Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014853.1 Kokia drynarioides strain JFW-HI SEQ_129896, 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: 115645
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Warning! 266 characters in sequence are not A, C, G, or T
Found at i:673 original size:31 final size:31
Alignment explanation
Indices: 613--676 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
603 CCTGAATTTT
* *
613 TTTTTATATTAATATTTGAATTTGATAATTA
1 TTTTTATATTAAGATTTGAATTAGATAATTA
644 TTTTTATATTAAGATTTGAATTA-AGTAATTA
1 TTTTTATATTAAGATTTGAATTAGA-TAATTA
675 TT
1 TT
677 CTCATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (31 bp):
TTTTTATATTAAGATTTGAATTAGATAATTA
Found at i:2715 original size:14 final size:16
Alignment explanation
Indices: 2696--2729 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
2686 AAGTAAAAAA
2696 ATAATATA-AAA-TTT
1 ATAATATATAAATTTT
2710 ATAATATATAAATTTT
1 ATAATATATAAATTTT
2726 ATAA
1 ATAA
2730 ATTATCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 3 0.17
16 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATATATAAATTTT
Found at i:2720 original size:16 final size:16
Alignment explanation
Indices: 2699--2729 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2689 TAAAAAAATA
2699 ATATAAAATTTATAAT
1 ATATAAAATTTATAAT
*
2715 ATATAAATTTTATAA
1 ATATAAAATTTATAA
2730 ATTATCCAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATAAAATTTATAAT
Found at i:3547 original size:16 final size:15
Alignment explanation
Indices: 3502--3550 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
3492 TAGTTTTAAA
3502 TTATATGTTTTATTAT
1 TTATATGTTTTATT-T
* *
3518 TTATTTGATGTTATTT
1 TTATATG-TTTTATTT
3534 TTATATGTTTTTATTT
1 TTATATG-TTTTATTT
3550 T
1 T
3551 ATGTTGTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 21 0.78
17 6 0.22
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.71
Consensus pattern (15 bp):
TTATATGTTTTATTT
Found at i:3553 original size:13 final size:14
Alignment explanation
Indices: 3514--3555 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
3504 ATATGTTTTA
*
3514 TTATTTATTTGATG
1 TTATTTATTTTATG
*
3528 TTATTT-TTATATG
1 TTATTTATTTTATG
3541 TT-TTTATTTTATG
1 TTATTTATTTTATG
3554 TT
1 TT
3556 GTTTCAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 3 0.12
13 15 0.62
14 6 0.25
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (14 bp):
TTATTTATTTTATG
Found at i:11138 original size:16 final size:17
Alignment explanation
Indices: 11110--11144 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
11100 ATTGAAATTC
11110 AAACAATAAAAAGAAGA
1 AAACAATAAAAAGAAGA
11127 AAACAA-AAAAAGAAGA
1 AAACAATAAAAAGAAGA
11143 AA
1 AA
11145 GAAAAAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.03
Consensus pattern (17 bp):
AAACAATAAAAAGAAGA
Found at i:15550 original size:24 final size:23
Alignment explanation
Indices: 15518--15564 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
15508 TATTATAAGC
*
15518 AAAAAAAAATTAGTATTAAAAAT
1 AAAAAAAAACTAGTATTAAAAAT
* *
15541 AAAAATAAAACTATTATTATAAAT
1 AAAAA-AAAACTAGTATTAAAAAT
15565 CAAGGCCGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAAAAAAACTAGTATTAAAAAT
Found at i:16256 original size:16 final size:16
Alignment explanation
Indices: 16220--16254 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
16210 AACAGTACAA
*
16220 TTTTATAATTTTATTT
1 TTTTAAAATTTTATTT
16236 TTTTAAAA-TTTATTT
1 TTTTAAAATTTTATTT
16251 TTTT
1 TTTT
16255 TATTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTAAAATTTTATTT
Found at i:18206 original size:22 final size:23
Alignment explanation
Indices: 18160--18207 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
18150 AATCAAAAGT
*
18160 TAAATTTTTAATTTATATTTAAA
1 TAAAATTTTAATTTATATTTAAA
*
18183 TAAAATTTTAATTTTTA-TTAAA
1 TAAAATTTTAATTTATATTTAAA
18205 TAA
1 TAA
18208 TTTGTAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TAAAATTTTAATTTATATTTAAA
Found at i:28460 original size:31 final size:29
Alignment explanation
Indices: 28417--28480 Score: 69
Period size: 31 Copynumber: 2.1 Consensus size: 29
28407 TATTTAATGG
*
28417 TTATATTTAA-TTTA-AAATACAGTTAATAT
1 TTATATTAAATTTTATAAATA-A-TTAATAT
28446 ATTATAATTAAATTTTATAAATAATTAATAT
1 -TTAT-ATTAAATTTTATAAATAATTAATAT
28477 TTAT
1 TTAT
28481 TGTTTAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
30 8 0.27
31 12 0.40
32 5 0.17
33 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
TTATATTAAATTTTATAAATAATTAATAT
Found at i:28468 original size:24 final size:23
Alignment explanation
Indices: 28441--28534 Score: 66
Period size: 23 Copynumber: 4.0 Consensus size: 23
28431 AAATACAGTT
28441 AATATATTATAATTAAATTTTATA
1 AATATATTA-AATTAAATTTTATA
* * *
28465 AATA-ATTAATATTTATTGTTTAAA
1 AATATATTAA-ATTAAAT-TTTATA
*
28489 AATAT-TTAAAATTAAATTTTGTA
1 AATATATT-AAATTAAATTTTATA
* * **
28512 TATATAATAAATTATTTTTTATA
1 AATATATTAAATTAAATTTTATA
28535 TTTTTACTAA
Statistics
Matches: 53, Mismatches: 12, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
22 1 0.02
23 29 0.55
24 21 0.40
25 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
AATATATTAAATTAAATTTTATA
Found at i:28982 original size:29 final size:30
Alignment explanation
Indices: 28920--28987 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
28910 AATTTACAAT
* * *
28920 AATTGGATCAAATCAAAATTTCATGTATAA
1 AATTGCATAAAATCAAAAGTTCATGTATAA
*
28950 AATTGCATAAAATC-AAAGTTCATGTATAC
1 AATTGCATAAAATCAAAAGTTCATGTATAA
28979 AATTGCATA
1 AATTGCATA
28988 TTAAACCATG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (30 bp):
AATTGCATAAAATCAAAAGTTCATGTATAA
Found at i:29005 original size:31 final size:29
Alignment explanation
Indices: 28939--29008 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
28929 AAATCAAAAT
*
28939 TTCATGTATAAAATTGCATAAAATCAAAG
1 TTCATGTATAAAATTGCATAAAACCAAAG
* **
28968 TTCATGTATACAATTGCATATTAAACCATGG
1 TTCATGTATAAAATTGCATA--AAACCAAAG
28999 TTCATGTATA
1 TTCATGTATA
29009 GTTTTAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (29 bp):
TTCATGTATAAAATTGCATAAAACCAAAG
Found at i:36924 original size:18 final size:18
Alignment explanation
Indices: 36898--36936 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
36888 GTTGGGAGTT
*
36898 TTTTGTCCTAAAACTCAA
1 TTTTATCCTAAAACTCAA
*
36916 TTTTATCCTAAAATTCAA
1 TTTTATCCTAAAACTCAA
36934 TTT
1 TTT
36937 AATTATCACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.46
Consensus pattern (18 bp):
TTTTATCCTAAAACTCAA
Found at i:41536 original size:28 final size:28
Alignment explanation
Indices: 41473--41536 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
41463 TCTAAAAAAG
*
41473 CATTT-AATATCATAATTTTACTTTATT
1 CATTTAAATATCATAATTTTACTTTAAT
***
41500 CAAAAAAATATCATAATTTTACTTTTAAT
1 CATTTAAATATCATAATTTTAC-TTTAAT
41529 -ATTTAAAT
1 CATTTAAAT
41537 TAAAACTTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
27 2 0.07
28 21 0.75
29 5 0.18
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (28 bp):
CATTTAAATATCATAATTTTACTTTAAT
Found at i:41878 original size:28 final size:29
Alignment explanation
Indices: 41830--41893 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
41820 TCAAAAATTG
* *
41830 ATTTTTATAAATATTTTAAATATTTAT-TT
1 ATTTTTATAAATAATATAAAT-TTTATATT
*
41859 ATTTTTATAAA-AATATAAATTTTTTATT
1 ATTTTTATAAATAATATAAATTTTATATT
41887 ATTTTTA
1 ATTTTTA
41894 ATTTATTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 4 0.13
28 16 0.52
29 11 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
ATTTTTATAAATAATATAAATTTTATATT
Found at i:41884 original size:29 final size:28
Alignment explanation
Indices: 41830--41893 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
41820 TCAAAAATTG
* *
41830 ATTTTTATAAATATTTTAAATATTTATTT
1 ATTTTTATAAATAATATAAATATTTA-TT
*
41859 ATTTTTATAAA-AATATAAATTTTTTATT
1 ATTTTTATAAATAATATAAA-TATTTATT
41887 ATTTTTA
1 ATTTTTA
41894 ATTTATTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTTTTATAAATAATATAAATATTTATT
Found at i:43403 original size:24 final size:24
Alignment explanation
Indices: 43342--43403 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
43332 TGAAATATGT
*
43342 ATTATATTA-AAATAAAAAAATAA
1 ATTAAATTATAAATAAAAAAATAA
* *
43365 ATTAAATTATGAATAAAACAA-AA
1 ATTAAATTATAAATAAAAAAATAA
*
43388 TTTAAATATATAAATA
1 ATTAAAT-TATAAATA
43404 CATCATTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (24 bp):
ATTAAATTATAAATAAAAAAATAA
Found at i:45965 original size:28 final size:28
Alignment explanation
Indices: 45896--45949 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
45886 TATGCTTTTT
45896 TTAA-TAATATTTTATAATATTTTTTAAA
1 TTAACTAA-ATTTTATAATATTTTTTAAA
45924 TTAACTAAATTTT-TAAATATTTTTTA
1 TTAACTAAATTTTAT-AATATTTTTTA
45950 TATTGTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 1 0.04
28 20 0.83
29 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
TTAACTAAATTTTATAATATTTTTTAAA
Found at i:46018 original size:18 final size:18
Alignment explanation
Indices: 45935--46045 Score: 57
Period size: 18 Copynumber: 6.0 Consensus size: 18
45925 TAACTAAATT
*
45935 TTTAAATATTTTTTAT-A
1 TTTATATATTTTTTATAA
* *
45952 TTGTA-ATACATTTTCATAA
1 TT-TATATA-TTTTTTATAA
* * *
45971 TTTTTACAATTTTTCATAA
1 TTTATA-TATTTTTTATAA
*
45990 -TAATATAATTTTTTATAA
1 TTTATAT-ATTTTTTATAA
**
46008 TTTATATATTTTTTAGGCA
1 TTTATATATTTTTTA-TAA
*
46027 TTTATAATAATTTTTATAA
1 TTTAT-ATATTTTTTATAA
46046 GTTTTGTAAT
Statistics
Matches: 70, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
17 5 0.07
18 30 0.43
19 25 0.36
20 10 0.14
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTATATATTTTTTATAA
Found at i:46050 original size:9 final size:9
Alignment explanation
Indices: 45961--46062 Score: 62
Period size: 9 Copynumber: 11.0 Consensus size: 9
45951 ATTGTAATAC
*
45961 ATTTTCATA
1 ATTTTTATA
*
45970 ATTTTTACA
1 ATTTTTATA
45979 ATTTTTCATA
1 ATTTTT-ATA
**
45989 A-TAATATA
1 ATTTTTATA
45997 ATTTTTTATA
1 A-TTTTTATA
*
46007 ATTTATATA
1 ATTTTTATA
* **
46016 TTTTTTAGGC
1 ATTTTTA-TA
*
46026 ATTTATAATA
1 ATTT-TTATA
46036 ATTTTTATA
1 ATTTTTATA
* *
46045 AGTTTTGTA
1 ATTTTTATA
46054 ATTTTTATA
1 ATTTTTATA
46063 TTGTTGCACT
Statistics
Matches: 67, Mismatches: 21, Indels: 10
0.68 0.21 0.10
Matches are distributed among these distances:
8 4 0.06
9 45 0.67
10 16 0.24
11 2 0.03
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (9 bp):
ATTTTTATA
Found at i:46117 original size:20 final size:20
Alignment explanation
Indices: 46092--46141 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
46082 ATATTTAAAT
*
46092 ATTTTTTATAATTTTC-TATG
1 ATTTTTAATAATTTTCAT-TG
*
46112 ATTTTTAATATTTTTCATTG
1 ATTTTTAATAATTTTCATTG
*
46132 ATTTTAAATA
1 ATTTTTAATA
46142 TAAAATATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (20 bp):
ATTTTTAATAATTTTCATTG
Found at i:80039 original size:7 final size:7
Alignment explanation
Indices: 80029--80056 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
80019 GGATTTTTAA
80029 TTTATTT
1 TTTATTT
80036 TTTATTT
1 TTTATTT
80043 TTTATTT
1 TTTATTT
80050 TTTATTT
1 TTTATTT
80057 GAAAGATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTATTT
Found at i:82213 original size:15 final size:15
Alignment explanation
Indices: 82193--82223 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
82183 GACATTGACA
82193 TTTTTTCCCTTTTTT
1 TTTTTTCCCTTTTTT
*
82208 TTTTTTCTCTTTTTT
1 TTTTTTCCCTTTTTT
82223 T
1 T
82224 CATGATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTCCCTTTTTT
Found at i:83862 original size:30 final size:31
Alignment explanation
Indices: 83808--83877 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
83798 ATTAGCATTT
83808 AATTATTTTTTAAAAAATTTAAAAAT-ATATAA
1 AATTA-TTTTTAAAAAATTTAAAAATCA-ATAA
83840 AATATATTTTT-AAAAA-TTAAAAATCAATAA
1 AAT-TATTTTTAAAAAATTTAAAAATCAATAA
83870 AATTATTT
1 AATTATTT
83878 AAAATTCTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
29 5 0.14
30 15 0.42
31 6 0.17
32 8 0.22
33 2 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (31 bp):
AATTATTTTTAAAAAATTTAAAAATCAATAA
Found at i:91244 original size:36 final size:36
Alignment explanation
Indices: 91204--91295 Score: 96
Period size: 36 Copynumber: 2.6 Consensus size: 36
91194 AAATTTCACT
* *
91204 AAAATTTTGCCTACAAGTGATCAACACAAGAGTGCA
1 AAAATTCTGCCTACAAGTAATCAACACAAGAGTGCA
* * * *
91240 AAAATCCTG-CTCACACGTAATCACCACAAGCGTGCA
1 AAAATTCTGCCT-ACAAGTAATCAACACAAGAGTGCA
* *
91276 AAAATTCTGCATACACGTAA
1 AAAATTCTGCCTACAAGTAA
91296 ATCTAATCCG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 2 0.04
36 43 0.93
37 1 0.02
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.21
Consensus pattern (36 bp):
AAAATTCTGCCTACAAGTAATCAACACAAGAGTGCA
Found at i:103931 original size:7 final size:8
Alignment explanation
Indices: 103914--103938 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
103904 CTAAATTTAA
103914 TTTATTTT
1 TTTATTTT
103922 TTTATTTT
1 TTTATTTT
103930 TTTATTTT
1 TTTATTTT
103938 T
1 T
103939 AAGTAAATAA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTATTTT
Found at i:105715 original size:52 final size:52
Alignment explanation
Indices: 105637--105740 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
105627 CATAGCATAC
105637 TAAACCAATTAATTTCGATGTCACCAAAGTATTAAAGCTAATAGAAACAAAG
1 TAAACCAATTAATTTCGATGTCACCAAAGTATTAAAGCTAATAGAAACAAAG
105689 TAAACCAATTAATTTCGATGTCACCAAAGTATTAAAGCTAATAGAAACAAAG
1 TAAACCAATTAATTTCGATGTCACCAAAGTATTAAAGCTAATAGAAACAAAG
105741 AATTTACGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.25
Consensus pattern (52 bp):
TAAACCAATTAATTTCGATGTCACCAAAGTATTAAAGCTAATAGAAACAAAG
Found at i:109922 original size:42 final size:42
Alignment explanation
Indices: 109860--109943 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
109850 TAGATCTATG
* *
109860 CAGTGTCGATGGTGTTTTTGTGTTTTTCATGCAACAAATTCT
1 CAGTGTCGATGCTGTATTTGTGTTTTTCATGCAACAAATTCT
* ** *
109902 CAGTGTTGATGCTGTATTTGTGTTTTTGGTGGAACAAATTCT
1 CAGTGTCGATGCTGTATTTGTGTTTTTCATGCAACAAATTCT
109944 ACGAAACCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (42 bp):
CAGTGTCGATGCTGTATTTGTGTTTTTCATGCAACAAATTCT
Found at i:110630 original size:48 final size:48
Alignment explanation
Indices: 110575--110669 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
110565 TAATAATCGT
*
110575 TTTCATTTTAGTCC-CCCAATTTTAACAAGCTTTCATTTTGATCACTCA
1 TTTCATTTTAG-CCACCCAACTTTAACAAGCTTTCATTTTGATCACTCA
** * * *
110623 TTTCATTTTAGCCATTCAACTTTAAGATGCTTTCATTTTGGTCACTC
1 TTTCATTTTAGCCACCCAACTTTAACAAGCTTTCATTTTGATCACTC
110670 GTTAATTCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
47 2 0.05
48 38 0.95
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.45
Consensus pattern (48 bp):
TTTCATTTTAGCCACCCAACTTTAACAAGCTTTCATTTTGATCACTCA
Found at i:110827 original size:29 final size:30
Alignment explanation
Indices: 110757--110829 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
110747 TAAATCTCAA
* *
110757 AATTATACA--TGAACTTTAATTTAATGTGC
1 AATTATACACTTGAACTTTAATTT-AGGTAC
* *
110786 AATTGTATACTTGAACTTTAATTT-GGTAC
1 AATTATACACTTGAACTTTAATTTAGGTAC
110815 AATTATACACTTGAA
1 AATTATACACTTGAA
110830 ACTCTAACTG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 23 0.64
31 13 0.36
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (30 bp):
AATTATACACTTGAACTTTAATTTAGGTAC
Found at i:111066 original size:29 final size:30
Alignment explanation
Indices: 111013--111069 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
111003 TAATTGGATC
*
111013 AAATCAAAATTTCATTTATAAAATTGCAAA
1 AAATCAAAATTTCATGTATAAAATTGCAAA
* *
111043 AAATTAAAA-TTCATGTATACAATTGCA
1 AAATCAAAATTTCATGTATAAAATTGCA
111070 CATTAAACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTGCAAA
Found at i:112821 original size:176 final size:178
Alignment explanation
Indices: 112525--112879 Score: 660
Period size: 176 Copynumber: 2.0 Consensus size: 178
112515 TGTTATTTAA
112525 AAAATTATAGTGGGAATTTTTAAATTCTCAAGTTATATTATAAAAGTGATACAATGTAGAAAAAA
1 AAAATTATAGTGGGAATTTTTAAATTCTCAAGTTATATTATAAAAGTGATACAATGTAGAAAAAA
*
112590 AAAATCAATCATTTCTATAAGTTCTGATTATATATATATTTTTATTCAATGTTTAGAACTACCCA
66 AAAATCAATCATTTCTATAAGTTCTGATTATATATATATTTTTATACAATGTTTAGAACTACCCA
*
112655 TAGCTCCTCTCAATCCATAAATAAAAAGATAATACGTTTTAGCGCACT
131 TAGCTCCTCTCAATCCATAAATAAAAAGATAATACGTTTCAGCGCACT
112703 AAAATTATAGTGGGAA-TTTTAAATTCTCAAGTTATATTATAAAAGTGATACAATGTAG-AAAAA
1 AAAATTATAGTGGGAATTTTTAAATTCTCAAGTTATATTATAAAAGTGATACAATGTAGAAAAAA
* *
112766 AAAATCAATCATTTCTATAAGTTTTGATTATATATATATTTTTATACAATGTTTAGAACTACTCA
66 AAAATCAATCATTTCTATAAGTTCTGATTATATATATATTTTTATACAATGTTTAGAACTACCCA
112831 TAGCTCCTCTCAATCCATAAATAAAAAGATAATACGTTTCAGCGCACT
131 TAGCTCCTCTCAATCCATAAATAAAAAGATAATACGTTTCAGCGCACT
112879 A
1 A
112880 GAATCCATGT
Statistics
Matches: 173, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
176 115 0.66
177 42 0.24
178 16 0.09
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (178 bp):
AAAATTATAGTGGGAATTTTTAAATTCTCAAGTTATATTATAAAAGTGATACAATGTAGAAAAAA
AAAATCAATCATTTCTATAAGTTCTGATTATATATATATTTTTATACAATGTTTAGAACTACCCA
TAGCTCCTCTCAATCCATAAATAAAAAGATAATACGTTTCAGCGCACT
Found at i:114080 original size:39 final size:39
Alignment explanation
Indices: 114017--114091 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
114007 CTCTTTTTTT
*
114017 TTCGACTCGATTTTTCGAGGCTGGAATCGAACAATCTTC
1 TTCGACTCGATTTTTCGAGACTGGAATCGAACAATCTTC
* *
114056 TTCGGCTCGATCTTTT-GAGACTGGAATCGAATAATC
1 TTCGACTCGAT-TTTTCGAGACTGGAATCGAACAATC
114092 CCACTTGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 28 0.88
40 4 0.12
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (39 bp):
TTCGACTCGATTTTTCGAGACTGGAATCGAACAATCTTC
Done.