Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007030.1 Kokia drynarioides strain JFW-HI SEQ_121638, 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: 51024
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:1299 original size:26 final size:26
Alignment explanation
Indices: 1244--1300 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1234 GCTAAACCTC
**
1244 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
1270 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
1296 ATTAA
1 ATTAA
1301 TTCCAACAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:4119 original size:25 final size:26
Alignment explanation
Indices: 4070--4119 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4060 AACCTTCTGT
*
4070 TTCCTTTTCTTCTTCAAAACTTTTGC
1 TTCCTTTTCTTCTTCAAAACATTTGC
4096 TTCC-TTTCTTTCTTCAAAA-ATTTG
1 TTCCTTTTC-TTCTTCAAAACATTTG
4120 TTGTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.18, C:0.24, G:0.04, T:0.54
Consensus pattern (26 bp):
TTCCTTTTCTTCTTCAAAACATTTGC
Found at i:4608 original size:32 final size:32
Alignment explanation
Indices: 4572--4636 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
4562 ATATTTATAT
*
4572 TATTTAAGT-TATTAATTTTATTTTTTGTATTA
1 TATTTAAGTGTATAAATTTT-TTTTTTGTATTA
**
4604 TATTTTGGTGTATAAATTTTTTTTTTGTATTA
1 TATTTAAGTGTATAAATTTTTTTTTTGTATTA
4636 T
1 T
4637 TTATGTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 20 0.69
33 9 0.31
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (32 bp):
TATTTAAGTGTATAAATTTTTTTTTTGTATTA
Found at i:4758 original size:27 final size:27
Alignment explanation
Indices: 4701--4762 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
4691 GGCTGCCAAG
* * *
4701 TAGGCAGCTTTGGTGCCGCCTAGCAGG
1 TAGGCACCTTTGGTGCCGCATAGCAGA
4728 TAGGCACCTTTGGTGCCGCAT-GTCAGA
1 TAGGCACCTTTGGTGCCGCATAG-CAGA
4755 TAGGCACC
1 TAGGCACC
4763 ACCCCTTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.03
27 30 0.97
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (27 bp):
TAGGCACCTTTGGTGCCGCATAGCAGA
Found at i:20302 original size:28 final size:28
Alignment explanation
Indices: 20261--20315 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
20251 AAATAAACTG
**
20261 TCACATAATCGCCATTAATGGCCACATT
1 TCACATAATCGCCAAAAATGGCCACATT
*
20289 TCACATAATTGCCAAAAATGGCCACAT
1 TCACATAATCGCCAAAAATGGCCACAT
20316 CTTCCACCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.25
Consensus pattern (28 bp):
TCACATAATCGCCAAAAATGGCCACATT
Found at i:21948 original size:23 final size:23
Alignment explanation
Indices: 21917--22243 Score: 456
Period size: 23 Copynumber: 14.2 Consensus size: 23
21907 ATGAAACTTG
*
21917 AGCATAAATCATATTAATATTTA
1 AGCACAAATCATATTAATATTTA
*
21940 AGCACAAATCATATTAATATTTG
1 AGCACAAATCATATTAATATTTA
*
21963 AGCTCAAATCATATTAATATTTA
1 AGCACAAATCATATTAATATTTA
* * *
21986 AGCATAAATCACATTAATATTTG
1 AGCACAAATCATATTAATATTTA
** *
22009 CTCACAAGTCATATTAATATTTA
1 AGCACAAATCATATTAATATTTA
* *
22032 TGCACAAATCATATTAATATTTG
1 AGCACAAATCATATTAATATTTA
*
22055 AGAACAAATCATATTAATATTTA
1 AGCACAAATCATATTAATATTTA
* * *
22078 AGCATAAATCACATTAATACTTA
1 AGCACAAATCATATTAATATTTA
22101 AGCACAAATCATATTAATATTTA
1 AGCACAAATCATATTAATATTTA
*
22124 AGCACAAATCACATTAATATTTA
1 AGCACAAATCATATTAATATTTA
* *
22147 ATCATAAATCATATTAATATTTA
1 AGCACAAATCATATTAATATTTA
*
22170 AGCACAAATCACATTAATATTTA
1 AGCACAAATCATATTAATATTTA
* * *
22193 AGCATAAATCACATTAATATTTG
1 AGCACAAATCATATTAATATTTA
22216 AGCACAAATCATATTAATATTTA
1 AGCACAAATCATATTAATATTTA
22239 AGCAC
1 AGCAC
22244 GGATATAAGA
Statistics
Matches: 264, Mismatches: 40, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 264 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.35
Consensus pattern (23 bp):
AGCACAAATCATATTAATATTTA
Found at i:35843 original size:41 final size:41
Alignment explanation
Indices: 35783--35967 Score: 225
Period size: 41 Copynumber: 4.6 Consensus size: 41
35773 GGGAAACCGT
* * * *
35783 CGCTAATGCTCTTATCTTTTGCGGCATTTTCTCAGAAACGC
1 CGCTAATGCTCATACCTTTTGCGGCGTTTTCTCATAAACGC
* * *
35824 TGCTAATGCTAATACCTTTTGCGGCGTTTTCTCATAAACAC
1 CGCTAATGCTCATACCTTTTGCGGCGTTTTCTCATAAACGC
35865 CGCTAATGCTCATACCTTTT-C--CGTTTTCTCATAAACGC
1 CGCTAATGCTCATACCTTTTGCGGCGTTTTCTCATAAACGC
* *
35903 CGCTAATGCTCATACCTTTTGCGACGTTTT-TCAATAAATGC
1 CGCTAATGCTCATACCTTTTGCGGCGTTTTCTC-ATAAACGC
* * *
35944 CACTAATGCTCTTATCTTTTGCGG
1 CGCTAATGCTCATACCTTTTGCGG
35968 TATTTTCCCC
Statistics
Matches: 125, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
38 36 0.29
39 1 0.01
40 3 0.02
41 85 0.68
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (41 bp):
CGCTAATGCTCATACCTTTTGCGGCGTTTTCTCATAAACGC
Found at i:35908 original size:79 final size:79
Alignment explanation
Indices: 35809--35963 Score: 213
Period size: 79 Copynumber: 2.0 Consensus size: 79
35799 TTTTGCGGCA
* * *
35809 TTTTCTCAGAAACGCTGCTAATGCTAATACCTTTTGCGGCGTTTTCTC-ATAAACACCGCTAATG
1 TTTTCTCAGAAACGCCGCTAATGCTAATACCTTTTGCGACGTTTT-TCAATAAACACCACTAATG
35873 CTCATACCTTTTCCG
65 CTCATACCTTTTCCG
* * **
35888 TTTTCTCATAAACGCCGCTAATGCTCATACCTTTTGCGACGTTTTTCAATAAATGCCACTAATGC
1 TTTTCTCAGAAACGCCGCTAATGCTAATACCTTTTGCGACGTTTTTCAATAAACACCACTAATGC
* *
35953 TCTTATCTTTT
66 TCATACCTTTT
35964 GCGGTATTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
78 2 0.03
79 64 0.97
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.38
Consensus pattern (79 bp):
TTTTCTCAGAAACGCCGCTAATGCTAATACCTTTTGCGACGTTTTTCAATAAACACCACTAATGC
TCATACCTTTTCCG
Found at i:36032 original size:40 final size:40
Alignment explanation
Indices: 35983--36079 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
35973 TCCCCATAAG
* * **
35983 CGCCACTATTATTTTACCTTTTACGGTGTTTATGAAAAAA
1 CGCCGCTATTACTTTACCTTTTACGGCATTTATGAAAAAA
* * *
36023 GGCCGCTATTGCTTTACCTTTTGCGGCATTTATGAAAAAA
1 CGCCGCTATTACTTTACCTTTTACGGCATTTATGAAAAAA
* *
36063 CGTCGCTATTGCTTTAC
1 CGCCGCTATTACTTTAC
36080 TTATTGCGGC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (40 bp):
CGCCGCTATTACTTTACCTTTTACGGCATTTATGAAAAAA
Found at i:36087 original size:40 final size:40
Alignment explanation
Indices: 35995--36089 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
35985 CCACTATTAT
* ** *
35995 TTTACCTTTTACGGTGTTTATGAAAAAAGGCCGCTATTGC
1 TTTACCTTTTGCGGCATTTATGAAAAAACGCCGCTATTGC
*
36035 TTTACCTTTTGCGGCATTTATGAAAAAACGTCGCTATTGC
1 TTTACCTTTTGCGGCATTTATGAAAAAACGCCGCTATTGC
36075 TTTA-CTTATTGCGGC
1 TTTACCTT-TTGCGGC
36090 GTTTTCTGTA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
39 3 0.06
40 46 0.94
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (40 bp):
TTTACCTTTTGCGGCATTTATGAAAAAACGCCGCTATTGC
Found at i:36720 original size:58 final size:58
Alignment explanation
Indices: 36620--36789 Score: 200
Period size: 58 Copynumber: 2.9 Consensus size: 58
36610 TTTATCAAAT
* *
36620 ATTATATATTATGATTTTTATTAATTCATATTTTAATAATAATTATAATAAGAATATTATTAA
1 ATTATATATT-T-ATTATTATTAATT-ATA-TTTAATAATAATTATAATAA-AATATGATTAA
* **
36683 ATTATATA-TTATT-TTATTAAATTGTATTTAATAATAATTATGTTAAAATATGATTAA
1 ATTATATATTTATTATTATT-AATTATATTTAATAATAATTATAATAAAATATGATTAA
* * *
36740 ATTATTTATTTATTATTATTAATTATATTTAATAATAATTTTATTAAAAT
1 ATTATATATTTATTATTATTAATTATATTTAATAATAATTATAATAAAAT
36790 TTAGTAAACA
Statistics
Matches: 96, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
57 17 0.18
58 50 0.52
59 12 0.12
60 7 0.07
61 1 0.01
62 1 0.01
63 8 0.08
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (58 bp):
ATTATATATTTATTATTATTAATTATATTTAATAATAATTATAATAAAATATGATTAA
Found at i:38459 original size:26 final size:24
Alignment explanation
Indices: 38426--38491 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
38416 AAAAACGTAT
38426 AAAAAACAACAACCAAAATAGAAGC
1 AAAAAACAACAA-CAAAATAGAAGC
* * *
38451 GAAACAACAACAA-AAATTAGCAGC
1 -AAAAAACAACAACAAAATAGAAGC
38475 AAAAAACAACAACAAAA
1 AAAAAACAACAACAAAA
38492 ATAACAGCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 11 0.32
24 12 0.35
26 11 0.32
ACGTcount: A:0.68, C:0.20, G:0.08, T:0.05
Consensus pattern (24 bp):
AAAAAACAACAACAAAATAGAAGC
Found at i:38492 original size:26 final size:25
Alignment explanation
Indices: 38426--38502 Score: 95
Period size: 26 Copynumber: 3.1 Consensus size: 25
38416 AAAAACGTAT
* *
38426 AAAAAACAACAACCAAAATAGAAGC
1 AAAAAACAACAACAAAAATAGCAGC
*
38451 --GAAACAACAACAAAAATTAGCAGC
1 AAAAAACAACAACAAAAA-TAGCAGC
*
38475 AAAAAACAACAACAAAAATAACAGC
1 AAAAAACAACAACAAAAATAGCAGC
38500 AAA
1 AAA
38503 GTAACACCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
23 14 0.32
24 6 0.14
25 9 0.20
26 15 0.34
ACGTcount: A:0.68, C:0.19, G:0.08, T:0.05
Consensus pattern (25 bp):
AAAAAACAACAACAAAAATAGCAGC
Found at i:40087 original size:88 final size:86
Alignment explanation
Indices: 39904--40089 Score: 196
Period size: 88 Copynumber: 2.1 Consensus size: 86
39894 AATCTCTTAA
* * * * *
39904 TTTAAAAAAAAATCAATAAAGCATTTTTTTTTTGCACTCATTTAGATACTTGAACTTTTAAAATG
1 TTTAAAAAAAAAGCAATAAAGCATTCTTTTTTTGCACTCAATTAGATACTTAAACTTTTAAAATA
*
39969 CATCAAATTGACCCTCAAATC
66 CATCAAATAGACCCTCAAATC
** * * * *
39990 TTTTCAAAAAAAGCAATTAAGCCTCTACTTTTTTTGCACTCAATTGGGTACTTAAACTTTTAAAA
1 TTTAAAAAAAAAGCAATAAAGCAT-T-CTTTTTTTGCACTCAATTAGATACTTAAACTTTTAAAA
* *
40055 TACATCAAA-AGATCTTCAAA-C
64 TACATCAAATAGACCCTCAAATC
40076 GGTTTAAAAAAAAA
1 --TTTAAAAAAAAA
40090 AAAAACAATT
Statistics
Matches: 80, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
86 20 0.25
87 9 0.11
88 51 0.64
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (86 bp):
TTTAAAAAAAAAGCAATAAAGCATTCTTTTTTTGCACTCAATTAGATACTTAAACTTTTAAAATA
CATCAAATAGACCCTCAAATC
Found at i:40130 original size:9 final size:9
Alignment explanation
Indices: 40116--40300 Score: 52
Period size: 9 Copynumber: 20.6 Consensus size: 9
40106 ATGATTTTAT
40116 TAAAAATTA
1 TAAAAATTA
40125 TAAAAAAATATA
1 T--AAAAAT-TA
*
40137 TAAAAAGT-
1 TAAAAATTA
*
40145 T-AAAATCAA
1 TAAAAAT-TA
**
40154 TAAATTTTA
1 TAAAAATTA
*
40163 TAAATATTA
1 TAAAAATTA
* *
40172 T-TAAATTT
1 TAAAAATTA
*
40180 TAATAAAAT-
1 TAA-AAATTA
*
40189 TAAATATT-
1 TAAAAATTA
40197 TAAAAATTA
1 TAAAAATTA
40206 TTAAAAATTA
1 -TAAAAATTA
* *
40216 GAAGAA--A
1 TAAAAATTA
*
40223 -AA-AATCA
1 TAAAAATTA
40230 TAAAAA-TA
1 TAAAAATTA
40238 TAAAAAATTA
1 T-AAAAATTA
*
40248 TAAAATTTTA
1 TAAAA-ATTA
40258 TAAAAAAATTA
1 T--AAAAATTA
40269 T-AAAATATA
1 TAAAAAT-TA
40278 TAAAAA-TA
1 TAAAAATTA
*
40286 TTAAAAAATA
1 -TAAAAATTA
40296 TAAAA
1 TAAAA
40301 TTTTATAAAG
Statistics
Matches: 133, Mismatches: 20, Indels: 46
0.67 0.10 0.23
Matches are distributed among these distances:
5 2 0.02
6 2 0.02
7 6 0.05
8 27 0.20
9 45 0.34
10 34 0.26
11 10 0.08
12 7 0.05
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (9 bp):
TAAAAATTA
Found at i:40178 original size:19 final size:19
Alignment explanation
Indices: 40154--40190 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
40144 TTAAAATCAA
40154 TAAATTTT-ATAAATATTAT
1 TAAATTTTAATAAA-ATTAT
40173 TAAATTTTAATAAAATTA
1 TAAATTTTAATAAAATTA
40191 AATATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTTTAATAAAATTAT
Found at i:40227 original size:39 final size:38
Alignment explanation
Indices: 40184--40292 Score: 87
Period size: 41 Copynumber: 2.8 Consensus size: 38
40174 AAATTTTAAT
40184 AAAATTAAATATTTAAAAATTATTAAAAATTAGAAGAAA
1 AAAATTAAATATTTAAAAATTATTAAAAATTAGAA-AAA
* * * *
40223 AAAATCATAAAAATATAAAAAATTA-TAAAATTTTATAAAAA
1 AAAAT--TAAATAT-TTAAAAATTATTAAAA-ATTAGAAAAA
* * *
40264 AATTATAAAATATATAAAAA-TATTAAAAA
1 AA-AATTAAATATTTAAAAATTATTAAAAA
40293 ATATAAAATT
Statistics
Matches: 54, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
38 2 0.04
39 15 0.28
40 5 0.09
41 16 0.30
42 16 0.30
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (38 bp):
AAAATTAAATATTTAAAAATTATTAAAAATTAGAAAAA
Found at i:40234 original size:10 final size:9
Alignment explanation
Indices: 40221--40300 Score: 65
Period size: 10 Copynumber: 8.4 Consensus size: 9
40211 AATTAGAAGA
40221 AAAAAATCAT
1 AAAAAAT-AT
40231 -AAAAATAT
1 AAAAAATAT
40239 AAAAAATTAT
1 AAAAAA-TAT
**
40249 AAAATTTTAT
1 AAAA-AATAT
40259 AAAAAA-ATT
1 AAAAAATA-T
*
40268 ATAAAATAT
1 AAAAAATAT
40277 ATAAAAATATT
1 A-AAAAATA-T
40288 AAAAAATAT
1 AAAAAATAT
40297 AAAA
1 AAAA
40301 TTTTATAAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
8 3 0.05
9 24 0.42
10 28 0.49
11 2 0.04
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAAAATAT
Found at i:40244 original size:18 final size:19
Alignment explanation
Indices: 40221--40300 Score: 94
Period size: 18 Copynumber: 4.2 Consensus size: 19
40211 AATTAGAAGA
*
40221 AAAAAATCATAAAA-ATAT
1 AAAAAATTATAAAATATAT
*
40239 AAAAAATTATAAAATTTTAT
1 AAAAAATTATAAAA-TATAT
40259 AAAAAAATTATAAAATATAT
1 -AAAAAATTATAAAATATAT
40279 AAAAATATTA-AAAA-ATAT
1 AAAAA-ATTATAAAATATAT
40297 AAAA
1 AAAA
40301 TTTTATAAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
18 21 0.38
19 9 0.16
20 11 0.20
21 14 0.25
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAATTATAAAATATAT
Found at i:40259 original size:20 final size:20
Alignment explanation
Indices: 40221--40294 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
40211 AATTAGAAGA
*
40221 AAAAAATCATAAAA--ATAT
1 AAAAAATTATAAAATTATAT
*
40239 AAAAAATTATAAAATTTTAT
1 AAAAAATTATAAAATTATAT
40259 AAAAAAATTATAAAA-TATAT
1 -AAAAAATTATAAAATTATAT
*
40279 AAAAATATTAAAAAAT
1 AAAAA-ATTATAAAAT
40295 ATAAAATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
18 13 0.28
19 5 0.11
20 15 0.32
21 14 0.30
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAAATTATAAAATTATAT
Found at i:40332 original size:48 final size:47
Alignment explanation
Indices: 40222--40347 Score: 137
Period size: 48 Copynumber: 2.6 Consensus size: 47
40212 ATTAGAAGAA
* *
40222 AAAAATCATAAAAATA-TAAAAAATTATAAAATTTTATAAAAAAATTAT
1 AAAAAT-ATAAAAATATTAAAAAA-TATAAAATTTTATAAAAAAATAAG
****
40270 AAAATATATAAAAATATTAAAAAATATAAAATTTTATAAAGTCGTAAG
1 AAAA-ATATAAAAATATTAAAAAATATAAAATTTTATAAAAAAATAAG
* *
40318 AAAAATATACAAAATGTAAAAAAATATAAA
1 AAAAATATA-AAAATATTAAAAAATATAAA
40348 TTTCGTAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
47 5 0.07
48 53 0.79
49 9 0.13
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (47 bp):
AAAAATATAAAAATATTAAAAAATATAAAATTTTATAAAAAAATAAG
Found at i:40355 original size:19 final size:19
Alignment explanation
Indices: 40311--40368 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
40301 TTTTATAAAG
40311 TCGTAAGAAAAATATACAAAA
1 TCGTAA-AAAAATATA-AAAA
**
40332 T-GTAAAAAAATATAAATT
1 TCGTAAAAAAATATAAAAA
*
40350 TCGTAAAAGAATTATAAAA
1 TCGTAAAA-AAATATAAAA
40369 TTTATAGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 3 0.10
19 15 0.48
20 12 0.39
21 1 0.03
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (19 bp):
TCGTAAAAAAATATAAAAA
Found at i:40566 original size:21 final size:21
Alignment explanation
Indices: 40540--40580 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40530 TTAAAGGGAA
40540 TTTTTTTTATGCATTT-TATAT
1 TTTTTTTTATG-ATTTCTATAT
40561 TTTTTTTTATGATTTCTATA
1 TTTTTTTTATGATTTCTATA
40581 AAATTGTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.71
Consensus pattern (21 bp):
TTTTTTTTATGATTTCTATAT
Found at i:40694 original size:19 final size:17
Alignment explanation
Indices: 40646--40714 Score: 50
Period size: 17 Copynumber: 3.9 Consensus size: 17
40636 TTAAATTTTT
40646 TTTATATTTTTATTAAAA
1 TTTATATTTTT-TTAAAA
* *
40664 TTTAATAATTTTTCTAAAG
1 TTT-AT-ATTTTTTTAAAA
***
40683 TTTAT-TATTTTTTATTT
1 TTTATAT-TTTTTTAAAA
40700 TTTATATTTTTTTAA
1 TTTATATTTTTTTAA
40715 TTTTTAATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
16 1 0.03
17 18 0.45
18 6 0.15
19 9 0.22
20 6 0.15
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (17 bp):
TTTATATTTTTTTAAAA
Found at i:40891 original size:89 final size:89
Alignment explanation
Indices: 40731--40905 Score: 237
Period size: 89 Copynumber: 2.0 Consensus size: 89
40721 ATAAGAAAAA
* * * * *
40731 GGGCTTAATTGCTTTTTTTTGAAAAATTTTAAGAGTTTTTTTTATGCATTTTGAAAGTTCAAGTA
1 GGGCTTAATTGCTTTTTTTTCAAAAAGTTTAAAAGTCTTTTTGATGCATTTTGAAAGTTCAAGTA
* * *
40796 TCCAATTTAGTGGAAAAAAAATAG
66 TCCAATTGAATGCAAAAAAAATAG
40820 GGGCTTAATTGC-TTTTTTTCAAAGAAGTTTAAAAGTCTTTTTGATGCATTTTGAAAGTTCAAGT
1 GGGCTTAATTGCTTTTTTTTCAAA-AAGTTTAAAAGTCTTTTTGATGCATTTTGAAAGTTCAAGT
*
40884 -GCTCAATTGAATGCAAAAAAAA
65 ATC-CAATTGAATGCAAAAAAAA
40906 AAAAAAAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
88 11 0.15
89 64 0.85
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (89 bp):
GGGCTTAATTGCTTTTTTTTCAAAAAGTTTAAAAGTCTTTTTGATGCATTTTGAAAGTTCAAGTA
TCCAATTGAATGCAAAAAAAATAG
Found at i:42114 original size:2 final size:2
Alignment explanation
Indices: 42109--42137 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42099 AAACTAATTC
42109 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 T
42138 GCTTTGTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44114 original size:20 final size:21
Alignment explanation
Indices: 44075--44114 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
44065 ATTTTTAATG
* *
44075 TTTAAATTTAAATTTATTTTT
1 TTTAAATATAAATATATTTTT
44096 TTTAAATAT-AATATATTTT
1 TTTAAATATAAATATATTTT
44115 ATCATTACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTAAATATAAATATATTTTT
Found at i:46946 original size:17 final size:17
Alignment explanation
Indices: 46915--46949 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
46905 TATTTTTATT
**
46915 TTTTAAATTTTTAAAAA
1 TTTTAAATTAATAAAAA
46932 TTTTAAATTAATAAAAA
1 TTTTAAATTAATAAAAA
46949 T
1 T
46950 AAAATTATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTAAATTAATAAAAA
Found at i:50714 original size:19 final size:20
Alignment explanation
Indices: 50668--50715 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
50658 CTTATTAAAA
50668 ATATTTAAATAAATTTTAAT
1 ATATTTAAATAAATTTTAAT
* *
50688 ATAATTAAATAGA-TTTAAT
1 ATATTTAAATAAATTTTAAT
*
50707 ATTTTTAAA
1 ATATTTAAA
50716 ATTGAATTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
ATATTTAAATAAATTTTAAT
Found at i:50994 original size:2 final size:2
Alignment explanation
Indices: 50987--51024 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
50977 TTAATTAGTG
50987 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.