Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003096.1 Kokia drynarioides strain JFW-HI SEQ_115658, 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: 31959
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:111 original size:20 final size:20
Alignment explanation
Indices: 86--130 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
76 TTCTTCTGTC
86 TTCTTTCTTTTT-TTATTTCT
1 TTCTTT-TTTTTCTTATTTCT
* *
106 TTCTTTTTTTTCTTTTTTTT
1 TTCTTTTTTTTCTTATTTCT
126 TTCTT
1 TTCTT
131 CAATTTTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84
Consensus pattern (20 bp):
TTCTTTTTTTTCTTATTTCT
Found at i:137 original size:14 final size:11
Alignment explanation
Indices: 89--130 Score: 57
Period size: 11 Copynumber: 3.5 Consensus size: 11
79 TTCTGTCTTC
89 TTTCTTTTTTT
1 TTTCTTTTTTT
100 ATTTCTTTCTTTTT
1 -TTTC-TT-TTTTT
114 TTTCTTTTTTT
1 TTTCTTTTTTT
125 TTTCTT
1 TTTCTT
131 CAATTTTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.39
12 6 0.21
13 6 0.21
14 5 0.18
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:4228 original size:19 final size:19
Alignment explanation
Indices: 4191--4229 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
4181 TTGATATTTG
* *
4191 TAAATATTATTATATATAT
1 TAAATATTATTAAAAATAT
*
4210 TAAATATTTTTAAAAATAT
1 TAAATATTATTAAAAATAT
4229 T
1 T
4230 GATATATTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAATATTATTAAAAATAT
Found at i:5028 original size:2 final size:2
Alignment explanation
Indices: 5021--5045 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5011 TAAAGTTAAT
5021 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5046 TACTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5604 original size:16 final size:17
Alignment explanation
Indices: 5569--5606 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
5559 ACAAATTTTT
5569 TTAACTATTAAATATAGA
1 TTAACTATT-AATATAGA
*
5587 TTAACTATT-ATATTGA
1 TTAACTATTAATATAGA
5603 TTAA
1 TTAA
5607 TATATCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (17 bp):
TTAACTATTAATATAGA
Found at i:5714 original size:42 final size:41
Alignment explanation
Indices: 5627--5801 Score: 219
Period size: 41 Copynumber: 4.3 Consensus size: 41
5617 AATATTTTTC
** *
5627 ACCTTTAGCGGCA-TTTTTTCATAAACACCGCTAATGCTCTG
1 ACCTTTAGCGGCACTTCCTT-ATAAACGCCGCTAATGCTCTG
*
5668 ACCTTTAGCGGCACTTCCTTATAAAACGTCGCTAATGCTCTG
1 ACCTTTAGCGGCACTTCCTTAT-AAACGCCGCTAATGCTCTG
* * * *
5710 ACCTTTAGCTGCGCTTCCTCATAAACGCCGCTAATGCTCTA
1 ACCTTTAGCGGCACTTCCTTATAAACGCCGCTAATGCTCTG
* *
5751 ATCTTTAGCGGCACTTCCTTATAAACGCCGCTAATGCT-TT
1 ACCTTTAGCGGCACTTCCTTATAAACGCCGCTAATGCTCTG
*
5791 ACCTTTTGCGG
1 ACCTTTAGCGG
5802 GGTTTATGAA
Statistics
Matches: 116, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
40 10 0.09
41 66 0.57
42 40 0.34
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (41 bp):
ACCTTTAGCGGCACTTCCTTATAAACGCCGCTAATGCTCTG
Found at i:5766 original size:83 final size:81
Alignment explanation
Indices: 5645--5796 Score: 241
Period size: 83 Copynumber: 1.9 Consensus size: 81
5635 CGGCATTTTT
* *
5645 TCATAAACACCGCTAATGCTCTGACCTTTAGCGGCACTTCCTTATAAAACGTCGCTAATGCTCTG
1 TCATAAACACCGCTAATGCTCTAACCTTTAGCGGCACTTCCTTAT-AAACGCCGCTAATGCT-TG
5710 ACCTTTAGCTGCGCTTCC
64 ACCTTTAGCTGCGCTTCC
* * *
5728 TCATAAACGCCGCTAATGCTCTAATCTTTAGCGGCACTTCCTTATAAACGCCGCTAATGCTTTAC
1 TCATAAACACCGCTAATGCTCTAACCTTTAGCGGCACTTCCTTATAAACGCCGCTAATGCTTGAC
5793 CTTT
66 CTTT
5797 TGCGGGGTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
81 7 0.11
82 15 0.23
83 42 0.66
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (81 bp):
TCATAAACACCGCTAATGCTCTAACCTTTAGCGGCACTTCCTTATAAACGCCGCTAATGCTTGAC
CTTTAGCTGCGCTTCC
Found at i:6986 original size:20 final size:21
Alignment explanation
Indices: 6953--6991 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
6943 CATGTGTCTT
6953 TTTTAAAATAAATT-TATTTA
1 TTTTAAAATAAATTATATTTA
* *
6973 TTTTAAATTTAATTATATT
1 TTTTAAAATAAATTATATT
6992 GCTTTCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTAAAATAAATTATATTTA
Found at i:7220 original size:31 final size:31
Alignment explanation
Indices: 7127--7228 Score: 90
Period size: 27 Copynumber: 3.5 Consensus size: 31
7117 TTAATATAAT
* * *
7127 ATTTGGTATCTGAATTTGACACTTTTT-TTA
1 ATTTGGTACCTAAATTTGACACTTTTTCCTA
* * *
7157 ATTTGGTACTTAAATTT-----TTTTGACCCA
1 ATTTGGTACCTAAATTTGACACTTTT-TCCTA
7184 ATTTGGTACCTAAATTTGACACTTTTTCCTA
1 ATTTGGTACCTAAATTTGACACTTTTTCCTA
*
7215 ATTTGGTACTTAAA
1 ATTTGGTACCTAAA
7229 CTTTTTTTGG
Statistics
Matches: 55, Mismatches: 10, Indels: 13
0.71 0.13 0.17
Matches are distributed among these distances:
25 4 0.07
27 17 0.31
30 14 0.25
31 16 0.29
32 4 0.07
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (31 bp):
ATTTGGTACCTAAATTTGACACTTTTTCCTA
Found at i:7264 original size:60 final size:58
Alignment explanation
Indices: 7127--7311 Score: 221
Period size: 60 Copynumber: 3.1 Consensus size: 58
7117 TTAATATAAT
* * *
7127 ATTTGGTATCTGAATTTGACACTTTTTTTAATTTGGTACTTAAA-TTTTTTTGACCCA
1 ATTTGGTATCAGAATTTGACACTTTTTCTAATTTGGTACTTAAACTTTTTTTGATCCA
*
7184 ATTTGGTACCTA-AATTTGACACTTTTTCCTAATTTGGTACTTAAACTTTTTTTGGATCCA
1 ATTTGGTATC-AGAATTTGACACTTTTT-CTAATTTGGTACTTAAACTTTTTTT-GATCCA
* * * * * *
7244 ATTTGATATCAGAACTTGACATATTTTTCTAATTTGGTACCTAAGCTTTTTTTAGATTCA
1 ATTTGGTATCAGAATTTGACA-CTTTTTCTAATTTGGTACTTAAACTTTTTTT-GATCCA
7304 ATTTGGTA
1 ATTTGGTA
7312 CCTAAATTTA
Statistics
Matches: 109, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
57 24 0.22
58 16 0.15
59 8 0.07
60 56 0.51
61 5 0.05
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (58 bp):
ATTTGGTATCAGAATTTGACACTTTTTCTAATTTGGTACTTAAACTTTTTTTGATCCA
Found at i:7594 original size:31 final size:30
Alignment explanation
Indices: 7520--7654 Score: 100
Period size: 31 Copynumber: 4.5 Consensus size: 30
7510 CCTAAAAAAA
* * *
7520 TTTAAGTACCAACTTTAAAAAAGTGTCAAG
1 TTTAAGTACCAAATTAAAAAAAATGTCAAG
*
7550 TTT-AGATAACAAATTAAGAAAAAATGTCAAG
1 TTTAAG-TACCAAATTAA-AAAAAATGTCAAG
*
7581 TTTAAGTACCAAATTAGACCAAAAA----AAG
1 TTTAAGTACCAAATTA-A-AAAAAATGTCAAG
* * *
7609 TTTAAGTATCAAATTAAAAAATATATATCAAA
1 TTTAAGTACCAAATTAAAAAA-A-ATGTCAAG
*
7641 TTTAAATACCAAAT
1 TTTAAGTACCAAAT
7655 ATTATATTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
26 3 0.04
27 2 0.02
28 19 0.23
29 2 0.02
30 11 0.13
31 24 0.29
32 22 0.27
ACGTcount: A:0.52, C:0.10, G:0.09, T:0.29
Consensus pattern (30 bp):
TTTAAGTACCAAATTAAAAAAAATGTCAAG
Found at i:13446 original size:17 final size:18
Alignment explanation
Indices: 13426--13459 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13416 TAAATTTTAT
*
13426 AAAATATAAAA-TAAATC
1 AAAATAAAAAAGTAAATC
13443 AAAATAAAAAAGTAAAT
1 AAAATAAAAAAGTAAAT
13460 TCCCATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
AAAATAAAAAAGTAAATC
Found at i:14480 original size:34 final size:32
Alignment explanation
Indices: 14421--14488 Score: 75
Period size: 34 Copynumber: 2.0 Consensus size: 32
14411 ATTATTTTAA
* *
14421 TTTTTAATCAATTTTTATGATTTTTTTATAATTT
1 TTTTTAATAAATTTTTATGA--TTTTTACAATTT
14455 TTTTTAATAAATTTTTCAATG-TTTTTACAATTT
1 TTTTTAATAAATTTTT--ATGATTTTTACAATTT
14488 T
1 T
14489 AAAATGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
33 12 0.40
34 15 0.50
36 3 0.10
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (32 bp):
TTTTTAATAAATTTTTATGATTTTTACAATTT
Found at i:19415 original size:16 final size:16
Alignment explanation
Indices: 19394--19447 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
19384 ATAAAATTTT
19394 AATTATTTATTACTAC
1 AATTATTTATTACTAC
**
19410 AATTA-TTATTTTTTATC
1 AATTATTTA-TTACTA-C
19427 AA--ATTTATTACTAC
1 AATTATTTATTACTAC
19441 AATTATT
1 AATTATT
19448 ATTTGACATA
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 15 0.52
17 3 0.10
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (16 bp):
AATTATTTATTACTAC
Found at i:19417 original size:19 final size:19
Alignment explanation
Indices: 19395--19451 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
19385 TAAAATTTTA
19395 ATTATTTATTACTACAATT
1 ATTATTTATTACTACAATT
*
19414 ATTATTTTTTA-T-C-A--
1 ATTATTTATTACTACAATT
19428 A--ATTTATTACTACAATT
1 ATTATTTATTACTACAATT
19445 ATTATTT
1 ATTATTT
19452 GACATAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 14
0.64 0.04 0.31
Matches are distributed among these distances:
12 7 0.24
13 1 0.03
14 2 0.07
15 1 0.03
16 1 0.03
17 2 0.07
18 1 0.03
19 14 0.48
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATTTATTACTACAATT
Found at i:19491 original size:17 final size:16
Alignment explanation
Indices: 19469--19524 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
19459 ATGCAACTTC
19469 AATATATTATATTATTT
1 AATATATTATATT-TTT
**
19486 AATATAAAATATTTTT
1 AATATATTATATTTTT
*
19502 TAT-TATTATATTTTT
1 AATATATTATATTTTT
19517 ACATATAT
1 A-ATATAT
19525 AAAAACTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 10 0.32
16 7 0.23
17 14 0.45
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
AATATATTATATTTTT
Found at i:20924 original size:17 final size:16
Alignment explanation
Indices: 20890--20939 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 16
20880 TGGGTGAGTG
*
20890 AAAA-AGAAA-ATTGA
1 AAAATAGAAAGATAGA
* *
20904 AAAATTGAAATGGTAGA
1 AAAATAGAAA-GATAGA
20921 AAAATAGAAAGATAGA
1 AAAATAGAAAGATAGA
20937 AAA
1 AAA
20940 TTATTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 4 0.14
15 4 0.14
16 8 0.29
17 12 0.43
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (16 bp):
AAAATAGAAAGATAGA
Found at i:23161 original size:56 final size:56
Alignment explanation
Indices: 23070--23181 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
23060 CTTTGATACG
* * *
23070 TTTATTATAATAATGTCATTACATGGCATTGGCAGCCAATAACATCACATAACAAC
1 TTTACTATAACAATGTCATGACATGGCATTGGCAGCCAATAACATCACATAACAAC
*
23126 TTTACTATAACAATGTCATGACATGGCATTGGCAGCTAATAACATCACATAACAAC
1 TTTACTATAACAATGTCATGACATGGCATTGGCAGCCAATAACATCACATAACAAC
23182 CTAAAATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.29
Consensus pattern (56 bp):
TTTACTATAACAATGTCATGACATGGCATTGGCAGCCAATAACATCACATAACAAC
Found at i:24332 original size:25 final size:26
Alignment explanation
Indices: 24295--24347 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
24285 TAACAAAAAT
* *
24295 AAAATCTATTCTAAAAA-GAAAAGAA
1 AAAACCTAATCTAAAAATGAAAAGAA
24320 AAAACCTAATCTAAAAATGAAAAGAA
1 AAAACCTAATCTAAAAATGAAAAGAA
24346 AA
1 AA
24348 GAAATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.66, C:0.09, G:0.08, T:0.17
Consensus pattern (26 bp):
AAAACCTAATCTAAAAATGAAAAGAA
Found at i:24898 original size:23 final size:23
Alignment explanation
Indices: 24872--24920 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
24862 TGAAAAACAT
*
24872 AAAAAAAACTCA-TAAATCACTTG
1 AAAAAAAACTCATTAAAT-ACTCG
* *
24895 AAAACAAATTCATTAAATACTCG
1 AAAAAAAACTCATTAAATACTCG
24918 AAA
1 AAA
24921 GAGCTTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.57, C:0.16, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAAAAAACTCATTAAATACTCG
Found at i:25503 original size:21 final size:20
Alignment explanation
Indices: 25475--25515 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
25465 TTTTTTTTGA
25475 AAATT-AAAAATATCTAAAAT
1 AAATTAAAAAAT-TCTAAAAT
25495 AAATATAAAAAATTCTAAAAT
1 AAAT-TAAAAAATTCTAAAAT
25516 TTTCTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATTAAAAAATTCTAAAAT
Found at i:26606 original size:14 final size:15
Alignment explanation
Indices: 26581--26610 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
26571 TTCATTCAGT
26581 TTTATATTTTATTTA
1 TTTATATTTTATTTA
26596 TTTAT-TTTTATTTA
1 TTTATATTTTATTTA
26610 T
1 T
26611 ATTCTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATATTTTATTTA
Found at i:28424 original size:59 final size:58
Alignment explanation
Indices: 28390--28551 Score: 173
Period size: 59 Copynumber: 2.8 Consensus size: 58
28380 AGTTCGGGGT
*
28390 TAAAAAATGGAA-CTTTAGACATCCGGGGGTAAAACGGTAACTTTTAGAAAAACCGGGA
1 TAAAAAACGGAATCTTTAGACATCCGGGGGTAAAACGGTAA-TTTTAGAAAAACCGGGA
* * * * * * *
28448 TCAAAAACGGAATTTTTGGACATCCGGGGGTAAAATGGTAATTTTTTGAGAAATCGGGA
1 TAAAAAACGGAATCTTTAGACATCCGGGGGTAAAACGGTAA-TTTTAGAAAAACCGGGA
* * * * * *
28507 TCAAAAACGAAATTTTTGGACATCCAGGGGTAAAAGGGTAATTTT
1 TAAAAAACGGAATCTTTAGACATCCGGGGGTAAAACGGTAATTTT
28552 TGAATGTTTC
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
58 14 0.15
59 77 0.85
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.26
Consensus pattern (58 bp):
TAAAAAACGGAATCTTTAGACATCCGGGGGTAAAACGGTAATTTTAGAAAAACCGGGA
Found at i:28553 original size:29 final size:28
Alignment explanation
Indices: 28316--28553 Score: 94
Period size: 29 Copynumber: 8.2 Consensus size: 28
28306 AAAATGAGAC
* *
28316 TTTTTGGATA-CCGGGGGTAAAATGGTAA
1 TTTTTGGACATCC-GGGGTAAAAAGGTAA
* * *
28344 -TTTTGGACTAT-AGGGGCAAAACGGTAA
1 TTTTTGGAC-ATCCGGGGTAAAAAGGTAA
* * *
28371 TTTTGGGAAAGTTCGGGGTTAAAAAATGG-AA
1 TTTTTGGACA-TCCGGGG-T-AAAAA-GGTAA
* * *
28402 -CTTTAGACATCCGGGGGTAAAACGGTAA
1 TTTTTGGACATCC-GGGGTAAAAAGGTAA
* * * * *
28430 CTTTTAGAAAAACCGGGATCAAAAACGG-AA
1 -TTTTTGGACATCCGGGGT-AAAAA-GGTAA
*
28460 TTTTTGGACATCCGGGGGTAAAATGGTAA
1 TTTTTGGACATCC-GGGGTAAAAAGGTAA
* * * *
28489 TTTTTTGAGAAAT-CGGGATCAAAAACGAAA
1 -TTTTTG-GACATCCGGGGT-AAAAAGGTAA
*
28519 TTTTTGGACATCCAGGGGTAAAAGGGTAA
1 TTTTTGGACATCC-GGGGTAAAAAGGTAA
28548 TTTTTG
1 TTTTTG
28554 AATGTTTCAA
Statistics
Matches: 150, Mismatches: 39, Indels: 41
0.65 0.17 0.18
Matches are distributed among these distances:
27 23 0.15
28 20 0.13
29 50 0.33
30 43 0.29
31 12 0.08
32 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.28
Consensus pattern (28 bp):
TTTTTGGACATCCGGGGTAAAAAGGTAA
Found at i:28570 original size:59 final size:57
Alignment explanation
Indices: 28407--28730 Score: 237
Period size: 59 Copynumber: 5.5 Consensus size: 57
28397 TGGAACTTTA
* * * ****
28407 GACATCCGGGGGTAAAACGGTAACTTTTAGAAAAACCGGGATCAAAAACGGAATTTTTG
1 GACATCCAGGGGTAAAATGGTAA-TTTTTGAAGTTTCGGG-TCAAAAACGGAATTTTTG
* ** *
28466 GACATCCGGGGGTAAAATGGTAATTTTTTG-AGAAATCGGGATCAAAAACGAAATTTTTG
1 GACATCCAGGGGTAAAATGGTAA-TTTTTGAAG-TTTCGGG-TCAAAAACGGAATTTTTG
* * *
28525 GACATCCAGGGGTAAAAGGGTAATTTTTGAATGTTTCAAGGTCAAAAATGGAATTTTTG
1 GACATCCAGGGGTAAAATGGTAATTTTTGAA-GTTTC-GGGTCAAAAACGGAATTTTTG
* * * * *
28584 GACATTCAAGGGTAAAATGGCAATTTTTGAAAGTTTCGGGGTC-AAAATGGAATTTTTA
1 GACATCCAGGGGTAAAATGGTAATTTTTG-AAGTTTC-GGGTCAAAAACGGAATTTTTG
* ** * *
28642 GA-AGTTC-GAGGGTAAAAAAT-GTAATTTTTTGAAAAATTAGGGTCAAAAACGGAATTTTGG
1 GACA-TCCAG-GGGT--AAAATGGTAA-TTTTTG-AAGTTTCGGGTCAAAAACGGAATTTTTG
*
28702 GA-AGTCCAAGGGTAAAATGGTAATTTTTG
1 GACA-TCCAGGGGTAAAATGGTAATTTTTG
28731 GTGAAATCAT
Statistics
Matches: 222, Mismatches: 30, Indels: 27
0.80 0.11 0.10
Matches are distributed among these distances:
57 1 0.00
58 41 0.18
59 137 0.62
60 43 0.19
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.29
Consensus pattern (57 bp):
GACATCCAGGGGTAAAATGGTAATTTTTGAAGTTTCGGGTCAAAAACGGAATTTTTG
Found at i:28625 original size:29 final size:27
Alignment explanation
Indices: 28533--28833 Score: 108
Period size: 29 Copynumber: 10.3 Consensus size: 27
28523 TGGACATCCA
* *
28533 GGGGTAAAAGGGTAATTTTTGAATGTTTC
1 GGGGTAAAATGG-AATTTTTGAAAG-TTC
** *
28562 AAGGTCAAAAATGGAATTTTTGGACA-TTC
1 GGGGT--AAAATGGAATTTTT-GAAAGTTC
*
28591 AAGGGTAAAATGGCAATTTTTGAAAGTTTC
1 -GGGGTAAAATGG-AATTTTTGAAAG-TTC
28621 GGGGTCAAAATGGAATTTTT-AGAAGTTC
1 GGGGT-AAAATGGAATTTTTGA-AAGTTC
* *
28649 GAGGGTAAAAAATGTAATTTTTTGAAAAATT-
1 G-GGGT--AAAATGGAA-TTTTTG-AAAGTTC
* * * * *
28680 AGGGTCAAAAACGGAATTTTGGGAAGTCC
1 GGGGT--AAAATGGAATTTTTGAAAGTTC
*
28709 AAGGGTAAAATGGTAATTTTTGGTGAAA--TC
1 -GGGGTAAAATGG-AA-TTTT--TGAAAGTTC
* * *
28739 ATGGTTAAAATGGAATTTTGGAAAGTTC
1 -GGGGTAAAATGGAATTTTTGAAAGTTC
* * * *
28767 GGGGGTAAAAATGTAAGTTTGGAAAGTTTA
1 -GGGGT-AAAATGGAATTTTTGAAAG-TTC
* * *
28797 GGGGTAAAATGTAATTTTGGAGAAGTTA
1 GGGGTAAAATGGAATTTTTGA-AAGTTC
28825 GGGGTAAAA
1 GGGGTAAAA
28834 ATATAATTTT
Statistics
Matches: 214, Mismatches: 33, Indels: 51
0.72 0.11 0.17
Matches are distributed among these distances:
26 4 0.02
28 60 0.28
29 65 0.30
30 64 0.30
31 13 0.06
32 7 0.03
33 1 0.00
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.32
Consensus pattern (27 bp):
GGGGTAAAATGGAATTTTTGAAAGTTC
Found at i:28661 original size:30 final size:28
Alignment explanation
Indices: 28546--28779 Score: 99
Period size: 30 Copynumber: 8.0 Consensus size: 28
28536 GTAAAAGGGT
*
28546 AATTTTTGAATGTTTC-AAGGTCAAAAATGG
1 AATTTTTGAA-G-TTCGAGGGT-AAAAATGG
*
28576 AATTTTTGGACA-TTCAAGGGT-AAAATGG
1 AATTTTT-GA-AGTTCGAGGGTAAAAATGG
*
28604 CAATTTTTGAAAGTTTCG-GGGTCAAAATGG
1 -AATTTTTG-AAG-TTCGAGGGTAAAAATGG
*
28634 AATTTTTAGAAGTTCGAGGGTAAAAAATGT
1 AATTTTT-GAAGTTCGAGGGT-AAAAATGG
* *
28664 AATTTTTTGAAAAATT--AGGGTCAAAAACGG
1 AA-TTTTTG--AAGTTCGAGGGT-AAAAATGG
* * *
28694 AATTTTGGGAAGTCCAAGGGT-AAAATGG
1 AATTTT-TGAAGTTCGAGGGTAAAAATGG
* * *
28722 TAATTTTTGGTGAA-ATC-ATGGTTAAAATGG
1 -AA-TTTT--TGAAGTTCGAGGGTAAAAATGG
* *
28752 AATTTTGGAAAGTTCGGGGGTAAAAATG
1 AATTTTTG-AAGTTCGAGGGTAAAAATG
28780 TAAGTTTGGA
Statistics
Matches: 159, Mismatches: 21, Indels: 49
0.69 0.09 0.21
Matches are distributed among these distances:
26 1 0.01
27 2 0.01
28 28 0.18
29 50 0.31
30 62 0.39
31 11 0.07
32 5 0.03
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.32
Consensus pattern (28 bp):
AATTTTTGAAGTTCGAGGGTAAAAATGG
Found at i:28814 original size:57 final size:58
Alignment explanation
Indices: 28744--28857 Score: 160
Period size: 57 Copynumber: 2.0 Consensus size: 58
28734 AAATCATGGT
* *
28744 TAAAATGGAATTTTGGA-AAGTTCGGGGGTAAAAATGTAA-GTTTGGAAAGTTTAGGGG
1 TAAAATGGAATTTTGGAGAAGTT-AGGGGTAAAAATATAATGTTTGGAAAGTTTAGGGG
* * *
28801 TAAAATGTAATTTTGGAGAAGTTAGGGGTAAAAATATAATTTTTGGATAGTTTAGGG
1 TAAAATGGAATTTTGGAGAAGTTAGGGGTAAAAATATAATGTTTGGAAAGTTTAGGG
28858 ACCTTTAGGG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 30 0.60
58 20 0.40
ACGTcount: A:0.36, C:0.01, G:0.30, T:0.33
Consensus pattern (58 bp):
TAAAATGGAATTTTGGAGAAGTTAGGGGTAAAAATATAATGTTTGGAAAGTTTAGGGG
Found at i:28834 original size:29 final size:29
Alignment explanation
Indices: 28621--28843 Score: 129
Period size: 29 Copynumber: 7.7 Consensus size: 29
28611 TGAAAGTTTC
* * * *
28621 GGGGTCAAAATGGAATTTT-TAGAAGTTC
1 GGGGTAAAAATGTAATTTTGGAGAAGTTA
* * *
28649 GAGGGTAAAAAATGTAATTTTTTGAAAAATTA
1 G-GGGT-AAAAATGTAA-TTTTGGAGAAGTTA
* * *
28681 -GGGTCAAAAACGGAATTTTGG-GAAGTCCA
1 GGGGT-AAAAATGTAATTTTGGAGAAGT-TA
* * * *
28710 AGGGT-AAAATGGTAATTTTTGGTGAAATCA
1 GGGGTAAAAAT-GTAA-TTTTGGAGAAGTTA
* * * *
28740 -TGGTTAAAATGGAATTTTGGA-AAGTTCG
1 GGGGTAAAAATGTAATTTTGGAGAAGTT-A
*
28768 GGGGTAAAAATGTAAGTTTGGA-AAGTTTA
1 GGGGTAAAAATGTAATTTTGGAGAAG-TTA
28797 GGGGT-AAAATGTAATTTTGGAGAAGTTA
1 GGGGTAAAAATGTAATTTTGGAGAAGTTA
*
28825 GGGGTAAAAATATAATTTT
1 GGGGTAAAAATGTAATTTT
28844 TGGATAGTTT
Statistics
Matches: 151, Mismatches: 29, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
27 3 0.02
28 37 0.25
29 59 0.39
30 39 0.26
31 8 0.05
32 5 0.03
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.32
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTGGAGAAGTTA
Found at i:28852 original size:29 final size:29
Alignment explanation
Indices: 28745--28857 Score: 140
Period size: 29 Copynumber: 3.9 Consensus size: 29
28735 AATCATGGTT
* **
28745 AAAATGGAATTTTGGAAAGTTCGGGGGTA
1 AAAATGTAATTTTGGAAAGTTTAGGGGTA
*
28774 AAAATGTAAGTTTGGAAAGTTTAGGGGT-
1 AAAATGTAATTTTGGAAAGTTTAGGGGTA
28802 AAAATGTAATTTTGGAGAAG-TTAGGGGTA
1 AAAATGTAATTTTGGA-AAGTTTAGGGGTA
* *
28831 AAAATATAATTTTTGGATAGTTTAGGG
1 AAAATGTAA-TTTTGGAAAGTTTAGGG
28858 ACCTTTAGGG
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
28 23 0.32
29 37 0.51
30 13 0.18
ACGTcount: A:0.36, C:0.01, G:0.30, T:0.33
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAGTTTAGGGGTA
Found at i:30784 original size:17 final size:17
Alignment explanation
Indices: 30729--30851 Score: 96
Period size: 17 Copynumber: 7.4 Consensus size: 17
30719 CTTTATTTAT
* *
30729 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
*
30746 TTTAAATTTGAAAATCAA
1 TTTAAATTT-AAAATAAA
* * *
30764 TTTAAACTCAAATTAAA
1 TTTAAATTTAAAATAAA
30781 TTT--A---AAAATAAA
1 TTTAAATTTAAAATAAA
*
30793 TTTAAATTTAAAAAAAA
1 TTTAAATTTAAAATAAA
*
30810 TTTAAATTTTTAAAACAAA
1 TTTAAA--TTTAAAATAAA
30829 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
30846 TTTAAA
1 TTTAAA
30852 ATGAGTTTGG
Statistics
Matches: 85, Mismatches: 11, Indels: 19
0.74 0.10 0.17
Matches are distributed among these distances:
12 10 0.12
14 1 0.01
15 1 0.01
16 1 0.01
17 43 0.51
18 16 0.19
19 13 0.15
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:30810 original size:29 final size:29
Alignment explanation
Indices: 30749--30815 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
30739 TAATAATTTT
* * **
30749 AAATTTGAAAATCAATTTAAACTCAAATT
1 AAATTTAAAAATAAATTTAAACTCAAAAA
* *
30778 AAATTTAAAAATAAATTTAAATTTAAAAA
1 AAATTTAAAAATAAATTTAAACTCAAAAA
30807 AAATTTAAA
1 AAATTTAAA
30816 TTTTTAAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (29 bp):
AAATTTAAAAATAAATTTAAACTCAAAAA
Found at i:30840 original size:36 final size:35
Alignment explanation
Indices: 30776--30851 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 35
30766 TAAACTCAAA
*
30776 TTAAATTTAAAAATAAATTTAAATTTAAAAAAAAT
1 TTAAATTTAAAAACAAATTTAAATTTAAAAAAAAT
* *
30811 TTAAATTTTTAAAACAAATTT-AATCTTAAAATAAAT
1 TTAAA-TTTAAAAACAAATTTAAAT-TTAAAAAAAAT
30847 TTAAA
1 TTAAA
30852 ATGAGTTTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 8 0.22
36 28 0.78
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (35 bp):
TTAAATTTAAAAACAAATTTAAATTTAAAAAAAAT
Found at i:30848 original size:65 final size:64
Alignment explanation
Indices: 30729--30852 Score: 160
Period size: 65 Copynumber: 1.9 Consensus size: 64
30719 CTTTATTTAT
* * * *
30729 TTTAAATTTATAATAATTTTAAATTTGAAAATCAATTTAAACTCAAATTAAATTTAAAAATAAA
1 TTTAAATTTAAAAAAAATTTAAATTTGAAAATCAATTTAAACTCAAAATAAATTTAAAAATAAA
* * *
30793 TTTAAATTTAAAAAAAATTTAAATTTTTAAAA-CAAATTTAATCTTAAAATAAATTTAAAA
1 TTTAAATTTAAAAAAAATTTAAA-TTTGAAAATC-AATTTAAACTCAAAATAAATTTAAAA
30853 TGAGTTTGGG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
64 21 0.41
65 30 0.59
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (64 bp):
TTTAAATTTAAAAAAAATTTAAATTTGAAAATCAATTTAAACTCAAAATAAATTTAAAAATAAA
Found at i:31777 original size:23 final size:22
Alignment explanation
Indices: 31745--31825 Score: 99
Period size: 23 Copynumber: 3.6 Consensus size: 22
31735 GCTGGGAAAA
*
31745 CAGTAAGCACACACAATGCAAT
1 CAGTAGGCACACACAATGCAAT
*
31767 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAATGCAAT
* * *
31790 CAGTAGGCGCACATAACGCAAAT
1 CAGTAGGCACACACAATGC-AAT
31813 CAGTAGGCACACA
1 CAGTAGGCACACA
31826 AAGTGCGAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 15 0.30
23 35 0.70
ACGTcount: A:0.40, C:0.28, G:0.20, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAATGCAAT
Found at i:31864 original size:23 final size:23
Alignment explanation
Indices: 31809--31866 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
31799 CACATAACGC
* *
31809 AAATCAGTAGGCACACAAAGTGCG
1 AAAT-AGTAAGCACACAAACTGCG
** *
31833 AAACGGTAAGCACACGAACTGCG
1 AAATAGTAAGCACACAAACTGCG
31856 AAATAGTAAGC
1 AAATAGTAAGC
31867 GCGCTAGCGT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 24 0.89
24 3 0.11
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AAATAGTAAGCACACAAACTGCG
Done.