Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011770.1 Kokia drynarioides strain JFW-HI SEQ_126765, 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: 28457
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:354 original size:15 final size:14
Alignment explanation
Indices: 302--361 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
292 TCCAAATCTC
*
302 TTTATAATTTT-TT
1 TTTAAAATTTTATT
* *
315 CTTAAAATTTAATT
1 TTTAAAATTTTATT
* *
329 TTTATATTTTTATT
1 TTTAAAATTTTATT
343 TTTAAGAATTTTATCT
1 TTTAA-AATTTTAT-T
359 TTT
1 TTT
362 CACTTTTTCA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
13 8 0.23
14 16 0.46
15 7 0.20
16 4 0.11
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTAAAATTTTATT
Found at i:361 original size:23 final size:23
Alignment explanation
Indices: 328--378 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
318 AAAATTTAAT
*
328 TTTTATATTTTTA-TTTTTAAGAA
1 TTTTATATTTTCACTTTTTAA-AA
* *
351 TTTTATCTTTTCACTTTTTCAAA
1 TTTTATATTTTCACTTTTTAAAA
374 TTTTA
1 TTTTA
379 AAATTTAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTATATTTTCACTTTTTAAAA
Found at i:580 original size:23 final size:23
Alignment explanation
Indices: 553--596 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
543 AACATGAATT
553 TTAAAAT-TTAAAAAGTAAAAAGA
1 TTAAAATCTTAAAAA-TAAAAAGA
*
576 TTAAATTCTTAAAAATAAAAA
1 TTAAAATCTTAAAAATAAAAA
597 TACAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (23 bp):
TTAAAATCTTAAAAATAAAAAGA
Found at i:1780 original size:9 final size:9
Alignment explanation
Indices: 1768--1832 Score: 53
Period size: 9 Copynumber: 7.4 Consensus size: 9
1758 ATAGAATTGA
1768 ATTAATTCG
1 ATTAATTCG
1777 ATTAA-TCG
1 ATTAATTCG
* **
1785 GTTAATTAA
1 ATTAATTCG
1794 ATTAATTCG
1 ATTAATTCG
1803 ATTAA-TCG
1 ATTAATTCG
* **
1811 GTTAATTAA
1 ATTAATTCG
*
1820 ATTAATTTG
1 ATTAATTCG
1829 ATTA
1 ATTA
1833 GAATAGGTTA
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
8 14 0.33
9 28 0.67
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (9 bp):
ATTAATTCG
Found at i:1848 original size:26 final size:26
Alignment explanation
Indices: 1762--1832 Score: 124
Period size: 26 Copynumber: 2.7 Consensus size: 26
1752 TAATCGATAG
*
1762 AATTGAATTAATTCGATTAATCGGTT
1 AATTAAATTAATTCGATTAATCGGTT
1788 AATTAAATTAATTCGATTAATCGGTT
1 AATTAAATTAATTCGATTAATCGGTT
*
1814 AATTAAATTAATTTGATTA
1 AATTAAATTAATTCGATTA
1833 GAATAGGTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (26 bp):
AATTAAATTAATTCGATTAATCGGTT
Found at i:2201 original size:26 final size:26
Alignment explanation
Indices: 2141--2197 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 26
2131 TAATCGATAG
* *
2141 AATTGAATTAATTTGATTAATCGGTT
1 AATTAAATTAATTTGATTAATAGGTT
2167 AATTAAATTAATTTGATTGGAATAGGTT
1 AATTAAATTAATTTGATT--AATAGGTT
2195 AAT
1 AAT
2198 AATTTTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 17 0.63
28 10 0.37
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.44
Consensus pattern (26 bp):
AATTAAATTAATTTGATTAATAGGTT
Found at i:3671 original size:16 final size:17
Alignment explanation
Indices: 3640--3672 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3630 TTTAAAAATA
*
3640 AAAACTAAAAATAAAGT
1 AAAACTAAAAAAAAAGT
3657 AAAAC-AAAAAAAAAGT
1 AAAACTAAAAAAAAAGT
3673 GTGAAGGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAACTAAAAAAAAAGT
Found at i:7306 original size:23 final size:23
Alignment explanation
Indices: 7280--7327 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
7270 TAAAATTTAA
* *
7280 TTAATGTTAATTTTATTCTATAT
1 TTAATGTAAAATTTATTCTATAT
*
7303 TTAATGTAAAATTTATTTTATAT
1 TTAATGTAAAATTTATTCTATAT
7326 TT
1 TT
7328 TAAGAGTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (23 bp):
TTAATGTAAAATTTATTCTATAT
Found at i:7948 original size:30 final size:31
Alignment explanation
Indices: 7912--7974 Score: 110
Period size: 30 Copynumber: 2.0 Consensus size: 31
7902 AAATTTGAAC
7912 TCAAGATAGAATCATTTATGTTA-TATATTT
1 TCAAGATAGAATCATTTATGTTATTATATTT
7942 TCAAGATAGAATCATTTATGTTATTTATATTT
1 TCAAGATAGAATCATTTATGTTA-TTATATTT
7974 T
1 T
7975 TTGAAGTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 23 0.74
32 8 0.26
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (31 bp):
TCAAGATAGAATCATTTATGTTATTATATTT
Found at i:10881 original size:21 final size:22
Alignment explanation
Indices: 10852--10895 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
10842 TGCAAGTAAA
* *
10852 ATTAAACATTTTTTAA-ATTTT
1 ATTAAACATGTCTTAATATTTT
*
10873 ATTAGACATGTCTTAATATTTT
1 ATTAAACATGTCTTAATATTTT
10895 A
1 A
10896 ATTTTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (22 bp):
ATTAAACATGTCTTAATATTTT
Found at i:12027 original size:45 final size:44
Alignment explanation
Indices: 11978--12065 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
11968 CCAAACAACC
* * *
11978 AAAATAACAACCAAAACAGTAGCAAAAATAATAGAAAAATAGCAA
1 AAAATAACAACAAAAACAGCA-CAAAAATAATAAAAAAATAGCAA
* *
12023 AAAATAACAACAAAAACAGCACCAAAATAGTAAAAAAATAGCA
1 AAAATAACAACAAAAACAGCACAAAAATAATAAAAAAATAGCA
12066 CCAAAACAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
44 19 0.50
45 19 0.50
ACGTcount: A:0.67, C:0.15, G:0.08, T:0.10
Consensus pattern (44 bp):
AAAATAACAACAAAAACAGCACAAAAATAATAAAAAAATAGCAA
Found at i:12066 original size:22 final size:22
Alignment explanation
Indices: 12002--12181 Score: 145
Period size: 22 Copynumber: 8.3 Consensus size: 22
11992 AACAGTAGCA
* * *
12002 AAAATAATAGAAAAATAGCA-A
1 AAAACAATAAAAAAATAGCACC
* * *
12023 AAAATAACAACAAAAACAGCACC
1 AAAACAATAA-AAAAATAGCACC
* *
12046 AAAATAGTAAAAAAATAGCACC
1 AAAACAATAAAAAAATAGCACC
* * *
12068 AAAACAATAAAAACACAACACC
1 AAAACAATAAAAAAATAGCACC
*
12090 AAAACAGT-AAAAAATAGCAACC
1 AAAACAATAAAAAAATAGC-ACC
*
12112 AAAACAATAAAAAAA-A-TACC
1 AAAACAATAAAAAAATAGCACC
* * * *
12132 AAAACAGTAAAAACACAACACC
1 AAAACAATAAAAAAATAGCACC
*
12154 AAAACAGT-AAAAAATAGCACC
1 AAAACAATAAAAAAATAGCACC
12175 AAAACAA
1 AAAACAA
12182 CAATATAATT
Statistics
Matches: 128, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
20 16 0.12
21 32 0.25
22 66 0.52
23 14 0.11
ACGTcount: A:0.67, C:0.19, G:0.06, T:0.08
Consensus pattern (22 bp):
AAAACAATAAAAAAATAGCACC
Found at i:12071 original size:11 final size:11
Alignment explanation
Indices: 12012--12071 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
12002 AAAATAATAG
12012 AAAAATAGCA-
1 AAAAATAGCAC
*
12022 AAAAATAACAAC
1 AAAAATAGC-AC
*
12034 AAAAACAGCAC
1 AAAAATAGCAC
* * *
12045 CAAAATAGTAA
1 AAAAATAGCAC
12056 AAAAATAGCACC
1 AAAAATAGCA-C
12068 AAAA
1 AAAA
12072 CAATAAAAAC
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
10 8 0.22
11 18 0.49
12 11 0.30
ACGTcount: A:0.68, C:0.17, G:0.07, T:0.08
Consensus pattern (11 bp):
AAAAATAGCAC
Found at i:12080 original size:42 final size:43
Alignment explanation
Indices: 12034--12180 Score: 181
Period size: 43 Copynumber: 3.4 Consensus size: 43
12024 AAATAACAAC
* *
12034 AAAAACAGCACCAAAATAGTAAAAAAATAGCACCAAAACAATA
1 AAAAACAACACCAAAACAGTAAAAAAATAGCACCAAAACAATA
12077 AAAACACAACACCAAAACAGT-AAAAAATAGCAACCAAAACAATA
1 AAAA-ACAACACCAAAACAGTAAAAAAATAGC-ACCAAAACAATA
* * * * *
12121 AAAAA-AATACCAAAACAGTAAAAACACAACACCAAAACAGTA
1 AAAAACAACACCAAAACAGTAAAAAAATAGCACCAAAACAATA
* *
12163 AAAAATAGCACCAAAACA
1 AAAAACAACACCAAAACA
12181 ACAATATAAT
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
42 29 0.32
43 32 0.35
44 30 0.33
ACGTcount: A:0.66, C:0.21, G:0.05, T:0.07
Consensus pattern (43 bp):
AAAAACAACACCAAAACAGTAAAAAAATAGCACCAAAACAATA
Found at i:12102 original size:64 final size:63
Alignment explanation
Indices: 12034--12181 Score: 224
Period size: 64 Copynumber: 2.3 Consensus size: 63
12024 AAATAACAAC
* * *
12034 AAAAACAGCACCAAAATAGTAAAAAAATAGCACCAAAACAATAAAAACACAACACCAAAACAGTA
1 AAAAATAGCACCAAAACAATAAAAAAA-A-CACCAAAACAATAAAAACACAACACCAAAACAGTA
* *
12099 AAAAATAGCAACCAAAACAATAAAAAAAATACCAAAACAGTAAAAACACAACACCAAAACAGTA
1 AAAAATAGC-ACCAAAACAATAAAAAAAACACCAAAACAATAAAAACACAACACCAAAACAGTA
12163 AAAAATAGCACCAAAACAA
1 AAAAATAGCACCAAAACAA
12182 CAATATAATT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
63 10 0.13
64 42 0.55
65 9 0.12
66 16 0.21
ACGTcount: A:0.66, C:0.21, G:0.05, T:0.07
Consensus pattern (63 bp):
AAAAATAGCACCAAAACAATAAAAAAAACACCAAAACAATAAAAACACAACACCAAAACAGTA
Found at i:13054 original size:20 final size:21
Alignment explanation
Indices: 13017--13055 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13007 TCATGAGCAA
*
13017 ATAGTGTTGAGTTTTGAAAAC
1 ATAGTATTGAGTTTTGAAAAC
13038 ATAGTATTGAG-TTTGAAA
1 ATAGTATTGAGTTTTGAAA
13056 GCACTACAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (21 bp):
ATAGTATTGAGTTTTGAAAAC
Found at i:13894 original size:36 final size:36
Alignment explanation
Indices: 13843--13973 Score: 106
Period size: 35 Copynumber: 3.6 Consensus size: 36
13833 ATCACAGTGA
* *
13843 CATGCTTAACGTGCGAATCAGAATA-AAAAATAATG
1 CATGCTTAACATGCGAATCAGAATACCAAAATAATG
* *
13878 CCATGCTTAACATGCGAGTCA-AA-ACCAAATTAATAG
1 -CATGCTTAACATGCGAATCAGAATACCAAAATAAT-G
* * * * * * *
13914 CATGCTTAACATACGATTCAAAATATCAGAATATTAA
1 CATGCTTAACATGCGAATCAGAATACCAAAATAAT-G
*
13951 CATGTTTAACATGCGAATCAGAA
1 CATGCTTAACATGCGAATCAGAA
13974 CATCAATAAT
Statistics
Matches: 76, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
34 1 0.01
35 27 0.36
36 21 0.28
37 27 0.36
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.25
Consensus pattern (36 bp):
CATGCTTAACATGCGAATCAGAATACCAAAATAATG
Found at i:14336 original size:49 final size:49
Alignment explanation
Indices: 14264--14361 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
14254 TTATATATTT
14264 TATCAAAGAAAGATTCCCACACCTGATTTCGCAAATCCAATCTGTTTCC
1 TATCAAAGAAAGATTCCCACACCTGATTTCGCAAATCCAATCTGTTTCC
14313 TATCAAAGAAAGATTCCCACACCTGATTTCGCAAATCCAATCTGTTTCC
1 TATCAAAGAAAGATTCCCACACCTGATTTCGCAAATCCAATCTGTTTCC
14362 AACTTCTAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.29
Consensus pattern (49 bp):
TATCAAAGAAAGATTCCCACACCTGATTTCGCAAATCCAATCTGTTTCC
Found at i:15530 original size:96 final size:96
Alignment explanation
Indices: 15351--15537 Score: 247
Period size: 96 Copynumber: 1.9 Consensus size: 96
15341 GGAAAAAAGA
* * *
15351 TATTCGATTATCTTGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCGCAGTATTTCAGAATC
1 TATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAGAATC
*
15416 GAAGATAAGAAAACATTGCCTCGATTAAGGG
66 GAAGACAAGAAAACATTGCCTCGATTAAGGG
* *
15447 TATTCGATTAT-TTCGATTTGAGGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTCGGAA
1 TATTCGATTATCTT-GATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTCAGAA
*
15510 CTCGAA-ACAA-AAAGATATTGCCTCGATT
64 -TCGAAGACAAGAAA-ACATTGCCTCGATT
15538 TTAAAGTTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
95 6 0.08
96 69 0.86
97 5 0.06
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (96 bp):
TATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAGAATC
GAAGACAAGAAAACATTGCCTCGATTAAGGG
Found at i:15941 original size:59 final size:59
Alignment explanation
Indices: 15878--16228 Score: 483
Period size: 59 Copynumber: 5.9 Consensus size: 59
15868 ACATTCGGGA
* * * ** * *
15878 GTAAAATAGTAATTTTTGGATGTTTCGAGGTTGAAAATGGGATTTTTGGGAGTTCGAGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGG
* *
15937 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTTGGGAGTTCGAGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGG
* * *
15996 GTAAAATAGTAATTTTTGGAAGGTTCGGGGTCAAAAATGATATTTTTGGAAGTTCGAGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGG
* * *
16055 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAATTTGGGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGG
* *
16114 GTAAAATGGTAAATTTTGGAAGGTTC-AGGGTCAAAAATG-GTATTTTTGGAAGTTAGAGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGA-GGTCAAAAATGAG-ATTTTTGGAAGTTCGAGG
* *
16173 GTAGAATGGTAATTTTTGGAAGGTT-TAGGGTCAAAAATGAGATTTTTGGAAGTTCG
1 GTAAAATGGTAATTTTTGGAAGGTTCGA-GGTCAAAAATGAGATTTTTGGAAGTTCG
16229 GGGACCTCCG
Statistics
Matches: 265, Mismatches: 23, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
58 2 0.01
59 262 0.99
60 1 0.00
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGG
Found at i:16131 original size:29 final size:29
Alignment explanation
Indices: 15878--16226 Score: 247
Period size: 30 Copynumber: 11.8 Consensus size: 29
15868 ACATTCGGGA
* *
15878 GTAAAATAGTAATTTTTGGATGTTTCGAGG
1 GTAAAATGGTAATTTTTGGAAGTTT-GAGG
* * * *
15908 TTGAAAATGG-GATTTTTGGGAGTTCGAGG
1 GT-AAAATGGTAATTTTTGGAAGTTTGAGG
*
15937 GTAAAATGGTAATTTTTGGAAGGTTCG-GG
1 GTAAAATGGTAATTTTTGGAA-GTTTGAGG
* *
15966 GTCAAAAAT-G-AGATTTTTGGGAGTTCGAGG
1 GT--AAAATGGTA-ATTTTTGGAAGTTTGAGG
* *
15996 GTAAAATAGTAATTTTTGGAAGGTTCG-GG
1 GTAAAATGGTAATTTTTGGAA-GTTTGAGG
* *
16025 GTCAAAAATGAT-ATTTTTGGAAGTTCGAGG
1 GT--AAAATGGTAATTTTTGGAAGTTTGAGG
*
16055 GTAAAATGGTAATTTTTGGAAGGTTCGA-G
1 GTAAAATGGTAATTTTTGGAA-GTTTGAGG
* *
16084 GTCAAAAAT-G-AGATTTTTGGAAATTTGGGG
1 GT--AAAATGGTA-ATTTTTGGAAGTTTGAGG
* * *
16114 GTAAAATGGTAAATTTTGGAAGGTTCAGG
1 GTAAAATGGTAATTTTTGGAAGTTTGAGG
*
16143 GTCAAAAATGGT-ATTTTTGGAAGTTAGAGG
1 GT--AAAATGGTAATTTTTGGAAGTTTGAGG
*
16173 GTAGAATGGTAATTTTTGGAAGGTTT-AGG
1 GTAAAATGGTAATTTTTGGAA-GTTTGAGG
16202 GTCAAAAAT-G-AGATTTTTGGAAGTT
1 GT--AAAATGGTA-ATTTTTGGAAGTT
16227 CGGGGACCTC
Statistics
Matches: 262, Mismatches: 29, Indels: 57
0.75 0.08 0.16
Matches are distributed among these distances:
28 31 0.12
29 95 0.36
30 102 0.39
31 34 0.13
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (29 bp):
GTAAAATGGTAATTTTTGGAAGTTTGAGG
Found at i:18107 original size:5 final size:5
Alignment explanation
Indices: 18099--18184 Score: 91
Period size: 5 Copynumber: 16.0 Consensus size: 5
18089 ATTGGACTTT
*
18099 TTAAA TTAAA TTAAA TTAAA TTAAA TTTAATA TTAAT TTAAA TTAAA TTTAATA
1 TTAAA TTAAA TTAAA TTAAA TTAAA -TTAA-A TTAAA TTAAA TTAAA -TTAA-A
* *
18153 TTAAT TTAAA TTTAAA TTTAAA TCAAA TTAAA
1 TTAAA TTAAA -TTAAA -TTAAA TTAAA TTAAA
18185 AAAGGCCCAG
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
5 41 0.59
6 27 0.39
7 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (5 bp):
TTAAA
Found at i:18139 original size:22 final size:22
Alignment explanation
Indices: 18099--18173 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
18089 ATTGGACTTT
*
18099 TTAAA-TTAA-ATTAAATTAAA
1 TTAAATTTAATATTAATTTAAA
18119 TTAAATTTAATATTAATTTAAA
1 TTAAATTTAATATTAATTTAAA
18141 TTAAATTTAATATTAATTTAAA
1 TTAAATTTAATATTAATTTAAA
18163 TTTAAATTTAA
1 -TTAAATTTAA
18174 ATCAAATTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
20 5 0.10
21 4 0.08
22 32 0.63
23 10 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAAATTTAATATTAATTTAAA
Found at i:18183 original size:22 final size:22
Alignment explanation
Indices: 18099--18184 Score: 115
Period size: 22 Copynumber: 4.0 Consensus size: 22
18089 ATTGGACTTT
18099 TTAAA-TTAA-ATTAAATTAAA
1 TTAAATTTAATATTAAATTAAA
*
18119 TTAAATTTAATATTAATTTAAA
1 TTAAATTTAATATTAAATTAAA
*
18141 TTAAATTTAATATTAATTTAAA
1 TTAAATTTAATATTAAATTAAA
*
18163 TTTAAATTTAA-ATCAAATTAAA
1 -TTAAATTTAATATTAAATTAAA
18185 AAAGGCCCAG
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
20 5 0.08
21 4 0.07
22 41 0.68
23 10 0.17
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAATTTAATATTAAATTAAA
Found at i:18854 original size:12 final size:12
Alignment explanation
Indices: 18839--18880 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
18829 TCTATATCAA
18839 CATCTGTATCTG
1 CATCTGTATCTG
* *
18851 CATCTGAATTTG
1 CATCTGTATCTG
18863 CATCTGTATCTG
1 CATCTGTATCTG
*
18875 TATCTG
1 CATCTG
18881 AACGTGTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (12 bp):
CATCTGTATCTG
Found at i:23499 original size:3 final size:3
Alignment explanation
Indices: 23491--23515 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
23481 AGTAAGGTTT
23491 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
23516 AAACCACTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28400 original size:4 final size:4
Alignment explanation
Indices: 28391--28457 Score: 57
Period size: 4 Copynumber: 16.5 Consensus size: 4
28381 CAAATAAACG
* * *
28391 AGAA AGAA AGAA AGAAA AGAA AAAA AGAA A-AGA AGAA GGAGA GGAA AGAA
1 AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AGA-A AGAA AGA-A AGAA AGAA
*
28441 AG-A AGAA GGAA AGAA AG
1 AGAA AGAA AGAA AGAA AG
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
3 4 0.08
4 39 0.75
5 9 0.17
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
AGAA
Done.