Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006852.1 Kokia drynarioides strain JFW-HI SEQ_121451, 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: 136573
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 101 characters in sequence are not A, C, G, or T
Found at i:1924 original size:18 final size:18
Alignment explanation
Indices: 1901--1946 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1891 GTGGTGATTT
*
1901 CGGGTCAGGACCACGTTC
1 CGGGTCAGGACCACGGTC
* *
1919 CGGGTCAAGACCAGGGTC
1 CGGGTCAGGACCACGGTC
*
1937 CGGATCAGGA
1 CGGGTCAGGA
1947 TCGGATTTCG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.28, G:0.37, T:0.13
Consensus pattern (18 bp):
CGGGTCAGGACCACGGTC
Found at i:6848 original size:33 final size:33
Alignment explanation
Indices: 6820--6900 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
6810 TTTCTTCTTC
*
6820 CTCCTCTTCTTCGTGTTTACTTCCTTCTTCCCG
1 CTCCTCTTCTTCGTGCTTACTTCCTTCTTCCCG
* *
6853 CTCCTCTTCTTCGTGCTTGCTTCCTTCTACCCG
1 CTCCTCTTCTTCGTGCTTACTTCCTTCTTCCCG
* *
6886 TTCCTCCTCTTCGTG
1 CTCCTCTTCTTCGTG
6901 TTTTATTGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.02, C:0.41, G:0.11, T:0.46
Consensus pattern (33 bp):
CTCCTCTTCTTCGTGCTTACTTCCTTCTTCCCG
Found at i:13204 original size:18 final size:17
Alignment explanation
Indices: 13162--13206 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
13152 TATTTAACAT
13162 TGCTTTTAATTTAAAAG
1 TGCTTTTAATTTAAAAG
* *
13179 TACTTTTTTATGTTAAAAG
1 TGC-TTTTAAT-TTAAAAG
13198 TGCTTTTAA
1 TGCTTTTAA
13207 AAAGCACTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 2 0.09
18 11 0.50
19 9 0.41
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.51
Consensus pattern (17 bp):
TGCTTTTAATTTAAAAG
Found at i:13919 original size:13 final size:13
Alignment explanation
Indices: 13901--13926 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13891 AACCTACATC
13901 CTCTTGCATTGTT
1 CTCTTGCATTGTT
13914 CTCTTGCATTGTT
1 CTCTTGCATTGTT
13927 AACAATACCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.15, T:0.54
Consensus pattern (13 bp):
CTCTTGCATTGTT
Found at i:16859 original size:13 final size:12
Alignment explanation
Indices: 16830--16868 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
16820 GTTCGAGTTT
*
16830 AATTTTGTTTGA
1 AATTTTGTTTAA
16842 AATTTTGATTTAA
1 AATTTTG-TTTAA
16855 AATTTTG-TTAA
1 AATTTTGTTTAA
16866 AAT
1 AAT
16869 CAAATTTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 7 0.28
12 7 0.28
13 11 0.44
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (12 bp):
AATTTTGTTTAA
Found at i:17346 original size:14 final size:13
Alignment explanation
Indices: 17327--17372 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
17317 CTTATAAATT
17327 ATTTTTTAATATTA
1 ATTTTTT-ATATTA
17341 ATTTTTTATAATT-
1 ATTTTTTAT-ATTA
*
17354 ATTTGTTATA-TA
1 ATTTTTTATATTA
17366 ATTTTTT
1 ATTTTTT
17373 TTTTAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 1 0.04
12 7 0.25
13 10 0.36
14 10 0.36
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
ATTTTTTATATTA
Found at i:17355 original size:27 final size:26
Alignment explanation
Indices: 17318--17372 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
17308 ATAAAAACTC
*
17318 TTATAAATTATTTTTTAATATTAATTTT
1 TTATAAATTATTTGTT-ATA-TAATTTT
17346 TTAT-AATTATTTGTTATATAATTTT
1 TTATAAATTATTTGTTATATAATTTT
17371 TT
1 TT
17373 TTTTAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 9 0.35
26 3 0.12
27 10 0.38
28 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTATAAATTATTTGTTATATAATTTT
Found at i:17365 original size:15 final size:14
Alignment explanation
Indices: 17318--17373 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
17308 ATAAAAACTC
17318 TTATA-AATTATTT
1 TTATATAATTATTT
17331 TT-TA-ATATTAATTT
1 TTATATA-ATT-ATTT
17345 TT-TATAATTATTT
1 TTATATAATTATTT
17358 GTTATATAATT-TTT
1 -TTATATAATTATTT
17372 TT
1 TT
17374 TTTAGAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.08
13 11 0.29
14 16 0.42
15 8 0.21
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTATATAATTATTT
Found at i:24441 original size:12 final size:12
Alignment explanation
Indices: 24424--24448 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24414 TAATCCAAAA
24424 TTTATTCTAGAT
1 TTTATTCTAGAT
24436 TTTATTCTAGAT
1 TTTATTCTAGAT
24448 T
1 T
24449 GAAGGTGAAG
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:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TTTATTCTAGAT
Found at i:28655 original size:31 final size:31
Alignment explanation
Indices: 28618--28686 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
28608 TGGAAGTGTA
28618 ATATAATGTGAATTCTCTGAAATAATAGCTT
1 ATATAATGTGAATTCTCTGAAATAATAGCTT
28649 ATATAATGTGAATTCTCTGAAATAATAGCTT
1 ATATAATGTGAATTCTCTGAAATAATAGCTT
*
28680 ACATAAT
1 ATATAAT
28687 TCCTATTGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.38
Consensus pattern (31 bp):
ATATAATGTGAATTCTCTGAAATAATAGCTT
Found at i:30915 original size:20 final size:20
Alignment explanation
Indices: 30890--30927 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
30880 ATGTTACAAG
30890 GTGGTGAAATAAGTGACGTA
1 GTGGTGAAATAAGTGACGTA
30910 GTGGTGAAATAAGTGACG
1 GTGGTGAAATAAGTGACG
30928 CAAGGACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.37, T:0.24
Consensus pattern (20 bp):
GTGGTGAAATAAGTGACGTA
Found at i:40447 original size:42 final size:42
Alignment explanation
Indices: 40401--40481 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
40391 AATGAGTCCG
* *
40401 GATCAGATTTTACAATATTCGCAGATTGAGTTCGCATATCCA
1 GATCAGATTTTACAATACTCGCAGATTGAATTCGCATATCCA
* *
40443 GATCAGATTTTACGATACTCGCAGGTTGAATTCGCATAT
1 GATCAGATTTTACAATACTCGCAGATTGAATTCGCATAT
40482 TGAGCTTACA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (42 bp):
GATCAGATTTTACAATACTCGCAGATTGAATTCGCATATCCA
Found at i:47539 original size:7 final size:7
Alignment explanation
Indices: 47527--47563 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
47517 TTAGATAAGG
47527 TTCAGAC
1 TTCAGAC
47534 TTCAGAC
1 TTCAGAC
47541 TTCAGAC
1 TTCAGAC
47548 TTCAGAC
1 TTCAGAC
47555 TTCAGAC
1 TTCAGAC
47562 TT
1 TT
47564 TTAGAGCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (7 bp):
TTCAGAC
Found at i:51525 original size:13 final size:13
Alignment explanation
Indices: 51503--51533 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
51493 ATGCGTTATC
51503 TTAA-TATTATTG
1 TTAATTATTATTG
51515 TTAATTATTATTG
1 TTAATTATTATTG
51528 TTAATT
1 TTAATT
51534 TCGAATTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (13 bp):
TTAATTATTATTG
Found at i:53569 original size:15 final size:17
Alignment explanation
Indices: 53549--53581 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
53539 GTACCGTGAA
53549 AGCAA-GAAGA-AGAAC
1 AGCAAGGAAGATAGAAC
53564 AGCAAGGAAGATAGAAC
1 AGCAAGGAAGATAGAAC
53581 A
1 A
53582 AGAAGCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.58, C:0.12, G:0.27, T:0.03
Consensus pattern (17 bp):
AGCAAGGAAGATAGAAC
Found at i:58717 original size:12 final size:11
Alignment explanation
Indices: 58695--58751 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
58685 ACTCAAAATC
58695 TTTTATTTTTT
1 TTTTATTTTTT
58706 TTTTATTTTTT
1 TTTTATTTTTT
*
58717 TTTTGGTTTTTT
1 TTTT-ATTTTTT
** *
58729 AATTATGTGTTT
1 TTTTAT-TTTTT
58741 TTTT-TTTTTT
1 TTTTATTTTTT
58751 T
1 T
58752 GCACAGTTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
10 5 0.14
11 17 0.47
12 14 0.39
ACGTcount: A:0.09, C:0.00, G:0.07, T:0.84
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:79995 original size:15 final size:16
Alignment explanation
Indices: 79965--79998 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
79955 TAAATAAAAA
*
79965 AATTTATATAAATTTT
1 AATTTAAATAAATTTT
79981 AATTTAAAT-AATTTT
1 AATTTAAATAAATTTT
79996 AAT
1 AAT
79999 ACAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTTAAATAAATTTT
Found at i:82753 original size:17 final size:18
Alignment explanation
Indices: 82712--82754 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
82702 ATAAGTCAAC
82712 TAAAAAT-TTAAAAATTA
1 TAAAAATATTAAAAATTA
*
82729 TAAAAATATTCAAAATTA
1 TAAAAATATTAAAAATTA
82747 -AAAAATAT
1 TAAAAATAT
82755 ATATATGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAATATTAAAAATTA
Found at i:86515 original size:2 final size:2
Alignment explanation
Indices: 86508--86538 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
86498 TCACAATCAT
86508 TA TA TA 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 TA TA TA T
86539 GCTCTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92182 original size:21 final size:21
Alignment explanation
Indices: 92157--92199 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
92147 ATTTTATATG
92157 TTAGATTAAAAAGATAATAAT
1 TTAGATTAAAAAGATAATAAT
92178 TTAGATTAAAAAGATAATAAT
1 TTAGATTAAAAAGATAATAAT
92199 T
1 T
92200 GGAGGGTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (21 bp):
TTAGATTAAAAAGATAATAAT
Found at i:92616 original size:2 final size:2
Alignment explanation
Indices: 92609--92644 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
92599 TCTTCTTCAT
*
92609 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
92645 TTGATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:96755 original size:21 final size:21
Alignment explanation
Indices: 96731--96779 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
96721 CAATTAAACG
96731 GTTAAATAATCAATT-TAATTT
1 GTTAAA-AATCAATTATAATTT
*
96752 GTTAAAAATTAATTAGTAATTT
1 GTTAAAAATCAATTA-TAATTT
*
96774 TTTAAA
1 GTTAAA
96780 CATTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (21 bp):
GTTAAAAATCAATTATAATTT
Found at i:96773 original size:22 final size:23
Alignment explanation
Indices: 96746--96794 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
96736 ATAATCAATT
*
96746 TAATTTGTTAAA-AATTAATTAG
1 TAATTTGTTAAACAATTAATTAA
* *
96768 TAATTTTTTAAACATTTAATTAA
1 TAATTTGTTAAACAATTAATTAA
96791 TAAT
1 TAAT
96795 AATTTAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
TAATTTGTTAAACAATTAATTAA
Found at i:97432 original size:23 final size:22
Alignment explanation
Indices: 97406--97459 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
97396 TAAATAAATT
*
97406 TTTTTAAATGTAATTATTTTTAA
1 TTTTTAAATAT-ATTATTTTTAA
* * *
97429 TTTTTAAAAATATTTTTTTTAT
1 TTTTTAAATATATTATTTTTAA
97451 TTTTTAAAT
1 TTTTTAAAT
97460 TTTGAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTTAAATATATTATTTTTAA
Found at i:97960 original size:18 final size:19
Alignment explanation
Indices: 97939--97980 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
97929 TCACGTTAAC
97939 AAAAAAAAATT-AAACTAA
1 AAAAAAAAATTAAAACTAA
* * *
97957 AAAACATAATTAAAATTAA
1 AAAAAAAAATTAAAACTAA
97976 AAAAA
1 AAAAA
97981 CAGTTAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAAAAAAATTAAAACTAA
Found at i:98694 original size:23 final size:23
Alignment explanation
Indices: 98664--98707 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
98654 CCCAAAACCC
*
98664 AAAATCTCCCAATTCAACAACTT
1 AAAATCTCCAAATTCAACAACTT
*
98687 AAAATCTCCAAATTCGACAAC
1 AAAATCTCCAAATTCAACAAC
98708 CATAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (23 bp):
AAAATCTCCAAATTCAACAACTT
Found at i:98714 original size:23 final size:23
Alignment explanation
Indices: 98664--98713 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
98654 CCCAAAACCC
* *
98664 AAAATCTCCCAATTCAACAACTT
1 AAAATCTCCAAATTCAACAACAT
*
98687 AAAATCTCCAAATTCGACAACCAT
1 AAAATCTCCAAATTCAACAA-CAT
98711 AAA
1 AAA
98714 TAATCCATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.48, C:0.28, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAATCTCCAAATTCAACAACAT
Found at i:102131 original size:19 final size:17
Alignment explanation
Indices: 102107--102141 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
102097 CTCTAATTAC
102107 TAAAAAAATAAAAGAAAAG
1 TAAAAAAA-AAAA-AAAAG
102126 TAAAAAAAAAAAAAAA
1 TAAAAAAAAAAAAAAA
102142 ACTTGGATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.86, C:0.00, G:0.06, T:0.09
Consensus pattern (17 bp):
TAAAAAAAAAAAAAAAG
Found at i:108116 original size:29 final size:29
Alignment explanation
Indices: 108057--108117 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
108047 TTTGACTTAT
* * *
108057 ATTTTTAAATATAAAATTAAAGGGATCAA
1 ATTTTTAAATATAAAAGTAAAAGAATCAA
*
108086 ATTTCTTAAA-ATAAAAGTAAAAGAATTAA
1 ATTT-TTAAATATAAAAGTAAAAGAATCAA
108115 ATT
1 ATT
108118 CCAAATGTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.34
Consensus pattern (29 bp):
ATTTTTAAATATAAAAGTAAAAGAATCAA
Found at i:108564 original size:4 final size:4
Alignment explanation
Indices: 108555--108595 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
108545 TAATAGAAAG
108555 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA T
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA T
108596 ATACATACCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (4 bp):
TCTA
Found at i:111039 original size:5 final size:5
Alignment explanation
Indices: 111029--111067 Score: 69
Period size: 5 Copynumber: 7.6 Consensus size: 5
111019 GCCAATCTGA
111029 TTGGG TTGGG TTGGG TTGGG TTGGG TTGGG TTTGGG TTG
1 TTGGG TTGGG TTGGG TTGGG TTGGG TTGGG -TTGGG TTG
111068 TAATCGGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.00, C:0.00, G:0.56, T:0.44
Consensus pattern (5 bp):
TTGGG
Found at i:112379 original size:2 final size:2
Alignment explanation
Indices: 112372--112410 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
112362 TTCAGGAATC
112372 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
112411 ATATATATGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:112704 original size:15 final size:15
Alignment explanation
Indices: 112673--112716 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
112663 AAAATTAATC
112673 ATGGAGGTG--GA-G
1 ATGGAGGTGATGATG
112685 ATGGAGGTGATGATG
1 ATGGAGGTGATGATG
*
112700 ATGGAGATGATGATG
1 ATGGAGGTGATGATG
112715 AT
1 AT
112717 TATTTTGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 9 0.32
14 2 0.07
15 17 0.61
ACGTcount: A:0.30, C:0.00, G:0.45, T:0.25
Consensus pattern (15 bp):
ATGGAGGTGATGATG
Found at i:116789 original size:4 final size:4
Alignment explanation
Indices: 116780--116829 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
116770 AGGTAATGCA
* * * *
116780 ACAT ACAT ACAG ACAT TCAT ACGT ACGT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
116828 AC
1 AC
116830 TGATGAGGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.44, C:0.26, G:0.06, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:123426 original size:3 final size:3
Alignment explanation
Indices: 123418--123449 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
123408 GGAGTTAGAA
123418 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC AC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC AC
123450 TTATATTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:128051 original size:30 final size:30
Alignment explanation
Indices: 128009--128080 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
127999 TGATACATAA
* * *
128009 TATATAATTTTTAAATGTTTTTAAA-TAAT
1 TATATAAATTTTAAATATTCTTAAAGTAAT
128038 TAATATAAATTTTAAATATTCTTAAAGTAAT
1 T-ATATAAATTTTAAATATTCTTAAAGTAAT
128069 TATAT-AATTTTA
1 TATATAAATTTTA
128081 TTTGTGCGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 8 0.21
30 25 0.66
31 5 0.13
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (30 bp):
TATATAAATTTTAAATATTCTTAAAGTAAT
Done.