Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015251.1 Kokia drynarioides strain JFW-HI SEQ_130296, whole genome shotgun sequence
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: 620055
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 406 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:3287 original size:28 final size:31
Alignment explanation
Indices: 3256--3313 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
3246 GCAATTCGAT
3256 ACAT-AAACTTG-ATT-TAGTGTAAT-TATAC
1 ACATAAAACTTGAATTGTAGT-TAATATATAC
3284 ACATAAAACTTGAATTGTAGTTAATATATA
1 ACATAAAACTTGAATTGTAGTTAATATATA
3314 TGCATGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 4 0.15
29 7 0.27
30 7 0.27
31 8 0.31
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (31 bp):
ACATAAAACTTGAATTGTAGTTAATATATAC
Found at i:3910 original size:12 final size:12
Alignment explanation
Indices: 3893--3933 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
3883 ATTAAAAAAA
3893 TTCAAAATAATT
1 TTCAAAATAATT
3905 TTCAAAA-AA-T
1 TTCAAAATAATT
3915 TT-AAAATAATT
1 TTCAAAATAATT
*
3926 TTTAAAAT
1 TTCAAAAT
3934 TCAAAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 4 0.15
10 5 0.19
11 5 0.19
12 12 0.46
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (12 bp):
TTCAAAATAATT
Found at i:3913 original size:21 final size:20
Alignment explanation
Indices: 3887--3951 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 20
3877 ACAAAAATTA
3887 AAAAAATTCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
*
3907 CAAAAAATTTAAAATAATTTT
1 -AAAAAATTCAAAATAATTTT
*
3928 -TAAAATTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTT-T
3947 AAAAA
1 AAAAA
3952 TTTAAATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
18 4 0.11
19 12 0.32
20 3 0.08
21 19 0.50
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:3951 original size:19 final size:19
Alignment explanation
Indices: 3888--3953 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 19
3878 CAAAAATTAA
3888 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
*
3907 CAAAAAATTTAAAATAATTTT
1 --AAAAATTCAAAATAATTTT
*
3928 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
3947 AAAAATT
1 AAAAATT
3954 TAAATTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.10
19 18 0.45
21 18 0.45
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:3958 original size:18 final size:18
Alignment explanation
Indices: 3909--3964 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
3899 ATAATTTTCA
3909 AAAAATTTAAAATAATTT-T
1 AAAAATTT-AAAT-ATTTAT
* *
3928 TAAAATTCAAAATATTTAT
1 AAAAATT-TAAATATTTAT
3947 AAAAATTTAAAT-TTTAT
1 AAAAATTTAAATATTTAT
3964 A
1 A
3965 TTTAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
17 6 0.19
18 8 0.26
19 17 0.55
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAAATTTAAATATTTAT
Found at i:3990 original size:18 final size:18
Alignment explanation
Indices: 3967--4018 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
3957 ATTTTATATT
* *
3967 TAAAAAATATACAAATTC
1 TAAAAAATATAAAAATCC
3985 TAAAAAA-ATAAAAATCC
1 TAAAAAATATAAAAATCC
4002 TAAAGAATATATAAAAA
1 TAAA-AA-ATATAAAAA
4019 ATTTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 12 0.41
18 9 0.31
19 1 0.03
20 7 0.24
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.23
Consensus pattern (18 bp):
TAAAAAATATAAAAATCC
Found at i:7247 original size:20 final size:21
Alignment explanation
Indices: 7210--7268 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
7200 GATTAGTATG
7210 GTTTATATTAAG-TGTAAATA-T
1 GTTTA-ATTAAGAT-TAAATAGT
7231 GTTTAATTAAGATTAAA-AGT
1 GTTTAATTAAGATTAAATAGT
* *
7251 GATTAATTAAGACTAAAT
1 GTTTAATTAAGATTAAAT
7269 GATGAAAGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 1 0.03
20 26 0.79
21 6 0.18
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.41
Consensus pattern (21 bp):
GTTTAATTAAGATTAAATAGT
Found at i:9035 original size:21 final size:21
Alignment explanation
Indices: 9009--9062 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
8999 GGAGTTTTTA
*
9009 GTATCGGTAGATG-CATCACTT
1 GTATCGGTAGAAGTCAT-ACTT
* *
9030 GTATCGATAGAAGTTATACTT
1 GTATCGGTAGAAGTCATACTT
9051 GTATCGGTAGAA
1 GTATCGGTAGAA
9063 CTAGCACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACTT
Found at i:10119 original size:214 final size:214
Alignment explanation
Indices: 9750--10158 Score: 800
Period size: 214 Copynumber: 1.9 Consensus size: 214
9740 AGGCCTTACA
9750 ATGGTTGGGATTTATGCTTAACTACATATTCTTGACAGCTCGTGTGAGTAGCACCGTTAGGGGAC
1 ATGGTTGGGATTTATGCTTAACTACATATTCTTGACAGCTCGTGTGAGTAGCACCGTTAGGGGAC
*
9815 AGTTTATAAACATACATCATATCGATGGCTGGGGTACTGCATATGTTGCGAGTCCTCGATAGCTC
66 AGTTTATAAACATACATCATATCGATGGCTGGGGTACTGCATATGTTGCGAGTCCTCGACAGCTC
9880 TTGTGAGCAGCATCGAATACTGGTAACCAAAAAAAAGCTATAGACAAAAAAGTTGAAATGCTTAA
131 TTGTGAGCAGCATCGAATACTGGTAACCAAAAAAAAGCTATAGACAAAAAAGTTGAAATGCTTAA
9945 CTACATATTCTTGACAACG
196 CTACATATTCTTGACAACG
9964 ATGGTTGGGATTTATGCTTAACTACATATTCTTGACAGCTCGTGTGAGTAGCACCGTTAGGGGAC
1 ATGGTTGGGATTTATGCTTAACTACATATTCTTGACAGCTCGTGTGAGTAGCACCGTTAGGGGAC
*
10029 AGTTTATAAACATACATCATATCGATGGCTGGGGTACTGCATATGTTGTGAGTCCTCGACAGCTC
66 AGTTTATAAACATACATCATATCGATGGCTGGGGTACTGCATATGTTGCGAGTCCTCGACAGCTC
10094 TTGTGAGCAGCATCGAATACTGGTAACCAAAAAAAAGCTATAGACAAAAAAGTTGAAATGCTTAA
131 TTGTGAGCAGCATCGAATACTGGTAACCAAAAAAAAGCTATAGACAAAAAAGTTGAAATGCTTAA
10159 TATGGCTTGA
Statistics
Matches: 193, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
214 193 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (214 bp):
ATGGTTGGGATTTATGCTTAACTACATATTCTTGACAGCTCGTGTGAGTAGCACCGTTAGGGGAC
AGTTTATAAACATACATCATATCGATGGCTGGGGTACTGCATATGTTGCGAGTCCTCGACAGCTC
TTGTGAGCAGCATCGAATACTGGTAACCAAAAAAAAGCTATAGACAAAAAAGTTGAAATGCTTAA
CTACATATTCTTGACAACG
Found at i:10733 original size:24 final size:26
Alignment explanation
Indices: 10698--10748 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
10688 GGTAATTGTA
*
10698 TAGAAGGTATCGGTAGT-TTTGTACT
1 TAGAAGGTATCGGTAGTCTATGTACT
10723 TAGAA-GTATCGGTAGTCTATGTACT
1 TAGAAGGTATCGGTAGTCTATGTACT
10748 T
1 T
10749 GTATTAGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.39
Consensus pattern (26 bp):
TAGAAGGTATCGGTAGTCTATGTACT
Found at i:11389 original size:18 final size:18
Alignment explanation
Indices: 11367--11409 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
11357 TAAATTCATA
*
11367 ATCATAATCATATTCTATT
1 ATCATAAT-ATATTCAATT
11386 -TCATAAATATATTCAATT
1 ATCAT-AATATATTCAATT
11404 ATCATA
1 ATCATA
11410 CTTGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (18 bp):
ATCATAATATATTCAATT
Found at i:13925 original size:19 final size:19
Alignment explanation
Indices: 13903--13973 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
13893 AAAATTACAA
13903 AAAAAATCAAAATAATTTT
1 AAAAAATCAAAATAATTTT
13922 AAAAAATTCAAAATAAATTTT
1 AAAAAA-TCAAAAT-AATTTT
*
13943 -AAAAATTAAAAT-ATTTAT
1 AAAAAATCAAAATAATTT-T
*
13961 AAAAATTCAAAAT
1 AAAAAATCAAAAT
13974 TTATATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 22 0.49
20 12 0.27
21 6 0.13
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAAATCAAAATAATTTT
Found at i:13948 original size:20 final size:19
Alignment explanation
Indices: 13903--13973 Score: 92
Period size: 20 Copynumber: 3.7 Consensus size: 19
13893 AAAATTACAA
*
13903 AAAAAATCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
13922 AAAAAATTCAAAATAAATTTT
1 -AAAAATTCAAAAT-AATTTT
13943 AAAAATT-AAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
13961 AAAAATTCAAAAT
1 AAAAATTCAAAAT
13974 TTATATTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
17 4 0.09
18 8 0.17
19 10 0.21
20 19 0.40
21 6 0.13
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:13972 original size:25 final size:24
Alignment explanation
Indices: 13944--13991 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
13934 ATAAATTTTA
13944 AAAATTAAAATATTTATAAAAATTC
1 AAAATTAAAATATTTA-AAAAATTC
* * *
13969 AAAATTTATATTTTTAAAAAATT
1 AAAATTAAAATATTTAAAAAATT
13992 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AAAATTAAAATATTTAAAAAATTC
Found at i:40013 original size:17 final size:17
Alignment explanation
Indices: 39991--40025 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
39981 ATTCAACCTT
39991 CTCTATTTTCCCATAAC
1 CTCTATTTTCCCATAAC
40008 CTCTATTTTCCCATAAC
1 CTCTATTTTCCCATAAC
40025 C
1 C
40026 ATGGCAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.37, G:0.00, T:0.40
Consensus pattern (17 bp):
CTCTATTTTCCCATAAC
Found at i:41326 original size:18 final size:18
Alignment explanation
Indices: 41303--41347 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
41293 GTTTTTAAGT
41303 TATTATTGTTT-TACATTA
1 TATTATT-TTTATACATTA
*
41321 TATTATTTTTATATATTA
1 TATTATTTTTATACATTA
*
41339 TGTTATTTT
1 TATTATTTT
41348 GTAATACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (18 bp):
TATTATTTTTATACATTA
Found at i:41507 original size:32 final size:33
Alignment explanation
Indices: 41431--41507 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 33
41421 ATTATACATA
* ** *
41431 AAATTTTAATAAATTAAAAATTCTATAAAATTATT
1 AAATTTT--TAAATGAAAAATAATATAAAAATATT
*
41466 AAA-TATTAAATGAAAAATAATATAAAAATA-T
1 AAATTTTTAAATGAAAAATAATATAAAAATATT
41497 AAATTTTTAAA
1 AAATTTTTAAA
41508 AATTTAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
31 4 0.11
32 26 0.74
34 2 0.06
35 3 0.09
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (33 bp):
AAATTTTTAAATGAAAAATAATATAAAAATATT
Found at i:52707 original size:15 final size:14
Alignment explanation
Indices: 52677--52703 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52667 ATGTCTTTCT
52677 TTTTTTAATATTTA
1 TTTTTTAATATTTA
52691 TTTTTTAATATTT
1 TTTTTTAATATTT
52704 TATTATAGTC
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTAATATTTA
Found at i:57324 original size:97 final size:97
Alignment explanation
Indices: 57131--57307 Score: 223
Period size: 96 Copynumber: 1.8 Consensus size: 97
57121 AATTTTGGAA
* * * *
57131 AAGGATATTTGATTATCTCGATTTGAAGAAAAAGTCGCACCCAGTAAGTTTACGTACAAATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAAGTCGCACCCAATAAGTTAACGGACAAATTTTC
* * *
57196 AGAATCTGAAATGAGAAACATTGCCTAGATTT
66 AAAATCTGAAATAAAAAACATTGCCTAGATTT
* ** * *
57228 AAGGATATTCGATTATTTCGATTTGAAGAAAAA-TCGTGCCTAATAAGTTAAGGGACAAATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAAGTCGCACCCAATAAGTTAACGGACAAATTTTC
57292 AAAAT-TCGAAATAAAA
66 AAAATCT-GAAATAAAA
57308 GAATATTGTC
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
95 1 0.01
96 35 0.52
97 31 0.46
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAAGTCGCACCCAATAAGTTAACGGACAAATTTTC
AAAATCTGAAATAAAAAACATTGCCTAGATTT
Found at i:57574 original size:29 final size:29
Alignment explanation
Indices: 57542--57608 Score: 66
Period size: 28 Copynumber: 2.3 Consensus size: 29
57532 AAAATGAGAC
*
57542 TTTTTGGATACCCGGGAGCAAAATGGTAA
1 TTTTTGGATACACGGGAGCAAAATGGTAA
* * *
57571 -TTTTGGACT-CATGGGGGCAAAATGGTCA
1 TTTTTGGA-TACACGGGAGCAAAATGGTAA
*
57599 TTTTGGGATA
1 TTTTTGGATA
57609 GTTTGGGGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
28 23 0.77
29 7 0.23
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.31
Consensus pattern (29 bp):
TTTTTGGATACACGGGAGCAAAATGGTAA
Found at i:57717 original size:29 final size:27
Alignment explanation
Indices: 57685--57779 Score: 84
Period size: 29 Copynumber: 3.3 Consensus size: 27
57675 TCAAAAACGA
*
57685 AATTTTTGGACATTCAGGGGTAAAAGGGT
1 AATTTTTGGA-ATTC-GGGGTAAAATGGT
* *
57714 AATTTTTGAGAGTTTCGAGGTAAAAAATGG-
1 AATTTTTG-GA-ATTCGGGGT--AAAATGGT
57744 AATTTTTGGAAGTTCGGGGGTAAAATGGT
1 AATTTTTGGAA-TTC-GGGGTAAAATGGT
57773 AATTTTT
1 AATTTTT
57780 TTTGAAGTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
28 7 0.13
29 24 0.44
30 17 0.31
31 6 0.11
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (27 bp):
AATTTTTGGAATTCGGGGTAAAATGGT
Found at i:57766 original size:30 final size:29
Alignment explanation
Indices: 57685--57875 Score: 115
Period size: 30 Copynumber: 6.4 Consensus size: 29
57675 TCAAAAACGA
*
57685 AATTTTTGGACA-TTC-AGGGGT-AAAAGGG
1 AATTTTTGGA-AGTTCGA-GGGTAAAAATGG
57713 TAATTTTT-GAGAGTTTCGA-GGTAAAAAATGG
1 -AATTTTTGGA-AG-TTCGAGGGT-AAAAATGG
*
57744 AATTTTTGGAAGTTCGGGGGT-AAAATGG
1 AATTTTTGGAAGTTCGAGGGTAAAAATGG
* ** * *
57772 TAATTTTTTTTGAAGTTTTAGGGTCAAAATCTAG
1 -AA--TTTTTGGAAGTTCGAGGGT-AAAA-ATGG
* *
57806 ATTTTTTGGAAGTTCGAGGGTAAAAATGT
1 AATTTTTGGAAGTTCGAGGGTAAAAATGG
* * **
57835 AATTTTTAGAAGTTTCAAGGCCAAAAATGG
1 AATTTTTGGAAG-TTCGAGGGTAAAAATGG
57865 AATTTTTGGAA
1 AATTTTTGGAA
57876 AAGCCGAGGG
Statistics
Matches: 125, Mismatches: 23, Indels: 27
0.71 0.13 0.15
Matches are distributed among these distances:
28 10 0.08
29 27 0.22
30 42 0.34
31 40 0.32
33 4 0.03
34 2 0.02
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (29 bp):
AATTTTTGGAAGTTCGAGGGTAAAAATGG
Found at i:57787 original size:31 final size:31
Alignment explanation
Indices: 57746--57841 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
57736 AAAAATGGAA
*
57746 TTTTTGGAAGTTCGGGGGT-AAAATGGTAATT
1 TTTTTGGAAGTTCGAGGGTAAAAAT-GTAATT
* ** * *
57777 TTTTTTGAAGTTTTAGGGTCAAAATCTAGA-T
1 TTTTTGGAAGTTCGAGGGTAAAAATGTA-ATT
57808 TTTTTGGAAGTTCGAGGGTAAAAATGTAATT
1 TTTTTGGAAGTTCGAGGGTAAAAATGTAATT
57839 TTT
1 TTT
57842 AGAAGTTTCA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
30 1 0.02
31 45 0.87
32 6 0.12
ACGTcount: A:0.28, C:0.04, G:0.25, T:0.43
Consensus pattern (31 bp):
TTTTTGGAAGTTCGAGGGTAAAAATGTAATT
Found at i:59780 original size:6 final size:6
Alignment explanation
Indices: 59771--59879 Score: 84
Period size: 6 Copynumber: 18.7 Consensus size: 6
59761 TTTAATTGAT
* * *
59771 TTTAAA TTTAAG TTTAAA ATT--A TTTCAAA TTTAAA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* ** *
59817 TTT-AT TTTAAA TTTAAA TTTAAAA AATGAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
59865 -GTAAA TTTAAT TTTA
1 TTTAAA TTTAAA TTTA
59880 GAAATAAATC
Statistics
Matches: 79, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
4 3 0.04
5 12 0.15
6 56 0.71
7 8 0.10
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:59813 original size:11 final size:11
Alignment explanation
Indices: 59797--59874 Score: 66
Period size: 11 Copynumber: 6.7 Consensus size: 11
59787 AAATTATTTC
*
59797 AAATTTAAACT
1 AAATTTAAATT
59808 AAATTTAAATT
1 AAATTTAAATT
* *
59819 TATTTTAAATTT
1 AAATTTAAA-TT
*
59831 AAATTTAAAAAAT
1 AAATTT--AAATT
*
59844 GAATTTAAATTT
1 AAATTTAAA-TT
*
59856 AAATTTAAAGT
1 AAATTTAAATT
59867 AAATTTAA
1 AAATTTAA
59875 TTTTAGAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
11 29 0.55
12 15 0.28
13 6 0.11
14 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (11 bp):
AAATTTAAATT
Found at i:59874 original size:17 final size:17
Alignment explanation
Indices: 59773--59858 Score: 75
Period size: 17 Copynumber: 4.9 Consensus size: 17
59763 TAATTGATTT
*
59773 TAAATTTAAGTTTAAAA
1 TAAATTTAAATTTAAAA
* *
59790 T-TATTTCAAATTTAAAC
1 TAAATTT-AAATTTAAAA
***
59807 TAAATTTAAATTTATTT
1 TAAATTTAAATTTAAAA
59824 TAAATTTAAATTTAAAAAA
1 TAAATTTAAATTT--AAAA
*
59843 TGAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
59859 TTTAAAGTAA
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
16 4 0.07
17 33 0.61
18 4 0.07
19 13 0.24
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:61444 original size:14 final size:14
Alignment explanation
Indices: 61418--61444 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
61408 AAATTTGATC
61418 CTTAAATCTTGAAT
1 CTTAAATCTTGAAT
61432 CTTAAATCTTGAA
1 CTTAAATCTTGAA
61445 CTCTAGATTC
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:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (14 bp):
CTTAAATCTTGAAT
Found at i:67167 original size:38 final size:38
Alignment explanation
Indices: 67116--67191 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
67106 AGTTATTATG
67116 CTCGCATGTTTATCAGCATAAGTTTTGTATAATTTTCA
1 CTCGCATGTTTATCAGCATAAGTTTTGTATAATTTTCA
67154 CTCGCATGTTTATCAGCATAAGTTTTGTATAATTTTCA
1 CTCGCATGTTTATCAGCATAAGTTTTGTATAATTTTCA
67192 TTCTTTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (38 bp):
CTCGCATGTTTATCAGCATAAGTTTTGTATAATTTTCA
Found at i:69117 original size:4 final size:4
Alignment explanation
Indices: 69110--69136 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
69100 CTACAATATA
69110 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
69137 AGTTTTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:81309 original size:19 final size:18
Alignment explanation
Indices: 81287--81322 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
81277 AAGTTTATAT
*
81287 AATTTTTATATATCTTTTA
1 AATTTTTAAATAT-TTTTA
81306 AATTTTTAAATATTTTT
1 AATTTTTAAATATTTTT
81323 GTTGAGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
AATTTTTAAATATTTTTA
Found at i:82424 original size:10 final size:9
Alignment explanation
Indices: 82399--82423 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
82389 ATAAACGCAC
82399 AAAAAAATA
1 AAAAAAATA
82408 AAAAAAATA
1 AAAAAAATA
82417 AAAAAAA
1 AAAAAAA
82424 AATAGCAAAC
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:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:85365 original size:30 final size:28
Alignment explanation
Indices: 85303--85368 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
85293 CAGTAAATTG
*
85303 AAAATTTAGTCTTATACTTTTATTTTTA
1 AAAATTTAGTCTTATACTTTTAATTTTA
*
85331 AAAATTTAGTCCTTTTACTTTTTAGATTTT-
1 AAAATTTAGT-CTTATAC-TTTTA-ATTTTA
85361 AAAATTTA
1 AAAATTTA
85369 AGTTCAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 10 0.30
29 6 0.18
30 13 0.39
31 4 0.12
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.55
Consensus pattern (28 bp):
AAAATTTAGTCTTATACTTTTAATTTTA
Found at i:86061 original size:18 final size:16
Alignment explanation
Indices: 86029--86072 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
86019 ATGGAATGAG
86029 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
86045 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
86059 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
86073 ATCCTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:87339 original size:54 final size:54
Alignment explanation
Indices: 87257--87366 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
87247 CGTTTCCGCT
87257 ATCTGTTTTGTCAAATTCGAACCCGAAGGCCTCATTTTGACTATTTTATTCTTA
1 ATCTGTTTTGTCAAATTCGAACCCGAAGGCCTCATTTTGACTATTTTATTCTTA
87311 ATCTGTTTTGTCAAATTCGAACCCGAAGGCCTCATTTTGACTATTTTATTCTTA
1 ATCTGTTTTGTCAAATTCGAACCCGAAGGCCTCATTTTGACTATTTTATTCTTA
87365 AT
1 AT
87367 TTTGTACTTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.43
Consensus pattern (54 bp):
ATCTGTTTTGTCAAATTCGAACCCGAAGGCCTCATTTTGACTATTTTATTCTTA
Found at i:89122 original size:21 final size:21
Alignment explanation
Indices: 89098--89137 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
89088 AACCTGTCGT
*
89098 ATAATTTAAATAAATTAATCG
1 ATAATATAAATAAATTAATCG
* *
89119 ATAATATAATTAATTTAAT
1 ATAATATAAATAAATTAAT
89138 TTGAAAACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (21 bp):
ATAATATAAATAAATTAATCG
Found at i:95886 original size:50 final size:49
Alignment explanation
Indices: 95832--95931 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 49
95822 GTCCAGAAAC
95832 AACCAAGGAAT-ATTTACTTAACCAAAAAACCAAGACCGAGATCAAGAATA
1 AACCAAGG-ATCA-TTACTTAACCAAAAAACCAAGACCGAGATCAAGAATA
* * *
95882 AACCAAGGATGCATTACTTAACCAAAAAAGCATGACCTAGATCAAGAATA
1 AACCAAGGAT-CATTACTTAACCAAAAAACCAAGACCGAGATCAAGAATA
95932 TAGCTTGACC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
49 2 0.04
50 42 0.93
51 1 0.02
ACGTcount: A:0.50, C:0.20, G:0.13, T:0.17
Consensus pattern (49 bp):
AACCAAGGATCATTACTTAACCAAAAAACCAAGACCGAGATCAAGAATA
Found at i:114732 original size:37 final size:38
Alignment explanation
Indices: 114679--114762 Score: 116
Period size: 38 Copynumber: 2.2 Consensus size: 38
114669 CTTCTTCAAA
* * *
114679 CCCTAAGCCACAAAATTAA-TTTCTTCCTGCACGAAAT
1 CCCTAACCCACAAAATTAATTTTATTCCTGCACAAAAT
*
114716 CCCTAACCCACCAAATTAATTTTATTCCTGCACAAAAT
1 CCCTAACCCACAAAATTAATTTTATTCCTGCACAAAAT
*
114754 CCCTGACCC
1 CCCTAACCC
114763 CATCCCTACT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 17 0.41
38 24 0.59
ACGTcount: A:0.33, C:0.35, G:0.06, T:0.26
Consensus pattern (38 bp):
CCCTAACCCACAAAATTAATTTTATTCCTGCACAAAAT
Found at i:116400 original size:2 final size:2
Alignment explanation
Indices: 116393--116419 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
116383 TTTCAGATTT
116393 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
116420 TTAAAAATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:127076 original size:91 final size:91
Alignment explanation
Indices: 126955--127167 Score: 272
Period size: 91 Copynumber: 2.3 Consensus size: 91
126945 AACCCCAATT
* * * *
126955 TTTTTTTTGCACTCACTTGAGTA-TTAGAACTTTCAAAATGCATAAAAAAAAA-CCCTCAACCTT
1 TTTTTTTTGTACTCAATTGGGTACTT-GAACTTTCAAAATGCATAAAAAAAAAGCCCTCAAACTT
*
127018 TTTCAGAAA-AAGCAATTAAGCCCTT-G
65 TTT-AAAAAGAAGCAATTAAGCCCTTAG
127044 CTTTATTTTTGTACTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAAAAAATGCCCTCAAAC
1 -TTT-TTTTTGTACTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAAAAAA-GCCCTCAAAC
127109 TTTTTAAAAAGAAGCAATTAAGCCCTTAG
63 TTTTTAAAAAGAAGCAATTAAGCCCTTAG
* * * *
127138 TTTTTTTTTTATTGAATTAGGTACTTGAAC
1 TTTTTTTTGTACTCAATTGGGTACTTGAAC
127168 CGCCCTTAAT
Statistics
Matches: 108, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
90 3 0.03
91 43 0.40
92 29 0.27
93 32 0.30
94 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (91 bp):
TTTTTTTTGTACTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAAAAAAGCCCTCAAACTTT
TTAAAAAGAAGCAATTAAGCCCTTAG
Found at i:127611 original size:21 final size:23
Alignment explanation
Indices: 127569--127614 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
127559 ATTTGATGCA
* *
127569 TTTTATAATATTGTTATGATTTT
1 TTTTATAAAATTGTTATCATTTT
127592 TTTTATAAAATT-TTA-CATTTT
1 TTTTATAAAATTGTTATCATTTT
127613 TT
1 TT
127615 ACGATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 3 0.14
23 11 0.52
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (23 bp):
TTTTATAAAATTGTTATCATTTT
Found at i:130014 original size:21 final size:20
Alignment explanation
Indices: 129967--130007 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
129957 TTTGATTAGT
*
129967 TTAATTAATCATGTTTTATGC
1 TTAATTAATCATGTTTAAT-C
129988 TTAATTAATCATAGTTTAAT
1 TTAATTAATCAT-GTTTAAT
130008 TATAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (20 bp):
TTAATTAATCATGTTTAATC
Found at i:134497 original size:321 final size:321
Alignment explanation
Indices: 133915--134551 Score: 1040
Period size: 321 Copynumber: 2.0 Consensus size: 321
133905 GGAGACACGT
133915 ACTGAGTTAAACTCGATGAAAGAGTAATTCAAGGAATATGTGGTAGAGGCCATTAGTTCCATTAT
1 ACTGAGTTAAACTCGATGAAAGAGTAATTCAAGGAATATGTGGTAGAGGCCATTAGTTCCATTAT
* * *
133980 GGACGCAATGGAAGCACTCCTCAATACTACTATAGATAAGCTAACAAAGAAAAATGATGCTCTTG
66 GAACGCAATGGAAGCACTCCTCAATACTACTATAGATAAGCTAACAAAGAAAAATGATGCTATTA
* * * *
134045 AAGCTAGGATAACCACTATGAAGGAAGAAATGAAGCCACAGTGACAACTTTGAACGCAAAAATCG
131 AAGCTAGGATAACAACTATGAAGGAAGAAATAAAGCCACAATGACAACTTTGAACGCAAAAATAG
134110 AGGAGCTCTAGGGAGAGCTTGTTATGTGCAGAGTTGTTATGGGTAAAAGAGTGTTGAGTGCAACA
196 AGGAGCTCTAGGGAGAGCTTGTTATGTGCAGAGTTGTTATGGGTAAAAGAGTGTTGAGTGCAACA
* * * * *
134175 CTAAATAGGAGATCGATGTCCCTAAACCGGAGAAGTTTAAAGGGGCAAGCGAGGGACATGC
261 CTAAACAAGAGATCGATGTCCCTAAACCGAAGAAGTTTAAAGAGGCAAGCAAGGGACATGC
* *
134236 ACTGAGTTAAACTCGATGAAAGAGTAATTCAATGAATATGTGGTAGATGCCATTAGTTCCATTAT
1 ACTGAGTTAAACTCGATGAAAGAGTAATTCAAGGAATATGTGGTAGAGGCCATTAGTTCCATTAT
* * * * *
134301 GAATGCAGTGGAAGCATTCCTCAATACTGCTATAGGTAAGCTAACAAAGAAAAATGATGCTATTA
66 GAACGCAATGGAAGCACTCCTCAATACTACTATAGATAAGCTAACAAAGAAAAATGATGCTATTA
* * * *
134366 AAGCTAGGATGACAACTATGAAGGAAGAAATAAAGCCACAATGACGATTTTGAATGCAAAAATAG
131 AAGCTAGGATAACAACTATGAAGGAAGAAATAAAGCCACAATGACAACTTTGAACGCAAAAATAG
*
134431 AGGAGCTCTAGGGAGAGCTTGTTATGTGCAGAGTTGTTATGGGTAAAGGAGTGTTGAGTGCAACA
196 AGGAGCTCTAGGGAGAGCTTGTTATGTGCAGAGTTGTTATGGGTAAAAGAGTGTTGAGTGCAACA
* *
134496 CTAAGCAAGAGATCGATGTCCCTAAATCGAAGAAGTTTAAAGAGGCAAGCAAGGGA
261 CTAAACAAGAGATCGATGTCCCTAAACCGAAGAAGTTTAAAGAGGCAAGCAAGGGA
134552 AGTAGATAAC
Statistics
Matches: 290, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
321 290 1.00
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.23
Consensus pattern (321 bp):
ACTGAGTTAAACTCGATGAAAGAGTAATTCAAGGAATATGTGGTAGAGGCCATTAGTTCCATTAT
GAACGCAATGGAAGCACTCCTCAATACTACTATAGATAAGCTAACAAAGAAAAATGATGCTATTA
AAGCTAGGATAACAACTATGAAGGAAGAAATAAAGCCACAATGACAACTTTGAACGCAAAAATAG
AGGAGCTCTAGGGAGAGCTTGTTATGTGCAGAGTTGTTATGGGTAAAAGAGTGTTGAGTGCAACA
CTAAACAAGAGATCGATGTCCCTAAACCGAAGAAGTTTAAAGAGGCAAGCAAGGGACATGC
Found at i:137869 original size:27 final size:27
Alignment explanation
Indices: 137818--137870 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
137808 ATGTTCATTA
* * *
137818 TTTCAAGTATGATTTGAATTTGAATCG
1 TTTCAAGTATGATCTGAACTCGAATCG
*
137845 TTTCAATTATGATCTGAACTCGAATC
1 TTTCAAGTATGATCTGAACTCGAATC
137871 ACTTTAATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (27 bp):
TTTCAAGTATGATCTGAACTCGAATCG
Found at i:142288 original size:2 final size:2
Alignment explanation
Indices: 142281--142316 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
142271 GAGATTGTAA
142281 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
142317 AAATTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:144099 original size:17 final size:17
Alignment explanation
Indices: 144077--144112 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
144067 TATACGAATC
*
144077 AATTCCTAACAATATTG
1 AATTCCTAACAATAATG
144094 AATTCCTAACAATAATG
1 AATTCCTAACAATAATG
144111 AA
1 AA
144113 AGATGAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.31
Consensus pattern (17 bp):
AATTCCTAACAATAATG
Found at i:149765 original size:20 final size:20
Alignment explanation
Indices: 149742--149818 Score: 55
Period size: 23 Copynumber: 3.6 Consensus size: 20
149732 AACAACATTA
149742 AAAACAATAAAAATAGCAAC
1 AAAACAATAAAAATAGCAAC
* * **
149762 AAAAATAACACGAAAATAATAATC
1 -AAAACAATA--AAAATAGCAA-C
* * *
149786 AAAACAGTAAAAAAAGCACC
1 AAAACAATAAAAATAGCAAC
149806 AAAACAATAAAAA
1 AAAACAATAAAAA
149819 AAACAACACA
Statistics
Matches: 41, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
20 13 0.32
21 13 0.32
23 14 0.34
24 1 0.02
ACGTcount: A:0.70, C:0.14, G:0.05, T:0.10
Consensus pattern (20 bp):
AAAACAATAAAAATAGCAAC
Found at i:149819 original size:22 final size:22
Alignment explanation
Indices: 149785--149868 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 22
149775 AAATAATAAT
*
149785 CAAAACAGT--AAAAAAAGCAC
1 CAAAACAGTAAAAAAAAAACAC
*
149805 CAAAACAATAAAAAAAACAACAC
1 CAAAACAGTAAAAAAAA-AACAC
* * * *
149828 AAAAATAGTAAAAACCAATA-AC
1 CAAAACAGTAAAAA-AAAAACAC
149850 CAAAACAGTAAAAAAAAAA
1 CAAAACAGTAAAAAAAAAA
149869 AAAACACCAA
Statistics
Matches: 49, Mismatches: 11, Indels: 7
0.73 0.16 0.10
Matches are distributed among these distances:
20 8 0.16
21 3 0.06
22 20 0.41
23 16 0.33
24 2 0.04
ACGTcount: A:0.71, C:0.17, G:0.05, T:0.07
Consensus pattern (22 bp):
CAAAACAGTAAAAAAAAAACAC
Found at i:149822 original size:32 final size:32
Alignment explanation
Indices: 149742--149831 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 32
149732 AACAACATTA
* * *
149742 AAAACAATAAAAATAGCAACAAAAATAACACG
1 AAAACAATAAAAAAAACAACAAAAATAACACC
* ** **
149774 AAAATAATAATCAAAACAGTAAAAA-AAGCACC
1 AAAACAATAAAAAAAACAACAAAAATAA-CACC
149806 AAAACAATAAAAAAAACAACACAAAA
1 AAAACAATAAAAAAAACAACA-AAAA
149832 ATAGTAAAAA
Statistics
Matches: 43, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
31 2 0.05
32 37 0.86
33 4 0.09
ACGTcount: A:0.71, C:0.16, G:0.04, T:0.09
Consensus pattern (32 bp):
AAAACAATAAAAAAAACAACAAAAATAACACC
Found at i:149834 original size:20 final size:20
Alignment explanation
Indices: 149785--149874 Score: 60
Period size: 20 Copynumber: 4.3 Consensus size: 20
149775 AAATAATAAT
* * *
149785 CAAAACAGTAAAAAAAGCAC
1 CAAAACAATAAAAAAAACAA
149805 CAAAACAATAAAAAAAACAA
1 CAAAACAATAAAAAAAACAA
*
149825 CACAAA-AATAGTAAAAACCAATAA
1 CA-AAACAATA--AAAAA--AACAA
*
149849 CCAAAACAGTAAAAAAAA-AA
1 -CAAAACAATAAAAAAAACAA
149869 -AAAACA
1 CAAAACA
149875 CCAAAACAAC
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
18 6 0.10
20 25 0.43
21 5 0.09
22 5 0.09
23 5 0.09
24 7 0.12
25 5 0.09
ACGTcount: A:0.72, C:0.17, G:0.04, T:0.07
Consensus pattern (20 bp):
CAAAACAATAAAAAAAACAA
Found at i:149864 original size:32 final size:31
Alignment explanation
Indices: 149774--149865 Score: 78
Period size: 32 Copynumber: 2.9 Consensus size: 31
149764 AAATAACACG
* *
149774 AAAATAATAATCAAAACAGTAAAAAAAGCACC
1 AAAACAATAAACAAAACAGTAAAAAAAGCA-C
* ** *
149806 AAAACAATAAAAAAAACAACACAAAAATAGTA-
1 AAAACAATAAACAAAACAGTA-AAAAA-AGCAC
*
149838 AAAACCAATAACCAAAACAGTAAAAAAA
1 AAAA-CAATAAACAAAACAGTAAAAAAA
149866 AAAAAAACAC
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
31 1 0.02
32 25 0.53
33 18 0.38
34 3 0.06
ACGTcount: A:0.71, C:0.15, G:0.04, T:0.10
Consensus pattern (31 bp):
AAAACAATAAACAAAACAGTAAAAAAAGCAC
Found at i:151708 original size:27 final size:27
Alignment explanation
Indices: 151677--151731 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
151667 CCGTCTTGAG
**
151677 TTGCCGGTTAACAGTGCCGATGAACAA
1 TTGCCGGTTAACAGCACCGATGAACAA
*
151704 TTGCCGGTTAGCAGCACCGATGAACAA
1 TTGCCGGTTAACAGCACCGATGAACAA
151731 T
1 T
151732 CTAGCAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (27 bp):
TTGCCGGTTAACAGCACCGATGAACAA
Found at i:155120 original size:19 final size:20
Alignment explanation
Indices: 155072--155111 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
155062 CAAAAGAAGC
155072 ATAAAAAA-TATAGGAAGTT
1 ATAAAAAATTATAGGAAGTT
155091 ATAAAAAATTATAGG-AGTT
1 ATAAAAAATTATAGGAAGTT
155110 AT
1 AT
155112 TATAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (20 bp):
ATAAAAAATTATAGGAAGTT
Found at i:155163 original size:20 final size:18
Alignment explanation
Indices: 155117--155163 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
155107 GTTATTATAA
155117 ATTAAAAATTATAAAAAT
1 ATTAAAAATTATAAAAAT
*
155135 A-TAAGAAATTTTAGAAAATT
1 ATTAA-AAATTATA-AAAA-T
155155 ATTAAAAAT
1 ATTAAAAAT
155164 AAAAGGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 3 0.12
18 8 0.33
19 4 0.17
20 6 0.25
21 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (18 bp):
ATTAAAAATTATAAAAAT
Found at i:155175 original size:28 final size:28
Alignment explanation
Indices: 155121--155180 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
155111 TTATAAATTA
* *
155121 AAAATTATAAAAATATAAGAAATTTTAG
1 AAAATTATAAAAATAAAAGAAATTTTAC
*
155149 AAAATTATTAAAAATAAAAGGAA-TTTAC
1 AAAATTA-TAAAAATAAAAGAAATTTTAC
155177 AAAA
1 AAAA
155181 AAATTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (28 bp):
AAAATTATAAAAATAAAAGAAATTTTAC
Found at i:155181 original size:29 final size:28
Alignment explanation
Indices: 155120--155194 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
155110 ATTATAAATT
*
155120 AAAAATTATAAAAATATAAGAAATTTTA
1 AAAAATTATAAAAATAAAAGAAATTTTA
* * *
155148 GAAAATTATTAAAAATAAAAGGAATTTACAA
1 AAAAATTA-TAAAAATAAAAGAAATTT--TA
155179 AAAAATTATATAAAAT
1 AAAAATTATA-AAAAT
155195 TACAAAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
28 7 0.18
29 16 0.42
30 2 0.05
31 13 0.34
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.29
Consensus pattern (28 bp):
AAAAATTATAAAAATAAAAGAAATTTTA
Found at i:155274 original size:21 final size:21
Alignment explanation
Indices: 155250--155297 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
155240 AAAAATATTA
155250 TAAAAAATTAT-AAAACAAGT-T
1 TAAAAAA-TATGAAAA-AAGTAT
*
155271 TAAAATATATGAAAAAAGTAT
1 TAAAAAATATGAAAAAAGTAT
155292 TAAAAA
1 TAAAAA
155298 GAATTTGTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (21 bp):
TAAAAAATATGAAAAAAGTAT
Found at i:155275 original size:20 final size:22
Alignment explanation
Indices: 155252--155297 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 22
155242 AAATATTATA
155252 AAAAAT-TAT-AAAACAAGT-TT
1 AAAAATATATGAAAA-AAGTATT
155272 -AAAATATATGAAAAAAGTATT
1 AAAAATATATGAAAAAAGTATT
155293 AAAAA
1 AAAAA
155298 GAATTTGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.23
20 7 0.32
21 6 0.27
22 4 0.18
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (22 bp):
AAAAATATATGAAAAAAGTATT
Found at i:176673 original size:17 final size:17
Alignment explanation
Indices: 176653--176686 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
176643 ATGATATTAA
*
176653 TAAATTAAATTTTAGGT
1 TAAATTAAATCTTAGGT
176670 TAAATTAAATCTTAGGT
1 TAAATTAAATCTTAGGT
176687 GTTCATCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (17 bp):
TAAATTAAATCTTAGGT
Found at i:177364 original size:22 final size:23
Alignment explanation
Indices: 177336--177378 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
177326 AAATATATAT
177336 ATATTT-A-AATTGTTTTATTTTA
1 ATATTTAATAATT-TTTTATTTTA
177358 ATATTTAATAATTTTTTATTT
1 ATATTTAATAATTTTTTATTT
177379 ATTGAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
ATATTTAATAATTTTTTATTTTA
Found at i:178796 original size:17 final size:17
Alignment explanation
Indices: 178765--178830 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 17
178755 TCCAATAAAC
**
178765 TTAAATTTATTTTTATT
1 TTAAATTTAAATTTATT
*
178782 TTAAATTTAAATTTAGT
1 TTAAATTTAAATTTATT
** *
178799 TGGAATTTAAGTTTATT
1 TTAAATTTAAATTTATT
*
178816 ATAAATTTAAATTTA
1 TTAAATTTAAATTTA
178831 AAGTTTATTT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTAAATTTAAATTTATT
Found at i:179547 original size:21 final size:23
Alignment explanation
Indices: 179522--179579 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 23
179512 TAAATGTTTT
*
179522 TAATAGCATTAATAGTA-A-TAA
1 TAATAGCATTAATAATACATTAA
**
179543 TAATAATATTAATAATATCATTAA
1 TAATAGCATTAATAATA-CATTAA
*
179567 TAATGGCATTAAT
1 TAATAGCATTAAT
179580 TAAATTAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 14 0.50
23 1 0.04
24 13 0.46
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (23 bp):
TAATAGCATTAATAATACATTAA
Found at i:179576 original size:12 final size:12
Alignment explanation
Indices: 179522--179579 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
179512 TAAATGTTTT
179522 TAATAGCATTAA
1 TAATAGCATTAA
*
179534 TAGTA--A-TAA
1 TAATAGCATTAA
**
179543 TAATAATATTAA
1 TAATAGCATTAA
*
179555 TAATATCATTAA
1 TAATAGCATTAA
*
179567 TAATGGCATTAA
1 TAATAGCATTAA
179579 T
1 T
179580 TAAATTAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 7 0.19
10 1 0.03
11 1 0.03
12 28 0.76
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (12 bp):
TAATAGCATTAA
Found at i:180676 original size:29 final size:28
Alignment explanation
Indices: 180636--181013 Score: 312
Period size: 29 Copynumber: 13.0 Consensus size: 28
180626 AGGGTCCCTA
180636 AACTATCCAAAAATTCCATTTTTACCCTCG
1 AACT-TCCAAAAATTCCATTTTTACCC-CG
* * *
180666 AACTTCTAAAAATCCCATTTTTACCCTTG
1 AACTTCCAAAAATTCCATTTTTACCC-CG
* *
180695 AACTTCTAAAAATCCCATTTTTACCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCG
* * * *
180723 AACTTCCAAAAATCCCATTTTCAATCCCA
1 AACTTCCAAAAATTCCATTTT-TACCCCG
*
180752 AACTTCCAAAAATTACATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTA-CCCCG
180781 AACTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTA-CCCCG
* * *
180810 AACTTCTAAAAA-TCTCATTTTCAACCTCG
1 AACTTCCAAAAATTC-CATTTT-TACCCCG
** * *
180839 AAACTTCCAAAAACCCCGTTTTTACCCCCA
1 -AACTTCCAAAAATTCCATTTTTA-CCCCG
* * **
180869 AACTTCTAAAAATCCCATTTTTTACCCTAA
1 AACTTCCAAAAATTCCA-TTTTTACCC-CG
* *
180899 AACTTCC-AAAATTACATTTTTAACCCCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCC-G
* *
180928 AACTTCTAAAAATTCTATTTTTAGCCCCG
1 AACTTCCAAAAATTCCATTTTTA-CCCCG
* **
180957 AACTTCCCAAAATTCCATTTTTGACTCCAA
1 AACTTCCAAAAATTCCATTTTT-AC-CCCG
*
180987 AACTTCCTAAAATTACCA-TTTTACCCC
1 AACTTCCAAAAATT-CCATTTTTACCCC
181014 CGGATGTCCA
Statistics
Matches: 290, Mismatches: 42, Indels: 34
0.79 0.11 0.09
Matches are distributed among these distances:
28 31 0.11
29 182 0.63
30 73 0.25
31 4 0.01
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.33
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTTACCCCG
Found at i:180800 original size:58 final size:58
Alignment explanation
Indices: 180635--181015 Score: 360
Period size: 59 Copynumber: 6.5 Consensus size: 58
180625 GAGGGTCCCT
* * * *
180635 AAACTATCCAAAAATTCCATTTTTACCCTCGAACTTCTAAAAATCCCATTTTT-ACCCTT
1 AAACT-TCTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCC-C
* * * *
180694 GAACTTCTAAAAATCCCATTTTTA-CCCCGAACTTCCAAAAATCCCATTTTCAATCCC
1 AAACTTCTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
* * * *
180751 AAACTTCCAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
* * * * * * *
180809 GAACTTCTAAAAA-TCTCATTTTCAACCTCGAAACTTCCAAAAACCCCGTTTTTACCCCC
1 AAACTTCTAAAAATTC-CATTTTTACCCCCG-AACTTCCAAAAATCCCATTTTTAACCCC
* *** **
180868 AAACTTCTAAAAATCCCATTTTTTACCCTAAAACTTCC-AAAATTACATTTTTAACCCC
1 AAACTTCTAAAAATTCCA-TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
* * * * * *
180926 AAAACTTCTAAAAATTCTATTTTTAGCCCCGAACTTCCCAAAATTCCATTTTTGACTCCA
1 -AAACTTCTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAAC-CCC
180986 AAACTTCCT-AAAATTACCA-TTTTACCCCCG
1 AAACTT-CTAAAAATT-CCATTTTTACCCCCG
181016 GATGTCCAAA
Statistics
Matches: 264, Mismatches: 47, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
57 45 0.17
58 101 0.38
59 103 0.39
60 15 0.06
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (58 bp):
AAACTTCTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
Found at i:181027 original size:88 final size:86
Alignment explanation
Indices: 180635--181015 Score: 294
Period size: 88 Copynumber: 4.4 Consensus size: 86
180625 GAGGGTCCCT
* * * * * **
180635 AAACTATCCAAAAATT-CCATTTTTACCCTCGAACTTCTAAAAATCCCATTTTTACCCTTGAACT
1 AAACT-TCCTAAAATTACCATTTTAACCCCCGAACTTCCAAAAAT-TCATTTTTACCCCCGAACT
* * *
180699 TCTAAAAATCCCATTTTTACCCC
64 TCCAAAAATTCCATTTTTACCCA
* * * * *
180722 GAACTTCC-AAAAATCCCATTTTCAA-TCCCAAACTTCCAAAAATTACATTTTTACCCCCGAACT
1 AAACTTCCTAAAATTACCATTTT-AACCCCCGAACTTCCAAAAATT-CATTTTTACCCCCGAACT
*
180785 TCCAAAAATTCCATTTTTACCCCC
64 TCCAAAAATTCCATTTTTA-CCCA
* * * ** * *
180809 GAACTT-CTAAAAAT-CTCATTTTCAA-CCTCGAAACTTCCAAAAACCCCGTTTTTACCCCCAAA
1 AAACTTCCTAAAATTAC-CATTTT-AACCCCCG-AACTTCCAAAAA-TTCATTTTTACCCCCGAA
* *
180871 CTTCTAAAAATCCCATTTTTTACCCTA
62 CTTCCAAAAATTCCA-TTTTTACCC-A
** * *
180898 AAACTTCC-AAAATTA-CATTTTTAACCCCAAAACTTCTAAAAATTCTATTTTTAGCCCCGAACT
1 AAACTTCCTAAAATTACCA-TTTTAACCCCCGAACTTCCAAAAATTC-ATTTTTACCCCCGAACT
*
180961 TCCCAAAATTCCATTTTTGACTCCA
64 TCCAAAAATTCCATTTTT-AC-CCA
180986 AAACTTCCTAAAATTACCATTTT-ACCCCCG
1 AAACTTCCTAAAATTACCATTTTAACCCCCG
181016 GATGTCCAAA
Statistics
Matches: 237, Mismatches: 38, Indels: 37
0.76 0.12 0.12
Matches are distributed among these distances:
85 5 0.02
86 59 0.25
87 38 0.16
88 97 0.41
89 35 0.15
90 3 0.01
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (86 bp):
AAACTTCCTAAAATTACCATTTTAACCCCCGAACTTCCAAAAATTCATTTTTACCCCCGAACTTC
CAAAAATTCCATTTTTACCCA
Found at i:181849 original size:18 final size:20
Alignment explanation
Indices: 181816--181858 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
181806 AAGTTTATAA
181816 TATTTTATATTATATTATGT
1 TATTTTATATTATATTATGT
181836 TATTTT-TA-TATATTATGT
1 TATTTTATATTATATTATGT
*
181854 AATTT
1 TATTT
181859 AAAAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.64
19 2 0.09
20 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (20 bp):
TATTTTATATTATATTATGT
Found at i:186190 original size:18 final size:18
Alignment explanation
Indices: 186167--186204 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
186157 TAATATAGTT
*
186167 TTATTCGATTTATTCAAA
1 TTATTCGAGTTATTCAAA
*
186185 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCAAA
186203 TT
1 TT
186205 CGAAAATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCAAA
Found at i:186291 original size:23 final size:23
Alignment explanation
Indices: 186247--186293 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
186237 GAAAAAAATT
*
186247 TAACTCGATTCGTTTAACTCGAA
1 TAACTCGATTCGTATAACTCGAA
*
186270 TAACTCGATTC-TAATAATTCGAA
1 TAACTCGATTCGT-ATAACTCGAA
186293 T
1 T
186294 TTTCTATTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (23 bp):
TAACTCGATTCGTATAACTCGAA
Found at i:189362 original size:17 final size:18
Alignment explanation
Indices: 189342--189377 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
189332 TATATTTTTA
189342 AAAAAAATTATAAA-AAT
1 AAAAAAATTATAAAGAAT
189359 AAAAAAATTATAAAGAAT
1 AAAAAAATTATAAAGAAT
189377 A
1 A
189378 TATAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (18 bp):
AAAAAAATTATAAAGAAT
Found at i:192026 original size:27 final size:26
Alignment explanation
Indices: 191977--192045 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 26
191967 TTACGGTTTT
*
191977 TTAGGATTAGGGTTTTATTTTTTAAAA
1 TTAGGATTAGGG-TTTATGTTTTAAAA
* *
192004 TTAGGGTTAGGGTTTAGTGTTTTTAAA
1 TTAGGATTAGGGTTTA-TGTTTTAAAA
* *
192031 GTAGGATTTGGGTTT
1 TTAGGATTAGGGTTT
192046 TTTTGGATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 4 0.11
27 31 0.89
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (26 bp):
TTAGGATTAGGGTTTATGTTTTAAAA
Found at i:206870 original size:27 final size:27
Alignment explanation
Indices: 206819--206871 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
206809 TACATATTTT
**
206819 CAATTTGATACTTGAATTTTTTTTTAC
1 CAATTTGATACTTGAATTTAGTTTTAC
206846 CAATTTGATACTT-AAGTTTAGTTTTA
1 CAATTTGATACTTGAA-TTTAGTTTTA
206872 ATGTTTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (27 bp):
CAATTTGATACTTGAATTTAGTTTTAC
Found at i:211160 original size:17 final size:18
Alignment explanation
Indices: 211138--211172 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
211128 GGTTTAGGGT
211138 TTAAAATT-TTTAATTAA
1 TTAAAATTATTTAATTAA
*
211155 TTAAAATTATTTCATTAA
1 TTAAAATTATTTAATTAA
211173 AGATTTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAAAATTATTTAATTAA
Found at i:214718 original size:52 final size:52
Alignment explanation
Indices: 214636--214790 Score: 215
Period size: 52 Copynumber: 3.0 Consensus size: 52
214626 ATGACACATT
* * * *
214636 ATAATCCAAAAAGGATTCATATGCTTACGATGACACAT-GATCATC-AGACTTC
1 ATAATCCATAAAGGATTCATATACTCACGATGACACATAG-TCATCGA-ACCTC
* *
214688 ATAATCCGTAAATGATTCATATACTCACGATGACACATAGTCATCGAACCTC
1 ATAATCCATAAAGGATTCATATACTCACGATGACACATAGTCATCGAACCTC
*
214740 ATAATCCATAAAGGATTCATATACTCACGATGACACATAGTCATCGGACCT
1 ATAATCCATAAAGGATTCATATACTCACGATGACACATAGTCATCGAACCT
214791 TTTGTATTTA
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
52 90 0.98
53 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (52 bp):
ATAATCCATAAAGGATTCATATACTCACGATGACACATAGTCATCGAACCTC
Found at i:217786 original size:3 final size:3
Alignment explanation
Indices: 217780--217808 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
217770 AGGAGGGAAA
217780 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
217809 ATGAATTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:219061 original size:26 final size:27
Alignment explanation
Indices: 219014--219079 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
219004 ATTTATGATT
219014 AATATAAAAATAATGATAATAAATTT-A
1 AATATAAAAATAATGATAAT-AATTTGA
*
219041 AATATTAAAATAAT-ACT-ATAATTTGA
1 AATATAAAAATAATGA-TAATAATTTGA
*
219067 AATAAAAAAATAA
1 AATATAAAAATAA
219080 ATTAAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 5 0.15
26 15 0.44
27 14 0.41
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (27 bp):
AATATAAAAATAATGATAATAATTTGA
Found at i:238496 original size:20 final size:20
Alignment explanation
Indices: 238471--238509 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
238461 TGTGAAGTTT
*
238471 ATTGATGAGTATTTTATATA
1 ATTGATGAATATTTTATATA
238491 ATTGATGAATATTTTATAT
1 ATTGATGAATATTTTATAT
238510 TATAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (20 bp):
ATTGATGAATATTTTATATA
Found at i:245371 original size:23 final size:22
Alignment explanation
Indices: 245338--245388 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
245328 CTTTATTTGA
245338 TAAAATA-TTTTGATATAACAAAT
1 TAAAATATTTTTGA-AT-ACAAAT
* *
245361 TAAAATGTTTTTGAATACAAGT
1 TAAAATATTTTTGAATACAAAT
245383 TAAAAT
1 TAAAAT
245389 TGACAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.44
23 8 0.32
24 6 0.24
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (22 bp):
TAAAATATTTTTGAATACAAAT
Found at i:245385 original size:22 final size:24
Alignment explanation
Indices: 245345--245388 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
245335 TGATAAAATA
245345 TTTTGATATAACAAATTAAAATGT
1 TTTTGATATAACAAATTAAAATGT
*
245369 TTTTGA-AT-ACAAGTTAAAAT
1 TTTTGATATAACAAATTAAAAT
245389 TGACAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAATGT
Found at i:246757 original size:16 final size:16
Alignment explanation
Indices: 246732--246778 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
246722 GTTGTTTCTA
*
246732 AATTTATATTTGAAAC
1 AATTTATATTTAAAAC
*
246748 AATTTTTATTTAAAAC
1 AATTTATATTTAAAAC
246764 AATTGTAT-TTTAAAA
1 AATT-TATATTTAAAA
246779 ATAGTTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 25 0.93
17 2 0.07
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (16 bp):
AATTTATATTTAAAAC
Found at i:253683 original size:5 final size:5
Alignment explanation
Indices: 253675--253701 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
253665 AATTTATTTT
253675 TTATA TTATA TTATA TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TT
253702 TCATCCTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:260421 original size:127 final size:125
Alignment explanation
Indices: 260167--260422 Score: 449
Period size: 125 Copynumber: 2.0 Consensus size: 125
260157 CGAGACAAGC
* *
260167 CCTCCGTTGCACCAAGATCTCACGCCCAAGTAACTTTGAAATCATAAGCCACAAGACCCTCACAC
1 CCTCCATTGCACCAAGATCTCACGCCCAAGTAACTTCGAAATCATAAGCCACAAGACCCTCACAC
* *
260232 CAAGAGTAGTTTGAGGAGTTCAAGAATGTCTACAAGTCACTCAGAAACGCCAAGATTTGG
66 CAAGAGTAGTTTGAGGAGTTCAAGAATGTCTACAAGTCACTCAGAAACCCCAAGATTAGG
*
260292 CCTCCATTGCACCAAGATCTCACGCCCAAGTAACTTCGGAATCATAAGCCACAAGACCCTCACAC
1 CCTCCATTGCACCAAGATCTCACGCCCAAGTAACTTCGAAATCATAAGCCACAAGACCCTCACA-
260357 CCTAAGAGTAGTTTGAGGAGTTCAAGAATGTCTACAAGTCACTCAGAAACCCCAAGATTAGG
65 CC-AAGAGTAGTTTGAGGAGTTCAAGAATGTCTACAAGTCACTCAGAAACCCCAAGATTAGG
260419 CCTC
1 CCTC
260423 TTCACGCCTT
Statistics
Matches: 124, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
125 61 0.49
126 2 0.02
127 61 0.49
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (125 bp):
CCTCCATTGCACCAAGATCTCACGCCCAAGTAACTTCGAAATCATAAGCCACAAGACCCTCACAC
CAAGAGTAGTTTGAGGAGTTCAAGAATGTCTACAAGTCACTCAGAAACCCCAAGATTAGG
Found at i:263795 original size:26 final size:26
Alignment explanation
Indices: 263766--263815 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
263756 TTGCTAGTAA
*
263766 AAATTCAT-AAATATTATAACAAAATT
1 AAATTC-TCAAATAATATAACAAAATT
*
263792 AAATTCTCAATTAATATAACAAAA
1 AAATTCTCAAATAATATAACAAAA
263816 GAAAAGAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (26 bp):
AAATTCTCAAATAATATAACAAAATT
Found at i:263861 original size:16 final size:16
Alignment explanation
Indices: 263829--263862 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
263819 AAGAGAATAA
*
263829 ATATAATATGTAAATG
1 ATATAATATATAAATG
*
263845 ATATAATATATAGATG
1 ATATAATATATAAATG
263861 AT
1 AT
263863 TAAATATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (16 bp):
ATATAATATATAAATG
Found at i:264478 original size:19 final size:20
Alignment explanation
Indices: 264451--264491 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
264441 AAAATTTTTG
*
264451 AATAATTATTA-TTTTTAAA
1 AATAATTATGATTTTTTAAA
*
264470 AATATTTATGATTTTTTAAA
1 AATAATTATGATTTTTTAAA
264490 AA
1 AA
264492 AAAATATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AATAATTATGATTTTTTAAA
Found at i:275169 original size:4 final size:4
Alignment explanation
Indices: 275160--275234 Score: 96
Period size: 4 Copynumber: 18.0 Consensus size: 4
275150 TTAAAAATAT
* * *
275160 TTTA TTTA TTTA TATATA TATA TTTA TTTA TTTA TTTTA ATTA TTTA GTTA
1 TTTA TTTA TTTA T-T-TA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA
275211 TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA
275235 CATCGTAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
4 54 0.87
5 5 0.08
6 3 0.05
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:276642 original size:54 final size:54
Alignment explanation
Indices: 276578--276688 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
276568 ATATTATTAT
*
276578 GTATGAATTTTTATAACCAATCATAAAGTAATCAATATAAGTTTGAAAGAATAA
1 GTATGAATTTTTATAACCAATCATAAAGTAATCAATATAAGTTCGAAAGAATAA
276632 GTATGAATTTTTATAACCAATCATAAAGTAATCAATATAAGTTCGAAAGAATAA
1 GTATGAATTTTTATAACCAATCATAAAGTAATCAATATAAGTTCGAAAGAATAA
276686 GTA
1 GTA
276689 ACTAACCTCG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (54 bp):
GTATGAATTTTTATAACCAATCATAAAGTAATCAATATAAGTTCGAAAGAATAA
Found at i:279646 original size:20 final size:21
Alignment explanation
Indices: 279607--279646 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
279597 AAGAATTGTT
*
279607 TTTATTTTGATTACTTTAAAA
1 TTTATTTTGATTAATTTAAAA
279628 TTTATTTTG-TTAATTTAAA
1 TTTATTTTGATTAATTTAAA
279647 TATCCTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTATTTTGATTAATTTAAAA
Found at i:284294 original size:76 final size:76
Alignment explanation
Indices: 284168--284321 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
284158 AATTACTCGC
284168 TAGCATGTATTTTGTGTTTTACTGAATATACCCTCAAGGGAAATGGCGCCTTCTACTATTACTCT
1 TAGCATGTATTTTGTGTTTTACTGAATATACCCTCAAGGGAAATGGCGCCTTCTACTATTACTCT
284233 CAAAACTTAAG
66 CAAAACTTAAG
284244 TAGCATGTATTTTGTGTTTTACTGAATATACCCTCAAGGGAAATGGCGCCTTCTACTATTACTCT
1 TAGCATGTATTTTGTGTTTTACTGAATATACCCTCAAGGGAAATGGCGCCTTCTACTATTACTCT
284309 CAAAACTTAAG
66 CAAAACTTAAG
284320 TA
1 TA
284322 ATCACACCTG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (76 bp):
TAGCATGTATTTTGTGTTTTACTGAATATACCCTCAAGGGAAATGGCGCCTTCTACTATTACTCT
CAAAACTTAAG
Found at i:286138 original size:3 final size:3
Alignment explanation
Indices: 286130--286155 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
286120 AAACGCCACA
286130 AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AG
286156 AAGAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:299204 original size:31 final size:31
Alignment explanation
Indices: 299169--299227 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
299159 GTTATCCAAA
* *
299169 TATTCTATAATTTTTATTTAAGTTATTGAAT
1 TATTCGATAATTTTTATTTAAATTATTGAAT
**
299200 TATTCGATTGTTTTTATTTAAATTATTG
1 TATTCGATAATTTTTATTTAAATTATTG
299228 GGTTTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.59
Consensus pattern (31 bp):
TATTCGATAATTTTTATTTAAATTATTGAAT
Found at i:300486 original size:30 final size:31
Alignment explanation
Indices: 300442--300514 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
300432 TTTAGTAGTT
* * *
300442 TATATTTTTA-TAATTTTTAAATAATTAAAT
1 TATAATTTTATTAATTTTTAAAGAATTAAAG
**
300472 TA-AATTTTATTAATTTTTTGAGAATTAAAG
1 TATAATTTTATTAATTTTTAAAGAATTAAAG
300502 TATAATTTTATTA
1 TATAATTTTATTA
300515 TTATTAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 6 0.17
30 20 0.56
31 10 0.28
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (31 bp):
TATAATTTTATTAATTTTTAAAGAATTAAAG
Found at i:305864 original size:15 final size:16
Alignment explanation
Indices: 305834--305872 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
305824 TAATAAAAAT
305834 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
305851 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
305866 ATAATTT
1 ATAATTT
305873 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:309158 original size:6 final size:6
Alignment explanation
Indices: 309140--309203 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
309130 TGAACTCAAT
* * * * *
309140 TTTAAA TTTTAAA TTTAAA TTTAAA CTT-AT TTTAAG TTTCAA TTT-AT
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
309187 TTTATA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
309204 TTAAAAAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
5 7 0.16
6 32 0.71
7 6 0.13
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:309200 original size:17 final size:16
Alignment explanation
Indices: 309152--309202 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
309142 TAAATTTTAA
* *
309152 ATTTAAATTTAAACTT
1 ATTTTAATTTAAATTT
*
309168 ATTTTAAGTTTCAATTT
1 ATTTTAA-TTTAAATTT
309185 ATTTTATATTTAAATTT
1 ATTTTA-ATTTAAATTT
309202 A
1 A
309203 ATTAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 6 0.21
17 22 0.76
18 1 0.03
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (16 bp):
ATTTTAATTTAAATTT
Found at i:310888 original size:30 final size:30
Alignment explanation
Indices: 310854--310919 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
310844 TTAAAAATCC
** *
310854 CATTTTGACCCTTAAACTTCTCTAAAATTA
1 CATTTTGACCCCAAAACTTCTCCAAAATTA
310884 CATTTTGACCCCAAAACTTCTCCAAAATTA
1 CATTTTGACCCCAAAACTTCTCCAAAATTA
310914 CATTTT
1 CATTTT
310920 TTCCTCCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (30 bp):
CATTTTGACCCCAAAACTTCTCCAAAATTA
Found at i:311065 original size:29 final size:29
Alignment explanation
Indices: 310885--311047 Score: 138
Period size: 29 Copynumber: 5.6 Consensus size: 29
310875 CTAAAATTAC
* *
310885 ATTTTGACCCCAAAACTTCTCCAAAATTACAT
1 ATTTTTACCCC-AAACTT-TCCAAAAAT-CAT
* *
310917 -TTTTT-CCTCCAAACTTAT-AAAAAATTAT
1 ATTTTTACC-CCAAACTT-TCCAAAAATCAT
* * *
310945 A-TTTTATCGCCGAACTTTCCAAAAATCAC
1 ATTTTTA-CCCCAAACTTTCCAAAAATCAT
* *
310974 ATTTTTACCCTCGAAC-TTCCAAAAATCAC
1 ATTTTTACCC-CAAACTTTCCAAAAATCAT
*
311003 ATTTTTACCCTAAACTTTCCAAAAATCAT
1 ATTTTTACCCCAAACTTTCCAAAAATCAT
311032 ATTTTTACCCCAAACT
1 ATTTTTACCCCAAACT
311048 CTTCGAAACG
Statistics
Matches: 108, Mismatches: 15, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
28 10 0.09
29 72 0.67
30 20 0.19
31 6 0.06
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.35
Consensus pattern (29 bp):
ATTTTTACCCCAAACTTTCCAAAAATCAT
Found at i:318299 original size:28 final size:28
Alignment explanation
Indices: 318268--318358 Score: 79
Period size: 28 Copynumber: 3.4 Consensus size: 28
318258 TTTGAATCCT
318268 GAACCCTGAACTTTAAACCCAAAATTCC
1 GAACCCTGAACTTTAAACCCAAAATTCC
* **
318296 GAACCCTGTAAATTT------TGAA-TCC
1 GAACCCTG-AACTTTAAACCCAAAATTCC
*
318318 TGAACCCTAAACTTTAAACCCAAAATTCC
1 -GAACCCTGAACTTTAAACCCAAAATTCC
318347 GAACCCTGAACT
1 GAACCCTGAACT
318359 ACTTAGGATT
Statistics
Matches: 46, Mismatches: 8, Indels: 18
0.64 0.11 0.25
Matches are distributed among these distances:
22 8 0.17
23 9 0.20
28 21 0.46
29 8 0.17
ACGTcount: A:0.37, C:0.30, G:0.09, T:0.24
Consensus pattern (28 bp):
GAACCCTGAACTTTAAACCCAAAATTCC
Found at i:318309 original size:51 final size:51
Alignment explanation
Indices: 318253--318354 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
318243 CCTTGAACCT
*
318253 TAAATTTTGAATCCTGAACCCTGAACTTTAAACCCAAAATTCCGAACCCTG
1 TAAATTTTGAATCCTGAACCCTAAACTTTAAACCCAAAATTCCGAACCCTG
318304 TAAATTTTGAATCCTGAACCCTAAACTTTAAACCCAAAATTCCGAACCCTG
1 TAAATTTTGAATCCTGAACCCTAAACTTTAAACCCAAAATTCCGAACCCTG
318355 AACTACTTAG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (51 bp):
TAAATTTTGAATCCTGAACCCTAAACTTTAAACCCAAAATTCCGAACCCTG
Found at i:322676 original size:24 final size:24
Alignment explanation
Indices: 322649--322723 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
322639 AGTTTGACTC
322649 AAACAAATAAAAAGAGTTTAATTG
1 AAACAAATAAAAAGAGTTTAATTG
* *
322673 AAACAAATAAATAGAGTTTAATTA
1 AAACAAATAAAAAGAGTTTAATTG
* * *
322697 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAAAAGAGTTTAATTG
322721 AAA
1 AAA
322724 GATTATTTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.57, C:0.07, G:0.11, T:0.25
Consensus pattern (24 bp):
AAACAAATAAAAAGAGTTTAATTG
Found at i:324667 original size:24 final size:24
Alignment explanation
Indices: 324652--324726 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
324642 AGTTTGACTC
324652 AAACAAATAAAAAGAGTTTAATTG
1 AAACAAATAAAAAGAGTTTAATTG
* *
324676 AAATAAATAAATAGAGTTTAATTG
1 AAACAAATAAAAAGAGTTTAATTG
* * *
324700 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAAAAGAGTTTAATTG
324724 AAA
1 AAA
324727 GATTATTTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.27
Consensus pattern (24 bp):
AAACAAATAAAAAGAGTTTAATTG
Found at i:325297 original size:16 final size:17
Alignment explanation
Indices: 325258--325298 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
325248 AATTATATTG
*
325258 TATAATTTTATTATTTT
1 TATAAATTTATTATTTT
*
325275 AAT-AATTTA-TATTTT
1 TATAAATTTATTATTTT
325290 TATAAATTT
1 TATAAATTT
325299 TAAAAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 8 0.40
16 10 0.50
17 2 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATAAATTTATTATTTT
Found at i:328578 original size:59 final size:59
Alignment explanation
Indices: 328486--328604 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
328476 GTAGTTGCTT
328486 TTTCAAAGATCTCCACTAGATATTCAGCAATTGTATGATAAAAGTAATTCATTTTGCAA
1 TTTCAAAGATCTCCACTAGATATTCAGCAATTGTATGATAAAAGTAATTCATTTTGCAA
328545 TTTCAAAGATCTCCACTAGATATTCAGCAATTGTATGATAAAAGTAATTCATTTTGCAA
1 TTTCAAAGATCTCCACTAGATATTCAGCAATTGTATGATAAAAGTAATTCATTTTGCAA
328604 T
1 T
328605 GACTGATGGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (59 bp):
TTTCAAAGATCTCCACTAGATATTCAGCAATTGTATGATAAAAGTAATTCATTTTGCAA
Found at i:334163 original size:13 final size:13
Alignment explanation
Indices: 334145--334188 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
334135 ATAAATAAAT
*
334145 AATTTATGTAATA
1 AATTTATATAATA
*
334158 AATTTATATAAAA
1 AATTTATATAATA
*
334171 AATTGATATAAT-
1 AATTTATATAATA
334183 AATTTA
1 AATTTA
334189 ATATTACTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (13 bp):
AATTTATATAATA
Found at i:334192 original size:26 final size:26
Alignment explanation
Indices: 334139--334188 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
334129 TTCTTAATAA
* * *
334139 ATAAATAATTTATGTAATAAATTTAT
1 ATAAAAAATTGATATAATAAATTTAT
334165 ATAAAAAATTGATATAAT-AATTTA
1 ATAAAAAATTGATATAATAAATTTA
334189 ATATTACTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
ATAAAAAATTGATATAATAAATTTAT
Found at i:345123 original size:53 final size:52
Alignment explanation
Indices: 345065--345170 Score: 140
Period size: 53 Copynumber: 2.0 Consensus size: 52
345055 CCACCCCCCC
* * *
345065 AAAGAGCTGTTACAGACAGCAAGCTCACAACCAAAACCACAAAAAACAGAACA
1 AAAGAGCTGCTACAAACAACAAGCTCACAACCAAAACCAC-AAAAACAGAACA
* * * *
345118 AAAGAGTTGCTACAAAGAACAAGCTCACAGCCAAAACCACAAATACAGAACA
1 AAAGAGCTGCTACAAACAACAAGCTCACAACCAAAACCACAAAAACAGAACA
345170 A
1 A
345171 CCGATCTGCA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 12 0.26
53 34 0.74
ACGTcount: A:0.53, C:0.25, G:0.13, T:0.08
Consensus pattern (52 bp):
AAAGAGCTGCTACAAACAACAAGCTCACAACCAAAACCACAAAAACAGAACA
Found at i:350297 original size:10 final size:10
Alignment explanation
Indices: 350276--350307 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
350266 CTTCAAATAA
350276 ATTTTCCTTTT
1 ATTTT-CTTTT
350287 ATTTTCTTTT
1 ATTTTCTTTT
350297 ATTTTCTTTT
1 ATTTTCTTTT
350307 A
1 A
350308 GGTCCAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.76
11 5 0.24
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (10 bp):
ATTTTCTTTT
Found at i:361536 original size:2 final size:2
Alignment explanation
Indices: 361531--361556 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
361521 AATAAAAAAT
361531 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
361557 ACACTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:364153 original size:3 final size:3
Alignment explanation
Indices: 364145--364186 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
364135 GTTAACTTCA
364145 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
364187 TTGGTTCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:368408 original size:29 final size:27
Alignment explanation
Indices: 368351--368411 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 27
368341 TGATTAACGA
368351 AAGTATCAACTTGAAAAAAAATAATTT
1 AAGTATCAACTTGAAAAAAAATAATTT
*
368378 AAGTATC-ACTTTCGAATAAAAATAAATTT
1 AAGTATCAAC-TT-GAAAAAAAAT-AATTT
368407 AAGTA
1 AAGTA
368412 CCAAAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 2 0.07
27 9 0.30
28 9 0.30
29 10 0.33
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (27 bp):
AAGTATCAACTTGAAAAAAAATAATTT
Found at i:369151 original size:4 final size:4
Alignment explanation
Indices: 369138--369167 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
369128 AAAAATGAAC
369138 GAAA -AAA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
369168 GAAGGAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:369186 original size:27 final size:26
Alignment explanation
Indices: 369139--369223 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 26
369129 AAAATGAACG
* *
369139 AAAAAAGAAAGAAAGA-AAGAA-AGA
1 AAAAAAGGAAGAAGGAGAAGAAGAGA
*
369163 AAGAAGAAGGAAGAAGGAGAAGAAGGGGA
1 AA-AA-AAGGAAGAAGGAGAAGAA-GAGA
* *
369192 AAAAAGGGAAGAAGGAGAAG--GAAA
1 AAAAAAGGAAGAAGGAGAAGAAGAGA
369216 AAAAAAGG
1 AAAAAAGG
369224 TAATGTGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
24 11 0.22
25 2 0.04
26 10 0.20
27 20 0.41
28 2 0.04
29 4 0.08
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (26 bp):
AAAAAAGGAAGAAGGAGAAGAAGAGA
Found at i:369638 original size:2 final size:2
Alignment explanation
Indices: 369631--369667 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
369621 NNNNNNNNNN
369631 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
369668 TCTTGAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:378459 original size:16 final size:16
Alignment explanation
Indices: 378438--378469 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
378428 TCCAAATCTA
378438 TTAACACATTCTCATG
1 TTAACACATTCTCATG
378454 TTAACACATTCTCATG
1 TTAACACATTCTCATG
378470 GTACCAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (16 bp):
TTAACACATTCTCATG
Found at i:387722 original size:7 final size:6
Alignment explanation
Indices: 387702--387737 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
387692 ACTCCTCAAC
387702 AGAAAA AG-AAA AGAAAAA AGAAAA AGAAAA AGAAAA
1 AGAAAA AGAAAA AG-AAAA AGAAAA AGAAAA AGAAAA
387738 TTTAAATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.18
6 18 0.64
7 5 0.18
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:387725 original size:18 final size:19
Alignment explanation
Indices: 387702--387737 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
387692 ACTCCTCAAC
387702 AGAAAAAG-AAAAGAAAAA
1 AGAAAAAGAAAAAGAAAAA
387720 AGAAAAAGAAAAAGAAAA
1 AGAAAAAGAAAAAGAAAA
387738 TTTAAATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AGAAAAAGAAAAAGAAAAA
Found at i:403078 original size:15 final size:17
Alignment explanation
Indices: 403058--403095 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
403048 AATCTTTTAA
403058 AAATTATAAAAAT-AT-
1 AAATTATAAAAATGATG
*
403073 AAATTATTAAAATGATG
1 AAATTATAAAAATGATG
403090 AAATTA
1 AAATTA
403096 CTGTTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (17 bp):
AAATTATAAAAATGATG
Found at i:433118 original size:12 final size:12
Alignment explanation
Indices: 433093--433205 Score: 62
Period size: 12 Copynumber: 9.8 Consensus size: 12
433083 ATCTACAAGA
433093 TAAATATTAAAT
1 TAAATATTAAAT
433105 TAAAT-TTAATAT
1 TAAATATTAA-AT
* * *
433117 TAAGATAATCACT
1 TAA-ATATTAAAT
*
433130 TTAATATTAAAT
1 TAAATATTAAAT
433142 T--A-A-TAAAT
1 TAAATATTAAAT
* *
433150 T-ACTATTAAAA
1 TAAATATTAAAT
*
433161 TAAGTATTAAAT
1 TAAATATTAAAT
433173 TAAAT-TTAATAT
1 TAAATATTAA-AT
*
433185 TAAATTATTAAAA
1 TAAA-TATTAAAT
433198 T-AATATTA
1 TAAATATTA
433206 TTTTTTGAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 21
0.70 0.12 0.19
Matches are distributed among these distances:
8 6 0.08
9 1 0.01
10 2 0.03
11 18 0.23
12 37 0.47
13 8 0.10
14 6 0.08
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:433144 original size:11 final size:11
Alignment explanation
Indices: 433130--433205 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
433120 GATAATCACT
433130 TTAATATTAAA
1 TTAATATTAAA
433141 TT-A-A-TAAA
1 TTAATATTAAA
*
433149 TTACTATTAAA
1 TTAATATTAAA
*
433160 ATAAGTATTAAA
1 TTAA-TATTAAA
433172 TTAA-ATTTAATA
1 TTAATA-TTAA-A
433184 TTAAATTATTAAA
1 TT-AA-TATTAAA
*
433197 ATAATATTA
1 TTAATATTA
433206 TTTTTTGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
8 6 0.12
9 1 0.02
10 3 0.06
11 17 0.33
12 15 0.29
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:433145 original size:20 final size:18
Alignment explanation
Indices: 433095--433204 Score: 84
Period size: 19 Copynumber: 5.9 Consensus size: 18
433085 CTACAAGATA
433095 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
433112 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
*
433132 AATATTAAATTAATAAATT
1 AATATTAAATTAAT-ATTT
* *
433151 ACTATTAAAATAAGTA-TT
1 AATATTAAATTAA-TATTT
*
433169 AA-ATTAAATTTAATATTA
1 AATATTAAA-TTAATATTT
*
433187 AATTATTAAAATAATATT
1 AA-TATTAAATTAATATT
433205 ATTTTTTGAA
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
17 19 0.25
18 10 0.13
19 23 0.31
20 23 0.31
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.43
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:438825 original size:27 final size:27
Alignment explanation
Indices: 438795--438863 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
438785 TTTAAAGTTG
*
438795 TTTAAACAATTTAATAAATTCTAATAT
1 TTTAAAGAATTTAATAAATTCTAATAT
438822 TTTAAAGAATTTAATAAATTCTAATAT
1 TTTAAAGAATTTAATAAATTCTAATAT
438849 TTTAAAGAATTTAAT
1 TTTAAAGAATTTAAT
438864 TAATGAAGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (27 bp):
TTTAAAGAATTTAATAAATTCTAATAT
Done.