Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012134.1 Kokia drynarioides strain JFW-HI SEQ_127133, 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: 116498
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 102 characters in sequence are not A, C, G, or T
Found at i:9068 original size:28 final size:28
Alignment explanation
Indices: 9037--9270 Score: 111
Period size: 28 Copynumber: 8.2 Consensus size: 28
9027 AGTTTCGGTT
9037 AGTTTGGGGTTAAAATGTAATTTTGGAA
1 AGTTTGGGGTTAAAATGTAATTTTGGAA
* *
9065 AGTTTAGGGGTAAAAATGTCATTTTGGGAA
1 AGTTT-GGGGTTAAAATGTAATTTT-GGAA
** ** *
9095 A-TTCAGGG-TAAAATACATTTTTTGG-A
1 AGTTTGGGGTTAAAATGTA-ATTTTGGAA
* ** *
9121 AGTTCGAGGGCAAAAATG-AGATTTTTGAA
1 AGTTTG-GGGTTAAAATGTA-ATTTTGGAA
** * *
9150 AGTTCAGGG-TAAAATGTGATTTTTGAA
1 AGTTTGGGGTTAAAATGTAATTTTGGAA
* * *
9177 AGTTCGAGGG-TAAAATGTGATTTTTGAGA
1 AGTTTG-GGGTTAAAATGTAATTTTGGA-A
* *
9206 AGTTTAAGGGTTAAAATGTAATTTTTGAGA
1 AGTTT-GGGGTTAAAATGTAATTTTGGA-A
* * * *
9236 AGTTTAGAGGTTAAAATATGATTTTTGGAC
1 AGTTT-GGGGTTAAAATGT-AATTTTGGAA
9266 AGTTT
1 AGTTT
9271 AAAGACCTTC
Statistics
Matches: 165, Mismatches: 28, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
26 2 0.01
27 30 0.18
28 44 0.27
29 38 0.23
30 44 0.27
31 7 0.04
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (28 bp):
AGTTTGGGGTTAAAATGTAATTTTGGAA
Found at i:9081 original size:29 final size:28
Alignment explanation
Indices: 9037--9271 Score: 124
Period size: 30 Copynumber: 8.2 Consensus size: 28
9027 AGTTTCGGTT
9037 AGTTT-GGGGTTAAAATGTAATTTTGGAA
1 AGTTTAGGGG-TAAAATGTAATTTTGGAA
*
9065 AGTTTAGGGGTAAAAATGTCATTTTGGGAA
1 AGTTTAGGGGT-AAAATGTAATTTT-GGAA
* ** *
9095 A-TTCA-GGGTAAAATACATTTTTTGG-A
1 AGTTTAGGGGTAAAATGTA-ATTTTGGAA
* ** *
9121 AGTTCGAGGGCAAAAATG-AGATTTTTGAA
1 AGTT-TAGGGGTAAAATGTA-ATTTTGGAA
* * *
9150 AGTTCA-GGGTAAAATGTGATTTTTGAA
1 AGTTTAGGGGTAAAATGTAATTTTGGAA
* * *
9177 AG-TTCGAGGGTAAAATGTGATTTTTGAGA
1 AGTTTAG-GGGTAAAATGTAATTTTGGA-A
* *
9206 AGTTTAAGGGTTAAAATGTAATTTTTGAGA
1 AGTTT-AGGGGTAAAATGTAATTTTGGA-A
* * * *
9236 AGTTTAGAGGTTAAAATATGATTTTTGGAC
1 AGTTTAG-GGGTAAAATGT-AATTTTGGAA
9266 AGTTTA
1 AGTTTA
9272 AAGACCTTCT
Statistics
Matches: 165, Mismatches: 26, Indels: 30
0.75 0.12 0.14
Matches are distributed among these distances:
26 3 0.02
27 28 0.17
28 42 0.25
29 36 0.22
30 48 0.29
31 8 0.05
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (28 bp):
AGTTTAGGGGTAAAATGTAATTTTGGAA
Found at i:9270 original size:60 final size:57
Alignment explanation
Indices: 9047--9272 Score: 180
Period size: 56 Copynumber: 3.9 Consensus size: 57
9037 AGTTTGGGGT
* * * *
9047 TAAAATGTAATTTTGGAAAGTTTAG-GGGTAAAA-ATG-TCATTTTGGGAA-ATTCAGGG
1 TAAAATGTAATTTTTGAAAG-TTAGAGGGTAAAATATGAT--TTTTGAGAAGTTTAAGGG
** * * * * *
9103 TAAAATACATTTTTTGGAAGTTCGAGGGCAAAA-ATGAGATTTTTGA-AAG-TTCAGGG
1 TAAAATGTAATTTTTGAAAGTTAGAGGGTAAAATAT--GATTTTTGAGAAGTTTAAGGG
* * *
9159 TAAAATGTGATTTTTGAAAGTTCGAGGGTAAAATGTGATTTTTGAGAAGTTTAAGGG
1 TAAAATGTAATTTTTGAAAGTTAGAGGGTAAAATATGATTTTTGAGAAGTTTAAGGG
*
9216 TTAAAATGTAATTTTTGAGAAGTTTAGAGGTTAAAATATGATTTTTG-GACAGTTTAA
1 -TAAAATGTAATTTTTGA-AAG-TTAGAGGGTAAAATATGATTTTTGAGA-AGTTTAA
9273 AGACCTTCTG
Statistics
Matches: 138, Mismatches: 20, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
55 12 0.09
56 63 0.46
57 12 0.09
58 17 0.12
59 6 0.04
60 28 0.20
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (57 bp):
TAAAATGTAATTTTTGAAAGTTAGAGGGTAAAATATGATTTTTGAGAAGTTTAAGGG
Found at i:10273 original size:3 final size:3
Alignment explanation
Indices: 10259--10313 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
10249 CGAATTTCTT
*
10259 TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA
10306 TTA -TA TTA
1 TTA TTA TTA
10314 AATGTGTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 40 0.85
4 4 0.09
5 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:11039 original size:6 final size:6
Alignment explanation
Indices: 11020--11096 Score: 78
Period size: 6 Copynumber: 13.7 Consensus size: 6
11010 GAACATTATT
11020 AATTTA AA--TA AATTTA AATTTA AATTTA TAA--TA AATTTA AATTTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AA-TTTA
*
11066 AA--TA AATTTA AATTTA AA-ATA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATT
11097 CTGTTGGGCC
Statistics
Matches: 60, Mismatches: 2, Indels: 18
0.75 0.03 0.22
Matches are distributed among these distances:
4 10 0.17
5 6 0.10
6 36 0.60
7 8 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:11054 original size:23 final size:23
Alignment explanation
Indices: 11020--11068 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 23
11010 GAACATTATT
11020 AATTTAAATAAATTTAAA-TTTA
1 AATTTAAATAAATTTAAATTTTA
11042 AATTTATAATAAATTTAAATTTTA
1 AATTTA-AATAAATTTAAATTTTA
11066 AAT
1 AAT
11069 AAATTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 6 0.24
23 12 0.48
24 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTTAAATAAATTTAAATTTTA
Found at i:11056 original size:17 final size:17
Alignment explanation
Indices: 11034--11096 Score: 101
Period size: 17 Copynumber: 3.7 Consensus size: 17
11024 TAAATAAATT
11034 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
11051 TAAATTTAAATTT-TAAA
1 TAAATTTAAATTTAT-AA
*
11068 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTATAA
11085 TAAATTTAAATT
1 TAAATTTAAATT
11097 CTGTTGGGCC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
16 1 0.02
17 42 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:11071 original size:11 final size:10
Alignment explanation
Indices: 11020--11095 Score: 74
Period size: 10 Copynumber: 7.9 Consensus size: 10
11010 GAACATTATT
11020 AATTTAAATA
1 AATTTAAATA
11030 AATTTAAATTTA
1 AATTTAAA--TA
11042 AATTTATAATA
1 AATTTA-AATA
11053 AATTTAAAT-
1 AATTTAAATA
11062 --TTTAAATA
1 AATTTAAATA
11070 AATTTAAAT-
1 AATTTAAATA
*
11079 --TTAAAATA
1 AATTTAAATA
11087 AATTTAAAT
1 AATTTAAAT
11096 TCTGTTGGGC
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
7 13 0.24
10 24 0.44
11 8 0.15
12 8 0.15
13 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
AATTTAAATA
Found at i:11077 original size:23 final size:23
Alignment explanation
Indices: 11026--11083 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
11016 TATTAATTTA
**
11026 AATAAATTTAAATTTAAATTTAT
1 AATAAATTTAAATTTAAATAAAT
11049 AATAAATTTAAATTTTAAATAAAT
1 AATAAATTTAAA-TTTAAATAAAT
*
11073 -TTAAATTTAAA
1 AATAAATTTAAA
11084 ATAAATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 22 0.71
24 9 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATAAATTTAAATTTAAATAAAT
Found at i:13771 original size:26 final size:26
Alignment explanation
Indices: 13742--13792 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
13732 AATTTTTTTT
* *
13742 AAATTGAGTCAAATGAAATGAAATTC
1 AAATCGAGTCAAATCAAATGAAATTC
* *
13768 AAATCGAGTCGAATCAATTGAAATT
1 AAATCGAGTCAAATCAAATGAAATT
13793 GTTTGAGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.27
Consensus pattern (26 bp):
AAATCGAGTCAAATCAAATGAAATTC
Found at i:14051 original size:23 final size:24
Alignment explanation
Indices: 14006--14051 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
13996 TTTCTTTATC
*
14006 TATTCTTTAAAAAAAAATTAATTA
1 TATTCTTTAAAAAAAAATAAATTA
* *
14030 TATT-TTTAAAAATATATAAATT
1 TATTCTTTAAAAAAAAATAAATT
14052 TTGAAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TATTCTTTAAAAAAAAATAAATTA
Found at i:14080 original size:19 final size:20
Alignment explanation
Indices: 14049--14086 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
14039 AAATATATAA
14049 ATTTTGAAATTTTTATAAAT
1 ATTTTGAAATTTTTATAAAT
*
14069 ATTTTG-AATTTTTTTAAA
1 ATTTTGAAATTTTTATAAA
14087 ATTATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
ATTTTGAAATTTTTATAAAT
Found at i:14088 original size:20 final size:22
Alignment explanation
Indices: 14049--14105 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
14039 AAATATATAA
*
14049 ATTTTGAA-ATTTTTATAAA-T
1 ATTTTGAATTTTTTTATAAATT
14069 ATTTTGAATTTTTTTA-AAATT
1 ATTTTGAATTTTTTTATAAATT
*
14090 ATTTTAAATCTTTTTT
1 ATTTTGAAT-TTTTTT
14106 GTAATTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.34
21 15 0.47
22 6 0.19
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (22 bp):
ATTTTGAATTTTTTTATAAATT
Found at i:17880 original size:7 final size:7
Alignment explanation
Indices: 17868--17892 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17858 AGGGATTAAG
17868 TTAAAAT
1 TTAAAAT
17875 TTAAAAT
1 TTAAAAT
17882 TTAAAAT
1 TTAAAAT
17889 TTAA
1 TTAA
17893 GTGACCATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTAAAAT
Found at i:24049 original size:12 final size:12
Alignment explanation
Indices: 24030--24080 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
24020 ATAACATCCA
24030 AACAACAAAAAT
1 AACAACAAAAAT
* *
24042 AGCAACAAAAAC
1 AACAACAAAAAT
24054 AACAA-AAAAAT
1 AACAACAAAAAT
* *
24065 AACAGCAAAAAC
1 AACAACAAAAAT
24077 AACA
1 AACA
24081 TGAAAACATC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 9 0.28
12 23 0.72
ACGTcount: A:0.73, C:0.20, G:0.04, T:0.04
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:24062 original size:23 final size:24
Alignment explanation
Indices: 24030--24080 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
24020 ATAACATCCA
*
24030 AACAACAAAAATAGCAACAAAAAC
1 AACAACAAAAATAACAACAAAAAC
*
24054 AACAA-AAAAATAACAGCAAAAAC
1 AACAACAAAAATAACAACAAAAAC
24077 AACA
1 AACA
24081 TGAAAACATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.73, C:0.20, G:0.04, T:0.04
Consensus pattern (24 bp):
AACAACAAAAATAACAACAAAAAC
Found at i:24086 original size:23 final size:21
Alignment explanation
Indices: 24016--24080 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 21
24006 AAAACGCATA
* *
24016 AAAAATAACATC-CAAACAAC
1 AAAAATAACAACAAAAACAAC
*
24036 AAAAATAGCAACAAAAACAAC
1 AAAAATAACAACAAAAACAAC
*
24057 AAAAAAATAACAGCAAAAACAAC
1 --AAAAATAACAACAAAAACAAC
24080 A
1 A
24081 TGAAAACATC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
20 10 0.27
21 8 0.22
23 19 0.51
ACGTcount: A:0.71, C:0.20, G:0.03, T:0.06
Consensus pattern (21 bp):
AAAAATAACAACAAAAACAAC
Found at i:24116 original size:21 final size:21
Alignment explanation
Indices: 24083--24145 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
24073 AAACAACATG
*
24083 AAAACATCAACCAAAACAGTAA
1 AAAACAAC-ACCAAAACAGTAA
24105 AAAA-AAGCACCAAAACAGTAA
1 AAAACAA-CACCAAAACAGTAA
24126 AAAACAACA-CAAAACAGTAA
1 AAAACAACACCAAAACAGTAA
24146 CCAAAATAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
20 11 0.29
21 20 0.53
22 7 0.18
ACGTcount: A:0.67, C:0.21, G:0.06, T:0.06
Consensus pattern (21 bp):
AAAACAACACCAAAACAGTAA
Found at i:24160 original size:31 final size:33
Alignment explanation
Indices: 24113--24173 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
24103 AAAAAAAAGC
24113 ACCAAAACAGTAAAAAACAACA-CAAAACAGTA
1 ACCAAAACAGTAAAAAACAACACCAAAACAGTA
* *
24145 ACCAAAATAGT-AAAAACAGCACCAAAACA
1 ACCAAAACAGTAAAAAACAACACCAAAACA
24174 ACAATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.64, C:0.23, G:0.07, T:0.07
Consensus pattern (33 bp):
ACCAAAACAGTAAAAAACAACACCAAAACAGTA
Found at i:32698 original size:3 final size:3
Alignment explanation
Indices: 32692--32731 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
32682 AAAAAAAACA
32692 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
32732 GTTATTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35960 original size:17 final size:17
Alignment explanation
Indices: 35922--35960 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
35912 AGGTGGAGAA
* *
35922 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
*
35939 TTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
35956 CTTGT
1 CTTGT
35961 CAAGGTGGAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:36007 original size:41 final size:41
Alignment explanation
Indices: 35950--36045 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
35940 TTGTTCGTAG
* *
35950 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGGTGATT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
35991 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
*
36032 AGAATTCTTATTAA
1 AGAATTCTTGTTAA
36046 AATAAAATTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.29, C:0.05, G:0.28, T:0.38
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
Found at i:36684 original size:21 final size:22
Alignment explanation
Indices: 36650--36703 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
36640 TAAAAATATT
*
36650 TAAAA-TTCAAAAAAAT-ATAAA
1 TAAAATTTCATAAAAATCA-AAA
36671 -AAAATTTCATAAAAATCAAAA
1 TAAAATTTCATAAAAATCAAAA
36692 TAAAATTATCAT
1 TAAAATT-TCAT
36704 GAATTACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.14
21 13 0.46
22 7 0.25
23 4 0.14
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (22 bp):
TAAAATTTCATAAAAATCAAAA
Found at i:44508 original size:84 final size:83
Alignment explanation
Indices: 44413--44579 Score: 316
Period size: 84 Copynumber: 2.0 Consensus size: 83
44403 AAAGATGAAA
44413 CCCAATAAAAAACGAGGCAAGTTAAAATGTTTTCTTTGTGACGGTCCACATTTACTGAAGAAATG
1 CCCAATAAAAAACGAGGCAAGTTAAAATGTTTTCTTTGTGACGGTCCACATTTACTGAAGAAATG
44478 TCCAAGGAAATCCGAATT
66 TCCAAGGAAATCCGAATT
*
44496 NCCCAATAAAAAACGAGGCAAGTTAAAATGTTTTCTTTGTGACGGTCCACATTTGCTGAAGAAAT
1 -CCCAATAAAAAACGAGGCAAGTTAAAATGTTTTCTTTGTGACGGTCCACATTTACTGAAGAAAT
44561 GTCCAAGGAAATCCGAATT
65 GTCCAAGGAAATCCGAATT
44580 GTCTAAGAGG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (83 bp):
CCCAATAAAAAACGAGGCAAGTTAAAATGTTTTCTTTGTGACGGTCCACATTTACTGAAGAAATG
TCCAAGGAAATCCGAATT
Found at i:47038 original size:19 final size:18
Alignment explanation
Indices: 47014--47064 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
47004 GAGACATTAG
47014 AGAAAAAGAAAAAAAGAAA
1 AGAAAAAGAAAAAAAG-AA
** *
47033 AGAAAAAGTGGAGAAAGAA
1 AGAAAAAG-AAAAAAAGAA
47052 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
47065 GAAGTGTGGG
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
18 2 0.08
19 18 0.72
20 5 0.20
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (18 bp):
AGAAAAAGAAAAAAAGAA
Found at i:49765 original size:31 final size:32
Alignment explanation
Indices: 49730--49792 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
49720 TTTTCTCTCC
*
49730 AAAAACAATCT-AATATCATAAATAT-ATAAAA
1 AAAAACAACCTAAAT-TCATAAATATCATAAAA
* *
49761 AAAAACTACCTAAATTCATAAATTTCATAAAA
1 AAAAACAACCTAAATTCATAAATATCATAAAA
49793 TTTCGACACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (32 bp):
AAAAACAACCTAAATTCATAAATATCATAAAA
Found at i:56694 original size:22 final size:22
Alignment explanation
Indices: 56669--56734 Score: 132
Period size: 22 Copynumber: 3.0 Consensus size: 22
56659 TTGGGGTTAG
56669 TTGAATAAAAAAATCTATTTTT
1 TTGAATAAAAAAATCTATTTTT
56691 TTGAATAAAAAAATCTATTTTT
1 TTGAATAAAAAAATCTATTTTT
56713 TTGAATAAAAAAATCTATTTTT
1 TTGAATAAAAAAATCTATTTTT
56735 AAGTGTAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (22 bp):
TTGAATAAAAAAATCTATTTTT
Found at i:56780 original size:12 final size:12
Alignment explanation
Indices: 56763--56801 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
56753 ATTTTTGGTG
*
56763 AATAAATAAATA
1 AATAAATATATA
56775 AATAAATATATA
1 AATAAATATATA
* *
56787 TATATATATATA
1 AATAAATATATA
56799 AAT
1 AAT
56802 CACAAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AATAAATATATA
Found at i:58866 original size:30 final size:27
Alignment explanation
Indices: 58800--58863 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
58790 TAACATACAA
58800 TAAATAATAAAATGTATGGTTTGAAAC
1 TAAATAATAAAATGTATGGTTTGAAAC
58827 TAAATAATAAAATGTATGGTTTGAAAC
1 TAAATAATAAAATGTATGGTTTGAAAC
*
58854 TAATTAATAA
1 TAAATAATAA
58864 TAACACGTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.34
Consensus pattern (27 bp):
TAAATAATAAAATGTATGGTTTGAAAC
Found at i:83525 original size:21 final size:21
Alignment explanation
Indices: 83509--83588 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
83499 ATCAACATAC
*
83509 TCAGATGCATCCACAAC-AAA
1 TCAGATGCAACCACAACAAAA
* * *
83529 GCAAGATGCAGCCACATCAAAA
1 TC-AGATGCAACCACAACAAAA
*
83551 TCAGATGCAACCAC-ACTAGAA
1 TCAGATGCAACCACAAC-AAAA
83572 TCAGATGCAACCACAAC
1 TCAGATGCAACCACAAC
83589 CCTCTTCAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 2 0.04
21 41 0.84
22 6 0.12
ACGTcount: A:0.44, C:0.30, G:0.14, T:0.12
Consensus pattern (21 bp):
TCAGATGCAACCACAACAAAA
Found at i:88846 original size:18 final size:18
Alignment explanation
Indices: 88804--88854 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
88794 GTTAGTACGT
* *
88804 ATTGTCATTTCA-TTCCA
1 ATTGTCATTGCATTTTCA
*
88821 ATTTTCATTGCATTTTCA
1 ATTGTCATTGCATTTTCA
88839 ATTGTCATTGCATTTT
1 ATTGTCATTGCATTTT
88855 AGTGTTAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 10 0.34
18 19 0.66
ACGTcount: A:0.22, C:0.18, G:0.08, T:0.53
Consensus pattern (18 bp):
ATTGTCATTGCATTTTCA
Found at i:91021 original size:10 final size:10
Alignment explanation
Indices: 90997--91043 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
90987 TTTAACACAA
90997 CACATATTAAT
1 CACAT-TTAAT
*
91008 CACATTTGAT
1 CACATTTAAT
*
91018 CACATATAAT
1 CACATTTAAT
91028 CACATTTAAT
1 CACATTTAAT
91038 CACATT
1 CACATT
91044 AGTCACATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
10 27 0.84
11 5 0.16
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.36
Consensus pattern (10 bp):
CACATTTAAT
Found at i:91029 original size:20 final size:20
Alignment explanation
Indices: 90997--91051 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
90987 TTTAACACAA
*
90997 CACATATTAATCACATTTGAT
1 CACATA-TAATCACATTTAAT
91018 CACATATAATCACATTTAAT
1 CACATATAATCACATTTAAT
*
91038 CACAT-TAGTCACAT
1 CACATATAATCACAT
91052 AAATATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.25
20 18 0.56
21 6 0.19
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.35
Consensus pattern (20 bp):
CACATATAATCACATTTAAT
Found at i:91065 original size:23 final size:23
Alignment explanation
Indices: 91046--91121 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
91036 ATCACATTAG
91046 TCACATAAATATTTCAACATTTA
1 TCACATAAATATTTCAACATTTA
*
91069 TCACATCACATATTAATC-ACA-TTA
1 TCACAT-AAATATT--TCAACATTTA
* *
91093 GCACATGAATATTTCAACATTTA
1 TCACATAAATATTTCAACATTTA
91116 TCACAT
1 TCACAT
91122 CACATATTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
21 2 0.05
22 3 0.07
23 19 0.44
24 14 0.33
25 3 0.07
26 2 0.05
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.36
Consensus pattern (23 bp):
TCACATAAATATTTCAACATTTA
Found at i:91079 original size:47 final size:48
Alignment explanation
Indices: 91026--91147 Score: 203
Period size: 47 Copynumber: 2.6 Consensus size: 48
91016 ATCACATATA
91026 ATCACAT-TTAATCACATTAGTCACATAAATATTTCAACATTTATCAC
1 ATCACATATTAATCACATTAGTCACATAAATATTTCAACATTTATCAC
*
91073 ATCACATATTAATCACATTAG-CACATGAATATTTCAACATTTATCAC
1 ATCACATATTAATCACATTAGTCACATAAATATTTCAACATTTATCAC
*
91120 ATCACATATTAATCACATTTAGTTACAT
1 ATCACATATTAATCACA-TTAGTCACAT
91148 TTAATCACAT
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
47 49 0.70
48 17 0.24
49 4 0.06
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.36
Consensus pattern (48 bp):
ATCACATATTAATCACATTAGTCACATAAATATTTCAACATTTATCAC
Found at i:91089 original size:16 final size:16
Alignment explanation
Indices: 91068--91137 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
91058 TTCAACATTT
91068 ATCACATCACATATTA
1 ATCACATCACATATTA
* * *
91084 ATCACATTAGCACATGA
1 ATCACATCA-CATATTA
**
91101 AT-ATTTCAACAT-TT-
1 ATCACATC-ACATATTA
91115 ATCACATCACATATTA
1 ATCACATCACATATTA
91131 ATCACAT
1 ATCACAT
91138 TTAGTTACAT
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
14 6 0.15
15 6 0.15
16 19 0.49
17 8 0.21
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.33
Consensus pattern (16 bp):
ATCACATCACATATTA
Found at i:91149 original size:10 final size:10
Alignment explanation
Indices: 91120--91164 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
91110 CATTTATCAC
91120 ATCACATATTA
1 ATCACAT-TTA
91131 ATCACATTTA
1 ATCACATTTA
* *
91141 GTTACATTTA
1 ATCACATTTA
91151 ATCACATTTA
1 ATCACATTTA
91161 ATCA
1 ATCA
91165 AATGAACATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
10 23 0.77
11 7 0.23
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (10 bp):
ATCACATTTA
Found at i:91198 original size:23 final size:23
Alignment explanation
Indices: 91182--91522 Score: 470
Period size: 23 Copynumber: 14.8 Consensus size: 23
91172 ATTTCAACAC
91182 AAATCACATTAATATTTAAGCAT
1 AAATCACATTAATATTTAAGCAT
* *
91205 AAATCATATTAACATTTAAGCAT
1 AAATCACATTAATATTTAAGCAT
91228 AAATCACATTAATATTTAAGCAT
1 AAATCACATTAATATTTAAGCAT
* * * * *
91251 AAATCATATTAACAATTAAACTT
1 AAATCACATTAATATTTAAGCAT
* * * *
91274 AAATCATATTAACATTTAAACTT
1 AAATCACATTAATATTTAAGCAT
91297 AAATCACATTAATATTTAAGCAT
1 AAATCACATTAATATTTAAGCAT
*
91320 AAATCACATTAACATTTAAGCAT
1 AAATCACATTAATATTTAAGCAT
*
91343 AAATCACATTAATATTTAAGCAC
1 AAATCACATTAATATTTAAGCAT
*
91366 AAATCACATTAATATTTAAGAAT
1 AAATCACATTAATATTTAAGCAT
*
91389 AAATCATATT-ATCATTTAAGCAT
1 AAATCACATTAAT-ATTTAAGCAT
* *
91412 AAATCATATTAACATTTAAGCAT
1 AAATCACATTAATATTTAAGCAT
91435 AAATCACATTAATATTTAAGCAT
1 AAATCACATTAATATTTAAGCAT
91458 AAATCACATTAATATTTAAG-ATT
1 AAATCACATTAATATTTAAGCA-T
*
91481 AAATCACATTAATATTTAAGTAT
1 AAATCACATTAATATTTAAGCAT
* *
91504 AAATCATATTAACATTTAA
1 AAATCACATTAATATTTAA
91523 TCTTTAAAAA
Statistics
Matches: 288, Mismatches: 26, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
22 3 0.01
23 283 0.98
24 2 0.01
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (23 bp):
AAATCACATTAATATTTAAGCAT
Found at i:91549 original size:10 final size:10
Alignment explanation
Indices: 91534--91647 Score: 122
Period size: 10 Copynumber: 11.5 Consensus size: 10
91524 CTTTAAAAAA
91534 CACATATAAT
1 CACATATAAT
* *
91544 CACATACAAC
1 CACATATAAT
*
91554 CACATATAGT
1 CACATATAAT
91564 CACATATAAT
1 CACATATAAT
* *
91574 CACATTTAAC
1 CACATATAAT
91584 CACATATAAT
1 CACATATAAT
*
91594 CACATTTAAT
1 CACATATAAT
* *
91604 TACATTTAAT
1 CACATATAAT
91614 CACATATAAT
1 CACATATAAT
* *
91624 CATATTTAAT
1 CACATATAAT
*
91634 CACAT-TAGT
1 CACATATAAT
91643 CACAT
1 CACAT
91648 GAATATTTCA
Statistics
Matches: 86, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
9 8 0.09
10 78 0.91
ACGTcount: A:0.44, C:0.22, G:0.02, T:0.32
Consensus pattern (10 bp):
CACATATAAT
Found at i:91570 original size:30 final size:30
Alignment explanation
Indices: 91534--91639 Score: 140
Period size: 30 Copynumber: 3.5 Consensus size: 30
91524 CTTTAAAAAA
** *
91534 CACATATAATCACATACAACCACATATAGT
1 CACATATAATCACATTTAACCACATATAAT
91564 CACATATAATCACATTTAACCACATATAAT
1 CACATATAATCACATTTAACCACATATAAT
* * *
91594 CACATTTAATTACATTTAATCACATATAAT
1 CACATATAATCACATTTAACCACATATAAT
* *
91624 CATATTTAATCACATT
1 CACATATAATCACATT
91640 AGTCACATGA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.44, C:0.22, G:0.01, T:0.33
Consensus pattern (30 bp):
CACATATAATCACATTTAACCACATATAAT
Found at i:91696 original size:10 final size:10
Alignment explanation
Indices: 91672--91843 Score: 63
Period size: 10 Copynumber: 16.4 Consensus size: 10
91662 TTATCACATT
91672 ACATATTAATC
1 ACAT-TTAATC
*
91683 ACATTTAGTC
1 ACATTTAATC
91693 ACA-TTAATC
1 ACATTTAATC
*
91702 ACATTTGATC
1 ACATTTAATC
* *
91712 ACATGAATATTTC
1 ACAT--TTA-ATC
91725 AACATTT-ATC
1 -ACATTTAATC
91735 AC----AA-C
1 ACATTTAATC
91740 ACATATTAATC
1 ACAT-TTAATC
*
91751 ACATTTAGTC
1 ACATTTAATC
91761 ACATTTAATC
1 ACATTTAATC
*
91771 ACATGAATGT-TTC
1 ACAT---T-TAATC
91784 AACATTTATCACATC
1 -ACA-TT-T-A-ATC
*
91799 ACATATTAATT
1 ACAT-TTAATC
*
91810 ACATTTAGTC
1 ACATTTAATC
91820 ACATTTAATC
1 ACATTTAATC
*
91830 ATATTTAATC
1 ACATTTAATC
91840 ACAT
1 ACAT
91844 GAATATTATA
Statistics
Matches: 120, Mismatches: 19, Indels: 45
0.65 0.10 0.24
Matches are distributed among these distances:
5 3 0.03
6 1 0.01
9 10 0.08
10 64 0.53
11 15 0.12
12 5 0.04
13 7 0.06
14 12 0.10
15 3 0.03
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.38
Consensus pattern (10 bp):
ACATTTAATC
Found at i:91717 original size:68 final size:68
Alignment explanation
Indices: 91605--91893 Score: 305
Period size: 68 Copynumber: 4.4 Consensus size: 68
91595 ACATTTAATT
* * * * **
91605 ACAT-TTAATCACATATAATCATATTTAATCACATTAG-TCACATGAATATTTCAGTATTTATCA
1 ACATATTAATCACATTTAGTCACA-TTAATCACATTTGATCACATGAATATTTCAACATTTATCA
*
91668 CATT
65 CATC
91672 ACATATTAATCACATTTAGTCACATTAATCACATTTGATCACATGAATATTTCAACATTTATCAC
1 ACATATTAATCACATTTAGTCACATTAATCACATTTGATCACATGAATATTTCAACATTTATCAC
*
91737 AAC
66 ATC
*
91740 ACATATTAATCACATTTAGTCACATT--T---A----ATCACATGAATGTTTCAACATTTATCAC
1 ACATATTAATCACATTTAGTCACATTAATCACATTTGATCACATGAATATTTCAACATTTATCAC
91796 ATC
66 ATC
* * * * * *
91799 ACATATTAATTACATTTAGTCACATTTAATCATATTTAATCACATGAATATTAT-AGCAATAATC
1 ACATATTAATCACATTTAGTCACA-TTAATCACATTTGATCACATGAATATT-TCAACATTTATC
91863 ACATC
64 ACATC
* * *
91868 ACATATTAATCGCATATAATCACATT
1 ACATATTAATCACATTTAGTCACATT
91894 TAATGATTCT
Statistics
Matches: 190, Mismatches: 19, Indels: 25
0.81 0.08 0.11
Matches are distributed among these distances:
59 52 0.27
60 2 0.01
62 1 0.01
63 1 0.01
65 1 0.01
66 1 0.01
67 16 0.08
68 70 0.37
69 45 0.24
70 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.37
Consensus pattern (68 bp):
ACATATTAATCACATTTAGTCACATTAATCACATTTGATCACATGAATATTTCAACATTTATCAC
ATC
Found at i:91763 original size:59 final size:59
Alignment explanation
Indices: 91682--91830 Score: 230
Period size: 59 Copynumber: 2.6 Consensus size: 59
91672 ACATATTAAT
* * *
91682 CACAT-TTAGTCACA-TTAATCACATTTGATCACATGAATATTTCAACATTTATCACAA
1 CACATATTAATCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCACAA
* *
91739 CACATATTAATCACATTTAGTCACATTTAATCACATGAATGTTTCAACATTTATCACAT
1 CACATATTAATCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCACAA
*
91798 CACATATTAATTACATTTAGTCACATTTAATCA
1 CACATATTAATCACATTTAGTCACATTTAATCA
91831 TATTTAATCA
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
57 5 0.06
58 8 0.10
59 71 0.85
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (59 bp):
CACATATTAATCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCACAA
Found at i:91836 original size:69 final size:69
Alignment explanation
Indices: 91739--91897 Score: 203
Period size: 69 Copynumber: 2.3 Consensus size: 69
91729 TTTATCACAA
* * * *
91739 CACATATTAATCACATTTAGTCACATTTAATCACATGAATGTT-TCAACATTTATCACATCACAT
1 CACAT-TTAATCACATTTAATCACATTTAATCACATGAATATTAT-AACAATAATCACATCACAT
91803 ATTAAT
64 ATTAAT
* * * *
91809 TACATTTAGTCACATTTAATCATATTTAATCACATGAATATTATAGCAATAATCACATCACATAT
1 CACATTTAATCACATTTAATCACATTTAATCACATGAATATTATAACAATAATCACATCACATAT
91874 TAAT
66 TAAT
* *
91878 CGCATATAATCACATTTAAT
1 CACATTTAATCACATTTAAT
91898 GATTCTTTAT
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
69 71 0.93
70 5 0.07
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.37
Consensus pattern (69 bp):
CACATTTAATCACATTTAATCACATTTAATCACATGAATATTATAACAATAATCACATCACATAT
TAAT
Found at i:91889 original size:26 final size:26
Alignment explanation
Indices: 91818--91892 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 26
91808 TTACATTTAG
** *
91818 TCACAT-TTAATCATATTTAATCACA
1 TCACATATTAATCGCATATAATCACA
* *
91843 TGA-ATATT-ATAGCA-ATAATCACA
1 TCACATATTAATCGCATATAATCACA
91866 TCACATATTAATCGCATATAATCACA
1 TCACATATTAATCGCATATAATCACA
91892 T
1 T
91893 TTAATGATTC
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
23 10 0.26
24 10 0.26
25 9 0.23
26 10 0.26
ACGTcount: A:0.43, C:0.19, G:0.04, T:0.35
Consensus pattern (26 bp):
TCACATATTAATCGCATATAATCACA
Found at i:92103 original size:67 final size:65
Alignment explanation
Indices: 91974--92107 Score: 180
Period size: 67 Copynumber: 2.0 Consensus size: 65
91964 GATACACAAA
* * * *
91974 TCTCCAAACACACCAAATGACTCATAGAGTCAACATATCTCATAAGTGAAGCATATAACTAACAC
1 TCTCCAAACACACAAAAAGACTCATAGAGTCAACATATCCCAAAAGTGAAGCATATAACTAACAC
* *
92039 TCTCCAAACACAACAAAAAGACTCATAGAGTCAAACATGTCCCAAAAGTGAAGTATA-AAGCTAA
1 TCTCCAAACAC-ACAAAAAGACTCATAGAGTC-AACATATCCCAAAAGTGAAGCATATAA-CTAA
92103 CAC
63 CAC
92106 TC
1 TC
92108 ACCTTATTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
65 11 0.18
66 20 0.33
67 29 0.48
ACGTcount: A:0.45, C:0.25, G:0.10, T:0.19
Consensus pattern (65 bp):
TCTCCAAACACACAAAAAGACTCATAGAGTCAACATATCCCAAAAGTGAAGCATATAACTAACAC
Found at i:92434 original size:36 final size:36
Alignment explanation
Indices: 92367--92627 Score: 270
Period size: 36 Copynumber: 6.9 Consensus size: 36
92357 ATAATCACTG
*
92367 TCACATGGCATGAAAAACATACCCACATATTTACTA
1 TCACATGGCATGAATAACATACCCACATATTTACTA
* * * * *
92403 TCACCTGACTTGAATAACACACCCACATATTTACCA
1 TCACATGGCATGAATAACATACCCACATATTTACTA
*
92439 TCACATGGCATGAATAACATACCCACATATTTACTG
1 TCACATGGCATGAATAACATACCCACATATTTACTA
* *
92475 TCTCATGGCATGAATAATATACCCACATATTTACCCACATATTTACTG
1 TCACATGGCATG----A-ATA---AC--A--TACCCACATATTTACTA
*
92523 TCACATGGCATGAATAACATACCCACATATTTACTG
1 TCACATGGCATGAATAACATACCCACATATTTACTA
* * *
92559 TCTCATGGCATGAATAACATACTCACATATTTACTG
1 TCACATGGCATGAATAACATACCCACATATTTACTA
* **
92595 TCACATGACATGAATAACATAGTCACATATTTA
1 TCACATGGCATGAATAACATACCCACATATTTA
92628 TTTTCACAAT
Statistics
Matches: 194, Mismatches: 19, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
36 152 0.78
38 1 0.01
40 3 0.02
41 3 0.02
43 3 0.02
44 3 0.02
46 1 0.01
48 28 0.14
ACGTcount: A:0.37, C:0.25, G:0.09, T:0.29
Consensus pattern (36 bp):
TCACATGGCATGAATAACATACCCACATATTTACTA
Found at i:92511 original size:12 final size:12
Alignment explanation
Indices: 92494--92520 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
92484 ATGAATAATA
92494 TACCCACATATT
1 TACCCACATATT
92506 TACCCACATATT
1 TACCCACATATT
92518 TAC
1 TAC
92521 TGTCACATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (12 bp):
TACCCACATATT
Found at i:92522 original size:48 final size:48
Alignment explanation
Indices: 92458--92556 Score: 180
Period size: 48 Copynumber: 2.1 Consensus size: 48
92448 ATGAATAACA
* *
92458 TACCCACATATTTACTGTCTCATGGCATGAATAATATACCCACATATT
1 TACCCACATATTTACTGTCACATGGCATGAATAACATACCCACATATT
92506 TACCCACATATTTACTGTCACATGGCATGAATAACATACCCACATATT
1 TACCCACATATTTACTGTCACATGGCATGAATAACATACCCACATATT
92554 TAC
1 TAC
92557 TGTCTCATGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.31
Consensus pattern (48 bp):
TACCCACATATTTACTGTCACATGGCATGAATAACATACCCACATATT
Found at i:92564 original size:84 final size:84
Alignment explanation
Indices: 92423--92592 Score: 304
Period size: 84 Copynumber: 2.0 Consensus size: 84
92413 TGAATAACAC
92423 ACCCACATATTTACCATCACATGGCATGAATAACATACCCACATATTTACTGTCTCATGGCATGA
1 ACCCACATATTTACCATCACATGGCATGAATAACATACCCACATATTTACTGTCTCATGGCATGA
*
92488 ATAATATACCCACATATTT
66 ATAACATACCCACATATTT
**
92507 ACCCACATATTTACTGTCACATGGCATGAATAACATACCCACATATTTACTGTCTCATGGCATGA
1 ACCCACATATTTACCATCACATGGCATGAATAACATACCCACATATTTACTGTCTCATGGCATGA
*
92572 ATAACATACTCACATATTT
66 ATAACATACCCACATATTT
92591 AC
1 AC
92593 TGTCACATGA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (84 bp):
ACCCACATATTTACCATCACATGGCATGAATAACATACCCACATATTTACTGTCTCATGGCATGA
ATAACATACCCACATATTT
Found at i:92647 original size:120 final size:120
Alignment explanation
Indices: 92386--92627 Score: 358
Period size: 120 Copynumber: 2.0 Consensus size: 120
92376 ATGAAAAACA
* * *
92386 TACCCACATATTTACTATCACCTGACTTGAATAACACACCCACATATTTACCATCACATGGCATG
1 TACCCACATATTTACTATCACATGGCATGAATAACACACCCACATATTTACCATCACATGGCATG
* * *
92451 AATAACATACCCACATATTTACTGTCTCATGGCATGAATAATATACCCACATATT
66 AATAACATACCCACATATTTACTGTCACATGACATGAATAACATACCCACATATT
* * ** *
92506 TACCCACATATTTACTGTCACATGGCATGAATAACATACCCACATATTTACTGTCTCATGGCATG
1 TACCCACATATTTACTATCACATGGCATGAATAACACACCCACATATTTACCATCACATGGCATG
* **
92571 AATAACATACTCACATATTTACTGTCACATGACATGAATAACATAGTCACATATT
66 AATAACATACCCACATATTTACTGTCACATGACATGAATAACATACCCACATATT
92626 TA
1 TA
92628 TTTTCACAAT
Statistics
Matches: 108, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (120 bp):
TACCCACATATTTACTATCACATGGCATGAATAACACACCCACATATTTACCATCACATGGCATG
AATAACATACCCACATATTTACTGTCACATGACATGAATAACATACCCACATATT
Found at i:94972 original size:33 final size:33
Alignment explanation
Indices: 94890--95031 Score: 92
Period size: 33 Copynumber: 4.4 Consensus size: 33
94880 ACGCTCATAA
* * *
94890 GAGCTAATCAGTCAGTATCCAATATGCTCGTAT
1 GAGCTAATCAATCAGTATACAATAAGCTCGTAT
* * * * *
94923 GAGTTGAGCATTCAGTATACAGTAAGCTCGTAT
1 GAGCTAATCAATCAGTATACAATAAGCTCGTAT
* * * *
94956 GAGCTAATCAACCAGTAAACAATATA-CTCATAA
1 GAGCTAATCAATCAGTATACAATA-AGCTCGTAT
* * * * * *
94989 GAG-TTATCAATCTGTAAACAGTATGCTCGTAA
1 GAGCTAATCAATCAGTATACAATAAGCTCGTAT
95021 GAGCT-ATCAAT
1 GAGCTAATCAAT
95032 ATGTAACCAA
Statistics
Matches: 84, Mismatches: 22, Indels: 7
0.74 0.19 0.06
Matches are distributed among these distances:
32 31 0.37
33 52 0.62
34 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (33 bp):
GAGCTAATCAATCAGTATACAATAAGCTCGTAT
Found at i:95517 original size:32 final size:32
Alignment explanation
Indices: 94942--95619 Score: 784
Period size: 32 Copynumber: 21.2 Consensus size: 32
94932 ATTCAGTATA
* * * * *
94942 CAGTAAGCTCGTATGAGCTAATCAACCAGTAAA
1 CAGTATGCTCGTAAGAGCT-ATCAATCTGTAAC
* * * * *
94975 CAATATACTCATAAGAGTTATCAATCTGTAAA
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
*
95007 CAGTATGCTCGTAAGAGCTATCAATATGTAAC
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
* * * *
95039 CAATATGCTAGTAAGAGCTATCATTCTGTAAT
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
* * *
95071 CAGTATGCTCATAAGAGCTAGCAATCTATAAC
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
*
95103 CAGTATACTCGTAAGAGCTATCAATCTGTAAC
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
* * * * *
95135 CATTATGCTCATAAGAGCTATTAATATGTAAT
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
* * * *
95167 CAATATGCTCGTAAGAGATATCAAACTATAAC
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
* * *
95199 CAATATGCTCGTAAGAGCTATCAAACTATAAC
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
* * * * *
95231 CAATATGCTAGTAAGAGCTATAAATATGTAAT
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
* *
95263 CAGTATGCTCGTAGGAGCTATCAATCTGTAAT
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
95295 CAGTATGCTCGTAAGAGCTATCAAT-TGGTAAC
1 CAGTATGCTCGTAAGAGCTATCAATCT-GTAAC
* *
95327 CAATATGCTCGTAAGAGCTATCAATCTGTAAT
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
* *
95359 CAGTATGCTCATAAGAGCTAGCAATCTGTAAC
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
* * *
95391 CAATATGCTCGTAAGAGCTATCAATATGTAAT
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
*
95423 CAGTATGCTCGTAAGAGCTATCAATCTGTAAT
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
*
95455 CAGTATGCTTGTAAGAGCTATCAAAT-TGTAAC
1 CAGTATGCTCGTAAGAGCTATC-AATCTGTAAC
* * * *
95487 CAATATGCTAGTAAGAGCTATCAATATGTAAT
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
* * *
95519 CAGTATGCTCGTATGAGATACCAATCTGTAAC
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
* *
95551 CAGTATGCTCGTAAGAGTTATCAATTTGTAAC
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
* * *
95583 TAGTATGCTCGTAAGAGCTATTAATCTGTAAT
1 CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
95615 CAGTA
1 CAGTA
95620 CACTTTATGC
Statistics
Matches: 548, Mismatches: 93, Indels: 9
0.84 0.14 0.01
Matches are distributed among these distances:
31 4 0.01
32 527 0.96
33 17 0.03
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (32 bp):
CAGTATGCTCGTAAGAGCTATCAATCTGTAAC
Found at i:101840 original size:29 final size:29
Alignment explanation
Indices: 101743--101823 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
101733 TATACCGGTC
* *
101743 ATTATAGCTATCAGGTACTTTGTATTGGT
1 ATTATAGTTATCAGGCACTTTGTATTGGT
101772 ATTATAGTTATCAGGCACTTTGTATTGGT
1 ATTATAGTTATCAGGCACTTTGTATTGGT
101801 ATTATAGTTATCAGGCACTTTGT
1 ATTATAGTTATCAGGCACTTTGT
101824 TCTAGTGTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (29 bp):
ATTATAGTTATCAGGCACTTTGTATTGGT
Found at i:104369 original size:13 final size:12
Alignment explanation
Indices: 104351--104403 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 12
104341 ACTCCAAATC
104351 CTTAAACCTTAAA
1 CTTAAACC-TAAA
104364 CTTAAATCCTAAA
1 CTTAAA-CCTAAA
104377 CTTAAACCTAAA
1 CTTAAACCTAAA
104389 CCTTAAACTCTAAA
1 -CTTAAAC-CTAAA
104403 C
1 C
104404 CTTAGGGTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.16
13 24 0.65
14 7 0.19
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.28
Consensus pattern (12 bp):
CTTAAACCTAAA
Found at i:104385 original size:26 final size:26
Alignment explanation
Indices: 104329--104403 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 26
104319 AACTTGCAAC
* *
104329 CCTAAACCCTAAACTCCAAATCCTTAAA
1 CCTAAACCTTAAACTCTAAA--CTTAAA
104357 CCTTAAA-CTTAAA-TCCTAAACTTAAA
1 CC-TAAACCTTAAACT-CTAAACTTAAA
104383 CCTAAACCTTAAACTCTAAAC
1 CCTAAACCTTAAACTCTAAAC
104404 CTTAGGGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
25 4 0.10
26 20 0.49
27 2 0.05
28 11 0.27
29 4 0.10
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (26 bp):
CCTAAACCTTAAACTCTAAACTTAAA
Done.