Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007344.1 Kokia drynarioides strain JFW-HI SEQ_121960, 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: 30154
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:452 original size:11 final size:10
Alignment explanation
Indices: 433--474 Score: 59
Period size: 11 Copynumber: 4.1 Consensus size: 10
423 ATATTTTAAA
433 AAATAATTTT
1 AAATAATTTT
443 AAATTAATTTT
1 AAA-TAATTTT
454 AAAATAATTTT
1 -AAATAATTTT
465 -AATAATTTT
1 AAATAATTTT
474 A
1 A
475 TATTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.31
10 3 0.10
11 14 0.48
12 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AAATAATTTT
Found at i:460 original size:22 final size:20
Alignment explanation
Indices: 414--474 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
404 ATGATGTTTT
414 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTT--AA
434 AATAATTTTAAATTAATTTTAA
1 AATAATTTT-AA-TAATTTTAA
456 AATAATTTTAATAATTTTA
1 AATAATTTTAATAATTTTA
475 TATTTTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
20 17 0.46
21 2 0.05
22 12 0.32
23 1 0.03
24 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATTTTAATAATTTTAA
Found at i:506 original size:50 final size:51
Alignment explanation
Indices: 410--513 Score: 176
Period size: 51 Copynumber: 2.1 Consensus size: 51
400 GATGATGATG
410 TTTTAATAATTTTATATTTTAAAAAATAATTTTAAATTAATTTTAAAATAA
1 TTTTAATAATTTTATATTTTAAAAAATAATTTTAAATTAATTTTAAAATAA
*
461 TTTTAATAATTTTATATTTTAAAAAAATAATTTT-AA-TAATTTTAAAATCA
1 TTTTAATAATTTTATATTTT-AAAAAATAATTTTAAATTAATTTTAAAATAA
511 TTT
1 TTT
514 GCTAACATGG
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
50 16 0.31
51 22 0.43
52 13 0.25
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (51 bp):
TTTTAATAATTTTATATTTTAAAAAATAATTTTAAATTAATTTTAAAATAA
Found at i:4345 original size:4 final size:4
Alignment explanation
Indices: 4332--4375 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
4322 TGATTTGAAG
*
4332 GAAA -AAA GAAA GAAA -AAA -AAA AAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
4376 GAAGGAAGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
3 9 0.24
4 28 0.76
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:4356 original size:18 final size:19
Alignment explanation
Indices: 4333--4378 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
4323 GATTTGAAGG
4333 AAAAAAGAAAGAAA-AAAA
1 AAAAAAGAAAGAAAGAAAA
*
4351 AAAAAAGAAAGAAAGAAAG
1 AAAAAAGAAAGAAAGAAAA
*
4370 AAAGAAGAA
1 AAAAAAGAA
4379 GGAAGAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAGAAAGAAAA
Found at i:4362 original size:22 final size:22
Alignment explanation
Indices: 4336--4391 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
4326 TTGAAGGAAA
4336 AAAGAAAGAAAAAAAAAAAAAG
1 AAAGAAAGAAAAAAAAAAAAAG
* * *
4358 AAAGAAAGAAAGAAAGAAGAAG
1 AAAGAAAGAAAAAAAAAAAAAG
* *
4380 GAAGAAGGAAAA
1 AAAGAAAGAAAA
4392 GGAGAAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAAAAAAAAAAAAG
Found at i:4567 original size:17 final size:18
Alignment explanation
Indices: 4533--4567 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4523 GGAAGAAAGG
4533 TAAGTTTGATTAAATTTT
1 TAAGTTTGATTAAATTTT
*
4551 TAAGTTTGGTT-AATTTT
1 TAAGTTTGATTAAATTTT
4568 AAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (18 bp):
TAAGTTTGATTAAATTTT
Found at i:5346 original size:23 final size:22
Alignment explanation
Indices: 5294--5347 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
5284 TTTAATTTAT
5294 AATTAAAATTAGTTATATAATA
1 AATTAAAATTAGTTATATAATA
**
5316 CGTGTAAAATTAGTTATATAATAA
1 AAT-TAAAATTAGTTATATAAT-A
5340 AATTAAAA
1 AATTAAAA
5348 AAATTTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.04
23 23 0.88
24 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (22 bp):
AATTAAAATTAGTTATATAATA
Found at i:5584 original size:16 final size:16
Alignment explanation
Indices: 5538--5586 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
5528 TAAACCTAGC
5538 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
5554 T-A-TAATATA--AAAA
1 TAATTAAT-TACCAAAA
5567 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
5583 TAAT
1 TAAT
5587 ATCCCCACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 5 0.18
14 7 0.25
15 7 0.25
16 9 0.32
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:5653 original size:30 final size:30
Alignment explanation
Indices: 5619--5713 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
5609 AAATGGTACA
*
5619 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATATATTTTGTACCATTTTAGT
** * * * * *
5649 AAAT-AAT-GGTGTGTGGATACTATTTTGGT
1 AAATAAATATATATTTTG-TACCATTTTAGT
*
5678 ATATAAATATATATTTTGTACCATTTTAGT
1 AAATAAATATATATTTTGTACCATTTTAGT
5708 AAATAA
1 AAATAA
5714 CCCATTTTGA
Statistics
Matches: 46, Mismatches: 16, Indels: 6
0.68 0.24 0.09
Matches are distributed among these distances:
28 4 0.09
29 16 0.35
30 22 0.48
31 4 0.09
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (30 bp):
AAATAAATATATATTTTGTACCATTTTAGT
Found at i:6964 original size:43 final size:43
Alignment explanation
Indices: 6882--6966 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
6872 ATTAACATGT
* * *
6882 TAAATTATATTACTTGACTTGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTTGTATTAATATGCTTACATGTTAC
*
6925 TAAATTATATTACTTTACTCT-TATTAATAT-CTATACATGTTA
1 TAAATTATATTACTTGACT-TGTATTAATATGCT-TACATGTTA
6967 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.03
43 34 0.94
44 1 0.03
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGACTTGTATTAATATGCTTACATGTTAC
Found at i:7842 original size:21 final size:21
Alignment explanation
Indices: 7818--7869 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
7808 TTATAACCTC
*
7818 AAACCTTAAAATCTAAACCCA-
1 AAACCTTAAAAT-TAAAACCAT
* *
7839 AAACCTTAGACTTAAAACCAT
1 AAACCTTAAAATTAAAACCAT
7860 AAACCTTAAA
1 AAACCTTAAA
7870 CCTTAGACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.52, C:0.25, G:0.02, T:0.21
Consensus pattern (21 bp):
AAACCTTAAAATTAAAACCAT
Found at i:7855 original size:14 final size:14
Alignment explanation
Indices: 7838--7888 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
7828 ATCTAAACCC
7838 AAAACCTTAGACTT
1 AAAACCTTAGACTT
* *
7852 AAAACCATAAACCTT
1 AAAACCTTAGA-CTT
7867 -AAACCTTAGACTT
1 AAAACCTTAGACTT
*
7880 GAAACCTTA
1 AAAACCTTA
7889 AACCCTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 3 0.10
14 25 0.81
15 3 0.10
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.25
Consensus pattern (14 bp):
AAAACCTTAGACTT
Found at i:7869 original size:7 final size:7
Alignment explanation
Indices: 7812--7897 Score: 52
Period size: 7 Copynumber: 12.3 Consensus size: 7
7802 TAAATTTTAT
*
7812 AACCTCA
1 AACCTTA
7819 AACCTTA
1 AACCTTA
*
7826 AA-ATCTA
1 AACCT-TA
**
7833 AACCCAA
1 AACCTTA
7840 AACCTTA
1 AACCTTA
*
7847 GA-CTTAA
1 AACCTT-A
*
7854 AACCATA
1 AACCTTA
7861 AACCTTA
1 AACCTTA
7868 AACCTTA
1 AACCTTA
*
7875 GA-CTTGA
1 AACCTT-A
7882 AACCTTA
1 AACCTTA
*
7889 AACCCTA
1 AACCTTA
7896 AA
1 AA
7898 TCCTATACAT
Statistics
Matches: 59, Mismatches: 14, Indels: 12
0.69 0.16 0.14
Matches are distributed among these distances:
6 7 0.12
7 47 0.80
8 5 0.08
ACGTcount: A:0.47, C:0.28, G:0.03, T:0.22
Consensus pattern (7 bp):
AACCTTA
Found at i:7897 original size:28 final size:28
Alignment explanation
Indices: 7822--7897 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
7812 AACCTCAAAC
* *
7822 CTTAAAATC-TAAACCCAAAACCTTAGA
1 CTTAAAACCATAAACCCTAAACCTTAGA
*
7849 CTTAAAACCATAAACCTTAAACCTTAGA
1 CTTAAAACCATAAACCCTAAACCTTAGA
* *
7877 CTTGAAACCTTAAACCCTAAA
1 CTTAAAACCATAAACCCTAAA
7898 TCCTATACAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 8 0.19
28 34 0.81
ACGTcount: A:0.46, C:0.26, G:0.04, T:0.24
Consensus pattern (28 bp):
CTTAAAACCATAAACCCTAAACCTTAGA
Found at i:7910 original size:28 final size:28
Alignment explanation
Indices: 7831--7912 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
7821 CCTTAAAATC
* * *
7831 TAAACCCAAAACCTTAGACTTAAAACCA
1 TAAACCCTAAACCTTAGACATGAAACCA
* * *
7859 TAAACCTTAAACCTTAGACTTGAAACCT
1 TAAACCCTAAACCTTAGACATGAAACCA
*
7887 TAAACCCTAAATCC-TATACATGAAAC
1 TAAACCCTAAA-CCTTAGACATGAAAC
7913 ATTTTTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
28 44 0.96
29 2 0.04
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.23
Consensus pattern (28 bp):
TAAACCCTAAACCTTAGACATGAAACCA
Found at i:10762 original size:4 final size:4
Alignment explanation
Indices: 10755--10779 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
10745 ATACATTACA
10755 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
10780 CGTTTATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:14871 original size:31 final size:30
Alignment explanation
Indices: 14836--14941 Score: 81
Period size: 31 Copynumber: 3.5 Consensus size: 30
14826 AATGTAATAA
*
14836 TTGGTACCTGAACTTGGCACTTTTTCCTAAT
1 TTGGTACCTAAACTTGG-ACTTTTTCCTAAT
* * * *
14867 TTGGTACTTAAACTTTG--TTTTGACCAAAT
1 TTGGTACCTAAACTTGGACTTTT-TCCTAAT
* * * *
14896 TTGGTACTTGAACTTGATACATTTTCCTAAT
1 TTGGTACCTAAACTTG-GACTTTTTCCTAAT
*
14927 TCGGTACCTAAACTT
1 TTGGTACCTAAACTT
14942 TTTTTAACCC
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
28 4 0.07
29 19 0.33
31 31 0.54
32 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (30 bp):
TTGGTACCTAAACTTGGACTTTTTCCTAAT
Found at i:14992 original size:59 final size:59
Alignment explanation
Indices: 14836--15005 Score: 223
Period size: 59 Copynumber: 2.9 Consensus size: 59
14826 AATGTAATAA
* ** * *
14836 TTGGTACCTGAACTTGGCACTTTTTCCTAATTTGGTACTTAAACTTTGTTTTGACCAAAT
1 TTGGTACTTGAACTTGATACTTTTTCCTAATTTGGTACCTAAACTTT-TTTTAACCAAAT
* * *
14896 TTGGTACTTGAACTTGATACATTTTCCTAATTCGGTACCTAAACTTTTTTTAACCCAAT
1 TTGGTACTTGAACTTGATACTTTTTCCTAATTTGGTACCTAAACTTTTTTTAACCAAAT
* * * *
14955 TTGGTACTTGAACTTGATATTTTTTTCTATTTTGGTACCTAAGCTTTTTTT
1 TTGGTACTTGAACTTGATACTTTTTCCTAATTTGGTACCTAAACTTTTTTT
15006 TTTTTTAGAT
Statistics
Matches: 96, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 55 0.57
60 41 0.43
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (59 bp):
TTGGTACTTGAACTTGATACTTTTTCCTAATTTGGTACCTAAACTTTTTTTAACCAAAT
Found at i:15309 original size:31 final size:31
Alignment explanation
Indices: 15256--15314 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
15246 CCAACTTTTA
*
15256 AAAAAGTGTCAAGGTTAGGTACCAAATTAGG
1 AAAAAGTGTCAAAGTTAGGTACCAAATTAGG
*
15287 AAAAAGTGTCAAA-TTTGAGTACCAAATT
1 AAAAAGTGTCAAAGTTAG-GTACCAAATT
15315 GTGTTGAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.25
Consensus pattern (31 bp):
AAAAAGTGTCAAAGTTAGGTACCAAATTAGG
Found at i:15413 original size:18 final size:17
Alignment explanation
Indices: 15392--15475 Score: 78
Period size: 17 Copynumber: 4.7 Consensus size: 17
15382 CATTTTGGGC
15392 TTAAATTTAATTTAAAGT
1 TTAAATTTAATTTAAA-T
**
15410 TTAAATTTTTCTTTTAAAT
1 TTAAA--TTTAATTTAAAT
* *
15429 TTAAATTTAAATTAAGT
1 TTAAATTTAATTTAAAT
* *
15446 TTAAAATTAATTTGAAT
1 TTAAATTTAATTTAAAT
15463 TTAAAATTTAATT
1 TT-AAATTTAATT
15476 AATTAAAAAA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
17 23 0.44
18 14 0.27
19 6 0.12
20 9 0.17
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (17 bp):
TTAAATTTAATTTAAAT
Found at i:15439 original size:12 final size:12
Alignment explanation
Indices: 15392--15473 Score: 62
Period size: 11 Copynumber: 6.8 Consensus size: 12
15382 CATTTTGGGC
15392 TTAAATTT-AAT
1 TTAAATTTAAAT
15403 TTAAAGTTTAAATT
1 TTAAA-TTTAAA-T
***
15417 TTTCTTTTAAAT
1 TTAAATTTAAAT
15429 TTAAATTTAAA-
1 TTAAATTTAAAT
* *
15440 TTAAGTTTAAAA
1 TTAAATTTAAAT
*
15452 TT-AATTTGAAT
1 TTAAATTTAAAT
15463 TTAAAATTTAA
1 TT-AAATTTAA
15474 TTAATTAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
11 23 0.43
12 14 0.26
13 14 0.26
14 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:15443 original size:5 final size:6
Alignment explanation
Indices: 15392--15473 Score: 62
Period size: 6 Copynumber: 13.7 Consensus size: 6
15382 CATTTTGGGC
***
15392 TTAAAT TT-AAT TTAAAGT TTAAATT TTTCTT TTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAA-T TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT
* * *
15440 TTAAGT TTAAAA TT-AAT TTGAAT TTAAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAA
15474 TTAATTAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
5 13 0.22
6 32 0.54
7 14 0.24
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:16164 original size:12 final size:12
Alignment explanation
Indices: 16147--16254 Score: 65
Period size: 12 Copynumber: 9.8 Consensus size: 12
16137 TCAAAATGTC
16147 ATTAATAATATT
1 ATTAATAATATT
16159 ATTAAT--TATT
1 ATTAATAATATT
**
16169 A-TGGTAATA--
1 ATTAATAATATT
*
16178 A-TAATAATAAT
1 ATTAATAATATT
* *
16189 ATTACTAATATC
1 ATTAATAATATT
16201 ATTAATAATATT
1 ATTAATAATATT
*
16213 A--AA-AACGA-T
1 ATTAATAA-TATT
* *
16222 AATAATAATAAT
1 ATTAATAATATT
16234 ATTAATAATATT
1 ATTAATAATATT
16246 ATTAATAAT
1 ATTAATAAT
16255 GGCAGTAATT
Statistics
Matches: 73, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
9 13 0.18
10 8 0.11
11 6 0.08
12 46 0.63
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (12 bp):
ATTAATAATATT
Found at i:16179 original size:3 final size:3
Alignment explanation
Indices: 16173--16254 Score: 58
Period size: 3 Copynumber: 27.3 Consensus size: 3
16163 ATTATTATGG
* * * * *
16173 TAA TAA TAA TAA TAA TAT TAC TAA T-A TCAT TAA TAA TAT TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
** * * *
16218 CGA TAA TAA TAA TAA TAT TAA TAA TAT TAT TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
16255 GGCAGTAATT
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
2 2 0.03
3 58 0.95
4 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:17340 original size:30 final size:29
Alignment explanation
Indices: 17269--17586 Score: 336
Period size: 30 Copynumber: 10.8 Consensus size: 29
17259 GAAGGTCCCT
17269 AAACTGTCCAAAAATTCCATTTTTATCCTCG
1 AAACT-TCCAAAAATTCCATTTTTA-CCTCG
* *
17300 -AACTTTCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
* **
17329 AAACTTCCAAAAATCCCATTTTTGACCTTA
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
*
17359 AAACTTCCAAAAATCCCATTTTTAACC-CG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
* *
17388 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCTCG
*
17417 AAACTTCCAAAAATTCCATTTTTTACCCCG
1 AAACTTCCAAAAATTCCA-TTTTTACCTCG
* * **
17447 AAACTTCTAAAAAATCTGTTTTTACCTTCG
1 AAACTTCCAAAAATTCCATTTTTACC-TCG
* * *
17477 -AACTGCTAAAAATTCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
* * *
17506 AAACTTCCAAAAATTCCAATTTTACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCTCG
* *
17535 AAACTTCCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
*
17565 AAACTTCCAAAAACTCCATTTT
1 AAACTTCCAAAAATTCCATTTT
17587 CAACCCCTAA
Statistics
Matches: 252, Mismatches: 27, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
28 3 0.01
29 117 0.46
30 132 0.52
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCTCG
Found at i:17608 original size:59 final size:59
Alignment explanation
Indices: 17269--17599 Score: 346
Period size: 59 Copynumber: 5.6 Consensus size: 59
17259 GAAGGTCCCT
* * * * *
17269 AAACTGTCCAAAAATTCCATTTTTA-TCCTCGAACTTTCAAAAATCCCATTTTTGACCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCCCT-AAACTTCCAAAAATTCCATTTTTGACCCCG
* * * *
17329 AAACTTCCAAAAATCCCATTTTTGA-CCTTAAAACTTCCAAAAATCCCATTTTT-AACCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCT-AAACTTCCAAAAATTCCATTTTTGACCCCG
* *
17388 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTTACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCG
* * ** * * * * * *
17447 AAACTTCTAAAAAATCTGTTTTTA-CCTTCGAACTGCTAAAAATTCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCCT-AAACTTCCAAAAATTCCATTTTTGACCCCG
* * *
17506 AAACTTCCAAAAATTCCAATTTTACCCCAAAACTTCCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCG
* *
17565 AAACTTCCAAAAACTCCATTTTCAACCCCTAAACT
1 AAACTTCCAAAAATTCCATTTT-TACCCCTAAACT
17600 CTCAAAATTA
Statistics
Matches: 225, Mismatches: 40, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
58 25 0.11
59 159 0.71
60 41 0.18
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCG
Found at i:18030 original size:96 final size:96
Alignment explanation
Indices: 17913--18104 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
17903 AAGACTTTAA
* * *
17913 AATCGAGGTAATATTTTTTTAT-TTCGTGTTTC-GAAA-ATTTGCGCCTTAACTTACTAAGTGCA
1 AATCGAGGCAATATTTCTTTATCTT-G-GATTCTGAAATA-TTGCGCCTTAACTTACTAAGTGCA
** *
17975 ATTTTTCTTCAAATTGA-AATAATCGAATACCCTT
63 ACCTTTCTTCAAATCGAGAA-AATCGAATACCCTT
* * *
18009 AATCGAGGCAATGTTTCTTTATCTTGGATTCTGAAATATTGCGCCTTAACTTACTAGGTGTAACC
1 AATCGAGGCAATATTTCTTTATCTTGGATTCTGAAATATTGCGCCTTAACTTACTAAGTGCAACC
*
18074 TTTCTTCAAATCGAGAAAATCGAATATCCTT
66 TTTCTTCAAATCGAGAAAATCGAATACCCTT
18105 TTCCCAAAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 4 0.05
96 73 0.89
97 5 0.06
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (96 bp):
AATCGAGGCAATATTTCTTTATCTTGGATTCTGAAATATTGCGCCTTAACTTACTAAGTGCAACC
TTTCTTCAAATCGAGAAAATCGAATACCCTT
Found at i:27529 original size:14 final size:15
Alignment explanation
Indices: 27503--27531 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
27493 CCATCATCTT
27503 CTTCTTCTTCCTCTG
1 CTTCTTCTTCCTCTG
27518 CTTCTT-TTCCTCTG
1 CTTCTTCTTCCTCTG
27532 GTTTTTGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.00, C:0.38, G:0.07, T:0.55
Consensus pattern (15 bp):
CTTCTTCTTCCTCTG
Found at i:29256 original size:17 final size:18
Alignment explanation
Indices: 29234--29270 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
29224 AGTTTGATTT
29234 TATAT-AATTTTTATTCA
1 TATATAAATTTTTATTCA
29251 TATATAAATTTTTATTCA
1 TATATAAATTTTTATTCA
29269 TA
1 TA
29271 CAATACTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATAAATTTTTATTCA
Done.