Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011686.1 Kokia drynarioides strain JFW-HI SEQ_126679, 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: 207212
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 64 characters in sequence are not A, C, G, or T
Found at i:1084 original size:23 final size:23
Alignment explanation
Indices: 1038--1187 Score: 103
Period size: 23 Copynumber: 6.4 Consensus size: 23
1028 ATGCTAACGC
**
1038 GCTTACTGTTTCGCACTTCATGT
1 GCTTACTGTTTCGCACTTTGTGT
1061 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
* * *
1084 GCCTACTGATTTGCGC-C-ATGTGC
1 GCTTACTG-TTT-CGCACTTTGTGT
* * *
1107 GCCTACTGATT-GCACTGTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
* * *
1129 GCCTACTGGATT-GCACTGTGTGT
1 GCTTACT-GTTTCGCACTTTGTGT
1152 GCTTACTGTTTCCCCAGCAC-TTGTGT
1 GCTTACTGTTT---C-GCACTTTGTGT
1178 GCTTACTGTT
1 GCTTACTGTT
1188 AAGCACTTCG
Statistics
Matches: 106, Mismatches: 11, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.02
21 1 0.01
22 16 0.15
23 61 0.58
24 4 0.04
25 3 0.03
26 15 0.14
27 4 0.04
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.39
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTTGTGT
Found at i:1159 original size:45 final size:46
Alignment explanation
Indices: 1058--1159 Score: 118
Period size: 45 Copynumber: 2.2 Consensus size: 46
1048 TCGCACTTCA
* * *
1058 TGTGCTTACTGTTTCGCACTTTGTGTGCCTACTGATTTGCGCCATG
1 TGTGCTTACTGATTCGCACTGTGTGTGCCTACTGATTTGCACCATG
* * **
1104 TGCGCCTACTGATT-GCACTGTGTGTGCCTACTGGA-TTGCACTGTG
1 TGTGCTTACTGATTCGCACTGTGTGTGCCTACT-GATTTGCACCATG
1149 TGTGCTTACTG
1 TGTGCTTACTG
1160 TTTCCCCAGC
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
45 33 0.72
46 13 0.28
ACGTcount: A:0.12, C:0.24, G:0.26, T:0.38
Consensus pattern (46 bp):
TGTGCTTACTGATTCGCACTGTGTGTGCCTACTGATTTGCACCATG
Found at i:7493 original size:2 final size:2
Alignment explanation
Indices: 7486--7532 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
7476 TTTTATCTTT
7486 TA TA TA TA TA TA 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 TA TA TA TA TA TA
7528 TA TA T
1 TA TA T
7533 TGATTGGAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8731 original size:18 final size:19
Alignment explanation
Indices: 8699--8741 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
8689 AACAATGCTG
* *
8699 TTAAGAAGTCTTTTTCACC
1 TTAAAAAGTCCTTTTCACC
*
8718 -TAAAAAGTCCTTTTTACC
1 TTAAAAAGTCCTTTTCACC
8736 TTAAAA
1 TTAAAA
8742 CAGTACTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.40
Consensus pattern (19 bp):
TTAAAAAGTCCTTTTCACC
Found at i:8732 original size:19 final size:18
Alignment explanation
Indices: 8699--8741 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
8689 AACAATGCTG
*
8699 TTAAGAAGTCTTTTTCACC
1 TTAAAAAGTCTTTTT-ACC
8718 -TAAAAAGTCCTTTTTACC
1 TTAAAAAGT-CTTTTTACC
8736 TTAAAA
1 TTAAAA
8742 CAGTACTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.40
Consensus pattern (18 bp):
TTAAAAAGTCTTTTTACC
Found at i:10559 original size:12 final size:10
Alignment explanation
Indices: 10526--10552 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
10516 TTTGCCCCTT
10526 ATTGTTGCCA
1 ATTGTTGCCA
10536 ATTGTTGCCA
1 ATTGTTGCCA
10546 ATTGTTG
1 ATTGTTG
10553 AGCCAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.44
Consensus pattern (10 bp):
ATTGTTGCCA
Found at i:12342 original size:22 final size:21
Alignment explanation
Indices: 12293--12342 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 21
12283 CTACTGGGGA
12293 AACAGAAGCACACACAGTGCT
1 AACAGAAGCACACACAGTGCT
12314 AATCAGAAGCACACACAGTGCT
1 AA-CAGAAGCACACACAGTGCT
12336 GAACAGA
1 -AACAGA
12343 GGGTGCACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.07
22 23 0.85
23 2 0.07
ACGTcount: A:0.44, C:0.26, G:0.20, T:0.10
Consensus pattern (21 bp):
AACAGAAGCACACACAGTGCT
Found at i:14547 original size:13 final size:13
Alignment explanation
Indices: 14531--14555 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14521 ATCAAAATTT
14531 TTAAAAATACTTC
1 TTAAAAATACTTC
14544 TTAAAAATACTT
1 TTAAAAATACTT
14556 TCCCACCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAAAAATACTTC
Found at i:15987 original size:25 final size:24
Alignment explanation
Indices: 15942--15992 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
15932 TATACTTTTA
**
15942 TTTTTAAAAATTTAATCTTTCGAT
1 TTTTTAAAAATTTAAAATTTCGAT
*
15966 TTTTTTAAAATTTATAAATTTCGAT
1 TTTTTAAAAATTTA-AAATTTCGAT
15991 TT
1 TT
15993 ATTTGTTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTTAAAAATTTAAAATTTCGAT
Found at i:40584 original size:12 final size:11
Alignment explanation
Indices: 40548--40590 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
40538 AGTTCAATAT
40548 TATTTTATTAA
1 TATTTTATTAA
40559 TATTTTACTT-A
1 TATTTTA-TTAA
40570 TATATTTATTAA
1 TAT-TTTATTAA
40582 TATTTTATT
1 TATTTTATT
40591 TAGAAAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:40898 original size:26 final size:26
Alignment explanation
Indices: 40845--40900 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
40835 GGAGAAAATG
* **
40845 AGAAGATAAATGAAGGAAAATGGTGA
1 AGAAGAGAAATGAAGGAAAATGAAGA
* *
40871 AGAAGAGAAATGCATGAAAATGAAGA
1 AGAAGAGAAATGAAGGAAAATGAAGA
40897 AGAA
1 AGAA
40901 AGGAAGAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.29, T:0.12
Consensus pattern (26 bp):
AGAAGAGAAATGAAGGAAAATGAAGA
Found at i:44845 original size:21 final size:24
Alignment explanation
Indices: 44812--44854 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
44802 AAGTATAAAT
44812 AAATTATCCAAAT-TT-TTATTTA
1 AAATTATCCAAATATTCTTATTTA
*
44834 AAATT-TCGAAATATTCTTATT
1 AAATTATCCAAATATTCTTATT
44855 AAATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (24 bp):
AAATTATCCAAATATTCTTATTTA
Found at i:51204 original size:207 final size:207
Alignment explanation
Indices: 50849--51268 Score: 831
Period size: 207 Copynumber: 2.0 Consensus size: 207
50839 AGAAGTGGTG
50849 GAATCCTTTCTTCCGAGAGGGATCTGAATATCGGGTCCTCCTGACAGTGCAACTGATACCTTAGC
1 GAATCCTTTCTTCCGAGAGGGATCTGAATATCGGGTCCTCCTGACAGTGCAACTGATACCTTAGC
50914 TGCTAAGGCAACAATATCTGCACATGAGGCCAGCCCTGGACACTTTGCTTCTAGTTTGTCTTTTA
66 TGCTAAGGCAACAATATCTGCACATGAGGCCAGCCCTGGACACTTTGCTTCTAGTTTGTCTTTTA
50979 TACTGTAAATAGCTTCCAACTTTCTAATACCCAAGTTCATTCCAGAAGCCATCTCAGAGTTGCCT
131 TACTGTAAATAGCTTCCAACTTTCTAATACCCAAGTTCATTCCAGAAGCCATCTCAGAGTTGCCT
51044 TTAACAGGTTTA
196 TTAACAGGTTTA
51056 GAATCCTTTCTTCCGAGAGGGATCTGAATATCGGGTCCTCCTGACAGTGCAACTGATACCTTAGC
1 GAATCCTTTCTTCCGAGAGGGATCTGAATATCGGGTCCTCCTGACAGTGCAACTGATACCTTAGC
*
51121 TGCTAAGGCAACAATATCTGCACATGAGGCCTGCCCTGGACACTTTGCTTCTAGTTTGTCTTTTA
66 TGCTAAGGCAACAATATCTGCACATGAGGCCAGCCCTGGACACTTTGCTTCTAGTTTGTCTTTTA
51186 TACTGTAAATAGCTTCCAACTTTCTAATACCCAAGTTCATTCCAGAAGCCATCTCAGAGTTGCCT
131 TACTGTAAATAGCTTCCAACTTTCTAATACCCAAGTTCATTCCAGAAGCCATCTCAGAGTTGCCT
51251 TTAACAGGTTTA
196 TTAACAGGTTTA
51263 GAATCC
1 GAATCC
51269 AACAGGATCG
Statistics
Matches: 212, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
207 212 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (207 bp):
GAATCCTTTCTTCCGAGAGGGATCTGAATATCGGGTCCTCCTGACAGTGCAACTGATACCTTAGC
TGCTAAGGCAACAATATCTGCACATGAGGCCAGCCCTGGACACTTTGCTTCTAGTTTGTCTTTTA
TACTGTAAATAGCTTCCAACTTTCTAATACCCAAGTTCATTCCAGAAGCCATCTCAGAGTTGCCT
TTAACAGGTTTA
Found at i:61897 original size:23 final size:22
Alignment explanation
Indices: 61868--61996 Score: 123
Period size: 23 Copynumber: 5.5 Consensus size: 22
61858 GAACACTAGC
*
61868 GTGCTCTCTGTTTAGCACGTCT
1 GTGCTCTCTGTTTAGCACGTGT
61890 CGTGCTCTCTGTTATTAGCACTGTGT
1 -GTGCTCTCTG-T-TTAGCAC-GTGT
* * *
61916 GTGCTGTCTGATTAGCACTTTGT
1 GTGCTCTCTGTTTAGCAC-GTGT
* * *
61939 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGTTTAGCAC-GTGT
*
61962 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGTTTAGCAC-GTGT
61985 GTGCTCTCTGTT
1 GTGCTCTCTGTT
61997 GCCCAGCACT
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
23 72 0.78
24 1 0.01
25 16 0.17
26 3 0.03
ACGTcount: A:0.11, C:0.22, G:0.23, T:0.44
Consensus pattern (22 bp):
GTGCTCTCTGTTTAGCACGTGT
Found at i:61977 original size:46 final size:47
Alignment explanation
Indices: 61871--61995 Score: 146
Period size: 46 Copynumber: 2.7 Consensus size: 47
61861 CACTAGCGTG
* *
61871 CTCTCTGTTTAGCACGTCT-CGTGCTCTCTGTTATTAGCACTGTGTGTG
1 CTCTCTGTTTAGCAC-TCTGTGTGCTCTCTG-TATTAGCACTGTGTGTA
* * * * *
61919 CTGTCTGATTAGCACTTTGTGTGCTCTCTG-ATTAGTACTTTGTGTA
1 CTCTCTGTTTAGCACTCTGTGTGCTCTCTGTATTAGCACTGTGTGTA
*
61965 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGT
1 CTCTCTGTTTAGCACTCTGTGTGCTCTCTGT
61996 TGCCCAGCAC
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
46 40 0.62
47 2 0.03
48 23 0.35
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (47 bp):
CTCTCTGTTTAGCACTCTGTGTGCTCTCTGTATTAGCACTGTGTGTA
Found at i:66495 original size:96 final size:96
Alignment explanation
Indices: 66321--66512 Score: 223
Period size: 96 Copynumber: 2.0 Consensus size: 96
66311 ATTTTGGGAA
* * * *
66321 AAGGATATTCGATTATCTCGATTTTAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCAATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
66386 GAATCGAAGAT-AAAGAAACATTGCCTCGATT
66 GAATCGAAGATAAAAG-AACATTACCTCGATT
* *
66417 AAGGGTATTCGATTATTTCAATTTGAAGGAAA-ATTGCACCTAGTAAGTTAAGGCACAA-ATTTT
1 AAGGATATTCGATTATCTCAATTTGAA-GAAAGATTGCACCTAGTAAGTTAAGGCACAATA-TTT
* *
66480 C-GAAACTTGAA-ATAAAAGAATATTACCTCGATT
64 CAG-AA-TCGAAGATAAAAGAACATTACCTCGATT
66513 TTAAAGTCTT
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
95 2 0.02
96 68 0.83
97 12 0.15
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCAATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAAGAACATTACCTCGATT
Found at i:66842 original size:29 final size:29
Alignment explanation
Indices: 66808--67033 Score: 237
Period size: 29 Copynumber: 7.7 Consensus size: 29
66798 TGGGGTTTAA
* *
66808 AAAAATGGAATTTTTAGACA-TTCGAGGGT
1 AAAAATGGAATTTTTGGA-AGTTTGAGGGT
* *
66837 AAAAATGGAATTTTTAGAAGTTTTAGGGT
1 AAAAATGGAATTTTTGGAAGTTTGAGGGT
* * *
66866 CAAAATTAGGATTTTTTAGAAGTTTTGA-GGT
1 -AAAAAT-GGAATTTTTGGAAG-TTTGAGGGT
* *
66897 CAAAAAATGGAATTTTTGGAAATTTTGAGGTT
1 --AAAAATGGAATTTTTGG-AAGTTTGAGGGT
*
66929 AAAAATGGAA-TTTTGGAAGTTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTT-GAGGGT
66958 AAAAATGGAATTTTTGGAAGTTTCG-GGGT
1 AAAAATGGAATTTTTGGAAGTTT-GAGGGT
*
66987 AAAAATGGGATTTTTGGAAGTTTG-GGGT
1 AAAAATGGAATTTTTGGAAGTTTGAGGGT
67015 AAAAATGGAATTTTTGGAA
1 AAAAATGGAATTTTTGGAA
67034 ATGGAATTTT
Statistics
Matches: 172, Mismatches: 16, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
28 29 0.17
29 71 0.41
30 29 0.17
31 30 0.17
32 13 0.08
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGAGGGT
Found at i:67037 original size:15 final size:15
Alignment explanation
Indices: 67017--67048 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
67007 TTTGGGGTAA
67017 AAATGGAATTTTTGG
1 AAATGGAATTTTTGG
67032 AAATGGAATTTTTGG
1 AAATGGAATTTTTGG
67047 AA
1 AA
67049 GTTTTAGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (15 bp):
AAATGGAATTTTTGG
Found at i:67041 original size:72 final size:73
Alignment explanation
Indices: 66960--67105 Score: 206
Period size: 72 Copynumber: 2.0 Consensus size: 73
66950 TCGGGGGTAA
* * * *
66960 AAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGGGATTTTTGGAAG-TTTGGGGTAAAAAT-GG
1 AAATGGAATTTTTGGAAGTTTCAGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGTAAAAATAGG
67023 AATTTTTGG
66 -ATTTTTGG
* * *
67032 AAATGGAATTTTTGGAAGTTTTAGGGTTAAAATGGAATTTTTAGAAGTTTTAGGGTCAAAATAGG
1 AAATGGAATTTTTGGAAGTTTCAGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGTAAAAATAGG
67097 ATTTTTGG
66 ATTTTTGG
67105 A
1 A
67106 GGTTTTAGGG
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
72 42 0.65
73 21 0.32
74 2 0.03
ACGTcount: A:0.32, C:0.01, G:0.29, T:0.38
Consensus pattern (73 bp):
AAATGGAATTTTTGGAAGTTTCAGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGTAAAAATAGG
ATTTTTGG
Found at i:67050 original size:43 final size:44
Alignment explanation
Indices: 66989--67073 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
66979 TTCGGGGTAA
* *
66989 AAATGGGATTTTTGGAAG-TTTGGGGTAAAAATGGAATTTTTGG
1 AAATGGAATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGG
*
67032 AAATGGAATTTTTGGAAGTTTTAGGGTTAAAATGGAATTTTT
1 AAATGGAATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTT
67074 AGAAGTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 17 0.45
44 21 0.55
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (44 bp):
AAATGGAATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGG
Found at i:67078 original size:29 final size:29
Alignment explanation
Indices: 67032--67251 Score: 234
Period size: 29 Copynumber: 7.6 Consensus size: 29
67022 GAATTTTTGG
*
67032 AAATGGAATTTTTGGAAGTTTTAGGGTTA
1 AAATGGAATTTTTGGAAGTTTTAGGGTAA
* *
67061 AAATGGAATTTTTAGAAGTTTTAGGGTCA
1 AAATGGAATTTTTGGAAGTTTTAGGGTAA
* *
67090 AAATAGG-ATTTTTGGAGGTTTTAGGGTTA
1 AAAT-GGAATTTTTGGAAGTTTTAGGGTAA
* **
67119 AAATGGAATTTTTGGAAG-TTTCGACATCAA
1 AAATGGAATTTTTGGAAGTTTTAG-GGT-AA
*
67149 AAATGGAA-TTTTGGAAGTTTTGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTT-AGGGTAA
* *
67178 AAATGGAATTTTTGGAAG-TTTCGGATTCAA
1 AAATGGAATTTTTGGAAGTTTTAGG-GT-AA
* *
67208 AAATGGGATTTTTGGAAG-TTTGGGGTAA
1 AAATGGAATTTTTGGAAGTTTTAGGGTAA
67236 AAATGGAATTTTTGGA
1 AAATGGAATTTTTGGA
67252 CAATTCAGGG
Statistics
Matches: 163, Mismatches: 19, Indels: 19
0.81 0.09 0.09
Matches are distributed among these distances:
28 25 0.15
29 89 0.55
30 48 0.29
31 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTTTAGGGTAA
Found at i:67105 original size:130 final size:131
Alignment explanation
Indices: 66901--67139 Score: 333
Period size: 130 Copynumber: 1.8 Consensus size: 131
66891 TGAGGTCAAA
* *
66901 AAATGGAATTTTTGGAAATTTTGAGGTTAAAAATGGAATTTTGGAAGTTTCGGGGGTAAAAATGG
1 AAATGGAATTTTTGGAAATTTTGAGGTTAAAAATGGAATTTTAGAAGTTTCGAGGGTAAAAATGG
* *
66966 AATTTTTGGAAGTTTCGGGGTAAAAATGGGATTTTTGGAAGTTTGGGGTAAAAATGGAATTTTTG
66 AATTTTTGGAAGTTTCAGGGTAAAAATGGAATTTTTGGAAGTTTGGGGTAAAAATGGAATTTTTG
67031 G
131 G
* * *
67032 AAATGGAATTTTTGGAAGTTTT-AGGGTT-AAAATGGAATTTTTAGAAGTTT-TAGGGTCAAAAT
1 AAATGGAATTTTTGGAAATTTTGA-GGTTAAAAATGGAA-TTTTAGAAGTTTCGAGGGTAAAAAT
* * *
67094 AGG-ATTTTTGGAGGTTTTAGGGTTAAAATGGAATTTTTGGAAGTTT
64 -GGAATTTTTGGAAGTTTCAGGGTAAAAATGGAATTTTTGGAAGTTT
67140 CGACATCAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
130 57 0.60
131 38 0.40
ACGTcount: A:0.32, C:0.01, G:0.29, T:0.38
Consensus pattern (131 bp):
AAATGGAATTTTTGGAAATTTTGAGGTTAAAAATGGAATTTTAGAAGTTTCGAGGGTAAAAATGG
AATTTTTGGAAGTTTCAGGGTAAAAATGGAATTTTTGGAAGTTTGGGGTAAAAATGGAATTTTTG
G
Found at i:67111 original size:58 final size:57
Alignment explanation
Indices: 67039--67251 Score: 259
Period size: 58 Copynumber: 3.7 Consensus size: 57
67029 TGGAAATGGA
* * * *
67039 ATTTTTGGAAGTTTTAGGGTTAAAATGGAATTTTTAGAAGTTTTAGGGTCAAAATAGG
1 ATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGGAAG-TTTCGGATCAAAATAGG
* * *
67097 ATTTTTGGAGGTTTTAGGGTTAAAATGGAATTTTTGGAAGTTTCGACATCAAAA-ATGG
1 ATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGGAAGTTTCG-GATCAAAATA-GG
* * *
67155 AATTTTGGAAGTTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGATTCAAAAATGGG
1 ATTTTTGGAAGTTTT-AGGGTAAAAATGGAATTTTTGGAAGTTTCGGA-TC-AAAATAGG
*
67215 ATTTTTGGAAG-TTTGGGGTAAAAATGGAATTTTTGGA
1 ATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGGA
67252 CAATTCAGGG
Statistics
Matches: 137, Mismatches: 12, Indels: 12
0.85 0.07 0.07
Matches are distributed among these distances:
57 5 0.04
58 83 0.61
59 33 0.24
60 16 0.12
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (57 bp):
ATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGGAAGTTTCGGATCAAAATAGG
Found at i:69092 original size:17 final size:16
Alignment explanation
Indices: 69066--69108 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
69056 ATTTTGAAAT
69066 TAAATTTAAATTTAAAA
1 TAAA-TTAAATTTAAAA
69083 TAAATCTAAATTTAAAA
1 TAAAT-TAAATTTAAAA
69100 TAAATTAAA
1 TAAATTAAA
69109 AAGAGGTCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATTAAATTTAAAA
Found at i:75898 original size:345 final size:353
Alignment explanation
Indices: 75484--76166 Score: 927
Period size: 365 Copynumber: 1.9 Consensus size: 353
75474 AATTAATATT
** * * * *** *
75484 TATTAGATTAAATTTTATATTAAATCTTATTAAAGTAATAAAATGTTTATCTTGTAGATAAA-TA
1 TATTAGATTAAATTCAATATTAAATATTATTAAAATAATAAAATATTTATCTACAAGATAAACAA
*
75548 TTAAATTTAATATTAAAATAATCACTTTAATATTAAATTAATAAAATACTACTAAAATAAGTATT
66 TTAAATTTAATATTAAAATAATCACTTTAATATTAAATTAATAAAATAATACTAAAATAAGTATT
75613 AAATTAAATTTAATATTAAACCATT-AAA-AATATTATTTTTTG-AATAG-TTC-AATT-A-T-C
131 AAATTAAATTTAATATTAAACCATTAAAATAATATTA-TTTTTGAAATAGTTTCAAATTAATTAC
* * *
75670 -CATTGAATCAATTGTCTGACTTGAAAATTAATTTATAAAAATATCATATTAATTTTAATTAATT
195 TCATTGAACCAATTGTATGACTTGAAAATTAATTTACAAAAATATCATATTAATTTTAATTAATT
* * *
75734 TAATTTTACTCGATCAAAATTAATTTTTCAAAAATCACTTAGATTTTTTTAAATTAATTTTTGAA
260 TAATTTTACTCAATCAAAATTAATTTTCCAAAAATCACTTAGA-ATTTTTAAATTAATTTTTGAA
75799 GAAAATTAATATAATATTTATCTTGATAAA
324 GAAAATTAATATAATATTTATCTTGATAAA
75829 TATTAGATTAAATTCAATATTAAATATTATTAAAATAATAAAATATTTATCTACAAGATAAACAT
1 TATTAGATTAAATTCAATATTAAATATTATTAAAATAATAAAATATTTATCTACAAGATAAAC--
* *
75894 TAAATTAAATTTAATATTAAGATAATCACTTTAATATTAAATTAATAAAATAATATTAAAATAAG
64 --AATTAAATTTAATATTAAAATAATCACTTTAATATTAAATTAATAAAATAATACTAAAATAAG
* *
75959 TATTAAATTTAATTTAATATTAAACTATTAAAATAATATTATTTTTGAAATAGTCTAATTTTCAA
127 TATTAAATTAAATTTAATATTAAACCATTAAAATAATATTATTTTTGAAATAG------TTTCAA
** * * *
76024 ATTCAATTACTCATTGGGCCAGTTGTATTACTTGAAAATTAATTTCCAAAAATATCATATTAATT
186 ATT-AATTACTCATTGAACCAATTGTATGACTTGAAAATTAATTTACAAAAATATCATATTAATT
* *
76089 TTAATTAATTTAATTTTACTTAATCAAAATTAATTTTCCAAAAATCACTTAGAATTTTTAAGTTA
250 TTAATTAATTTAATTTTACTCAATCAAAATTAATTTTCCAAAAATCACTTAGAATTTTTAAATTA
*
76154 ATTTTTGATGAAA
315 ATTTTTGAAGAAA
76167 TTTTTTTAAT
Statistics
Matches: 289, Mismatches: 28, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
345 54 0.19
350 86 0.30
351 9 0.03
352 12 0.04
359 3 0.01
360 4 0.01
362 1 0.00
363 1 0.00
364 23 0.08
365 96 0.33
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (353 bp):
TATTAGATTAAATTCAATATTAAATATTATTAAAATAATAAAATATTTATCTACAAGATAAACAA
TTAAATTTAATATTAAAATAATCACTTTAATATTAAATTAATAAAATAATACTAAAATAAGTATT
AAATTAAATTTAATATTAAACCATTAAAATAATATTATTTTTGAAATAGTTTCAAATTAATTACT
CATTGAACCAATTGTATGACTTGAAAATTAATTTACAAAAATATCATATTAATTTTAATTAATTT
AATTTTACTCAATCAAAATTAATTTTCCAAAAATCACTTAGAATTTTTAAATTAATTTTTGAAGA
AAATTAATATAATATTTATCTTGATAAA
Found at i:75938 original size:11 final size:11
Alignment explanation
Indices: 75924--75999 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
75914 GATAATCACT
75924 TTAATATTAAA
1 TTAATATTAAA
75935 TTAATA--AAA
1 TTAATATTAAA
75944 -TAATATTAAA
1 TTAATATTAAA
*
75954 ATAAGTATTAAA
1 TTAA-TATTAAA
75966 TTTAAT-TTAATA
1 -TTAATATTAA-A
75978 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
75991 ATAATATTA
1 TTAATATTA
76000 TTTTTGAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
8 5 0.09
9 3 0.06
10 3 0.06
11 20 0.37
12 13 0.24
13 6 0.11
14 4 0.07
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:75939 original size:20 final size:18
Alignment explanation
Indices: 75892--75998 Score: 76
Period size: 19 Copynumber: 5.8 Consensus size: 18
75882 CAAGATAAAC
75892 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
75909 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
**
75929 ATTAAATTAATAAAATAAT
1 ATTAAATTAAT-ATTTAAT
* *
75948 ATTAAAATAAGTATTAAAT
1 ATTAAATTAA-TATTTAAT
* *
75967 -TTAATTTAATATTAAACT
1 ATTAAATTAATATTTAA-T
*
75985 ATTAAAATAATATT
1 ATTAAATTAATATT
75999 ATTTTTGAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
17 15 0.21
18 9 0.13
19 30 0.42
20 17 0.24
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:76103 original size:15 final size:15
Alignment explanation
Indices: 76083--76112 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
76073 AAATATCATA
76083 TTAATTTTAATTAAT
1 TTAATTTTAATTAAT
*
76098 TTAATTTTACTTAAT
1 TTAATTTTAATTAAT
76113 CAAAATTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAATTTTAATTAAT
Found at i:77847 original size:29 final size:30
Alignment explanation
Indices: 77772--77848 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
77762 ATTAGACTTG
* *
77772 AATTTTGAAATCTAAAAAATAAAGAGATTA
1 AATTTTGAAATATAAAAAATAAAGAGATCA
*
77802 AATTTTTGAAA-AT-AAAAATATAGAGATCA
1 AA-TTTTGAAATATAAAAAATAAAGAGATCA
*
77831 AATTTT-AAATTTAAAAAA
1 AATTTTGAAATATAAAAAA
77849 AGTATAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 3 0.08
28 5 0.12
29 21 0.52
30 3 0.08
31 8 0.20
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (30 bp):
AATTTTGAAATATAAAAAATAAAGAGATCA
Found at i:82526 original size:21 final size:21
Alignment explanation
Indices: 82502--82559 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
82492 GTAATTGATC
82502 AAATATATTTAAAAATTTTTA
1 AAATATATTTAAAAATTTTTA
*
82523 AAAT-TAATTATAAAAA-TTTTC
1 AAATAT-ATT-TAAAAATTTTTA
*
82544 AAATACATTTAAAAAT
1 AAATATATTTAAAAAT
82560 GAAAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
20 7 0.23
21 18 0.58
22 6 0.19
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATATATTTAAAAATTTTTA
Found at i:90903 original size:23 final size:23
Alignment explanation
Indices: 90859--90904 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
90849 AAAAAAAAAT
**
90859 TAACTCGATTCGTTTAACTCGAA
1 TAACTCGATTCGAATAACTCGAA
*
90882 TAACTCGATTCGAATAATTCGAA
1 TAACTCGATTCGAATAACTCGAA
90905 ATTCGAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (23 bp):
TAACTCGATTCGAATAACTCGAA
Found at i:100210 original size:5 final size:6
Alignment explanation
Indices: 100187--100216 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
100177 TAAAAATCTA
*
100187 TATTTT TATTTT TGTTTT TATTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT
100217 CAATGTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:108463 original size:4 final size:4
Alignment explanation
Indices: 108454--108486 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
108444 TAACCAGCTG
108454 ACCA ACCA ACCA ACCA ACCA ACCA ACCA ACCA A
1 ACCA ACCA ACCA ACCA ACCA ACCA ACCA ACCA A
108487 GTTATGACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (4 bp):
ACCA
Found at i:118912 original size:30 final size:31
Alignment explanation
Indices: 118863--118920 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
118853 AGAATGACCA
*
118863 AAAACATATCTAAATTTTAAAATATAAAAAAT
1 AAAACATATCTAAACTTTAAAATA-AAAAAAT
118895 AAAACA-A-CTAAACTTTAAAATAAAAA
1 AAAACATATCTAAACTTTAAAATAAAAA
118921 TATATAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 4 0.16
30 14 0.56
31 1 0.04
32 6 0.24
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (31 bp):
AAAACATATCTAAACTTTAAAATAAAAAAAT
Found at i:121601 original size:23 final size:22
Alignment explanation
Indices: 121553--121623 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 22
121543 AGTATTAACA
*
121553 AATTTAGTTTA-TTATTAACAAGT
1 AATTTAGTTTATTTATTTA-AA-T
121576 AATTTAGTTTATTTAATTTAAAT
1 AATTTAGTTTATTT-ATTTAAAT
121599 AATATTA-TATTATTTATTTAAAT
1 AAT-TTAGT-TTATTTATTTAAAT
121622 AA
1 AA
121624 AATAAATTGA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
23 26 0.60
24 13 0.30
25 4 0.09
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (22 bp):
AATTTAGTTTATTTATTTAAAT
Found at i:121614 original size:28 final size:27
Alignment explanation
Indices: 121586--121640 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
121576 AATTTAGTTT
* *
121586 ATTTAATTTAAATAATATT-ATATTATTT
1 ATTTAAATAAAATAA-ATTGATA-TATTT
121614 ATTTAAATAAAATAAATTGATATATTT
1 ATTTAAATAAAATAAATTGATATATTT
121641 GTTTCAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
ATTTAAATAAAATAAATTGATATATTT
Found at i:121639 original size:23 final size:23
Alignment explanation
Indices: 121591--121640 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
121581 AGTTTATTTA
* * *
121591 ATTTAAATAATATTATATTATTT
1 ATTTAAATAATAATAAATTATAT
121614 ATTTAAATAA-AATAAATTGATAT
1 ATTTAAATAATAATAAATT-ATAT
121637 ATTT
1 ATTT
121641 GTTTCAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTTAAATAATAATAAATTATAT
Found at i:123296 original size:29 final size:27
Alignment explanation
Indices: 123263--123317 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
123253 CTTATATACG
123263 TACAACT-AAATGCAACTAACTTCAACTGA
1 TACAACTAAAAT--AACTAACT-CAACTGA
123292 TACAACTAAAATAACTAACTCAACTG
1 TACAACTAAAATAACTAACTCAACTG
123318 CAATTGACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.24
28 8 0.32
29 7 0.28
30 4 0.16
ACGTcount: A:0.47, C:0.24, G:0.05, T:0.24
Consensus pattern (27 bp):
TACAACTAAAATAACTAACTCAACTGA
Found at i:133605 original size:15 final size:15
Alignment explanation
Indices: 133587--133635 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
133577 CGCCATGGGA
133587 ACCACCACCTCCCCC
1 ACCACCACCTCCCCC
* *
133602 ACCACCACCGCCTCC
1 ACCACCACCTCCCCC
* * *
133617 ACCTCCTCCTCCGCC
1 ACCACCACCTCCCCC
133632 ACCA
1 ACCA
133636 AGCCCTCCAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.18, C:0.67, G:0.04, T:0.10
Consensus pattern (15 bp):
ACCACCACCTCCCCC
Found at i:133720 original size:6 final size:6
Alignment explanation
Indices: 133705--133751 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
133695 ACCACCATTG
* *
133705 CCACCC CCACCT CCACCT CCACCT CCACCT CCACCT CCACCG CCACC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACC
133752 ACCAACTGGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.17, C:0.70, G:0.02, T:0.11
Consensus pattern (6 bp):
CCACCT
Found at i:136728 original size:28 final size:29
Alignment explanation
Indices: 136679--136743 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
136669 ATAAACTATT
*
136679 AAAATAATAAAATTATACTTTT-ACTATCAA
1 AAAAT-ATAAAATTATAATTTTAACTAT-AA
* *
136709 AAAATATATAATT-TAATTTTAACTCTAA
1 AAAATATAAAATTATAATTTTAACTATAA
136737 AAAATAT
1 AAAATAT
136744 TTCAAACGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 15 0.48
29 11 0.35
30 5 0.16
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAATATAAAATTATAATTTTAACTATAA
Found at i:141011 original size:15 final size:15
Alignment explanation
Indices: 140991--141044 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
140981 ATACTACAAA
140991 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
141006 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
141023 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
141040 ATATT
1 ATATT
141045 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:141028 original size:34 final size:32
Alignment explanation
Indices: 140989--141056 Score: 100
Period size: 34 Copynumber: 2.1 Consensus size: 32
140979 TTATACTACA
* *
140989 AAATATTTATTATTAATATATTTATAATTGTAAT
1 AAATATTTATTATTAAAATATTAAT-ATTG-AAT
141023 AAATATTTATTATTAAAATATTAATATTGAAT
1 AAATATTTATTATTAAAATATTAATATTGAAT
141055 AA
1 AA
141057 TTTCAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 5 0.16
33 4 0.12
34 23 0.72
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (32 bp):
AAATATTTATTATTAAAATATTAATATTGAAT
Found at i:142899 original size:26 final size:26
Alignment explanation
Indices: 142863--142918 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
142853 CTTAGCTCAA
142863 AATTCACTAGCTTCATTAACAATTAG
1 AATTCACTAGCTTCATTAACAATTAG
142889 AATTCACTAGCTTCATTAACAATTAG
1 AATTCACTAGCTTCATTAACAATTAG
142915 AATT
1 AATT
142919 TGTAATAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (26 bp):
AATTCACTAGCTTCATTAACAATTAG
Found at i:152236 original size:51 final size:51
Alignment explanation
Indices: 152139--152241 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 51
152129 AAAAAAATAT
*
152139 ATTTTTTTATCAGATAAAGGAAGTGTCAGCCATGGTAGGAGCGACACAAAA
1 ATTTTTTTATCAGATAAAGGAAGTGTCAGCCATGGCAGGAGCGACACAAAA
* * * *
152190 ATTTTTTTATCTGATAAATGG-AGTGTCGGCTATGGCATGG-GTGACACAAAA
1 ATTTTTTTATCAGATAAA-GGAAGTGTCAGCCATGGCA-GGAGCGACACAAAA
152241 A
1 A
152242 AATATTTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
51 41 0.91
52 4 0.09
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (51 bp):
ATTTTTTTATCAGATAAAGGAAGTGTCAGCCATGGCAGGAGCGACACAAAA
Found at i:164067 original size:3 final size:3
Alignment explanation
Indices: 164059--164083 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
164049 AGATGATCCC
164059 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
164084 TGCGTTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:170317 original size:22 final size:23
Alignment explanation
Indices: 170260--170319 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 23
170250 GGGATCGAAG
**
170260 TTAAATTGTAATTTTTAAGATAA
1 TTAAATTAAAATTTTTAAGATAA
* * * *
170283 TAAAAGTACAATTTTTAA-ATGA
1 TTAAATTAAAATTTTTAAGATAA
170305 TTAAATTAAAATTTT
1 TTAAATTAAAATTTT
170320 ATCATTTTTA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (23 bp):
TTAAATTAAAATTTTTAAGATAA
Found at i:201803 original size:13 final size:14
Alignment explanation
Indices: 201785--201814 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
201775 AGCATTAGGA
201785 TTGTCCGAAAAT-T
1 TTGTCCGAAAATCT
201798 TTGTCCGAAAATCT
1 TTGTCCGAAAATCT
201812 TTG
1 TTG
201815 ACCAAGAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (14 bp):
TTGTCCGAAAATCT
Found at i:205374 original size:12 final size:12
Alignment explanation
Indices: 205357--205387 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
205347 CCTTCCCCAT
205357 GGACCCATTCCC
1 GGACCCATTCCC
205369 GGACCCATTCCC
1 GGACCCATTCCC
205381 GGACCCA
1 GGACCCA
205388 ACTCTGTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.13
Consensus pattern (12 bp):
GGACCCATTCCC
Found at i:206077 original size:12 final size:13
Alignment explanation
Indices: 206052--206076 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
206042 TTTTAATAAA
206052 AAAATATTTTTTT
1 AAAATATTTTTTT
206065 AAAATATTTTTT
1 AAAATATTTTTT
206077 ATATCAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AAAATATTTTTTT
Done.