Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 1 of 325
Found at i:4954 original size:26 final size:26
Alignment explanation
Indices: 4918--5054 Score: 247
Period size: 26 Copynumber: 5.3 Consensus size: 26
4908 ACATGAAATT
4918 ATTATCATGAAACATTTACCTAACCC
1 ATTATCATGAAACATTTACCTAACCC
*
4944 ATTATCATGAAACATTTACCTAACAC
1 ATTATCATGAAACATTTACCTAACCC
4970 ATTATCATGAAACATTTACCTAACCC
1 ATTATCATGAAACATTTACCTAACCC
*
4996 ATTATCATGAAACATTTACCTAACAC
1 ATTATCATGAAACATTTACCTAACCC
*
5022 ATTATCATGAAACATTTACCTAACCT
1 ATTATCATGAAACATTTACCTAACCC
5048 ATTATCA
1 ATTATCA
5055 ATTTGTACCA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 106 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (26 bp):
ATTATCATGAAACATTTACCTAACCC
Found at i:4959 original size:13 final size:13
Alignment explanation
Indices: 4943--5037 Score: 58
Period size: 13 Copynumber: 7.3 Consensus size: 13
4933 TTACCTAACC
4943 CATTATCATGAAA
1 CATTATCATGAAA
*
4956 CATT-TACCT-AACA
1 CATTAT-CATGAA-A
4969 CATTATCATGAAA
1 CATTATCATGAAA
* *
4982 CATT-TACCT-AACC
1 CATTAT-CATGAA-A
4995 CATTATCATGAAA
1 CATTATCATGAAA
*
5008 CATT-TACCT-AACA
1 CATTAT-CATGAA-A
5021 CATTATCATGAAA
1 CATTATCATGAAA
5034 CATT
1 CATT
5038 TACCTAACCT
Statistics
Matches: 62, Mismatches: 8, Indels: 24
0.66 0.09 0.26
Matches are distributed among these distances:
12 9 0.15
13 44 0.71
14 9 0.15
ACGTcount: A:0.41, C:0.23, G:0.04, T:0.32
Consensus pattern (13 bp):
CATTATCATGAAA
Found at i:5905 original size:33 final size:33
Alignment explanation
Indices: 5863--5929 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
5853 TTTGGATGAC
*
5863 CCAGCGGAAATAGCCAGGTTGAGAACAGACGAT
1 CCAGCGGAAATAGCCAGGTCGAGAACAGACGAT
5896 CCAGCGGAAATAGCCAGGTCGAGAACAGACGAT
1 CCAGCGGAAATAGCCAGGTCGAGAACAGACGAT
5929 C
1 C
5930 ATGAGGCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.24, G:0.30, T:0.10
Consensus pattern (33 bp):
CCAGCGGAAATAGCCAGGTCGAGAACAGACGAT
Found at i:13925 original size:70 final size:71
Alignment explanation
Indices: 13646--14000 Score: 336
Period size: 74 Copynumber: 4.9 Consensus size: 71
13636 TTTAGGTACT
* * ** **
13646 CTGAGGTATCTTTAATTCATGTTTTCAAAAATCAACTCATATTATGAGAAATGAGTTGAGCCTCA
1 CTGAGGTATTTTTAATTTATG-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
13711 GGTCACACG
65 GG--ACACG
* ** **
13720 CTGAGGTATTTTTAGTTTATGTTTCAAAAAAAATTGACTCATATTGCGAGAGGTGAGTCAAGCCT
1 CTGAGGTATTTTTAATTTATGTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
*
13785 CAGGTCACG
63 CAGGACACG
* * *
13794 CTGAGGTGTTTTTAATTCCTGTTGTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCT
1 CTGAGGTATTTTTAATT--T-ATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
*
13859 CAAGACACG
63 CAGGACACG
* * * * *
13868 TTGAGGTAATTTCAATTTATG-TTCCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 CTGAGGTATTTTTAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
*
13932 GGCACG
66 GACACG
* ** * * * *
13938 CTGAGGTATTTTTTAGTTTATGTTT-AGAAAATTGACTCATCTTGCGAAAAGTGAGTTAAGCCT
1 CTGAGGTA-TTTTTAATTTATGTTTCA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
14001 TTCAATTTAT
Statistics
Matches: 229, Mismatches: 43, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
70 51 0.22
71 12 0.05
72 33 0.14
73 4 0.02
74 89 0.39
76 34 0.15
77 6 0.03
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (71 bp):
CTGAGGTATTTTTAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
GACACG
Found at i:13940 original size:144 final size:145
Alignment explanation
Indices: 13646--13950 Score: 364
Period size: 144 Copynumber: 2.1 Consensus size: 145
13636 TTTAGGTACT
* *
13646 CTGAGGTATCTTTAATTCATGTTTTCAAAAATCAACTCATATTATGAGAAATGAGTTGAGCCTCA
1 CTGAGGTATTTTTAATTCATGTTTTCAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCA
* * * * **
13711 GGTCACACGCTGAGGTATTTTTAGTTTATGTTTCAAAAAAAATTGACTCATATTGCGAGAGGTGA
66 AG-CACACGCTGAGGTAATTTCAATTTATGTTTC--AAAAAATCAACTCATATTGCGAGAGGTGA
*
13776 GTCAAGCCTCAGGTCACG
128 GTCAAGCCTCAGGGCACG
* * * * **
13794 CTGAGGTGTTTTTAATTCCTGTTGTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCT
1 CTGAGGTATTTTTAATTCATG-T-TTTCAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCT
* *
13859 CAAG-ACACGTTGAGGTAATTTCAATTTATG-TTC-CAAAATCAACTCATATTGCGAGAGGTGAG
64 CAAGCACACGCTGAGGTAATTTCAATTTATGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAG
** *
13921 TTGAGCCTCGGGGCACG
129 TCAAGCCTCAGGGCACG
13938 CTGAGGTATTTTT
1 CTGAGGTATTTTT
13951 TAGTTTATGT
Statistics
Matches: 134, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
144 51 0.38
147 3 0.02
148 40 0.30
149 1 0.01
150 39 0.29
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (145 bp):
CTGAGGTATTTTTAATTCATGTTTTCAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCA
AGCACACGCTGAGGTAATTTCAATTTATGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTC
AAGCCTCAGGGCACG
Found at i:14035 original size:52 final size:52
Alignment explanation
Indices: 13954--14052 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 52
13944 TATTTTTTAG
** *
13954 TTTATGTTTAGAAAATTGACTCATCTTGCGAAAAGTGAGTTAAGCCTTTCAA
1 TTTATGTTTAGAAAATCAACTCATATTGCGAAAAGTGAGTTAAGCCTTTCAA
* * *
14006 TTTATGTTTCA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTATGTTT-AGAAAATCAACTCATATTGCGAAAAGTGAGTTAAGCCT
14053 CGGGGCACGC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
52 39 0.98
53 1 0.03
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.35
Consensus pattern (52 bp):
TTTATGTTTAGAAAATCAACTCATATTGCGAAAAGTGAGTTAAGCCTTTCAA
Found at i:14242 original size:54 final size:53
Alignment explanation
Indices: 14098--14297 Score: 234
Period size: 56 Copynumber: 3.8 Consensus size: 53
14088 AATTCCTGTT
* * * *
14098 TTTTTCAAAAATTAACTCATATTGCGAGAGGTGAGTTAAGCCTTTCAATTTATA
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTT-TG
14152 TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTG
1 TTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTT-TG
*
14208 TTTTTCAAAAAGCAACTCATATTGCGAGAGGTGAGTTGTA-CC---T--TTTTG
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG-AGCCTTTTAATTTTG
* * *
14256 TTTTGC-AAAATCAACTCATATTGCAAGAGATGAGTTGAGCCT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
14298 CGGGTCACAT
Statistics
Matches: 131, Mismatches: 10, Indels: 16
0.83 0.06 0.10
Matches are distributed among these distances:
46 1 0.01
47 30 0.23
48 7 0.05
49 3 0.02
51 1 0.01
54 39 0.30
55 1 0.01
56 49 0.37
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36
Consensus pattern (53 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTG
Found at i:14338 original size:14 final size:14
Alignment explanation
Indices: 14319--14345 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14309 TCAAAGTATT
14319 TTCAAATTCTGTTA
1 TTCAAATTCTGTTA
14333 TTCAAATTCTGTT
1 TTCAAATTCTGTT
14346 TTTAATTTTT
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:0.15, G:0.07, T:0.52
Consensus pattern (14 bp):
TTCAAATTCTGTTA
Found at i:14573 original size:71 final size:71
Alignment explanation
Indices: 14452--14701 Score: 288
Period size: 71 Copynumber: 3.5 Consensus size: 71
14442 GTTTTCCAAG
* * * *
14452 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGAACGTTGAGGTAATTTCAATT-TA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATTCTA
14516 TATTTCA
66 T-TTTCA
* * * *
14523 AAAATCAACTCATATTGTGAGAAGTGAGTTGAACCTCGGGGCACGCTGAGGTAATTTCAATTCT-
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATTCTA
*
14587 TGTTAAATCT
66 T-TT---TCA
* * * *
14597 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGCGGCACGCTAAGGTATTTTCAAATTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTC-AATTCT
14662 ATTTTCA
65 ATTTTCA
* * *
14669 AAATTCAATTCATATTACGAGAGGTGAGTTGAG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAG
14702 TCTTTTTAAT
Statistics
Matches: 152, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
71 57 0.38
72 33 0.22
74 53 0.35
75 8 0.05
76 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATTCTA
TTTTCA
Found at i:14725 original size:13 final size:13
Alignment explanation
Indices: 14704--14739 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
14694 GAGTTGAGTC
14704 TTTTTAATTTCTA
1 TTTTTAATTTCTA
* *
14717 TTTTCAATTTCTG
1 TTTTTAATTTCTA
14730 TTTTTAATTT
1 TTTTTAATTT
14740 TTCAAAGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.08, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTTAATTTCTA
Found at i:14865 original size:13 final size:13
Alignment explanation
Indices: 14847--14871 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14837 TGAGTTGAGC
14847 CTTTTAATTTCTG
1 CTTTTAATTTCTG
14860 CTTTTAATTTCT
1 CTTTTAATTTCT
14872 ATGTTTCAAA
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:0.16, C:0.16, G:0.04, T:0.64
Consensus pattern (13 bp):
CTTTTAATTTCTG
Found at i:15581 original size:23 final size:21
Alignment explanation
Indices: 15555--15603 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
15545 AAACAAACTG
*
15555 ACCCATTACAAACTAAACCCAA
1 ACCCATTAC-AACCAAACCCAA
*
15577 TACCCCTTTACAACCAAACCCAA
1 -A-CCCATTACAACCAAACCCAA
15600 ACCC
1 ACCC
15604 CAAAACCCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 3 0.13
22 1 0.04
23 12 0.52
24 7 0.30
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (21 bp):
ACCCATTACAACCAAACCCAA
Found at i:15587 original size:24 final size:22
Alignment explanation
Indices: 15560--15604 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
15550 AACTGACCCA
*
15560 TTACAAACTAAACCCAATACCCCT
1 TTAC-AACCAAACCCAA-ACCCCT
15584 TTACAACCAAACCCAAACCCC
1 TTACAACCAAACCCAAACCCC
15605 AAAACCCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 11 0.55
24 4 0.20
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (22 bp):
TTACAACCAAACCCAAACCCCT
Found at i:17078 original size:2 final size:2
Alignment explanation
Indices: 17071--17109 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
17061 ATTTTTGTTC
*
17071 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17110 TTCCATACGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20449 original size:23 final size:22
Alignment explanation
Indices: 20430--20492 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
20420 TAAAAAATGC
20430 TAATACAATTACATATAAAATTT
1 TAATACAATTACATATAAAA-TT
* *
20453 TAATA-AATATAAATTTAAAATT
1 TAATACAAT-TACATATAAAATT
20475 TAAATACAATTACATATA
1 T-AATACAATTACATATA
20493 TAGGATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 6 0.18
23 24 0.73
24 3 0.09
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (22 bp):
TAATACAATTACATATAAAATT
Found at i:21110 original size:21 final size:21
Alignment explanation
Indices: 21084--21167 Score: 87
Period size: 21 Copynumber: 3.8 Consensus size: 21
21074 CTCCTAAACT
*
21084 TTAAACCCTAAACCATATATC
1 TTAAACCATAAACCATATATC
* *
21105 TTAAACCATAGTTAACTCAAAAATC
1 TTAAACCATA---AAC-CATATATC
* *
21130 TTAAACCCTAAACTATATATC
1 TTAAACCATAAACCATATATC
21151 TTAAACCATAAACCATA
1 TTAAACCATAAACCATA
21168 AACTATAATG
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
21 29 0.58
22 3 0.06
24 3 0.06
25 15 0.30
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.29
Consensus pattern (21 bp):
TTAAACCATAAACCATATATC
Found at i:21119 original size:46 final size:46
Alignment explanation
Indices: 21067--21160 Score: 145
Period size: 46 Copynumber: 2.0 Consensus size: 46
21057 CTTCAAATAC
**
21067 TAGTTAACTCCTAAA-CTTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCAAAAATC-TTAAACCCTAAACCATATATCTTAAACCA
*
21113 TAGTTAACTCAAAAATCTTAAACCCTAAACTATATATCTTAAACCA
1 TAGTTAACTCAAAAATCTTAAACCCTAAACCATATATCTTAAACCA
21159 TA
1 TA
21161 AACCATAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 43 0.98
47 1 0.02
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.31
Consensus pattern (46 bp):
TAGTTAACTCAAAAATCTTAAACCCTAAACCATATATCTTAAACCA
Found at i:21352 original size:42 final size:40
Alignment explanation
Indices: 21307--21486 Score: 209
Period size: 41 Copynumber: 4.4 Consensus size: 40
21297 GTTTATGATT
21307 TTTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCT-G
* * *
21348 TTTTTAGCGGCATTTTTTCCAAAAGCGCCGTTAATGCTCTGG
1 TTTTTAGCGGC-GTTTTGCCAAAAGCGCCGCTAATGCTCT-G
* *
21390 TTTTTAGTGGCGTTTTGCCAAAAGCGCCGCTAATTCTCTG
1 TTTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTG
* * * * *
21430 TTTTTTGCGGCATTTTTTACTAAAA-CGCCGCTATTGCTCTG
1 TTTTTAGCGGC--GTTTTGCCAAAAGCGCCGCTAATGCTCTG
*
21471 TTTTTAGTGGCGTTTT
1 TTTTTAGCGGCGTTTT
21487 TGGTAAAACA
Statistics
Matches: 118, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
39 4 0.03
40 10 0.08
41 58 0.49
42 46 0.39
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTG
Found at i:21405 original size:83 final size:81
Alignment explanation
Indices: 21307--21486 Score: 272
Period size: 83 Copynumber: 2.2 Consensus size: 81
21297 GTTTATGATT
*
21307 TTTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCATTTTTT-CCAAA
1 TTTTTAGTGGCGTTTTGCCAAAAGCGCCGCTAATGCTCT-GTTTTTAGCGGCATTTTTTACCAAA
*
21371 AGCGCCGTTAATGCTCTGG
65 A-CGCCGCTAATGCTCT-G
* * *
21390 TTTTTAGTGGCGTTTTGCCAAAAGCGCCGCTAATTCTCTGTTTTTTGCGGCATTTTTTACTAAAA
1 TTTTTAGTGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGTTTTTAGCGGCATTTTTTACCAAAA
*
21455 CGCCGCTATTGCTCTG
66 CGCCGCTAATGCTCTG
21471 TTTTTAGTGGCGTTTT
1 TTTTTAGTGGCGTTTT
21487 TGGTAAAACA
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
81 17 0.19
82 31 0.34
83 42 0.47
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (81 bp):
TTTTTAGTGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGTTTTTAGCGGCATTTTTTACCAAAA
CGCCGCTAATGCTCTG
Found at i:21487 original size:41 final size:41
Alignment explanation
Indices: 21307--21517 Score: 198
Period size: 41 Copynumber: 5.1 Consensus size: 41
21297 GTTTATGATT
* *
21307 TTTTTAGCGGC-GTTTTGCCAAAAGCGCCGCTAATGCTCTGG
1 TTTTTAGCGGCATTTTTGCCAAAAGCGCCGCTATTGCTCT-G
* * *
21348 TTTTTAGCGGCATTTTTTCCAAAAGCGCCGTTAATGCTCTGG
1 TTTTTAGCGGCATTTTTGCCAAAAGCGCCGCTATTGCTCT-G
* *
21390 TTTTTAGTGGC-GTTTTGCCAAAAGCGCCGCTAATT-CTCTG
1 TTTTTAGCGGCATTTTTGCCAAAAGCGCCGCT-ATTGCTCTG
* * *
21430 TTTTTTGCGGCATTTTTTACTAAAA-CGCCGCTATTGCTCTG
1 TTTTTAGCGGCA-TTTTTGCCAAAAGCGCCGCTATTGCTCTG
* * ** * *
21471 TTTTTAGTGGCGTTTTTGGTAAAA-CACCGCTATTGCTATG
1 TTTTTAGCGGCATTTTTGCCAAAAGCGCCGCTATTGCTCTG
21511 TGTTTTA
1 T-TTTTA
21518 CAATTTTTGC
Statistics
Matches: 144, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
40 38 0.26
41 58 0.40
42 48 0.33
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (41 bp):
TTTTTAGCGGCATTTTTGCCAAAAGCGCCGCTATTGCTCTG
Found at i:21556 original size:12 final size:12
Alignment explanation
Indices: 21541--21566 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21531 GTTTTTTGAT
21541 AAAACGCCGCTA
1 AAAACGCCGCTA
21553 AAAACGCCGCTA
1 AAAACGCCGCTA
21565 AA
1 AA
21567 GCCCTATTTT
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:21886 original size:34 final size:34
Alignment explanation
Indices: 21839--21919 Score: 117
Period size: 34 Copynumber: 2.4 Consensus size: 34
21829 GCATGACTGC
21839 TACTGATACTGTGATAGGCTAAAGCCCTAATGCA
1 TACTGATACTGTGATAGGCTAAAGCCCTAATGCA
* * *
21873 TACTGATATTGTGATGGGCTAAAGCCCTACTGCA
1 TACTGATACTGTGATAGGCTAAAGCCCTAATGCA
*
21907 TATTTGATACTGT
1 TA-CTGATACTGT
21920 ATTGAGATGG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 33 0.80
35 8 0.20
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (34 bp):
TACTGATACTGTGATAGGCTAAAGCCCTAATGCA
Found at i:23990 original size:39 final size:40
Alignment explanation
Indices: 23910--23990 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
23900 ATATTATAAG
* * **
23910 ATTGATTTATATTTAAATTTAAATACAAAATTGGGTTGTT
1 ATTGAATTATATATAAATTTAAATACAAAATTAAGTTGTT
23950 ATTGAATTATATATAAATTTAAATA-AAAATTAAGTTGTT
1 ATTGAATTATATATAAATTTAAATACAAAATTAAGTTGTT
23989 AT
1 AT
23991 AAATAGATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 14 0.38
40 23 0.62
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (40 bp):
ATTGAATTATATATAAATTTAAATACAAAATTAAGTTGTT
Found at i:28460 original size:17 final size:17
Alignment explanation
Indices: 28434--28468 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28424 ATCAAGAAAT
*
28434 AATTTTAAATTATAAAA
1 AATTTAAAATTATAAAA
*
28451 AATTTAAAATTTTAAAA
1 AATTTAAAATTATAAAA
28468 A
1 A
28469 GTCAATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTTAAAATTATAAAA
Found at i:30035 original size:15 final size:15
Alignment explanation
Indices: 30015--30044 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30005 CATTTTATTT
*
30015 ATATTAGGATAATTA
1 ATATTAAGATAATTA
30030 ATATTAAGATAATTA
1 ATATTAAGATAATTA
30045 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:30072 original size:27 final size:26
Alignment explanation
Indices: 30011--30073 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
30001 ACTCCATTTT
30011 ATTTATATTAGGATAATTAATATTAAG
1 ATTT-TATTAGGATAATTAATATTAAG
* * * *
30038 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
30066 ATTTTATT
1 ATTTTATT
30074 TTATTTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:30086 original size:10 final size:10
Alignment explanation
Indices: 30068--30115 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
30058 ATTTTAGGAT
30068 TTTAT-TTTA
1 TTTATCTTTA
30077 TTTATCTTTA
1 TTTATCTTTA
30087 TTTATCTTTA
1 TTTATCTTTA
* ** *
30097 ATTAAATGTA
1 TTTATCTTTA
30107 TTTATCTTT
1 TTTATCTTT
30116 TTAGAATTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 5 0.17
10 25 0.83
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:30703 original size:26 final size:26
Alignment explanation
Indices: 30666--30775 Score: 202
Period size: 26 Copynumber: 4.2 Consensus size: 26
30656 TGATACAAAT
*
30666 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
30692 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
30718 TGATAATGTGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
30744 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
30770 TGATAA
1 TGATAA
30776 GAATTTCATG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.39
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:36962 original size:5 final size:5
Alignment explanation
Indices: 36946--36996 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
36936 GCAACCCAAT
*
36946 TTTTA -TTT- TTTTA TTTTTA TTTTA TTTTAA TTTTA -TTTA TTTTA TCTTA
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA
36995 TT
1 TT
36997 ATTTATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 10 0.26
5 19 0.49
6 10 0.26
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:36970 original size:11 final size:11
Alignment explanation
Indices: 36954--37000 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
36944 ATTTTTATTT
36954 TTTTATTTTTA
1 TTTTATTTTTA
*
36965 TTTTATTTTAA
1 TTTTATTTTTA
36976 TTTTA--TTTA
1 TTTTATTTTTA
36985 TTTTATCTTATTA
1 TTTTAT-TT-TTA
36998 TTT
1 TTT
37001 ATTATTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 8 0.27
11 15 0.50
12 1 0.03
13 6 0.20
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:36978 original size:25 final size:25
Alignment explanation
Indices: 36944--36996 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
36934 ACGCAACCCA
* *
36944 ATTTTTATTTT-TTTATTTTTATTTT
1 ATTTTAATTTTATTTA-TTTTATCTT
36969 ATTTTAATTTTATTTATTTTATCTT
1 ATTTTAATTTTATTTATTTTATCTT
36994 ATT
1 ATT
36997 ATTTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (25 bp):
ATTTTAATTTTATTTATTTTATCTT
Found at i:36984 original size:20 final size:21
Alignment explanation
Indices: 36961--37008 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
36951 TTTTTTTATT
*
36961 TTTATTTTATTTTAAT-TTTA
1 TTTATTTTATCTTAATATTTA
*
36981 TTTATTTTATCTTATTATTTA
1 TTTATTTTATCTTAATATTTA
37002 -TTATTTT
1 TTTATTTT
37009 CAGATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTATTTTATCTTAATATTTA
Found at i:36998 original size:17 final size:15
Alignment explanation
Indices: 36944--37003 Score: 77
Period size: 15 Copynumber: 3.9 Consensus size: 15
36934 ACGCAACCCA
36944 ATTTTTATTT-TTTT
1 ATTTTTATTTATTTT
36958 ATTTTTATTTTATTTT
1 ATTTTTA-TTTATTTT
*
36974 AATTTTATTTATTTT
1 ATTTTTATTTATTTT
36989 ATCTTATTATTTATT
1 AT-TT-TTATTTATT
37004 ATTTTCAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.17
15 12 0.30
16 12 0.30
17 9 0.22
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.77
Consensus pattern (15 bp):
ATTTTTATTTATTTT
Found at i:37933 original size:20 final size:20
Alignment explanation
Indices: 37905--37942 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
37895 TATTCCTAAG
37905 GAAAGTAAA-TAAATAAAGTT
1 GAAAGTAAAGTAAA-AAAGTT
*
37925 GAAATTAAAGTAAAAAAG
1 GAAAGTAAAGTAAAAAAG
37943 AAAAAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.63, C:0.00, G:0.16, T:0.21
Consensus pattern (20 bp):
GAAAGTAAAGTAAAAAAGTT
Found at i:39204 original size:2 final size:2
Alignment explanation
Indices: 39197--39237 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
39187 TACAATTTTG
39197 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
39238 TATATATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:39472 original size:22 final size:25
Alignment explanation
Indices: 39422--39472 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 25
39412 AAAATTTGTG
* *
39422 ATATTTAATAATAGATATAAAAAAC
1 ATATTTAATAAGAGATATAAAAAAA
39447 ATATTT-ATAAGA-ATA-AAAAAAA
1 ATATTTAATAAGAGATATAAAAAAA
39469 ATAT
1 ATAT
39473 ATTGGTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.42
23 3 0.12
24 5 0.21
25 6 0.25
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (25 bp):
ATATTTAATAAGAGATATAAAAAAA
Found at i:39717 original size:3 final size:3
Alignment explanation
Indices: 39709--39832 Score: 67
Period size: 3 Copynumber: 38.7 Consensus size: 3
39699 ACAAGTAAAA
* * *
39709 AAT AAT AAT AAT ATAT AAAT AAT GAGT AA- AAT AAT AAT AATT TAT GAAA
1 AAT AAT AAT AAT A-AT -AAT AAT -AAT AAT AAT AAT AAT AA-T AAT -AAT
39758 AAT AAT ATAT AAT AAAT AAT AAT AAT -AT AAAT AAT ATAT AAAT AAAT
1 AAT AAT A-AT AAT -AAT AAT AAT AAT AAT -AAT AAT A-AT -AAT -AAT
* *
39805 AAT TAT -AT AAT ATAT AAT -AT AAA AAT AA
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA
39833 GGTTTAAAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 30
0.71 0.07 0.22
Matches are distributed among these distances:
2 8 0.08
3 59 0.61
4 28 0.29
5 2 0.02
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:39771 original size:7 final size:7
Alignment explanation
Indices: 39759--39825 Score: 73
Period size: 7 Copynumber: 9.1 Consensus size: 7
39749 TTTATGAAAA
39759 ATAATAT
1 ATAATAT
*
39766 ATAATAA
1 ATAATAT
39773 ATAATA-
1 ATAATAT
39779 ATAATAT
1 ATAATAT
39786 AAATAATAT
1 --ATAATAT
*
39795 ATAAATAA
1 AT-AATAT
39803 ATAATTAT
1 ATAA-TAT
39811 ATAATAT
1 ATAATAT
39818 ATAATAT
1 ATAATAT
39825 A
1 A
39826 AAAATAAGGT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
6 6 0.12
7 27 0.52
8 12 0.23
9 7 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
ATAATAT
Found at i:39804 original size:30 final size:29
Alignment explanation
Indices: 39674--39832 Score: 132
Period size: 30 Copynumber: 5.3 Consensus size: 29
39664 AATTATTAAC
*
39674 ATATAAATAAA-AATAAGTATATAATACAAGT
1 ATATAAATAAATAATAA-TATATAA-ATAA-T
*
39705 A-AAAAAT-AATAATAATATATAAATAAT
1 ATATAAATAAATAATAATATATAAATAAT
*
39732 GAGTA-AAAT-AATAATAATTTATGAAA-AAT
1 -A-TATAAATAAATAATAATATAT-AAATAAT
39761 AATATATAATAAATAATAATAATATAAATAAT
1 -ATATA-AATAAATAATAAT-ATATAAATAAT
* *
39793 ATATAAATAAATAATTATATAATATATAAT
1 ATATAAATAAATAATAATAT-ATAAATAAT
*
39823 ATAAAAATAA
1 ATATAAATAA
39833 GGTTTAAAAA
Statistics
Matches: 109, Mismatches: 8, Indels: 23
0.78 0.06 0.16
Matches are distributed among these distances:
27 1 0.01
28 6 0.06
29 32 0.29
30 46 0.42
31 18 0.17
32 6 0.06
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (29 bp):
ATATAAATAAATAATAATATATAAATAAT
Found at i:39815 original size:72 final size:74
Alignment explanation
Indices: 39682--39833 Score: 178
Period size: 72 Copynumber: 2.1 Consensus size: 74
39672 ACATATAAAT
*
39682 AAAAATAAGTATATAATACAAGTAAAAAATAATAATAATATATAAATAATGAGTAAAATAATA-A
1 AAAAATAAGTATATAATACAAGTAAAAAATAATAATAATATATAAATAATGAATAAAATAATATA
39746 TAATTTATG
66 TAATTTATG
* *
39755 AAAAATAA-TATATAATA-AA-TAATAATAAT-ATAAATAATATATAAATAAAT-AATTATATAA
1 AAAAATAAGTATATAATACAAGTAA-AA-AATAAT-AATAATATATAAAT-AATGAATAAAATAA
39815 TATATAA--TAT-
62 TATATAATTTATG
39825 AAAAATAAG
1 AAAAATAAG
39834 GTTTAAAAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 14
0.80 0.03 0.16
Matches are distributed among these distances:
70 11 0.16
71 9 0.13
72 35 0.50
73 15 0.21
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.32
Consensus pattern (74 bp):
AAAAATAAGTATATAATACAAGTAAAAAATAATAATAATATATAAATAATGAATAAAATAATATA
TAATTTATG
Found at i:39831 original size:15 final size:16
Alignment explanation
Indices: 39712--39823 Score: 89
Period size: 14 Copynumber: 7.2 Consensus size: 16
39702 AGTAAAAAAT
39712 AATAATA-AT-ATATA
1 AATAATATATAATATA
*
39726 AATAATGAGTAAAATA-A
1 AATAAT-A-TATAATATA
* *
39743 TAATAATTTATGA-A-A
1 -AATAATATATAATATA
39758 AATAATATAT-A-ATA
1 AATAATATATAATATA
39772 AATAATA-ATAATATA
1 AATAATATATAATATA
39787 AATAATATATAA-ATA
1 AATAATATATAATATA
39802 AATAATTATATAATATA
1 AATAA-TATATAATATA
39819 TAATA
1 -AATA
39824 TAAAAATAAG
Statistics
Matches: 81, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
13 4 0.05
14 24 0.30
15 21 0.26
16 14 0.17
17 5 0.06
18 13 0.16
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
AATAATATATAATATA
Found at i:40439 original size:9 final size:9
Alignment explanation
Indices: 40427--40463 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
40417 GCAGTACCTG
40427 CACACGCGC
1 CACACGCGC
*
40436 CACACACGC
1 CACACGCGC
40445 CACACGCGC
1 CACACGCGC
*
40454 CTCACGCGC
1 CACACGCGC
40463 C
1 C
40464 GTCATATACG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.22, C:0.57, G:0.19, T:0.03
Consensus pattern (9 bp):
CACACGCGC
Found at i:41528 original size:15 final size:15
Alignment explanation
Indices: 41508--41537 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41498 CATTTTATTT
*
41508 ATATTAGGATAATTA
1 ATATTAAGATAATTA
41523 ATATTAAGATAATTA
1 ATATTAAGATAATTA
41538 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:57145 original size:16 final size:17
Alignment explanation
Indices: 57121--57153 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
57111 ACTATTGTGC
*
57121 CACATATAA-AATTTGT
1 CACAAATAATAATTTGT
57137 CACAAATAATAATTTGT
1 CACAAATAATAATTTGT
57154 GATGAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
CACAAATAATAATTTGT
Found at i:64882 original size:18 final size:18
Alignment explanation
Indices: 64843--64882 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
64833 GCATCCATGT
*
64843 ATTAAGGGATAGAATTTA
1 ATTAAGGGATAGAATTCA
* *
64861 ATTAAGGGGTAGAATTCG
1 ATTAAGGGATAGAATTCA
64879 ATTA
1 ATTA
64883 TTGATAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.33
Consensus pattern (18 bp):
ATTAAGGGATAGAATTCA
Found at i:67489 original size:17 final size:17
Alignment explanation
Indices: 67430--67489 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
67420 TAATAAATTT
67430 AAAATATAATATATAATAA
1 AAAATATAAT-TAT-ATAA
67449 AAAATAT-ATT-TAT-A
1 AAAATATAATTATATAA
*
67463 AGAATAATAATTATATAA
1 AAAAT-ATAATTATATAA
67481 AAAATATAA
1 AAAATATAA
67490 AATATATTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
17 8 0.23
18 7 0.20
19 7 0.20
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATATAATTATATAA
Found at i:68025 original size:17 final size:18
Alignment explanation
Indices: 67972--68069 Score: 137
Period size: 18 Copynumber: 5.5 Consensus size: 18
67962 AATCATATCT
*
67972 TCTAAGATTGTATATCATA
1 TCTAAGATTG-CTATCATA
*
67991 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
68009 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
68026 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
*
68044 TTTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
68061 TCTAAGATT
1 TCTAAGATT
68070 ACATATCATT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
17 30 0.42
18 31 0.44
19 10 0.14
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:68030 original size:35 final size:35
Alignment explanation
Indices: 67972--68078 Score: 169
Period size: 35 Copynumber: 3.0 Consensus size: 35
67962 AATCATATCT
67972 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
68009 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
* *
68044 TTTAAGATTGTATCATATCTAAGATTACATATCAT
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCAT
68079 TGAAGATTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
35 52 0.78
36 5 0.07
37 10 0.15
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.39
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:69639 original size:108 final size:108
Alignment explanation
Indices: 69443--69639 Score: 247
Period size: 108 Copynumber: 1.8 Consensus size: 108
69433 TGTATGGTCA
* *
69443 GGCCGTGTGACTCAAAATCCTCGAATCCCTAATTCTAAAATTCACACACCCGTGTGCCCAGTGGA
1 GGCCATGTGACTCAAAATCCTCAAATCCCTAATTCTAAAATTCACACACCCGTGTGCCCAGTGGA
*
69508 CACGGCCATGTGAAAATCAACAAAATCACCAAATCGGCTACAC
66 CACGACCATGTGAAAATCAACAAAATCACCAAATCGGCTACAC
* * * *
69551 GGCCATGTGACTCCAAATCC-CTAAATCCTTAATTCCT-AATTTCACACACTCGTGTGCCCAAG-
1 GGCCATGTGACTCAAAATCCTC-AAATCCCTAATT-CTAAAATTCACACACCCGTGTGCCC-AGT
*** *
69613 GGACACGATTGTGTGAAAATCGACAAA
63 GGACACGACCATGTGAAAATCAACAAA
69640 TCCCCATATC
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
107 1 0.01
108 70 0.93
109 4 0.05
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (108 bp):
GGCCATGTGACTCAAAATCCTCAAATCCCTAATTCTAAAATTCACACACCCGTGTGCCCAGTGGA
CACGACCATGTGAAAATCAACAAAATCACCAAATCGGCTACAC
Found at i:70077 original size:21 final size:21
Alignment explanation
Indices: 70051--70101 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
70041 TGAAAGAAGA
*
70051 AAAATAGAAA-TAAAAGAAATC
1 AAAATA-AAATTAAAACAAATC
*
70072 AAAATAAAATTAAAACAAATA
1 AAAATAAAATTAAAACAAATC
70093 ATAAATAAA
1 A-AAATAAA
70102 TAACATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.12
21 16 0.62
22 7 0.27
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (21 bp):
AAAATAAAATTAAAACAAATC
Found at i:71222 original size:21 final size:21
Alignment explanation
Indices: 71193--71232 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
71183 TTCCCTATCC
* *
71193 ATTTTCATCATTTTCCATACA
1 ATTTCCATCATTTCCCATACA
71214 ATTTCCATCATTTCCCATA
1 ATTTCCATCATTTCCCATA
71233 ACCTTCAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTCCATCATTTCCCATACA
Found at i:71837 original size:23 final size:24
Alignment explanation
Indices: 71811--71855 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
71801 TTTATAAAAT
* *
71811 TTTAAATTTATT-TTCGTTTTACA
1 TTTAAATTAATTGTTCATTTTACA
*
71834 TTTATATTAATTGTTCATTTTA
1 TTTAAATTAATTGTTCATTTTA
71856 TATTATTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTAAATTAATTGTTCATTTTACA
Found at i:73517 original size:24 final size:25
Alignment explanation
Indices: 73490--73546 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
73480 GATAAGTCTG
73490 TATCTATTA-TTTTCAGCAGATTTC
1 TATCTATTATTTTTCAGCAGATTTC
*
73514 TATCTATTATTTTTTAGCAGATTTC
1 TATCTATTATTTTTCAGCAGATTTC
73539 TATCTATT
1 TATCTATT
73547 TTTAGTAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 9 0.29
25 22 0.71
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (25 bp):
TATCTATTATTTTTCAGCAGATTTC
Found at i:73540 original size:21 final size:21
Alignment explanation
Indices: 73492--73560 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 21
73482 TAAGTCTGTA
*
73492 TCTAT-TATTTTCAGCAGATT
1 TCTATCTATTTTTAGCAGATT
73512 TCTATCTATTATTTTTTAGCAGATT
1 TCTATC---TA-TTTTTAGCAGATT
*
73537 TCTATCTATTTTTAGTAGATT
1 TCTATCTATTTTTAGCAGATT
73558 TCT
1 TCT
73561 TGGCATGCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 5 0.12
21 15 0.36
22 2 0.05
24 2 0.05
25 18 0.43
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (21 bp):
TCTATCTATTTTTAGCAGATT
Found at i:83503 original size:50 final size:51
Alignment explanation
Indices: 83420--83516 Score: 169
Period size: 50 Copynumber: 1.9 Consensus size: 51
83410 GAGCTAAGAC
*
83420 TCAATAATTGAACAATTTTTTTGTCTTTATTTTCATTTTCTTGGCCATAAA
1 TCAATAATTGAACAATCTTTTTGTCTTTATTTTCATTTTCTTGGCCATAAA
*
83471 TCAATAATTGAATAA-CTTTTTGTCTTTATTTTCATTTTCTTGGCCA
1 TCAATAATTGAACAATCTTTTTGTCTTTATTTTCATTTTCTTGGCCA
83517 AAAGTGGAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 30 0.68
51 14 0.32
ACGTcount: A:0.26, C:0.14, G:0.08, T:0.52
Consensus pattern (51 bp):
TCAATAATTGAACAATCTTTTTGTCTTTATTTTCATTTTCTTGGCCATAAA
Found at i:83596 original size:67 final size:68
Alignment explanation
Indices: 83464--83604 Score: 221
Period size: 67 Copynumber: 2.0 Consensus size: 68
83454 ATTTTCTTGG
* *
83464 CCATAAATCAATAATTGAATAACTTTTTGTCTTTATTTTCATTTTCTTGGCCAAAAGTGGAATTA
1 CCATAAATCAATAATTGAACAACTTTTTGTC--T-TTTTCATTTTCTTGGCCAAAAGTGAAATTA
83529 ATGAAA
63 ATGAAA
*
83535 CCATAAATCAATAATTTAACAACTTTTTGTC-TTTTCATTTTCTTGGCCAAAAGTGAAATTAATG
1 CCATAAATCAATAATTGAACAACTTTTTGTCTTTTTCATTTTCTTGGCCAAAAGTGAAATTAATG
83599 AAA
66 AAA
83602 CCA
1 CCA
83605 GGCTAGGATT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
67 38 0.57
71 29 0.43
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (68 bp):
CCATAAATCAATAATTGAACAACTTTTTGTCTTTTTCATTTTCTTGGCCAAAAGTGAAATTAATG
AAA
Found at i:83832 original size:39 final size:40
Alignment explanation
Indices: 83752--83832 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
83742 ATATTATAAG
* *
83752 ATTGATTTATATTTAAATTTAAATACAAAATTAAGTTGTT
1 ATTGAATTATATATAAATTTAAATACAAAATTAAGTTGTT
83792 ATTGAATTATATATAAATTTAAATA-AAAATTAAGTTGTT
1 ATTGAATTATATATAAATTTAAATACAAAATTAAGTTGTT
83831 AT
1 AT
83833 AAATAGATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 16 0.41
40 23 0.59
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (40 bp):
ATTGAATTATATATAAATTTAAATACAAAATTAAGTTGTT
Found at i:84335 original size:2 final size:2
Alignment explanation
Indices: 84328--84352 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
84318 CTTTATATTT
84328 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 T
84353 TTAAGCGTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:84729 original size:39 final size:39
Alignment explanation
Indices: 84678--84760 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
84668 TAAAATATTA
* ** *
84678 ATATTTATTACTTCC-AAGTACGAGTTGTTGGACCTCAAT
1 ATATTTAATACTTCCAAAAAACGAGTTGTTAGACCT-AAT
*
84717 ATATTTAATACTTCCAAAAAACGAGTTGTTAGACCTAGT
1 ATATTTAATACTTCCAAAAAACGAGTTGTTAGACCTAAT
84756 ATATT
1 ATATT
84761 ATTTTGGTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 21 0.55
40 17 0.45
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (39 bp):
ATATTTAATACTTCCAAAAAACGAGTTGTTAGACCTAAT
Found at i:85695 original size:19 final size:19
Alignment explanation
Indices: 85670--85724 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
85660 TTCTCCTCCA
*
85670 CTTCTTCTTTTTTCATTT-T
1 CTTCTTCTTCTTTC-TTTCT
*
85689 TTTCTTCTTCTTTCTTTCT
1 CTTCTTCTTCTTTCTTTCT
85708 CTTCTTC-TCTGTTCTTT
1 CTTCTTCTTCT-TTCTTT
85725 GCCGAATTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 6 0.19
19 25 0.81
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.71
Consensus pattern (19 bp):
CTTCTTCTTCTTTCTTTCT
Found at i:86710 original size:34 final size:34
Alignment explanation
Indices: 86663--86732 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
86653 GCATGACTGC
86663 TACTGATATTGTGATGGGCTAAGACCCTAATGCA
1 TACTGATATTGTGATGGGCTAAGACCCTAATGCA
* *
86697 TACTGAT-TCTGTGATGGGCTAAGGCCCTACTGCA
1 TACTGATAT-TGTGATGGGCTAAGACCCTAATGCA
86731 TA
1 TA
86733 TTTGATACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 1 0.03
34 32 0.97
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (34 bp):
TACTGATATTGTGATGGGCTAAGACCCTAATGCA
Found at i:88833 original size:40 final size:39
Alignment explanation
Indices: 88758--88834 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
88748 TATAAGATTC
* **
88758 AATTATATTTAAATTTAAATAAAAATTGGGTTGTTATTG
1 AATTATATATAAATTTAAATAAAAATTAAGTTGTTATTG
88797 AATTATATATAAATTTAAATAAAAAATTAAGTTGTTAT
1 AATTATATATAAATTTAAAT-AAAAATTAAGTTGTTAT
88835 AAATAGATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 19 0.56
40 15 0.44
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (39 bp):
AATTATATATAAATTTAAATAAAAATTAAGTTGTTATTG
Found at i:93033 original size:17 final size:18
Alignment explanation
Indices: 93011--93049 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
93001 TCAAGACCCA
*
93011 AAATT-AACTTTTTTTTT
1 AAATTAAACTTTCTTTTT
93028 AAATTAAAACTTTCTTTTT
1 AAATT-AAACTTTCTTTTT
93047 AAA
1 AAA
93050 AAATGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
19 14 0.74
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATTAAACTTTCTTTTT
Found at i:94267 original size:30 final size:30
Alignment explanation
Indices: 94187--94276 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
94177 CCATATACAG
**
94187 TCTCAATACCACCATTCTTGACAAAAGAAA
1 TCTCAATACCACCACACTTGACAAAAGAAA
* * **
94217 TCGCAATACCACTAGGCTTGACAAAAGAAA
1 TCTCAATACCACCACACTTGACAAAAGAAA
94247 TCTCAATACCACCACACTTGA-AAAGAGAAA
1 TCTCAATACCACCACACTTGACAAA-AGAAA
94277 GCTCTGATGG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 3 0.06
30 48 0.94
ACGTcount: A:0.44, C:0.26, G:0.11, T:0.19
Consensus pattern (30 bp):
TCTCAATACCACCACACTTGACAAAAGAAA
Found at i:96414 original size:18 final size:17
Alignment explanation
Indices: 96393--96445 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
96383 TTGTAAATAT
*
96393 TTTTATATTTTTTATGCA
1 TTTTATATTTTTTAT-AA
*
96411 TTTTATAATTTTTATAA
1 TTTTATATTTTTTATAA
96428 TTTTATATGTATTTTATA
1 TTTTATAT-T-TTTTATA
96446 GTTTACTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 8 0.27
18 15 0.50
19 7 0.23
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (17 bp):
TTTTATATTTTTTATAA
Found at i:96436 original size:28 final size:27
Alignment explanation
Indices: 96391--96445 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
96381 ATTTGTAAAT
*
96391 ATTTTTATATTTTTTATGCATTTTATA
1 ATTTTTATATTTTATATGCATTTTATA
*
96418 ATTTTTATAATTTTATATGTATTTTATA
1 ATTTTTAT-ATTTTATATGCATTTTATA
96446 GTTTACTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (27 bp):
ATTTTTATATTTTATATGCATTTTATA
Found at i:100897 original size:51 final size:53
Alignment explanation
Indices: 100817--100948 Score: 160
Period size: 51 Copynumber: 2.5 Consensus size: 53
100807 ACATATATAT
* * * *
100817 ATAATTTATTGCTTGAACACTTCAACATAGCATAAC-AAAAG-CGTAGCATGC
1 ATAATTCATTCCTTGAACACTTTAACATAGCATAACAAAAAGCCATAGCATGC
* * *
100868 ATAATTCCTTTCTTGAACACTTTAGCATAGCATAACAAAAAGCTCCATAGCATGC
1 ATAATTCATTCCTTGAACACTTTAACATAGCATAACAAAAAG--CCATAGCATGC
*
100923 ATAATTCATTCCTTGAAGACTTTAAC
1 ATAATTCATTCCTTGAACACTTTAAC
100949 TTATACTTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
51 31 0.46
52 5 0.07
55 31 0.46
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.30
Consensus pattern (53 bp):
ATAATTCATTCCTTGAACACTTTAACATAGCATAACAAAAAGCCATAGCATGC
Found at i:101127 original size:27 final size:28
Alignment explanation
Indices: 101097--101149 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
101087 ATTTATAAAT
*
101097 ATTTTTATATTTTTATATG-ATTTTATA
1 ATTTTTATAATTTTATATGTATTTTATA
*
101124 ATTTTTATAATTTTATGTGTATTTTA
1 ATTTTTATAATTTTATATGTATTTTA
101150 AAGTTTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (28 bp):
ATTTTTATAATTTTATATGTATTTTATA
Found at i:101129 original size:9 final size:8
Alignment explanation
Indices: 101095--101139 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
101085 TTATTTATAA
101095 ATATTTTT
1 ATATTTTT
101103 ATATTTTT
1 ATATTTTT
101111 ATATGATTTT
1 ATAT--TTTT
101121 ATAATTTTT
1 AT-ATTTTT
*
101130 ATAATTTT
1 ATATTTTT
101138 AT
1 AT
101140 GTGTATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 19 0.58
9 6 0.18
10 6 0.18
11 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (8 bp):
ATATTTTT
Found at i:101806 original size:21 final size:20
Alignment explanation
Indices: 101757--101807 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
101747 CGATTTTAGG
101757 TTTTT-TTTTCCTTTTTCCT
1 TTTTTATTTTCCTTTTTCCT
*
101776 TTTTACATTTTCCATTTTT-CT
1 TTTT-TATTTTCC-TTTTTCCT
101797 TCTTTTATTTT
1 T-TTTTATTTT
101808 TTCCTAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 4 0.15
21 14 0.54
22 8 0.31
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTATTTTCCTTTTTCCT
Found at i:104710 original size:16 final size:16
Alignment explanation
Indices: 104689--104735 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
104679 GTTCGAGTCA
104689 AGTTCAATTTATTTTG
1 AGTTCAATTTATTTTG
*
104705 AGTTCAGA-TCATTTTG
1 AGTTCA-ATTTATTTTG
*
104721 AATTCAATTTATTTT
1 AGTTCAATTTATTTT
104736 AATTTGGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.53
Consensus pattern (16 bp):
AGTTCAATTTATTTTG
Found at i:110673 original size:5 final size:6
Alignment explanation
Indices: 110661--110685 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
110651 AATAATTAAA
110661 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
110686 GTTGAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:115706 original size:266 final size:267
Alignment explanation
Indices: 115230--115756 Score: 1020
Period size: 266 Copynumber: 2.0 Consensus size: 267
115220 CAGGCTAATA
*
115230 TATTGAACAAAAAAGACATAAAAATGATAAGAAATGGTAATTTCTTCAAAAAAAAAAAGGAAGTG
1 TATTGAACAAAAAAGACATAAAAATCATAAGAAATGGTAATTTCTTC-AAAAAAAAAAGGAAGTG
115295 AATAGAGAACAGATTAAAATGAAATATGGATATGATCTTGTTCTTTCATCGGATCAATCAGTTTT
65 AATAGAGAACAGATTAAAATGAAATATGGATATGATCTTGTTCTTTCATCGGATCAATCAGTTTT
*
115360 CACCGGTCGCCCTGTAGCTTGGCCCGGTTCCTTTGGCATTTTCTTCGATCAGGCATCTTTGATGT
130 CACCGGTCGCCCTGTAGCTTGGCCCGGTTCCTTCGGCATTTTCTTCGATCAGGCATCTTTGATGT
115425 CTTTCATTTGGTAGTAATGTGGGGCTATTTCGACCAGCCATTCCGGTTTCAGCTCAGTTACATTT
195 CTTTCATTTGGTAGTAATGTGGGGCTATTTCGACCAGCCATTCCGGTTTCAGCTCAGTTACATTT
115490 CGACCAGC
260 CGACCAGC
115498 TATTGAACAAAAAAGACATAAAAATCATAAGAAATGGTAATTTCTTC-AAAAAAAAAGGAAGTGA
1 TATTGAACAAAAAAGACATAAAAATCATAAGAAATGGTAATTTCTTCAAAAAAAAAAGGAAGTGA
115562 ATAGAGAACAGATTAAAATGAAATATGGATATGATCTTGTTCTTTCATCGGATCAATCAGTTTTC
66 ATAGAGAACAGATTAAAATGAAATATGGATATGATCTTGTTCTTTCATCGGATCAATCAGTTTTC
115627 ACCGGTCGCCCTGTAGCTTGGCCCGGTTCCTTCGGCATTTTCTTCGATCAGGCATCTTTGATGTC
131 ACCGGTCGCCCTGTAGCTTGGCCCGGTTCCTTCGGCATTTTCTTCGATCAGGCATCTTTGATGTC
115692 TTTCATTTGGTAGTAATGTGGGGCTATTTCGACCAGCCATTCCGGTTTCAGCTCAGTTACATTTC
196 TTTCATTTGGTAGTAATGTGGGGCTATTTCGACCAGCCATTCCGGTTTCAGCTCAGTTACATTTC
115757 TCATGTATTC
Statistics
Matches: 257, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
266 211 0.82
268 46 0.18
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (267 bp):
TATTGAACAAAAAAGACATAAAAATCATAAGAAATGGTAATTTCTTCAAAAAAAAAAGGAAGTGA
ATAGAGAACAGATTAAAATGAAATATGGATATGATCTTGTTCTTTCATCGGATCAATCAGTTTTC
ACCGGTCGCCCTGTAGCTTGGCCCGGTTCCTTCGGCATTTTCTTCGATCAGGCATCTTTGATGTC
TTTCATTTGGTAGTAATGTGGGGCTATTTCGACCAGCCATTCCGGTTTCAGCTCAGTTACATTTC
GACCAGC
Found at i:125723 original size:7 final size:8
Alignment explanation
Indices: 125698--125742 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
125688 AGACTATTTA
125698 TAAATTAT
1 TAAATTAT
125706 TAAATTAT
1 TAAATTAT
125714 TAAATT-T
1 TAAATTAT
125721 TAAATTA-
1 TAAATTAT
*
125728 AAAATTAT
1 TAAATTAT
*
125736 AAAATTA
1 TAAATTA
125743 CACTTTTCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
7 13 0.38
8 21 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
TAAATTAT
Found at i:125723 original size:15 final size:16
Alignment explanation
Indices: 125698--125742 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
125688 AGACTATTTA
125698 TAAATTATTAAATTAT
1 TAAATTATTAAATTAT
125714 TAAATT-TTAAATTA-
1 TAAATTATTAAATTAT
* *
125728 AAAATTATAAAATTA
1 TAAATTATTAAATTA
125743 CACTTTTCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 5 0.19
15 15 0.58
16 6 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTATTAAATTAT
Found at i:128028 original size:40 final size:39
Alignment explanation
Indices: 127954--128039 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 39
127944 AATTAATAAA
* *
127954 AATAAAA-TTACATTTTAATTTTTAAAAATAATAAAAAAT
1 AATAAAATTTAAATTTAAATTTTTAAAAATAAT-AAAAAT
*
127993 AATAAAATTTAAATTTAAATTTTTAAAAATTATAAAAAT
1 AATAAAATTTAAATTTAAATTTTTAAAAATAATAAAAAT
*
128032 AAAAAAAT
1 AATAAAAT
128040 GTAATTTCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 20 0.48
40 22 0.52
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (39 bp):
AATAAAATTTAAATTTAAATTTTTAAAAATAATAAAAAT
Found at i:130115 original size:23 final size:23
Alignment explanation
Indices: 130083--130150 Score: 81
Period size: 22 Copynumber: 3.1 Consensus size: 23
130073 TTCCATTACA
130083 ATAAAT-TATAAATTTTAATTTT
1 ATAAATATATAAATTTTAATTTT
*
130105 ATAAATATATAAATATTAA-TTT
1 ATAAATATATAAATTTTAATTTT
*
130127 ATAAA-ATA-AAATTTAATATTTT
1 ATAAATATATAAATTTTA-ATTTT
130149 AT
1 AT
130151 TTATTAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 6 0.15
21 4 0.10
22 19 0.47
23 11 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAAATATATAAATTTTAATTTT
Found at i:134026 original size:21 final size:20
Alignment explanation
Indices: 133993--134033 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
133983 AGAGATATAT
133993 AAAAATAAATAAT-ATTTTA
1 AAAAATAAATAATAATTTTA
134012 AAAATATATAATAATAATTTTA
1 AAAA-ATA-AATAATAATTTTA
134034 TAGTTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 6 0.32
22 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATAAATAATAATTTTA
Found at i:134345 original size:11 final size:11
Alignment explanation
Indices: 134329--134354 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
134319 TGAAAGGCAT
134329 AGGTCTTAGGA
1 AGGTCTTAGGA
134340 AGGTCTTAGGA
1 AGGTCTTAGGA
134351 AGGT
1 AGGT
134355 GAGATAATTT
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:0.27, C:0.08, G:0.38, T:0.27
Consensus pattern (11 bp):
AGGTCTTAGGA
Found at i:136477 original size:60 final size:58
Alignment explanation
Indices: 136347--136480 Score: 146
Period size: 60 Copynumber: 2.3 Consensus size: 58
136337 AATATAATAT
* * *
136347 TTGATATTTAAATTTGACATTTTTTTTAATTTGGCATCTAAACTTTTTTGGGTCCAAA
1 TTGATACTTAAATTTAACATTTTTTTTAATTTGGCATCTAAACTTTTTTAGGTCCAAA
* * * * *
136405 TTAATACCTAAATTTAACATTTTTTTCTTAATTTTGTA-CTTAAACTTTTTTTAGGTTC-AA
1 TTGATACTTAAATTTAACA-TTTTTT-TTAATTTGGCATC-TAAAC-TTTTTTAGGTCCAAA
136465 TTGATACTTAAATTTA
1 TTGATACTTAAATTTA
136481 TTAAATGTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
58 15 0.24
59 7 0.11
60 30 0.48
61 10 0.16
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.51
Consensus pattern (58 bp):
TTGATACTTAAATTTAACATTTTTTTTAATTTGGCATCTAAACTTTTTTAGGTCCAAA
Found at i:136889 original size:31 final size:31
Alignment explanation
Indices: 136853--137039 Score: 108
Period size: 31 Copynumber: 6.3 Consensus size: 31
136843 TAAAGATTAT
136853 GTACCAAATTAAGAAAAAGAGTCAAGTTTAG
1 GTACCAAATTAAGAAAAAGAGTCAAGTTTAG
* ***** ** *
136884 GTACCAAATT-GGACTCTCA-AAAAGTTTAA
1 GTACCAAATTAAGAAAAAGAGTCAAGTTTAG
136913 GTA-CAAATTTAAGAAAAA-ATGTCAAGTTTAG
1 GTACCAAA-TTAAGAAAAAGA-GTCAAGTTTAG
* *
136944 GTACCAAATTAAG-AAAAGTGTCAAGTTTGG
1 GTACCAAATTAAGAAAAAGAGTCAAGTTTAG
* *
136974 GTATCAAATT-GGACAAAA-A---AA-TTTAG
1 GTACCAAATTAAGA-AAAAGAGTCAAGTTTAG
* * * * *
137000 ATACCAAATTAAGAAAAAGTGTGAAGTTCAA
1 GTACCAAATTAAGAAAAAGAGTCAAGTTTAG
137031 GTACCAAAT
1 GTACCAAAT
137040 GTTATATTAA
Statistics
Matches: 112, Mismatches: 30, Indels: 28
0.66 0.18 0.16
Matches are distributed among these distances:
26 16 0.14
27 4 0.04
28 4 0.04
29 14 0.12
30 30 0.27
31 40 0.36
32 4 0.04
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.26
Consensus pattern (31 bp):
GTACCAAATTAAGAAAAAGAGTCAAGTTTAG
Found at i:142459 original size:21 final size:22
Alignment explanation
Indices: 142435--142491 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
142425 AAATTAAAAT
*
142435 AAAATTAATATTTACTATTTAA
1 AAAATTAATATTCACTATTTAA
*
142457 AAAA-T-ATCATCCACTATTTAGA
1 AAAATTAAT-ATTCACTATTTA-A
142479 AAAATTAATATTC
1 AAAATTAATATTC
142492 TTAAAGTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 2 0.07
21 11 0.39
22 9 0.32
23 4 0.14
24 2 0.07
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.39
Consensus pattern (22 bp):
AAAATTAATATTCACTATTTAA
Found at i:143894 original size:9 final size:9
Alignment explanation
Indices: 143880--143921 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
143870 TCTATAAAAA
143880 TTTTAATTT
1 TTTTAATTT
143889 TTTTAA-TT
1 TTTTAATTT
* *
143897 TTATAAATT
1 TTTTAATTT
143906 TTTTAATTT
1 TTTTAATTT
143915 TATTTAA
1 T-TTTAA
143922 CTATTATTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
8 7 0.25
9 16 0.57
10 5 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTAATTT
Found at i:147698 original size:13 final size:13
Alignment explanation
Indices: 147680--147705 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
147670 GGAAAGGCCG
147680 TTTGATTATGCAT
1 TTTGATTATGCAT
147693 TTTGATTATGCAT
1 TTTGATTATGCAT
147706 CTCTTTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
TTTGATTATGCAT
Found at i:151525 original size:21 final size:21
Alignment explanation
Indices: 151499--151541 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
151489 CATGAGTATT
151499 CAATTAGGGATTTAAATTAAA
1 CAATTAGGGATTTAAATTAAA
151520 CAATTAGGGATTTAAATTAAA
1 CAATTAGGGATTTAAATTAAA
151541 C
1 C
151542 GGAGAGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.33
Consensus pattern (21 bp):
CAATTAGGGATTTAAATTAAA
Found at i:154740 original size:21 final size:20
Alignment explanation
Indices: 154714--154752 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
154704 CTTGATCTTA
154714 AAATCTTGAACCCTAAACCTC
1 AAATCTTGAACCC-AAACCTC
*
154735 AAATCTTGAATCCAAACC
1 AAATCTTGAACCCAAACC
154753 CTTTATGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.41, C:0.31, G:0.05, T:0.23
Consensus pattern (20 bp):
AAATCTTGAACCCAAACCTC
Found at i:158815 original size:8 final size:8
Alignment explanation
Indices: 158802--158830 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
158792 GTTTTTAAGC
158802 TAATGATT
1 TAATGATT
158810 TAATGATT
1 TAATGATT
158818 TAATGATT
1 TAATGATT
158826 TAATG
1 TAATG
158831 GTAAGAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (8 bp):
TAATGATT
Found at i:159056 original size:17 final size:18
Alignment explanation
Indices: 159034--159070 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
159024 AGTAGAGGTT
159034 TAGAGATGACACG-TGGA
1 TAGAGATGACACGCTGGA
159051 TAGAGATGACACGCTGGA
1 TAGAGATGACACGCTGGA
159069 TA
1 TA
159071 ATATAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.35, C:0.14, G:0.32, T:0.19
Consensus pattern (18 bp):
TAGAGATGACACGCTGGA
Found at i:163616 original size:2 final size:2
Alignment explanation
Indices: 163609--163633 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
163599 AGTCCAAAAC
163609 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 T
163634 GGGAAGGATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:167179 original size:40 final size:39
Alignment explanation
Indices: 167126--167201 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
167116 TAAAAATTAT
*
167126 ATTTTAATTAATATTTTATATAATTTTATAATTAAATTTAA
1 ATTTTAATAAATATTTTATATAA-TTTA-AATTAAATTTAA
* *
167167 ATTTTAA-AAATATTTTTTATTATTTAAATTAAATT
1 ATTTTAATAAATATTTTATATAATTTAAATTAAATT
167202 CAAGTATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 9 0.28
39 4 0.12
40 12 0.38
41 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (39 bp):
ATTTTAATAAATATTTTATATAATTTAAATTAAATTTAA
Found at i:172320 original size:5 final size:5
Alignment explanation
Indices: 172310--172338 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
172300 CATTATTATT
172310 CAAAC CAAAC CAAAC CAAAC CAAAC CAAA
1 CAAAC CAAAC CAAAC CAAAC CAAAC CAAA
172339 TTCAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAC
Found at i:172622 original size:21 final size:21
Alignment explanation
Indices: 172583--172622 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
172573 CCCCAATTTC
*
172583 TTTTATTAGTATATGTTTTTA
1 TTTTATTAGTATATATTTTTA
172604 TTTTATT-GTATTATATTTT
1 TTTTATTAGTA-TATATTTT
172623 ATAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTATTAGTATATATTTTTA
Found at i:173726 original size:28 final size:28
Alignment explanation
Indices: 173673--173733 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
173663 AGAAAAATTT
*
173673 TAAAAAAAATTATTAAACCCTTTAAAAA
1 TAAAAAAAATTATTAAACCCTCTAAAAA
*
173701 TAAAAAAAATTAATTAAACCC-CTAAAAT
1 TAAAAAAAATT-ATTAAACCCTCTAAAAA
173729 TAAAA
1 TAAAA
173734 TTTTAAGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.26
Consensus pattern (28 bp):
TAAAAAAAATTATTAAACCCTCTAAAAA
Found at i:176275 original size:2 final size:2
Alignment explanation
Indices: 176259--176302 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
176249 TCTTAGCCGC
*
176259 AT AT TT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
176299 AT AT
1 AT AT
176303 TCAGAGGACC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:184242 original size:27 final size:27
Alignment explanation
Indices: 184212--184268 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
184202 GATGAAAAAA
184212 AGTGCATTTAACTTGTATTGTCGATTG
1 AGTGCATTTAACTTGTATTGTCGATTG
184239 AGTGCATTTAACTTGTATTGTCGATTG
1 AGTGCATTTAACTTGTATTGTCGATTG
184266 AGT
1 AGT
184269 CTTAGCTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.44
Consensus pattern (27 bp):
AGTGCATTTAACTTGTATTGTCGATTG
Found at i:187191 original size:2 final size:2
Alignment explanation
Indices: 187186--187217 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
187176 AATCAATGAA
187186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
187218 TTTAAATGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:188637 original size:22 final size:24
Alignment explanation
Indices: 188601--188644 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
188591 TAATCGAGCT
*
188601 TTTTTTAAAACATATTTTAATTGG
1 TTTTTTAAAACATATCTTAATTGG
188625 TTTTTT-AAA-ATATCTTAATT
1 TTTTTTAAAACATATCTTAATT
188645 TAAATTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 3 0.16
24 6 0.32
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (24 bp):
TTTTTTAAAACATATCTTAATTGG
Found at i:191030 original size:31 final size:31
Alignment explanation
Indices: 190995--191061 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
190985 AGGAACTTCA
* *
190995 AAAAAAAGTTCAAG-ACTTAATTAAAATTTTC
1 AAAAAAACTTCAAGTAC-TAATTAAAACTTTC
* *
191026 -AAAAAACTTGAGGTACTAATTAAAACTTTC
1 AAAAAAACTTCAAGTACTAATTAAAACTTTC
191056 AAAAAA
1 AAAAAA
191062 CTTTCAGGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.28
Consensus pattern (31 bp):
AAAAAAACTTCAAGTACTAATTAAAACTTTC
Found at i:194072 original size:33 final size:33
Alignment explanation
Indices: 194030--194098 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
194020 CAAAATATTT
194030 TCTCTACCTAAACATGCATTGTACACCATTAAA
1 TCTCTACCTAAACATGCATTGTACACCATTAAA
194063 TCTCTACCTAAACATGCATTGTACACCATTAAA
1 TCTCTACCTAAACATGCATTGTACACCATTAAA
194096 TCT
1 TCT
194099 AAATACATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.32
Consensus pattern (33 bp):
TCTCTACCTAAACATGCATTGTACACCATTAAA
Found at i:205394 original size:16 final size:16
Alignment explanation
Indices: 205373--205404 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
205363 TCCAACACTC
205373 ATATCAATATACATTT
1 ATATCAATATACATTT
205389 ATATCAATATACATTT
1 ATATCAATATACATTT
205405 GAACATGGTA
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:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATCAATATACATTT
Found at i:205710 original size:21 final size:19
Alignment explanation
Indices: 205662--205710 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
205652 AACAATCGTC
205662 AATGCATATTCAGACATGG
1 AATGCATATTCAGACATGG
*
205681 -ATACATATTCAGACATGGGG
1 AATGCATATTCAGACAT--GG
205701 AATGCATATT
1 AATGCATATT
205711 GTACCTACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 15 0.60
20 2 0.08
21 8 0.32
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (19 bp):
AATGCATATTCAGACATGG
Found at i:211947 original size:10 final size:10
Alignment explanation
Indices: 211932--211965 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
211922 TTAATAATTA
211932 AAAATTTTAT
1 AAAATTTTAT
*
211942 AAAATTTAATT
1 AAAATTTTA-T
211953 AAAATTTTAT
1 AAAATTTTAT
211963 AAA
1 AAA
211966 TTTGTTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AAAATTTTAT
Found at i:212025 original size:19 final size:20
Alignment explanation
Indices: 211993--212031 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
211983 ACCATCTATT
* *
211993 TTTTTTCTAGATTTTTAATG
1 TTTTTACTAGATTTTGAATG
212013 TTTTTACTA-ATTTTGAATG
1 TTTTTACTAGATTTTGAATG
212032 ATTCAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (20 bp):
TTTTTACTAGATTTTGAATG
Found at i:214833 original size:109 final size:109
Alignment explanation
Indices: 214631--214843 Score: 286
Period size: 109 Copynumber: 2.0 Consensus size: 109
214621 TAGTCCAATG
* *
214631 AGGGTATGTTCAATCTCAGTTTTGTATAATATATGCATACTTTATGAATGCCAATTTGTTACCCG
1 AGGGTACGTTCAATCTCAGTTTTGTATAATATATGCATACATTATGAATGCCAATTTGTTACCCG
214696 AACTTGGGGTGAGTATTGGATATGTGTATGAGTATATTTCTGATA
66 AACTTGGGGTGAGTATTGGATATGTGTATGAGTAT-TTTCTGATA
* * * * * **
214741 AGGGTACGTTCAATGTCAGTTTTGTATAATATATGTATACATTA-GGATGCTAGTTTGTTACTTG
1 AGGGTACGTTCAATCTCAGTTTTGTATAATATATGCATACATTATGAATGCCAATTTGTTACCCG
* * *
214805 GACTTGGGGTGAGTATTGGATGCT-TGTATGATTATTTTC
66 AACTTGGGGTGAGTATTGGAT-ATGTGTATGAGTATTTTC
214844 GGAGAATGTG
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
108 4 0.04
109 45 0.50
110 41 0.46
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.41
Consensus pattern (109 bp):
AGGGTACGTTCAATCTCAGTTTTGTATAATATATGCATACATTATGAATGCCAATTTGTTACCCG
AACTTGGGGTGAGTATTGGATATGTGTATGAGTATTTTCTGATA
Found at i:219861 original size:17 final size:17
Alignment explanation
Indices: 219835--219868 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
219825 GTTTTGGTGA
*
219835 GTGTTAGATACGGGTAC
1 GTGTTAGATACGAGTAC
*
219852 GTGTTCGATACGAGTAC
1 GTGTTAGATACGAGTAC
219869 CTTTTTTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (17 bp):
GTGTTAGATACGAGTAC
Found at i:232885 original size:21 final size:22
Alignment explanation
Indices: 232845--232885 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
232835 ATCCTAAAAG
232845 CTTAAAATGTTCTGATTAAGTC
1 CTTAAAATGTTCTGATTAAGTC
232867 CTTAAAA-GTATCT-ATTAAG
1 CTTAAAATGT-TCTGATTAAG
232886 GTCTTCCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (22 bp):
CTTAAAATGTTCTGATTAAGTC
Found at i:233113 original size:17 final size:16
Alignment explanation
Indices: 233091--233134 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
233081 AAAATATATA
233091 TTTATATTATTATTATT
1 TTTATATT-TTATTATT
* *
233108 TTTATATTTAATAATT
1 TTTATATTTTATTATT
233124 TTATATATTTT
1 TT-TATATTTT
233135 TATTTATTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATATTTTATTATT
Found at i:233138 original size:23 final size:25
Alignment explanation
Indices: 233107--233157 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
233097 TTATTATTAT
233107 TTTTATATTTAAT-AATTTTATATA
1 TTTTATATTTAATGAATTTTATATA
*
233131 TTTT-TATTTATTGGAATTTTATATA
1 TTTTATATTTAAT-GAATTTTATATA
233156 TT
1 TT
233158 GATATCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
24 4 0.17
25 13 0.54
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (25 bp):
TTTTATATTTAATGAATTTTATATA
Found at i:234430 original size:6 final size:6
Alignment explanation
Indices: 234421--234457 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
234411 TTATTTTTAT
234421 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA T
234458 ATTTTTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTAATA
Found at i:240474 original size:16 final size:16
Alignment explanation
Indices: 240443--240479 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
240433 CTTCAAATAA
240443 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
240459 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
240475 TATTA
1 TATTA
240480 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:240497 original size:19 final size:18
Alignment explanation
Indices: 240465--240500 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
240455 TTATTATTTT
*
240465 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
240483 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
240501 CAAATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:252703 original size:10 final size:10
Alignment explanation
Indices: 252688--252719 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
252678 GCTAGCACTT
252688 GAGAATTTAA
1 GAGAATTTAA
252698 GAGAATTTAA
1 GAGAATTTAA
252708 GAGAATTTAA
1 GAGAATTTAA
252718 GA
1 GA
252720 TCTAGCGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (10 bp):
GAGAATTTAA
Found at i:255281 original size:12 final size:12
Alignment explanation
Indices: 255261--255295 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
255251 GTCCTTCCAC
*
255261 TCTTATTCTTCT
1 TCTTGTTCTTCT
255273 TCTTGTTCTTCT
1 TCTTGTTCTTCT
255285 TCTTGTTCTTC
1 TCTTGTTCTTC
255296 GAAGTTTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.03, C:0.26, G:0.06, T:0.66
Consensus pattern (12 bp):
TCTTGTTCTTCT
Found at i:257032 original size:31 final size:31
Alignment explanation
Indices: 256997--257090 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 31
256987 TTACAAAATG
256997 GTCACTGAA-TCATTCAAAAGTTTTCATTTAA
1 GTCACTGAACT-ATTCAAAAGTTTTCATTTAA
* * *
257028 GTCACTCAACTATTTAAAAGTTTTTATTTAA
1 GTCACTGAACTATTCAAAAGTTTTCATTTAA
** * *
257059 GTCACTGGGCTATT-AAAAATTTT-TTTTAA
1 GTCACTGAACTATTCAAAAGTTTTCATTTAA
257088 GTC
1 GTC
257091 CTACCAGTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 8 0.15
30 8 0.15
31 37 0.69
32 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (31 bp):
GTCACTGAACTATTCAAAAGTTTTCATTTAA
Found at i:257082 original size:30 final size:31
Alignment explanation
Indices: 257012--257090 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
257002 TGAATCATTC
*
257012 AAAAGTTTTCATTTAAGTCACTCAACTATTT
1 AAAAGTTTTTATTTAAGTCACTCAACTATTT
***
257043 AAAAGTTTTTATTTAAGTCACTGGGCTA-TT
1 AAAAGTTTTTATTTAAGTCACTCAACTATTT
*
257073 AAAAATTTTT-TTTAAGTC
1 AAAAGTTTTTATTTAAGTC
257091 CTACCAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 8 0.19
30 11 0.26
31 24 0.56
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (31 bp):
AAAAGTTTTTATTTAAGTCACTCAACTATTT
Found at i:275946 original size:17 final size:19
Alignment explanation
Indices: 275911--275952 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
275901 AACAATATAT
275911 TTTATAATAAATATTTAAA
1 TTTATAATAAATATTTAAA
275930 TTTATAAT-AAT-TTTAAA
1 TTTATAATAAATATTTAAA
*
275947 ATTATA
1 TTTATA
275953 GCATAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.50
18 3 0.14
19 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTATAATAAATATTTAAA
Found at i:276126 original size:4 final size:4
Alignment explanation
Indices: 276117--276142 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
276107 TCTAATTTTT
276117 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
276143 TTTGTTCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:276307 original size:25 final size:26
Alignment explanation
Indices: 276272--276321 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
276262 TTTGTTTTTT
276272 TTTTTTGTTAAATATAAAATAATGGG
1 TTTTTTGTTAAATATAAAATAATGGG
*
276298 TTTTTT-TTAAATATAAAATTATGG
1 TTTTTTGTTAAATATAAAATAATGG
276322 CTTTAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (26 bp):
TTTTTTGTTAAATATAAAATAATGGG
Found at i:277410 original size:2 final size:2
Alignment explanation
Indices: 277403--277429 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
277393 ATTGTGAAAG
277403 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
277430 ATGAACTGTA
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:285003 original size:95 final size:95
Alignment explanation
Indices: 284839--285014 Score: 241
Period size: 95 Copynumber: 1.9 Consensus size: 95
284829 TAACTCAACA
* * * * *
284839 TTTTGACGTTTGAGACTAAATTAAAATTTTAGTTATAGTTTAAGGGTTTTTAGTAAATTAATTCT
1 TTTTGAAGTTTGAGACTAAATTAAAATTTTAGTTATAGTTTAAGGGTTCTAAGCAAATTAATTCA
*
284904 TTTTTTATTGCATATTTTGGTAAGTCAGCG
66 TTTTTCATTGCATATTTTGGTAAGTCAGCG
*
284934 TTTTGAAGTTTGGGACTAAATTAAGAATTTTAGTTATAGTTT-AGGGTGTCTAATGCAAA-TAAT
1 TTTTGAAGTTTGAGACTAAATTAA-AATTTTAGTTATAGTTTAAGGGT-TCTAA-GCAAATTAAT
284997 T-ATTTTTCATTGCATATT
63 TCATTTTTCATTGCATATT
285015 CATAATTACA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
95 42 0.59
96 25 0.35
97 4 0.06
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (95 bp):
TTTTGAAGTTTGAGACTAAATTAAAATTTTAGTTATAGTTTAAGGGTTCTAAGCAAATTAATTCA
TTTTTCATTGCATATTTTGGTAAGTCAGCG
Done.