Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 31 of 45
Found at i:5477632 original size:22 final size:21
Alignment explanation
Indices: 5477596--5477637 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
5477586 ATAATTAGAA
*
5477596 TTTAATTAATTTTAAAGTTATC
1 TTTAATTAATATTAAA-TTATC
*
5477618 TTTAATTACTATTAAATTAT
1 TTTAATTAATATTAAATTAT
5477638 ATTATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTAATTAATATTAAATTATC
Found at i:5477646 original size:16 final size:16
Alignment explanation
Indices: 5477622--5477656 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5477612 GTTATCTTTA
5477622 ATTACTATTAAATTAT
1 ATTACTATTAAATTAT
* *
5477638 ATTATTATTAAGTTAT
1 ATTACTATTAAATTAT
5477654 ATT
1 ATT
5477657 CTAATTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTACTATTAAATTAT
Found at i:5477956 original size:24 final size:28
Alignment explanation
Indices: 5477920--5477990 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 28
5477910 AATATTTATT
*
5477920 TAAATTT-TATTTTAAATATTAAAAAT-A
1 TAAATTTAT-TTTTAAATAATAAAAATAA
*
5477947 T-AA-TT-TTTTTAAATAATAATAATAA
1 TAAATTTATTTTTAAATAATAAAAATAA
5477972 TAAATTTATTTTTAAATAA
1 TAAATTTATTTTTAAATAA
5477991 AAATAACATA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 15 0.39
25 5 0.13
26 4 0.11
27 3 0.08
28 11 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TAAATTTATTTTTAAATAATAAAAATAA
Found at i:5477964 original size:27 final size:28
Alignment explanation
Indices: 5477934--5477996 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
5477924 TTTTATTTTA
*
5477934 AATATTAAAAATATAA-TT-TTTTTAAAT
1 AATAATAAAAATA-AATTTATTTTTAAAT
*
5477961 AATAATAATAATAAATTTATTTTTAAAT
1 AATAATAAAAATAAATTTATTTTTAAAT
*
5477989 AAAAATAA
1 AATAATAA
5477997 CATAATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 2 0.06
27 13 0.42
28 16 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
AATAATAAAAATAAATTTATTTTTAAAT
Found at i:5477989 original size:25 final size:24
Alignment explanation
Indices: 5477920--5477996 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 24
5477910 AATATTTATT
* *
5477920 TAAATTTTATTTTAAATATTAAAAA
1 TAAATTTT-TTTTAAATAATAATAA
*
5477945 TATAATTTTTTTAAATAATAATAATAA
1 TA-AATTTTTTT-TA-AATAATAATAA
*
5477972 TAAATTTATTTTTAAATAAAAATAA
1 TAAATTT-TTTTTAAATAATAATAA
5477997 CATAATATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
25 15 0.35
26 13 0.30
27 15 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAATTTTTTTTAAATAATAATAA
Found at i:5478225 original size:16 final size:16
Alignment explanation
Indices: 5478204--5478235 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5478194 AATAAGAATA
*
5478204 TAATTTAATTATATTT
1 TAATTTAATAATATTT
5478220 TAATTTAATAATATTT
1 TAATTTAATAATATTT
5478236 AAAGATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTAATAATATTT
Found at i:5478394 original size:29 final size:27
Alignment explanation
Indices: 5478362--5478420 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
5478352 ATCAAATATT
5478362 TAAAAAA-TATTAATTTAAATTTTAAAAAA
1 TAAAAAACTATT--TTTAAA-TTTAAAAAA
5478391 TAAAAAAACTATTTTTAAATTTAAAAAA
1 T-AAAAAACTATTTTTAAATTTAAAAAA
5478419 TA
1 TA
5478421 TTACATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
27 1 0.04
28 10 0.36
29 7 0.25
30 6 0.21
31 4 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
TAAAAAACTATTTTTAAATTTAAAAAA
Found at i:5478820 original size:6 final size:6
Alignment explanation
Indices: 5478786--5478818 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
5478776 TTAGTACACA
5478786 TTTTCT TTTTCT TTTTCT TTTTCT TTTT-T TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
5478819 TTCGTGTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTCT
Found at i:5478903 original size:11 final size:11
Alignment explanation
Indices: 5478889--5478997 Score: 50
Period size: 12 Copynumber: 9.6 Consensus size: 11
5478879 ATTGAATTTA
5478889 TATATTTTAAT
1 TATATTTTAAT
5478900 TATATTTATATAT
1 TATATTT-TA-AT
5478913 T-TATATTTATAT
1 TATAT-TTTA-AT
5478925 TA-ATTTTAAAT
1 TATATTTT-AAT
**
5478936 TAT-TAATAAT
1 TATATTTTAAT
* *
5478946 T-TATATTAAA
1 TATATTTTAAT
*
5478956 TAAATTTTTAA-
1 TATA-TTTTAAT
5478967 -ATATTTTATAT
1 TATATTTTA-AT
5478978 TATATTTTTATAT
1 TATA-TTTTA-AT
5478991 TATATTT
1 TATATTT
5478998 AATATTTTCG
Statistics
Matches: 78, Mismatches: 7, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
9 6 0.08
10 13 0.17
11 17 0.22
12 25 0.32
13 17 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTTTAAT
Found at i:5478906 original size:19 final size:20
Alignment explanation
Indices: 5478884--5478925 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
5478874 CGCATATTGA
5478884 ATTTATATATTT-TAATTAT
1 ATTTATATATTTATAATTAT
*
5478903 ATTTATATATTTATATTTAT
1 ATTTATATATTTATAATTAT
5478923 ATT
1 ATT
5478926 AATTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTATATATTTATAATTAT
Found at i:5478921 original size:33 final size:32
Alignment explanation
Indices: 5478884--5479002 Score: 93
Period size: 33 Copynumber: 3.6 Consensus size: 32
5478874 CGCATATTGA
5478884 ATTTATATATTTTAATTATATTTATATATTTAT
1 ATTTATATATTTTAA-TATATTTATATATTTAT
*
5478917 ATTTATATTAATTTTAA-ATTATTAATA-ATTTAT
1 ATTTATA-T-ATTTTAATA-TATTTATATATTTAT
* *
5478950 ATTAAATAAATTTTTAA-ATATTT-TATATTATAT
1 ATT-TATATA-TTTTAATATATTTATATATT-TAT
*
5478983 TTTTATATTATATTTAATAT
1 ATTTATA-TAT-TTTAATAT
5479003 TTTCGAATCT
Statistics
Matches: 69, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
31 2 0.03
32 12 0.17
33 35 0.51
34 13 0.19
35 7 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
ATTTATATATTTTAATATATTTATATATTTAT
Found at i:5478926 original size:25 final size:24
Alignment explanation
Indices: 5478889--5479003 Score: 65
Period size: 25 Copynumber: 4.5 Consensus size: 24
5478879 ATTGAATTTA
*
5478889 TATATTT-TAATTATATTTATATATT
1 TATATTTAT-ATTA-ATTTAAATATT
5478914 TATATTTATATTAATTTTAAATTATT
1 TATATTTATATTAA-TTTAAA-TATT
* * *
5478940 AATAATTTATATTAA-ATAAATTTT
1 TAT-ATTTATATTAATTTAAATATT
**
5478964 TAAATATTTTATATTATATTTTTATA-T
1 T--ATA-TTTATATTA-ATTTAAATATT
5478991 TATATTTAATATT
1 TATATTT-ATATT
5479004 TTCGAATCTT
Statistics
Matches: 71, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
24 7 0.10
25 29 0.41
26 18 0.25
27 14 0.20
28 3 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATATTTATATTAATTTAAATATT
Found at i:5478976 original size:26 final size:25
Alignment explanation
Indices: 5478917--5478979 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
5478907 ATATATTTAT
*
5478917 ATTTATATTAATTTTAAATTATTAATA
1 ATTTATATTAA--ATAAATTATTAATA
*
5478944 ATTTATATTAAATAAATTTTTAAATA
1 ATTTATATTAAATAAATTATT-AATA
*
5478970 TTTTATATTA
1 ATTTATATTA
5478980 TATTTTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.25
26 13 0.41
27 11 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTTATATTAAATAAATTATTAATA
Found at i:5481953 original size:15 final size:15
Alignment explanation
Indices: 5481921--5481960 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
5481911 AAATAATAAA
*
5481921 AATTTAAAATAATTTG
1 AATTT-AAATAATCTG
5481937 AATTTAAATAATCTG
1 AATTTAAATAATCTG
5481952 AATTTAAAT
1 AATTTAAAT
5481961 GATATTCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (15 bp):
AATTTAAATAATCTG
Found at i:5481998 original size:17 final size:17
Alignment explanation
Indices: 5481969--5482025 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 17
5481959 ATGATATTCG
5481969 AATAATCTAAATTTAAAA
1 AATAAT-TAAATTTAAAA
5481987 AATAATTAAATTTTAAAA
1 AATAATTAAA-TTTAAAA
*
5482005 AAT--TTAAA-TAAAAA
1 AATAATTAAATTTAAAA
5482019 AATAATT
1 AATAATT
5482026 TAAAAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 8 0.23
16 7 0.20
17 4 0.11
18 16 0.46
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAATTAAATTTAAAA
Found at i:5482027 original size:17 final size:17
Alignment explanation
Indices: 5481969--5482029 Score: 63
Period size: 16 Copynumber: 3.6 Consensus size: 17
5481959 ATGATATTCG
*
5481969 AATAATCTAAATTTAAAA
1 AATAATTTAAA-TTAAAA
**
5481987 AATAA-TTAAATTTTAA
1 AATAATTTAAATTAAAA
*
5482003 AA-AATTTAAATAAAAA
1 AATAATTTAAATTAAAA
5482019 AATAATTTAAA
1 AATAATTTAAA
5482030 AAATTTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 2 0.06
16 16 0.46
17 12 0.34
18 5 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAATTTAAATTAAAA
Found at i:5482693 original size:17 final size:18
Alignment explanation
Indices: 5482671--5482705 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5482661 TCACTTTTTT
5482671 AAAAATTAATATA-AATA
1 AAAAATTAATATATAATA
*
5482688 AAAAATTATTATATAATA
1 AAAAATTAATATATAATA
5482706 TAATAACCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTAATATATAATA
Found at i:5483080 original size:132 final size:129
Alignment explanation
Indices: 5482862--5483112 Score: 312
Period size: 132 Copynumber: 1.9 Consensus size: 129
5482852 AGGTCAGTCC
* *
5482862 AGTTAAATTTCAAGGAATGAGAGGGTGTGGGAATATTTTGATGGGTTTGTTTAACTACGACAAGT
1 AGTTAAATTTCAAGGAA-GAGAGAGTGTGGGAATATTTTGATGGGTTTGATTAACTACGACAAGT
*
5482927 AAAATTAAAAAAATATTATATATTTTATTT-TTTATTTAATTTTTTAAAATATATAATAATTTAT
65 AAAATTAAAAAAATATAATATATTTTATTTATTT-TTT-ATTTTTT-AAATATATAATAATTTAT
5482991 TAA
127 TAA
* * * *
5482994 AGTTAAATTTCGAGGAA-AGAGAGTG-GGAGAATATTTTTGA-GGGTTTGATTACCTATATGGCA
1 AGTTAAATTTCAAGGAAGAGAGAGTGTGG-GAATA-TTTTGATGGGTTTGATTAAC--TACGACA
* * *
5483056 AGTAGATTTAAAAAACTATAATATATTTTATTTATTTTTTATTTTTTAAATATATAA
62 AGTAAAATTAAAAAAATATAATATATTTTATTTATTTTTTATTTTTTAAATATATAA
5483113 ATTAAAAATA
Statistics
Matches: 104, Mismatches: 10, Indels: 12
0.83 0.08 0.10
Matches are distributed among these distances:
129 2 0.02
130 33 0.32
131 13 0.12
132 53 0.51
133 3 0.03
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.43
Consensus pattern (129 bp):
AGTTAAATTTCAAGGAAGAGAGAGTGTGGGAATATTTTGATGGGTTTGATTAACTACGACAAGTA
AAATTAAAAAAATATAATATATTTTATTTATTTTTTATTTTTTAAATATATAATAATTTATTAA
Found at i:5484993 original size:14 final size:13
Alignment explanation
Indices: 5484940--5484989 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
5484930 ACACAACACT
*
5484940 TTTTTAAAAAAAA
1 TTTTTAAAAATAA
*
5484953 TTTGTAAAAATAA
1 TTTTTAAAAATAA
* *
5484966 TGTATTAAATATAA
1 T-TTTTAAAAATAA
5484980 TTTTTAAAAA
1 TTTTTAAAAA
5484990 ATAAAAATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (13 bp):
TTTTTAAAAATAA
Found at i:5486937 original size:8 final size:8
Alignment explanation
Indices: 5486924--5486953 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
5486914 GCTGGCCTTC
5486924 TTTTTTCT
1 TTTTTTCT
5486932 TTTTTTCT
1 TTTTTTCT
5486940 TTTTTT-T
1 TTTTTTCT
5486947 TTTTTTC
1 TTTTTTC
5486954 ACTTTTAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTCT
Found at i:5486941 original size:15 final size:15
Alignment explanation
Indices: 5486921--5486953 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5486911 TTAGCTGGCC
5486921 TTCTTTTTTCTTTTT
1 TTCTTTTTTCTTTTT
*
5486936 TTCTTTTTTTTTTTT
1 TTCTTTTTTCTTTTT
5486951 TTC
1 TTC
5486954 ACTTTTAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTCTTTTTTCTTTTT
Found at i:5490517 original size:2 final size:2
Alignment explanation
Indices: 5490510--5490547 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5490500 AAAGAGTTGC
5490510 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
5490548 TATATATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5492576 original size:65 final size:64
Alignment explanation
Indices: 5492498--5492768 Score: 170
Period size: 74 Copynumber: 3.9 Consensus size: 64
5492488 AATTTAAGTA
* * * *
5492498 TTTATTAAGTGATTTTATCAGTTAATTTTTTGTAAGATATAAATTATTTTTATTTGTAAAAATAT
1 TTTAGTAA-TGATTATATCAGTTAATTTTTT-TAAGATATGATTTATTTTTATTTGTAAAAATAT
5492563 T
64 T
* * *
5492564 TTT-GGATATGATTATATCAATTTAAAATTTTTACAAATTTTAAAATATGATTTATTTTTATTTG
1 TTTAGTA-ATGATTATATC-AGTT--AA--TTT-----TTTTAAGATATGATTTATTTTTATTTG
*
5492628 TAAAATTATT
55 TAAAAATATT
* * *
5492638 TTTAGTAATGATTATATGAGTTTATATTTTTTAAGTTATGATTTATTTTTATTTGTAAAATTTAA
1 TTTAGTAATGATTATATCAGTTAAT-TTTTTTAAGATATGATTTATTTTTATTTGT---A---AA
5492703 AATTTATTT
59 AA--TA-TT
* * *
5492712 TTTAGT-TTGATTATA-CGAGTTTAAATTTTTTAAGGTATGATTTATTTTTATTTGTAA
1 TTTAGTAATGATTATATC-AG-TTAATTTTTTTAAGATATGATTTATTTTTATTTGTAA
5492769 GATTAATTTG
Statistics
Matches: 161, Mismatches: 20, Indels: 47
0.71 0.09 0.21
Matches are distributed among these distances:
65 36 0.22
66 7 0.04
67 1 0.01
68 3 0.02
69 1 0.01
70 6 0.04
71 4 0.02
73 44 0.27
74 54 0.34
75 5 0.03
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.55
Consensus pattern (64 bp):
TTTAGTAATGATTATATCAGTTAATTTTTTTAAGATATGATTTATTTTTATTTGTAAAAATATT
Found at i:5492732 original size:73 final size:72
Alignment explanation
Indices: 5492628--5492768 Score: 221
Period size: 73 Copynumber: 1.9 Consensus size: 72
5492618 TTTTTATTTG
* * *
5492628 TAAAATTATTTTTAGTAATGATTATATGAGTTTATATTTTTTAAGTTATGATTTATTTTTATTTG
1 TAAAATTATTTTTAGTAATGATTATACGAGTTTAAATTTTTTAAGGTATGATTTATTTTTATTTG
5492693 TAAAATT
66 TAAAATT
*
5492700 TAAAATTTATTTTTTAGT-TTGATTATACGAGTTTAAATTTTTTAAGGTATGATTTATTTTTATT
1 TAAAA-TTA-TTTTTAGTAATGATTATACGAGTTTAAATTTTTTAAGGTATGATTTATTTTTATT
5492764 TGTAA
64 TGTAA
5492769 GATTAATTTG
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
72 5 0.08
73 50 0.79
74 8 0.13
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.57
Consensus pattern (72 bp):
TAAAATTATTTTTAGTAATGATTATACGAGTTTAAATTTTTTAAGGTATGATTTATTTTTATTTG
TAAAATT
Found at i:5495919 original size:22 final size:24
Alignment explanation
Indices: 5495889--5495932 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
5495879 CCTCTGAATC
*
5495889 TCTTCAAGA-ATTATACCCCAAAT
1 TCTTCAAGAGATTATAACCCAAAT
5495912 TCTT-AAGAGATTATAACCCAA
1 TCTTCAAGAGATTATAACCCAA
5495933 GATTGAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.30
Consensus pattern (24 bp):
TCTTCAAGAGATTATAACCCAAAT
Found at i:5496454 original size:20 final size:19
Alignment explanation
Indices: 5496416--5496463 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
5496406 ATTCTTTATG
*
5496416 TATCGATACAATGAATATA
1 TATCGATACAAAGAATATA
5496435 TATCGATACAAAGCAATATA
1 TATCGATACAAAG-AATATA
5496455 TATCGATAC
1 TATCGATAC
5496464 TTCTAGGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (19 bp):
TATCGATACAAAGAATATA
Found at i:5498737 original size:33 final size:33
Alignment explanation
Indices: 5498700--5498766 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5498690 TTCAACGATT
5498700 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
5498733 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
5498766 T
1 T
5498767 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:5498738 original size:13 final size:13
Alignment explanation
Indices: 5498720--5498744 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5498710 CATAAAATGT
5498720 TGTATCGATACAA
1 TGTATCGATACAA
5498733 TGTATCGATACA
1 TGTATCGATACA
5498745 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5498825 original size:13 final size:13
Alignment explanation
Indices: 5498807--5498831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5498797 ATTACTCAAA
5498807 TGTATCGATACAT
1 TGTATCGATACAT
5498820 TGTATCGATACA
1 TGTATCGATACA
5498832 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5498933 original size:52 final size:52
Alignment explanation
Indices: 5498840--5498967 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
5498830 CACTGATCTT
*
5498840 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
*
5498891 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
5498943 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
5498968 TCATATTTCG
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
51 18 0.25
52 51 0.71
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:5503859 original size:38 final size:39
Alignment explanation
Indices: 5503718--5503862 Score: 130
Period size: 39 Copynumber: 3.7 Consensus size: 39
5503708 ATATATTCAA
* * ** *
5503718 AAAAAAATCATACATTAGTTTCATCTTTCAAATTCTAAT
1 AAAAAATTTATACATTAGTCACATCTTTTAAATTCTAAT
** * *
5503757 AAAAAATTTATGTATTAATCACATCTTTTAAATTCCAAT
1 AAAAAATTTATACATTAGTCACATCTTTTAAATTCTAAT
** * * * * *
5503796 AATTAATCTATACATTACTAACATCTTTTAAATTTTTAT
1 AAAAAATTTATACATTAGTCACATCTTTTAAATTCTAAT
*
5503835 AAAGAATTTAT-CATTAGTCACATCTTTT
1 AAAAAATTTATACATTAGTCACATCTTTT
5503863 GGATTTTTAT
Statistics
Matches: 82, Mismatches: 24, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
38 15 0.18
39 67 0.82
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.43
Consensus pattern (39 bp):
AAAAAATTTATACATTAGTCACATCTTTTAAATTCTAAT
Found at i:5504446 original size:21 final size:21
Alignment explanation
Indices: 5504420--5504464 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5504410 AAAAATAATA
*
5504420 ATAACGATAAAATTAATTATT
1 ATAACGATAAAATTAAATATT
* * *
5504441 ATAACGGTGAGATTAAATATT
1 ATAACGATAAAATTAAATATT
5504462 ATA
1 ATA
5504465 GTAATGAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (21 bp):
ATAACGATAAAATTAAATATT
Found at i:5509749 original size:41 final size:42
Alignment explanation
Indices: 5509696--5509780 Score: 136
Period size: 41 Copynumber: 2.0 Consensus size: 42
5509686 AGTGTAAGAA
* *
5509696 TGATTCATTGGGATGCATTAATTGTAATG-CACTTATGTATT
1 TGATTCAATGGGATGCATTAATTGTAAAGTCACTTATGTATT
*
5509737 TGATTCAATGGGATGGATTAATTGTAAAGTCACTTATGTATT
1 TGATTCAATGGGATGCATTAATTGTAAAGTCACTTATGTATT
5509779 TG
1 TG
5509781 TCCCTCATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 26 0.65
42 14 0.35
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.42
Consensus pattern (42 bp):
TGATTCAATGGGATGCATTAATTGTAAAGTCACTTATGTATT
Found at i:5511166 original size:177 final size:177
Alignment explanation
Indices: 5510870--5511222 Score: 661
Period size: 177 Copynumber: 2.0 Consensus size: 177
5510860 AATAAGTCCT
*
5510870 TTCGTAAGTGTTGTGACACCTAATGTCTGGCCATTTTTCCCTGAAAACCACTCTTTTATTTAAAA
1 TTCGTAAGTGTTGTGACACCTAATGTCTGGCCATATTTCCCTGAAAACCACTCTTTTATTTAAAA
5510935 TTTTGACATTTATGAGTTGATAAGCAAAGCATAAAAGTGTCATGATGGATTGATTTTCTTTATTA
66 TTTTGACATTTATGAGTTGATAAGCAAAGCATAAAAGTGTCATGATGGATTGATTTTCTTTATTA
5511000 TGACGTAGGTTGTGTTATGTGGTATGGCATTTGATGGTGTAGGATTA
131 TGACGTAGGTTGTGTTATGTGGTATGGCATTTGATGGTGTAGGATTA
* * *
5511047 TTCGTAAGTGTTGTGGCACGTAATGTCTGGCTATATTTCCCTGAAAACCACTCTTTTATTTAAAA
1 TTCGTAAGTGTTGTGACACCTAATGTCTGGCCATATTTCCCTGAAAACCACTCTTTTATTTAAAA
*
5511112 TTTTGACATTTATGAGTTGATTAGCAAAGCATAAAAGTGTCATGATGGATTGATTTTCTTTATTA
66 TTTTGACATTTATGAGTTGATAAGCAAAGCATAAAAGTGTCATGATGGATTGATTTTCTTTATTA
5511177 TGACGTAGGTTGTGTTATGTGGTATGGCATTTGATGGTGTAGGATT
131 TGACGTAGGTTGTGTTATGTGGTATGGCATTTGATGGTGTAGGATT
5511223 TCGAGTTTTA
Statistics
Matches: 171, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
177 171 1.00
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (177 bp):
TTCGTAAGTGTTGTGACACCTAATGTCTGGCCATATTTCCCTGAAAACCACTCTTTTATTTAAAA
TTTTGACATTTATGAGTTGATAAGCAAAGCATAAAAGTGTCATGATGGATTGATTTTCTTTATTA
TGACGTAGGTTGTGTTATGTGGTATGGCATTTGATGGTGTAGGATTA
Found at i:5516554 original size:14 final size:14
Alignment explanation
Indices: 5516537--5516563 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5516527 TATTCAAAAT
5516537 TTTATATATATATA
1 TTTATATATATATA
5516551 TTTATATATATAT
1 TTTATATATATAT
5516564 TTAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATATATATATA
Found at i:5516558 original size:12 final size:12
Alignment explanation
Indices: 5516541--5516566 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5516531 CAAAATTTTA
5516541 TATATATATATT
1 TATATATATATT
5516553 TATATATATATT
1 TATATATATATT
5516565 TA
1 TA
5516567 AAAAAATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATATATATATT
Found at i:5520663 original size:18 final size:17
Alignment explanation
Indices: 5520620--5520664 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
5520610 TTTTAACTTA
5520620 AAAAATATATA-TATAT
1 AAAAATATATATTATAT
*
5520636 ACAAA-A-ATATTACTAT
1 AAAAATATATATTA-TAT
5520652 AAAAATATATATT
1 AAAAATATATATT
5520665 TAATTTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 3 0.13
15 3 0.13
16 11 0.48
17 1 0.04
18 5 0.22
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAAATATATATTATAT
Found at i:5520877 original size:19 final size:22
Alignment explanation
Indices: 5520835--5520879 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
5520825 TCGTGAGATA
*
5520835 AAACAATAATAACATATTATTC
1 AAACAATAATAACATAATATTC
5520857 AAACAATAAT-A-ATAATA-TC
1 AAACAATAATAACATAATATTC
5520876 AAAC
1 AAAC
5520880 TTCCAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 5 0.23
21 1 0.05
22 10 0.45
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (22 bp):
AAACAATAATAACATAATATTC
Found at i:5520970 original size:12 final size:12
Alignment explanation
Indices: 5520953--5520977 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5520943 CTCATCGAAG
5520953 ACAATAATAATA
1 ACAATAATAATA
5520965 ACAATAATAATA
1 ACAATAATAATA
5520977 A
1 A
5520978 ACACAGATTT
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
ACAATAATAATA
Found at i:5521127 original size:99 final size:99
Alignment explanation
Indices: 5520956--5521138 Score: 294
Period size: 99 Copynumber: 1.8 Consensus size: 99
5520946 ATCGAAGACA
* *
5520956 ATAATAATAACAATAATAATAAACACAGATTTTTAAAGTGAAATATTCAAAAGACAAAATTTCCT
1 ATAATAATAACAATAATAATAAACACAGATTTCTAAAGTGAAATATTCAAAAGACAAAATTTCCC
* * * *
5521021 TAGTCAGAATTTTAGAAATATTCAAAATTTTAAT
66 GAATCAGAATCTCAGAAATATTCAAAATTTTAAT
* *
5521055 ATAATAATAATAATAATAATAAACGCAGATTTCTAAAGTGAAATATTCAAAAGACAAAATTTCCC
1 ATAATAATAACAATAATAATAAACACAGATTTCTAAAGTGAAATATTCAAAAGACAAAATTTCCC
5521120 GAATCAGAATCTCAGAAAT
66 GAATCAGAATCTCAGAAAT
5521139 GCCCCATATA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 76 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (99 bp):
ATAATAATAACAATAATAATAAACACAGATTTCTAAAGTGAAATATTCAAAAGACAAAATTTCCC
GAATCAGAATCTCAGAAATATTCAAAATTTTAAT
Found at i:5522083 original size:16 final size:16
Alignment explanation
Indices: 5522033--5522085 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
5522023 ATATGTAACT
5522033 TAAAATTTATATAATA
1 TAAAATTTATATAATA
* *
5522049 TAAATTATTAT-TTAT-
1 TAAAAT-TTATATAATA
5522064 TAAAATTTATATAATA
1 TAAAATTTATATAATA
5522080 TAAAAT
1 TAAAAT
5522086 GCTTTAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 4 0.13
15 8 0.27
16 14 0.47
17 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAAATTTATATAATA
Found at i:5522261 original size:2 final size:2
Alignment explanation
Indices: 5522203--5522244 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5522193 ATTAACAATT
5522203 TA TA T- 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
5522244 T
1 T
5522245 GAAAGGTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5522557 original size:34 final size:35
Alignment explanation
Indices: 5522499--5522571 Score: 121
Period size: 34 Copynumber: 2.1 Consensus size: 35
5522489 GATTTATACA
*
5522499 ATGAAATCTTTTTAAAAATAATTTATGTATTTATT
1 ATGAAATCTTTTTAAAAATAATTTATATATTTATT
*
5522534 ATGAAATCTTTTT-TAAATAATTTATATATTTATT
1 ATGAAATCTTTTTAAAAATAATTTATATATTTATT
5522568 ATGA
1 ATGA
5522572 GTTAAAATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 23 0.64
35 13 0.36
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (35 bp):
ATGAAATCTTTTTAAAAATAATTTATATATTTATT
Found at i:5522780 original size:20 final size:20
Alignment explanation
Indices: 5522755--5522792 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5522745 TTAATGCAAA
5522755 AATCAAAAATTATTTTTTAT
1 AATCAAAAATTATTTTTTAT
5522775 AATCAAAAATTATTTTTT
1 AATCAAAAATTATTTTTT
5522793 TAAATCGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
AATCAAAAATTATTTTTTAT
Found at i:5522798 original size:20 final size:19
Alignment explanation
Indices: 5522754--5522798 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
5522744 TTTAATGCAA
5522754 AAATCAAAAATTATTTTTT
1 AAATCAAAAATTATTTTTT
5522773 ATAATCAAAAATTATTTTTTT
1 A-AATCAAAAATTA-TTTTTT
5522794 AAATC
1 AAATC
5522799 GAAACTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 16 0.67
21 7 0.29
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATCAAAAATTATTTTTT
Found at i:5524114 original size:2 final size:2
Alignment explanation
Indices: 5524068--5524094 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5524058 TAATTCTGTG
5524068 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5524095 CACACCAAGT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5530367 original size:13 final size:13
Alignment explanation
Indices: 5530349--5530374 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5530339 CATTATTCAA
5530349 TGTATCGATACAT
1 TGTATCGATACAT
5530362 TGTATCGATACAT
1 TGTATCGATACAT
5530375 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5530438 original size:20 final size:19
Alignment explanation
Indices: 5530413--5530486 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 19
5530403 TTTACCCAGA
5530413 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
5530433 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
5530453 TGTATCGATACATTTTCCAA
1 TGTATCGATACATTTT-CAT
5530473 TGTATCGATACATT
1 TGTATCGATACATT
5530487 CTGGCATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:5532870 original size:51 final size:51
Alignment explanation
Indices: 5532805--5532952 Score: 172
Period size: 51 Copynumber: 2.9 Consensus size: 51
5532795 CTAATCCCGG
** * * *
5532805 TTTCATTTCCAAAACATTAATTTTTCTTAATCGGGGATACTCCAACTTCGAT
1 TTTC-TTTCCAAAACACCAATTTTCCATAATCGGGGATACTCCAACTCCGAT
* *
5532857 TTTCTTTCTAAAACACCCATTTTCCATAATCGGGGATACTCCAACTCCGAT
1 TTTCTTTCCAAAACACCAATTTTCCATAATCGGGGATACTCCAACTCCGAT
* * * *
5532908 TTTATTTCCAAAACACCGACTTTT-CACAATCGGAGATACTCCAAC
1 TTTCTTTCCAAAACACC-AATTTTCCATAATCGGGGATACTCCAAC
5532953 CCCGTTATTT
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
51 74 0.90
52 8 0.10
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.34
Consensus pattern (51 bp):
TTTCTTTCCAAAACACCAATTTTCCATAATCGGGGATACTCCAACTCCGAT
Found at i:5533135 original size:79 final size:78
Alignment explanation
Indices: 5532888--5533315 Score: 495
Period size: 79 Copynumber: 5.5 Consensus size: 78
5532878 TTCCATAATC
* * * * * * * *
5532888 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCGACTTTTCACAATCGGAGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATC-AATTTTCATAATCGGGGATACTCCAAC
*
5532953 CCCGTTATTTCTGA
65 CCCGTTATTTCCGA
* * *
5532967 GGGGACACTCCAACCCCGGTTTTATTTCTAAAATATAAATTTT--TCATCGGGGATACTCCAACC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATCAATTTTCATAATCGGGGATACTCCAACC
*
5533030 CCGTTATTTTCGA
66 CCGTTATTTCCGA
* * * *
5533043 GAGGATACCCCAACCCCGGTTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCTAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATCAATTT-TCATAATCGGGGATACTCCAAC
5533108 CCCGTTATTTCCGA
65 CCCGTTATTTCCGA
* * * * *
5533122 GGAGATACTCCAACCCCGGTTTTATTTCTAAAACATCGATTTTTTATAGTCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATC-AATTTTCATAATCGGGGATACTCCAAC
5533187 CCCGTTATTTCCGA
65 CCCGTTATTTCCGA
* * * * *
5533201 GGGGATACTCTAATCCCGATTTTATTTC-GAAATCATCGATTTTTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAAT-ATC-AATTTTCATAATCGGGGATACTCCAA
* *
5533265 CCCCGTTATTTTCAA
64 CCCCGTTATTTCCGA
* *
5533280 GGGGATACTCCAACCCC-GTTATTATCTCCAAAATAT
1 GGGGATACTCCAACCCCGGTT-TTATTTCTAAAATAT
5533316 TAAATTTCTC
Statistics
Matches: 298, Mismatches: 44, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
76 66 0.22
77 1 0.00
78 10 0.03
79 213 0.71
80 8 0.03
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATCAATTTTCATAATCGGGGATACTCCAACC
CCGTTATTTCCGA
Found at i:5536247 original size:52 final size:52
Alignment explanation
Indices: 5536181--5536291 Score: 179
Period size: 52 Copynumber: 2.1 Consensus size: 52
5536171 TTGAATCCTG
*
5536181 ATCGCCACCAAGGCATCATCACTCTTAGTGACATCAAGTCAC-TCTAAATTTA
1 ATCGCCACCAAGGCATCATCACTCTTAGTGACACCAAGTCACTTC-AAATTTA
* *
5536233 ATTGCCACCAAGGCATCATCACTTTTAGTGACACCAAGTCACTTCAAATTTA
1 ATCGCCACCAAGGCATCATCACTCTTAGTGACACCAAGTCACTTCAAATTTA
5536285 ATCGCCA
1 ATCGCCA
5536292 TGAAGAACAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 52 0.96
53 2 0.04
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (52 bp):
ATCGCCACCAAGGCATCATCACTCTTAGTGACACCAAGTCACTTCAAATTTA
Found at i:5536267 original size:26 final size:26
Alignment explanation
Indices: 5536186--5536270 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
5536176 TCCTGATCGC
*
5536186 CACCAAGGCATCATCACTCTTAGTGA
1 CACCAAGGCATCATCACTTTTAGTGA
* * * * * * *
5536212 CATCAAGTCACTC-TAAATTTAATTGC
1 CACCAAGGCA-TCATCACTTTTAGTGA
5536238 CACCAAGGCATCATCACTTTTAGTGA
1 CACCAAGGCATCATCACTTTTAGTGA
5536264 CACCAAG
1 CACCAAG
5536271 TCACTTCAAA
Statistics
Matches: 42, Mismatches: 15, Indels: 4
0.69 0.25 0.07
Matches are distributed among these distances:
25 2 0.05
26 38 0.90
27 2 0.05
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (26 bp):
CACCAAGGCATCATCACTTTTAGTGA
Found at i:5536902 original size:15 final size:15
Alignment explanation
Indices: 5536882--5536942 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
5536872 CTCACAGTAA
*
5536882 CCTCCTTAGTGGCAG
1 CCTCCTCAGTGGCAG
5536897 CCTCCTCAGTGGCAG
1 CCTCCTCAGTGGCAG
* * **
5536912 CCTTCTCTGCAGCTA-
1 CCTCCTCAGTGGC-AG
5536927 CCTCCTCAGTGGCAG
1 CCTCCTCAGTGGCAG
5536942 C
1 C
5536943 TTTTCCAACT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
14 1 0.03
15 33 0.94
16 1 0.03
ACGTcount: A:0.13, C:0.39, G:0.23, T:0.25
Consensus pattern (15 bp):
CCTCCTCAGTGGCAG
Found at i:5541213 original size:31 final size:31
Alignment explanation
Indices: 5541177--5541237 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
5541167 TAATATAAAG
*
5541177 TATATAGTAATATAGTAACGTAAAATATATT
1 TATATAGTAATATAGTAACATAAAATATATT
*
5541208 TATATAGTAATATTGTAACATAAAATATAT
1 TATATAGTAATATAGTAACATAAAATATAT
5541238 AGTAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.39
Consensus pattern (31 bp):
TATATAGTAATATAGTAACATAAAATATATT
Found at i:5541454 original size:17 final size:19
Alignment explanation
Indices: 5541425--5541475 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 19
5541415 AAATATTACA
*
5541425 TGATAATA-AATTACATAC
1 TGATAATAGTATTACATAC
5541443 T-ATAAT-GTATTA-ATAC
1 TGATAATAGTATTACATAC
*
5541459 TGTTAATAGTATTACAT
1 TGATAATAGTATTACAT
5541476 TCTAAGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 5 0.19
17 13 0.48
18 7 0.26
19 2 0.07
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (19 bp):
TGATAATAGTATTACATAC
Found at i:5541522 original size:18 final size:18
Alignment explanation
Indices: 5541484--5541527 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5541474 ATTCTAAGTA
*
5541484 TATAATACTATTGATATT
1 TATAATAGTATTGATATT
*
5541502 TATTATAGTATT-ATATAT
1 TATAATAGTATTGATAT-T
5541520 TATAATAG
1 TATAATAG
5541528 GAGGGATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (18 bp):
TATAATAGTATTGATATT
Found at i:5541945 original size:15 final size:14
Alignment explanation
Indices: 5541924--5541973 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
5541914 GTCTTATAAT
5541924 TATATTATATTAAA
1 TATATTATATTAAA
5541938 TAATATTATA-T-AA
1 T-ATATTATATTAAA
*
5541951 TATATAATATTTAAA
1 TATATTATA-TTAAA
5541966 TATATTAT
1 TATATTAT
5541974 TTATATGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
14 3 0.10
15 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATTATATTAAA
Found at i:5541960 original size:27 final size:27
Alignment explanation
Indices: 5541918--5542006 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 27
5541908 CTTCTTGTCT
*
5541918 TATAATTATATTATATTAAATAATATTA
1 TATAA-TATATAATATTAAATAATATTA
5541946 TATAATATATAATATTTAAAT-ATATTA
1 TATAATATATAATA-TTAAATAATATTA
* * *
5541973 T-TTATATGTAA-ATTATA-AATATTTA
1 TATAATATATAATATTAAATAATA-TTA
5541998 TATAA-ATAT
1 TATAATATAT
5542007 TATGTGTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
24 7 0.14
25 8 0.16
26 10 0.20
27 15 0.29
28 11 0.22
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
TATAATATATAATATTAAATAATATTA
Found at i:5543965 original size:165 final size:165
Alignment explanation
Indices: 5543699--5544438 Score: 869
Period size: 165 Copynumber: 4.5 Consensus size: 165
5543689 GAGTTTTTTA
* * * *** * * **
5543699 TTTTTTTCTGAAATACGGTGTTTCCTATTTTATAAATTTTTTTGAGGGGATTTTTCTTACTTTTT
1 TTTTTTTCCGAAATACGGTGTTTTCTACTCCGTAAATTTTTTCGAGAGGATTTTTCTT--GGTTT
* * * * * * *
5543764 TTTATTTTTAAAATTCATAAAATATCATTATTTATTTTACATTAATTCATTTTTAAAAAACGAAT
64 TTAATTTTTAAAATTCATCAAACATCATTATTTATTTCATATTAATTCAGTGTT-AAAAA--AAT
*
5543829 TCATTTTCAT-AATTTTTGA-TTTTTTCTTTGAAA-TTCT
126 TCATTTTCATGAGTTTTTGATTTTTTTCTTTGAAATTTCT
* * * * *
5543866 TTTTTTTCCCAAATACAGTATTTTTTACTCTGTAAATTTTTTCGAGAGGATTTTTCTTGGTTTTT
1 TTTTTTTCCGAAATACGGTGTTTTCTACTCCGTAAATTTTTTCGAGAGGATTTTTCTTGGTTTTT
*
5543931 AATTTTTAAAATTCATCAAACATCATTATTTATTTCATATTAATTCAGTGTTAAAAAAATTTATT
66 AATTTTTAAAATTCATCAAACATCATTATTTATTTCATATTAATTCAGTGTTAAAAAAATTCATT
*
5543996 TTCATGAGTTTTTCATTTTTTTCTTTGAAATTTCT
131 TTCATGAGTTTTTGATTTTTTTCTTTGAAATTTCT
* * *
5544031 TTTTTTTCCGAAATACGGTGTTTTCTACTCCGTAATTTTTTTTGAG-GAGATTTTTCTTGGGTTT
1 TTTTTTTCCGAAATACGGTGTTTTCTACTCCGTAAATTTTTTCGAGAG-GATTTTTCTTGGTTTT
* * *
5544095 TAATTTTTAAAATTCATCAAACATCATTATTTATTTCATATTAGTTCAGTTTTAAAAAAAAAATC
65 TAATTTTTAAAATTCATCAAACATCATTATTTATTTCATATTAATTCAGTGTT--AAAAAAATTC
*
5544160 ATTTTTATGAGTTTTT-A--TTTTTCTTTGAAATTTCT
128 ATTTTCATGAGTTTTTGATTTTTTTCTTTGAAATTTCT
* *
5544195 CTTTTTTT--GAAATACGGTGTTTTTTACTCCGTAAATTTTTTCGAGGGGATTTTTTCTT-GTTT
1 -TTTTTTTCCGAAATACGGTGTTTTCTACTCCGTAAATTTTTTCGAGAGGA-TTTTTCTTGGTTT
* *
5544257 TCAA-TTTTAAAATTCATCAAACATCATTATTTATTTCATATTAATTCAGTGTTAAAAAAATTCG
64 TTAATTTTTAAAATTCATCAAACATCATTATTTATTTCATATTAATTCAGTGTTAAAAAAATTCA
*
5544321 TTTTCATGAGTTTTTGATTTTTTTCCTTGAAATTT-T
129 TTTTCATGAGTTTTTGATTTTTTTCTTTGAAATTTCT
* * * * *
5544357 TCTTTTTT-CGAAATGCGGTGTTTTCTATTCCATAAATTTTTTCGGGAGGA-TTTTCTTTGGTCT
1 T-TTTTTTCCGAAATACGGTGTTTTCTACTCCGTAAATTTTTTCGAGAGGATTTTTC-TTGGTTT
** *
5544420 AAAATTTTTAAAATGCATC
64 TTAATTTTTAAAATTCATC
5544439 TAATATTGTC
Statistics
Matches: 499, Mismatches: 57, Indels: 37
0.84 0.10 0.06
Matches are distributed among these distances:
160 23 0.05
161 7 0.01
162 68 0.14
163 104 0.21
164 60 0.12
165 166 0.33
166 1 0.00
167 70 0.14
ACGTcount: A:0.27, C:0.11, G:0.10, T:0.53
Consensus pattern (165 bp):
TTTTTTTCCGAAATACGGTGTTTTCTACTCCGTAAATTTTTTCGAGAGGATTTTTCTTGGTTTTT
AATTTTTAAAATTCATCAAACATCATTATTTATTTCATATTAATTCAGTGTTAAAAAAATTCATT
TTCATGAGTTTTTGATTTTTTTCTTTGAAATTTCT
Found at i:5546245 original size:158 final size:157
Alignment explanation
Indices: 5545858--5546452 Score: 712
Period size: 152 Copynumber: 3.8 Consensus size: 157
5545848 ATCATTTTTA
* * * *
5545858 AATCTTTTATGTTCCTATGGGCATCCGTTGGGGTATAAAAGATTTCAAAAATA-TTTCGTATCCT
1 AATCTTTTATATTCCTATGGGCATCCATAGGGGTATAAAAGATTTCAAAAACATTTTCGTATCCT
* * *
5545922 TTCGGGCTTCTATTAGAGTACGAAATAGTATTTTTGAAAATAAATAAAATTAAATTGAATTAATA
66 TTCGGGCTTCCATTAGGGTACGAAATAGTATTTTCGAAAATAAATAAAA-TAAATTGAATTAATA
5545987 CTTTCGGATTAAATTTTAA--TTTTT-T
130 CTTTCGGATTAAATTTTAATTTTTTTCT
* * * * *
5546012 --TC-TTTATATTCCTATGAGCATTCGTAGGGGTATAAAAGATTTCAAAAACATTTTTGTATTCT
1 AATCTTTTATATTCCTATGGGCATCCATAGGGGTATAAAAGATTTCAAAAACATTTTCGTATCCT
* ** * *
5546074 TTTGGGCTTCCATTAGGGTACGAAATAACATTTTCGAAAATAAATAAAATCAAATTTAATTAACA
66 TTCGGGCTTCCATTAGGGTACGAAATAGTATTTTCGAAAATAAATAAAAT-AAATTGAATTAATA
5546139 CTTTCGGATTAAATTTTAATTTTTTTCT
130 CTTTCGGATTAAATTTTAATTTTTTTCT
** * *
5546167 AATCTTTTATATTCCTATGGGCATTTATAGGGGTATAAAAGATTTCAAAAACGTTTTTGTATCCT
1 AATCTTTTATATTCCTATGGGCATCCATAGGGGTATAAAAGATTTCAAAAACATTTTCGTATCCT
*
5546232 TTCGGGCTTCCATTAGGATACGAAATAGTATTTTC---AA-AAAT-AAATAAATTGAATTAATAC
66 TTCGGGCTTCCATTAGGGTACGAAATAGTATTTTCGAAAATAAATAAAATAAATTGAATTAATAC
*
5546292 TTGCGGATTAAATTTTAATTTCTTTTTTTTTTCT
131 TTTCGGATTAAATTTTAA-------TTTTTTTCT
** * *
5546326 AATCTTTTATATTATTATGGGCATCCGA-AGGGGTAAAAAAGGTTTCAAAAACATTTTCGTATCC
1 AATCTTTTATATTCCTATGGGCATCC-ATAGGGGTATAAAAGATTTCAAAAACATTTTCGTATCC
* * * * *
5546390 TTTCCGGCTTCTATTAAGGTACGAAATTGTATTTTCGAAAATAAATAAAAGTAAATCGAATTA
65 TTTCGGGCTTCCATTAGGGTACGAAATAGTATTTTCGAAAATAAATAAAA-TAAATTGAATTA
5546453 CTGTTCTCAA
Statistics
Matches: 378, Mismatches: 41, Indels: 33
0.84 0.09 0.07
Matches are distributed among these distances:
151 44 0.12
152 115 0.30
153 4 0.01
154 9 0.02
155 3 0.01
157 2 0.01
158 86 0.23
159 94 0.25
160 1 0.00
162 2 0.01
163 4 0.01
164 3 0.01
165 11 0.03
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (157 bp):
AATCTTTTATATTCCTATGGGCATCCATAGGGGTATAAAAGATTTCAAAAACATTTTCGTATCCT
TTCGGGCTTCCATTAGGGTACGAAATAGTATTTTCGAAAATAAATAAAATAAATTGAATTAATAC
TTTCGGATTAAATTTTAATTTTTTTCT
Found at i:5546471 original size:159 final size:156
Alignment explanation
Indices: 5545858--5546454 Score: 617
Period size: 159 Copynumber: 3.8 Consensus size: 156
5545848 ATCATTTTTA
* ** *
5545858 AATCTTTTATGTTCCTATGGGCATCCGTTGGGGTATAAAAGATTTCAAAAATA-TTTCGTATCCT
1 AATCTTTTATATTCCTATGGGCATCCGAAGGGGTATAAAAGATTTCAAAAACATTTTCGTATCCT
* * *
5545922 TTCGGGCTTCTATTAGAGTACGAAATAGTATTTTTGAAAATAAATAAAATTAAATTGAATTAATA
66 TTCGGGCTTCCATTAG-GTACGAAATAGTATTTTCGAAAATAAATAAAATTAAATTGAATTACT-
* **
5545987 CTTTCGGATTAAA--TTTTAATTTTT-T
129 CTTTCGGATAAAATTTTTTTTTTTTTCT
* * * * *
5546012 --TC-TTTATATTCCTATGAGCATTCGTAGGGGTATAAAAGATTTCAAAAACATTTTTGTATTCT
1 AATCTTTTATATTCCTATGGGCATCCGAAGGGGTATAAAAGATTTCAAAAACATTTTCGTATCCT
* ** * * *
5546074 TTTGGGCTTCCATTAGGGTACGAAATAACATTTTCGAAAATAAATAAAATCAAATTTAATTAACA
66 TTCGGGCTTCCATTA-GGTACGAAATAGTATTTTCGAAAATAAATAAAATTAAATTGAATT-ACT
* **
5546139 CTTTCGGATTAAATTTTAATTTTTTTCT
129 CTTTCGGATAAAATTTTTTTTTTTTTCT
** * *
5546167 AATCTTTTATATTCCTATGGGCAT-TTATAGGGGTATAAAAGATTTCAAAAACGTTTTTGTATCC
1 AATCTTTTATATTCCTATGGGCATCCGA-AGGGGTATAAAAGATTTCAAAAACATTTTCGTATCC
* *
5546231 TTTCGGGCTTCCATTAGGATACGAAATAGTATTTTCAAAAATAAAT-AAATTGAATT-AA-TA--
65 TTTCGGGCTTCCATTAGG-TACGAAATAGTATTTTCGAAAATAAATAAAATTAAATTGAATTACT
*
5546291 CTTGCGGATTAAATTTTAATTTCTTTTTTTTTTCT
129 CTTTCGGA-T-AA----AATTT-TTTTTTTTTTCT
** * *
5546326 AATCTTTTATATTATTATGGGCATCCGAAGGGGTAAAAAAGGTTTCAAAAACATTTTCGTATCCT
1 AATCTTTTATATTCCTATGGGCATCCGAAGGGGTATAAAAGATTTCAAAAACATTTTCGTATCCT
* * * * *
5546391 TTCCGGCTTCTATTAAGGTACGAAATTGTATTTTCGAAAATAAATAAAAGTAAATCGAATTACT
66 TTCGGGCTTCCATT-AGGTACGAAATAGTATTTTCGAAAATAAATAAAATTAAATTGAATTACT
5546455 GTTCTCAAGA
Statistics
Matches: 367, Mismatches: 51, Indels: 40
0.80 0.11 0.09
Matches are distributed among these distances:
151 43 0.12
152 83 0.23
153 3 0.01
154 9 0.02
155 2 0.01
156 2 0.01
157 12 0.03
158 96 0.26
159 102 0.28
160 11 0.03
161 2 0.01
162 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (156 bp):
AATCTTTTATATTCCTATGGGCATCCGAAGGGGTATAAAAGATTTCAAAAACATTTTCGTATCCT
TTCGGGCTTCCATTAGGTACGAAATAGTATTTTCGAAAATAAATAAAATTAAATTGAATTACTCT
TTCGGATAAAATTTTTTTTTTTTTCT
Found at i:5549047 original size:4 final size:4
Alignment explanation
Indices: 5549026--5549078 Score: 56
Period size: 4 Copynumber: 13.5 Consensus size: 4
5549016 TATAAAAAAA
* * *
5549026 TTCT TT-T TT-T TTCC TTCT TTCT TTCT TTCCT TTTT TTCT TTCT TTCC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTCT TTCT
5549073 TTCT TT
1 TTCT TT
5549079 TTCACCTGCG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 6 0.15
4 31 0.76
5 4 0.10
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTCT
Found at i:5549065 original size:17 final size:18
Alignment explanation
Indices: 5549035--5549081 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 18
5549025 ATTCTTTTTT
5549035 TTTCCTTC--TTTCTTTC
1 TTTCCTTCTTTTTCTTTC
5549051 TTTCCTT-TTTTTCTTTC
1 TTTCCTTCTTTTTCTTTC
5549068 TTTCCTTCTTTTTC
1 TTTCCTTCTTTTTC
5549082 ACCTGCGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.25
17 15 0.54
18 6 0.21
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCCTTCTTTTTCTTTC
Found at i:5549068 original size:25 final size:25
Alignment explanation
Indices: 5549031--5549078 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
5549021 AAAAATTCTT
*
5549031 TTTTTTTCCTTCTTTCTTTCTTTCC
1 TTTTTTTCCTTCTTTCCTTCTTTCC
*
5549056 TTTTTTTCTTTCTTTCCTTCTTT
1 TTTTTTTCCTTCTTTCCTTCTTT
5549079 TTCACCTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTTTTCCTTCTTTCCTTCTTTCC
Found at i:5549285 original size:13 final size:11
Alignment explanation
Indices: 5549256--5549281 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5549246 ATTATATTAT
5549256 TATAATATAAA
1 TATAATATAAA
5549267 TATAATATAAA
1 TATAATATAAA
5549278 TATA
1 TATA
5549282 TAATTATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TATAATATAAA
Found at i:5549984 original size:12 final size:12
Alignment explanation
Indices: 5549960--5549993 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5549950 TTTTCAATCA
5549960 TCTCTTT-TTTC
1 TCTCTTTCTTTC
5549971 TCTCTTTCTTTC
1 TCTCTTTCTTTC
*
5549983 TCTCTCTCTTT
1 TCTCTTTCTTT
5549994 GCCTTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TCTCTTTCTTTC
Found at i:5551043 original size:8 final size:8
Alignment explanation
Indices: 5551030--5551066 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
5551020 ATTTTAAAAT
5551030 AAAATTAA
1 AAAATTAA
5551038 AAAATT--
1 AAAATTAA
5551044 AAAATTAA
1 AAAATTAA
*
5551052 AAAATAAA
1 AAAATTAA
5551060 AAAATTA
1 AAAATTA
5551067 TTTTAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
6 6 0.24
8 19 0.76
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATTAA
Found at i:5551061 original size:14 final size:13
Alignment explanation
Indices: 5551025--5551060 Score: 63
Period size: 14 Copynumber: 2.7 Consensus size: 13
5551015 ACATTATTTT
5551025 AAAATAAAATTAA
1 AAAATAAAATTAA
5551038 AAAATTAAAATTAA
1 AAAA-TAAAATTAA
5551052 AAAATAAAA
1 AAAATAAAA
5551061 AAATTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATAAAATTAA
Found at i:5551194 original size:15 final size:14
Alignment explanation
Indices: 5551151--5551206 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
5551141 TTTTAAAATT
*
5551151 AAATTAAAACTT-A
1 AAATAAAAACTTAA
* **
5551164 AAAGAAAATTTTAA
1 AAATAAAAACTTAA
5551178 AAATACAAAACTTAA
1 AAATA-AAAACTTAA
*
5551193 AAATAAAATCTTAA
1 AAATAAAAACTTAA
5551207 GTGATTTAGT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
13 8 0.24
14 13 0.39
15 12 0.36
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (14 bp):
AAATAAAAACTTAA
Found at i:5551395 original size:25 final size:25
Alignment explanation
Indices: 5551367--5551414 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5551357 TAAATATAAT
5551367 AATTTAAAATAAAATAAAATTTTAA
1 AATTTAAAATAAAATAAAATTTTAA
*** *
5551392 AATTTGTTATAAAATAATATTTT
1 AATTTAAAATAAAATAAAATTTT
5551415 TTTAATAAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
AATTTAAAATAAAATAAAATTTTAA
Found at i:5551513 original size:13 final size:12
Alignment explanation
Indices: 5551489--5551538 Score: 66
Period size: 13 Copynumber: 4.0 Consensus size: 12
5551479 ATATATTATT
5551489 TTAAAA-TAAAA
1 TTAAAATTAAAA
5551500 TTAAAAGTTAAAA
1 TTAAAA-TTAAAA
5551513 TTAAAATATAAAA
1 TTAAAAT-TAAAA
5551526 TATAAAATTAAAA
1 T-TAAAATTAAAA
5551539 AATTATTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.17
12 1 0.03
13 22 0.63
14 6 0.17
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (12 bp):
TTAAAATTAAAA
Found at i:5551516 original size:6 final size:6
Alignment explanation
Indices: 5551489--5551538 Score: 66
Period size: 7 Copynumber: 8.0 Consensus size: 6
5551479 ATATATTATT
5551489 TTAAAA -TAAAA TTAAAA GTTAAAA TTAAAA TATAAAA TATAAAA TTAAAA
1 TTAAAA TTAAAA TTAAAA -TTAAAA TTAAAA T-TAAAA T-TAAAA TTAAAA
5551539 AATTATTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.12
6 17 0.41
7 19 0.46
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (6 bp):
TTAAAA
Found at i:5551776 original size:19 final size:18
Alignment explanation
Indices: 5551754--5551794 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
5551744 TCTAAATTTA
5551754 TTATTTATATATAAATAAT
1 TTATTTATATATAAAT-AT
*
5551773 TTATTTTTATATAAATAT
1 TTATTTATATATAAATAT
5551791 TTAT
1 TTAT
5551795 ATGTTTGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTTATATATAAATAT
Found at i:5551833 original size:17 final size:18
Alignment explanation
Indices: 5551813--5551849 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5551803 TGTATTTCTG
*
5551813 TTTATGTCATATTA-ATT
1 TTTATATCATATTATATT
5551830 TTTATATCATATTATATT
1 TTTATATCATATTATATT
5551848 TT
1 TT
5551850 AATTATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTATATCATATTATATT
Found at i:5551991 original size:16 final size:16
Alignment explanation
Indices: 5551962--5552015 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
5551952 ATTTTTAAAT
5551962 AAATTTTA-TTAATTA
1 AAATTTTATTTAATTA
*
5551977 CAATTTTATTTAATTA
1 AAATTTTATTTAATTA
**
5551993 AAATTTTATAAATATTA
1 AAATTTTATTTA-ATTA
5552010 AAATTT
1 AAATTT
5552016 CAAGCGAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 7 0.21
16 16 0.48
17 10 0.30
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
AAATTTTATTTAATTA
Found at i:5552288 original size:18 final size:18
Alignment explanation
Indices: 5552250--5552286 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5552240 ACATGACACG
*
5552250 AATATACATACATATAAA
1 AATATACATAAATATAAA
5552268 AATATACATAAA-ATAAA
1 AATATACATAAATATAAA
5552285 AA
1 AA
5552287 ATTATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (18 bp):
AATATACATAAATATAAA
Found at i:5552377 original size:8 final size:8
Alignment explanation
Indices: 5552358--5552407 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
5552348 AATATATAAA
5552358 TTTTTTTC
1 TTTTTTTC
5552366 TTTTTCTT-
1 TTTTT-TTC
*
5552374 TTTTTCTC
1 TTTTTTTC
5552382 ATTTTTTTC
1 -TTTTTTTC
*
5552391 -ATTTTTC
1 TTTTTTTC
5552398 TTTTTTTC
1 TTTTTTTC
5552406 TT
1 TT
5552408 CAAAATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
7 7 0.21
8 18 0.53
9 9 0.26
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:5552395 original size:25 final size:26
Alignment explanation
Indices: 5552357--5552406 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
5552347 GAATATATAA
5552357 ATTTTTTTC-TTTTTCTTTTTTTCTC
1 ATTTTTTTCATTTTTCTTTTTTTCTC
5552382 ATTTTTTTCATTTTTCTTTTTTTCT
1 ATTTTTTTCATTTTTCTTTTTTTCT
5552407 TCAAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (26 bp):
ATTTTTTTCATTTTTCTTTTTTTCTC
Found at i:5552604 original size:38 final size:37
Alignment explanation
Indices: 5552534--5552605 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 37
5552524 TAACAATATG
* * *
5552534 AAAAATAACATAAATATGATATTTGTAAAATATATTT
1 AAAAATAACATAAAAATGATATGTATAAAATATATTT
* *
5552571 AAAATATAATATAAAAATGATATGTATATAATATA
1 AAAA-ATAACATAAAAATGATATGTATAAAATATA
5552606 AATGCAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 4 0.14
38 25 0.86
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (37 bp):
AAAAATAACATAAAAATGATATGTATAAAATATATTT
Found at i:5552615 original size:22 final size:20
Alignment explanation
Indices: 5552574--5552621 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
5552564 TATATTTAAA
*
5552574 ATATAATATAAAAATGATATGT
1 ATATAATAT--AAATGATATAT
5552596 ATATAATATAAATGCA-ATAT
1 ATATAATATAAATG-ATATAT
5552616 ATATAA
1 ATATAA
5552622 AAATATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 14 0.58
21 1 0.04
22 9 0.38
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (20 bp):
ATATAATATAAATGATATAT
Found at i:5552681 original size:22 final size:22
Alignment explanation
Indices: 5552627--5552684 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
5552617 TATAAAAATA
5552627 TAAATA-AAATAAAATAAATTAT
1 TAAATATAAA-AAAATAAATTAT
*
5552649 TAATATATAAAAATATAATATT-T
1 TAA-ATATAAAAAAATAA-ATTAT
5552672 TAAATATAAAAAA
1 TAAATATAAAAAA
5552685 TTAACATGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 12 0.39
23 13 0.42
24 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAATATAAAAAAATAAATTAT
Found at i:5552688 original size:37 final size:37
Alignment explanation
Indices: 5552614--5552688 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
5552604 TAAATGCAAT
**
5552614 ATATATAAAAATATAAATAAAATAAAATAAATTATTA
1 ATATATAAAAATATAAATAAAATAAAATAAAAAATTA
***
5552651 ATATATAAAAATAT-AATATTTTAAATATAAAAAATTA
1 ATATATAAAAATATAAATAAAATAAA-ATAAAAAATTA
5552688 A
1 A
5552689 CATGTATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 8 0.25
37 24 0.75
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (37 bp):
ATATATAAAAATATAAATAAAATAAAATAAAAAATTA
Found at i:5552698 original size:23 final size:21
Alignment explanation
Indices: 5552625--5552699 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 21
5552615 TATATAAAAA
*
5552625 TATAAATA-AAATAAAATAAAT
1 TATAAATATAAA-AAATTAAAT
*
5552646 TATTAATATATAAAAATATAATAT
1 TATAAATATA-AAAAAT-TAA-AT
*
5552670 TTTAAATATAAAAAATTAACAT
1 TATAAATATAAAAAATTAA-AT
5552692 GTATAAAT
1 -TATAAAT
5552700 TTTTTTTTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
21 7 0.16
22 9 0.21
23 17 0.40
24 10 0.23
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (21 bp):
TATAAATATAAAAAATTAAAT
Found at i:5553517 original size:2 final size:2
Alignment explanation
Indices: 5553510--5553539 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5553500 CATTGAAAAT
5553510 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
5553540 GAAAAAAAAT
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:5554942 original size:14 final size:14
Alignment explanation
Indices: 5554925--5554970 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 14
5554915 TTTTATTTTT
5554925 ATTTTTATTTTAAA
1 ATTTTTATTTTAAA
*
5554939 ATTTTTATTTATATA
1 ATTTTTATTT-TAAA
5554954 ATTTTATATTTTAAA
1 ATTTT-TATTTTAAA
5554969 AT
1 AT
5554971 ATGATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 10 0.36
15 13 0.46
16 5 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTTTATTTTAAA
Found at i:5554961 original size:8 final size:7
Alignment explanation
Indices: 5554909--5554966 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 7
5554899 TCAACTTATA
5554909 TATATTT
1 TATATTT
*
5554916 TTTATTT
1 TATATTT
5554923 T-TATTT
1 TATATTT
5554929 T-TATTT
1 TATATTT
*
5554935 TAAAATTT
1 T-ATATTT
5554943 T-TATTT
1 TATATTT
5554949 ATATAATTT
1 -TAT-ATTT
5554958 TATATTT
1 TATATTT
5554965 TA
1 TA
5554967 AAATATGATA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
6 16 0.37
7 14 0.33
8 9 0.21
9 4 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TATATTT
Found at i:5554964 original size:30 final size:26
Alignment explanation
Indices: 5554914--5554970 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 26
5554904 TTATATATAT
5554914 TTTTTATTTTTATTTTTATTTTAAAA
1 TTTTTATTTTTATTTTTATTTTAAAA
5554940 TTTTTATTTATATAATTTTATATTTTAAAA
1 TTTTTATTT-T-T-ATTTT-TATTTTAAAA
5554970 T
1 T
5554971 ATGATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 9 0.33
27 1 0.04
28 1 0.04
29 5 0.19
30 11 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTTATTTTTATTTTTATTTTAAAA
Found at i:5554980 original size:29 final size:28
Alignment explanation
Indices: 5554925--5554985 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
5554915 TTTTATTTTT
* * *
5554925 ATTTTTATTTTAAAATTTTTATTTATATA
1 ATTTTTATTTTAAAATTATGATATATA-A
5554954 ATTTTATATTTTAAAA-TATGATATATAA
1 ATTTT-TATTTTAAAATTATGATATATAA
5554982 ATTT
1 ATTT
5554986 AATTTGAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.18
29 13 0.46
30 10 0.36
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
ATTTTTATTTTAAAATTATGATATATAA
Found at i:5555685 original size:26 final size:24
Alignment explanation
Indices: 5555650--5555704 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
5555640 AATTTATATA
* *
5555650 ATATTTATAAATATTTTTATGTTTGT
1 ATATTCAT-AATATATTTAT-TTTGT
*
5555676 ATATTCATAATATATTTATTTTTT
1 ATATTCATAATATATTTATTTTGT
5555700 ATATT
1 ATATT
5555705 GTATTTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 9 0.35
25 10 0.38
26 7 0.27
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (24 bp):
ATATTCATAATATATTTATTTTGT
Found at i:5556154 original size:20 final size:20
Alignment explanation
Indices: 5556129--5556186 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
5556119 ATAATTAATA
5556129 TTATGTATATTTTGA-CATAT
1 TTATGTATATTTT-ATCATAT
*
5556149 TTATGTAT-TTATATCATAT
1 TTATGTATATTTTATCATAT
*
5556168 TTATG-ATATTTTTTCATAT
1 TTATGTATATTTTATCATAT
5556187 AGTATTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 3 0.09
19 22 0.67
20 8 0.24
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.59
Consensus pattern (20 bp):
TTATGTATATTTTATCATAT
Found at i:5556696 original size:22 final size:21
Alignment explanation
Indices: 5556656--5556706 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
5556646 AATAATAATT
5556656 ATTTAATATAATTTAATTTAA
1 ATTTAATATAATTTAATTTAA
5556677 ATTT-ATATAATTATTAATTT-A
1 ATTTAATATAA-T-TTAATTTAA
*
5556698 ATTAAATAT
1 ATTTAATAT
5556707 GTGAAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 9 0.35
22 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAATATAATTTAATTTAA
Found at i:5559420 original size:11 final size:11
Alignment explanation
Indices: 5559400--5559437 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5559390 TATTTTTTAA
5559400 TAAATAAAAAT
1 TAAATAAAAAT
*
5559411 TAATTAAAAA-
1 TAAATAAAAAT
5559421 TAAATAAAAAT
1 TAAATAAAAAT
*
5559432 AAAATA
1 TAAATA
5559438 TATGATAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
TAAATAAAAAT
Found at i:5559428 original size:10 final size:10
Alignment explanation
Indices: 5559398--5559434 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
5559388 TATATTTTTT
5559398 AATAAATAAA
1 AATAAATAAA
*
5559408 AATTAATTAAA
1 AA-TAAATAAA
5559419 AATAAATAAA
1 AATAAATAAA
5559429 AATAAA
1 AATAAA
5559435 ATATATGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AATAAATAAA
Found at i:5562201 original size:32 final size:32
Alignment explanation
Indices: 5562164--5562234 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
5562154 ACGGCTCTTG
* *
5562164 TTTAAAACAGTCCATAGTAAGAATAATTTTTA
1 TTTAAAACAATCCATAGTAAAAATAATTTTTA
* ** **
5562196 TTTAAAATAATTTATTTTAAAAATAATTTTTA
1 TTTAAAACAATCCATAGTAAAAATAATTTTTA
5562228 TTTAAAA
1 TTTAAAA
5562235 TAATTTTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (32 bp):
TTTAAAACAATCCATAGTAAAAATAATTTTTA
Found at i:5562235 original size:32 final size:32
Alignment explanation
Indices: 5562185--5562278 Score: 140
Period size: 32 Copynumber: 3.0 Consensus size: 32
5562175 CCATAGTAAG
5562185 AATAATTTTTATTTAAAATAATTTATTTTAAA
1 AATAATTTTTATTTAAAATAATTTATTTTAAA
*
5562217 AATAATTTTTATTTAAAATAATTT-TTTTTAA
1 AATAATTTTTATTTAAAATAATTTATTTTAAA
* *
5562248 AATAA-TTTT-TTTAAAATAACTCATTTTAAA
1 AATAATTTTTATTTAAAATAATTTATTTTAAA
5562278 A
1 A
5562279 TTCTTTCATA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 11 0.19
32 24 0.42
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (32 bp):
AATAATTTTTATTTAAAATAATTTATTTTAAA
Found at i:5562279 original size:15 final size:15
Alignment explanation
Indices: 5562185--5562266 Score: 121
Period size: 16 Copynumber: 5.3 Consensus size: 15
5562175 CCATAGTAAG
5562185 AATAATTTTTATTTAA
1 AATAATTTTT-TTTAA
*
5562201 AATAATTTATTTTAAA
1 AATAATTT-TTTTTAA
5562217 AATAATTTTTATTTAA
1 AATAATTTTT-TTTAA
5562233 AATAATTTTTTTTAA
1 AATAATTTTTTTTAA
5562248 AATAA-TTTTTTTAA
1 AATAATTTTTTTTAA
5562262 AATAA
1 AATAA
5562267 CTCATTTTAA
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
14 14 0.23
15 12 0.19
16 34 0.55
17 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATAATTTTTTTTAA
Found at i:5566104 original size:28 final size:29
Alignment explanation
Indices: 5566072--5566150 Score: 112
Period size: 28 Copynumber: 2.9 Consensus size: 29
5566062 CAAATGACAC
5566072 CCTTTGTATTTGTCAAATATGGTGGTT-T
1 CCTTTGTATTTGTCAAATATGGTGGTTAT
5566100 CCTTTGTATTTGTCAAATATGGTGGTTAT
1 CCTTTGTATTTGTCAAATATGGTGGTTAT
* *
5566129 --TTT-TATTTGTAAAAAATGGTGG
1 CCTTTGTATTTGTCAAATATGGTGG
5566151 CTTGTTGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
26 17 0.35
27 3 0.06
28 27 0.56
29 1 0.02
ACGTcount: A:0.23, C:0.08, G:0.22, T:0.48
Consensus pattern (29 bp):
CCTTTGTATTTGTCAAATATGGTGGTTAT
Found at i:5567655 original size:14 final size:14
Alignment explanation
Indices: 5567636--5567665 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5567626 ATTCATATAA
5567636 AAAATATTTGTGTC
1 AAAATATTTGTGTC
*
5567650 AAAATATTTTTGTC
1 AAAATATTTGTGTC
5567664 AA
1 AA
5567666 GTACTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (14 bp):
AAAATATTTGTGTC
Found at i:5568140 original size:13 final size:13
Alignment explanation
Indices: 5568122--5568147 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5568112 ATTTTTACAA
5568122 TACTAGATATTTG
1 TACTAGATATTTG
5568135 TACTAGATATTTG
1 TACTAGATATTTG
5568148 CTGGTCCACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
TACTAGATATTTG
Found at i:5568752 original size:155 final size:154
Alignment explanation
Indices: 5568577--5568893 Score: 465
Period size: 155 Copynumber: 2.1 Consensus size: 154
5568567 CTTAATACAA
*
5568577 TTATACATTCATATTGTATTATTATTATTTTTTGTATTATATCTAATTTTAATCATTTTTCATAC
1 TTATACATTCATATTGTATTACTATTATTTTTTGTATTATATCTAATTTTAATCATTTTTCATAC
* * * *
5568642 TCAAGTTGTATTTAAAATTGTCAAATCTAATT-GACACTATACAAATTACTTGTCACATAGTAAG
66 TCAAGTCGTATTTAAAATTATCAAATCTAATTAG-CACTAT-CAAATTACTCGTCACATAGCAAG
*
5568706 CAATTATAAGTTTTCTTTCTAGGTTT
129 CAATTATAAGTTTTCTTTCGAGGTTT
* *
5568732 TTATACATTCGTATTGTATTACTATTATTTTTTGTATTATATCTAATTTTAATCATTTTTCATGC
1 TTATACATTCATATTGTATTACTATTATTTTTTGTATTATATCTAATTTTAATCATTTTTCATAC
* * * * * * * *
5568797 TTAAGTCGTATTTGAAATTATTAGATCTAATTAGCATTATTAAATTGCTCGTCACGTAGCAAGCA
66 TCAAGTCGTATTTAAAATTATCAAATCTAATTAGCACTATCAAATTACTCGTCACATAGCAAGCA
5568862 ATTATAAGTTTTCTTTCGAGGTTT
131 ATTATAAGTTTTCTTTCGAGGTTT
5568886 TTATACAT
1 TTATACAT
5568894 AATTATGTGT
Statistics
Matches: 145, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
154 51 0.35
155 93 0.64
156 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (154 bp):
TTATACATTCATATTGTATTACTATTATTTTTTGTATTATATCTAATTTTAATCATTTTTCATAC
TCAAGTCGTATTTAAAATTATCAAATCTAATTAGCACTATCAAATTACTCGTCACATAGCAAGCA
ATTATAAGTTTTCTTTCGAGGTTT
Found at i:5569735 original size:33 final size:33
Alignment explanation
Indices: 5569692--5569767 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 33
5569682 TTTATATCAT
* *
5569692 AAATATATTAAGATATAAAAAATAAATATTTTA-A
1 AAATA-ATTAA-ATATAAAAAATAAAAATATTATA
* * *
5569726 AAATAATTAATTATAAAAATTAAAAATATTATT
1 AAATAATTAAATATAAAAAATAAAAATATTATA
5569759 AAATAATTA
1 AAATAATTA
5569768 CCTATAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 17 0.47
33 14 0.39
34 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (33 bp):
AAATAATTAAATATAAAAAATAAAAATATTATA
Found at i:5569926 original size:2 final size:2
Alignment explanation
Indices: 5569919--5569950 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5569909 TTTATTTTGG
5569919 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
5569951 CTATCTTAGG
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):
TA
Found at i:5570700 original size:22 final size:20
Alignment explanation
Indices: 5570647--5570700 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
5570637 AAAGGTTAGT
5570647 TTTTTTTTATTTTATTTAATA
1 TTTTTTTT-TTTTATTTAATA
*
5570668 TTTTGTATTTTTTTATTTGGATA
1 TTTT-T-TTTTTTTATTT-AATA
*
5570691 TTTATTTTTT
1 TTTTTTTTTT
5570701 CAAGTTGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 9 0.32
22 10 0.36
23 9 0.32
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.76
Consensus pattern (20 bp):
TTTTTTTTTTTTATTTAATA
Found at i:5572231 original size:32 final size:33
Alignment explanation
Indices: 5572195--5572260 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
5572185 TTAATACAAG
*
5572195 GGGCTGTTGTT-GTCCGATTTAACCGCATAAGT
1 GGGCTGTTGTTGGTCCGATTTAACCACATAAGT
*
5572227 GGGCTGTTGTTGGTCTGATTTAACCACATAAGT
1 GGGCTGTTGTTGGTCCGATTTAACCACATAAGT
5572260 G
1 G
5572261 CACGTATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 11 0.35
33 20 0.65
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.35
Consensus pattern (33 bp):
GGGCTGTTGTTGGTCCGATTTAACCACATAAGT
Found at i:5577438 original size:7 final size:7
Alignment explanation
Indices: 5577426--5577455 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5577416 ATATATTAAT
5577426 ATCAATA
1 ATCAATA
5577433 ATCAATA
1 ATCAATA
5577440 ATCAATA
1 ATCAATA
5577447 ATCAATA
1 ATCAATA
5577454 AT
1 AT
5577456 ATATAAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (7 bp):
ATCAATA
Found at i:5579742 original size:45 final size:45
Alignment explanation
Indices: 5579691--5579792 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
5579681 TTTTTCCTCC
*
5579691 TTATAAATAAATACAA-AAATTATAA-TATAATAATTTGAATTAATT
1 TTATAAA-AAATA-AATAAATTATAAGAATAATAATTTGAATTAATT
* * * * *
5579736 TTATAAAAATTAAATAATTTATAAGAATATTTATTTGCATTAATT
1 TTATAAAAAATAAATAAATTATAAGAATAATAATTTGAATTAATT
5579781 TTATAAAAAATA
1 TTATAAAAAATA
5579793 TTTAAAGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
43 2 0.04
44 12 0.25
45 34 0.71
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (45 bp):
TTATAAAAAATAAATAAATTATAAGAATAATAATTTGAATTAATT
Found at i:5580197 original size:24 final size:23
Alignment explanation
Indices: 5580169--5580215 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
5580159 AAAAAACTCA
5580169 AAATATTTTT-ATAAAATTAATTAT
1 AAATATTTTTAAT-AAATT-ATTAT
5580193 AAATATTTTTAATAAATTATTAT
1 AAATATTTTTAATAAATTATTAT
5580216 TTTTTATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.23
24 15 0.68
25 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATATTTTTAATAAATTATTAT
Found at i:5580372 original size:15 final size:16
Alignment explanation
Indices: 5580348--5580380 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5580338 AATATTTTAC
5580348 ATTTTATAG-TAATTT
1 ATTTTATAGTTAATTT
*
5580363 ATTTTTTAGTTAATTT
1 ATTTTATAGTTAATTT
5580379 AT
1 AT
5580381 AAAGATGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
ATTTTATAGTTAATTT
Found at i:5581085 original size:29 final size:31
Alignment explanation
Indices: 5581038--5581100 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
5581028 ATCGGGTTAC
5581038 AATTTAATTTTTTATTTTAAATT-AT-TTAA
1 AATTTAATTTTTTATTTTAAATTAATATTAA
* *
5581067 AATTTTATTTTATTA-TTTATATTAATATTAA
1 AATTTAATTTT-TTATTTTAAATTAATATTAA
5581098 AAT
1 AAT
5581101 ATGTATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 17 0.59
30 5 0.17
31 7 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
AATTTAATTTTTTATTTTAAATTAATATTAA
Found at i:5581160 original size:5 final size:5
Alignment explanation
Indices: 5581150--5581180 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
5581140 TATTAAAAAA
*
5581150 TAAAT TAAAT TAAAT TAAAT TAATT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T
5581181 TATAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
TAAAT
Found at i:5581349 original size:15 final size:15
Alignment explanation
Indices: 5581249--5581349 Score: 69
Period size: 15 Copynumber: 6.6 Consensus size: 15
5581239 TTTAAATTGT
5581249 ATTTAAAATTAATTAA
1 ATTTAAAA-TAATTAA
*
5581265 ATTTTAAATAATTTAA
1 ATTTAAAATAA-TTAA
*
5581281 ATTAAAAATAATTAA
1 ATTTAAAATAATTAA
* ** *
5581296 ATTTATAATGTTTGA
1 ATTTAAAATAATTAA
** *
5581311 A-CCAAGATAATTAAA
1 ATTTAAAATAATT-AA
* *
5581326 ATCTAAAATAATTTA
1 ATTTAAAATAATTAA
5581341 ATTTAAAAT
1 ATTTAAAAT
5581350 TATCAAAATA
Statistics
Matches: 63, Mismatches: 19, Indels: 7
0.71 0.21 0.08
Matches are distributed among these distances:
14 5 0.08
15 29 0.46
16 29 0.46
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
ATTTAAAATAATTAA
Found at i:5582935 original size:16 final size:14
Alignment explanation
Indices: 5582913--5582950 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
5582903 AATATACTTA
5582913 ATTTAAATTTATATT
1 ATTTAAATTTA-ATT
5582928 ATTTTAAA-TTAATT
1 A-TTTAAATTTAATT
5582942 ATTTAAATT
1 ATTTAAATT
5582951 ATTTCAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 6 0.29
14 5 0.24
15 4 0.19
16 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTAAATTTAATT
Found at i:5582995 original size:16 final size:16
Alignment explanation
Indices: 5582976--5583006 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5582966 TAATTTAATT
5582976 TTAAAATATTTTATAC
1 TTAAAATATTTTATAC
*
5582992 TTAAATTATTTTATA
1 TTAAAATATTTTATA
5583007 TTATTGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAAATATTTTATAC
Found at i:5583049 original size:6 final size:5
Alignment explanation
Indices: 5583022--5583060 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
5583012 GATTTTTATT
5583022 ATTAA ATTAA ATTAA ATTAA ATTTAA ATTTAA A-TAA ATT
1 ATTAA ATTAA ATTAA ATTAA A-TTAA A-TTAA ATTAA ATT
5583061 GATTAACTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 17 0.53
6 11 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
ATTAA
Found at i:5583053 original size:27 final size:27
Alignment explanation
Indices: 5583023--5583082 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
5583013 ATTTTTATTA
5583023 TTAAATTAAATTAAATTAA-ATTTAAAT
1 TTAAATTAAATT-AATTAACATTTAAAT
* *
5583050 TTAAA-TAAATTGATTAACTTTTTAAAT
1 TTAAATTAAATTAATTAAC-ATTTAAAT
5583077 TTAAAT
1 TTAAAT
5583083 AAAAATGGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 5 0.18
26 6 0.21
27 17 0.61
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
TTAAATTAAATTAATTAACATTTAAAT
Found at i:5583373 original size:2 final size:2
Alignment explanation
Indices: 5583368--5583392 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5583358 AAAGGCAAGC
5583368 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
5583393 GGATGATTTC
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:5584711 original size:21 final size:20
Alignment explanation
Indices: 5584685--5584724 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
5584675 TATTTTGATA
*
5584685 TTTTTAATTTAATCATAATTT
1 TTTTTAATTCAATC-TAATTT
5584706 TTTTTAATTCAATCTAATT
1 TTTTTAATTCAATCTAATT
5584725 AACTTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTAATTCAATCTAATTT
Found at i:5587660 original size:2 final size:2
Alignment explanation
Indices: 5587653--5587686 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5587643 GAGATACTAC
*
5587653 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5587687 TACATCAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5588663 original size:30 final size:33
Alignment explanation
Indices: 5588627--5588699 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 33
5588617 AAAAATTTAT
*
5588627 TATATATTTAATTT-TTAA-A-TAATTTTAAAA
1 TATATATTTAATTTATTAATATTAATTATAAAA
*
5588657 TATATA-TTATTTTATTAATATTAATTATAAAA
1 TATATATTTAATTTATTAATATTAATTATAAAA
*
5588689 TTTAATATTTA
1 TAT-ATATTTA
5588700 TTCTGTCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
29 6 0.17
30 10 0.29
31 1 0.03
32 12 0.34
33 3 0.09
34 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
TATATATTTAATTTATTAATATTAATTATAAAA
Found at i:5593574 original size:15 final size:15
Alignment explanation
Indices: 5593554--5593590 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
5593544 CAAGTATTTT
5593554 CTATCTTTCATCATA
1 CTATCTTTCATCATA
5593569 CTATCTTTCATCATA
1 CTATCTTTCATCATA
*
5593584 CTCTCTT
1 CTATCTT
5593591 AATTGCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.49
Consensus pattern (15 bp):
CTATCTTTCATCATA
Done.