Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014950.1 Kokia drynarioides strain JFW-HI SEQ_129993, 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: 198327
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
Found at i:2653 original size:21 final size:20
Alignment explanation
Indices: 2628--2684 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
2618 AAACCAAACC
2628 AAATATATATTATAAAATTAA
1 AAATATATATTATAAAATT-A
* *
2649 AAATATAAAATATAAAATTA
1 AAATATATATTATAAAATTA
*
2669 AAATATATGTTATAAA
1 AAATATATATTATAAA
2685 TTCTTATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
AAATATATATTATAAAATTA
Found at i:2672 original size:6 final size:7
Alignment explanation
Indices: 2628--2675 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
2618 AAACCAAACC
2628 AAATATA
1 AAATATA
* *
2635 TATTATA
1 AAATATA
2642 AAAT-TAA
1 AAATAT-A
2649 AAATATA
1 AAATATA
2656 AAATATA
1 AAATATA
2663 AAAT-TA
1 AAATATA
2669 AAATATA
1 AAATATA
2676 TGTTATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 7 0.21
7 26 0.76
8 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
AAATATA
Found at i:6948 original size:17 final size:15
Alignment explanation
Indices: 6899--6953 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
6889 TTCTTTTAAC
*
6899 CTTCTTTTGTTT-TT
1 CTTCTTTTTTTTCTT
* *
6913 -TTGTTTTTCTTCTT
1 CTTCTTTTTTTTCTT
6927 CTTCTTTTTTTTCTCT
1 CTTCTTTTTTTTCT-T
6943 CATTCTTTTTT
1 C-TTCTTTTTT
6954 CTATCTTCTC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 8 0.25
14 2 0.06
15 11 0.34
16 2 0.06
17 9 0.28
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (15 bp):
CTTCTTTTTTTTCTT
Found at i:17329 original size:10 final size:8
Alignment explanation
Indices: 17294--17337 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
17284 AGAAATAATT
17294 TATA-TTA
1 TATATTTA
17301 TAATATTTA
1 T-ATATTTA
17310 TATATTTA
1 TATATTTA
*
17318 TATATTCA
1 TATATTTA
*
17326 TATATTTT
1 TATATTTA
17334 TATA
1 TATA
17338 ATGATGTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
7 1 0.03
8 27 0.84
9 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (8 bp):
TATATTTA
Found at i:18246 original size:18 final size:17
Alignment explanation
Indices: 18223--18259 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
18213 TTTTTATTAA
*
18223 TTTAAAATTTTAAAAATT
1 TTTAAAAATTT-AAAATT
18241 TTTAAAAATTTAAAATT
1 TTTAAAAATTTAAAATT
18258 TT
1 TT
18260 CATTTTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAAAAATTTAAAATT
Found at i:18478 original size:46 final size:46
Alignment explanation
Indices: 18424--18515 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
18414 TTAGATTTTT
*
18424 TATAAATTTATTTTGGTTTAATCATTATAATTACAATGTGACTATA
1 TATAAATTTATTTTGGTTTAATCATTATAATTACAACGTGACTATA
18470 TATAAATTTATTTTGGTTTAATCATTATAATTACAACGTGACTATA
1 TATAAATTTATTTTGGTTTAATCATTATAATTACAACGTGACTATA
18516 CTTATAACTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.47
Consensus pattern (46 bp):
TATAAATTTATTTTGGTTTAATCATTATAATTACAACGTGACTATA
Found at i:19076 original size:17 final size:18
Alignment explanation
Indices: 19043--19080 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
19033 AAATTTAAAA
19043 TATTTAATCAAATAAATT
1 TATTTAATCAAATAAATT
19061 TATTTAAT-AAGA-AAATT
1 TATTTAATCAA-ATAAATT
19078 TAT
1 TAT
19081 CATACTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
TATTTAATCAAATAAATT
Found at i:28584 original size:18 final size:17
Alignment explanation
Indices: 28554--28587 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28544 GAGAAAAATA
28554 AAAATATTTTTATTTTC
1 AAAATATTTTTATTTTC
*
28571 AAAATTTTTGTTATTTT
1 AAAATATTT-TTATTTT
28588 ATAGGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
AAAATATTTTTATTTTC
Found at i:29331 original size:9 final size:9
Alignment explanation
Indices: 29270--29368 Score: 54
Period size: 9 Copynumber: 10.0 Consensus size: 9
29260 ATAGCTACAC
29270 TAAAAAATA
1 TAAAAAATA
*
29279 TAAATAAATG
1 TAAA-AAATA
* *
29289 GAAATAAATT
1 TAAA-AAATA
29299 TAAAAAATTCA
1 TAAAAAA-T-A
29310 TAAAATAAATA
1 T-AAA-AAATA
*
29321 TAAAAACTA
1 TAAAAAATA
29330 TAAAAAATA
1 TAAAAAATA
*
29339 TATATAAATTTA
1 TA-A-AAA-ATA
*
29351 TAAAAAATT
1 TAAAAAATA
*
29360 TATAAAATA
1 TAAAAAATA
29369 AAATTTACAA
Statistics
Matches: 70, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
9 29 0.41
10 23 0.33
11 7 0.10
12 8 0.11
13 3 0.04
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (9 bp):
TAAAAAATA
Found at i:29558 original size:21 final size:20
Alignment explanation
Indices: 29525--29578 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
29515 TTACTTGAAA
*
29525 TTTA-AATACTTTTTTTAATT
1 TTTATAATA-TTTTTTCAATT
29545 TTTATAATA-TTTTTCAATT
1 TTTATAATATTTTTTCAATT
29564 TTTAT-ATATTATTTT
1 TTTATAATATT-TTTT
29579 GATTTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 3 0.10
19 15 0.50
20 8 0.27
21 4 0.13
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATAATATTTTTTCAATT
Found at i:29583 original size:19 final size:19
Alignment explanation
Indices: 29535--29585 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
29525 TTTAAATACT
29535 TTTTTTAATTTTTATAATA
1 TTTTTTAATTTTTATAATA
*
29554 TTTTTCAATTTTTAT-ATA
1 TTTTTTAATTTTTATAATA
*
29572 TTATTTTGATTTTT
1 TT-TTTTAATTTTT
29586 TAAAATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTTAATTTTTATAATA
Found at i:29635 original size:20 final size:18
Alignment explanation
Indices: 29599--29634 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
29589 AATTTATAAT
29599 TATATATTTTAAATTTTG
1 TATATATTTTAAATTTTG
29617 TATATATTTTCAAATTTT
1 TATATATTTT-AAATTTT
29635 TAAAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (18 bp):
TATATATTTTAAATTTTG
Found at i:32050 original size:11 final size:10
Alignment explanation
Indices: 32024--32049 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
32014 AAAGAAGAGG
32024 AAAAAAGAAA
1 AAAAAAGAAA
32034 AAAAAAGAAA
1 AAAAAAGAAA
32044 AAAAAA
1 AAAAAA
32050 AAGGAAGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:34047 original size:6 final size:6
Alignment explanation
Indices: 34036--34071 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
34026 AATAATACTA
*
34036 TAATAG TAATAG TAATAA TAATAG TAAATAG TAATA
1 TAATAG TAATAG TAATAG TAATAG T-AATAG TAATA
34072 AATCAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (6 bp):
TAATAG
Found at i:34103 original size:29 final size:29
Alignment explanation
Indices: 34070--34127 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
34060 TAAATAGTAA
*
34070 TAAATCAAAATTGGTTTTGGAATAGCGGC
1 TAAATCAAAATTGGTTTAGGAATAGCGGC
34099 TAAATCAAAATTGGTTTAGGAATAGCGGC
1 TAAATCAAAATTGGTTTAGGAATAGCGGC
34128 CTTCACACGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.29
Consensus pattern (29 bp):
TAAATCAAAATTGGTTTAGGAATAGCGGC
Found at i:37113 original size:18 final size:19
Alignment explanation
Indices: 37074--37114 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
37064 TAGAAGAAGC
* *
37074 ATTTTTATAATTAATTATA
1 ATTTTTATAACTAATTACA
37093 ATTTTTATAACTAA-TACA
1 ATTTTTATAACTAATTACA
37111 ATTT
1 ATTT
37115 AATAATAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTTATAACTAATTACA
Found at i:39663 original size:18 final size:19
Alignment explanation
Indices: 39626--39671 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
39616 AGCTCCTTTA
39626 ATTTTGTTTTTATATATTTT
1 ATTTTG-TTTTATATATTTT
* *
39646 TTTTTGTTTTATGT-TTTT
1 ATTTTGTTTTATATATTTT
39664 ATTTTGTT
1 ATTTTGTT
39672 GAATTGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 11 0.48
19 7 0.30
20 5 0.22
ACGTcount: A:0.13, C:0.00, G:0.09, T:0.78
Consensus pattern (19 bp):
ATTTTGTTTTATATATTTT
Found at i:58973 original size:15 final size:16
Alignment explanation
Indices: 58943--58981 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
58933 CTTGTTGGTT
58943 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
58960 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
58975 ATAATTT
1 ATAATTT
58982 TTAAAGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:62945 original size:29 final size:29
Alignment explanation
Indices: 62904--62965 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
62894 TGGATTGCCT
* *
62904 GCCACTTTAGCTTGCACTTCAGACTGTCC
1 GCCACTTTAGCTTACACTTCAGACGGTCC
* **
62933 GCCACTTTGGCTTACACTTTGGACGGTCC
1 GCCACTTTAGCTTACACTTCAGACGGTCC
62962 GCCA
1 GCCA
62966 AATAATTTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.16, C:0.34, G:0.21, T:0.29
Consensus pattern (29 bp):
GCCACTTTAGCTTACACTTCAGACGGTCC
Found at i:66175 original size:87 final size:87
Alignment explanation
Indices: 66051--66286 Score: 418
Period size: 87 Copynumber: 2.7 Consensus size: 87
66041 TTTTTTTTAC
* * * *
66051 TCTTGATGAATTCATAGCCCAGATTTTGGGTGGTCCTATTGAGAAGGACTTGATGAATTCACCGA
1 TCTTAATGAGTTCATATCCCAAATTTTGGGTGGTCCTATTGAGAAGGACTTGATGAATTCACCGA
66116 CTTGAGAGGTTGAATTTATTAT
66 CTTGAGAGGTTGAATTTATTAT
66138 TCTTAATGAGTTCATATCCCAAATTTTGGGTGGTCCTATTGAGAAGGACTTGATGAATTCACCGA
1 TCTTAATGAGTTCATATCCCAAATTTTGGGTGGTCCTATTGAGAAGGACTTGATGAATTCACCGA
66203 CTTGAGAGGTTGAATTTATTAT
66 CTTGAGAGGTTGAATTTATTAT
**
66225 TCTTAATGAGTTCATATCCCAAATTTTGGGTGGTCCTATTGAGGCGGACTTGATGAATTCAC
1 TCTTAATGAGTTCATATCCCAAATTTTGGGTGGTCCTATTGAGAAGGACTTGATGAATTCAC
66287 TGAACTTAAA
Statistics
Matches: 143, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 143 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (87 bp):
TCTTAATGAGTTCATATCCCAAATTTTGGGTGGTCCTATTGAGAAGGACTTGATGAATTCACCGA
CTTGAGAGGTTGAATTTATTAT
Found at i:111179 original size:22 final size:22
Alignment explanation
Indices: 111137--111179 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
111127 ATAATATCAC
*
111137 AATAATATAAAAGCATGCAAAT
1 AATAATATAAAAGCATACAAAT
*
111159 AATAATAATAATA-CATACAAA
1 AATAAT-ATAAAAGCATACAAA
111180 AGCATGCGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.63, C:0.09, G:0.05, T:0.23
Consensus pattern (22 bp):
AATAATATAAAAGCATACAAAT
Found at i:111241 original size:28 final size:30
Alignment explanation
Indices: 111210--111295 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 30
111200 TGGCAAATGC
* *
111210 AAAGCAAAACATGTAGATGCAC-T-TATGT
1 AAAGCAAAACATGTAGACGCACATACATGT
111238 AAAGCAAAACATGTAGACGCACATACATGT
1 AAAGCAAAACATGTAGACGCACATACATGT
*
111268 AAAGCAAAACATGTAGACGCACGTACAT
1 AAAGCAAAACATGTAGACGCACATACAT
111296 AAACATGTGC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
28 21 0.40
29 1 0.02
30 31 0.58
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (30 bp):
AAAGCAAAACATGTAGACGCACATACATGT
Found at i:111251 original size:14 final size:14
Alignment explanation
Indices: 111234--111282 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
111224 AGATGCACTT
111234 ATGTAAAGCAAAAC
1 ATGTAAAGCAAAAC
* *
111248 ATGTAGACGCACATAC
1 ATGTA-AAGCA-AAAC
111264 ATGTAAAGCAAAAC
1 ATGTAAAGCAAAAC
111278 ATGTA
1 ATGTA
111283 GACGCACGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 13 0.45
15 8 0.28
16 8 0.28
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.18
Consensus pattern (14 bp):
ATGTAAAGCAAAAC
Found at i:111267 original size:16 final size:16
Alignment explanation
Indices: 111246--111295 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
111236 GTAAAGCAAA
111246 ACATGTAGACGCACAT
1 ACATGTAGACGCACAT
* *
111262 ACATGTA-AAGCA-AA
1 ACATGTAGACGCACAT
*
111276 ACATGTAGACGCACGT
1 ACATGTAGACGCACAT
111292 ACAT
1 ACAT
111296 AAACATGTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 8 0.30
15 8 0.30
16 11 0.41
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (16 bp):
ACATGTAGACGCACAT
Found at i:111388 original size:56 final size:56
Alignment explanation
Indices: 111328--111446 Score: 229
Period size: 56 Copynumber: 2.1 Consensus size: 56
111318 TAGGAAAGGG
111328 TAAAATTAAATTGTAATTTTTACAATAGTAAAAATATTATTTTTAAAAGATTAAAT
1 TAAAATTAAATTGTAATTTTTACAATAGTAAAAATATTATTTTTAAAAGATTAAAT
111384 TAAAATTAAATTGTAATTTTTACAATAGTAAAAATATTATTTTTAAAAGATTAAAT
1 TAAAATTAAATTGTAATTTTTACAATAGTAAAAATATTATTTTTAAAAGATTAAAT
*
111440 CAAAATT
1 TAAAATT
111447 TATCATTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (56 bp):
TAAAATTAAATTGTAATTTTTACAATAGTAAAAATATTATTTTTAAAAGATTAAAT
Found at i:112881 original size:52 final size:52
Alignment explanation
Indices: 112801--112939 Score: 181
Period size: 52 Copynumber: 2.7 Consensus size: 52
112791 ATGAAAAGGG
* * *
112801 TCCGATGACTAATTGTCATCGTGAGTACATGAATTATTCATGGATTATAAGA
1 TCCGATGTCTAAGTGTCATCGTGAGTACATGAATTATTCACGGATTATAAGA
* * ** *
112853 TTCGATGTCTAAGTGTCATCTTGAGTACATGAATCCTTCACGGATTATAAGG
1 TCCGATGTCTAAGTGTCATCGTGAGTACATGAATTATTCACGGATTATAAGA
*
112905 TCCGATGAT-TAAGTGTCATCGTGAGTATATGAATT
1 TCCGATG-TCTAAGTGTCATCGTGAGTACATGAATT
112940 CCTTTACGAA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
52 73 0.99
53 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.35
Consensus pattern (52 bp):
TCCGATGTCTAAGTGTCATCGTGAGTACATGAATTATTCACGGATTATAAGA
Found at i:113035 original size:60 final size:61
Alignment explanation
Indices: 112933--113051 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 61
112923 TCGTGAGTAT
* *
112933 ATGAATTCCTTTACGAAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAA
1 ATGAATTCCATTACGAAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATCAAATGAA
* ** * *
112994 ATGAATTCCATTACGGATTAAG-GGTCCGATGACTTTGTGTCATCGTGAGTATCAAATG
1 ATGAATTCCATTACGAAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATCAAATG
113052 CGAGTTGAGG
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 33 0.65
61 18 0.35
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (61 bp):
ATGAATTCCATTACGAAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATCAAATGAA
Found at i:113592 original size:21 final size:22
Alignment explanation
Indices: 113565--113624 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
113555 TAGATGCATG
*
113565 ACATGTATCGGTAGAAATTA-T
1 ACATGTATCGGTAGAAATTAGC
* *
113586 ACTTGTATCGGTA-AAACTAGC
1 ACATGTATCGGTAGAAATTAGC
*
113607 ACAGGTATCGGTAGAAAT
1 ACATGTATCGGTAGAAAT
113625 CTGCATCGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 5 0.16
21 23 0.74
22 3 0.10
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (22 bp):
ACATGTATCGGTAGAAATTAGC
Found at i:119248 original size:18 final size:16
Alignment explanation
Indices: 119209--119238 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
119199 TTTATAATAC
119209 TTTATATTATATTATT
1 TTTATATTATATTATT
119225 TTTATA-TATATTAT
1 TTTATATTATATTAT
119239 GTAATTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATATTATATTATT
Found at i:119406 original size:23 final size:23
Alignment explanation
Indices: 119340--119407 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 23
119330 TTTCAATAAA
* *
119340 TAAAAAATATAAAACTATTAAATAT
1 TAAAAAATA-AAAA-TAATATATAT
*
119365 TAATAAAAT-AAAATAAATATATTT
1 TAA-AAAATAAAAAT-AATATATAT
119389 TAAAAAATAAAAATAATAT
1 TAAAAAATAAAAATAATAT
119408 GGATGGACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 11 0.30
24 18 0.49
25 3 0.08
26 5 0.14
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAAAAATAAAAATAATATATAT
Found at i:124391 original size:26 final size:26
Alignment explanation
Indices: 124356--124409 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
124346 ACATTTAATT
*
124356 AAACTTATATGTA-AATAAATAATTAA
1 AAACTGATATGTACAATAAATAA-TAA
* *
124382 AAACTGATATTTACATTAAATAATAA
1 AAACTGATATGTACAATAAATAATAA
124408 AA
1 AA
124410 TGTACACTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (26 bp):
AAACTGATATGTACAATAAATAATAA
Found at i:126828 original size:27 final size:26
Alignment explanation
Indices: 126765--126835 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 26
126755 TTAAAATTTG
*
126765 AAAAATAT-AAATT-TTAAAAAAATT
1 AAAAATATAAAATTATTTAAAAAATT
* *
126789 AAAAACCATTAAAATTATTTAAAAAGTAT
1 AAAAA-TA-TAAAATTATTTAAAAAAT-T
*
126818 AAAAATATAAAAATATTT
1 AAAAATATAAAATTATTT
126836 TTAATATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 5 0.14
25 1 0.03
26 1 0.03
27 15 0.41
28 9 0.24
29 6 0.16
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (26 bp):
AAAAATATAAAATTATTTAAAAAATT
Found at i:128359 original size:22 final size:22
Alignment explanation
Indices: 128334--128392 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
128324 AAATTGAAAT
** *
128334 TAAATTATAATTTTTGTAATAG
1 TAAATTATAATTTTTAAAAAAG
* *
128356 TAAAAATATAATTTTTAAAAAAT
1 T-AAATTATAATTTTTAAAAAAG
128379 TAAATTATAATTTT
1 TAAATTATAATTTT
128393 ATTATTTTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (22 bp):
TAAATTATAATTTTTAAAAAAG
Found at i:133202 original size:43 final size:43
Alignment explanation
Indices: 133154--133262 Score: 218
Period size: 43 Copynumber: 2.5 Consensus size: 43
133144 CTGAACTTAG
133154 TAAAAAACTCCACAACTAATTTTATTATCTTTTTGTTATTATT
1 TAAAAAACTCCACAACTAATTTTATTATCTTTTTGTTATTATT
133197 TAAAAAACTCCACAACTAATTTTATTATCTTTTTGTTATTATT
1 TAAAAAACTCCACAACTAATTTTATTATCTTTTTGTTATTATT
133240 TAAAAAACTCCACAACTAATTTT
1 TAAAAAACTCCACAACTAATTTT
133263 TTTTTTATGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.45
Consensus pattern (43 bp):
TAAAAAACTCCACAACTAATTTTATTATCTTTTTGTTATTATT
Found at i:137120 original size:28 final size:29
Alignment explanation
Indices: 137080--137136 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
137070 AATAATAATA
*
137080 TTTATGCATTAATTTATAATGGTTTATTT
1 TTTATGCAATAATTTATAATGGTTTATTT
*
137109 TTTATG-AATAATTTATAATGTTTTATTT
1 TTTATGCAATAATTTATAATGGTTTATTT
137137 ATAGTTATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.60
Consensus pattern (29 bp):
TTTATGCAATAATTTATAATGGTTTATTT
Found at i:137823 original size:16 final size:16
Alignment explanation
Indices: 137802--137836 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
137792 ATGGAATAAA
137802 TTTTAA-AAGAAAATAT
1 TTTTAACAA-AAAATAT
137818 TTTTAACAAAAAATAT
1 TTTTAACAAAAAATAT
137834 TTT
1 TTT
137837 ATTTCACCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (16 bp):
TTTTAACAAAAAATAT
Found at i:138320 original size:2 final size:2
Alignment explanation
Indices: 138315--138339 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
138305 ACACACACGC
138315 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 A
138340 GATTTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:140618 original size:30 final size:30
Alignment explanation
Indices: 140584--140670 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
140574 GTTATAAAAT
* **
140584 AATTATTAAACTATTAAAATTTTTTATTTG
1 AATTATTAAATTATTAAAATTTTTTATTCA
*
140614 AATTATTGAATTAATT-AAATTTTTTATTCA
1 AATTATTAAATT-ATTAAAATTTTTTATTCA
* *
140644 AATTA-TAAATTATTAAAGTTTATTATT
1 AATTATTAAATTATTAAAATTTTTTATT
140671 ATTATTATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 3 0.06
29 15 0.31
30 27 0.56
31 3 0.06
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (30 bp):
AATTATTAAATTATTAAAATTTTTTATTCA
Found at i:143302 original size:6 final size:6
Alignment explanation
Indices: 143291--143329 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
143281 GAAAGGCTTA
143291 ATTTCT ATTTCT ATTTCT ATTTCT ATTTCT ATTTCT ATT
1 ATTTCT ATTTCT ATTTCT ATTTCT ATTTCT ATTTCT ATT
143330 GCTGATAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTCT
Found at i:146659 original size:109 final size:109
Alignment explanation
Indices: 146468--146687 Score: 440
Period size: 109 Copynumber: 2.0 Consensus size: 109
146458 TATATCCCCC
146468 AGCAACATTGCTTGTTTTGCATACATCATGAGGCACTTATGTTGCTGAATGTTGTTTATGGATGA
1 AGCAACATTGCTTGTTTTGCATACATCATGAGGCACTTATGTTGCTGAATGTTGTTTATGGATGA
146533 TAACGTGAAGCAGGCTATTGAACACACTCACACAAGCACTGCAG
66 TAACGTGAAGCAGGCTATTGAACACACTCACACAAGCACTGCAG
146577 AGCAACATTGCTTGTTTTGCATACATCATGAGGCACTTATGTTGCTGAATGTTGTTTATGGATGA
1 AGCAACATTGCTTGTTTTGCATACATCATGAGGCACTTATGTTGCTGAATGTTGTTTATGGATGA
146642 TAACGTGAAGCAGGCTATTGAACACACTCACACAAGCACTGCAG
66 TAACGTGAAGCAGGCTATTGAACACACTCACACAAGCACTGCAG
146686 AG
1 AG
146688 AACGGGTTTG
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 111 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (109 bp):
AGCAACATTGCTTGTTTTGCATACATCATGAGGCACTTATGTTGCTGAATGTTGTTTATGGATGA
TAACGTGAAGCAGGCTATTGAACACACTCACACAAGCACTGCAG
Found at i:149601 original size:48 final size:48
Alignment explanation
Indices: 149542--149648 Score: 187
Period size: 48 Copynumber: 2.2 Consensus size: 48
149532 GCATATTGAC
149542 ATCAAATGTAAGAGAGAGAAAGCCACAAAGAGTCCAAAGCAACAAGAT
1 ATCAAATGTAAGAGAGAGAAAGCCACAAAGAGTCCAAAGCAACAAGAT
*
149590 ATCAAATGTAAGAGAGAGAAAGCCACAAAGAGTCCAAAGCATCAAGAT
1 ATCAAATGTAAGAGAGAGAAAGCCACAAAGAGTCCAAAGCAACAAGAT
* *
149638 ATTAAAAGTAA
1 ATCAAATGTAA
149649 CTGTATCATA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.52, C:0.15, G:0.20, T:0.13
Consensus pattern (48 bp):
ATCAAATGTAAGAGAGAGAAAGCCACAAAGAGTCCAAAGCAACAAGAT
Found at i:153007 original size:59 final size:59
Alignment explanation
Indices: 152915--153026 Score: 206
Period size: 59 Copynumber: 1.9 Consensus size: 59
152905 TGATACTAAC
*
152915 ACTCTTGTTTGCACTCATTGAAAATATCTTAAAGGTTTGATTATTTAATTAAACTTGAA
1 ACTCTTGTTCGCACTCATTGAAAATATCTTAAAGGTTTGATTATTTAATTAAACTTGAA
*
152974 ACTCTTGTTCGCACTCATTGAAAATATTTTAAAGGTTTGATTATTTAATTAAA
1 ACTCTTGTTCGCACTCATTGAAAATATCTTAAAGGTTTGATTATTTAATTAAA
153027 TTCGAAAGCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (59 bp):
ACTCTTGTTCGCACTCATTGAAAATATCTTAAAGGTTTGATTATTTAATTAAACTTGAA
Found at i:153201 original size:21 final size:23
Alignment explanation
Indices: 153157--153204 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
153147 AAGTTTACGA
* *
153157 TATATGAATAATATAATTTATAT
1 TATATGAAAAATATAATATATAT
153180 TATATGAAAAAT-TAA-ATATAT
1 TATATGAAAAATATAATATATAT
153201 TATA
1 TATA
153205 ATGTAAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 3 0.13
23 11 0.48
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TATATGAAAAATATAATATATAT
Found at i:164599 original size:31 final size:32
Alignment explanation
Indices: 164556--164642 Score: 108
Period size: 31 Copynumber: 2.8 Consensus size: 32
164546 ACAAAAAATT
*
164556 AAATGGAAGGCTAAAATAATATT-TTCT-AAAA
1 AAATGGAGGGCTAAAATAAT-TTATTCTAAAAA
*
164587 AAATGGAGGGCTAAAATGATTTATTCTAAAAAA
1 AAATGGAGGGCTAAAATAATTTATTCT-AAAAA
*
164620 AAATGGAGGGCT-AAATAAGTTAT
1 AAATGGAGGGCTAAAATAATTTAT
164643 CATGTCAGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 2 0.04
31 22 0.45
32 9 0.18
33 16 0.33
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (32 bp):
AAATGGAGGGCTAAAATAATTTATTCTAAAAA
Found at i:166495 original size:15 final size:15
Alignment explanation
Indices: 166471--166507 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
166461 ATTTTTAAGT
*
166471 TTATAATATTTTTTA
1 TTATATTATTTTTTA
166486 TTATATTA-TTTTTA
1 TTATATTATTTTTTA
166500 -TATATTAT
1 TTATATTAT
166508 GTAATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 7 0.35
14 6 0.30
15 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATATTATTTTTTA
Found at i:169436 original size:118 final size:118
Alignment explanation
Indices: 169279--169513 Score: 461
Period size: 118 Copynumber: 2.0 Consensus size: 118
169269 TGTTGGTAGA
*
169279 ATGTTTGGAGGTGATGCCTAGAGTGACTTATATGAATATATAGGAGATTAGAAGGGTTATGGGTA
1 ATGTTTGGAGGTGATGCCTAGAGTGACTCATATGAATATATAGGAGATTAGAAGGGTTATGGGTA
169344 AGGTCGGATCAGGTTGGATTGAATTGGGTTTAAATATGATATTAATATATTTT
66 AGGTCGGATCAGGTTGGATTGAATTGGGTTTAAATATGATATTAATATATTTT
169397 ATGTTTGGAGGTGATGCCTAGAGTGACTCATATGAATATATAGGAGATTAGAAGGGTTATGGGTA
1 ATGTTTGGAGGTGATGCCTAGAGTGACTCATATGAATATATAGGAGATTAGAAGGGTTATGGGTA
169462 AGGTCGGATCAGGTTGGATTGAATTGGGTTTAAATATGATATTAATATATTT
66 AGGTCGGATCAGGTTGGATTGAATTGGGTTTAAATATGATATTAATATATTT
169514 GTCCAAATTC
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 116 1.00
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.36
Consensus pattern (118 bp):
ATGTTTGGAGGTGATGCCTAGAGTGACTCATATGAATATATAGGAGATTAGAAGGGTTATGGGTA
AGGTCGGATCAGGTTGGATTGAATTGGGTTTAAATATGATATTAATATATTTT
Found at i:169626 original size:4 final size:4
Alignment explanation
Indices: 169614--169668 Score: 65
Period size: 4 Copynumber: 13.8 Consensus size: 4
169604 TTCGTCTATA
* * * *
169614 TTAT TTAT ATAT ATAT ATAT ATAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
*
169662 ATAT TTA
1 TTAT TTA
169669 ATAATTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (4 bp):
TTAT
Found at i:169636 original size:12 final size:12
Alignment explanation
Indices: 169610--169679 Score: 67
Period size: 12 Copynumber: 6.2 Consensus size: 12
169600 TGGGTTCGTC
169610 TATAT-TATTTA
1 TATATATATTTA
*
169621 TATATATATATA
1 TATATATATTTA
*
169633 TATATTTATTTA
1 TATATATATTTA
* *
169645 TTTATTTATTTA
1 TATATATATTTA
*
169657 TTTATATATTTA
1 TATATATATTTA
169669 -ATA-AT-TTTA
1 TATATATATTTA
169678 TA
1 TA
169680 CATTTTTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
9 4 0.08
10 3 0.06
11 7 0.14
12 37 0.73
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATATATATTTA
Found at i:177192 original size:2 final size:2
Alignment explanation
Indices: 177185--177214 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
177175 TCTATCTATC
177185 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
177215 GGTCCTTTGA
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:177563 original size:20 final size:20
Alignment explanation
Indices: 177540--177588 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 20
177530 TAATTTTGGA
*
177540 CTATTGTCCATAGATTTGAC
1 CTATTGTACATAGATTTGAC
177560 CTATTGTGTACATAGATTTGAC
1 CTA-T-TGTACATAGATTTGAC
177582 CTATTGT
1 CTATTGT
177589 GTATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 2 0.08
22 18 0.69
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (20 bp):
CTATTGTACATAGATTTGAC
Found at i:177576 original size:22 final size:22
Alignment explanation
Indices: 177548--177591 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
177538 GACTATTGTC
177548 CATAGATTTGACCTATTGTGTA
1 CATAGATTTGACCTATTGTGTA
177570 CATAGATTTGACCTATTGTGTA
1 CATAGATTTGACCTATTGTGTA
177592 TATATATACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (22 bp):
CATAGATTTGACCTATTGTGTA
Found at i:178073 original size:7 final size:6
Alignment explanation
Indices: 178062--178113 Score: 52
Period size: 6 Copynumber: 8.2 Consensus size: 6
178052 ATTTTTAAGA
*
178062 ATTTTT ATTTTT ACTTTTT ATTTTT -TTTTGAT AATTTT ATTTTT ACTTTTT
1 ATTTTT ATTTTT A-TTTTT ATTTTT ATTTT--T ATTTTT ATTTTT A-TTTTT
178113 A
1 A
178114 ATTCATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
5 4 0.10
6 19 0.49
7 13 0.33
8 3 0.08
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (6 bp):
ATTTTT
Found at i:178115 original size:19 final size:18
Alignment explanation
Indices: 178062--178130 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 18
178052 ATTTTTAAGA
*
178062 ATTTTTATTTTTACTTTTT
1 ATTTTTATTTTTA-ATTTT
178081 ATTTTT-TTTTGATAATTTT
1 ATTTTTATTTT--TAATTTT
178100 ATTTTTACTTTTTAATTCATT
1 ATTTTTA-TTTTTAATT--TT
*
178121 TTTTTTATTT
1 ATTTTTATTT
178131 ACACAAACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
18 4 0.10
19 21 0.50
20 5 0.12
21 12 0.29
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.75
Consensus pattern (18 bp):
ATTTTTATTTTTAATTTT
Found at i:180628 original size:16 final size:14
Alignment explanation
Indices: 180607--180640 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
180597 GACACGTGTC
*
180607 TTTTTTTAAATATT
1 TTTTTTTTAATATT
180621 TATTTTTTTAATATT
1 T-TTTTTTTAATATT
180636 TTTTT
1 TTTTT
180641 ACGCCACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTTTTAATATT
Found at i:183496 original size:16 final size:16
Alignment explanation
Indices: 183472--183508 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
183462 CATGGTGTTC
183472 TTTTAAAAATGGTAAA
1 TTTTAAAAATGGTAAA
*
183488 TTTTGAAAATGGTAAA
1 TTTTAAAAATGGTAAA
*
183504 ATTTA
1 TTTTA
183509 CAAGTTGTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.41
Consensus pattern (16 bp):
TTTTAAAAATGGTAAA
Found at i:183711 original size:2 final size:2
Alignment explanation
Indices: 183704--183732 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
183694 ATTTTACATA
183704 AT 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 AT A
183733 AAGAGAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.