Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 41 of 199
Found at i:11761172 original size:50 final size:50
Alignment explanation
Indices: 11760985--11761223 Score: 165
Period size: 50 Copynumber: 4.7 Consensus size: 50
11760975 GATAATAACA
* * * ** ** * * *
11760985 TGCCAAAGCCATGTCCTAGCCATGGTCTTACATGGGATGTTTCTTAT-AC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCCCATCTCAG
* * ** * * *
11761034 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGATTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCCCATCTCAG
* * * * ***
11761084 TGCCCATGCTATGTTCGAGACATGGTCTTATGGGGGACCTCCCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCCCATCTCAG
* * *
11761134 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATGATCTCAATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTC-C--CATCTC-A-G
*
11761189 ATGCCAATGCCATGTCCCAGACATCGTCTTACATG
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATG
11761224 AGATCTCTTT
Statistics
Matches: 146, Mismatches: 37, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
49 39 0.27
50 68 0.47
51 1 0.01
53 5 0.03
54 1 0.01
55 1 0.01
56 31 0.21
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCCCATCTCAG
Found at i:11762737 original size:13 final size:13
Alignment explanation
Indices: 11762719--11762743 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11762709 GAATTAATAT
11762719 GTGTGAAAATTTC
1 GTGTGAAAATTTC
11762732 GTGTGAAAATTT
1 GTGTGAAAATTT
11762744 TATTTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:11763915 original size:43 final size:42
Alignment explanation
Indices: 11763852--11763976 Score: 130
Period size: 43 Copynumber: 2.9 Consensus size: 42
11763842 AAGATTCCGT
*
11763852 TATGTGTTATCGTGTAAGACCAGGTCTGGGACGTTGGCATCAAC
1 TATGTGTTA-CGTGTAAGACCACGTCTGGGACGTTGGCATC-AC
**
11763896 T-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGT
1 TATGTG-TTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCAC
**
11763938 TATGTGATTACACGTAAGACCACGTCTGGGACGTTGGCA
1 TATGTG-TTACGTGTAAGACCACGTCTGGGACGTTGGCA
11763977 CTGTACGATA
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
42 2 0.03
43 61 0.88
44 6 0.09
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (42 bp):
TATGTGTTACGTGTAAGACCACGTCTGGGACGTTGGCATCAC
Found at i:11765726 original size:102 final size:101
Alignment explanation
Indices: 11765550--11765893 Score: 478
Period size: 102 Copynumber: 3.4 Consensus size: 101
11765540 TATCGATGAA
* * *
11765550 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGGATCGCTAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGATCACATGTGTAGTAC
* *
11765615 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TATGTGAAGGCTACTATGTGTACCGA-AAGCTTTGGT
*
11765652 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGATCACATGTGTAGTAC
11765717 TATGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TATGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
* * * * *
11765754 TACGTGTGTAGTACTATGTGAAGGCTACTACATGAACCG-TAAA-ACTTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGATCACATGTGTAGTA
* * * *
11765817 CTATGTGAAGGCTACTACGTGAACCGTAAAAC-TTGAT
65 CTATGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
* *
11765854 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
11765894 ATGATAAAAG
Statistics
Matches: 217, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
100 38 0.18
101 48 0.22
102 130 0.60
103 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGATCACATGTGTAGTAC
TATGTGAAGGCTACTATGTGTACCGAAAGCTTTGGT
Found at i:11765830 original size:50 final size:50
Alignment explanation
Indices: 11765550--11765887 Score: 394
Period size: 51 Copynumber: 6.7 Consensus size: 50
11765540 TATCGATGAA
* * * *
11765550 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGGATCGCTAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGAT
* * * * * * *
11765601 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGAT
* ***
11765652 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGAT
* * * *
11765703 CACATGTGTAGTACTATGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGAT
* *
11765754 TACGTGTGTAGTACTATGTGAAGGCTACTACATGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
11765804 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
*
11765854 CACATGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
11765888 TATCGAATGA
Statistics
Matches: 244, Mismatches: 35, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
49 4 0.02
50 87 0.36
51 146 0.60
52 6 0.02
53 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
Found at i:11767721 original size:15 final size:15
Alignment explanation
Indices: 11767701--11767731 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11767691 TTAATGATAA
11767701 ATTATGAATTGGTTT
1 ATTATGAATTGGTTT
11767716 ATTATGAATTGGTTT
1 ATTATGAATTGGTTT
11767731 A
1 A
11767732 AAAGTGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (15 bp):
ATTATGAATTGGTTT
Found at i:11767919 original size:47 final size:46
Alignment explanation
Indices: 11767860--11767997 Score: 161
Period size: 47 Copynumber: 2.9 Consensus size: 46
11767850 TATATATATA
11767860 CTGTCCAATTTGGTGTATCAATACTGTCCAATTTGGTGTATAAAATG
1 CTGTCCAATTTGGTGTAT-AATACTGTCCAATTTGGTGTATAAAATG
* *
11767907 CTGTCCAATTTGGTGTATATATGA-TGTCCAATTTGGTATATATATATG
1 CTGTCCAATTTGGTGTATA-AT-ACTGTCCAATTTGGTGTATA-AAATG
* * * * *
11767955 CTGTCCGATTTGATGTATAAGAGCTGTCCGATTTGATGTATAA
1 CTGTCCAATTTGGTGTATAATA-CTGTCCAATTTGGTGTATAA
11767998 GAGTTGTCCA
Statistics
Matches: 78, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
46 2 0.03
47 39 0.50
48 37 0.47
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (46 bp):
CTGTCCAATTTGGTGTATAATACTGTCCAATTTGGTGTATAAAATG
Found at i:11767998 original size:23 final size:23
Alignment explanation
Indices: 11767860--11768008 Score: 142
Period size: 23 Copynumber: 6.3 Consensus size: 23
11767850 TATATATATA
*
11767860 CTGTCCAATTTGGTGTATCAATA-
1 CTGTCCAATTTGGTGTAT-AAGAG
*
11767883 CTGTCCAATTTGGTGTATAAAATG
1 CTGTCCAATTTGGTGTATAAGA-G
11767907 CTGTCCAATTTGGTGTATATATGA-
1 CTGTCCAATTTGGTGTATA-A-GAG
* *
11767931 -TGTCCAATTTGGTATATATATATG
1 CTGTCCAATTTGGTGTATA-AGA-G
* *
11767955 CTGTCCGATTTGATGTATAAGAG
1 CTGTCCAATTTGGTGTATAAGAG
* *
11767978 CTGTCCGATTTGATGTATAAGAG
1 CTGTCCAATTTGGTGTATAAGAG
*
11768001 TTGTCCAA
1 CTGTCCAA
11768009 ACAGGGTAGA
Statistics
Matches: 109, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
22 4 0.04
23 67 0.61
24 21 0.19
25 16 0.15
26 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (23 bp):
CTGTCCAATTTGGTGTATAAGAG
Found at i:11776693 original size:11 final size:11
Alignment explanation
Indices: 11776679--11776735 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
11776669 ATTGAATTAA
*
11776679 TAAAATACTAT
1 TAAAATAATAT
11776690 TAAAATAAGTAT
1 TAAAATAA-TAT
*
11776702 TAAATTTAATAT
1 TAAA-ATAATAT
*
11776714 T-AAAT-TTAT
1 TAAAATAATAT
11776723 TAAAATAATAT
1 TAAAATAATAT
11776734 TA
1 TA
11776736 TTTTTGAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
9 4 0.11
10 5 0.14
11 14 0.38
12 11 0.30
13 3 0.08
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
TAAAATAATAT
Found at i:11779563 original size:90 final size:90
Alignment explanation
Indices: 11779456--11779635 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
11779446 AGTAAACTTG
11779456 TTAATGAGTTGCTTGTCTTTGTGATAAATGATTTAATCACTATTTGATAGTAATTGACTTTTCAT
1 TTAATGAGTTGCTTGTCTTTGTGATAAATGATTTAATCACTATTTGATAGTAATTGACTTTTCAT
11779521 AAAAGAAGATGTAATAGTTACCATA
66 AAAAGAAGATGTAATAGTTACCATA
11779546 TTAATGAGTTGCTTGTCTTTGTGATAAATGATTTAATCACTATTTGATAGTAATTGACTTTTCAT
1 TTAATGAGTTGCTTGTCTTTGTGATAAATGATTTAATCACTATTTGATAGTAATTGACTTTTCAT
*
11779611 AAAAGAAGATGTAATGGTTACCATA
66 AAAAGAAGATGTAATAGTTACCATA
11779636 CGATAAAATA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (90 bp):
TTAATGAGTTGCTTGTCTTTGTGATAAATGATTTAATCACTATTTGATAGTAATTGACTTTTCAT
AAAAGAAGATGTAATAGTTACCATA
Found at i:11779670 original size:90 final size:90
Alignment explanation
Indices: 11779481--11779670 Score: 224
Period size: 90 Copynumber: 2.1 Consensus size: 90
11779471 TCTTTGTGAT
11779481 AAATGATTTAATCACTATTTGATAGTAATTGACTTTTCATAAAAGAAGATGTAATAGTTACCATA
1 AAATGATTTAATCACTATTTGATAGTAATTGACTTTTCATAAAAGAAGATGTAATAGTTACCATA
* * ** *** * * *
11779546 TTAATGAGTTGCTTGTCTTTGTGAT
66 TCAATAAAATGAAGGTCATTGAGAG
*
11779571 AAATGATTTAATCACTATTTGATAGTAATTGACTTTTCATAAAAGAAGATGTAATGGTTACCATA
1 AAATGATTTAATCACTATTTGATAGTAATTGACTTTTCATAAAAGAAGATGTAATAGTTACCATA
*
11779636 -CGATAAAAT-AAGGTCCAATTGAGAG
66 TCAATAAAATGAAGGT-C-ATTGAGAG
11779661 AATAT-ATTTA
1 AA-ATGATTTA
11779671 TCCTAAAGAG
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
88 2 0.02
89 5 0.06
90 76 0.89
91 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (90 bp):
AAATGATTTAATCACTATTTGATAGTAATTGACTTTTCATAAAAGAAGATGTAATAGTTACCATA
TCAATAAAATGAAGGTCATTGAGAG
Found at i:11789745 original size:50 final size:50
Alignment explanation
Indices: 11789691--11789870 Score: 195
Period size: 50 Copynumber: 3.6 Consensus size: 50
11789681 TGTGAGCCAT
* ** *
11789691 GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCTCCC
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCTCAC
* * *
11789741 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCTCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCTCAC
* * * * * *
11789791 GTAAGACTATATCTGGGATATGGCATTGGCA--GTACA-GAAAACATCCCAC
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAAC-TCTCAC
*
11789840 GTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA
11789871 TGTTATTATC
Statistics
Matches: 109, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
48 6 0.06
49 33 0.30
50 70 0.64
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCTCAC
Found at i:11799328 original size:18 final size:18
Alignment explanation
Indices: 11799307--11799343 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
11799297 AAAATTCGAA
11799307 TTTATTTCCTAAT-TTAAT
1 TTTATTTCC-AATATTAAT
11799325 TTTATTTCCAATATTAAT
1 TTTATTTCCAATATTAAT
11799343 T
1 T
11799344 GTTTATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTATTTCCAATATTAAT
Found at i:11809196 original size:3 final size:3
Alignment explanation
Indices: 11809188--11809216 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11809178 GCCTTGTCTT
11809188 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11809217 TTCTTTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11813876 original size:34 final size:34
Alignment explanation
Indices: 11813833--11813900 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
11813823 GCATTTTTGA
* *
11813833 CACTGTACTGAGATGGGCTAAGGCCCAA-ACTGT
1 CACTGTACTGAAAAGGGCTAAGGCCCAAGACTGT
*
11813866 CACTGATACTGAAAAGGGCTTAGGCCCAAGACTGT
1 CACTG-TACTGAAAAGGGCTAAGGCCCAAGACTGT
11813901 TCAACTGTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (34 bp):
CACTGTACTGAAAAGGGCTAAGGCCCAAGACTGT
Found at i:11816142 original size:11 final size:12
Alignment explanation
Indices: 11816120--11816145 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11816110 TATATATATA
11816120 TTTTAAATTTTT
1 TTTTAAATTTTT
11816132 TTTTAAATTTTT
1 TTTTAAATTTTT
11816144 TT
1 TT
11816146 ATTTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTAAATTTTT
Found at i:11822183 original size:72 final size:72
Alignment explanation
Indices: 11822061--11822206 Score: 193
Period size: 72 Copynumber: 2.0 Consensus size: 72
11822051 TTTATTATGA
* **
11822061 CCTGACAAATGGTCGTGTCCTTATTGTTGGGTATTTTACACGTCAAACACACGACCTCAGGCTGT
1 CCTGACAAATAGTCGTGTCCTTATCATTGGGTATTTTACACGTCAAACACACGACCTCAGGCTGT
11822126 TACACGG
66 TACACGG
* * ** * * * *
11822133 CCTGACACATAGTCGTGTCCTTATCATTGGGTATTTTGCACGTCGTACACATGGCTTTAGGCTGT
1 CCTGACAAATAGTCGTGTCCTTATCATTGGGTATTTTACACGTCAAACACACGACCTCAGGCTGT
11822198 TACACGG
66 TACACGG
11822205 CC
1 CC
11822207 GTGTACCCCC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (72 bp):
CCTGACAAATAGTCGTGTCCTTATCATTGGGTATTTTACACGTCAAACACACGACCTCAGGCTGT
TACACGG
Found at i:11827106 original size:13 final size:14
Alignment explanation
Indices: 11827072--11827105 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
11827062 ATTTGAAATT
*
11827072 TTAAAAATATATTA
1 TTAAAAAGATATTA
11827086 TTAAAAAGATATTA
1 TTAAAAAGATATTA
11827100 TTAAAA
1 TTAAAA
11827106 GGTTTAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
TTAAAAAGATATTA
Found at i:11827440 original size:10 final size:10
Alignment explanation
Indices: 11827415--11827470 Score: 53
Period size: 10 Copynumber: 5.8 Consensus size: 10
11827405 TATTTTTAGG
*
11827415 ATTTTTATAA
1 ATTTTTATAT
*
11827425 AATTTTATAT
1 ATTTTTATAT
*
11827435 ATTTTTA-CT
1 ATTTTTATAT
11827444 ATTTTTATA-
1 ATTTTTATAT
* *
11827453 AATTTTAAAT
1 ATTTTTATAT
11827463 ATTTTTAT
1 ATTTTTAT
11827471 TAAAATTTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
9 15 0.43
10 20 0.57
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:11827447 original size:29 final size:28
Alignment explanation
Indices: 11827405--11827469 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
11827395 TTTATAATTT
* *
11827405 TATTTTTAGGATTTTTATAAAATTTTATA
1 TATTTTTACGATTTTTAT-AAATTTTAAA
*
11827434 TATTTTTACTATTTTTATAAATTTTAAA
1 TATTTTTACGATTTTTATAAATTTTAAA
11827462 TATTTTTA
1 TATTTTTA
11827470 TTAAAATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.62
Consensus pattern (28 bp):
TATTTTTACGATTTTTATAAATTTTAAA
Found at i:11827449 original size:19 final size:19
Alignment explanation
Indices: 11827427--11827480 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
11827417 TTTTATAAAA
* * *
11827427 TTTTATATATTTTTACTAT
1 TTTTATAAATTTTAAATAT
11827446 TTTTATAAATTTTAAATAT
1 TTTTATAAATTTTAAATAT
*
11827465 TTTTATTAAAATTTAA
1 TTTTA-TAAATTTTAA
11827481 TAACTTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 21 0.70
20 9 0.30
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTATAAATTTTAAATAT
Found at i:11827474 original size:20 final size:19
Alignment explanation
Indices: 11827443--11827480 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
11827433 ATATTTTTAC
*
11827443 TATTTTTATAAATTTTAAA
1 TATTTTTATAAAATTTAAA
11827462 TATTTTTATTAAAATTTAA
1 TATTTTTA-TAAAATTTAA
11827481 TAACTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTTTATAAAATTTAAA
Found at i:11827791 original size:87 final size:87
Alignment explanation
Indices: 11827628--11827832 Score: 239
Period size: 87 Copynumber: 2.3 Consensus size: 87
11827618 ATTAAATGGT
* * * * *
11827628 CTTTTTGATGCATTTTCACAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAAAGGATTAATTGCT
1 CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAACTAAGTGCAAAAAAAAAAAGGATTAATTGCA
* * **
11827693 TTTTTTGAAAAAGTTTGTGGGC
66 TTTTGTAAAAAAGTTTGAAGGC
* * * * *
11827715 CTTTTTGATACATTTTGAAAGTTCAAGTGCCCAACTAAGTGCAAAAAAAAGTAGGGCTTAATTGC
1 CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAACTAAGTGCAAAAAAAA-AAAGGATTAATTGC
11827780 ATTTTGTAAAAAAGTTTGAAGGC
65 ATTTTGTAAAAAAGTTTGAAGGC
* * *
11827803 CTTTTTTTATGCACTTTGAAAGTTTAAGTA
1 C-TTTTTGATGCATTTTGAAAGTTCAAGTA
11827833 TCGAATTGAG
Statistics
Matches: 97, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
87 44 0.45
88 30 0.31
89 23 0.24
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (87 bp):
CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAACTAAGTGCAAAAAAAAAAAGGATTAATTGCA
TTTTGTAAAAAAGTTTGAAGGC
Found at i:11834018 original size:13 final size:13
Alignment explanation
Indices: 11834000--11834025 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11833990 AGGTGGTGGC
11834000 AGAGGCTAGGGTT
1 AGAGGCTAGGGTT
11834013 AGAGGCTAGGGTT
1 AGAGGCTAGGGTT
11834026 TCTTTGTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.46, T:0.23
Consensus pattern (13 bp):
AGAGGCTAGGGTT
Found at i:11843694 original size:18 final size:18
Alignment explanation
Indices: 11843668--11843702 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11843658 ATGATATGCC
*
11843668 AAACTATTTTCATGCTTG
1 AAACCATTTTCATGCTTG
*
11843686 AAACCATTTTGATGCTT
1 AAACCATTTTCATGCTT
11843703 ACCATTCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (18 bp):
AAACCATTTTCATGCTTG
Found at i:11848592 original size:54 final size:54
Alignment explanation
Indices: 11848534--11848655 Score: 131
Period size: 54 Copynumber: 2.3 Consensus size: 54
11848524 GTCCTCACCT
* *
11848534 GTGTAACTCACTGGGCTGCCACACACGCCCCTGT-TCCAGACCGTGTGCTAAGCC
1 GTGTAACTCACTGAGCTACCACACACGCCCCTGTGT-CAGACCGTGTGCTAAGCC
* * * * * *
11848588 GTGTAACAT-ACTGAGTTACCATACACGCCCGTGTGTCAGGCCGTGTGTTAGGCC
1 GTGTAAC-TCACTGAGCTACCACACACGCCCCTGTGTCAGACCGTGTGCTAAGCC
*
11848642 GTTTAACTCACTGA
1 GTGTAACTCACTGA
11848656 CTTTAAACAT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
53 1 0.02
54 53 0.95
55 2 0.04
ACGTcount: A:0.20, C:0.30, G:0.25, T:0.25
Consensus pattern (54 bp):
GTGTAACTCACTGAGCTACCACACACGCCCCTGTGTCAGACCGTGTGCTAAGCC
Found at i:11854269 original size:34 final size:34
Alignment explanation
Indices: 11854231--11854298 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
11854221 ATCAAGCTAA
* * *
11854231 AACTTACACATTTAAATCACATCATTTGTACAAG
1 AACTTAAACATTTAAAACACATCATTTGCACAAG
11854265 AACTTAAACATTTAAAACACATCATTTGCACAAG
1 AACTTAAACATTTAAAACACATCATTTGCACAAG
11854299 CATTCATAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (34 bp):
AACTTAAACATTTAAAACACATCATTTGCACAAG
Found at i:11855376 original size:40 final size:40
Alignment explanation
Indices: 11855331--11855594 Score: 255
Period size: 40 Copynumber: 6.6 Consensus size: 40
11855321 GTAGATGTAG
* * *
11855331 AACAGGGGCACACATGTGAATTCAGGGGTACCAAAGTATA
1 AACAGGGGCACATATGTGCATTCAGGGGTACCAAAGTACA
* * *
11855371 AACAGGGGCACGTATGTGCATTTAGGGGGTA-CTAAGTACA
1 AACAGGGGCACATATGTGCATTCA-GGGGTACCAAAGTACA
* * * **
11855411 AACAGGAGCACATGTGTGCATTCTGGTCTACCAAAGTACA
1 AACAGGGGCACATATGTGCATTCAGGGGTACCAAAGTACA
* * * * *
11855451 AACAGGGGCGCGTATGTGCATTTAGGGGTACCGAAGTACG
1 AACAGGGGCACATATGTGCATTCAGGGGTACCAAAGTACA
* ** * *
11855491 AATAGGGGCATGTATGTGTATTCAGGGGTACCGAAGTACA
1 AACAGGGGCACATATGTGCATTCAGGGGTACCAAAGTACA
**
11855531 AACAGGGGCACGA-ATGTGCATTCAGGGGTATTGAAA-TACA
1 AACAGGGGCAC-ATATGTGCATTCAGGGGTA-CCAAAGTACA
* *
11855571 AATAGGGGCACACATGTGCATTCA
1 AACAGGGGCACATATGTGCATTCA
11855595 AGTACATTTT
Statistics
Matches: 181, Mismatches: 38, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
39 5 0.03
40 168 0.93
41 8 0.04
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (40 bp):
AACAGGGGCACATATGTGCATTCAGGGGTACCAAAGTACA
Found at i:11855465 original size:80 final size:79
Alignment explanation
Indices: 11855334--11855594 Score: 297
Period size: 80 Copynumber: 3.3 Consensus size: 79
11855324 GATGTAGAAC
* * * *
11855334 AGGGGCACACATGTGAATTCAGGGGTACCAAAGTATAAACAGGGGCACGTATGTGCATTTAGGGG
1 AGGGGCACATATGTGCATTCAGGGCTACCAAAGTACAAACAGGGGCACGTATGTGCATTTA-GGG
*
11855399 GTACTAAGTACAAAC
65 GTACTAAGTACAAAT
* * * * *
11855414 AGGAGCACATGTGTGCATTCTGGTCTACCAAAGTACAAACAGGGGCGCGTATGTGCATTTAGGGG
1 AGGGGCACATATGTGCATTCAGGGCTACCAAAGTACAAACAGGGGCACGTATGTGCATTTAGGGG
* *
11855479 TACCGAAGTACGAAT
66 TA-CTAAGTACAAAT
** * * * * *
11855494 AGGGGCATGTATGTGTATTCAGGGGTACCGAAGTACAAACAGGGGCACGAATGTGCATTCAGGGG
1 AGGGGCACATATGTGCATTCAGGGCTACCAAAGTACAAACAGGGGCACGTATGTGCATTTAGGGG
* *
11855559 TATTGAAATACAAAT
66 TACT-AAGTACAAAT
*
11855574 AGGGGCACACATGTGCATTCA
1 AGGGGCACATATGTGCATTCA
11855595 AGTACATTTT
Statistics
Matches: 147, Mismatches: 32, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
79 6 0.04
80 141 0.96
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.21
Consensus pattern (79 bp):
AGGGGCACATATGTGCATTCAGGGCTACCAAAGTACAAACAGGGGCACGTATGTGCATTTAGGGG
TACTAAGTACAAAT
Found at i:11855588 original size:120 final size:120
Alignment explanation
Indices: 11855331--11855594 Score: 291
Period size: 120 Copynumber: 2.2 Consensus size: 120
11855321 GTAGATGTAG
* * *
11855331 AACAGGGGCACACATGTGAATTCAGGGGTACCAAAGTATAAACAGGGGCACGTATGTGCATTTAG
1 AACAGGGGCACACATGTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCATTCAG
* * * *
11855396 GGGGTACTAAGTACAAACAGGAGCACATGTGTGCATTCTGGTCTACCAAAGTACA
66 GGGGTACGAAGTACAAACAGGAGCACATATGTGCATTCAGGGCTACCAAAGTACA
* ** * * * * * *
11855451 AACAGGGGCGCGTATGTGCATTTAGGGGTACCGAAGTACGAATAGGGGCATGTATGTGTATTCA-
1 AACAGGGGCACACATGTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCATTCAG
* * **
11855515 GGGGTACCGAAGTACAAACAGGGGCACGA-ATGTGCATTCAGGGGTATTGAAA-TACA
66 GGGGTA-CGAAGTACAAACAGGAGCAC-ATATGTGCATTCAGGGCTA-CCAAAGTACA
*
11855571 AATAGGGGCACACATGTGCATTCA
1 AACAGGGGCACACATGTGCATTCA
11855595 AGTACATTTT
Statistics
Matches: 116, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
119 6 0.05
120 106 0.91
121 4 0.03
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (120 bp):
AACAGGGGCACACATGTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCATTCAG
GGGGTACGAAGTACAAACAGGAGCACATATGTGCATTCAGGGCTACCAAAGTACA
Found at i:11856049 original size:15 final size:14
Alignment explanation
Indices: 11856033--11856068 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
11856023 GATACCTTAT
11856033 TTTAATTTTATTTA
1 TTTAATTTTATTTA
*
11856047 TTTATGTTTTATTTA
1 TTTA-ATTTTATTTA
11856062 TTTAATT
1 TTTAATT
11856069 ACAAGTTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTAATTTTATTTA
Found at i:11860136 original size:91 final size:91
Alignment explanation
Indices: 11860032--11860200 Score: 320
Period size: 91 Copynumber: 1.9 Consensus size: 91
11860022 TGACTTACTA
11860032 GACTAACAATAAATCAGATTGGACCCAAGAAGAATAGATCTTGAATCCGTTTATGGATTTATTCA
1 GACTAACAATAAATCAGATTGGACCCAAGAAGAATAGATCTTGAATCCGTTTATGGATTTATTCA
11860097 CTTATGACATTCAGAGTGTGATATTG
66 CTTATGACATTCAGAGTGTGATATTG
11860123 GACTAACAATAAATCAGATTGGACCCAAGAAGAATAGATCTTGAATCCGTTTATGGATTTATTCA
1 GACTAACAATAAATCAGATTGGACCCAAGAAGAATAGATCTTGAATCCGTTTATGGATTTATTCA
* *
11860188 CTTGTGACGTTCA
66 CTTATGACATTCA
11860201 AAATGTGACA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 76 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (91 bp):
GACTAACAATAAATCAGATTGGACCCAAGAAGAATAGATCTTGAATCCGTTTATGGATTTATTCA
CTTATGACATTCAGAGTGTGATATTG
Found at i:11864083 original size:7 final size:7
Alignment explanation
Indices: 11864071--11864116 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
11864061 GTATGTAAAC
11864071 ATATAAT
1 ATATAAT
11864078 ATATAAT
1 ATATAAT
11864085 ATATAAT
1 ATATAAT
11864092 ATATAAT
1 ATATAAT
*
11864099 ATATAGT
1 ATATAAT
11864106 ATATAAT
1 ATATAAT
11864113 ATAT
1 ATAT
11864117 GATAAAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (7 bp):
ATATAAT
Found at i:11864145 original size:12 final size:12
Alignment explanation
Indices: 11864128--11864165 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
11864118 ATAAAAACAA
11864128 AATAAAAGAAAT
1 AATAAAAGAAAT
11864140 AATAAAAGAAAT
1 AATAAAAGAAAT
*
11864152 AATAAAAGAGAT
1 AATAAAAGAAAT
11864164 AA
1 AA
11864166 AAAGAAAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (12 bp):
AATAAAAGAAAT
Found at i:11864157 original size:24 final size:22
Alignment explanation
Indices: 11864128--11864172 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
11864118 ATAAAAACAA
11864128 AATAAAAGAAATAATAAAAGAAAT
1 AATAAAAGAAAT-A-AAAAGAAAT
*
11864152 AATAAAAGAGATAAAAAGAAA
1 AATAAAAGAAATAAAAAGAAA
11864173 GCTAAGTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 1 0.05
24 11 0.55
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (22 bp):
AATAAAAGAAATAAAAAGAAAT
Found at i:11879056 original size:43 final size:44
Alignment explanation
Indices: 11879008--11879125 Score: 141
Period size: 44 Copynumber: 2.7 Consensus size: 44
11878998 AATCTGCCTA
* *
11879008 AAAAAGAGAAGAAGATAATCTTGGGTTGTTG-AAAACATAA-TTT
1 AAAAAGAG-AGAAGATAATCTTGGGTTGTTGAAAAAAAGAATTTT
* **
11879051 AAAAAGAGGAGAAGATAATCCTAAGTTGTTGAAAAAAAGAATTTT
1 AAAAAGA-GAGAAGATAATCTTGGGTTGTTGAAAAAAAGAATTTT
* *
11879096 AAAAAAAGAGAAGATAAACTTGGGTTGTTG
1 AAAAAGAGAGAAGATAATCTTGGGTTGTTG
11879126 GATTTTCCCT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
43 26 0.42
44 27 0.44
45 9 0.15
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.25
Consensus pattern (44 bp):
AAAAAGAGAGAAGATAATCTTGGGTTGTTGAAAAAAAGAATTTT
Found at i:11885600 original size:9 final size:9
Alignment explanation
Indices: 11885586--11885610 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11885576 CGTTTCAAAA
11885586 TCATTCAAT
1 TCATTCAAT
11885595 TCATTCAAT
1 TCATTCAAT
11885604 TCATTCA
1 TCATTCA
11885611 TCCATTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (9 bp):
TCATTCAAT
Found at i:11886476 original size:13 final size:13
Alignment explanation
Indices: 11886460--11886492 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
11886450 AAATATTTTT
11886460 TTAGTTTATTAAA
1 TTAGTTTATTAAA
*
11886473 TTAGTTTGTTAAA
1 TTAGTTTATTAAA
11886486 TTAGTTT
1 TTAGTTT
11886493 TATTTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (13 bp):
TTAGTTTATTAAA
Found at i:11896767 original size:11 final size:11
Alignment explanation
Indices: 11896751--11896779 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
11896741 TGCCAACACT
11896751 AATGCCATGGA
1 AATGCCATGGA
11896762 AATGCCATGGA
1 AATGCCATGGA
11896773 AATGCCA
1 AATGCCA
11896780 GTAAGATGCC
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:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (11 bp):
AATGCCATGGA
Found at i:11899634 original size:22 final size:22
Alignment explanation
Indices: 11899604--11899714 Score: 102
Period size: 22 Copynumber: 5.0 Consensus size: 22
11899594 ACTCTGCATA
11899604 ACATGCGAGCCTATATGTTAGT
1 ACATGCGAGCCTATATGTTAGT
* *
11899626 -CTATGCGAGCTTATACGTTAGT
1 AC-ATGCGAGCCTATATGTTAGT
* *** *
11899648 ACATGCAAGCCTATCCATTA-C
1 ACATGCGAGCCTATATGTTAGT
*
11899669 ATCAT-CTGAACCTATATGTTAGT
1 A-CATGC-GAGCCTATATGTTAGT
11899692 ACATGCGAGCCTATATGTTAGT
1 ACATGCGAGCCTATATGTTAGT
11899714 A
1 A
11899715 TGTACGAACC
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
21 3 0.04
22 63 0.91
23 3 0.04
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (22 bp):
ACATGCGAGCCTATATGTTAGT
Found at i:11899742 original size:15 final size:15
Alignment explanation
Indices: 11899721--11899760 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
11899711 AGTATGTACG
11899721 AACCCCTAAGG-TAA
1 AACCCCTAAGGTTAA
*
11899735 ACACCCCTAAGGTTCA
1 A-ACCCCTAAGGTTAA
11899751 AACCCCTAAG
1 AACCCCTAAG
11899761 TTTGCAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 19 0.83
16 3 0.13
ACGTcount: A:0.38, C:0.35, G:0.12, T:0.15
Consensus pattern (15 bp):
AACCCCTAAGGTTAA
Found at i:11903216 original size:12 final size:12
Alignment explanation
Indices: 11903201--11903225 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11903191 GTGGTTTTTG
11903201 ATGTTTTATGGA
1 ATGTTTTATGGA
11903213 ATGTTTTATGGA
1 ATGTTTTATGGA
11903225 A
1 A
11903226 GAAAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (12 bp):
ATGTTTTATGGA
Found at i:11905869 original size:28 final size:28
Alignment explanation
Indices: 11905824--11905884 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
11905814 CTTTCCAGAA
* *
11905824 ACAGT-ACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGAGCCTTAGCCCAAT
11905851 ACAGTAACAATGTGAGCCTTAGCCCAAT
1 ACAGTAACAATGTGAGCCTTAGCCCAAT
11905879 ACAGTA
1 ACAGTA
11905885 TCGATACAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (28 bp):
ACAGTAACAATGTGAGCCTTAGCCCAAT
Found at i:11911039 original size:42 final size:40
Alignment explanation
Indices: 11910992--11911073 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
11910982 TTGATTTTCT
*
11910992 TCAAGGACTCATAAGAAATTATTCTTTATCCTTCAATTTATC
1 TCAAGGAATCAT-A-AAATTATTCTTTATCCTTCAATTTATC
** *
11911034 TCAAGGAATCATAACTTTATTCTTTGTCCTTCAATTTATC
1 TCAAGGAATCATAAAATTATTCTTTATCCTTCAATTTATC
11911074 AAGGATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 24 0.67
41 1 0.03
42 11 0.31
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (40 bp):
TCAAGGAATCATAAAATTATTCTTTATCCTTCAATTTATC
Found at i:11911276 original size:20 final size:20
Alignment explanation
Indices: 11911234--11911274 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
11911224 TGTTTAGTTA
11911234 TTATTTTGAATATTTATTAT
1 TTATTTTGAATATTTATTAT
* *
11911254 TTATTTTTAA-ATTTCTTAT
1 TTATTTTGAATATTTATTAT
11911273 TT
1 TT
11911275 TAGTTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TTATTTTGAATATTTATTAT
Found at i:11911845 original size:18 final size:18
Alignment explanation
Indices: 11911822--11911859 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
11911812 TGGAACTTAC
11911822 TTCCTTTGGAGTCGAGTT
1 TTCCTTTGGAGTCGAGTT
11911840 TTCCTTTGGAGTCGAGTT
1 TTCCTTTGGAGTCGAGTT
11911858 TT
1 TT
11911860 GTTAAAGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.16, G:0.26, T:0.47
Consensus pattern (18 bp):
TTCCTTTGGAGTCGAGTT
Found at i:11927672 original size:20 final size:20
Alignment explanation
Indices: 11927647--11927687 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
11927637 CTTCTAGTTG
11927647 TATTTATATATATTATT-ATA
1 TATTTATATA-ATTATTGATA
11927667 TATTTATATAATTATTGATA
1 TATTTATATAATTATTGATA
11927687 T
1 T
11927688 GCTAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TATTTATATAATTATTGATA
Found at i:11928635 original size:16 final size:15
Alignment explanation
Indices: 11928614--11928643 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
11928604 TATTAATATG
11928614 ATAAATAAATCAAAAA
1 ATAAATAAAT-AAAAA
11928630 ATAAATAAATAAAA
1 ATAAATAAATAAAA
11928644 TAAAAATGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (15 bp):
ATAAATAAATAAAAA
Found at i:11930430 original size:44 final size:44
Alignment explanation
Indices: 11930358--11930480 Score: 111
Period size: 44 Copynumber: 2.8 Consensus size: 44
11930348 ATTCCAACCC
* * * * * * *
11930358 ACTACAACTTCAGGGGTATAGGAATTGTAGCTTTAATCTGATCA
1 ACTACAAATTTAGGGATATAAGATTTGTAGCTTTAACCCGATCA
* * * *
11930402 ACTATAAATTTAGGGATATAAGATTTGTAACTTCAACCCGATCC
1 ACTACAAATTTAGGGATATAAGATTTGTAGCTTTAACCCGATCA
* * * *
11930446 ACTACCACTTTAGGGATATAGGATTCGTAGCTTTA
1 ACTACAAATTTAGGGATATAAGATTTGTAGCTTTA
11930481 TCTTCTTCCA
Statistics
Matches: 61, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
44 61 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (44 bp):
ACTACAAATTTAGGGATATAAGATTTGTAGCTTTAACCCGATCA
Found at i:11930585 original size:94 final size:94
Alignment explanation
Indices: 11930457--11930701 Score: 305
Period size: 94 Copynumber: 2.6 Consensus size: 94
11930447 CTACCACTTT
* * *
11930457 AGGGATATAGGATTCGTAGCTTTATCTT-CTTCCACTGCAACTTTAAGGAGATAAGATTCGATAT
1 AGGG-TATAGGATTTGTAGCTTCATCTTGC-TCCACTGCAACTTTAAGGAGATAAGATTCGACAT
*
11930521 CATTATTTCATTCCAACCAACTGCAACTTCA
64 CATAATTTCATTCCAACCAACTGCAACTTCA
* * * *
11930552 AGGGTATAGGATTTGTAGCTTCATATTGCTCCACTGCAAC-TTCAGAGAGATAAGATTCGCCATT
1 AGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTTAAG-GAGATAAGATTCGACATC
* *
11930616 GTAATTTCATTCCAACCCACTGCAACTTCA
65 ATAATTTCATTCCAACCAACTGCAACTTCA
* * * * * *
11930646 AGAGTATAGAAATTGTAGCTTCATCTTGCTCCACTGTAACTTCAGGGAGATAAGAT
1 AGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTTAAGGAGATAAGAT
11930702 CCGCTATGGC
Statistics
Matches: 129, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
93 4 0.03
94 118 0.91
95 7 0.05
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (94 bp):
AGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTTAAGGAGATAAGATTCGACATCA
TAATTTCATTCCAACCAACTGCAACTTCA
Found at i:11930680 original size:44 final size:44
Alignment explanation
Indices: 11930540--11930689 Score: 115
Period size: 44 Copynumber: 3.3 Consensus size: 44
11930530 ATTCCAACCA
* * * *
11930540 ACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCATATTGCTCC
1 ACTGCAACTTCAAGAGTATAGAAATTGTAGCTTCATCTTGCTCC
* ** ***
11930584 ACTGCAACTTCAGAGAG-ATAAGATTCGCCATTGTAATTTCATTCCAAC-CC
1 ACTGCAACTTCA-AGAGTAT-AGA-----AATTGTAGCTTCA-TCTTGCTCC
11930634 ACTGCAACTTCAAGAGTATAGAAATTGTAGCTTCATCTTGCTCC
1 ACTGCAACTTCAAGAGTATAGAAATTGTAGCTTCATCTTGCTCC
*
11930678 ACTGTAACTTCA
1 ACTGCAACTTCA
11930690 GGGAGATAAG
Statistics
Matches: 79, Mismatches: 17, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 37 0.47
45 5 0.06
49 7 0.09
50 25 0.32
51 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (44 bp):
ACTGCAACTTCAAGAGTATAGAAATTGTAGCTTCATCTTGCTCC
Found at i:11930728 original size:94 final size:94
Alignment explanation
Indices: 11930525--11930730 Score: 270
Period size: 94 Copynumber: 2.2 Consensus size: 94
11930515 CGATATCATT
* * * * *
11930525 ATTTCATTCCAACCAACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCATATTGCTCCACTGCA
1 ATTTCAATCCAACCCACTGCAACTTCAAGAGTATAGAAATTGTAGCTTCATATTGCTCCACTGCA
* * *
11930590 ACTTCAGAGAGATAAGATTCGCCATTGTA
66 ACTTCAGAGAGATAAGATCCGCCATGGCA
* * *
11930619 ATTTCATTCCAACCCACTGCAACTTCAAGAGTATAGAAATTGTAGCTTCATCTTGCTCCACTGTA
1 ATTTCAATCCAACCCACTGCAACTTCAAGAGTATAGAAATTGTAGCTTCATATTGCTCCACTGCA
* *
11930684 ACTTCAGGGAGATAAGATCCGCTATGGCA
66 ACTTCAGAGAGATAAGATCCGCCATGGCA
*
11930713 GA-TTCAATCCGACCCACT
1 -ATTTCAATCCAACCCACT
11930731 AACACTTTAG
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
94 97 0.99
95 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (94 bp):
ATTTCAATCCAACCCACTGCAACTTCAAGAGTATAGAAATTGTAGCTTCATATTGCTCCACTGCA
ACTTCAGAGAGATAAGATCCGCCATGGCA
Found at i:11937218 original size:28 final size:27
Alignment explanation
Indices: 11937185--11937283 Score: 119
Period size: 28 Copynumber: 3.6 Consensus size: 27
11937175 TAATGAGATT
11937185 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTTTAATTGAA
* **
11937212 ATGCACTAAGTGTGCGAGTATAAGGGTAA
1 A-GCACTAAGTGTGCGAGTTTAATTG-AA
*
11937241 AGCACTAAGTGTGCGAGTTTGATT-ATTA
1 AGCACTAAGTGTGCGAGTTTAATTGA--A
11937269 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
11937284 TACTTGTTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 56 0.92
29 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTTAATTGAA
Found at i:11938250 original size:22 final size:22
Alignment explanation
Indices: 11938219--11938345 Score: 123
Period size: 22 Copynumber: 5.5 Consensus size: 22
11938209 GTGTTATAAA
**
11938219 TTTAATGTATAATGCAATCCAAT
1 TTTAA-GTATAATGCTGTCCAAT
*
11938242 TTTGAGTATATTGATGCTGTCC-AT
1 TTTAAGTATA---ATGCTGTCCAAT
11938266 TTTAATGTATAATGCTGTCCAAT
1 TTTAA-GTATAATGCTGTCCAAT
11938289 TTTAAGTATATTGATGCTGTCC-AT
1 TTTAAGTATA---ATGCTGTCCAAT
11938313 TTTAATGTATAATGCTGTCCAAT
1 TTTAA-GTATAATGCTGTCCAAT
*
11938336 TTTGAGTATA
1 TTTAAGTATA
11938346 TTTAAGCTGT
Statistics
Matches: 89, Mismatches: 5, Indels: 21
0.77 0.04 0.18
Matches are distributed among these distances:
22 33 0.37
23 17 0.19
24 13 0.15
25 26 0.29
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (22 bp):
TTTAAGTATAATGCTGTCCAAT
Found at i:11938264 original size:25 final size:24
Alignment explanation
Indices: 11938236--11938408 Score: 141
Period size: 25 Copynumber: 7.3 Consensus size: 24
11938226 TATAATGCAA
11938236 TCCAATTTTGAGTATATTGATGCTG
1 TCCAATTTTGAGTATATT-ATGCTG
*
11938261 TCC-ATTTTAATGTATA--ATGCTG
1 TCCAATTTTGA-GTATATTATGCTG
*
11938283 TCCAATTTTAAGTATATTGATGCTG
1 TCCAATTTTGAGTATATT-ATGCTG
*
11938308 TCC-ATTTTAATGTATA--ATGCTG
1 TCCAATTTTGA-GTATATTATGCTG
*
11938330 TCCAATTTTGAGTATATTTAAGCTG
1 TCCAATTTTGAGTATA-TTATGCTG
* *
11938355 TCTAA-TTTGATGTATA--ATGCTA
1 TCCAATTTTGA-GTATATTATGCTG
* *
11938377 TCC-ATTTAGAGCATATTATTGCTG
1 TCCAATTTTGAGTATATTA-TGCTG
11938401 TCCAATTT
1 TCCAATTT
11938409 GATGAATAAT
Statistics
Matches: 122, Mismatches: 10, Indels: 32
0.74 0.06 0.20
Matches are distributed among these distances:
21 5 0.04
22 38 0.31
23 14 0.11
24 25 0.20
25 40 0.33
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (24 bp):
TCCAATTTTGAGTATATTATGCTG
Found at i:11938288 original size:47 final size:47
Alignment explanation
Indices: 11938217--11938428 Score: 266
Period size: 47 Copynumber: 4.5 Consensus size: 47
11938207 TTGTGTTATA
**
11938217 AATTTAATGTATAATGCAATCCAATTTTGAGTATATTGATGCTGTCC
1 AATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
* *
11938264 ATTTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCC
1 AATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
* * * *
11938311 ATTTTAATGTATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCT
1 AATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
* * * *
11938358 AATTTGATGTATAATGCTATCC-ATTTAGAGCATATT-ATTGCTGTCC
1 AATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGA-TGCTGTCC
* *
11938404 AATTTGATGAATAATTGCTGTCCAA
1 AATTTAATGTATAA-TGCTGTCCAA
11938429 AACAGGATTG
Statistics
Matches: 145, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
45 1 0.01
46 31 0.21
47 112 0.77
48 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (47 bp):
AATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGCTGTCC
Found at i:11943605 original size:21 final size:21
Alignment explanation
Indices: 11943581--11943645 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
11943571 TTTTTTGGTC
11943581 AAATTTTATATTTTTGTATAT
1 AAATTTTATATTTTTGTATAT
* *
11943602 AAATTTTATACTTTGGTATAT
1 AAATTTTATATTTTTGTATAT
11943623 AAATTTTATATATTTTCGTATAT
1 AAATTTTATAT-TTTT-GTATAT
11943646 TAGTTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 29 0.76
22 3 0.08
23 6 0.16
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (21 bp):
AAATTTTATATTTTTGTATAT
Found at i:11952183 original size:20 final size:20
Alignment explanation
Indices: 11952142--11952186 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
11952132 TTATGATATT
*
11952142 TTTTTAAAATTTTTTGAATA
1 TTTTTAAAATTTTTTAAATA
*
11952162 TTTTTATAA-TTTTTAAATTA
1 TTTTTAAAATTTTTTAAA-TA
11952182 TTTTT
1 TTTTT
11952187 TGACATGGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTAAAATTTTTTAAATA
Found at i:11956702 original size:25 final size:24
Alignment explanation
Indices: 11956647--11956702 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
11956637 ATATTTATGA
* *
11956647 TTTTTAAACATTAAATATAATCTC
1 TTTTTTAACATAAAATATAATCTC
* *
11956671 TTATTTTAACATAAAATTATGATTTC
1 TT-TTTTAACATAAAA-TATAATCTC
11956697 TTTTTT
1 TTTTTT
11956703 TCTTTTTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 2 0.08
25 15 0.58
26 9 0.35
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTTTTAACATAAAATATAATCTC
Found at i:11969156 original size:22 final size:22
Alignment explanation
Indices: 11969125--11969175 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
11969115 TTTATCTACT
11969125 AATTAATGAGATGATATTAATGA
1 AATT-ATGAGATGATATTAATGA
11969148 AATTATGAGATGATATTAATGA
1 AATTATGAGATGATATTAATGA
11969170 AATTAT
1 AATTAT
11969176 AAACAGATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (22 bp):
AATTATGAGATGATATTAATGA
Found at i:11973382 original size:2 final size:2
Alignment explanation
Indices: 11973375--11973402 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11973365 AAATTTTGAA
11973375 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
11973403 TGAATTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11974043 original size:2 final size:2
Alignment explanation
Indices: 11974036--11974079 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
11974026 NNNNNNNNCT
* **
11974036 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TT TA GG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11974077 TA T
1 TA T
11974080 TCTAATACGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11979271 original size:30 final size:30
Alignment explanation
Indices: 11979235--11979295 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
11979225 CTGCCCAGTG
11979235 TTAGTGGACACATCCGGTAAAAGGAAAGGA
1 TTAGTGGACACATCCGGTAAAAGGAAAGGA
*
11979265 TTAGTGGATACATCCGGTAAAAGGAAAGGA
1 TTAGTGGACACATCCGGTAAAAGGAAAGGA
11979295 T
1 T
11979296 CCCAAGTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.30, T:0.20
Consensus pattern (30 bp):
TTAGTGGACACATCCGGTAAAAGGAAAGGA
Found at i:11995972 original size:3 final size:3
Alignment explanation
Indices: 11995966--11995994 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11995956 ATAAATTATT
11995966 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
11995995 ATTAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:11997082 original size:23 final size:24
Alignment explanation
Indices: 11997052--11997119 Score: 86
Period size: 23 Copynumber: 2.9 Consensus size: 24
11997042 CTTGATTGTT
* *
11997052 AGAATATGTCACACAGGCTTT-CC
1 AGAATATGCCACAAAGGCTTTACC
*
11997075 AGAATATGCCACATAGGCTTTACC
1 AGAATATGCCACAAAGGCTTTACC
*
11997099 -GAATACGCCACAAAGGCTTTA
1 AGAATATGCCACAAAGGCTTTA
11997120 TAGGACATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 38 0.95
24 2 0.05
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (24 bp):
AGAATATGCCACAAAGGCTTTACC
Found at i:12001121 original size:14 final size:15
Alignment explanation
Indices: 12001102--12001131 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12001092 ATCGTTATCG
12001102 AGTTTAAAA-CTTTC
1 AGTTTAAAATCTTTC
12001116 AGTTTAAAATCTTTC
1 AGTTTAAAATCTTTC
12001131 A
1 A
12001132 TTTGGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (15 bp):
AGTTTAAAATCTTTC
Found at i:12001941 original size:20 final size:19
Alignment explanation
Indices: 12001903--12001947 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
12001893 GGTTTGACCA
* *
12001903 AGTTTAGGGTCTTGGTCCC
1 AGTTTTGGGTCTAGGTCCC
12001922 AGTTTTGGGCTCTAGGTCCC
1 AGTTTTGGG-TCTAGGTCCC
*
12001942 AATTTT
1 AGTTTT
12001948 CGATCTCAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (19 bp):
AGTTTTGGGTCTAGGTCCC
Found at i:12003152 original size:27 final size:27
Alignment explanation
Indices: 12003121--12003177 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
12003111 ATCCATTCAC
12003121 TCAATACAATTTTATTTTATCTCAATG
1 TCAATACAATTTTATTTTATCTCAATG
12003148 TCAATACAATTTTATTTTATCTCAATG
1 TCAATACAATTTTATTTTATCTCAATG
12003175 TCA
1 TCA
12003178 CCATTGTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.47
Consensus pattern (27 bp):
TCAATACAATTTTATTTTATCTCAATG
Found at i:12003966 original size:27 final size:27
Alignment explanation
Indices: 12003912--12003967 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
12003902 CTTTCAATCG
* *
12003912 TTCAAATAAATAGAAAATAGTTATAAA
1 TTCAAATAAATAGAAAATAGCTAAAAA
*
12003939 TTCAAATAAATATAAAATA-CTACAAAA
1 TTCAAATAAATAGAAAATAGCTA-AAAA
12003966 TT
1 TT
12003968 TCCCAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (27 bp):
TTCAAATAAATAGAAAATAGCTAAAAA
Found at i:12009339 original size:22 final size:22
Alignment explanation
Indices: 12009311--12009353 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12009301 CTTATATATA
12009311 GATATTG-TAAACCTTTTGTTTG
1 GATATTGTTAAA-CTTTTGTTTG
*
12009333 GATATTGTTGAACTTTTGTTT
1 GATATTGTTAAACTTTTGTTT
12009354 AAAAGCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.21, C:0.07, G:0.19, T:0.53
Consensus pattern (22 bp):
GATATTGTTAAACTTTTGTTTG
Found at i:12038505 original size:85 final size:83
Alignment explanation
Indices: 12038410--12038577 Score: 300
Period size: 85 Copynumber: 2.0 Consensus size: 83
12038400 ACTAATATCG
12038410 AATTCGAATGATATAAGAGGAGTTTAGAGTACATCTATTTATAGCTTAAAAAAAACCTTATTCTA
1 AATTCGAATGATATAAGAGGAGTTTAGAGTACATCTATTTATAGCTT--AAAAAACCTTATTCTA
12038475 ATCAATGTCAAATAGATGAA
64 ATCAATGTCAAATAGATGAA
* *
12038495 AATTCGAATGATATAAGAGGAGTTTAGAGTACATCTATTTATAGCTTAAATAATCTTATTCTAAT
1 AATTCGAATGATATAAGAGGAGTTTAGAGTACATCTATTTATAGCTTAAAAAACCTTATTCTAAT
12038560 CAATGTCAAATAGATGAA
66 CAATGTCAAATAGATGAA
12038578 GTGTAGTAAT
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
83 34 0.42
85 47 0.58
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (83 bp):
AATTCGAATGATATAAGAGGAGTTTAGAGTACATCTATTTATAGCTTAAAAAACCTTATTCTAAT
CAATGTCAAATAGATGAA
Found at i:12041780 original size:37 final size:35
Alignment explanation
Indices: 12041723--12041794 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 35
12041713 TCTCTATAAT
*
12041723 ATTAAATTAATAAAATACTATTAAGATAAGTATTAA
1 ATTAAATTAATAAAATACTATTAAAATAA-TATTAA
*
12041759 ATTAAATTTAATATTAA-ACTATTAAAATAATATTAA
1 ATTAAA-TTAATA-AAATACTATTAAAATAATATTAA
12041795 TTTTAGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 12 0.38
37 18 0.56
38 2 0.06
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (35 bp):
ATTAAATTAATAAAATACTATTAAAATAATATTAA
Found at i:12043224 original size:77 final size:77
Alignment explanation
Indices: 12043131--12043285 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
12043121 CTTCTCAGTA
12043131 TTTGAATCAAATTCTCACTTTGATTCTTTTACGGGATTACGAATTTATTTAGATTATCTACTGAA
1 TTTGAATCAAATTCTCACTTTGATTCTTTTACGGGATTACGAATTTATTTAGATTATCTACTGAA
12043196 GTAAGTTGTCTT
66 GTAAGTTGTCTT
12043208 TTTGAATCAAATTCTCACTTTGATTCTTTTACGGGATTACGAATTTATTTAGATTATCTACTGAA
1 TTTGAATCAAATTCTCACTTTGATTCTTTTACGGGATTACGAATTTATTTAGATTATCTACTGAA
12043273 GTAAGTTGTCTT
66 GTAAGTTGTCTT
12043285 T
1 T
12043286 CTCGCAATGT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (77 bp):
TTTGAATCAAATTCTCACTTTGATTCTTTTACGGGATTACGAATTTATTTAGATTATCTACTGAA
GTAAGTTGTCTT
Found at i:12044707 original size:23 final size:23
Alignment explanation
Indices: 12044681--12044735 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
12044671 GTCAATGTCG
12044681 AAGGCATCTCATCTAACCTTAGC
1 AAGGCATCTCATCTAACCTTAGC
12044704 AAGGCATCTCATCTAACCTTAGC
1 AAGGCATCTCATCTAACCTTAGC
12044727 AAGGCATCT
1 AAGGCATCT
12044736 TTCAAATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (23 bp):
AAGGCATCTCATCTAACCTTAGC
Found at i:12046058 original size:21 final size:22
Alignment explanation
Indices: 12046034--12046080 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
12046024 GGTTCGCATT
* *
12046034 ACATATAGGCTT-GCATATGAC
1 ACATATAAGCTTCACATATGAC
*
12046055 ACATATAAGCTTCACATATTAC
1 ACATATAAGCTTCACATATGAC
12046077 ACAT
1 ACAT
12046081 GTTATAGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (22 bp):
ACATATAAGCTTCACATATGAC
Found at i:12046360 original size:38 final size:38
Alignment explanation
Indices: 12046305--12046382 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
12046295 TTCACATGTA
* **
12046305 ATATTTTGACTCACATGTAATAATTACAGGTGACTCGC
1 ATATATTGACTCACATGTAATAACAACAGGTGACTCGC
*
12046343 ATATATTGACTCTCATGTAATAACAACAGGTGACTCGC
1 ATATATTGACTCACATGTAATAACAACAGGTGACTCGC
12046381 AT
1 AT
12046383 GGCATAACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (38 bp):
ATATATTGACTCACATGTAATAACAACAGGTGACTCGC
Found at i:12046383 original size:24 final size:24
Alignment explanation
Indices: 12046349--12046414 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 24
12046339 TCGCATATAT
* * *
12046349 TGACTCTCATGTAATAACAACAGG
1 TGACTCACATGGAATAACAACAAG
* *
12046373 TGACTCGCATGGCATAACAACAAG
1 TGACTCACATGGAATAACAACAAG
*
12046397 TGACTCACATGGTATAAC
1 TGACTCACATGGAATAAC
12046415 CTAGGGTTCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (24 bp):
TGACTCACATGGAATAACAACAAG
Found at i:12046592 original size:53 final size:53
Alignment explanation
Indices: 12046535--12046636 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
12046525 GCACACATGT
*
12046535 TCACACACAT-GCTCACACACGGGCTCGCACCTATAGGGGGTTCGCACATAGGC
1 TCACACAC-TGGCTCACACACGGACTCGCACCTATAGGGGGTTCGCACATAGGC
* *
12046588 TCACACACTGGCTCGCACACGGACTCGCACCTATAGGGGGTTTGCACAT
1 TCACACACTGGCTCACACACGGACTCGCACCTATAGGGGGTTCGCACAT
12046637 GCTAGTTCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.02
53 44 0.98
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.19
Consensus pattern (53 bp):
TCACACACTGGCTCACACACGGACTCGCACCTATAGGGGGTTCGCACATAGGC
Found at i:12065014 original size:31 final size:31
Alignment explanation
Indices: 12064987--12065047 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
12064977 TAATTTATAT
12064987 TTTATGTATCATTATATTAAATTATTTAAAC
1 TTTATGTATCATTATATTAAATTATTTAAAC
* * * *
12065018 TTTATTTATTATTATATTTAATTTTTTAAA
1 TTTATGTATCATTATATTAAATTATTTAAA
12065048 ATATTTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (31 bp):
TTTATGTATCATTATATTAAATTATTTAAAC
Found at i:12076512 original size:23 final size:23
Alignment explanation
Indices: 12076472--12076516 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12076462 ATAGAAAAAG
*
12076472 ATATATATGCAACGATATATATT
1 ATATATATGAAACGATATATATT
12076495 ATATATTATGAAAC-ATATATAT
1 ATATA-TATGAAACGATATATAT
12076517 ATTAATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (23 bp):
ATATATATGAAACGATATATATT
Found at i:12078635 original size:92 final size:92
Alignment explanation
Indices: 12078478--12078951 Score: 905
Period size: 92 Copynumber: 5.1 Consensus size: 92
12078468 GTTTAAAAGC
12078478 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
12078543 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
12078570 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
12078635 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
*
12078662 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAATA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
12078727 TTACTATTTTTTTAATATTATAACATAT
66 TTACTATTTTTTTAATATTAT-ACATAT
12078755 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAAATTTATAACTTAAATAAGT
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAAT-AAATTTATAACTTAAATAAGT
*
12078820 ATTACTA-TTTTTCAATATTATACATAT
65 ATTACTATTTTTTTAATATTATACATAT
12078847 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
12078912 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
12078939 ATTCATTTACGTA
1 ATTCATTTACGTA
12078952 ACACATAACT
Statistics
Matches: 375, Mismatches: 4, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
91 28 0.07
92 258 0.69
93 62 0.17
94 27 0.07
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (92 bp):
ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
TTACTATTTTTTTAATATTATACATAT
Found at i:12078805 original size:42 final size:42
Alignment explanation
Indices: 12078759--12078896 Score: 95
Period size: 42 Copynumber: 3.1 Consensus size: 42
12078749 ACATATATTC
12078759 ATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAA
1 ATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAA
* * * * **
12078801 ATTTATAACTTAAATAAGTATTA-CTATTTTTCAATATTA-TACAT-ATATTC
1 A-TT-T-ACGT--AT--GTA--AGCTATATTTAAATTTTATTA-ATAATA-AA
12078851 ATTTACGTATGTAAGCTATATTTAAATTTTATTAATAAT-AA
1 ATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAA
12078892 ATTTA
1 ATTTA
12078897 TAACTTAAAT
Statistics
Matches: 70, Mismatches: 12, Indels: 29
0.63 0.11 0.26
Matches are distributed among these distances:
41 6 0.09
42 16 0.23
43 9 0.13
44 1 0.01
45 5 0.07
47 5 0.07
48 1 0.01
49 10 0.14
50 16 0.23
51 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (42 bp):
ATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAA
Found at i:12078866 original size:185 final size:184
Alignment explanation
Indices: 12078478--12078951 Score: 905
Period size: 185 Copynumber: 2.6 Consensus size: 184
12078468 GTTTAAAAGC
12078478 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
12078543 TTACTATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTA
66 TTACTATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTA
*
12078608 ATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATAT
131 ATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTCAATATTATACATAT
*
12078662 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAATA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
12078727 TTACTATTTTTTTAATATTATAACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATT
66 TTACTATTTTTTTAATATTAT-ACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATT
12078792 AATAATAAAATTTATAACTTAAATAAGTATTACTA-TTTTTCAATATTATACATAT
130 AATAAT-AAATTTATAACTTAAATAAGTATTACTATTTTTTCAATATTATACATAT
12078847 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
12078912 TTACTATTTTTTTAATATTATACATATATTCATTTACGTA
66 TTACTATTTTTTTAATATTATACATATATTCATTTACGTA
12078952 ACACATAACT
Statistics
Matches: 285, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
184 104 0.36
185 153 0.54
186 28 0.10
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (184 bp):
ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
TTACTATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTA
ATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTCAATATTATACATAT
Found at i:12078968 original size:9 final size:9
Alignment explanation
Indices: 12078954--12079347 Score: 134
Period size: 9 Copynumber: 45.7 Consensus size: 9
12078944 TTTACGTAAC
12078954 ACATAACTT
1 ACATAACTT
*
12078963 ACATAACCT
1 ACATAACTT
*
12078972 ACTTAA--T
1 ACATAACTT
*
12078979 ATATAACTT
1 ACATAACTT
*
12078988 GCATAACTT
1 ACATAACTT
* *
12078997 AAATAAGTT
1 ACATAACTT
*
12079006 ACGTAA-TAAT
1 ACATAACT--T
12079016 ACATAA--T
1 ACATAACTT
*
12079023 ACACAACTT
1 ACATAACTT
* *
12079032 ACAT-GCGT
1 ACATAACTT
*
12079040 AAATAA--T
1 ACATAACTT
* *
12079047 ACAGAGCTT
1 ACATAACTT
12079056 ACATAACTT
1 ACATAACTT
* *
12079065 ACATACCCT
1 ACATAACTT
*
12079074 ACATAAATT
1 ACATAACTT
* *
12079083 AAATAAGTT
1 ACATAACTT
12079092 ACATAA-TAAT
1 ACATAACT--T
* * *
12079102 ACGTACCCT
1 ACATAACTT
*
12079111 ACATAAATT
1 ACATAACTT
* *
12079120 AAATAAGTT
1 ACATAACTT
*
12079129 ACATAAATT
1 ACATAACTT
* *
12079138 AAATAAGTT
1 ACATAACTT
12079147 ACATAA-TAAT
1 ACATAACT--T
* *
12079157 ACATACCCT
1 ACATAACTT
12079166 ACATAACTT
1 ACATAACTT
*
12079175 ACATAA--G
1 ACATAACTT
12079182 ACATAACTT
1 ACATAACTT
*
12079191 TCATAA--T
1 ACATAACTT
*
12079198 ACACAACTT
1 ACATAACTT
**
12079207 ACGCAACTT
1 ACATAACTT
*
12079216 ACATAA--G
1 ACATAACTT
12079223 ACATAACTT
1 ACATAACTT
*
12079232 ACAT--GTGT
1 ACATAACT-T
*
12079240 AAATAA--T
1 ACATAACTT
**
12079247 ACATATTTT
1 ACATAACTT
12079256 ACATAACTT
1 ACATAACTT
*
12079265 ACATAA--G
1 ACATAACTT
12079272 ACATAACTT
1 ACATAACTT
*
12079281 ACATAAGTT
1 ACATAACTT
*
12079290 TCATAA--T
1 ACATAACTT
* *
12079297 ACACATCTT
1 ACATAACTT
**
12079306 ACGCAACTT
1 ACATAACTT
*
12079315 ACACAACTT
1 ACATAACTT
12079324 ACATAACTT
1 ACATAACTT
12079333 ACATAACTT
1 ACATAACTT
12079342 ACATAA
1 ACATAA
12079348 TGTATACCTT
Statistics
Matches: 279, Mismatches: 76, Indels: 60
0.67 0.18 0.14
Matches are distributed among these distances:
7 48 0.17
8 12 0.04
9 202 0.72
10 17 0.06
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (9 bp):
ACATAACTT
Found at i:12079181 original size:55 final size:55
Alignment explanation
Indices: 12079041--12079181 Score: 201
Period size: 55 Copynumber: 2.6 Consensus size: 55
12079031 TACATGCGTA
* * * **
12079041 AATAATACAGAGCTTACATAACTTACATACCCTACATAAATTAAATAAGTTACAT
1 AATAATACATACCCTACATAACTTACATAAGCTACATAAATTAAATAAGTTACAT
* * * *
12079096 AATAATACGTACCCTACATAAATTAAATAAGTTACATAAATTAAATAAGTTACAT
1 AATAATACATACCCTACATAACTTACATAAGCTACATAAATTAAATAAGTTACAT
12079151 AATAATACATACCCTACATAACTTACATAAG
1 AATAATACATACCCTACATAACTTACATAAG
12079182 ACATAACTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 74 1.00
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (55 bp):
AATAATACATACCCTACATAACTTACATAAGCTACATAAATTAAATAAGTTACAT
Found at i:12079185 original size:16 final size:16
Alignment explanation
Indices: 12079166--12079287 Score: 82
Period size: 16 Copynumber: 8.0 Consensus size: 16
12079156 TACATACCCT
12079166 ACATAACTTACATAAG
1 ACATAACTTACATAAG
* *
12079182 ACATAACTTTCATAAT
1 ACATAACTTACATAAG
*
12079198 ACACAACTTAC----G
1 ACATAACTTACATAAG
12079210 -C--AACTTACATAAG
1 ACATAACTTACATAAG
**
12079223 ACATAACTTACATGTG
1 ACATAACTTACATAAG
* **
12079239 TAAATAA--TACATATTTT
1 -ACATAACTTACATA--AG
12079256 ACATAACTTACATAAG
1 ACATAACTTACATAAG
12079272 ACATAACTTACATAAG
1 ACATAACTTACATAAG
12079288 TTTCATAATA
Statistics
Matches: 81, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
9 7 0.09
11 1 0.01
13 1 0.01
14 1 0.01
15 5 0.06
16 54 0.67
17 6 0.07
18 6 0.07
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.30
Consensus pattern (16 bp):
ACATAACTTACATAAG
Found at i:12079214 original size:25 final size:25
Alignment explanation
Indices: 12079186--12079317 Score: 70
Period size: 25 Copynumber: 5.3 Consensus size: 25
12079176 CATAAGACAT
* *
12079186 AACTTTCATAATACACAACTTACGC
1 AACTTACATAAGACACAACTTACGC
*
12079211 AACTTACATAAGACATAACTTA--C
1 AACTTACATAAGACACAACTTACGC
** * * * ** **
12079234 ATGTGTAAATAATACATATTTTACAT
1 AACT-TACATAAGACACAACTTACGC
* **
12079260 AACTTACATAAGACATAACTTACAT
1 AACTTACATAAGACACAACTTACGC
* * * *
12079285 AAGTTTCATAATACACATCTTACGC
1 AACTTACATAAGACACAACTTACGC
12079310 AACTTACA
1 AACTTACA
12079318 CAACTTACAT
Statistics
Matches: 79, Mismatches: 25, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
23 3 0.04
24 14 0.18
25 60 0.76
26 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.31
Consensus pattern (25 bp):
AACTTACATAAGACACAACTTACGC
Found at i:12084872 original size:66 final size:65
Alignment explanation
Indices: 12084765--12084935 Score: 218
Period size: 66 Copynumber: 2.6 Consensus size: 65
12084755 GAGCAAATTA
* * * *
12084765 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
12084829 G
65 G
* *
12084830 CTACAACTAAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
12084895 G
65 G
* * * *
12084896 CAGCAGCTTAAAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
12084936 CGGCAGCGAG
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 2 0.02
66 86 0.93
67 4 0.04
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.12
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:12084932 original size:21 final size:21
Alignment explanation
Indices: 12084906--12085014 Score: 74
Period size: 21 Copynumber: 5.2 Consensus size: 21
12084896 CAGCAGCTTA
*
12084906 AAGCAGATGCGGCAGCAAGAG
1 AAGCAGAGGCGGCAGCAAGAG
*
12084927 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAGCAAGAG
* * * * * *
12084948 AAGTACAGGCTGCAACGAGGG
1 AAGCAGAGGCGGCAGCAAGAG
*** * *
12084969 AAGCAGAGGCTAAAGCGAGGG
1 AAGCAGAGGCGGCAGCAAGAG
* * *
12084990 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAGCAAGAG
12085011 AAGC
1 AAGC
12085015 CAAGCAGCGT
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.35, C:0.18, G:0.42, T:0.05
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:12084972 original size:42 final size:42
Alignment explanation
Indices: 12084926--12085014 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
12084916 GGCAGCAAGA
** *
12084926 GAAGCAGAGGCGGCAGCGAGAGAAGTACAGGCTGCAACGAGG
1 GAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCTGCAACGAGG
* * * *
12084968 GAAGCAGAGGCTAAAGCGAGGGAAGCAGAGGCTGCAGCGAGG
1 GAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCTGCAACGAGG
12085010 GAAGC
1 GAAGC
12085015 CAAGCAGCGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.44, T:0.04
Consensus pattern (42 bp):
GAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCTGCAACGAGG
Found at i:12085437 original size:43 final size:44
Alignment explanation
Indices: 12085390--12085584 Score: 195
Period size: 43 Copynumber: 4.5 Consensus size: 44
12085380 ATTTTTGGTC
*
12085390 AAAGCGCCGCTAAAGATAAGGGTT-TTTAGCGGCGTTTGTGGGG
1 AAAGCGCCGCTAAAGATCAGGGTTCTTTAGCGGCGTTTGTGGGG
* * **
12085433 AAAGCGCCGCTAAAGATTA-GGTTCTTTAGTGGCGTTTTGTTGTCG
1 AAAGCGCCGCTAAAGATCAGGGTTCTTTAGCGGCG-TTTG-TGGGG
* * *
12085478 -AAGCGCCGCTATAGATCAGGGTT-ATT-GCGGCGTTTGAGGGG
1 AAAGCGCCGCTAAAGATCAGGGTTCTTTAGCGGCGTTTGTGGGG
* * * **
12085519 AAAGCGCCGCTAAAGATTA-GGTTCTTTCGTGGCGTTTGTGGTC
1 AAAGCGCCGCTAAAGATCAGGGTTCTTTAGCGGCGTTTGTGGGG
* *
12085562 AAAGTGCCGCTATAGATCAGGGT
1 AAAGCGCCGCTAAAGATCAGGGT
12085585 CTATTACGAC
Statistics
Matches: 123, Mismatches: 21, Indels: 15
0.77 0.13 0.09
Matches are distributed among these distances:
41 6 0.05
42 26 0.21
43 59 0.48
44 25 0.20
45 7 0.06
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.29
Consensus pattern (44 bp):
AAAGCGCCGCTAAAGATCAGGGTTCTTTAGCGGCGTTTGTGGGG
Found at i:12085509 original size:86 final size:85
Alignment explanation
Indices: 12085370--12085620 Score: 322
Period size: 86 Copynumber: 2.9 Consensus size: 85
12085360 AGGTGTTGGC
* * * * * * *
12085370 CTTTATTGGCATTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTTTTTAGCGGCGTTTGTGGGGAA
1 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTTATT-GCGGCGTTTGAGGGGAA
12085435 AGCGCCGCTAAAGATTAGGTT
65 AGCGCCGCTAAAGATTAGGTT
* *
12085456 CTTTAGTGGCGTTTTGTTGTCGAAGCGCCGCTATAGATCAGGGTTATTGCGGCGTTTGAGGGGAA
1 CTTTAGTGGCG-TTTGTGGTCAAAGCGCCGCTATAGATCAGGGTTATTGCGGCGTTTGAGGGGAA
12085521 AGCGCCGCTAAAGATTAGGTT
65 AGCGCCGCTAAAGATTAGGTT
* * * * ***
12085542 CTTTCGTGGCGTTTGTGGTCAAAGTGCCGCTATAGATCAGGGTCTATTACGACGTTTGAGAAAAA
1 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGT-TATTGCGGCGTTTGAGGGGAA
*
12085607 AACGCCGCTAAAGA
65 AGCGCCGCTAAAGA
12085621 CCCTGATCTT
Statistics
Matches: 144, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
85 29 0.20
86 85 0.59
87 30 0.21
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (85 bp):
CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTTATTGCGGCGTTTGAGGGGAAA
GCGCCGCTAAAGATTAGGTT
Found at i:12085842 original size:22 final size:22
Alignment explanation
Indices: 12085814--12085856 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
12085804 CTGCGGCGCT
*
12085814 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
12085836 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
12085857 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:12094875 original size:15 final size:15
Alignment explanation
Indices: 12094855--12094884 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12094845 TAATCAAACC
12094855 CTCAAGAATGTCTAA
1 CTCAAGAATGTCTAA
12094870 CTCAAGAATGTCTAA
1 CTCAAGAATGTCTAA
12094885 GGGTACCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
CTCAAGAATGTCTAA
Found at i:12098125 original size:46 final size:41
Alignment explanation
Indices: 12098058--12098248 Score: 177
Period size: 36 Copynumber: 4.7 Consensus size: 41
12098048 TTTGAGTAAT
* *
12098058 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACAATTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGT-GC-TTAG-TAC--TTA
12098104 TCTGATCAAGTGAAAAAGTGATAA---GTGC-TAG-ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTGCTTAGTACTTA
* * *
12098140 TCTGATCAAGAGACAATGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGT-GC-TTAG-T--ACTTA
12098186 TCTGATCAAGTGAAAAAGTGATAA---GTG-TTA-TACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTGCTTAGTACTTA
12098222 TCTGATCAAGTGAAAAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
12098249 CTATACTTAT
Statistics
Matches: 124, Mismatches: 8, Indels: 33
0.75 0.05 0.20
Matches are distributed among these distances:
36 53 0.43
38 3 0.02
39 2 0.02
40 8 0.06
42 6 0.05
43 4 0.03
46 48 0.39
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (41 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTGCTTAGTACTTA
Found at i:12098142 original size:36 final size:36
Alignment explanation
Indices: 12098101--12098265 Score: 186
Period size: 36 Copynumber: 4.3 Consensus size: 36
12098091 TTAGCTACAA
12098101 TTATCTGATCAAGTGAAAAAGTGATAAGTGCTAGAC
1 TTATCTGATCAAGTGAAAAAGTGATAAGTGCTAGAC
* * *
12098137 TTATCTGATCAAGAGACAATGTGATAAGTGGTAGCTTTAGCTACAC
1 TTATCTGATCAAGTGAAAAAGTGATAA---GT-GC--TAG----AC
* *
12098183 TTATCTGATCAAGTGAAAAAGTGATAAGTGTTATAC
1 TTATCTGATCAAGTGAAAAAGTGATAAGTGCTAGAC
*
12098219 TTATCTGATCAAGTGAAAAAGTGATAAGTGCTATAC
1 TTATCTGATCAAGTGAAAAAGTGATAAGTGCTAGAC
12098255 TTATCTGATCA
1 TTATCTGATCA
12098266 GGGACAAATG
Statistics
Matches: 110, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
36 72 0.65
39 2 0.02
40 4 0.04
42 4 0.04
43 2 0.02
46 26 0.24
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (36 bp):
TTATCTGATCAAGTGAAAAAGTGATAAGTGCTAGAC
Found at i:12098195 original size:82 final size:82
Alignment explanation
Indices: 12098058--12098248 Score: 319
Period size: 82 Copynumber: 2.3 Consensus size: 82
12098048 TTTGAGTAAT
*
12098058 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACAATTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACAATTATCTGATCAAGTGAAAAAGT
12098123 GATAAGTGCTAGACTTA
66 GATAAGTGCTAGACTTA
* * *
12098140 TCTGATCAAGAGACAATGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACAATTATCTGATCAAGTGAAAAAGT
* *
12098205 GATAAGTGTTATACTTA
66 GATAAGTGCTAGACTTA
*
12098222 TCTGATCAAGTGAAAAAGTGATAAGTG
1 TCTGATCAAGAGAAAAAGTGATAAGTG
12098249 CTATACTTAT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 101 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (82 bp):
TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACAATTATCTGATCAAGTGAAAAAGT
GATAAGTGCTAGACTTA
Found at i:12105945 original size:46 final size:45
Alignment explanation
Indices: 12105878--12106111 Score: 247
Period size: 36 Copynumber: 5.6 Consensus size: 45
12105868 TTTGAGTAAT
* *
12105878 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
12105924 TCTGATCAAGTGAAAAAGTGATAA---GT-G--T---TACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
12105960 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
12106006 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
12106042 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
12106087 TCTAATC-AGGGACAAA-TGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
12106112 ATCATACGTA
Statistics
Matches: 160, Mismatches: 9, Indels: 41
0.76 0.04 0.20
Matches are distributed among these distances:
36 58 0.36
38 1 0.01
39 5 0.03
40 5 0.03
41 2 0.01
42 3 0.02
43 15 0.09
44 8 0.05
45 11 0.07
46 52 0.32
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:12106015 original size:82 final size:82
Alignment explanation
Indices: 12105878--12106111 Score: 384
Period size: 82 Copynumber: 2.9 Consensus size: 82
12105868 TTTGAGTAAT
*
12105878 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
12105943 GATAAGTGTTACACTTA
66 GATAAGTGCTACACTTA
12105960 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
12106025 GATAAGTGCTATACTTA
66 GATAAGTGCTACACTTA
* * * *
12106042 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTAATC-AGGGACAAA-T
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
12106104 GATAAGTG
66 GATAAGTG
12106112 ATCATACGTA
Statistics
Matches: 145, Mismatches: 7, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
79 9 0.06
80 7 0.05
81 19 0.13
82 110 0.76
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:12106806 original size:11 final size:11
Alignment explanation
Indices: 12106780--12106857 Score: 78
Period size: 11 Copynumber: 7.4 Consensus size: 11
12106770 TTAAAAATTA
12106780 AAAAATATAATTT
1 AAAAATAT--TTT
12106793 AAAAATATTTT
1 AAAAATATTTT
12106804 AAAAATATTTT
1 AAAAATATTTT
12106815 --AAA-A--TT
1 AAAAATATTTT
*
12106821 AAAAA-AATTT
1 AAAAATATTTT
12106831 AAAAATTATTTT
1 AAAAA-TATTTT
12106843 AAAAATATTTT
1 AAAAATATTTT
12106854 AAAA
1 AAAA
12106858 TTGAAAAATA
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
6 2 0.03
8 5 0.09
9 3 0.05
10 7 0.12
11 24 0.41
12 9 0.16
13 8 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:12106825 original size:28 final size:28
Alignment explanation
Indices: 12106791--12106846 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
12106781 AAAATATAAT
*
12106791 TTAAAAATATTTTAAAAA-TATTTTAAAA
1 TTAAAAA-AATTTAAAAATTATTTTAAAA
12106819 TTAAAAAAATTTAAAAATTATTTTAAAA
1 TTAAAAAAATTTAAAAATTATTTTAAAA
12106847 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
TTAAAAAAATTTAAAAATTATTTTAAAA
Found at i:12106852 original size:39 final size:38
Alignment explanation
Indices: 12106788--12106912 Score: 189
Period size: 39 Copynumber: 3.2 Consensus size: 38
12106778 TAAAAAATAT
12106788 AATTTAAAAA-TATTTTAAAAATATTTTAAAATTAAAAA
1 AATTTAAAAATTATTTTAAAAATATTTTAAAATT-AAAA
*
12106826 AATTTAAAAATTATTTTAAAAATATTTTAAAATTGAAA
1 AATTTAAAAATTATTTTAAAAATATTTTAAAATTAAAA
**
12106864 AATAAAAAAATTTATTTTAAAAATATTTTAAAATTTAAAA
1 AATTTAAAAA-TTATTTTAAAAATATTTTAAAA-TTAAAA
12106904 AATTTAAAA
1 AATTTAAAA
12106913 TAAATATATT
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
38 21 0.27
39 45 0.58
40 12 0.15
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (38 bp):
AATTTAAAAATTATTTTAAAAATATTTTAAAATTAAAA
Found at i:12106902 original size:18 final size:16
Alignment explanation
Indices: 12106879--12106913 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
12106869 AAAAATTTAT
12106879 TTTAAAAATATTTTAAAA
1 TTTAAAAA-A-TTTAAAA
12106897 TTTAAAAAATTTAAAA
1 TTTAAAAAATTTAAAA
12106913 T
1 T
12106914 AAATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 1 0.06
18 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTAAAAAATTTAAAA
Found at i:12108854 original size:21 final size:21
Alignment explanation
Indices: 12108809--12108855 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
12108799 AAACAATAAA
*
12108809 ATAG-ATTATATAGTATTTTT
1 ATAGTATTATATAGTATATTT
*
12108829 ATAGTATTATATATTATGATTT
1 ATAGTATTATATAGTAT-ATTT
12108851 -TAGTA
1 ATAGTA
12108856 AATTCATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 16 0.70
22 3 0.13
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (21 bp):
ATAGTATTATATAGTATATTT
Found at i:12108911 original size:26 final size:26
Alignment explanation
Indices: 12108882--12108975 Score: 71
Period size: 26 Copynumber: 3.4 Consensus size: 26
12108872 ATATTAAGAG
12108882 TTTTATTAAATTATATTTAATAATAA
1 TTTTATTAAATTATATTTAATAATAA
* * ** *
12108908 TTTTGTTAAAATATGGTTAGATTATTTATTAT
1 TTTTATTAAATTATATTTA-A-TA---A-TAA
*
12108940 TTTTATTAAATTATTTTTAATAATAA
1 TTTTATTAAATTATATTTAATAATAA
*
12108966 TATTATTAAA
1 TTTTATTAAA
12108976 ATTTAATAAC
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
26 26 0.51
27 2 0.04
28 2 0.04
30 2 0.04
31 2 0.04
32 17 0.33
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (26 bp):
TTTTATTAAATTATATTTAATAATAA
Found at i:12108991 original size:6 final size:6
Alignment explanation
Indices: 12108980--12109008 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12108970 ATTAAAATTT
12108980 AATAAC AATAAC AATAAC AATAAC AATAA
1 AATAAC AATAAC AATAAC AATAAC AATAA
12109009 TCATCTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAC
Found at i:12109575 original size:21 final size:21
Alignment explanation
Indices: 12109549--12109591 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12109539 TGGTTGTTAT
12109549 ACACCTATAACAACACTTGAG
1 ACACCTATAACAACACTTGAG
* *
12109570 ACACCTATAATAACATTTGAG
1 ACACCTATAACAACACTTGAG
12109591 A
1 A
12109592 TTTAGGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.23
Consensus pattern (21 bp):
ACACCTATAACAACACTTGAG
Found at i:12109709 original size:15 final size:15
Alignment explanation
Indices: 12109687--12109730 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
12109677 AATGTAATTC
12109687 TATTAATTAAAAATA
1 TATTAATTAAAAATA
*
12109702 TTTTAATTTAAATAATA
1 TATTAA-TTAAA-AATA
12109719 TATTAATTAAAA
1 TATTAATTAAAA
12109731 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 6 0.24
16 10 0.40
17 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTAATTAAAAATA
Found at i:12109724 original size:17 final size:17
Alignment explanation
Indices: 12109687--12109731 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
12109677 AATGTAATTC
12109687 TATTAA-TTAAA-AATA
1 TATTAATTTAAATAATA
*
12109702 TTTTAATTTAAATAATA
1 TATTAATTTAAATAATA
*
12109719 TATTAATTAAAAT
1 TATTAATTTAAAT
12109732 TTATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 5 0.20
16 5 0.20
17 15 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTAATTTAAATAATA
Found at i:12110543 original size:32 final size:32
Alignment explanation
Indices: 12110502--12110566 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
12110492 AAAGATGAAA
*
12110502 AATTAAATAAAAGGTTAAAATGACTTTTTTTT
1 AATTAAATAAAAGGTTAAAATGAATTTTTTTT
12110534 AATTAAATAAAAGGTTAAAATGAATTTTTTTT
1 AATTAAATAAAAGGTTAAAATGAATTTTTTTT
12110566 A
1 A
12110567 TAAAATTGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (32 bp):
AATTAAATAAAAGGTTAAAATGAATTTTTTTT
Found at i:12112521 original size:196 final size:196
Alignment explanation
Indices: 12112187--12112587 Score: 658
Period size: 196 Copynumber: 2.0 Consensus size: 196
12112177 GAAGATACCC
* *
12112187 CACAATTCCGTTAATAATGCAAATTTCACAAAGGATTGAGAAGCCAACATTCTTAGCTCCATGGT
1 CACAATTCCGTTAATAATGCAAATTCCACAAAGGATTGAGAAGCCAACATTCTTAGCTCCATGGC
* *
12112252 AGTCCCAAATAGCTCCACCTGCCCTAACTTTCTCACCTAAAAAGACTCAACTACCATCAACATTC
66 AATCCCAAATAGCTCCACCTGCCCTAACTCTCTCACCTAAAAAGACTCAACTACCATCAACATTC
* * *
12112317 AACTTAAACCAATCATGTGGAGGTTTCTCCCAACTTAACATCACAGTACTCTTTTTCCTTATCAT
131 AACTTAAACCAATCATGTGGAGGTTTCTCCCAACATAACATCACAATACTCTTTTTCCTTAGCAT
12112382 A
196 A
* *
12112383 CACAATTCTGTTAATACTGCAAATTCCACAAAGGATTGAGAAGCCAACATTCTTAGCTCCATGGC
1 CACAATTCCGTTAATAATGCAAATTCCACAAAGGATTGAGAAGCCAACATTCTTAGCTCCATGGC
* * * *
12112448 AATCCCGAATAGCTCCACCTGCCCTAGCTCTCTTACCTAAAAAGACTCAACTACCATTAACATTC
66 AATCCCAAATAGCTCCACCTGCCCTAACTCTCTCACCTAAAAAGACTCAACTACCATCAACATTC
*
12112513 AACTTAAACCAATCATGTGGAGGTTTCTCCCAACATAACATCATAATACTCTTTTTCCTTAGCAT
131 AACTTAAACCAATCATGTGGAGGTTTCTCCCAACATAACATCACAATACTCTTTTTCCTTAGCAT
12112578 A
196 A
*
12112579 GACTAATTC
1 CAC-AATTC
12112588 GTTCAAAATT
Statistics
Matches: 189, Mismatches: 15, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
196 184 0.97
197 5 0.03
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.28
Consensus pattern (196 bp):
CACAATTCCGTTAATAATGCAAATTCCACAAAGGATTGAGAAGCCAACATTCTTAGCTCCATGGC
AATCCCAAATAGCTCCACCTGCCCTAACTCTCTCACCTAAAAAGACTCAACTACCATCAACATTC
AACTTAAACCAATCATGTGGAGGTTTCTCCCAACATAACATCACAATACTCTTTTTCCTTAGCAT
A
Found at i:12115534 original size:24 final size:25
Alignment explanation
Indices: 12115502--12115549 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
12115492 GGATGTTGCA
* *
12115502 AAGAGCTAT-TAACGGTAAGCTCGC
1 AAGAACTATATAACGGGAAGCTCGC
*
12115526 AAGAACTATATAATGGGAAGCTCG
1 AAGAACTATATAACGGGAAGCTCG
12115550 AGTGGGCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (25 bp):
AAGAACTATATAACGGGAAGCTCGC
Found at i:12115630 original size:164 final size:163
Alignment explanation
Indices: 12115425--12115916 Score: 664
Period size: 164 Copynumber: 3.0 Consensus size: 163
12115415 CTCATGAAGA
* * * * * *
12115425 GCCATATAACGGGATGCTTATAAAAGTTACGGTGTGTCTACAACACACGTAGGATCACAACCGAT
1 GCCATATAACGAGATGCTCATAAGAGCTACGGTGTGTCTACAACACATGCAGGATCACAACCGAT
* * * * *
12115490 CGGGATGTTGCAAAGAGCTATTAACGGTAAGCTCGCAAGAACTATATAATGGGAAGCTCGAGTGG
66 CGGGATGTTGC-AAGAGCTATTAACGGTAAGCTCGCAATAACCATATAACGAGAAGCTCGAGAGG
* *
12115555 GCTAAATATCAGGATGCTCATTAGAGATAATAAC
130 GCCAAATATCAGGATGCTCATGAGAGATAATAAC
12115589 GCCATATAACGAGATGCTCATAAGAGCTACGGTGTGTCTACAACACATGCAGGATCACAACCGAT
1 GCCATATAACGAGATGCTCATAAGAGCTACGGTGTGTCTACAACACATGCAGGATCACAACCGAT
*
12115654 CGGGATGCTTTG-AATAGCTATTAACGGTAAGCTCGCAATAACCATATAAC-ATGAAGCTCGAGA
66 CGGGATG--TTGCAAGAGCTATTAACGGTAAGCTCGCAATAACCATATAACGA-GAAGCTCGAGA
**
12115717 ATGCCAAATATCAGGATGCTCATGAGAGATAATAAC
128 GGGCCAAATATCAGGATGCTCATGAGAGATAATAAC
* ** * * *
12115753 GTCATATAACGAGATGCTCATAAGAGCTGTGGTGTGTCCACAACACATGCAGAATCACAACCAAT
1 GCCATATAACGAGATGCTCATAAGAGCTACGGTGTGTCTACAACACATGCAGGATCACAACCGAT
* * * * *
12115818 CGGGATGCTCCGAAGAGCTATTAACGGTAAGCTTGCAATAACCATATAACGAGAAGTTCAAGAGG
66 CGGGATGTTGC-AAGAGCTATTAACGGTAAGCTCGCAATAACCATATAACGAGAAGCTCGAGAGG
**
12115883 GCCAAATATCAATATGCTCATGAGAGATAATAAC
130 GCCAAATATCAGGATGCTCATGAGAGATAATAAC
12115917 AGGATGCTCT
Statistics
Matches: 290, Mismatches: 32, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
162 1 0.00
164 285 0.98
165 1 0.00
166 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (163 bp):
GCCATATAACGAGATGCTCATAAGAGCTACGGTGTGTCTACAACACATGCAGGATCACAACCGAT
CGGGATGTTGCAAGAGCTATTAACGGTAAGCTCGCAATAACCATATAACGAGAAGCTCGAGAGGG
CCAAATATCAGGATGCTCATGAGAGATAATAAC
Found at i:12116265 original size:21 final size:21
Alignment explanation
Indices: 12116241--12116282 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12116231 TAAATTTAAA
*
12116241 TCAATTTAATACAATTCACAT
1 TCAACTTAATACAATTCACAT
* *
12116262 TCAACTTATTCCAATTCACAT
1 TCAACTTAATACAATTCACAT
12116283 CTTAGGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (21 bp):
TCAACTTAATACAATTCACAT
Found at i:12118568 original size:54 final size:54
Alignment explanation
Indices: 12118502--12118607 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 54
12118492 CCATGTGACC
* * * *
12118502 CAAGTCAGTGAGTTACACAGGTAGAGACACGATCTGGGACACGA-CTGTGTGTTT
1 CAAGTCAATGAGTTACACAGGCAAAGACACGAGCTGGGACACGATC-GTGTGTTT
* *
12118556 CAAGTCAATGAGTTACACGGGCAAAGACACGGGCTGGGACACGATCGTGTGT
1 CAAGTCAATGAGTTACACAGGCAAAGACACGAGCTGGGACACGATCGTGTGT
12118608 CCCAACTTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 44 0.98
55 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.21
Consensus pattern (54 bp):
CAAGTCAATGAGTTACACAGGCAAAGACACGAGCTGGGACACGATCGTGTGTTT
Found at i:12120124 original size:50 final size:50
Alignment explanation
Indices: 12120000--12120240 Score: 198
Period size: 50 Copynumber: 4.7 Consensus size: 50
12119990 AATATAACAG
* * * ** * * *
12120000 GCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGT-TCCTTGTA-CT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT-CATATAGGT
* * **
12120049 GCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATAGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGT
* * * * * *
12120099 GCCCATGCCATGTCCGAGACATGGTCTTATAGGGGACCTCTCATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGT
* * * *
12120149 GCCAACGCCATGTCCCAGACATGATCTTACATAGGACCTCTCATAATCTCAATGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T--A-GGT
*
12120205 GCCAATGCCATGTCCCAGACATGGTCTTATATGGGA
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
12120241 TCTCATCCTC
Statistics
Matches: 150, Mismatches: 34, Indels: 9
0.78 0.18 0.05
Matches are distributed among these distances:
49 36 0.24
50 79 0.53
53 1 0.01
56 34 0.23
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (50 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGT
Found at i:12120165 original size:100 final size:102
Alignment explanation
Indices: 12120048--12120247 Score: 237
Period size: 100 Copynumber: 2.0 Consensus size: 102
12120038 TTCCTTGTAC
* * * * ** * *
12120048 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCAT-A-T-A-GGTGCCCATGCCA
1 TGCCAACGCCATATCCCAGACATGATCTTACATAGGACCTCTCATAACTAATGATGCCAATGCCA
*
12120109 TGTCCGAGACATGGTCTTATAGGGGACCTCTCATCTCGG
66 TGTCCCAGACATGGTCTTATAGGGGA--TCTCATCTCGG
*
12120148 TGCCAACGCCATGTCCCAGACATGATCTTACATAGGACCTCTCATAATCTCAATGATGCCAATGC
1 TGCCAACGCCATATCCCAGACATGATCTTACATAGGACCTCTCATAA-CT-AATGATGCCAATGC
*
12120213 CATGTCCCAGACATGGTCTTATATGGGATCTCATC
64 CATGTCCCAGACATGGTCTTATAGGGGATCTCATC
12120248 CTCTTAATGT
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
100 38 0.46
101 1 0.01
103 1 0.01
104 7 0.08
105 1 0.01
106 35 0.42
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (102 bp):
TGCCAACGCCATATCCCAGACATGATCTTACATAGGACCTCTCATAACTAATGATGCCAATGCCA
TGTCCCAGACATGGTCTTATAGGGGATCTCATCTCGG
Found at i:12121576 original size:81 final size:82
Alignment explanation
Indices: 12121441--12121602 Score: 290
Period size: 81 Copynumber: 2.0 Consensus size: 82
12121431 ATCAGGATGT
* *
12121441 TACAAATTTACCTTAAACTTTTAGAATTATTTCAAATTATCCCCTATTTTTTCTTAGA-ATTTTT
1 TACAAATTTACCCTAAACTTTTAGAATTATTTCAAATTAGCCCCTATTTTTTCTTAGACATTTTT
12121505 AGCCCCTATTTTTCTTA
66 AGCCCCTATTTTTCTTA
*
12121522 TACAAATTTACCCTAAACTTTTAGAATTATTTCAAATTAGCCCCTATTTTTTCTTAGACTTTTTT
1 TACAAATTTACCCTAAACTTTTAGAATTATTTCAAATTAGCCCCTATTTTTTCTTAGACATTTTT
12121587 AGCCCCTATTTTTCTT
66 AGCCCCTATTTTTCTT
12121603 GTACTTTTTT
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
81 56 0.73
82 21 0.27
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (82 bp):
TACAAATTTACCCTAAACTTTTAGAATTATTTCAAATTAGCCCCTATTTTTTCTTAGACATTTTT
AGCCCCTATTTTTCTTA
Found at i:12121615 original size:27 final size:27
Alignment explanation
Indices: 12121558--12121612 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
12121548 TTATTTCAAA
12121558 TTAGCCCCTATTTTTTCTTAGACTTTT
1 TTAGCCCCTATTTTTTCTTAGACTTTT
12121585 TTAGCCCCTA-TTTTTCTT-GTACTTTT
1 TTAGCCCCTATTTTTTCTTAG-ACTTTT
12121611 TT
1 TT
12121613 TAGGGTCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 1 0.04
26 16 0.59
27 10 0.37
ACGTcount: A:0.13, C:0.22, G:0.07, T:0.58
Consensus pattern (27 bp):
TTAGCCCCTATTTTTTCTTAGACTTTT
Found at i:12123305 original size:2 final size:2
Alignment explanation
Indices: 12123300--12123324 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12123290 AAGCAAAAAA
12123300 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
12123325 AAAAGCTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.