Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011144.1 Kokia drynarioides strain JFW-HI SEQ_126117, 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: 197758
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:3863 original size:18 final size:18
Alignment explanation
Indices: 3842--3877 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3832 ATCAAAAAGT
3842 CGAGAAAAA-AGAAAAATA
1 CGAGAAAAATA-AAAAATA
3860 CGAGAAAAATAAAAAATA
1 CGAGAAAAATAAAAAATA
3878 AAAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.72, C:0.06, G:0.14, T:0.08
Consensus pattern (18 bp):
CGAGAAAAATAAAAAATA
Found at i:5510 original size:23 final size:24
Alignment explanation
Indices: 5484--5536 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 24
5474 GGAGAGTTCT
5484 CAAGAGAAAAAA-GAAAATG-AAAA
1 CAAGA-AAAAAATGAAAATGAAAAA
5507 CAAGAAAAAAATGAAAATGAAAAA
1 CAAGAAAAAAATGAAAATGAAAAA
5531 CAAGAA
1 CAAGAA
5537 GATACCTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 6 0.21
23 12 0.43
24 10 0.36
ACGTcount: A:0.74, C:0.06, G:0.15, T:0.06
Consensus pattern (24 bp):
CAAGAAAAAAATGAAAATGAAAAA
Found at i:17757 original size:18 final size:18
Alignment explanation
Indices: 17734--17777 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
17724 TCATGCATTC
17734 CATGCATTTCATACAACT
1 CATGCATTTCATACAACT
* * * *
17752 CGTGCACTTCTTGCAACT
1 CATGCATTTCATACAACT
17770 CATGCATT
1 CATGCATT
17778 CCATGCAATG
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (18 bp):
CATGCATTTCATACAACT
Found at i:17784 original size:18 final size:17
Alignment explanation
Indices: 17734--17785 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
17724 TCATGCATTC
*
17734 CATGCATTTCATACAACT
1 CATGCA-TTCATGCAACT
* *
17752 CGTGCACTTCTTGCAACT
1 CATGCA-TTCATGCAACT
17770 CATGCATTCCATGCAA
1 CATGCATT-CATGCAA
17786 TGTGTTGAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.31
Consensus pattern (17 bp):
CATGCATTCATGCAACT
Found at i:23684 original size:18 final size:17
Alignment explanation
Indices: 23635--23678 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
23625 CAATATATAC
23635 TTTTTT-TTTGCTTTTCT
1 TTTTTTCTTTGC-TTTCT
23652 TTTTTTCTTTGCTTTCT
1 TTTTTTCTTTGCTTTCT
23669 TTTTCTTCTT
1 TTTT-TTCTT
23679 CTCTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.80
Consensus pattern (17 bp):
TTTTTTCTTTGCTTTCT
Found at i:24183 original size:17 final size:16
Alignment explanation
Indices: 24163--24218 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
24153 ACCACAATCC
*
24163 AAATGAACTAACAAGTA
1 AAATGAACTGACAA-TA
24180 AAATGCAAC-GACAACTA
1 AAATG-AACTGACAA-TA
*
24197 AAATGAAATGACAATA
1 AAATGAACTGACAATA
24213 AAATGA
1 AAATGA
24219 GATGCATGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 10 0.29
17 21 0.62
18 3 0.09
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.16
Consensus pattern (16 bp):
AAATGAACTGACAATA
Found at i:24201 original size:34 final size:33
Alignment explanation
Indices: 24134--24217 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 33
24124 AATATTATAC
* *
24134 AAATAAGAATGAAAATGCAACCACAATCCAAATG
1 AAATAACAAT-AAAATGCAACCACAATCAAAATG
* *
24168 AACTAACAAGTAAAATGCAACGACAA-CTAAAATG
1 AAATAACAA-TAAAATGCAACCACAATC-AAAATG
*
24202 AAATGACAATAAAATG
1 AAATAACAATAAAATG
24218 AGATGCATGT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
33 8 0.19
34 33 0.79
35 1 0.02
ACGTcount: A:0.57, C:0.15, G:0.12, T:0.15
Consensus pattern (33 bp):
AAATAACAATAAAATGCAACCACAATCAAAATG
Found at i:38596 original size:25 final size:25
Alignment explanation
Indices: 38562--38610 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
38552 GTTTAGAAAG
38562 TAGTAGATTCTTCAAGAAAGTATAT
1 TAGTAGATTCTTCAAGAAAGTATAT
38587 TAGTAGATTCTTCAAGAAAGTATA
1 TAGTAGATTCTTCAAGAAAGTATA
38611 ATTAAAGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (25 bp):
TAGTAGATTCTTCAAGAAAGTATAT
Found at i:40837 original size:23 final size:23
Alignment explanation
Indices: 40807--40951 Score: 200
Period size: 23 Copynumber: 6.3 Consensus size: 23
40797 TATATCCATA
* *
40807 CTTAAATATTAATGCGATTTGTG
1 CTTAAATATTAATGTGATTTATG
* *
40830 CTTAAATATTAATATGATTTGTG
1 CTTAAATATTAATGTGATTTATG
*
40853 CTTAAATATTAATTTTGATTTATG
1 CTTAAATATTAA-TGTGATTTATG
40877 CTTAAATATTAATGTGATTTATG
1 CTTAAATATTAATGTGATTTATG
* *
40900 CTTAAATATTAATATAATTTATG
1 CTTAAATATTAATGTGATTTATG
* *
40923 ATTAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTATG
40946 CTTAAA
1 CTTAAA
40952 GAATAAGATG
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
23 88 0.81
24 21 0.19
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (23 bp):
CTTAAATATTAATGTGATTTATG
Found at i:40896 original size:70 final size:69
Alignment explanation
Indices: 40807--40951 Score: 218
Period size: 70 Copynumber: 2.1 Consensus size: 69
40797 TATATCCATA
* * * * *
40807 CTTAAATATTAATGCGATTTGTGCTTAAATATTAATATGATTTGTGCTTAAATATTAATTTTGAT
1 CTTAAATATTAATGCGATTTATGCTTAAATATTAATATAATTTATGATTAAATATTAA-TGTGAT
40872 TTATG
65 TTATG
*
40877 CTTAAATATTAATGTGATTTATGCTTAAATATTAATATAATTTATGATTAAATATTAATGTGATT
1 CTTAAATATTAATGCGATTTATGCTTAAATATTAATATAATTTATGATTAAATATTAATGTGATT
*
40942 TGTG
66 TATG
40946 CTTAAA
1 CTTAAA
40952 GAATAAGATG
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
69 15 0.22
70 53 0.78
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (69 bp):
CTTAAATATTAATGCGATTTATGCTTAAATATTAATATAATTTATGATTAAATATTAATGTGATT
TATG
Found at i:41097 original size:36 final size:36
Alignment explanation
Indices: 41020--41097 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
41010 TGATGACTGT
* *
41020 TGTGAAAGTAAATATGTGGGTATGTTCTTCATGCCA
1 TGTGACAGAAAATATGTGGGTATGTTCTTCATGCCA
*
41056 TGTGACAGAAAATATGTGGGTATGTTCTTCGTGCCA
1 TGTGACAGAAAATATGTGGGTATGTTCTTCATGCCA
41092 TGTGAC
1 TGTGAC
41098 TGATTATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.35
Consensus pattern (36 bp):
TGTGACAGAAAATATGTGGGTATGTTCTTCATGCCA
Found at i:45133 original size:16 final size:17
Alignment explanation
Indices: 45112--45146 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
45102 TTTTGAGGTT
45112 TGTTTTATA-TGATAAA
1 TGTTTTATAGTGATAAA
45128 TGTTTTATAGTTGATAAA
1 TGTTTTATAG-TGATAAA
45146 T
1 T
45147 CGATGAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (17 bp):
TGTTTTATAGTGATAAA
Found at i:45692 original size:23 final size:23
Alignment explanation
Indices: 45662--45738 Score: 127
Period size: 23 Copynumber: 3.3 Consensus size: 23
45652 CTTATATCAA
45662 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
45685 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
45708 TGCTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
45731 AGCTTAAA
1 TGCTTAAA
45739 GAATTAAGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:45865 original size:34 final size:36
Alignment explanation
Indices: 45818--45919 Score: 154
Period size: 34 Copynumber: 2.9 Consensus size: 36
45808 TGTGAAAGTG
* *
45818 AATATATAAGTATGTTCTTCATGTCATGTGACA-AA
1 AATATGTAGGTATGTTCTTCATGTCATGTGACAGAA
*
45853 AA-ATGTAGGTATGTTCTTCATGCCATGTGACAGAA
1 AATATGTAGGTATGTTCTTCATGTCATGTGACAGAA
*
45888 AATATGTAGGTATTTTCTTCATGTCATGTGAC
1 AATATGTAGGTATGTTCTTCATGTCATGTGAC
45920 TAATTATATT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
34 27 0.45
35 6 0.10
36 27 0.45
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (36 bp):
AATATGTAGGTATGTTCTTCATGTCATGTGACAGAA
Found at i:50382 original size:10 final size:10
Alignment explanation
Indices: 50367--50392 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
50357 TTTCACAAGG
50367 AACAGGTGAC
1 AACAGGTGAC
50377 AACAGGTGAC
1 AACAGGTGAC
50387 AACAGG
1 AACAGG
50393 CTGTACCCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.31, T:0.08
Consensus pattern (10 bp):
AACAGGTGAC
Found at i:52029 original size:27 final size:27
Alignment explanation
Indices: 51995--52050 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
51985 TATGATCTCA
51995 TTTTATCTCATGATAACCATTACATCT
1 TTTTATCTCATGATAACCATTACATCT
52022 TTTTATCTCATGATAACCATTACATCT
1 TTTTATCTCATGATAACCATTACATCT
52049 TT
1 TT
52051 CTTCATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (27 bp):
TTTTATCTCATGATAACCATTACATCT
Found at i:52258 original size:15 final size:15
Alignment explanation
Indices: 52238--52272 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
52228 ACTTTCAATT
52238 CCTTATCTATTTGAA
1 CCTTATCTATTTGAA
52253 CCTTATCTATTTGAA
1 CCTTATCTATTTGAA
52268 -CTTAT
1 CCTTAT
52273 GCTTTCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.49
Consensus pattern (15 bp):
CCTTATCTATTTGAA
Found at i:55852 original size:39 final size:39
Alignment explanation
Indices: 55842--55936 Score: 154
Period size: 39 Copynumber: 2.4 Consensus size: 39
55832 TCAGTATAGT
*
55842 ATTGCAGTGTTTACAGTGTCACTGCCAATTCAATATGTC
1 ATTGCAGTGTTTACAGTGTCACTACCAATTCAATATGTC
* * *
55881 ATTGCAGTGTTTACAGTGTCACTGCCAATTCAACATATC
1 ATTGCAGTGTTTACAGTGTCACTACCAATTCAATATGTC
55920 ATTGCAGTGTTTACAGT
1 ATTGCAGTGTTTACAGT
55937 ATCATTGCAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (39 bp):
ATTGCAGTGTTTACAGTGTCACTACCAATTCAATATGTC
Found at i:55941 original size:20 final size:20
Alignment explanation
Indices: 55879--55954 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
55869 ATTCAATATG
* *
55879 TCATTGCAGTGTTTACAGTG
1 TCATTGCAATGTTTACAGTA
* **
55899 TCACTGCCAAT-TCAACA-TA
1 TCATTG-CAATGTTTACAGTA
*
55918 TCATTGCAGTGTTTACAGTA
1 TCATTGCAATGTTTACAGTA
55938 TCATTGCAATGTTTACA
1 TCATTGCAATGTTTACA
55955 ATGTCACTGC
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
18 3 0.07
19 10 0.23
20 27 0.63
21 3 0.07
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.37
Consensus pattern (20 bp):
TCATTGCAATGTTTACAGTA
Found at i:55978 original size:59 final size:59
Alignment explanation
Indices: 55879--55993 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 59
55869 ATTCAATATG
* * *
55879 TCATTGCAGTGTTTACAGTGTCACTGCCAATTCAACATATCATTGCAGTGTTTACAGTA
1 TCATTGCAATGTTTACAATGTCACTGCCAATTCAACATATCATTACAGTGTTTACAGTA
* **
55938 TCATTGCAATGTTTACAATGTCACTGCCAGTTCAGTATATCATTACAGTGTTTACA
1 TCATTGCAATGTTTACAATGTCACTGCCAATTCAACATATCATTACAGTGTTTACA
55994 ATGTCACTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.37
Consensus pattern (59 bp):
TCATTGCAATGTTTACAATGTCACTGCCAATTCAACATATCATTACAGTGTTTACAGTA
Found at i:55990 original size:39 final size:39
Alignment explanation
Indices: 55936--56059 Score: 194
Period size: 39 Copynumber: 3.2 Consensus size: 39
55926 GTGTTTACAG
* * *
55936 TATCATTGCAATGTTTACAATGTCACTGCCAGTTCAGTA
1 TATCATTACAGTGTTTACAATGTCACTGTCAGTTCAGTA
55975 TATCATTACAGTGTTTACAATGTCACTGTCAGTTCAGTA
1 TATCATTACAGTGTTTACAATGTCACTGTCAGTTCAGTA
* * *
56014 TATCATTATAGTGTTTACAGTGTCACTGTCAGTTTAGTA
1 TATCATTACAGTGTTTACAATGTCACTGTCAGTTCAGTA
56053 TATCATT
1 TATCATT
56060 GCAGAGCAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (39 bp):
TATCATTACAGTGTTTACAATGTCACTGTCAGTTCAGTA
Found at i:56017 original size:98 final size:98
Alignment explanation
Indices: 55842--56034 Score: 269
Period size: 98 Copynumber: 2.0 Consensus size: 98
55832 TCAGTATAGT
* * * * *
55842 ATTGCAGTGTTTACAGTGTCACTGCCAATTCAATATGTCATTGCAGTGTTTACAGTGTCACTGCC
1 ATTGCAATGTTTACAATGTCACTGCCAATTCAATATATCATTACAGTGTTTACAATGTCACTGCC
*
55907 AATTCAACATATCATTGCAGTGTTTACAGTATC
66 AATTCAACATATCATTACAGTGTTTACAGTATC
* * *
55940 ATTGCAATGTTTACAATGTCACTGCCAGTTCAGTATATCATTACAGTGTTTACAATGTCACTGTC
1 ATTGCAATGTTTACAATGTCACTGCCAATTCAATATATCATTACAGTGTTTACAATGTCACTGCC
* ** *
56005 AGTTCAGTATATCATTATAGTGTTTACAGT
66 AATTCAACATATCATTACAGTGTTTACAGT
56035 GTCACTGTCA
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
98 82 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (98 bp):
ATTGCAATGTTTACAATGTCACTGCCAATTCAATATATCATTACAGTGTTTACAATGTCACTGCC
AATTCAACATATCATTACAGTGTTTACAGTATC
Found at i:58973 original size:75 final size:75
Alignment explanation
Indices: 58848--59001 Score: 218
Period size: 75 Copynumber: 2.1 Consensus size: 75
58838 TTAGTTAAGA
* * * * * *
58848 ATACCTTCTTGGTCTCACCTAGACATATAGATACGCTCTTAGTCTTATTGCTTGGCACAAATTAT
1 ATACCCTCTCGGTCTCACCAAGACATATAGATACCCTCTCAGTCTCATTGCTTGGCACAAATTAT
*
58913 ACTCAACAGG
66 ACTCAACAAG
* *
58923 ATACCCTCTCGGTCTCACCAAGACATATAGATACCCTCTCAGTCTCATTGCTTTGCACAAGTTAT
1 ATACCCTCTCGGTCTCACCAAGACATATAGATACCCTCTCAGTCTCATTGCTTGGCACAAATTAT
*
58988 ACTCGACAAG
66 ACTCAACAAG
58998 ATAC
1 ATAC
59002 TCTCGCTATC
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (75 bp):
ATACCCTCTCGGTCTCACCAAGACATATAGATACCCTCTCAGTCTCATTGCTTGGCACAAATTAT
ACTCAACAAG
Found at i:59058 original size:45 final size:44
Alignment explanation
Indices: 58951--59059 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 44
58941 CAAGACATAT
*
58951 AGATACCCTCTCAGTCTCATTGCTTTGCACAAGTTATACTCGACA
1 AGATACCCTCTCA-TCTCATCGCTTTGCACAAGTTATACTCGACA
* * * *
58996 AGATACTCTCGCTATCTCATCGTTTTGCACAAGTTATACTCGATA
1 AGATACCCTCTC-ATCTCATCGCTTTGCACAAGTTATACTCGACA
*
59041 GGATACCCTCTCGATCTCA
1 AGATACCCTCTC-ATCTCA
59060 CCTGTTTGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 53 0.98
46 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (44 bp):
AGATACCCTCTCATCTCATCGCTTTGCACAAGTTATACTCGACA
Found at i:64413 original size:18 final size:17
Alignment explanation
Indices: 64390--64429 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
64380 ATAAAACAAT
64390 AAAATAACAAAATTAA-TA
1 AAAAT-ACAAAA-TAATTA
64408 AAAATACAAAATAATTA
1 AAAATACAAAATAATTA
64425 AAAAT
1 AAAAT
64430 TAGCACACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.14
17 13 0.62
18 5 0.24
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATACAAAATAATTA
Found at i:66223 original size:50 final size:49
Alignment explanation
Indices: 66169--66322 Score: 119
Period size: 50 Copynumber: 3.2 Consensus size: 49
66159 TAACCAATTG
66169 TATAATTTACCCTTTTAATAATGATTTTCAATTTAATAATGCGAAATTAT
1 TATAATTTACCCTTTTAATAATGATTTTCAATTTAATAATG-GAAATTAT
* * ** * *
66219 TATAATTTA---TTCATGAGGATAGTTTTATCAGA--T-ATAA---ATATTAT
1 TATAATTTACCCTT-TTAATAAT-GATTT-TCA-ATTTAATAATGGAAATTAT
*
66263 ATATAATTTACCCTTTTAATAATGATTTTAAATTTAATAATGTGAAATTAT
1 -TATAATTTACCCTTTTAATAATGATTTTCAATTTAATAATG-GAAATTAT
66314 TATAATTTA
1 TATAATTTA
66323 TTCATGAGGA
Statistics
Matches: 76, Mismatches: 13, Indels: 30
0.64 0.11 0.25
Matches are distributed among these distances:
44 7 0.09
45 11 0.14
46 5 0.07
47 10 0.13
48 10 0.13
49 5 0.07
50 21 0.28
51 7 0.09
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (49 bp):
TATAATTTACCCTTTTAATAATGATTTTCAATTTAATAATGGAAATTAT
Found at i:66332 original size:95 final size:95
Alignment explanation
Indices: 66169--66362 Score: 345
Period size: 95 Copynumber: 2.0 Consensus size: 95
66159 TAACCAATTG
*
66169 TATAATTTACCCTTTTAATAATGATTTTCAATTTAATAATGCGAAATTATTATAATTTATTCATG
1 TATAATTTACCCTTTTAATAATGATTTTAAATTTAATAATGCGAAATTATTATAATTTATTCATG
66234 AGGATAGTTTTATCAGATATAAATAT-TATA
66 AGGATAGTTTTAT-AGATATAAATATATATA
*
66264 TATAATTTACCCTTTTAATAATGATTTTAAATTTAATAATGTGAAATTATTATAATTTATTCATG
1 TATAATTTACCCTTTTAATAATGATTTTAAATTTAATAATGCGAAATTATTATAATTTATTCATG
*
66329 AGGATAGTTTTATAGATATATATATATATA
66 AGGATAGTTTTATAGATATAAATATATATA
66359 TATA
1 TATA
66363 TATATATTTC
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
94 11 0.12
95 84 0.88
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (95 bp):
TATAATTTACCCTTTTAATAATGATTTTAAATTTAATAATGCGAAATTATTATAATTTATTCATG
AGGATAGTTTTATAGATATAAATATATATA
Found at i:66351 original size:2 final size:2
Alignment explanation
Indices: 66339--66369 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
66329 AGGATAGTTT
*
66339 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66370 TTCAAGCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:66864 original size:14 final size:14
Alignment explanation
Indices: 66824--66867 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
66814 GAAGGACTTT
66824 AAAAAGTGTTTTTG
1 AAAAAGTGTTTTTG
66838 AAAATA-TGTTTTTG
1 AAAA-AGTGTTTTTG
*
66852 AAAAAGTGATTTTG
1 AAAAAGTGTTTTTG
66866 AA
1 AA
66868 CTTTTGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (14 bp):
AAAAAGTGTTTTTG
Found at i:67680 original size:24 final size:24
Alignment explanation
Indices: 67645--67693 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
67635 TTTTTTGTAC
* * *
67645 TTAATTACAAATGTGTTAAAATAA
1 TTAATTAAAAATATATTAAAATAA
67669 TTAATTAAAAATATATTAAAATAA
1 TTAATTAAAAATATATTAAAATAA
67693 T
1 T
67694 ACAAATGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (24 bp):
TTAATTAAAAATATATTAAAATAA
Found at i:68036 original size:24 final size:24
Alignment explanation
Indices: 68009--68054 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
67999 TAATTAATCT
*
68009 TTTATAAA-TAATTAATATTTATTG
1 TTTA-AAAGTAATTAAAATTTATTG
*
68033 TTTAAAAGTATTTAAAATTTAT
1 TTTAAAAGTAATTAAAATTTAT
68055 ATTTCATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
TTTAAAAGTAATTAAAATTTATTG
Found at i:68646 original size:34 final size:36
Alignment explanation
Indices: 68606--68674 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
68596 TCTATAATCT
68606 TTTTTATATTTAA-AATTTAGTATTTTTA-TTTTTA
1 TTTTTATATTTAATAATTTAGTATTTTTACTTTTTA
* * *
68640 TTTTTATTTTTAATATTTTTGTATTTTTACTTTTT
1 TTTTTATATTTAATAATTTAGTATTTTTACTTTTT
68675 TGAGATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 12 0.40
35 13 0.43
36 5 0.17
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.72
Consensus pattern (36 bp):
TTTTTATATTTAATAATTTAGTATTTTTACTTTTTA
Found at i:68673 original size:7 final size:6
Alignment explanation
Indices: 68626--68674 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
68616 TAAAATTTAG
* * *
68626 TATTTT TATTTT TATTTT TATTTT TAATAT T-TTTG TATTTT TACTTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TA-TTTT
68674 T
1 T
68675 TGAGATAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
5 2 0.06
6 28 0.80
7 5 0.14
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:77552 original size:3 final size:3
Alignment explanation
Indices: 77544--77576 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
77534 TCAGTGTGAT
77544 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
77577 GTTACTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:78979 original size:26 final size:26
Alignment explanation
Indices: 78946--79009 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
78936 TGCAAAAATA
*
78946 TTTTTGAATTATTCAATTTTTATATT
1 TTTTTGAATTATTAAATTTTTATATT
*
78972 TTTTTGAAATT-TTAAATTTTTTTATT
1 TTTTTG-AATTATTAAATTTTTATATT
*
78998 TTTTTAAATTAT
1 TTTTTGAATTAT
79010 ATATATCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 4 0.12
26 25 0.76
27 4 0.12
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTTTGAATTATTAAATTTTTATATT
Found at i:80277 original size:21 final size:21
Alignment explanation
Indices: 80253--80295 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
80243 AATTTAAACC
*
80253 AAAATTTATATTTT-TAAAAAT
1 AAAATGTA-ATTTTATAAAAAT
80274 AAAATGTAATTTTATAAAAAT
1 AAAATGTAATTTTATAAAAAT
80295 A
1 A
80296 TCATAAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
AAAATGTAATTTTATAAAAAT
Found at i:81505 original size:6 final size:6
Alignment explanation
Indices: 81491--81567 Score: 79
Period size: 6 Copynumber: 13.0 Consensus size: 6
81481 TTTCATTTAT
* *
81491 TTTAAA TTTAGA TTT-AT TTTAAA TTT-AA TCTTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
* *
81537 TCTTAAA TTTAAA TTTAAT TTTAAA ATTAAA
1 T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA
81568 AAGTCCATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
5 9 0.15
6 44 0.75
7 6 0.10
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:81531 original size:18 final size:18
Alignment explanation
Indices: 81491--81567 Score: 104
Period size: 18 Copynumber: 4.3 Consensus size: 18
81481 TTTCATTTAT
*
81491 TTTAAATTTAGAT-TT-AT
1 TTTAAATTTA-ATCTTAAA
81508 TTTAAATTTAATCTTAAA
1 TTTAAATTTAATCTTAAA
81526 TTTAAATTTAATCTTAAA
1 TTTAAATTTAATCTTAAA
*
81544 TTTAAATTTAATTTTAAA
1 TTTAAATTTAATCTTAAA
*
81562 ATTAAA
1 TTTAAA
81568 AAGTCCATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
16 2 0.04
17 12 0.22
18 41 0.75
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (18 bp):
TTTAAATTTAATCTTAAA
Found at i:81640 original size:35 final size:35
Alignment explanation
Indices: 81588--81664 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
81578 AAAATGTCCA
81588 AATTACAAAGGACCCAAAGACTAACCCAATGACCC
1 AATTACAAAGGACCCAAAGACTAACCCAATGACCC
** * **
81623 AATTACAAAGGGTCCAAAGACTAGCCCAATGACTT
1 AATTACAAAGGACCCAAAGACTAACCCAATGACCC
81658 AATTACA
1 AATTACA
81665 CCCAACACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.44, C:0.26, G:0.13, T:0.17
Consensus pattern (35 bp):
AATTACAAAGGACCCAAAGACTAACCCAATGACCC
Found at i:83467 original size:29 final size:29
Alignment explanation
Indices: 83421--83790 Score: 347
Period size: 29 Copynumber: 12.7 Consensus size: 29
83411 CCGTAAATTG
*
83421 TCCAAAAATCTCATTTTTACCCCCAAACT
1 TCCAAAAATCCCATTTTTACCCCCAAACT
* ** *
83450 TCCAAAAATCCCAATTTTGACCCTAAAAAT
1 TCCAAAAATCCC-ATTTTTACCCCCAAACT
* *
83480 TCCAAAAAAATCCCATTTTTA-CCTCGAACT
1 TCC--AAAAATCCCATTTTTACCCCCAAACT
*
83510 TCCAAAAATCCCATTTTTGACCCCAAAACT
1 TCCAAAAATCCCATTTTT-ACCCCCAAACT
* *
83540 TCCAAAAATCCTATTTTTACCCCCAAAAT
1 TCCAAAAATCCCATTTTTACCCCCAAACT
** *
83569 TCCAAAAATCTTATTTTTGACCCCAAAACT
1 TCCAAAAATCCCATTTTT-ACCCCCAAACT
* *
83599 TCCAAAAATCCCATTTTTA-CACTAGAACT
1 TCCAAAAATCCCATTTTTACCCCCA-AACT
* * **
83628 TCCAAAAATTCCATTTTAACCCTAAAACT
1 TCCAAAAATCCCATTTTTACCCCCAAACT
**
83657 TCCAAAAATCCCATTTTTGGCCCCAAACT
1 TCCAAAAATCCCATTTTTACCCCCAAACT
* * *
83686 TCCAAAAATCCCATTTTGACCTCGAAACT
1 TCCAAAAATCCCATTTTTACCCCCAAACT
*
83715 TCCAAAAATTCCATTTTT-CCCCCTGAAACT
1 TCCAAAAATCCCATTTTTACCCCC--AAACT
* **
83745 TCC--AAATTCCATTTTTACCCTTAAA-T
1 TCCAAAAATCCCATTTTTACCCCCAAACT
* *
83771 GTCTAAAAATTCCATTTTTA
1 -TCCAAAAATCCCATTTTTA
83791 AACCTCAAAT
Statistics
Matches: 282, Mismatches: 45, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
26 1 0.00
27 5 0.02
28 34 0.12
29 144 0.51
30 83 0.29
31 6 0.02
32 9 0.03
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (29 bp):
TCCAAAAATCCCATTTTTACCCCCAAACT
Found at i:83673 original size:58 final size:57
Alignment explanation
Indices: 83421--83790 Score: 388
Period size: 58 Copynumber: 6.3 Consensus size: 57
83411 CCGTAAATTG
* *
83421 TCCAAAAATCTCATTTTTACCCCCAAACTTCCAAAAATCCCAATTTTGACCCTAAAAAT
1 TCCAAAAATCCCATTTTTA-CCCCAAACTTCCAAAAATCCC-ATTTTGACCCTAAAACT
* * *
83480 TCCAAAAAAATCCCATTTTTACCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACT
1 TCC--AAAAATCCCATTTTTACCCCAAACTTCCAAAAATCCCA-TTTTGACCCTAAAACT
* * ** *
83540 TCCAAAAATCCTATTTTTACCCCCAAAATTCCAAAAATCTTATTTTTGACCCCAAAACT
1 TCCAAAAATCCCATTTTTA-CCCCAAACTTCCAAAAATCCCA-TTTTGACCCTAAAACT
* * * *
83599 TCCAAAAATCCCATTTTTACACTAGAACTTCCAAAAATTCCATTTTAACCCTAAAACT
1 TCCAAAAATCCCATTTTTACCCCA-AACTTCCAAAAATCCCATTTTGACCCTAAAACT
* *
83657 TCCAAAAATCCCATTTTTGGCCCCAAACTTCCAAAAATCCCATTTTGA-CCTCGAAACT
1 TCCAAAAATCCCATTTTT-ACCCCAAACTTCCAAAAATCCCATTTTGACCCT-AAAACT
* * * * *
83715 TCCAAAAATTCCATTTTTCCCCCTGAAACTTCC--AAATTCCATTTTTACCCTTAAA-T
1 TCCAAAAATCCCATTTTTACCCC--AAACTTCCAAAAATCCCATTTTGACCCTAAAACT
* *
83771 GTCTAAAAATTCCATTTTTA
1 -TCCAAAAATCCCATTTTTA
83791 AACCTCAAAT
Statistics
Matches: 267, Mismatches: 33, Indels: 24
0.82 0.10 0.07
Matches are distributed among these distances:
56 1 0.00
57 39 0.15
58 96 0.36
59 80 0.30
60 36 0.13
61 15 0.06
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (57 bp):
TCCAAAAATCCCATTTTTACCCCAAACTTCCAAAAATCCCATTTTGACCCTAAAACT
Found at i:83857 original size:28 final size:29
Alignment explanation
Indices: 83808--83867 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
83798 AATTTTCCCC
* *
83808 AAATTACCATTTTTACCTTGAGAATCC-A
1 AAATTACCATTTTGACCCTGAGAATCCGA
* *
83836 AAATTACCATTTTGCCCCTGAGTATCCGA
1 AAATTACCATTTTGACCCTGAGAATCCGA
83865 AAA
1 AAA
83868 GTCTCATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (29 bp):
AAATTACCATTTTGACCCTGAGAATCCGA
Found at i:85410 original size:29 final size:28
Alignment explanation
Indices: 85378--85437 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
85368 AAAATGAGAC
* *
85378 TTTTCGGATACTCAGGGGCAAAATGGTAA
1 TTTT-GGATACTCAAGGGAAAAATGGTAA
* *
85407 TTTTGGATTCTCAAGGTAAAAATGGTAA
1 TTTTGGATACTCAAGGGAAAAATGGTAA
85435 TTT
1 TTT
85438 GGGGAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (28 bp):
TTTTGGATACTCAAGGGAAAAATGGTAA
Found at i:85523 original size:57 final size:55
Alignment explanation
Indices: 85456--85824 Score: 201
Period size: 59 Copynumber: 6.3 Consensus size: 55
85446 TTTGAGGTTT
* *
85456 AAAAATGGAATTTTTAGACA-TTTAAGGGTAAAAATGGAATTTGGAAGTTTCAGGGG-G
1 AAAAATGGAATTTTTGGA-AGTTT-AGGGTAAAAATGGAATTTGGAAGTTT--GGGGCC
* * *
85513 AAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAATGGGATTTTTGGAAGTTTGGGGCC
1 AAAAATGGAATTTTTGGAAGTTTAG-GGTAAAAAT-GGA-ATTTGGAAGTTTGGGGCC
* * * * *
85571 AAAAATGGGATTTTTGGAAGTTTTAGGGTTAAAATGGAATTTTTGGAAGTTCTAGTG-T
1 AAAAATGGAATTTTTGGAAG-TTTAGGGTAAAAATGGAA--TTTGGAAGTT-TGGGGCC
* * * * * **
85629 AAAAATGGGATTTTTGGAAGTTTTGGGGTCAAAAATAAGATTTTTGGAATTTTGGGGGT
1 AAAAATGGAATTTTTGGAAG-TTTAGGGT-AAAAAT-GGA-ATTTGGAAGTTTGGGGCC
* * * * *
85688 AAAAATAGG-ATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGG-T
1 AAAAAT-GGAATTTTTGGAAG-TTTAGGGT-AAAAAT-GGA-ATTTGGAAGTTTGGGGCC
* * * * **
85746 AAAAATGGGATTTTTTTGGAATTTTTAGGGTCAAAATTGGGATTTTTGGAAGTTTGGGGGT
1 AAAAAT-GGA-ATTTTTGGAA-GTTTAGGGT-AAAAAT-GGA-ATTTGGAAGTTTGGGGCC
85807 AAAAAT-GAGATTTTTGGA
1 AAAAATGGA-ATTTTTGGA
85825 CAATTTACGG
Statistics
Matches: 261, Mismatches: 33, Indels: 34
0.80 0.10 0.10
Matches are distributed among these distances:
56 2 0.01
57 35 0.13
58 80 0.31
59 92 0.35
60 45 0.17
61 7 0.03
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.36
Consensus pattern (55 bp):
AAAAATGGAATTTTTGGAAGTTTAGGGTAAAAATGGAATTTGGAAGTTTGGGGCC
Found at i:85555 original size:29 final size:29
Alignment explanation
Indices: 85455--85824 Score: 347
Period size: 29 Copynumber: 12.7 Consensus size: 29
85445 ATTTGAGGTT
* * **
85455 TAAAAATGGAATTTTTAGACA-TTTAAGGG
1 TAAAAATGGGATTTTTGGA-AGTTTCGGGG
*
85484 TAAAAAT-GGA-ATTTGGAAGTTTCAGGGG
1 TAAAAATGGGATTTTTGGAAGTTTC-GGGG
* * *
85512 GAAAAATGGAATTTTTGGAAGTTTCGAGG
1 TAAAAATGGGATTTTTGGAAGTTTCGGGG
*
85541 TCAAAATGGGATTTTTGGAAGTTT-GGGG
1 TAAAAATGGGATTTTTGGAAGTTTCGGGG
* **
85569 CCAAAAATGGGATTTTTGGAAGTTTTAGGG
1 -TAAAAATGGGATTTTTGGAAGTTTCGGGG
* * * *
85599 TTAAAATGGAATTTTTGGAAG-TTCTAGTG
1 TAAAAATGGGATTTTTGGAAGTTTC-GGGG
*
85628 TAAAAATGGGATTTTTGGAAGTTTTGGGG
1 TAAAAATGGGATTTTTGGAAGTTTCGGGG
** * *
85657 TCAAAAATAAGATTTTTGGAATTTTGGGGG
1 T-AAAAATGGGATTTTTGGAAGTTTCGGGG
* *
85687 TAAAAATAGGATTTTTGGAAGTTTTGGGG
1 TAAAAATGGGATTTTTGGAAGTTTCGGGG
*
85716 TCAAAAATGGGATTTTTGGAAG-TTCGAGG
1 T-AAAAATGGGATTTTTGGAAGTTTCGGGG
* **
85745 TAAAAATGGGATTTTTTTGGAATTTTTAGGG
1 TAAAAATGGGA--TTTTTGGAAGTTTCGGGG
* *
85776 TCAAAATTGGGATTTTTGGAAGTTTGGGGG
1 T-AAAAATGGGATTTTTGGAAGTTTCGGGG
*
85806 TAAAAATGAGATTTTTGGA
1 TAAAAATGGGATTTTTGGA
85825 CAATTTACGG
Statistics
Matches: 281, Mismatches: 46, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
26 1 0.00
27 8 0.03
28 26 0.09
29 146 0.52
30 86 0.31
31 5 0.02
32 9 0.03
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (29 bp):
TAAAAATGGGATTTTTGGAAGTTTCGGGG
Found at i:87629 original size:35 final size:35
Alignment explanation
Indices: 87581--87657 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
87571 TTGTGTTGGG
87581 TGTAATTAAGTCATTGGGCTAGTCTTTGGACCCTT
1 TGTAATTAAGTCATTGGGCTAGTCTTTGGACCCTT
** * **
87616 TGTAATTGGGTCATTGGGTTAGTCTTTGGGTCCTT
1 TGTAATTAAGTCATTGGGCTAGTCTTTGGACCCTT
87651 TGTAATT
1 TGTAATT
87658 TGGACATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.17, C:0.13, G:0.26, T:0.44
Consensus pattern (35 bp):
TGTAATTAAGTCATTGGGCTAGTCTTTGGACCCTT
Found at i:87694 original size:12 final size:12
Alignment explanation
Indices: 87679--87754 Score: 75
Period size: 12 Copynumber: 6.4 Consensus size: 12
87669 AATGGACTTT
*
87679 TTAATTTTAAAA
1 TTAAATTTAAAA
*
87691 TTAAATTTAAAT
1 TTAAATTTAAAA
*
87703 TTAAGA-TTAAAT
1 TTAA-ATTTAAAA
*
87715 TTAAATTTAAGA
1 TTAAATTTAAAA
87727 TTAAATTTAAAA
1 TTAAATTTAAAA
* *
87739 -TAAATCTAAAT
1 TTAAATTTAAAA
87750 TTAAA
1 TTAAA
87755 ATAAATGAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
11 10 0.19
12 43 0.80
13 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (12 bp):
TTAAATTTAAAA
Found at i:87699 original size:18 final size:18
Alignment explanation
Indices: 87678--87754 Score: 104
Period size: 18 Copynumber: 4.3 Consensus size: 18
87668 TAATGGACTT
* *
87678 TTTAATTTTAAAATTAAA
1 TTTAAATTTAAGATTAAA
87696 TTTAAATTTAAGATTAAA
1 TTTAAATTTAAGATTAAA
87714 TTTAAATTTAAGATTAAA
1 TTTAAATTTAAGATTAAA
*
87732 TTTAAA-ATAA-ATCTAAA
1 TTTAAATTTAAGAT-TAAA
87749 TTTAAA
1 TTTAAA
87755 ATAAATGAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
16 2 0.04
17 13 0.24
18 40 0.73
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (18 bp):
TTTAAATTTAAGATTAAA
Found at i:88187 original size:16 final size:18
Alignment explanation
Indices: 88148--88181 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
88138 TAAGTTTATA
88148 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
88165 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
88182 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:88976 original size:21 final size:21
Alignment explanation
Indices: 88950--88992 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
88940 AAGTTTATGA
*
88950 TATTTTTATAAAAT-TACATTT
1 TATTTTTA-AAAATATAAATTT
88971 TATTTTTAAAAATATAAATTT
1 TATTTTTAAAAATATAAATTT
88992 T
1 T
88993 GGTTTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTTTAAAAATATAAATTT
Found at i:90272 original size:26 final size:27
Alignment explanation
Indices: 90236--90299 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 27
90226 TTGGATATAT
*
90236 ATAATTT-AAAAAAATAAAAAAATTTA
1 ATAATTTCAAAAAAATAAAAAAATTGA
*
90262 A-AATTTCAAAAAAATATAAAAATTGA
1 ATAATTTCAAAAAAATAAAAAAATTGA
90288 ATAA-TTCAAAAA
1 ATAATTTCAAAAA
90300 TATTTTTGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 5 0.15
26 27 0.79
27 2 0.06
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (27 bp):
ATAATTTCAAAAAAATAAAAAAATTGA
Found at i:90421 original size:17 final size:16
Alignment explanation
Indices: 90398--90436 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
90388 GTTTAAATTT
*
90398 TAAAAATTACAAAAAA
1 TAAAAAATACAAAAAA
**
90414 TAAAAAATATTAAAAA
1 TAAAAAATACAAAAAA
90430 TAAAAAA
1 TAAAAAA
90437 ATTGACCTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (16 bp):
TAAAAAATACAAAAAA
Found at i:91450 original size:23 final size:21
Alignment explanation
Indices: 91424--91467 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
91414 TAAACCATTT
*
91424 TATTAATTACTAATAATTTTAAA
1 TATTAATTAAT-AT-ATTTTAAA
*
91447 TATTAGTTAATATATTTTAAA
1 TATTAATTAATATATTTTAAA
91468 AGGCTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 2 0.11
23 9 0.47
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TATTAATTAATATATTTTAAA
Found at i:91677 original size:3 final size:3
Alignment explanation
Indices: 91669--91701 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
91659 ATTTAGTAAC
91669 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
91702 ATCACACTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:93088 original size:29 final size:28
Alignment explanation
Indices: 93056--93176 Score: 82
Period size: 28 Copynumber: 4.2 Consensus size: 28
93046 AAAATGAGAC
93056 TTTTCGGATACTCGGGGGTAAAATGGTAA
1 TTTT-GGATACTCGGGGGTAAAATGGTAA
* * * *
93085 TTTTGAATTCTCGGGGGCAAAGTGGTAA
1 TTTTGGATACTCGGGGGTAAAATGGTAA
* * * *
93113 TTTTGGGAAAATTCGGGGTTAAAAATTG-AA
1 TTTT-GG-ATACTCGGGGGT-AAAATGGTAA
* * * *
93143 TTTTTAGACATTCGGGGGTAAAAGGGTAA
1 -TTTTGGATACTCGGGGGTAAAATGGTAA
93172 TTTTG
1 TTTTG
93177 AGAGTTTCGA
Statistics
Matches: 69, Mismatches: 18, Indels: 11
0.70 0.18 0.11
Matches are distributed among these distances:
28 33 0.48
29 17 0.25
30 10 0.14
31 9 0.13
ACGTcount: A:0.29, C:0.07, G:0.30, T:0.34
Consensus pattern (28 bp):
TTTTGGATACTCGGGGGTAAAATGGTAA
Found at i:93185 original size:29 final size:28
Alignment explanation
Indices: 93067--93179 Score: 79
Period size: 29 Copynumber: 3.9 Consensus size: 28
93057 TTTCGGATAC
* *
93067 TCGGGGGTAAAATGGTAATTTTGA-ATT
1 TCGGGGGTAAAAGGGTAATTTTGAGAAT
* *
93094 CTCGGGGG-CAAAGTGGTAATTTTGGGAAAAT
1 -TCGGGGGTAAAAG-GGTAATTTT--GAGAAT
* ** *
93125 TCGGGGTTAAAA-ATTGAATTTTTAGACAT
1 TCGGGGGTAAAAGGGT-AATTTTGAGA-AT
93154 TCGGGGGTAAAAGGGTAATTTTGAGA
1 TCGGGGGTAAAAGGGTAATTTTGAGA
93180 GTTTCGAGGT
Statistics
Matches: 64, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
27 3 0.05
28 18 0.28
29 23 0.36
30 15 0.23
31 5 0.08
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.32
Consensus pattern (28 bp):
TCGGGGGTAAAAGGGTAATTTTGAGAAT
Found at i:93251 original size:29 final size:29
Alignment explanation
Indices: 93219--93424 Score: 177
Period size: 30 Copynumber: 7.0 Consensus size: 29
93209 ATCCGAGGGC
93219 AAAATGGTAATTTTTGAAAGTTTCGGGGTAA
1 AAAATGG-AATTTTTGAAAGTTTCGGGGT-A
** * * **
93250 AAAATGGAAAATTTGGATG-TAAGAGGGTA
1 AAAATGGAATTTTTGAAAGTTTCG-GGGTA
* *
93279 AAAATGGAATTTTTGGAAGTTTTGGGGGTA
1 AAAATGGAATTTTTGAAAG-TTTCGGGGTA
* * *
93309 AAAATGAAATTTTTGGAAGTTTCGGGGTC
1 AAAATGGAATTTTTGAAAGTTTCGGGGTA
* *
93338 AAAATGGAATTTTTAGAAA-CTTCGAGGTTA
1 AAAATGGAATTTTT-GAAAGTTTCG-GGGTA
*
93368 AAAATGGAATTTTTGGAAA-TTTCGAGGTTA
1 AAAATGGAATTTTT-GAAAGTTTCG-GGGTA
*
93398 AAATTGGAATTTTTGAAAG-TTCGGGGT
1 AAAATGGAATTTTTGAAAGTTTCGGGGT
93425 CTCCGGGATA
Statistics
Matches: 146, Mismatches: 23, Indels: 15
0.79 0.12 0.08
Matches are distributed among these distances:
28 3 0.02
29 52 0.36
30 82 0.56
31 9 0.06
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGAAAGTTTCGGGGTA
Found at i:93324 original size:59 final size:58
Alignment explanation
Indices: 93219--93423 Score: 153
Period size: 59 Copynumber: 3.4 Consensus size: 58
93209 ATCCGAGGGC
* * * *
93219 AAAATGGTAATTTTTGAAAGTTTCGGGGTAAAAAATGGAAA-ATTTGGATG-TAAGAGGGTA
1 AAAATGG-AATTTTTGGAAGTTTGGGGGT-AAAAAT-GAAATTTTTGGAAGTTAAG-GGGTA
** *
93279 AAAATGGAATTTTTGGAAGTTTTGGGGGTAAAAATGAAATTTTTGGAAGTTTCGGGGTC
1 AAAATGGAATTTTTGGAAG-TTTGGGGGTAAAAATGAAATTTTTGGAAGTTAAGGGGTA
* * * * * * * ** *
93338 AAAATGGAATTTTTAGAAACTTCGAGGTTAAAAATGGAATTTTTGGAAATTTCGAGGTTA
1 AAAATGGAATTTTT-GGAAGTTTGGGGGTAAAAATGAAATTTTTGGAAGTTAAG-GGGTA
* * *
93398 AAATTGGAATTTTTGAAAGTTCGGGG
1 AAAATGGAATTTTTGGAAGTTTGGGG
93424 TCTCCGGGAT
Statistics
Matches: 121, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
58 4 0.03
59 81 0.67
60 36 0.30
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGAAATTTTTGGAAGTTAAGGGGTA
Found at i:95264 original size:17 final size:18
Alignment explanation
Indices: 95242--95353 Score: 79
Period size: 17 Copynumber: 6.4 Consensus size: 18
95232 GGCTTTATTT
**
95242 ATTTTAAATTT-ATGATA
1 ATTTTAAATTTGAAAATA
95259 ATTTTAAATTTGAAAATA
1 ATTTTAAATTTGAAAATA
* *
95277 ATTTTAAACTT-AAATTA
1 ATTTTAAATTTGAAAATA
*
95294 AATTTAAATTT-AAAATA
1 ATTTTAAATTTGAAAATA
** ** *
95311 AAATTAAATTTTTAAACA
1 ATTTTAAATTTGAAAATA
* *
95329 AATTT-AATTTTAAAATA
1 ATTTTAAATTTGAAAATA
*
95346 AATTTAAA
1 ATTTTAAA
95354 GGGAGTTTAG
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
17 55 0.70
18 24 0.30
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTTTAAATTTGAAAATA
Found at i:95321 original size:52 final size:52
Alignment explanation
Indices: 95244--95353 Score: 121
Period size: 52 Copynumber: 2.1 Consensus size: 52
95234 CTTTATTTAT
** ** * * *
95244 TTTAAATTTATGATAATTTTAAATTTGAAAATAATTTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAAATTAAATTTGAAAACAAATTTAAACTTAAAATAAA
** **
95296 TTTAAATTTAAAATAAAATTAAATTTTTAAACAAATTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAAATTAAATTTGAAAACAAATTTAAACTTAAAATAAA
95348 TTTAAA
1 TTTAAA
95354 GGGAGTTTAG
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (52 bp):
TTTAAATTTAAAATAAAATTAAATTTGAAAACAAATTTAAACTTAAAATAAA
Found at i:96213 original size:31 final size:31
Alignment explanation
Indices: 96175--96233 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
96165 TTTCGTTATT
* *
96175 ATATTACTAC-TATTTTGTTGTTATTTTTTGG
1 ATATTACT-CTTATTTTATTGTTAATTTTTGG
96206 ATATTACTCTTATTTTATTGTTAATTTT
1 ATATTACTCTTATTTTATTGTTAATTTT
96234 ACTACTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.22, C:0.07, G:0.08, T:0.63
Consensus pattern (31 bp):
ATATTACTCTTATTTTATTGTTAATTTTTGG
Found at i:96357 original size:25 final size:25
Alignment explanation
Indices: 96328--96382 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
96318 AATTTGTTTA
*
96328 TTTAATGTA-TTATATGTATTATATT
1 TTTAACGTATTTA-ATGTATTATATT
96353 TTTAACGTATTTAATGTATTATATT
1 TTTAACGTATTTAATGTATTATATT
96378 TTTAA
1 TTTAA
96383 AATTTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 25 0.89
26 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (25 bp):
TTTAACGTATTTAATGTATTATATT
Found at i:98541 original size:21 final size:21
Alignment explanation
Indices: 98517--98575 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
98507 TAATAAGATA
98517 TATGTTAAGTATGATCTG-TAT
1 TATG-TAAGTATGATCTGTTAT
* *
98538 TATGTAAATACGATCTGTTAT
1 TATGTAAGTATGATCTGTTAT
*
98559 T-TGCTAAGCATGATCTG
1 TATG-TAAGTATGATCTG
98576 AATCTGTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (21 bp):
TATGTAAGTATGATCTGTTAT
Found at i:105002 original size:2 final size:2
Alignment explanation
Indices: 104995--105024 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
104985 CGTATCTGGC
104995 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
105025 TAAATACTAG
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:109863 original size:64 final size:64
Alignment explanation
Indices: 109740--109865 Score: 175
Period size: 64 Copynumber: 2.0 Consensus size: 64
109730 CTCGAACCTT
* * * *
109740 AAAACTCCATTATTATCTAAAATCGAAGCTTCCTTGTTAGCTACCCAAATGATGTTGGTGTTTA
1 AAAACTCCATTATTATATAAAATCGAAGCTTCCTTGTTAGCGACACAAATGATGGTGGTGTTTA
*
109804 AAAACTCCATTATTATATGAAATCGAAGCTTCGCTT-TTAGCGACACAAACT-ATGGTGGTGTT
1 AAAACTCCATTATTATATAAAATCGAAGCTTC-CTTGTTAGCGACACAAA-TGATGGTGGTGTT
109866 AGAAAATTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
64 51 0.93
65 4 0.07
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (64 bp):
AAAACTCCATTATTATATAAAATCGAAGCTTCCTTGTTAGCGACACAAATGATGGTGGTGTTTA
Found at i:110963 original size:15 final size:16
Alignment explanation
Indices: 110943--110973 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
110933 CGAATTAAAT
110943 TTTTTC-CAAAATCCA
1 TTTTTCTCAAAATCCA
110958 TTTTTCTCAAAATCCA
1 TTTTTCTCAAAATCCA
110974 ATTACCCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTTTCTCAAAATCCA
Found at i:112384 original size:28 final size:27
Alignment explanation
Indices: 112327--112384 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
112317 CGATTAAATC
*
112327 TTTTTTTATTTTTGATTTATTTTGTCA
1 TTTTTTTATTTTTGATTTATTTTGTAA
112354 TTTTATTTATTATTT-ATTT-TTTGTGTAA
1 TTTT-TTTATT-TTTGATTTATTT-TGTAA
112382 TTT
1 TTT
112385 ACATTTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 7 0.26
28 17 0.63
29 3 0.11
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (27 bp):
TTTTTTTATTTTTGATTTATTTTGTAA
Found at i:112536 original size:13 final size:14
Alignment explanation
Indices: 112518--112551 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
112508 CATACTCGTA
112518 TTATTATC-TTTAT
1 TTATTATCATTTAT
*
112531 TTATTATCATTTTT
1 TTATTATCATTTAT
112545 TTATTAT
1 TTATTAT
112552 TTTCTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTATCATTTAT
Found at i:112584 original size:25 final size:25
Alignment explanation
Indices: 112556--112603 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
112546 TATTATTTTC
112556 TTATTTATGTTATTAATTGTATTAT
1 TTATTTATGTTATTAATTGTATTAT
* * *
112581 TTATTTGTGTTATTTATTTTATT
1 TTATTTATGTTATTAATTGTATT
112604 TTATTATTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (25 bp):
TTATTTATGTTATTAATTGTATTAT
Found at i:112593 original size:13 final size:13
Alignment explanation
Indices: 112556--112599 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
112546 TATTATTTTC
*
112556 TTATTTATGTTA-
1 TTATTTGTGTTAT
* *
112568 TTAATTGTATTAT
1 TTATTTGTGTTAT
112581 TTATTTGTGTTAT
1 TTATTTGTGTTAT
112594 TTATTT
1 TTATTT
112600 TATTTTATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (13 bp):
TTATTTGTGTTAT
Found at i:116898 original size:2 final size:2
Alignment explanation
Indices: 116891--116924 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
116881 CTGACATTAT
116891 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
116925 GAAATGCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:116965 original size:17 final size:17
Alignment explanation
Indices: 116926--116983 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
116916 ATATATATAG
**
116926 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
116943 AGATGCAGTGACAATAA
1 AAATGCAATGACAATAA
*
116960 AAATGCAATGACATTAA
1 AAATGCAATGACAATAA
*
116977 TAATGCA
1 AAATGCA
116984 GGGATAATTA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.22
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:132198 original size:15 final size:16
Alignment explanation
Indices: 132178--132209 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
132168 GATTGTTTTG
132178 GTAACTCCCTTG-TTT
1 GTAACTCCCTTGATTT
132193 GTAACTCCCTTGATTT
1 GTAACTCCCTTGATTT
132209 G
1 G
132210 AGGAATTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.44
Consensus pattern (16 bp):
GTAACTCCCTTGATTT
Found at i:138238 original size:51 final size:52
Alignment explanation
Indices: 138112--138239 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
138102 TTCATGATTT
*
138112 AATTAAGTCATGCATTATGTAACTCTCATGTTAGTTAAAGTTTGCATCATTA
1 AATTAAGTCATGCATTATGTAACTCTCATATTAGTTAAAGTTTGCATCATTA
*
138164 AATTAAGTCATGCATTATGTAACTCTTATATTAGTTAAAGTTTGCATCA-TA
1 AATTAAGTCATGCATTATGTAACTCTCATATTAGTTAAAGTTTGCATCATTA
*
138215 AATTAAGTCATGCATTAAGTAACTC
1 AATTAAGTCATGCATTATGTAACTC
138240 ATTTGTTGAA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 26 0.36
52 47 0.64
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (52 bp):
AATTAAGTCATGCATTATGTAACTCTCATATTAGTTAAAGTTTGCATCATTA
Found at i:149627 original size:27 final size:27
Alignment explanation
Indices: 149585--149654 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
149575 TGCTAGAAAG
* *
149585 TGGAAACCTTTTTGGCCATCTT-TAAAA
1 TGGAAACCTTTATGGCAAT-TTCTAAAA
*
149612 TGGAAACCTTTATGGCAATTTCTGAAA
1 TGGAAACCTTTATGGCAATTTCTAAAA
*
149639 TGGAAACCTTTGTGGC
1 TGGAAACCTTTATGGC
149655 GTAATCTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 2 0.05
27 36 0.95
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (27 bp):
TGGAAACCTTTATGGCAATTTCTAAAA
Found at i:149764 original size:28 final size:27
Alignment explanation
Indices: 149671--149764 Score: 68
Period size: 28 Copynumber: 3.4 Consensus size: 27
149661 TGAATGAAGA
*
149671 GCCTTTGTGGTGAT-TCATGAAAGGAAAT
1 GCCTTTGTGGCGATCT-ATGAAAGG-AAT
* * *
149699 GTCTTTGTGGC-A-CAATCTGAATGGAAT
1 GCCTTTGTGGCGATC--TATGAAAGGAAT
* *
149726 GCCTCTATGGCGATCTATGGAAAGGAAT
1 GCCTTTGTGGCGATCTAT-GAAAGGAAT
149754 GCCTTTGTGGC
1 GCCTTTGTGGC
149765 TCACTCTATG
Statistics
Matches: 49, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
27 14 0.29
28 33 0.67
29 2 0.04
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (27 bp):
GCCTTTGTGGCGATCTATGAAAGGAAT
Found at i:149865 original size:54 final size:54
Alignment explanation
Indices: 149798--149924 Score: 164
Period size: 54 Copynumber: 2.4 Consensus size: 54
149788 AGCAACTATC
* * * *
149798 TGAAGGAAAAGCCTCTGTGACAATTCTCGAATGAAATGTCTTTGTAGCGTAGTA
1 TGAAAGAAAAGCCTCTATGACAATTCTCGAATGAAATGCCTTTGTAGCGTAATA
*** * *
149852 TGAAAGAAAAGCCTCTATGGTGATTCTTGAATGAAATGCCTTTGTGGCGTAATA
1 TGAAAGAAAAGCCTCTATGACAATTCTCGAATGAAATGCCTTTGTAGCGTAATA
*
149906 TGAAAGAAAAGCCTTTATG
1 TGAAAGAAAAGCCTCTATG
149925 GCATATCATG
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (54 bp):
TGAAAGAAAAGCCTCTATGACAATTCTCGAATGAAATGCCTTTGTAGCGTAATA
Found at i:149909 original size:27 final size:27
Alignment explanation
Indices: 149844--149980 Score: 91
Period size: 27 Copynumber: 5.0 Consensus size: 27
149834 TGTCTTTGTA
* *
149844 GCGTAGTATGAAAGAAAAGCCTCTATG
1 GCGTAATATGAAAGAAAAGCCTTTATG
* * * * * *
149871 GTG-ATTCTTGAATGAAATGCCTTTGTG
1 GCGTAAT-ATGAAAGAAAAGCCTTTATG
149898 GCGTAATATGAAAGAAAAGCCTTTATG
1 GCGTAATATGAAAGAAAAGCCTTTATG
* *
149925 GCAT-ATCATGAAA-ATAAGTTCCTTTATG
1 GCGTAAT-ATGAAAGAAAAG--CCTTTATG
* * * *
149953 GCATAGTGTGAAAGAAAAGCCTATATG
1 GCGTAATATGAAAGAAAAGCCTTTATG
149980 G
1 G
149981 TGAGCCCTAA
Statistics
Matches: 84, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
26 8 0.10
27 52 0.62
28 19 0.23
29 5 0.06
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.29
Consensus pattern (27 bp):
GCGTAATATGAAAGAAAAGCCTTTATG
Found at i:149925 original size:54 final size:54
Alignment explanation
Indices: 149820--149925 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 54
149810 CTCTGTGACA
* *
149820 ATTCTCGAATGAAATGTCTTTGTAGCGTAGTATGAAAGAAAAGCCTCTATGGTG
1 ATTCTCGAATGAAATGCCTTTGTAGCGTAATATGAAAGAAAAGCCTCTATGGTG
* * *
149874 ATTCTTGAATGAAATGCCTTTGTGGCGTAATATGAAAGAAAAGCCTTTATGG
1 ATTCTCGAATGAAATGCCTTTGTAGCGTAATATGAAAGAAAAGCCTCTATGG
149926 CATATCATGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (54 bp):
ATTCTCGAATGAAATGCCTTTGTAGCGTAATATGAAAGAAAAGCCTCTATGGTG
Found at i:151300 original size:40 final size:40
Alignment explanation
Indices: 151241--151357 Score: 137
Period size: 40 Copynumber: 2.9 Consensus size: 40
151231 ACTTGGATAA
* * *
151241 AATTTCAACCTACGGCTTAGCAGGCTTTGTGCCT-GTGTCT
1 AATTTCAAGCTACGGCTTAGCAGGCTTTGAG-CTGGTGACT
* *
151281 AATTTCAAGCTACGACTTAGCAGGCTTTGAGTTGGTGACT
1 AATTTCAAGCTACGGCTTAGCAGGCTTTGAGCTGGTGACT
** * *
151321 AAACTCAAGCTACGGCTTAGCAGGCTATGAGCCGGTG
1 AATTTCAAGCTACGGCTTAGCAGGCTTTGAGCTGGTG
151358 TTGAAATTGA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 1 0.02
40 64 0.98
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (40 bp):
AATTTCAAGCTACGGCTTAGCAGGCTTTGAGCTGGTGACT
Found at i:154268 original size:19 final size:18
Alignment explanation
Indices: 154241--154388 Score: 94
Period size: 18 Copynumber: 8.1 Consensus size: 18
154231 TTTCTCATAA
*
154241 AAAAGATTAAAAAATTAT
1 AAAATATTAAAAAATTAT
*
154259 AAAATCATT-AAAAA-TAA
1 AAAAT-ATTAAAAAATTAT
**
154276 AAAATAAGAAAAAAATTAT
1 AAAAT-ATTAAAAAATTAT
154295 AAAATATTAAAAAA-TATT
1 AAAATATTAAAAAATTA-T
*
154313 AAAAT-TGATAAAAACTTAT
1 AAAATAT--TAAAAAATTAT
154332 AAAA-ATATAAAAAACTTAT
1 AAAATAT-TAAAAAA-TTAT
*
154351 -AAATATTATAAATATCTAAT
1 AAAATATTA-AAAAAT-T-AT
*
154371 AAAAT-TTAATAAATTAT
1 AAAATATTAAAAAATTAT
154388 A
1 A
154389 TTTTTTATAA
Statistics
Matches: 103, Mismatches: 13, Indels: 29
0.71 0.09 0.20
Matches are distributed among these distances:
17 14 0.14
18 41 0.40
19 37 0.36
20 7 0.07
21 4 0.04
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAATATTAAAAAATTAT
Found at i:154308 original size:36 final size:37
Alignment explanation
Indices: 154237--154345 Score: 120
Period size: 36 Copynumber: 3.0 Consensus size: 37
154227 ATATTTTCTC
154237 ATAAAAA-AGATTAAAAAATTATAAAATCATT-AAAAAT
1 ATAAAAATAGA-TAAAAAATTATAAAAT-ATTAAAAAAT
154274 A-AAAAATAAGA-AAAAAATTATAAAATATTAAAAAAT
1 ATAAAAAT-AGATAAAAAATTATAAAATATTAAAAAAT
* * *
154310 ATTAAAATTGATAAAAACTTATAAAA-ATATAAAAAA
1 ATAAAAATAGATAAAAAATTATAAAATAT-TAAAAAA
154346 CTTATAAATA
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
35 3 0.05
36 31 0.49
37 26 0.41
38 3 0.05
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.26
Consensus pattern (37 bp):
ATAAAAATAGATAAAAAATTATAAAATATTAAAAAAT
Found at i:154316 original size:28 final size:28
Alignment explanation
Indices: 154285--154376 Score: 79
Period size: 28 Copynumber: 3.3 Consensus size: 28
154275 AAAAATAAGA
154285 AAAAAATTATAAAATATTAAAAAATATT
1 AAAAAATTATAAAATATTAAAAAATATT
154313 --AAAATTGATAAAA-ACTTATAAAAATA-T
1 AAAAAATT-ATAAAATA-TTA-AAAAATATT
*
154340 AAAAAACTTAT-AAATATT-ATAAATATCT
1 AAAAAA-TTATAAAATATTAAAAAATAT-T
154368 AATAAAATT
1 AA-AAAATT
154377 TAATAAATTA
Statistics
Matches: 53, Mismatches: 1, Indels: 20
0.72 0.01 0.27
Matches are distributed among these distances:
26 13 0.25
27 10 0.19
28 17 0.32
29 11 0.21
30 2 0.04
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (28 bp):
AAAAAATTATAAAATATTAAAAAATATT
Found at i:154442 original size:21 final size:21
Alignment explanation
Indices: 154417--154487 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
154407 GAACATATTT
*
154417 AAAATAT-TTAAAATTTTATAA
1 AAAATATATTAAAATTCT-TAA
*
154438 AAAATATATTATAATTCTT-A
1 AAAATATATTAAAATTCTTAA
** * *
154458 AAAATCATAAAAAAATTGTAAA
1 AAAAT-ATATTAAAATTCTTAA
154480 AAAATATA
1 AAAATATA
154488 AAAATTATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
20 6 0.15
21 20 0.50
22 14 0.35
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (21 bp):
AAAATATATTAAAATTCTTAA
Found at i:155640 original size:17 final size:17
Alignment explanation
Indices: 155618--155662 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
155608 AACCATGCAA
155618 AAAAAATTATAAAAGAT
1 AAAAAATTATAAAAGAT
** *
155635 AAAAAAAAATAAAAGTT
1 AAAAAATTATAAAAGAT
155652 ATAAAAATTAT
1 A-AAAAATTAT
155663 TAAATTTTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (17 bp):
AAAAAATTATAAAAGAT
Found at i:155640 original size:19 final size:18
Alignment explanation
Indices: 155616--155662 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
155606 GCAACCATGC
155616 AAAAAAAATTATAAAAGAT
1 AAAAAAAATTATAAAAG-T
155635 AAAAAAAA--ATAAAAGT
1 AAAAAAAATTATAAAAGT
* *
155651 TATAAAAATTAT
1 AAAAAAAATTAT
155663 TAAATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 7 0.29
17 7 0.29
18 2 0.08
19 8 0.33
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (18 bp):
AAAAAAAATTATAAAAGT
Found at i:155682 original size:27 final size:27
Alignment explanation
Indices: 155652--155704 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
155642 AATAAAAGTT
*
155652 ATAAAAAT-TATTAAATTTTAATAAAAA
1 ATAAAAATAT-TTAAAATTTAATAAAAA
*
155679 ATAAAAATATTTAAAATTTATTAAAA
1 ATAAAAATATTTAAAATTTAATAAAA
155705 TTAGAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
ATAAAAATATTTAAAATTTAATAAAAA
Found at i:155722 original size:46 final size:46
Alignment explanation
Indices: 155617--155723 Score: 108
Period size: 46 Copynumber: 2.3 Consensus size: 46
155607 CAACCATGCA
* * *
155617 AAAAAAATTATAAAAGATAAAAAAAAATAAAAGTTATAAAAATTAT
1 AAAATAATTATAAAAAATAAAAAAAAATAAAAGTTATAAAAATTAG
* * * ** * *
155663 TAAAT-TTTAATAAAAAATAAAAATATTTAAAATTTATTAAAATTAG
1 AAAATAATT-ATAAAAAATAAAAAAAAATAAAAGTTATAAAAATTAG
155709 AAAATAATTATAAAA
1 AAAATAATTATAAAA
155724 TTCGTAAAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
45 2 0.04
46 43 0.91
47 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (46 bp):
AAAATAATTATAAAAAATAAAAAAAAATAAAAGTTATAAAAATTAG
Found at i:155959 original size:19 final size:20
Alignment explanation
Indices: 155922--155959 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
155912 TTTAGTATGA
*
155922 TAATTTTATAATTTGTTTAC
1 TAATTTTATAATTTCTTTAC
155942 TAATTTTAT-ATTTCTTTA
1 TAATTTTATAATTTCTTTA
155960 TATTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TAATTTTATAATTTCTTTAC
Found at i:155976 original size:10 final size:10
Alignment explanation
Indices: 155925--156052 Score: 54
Period size: 10 Copynumber: 12.9 Consensus size: 10
155915 AGTATGATAA
155925 TTTTATAATT
1 TTTTATAATT
155935 TGTTTACTAA--
1 T-TTTA-TAATT
155945 TTTTAT-ATT
1 TTTTATAATT
*
155954 TCTTTATATTT
1 T-TTTATAATT
155965 TTTTATAATT
1 TTTTATAATT
* *
155975 TTCTTATGACT
1 TT-TTATAATT
* * *
155986 TTATAAAACT
1 TTTTATAATT
* *
155996 GTATA-ATATT
1 TTTTATA-ATT
156006 TTTTAT-A-T
1 TTTTATAATT
* *
156014 TTCTAT-ATG
1 TTTTATAATT
156023 TTTTATAATTT
1 TTTTATAA-TT
*
156034 TTTTACAATT
1 TTTTATAATT
156044 TTTTATAAT
1 TTTTATAAT
156053 AGTTTTACGA
Statistics
Matches: 89, Mismatches: 17, Indels: 24
0.68 0.13 0.18
Matches are distributed among these distances:
7 1 0.01
8 8 0.09
9 12 0.13
10 42 0.47
11 23 0.26
12 3 0.03
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTTATAATT
Found at i:156169 original size:4 final size:4
Alignment explanation
Indices: 156160--156189 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
156150 TTATAGATAC
156160 AAAT AAAT AAAT AAAT AAAT AAAT -AAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
156190 GTAATAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:168156 original size:25 final size:25
Alignment explanation
Indices: 168125--168184 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
168115 AACATGAATT
*
168125 TTTTATTTATTCTGTTTAATATATG
1 TTTTATTTATTATGTTTAATATATG
168150 TTTTATTTATTATGTTTAATATATG
1 TTTTATTTATTATGTTTAATATATG
168175 TTTTATTTAT
1 TTTTATTTAT
168185 ACCTATTCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.67
Consensus pattern (25 bp):
TTTTATTTATTATGTTTAATATATG
Found at i:171197 original size:17 final size:17
Alignment explanation
Indices: 171162--171204 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
171152 CTCCCTTGAC
* *
171162 CTTTAACCTTCCATCTT
1 CTTTAACTTTCCATATT
*
171179 CTTTAACTTTTCATATT
1 CTTTAACTTTCCATATT
171196 CTTGTAACT
1 CTT-TAACT
171205 ACTTTTTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (17 bp):
CTTTAACTTTCCATATT
Found at i:174701 original size:14 final size:14
Alignment explanation
Indices: 174682--174708 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
174672 TTATAAAATA
174682 AAAGAACAAAGAGT
1 AAAGAACAAAGAGT
174696 AAAGAACAAAGAG
1 AAAGAACAAAGAG
174709 AATGGGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.22, T:0.04
Consensus pattern (14 bp):
AAAGAACAAAGAGT
Found at i:175768 original size:9 final size:9
Alignment explanation
Indices: 175750--175781 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
175740 CTAATTATGG
175750 TAAA-ATTT
1 TAAATATTT
175758 TAAATATTT
1 TAAATATTT
175767 TAAATATTT
1 TAAATATTT
175776 TAAATA
1 TAAATA
175782 AATGAACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TAAATATTT
Found at i:176856 original size:3 final size:3
Alignment explanation
Indices: 176848--176881 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
176838 AATATTAAAA
*
176848 ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
176882 AGTCATTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:193105 original size:16 final size:16
Alignment explanation
Indices: 193084--193121 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
193074 TAACAGTCTT
193084 GTTGACGTGGCGGTTA
1 GTTGACGTGGCGGTTA
193100 GTTGACGTGGCGGTTA
1 GTTGACGTGGCGGTTA
193116 GTTGAC
1 GTTGAC
193122 TAACTACACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.13, C:0.13, G:0.42, T:0.32
Consensus pattern (16 bp):
GTTGACGTGGCGGTTA
Found at i:193243 original size:20 final size:19
Alignment explanation
Indices: 193222--193322 Score: 71
Period size: 20 Copynumber: 5.6 Consensus size: 19
193212 AGCAAATGAT
193222 TTTAAAATTATTAAAATTA
1 TTTAAAATTATTAAAATTA
193241 TTT----TT-TTAAAA-TA
1 TTTAAAATTATTAAAATTA
193254 --TAAAATTATTAAAATTA
1 TTTAAAATTATTAAAATTA
193271 TTTTAAAATTATTTTTTAAAA-TA
1 -TTTAAAATTA----TTAAAATTA
193294 --TAAAATTATTAAAATTA
1 TTTAAAATTATTAAAATTA
193311 TTTTAAAATTAT
1 -TTTAAAATTAT
193323 AATCATCATC
Statistics
Matches: 65, Mismatches: 0, Indels: 33
0.66 0.00 0.34
Matches are distributed among these distances:
11 1 0.02
13 2 0.03
14 6 0.09
15 4 0.06
16 12 0.18
17 4 0.06
19 3 0.05
20 25 0.38
23 2 0.03
24 6 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAAAATTATTAAAATTA
Found at i:193278 original size:11 final size:10
Alignment explanation
Indices: 193254--193322 Score: 58
Period size: 11 Copynumber: 6.9 Consensus size: 10
193244 TTTTAAAATA
193254 TAAAATTA-T
1 TAAAATTATT
193263 TAAAATTATTT
1 TAAAATTA-TT
193274 TAAAATTATTTTT
1 TAAAATTA---TT
193287 TAAAA-TA--
1 TAAAATTATT
193294 TAAAATTA-T
1 TAAAATTATT
193303 TAAAATTATTT
1 TAAAATTA-TT
193314 TAAAATTAT
1 TAAAATTAT
193323 AATCATCATC
Statistics
Matches: 52, Mismatches: 0, Indels: 15
0.78 0.00 0.22
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 16 0.31
10 1 0.02
11 18 0.35
12 2 0.04
13 8 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TAAAATTATT
Found at i:193297 original size:40 final size:40
Alignment explanation
Indices: 193223--193322 Score: 177
Period size: 40 Copynumber: 2.5 Consensus size: 40
193213 GCAAATGATT
193223 TTAAAATTA--TTAAAATTATTTTTTTAAAATATAAAATTA
1 TTAAAATTATTTTAAAATTA-TTTTTTAAAATATAAAATTA
193262 TTAAAATTATTTTAAAATTATTTTTTAAAATATAAAATTA
1 TTAAAATTATTTTAAAATTATTTTTTAAAATATAAAATTA
193302 TTAAAATTATTTTAAAATTAT
1 TTAAAATTATTTTAAAATTAT
193323 AATCATCATC
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
39 9 0.15
40 41 0.69
41 9 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (40 bp):
TTAAAATTATTTTAAAATTATTTTTTAAAATATAAAATTA
Found at i:193373 original size:6 final size:6
Alignment explanation
Indices: 193362--193396 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
193352 GGTTTTTTTT
193362 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTT
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTT
193397 GTTTCTCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CCCTTC
Found at i:194172 original size:30 final size:31
Alignment explanation
Indices: 194138--194200 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 31
194128 GGTGAATTTA
194138 ATGAG-AAGAAGTGGTGTTAGACGGAAAATG
1 ATGAGAAAGAAGTGGTGTTAGACGGAAAATG
*
194168 ATGAGAATAAGAAGTGGTGTTAGATGGAAAATG
1 ATGAG-A-AAGAAGTGGTGTTAGACGGAAAATG
194201 GGTTAGAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 5 0.17
33 24 0.83
ACGTcount: A:0.41, C:0.02, G:0.35, T:0.22
Consensus pattern (31 bp):
ATGAGAAAGAAGTGGTGTTAGACGGAAAATG
Found at i:195989 original size:43 final size:43
Alignment explanation
Indices: 195928--196205 Score: 258
Period size: 43 Copynumber: 6.5 Consensus size: 43
195918 CGCTTTCCCA
* ** *
195928 TTTTCTCACAAATACCGCTAAATAACATAGTCTTTAGCGACGC
1 TTTTCCCACAAACGCCGCTAAAGAACATAGTCTTTAGCGACGC
* * *
195971 TTCTCCCACAAACGCCGCTAAAGAACATAGTCTTTAGCGGCGA
1 TTTTCCCACAAACGCCGCTAAAGAACATAGTCTTTAGCGACGC
* *
196014 TTTTCCAACAAATGCCGCTAAAGAACAT-GATCTTTAGCGACGC
1 TTTTCCCACAAACGCCGCTAAAGAACATAG-TCTTTAGCGACGC
* *
196057 TTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCTG-CGT
1 TTTTCCCACAAACGCCGCTAAAGAACATAGTCTTTAGC-GACGC
* * * * * * *
196100 TTTTACCACAAGCGCCACTAAAGAACATGGTCTTTAGTTG-TGT
1 TTTTCCCACAAACGCCGCTAAAGAACATAGTCTTTAG-CGACGC
* * * * *
196143 TTTTCACGCAAACGCCACTATAGAACAT-GATCTTTAGCGACGT
1 TTTTCCCACAAACGCCGCTAAAGAACATAG-TCTTTAGCGACGC
* * *
196186 TTTTTCCATAAACACCGCTA
1 TTTTCCCACAAACGCCGCTA
196206 TCATTAACAG
Statistics
Matches: 196, Mismatches: 33, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
42 3 0.02
43 191 0.97
44 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (43 bp):
TTTTCCCACAAACGCCGCTAAAGAACATAGTCTTTAGCGACGC
Found at i:196072 original size:86 final size:85
Alignment explanation
Indices: 195927--196136 Score: 287
Period size: 86 Copynumber: 2.4 Consensus size: 85
195917 GCGCTTTCCC
* *
195927 ATTTTCTCACAAATACCGCTAAATAACAT-AGTCTTTAGCGACGCTTCTCCCACAAACGCCGCTA
1 ATTTTC-CACAAATGCCGCTAAAGAACATGA-TCTTTAGCGACGCTTCTCCCACAAACGCCGCTA
195991 AAGAACATAGTCTTTAGCGGCG
64 AAGAACATAGTCTTTAGCGGCG
*
196013 ATTTTCCAACAAATGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTCCCACAAACGCCGCTAA
1 ATTTTCC-ACAAATGCCGCTAAAGAACATGATCTTTAGCGACGCTTCTCCCACAAACGCCGCTAA
* *
196078 AGAACATGGTCTTTAGCTGCG
65 AGAACATAGTCTTTAGCGGCG
* ** * *
196099 TTTTTACCACAAGCGCCACTAAAGAACATGGTCTTTAG
1 ATTTT-CCACAAATGCCGCTAAAGAACATGATCTTTAG
196137 TTGTGTTTTT
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
85 1 0.01
86 107 0.96
87 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (85 bp):
ATTTTCCACAAATGCCGCTAAAGAACATGATCTTTAGCGACGCTTCTCCCACAAACGCCGCTAAA
GAACATAGTCTTTAGCGGCG
Found at i:196133 original size:129 final size:129
Alignment explanation
Indices: 195928--196205 Score: 326
Period size: 129 Copynumber: 2.2 Consensus size: 129
195918 CGCTTTCCCA
* * * * *
195928 TTTTCTCACAAATACCGCTAAATAACATAGTCTTTAGCGACGCTTCTCCCACAAACGCCGCTAAA
1 TTTTCCCACAAACACCGCTAAAGAACATAGTCTTTAGCGACGCTTCTACCACAAACGCCACTAAA
* *
195993 GAACATAGTCTTTAGCGGCGATTTTCCA-ACAAATGCCGCTAAAGAACATGATCTTTAGCGACGC
66 GAACATAGTCTTTAGCGGCG-TTTTCCACACAAACGCCACTAAAGAACATGATCTTTAGCGACGC
* * * * *
196057 TTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCTG-CGTTTTTACCACAAGCGCCACTAA
1 TTTTCCCACAAACACCGCTAAAGAACATAGTCTTTAGC-GACGCTTCTACCACAAACGCCACTAA
* ** * * * * *
196121 AGAACATGGTCTTTAGTTGTGTTTTTCACGCAAACGCCACTATAGAACATGATCTTTAGCGACGT
65 AGAACATAGTCTTTAGCGGCGTTTTCCACACAAACGCCACTAAAGAACATGATCTTTAGCGACGC
* *
196186 TTTTTCCATAAACACCGCTA
1 TTTTCCCACAAACACCGCTA
196206 TCATTAACAG
Statistics
Matches: 124, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
128 6 0.05
129 117 0.94
130 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (129 bp):
TTTTCCCACAAACACCGCTAAAGAACATAGTCTTTAGCGACGCTTCTACCACAAACGCCACTAAA
GAACATAGTCTTTAGCGGCGTTTTCCACACAAACGCCACTAAAGAACATGATCTTTAGCGACGC
Done.