Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009732.1 Kokia drynarioides strain JFW-HI SEQ_124451, 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: 104845
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:187 original size:14 final size:14
Alignment explanation
Indices: 170--205 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
160 CTGTTTGACT
*
170 GAAAATGATTTCTG
1 GAAAATGATTTCTA
184 GAAAATGATTTCTA
1 GAAAATGATTTCTA
198 GAAAATGA
1 GAAAATGA
206 ATTGCTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (14 bp):
GAAAATGATTTCTA
Found at i:20131 original size:22 final size:22
Alignment explanation
Indices: 20103--20148 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
20093 AAGCCAAACA
20103 AAAATAGAAAATAAAAAAAATT
1 AAAATAGAAAATAAAAAAAATT
* *
20125 AAAATAGAAAATAATAAAATTT
1 AAAATAGAAAATAAAAAAAATT
20147 AA
1 AA
20149 CATCGTGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAATAGAAAATAAAAAAAATT
Found at i:27976 original size:33 final size:32
Alignment explanation
Indices: 27925--27987 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
27915 AGTTAGAAGT
* * *
27925 AAAACTAGATGTCATTATTCTATAAAAATTACA
1 AAAAATAGATATCATTATTCT-GAAAAATTACA
*
27958 AAAAATAGATATCGTTATTCTGAAAAATTA
1 AAAAATAGATATCATTATTCTGAAAAATTA
27988 AAAGTTCACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (32 bp):
AAAAATAGATATCATTATTCTGAAAAATTACA
Found at i:45265 original size:18 final size:19
Alignment explanation
Indices: 45247--45282 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
45237 ATGAAGGAGA
45247 AAGAAAA-GAAGA-GAAAG
1 AAGAAAAGGAAGAGGAAAG
45264 AAGAAAAGGAAGAGGAAAG
1 AAGAAAAGGAAGAGGAAAG
45283 GGAGAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 5 0.29
19 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (19 bp):
AAGAAAAGGAAGAGGAAAG
Found at i:45296 original size:21 final size:21
Alignment explanation
Indices: 45242--45303 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
45232 ACGAGATGAA
45242 GGAGAAAGAAAAGAAGA-GAAA-
1 GGAG-AAG-AAAGAAGAGGAAAG
* *
45263 GAAGAA-AAGGAAGAGGAAAG
1 GGAGAAGAAAGAAGAGGAAAG
*
45283 GGAGAAGAAAGAAGAGCAAAG
1 GGAGAAGAAAGAAGAGGAAAG
45304 TATTGCCATG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
18 7 0.21
19 4 0.12
20 7 0.21
21 15 0.45
ACGTcount: A:0.61, C:0.02, G:0.37, T:0.00
Consensus pattern (21 bp):
GGAGAAGAAAGAAGAGGAAAG
Found at i:45720 original size:17 final size:17
Alignment explanation
Indices: 45695--45733 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
45685 CATTCATTTC
45695 TTTTAATTGTCAT-TGCA
1 TTTTAATTGTC-TCTGCA
*
45712 TTTTTATTGTCTCTGCA
1 TTTTAATTGTCTCTGCA
45729 TTTTA
1 TTTTA
45734 CTTTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (17 bp):
TTTTAATTGTCTCTGCA
Found at i:58850 original size:14 final size:14
Alignment explanation
Indices: 58833--58873 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
58823 AAATATAAAA
58833 TCATATTAAATAAT
1 TCATATTAAATAAT
* *
58847 TCATTTTAAATATT
1 TCATATTAAATAAT
58861 TC--ATTAAATAAT
1 TCATATTAAATAAT
58873 T
1 T
58874 TGGGTTGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 9 0.39
14 14 0.61
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (14 bp):
TCATATTAAATAAT
Found at i:58899 original size:23 final size:22
Alignment explanation
Indices: 58863--58906 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
58853 TAAATATTTC
*
58863 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
58886 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
58907 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:59383 original size:36 final size:36
Alignment explanation
Indices: 59343--59414 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
59333 CCCATTTCTC
59343 ACGCCTAGCATCATCTCTTCATAGAGATTTTAGCAA
1 ACGCCTAGCATCATCTCTTCATAGAGATTTTAGCAA
59379 ACGCCTAGCATCATCTCTTCATAGAGATTTTAGCAA
1 ACGCCTAGCATCATCTCTTCATAGAGATTTTAGCAA
59415 TTAAGCCTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (36 bp):
ACGCCTAGCATCATCTCTTCATAGAGATTTTAGCAA
Found at i:63435 original size:12 final size:12
Alignment explanation
Indices: 63414--63460 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
63404 TTGCTACAAA
63414 TTCTTCTTCTTT
1 TTCTTCTTCTTT
*
63426 TTCTTTTTCTTT
1 TTCTTCTTCTTT
* *
63438 TGCTTCTTCTCTC
1 TTCTTCTTCT-TT
63451 TTC-TCTTCTT
1 TTCTTCTTCTT
63461 CCTCCACTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 1 0.03
12 25 0.86
13 3 0.10
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:74121 original size:44 final size:44
Alignment explanation
Indices: 74058--74147 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
74048 GGCTTCATTG
74058 TGACATCGTCCTCAGTTCCGATTTATCATCCAGTTTACACTCTA
1 TGACATCGTCCTCAGTTCCGATTTATCATCCAGTTTACACTCTA
*
74102 TGACATCGTCCTCAGTTCCGATTTATCATCCAGTTTGCACTCTA
1 TGACATCGTCCTCAGTTCCGATTTATCATCCAGTTTACACTCTA
74146 TG
1 TG
74148 TCGTAACATG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (44 bp):
TGACATCGTCCTCAGTTCCGATTTATCATCCAGTTTACACTCTA
Found at i:81481 original size:82 final size:82
Alignment explanation
Indices: 81344--81564 Score: 334
Period size: 82 Copynumber: 2.7 Consensus size: 82
81334 GGATTCCTCT
* * *
81344 GATGGCTAAGTCTTCACATATGTTGCGGATTCTCATCAGCTTGTATGAGCAGCATCGAGAGTGAG
1 GATGGCTGAGTCTTCGCATATGTTGCGGATTCTCATCAGCTTGTGTGAGCAGCATCGAGAGTGAG
* *
81409 AAATTCTAGACTGTTTC
66 AAATTCTAGACCGTATC
* * *
81426 GATGGTTGAGTCTTCGCATATGTTGCGGATTCTCATCAGCTTGTGTAAGCAGCATCAAGAGTGAG
1 GATGGCTGAGTCTTCGCATATGTTGCGGATTCTCATCAGCTTGTGTGAGCAGCATCGAGAGTGAG
81491 AAATTCTAGACCGTATC
66 AAATTCTAGACCGTATC
* * * *
81508 GATGGCTGAGACTTTGCATATGTTACGGGTTCTCATCAGCTTGTGTGAGCAGCATCG
1 GATGGCTGAGTCTTCGCATATGTTGCGGATTCTCATCAGCTTGTGTGAGCAGCATCG
81565 TATACTGGTT
Statistics
Matches: 124, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 124 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (82 bp):
GATGGCTGAGTCTTCGCATATGTTGCGGATTCTCATCAGCTTGTGTGAGCAGCATCGAGAGTGAG
AAATTCTAGACCGTATC
Found at i:84776 original size:10 final size:10
Alignment explanation
Indices: 84761--84790 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
84751 ACTTTTTTAT
84761 TTAATATAAA
1 TTAATATAAA
*
84771 TTAATATAAT
1 TTAATATAAA
84781 TTAATATAAA
1 TTAATATAAA
84791 ATATTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TTAATATAAA
Found at i:94822 original size:15 final size:15
Alignment explanation
Indices: 94802--94832 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
94792 CATCCCTTTA
94802 TCCTCTCTTCCCAAC
1 TCCTCTCTTCCCAAC
*
94817 TCCTCTCTTCTCAAC
1 TCCTCTCTTCCCAAC
94832 T
1 T
94833 TAACTCCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.48, G:0.00, T:0.39
Consensus pattern (15 bp):
TCCTCTCTTCCCAAC
Found at i:97607 original size:23 final size:22
Alignment explanation
Indices: 97572--97651 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
97562 AAGCACTTAA
* *
97572 CAGTAAGCGCACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
97594 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * **
97617 CAGTAGGCGCACATAACGCATAT
1 CAGTAGGCACACACAGTGCA-AT
97640 CAGTAGGCACAC
1 CAGTAGGCACAC
97652 GAGGTGCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
22 16 0.33
23 33 0.67
ACGTcount: A:0.35, C:0.29, G:0.23, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:97667 original size:23 final size:23
Alignment explanation
Indices: 97640--97693 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
97630 TAACGCATAT
* *
97640 CAGTAGGCACACGAGGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
97663 TAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
97686 CAGTAAGC
1 CAGTAAGC
97694 GCGCTAGTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.30, T:0.11
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:102715 original size:29 final size:29
Alignment explanation
Indices: 102682--102974 Score: 322
Period size: 29 Copynumber: 10.0 Consensus size: 29
102672 CGGATACTTG
*
102682 GGGGT-AAAATGGTAATTTTTGGAAGTTTT
1 GGGGTAAAAATGG-GATTTTTGGAAGTTTT
* * * **
102711 CGGGTCAAGAATGAGATTTTTGGAAGTTCA
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTT
*
102741 GGGGTAAAAATGGGATTTTTGGAAGTTTC
1 GGGGTAAAAATGGGATTTTTGGAAGTTTT
* * *
102770 GAGGTAAAAAATGGGATTTTTAGAAG-TTC
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTT
102799 GAGGGTAAAAATGGGATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGGATTTTTGGAAGTTTT
* *
102829 GGGGTTAAAAATGGGATTTATGGAAG-TTC
1 GGGG-TAAAAATGGGATTTTTGGAAGTTTT
* *
102858 GAGGGAAAAAATGGGATTTTTTGAAGTTTT
1 G-GGGTAAAAATGGGATTTTTGGAAGTTTT
* * * *
102888 AGGGTCAAATTGGGATTTTTGGAAGTTTA
1 GGGGTAAAAATGGGATTTTTGGAAGTTTT
*
102917 GGGGTCAAAATGGGATTTTTGGAAGTTTT
1 GGGGTAAAAATGGGATTTTTGGAAGTTTT
*
102946 GGGGTTAAAATGGGATTTTTGGACAGTTT
1 GGGGTAAAAATGGGATTTTTGGA-AGTTT
102975 AGGGACCTTC
Statistics
Matches: 223, Mismatches: 32, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
29 146 0.65
30 72 0.32
31 5 0.02
ACGTcount: A:0.29, C:0.03, G:0.32, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGGGATTTTTGGAAGTTTT
Found at i:102759 original size:59 final size:58
Alignment explanation
Indices: 102682--102978 Score: 350
Period size: 59 Copynumber: 5.1 Consensus size: 58
102672 CGGATACTTG
* *
102682 GGGGT-AAAATGGTAATTTTTGGAAGTTTTCGGGTCAAGAATGAGATTTTTGGAAGTTCA
1 GGGGTAAAAATGG-GATTTTTGGAAGTTTTCGGGTCAA-AATGGGATTTTTGGAAGTTCA
* *
102741 GGGGTAAAAATGGGATTTTTGGAAG-TTTCGAGGTAAAAAATGGGATTTTTAGAAGTTC-
1 GGGGTAAAAATGGGATTTTTGGAAGTTTTCG-GGT-CAAAATGGGATTTTTGGAAGTTCA
* * *
102799 GAGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTATGGAAGTTC-
1 G-GGGTAAAAATGGGATTTTTGGAAGTTTTCGGG-TCAAAATGGGATTTTTGGAAGTTCA
* * * * *
102858 GAGGGAAAAAATGGGATTTTTTGAAGTTTTAGGGTCAAATTGGGATTTTTGGAAGTTTA
1 G-GGGTAAAAATGGGATTTTTGGAAGTTTTCGGGTCAAAATGGGATTTTTGGAAGTTCA
* * * *
102917 GGGGTCAAAATGGGATTTTTGGAAGTTTTGGGGTTAAAATGGGATTTTTGGACAGTTTA
1 GGGGTAAAAATGGGATTTTTGGAAGTTTTCGGGTCAAAATGGGATTTTTGGA-AGTTCA
102976 GGG
1 GGG
102979 ACCTTCAGGG
Statistics
Matches: 210, Mismatches: 20, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
58 71 0.34
59 125 0.60
60 14 0.07
ACGTcount: A:0.29, C:0.03, G:0.33, T:0.35
Consensus pattern (58 bp):
GGGGTAAAAATGGGATTTTTGGAAGTTTTCGGGTCAAAATGGGATTTTTGGAAGTTCA
Found at i:102822 original size:88 final size:88
Alignment explanation
Indices: 102720--102965 Score: 343
Period size: 88 Copynumber: 2.8 Consensus size: 88
102710 TCGGGTCAAG
* *
102720 AATGAGATTTTTGGAAGTTCAGGGGTAAAAATGGGATTTTTGGAAGTTTCGAGGTAAAAAATGGG
1 AATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGGATTTTTGGAAGTTTCGAGGTAAAAAATGGG
102785 ATTTTTAGAAGTTCGAGGGTAAA
66 ATTTTTAGAAGTTCGAGGGTAAA
* * *
102808 AATGGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTATGGAAG-TTCGAGGGAAAAAATGG
1 AATGGGATTTTTGGAAGTTTAGGGG-TAAAAATGGGATTTTTGGAAGTTTCGAGGTAAAAAATGG
* ** *
102872 GATTTTTTGAAGTTTTAGGGTCAA
65 GATTTTTAGAAGTTCGAGGGTAAA
* * * * *
102896 ATTGGGATTTTTGGAAGTTTAGGGGTCAAAATGGGATTTTTGGAAGTTTTGGGGT-TAAAATGGG
1 AATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGGATTTTTGGAAGTTTCGAGGTAAAAAATGGG
102960 ATTTTT
66 ATTTTT
102966 GGACAGTTTA
Statistics
Matches: 139, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
87 33 0.24
88 86 0.62
89 20 0.14
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (88 bp):
AATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGGATTTTTGGAAGTTTCGAGGTAAAAAATGGG
ATTTTTAGAAGTTCGAGGGTAAA
Found at i:103998 original size:13 final size:13
Alignment explanation
Indices: 103980--104006 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
103970 ATTATTATTA
103980 TCAAAACATTTAT
1 TCAAAACATTTAT
103993 TCAAAACATTTAT
1 TCAAAACATTTAT
104006 T
1 T
104007 ATTATTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TCAAAACATTTAT
Found at i:104770 original size:11 final size:11
Alignment explanation
Indices: 104754--104821 Score: 66
Period size: 11 Copynumber: 6.0 Consensus size: 11
104744 TTTTTTAATT
104754 TTAAATTTAAA
1 TTAAATTTAAA
104765 TTAAATTTAAA
1 TTAAATTTAAA
*
104776 TTTAAGA-TTAAT
1 -TTAA-ATTTAAA
104788 TTAAATTTAAA
1 TTAAATTTAAA
* *
104799 ATAAATCTAAA
1 TTAAATTTAAA
*
104810 TTTAAAATTAAA
1 -TTAAATTTAAA
104822 AAGGGGCCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
10 1 0.02
11 28 0.61
12 16 0.35
13 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:104773 original size:17 final size:17
Alignment explanation
Indices: 104748--104821 Score: 96
Period size: 17 Copynumber: 4.3 Consensus size: 17
104738 TTGAACTTTT
*
104748 TTAATTTTAAATTTAAA
1 TTAAATTTAAATTTAAA
104765 TTAAATTTAAATTTAAGA
1 TTAAATTTAAATTTAA-A
104783 TT-AATTTAAATTTAAA
1 TTAAATTTAAATTTAAA
* *
104799 ATAAATCTAAATTTAAAA
1 TTAAATTTAAATTT-AAA
104817 TTAAA
1 TTAAA
104822 AAGGGGCCCA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
16 2 0.04
17 38 0.76
18 10 0.20
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:104779 original size:6 final size:6
Alignment explanation
Indices: 104747--104821 Score: 77
Period size: 6 Copynumber: 13.0 Consensus size: 6
104737 TTTGAACTTT
*
104747 TTTAAT TTTAAA TTTAAA -TTAAA TTTAAA TTTAAGA -TT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
* * *
104793 TTTAAA -ATAAA TCTAAA TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
104822 AAGGGGCCCA
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
4 1 0.02
5 12 0.20
6 45 0.76
7 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:104798 original size:23 final size:23
Alignment explanation
Indices: 104748--104821 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 23
104738 TTGAACTTTT
*
104748 TTAATTTTAAATTTAAA-TTAAAT
1 TTAAATTTAAA-TTAAATTTAAAT
104771 TTAAATTTAAGATT-AATTTAAAT
1 TTAAATTTAA-ATTAAATTTAAAT
* *
104794 TTAAA-ATAAATCTAAATTTAAAA
1 TTAAATTTAAAT-TAAATTTAAAT
104817 TTAAA
1 TTAAA
104822 AAGGGGCCCA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
21 2 0.05
22 6 0.14
23 35 0.80
24 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (23 bp):
TTAAATTTAAATTAAATTTAAAT
Done.