Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014090.1 Kokia drynarioides strain JFW-HI SEQ_129121, 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: 181580
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:6758 original size:17 final size:17
Alignment explanation
Indices: 6717--6759 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
6707 TTAACATAAT
6717 ATTAATATT-TATCAAA
1 ATTAATATTATATCAAA
* *
6733 ATAAATATTATATTAAA
1 ATTAATATTATATCAAA
*
6750 TTTAATATTA
1 ATTAATATTA
6760 AATCTTATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTAATATTATATCAAA
Found at i:6811 original size:62 final size:60
Alignment explanation
Indices: 6706--6906 Score: 167
Period size: 62 Copynumber: 3.2 Consensus size: 60
6696 TTAGTGTTAA
* * * *
6706 ATTAACATAATATTAATATTTATCAAAATAAATATTATATTAAATTTAATATTAAATCTT
1 ATTAAAATAATATAAATATTTATCAAAATAAACATTAAATTAAATTTAATATTAAATCTT
* *
6766 ATTAAAATAATA-AAATATTTATCTAAAAGATAAACATTAAATTAAATTTAATATTAAGATAATC
1 ATTAAAATAATATAAATATTTATC--AAA-ATAAACATTAAATTAAATTTAATATTAA-AT-CTT
* * * **
6830 ACTTTAATATTAAATTAATAAA-ATCCTATTAAAATAAGTATTAAATTAAATTTAATATTAAA-C
1 A--TTAA-AAT-AA-T-ATAAATAT-TTATCAAAATAAACATTAAATTAAATTTAATATTAAATC
6893 -T
59 TT
6894 ATTAAAATAATAT
1 ATTAAAATAATAT
6907 TTATTTTGGA
Statistics
Matches: 114, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
58 2 0.02
59 11 0.10
60 13 0.11
61 5 0.04
62 30 0.26
63 2 0.02
64 3 0.03
66 4 0.04
67 3 0.03
68 28 0.25
69 4 0.04
70 3 0.03
71 6 0.05
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (60 bp):
ATTAAAATAATATAAATATTTATCAAAATAAACATTAAATTAAATTTAATATTAAATCTT
Found at i:6848 original size:20 final size:18
Alignment explanation
Indices: 6801--6909 Score: 64
Period size: 20 Copynumber: 5.9 Consensus size: 18
6791 AAAGATAAAC
6801 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
6818 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** **
6838 ATTAAATTAATAAAATCCT
1 ATTAAATTAAT-ATTTAAT
*
6857 ATTAAAATAAGTA-TTAA-
1 ATTAAATTAA-TATTTAAT
*
6874 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
6894 ATTAAAATAATATTTA
1 ATTAAATTAATATTTA
6910 TTTTGGAAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
17 16 0.23
18 8 0.12
19 22 0.32
20 23 0.33
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:8705 original size:33 final size:32
Alignment explanation
Indices: 8656--8724 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
8646 CTTAATTTAA
*
8656 AATTTAAATTAATCCTTTT-ACAATCCTAACTAG
1 AATTCAAATTAATCCTTTTCA-AATCCTAA-TAG
*
8689 AATTCAAATTACTCCTTTTCAAATCCTAATAG
1 AATTCAAATTAATCCTTTTCAAATCCTAATAG
8721 AATT
1 AATT
8725 TATCTTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 7 0.21
33 25 0.76
34 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (32 bp):
AATTCAAATTAATCCTTTTCAAATCCTAATAG
Found at i:9243 original size:29 final size:28
Alignment explanation
Indices: 9199--9304 Score: 79
Period size: 29 Copynumber: 3.7 Consensus size: 28
9189 TTTTTTACAA
*
9199 TTTTGCCATTACTTTTTCAAATTTTATAG
1 TTTTGCCACTA-TTTTTCAAATTTTATAG
* * *
9228 TTTTGCCACTAGTTTTCCAGATTTT-TCAA
1 TTTTGCCACTA-TTTTTCAAATTTTAT-AG
* *** *
9257 TTATGTTTCTATTTTTCAAATTTCATAG
1 TTTTGCCACTATTTTTCAAATTTTATAG
* *
9285 TTTTACCTCTATTTTTCAAA
1 TTTTGCCACTATTTTTCAAA
9305 AAAAAAAATA
Statistics
Matches: 58, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
28 28 0.48
29 30 0.52
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.54
Consensus pattern (28 bp):
TTTTGCCACTATTTTTCAAATTTTATAG
Found at i:10014 original size:110 final size:110
Alignment explanation
Indices: 9791--10072 Score: 343
Period size: 110 Copynumber: 2.6 Consensus size: 110
9781 TTGTCGCTGG
* * * *
9791 GTATTCACAAATTAGCAGATTCCAACTGCGACTGTATGAACGAAGCATCCACGATTTTCTCTGAC
1 GTATTCACAGATTAACAGATTCCAACTGCGACTGTATGAACGAAGCATCCACGATTTCCTCTAAC
*
9856 AACTTTTATTTGCAAGGGATTGTGGATCCTCAATCAATCCATTGT
66 AACTTTTATTTGCAAGGGATTGTGGATCCTCAATCAATCCATTCT
* * * * * *
9901 GTATTCACAGATTAACGGGTTCCAATTGCGACTTTATGAATGAAGCATCCATGATTTCCTCTAAC
1 GTATTCACAGATTAACAGATTCCAACTGCGACTGTATGAACGAAGCATCCACGATTTCCTCTAAC
*
9966 AACTTTTATTTGCAAGGGATTGTGGATCCTCAATCAATCTGA-TCT
66 AACTTTTATTTGCAAGGGATTGTGGATCCTCAATCAATC-CATTCT
* ** * * * * * *
10011 GTATTCATAGATTAGTATATTCCAA-TAGCGACTATACGAATGGAGCATCCACGATTTTCTCT
1 GTATTCACAGATTAACAGATTCCAACT-GCGACTGTATGAACGAAGCATCCACGATTTCCTCT
10073 TGTAGCATTT
Statistics
Matches: 147, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
109 1 0.01
110 145 0.99
111 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (110 bp):
GTATTCACAGATTAACAGATTCCAACTGCGACTGTATGAACGAAGCATCCACGATTTCCTCTAAC
AACTTTTATTTGCAAGGGATTGTGGATCCTCAATCAATCCATTCT
Found at i:11723 original size:57 final size:55
Alignment explanation
Indices: 11662--11779 Score: 150
Period size: 56 Copynumber: 2.1 Consensus size: 55
11652 ATAGAAATGG
* *
11662 TGAAATGGAGAAATAGGAAA-CATTTGGAAATGAT-TAAGGTTTTCTCCAAAATGAAAA
1 TGAAATGGA-AAA-AGGAAATCATTTGAAAATAATGT--GGTTTTCTCCAAAATGAAAA
*
11719 TGAAAATGGAAAAATGAAATCATTTGAAAATAATGTGGTTTTCTCCAAAATGAAAA
1 TG-AAATGGAAAAAGGAAATCATTTGAAAATAATGTGGTTTTCTCCAAAATGAAAA
11775 TGAAA
1 TGAAA
11780 AATGAAAATG
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
55 3 0.05
56 27 0.49
57 17 0.31
58 8 0.15
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.27
Consensus pattern (55 bp):
TGAAATGGAAAAAGGAAATCATTTGAAAATAATGTGGTTTTCTCCAAAATGAAAA
Found at i:11783 original size:13 final size:13
Alignment explanation
Indices: 11765--11790 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11755 GGTTTTCTCC
11765 AAAATGAAAATGA
1 AAAATGAAAATGA
11778 AAAATGAAAATGA
1 AAAATGAAAATGA
11791 CCTAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAATGAAAATGA
Found at i:14865 original size:3 final size:3
Alignment explanation
Indices: 14857--14895 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
14847 GGTGAGTTGA
*
14857 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
14896 TCAAACAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:15715 original size:13 final size:13
Alignment explanation
Indices: 15697--15721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15687 TTTTTATCAA
15697 AAAAAATATTTTC
1 AAAAAATATTTTC
15710 AAAAAATATTTT
1 AAAAAATATTTT
15722 GAGAGTGATT
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAAATATTTTC
Found at i:15761 original size:30 final size:30
Alignment explanation
Indices: 15717--15780 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
15707 TTCAAAAAAT
* *
15717 ATTTTGAGAGTGATTTGAGAATTTGAGAGA
1 ATTTTGAGAATGATTTAAGAATTTGAGAGA
* *
15747 ATTTTTAGAATGATTTAAGATTTTGAGAGA
1 ATTTTGAGAATGATTTAAGAATTTGAGAGA
15777 ATTT
1 ATTT
15781 AAGAGATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.42
Consensus pattern (30 bp):
ATTTTGAGAATGATTTAAGAATTTGAGAGA
Found at i:26259 original size:104 final size:104
Alignment explanation
Indices: 26079--26282 Score: 363
Period size: 104 Copynumber: 2.0 Consensus size: 104
26069 CAAACCGAAT
*
26079 TTTTCAGAAACATTCTTCTCAAAATCACTTATCAAAAACAATGCTAACTAGCCCTTAATCTAAGT
1 TTTTCAGAAACATTCTTCTCAAAATCACTTATCAAAAACAATGCTAACTAGCCCTTAATCTAAGG
26144 CATACATCCGCTAAATTATAAAGTGGTGTAAGCACCAAC
66 CATACATCCGCTAAATTATAAAGTGGTGTAAGCACCAAC
* *
26183 TTTTCAGAAACATTCTTCTCAAAATCACTTATCAAAAGCAATGCTAACTAGCCCTTAATTTAAGG
1 TTTTCAGAAACATTCTTCTCAAAATCACTTATCAAAAACAATGCTAACTAGCCCTTAATCTAAGG
* *
26248 CATCCATCCGCTAGATTATAAAGTGGTGTAAGCAC
66 CATACATCCGCTAAATTATAAAGTGGTGTAAGCAC
26283 TGCATTGGCA
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
104 95 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (104 bp):
TTTTCAGAAACATTCTTCTCAAAATCACTTATCAAAAACAATGCTAACTAGCCCTTAATCTAAGG
CATACATCCGCTAAATTATAAAGTGGTGTAAGCACCAAC
Found at i:38386 original size:182 final size:182
Alignment explanation
Indices: 38079--38440 Score: 643
Period size: 182 Copynumber: 2.0 Consensus size: 182
38069 AAAAGCGTCT
38079 CATTGGGATCAATCTATCAAATGGGGCTCATTTAACCCACTTAAACTAACTCAATTCGAAGAACA
1 CATTGGGATCAATCTATCAAATGGGGCTCATTTAACCCACTTAAACTAACTCAATTCGAAGAACA
* *
38144 AGTGACGAAGCTAATCCACTTGAAGCCTTGGTGGCCAACTAAAGCACTTAAAAAAAACTAAAGTT
66 AGTGACGAAGCTAATCCACTTGAACCCTTGGTGGCCAACTAAAGCACTTAAAAAAAACTAAAGCT
* *
38209 TTCTTGGTAAATAGAAAAATTAATTTTAAAATATTATAATCTGATAAGATCC
131 ATCTTGGTAAATAGAAAAATTAATCTTAAAATATTATAATCTGATAAGATCC
*
38261 CATTGGGATCAATCTATCAAATGGGGCTCATTTGACCCACTTAAACTAACTCAATTCGAAGAACA
1 CATTGGGATCAATCTATCAAATGGGGCTCATTTAACCCACTTAAACTAACTCAATTCGAAGAACA
* * *
38326 AGTGACGAAGCTCATCCACTTGAACCCTTGGTGGCCAACTAAAGCACTTCAGAAAAACTAAAGCT
66 AGTGACGAAGCTAATCCACTTGAACCCTTGGTGGCCAACTAAAGCACTTAAAAAAAACTAAAGCT
*
38391 ATCTTGGTAAATAGAAAAATTAATCTTAAAATATTATAATTTGATAAGAT
131 ATCTTGGTAAATAGAAAAATTAATCTTAAAATATTATAATCTGATAAGAT
38441 TTGATTTTTG
Statistics
Matches: 171, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
182 171 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.28
Consensus pattern (182 bp):
CATTGGGATCAATCTATCAAATGGGGCTCATTTAACCCACTTAAACTAACTCAATTCGAAGAACA
AGTGACGAAGCTAATCCACTTGAACCCTTGGTGGCCAACTAAAGCACTTAAAAAAAACTAAAGCT
ATCTTGGTAAATAGAAAAATTAATCTTAAAATATTATAATCTGATAAGATCC
Found at i:51970 original size:26 final size:26
Alignment explanation
Indices: 51931--51987 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
51921 TATAGTCTGT
* * *
51931 ATCACTGACTCAAAACTTGATATATA
1 ATCACTGACACAAAACCTAATATATA
* *
51957 ATCATTGACACAAAGCCTAATATATA
1 ATCACTGACACAAAACCTAATATATA
51983 ATCAC
1 ATCAC
51988 CGGCATAAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (26 bp):
ATCACTGACACAAAACCTAATATATA
Found at i:51997 original size:26 final size:26
Alignment explanation
Indices: 51950--52027 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
51940 TCAAAACTTG
**
51950 ATATATAATCATTGACACAAAGCCTA
1 ATATATAATCACCGACACAAAGCCTA
* * *
51976 ATATATAATCACCGGCATAAAGCCTG
1 ATATATAATCACCGACACAAAGCCTA
** *
52002 ATAGGTAATCACCGAAACAAAGCCTA
1 ATATATAATCACCGACACAAAGCCTA
52028 CTACTCAGAA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.22
Consensus pattern (26 bp):
ATATATAATCACCGACACAAAGCCTA
Found at i:55707 original size:12 final size:13
Alignment explanation
Indices: 55685--55713 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
55675 TTGCCTGGGA
55685 TTGTCAAAATTAT
1 TTGTCAAAATTAT
55698 TTGT-AAAATTAT
1 TTGTCAAAATTAT
55710 TTGT
1 TTGT
55714 TTACATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.52
Consensus pattern (13 bp):
TTGTCAAAATTAT
Found at i:66258 original size:18 final size:17
Alignment explanation
Indices: 66230--66265 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
66220 ACATAAAAAG
66230 AAAGAAAAAGAAAAGAA
1 AAAGAAAAAGAAAAGAA
66247 AAAGAGAAAAGAAAAGAA
1 AAAGA-AAAAGAAAAGAA
66265 A
1 A
66266 GTATTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAAAGAA
Found at i:69654 original size:18 final size:19
Alignment explanation
Indices: 69617--69654 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
69607 CCCAACTATC
69617 AAAAAATATCGATACCATTT
1 AAAAAATATCGATA-CATTT
*
69637 AAAAAGTATCGATA-ATTT
1 AAAAAATATCGATACATTT
69655 CACCCTGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (19 bp):
AAAAAATATCGATACATTT
Found at i:82398 original size:271 final size:271
Alignment explanation
Indices: 81908--82450 Score: 917
Period size: 271 Copynumber: 2.0 Consensus size: 271
81898 TAAATACTAA
81908 CCTATGCCTAAACCTCTTTAAACACTTATATCTACTCCAAACTCTCTCATCCACTCTCAACCATA
1 CCTATGCCTAAACCTCTTTAAACACTTATATCTACTCCAAACTCTCTCATCCACTCTCAACCATA
*
81973 CCCAAAATCCACCAAACTTTCATACCCATTGTTCAAAGAATAAGAGGACGGAAGTAACAAGTTCA
66 CCCAAAATCCACCAAACTTTCATACCCATTGTTCAAAGAATAAGAGGACGAAAGTAACAAGTTCA
* * *
82038 ATATTGAAGAGATAGTCGAGTGATTCAGCAAGCACGAAATTAGGATTAAGGTATCTCTTGACTAT
131 ATATTAAAGAGATAGTCGAGTGATTCAGCAAGCACAAAATTAGGATTAAGGTATCTCCTGACTAT
* * *
82103 TACTATTCCATTGATTATTGTTCATCCCTATTCATTATTTGCAGATTATAATTCCTCCACCAAAA
196 CACTATTCCATTGATTACTGTTCATCCCTATTCATTATTTGCAGATTATAATTACTCCACCAAAA
82168 AGGAAGAAAAC
261 AGGAAGAAAAC
*
82179 CCTATGCCTAAACCTCTTTAAACACTTATATCTCCTCCAAACTCTCTCATCCACTCTCAACCATA
1 CCTATGCCTAAACCTCTTTAAACACTTATATCTACTCCAAACTCTCTCATCCACTCTCAACCATA
* *
82244 CGCAAAATTCC-TCAAACTTTCATACCCATTGTTCAAAGAATAAGAGGACGAAAGTAACAAGTTC
66 CCCAAAA-TCCACCAAACTTTCATACCCATTGTTCAAAGAATAAGAGGACGAAAGTAACAAGTTC
* *
82308 AATATTAAAGAGATAGTCGAGTGATTCAGCAAGCACAAAATTGGGATTAAGGTATCTCCTGACTG
130 AATATTAAAGAGATAGTCGAGTGATTCAGCAAGCACAAAATTAGGATTAAGGTATCTCCTGACTA
* * * **
82373 TCACTGTTCCATTGATTACTGTTCATCCTTGTTCATTATTTGCAGATTATAATTACTCCATGAAA
195 TCACTATTCCATTGATTACTGTTCATCCCTATTCATTATTTGCAGATTATAATTACTCCACCAAA
82438 AAGGAAGAAAAC
260 AAGGAAGAAAAC
82450 C
1 C
82451 GCAATTCAGC
Statistics
Matches: 254, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
271 251 0.99
272 3 0.01
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.29
Consensus pattern (271 bp):
CCTATGCCTAAACCTCTTTAAACACTTATATCTACTCCAAACTCTCTCATCCACTCTCAACCATA
CCCAAAATCCACCAAACTTTCATACCCATTGTTCAAAGAATAAGAGGACGAAAGTAACAAGTTCA
ATATTAAAGAGATAGTCGAGTGATTCAGCAAGCACAAAATTAGGATTAAGGTATCTCCTGACTAT
CACTATTCCATTGATTACTGTTCATCCCTATTCATTATTTGCAGATTATAATTACTCCACCAAAA
AGGAAGAAAAC
Found at i:86358 original size:22 final size:23
Alignment explanation
Indices: 86328--86370 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
86318 TACATGTCCA
86328 TTAAATAATATAATTT-CATGCT
1 TTAAATAATATAATTTGCATGCT
* *
86350 TTAATTAATTTAATTTGCATG
1 TTAAATAATATAATTTGCATG
86371 GCCGACTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (23 bp):
TTAAATAATATAATTTGCATGCT
Found at i:93507 original size:26 final size:26
Alignment explanation
Indices: 93478--93535 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
93468 AATTCTAGGC
93478 ACAATTCTCGACA-TGCTCATACAGTG
1 ACAATTCTCGACATTG-TCATACAGTG
* * **
93504 ACAACTCTGGACATTGTCATGTAGTG
1 ACAATTCTCGACATTGTCATACAGTG
93530 ACAATT
1 ACAATT
93536 TTAGGTTGCA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (26 bp):
ACAATTCTCGACATTGTCATACAGTG
Found at i:94626 original size:17 final size:17
Alignment explanation
Indices: 94601--94655 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
94591 TATAAGGACA
*
94601 AATGGAAATGCAATGAC
1 AATGAAAATGCAATGAC
* *
94618 AATGCAAATGCTATGAC
1 AATGAAAATGCAATGAC
* *
94635 AATTAAAATGTAATGAC
1 AATGAAAATGCAATGAC
94652 AATG
1 AATG
94656 GGAATACGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (17 bp):
AATGAAAATGCAATGAC
Found at i:94668 original size:34 final size:34
Alignment explanation
Indices: 94606--94671 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
94596 GGACAAATGG
* *
94606 AAATGCAATGACAATGCAAATGCTATGACAATTA
1 AAATGCAATGACAATGCAAATACGATGACAATTA
* **
94640 AAATGTAATGACAATGGGAATACGATGACAAT
1 AAATGCAATGACAATGCAAATACGATGACAAT
94672 GCTTATTAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (34 bp):
AAATGCAATGACAATGCAAATACGATGACAATTA
Found at i:94858 original size:38 final size:35
Alignment explanation
Indices: 94773--94844 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
94763 ATCGATGTAG
94773 CTGCATGGTGCTTTTCTTCCTTCTCTTCTTCTCCT
1 CTGCATGGTGCTTTTCTTCCTTCTCTTCTTCTCCT
94808 CTGCATGGTGCTTTTCTTCCTTCTCTTCTTCTCCT
1 CTGCATGGTGCTTTTCTTCCTTCTCTTCTTCTCCT
94843 CT
1 CT
94845 TTCTTTCTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.03, C:0.35, G:0.11, T:0.51
Consensus pattern (35 bp):
CTGCATGGTGCTTTTCTTCCTTCTCTTCTTCTCCT
Found at i:129860 original size:18 final size:18
Alignment explanation
Indices: 129837--129882 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
129827 GCACAACTTG
129837 ATCAGATGC-GATCATAAA
1 ATCAGATGCAG-TCATAAA
*
129855 ATCAGATGCAGTCATATA
1 ATCAGATGCAGTCATAAA
*
129873 ATCAAATGCA
1 ATCAGATGCA
129883 TCCACAAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.24
Consensus pattern (18 bp):
ATCAGATGCAGTCATAAA
Found at i:131962 original size:51 final size:50
Alignment explanation
Indices: 131885--131987 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 50
131875 GAAGGATCAA
131885 GCAAAGACGACTTTCACCTACCCATTTGGAACCTTTTCTTTTCGACGAAT
1 GCAAAGACGACTTTCACCTACCCATTTGGAACCTTTTCTTTTCGACGAAT
*
131935 GNCAAAGACGACTTTCACCTGCCCATTTGGAACCTTTTCTTTTCGACGAAT
1 G-CAAAGACGACTTTCACCTACCCATTTGGAACCTTTTCTTTTCGACGAAT
131986 GC
1 GC
131988 CATTTGGATT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 2 0.04
51 49 0.96
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.31
Consensus pattern (50 bp):
GCAAAGACGACTTTCACCTACCCATTTGGAACCTTTTCTTTTCGACGAAT
Found at i:136515 original size:17 final size:17
Alignment explanation
Indices: 136489--136528 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
136479 GCATGTATTT
136489 ATTTTAATTGTCAT-TGC
1 ATTTTAATTGTC-TCTGC
*
136506 ATTTTTATTGTCTCTGC
1 ATTTTAATTGTCTCTGC
136523 ATTTTA
1 ATTTTA
136529 TTTATTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (17 bp):
ATTTTAATTGTCTCTGC
Found at i:147515 original size:17 final size:16
Alignment explanation
Indices: 147493--147537 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
147483 TGGCAATATA
147493 TTTCTTTTCTTTTCTCT
1 TTTCTTTTCTTTTCT-T
147510 TTTCTTCTTC-TTTCTT
1 TTTCTT-TTCTTTTCTT
147526 TTTC-TTTCTTTT
1 TTTCTTTTCTTTT
147538 ATGAATTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.12
15 4 0.15
16 5 0.19
17 11 0.42
18 3 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCTTTTCTTTTCTT
Found at i:147536 original size:10 final size:11
Alignment explanation
Indices: 147493--147537 Score: 58
Period size: 10 Copynumber: 4.2 Consensus size: 11
147483 TGGCAATATA
147493 TTTCTTTTCTT
1 TTTCTTTTCTT
147504 TTCTCTTTTCTT
1 TT-TCTTTTCTT
*
147516 CTTC-TTTCTT
1 TTTCTTTTCTT
147526 TTTC-TTTCTT
1 TTTCTTTTCTT
147536 TT
1 TT
147538 ATGAATTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
10 17 0.55
11 4 0.13
12 10 0.32
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:148078 original size:17 final size:18
Alignment explanation
Indices: 148057--148116 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 18
148047 TATAAGAATG
148057 GAAATGCAACT-AC-AAT
1 GAAATGCAACTAACAAAT
148073 GCAAATGC-ACTAACAAAT
1 G-AAATGCAACTAACAAAT
*
148091 GAAATGCAA-TGACAAAT
1 GAAATGCAACTAACAAAT
*
148108 AAAATGCAA
1 GAAATGCAA
148117 TGACAACTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.11
17 29 0.76
18 5 0.13
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (18 bp):
GAAATGCAACTAACAAAT
Found at i:148117 original size:17 final size:17
Alignment explanation
Indices: 148075--148127 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
148065 ACTACAATGC
* * *
148075 AAATGCACTAACAAATG
1 AAATGCAATGACAAATA
148092 AAATGCAATGACAAATA
1 AAATGCAATGACAAATA
*
148109 AAATGCAATGACAACTA
1 AAATGCAATGACAAATA
148126 AA
1 AA
148128 TAAGATGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.17
Consensus pattern (17 bp):
AAATGCAATGACAAATA
Found at i:148144 original size:19 final size:21
Alignment explanation
Indices: 148104--148145 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
148094 ATGCAATGAC
148104 AAATAAAATGCAATGACAACT
1 AAATAAAATGCAATGACAACT
*
148125 AAATAAGATGC-ATG-CAACT
1 AAATAAAATGCAATGACAACT
148144 AA
1 AA
148146 CTACTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 10 0.50
ACGTcount: A:0.55, C:0.14, G:0.12, T:0.19
Consensus pattern (21 bp):
AAATAAAATGCAATGACAACT
Found at i:173595 original size:18 final size:18
Alignment explanation
Indices: 173568--173615 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
173558 ATACATCAAA
173568 TTGCGTCGACATCTTTGG
1 TTGCGTCGACATCTTTGG
*
173586 TTGTGTCGACATCTTTGG
1 TTGCGTCGACATCTTTGG
173604 TTGCGTCGACAT
1 TTGCGTCGACAT
173616 TTTCTAAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.12, C:0.21, G:0.27, T:0.40
Consensus pattern (18 bp):
TTGCGTCGACATCTTTGG
Found at i:176212 original size:26 final size:26
Alignment explanation
Indices: 176174--176231 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
176164 GGTGCAATTT
* *
176174 TGGACATGCTCATATAGCGACAACTC
1 TGGACATACTCATACAGCGACAACTC
* * * *
176200 TGGACATATTCATACAGTGATAATTC
1 TGGACATACTCATACAGCGACAACTC
176226 TGGACA
1 TGGACA
176232 AGTTTCTCCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (26 bp):
TGGACATACTCATACAGCGACAACTC
Found at i:178959 original size:26 final size:27
Alignment explanation
Indices: 178905--178970 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
178895 ATCACTCATA
* *
178905 ATTTTTTTTTCTCTTTTGATTCTACTC
1 ATTTTTTCTTCTCTTTGGATTCTACTC
*
178932 ATCTTTTTCTTCTCTTTGGATT-T-TTC
1 AT-TTTTTCTTCTCTTTGGATTCTACTC
178958 ATTGTTTTCTTCT
1 ATT-TTTTCTTCT
178971 TTATGGCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 1 0.03
26 13 0.38
27 3 0.09
28 17 0.50
ACGTcount: A:0.09, C:0.18, G:0.06, T:0.67
Consensus pattern (27 bp):
ATTTTTTCTTCTCTTTGGATTCTACTC
Done.