Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013606.1 Kokia drynarioides strain JFW-HI SEQ_128633, 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: 122222
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:769 original size:34 final size:33
Alignment explanation
Indices: 719--782 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
709 TGGTATCTTA
*
719 ATTTTTTTATCCAATTT-GTTACTTGAATTTGAT
1 ATTTTTTTATCCAATTTAG-TACTTAAATTTGAT
*
752 ATTTTTTTTTCCTAATTTAGTACTTAAATTT
1 ATTTTTTTATCC-AATTTAGTACTTAAATTT
783 TTTTAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 11 0.41
34 15 0.56
35 1 0.04
ACGTcount: A:0.25, C:0.09, G:0.06, T:0.59
Consensus pattern (33 bp):
ATTTTTTTATCCAATTTAGTACTTAAATTTGAT
Found at i:10527 original size:9 final size:9
Alignment explanation
Indices: 10499--10561 Score: 63
Period size: 9 Copynumber: 7.0 Consensus size: 9
10489 TTTGCATTGC
*
10499 CATCACCAT
1 CATCATCAT
*
10508 CACCATCAT
1 CATCATCAT
*
10517 CATCATTAT
1 CATCATCAT
* *
10526 CACCATCAC
1 CATCATCAT
*
10535 CATCTTCAT
1 CATCATCAT
10544 CATCATCAT
1 CATCATCAT
*
10553 CATCTTCAT
1 CATCATCAT
10562 GTGAGAATCC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.30, C:0.38, G:0.00, T:0.32
Consensus pattern (9 bp):
CATCATCAT
Found at i:10528 original size:24 final size:24
Alignment explanation
Indices: 10499--10556 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
10489 TTTGCATTGC
10499 CATCACCATCACCATCATCATCAT
1 CATCACCATCACCATCATCATCAT
* *
10523 TATCACCATCACCATCTTCATCAT
1 CATCACCATCACCATCATCATCAT
*
10547 CATCATCATC
1 CATCACCATC
10557 TTCATGTGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.31, C:0.40, G:0.00, T:0.29
Consensus pattern (24 bp):
CATCACCATCACCATCATCATCAT
Found at i:10544 original size:6 final size:6
Alignment explanation
Indices: 10499--10561 Score: 63
Period size: 6 Copynumber: 10.5 Consensus size: 6
10489 TTTGCATTGC
* * * * * *
10499 CATCAC CATCAC CATCAT CATCAT TATCAC CATCAC CATCTT CATCAT
1 CATCAT CATCAT CATCAT CATCAT CATCAT CATCAT CATCAT CATCAT
*
10547 CATCAT CATCTT CAT
1 CATCAT CATCAT CAT
10562 GTGAGAATCC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.30, C:0.38, G:0.00, T:0.32
Consensus pattern (6 bp):
CATCAT
Found at i:10557 original size:18 final size:18
Alignment explanation
Indices: 10505--10561 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
10495 TTGCCATCAC
10505 CATCACCATCATCATCATT
1 CATCACCATCATCATC-TT
*
10524 -ATCACCATCACCATCTT
1 CATCACCATCATCATCTT
*
10541 CATCATCATCATCATCTT
1 CATCACCATCATCATCTT
10559 CAT
1 CAT
10562 GTGAGAATCC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.06
18 32 0.94
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (18 bp):
CATCACCATCATCATCTT
Found at i:18323 original size:15 final size:16
Alignment explanation
Indices: 18296--18325 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18286 GGGGAAAAAA
18296 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
18312 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
18326 AATAGGAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:19154 original size:19 final size:19
Alignment explanation
Indices: 19130--19172 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
19120 AAACATGAAT
19130 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
19149 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
19168 TAAAT
1 TAAAT
19173 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:20471 original size:19 final size:19
Alignment explanation
Indices: 20394--20464 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
20384 AGATTAGGGA
*
20394 TGCTTACACAAGCTAACAT
1 TGCTCACACAAGCTAACAT
* *
20413 TGCTTACACAATCTAACAT
1 TGCTCACACAAGCTAACAT
* * *
20432 TACTCACACAAGCTGATAT
1 TGCTCACACAAGCTAACAT
20451 TGCTCACACAAGCT
1 TGCTCACACAAGCT
20465 GATATTGTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.35, C:0.28, G:0.10, T:0.27
Consensus pattern (19 bp):
TGCTCACACAAGCTAACAT
Found at i:22598 original size:16 final size:16
Alignment explanation
Indices: 22569--22599 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22559 AGGTTTTGAA
*
22569 AATTTGGGGTTTTTAG
1 AATTTAGGGTTTTTAG
22585 AATTTAGGGTTTTTA
1 AATTTAGGGTTTTTA
22600 AGTTTGAGCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.52
Consensus pattern (16 bp):
AATTTAGGGTTTTTAG
Found at i:31540 original size:22 final size:22
Alignment explanation
Indices: 31515--31558 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
31505 TGCTACCTTA
31515 GGTTTTAGTTATGATGGTAGAT
1 GGTTTTAGTTATGATGGTAGAT
31537 GGTTTTAGTTATGATGGTAGAT
1 GGTTTTAGTTATGATGGTAGAT
31559 ATAACTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (22 bp):
GGTTTTAGTTATGATGGTAGAT
Found at i:37089 original size:12 final size:12
Alignment explanation
Indices: 37072--37096 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37062 ATTATACTTA
37072 TATATATTTTTG
1 TATATATTTTTG
37084 TATATATTTTTG
1 TATATATTTTTG
37096 T
1 T
37097 CTTAAAGTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TATATATTTTTG
Found at i:47134 original size:13 final size:13
Alignment explanation
Indices: 47104--47136 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
47094 AGTTTTAAAT
*
47104 ACTTTTTTTTTTA
1 ACTTTTTATTTTA
47117 A-TTTTTATTTTA
1 ACTTTTTATTTTA
47129 ACTTTTTA
1 ACTTTTTA
47137 AAATTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (13 bp):
ACTTTTTATTTTA
Found at i:50320 original size:2 final size:2
Alignment explanation
Indices: 50313--50345 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
50303 TTTAAACTAT
50313 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
50346 GTGAGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:65478 original size:29 final size:31
Alignment explanation
Indices: 65426--65500 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 31
65416 ATTTTAAATT
* *
65426 AATAAT-AAAATTATACTTTGATC-TCCAAA
1 AATAATAAAAATTATAATTTAATCTTCCAAA
**
65455 AATAATAAAAATT-TAATTTAATCTTTTAAA
1 AATAATAAAAATTATAATTTAATCTTCCAAA
*
65485 AATATTAAAAA-TATAA
1 AATAATAAAAATTATAA
65501 ACTATTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
29 15 0.39
30 23 0.61
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (31 bp):
AATAATAAAAATTATAATTTAATCTTCCAAA
Found at i:66040 original size:14 final size:15
Alignment explanation
Indices: 66009--66046 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
65999 TATTTTTTAT
*
66009 TTAAATAAACATTAA
1 TTAAATAAACAATAA
66024 TTAAATAAA-AATAA
1 TTAAATAAACAATAA
66038 TTAAATAAA
1 TTAAATAAA
66047 TTATCTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAATAAACAATAA
Found at i:66487 original size:26 final size:26
Alignment explanation
Indices: 66455--66525 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 26
66445 TATATTATCT
* *
66455 TAAATATTTAATTAGATAATCAGAAA
1 TAAATATTTAATTAGATAATAAAAAA
66481 TAAATATTTAATTAGATAATAAAAAA
1 TAAATATTTAATTAGATAATAAAAAA
*
66507 TAAATATTTAATTAAATAA
1 TAAATATTTAATTAGATAA
66526 AAATAGATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (26 bp):
TAAATATTTAATTAGATAATAAAAAA
Found at i:71014 original size:25 final size:26
Alignment explanation
Indices: 70960--71025 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 26
70950 AATAATTTGA
* *
70960 AAAAAAATTACCATTA-ATTTTCATT
1 AAAAAAATTACCATTAGACTTTCATG
*
70985 TAAAAAATTACCATTAGACTTTCA-G
1 AAAAAAATTACCATTAGACTTTCATG
*
71010 AAAAAAA-TACTATTAG
1 AAAAAAATTACCATTAG
71026 TTTTGTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 8 0.23
25 21 0.60
26 6 0.17
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAAAAATTACCATTAGACTTTCATG
Found at i:75297 original size:40 final size:40
Alignment explanation
Indices: 75215--75303 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
75205 AAAATTTATA
* * * * *
75215 TTTAATACAATAAAATATTTATTATATTTATTTGTGTTTT
1 TTTAATATAATAAAACATTTATTATATTCATTGGTGTGTT
75255 TTTAATATAATAAAACATTTATTATATTCA-TGGTAGTGTT
1 TTTAATATAATAAAACATTTATTATATTCATTGGT-GTGTT
75295 TTT-ATATAA
1 TTTAATATAA
75304 ATATATTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 9 0.21
40 34 0.79
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (40 bp):
TTTAATATAATAAAACATTTATTATATTCATTGGTGTGTT
Found at i:81385 original size:24 final size:24
Alignment explanation
Indices: 81358--81405 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
81348 TCAATTTCCG
81358 CTTATGGTTGCATTTCGAAGTATT
1 CTTATGGTTGCATTTCGAAGTATT
81382 CTTATGGTTGCATTTCGAAGTATT
1 CTTATGGTTGCATTTCGAAGTATT
81406 AAAGCTGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.46
Consensus pattern (24 bp):
CTTATGGTTGCATTTCGAAGTATT
Found at i:84372 original size:22 final size:22
Alignment explanation
Indices: 84347--84399 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
84337 CAAATGAACG
*
84347 GAGAGCACTAAGATGTTAAACA
1 GAGAGCACTAAGATGCTAAACA
* *
84369 GAGAGCACAAATATGCTAAACA
1 GAGAGCACTAAGATGCTAAACA
84391 GAGAGCACT
1 GAGAGCACT
84400 TTACGTGCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (22 bp):
GAGAGCACTAAGATGCTAAACA
Found at i:88452 original size:25 final size:24
Alignment explanation
Indices: 88407--88457 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
88397 ACTAAATCGA
88407 AAAATTTAAAATTGAAAAAAATCAG
1 AAAATTTAAAATTGAAAAAAAT-AG
* **
88432 AAAATTTAATATTGACCAAAATAG
1 AAAATTTAAAATTGAAAAAAATAG
88456 AA
1 AA
88458 TTTTCACTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.61, C:0.06, G:0.08, T:0.25
Consensus pattern (24 bp):
AAAATTTAAAATTGAAAAAAATAG
Found at i:90817 original size:24 final size:24
Alignment explanation
Indices: 90786--90846 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
90776 AAGTTCACAG
90786 ACTACCGATACTTCTATAAGTAGA
1 ACTACCGATACTTCTATAAGTAGA
90810 ACTACCGATACTTCTATAAGTAGA
1 ACTACCGATACTTCTATAAGTAGA
90834 ACTACCGATACTT
1 ACTACCGATACTT
90847 ATCTTACATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (24 bp):
ACTACCGATACTTCTATAAGTAGA
Found at i:91971 original size:52 final size:52
Alignment explanation
Indices: 91576--91970 Score: 601
Period size: 52 Copynumber: 7.6 Consensus size: 52
91566 TTCTCATTTG
* **
91576 ATACTCACGATGATACATAGTCATCGAACCTCATAATCCAAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
* * * **
91628 ATGCTTACGATGACACATAGTCATTGGCCCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
* *
91680 ATACTCATGATGACACATAGTCATCGAACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
* * *
91732 ATACTCACGATGACACATAGTCACCGGACCTCATAATCCGTAAAGGATCCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
* * *
91784 ATACTTACGATGACACATAGTTATCGAACCTCATAATCCGTAAAGGATCCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
91836 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
* *
91888 ATACTCACGATGACACATAGTCATCGAACCTTATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
* * *
91940 ATACTCACGTTAACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGAACCT
91971 TTTGCATTTA
Statistics
Matches: 311, Mismatches: 32, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 311 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
Found at i:97108 original size:16 final size:17
Alignment explanation
Indices: 97087--97122 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
97077 TTTTCATGTA
*
97087 AATCGAGTTAAAATT-T
1 AATCGACTTAAAATTAT
97103 AATCGACTTAAAATTAT
1 AATCGACTTAAAATTAT
97120 AAT
1 AAT
97123 TTTATTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.36
Consensus pattern (17 bp):
AATCGACTTAAAATTAT
Found at i:102767 original size:12 final size:12
Alignment explanation
Indices: 102752--102776 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
102742 CTAAGATATT
102752 TCCCCTTATTTC
1 TCCCCTTATTTC
102764 TCCCCTTATTTC
1 TCCCCTTATTTC
102776 T
1 T
102777 AAATAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.40, G:0.00, T:0.52
Consensus pattern (12 bp):
TCCCCTTATTTC
Found at i:104622 original size:19 final size:19
Alignment explanation
Indices: 104580--104710 Score: 88
Period size: 21 Copynumber: 6.6 Consensus size: 19
104570 CAAAATTATT
*
104580 TTTTTAGAATTTTTT-TAAA
1 TTTTTA-AATTTTTTATATA
* *
104599 ATTTTAACTTTTTTATATA
1 TTTTTAAATTTTTTATATA
104618 TTTTTAGAATTTTTTA-AT-
1 TTTTTA-AATTTTTTATATA
104636 TTTTATAAATTTTTTAATATAA
1 TTTT-TAAATTTTTT-ATAT-A
* * *
104658 ATTTTGAATTTTTATAGATA
1 TTTTTAAATTTTT-TATATA
* *
104678 TTTTTAATTTTATTTATTTTA
1 TTTTTAAATTT-TTTA-TATA
*
104699 TTTTTGAATTTT
1 TTTTTAAATTTT
104711 ATTTTAAATT
Statistics
Matches: 87, Mismatches: 15, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
18 19 0.22
19 18 0.21
20 22 0.25
21 24 0.28
22 4 0.05
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTTTAAATTTTTTATATA
Found at i:104691 original size:12 final size:12
Alignment explanation
Indices: 104676--104734 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
104666 TTTTTATAGA
104676 TATTTTTAATTT
1 TATTTTTAATTT
104688 TA--TTT-ATTT
1 TATTTTTAATTT
104697 TATTTTTGAATTT
1 TATTTTT-AATTT
*
104710 TATTTTAAATTAT
1 TATTTTTAATT-T
*
104723 T-TTTGTAATTT
1 TATTTTTAATTT
104734 T
1 T
104735 TGTTGAGAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
9 6 0.15
10 3 0.08
11 5 0.13
12 13 0.33
13 12 0.31
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.71
Consensus pattern (12 bp):
TATTTTTAATTT
Found at i:104722 original size:23 final size:22
Alignment explanation
Indices: 104659--104734 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
104649 TTAATATAAA
* *
104659 TTTTGAATTTT-TATAGA-TAT
1 TTTTGAATTTTATTTAAATTAT
**
104679 TTTT-AATTTTATTTATTTTAT
1 TTTTGAATTTTATTTAAATTAT
104700 TTTTGAATTTTATTTTAAATTAT
1 TTTTGAATTTTA-TTTAAATTAT
104723 TTTTGTAATTTT
1 TTTTG-AATTTT
104735 TGTTGAGAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
19 6 0.13
20 7 0.15
21 7 0.15
22 7 0.15
23 13 0.28
24 6 0.13
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTGAATTTTATTTAAATTAT
Found at i:116508 original size:25 final size:25
Alignment explanation
Indices: 116437--116515 Score: 115
Period size: 25 Copynumber: 3.2 Consensus size: 25
116427 CGAAATACTT
* *
116437 AACAGAAGCGCATAAGTGCTGAAGA
1 AACAGAAGCACATAAGTGCTGGAGA
* *
116462 AAAAGAAGCACGTAAGTGCTGGAGA
1 AACAGAAGCACATAAGTGCTGGAGA
116487 AACAGAAGCACATAAGTGCTGG-GA
1 AACAGAAGCACATAAGTGCTGGAGA
116511 AACAG
1 AACAG
116516 TAGGCACACA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 7 0.15
25 41 0.85
ACGTcount: A:0.44, C:0.15, G:0.29, T:0.11
Consensus pattern (25 bp):
AACAGAAGCACATAAGTGCTGGAGA
Found at i:116545 original size:22 final size:23
Alignment explanation
Indices: 116510--116564 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
116500 AAGTGCTGGG
*
116510 AAACAGTAGGCACACACAGTGCT
1 AAACAGTAAGCACACACAGTGCT
116533 AAACA-TAAGCACACACAGTGC-
1 AAACAGTAAGCACACACAGTGCT
116554 AGAACAGTAAG
1 A-AACAGTAAG
116565 TACGCTAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 1 0.03
22 19 0.66
23 9 0.31
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (23 bp):
AAACAGTAAGCACACACAGTGCT
Found at i:120881 original size:27 final size:27
Alignment explanation
Indices: 120842--120926 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 27
120832 GGTAAAAAAA
* *
120842 AGTCAAAG-GTCAAAGTAAACGGGTC-
1 AGTCAATGAGTCAAAGTCAACGGGTCG
* *
120867 AGGTCAATGAGTCAAAATCAATGGGTCG
1 A-GTCAATGAGTCAAAGTCAACGGGTCG
*
120895 AGTCAATGGGTCAAAGTCAACGGGTCG
1 AGTCAATGAGTCAAAGTCAACGGGTCG
120922 A-TCAA
1 AGTCAA
120927 CTCGGGTTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
25 1 0.02
26 10 0.20
27 38 0.76
28 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.19
Consensus pattern (27 bp):
AGTCAATGAGTCAAAGTCAACGGGTCG
Found at i:120902 original size:13 final size:13
Alignment explanation
Indices: 120884--120926 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
120874 TGAGTCAAAA
120884 TCAATGGGTCGAG
1 TCAATGGGTCGAG
*
120897 TCAATGGGTCAAAG
1 TCAATGGGTC-GAG
*
120911 TCAACGGGTCGA-
1 TCAATGGGTCGAG
120923 TCAA
1 TCAA
120927 CTCGGGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 4 0.15
13 11 0.42
14 11 0.42
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (13 bp):
TCAATGGGTCGAG
Found at i:120914 original size:14 final size:14
Alignment explanation
Indices: 120840--120920 Score: 69
Period size: 13 Copynumber: 6.0 Consensus size: 14
120830 TTGGTAAAAA
*
120840 AAAGTCAA-AGGTC
1 AAAGTCAATGGGTC
* *
120853 AAAGTAAACGGGTC
1 AAAGTCAATGGGTC
* *
120867 -AGGTCAATGAGTC
1 AAAGTCAATGGGTC
*
120880 AAAATCAATGGGTC
1 AAAGTCAATGGGTC
*
120894 -GAGTCAATGGGTC
1 AAAGTCAATGGGTC
*
120907 AAAGTCAACGGGTC
1 AAAGTCAATGGGTC
120921 GATCAACTCG
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
13 27 0.52
14 25 0.48
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (14 bp):
AAAGTCAATGGGTC
Done.