Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015315.1 Kokia drynarioides strain JFW-HI SEQ_130360, 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: 547892
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 536 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:3443 original size:56 final size:58
Alignment explanation
Indices: 3316--3466 Score: 184
Period size: 56 Copynumber: 2.6 Consensus size: 58
3306 TATATTATGA
* * * *
3316 TTTTTATT-AATTCATATTTTAATAATAATTATATTAAGAATGTTATTAAATTATATACT
1 TTTTTATTAAATT-ATA-TTTAATAATAATCATATTAAGAATATGATTAAAATATATACT
* *
3375 ATTTTATTAAATTATATTTAATAATAATCA-AGTTAA-AATATGATTAAAATATTTA-T
1 TTTTTATTAAATTATATTTAATAATAATCATA-TTAAGAATATGATTAAAATATATACT
*
3431 TTTTTATTAAATTATATTTAATAATAATCTTATTAA
1 TTTTTATTAAATTATATTTAATAATAATCATATTAA
3467 AAGTTAACAA
Statistics
Matches: 81, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
56 33 0.41
57 17 0.21
58 17 0.21
59 10 0.12
60 4 0.05
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (58 bp):
TTTTTATTAAATTATATTTAATAATAATCATATTAAGAATATGATTAAAATATATACT
Found at i:3657 original size:16 final size:16
Alignment explanation
Indices: 3636--3689 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
3626 TGAAATACTA
* *
3636 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTAC
*
3652 ATTACAGTTCTATTAC
1 ATTACAGCTCTATTAC
* *
3668 ATTACAGCTCTGTTTC
1 ATTACAGCTCTATTAC
3684 ATTACA
1 ATTACA
3690 ACGAACCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTAC
Found at i:4761 original size:19 final size:19
Alignment explanation
Indices: 4737--4787 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
4727 CCCTTCAAAT
4737 TTCGAAGATTCTCCATATA
1 TTCGAAGATTCTCCATATA
4756 TTCGAAGATTCTCCATATA
1 TTCGAAGATTCTCCATATA
4775 TTCGAAGATTCTC
1 TTCGAAGATTCTC
4788 TTGATTCTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (19 bp):
TTCGAAGATTCTCCATATA
Found at i:10242 original size:18 final size:18
Alignment explanation
Indices: 10219--10261 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
10209 TTTTCAGTTG
*
10219 TAATTAATTTAAA-ATTTT
1 TAATTAA-TTAAATATATT
10237 TAATTAATTAAATATATT
1 TAATTAATTAAATATATT
10255 TAATTAA
1 TAATTAA
10262 AAAATTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTAAATATATT
Found at i:16168 original size:21 final size:20
Alignment explanation
Indices: 16143--16182 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16133 AAGTTTAGTT
16143 TTTATTAAATTATTTTAGAAC
1 TTTATTAAATT-TTTTAGAAC
**
16164 TTTATTGTATTTTTTAGAA
1 TTTATTAAATTTTTTAGAA
16183 ATTTTAGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTATTAAATTTTTTAGAAC
Found at i:16933 original size:30 final size:31
Alignment explanation
Indices: 16884--16948 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
16874 AAAGTTGTAG
* *
16884 ATTTAGTTCTTTGTATTTTT-ATTTAATCAA
1 ATTTAGTTCTTTATATTTTTGAATTAATCAA
*
16914 ATTTAGTTC-TTATATTTTTTGAATTGATCAA
1 ATTTAGTTCTTTATA-TTTTTGAATTAATCAA
16945 ATTT
1 ATTT
16949 TAATCTTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 4 0.13
30 14 0.47
31 12 0.40
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (31 bp):
ATTTAGTTCTTTATATTTTTGAATTAATCAA
Found at i:17396 original size:24 final size:23
Alignment explanation
Indices: 17364--17410 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
17354 CCCAGCCCGG
17364 ATTTATAATAATAATTTTATTTTA
1 ATTTATAATAATAATTTT-TTTTA
* *
17388 ATTTTTAATATTAATTTTTTTTA
1 ATTTATAATAATAATTTTTTTTA
17411 CTTGTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTTATAATAATAATTTTTTTTA
Found at i:18086 original size:20 final size:19
Alignment explanation
Indices: 18047--18090 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
18037 ATATAAAGGG
*
18047 TGTTTATTGTATTTTCAATT
1 TGTTTATTGTATTTACAA-T
18067 TGTTTATTGT-TTTACGAAT
1 TGTTTATTGTATTTAC-AAT
18086 TGTTT
1 TGTTT
18091 TAATATCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.18, C:0.05, G:0.14, T:0.64
Consensus pattern (19 bp):
TGTTTATTGTATTTACAAT
Found at i:18108 original size:41 final size:41
Alignment explanation
Indices: 18058--18137 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
18048 GTTTATTGTA
*
18058 TTTTCAATTTGTTTATTGTTTTACGAATTGTTTTAATATCG
1 TTTTCAATTTGTTTATTGTTTTAAGAATTGTTTTAATATCG
* * * *
18099 TTTTTAATTTGTTTGTTGTTTTAATATTTGTTTTAATAT
1 TTTTCAATTTGTTTATTGTTTTAAGAATTGTTTTAATAT
18138 TTTTAAGTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.21, C:0.04, G:0.11, T:0.64
Consensus pattern (41 bp):
TTTTCAATTTGTTTATTGTTTTAAGAATTGTTTTAATATCG
Found at i:18131 original size:12 final size:12
Alignment explanation
Indices: 18114--18139 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18104 AATTTGTTTG
18114 TTGTTTTAATAT
1 TTGTTTTAATAT
18126 TTGTTTTAATAT
1 TTGTTTTAATAT
18138 TT
1 TT
18140 TTAAGTGTAT
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:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:20582 original size:19 final size:21
Alignment explanation
Indices: 20544--20584 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
20534 TAAAAAAGTT
20544 AAGGACTAAATTTAGATAAAA
1 AAGGACTAAATTTAGATAAAA
20565 AAGGACTAAA-TT-GATAAAA
1 AAGGACTAAATTTAGATAAAA
20584 A
1 A
20585 CATAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 2 0.10
21 10 0.50
ACGTcount: A:0.59, C:0.05, G:0.15, T:0.22
Consensus pattern (21 bp):
AAGGACTAAATTTAGATAAAA
Found at i:27137 original size:12 final size:12
Alignment explanation
Indices: 27120--27145 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27110 AAAAGTAAAT
27120 AACCTCTAGAAA
1 AACCTCTAGAAA
27132 AACCTCTAGAAA
1 AACCTCTAGAAA
27144 AA
1 AA
27146 GTTGGAGAAT
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:0.54, C:0.23, G:0.08, T:0.15
Consensus pattern (12 bp):
AACCTCTAGAAA
Found at i:29952 original size:34 final size:32
Alignment explanation
Indices: 29913--29989 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 32
29903 AAGTCCAAAT
*
29913 TTTAAATTTTAAATAAGTTTGAATTTATTTTAAA
1 TTTAAATTTT--ATAAGTTTGAATTTACTTTAAA
* *
29947 TTTAAATTCATTTTGAGTTTGAATTTACTTTAAA
1 TTTAAATT--TTATAAGTTTGAATTTACTTTAAA
29981 TTTAAATTT
1 TTTAAATTT
29990 ATTCTAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
32 1 0.03
34 35 0.92
36 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (32 bp):
TTTAAATTTTATAAGTTTGAATTTACTTTAAA
Found at i:29954 original size:17 final size:17
Alignment explanation
Indices: 29934--30004 Score: 79
Period size: 17 Copynumber: 4.2 Consensus size: 17
29924 AATAAGTTTG
29934 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* * * *
29951 AATTCATTTTGAGTTTG
1 AATTTATTTTAAATTTA
*
29968 AATTTACTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
29985 AATTTATTCTAAATTAA
1 AATTTATTTTAAATTTA
30002 AAT
1 AAT
30005 AAAACTAAAA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:31938 original size:58 final size:57
Alignment explanation
Indices: 31839--32235 Score: 400
Period size: 58 Copynumber: 6.8 Consensus size: 57
31829 CAAACTTTCC
* *
31839 AAAATTCCATTTTTGACCCTAAACTTTC-CAAAAAATACCATTTTACCCTCGAATGTCTA
1 AAAATTCCA-TTTTAACCC-AAAC-TTCACAAAAATTACCATTTTACCCTCGAATGTCTA
* * *
31898 AAAATTCCATTTTAACCCAAAACTTCACAAAAGTTGCCATTTTACCCCCGAATGTCTA
1 AAAATTCCATTTTAACCC-AAACTTCACAAAAATTACCATTTTACCCTCGAATGTCTA
* *
31956 AAAATTCCATTTTAACCTCGAACTTCAAAAAAATTACCATTTTACCCTCGAATGTCTA
1 AAAATTCCATTTTAACC-CAAACTTCACAAAAATTACCATTTTACCCTCGAATGTCTA
*
32014 AAAATTTCATTTTAACCCCAAACTTCACAAAAATTACCATTTTA-CCTCCGAATGTCTA
1 AAAATTCCATTTTAA-CCCAAACTTCACAAAAATTACCATTTTACCCT-CGAATGTCTA
* * * *
32072 AAAATTCTATTTTTGACCTCGAACTTTC-CAAAAATTACTATTTTA-CCTCCGAATGTCTA
1 AAAATTCCA-TTTTAACC-CAAAC-TTCACAAAAATTACCATTTTACCCT-CGAATGTCTA
* * * *
32131 AAAATTCCATTTTTAACTTCGAACTTCACAAAAA-TA-CATTTTTACCCTTGAACT-TCCA
1 AAAATTCCA-TTTTAAC-CCAAACTTCACAAAAATTACCA-TTTTACCCTCGAA-TGTCTA
* * *
32189 AAAATTCCATTTTTGACCCAGACCTTC-C-AAAATTACC-GTTTACCCTC
1 AAAATTCCA-TTTTAACCCA-AACTTCACAAAAATTACCATTTTACCCTC
32236 AGGCATCTAA
Statistics
Matches: 292, Mismatches: 31, Indels: 33
0.82 0.09 0.09
Matches are distributed among these distances:
56 12 0.04
57 11 0.04
58 185 0.63
59 81 0.28
60 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (57 bp):
AAAATTCCATTTTAACCCAAACTTCACAAAAATTACCATTTTACCCTCGAATGTCTA
Found at i:32044 original size:116 final size:117
Alignment explanation
Indices: 31839--32202 Score: 456
Period size: 116 Copynumber: 3.1 Consensus size: 117
31829 CAAACTTTCC
* *
31839 AAAATTCCATTTTTGACC-CTAAACTTTCCAAAAAA-TACCATTTTACCCTCGAATGTCTAAAAA
1 AAAATTCCATTTTTAACCTC-GAACTTT-CAAAAAATTACCATTTTACCCTCGAATGTCTAAAAA
* * *
31902 TTCCATTTTAACCCAAAACTTCACAAAAGTTGCCATTTTACCCCCGAATGTCTA
64 TTCCATTTTAACCCCAAACTTCACAAAAATTACCATTTTACCCCCGAATGTCTA
31956 AAAATTCCA-TTTTAACCTCGAAC-TTCAAAAAAATTACCATTTTACCCTCGAATGTCTAAAAAT
1 AAAATTCCATTTTTAACCTCGAACTTTC-AAAAAATTACCATTTTACCCTCGAATGTCTAAAAAT
* *
32019 TTCATTTTAACCCCAAACTTCACAAAAATTACCATTTTACCTCCGAATGTCTA
65 TCCATTTTAACCCCAAACTTCACAAAAATTACCATTTTACCCCCGAATGTCTA
* * * *
32072 AAAATTCTATTTTTGACCTCGAACTTTCCAAAAATTACTATTTTA-CCTCCGAATGTCTAAAAAT
1 AAAATTCCATTTTTAACCTCGAACTTTCAAAAAATTACCATTTTACCCT-CGAATGTCTAAAAAT
** * ** *
32136 TCCATTTTTAACTTCGAACTTCACAAAAA-TA-CATTTTTACCCTTGAACT-TCCA
65 TCCA-TTTTAACCCCAAACTTCACAAAAATTACCA-TTTTACCCCCGAA-TGTCTA
32189 AAAATTCCATTTTT
1 AAAATTCCATTTTT
32203 GACCCAGACC
Statistics
Matches: 218, Mismatches: 20, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
114 1 0.00
115 8 0.04
116 100 0.46
117 84 0.39
118 25 0.11
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (117 bp):
AAAATTCCATTTTTAACCTCGAACTTTCAAAAAATTACCATTTTACCCTCGAATGTCTAAAAATT
CCATTTTAACCCCAAACTTCACAAAAATTACCATTTTACCCCCGAATGTCTA
Found at i:32153 original size:29 final size:28
Alignment explanation
Indices: 31869--32153 Score: 215
Period size: 29 Copynumber: 9.8 Consensus size: 28
31859 AAACTTTCCA
* *
31869 AAAAATACCATTTTACCCTCGAATGTCT
1 AAAAATTCCATTTTAACCTCGAATGTCT
*
31897 AAAAATTCCATTTTAACC-CAAAACT-TC-
1 AAAAATTCCATTTTAACCTC-GAA-TGTCT
* *
31924 ACAAAAGTTGCCATTTTACCCCCGAATGTCT
1 A-AAAA-TT-CCATTTTAACCTCGAATGTCT
*
31955 AAAAATTCCATTTTAACCTCGAACT-TCAA
1 AAAAATTCCATTTTAACCTCGAA-TGTC-T
*
31984 AAAAATTACCATTTTACCCTCGAATGTCT
1 AAAAATT-CCATTTTAACCTCGAATGTCT
* * * *
32013 AAAAATTTCATTTTAACCCCAAACT-TCAC
1 AAAAATTCCATTTTAACCTCGAA-TGTC-T
32042 AAAAATTACCATTTT-ACCTCCGAATGTCT
1 AAAAATT-CCATTTTAACCT-CGAATGTCT
* * * *
32071 AAAAATTCTATTTTTGACCTCGAACTTTCC
1 AAAAATTCCA-TTTTAACCTCGAA-TGTCT
*
32101 AAAAATTACTATTTT-ACCTCCGAATGTCT
1 AAAAATT-CCATTTTAACCT-CGAATGTCT
*
32130 AAAAATTCCATTTTTAACTTCGAA
1 AAAAATTCCA-TTTTAACCTCGAA
32154 CTTCACAAAA
Statistics
Matches: 207, Mismatches: 26, Indels: 47
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.01
28 58 0.28
29 71 0.34
30 71 0.34
31 5 0.02
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (28 bp):
AAAAATTCCATTTTAACCTCGAATGTCT
Found at i:32163 original size:29 final size:30
Alignment explanation
Indices: 31838--32202 Score: 163
Period size: 29 Copynumber: 12.5 Consensus size: 30
31828 CCAAACTTTC
* * *
31838 CAAAATTCCATTTTTGACC-CTAAACTTTCCA
1 CAAAATTCCATTTTTAACCTC-GAAC-TTCTA
* * *
31869 AAAAATACCA-TTTTACCCTCGAA-TGTCTA
1 CAAAATTCCATTTTTAACCTCGAACT-TCTA
*
31898 -AAAATTCCA-TTTTAACC-CAAAACTTC-A
1 CAAAATTCCATTTTTAACCTC-GAACTTCTA
* *
31925 CAAAAGTTGCCA-TTTTACCCCCGAA-TGTCTA
1 CAAAA-TT-CCATTTTTAACCTCGAACT-TCTA
*
31956 -AAAATTCCA-TTTTAACCTCGAACTTCAA
1 CAAAATTCCATTTTTAACCTCGAACTTCTA
* *
31984 AAAAATTACCA-TTTTACCCTCGAA-TGTCTA
1 CAAAATT-CCATTTTTAACCTCGAACT-TCTA
* * *
32014 -AAAATTTCA-TTTTAACCCCAAACTTC-A
1 CAAAATTCCATTTTTAACCTCGAACTTCTA
32041 CAAAAATTACCA-TTTT-ACCTCCGAA-TGTCTA
1 C-AAAATT-CCATTTTTAACCT-CGAACT-TCTA
* * *
32072 -AAAATTCTATTTTTGACCTCGAACTT-TC
1 CAAAATTCCATTTTTAACCTCGAACTTCTA
*
32100 CAAAAATTAC-TATTTT-ACCTCCGAA-TGTCTA
1 C-AAAATTCCAT-TTTTAACCT-CGAACT-TCTA
*
32131 -AAAATTCCATTTTTAACTTCGAACTTC-A
1 CAAAATTCCATTTTTAACCTCGAACTTCTA
* * * * *
32159 CAAAAATACATTTTTACCCTTGAACTTCCA
1 CAAAATTCCATTTTTAACCTCGAACTTCTA
32189 -AAAATTCCATTTTT
1 CAAAATTCCATTTTT
32203 GACCCAGACC
Statistics
Matches: 262, Mismatches: 37, Indels: 72
0.71 0.10 0.19
Matches are distributed among these distances:
27 3 0.01
28 59 0.23
29 106 0.40
30 81 0.31
31 13 0.05
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (30 bp):
CAAAATTCCATTTTTAACCTCGAACTTCTA
Found at i:36168 original size:23 final size:22
Alignment explanation
Indices: 36137--36200 Score: 56
Period size: 25 Copynumber: 2.7 Consensus size: 22
36127 TTCAAAATCA
*
36137 ATGCCTTTTTTTGCATTACATAC
1 ATGCATTTTTTTGCATTACAT-C
*
36160 ATGCATTTTTATTTGCATTGCATC
1 ATGCA-TTTT-TTTGCATTACATC
* *
36184 TTCGCATATTTTTGCAT
1 AT-GCATTTTTTTGCAT
36201 AATAATTCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 11 0.32
24 9 0.26
25 14 0.41
ACGTcount: A:0.20, C:0.19, G:0.11, T:0.50
Consensus pattern (22 bp):
ATGCATTTTTTTGCATTACATC
Found at i:44030 original size:37 final size:37
Alignment explanation
Indices: 43980--44053 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
43970 AATGAGCTGG
*
43980 TCGTCTTCCTGATGAGATACTGAGAAGTGGACAAAAT
1 TCGTCTTCCTGATGAGATACTGAGAAGAGGACAAAAT
*
44017 TCGTCTTCCTGATGAGATACTGAGAAGAGGACTAAAT
1 TCGTCTTCCTGATGAGATACTGAGAAGAGGACAAAAT
44054 CAATGAAGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (37 bp):
TCGTCTTCCTGATGAGATACTGAGAAGAGGACAAAAT
Found at i:44380 original size:209 final size:209
Alignment explanation
Indices: 44020--45107 Score: 1631
Period size: 209 Copynumber: 5.2 Consensus size: 209
44010 ACAAAATTCG
* * * * *
44020 TCTTCCTGATGAGATACTGAGAAGAGGACTAAATCAATGAAGCCAAGCTCAAAGTGAGTAAATCT
1 TCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACTAAGCTCAAAGTGAGCAAATCT
* * * *
44085 TCGAGCCCCAACTTCCTGATGAGATATTGAGAAGCAGGTTGAAGTAATAAAATGGTTAGCTTCCT
66 TCGAACTCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAAATGGTTAGCTTCCT
*
44150 GATGAAGTACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAC
131 GATGAAATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAC
*
44215 AAGTGATGTGGTCA
196 AAGTGATGCGGTCA
*
44229 TCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACTAAGCTCAAAGTGAGCAAATAT
1 TCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACTAAGCTCAAAGTGAGCAAATCT
** *
44294 TCGAACTTTAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCAATAAAATGGTTAGCTTCCT
66 TCGAACTCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAAATGGTTAGCTTCCT
* * * *
44359 GATGAAATACTGAGAAGTGGACCAAATTTGTCTTCCTGATAATATACAGAGAAGCGGATTGAAAC
131 GATGAAATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAC
* *
44424 AAATGATGCAGTCA
196 AAGTGATGCGGTCA
*
44438 TCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACTAAGCTCAAAGTGAACAAATCT
1 TCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACTAAGCTCAAAGTGAGCAAATCT
44503 TCGAACTCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAAATGGTTAGCTTCCT
66 TCGAACTCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAAATGGTTAGCTTCCT
*
44568 GATGAAGTACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAC
131 GATGAAATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAC
44633 AAGTGATGCGGTCA
196 AAGTGATGCGGTCA
*
44647 TCTTCCTGATGAGATACTGAGAAGAATACCAAATCAATGAAACTAAGCTCAAAGTGAGCAAATCT
1 TCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACTAAGCTCAAAGTGAGCAAATCT
* * * * * * *
44712 TCGAACTCTAGCTTTCTGATGAGATATTGAGAAGCATGTCGAAGCAATAAAATGGTTAGCTTTCT
66 TCGAACTCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAAATGGTTAGCTTCCT
* * *
44777 GATGAAATACTGAGAAGTGGACCAAATTTGTCTTCCTGATAAGATACAGAGAAGCGGATTGAAAC
131 GATGAAATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAC
* *
44842 AAATGATGCAGTCA
196 AAGTGATGCGGTCA
*
44856 TCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACTAAGCTCAAAGTGAACAAATCT
1 TCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACTAAGCTCAAAGTGAGCAAATCT
* * *
44921 TCGAACTCCAGCTGCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAGA-GGTTACCTTCC
66 TCGAACTCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAA-ATGGTTAGCTTCC
* * * * * * * * * * *
44985 TAATGAGATACAAAAAAGTGAACCAGA-TCAGTCTTCCTGGTGAGACATAGAGAAGTGGATCAAA
130 TGATGAAATACTAAGAAGTGGACCAAATTC-GTCTTCCTGATGAGATACAGAGAAGCGGAT---T
*
45049 AAAACAAGTGATGCGGTCA
191 GAAACAAGTGATGCGGTCA
* *
45068 TCTTCCTGATGAGATACTGAGAAGTAGATCAAATCAATGA
1 TCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGA
45108 CATGAAACCA
Statistics
Matches: 797, Mismatches: 77, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
208 1 0.00
209 741 0.93
210 1 0.00
212 54 0.07
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (209 bp):
TCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACTAAGCTCAAAGTGAGCAAATCT
TCGAACTCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAAATGGTTAGCTTCCT
GATGAAATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAC
AAGTGATGCGGTCA
Found at i:47482 original size:58 final size:56
Alignment explanation
Indices: 47387--47686 Score: 254
Period size: 58 Copynumber: 5.2 Consensus size: 56
47377 CGAACTTTCC
* * *
47387 AAAATTCCATTTTTAACCTCAAACTTTC-CAAAAATTACTGTTTTACACTCGGATGTCTA
1 AAAATTCCA-TTTTAA-CTCGAAC-TTCACAAAAATTACTATTTTAC-CTCGAATGTCTA
* * *
47446 AAAATTCCATTTTAAACTCGAACTTCACAAAGATTACCATTTTACCCTCTAATGTCTA
1 AAAATTCCATTTT-AACTCGAACTTCACAAAAATTACTATTTTA-CCTCGAATGTCTA
* * * *
47504 AAAATTCCATTTTAACCCTGAACTTCACAAAAATTAC-AATTTACCCCAAATGT-TA
1 AAAATTCCATTTTAACTC-GAACTTCACAAAAATTACTATTTTACCTCGAATGTCTA
** * * *
47559 AAAATTATATTTTGACCTCGAACTTTC-CAAAAATTA-TCGTTTTACCTCTGGATGTCTA
1 AAAATTCCATTTT-AACTCGAAC-TTCACAAAAATTACT-ATTTTACCTC-GAATGTCTA
* * * *
47617 AAAATTCCATTTTAACCCTAACTTCACAAAAATTAC-ATTTTTACCCCCGAACT-TCCA
1 AAAATTCCATTTTAACTCGAACTTCACAAAAATTACTA-TTTTA-CCTCGAA-TGTCTA
47674 AAAATTCCATTTT
1 AAAATTCCATTTT
47687 TGACCTTGGA
Statistics
Matches: 197, Mismatches: 29, Indels: 32
0.76 0.11 0.12
Matches are distributed among these distances:
55 26 0.13
56 24 0.12
57 54 0.27
58 81 0.41
59 12 0.06
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.35
Consensus pattern (56 bp):
AAAATTCCATTTTAACTCGAACTTCACAAAAATTACTATTTTACCTCGAATGTCTA
Found at i:47535 original size:29 final size:28
Alignment explanation
Indices: 47445--47686 Score: 117
Period size: 29 Copynumber: 8.5 Consensus size: 28
47435 TCGGATGTCT
*
47445 AAAAATTCCATTTTAA-ACTCGAACTTCAC
1 AAAAATTCCATTTTAACCCT-GAACTTC-C
* * *
47474 AAAGATTACCATTTT-ACCCTCTAA-TGTCT
1 AAAAATT-CCATTTTAACCCT-GAACT-TCC
47503 AAAAATTCCATTTTAACCCTGAACTTCAC
1 AAAAATTCCATTTTAACCCTGAACTTC-C
* * * * *
47532 AAAAATTACAATTT-ACCC-CAAATGT-T
1 AAAAATTCCATTTTAACCCTGAACT-TCC
** *
47558 AAAAATTATATTTTGA-CCTCGAACTTTCC
1 AAAAATTCCATTTTAACCCT-GAAC-TTCC
* * * *
47587 AAAAATTATCGTTTT-ACCTCTGGA-TGTCT
1 AAAAATT-CCATTTTAACC-CTGAACT-TCC
47616 AAAAATTCCATTTTAACCCT-AACTTCAC
1 AAAAATTCCATTTTAACCCTGAACTTC-C
* * *
47644 AAAAATTACATTTTTACCCCCGAACTTCC
1 AAAAATTCCA-TTTTAACCCTGAACTTCC
47673 AAAAATTCCATTTT
1 AAAAATTCCATTTT
47687 TGACCTTGGA
Statistics
Matches: 162, Mismatches: 30, Indels: 43
0.69 0.13 0.18
Matches are distributed among these distances:
26 14 0.09
27 7 0.04
28 41 0.25
29 71 0.44
30 27 0.17
31 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (28 bp):
AAAAATTCCATTTTAACCCTGAACTTCC
Found at i:47602 original size:113 final size:114
Alignment explanation
Indices: 47387--47663 Score: 314
Period size: 113 Copynumber: 2.4 Consensus size: 114
47377 CGAACTTTCC
* * * **
47387 AAAATTCCATTTTTAACCTCAAACTTTC-CAAAAATTAC-TGTTTTACACTCGGATGTCTAAAAA
1 AAAATTCCA-TTTTAACC-CTAAC-TTCACAAAAATTACAT-ATTTAC-CCCAAATGTCTAAAAA
* *
47450 TTCCATTTTAAACTCGAACTTCACAAAGATTACCATTTTACCCTCT-AATGTCTA
61 TTACATTTTAAACTCGAACTTCACAAAAATTACCATTTTA-CCTCTGAATGTCTA
*
47504 AAAATTCCATTTTAACCCTGAACTTCACAAAAATTACA-ATTTACCCCAAATGT-TAAAAATTAT
1 AAAATTCCATTTTAACCCT-AACTTCACAAAAATTACATATTTACCCCAAATGTCTAAAAATTAC
* * * * *
47567 ATTTTGACCTCGAACTTTC-CAAAAATTATCGTTTTACCTCTGGATGTCTA
65 ATTTTAAACTCGAAC-TTCACAAAAATTACCATTTTACCTCTGAATGTCTA
*
47617 AAAATTCCATTTTAACCCTAACTTCACAAAAATTACATTTTTACCCC
1 AAAATTCCATTTTAACCCTAACTTCACAAAAATTACATATTTACCCC
47664 CGAACTTCCA
Statistics
Matches: 140, Mismatches: 14, Indels: 16
0.82 0.08 0.09
Matches are distributed among these distances:
112 23 0.16
113 69 0.49
114 9 0.06
115 9 0.06
116 21 0.15
117 9 0.06
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.35
Consensus pattern (114 bp):
AAAATTCCATTTTAACCCTAACTTCACAAAAATTACATATTTACCCCAAATGTCTAAAAATTACA
TTTTAAACTCGAACTTCACAAAAATTACCATTTTACCTCTGAATGTCTA
Found at i:56912 original size:17 final size:17
Alignment explanation
Indices: 56890--56942 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
56880 AACTGCAAAT
**
56890 TCACCAAGTGTGCGAGC
1 TCACCAAGACTGCGAGC
56907 TCACCAAGACTGCGAGC
1 TCACCAAGACTGCGAGC
* * *
56924 TTACCAAGATTGGGAGC
1 TCACCAAGACTGCGAGC
56941 TC
1 TC
56943 GCACACTAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (17 bp):
TCACCAAGACTGCGAGC
Found at i:57787 original size:24 final size:22
Alignment explanation
Indices: 57760--57805 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
57750 CTCGGCCTGA
57760 ATTTATAATAATAATTTTATTTTT
1 ATTTATAATAAT-ATTTT-TTTTT
* *
57784 ATTTTTAATACTATTTTTTTTT
1 ATTTATAATAATATTTTTTTTT
57806 GCTTGTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 5 0.25
24 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTATAATAATATTTTTTTTT
Found at i:58179 original size:41 final size:41
Alignment explanation
Indices: 58129--58208 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
58119 TCTTATTGTA
* *
58129 TTTTCAATTTGTTTGTTGTTTT-ATGAATTGTTTTAATATCG
1 TTTTCAATTTATTTGTTATTTTAAT-AATTGTTTTAATATCG
* *
58170 TTTTTAATTTATTTGTTATTTTAATATTTGTTTTAATAT
1 TTTTCAATTTATTTGTTATTTTAATAATTGTTTTAATAT
58209 TTTTAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.65
Consensus pattern (41 bp):
TTTTCAATTTATTTGTTATTTTAATAATTGTTTTAATATCG
Found at i:58221 original size:24 final size:26
Alignment explanation
Indices: 58194--58242 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
58184 GTTATTTTAA
*
58194 TATTTG-TTT-TAATATTTTTAAATG
1 TATTTGATTTATAATATTTTAAAATG
*
58218 TATTTGATTTATCATATTTTAAAAT
1 TATTTGATTTATAATATTTTAAAAT
58243 TACTTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (26 bp):
TATTTGATTTATAATATTTTAAAATG
Found at i:71245 original size:7 final size:6
Alignment explanation
Indices: 71229--71291 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
71219 AGTTTTTGAA
* * * * *
71229 ATTTTT ATTTTT CATTTTT ATTGTT GTTTTT AATTTT AATTTT ACTTTT
1 ATTTTT ATTTTT -ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
*
71278 ATTGTTT ATGTTT A
1 ATT-TTT ATTTTT A
71292 ATAAAGGGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
6 36 0.77
7 11 0.23
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.71
Consensus pattern (6 bp):
ATTTTT
Found at i:83573 original size:13 final size:13
Alignment explanation
Indices: 83555--83579 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83545 TAAAGCACAC
83555 ATAAAAATAAAAA
1 ATAAAAATAAAAA
83568 ATAAAAATAAAA
1 ATAAAAATAAAA
83580 TATGTGTGCC
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
ATAAAAATAAAAA
Found at i:83914 original size:3 final size:3
Alignment explanation
Indices: 83906--83932 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
83896 TAAATGAATA
83906 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
83933 GAAAAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:86701 original size:24 final size:24
Alignment explanation
Indices: 86672--86729 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
86662 CCCACACGCC
*
86672 CGTGTGTCAAACCGTGTTCTGGAT
1 CGTGTGTCAAACCGTGTTCTAGAT
*
86696 CTTGTGTCAAACCGTGTTCTAGAT
1 CGTGTGTCAAACCGTGTTCTAGAT
86720 CGTGTGTCAA
1 CGTGTGTCAA
86730 CTCGAAATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (24 bp):
CGTGTGTCAAACCGTGTTCTAGAT
Found at i:93498 original size:28 final size:28
Alignment explanation
Indices: 93466--93523 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
93456 TTAAGTATGC
*
93466 TTTAATAGATGAAATGTTCAGAAAAATT
1 TTTAATAAATGAAATGTTCAGAAAAATT
93494 TTTAATAAATGAAATGTTCAGAAAAATT
1 TTTAATAAATGAAATGTTCAGAAAAATT
93522 TT
1 TT
93524 CTTTGTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (28 bp):
TTTAATAAATGAAATGTTCAGAAAAATT
Found at i:97865 original size:23 final size:23
Alignment explanation
Indices: 97835--97915 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
97825 CTGACAAGGC
*
97835 ATCCAGTCAGCAGCTTTTAGAAG
1 ATCCAGTCAGCAGCTTCTAGAAG
97858 ATCCAGTCAGCAGCTTCTAGAAG
1 ATCCAGTCAGCAGCTTCTAGAAG
* ** * *
97881 GTTTAGTCAGCAGCTTCCATAAG
1 ATCCAGTCAGCAGCTTCTAGAAG
* *
97904 GTCTAGTCAGCA
1 ATCCAGTCAGCA
97916 AGGATGGACA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.26
Consensus pattern (23 bp):
ATCCAGTCAGCAGCTTCTAGAAG
Found at i:103026 original size:47 final size:47
Alignment explanation
Indices: 102974--103070 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
102964 ATATGGTCAA
*
102974 TTATTTGGCTACAGGTAAATTACCTTTAGACTTGCCCAGAGTTGAAG
1 TTATTTGGCTACAGGTAAATTACCTTTAGACTTGCCCAAAGTTGAAG
103021 TTATTTGGCTACAGGTAAATTACCTTTAGACTTGCCCAAAGTTGAAG
1 TTATTTGGCTACAGGTAAATTACCTTTAGACTTGCCCAAAGTTGAAG
103068 TTA
1 TTA
103071 ACCGAATAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (47 bp):
TTATTTGGCTACAGGTAAATTACCTTTAGACTTGCCCAAAGTTGAAG
Found at i:118775 original size:17 final size:18
Alignment explanation
Indices: 118753--118786 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
118743 ACTAAGCTTT
118753 AATAT-ATTTAATTCACC
1 AATATAATTTAATTCACC
118770 AATATAATTTAATTCAC
1 AATATAATTTAATTCAC
118787 TTAATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATAATTTAATTCACC
Found at i:123396 original size:21 final size:22
Alignment explanation
Indices: 123352--123394 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
123342 TGAATCAGAT
123352 AGTAATATATGATAATTTTTTTA
1 AGTAATATATGATAA-TTTTTTA
123375 AGTAATATATGATAATTTTT
1 AGTAATATATGATAATTTTT
123395 AATTTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
AGTAATATATGATAATTTTTTA
Found at i:125724 original size:12 final size:12
Alignment explanation
Indices: 125709--125733 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
125699 GCGTTCGCGA
125709 ACATGTTCGTTT
1 ACATGTTCGTTT
125721 ACATGTTCGTTT
1 ACATGTTCGTTT
125733 A
1 A
125734 TACGTTCGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (12 bp):
ACATGTTCGTTT
Found at i:125743 original size:36 final size:35
Alignment explanation
Indices: 125691--125758 Score: 109
Period size: 36 Copynumber: 1.9 Consensus size: 35
125681 TCAGGCTCGA
* *
125691 TTCGTTTAGCGTTCGCGAACATGTTCGTTTACATG
1 TTCGTTTAACGTTCGCGAACATGTTCATTTACATG
125726 TTCGTTTATACGTTCGCGAACATGTTCATTTAC
1 TTCGTTTA-ACGTTCGCGAACATGTTCATTTAC
125759 GTTCGCGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 8 0.27
36 22 0.73
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (35 bp):
TTCGTTTAACGTTCGCGAACATGTTCATTTACATG
Found at i:125816 original size:19 final size:19
Alignment explanation
Indices: 125794--125832 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
125784 AAACAAAAAT
*
125794 TAAATAAAACAAAACCAAG
1 TAAATAAAAAAAAACCAAG
*
125813 TAAATAAAAAAAAACTAAG
1 TAAATAAAAAAAAACCAAG
125832 T
1 T
125833 TGCAAACAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.69, C:0.10, G:0.05, T:0.15
Consensus pattern (19 bp):
TAAATAAAAAAAAACCAAG
Found at i:132106 original size:22 final size:22
Alignment explanation
Indices: 132042--132107 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
132032 ATATAATTTT
*
132042 AATAA-ATAAA-A-ATATTTAA
1 AATAATATAAATATATATTAAA
* *
132061 AATTAT-TAAATATTAAATTAAA
1 AATAATATAAATA-TATATTAAA
*
132083 AATAATATAAATATATATTGAA
1 AATAATATAAATATATATTAAA
132105 AAT
1 AAT
132108 GGACAAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 8 0.22
20 1 0.03
22 21 0.58
23 6 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AATAATATAAATATATATTAAA
Found at i:133365 original size:30 final size:30
Alignment explanation
Indices: 133331--133395 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
133321 CAACCTAATA
*
133331 AACAAATACTTCTAAAATAGTAACAAAAGT
1 AACAAATACTTCTAAAATAATAACAAAAGT
* * *
133361 AACAAATGCTTCTAAAATAATAATAAAATT
1 AACAAATACTTCTAAAATAATAACAAAAGT
133391 AACAA
1 AACAA
133396 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.25
Consensus pattern (30 bp):
AACAAATACTTCTAAAATAATAACAAAAGT
Found at i:134008 original size:31 final size:31
Alignment explanation
Indices: 133950--134008 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
133940 TATAATTATT
*
133950 AATTTATTCATTTTATGAAGAATAAAATGCA
1 AATTTATTCATTTTATGAAGAACAAAATGCA
* * *
133981 AATTTATTGATTTTGTGAAGGACAAAAT
1 AATTTATTCATTTTATGAAGAACAAAAT
134009 ACGAACCAAT
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:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (31 bp):
AATTTATTCATTTTATGAAGAACAAAATGCA
Found at i:134345 original size:16 final size:16
Alignment explanation
Indices: 134324--134359 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
134314 TGATTCGTTA
*
134324 TAATGTAATAGAGTTG
1 TAATGTAATAAAGTTG
134340 TAATGTAATAAAGTTG
1 TAATGTAATAAAGTTG
134356 TAAT
1 TAAT
134360 AAAAATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (16 bp):
TAATGTAATAAAGTTG
Found at i:134616 original size:56 final size:57
Alignment explanation
Indices: 134533--134683 Score: 175
Period size: 56 Copynumber: 2.6 Consensus size: 57
134523 TTGTTAAATT
* * * *
134533 TTAATA-AGATTATTATTAAATATAATTTAATAAAAAATAAATATTTTAATCATATT-
1 TTAATATA-ATTATTATTAAATACAATTTAATAAAAAATAAATAATTTAATAACATTC
*
134589 TTAACT-TAATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAACATTC
1 TTAA-TATAATTATTATTAAATACAATTTAATAAAA-AATAAATAATTTAATAACATTC
*
134647 TTAATATAATTATTATTAAAATATGAA-TTAATAAAAA
1 TTAATATAATTATTATT-AAATA-CAATTTAATAAAAA
134684 TCATAATATA
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
56 30 0.37
57 20 0.24
58 16 0.20
59 14 0.17
60 2 0.02
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (57 bp):
TTAATATAATTATTATTAAATACAATTTAATAAAAAATAAATAATTTAATAACATTC
Found at i:148320 original size:39 final size:39
Alignment explanation
Indices: 148275--148449 Score: 140
Period size: 39 Copynumber: 4.5 Consensus size: 39
148265 ATTTAATATT
* * *
148275 AGTGTTTACAGTGTCACTACTACTTCAGTATAGCGTTGCG
1 AGTGTTTACAATGTCACTGCTAGTTCAGTATAGCGTTG-G
* * * * *
148315 A-TGTTTACAATATCACCGCCAGTTCAGTATGGCGTTGT
1 AGTGTTTACAATGTCACTGCTAGTTCAGTATAGCGTTGG
* * *
148353 AGTGTTTACAATGTCACTGCTAGTTCAGTATATCTTTGT
1 AGTGTTTACAATGTCACTGCTAGTTCAGTATAGCGTTGG
* * * * * *
148392 AGTGTTTTCAGTGTCA-TCGCTAGTTTAAG-ATAACTTTGT
1 AGTGTTTACAATGTCACT-GCTAG-TTCAGTATAGCGTTGG
*
148431 AGTGTTTACAGTGTCACTG
1 AGTGTTTACAATGTCACTG
148450 TCGATAACAT
Statistics
Matches: 112, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
38 2 0.02
39 104 0.93
40 6 0.05
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (39 bp):
AGTGTTTACAATGTCACTGCTAGTTCAGTATAGCGTTGG
Found at i:149838 original size:17 final size:17
Alignment explanation
Indices: 149816--149849 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
149806 ACATATAAAA
149816 CATGTATATATCCACCT
1 CATGTATATATCCACCT
149833 CATGTATATATCCACCT
1 CATGTATATATCCACCT
149850 AAGAAAGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (17 bp):
CATGTATATATCCACCT
Found at i:152808 original size:84 final size:84
Alignment explanation
Indices: 152666--152834 Score: 295
Period size: 84 Copynumber: 2.0 Consensus size: 84
152656 GCTAAACAGA
*
152666 TTTACTCTCTAGTAGCTTAGCATGTAAGGCCAAAAGACTTACCTTACAAGGGGCATCTCAAGAAT
1 TTTACTCTCTAGTAGCTTAGCATGTAAGGCCAAAAGACTTACCTTACAAGGGGAATCTCAAGAAT
152731 GGTCCTCCCATTCCGAGCT
66 GGTCCTCCCATTCCGAGCT
*
152750 TTTACTCTGC-AGTAGCTTAGCATGTAAGGCCAAAAGACTTACCTTACAAGGGGAATCTCAAGGA
1 TTTACTCT-CTAGTAGCTTAGCATGTAAGGCCAAAAGACTTACCTTACAAGGGGAATCTCAAGAA
*
152814 TGGTCCTCCCATTCCGGGCT
65 TGGTCCTCCCATTCCGAGCT
152834 T
1 T
152835 ATCCTAAAGG
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
84 80 0.99
85 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (84 bp):
TTTACTCTCTAGTAGCTTAGCATGTAAGGCCAAAAGACTTACCTTACAAGGGGAATCTCAAGAAT
GGTCCTCCCATTCCGAGCT
Found at i:155910 original size:337 final size:337
Alignment explanation
Indices: 155280--155944 Score: 985
Period size: 337 Copynumber: 2.0 Consensus size: 337
155270 TGTGCCACCA
* * *
155280 CATCGCACATAGCAAGCATTATCAGTCATGCATCGATGAACCCACTCTGAATTTGTGAGCAACCT
1 CATCGCACATAGCAAGCATCATCAGTCATGCATCGACGAACCCACTATGAATTTGTGAGCAACCT
* * * * **
155345 TTGTCTGCGAATGAGCCAAAGGAAATGCTGGATACGTAGAGGCAAGGAACTTTCCCAAATCATAG
66 CTGCCTACGAACGAGCCAAAGGAAATGCTGGATACACAGAGGCAAGGAACTTTCCCAAATCATAG
*
155410 TCCACCCATTCAGACCACTCAAATTATCCATCATTTCCAAACTCCTATACACTGTACGGACTAAA
131 TCCACCCATTCAGACCACTCAAATTATCCATCATGTCCAAACTCCTATACACTGTACGGACTAAA
*
155475 TAGGCCCCATTGGTGCTCATCTTCCATATGATTTTGTCACAACCTAAGGCTTCATTGGAAGGGTG
196 TAGGCCCCATTGGTGCTCATCTTCCATATGATTTTGTCACAACCTAAGGCTTCATTGGAAGGGTC
* * * *
155540 TGAGCCCAAAATACTATCCAATGCTTGCTTAGGGAACAACTAGGATAGCAACCCCACATTCCAAA
261 CGAGCCCAAAATACTATCCAATGCCTCCTTAGGGAACAACTAGGACAGCAACCCCACATTCCAAA
155605 CACATTGGTGCT
326 CACATTGGTGCT
* * **
155617 CATCGCACACT-GTAAGCATCATCAGTCATGCATCGACGGACCCTTTATGAATTTGTGAGCAACC
1 CATCGCACA-TAGCAAGCATCATCAGTCATGCATCGACGAACCCACTATGAATTTGTGAGCAACC
* *
155681 TCTGCCTACGAACGAGCCAAAGGAAATGCTGGATACACGGAGGCAAGGAACTTTCCCAAATCGTA
65 TCTGCCTACGAACGAGCCAAAGGAAATGCTGGATACACAGAGGCAAGGAACTTTCCCAAATCATA
* * * *
155746 GTCCACCCATTCGGACCTCTCAAATTATTCATCATGTCCAAACTCCTATACGCTGTACGGACTAA
130 GTCCACCCATTCAGACCACTCAAATTATCCATCATGTCCAAACTCCTATACACTGTACGGACTAA
* * * *
155811 ATAGGCTCCATTGGTGCTCTTCTTCCATATGATTTTGTCAC-ACCTTAAGGTTTCATTGGGAGGG
195 ATAGGCCCCATTGGTGCTCATCTTCCATATGATTTTGTCACAACC-TAAGGCTTCATTGGAAGGG
* * * *
155875 TCCGAGGCCGAAATA-TAGTCCAATTCCTCCTTAGGGAACAACTGGGACAGCAACCCCACATTCC
259 TCCGAGCCCAAAATACTA-TCCAATGCCTCCTTAGGGAACAACTAGGACAGCAACCCCACATTCC
155939 AAACAC
323 AAACAC
155945 CAGTAGTAGT
Statistics
Matches: 292, Mismatches: 33, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
336 5 0.02
337 286 0.98
338 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (337 bp):
CATCGCACATAGCAAGCATCATCAGTCATGCATCGACGAACCCACTATGAATTTGTGAGCAACCT
CTGCCTACGAACGAGCCAAAGGAAATGCTGGATACACAGAGGCAAGGAACTTTCCCAAATCATAG
TCCACCCATTCAGACCACTCAAATTATCCATCATGTCCAAACTCCTATACACTGTACGGACTAAA
TAGGCCCCATTGGTGCTCATCTTCCATATGATTTTGTCACAACCTAAGGCTTCATTGGAAGGGTC
CGAGCCCAAAATACTATCCAATGCCTCCTTAGGGAACAACTAGGACAGCAACCCCACATTCCAAA
CACATTGGTGCT
Found at i:162846 original size:87 final size:86
Alignment explanation
Indices: 162689--162848 Score: 200
Period size: 87 Copynumber: 1.8 Consensus size: 86
162679 CATCTCAATA
* * * * *
162689 GGACCACCCAAACTCTGGGATTTGAATTCATTAAGAGTAATAAACTCAACCTGTCATGTCATTGA
1 GGACCACCCAAACTCTGGGATATGAAGTCATTAAGAGTAATAAACGCAACCTATCATGTCATCG-
162754 ATTCATCAAGTCTCTTTTAATT
65 ATTCATCAAGTCTCTTTTAATT
*
162776 GGACCACCCAAA-TCTTGGGATATGAAGTCATTAAGAGTAA-GAACGCAACCTTATGCATGTACA
1 GGACCACCCAAACTC-TGGGATATGAAGTCATTAAGAGTAATAAACGCAACC-TAT-CATGT-CA
162839 TCG-TTCATCA
62 TCGATTCATCA
162849 TAGGGATAGG
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
86 10 0.16
87 44 0.70
88 5 0.08
89 4 0.06
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Consensus pattern (86 bp):
GGACCACCCAAACTCTGGGATATGAAGTCATTAAGAGTAATAAACGCAACCTATCATGTCATCGA
TTCATCAAGTCTCTTTTAATT
Found at i:164301 original size:12 final size:12
Alignment explanation
Indices: 164286--164310 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
164276 ATTAAAGAAT
164286 TAATAGCATTCA
1 TAATAGCATTCA
164298 TAATAGCATTCA
1 TAATAGCATTCA
164310 T
1 T
164311 CATATAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:167146 original size:21 final size:18
Alignment explanation
Indices: 167103--167138 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
167093 TCTTCCTCGG
167103 GATCTTCTTCTTCTTTAA
1 GATCTTCTTCTTCTTTAA
*
167121 GATCTTCTTTTTCTTTAA
1 GATCTTCTTCTTCTTTAA
167139 CAGAATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.19, G:0.06, T:0.58
Consensus pattern (18 bp):
GATCTTCTTCTTCTTTAA
Found at i:167987 original size:22 final size:22
Alignment explanation
Indices: 167946--167994 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
167936 AAATTAAAAT
*
167946 AAATTAAAAAGTTAATAAATTA
1 AAATTAAAAAGTTAATAAATAA
167968 AAATTAGAAAA-TTAGA-AAATAA
1 AAATTA-AAAAGTTA-ATAAATAA
167990 AAATT
1 AAATT
167995 TTTACCACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
AAATTAAAAAGTTAATAAATAA
Found at i:168634 original size:108 final size:108
Alignment explanation
Indices: 168506--168729 Score: 328
Period size: 108 Copynumber: 2.1 Consensus size: 108
168496 TCAAAATATT
* * *
168506 TAAAACAAATCCTAATTCAAACTTTGGATAGTAATTAATATAAATTAGAAAATTCAATTTATAAC
1 TAAAAAAAATCCTAATTCAAACTTTGGATAATAATTAATATAAATTACAAAATTCAATTTATAAC
* *
168571 TAATATTAAAGATTATCAAAA-TTCTGAAAAATAAAAATTTAAA
66 TAATATTAAAAATTATCAAAACTT-TGAAAAATAAAAATTGAAA
* *
168614 TAAAAAAAAT-CTAATCTCAAACTTTTGATAATAATTAATATAAATTACAAAATTTAATTTATAA
1 TAAAAAAAATCCTAAT-TCAAACTTTGGATAATAATTAATATAAATTACAAAATTCAATTTATAA
* *
168678 TTAATATTAAAAATTATCAAAACTTTGAAAAATAAGAATTGAAA
65 CTAATATTAAAAATTATCAAAACTTTGAAAAATAAAAATTGAAA
168722 -AAAAAAAA
1 TAAAAAAAA
168730 CTTGATAATA
Statistics
Matches: 105, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
107 13 0.12
108 90 0.86
109 2 0.02
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.33
Consensus pattern (108 bp):
TAAAAAAAATCCTAATTCAAACTTTGGATAATAATTAATATAAATTACAAAATTCAATTTATAAC
TAATATTAAAAATTATCAAAACTTTGAAAAATAAAAATTGAAA
Found at i:169054 original size:29 final size:30
Alignment explanation
Indices: 168997--169054 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
168987 TGTTTTAAAA
* * *
168997 ATATTTACAAAAAATGACAGCTAATTTTTC
1 ATATTTACAAAAAATCACAACTAAATTTTC
*
169027 ATATTTAC-AAAATTCACAACTAAATTTT
1 ATATTTACAAAAAATCACAACTAAATTTT
169055 ACAAAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (30 bp):
ATATTTACAAAAAATCACAACTAAATTTTC
Found at i:178296 original size:51 final size:50
Alignment explanation
Indices: 178236--178358 Score: 174
Period size: 51 Copynumber: 2.4 Consensus size: 50
178226 AATAGTAGAG
* *
178236 GATTTTTCTCAGATGAAAATACTCTAAAAATATTTTCTGTAACAGTCAAAA
1 GATTTTTCTCA-ATGAAAATACTCTAAAAATATTTTCTATAACAATCAAAA
* *
178287 GATTTTTCTCAAATGAAAATATTCTGAAAATATTTTCTATAACAATCAAAA
1 GATTTTTCTC-AATGAAAATACTCTAAAAATATTTTCTATAACAATCAAAA
*
178338 GAATTTTCTCAATTGAAAATA
1 GATTTTTCTCAA-TGAAAATA
178359 TTATTTTACA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
50 2 0.03
51 62 0.95
52 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (50 bp):
GATTTTTCTCAATGAAAATACTCTAAAAATATTTTCTATAACAATCAAAA
Found at i:180749 original size:53 final size:53
Alignment explanation
Indices: 180682--180789 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
180672 TTTTAGGATG
180682 CTGGTATTGAAATTAACAAATTTTAAATTCAAATGACAACATTTTTAAAAATT
1 CTGGTATTGAAATTAACAAATTTTAAATTCAAATGACAACATTTTTAAAAATT
180735 CTGGTATTGAAATTAACAAATTTTAAATTCAAATGACAACATTTTTAAAAATT
1 CTGGTATTGAAATTAACAAATTTTAAATTCAAATGACAACATTTTTAAAAATT
180788 CT
1 CT
180790 ATCACACACG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.38
Consensus pattern (53 bp):
CTGGTATTGAAATTAACAAATTTTAAATTCAAATGACAACATTTTTAAAAATT
Found at i:181610 original size:18 final size:18
Alignment explanation
Indices: 181587--181622 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
181577 CTTAATTAAG
*
181587 GATTTAAATAATAATATT
1 GATTTAAACAATAATATT
*
181605 GATTTAAGCAATAATATT
1 GATTTAAACAATAATATT
181623 TAGAACATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (18 bp):
GATTTAAACAATAATATT
Found at i:185747 original size:30 final size:30
Alignment explanation
Indices: 185711--185823 Score: 138
Period size: 30 Copynumber: 3.7 Consensus size: 30
185701 TGTCCTTTTT
185711 CACATTTTGACCCCTAAACTTTTCCAAATA-
1 CACATTTTGACCCCTAAACTTTTCCAAA-AG
* *
185741 CACATTTTGACCCTTAAACTTTTCCAAAAT
1 CACATTTTGACCCCTAAACTTTTCCAAAAG
* * *
185771 TACATTTTAACCCCTTAAACTTTCCCAAAAG
1 CACATTTTGACCCC-TAAACTTTTCCAAAAG
* *
185802 CATATTTTGACCCCCAAACTTT
1 CACATTTTGACCCCTAAACTTT
185824 CTTAAAATTA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
29 1 0.01
30 45 0.63
31 25 0.35
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.35
Consensus pattern (30 bp):
CACATTTTGACCCCTAAACTTTTCCAAAAG
Found at i:185809 original size:61 final size:60
Alignment explanation
Indices: 185712--185838 Score: 159
Period size: 61 Copynumber: 2.1 Consensus size: 60
185702 GTCCTTTTTC
* * **
185712 ACATTTTGACCCCTAAACTTTTCCAAATACACATTTTGACCCTTAAACTTT-TCCAAAATT
1 ACATTTTAACCCCTAAACTTTCCCAAATACACATTTTGACCCCCAAACTTTCT-CAAAATT
* *
185772 ACATTTTAACCCCTTAAACTTTCCCAAA-AGCATATTTTGACCCCCAAACTTTCTTAAAATT
1 ACATTTTAACCCC-TAAACTTTCCCAAATA-CACATTTTGACCCCCAAACTTTCTCAAAATT
185833 ACATTT
1 ACATTT
185839 GATACTCAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
60 13 0.22
61 44 0.76
62 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (60 bp):
ACATTTTAACCCCTAAACTTTCCCAAATACACATTTTGACCCCCAAACTTTCTCAAAATT
Found at i:197870 original size:21 final size:19
Alignment explanation
Indices: 197820--197872 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
197810 TGTTTGCTAG
* *
197820 TTTTTTTACCAACATTTGC
1 TTTTTTTACCAATACTTGC
* *
197839 TATTTTGACCAATACTTGC
1 TTTTTTTACCAATACTTGC
197858 ATTTTTTTTACCAAT
1 --TTTTTTTACCAAT
197873 GTTTGATATC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 15 0.58
21 11 0.42
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.51
Consensus pattern (19 bp):
TTTTTTTACCAATACTTGC
Found at i:198523 original size:50 final size:50
Alignment explanation
Indices: 198469--198632 Score: 145
Period size: 50 Copynumber: 3.1 Consensus size: 50
198459 AAATGGAGTA
198469 AATGGAGTAAAACAAGTAGCAAATCTCATTATCCACTAAAATTGCAATGG
1 AATGGAGTAAAACAAGTAGCAAATCTCATTATCCACTAAAATTGCAATGG
* * * * *
198519 AATGGGGTGAAGTGATAGATCAGTGAAACAACAAT-TCCTATATCC-CTAAAGTTGCAA-GG
1 AATGGAGT-AA---A-ACA--AGT--AGC-A-AATCTCAT-TATCCACTAAAATTGCAATGG
198578 AAATGGAGTAAAACAAGTAGCAAATCTCATTATCCACTAAAATTGCAATGG
1 -AATGGAGTAAAACAAGTAGCAAATCTCATTATCCACTAAAATTGCAATGG
198629 AATG
1 AATG
198633 ATGTGAAGCC
Statistics
Matches: 88, Mismatches: 10, Indels: 32
0.68 0.08 0.25
Matches are distributed among these distances:
49 8 0.09
50 26 0.30
51 6 0.07
53 3 0.03
54 1 0.01
55 4 0.05
56 1 0.01
57 3 0.03
59 6 0.07
60 22 0.25
61 8 0.09
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (50 bp):
AATGGAGTAAAACAAGTAGCAAATCTCATTATCCACTAAAATTGCAATGG
Found at i:198815 original size:97 final size:97
Alignment explanation
Indices: 198564--198832 Score: 297
Period size: 97 Copynumber: 2.8 Consensus size: 97
198554 TCCTATATCC
* * * * * * *
198564 CTAAAGTTGCAAGGAAATGGAGTAAAACAAGTAGCAAATCTCATTATCCACTAAAATTGCAATGG
1 CTAAAGTTGCAATGAAACGAATTAAAACAAGTAGCAAATCTCAATCTCCACTAAAGTTGCAATGG
*
198629 AAT-GATGTGAAGCCACACCAAATTCTATCTAC
66 AATAGA-GTGAAGCCACACCAAATTCTATCTAA
* * * * * ** *
198661 CTAAAGTTGCAATGAAACGAATTAAAACAAGTAACAGATCTCAAACCCCACTGAAGTTATAGTGG
1 CTAAAGTTGCAATGAAACGAATTAAAACAAGTAGCAAATCTCAATCTCCACTAAAGTTGCAATGG
* ***
198726 AATAGAGTGAAGCCATATTGAATTCTATCTAA
66 AATAGAGTGAAGCCACACCAAATTCTATCTAA
* * * * *
198758 CTGAAGTTGCAGTGAAGCGAATTAAAAAAAGTAGCAAATCTCAATCTCAACTAAAGTTGCAATGG
1 CTAAAGTTGCAATGAAACGAATTAAAACAAGTAGCAAATCTCAATCTCCACTAAAGTTGCAATGG
198823 AATAGAGTGA
66 AATAGAGTGA
198833 GACCACAAAA
Statistics
Matches: 138, Mismatches: 33, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
97 136 0.99
98 2 0.01
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (97 bp):
CTAAAGTTGCAATGAAACGAATTAAAACAAGTAGCAAATCTCAATCTCCACTAAAGTTGCAATGG
AATAGAGTGAAGCCACACCAAATTCTATCTAA
Found at i:200477 original size:21 final size:21
Alignment explanation
Indices: 200453--200498 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
200443 CCTTCCACAG
200453 TTTTACTTT-GTTTTAATTTCA
1 TTTTACTTTAGTTTTAATTT-A
* *
200474 TTTT-TTTTATTTTTAATTTA
1 TTTTACTTTAGTTTTAATTTA
200494 TTTTA
1 TTTTA
200499 ATTTTAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTACTTTAGTTTTAATTTA
Found at i:200497 original size:16 final size:16
Alignment explanation
Indices: 200453--200505 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
200443 CCTTCCACAG
* *
200453 TTTTACTTTGTTTTAA
1 TTTTAATTTATTTTAA
* * *
200469 -TTTCATTTTTTTTAT
1 TTTTAATTTATTTTAA
200484 TTTTAATTTATTTTAA
1 TTTTAATTTATTTTAA
200500 TTTTAA
1 TTTTAA
200506 CCTTAAATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTAATTTATTTTAA
Found at i:201552 original size:30 final size:30
Alignment explanation
Indices: 201507--201573 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
201497 CAATTGAGTA
201507 AATAGCTAACAAGTAATGTTAAGTAATAATT
1 AATA-CTAACAAGTAATGTTAAGTAATAATT
* * * *
201538 AGTACTAACTAGTAATGTTAGGTAATGATT
1 AATACTAACAAGTAATGTTAAGTAATAATT
201568 AATACT
1 AATACT
201574 GGTTAGACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.34
Consensus pattern (30 bp):
AATACTAACAAGTAATGTTAAGTAATAATT
Found at i:208111 original size:9 final size:9
Alignment explanation
Indices: 208097--208266 Score: 65
Period size: 10 Copynumber: 17.1 Consensus size: 9
208087 TGATTTAAAC
*
208097 TTATAAATA
1 TTATAAAAA
208106 TTATAAAAAA
1 TTAT-AAAAA
*
208116 TCATAAAAA
1 TTATAAAAA
*
208125 CTTATAAATA
1 -TTATAAAAA
208135 TTATAAAAAA
1 TTAT-AAAAA
*
208145 TATCTAATAAA
1 T-TATAA-AAA
*
208156 TTTTAAAAAA
1 TTAT-AAAAA
208166 TTAT-AAAA
1 TTATAAAAA
*
208174 TAACTATAAAA
1 TTA-TA-AAAA
208185 TTAATAAAACA
1 TT-ATAAAA-A
* *
208196 TATTTAAAATT
1 T-TATAAAA-A
208207 TTATAAAAAAA
1 TTAT--AAAAA
*
208218 CTTACAAATAA
1 -TTATAAA-AA
*
208229 -TATAAATA
1 TTATAAAAA
*
208237 TTCTAATAAA
1 TTATAA-AAA
208247 TTATAAAAA
1 TTATAAAAA
208256 TTATTAAAAA
1 TTA-TAAAAA
208266 T
1 T
208267 CATTTAAACT
Statistics
Matches: 121, Mismatches: 21, Indels: 37
0.68 0.12 0.21
Matches are distributed among these distances:
8 7 0.06
9 29 0.24
10 51 0.42
11 25 0.21
12 9 0.07
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:208175 original size:22 final size:23
Alignment explanation
Indices: 208099--208176 Score: 61
Period size: 29 Copynumber: 3.2 Consensus size: 23
208089 ATTTAAACTT
208099 ATAAATATTATAAAAAATCATAAAAA
1 ATAAATATTATAAAAAAT-AT--AAA
**
208125 CTTATAAATATTATAAAAAATATCTA
1 ---ATAAATATTATAAAAAATATAAA
208151 ATAAAT-TT-TAAAAAATTATAAA
1 ATAAATATTATAAAAAA-TATAAA
208173 ATAA
1 ATAA
208177 CTATAAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 7 0.16
22 10 0.23
23 6 0.14
26 1 0.02
28 2 0.05
29 18 0.41
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAAATATTATAAAAAATATAAA
Found at i:208202 original size:41 final size:39
Alignment explanation
Indices: 208153--208255 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 39
208143 AATATCTAAT
*
208153 AAAT-TTTAAAAAATTATAAAATAACTATA-AAATTAATAA
1 AAATATTTAAAAAATTATAAAAAAACT-TACAAA-TAATAA
** *
208192 AACATATTTAAAATTTTATAAAAAAACTTACAAATAATAT
1 AA-ATATTTAAAAAATTATAAAAAAACTTACAAATAATAA
*
208232 AAATATTCTAATAAATTATAAAAA
1 AAATATT-TAAAAAATTATAAAAA
208256 TTATTAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
39 7 0.13
40 24 0.45
41 22 0.42
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (39 bp):
AAATATTTAAAAAATTATAAAAAAACTTACAAATAATAA
Found at i:208266 original size:19 final size:19
Alignment explanation
Indices: 208071--208193 Score: 61
Period size: 19 Copynumber: 6.3 Consensus size: 19
208061 TTAATAAAAA
* *
208071 TAAAAAATATTAAAATTGAT
1 TAAAAATTATAAAAATT-AT
* * *
208091 TTAAACTTATAAATATTAT
1 TAAAAATTATAAAAATTAT
* *
208110 AAAAAATCATAAAAACTTA-
1 TAAAAATTATAAAAA-TTAT
* *
208129 TAAATATTATAAAAAATAT
1 TAAAAATTATAAAAATTAT
*
208148 CTAATAAATTTTAAAAAATTAT
1 -TAA-AAATTAT-AAAAATTAT
* * *
208170 AAAATAACTAT-AAAATTAA
1 TAAA-AATTATAAAAATTAT
208189 TAAAA
1 TAAAA
208194 CATATTTAAA
Statistics
Matches: 75, Mismatches: 22, Indels: 14
0.68 0.20 0.13
Matches are distributed among these distances:
18 3 0.04
19 34 0.45
20 19 0.25
21 11 0.15
22 8 0.11
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (19 bp):
TAAAAATTATAAAAATTAT
Found at i:212444 original size:14 final size:15
Alignment explanation
Indices: 212425--212457 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
212415 GGAGTCAAAC
*
212425 TAAAAAT-TTTATAT
1 TAAAAATGTTTAAAT
212439 TAAAAATGTTTAAAT
1 TAAAAATGTTTAAAT
212454 TAAA
1 TAAA
212458 TTATAATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TAAAAATGTTTAAAT
Found at i:212695 original size:9 final size:9
Alignment explanation
Indices: 212688--212717 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
212678 ATTAATTTTA
212688 AAAATT-TT
1 AAAATTATT
212696 AAAATTATT
1 AAAATTATT
212705 AAAATTATT
1 AAAATTATT
212714 AAAA
1 AAAA
212718 AGTATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.29
9 15 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAAATTATT
Found at i:214803 original size:18 final size:18
Alignment explanation
Indices: 214776--214816 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
214766 GGCTGCGGTT
*
214776 CAGCAGCAGGACGAGGAG
1 CAGCAACAGGACGAGGAG
* *
214794 TAGCAACAGGACGGGGAG
1 CAGCAACAGGACGAGGAG
214812 CAGCA
1 CAGCA
214817 GCTGCCGAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.22, G:0.41, T:0.02
Consensus pattern (18 bp):
CAGCAACAGGACGAGGAG
Found at i:218475 original size:15 final size:15
Alignment explanation
Indices: 218455--218490 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
218445 GGTATGTTTG
218455 TGCACTTAATCACTT
1 TGCACTTAATCACTT
218470 TGCACTTAATCACTT
1 TGCACTTAATCACTT
218485 TGCACT
1 TGCACT
218491 ATTAAGGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.39
Consensus pattern (15 bp):
TGCACTTAATCACTT
Found at i:221410 original size:3 final size:3
Alignment explanation
Indices: 221404--221439 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
221394 TGATAATGAT
* *
221404 GAG GAG GAG GAG GAG AAG GAG GAG GAG GAA GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
221440 ACCCCAATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:230393 original size:51 final size:51
Alignment explanation
Indices: 230277--230518 Score: 270
Period size: 51 Copynumber: 4.7 Consensus size: 51
230267 TTTCATTTAA
* ** * * *
230277 TACTCACGATGACA-TATAGTCATCGGACCTCTTGTTCCATATAAGAATTCATG
1 TACTCACGATGACACT-TAGTCATCAGACCT-TTAATCCGTA-AAGGATTCATT
* * * * * *
230330 TACTCACAATGACTCTAAGTCATCAGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
* *
230381 TACTCACGATGACACTTACTGATCAGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
* *
230432 TACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
* * *
230483 TACTCACGATGGCACGTAGTCATCGGACCCTTTAAT
1 TACTCACGATGACACTTAGTCATCAGA-CCTTTAAT
230519 TTATAGTTCG
Statistics
Matches: 162, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
51 122 0.75
52 15 0.09
53 24 0.15
54 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
Found at i:237665 original size:51 final size:51
Alignment explanation
Indices: 237540--237828 Score: 395
Period size: 51 Copynumber: 5.6 Consensus size: 51
237530 TTTCATTTAA
** ** * *
237540 TACTCACGATGACA-TATAGTCATCAAACCTCTTGTTCCGTATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCGTAAAGG-ATTCATT
* * *
237593 TACTCACGATGAC-TTTGAGTCATCGGACCTTTAATCCATCATA-GATTCATT
1 TACTCACGATGACACTT-AGTCATCGGACCTTTAATCCGT-AAAGGATTCATT
*
237644 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAAGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
237695 TACTCACGATAACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
237746 TACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
237797 TACTCACGATGACACTTAGTCATCTGACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
237829 TAGTTTATAG
Statistics
Matches: 216, Mismatches: 15, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
50 2 0.01
51 176 0.81
52 10 0.05
53 28 0.13
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:248640 original size:60 final size:56
Alignment explanation
Indices: 248469--248669 Score: 264
Period size: 54 Copynumber: 3.5 Consensus size: 56
248459 AGCCATGTAA
* * *
248469 ACCACTTTTTTTATCAGATAAAAAAAACTTTTTGGTGTTGGCCAATGCTTGGTAGAC
1 ACCACTTTTTTTATCAGATAAAAAAAA-TTTTTTGTGTTGGCCAATGCTTGATCGAC
* *
248526 ACTACTTTTTTTATCAGATAAAAAAAA--TTTTGTGTTGGCCAATGCTTGACCGAC
1 ACCACTTTTTTTATCAGATAAAAAAAATTTTTTGTGTTGGCCAATGCTTGATCGAC
* *
248580 ACCACATTTTTTATCAGATAAAAAAATAATTTTTTTTGTATTGGCC-ATGCATTGATCGAC
1 ACCACTTTTTTTATCAGAT-AAAAAA-AA--TTTTTTGTGTTGGCCAATGC-TTGATCGAC
248640 ACCACTTTTTTTATCAGATAAAAAAAATTT
1 ACCACTTTTTTTATCAGATAAAAAAAATTT
248670 GGTGTTAGCC
Statistics
Matches: 127, Mismatches: 10, Indels: 15
0.84 0.07 0.10
Matches are distributed among these distances:
54 40 0.31
55 6 0.05
56 5 0.04
57 26 0.20
58 2 0.02
59 10 0.08
60 38 0.30
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (56 bp):
ACCACTTTTTTTATCAGATAAAAAAAATTTTTTGTGTTGGCCAATGCTTGATCGAC
Found at i:248666 original size:114 final size:111
Alignment explanation
Indices: 248469--248697 Score: 300
Period size: 114 Copynumber: 2.0 Consensus size: 111
248459 AGCCATGTAA
* * * *
248469 ACCACTTTTTTTATCAGATAAAAAAAACTTTTTGGTGTTGGCCAATGCTTGGTAGACACTACTTT
1 ACCACATTTTTTATCAGATAAAAAAAACTTTTTGGTATTGGCCAATGCTTGATAGACACCACTTT
* *
248534 TTTTATCAGATAAAAAAAATTTTGTGTTGGCCAATGC-TTGACCGAC
66 TTTTATCAGATAAAAAAAATTTGGTGTTAGCC-ATGCATTGACCGAC
* * *
248580 ACCACATTTTTTATCAGATAAAAAAATAATTTTTTTTGTATTGGCC-ATGCATTGATCGACACCA
1 ACCACATTTTTTATCAGAT-AAAAAA-AA-CTTTTTGGTATTGGCCAATGC-TTGATAGACACCA
* *
248644 CTTTTTTTATCAGATAAAAAAAATTTGGTGTTAGCCATGCATTGGCTGAC
62 CTTTTTTTATCAGATAAAAAAAATTTGGTGTTAGCCATGCATTGACCGAC
248694 ACCA
1 ACCA
248698 ACTTTCCCTC
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
111 18 0.18
112 6 0.06
113 10 0.10
114 68 0.67
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (111 bp):
ACCACATTTTTTATCAGATAAAAAAAACTTTTTGGTATTGGCCAATGCTTGATAGACACCACTTT
TTTTATCAGATAAAAAAAATTTGGTGTTAGCCATGCATTGACCGAC
Found at i:248695 original size:54 final size:56
Alignment explanation
Indices: 248469--248702 Score: 241
Period size: 54 Copynumber: 4.1 Consensus size: 56
248459 AGCCATGTAA
248469 ACCACTTTTTTTATCAGATAAAAAAAACTTTTTGGTGTTGGCCAATGCTTGG-TAGAC
1 ACCACTTTTTTTATCAGATAAAAAAAA--TTTTGGTGTTGGCCAATGCTTGGCTAGAC
* * *
248526 ACTACTTTTTTTATCAGATAAAAAAAATTTT-GTGTTGGCCAATGCTTGAC-CGAC
1 ACCACTTTTTTTATCAGATAAAAAAAATTTTGGTGTTGGCCAATGCTTGGCTAGAC
* * * * *
248580 ACCACATTTTTTATCAGATAAAAAAATAATTTTTTTTGTATTGGCC-ATGCATT-GATCGAC
1 ACCACTTTTTTTATCAGAT-AAAAAA-AA---TTTTGGTGTTGGCCAATGC-TTGGCTAGAC
*
248640 ACCACTTTTTTTATCAGATAAAAAAAA-TTTGGTGTTAGCC-ATGCATTGGCT-GAC
1 ACCACTTTTTTTATCAGATAAAAAAAATTTTGGTGTTGGCCAATGC-TTGGCTAGAC
248694 ACCAACTTT
1 ACC-ACTTT
248703 CCCTCCTATC
Statistics
Matches: 153, Mismatches: 13, Indels: 24
0.81 0.07 0.13
Matches are distributed among these distances:
54 60 0.39
55 17 0.11
56 2 0.01
57 26 0.17
58 2 0.01
59 14 0.09
60 32 0.21
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (56 bp):
ACCACTTTTTTTATCAGATAAAAAAAATTTTGGTGTTGGCCAATGCTTGGCTAGAC
Found at i:252629 original size:17 final size:16
Alignment explanation
Indices: 252607--252641 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
252597 ATTTATGTAA
*
252607 AAATTAATTTGAAAATT
1 AAATTAAGTTG-AAATT
252624 AAATTAAGTTGAAATT
1 AAATTAAGTTGAAATT
252640 AA
1 AA
252642 TTTCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (16 bp):
AAATTAAGTTGAAATT
Found at i:252722 original size:19 final size:19
Alignment explanation
Indices: 252694--252730 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
252684 TAATTATACA
*
252694 AGTTTGAATTTAAAATTAT
1 AGTTTAAATTTAAAATTAT
*
252713 AGTTTAAATTTGAAATTA
1 AGTTTAAATTTAAAATTA
252731 AAATTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (19 bp):
AGTTTAAATTTAAAATTAT
Found at i:253014 original size:93 final size:93
Alignment explanation
Indices: 252853--253466 Score: 987
Period size: 93 Copynumber: 6.6 Consensus size: 93
252843 TAACCAACAT
* * *
252853 TATTTCAATTTATATCAAATAA-AGTGTTGATTTGATAATATATTATTTACTAAATTCAAATATT
1 TATTTCAATTTATATCAAATAATA-TGTTGATTTGACAATACATTATTTACCAAATTCAAATATT
*
252917 AAAATTATTTAAATAAAAAATTATTATAA
65 AAAATTATTTAAATTAAAAATTATTATAA
* * * *
252946 TATTTCAATTTATATCAAATAATATATTGATTTGATAATACATTTTTTACCAAATTCAAATATCA
1 TATTTCAATTTATATCAAATAATATGTTGATTTGACAATACATTATTTACCAAATTCAAATATTA
253011 AAATTATTTAAATTAAAAATTATTATAA
66 AAATTATTTAAATTAAAAATTATTATAA
* * *
253039 TATTTTAATTTATATCAAATAATATGTTGATTTAACAATACAGTATTTACCAAATTCAAATATTA
1 TATTTCAATTTATATCAAATAATATGTTGATTTGACAATACATTATTTACCAAATTCAAATATTA
253104 AAATTATTTAAATTAAAAATTATTATAA
66 AAATTATTTAAATTAAAAATTATTATAA
*
253132 TATTTCAATTTATATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAATTCAAATATTA
1 TATTTCAATTTATATCAAATAATATGTTGATTTGACAATACATTATTTACCAAATTCAAATATTA
* *
253197 ATATTATTTAGATTAAAAATTATTATAA
66 AAATTATTTAAATTAAAAATTATTATAA
* * * * *
253225 TATTTTAATTAATATAAAATAATATGTTGATTTGACAATATATTATTTAACAAATTCAAATATTA
1 TATTTCAATTTATATCAAATAATATGTTGATTTGACAATACATTATTTACCAAATTCAAATATTA
*
253290 AAATTATTTAAATTAAAATTTATTATAA
66 AAATTATTTAAATTAAAAATTATTATAA
* *
253318 TATTTCAATTTATATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAATTCAAATTTTA
1 TATTTCAATTTATATCAAATAATATGTTGATTTGACAATACATTATTTACCAAATTCAAATATTA
253383 AAATTATTTAAATTAAAAATTATTATAA
66 AAATTATTTAAATTAAAAATTATTATAA
* * *
253411 TATTTCAATTTATATCAAATAATGTGTTGATTTGATAATAGATTATTTACCAAATT
1 TATTTCAATTTATATCAAATAATATGTTGATTTGACAATACATTATTTACCAAATT
253467 ACCCTTAATT
Statistics
Matches: 482, Mismatches: 38, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
93 481 1.00
94 1 0.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (93 bp):
TATTTCAATTTATATCAAATAATATGTTGATTTGACAATACATTATTTACCAAATTCAAATATTA
AAATTATTTAAATTAAAAATTATTATAA
Found at i:254760 original size:20 final size:20
Alignment explanation
Indices: 254711--254760 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
254701 AAATTTTTTA
*
254711 AAATATTTTTTTCTATTTTCG
1 AAAT-TTTTTTTATATTTTCG
* *
254732 AAATGTTTTTTATATTTTTG
1 AAATTTTTTTTATATTTTCG
254752 -AATTTTTTT
1 AAATTTTTTT
254761 AAAATAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 8 0.32
20 13 0.52
21 4 0.16
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.66
Consensus pattern (20 bp):
AAATTTTTTTTATATTTTCG
Found at i:254849 original size:35 final size:36
Alignment explanation
Indices: 254810--254878 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
254800 TAGTTTTTCG
254810 AATTTTTTAAA-AT-TATTTTTATATCTTCGAAATGA
1 AATTTTTTAAATATAT-TTTTTATATCTTCGAAATGA
* *
254845 AATTTTTTACATATATTTTTTATATTTTCGAAAT
1 AATTTTTTAAATATATTTTTTATATCTTCGAAAT
254879 ATTAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 10 0.33
36 19 0.63
37 1 0.03
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (36 bp):
AATTTTTTAAATATATTTTTTATATCTTCGAAATGA
Found at i:255074 original size:153 final size:154
Alignment explanation
Indices: 254792--255107 Score: 562
Period size: 153 Copynumber: 2.1 Consensus size: 154
254782 TTTTTTACAT
* * *
254792 ATATTTTTTAGTTTTTCGAATTTTTTAAAATTATTTTTATATCTTCGAAATGAAATTTTTTACAT
1 ATATTTTTTAGCTTTTCGAATTTTTTAAAATTATTTTTATATCTTCAAAATGAAAATTTTTACAT
254857 ATATTTTTTATATTTTCGAAATATTAAAAAATACATTTTCGAAATATTTTTTTACAAATTAAAAA
66 ATATTTTTTATATTTTCGAAATATTAAAAAATACATTTTCGAAATATTTTTTTACAAATTAAAAA
*
254922 TCTTATATATTTTATATTTTCAAA
131 TCTTATATATTTTACATTTTCAAA
*
254946 ATATTTTTTAGCTTTTCGATTTTTTTAAAATTATTTTTATATCTTCAAAATGAAAATTTTTACAT
1 ATATTTTTTAGCTTTTCGAATTTTTTAAAATTATTTTTATATCTTCAAAATGAAAATTTTTACAT
*
255011 ATA-TTTTTATATTTTCGAAATATTAAAAAATACATTTTTGAAATATTTTTTTACAAATTAAAAA
66 ATATTTTTTATATTTTCGAAATATTAAAAAATACATTTTCGAAATATTTTTTTACAAATTAAAAA
*
255075 TCTTATATTTTTTACATTTTCAAA
131 TCTTATATATTTTACATTTTCAAA
255099 ATATTTTTT
1 ATATTTTTT
255108 TACAAATAAA
Statistics
Matches: 155, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
153 91 0.59
154 64 0.41
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (154 bp):
ATATTTTTTAGCTTTTCGAATTTTTTAAAATTATTTTTATATCTTCAAAATGAAAATTTTTACAT
ATATTTTTTATATTTTCGAAATATTAAAAAATACATTTTCGAAATATTTTTTTACAAATTAAAAA
TCTTATATATTTTACATTTTCAAA
Found at i:256197 original size:31 final size:29
Alignment explanation
Indices: 256161--256243 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 29
256151 TTTTGATTTT
256161 TTTTAAAATTTAATTTGTAATTTCGTTTATA
1 TTTT-AAATTTAATTT-TAATTTCGTTTATA
256192 TTTTAAATTTAAAATTTTAATTTCGTTTATA
1 TTTTAAATTT--AATTTTAATTTCGTTTATA
*
256223 TTTTAAATTTCATTTCTAATT
1 TTTTAAATTTAATTT-TAATT
256244 ATTATTTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
29 4 0.08
30 11 0.23
31 28 0.58
32 5 0.10
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.59
Consensus pattern (29 bp):
TTTTAAATTTAATTTTAATTTCGTTTATA
Found at i:257262 original size:52 final size:55
Alignment explanation
Indices: 257126--257282 Score: 169
Period size: 52 Copynumber: 2.9 Consensus size: 55
257116 ATTTATTTTT
** * *
257126 TTATCTGATAAAAAAGGTAGTGTCGACCAAGCATTTGTCAACACCAAAAAAAAAAA
1 TTATCTGATAAAAAA-GTAGTGTCGGTCAAGCATTGGCCAACACCAAAAAAAAAAA
* * * *
257182 TTATCTAATAAAAAAGTTGTTGTTGGTCAAGCATTGGCCAATA-C-AAAAAAAAAA
1 TTATCTGATAAAAAAGTAG-TGTCGGTCAAGCATTGGCCAACACCAAAAAAAAAAA
* *
257236 -T-TCTGATAAAAAAGATAGTGTCGGTCAAGTATTGGTCAACACCAAAA
1 TTATCTGATAAAAAAG-TAGTGTCGGTCAAGCATTGGCCAACACCAAAA
257283 TTTTTTTTAT
Statistics
Matches: 83, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
52 31 0.37
53 4 0.05
54 13 0.16
55 4 0.05
56 31 0.37
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (55 bp):
TTATCTGATAAAAAAGTAGTGTCGGTCAAGCATTGGCCAACACCAAAAAAAAAAA
Found at i:257538 original size:116 final size:114
Alignment explanation
Indices: 257398--257688 Score: 345
Period size: 116 Copynumber: 2.5 Consensus size: 114
257388 AACACCAATT
* *
257398 TTTTTATCTGATAAAAAAGATGGTGTCGGCCAAGCATTGACCAACACCAAAATTTTTTTTTATCT
1 TTTTTATCTGATAAAAAAGGTGGTGTCGGCCAAGCATTGGCCAACACCAAAATTTTTTTTTATC-
* *
257463 AAATAAAAAA-G-TGGTGTCGACCAATCCATGGCCAATACTAAAAAAAATCAG
65 AAATAAAAAATGCTGATGTCGACCAATCCATGACCAATAC--AAAAAAAT-AG
* * *
257514 TTTTTATCTGATTAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACC-AAATTTTTTTTTATCG
1 TTTTTATCTGATAAAAAAGGTGGTGTCGGCCAAGCATTGGCCAACACCAAAATTTTTTTTTATCA
* * * ** * * **
257578 GATAAAAAATGCTGATGTTGGCCAATGTATGACCAATACCAAGAAATTT
66 AATAAAAAATGCTGATGTCGACCAATCCATGACCAATACAAAAAAATAG
* *
257627 TTTTTATCTGATAAAAAAAGTGGTGTCGGCCAAGCATTGGCCAACACTATTAAATTTTTTTT
1 TTTTTATCTGATAAAAAAGGTGGTGTCGGCCAAGCATTGGCCAACACCA--AAATTTTTTTT
257689 CAAAATCTCG
Statistics
Matches: 150, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
113 44 0.29
114 14 0.09
115 16 0.11
116 76 0.51
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (114 bp):
TTTTTATCTGATAAAAAAGGTGGTGTCGGCCAAGCATTGGCCAACACCAAAATTTTTTTTTATCA
AATAAAAAATGCTGATGTCGACCAATCCATGACCAATACAAAAAAATAG
Found at i:257555 original size:60 final size:57
Alignment explanation
Indices: 257335--257557 Score: 174
Period size: 60 Copynumber: 4.0 Consensus size: 57
257325 TAACCAACAC
* * * *
257335 CAAAAAAATTA-TTTTTATCTGATAAAAAAGGTGGTGTCAACCAAGTATTGGCC-AA
1 CAAAAAAATCAGTTTTTATCTGATTAAAAAGGTGGTGTCGACCAAGCATTGGCCAAA
** * * * * *
257390 C--ACCAAT--TTTTTTATCTGATAAAAAAGATGGTGTCGGCCAAGCATTGACC-AA
1 CAAAAAAATCAGTTTTTATCTGATTAAAAAGGTGGTGTCGACCAAGCATTGGCCAAA
** *** * * * *
257442 CACCAAAATTTTTTTTTATCTAAATAAAAAAGTGGTGTCGACCAATCCA-TGGCCAATA
1 CAAAAAAATCAGTTTTTATCTGATTAAAAAGGTGGTGTCGACCAA-GCATTGGCCAA-A
257500 CTAAAAAAAATCAGTTTTTATCTGATTAAAAAGGTGGTGTCGACCAAGCATTGGCCAA
1 C--AAAAAAATCAGTTTTTATCTGATTAAAAAGGTGGTGTCGACCAAGCATTGGCCAA
257558 CACCAAATTT
Statistics
Matches: 130, Mismatches: 27, Indels: 17
0.75 0.16 0.10
Matches are distributed among these distances:
52 40 0.31
53 4 0.03
54 3 0.02
55 1 0.01
56 32 0.25
57 3 0.02
58 2 0.02
59 2 0.02
60 43 0.33
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (57 bp):
CAAAAAAATCAGTTTTTATCTGATTAAAAAGGTGGTGTCGACCAAGCATTGGCCAAA
Found at i:257561 original size:168 final size:167
Alignment explanation
Indices: 257237--257659 Score: 478
Period size: 167 Copynumber: 2.5 Consensus size: 167
257227 AAAAAAAAAT
* * ** *
257237 TCTGATAAAAAAGATAGTGTCGGTCAAGTATTGGTCAACACCAAAATTTTTTTTATTTGATAA-A
1 TCTGATAAAAAAGATGGTGTCGGCCAAGTATTGACCAACACCAAAATTTTTTTTATCT-A-AATA
* * * * * *
257301 AAAATGCTGATGTTGGCCAATGCATAACCAACACCAAAAAAATTATTTTTATCTGATAAAAAAGG
64 AAAAAG-TGGTGTCGGCCAATCCATAACCAACACAAAAAAAATCATTTTTATCTGATAAAAAAGG
*
257366 TGGTGTCAACCAAGTATTGGCCAACACC-AA-TTTTTTTA
128 TGGTGTCAACCAAGCATTGGCCAACACCAAATTTTTTTTA
*
257404 TCTGATAAAAAAGATGGTGTCGGCCAAGCATTGACCAACACCAAAATTTTTTTTTATCTAAATAA
1 TCTGATAAAAAAGATGGTGTCGGCCAAGTATTGACCAACACCAAAA-TTTTTTTTATCTAAATAA
* ** * *
257469 AAAAGTGGTGTCGACCAATCCATGGCCAATACTAAAAAAAATCAGTTTTTATCTGATTAAAAAGG
65 AAAAGTGGTGTCGGCCAATCCATAACCAACAC-AAAAAAAATCA-TTTTTATCTGATAAAAAAGG
*
257534 TGGTGTCGACCAAGCATTGGCCAACACCAAATTTTTTTTTA
128 TGGTGTCAACCAAGCATTGGCCAACACCAAA-TTTTTTTTA
* * * * * *
257575 TCGGATAAAAAATGCTGATGTTGGCCAATGTA-TGACCAATACCAAGAAATTTTTTTTATCT-GA
1 TCTGATAAAAAA-GATGGTGTCGGCCAA-GTATTGACCAACACC-A-AAATTTTTTTTATCTAAA
257638 TAAAAAAAGTGGTGTCGGCCAA
62 T-AAAAAAGTGGTGTCGGCCAA
257660 GCATTGGCCA
Statistics
Matches: 217, Mismatches: 27, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
166 22 0.10
167 57 0.26
168 56 0.26
169 2 0.01
171 19 0.09
172 24 0.11
173 34 0.16
174 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (167 bp):
TCTGATAAAAAAGATGGTGTCGGCCAAGTATTGACCAACACCAAAATTTTTTTTATCTAAATAAA
AAAGTGGTGTCGGCCAATCCATAACCAACACAAAAAAAATCATTTTTATCTGATAAAAAAGGTGG
TGTCAACCAAGCATTGGCCAACACCAAATTTTTTTTA
Found at i:259930 original size:49 final size:46
Alignment explanation
Indices: 259854--259953 Score: 137
Period size: 49 Copynumber: 2.1 Consensus size: 46
259844 TAAGAAAGGG
* *
259854 CAAAACCACGTCGTTTTGATAAGTGTTTACCTTCTTTAAAGTTAAAAGA
1 CAAAACCACGTCGTTTTGATAAATGTTTA-CTT-ATT-AAGTTAAAAGA
* *
259903 CAAAACTATGTCGTTTTGATAAATGTTTACTTATTAAGTTAAAAGA
1 CAAAACCACGTCGTTTTGATAAATGTTTACTTATTAAGTTAAAAGA
259949 CAAAA
1 CAAAA
259954 TCATTATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
46 16 0.34
47 2 0.04
48 3 0.06
49 26 0.55
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (46 bp):
CAAAACCACGTCGTTTTGATAAATGTTTACTTATTAAGTTAAAAGA
Found at i:260575 original size:18 final size:16
Alignment explanation
Indices: 260543--260578 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
260533 ATGGGATGAG
260543 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
260559 AATAAATTTAATTAATTA
1 AATAAATTT--TTAATTA
260577 AA
1 AA
260579 AATTTTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:262876 original size:25 final size:24
Alignment explanation
Indices: 262848--262899 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
262838 ACTATATAAA
262848 AAAATTTAATAAATA-AAAAATATAT
1 AAAA-TTAATAAATATAAAAA-ATAT
*
262873 AAAATTATTAAATATTAAAAAATAT
1 AAAATTAATAAATA-TAAAAAATAT
262898 AA
1 AA
262900 TATATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 9 0.38
25 10 0.42
26 5 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAATTAATAAATATAAAAAATAT
Found at i:262886 original size:28 final size:27
Alignment explanation
Indices: 262840--262898 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
262830 TTAATATAAC
*
262840 TATATAAAAAAATTTAATAAATAAAAAA
1 TATATAAAAAAATTAAAT-AATAAAAAA
** *
262868 TATATAAAATTATTAAATATTAAAAAA
1 TATATAAAAAAATTAAATAATAAAAAA
262895 TATA
1 TATA
262899 ATATATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
TATATAAAAAAATTAAATAATAAAAAA
Found at i:262913 original size:29 final size:29
Alignment explanation
Indices: 262853--262932 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
262843 ATAAAAAAAT
262853 TTAATAAA-TAAAAAATAT-ATA-AAATTA
1 TTAA-AAATTAAAAAATATAATATAAATTA
* * *
262880 TTAAATATTAAAAAATATAATATATATTT
1 TTAAAAATTAAAAAATATAATATAAATTA
262909 TTAAAAATTAAAAAA-ATAATATAA
1 TTAAAAATTAAAAAATATAATATAA
262933 GCAGACTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.04
27 14 0.31
28 11 0.24
29 18 0.40
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
TTAAAAATTAAAAAATATAATATAAATTA
Found at i:262921 original size:28 final size:28
Alignment explanation
Indices: 262852--262932 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
262842 TATAAAAAAA
*
262852 TTTAATAAATAAAAAATAT-ATA-AAATT
1 TTTAA-AAATTAAAAATATAATATAAATT
* * *
262879 ATTAAATATTAAAAAATATAATATATATT
1 TTTAAAAATT-AAAAATATAATATAAATT
*
262908 TTTAAAAATTAAAAAAATAATATAA
1 TTTAAAAATTAAAAATATAATATAA
262933 GCAGACTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
26 3 0.07
27 12 0.28
28 16 0.37
29 12 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
TTTAAAAATTAAAAATATAATATAAATT
Found at i:262923 original size:30 final size:27
Alignment explanation
Indices: 262853--262932 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 27
262843 ATAAAAAAAT
262853 TTAATAAA-TAAAAAATATATAAAATTA
1 TTAA-AAATTAAAAAATATATAAAATTA
* * *
262880 TTAAATATTAAAAAATATAATATATATTT
1 TTAAAAATTAAAAAATAT-ATA-AAATTA
262909 TTAAAAATTAAAAAAATAATATAA
1 TTAAAAATT-AAAAAAT-ATATAA
262933 GCAGACTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
26 2 0.05
27 14 0.32
28 3 0.07
29 13 0.30
30 10 0.23
31 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
TTAAAAATTAAAAAATATATAAAATTA
Found at i:263997 original size:6 final size:6
Alignment explanation
Indices: 263980--264031 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
263970 AAGTGCGCCG
* * * * *
263980 GAGGGA GAGGCA GTGGCA GTGGCA GAGGCA GAGGCA GAGGGA GAGGAA
1 GAGGCA GAGGCA GAGGCA GAGGCA GAGGCA GAGGCA GAGGCA GAGGCA
264028 GAGG
1 GAGG
264032 GAGCACCAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.31, C:0.10, G:0.56, T:0.04
Consensus pattern (6 bp):
GAGGCA
Found at i:264024 original size:18 final size:18
Alignment explanation
Indices: 263980--264031 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
263970 AAGTGCGCCG
*
263980 GAGGGAGAGGCAGTGGCA
1 GAGGGAGAGGCAGAGGCA
* *
263998 GTGGCAGAGGCAGAGGCA
1 GAGGGAGAGGCAGAGGCA
*
264016 GAGGGAGAGGAAGAGG
1 GAGGGAGAGGCAGAGG
264032 GAGCACCAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.31, C:0.10, G:0.56, T:0.04
Consensus pattern (18 bp):
GAGGGAGAGGCAGAGGCA
Found at i:264032 original size:12 final size:12
Alignment explanation
Indices: 263980--264034 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
263970 AAGTGCGCCG
263980 GAGGGAGAGGCA
1 GAGGGAGAGGCA
* * *
263992 GTGGCAGTGGCA
1 GAGGGAGAGGCA
*
264004 GAGGCAGAGGCA
1 GAGGGAGAGGCA
*
264016 GAGGGAGAGGAA
1 GAGGGAGAGGCA
264028 GAGGGAG
1 GAGGGAG
264035 CACCAGAAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.31, C:0.09, G:0.56, T:0.04
Consensus pattern (12 bp):
GAGGGAGAGGCA
Found at i:265212 original size:30 final size:30
Alignment explanation
Indices: 265178--265235 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
265168 CACTCAAGGC
*
265178 ACACGCCCGTGTAAGTTG-TCCGTGTGCACA
1 ACACGCCCATGTAAGTTGCT-CGTGTGCACA
*
265208 ACACGCCCATGTGAGTTGCTCGTGTGCA
1 ACACGCCCATGTAAGTTGCTCGTGTGCA
265236 TGCCGTGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.19, C:0.29, G:0.28, T:0.24
Consensus pattern (30 bp):
ACACGCCCATGTAAGTTGCTCGTGTGCACA
Found at i:265849 original size:20 final size:20
Alignment explanation
Indices: 265792--265849 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
265782 GTCCACTAAA
265792 TAAAATCCAATGT--CCAAAC
1 TAAAATCCAAT-TACCCAAAC
* *
265811 TACAAATCCAAACTACCCAAAT
1 TA-AAATCC-AATTACCCAAAC
265833 TAAAATCCAATTACCCA
1 TAAAATCCAATTACCCA
265850 CTACAAGCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.06
20 15 0.47
21 8 0.25
22 7 0.22
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.21
Consensus pattern (20 bp):
TAAAATCCAATTACCCAAAC
Found at i:268395 original size:76 final size:77
Alignment explanation
Indices: 268303--268534 Score: 281
Period size: 77 Copynumber: 3.0 Consensus size: 77
268293 AAAAAATCTT
* * * * * *
268303 ATTCAGTATAATTAGTGGATAATGCTCG-TTTGAGCAAACATTCAGTATGATCAGTAGTTATCGC
1 ATTCAGTAAAATTAGTGGAT-TTGCTCGTTTTGACCAAGCATTCAGTATAATCAGTAGAT-TCGC
268367 CCG-TTGAGCAA-C
64 CCGCTTGAGCAAGC
* * **
268379 ATTCAGTAAAATTAGTGGATTTGCTCGTTTTGATCAAGCACTCAGTATAATCAGTAGATTCGCTT
1 ATTCAGTAAAATTAGTGGATTTGCTCGTTTTGACCAAGCATTCAGTATAATCAGTAGATTCGCCC
*
268444 GCTTGAGTAAGC
66 GCTTGAGCAAGC
* * * *
268456 TTTCAGTAAAATTAGTGGATTTGCTCGTTTTGACCAAGCATTCAGTATAATCAATAAATTCGCTC
1 ATTCAGTAAAATTAGTGGATTTGCTCGTTTTGACCAAGCATTCAGTATAATCAGTAGATTCGCCC
*
268521 GCTTTAGCAAGC
66 GCTTGAGCAAGC
268533 AT
1 AT
268535 ATAAATAAAA
Statistics
Matches: 134, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
75 11 0.08
76 52 0.39
77 71 0.53
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (77 bp):
ATTCAGTAAAATTAGTGGATTTGCTCGTTTTGACCAAGCATTCAGTATAATCAGTAGATTCGCCC
GCTTGAGCAAGC
Found at i:268521 original size:39 final size:39
Alignment explanation
Indices: 268303--268534 Score: 172
Period size: 39 Copynumber: 6.1 Consensus size: 39
268293 AAAAAATCTT
* * *
268303 ATTCAGTATAATTAGTGGATAAT-GCTCG-TTTGAGCAAAC
1 ATTCAGTATAATCAGTAGAT--TCGCTCGTTTTGAGCAAGC
* * *
268342 ATTCAGTATGATCAGTAGTTATCGCCCG--TTGAGCAA-C
1 ATTCAGTATAATCAGTAGAT-TCGCTCGTTTTGAGCAAGC
* * * * *
268379 ATTCAGTAAAATTAGTGGATTTGCTCGTTTTGATCAAGC
1 ATTCAGTATAATCAGTAGATTCGCTCGTTTTGAGCAAGC
* * * *
268418 ACTCAGTATAATCAGTAGATTCGCTTG-CTTGAGTAAGC
1 ATTCAGTATAATCAGTAGATTCGCTCGTTTTGAGCAAGC
* * * * * *
268456 TTTCAGTAAAATTAGTGGATTTGCTCGTTTTGACCAAGC
1 ATTCAGTATAATCAGTAGATTCGCTCGTTTTGAGCAAGC
* * *
268495 ATTCAGTATAATCAATAAATTCGCTCGCTTT-AGCAAGC
1 ATTCAGTATAATCAGTAGATTCGCTCGTTTTGAGCAAGC
268533 AT
1 AT
268535 ATAAATAAAA
Statistics
Matches: 147, Mismatches: 41, Indels: 11
0.74 0.21 0.06
Matches are distributed among these distances:
36 5 0.03
37 16 0.11
38 53 0.36
39 73 0.50
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (39 bp):
ATTCAGTATAATCAGTAGATTCGCTCGTTTTGAGCAAGC
Found at i:270790 original size:10 final size:10
Alignment explanation
Indices: 270775--270803 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
270765 TAAGAATAGA
270775 TTAGTAATTT
1 TTAGTAATTT
270785 TTAGTAA-TT
1 TTAGTAATTT
270794 TTAGTAATTT
1 TTAGTAATTT
270804 ATTGGTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (10 bp):
TTAGTAATTT
Found at i:272071 original size:16 final size:18
Alignment explanation
Indices: 272045--272077 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
272035 TTAAATTAAC
272045 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
272062 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
272078 CTCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:285048 original size:11 final size:11
Alignment explanation
Indices: 285032--285072 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
285022 AGTTTTCAAT
285032 TTTTTTAATTA
1 TTTTTTAATTA
*
285043 TTTTTT-ATAA
1 TTTTTTAATTA
*
285053 TTTTTAAATTA
1 TTTTTTAATTA
285064 TTTTTTAAT
1 TTTTTTAAT
285073 GTGACTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTTAATTA
Found at i:289466 original size:11 final size:11
Alignment explanation
Indices: 289450--289478 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
289440 TCTGGCTTCT
289450 CCTTTCTGATA
1 CCTTTCTGATA
289461 CCTTTCTGATA
1 CCTTTCTGATA
289472 CCTTTCT
1 CCTTTCT
289479 CGTCAATGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.31, G:0.07, T:0.48
Consensus pattern (11 bp):
CCTTTCTGATA
Found at i:293920 original size:3 final size:3
Alignment explanation
Indices: 293912--293951 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
293902 CAGAACAAAT
293912 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
293952 ACTAAAGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:299204 original size:19 final size:18
Alignment explanation
Indices: 299161--299204 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
299151 AAACTTATTT
299161 AATATA-TCACATCAATA
1 AATATACTCACATCAATA
*
299178 AATAATACTCAGATCATATA
1 AAT-ATACTCACATCA-ATA
299198 AATATAC
1 AATATAC
299205 AACCTTACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 3 0.13
19 11 0.48
20 6 0.26
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (18 bp):
AATATACTCACATCAATA
Found at i:311684 original size:17 final size:17
Alignment explanation
Indices: 311662--311696 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
311652 TTTTTCTCCA
311662 AAAATATTTG-TAAAAAT
1 AAAATA-TTGATAAAAAT
311679 AAAATATTGATAAAAAT
1 AAAATATTGATAAAAAT
311696 A
1 A
311697 TTCAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
AAAATATTGATAAAAAT
Found at i:315272 original size:33 final size:33
Alignment explanation
Indices: 315225--315291 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
315215 GATAAGATAA
315225 AGATACATCCTTTGCCATCATTAAAAAGCTTCT
1 AGATACATCCTTTGCCATCATTAAAAAGCTTCT
*
315258 AGATGCATCCTTTGCCATCATTAAAAAGCTTCT
1 AGATACATCCTTTGCCATCATTAAAAAGCTTCT
315291 A
1 A
315292 CTTGTAGAAT
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:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (33 bp):
AGATACATCCTTTGCCATCATTAAAAAGCTTCT
Found at i:316286 original size:17 final size:16
Alignment explanation
Indices: 316244--316287 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
316234 ATTAATTATT
316244 TTTTAATT-TTTAAAA
1 TTTTAATTATTTAAAA
* *
316259 TTATAAATATTATAAAA
1 TTTTAATTATT-TAAAA
316276 TTTTAATTATTT
1 TTTTAATTATTT
316288 TTTAAAGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 6 0.26
16 3 0.13
17 14 0.61
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAATTATTTAAAA
Found at i:317299 original size:31 final size:31
Alignment explanation
Indices: 317262--317329 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
317252 TTTAAAAGTC
* * *
317262 AAAAAAATATTTTTACCAACTTTTAAAGGATTT
1 AAAAAAAT-TGTTT-CCAACTTTTAAAGAACTT
*
317295 AAAAAAATTGTTTCCAATTTTTAAAGAACTT
1 AAAAAAATTGTTTCCAACTTTTAAAGAACTT
317326 AAAA
1 AAAA
317330 CCTCATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 19 0.61
32 4 0.13
33 8 0.26
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (31 bp):
AAAAAAATTGTTTCCAACTTTTAAAGAACTT
Found at i:320918 original size:327 final size:327
Alignment explanation
Indices: 320324--320981 Score: 1111
Period size: 327 Copynumber: 2.0 Consensus size: 327
320314 AAACTTGGTC
320324 TCAAAATTTTCCCTATATTCATAGGACACTTCATTAAGAGAACAATACTGAGGTTCCTTTGTTTC
1 TCAAAATTTTCCCTATATTCATAGGACACTTCATTAAGAGAACAATACTGAGGTTCCTTTGTTTC
* * *
320389 ACAACCAGAAAGCTCCACGTCAAGCCTGGTCTCAGAATCTTCCGTGTATTCATATGACACTTCAT
66 ACAACCAGAAAGCCCCAAGTCAAGCCTGGTCTCAGAATCTTCCGTGTATTCATAGGACACTTCAT
* * * *
320454 TAATAGAACTGCATTGGAGTTCCGTTGTATGATAAGGCACATCAGTCCTCAAAATATTTACATTA
131 TAAGAGAACAGCATTGGAGTTCCGTTGTAGGATAAGACACATCAGTCCTCAAAATATTTACATTA
* *
320519 GCGGTTTCACTTTCAGGAACCTCAACTTTAACATCAATAGATGCAGGCCAATCCCGATTTAGTTC
196 GCAGTTTCACTTTCAGGAACCTCAACTTTAACATCAATAGACGCAGGCCAATCCCGATTTAGTTC
* *
320584 AAGCAAATCCTCATCGCTACTCTTGATATTCTTGAAACGTTTAGATTTCCAACCGATAAGAGGAT
261 AAGCAAATCCTCATCACTACTCTTGATATTCTTGAAAAGTTTAGATTTCCAACCGATAAGAGGAT
320649 CT
326 CT
*
320651 TCAAAATTTTCCCTATATTCATAGGACGCTTCATTAAGAGAACAATACTGAGGTTCCTTTGTTTC
1 TCAAAATTTTCCCTATATTCATAGGACACTTCATTAAGAGAACAATACTGAGGTTCCTTTGTTTC
320716 ACAACCAGAAAGCCCCAAGTCAAGCCTGGTCTCAGAATCTTCCGTGTATTCATAGGACACTTCAT
66 ACAACCAGAAAGCCCCAAGTCAAGCCTGGTCTCAGAATCTTCCGTGTATTCATAGGACACTTCAT
* * * * *
320781 TAAGAGTACAGTATTGGGGTTCC-TCTGTAGGATAAGACACGTCAGTCTTCAAAATATTTACATT
131 TAAGAGAACAGCATTGGAGTTCCGT-TGTAGGATAAGACACATCAGTCCTCAAAATATTTACATT
*
320845 AGCAGTTTCACTTTCAGGAACCTCAACTTTAACATCAATAGGCGCAGGCCAATCCCGATTTAGTT
195 AGCAGTTTCACTTTCAGGAACCTCAACTTTAACATCAATAGACGCAGGCCAATCCCGATTTAGTT
** *
320910 CAAGCAAATTTTCATCACTGCTCTTGATATTCTTGAAAAGTTTAGATTTCCAACCGATAAGAGGA
260 CAAGCAAATCCTCATCACTACTCTTGATATTCTTGAAAAGTTTAGATTTCCAACCGATAAGAGGA
320975 TCT
325 TCT
320978 TCAA
1 TCAA
320982 GATCATCGTG
Statistics
Matches: 309, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
326 1 0.00
327 308 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (327 bp):
TCAAAATTTTCCCTATATTCATAGGACACTTCATTAAGAGAACAATACTGAGGTTCCTTTGTTTC
ACAACCAGAAAGCCCCAAGTCAAGCCTGGTCTCAGAATCTTCCGTGTATTCATAGGACACTTCAT
TAAGAGAACAGCATTGGAGTTCCGTTGTAGGATAAGACACATCAGTCCTCAAAATATTTACATTA
GCAGTTTCACTTTCAGGAACCTCAACTTTAACATCAATAGACGCAGGCCAATCCCGATTTAGTTC
AAGCAAATCCTCATCACTACTCTTGATATTCTTGAAAAGTTTAGATTTCCAACCGATAAGAGGAT
CT
Found at i:324899 original size:3 final size:3
Alignment explanation
Indices: 324891--324917 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
324881 ACCCGACTGT
324891 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
324918 ACAATTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:331053 original size:12 final size:12
Alignment explanation
Indices: 331036--331065 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
331026 AAAAAAGTAA
*
331036 TAATAATAATAT
1 TAATAATAATAG
331048 TAATAATAATAG
1 TAATAATAATAG
331060 TAATAA
1 TAATAA
331066 AACATATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
TAATAATAATAG
Found at i:338436 original size:12 final size:12
Alignment explanation
Indices: 338419--338544 Score: 77
Period size: 12 Copynumber: 10.8 Consensus size: 12
338409 ATAACATCCA
338419 AACAACAAAAAT
1 AACAACAAAAAT
* *
338431 AACAACCAAAGT
1 AACAACAAAAAT
* *
338443 AGCAGCAAAAAT
1 AACAACAAAAAT
*
338455 ---AACAATAA-
1 AACAACAAAAAT
*
338463 AACAACATTAAA-
1 AACAACA-AAAAT
338475 AACAACAAAAAT
1 AACAACAAAAAT
*
338487 AGCAACAAAAA-
1 AACAACAAAAAT
*
338498 AAGGAACAAAAAT
1 AA-CAACAAAAAT
*
338511 AACAATAAAAAT
1 AACAACAAAAAT
*
338523 AAC-ACGAAAAT
1 AACAACAAAAAT
*
338534 AGCAATCAAAA
1 AACAA-CAAAA
338545 CAATAAAAAA
Statistics
Matches: 85, Mismatches: 20, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
9 6 0.07
11 16 0.19
12 57 0.67
13 6 0.07
ACGTcount: A:0.68, C:0.16, G:0.06, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:338458 original size:44 final size:44
Alignment explanation
Indices: 338405--338497 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
338395 AAAACGCATA
* * * *
338405 AAAAATAAC-ATCCAAACAACA-AAAATAACAACCAAAGTAGCAGC
1 AAAAATAACAAT-AAAACAACATAAAA-AACAACAAAAATAGCAAC
*
338449 AAAAATAACAATAAAACAACATTAAAAACAACAAAAATAGCAAC
1 AAAAATAACAATAAAACAACATAAAAAACAACAAAAATAGCAAC
338493 AAAAA
1 AAAAA
338498 AAGGAACAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 37 0.88
45 5 0.12
ACGTcount: A:0.68, C:0.18, G:0.04, T:0.10
Consensus pattern (44 bp):
AAAAATAACAATAAAACAACATAAAAAACAACAAAAATAGCAAC
Done.