Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011779.1 Kokia drynarioides strain JFW-HI SEQ_126774, 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: 390585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
Found at i:2659 original size:4 final size:4
Alignment explanation
Indices: 2650--2716 Score: 73
Period size: 4 Copynumber: 16.5 Consensus size: 4
2640 AAACACATTA
* * * *
2650 TCTT TCTT TCAT TCTT T-TT TCTT TCCTC TCCT TCTT CCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT TCTT TCTT TCTT
2698 TCTT TCCTT TCTT TCTT TC
1 TCTT T-CTT TCTT TCTT TC
2717 CCGTTTATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
3 3 0.06
4 42 0.81
5 7 0.13
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.67
Consensus pattern (4 bp):
TCTT
Found at i:2704 original size:17 final size:16
Alignment explanation
Indices: 2650--2716 Score: 73
Period size: 17 Copynumber: 4.1 Consensus size: 16
2640 AAACACATTA
*
2650 TCTTTCTTTCATTCTT
1 TCTTTCTTTCTTTCTT
* *
2666 T-TTTCTTTCCTCTCCT
1 TCTTTCTTT-CTTTCTT
*
2682 TCTTCCTTTCTTTCTT
1 TCTTTCTTTCTTTCTT
2698 TCTTTCCTTTCTTTCTT
1 TCTTT-CTTTCTTTCTT
2715 TC
1 TC
2717 CCGTTTATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
15 7 0.17
16 15 0.37
17 19 0.46
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.67
Consensus pattern (16 bp):
TCTTTCTTTCTTTCTT
Found at i:6157 original size:7 final size:7
Alignment explanation
Indices: 6145--6182 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
6135 TAAGAAATTT
6145 AAAA-AA
1 AAAAGAA
6151 AAAA-AA
1 AAAAGAA
6157 AAAAGAA
1 AAAAGAA
6164 AAAAGAA
1 AAAAGAA
6171 AAAAGAA
1 AAAAGAA
6178 AAAAG
1 AAAAG
6183 TGGGTATGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 10 0.32
7 21 0.68
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:12021 original size:6 final size:6
Alignment explanation
Indices: 12010--12039 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
12000 TCCCTTGAAG
12010 AACAGA AACAGA AACAGA AACAGA AACAGA
1 AACAGA AACAGA AACAGA AACAGA AACAGA
12040 GAGTTTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.17, G:0.17, T:0.00
Consensus pattern (6 bp):
AACAGA
Found at i:19943 original size:22 final size:22
Alignment explanation
Indices: 19915--20001 Score: 79
Period size: 22 Copynumber: 3.9 Consensus size: 22
19905 GCAACAGTAG
19915 GCACACAAAGTGCTAAACAGAA
1 GCACACAAAGTGCTAAACAGAA
* *
19937 GCACACACAA-TGCTGAATAGAA
1 GCACACA-AAGTGCTAAACAGAA
* *
19959 GCACACATAGTGCTGAACA-AA
1 GCACACAAAGTGCTAAACAGAA
**
19980 GGGCACGAAACGTGCTAAACAG
1 GCACAC-AAA-GTGCTAAACAG
20002 TAGGCGCGCA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
21 7 0.13
22 34 0.65
23 11 0.21
ACGTcount: A:0.44, C:0.23, G:0.22, T:0.11
Consensus pattern (22 bp):
GCACACAAAGTGCTAAACAGAA
Found at i:51627 original size:111 final size:111
Alignment explanation
Indices: 51337--51798 Score: 611
Period size: 111 Copynumber: 4.1 Consensus size: 111
51327 GTGAGTGGGC
* *
51337 CTGCTGCTGCCGAACCAGCTGGCCATTCCAGGCAGGACCTGTGCCTTGAGCATTTGACTGCTCAT
1 CTGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTGCCTTGAGCATATGACTGCTCAT
** * *
51402 ATCGAGGCAAGCCCATGTTTGATACACTTCCATTTC-CATGAAAGTTATT
66 ATCGAGGTGATCCCATGTTTGATACAGTTCCA-TTCGCATGAAA---ATT
* * *
51451 CTGATGATGCTGCTGAACCAGCTGACCATTCCAGGCAGGACCTGTGCCTTGAGCATATGTCTGCT
1 C---TGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTGCCTTGAGCATATGACTGCT
* * *
51516 CATATCGAGGTGATCCCATGTTCGATACAGTTCCGTTCACATGAAAATT
63 CATATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
* * * * *
51565 CTGCTGCTGCTGAACCATCTGGCCATTCCAGGTAGGACCTGTCCCTTGAGCATACGAATGCTCAT
1 CTGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTGCCTTGAGCATATGACTGCTCAT
* *
51630 ATCGAGGTGATCCCATGTTTGGTATAGTTCCATTCGCATGAAAATT
66 ATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
* * * ** * *
51676 CTGCTGCTGCTGAACCATCTGGCCATTACAGGCATGACCCATACCTTGAACATATGACTGCTCAT
1 CTGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTGCCTTGAGCATATGACTGCTCAT
*
51741 ATCGAGGTGATCCCATGTTAGATACAGTTCCATTCGCATGAAAATT
66 ATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
51787 CTGCTGCTGCTG
1 CTGCTGCTGCTG
51799 CTGCTGAATT
Statistics
Matches: 308, Mismatches: 36, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
111 208 0.68
114 5 0.02
116 3 0.01
117 92 0.30
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (111 bp):
CTGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTGCCTTGAGCATATGACTGCTCAT
ATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
Found at i:58128 original size:6 final size:6
Alignment explanation
Indices: 58117--58143 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
58107 AGCACAGCCA
58117 CCCCCT CCCCCT CCCCCT CCCCCT CCC
1 CCCCCT CCCCCT CCCCCT CCCCCT CCC
58144 GAGCTCCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.85, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCCCT
Found at i:80979 original size:20 final size:19
Alignment explanation
Indices: 80936--80980 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
80926 ATTTAAAGAG
80936 GTATAAATCTTAAAATTAT
1 GTATAAATCTTAAAATTAT
* * *
80955 ATATAAATTTTTAAATTAAT
1 GTATAAATCTTAAAATT-AT
80975 GTATAA
1 GTATAA
80981 TTATGTTCGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (19 bp):
GTATAAATCTTAAAATTAT
Found at i:84028 original size:16 final size:16
Alignment explanation
Indices: 83992--84033 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
83982 CACCGCCTAA
*
83992 CCCTTTTCTTTTTCTTT
1 CCCTTTT-TTTTTCTTG
*
84009 CCCTTTTTTTTTGTTG
1 CCCTTTTTTTTTCTTG
84025 CCCTTTTTT
1 CCCTTTTTT
84034 GCGAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.00, C:0.26, G:0.05, T:0.69
Consensus pattern (16 bp):
CCCTTTTTTTTTCTTG
Found at i:86927 original size:25 final size:23
Alignment explanation
Indices: 86890--86990 Score: 98
Period size: 23 Copynumber: 4.3 Consensus size: 23
86880 ACACTAGCGC
86890 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTCT-GT
*
86913 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTCTGT
* * * *
86938 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
*
86961 ACTCTCTGTTTAGCACTG-CGTGT
1 GCTCTCTGTTTAGCACTGTC-TGT
86984 GCTCTCT
1 GCTCTCT
86991 ATTGCCCAGC
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
23 43 0.67
24 1 0.02
25 17 0.27
26 3 0.05
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTCTGT
Found at i:87014 original size:48 final size:46
Alignment explanation
Indices: 86911--87018 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 46
86901 AGCACGTCTC
* * *
86911 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTG-T-TTAGCACTGCGTGTGCTCTCTGATTAGCACTTTAT
*
86959 GTACTCTCTGTTTAGCACTGCGTGTGCTCTCT-ATT-GCCCAGCATTTAT
1 GTGCTCTCTGTTTAGCACTGCGTGTGCTCTCTGATTAG--CA-C-TTTAT
87007 GTGCTCTCTGTT
1 GTGCTCTCTGTT
87019 AGTACTTTGG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
44 1 0.02
45 3 0.06
46 21 0.41
47 2 0.04
48 24 0.47
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (46 bp):
GTGCTCTCTGTTTAGCACTGCGTGTGCTCTCTGATTAGCACTTTAT
Found at i:88291 original size:31 final size:31
Alignment explanation
Indices: 88224--88292 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
88214 AAGATTTTTT
*
88224 ATTTATTTAATATTAATATTAATATAATTAT
1 ATTTATTTAATATTAATATTAATATAATTAA
* * * *
88255 TTTTATTTAGTATTTATA-TAATATATTTTAA
1 ATTTATTTAATATTAATATTAATATA-ATTAA
88286 ATTTATT
1 ATTTATT
88293 ATTTTATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (31 bp):
ATTTATTTAATATTAATATTAATATAATTAA
Found at i:92465 original size:2 final size:2
Alignment explanation
Indices: 92460--92493 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
92450 TATATACAGG
*
92460 GA GA GA GA GA GA GA GA GA CA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
92494 AGCGAGAGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:100911 original size:24 final size:24
Alignment explanation
Indices: 100883--100933 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
100873 AAAAATAATC
* *
100883 TTTCAGTTAAATTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
* *
100907 TTTCAATTAAACTGTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
100931 TTT
1 TTT
100934 GAGTCAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:100942 original size:24 final size:24
Alignment explanation
Indices: 100897--100943 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
100887 AGTTAAATTC
*
100897 TGTTTAATTGTTTCAATTAAACTG
1 TGTTTAATTGTTTCAATCAAACTG
* * *
100921 TGTTTATTTGTTTGAGTCAAACT
1 TGTTTAATTGTTTCAATCAAACT
100944 CTTATTAGTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.51
Consensus pattern (24 bp):
TGTTTAATTGTTTCAATCAAACTG
Found at i:102896 original size:24 final size:24
Alignment explanation
Indices: 102869--102915 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
102859 ATAATATGTA
102869 AATTAAACTCTGTTTAATTGTTTC
1 AATTAAACTCTGTTTAATTGTTTC
* *
102893 AATTAAACTTTGTTTATTTGTTT
1 AATTAAACTCTGTTTAATTGTTT
102916 TAGTCAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.55
Consensus pattern (24 bp):
AATTAAACTCTGTTTAATTGTTTC
Found at i:102924 original size:24 final size:24
Alignment explanation
Indices: 102873--102927 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
102863 TATGTAAATT
*
102873 AAACTCTGTTTAATTGTTTCAATT
1 AAACTCTGTTTAATTGTTTCAATC
* * * *
102897 AAACTTTGTTTATTTGTTTTAGTC
1 AAACTCTGTTTAATTGTTTCAATC
102921 AAACTCT
1 AAACTCT
102928 TATTAGTCTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (24 bp):
AAACTCTGTTTAATTGTTTCAATC
Found at i:121173 original size:13 final size:13
Alignment explanation
Indices: 121151--121182 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
121141 AATTAATAAT
*
121151 ATTAACTATTTGG
1 ATTAAATATTTGG
121164 ATTAAATATTTGG
1 ATTAAATATTTGG
121177 ATTAAA
1 ATTAAA
121183 CATTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (13 bp):
ATTAAATATTTGG
Found at i:125041 original size:2 final size:2
Alignment explanation
Indices: 125034--125062 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
125024 GTCATGTCTT
125034 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
125063 GTATGTCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:129610 original size:46 final size:47
Alignment explanation
Indices: 129543--129636 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
129533 TCCATGCAAC
129543 ACTAACTTTTAGATTCCCTTT-CCATTGTATTGTTCTTTCTTTCTAT
1 ACTAACTTTTAGATTCCCTTTCCCATTGTATTGTTCTTTCTTTCTAT
129589 ACTAACTTTTAGATTCCCTTTCCCATTGTATTGTTCTTTCTTTCTAT
1 ACTAACTTTTAGATTCCCTTTCCCATTGTATTGTTCTTTCTTTCTAT
129636 A
1 A
129637 GAATTAGTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 21 0.45
47 26 0.55
ACGTcount: A:0.18, C:0.22, G:0.06, T:0.53
Consensus pattern (47 bp):
ACTAACTTTTAGATTCCCTTTCCCATTGTATTGTTCTTTCTTTCTAT
Found at i:130447 original size:60 final size:60
Alignment explanation
Indices: 130377--130597 Score: 354
Period size: 60 Copynumber: 3.7 Consensus size: 60
130367 AGGAAAAGGG
* *
130377 AAGCCTGGGGGTGGCACCCATGTGAACGTTGGAGGCAAACGAGTTGGAGTGAACACGGGA
1 AAGCCAGGGGGTGGCACCCATGTGAACGTTGGAGGCAAAGGAGTTGGAGTGAACACGGGA
*
130437 AAGCCAGGGGGTGGCACTCATGTGAACGTTGG-GCGCAAAGGAGTTGGAGTGAACACGGGA
1 AAGCCAGGGGGTGGCACCCATGTGAACGTTGGAG-GCAAAGGAGTTGGAGTGAACACGGGA
* * * *
130497 AAGCCAGGGGGTGGCACTCATGTGAATGTTGGAGGCAAAGGAGTTGGGGTGAACACTGGA
1 AAGCCAGGGGGTGGCACCCATGTGAACGTTGGAGGCAAAGGAGTTGGAGTGAACACGGGA
*
130557 AAGCCAGGAGGTGGCACCCATGTGAACGTTGGAGGCAAAGG
1 AAGCCAGGGGGTGGCACCCATGTGAACGTTGGAGGCAAAGG
130598 TGGAGGAGTA
Statistics
Matches: 150, Mismatches: 9, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
59 1 0.01
60 148 0.99
61 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.41, T:0.15
Consensus pattern (60 bp):
AAGCCAGGGGGTGGCACCCATGTGAACGTTGGAGGCAAAGGAGTTGGAGTGAACACGGGA
Found at i:134002 original size:15 final size:18
Alignment explanation
Indices: 133984--134033 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
133974 AATTTTACCA
133984 TTTATAATT-T-AA-AAT
1 TTTATAATTATAAAGAAT
133999 TTTATAAATTATAAAGAAT
1 TTTAT-AATTATAAAGAAT
134018 TTTATAAATTATAAAG
1 TTTAT-AATTATAAAG
134034 GACATAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.16
16 4 0.13
17 1 0.03
18 2 0.06
19 19 0.61
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (18 bp):
TTTATAATTATAAAGAAT
Found at i:134020 original size:19 final size:19
Alignment explanation
Indices: 133996--134033 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
133986 TATAATTTAA
133996 AATTTTATAAATTATAAAG
1 AATTTTATAAATTATAAAG
134015 AATTTTATAAATTATAAAG
1 AATTTTATAAATTATAAAG
134034 GACATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
AATTTTATAAATTATAAAG
Found at i:135105 original size:18 final size:18
Alignment explanation
Indices: 135071--135106 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 18
135061 ATACAAGTCA
135071 ATACATATATATATTATT
1 ATACATATATATATTATT
135089 ATACA-ATAT-TATT-TT
1 ATACATATATATATTATT
135104 ATA
1 ATA
135107 ATGTACATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.28
16 4 0.22
17 4 0.22
18 5 0.28
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
ATACATATATATATTATT
Found at i:151363 original size:5 final size:5
Alignment explanation
Indices: 151353--151379 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
151343 TCGAGGCCTG
151353 TCCCA TCCCA TCCCA TCCCA TCCCA TC
1 TCCCA TCCCA TCCCA TCCCA TCCCA TC
151380 AGATGTGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.59, G:0.00, T:0.22
Consensus pattern (5 bp):
TCCCA
Found at i:159244 original size:122 final size:122
Alignment explanation
Indices: 159013--159251 Score: 383
Period size: 122 Copynumber: 2.0 Consensus size: 122
159003 TCAATAGCAC
159013 GATCATATTCATCTGCATGATTATAAACCCATCATAAGTCAATCAATGTGCATTTACTAAAAAAC
1 GATCATATTCATCTGCATGATTATAAACCCATCATAAGTCAATCAATGTGCATTTACTAAAAAAC
* * *
159078 AAATGCTAAAGTTTAACTAGACTAAGAGCATAAGCTGAGTAGATCAATACTATTGAT
66 AAATGCTAAAGTTTAACTAGACTAAGAGCAAAAGCCGAGCAGATCAATACTATTGAT
** *
159135 GATCATATTCATCTGCATGATTATAAACCCATCATAAGTTGATCAATGTGCATTTAATTAAAAAA
1 GATCATATTCATCTGCATGATTATAAACCCATCATAAGTCAATCAATGTGCATTT-ACTAAAAAA
*
159200 -AAATGCTACAGTTTAACTAGACTACA-AGCAAAAGCCGAGCAGATCAATACTA
65 CAAATGCTAAAGTTTAACTAGACTA-AGAGCAAAAGCCGAGCAGATCAATACTA
159252 AGATTCAACT
Statistics
Matches: 108, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
122 99 0.92
123 9 0.08
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (122 bp):
GATCATATTCATCTGCATGATTATAAACCCATCATAAGTCAATCAATGTGCATTTACTAAAAAAC
AAATGCTAAAGTTTAACTAGACTAAGAGCAAAAGCCGAGCAGATCAATACTATTGAT
Found at i:159404 original size:32 final size:32
Alignment explanation
Indices: 159363--159425 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
159353 AAGAGACATT
159363 TCCTTCATCCTGTTAGACATGTATGACAGGAC
1 TCCTTCATCCTGTTAGACATGTATGACAGGAC
159395 TCCTTCATCCTGTTAGACATGTATGACAGGA
1 TCCTTCATCCTGTTAGACATGTATGACAGGA
159426 AATAAAGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (32 bp):
TCCTTCATCCTGTTAGACATGTATGACAGGAC
Found at i:186437 original size:31 final size:30
Alignment explanation
Indices: 186382--186451 Score: 106
Period size: 32 Copynumber: 2.3 Consensus size: 30
186372 ATGAATTTTG
*
186382 TATTCTAATTGTGATTCATTATATGGATTTT
1 TATTATAATTGTGATTCATTATATGGA-TTT
186413 TAATTATAATTGTGATT-ATTATATGGATTT
1 T-ATTATAATTGTGATTCATTATATGGATTT
186443 TATTATAAT
1 TATTATAAT
186452 AAATTTCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 8 0.22
30 4 0.11
31 11 0.30
32 14 0.38
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.54
Consensus pattern (30 bp):
TATTATAATTGTGATTCATTATATGGATTT
Found at i:186462 original size:29 final size:29
Alignment explanation
Indices: 186396--186485 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
186386 CTAATTGTGA
*
186396 TTCATTATATGGATTTTTAATTATAAT-TGT
1 TTCATTATATGGA-TTTT-ATTATAATATAT
*
186426 GATT-ATTATATGGATTTTATTATAATAAAT
1 --TTCATTATATGGATTTTATTATAATATAT
*
186456 TTCATTATAGGGATTTTA-TATAATATAT
1 TTCATTATATGGATTTTATTATAATATAT
186484 TT
1 TT
186486 AGAATATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
28 13 0.25
29 22 0.42
30 5 0.10
31 10 0.19
32 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.53
Consensus pattern (29 bp):
TTCATTATATGGATTTTATTATAATATAT
Found at i:187475 original size:25 final size:28
Alignment explanation
Indices: 187447--187505 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 28
187437 AAAAGGGATA
187447 AATTT-TAAAATTATATA-T-AAACTTT
1 AATTTATAAAATTATATACTGAAACTTT
*
187472 AATTTGATATAATTATATACGTGAAACTTT
1 AATTT-ATAAAATTATATAC-TGAAACTTT
187502 AATT
1 AATT
187506 GTACTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 5 0.18
27 11 0.39
29 1 0.04
30 11 0.39
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (28 bp):
AATTTATAAAATTATATACTGAAACTTT
Found at i:189239 original size:19 final size:20
Alignment explanation
Indices: 189202--189239 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
189192 CATTGTGCTC
*
189202 TTTTTATTTTCCAGTTTTCT
1 TTTTTATTTTCCAGCTTTCT
*
189222 TTTTTTTTTTCCA-CTTTC
1 TTTTTATTTTCCAGCTTTC
189240 ACTTTCTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTTTATTTTCCAGCTTTCT
Found at i:200761 original size:18 final size:16
Alignment explanation
Indices: 200729--200764 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
200719 ATGAGATGAG
200729 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
200745 AATAAATTTAATTAATTA
1 AATAAATTT--TTAATTA
200763 AA
1 AA
200765 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:201056 original size:292 final size:291
Alignment explanation
Indices: 200499--201073 Score: 925
Period size: 292 Copynumber: 2.0 Consensus size: 291
200489 GGAAGATGGG
* ** * * * *
200499 AAATGTTACTACTAATTAAAGAAGGGTAAATTTAAAAATAGTCACTTTAGTTTGCCTCAAGTTAT
1 AAATGTTACTACTAATTAAAAAAGGGTAAATGCAAAAATAATCACTTTAATTTACCTCAAGTTAC
* *
200564 ATTTTAATCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGTTATTATTTTGTTACGAAGT
66 ATTTTAATCACTTATGTTTGAAACGTTACATTTTAGTCACTTATGTTATTATTTTGTTACGAAGT
* *
200629 GATCACTCTACCGTTAAGTTCCATTATCTCCCTAACGGTAATCCTACGTGGCAGTTCAATTAGAT
131 GATCACTCTACCGTTAAGTTCCATTATCTCCCTAACGGTAATCCTACGTGGCAGTCCAATTAGAA
*
200694 TTTAAGTGCCAACTTGAATTTCCAGATGAGATGAGAATAAATTTTTAATTAAATAAATTTAATTA
196 TTTAAGTGCCAACTTGAATTTCCAAATGAGATGAGAATAAATTTTTAATTAAATAAATTTAATTA
200759 ATTAAAAATTTTAAACCTAAACCTTAGCTTA
261 ATTAAAAATTTTAAACCTAAACCTTAGCTTA
* *
200790 AAATGTTACTACTAATTAAAAAAGGGTTAACTGCAAAAATAATCACTTTAATTTATCTCAAGTTA
1 AAATGTTACTACTAATTAAAAAAGGG-TAAATGCAAAAATAATCACTTTAATTTACCTCAAGTTA
* *
200855 CATTTTAGTCACTTATGTTTGAAACGTTACATTTTAGTGACTTATGTTATTATTTTGTTACGAAG
65 CATTTTAATCACTTATGTTTGAAACGTTACATTTTAGTCACTTATGTTATTATTTTGTTACGAAG
* * * * * *
200920 TGATCATTCTACCTTTAAGTTCCGTTGTCTCCCTAACGGTAATCTTACGTGGTAGTCCAATTAGA
130 TGATCACTCTACCGTTAAGTTCCATTATCTCCCTAACGGTAATCCTACGTGGCAGTCCAATTAGA
* *
200985 ATTTAAGTGCCAACTTGAATTTCCAAATGGGATGAGAATAGATTTTTAATTAAATAAATTTAATT
195 ATTTAAGTGCCAACTTGAATTTCCAAATGAGATGAGAATAAATTTTTAATTAAATAAATTTAATT
201050 AATTAAAAATTTTAAACCTAAACC
260 AATTAAAAATTTTAAACCTAAACC
201074 AAAGTGATTA
Statistics
Matches: 259, Mismatches: 24, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
291 25 0.10
292 234 0.90
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39
Consensus pattern (291 bp):
AAATGTTACTACTAATTAAAAAAGGGTAAATGCAAAAATAATCACTTTAATTTACCTCAAGTTAC
ATTTTAATCACTTATGTTTGAAACGTTACATTTTAGTCACTTATGTTATTATTTTGTTACGAAGT
GATCACTCTACCGTTAAGTTCCATTATCTCCCTAACGGTAATCCTACGTGGCAGTCCAATTAGAA
TTTAAGTGCCAACTTGAATTTCCAAATGAGATGAGAATAAATTTTTAATTAAATAAATTTAATTA
ATTAAAAATTTTAAACCTAAACCTTAGCTTA
Found at i:202055 original size:2 final size:2
Alignment explanation
Indices: 202048--202077 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
202038 AAGAAATTCC
202048 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
202078 TTGAGATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:212201 original size:28 final size:28
Alignment explanation
Indices: 212161--212219 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
212151 AGTTTAAAAC
* *
212161 TTGTCCACATGTCGTTCGACATCCTATG
1 TTGTCCACATGTCATTCGACACCCTATG
**
212189 TTGTCCATGTGTCATTCGACACCCTATG
1 TTGTCCACATGTCATTCGACACCCTATG
212217 TTG
1 TTG
212220 AAAGCTTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (28 bp):
TTGTCCACATGTCATTCGACACCCTATG
Found at i:214268 original size:46 final size:46
Alignment explanation
Indices: 214210--214297 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 46
214200 AAGCGAATTG
* ** * * *
214210 ATGATAACTACAATATTTTTCAAGTGTATAACTAGTATTACACCAC
1 ATGATAACTACAACATCGTCCAAGTGCATAACTAATATTACACCAC
*
214256 ATGATAATTACAACATCGTCCAAGTGCATAACTAATATTACA
1 ATGATAACTACAACATCGTCCAAGTGCATAACTAATATTACA
214298 AATTAGTAGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 35 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (46 bp):
ATGATAACTACAACATCGTCCAAGTGCATAACTAATATTACACCAC
Found at i:226293 original size:29 final size:31
Alignment explanation
Indices: 226251--226323 Score: 114
Period size: 29 Copynumber: 2.4 Consensus size: 31
226241 CAAATGATTT
226251 TAAAATTATTAAAACTA-TTTTTTAAAAT-A
1 TAAAATTATTAAAACTATTTTTTTAAAATAA
* *
226280 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAACTATTTTTTTAAAATAA
226311 TAAAATTATTAAA
1 TAAAATTATTAAA
226324 TAATTTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 16 0.40
30 10 0.25
31 14 0.35
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (31 bp):
TAAAATTATTAAAACTATTTTTTTAAAATAA
Found at i:226330 original size:30 final size:29
Alignment explanation
Indices: 226251--226330 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
226241 CAAATGATTT
*
226251 TAAAATTATTAAA-ACTATTTTTTAAAATA
1 TAAAATTATTAAATAAT-TTTTTTAAAATA
* *
226280 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATT-AAATAATTTTTTTAAAAT-A
226311 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATAATTTT
226331 AATTTTCAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 10 0.23
30 22 0.50
31 12 0.27
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (29 bp):
TAAAATTATTAAATAATTTTTTTAAAATA
Found at i:228018 original size:67 final size:67
Alignment explanation
Indices: 227910--228055 Score: 274
Period size: 67 Copynumber: 2.2 Consensus size: 67
227900 TCATTATGCC
* *
227910 TATTTAGATTTTAGCCATCTTTTTATAGTGCAAGTTACAAATGCAAAGCTTTATTCCTAACCTAT
1 TATTTGGATTTTAGCCATCTTTATATAGTGCAAGTTACAAATGCAAAGCTTTATTCCTAACCTAT
227975 GA
66 GA
227977 TATTTGGATTTTAGCCATCTTTATATAGTGCAAGTTACAAATGCAAAGCTTTATTCCTAACCTAT
1 TATTTGGATTTTAGCCATCTTTATATAGTGCAAGTTACAAATGCAAAGCTTTATTCCTAACCTAT
228042 GA
66 GA
228044 TATTTGGATTTT
1 TATTTGGATTTT
228056 TTTCTTTTAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 77 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (67 bp):
TATTTGGATTTTAGCCATCTTTATATAGTGCAAGTTACAAATGCAAAGCTTTATTCCTAACCTAT
GA
Found at i:240656 original size:21 final size:22
Alignment explanation
Indices: 240616--240670 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
240606 ATCTAAAAAT
*
240616 AATATAAAATA-TATATTTAAA
1 AATATTAAATATTATATTTAAA
*
240637 AATATTAAATATTATA-TTAAT
1 AATATTAAATATTATATTTAAA
*
240658 AAGATTAAA-ATTA
1 AATATTAAATATTA
240671 AAAAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.13
21 22 0.73
22 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AATATTAAATATTATATTTAAA
Found at i:247569 original size:23 final size:22
Alignment explanation
Indices: 247537--247580 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
247527 TTTTTAATCT
*
247537 ATTAAAAATGATGAAATTATAA
1 ATTAAAAATGATAAAATTATAA
247559 ATTAATAAATGATAAAATTATA
1 ATTAA-AAATGATAAAATTATA
247581 TTTTTAACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (22 bp):
ATTAAAAATGATAAAATTATAA
Found at i:261895 original size:27 final size:27
Alignment explanation
Indices: 261865--261923 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
261855 ATCAATTTAA
261865 ATGTTTAAAAAGATACATGGAATTCAT
1 ATGTTTAAAAAGATACATGGAATTCAT
* * * *
261892 ATGTTTAAAATGTTAGATGGCATTCAT
1 ATGTTTAAAAAGATACATGGAATTCAT
261919 ATGTT
1 ATGTT
261924 ATATCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (27 bp):
ATGTTTAAAAAGATACATGGAATTCAT
Found at i:262314 original size:19 final size:19
Alignment explanation
Indices: 262269--262315 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
262259 AAATTGACTG
262269 AAATAATTAAAAATAAATTT
1 AAATAA-TAAAAATAAATTT
*
262289 TAA-AATAAAAATCAAA-TT
1 AAATAATAAAAAT-AAATTT
262307 AAATAATAA
1 AAATAATAA
262316 TAATGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 11 0.48
19 10 0.43
20 2 0.09
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATAATAAAAATAAATTT
Found at i:262350 original size:22 final size:21
Alignment explanation
Indices: 262325--262392 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 21
262315 ATAATGATTT
262325 TTTAAAATGTAATTATAATAAA
1 TTTAAAAT-TAATTATAATAAA
* *
262347 TTTAAATATTAAGGTA-AATAATTT
1 TTTAAA-ATTAA-TTATAATAA--A
262371 TTTAAAATTAATTATAATAAA
1 TTTAAAATTAATTATAATAAA
262392 T
1 T
262393 AATATTTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
21 1 0.03
22 16 0.43
23 14 0.38
24 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
TTTAAAATTAATTATAATAAA
Found at i:262737 original size:10 final size:10
Alignment explanation
Indices: 262712--262741 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
262702 TCTTAGCATA
262712 AAATTTATAT
1 AAATTTATAT
262722 -AATTTATAT
1 AAATTTATAT
262731 AAATTTATAT
1 AAATTTATAT
262741 A
1 A
262742 GTTTTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AAATTTATAT
Found at i:263476 original size:9 final size:9
Alignment explanation
Indices: 263462--263521 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
263452 GCAAATGATT
263462 TTAAAATTA
1 TTAAAATTA
263471 TTAAAATTA
1 TTAAAATTA
263480 TT----TT-
1 TTAAAATTA
*
263484 TTAAAAATA
1 TTAAAATTA
263493 -TAAAATTA
1 TTAAAATTA
263501 TTAAAATTA
1 TTAAAATTA
263510 TTTTAAAATTA
1 --TTAAAATTA
263521 T
1 T
263522 AATCATTGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 16
0.69 0.03 0.27
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
8 8 0.20
9 20 0.49
11 9 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAAAATTA
Found at i:263496 original size:21 final size:22
Alignment explanation
Indices: 263460--263502 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
263450 CAGCAAATGA
*
263460 TTTTAAAATTATTAAAATTATT
1 TTTTAAAAATATTAAAATTATT
263482 TTTTAAAAATA-TAAAATTATT
1 TTTTAAAAATATTAAAATTATT
263503 AAAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAAATATTAAAATTATT
Found at i:263522 original size:28 final size:29
Alignment explanation
Indices: 263463--263523 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
263453 CAAATGATTT
263463 TAAAATTATTAAAATTATTTTTTAAAAATA
1 TAAAATTATTAAAATTA-TTTTTAAAAATA
*
263493 TAAAATTATTAAAATTA-TTTTAAAATTA
1 TAAAATTATTAAAATTATTTTTAAAAATA
263521 TAA
1 TAA
263524 TCATTGTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 13 0.43
30 17 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTAAAAATA
Found at i:271404 original size:36 final size:36
Alignment explanation
Indices: 271357--271430 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
271347 AGGTCAGAGC
271357 GGAGAGGTGGTTGTTGGGGTTTTGTTAGATAATGAA
1 GGAGAGGTGGTTGTTGGGGTTTTGTTAGATAATGAA
271393 GGAGAGGTGGTTGTTGGGGTTTTGTTAGATAATGAA
1 GGAGAGGTGGTTGTTGGGGTTTTGTTAGATAATGAA
271429 GG
1 GG
271431 TAGTGGAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.22, C:0.00, G:0.43, T:0.35
Consensus pattern (36 bp):
GGAGAGGTGGTTGTTGGGGTTTTGTTAGATAATGAA
Found at i:273532 original size:31 final size:31
Alignment explanation
Indices: 273494--273558 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
273484 TTTTAAGAAT
273494 GCTTTGCAAGATTGTCAATTAATGGACTTAG
1 GCTTTGCAAGATTGTCAATTAATGGACTTAG
273525 GCTTTGCAAGATTGTCAATTAATGGACTTAG
1 GCTTTGCAAGATTGTCAATTAATGGACTTAG
273556 GCT
1 GCT
273559 ATTCTGGTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (31 bp):
GCTTTGCAAGATTGTCAATTAATGGACTTAG
Found at i:275663 original size:38 final size:38
Alignment explanation
Indices: 275620--275697 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
275610 TATTGCATAG
275620 TTAGCTAAACAAGGTTGGCGTTTATTTACTTATCCGAA
1 TTAGCTAAACAAGGTTGGCGTTTATTTACTTATCCGAA
275658 TTAGCTAAACAAGGTTGGCGTTTATTTACTTATCCGAA
1 TTAGCTAAACAAGGTTGGCGTTTATTTACTTATCCGAA
275696 TT
1 TT
275698 CATTATTAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (38 bp):
TTAGCTAAACAAGGTTGGCGTTTATTTACTTATCCGAA
Found at i:276849 original size:23 final size:23
Alignment explanation
Indices: 276776--276928 Score: 123
Period size: 23 Copynumber: 6.6 Consensus size: 23
276766 TATACGGAAC
* *
276776 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
276798 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
** *
276819 AGGCAACAGAGAGCACACTCAGTGTT
1 A---AACAGAGAGCACACAAAGTGCT
* *
276845 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
276868 AATCAGAGAGCACGCAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
276891 AATCAAAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
276914 AATAACAGAGAGCAC
1 -A-AACAGAGAGCAC
276929 GAGACGTGCT
Statistics
Matches: 104, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
21 17 0.16
23 56 0.54
24 1 0.01
25 23 0.22
26 7 0.07
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:276901 original size:69 final size:68
Alignment explanation
Indices: 276776--276925 Score: 180
Period size: 69 Copynumber: 2.1 Consensus size: 68
276766 TATACGGAAC
* *
276776 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTAGGCAACAGAGAGCACACTCAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTA-G-AACAAAGAGCACACACAG
*
276841 TG-TT
64 TGCTA
*
276845 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACGCA-AAGTGCTA-ATCAAAGAGCACACAC
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCA--CATAAGTGCTAGAACAAAGAGCACACAC
276908 AGTGCTA
62 AGTGCTA
276915 ATAACAGAGAG
1 A-AACAGAGAG
276926 CACGAGACGT
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
69 30 0.42
70 13 0.18
71 18 0.25
72 8 0.11
73 2 0.03
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (68 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTAGAACAAAGAGCACACACAGTG
CTA
Found at i:276937 original size:25 final size:22
Alignment explanation
Indices: 276866--276949 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 22
276856 ACACAAAGTA
*
276866 CTAATCAGAGAGCACGCAAAGTG
1 CTAATCAGAGAGCACG-AACGTG
*
276889 CTAATCAAAGAGCAC-ACACAGTG
1 CTAATCAGAGAGCACGA-AC-GTG
276912 CTAATAACAGAGAGCACGAGACGTG
1 CTAAT--CAGAGAGCACGA-ACGTG
* *
276937 CTAAACTGAGAGC
1 CTAATCAGAGAGC
276950 GAGCTAGTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
21 1 0.02
22 1 0.02
23 29 0.58
25 16 0.32
26 3 0.06
ACGTcount: A:0.40, C:0.23, G:0.24, T:0.13
Consensus pattern (22 bp):
CTAATCAGAGAGCACGAACGTG
Found at i:276949 original size:48 final size:46
Alignment explanation
Indices: 276825--276949 Score: 117
Period size: 46 Copynumber: 2.7 Consensus size: 46
276815 TGCTAGGCAA
* ** * *
276825 CAGAGAGCACACTCAGTGTTAAACAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACGCAAAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* * * *
276871 CAGAGAGCACGCAAAGTGCTAATCAAAGAGCACACACAGTGCTAAT
1 CAGAGAGCACGCAAAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* *
276917 AACAGAGAGCACG-AGACGTGCTAAACTGAGAGC
1 --CAGAGAGCACGCA-AAGTGCTAAACAGAGAGC
276950 GAGCTAGTGT
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
46 37 0.59
47 1 0.02
48 25 0.40
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.14
Consensus pattern (46 bp):
CAGAGAGCACGCAAAGTGCTAAACAGAGAGCACACAAAGTACTAAT
Found at i:279482 original size:267 final size:267
Alignment explanation
Indices: 279000--279533 Score: 865
Period size: 267 Copynumber: 2.0 Consensus size: 267
278990 TTCGTCTACC
*
279000 CAGATCTGGTCTCCCCCACCGTGCTTGGTCACAAAAAAAATTTTTGATACCGCATATTGTCAAAA
1 CAGATCTCGTCTCCCCCACCGTGCTTGGTCACAAAAAAAATTTTTGATACCGCATATTGTCAAAA
* *
279065 GGAAGCAAAATCGGGCTTTGGAGTGGTCGATCGGAATCATCAAGGAGAGATACTGGCATATGGAC
66 GGAAGCAAAATCGAGCTCTGGAGTGGTCGATCGGAATCATCAAGGAGAGATACTGGCATATGGAC
*
279130 AATATTTGCACTTAAATGTTGACTCACCATTTGCTGCAAAAGGGGTTGCGTGTCTTCGTGCAATC
131 AATATTTGCACTTAAATGTTGACTCACCATTCGCTGCAAAAGGGGTTGCGTGTCTTCGTGCAATC
*
279195 CAGATGGGTGCACAACTTGGTCTCTACTCCGTCATCATTGAAGGCGACGCAAAGACCATAATAAA
196 CAGATGGGTGCACAACTTGGTCTCTACTCCGTCATCATTGAAGGCGACACAAAGACCATAATAAA
279260 AAAATGT
261 AAAATGT
* * * *
279267 CAGATCTCGTCTCCCCCGCCGTGCTTGGTCACGAAAATAAA-TTTTGATGCCGCATATTGTTAAA
1 CAGATCTCGTCTCCCCCACCGTGCTTGGTCAC-AAAAAAAATTTTTGATACCGCATATTGTCAAA
* **
279331 AGGAAGCAAAATCGAGCTCTGGAGTGGTCGCTCGGAATCATTGAGGAGAGATACTGGCATATGGA
65 AGGAAGCAAAATCGAGCTCTGGAGTGGTCGATCGGAATCATCAAGGAGAGATACTGGCATATGGA
* * *
279396 CAATATTTGCACTTAAATGTTGACTCACCATTCGCTGCAGAAGGGTTTGCGTGTC-TCTGTGCGA
130 CAATATTTGCACTTAAATGTTGACTCACCATTCGCTGCAAAAGGGGTTGCGTGTCTTC-GTGCAA
** * *
279460 TCCAGATGGGTGCATGACTTGGTCTCTAGTCCGTCATCATTGAAGGCGACATAAAGACCATAATA
194 TCCAGATGGGTGCACAACTTGGTCTCTACTCCGTCATCATTGAAGGCGACACAAAGACCATAATA
279525 AAAAAATGT
259 AAAAAATGT
279534 TAGTCTAGCG
Statistics
Matches: 246, Mismatches: 19, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
266 2 0.01
267 237 0.96
268 7 0.03
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (267 bp):
CAGATCTCGTCTCCCCCACCGTGCTTGGTCACAAAAAAAATTTTTGATACCGCATATTGTCAAAA
GGAAGCAAAATCGAGCTCTGGAGTGGTCGATCGGAATCATCAAGGAGAGATACTGGCATATGGAC
AATATTTGCACTTAAATGTTGACTCACCATTCGCTGCAAAAGGGGTTGCGTGTCTTCGTGCAATC
CAGATGGGTGCACAACTTGGTCTCTACTCCGTCATCATTGAAGGCGACACAAAGACCATAATAAA
AAAATGT
Found at i:281739 original size:15 final size:15
Alignment explanation
Indices: 281719--281769 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
281709 AAAATAATAC
281719 AAAATACAAAAATTT
1 AAAATACAAAAATTT
* * **
281734 AAAATATAATAATAG
1 AAAATACAAAAATTT
*
281749 AAAATACAAAATTTT
1 AAAATACAAAAATTT
281764 AAAATA
1 AAAATA
281770 TAATATACAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (15 bp):
AAAATACAAAAATTT
Found at i:281759 original size:22 final size:21
Alignment explanation
Indices: 281734--281782 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
281724 ACAAAAATTT
281734 AAAATATAATAATAGAAAATAC
1 AAAATATAA-AATAGAAAATAC
* * *
281756 AAAATTTTAAAATATAATATAC
1 AAAA-TATAAAATAGAAAATAC
281778 AAAAT
1 AAAAT
281783 TTTAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.78
23 4 0.17
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATATAAAATAGAAAATAC
Found at i:281791 original size:30 final size:30
Alignment explanation
Indices: 281711--281782 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
281701 CATCATTCAA
*
281711 AATAATACAAAATACAAAAATTTAAAATAT
1 AATAATACAAAATACAAAATTTTAAAATAT
*
281741 AATAATAGAAAATACAAAATTTTAAAATAT
1 AATAATACAAAATACAAAATTTTAAAATAT
281771 AAT-ATACAAAAT
1 AATAATACAAAAT
281783 TTTAAAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 8 0.21
30 31 0.79
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.28
Consensus pattern (30 bp):
AATAATACAAAATACAAAATTTTAAAATAT
Found at i:286578 original size:29 final size:30
Alignment explanation
Indices: 286525--286597 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
286515 TCTTCAAAGA
286525 TTTA-AAATTTAGTCATTATA-CTTTTATT
1 TTTATAAATTTAGTCATTATATCTTTTATT
* * *
286553 TTTATAAATTTAGTCTTTCTATTTTTTATT
1 TTTATAAATTTAGTCATTATATCTTTTATT
*
286583 TATATCAAAATTTAG
1 TTTAT--AAATTTAG
286598 GTACAATGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.11
29 14 0.38
30 11 0.30
32 8 0.22
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.58
Consensus pattern (30 bp):
TTTATAAATTTAGTCATTATATCTTTTATT
Found at i:286586 original size:28 final size:30
Alignment explanation
Indices: 286524--286586 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
286514 CTCTTCAAAG
286524 ATTTA-AAATTTAGTCATTATACTTTTATT
1 ATTTATAAATTTAGTCATTATACTTTTATT
* *
286553 -TTTATAAATTTAGTCTTTCTA-TTTT-TT
1 ATTTATAAATTTAGTCATTATACTTTTATT
286580 ATTTATA
1 ATTTATA
286587 TCAAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 2 0.07
28 14 0.47
29 14 0.47
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.60
Consensus pattern (30 bp):
ATTTATAAATTTAGTCATTATACTTTTATT
Found at i:286926 original size:4 final size:4
Alignment explanation
Indices: 286917--286947 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
286907 TTTATATTTA
286917 TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TAT
286948 ATATAGATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:307725 original size:21 final size:22
Alignment explanation
Indices: 307699--307748 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
307689 GTACATTCTA
*
307699 ATATATATTA-ATTTAATTTAT
1 ATATATATTACATCTAATTTAT
*
307720 ATATAT-TTACATCTAGTTTAT
1 ATATATATTACATCTAATTTAT
*
307741 ACATATAT
1 ATATATAT
307749 ATATATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 20 0.83
22 1 0.04
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATATATTACATCTAATTTAT
Found at i:315065 original size:25 final size:23
Alignment explanation
Indices: 315037--315098 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 23
315027 TTTTTAATTG
315037 AATTATAAATTAATTAAATATTCCA
1 AATTATAAATTAATTAAA-A-TCCA
*
315062 AATT-TCAAATTTAATTTAAATCCA
1 AATTAT-AAA-TTAATTAAAATCCA
315086 AATTCATAAATTA
1 AATT-ATAAATTA
315099 GTTGAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
24 12 0.38
25 11 0.34
26 9 0.28
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTATAAATTAATTAAAATCCA
Found at i:315665 original size:19 final size:20
Alignment explanation
Indices: 315643--315682 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
315633 AAATAATATT
* *
315643 AAAAAAA-CGAAACAATAAA
1 AAAAAAATCAAAACAACAAA
315662 AAAAAAATCAAAACAACAAA
1 AAAAAAATCAAAACAACAAA
315682 A
1 A
315683 GCATCACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.80, C:0.12, G:0.03, T:0.05
Consensus pattern (20 bp):
AAAAAAATCAAAACAACAAA
Found at i:315729 original size:33 final size:30
Alignment explanation
Indices: 315690--315757 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 30
315680 AAAGCATCAC
*
315690 CAAAACAATAA-AAAATAACACTAAAATAACAA
1 CAAAACAACAACAAAA-AACAC-AAAA-AACAA
315722 TCAAAACAACAACAAAAAACACAAAAAACAA
1 -CAAAACAACAACAAAAAACACAAAAAACAA
315753 CAAAA
1 CAAAA
315758 AGGATAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
30 5 0.15
31 5 0.15
32 4 0.12
33 15 0.45
34 4 0.12
ACGTcount: A:0.74, C:0.19, G:0.00, T:0.07
Consensus pattern (30 bp):
CAAAACAACAACAAAAAACACAAAAAACAA
Found at i:315748 original size:10 final size:10
Alignment explanation
Indices: 315712--315758 Score: 60
Period size: 10 Copynumber: 4.5 Consensus size: 10
315702 AAATAACACT
315712 AAAATAACAATC
1 AAAA-AACAA-C
315724 AAAACAACAAC
1 AAAA-AACAAC
315735 AAAAAAC-AC
1 AAAAAACAAC
315744 AAAAAACAAC
1 AAAAAACAAC
315754 AAAAA
1 AAAAA
315759 GGATAGAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
9 9 0.27
10 10 0.30
11 5 0.15
12 9 0.27
ACGTcount: A:0.77, C:0.19, G:0.00, T:0.04
Consensus pattern (10 bp):
AAAAAACAAC
Found at i:321741 original size:33 final size:33
Alignment explanation
Indices: 321680--321743 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
321670 CACAAGGGTT
* *
321680 AATAAAAAATTAGTCATGCTAGAACAAAAAATA
1 AATAAAAAACTAGTCATGCTAAAACAAAAAATA
* *
321713 AATAAATAACTAGTCATGC-AAAACCAAAAAT
1 AATAAAAAACTAGTCATGCTAAAACAAAAAAT
321744 CATATTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 10 0.37
33 17 0.63
ACGTcount: A:0.59, C:0.12, G:0.08, T:0.20
Consensus pattern (33 bp):
AATAAAAAACTAGTCATGCTAAAACAAAAAATA
Found at i:324246 original size:12 final size:12
Alignment explanation
Indices: 324231--324261 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
324221 AGAGAGGCTC
*
324231 AGACAGAGACAG
1 AGACAAAGACAG
324243 AGACAAAGACAG
1 AGACAAAGACAG
324255 AGACAAA
1 AGACAAA
324262 TAAAAGGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.16, G:0.26, T:0.00
Consensus pattern (12 bp):
AGACAAAGACAG
Found at i:324672 original size:18 final size:17
Alignment explanation
Indices: 324629--324673 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
324619 TTTGTTTAGT
324629 AATATTTTTATCTCAAA
1 AATATTTTTATCTCAAA
*
324646 AGTATTTTTTATCTCAAA
1 AATA-TTTTTATCTCAAA
*
324664 AATACTTTTA
1 AATATTTTTA
324674 AGAAGTAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (17 bp):
AATATTTTTATCTCAAA
Found at i:324772 original size:32 final size:35
Alignment explanation
Indices: 324736--324805 Score: 110
Period size: 32 Copynumber: 2.1 Consensus size: 35
324726 ACCCTTCAAT
*
324736 TTTATTTTATTTTTT-AT-TTTTTAAT-ATTTAAA
1 TTTATGTTATTTTTTAATGTTTTTAATAATTTAAA
324768 TTTATGTTATTTTTTAATGTTTTTAATAATTTAAA
1 TTTATGTTATTTTTTAATGTTTTTAATAATTTAAA
324803 TTT
1 TTT
324806 TTAATTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.41
33 2 0.06
34 8 0.24
35 10 0.29
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (35 bp):
TTTATGTTATTTTTTAATGTTTTTAATAATTTAAA
Found at i:340252 original size:5 final size:5
Alignment explanation
Indices: 340242--340269 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
340232 ACCAAATTAA
340242 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
340270 TTGAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:348578 original size:25 final size:24
Alignment explanation
Indices: 348532--348579 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
348522 GTTTCCACAC
*
348532 TTTATCTCTTAAATTTTTTTATTT
1 TTTATCTCTGAAATTTTTTTATTT
348556 TTTAT-TCTGAAATATTTTATTATT
1 TTTATCTCTGAAAT-TTTT-TTATT
348580 AATTCTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 9 0.43
25 5 0.24
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTATCTCTGAAATTTTTTTATTT
Found at i:354175 original size:18 final size:18
Alignment explanation
Indices: 354127--354179 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
354117 TTTCGGGTAA
*
354127 AATCGAATTAATTCAGTT
1 AATCGAATTAATTCGGTT
* *
354145 AACCG-ATCGAATTCGGTT
1 AATCGAAT-TAATTCGGTT
354163 AATCGAATTAATTCGGT
1 AATCGAATTAATTCGGT
354180 CGGGGTGGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 2 0.07
18 24 0.86
19 2 0.07
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (18 bp):
AATCGAATTAATTCGGTT
Found at i:355688 original size:26 final size:28
Alignment explanation
Indices: 355638--355700 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 28
355628 ATTTAGTTAT
*
355638 TTTTTAAAATTAAAAATTCAAAAAA-TA
1 TTTTAAAAATTAAAAATTCAAAAAATTA
*
355665 -TTTAAAAATTAAAAA-TCATTAAAATTA
1 TTTTAAAAATTAAAAATTCA-AAAAATTA
355692 TTTTAAAAA
1 TTTTAAAAA
355701 ATATTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 3 0.10
26 18 0.58
27 2 0.06
28 8 0.26
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (28 bp):
TTTTAAAAATTAAAAATTCAAAAAATTA
Found at i:356604 original size:23 final size:23
Alignment explanation
Indices: 356578--356704 Score: 139
Period size: 23 Copynumber: 5.4 Consensus size: 23
356568 AGTGCTGGGC
356578 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
356601 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
** *
356624 ATTAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
356647 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
* *
356671 TAACAGATAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
356695 AACAGAGAGC
1 AACAGAGAGC
356705 GCGCTAGTGT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
23 68 0.77
24 2 0.02
25 15 0.17
26 3 0.03
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:365644 original size:21 final size:21
Alignment explanation
Indices: 365597--365646 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
365587 AACGGTGCAG
**
365597 ATTTCTACCGATACCTGTACT
1 ATTTCTACCGATACAAGTACT
*
365618 AGTTCTACCGATACAAGTA-T
1 ATTTCTACCGATACAAGTACT
365638 AATTTCTAC
1 -ATTTCTAC
365647 TAATACATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (21 bp):
ATTTCTACCGATACAAGTACT
Found at i:366450 original size:52 final size:52
Alignment explanation
Indices: 366368--366561 Score: 291
Period size: 52 Copynumber: 3.7 Consensus size: 52
366358 TTCATTTCAG
* * ** *
366368 GGATTCTTATACTCACGATGACACAGAGTCATCGGACCTCTTAATCCGTAAA
1 GGATTCATATACTCACAATGACACTTAGTCATCGGACCTTTTAATCCGTAAA
* *
366420 TGATTTATATACTCACAATGACACTTAGTCATCGGACCTTTTAATCCGTAAA
1 GGATTCATATACTCACAATGACACTTAGTCATCGGACCTTTTAATCCGTAAA
*
366472 GGATTCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAA
1 GGATTCATATACTCACAATGACACTTAGTCATCGGACCTTTTAATCCGTAAA
*
366524 GGATTCATATACTTA-AGATGACACTTAGTCATCGGACC
1 GGATTCATATACTCACA-ATGACACTTAGTCATCGGACC
366562 CCTTTTCATT
Statistics
Matches: 129, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
52 129 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Consensus pattern (52 bp):
GGATTCATATACTCACAATGACACTTAGTCATCGGACCTTTTAATCCGTAAA
Found at i:368145 original size:20 final size:20
Alignment explanation
Indices: 368108--368145 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
368098 CTCCAGTGAG
* *
368108 ACTTCTACCGGTAGAACTCC
1 ACTTCTACCGATACAACTCC
368128 ACTTCTACCGATACAACT
1 ACTTCTACCGATACAACT
368146 ATAGTTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.11, T:0.26
Consensus pattern (20 bp):
ACTTCTACCGATACAACTCC
Found at i:368382 original size:20 final size:20
Alignment explanation
Indices: 368366--368423 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
368356 TAGAACTCCT
368366 CTTCTACCGATACAACTACA
1 CTTCTACCGATACAACTACA
* * **
368386 GTTCTACCGATACAAGTATG
1 CTTCTACCGATACAACTACA
368406 CTTCTACCGGA-ACAACTA
1 CTTCTACC-GATACAACTA
368424 AGTTGCAGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (20 bp):
CTTCTACCGATACAACTACA
Found at i:371280 original size:25 final size:24
Alignment explanation
Indices: 371252--371298 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
371242 CTCAATTTTT
371252 TACTT-TTATCGATTTAAAATGATTA
1 TACTTATTATCGA-TT-AAATGATTA
*
371277 TACTTATTTTCGATTAAATGAT
1 TACTTATTATCGATTAAATGAT
371299 ACAAACTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 7 0.35
26 6 0.30
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (24 bp):
TACTTATTATCGATTAAATGATTA
Found at i:373374 original size:57 final size:57
Alignment explanation
Indices: 373286--373399 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
373276 ACAAGCTGAG
373286 TATGTTTCCTTTCTGATGCAGTGTGTCGTCATTGATGACAACTACCGAAGCTATTGT
1 TATGTTTCCTTTCTGATGCAGTGTGTCGTCATTGATGACAACTACCGAAGCTATTGT
373343 TATGTTTCCTTTCTGATGCAGTGTGTCGTCATTGATGACAACTACCGAAGCTATTGT
1 TATGTTTCCTTTCTGATGCAGTGTGTCGTCATTGATGACAACTACCGAAGCTATTGT
373400 AGTCGAACTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (57 bp):
TATGTTTCCTTTCTGATGCAGTGTGTCGTCATTGATGACAACTACCGAAGCTATTGT
Found at i:376614 original size:7 final size:7
Alignment explanation
Indices: 376599--376636 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
376589 CTAACCCCCT
*
376599 ATTTTCC
1 ATTTCCC
376606 ATTTCCC
1 ATTTCCC
376613 ATTTCCC
1 ATTTCCC
376620 ATTTCCC
1 ATTTCCC
376627 ATTTCCC
1 ATTTCCC
376634 ATT
1 ATT
376637 CCATATACTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.16, C:0.37, G:0.00, T:0.47
Consensus pattern (7 bp):
ATTTCCC
Found at i:387246 original size:16 final size:16
Alignment explanation
Indices: 387225--387262 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
387215 GAAGAAGCAG
*
387225 AAAAAA-ATGAAAAATA
1 AAAAAACAT-AAAAAGA
387241 AAAAAACATAAAAAGA
1 AAAAAACATAAAAAGA
387257 AAAAAA
1 AAAAAA
387263 TAATTACTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.84, C:0.03, G:0.05, T:0.08
Consensus pattern (16 bp):
AAAAAACATAAAAAGA
Found at i:387483 original size:51 final size:51
Alignment explanation
Indices: 387397--387499 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 51
387387 CGGCTCAGTG
* * *
387397 ATTAAAATGTTATAACACGTTAACATAAATAACTAAAATATAACATTTCAA
1 ATTAAAATATTACAACACATTAACATAAATAACTAAAATATAACATTTCAA
* * *
387448 ATTAAAATATTACAACATATTAATATAAGTAACTAAAATATAACATTTCAA
1 ATTAAAATATTACAACACATTAACATAAATAACTAAAATATAACATTTCAA
387499 A
1 A
387500 CATAAATATT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.32
Consensus pattern (51 bp):
ATTAAAATATTACAACACATTAACATAAATAACTAAAATATAACATTTCAA
Found at i:389961 original size:20 final size:20
Alignment explanation
Indices: 389936--389974 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
389926 AAAATCTATG
* *
389936 TATTAAATTAATTAATTTAT
1 TATTAAATGAATCAATTTAT
389956 TATTAAATGAATCAATTTA
1 TATTAAATGAATCAATTTA
389975 ATTCATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TATTAAATGAATCAATTTAT
Done.