Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008307.1 Kokia drynarioides strain JFW-HI SEQ_122972, 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: 118049
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2916 original size:34 final size:34
Alignment explanation
Indices: 2873--2942 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
2863 AATAATAATA
2873 ATAATTTATATTACCCCCAGACTTTAGTCAGCAC
1 ATAATTTATATTACCCCCAGACTTTAGTCAGCAC
2907 ATAATTTATATTACCCCCAGACTTTAGTCAGCAC
1 ATAATTTATATTACCCCCAGACTTTAGTCAGCAC
2941 AT
1 AT
2943 TGTCCTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.33
Consensus pattern (34 bp):
ATAATTTATATTACCCCCAGACTTTAGTCAGCAC
Found at i:18532 original size:24 final size:24
Alignment explanation
Indices: 18499--18544 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
18489 TTTTAACATA
* *
18499 TAAAATATAAATTTTAAATATTTT
1 TAAAAAATAAATATTAAATATTTT
*
18523 TAAAAAATAAATATTAATTATT
1 TAAAAAATAAATATTAAATATT
18545 CATAAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAAAAATAAATATTAAATATTTT
Found at i:18550 original size:24 final size:24
Alignment explanation
Indices: 18498--18551 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
18488 ATTTTAACAT
* * *
18498 ATAAAATATAAATTTTAAATATTT
1 ATAAAAAATAAATATTAAATATTC
* *
18522 TTAAAAAATAAATATTAATTATTC
1 ATAAAAAATAAATATTAAATATTC
18546 ATAAAA
1 ATAAAA
18552 TTTTATTCGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
ATAAAAAATAAATATTAAATATTC
Found at i:46073 original size:15 final size:16
Alignment explanation
Indices: 46043--46080 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
46033 GGTAATACGA
**
46043 AAATTTAAATTTTGTT
1 AAATTTAAATACTGTT
46059 -AATTTAAATACTGTT
1 AAATTTAAATACTGTT
46074 AAATTTA
1 AAATTTA
46081 TTTTATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (16 bp):
AAATTTAAATACTGTT
Found at i:48372 original size:4 final size:4
Alignment explanation
Indices: 48363--48477 Score: 74
Period size: 4 Copynumber: 28.5 Consensus size: 4
48353 TTTACGATTT
* * * *
48363 AATA AATA AATA AGTA AGTA AATA AGTA AATA AATA AGTA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* * * *
48411 ACA-A CATA AAT- AATCA AACA AATAA AATA ATTA AAT- AATAA AACA
1 A-ATA AATA AATA AAT-A AATA AAT-A AATA AATA AATA AAT-A AATA
* * *
48456 AATA ACTA ATTA ACTA AATA AA
1 AATA AATA AATA AATA AATA AA
48478 AGATTTTTAA
Statistics
Matches: 86, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
3 7 0.08
4 70 0.81
5 9 0.10
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:48386 original size:12 final size:12
Alignment explanation
Indices: 48365--48411 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
48355 TACGATTTAA
48365 TAAATAAATAAG
1 TAAATAAATAAG
*
48377 TAAGTAAATAAG
1 TAAATAAATAAG
48389 TAAATAAATAAG
1 TAAATAAATAAG
48401 TAAATAAATAA
1 TAAATAAATAA
48412 CAACATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (12 bp):
TAAATAAATAAG
Found at i:48419 original size:24 final size:24
Alignment explanation
Indices: 48366--48423 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
48356 ACGATTTAAT
* *
48366 AAATAAATAAGTAAGTAAATAAGT
1 AAATAAATAAGTAAATAAATAAGC
48390 AAATAAATAAGTAAATAAATAA-C
1 AAATAAATAAGTAAATAAATAAGC
48413 AACATAAATAA
1 AA-ATAAATAA
48424 TCAAACAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 2 0.06
24 29 0.94
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.22
Consensus pattern (24 bp):
AAATAAATAAGTAAATAAATAAGC
Found at i:48454 original size:25 final size:24
Alignment explanation
Indices: 48417--48478 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
48407 AATAACAACA
*
48417 TAAATAATCAAACAAATAAAATAAT
1 TAAATAATAAAACAAAT-AAATAAT
*
48442 TAAATAATAAAACAAATAACTAAT
1 TAAATAATAAAACAAATAAATAAT
*
48466 TAACTAAATAAAA
1 TAAAT-AATAAAA
48479 GATTTTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 10 0.30
25 23 0.70
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (24 bp):
TAAATAATAAAACAAATAAATAAT
Found at i:55448 original size:40 final size:43
Alignment explanation
Indices: 55337--55876 Score: 199
Period size: 40 Copynumber: 12.8 Consensus size: 43
55327 TGAGATGGTA
* * *
55337 GCTTCAATCTGCCCCTCTTGATTAGGGCAAAAGATTGGATAGTG
1 GCTTCAATCTG-CCCTCATGATTAGGGTAAAAGATTGAATAGTG
* *
55381 GCTTCAATCTGCCC-CATGA-TCGAGGTAAGAGATT-AAT-GTG
1 GCTTCAATCTGCCCTCATGATTAG-GGTAAAAGATTGAATAGTG
* * *
55421 TCTTCAATCTGCCCTC-CGATTAGGGTAAAAGATTG----GAG
1 GCTTCAATCTGCCCTCATGATTAGGGTAAAAGATTGAATAGTG
* ** * *
55459 GCTTCAATCTGACC-CATGATCGGGGTAAGAGATTG-GT-GTG
1 GCTTCAATCTGCCCTCATGATTAGGGTAAAAGATTGAATAGTG
* * ** * * * *
55499 TCTTCAATTTGTTCT-TTGATTAAGGTAAAAGATTGGATGGTG
1 GCTTCAATCTGCCCTCATGATTAGGGTAAAAGATTGAATAGTG
* * * *
55541 ACTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTG
1 GCTTCAATCTG-CCCTCATGA-TTA-GGGTAAAAGATTGAATAGTG
* * * * * *
55587 GCTTCAATTTGTCGCTCTTGAAATAGGGCTAAAAGATTGGATGGTG
1 GCTTCAATCTG-CCCTCATG-ATTAGGG-TAAAAGATTGAATAGTG
* * * * *
55633 ACTTAAATCTGTCCCTCTTAACTTAGGGGGTAAAAGATTG--GA-T-
1 GCTTCAATCTG-CCCTCATGA-TTA--GGGTAAAAGATTGAATAGTG
* * *
55676 GCTTCAATTTGCCCT-ATGA-TCGAGG-AAAGAGATTG-GT-GTG
1 GCTTCAATCTGCCCTCATGATTAG-GGTAAA-AGATTGAATAGTG
* * ** *
55716 TCTTCAATTTG-CCTTTTGATTAGGGTAAAAGATTG--GA-T-
1 GCTTCAATCTGCCCTCATGATTAGGGTAAAAGATTGAATAGTG
* * *
55754 GCTTCAATCTGCCCT-ATGATTGGGGTAAGAGATTG-GTA-TG
1 GCTTCAATCTGCCCTCATGATTAGGGTAAAAGATTGAATAGTG
* * *
55794 TCTTCAATCTGCCCCTCTTGATTTAGGGGTAAAAGATTGGAT-G-G
1 GCTTCAATCTG-CCCTCATGA-TTA-GGGTAAAAGATTGAATAGTG
* * *
55838 TCTTCAATTTGCCCCTCTTGACTTAGGGGTAAAAGATTG
1 GCTTCAATCTG-CCCTCATGA-TTA-GGGTAAAAGATTG
55877 GATGGTCTTT
Statistics
Matches: 390, Mismatches: 69, Indels: 74
0.73 0.13 0.14
Matches are distributed among these distances:
37 5 0.01
38 63 0.16
39 11 0.03
40 86 0.22
41 19 0.05
42 32 0.08
43 15 0.04
44 66 0.17
45 8 0.02
46 71 0.18
47 11 0.03
48 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (43 bp):
GCTTCAATCTGCCCTCATGATTAGGGTAAAAGATTGAATAGTG
Found at i:55477 original size:78 final size:79
Alignment explanation
Indices: 55338--55551 Score: 250
Period size: 78 Copynumber: 2.6 Consensus size: 79
55328 GAGATGGTAG
* *
55338 CTTCAATCTGCCCCTCTTGATTAGGGCAAAAGATTGGATAGTGGCTTCAATCTGCCCCATGATCG
1 CTTCAATCTG-CCCTC-TGATTAGGGTAAAAGATTGG--AG-GGCTTCAATCTGACCCATGATCG
55403 AGGTAAGAGATTAATGTGT
61 AGGTAAGAGATTAATGTGT
* *
55422 CTTCAATCTGCCCTCCGATTAGGGTAAAAGATTGGA-GGCTTCAATCTGACCCATGATCGGGGTA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGAGGGCTTCAATCTGACCCATGATCGAGGTA
**
55486 AGAGATTGGTGTGT
66 AGAGATTAATGTGT
* ** * *
55500 CTTCAATTTGTTCTTTGATTAAGGTAAAAGATTGGATGGTGACTTCAATCTG
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGA-GG-G-CTTCAATCTG
55552 CCCCTCTTGA
Statistics
Matches: 114, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
78 68 0.60
80 2 0.02
81 1 0.01
82 28 0.25
83 5 0.04
84 10 0.09
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (79 bp):
CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGAGGGCTTCAATCTGACCCATGATCGAGGTA
AGAGATTAATGTGT
Found at i:55752 original size:78 final size:81
Alignment explanation
Indices: 55542--55851 Score: 283
Period size: 78 Copynumber: 3.7 Consensus size: 81
55532 TGGATGGTGA
*
55542 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGTCGCTCT-T
1 CTTCAATCTG-CCCTCTTGATTTAGGGGTAAAAGATTGGA---T-GCTTCAATTTG-C-C-CTAT
*
55606 GAAATAG-GGCTAAA-AGATTGG-ATGGT
58 G--ATCGAGG--AAAGAGATTGGTAT-GT
* * *
55632 GACTTAAATCTGTCCCTCTTAACTTAGGGGGTAAAAGATTGGATGCTTCAATTTGCCCTATGATC
1 --CTTCAATCTG-CCCTCTTGATTTA-GGGGTAAAAGATTGGATGCTTCAATTTGCCCTATGATC
*
55697 GAGGAAAGAGATTGGTGTGT
62 GAGGAAAGAGATTGGTATGT
* * * * *
55717 CTTCAATTTG-CCTTTTGA-TTA-GGGTAAAAGATTGGATGCTTCAATCTGCCCTATGATTGGGG
1 CTTCAATCTGCCCTCTTGATTTAGGGGTAAAAGATTGGATGCTTCAATTTGCCCTATGATCGAGG
*
55779 TAAGAGATTGGTATGT
66 AAAGAGATTGGTATGT
55795 CTTCAATCTGCCCCTCTTGATTTAGGGGTAAAAGATTGGATGGTCTTCAATTTGCCC
1 CTTCAATCTG-CCCTCTTGATTTAGGGGTAAAAGATTGGAT-G-CTTCAATTTGCCC
55852 CTCTTGACTT
Statistics
Matches: 190, Mismatches: 17, Indels: 30
0.80 0.07 0.13
Matches are distributed among these distances:
78 61 0.32
80 10 0.05
81 9 0.05
82 16 0.08
83 9 0.05
84 15 0.08
85 12 0.06
86 5 0.03
87 3 0.02
88 1 0.01
89 11 0.06
90 1 0.01
92 21 0.11
93 16 0.08
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (81 bp):
CTTCAATCTGCCCTCTTGATTTAGGGGTAAAAGATTGGATGCTTCAATTTGCCCTATGATCGAGG
AAAGAGATTGGTATGT
Found at i:58759 original size:18 final size:18
Alignment explanation
Indices: 58736--58770 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
58726 ACCTCGGCAG
*
58736 TTCTTCTTTTTCTTTCTA
1 TTCTTCTTTCTCTTTCTA
58754 TTCTTCTTTCTCTTTCT
1 TTCTTCTTTCTCTTTCT
58771 CGTCTTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (18 bp):
TTCTTCTTTCTCTTTCTA
Found at i:58776 original size:18 final size:18
Alignment explanation
Indices: 58737--58776 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
58727 CCTCGGCAGT
* *
58737 TCTTCTTTTTCTTTCTAT
1 TCTTCTTTCTCTTTCTAG
*
58755 TCTTCTTTCTCTTTCTCG
1 TCTTCTTTCTCTTTCTAG
58773 TCTT
1 TCTT
58777 GATCCTTCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.28, G:0.03, T:0.68
Consensus pattern (18 bp):
TCTTCTTTCTCTTTCTAG
Found at i:67659 original size:44 final size:44
Alignment explanation
Indices: 67485--67659 Score: 242
Period size: 44 Copynumber: 4.0 Consensus size: 44
67475 ATACCATCAG
* *
67485 TCTTCAAACTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATCT
1 TCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGT
* * * *
67529 TCTTCAATCTGCCCCTCTTTACTTAAGGGTAAAAGATTGGACGG
1 TCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGT
* * * *
67573 TCTTCATTTTTCCTCTCTTGACTTAGGGGTAAAAGATTGGATGT
1 TCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGT
* *
67617 TCTTCAATCTGCCCCTCTTGAATTTGGGGTAAAAGATTGGATG
1 TCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATG
67660 GTGATGTAAC
Statistics
Matches: 111, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 111 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (44 bp):
TCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGT
Found at i:68790 original size:6 final size:6
Alignment explanation
Indices: 68770--68830 Score: 51
Period size: 6 Copynumber: 11.0 Consensus size: 6
68760 TCTCGACCTC
* * *
68770 TCTTTT T-TCTT TCTTTT TCTTTT TCTTCT TC-TTT T-TTTT TC-TCT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
*
68814 TCGTTT TCTTTT T-TTTT
1 TCTTTT TCTTTT TCTTTT
68831 AGGGTGAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
5 19 0.43
6 25 0.57
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:68794 original size:16 final size:16
Alignment explanation
Indices: 68773--68826 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
68763 CGACCTCTCT
68773 TTTTTCTTTCTTTTTC
1 TTTTTCTTTCTTTTTC
*
68789 TTTTTC-TTCTTCTTTT
1 TTTTTCTTTCTT-TTTC
*
68805 TTTTTCTCTTCGTTTTC
1 TTTTTCT-TTCTTTTTC
68822 TTTTT
1 TTTTT
68827 TTTTAGGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 5 0.16
16 15 0.47
17 8 0.25
18 4 0.12
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTTTCTTTCTTTTTC
Found at i:73659 original size:18 final size:18
Alignment explanation
Indices: 73636--73679 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
73626 AGACAAAAGT
73636 GAAATCGTTTTAAAGATA
1 GAAATCGTTTTAAAGATA
*
73654 GAAATCATTTTAAAGATA
1 GAAATCGTTTTAAAGATA
*
73672 AAAATCGT
1 GAAATCGT
73680 ATATTAGGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.32
Consensus pattern (18 bp):
GAAATCGTTTTAAAGATA
Found at i:74427 original size:30 final size:31
Alignment explanation
Indices: 74350--74556 Score: 204
Period size: 30 Copynumber: 7.0 Consensus size: 31
74340 GGGAAGCTTG
* *
74350 GGGGTCAAAATG-TAACTTTCAGAAAGTTT-
1 GGGGTCAAAATGATAATTTTTAGAAAGTTTA
* * *
74379 GAGGTTAAAATG-TAATTTTCA-AATAGTTTA
1 GGGGTCAAAATGATAATTTTTAGAA-AGTTTA
74409 GGGGTCAAAATGAT-ATTTTTAGAAAGTTTA
1 GGGGTCAAAATGATAATTTTTAGAAAGTTTA
74439 GGGGTCAAAATG-TAATTTTTAGAAAGTTTA
1 GGGGTCAAAATGATAATTTTTAGAAAGTTTA
* * *
74469 AGGGTCAAAATCA-AACTTTTAGAAAGTTTA
1 GGGGTCAAAATGATAATTTTTAGAAAGTTTA
*
74499 GGGG-CTAAAAT-ATAATTTTTAAAAAGTTT-
1 GGGGTC-AAAATGATAATTTTTAGAAAGTTTA
* *
74528 GAGGTCAAAAT-ATAGTTTTT-GAAAAGTTT
1 GGGGTCAAAATGATAATTTTTAG-AAAGTTT
74557 GAAGGTTGAA
Statistics
Matches: 153, Mismatches: 15, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
28 2 0.01
29 49 0.32
30 99 0.65
31 3 0.02
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (31 bp):
GGGGTCAAAATGATAATTTTTAGAAAGTTTA
Found at i:77764 original size:46 final size:47
Alignment explanation
Indices: 77680--77769 Score: 128
Period size: 46 Copynumber: 1.9 Consensus size: 47
77670 CACATTTTTG
* *
77680 TCTGGCAGCTTGTCTGCAATTATAGTGGCTCAACCACATATATCTGT
1 TCTGCCAGCTTGACTGCAATTATAGTGGCTCAACCACATATATCTGT
* **
77727 TCTGCCAGCTTGACTGCAA-TATAGTGGTTCGGCCACATATATC
1 TCTGCCAGCTTGACTGCAATTATAGTGGCTCAACCACATATATC
77770 CGATCTGGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
46 21 0.55
47 17 0.45
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.32
Consensus pattern (47 bp):
TCTGCCAGCTTGACTGCAATTATAGTGGCTCAACCACATATATCTGT
Found at i:79807 original size:2 final size:2
Alignment explanation
Indices: 79802--79830 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
79792 AAAAAAAAAA
79802 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
79831 CTTAGAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:88745 original size:8 final size:8
Alignment explanation
Indices: 88727--88770 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
88717 AATTAAATTT
88727 TTATAAAAA
1 TTAT-AAAA
88736 TTATAAAA
1 TTATAAAA
88744 TTAT-AAA
1 TTATAAAA
*
88751 TTAATATAA
1 TT-ATAAAA
88760 TTATAAAA
1 TTATAAAA
88768 TTA
1 TTA
88771 CATTTGGACT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
7 5 0.16
8 18 0.58
9 8 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TTATAAAA
Found at i:88768 original size:17 final size:17
Alignment explanation
Indices: 88727--88770 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
88717 AATTAAATTT
88727 TTATAAAAATT-ATAAAA
1 TTAT-AAAATTAATAAAA
*
88744 TTAT-AAATTAATATAA
1 TTATAAAATTAATAAAA
88760 TTATAAAATTA
1 TTATAAAATTA
88771 CATTTGGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.21
16 9 0.38
17 10 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTATAAAATTAATAAAA
Found at i:97531 original size:215 final size:215
Alignment explanation
Indices: 97158--97586 Score: 707
Period size: 215 Copynumber: 2.0 Consensus size: 215
97148 GAACGGCTAC
* *
97158 AGTCTTTAAGCCATCTATTGAAGAAGCTCCTAATCTGGAGTTGAAGCTTTTGCTTACCCATCTAA
1 AGTCTTTAAGCCATCTATTGAAGAAGCTCCTAATCTGGAGTTAAAGCTATTGCTTACCCATCTAA
* *
97223 AGTATGTTTTTCTTGGTGATACTGATACACTGCCAGTTATTGTGTCTGTAACCCTCGACACAACT
66 AGTATGTTTTTCTTGGTGATAATGATACACTGCCAGTTATTGTGTCTGCAACCCTCGACACAACT
* * *
97288 CGGGAAGAAAAATTAATTCATATATTGAAGCAGCATAAGTGTGCAATTGCTTAGAGTATTATTGA
131 CAGGAAGAAAAATTAATTCATATATTGAAGCAGCATAAGCGTGCAATTGCTTAGAGTATTACTGA
97353 TATTAGAGACATTAGTCCTT
196 TATTAGAGACATTAGTCCTT
*
97373 AGTCTTTAAGCCATCTATTGAAGAAGCTCCTAATCTGGAGTTAAAG-TCATTGCTTACCCATCTG
1 AGTCTTTAAGCCATCTATTGAAGAAGCTCCTAATCTGGAGTTAAAGCT-ATTGCTTACCCATCTA
* *
97437 AAGTATGTTTTTCTTGGTGATAATGATACACTGCCAGTTATTGTGTTTGCAACTCTCGACACAAC
65 AAGTATGTTTTTCTTGGTGATAATGATACACTGCCAGTTATTGTGTCTGCAACCCTCGACACAAC
* * * *
97502 TCAGGAAGAAAAATTGATTCATTTATTGAAGCAGCATAAGCGTGCGATTGCTTAGAGTATTGCTG
130 TCAGGAAGAAAAATTAATTCATATATTGAAGCAGCATAAGCGTGCAATTGCTTAGAGTATTACTG
*
97567 ATATTAGAGGCATTAGTCCT
195 ATATTAGAGACATTAGTCCT
97587 CTTTCTGCAT
Statistics
Matches: 198, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
214 1 0.01
215 197 0.99
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (215 bp):
AGTCTTTAAGCCATCTATTGAAGAAGCTCCTAATCTGGAGTTAAAGCTATTGCTTACCCATCTAA
AGTATGTTTTTCTTGGTGATAATGATACACTGCCAGTTATTGTGTCTGCAACCCTCGACACAACT
CAGGAAGAAAAATTAATTCATATATTGAAGCAGCATAAGCGTGCAATTGCTTAGAGTATTACTGA
TATTAGAGACATTAGTCCTT
Found at i:102104 original size:12 final size:13
Alignment explanation
Indices: 102085--102122 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
102075 ACATGTGGAG
102085 ACAGAGGAAGGAA
1 ACAGAGGAAGGAA
102098 A-AGAGGAA-GAA
1 ACAGAGGAAGGAA
*
102109 ACAAAGGAAGGAA
1 ACAGAGGAAGGAA
102122 A
1 A
102123 TGATGTCGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 4 0.18
12 13 0.59
13 5 0.23
ACGTcount: A:0.61, C:0.05, G:0.34, T:0.00
Consensus pattern (13 bp):
ACAGAGGAAGGAA
Found at i:102536 original size:24 final size:23
Alignment explanation
Indices: 102479--102528 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
102469 ACAACTAATG
102479 GAGTTAGTTTTATTTCTGTTTTT
1 GAGTTAGTTTTATTTCTGTTTTT
102502 GAGTTAGTTTTATTTCTGTTTTT
1 GAGTTAGTTTTATTTCTGTTTTT
102525 -AGTT
1 GAGTT
102529 TTAGTTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.14, C:0.04, G:0.18, T:0.64
Consensus pattern (23 bp):
GAGTTAGTTTTATTTCTGTTTTT
Found at i:105588 original size:26 final size:26
Alignment explanation
Indices: 105557--105639 Score: 139
Period size: 26 Copynumber: 3.2 Consensus size: 26
105547 AGCCCAGAAT
105557 AGAGTTTAGCTCATACAAGTCCAAAC
1 AGAGTTTAGCTCATACAAGTCCAAAC
105583 AGAGTTTAGCTCATACAAGTCCAAAC
1 AGAGTTTAGCTCATACAAGTCCAAAC
* * *
105609 AGCGTTTAGCTCATTCAAGCCCAAAC
1 AGAGTTTAGCTCATACAAGTCCAAAC
105635 AGAGT
1 AGAGT
105640 AACACTCTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (26 bp):
AGAGTTTAGCTCATACAAGTCCAAAC
Found at i:106217 original size:16 final size:16
Alignment explanation
Indices: 106196--106227 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
106186 TAATAATCTT
106196 TCACAAATGCTCAAGA
1 TCACAAATGCTCAAGA
*
106212 TCACAAATGCTTAAGA
1 TCACAAATGCTCAAGA
106228 ATAACTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (16 bp):
TCACAAATGCTCAAGA
Found at i:107028 original size:40 final size:40
Alignment explanation
Indices: 106961--107189 Score: 280
Period size: 40 Copynumber: 5.8 Consensus size: 40
106951 CAATAACACT
* * *
106961 GGCT-AAAGCCTGCTAGGTCATAACCTGAATCATCTCACC
1 GGCTCAAAGCCTGCTAGGCCGTAGCCTGAATCATCTCACC
** * * *
107000 GGCTCAGTGCCTGCTAAGCTGTAGCCTGAATCATCTCACT
1 GGCTCAAAGCCTGCTAGGCCGTAGCCTGAATCATCTCACC
* *
107040 AGCTCAAAGCCTGCTAGGCCGTAGCCTAAATCATCTCACC
1 GGCTCAAAGCCTGCTAGGCCGTAGCCTGAATCATCTCACC
* * ** * *
107080 GGCTCAAAGTCTACTAGATCGTAGCTTGAACCATCTCACC
1 GGCTCAAAGCCTGCTAGGCCGTAGCCTGAATCATCTCACC
* *
107120 GGCTCAAAGCTTGCTAGGCCGTAGCTTGAATCATCTCACC
1 GGCTCAAAGCCTGCTAGGCCGTAGCCTGAATCATCTCACC
*
107160 GGCTCAAAGCCTGCTAGGCCGTAGCTTGAA
1 GGCTCAAAGCCTGCTAGGCCGTAGCCTGAA
107190 CTATATGCAT
Statistics
Matches: 159, Mismatches: 30, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
39 4 0.03
40 155 0.97
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.24
Consensus pattern (40 bp):
GGCTCAAAGCCTGCTAGGCCGTAGCCTGAATCATCTCACC
Found at i:115109 original size:20 final size:19
Alignment explanation
Indices: 115084--115135 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
115074 GGTCAGACCA
*
115084 AAAAATTATAAAAATATATT
1 AAAAATTATAAAAA-AAATT
*
115104 AAAAATCATAAAAAAAATT
1 AAAAATTATAAAAAAAATT
115123 AAAAATATATAAA
1 AAAAAT-TATAAA
115136 TATTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAATTATAAAAAAAATT
Found at i:115126 original size:30 final size:30
Alignment explanation
Indices: 115083--115166 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 30
115073 TGGTCAGACC
*
115083 AAAAAATTATAAAAATATATTAAAAATCATA
1 AAAAAAAT-TAAAAATATATTAAAAATCATA
* **
115114 AAAAAAATTAAAAATATA-TAAATATTGTA
1 AAAAAAATTAAAAATATATTAAAAATCATA
*
115143 AAAAAACATT-TAAAT-TATTAAAAA
1 AAAAAA-ATTAAAAATATATTAAAAA
115167 ATATTAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
28 2 0.04
29 23 0.51
30 13 0.29
31 7 0.16
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (30 bp):
AAAAAAATTAAAAATATATTAAAAATCATA
Found at i:115146 original size:20 final size:19
Alignment explanation
Indices: 115123--115262 Score: 69
Period size: 19 Copynumber: 7.3 Consensus size: 19
115113 AAAAAAAATT
115123 AAAAATATATAAATATTGTAA
1 AAAAATAT-TAAATATTGT-A
*
115144 AAAAACATTTAAAT-TAT-TA
1 AAAAATA-TTAAATAT-TGTA
* *
115163 AAAAATATTAAAAATTGCA
1 AAAAATATTAAATATTGTA
*
115182 AAAAAAATTAAA-ACTTGT-
1 AAAAATATTAAATA-TTGTA
* *
115200 GAAAA-ATTAAATACAT-TA
1 AAAAATATTAAATA-TTGTA
* *
115218 AATAATTAATAAATATTGTTA
1 AA-AAATATTAAATATTG-TA
*
115239 AAAATATTTTAAA-ATTGTA
1 AAAA-ATATTAAATATTGTA
115258 AAAAA
1 AAAAA
115263 GTTATTAAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
17 7 0.08
18 16 0.17
19 32 0.35
20 15 0.16
21 21 0.23
22 1 0.01
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (19 bp):
AAAAATATTAAATATTGTA
Found at i:115205 original size:39 final size:40
Alignment explanation
Indices: 115123--115205 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 40
115113 AAAAAAAATT
* * * *
115123 AAAAATATATAAATATTGTAAAAAAACATTTAAATTATTA
1 AAAAATATATAAAAATTGCAAAAAAACATTAAAATTATGA
*
115163 AAAAATAT-TAAAAATTGCAAAAAAA-ATTAAAACTTGTGA
1 AAAAATATATAAAAATTGCAAAAAAACATTAAAA-TTATGA
115202 AAAA
1 AAAA
115206 TTAAATACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 6 0.16
39 23 0.62
40 8 0.22
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.29
Consensus pattern (40 bp):
AAAAATATATAAAAATTGCAAAAAAACATTAAAATTATGA
Found at i:115272 original size:10 final size:9
Alignment explanation
Indices: 115259--115331 Score: 56
Period size: 10 Copynumber: 7.4 Consensus size: 9
115249 AAAATTGTAA
115259 AAAAGTTATT
1 AAAA-TTATT
*
115269 AAAATTTATA
1 AAAA-TTATT
115279 AAACATTATTT
1 AAA-ATTA-TT
*
115290 AAAATTTATA
1 AAAA-TTATT
115300 AAAATTATT
1 AAAATTATT
* *
115309 AACATTTTT
1 AAAATTATT
115318 GAAAATTATT
1 -AAAATTATT
115328 AAAA
1 AAAA
115332 AATGGAAATG
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
9 15 0.30
10 27 0.54
11 8 0.16
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (9 bp):
AAAATTATT
Found at i:115315 original size:19 final size:19
Alignment explanation
Indices: 115237--115331 Score: 102
Period size: 20 Copynumber: 4.8 Consensus size: 19
115227 TAAATATTGT
*
115237 TAAAAATATTTTAAAATTGTA
1 TAAAAAT-TATTAAAATT-TA
115258 -AAAAAGTTATTAAAATTTA
1 TAAAAA-TTATTAAAATTTA
115277 TAAAACATTATTTAAAATTTA
1 TAAAA-ATTA-TTAAAATTTA
* *
115298 TAAAAATTATTAACATTTT
1 TAAAAATTATTAAAATTTA
*
115317 TGAAAATTATTAAAA
1 TAAAAATTATTAAAA
115332 AATGGAAATG
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
19 23 0.35
20 25 0.38
21 17 0.26
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (19 bp):
TAAAAATTATTAAAATTTA
Found at i:115347 original size:20 final size:20
Alignment explanation
Indices: 115322--115391 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
115312 ATTTTTGAAA
*
115322 ATTATTAAAAAATGGAAATG
1 ATTATTAAAAAATGAAAATG
* * *
115342 ATTATTAAAAAGTGTAAATA
1 ATTATTAAAAAATGAAAATG
* *
115362 ATCATT-AAAAATGAAAAAG
1 ATTATTAAAAAATGAAAATG
*
115381 AGTATTAAAAA
1 ATTATTAAAAA
115392 TTCTTTAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 13 0.33
20 26 0.67
ACGTcount: A:0.59, C:0.01, G:0.11, T:0.29
Consensus pattern (20 bp):
ATTATTAAAAAATGAAAATG
Found at i:115642 original size:10 final size:10
Alignment explanation
Indices: 115629--115762 Score: 62
Period size: 10 Copynumber: 13.3 Consensus size: 10
115619 AATTATATAC
115629 AATTTTTAAT
1 AATTTTTAAT
* *
115639 AA-TTATATAC
1 AATTTTTA-AT
115649 AATTTTTAAT
1 AATTTTTAAT
115659 AATTATTT-AT
1 AATT-TTTAAT
* **
115669 GATTTTTTTT
1 AATTTTTAAT
115679 AATTTTTAA-
1 AATTTTTAAT
*
115688 AGATTTTAAAT
1 A-ATTTTTAAT
* *
115699 ATTTTTTTAT
1 AATTTTTAAT
*
115709 AATTTTTTAT
1 AATTTTTAAT
*
115719 AACTTCTTT-AC
1 AA-TT-TTTAAT
*
115730 AA-TTTTAAA
1 AATTTTTAAT
*
115739 ATATTTTTAAC
1 A-ATTTTTAAT
*
115750 AATATTTAAT
1 AATTTTTAAT
115760 AAT
1 AAT
115763 CATTTACAAT
Statistics
Matches: 94, Mismatches: 19, Indels: 22
0.70 0.14 0.16
Matches are distributed among these distances:
8 3 0.03
9 11 0.12
10 57 0.61
11 20 0.21
12 3 0.03
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:115643 original size:20 final size:20
Alignment explanation
Indices: 115618--115664 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
115608 TTTAAGTTAT
115618 TAATTATATACAATTTTTAA
1 TAATTATATACAATTTTTAA
115638 TAATTATATACAATTTTTAA
1 TAATTATATACAATTTTTAA
115658 TAATTAT
1 TAATTAT
115665 TTATGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATTATATACAATTTTTAA
Found at i:115673 original size:20 final size:20
Alignment explanation
Indices: 115618--115735 Score: 85
Period size: 20 Copynumber: 5.8 Consensus size: 20
115608 TTTAAGTTAT
* *
115618 TAATTATATACAATTTTTAA
1 TAATTATTTATAATTTTTAA
* *
115638 TAATTATATACAATTTTTAA
1 TAATTATTTATAATTTTTAA
* **
115658 TAATTATTTATGATTTTTTT
1 TAATTATTTATAATTTTTAA
* *
115678 TAATT-TTTAAAGATTTTAAA
1 TAATTATTTATA-ATTTTTAA
* * *
115698 TATTTTTTTATAATTTTTTA
1 TAATTATTTATAATTTTTAA
* *
115718 TAACTTCTTTACAATTTT
1 TAA-TTATTTATAATTTT
115736 AAAATATTTT
Statistics
Matches: 78, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
19 4 0.05
20 57 0.73
21 17 0.22
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (20 bp):
TAATTATTTATAATTTTTAA
Found at i:115682 original size:40 final size:39
Alignment explanation
Indices: 115618--115738 Score: 116
Period size: 40 Copynumber: 3.0 Consensus size: 39
115608 TTTAAGTTAT
* * * * *
115618 TAATTATATACAATTTTTAATAATTATATACAATTTTTAA
1 TAATTATTTATAATTTTTTATAATT-TTTACAATTTTAAA
* * *
115658 TAATTATTTATGATTTTTTTTAATTTTTAAAGATTTTAAA
1 TAATTATTTATAATTTTTTATAATTTTTACA-ATTTTAAA
* *
115698 TATTTTTTTATAATTTTTTATAACTTCTTTACAATTTTAAA
1 TAATTATTTATAATTTTTTATAA-TT-TTTACAATTTTAAA
115739 ATATTTTTAA
Statistics
Matches: 65, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
39 4 0.06
40 46 0.71
41 10 0.15
42 5 0.08
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (39 bp):
TAATTATTTATAATTTTTTATAATTTTTACAATTTTAAA
Found at i:115685 original size:30 final size:30
Alignment explanation
Indices: 115649--115720 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
115639 AATTATATAC
*
115649 AATTTTTAATAATTATT-TATGATTTTTTT-T
1 AATTTTTAATAATT-TTAAAT-ATTTTTTTAT
115679 AATTTTTAA-AGATTTTAAATATTTTTTTAT
1 AATTTTTAATA-ATTTTAAATATTTTTTTAT
*
115709 AATTTTTTATAA
1 AATTTTTAATAA
115721 CTTCTTTACA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
29 11 0.31
30 24 0.67
31 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (30 bp):
AATTTTTAATAATTTTAAATATTTTTTTAT
Found at i:115804 original size:20 final size:19
Alignment explanation
Indices: 115690--115841 Score: 82
Period size: 20 Copynumber: 7.8 Consensus size: 19
115680 ATTTTTAAAG
*
115690 ATTTTAAATATTTTTTTATA
1 ATTTTAAATA-TTTTTTACA
** *
115710 ATTTTTTATAACTTCTTTACA
1 ATTTTAAAT-A-TTTTTTACA
*
115731 ATTTTAAAATATTTTTAACA
1 ATTTT-AAATATTTTTTACA
**
115751 ATATTT-AATAATCATTTACA
1 AT-TTTAAAT-ATTTTTTACA
* *
115771 ATATT---TATTATTTACA
1 ATTTTAAATATTTTTTACA
115787 ATTTCTAAATATTTTTTACA
1 ATTT-TAAATATTTTTTACA
* *
115807 ACTTTTTAATATTTTAATA-A
1 A-TTTTAAATATTTT-TTACA
115827 A-TTTAAATATTTTTT
1 ATTTTAAATATTTTTT
115842 TTTTACAATT
Statistics
Matches: 102, Mismatches: 20, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
16 12 0.12
17 3 0.03
18 11 0.11
19 5 0.05
20 47 0.46
21 22 0.22
22 2 0.02
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTAAATATTTTTTACA
Found at i:117066 original size:162 final size:161
Alignment explanation
Indices: 116869--118047 Score: 1320
Period size: 162 Copynumber: 7.4 Consensus size: 161
116859 AAGCACAGAA
* * *
116869 ATTTA-ATAAGACATAAATTTTAGACTTATCAATTCAAATATGATAGCATATTAATAAGAAGACG
1 ATTTAGATAA-ACATAAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGACG
* * * *
116933 TATAAATAATGGCATATTCGTGATAAAGCATGAAAATTTATTTAGTTCAATATAAAAATTGTAAA
65 TATAAATAAT-GCATATTCGTGATAAAGCATGAGAATTTGTTTAGTTAAATATAAAATTTGTAAA
*
116998 CTTATCAACTCAAGTACAAAAGTGCACGAATTT
129 CTTATCAATTCAAGTACAAAAGTGCACGAATTT
* * * *
117031 ATTTAGTTAAACAAAAACTTTAAATTTTACAATTCAAATATGATAGCATATTAATAAGAAGACGT
1 ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGACGT
* * * *
117096 AAAAATAATGACATATTCGTTATAAAGCATGAGAATTTATTTAGTTAAATATAACATTTGTAAAC
66 ATAAATAATG-CATATTCGTGATAAAGCATGAGAATTTGTTTAGTTAAATATAAAATTTGTAAAC
*
117161 TTATCAACTCAAGTACAAAA-T-CACGCGAATTT
130 TTATCAATTCAAGTACAAAAGTGCA--CGAATTT
* * * *
117193 ATTTAGATAAACATTAATTTTAAACTTAACAATTCAAATATGATAGCATACTAATAAGAAG--GC
1 ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGACGT
* ** *
117256 ATAGA-AAT--AT-TT-GTGATAAAGCCCGAGAATTTGTTTAGTTAAATATAAAACTTGTAAACT
66 ATAAATAATGCATATTCGTGATAAAGCATGAGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
* *
117316 TATCAATTCAAGTACAACAGT--AGGTAAATTT
131 TATCAATTCAAGTACAAAAGTGCACG--AATTT
* ** * *
117347 ATTTAGATAAACATAAGCTTTAAACTTAACAATTCAAATATGATAATATATTAATAAGAAGGCAT
1 ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGACGT
* *
117412 AGAAATAATGTCATATTCGTGATAAAGCGT-AGGAATTTGTTTAGTTAAATATAAAATTTGTAAA
66 ATAAATAATG-CATATTCGTGATAAAGCATGA-GAATTTGTTTAGTTAAATATAAAATTTGTAAA
** * *
117476 CTTATCAATTCAAGTACAAAAGAACGCAAATTT
129 CTTATCAATTCAAGTACAAAAGTGCACGAATTT
* * *
117509 ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATTTGAGAGCATATTATTAAGAAGACGT
1 ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGACGT
* * ** * *
117574 AGAAATAATGACATATTCATGATAAAGCGCGGGAATTTGTTTAGTTAAATATAACATTTGTAAAC
66 ATAAATAATG-CATATTCGTGATAAAGCATGAGAATTTGTTTAGTTAAATATAAAATTTGTAAAC
*
117639 TTATCAACTCAAGTACAAAAGCATGCA--AATTT
130 TTATCAATTCAAGTACAAAAG--TGCACGAATTT
* * * *
117671 ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATATCATTTTAAAAAGAAGGCG-
1 ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGACGT
** *
117735 -TAAA-AAT--AT-TT-AAGATAAA--ATGCGAGAATTTTTTTAGTTAAATATAAAATTTGTAAA
66 ATAAATAATGCATATTCGTGATAAAGCAT--GAGAATTTGTTTAGTTAAATATAAAATTTGTAAA
117792 CTTATCAATTCGAA-TACAGAACCAG-GCA--AATTT
129 CTTATCAATTC-AAGTACA-AA--AGTGCACGAATTT
* * ** ** * *
117825 ATTTAGATAAACGTAAGCTTTAAACTCGACAATTCAAATATGATAATATATTAATAAAAAGGCGT
1 ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGACGT
*
117890 AAAAATAATGTCATATTCGTGATAAAACGCA--AGAATTTGTTTAGTTAAATATAAAATTTGTAA
66 ATAAATAATG-CATATTCGTGAT-AAA-GCATGAGAATTTGTTTAGTTAAATATAAAATTTGTAA
** *
117953 ACTTATCAATTCAAGTACAAAAACGCACAAATTT
128 ACTTATCAATTCAAGTACAAAAGTGCACGAATTT
* ** *
117987 ATTTATATAAACATATGCTTTAAACTTAACTATTCAAATATGATAGCATATTAATAAGAAG
1 ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAG
118048 GC
Statistics
Matches: 869, Mismatches: 105, Indels: 86
0.82 0.10 0.08
Matches are distributed among these distances:
152 1 0.00
154 235 0.27
155 9 0.01
156 10 0.01
157 8 0.01
159 7 0.01
160 16 0.02
161 11 0.01
162 564 0.65
163 6 0.01
164 1 0.00
166 1 0.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (161 bp):
ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGACGT
ATAAATAATGCATATTCGTGATAAAGCATGAGAATTTGTTTAGTTAAATATAAAATTTGTAAACT
TATCAATTCAAGTACAAAAGTGCACGAATTT
Found at i:117400 original size:316 final size:318
Alignment explanation
Indices: 116869--118049 Score: 1363
Period size: 316 Copynumber: 3.7 Consensus size: 318
116859 AAGCACAGAA
* * *
116869 ATTTA-ATAAGACATAAATTTTAGACTTATCAATTCAAATATGATAGCATATTAATAAGAAGACG
1 ATTTAGATAA-ACATAAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAG--G
* ** * * * *
116933 TATAAATAATGGCATATTCGTGATAAAGCATGAAAATTTATTTAGTTCAATATAAAAATTGTAAA
63 CATAAATAAT--CATATTCGTGATAAAGCGCGAGAATTTGTTTAGTTAAATATAAAATTTGTAAA
* * * *
116998 CTTATCAACTCAAGTACAAAAGT--GCACGAATTTATTTAGTTAAACAAAAACTTTAAATTTTAC
126 CTTATCAACTCAAGTACAAAAGTAGGCA--AATTTATTTAGATAAACATAAACTTTAAACTTAAC
* *
117061 AATTCAAATATGATAGCATATTAATAAGAAGACGTAAAAATAATGACATATTCGTTATAAAGCAT
189 AATTCAAATATGATAACATATTAATAAGAAGGCGTAAAAATAATG-CATATTCGTTATAAAGC-T
* * * *
117126 GAGAATTTATTTAGTTAAATATAACATTTGTAAACTTATCAACTCAAGTACAAAATCACGCGAAT
252 GAGAATTTATTTAGTTAAATATAAAATTTGTAAACTTATCAATTCAAGTACAAAACCACGCAAAT
117191 TT
317 TT
* * *
117193 ATTTAGATAAACATTAATTTTAAACTTAACAATTCAAATATGATAGCATACTAATAAGAAGGCAT
1 ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGGCAT
* * *
117258 AGA-AAT-AT-TT-GTGATAAAGCCCGAGAATTTGTTTAGTTAAATATAAAACTTGTAAACTTAT
66 AAATAATCATATTCGTGATAAAGCGCGAGAATTTGTTTAGTTAAATATAAAATTTGTAAACTTAT
* * * *
117319 CAATTCAAGTACAACAGTAGGTAAATTTATTTAGATAAACATAAGCTTTAAACTTAACAATTCAA
131 CAACTCAAGTACAAAAGTAGGCAAATTTATTTAGATAAACATAAACTTTAAACTTAACAATTCAA
* * * *
117384 ATATGATAATATATTAATAAGAAGGCATAGAAATAATGTCATATTCGTGATAAAGC-GTAGGAAT
196 ATATGATAACATATTAATAAGAAGGCGTAAAAATAATG-CATATTCGTTATAAAGCTG-A-GAAT
* **
117448 TTGTTTAGTTAAATATAAAATTTGTAAACTTATCAATTCAAGTACAAAAGAACGCAAATTT
258 TTATTTAGTTAAATATAAAATTTGTAAACTTATCAATTCAAGTACAAAACCACGCAAATTT
* * * *
117509 ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATTTGAGAGCATATTATTAAGAAGACGT
1 ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAG--GC
* * * *
117574 AGAAATAATGACATATTCATGATAAAGCGCGGGAATTTGTTTAGTTAAATATAACATTTGTAAAC
64 ATAAATAAT--CATATTCGTGATAAAGCGCGAGAATTTGTTTAGTTAAATATAAAATTTGTAAAC
* *
117639 TTATCAACTCAAGTACAAAAGCATGCAAATTTATTTAGATAAACATAAACTTTAAACTTAACAAT
127 TTATCAACTCAAGTACAAAAGTAGGCAAATTTATTTAGATAAACATAAACTTTAAACTTAACAAT
* * * ** *
117704 TCAAATATGATATCATTTTAAAAAGAAGGCGTAAAAAT-AT---T-TAAGATA-AAATGC-GAGA
192 TCAAATATGATAACATATTAATAAGAAGGCGTAAAAATAATGCATATTCGTTATAAA-GCTGAGA
* * *
117762 ATTTTTTTAGTTAAATATAAAATTTGTAAACTTATCAATTCGAA-TACAGAACCAGGCAAATTT
256 ATTTATTTAGTTAAATATAAAATTTGTAAACTTATCAATTC-AAGTACAAAACCACGCAAATTT
* * ** ** *
117825 ATTTAGATAAACGTAAGCTTTAAACTCGACAATTCAAATATGATAATATATTAATAAAAAGGCGT
1 ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGGC--
* * *
117890 AAAAATAATGTCATATTCGTGATAAAACGCAAGAATTTGTTTAGTTAAATATAAAATTTGTAAAC
64 ATAAATAA--TCATATTCGTGATAAAGCGCGAGAATTTGTTTAGTTAAATATAAAATTTGTAAAC
* * * ** *
117955 TTATCAATTCAAGTACAAAA--ACGCACAAATTTATTTATATAAACATATGCTTTAAACTTAACT
127 TTATCAACTCAAGTACAAAAGTA-G-GCAAATTTATTTAGATAAACATAAACTTTAAACTTAACA
*
118018 ATTCAAATATGATAGCATATTAATAAGAAGGC
190 ATTCAAATATGATAACATATTAATAAGAAGGC
Statistics
Matches: 741, Mismatches: 95, Indels: 50
0.84 0.11 0.06
Matches are distributed among these distances:
314 3 0.00
315 1 0.00
316 507 0.68
317 8 0.01
318 15 0.02
319 4 0.01
321 3 0.00
322 7 0.01
323 4 0.01
324 185 0.25
325 4 0.01
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (318 bp):
ATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATATTAATAAGAAGGCAT
AAATAATCATATTCGTGATAAAGCGCGAGAATTTGTTTAGTTAAATATAAAATTTGTAAACTTAT
CAACTCAAGTACAAAAGTAGGCAAATTTATTTAGATAAACATAAACTTTAAACTTAACAATTCAA
ATATGATAACATATTAATAAGAAGGCGTAAAAATAATGCATATTCGTTATAAAGCTGAGAATTTA
TTTAGTTAAATATAAAATTTGTAAACTTATCAATTCAAGTACAAAACCACGCAAATTT
Found at i:117712 original size:478 final size:478
Alignment explanation
Indices: 116869--118047 Score: 1659
Period size: 478 Copynumber: 2.5 Consensus size: 478
116859 AAGCACAGAA
** * * ** *
116869 ATTTA-ATAAGACATAAATTTTAGACTTATCAATTCAAATATGATAGCATATTAATAAGAAGACG
1 ATTTAGATAA-ACATAAGCTTTAAACTTAACAATTCAAATATGATAATATATTAATAAGAAGGCG
* * * * * * *
116933 TATAAATAATGGCATATTCGTGATAAAGCAT-GAAAATTTATTTAGTTCAATATAAAAATTGTAA
65 TAAAAATAATGTCATATTCGTGATAAAGCGTAG-GAATTTGTTTAGTTAAATATAAAATTTGTAA
* ** * * * * * *
116997 ACTTATCAACTCAAGTACAAAAGTGCACGAATTTATTTAGTTAAACAAAAACTTTAAATTTTACA
129 ACTTATCAATTCAAGTACAAAAGAACGCAAATTTATTTAGATAAACATAAACTTTAAACTTAACA
* * *
117062 ATTCAAATATGATAGCATATTAATAAGAAGACGTAAAAATAATGACATATTCGTTATAAAGCATG
194 ATTCAAATATGATAGCATATTAATAAGAAGACGTAAAAATAATGACATATTCATGATAAAGCACG
* *
117127 AGAATTTATTTAGTTAAATATAACATTTGTAAACTTATCAACTCAAGTACAAAATCACGCGAATT
259 AGAATTTATTTAGTTAAATATAACATTTGTAAACTTATCAACTCAAGTACAAAAGCACGCAAATT
* * *
117192 TATTTAGATAAACATTAATTTTAAACTTAACAATTCAAATATGATAGCATACTAATAAGAAGGCA
324 TATTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATACTAAAAAGAAGGCA
* ** *
117257 TAGAAATATTTGTGATAAAGCCCGAGAATTTGTTTAGTTAAATATAAAACTTGTAAACTTATCAA
389 TAAAAATATTTAAGATAAAACCCGAGAATTTGTTTAGTTAAATATAAAACTTGTAAACTTATCAA
** *
117322 TTC-AAGTACA-ACAGTAGGTAAATTT
454 TTCGAA-TACAGA-ACCAGGCAAATTT
*
117347 ATTTAGATAAACATAAGCTTTAAACTTAACAATTCAAATATGATAATATATTAATAAGAAGGCAT
1 ATTTAGATAAACATAAGCTTTAAACTTAACAATTCAAATATGATAATATATTAATAAGAAGGCGT
*
117412 AGAAATAATGTCATATTCGTGATAAAGCGTAGGAATTTGTTTAGTTAAATATAAAATTTGTAAAC
66 AAAAATAATGTCATATTCGTGATAAAGCGTAGGAATTTGTTTAGTTAAATATAAAATTTGTAAAC
117477 TTATCAATTCAAGTACAAAAGAACGCAAATTTATTTAGATAAACATAAACTTTAAACTTAACAAT
131 TTATCAATTCAAGTACAAAAGAACGCAAATTTATTTAGATAAACATAAACTTTAAACTTAACAAT
* * * * * *
117542 TCAAATTTGAGAGCATATTATTAAGAAGACGTAGAAATAATGACATATTCATGATAAAGCGCGGG
196 TCAAATATGATAGCATATTAATAAGAAGACGTAAAAATAATGACATATTCATGATAAAGCACGAG
* *
117607 AATTTGTTTAGTTAAATATAACATTTGTAAACTTATCAACTCAAGTACAAAAGCATGCAAATTTA
261 AATTTATTTAGTTAAATATAACATTTGTAAACTTATCAACTCAAGTACAAAAGCACGCAAATTTA
* ** *
117672 TTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATATCATTTTAAAAAGAAGGCGTA
326 TTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATACTAAAAAGAAGGCATA
** * *
117737 AAAATATTTAAGATAAAATGCGAGAATTTTTTTAGTTAAATATAAAATTTGTAAACTTATCAATT
391 AAAATATTTAAGATAAAACCCGAGAATTTGTTTAGTTAAATATAAAACTTGTAAACTTATCAATT
117802 CGAATACAGAACCAGGCAAATTT
456 CGAATACAGAACCAGGCAAATTT
* ** *
117825 ATTTAGATAAACGTAAGCTTTAAACTCGACAATTCAAATATGATAATATATTAATAAAAAGGCGT
1 ATTTAGATAAACATAAGCTTTAAACTTAACAATTCAAATATGATAATATATTAATAAGAAGGCGT
* * *
117890 AAAAATAATGTCATATTCGTGATAAAACGCAAGAATTTGTTTAGTTAAATATAAAATTTGTAAAC
66 AAAAATAATGTCATATTCGTGATAAAGCGTAGGAATTTGTTTAGTTAAATATAAAATTTGTAAAC
* ** *
117955 TTATCAATTCAAGTAC-AAA-AACGCACAAATTTATTTATATAAACATATGCTTTAAACTTAACT
131 TTATCAATTCAAGTACAAAAGAACG--CAAATTTATTTAGATAAACATAAACTTTAAACTTAACA
118018 ATTCAAATATGATAGCATATTAATAAGAAG
194 ATTCAAATATGATAGCATATTAATAAGAAG
118048 GC
Statistics
Matches: 624, Mismatches: 71, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
476 4 0.01
477 3 0.00
478 609 0.98
479 8 0.01
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (478 bp):
ATTTAGATAAACATAAGCTTTAAACTTAACAATTCAAATATGATAATATATTAATAAGAAGGCGT
AAAAATAATGTCATATTCGTGATAAAGCGTAGGAATTTGTTTAGTTAAATATAAAATTTGTAAAC
TTATCAATTCAAGTACAAAAGAACGCAAATTTATTTAGATAAACATAAACTTTAAACTTAACAAT
TCAAATATGATAGCATATTAATAAGAAGACGTAAAAATAATGACATATTCATGATAAAGCACGAG
AATTTATTTAGTTAAATATAACATTTGTAAACTTATCAACTCAAGTACAAAAGCACGCAAATTTA
TTTAGATAAACATAAACTTTAAACTTAACAATTCAAATATGATAGCATACTAAAAAGAAGGCATA
AAAATATTTAAGATAAAACCCGAGAATTTGTTTAGTTAAATATAAAACTTGTAAACTTATCAATT
CGAATACAGAACCAGGCAAATTT
Done.