Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 31 of 33
Found at i:5264753 original size:2 final size:2
Alignment explanation
Indices: 5264709--5264738 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5264699 TGCTTTTTCT
5264709 TA TA 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 TA TA
5264739 CACATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5274152 original size:22 final size:22
Alignment explanation
Indices: 5274118--5274161 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5274108 ACTCGTGAGA
* * *
5274118 TTTTTATCTATTTGTTTTTTTT
1 TTTTTATCAATTTCTTTATTTT
*
5274140 TTTTTGTCAATTTCTTTATTTT
1 TTTTTATCAATTTCTTTATTTT
5274162 CAATTTTTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.11, C:0.07, G:0.05, T:0.77
Consensus pattern (22 bp):
TTTTTATCAATTTCTTTATTTT
Found at i:5274193 original size:31 final size:31
Alignment explanation
Indices: 5274158--5274222 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
5274148 AATTTCTTTA
* *
5274158 TTTTCAATTTTTAATTTCTTT-TTTATGCTAT
1 TTTTCAATTTTTAATTTATTTGTTT-TGATAT
* *
5274189 TTTTCGATTTTTCATTTATTTGTTTTGATAT
1 TTTTCAATTTTTAATTTATTTGTTTTGATAT
5274220 TTT
1 TTT
5274223 CCATGCTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.69
Consensus pattern (31 bp):
TTTTCAATTTTTAATTTATTTGTTTTGATAT
Found at i:5274509 original size:2 final size:2
Alignment explanation
Indices: 5274502--5274530 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5274492 TGTTTTCTTT
5274502 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
5274531 CTGAGTAGAG
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:5276149 original size:2 final size:2
Alignment explanation
Indices: 5276089--5276131 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
5276079 TAATGCTTTC
*
5276089 TA TA TA -A TA TA TG TA 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 TA TA TA TA TA TA TA TA
5276130 TA
1 TA
5276132 CCCACACATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5284002 original size:18 final size:20
Alignment explanation
Indices: 5283961--5284003 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 20
5283951 TATTTTGGTG
5283961 TAAAACTATTACAAATGTTA
1 TAAAACTATTACAAATGTTA
5283981 TAAAA-TATT-CAAAT-TTA
1 TAAAACTATTACAAATGTTA
5283998 TTAAAA
1 -TAAAA
5284004 AGAAAGCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.14
18 10 0.45
19 4 0.18
20 5 0.23
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAAACTATTACAAATGTTA
Found at i:5284107 original size:21 final size:21
Alignment explanation
Indices: 5284083--5284218 Score: 76
Period size: 21 Copynumber: 6.5 Consensus size: 21
5284073 TAATGGTCAT
*
5284083 TAAAATTATATCAAATGTTAG
1 TAAAATTATATCAAATGTTAC
* * * *
5284104 TAAAAATATAGCAGATGTAAC
1 TAAAATTATATCAAATGTTAC
* *
5284125 T-AAATTATATGAAATGTTAT
1 TAAAATTATATCAAATGTTAC
* * * **
5284145 TATAATTACATTAAAACTTAC
1 TAAAATTATATCAAATGTTAC
** * * **
5284166 TAAAATTAGGTTAAAGGTTGT
1 TAAAATTATATCAAATGTTAC
* * *
5284187 TAAAATAATATCAAATATTAT
1 TAAAATTATATCAAATGTTAC
5284208 TAAAATTATAT
1 TAAAATTATAT
5284219 TAAAATTGTT
Statistics
Matches: 82, Mismatches: 32, Indels: 2
0.71 0.28 0.02
Matches are distributed among these distances:
20 14 0.17
21 68 0.83
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.38
Consensus pattern (21 bp):
TAAAATTATATCAAATGTTAC
Found at i:5284235 original size:21 final size:21
Alignment explanation
Indices: 5284183--5284236 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
5284173 AGGTTAAAGG
*
5284183 TTGTTAAAATAATATCAAATA
1 TTGTTAAAATTATATCAAATA
* *
5284204 TTATTAAAATTATATTAAA-A
1 TTGTTAAAATTATATCAAATA
5284224 TTGTTAATAATTA
1 TTGTTAA-AATTA
5284237 GAGATATCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (21 bp):
TTGTTAAAATTATATCAAATA
Found at i:5286942 original size:165 final size:165
Alignment explanation
Indices: 5286654--5286973 Score: 579
Period size: 165 Copynumber: 1.9 Consensus size: 165
5286644 AGCTTCGGTC
* * *
5286654 GGCTTCCCTGCAAAATTAATCTTCTTCTTAACTTTTTGGGTTCTTCTTCCTTCTTTGTTTTATCG
1 GGCTCCCCTACAAAACTAATCTTCTTCTTAACTTTTTGGGTTCTTCTTCCTTCTTTGTTTTATCG
5286719 CTTTGTTTTGTTGAAGTTTATGTGATCGCAATACCCAATGCCCACTGTGTTGTTCTGGAAGAAGA
66 CTTTGTTTTGTTGAAGTTTATGTGATCGCAATACCCAATGCCCACTGTGTTGTTCTGGAAGAAGA
5286784 AGAAGAAACTCTGTTATCTCCTCCTTTAGCTGGTG
131 AGAAGAAACTCTGTTATCTCCTCCTTTAGCTGGTG
* *
5286819 GGCTCCCCTACAAAACTAATCTTCTTCTTTACTTTTTGGGTTCTTCTTCCTTCTTTGTTTTTTTC
1 GGCTCCCCTACAAAACTAATCTTCTTCTTAACTTTTTGGGTTCTTCTTCCTTCTTTG-TTTTATC
5286884 -CTTTGTTTTGTTGAAGTTTATGTGATCGCAATACCCAATGCCCACTGTGTTGTTCTGGAAGAAG
65 GCTTTGTTTTGTTGAAGTTTATGTGATCGCAATACCCAATGCCCACTGTGTTGTTCTGGAAGAAG
5286948 AAGAAGAAACTCTGTTATCTCCTCCT
130 AAGAAGAAACTCTGTTATCTCCTCCT
5286974 CTTCAACCCA
Statistics
Matches: 149, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
165 143 0.96
166 6 0.04
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (165 bp):
GGCTCCCCTACAAAACTAATCTTCTTCTTAACTTTTTGGGTTCTTCTTCCTTCTTTGTTTTATCG
CTTTGTTTTGTTGAAGTTTATGTGATCGCAATACCCAATGCCCACTGTGTTGTTCTGGAAGAAGA
AGAAGAAACTCTGTTATCTCCTCCTTTAGCTGGTG
Found at i:5287839 original size:2 final size:2
Alignment explanation
Indices: 5287832--5287857 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5287822 AATGGATTTC
5287832 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
5287858 TTTTATAATT
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5294884 original size:12 final size:12
Alignment explanation
Indices: 5294863--5294904 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
5294853 AGATAGTGTG
5294863 TGTATATATGTA
1 TGTATATATGTA
*
5294875 TGTATGTATGTA
1 TGTATATATGTA
5294887 TGTATTATATGTA
1 TGTA-TATATGTA
*
5294900 CGTAT
1 TGTAT
5294905 CTCATCTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.50
Consensus pattern (12 bp):
TGTATATATGTA
Found at i:5296052 original size:202 final size:201
Alignment explanation
Indices: 5295700--5296108 Score: 773
Period size: 202 Copynumber: 2.0 Consensus size: 201
5295690 TGACGTCCTC
5295700 TATCTTGCTCTCTCTCCAGTTTACTCCTCACCCTCAAGCTGGGGATAAGTGGTGCGTTTATCCAA
1 TATCTTGCTCTCTCTCCAGTTTACTCCTCACCCTCAAGCTGGGGATAAGTGGTGCGTTTATCCAA
5295765 GCTATGATTATGCTCACTGCATTGTGGACTTTCTTGAGAACATCACACATTCAGTATGTTGTCTT
66 GCTATGATTATGCTCACTGCATTGTGGACTTTCTTGAGAACATCACACATTCAGTATGTTGTCTT
* *
5295830 TTTTAGCTATATTTAATTTTGCCATTTTCAAGGAAAACTTTGGGTAATTTTCCTTTTATTTTTAA
131 TTTTAGCTATATTTAATTTTGCAACTTTCAAGGAAAACTTTGGGTAATTTTCCTTTTATTTTTAA
5295895 CCAGTG
196 CCAGTG
*
5295901 TATCTTTCTCTCTCTCCAGTTTACTCCTCACCCTCAAGCTGGGGATAAGTGGTGCGTTTATCCAA
1 TATCTTGCTCTCTCTCCAGTTTACTCCTCACCCTCAAGCTGGGGATAAGTGGTGCGTTTATCCAA
*
5295966 GCTATGATTAATGCTCACTGCATTGTGGACTTTCTTGAGAACATCACACATTCAGTTTGTTGTCT
66 GCTATGATT-ATGCTCACTGCATTGTGGACTTTCTTGAGAACATCACACATTCAGTATGTTGTCT
5296031 TTTTTAGCTATATTTAATTTTGCAACTTTCAAGGAAAACTTTGGGTAATTTTCCTTTTATTTTTA
130 TTTTTAGCTATATTTAATTTTGCAACTTTCAAGGAAAACTTTGGGTAATTTTCCTTTTATTTTTA
5296096 ACCAGTG
195 ACCAGTG
5296103 TATCTT
1 TATCTT
5296109 CTAAAGGCAT
Statistics
Matches: 203, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
201 73 0.36
202 130 0.64
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.41
Consensus pattern (201 bp):
TATCTTGCTCTCTCTCCAGTTTACTCCTCACCCTCAAGCTGGGGATAAGTGGTGCGTTTATCCAA
GCTATGATTATGCTCACTGCATTGTGGACTTTCTTGAGAACATCACACATTCAGTATGTTGTCTT
TTTTAGCTATATTTAATTTTGCAACTTTCAAGGAAAACTTTGGGTAATTTTCCTTTTATTTTTAA
CCAGTG
Found at i:5299546 original size:21 final size:21
Alignment explanation
Indices: 5299512--5299555 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
5299502 GAGTGAAATA
* * * *
5299512 TTTTCTTTCTATTTGTTTTTT
1 TTTTCTGTCAATTTCTTTATT
5299533 TTTTCTGTCAATTTCTTTATT
1 TTTTCTGTCAATTTCTTTATT
5299554 TT
1 TT
5299556 CAATTTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.11, G:0.05, T:0.75
Consensus pattern (21 bp):
TTTTCTGTCAATTTCTTTATT
Found at i:5299567 original size:22 final size:23
Alignment explanation
Indices: 5299542--5299586 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
5299532 TTTTTCTGTC
*
5299542 AATTTCTTTATT-TTCAATTTTT
1 AATTCCTTTATTATTCAATTTTT
* *
5299564 AATTCCTTTTTTATTCTATTTTT
1 AATTCCTTTATTATTCAATTTTT
5299587 CGATTTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (23 bp):
AATTCCTTTATTATTCAATTTTT
Found at i:5304586 original size:12 final size:12
Alignment explanation
Indices: 5304569--5304596 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5304559 ATTCTCAAAA
5304569 TTTTGATATTTT
1 TTTTGATATTTT
5304581 TTTTGATATTTT
1 TTTTGATATTTT
5304593 TTTT
1 TTTT
5304597 TCAAAGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTGATATTTT
Found at i:5305683 original size:20 final size:21
Alignment explanation
Indices: 5305660--5305698 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5305650 ATTCTTATGC
5305660 CATTT-CCAAAATTTTGTTAT
1 CATTTGCCAAAATTTTGTTAT
* *
5305680 CATTTGTCAAAGTTTTGTT
1 CATTTGCCAAAATTTTGTT
5305699 CGACTTTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (21 bp):
CATTTGCCAAAATTTTGTTAT
Found at i:5306867 original size:41 final size:42
Alignment explanation
Indices: 5306779--5306866 Score: 151
Period size: 41 Copynumber: 2.1 Consensus size: 42
5306769 GGATATTCAT
* *
5306779 ATTTTTATATTAAAAATTTTATTAA-TTTTTTAAAAATATCA
1 ATTTTTATATTAAAAAATTTATTAATTTTTTTTAAAATATCA
5306820 ATTTTTATATTAAAAAATTTATTAATTTTTTTTAAAATATCA
1 ATTTTTATATTAAAAAATTTATTAATTTTTTTTAAAATATCA
5306862 ATTTT
1 ATTTT
5306867 AGTAAAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 24 0.55
42 20 0.45
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (42 bp):
ATTTTTATATTAAAAAATTTATTAATTTTTTTTAAAATATCA
Found at i:5306876 original size:41 final size:41
Alignment explanation
Indices: 5306779--5306899 Score: 131
Period size: 41 Copynumber: 3.0 Consensus size: 41
5306769 GGATATTCAT
* *
5306779 ATTTTTATATTAAAAATTTTATTAATTTTTTAAAAATATCA
1 ATTTTTATATAAAAAAATTTATTAATTTTTTAAAAATATCA
* *
5306820 ATTTTTATATTAAAAAATTTATTAATTTTTTTTAAAATATCA
1 ATTTTTATATAAAAAAATTTATTAA-TTTTTTAAAAATATCA
* * * *
5306862 A-TTTTA-GTAAAAAAACTTACTT-TTTTTTTAAAATTATC
1 ATTTTTATATAAAAAAATTTA-TTAATTTTTTAAAAATATC
5306900 TACTTTAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
39 13 0.19
40 10 0.14
41 31 0.44
42 16 0.23
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (41 bp):
ATTTTTATATAAAAAAATTTATTAATTTTTTAAAAATATCA
Found at i:5307600 original size:17 final size:16
Alignment explanation
Indices: 5307578--5307630 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
5307568 TTTCATTTTT
5307578 TTTTTCAAATTTTTATC
1 TTTTTC-AATTTTTATC
*
5307595 TTTTTCAGTTTTTCAT-
1 TTTTTCAATTTTT-ATC
*
5307611 TTTTT-TATTTTTATC
1 TTTTTCAATTTTTATC
5307626 TTTTT
1 TTTTT
5307631 GTGCTTTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 2 0.06
15 10 0.32
16 11 0.35
17 8 0.26
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTTTCAATTTTTATC
Found at i:5310694 original size:26 final size:25
Alignment explanation
Indices: 5310665--5310713 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
5310655 TAAATTTTTA
*
5310665 TAATTTTTTATTTA-ATATAATTTACT
1 TAATGTTTT-TTTATATAT-ATTTACT
5310691 TAATGTTTTTTTATATATATTTA
1 TAATGTTTTTTTATATATATTTA
5310714 TAATAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
TAATGTTTTTTTATATATATTTACT
Found at i:5312979 original size:102 final size:102
Alignment explanation
Indices: 5312798--5312991 Score: 291
Period size: 102 Copynumber: 1.9 Consensus size: 102
5312788 GGTCAGTATA
* ** *
5312798 TTTTGGTTAAAATAGTCTATTGGTGTCTTAGCCTATTCTTTTACCTGTATGATAATGACTAATGT
1 TTTTGGTTAAAATAGTCTATTGGTATCTTAGCCTATTCTTTTACCTACAAGATAATGACTAATGT
5312863 CTCAAATATATTTGGTTGCAGGATATTTCTTCAGATT
66 CTCAAATATATTTGGTTGCAGGATATTTCTTCAGATT
* * * *
5312900 TTTTGGTTTAAATAGTCTATTGGTATCTTAGCTTATTCTGTTT-CCTACAAGATAATGGCTAGTG
1 TTTTGGTTAAAATAGTCTATTGGTATCTTAGCCTATTCT-TTTACCTACAAGATAATGACTAATG
*
5312964 TCTCAAATATGTTTGGTTGCAGGATATT
65 TCTCAAATATATTTGGTTGCAGGATATT
5312992 CATACTTCCT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 79 0.96
103 3 0.04
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (102 bp):
TTTTGGTTAAAATAGTCTATTGGTATCTTAGCCTATTCTTTTACCTACAAGATAATGACTAATGT
CTCAAATATATTTGGTTGCAGGATATTTCTTCAGATT
Found at i:5327428 original size:141 final size:142
Alignment explanation
Indices: 5327249--5327521 Score: 503
Period size: 141 Copynumber: 1.9 Consensus size: 142
5327239 TTTGATGGAT
5327249 CCACTCATTTCTTTTTTTTTTTTGTTTTTTAATTAATTTTTTTGTATTTTTTTAAATAAGTCTAA
1 CCACTCATTTC-TTTTTTTTTTTGTTTTTTAATTAATTTTTTTGTATTTTTTTAAATAAGTCTAA
5327314 ATTAAAATGAATTAAGCCCAATTAATTTGGATCCAATAAATCCAAATTAAAGATAACTTGATAAA
65 ATTAAAATGAATTAAGCCCAATTAATTTGGATCCAATAAATCCAAATTAAAGATAACTTGATAAA
5327379 TTCAAATCCCAAG
130 TTCAAATCCCAAG
5327392 CCACTCATTTC-TTTTTTTTTTGTTTTTTAATTAATTTTTTTGTATTTTTTTAAATAAGTCTAAA
1 CCACTCATTTCTTTTTTTTTTTGTTTTTTAATTAATTTTTTTGTATTTTTTTAAATAAGTCTAAA
* * *
5327456 TTAAAATGAATTAAGCCCAATTAATTTGGATCCAATAAATCTAAATTAAAGATGACTTGATTAAT
66 TTAAAATGAATTAAGCCCAATTAATTTGGATCCAATAAATCCAAATTAAAGATAACTTGATAAAT
5327521 T
131 T
5327522 GAATTATTTT
Statistics
Matches: 127, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
141 116 0.91
143 11 0.09
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (142 bp):
CCACTCATTTCTTTTTTTTTTTGTTTTTTAATTAATTTTTTTGTATTTTTTTAAATAAGTCTAAA
TTAAAATGAATTAAGCCCAATTAATTTGGATCCAATAAATCCAAATTAAAGATAACTTGATAAAT
TCAAATCCCAAG
Found at i:5328326 original size:35 final size:35
Alignment explanation
Indices: 5328275--5328345 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
5328265 ATTACGTGTA
5328275 CGAGTATAATTATATTGTTAAATCTAATGGTCAGT
1 CGAGTATAATTATATTGTTAAATCTAATGGTCAGT
* *
5328310 CGAGTATAATTTTATTGTTAAATCTAATTGTCAGT
1 CGAGTATAATTATATTGTTAAATCTAATGGTCAGT
5328345 C
1 C
5328346 TGTTAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (35 bp):
CGAGTATAATTATATTGTTAAATCTAATGGTCAGT
Found at i:5333039 original size:15 final size:18
Alignment explanation
Indices: 5332992--5333063 Score: 64
Period size: 19 Copynumber: 4.2 Consensus size: 18
5332982 TTATTATGAC
*
5332992 ATATAATAATAAA--AAT
1 ATATATTAATAAATTAAT
* *
5333008 TTATATTTAATATATTAAT
1 ATATA-TTAATAAATTAAT
5333027 -TA-A-TAATAAATTAAT
1 ATATATTAATAAATTAAT
5333042 ATATTATTAATAAATTAAT
1 ATA-TATTAATAAATTAAT
5333061 ATA
1 ATA
5333064 AATTTTAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
15 11 0.24
16 6 0.13
17 7 0.16
18 3 0.07
19 18 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTAATAAATTAAT
Found at i:5333040 original size:11 final size:11
Alignment explanation
Indices: 5333014--5333067 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
5333004 AAATTTATAT
*
5333014 TTAATATATTAA
1 TTAATA-ATAAA
5333026 TTAATAATAAA
1 TTAATAATAAA
5333037 TTAAT-AT--A
1 TTAATAATAAA
*
5333045 TTATTAATAAA
1 TTAATAATAAA
5333056 TTAAT-ATAAA
1 TTAATAATAAA
5333066 TT
1 TT
5333068 TTAAAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
8 5 0.14
9 2 0.06
10 9 0.25
11 14 0.39
12 6 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TTAATAATAAA
Found at i:5333052 original size:19 final size:19
Alignment explanation
Indices: 5333025--5333063 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5333015 TAATATATTA
5333025 ATTAATAATAAATTAATAT
1 ATTAATAATAAATTAATAT
*
5333044 ATTATTAATAAATTAATAT
1 ATTAATAATAAATTAATAT
5333063 A
1 A
5333064 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTAATAATAAATTAATAT
Found at i:5333058 original size:30 final size:30
Alignment explanation
Indices: 5332998--5333067 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
5332988 TGACATATAA
* *
5332998 TAATAA-AAATTTATATTTAATATATTAAT
1 TAATAATAAATTAATATTTAATATATAAAT
*
5333027 TAATAATAAATTAATATATTATTA-ATAAAT
1 TAATAATAAATTAATAT-TTAATATATAAAT
5333057 TAAT-ATAAATT
1 TAATAATAAATT
5333068 TTAAAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 13 0.36
30 18 0.50
31 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TAATAATAAATTAATATTTAATATATAAAT
Found at i:5333076 original size:10 final size:10
Alignment explanation
Indices: 5333063--5333111 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
5333053 AAATTAATAT
5333063 AAATTTTAAA
1 AAATTTTAAA
5333073 AAA-TTT-AA
1 AAATTTTAAA
5333081 AAATTTTAAA
1 AAATTTTAAA
5333091 AAATTTATAAA
1 AAATTT-TAAA
* *
5333102 TAATTATAAA
1 AAATTTTAAA
5333112 TTTTAACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 5 0.15
9 6 0.18
10 15 0.44
11 8 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AAATTTTAAA
Found at i:5333081 original size:9 final size:9
Alignment explanation
Indices: 5333067--5333111 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
5333057 TAATATAAAT
5333067 TTTAAAAAA
1 TTTAAAAAA
*
5333076 TTTAAAAAT
1 TTTAAAAAA
5333085 TTTAAAAAA
1 TTTAAAAAA
5333094 TTTATAAATAA
1 TTTA-AAA-AA
5333105 TTATAAA
1 TT-TAAA
5333112 TTTTAACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 20 0.65
10 3 0.10
11 6 0.19
12 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:5333086 original size:18 final size:18
Alignment explanation
Indices: 5333063--5333102 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
5333053 AAATTAATAT
5333063 AAATTTTAAAAAATTTAA
1 AAATTTTAAAAAATTTAA
*
5333081 AAATTTTAAAAAATTTAT
1 AAATTTTAAAAAATTTAA
5333099 AAAT
1 AAAT
5333103 AATTATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTTTAAAAAATTTAA
Found at i:5335589 original size:2 final size:2
Alignment explanation
Indices: 5335582--5335629 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5335572 TGGTGAGTTC
5335582 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
5335624 AT AT AT
1 AT AT AT
5335630 TTCTGTATCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5338535 original size:2 final size:2
Alignment explanation
Indices: 5338528--5338556 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5338518 TCTCATACAA
5338528 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5338557 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5345074 original size:17 final size:19
Alignment explanation
Indices: 5345024--5345074 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
5345014 TAAGTTTTTT
5345024 AAATAAATTATTTAAAATTA
1 AAAT-AATTATTTAAAATTA
*
5345044 AAATAATTA-ATAAAA-TA
1 AAATAATTATTTAAAATTA
*
5345061 AAAT-TTTATTTAAA
1 AAATAATTATTTAAA
5345075 GTTTTTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 3 0.11
17 10 0.37
18 5 0.19
19 5 0.19
20 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATAATTATTTAAAATTA
Found at i:5345204 original size:29 final size:29
Alignment explanation
Indices: 5345144--5345204 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
5345134 TATATTATTA
* ***
5345144 AAAAATAAAATTAACGTAATGAATACTCT
1 AAAAATAAAATTAAAGTAATGAATAAAAT
5345173 AAAAATAAAATTAAAGTAAGTG-ATAAAAT
1 AAAAATAAAATTAAAGTAA-TGAATAAAAT
5345202 AAA
1 AAA
5345205 TATTATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (29 bp):
AAAAATAAAATTAAAGTAATGAATAAAAT
Found at i:5345754 original size:22 final size:21
Alignment explanation
Indices: 5345729--5345779 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
5345719 ACTAATTTTT
5345729 TAAAAAATATT-ATTTAAAAAAA
1 TAAAAAAT-TTAATTT-AAAAAA
*
5345751 TAAAAAATTTAAATTTAAATAA
1 TAAAAAATTT-AATTTAAAAAA
5345773 TAAAAAA
1 TAAAAAA
5345780 CTATCTCGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 20 0.77
23 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAAAATTTAATTTAAAAAA
Found at i:5346122 original size:3 final size:3
Alignment explanation
Indices: 5346114--5346139 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5346104 TTTAAATCTC
5346114 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
5346140 TATTCATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5347715 original size:56 final size:56
Alignment explanation
Indices: 5347630--5347789 Score: 304
Period size: 56 Copynumber: 2.9 Consensus size: 56
5347620 ATCAACTTTT
5347630 ATGTTATTG-ATCTAAATATCAAATAGCTTACAATAAAAATGAGGACTTAGTGATC
1 ATGTTATTGAATCTAAATATCAAATAGCTTACAATAAAAATGAGGACTTAGTGATC
5347685 ATGTTATTGAATCTAAATATCAAATAGCTTACAATAAAAATGAGGACTTAGTGATC
1 ATGTTATTGAATCTAAATATCAAATAGCTTACAATAAAAATGAGGACTTAGTGATC
*
5347741 ATGTTATTGAATCTAAATATCAAATAGCTTACAATAAAAATGGGGACTT
1 ATGTTATTGAATCTAAATATCAAATAGCTTACAATAAAAATGAGGACTT
5347790 TGGAATCAAT
Statistics
Matches: 103, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
55 9 0.09
56 94 0.91
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (56 bp):
ATGTTATTGAATCTAAATATCAAATAGCTTACAATAAAAATGAGGACTTAGTGATC
Found at i:5353332 original size:70 final size:70
Alignment explanation
Indices: 5353215--5353354 Score: 262
Period size: 70 Copynumber: 2.0 Consensus size: 70
5353205 ACGGGTTTAA
5353215 AATTGAGTTTGATATGATGGGGAAATTTGGAAGTAGTTTTACAGTTGTGTTATCCTTTGTTCTTC
1 AATTGAGTTTGATATGATGGGGAAATTTGGAAGTAGTTTTACAGTTGTGTTATCCTTTGTTCTTC
5353280 ACTTT
66 ACTTT
*
5353285 AATTGAGTTTGATATGATGGGGAAATTTGGAAGTAGTTTTACGGTTGTGTTATCCTTTGTTCTTC
1 AATTGAGTTTGATATGATGGGGAAATTTGGAAGTAGTTTTACAGTTGTGTTATCCTTTGTTCTTC
*
5353350 GCTTT
66 ACTTT
5353355 TTCGAGTGTC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.21, C:0.09, G:0.24, T:0.46
Consensus pattern (70 bp):
AATTGAGTTTGATATGATGGGGAAATTTGGAAGTAGTTTTACAGTTGTGTTATCCTTTGTTCTTC
ACTTT
Found at i:5353385 original size:2 final size:2
Alignment explanation
Indices: 5353378--5353421 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
5353368 CGGTTCCAAC
*
5353378 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5353420 AT
1 AT
5353422 CTAGACCTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5353852 original size:2 final size:2
Alignment explanation
Indices: 5353847--5353885 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5353837 TGCGTGTGTC
5353847 TA TA TA TA TA 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 TA TA TA TA TA T
5353886 CGATCGAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5360335 original size:2 final size:2
Alignment explanation
Indices: 5360330--5360358 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5360320 ACCAGAATAC
5360330 AG AG 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 AG AG A
5360359 AAAAAAAAAC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5360772 original size:3 final size:3
Alignment explanation
Indices: 5360764--5360801 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
5360754 ATTATGGTCC
*
5360764 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
5360802 CACTTCATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:5368603 original size:65 final size:65
Alignment explanation
Indices: 5368520--5368647 Score: 170
Period size: 65 Copynumber: 2.0 Consensus size: 65
5368510 AAGTTAAATA
* * * *
5368520 TTATAGTGAGAGAAAAACCATCACA-CGCTACGAATACTGTCCATGACAAACTACGTGCTTCAAT
1 TTATAGTGAGAGAAAAACCATCACATC-CTAAGAAGACTATCCATGACAAACTACATGCTTCAAT
5368584 T
65 T
**
5368585 TTATAGTGTA-AGAAAAACCATCACATCCTAAGAAGACTATCCATGACAAGTTACATGCTTCAA
1 TTATAGTG-AGAGAAAAACCATCACATCCTAAGAAGACTATCCATGACAAACTACATGCTTCAA
5368648 ATTTCTAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
65 53 0.96
66 2 0.04
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (65 bp):
TTATAGTGAGAGAAAAACCATCACATCCTAAGAAGACTATCCATGACAAACTACATGCTTCAATT
Found at i:5369287 original size:2 final size:2
Alignment explanation
Indices: 5369241--5369271 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5369231 ATTGAACTAC
5369241 TA 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 TA T
5369272 TGATAACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5369391 original size:105 final size:105
Alignment explanation
Indices: 5369184--5369384 Score: 233
Period size: 105 Copynumber: 1.9 Consensus size: 105
5369174 TCACCAAACA
* * * * * **
5369184 ATACTATATTCTGATACACCTTAACCAGAAAGCATTTTCATGGCAAAATTGAACTACTATATATA
1 ATACTAGATTCTAATAAACCCTAACCAGAAAGCATTTTCATGGCAAAATTGAACAAAAATATATA
* * **
5369249 TATATATATATATATATATATATTGATAACATATATATAC
66 AATATATATATATACATATATATACATAACATATATATAC
* * *
5369289 ATACTAGATTCTAATAAACCCTAACCGGAAAGCATTTTCTTGGGAAAATTGAACAAAAATATATC
1 ATACTAGATTCTAATAAACCCTAACCAGAAAGCATTTTCATGGCAAAATTGAACAAAAATATAT-
*
5369354 AAATATAT-TTTGATGACATATATATACATAA
65 AAATATATATAT-AT-ACATATATATACATAA
5369385 ACTATATCAT
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
105 56 0.72
106 9 0.12
107 13 0.17
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.34
Consensus pattern (105 bp):
ATACTAGATTCTAATAAACCCTAACCAGAAAGCATTTTCATGGCAAAATTGAACAAAAATATATA
AATATATATATATACATATATATACATAACATATATATAC
Found at i:5371275 original size:29 final size:29
Alignment explanation
Indices: 5371241--5371298 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
5371231 GTTTTCTAAA
*
5371241 AATTAAAAGT-ATTATTTAT-AATTTAATT
1 AATTTAAAGTAATT-TTTATAAATTTAATT
*
5371269 AATTTAAATTAATTTTTATAAATTTAATT
1 AATTTAAAGTAATTTTTATAAATTTAATT
5371298 A
1 A
5371299 CGTTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
AATTTAAAGTAATTTTTATAAATTTAATT
Found at i:5371323 original size:30 final size:28
Alignment explanation
Indices: 5371253--5371325 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 28
5371243 TTAAAAGTAT
*
5371253 TATTTATAATTTAATTAATTTAAATTAA
1 TATTTTTAATTTAATTAATTTAAATTAA
*
5371281 T-TTTTATAAATTTAATTACGTTTAAATTAA
1 TATTTT-T-AATTTAATTA-ATTTAAATTAA
5371311 TGATTTTTAATTTAA
1 T-ATTTTTAATTTAA
5371326 AAAAATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 3 0.08
28 2 0.05
29 10 0.26
30 18 0.47
31 1 0.03
32 4 0.11
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (28 bp):
TATTTTTAATTTAATTAATTTAAATTAA
Found at i:5371513 original size:18 final size:18
Alignment explanation
Indices: 5371464--5371523 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
5371454 ATTAAAATCA
5371464 TAATAAATTTAAA-AAAT
1 TAATAAATTTAAATAAAT
* *
5371481 TAAATAACA-TCAAATCAAT
1 T-AATAA-ATTTAAATAAAT
*
5371500 TAATAAATTTAAATTAAT
1 TAATAAATTTAAATAAAT
*
5371518 TCATAA
1 TAATAA
5371524 TTTTCTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 2 0.06
18 27 0.79
19 5 0.15
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATAAATTTAAATAAAT
Found at i:5372498 original size:26 final size:28
Alignment explanation
Indices: 5372469--5372520 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
5372459 TAAATTATTT
**
5372469 TTTTATTTTTATT-AATTA-AAAATATA
1 TTTTATTTACATTAAATTATAAAATATA
5372495 TTTTATTTACATTAAATTATAAAATA
1 TTTTATTTACATTAAATTATAAAATA
5372521 ATATAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.50
27 5 0.23
28 6 0.27
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTTATTTACATTAAATTATAAAATATA
Found at i:5372535 original size:21 final size:21
Alignment explanation
Indices: 5372511--5372561 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
5372501 TTACATTAAA
5372511 TTATAAA-ATAATATAATTTTT
1 TTATAAATATAATAT-ATTTTT
*
5372532 TTATAATATTTAATATATTTTT
1 TTATAA-ATATAATATATTTTT
*
5372554 TAATAAAT
1 TTATAAAT
5372562 TCAAATTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 8 0.31
22 12 0.46
23 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATAAATATAATATATTTTT
Found at i:5373737 original size:17 final size:17
Alignment explanation
Indices: 5373710--5373750 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
5373700 TTTTTTTAAA
*
5373710 TTAATTAATA-TATTAT
1 TTAAATAATATTATTAT
5373726 TTACAATAATATTATTAT
1 TTA-AATAATATTATTAT
5373744 TTAAATA
1 TTAAATA
5373751 TAATCATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 10 0.45
18 9 0.41
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAATAATATTATTAT
Found at i:5374179 original size:5 final size:5
Alignment explanation
Indices: 5374169--5374203 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
5374159 TTTTTACATG
*
5374169 AATTA AATTA AATTT AATTA AATTA AATT- AATTA A
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA A
5374204 CGATTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
AATTA
Found at i:5374189 original size:15 final size:14
Alignment explanation
Indices: 5374169--5374203 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
5374159 TTTTTACATG
5374169 AATTAAATTAAATTT
1 AATTAAATTAAA-TT
5374184 AATTAAATTAAATT
1 AATTAAATTAAATT
5374198 AATTAA
1 AATTAA
5374204 CGATTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTAAATTAAATT
Found at i:5374286 original size:31 final size:30
Alignment explanation
Indices: 5374240--5374297 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5374230 TTTAATCGTC
* *
5374240 AATCGTCAATTAATTTTAAATTAAATTTTTT
1 AATCATCAATCAA-TTTAAATTAAATTTTTT
*
5374271 AATCATCAATCAATTTAATTTAAATTT
1 AATCATCAATCAATTTAAATTAAATTT
5374298 GATTTGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (30 bp):
AATCATCAATCAATTTAAATTAAATTTTTT
Found at i:5378982 original size:2 final size:2
Alignment explanation
Indices: 5378975--5379000 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5378965 GTCGACATGA
5378975 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
5379001 GGTGCATAAA
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):
AT
Found at i:5379545 original size:23 final size:23
Alignment explanation
Indices: 5379515--5379565 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
5379505 CATTTTTTTC
*
5379515 ATAAGAAAAGTTAAGACTTGAAT
1 ATAAGAAAAGTTAAAACTTGAAT
5379538 ATAAGAAAAGTTAAAACTTGAAT
1 ATAAGAAAAGTTAAAACTTGAAT
5379561 ATAAG
1 ATAAG
5379566 TGAAAGATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.25
Consensus pattern (23 bp):
ATAAGAAAAGTTAAAACTTGAAT
Found at i:5381332 original size:12 final size:12
Alignment explanation
Indices: 5381315--5381380 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 12
5381305 GTCAATTCAT
5381315 TATTTAAAATAA
1 TATTTAAAATAA
5381327 TATTTAAAAT-A
1 TATTTAAAATAA
*
5381338 T-TTTAAAAATTA
1 TATTT-AAAATAA
* * *
5381350 TTTTTATATTAA
1 TATTTAAAATAA
5381362 TA-TTATAAATAA
1 TATTTA-AAATAA
5381374 -ATTTAAA
1 TATTTAAA
5381381 TAAAAATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
10 3 0.07
11 13 0.30
12 24 0.56
13 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TATTTAAAATAA
Found at i:5381853 original size:2 final size:2
Alignment explanation
Indices: 5381846--5381873 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5381836 TATAATACCA
5381846 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
5381874 GAACTCAAAC
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:5385258 original size:7 final size:7
Alignment explanation
Indices: 5385246--5385279 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
5385236 GTCACCTCAT
5385246 AAATTTA
1 AAATTTA
5385253 AAATTTA
1 AAATTTA
*
5385260 AATTTTA
1 AAATTTA
*
5385267 ATATTTA
1 AAATTTA
5385274 AAATTT
1 AAATTT
5385280 TTATCTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
AAATTTA
Found at i:5388451 original size:263 final size:264
Alignment explanation
Indices: 5387925--5388452 Score: 828
Period size: 263 Copynumber: 2.0 Consensus size: 264
5387915 ACAATAAATC
* * * *
5387925 TTAGGTAACAACATACTCAACTTTTCGGACTTTGTTCGGTGGTATTTGCCAGAATGGAGGTAAGT
1 TTAGGTAACAACATACTCAACTTCTAGGACTTCGTTCGGTGGTATTTGCCAGAATGAAGGTAAGT
* *
5387990 TCCAACCATAAGCAGGTGACAGGAAAACAAGTTAAATTAAACACTATTTCTTGCCATACAAGAGA
66 TCCAACCATAAGCAGGTGACAGGAAAACAAGTTAAACTAAACACTATTTCTTGACATACAAGAGA
* *
5388055 GGGCTGGTTCTTGCAACTGATGGAAGAGAGGGGAAAAAGGACAATGACAATGGCTTATGCAACCA
131 GGGCTAGTTCTTGCAACTGATGGAAGAGAGAGGAAAAAGGACAATGACAATGGCTTATGCAACCA
5388120 TTGATTAATGAATCAAAGCCAAAACAGTCCTTGTCAGTATAAAATCACAAGCTAAGCAAATATTT
196 TTGATTAATGAATCAAAGCCAAAACAGTCCTTGTCAGTATAAAATCACAAGCTAAGCAAATATTT
5388185 TAAT
261 TAAT
* *
5388189 TTAGGTAACAATATACTCAACTTCTAGGACTTCGTTTGGT-GTATTTGCCAGAATGAAGGTAAGT
1 TTAGGTAACAACATACTCAACTTCTAGGACTTCGTTCGGTGGTATTTGCCAGAATGAAGGTAAGT
* * **
5388253 TCCAACCATATGCAGGTGACAGGAACACAAGTTAAACTATGCACTATTTCTTGACATACAAGAGA
66 TCCAACCATAAGCAGGTGACAGGAAAACAAGTTAAACTAAACACTATTTCTTGACATACAAGAGA
*
5388318 GGTGC-AGTTCTTGCAACTGATGGAAGAGAGAGGAAAAAGGACAATGACAATGGCTTATGCAGCC
131 GG-GCTAGTTCTTGCAACTGATGGAAGAGAGAGGAAAAAGGACAATGACAATGGCTTATGCAACC
* * * * * *
5388382 ATTGA-TCATGTATCAAAGCTAAGACAGTCTTTGTCAGTATAAAATCACAAGCTAAGTAAATACT
195 ATTGATTAATGAATCAAAGCCAAAACAGTCCTTGTCAGTATAAAATCACAAGCTAAGCAAATA-T
5388446 TTTAAT
259 TTTAAT
5388452 T
1 T
5388453 AGCTATGTTT
Statistics
Matches: 241, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
262 51 0.21
263 153 0.63
264 37 0.15
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (264 bp):
TTAGGTAACAACATACTCAACTTCTAGGACTTCGTTCGGTGGTATTTGCCAGAATGAAGGTAAGT
TCCAACCATAAGCAGGTGACAGGAAAACAAGTTAAACTAAACACTATTTCTTGACATACAAGAGA
GGGCTAGTTCTTGCAACTGATGGAAGAGAGAGGAAAAAGGACAATGACAATGGCTTATGCAACCA
TTGATTAATGAATCAAAGCCAAAACAGTCCTTGTCAGTATAAAATCACAAGCTAAGCAAATATTT
TAAT
Found at i:5388622 original size:41 final size:41
Alignment explanation
Indices: 5388565--5388662 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
5388555 ATGGAATACT
* * *
5388565 TTTGCAGACTGAAATCCTCTGTAGTAATTACAAGTTCTTAA
1 TTTGCAAACTGAAATCCTCTATAGTAAGTACAAGTTCTTAA
* * *
5388606 TTTGCAAATTGAAATCCTCTATGGTAAGTACAATTTCTTAA
1 TTTGCAAACTGAAATCCTCTATAGTAAGTACAAGTTCTTAA
5388647 TTTGCAGAAC-GAAATC
1 TTTGCA-AACTGAAATC
5388663 TGCAATGAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
41 47 0.96
42 2 0.04
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (41 bp):
TTTGCAAACTGAAATCCTCTATAGTAAGTACAAGTTCTTAA
Found at i:5393747 original size:17 final size:18
Alignment explanation
Indices: 5393725--5393758 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5393715 TTAAAAATGC
5393725 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
5393742 AATTATATTATTTATTT
1 AATTATATTATTTATTT
5393759 ATTAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:5395064 original size:23 final size:24
Alignment explanation
Indices: 5395028--5395073 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
5395018 AATTTTTTAA
*
5395028 AAATATAAAAATATTAAA-ATATT
1 AAATATAAAAATATCAAATATATT
**
5395051 AAATATAATTATATCAAATATAT
1 AAATATAAAAATATCAAATATAT
5395074 ATTTATCGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAATATAAAAATATCAAATATATT
Found at i:5395322 original size:3 final size:3
Alignment explanation
Indices: 5395314--5395353 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5395304 TAAATTTTCG
5395314 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5395354 CATGCAAGTA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5395627 original size:3 final size:3
Alignment explanation
Indices: 5395619--5395643 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5395609 ACTTAAAGTT
5395619 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
5395644 ATGTTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5396027 original size:43 final size:45
Alignment explanation
Indices: 5395977--5396068 Score: 161
Period size: 46 Copynumber: 2.1 Consensus size: 45
5395967 TATCCCTTTA
5395977 ATTATTTTCTGT-C-CTTTAATCTCTAATTATTTACCATTGGTCG
1 ATTATTTTCTGTCCTCTTTAATCTCTAATTATTTACCATTGGTCG
5396020 ATTATTTTCTGTCCTTCTTTAATCTCTAATTATTTACCATTGGTCG
1 ATTATTTTCTGTCC-TCTTTAATCTCTAATTATTTACCATTGGTCG
5396066 ATT
1 ATT
5396069 CTTAAAGTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
43 12 0.26
44 1 0.02
46 33 0.72
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.52
Consensus pattern (45 bp):
ATTATTTTCTGTCCTCTTTAATCTCTAATTATTTACCATTGGTCG
Found at i:5396758 original size:2 final size:2
Alignment explanation
Indices: 5396717--5396741 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5396707 CCATTATCTA
5396717 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 A
5396742 CACACACATA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5399410 original size:34 final size:34
Alignment explanation
Indices: 5399364--5399548 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
5399354 GTAAAAACCA
*
5399364 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
5399398 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
5399432 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
5399466 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
5399500 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
5399533 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
5399549 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:5403644 original size:20 final size:20
Alignment explanation
Indices: 5403619--5403677 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
5403609 TGTACAGTAA
*
5403619 CCGTATACTTGAATAGTACC
1 CCGTATACGTGAATAGTACC
5403639 CCGTATACGTGAATAGTA-C
1 CCGTATACGTGAATAGTACC
**
5403658 CTATATACGTGAATAGTACC
1 CCGTATACGTGAATAGTACC
5403678 TCGACAACCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (20 bp):
CCGTATACGTGAATAGTACC
Found at i:5403666 original size:19 final size:19
Alignment explanation
Indices: 5403622--5403678 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
5403612 ACAGTAACCG
* **
5403622 TATACTTGAATAGTACCCCG
1 TATACGTGAATAGTA-CCTA
5403642 TATACGTGAATAGTACCTA
1 TATACGTGAATAGTACCTA
5403661 TATACGTGAATAGTACCT
1 TATACGTGAATAGTACCT
5403679 CGACAACCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (19 bp):
TATACGTGAATAGTACCTA
Found at i:5404028 original size:34 final size:34
Alignment explanation
Indices: 5403982--5404164 Score: 246
Period size: 34 Copynumber: 5.4 Consensus size: 34
5403972 GTAAAAACCA
5403982 CCATTTAATCAACAAT-GTCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
5404016 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
5404050 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
5404084 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
5404118 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
5404151 CCATTTAATCAACA
1 CCATTTAATCAACA
5404165 GTTTCTTGAT
Statistics
Matches: 133, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.12
34 111 0.83
35 6 0.05
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:5404435 original size:20 final size:20
Alignment explanation
Indices: 5404396--5404451 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
5404386 TATTATTTTT
*
5404396 ATATTATA-ATTATATTTAAA
1 ATATTATATATTA-ATATAAA
5404416 ATATTATATATTAATATAAA
1 ATATTATATATTAATATAAA
* *
5404436 TTTTTATATATTAATA
1 ATATTATATATTAATA
5404452 GTTTATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTATATATTAATATAAA
Found at i:5404487 original size:17 final size:17
Alignment explanation
Indices: 5404377--5404495 Score: 55
Period size: 17 Copynumber: 6.8 Consensus size: 17
5404367 TTCACAATCA
*
5404377 ATATATTTATATTATTTTT
1 ATAT-TTTA-ATTATATTT
*
5404396 ATATTATAATTATATTT
1 ATATTTTAATTATATTT
* *
5404413 AAAATATTATATATTA-ATAT
1 ---ATATTTTA-ATTATATTT
* * *
5404433 AAATTTTTA-TATATTA
1 ATATTTTAATTATATTT
* * *
5404449 ATAGTTT-ATAATATAT
1 ATATTTTAATTATATTT
*
5404465 AAATTTTAATTATATTT
1 ATATTTTAATTATATTT
*
5404482 ATATTTTATTTATA
1 ATATTTTAATTATA
5404496 CAATATAATC
Statistics
Matches: 74, Mismatches: 19, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
15 3 0.04
16 17 0.23
17 32 0.43
18 3 0.04
19 4 0.05
20 11 0.15
21 4 0.05
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
ATATTTTAATTATATTT
Found at i:5404490 original size:33 final size:34
Alignment explanation
Indices: 5404402--5404490 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 34
5404392 TTTTATATTA
* *
5404402 TAATTATATTTAAAATATTATATATTAATATAAATTT
1 TAATTATATTT---ATATTTTATAATAATATAAATTT
* * *
5404439 TTA-TATATTAATAGTTTATAAT-ATATAAATTT
1 TAATTATATTTATATTTTATAATAATATAAATTT
5404471 TAATTATATTTATATTTTAT
1 TAATTATATTTATATTTTAT
5404491 TTATACAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
32 12 0.28
33 23 0.53
36 6 0.14
37 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (34 bp):
TAATTATATTTATATTTTATAATAATATAAATTT
Found at i:5405333 original size:33 final size:30
Alignment explanation
Indices: 5405286--5405348 Score: 90
Period size: 33 Copynumber: 2.0 Consensus size: 30
5405276 GTTAATATTT
*
5405286 TTAAAAAATTATATATTTAATATATTATTTTTA
1 TTAAAAAATAATATA-TTAAT-TA-TATTTTTA
5405319 TTAAAAAATAATATATTAATTATATTTTTA
1 TTAAAAAATAATATATTAATTATATTTTTA
5405349 CATGCGTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 8 0.28
31 2 0.07
32 5 0.17
33 14 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TTAAAAAATAATATATTAATTATATTTTTA
Found at i:5409444 original size:20 final size:20
Alignment explanation
Indices: 5409391--5409436 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5409381 AAGTAATTAT
* * *
5409391 ATATATATATATATATATGC
1 ATATGTATATGTATACATGC
5409411 ATATGTATATGTATACATGC
1 ATATGTATATGTATACATGC
5409431 ATATGT
1 ATATGT
5409437 GTCTGTATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (20 bp):
ATATGTATATGTATACATGC
Found at i:5414459 original size:16 final size:16
Alignment explanation
Indices: 5414415--5414459 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
5414405 TCTTAAAATT
5414415 CATATAATATAAATTTA
1 CATA-AATATAAATTTA
*
5414432 CA-AAGTATTAAATTTA
1 CATAAATA-TAAATTTA
5414448 CATAAATATAAA
1 CATAAATATAAA
5414460 ATATCTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 3 0.12
16 15 0.62
17 6 0.25
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (16 bp):
CATAAATATAAATTTA
Found at i:5422785 original size:2 final size:2
Alignment explanation
Indices: 5422778--5422805 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5422768 AATTGGCAAA
5422778 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
5422806 TAATAGTAAA
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:5426007 original size:458 final size:458
Alignment explanation
Indices: 5425148--5426503 Score: 2292
Period size: 458 Copynumber: 2.9 Consensus size: 458
5425138 GTACTGACGA
5425148 TCTTGATCAGGCAATCCAAAAATGAAAGCTTTTTTATCTCTTTGCCTATGAATGTTTAGTTACCC
1 TCTTGATCAGGCAATCCAAAAATGAAAGCTTTTTTATCTCTTTGCCTATGAATGTTTAGTTACCC
5425213 TAAAAAATAGAAAACCTTACAATTACCCCTTTCCCTAAAGATTACTTCAATTTTGTTGAGAAGCC
66 TAAAAAATAGAAAACCTTACAATTACCCCTTTCCCTAAAGATTACTTCAATTTTGTTGAGAAGCC
* * *
5425278 ATCTCTTTAGACAAAAGCTTTCTCCAACAAATTATATATTTGACAGCTCCAAAATCCATAACATA
131 ATCTCTTTAGACAAAAGCTTTCTCCAA-AAAAT-TATATTTGACAGCTCCAAAGTCAATAACATA
* *
5425343 TTCCAAAGGCAAATAGGCCTTTCCTTTCCTTGCTTCTAGACCAAATGTAGACACTCATCTATGAT
194 TTCCAAAGGCAAATAGGCCTTTCCTTTCCTTGCTTCTAGACCAAATCTAGAGACTCATCTATGAT
5425408 CTATCTACATTGGAATTCACATCCCGACCGTTTTTATGCTTTTAACTTTTATTGGTGATATACAT
259 CTATCTACATTGGAATTCACATCCCGACCGTTTTTATGCTTTTAACTTTTATTGGTGATATACAT
*
5425473 AGAAGCTAGAAGCATTCTCCAATCTGTAAATAGAAATCATATACTCACAAGAAGAAAGTTTGTAC
324 AGAAGCTAGAAGCATTCTCCAATCTGTAAATAGAAATCATATACTCCCAAGAAGAAAGTTTGTAC
5425538 TTTGCAATATCCAGAAGAGAAACATCTATTGGTGCATATAAATTTCACATGGGATT-TCACTTGC
389 TTTGCAATATCCAGAAGAGAAACATCTATTGGTGCATATAAATTTCACATGGGATTGT-ACTTGC
5425602 TAAGTT
453 TAAGTT
*
5425608 TCTTGATCAGGCAATCCAAAAATGAAAGCTTTTTTATCTCTTTGCCTATGAATGTTTAGTTATCC
1 TCTTGATCAGGCAATCCAAAAATGAAAGCTTTTTTATCTCTTTGCCTATGAATGTTTAGTTACCC
5425673 TAAAAAATAGAAAACCTTACAATTACCCCTTTCCCTAAAGATTACTTCAATTTTGTTGAGAAGCC
66 TAAAAAATAGAAAACCTTACAATTACCCCTTTCCCTAAAGATTACTTCAATTTTGTTGAGAAGCC
*
5425738 ATCTCTTTAGACAAAAGCTTTCTCCAAAAAATTATATTTGACATCTCCAAAGTCAATAACATATT
131 ATCTCTTTAGACAAAAGCTTTCTCCAAAAAATTATATTTGACAGCTCCAAAGTCAATAACATATT
5425803 CCAAAGGCAAATAGGCCTTTCCTTTCCTTGCTTCTAGACCAAATCTAGAGACTCATCTATGATCT
196 CCAAAGGCAAATAGGCCTTTCCTTTCCTTGCTTCTAGACCAAATCTAGAGACTCATCTATGATCT
* *
5425868 ATCTACATTGGAATTCACATCCCGACTGTTTTTATGCTTTTAACTTTTATTGGTGATAAACATAG
261 ATCTACATTGGAATTCACATCCCGACCGTTTTTATGCTTTTAACTTTTATTGGTGATATACATAG
*
5425933 AAGCTAGAAGCATTCTCCAATCTGTAAATAGAAATCATATACTCCCAAGAAGAAAGTTTGCACTT
326 AAGCTAGAAGCATTCTCCAATCTGTAAATAGAAATCATATACTCCCAAGAAGAAAGTTTGTACTT
5425998 TGCAATATCCAGAAGAGAAACATCTATTGGTGCATATAAATTTCACATGGGATTGTACTTGCTAA
391 TGCAATATCCAGAAGAGAAACATCTATTGGTGCATATAAATTTCACATGGGATTGTACTTGCTAA
5426063 GTT
456 GTT
*
5426066 TCTTGATCAGGCAATCCAAAAAT-AAAGGCTTTTTTATCTTTTTGCCTATGAACTGTTTAGTTAC
1 TCTTGATCAGGCAATCCAAAAATGAAA-GCTTTTTTATCTCTTTGCCTATGAA-TGTTTAGTTAC
* * *
5426130 CCTAAAAAATAGAAAACCTTACAATTACGCCTTTCCCTAAGGATTACTTCAATTTTGTTGAGAAA
64 CCTAAAAAATAGAAAACCTTACAATTACCCCTTTCCCTAAAGATTACTTCAATTTTGTTGAGAAG
* *
5426195 CTATCTCTTTAGACAAAAGCTTTCTCCAACAAATTATAAATTTGACAGCTCCAAAGTCAATAACA
129 CCATCTCTTTAGACAAAAGCTTTCTCCAAAAAATTAT--ATTTGACAGCTCCAAAGTCAATAACA
*
5426260 TATTCCTAAGGCAAAATAGGCCTTTCCTTTCCTTGCTTCTAGACCAAAATCTAGAGACTCATCTA
192 TATTCCAAAGGC-AAATAGGCCTTTCCTTTCCTTGCTTCTAGACC-AAATCTAGAGACTCATCTA
* *
5426325 TGATCTATCTACATTGGAATTCACATCCCAACCGTTTTTATGCGTTTAACTTTTATTGGTGATAT
255 TGATCTATCTACATTGGAATTCACATCCCGACCGTTTTTATGCTTTTAACTTTTATTGGTGATAT
* * *
5426390 ACACAGAAGCTAGAAGCA-CCTCCAATGTCGT-AATAGAAA-CAATATTACT-CCAAGAAGAAAG
320 ACATAGAAGCTAGAAGCATTCTCCAATCT-GTAAATAGAAATC-ATA-TACTCCCAAGAAGAAAG
* * * * * *
5426451 TCTATACTTTGCAATATCCAGAAGAAAAAGCATCTATAGTTGCAAATAAATTT
382 TTTGTACTTTGCAATATCCAGAAGAGAAA-CATCTATTGGTGCATATAAATTT
5426504 GCATAGTTTT
Statistics
Matches: 851, Mismatches: 34, Indels: 19
0.94 0.04 0.02
Matches are distributed among these distances:
457 3 0.00
458 332 0.39
459 112 0.13
460 156 0.18
461 37 0.04
462 88 0.10
463 123 0.14
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (458 bp):
TCTTGATCAGGCAATCCAAAAATGAAAGCTTTTTTATCTCTTTGCCTATGAATGTTTAGTTACCC
TAAAAAATAGAAAACCTTACAATTACCCCTTTCCCTAAAGATTACTTCAATTTTGTTGAGAAGCC
ATCTCTTTAGACAAAAGCTTTCTCCAAAAAATTATATTTGACAGCTCCAAAGTCAATAACATATT
CCAAAGGCAAATAGGCCTTTCCTTTCCTTGCTTCTAGACCAAATCTAGAGACTCATCTATGATCT
ATCTACATTGGAATTCACATCCCGACCGTTTTTATGCTTTTAACTTTTATTGGTGATATACATAG
AAGCTAGAAGCATTCTCCAATCTGTAAATAGAAATCATATACTCCCAAGAAGAAAGTTTGTACTT
TGCAATATCCAGAAGAGAAACATCTATTGGTGCATATAAATTTCACATGGGATTGTACTTGCTAA
GTT
Found at i:5426859 original size:2 final size:2
Alignment explanation
Indices: 5426852--5426895 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
5426842 CAAGTCTATA
*
5426852 TG TG TG TG TG TG AG TG 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 TG TG TG TG TG TG TG TG
5426894 TG
1 TG
5426896 CATATGCATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.02, C:0.00, G:0.50, T:0.48
Consensus pattern (2 bp):
TG
Found at i:5437144 original size:2 final size:2
Alignment explanation
Indices: 5437137--5437163 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5437127 GGGAAACAAT
5437137 AG 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 AG A
5437164 AAAAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5438386 original size:24 final size:24
Alignment explanation
Indices: 5438359--5438406 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
5438349 GTATATTTTT
*
5438359 ATTTTATTTTATTTTATTATTATA
1 ATTTTAATTTATTTTATTATTATA
*
5438383 ATTTTAATTTATTTTTTTATTATA
1 ATTTTAATTTATTTTATTATTATA
5438407 TCCACCACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
ATTTTAATTTATTTTATTATTATA
Found at i:5438388 original size:29 final size:27
Alignment explanation
Indices: 5438350--5438405 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
5438340 AAAAAATCAG
* *
5438350 TATATTTTTATTTTATTTTATTTTATTAT
1 TATAATTTTAATTTA-TTT-TTTTATTAT
5438379 TATAATTTTAATTTATTTTTTTATTAT
1 TATAATTTTAATTTATTTTTTTATTAT
5438406 ATCCACCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.36
28 3 0.12
29 13 0.52
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (27 bp):
TATAATTTTAATTTATTTTTTTATTAT
Found at i:5439396 original size:86 final size:86
Alignment explanation
Indices: 5439246--5439419 Score: 233
Period size: 86 Copynumber: 2.0 Consensus size: 86
5439236 ACTCTATTCA
* * * * * * *
5439246 TTCACCAACCAATTTGTGACGTTAAATACCGCAATGCTAAGGAAGATCAAGCTGATTTGGTTTGA
1 TTCACCAACCAACTTGTGACATTAAACACCGCAATGCTAAGAAAAATCAAGCTGATTAGATTTGA
5439311 ACTATATCTTCATCAATAATG
66 ACTATATCTTCATCAATAATG
* * *
5439332 TTCACCAACCAGCTTGTGACATTAAACACGGCAATGCTAAGAAAAATTAA-CTTGATTAGATTTG
1 TTCACCAACCAACTTGTGACATTAAACACCGCAATGCTAAGAAAAATCAAGC-TGATTAGATTTG
*
5439396 AAGTATATCTTCATCAATAATG
65 AACTATATCTTCATCAATAATG
5439418 TT
1 TT
5439420 ATCTCATTTA
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
85 1 0.01
86 75 0.99
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (86 bp):
TTCACCAACCAACTTGTGACATTAAACACCGCAATGCTAAGAAAAATCAAGCTGATTAGATTTGA
ACTATATCTTCATCAATAATG
Found at i:5440516 original size:20 final size:20
Alignment explanation
Indices: 5440491--5440529 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
5440481 GCAGTTCCAA
5440491 ACTGCACATTCATAAAGGGG
1 ACTGCACATTCATAAAGGGG
5440511 ACTGCACATTCATAAAGGG
1 ACTGCACATTCATAAAGGG
5440530 AATCACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (20 bp):
ACTGCACATTCATAAAGGGG
Found at i:5440716 original size:17 final size:18
Alignment explanation
Indices: 5440696--5440734 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5440686 TTATCGAATA
5440696 TAAATATTTTTAAAT-TT
1 TAAATATTTTTAAATATT
* *
5440713 TAAATTTTTTTATATATT
1 TAAATATTTTTAAATATT
5440731 TAAA
1 TAAA
5440735 AAGTATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TAAATATTTTTAAATATT
Found at i:5448764 original size:13 final size:14
Alignment explanation
Indices: 5448746--5448801 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 14
5448736 ATAAATTTTT
5448746 TATATATTTAAAAA
1 TATATATTTAAAAA
*
5448760 T-TATATATTATAAA
1 TATATAT-TTAAAAA
*
5448774 TATATA-TTAAATA
1 TATATATTTAAAAA
*
5448787 TAAATATTTTAAAAA
1 TATATA-TTTAAAAA
5448802 ATTAAAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
13 15 0.45
14 8 0.24
15 10 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATATTTAAAAA
Found at i:5448765 original size:15 final size:15
Alignment explanation
Indices: 5448745--5448781 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
5448735 TATAAATTTT
5448745 TTATATATTTAAAAA
1 TTATATATTTAAAAA
*
5448760 TTATATA-TTATAAA
1 TTATATATTTAAAAA
5448774 -TATATATT
1 TTATATATT
5448782 AAATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 6 0.30
14 7 0.35
15 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATATATTTAAAAA
Found at i:5448793 original size:26 final size:28
Alignment explanation
Indices: 5448746--5448799 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
5448736 ATAAATTTTT
*
5448746 TATATATTTAAAAATTATATATTATAAA
1 TATATATTTAAAAATTAAATATTATAAA
* *
5448774 TATATA-TTAAATA-TAAATATTTTAAA
1 TATATATTTAAAAATTAAATATTATAAA
5448800 AAATTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 11 0.48
27 6 0.26
28 6 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TATATATTTAAAAATTAAATATTATAAA
Found at i:5451024 original size:21 final size:21
Alignment explanation
Indices: 5450968--5451027 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
5450958 TTTAGGTTAT
*
5450968 TTTTAT-ATAATTTTAATAAA
1 TTTTATAATAATTTTGATAAA
*
5450988 TTTAATAA-AATTTTTGATAAA
1 TTTTATAATAA-TTTTGATAAA
5451009 TTTTATAATAATTTTGATA
1 TTTTATAATAATTTTGATA
5451028 GCATTTGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 7 0.21
21 25 0.74
22 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TTTTATAATAATTTTGATAAA
Found at i:5458904 original size:3 final size:3
Alignment explanation
Indices: 5458896--5458937 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
5458886 TAATGCTCAA
5458896 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5458938 GGTAGGGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5459010 original size:13 final size:14
Alignment explanation
Indices: 5458972--5459010 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
5458962 AAAAAATTAC
*
5458972 AAAAAGAAAAAGCA
1 AAAAAAAAAAAGCA
*
5458986 AATAAAAAAAAG-A
1 AAAAAAAAAAAGCA
5458999 AAAAAAAAAAAG
1 AAAAAAAAAAAG
5459011 GTGGAGACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAAAGCA
Found at i:5464312 original size:12 final size:12
Alignment explanation
Indices: 5464293--5464326 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5464283 GGTTGTGGTG
*
5464293 GCTGTGGAGGTA
1 GCTGTGGAGGAA
*
5464305 GTTGTGGAGGAA
1 GCTGTGGAGGAA
5464317 GCTGTGGAGG
1 GCTGTGGAGG
5464327 GCACTGTTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.06, G:0.53, T:0.24
Consensus pattern (12 bp):
GCTGTGGAGGAA
Found at i:5468859 original size:1 final size:1
Alignment explanation
Indices: 5468853--5468879 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
5468843 AGGGTTTTAC
5468853 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
5468880 CCTATCGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5471843 original size:2 final size:2
Alignment explanation
Indices: 5471836--5471878 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5471826 ATCACAAAAT
*
5471836 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5471878 T
1 T
5471879 TTGAAGTTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5471948 original size:2 final size:2
Alignment explanation
Indices: 5471941--5471972 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5471931 ATGACTACAG
5471941 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
5471973 CCTGGCGAAA
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
Found at i:5473074 original size:2 final size:2
Alignment explanation
Indices: 5473067--5473120 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
5473057 AGATCGATGC
*
5473067 AT AT AT AT TT 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
5473109 AT AT AT AT AT AT
1 AT AT AT AT AT AT
5473121 TCGAAAAGCA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5474420 original size:26 final size:26
Alignment explanation
Indices: 5474391--5474446 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
5474381 ATTTGGAGTA
*
5474391 GTTGAGACAAATAATATAAAGGATAG
1 GTTGAGACAAATAATACAAAGGATAG
* *
5474417 GTTGAGACAAATAATACGAGGGATAG
1 GTTGAGACAAATAATACAAAGGATAG
5474443 GTTG
1 GTTG
5474447 CTCATAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.23
Consensus pattern (26 bp):
GTTGAGACAAATAATACAAAGGATAG
Found at i:5476100 original size:29 final size:29
Alignment explanation
Indices: 5476058--5476134 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
5476048 ACTAAAAAAT
* *
5476058 TTATA-AATTTTATTATATTTGTCTCATA
1 TTATATAATTATATTATATTTATCTCATA
* *
5476086 TTATATAATTATATTATTTTTATCTTATA
1 TTATATAATTATATTATATTTATCTCATA
*
5476115 TTATATATTTATATTA-ATTT
1 TTATATAATTATATTATATTT
5476135 TGATAAATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 8 0.19
29 34 0.81
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (29 bp):
TTATATAATTATATTATATTTATCTCATA
Found at i:5478719 original size:3 final size:3
Alignment explanation
Indices: 5478711--5478735 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5478701 ATTCAAAACG
5478711 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
5478736 TGGCAGAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5479574 original size:17 final size:18
Alignment explanation
Indices: 5479541--5479574 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5479531 TAAAAATAAC
*
5479541 TTTTAAATATTTTATTTT
1 TTTTAAATATTTAATTTT
5479559 TTTTAAATA-TTAATTT
1 TTTTAAATATTTAATTT
5479575 AAGTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTAAATATTTAATTTT
Found at i:5479956 original size:36 final size:35
Alignment explanation
Indices: 5479915--5479992 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 35
5479905 CCCTACATAT
*
5479915 TTTTAAAAACAATTTATATTTTATATTA-TTAATTTA
1 TTTTAAAAACAATAT-TATTTTA-ATTATTTAATTTA
*
5479951 TTTT-AAAATAATATTATTTTAATTATTTTAATTTA
1 TTTTAAAAACAATATTATTTTAATTA-TTTAATTTA
5479986 TTTTAAA
1 TTTTAAA
5479993 TATAAATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
33 4 0.11
34 7 0.19
35 20 0.54
36 6 0.16
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (35 bp):
TTTTAAAAACAATATTATTTTAATTATTTAATTTA
Found at i:5479985 original size:35 final size:36
Alignment explanation
Indices: 5479931--5480007 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 36
5479921 AAACAATTTA
5479931 TATTTTATATTATTAATTTATTTTAAA-AT-AATAT
1 TATTTTATATTATTAATTTATTTTAAATATAAATAT
5479965 TATTTTA-ATTATTTTAATTTATTTTAAATATAAATAT
1 TATTTTATATTA--TTAATTTATTTTAAATATAAATAT
*
5480002 AATTTT
1 TATTTT
5480008 TAAAATATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
33 4 0.11
34 7 0.18
35 15 0.39
36 2 0.05
37 10 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (36 bp):
TATTTTATATTATTAATTTATTTTAAATATAAATAT
Found at i:5480008 original size:19 final size:19
Alignment explanation
Indices: 5479986--5480095 Score: 64
Period size: 19 Copynumber: 6.3 Consensus size: 19
5479976 TTTTAATTTA
5479986 TTTTAAATATAAATATAAT
1 TTTTAAATATAAATATAAT
*
5480005 TTTTAAA-AT--ATA-AGT
1 TTTTAAATATAAATATAAT
* *
5480020 TTTTTAGTATAAA-AGTAAAT
1 TTTTAAATATAAATA-T-AAT
*
5480040 TTTT-AATATAAACATAA-
1 TTTTAAATATAAATATAAT
* *
5480057 TTTT-AAT-T-TAT-TTAT
1 TTTTAAATATAAATATAAT
5480072 TTTTAAA-ATAAATATAAT
1 TTTTAAATATAAATATAAT
5480090 TTTTAA
1 TTTTAA
5480096 TTATTATTTA
Statistics
Matches: 69, Mismatches: 10, Indels: 25
0.66 0.10 0.24
Matches are distributed among these distances:
14 2 0.03
15 12 0.17
16 9 0.13
17 10 0.14
18 14 0.20
19 15 0.22
20 7 0.10
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTTAAATATAAATATAAT
Found at i:5480083 original size:32 final size:31
Alignment explanation
Indices: 5480038--5480104 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 31
5480028 ATAAAAGTAA
*
5480038 ATTTTTAATATAAACATAA-TTTTAATTTATTT
1 ATTTTTAAAATAAACATAATTTTTAA-TTA-TT
*
5480070 ATTTTTAAAATAAATATAATTTTTAATTATT
1 ATTTTTAAAATAAACATAATTTTTAATTATT
5480101 ATTT
1 ATTT
5480105 AACATAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 6 0.19
32 20 0.62
33 6 0.19
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTTTTAAAATAAACATAATTTTTAATTATT
Found at i:5480115 original size:29 final size:28
Alignment explanation
Indices: 5480063--5480118 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
5480053 ATAATTTTAA
*
5480063 TTTATTTATTTTTAAAATAAATATAATT
1 TTTAATTATTTTTAAAATAAATATAATT
*
5480091 TTTAATTATTATTTAACATAAATATAAT
1 TTTAATTATT-TTTAAAATAAATATAAT
5480119 GTTATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTAATTATTTTTAAAATAAATATAATT
Found at i:5480134 original size:29 final size:27
Alignment explanation
Indices: 5480050--5480134 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 27
5480040 TTTTAATATA
* *
5480050 AACATAATTTTAATTTA-TTTATTTTT
1 AACATAAATATAATTTATTTTATTTTT
*
5480076 AAAATAAATATAATTT-TTAATTATTATTT
1 AACATAAATATAATTTATT--TTATT-TTT
5480105 AACATAAATATAATGTTATTTTATATTTT
1 AACATAAATATAAT-TTATTTTAT-TTTT
5480134 A
1 A
5480135 TTATTTTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
26 14 0.29
28 5 0.10
29 24 0.50
30 3 0.06
31 2 0.04
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (27 bp):
AACATAAATATAATTTATTTTATTTTT
Found at i:5480161 original size:14 final size:14
Alignment explanation
Indices: 5480142--5480210 Score: 72
Period size: 13 Copynumber: 4.9 Consensus size: 14
5480132 TTATTATTTT
5480142 TAAATAATTTTTAA
1 TAAATAATTTTTAA
*
5480156 TAAAT-ATTTTAACA
1 TAAATAATTTTTA-A
*
5480170 TAAATATATATTTCAA
1 TAAATA-AT-TTTTAA
5480186 TAAAT-ATTTTTAA
1 TAAATAATTTTTAA
5480199 T-AATAATTTTTA
1 TAAATAATTTTTA
5480211 TTCTCATCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
12 3 0.06
13 19 0.40
14 13 0.28
16 8 0.17
17 4 0.09
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
TAAATAATTTTTAA
Found at i:5481962 original size:2 final size:2
Alignment explanation
Indices: 5481955--5481988 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5481945 GGAGTAGATA
5481955 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
5481989 GATCTAGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5486430 original size:10 final size:10
Alignment explanation
Indices: 5486415--5486455 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
5486405 AATTCACACA
5486415 ATATATACAT
1 ATATATACAT
5486425 ATATAT--AT
1 ATATATACAT
*
5486433 ATATATATAT
1 ATATATACAT
*
5486443 ATAAATACAT
1 ATATATACAT
5486453 ATA
1 ATA
5486456 AAAGAGGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 8 0.30
10 19 0.70
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATACAT
Found at i:5486432 original size:4 final size:4
Alignment explanation
Indices: 5486415--5486455 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
5486405 AATTCACACA
* * *
5486415 ATAT ATAC ATAT ATAT ATAT ATAT ATAT ATAA ATAC ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
5486456 AAAGAGGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (4 bp):
ATAT
Found at i:5488423 original size:108 final size:110
Alignment explanation
Indices: 5488313--5488516 Score: 276
Period size: 112 Copynumber: 1.9 Consensus size: 110
5488303 TTTAATTATA
*
5488313 TATATATATGCCCCCAC-AAATTGAAAATCTTCAAGC-A-A-AG-G-TTACAAACGTTTCTGAGG
1 TATATATATGCCCCCACAAAATTCAAAATCTTCAAGCAATACAGAGCTTACAAACGTTTCTGAGG
* *
5488372 CCAATTAGCTTTCCCAACAAGACAAGCAAGTGATGAAATTTTAAT
66 CCAATTAACTTTCCCAACAAGACAAGCAAGTGATGAAAGTTTAAT
* * *
5488417 TATATATGTGCCCCCACAAAATTCAAAATCTTCTAGCAAAATACAGAGCTTACAAACGTTTCTTA
1 TATATATATGCCCCCACAAAATTCAAAATCTTCAAGC--AATACAGAGCTTACAAACGTTTCTGA
* *
5488482 TGCCAATTAACTTTCCCAACATGACAAGCAAGTGA
64 GGCCAATTAACTTTCCCAACAAGACAAGCAAGTGA
5488517 AACAATCTGT
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
104 16 0.19
105 17 0.20
108 1 0.01
109 1 0.01
110 2 0.02
111 1 0.01
112 47 0.55
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (110 bp):
TATATATATGCCCCCACAAAATTCAAAATCTTCAAGCAATACAGAGCTTACAAACGTTTCTGAGG
CCAATTAACTTTCCCAACAAGACAAGCAAGTGATGAAAGTTTAAT
Found at i:5489950 original size:15 final size:15
Alignment explanation
Indices: 5489930--5489959 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5489920 CCATTGAAAT
5489930 CACTAGCAGACAAAA
1 CACTAGCAGACAAAA
*
5489945 CACTAGCTGACAAAA
1 CACTAGCAGACAAAA
5489960 TTTAGACAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.27, G:0.13, T:0.10
Consensus pattern (15 bp):
CACTAGCAGACAAAA
Found at i:5490332 original size:2 final size:2
Alignment explanation
Indices: 5490247--5490312 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
5490237 CATTGTCGAC
5490247 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
5490289 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
5490313 CATACATACA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5490388 original size:23 final size:19
Alignment explanation
Indices: 5490345--5490384 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
5490335 CCAGCATATC
5490345 AATTTATATATTTTTAATA
1 AATTTATATATTTTTAATA
5490364 AATTATATGATATTCTTTAAT
1 AATT-TAT-ATATT-TTTAAT
5490385 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 3 0.17
21 5 0.28
22 6 0.33
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (19 bp):
AATTTATATATTTTTAATA
Found at i:5492312 original size:9 final size:8
Alignment explanation
Indices: 5492297--5492322 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5492287 GAGGATTTAA
5492297 ATTTTTTT
1 ATTTTTTT
5492305 ATTTTTTT
1 ATTTTTTT
5492313 ATTTTTTT
1 ATTTTTTT
5492321 AT
1 AT
5492323 CTCCAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
ATTTTTTT
Found at i:5492653 original size:16 final size:16
Alignment explanation
Indices: 5492634--5492773 Score: 84
Period size: 16 Copynumber: 9.1 Consensus size: 16
5492624 AAATTAATTA
5492634 AAATATAATATAATAT
1 AAATATAATATAATAT
*
5492650 AAATATGATATAA-AT
1 AAATATAATATAATAT
* * *
5492665 ATATA-AATAT-TTTT
1 AAATATAATATAATAT
*
5492679 AAATAT-ATATAATAA
1 AAATATAATATAATAT
*
5492694 AAATTATTAATATATTA-
1 AAA-TA-TAATATAATAT
*
5492711 AAAT-TTATATAAATAT
1 AAATATAATAT-AATAT
* *
5492727 AAAT-TATTTTAAATAT
1 AAATATAATAT-AATAT
*
5492743 AAATATAATACAATA-
1 AAATATAATATAATAT
5492758 AAATA-AATA-AATAT
1 AAATATAATATAATAT
5492772 AA
1 AA
5492774 CATAAATTTC
Statistics
Matches: 96, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
13 4 0.04
14 24 0.25
15 18 0.19
16 36 0.38
17 7 0.07
18 7 0.07
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (16 bp):
AAATATAATATAATAT
Found at i:5492670 original size:19 final size:18
Alignment explanation
Indices: 5492636--5492772 Score: 63
Period size: 20 Copynumber: 7.6 Consensus size: 18
5492626 ATTAATTAAA
5492636 ATATAATATAATATAAATAT
1 ATATAA-AT-ATATAAATAT
5492656 GATATAAATATATAAATAT
1 -ATATAAATATATAAATAT
* *
5492675 TTTTAAATATAT--ATA-
1 ATATAAATATATAAATAT
* *
5492690 ATAAAAAT-TATTAATAT
1 ATATAAATATATAAATAT
* * *
5492707 AT-TAAA-ATTTATATAA
1 ATATAAATATATAAATAT
*
5492723 ATATAAATTATTTTAAATAT
1 ATATAAA-TA-TATAAATAT
* *
5492743 AAATATAATACAATAAA-AT
1 ATATA-AATA-TATAAATAT
*
5492762 AAATAAATATA
1 ATATAAATATA
5492773 ACATAAATTT
Statistics
Matches: 90, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
14 3 0.03
15 5 0.06
16 16 0.18
17 7 0.08
18 14 0.16
19 18 0.20
20 19 0.21
21 8 0.09
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (18 bp):
ATATAAATATATAAATAT
Found at i:5492688 original size:22 final size:22
Alignment explanation
Indices: 5492635--5492708 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
5492625 AATTAATTAA
*
5492635 AATATAATATAATATAAA-TA-T
1 AATAT-ATATAATAAAAATTATT
* * * *
5492656 GATATAAATATATAAATATTTTT
1 AATATATATA-ATAAAAATTATT
5492679 AAATATATATAATAAAAATTATT
1 -AATATATATAATAAAAATTATT
5492702 AATATAT
1 AATATAT
5492709 TAAAATTTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
20 4 0.10
21 9 0.22
22 8 0.20
23 11 0.28
24 8 0.20
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (22 bp):
AATATATATAATAAAAATTATT
Found at i:5492706 original size:18 final size:20
Alignment explanation
Indices: 5492636--5492728 Score: 59
Period size: 22 Copynumber: 4.6 Consensus size: 20
5492626 ATTAATTAAA
*
5492636 ATAT-AATATAATATAAATATG
1 ATATAAATATAATA-AAA-ATT
*
5492657 ATATAAATAT-ATAAATATTTTT
1 ATATAAATATAATAAA-A--ATT
* *
5492679 AAATATATATAATAAAAATT
1 ATATAAATATAATAAAAATT
* *
5492699 AT-T-AATATATTAAAATTT
1 ATATAAATATAATAAAAATT
5492717 ATATAAATATAA
1 ATATAAATATAA
5492729 ATTATTTTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
18 14 0.25
19 2 0.04
20 11 0.20
21 8 0.14
22 16 0.29
23 5 0.09
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (20 bp):
ATATAAATATAATAAAAATT
Done.