Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000886.1 Kokia drynarioides strain JFW-HI SEQ_112009, 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: 59537
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:4633 original size:82 final size:82
Alignment explanation
Indices: 4490--4645 Score: 258
Period size: 82 Copynumber: 1.9 Consensus size: 82
4480 CGCAAAACCT
* * * *
4490 TTGGTTAATCCAACTAGAGCTGGGCTCACTTATTGCGGTTTATCTGCTAGGCACTGTGTGCCAGG
1 TTGGTTAATCCAACTAGAGCTGGGCTCACTTATTGCGGTTTATCCGCTAGACACCGAGTGCCAGG
4555 AATTGACGGAATTATCG
66 AATTGACGGAATTATCG
*
4572 TTGGTTAATCCAACTAGAGCTGGGCTCACTTATTGCGGTTTATCCGCTAGACACCGAGTGCCATG
1 TTGGTTAATCCAACTAGAGCTGGGCTCACTTATTGCGGTTTATCCGCTAGACACCGAGTGCCAGG
*
4637 AATTTACGG
66 AATTGACGG
4646 GTTTATACGG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 68 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (82 bp):
TTGGTTAATCCAACTAGAGCTGGGCTCACTTATTGCGGTTTATCCGCTAGACACCGAGTGCCAGG
AATTGACGGAATTATCG
Found at i:5363 original size:18 final size:18
Alignment explanation
Indices: 5340--5374 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5330 ATACTCTAGT
5340 AACTAAATT-CTAATTGAA
1 AACT-AATTCCTAATTGAA
5358 AACTAATTCCTAATTGA
1 AACTAATTCCTAATTGA
5375 TGATGGGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (18 bp):
AACTAATTCCTAATTGAA
Found at i:8320 original size:10 final size:9
Alignment explanation
Indices: 8281--8584 Score: 90
Period size: 10 Copynumber: 32.6 Consensus size: 9
8271 TTTTCTCATA
*
8281 AAAAAATAT
1 AAAAATTAT
*
8290 TAAAATTATT
1 AAAAATTA-T
**
8300 AAAAACAAT
1 AAAAATTAT
8309 AAAAACTTAT
1 AAAAA-TTAT
*
8319 AAATATTAT
1 AAAAATTAT
*
8328 AAAGATATAT
1 AAAAAT-TAT
*
8338 AAAAGTTAT
1 AAAAATTAT
8347 AATAAATTAT
1 AA-AAATTAT
****
8357 ATTTTTTAT
1 AAAAATTAT
*
8366 AAAATTTTAT
1 AAAA-ATTAT
8376 GAAAACA-TAT
1 -AAAA-ATTAT
*
8386 AAAAATTGTT
1 AAAAATT-AT
8396 AAAAATT-T
1 AAAAATTAT
* *
8404 ATATA-TA-
1 AAAAATTAT
8411 AAAAATT-T
1 AAAAATTAT
*
8419 ATTAAA-TATT
1 A-AAAATTA-T
*
8429 AATAA-TAT
1 AAAAATTAT
*
8437 TAAAATTGAT
1 AAAAATT-AT
*
8447 ATAAACTTAT
1 A-AAAATTAT
8457 -AAAA-TAT
1 AAAAATTAT
**
8464 AAGAAACCAT
1 AA-AAATTAT
8474 AAAAATTTAT
1 AAAAA-TTAT
8484 AAAAATTAT
1 AAAAATTAT
8493 -AAAATATATT
1 AAAAAT-TA-T
* *
8503 TAAAATTTT
1 AAAAATTAT
*
8512 ATGAAATTAT
1 A-AAAATTAT
*
8522 GAAAATTCAT
1 AAAAATT-AT
8532 AAAAACTTAT
1 AAAAA-TTAT
8542 AAATAA-TAT
1 AAA-AATTAT
*
8551 AATAAATTCTT
1 AA-AAATT-AT
*
8562 ATAAATTAT
1 AAAAATTAT
8571 AAAAATTAT
1 AAAAATTAT
8580 AAAAA
1 AAAAA
8585 AAATCATTTA
Statistics
Matches: 216, Mismatches: 48, Indels: 62
0.66 0.15 0.19
Matches are distributed among these distances:
7 7 0.03
8 21 0.10
9 83 0.38
10 85 0.39
11 20 0.09
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (9 bp):
AAAAATTAT
Found at i:8492 original size:9 final size:9
Alignment explanation
Indices: 8472--8584 Score: 77
Period size: 9 Copynumber: 11.8 Consensus size: 9
8462 ATAAGAAACC
8472 ATAAAAATTT
1 ATAAAAA-TT
8482 ATAAAAATT
1 ATAAAAATT
8491 AT-AAAATAT
1 ATAAAAAT-T
*
8500 ATTTAAAATT
1 A-TAAAAATT
* *
8510 TTATGAAATT
1 ATA-AAAATT
*
8520 ATGAAAATT
1 ATAAAAATT
8529 CATAAAAACTT
1 -ATAAAAA-TT
8540 ATAAATAA-T
1 ATAAA-AATT
8549 ATAATAAATT
1 ATAA-AAATT
* *
8559 CTTATAAATT
1 -ATAAAAATT
8569 ATAAAAATT
1 ATAAAAATT
8578 ATAAAAA
1 ATAAAAA
8585 AAATCATTTA
Statistics
Matches: 82, Mismatches: 11, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
8 5 0.06
9 33 0.40
10 33 0.40
11 11 0.13
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (9 bp):
ATAAAAATT
Found at i:8507 original size:29 final size:29
Alignment explanation
Indices: 8475--8583 Score: 79
Period size: 29 Copynumber: 3.8 Consensus size: 29
8465 AGAAACCATA
8475 AAAATTTATAAAAATTATAAAATATATTT
1 AAAATTTATAAAAATTATAAAATATATTT
* *
8504 AAAATTT-TATGAAATTATGAAAAT-TCA-TA
1 AAAATTTATA-AAAATTAT-AAAATAT-ATTT
*
8533 AAAACTTATAAATAA-TATAATAA-AT-TCTT
1 AAAATTTATAAA-AATTATAA-AATATAT-TT
8562 ATAAA-TTATAAAAATTATAAAA
1 A-AAATTTATAAAAATTATAAAA
8584 AAAATCATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 23
0.70 0.05 0.25
Matches are distributed among these distances:
28 8 0.12
29 43 0.67
30 13 0.20
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATTTATAAAAATTATAAAATATATTT
Found at i:8568 original size:49 final size:47
Alignment explanation
Indices: 8472--8584 Score: 133
Period size: 48 Copynumber: 2.3 Consensus size: 47
8462 ATAAGAAACC
*
8472 ATAAAAATTTATAAAAATTATAAAATATATTTAAAATTTTATGAAATT
1 ATAAAAA-TTATAAAAATTATAAAATATATATAAAATTTTATGAAATT
*
8520 ATGAAAATTCATAAAAACTTAT-AAATA-ATATAATAAATTCTTAT-AAATT
1 ATAAAAATT-ATAAAAA-TTATAAAATATATAT-A-AAATT-TTATGAAATT
8569 ATAAAAATTATAAAAA
1 ATAAAAATTATAAAAA
8585 AAATCATTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
47 5 0.09
48 26 0.46
49 22 0.39
50 4 0.07
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (47 bp):
ATAAAAATTATAAAAATTATAAAATATATATAAAATTTTATGAAATT
Found at i:8585 original size:49 final size:48
Alignment explanation
Indices: 8472--8585 Score: 128
Period size: 49 Copynumber: 2.4 Consensus size: 48
8462 ATAAGAAACC
*
8472 ATAAAAATT-TATAAAAATTATAAAATATATTTAAAATTTTATGAAATT
1 ATAAAAATTATA-AAAAATTATAAAATATATATAAAATTTTATGAAATT
* *
8520 ATGAAAATTCATAAAAACTTAT-AAATA-ATATAATAAATTCTTAT-AAATT
1 ATAAAAATT-ATAAAAAATTATAAAATATATAT-A-AAATT-TTATGAAATT
8569 ATAAAAATTATAAAAAA
1 ATAAAAATTATAAAAAA
8586 AATCATTTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
47 3 0.05
48 21 0.38
49 26 0.46
50 6 0.11
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (48 bp):
ATAAAAATTATAAAAAATTATAAAATATATATAAAATTTTATGAAATT
Found at i:9185 original size:17 final size:18
Alignment explanation
Indices: 9163--9197 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
9153 TAAATTTATA
9163 TCAATTTTAAT-ATTTTT
1 TCAATTTTAATCATTTTT
*
9180 TCAATTTTTATCATTTTT
1 TCAATTTTAATCATTTTT
9198 AAGGATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TCAATTTTAATCATTTTT
Found at i:13214 original size:16 final size:15
Alignment explanation
Indices: 13164--13217 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
13154 AAATATATAT
13164 ATTAAAATT-ACTAAA
1 ATTAAAATTAAC-AAA
* * *
13179 AATAAATTTAACAAT
1 ATTAAAATTAACAAA
13194 ATTAAAATTAACAAA
1 ATTAAAATTAACAAA
*
13209 ATTTAAATT
1 ATTAAAATT
13218 TTCGTATTAC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
15 29 0.94
16 2 0.06
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTAAAATTAACAAA
Found at i:19459 original size:21 final size:22
Alignment explanation
Indices: 19425--19474 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
19415 TGAACAGAAC
*
19425 GTTCGATGAACCATTTGTA-AACT
1 GTTCG-TGAACCATTCGTATAA-T
19448 GTTCGTG-ACCATTCGTATAAT
1 GTTCGTGAACCATTCGTATAAT
19469 GTTCGT
1 GTTCGT
19475 TTACTAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 16 0.64
22 4 0.16
23 5 0.20
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (22 bp):
GTTCGTGAACCATTCGTATAAT
Found at i:19844 original size:30 final size:30
Alignment explanation
Indices: 19796--19876 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
19786 TTCTTGAACA
* * * *
19796 TTAAACAAATGAATATGAACACGCATAATT
1 TTAAATAAACGAACATGAACACACATAATT
19826 TTAAATAAACGAACATGAACACACATAATT
1 TTAAATAAACGAACATGAACACACATAATT
* *
19856 TTAGATAAACAAACATGAACA
1 TTAAATAAACGAACATGAACA
19877 AAAAATTGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.53, C:0.15, G:0.09, T:0.23
Consensus pattern (30 bp):
TTAAATAAACGAACATGAACACACATAATT
Found at i:23050 original size:15 final size:15
Alignment explanation
Indices: 23030--23062 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
23020 ATTTGAGTAA
23030 GTTCTCTCTTGCAAG
1 GTTCTCTCTTGCAAG
*
23045 GTTCTCTCTTGTAAG
1 GTTCTCTCTTGCAAG
23060 GTT
1 GTT
23063 TTCATCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (15 bp):
GTTCTCTCTTGCAAG
Found at i:25971 original size:14 final size:16
Alignment explanation
Indices: 25954--25993 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
25944 AAATTTACAA
*
25954 TTTAGTCTTT-ATA-T
1 TTTAGTCTTTGAGATT
25968 TTTAGT-TTTGAGATT
1 TTTAGTCTTTGAGATT
25983 TTTAGTCTTTG
1 TTTAGTCTTTG
25994 TACTTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 3 0.14
14 8 0.36
15 7 0.32
16 4 0.18
ACGTcount: A:0.17, C:0.05, G:0.15, T:0.62
Consensus pattern (16 bp):
TTTAGTCTTTGAGATT
Found at i:27222 original size:25 final size:25
Alignment explanation
Indices: 27177--27240 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 25
27167 GAGAATTTTG
27177 TTTATGTTTTAAAAATCTTTTTTATTT
1 TTTAT-TTTTAAAAA-CTTTTTTATTT
*
27204 TTTATTTTTAAAGA-TTTTTTATTT
1 TTTATTTTTAAAAACTTTTTTATTT
27228 TTATATTATTTAA
1 TT-TATT-TTTAA
27241 TTTTAAAGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
24 12 0.35
25 4 0.12
26 13 0.38
27 5 0.15
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (25 bp):
TTTATTTTTAAAAACTTTTTTATTT
Found at i:27244 original size:23 final size:23
Alignment explanation
Indices: 27194--27240 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 23
27184 TTTAAAAATC
27194 TTTTTTATTTTTTATTTTTAAAGA
1 TTTTTTATTTTTTATTTTT-AAGA
27218 TTTTTTATTTTTATATTATTTAA
1 TTTTTTATTTTT-TATT-TTTAA
27241 TTTTAAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 12 0.57
25 6 0.29
26 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTTTATTTTTTATTTTTAAGA
Found at i:29786 original size:14 final size:15
Alignment explanation
Indices: 29767--29795 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29757 GTGTATAGTT
29767 AAATA-TTAAAAAAA
1 AAATATTTAAAAAAA
29781 AAATATTTAAAAAAA
1 AAATATTTAAAAAAA
29796 GAGAAGCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATATTTAAAAAAA
Found at i:33333 original size:7 final size:7
Alignment explanation
Indices: 33323--33355 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
33313 CACCATGATT
33323 TAAAATA
1 TAAAATA
33330 TAAAATA
1 TAAAATA
33337 TAAAATA
1 TAAAATA
33344 TAAAATA
1 TAAAATA
33351 TAAAA
1 TAAAA
33356 AGATCTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAATA
Found at i:33917 original size:12 final size:12
Alignment explanation
Indices: 33900--33924 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33890 ATATATAAAG
33900 GGAGAAGAAGAA
1 GGAGAAGAAGAA
33912 GGAGAAGAAGAA
1 GGAGAAGAAGAA
33924 G
1 G
33925 AAGCAACAGT
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:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (12 bp):
GGAGAAGAAGAA
Found at i:40360 original size:28 final size:28
Alignment explanation
Indices: 40253--40455 Score: 106
Period size: 28 Copynumber: 7.7 Consensus size: 28
40243 AAAAGTGCGC
* *
40253 AAGCTGGCGAGCGTAAACGCATATATAT
1 AAGCTGACGAGCGTAAACGCATACATAT
* * * * **
40281 AAACTGACAATCGTAAACG--T--TTGC
1 AAGCTGACGAGCGTAAACGCATACATAT
* * * *
40305 AAGCTGGCAAGCGTAAACACATATATAT
1 AAGCTGACGAGCGTAAACGCATACATAT
* *
40333 AAGTTGACGAGTGTAAACGCATACATAT
1 AAGCTGACGAGCGTAAACGCATACATAT
* **
40361 AAGCTGACGAGCGTAAACG--T--GTGC
1 AAGCTGACGAGCGTAAACGCATACATAT
* * **
40385 AAGCTGACGAGCGTAAATG--T--GTGC
1 AAGCTGACGAGCGTAAACGCATACATAT
* *
40409 AAGCTAACGAGCATAAACGCATACATAT
1 AAGCTGACGAGCGTAAACGCATACATAT
*
40437 AAGCTGGCGAGCGTAAACG
1 AAGCTGACGAGCGTAAACG
40456 TGTGCAAACT
Statistics
Matches: 132, Mismatches: 35, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
24 56 0.42
26 4 0.03
28 72 0.55
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (28 bp):
AAGCTGACGAGCGTAAACGCATACATAT
Found at i:40393 original size:24 final size:24
Alignment explanation
Indices: 40361--40427 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
40351 GCATACATAT
40361 AAGCTGACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
*
40385 AAGCTGACGAGCGTAAATGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* *
40409 AAGCTAACGAGCATAAACG
1 AAGCTGACGAGCGTAAACG
40428 CATACATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.16
Consensus pattern (24 bp):
AAGCTGACGAGCGTAAACGTGTGC
Found at i:40441 original size:52 final size:52
Alignment explanation
Indices: 40385--40530 Score: 184
Period size: 52 Copynumber: 2.8 Consensus size: 52
40375 AAACGTGTGC
*
40385 AAGCTGACGAGCGTAAATGTGTGCAAGCTAACGAGCATAAACGCATACATAT
1 AAGCTGACGAGCGTAAACGTGTGCAAGCTAACGAGCATAAACGCATACATAT
* * **** *
40437 AAGCTGGCGAGCGTAAACGTGTGCAAACTGGTAAGCATAAACGCATATATAT
1 AAGCTGACGAGCGTAAACGTGTGCAAGCTAACGAGCATAAACGCATACATAT
* * *
40489 ATAGCCGACGAGCATAAACATGTGCAAGCTAACGAGCATAAA
1 A-AGCTGACGAGCGTAAACGTGTGCAAGCTAACGAGCATAAA
40531 AGTTTGAAAG
Statistics
Matches: 76, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
52 45 0.59
53 31 0.41
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.18
Consensus pattern (52 bp):
AAGCTGACGAGCGTAAACGTGTGCAAGCTAACGAGCATAAACGCATACATAT
Found at i:40541 original size:24 final size:24
Alignment explanation
Indices: 40496--40543 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
40486 TATATAGCCG
*
40496 ACGAGCATAAACATGTGCAAGCTA
1 ACGAGCATAAACATGTGAAAGCTA
*
40520 ACGAGCATAAA-AGTTTGAAAGCTA
1 ACGAGCATAAACA-TGTGAAAGCTA
40544 GTGAGTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.19
Consensus pattern (24 bp):
ACGAGCATAAACATGTGAAAGCTA
Found at i:43915 original size:18 final size:19
Alignment explanation
Indices: 43869--43935 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
43859 AAAAGTGATT
*
43869 TTTAATATTTAAATATTTAAAA
1 TTTAA-ATTT-AATATTT-TAA
*
43891 TTATAAATTT-ATTTTTTAA
1 TT-TAAATTTAATATTTTAA
*
43910 TTTAAATTTAATATTTTAT
1 TTTAAATTTAATATTTTAA
43929 TTTAAAT
1 TTTAAAT
43936 AAACTTTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 7 0.18
19 18 0.46
20 5 0.13
22 6 0.15
23 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAAATTTAATATTTTAA
Found at i:44536 original size:18 final size:18
Alignment explanation
Indices: 44513--44547 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44503 TTTTATTTGC
44513 TTTCAAAAAATTTTTTTT
1 TTTCAAAAAATTTTTTTT
**
44531 TTTCAATTAATTTTTTT
1 TTTCAAAAAATTTTTTT
44548 GTAAATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTCAAAAAATTTTTTTT
Found at i:46226 original size:29 final size:29
Alignment explanation
Indices: 46193--46254 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
46183 TAATTTATGA
* *
46193 AAAATAAATCAAATTAAAATTTCATGTGT
1 AAAATAAATCAAATTAAAAGTTCATGCGT
* * *
46222 AAAATTATTCAAATTCAAAGTTCATGCGT
1 AAAATAAATCAAATTAAAAGTTCATGCGT
46251 AAAA
1 AAAA
46255 ACACATATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32
Consensus pattern (29 bp):
AAAATAAATCAAATTAAAAGTTCATGCGT
Found at i:49367 original size:17 final size:18
Alignment explanation
Indices: 49340--49375 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
49330 AAAATTCAAA
49340 AAAATTTTCAAAATTTAT
1 AAAATTTTCAAAATTTAT
49358 AAAA-TTTCAAAATTTAT
1 AAAATTTTCAAAATTTAT
49375 A
1 A
49376 TTTTGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATTTTCAAAATTTAT
Found at i:51228 original size:59 final size:60
Alignment explanation
Indices: 51118--51308 Score: 231
Period size: 60 Copynumber: 3.2 Consensus size: 60
51108 TTAATACAAC
* *
51118 ATTTAGTATCTGAACTTGACATTTTTTTTTAATTTGGTACCTAAACTTTTTTT-GACCCA
1 ATTTGGTACCTGAACTTGACATTTTTTTTTAATTTGGTACCTAAACTTTTTTTGGACCCA
*
51177 ATTTGGTACCTGAACTTGATACTTTTTTTTTAATTTGGTACCTAAACTTTTTTTGGACCCA
1 ATTTGGTACCTGAACTTGACA-TTTTTTTTTAATTTGGTACCTAAACTTTTTTTGGACCCA
* * * * *** ** * **
51238 ATTTGATACCTGAATTTGGCATCTTTTCCGAATTTGGTACCTAAGTTTTTTTTAGATTCA
1 ATTTGGTACCTGAACTTGACATTTTTTTTTAATTTGGTACCTAAACTTTTTTTGGACCCA
51298 ATTTGGTACCT
1 ATTTGGTACCT
51309 AATTTTATTA
Statistics
Matches: 113, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
59 18 0.16
60 72 0.64
61 23 0.20
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.48
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGACATTTTTTTTTAATTTGGTACCTAAACTTTTTTTGGACCCA
Found at i:51582 original size:32 final size:32
Alignment explanation
Indices: 51508--51646 Score: 123
Period size: 31 Copynumber: 4.5 Consensus size: 32
51498 GGACCCCAAA
* * *
51508 AAGTTTAAGTAACAACTTAGAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGGAAAAAAGTGTC
*
51540 AAATTT-AGTACCAAATTAGGAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGGAAAAAAGTGTC
*
51571 AAGTTTAAGTACCAAATT-GGACAAAAA----A
1 AAGTTTAAGTACCAAATTAGGA-AAAAAGTGTC
* *
51599 AAATTT-AGATACCAAATTAAG-AAAAAGTGTC
1 AAGTTTAAG-TACCAAATTAGGAAAAAAGTGTC
* *
51630 AAGTTCAAATACCAAAT
1 AAGTTTAAGTACCAAAT
51647 GTTATTTTAA
Statistics
Matches: 86, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
27 7 0.08
28 14 0.16
29 1 0.01
31 42 0.49
32 22 0.26
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (32 bp):
AAGTTTAAGTACCAAATTAGGAAAAAAGTGTC
Found at i:53037 original size:13 final size:13
Alignment explanation
Indices: 53019--53043 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53009 AATATCACAC
53019 AAATAAAATTAAT
1 AAATAAAATTAAT
53032 AAATAAAATTAA
1 AAATAAAATTAA
53044 CAAAATTAAC
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAAAATTAAT
Found at i:53060 original size:22 final size:22
Alignment explanation
Indices: 53023--53065 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
53013 TCACACAAAT
*
53023 AAAATTAATAAATAAAATTAAC
1 AAAATTAACAAATAAAATTAAC
* *
53045 AAAATTAACAATTAAACTTAA
1 AAAATTAACAAATAAAATTAA
53066 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATTAACAAATAAAATTAAC
Found at i:53419 original size:30 final size:30
Alignment explanation
Indices: 53383--53444 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
53373 TTAATTAATC
53383 TCCCTAAGGTGTGAACGGTGACCTTCAATT
1 TCCCTAAGGTGTGAACGGTGACCTTCAATT
53413 TCCCTAAGGTGTGAACGGTGACCTTCAATT
1 TCCCTAAGGTGTGAACGGTGACCTTCAATT
53443 TC
1 TC
53445 AGTTTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (30 bp):
TCCCTAAGGTGTGAACGGTGACCTTCAATT
Found at i:59090 original size:4 final size:4
Alignment explanation
Indices: 59081--59166 Score: 77
Period size: 4 Copynumber: 21.2 Consensus size: 4
59071 AAATAAACGG
* * *
59081 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGA GAAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA GAAA
* * *
59131 G-AA GAAG GAGAG GAAA GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
59167 TTAATGTGTT
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
3 6 0.09
4 50 0.75
5 11 0.16
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:59103 original size:17 final size:17
Alignment explanation
Indices: 59081--59166 Score: 99
Period size: 16 Copynumber: 5.3 Consensus size: 17
59071 AAATAAACGG
59081 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
59098 GAAAGAAAGAAAGG-AA
1 GAAAGAAAGAAAGGAAA
* * *
59114 GAAGGAGAGAAAAGAAA
1 GAAAGAAAGAAAGGAAA
* *
59131 G-AAGAAGGAGAGGAAA
1 GAAAGAAAGAAAGGAAA
59147 GAAAG-AAG-AAGGAAA
1 GAAAGAAAGAAAGGAAA
59162 GAAAG
1 GAAAG
59167 TTAATGTGTT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
15 11 0.19
16 26 0.46
17 20 0.35
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Found at i:59134 original size:20 final size:20
Alignment explanation
Indices: 59103--59165 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
59093 GGAAAGAAAG
59103 AAAGAAAGGAAGAAGGAGAGA
1 AAAGAAA-GAAGAAGGAGAGA
*
59124 AAAGAAAGAAGAAGGAGAGG
1 AAAGAAAGAAGAAGGAGAGA
*
59144 AAAGAAAGAAGAAGGAAAGA
1 AAAGAAAGAAGAAGGAGAGA
59164 AA
1 AA
59166 GTTAATGTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 32 0.82
21 7 0.18
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAAGAAGGAGAGA
Done.