Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004317.1 Kokia drynarioides strain JFW-HI SEQ_117633, 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: 98817
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Warning! 62 characters in sequence are not A, C, G, or T
Found at i:1223 original size:31 final size:31
Alignment explanation
Indices: 1161--1243 Score: 105
Period size: 31 Copynumber: 2.6 Consensus size: 31
1151 CTTAATATAA
1161 TATTTGGTACTTGAATATTTGACAATTTTTTTT
1 TATTTGGTACTT-AA-ATTTGACAATTTTTTTT
*
1194 TAATTTGGTACCTAAATTTGAC-ATTTTTTTT
1 T-ATTTGGTACTTAAATTTGACAATTTTTTTT
*
1225 TATGTTGGTAATTAAATTT
1 TAT-TTGGTACTTAAATTT
1244 TGTGAGGGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
30 2 0.04
31 23 0.51
32 7 0.16
33 3 0.07
34 10 0.22
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (31 bp):
TATTTGGTACTTAAATTTGACAATTTTTTTT
Found at i:18591 original size:17 final size:16
Alignment explanation
Indices: 18549--18591 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
18539 AATTCAATTT
*
18549 TAATATAAATATTCAA
1 TAATATAAACATTCAA
*
18565 TAAGATTAAACATTTCAA
1 TAATA-TAAACA-TTCAA
18583 TAATATAAA
1 TAATATAAA
18592 TAGTACAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 9 0.41
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (16 bp):
TAATATAAACATTCAA
Found at i:37418 original size:17 final size:17
Alignment explanation
Indices: 37389--37447 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 17
37379 CAGCAGAATA
* *
37389 TAAATTTAATTTAAAAT
1 TAAATTTATTTTAAATT
*
37406 TAAGTTTATTTTAAATT
1 TAAATTTATTTTAAATT
*
37423 TAAATTTATTATAAATT
1 TAAATTTATTTTAAATT
37440 TAAATTTA
1 TAAATTTA
37448 AATTTATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TAAATTTATTTTAAATT
Found at i:37424 original size:6 final size:6
Alignment explanation
Indices: 37389--37453 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
37379 CAGCAGAATA
* * *
37389 TAAATT T-AATT TAAAAT TAAGTT T-ATTT TAAATT TAAATT T--ATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
37433 ATAAATT TAAATT TAAATT TA
1 -TAAATT TAAATT TAAATT TA
37454 TTTAAATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
4 3 0.06
5 10 0.20
6 33 0.67
7 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:37441 original size:23 final size:22
Alignment explanation
Indices: 37389--37460 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 22
37379 CAGCAGAATA
*
37389 TAAATTT-AATTTAAAATTAAGTT
1 TAAATTTAAATTT-AAATTTA-TT
*
37412 T-ATTTTAAATTTAAATTTATT
1 TAAATTTAAATTTAAATTTATT
37433 ATAAATTTAAATTTAAATTTATT
1 -TAAATTTAAATTTAAATTTATT
37456 TAAAT
1 TAAAT
37461 AAAGTCCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.05
22 16 0.37
23 25 0.58
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (22 bp):
TAAATTTAAATTTAAATTTATT
Found at i:37478 original size:14 final size:14
Alignment explanation
Indices: 37461--37490 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
37451 TTATTTAAAT
37461 AAAGTCCAAATACA
1 AAAGTCCAAATACA
*
37475 AAAGTCCAATTACA
1 AAAGTCCAAATACA
37489 AA
1 AA
37491 TTGGACCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.20, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAGTCCAAATACA
Found at i:38140 original size:3 final size:3
Alignment explanation
Indices: 38127--38164 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
38117 AAATATAGTC
*
38127 ATA ATTA ATA ATA ATA ATA TTA ATA ATA ATA ATA ATA A
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38165 AAAGAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:39212 original size:29 final size:30
Alignment explanation
Indices: 39156--39259 Score: 108
Period size: 29 Copynumber: 3.5 Consensus size: 30
39146 CTTGAAGGTT
* * *
39156 CCTAAACTGTCCAAAAATAATATTTTGACC
1 CCTAAACTTTCCAAAAATTACATTTTGACC
39186 CCTAAACTTTCCAAAAATTACA-TTTGACC
1 CCTAAACTTTCCAAAAATTACATTTTGACC
* *
39215 CCCAAACTTTCC-AAAATTAC-TTCTTTA-C
1 CCTAAACTTTCCAAAAATTACATT-TTGACC
*
39243 CCTCGAACTTTCCAAAA
1 CCT-AAACTTTCCAAAA
39260 TTCTATTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
28 12 0.19
29 29 0.46
30 22 0.35
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.31
Consensus pattern (30 bp):
CCTAAACTTTCCAAAAATTACATTTTGACC
Found at i:39260 original size:29 final size:30
Alignment explanation
Indices: 39190--39417 Score: 161
Period size: 29 Copynumber: 7.7 Consensus size: 30
39180 TTGACCCCTA
* * *
39190 AACTTTCCAAAAATTACA-TTTGACCCCCA
1 AACTTTCCAAAAATTACATTTTTACCCTCG
39219 AACTTTCC-AAAATTAC-TTCTTTACCCTCG
1 AACTTTCCAAAAATTACATT-TTTACCCTCG
*
39248 AACTTTCC-AAAATT-CTATTTTTAACCTCG
1 AACTTTCCAAAAATTAC-ATTTTTACCCTCG
* * * * *
39277 AATTTTCTAAAATTTACATTTTTACCTTCA
1 AACTTTCCAAAAATTACATTTTTACCCTCG
* * *
39307 AAC-TTCCTAAAATTCCATTTTTTACCAT-G
1 AACTTTCCAAAAATTACA-TTTTTACCCTCG
* *
39336 AATTTTCCAAAAATTACATTTTTACCC-CC
1 AACTTTCCAAAAATTACATTTTTACCCTCG
*** *
39365 AAAAATCTAAAAATTTA-ATTTTTAACCC-CG
1 AACTTTCCAAAAA-TTACATTTTT-ACCCTCG
*
39395 AACCTTCCAAAAATTACCATTTT
1 AACTTTCCAAAAATTA-CATTTT
39418 ACTCCAGATG
Statistics
Matches: 155, Mismatches: 31, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
28 10 0.06
29 82 0.53
30 57 0.37
31 6 0.04
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (30 bp):
AACTTTCCAAAAATTACATTTTTACCCTCG
Found at i:39319 original size:59 final size:58
Alignment explanation
Indices: 39222--39367 Score: 172
Period size: 59 Copynumber: 2.5 Consensus size: 58
39212 ACCCCCAAAC
* *
39222 TTTCCAAAATTAC-TTCTTTACCCTCGAACTTTCCAAAATTCTATTTTTAACC-TCGAAT
1 TTTCCAAAATTACATT-TTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCAT-GAAT
* * *
39280 TTTCTAAAATTTACATTTTTACCTTCAAAC-TTCCTAAAATTCCATTTTTTACCATGAAT
1 TTTCCAAAA-TTACATTTTTACCCTCAAACTTTCC-AAAATTCCATTTTTAACCATGAAT
*
39339 TTTCCAAAAATTACATTTTTACCCCCAAA
1 TTTCC-AAAATTACATTTTTACCCTCAAA
39368 AATCTAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
58 12 0.16
59 56 0.75
60 7 0.09
ACGTcount: A:0.32, C:0.24, G:0.02, T:0.42
Consensus pattern (58 bp):
TTTCCAAAATTACATTTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCATGAAT
Found at i:39378 original size:59 final size:58
Alignment explanation
Indices: 39256--39417 Score: 155
Period size: 59 Copynumber: 2.7 Consensus size: 58
39246 CGAACTTTCC
* * * ** **
39256 AAAATTCTATTTTTAACCTCGAATTTTCTAAAATTTACATTTTTACCTTCAAACTTCCT
1 AAAATTCAATTTTTAACCT-GAATTTTCCAAAAATTACATTTTTACCCCCAAAAATCCT
* *
39315 AAAATTCCATTTTTTACCATGAATTTTCCAAAAATTACATTTTTACCCCCAAAAAT-CT
1 AAAATTCAATTTTTAACC-TGAATTTTCCAAAAATTACATTTTTACCCCCAAAAATCCT
* * **
39373 AAAAATTTAATTTTTAACCCCGAACCTTCCAAAAATTACCATTTT
1 -AAAATTCAATTTTTAA-CCTGAATTTTCCAAAAATTA-CATTTT
39418 ACTCCAGATG
Statistics
Matches: 85, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
58 2 0.02
59 74 0.87
60 9 0.11
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (58 bp):
AAAATTCAATTTTTAACCTGAATTTTCCAAAAATTACATTTTTACCCCCAAAAATCCT
Found at i:39444 original size:58 final size:58
Alignment explanation
Indices: 39340--39550 Score: 200
Period size: 58 Copynumber: 3.6 Consensus size: 58
39330 ACCATGAATT
* ** *
39340 TTCCAAAAATTA-CATTTTTACCCCCAAAAATCTAAAAATTTAATTTTTAACCCCGAACC
1 TTCCAAAAATTACCA-TTTTA-CCCCAGATGTCTAAAAATTTCATTTTTAACCCCGAACC
* * *
39399 TTCCAAAAATTACCATTTTACTCCAGATGTTTAAAAATTTCATTTTTAATCCCGAA--
1 TTCCAAAAATTACCATTTTACCCCAGATGTCTAAAAATTTCATTTTTAACCCCGAACC
* * * *
39455 TTCTCTAAAAATTACCA-TTTACCCTCAAATGTCTAAAAA-TCCTATTTTTGACCTCGAACC
1 TTC-C-AAAAATTACCATTTTACCC-CAGATGTCTAAAAATTTC-ATTTTTAACCCCGAACC
* *
39515 TTTC-AAAATTACCATTTTACCCCAGAATGTCCAAAA
1 TTCCAAAAATTACCATTTTACCCCAG-ATGTCTAAAA
39551 TTATTGTTTT
Statistics
Matches: 126, Mismatches: 17, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
56 3 0.02
57 21 0.17
58 80 0.63
59 18 0.14
60 4 0.03
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (58 bp):
TTCCAAAAATTACCATTTTACCCCAGATGTCTAAAAATTTCATTTTTAACCCCGAACC
Found at i:48874 original size:23 final size:24
Alignment explanation
Indices: 48844--48907 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
48834 GATATAAAAA
* * *
48844 TATTTTTAAATAAT-CAAATTGGC
1 TATTTTTAAATAATAAAAAGTGAC
*
48867 TATTTTTAATTAATAAAAAGTGAC
1 TATTTTTAAATAATAAAAAGTGAC
48891 TATTTTGTAAAT-ATAAA
1 TATTTT-TAAATAATAAA
48908 TGATTAAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 13 0.38
24 17 0.50
25 4 0.12
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (24 bp):
TATTTTTAAATAATAAAAAGTGAC
Found at i:48893 original size:24 final size:23
Alignment explanation
Indices: 48844--48907 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
48834 GATATAAAAA
* * *
48844 TATTTTTAAATAATCAAATTGGC
1 TATTTTTAAATAATAAAAGTGAC
*
48867 TATTTTTAATTAATAAAAAGTGAC
1 TATTTTTAAATAAT-AAAAGTGAC
48891 TATTTTGTAAAT-ATAAA
1 TATTTT-TAAATAATAAA
48908 TGATTAAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 16 0.47
24 14 0.41
25 4 0.12
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (23 bp):
TATTTTTAAATAATAAAAGTGAC
Found at i:50062 original size:30 final size:29
Alignment explanation
Indices: 50014--50082 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
50004 CAACATGAAC
* *
50014 TAAAAACTT-AAA-AATATGTTTGTTAAT
1 TAAAAACTTAAAATAATATGTATATTAAT
50041 TAAAAACTTGAAAATAATATGTATATTAAT
1 TAAAAACTT-AAAATAATATGTATATTAAT
50071 TAAAAA-TTAAAA
1 TAAAAACTTAAAA
50083 ATTAAAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 9 0.24
28 4 0.11
29 5 0.14
30 19 0.51
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (29 bp):
TAAAAACTTAAAATAATATGTATATTAAT
Found at i:50635 original size:13 final size:14
Alignment explanation
Indices: 50600--50634 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
50590 AGAAAGTAAG
50600 TCATTTTTCAAAAA
1 TCATTTTTCAAAAA
* *
50614 TTATTTTTCGAAAA
1 TCATTTTTCAAAAA
50628 TCATTTT
1 TCATTTT
50635 CAGTAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.51
Consensus pattern (14 bp):
TCATTTTTCAAAAA
Found at i:53751 original size:20 final size:20
Alignment explanation
Indices: 53726--53765 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
53716 TATGAGTACC
*
53726 AAAATTATACCTCGGGAAAA
1 AAAATTATACCTCAGGAAAA
53746 AAAATTATACCTCAGGAAAA
1 AAAATTATACCTCAGGAAAA
53766 GCCTCTTGGC
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:0.53, C:0.15, G:0.12, T:0.20
Consensus pattern (20 bp):
AAAATTATACCTCAGGAAAA
Found at i:54961 original size:47 final size:47
Alignment explanation
Indices: 54892--54987 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
54882 TTTTTCCGTA
*
54892 CTCAAGTATAGATAAAATGGATATTCTGAGTATTATATAATTAATAT
1 CTCAAATATAGATAAAATGGATATTCTGAGTATTATATAATTAATAT
54939 CTCAAATATAGATAAAATGGATATTCTGAGTATTATATAATTAATAT
1 CTCAAATATAGATAAAATGGATATTCTGAGTATTATATAATTAATAT
54986 CT
1 CT
54988 TACTTGAACA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (47 bp):
CTCAAATATAGATAAAATGGATATTCTGAGTATTATATAATTAATAT
Found at i:54962 original size:24 final size:24
Alignment explanation
Indices: 54892--54962 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
54882 TTTTTCCGTA
54892 CTCAAGTATAGATAAAATGGATAT
1 CTCAAGTATAGATAAAATGGATAT
* * * **
54916 -TCTGAGTAT-TATATAATTAATAT
1 CTC-AAGTATAGATAAAATGGATAT
*
54939 CTCAAATATAGATAAAATGGATAT
1 CTCAAGTATAGATAAAATGGATAT
54963 TCTGAGTATT
Statistics
Matches: 33, Mismatches: 11, Indels: 6
0.66 0.22 0.12
Matches are distributed among these distances:
23 16 0.48
24 17 0.52
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (24 bp):
CTCAAGTATAGATAAAATGGATAT
Found at i:57038 original size:8 final size:8
Alignment explanation
Indices: 57025--57060 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
57015 CTTTTGTAAC
57025 AAAAAAAT
1 AAAAAAAT
57033 AAAAAAAAT
1 -AAAAAAAT
57042 AAAAAAAT
1 AAAAAAAT
57050 -AAAAAAT
1 AAAAAAAT
57057 AAAA
1 AAAA
57061 CCCCAATCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.27
8 11 0.42
9 8 0.31
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:57039 original size:9 final size:9
Alignment explanation
Indices: 57025--57055 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
57015 CTTTTGTAAC
57025 AAAAAAATA
1 AAAAAAATA
57034 AAAAAAAT-
1 AAAAAAATA
57042 AAAAAAATA
1 AAAAAAATA
57051 AAAAA
1 AAAAA
57056 TAAAACCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:57674 original size:12 final size:12
Alignment explanation
Indices: 57657--57691 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
57647 TTGAATTATC
* *
57657 AAAATATTATGT
1 AAAATATAATAT
57669 AAAATATAATAT
1 AAAATATAATAT
57681 AAAATATAATA
1 AAAATATAATA
57692 ATTAAATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (12 bp):
AAAATATAATAT
Found at i:58414 original size:24 final size:24
Alignment explanation
Indices: 58353--58405 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
58343 TGGGTTTTTC
58353 AAATAAAAATATTAAAATACTCTT
1 AAATAAAAATATTAAAATACTCTT
58377 AAATAAAAATATTAAAATACTCTT
1 AAATAAAAATATTAAAATACTCTT
58401 AAATA
1 AAATA
58406 GTATAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATAAAAATATTAAAATACTCTT
Found at i:76865 original size:24 final size:24
Alignment explanation
Indices: 76831--76877 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
76821 AACTAGAGGC
* *
76831 AGGTTCGCAAACATGTTTGCAAGT
1 AGGTTCACAAACAGGTTTGCAAGT
76855 AGGTTCACAAACAGGTTTGCAAG
1 AGGTTCACAAACAGGTTTGCAAG
76878 ATCTAAGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (24 bp):
AGGTTCACAAACAGGTTTGCAAGT
Found at i:78578 original size:14 final size:16
Alignment explanation
Indices: 78549--78580 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
78539 AACTTTTTTC
78549 ATAAAGATTATATATT
1 ATAAAGATTATATATT
78565 ATAAA-ATT-TATATT
1 ATAAAGATTATATATT
78579 AT
1 AT
78581 TATTATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAGATTATATATT
Found at i:78583 original size:3 final size:3
Alignment explanation
Indices: 78575--78614 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
78565 ATAAAATTTA
78575 TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T-T TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
78615 TACATATCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.18
3 28 0.82
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:80950 original size:19 final size:20
Alignment explanation
Indices: 80911--80964 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
80901 ACAGTAATGA
*
80911 TAAAATTAATGTATAAATTT
1 TAAAATTAATATATAAATTT
*
80931 TAAAATT-ATATATGAATTT
1 TAAAATTAATATATAAATTT
* *
80950 T-GATTTAATATATAA
1 TAAAATTAATATATAA
80965 TTGTATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 3 0.11
19 18 0.64
20 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (20 bp):
TAAAATTAATATATAAATTT
Found at i:81231 original size:29 final size:29
Alignment explanation
Indices: 81199--81256 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
81189 GAATTGGATC
*
81199 AAATTAAAATTTCACGTATA-AATTACATA
1 AAATTAAAA-TTCACATATATAATTACATA
*
81228 AAATTAAAATTCATATATATAATTACATA
1 AAATTAAAATTCACATATATAATTACATA
81257 TTAAATCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (29 bp):
AAATTAAAATTCACATATATAATTACATA
Found at i:86118 original size:23 final size:26
Alignment explanation
Indices: 86088--86142 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
86078 ATTGTAAGTT
86088 AAAT-AATTTTT-TTA-A-TATAGTA
1 AAATGAATTTTTGTTATAGTATAGTA
*
86110 AAATGAATTTTTGTTATAGTATATTA
1 AAATGAATTTTTGTTATAGTATAGTA
86136 AAATGAA
1 AAATGAA
86143 ATTTAAACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 4 0.14
23 7 0.25
24 3 0.11
25 1 0.04
26 13 0.46
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (26 bp):
AAATGAATTTTTGTTATAGTATAGTA
Found at i:92579 original size:42 final size:42
Alignment explanation
Indices: 92518--92617 Score: 139
Period size: 43 Copynumber: 2.4 Consensus size: 42
92508 GGAAAAACGT
* *
92518 CGCTATAGAACATGATCTTTAGCG-GCTCTTATCCACAAATGC
1 CGCTAAAGAACATGGTCTTTAGCGAGCTC-TATCCACAAATGC
*
92560 CGCTAAAGAACATGGTCTTTAGCGACGCTCTCTCCACAAATGC
1 CGCTAAAGAACATGGTCTTTAGCGA-GCTCTATCCACAAATGC
*
92603 CGATAAAGAACATGG
1 CGCTAAAGAACATGG
92618 CTGATAAAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
42 22 0.42
43 26 0.50
44 4 0.08
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (42 bp):
CGCTAAAGAACATGGTCTTTAGCGAGCTCTATCCACAAATGC
Found at i:92809 original size:42 final size:42
Alignment explanation
Indices: 92730--92830 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
92720 CATTTTCCCA
* * *
92730 ACAAACGCCGCTAAAGAACATGATCTTTAATGGCGCTTTTCC
1 ACAAACGCCGCTAAAAAACATGATCTTTAACGACGCTTTTCC
* * *
92772 ACAAACGCCGTTAAAAAACATGGTCTTTAACGACGCTTCTCCC
1 ACAAACGCCGCTAAAAAACATGATCTTTAACGACGCTT-TTCC
* *
92815 ATAAACTCCGCTAAAA
1 ACAAACGCCGCTAAAA
92831 TTAATTAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 33 0.67
43 16 0.33
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.24
Consensus pattern (42 bp):
ACAAACGCCGCTAAAAAACATGATCTTTAACGACGCTTTTCC
Found at i:95563 original size:20 final size:20
Alignment explanation
Indices: 95535--95577 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
95525 TTTATATAAG
*
95535 TTTTAAAATTTAATAATTTT
1 TTTTAAAATTTAAGAATTTT
* *
95555 TTTTTAAATTTTAGAATTTT
1 TTTTAAAATTTAAGAATTTT
95575 TTT
1 TTT
95578 CGTTTATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTAAAATTTAAGAATTTT
Found at i:95704 original size:40 final size:41
Alignment explanation
Indices: 95652--95851 Score: 127
Period size: 41 Copynumber: 4.9 Consensus size: 41
95642 TTTAAATAAA
* * *
95652 TTAGCGGTGTTTACGAAAAAACGCCGCTATTG-TTTAACCT
1 TTAGCGGCGTTTACGAAAAAACGCCGCTAATGCTCTAACCT
* * * *
95692 TTAGCGGCGTTTATGAGAAAGCGCCGCTAATGCTCTGACCT
1 TTAGCGGCGTTTACGAAAAAACGCCGCTAATGCTCTAACCT
* ** * ** * * * *
95733 TTAGCGGTGCTTT-CTCATAAATACCGTTAATGCTTTGACTT
1 TTAGCGGCG-TTTACGAAAAAACGCCGCTAATGCTCTAACCT
** * *
95774 TTAGCGGCGCTTT-CTCATAAATGCCGCTAATGCTCTAACCT
1 TTAGCGGCG-TTTACGAAAAAACGCCGCTAATGCTCTAACCT
* * * *
95815 TTAGCGGTGTTTATGAGAAAAACGTCACTAATGCTCT
1 TTAGCGGCGTTTACGA-AAAAACGCCGCTAATGCTCT
95852 TTCCCATATT
Statistics
Matches: 123, Mismatches: 33, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
40 30 0.24
41 74 0.60
42 19 0.15
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (41 bp):
TTAGCGGCGTTTACGAAAAAACGCCGCTAATGCTCTAACCT
Found at i:95764 original size:41 final size:41
Alignment explanation
Indices: 95715--95823 Score: 164
Period size: 41 Copynumber: 2.7 Consensus size: 41
95705 TGAGAAAGCG
95715 CCGCTAATGCTCTGACCTTTAGCGGTGCTTTCTCATAAATA
1 CCGCTAATGCTCTGACCTTTAGCGGTGCTTTCTCATAAATA
* * * * *
95756 CCGTTAATGCTTTGACTTTTAGCGGCGCTTTCTCATAAATG
1 CCGCTAATGCTCTGACCTTTAGCGGTGCTTTCTCATAAATA
*
95797 CCGCTAATGCTCTAACCTTTAGCGGTG
1 CCGCTAATGCTCTGACCTTTAGCGGTG
95824 TTTATGAGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (41 bp):
CCGCTAATGCTCTGACCTTTAGCGGTGCTTTCTCATAAATA
Found at i:98271 original size:41 final size:41
Alignment explanation
Indices: 98220--98371 Score: 160
Period size: 41 Copynumber: 3.7 Consensus size: 41
98210 AAATCCGCGG
* * * **
98220 CGCTAATGCTCTGATCTTTAGCAGCGCTTGCCCATAAACAC
1 CGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAACGT
* * * * **
98261 CGCAATTGCTCTTACCTTTAGCGGCGCTTTCACATAGGCGT
1 CGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAACGT
* *
98302 CGCTATTGCTCTAACCTTTAGCGACGCTTGCCCATAAACGT
1 CGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAACGT
* * *
98343 AGCTATTGCTCTGTCTTTTAGCGGCGCTT
1 CGCTATTGCTCTGACCTTTAGCGGCGCTT
98372 TCCATAAGCA
Statistics
Matches: 88, Mismatches: 23, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
41 88 1.00
ACGTcount: A:0.19, C:0.30, G:0.20, T:0.32
Consensus pattern (41 bp):
CGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAACGT
Found at i:98351 original size:82 final size:81
Alignment explanation
Indices: 98220--98377 Score: 203
Period size: 82 Copynumber: 1.9 Consensus size: 81
98210 AAATCCGCGG
* * *
98220 CGCTAATGCTCTGATCTTTAGCAGCGCTTGCCCATAAACACCGCAATTGCTCT-TACCTTTAGCG
1 CGCTAATGCTCTAACCTTTAGCAGCGCTTGCCCATAAACACAGCAATTGCTCTGT-CCTTTAGCG
98284 GCGCTTTCACATAGGCGT
65 GCGCTTTC-CATAGGCGT
* ** * *
98302 CGCTATTGCTCTAACCTTTAGC-GACGCTTGCCCATAAACGTAGCTATTGCTCTGTCTTTTAGCG
1 CGCTAATGCTCTAACCTTTAGCAG-CGCTTGCCCATAAACACAGCAATTGCTCTGTCCTTTAGCG
98366 GCGCTTTCCATA
65 GCGCTTTCCATA
98378 AGCACTGCTA
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
81 5 0.08
82 60 0.91
83 1 0.02
ACGTcount: A:0.20, C:0.30, G:0.19, T:0.32
Consensus pattern (81 bp):
CGCTAATGCTCTAACCTTTAGCAGCGCTTGCCCATAAACACAGCAATTGCTCTGTCCTTTAGCGG
CGCTTTCCATAGGCGT
Done.