Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004387.1 Kokia drynarioides strain JFW-HI SEQ_117763, 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: 62776
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:862 original size:35 final size:35
Alignment explanation
Indices: 823--894 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
813 ACAAGAATAT
* * *
823 GAGAGGTTGAGGAAGATGAAAGGTTAAAGGTCAAG
1 GAGAGGTTAAGGAAGAAGAAAGGTTAAAAGTCAAG
*
858 GAGAGGTTAAGGAAGAAGGAAGGTTAAAAGTCAAG
1 GAGAGGTTAAGGAAGAAGAAAGGTTAAAAGTCAAG
893 GA
1 GA
895 AGATGAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.43, C:0.03, G:0.39, T:0.15
Consensus pattern (35 bp):
GAGAGGTTAAGGAAGAAGAAAGGTTAAAAGTCAAG
Found at i:893 original size:17 final size:17
Alignment explanation
Indices: 842--896 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
832 AGGAAGATGA
*
842 AAGGTTAAAGGTCAAGG
1 AAGGTTAAAAGTCAAGG
859 AGAGGTTAAGGAAG--AAGG
1 A-AGGTTAA--AAGTCAAGG
877 AAGGTTAAAAGTCAAGG
1 AAGGTTAAAAGTCAAGG
894 AAG
1 AAG
897 ATGAAAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
15 3 0.09
17 15 0.47
18 12 0.38
20 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.36, T:0.15
Consensus pattern (17 bp):
AAGGTTAAAAGTCAAGG
Found at i:3865 original size:19 final size:19
Alignment explanation
Indices: 3841--3878 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3831 TCTTACATGT
3841 GTCTCGCATGCCTAAGGGC
1 GTCTCGCATGCCTAAGGGC
3860 GTCTCGCATGCCTAAGGGC
1 GTCTCGCATGCCTAAGGGC
3879 TGCAAACTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.32, T:0.21
Consensus pattern (19 bp):
GTCTCGCATGCCTAAGGGC
Found at i:11992 original size:10 final size:10
Alignment explanation
Indices: 11977--12001 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11967 TACATGTATA
11977 TATATATATG
1 TATATATATG
11987 TATATATATG
1 TATATATATG
11997 TATAT
1 TATAT
12002 TTGAAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (10 bp):
TATATATATG
Found at i:15880 original size:105 final size:105
Alignment explanation
Indices: 15756--15961 Score: 272
Period size: 105 Copynumber: 2.0 Consensus size: 105
15746 TATTTTCATG
* * *
15756 TATACTATATTGATTGATGCACATTGCAAGGATGGAAAGATTTCTGAAGCAT-TAGATACCACTG
1 TATAATATATTGATTGATGCACATTGCAAGGAGGGAAAGATTTCTGAAGC-TGAAGATACCACTG
15820 ACACAATGAAAAAGCA-AGGCATTGAGCCTAATGTTGTCACA
65 ACACAATGAAAAAGCATA-GCATTGAGCCTAATGTTGTCACA
* * * * ****
15861 TATAATATATTGGTTGATGCGCATTGCAAGGAGGGGAAGGTTTCTGAAGCTGAAGATATTGTTGA
1 TATAATATATTGATTGATGCACATTGCAAGGAGGGAAAGATTTCTGAAGCTGAAGATACCACTGA
*
15926 CACAATGATAAAGCATAGCATTGAGCCTAATGTTGT
66 CACAATGAAAAAGCATAGCATTGAGCCTAATGTTGT
15962 TACCTATGGT
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
104 1 0.01
105 85 0.98
106 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (105 bp):
TATAATATATTGATTGATGCACATTGCAAGGAGGGAAAGATTTCTGAAGCTGAAGATACCACTGA
CACAATGAAAAAGCATAGCATTGAGCCTAATGTTGTCACA
Found at i:18985 original size:26 final size:26
Alignment explanation
Indices: 18955--19013 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
18945 AGAAGTGTAT
18955 AACTAATTTGGTTTAAATTATGTTTG
1 AACTAATTTGGTTTAAATTATGTTTG
18981 AACTAATTTGGTTTAAATTATGTTTG
1 AACTAATTTGGTTTAAATTATGTTTG
*
19007 AATTAAT
1 AACTAAT
19014 AGAAATTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (26 bp):
AACTAATTTGGTTTAAATTATGTTTG
Found at i:20856 original size:109 final size:109
Alignment explanation
Indices: 20711--20924 Score: 308
Period size: 109 Copynumber: 2.0 Consensus size: 109
20701 AACAAAGAAT
* * *
20711 ATTTATCGATTTTAAATAAAATATTCAATTATTTAGGTTCAAAGAAAAATCATACCCAATATGTT
1 ATTTATCAATTTTAAATAAAATATTCAATTACTTAGGTTCAAAGAAAAATAATACCCAATATGTT
* * *
20776 -AGAGCACAATTTCT-TGAGTTCTCTAAAATAAAATAACATTGAAC
66 AAG-GCACAATTTCTAT-AATTCCCCAAAATAAAATAACATTGAAC
* *
20820 ATTTATCAATTTTAAA-AAGGATATTCAATTACTTAGGTTCAACGAAAAATAATACCCAATATGT
1 ATTTATCAATTTTAAATAA-AATATTCAATTACTTAGGTTCAAAGAAAAATAATACCCAATATGT
20884 TAAGGCACAATTTCTATAATTCCCCAAAATAAAATAACATT
65 TAAGGCACAATTTCTATAATTCCCCAAAATAAAATAACATT
20925 ATCTCGGTTT
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
108 2 0.02
109 89 0.95
110 3 0.03
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (109 bp):
ATTTATCAATTTTAAATAAAATATTCAATTACTTAGGTTCAAAGAAAAATAATACCCAATATGTT
AAGGCACAATTTCTATAATTCCCCAAAATAAAATAACATTGAAC
Found at i:23117 original size:46 final size:46
Alignment explanation
Indices: 23038--23279 Score: 241
Period size: 45 Copynumber: 5.4 Consensus size: 46
23028 GCTTCTGTGA
* * * * *
23038 GATGGTAGCTTCAATCTTCCCCTTTTGATTTAGGGGGT-AAATATTG
1 GATGGTGGCTTCAATCTACCCCTATTGAATTA-GGGGTAAAAGATTG
** * * *
23084 GACAGTGGCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTACCCCTATTGAATTAGGGGTAAAAGATTG
* * *
23130 AATGGTGACTTCAATCTACCCCTATT-AATTAGGGGTAAAATATTG
1 GATGGTGGCTTCAATCTACCCCTATTGAATTAGGGGTAAAAGATTG
* *
23175 GATGGTGACTTCAATCCACCCCTATT-AATTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTACCCCTATTGAATTAGGGGTAAAAGATTG
** *
23220 GATGGTGGCTTCAATCTGTCCCTCTTG--TTA-GGGTAAAAGATT-
1 GATGGTGGCTTCAATCTACCCCTATTGAATTAGGGGTAAAAGATTG
*
23262 -A-GATGGCTTCAATCTACC
1 GATGGTGGCTTCAATCTACC
23280 TCGATACCTC
Statistics
Matches: 168, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
40 14 0.08
41 1 0.01
43 12 0.07
44 3 0.02
45 85 0.51
46 53 0.32
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (46 bp):
GATGGTGGCTTCAATCTACCCCTATTGAATTAGGGGTAAAAGATTG
Found at i:26779 original size:105 final size:104
Alignment explanation
Indices: 26597--26819 Score: 313
Period size: 105 Copynumber: 2.1 Consensus size: 104
26587 CACTTAATAC
* * *
26597 TGTCACATATAATATATTGATCGATGCACATTGTAAGGATGGGAAGATTTTTGAAGCAATGGATA
1 TGTCACATATAATATATTGATCGATGCACATTGCAAAGATGGGAAGATTTCTGAAGCAA-GGATA
26662 CTGTTGACACAATGGAAAAGCAAGGCATTGAGCCTAATGT
65 CTGTTGACACAATGGAAAAGCAAGGCATTGAGCCTAATGT
* * *
26702 TGTCACATATAATATATTGGTTGATGCACATTGCAAAGATGGGAAGGTTTCTGAAGCTGAA-GAT
1 TGTCACATATAATATATTGATCGATGCACATTGCAAAGATGGGAAGATTTCTGAAGC--AAGGAT
* * *
26766 ATTGTTGACACAATGGTAAAGCATGGCATTGAGCCTAATGT
64 ACTGTTGACACAATGGAAAAGCAAGGCATTGAGCCTAATGT
* *
26807 TGTTACCTATAAT
1 TGTCACATATAAT
26820 GCTTTAATAA
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
105 103 0.98
107 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (104 bp):
TGTCACATATAATATATTGATCGATGCACATTGCAAAGATGGGAAGATTTCTGAAGCAAGGATAC
TGTTGACACAATGGAAAAGCAAGGCATTGAGCCTAATGT
Found at i:31960 original size:18 final size:16
Alignment explanation
Indices: 31937--32009 Score: 65
Period size: 18 Copynumber: 4.2 Consensus size: 16
31927 CTCAACCCAT
31937 TTTAAATTTATTCTAAAA
1 TTTAAATTTATT-T-AAA
*
31955 TTTAAATTTAATTTAAG
1 TTTAAATTT-ATTTAAA
31972 TTTAAATTTATATTTAAA
1 TTTAAA-TT-TATTTAAA
**
31990 TTTAAAACTATTATAAA
1 TTTAAATTTATT-TAAA
32007 TTT
1 TTT
32010 GAATGTACAG
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
16 4 0.09
17 15 0.32
18 24 0.51
19 4 0.09
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:31961 original size:6 final size:6
Alignment explanation
Indices: 31952--31995 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
31942 ATTTATTCTA
* *
31952 AAATTT AAATTT -AATTT AAGTTT AAATTT ATATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAA
31996 ACTATTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:31981 original size:12 final size:11
Alignment explanation
Indices: 31937--31994 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 11
31927 CTCAACCCAT
31937 TTTAAATTT-A
1 TTTAAATTTAA
31947 TTCTAAAATTTAAA
1 TT-T-AAATTT-AA
31961 TTT-AATTTAA
1 TTTAAATTTAA
31971 GTTTAAATTTATA
1 -TTTAAATTTA-A
31984 TTTAAATTTAA
1 TTTAAATTTAA
31995 AACTATTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
10 4 0.10
11 10 0.24
12 22 0.54
13 2 0.05
14 3 0.07
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:32766 original size:3 final size:3
Alignment explanation
Indices: 32758--32844 Score: 63
Period size: 3 Copynumber: 29.0 Consensus size: 3
32748 AAATGAACAT
* * * *
32758 TAA TAA TAA TAA TAA TGA TGA TGA TGAA T-A TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* * *
32803 TAA TAG TAA TGAA T-T TAT TAA TAA TAA TAAA TAA T-A TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
32845 ATAAAGAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
2 5 0.07
3 57 0.81
4 8 0.11
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:32794 original size:30 final size:30
Alignment explanation
Indices: 32749--32847 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 30
32739 ATATGCATTA
* *
32749 AATGAACATTAATAATAATAATAATGAT-GAT
1 AATGAATA-TAATAATAATAATAATAATAG-T
* *
32780 GATGAATATAATAATATTAATAATAATAGT
1 AATGAATATAATAATAATAATAATAATAGT
* *
32810 AATGAATTTATTAATAATAATAAATAATA-T
1 AATGAATATAATAATAATAAT-AATAATAGT
*
32840 AATAAATA
1 AATGAATA
32848 AAGAAAATAG
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
30 42 0.75
31 14 0.25
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.35
Consensus pattern (30 bp):
AATGAATATAATAATAATAATAATAATAGT
Found at i:34058 original size:29 final size:29
Alignment explanation
Indices: 33989--34088 Score: 112
Period size: 29 Copynumber: 3.4 Consensus size: 29
33979 GGAGGTCCCT
** *
33989 AAACTTCCAAAATTTTATTTTTGACCTCA
1 AAACTTCCAAAATTACATTTTTGACCCCA
* ** *
34018 AAAATTTTAAAATTAACATTTTT-ACCCCT
1 AAACTTCCAAAATT-ACATTTTTGACCCCA
34047 AAACTTCCAAAAATTACATTTTTGACCCCA
1 AAACTTCC-AAAATTACATTTTTGACCCCA
34077 AAACTTCCAAAA
1 AAACTTCCAAAA
34089 AATACTAATT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 32 0.56
30 25 0.44
ACGTcount: A:0.41, C:0.22, G:0.02, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAATTACATTTTTGACCCCA
Found at i:34060 original size:30 final size:30
Alignment explanation
Indices: 33989--34089 Score: 109
Period size: 30 Copynumber: 3.4 Consensus size: 30
33979 GGAGGTCCCT
** *
33989 AAACTTCC-AAAATTTTATTTTTGACCTCA
1 AAACTTCCAAAAATTACATTTTTGACCCCA
* ** *
34018 AAAATT-TTAAAATTAACATTTTT-ACCCCT
1 AAACTTCCAAAAATT-ACATTTTTGACCCCA
34047 AAACTTCCAAAAATTACATTTTTGACCCCA
1 AAACTTCCAAAAATTACATTTTTGACCCCA
34077 AAACTTCCAAAAA
1 AAACTTCCAAAAA
34090 ATACTAATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
29 28 0.48
30 30 0.52
ACGTcount: A:0.42, C:0.22, G:0.02, T:0.35
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTGACCCCA
Found at i:34104 original size:29 final size:29
Alignment explanation
Indices: 34033--34104 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
34023 TTTAAAATTA
* * *
34033 ACATTTTTACCCCTAAACTTCCAAAAATT
1 ACATATTTACCCCAAAACTTCCAAAAAAT
*
34062 ACATTTTTGACCCCAAAACTTCCAAAAAAT
1 ACATATTT-ACCCCAAAACTTCCAAAAAAT
34092 AC-TAATTTACCCC
1 ACAT-ATTTACCCC
34105 CGGAAGTCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 14 0.37
30 24 0.63
ACGTcount: A:0.39, C:0.29, G:0.01, T:0.31
Consensus pattern (29 bp):
ACATATTTACCCCAAAACTTCCAAAAAAT
Found at i:34115 original size:59 final size:59
Alignment explanation
Indices: 34052--34189 Score: 150
Period size: 59 Copynumber: 2.3 Consensus size: 59
34042 CCCCTAAACT
* *
34052 TCCAAAAATTACATTTTTGACCCCAAAACTTCCAAAAAATACTAATTTACCCCCGGAAG
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAAATACCAATTTACCCCCGGAAG
* * * *** * * * * *
34111 TCCAAAAATTCCTTTTTTGATCTCAATTTTTCTAAAAATTACCATTTTACCCTCGGATG
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAAATACCAATTTACCCCCGGAAG
*
34170 TCCAAAAATTCCGTTTTTGA
1 TCCAAAAATTCCATTTTTGA
34190 TCCAATTTTT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.35
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAAATACCAATTTACCCCCGGAAG
Found at i:34203 original size:58 final size:59
Alignment explanation
Indices: 34097--34221 Score: 198
Period size: 59 Copynumber: 2.1 Consensus size: 59
34087 AAAATACTAA
*
34097 TTTACCCCCGGAAGTCCAAAAATTCCTTTTTTGATCTCAATTTTTCTAAAAATTACCAT
1 TTTACCCCCGGAAGTCCAAAAATTCCGTTTTTGATCTCAATTTTTCTAAAAATTACCAT
* * * *
34156 TTTACCCTCGGATGTCCAAAAATTCCGTTTTTGATC-CAATTTTTCTAAAAATTATCGT
1 TTTACCCCCGGAAGTCCAAAAATTCCGTTTTTGATCTCAATTTTTCTAAAAATTACCAT
34214 TTTACCCC
1 TTTACCCC
34222 TAATGTTTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
58 27 0.45
59 33 0.55
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (59 bp):
TTTACCCCCGGAAGTCCAAAAATTCCGTTTTTGATCTCAATTTTTCTAAAAATTACCAT
Found at i:36255 original size:15 final size:15
Alignment explanation
Indices: 36216--36255 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
36206 TGAGAAAATT
36216 AAAAAAAAAATCACA
1 AAAAAAAAAATCACA
* *
36231 AAACAAAAAATCAGA
1 AAAAAAAAAATCACA
36246 AAAAAAAAAA
1 AAAAAAAAAA
36256 GTTATGGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.82, C:0.10, G:0.03, T:0.05
Consensus pattern (15 bp):
AAAAAAAAAATCACA
Found at i:36289 original size:30 final size:30
Alignment explanation
Indices: 36255--36315 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
36245 AAAAAAAAAA
36255 AGTTATGGAAGTTCTAAAAAATGAGAAATT
1 AGTTATGGAAGTTCTAAAAAATGAGAAATT
36285 AGTTATGGAAGTTCTAAAAAATGAGAAATT
1 AGTTATGGAAGTTCTAAAAAATGAGAAATT
36315 A
1 A
36316 TAAAATATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.03, G:0.20, T:0.30
Consensus pattern (30 bp):
AGTTATGGAAGTTCTAAAAAATGAGAAATT
Found at i:36364 original size:19 final size:18
Alignment explanation
Indices: 36342--36381 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
36332 AAAAATACAT
36342 AAAATACAAAAAAAAAACG
1 AAAATACAAAAAAAAAA-G
* *
36361 AAAATTCAAAATAAAAAG
1 AAAATACAAAAAAAAAAG
36379 AAA
1 AAA
36382 TATGTAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.78, C:0.07, G:0.05, T:0.10
Consensus pattern (18 bp):
AAAATACAAAAAAAAAAG
Found at i:39349 original size:24 final size:24
Alignment explanation
Indices: 39292--39350 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
39282 TTTAGCCAAC
* *
39292 ACGAGCCCAAAATGATTAGCTTTT
1 ACGAGCCCAGAATGATTAGCTCTT
*
39316 ACAAGCCCAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
39340 ACGAGCCCAGA
1 ACGAGCCCAGA
39351 CAGAGTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (24 bp):
ACGAGCCCAGAATGATTAGCTCTT
Found at i:43503 original size:24 final size:24
Alignment explanation
Indices: 43475--43525 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
43465 AGAAATTATC
* *
43475 TTTCAGTTAGACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
43499 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
43523 TTT
1 TTT
43526 GAGTCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:43534 original size:24 final size:24
Alignment explanation
Indices: 43485--43537 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
43475 TTTCAGTTAG
*
43485 ACTCTGTTTATTTGTTTCAATTAA
1 ACTCTGTTTATTTGTTTCAATCAA
* *
43509 ACTCTGTTTATTTGTTTGAGTCAA
1 ACTCTGTTTATTTGTTTCAATCAA
43533 ACTCT
1 ACTCT
43538 TATTAGTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.11, T:0.51
Consensus pattern (24 bp):
ACTCTGTTTATTTGTTTCAATCAA
Found at i:45447 original size:24 final size:24
Alignment explanation
Indices: 45396--45450 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
45386 TCTTTCGGTT
*
45396 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTGTTTCAATA
* *
45420 AAACTCTGTTTATTTGTTTGAGTA
1 AAACTCTGTTTATTTGTTTCAATA
45444 AAACTCT
1 AAACTCT
45451 TATTAGTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTCAATA
Found at i:47447 original size:20 final size:22
Alignment explanation
Indices: 47408--47448 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
47398 AGATCAAATT
47408 GATAAAATGTATAATATTAGAGG
1 GATAAAATGTAT-ATATTAGAGG
47431 GATAAAAT-TAT-TATTAGA
1 GATAAAATGTATATATTAGA
47449 CCAATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (22 bp):
GATAAAATGTATATATTAGAGG
Found at i:47953 original size:20 final size:21
Alignment explanation
Indices: 47925--48000 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 21
47915 TATACACATT
*
47925 TAAAAATATAAAAAT-AAATA
1 TAAATATATAAAAATAAAATA
* *
47945 TAAATATATAAAAATTCAAATT
1 TAAATATATAAAAA-TAAAATA
* *
47967 TATATAATCTAAAAATAAAATA
1 TAAAT-ATATAAAAATAAAATA
47989 TAAA-ATATAAAA
1 TAAATATATAAAA
48001 GAATTATAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 20 0.44
21 1 0.02
22 16 0.36
23 8 0.18
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAATATATAAAAATAAAATA
Found at i:49959 original size:60 final size:59
Alignment explanation
Indices: 49872--50060 Score: 236
Period size: 60 Copynumber: 3.2 Consensus size: 59
49862 TTAATATAAC
* * *
49872 ATTTCGTACCTGAACTTGACACTTTTTCTTAATTTGGTACCTAAATATTTTTTGGATCCA
1 ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAAT-TTTTTTGGATCCA
* *
49932 ATTTGGTACTTGAACTTGACACATTTTCCTAATTTGGTACCTAAACTTTTTTTGGACCCA
1 ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAA-TTTTTTTGGATCCA
* * * * * *
49992 ATTTGGTACTTAAACTTGGC-CTTTTTTCCTAATTTGGCACCTAAGCTTTTTTTAGATTCA
1 ATTTGGTACTTGAACTTGACAC-TTTTTCCTAATTTGGTACCTAA-ATTTTTTTGGATCCA
50052 ATTTGGTAC
1 ATTTGGTAC
50061 CTAAATTTAT
Statistics
Matches: 113, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
59 1 0.01
60 111 0.98
61 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (59 bp):
ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAATTTTTTTGGATCCA
Found at i:50337 original size:28 final size:28
Alignment explanation
Indices: 50271--50340 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
50261 AAATTGTCAC
* *
50271 GTTTGAGTAACAAATTGGACCCAAAAAAA
1 GTTTAAGTACCAAATTGGACCC-AAAAAA
*
50300 GTTTAGGTACCAAATTGGATCCC-AAAAA
1 GTTTAAGTACCAAATTGGA-CCCAAAAAA
50328 GTTTAAGTACCAA
1 GTTTAAGTACCAA
50341 CTTTAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 17 0.47
29 16 0.44
30 3 0.08
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (28 bp):
GTTTAAGTACCAAATTGGACCCAAAAAA
Found at i:50363 original size:31 final size:31
Alignment explanation
Indices: 50326--50406 Score: 83
Period size: 32 Copynumber: 2.6 Consensus size: 31
50316 GGATCCCAAA
*
50326 AAGTTTAAGTACCAACTTTA-AAAAAAGTGTC
1 AAGTTTAAGTACCAA-ATTAGAAAAAAGTGTC
* *
50357 AAGTTTAGGCACCAAATTAGGAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTA-GAAAAAAGTGTC
* * *
50389 AAATTTGAGTACAAAATT
1 AAGTTTAAGTACCAAATT
50407 GAACAGAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
30 3 0.08
31 13 0.32
32 24 0.60
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAGTGTC
Found at i:50819 original size:21 final size:22
Alignment explanation
Indices: 50789--50836 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
50779 GAAAAATATT
**
50789 TATATCATATTTTAATAATAAA
1 TATATCATATTGCAATAATAAA
*
50811 TATAT-ATATTGCAATTATAAA
1 TATATCATATTGCAATAATAAA
50832 TATAT
1 TATAT
50837 TAATAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (22 bp):
TATATCATATTGCAATAATAAA
Found at i:51442 original size:13 final size:13
Alignment explanation
Indices: 51424--51449 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51414 ATGCATTAAA
51424 TTAAAATTAAAAT
1 TTAAAATTAAAAT
51437 TTAAAATTAAAAT
1 TTAAAATTAAAAT
51450 CTCAACACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAATTAAAAT
Done.