Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015182.1 Kokia drynarioides strain JFW-HI SEQ_130226, 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: 65699
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:1572 original size:5 final size:5
Alignment explanation
Indices: 1562--1606 Score: 69
Period size: 5 Copynumber: 9.6 Consensus size: 5
1552 TATGATTAAC
1562 TTTCT TTTCT TTTC- TTTCT TTTCT TTTC- TTTCT TTT-T TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1607 AAAATATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 12 0.32
5 25 0.68
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:1573 original size:9 final size:9
Alignment explanation
Indices: 1561--1606 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
1551 GTATGATTAA
1561 CTTTCTTTT
1 CTTTCTTTT
1570 CTTT-TCTTT
1 CTTTCT-TTT
1579 CTTTTCTTTT
1 C-TTTCTTTT
1589 CTTTCTTTT
1 CTTTCTTTT
*
1598 TTTTCTTTT
1 CTTTCTTTT
1607 AAAATATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 1 0.03
9 24 0.73
10 7 0.21
11 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
CTTTCTTTT
Found at i:1580 original size:14 final size:14
Alignment explanation
Indices: 1561--1605 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
1551 GTATGATTAA
1561 CTTTCTTTTCTTTT
1 CTTTCTTTTCTTTT
1575 CTTTCTTTTCTTTT
1 CTTTCTTTTCTTTT
1589 CTTTCTTTT-TTTT
1 CTTTCTTTTCTTTT
1602 CTTT
1 CTTT
1606 TAAAATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 8 0.26
14 23 0.74
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
CTTTCTTTTCTTTT
Found at i:7260 original size:23 final size:24
Alignment explanation
Indices: 7217--7261 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
7207 TTTTTACCAC
*
7217 AAATTTATCATAACAAACAAAAAA
1 AAATTTATCAAAACAAACAAAAAA
*
7241 AAATTTA-CAAAACAAGCAAAA
1 AAATTTATCAAAACAAACAAAA
7262 TCTAAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.67, C:0.13, G:0.02, T:0.18
Consensus pattern (24 bp):
AAATTTATCAAAACAAACAAAAAA
Found at i:11393 original size:11 final size:11
Alignment explanation
Indices: 11377--11405 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
11367 AACCCCTCTG
11377 GCTTCTCCCCA
1 GCTTCTCCCCA
11388 GCTTCTCCCCA
1 GCTTCTCCCCA
11399 GCTTCTC
1 GCTTCTC
11406 GCTTTTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.52, G:0.10, T:0.31
Consensus pattern (11 bp):
GCTTCTCCCCA
Found at i:15014 original size:30 final size:31
Alignment explanation
Indices: 14978--15037 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
14968 ATGATCTCTC
*
14978 AACTATTCGACTCTTTTTTTT-TGGTCACCT
1 AACTATTCGAATCTTTTTTTTGTGGTCACCT
*
15008 AACTATTTGAATCTTTTTTTTGTGGTCACC
1 AACTATTCGAATCTTTTTTTTGTGGTCACC
15038 AACAGTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.50
Consensus pattern (31 bp):
AACTATTCGAATCTTTTTTTTGTGGTCACCT
Found at i:15537 original size:9 final size:8
Alignment explanation
Indices: 15525--15549 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
15515 ACGAAAACAG
15525 AAAAAATT
1 AAAAAATT
15533 AAAAAATT
1 AAAAAATT
15541 AAAAAATT
1 AAAAAATT
15549 A
1 A
15550 TTTTATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAAAATT
Found at i:16893 original size:24 final size:24
Alignment explanation
Indices: 16866--16912 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
16856 ATTAAAATTT
16866 TTATATATT-TTATTCAAAAAAAAA
1 TTATATATTATT-TTCAAAAAAAAA
*
16890 TTATATATTATTTTTAAAAAAAA
1 TTATATATTATTTTCAAAAAAAA
16913 TAAATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TTATATATTATTTTCAAAAAAAAA
Found at i:18924 original size:11 final size:10
Alignment explanation
Indices: 18904--18961 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
18894 GCCCAACAGC
18904 ATTTAAATTT
1 ATTTAAATTT
*
18914 ATTTGAA---
1 ATTTAAATTT
18921 ATTTAAATTT
1 ATTTAAATTT
18931 ATTATAAATTT
1 ATT-TAAATTT
18942 AAATTTAAATTT
1 --ATTTAAATTT
18954 ATTTAAAT
1 ATTTAAAT
18962 AATGTCCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 6 0.15
10 17 0.43
11 7 0.17
12 7 0.17
13 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:18926 original size:17 final size:17
Alignment explanation
Indices: 18904--18948 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 17
18894 GCCCAACAGC
18904 ATTTAAATTTATT-TGAA
1 ATTTAAATTTATTAT-AA
18921 ATTTAAATTTATTATAA
1 ATTTAAATTTATTATAA
18938 ATTTAAATTTA
1 ATTTAAATTTA
18949 AATTTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 26 0.96
18 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATTATAA
Found at i:18928 original size:6 final size:6
Alignment explanation
Indices: 18904--18954 Score: 56
Period size: 6 Copynumber: 8.8 Consensus size: 6
18894 GCCCAACAGC
18904 ATTTAA ATTT-- ATTTGAA ATTTAA ATTT-- ATTATAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATT-TAA ATTTAA ATTTAA
18950 ATTTA
1 ATTTA
18955 TTTAAATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
4 7 0.18
5 1 0.03
6 24 0.62
7 7 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:18931 original size:23 final size:22
Alignment explanation
Indices: 18914--18961 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
18904 ATTTAAATTT
18914 ATTTGAAATTTAAATTTATTATAA
1 ATTT-AAATTTAAATTTATT-TAA
18938 ATTTAAATTTAAATTTATTTAA
1 ATTTAAATTTAAATTTATTTAA
18960 AT
1 AT
18962 AATGTCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTTAAATTTAAATTTATTTAA
Found at i:20890 original size:29 final size:29
Alignment explanation
Indices: 20839--21116 Score: 270
Period size: 29 Copynumber: 9.8 Consensus size: 29
20829 GAAGGTCCCT
* * *
20839 AAACTATCCGAAAATTACA-TTTTCCCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCC
*
20868 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * *
20897 AAACTTACAAAAATTCCATTATTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* ** * *
20926 GAACTTCCAAAAAACCCATTTTTTACCTCA
1 AAACTTCCAAAAATTCCA-TTTTTACCCCC
20956 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * *
20985 GAACTTCCAAAAATTCCATTTTCGACCCCA
1 AAACTTCCAAAAATTCCATTTT-TACCCCC
*
21015 AAACTTCAAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * *
21044 GAACCTCCAAAAGTTCCATTTTTA-ACCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
21072 --A-----AAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
21094 GAAAC-TCCAAAAATTCCATTTTT
1 -AAACTTCCAAAAATTCCATTTTT
21117 GGCCTAAAAA
Statistics
Matches: 206, Mismatches: 32, Indels: 22
0.79 0.12 0.08
Matches are distributed among these distances:
21 15 0.07
22 3 0.01
25 1 0.00
26 1 0.00
28 14 0.07
29 124 0.60
30 48 0.23
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.31
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:20967 original size:59 final size:59
Alignment explanation
Indices: 20839--21116 Score: 301
Period size: 59 Copynumber: 4.9 Consensus size: 59
20829 GAAGGTCCCT
* * * * *
20839 AAACTATCCGAAAATTACA-TTTTCCCCCCAAACTTCCAAAAATTCCA-TTTTTACCCCT
1 AAACT-TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTTACCCCA
* * * ** *
20897 AAACTTACAAAAATTCCATTATTACCCCTGAACTTCCAAAAAACCCATTTTTTACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTTACCCCA
**
20956 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTCGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTTACCCCA
* * * *
21015 AAACTTCAAAAAATTCCATTTTTACCCCCGAACCTCCAAAAGTTCCA-TTTTTAACCC-
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTTACCCCA
21072 --A-----AAAAATTCCATTTTTACCCCCGAAAC-TCCAAAAATTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTTACCCCCG-AACTTCCAAAAATTCCATTTTT
21117 GGCCTAAAAA
Statistics
Matches: 190, Mismatches: 26, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
50 34 0.18
51 7 0.04
55 1 0.01
57 10 0.05
58 34 0.18
59 104 0.55
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.31
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTTACCCCA
Found at i:21025 original size:88 final size:88
Alignment explanation
Indices: 20858--21067 Score: 255
Period size: 88 Copynumber: 2.4 Consensus size: 88
20848 GAAAATTACA
* * *
20858 TTTTCCCCCCAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTACAAAAATTCCATTATTACC
1 TTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTACAAAAATTCCATTATTACC
**
20923 CCTGAACTTCCAAAAAA-CCCATT
66 CCAAAACTTCCAAAAAATCCCA-T
* * *
20946 TTTTACCTCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATT-TTCGA
1 TTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTACAAAAATTCCATTATT--A
*
21010 CCCCAAAACTT-CAAAAAATTCCAT
64 CCCCAAAACTTCCAAAAAATCCCAT
** * *
21034 TTTTACCCCCGAACCTCCAAAAGTTCCATTTTTA
1 TTTTACCCCAAAACTTCCAAAAATTCCATTTTTA
21068 ACCCAAAAAA
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
87 2 0.02
88 90 0.86
89 13 0.12
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.31
Consensus pattern (88 bp):
TTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTACAAAAATTCCATTATTACC
CCAAAACTTCCAAAAAATCCCAT
Found at i:21156 original size:50 final size:50
Alignment explanation
Indices: 21021--21116 Score: 174
Period size: 50 Copynumber: 1.9 Consensus size: 50
21011 CCCAAAACTT
* *
21021 CAAAAAATTCCATTTTTACCCCCGAACCTCCAAAAGTTCCATTTTTAACC
1 CAAAAAATTCCATTTTTACCCCCGAAACTCCAAAAATTCCATTTTTAACC
21071 CAAAAAATTCCATTTTTACCCCCGAAACTCCAAAAATTCCATTTTT
1 CAAAAAATTCCATTTTTACCCCCGAAACTCCAAAAATTCCATTTTT
21117 GGCCTAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.31
Consensus pattern (50 bp):
CAAAAAATTCCATTTTTACCCCCGAAACTCCAAAAATTCCATTTTTAACC
Found at i:33907 original size:206 final size:206
Alignment explanation
Indices: 33527--33931 Score: 504
Period size: 206 Copynumber: 2.0 Consensus size: 206
33517 CAACTCAGGA
* * * * *
33527 CTCGATGCGAGCAAATCTTCGAACCTCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAA
1 CTCGATGCGAACAAATCCTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGAAGGTCGAAGCAA
* * ** ** * * * *
33592 TAAAATGGTTAGCTTCCTGATGAGATATTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAT
66 TAAAATGGTTAGCTTCCTGACGAAATACGGAGAAGTGAACCAAAACCATATTCCTGATGAAATAC
** * * *
33657 AGAGAAGCGGATTGAAACAAGCGATGCAGTTATCTTCCTGATGAGACACTGAGAAGAAGACCAAA
131 AGAGAAGCGGATCAAAACAAGCGATACAGTCATCTTCCTGATGAGACACTGAAAAGAAGACCAAA
33722 TCAAACCCATG
196 TCAAACCCATG
* * *
33733 CTCGATGTGAACAAATCCTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGAAGGTTGAAGTAA
1 CTCGATGCGAACAAATCCTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGAAGGTCGAAGCAA
*
33798 TAAAATGGTTAGCTTCCTGACGAAATACGGGGAAGTGAACCAAAACCATATTCCTGATGAAATAC
66 TAAAATGGTTAGCTTCCTGACGAAATACGGAGAAGTGAACCAAAACCATATTCCTGATGAAATAC
* * ** * ** * * *
33863 AGAGAAGTGGATCAAAACAAGTGATATGGTCGTCTTTTTGATGAGATACTGAAAAGAAGGCCAAG
131 AGAGAAGCGGATCAAAACAAGCGATACAGTCATCTTCCTGATGAGACACTGAAAAGAAGACCAAA
33928 TCAA
196 TCAA
33932 TGAAACCAGA
Statistics
Matches: 165, Mismatches: 34, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
206 165 1.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (206 bp):
CTCGATGCGAACAAATCCTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGAAGGTCGAAGCAA
TAAAATGGTTAGCTTCCTGACGAAATACGGAGAAGTGAACCAAAACCATATTCCTGATGAAATAC
AGAGAAGCGGATCAAAACAAGCGATACAGTCATCTTCCTGATGAGACACTGAAAAGAAGACCAAA
TCAAACCCATG
Found at i:34273 original size:17 final size:17
Alignment explanation
Indices: 34245--34307 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
34235 GGCCCAACAG
*
34245 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTGA
* *
34262 AAATTAAGTTTATTTGA
1 AATTTAAATTTATTTGA
*
34279 AATTTAATTTTATTTGA
1 AATTTAAATTTATTTGA
34296 AATTTAAATTTA
1 AATTTAAATTTA
34308 AATTTATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTTGA
Found at i:34284 original size:23 final size:22
Alignment explanation
Indices: 34258--34320 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 22
34248 TTAAATTTAT
34258 TTTAAAATTAAGTTTATTTGAAA
1 TTTAAAATTAA-TTTATTTGAAA
34281 TTT--AA-T--TTTATTTGAAA
1 TTTAAAATTAATTTATTTGAAA
*
34298 TTTAAATTTAAATTTATTT-AAA
1 TTTAAAATT-AATTTATTTGAAA
34320 T
1 T
34321 AATGTCCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 13
0.70 0.02 0.28
Matches are distributed among these distances:
17 14 0.42
19 1 0.03
20 2 0.06
21 2 0.06
22 4 0.12
23 10 0.30
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTAAAATTAATTTATTTGAAA
Found at i:34288 original size:12 final size:11
Alignment explanation
Indices: 34245--34320 Score: 52
Period size: 12 Copynumber: 6.8 Consensus size: 11
34235 GGCCCAACAG
34245 AATTTAAATTT
1 AATTTAAATTT
* *
34256 ATTTTAAAATT
1 AATTTAAATTT
34267 AAGTTT--ATTT
1 AA-TTTAAATTT
34277 GAAATTT-AATTT
1 --AATTTAAATTT
*
34289 TATTTGAAATTT
1 AATTT-AAATTT
34301 AAATTTAAATTT
1 -AATTTAAATTT
34313 -ATTTAAAT
1 AATTTAAAT
34321 AATGTCCAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
10 15 0.29
11 13 0.25
12 20 0.38
13 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:34343 original size:13 final size:13
Alignment explanation
Indices: 34325--34349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34315 TTAAATAATG
34325 TCCAATTACAAAA
1 TCCAATTACAAAA
34338 TCCAATTACAAA
1 TCCAATTACAAA
34350 TCAAGCCCAA
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:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (13 bp):
TCCAATTACAAAA
Found at i:36268 original size:34 final size:36
Alignment explanation
Indices: 36216--36282 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
36206 CCCTGAAGGT
36216 CCCTAAACTATCCAAAAATTAC-ATTTTACCCCTAA
1 CCCTAAACTATCCAAAAATTACAATTTTACCCCTAA
*
36251 CCCTAAACT-TCCAAAAATTCCAATTTTACCCC
1 CCCTAAACTATCCAAAAATTACAATTTTACCCC
36283 CAAATTTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 11 0.37
35 19 0.63
ACGTcount: A:0.37, C:0.34, G:0.00, T:0.28
Consensus pattern (36 bp):
CCCTAAACTATCCAAAAATTACAATTTTACCCCTAA
Found at i:36328 original size:30 final size:29
Alignment explanation
Indices: 36255--36349 Score: 127
Period size: 30 Copynumber: 3.2 Consensus size: 29
36245 CCCTAACCCT
* *
36255 AAACTTCCAAAAATTCCAATTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* *
36284 AAATTTCCAAAAATTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
*
36314 AAACTTCTAAAAATTCCATTTTTTACCCCA
1 AAACTTCCAAAAATTCCA-TTTTTACCCCA
36344 AAACTT
1 AAACTT
36350 TCATTTTGCC
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
29 21 0.37
30 31 0.54
31 5 0.09
ACGTcount: A:0.38, C:0.27, G:0.01, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:37433 original size:36 final size:33
Alignment explanation
Indices: 37393--37458 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
37383 TTTTATGTAT
* *
37393 ATTTTAATATATTTATATATTCATGTTTATATTAAA
1 ATTTTAATAT-TTT-CATATT-ATGTTGATATTAAA
37429 ATTTTAATATTTTCATATTATGTTGATATT
1 ATTTTAATATTTTCATATTATGTTGATATT
37459 GTGTTACTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 10 0.36
34 5 0.18
35 3 0.11
36 10 0.36
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.58
Consensus pattern (33 bp):
ATTTTAATATTTTCATATTATGTTGATATTAAA
Found at i:37443 original size:28 final size:28
Alignment explanation
Indices: 37381--37444 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
37371 GATAATACTT
* *
37381 TATTTT-ATGTATATTTTAATATATTTA
1 TATTTTCATGTATATATTAAAATATTTA
* *
37408 TATATTCATGTTTATATTAAAAT-TTTAA
1 TATTTTCATGTATATATTAAAATATTT-A
37436 TATTTTCAT
1 TATTTTCAT
37445 ATTATGTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (28 bp):
TATTTTCATGTATATATTAAAATATTTA
Found at i:38492 original size:8 final size:8
Alignment explanation
Indices: 38479--38525 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
38469 GCTTTTAGTA
38479 ATTTTTAT
1 ATTTTTAT
38487 ATTTTTAAT
1 ATTTTT-AT
38496 AGTTTTTAT
1 A-TTTTTAT
*
38505 TTTTTTAT
1 ATTTTTAT
*
38513 AATTTTA-
1 ATTTTTAT
38520 ATTTTT
1 ATTTTT
38526 TAAAATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
7 5 0.15
8 18 0.55
9 5 0.15
10 5 0.15
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (8 bp):
ATTTTTAT
Found at i:38509 original size:17 final size:17
Alignment explanation
Indices: 38471--38528 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
38461 TGAAAAAAGC
*
38471 TTTTAGTAATTTTTATAT
1 TTTTAATAATTTTTAT-T
*
38489 TTTTAATAGTTTTTATT
1 TTTTAATAATTTTTATT
* *
38506 TTTTTATAATTTTAATT
1 TTTTAATAATTTTTATT
38523 TTTTAA
1 TTTTAA
38529 AATATATGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 20 0.59
18 14 0.41
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTAATAATTTTTATT
Found at i:40641 original size:30 final size:30
Alignment explanation
Indices: 40607--40663 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
40597 TTTATGGAAC
* *
40607 AATTTTTTAATATAAATTCAACACTTATAA
1 AATTTTGTAATAAAAATTCAACACTTATAA
*
40637 AATTTTGTAATAAAAATTCAGCACTTA
1 AATTTTGTAATAAAAATTCAACACTTA
40664 ATTTCTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.40
Consensus pattern (30 bp):
AATTTTGTAATAAAAATTCAACACTTATAA
Done.