Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 11 of 79
Found at i:3750226 original size:32 final size:32
Alignment explanation
Indices: 3750162--3750226 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
3750152 TAATTTATAA
* * *
3750162 TATAATAAAATAATAATAATAATAATATATTT
1 TATAATAAAACAATAATAAAAATAATAGATTT
*
3750194 TATAATAAAACAATCATAAAAATTAA-AGATTT
1 TATAATAAAACAATAATAAAAA-TAATAGATTT
3750226 T
1 T
3750227 TATGCTTTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (32 bp):
TATAATAAAACAATAATAAAAATAATAGATTT
Found at i:3755202 original size:109 final size:109
Alignment explanation
Indices: 3755100--3755392 Score: 466
Period size: 109 Copynumber: 2.7 Consensus size: 109
3755090 TTTTTGATTG
* *
3755100 AGGCAATATTTCGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
3755165 CGTTCAACCAAATAGCTAAATATCCTTTTAAAAATTTTAAAATA
66 CGTTCAACCAAATAGCTAAATATCCTTTCAAAAATTTTAAAATA
3755209 AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* *
3755274 CATTCAACCAAATAGCTAAATATCCTTTCAAAAATTTCAAAATA
66 CGTTCAACCAAATAGCTAAATATCCTTTCAAAAATTTTAAAATA
* * * * *
3755318 AAGCAATGTTTTGCGTTTGAAAATTCAAG-GAACGTGCCCTAAGGTGCTGGGTTTCGA--TTTCT
1 AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
3755380 CGTTTAACCAAAT
66 CGTTCAACCAAAT
3755393 TGNNNNNNNN
Statistics
Matches: 172, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
106 16 0.09
108 25 0.15
109 131 0.76
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (109 bp):
AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATAGCTAAATATCCTTTCAAAAATTTTAAAATA
Found at i:3758950 original size:45 final size:45
Alignment explanation
Indices: 3758884--3758979 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
3758874 CCAACTACTA
* **
3758884 TTACTGTTACCGATTTGACACTTTGTGTGTCGAATACTGTTACCG
1 TTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTTACCG
* **
3758929 TTACTGTTACAGATTCAACACTTTGTGTGTTGAATACTGTTATTG
1 TTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTTACCG
3758974 TTACTG
1 TTACTG
3758980 CTATCGTTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (45 bp):
TTACTGTTACAGATTCAACACTTTGTGTGTCGAATACTGTTACCG
Found at i:3760766 original size:21 final size:22
Alignment explanation
Indices: 3760736--3760800 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
3760726 TTTTTCTTTT
3760736 TGTAATTATTTTTTATTTATATA
1 TGTAA-TATTTTTTATTTATATA
* *
3760759 TGT-ATATTTGTTGTTT-T-TA
1 TGTAATATTTTTTATTTATATA
3760778 TGTACATATTTATTTATTTATAT
1 TGTA-ATATTT-TTTATTTATAT
3760801 TTTTTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
19 5 0.15
20 1 0.03
21 16 0.48
22 6 0.18
23 4 0.12
24 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.65
Consensus pattern (22 bp):
TGTAATATTTTTTATTTATATA
Found at i:3762975 original size:24 final size:25
Alignment explanation
Indices: 3762948--3762994 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3762938 ACATCAAAAA
3762948 TTCT-AAAAACATT-AAAACAAATGT
1 TTCTCAAAAA-ATTGAAAACAAATGT
*
3762972 TTCTCAAAAAATTGAAAAGAAAT
1 TTCTCAAAAAATTGAAAACAAAT
3762995 TAAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (25 bp):
TTCTCAAAAAATTGAAAACAAATGT
Found at i:3771743 original size:7 final size:7
Alignment explanation
Indices: 3771731--3771771 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
3771721 TTATATTTGT
3771731 TTTTTTA
1 TTTTTTA
3771738 TTTTTTA
1 TTTTTTA
3771745 TTTTTTA
1 TTTTTTA
3771752 TTTTTTA
1 TTTTTTA
3771759 TTTTTTA
1 TTTTTTA
3771766 TTTTTT
1 TTTTTT
3771772 TCATTCTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:3771745 original size:21 final size:21
Alignment explanation
Indices: 3771720--3771769 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
3771710 ACAACCAATG
3771720 TTTATATTTGT-TTTTTTATTT
1 TTTAT-TTTGTATTTTTTATTT
*
3771741 TTTATTTTTTATTTTTTATTT
1 TTTATTTTGTATTTTTTATTT
3771762 TTTATTTT
1 TTTATTTT
3771770 TTTCATTCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.84
Consensus pattern (21 bp):
TTTATTTTGTATTTTTTATTT
Found at i:3772230 original size:28 final size:27
Alignment explanation
Indices: 3772184--3772260 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 27
3772174 ATTTAATTAA
*
3772184 TTTTTTAAAATTTAAAAAATTATAAAAT
1 TTTTTTAAAAATT-AAAAATTATAAAAT
*
3772212 TATTTTTAAAAATTAAAAATTATTAAAT
1 T-TTTTTAAAAATTAAAAATTATAAAAT
*
3772240 TTATTTAAAAAGTATAAAAAT
1 TTTTTTAAAAA-T-TAAAAAT
3772261 ATATTTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 9 0.21
28 16 0.37
29 18 0.42
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
TTTTTTAAAAATTAAAAATTATAAAAT
Found at i:3772248 original size:49 final size:53
Alignment explanation
Indices: 3772193--3772292 Score: 129
Period size: 49 Copynumber: 2.0 Consensus size: 53
3772183 ATTTTTTAAA
*
3772193 ATTTAAAAAAT-TATAAAAT-TA-TTTTTAAAAATTAAA-AATT-ATTAAATTT
1 ATTTAAAAAGTATA-AAAATATATTTTTTAAAAATTAAAGAATTGATTAAATTT
**
3772242 ATTTAAAAAGTATAAAAATATATTTTTTAAATGTTAAAGAATTGATTAAAT
1 ATTTAAAAAGTATAAAAATATATTTTTTAAAAATTAAAGAATTGATTAAAT
3772293 GTTGACATGT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
49 15 0.35
50 4 0.09
51 13 0.30
52 4 0.09
53 7 0.16
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (53 bp):
ATTTAAAAAGTATAAAAATATATTTTTTAAAAATTAAAGAATTGATTAAATTT
Found at i:3773464 original size:21 final size:21
Alignment explanation
Indices: 3773438--3773480 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3773428 TAAACTAGTC
*
3773438 TGCTGGTATCATCCGAGACCA
1 TGCTGGTATCACCCGAGACCA
*
3773459 TGCTGGTATTACCCGAGACCA
1 TGCTGGTATCACCCGAGACCA
3773480 T
1 T
3773481 ATATCCTTAG
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:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (21 bp):
TGCTGGTATCACCCGAGACCA
Found at i:3776244 original size:24 final size:24
Alignment explanation
Indices: 3776212--3776257 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3776202 ACTTAAAAAA
* *
3776212 ATTAATTCTTTTTTTTTCTTTTAC
1 ATTAATTCTCTTTCTTTCTTTTAC
*
3776236 ATTATTTCTCTTTCTTTCTTTT
1 ATTAATTCTCTTTCTTTCTTTT
3776258 TCTTTTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (24 bp):
ATTAATTCTCTTTCTTTCTTTTAC
Found at i:3782304 original size:16 final size:17
Alignment explanation
Indices: 3782274--3782315 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
3782264 TAGAATTTAT
3782274 TTTTATTATACTAA-TAG
1 TTTT-TTATACTAATTAG
*
3782291 TTTTTTATAGTAATTAG
1 TTTTTTATACTAATTAG
3782308 TATTTTTA
1 T-TTTTTA
3782316 AAAATATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 8 0.36
18 6 0.27
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (17 bp):
TTTTTTATACTAATTAG
Found at i:3784214 original size:35 final size:35
Alignment explanation
Indices: 3784174--3784245 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
3784164 TCGCGTATTT
*
3784174 AGATTCATCGTGAAAATTGAAACCCAGTAAGTTAG
1 AGATTCATCGTGAAAATTAAAACCCAGTAAGTTAG
3784209 AGATTCATCGTGAAAATTAAAACCCAGTAAGTTAG
1 AGATTCATCGTGAAAATTAAAACCCAGTAAGTTAG
3784244 AG
1 AG
3784246 TACGACCTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (35 bp):
AGATTCATCGTGAAAATTAAAACCCAGTAAGTTAG
Found at i:3784786 original size:18 final size:18
Alignment explanation
Indices: 3784763--3784798 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3784753 TATATGTAAG
*
3784763 TATATATGTACGTATAAA
1 TATATATATACGTATAAA
*
3784781 TATATATATACTTATAAA
1 TATATATATACGTATAAA
3784799 AAATTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (18 bp):
TATATATATACGTATAAA
Found at i:3784861 original size:20 final size:18
Alignment explanation
Indices: 3784833--3784891 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 18
3784823 CATAGATATG
3784833 AATATATGTATATATATAA
1 AATA-ATGTATATATATAA
3784852 ATTATAATGTATATATA-AA
1 A--ATAATGTATATATATAA
3784871 AATAA-GTATATATATATA
1 AATAATGTATATATATA-A
3784889 AAT
1 AAT
3784892 CAAAGATATG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
16 9 0.25
17 5 0.14
18 4 0.11
19 4 0.11
20 11 0.31
21 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
AATAATGTATATATATAA
Found at i:3784879 original size:16 final size:18
Alignment explanation
Indices: 3784843--3784889 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
3784833 AATATATGTA
*
3784843 TATATATAAATTATAATG
1 TATATATAAATAATAATG
3784861 TATATATAAA-AATAA-G
1 TATATATAAATAATAATG
*
3784877 TATATATATATAA
1 TATATATAAATAA
3784890 ATCAAAGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 10 0.38
17 6 0.23
18 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
TATATATAAATAATAATG
Found at i:3785055 original size:3 final size:3
Alignment explanation
Indices: 3785049--3785101 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
3785039 TAAAATGATG
* * *
3785049 ATA ATA ATA ATA GTA ATA ATAA ATA ATA ATA ATA TATT TTA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA -ATA ATA ATA ATA
3785096 A-A ATA A
1 ATA ATA A
3785102 CCAAAATACA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 34 0.83
4 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:3792752 original size:8 final size:8
Alignment explanation
Indices: 3792728--3792761 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
3792718 AATAATGTCC
3792728 TATAAAATA
1 TATAAAA-A
3792737 TAATAAAAA
1 T-ATAAAAA
3792746 TATAAAAA
1 TATAAAAA
3792754 TATAAAAA
1 TATAAAAA
3792762 AAATGTGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 15 0.62
9 3 0.12
10 6 0.25
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
TATAAAAA
Found at i:3797015 original size:20 final size:18
Alignment explanation
Indices: 3796970--3797020 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
3796960 AAAAAATAAG
3796970 ATAAAAATAAATTTGAAA
1 ATAAAAATAAATTTGAAA
3796988 ATGCAAAAATAAATTTAAGAAA
1 AT--AAAAATAAATTT--GAAA
3797010 AT-AAAATAAAT
1 ATAAAAATAAAT
3797021 GGAAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.07
19 9 0.31
20 12 0.41
22 6 0.21
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAAATTTGAAA
Found at i:3797632 original size:28 final size:28
Alignment explanation
Indices: 3797600--3797657 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3797590 CTAAAAAGAG
3797600 TTTAGTTAATAATAAAGAAAATTATGCT
1 TTTAGTTAATAATAAAGAAAATTATGCT
3797628 TTTAGTTAATAATAAAGAAAATTATGCT
1 TTTAGTTAATAATAAAGAAAATTATGCT
3797656 TT
1 TT
3797658 GAAAATAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.41
Consensus pattern (28 bp):
TTTAGTTAATAATAAAGAAAATTATGCT
Found at i:3797918 original size:13 final size:13
Alignment explanation
Indices: 3797900--3797965 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
3797890 TAGATTTTTC
3797900 CTAAATATTATCA
1 CTAAATATTATCA
3797913 CTAAATA--AT-A
1 CTAAATATTATCA
*
3797923 CTAAATATTATCG
1 CTAAATATTATCA
* *
3797936 CTAAACA--AT-T
1 CTAAATATTATCA
3797946 CTAAATATTATCA
1 CTAAATATTATCA
3797959 CTAAATA
1 CTAAATA
3797966 ATTCAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
10 14 0.33
11 4 0.10
12 4 0.10
13 20 0.48
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:3797968 original size:23 final size:23
Alignment explanation
Indices: 3797900--3797974 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
3797890 TAGATTTTTC
*
3797900 CTAAATATTATCACTAAATAATA
1 CTAAATATTATCACTAAATAATT
* *
3797923 CTAAATATTATCGCTAAACAATT
1 CTAAATATTATCACTAAATAATT
3797946 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
3797969 CAAAAT
1 CTAAAT
3797975 TTAAAAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:3798000 original size:18 final size:18
Alignment explanation
Indices: 3797979--3798013 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3797969 CAAAATTTAA
3797979 AAATTAAATTTAAACTAG
1 AAATTAAATTTAAACTAG
3797997 AAATTAAATTTAAACTA
1 AAATTAAATTTAAACTA
3798014 ATTACAGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (18 bp):
AAATTAAATTTAAACTAG
Found at i:3814480 original size:13 final size:12
Alignment explanation
Indices: 3814459--3814485 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3814449 TTATTATTTG
3814459 TTATTTTTTTCT
1 TTATTTTTTTCT
3814471 TTATTTTTTTCT
1 TTATTTTTTTCT
3814483 TTA
1 TTA
3814486 CTTTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.81
Consensus pattern (12 bp):
TTATTTTTTTCT
Found at i:3814509 original size:12 final size:12
Alignment explanation
Indices: 3814459--3814509 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
3814449 TTATTATTTG
*
3814459 TTATTTTTTTCT
1 TTATTTTATTCT
*
3814471 TTATTTTTTTCT
1 TTATTTTATTCT
*
3814483 TTACTTTA-T-T
1 TTATTTTATTCT
*
3814493 TTATTTTATTAT
1 TTATTTTATTCT
3814505 TTATT
1 TTATT
3814510 ACTTATTTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 8 0.24
11 2 0.06
12 24 0.71
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (12 bp):
TTATTTTATTCT
Found at i:3825067 original size:3 final size:3
Alignment explanation
Indices: 3825059--3825096 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3825049 CATAAAATTT
*
3825059 TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3825097 TGGAGTCAGA
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:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:3825703 original size:16 final size:16
Alignment explanation
Indices: 3825682--3825727 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
3825672 TTGATTACTG
*
3825682 ATTACAACGT-TATTCC
1 ATTACAAC-TCTATTAC
*
3825698 ATTACATCTCTATTAC
1 ATTACAACTCTATTAC
3825714 ATTACAACTCTATT
1 ATTACAACTCTATT
3825728 CTATTCCAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 1 0.04
16 25 0.96
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (16 bp):
ATTACAACTCTATTAC
Found at i:3827236 original size:22 final size:22
Alignment explanation
Indices: 3827211--3827259 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3827201 TGTTTTCTTC
*
3827211 TTATTTTGCTACTATTTCACTA
1 TTATTATGCTACTATTTCACTA
* * *
3827233 TTATAATGCTACTATTTTACTG
1 TTATTATGCTACTATTTCACTA
3827255 TTATT
1 TTATT
3827260 GTTTAGATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.14, G:0.06, T:0.55
Consensus pattern (22 bp):
TTATTATGCTACTATTTCACTA
Found at i:3827805 original size:23 final size:24
Alignment explanation
Indices: 3827775--3827830 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 24
3827765 TAATATATAT
3827775 AATATATATTTGATTAAAAAT-AA
1 AATATATATTTGATTAAAAATAAA
*
3827798 AATATATATTTGTTTAAAAATAAA
1 AATATATATTTGATTAAAAATAAA
3827822 AATATATAT
1 AATATATAT
3827831 ATTTAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 20 0.65
24 11 0.35
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
AATATATATTTGATTAAAAATAAA
Found at i:3827843 original size:23 final size:22
Alignment explanation
Indices: 3827756--3827836 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 22
3827746 CCCATATTAA
* *
3827756 ATATATATTT-AATATATATAAT
1 ATATATATTTAAAAATA-AAAAT
*
3827778 ATATATTTGATTAAAAATAAAATAT
1 ATATATAT--TTAAAAATAAAA-AT
* *
3827803 ATATTTGTTTAAAAATAAAAAT
1 ATATATATTTAAAAATAAAAAT
3827825 ATATATATTTAA
1 ATATATATTTAA
3827837 TATATAATTC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
22 19 0.40
23 12 0.25
24 4 0.08
25 13 0.27
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATATATTTAAAAATAAAAAT
Found at i:3834496 original size:10 final size:9
Alignment explanation
Indices: 3834476--3834543 Score: 57
Period size: 10 Copynumber: 7.3 Consensus size: 9
3834466 TATGATTTTG
3834476 TTTATAATT
1 TTTATAATT
3834485 TTTATAAATT
1 TTTAT-AATT
3834495 TTTATTAATT
1 TTTA-TAATT
* *
3834505 TTAATACTT
1 TTTATAATT
* *
3834514 TTAATCA-T
1 TTTATAATT
3834522 TTTATAATT
1 TTTATAATT
*
3834531 TTCAATAATT
1 TT-TATAATT
3834541 TTT
1 TTT
3834544 TATGAATCGT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
8 6 0.13
9 17 0.36
10 23 0.49
11 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTATAATT
Found at i:3834541 original size:18 final size:17
Alignment explanation
Indices: 3834479--3834542 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
3834469 GATTTTGTTT
3834479 ATAATTTTTATAAATTTTTA
1 ATAA-TTTTAT-AA-TTTTA
* *
3834499 TTAATTTTAATACTTTTA
1 ATAATTTT-ATAATTTTA
*
3834517 ATCATTTTATAATTTTCA
1 ATAATTTTATAATTTT-A
3834535 ATAATTTT
1 ATAATTTT
3834543 TTATGAATCG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 7 0.19
18 19 0.53
19 5 0.14
20 5 0.14
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
ATAATTTTATAATTTTA
Found at i:3834586 original size:23 final size:23
Alignment explanation
Indices: 3834535--3834587 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
3834525 ATAATTTTCA
3834535 ATAATTTTTTATGAATCGTTTTTT
1 ATAATTTTTTAT-AATCGTTTTTT
*
3834559 A-AATTTTTTAT-ATGGTTTTATT
1 ATAATTTTTTATAATCGTTTT-TT
3834581 ATAATTT
1 ATAATTT
3834588 ATTCTGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 7 0.27
22 3 0.12
23 15 0.58
24 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62
Consensus pattern (23 bp):
ATAATTTTTTATAATCGTTTTTT
Found at i:3841678 original size:17 final size:17
Alignment explanation
Indices: 3841643--3841676 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3841633 AGCTTAACCC
*
3841643 ATATTATTTTTTCTTTT
1 ATATTATTTTCTCTTTT
3841660 ATATTATTTCTCTCTTT
1 ATATTATTT-TCTCTTT
3841677 ATTTTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.71
Consensus pattern (17 bp):
ATATTATTTTCTCTTTT
Found at i:3847231 original size:2 final size:2
Alignment explanation
Indices: 3847224--3847253 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3847214 CCAATATCCA
*
3847224 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3847254 CCTCTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3851937 original size:26 final size:26
Alignment explanation
Indices: 3851901--3851955 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
3851891 AATTTCCTTA
3851901 AACAAGTATCTCACCTTTTGCCTAGG
1 AACAAGTATCTCACCTTTTGCCTAGG
3851927 AACAAGTATCTCACCTTTTGCCTAGG
1 AACAAGTATCTCACCTTTTGCCTAGG
3851953 AAC
1 AAC
3851956 CGCCCCATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (26 bp):
AACAAGTATCTCACCTTTTGCCTAGG
Found at i:3855914 original size:16 final size:16
Alignment explanation
Indices: 3855893--3855934 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
3855883 ATTTAGTGAA
3855893 CTAAATATCTA-AATAT
1 CTAAATAT-TAGAATAT
3855909 CTAAAT-TTAGTAATAT
1 CTAAATATTAG-AATAT
3855925 CTAAATATTA
1 CTAAATATTA
3855935 ATTTGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.09
15 1 0.04
16 17 0.74
17 3 0.13
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (16 bp):
CTAAATATTAGAATAT
Found at i:3856634 original size:156 final size:157
Alignment explanation
Indices: 3856463--3856780 Score: 620
Period size: 156 Copynumber: 2.0 Consensus size: 157
3856453 TATAATAATA
3856463 TTATTTTTTATAAAAAAAATTAAATTAATTGCAACAACGAATTATTAAATTATTGGATTAGTTGT
1 TTATTTTTTATAAAAAAAATTAAATTAATTGCAACAACGAATTATTAAATTATTGGATTAGTTGT
3856528 ATAGCATTAAATTTAAGGTTTTGTACTTATCTTCAACATAGAAACCTTTATGTAATCCCCACCAA
66 ATAGCATTAAATTTAAGGTTTTGTACTTATCTTCAACATAGAAACCTTTATGTAATCCCCACCAA
3856593 ATAAATTGAGTTGATATGTAGCTTTGT
131 ATAAATTGAGTTGATATGTAGCTTTGT
3856620 TTATTTTTTA-AAAAAAAATTAAATTAATTGCAACAACGAATTATTAAATTATTGGATTAGTTGT
1 TTATTTTTTATAAAAAAAATTAAATTAATTGCAACAACGAATTATTAAATTATTGGATTAGTTGT
3856684 ATAGCATTAAATTTAAGGTTTTGTACTTATCTTCAACATAGAAACCTTTATGTAATCCCCACCAA
66 ATAGCATTAAATTTAAGGTTTTGTACTTATCTTCAACATAGAAACCTTTATGTAATCCCCACCAA
3856749 ATAAATTGAGTTGATATGTAGCTTTGT
131 ATAAATTGAGTTGATATGTAGCTTTGT
*
3856776 CTATT
1 TTATT
3856781 GTTTCAATTT
Statistics
Matches: 160, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
156 150 0.94
157 10 0.06
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (157 bp):
TTATTTTTTATAAAAAAAATTAAATTAATTGCAACAACGAATTATTAAATTATTGGATTAGTTGT
ATAGCATTAAATTTAAGGTTTTGTACTTATCTTCAACATAGAAACCTTTATGTAATCCCCACCAA
ATAAATTGAGTTGATATGTAGCTTTGT
Found at i:3864253 original size:9 final size:9
Alignment explanation
Indices: 3864236--3864266 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3864226 TCGAGTTGAT
3864236 TCGAATAAC
1 TCGAATAAC
*
3864245 TCGATTAAC
1 TCGAATAAC
3864254 TCGAATAAC
1 TCGAATAAC
3864263 TCGA
1 TCGA
3864267 TTCATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:3870577 original size:15 final size:15
Alignment explanation
Indices: 3870557--3870586 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3870547 TTTAATTATT
3870557 TTTCTTTTCCTTTTA
1 TTTCTTTTCCTTTTA
*
3870572 TTTCTTTTCTTTTTA
1 TTTCTTTTCCTTTTA
3870587 AAATTGAGAA
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:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTCTTTTCCTTTTA
Found at i:3872689 original size:16 final size:16
Alignment explanation
Indices: 3872670--3872703 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3872660 AAAAAATTCT
3872670 AAAAACCA-AAAACCC
1 AAAAACCATAAAACCC
*
3872685 AAAAACGATAAAACCC
1 AAAAACCATAAAACCC
3872701 AAA
1 AAA
3872704 TTAAAGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.68, C:0.26, G:0.03, T:0.03
Consensus pattern (16 bp):
AAAAACCATAAAACCC
Found at i:3873398 original size:27 final size:27
Alignment explanation
Indices: 3873368--3873428 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
3873358 GGAAGGTGCT
3873368 AATGGTGGTGCCTACTTGGGAGGCGCC
1 AATGGTGGTGCCTACTTGGGAGGCGCC
**
3873395 AATGGTGGTGCCTGTTTGGGAGGCGCC
1 AATGGTGGTGCCTACTTGGGAGGCGCC
3873422 AATGGTG
1 AATGGTG
3873429 AACAAAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.15, C:0.18, G:0.43, T:0.25
Consensus pattern (27 bp):
AATGGTGGTGCCTACTTGGGAGGCGCC
Found at i:3873510 original size:21 final size:22
Alignment explanation
Indices: 3873472--3873512 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3873462 ACAAATTAAT
*
3873472 TATAAAATAATTATAATATTCA
1 TATAAAATAATTACAATATTCA
3873494 TATAAAA-AATTACAATATT
1 TATAAAATAATTACAATATT
3873513 ACAATATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
TATAAAATAATTACAATATTCA
Found at i:3874002 original size:27 final size:27
Alignment explanation
Indices: 3873971--3874049 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
3873961 ATATTTTGTT
3873971 CACCATTGGCGCCTCCCAAATAGGCAC
1 CACCATTGGCGCCTCCCAAATAGGCAC
*
3873998 CACCATTGGCGCCTCCCAAGTAGGCAC
1 CACCATTGGCGCCTCCCAAATAGGCAC
* *
3874025 CACCATTGGCGCCTTCCAGATAGGC
1 CACCATTGGCGCCTCCCAAATAGGC
3874050 GCCAATACTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.23, C:0.39, G:0.22, T:0.16
Consensus pattern (27 bp):
CACCATTGGCGCCTCCCAAATAGGCAC
Found at i:3877583 original size:19 final size:20
Alignment explanation
Indices: 3877569--3877619 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
3877559 CTTAATATTT
3877569 AAGTAAATATATAATATAATA
1 AAGTAAATATATAATAT-ATA
* *
3877590 AAGTAAATATAATAAAATAAA
1 AAGTAAATAT-ATAATATATA
3877611 TAAGTAAAT
1 -AAGTAAAT
3877620 GAAATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (20 bp):
AAGTAAATATATAATATATA
Found at i:3877587 original size:5 final size:4
Alignment explanation
Indices: 3877572--3877631 Score: 50
Period size: 4 Copynumber: 14.0 Consensus size: 4
3877562 AATATTTAAG
* *
3877572 TAAA TATA T-AA TATAA TAAA GTAAA TATAA TAAAA TAAA TAAG TAAA
1 TAAA TAAA TAAA TA-AA TAAA -TAAA TA-AA T-AAA TAAA TAAA TAAA
3877619 TGAAA TAAA TAAA
1 T-AAA TAAA TAAA
3877632 GAAAAGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
3 2 0.04
4 25 0.54
5 18 0.39
6 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:3877598 original size:14 final size:13
Alignment explanation
Indices: 3877581--3877632 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
3877571 GTAAATATAT
3877581 AATATAATAAAGTA
1 AATA-AATAAAGTA
*
3877595 AATATAATAAAATA
1 AATA-AATAAAGTA
*
3877609 AATAAGTAAA-TGA
1 AATAAATAAAGT-A
3877622 AATAAATAAAG
1 AATAAATAAAG
3877633 AAAAGAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 1 0.03
13 15 0.45
14 17 0.52
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (13 bp):
AATAAATAAAGTA
Found at i:3877609 original size:22 final size:22
Alignment explanation
Indices: 3877568--3877631 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
3877558 ACTTAATATT
*
3877568 TAAGTAAATAT-ATAATAT-AA
1 TAAGTAAATATAATAAAATAAA
3877588 TAAAGTAAATATAATAAAATAAA
1 T-AAGTAAATATAATAAAATAAA
3877611 TAAGTAAATGA-AAT-AAATAAA
1 TAAGTAAAT-ATAATAAAATAAA
3877632 GAAAAGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
20 1 0.03
21 17 0.44
22 17 0.44
23 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (22 bp):
TAAGTAAATATAATAAAATAAA
Found at i:3878687 original size:40 final size:39
Alignment explanation
Indices: 3878558--3878691 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 39
3878548 GACTTCAAGT
* *
3878558 CGATGAGACACTGGGTGTCAATTTATTACTTCGGATATATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTC-GAT-TATC
* * * * * *
3878599 TGATGGGGCACTGGGTG-CCAA-T-TTACTTCGGTTAGC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGATTATC
*
3878635 CGATGAGACACTGGGTGTTAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCG-ATTATC
*
3878675 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
3878692 CCAAGTTGGT
Statistics
Matches: 73, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
36 16 0.22
37 4 0.05
38 8 0.11
39 9 0.12
40 22 0.30
41 14 0.19
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGATTATC
Found at i:3879373 original size:120 final size:121
Alignment explanation
Indices: 3879228--3879468 Score: 475
Period size: 120 Copynumber: 2.0 Consensus size: 121
3879218 TCACATTATG
3879228 ACATGTTTAAGTTAATGTTTAAATGAACATGAAATAGGTAAAATAGATTAAATTTGGCATGTTTA
1 ACATGTTTAAGTTAATGTTTAAATGAACATGAAATAGGTAAAATAGATTAAATTTGGCATGTTTA
3879293 CAAGTTCGATTTGAATGATGTTCTATTGATATGTTTTATTGATATAATTGTGGTAC
66 CAAGTTCGATTTGAATGATGTTCTATTGATATGTTTTATTGATATAATTGTGGTAC
3879349 ACATGTTTAA-TTAATGTTTAAATGAACATGAAATAGGTAAAATAGATTAAATTTGGCATGTTTA
1 ACATGTTTAAGTTAATGTTTAAATGAACATGAAATAGGTAAAATAGATTAAATTTGGCATGTTTA
3879413 CAAGTTCGATTTGAATGATGTTCTATTGATATGTTTTATTGATATAATTGTGGTAC
66 CAAGTTCGATTTGAATGATGTTCTATTGATATGTTTTATTGATATAATTGTGGTAC
3879469 CTATGAGGGT
Statistics
Matches: 120, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
120 110 0.92
121 10 0.08
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (121 bp):
ACATGTTTAAGTTAATGTTTAAATGAACATGAAATAGGTAAAATAGATTAAATTTGGCATGTTTA
CAAGTTCGATTTGAATGATGTTCTATTGATATGTTTTATTGATATAATTGTGGTAC
Found at i:3893123 original size:17 final size:16
Alignment explanation
Indices: 3893102--3893140 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
3893092 TTATATTATA
3893102 AAAATTTAA-AAAACAT
1 AAAATTTAATAAAA-AT
3893118 ATAAATTTAATAAAAAT
1 A-AAATTTAATAAAAAT
3893135 AAAATT
1 AAAATT
3893141 CATTTTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.29
17 11 0.52
18 4 0.19
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATTTAATAAAAAT
Found at i:3898958 original size:7 final size:7
Alignment explanation
Indices: 3898946--3898987 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
3898936 CACGGGGTCG
3898946 GGGAAAT
1 GGGAAAT
3898953 GGGAAAT
1 GGGAAAT
3898960 GGGAAAT
1 GGGAAAT
*
3898967 GGG-AAG
1 GGGAAAT
3898973 GGGAAAT
1 GGGAAAT
3898980 GGGAAAT
1 GGGAAAT
3898987 G
1 G
3898988 TAAAATAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.40, C:0.00, G:0.48, T:0.12
Consensus pattern (7 bp):
GGGAAAT
Found at i:3898978 original size:13 final size:13
Alignment explanation
Indices: 3898945--3898984 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
3898935 ACACGGGGTC
3898945 GGGGAAATGGGAAA
1 GGGGAAATGGG-AA
*
3898959 TGGGAAATGGGAA
1 GGGGAAATGGGAA
3898972 GGGGAAATGGGAA
1 GGGGAAATGGGAA
3898985 ATGTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.50, T:0.10
Consensus pattern (13 bp):
GGGGAAATGGGAA
Found at i:3902531 original size:5 final size:5
Alignment explanation
Indices: 3902515--3902560 Score: 83
Period size: 5 Copynumber: 9.0 Consensus size: 5
3902505 GAAAGGACCA
3902515 TATAT ATATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
3902561 ATTATTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 35 0.88
6 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:3903116 original size:20 final size:20
Alignment explanation
Indices: 3903088--3903125 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3903078 ATATTTTCTA
*
3903088 TAAATCATTTTACAGAAAAG
1 TAAAACATTTTACAGAAAAG
*
3903108 TAAAACATTTTCCAGAAA
1 TAAAACATTTTACAGAAA
3903126 TCATTTTACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (20 bp):
TAAAACATTTTACAGAAAAG
Found at i:3903127 original size:34 final size:34
Alignment explanation
Indices: 3903075--3903140 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
3903065 CAAACACTAG
* * *
3903075 AAAATATTTTCTATAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGAAATCATTTTACAGAAAAGT
*
3903109 AAAACATTTTCCAGAAATCATTTTACGGAAAA
1 AAAACATTTTCCAGAAATCATTTTACAGAAAA
3903141 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (34 bp):
AAAACATTTTCCAGAAATCATTTTACAGAAAAGT
Found at i:3905138 original size:18 final size:18
Alignment explanation
Indices: 3905117--3905166 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
3905107 ATGCCTCTAA
3905117 AATAGCAACAAAATTA-AC
1 AATA-CAACAAAATTATAC
* *
3905135 AATAAAACAAAGTTATAC
1 AATACAACAAAATTATAC
3905153 AATAACAACAAAAT
1 AAT-ACAACAAAAT
3905167 AATTAAATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 9 0.35
18 9 0.35
19 8 0.31
ACGTcount: A:0.64, C:0.14, G:0.04, T:0.18
Consensus pattern (18 bp):
AATACAACAAAATTATAC
Found at i:3907966 original size:20 final size:20
Alignment explanation
Indices: 3907943--3907997 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
3907933 CTAATTTTTT
3907943 GTTAATTAA-GCTTAGTATTA
1 GTTAATTAAGGCTTAGT-TTA
*
3907963 GTTAATTAAGGTTTAGTTTA
1 GTTAATTAAGGCTTAGTTTA
*
3907983 ATTAATTAAGGCTTA
1 GTTAATTAAGGCTTA
3907998 TTAATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 25 0.81
21 6 0.19
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (20 bp):
GTTAATTAAGGCTTAGTTTA
Found at i:3915596 original size:12 final size:12
Alignment explanation
Indices: 3915579--3915613 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
3915569 CGGCCCGCCC
3915579 ATATTAATTTTT
1 ATATTAATTTTT
3915591 ATATT-ATTTTT
1 ATATTAATTTTT
3915602 ATA-TAATTTTT
1 ATATTAATTTTT
3915613 A
1 A
3915614 AATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 16 0.73
12 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:3915761 original size:35 final size:35
Alignment explanation
Indices: 3915651--3915765 Score: 115
Period size: 35 Copynumber: 3.3 Consensus size: 35
3915641 AAAACATCAA
3915651 AAAAAATATTTCTCAACAAATTGAAAATAAATTTT
1 AAAAAATATTTCTCAACAAATTGAAAATAAATTTT
* * * ** * * ***
3915686 AAAAACTATGTATCATTAAAATGCTAAAA-ACATCAA
1 AAAAAATATTTCTCAACAAATTG--AAAATAAATTTT
3915722 AAAAAATATTTCTCAACAAATTGAAAATAAATTTT
1 AAAAAATATTTCTCAACAAATTGAAAATAAATTTT
3915757 AAAAAATAT
1 AAAAAATAT
3915766 GTATACTTAA
Statistics
Matches: 57, Mismatches: 20, Indels: 6
0.69 0.24 0.07
Matches are distributed among these distances:
34 4 0.07
35 29 0.51
36 20 0.35
37 4 0.07
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (35 bp):
AAAAAATATTTCTCAACAAATTGAAAATAAATTTT
Found at i:3915761 original size:36 final size:36
Alignment explanation
Indices: 3915650--3915762 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 36
3915640 AAAAACATCA
3915650 AAAAAAATATTTCTCAACAAATTGAAAATAAATTTT
1 AAAAAAATATTTCTCAACAAATTGAAAATAAATTTT
* * * ** * * **
3915686 -AAAAACTATGTATCATTAAAATGCTAAAA-ACA-TCA
1 AAAAAAATATTTCTCAACAAATTG--AAAATAAATTTT
3915721 AAAAAAATATTTCTCAACAAATTGAAAATAAATTTT
1 AAAAAAATATTTCTCAACAAATTGAAAATAAATTTT
3915757 AAAAAA
1 AAAAAA
3915763 TATGTATACT
Statistics
Matches: 54, Mismatches: 18, Indels: 10
0.66 0.22 0.12
Matches are distributed among these distances:
34 4 0.07
35 20 0.37
36 26 0.48
37 4 0.07
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.29
Consensus pattern (36 bp):
AAAAAAATATTTCTCAACAAATTGAAAATAAATTTT
Found at i:3915776 original size:71 final size:71
Alignment explanation
Indices: 3915632--3915769 Score: 267
Period size: 71 Copynumber: 1.9 Consensus size: 71
3915622 TAATACATCA
*
3915632 AAAATGCTAAAAACATCAAAAAAAATATTTCTCAACAAATTGAAAATAAATTTTAAAAACTATGT
1 AAAATGCTAAAAACATCAAAAAAAATATTTCTCAACAAATTGAAAATAAATTTTAAAAAATATGT
3915697 ATCATT
66 ATCATT
3915703 AAAATGCTAAAAACATCAAAAAAAATATTTCTCAACAAATTGAAAATAAATTTTAAAAAATATGT
1 AAAATGCTAAAAACATCAAAAAAAATATTTCTCAACAAATTGAAAATAAATTTTAAAAAATATGT
3915768 AT
66 AT
3915770 ACTTAAATAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (71 bp):
AAAATGCTAAAAACATCAAAAAAAATATTTCTCAACAAATTGAAAATAAATTTTAAAAAATATGT
ATCATT
Found at i:3915843 original size:30 final size:30
Alignment explanation
Indices: 3915809--3915867 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
3915799 TAACAAGCAA
3915809 ATACCTCTAAAATAATAACAAAATTAACAG
1 ATACCTCTAAAATAATAACAAAATTAACAG
*
3915839 ATACCTTTAAAATAATAACAAAATTAACA
1 ATACCTCTAAAATAATAACAAAATTAACA
3915868 ATAAAATAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (30 bp):
ATACCTCTAAAATAATAACAAAATTAACAG
Found at i:3917140 original size:19 final size:19
Alignment explanation
Indices: 3917093--3917132 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3917083 AAAAGTTTCT
3917093 ATATAACTTTAATATCTAAA
1 ATATAA-TTTAATATCTAAA
3917113 ATATAATTTATATAT-TAAA
1 ATATAATTTA-ATATCTAAA
3917132 A
1 A
3917133 GTAAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATAATTTAATATCTAAA
Found at i:3924560 original size:42 final size:42
Alignment explanation
Indices: 3924512--3924646 Score: 137
Period size: 42 Copynumber: 3.2 Consensus size: 42
3924502 ATAAGTGTTA
* * *
3924512 AACAGAAACTCGTAAGGGTTGAACGGAAGCTCATAACAGCTG
1 AACAGAAACCCATAAGGGTTGAACGGAAGCTCATAAGAGCTG
* * *
3924554 AACAGAAACCCATAAAGGTTAAACTGAAGCTCA-ATAGAGCTG
1 AACAGAAACCCATAAGGGTTGAACGGAAGCTCATA-AGAGCTG
* * * ** * *
3924596 AATAGAAACCCATTAGGGTTGAACGAAAATTCATATGAGTTG
1 AACAGAAACCCATAAGGGTTGAACGGAAGCTCATAAGAGCTG
3924638 AACAGAAAC
1 AACAGAAAC
3924647 TTGTGAGAGC
Statistics
Matches: 74, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
41 1 0.01
42 72 0.97
43 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (42 bp):
AACAGAAACCCATAAGGGTTGAACGGAAGCTCATAAGAGCTG
Found at i:3926888 original size:23 final size:25
Alignment explanation
Indices: 3926844--3926889 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
3926834 TTTTCAAAAA
*
3926844 ATATATAATAATAAATTTAAATTTT
1 ATATATAATAATAAATTAAAATTTT
*
3926869 ATAT-TAATATTAAA-TAAAATT
1 ATATATAATAATAAATTAAAATT
3926890 ANNNNNNNNN
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 9 0.47
25 4 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
ATATATAATAATAAATTAAAATTTT
Found at i:3930885 original size:246 final size:238
Alignment explanation
Indices: 3930480--3930919 Score: 544
Period size: 246 Copynumber: 1.8 Consensus size: 238
3930470 GAAAGTTAAG
* * * * *
3930480 GGAATGCCCTTCAGTAATTAAAATAAATAATATTATTTGAGGGTATTTTAGTCTTTTTATTTTTA
1 GGAATGCCCTTCAGTAATCAAAATAAATAATATTATTTGAGGATACTTTAGTCCTTTTATTTTGA
* * * * * *
3930545 AAAAAACAATAAAATATGCATATGATGAGTTTTGTTCAATTGCATCATTAAACTCTTTAATTTAC
66 AAAAAACAATAAAACATGCATATGATGAGATTCGTCCAATTGCATAATAAAACTCTTTAATTTAC
*** * * *
3930610 CATTTAGCTAAAATTTTATTTTTATATTTTTATACATTTTAATTTTATTACGAACACTTTATTAG
131 CACACAACTAAAATCTTATTTTAATATTTTTATACATTTTAATTTTATTACGAACACTTTATTAG
3930675 GTGTCACGAGTCAATCGAACACCAACTTAGTTGAGAAATTACA
196 GTGTCACGAGTCAATCGAACACCAACTTAGTTGAGAAATTACA
* * *
3930718 GGAATGTCCTTCCGTAATCAAAATAAGTAATATTATTTGAGGATACTTTAG-CCTTTTATTTTGA
1 GGAATGCCCTTCAGTAATCAAAATAAATAATATTATTTGAGGATACTTTAGTCCTTTTATTTTGA
3930782 AAAAAATCAATAAAAACATGCATATGATGAGATTCGAACTCAAACCAATTGCATTAATAAAACT-
66 AAAAAA-CAAT-AAAACATGCATATGATGAGATTCG---T----CCAATTGCA-TAATAAAACTC
* * **
3930846 TTTAATTTTCCACACAACT-AAATCCTTATTTTAATATTTTTATCCATTTTAATTTTATTATTAA
121 TTTAATTTACCACACAACTAAAAT-CTTATTTTAATATTTTTATACATTTTAATTTTATTACGAA
3930910 CACTTTATTA
185 CACTTTATTA
3930920 CTTCCACCAA
Statistics
Matches: 167, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
237 17 0.10
238 49 0.29
239 21 0.13
242 1 0.01
245 4 0.02
246 67 0.40
247 8 0.05
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (238 bp):
GGAATGCCCTTCAGTAATCAAAATAAATAATATTATTTGAGGATACTTTAGTCCTTTTATTTTGA
AAAAAACAATAAAACATGCATATGATGAGATTCGTCCAATTGCATAATAAAACTCTTTAATTTAC
CACACAACTAAAATCTTATTTTAATATTTTTATACATTTTAATTTTATTACGAACACTTTATTAG
GTGTCACGAGTCAATCGAACACCAACTTAGTTGAGAAATTACA
Found at i:3934959 original size:24 final size:25
Alignment explanation
Indices: 3934914--3934961 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
3934904 AATAATTTTA
** *
3934914 ATTTTATTATAAATGTATTAAAATC
1 ATTTTATTATAAATAAAGTAAAATC
3934939 ATTTT-TTATAAATAAAGTAAAAT
1 ATTTTATTATAAATAAAGTAAAAT
3934962 ATTATCTGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
ATTTTATTATAAATAAAGTAAAATC
Found at i:3944092 original size:3 final size:3
Alignment explanation
Indices: 3944084--3944114 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3944074 CCTTCCTCAT
3944084 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
3944115 AACAGAGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:3968838 original size:12 final size:11
Alignment explanation
Indices: 3968811--3968858 Score: 64
Period size: 11 Copynumber: 4.4 Consensus size: 11
3968801 ATTTTTTTAA
3968811 TTTTAAAATAT
1 TTTTAAAATAT
3968822 TTTTAAAATACT
1 TTTTAAAATA-T
3968834 TTTT-AAA-AT
1 TTTTAAAATAT
3968843 TTTTAAAATAAT
1 TTTTAAAAT-AT
3968855 TTTT
1 TTTT
3968859 TGGTATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
9 5 0.15
10 4 0.12
11 13 0.39
12 11 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3968846 original size:21 final size:22
Alignment explanation
Indices: 3968808--3968858 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
3968798 TTAATTTTTT
*
3968808 TAATTTTAAAATATTTTTAAAA
1 TAATTTTTAAATATTTTTAAAA
*
3968830 TACTTTTTAAA-ATTTTTAAAA
1 TAATTTTTAAATATTTTTAAAA
3968851 TAATTTTT
1 TAATTTTT
3968859 TGGTATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATTTTTAAATATTTTTAAAA
Found at i:3969317 original size:8 final size:9
Alignment explanation
Indices: 3969297--3969321 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3969287 ATTAAGTTAA
3969297 TTTTAAAGT
1 TTTTAAAGT
3969306 TTTTAAAGT
1 TTTTAAAGT
3969315 TTTTAAA
1 TTTTAAA
3969322 AATTTTTTAT
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:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (9 bp):
TTTTAAAGT
Found at i:3976026 original size:15 final size:15
Alignment explanation
Indices: 3976006--3976034 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3975996 TAGAATTACG
3976006 TTTGAATGTGTTTAA
1 TTTGAATGTGTTTAA
3976021 TTTGAATGTGTTTA
1 TTTGAATGTGTTTA
3976035 GATCAATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (15 bp):
TTTGAATGTGTTTAA
Found at i:3976452 original size:43 final size:44
Alignment explanation
Indices: 3976345--3976461 Score: 132
Period size: 44 Copynumber: 2.7 Consensus size: 44
3976335 TATGTGTTGT
* * *
3976345 CATGTAAGACCACGTCTGAGACGTTGGCATAGATTTGTGATTTA
1 CATGTAAGACCACGTCTGGGACGATGGCATAGATATGTGATTTA
* * *
3976389 CGTGTAAGACC-CTGTCTGGGAC-AGTGGCATCGATATGTTA-TTA
1 CATGTAAGACCAC-GTCTGGGACGA-TGGCATAGATATGTGATTTA
*
3976432 CATGTAAGACCACGTTTGGGACGATGGCAT
1 CATGTAAGACCACGTCTGGGACGATGGCAT
3976462 TATACGAAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
43 28 0.46
44 33 0.54
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (44 bp):
CATGTAAGACCACGTCTGGGACGATGGCATAGATATGTGATTTA
Found at i:3976897 original size:311 final size:311
Alignment explanation
Indices: 3976472--3977102 Score: 1208
Period size: 311 Copynumber: 2.0 Consensus size: 311
3976462 TATACGAAAC
*
3976472 GTTTGATATTCTGAGTATCCTTTTAATTCCGAATGGTTCAATGGGTTGTAATAAATTAAGATCGA
1 GTTTGATATTCTGAGTATCCTTTTAATTCCGAATGGTTCAATGGGCTGTAATAAATTAAGATCGA
* *
3976537 GTATAAAAATTCAGATTAGAAAGGCTCAGGTATATATTTATTCGAGTTATAAAAATATGGTAAGT
66 GTATAAAAAATCAAATTAGAAAGGCTCAGGTATATATTTATTCGAGTTATAAAAATATGGTAAGT
3976602 CGAATATATGAATTGATGATATAATATCATATTTTAATGTGAATTATGTGTATGTATATGTGAAT
131 CGAATATATGAATTGATGATATAATATCATATTTTAATGTGAATTATGTGTATGTATATGTGAAT
3976667 GTATATATATATTCGGCCAATGATGTTTCTTTTTGTTAGTGTTGAAGCAAAGGTTGAATATACTA
196 GTATATATATATTCGGCCAATGATGTTTCTTTTTGTTAGTGTTGAAGCAAAGGTTGAATATACTA
3976732 ATGTTTCCTTATGTATTCGACCTAAGTAAAATTTATGCCAAATATATATAT
261 ATGTTTCCTTATGTATTCGACCTAAGTAAAATTTATGCCAAATATATATAT
*
3976783 GTTTGATTTTCTGAGTATCCTTTTAATTCCGAATGGTTCAATGGGCTGTAATAAATTAAGATCGA
1 GTTTGATATTCTGAGTATCCTTTTAATTCCGAATGGTTCAATGGGCTGTAATAAATTAAGATCGA
*
3976848 GTATAAAAAATCAAATTAGAAAGGCTCAGGTATGTATTTATTCGAGTTATAAAAATATGGTAAGT
66 GTATAAAAAATCAAATTAGAAAGGCTCAGGTATATATTTATTCGAGTTATAAAAATATGGTAAGT
*
3976913 TGAATATATGAATTGATGATATAATATCATATTTTAATGTGAATTATGTGTATGTATATGTGAAT
131 CGAATATATGAATTGATGATATAATATCATATTTTAATGTGAATTATGTGTATGTATATGTGAAT
3976978 GTATATATATATTCGGCCAATGATGTTTCTTTTTGTTAGTGTTGAAGCAAAGGTTGAATATACTA
196 GTATATATATATTCGGCCAATGATGTTTCTTTTTGTTAGTGTTGAAGCAAAGGTTGAATATACTA
3977043 ATGTTTCCTTATGTATTCGACCTAAGTAAAATTTATGCCAAATATATATAT
261 ATGTTTCCTTATGTATTCGACCTAAGTAAAATTTATGCCAAATATATATAT
3977094 GTTTGATAT
1 GTTTGATAT
3977103 ATGAAATTAT
Statistics
Matches: 313, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
311 313 1.00
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.40
Consensus pattern (311 bp):
GTTTGATATTCTGAGTATCCTTTTAATTCCGAATGGTTCAATGGGCTGTAATAAATTAAGATCGA
GTATAAAAAATCAAATTAGAAAGGCTCAGGTATATATTTATTCGAGTTATAAAAATATGGTAAGT
CGAATATATGAATTGATGATATAATATCATATTTTAATGTGAATTATGTGTATGTATATGTGAAT
GTATATATATATTCGGCCAATGATGTTTCTTTTTGTTAGTGTTGAAGCAAAGGTTGAATATACTA
ATGTTTCCTTATGTATTCGACCTAAGTAAAATTTATGCCAAATATATATAT
Found at i:3977127 original size:2 final size:2
Alignment explanation
Indices: 3977120--3977161 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
3977110 TATGATTTGG
* * *
3977120 AT AT AT AT AT AT AT AT TT AT AT AC AT AT AT AT TT 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
3977162 GAAATTATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3977247 original size:47 final size:47
Alignment explanation
Indices: 3977196--3977426 Score: 313
Period size: 46 Copynumber: 5.0 Consensus size: 47
3977186 TTATCTAGAT
* *
3977196 CAATTTTATATATATATGCTGTCAAATTTTGGTGTGTAAATGCTGTC
1 CAATTTTGTATATATATGCTGTCAAATTTTGGTGTATAAATGCTGTC
3977243 CAATTTTGTATATATATGCTGTCAAATTTTGGTGTATAAATGCTGTC
1 CAATTTTGTATATATATGCTGTCAAATTTTGGTGTATAAATGCTGTC
* * * * *
3977290 CAAATTGGTATATATATGCTGCCCAA-TTTCGTGTATAAATGCTGTC
1 CAATTTTGTATATATATGCTGTCAAATTTTGGTGTATAAATGCTGTC
* * ** * * *
3977336 CAAATTGGTATATATATGCTACCCAA-TTTCGTGTATAAATGCTATC
1 CAATTTTGTATATATATGCTGTCAAATTTTGGTGTATAAATGCTGTC
*
3977382 CAATTTTGTATATATATGCCGTCAAATTTTGGTGTATAAATGCTG
1 CAATTTTGTATATATATGCTGTCAAATTTTGGTGTATAAATGCTG
3977427 ACCGATTTGA
Statistics
Matches: 166, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
46 83 0.50
47 83 0.50
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (47 bp):
CAATTTTGTATATATATGCTGTCAAATTTTGGTGTATAAATGCTGTC
Found at i:3977265 original size:23 final size:23
Alignment explanation
Indices: 3977196--3977426 Score: 201
Period size: 23 Copynumber: 9.9 Consensus size: 23
3977186 TTATCTAGAT
* *
3977196 CAATTTTATATATATATGCTGTC
1 CAATTTTGTATATAAATGCTGTC
* * *
3977219 AAATTTTGGTGTGTAAATGCTGTC
1 CAATTTT-GTATATAAATGCTGTC
*
3977243 CAATTTTGTATATATATGCTGTC
1 CAATTTTGTATATAAATGCTGTC
* *
3977266 AAATTTTGGTGTATAAATGCTGTC
1 CAATTTT-GTATATAAATGCTGTC
* * * *
3977290 CAAATTGGTATATATATGCTGCC
1 CAATTTTGTATATAAATGCTGTC
* *
3977313 CAATTTCGTGTATAAATGCTGTC
1 CAATTTTGTATATAAATGCTGTC
* * * **
3977336 CAAATTGGTATATATATGCTACC
1 CAATTTTGTATATAAATGCTGTC
* * *
3977359 CAATTTCGTGTATAAATGCTATC
1 CAATTTTGTATATAAATGCTGTC
* *
3977382 CAATTTTGTATATATATGCCGTC
1 CAATTTTGTATATAAATGCTGTC
* *
3977405 AAATTTTGGTGTATAAATGCTG
1 CAATTTT-GTATATAAATGCTG
3977427 ACCGATTTGA
Statistics
Matches: 162, Mismatches: 43, Indels: 5
0.77 0.20 0.02
Matches are distributed among these distances:
23 115 0.71
24 47 0.29
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (23 bp):
CAATTTTGTATATAAATGCTGTC
Found at i:3977740 original size:91 final size:91
Alignment explanation
Indices: 3977627--3977808 Score: 337
Period size: 91 Copynumber: 2.0 Consensus size: 91
3977617 ATAAATGATA
3977627 ATGACTTGGTTGAATTTTGAAACATGGTTGGTATATGTAATTTGATTAATGATGCATGTTTGATT
1 ATGACTTGGTTGAATTTTGAAACATGGTTGGTATATGTAATTTGATTAATGATGCATGTTTGATT
*
3977692 TTAATTGGTTATGTTCTTATATATAT
66 TTAATTAGTTATGTTCTTATATATAT
* *
3977718 ATGAGTTGGTTGAATTTTGAAACATGGTTGGTATATGTAATTTGATTAATGATGCATGTTTTATT
1 ATGACTTGGTTGAATTTTGAAACATGGTTGGTATATGTAATTTGATTAATGATGCATGTTTGATT
3977783 TTAATTAGTTATGTTCTTATATATAT
66 TTAATTAGTTATGTTCTTATATATAT
3977809 TTATATATAT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.49
Consensus pattern (91 bp):
ATGACTTGGTTGAATTTTGAAACATGGTTGGTATATGTAATTTGATTAATGATGCATGTTTGATT
TTAATTAGTTATGTTCTTATATATAT
Found at i:3979527 original size:28 final size:28
Alignment explanation
Indices: 3979495--3979597 Score: 145
Period size: 28 Copynumber: 3.7 Consensus size: 28
3979485 TATAATGAAT
* *
3979495 GCCTTATCCCAATTCAGTAGT-AGTGTGG
1 GCCTTAGCCCAATACAGTA-TCAGTGTGG
*
3979523 GCCTTAGCCCAATACAGCATCAGTGTGG
1 GCCTTAGCCCAATACAGTATCAGTGTGG
*
3979551 GCCTTAGCCCAATACAATATCAGTGTGG
1 GCCTTAGCCCAATACAGTATCAGTGTGG
*
3979579 GCCTTAGCCCAATATAGTA
1 GCCTTAGCCCAATACAGTA
3979598 ACATTACAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 1 0.01
28 66 0.99
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (28 bp):
GCCTTAGCCCAATACAGTATCAGTGTGG
Found at i:3980379 original size:27 final size:27
Alignment explanation
Indices: 3979969--3980371 Score: 421
Period size: 27 Copynumber: 14.9 Consensus size: 27
3979959 GGTATAAAAA
*
3979969 TCATTTTACCCTAT-GGGGGTATTTCAG
1 TCATTTTACCCT-TCGAGGGTATTTCAG
* * *
3979996 TTATTTTACCCTTCGGGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * * *
3980023 TCATTTTGCCCTTCGGGGGCATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
** *
3980050 TCATTTTACCCTTTAAGGGTATTTCAA
1 TCATTTTACCCTTCGAGGGTATTTCAG
**
3980077 TCATTTTACCCTTCGAGGGTATTTTTG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
3980104 TCATTTTACCCTTCGCGAGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
*
3980131 TTATTTTACCCTTCGAGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * * *
3980158 TTATTTTACCATTCAAGGGTATTTTAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * *
3980185 TCATTTTACCTTTTGAGGGTATTTCAC
1 TCATTTTACCCTTCGAGGGTATTTCAG
* **
3980212 TCATTTTACCCTTCGGGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * * *
3980239 TTATTTTACCTTTCTAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * * * **
3980266 TCATTTTATCTTTAGGGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
3980293 TCATTTTACCCTTCGAGGCTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
**
3980320 TCATTTTGTCCTTCGAGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
*
3980347 TCATTTTACCCTTCAAGGGTATTTC
1 TCATTTTACCCTTCGAGGGTATTTC
3980372 GGTTATTTAC
Statistics
Matches: 312, Mismatches: 63, Indels: 2
0.83 0.17 0.01
Matches are distributed among these distances:
26 1 0.00
27 311 1.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.45
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCAG
Found at i:3980697 original size:18 final size:18
Alignment explanation
Indices: 3980674--3980716 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3980664 ACCCAATCCA
*
3980674 AACCCAAGTA-TTCAACCC
1 AACCCAAGTACCT-AACCC
*
3980692 AACCCAATTACCTAACCC
1 AACCCAAGTACCTAACCC
3980710 AACCCAA
1 AACCCAA
3980717 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.42, C:0.42, G:0.02, T:0.14
Consensus pattern (18 bp):
AACCCAAGTACCTAACCC
Found at i:3980767 original size:6 final size:6
Alignment explanation
Indices: 3980758--3980786 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3980748 GAATAAAATT
3980758 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
3980787 GTCTAAAAGT
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:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:3980840 original size:9 final size:9
Alignment explanation
Indices: 3980826--3980876 Score: 84
Period size: 9 Copynumber: 5.7 Consensus size: 9
3980816 GTAGTGATTC
3980826 AATTCGGTT
1 AATTCGGTT
*
3980835 AATTCGGGT
1 AATTCGGTT
3980844 AATTCGGTT
1 AATTCGGTT
3980853 AATTCGGTT
1 AATTCGGTT
*
3980862 AATTCGGGT
1 AATTCGGTT
3980871 AATTCG
1 AATTCG
3980877 AACCAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (9 bp):
AATTCGGTT
Found at i:3988598 original size:7 final size:7
Alignment explanation
Indices: 3988586--3988617 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
3988576 ATGCAATTTA
3988586 ATGTATT
1 ATGTATT
3988593 ATGTATT
1 ATGTATT
3988600 ATGTATT
1 ATGTATT
3988607 ATGTATT
1 ATGTATT
3988614 ATGT
1 ATGT
3988618 TTTTGCCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
ATGTATT
Found at i:3991651 original size:10 final size:9
Alignment explanation
Indices: 3991628--3991677 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
3991618 TACGTAAGAT
3991628 ATTTTTAAA
1 ATTTTTAAA
3991637 ATTTTTGAAA
1 ATTTTT-AAA
* *
3991647 CTTTTTATAT
1 ATTTTTA-AA
3991657 ATTTTTAAA
1 ATTTTTAAA
*
3991666 ATTCTTAAA
1 ATTTTTAAA
3991675 ATT
1 ATT
3991678 CTTTTCATCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 19 0.56
10 15 0.44
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:3994294 original size:110 final size:111
Alignment explanation
Indices: 3994100--3994320 Score: 435
Period size: 110 Copynumber: 2.0 Consensus size: 111
3994090 CAGAAAAAAT
3994100 TTTCGGCCCGCCTCCTAGGCCCGGGCTCGGTCTGGCCCGAAAAAATATCATAAGCCCAAGCCCGA
1 TTTCGGCCCGCCTCCTAGGCCCGGGCTCGGTCTGGCCCGAAAAAATATCATAAGCCCAAGCCCGA
3994165 CCCGGCCCGGCCCATTTTTAAAATAAACATTAAAAAATTATTTTAA
66 CCCGGCCCGGCCCATTTTTAAAATAAACATTAAAAAATTATTTTAA
3994211 TTTCGGCCCG-CTCCTAGGCCCGGGCTCGGTCTGGCCCGAAAAAATATCATAAGCCCAAGCCCGA
1 TTTCGGCCCGCCTCCTAGGCCCGGGCTCGGTCTGGCCCGAAAAAATATCATAAGCCCAAGCCCGA
3994275 CCCGGCCCGGCCCATTTTTAAAATAAACATTAAAAAATTATTTTAA
66 CCCGGCCCGGCCCATTTTTAAAATAAACATTAAAAAATTATTTTAA
3994321 AAATAAAAAA
Statistics
Matches: 110, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
110 100 0.91
111 10 0.09
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (111 bp):
TTTCGGCCCGCCTCCTAGGCCCGGGCTCGGTCTGGCCCGAAAAAATATCATAAGCCCAAGCCCGA
CCCGGCCCGGCCCATTTTTAAAATAAACATTAAAAAATTATTTTAA
Found at i:3994360 original size:19 final size:19
Alignment explanation
Indices: 3994305--3994341 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3994295 AAATAAACAT
3994305 TAAAAAATTATTTTAAAAA
1 TAAAAAATTATTTTAAAAA
3994324 TAAAAAATTATTTTAAAA
1 TAAAAAATTATTTTAAAA
3994342 GTATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAATTATTTTAAAAA
Found at i:3995436 original size:3 final size:3
Alignment explanation
Indices: 3995417--3995466 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
3995407 ATATAGGAAC
* *
3995417 AAT AAT AGT AAT GAT AAT AAT AAT AAT AAAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
3995462 AAT AA
1 AAT AA
3995467 ATAAAAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3995467 original size:21 final size:22
Alignment explanation
Indices: 3995417--3995470 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
3995407 ATATAGGAAC
* *
3995417 AATAAT-AGTAATGATAATAAT
1 AATAATAAATAATAATAATAAT
3995438 AATAATAAATAATAATAAT-AT
1 AATAATAAATAATAATAATAAT
3995459 AATAATAAATAA
1 AATAATAAATAA
3995471 AAGAAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
AATAATAAATAATAATAATAAT
Found at i:3997300 original size:30 final size:29
Alignment explanation
Indices: 3997252--3997324 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
3997242 TTAATTTCTC
* * * *
3997252 CCTTGAAATTTTCAGAAAATTTTTATTAGAA
1 CCTTTAAATTTT-TGAAAATTCTCATT-GAA
*
3997283 CCTTTAAATTTTTGAAAATTCTCATTGTA
1 CCTTTAAATTTTTGAAAATTCTCATTGAA
*
3997312 CCTTTTAATTTTT
1 CCTTTAAATTTTT
3997325 TTTGAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 14 0.39
30 11 0.31
31 11 0.31
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (29 bp):
CCTTTAAATTTTTGAAAATTCTCATTGAA
Found at i:4000531 original size:45 final size:45
Alignment explanation
Indices: 4000465--4000631 Score: 208
Period size: 45 Copynumber: 3.7 Consensus size: 45
4000455 TGTATTGAGT
** * **
4000465 ATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCATCGGGT
1 ATCATTGAAAATAAAGGTGGTTGCTATGTGCTGACTCCATCGGAA
* ** * *
4000510 ACCATTGATTATAAAGGTGGTTGCTATGTGTTGACTCCATCAGAA
1 ATCATTGAAAATAAAGGTGGTTGCTATGTGCTGACTCCATCGGAA
* *
4000555 ATCATTGAAAATAAAGGTGGCTGCTATGTGCTGACTCCACCGGAA
1 ATCATTGAAAATAAAGGTGGTTGCTATGTGCTGACTCCATCGGAA
* *
4000600 ATCATTAAAAATAAAGGTGGTTGCTATATGCT
1 ATCATTGAAAATAAAGGTGGTTGCTATGTGCT
4000632 AATTCTACCG
Statistics
Matches: 106, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 106 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.32
Consensus pattern (45 bp):
ATCATTGAAAATAAAGGTGGTTGCTATGTGCTGACTCCATCGGAA
Found at i:4000652 original size:45 final size:45
Alignment explanation
Indices: 4000520--4000652 Score: 124
Period size: 45 Copynumber: 3.0 Consensus size: 45
4000510 ACCATTGATT
* * * * * * * *
4000520 ATAAAGGTGGTTGCTATGTGTTGACTCCATCAGAAATCATTGAAA
1 ATAAAGGTGGCTGCTATATGCTAACTCCACCGGAAATAATTAAAA
* * *
4000565 ATAAAGGTGGCTGCTATGTGCTGACTCCACCGGAAATCATTAAAA
1 ATAAAGGTGGCTGCTATATGCTAACTCCACCGGAAATAATTAAAA
* * *
4000610 ATAAAGGTGGTTGCTATATGCTAATTCTACC-GAATATAATTAA
1 ATAAAGGTGGCTGCTATATGCTAACTCCACCGGAA-ATAATTAA
4000653 TTATAAGGGT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
44 3 0.04
45 73 0.96
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (45 bp):
ATAAAGGTGGCTGCTATATGCTAACTCCACCGGAAATAATTAAAA
Found at i:4001676 original size:38 final size:39
Alignment explanation
Indices: 4001618--4001694 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 39
4001608 ATCCAACCAA
*
4001618 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
4001657 ACCCAATTA-CCAACCCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
4001695 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 28 0.76
39 9 0.24
ACGTcount: A:0.51, C:0.29, G:0.03, T:0.18
Consensus pattern (39 bp):
ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
Found at i:4001934 original size:12 final size:12
Alignment explanation
Indices: 4001917--4001941 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4001907 TGTTATTTCG
4001917 GGTCGGTTAACC
1 GGTCGGTTAACC
4001929 GGTCGGTTAACC
1 GGTCGGTTAACC
4001941 G
1 G
4001942 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:4003217 original size:30 final size:30
Alignment explanation
Indices: 4003169--4003244 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
4003159 GGTGAACTAT
* * *
4003169 GTTGATCACATAACCTGAAATTACATCAGG
1 GTTGATCACACAAGCTGAAATTACATCAAG
* * * *
4003199 GTTGCTCACACAAGCTGAATTTATATTAAG
1 GTTGATCACACAAGCTGAAATTACATCAAG
*
4003229 ATTGATCACACAAGCT
1 GTTGATCACACAAGCT
4003245 AAGTTTATAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (30 bp):
GTTGATCACACAAGCTGAAATTACATCAAG
Found at i:4004632 original size:29 final size:29
Alignment explanation
Indices: 4004595--4004653 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
4004585 TTTGGTCTCT
* *
4004595 ATATTTTTATAATGTTCTTAATTAGTTCA
1 ATATTTTTATAATGTTATTAATTAGCTCA
4004624 ATATTTTTATAATGTTATTAATTAGCTCA
1 ATATTTTTATAATGTTATTAATTAGCTCA
4004653 A
1 A
4004654 ATTGTTAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.53
Consensus pattern (29 bp):
ATATTTTTATAATGTTATTAATTAGCTCA
Found at i:4009415 original size:20 final size:20
Alignment explanation
Indices: 4009354--4009417 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
4009344 GTACATACAA
*
4009354 GGGCACAAGAGTGCAAATCAG
1 GGGCACTAGAGTGC-AATCAG
*
4009375 AGGCACTAGAGTGCAATCAG
1 GGGCACTAGAGTGCAATCAG
* *
4009395 GGGCATTGGAGTGCAATCAG
1 GGGCACTAGAGTGCAATCAG
4009415 GGG
1 GGG
4009418 TGTTGAACTG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
20 26 0.68
21 12 0.32
ACGTcount: A:0.31, C:0.17, G:0.38, T:0.14
Consensus pattern (20 bp):
GGGCACTAGAGTGCAATCAG
Found at i:4009429 original size:20 final size:20
Alignment explanation
Indices: 4009386--4009433 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
4009376 GGCACTAGAG
* *
4009386 TGCAATCAGGGGCATTGGAG
1 TGCAATCAGGGGCATTGAAC
**
4009406 TGCAATCAGGGGTGTTGAAC
1 TGCAATCAGGGGCATTGAAC
4009426 TGCAATCA
1 TGCAATCA
4009434 TATACATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (20 bp):
TGCAATCAGGGGCATTGAAC
Found at i:4011521 original size:19 final size:19
Alignment explanation
Indices: 4011492--4011542 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
4011482 GAACATTAAA
*
4011492 AAATAAAATAAATACAATAT
1 AAATAAAATAAAT-CAAAAT
4011512 AAAT-AAATAAATCAAAAT
1 AAATAAAATAAATCAAAAT
*
4011530 ACATAAAATAAAT
1 AAATAAAATAAAT
4011543 TACTAACTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 8 0.29
19 16 0.57
20 4 0.14
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAAATAAATCAAAAT
Found at i:4011523 original size:23 final size:24
Alignment explanation
Indices: 4011484--4011542 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
4011474 AATTATATGA
4011484 ACAT-TAAA-AAATAAAAT-AAAT
1 ACATATAAATAAATAAAATAAAAT
4011505 ACAATATAAATAAAT-AAATCAAAAT
1 AC-ATATAAATAAATAAAAT-AAAAT
4011530 ACATA-AAATAAAT
1 ACATATAAATAAAT
4011543 TACTAACTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
21 2 0.06
22 2 0.06
23 16 0.48
24 7 0.21
25 6 0.18
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (24 bp):
ACATATAAATAAATAAAATAAAAT
Found at i:4011529 original size:14 final size:13
Alignment explanation
Indices: 4011488--4011541 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 13
4011478 ATATGAACAT
4011488 TAAA-AAATAAAA
1 TAAATAAATAAAA
4011500 TAAATACAATATAAA
1 TAAATA-AATA-AAA
4011515 TAAATAAATCAAAA
1 TAAATAAAT-AAAA
*
4011529 TACATAAAATAAA
1 TAAAT-AAATAAA
4011542 TTACTAACTC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
12 4 0.11
13 1 0.03
14 17 0.47
15 14 0.39
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:4012987 original size:38 final size:39
Alignment explanation
Indices: 4012911--4012987 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 39
4012901 ACACTAATCA
* **
4012911 ATTTACATAATTAACCACTTGTGACATTAAACGCAATGC
1 ATTTACATAATTAACAACTTGTGACATTAAACAAAATGC
* *
4012950 ATTTACA-ACTTAACAACTTGTGACATTAAATAAAATGC
1 ATTTACATAATTAACAACTTGTGACATTAAACAAAATGC
4012988 CCCTAGGTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
38 26 0.79
39 7 0.21
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (39 bp):
ATTTACATAATTAACAACTTGTGACATTAAACAAAATGC
Found at i:4017891 original size:28 final size:28
Alignment explanation
Indices: 4017859--4017914 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
4017849 TTCTCTTTTG
* *
4017859 TCCATTTTATATTTCTTTTAGTTTTATA
1 TCCATTCTATATTTCTTTTAATTTTATA
4017887 TCCATTCTATATTTCTTTTAATTTTATA
1 TCCATTCTATATTTCTTTTAATTTTATA
4017915 ACATGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.02, T:0.62
Consensus pattern (28 bp):
TCCATTCTATATTTCTTTTAATTTTATA
Found at i:4026866 original size:28 final size:28
Alignment explanation
Indices: 4026782--4026867 Score: 111
Period size: 28 Copynumber: 3.1 Consensus size: 28
4026772 TTATGAAAAA
*
4026782 ATATGTGGAAGTTCG-CAGGACTATTTT
1 ATATGTGGAAGTCCGTCAGGACTATTTT
* * * *
4026809 ATATGTTGAAGTCCATCAAGACGATTTT
1 ATATGTGGAAGTCCGTCAGGACTATTTT
*
4026837 ATATGTGGAAGTCCGTCAGGACTATCTT
1 ATATGTGGAAGTCCGTCAGGACTATTTT
4026865 ATA
1 ATA
4026868 AGTAGGATTC
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 12 0.25
28 36 0.75
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (28 bp):
ATATGTGGAAGTCCGTCAGGACTATTTT
Found at i:4028684 original size:51 final size:52
Alignment explanation
Indices: 4028617--4028724 Score: 175
Period size: 52 Copynumber: 2.1 Consensus size: 52
4028607 ACCCTAATTC
* *
4028617 ATAGTAAAATTTACTCTTACA--CCTCTATTACTAGTCTACGATACCCTAAAA
1 ATAGTAAAATTTACTCTTACAGCCCT-TATTACAAGTCTACGAGACCCTAAAA
4028668 ATAGTAAAATTTACTCTTACAGCCCTTATTACAAGTCTACGAGACCCTAAAA
1 ATAGTAAAATTTACTCTTACAGCCCTTATTACAAGTCTACGAGACCCTAAAA
4028720 ATAGT
1 ATAGT
4028725 CTAAAAAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
51 21 0.40
52 29 0.55
53 3 0.06
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.31
Consensus pattern (52 bp):
ATAGTAAAATTTACTCTTACAGCCCTTATTACAAGTCTACGAGACCCTAAAA
Found at i:4029218 original size:25 final size:24
Alignment explanation
Indices: 4029166--4029219 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 24
4029156 CTTTTAAAGT
4029166 TACC-AAATATGAAACTAAGCACA
1 TACCAAAATATGAAACTAAGCACA
*
4029189 TACCAAAATAT-AAACTAGGCTAGCA
1 TACCAAAATATGAAACTAAGC-A-CA
4029214 TACCAA
1 TACCAA
4029220 CATAACCTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 12 0.44
24 7 0.26
25 8 0.30
ACGTcount: A:0.50, C:0.22, G:0.09, T:0.19
Consensus pattern (24 bp):
TACCAAAATATGAAACTAAGCACA
Found at i:4029802 original size:37 final size:36
Alignment explanation
Indices: 4029735--4029809 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
4029725 TTCATATATC
* *
4029735 ATATCTCATCTCATTTCTCATATTTTTCATTTCAAT
1 ATATCTCATCTCATTTATCATATTTGTCATTTCAAT
* *
4029771 ATATCTCATATTCATTTATCATCTTTGTCATTTCAAT
1 ATATCTCAT-CTCATTTATCATATTTGTCATTTCAAT
4029808 AT
1 AT
4029810 CAATCACATA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
36 9 0.26
37 25 0.74
ACGTcount: A:0.27, C:0.20, G:0.01, T:0.52
Consensus pattern (36 bp):
ATATCTCATCTCATTTATCATATTTGTCATTTCAAT
Found at i:4030281 original size:17 final size:17
Alignment explanation
Indices: 4030256--4030296 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
4030246 TCCATTTCAT
* *
4030256 TTCACTTATGAATTTAA
1 TTCAATTATGAATATAA
4030273 TTCAATTATGAATATAA
1 TTCAATTATGAATATAA
4030290 TTCAATT
1 TTCAATT
4030297 TTAAAGTACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (17 bp):
TTCAATTATGAATATAA
Found at i:4032802 original size:16 final size:17
Alignment explanation
Indices: 4032777--4032811 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4032767 AGATATAAGA
4032777 TTCCTCCTA-TTAAAGG
1 TTCCTCCTATTTAAAGG
*
4032793 TTCCTTCTATTTAAAGG
1 TTCCTCCTATTTAAAGG
4032810 TT
1 TT
4032812 TAATAACGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (17 bp):
TTCCTCCTATTTAAAGG
Found at i:4033817 original size:12 final size:13
Alignment explanation
Indices: 4033770--4033815 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
4033760 TTTTGCTTTC
4033770 AATTAAAATTATA
1 AATTAAAATTATA
*
4033783 AATTAAAA-AATA
1 AATTAAAATTATA
*
4033795 ATTTAAGAATTATA
1 AATTAA-AATTATA
4033809 AATTAAA
1 AATTAAA
4033816 TTGTATTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 8 0.30
13 11 0.41
14 8 0.30
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
AATTAAAATTATA
Found at i:4034934 original size:22 final size:23
Alignment explanation
Indices: 4034885--4034937 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
4034875 TAGATTTTTT
*
4034885 TTTAGAAATATTTATGAAACAATT
1 TTTA-AAATATTTATGAAACAATA
* *
4034909 TTTAAAAT-TTTATTAAATAATA
1 TTTAAAATATTTATGAAACAATA
4034931 TTTAAAA
1 TTTAAAA
4034938 ATCACTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 18 0.69
23 4 0.15
24 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (23 bp):
TTTAAAATATTTATGAAACAATA
Found at i:4035246 original size:35 final size:33
Alignment explanation
Indices: 4035206--4035276 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 33
4035196 ATATATAGTA
*
4035206 TATTAAATAGTATAAAAAGAAAAAAATATTATATT
1 TATTAAATA-TATAAAAAGAAAAAAATA-AATATT
* * **
4035241 TATTAATTATTTTGAAAGAAAAAAATAAATATT
1 TATTAAATATATAAAAAGAAAAAAATAAATATT
4035274 TAT
1 TAT
4035277 CTAATTCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 8 0.26
34 15 0.48
35 8 0.26
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (33 bp):
TATTAAATATATAAAAAGAAAAAAATAAATATT
Found at i:4035817 original size:5 final size:5
Alignment explanation
Indices: 4035807--4035832 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4035797 TAATTTAGAC
4035807 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
4035833 GACATGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:4039229 original size:6 final size:7
Alignment explanation
Indices: 4039212--4039236 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4039202 TTTATGGAAT
4039212 AAAAAGC
1 AAAAAGC
4039219 AAAAAGC
1 AAAAAGC
4039226 AAAAAGC
1 AAAAAGC
4039233 AAAA
1 AAAA
4039237 TCTACTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGC
Found at i:4040031 original size:111 final size:111
Alignment explanation
Indices: 4039881--4040093 Score: 275
Period size: 111 Copynumber: 1.9 Consensus size: 111
4039871 AAAAAAACTT
* *
4039881 GAGAAGTAACTTAAATAAAAAATTAAACTCGTTTAAAATATAAATCAGATACGAG-TCTAATATC
1 GAGAAGTAACTTAAACAAAAAATTAAACTCGTTTAAAATACAAATCAGATACGAGAT-TAATATC
* *
4039945 CAAAGTTTAAGCTTAAACTATTTTTAAGTTTATAATATATAAAGCTC
65 CAAAGCTTAAGCTCAAACTATTTTTAAGTTTATAATATATAAAGCTC
* * * * * ** * *
4039992 GAGAAGTGACTTGAACAAAAATTTAATCTTGTTTAAAATACAAATTGGGTGCGAGATTAATATCC
1 GAGAAGTAACTTAAACAAAAAATTAAACTCGTTTAAAATACAAATCAGATACGAGATTAATATCC
* *
4040057 AAAGCTTAAGCTCAACCTATTTTTATGTTTATAATAT
66 AAAGCTTAAGCTCAAACTATTTTTAAGTTTATAATAT
4040094 GAATTATGTA
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
111 85 0.99
112 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (111 bp):
GAGAAGTAACTTAAACAAAAAATTAAACTCGTTTAAAATACAAATCAGATACGAGATTAATATCC
AAAGCTTAAGCTCAAACTATTTTTAAGTTTATAATATATAAAGCTC
Found at i:4046542 original size:21 final size:21
Alignment explanation
Indices: 4046493--4046544 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
4046483 CAAATAAAAG
4046493 CTGCTCAAACGGTGTGAATAAA
1 CTGCTC-AACGGTGTGAATAAA
**
4046515 CCACTCAACGGTGT-AGATAAA
1 CTGCTCAACGGTGTGA-ATAAA
4046536 CTGCTCAAC
1 CTGCTCAAC
4046545 TTCCTCCGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 20 0.80
22 4 0.16
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (21 bp):
CTGCTCAACGGTGTGAATAAA
Found at i:4046985 original size:28 final size:25
Alignment explanation
Indices: 4046937--4047000 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 25
4046927 AATTTTGGGT
*
4046937 AAAACTATAAAAGTTGGAAAATAGGGG
1 AAAACTATAAAAGTT--AAAAAAGGGG
4046964 CAAAACTATAAAA-TCTAAAAAAGGGG
1 -AAAACTATAAAAGT-TAAAAAAGGGG
*
4046990 AAAATTATAAA
1 AAAACTATAAA
4047001 TTTGAGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 10 0.30
26 9 0.27
27 1 0.03
28 13 0.39
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.19
Consensus pattern (25 bp):
AAAACTATAAAAGTTAAAAAAGGGG
Found at i:4055463 original size:7 final size:6
Alignment explanation
Indices: 4055371--4055504 Score: 51
Period size: 6 Copynumber: 22.5 Consensus size: 6
4055361 ATTTCATATG
* * * * ** *
4055371 TTTTAT TTTTAT TTTTTA TTTTAA ATTTAA -GATAA TTTTGA TTTTAAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT-AA
* * * * *
4055419 TTTGAA TTTTAA CTGTGA TGTTAA TTTT-- TTTTAA TTTTAA GTTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA -TTTTAA
*** * * *
4055466 CTTTGGG TTTTAA TTTTGA TGTT-A TATTAA TTTTAA TTT
1 -TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTT
4055505 AGTAAATATT
Statistics
Matches: 91, Mismatches: 31, Indels: 12
0.68 0.23 0.09
Matches are distributed among these distances:
4 4 0.04
5 7 0.08
6 67 0.74
7 13 0.14
ACGTcount: A:0.28, C:0.01, G:0.09, T:0.62
Consensus pattern (6 bp):
TTTTAA
Found at i:4055483 original size:13 final size:13
Alignment explanation
Indices: 4055403--4055484 Score: 57
Period size: 13 Copynumber: 6.7 Consensus size: 13
4055393 AAATTTAAGA
4055403 TAATTTTGA-TTT
1 TAATTTTGAGTTT
* *
4055415 TAAATTTGAATTT
1 TAATTTTGAGTTT
* * *
4055428 TAACTGTGA-TGT
1 TAATTTTGAGTTT
4055440 TAATTTT---TTT
1 TAATTTTGAGTTT
*
4055450 TAATTTTAAGTTT
1 TAATTTTGAGTTT
* *
4055463 TAACTTTGGGTTT
1 TAATTTTGAGTTT
4055476 TAATTTTGA
1 TAATTTTGA
4055485 TGTTATATTA
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
10 9 0.17
12 15 0.28
13 30 0.56
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (13 bp):
TAATTTTGAGTTT
Done.