Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001125.1 Kokia drynarioides strain JFW-HI SEQ_112411, 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: 75514
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:1278 original size:82 final size:82
Alignment explanation
Indices: 1141--1298 Score: 253
Period size: 82 Copynumber: 1.9 Consensus size: 82
1131 TTAGAAAAAC
* * *
1141 ATGTCCCATGAAAATAAAATGTAACCGTTGAAAAAATTATCACTTTTTAATAAATGAATAATTAT
1 ATGTCCCATGAAAATAAAATATAACCATTGAAAAAATCATCACTTTTTAATAAATGAATAATTAT
*
1206 GAATTTGCAATCTATTT
66 GAATTTACAATCTATTT
* * *
1223 ATGTCCCATGGAAATCAAATATAACCATTGAATAAATCATCACTTTTTAATAAATGAATAATTAT
1 ATGTCCCATGAAAATAAAATATAACCATTGAAAAAATCATCACTTTTTAATAAATGAATAATTAT
1288 GAATTTACAAT
66 GAATTTACAAT
1299 TTATAAATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 69 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (82 bp):
ATGTCCCATGAAAATAAAATATAACCATTGAAAAAATCATCACTTTTTAATAAATGAATAATTAT
GAATTTACAATCTATTT
Found at i:3650 original size:22 final size:22
Alignment explanation
Indices: 3622--3691 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
3612 AAATGTTTCG
**
3622 AACGCATATGCTGACGAGCGTA
1 AACGCATATGCTGGTGAGCGTA
3644 AACGCATATGCTGGTGAGCGTA
1 AACGCATATGCTGGTGAGCGTA
3666 AACGCATATGCTGGTGAGCGTA
1 AACGCATATGCTGGTGAGCGTA
3688 AACG
1 AACG
3692 TACTAAACGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AACGCATATGCTGGTGAGCGTA
Found at i:7302 original size:27 final size:27
Alignment explanation
Indices: 7264--7348 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 27
7254 TTCAATAATA
**
7264 ACAGAATATCGCTTGTTCGAGCCAGTT
1 ACAGAATATCGCTCATTCGAGCCAGTT
*
7291 ACAGAATATCGCTCATTTGAGCCAGTT
1 ACAGAATATCGCTCATTCGAGCCAGTT
* * * * *
7318 ACATAAAAATGGCTCATTTGAGCCAGAT
1 ACA-GAATATCGCTCATTCGAGCCAGTT
7346 ACA
1 ACA
7349 AATTTTTGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 27 0.54
28 23 0.46
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (27 bp):
ACAGAATATCGCTCATTCGAGCCAGTT
Found at i:7340 original size:28 final size:27
Alignment explanation
Indices: 7282--7350 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 27
7272 TCGCTTGTTC
* *
7282 GAGCCAGTTACAGAATATCGCTCATTT
1 GAGCCAGTTACAAAAAATCGCTCATTT
*
7309 GAGCCAGTTACATAAAAATGGCTCATTT
1 GAGCCAGTTACA-AAAAATCGCTCATTT
*
7337 GAGCCAGATACAAA
1 GAGCCAGTTACAAA
7351 TTTTTGACTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 14 0.38
28 23 0.62
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (27 bp):
GAGCCAGTTACAAAAAATCGCTCATTT
Found at i:17457 original size:26 final size:25
Alignment explanation
Indices: 17427--17478 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
17417 TTGAATTTAA
*
17427 TTACTCA-ATTTTGTTAATTTATTTTT
1 TTACTCAGATTTT-TT-ATTAATTTTT
17453 TTACTCAGATTTTTTATTAATTTTT
1 TTACTCAGATTTTTTATTAATTTTT
17478 T
1 T
17479 ATATATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 10 0.42
26 9 0.38
27 5 0.21
ACGTcount: A:0.23, C:0.08, G:0.04, T:0.65
Consensus pattern (25 bp):
TTACTCAGATTTTTTATTAATTTTT
Found at i:18310 original size:42 final size:42
Alignment explanation
Indices: 18238--18331 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 42
18228 CGGTTCTGCT
* * *
18238 GTTTCCGTCGACGGTTTCGCTGCTGATTGTTTAGATTCCGAA
1 GTTTCCGTCGAAGGTTTCGCTGCCGATTGTTCAGATTCCGAA
* * * **
18280 GTTTCTGTCGAAGGTTTCG-TCGCCGGTTGTTCGGATTCCGGG
1 GTTTCCGTCGAAGGTTTCGCT-GCCGATTGTTCAGATTCCGAA
18322 GTTTCCGTCG
1 GTTTCCGTCG
18332 CCGATTGCTT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
41 1 0.02
42 41 0.98
ACGTcount: A:0.10, C:0.22, G:0.31, T:0.37
Consensus pattern (42 bp):
GTTTCCGTCGAAGGTTTCGCTGCCGATTGTTCAGATTCCGAA
Found at i:18332 original size:30 final size:30
Alignment explanation
Indices: 18321--18394 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 30
18311 CGGATTCCGG
18321 GGTTTCCGTCGCCGATTGCTTGGAGTCAGC
1 GGTTTCCGTCGCCGATTGCTTGGAGTCAGC
* *
18351 GGTTTCCGTCGTTGCC-AGTGGTTTGGAGTCAGC
1 GGTTTCCGTC---GCCGA-TTGCTTGGAGTCAGC
18384 GGTTTCCGTCG
1 GGTTTCCGTCG
18395 TCTCCGGTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 11 0.29
32 1 0.03
33 26 0.68
ACGTcount: A:0.08, C:0.24, G:0.35, T:0.32
Consensus pattern (30 bp):
GGTTTCCGTCGCCGATTGCTTGGAGTCAGC
Found at i:18382 original size:33 final size:33
Alignment explanation
Indices: 18340--18458 Score: 168
Period size: 33 Copynumber: 3.6 Consensus size: 33
18330 CGCCGATTGC
* *
18340 TTGGAGTCAGCGGTTTCCGTCGTTGCCAGTGGT
1 TTGGAATCAGCGGTTTCCGTCGTTGCCGGTGGT
*
18373 TTGGAGTCAGCGGTTTCCGTCGTCT-CCGGTGGT
1 TTGGAATCAGCGGTTTCCGTCGT-TGCCGGTGGT
* * *
18406 TTGGAACCAGCGGTTTCCGTCGTCGCTGGTGGT
1 TTGGAATCAGCGGTTTCCGTCGTTGCCGGTGGT
18439 TTGGAATCAGCGGTTTCCGT
1 TTGGAATCAGCGGTTTCCGT
18459 GGAAGGTTTG
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
33 77 0.99
34 1 0.01
ACGTcount: A:0.09, C:0.23, G:0.35, T:0.33
Consensus pattern (33 bp):
TTGGAATCAGCGGTTTCCGTCGTTGCCGGTGGT
Found at i:23990 original size:16 final size:16
Alignment explanation
Indices: 23971--24004 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23961 TTAAATTTTC
23971 TTATAAATAAAAAAAA
1 TTATAAATAAAAAAAA
* *
23987 TTATAAATCAATAAAA
1 TTATAAATAAAAAAAA
24003 TT
1 TT
24005 GCACTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
TTATAAATAAAAAAAA
Found at i:33378 original size:21 final size:22
Alignment explanation
Indices: 33332--33399 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
33322 CCATGCCTTG
* * *
33332 AGACATATA-AGCTTTTGTATCG
1 AGACATATAGA-CTTTTATCTCA
*
33354 AGACA-ATAGGCTTTTATCTCA
1 AGACATATAGACTTTTATCTCA
* *
33375 AGACATGTAGACTTTTGTCTCA
1 AGACATATAGACTTTTATCTCA
33397 AGA
1 AGA
33400 AAGCAACCCT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 16 0.43
22 21 0.57
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (22 bp):
AGACATATAGACTTTTATCTCA
Found at i:33657 original size:2 final size:2
Alignment explanation
Indices: 33650--33685 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
33640 AGGACAAATA
33650 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33686 GTAATTTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36844 original size:5 final size:5
Alignment explanation
Indices: 36834--36864 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
36824 TTTTTCGTCG
36834 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT T
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT T
36865 TTCCCCTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TCCTT
Found at i:39959 original size:13 final size:13
Alignment explanation
Indices: 39941--39965 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39931 TCTTTGGGTT
39941 TTTAATAAATAAC
1 TTTAATAAATAAC
39954 TTTAATAAATAA
1 TTTAATAAATAA
39966 AAAAAAATAT
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):
TTTAATAAATAAC
Found at i:62185 original size:18 final size:18
Alignment explanation
Indices: 62162--62204 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
62152 AAATACACTT
62162 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
62180 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
62198 TTAATTA
1 TTAATTA
62205 TACCTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:65491 original size:93 final size:93
Alignment explanation
Indices: 65218--65725 Score: 315
Period size: 93 Copynumber: 5.4 Consensus size: 93
65208 AAAAAGGAAG
* * * * * *
65218 AAACTCAAAG-AGTAGCTTGCAAAGGTGACAGAAAGCTATAAACTTAAACAAAAACGATCATCAT
1 AAACTCGAAGAAG-AGCTTGAAAAGGTGACAAAAAGCTATAAACTTAAACAGAAACAACCATCAT
* * *
65282 -TGTCATTGGAACCTGAAAAGGATATCAAT
65 CT-TCATTGGAACCCGAAAAGGAGATCGAT
* * * * * *
65311 AAA-TCCGAAGAAGAAGAGCCT-AGAAAGGTAACAAAAAGGTATAAACGTAAACAAAAAGCAGCC
1 AAACT-C---GAAGAAGAGCTTGA-AAAGGTGACAAAAAGCTATAAACTTAAACAGAAA-CAACC
* * * *
65374 ATCATATTCATTAGAACCCG-AAAGGAGATTGGT
60 ATCATCTTCATTGGAACCCGAAAAGGAGATCGAT
* *
65407 AAACTCGAAGAAGAGCTTGAAAAGGTGACAAAAAGTTATAAACTTAAATAGAAACAACCATCATC
1 AAACTCGAAGAAGAGCTTGAAAAGGTGACAAAAAGCTATAAACTTAAACAGAAACAACCATCATC
* *
65472 TTCATCGGAACCCGAAAAGGAGATTGAT
66 TTCATTGGAACCCGAAAAGGAGATCGAT
* * * * * * **
65500 AAACAT-GAAGAATAAGGGCTTAAAAAGGTAACAGAAAGGTA-AAACTTAAA-TGAAAACGGCCA
1 AAAC-TCGAAG---AAGAGCTTGAAAAGGTGACAAAAAGCTATAAACTTAAACAG-AAACAACCA
* ** ** * *
65562 TCATCTTCATTGAAACTTGAAAAAAACACCG-T
61 TCATCTTCATTGGAACCCGAAAAGGAGATCGAT
* * *
65594 AAAC-CTGAAGAAGAGCTTTTAAAA-GTGACAGAAAGCTATAAACTTAAAC-GAAACCGAA-TAT
1 AAACTC-GAAGAAGAGC-TTGAAAAGGTGACAAAAAGCTATAAACTTAAACAGAAA-C-AACCAT
* *** * *
65655 AATCTTCATCAAAATCCAAAAAGGAGATCGAT
62 CATCTTCATTGGAACCCGAAAAGGAGATCGAT
* *
65687 AAACCCGAAGAAGAG-TTCGAAAACGTGACAAAAAGCTAT
1 AAACTCGAAGAAGAGCTT-GAAAAGGTGACAAAAAGCTAT
65726 CATCTTCTAC
Statistics
Matches: 324, Mismatches: 64, Indels: 54
0.73 0.14 0.12
Matches are distributed among these distances:
91 22 0.07
92 64 0.20
93 92 0.28
94 13 0.04
95 38 0.12
96 73 0.23
97 21 0.06
98 1 0.00
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.19
Consensus pattern (93 bp):
AAACTCGAAGAAGAGCTTGAAAAGGTGACAAAAAGCTATAAACTTAAACAGAAACAACCATCATC
TTCATTGGAACCCGAAAAGGAGATCGAT
Found at i:65540 original size:189 final size:187
Alignment explanation
Indices: 65218--65572 Score: 428
Period size: 189 Copynumber: 1.9 Consensus size: 187
65208 AAAAAGGAAG
* * * *
65218 AAACTCAAAGAGTAGCTTGCAAAGGTGACAGAAAGCTATAAACTTAAACAAAAACGATCATCATT
1 AAACTCAAAGAGTAGCTTGAAAAGGTGACAAAAAGCTATAAACTTAAACAAAAACAACCATCATT
* * * *
65283 GTCATTGGAACCTGAAAAGGATATCAATAAATCCGAAGAAGAAGAGCCTAGAAAGGTAACAAAAA
66 GTCATCGGAACCCGAAAAGGAGATCAATAAATCCGAAGAAGAAGAGCCTAAAAAGGTAACAAAAA
65348 GGTATAAACGTAAACAAAAAGCAGCCATCATATTCATTAGAACCCGAAAGGAGATTGGT
131 GGTA-AAACGTAAACAAAAA-CAGCCATCATATTCATTAGAACCCGAAAGGAGATTGGT
* * * *
65407 AAACTCGAAGAAG-AGCTTGAAAAGGTGACAAAAAGTTATAAACTTAAATAGAAACAACCATCAT
1 AAACTCAAAG-AGTAGCTTGAAAAGGTGACAAAAAGCTATAAACTTAAACAAAAACAACCATCAT
** * * * * *
65471 CT-TCATCGGAACCCGAAAAGGAGATTGATAAA-CATGAAGAATAAGGGCTTAAAAAGGTAACAG
65 -TGTCATCGGAACCCGAAAAGGAGATCAATAAATC-CGAAGAAGAAGAGCCTAAAAAGGTAACAA
* ** * *
65534 AAAGGTAAAACTTAAATGAAAACGGCCATCATCTTCATT
128 AAAGGTAAAACGTAAACAAAAACAGCCATCATATTCATT
65573 GAAACTTGAA
Statistics
Matches: 139, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
187 15 0.11
188 13 0.09
189 108 0.78
190 3 0.02
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (187 bp):
AAACTCAAAGAGTAGCTTGAAAAGGTGACAAAAAGCTATAAACTTAAACAAAAACAACCATCATT
GTCATCGGAACCCGAAAAGGAGATCAATAAATCCGAAGAAGAAGAGCCTAAAAAGGTAACAAAAA
GGTAAAACGTAAACAAAAACAGCCATCATATTCATTAGAACCCGAAAGGAGATTGGT
Found at i:68634 original size:30 final size:30
Alignment explanation
Indices: 68600--68657 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
68590 ATCACCATCT
*
68600 CCATCACCGGCACCATCACCTGTCGAAGTG
1 CCATCACCGGCACCATCACCTGTAGAAGTG
* *
68630 CCATCACCGGCACCGTCGCCTGTAGAAG
1 CCATCACCGGCACCATCACCTGTAGAAG
68658 CTCCACCTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.22, C:0.40, G:0.22, T:0.16
Consensus pattern (30 bp):
CCATCACCGGCACCATCACCTGTAGAAGTG
Found at i:71721 original size:30 final size:30
Alignment explanation
Indices: 71687--72224 Score: 554
Period size: 30 Copynumber: 17.9 Consensus size: 30
71677 ATCACCACCT
* *
71687 CCATCACCAGCACCATCACTTGTAGAAGTG
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
* * *
71717 CCATCACCAGCACCGTTATCTGTAGAAATG
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
**
71747 CCATCACCAGGTCCGTCACCTGTAGAAGTG
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
*
71777 CCATCACCAGCACCGACACCTGTAGAAGTG
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
* ** * *
71807 CCATTACCAGCACTATCACCTGTAGAATTT
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
* *
71837 CCATCACCAACATCGTCACCTGTAGAAGTG
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
* *
71867 CCATCACCAACATCGTCACCTGTAGAAGTG
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
** * *
71897 CCATCACCAGCACTTTCACCTGTACAAGTA
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
* * * *
71927 CCATCACCTGCACCATCATCTGCAGAAGTG
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
* * * *
71957 CCATTACCAGCACTGTCACCTGTAGAATTT
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
* * * *
71987 CCATTACCAGCACTGTCACCTATAGAAATG
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
* * **
72017 CCATCACCAGCACTGTCACCTGTTGAAGCA
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
* * * *
72047 CCATCACTAGCATCATCATCTGTAGAAGTG
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
* * * * * *
72077 CCATTACCTGCACTGTCACTTGTAGAATTT
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
72107 CCATCACCAGCACCGTCACCTGTAGAAGTG
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
* * *
72137 TCATCACCAGCAGCGTCACCTGTAGAATTG
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
* * ** * *
72167 TCAACACCAAAAGCGTCACCTGTAAAAGTG
1 CCATCACCAGCACCGTCACCTGTAGAAGTG
* *
72197 CCATCACCGGCACCGTCGCCTGTAGAAG
1 CCATCACCAGCACCGTCACCTGTAGAAG
72225 CTCCACATTC
Statistics
Matches: 412, Mismatches: 96, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 412 1.00
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.22
Consensus pattern (30 bp):
CCATCACCAGCACCGTCACCTGTAGAAGTG
Found at i:73053 original size:23 final size:23
Alignment explanation
Indices: 73027--73071 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
73017 GTGATTGAAA
*
73027 ATAATTTAAGAATATTTAAAAAG
1 ATAATATAAGAATATTTAAAAAG
*
73050 ATAATATAAGAATTTTTAAAAA
1 ATAATATAAGAATATTTAAAAA
73072 TTATTTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (23 bp):
ATAATATAAGAATATTTAAAAAG
Found at i:74778 original size:30 final size:30
Alignment explanation
Indices: 74744--74809 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
74734 ACCGTCACCC
74744 GTAGAAGTGCCATCACCGGTACAGTCGCCT
1 GTAGAAGTGCCATCACCGGTACAGTCGCCT
74774 GTAGAAGTGCCATCACCGGTACAGTCGCCT
1 GTAGAAGTGCCATCACCGGTACAGTCGCCT
74804 GTAGAA
1 GTAGAA
74810 ACTCCAACAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.26, C:0.27, G:0.27, T:0.20
Consensus pattern (30 bp):
GTAGAAGTGCCATCACCGGTACAGTCGCCT
Found at i:74821 original size:30 final size:30
Alignment explanation
Indices: 74744--74822 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
74734 ACCGTCACCC
* *
74744 GTAGAAGTGCCATCACCGGTACAGTCGCCT
1 GTAGAACTGCCAACACCGGTACAGTCGCCT
* *
74774 GTAGAAGTGCCATCACCGGTACAGTCGCCT
1 GTAGAACTGCCAACACCGGTACAGTCGCCT
74804 GTAGAAACT-CCAACACCGG
1 GTAG-AACTGCCAACACCGG
74823 CAGAACGGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 43 0.93
31 3 0.07
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (30 bp):
GTAGAACTGCCAACACCGGTACAGTCGCCT
Found at i:75466 original size:17 final size:17
Alignment explanation
Indices: 75444--75476 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
75434 TACAATGATC
75444 AAAATAA-ATTTAAATTG
1 AAAATAACA-TTAAATTG
75461 AAAATAACATTAAATT
1 AAAATAACATTAAATT
75477 ATTTGGACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAATAACATTAAATTG
Done.