Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001611.1 Kokia drynarioides strain JFW-HI SEQ_113244, 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: 88849
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:4429 original size:9 final size:9
Alignment explanation
Indices: 4415--4447 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
4405 AGATATATTT
4415 TTTTTTGAA
1 TTTTTTGAA
4424 TTTTTTGAA
1 TTTTTTGAA
*
4433 TTTTTTAAA
1 TTTTTTGAA
4442 TTTTTT
1 TTTTTT
4448 TAAAAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (9 bp):
TTTTTTGAA
Found at i:8053 original size:7 final size:7
Alignment explanation
Indices: 8041--8103 Score: 74
Period size: 7 Copynumber: 9.1 Consensus size: 7
8031 TGACTCGGAC
8041 CCGTTGA
1 CCGTTGA
8048 CCGTTGA
1 CCGTTGA
**
8055 TAGTTGA
1 CCGTTGA
*
8062 CCATTGA
1 CCGTTGA
8069 CCGTTGA
1 CCGTTGA
8076 CCGTTGA
1 CCGTTGA
8083 CCGTTGA
1 CCGTTGA
*
8090 -CTTTGA
1 CCGTTGA
*
8096 TCGTTGA
1 CCGTTGA
8103 C
1 C
8104 TTTTTACGGG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
6 5 0.11
7 41 0.89
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.33
Consensus pattern (7 bp):
CCGTTGA
Found at i:9089 original size:21 final size:21
Alignment explanation
Indices: 9065--9116 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
9055 TGAGACAATA
9065 CTACCGATACAAG-TATGACTT
1 CTACCGATACAAGTTATG-CTT
* *
9086 CTACCGAAACATGTTATGCTT
1 CTACCGATACAAGTTATGCTT
9107 CTACCGATAC
1 CTACCGATAC
9117 TAAAAACTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (21 bp):
CTACCGATACAAGTTATGCTT
Found at i:15406 original size:22 final size:21
Alignment explanation
Indices: 15373--15489 Score: 96
Period size: 22 Copynumber: 5.4 Consensus size: 21
15363 AATTTATATT
15373 GTTG-TTTTTTTACTGTTTTA
1 GTTGCTTTTTTTACTGTTTTA
15393 GTTGCTATTTTTTACTGTTTT-
1 GTTGCT-TTTTTTACTGTTTTA
* *
15414 GGTGCTTTTTTTCACTATTTTA
1 GTTGCTTTTTTT-ACTGTTTTA
* * **
15436 GTTACTGTTTTGATGTTGTTTTA
1 GTTGCT-TTTT-TTACTGTTTTA
*
15459 G-TGCTTTTTTTATTGTTTTA
1 GTTGCTTTTTTTACTGTTTTA
15479 GTGTTGCTTTT
1 --GTTGCTTTT
15490 ACAGTTATTT
Statistics
Matches: 77, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
20 19 0.25
21 17 0.22
22 22 0.29
23 18 0.23
24 1 0.01
ACGTcount: A:0.10, C:0.08, G:0.17, T:0.65
Consensus pattern (21 bp):
GTTGCTTTTTTTACTGTTTTA
Found at i:15478 original size:43 final size:42
Alignment explanation
Indices: 15377--15480 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 42
15367 TATATTGTTG
* * *
15377 TTTTTTTACTGTTTTAGTTGCTATTTTTTACTGTTTTGGTGC
1 TTTTTTTACTGTTTTAGTTACTATTTTATACTGTTTTAGTGC
* * **
15419 TTTTTTTCACTATTTTAGTTACTGTTTTGATGTTGTTTTAGTGC
1 TTTTTTT-ACTGTTTTAGTTACTATTTT-ATACTGTTTTAGTGC
*
15463 TTTTTTTATTGTTTTAGT
1 TTTTTTTACTGTTTTAGT
15481 GTTGCTTTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 7 0.14
43 26 0.51
44 18 0.35
ACGTcount: A:0.12, C:0.08, G:0.15, T:0.65
Consensus pattern (42 bp):
TTTTTTTACTGTTTTAGTTACTATTTTATACTGTTTTAGTGC
Found at i:15489 original size:20 final size:20
Alignment explanation
Indices: 15451--15490 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
15441 TGTTTTGATG
*
15451 TTGTTTTAGTGCTTTTTTTA
1 TTGTTTTAGTGCTTCTTTTA
15471 TTGTTTTAGTG-TTGCTTTTA
1 TTGTTTTAGTGCTT-CTTTTA
15491 CAGTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.10, C:0.05, G:0.17, T:0.68
Consensus pattern (20 bp):
TTGTTTTAGTGCTTCTTTTA
Found at i:15534 original size:33 final size:33
Alignment explanation
Indices: 15497--15565 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
15487 TTTACAGTTA
* *
15497 TTTTTGTTGCTG-TTTGTGTTGTT-TTTGTTGTTG
1 TTTTTGCTGCTGTTTTG-GTTGTTATTT-TTATTG
15530 TTTTTGCTGCTGTTTTGGTTGTTATTTTTATTG
1 TTTTTGCTGCTGTTTTGGTTGTTATTTTTATTG
15563 TTT
1 TTT
15566 GAATGTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.03, C:0.04, G:0.23, T:0.70
Consensus pattern (33 bp):
TTTTTGCTGCTGTTTTGGTTGTTATTTTTATTG
Found at i:15564 original size:21 final size:23
Alignment explanation
Indices: 15540--15588 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 23
15530 TTTTTGCTGC
**
15540 TGTTTTGGTTGTTA-TTTTTAT-
1 TGTTTTGAATGTTATTTTTTATG
15561 TG-TTTGAATGTTATTTTTTATG
1 TGTTTTGAATGTTATTTTTTATG
15583 TGTTTT
1 TGTTTT
15589 TACTGTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 9 0.39
21 9 0.39
22 2 0.09
23 3 0.13
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.69
Consensus pattern (23 bp):
TGTTTTGAATGTTATTTTTTATG
Found at i:15744 original size:24 final size:24
Alignment explanation
Indices: 15695--15744 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
15685 ATATAAAGAA
*
15695 TTTTTAATGTATTTTAAATTTATT
1 TTTTTAATGTATTTTAAATGTATT
15719 TTTTTAATGTTTATTTT-AATGT-TT
1 TTTTTAATG--TATTTTAAATGTATT
15743 TT
1 TT
15745 AAGTGTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 13 0.57
25 4 0.17
26 6 0.26
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (24 bp):
TTTTTAATGTATTTTAAATGTATT
Found at i:20901 original size:24 final size:24
Alignment explanation
Indices: 20867--20915 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
20857 TGGATTTTTT
* *
20867 ATGCTCTCTACAAACAGTAAGACA
1 ATGCTCCCTACAAACAGTAACACA
*
20891 ATGCTCCCTACAAAGAGTAACACA
1 ATGCTCCCTACAAACAGTAACACA
20915 A
1 A
20916 CCCCTTCTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.18
Consensus pattern (24 bp):
ATGCTCCCTACAAACAGTAACACA
Found at i:34382 original size:81 final size:81
Alignment explanation
Indices: 34256--34475 Score: 341
Period size: 81 Copynumber: 2.7 Consensus size: 81
34246 CGACTACTGT
* *
34256 CCTACCCAGCAGCAATTCGATCACCGGCCTACCCAACAGCAATTCGATCACCGGCCTACCCAACA
1 CCTACCCAGCAGCAATTCGATCACCGGCCTACCCAACAGCAATTCGAACACCGGCCTAACCAACA
34321 GCCATTCGAACACCGG
66 GCCATTCGAACACCGG
* * * *
34337 CCTACCCAGCAGCAATTTGATCACCGGCCTAACCAACAGCCATTCGAACACAGGCCTAACCAACA
1 CCTACCCAGCAGCAATTCGATCACCGGCCTACCCAACAGCAATTCGAACACCGGCCTAACCAACA
34402 GCCATTCGAACACCGG
66 GCCATTCGAACACCGG
* * * * *
34418 CCTAACCAGCAGCAATTCGATCATCGGTCTACCCAGCAGCAATTCGAACACCAGCCTA
1 CCTACCCAGCAGCAATTCGATCACCGGCCTACCCAACAGCAATTCGAACACCGGCCTA
34476 GTCAGCAGCA
Statistics
Matches: 124, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 124 1.00
ACGTcount: A:0.30, C:0.39, G:0.16, T:0.15
Consensus pattern (81 bp):
CCTACCCAGCAGCAATTCGATCACCGGCCTACCCAACAGCAATTCGAACACCGGCCTAACCAACA
GCCATTCGAACACCGG
Found at i:34497 original size:27 final size:27
Alignment explanation
Indices: 34238--34496 Score: 286
Period size: 27 Copynumber: 9.6 Consensus size: 27
34228 CCATAACCCC
* *
34238 CAGCAATTCG-ACTACTGTCCTACCCAG
1 CAGCAATTCGAAC-ACCGGCCTACCCAG
* *
34265 CAGCAATTCGATCACCGGCCTACCCAA
1 CAGCAATTCGAACACCGGCCTACCCAG
* *
34292 CAGCAATTCGATCACCGGCCTACCCAA
1 CAGCAATTCGAACACCGGCCTACCCAG
*
34319 CAGCCATTCGAACACCGGCCTACCCAG
1 CAGCAATTCGAACACCGGCCTACCCAG
* * * *
34346 CAGCAATTTGATCACCGGCCTAACCAA
1 CAGCAATTCGAACACCGGCCTACCCAG
* * * *
34373 CAGCCATTCGAACACAGGCCTAACCAA
1 CAGCAATTCGAACACCGGCCTACCCAG
* *
34400 CAGCCATTCGAACACCGGCCTAACCAG
1 CAGCAATTCGAACACCGGCCTACCCAG
* * *
34427 CAGCAATTCGATCATCGGTCTACCCAG
1 CAGCAATTCGAACACCGGCCTACCCAG
* **
34454 CAGCAATTCGAACACCAGCCTAGTCAG
1 CAGCAATTCGAACACCGGCCTACCCAG
*
34481 CAGCAATTTGAACACC
1 CAGCAATTCGAACACC
34497 AACCTGGCAA
Statistics
Matches: 201, Mismatches: 30, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
27 200 1.00
28 1 0.00
ACGTcount: A:0.31, C:0.37, G:0.16, T:0.16
Consensus pattern (27 bp):
CAGCAATTCGAACACCGGCCTACCCAG
Found at i:34958 original size:35 final size:35
Alignment explanation
Indices: 34919--34989 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
34909 AACTGAAGAA
34919 TCCGTAAGCCATTATCATTTTCTTTGCAATTTTTT
1 TCCGTAAGCCATTATCATTTTCTTTGCAATTTTTT
34954 TCCGTAAGCCATTATCATTTTCTTTGCAATTTTTT
1 TCCGTAAGCCATTATCATTTTCTTTGCAATTTTTT
34989 T
1 T
34990 AGTCATTGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.20, C:0.20, G:0.08, T:0.52
Consensus pattern (35 bp):
TCCGTAAGCCATTATCATTTTCTTTGCAATTTTTT
Found at i:41535 original size:82 final size:82
Alignment explanation
Indices: 41398--41561 Score: 301
Period size: 82 Copynumber: 2.0 Consensus size: 82
41388 ATCTTTTGAT
*
41398 AAGGCACACACAGGTGCTCGAACCCAAATGTTTTAAGATGAACAATATTCTCTTTATCATTGAAG
1 AAGGCACACACAGGTGCTCGAACCCAAATGTTTTAAGATGAACAATATTCTCTTTATCACTGAAG
*
41463 CCATTCGCTGGGTTCAA
66 CCACTCGCTGGGTTCAA
41480 AAGGCACACACAGGTGCTCGAACCCAAATGTTTTAAGATGAACAATATTCTCTTTATCACTGAAG
1 AAGGCACACACAGGTGCTCGAACCCAAATGTTTTAAGATGAACAATATTCTCTTTATCACTGAAG
*
41545 CCACTCGTTGGGTTCAA
66 CCACTCGCTGGGTTCAA
41562 TCTTAATTCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (82 bp):
AAGGCACACACAGGTGCTCGAACCCAAATGTTTTAAGATGAACAATATTCTCTTTATCACTGAAG
CCACTCGCTGGGTTCAA
Found at i:43722 original size:8 final size:8
Alignment explanation
Indices: 43711--43755 Score: 54
Period size: 8 Copynumber: 5.1 Consensus size: 8
43701 TTTTAAACTT
43711 TTTTAATA
1 TTTTAATA
43719 TTTTAATAA
1 TTTTAAT-A
43728 TTTTATATA
1 TTTTA-ATA
43737 TTTTGTAATA
1 -TTT-TAATA
43747 TTTTAATA
1 TTTTAATA
43755 T
1 T
43756 ATATTTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 13 0.39
9 10 0.30
10 8 0.24
11 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TTTTAATA
Found at i:43745 original size:17 final size:17
Alignment explanation
Indices: 43711--43755 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
43701 TTTTAAACTT
43711 TTTTAATATTTTAATAA
1 TTTTAATATTTTAATAA
43728 TTTTATATATTTTGTAAT-A
1 TTTTA-ATA-TTT-TAATAA
43747 TTTTAATAT
1 TTTTAATAT
43756 ATATTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.24
18 6 0.24
19 9 0.36
20 4 0.16
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTTAATATTTTAATAA
Found at i:46963 original size:30 final size:30
Alignment explanation
Indices: 46904--46963 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
46894 TCAATGACTG
* *
46904 TTTTGTCACTTTTAGTTAATGTTAGTGATTA
1 TTTTGTCACATTTA-TTAAAGTTAGTGATTA
46935 TTTTGTCACATTT-TTAAAGTTGAGTGATT
1 TTTTGTCACATTTATTAAAGTT-AGTGATT
46964 GTTGTGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 7 0.27
30 7 0.27
31 12 0.46
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (30 bp):
TTTTGTCACATTTATTAAAGTTAGTGATTA
Found at i:61082 original size:17 final size:17
Alignment explanation
Indices: 61056--61089 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
61046 TACCTTACGC
61056 CCTCTCCTTCTCTCTTT
1 CCTCTCCTTCTCTCTTT
*
61073 CCTCTTCTTCTCTCTTT
1 CCTCTCCTTCTCTCTTT
61090 TTTTCTCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (17 bp):
CCTCTCCTTCTCTCTTT
Found at i:63448 original size:58 final size:58
Alignment explanation
Indices: 63378--63499 Score: 235
Period size: 58 Copynumber: 2.1 Consensus size: 58
63368 CATATGCATT
63378 TTAGAACTACAATGCAAAAATTGAGTGTGTTTGAATTAATTGATGTAGGCTGAGGCTA
1 TTAGAACTACAATGCAAAAATTGAGTGTGTTTGAATTAATTGATGTAGGCTGAGGCTA
*
63436 TTAGAACTACAATGCGAAAATTGAGTGTGTTTGAATTAATTGATGTAGGCTGAGGCTA
1 TTAGAACTACAATGCAAAAATTGAGTGTGTTTGAATTAATTGATGTAGGCTGAGGCTA
63494 TTAGAA
1 TTAGAA
63500 AAATACTTGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 63 1.00
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.33
Consensus pattern (58 bp):
TTAGAACTACAATGCAAAAATTGAGTGTGTTTGAATTAATTGATGTAGGCTGAGGCTA
Found at i:64604 original size:21 final size:21
Alignment explanation
Indices: 64580--64619 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
64570 TTTATTTTTT
64580 TTAAATT-AAAAGTCAAAATCA
1 TTAAATTAAAAAGT-AAAATCA
64601 TTAAATTAAAAAGTAAAAT
1 TTAAATTAAAAAGTAAAAT
64620 TGTGTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (21 bp):
TTAAATTAAAAAGTAAAATCA
Found at i:68299 original size:25 final size:25
Alignment explanation
Indices: 68245--68299 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
68235 ACTTTCATCA
68245 TTTT-TCATTCTTTCAGTTTATTAT
1 TTTTCTCATTCTTTCAGTTTATTAT
* * *
68269 TGTTCTCATTCTTTCATTTTATTCT
1 TTTTCTCATTCTTTCAGTTTATTAT
68294 TTTTCT
1 TTTTCT
68300 TTGAATTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 3 0.12
25 23 0.88
ACGTcount: A:0.13, C:0.16, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTTCTCATTCTTTCAGTTTATTAT
Found at i:82935 original size:29 final size:30
Alignment explanation
Indices: 82880--82945 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
82870 GTTTAATATG
* *
82880 TAATTGTATACATGAACTTTAATTTTG-TA
1 TAATTTTATACATAAACTTTAATTTTGATA
* *
82909 TAATTTTATACATTAAATTTTAA-TTTGATG
1 TAATTTTATACA-TAAACTTTAATTTTGATA
82939 TAATTTT
1 TAATTTT
82946 TGTAAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.53
Consensus pattern (30 bp):
TAATTTTATACATAAACTTTAATTTTGATA
Found at i:82943 original size:30 final size:30
Alignment explanation
Indices: 82877--82945 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
82867 CTGGTTTAAT
* *
82877 ATGTAATTGTATACATGAACTTTAATTTTG
1 ATGTAATTTTATACATAAACTTTAATTTTG
* *
82907 -TATAATTTTATACATTAAATTTTAA-TTTG
1 ATGTAATTTTATACA-TAAACTTTAATTTTG
82936 ATGTAATTTT
1 ATGTAATTTT
82946 TGTAAATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (30 bp):
ATGTAATTTTATACATAAACTTTAATTTTG
Found at i:83113 original size:31 final size:30
Alignment explanation
Indices: 83077--83162 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 30
83067 GATTAAATCA
* *
83077 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGATTCAAGTATACAATTGAACC
* * * * *
83107 ACAATTAGAGCTTCACGTATATAATTGCACC
1 A-AATTAAAGATTCAAGTATACAATTGAACC
*
83138 AAATTAAA-ATTCATGTATACAATTG
1 AAATTAAAGATTCAAGTATACAATTG
83163 CACATTAAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 14 0.31
30 7 0.16
31 24 0.53
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (30 bp):
AAATTAAAGATTCAAGTATACAATTGAACC
Found at i:85071 original size:21 final size:20
Alignment explanation
Indices: 85039--85077 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
85029 TCTCTACAAA
*
85039 TTATAATACATTTTCCTTTG
1 TTATAATACATTTACCTTTG
*
85059 TTATGAATGCATTTACCTT
1 TTAT-AATACATTTACCTT
85078 CCATAGATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (20 bp):
TTATAATACATTTACCTTTG
Found at i:88301 original size:17 final size:18
Alignment explanation
Indices: 88268--88316 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
88258 TTTAAAAGTA
*
88268 TTTTATTT-AATAATA-T
1 TTTTATTTCAAAAATATT
88284 TTTTATTTCAAAAATATT
1 TTTTATTTCAAAAATATT
*
88302 TTTTATCTCAAAAAT
1 TTTTATTTCAAAAAT
88317 TGATTTTGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.28
17 6 0.21
18 15 0.52
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTATTTCAAAAATATT
Found at i:88799 original size:14 final size:14
Alignment explanation
Indices: 88777--88819 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
88767 TTTTTTACAT
88777 AAATAATACAAAAA
1 AAATAATACAAAAA
* *
88791 AAATTATACACCAAA
1 AAATAATACA-AAAA
*
88806 ATATAATACAAAAA
1 AAATAATACAAAAA
88820 TTAAAATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAATACAAAAA
Done.