Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012571.1 Kokia drynarioides strain JFW-HI SEQ_127580, 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: 190773
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:823 original size:48 final size:47
Alignment explanation
Indices: 752--844 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 47
742 TTGGCACCGT
*
752 AATTGTTTCGATCCATTTTGAGACATAATCAAGAGCCAATTAAGATGC
1 AATTGTTTCGATCCATTTCGAGACATAATCAAGAGCC-ATTAAGATGC
*
800 AATTGCTTT-GATCCATTTCGAGACATAGTCAAGAGCCATTAAGAT
1 AATTG-TTTCGATCCATTTCGAGACATAATCAAGAGCCATTAAGAT
845 ATACACATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
47 8 0.19
48 31 0.74
49 3 0.07
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (47 bp):
AATTGTTTCGATCCATTTCGAGACATAATCAAGAGCCATTAAGATGC
Found at i:2975 original size:42 final size:42
Alignment explanation
Indices: 2912--3064 Score: 243
Period size: 42 Copynumber: 3.6 Consensus size: 42
2902 AAAAAGTTTA
* *
2912 TATGATTAAAGGAAGAATCATGTCTCGGGATGAGAAAGAGAT
1 TATGATTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGAT
*
2954 TATGATTAAAGGAAGACTCATGTCTCAGGATGAGAATGAGAT
1 TATGATTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGAT
* * *
2996 TATGAATAAAGGAAGACTAATGTCTCGGGATGAGAATGAGAA
1 TATGATTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGAT
*
3038 TATGATTAAAGGAAGACTTATGTCTCG
1 TATGATTAAAGGAAGACTCATGTCTCG
3065 ATAGAGCATA
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 102 1.00
ACGTcount: A:0.39, C:0.08, G:0.27, T:0.25
Consensus pattern (42 bp):
TATGATTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGAT
Found at i:15067 original size:19 final size:19
Alignment explanation
Indices: 15043--15086 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
15033 AGTATTATTG
*
15043 TGCAAGCGTACACTATCAA
1 TGCAAGCATACACTATCAA
*
15062 TGCAAGTATACACTATCAA
1 TGCAAGCATACACTATCAA
15081 TGCAAG
1 TGCAAG
15087 TATAGTAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (19 bp):
TGCAAGCATACACTATCAA
Found at i:15087 original size:19 final size:19
Alignment explanation
Indices: 15051--15090 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
15041 TGTGCAAGCG
15051 TACACTATCAATGCAAGTA
1 TACACTATCAATGCAAGTA
15070 TACACTATCAATGCAAGTA
1 TACACTATCAATGCAAGTA
15089 TA
1 TA
15091 GTAGACAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (19 bp):
TACACTATCAATGCAAGTA
Found at i:17559 original size:18 final size:18
Alignment explanation
Indices: 17536--17579 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
17526 TTCAATAAGG
17536 ACTTCCTCCTCTCTAACA
1 ACTTCCTCCTCTCTAACA
17554 ACTTCCTCCTCTCTAACA
1 ACTTCCTCCTCTCTAACA
17572 ACTTCCTC
1 ACTTCCTC
17580 TTGACTAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.20, C:0.45, G:0.00, T:0.34
Consensus pattern (18 bp):
ACTTCCTCCTCTCTAACA
Found at i:17992 original size:27 final size:27
Alignment explanation
Indices: 17954--18012 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
17944 CCTGCATCCT
17954 TCATTGTCAGTGTATCTTTACCACAAG
1 TCATTGTCAGTGTATCTTTACCACAAG
17981 TCATTGTCAGTGTATCTTTACCACAAG
1 TCATTGTCAGTGTATCTTTACCACAAG
18008 TCATT
1 TCATT
18013 CTTTCAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (27 bp):
TCATTGTCAGTGTATCTTTACCACAAG
Found at i:19276 original size:5 final size:5
Alignment explanation
Indices: 19268--19292 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
19258 AACAAAAACA
19268 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
19293 TATAGAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:33133 original size:21 final size:21
Alignment explanation
Indices: 33103--33153 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
33093 GTGCTAGTTT
33103 TACCGATACAAGT-ATAACTTC
1 TACCGATACAAGTCAT-ACTTC
* *
33124 TACTGATACAAGTCATGCTTC
1 TACCGATACAAGTCATACTTC
33145 TACCGATAC
1 TACCGATAC
33154 TAAAAACTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.29
Consensus pattern (21 bp):
TACCGATACAAGTCATACTTC
Found at i:38523 original size:52 final size:52
Alignment explanation
Indices: 38441--38578 Score: 195
Period size: 52 Copynumber: 2.7 Consensus size: 52
38431 CCGTAAATGA
*
38441 AAAAGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGACT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGACT
** * * * *
38493 ATGAGGTCCGATGACTATGTGTTATTGTGAGTATATGATTCCTTTACGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGACT
* *
38545 AAAAGGTCCGATGACTATGTGTCTTCGTAAGTAT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTAT
38579 TAAATAAAAT
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (52 bp):
AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGACT
Found at i:50407 original size:52 final size:48
Alignment explanation
Indices: 50304--50423 Score: 152
Period size: 52 Copynumber: 2.4 Consensus size: 48
50294 TAAATGAAAA
* * *
50304 AGGTCCGATGACTACGTGTCATCGTGTATGAATCCTTTACGGATTATG
1 AGGTTCGATGACTATGTGTCATCGTGTATGAATCCTTTACGGATTAAG
*
50352 AGGTTCGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTAAG
1 AGGTTCGATGACTATGTGTCATCGT--G--TATGAATCCTTTACGGATTAAG
50404 AGG-TCTGATGACTATGTGTC
1 AGGTTC-GATGACTATGTGTC
50424 TTCAAGAGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
48 23 0.37
50 1 0.02
51 2 0.03
52 37 0.59
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (48 bp):
AGGTTCGATGACTATGTGTCATCGTGTATGAATCCTTTACGGATTAAG
Found at i:50433 original size:52 final size:52
Alignment explanation
Indices: 50330--50434 Score: 149
Period size: 52 Copynumber: 2.0 Consensus size: 52
50320 TGTCATCGTG
* **
50330 TATGAATCCTTTACGGATTATGAGGTTCGATGACTATGTGTCATCGTGAGTA
1 TATGAATCCTTTACGGATTAAGAGGTTCGATGACTATGTGTCATCAAGAGTA
* *
50382 TATGATTCCTTTACGGATTAAGAGG-TCTGATGACTATGTGTCTTCAAGAGTA
1 TATGAATCCTTTACGGATTAAGAGGTTC-GATGACTATGTGTCATCAAGAGTA
50434 T
1 T
50435 TAAATGAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.04
52 45 0.96
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (52 bp):
TATGAATCCTTTACGGATTAAGAGGTTCGATGACTATGTGTCATCAAGAGTA
Found at i:60214 original size:28 final size:28
Alignment explanation
Indices: 60148--60218 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
60138 TTTGAACTTT
* * *
60148 GGCTTGTATGAGCT--AAATTCTGTCTA
1 GGCTCGTATGAGCTAAAAACTCTATCTA
* * *
60174 GGCTCATAAGAGCTAAAAACTCTATCTG
1 GGCTCGTATGAGCTAAAAACTCTATCTA
60202 GGCTCGTATGAGCTAAA
1 GGCTCGTATGAGCTAAA
60219 TATTCTGGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 11 0.31
28 24 0.69
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (28 bp):
GGCTCGTATGAGCTAAAAACTCTATCTA
Found at i:61309 original size:7 final size:7
Alignment explanation
Indices: 61297--61322 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
61287 AGGAAAGAAA
61297 GATGAGG
1 GATGAGG
61304 GATGAGG
1 GATGAGG
61311 GATGAGG
1 GATGAGG
61318 GATGA
1 GATGA
61323 TTAGGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.15
Consensus pattern (7 bp):
GATGAGG
Found at i:88942 original size:42 final size:42
Alignment explanation
Indices: 88876--89441 Score: 785
Period size: 42 Copynumber: 13.5 Consensus size: 42
88866 TTGTGTCACT
* * *
88876 TTATGTATAAATGAATGACTCATGTCTCGGGATGAGCATGAGA
1 TTATGTTTAAAGGAA-GACTCGTGTCTCGGGATGAGCATGAGA
* * * * *
88919 TTATGTTTAAAGGAAGATTCATGTCTCAGGATGAGCATCAAA
1 TTATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGA
* *
88961 TTATGTTTAAAGGAAGACTCATATCTCGGGATGAGCATGAGA
1 TTATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGA
* *
89003 TTATGTTTAAAGGAAGACTCGTGACTCGGGATGAGCATGAAA
1 TTATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGA
* * *
89045 TTATGTTTAAAGGAAGACTCTTATCTCGGGATGAACATGAGA
1 TTATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGA
* * **
89087 TTGTGTTTAAAGGAAGACTCGTGACTCTAGATGAGCATGAGA
1 TTATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGA
*
89129 TTATGTTTAAAGGAAGACTCGTGACTCGGGATGAGCATGAGA
1 TTATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGA
* *
89171 TTATGTTTAAAGGAAGATTCGTGTCTCAGGATGAGCATGAGA
1 TTATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGA
*
89213 TTATGTTTAAAGGAAGACTCGTGACTCGGGATGAGCATGAGA
1 TTATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGA
* * *
89255 TTATGTTTAAAGGAAGACTCTTGTCTTGGGATGAGCATGAAA
1 TTATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGA
*
89297 TTATGTTTAAAGGAAGACTCGTGACTCGGGATGAGCATGAGA
1 TTATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGA
* *
89339 TTATGTTTAAAGGAAGACTCATGTCTCAGGATGAGCATGAGA
1 TTATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGA
** * * *
89381 TTATGTTTAAAGGAAGACTTATGTCTCCGTA-GAGCATAAGA
1 TTATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGA
89422 TT-TGTTTAAAATGGAAGACT
1 TTATGTTT-AAA-GGAAGACT
89442 TATGACTCAG
Statistics
Matches: 470, Mismatches: 51, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
40 5 0.01
41 14 0.03
42 438 0.93
43 13 0.03
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.30
Consensus pattern (42 bp):
TTATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGA
Found at i:90518 original size:23 final size:23
Alignment explanation
Indices: 90488--90534 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
90478 TGATTGATTC
90488 GATCTAACTCCTGTTTATTTGTA
1 GATCTAACTCCTGTTTATTTGTA
90511 GATCTAACTCCTGTTTATTTGTA
1 GATCTAACTCCTGTTTATTTGTA
90534 G
1 G
90535 CTTCTAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.15, T:0.47
Consensus pattern (23 bp):
GATCTAACTCCTGTTTATTTGTA
Found at i:94350 original size:42 final size:42
Alignment explanation
Indices: 94281--94508 Score: 264
Period size: 42 Copynumber: 5.4 Consensus size: 42
94271 GAATCACTTG
* * *
94281 ATGTATAAATGGAAGACTCATGTCTCGAGATGAGTATGATATT
1 ATGTTTAAA-GGAAGACTCATGTCTCGAGATGAGCATGAGATT
* *
94324 ATGTTTAAAGGAAGACTCATGTCTCGAGATAAGGATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATT
* * * *
94366 ATGTTTAAAGGAAGACTCGTGACTCGGGATGAGCATGATATT
1 ATGTTTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATT
* *
94408 ATGTTTAAAGGAAGACTCGTGTCTCAAGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATT
* * *
94450 ATGTTTAAACGAAGACTTATGTCTC-AG-TAGAGCATAAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCGAGAT-GAGCATGAGATT
*
94491 -TGTCTAAAAAGGAAGACT
1 ATGT-T-TAAAGGAAGACT
94509 TATGACTCCG
Statistics
Matches: 162, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
40 4 0.02
41 14 0.09
42 136 0.84
43 8 0.05
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (42 bp):
ATGTTTAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATT
Found at i:94516 original size:126 final size:127
Alignment explanation
Indices: 94281--94516 Score: 309
Period size: 126 Copynumber: 1.9 Consensus size: 127
94271 GAATCACTTG
* * * *
94281 ATGTATAAATGGAAGACTCATGTCTCGAGATGAGTATGATATTATGTTTAAAGGAAGACTCATGT
1 ATGTATAAATGGAAGACTCATGTCTCAAGATGAGCATGAGATTATGTTTAAACGAAGACTCATGT
* * * *
94346 CTCGAGATAAGGATGAGATTATGTTTAAAGGAAGACTCGTGACTCGGGATGAGCATGATATT
66 CTCGAGATAAGCATAAGATTATGTTAAAAGGAAGACTCATGACTCGGGATGAGCATGATATT
* * *
94408 ATGTTTAAA-GGAAGACTCGTGTCTCAAGATGAGCATGAGATTATGTTTAAACGAAGACTTATGT
1 ATGTATAAATGGAAGACTCATGTCTCAAGATGAGCATGAGATTATGTTTAAACGAAGACTCATGT
*
94472 CTC-AG-TAGAGCATAAGATT-TGTCTAAAAAGGAAGACTTATGACTC
66 CTCGAGATA-AGCATAAGATTATGT-T-AAAAGGAAGACTCATGACTC
94517 CGTTGGAGCA
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
124 5 0.05
125 12 0.13
126 69 0.73
127 8 0.09
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (127 bp):
ATGTATAAATGGAAGACTCATGTCTCAAGATGAGCATGAGATTATGTTTAAACGAAGACTCATGT
CTCGAGATAAGCATAAGATTATGTTAAAAGGAAGACTCATGACTCGGGATGAGCATGATATT
Found at i:101996 original size:3 final size:3
Alignment explanation
Indices: 101988--102047 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
101978 CGGGGCCACA
* *
101988 TCT TCT TCT TCT TTT TCT TCCT TC- TCT TCT TTT TCT TCT TCT T-T
1 TCT TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT
*
102032 ACTT TCT TCT TCT TCT
1 TC-T TCT TCT TCT TCT
102048 ACCTCAATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 3 0.06
3 39 0.83
4 5 0.11
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:102015 original size:24 final size:24
Alignment explanation
Indices: 101988--102047 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
101978 CGGGGCCACA
* *
101988 TCTTCTTCTTCTTTTTC-TTCCTT
1 TCTTCTTCTTCTTCTTCTTTACTT
*
102011 CTCTTCTTTTTCTTCTTCTTTACTT
1 -TCTTCTTCTTCTTCTTCTTTACTT
102036 TCTTCTTCTTCT
1 TCTTCTTCTTCT
102048 ACCTCAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (24 bp):
TCTTCTTCTTCTTCTTCTTTACTT
Found at i:126960 original size:30 final size:29
Alignment explanation
Indices: 126926--126990 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
126916 ATTTTTAAGG
* *
126926 AATTTAGGGTTAAAATTAAAATTGTTGGAA
1 AATTTAGGATTAAAATCAAAATT-TTGGAA
*
126956 AATTTAGGATTAAAATCAAACTTTTGGAA
1 AATTTAGGATTAAAATCAAAATTTTGGAA
126985 AATTTA
1 AATTTA
126991 AGGTCGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 12 0.38
30 20 0.62
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.37
Consensus pattern (29 bp):
AATTTAGGATTAAAATCAAAATTTTGGAA
Found at i:127122 original size:30 final size:30
Alignment explanation
Indices: 126977--127128 Score: 136
Period size: 30 Copynumber: 5.1 Consensus size: 30
126967 AAAATCAAAC
*
126977 TTTTGGAAAA-TTTAA-GGTCGAAAATGTGAC
1 TTTTGGAAAAGTTTAAGGGTC-AAAATGT-AA
* *
127007 TTTTGG-AAA-TTCAGGGGT-AAAATGGTAA
1 TTTTGGAAAAGTTTAAGGGTCAAAAT-GTAA
** *
127035 TTTTGGATGAGTTTAAGAGTCAAAAATGTAA
1 TTTTGGAAAAGTTTAAGGGTC-AAAATGTAA
* * *
127066 TTTTAGAAAAGTTTGA-GGTTAAAATGTAA
1 TTTTGGAAAAGTTTAAGGGTCAAAATGTAA
*
127095 TTTTGGAAAAGTTCAAGGGTCAAAATGTAA
1 TTTTGGAAAAGTTTAAGGGTCAAAATGTAA
127125 TTTT
1 TTTT
127129 TGTGAAGTTC
Statistics
Matches: 97, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
28 12 0.12
29 31 0.32
30 33 0.34
31 16 0.16
32 5 0.05
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.36
Consensus pattern (30 bp):
TTTTGGAAAAGTTTAAGGGTCAAAATGTAA
Found at i:128077 original size:10 final size:10
Alignment explanation
Indices: 128035--128095 Score: 54
Period size: 10 Copynumber: 5.9 Consensus size: 10
128025 TGATTAATGA
128035 ATATATTAAT
1 ATATATTAAT
*
128045 ATATAATAA-
1 ATATATTAAT
*
128054 ATAATAAGTAAAT
1 AT-AT-A-TTAAT
128067 ATATATTAAT
1 ATATATTAAT
128077 ATATA-TATAT
1 ATATATTA-AT
128087 ATATATTAA
1 ATATATTAA
128096 AAACGTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
9 4 0.10
10 27 0.66
11 4 0.10
12 4 0.10
13 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (10 bp):
ATATATTAAT
Found at i:128571 original size:18 final size:19
Alignment explanation
Indices: 128548--128586 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
128538 TTGTAGGTAC
*
128548 CAGTGGCGA-TGCTGGTGG
1 CAGTGGCAACTGCTGGTGG
128566 CAGTGGCAACTTGCTGGTGG
1 CAGTGGCAAC-TGCTGGTGG
128586 C
1 C
128587 GGTGTTGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.13, C:0.21, G:0.44, T:0.23
Consensus pattern (19 bp):
CAGTGGCAACTGCTGGTGG
Found at i:129359 original size:39 final size:39
Alignment explanation
Indices: 129309--130097 Score: 223
Period size: 39 Copynumber: 20.2 Consensus size: 39
129299 CTTTTTTTTT
*
129309 GTAAGATATTGGATGGTTACAATCTGCCCCAAGCTCGGG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
* * * * * *
129348 GCAAGAGATTGGCTAACGG-T--GATCTGCCCCATGATCGAG
1 GTAAGAGATTGG---ATGGTTACAATCTGCCCCAAGCTCGGG
* * ** *
129387 GTAAAAGATCT-AATAATTACAATCTGCCCCAAGCTCGAG
1 GTAAGAGAT-TGGATGGTTACAATCTGCCCCAAGCTCGGG
* * * * * *
129426 GCAAGAGATTGGCT-GATAGCGATCTGCCCCATGATCGGG
1 GTAAGAGATTGGATGGTTA-CAATCTGCCCCAAGCTCGGG
* * * * * * *
129465 GTAAAAGATCGGATGGCTATAATCTGCCCTAGGCTCGAG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
* * * **** *
129504 GTAAGAAATTGGTTGATGGTGATCTACCCCAAGCTCGAGG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCG-GG
* * * * * * *
129544 GTAAAAGATCGGATAGCTGCAATCTGCCCCAGGCTCAGG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
*
129583 GTAAGAGATTGGCTAATGG-T--GATCTGCCCCAAGCTCGGG
1 GTAAGAGATTGG---ATGGTTACAATCTGCCCCAAGCTCGGG
* ** * * * * * *
129622 GTAAAAGATCAGATGATTGCAATCTGCTCTAGGCTCGAG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
* * * * *
129661 GTAAGAGATTGGCTGACGGT--GATCTGCCCCAGGCTCGAG
1 GTAAGAGATTGGATG--GTTACAATCTGCCCCAAGCTCGGG
* * * * * * * **
129700 GTAAAAGATTGGATCGCTGCTATCTACCCCATGCTCAAG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
* * **** * *
129739 GTAAGAGATTGGCTGATGGTGATCTGCCGCAGGCTCGGG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
* * * * * * *
129778 GTAAAAGATCGGATCGCTGCAATTTGCCCCAGGCTCGGG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
* * *** ** * *
129817 CTAAGAGATTGGCTGACGATGATCTGCCCCATGATCGGG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
* * ** * *
129856 GTAAAAGATTGAATAATTACAATCTACCCCAGGCTCGGG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
* * ** * * *
129895 GTAAGAGATTGGCTGATGGCGATCTGCCCCATGATCGGG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
* * ** * * *
129934 CTAAAAGA-TGGATGACTACAATCTACCCTAGGCTCGGG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
* * **** * * *
129972 GTAAGAGATTGGCTGATGGTGATTTGCCCCAGGCTCAGG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
* * ** * *
130011 GTAAAAGATCGGATGGTTGTAATCTGCCCCAGGCTCAGG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
* * * * * * * *
130050 GTAAAAGATCGTATGGCTGCAATCTACCCCAGGCTCGAG
1 GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
130089 GTAAGAGAT
1 GTAAGAGAT
130098 AGAATCTTCA
Statistics
Matches: 537, Mismatches: 191, Indels: 44
0.70 0.25 0.06
Matches are distributed among these distances:
36 4 0.01
37 4 0.01
38 30 0.06
39 461 0.86
40 29 0.05
41 3 0.01
42 6 0.01
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (39 bp):
GTAAGAGATTGGATGGTTACAATCTGCCCCAAGCTCGGG
Found at i:129534 original size:117 final size:116
Alignment explanation
Indices: 129408--130094 Score: 436
Period size: 117 Copynumber: 5.9 Consensus size: 116
129398 AATAATTACA
* * * * * * * *
129408 ATCTGCCCCAAGCTCGAGGCAAGAGATTGGCTGATAGCGATCTGCCCCATGATCGGGGTAAAAGA
1 ATCTGCCCCAGGCTCGAGGTAAAAGATCGGATGAT-GCAATCTGCCCCAGGCTCGGGGTAAAAGA
* * * *
129473 TCGGATGGCTATAATCTGCCCTAGGCTCGAGGTAAGAAATTGGTTGATGGTG
65 TTGGATGGCTATAATCTACCCCAGGCTCGAGGTAAGAAATTGGATGATGGTG
* * * * *
129525 ATCTACCCCAAGCTCGAGGGTAAAAGATCGGATAGCTGCAATCTGCCCCAGGCTCAGGGTAAGAG
1 ATCTGCCCCAGGCTCGA-GGTAAAAGATCGGAT-GATGCAATCTGCCCCAGGCTCGGGGTAAAAG
* * * * ** * **
129590 ATTGGCTAATGG---TGATCTGCCCCAAGCTCGGGGTAA-AAGATCAGATGATTGCA
64 ATTGG---ATGGCTATAATCTACCCCAGGCTCGAGGTAAGAA-ATTGGATGATGGTG
* * * * * * ** *
129643 ATCTGCTCTAGGCTCGAGGTAAGAGATTGGCTGACGGTGATCTGCCCCAGGCTCGAGGTAAAAGA
1 ATCTGCCCCAGGCTCGAGGTAAAAGATCGGATGA-TGCAATCTGCCCCAGGCTCGGGGTAAAAGA
* * * * * *
129708 TTGGATCGCTGCT-ATCTACCCCATGCTCAAGGTAAGAGATTGGCTGATGGTG
65 TTGGATGGCT-ATAATCTACCCCAGGCTCGAGGTAAGAAATTGGATGATGGTG
* * * * * *
129760 ATCTGCCGCAGGCTCGGGGTAAAAGATCGGATCGCTGCAATTTGCCCCAGGCTCGGGCTAAGAGA
1 ATCTGCCCCAGGCTCGAGGTAAAAGATCGGAT-GATGCAATCTGCCCCAGGCTCGGGGTAAAAGA
* * * * * * * * * * ****
129825 TTGGCTGACGATGATCTGCCCCATGATCGGGGTAA-AAGATTGAATAATTACA
65 TTGGATGGCTATAATCTACCCCAGGCTCGAGGTAAGAA-ATTGGATGATGGTG
* * * * * * * * *
129877 ATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGGCGATCTGCCCCATGATCGGGCTAAAAGA
1 ATCTGCCCCAGGCTCGAGGTAAAAGATCGGATGAT-GCAATCTGCCCCAGGCTCGGGGTAAAAGA
* * * * * *
129942 -TGGATGACTACAATCTACCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
65 TTGGATGGCTATAATCTACCCCAGGCTCGAGGTAAGAAATTGGATGATGGTG
* * * *
129993 ATTTGCCCCAGGCTC-AGGGTAAAAGATCGGATGGTTGTAATCTGCCCCAGGCTCAGGGTAAAAG
1 ATCTGCCCCAGGCTCGA-GGTAAAAGATCGGAT-GATGCAATCTGCCCCAGGCTCGGGGTAAAAG
* * **
130057 ATCGTATGGCTGCAATCTACCCCAGGCTCGAGGTAAGA
64 ATTGGATGGCTATAATCTACCCCAGGCTCGAGGTAAGA
130095 GATAGAATCT
Statistics
Matches: 424, Mismatches: 126, Indels: 40
0.72 0.21 0.07
Matches are distributed among these distances:
114 3 0.01
116 86 0.20
117 247 0.58
118 82 0.19
119 2 0.00
121 4 0.01
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (116 bp):
ATCTGCCCCAGGCTCGAGGTAAAAGATCGGATGATGCAATCTGCCCCAGGCTCGGGGTAAAAGAT
TGGATGGCTATAATCTACCCCAGGCTCGAGGTAAGAAATTGGATGATGGTG
Found at i:129782 original size:156 final size:156
Alignment explanation
Indices: 129326--130024 Score: 778
Period size: 156 Copynumber: 4.5 Consensus size: 156
129316 ATTGGATGGT
* * * * * * *
129326 TACAATCTGCCCCAAGCTCGGGGCAAGAGATTGGCTAACGGTGATCTGCCCCATGATCGAGGTAA
1 TACAATCTGCCCTAGGCTCGAGGTAAGAGATTGGCTGACGGTGATCTGCCCCAGGCTCGAGGTAA
* * * * * * *
129391 AAGATCT-AATAATTACAATCTGCCCCAAGCTCGAGGCAAGAGATTGGCTGATAGCGATCTGCCC
66 AAGAT-TGGATAACTACAATCTACCCCAGGCTCAAGGTAAGAGATTGGCTGATGGCGATCTGCCC
*
129455 CATGATCGGGGTAAAAGATCGGATGGC
130 CATGATCGGGGTAAAAGATCGGATGAC
* * * * * *
129482 TATAATCTGCCCTAGGCTCGAGGTAAGAAATTGGTTGATGGTGATCTACCCCAAGCTCGAGGGTA
1 TACAATCTGCCCTAGGCTCGAGGTAAGAGATTGGCTGACGGTGATCTGCCCCAGGCTCGA-GGTA
* * * * * * *
129547 AAAGATCGGATAGCTGCAATCTGCCCCAGGCTCAGGGTAAGAGATTGGCTAATGGTGATCTGCCC
65 AAAGATTGGATAACTACAATCTACCCCAGGCTCAAGGTAAGAGATTGGCTGATGGCGATCTGCCC
* * * *
129612 CAAGCTCGGGGTAAAAGATCAGATGAT
130 CATGATCGGGGTAAAAGATCGGATGAC
* *
129639 TGCAATCTGCTCTAGGCTCGAGGTAAGAGATTGGCTGACGGTGATCTGCCCCAGGCTCGAGGTAA
1 TACAATCTGCCCTAGGCTCGAGGTAAGAGATTGGCTGACGGTGATCTGCCCCAGGCTCGAGGTAA
** * * * * *
129704 AAGATTGGATCGCTGCTATCTACCCCATGCTCAAGGTAAGAGATTGGCTGATGGTGATCTGCCGC
66 AAGATTGGATAACTACAATCTACCCCAGGCTCAAGGTAAGAGATTGGCTGATGGCGATCTGCCCC
* *
129769 AGGCTCGGGGTAAAAGATCGGATCG-C
131 ATGATCGGGGTAAAAGATCGGAT-GAC
* * * * * * *
129795 TGCAATTTGCCCCAGGCTCG-GGCTAAGAGATTGGCTGACGATGATCTGCCCCATGATCGGGGTA
1 TACAATCTGCCCTAGGCTCGAGG-TAAGAGATTGGCTGACGGTGATCTGCCCCAGGCTCGAGGTA
* * **
129859 AAAGATTGAATAATTACAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGGCGATCTGCCC
65 AAAGATTGGATAACTACAATCTACCCCAGGCTCAAGGTAAGAGATTGGCTGATGGCGATCTGCCC
*
129924 CATGATCGGGCTAAAAGAT-GGATGAC
130 CATGATCGGGGTAAAAGATCGGATGAC
* * * *
129950 TACAATCTACCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCCAGGCTC-AGGGTA
1 TACAATCTGCCCTAGGCTCGAGGTAAGAGATTGGCTGACGGTGATCTGCCCCAGGCTCGA-GGTA
*
130014 AAAGATCGGAT
65 AAAGATTGGAT
130025 GGTTGTAATC
Statistics
Matches: 455, Mismatches: 81, Indels: 15
0.83 0.15 0.03
Matches are distributed among these distances:
154 1 0.00
155 66 0.15
156 257 0.56
157 131 0.29
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.22
Consensus pattern (156 bp):
TACAATCTGCCCTAGGCTCGAGGTAAGAGATTGGCTGACGGTGATCTGCCCCAGGCTCGAGGTAA
AAGATTGGATAACTACAATCTACCCCAGGCTCAAGGTAAGAGATTGGCTGATGGCGATCTGCCCC
ATGATCGGGGTAAAAGATCGGATGAC
Found at i:130092 original size:78 final size:77
Alignment explanation
Indices: 129319--130097 Score: 706
Period size: 78 Copynumber: 10.0 Consensus size: 77
129309 GTAAGATATT
* * * * * * * *
129319 GGATGGTTACAATCTGCCCCAAGCTCGGGGCAAGAGATTGGCTAACGGTGATCTGCCCCATGATC
1 GGATGGCTGCAATCTGCCCCAGGCTC-GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
129384 GAGGTAAAAGATC
65 GAGGTAAAAGATC
** *** * * * * * * *
129397 TAATAATTACAATCTGCCCCAAGCTCGAGGCAAGAGATTGGCTGATAGCGATCTGCCCCATGATC
1 GGATGGCTGCAATCTGCCCCAGGCTCG-GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
*
129462 GGGGTAAAAGATC
65 GAGGTAAAAGATC
** * * * * *
129475 GGATGGCTATAATCTGCCCTAGGCTCGAGGTAAGAAATTGGTTGATGGTGATCTACCCCAAGCTC
1 GGATGGCTGCAATCTGCCCCAGGCTCG-GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
129540 GAGGGTAAAAGATC
65 GA-GGTAAAAGATC
* * *
129554 GGATAGCTGCAATCTGCCCCAGGCTCAGGGTAAGAGATTGGCTAATGGTGATCTGCCCCAAGCTC
1 GGATGGCTGCAATCTGCCCCAGGCTC-GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
*
129619 GGGGTAAAAGATC
65 GAGGTAAAAGATC
* ** * * *
129632 AGATGATTGCAATCTGCTCTAGGCTCGAGGTAAGAGATTGGCTGACGGTGATCTGCCCCAGGCTC
1 GGATGGCTGCAATCTGCCCCAGGCTCG-GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
*
129697 GAGGTAAAAGATT
65 GAGGTAAAAGATC
* * * * * *
129710 GGATCGCTGCTATCTACCCCATGCTCAAGGTAAGAGATTGGCTGATGGTGATCTGCCGCAGGCTC
1 GGATGGCTGCAATCTGCCCCAGGCTC-GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
*
129775 GGGGTAAAAGATC
65 GAGGTAAAAGATC
* * * * * *
129788 GGATCGCTGCAATTTGCCCCAGGCTCGGGCTAAGAGATTGGCTGACGATGATCTGCCCCATGATC
1 GGATGGCTGCAATCTGCCCCAGGCTCGGG-TAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* *
129853 GGGGTAAAAGATT
65 GAGGTAAAAGATC
* *** * * * * *
129866 GAATAATTACAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGGCGATCTGCCCCATGATC
1 GGATGGCTGCAATCTGCCCCAGGCTC-GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
129931 G-GGCTAAAAGAT-
65 GAGG-TAAAAGATC
* * * * *
129943 GGATGACTACAATCTACCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCCAGGCTC
1 GGATGGCTGCAATCTGCCCCAGGCTC-GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
130008 -AGGGTAAAAGATC
65 GA-GGTAAAAGATC
* * * * *
130021 GGATGGTTGTAATCTGCCCCAGGCTCAGGGTAAAAGA-TCG-T-ATGGCTGCAATCTACCCCAGG
1 GGATGGCTGCAATCTGCCCCAGGCTC-GGGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAGG
*
130083 CTCGAGGTAAGAGAT
62 CTCGAGGTAAAAGAT
130098 AGAATCTTCA
Statistics
Matches: 585, Mismatches: 101, Indels: 30
0.82 0.14 0.04
Matches are distributed among these distances:
75 4 0.01
76 3 0.01
77 73 0.12
78 433 0.74
79 71 0.12
80 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.22
Consensus pattern (77 bp):
GGATGGCTGCAATCTGCCCCAGGCTCGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCG
AGGTAAAAGATC
Found at i:131850 original size:22 final size:22
Alignment explanation
Indices: 131825--131870 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
131815 TAGACTAACG
**
131825 AGAACAGTGTTGCCTTAGTAGA
1 AGAACAGTGTTGCCCAAGTAGA
*
131847 AGAACGGTGTTGCCCAAGTAGA
1 AGAACAGTGTTGCCCAAGTAGA
131869 AG
1 AG
131871 TTCTGACTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (22 bp):
AGAACAGTGTTGCCCAAGTAGA
Found at i:139335 original size:30 final size:30
Alignment explanation
Indices: 139301--139404 Score: 83
Period size: 29 Copynumber: 3.5 Consensus size: 30
139291 ATTTTCGAGG
*
139301 AATTTGGGGTCAAAATTGAAATTTTTGGAA
1 AATTTGGGGTCAAAATTGAAACTTTTGGAA
** * * *
139331 AATTTTTGAT-AAAAATCAAACTTTTGGAA
1 AATTTGGGGTCAAAATTGAAACTTTTGGAA
*
139360 AATTTGAGGTCGAAAATGTG--ACTTTTGG-A
1 AATTTGGGGTC-AAAAT-TGAAACTTTTGGAA
139389 AATTATGGGG-CAAAAT
1 AATT-TGGGGTCAAAAT
139405 GGTAATTTTA
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
28 5 0.09
29 29 0.50
30 19 0.33
31 4 0.07
32 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (30 bp):
AATTTGGGGTCAAAATTGAAACTTTTGGAA
Found at i:139533 original size:30 final size:30
Alignment explanation
Indices: 139480--139562 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 30
139470 TTTTGGAATT
*
139480 ATTTTTGA-GAAGTTTCAAGGGTCAAAATGTA
1 ATTTTT-ATGAAG-TTCGAGGGTCAAAATGTA
139511 ATTTTTATGAAGTTCGAGGGTCAAAATGTA
1 ATTTTTATGAAGTTCGAGGGTCAAAATGTA
* *
139541 ATTTTTGTGAAGTTTGAGGGTC
1 ATTTTTATGAAGTTCGAGGGTC
139563 TTCTGAGCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
30 38 0.79
31 10 0.21
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.39
Consensus pattern (30 bp):
ATTTTTATGAAGTTCGAGGGTCAAAATGTA
Found at i:140673 original size:11 final size:11
Alignment explanation
Indices: 140650--140691 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
140640 TGAATATATT
140650 AATATATAATA
1 AATATATAATA
140661 AATA-ATAAGTA
1 AATATATAA-TA
140672 AATATATATATA
1 AATATATA-ATA
*
140684 CATATATA
1 AATATATA
140692 TATTTAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.15
11 10 0.37
12 12 0.44
13 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (11 bp):
AATATATAATA
Found at i:141373 original size:7 final size:7
Alignment explanation
Indices: 141355--141396 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
141345 AATTTTGGAC
141355 ATTTTAA
1 ATTTTAA
141362 A-TTTAA
1 ATTTTAA
141368 ATTTTAA
1 ATTTTAA
141375 ATTTTAA
1 ATTTTAA
*
141382 A-TCTAA
1 ATTTTAA
*
141388 ATTTAAA
1 ATTTTAA
141395 AT
1 AT
141397 GTATTTAGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 11 0.37
7 19 0.63
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (7 bp):
ATTTTAA
Found at i:141373 original size:13 final size:13
Alignment explanation
Indices: 141355--141394 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
141345 AATTTTGGAC
141355 ATTTTAAATTTAA
1 ATTTTAAATTTAA
141368 ATTTTAAATTTTAA
1 ATTTTAAA-TTTAA
*
141382 A-TCTAAATTTAA
1 ATTTTAAATTTAA
141394 A
1 A
141395 ATGTATTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 6 0.24
13 13 0.52
14 6 0.24
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTTAAATTTAA
Found at i:141380 original size:20 final size:20
Alignment explanation
Indices: 141355--141396 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
141345 AATTTTGGAC
* *
141355 ATTTTAAATTTAAATTTTAA
1 ATTTTAAATCTAAATTTAAA
141375 ATTTTAAATCTAAATTTAAA
1 ATTTTAAATCTAAATTTAAA
141395 AT
1 AT
141397 GTATTTAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTAAATCTAAATTTAAA
Found at i:142653 original size:18 final size:18
Alignment explanation
Indices: 142630--142666 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
142620 ACAATTCATA
142630 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
142648 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
142666 T
1 T
142667 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:148533 original size:18 final size:18
Alignment explanation
Indices: 148510--148546 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
148500 ACAATTCATA
148510 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
148528 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
148546 T
1 T
148547 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:152418 original size:71 final size:71
Alignment explanation
Indices: 152302--152440 Score: 251
Period size: 71 Copynumber: 2.0 Consensus size: 71
152292 CTTCGCAATG
*
152302 CCACTTCCTTGATATGTTCTTTACCCAAATTTATTGGATTCTCAGTATCGTTCGGAAAGGTTCCT
1 CCACTACCTTGATATGTTCTTTACCCAAATTTATTGGATTCTCAGTATCGTTCGGAAAGGTTCCT
152367 TGCAGT
66 TGCAGT
* *
152373 CCACTACCTTGATATGTTCTTTACCTAAATTTATTGGATTCTCAGTATCGTTCGGCAAGGTTCCT
1 CCACTACCTTGATATGTTCTTTACCCAAATTTATTGGATTCTCAGTATCGTTCGGAAAGGTTCCT
152438 TGC
66 TGC
152441 GGTCTATTAC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.40
Consensus pattern (71 bp):
CCACTACCTTGATATGTTCTTTACCCAAATTTATTGGATTCTCAGTATCGTTCGGAAAGGTTCCT
TGCAGT
Found at i:157105 original size:43 final size:43
Alignment explanation
Indices: 156966--157122 Score: 154
Period size: 43 Copynumber: 3.7 Consensus size: 43
156956 TATGCTCCAA
* * * * *
156966 CCGAGTCATAAGTTCTTCCATTTACACATAATCTTATGCTCTTG
1 CCGAGACATAAG-TCTTCCATTTATAAATAATCTTATGCACTTC
* * * * *
157010 CCAAAAAATAGGTCTTCCATTTAT-AATAATCTTATGCACTTT
1 CCGAGACATAAGTCTTCCATTTATAAATAATCTTATGCACTTC
* * * * *
157052 TCGAGTCATAAGTCTTCCATTTATAAACAATCTTATGCCCTAC
1 CCGAGACATAAGTCTTCCATTTATAAATAATCTTATGCACTTC
*
157095 CCGAGACATAAGTCTTCCATTTAAAAAT
1 CCGAGACATAAGTCTTCCATTTATAAAT
157123 CTCCGAGTCT
Statistics
Matches: 89, Mismatches: 23, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
42 33 0.37
43 49 0.55
44 7 0.08
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.36
Consensus pattern (43 bp):
CCGAGACATAAGTCTTCCATTTATAAATAATCTTATGCACTTC
Found at i:157110 original size:85 final size:84
Alignment explanation
Indices: 156967--157124 Score: 201
Period size: 85 Copynumber: 1.9 Consensus size: 84
156957 ATGCTCCAAC
* * * ** *
156967 CGAGTCATAAGTTCTTCCATTTACACATAATCTTATGCTCTTGCCAAAAAATAGGTCTTCCATTT
1 CGAGTCATAAGTTCTTCCATTTACAAACAATCTTATGCCCTACCCAAAAAATAAGTCTTCCATTT
157032 ATAATAATCTTATGCACTTTT
66 A-AA-AATCTTATGCACTTTT
* * * *
157053 CGAGTCATAAG-TCTTCCATTTATAAACAATCTTATGCCCTACCCGAGACATAAGTCTTCCATTT
1 CGAGTCATAAGTTCTTCCATTTACAAACAATCTTATGCCCTACCCAAAAAATAAGTCTTCCATTT
157117 AAAAATCT
66 AAAAATCT
157125 CCGAGTCTTC
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
83 5 0.08
84 2 0.03
85 44 0.71
86 11 0.18
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (84 bp):
CGAGTCATAAGTTCTTCCATTTACAAACAATCTTATGCCCTACCCAAAAAATAAGTCTTCCATTT
AAAAATCTTATGCACTTTT
Found at i:158196 original size:22 final size:22
Alignment explanation
Indices: 158171--158213 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
158161 AAAATATTTC
*
158171 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
158193 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
158214 TTATTCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:168510 original size:22 final size:22
Alignment explanation
Indices: 168485--168527 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
168475 AAAATATTTC
*
168485 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
168507 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
168528 TTATTCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:169290 original size:24 final size:24
Alignment explanation
Indices: 169255--169307 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
169245 TTAAATAATA
*
169255 TTTGTTTTATTCATACTTATGATG
1 TTTGTTTGATTCATACTTATGATG
*
169279 TTTGTTTGATTCATGCTTATGATG
1 TTTGTTTGATTCATACTTATGATG
169303 TTTGT
1 TTTGT
169308 GCCTCAATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.17, C:0.08, G:0.17, T:0.58
Consensus pattern (24 bp):
TTTGTTTGATTCATACTTATGATG
Found at i:170645 original size:12 final size:12
Alignment explanation
Indices: 170628--170652 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
170618 GAAATTTATA
170628 TGGTTAAATCCT
1 TGGTTAAATCCT
170640 TGGTTAAATCCT
1 TGGTTAAATCCT
170652 T
1 T
170653 AATGAGTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (12 bp):
TGGTTAAATCCT
Found at i:171183 original size:25 final size:23
Alignment explanation
Indices: 171138--171239 Score: 134
Period size: 23 Copynumber: 4.4 Consensus size: 23
171128 GGACCTTAGC
171138 GTGCTCTCCATTTAGCACTTTGT
1 GTGCTCTCCATTTAGCACTTTGT
*
171161 GTGCTCTTCATTATTAGCACTTTGT
1 GTGCTCTCCA-T-TTAGCACTTTGT
*
171186 GTGCTCTCCATTTAGCAATTTGT
1 GTGCTCTCCATTTAGCACTTTGT
** *
171209 GTGCTCTCTGTTTAGCACATT-T
1 GTGCTCTCCATTTAGCACTTTGT
171231 GTGCTCTCC
1 GTGCTCTCC
171240 GTTCATTTGT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
22 9 0.13
23 37 0.54
24 2 0.03
25 21 0.30
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (23 bp):
GTGCTCTCCATTTAGCACTTTGT
Found at i:171190 original size:48 final size:45
Alignment explanation
Indices: 171138--171239 Score: 143
Period size: 48 Copynumber: 2.2 Consensus size: 45
171128 GGACCTTAGC
* *
171138 GTGCTCTCCATTTAGCACTTTGTGTGCTCTTCAT-TATTAGCACTTTGT
1 GTGCTCTCCATTTAGCAATTTGTGTGCTC-TC-TGT-TTAGCACATT-T
171186 GTGCTCTCCATTTAGCAATTTGTGTGCTCTCTGTTTAGCACATTT
1 GTGCTCTCCATTTAGCAATTTGTGTGCTCTCTGTTTAGCACATTT
171231 GTGCTCTCC
1 GTGCTCTCC
171240 GTTCATTTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
45 10 0.20
46 10 0.20
47 3 0.06
48 28 0.55
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (45 bp):
GTGCTCTCCATTTAGCAATTTGTGTGCTCTCTGTTTAGCACATTT
Found at i:172081 original size:16 final size:16
Alignment explanation
Indices: 172060--172104 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
172050 GCATACTTAA
172060 GATAATTTGCATTAGG
1 GATAATTTGCATTAGG
172076 GATAATTTGCATTAGG
1 GATAATTTGCATTAGG
172092 GATAATTTGCATT
1 GATAATTTGCATT
172105 TAGTTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (16 bp):
GATAATTTGCATTAGG
Found at i:179207 original size:35 final size:35
Alignment explanation
Indices: 179162--179250 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 35
179152 TATGATCCTA
* * *
179162 TTTCGCATGTTAAGCATGCAATAAATCTGAGTCTG
1 TTTCACATGTTAAGCATGCAATAAATCTAACTCTG
* * *
179197 TTTCATATGTTAAGCATACCATAAATCTAACTCTG
1 TTTCACATGTTAAGCATGCAATAAATCTAACTCTG
*
179232 TTTCGCATGTTAAGCATGC
1 TTTCACATGTTAAGCATGC
179251 CACTCTGTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (35 bp):
TTTCACATGTTAAGCATGCAATAAATCTAACTCTG
Found at i:180675 original size:29 final size:29
Alignment explanation
Indices: 180637--180720 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
180627 TACTATGGAA
*
180637 TATGAAACTTTAGATT-TGGAAAATTATAT
1 TATGAAACTTTAGATTATGG-AAACTATAT
* *
180666 TATGAAACTTTATATTATGGAGACTATAT
1 TATGAAACTTTAGATTATGGAAACTATAT
* * *
180695 TGTGAAACTTTAGATTCTGAAAACTA
1 TATGAAACTTTAGATTATGGAAACTA
180721 AATATATTGA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 43 0.93
30 3 0.07
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (29 bp):
TATGAAACTTTAGATTATGGAAACTATAT
Found at i:180680 original size:15 final size:15
Alignment explanation
Indices: 180637--180716 Score: 60
Period size: 15 Copynumber: 5.5 Consensus size: 15
180627 TACTATGGAA
*
180637 TATGAAACTTTAGAT
1 TATGAAACTTTATAT
*
180652 T-TGGAAA-ATTATAT
1 TAT-GAAACTTTATAT
180666 TATGAAACTTTATAT
1 TATGAAACTTTATAT
*
180681 TATGGAGAC--TATAT
1 TAT-GAAACTTTATAT
* *
180695 TGTGAAACTTTAGAT
1 TATGAAACTTTATAT
*
180710 TCTGAAA
1 TATGAAA
180717 ACTAAATATA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
13 4 0.08
14 18 0.35
15 25 0.49
16 4 0.08
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (15 bp):
TATGAAACTTTATAT
Found at i:183405 original size:20 final size:20
Alignment explanation
Indices: 183376--183415 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
183366 GTACTTGTTC
183376 AGTTTCAGGTTTAGTTCTTT
1 AGTTTCAGGTTTAGTTCTTT
*
183396 AGTTTTAGGTTTAGTTCTTT
1 AGTTTCAGGTTTAGTTCTTT
183416 CTTCCAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.07, G:0.20, T:0.57
Consensus pattern (20 bp):
AGTTTCAGGTTTAGTTCTTT
Found at i:189708 original size:26 final size:27
Alignment explanation
Indices: 189653--189713 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
189643 CAATTTTCAA
* *
189653 TTAATGATTGTTTTCTTTGACCCTCTTT
1 TTAAT-ATTGTTTCCTTCGACCCTCTTT
*
189681 TTAATATTGTTTCCTTCGATCCTCTTT
1 TTAATATTGTTTCCTTCGACCCTCTTT
189708 TTAATA
1 TTAATA
189714 GAATTCTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.56
Consensus pattern (27 bp):
TTAATATTGTTTCCTTCGACCCTCTTT
Found at i:190394 original size:205 final size:206
Alignment explanation
Indices: 190012--190463 Score: 710
Period size: 205 Copynumber: 2.2 Consensus size: 206
190002 ATTATCCACA
* * *
190012 AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACACTCGATG
1 AAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACTCACACCCGATG
* **
190077 TGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACTTCGAAGAAGGTCAAAGCAATAAAACG
66 TGAGCAAATCTTCGAACCACAACTTCCTGATGAGACACTGAGAAGAAGGTCAAAGCAATAAAACG
* *
190142 GTTAGCTTCCTGATGAGATACGGAGAAGTTGACCAAATTCGTCTTCCTGATGAGATATAGAGAAG
131 GTTAGCTTCCTAATGAGATACGGAGAAGTTGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
190207 CGAATTGAAAC
196 CGAATTGAAAC
* * * *
190218 AAACGACGAAGTCATCTTCCCAATGAGATACTGAGAAGAAGACCAAATCAAACTCGCGCCCGATG
1 AAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACTCACACCCGATG
* * * *
190283 TGAGTAAATCTTCGAA-CACAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAACG
66 TGAGCAAATCTTCGAACCACAACTTCCTGATGAGACACTGAGAAGAAGGTCAAAGCAATAAAACG
* *
190347 GTTAGCTTCCTAATGAGATACTGAGAAG-TGAATCAAATTCGTCTTCCTGATGAGATACAGAGAA
131 GTTAGCTTCCTAATGAGATACGGAGAAGTTG-ACCAAATTCGTCTTCCTGATGAGATACAGAGAA
190411 GCGAATTGAAAC
195 GCGAATTGAAAC
*
190423 AAACAACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAG
1 AAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAG
190464 GTCAAGTCAA
Statistics
Matches: 224, Mismatches: 21, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
204 2 0.01
205 149 0.67
206 73 0.33
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (206 bp):
AAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACTCACACCCGATG
TGAGCAAATCTTCGAACCACAACTTCCTGATGAGACACTGAGAAGAAGGTCAAAGCAATAAAACG
GTTAGCTTCCTAATGAGATACGGAGAAGTTGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
CGAATTGAAAC
Done.