Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014962.1 Kokia drynarioides strain JFW-HI SEQ_130006, 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: 190410
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 275 characters in sequence are not A, C, G, or T
Found at i:7325 original size:18 final size:18
Alignment explanation
Indices: 7302--7336 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
7292 GTTCAAATAT
*
7302 TTTTATTTTTAATATAAA
1 TTTTATTTTTAAAATAAA
7320 TTTTATTTTTAAAATAA
1 TTTTATTTTTAAAATAA
7337 TATTGAAAAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATTTTTAAAATAAA
Found at i:9520 original size:87 final size:87
Alignment explanation
Indices: 9364--9620 Score: 290
Period size: 87 Copynumber: 3.0 Consensus size: 87
9354 CGATATTACA
* * *
9364 ACGATTAGTAAGGAATTGATTCACTTTGTGTTGAAGCAGTTGAAATTACTTGGCGCTATTGTTTT
1 ACGATTAGTAAGGAATTGATTCACTTTGTGTTTAAGTAGTTGAAATTACTTGGCACTATTGTTTT
9429 TCTAGATTCTCTTATGTTGCAT
66 TCTAGATTCTCTTATGTTGCAT
* * **
9451 ACGATTACTAAGGAATTGATTTACTTTGTGTTTAAGTAGTTGAAATTGGTCT-GCACT-TCT-TT
1 ACGATTAGTAAGGAATTGATTCACTTTGTGTTTAAGTAGTTGAAATTACT-TGGCACTAT-TGTT
*
9513 TTCTCTAGATTCTTTTATGTTGCAT
64 TT-TCTAGATTCTCTTATGTTGCAT
* * * * *** *
9538 ACGATTAGTAAGGAACTGCA-TCACTTCGTGTTTAAGTAGTTGAAATCACTCGATTCT-TTTTTT
1 ACGATTAGTAAGGAATTG-ATTCACTTTGTGTTTAAGTAGTTGAAATTACTTGGCACTATTGTTT
*
9601 TTCTAGATTCTTTTATGTTG
65 TTCTAGATTCTCTTATGTTG
9621 AATAGGAATT
Statistics
Matches: 145, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
86 25 0.17
87 118 0.81
88 2 0.01
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (87 bp):
ACGATTAGTAAGGAATTGATTCACTTTGTGTTTAAGTAGTTGAAATTACTTGGCACTATTGTTTT
TCTAGATTCTCTTATGTTGCAT
Found at i:13088 original size:2 final size:2
Alignment explanation
Indices: 13081--13107 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13071 TAGTCTTTTC
13081 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
13108 GAATCCTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15074 original size:2 final size:2
Alignment explanation
Indices: 15067--15093 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15057 TGTTGGTGAG
15067 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
15094 GATTGTCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21336 original size:6 final size:6
Alignment explanation
Indices: 21325--21354 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
21315 TTGCATCAAC
21325 AAAATT AAAATT AAAATT ATAAATT AAAAT
1 AAAATT AAAATT AAAATT A-AAATT AAAAT
21355 AATGTCCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAAATT
Found at i:21350 original size:13 final size:12
Alignment explanation
Indices: 21325--21354 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
21315 TTGCATCAAC
21325 AAAATTAAAATT
1 AAAATTAAAATT
21337 AAAATTATAAATT
1 AAAATTA-AAATT
21350 AAAAT
1 AAAAT
21355 AATGTCCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAAAATT
Found at i:34244 original size:26 final size:24
Alignment explanation
Indices: 34215--34278 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 24
34205 AAAGTTTAAG
*
34215 AATTTATTTATAATAAATTGTTATTT
1 AATTTATTTATAATAAA--GTTATTA
*
34241 AATTATGTTTA-AATAAAGTTATTA
1 AATT-TATTTATAATAAAGTTATTA
34265 ATATTTATTTATAA
1 A-ATTTATTTATAA
34279 GCCCTCTCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 12 0.38
25 5 0.16
26 10 0.31
27 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (24 bp):
AATTTATTTATAATAAAGTTATTA
Found at i:36597 original size:56 final size:58
Alignment explanation
Indices: 36451--36634 Score: 214
Period size: 59 Copynumber: 3.2 Consensus size: 58
36441 ATTTATATAT
* * *
36451 TAAAAATAATATTATATTAATGAATGATTATCAAATGACGGTATTACATGGAAAAAAA
1 TAAAAATAATATTATATTAATGAATGATTATCAAATGGCAGTATTACATAGAAAAAAA
* **
36509 TAAAATAAAATATTATATTAATGAAGTG-TTATCAAATGGCAGTATTGTA-AG-AAAAAA
1 TAAAA-ATAATATTATATTAATGAA-TGATTATCAAATGGCAGTATTACATAGAAAAAAA
** * ** *
36566 TAAAAATAATATTATATTAATGAATGATTATCAAATGGTGGCACCACA-GGAAAAAAA
1 TAAAAATAATATTATATTAATGAATGATTATCAAATGGCAGTATTACATAGAAAAAAA
36623 TAAAAATAATAT
1 TAAAAATAATAT
36635 ATCAGTGTAG
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
55 2 0.02
56 33 0.31
57 29 0.27
58 6 0.06
59 35 0.33
60 2 0.02
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.30
Consensus pattern (58 bp):
TAAAAATAATATTATATTAATGAATGATTATCAAATGGCAGTATTACATAGAAAAAAA
Found at i:36784 original size:7 final size:7
Alignment explanation
Indices: 36774--36824 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
36764 CTTAAAAATT
36774 AAATAAC
1 AAATAAC
36781 AAATAA-
1 AAATAAC
**
36787 AAATATT
1 AAATAAC
36794 AAATAAC
1 AAATAAC
36801 AAATAA-
1 AAATAAC
**
36807 AAATATT
1 AAATAAC
36814 AAATAAC
1 AAATAAC
36821 AAAT
1 AAAT
36825 CAATTAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
6 10 0.28
7 26 0.72
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (7 bp):
AAATAAC
Found at i:36796 original size:20 final size:20
Alignment explanation
Indices: 36767--37073 Score: 133
Period size: 20 Copynumber: 13.9 Consensus size: 20
36757 AAAATAACTT
36767 AAAA-ATTAAATAACAAATA
1 AAAATATTAAATAACAAATA
36786 AAAATATTAAATAACAAATA
1 AAAATATTAAATAACAAATA
36806 AAAATATTAAATAACAAATCA
1 AAAATATTAAATAACAAAT-A
*
36827 ATTAAAAATTAAATTTACTTAACTAAATA
1 A--AAATATT-AA---A--TAAC-AAATA
*
36856 AAAACATTAAATAACAAATCA
1 AAAATATTAAATAACAAAT-A
*
36877 ATTAAAAATTAAATTTACTCAACTAAATAA
1 A--AAATATT-AA---A-T-AAC-AAAT-A
* *
36907 AAAACATTAAATAAAAAATCA
1 AAAATATTAAATAACAAAT-A
*
36928 ATTAAAAATTAAATAACAAATA
1 A--AAATATTAAATAACAAATA
*
36950 AAAACATTAAATAACAAATCAATTA
1 AAAATATTAAATAAC--A--AA-TA
*
36975 AAAATAACTTAAA-AATTAAATAA
1 AAAAT-A-TTAAATAA-CAAAT-A
36998 AAAATACATTAAATAACAAAT-
1 AAAAT--ATTAAATAACAAATA
* * * *
37019 CAATTA-AAAATAAC--TTA
1 AAAATATTAAATAACAAATA
37036 AAAA-ATTAAATAACAAATA
1 AAAATATTAAATAACAAATA
*
37055 AAAATATCAAATAACAAAT
1 AAAATATTAAATAACAAAT
37074 CAATTAAAAA
Statistics
Matches: 226, Mismatches: 23, Indels: 77
0.69 0.07 0.24
Matches are distributed among these distances:
16 2 0.01
17 9 0.04
18 7 0.03
19 11 0.05
20 64 0.28
21 17 0.08
22 6 0.03
23 47 0.21
24 10 0.04
25 7 0.03
26 5 0.02
27 15 0.07
28 7 0.03
29 9 0.04
30 10 0.04
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATATTAAATAACAAATA
Found at i:36810 original size:13 final size:13
Alignment explanation
Indices: 36774--36824 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
36764 CTTAAAAATT
36774 AAATAACAAATAA
1 AAATAACAAATAA
**
36787 AAATATTAAATAA
1 AAATAACAAATAA
*
36800 CAAATAA-AAATATT
1 -AAATAACAAATA-A
36814 AAATAACAAAT
1 AAATAACAAAT
36825 CAATTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 22 0.71
14 9 0.29
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAACAAATAA
Found at i:36857 original size:25 final size:24
Alignment explanation
Indices: 36829--36909 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 24
36819 ACAAATCAAT
36829 TAAAAATTAAATTTACTTAACTAAA
1 TAAAAATTAAATTTAC-TAACTAAA
* * *
36854 TAAAAACATTAAA-TAAC-AAATCAAT
1 T-AAAA-ATTAAATTTACTAACT-AAA
36879 TAAAAATTAAATTTACTCAACTAAA
1 TAAAAATTAAATTTACT-AACTAAA
36904 TAAAAA
1 TAAAAA
36910 ACATTAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
23 6 0.14
24 10 0.23
25 12 0.27
26 10 0.23
27 6 0.14
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (24 bp):
TAAAAATTAAATTTACTAACTAAA
Found at i:36858 original size:50 final size:50
Alignment explanation
Indices: 36797--37140 Score: 404
Period size: 50 Copynumber: 6.9 Consensus size: 50
36787 AAATATTAAA
*
36797 TAAC-AAATAAAAATATTAAATAACAAATCAATTAAAAATTAAATTTACT
1 TAACTAAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATTTACT
36846 TAACTAAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATTTACT
1 TAACTAAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATTTACT
* *
36896 CAACTAAATAAAAAACATTAAATAAAAAATCAATTAAAAATT-AA---A--
1 TAACTAAAT-AAAAACATTAAATAACAAATCAATTAAAAATTAAATTTACT
* * *
36941 TAAC-AAATAAAAACATTAAATAACAAATCAATTAAAAA-TAACTTAAAAAT
1 TAACTAAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATT--TACT
* * * **
36991 TAAATAAA-AAATACATTAAATAACAAATCAATTAAAAATAACTTAAAAAATTAAA
1 TAACTAAATAAAAACATTAAATAACAAATCAATT--AAA-AA-TT--AAATTTACT
* *
37046 TAAC-AAATAAAAATATCAAATAACAAATCAATTAAAAATTAAATTTACT
1 TAACTAAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATTTACT
*
37095 CAACTAAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATT
1 TAACTAAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATT
37141 AAACAAAACA
Statistics
Matches: 253, Mismatches: 22, Indels: 39
0.81 0.07 0.12
Matches are distributed among these distances:
42 1 0.00
43 30 0.12
44 4 0.02
45 3 0.01
47 1 0.00
48 1 0.00
49 13 0.05
50 120 0.47
51 36 0.14
52 5 0.02
53 5 0.02
54 3 0.01
55 28 0.11
57 3 0.01
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (50 bp):
TAACTAAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATTTACT
Found at i:37040 original size:105 final size:106
Alignment explanation
Indices: 36918--37143 Score: 309
Period size: 105 Copynumber: 2.2 Consensus size: 106
36908 AAACATTAAA
* * *
36918 TAAAAAATCAATT-AAAAATTAAATAACAAATAAAAACATTAAATAACAAATCAATTAAAAA-T-
1 TAAAAATTAAATTAAAAAATTAAATAACAAATAAAAACATCAAATAACAAATCAATTAAAAATTA
*
36980 AACTTA-AAAATTAAATAAAAAATACATTAAATAACAAATCAAT
66 AACTTACAAAACTAAAT--AAAA-ACATTAAATAACAAATCAAT
* *
37023 TAAAAA-TAACTTAAAAAATTAAATAACAAATAAAAATATCAAATAACAAATCAATTAAAAATTA
1 TAAAAATTAAATTAAAAAATTAAATAACAAATAAAAACATCAAATAACAAATCAATTAAAAATTA
* **
37087 AATTTACTCAACTAAATAAAAACATTAAATAACAAATCAAT
66 AACTTACAAAACTAAATAAAAACATTAAATAACAAATCAAT
37128 TAAAAATTAAATTAAA
1 TAAAAATTAAATTAAA
37144 CAAAACAATA
Statistics
Matches: 107, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
104 4 0.04
105 78 0.73
106 13 0.12
107 5 0.05
108 7 0.07
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (106 bp):
TAAAAATTAAATTAAAAAATTAAATAACAAATAAAAACATCAAATAACAAATCAATTAAAAATTA
AACTTACAAAACTAAATAAAAACATTAAATAACAAATCAAT
Found at i:37145 original size:25 final size:25
Alignment explanation
Indices: 37067--37152 Score: 86
Period size: 24 Copynumber: 3.4 Consensus size: 25
37057 AATATCAAAT
37067 AACAAATCAATTAAAAATTAAATTTA
1 AACAAATCAATTAAAAATTAAA-TTA
** * * *
37093 CTCAACTAAATAAAAACATTAAA-T-
1 AACAAATCAATTAAAA-ATTAAATTA
37117 AACAAATCAATTAAAAATTAAATTA
1 AACAAATCAATTAAAAATTAAATTA
*
37142 AACAAAACAAT
1 AACAAATCAAT
37153 AAATACTAAA
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
23 6 0.13
24 12 0.26
25 11 0.24
26 11 0.24
27 6 0.13
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (25 bp):
AACAAATCAATTAAAAATTAAATTA
Found at i:43161 original size:51 final size:51
Alignment explanation
Indices: 43101--43199 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 51
43091 ACAAGGTCTG
43101 GCACACAGTTTGGGGCACAACCGTGTGACCCATTTTTTAATGAATTCTCTA
1 GCACACAGTTTGGGGCACAACCGTGTGACCCATTTTTTAATGAATTCTCTA
*
43152 GCACACAGTTTGGGGCACAACCGTGTGACCTATTTTTTAATGAATTCT
1 GCACACAGTTTGGGGCACAACCGTGTGACCCATTTTTTAATGAATTCT
43200 ATGTATAATC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.32
Consensus pattern (51 bp):
GCACACAGTTTGGGGCACAACCGTGTGACCCATTTTTTAATGAATTCTCTA
Found at i:49290 original size:36 final size:36
Alignment explanation
Indices: 49254--49442 Score: 200
Period size: 36 Copynumber: 5.2 Consensus size: 36
49244 TATAAAGTTA
* * *
49254 CATACGTCTTGGTTAGAGCGTGTTACTATGATGTTA
1 CATACGTCTCGGTTAGAGCGTATTACTATGATGTTG
* * *
49290 CATATGTCTCGGTTATAGCGTATTGCTATGATGTTG
1 CATACGTCTCGGTTAGAGCGTATTACTATGATGTTG
* * *
49326 CATACGTCTCGATTAGAGCATATTATTATGATGTTG
1 CATACGTCTCGGTTAGAGCGTATTACTATGATGTTG
* * * * * *
49362 CATACATCTCGGTAAAAACGTA-TAGCAAAGATGTTG
1 CATACGTCTCGGTTAGAGCGTATTA-CTATGATGTTG
* * *
49398 CATACATCTCGGTTAGAGCGTATTATTATGAAGTTG
1 CATACGTCTCGGTTAGAGCGTATTACTATGATGTTG
49434 CATACGTCT
1 CATACGTCT
49443 ACGTCCCAGT
Statistics
Matches: 122, Mismatches: 29, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
35 2 0.02
36 118 0.97
37 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (36 bp):
CATACGTCTCGGTTAGAGCGTATTACTATGATGTTG
Found at i:49356 original size:72 final size:72
Alignment explanation
Indices: 49254--49442 Score: 234
Period size: 72 Copynumber: 2.6 Consensus size: 72
49244 TATAAAGTTA
* * * * * * * * * * *
49254 CATACGTCTTGGTTAGAGCGTGTTACTATGATGTTACATATGTCTCGGTTATAGCGTATTGCTAT
1 CATACGTCTCGGTTAGAGCGTATTATTATGATGTTGCATACGTCTCGGTAAAAACGTATAGCAAA
49319 GATGTTG
66 GATGTTG
* * *
49326 CATACGTCTCGATTAGAGCATATTATTATGATGTTGCATACATCTCGGTAAAAACGTATAGCAAA
1 CATACGTCTCGGTTAGAGCGTATTATTATGATGTTGCATACGTCTCGGTAAAAACGTATAGCAAA
49391 GATGTTG
66 GATGTTG
* *
49398 CATACATCTCGGTTAGAGCGTATTATTATGAAGTTGCATACGTCT
1 CATACGTCTCGGTTAGAGCGTATTATTATGATGTTGCATACGTCT
49443 ACGTCCCAGT
Statistics
Matches: 98, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 98 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (72 bp):
CATACGTCTCGGTTAGAGCGTATTATTATGATGTTGCATACGTCTCGGTAAAAACGTATAGCAAA
GATGTTG
Found at i:49503 original size:36 final size:36
Alignment explanation
Indices: 49451--49536 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
49441 CTACGTCCCA
* *
49451 GTTAGAGCATATTGCT-A-TGAATTTGCTTATGTCTTG
1 GTTAGAGCATAATGCTAAGTG-A-TTGCTTATGTCTCG
* *
49487 GTTAGAGCTTAATGCTAAGTGATTGTTTATGTCTCG
1 GTTAGAGCATAATGCTAAGTGATTGCTTATGTCTCG
49523 GTTAGAGCATAATG
1 GTTAGAGCATAATG
49537 TCATTTTAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
36 39 0.91
37 2 0.05
38 2 0.05
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (36 bp):
GTTAGAGCATAATGCTAAGTGATTGCTTATGTCTCG
Found at i:53641 original size:21 final size:21
Alignment explanation
Indices: 53617--53657 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
53607 AGCTTTAAAG
*
53617 ATTACATAATTGAAAAGAATA
1 ATTACAAAATTGAAAAGAATA
* *
53638 ATTATAAAATTTAAAAGAAT
1 ATTACAAAATTGAAAAGAAT
53658 TAATATTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (21 bp):
ATTACAAAATTGAAAAGAATA
Found at i:55503 original size:30 final size:30
Alignment explanation
Indices: 55467--55524 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
55457 TTAATAAAAG
55467 TAAAA-TTACACTTTAATCTTTTAAAAATAA
1 TAAAATTTACA-TTTAATCTTTTAAAAATAA
**
55497 TAAAATTTTGATTTAATCTTTTAAAAAT
1 TAAAATTTACATTTAATCTTTTAAAAAT
55525 TATATTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (30 bp):
TAAAATTTACATTTAATCTTTTAAAAATAA
Found at i:67808 original size:21 final size:19
Alignment explanation
Indices: 67784--67836 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
67774 AGAGTTTTTG
67784 GTATCGGTAGATGCATGACTT
1 GTATCGGTAGAT-CAT-ACTT
*
67805 GTATCGATAGAAATCATACTT
1 GTATCGGTAG--ATCATACTT
*
67826 GTATCAGTAGA
1 GTATCGGTAGA
67837 GCTAGCACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 1 0.04
21 21 0.78
22 3 0.11
23 2 0.07
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (19 bp):
GTATCGGTAGATCATACTT
Found at i:71458 original size:28 final size:28
Alignment explanation
Indices: 71414--71470 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
71404 TTTTATTCAA
71414 AATACATCATTTCAATTCATCAACTCGT
1 AATACATCATTTCAATTCATCAACTCGT
*
71442 AATACATCATTTTAATTCATCAACTCGT
1 AATACATCATTTCAATTCATCAACTCGT
71470 A
1 A
71471 GTAATCCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.37
Consensus pattern (28 bp):
AATACATCATTTCAATTCATCAACTCGT
Found at i:71878 original size:21 final size:22
Alignment explanation
Indices: 71852--71987 Score: 114
Period size: 23 Copynumber: 6.0 Consensus size: 22
71842 CGAAACAAAT
* *
71852 AGAGAGTAC-CAAAGTACTAAC
1 AGAGAGCACACAAAGTGCTAAC
*
71873 AGAGAGCACA-TAAGTGCTGGGCAAC
1 AGAGAGCACACAAAGTGCT----AAC
* *
71898 AGAGAGCGCACACAGTGCTAAAC
1 AGAGAGCACACAAAGTGCT-AAC
* *
71921 AGAGAGTACACAAAGTACTAATC
1 AGAGAGCACACAAAGTGCTAA-C
71944 AGAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACAAAGTGCTAA-C
* *
71967 AGAGAGCATACACAGTGCTAA
1 AGAGAGCACACAAAGTGCTAA
71988 TAACAGAGAG
Statistics
Matches: 93, Mismatches: 15, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
21 14 0.15
22 2 0.02
23 59 0.63
25 12 0.13
26 6 0.06
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.13
Consensus pattern (22 bp):
AGAGAGCACACAAAGTGCTAAC
Found at i:71921 original size:23 final size:23
Alignment explanation
Indices: 71895--72021 Score: 139
Period size: 23 Copynumber: 5.4 Consensus size: 23
71885 AGTGCTGGGC
*
71895 AACAGAGAGCGCACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
71918 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* *
71941 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* *
71964 ATCAGAGAGCATACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
71988 TAACAGAGAGCACGAGACA-TGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
72012 AACAGAGAGC
1 AACAGAGAGC
72022 GCGCTAGTGT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 69 0.78
24 2 0.02
25 14 0.16
26 4 0.04
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:71970 original size:69 final size:68
Alignment explanation
Indices: 71852--71997 Score: 181
Period size: 69 Copynumber: 2.1 Consensus size: 68
71842 CGAAACAAAT
* *
71852 AGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCGCACACAGTGCT
1 AGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACACAGTGCT
71917 -A-AAC
63 AATAAC
*
71921 AGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCATACACAGTGC
1 AGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACACAGTGC
71985 TAATAAC
62 TAATAAC
71992 AGAGAG
1 AGAGAG
71998 CACGAGACAT
Statistics
Matches: 68, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
68 2 0.03
69 27 0.40
70 12 0.18
71 20 0.29
72 7 0.10
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (68 bp):
AGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACACACAGTGCTAAT
AAC
Found at i:82358 original size:23 final size:22
Alignment explanation
Indices: 82316--82359 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
82306 AATAAATTTA
82316 TAAATCCAAAAGATAAAAGAAT
1 TAAATCCAAAAGATAAAAGAAT
82338 TAAATCCTTAAAA-ATAAAAGAA
1 TAAATCC--AAAAGATAAAAGAA
82360 GAATTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 9 0.45
24 4 0.20
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (22 bp):
TAAATCCAAAAGATAAAAGAAT
Found at i:83026 original size:25 final size:27
Alignment explanation
Indices: 82989--83039 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
82979 CCAACATGTG
* *
82989 AACATTGATTGAGAAT-G-AAATGAAC
1 AACATGGAATGAGAATGGAAAATGAAC
83014 AACATGGAATGAGAATGGAAAATGAA
1 AACATGGAATGAGAATGGAAAATGAA
83040 TTTATGGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
26 1 0.05
27 7 0.32
ACGTcount: A:0.51, C:0.06, G:0.24, T:0.20
Consensus pattern (27 bp):
AACATGGAATGAGAATGGAAAATGAAC
Found at i:86286 original size:2 final size:2
Alignment explanation
Indices: 86279--86305 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
86269 ACATACATTC
86279 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
86306 CTCTATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:90600 original size:4 final size:4
Alignment explanation
Indices: 90591--90621 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
90581 CATACACACA
*
90591 TATT TATT TATT TACT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
90622 ATTCATATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:108354 original size:11 final size:11
Alignment explanation
Indices: 108338--108383 Score: 69
Period size: 11 Copynumber: 4.4 Consensus size: 11
108328 TCACGTCAGT
108338 AAATTATTTTA
1 AAATTATTTTA
108349 AAATTA--TTA
1 AAATTATTTTA
108358 AAATTATTTTA
1 AAATTATTTTA
*
108369 AAATTAATTTA
1 AAATTATTTTA
108380 AAAT
1 AAAT
108384 ATAAAACGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 9 0.28
11 23 0.72
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:109458 original size:18 final size:16
Alignment explanation
Indices: 109427--109480 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 16
109417 TTAAAATGAT
109427 TATTTTAATAATTTTA
1 TATTTTAATAATTTTA
109443 TATTTTAAATTAATTTTAAAA
1 TATTTT-AA-TAATTTT---A
109464 TCATTTTAATAATTTTA
1 T-ATTTTAATAATTTTA
109481 AAATCATTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 6 0.19
17 3 0.09
18 7 0.22
20 7 0.22
21 4 0.12
22 5 0.16
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTTAATAATTTTA
Found at i:109478 original size:20 final size:20
Alignment explanation
Indices: 109428--109489 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
109418 TAAAATGATT
109428 ATTTTAATAATTTT---AT-
1 ATTTTAATAATTTTAAAATC
109444 ATTTTAAATTAATTTTAAAATC
1 ATTTT-AA-TAATTTTAAAATC
109466 ATTTTAATAATTTTAAAATC
1 ATTTTAATAATTTTAAAATC
109486 ATTT
1 ATTT
109490 GTTCACGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.12
17 2 0.05
18 7 0.17
20 17 0.43
21 4 0.10
22 5 0.12
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTAATAATTTTAAAATC
Found at i:109489 original size:11 final size:11
Alignment explanation
Indices: 109444--109489 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
109434 ATAATTTTAT
*
109444 ATTTTAAATTA
1 ATTTTAAAATA
*
109455 ATTTTAAAATC
1 ATTTTAAAATA
109466 ATTTT--AATA
1 ATTTTAAAATA
*
109475 ATTTTAAAATC
1 ATTTTAAAATA
109486 ATTT
1 ATTT
109490 GTTCACGTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 8 0.28
11 21 0.72
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTTAAAATA
Found at i:109671 original size:30 final size:30
Alignment explanation
Indices: 109635--109695 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
109625 CTATTTGACC
* * *
109635 AAAAAAAAGGTTAAGGGCCAACGTGAGCAA
1 AAAAAAAAGGATAAGGGCCAAAGTGACCAA
*
109665 AAAAAAAATGATAAGGGCCAAAGTGACCAA
1 AAAAAAAAGGATAAGGGCCAAAGTGACCAA
109695 A
1 A
109696 CATCCAAACG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.54, C:0.13, G:0.23, T:0.10
Consensus pattern (30 bp):
AAAAAAAAGGATAAGGGCCAAAGTGACCAA
Found at i:117984 original size:16 final size:16
Alignment explanation
Indices: 117960--118002 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
117950 ACTTTTTTAA
*
117960 TTTTGATTTATATATT
1 TTTTGATTTATATAAT
* *
117976 TTTTTATTTTTATAAT
1 TTTTGATTTATATAAT
117992 TTTTGATTTAT
1 TTTTGATTTAT
118003 TTGTTGGCAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (16 bp):
TTTTGATTTATATAAT
Found at i:125336 original size:247 final size:247
Alignment explanation
Indices: 124900--125394 Score: 963
Period size: 247 Copynumber: 2.0 Consensus size: 247
124890 AGAATCATAA
*
124900 TAGCTCGAATAAAAAGTTAATGATATCTTCTTAATGATATATATCTGTTTATGAAACTGAAACAT
1 TAGCTCGAATAAAAAGTTAATGATATCTTCTCAATGATATATATCTGTTTATGAAACTGAAACAT
*
124965 GATCATAGATTATTTTTTTTGAATAAATGATTTAATCTTTACTTATTACAAATACAATGCAACGT
66 GACCATAGATTATTTTTTTTGAATAAATGATTTAATCTTTACTTATTACAAATACAATGCAACGT
125030 TGAGATAAAAGTGATCAAATTAATTGAAAAAAATACACAAATATCATAGTCATATTTTCAAATAT
131 TGAGATAAAAGTGATCAAATTAATTGAAAAAAATACACAAATATCATAGTCATATTTTCAAATAT
125095 AGTTTTTTTTGTAATTTTATATATAATTGGGAGTTCTGTCATCATACTTTAG
196 AGTTTTTTTTGTAATTTTATATATAATTGGGAGTTCTGTCATCATACTTTAG
*
125147 TAGCTCGAATAAAAAGTTAATGATATCTTCTCAATGATATATATTTGTTTATGAAACTGAAACAT
1 TAGCTCGAATAAAAAGTTAATGATATCTTCTCAATGATATATATCTGTTTATGAAACTGAAACAT
125212 GACCATAGATTATTTTTTTTGAATAAATGATTTAATCTTTACTTATTACAAATACAATGCAACGT
66 GACCATAGATTATTTTTTTTGAATAAATGATTTAATCTTTACTTATTACAAATACAATGCAACGT
125277 TGAGATAAAAGTGATCAAATTAATTGAAAAAAATACACAAATATCATAGTCATATTTTCAAATAT
131 TGAGATAAAAGTGATCAAATTAATTGAAAAAAATACACAAATATCATAGTCATATTTTCAAATAT
125342 AGTTTTTTTTGTAATTTTATATATAATTGGGAGTTCTGTCATCATACTTTAG
196 AGTTTTTTTTGTAATTTTATATATAATTGGGAGTTCTGTCATCATACTTTAG
125394 T
1 T
125395 GGTAAGGTTA
Statistics
Matches: 245, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
247 245 1.00
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (247 bp):
TAGCTCGAATAAAAAGTTAATGATATCTTCTCAATGATATATATCTGTTTATGAAACTGAAACAT
GACCATAGATTATTTTTTTTGAATAAATGATTTAATCTTTACTTATTACAAATACAATGCAACGT
TGAGATAAAAGTGATCAAATTAATTGAAAAAAATACACAAATATCATAGTCATATTTTCAAATAT
AGTTTTTTTTGTAATTTTATATATAATTGGGAGTTCTGTCATCATACTTTAG
Found at i:127799 original size:30 final size:31
Alignment explanation
Indices: 127738--127799 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
127728 GGGGGTGGAA
* * *
127738 TGGGAATGAAGTAAAAGTTTTGGGGGTAAAG
1 TGGGAATGAAGTAAAAGTTTTAGGAGAAAAG
*
127769 TGGGAA-GGAGTAAAAGTTTTAGGAGAAAAG
1 TGGGAATGAAGTAAAAGTTTTAGGAGAAAAG
127799 T
1 T
127800 AAAAAGGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.39, C:0.00, G:0.37, T:0.24
Consensus pattern (31 bp):
TGGGAATGAAGTAAAAGTTTTAGGAGAAAAG
Found at i:128482 original size:20 final size:20
Alignment explanation
Indices: 128459--128506 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
128449 AAAACTTATA
* *
128459 AAAAATAACATCCAAACAAC
1 AAAAATAACAACCAAAAAAC
128479 AAAAATAACAACCAAAAAAC
1 AAAAATAACAACCAAAAAAC
128499 AACAAATA
1 AA-AAATA
128507 TAACAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.71, C:0.21, G:0.00, T:0.08
Consensus pattern (20 bp):
AAAAATAACAACCAAAAAAC
Found at i:128490 original size:12 final size:12
Alignment explanation
Indices: 128473--128573 Score: 68
Period size: 12 Copynumber: 8.8 Consensus size: 12
128463 ATAACATCCA
128473 AACAACAAAAAT
1 AACAACAAAAAT
*
128485 AACAACCAAAA-
1 AACAACAAAAAT
*
128496 AACAACAAATAT
1 AACAACAAAAAT
** *
128508 AAC-AGTAAAAC
1 AACAACAAAAAT
128519 AACAAC--AAA-
1 AACAACAAAAAT
* *
128528 AACGATAAAAAT
1 AACAACAAAAAT
*
128540 ATCAACAAAAAT
1 AACAACAAAAAT
* *
128552 AACAGCGAAAAT
1 AACAACAAAAAT
*
128564 AACACCAAAA
1 AACAACAAAA
128574 CAGTAAAAAA
Statistics
Matches: 66, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
9 4 0.06
10 3 0.05
11 19 0.29
12 40 0.61
ACGTcount: A:0.68, C:0.19, G:0.04, T:0.09
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:128502 original size:23 final size:22
Alignment explanation
Indices: 128472--128529 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
128462 AATAACATCC
128472 AAACAACAAAAATAACAACCAAA
1 AAACAACAAAAATAAC-ACCAAA
* **
128495 AAACAACAAATATAACAGTAAA
1 AAACAACAAAAATAACACCAAA
128517 ACAACAACAAAAA
1 A-AACAACAAAAA
128530 CGATAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.72, C:0.19, G:0.02, T:0.07
Consensus pattern (22 bp):
AAACAACAAAAATAACACCAAA
Found at i:128574 original size:44 final size:44
Alignment explanation
Indices: 128498--128582 Score: 102
Period size: 44 Copynumber: 1.9 Consensus size: 44
128488 AACCAAAAAA
* *
128498 CAACAAATATAACAGTAAAACAACAACAAAAAC-GATAAAAATAT
1 CAACAAAAATAACAGGAAAACAACAACAAAAACAG-TAAAAATAT
* *
128542 CAACAAAAATAACAGCGAAAATAAC-ACCAAAACAGTAAAAA
1 CAACAAAAATAACAG-GAAAACAACAACAAAAACAGTAAAAA
128583 AAAGCACCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
44 27 0.77
45 8 0.23
ACGTcount: A:0.66, C:0.18, G:0.06, T:0.11
Consensus pattern (44 bp):
CAACAAAAATAACAGGAAAACAACAACAAAAACAGTAAAAATAT
Found at i:131361 original size:33 final size:32
Alignment explanation
Indices: 131324--131421 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 32
131314 GTTTAAAACC
131324 CCCATTTTCATCTTTTTTCCAAACTCTTCAACT
1 CCCATTTTCATCTTTTTTCC-AACTCTTCAACT
* *
131357 CCCA--TT--T-TGTTTT-C--CT-TTAAAACT
1 CCCATTTTCATCTTTTTTCCAACTCTT-CAACT
131381 CCCATTTTCATCTTTTTTTCCAACTCTTCAACT
1 CCCATTTTCATC-TTTTTTCCAACTCTTCAACT
131414 CCCATTTT
1 CCCATTTT
131422 GTTTTCCCTC
Statistics
Matches: 50, Mismatches: 4, Indels: 22
0.66 0.05 0.29
Matches are distributed among these distances:
23 2 0.04
24 10 0.20
26 2 0.04
27 1 0.02
28 6 0.12
29 1 0.02
30 5 0.10
31 3 0.06
33 18 0.36
34 2 0.04
ACGTcount: A:0.19, C:0.32, G:0.01, T:0.48
Consensus pattern (32 bp):
CCCATTTTCATCTTTTTTCCAACTCTTCAACT
Found at i:131392 original size:57 final size:57
Alignment explanation
Indices: 131315--131428 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
131305 TTTTGTTAGG
131315 TTTAAAACCCCCATTTTCATC-TTTTTTCCAAACTCTTCAACTCCCATTTTGTTTTCC
1 TTTAAAACCCCCATTTTCATCTTTTTTTCC-AACTCTTCAACTCCCATTTTGTTTTCC
*
131372 TTTAAAACTCCCATTTTCATCTTTTTTTCCAACTCTTCAACTCCCATTTTGTTTTCC
1 TTTAAAACCCCCATTTTCATCTTTTTTTCCAACTCTTCAACTCCCATTTTGTTTTCC
131429 CTCAACTGAT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 47 0.85
58 8 0.15
ACGTcount: A:0.20, C:0.31, G:0.02, T:0.47
Consensus pattern (57 bp):
TTTAAAACCCCCATTTTCATCTTTTTTTCCAACTCTTCAACTCCCATTTTGTTTTCC
Found at i:131918 original size:19 final size:19
Alignment explanation
Indices: 131894--131932 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
131884 GCCAAACTAG
131894 CCAAGCCTAAGACCCAATT
1 CCAAGCCTAAGACCCAATT
131913 CCAAGCCTAAGACCCAATT
1 CCAAGCCTAAGACCCAATT
131932 C
1 C
131933 GAAGAGGCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.38, G:0.10, T:0.15
Consensus pattern (19 bp):
CCAAGCCTAAGACCCAATT
Found at i:132588 original size:29 final size:29
Alignment explanation
Indices: 132556--132611 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
132546 CCACACCTTG
* *
132556 TATGATATTATTTTGTGTTGTATTATCTA
1 TATGATATTAATCTGTGTTGTATTATCTA
* *
132585 TATGATTTTAATCTGTGTTGTGTTATC
1 TATGATATTAATCTGTGTTGTATTATC
132612 ACATGTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.21, C:0.05, G:0.16, T:0.57
Consensus pattern (29 bp):
TATGATATTAATCTGTGTTGTATTATCTA
Found at i:136350 original size:42 final size:41
Alignment explanation
Indices: 136303--136447 Score: 143
Period size: 42 Copynumber: 3.5 Consensus size: 41
136293 CGTAATCAAC
*
136303 CGAGTCATAAGTCTTCCTTTAAACGA-AATCTCATGCTCATTT
1 CGAGTCACAAGTCTTCCTTTAAAC-ATAATCTCATGCTC-TTT
* *
136345 CGAGTCACAAGTCATCCTTTAAAACATAACCTCAT-CTCTTT
1 CGAGTCACAAGTCTTCCTTT-AAACATAATCTCATGCTCTTT
* ** * *
136386 CTAAGTCATGAGTCTTCC-TTAATCATAATCTCATGCTCCTCT
1 C-GAGTCACAAGTCTTCCTTTAAACATAATCTCATGCT-CTTT
*
136428 CGAGTCACGAGTCTTCCTTT
1 CGAGTCACAAGTCTTCCTTT
136448 TTTTATATAA
Statistics
Matches: 85, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
40 12 0.14
41 22 0.26
42 40 0.47
43 11 0.13
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (41 bp):
CGAGTCACAAGTCTTCCTTTAAACATAATCTCATGCTCTTT
Found at i:136440 original size:41 final size:42
Alignment explanation
Indices: 136303--136535 Score: 190
Period size: 41 Copynumber: 5.5 Consensus size: 42
136293 CGTAATCAAC
* * *
136303 CGAGTCATAAGTCTTCCTTTAAACGA-AATCTCATGCTCATTT
1 CGAGTCATGAGTCTTCCTTTAATC-ATAATCTCATGCTCATCT
** * * * *
136345 CGAGTCACAAGTCATCCTTTAAAACATAACCTCAT-CTC-TTT
1 CGAGTCATGAGTCTTCCTTT-AATCATAATCTCATGCTCATCT
* *
136386 CTAAGTCATGAGTCTTCC-TTAATCATAATCTCATGCTCCTCT
1 C-GAGTCATGAGTCTTCCTTTAATCATAATCTCATGCTCATCT
* * *
136428 CGAGTCACGAGTCTTCCTTTTTTTAT-ATAATCTCATGCTCATCC
1 CGAGTCATGAGTCTTCC---TTTAATCATAATCTCATGCTCATCT
* * * * *
136472 CAAGACATGAGTCTTCCTTTAAT-ATATTCTCATGTTCATCC
1 CGAGTCATGAGTCTTCCTTTAATCATAATCTCATGCTCATCT
*
136513 CGAGACATGAGTCTTCCTTTAAT
1 CGAGTCATGAGTCTTCCTTTAAT
136536 ATGCATCAAG
Statistics
Matches: 160, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
40 12 0.08
41 66 0.41
42 37 0.23
43 11 0.07
44 30 0.19
45 4 0.03
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (42 bp):
CGAGTCATGAGTCTTCCTTTAATCATAATCTCATGCTCATCT
Found at i:136869 original size:22 final size:22
Alignment explanation
Indices: 136843--136884 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
136833 TGTGACTTTC
*
136843 TTTA-TTAAGCTTAATTAATCCT
1 TTTATTTAA-CTTAATAAATCCT
136865 TTTATTTAACTTAATAAATC
1 TTTATTTAACTTAATAAATC
136885 ACACTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTATTTAACTTAATAAATCCT
Found at i:146518 original size:14 final size:14
Alignment explanation
Indices: 146499--146529 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
146489 CATATAACCA
*
146499 TTTCATATATCTAT
1 TTTCATATATATAT
146513 TTTCATATATATAT
1 TTTCATATATATAT
146527 TTT
1 TTT
146530 GTATAATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTCATATATATAT
Found at i:147245 original size:23 final size:24
Alignment explanation
Indices: 147198--147250 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
147188 TACGGAACAG
*
147198 AATAGAACACCATCCAAGCAAAT-
1 AATAGAACACCACCCAAGCAAATA
**
147221 AATAGAACACCACCCAAGCGGATA
1 AATAGAACACCACCCAAGCAAATA
147245 AATAGA
1 AATAGA
147251 TAGCACAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.51, C:0.25, G:0.13, T:0.11
Consensus pattern (24 bp):
AATAGAACACCACCCAAGCAAATA
Found at i:148529 original size:29 final size:29
Alignment explanation
Indices: 148487--148547 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
148477 TCGGAAACAA
148487 TTTAATTATCTTTAAAATCTCATTATTTT
1 TTTAATTATCTTTAAAATCTCATTATTTT
148516 TTTAATTATCTTTAAAATCTCATTATTTT
1 TTTAATTATCTTTAAAATCTCATTATTTT
148545 TTT
1 TTT
148548 CTTTCTTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTAATTATCTTTAAAATCTCATTATTTT
Found at i:155627 original size:43 final size:43
Alignment explanation
Indices: 155580--155666 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
155570 ATATGGAGTA
155580 TCCGAGCGATATCCATAATATTGTAATTTCTT-ATTCTATTAAT
1 TCCGAGCGATATCCATAATATTGTAATTT-TTGATTCTATTAAT
155623 TCCGAGCGATATCCATAATATTGTAATTTTTGATTCTATTAAT
1 TCCGAGCGATATCCATAATATTGTAATTTTTGATTCTATTAAT
155666 T
1 T
155667 GATGAGGTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 2 0.05
43 41 0.95
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (43 bp):
TCCGAGCGATATCCATAATATTGTAATTTTTGATTCTATTAAT
Found at i:156028 original size:26 final size:26
Alignment explanation
Indices: 155992--156044 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
155982 TAACCATAAA
155992 TGCTCACACGAGCTATGAAATGGGTC
1 TGCTCACACGAGCTATGAAATGGGTC
156018 TGCTCACACGAGCTATGAAATGGGTC
1 TGCTCACACGAGCTATGAAATGGGTC
156044 T
1 T
156045 AGATGTTGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (26 bp):
TGCTCACACGAGCTATGAAATGGGTC
Found at i:161208 original size:35 final size:37
Alignment explanation
Indices: 161145--161213 Score: 115
Period size: 35 Copynumber: 1.9 Consensus size: 37
161135 GACTTGGTTT
*
161145 GTATGAGCTAAAATTTACTGGGAGACTTGAAGAGCTC
1 GTATGAGCTAAAATTTACTGGGAAACTTGAAGAGCTC
161182 GTATGAGCT-AAA-TTACTGGGAAACTTGAAGAG
1 GTATGAGCTAAAATTTACTGGGAAACTTGAAGAG
161214 ATCATTTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 19 0.61
36 3 0.10
37 9 0.29
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.26
Consensus pattern (37 bp):
GTATGAGCTAAAATTTACTGGGAAACTTGAAGAGCTC
Found at i:163397 original size:5 final size:5
Alignment explanation
Indices: 163384--163426 Score: 50
Period size: 5 Copynumber: 7.8 Consensus size: 5
163374 CTATTTGGAC
163384 TTTACT TTTAT TTTAT TTTAT TTTAT CACTTTAT TTTAT TTTA
1 TTTA-T TTTAT TTTAT TTTAT TTTAT ---TTTAT TTTAT TTTA
163427 ATAAGAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 25 0.74
6 4 0.12
8 5 0.15
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (5 bp):
TTTAT
Found at i:165901 original size:27 final size:27
Alignment explanation
Indices: 165779--165888 Score: 148
Period size: 27 Copynumber: 4.1 Consensus size: 27
165769 AAGTTTGAGC
* * *
165779 AAAGAGCGATACTCTATTTTTGGCTCG
1 AAAGAGCAATACTCTATTTCTAGCTCG
* *
165806 AAAGAGCAATACTCTGTTTCTAGCTCT
1 AAAGAGCAATACTCTATTTCTAGCTCG
* *
165833 TAAGAGCAATACTCTGTTTCTAGCTCG
1 AAAGAGCAATACTCTATTTCTAGCTCG
*
165860 AAAGAGCAATACTCTATTTCTGGCTCG
1 AAAGAGCAATACTCTATTTCTAGCTCG
165887 AA
1 AA
165889 TTACTAATAC
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (27 bp):
AAAGAGCAATACTCTATTTCTAGCTCG
Found at i:165956 original size:27 final size:27
Alignment explanation
Indices: 165893--165969 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 27
165883 CTCGAATTAC
* ** *
165893 TAATACTCTGTACACGGCTCAAATGAG
1 TAATACTTTGTACTTGGCTCAAATGAA
*
165920 TTATACTTTGTACTTGGCTCAAATGAA
1 TAATACTTTGTACTTGGCTCAAATGAA
* *
165947 TAATATTTTGTATTTGGCTCAAA
1 TAATACTTTGTACTTGGCTCAAA
165970 AAAGCAACAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (27 bp):
TAATACTTTGTACTTGGCTCAAATGAA
Found at i:169599 original size:35 final size:35
Alignment explanation
Indices: 169556--169626 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
169546 ATATTTGAAC
*
169556 TCAGGGTATAAGATTATTAATATAACAATGAGCAT
1 TCAGGGTATAAGATTATTAATATAACAATAAGCAT
169591 TCAGGGTATAAGATTATTAATATAACAATAAGCAT
1 TCAGGGTATAAGATTATTAATATAACAATAAGCAT
169626 T
1 T
169627 ATATTAACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.32
Consensus pattern (35 bp):
TCAGGGTATAAGATTATTAATATAACAATAAGCAT
Found at i:170242 original size:21 final size:21
Alignment explanation
Indices: 170218--170257 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
170208 TTTCATTTTA
170218 AAATTTTAAACTT-TTTTCAAG
1 AAATTTTAAA-TTATTTTCAAG
170239 AAATTTTAAATTATTTTCA
1 AAATTTTAAATTATTTTCA
170258 CTATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (21 bp):
AAATTTTAAATTATTTTCAAG
Found at i:171172 original size:22 final size:22
Alignment explanation
Indices: 171120--171172 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 22
171110 GTAGGGGATC
* * * *
171120 GAAATTAAATTGTAATTTTTAT
1 GAAATAAAAATGTAATTTTAAA
*
171142 GATAGTAAAAATGTAATTTTAAA
1 GA-AATAAAAATGTAATTTTAAA
171165 GAAATAAA
1 GAAATAAA
171173 TCAAAATTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (22 bp):
GAAATAAAAATGTAATTTTAAA
Found at i:171812 original size:56 final size:57
Alignment explanation
Indices: 171664--171831 Score: 171
Period size: 56 Copynumber: 2.9 Consensus size: 57
171654 ATATCTAAAT
* * * * * * * *
171664 TTGATATTTTTATTAATTTGGTATTTAAATTTTTTTAACTCAATTTGATACATGTAC
1 TTGACATTTTTTTTAATTTGGTATCTAACTTTTTTTGACTCAATTTGGTACCTGAAC
* *
171721 TTGACATTTTTTCTTAATTTGATATCTAAAC-TTTTTTGA-TCCA-TTGGTACCTGAAC
1 TTGACATTTTTT-TTAATTTGGTATCT-AACTTTTTTTGACTCAATTTGGTACCTGAAC
* *
171777 TTGGCATTTTTTTTAATTTGGTATCTAAGCTTTTTTTAGATTCAATTTGGTACCT
1 TTGACATTTTTTTTAATTTGGTATCTAA-CTTTTTTT-GACTCAATTTGGTACCT
171832 AAATTTATTA
Statistics
Matches: 91, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
54 2 0.02
55 14 0.15
56 27 0.30
57 15 0.16
58 22 0.24
59 11 0.12
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.52
Consensus pattern (57 bp):
TTGACATTTTTTTTAATTTGGTATCTAACTTTTTTTGACTCAATTTGGTACCTGAAC
Found at i:172105 original size:26 final size:26
Alignment explanation
Indices: 172066--172119 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
172056 AAAAAAAGTC
*
172066 AAATTTGAGTACCAAATTAAACAAAAA
1 AAATTAGAGTACCAAATTAAA-AAAAA
172093 AAATTAGA-TACCAAATTAAAAAAAA
1 AAATTAGAGTACCAAATTAAAAAAAA
172118 AA
1 AA
172120 TGTATACCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 7 0.27
26 12 0.46
27 7 0.27
ACGTcount: A:0.65, C:0.09, G:0.06, T:0.20
Consensus pattern (26 bp):
AAATTAGAGTACCAAATTAAAAAAAA
Found at i:173765 original size:53 final size:53
Alignment explanation
Indices: 173685--173791 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
173675 TTTTTTTGAA
173685 ATTATAGTTAAATTTTTAAAAATAATGGTATTAGAATTTCATCAACTGTTCGT
1 ATTATAGTTAAATTTTTAAAAATAATGGTATTAGAATTTCATCAACTGTTCGT
173738 ATTATAGTTAAATTTTTAAAAATAATGGTATTAGAATTTCATCAACTGTTCGT
1 ATTATAGTTAAATTTTTAAAAATAATGGTATTAGAATTTCATCAACTGTTCGT
173791 A
1 A
173792 AAGGTTTGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.43
Consensus pattern (53 bp):
ATTATAGTTAAATTTTTAAAAATAATGGTATTAGAATTTCATCAACTGTTCGT
Found at i:174061 original size:23 final size:23
Alignment explanation
Indices: 174000--174087 Score: 70
Period size: 23 Copynumber: 3.8 Consensus size: 23
173990 TCATTAACAT
* *
174000 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCGATTA-A
** * *
174024 TACTCATGAATATGTTCGTTTAA
1 TGTTCATGAACATGTTCGATTAA
*
174047 TGTTCATGAACATGTTTGATT-A
1 TGTTCATGAACATGTTCGATTAA
* *
174069 TGTTAAATGAATATGTTCG
1 TGTT-CATGAACATGTTCG
174088 TGAACATTAA
Statistics
Matches: 49, Mismatches: 14, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
22 5 0.10
23 28 0.57
24 16 0.33
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (23 bp):
TGTTCATGAACATGTTCGATTAA
Found at i:175280 original size:87 final size:87
Alignment explanation
Indices: 175134--175307 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
175124 CCTGATCATA
175134 GGAACAATCAAAATTAATTTTGACTGAGTCATGTACTGGTGGTTTCCATATAGTCGAATGACGAA
1 GGAACAATCAAAATTAATTTTGACTGAGTCATGTACTGGTGGTTTCCATATAGTCGAATGACGAA
175199 CAGGGGTAGCAAGGTTAATAGT
66 CAGGGGTAGCAAGGTTAATAGT
175221 GGAACAATCAAAATTAATTTTGACTGAGTCATGTACTGGTGGTTTCCATATAGTCGAATGACGAA
1 GGAACAATCAAAATTAATTTTGACTGAGTCATGTACTGGTGGTTTCCATATAGTCGAATGACGAA
175286 CAGGGGTAGCAAGGTTAATAGT
66 CAGGGGTAGCAAGGTTAATAGT
175308 ATTCATAGCT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (87 bp):
GGAACAATCAAAATTAATTTTGACTGAGTCATGTACTGGTGGTTTCCATATAGTCGAATGACGAA
CAGGGGTAGCAAGGTTAATAGT
Found at i:182121 original size:2 final size:2
Alignment explanation
Indices: 182114--182143 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
182104 ATAATCAAAT
182114 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
182144 CACCGTAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:189426 original size:30 final size:30
Alignment explanation
Indices: 189390--189686 Score: 115
Period size: 29 Copynumber: 9.8 Consensus size: 30
189380 AAATTGATAT
189390 AAACTTATAAA-ATTTATTAAAAA-ATAATAA
1 AAACTTATAAATA-TTATTAAAAATAT-ATAA
189420 AAACTTATAAATATTATTAAAAATATAT-A
1 AAACTTATAAATATTATTAAAAATATATAA
*
189449 AAA-TTATAATAAATTA-TAAAAAT-TAT-A
1 AAACTTATAA-ATATTATTAAAAATATATAA
* *
189476 AAA-TTAATAAAGTA-TATTTAAAATATTTAA
1 AAACTT-ATAAA-TATTATTAAAAATATATAA
* * * *
189506 AATTATCATATATATATATATTTAAAATTTTATAA
1 AA--A-CTTATAAATAT-TA-TTAAAAATATATAA
* * * *
189541 AAACGTATAAAAATTCTTTAAAACT-TA-AA
1 AAACTTATAAATATT-ATTAAAAATATATAA
**
189570 AAAAATA-AAAT-TTCATTAAAAATCATA-AA
1 AAACTTATAAATATT-ATTAAAAAT-ATATAA
* *
189599 AATA-TTATAAATATTATTAAATATTAAAATTTATAT
1 AA-ACTTATAAATATTA-T---TA--AAAATATATAA
*
189635 AAACTTATAAAAATTATTAAAAATCATA-AA
1 AAACTTATAAATATTATTAAAAAT-ATATAA
* * *
189665 ATA-TTATAAAAATTATAAAAAA
1 AAACTTATAAATATTATTAAAAA
189687 AATCCTAATA
Statistics
Matches: 209, Mismatches: 28, Indels: 61
0.70 0.09 0.20
Matches are distributed among these distances:
27 22 0.11
28 27 0.13
29 44 0.21
30 42 0.20
31 16 0.08
32 13 0.06
33 5 0.02
34 5 0.02
35 16 0.08
36 19 0.09
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (30 bp):
AAACTTATAAATATTATTAAAAATATATAA
Found at i:189452 original size:38 final size:36
Alignment explanation
Indices: 189410--189486 Score: 93
Period size: 38 Copynumber: 2.1 Consensus size: 36
189400 AATTTATTAA
*
189410 AAAATAATAA-AAACTTATAAATATTATTAAAAATATAT
1 AAAATAATAATAAA-TTATAAAAATTA-TAAAAATA-AT
* *
189448 AAAATTATAATAAATTATAAAAATTATAAAATTAAT
1 AAAATAATAATAAATTATAAAAATTATAAAAATAAT
189484 AAA
1 AAA
189487 GTATATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 5 0.14
37 7 0.20
38 20 0.57
39 3 0.09
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (36 bp):
AAAATAATAATAAATTATAAAAATTATAAAAATAAT
Found at i:189486 original size:56 final size:58
Alignment explanation
Indices: 189374--189511 Score: 151
Period size: 56 Copynumber: 2.4 Consensus size: 58
189364 TAAATATTAA
* * *
189374 ATATTAAAATTGATATAAACTTATAAAATTTATTAAAAAATAATAAAAACTTATAAA-T
1 ATATTAAAAAT-ATATAAAATTATAAAAATTATTAAAAAATAATAAAAACTTATAAAGT
*
189432 ATTATTAAAAATATATAAAATTATAATAAATTA-T-AAAAATTAT-AAAA-TTAATAAAGT
1 A-TATTAAAAATATATAAAATTATAA-AAATTATTAAAAAATAATAAAAACTT-ATAAAGT
* *
189489 ATATTTAAAATATTTAAAATTAT
1 ATATTAAAAATATATAAAATTAT
189512 CATATATATA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
55 2 0.03
56 29 0.41
57 10 0.14
58 15 0.21
59 14 0.20
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (58 bp):
ATATTAAAAATATATAAAATTATAAAAATTATTAAAAAATAATAAAAACTTATAAAGT
Found at i:189563 original size:94 final size:95
Alignment explanation
Indices: 189453--189667 Score: 212
Period size: 94 Copynumber: 2.3 Consensus size: 95
189443 TATATAAAAT
* * * *
189453 TATAATAAATTA-TAAAAATTATAAAATTAATAAAGTAT-ATTTAAAATAT-TTAAAATTATCAT
1 TATAA-AAATTATTAAAAATTATAAAATAAATAAAATATCA-TTAAAA-ATCATAAAAATATCAT
* *
189515 ATATA-TA-TATAT-TTAAAATTTTATAAAAACG
63 AAATATTATTAAATATTAAAA-TTTATAAAAACG
* * * *
189546 TATAAAAATTCTTTAAAACTTA-AAAA-AAATAAAATTTCATTAAAAATCATAAAAATATTATAA
1 TATAAAAATT-ATTAAAAATTATAAAATAAATAAAATATCATTAAAAATCATAAAAATATCATAA
* *
189609 ATATTATTAAATATTAAAATTTATATAAACT
65 ATATTATTAAATATTAAAATTTATAAAAACG
*
189640 TATAAAAATTATTAAAAATCATAAAATA
1 TATAAAAATTATTAAAAATTATAAAATA
189668 TTATAAAAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
91 2 0.02
92 33 0.34
93 20 0.20
94 36 0.37
95 7 0.07
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (95 bp):
TATAAAAATTATTAAAAATTATAAAATAAATAAAATATCATTAAAAATCATAAAAATATCATAAA
TATTATTAAATATTAAAATTTATAAAAACG
Found at i:189622 original size:19 final size:19
Alignment explanation
Indices: 189597--189683 Score: 83
Period size: 19 Copynumber: 4.6 Consensus size: 19
189587 AAAAATCATA
189597 AAAATATTATAAATATTATT
1 AAAA-ATTATAAATATTATT
*
189617 AAATATTA-AAAT-TTA-T
1 AAAAATTATAAATATTATT
* *
189633 ATAAACTTATAAAAATTATT
1 A-AAAATTATAAATATTATT
*
189653 AAAAATCATAAAATATTA-T
1 AAAAATTAT-AAATATTATT
189672 AAAAATTATAAA
1 AAAAATTATAAA
189684 AAAAATCCTA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
16 2 0.04
17 8 0.15
18 10 0.19
19 22 0.41
20 12 0.22
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTATAAATATTATT
Found at i:189686 original size:10 final size:9
Alignment explanation
Indices: 189379--189685 Score: 123
Period size: 10 Copynumber: 32.4 Consensus size: 9
189369 ATTAAATATT
189379 AAAATTGATA
1 AAAATT-ATA
*
189389 TAAACTTATA
1 -AAAATTATA
*
189399 AAATTTATTAA
1 AAAATTA-T-A
*
189410 AAAATAATA
1 AAAATTATA
189419 AAAACTTATA
1 AAAA-TTATA
*
189429 AATATTATTA
1 AAAATTA-TA
189439 AAAA-TATA
1 AAAATTATA
189447 TAAAATTATA
1 -AAAATTATA
189457 ATAAATTATA
1 A-AAATTATA
189467 AAAATTAT-
1 AAAATTATA
189475 AAAATTAATA
1 AAAATT-ATA
189485 AAGTATATT-TA
1 AA--A-ATTATA
189496 AAATATT-T-
1 AAA-ATTATA
189504 AAAATTAT-
1 AAAATTATA
* *
189512 CATATATATA
1 AAAAT-TATA
* *
189522 TATATT-TA
1 AAAATTATA
*
189530 AAATTTTATA
1 AAA-ATTATA
*
189540 AAAACGTATA
1 AAAA-TTATA
*
189550 AAAATTCTTTA
1 AAAA-T-TATA
*
189561 AAACTTA-A
1 AAAATTATA
*
189569 AAAA-AATA
1 AAAATTATA
*
189577 AAATTTCATTA
1 AAAATT-A-TA
*
189588 AAAATCATAA
1 AAAATTAT-A
189598 AAATATTATA
1 AAA-ATTATA
*
189608 AATATTAT-
1 AAAATTATA
*
189616 TAAA-TATTA
1 AAAATTA-TA
*
189625 AAATTTATA
1 AAAATTATA
*
189634 TAAACTTATA
1 -AAAATTATA
189644 AAAATTATTA
1 AAAATTA-TA
*
189654 AAAATCATA
1 AAAATTATA
189663 AAATATTATA
1 AAA-ATTATA
189673 AAAATTATA
1 AAAATTATA
189682 AAAA
1 AAAA
189686 AAATCCTAAT
Statistics
Matches: 229, Mismatches: 36, Indels: 64
0.70 0.11 0.19
Matches are distributed among these distances:
7 6 0.03
8 29 0.13
9 74 0.32
10 85 0.37
11 31 0.14
12 1 0.00
13 3 0.01
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (9 bp):
AAAATTATA
Found at i:189716 original size:10 final size:10
Alignment explanation
Indices: 189685--189719 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
189675 AATTATAAAA
189685 AAAATCCTAAT
1 AAAAT-CTAAT
189696 AAAATTCTAAT
1 AAAA-TCTAAT
189707 AAAATCTAAT
1 AAAATCTAAT
189717 AAA
1 AAA
189720 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.39
11 13 0.57
12 1 0.04
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAATCTAAT
Found at i:189744 original size:27 final size:29
Alignment explanation
Indices: 189708--189766 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
189698 AATTCTAATA
189708 AAATCTAAT-AAAT-TATTTAAAAAATTAT
1 AAATCTAATAAAATATATTTAAAAAATT-T
*
189736 AAAT-TAATAAAATATATTTAAAATATTT
1 AAATCTAATAAAATATATTTAAAAAATTT
189764 AAA
1 AAA
189767 ATTTTATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 4 0.14
28 12 0.43
29 12 0.43
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
AAATCTAATAAAATATATTTAAAAAATTT
Found at i:189767 original size:38 final size:37
Alignment explanation
Indices: 189703--189776 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 37
189693 AATAAAATTC
* *
189703 TAATAAAATCTAATAAATTATTTAAAAAATTATAAAT
1 TAATAAAATATAATAAAATATTTAAAAAATTATAAAT
* **
189740 TAATAAAATATATTTAAAATATTTAAAATTTTATAAA
1 TAATAAAATATA-ATAAAATATTTAAAAAATTATAAA
189777 AACTTATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
37 11 0.35
38 20 0.65
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (37 bp):
TAATAAAATATAATAAAATATTTAAAAAATTATAAAT
Found at i:189768 original size:29 final size:26
Alignment explanation
Indices: 189706--189769 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 26
189696 AAAATTCTAA
189706 TAAAATCTAATAAATTATTTAAAAAAT
1 TAAAAT-TAATAAATTATTTAAAAAAT
*
189733 TATAAATTAATAAAATATATTTAAAATATT
1 TA-AAATTAAT-AAAT-TATTTAAAA-AAT
189763 TAAAATT
1 TAAAATT
189770 TTATAAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 6 0.19
28 8 0.25
29 14 0.44
30 4 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
TAAAATTAATAAATTATTTAAAAAAT
Done.