Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012027.1 Kokia drynarioides strain JFW-HI SEQ_127025, 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: 144542
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:9636 original size:96 final size:96
Alignment explanation
Indices: 9463--9643 Score: 251
Period size: 96 Copynumber: 1.9 Consensus size: 96
9453 AGGATGTTCG
** * *
9463 ATTATTTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGAT
1 ATTATTTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGAT
*
9528 AAGGAAACATTGCCTCGATTAAGGGTATTCT
66 AAAGAAACATTGCCTCGATTAAGGGTATTCT
*
9559 ATTATTTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTT-TGAAACTCGAA-
1 ATTATTTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAG-AA-TCGAAG
*
9622 ATAAA-AGAATATTGCCTCGATT
64 ATAAAGA-AACATTGCCTCGATT
9644 TTAAAGTTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
95 2 0.03
96 68 0.91
97 5 0.07
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (96 bp):
ATTATTTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGAT
AAAGAAACATTGCCTCGATTAAGGGTATTCT
Found at i:10057 original size:29 final size:29
Alignment explanation
Indices: 10036--10281 Score: 279
Period size: 29 Copynumber: 8.4 Consensus size: 29
10026 AAAATGATAA
*
10036 TTTTGGAAGTTTCAGAGTCAAAAATGGAAT
1 TTTTGGAAGTTTCAGGGTC-AAAATGGAAT
*
10066 TTTTGGAAG-TTCGAGGGTAAAAATGGAAT
1 TTTTGGAAGTTTC-AGGGTCAAAATGGAAT
* *
10095 TTTTGGAAG-TTCGGGGGTAAAAATGGAAT
1 TTTTGGAAGTTTC-AGGGTCAAAATGGAAT
10124 TTTTGGAAGTTTC-GTGGTCAAAATGGAAT
1 TTTTGGAAGTTTCAG-GGTCAAAATGGAAT
**
10153 TTTTGGAAGTTAGAGGGT-AAAATTGGAAT
1 TTTTGGAAGTTTCAGGGTCAAAA-TGGAAT
* *
10182 TTTTTGAAGTTTCGGGGTCAAAATGGAAT
1 TTTTGGAAGTTTCAGGGTCAAAATGGAAT
* *
10211 TTTTGGAAG-TTCAAGGGTAAAAATGAAAT
1 TTTTGGAAGTTTC-AGGGTCAAAATGGAAT
*
10240 TTTTTGAAGTTTC-GAGGTCAAAAATGGAAT
1 TTTTGGAAGTTTCAG-GGTC-AAAATGGAAT
10270 TTTTGGAAGTTT
1 TTTTGGAAGTTT
10282 TGGGACCTCA
Statistics
Matches: 188, Mismatches: 18, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
28 9 0.05
29 135 0.72
30 44 0.23
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
TTTTGGAAGTTTCAGGGTCAAAATGGAAT
Found at i:10098 original size:87 final size:87
Alignment explanation
Indices: 10036--10280 Score: 320
Period size: 87 Copynumber: 2.8 Consensus size: 87
10026 AAAATGATAA
* *
10036 TTTTGGAAGTTTCAGAGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGG
1 TTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTCG
*
10101 AAGTTCGGGGGTAAAAATGGAAT
66 AAGTTC-GGGGTCAAAATGGAAT
* * *
10124 TTTTGGAAGTTTC-GTGGTC-AAAATGGAATTTTTGGAAGTTAGAGGGTAAAATTGGAATTTTTT
1 TTTTGGAAGTTTCAG-GGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTC
10187 GAAGTTTCGGGGTCAAAATGGAAT
65 GAAG-TTCGGGGTCAAAATGGAAT
* *
10211 TTTTGGAAG-TTCAAGGGT-AAAAATGAAATTTTTTGAAGTTTCGA-GGTCAAAAATGGAATTTT
1 TTTTGGAAGTTTC-AGGGTCAAAAATGGAATTTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTT
*
10273 TGGAAGTT
63 TCGAAGTT
10281 TTGGGACCTC
Statistics
Matches: 140, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
86 3 0.02
87 95 0.68
88 42 0.30
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (87 bp):
TTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTCG
AAGTTCGGGGTCAAAATGGAAT
Found at i:11359 original size:3 final size:3
Alignment explanation
Indices: 11353--11465 Score: 106
Period size: 3 Copynumber: 36.7 Consensus size: 3
11343 CTTTTTTTTA
* * *
11353 TAT TAT TAAT TACT AAT TAT TAT TAT TAT TAT TA- CACT TAT TAA TAT
1 TAT TAT T-AT TA-T TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* *
11400 TAT TA- AAGC TA- TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11445 TAT TAT TAT TAT TACT TAT TA
1 TAT TAT TAT TAT TA-T TAT TA
11466 CAAACAATGT
Statistics
Matches: 93, Mismatches: 8, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.04
3 77 0.83
4 12 0.13
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:12149 original size:6 final size:6
Alignment explanation
Indices: 12138--12207 Score: 60
Period size: 6 Copynumber: 12.2 Consensus size: 6
12128 ATTATTTAAA
* *
12138 TAAATT TAAATT TAAATT TCAAA-- TAAATT TAAATT TAAA-A TAAACT
1 TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT
*
12184 TAATTT TAAGA-- TAAATT TAAATT T
1 TAAATT TAA-ATT TAAATT TAAATT T
12208 TGTTGGGCCC
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
4 4 0.08
5 8 0.15
6 37 0.71
7 3 0.06
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:12161 original size:23 final size:22
Alignment explanation
Indices: 12131--12176 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 22
12121 ATTGGACATT
12131 ATTTAAATAAATTTAAATTTAA
1 ATTTAAATAAATTTAAATTTAA
12153 ATTTCAAATAAATTTAAATTTAA
1 ATTT-AAATAAATTTAAATTTAA
12176 A
1 A
12177 ATAAACTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTAAATAAATTTAAATTTAA
Found at i:12166 original size:17 final size:17
Alignment explanation
Indices: 12144--12207 Score: 92
Period size: 17 Copynumber: 3.8 Consensus size: 17
12134 TAAATAAATT
*
12144 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
12161 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* * *
12178 TAAACTTAATTTTAAGA
1 TAAATTTAAATTTAAAA
12195 TAAATTTAAATTT
1 TAAATTTAAATTT
12208 TGTTGGGCCC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:13606 original size:24 final size:24
Alignment explanation
Indices: 13555--13606 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
13545 TTCGTAAGTC
* *
13555 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
13579 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
13603 AAAT
1 AAAT
13607 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:15236 original size:27 final size:28
Alignment explanation
Indices: 15205--15258 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
15195 ACTTCATAAA
15205 TTTTA-AATTTAGTCTCC-CTACTTTTAT
1 TTTTAGAATTTAGTC-CCTCTACTTTTAT
15232 TTTTAGGAATTTAGTCCCTCTACTTTT
1 TTTTA-GAATTTAGTCCCTCTACTTTT
15259 CAAATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 5 0.21
28 2 0.08
29 17 0.71
ACGTcount: A:0.20, C:0.19, G:0.07, T:0.54
Consensus pattern (28 bp):
TTTTAGAATTTAGTCCCTCTACTTTTAT
Found at i:17939 original size:18 final size:20
Alignment explanation
Indices: 17898--17940 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
17888 CATCATTAAT
*
17898 AATTCAATTTTAATATAAAC
1 AATTCAATTATAATATAAAC
17918 -ATTCAA-TATAAT-TAAAC
1 AATTCAATTATAATATAAAC
17935 AATTCA
1 AATTCA
17941 CTAATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.24
18 10 0.48
19 6 0.29
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTCAATTATAATATAAAC
Found at i:18188 original size:30 final size:29
Alignment explanation
Indices: 18154--18296 Score: 135
Period size: 29 Copynumber: 4.8 Consensus size: 29
18144 GGATTGGAGG
*
18154 GAGTAAAAGTTTTAGGGGGAAAGTGAGAGA
1 GAGTAAAAGTTTT-GGGGGAAAATGAGAGA
*
18184 GAGTAAAAGTTTTGGGGGAAAAT-AAAGA
1 GAGTAAAAGTTTTGGGGGAAAATGAGAGA
** ** * * * *
18212 GTTTTGAAGTTTTTTGGGGAAAATAAATAGGG
1 GAGTAAAAG-TTTTGGGGGAAAAT-GAGA-GA
*
18244 GAGTAAAAGTTTTAGGGGGAAAGTGAGAGA
1 GAGTAAAAGTTTT-GGGGGAAAATGAGAGA
18274 GAGTAAAAGTTTTGGGGGAAAAT
1 GAGTAAAAGTTTTGGGGGAAAAT
18297 AAAGAGTTTT
Statistics
Matches: 89, Mismatches: 19, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
28 9 0.10
29 31 0.35
30 27 0.30
31 8 0.09
32 14 0.16
ACGTcount: A:0.39, C:0.00, G:0.36, T:0.25
Consensus pattern (29 bp):
GAGTAAAAGTTTTGGGGGAAAATGAGAGA
Found at i:18305 original size:90 final size:91
Alignment explanation
Indices: 18152--18327 Score: 327
Period size: 90 Copynumber: 1.9 Consensus size: 91
18142 TTGGATTGGA
18152 GGGAGTAAAAGTTTTAGGGGGAAAGTGAGAGAGAGTAAAAGTTTTGGGGGAAAATAAAGAGTTTT
1 GGGAGTAAAAGTTTTAGGGGGAAAGTGAGAGAGAGTAAAAGTTTTGGGGGAAAATAAAGAGTTTT
* *
18217 GAAGTTTTTTG-GGGAAAATAAATAG
66 GAAGATTTTGGAGGGAAAATAAATAG
18242 GGGAGTAAAAGTTTTAGGGGGAAAGTGAGAGAGAGTAAAAGTTTTGGGGGAAAATAAAGAGTTTT
1 GGGAGTAAAAGTTTTAGGGGGAAAGTGAGAGAGAGTAAAAGTTTTGGGGGAAAATAAAGAGTTTT
18307 GAAGATTTTGGAGGGAAAATA
66 GAAGATTTTGGAGGGAAAATA
18328 TTAAATAAAA
Statistics
Matches: 83, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
90 74 0.89
91 9 0.11
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (91 bp):
GGGAGTAAAAGTTTTAGGGGGAAAGTGAGAGAGAGTAAAAGTTTTGGGGGAAAATAAAGAGTTTT
GAAGATTTTGGAGGGAAAATAAATAG
Found at i:18406 original size:30 final size:30
Alignment explanation
Indices: 18370--18431 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
18360 AAATGGGAGG
* *
18370 GGAGTAAAAGTTTGGAGGGGAAAGTGAAAA
1 GGAGTAAAAGTTTGGAGGGAAAAGTAAAAA
*
18400 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
1 GGAGTAAAAGTTTGGAGGGAAAAGTAAAAA
18430 GG
1 GG
18432 TTTGGAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.37, T:0.18
Consensus pattern (30 bp):
GGAGTAAAAGTTTGGAGGGAAAAGTAAAAA
Found at i:19597 original size:6 final size:6
Alignment explanation
Indices: 19588--19650 Score: 69
Period size: 6 Copynumber: 11.0 Consensus size: 6
19578 AATTTATTCA
* **
19588 TAAATT TAAATT T-ATTT TAAATT TAAATT TAAATT T-GTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
19634 TAAATT T-AGTT TAAATT
1 TAAATT TAAATT TAAATT
19651 CGGAATGATT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
5 11 0.24
6 35 0.76
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (6 bp):
TAAATT
Found at i:19606 original size:23 final size:21
Alignment explanation
Indices: 19588--19641 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
19578 AATTTATTCA
19588 TAAATTTAAATTTATTTTAAATT
1 TAAATTTAAATTTATTTT--ATT
*
19611 TAAATTTAAATTTGTTTTAAATT
1 TAAATTTAAATTTATTTT--ATT
19634 TAAATTTA
1 TAAATTTA
19642 GTTTAAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TAAATTTAAATTTATTTTATT
Found at i:19610 original size:17 final size:17
Alignment explanation
Indices: 19574--19650 Score: 73
Period size: 17 Copynumber: 4.1 Consensus size: 17
19564 TTAAATTGGT
*
19574 TTTAAATTTATTCATAAA
1 TTTAAATTTATT-TTAAA
19592 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
19609 TTTAAATTTAAATTTGTTTTAAA
1 TTTAAATTT--A----TTTTAAA
*
19632 TTTAAATTTAGTTTAAA
1 TTTAAATTTATTTTAAA
19649 TT
1 TT
19651 CGGAATGATT
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
17 21 0.41
18 12 0.24
19 1 0.02
21 1 0.02
23 16 0.31
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:21587 original size:29 final size:29
Alignment explanation
Indices: 21534--21639 Score: 83
Period size: 29 Copynumber: 3.6 Consensus size: 29
21524 AACAGTCTAG
* *
21534 AAATTACATTTTAG-CCTTCGAACTTTCCA
1 AAATTTCATTTTTGACCTT-GAACTTTCCA
* **
21563 AAATTTCATTTTTGACCTTGCACTTTTTGA
1 AAATTTCATTTTTGACCTTGAAC-TTTCCA
* *
21593 AAATTTCATTTTT-ACCCATGAACTTTCTA
1 AAATTTCATTTTTGA-CCTTGAACTTTCCA
*
21622 AAA-TTCTATTTATGACCT
1 AAATTTC-ATTTTTGACCT
21640 CAAAAGTTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
28 3 0.05
29 30 0.49
30 28 0.46
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (29 bp):
AAATTTCATTTTTGACCTTGAACTTTCCA
Found at i:21618 original size:30 final size:30
Alignment explanation
Indices: 21562--21677 Score: 80
Period size: 30 Copynumber: 3.9 Consensus size: 30
21552 CGAACTTTCC
* *
21562 AAAATTTCATTTTTGA-CCTTGCACTTTTTG
1 AAAATTTCATTTTT-ACCCATGAACTTTTTG
*
21592 AAAATTTCATTTTTACCCATGAACTTTCT-
1 AAAATTTCATTTTTACCCATGAACTTTTTG
* **
21621 AAAA-TTCTATTTATGACCTCA--AAAGTTTTG
1 AAAATTTC-ATTT-TTACC-CATGAACTTTTTG
* * *
21651 AAAATTACATTTTTACCCCTAAACTTT
1 AAAATTTCATTTTTACCCATGAACTTT
21678 CAAGAATTCC
Statistics
Matches: 66, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
28 4 0.06
29 18 0.27
30 40 0.61
31 4 0.06
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (30 bp):
AAAATTTCATTTTTACCCATGAACTTTTTG
Found at i:21626 original size:59 final size:58
Alignment explanation
Indices: 21534--21785 Score: 163
Period size: 59 Copynumber: 4.3 Consensus size: 58
21524 AACAGTCTAG
* * *** **
21534 AAATTACA-TTTTAGCCTTCGAACTTTCCAAAATTTCATTTTTGACCTTGCACTTTTTGA
1 AAATTACATTTTTACCCAT-GAACTTT-CAAAATTTCATTTTTGACCTCAAAAGTTTTGA
* *
21593 AAATTTCATTTTTACCCATGAACTTTCTAAAA-TTCTATTTATGACCTCAAAAGTTTTGA
1 AAATTACATTTTTACCCATGAACTTTC-AAAATTTC-ATTTTTGACCTCAAAAGTTTTGA
* * * * * * **
21652 AAATTACATTTTTACCCCTAAACTTTCAAGAATTCCAATTTTGACCCCAAAA-CTTCCA
1 AAATTACATTTTTACCCATGAACTTTCAA-AATTTCATTTTTGACCTCAAAAGTTTTGA
* * * * * *
21710 AAATTACCATTTTT-CCCATGGA-TGTCTAAAAATTCCATTTTTAACCTCAAAACTTTTAA
1 AAATTA-CATTTTTACCCATGAACT-T-TCAAAATTTCATTTTTGACCTCAAAAGTTTTGA
* **
21769 AAACTACCCTTTTACCC
1 AAATTACATTTTTACCC
21786 TCAAATGTCC
Statistics
Matches: 151, Mismatches: 32, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
57 1 0.01
58 45 0.30
59 95 0.63
60 10 0.07
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.39
Consensus pattern (58 bp):
AAATTACATTTTTACCCATGAACTTTCAAAATTTCATTTTTGACCTCAAAAGTTTTGA
Found at i:21721 original size:29 final size:29
Alignment explanation
Indices: 21651--21722 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
21641 AAAAGTTTTG
* * *
21651 AAAATTA-CATTTTTACCCCTAAACTTTC
1 AAAATTACCATTTTGACCCCAAAACTTCC
21679 AAGAATT-CCAATTTTGACCCCAAAACTTCC
1 AA-AATTACC-ATTTTGACCCCAAAACTTCC
21709 AAAATTACCATTTT
1 AAAATTACCATTTT
21723 TCCCATGGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 2 0.05
29 14 0.38
30 21 0.57
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTACCATTTTGACCCCAAAACTTCC
Found at i:21770 original size:29 final size:27
Alignment explanation
Indices: 21587--21770 Score: 84
Period size: 29 Copynumber: 6.3 Consensus size: 27
21577 ACCTTGCACT
* *
21587 TTTTGAAAATTTCATTTTTACCCATGAAC
1 TTTT-AAAATTCCATTTTTACCCA-AAAC
* * *
21616 TTTCTAAAATTCTATTTATGACCTCAAAAG
1 TTT-TAAAATTCCATTT-TTACC-CAAAAC
* *
21646 TTTTGAAAATTACATTTTTACCCCTAAAC
1 TTTT-AAAATTCCATTTTTA-CCCAAAAC
* *
21675 TTTCAAGAATTCCAATTTTGACCCCAAAAC
1 TTTTAA-AATTCC-ATTTTTA-CCCAAAAC
** **
21705 TTCCAAAATTACCATTTTT-CCCATGGA-
1 TTTTAAAATT-CCATTTTTACCCA-AAAC
*
21732 TGTCTAAAAATTCCATTTTTAACCTCAAAAC
1 T-T-TTAAAATTCCATTTTT-ACC-CAAAAC
21763 TTTTAAAA
1 TTTTAAAA
21771 ACTACCCTTT
Statistics
Matches: 117, Mismatches: 23, Indels: 30
0.69 0.14 0.18
Matches are distributed among these distances:
27 5 0.04
28 12 0.10
29 48 0.41
30 47 0.40
31 5 0.04
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (27 bp):
TTTTAAAATTCCATTTTTACCCAAAAC
Found at i:21803 original size:117 final size:118
Alignment explanation
Indices: 21599--21810 Score: 252
Period size: 117 Copynumber: 1.8 Consensus size: 118
21589 TTGAAAATTT
* * * * * * *
21599 CATTTTTACCCATGAACTTTCTAAAATTCTATTTATGACCTCAAAAGTTTTGAAAATTACATTTT
1 CATTTTTACCCATGAACTGTCTAAAATTCCATTTATAACCTCAAAACTTTTAAAAACTACACTTT
* *
21664 TACCCCTAAACTTTCAAGAATTCCAATTTTGACCCCAAAACTTCCAAAATTAC
66 TACCCCTAAACTTCCAAAAATTCCAATTTTGACCCCAAAACTTCCAAAATTAC
* * *
21717 CATTTTT-CCCATGGA-TGTCTAAAAATTCCATTTTTAACCTCAAAACTTTTAAAAACTACCCTT
1 CATTTTTACCCATGAACTGTCT-AAAATTCCATTTATAACCTCAAAACTTTTAAAAACTACACTT
*
21780 TTA-CCCTCAAA-TGTCCAAAAATTCCATTTTT
65 TTACCCCT-AAACT-TCCAAAAATTCCAATTTT
21811 TTATCCAATT
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
116 9 0.12
117 62 0.79
118 7 0.09
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (118 bp):
CATTTTTACCCATGAACTGTCTAAAATTCCATTTATAACCTCAAAACTTTTAAAAACTACACTTT
TACCCCTAAACTTCCAAAAATTCCAATTTTGACCCCAAAACTTCCAAAATTAC
Found at i:27613 original size:65 final size:63
Alignment explanation
Indices: 27508--27668 Score: 180
Period size: 65 Copynumber: 2.4 Consensus size: 63
27498 TAGAATTTTA
*
27508 AGTTAATTGAATTGAATTATTTGAATAAATTTAAATATGTAATTTGAATTTTTAAGTTTGATTTG
1 AGTTAATTGAATTGAATTATTTGAATAAATTTAAATATGTAATTTG-A-TTTTAAGTTTGAGTTG
* * * * *
27573 GGTTAATTGATTTGAATTATTTGAGGT-AATTTGAATATGTAATTTGATTTTGAGTTTGAGTTG
1 AGTTAATTGAATTGAATTATTTGA-ATAAATTTAAATATGTAATTTGATTTTAAGTTTGAGTTG
*
27636 AGTTAAATTTTGCAATTCGAATTATTTAAATAA
1 AGTT-AA--TTG-AATT-GAATTATTTGAATAA
27669 CTCAAATAGC
Statistics
Matches: 79, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
63 17 0.22
64 3 0.04
65 40 0.51
66 4 0.05
67 4 0.05
68 11 0.14
ACGTcount: A:0.34, C:0.01, G:0.17, T:0.48
Consensus pattern (63 bp):
AGTTAATTGAATTGAATTATTTGAATAAATTTAAATATGTAATTTGATTTTAAGTTTGAGTTG
Found at i:32994 original size:17 final size:16
Alignment explanation
Indices: 32964--33007 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
32954 AAACCGAAAA
*
32964 TAAAAAAT-AT-ATTT
1 TAAAAAATAATAAATT
32978 TAAAAAATAATAAATT
1 TAAAAAATAATAAATT
32994 TAAAATAATAATAA
1 TAAAA-AATAATAA
33008 TAAGGGCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 8 0.31
15 2 0.08
16 8 0.31
17 8 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAAAATAATAAATT
Found at i:34542 original size:10 final size:10
Alignment explanation
Indices: 34511--34545 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
34501 ATTGAAATAT
34511 AATTATATAA
1 AATTATATAA
*
34521 AATT-TATGA
1 AATTATATAA
34530 AATTATATAA
1 AATTATATAA
34540 AATTAT
1 AATTAT
34546 TTAATTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (10 bp):
AATTATATAA
Found at i:38265 original size:43 final size:43
Alignment explanation
Indices: 38170--38474 Score: 295
Period size: 43 Copynumber: 7.3 Consensus size: 43
38160 TTGTGAGGAA
* *** * *
38170 AAACGCCGCTAAAAAACATGGTCTTTATTAGCGC-TTTCCTAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGCTTTTCCCAC
* *
38212 AAACGCCGCTAAAGAACATTGTCTTTAGCGGTGCTTTTCCTAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGCTTTTCCCAC
* * ** **
38255 AAATGCCGCTAAAGAACATGATCTTTAGCGGCACTACTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGCTTTTCCCAC
* * * *
38298 AAATGCCGCTAAAGGATATAGTCTTTAGCGGTGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGCTTTTCCCAC
* ** * *
38341 AAACGCCGTTAAAG-AC-----CTTTAGCGACGCTTTCCCCAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGCTTTTCCCAC
* *
38378 AAACGCCGGTAAAGAACATGGTCTTTAGCGGTGCTTTTACCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGCTTTTCCCAC
* * *
38421 AAACGCCACTAAAGAACATGGTCTTTAGC-G-ACTTTTGCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGCTTTTCCCAC
38462 AAACGCCGCTAAA
1 AAACGCCGCTAAA
38475 AATCACGCCA
Statistics
Matches: 216, Mismatches: 40, Indels: 15
0.80 0.15 0.06
Matches are distributed among these distances:
37 30 0.14
38 2 0.01
41 21 0.10
42 30 0.14
43 133 0.62
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGCTTTTCCCAC
Found at i:38371 original size:37 final size:37
Alignment explanation
Indices: 38320--38392 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
38310 AGGATATAGT
** * * *
38320 CTTTAGCGGTGCTTTTCCCACAAACGCCGTTAAAGAC
1 CTTTAGCGACGCTTTCCCCAAAAACGCCGGTAAAGAC
38357 CTTTAGCGACGCTTTCCCCAAAAACGCCGGTAAAGA
1 CTTTAGCGACGCTTTCCCCAAAAACGCCGGTAAAGA
38393 ACATGGTCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.23
Consensus pattern (37 bp):
CTTTAGCGACGCTTTCCCCAAAAACGCCGGTAAAGAC
Found at i:38413 original size:80 final size:82
Alignment explanation
Indices: 38212--38438 Score: 253
Period size: 80 Copynumber: 2.7 Consensus size: 82
38202 GCTTTCCTAC
* * *
38212 AAACGCCGCTAAAGAACATTGTCTTTAGCGGTGCTTTTCCTACAAATGCCGCTAAAGAACATGAT
1 AAACGCCGCTAAAGAACATAGTCTTTAGCGGTGCTTTTCCCACAAACGCCGCTAAAGAAC---A-
* *
38277 CTTTAGCGGCACTACTCCCAC
62 CTTTAGCGACACTACTCCCAA
* * * *
38298 AAATGCCGCTAAAGGATATAGTCTTTAGCGGTGCTTTTCCCACAAACGCCGTTAAAG-AC-CTTT
1 AAACGCCGCTAAAGAACATAGTCTTTAGCGGTGCTTTTCCCACAAACGCCGCTAAAGAACACTTT
* *
38361 AGCGACGCT-TTCCCCAA
66 AGCGACACTACT-CCCAA
* * * *
38378 AAACGCCGGTAAAGAACATGGTCTTTAGCGGTGCTTTTACCACAAACGCCACTAAAGAACA
1 AAACGCCGCTAAAGAACATAGTCTTTAGCGGTGCTTTTCCCACAAACGCCGCTAAAGAACA
38439 TGGTCTTTAG
Statistics
Matches: 119, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
79 1 0.01
80 64 0.54
81 2 0.02
85 2 0.02
86 50 0.42
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (82 bp):
AAACGCCGCTAAAGAACATAGTCTTTAGCGGTGCTTTTCCCACAAACGCCGCTAAAGAACACTTT
AGCGACACTACTCCCAA
Found at i:50840 original size:15 final size:16
Alignment explanation
Indices: 50820--50849 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
50810 ACTTAAAACA
50820 ATTTACAAT-TTAACC
1 ATTTACAATATTAACC
50835 ATTTACAATATTAAC
1 ATTTACAATATTAAC
50850 TAAATTGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTTACAATATTAACC
Found at i:54771 original size:33 final size:35
Alignment explanation
Indices: 54710--54777 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 35
54700 ATATGTTCTA
54710 CTTAGAGTAGAACTTCTATTTTTTATTAAAATATT
1 CTTAGAGTAGAACTTCTATTTTTTATTAAAATATT
* * *
54745 CTTA-AGTAGAATTTGTA-TTTTTATTAAATTATT
1 CTTAGAGTAGAACTTCTATTTTTTATTAAAATATT
54778 ATTATTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 15 0.50
34 11 0.37
35 4 0.13
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (35 bp):
CTTAGAGTAGAACTTCTATTTTTTATTAAAATATT
Found at i:55836 original size:95 final size:95
Alignment explanation
Indices: 55673--55863 Score: 373
Period size: 95 Copynumber: 2.0 Consensus size: 95
55663 AAATATCTAC
*
55673 AATGGTTAAAAAGCAGTGGGTGAGCTTAACAAGCTCAGTGAGTGCCCGGGATAACCACTACATAA
1 AATGGTTAAAAAGCAGTGGGTGAGCTTAACAAGCTCAGTGAGTGCCCGAGATAACCACTACATAA
55738 AAAATCATCATGCATCAACCCAACAATCAT
66 AAAATCATCATGCATCAACCCAACAATCAT
55768 AATGGTTAAAAAGCAGTGGGTGAGCTTAACAAGCTCAGTGAGTGCCCGAGATAACCACTACATAA
1 AATGGTTAAAAAGCAGTGGGTGAGCTTAACAAGCTCAGTGAGTGCCCGAGATAACCACTACATAA
55833 AAAATCATCATGCATCAACCCAACAATCAT
66 AAAATCATCATGCATCAACCCAACAATCAT
55863 A
1 A
55864 CAACATATTC
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (95 bp):
AATGGTTAAAAAGCAGTGGGTGAGCTTAACAAGCTCAGTGAGTGCCCGAGATAACCACTACATAA
AAAATCATCATGCATCAACCCAACAATCAT
Found at i:59479 original size:18 final size:17
Alignment explanation
Indices: 59455--59494 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
59445 AATATGCTAT
59455 CTCTCTTTTGTTCTCTTA
1 CTCTCTTTTGTTCT-TTA
*
59473 TTCTC-TTTGTTCTTTA
1 CTCTCTTTTGTTCTTTA
59489 CTCTCT
1 CTCTCT
59495 ATCATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.05, C:0.28, G:0.05, T:0.62
Consensus pattern (17 bp):
CTCTCTTTTGTTCTTTA
Found at i:71505 original size:40 final size:40
Alignment explanation
Indices: 71450--71608 Score: 230
Period size: 40 Copynumber: 4.0 Consensus size: 40
71440 AAGTTACGTT
* *
71450 TGATAAAGTTCAAGCTACGGCTCAGCAGGCTATGAGCCGG
1 TGATAGAGTTCAAGCTACGGCTTAGCAGGCTATGAGCCGG
* *
71490 TGATAGAGTTCAAGCTATGGCTTAGCAGACTATGAGCCGG
1 TGATAGAGTTCAAGCTACGGCTTAGCAGGCTATGAGCCGG
*
71530 TGATAGAGTTCAAGCTACAGCTTAGCAGGCTATGAGCCGG
1 TGATAGAGTTCAAGCTACGGCTTAGCAGGCTATGAGCCGG
** *
71570 TGATAG-GAAACAAGCTATGGCTTAGCAGGCTATGAGCCG
1 TGATAGAG-TTCAAGCTACGGCTTAGCAGGCTATGAGCCG
71609 ATGTTAAAAC
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.22
Consensus pattern (40 bp):
TGATAGAGTTCAAGCTACGGCTTAGCAGGCTATGAGCCGG
Found at i:72840 original size:21 final size:20
Alignment explanation
Indices: 72797--72840 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
72787 GTGATGATTT
* *
72797 TTAAATTATTTGAAATGTAA
1 TTAAATTAATTAAAATGTAA
*
72817 TTAAATTAATTAAAGATGTCA
1 TTAAATTAATTAAA-ATGTAA
72838 TTA
1 TTA
72841 TATGCTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (20 bp):
TTAAATTAATTAAAATGTAA
Found at i:79665 original size:18 final size:17
Alignment explanation
Indices: 79642--79676 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
79632 TAATAAAAAA
*
79642 ATAAAAATTATAATTTAG
1 ATAAAAA-TAAAATTTAG
79660 ATAAAAATAAAATTTAG
1 ATAAAAATAAAATTTAG
79677 GAAAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
ATAAAAATAAAATTTAG
Found at i:100281 original size:27 final size:26
Alignment explanation
Indices: 100202--100281 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 26
100192 AGCAACTAAT
100202 CACACAATTTCTATTCAGCATCATATA
1 CACACAA-TTCTATTCAGCATCATATA
*
100229 CACTA-AATATC-A-T-AGCAAGCA-A-A
1 CAC-ACAAT-TCTATTCAGC-ATCATATA
100252 CACACAACTTCTATTCAGCATCATATA
1 CACACAA-TTCTATTCAGCATCATATA
100279 CAC
1 CAC
100282 TAAATATCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 20
0.65 0.03 0.32
Matches are distributed among these distances:
22 1 0.02
23 8 0.20
24 6 0.15
25 8 0.20
26 6 0.15
27 11 0.27
28 1 0.02
ACGTcount: A:0.41, C:0.28, G:0.05, T:0.26
Consensus pattern (26 bp):
CACACAATTCTATTCAGCATCATATA
Found at i:101338 original size:46 final size:46
Alignment explanation
Indices: 101280--101399 Score: 177
Period size: 46 Copynumber: 2.6 Consensus size: 46
101270 GGACATGATG
* *
101280 CCATAGTGTCTTTCAACTATGGTCTTATTTATTTCCCGTCATGTTA
1 CCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCCGTCATGTCA
* * * *
101326 CCATAGTGTCTTTCAACCATGATCTTATTCATTTCTCGTCATGTCG
1 CCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCCGTCATGTCA
*
101372 CCATAATGTCTTTCAACTATGGTCTTAT
1 CCATAGTGTCTTTCAACTATGGTCTTAT
101400 GTCACGAGCC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.43
Consensus pattern (46 bp):
CCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCCGTCATGTCA
Found at i:106711 original size:45 final size:45
Alignment explanation
Indices: 106640--106773 Score: 187
Period size: 45 Copynumber: 3.0 Consensus size: 45
106630 CATTTAGACG
* * * * *
106640 TTTGAATCGTGATGTCGTAACGTCTTTCAACTATGGTCTTACTTA
1 TTTGAATCATGATGCCATAACGTCTTTCAGCTATGGTCTTACTCA
* **
106685 TTTGAATCATGATGCCATAACATCTTTCAGCTATTATCTTACTCA
1 TTTGAATCATGATGCCATAACGTCTTTCAGCTATGGTCTTACTCA
*
106730 TTTGAATCATGATGCCATAACGTCTTTCAGTTATGGTCTTACTC
1 TTTGAATCATGATGCCATAACGTCTTTCAGCTATGGTCTTACTC
106774 GTTTTCGATA
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 77 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (45 bp):
TTTGAATCATGATGCCATAACGTCTTTCAGCTATGGTCTTACTCA
Found at i:106801 original size:90 final size:90
Alignment explanation
Indices: 106640--106860 Score: 211
Period size: 90 Copynumber: 2.5 Consensus size: 90
106630 CATTTAGACG
* * *
106640 TTTGAATCGTGATGTCGTAACGTCTTTCAACTATGGTCTTACTTATTTGAATCATGATGCCATAA
1 TTTGAATCATGATGCCATAACGTCTTTCAACTATGGTCTTACTTATTTGAATCATGATGCCATAA
* *
106705 CATCTTTCAGCTATTATCTTACTCA
66 CATCTTTCAACTATGATCTTACTCA
** *
106730 TTTGAATCATGATGCCATAACGTCTTTCAGTTATGGTCTTACTCGT-TTTCG-AT-ATGATGTCA
1 TTTGAATCATGATGCCATAACGTCTTTCAACTATGGTCTTACT--TATTT-GAATCATGATGCCA
*** * *
106792 TAGTTTCTTTCAACTATGATCTTATTTAA
63 TAACATCTTTCAACTATGATCTTA-CTCA
* *
106821 TTATG-GT-AT-AGTGCCATAGCGTCTTTCAACTATGGTCTTA
1 TT-TGAATCATGA-TGCCATAACGTCTTTCAACTATGGTCTTA
106861 ACCATTTCCT
Statistics
Matches: 108, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
89 1 0.01
90 93 0.86
91 10 0.09
92 4 0.04
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (90 bp):
TTTGAATCATGATGCCATAACGTCTTTCAACTATGGTCTTACTTATTTGAATCATGATGCCATAA
CATCTTTCAACTATGATCTTACTCA
Found at i:125763 original size:8 final size:8
Alignment explanation
Indices: 125750--125774 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
125740 TCAACACAAC
125750 TTCAAAAG
1 TTCAAAAG
125758 TTCAAAAG
1 TTCAAAAG
125766 TTCAAAAG
1 TTCAAAAG
125774 T
1 T
125775 CTAAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (8 bp):
TTCAAAAG
Found at i:126648 original size:27 final size:27
Alignment explanation
Indices: 126618--126675 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
126608 CTAAAAATGG
126618 TTATATAGTTAAATGTGCTTTATTAAT
1 TTATATAGTTAAATGTGCTTTATTAAT
*
126645 TTATGTAGTTAAATGTGCTTTATTAAT
1 TTATATAGTTAAATGTGCTTTATTAAT
126672 TTAT
1 TTAT
126676 TTCAACAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.53
Consensus pattern (27 bp):
TTATATAGTTAAATGTGCTTTATTAAT
Found at i:134416 original size:23 final size:23
Alignment explanation
Indices: 134390--134433 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
134380 AATATTATAA
134390 AAACTCGT-AAATTACTTGAGAAC
1 AAACTCGTCAAA-TACTTGAGAAC
*
134413 AAACTCGTCAAATATTTGAGA
1 AAACTCGTCAAATACTTGAGA
134434 GAACCTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (23 bp):
AAACTCGTCAAATACTTGAGAAC
Found at i:135489 original size:15 final size:15
Alignment explanation
Indices: 135469--135504 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
135459 ACTTACTTAC
135469 AAAGTCTCGAGACTT
1 AAAGTCTCGAGACTT
135484 AAAGTCTCGAGACTT
1 AAAGTCTCGAGACTT
*
135499 AGAGTC
1 AAAGTC
135505 ACGGGTCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (15 bp):
AAAGTCTCGAGACTT
Found at i:136859 original size:18 final size:17
Alignment explanation
Indices: 136836--136880 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
136826 CATTTTTCAC
*
136836 TAATTAATTTAGAAAATT
1 TAATTAATTTA-AAAAAT
136854 TAATTAA-TTAAAAAAT
1 TAATTAATTTAAAAAAT
*
136870 CAATTAATTTA
1 TAATTAATTTA
136881 TTTGGTTAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.46
17 6 0.25
18 7 0.29
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TAATTAATTTAAAAAAT
Found at i:137014 original size:15 final size:15
Alignment explanation
Indices: 136994--137044 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
136984 ACAAAATAAT
136994 AATATAAATAATTAA
1 AATATAAATAATTAA
* *
137009 AATAT-AATATTTTA
1 AATATAAATAATTAA
*
137023 AATACAAATAATTAA
1 AATATAAATAATTAA
137038 AATATAA
1 AATATAA
137045 TTCGAAACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:142541 original size:30 final size:30
Alignment explanation
Indices: 142507--142567 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
142497 ACTTATTTTA
* * *
142507 TTGTTAATTTTGTTATTGTTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTACAGGCAT
142537 TTGTTAATTTTGTTACTATTTTACAGGCAT
1 TTGTTAATTTTGTTACTATTTTACAGGCAT
142567 T
1 T
142568 GCCTTCTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.21, C:0.07, G:0.16, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTACAGGCAT
Done.