Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008023.1 Kokia drynarioides strain JFW-HI SEQ_122677, 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: 84267
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:95 original size:25 final size:26
Alignment explanation
Indices: 58--110 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 26
48 ATGTTGTATT
*
58 TAATTTGTGGTGTTTATATTTTCGCA
1 TAATTTGTGGTGTGTATATTTTCGCA
84 TAATTT-TGGTGTGTATATTTTCGCA
1 TAATTTGTGGTGTGTATATTTTCGCA
109 TA
1 TA
111 CATTGCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 20 0.77
26 6 0.23
ACGTcount: A:0.21, C:0.08, G:0.19, T:0.53
Consensus pattern (26 bp):
TAATTTGTGGTGTGTATATTTTCGCA
Found at i:8483 original size:36 final size:36
Alignment explanation
Indices: 8431--8510 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
8421 TATTGAGTTT
* *
8431 GATGTAATTTTGGGAATGGACTAGTTAACTGAGCAC
1 GATGCAATTTTGGGAATGGACTAGTTAACTAAGCAC
*
8467 GATGCAATTTTGGGAATGGACTAGTTAACTAAGCAT
1 GATGCAATTTTGGGAATGGACTAGTTAACTAAGCAC
8503 GATGCAAT
1 GATGCAAT
8511 GGTTAATTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (36 bp):
GATGCAATTTTGGGAATGGACTAGTTAACTAAGCAC
Found at i:11774 original size:2 final size:2
Alignment explanation
Indices: 11767--11797 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11757 TTTAACATTA
11767 AT 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 AT A
11798 ATTAAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12689 original size:51 final size:51
Alignment explanation
Indices: 12607--12748 Score: 167
Period size: 51 Copynumber: 2.8 Consensus size: 51
12597 GCTATAAACG
* * * *
12607 AAAAGGTCAGATGACTAAGTGTCATCTTGAGTAAATGAATCCTTTACGGATT
1 AAAA-GTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCATGACGGATT
*
12659 AAAAGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCATGATGGATT
1 AAAAGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCATGACGGATT
** ** ** *
12710 AAGGGTCCGATGACTTTGTGTCATGGTGAGTATATGAAT
1 AAAAGTCCGATGACTAAGTGTCATCATGAGTAAATGAAT
12749 TCCTATATGA
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
51 74 0.95
52 4 0.05
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (51 bp):
AAAAGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCATGACGGATT
Found at i:16864 original size:52 final size:52
Alignment explanation
Indices: 16786--17123 Score: 473
Period size: 52 Copynumber: 6.5 Consensus size: 52
16776 AAATAAGTCT
* *
16786 GATGACTATGTGTCATCGTGAGTATATGAATGCTTTACGGATTATGAGGTTC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
*
16838 GATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
* * *
16890 GTTGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
* * *
16942 AATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATAAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
* * * *
16994 AATGACTATGTGTCATCGTGAGTATACGAATCCTTTACAGATTATGAGGTTC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
* * **
17046 GATGACTATGTGTCATCGTTAGTATATGATTCCCAATACGGATTA--ATGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAAT-CCTTTACGGATTATGA-GGTCC
* *
17098 GATGACTCTGTGTCATCGTGATTATA
1 GATGACTATGTGTCATCGTGAGTATA
17124 AAAAATGCAT
Statistics
Matches: 257, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
51 1 0.00
52 246 0.96
53 10 0.04
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (52 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
Found at i:17761 original size:116 final size:116
Alignment explanation
Indices: 17617--17828 Score: 277
Period size: 116 Copynumber: 1.8 Consensus size: 116
17607 GATCCATTGG
* * * *
17617 TGTATCGATAGAAATACAGGGTAGGAGAGAGATTGTTC-T-CTGACTTGGGTTGTATCAGTAGTT
1 TGTATCGATAGAAATACAGGGTAGGAGAGAGATTG--CATACTAACCTAGGTTGTATCAGTAGAT
*
17680 GAATAACAAGTATCAGTAGTTATGTATTTAGAATTATTGGTATTTTGCATGTT
64 GAATAACAAGTATCAGTAGTCATGTATTTAGAATTATTGGTATTTTGCATGTT
* * * *
17733 TGTATCGGTAGAAGTACAGGAG-AGGAGAGAGGTTGCATACTAACCTAGGTTGTATCGGTAGATG
1 TGTATCGATAGAAATACAGG-GTAGGAGAGAGATTGCATACTAACCTAGGTTGTATCAGTAGATG
* *
17797 AATACCAAGTATCGGTAGTCATGTATTTAGAA
65 AATAACAAGTATCAGTAGTCATGTATTTAGAA
17829 ATATCGATAG
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
114 1 0.01
115 1 0.01
116 79 0.96
117 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.27, T:0.33
Consensus pattern (116 bp):
TGTATCGATAGAAATACAGGGTAGGAGAGAGATTGCATACTAACCTAGGTTGTATCAGTAGATGA
ATAACAAGTATCAGTAGTCATGTATTTAGAATTATTGGTATTTTGCATGTT
Found at i:17939 original size:21 final size:21
Alignment explanation
Indices: 17915--17966 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
17905 TAGAGGTGAA
17915 ACTTGTATCGGTAGAA-TAGTC
1 ACTTGTATCGGTAGAATTA-TC
*
17936 ACTTATATCGGTAGAATTATC
1 ACTTGTATCGGTAGAATTATC
*
17957 ATTTGTATCG
1 ACTTGTATCG
17967 TTAAAAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.38
Consensus pattern (21 bp):
ACTTGTATCGGTAGAATTATC
Found at i:24251 original size:52 final size:52
Alignment explanation
Indices: 24173--24405 Score: 297
Period size: 52 Copynumber: 4.5 Consensus size: 52
24163 AATAGGTTCA
*
24173 ATGACTATGTGTCATCGTGAGTATATGAATCATTTACGGATTATGAGGTCCG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCG
*
24225 ATGACTATGTGTCATCGTGAGTATATGAATCCTGTACGGATTATGAGGTCCG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCG
* * * * *
24277 ATAACTATGTGTCATCGTGAGTATACGAAGCCTTTACAGATTATGAGGTCTG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCG
* * ** * * *
24329 ATGATTATGTGTCATCGTGAGTATATGATTCCCAATACAGATTA-AAGGTCCA
1 ATGACTATGTGTCATCGTGAGTATATGAAT-CCTTTACGGATTATGAGGTCCG
* * *
24381 ATGACTCTGTGTCATCATAAGTATA
1 ATGACTATGTGTCATCGTGAGTATA
24406 AAAAATTCAT
Statistics
Matches: 158, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
52 147 0.93
53 11 0.07
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (52 bp):
ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCG
Found at i:28293 original size:24 final size:24
Alignment explanation
Indices: 28244--28294 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
28234 GTATACCCGT
* *
28244 TAACCATTCTAGGCTCGTAAGTGC
1 TAACCATTCTAGGCTCGCAAGAGC
* *
28268 TAACCATTCTAGGCTTGCGAGAGC
1 TAACCATTCTAGGCTCGCAAGAGC
28292 TAA
1 TAA
28295 TATTATCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (24 bp):
TAACCATTCTAGGCTCGCAAGAGC
Found at i:36005 original size:21 final size:23
Alignment explanation
Indices: 35981--36026 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
35971 CCTTTGCTAG
35981 TTCTACCGATACAAGT-ATG-AT
1 TTCTACCGATACAAGTCATGCAT
*
36002 TTCTACCGGTACAAGTCATGCAT
1 TTCTACCGATACAAGTCATGCAT
36025 TT
1 TT
36027 ACCAATACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.68
22 3 0.14
23 4 0.18
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (23 bp):
TTCTACCGATACAAGTCATGCAT
Found at i:42049 original size:37 final size:36
Alignment explanation
Indices: 41958--42053 Score: 129
Period size: 36 Copynumber: 2.6 Consensus size: 36
41948 CAGACAAGAT
* * *
41958 CTTTGGGTCAATAGGGAGAAAAATGAGCATAATGAC
1 CTTTGGGTCAACAGGGAGTAAAACGAGCATAATGAC
** *
41994 CTTCAGGTCAACAGGGAGTAAAACGAGCATCATGAC
1 CTTTGGGTCAACAGGGAGTAAAACGAGCATAATGAC
42030 CTTTGGGGTCAACAGGGAGTAAAA
1 CTTT-GGGTCAACAGGGAGTAAAA
42054 TGAATAACGA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 33 0.65
37 18 0.35
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (36 bp):
CTTTGGGTCAACAGGGAGTAAAACGAGCATAATGAC
Found at i:45474 original size:49 final size:49
Alignment explanation
Indices: 45417--46045 Score: 288
Period size: 49 Copynumber: 12.9 Consensus size: 49
45407 CTAGAGTTTG
* * * *
45417 AGAGGGATAGGTTGAAGCTGCAATGGTGGACCTAACACCCTAAAATCGA
1 AGAGGGATAGGTTGAAGCTGCAATGATAGATCTAACACCTTAAAATCGA
* * * ** * *
45466 AGAGGGATAGATTGAAGCCGTAATGGCAGATCTAACA--TAAAAAACTGA
1 AGAGGGATAGGTTGAAGCTGCAATGATAGATCTAACACCTTAAAATC-GA
* * * * * * * **
45514 AGAGGGAAAGATTGAAGCCGTAACGA-CGAATCTTACACCTTAAAATTAA
1 AGAGGGATAGGTTGAAGCTGCAATGATAG-ATCTAACACCTTAAAATCGA
* * * *
45563 AAAAGGATAGGTTAAAGCTGCAATGATAGA-CTTAACACCCTAAAATCGA
1 AGAGGGATAGGTTGAAGCTGCAATGATAGATC-TAACACCTTAAAATCGA
* * * * ** * * *
45612 AGAGGGAAAGATTAAAGTTGCAACAATAAATCTTACACCTTAAAA-CTAA
1 AGAGGGATAGGTTGAAGCTGCAATGATAGATCTAACACCTTAAAATC-GA
* ** *
45661 AGAGGGATAGGTTGAAGCCGCAATG-GCGAACCTAACACC-TAAAATCGA
1 AGAGGGATAGGTTGAAGCTGCAATGATAG-ATCTAACACCTTAAAATCGA
* * * *
45709 AGAGGGA-AGGATTGAAG-TCGCAATGACAAATCTTACACCTTAAAATTGA
1 AGAGGGATAGG-TTGAAGCT-GCAATGATAGATCTAACACCTTAAAATCGA
* * * * * *
45758 AGAGGGATAGGTTAAAGCCGCAACGACAAACCTAACACCTTAAAATCGA
1 AGAGGGATAGGTTGAAGCTGCAATGATAGATCTAACACCTTAAAATCGA
* *** ** *
45807 AGAGGG-TAGATTGAAGCAATAATGACGGATCTAA-ACCTTAAAACCGA
1 AGAGGGATAGGTTGAAGCTGCAATGATAGATCTAACACCTTAAAATCGA
* * * * * * * * *
45854 AAAGGGGA-AGATTAAAGCCGCAACGGTGGATCTTACACCTTAAAATTGA
1 AGA-GGGATAGGTTGAAGCTGCAATGATAGATCTAACACCTTAAAATCGA
* * * *
45903 AGAGGGATAGGTTTAAG-TCCGAATGATGGACCTAACA-CTCTAAAA-CTGA
1 AGAGGGATAGGTTGAAGCTGC-AATGATAGATCTAACACCT-TAAAATC-GA
* * * * *
45952 AGAGGGAACTA--TTCAAG-T-CACTATAATAGATTTTATACCTTAAAATCGA
1 AGAGGG-A-TAGGTTGAAGCTGCA--ATGATAGATCTAACACCTTAAAATCGA
* * * * * *
46001 AGAGGGATAGGTTGAAGTTGTAAGGGTAGACCTAACACCCTAAAA
1 AGAGGGATAGGTTGAAGCTGCAATGATAGATCTAACACCTTAAAA
46046 CCAAAAAGAG
Statistics
Matches: 431, Mismatches: 116, Indels: 66
0.70 0.19 0.11
Matches are distributed among these distances:
47 26 0.06
48 117 0.27
49 270 0.63
50 15 0.03
51 3 0.01
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.20
Consensus pattern (49 bp):
AGAGGGATAGGTTGAAGCTGCAATGATAGATCTAACACCTTAAAATCGA
Found at i:45704 original size:146 final size:146
Alignment explanation
Indices: 45421--45794 Score: 333
Period size: 146 Copynumber: 2.6 Consensus size: 146
45411 AGTTTGAGAG
* * * * *
45421 GGATAGGTTGAAGCTGCAATGGTGGACCTAACACCCTAAAATCGAAGAGGGATAGATTGAAGCCG
1 GGATAGGTTAAAGCTGCAATGATAGACCTAACACCCTAAAATCGAAGAGGGAAAGATTAAAGCCG
* *** * * * * *
45486 TAATGGCAGATCTAACATAAAAAACTGAAGAGGGAAAGATTGAAGCCGTAACGACGAATCTTACA
66 CAACAACAAATCTAACATAAAAAACTAAAGAGGGAAAGATTGAAGCCGCAACGACGAACCTAACA
45551 CCTTAAAATTAAAAAA
131 CCTTAAAATTAAAAAA
* **
45567 GGATAGGTTAAAGCTGCAATGATAGACTTAACACCCTAAAATCGAAGAGGGAAAGATTAAAGTTG
1 GGATAGGTTAAAGCTGCAATGATAGACCTAACACCCTAAAATCGAAGAGGGAAAGATTAAAGCCG
* * * * * * *
45632 CAACAATAAATCTTACACCT-TAAAACTAAAGAGGGATAGGTTGAAGCCGCAATGGCGAACCTAA
66 CAACAACAAATC-TA-ACATAAAAAACTAAAGAGGGAAAGATTGAAGCCGCAACGACGAACCTAA
** * *
45696 CACC-TAAAATCGAAGAG
129 CACCTTAAAATTAAAAAA
* * * * * * * * *
45713 GGA-AGGATTGAAG-TCGCAATGACAAATCTTACACCTTAAAATTGAAGAGGGATAGGTTAAAGC
1 GGATAGG-TTAAAGCT-GCAATGATAGACCTAACACCCTAAAATCGAAGAGGGAAAGATTAAAGC
* *
45776 CGCAACGACAAACCTAACA
64 CGCAACAACAAATCTAACA
45795 CCTTAAAATC
Statistics
Matches: 180, Mismatches: 44, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
144 2 0.01
145 6 0.03
146 128 0.71
147 41 0.23
148 3 0.02
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (146 bp):
GGATAGGTTAAAGCTGCAATGATAGACCTAACACCCTAAAATCGAAGAGGGAAAGATTAAAGCCG
CAACAACAAATCTAACATAAAAAACTAAAGAGGGAAAGATTGAAGCCGCAACGACGAACCTAACA
CCTTAAAATTAAAAAA
Found at i:45831 original size:97 final size:98
Alignment explanation
Indices: 45451--45876 Score: 359
Period size: 97 Copynumber: 4.4 Consensus size: 98
45441 GGTGGACCTA
* * * * * * * * * *
45451 ACACCCTAAAATCGAAGAGGGATAGATTGAAGCCGTAATGGCAGATCTAACA--TAAAAAACTGA
1 ACACCTTAAAATTGAAGAGGGATAGGTTAAAGCCGCAATGACAAACCTAACACCTTAAAATC-GA
*** * *
45514 AGAGGGAAAGATTGAAGCCGTAACGACGAATCTT
65 AGAGGGAAAGATTGAAGCAACAATGACAAATCTT
* * * * * * * *
45548 ACACCTTAAAATTAAAAAAGGATAGGTTAAAGCTGCAATGATAGACTTAACACCCTAAAATCGAA
1 ACACCTTAAAATTGAAGAGGGATAGGTTAAAGCCGCAATGACAAACCTAACACCTTAAAATCGAA
*
45613 GAGGGAAAGATTAAAGTTGCAACAAT---AAATCTT
66 GAGGGAAAGATTGAA---GCAACAATGACAAATCTT
* * * * *
45646 ACACCTTAAAACTAAAGAGGGATAGGTTGAAGCCGCAATGGCGAACCTAACACC-TAAAATCGAA
1 ACACCTTAAAATTGAAGAGGGATAGGTTAAAGCCGCAATGACAAACCTAACACCTTAAAATCGAA
* *
45710 GAGGGAAGGATTGAAGTC-GCAATGACAAATCTT
66 GAGGGAAAGATTGAAG-CAACAATGACAAATCTT
*
45743 ACACCTTAAAATTGAAGAGGGATAGGTTAAAGCCGCAACGACAAACCTAACACCTTAAAATCGAA
1 ACACCTTAAAATTGAAGAGGGATAGGTTAAAGCCGCAATGACAAACCTAACACCTTAAAATCGAA
* * **
45808 GAGGG-TAGATTGAAGCAATAATGACGGATC-T
66 GAGGGAAAGATTGAAGCAACAATGACAAATCTT
* ** * *
45839 AAACCTTAAAACCGAAAAGGGGA-AGATTAAAGCCGCAA
1 ACACCTTAAAATTGAAGA-GGGATAGGTTAAAGCCGCAA
45877 CGGTGGATCT
Statistics
Matches: 265, Mismatches: 52, Indels: 25
0.77 0.15 0.07
Matches are distributed among these distances:
94 5 0.02
95 1 0.00
96 30 0.11
97 138 0.52
98 82 0.31
99 5 0.02
101 4 0.02
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.18
Consensus pattern (98 bp):
ACACCTTAAAATTGAAGAGGGATAGGTTAAAGCCGCAATGACAAACCTAACACCTTAAAATCGAA
GAGGGAAAGATTGAAGCAACAATGACAAATCTT
Found at i:46200 original size:52 final size:52
Alignment explanation
Indices: 46097--46200 Score: 154
Period size: 52 Copynumber: 2.0 Consensus size: 52
46087 CCCTAAAACC
* * * **
46097 AAAGAGGGAACAGATTGAATCTGCAACGGCAAATCTTACACCTTTTGAAAAA
1 AAAGAGGGAACAGATTAAAGCTGCAACGGCAAATCTTACACCCTTAAAAAAA
*
46149 AAAGAGGGAACAGATTAAAGCTGCAACGGTAAATCTTACACCCTTAAAAAAA
1 AAAGAGGGAACAGATTAAAGCTGCAACGGCAAATCTTACACCCTTAAAAAAA
46201 CTATAGAGGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.45, C:0.17, G:0.18, T:0.19
Consensus pattern (52 bp):
AAAGAGGGAACAGATTAAAGCTGCAACGGCAAATCTTACACCCTTAAAAAAA
Found at i:46805 original size:17 final size:17
Alignment explanation
Indices: 46754--46811 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
46744 GAGGATTTTT
46754 TTTTTTGTTCAGAGAGAA
1 TTTTTTGTTCAGAGA-AA
***
46772 TTTTTT-TAGGGAGGAAA
1 TTTTTTGTTCAGA-GAAA
46789 TTTTTTGTTCAGAGAAA
1 TTTTTTGTTCAGAGAAA
46806 TTTTTT
1 TTTTTT
46812 TGAAATAAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 21 0.66
18 11 0.34
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (17 bp):
TTTTTTGTTCAGAGAAA
Found at i:46832 original size:24 final size:25
Alignment explanation
Indices: 46796--46883 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 25
46786 AAATTTTTTG
* *
46796 TTCAGAGAAATTTTTTTGAAATAAGA
1 TTCAGA-AAATTTTTTTGAAACAACA
* *
46822 TTCA-AAGATTTTTTT-ATACAACA
1 TTCAGAAAATTTTTTTGAAACAACA
*
46845 TTCAGAAAATTTTTTTGAGACATACA
1 TTCAGAAAATTTTTTTGAAACA-ACA
46871 TTCAAAGAAAATT
1 TTC--AGAAAATT
46884 CAAAGCAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
23 9 0.18
24 19 0.37
25 5 0.10
26 10 0.20
28 8 0.16
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (25 bp):
TTCAGAAAATTTTTTTGAAACAACA
Found at i:47136 original size:20 final size:20
Alignment explanation
Indices: 47082--47136 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
47072 CGTCTTATTA
47082 TTATTA-TTA-TTATTTAAT
1 TTATTATTTATTTATTTAAT
*
47100 TGT-TTATTT-TTGCATTTAAT
1 T-TATTATTTATT-TATTTAAT
47120 TTATTATTTATTTATTT
1 TTATTATTTATTTATTT
47137 GTCATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 4 0.14
19 5 0.17
20 18 0.62
21 2 0.07
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (20 bp):
TTATTATTTATTTATTTAAT
Found at i:48987 original size:66 final size:66
Alignment explanation
Indices: 48892--49025 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
48882 TTTTTCTCTC
48892 TTTATCGTATCATCCAAAAGACCCTCTAAATTTCCTCAGGTAATTCCTACTTATATTCTCTCTCA
1 TTTATCGTATCATCCAAAAGACCCTCTAAATTTCCTCAGGTAATTCCTACTTATATTCTCTCTCA
48957 G
66 G
48958 TTTATCGTATCATCCAAAAGACCCTCTAAATTTCCTCAGGTAATTCCTACTTATATTCTCTCTCA
1 TTTATCGTATCATCCAAAAGACCCTCTAAATTTCCTCAGGTAATTCCTACTTATATTCTCTCTCA
49023 G
66 G
49024 TT
1 TT
49026 ACCTGTTTTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.39
Consensus pattern (66 bp):
TTTATCGTATCATCCAAAAGACCCTCTAAATTTCCTCAGGTAATTCCTACTTATATTCTCTCTCA
G
Found at i:52344 original size:40 final size:40
Alignment explanation
Indices: 52300--52381 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
52290 TGATAATAAG
52300 AGAAAAAGGTTTCAAAGTGGAAACCGAAGTTAAGAAGAAA
1 AGAAAAAGGTTTCAAAGTGGAAACCGAAGTTAAGAAGAAA
52340 AGAAAAAGGTTTCAAAGTGGAAACCGAAGTTAAGAAGAAA
1 AGAAAAAGGTTTCAAAGTGGAAACCGAAGTTAAGAAGAAA
52380 AG
1 AG
52382 GGTTTTATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.52, C:0.07, G:0.26, T:0.15
Consensus pattern (40 bp):
AGAAAAAGGTTTCAAAGTGGAAACCGAAGTTAAGAAGAAA
Found at i:61977 original size:21 final size:21
Alignment explanation
Indices: 61951--61993 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
61941 GTATCCCAAA
61951 GATTCATCATTTAGTTTGCAT
1 GATTCATCATTTAGTTTGCAT
61972 GATTCATCATTTAGTTTGCAT
1 GATTCATCATTTAGTTTGCAT
61993 G
1 G
61994 CTTACTTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (21 bp):
GATTCATCATTTAGTTTGCAT
Found at i:63462 original size:15 final size:17
Alignment explanation
Indices: 63442--63476 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
63432 TCTTAAATGG
63442 TTAATTAATT-T-TTAA
1 TTAATTAATTATGTTAA
63457 TTAATTAATTATGTTAA
1 TTAATTAATTATGTTAA
63474 TTA
1 TTA
63477 TAAGAAGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 1 0.06
17 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTAATTAATTATGTTAA
Found at i:64949 original size:21 final size:21
Alignment explanation
Indices: 64920--64959 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
64910 AACGTTATAT
64920 GTGTAATGTGATCTATGATAA
1 GTGTAATGTGATCTATGATAA
* *
64941 GTGTTATGTGATGTATGAT
1 GTGTAATGTGATCTATGAT
64960 GTGTGAACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.42
Consensus pattern (21 bp):
GTGTAATGTGATCTATGATAA
Found at i:65155 original size:7 final size:7
Alignment explanation
Indices: 65131--65173 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
65121 ATACATGCTA
65131 AAATGTGG
1 AAATGT-G
65139 AAATTGTG
1 AAA-TGTG
65147 AAATGTG
1 AAATGTG
65154 AAATGTG
1 AAATGTG
*
65161 ATATGTG
1 AAATGTG
65168 AGAATG
1 A-AATG
65174 ATACATGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 18 0.58
8 10 0.32
9 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (7 bp):
AAATGTG
Found at i:65213 original size:53 final size:53
Alignment explanation
Indices: 65098--65214 Score: 157
Period size: 53 Copynumber: 2.2 Consensus size: 53
65088 GTGAAATTAT
* * *
65098 GTGATATGTGATATGTGAGCACGATACATGCTAAAATGTGGAAATTGTGAAAT
1 GTGATATGTGATATGTGAGAACGATACATGCTAAAATGTGGAAATCGTGAAAA
* *
65151 GTGAAATGTGATATGTGAGAATGATACATGCTAAAATGT-GAAAGTCGT-AACAA
1 GTGATATGTGATATGTGAGAACGATACATGCTAAAATGTGGAAA-TCGTGAA-AA
65204 GTGATATGTGA
1 GTGATATGTGA
65215 GCATGAAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
52 6 0.11
53 50 0.89
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (53 bp):
GTGATATGTGATATGTGAGAACGATACATGCTAAAATGTGGAAATCGTGAAAA
Found at i:66790 original size:25 final size:25
Alignment explanation
Indices: 66736--66791 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
66726 TCAGTCACTT
* *
66736 GAAAAAGGAAAATGAGAAAAAGGAA
1 GAAAAAGGAAAATGAAAAAAAAGAA
66761 GAAAAAGGAAAGA-GAAAAGAAAAGAA
1 GAAAAAGGAAA-ATGAAAA-AAAAGAA
66787 -AAAAA
1 GAAAAA
66792 TGTTTGCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 20 0.74
26 7 0.26
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (25 bp):
GAAAAAGGAAAATGAAAAAAAAGAA
Found at i:83996 original size:23 final size:23
Alignment explanation
Indices: 83970--84014 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
83960 ATTCTCCCAG
*
83970 AAATTCTACATCTTTGCCACCAT
1 AAATTCTACATCTTTGACACCAT
* *
83993 AAATTTTGCATCTTTGACACCA
1 AAATTCTACATCTTTGACACCA
84015 AAGAATCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.36
Consensus pattern (23 bp):
AAATTCTACATCTTTGACACCAT
Done.