Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009446.1 Kokia drynarioides strain JFW-HI SEQ_124153, 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: 182614
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:664 original size:30 final size:30
Alignment explanation
Indices: 628--692 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
618 CAACATAACA
*
628 AACAAATATCTCTAAAATAGTAACAAAATT
1 AACAAATATCTCTAAAATAATAACAAAATT
* *
658 AACAAATGTCTCTTAAATAATAACAAAATT
1 AACAAATATCTCTAAAATAATAACAAAATT
688 AACAA
1 AACAA
693 TAAAATAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.26
Consensus pattern (30 bp):
AACAAATATCTCTAAAATAATAACAAAATT
Found at i:2042 original size:44 final size:44
Alignment explanation
Indices: 1979--2066 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
1969 AAACCATAAA
1979 ATAAGTTCGAGAGTCGATTACACATAAGGAAGGATTAGCACTCT
1 ATAAGTTCGAGAGTCGATTACACATAAGGAAGGATTAGCACTCT
2023 ATAAGTTCGAGAGTCGATTACACATAAGGAAGGATTAGCACTCT
1 ATAAGTTCGAGAGTCGATTACACATAAGGAAGGATTAGCACTCT
2067 TACATGCTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (44 bp):
ATAAGTTCGAGAGTCGATTACACATAAGGAAGGATTAGCACTCT
Found at i:2687 original size:30 final size:30
Alignment explanation
Indices: 2651--2880 Score: 202
Period size: 30 Copynumber: 7.7 Consensus size: 30
2641 CATTAAAATT
* *
2651 GGGTCAAAATTGAACTTTTGGAAACTTTAA
1 GGGTCAAAATTGAATTTTTGGAAAATTTAA
*
2681 GGGTC-AAATCGAAATTTTTGGAAAATTTAA
1 GGGTCAAAATTG-AATTTTTGGAAAATTTAA
**
2711 GGGTC-AAATAAAATTTTTTGGAAAATTTAA
1 GGGTCAAAATTGAA-TTTTTGGAAAATTTAA
** * **
2741 -GGTCAATTTTGAATTTTT-GAAAAGATCGA
1 GGGTCAAAATTGAATTTTTGGAAAA-TTTAA
* * *
2770 GGGTCAAATTTGAATTTTTTGAAAATTTGA
1 GGGTCAAAATTGAATTTTTGGAAAATTTAA
* * *
2800 GGGTC-AAATTAAAATTTTTGGAAAGTTTTA
1 GGGTCAAAATT-GAATTTTTGGAAAATTTAA
* *
2830 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
1 GGGTCAAAATTGAATTTTTGGAAAATTTAA
* *
2860 GGGTTAAAACT-AATTTTTGGA
1 GGGTCAAAATTGAATTTTTGGA
2881 TAGTTTGGGG
Statistics
Matches: 166, Mismatches: 26, Indels: 17
0.79 0.12 0.08
Matches are distributed among these distances:
28 5 0.03
29 32 0.19
30 120 0.72
31 9 0.05
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (30 bp):
GGGTCAAAATTGAATTTTTGGAAAATTTAA
Found at i:2875 original size:89 final size:88
Alignment explanation
Indices: 2651--2926 Score: 286
Period size: 89 Copynumber: 3.1 Consensus size: 88
2641 CATTAAAATT
* * * * *
2651 GGGTCAAAATTGAACTTTTGGAAACTTTAAGGGTCAAATCGAAATTTTTGGAAAATTTAAGGGTC
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAAGGGTCAAATC-TAATTTTTGGAAAATTTGAGGGTC
*
2716 AAATAAAATTTTTTGGAAA-ATTTA
65 AAATAAAA-TTTTTGGAAAGTTTTA
* * * * ** * *
2740 AGGTCAATTTTGAATTTTTGAAAAGATCGAGGGTCAAATTTGAATTTTTTGAAAATTTGAGGGTC
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAAGGGTCAAATCT-AATTTTTGGAAAATTTGAGGGTC
2805 AAATTAAAATTTTTGGAAAGTTTTA
65 AAA-TAAAATTTTTGGAAAGTTTTA
* * * * *
2830 GGGTCAAATTTGAATTTTTGGAAAGTTTAAGGGTTAAAACTAATTTTTGGATAGTTTGGGGGTCA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAAGGGTCAAATCTAATTTTTGGAAAATTTGAGGGTCA
* *
2895 AA-ACATAATTTTTGGATAGTTTGA
66 AATA-A-AATTTTTGGAAAGTTTTA
*
2919 TGGTCAAA
1 GGGTCAAA
2927 ACATAATTTT
Statistics
Matches: 152, Mismatches: 30, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
87 1 0.01
88 1 0.01
89 109 0.72
90 41 0.27
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (88 bp):
GGGTCAAATTTGAATTTTTGGAAAGTTTAAGGGTCAAATCTAATTTTTGGAAAATTTGAGGGTCA
AATAAAATTTTTGGAAAGTTTTA
Found at i:2885 original size:29 final size:30
Alignment explanation
Indices: 2666--2966 Score: 179
Period size: 30 Copynumber: 10.1 Consensus size: 30
2656 AAAATTGAAC
* * *
2666 TTTTGGAAACTTTAAGGGTCAAATCGA-AAT
1 TTTTGGAAAGTTTGAGGGTCAAAAC-ATAAT
* *
2696 TTTTGGAAAATTTAAGGGTCAAATA-A-AATT
1 TTTTGGAAAGTTTGAGGGTCAAA-ACATAA-T
* * ***
2726 TTTTGGAAAATTT-AAGGTC-AATTTTGAAT
1 TTTTGGAAAGTTTGAGGGTCAAAACAT-AAT
* * * **
2755 TTTTGAAAAGATCGAGGGTC-AAATTTGAAT
1 TTTTGGAAAGTTTGAGGGTCAAAACAT-AAT
* * ** *
2785 TTTTTGAAAATTTGAGGGTCAAATTAAAAT
1 TTTTGGAAAGTTTGAGGGTCAAAACATAAT
* **
2815 TTTTGGAAAGTTTTAGGGTC-AAATTTGAAT
1 TTTTGGAAAGTTTGAGGGTCAAAACAT-AAT
* *
2845 TTTTGGAAAGTTTAAGGGTTAAAAC-TAAT
1 TTTTGGAAAGTTTGAGGGTCAAAACATAAT
* *
2874 TTTTGGATAGTTTGGGGGTCAAAACATAAT
1 TTTTGGAAAGTTTGAGGGTCAAAACATAAT
* *
2904 TTTTGGATAGTTTGATGGTCAAAACATAAT
1 TTTTGGAAAGTTTGAGGGTCAAAACATAAT
* * * *
2934 TTTT-AAATAGATTGGGGGTCAAAAAATAAT
1 TTTTGGAA-AGTTTGAGGGTCAAAACATAAT
2964 TTT
1 TTT
2967 AAAATAAAGT
Statistics
Matches: 220, Mismatches: 40, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
28 2 0.01
29 46 0.21
30 166 0.75
31 6 0.03
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (30 bp):
TTTTGGAAAGTTTGAGGGTCAAAACATAAT
Found at i:2896 original size:119 final size:119
Alignment explanation
Indices: 2651--2878 Score: 280
Period size: 119 Copynumber: 1.9 Consensus size: 119
2641 CATTAAAATT
* *
2651 GGGTCAAAATTGAACTTTTGGAAACTTTAAGGGTCAAATCGAAATTTTTGGAAAATTTAAGGGTC
1 GGGTCAAAATTGAACTTTTGGAAAATTTAAGGGTCAAATCAAAATTTTTGGAAAATTTAAGGGTC
***
2716 AAATAAAATTTTTTGGAAAATTTAAGGTCAATTTTGAATTTTTGAAAAGATCGA
66 AAATAAAATTTTTTGGAAAATTTAAGGTCAAAACTGAATTTTTGAAAAGATCGA
* * * * * * *
2770 GGGTCAAATTTGAATTTTTTGAAAATTTGAGGGTCAAATTAAAATTTTTGGAAAGTTTTAGGGTC
1 GGGTCAAAATTGAACTTTTGGAAAATTTAAGGGTCAAATCAAAATTTTTGGAAAATTTAAGGGTC
** * *
2835 AAATTTGAA-TTTTTGGAAAGTTTAAGGGTTAAAACT-AATTTTTG
66 AAA-TAAAATTTTTTGGAAAATTTAA-GGTCAAAACTGAATTTTTG
2879 GATAGTTTGG
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
119 82 0.90
120 9 0.10
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.38
Consensus pattern (119 bp):
GGGTCAAAATTGAACTTTTGGAAAATTTAAGGGTCAAATCAAAATTTTTGGAAAATTTAAGGGTC
AAATAAAATTTTTTGGAAAATTTAAGGTCAAAACTGAATTTTTGAAAAGATCGA
Found at i:4915 original size:79 final size:78
Alignment explanation
Indices: 4789--4982 Score: 230
Period size: 79 Copynumber: 2.5 Consensus size: 78
4779 TAGCTTTAGG
* * *
4789 GGTAAAAGATTAGATGATCTTTAATCT--GCCATGTAGTTAGGGTAAAGATCAGATGGTCTTCAA
1 GGTAAAAGATTAGATTA-CTTCAATCTACCCCATG--GTTAGGGTAAAGATCAGATGGTCTTCAA
4852 TCTGCCCTCTAGTTAA
63 TCTGCCCTCTAGTTAA
* * * **
4868 GGTAAAATATTGGATTACTTCAGTCTGTCCCATGGTTAGGGTAAAAGATCAGATGGTCTTCAATC
1 GGTAAAAGATTAGATTACTTCAATCTACCCCATGGTTAGGGT-AAAGATCAGATGGTCTTCAATC
* * *
4933 TGCCCTTTGGTTAT
65 TGCCCTCTAGTTAA
*
4947 GGTAAAAGATTAGATTGCTTCAATCTACCCCATGGT
1 GGTAAAAGATTAGATTACTTCAATCTACCCCATGGT
4983 CGAGGTAAGA
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
78 15 0.15
79 77 0.79
80 5 0.05
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (78 bp):
GGTAAAAGATTAGATTACTTCAATCTACCCCATGGTTAGGGTAAAGATCAGATGGTCTTCAATCT
GCCCTCTAGTTAA
Found at i:4990 original size:39 final size:39
Alignment explanation
Indices: 4788--4982 Score: 148
Period size: 39 Copynumber: 4.9 Consensus size: 39
4778 ATAGCTTTAG
*
4788 GGGTAAAAGATTAGA-TGATCTTTAATCTG--CCATGTAGTTA
1 GGGTAAAAGATTAGATTG--CTTCAATCTGCCCCATG--GTTA
* * *
4828 GGGT-AAAGATCAGATGGTCTTCAATCTGCCCTC-TAGTTA
1 GGGTAAAAGATTAGATTG-CTTCAATCTGCCC-CATGGTTA
* * * * * *
4867 AGGTAAAATATTGGATTACTTCAGTCTGTCCCATGGTTA
1 GGGTAAAAGATTAGATTGCTTCAATCTGCCCCATGGTTA
* * **
4906 GGGTAAAAGATCAGATGGTCTTCAATCTGCCCTTTGGTTA
1 GGGTAAAAGATTAGATTG-CTTCAATCTGCCCCATGGTTA
* *
4946 TGGTAAAAGATTAGATTGCTTCAATCTACCCCATGGT
1 GGGTAAAAGATTAGATTGCTTCAATCTGCCCCATGGT
4983 CGAGGTAAGA
Statistics
Matches: 119, Mismatches: 29, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
38 1 0.01
39 70 0.59
40 45 0.38
41 2 0.02
42 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (39 bp):
GGGTAAAAGATTAGATTGCTTCAATCTGCCCCATGGTTA
Found at i:5088 original size:50 final size:50
Alignment explanation
Indices: 5032--5242 Score: 219
Period size: 50 Copynumber: 4.2 Consensus size: 50
5022 AGCTTCAGGA
* * * *
5032 GTATAAGATTTGTCC-TTGCGACTTCAATCTTCCCCTCTATAGCTTTAGGT
1 GTATAAGATTCG-CCTTTGCGACTTCAATCTGCCCCTCTACAACTTTAGGT
* * *
5082 GAATAAGATTCGCCTTTACGACTTCAATCTGCCTCTCTACAACTTTAGGT
1 GTATAAGATTCGCCTTTGCGACTTCAATCTGCCCCTCTACAACTTTAGGT
* * * *
5132 GTATGAGATTCGTCTTTGC-ATTTTCAATCTGCCCCTCTGCAACTTTAGGT
1 GTATAAGATTCGCCTTTGCGA-CTTCAATCTGCCCCTCTACAACTTTAGGT
* * * ** * *
5182 GTATGAGATTCGCCTTTGCGGCTTCAATCCGTTCCTCTACAGCTTTAGGG
1 GTATAAGATTCGCCTTTGCGACTTCAATCTGCCCCTCTACAACTTTAGGT
*
5232 GTATAGGATTC
1 GTATAAGATTC
5243 ATCGTTCTAT
Statistics
Matches: 133, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
49 3 0.02
50 130 0.98
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.37
Consensus pattern (50 bp):
GTATAAGATTCGCCTTTGCGACTTCAATCTGCCCCTCTACAACTTTAGGT
Found at i:16919 original size:29 final size:29
Alignment explanation
Indices: 16798--16950 Score: 141
Period size: 30 Copynumber: 5.2 Consensus size: 29
16788 CATTAAAATC
* *
16798 GGGTCAAATTTGAACTTTTGGAAACTTTAG
1 GGGTCAAATTTGAATTTTTGGAAA-TTTAA
***
16828 GGGTCAAATCAAAATTTTTGGAAAATTT-A
1 GGGTCAAATTTGAATTTTTGG-AAATTTAA
* * *
16857 GGGATCAATTTTGACTTTTTGGAAAGTTCAA
1 GGG-TCAAATTTGAATTTTTGGAAA-TTTAA
16888 GGGTCAAATTTGAATTTTTGGAAATTTAA
1 GGGTCAAATTTGAATTTTTGGAAATTTAA
**
16917 GGGTCAAAAAAT-AATTTTTGGACAATTT-A
1 GGGTC-AAATTTGAATTTTTGGA-AATTTAA
16946 GGGTC
1 GGGTC
16951 GAAACATAAT
Statistics
Matches: 101, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
29 31 0.31
30 63 0.62
31 7 0.07
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.37
Consensus pattern (29 bp):
GGGTCAAATTTGAATTTTTGGAAATTTAA
Found at i:16959 original size:29 final size:29
Alignment explanation
Indices: 16900--17023 Score: 124
Period size: 29 Copynumber: 4.2 Consensus size: 29
16890 GTCAAATTTG
16900 AATTTTTGGA-AATTTAAGGGTCAAAAAAT
1 AATTTTTGGACAATTT-AGGGTCAAAAAAT
* *
16929 AATTTTTGGACAATTTAGGGTCGAAACAT
1 AATTTTTGGACAATTTAGGGTCAAAAAAT
* * * * * *
16958 AATTTTTAGATAGTTTGGTGGTTAAAATAT
1 AATTTTTGGACAATTTAG-GGTCAAAAAAT
* *
16988 AATTTTTTGAACAATTTGGGGTCAAAAAAT
1 AA-TTTTTGGACAATTTAGGGTCAAAAAAT
17018 AATTTT
1 AATTTT
17024 AAAATAAAGC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
29 39 0.51
30 26 0.34
31 12 0.16
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.40
Consensus pattern (29 bp):
AATTTTTGGACAATTTAGGGTCAAAAAAT
Found at i:17020 original size:30 final size:29
Alignment explanation
Indices: 16900--17023 Score: 115
Period size: 30 Copynumber: 4.2 Consensus size: 29
16890 GTCAAATTTG
* *
16900 AATTTTTGGA-AATTTAAGGGTCAAAAAAT
1 AATTTTTTGACAATTT-GGGGTCAAAAAAT
* * * *
16929 AATTTTTGGACAATTTAGGGTCGAAACAT
1 AATTTTTTGACAATTTGGGGTCAAAAAAT
* * * * *
16958 AATTTTTAGATAGTTTGGTGGTTAAAATAT
1 AATTTTTTGACAATTTGG-GGTCAAAAAAT
16988 AATTTTTTGAACAATTTGGGGTCAAAAAAT
1 AATTTTTTG-ACAATTTGGGGTCAAAAAAT
17018 AATTTT
1 AATTTT
17024 AAAATAAAGC
Statistics
Matches: 78, Mismatches: 14, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
29 35 0.45
30 36 0.46
31 7 0.09
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.40
Consensus pattern (29 bp):
AATTTTTTGACAATTTGGGGTCAAAAAAT
Found at i:17929 original size:18 final size:18
Alignment explanation
Indices: 17886--17930 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
17876 TTCTTTTGTA
*
17886 TATATATATTTTCCTTTT
1 TATATATATTTTCCTGTT
* * *
17904 TGTGTATATTTTCGTGTT
1 TATATATATTTTCCTGTT
17922 TATATATAT
1 TATATATAT
17931 CTTTTTACAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.62
Consensus pattern (18 bp):
TATATATATTTTCCTGTT
Found at i:18158 original size:24 final size:22
Alignment explanation
Indices: 18120--18172 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 22
18110 TTTAGGTTAC
18120 TTGGGCTTAGTTTAGGTTGGGCTT
1 TTGGG-TTAGTTTAGGTTGGG-TT
*
18144 TTAGGGTTAGTTTAGTTTGGGTT
1 TT-GGGTTAGTTTAGGTTGGGTT
18167 TTGGGT
1 TTGGGT
18173 AAATGGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 16 0.59
25 3 0.11
ACGTcount: A:0.09, C:0.04, G:0.38, T:0.49
Consensus pattern (22 bp):
TTGGGTTAGTTTAGGTTGGGTT
Found at i:18227 original size:16 final size:16
Alignment explanation
Indices: 18206--18236 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18196 GTTTTTTAAT
18206 TTTATTTATTTATTTG
1 TTTATTTATTTATTTG
*
18222 TTTATTTGTTTATTT
1 TTTATTTATTTATTT
18237 ATCTATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTATTTATTTATTTG
Found at i:18265 original size:19 final size:17
Alignment explanation
Indices: 18241--18284 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
18231 TTATTTATCT
18241 ATAAAATAATAATAAATAA
1 ATAAAATAA-AATAAA-AA
18260 ATAAAAATAAAATAAAAA
1 AT-AAAATAAAATAAAAA
*
18278 ACAAAAT
1 ATAAAAT
18285 TGGATTGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 8 0.35
20 7 0.30
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (17 bp):
ATAAAATAAAATAAAAA
Found at i:18595 original size:13 final size:13
Alignment explanation
Indices: 18571--18602 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
18561 TATTAAAGAG
18571 TTTAAA-CAAAAT
1 TTTAAATCAAAAT
18583 TTTAAATCAAAAT
1 TTTAAATCAAAAT
18596 TTTAAAT
1 TTTAAAT
18603 TAAACCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTAAATCAAAAT
Found at i:19438 original size:16 final size:18
Alignment explanation
Indices: 19399--19432 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19389 TAAGTTTATA
19399 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
19416 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
19433 AATTTAGAAC
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:20165 original size:22 final size:23
Alignment explanation
Indices: 20137--20185 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
20127 GGTGATTTAA
*
20137 GAAAAAAAATACAAAAA-TAAAT
1 GAAAAAAAAGACAAAAATTAAAT
20159 GAAAAAAAAGACAAAAATTTAAAT
1 GAAAAAAAAGACAAAAA-TTAAAT
20183 GAA
1 GAA
20186 TTAATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 16 0.67
24 8 0.33
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.14
Consensus pattern (23 bp):
GAAAAAAAAGACAAAAATTAAAT
Found at i:20936 original size:16 final size:17
Alignment explanation
Indices: 20899--20939 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
20889 TATTATATTA
*
20899 TTTTA-ATATTTAATAT
1 TTTTATATATTGAATAT
20915 TTTTATATATTGAAT-T
1 TTTTATATATTGAATAT
20931 TTTTATATA
1 TTTTATATA
20940 ATTGTCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTATATATTGAATAT
Found at i:21056 original size:15 final size:16
Alignment explanation
Indices: 21031--21062 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
21021 ATTTTATGAT
21031 ATATAAAAATATTATA
1 ATATAAAAATATTATA
21047 ATAT-AAAATATTATA
1 ATATAAAAATATTATA
21062 A
1 A
21063 ACATAAAATG
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAAATATTATA
Found at i:21068 original size:16 final size:15
Alignment explanation
Indices: 21036--21071 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
21026 ATGATATATA
*
21036 AAAATATTATAATAT
1 AAAATATTATAACAT
21051 AAAATATTATAAACAT
1 AAAATATTAT-AACAT
21067 AAAAT
1 AAAAT
21072 GAGTTAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATATTATAACAT
Found at i:22177 original size:59 final size:61
Alignment explanation
Indices: 22080--22277 Score: 185
Period size: 62 Copynumber: 3.3 Consensus size: 61
22070 ATTTTTTAGG
* * * * * * *
22080 TAAATAA-TTATTATTATTATAATT-TATTACTATCAAATATAATTTAATTAA-A-AGTAA
1 TAAATAATTTAATAATATTTTAATTATATTATTATTAAATATAATTTAATAAATATAATAA
*
22137 TAAATAATTTAATCATATTTTAATTATATTATTATTAAATATAATTTAATAAATATAATAA
1 TAAATAATTTAATAATATTTTAATTATATTATTATTAAATATAATTTAATAAATATAATAA
* * * *
22198 TATATAATTTAATAATATTTTTAA-TATAATTATTATTAAAATATGAA-CTAGTAAA-ATAAAAA
1 TAAATAATTTAATAATA-TTTTAATTAT-ATTATTATT-AAATAT-AATTTAATAAATATAATAA
*
22260 TATATAATATTAATAATA
1 TAAATAAT-TTAATAATA
22278 AATTTTAAAA
Statistics
Matches: 119, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
57 7 0.06
58 13 0.11
59 24 0.20
60 1 0.01
61 22 0.18
62 29 0.24
63 21 0.18
64 2 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (61 bp):
TAAATAATTTAATAATATTTTAATTATATTATTATTAAATATAATTTAATAAATATAATAA
Found at i:22179 original size:15 final size:15
Alignment explanation
Indices: 22151--22237 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 15
22141 TAATTTAATC
*
22151 ATATT-TTAATTATA
1 ATATTATTAAATATA
*
22165 TTATTATTAAATATA
1 ATATTATTAAATATA
*
22180 AT-TTAATAAATATA
1 ATATTATTAAATATA
* *
22194 ATAATATATAATTTAATA
1 ATATTAT-TAA-AT-ATA
*
22212 ATATT-TTTAATATA
1 ATATTATTAAATATA
22226 ATTATTATTAAA
1 A-TATTATTAAA
22238 ATATGAACTA
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
14 21 0.38
15 16 0.29
16 9 0.16
17 2 0.04
18 7 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTATTAAATATA
Found at i:22222 original size:24 final size:24
Alignment explanation
Indices: 22166--22225 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
22156 TTAATTATAT
22166 TATTATTAA-ATATAATTTAATAA
1 TATTATTAATATATAATTTAATAA
*
22189 -ATATAATAATATATAATTTAATAA
1 TAT-TATTAATATATAATTTAATAA
*
22213 TATTTTTAATATA
1 TATTATTAATATA
22226 ATTATTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 2 0.06
23 5 0.16
24 22 0.71
25 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TATTATTAATATATAATTTAATAA
Found at i:30541 original size:20 final size:20
Alignment explanation
Indices: 30516--30554 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
30506 GTGTACCTAA
30516 TTGCACATTT-GTGCCCCTGT
1 TTGCAC-TTTAGTGCCCCTGT
30536 TTGCACTTTAGTGCCCCTG
1 TTGCACTTTAGTGCCCCTG
30555 AATGCACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.10, C:0.31, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCACTTTAGTGCCCCTGT
Found at i:30560 original size:20 final size:19
Alignment explanation
Indices: 30479--30561 Score: 53
Period size: 20 Copynumber: 4.3 Consensus size: 19
30469 TGCTTTTGGT
*
30479 TGCACCTTAGTGCCCCT-A
1 TGCACTTTAGTGCCCCTAA
* * **
30497 TACACTTCAGTGTACCTAA
1 TGCACTTTAGTGCCCCTAA
**
30516 TTGCACATTT-GTGCCCCTGTT
1 -TGCAC-TTTAGTGCCCCT-AA
30537 TGCACTTTAGTGCCCCTGAA
1 TGCACTTTAGTGCCCCT-AA
30557 TGCAC
1 TGCAC
30562 AAATGTGTCC
Statistics
Matches: 47, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
18 12 0.26
19 4 0.09
20 29 0.62
21 2 0.04
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (19 bp):
TGCACTTTAGTGCCCCTAA
Found at i:30593 original size:20 final size:20
Alignment explanation
Indices: 30526--30594 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
30516 TTGCACATTT
* **
30526 GTGCCCCTGTTTGCACTTTA
1 GTGCCCCTGTATGCACTAAA
*
30546 GTGCCCCTGAATGCAC-AAA
1 GTGCCCCTGTATGCACTAAA
* **
30565 TGTGTCCCTGTATGCACTCCA
1 -GTGCCCCTGTATGCACTAAA
30586 GTGCCCCTG
1 GTGCCCCTG
30595 ATGATACATT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
19 1 0.03
20 36 0.95
21 1 0.03
ACGTcount: A:0.16, C:0.33, G:0.22, T:0.29
Consensus pattern (20 bp):
GTGCCCCTGTATGCACTAAA
Found at i:32135 original size:58 final size:61
Alignment explanation
Indices: 32068--32190 Score: 189
Period size: 58 Copynumber: 2.1 Consensus size: 61
32058 GCTCATCAAC
*
32068 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATT-ATTAA-AA-AACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCATAAATAACAACACTCAT
* * *
32126 AAACTAAACCCAAATATTTTTAAACTCAAATATAATTTTATTCCTAAATAACAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCATAAATAACAACACTCAT
32187 AAAC
1 AAAC
32191 AATTCCTTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
58 40 0.69
59 3 0.05
60 2 0.03
61 13 0.22
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.31
Consensus pattern (61 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCATAAATAACAACACTCAT
Found at i:32291 original size:25 final size:25
Alignment explanation
Indices: 32254--32303 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
32244 TTCTTCTTCT
*
32254 TTGTTGTGGTTGCTCTCGCACTGAA
1 TTGTTGTGATTGCTCTCGCACTGAA
*
32279 TTGTTGTGATTGCTCTTGCACTGAA
1 TTGTTGTGATTGCTCTCGCACTGAA
32304 CCAGCAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.18, G:0.26, T:0.42
Consensus pattern (25 bp):
TTGTTGTGATTGCTCTCGCACTGAA
Found at i:33377 original size:40 final size:38
Alignment explanation
Indices: 33305--33382 Score: 93
Period size: 40 Copynumber: 2.0 Consensus size: 38
33295 GTCAATAATT
* ** *
33305 TCAATATCCAACAAGTTTAAAGCATAATAATTTCAATA
1 TCAATATCCAACAAATTTAAAAAATAAAAATTTCAATA
*
33343 TCAATATCCAACCAACATTTAAAAAATAAAAATTTTAATA
1 TCAATATCCAA-CAA-ATTTAAAAAATAAAAATTTCAATA
33383 CTAAAACATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 11 0.33
39 3 0.09
40 19 0.58
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (38 bp):
TCAATATCCAACAAATTTAAAAAATAAAAATTTCAATA
Found at i:34635 original size:22 final size:22
Alignment explanation
Indices: 34593--34636 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
34583 CCTTCCTAGT
*
34593 TTTTAATATTTTTATTAAAAGA
1 TTTTAATATTTTTATCAAAAGA
*
34615 TTTTAAT-TTTTTAATCCAAAGA
1 TTTTAATATTTTT-ATCAAAAGA
34637 GCCCAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (22 bp):
TTTTAATATTTTTATCAAAAGA
Found at i:35337 original size:15 final size:15
Alignment explanation
Indices: 35317--35359 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
35307 CGATTTTGTC
35317 TAAATTTAAATGATT
1 TAAATTTAAATGATT
35332 TAAATTTAAATTGATT
1 TAAATTTAAA-TGATT
* *
35348 CAAATTAAAATG
1 TAAATTTAAATG
35360 TCAAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (15 bp):
TAAATTTAAATGATT
Found at i:36985 original size:14 final size:14
Alignment explanation
Indices: 36966--37038 Score: 60
Period size: 14 Copynumber: 5.2 Consensus size: 14
36956 GGCAAGGAAG
36966 GGGAAAGGAGAAAA
1 GGGAAAGGAGAAAA
36980 GGGAAAGGA-AAAA
1 GGGAAAGGAGAAAA
**
36993 GAAAAAAGGAGAAAA
1 G-GGAAAGGAGAAAA
* **
37008 GAGAAAGG-GGGAA
1 GGGAAAGGAGAAAA
*
37021 GGGAAAGGGGAAAGA
1 GGGAAAGGAGAAA-A
37036 GGG
1 GGG
37039 GGAGAGGTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
13 15 0.32
14 23 0.49
15 9 0.19
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (14 bp):
GGGAAAGGAGAAAA
Found at i:52160 original size:21 final size:21
Alignment explanation
Indices: 52122--52161 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
52112 GTTTTTAGTA
*
52122 TCGGTAGAAGTAGGACTTGTT
1 TCGGTAGAAGTAGCACTTGTT
52143 TCGGTAGAAG-AGTCACTTG
1 TCGGTAGAAGTAG-CACTTG
52162 AATCGATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.30
Consensus pattern (21 bp):
TCGGTAGAAGTAGCACTTGTT
Found at i:59515 original size:7 final size:7
Alignment explanation
Indices: 59503--59541 Score: 51
Period size: 7 Copynumber: 5.1 Consensus size: 7
59493 CCACGAAATA
59503 TTTTTTC
1 TTTTTTC
59510 TTTTTTC
1 TTTTTTC
59517 TTTTTCTC
1 TTTTT-TC
59525 GTATTTTTC
1 -T-TTTTTC
59534 TTTTTTC
1 TTTTTTC
59541 T
1 T
59542 CTACTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 19 0.66
8 3 0.10
9 3 0.10
10 4 0.14
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:59549 original size:17 final size:17
Alignment explanation
Indices: 59512--59549 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
59502 ATTTTTTCTT
*
59512 TTTTCTTTTTCTCGTAT
1 TTTTCTTTTTCTCGTAC
59529 TTTTCTTTTTTCTC-TAC
1 TTTTC-TTTTTCTCGTAC
59546 TTTT
1 TTTT
59550 TTGATCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTCTTTTTCTCGTAC
Found at i:64644 original size:22 final size:22
Alignment explanation
Indices: 64619--64661 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
64609 CAAACCACTG
64619 TTGAACCTCTACTGGATCGCCA
1 TTGAACCTCTACTGGATCGCCA
*
64641 TTGAACCTCTATTGGATCGCC
1 TTGAACCTCTACTGGATCGCC
64662 GTTGGACCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (22 bp):
TTGAACCTCTACTGGATCGCCA
Found at i:66933 original size:25 final size:26
Alignment explanation
Indices: 66905--66953 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
66895 AGGACCAAAG
* *
66905 AATTAAATTAAC-CCAATTATTAAAC
1 AATTAAATAAACACAAATTATTAAAC
66930 AATTAAATAAACACAAATTATTAA
1 AATTAAATAAACACAAATTATTAA
66954 TGAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (26 bp):
AATTAAATAAACACAAATTATTAAAC
Found at i:70915 original size:26 final size:27
Alignment explanation
Indices: 70880--70933 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
70870 AGAATTGTCA
* *
70880 TTGCAGGAATTTGTTCAGAATTATCGC
1 TTGCAGGAATATGTCCAGAATTATCGC
*
70907 TTGCA-GAATATGTCCAGAGTTATCGC
1 TTGCAGGAATATGTCCAGAATTATCGC
70933 T
1 T
70934 GCATAAGCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (27 bp):
TTGCAGGAATATGTCCAGAATTATCGC
Found at i:79529 original size:43 final size:43
Alignment explanation
Indices: 79468--79553 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
79458 AAAAACTCAA
79468 GTTTGGGGTTGTGATAGTACTAGAAAAAACCATGGATTTATCT
1 GTTTGGGGTTGTGATAGTACTAGAAAAAACCATGGATTTATCT
*
79511 GTTTGGGGTTGTGATAGTACTAGAAAGAACCATGGATTTATCT
1 GTTTGGGGTTGTGATAGTACTAGAAAAAACCATGGATTTATCT
79554 TTACTTATTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.35
Consensus pattern (43 bp):
GTTTGGGGTTGTGATAGTACTAGAAAAAACCATGGATTTATCT
Found at i:91346 original size:20 final size:21
Alignment explanation
Indices: 91310--91348 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
91300 CATTTATTGA
*
91310 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
91331 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
91349 AATTCCTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:99153 original size:17 final size:18
Alignment explanation
Indices: 99115--99159 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
99105 GCAAATGTGC
99115 TGACAAATAAAATGCAGA
1 TGACAAATAAAATGCAGA
*
99133 -GACAAATAAAATGTA-A
1 TGACAAATAAAATGCAGA
*
99149 TGACAACTAAA
1 TGACAAATAAA
99160 TGGATGTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (18 bp):
TGACAAATAAAATGCAGA
Found at i:99572 original size:21 final size:21
Alignment explanation
Indices: 99548--99592 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
99538 GCACAAACTA
*
99548 TTCT-TTTTCTTTTTCTTTCTC
1 TTCTCTTTTC-TTTTCTTCCTC
99569 TTCTCTTTTCTTTTCTTCCTC
1 TTCTCTTTTCTTTTCTTCCTC
99590 TTC
1 TTC
99593 AATACCCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
TTCTCTTTTCTTTTCTTCCTC
Found at i:111881 original size:25 final size:26
Alignment explanation
Indices: 111853--111901 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
111843 AGGACCAAAG
**
111853 AATTAAATTAACCC-AATTATTAAAC
1 AATTAAAAAAACCCAAATTATTAAAC
111878 AATTAAAAAAACCCAAATTATTAA
1 AATTAAAAAAACCCAAATTATTAA
111902 TGAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (26 bp):
AATTAAAAAAACCCAAATTATTAAAC
Found at i:112523 original size:22 final size:22
Alignment explanation
Indices: 112495--112567 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
112485 AGGAGGAATA
112495 TATGTGGCAGTTTATCTACAAT
1 TATGTGGCAGTTTATCTACAAT
* * *
112517 TATGTGGTAGTTCATCTGCAAT
1 TATGTGGCAGTTTATCTACAAT
* * *
112539 TATGTAGTC-GTTTATCGACTAT
1 TATGT-GGCAGTTTATCTACAAT
112561 TATGTGG
1 TATGTGG
112568 TGGCTTGTCC
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
21 1 0.03
22 38 0.95
23 1 0.03
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.42
Consensus pattern (22 bp):
TATGTGGCAGTTTATCTACAAT
Found at i:113864 original size:17 final size:17
Alignment explanation
Indices: 113842--113875 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
113832 ACTCATGAAG
113842 AGTCGAGTCAAGGAACC
1 AGTCGAGTCAAGGAACC
113859 AGTCGAGTCAAGGAACC
1 AGTCGAGTCAAGGAACC
113876 TACATTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.29, T:0.12
Consensus pattern (17 bp):
AGTCGAGTCAAGGAACC
Found at i:115890 original size:13 final size:13
Alignment explanation
Indices: 115872--115896 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
115862 GCAATATTTC
115872 TTTTTCTTTTCTG
1 TTTTTCTTTTCTG
115885 TTTTTCTTTTCT
1 TTTTTCTTTTCT
115897 TTTCCTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTCTG
Found at i:116528 original size:18 final size:17
Alignment explanation
Indices: 116493--116540 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
116483 AACTAAATTA
* **
116493 ACAAAACAAATGCAATG
1 ACAAAAAAAATGTGATG
116510 ACAAAATAAAATGTGATG
1 ACAAAA-AAAATGTGATG
*
116528 ACAATAAAAATGT
1 ACAAAAAAAATGT
116541 ATGCAATTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.19
Consensus pattern (17 bp):
ACAAAAAAAATGTGATG
Found at i:116539 original size:17 final size:18
Alignment explanation
Indices: 116507--116540 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
116497 AACAAATGCA
116507 ATGACAAAATAAAATGTG
1 ATGACAAAATAAAATGTG
*
116525 ATGACAATA-AAAATGT
1 ATGACAAAATAAAATGT
116541 ATGCAATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (18 bp):
ATGACAAAATAAAATGTG
Found at i:117873 original size:18 final size:18
Alignment explanation
Indices: 117846--117882 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
117836 TTAATTTTGA
*
117846 GTGTAGAAGGTAGGATAT
1 GTGTAAAAGGTAGGATAT
117864 GTGTAAAAGGTAGGATAT
1 GTGTAAAAGGTAGGATAT
117882 G
1 G
117883 GCTATTCACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.27
Consensus pattern (18 bp):
GTGTAAAAGGTAGGATAT
Found at i:123301 original size:14 final size:15
Alignment explanation
Indices: 123272--123301 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
123262 ACTATTGTTG
123272 TAACTCCCTTGTCTA
1 TAACTCCCTTGTCTA
123287 TAACTCCCTTG-CTA
1 TAACTCCCTTGTCTA
123301 T
1 T
123302 GAGGAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (15 bp):
TAACTCCCTTGTCTA
Found at i:136010 original size:32 final size:32
Alignment explanation
Indices: 135952--136012 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
135942 AATCACACAT
*
135952 CCTCTCAACATATCCTCAAGAATATGGATGAC
1 CCTCTCAAAATATCCTCAAGAATATGGATGAC
* *
135984 CCTCTCAAAATGTCCATCAA-ACTATGGAT
1 CCTCTCAAAATATCC-TCAAGAATATGGAT
136013 TATAAGTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 21 0.84
33 4 0.16
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.26
Consensus pattern (32 bp):
CCTCTCAAAATATCCTCAAGAATATGGATGAC
Found at i:140357 original size:25 final size:25
Alignment explanation
Indices: 140316--140394 Score: 95
Period size: 25 Copynumber: 3.1 Consensus size: 25
140306 TGTATACTGT
140316 TAAACTCTATCTGGGCTCATAAGAGC
1 TAAAC-CTATCTGGGCTCATAAGAGC
* * *
140342 TAACCCTATCTAGGCTCATTAGAGC
1 TAAACCTATCTGGGCTCATAAGAGC
* * *
140367 TAAACTTATCTGGGCTCGTATGAGC
1 TAAACCTATCTGGGCTCATAAGAGC
140392 TAA
1 TAA
140395 TTTCTAGAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
25 40 0.91
26 4 0.09
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (25 bp):
TAAACCTATCTGGGCTCATAAGAGC
Found at i:144225 original size:35 final size:36
Alignment explanation
Indices: 144177--144253 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
144167 AATATAATCA
*
144177 GTCACATGACATGAA-AAAATACCCACATATTTACT
1 GTCACATGACATGAATAAAATACCCACATATTCACT
* * *
144212 GTCACATGGCATGAATAACATACCCTCATATTCACT
1 GTCACATGACATGAATAAAATACCCACATATTCACT
*
144248 TTCACA
1 GTCACA
144254 ATAGTCATCA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 14 0.39
36 22 0.61
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.27
Consensus pattern (36 bp):
GTCACATGACATGAATAAAATACCCACATATTCACT
Found at i:172047 original size:198 final size:198
Alignment explanation
Indices: 171709--172110 Score: 768
Period size: 198 Copynumber: 2.0 Consensus size: 198
171699 TGTCATCAAT
171709 AAATACAACTACAAACCTATCCAATTGAGGCTGGAATACTCTGTTCATCAGATCCATGAATGCTG
1 AAATACAACTACAAACCTATCCAATTGAGGCTGGAATACTCTGTTCATCAGATCCATGAATGCTG
* *
171774 CTGGAGCGTTAGTCAACCCAAATGACATAACTAGAAACTCGTAAAGTCCATACCGGGTCCTAAAT
66 CTGGAGCATTAGTCAACCCAAACGACATAACTAGAAACTCGTAAAGTCCATACCGGGTCCTAAAT
*
171839 GTTGTTTTCGATACATCAAAATCTTTCACTGGCATCTGATTGTAACCTAATCAAAGATCTACCTA
131 GTTGTTTTCGATACATCAAAATCTTTCACTGGCATCTGATAGTAACCTAATCAAAGATCTACCTA
171904 GGA
196 GGA
171907 AAATACAACTACAAACCTATCCAATTGAGGCTGGAATACTCTGTTCATCAGATCCATGAATGCTG
1 AAATACAACTACAAACCTATCCAATTGAGGCTGGAATACTCTGTTCATCAGATCCATGAATGCTG
171972 CTGGAGCATTAGTCAACCCAAACGACATAACTAGAAACTCGTAAAGTCCATACCGGGTCCTAAAT
66 CTGGAGCATTAGTCAACCCAAACGACATAACTAGAAACTCGTAAAGTCCATACCGGGTCCTAAAT
*
172037 GTTGTTTTCGATACATCAAAATCTTTCACTGGCATCTGATAGTAACCTAATCGAAGATCTACCTA
131 GTTGTTTTCGATACATCAAAATCTTTCACTGGCATCTGATAGTAACCTAATCAAAGATCTACCTA
172102 GGA
196 GGA
172105 AAATAC
1 AAATAC
172111 GATTACACCT
Statistics
Matches: 200, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
198 200 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (198 bp):
AAATACAACTACAAACCTATCCAATTGAGGCTGGAATACTCTGTTCATCAGATCCATGAATGCTG
CTGGAGCATTAGTCAACCCAAACGACATAACTAGAAACTCGTAAAGTCCATACCGGGTCCTAAAT
GTTGTTTTCGATACATCAAAATCTTTCACTGGCATCTGATAGTAACCTAATCAAAGATCTACCTA
GGA
Found at i:174537 original size:7 final size:7
Alignment explanation
Indices: 174515--174566 Score: 61
Period size: 7 Copynumber: 7.3 Consensus size: 7
174505 ATTTACAACA
174515 CATTCATT
1 CATTCA-T
174523 CGATTCAT
1 C-ATTCAT
174531 CATTCAT
1 CATTCAT
174538 CATTCAT
1 CATTCAT
*
174545 CATTTAT
1 CATTCAT
*
174552 CATTTAT
1 CATTCAT
174559 CA-TCAT
1 CATTCAT
174565 CA
1 CA
174567 CATGCAAGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 5 0.12
7 28 0.68
8 3 0.07
9 5 0.12
ACGTcount: A:0.29, C:0.25, G:0.02, T:0.44
Consensus pattern (7 bp):
CATTCAT
Found at i:180211 original size:41 final size:40
Alignment explanation
Indices: 180165--180243 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
180155 GTTATTAGCG
180165 GCATTTGGACAGAAAACGCCGCAAAAGATAAAGCAATAGTA
1 GCATTTGGACA-AAAACGCCGCAAAAGATAAAGCAATAGTA
** * * *
180206 GCATTTTTACATAAACGCCGCAAAAGGTAGAGCAATAG
1 GCATTTGGACAAAAACGCCGCAAAAGATAAAGCAATAG
180244 CGGCGCTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
40 24 0.73
41 9 0.27
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.18
Consensus pattern (40 bp):
GCATTTGGACAAAAACGCCGCAAAAGATAAAGCAATAGTA
Found at i:180284 original size:41 final size:41
Alignment explanation
Indices: 180223--180374 Score: 218
Period size: 41 Copynumber: 3.7 Consensus size: 41
180213 TACATAAACG
* *
180223 CCGCAAAAGGT-AGAGCAATAGCGGCGCTTATGGGAAACCA
1 CCGCTAAAGGTCAGAGCAATAGCAGCGCTTATGGGAAACCA
* *
180263 CCGCTAAAGGTCAGAGCAATAGCAGCGTTTATGGGAAAGCA
1 CCGCTAAAGGTCAGAGCAATAGCAGCGCTTATGGGAAACCA
* *
180304 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCC-
1 CCGCTAAAGGTCAGAGCAATAGCAGCGCTTATGGG-AAACCA
*
180345 CCGCTAAAGGTTAGAGCAATAGCAGCGCTT
1 CCGCTAAAGGTCAGAGCAATAGCAGCGCTT
180375 CCGCTAAAGG
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
40 10 0.10
41 87 0.87
42 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.30, T:0.16
Consensus pattern (41 bp):
CCGCTAAAGGTCAGAGCAATAGCAGCGCTTATGGGAAACCA
Found at i:180381 original size:30 final size:30
Alignment explanation
Indices: 180345--180427 Score: 157
Period size: 30 Copynumber: 2.8 Consensus size: 30
180335 TGGGCAAGCC
*
180345 CCGCTAAAGGTTAGAGCAATAGCAGCGCTT
1 CCGCTAAAGGTCAGAGCAATAGCAGCGCTT
180375 CCGCTAAAGGTCAGAGCAATAGCAGCGCTT
1 CCGCTAAAGGTCAGAGCAATAGCAGCGCTT
180405 CCGCTAAAGGTCAGAGCAATAGC
1 CCGCTAAAGGTCAGAGCAATAGC
180428 GATGCTTATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (30 bp):
CCGCTAAAGGTCAGAGCAATAGCAGCGCTT
Found at i:180462 original size:41 final size:40
Alignment explanation
Indices: 180405--180577 Score: 184
Period size: 41 Copynumber: 4.2 Consensus size: 40
180395 AGCAGCGCTT
* *
180405 CCGCTAAAGGTCAGAGCAATAGCGATGCTTATAAGAAAGCG
1 CCGCTAAAGGTCAGAGCATTAGCG-CGCTTATAAGAAAGCG
* * * *
180446 CCGTTAAAGGTTAGAGCATTAGTGGCGCCTATAAGAAAGCG
1 CCGCTAAAGGTCAGAGCATTAG-CGCGCTTATAAGAAAGCG
* *
180487 CCGCTAAAGATCAGAGCATTAGCTGCGCTTATAAGAAAGTG
1 CCGCTAAAGGTCAGAGCATTAGC-GCGCTTATAAGAAAGCG
* * ** *
180528 TCGCTAAAGGTCAGATCATTAGCGGCGCTTATTTGAAAAACG
1 CCGCTAAAGGTCAGAGCATTAGC-GCGCTTATAAG-AAAGCG
180570 CCGCTAAA
1 CCGCTAAA
180578 AGTTAAACTA
Statistics
Matches: 108, Mismatches: 21, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
41 96 0.89
42 12 0.11
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (40 bp):
CCGCTAAAGGTCAGAGCATTAGCGCGCTTATAAGAAAGCG
Found at i:180548 original size:82 final size:82
Alignment explanation
Indices: 180405--180555 Score: 205
Period size: 82 Copynumber: 1.8 Consensus size: 82
180395 AGCAGCGCTT
* * * * *
180405 CCGCTAAAGGTCAGAGCAATAGCGATGCTTATAAGAAAGCGCCGTTAAAGGTTAGAGCATTAGTG
1 CCGCTAAAGATCAGAGCAATAGCGACGCTTATAAGAAAGCGCCGCTAAAGGTCAGAGCATTAGCG
180470 GCGCCTATAAGAAAGCG
66 GCGCCTATAAGAAAGCG
* * * *
180487 CCGCTAAAGATCAGAGCATTAGCTG-CGCTTATAAGAAAGTGTCGCTAAAGGTCAGATCATTAGC
1 CCGCTAAAGATCAGAGCAATAGC-GACGCTTATAAGAAAGCGCCGCTAAAGGTCAGAGCATTAGC
180551 GGCGC
65 GGCGC
180556 TTATTTGAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
82 58 0.98
83 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (82 bp):
CCGCTAAAGATCAGAGCAATAGCGACGCTTATAAGAAAGCGCCGCTAAAGGTCAGAGCATTAGCG
GCGCCTATAAGAAAGCG
Found at i:180671 original size:27 final size:28
Alignment explanation
Indices: 180641--180721 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 28
180631 ACAATTATTT
180641 TAAAACTTATATAAACTAAAA-AAATTC
1 TAAAACTTATATAAACTAAAATAAATTC
** *
180668 TAAAA-TT-TA-AAAAAAAAATTTAAATTT
1 TAAAACTTATATAAACTAAAA--TAAATTC
180695 TAAAACTTATATAAACTAAAATAAATT
1 TAAAACTTATATAAACTAAAATAAATT
180722 AAATTATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
24 7 0.16
25 2 0.05
26 2 0.05
27 15 0.35
28 8 0.19
29 2 0.05
30 7 0.16
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (28 bp):
TAAAACTTATATAAACTAAAATAAATTC
Found at i:180683 original size:20 final size:20
Alignment explanation
Indices: 180658--180699 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
180648 TATATAAACT
180658 AAAAAAATTCTAAAATTTAAA
1 AAAAAAATT-TAAAATTTAAA
*
180679 AAAAAAATTTAAATTTTAAA
1 AAAAAAATTTAAAATTTAAA
180699 A
1 A
180700 CTTATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAAATTTAAAATTTAAA
Found at i:180693 original size:19 final size:22
Alignment explanation
Indices: 180658--180699 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
180648 TATATAAACT
180658 AAAAAAATTCTAAAA-TTTAAA
1 AAAAAAATTCTAAAATTTTAAA
180679 AAAAAAATT-T-AAATTTTAAA
1 AAAAAAATTCTAAAATTTTAAA
180699 A
1 A
180700 CTTATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.15
20 8 0.40
21 9 0.45
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAAAAATTCTAAAATTTTAAA
Found at i:180856 original size:26 final size:26
Alignment explanation
Indices: 180827--180888 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
180817 TTTGCTCCCA
*
180827 GTTAGTTTTCTTCTCTCTACTTATTT
1 GTTATTTTTCTTCTCTCTACTTATTT
180853 GTTATTTTTCTTCTCTCTACTTATTT
1 GTTATTTTTCTTCTCTCTACTTATTT
180879 GTTATTTTTC
1 GTTATTTTTC
180889 CATCGCCATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.11, C:0.18, G:0.06, T:0.65
Consensus pattern (26 bp):
GTTATTTTTCTTCTCTCTACTTATTT
Done.