Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012747.1 Kokia drynarioides strain JFW-HI SEQ_127758, 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: 62510
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:3866 original size:21 final size:21
Alignment explanation
Indices: 3842--3903 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3832 GTATTTTGAG
3842 TGTATAATCTGTTTTAATAAA
1 TGTATAATCTGTTTTAATAAA
* *
3863 TG--TAA--GGTATTT--TAAG
1 TGTATAATCTGT-TTTAATAAA
3879 TGTATAATCTGTTTTAATAAA
1 TGTATAATCTGTTTTAATAAA
3900 TGTA
1 TGTA
3904 ATCAATAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 14
0.62 0.08 0.29
Matches are distributed among these distances:
16 5 0.17
17 2 0.07
18 6 0.20
19 6 0.20
20 2 0.07
21 9 0.30
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (21 bp):
TGTATAATCTGTTTTAATAAA
Found at i:3881 original size:37 final size:37
Alignment explanation
Indices: 3830--3904 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
3820 AAATTCCGTG
*
3830 AGGTATTTTGAGTGTATAATCTGTTTTAATAAATGTA
1 AGGTATTTTAAGTGTATAATCTGTTTTAATAAATGTA
3867 AGGTATTTTAAGTGTATAATCTGTTTTAATAAATGTA
1 AGGTATTTTAAGTGTATAATCTGTTTTAATAAATGTA
3904 A
1 A
3905 TCAATAATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (37 bp):
AGGTATTTTAAGTGTATAATCTGTTTTAATAAATGTA
Found at i:8416 original size:3 final size:3
Alignment explanation
Indices: 8410--8436 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
8400 TATTTTTTTA
8410 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
8437 GTAATACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9285 original size:15 final size:16
Alignment explanation
Indices: 9261--9291 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
9251 ATTTGTTTTT
9261 AAAATAATTTTTTATA
1 AAAATAATTTTTTATA
9277 AAAAT-ATTTTTTATA
1 AAAATAATTTTTTATA
9292 TAATTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AAAATAATTTTTTATA
Found at i:11291 original size:27 final size:27
Alignment explanation
Indices: 11251--11307 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
11241 AGGTGGAGAA
* *
11251 GAAGCCTAACAAAGTTGCTAATGAAAT
1 GAAGCCCAACAAAGCTGCTAATGAAAT
* * *
11278 GAAGCCCAATAAAGCTGTTAATGAAGT
1 GAAGCCCAACAAAGCTGCTAATGAAAT
11305 GAA
1 GAA
11308 AAAGTTGCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (27 bp):
GAAGCCCAACAAAGCTGCTAATGAAAT
Found at i:13588 original size:15 final size:15
Alignment explanation
Indices: 13570--13599 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13560 AAAATCCGAT
*
13570 TTGATTTAATCCAAA
1 TTGATTTAACCCAAA
13585 TTGATTTAACCCAAA
1 TTGATTTAACCCAAA
13600 AACCAACTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.37
Consensus pattern (15 bp):
TTGATTTAACCCAAA
Found at i:18211 original size:3 final size:3
Alignment explanation
Indices: 18203--18231 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
18193 TCAGCATTCA
18203 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
18232 ACTAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:29034 original size:39 final size:40
Alignment explanation
Indices: 28980--29066 Score: 149
Period size: 40 Copynumber: 2.2 Consensus size: 40
28970 GTCAATGGAA
*
28980 ACCTTTTGAAGAGTCACAACCC-TTTCATATTGGATGAAC
1 ACCTTTTGAAAAGTCACAACCCTTTTCATATTGGATGAAC
*
29019 ACCTTTTGAAAAGTCACAACCCTTTTCATATTGGATGGAC
1 ACCTTTTGAAAAGTCACAACCCTTTTCATATTGGATGAAC
29059 ACCTTTTG
1 ACCTTTTG
29067 GAAGAGACTT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 21 0.47
40 24 0.53
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (40 bp):
ACCTTTTGAAAAGTCACAACCCTTTTCATATTGGATGAAC
Found at i:29061 original size:40 final size:39
Alignment explanation
Indices: 28974--29066 Score: 150
Period size: 39 Copynumber: 2.4 Consensus size: 39
28964 TATGCAGTCA
* *
28974 ATGGAAACCTTTTGAAGAGTCACAACCCTTTCATATTGG
1 ATGGACACCTTTTGAAAAGTCACAACCCTTTCATATTGG
*
29013 ATGAACACCTTTTGAAAAGTCACAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAAAGTCACAACCC-TTTCATATTGG
29053 ATGGACACCTTTTG
1 ATGGACACCTTTTG
29067 GAAGAGACTT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 25 0.51
40 24 0.49
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (39 bp):
ATGGACACCTTTTGAAAAGTCACAACCCTTTCATATTGG
Found at i:33938 original size:39 final size:40
Alignment explanation
Indices: 33879--33965 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
33869 CTCAATGGAA
* **
33879 ACCTTTTGAAGAGTTGCAA-CCTTTTCATATTGGATAGAC
1 ACCTTTTGAAAAGTCACAACCCTTTTCATATTGGATAGAC
*
33918 ACCTTTTGAAAAGTCACAACCCTTTTCATATTGGATGGAC
1 ACCTTTTGAAAAGTCACAACCCTTTTCATATTGGATAGAC
33958 ACCTTTTG
1 ACCTTTTG
33966 GAAGAGACTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 16 0.37
40 27 0.63
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.36
Consensus pattern (40 bp):
ACCTTTTGAAAAGTCACAACCCTTTTCATATTGGATAGAC
Found at i:34626 original size:89 final size:89
Alignment explanation
Indices: 34435--34659 Score: 245
Period size: 89 Copynumber: 2.5 Consensus size: 89
34425 CAAAAAAAAT
* * * * * *
34435 TTGCAGGTTAATACATTGCTAGAAGGTTGTGAATTCACAACATATTTGCATATGAGAGCTGCCAA
1 TTGCAGGTTAATACACTGCTAGATGGTTGTGAATGCACAACATA-TTACAGATAAGAGCTGCCAA
* * **
34500 AAATTTGGTGGATGAACCATTAGTG
65 AAAATGGGTGGATGAACCACCAGTG
** * * * * *
34525 TTATAGGTTAATACACTGTTAGATGGTTTTGAATGCACAACATATTACAGATAATAGTTGCTAAA
1 TTGCAGGTTAATACACTGCTAGATGGTTGTGAATGCACAACATATTACAGATAAGAGCTGCCAAA
34590 AAATGGGTGGATGAACCACCAGTG
66 AAATGGGTGGATGAACCACCAGTG
* * *
34614 TTGCAGGTTAATACGCTACCAGATGGTTGTGAATGCA-AACCATATT
1 TTGCAGGTTAATACACTGCTAGATGGTTGTGAATGCACAA-CATATT
34660 TGCATATAAA
Statistics
Matches: 110, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
88 2 0.02
89 71 0.65
90 37 0.34
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (89 bp):
TTGCAGGTTAATACACTGCTAGATGGTTGTGAATGCACAACATATTACAGATAAGAGCTGCCAAA
AAATGGGTGGATGAACCACCAGTG
Found at i:37114 original size:89 final size:89
Alignment explanation
Indices: 36962--37323 Score: 436
Period size: 89 Copynumber: 4.1 Consensus size: 89
36952 TTTAGAGAAT
* * * *
36962 TGAGTCAGCCATATCATGAATCTTCTTTTATGAATTCACATATATGAGTCCACCATATCTACGAA
1 TGAGTCTGCCATATCATGAATCTTCTTCTATGAATTCACATGTATGAGTCCATCATATCTACGAA
37027 TCCTCTTCTATGAATCCGCATGTA
66 TCCTCTTCTATGAATCCGCATGTA
* * * *
37051 AGAGTCTGCCATATCATGAATCTTCTTCTATGAACTCGCATGTATGACTCCATCATATCTACGAA
1 TGAGTCTGCCATATCATGAATCTTCTTCTATGAATTCACATGTATGAGTCCATCATATCTACGAA
* *
37116 TCCTCTTTTATGAATCCGCATGCA
66 TCCTCTTCTATGAATCCGCATGTA
* * **
37140 TGAGTCTGCCATATCATGAATCTTCTTCTACGAATTCACTTGTATGAGTCTGTCATATCTACGAA
1 TGAGTCTGCCATATCATGAATCTTCTTCTATGAATTCACATGTATGAGTCCATCATATCTACGAA
* *
37205 TCCTCTTCTATGAATTCACATGTA
66 TCCTCTTCTATGAATCCGCATGTA
* * * * * * ** ***
37229 TGAGCCTGTCATATCTACGAATCCTCTTTTATGAATCCGTATGTATGAGTTTGTCATATCTACGA
1 TGAGTCTGCCATATC-ATGAATCTTCTTCTATGAATTCACATGTATGAGTCCATCATATCTACGA
* * * *
37294 ATCTTCTTCTACGAGTTCGCATGTA
65 ATCCTCTTCTATGAATCCGCATGTA
37319 TGAGT
1 TGAGT
37324 TCTAATATAA
Statistics
Matches: 234, Mismatches: 38, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
89 169 0.72
90 65 0.28
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.36
Consensus pattern (89 bp):
TGAGTCTGCCATATCATGAATCTTCTTCTATGAATTCACATGTATGAGTCCATCATATCTACGAA
TCCTCTTCTATGAATCCGCATGTA
Found at i:37212 original size:134 final size:134
Alignment explanation
Indices: 36971--37323 Score: 433
Period size: 134 Copynumber: 2.6 Consensus size: 134
36961 TTGAGTCAGC
* * * * * ** *
36971 CATATC-ATGAATCTTCTTTTATGAATTCACATATATGAGTCCACCATATCTACGAATCCTCTTC
1 CATATCTACGAATCCTCTTTTATGAATCCGCATGTATGAGTCTGCCATATCTACGAATCTTCTTC
* * * * * *
37035 TATGAATCCGCATGTAAGAGTCTGCCATATCATGAATCTTCTTCTATGAACTCGCATGTATGA-C
66 TACGAATTCGCATGTATGAGTCTGCCATATCACGAATCCTCTTCTATGAACTCACATGTATGAGC
37099 TCCAT
131 -CCAT
* *
37104 CATATCTACGAATCCTCTTTTATGAATCCGCATGCATGAGTCTGCCATATC-ATGAATCTTCTTC
1 CATATCTACGAATCCTCTTTTATGAATCCGCATGTATGAGTCTGCCATATCTACGAATCTTCTTC
* * * *
37168 TACGAATTCACTTGTATGAGTCTGTCATATCTACGAATCCTCTTCTATGAATTCACATGTATGAG
66 TACGAATTCGCATGTATGAGTCTGCCATATC-ACGAATCCTCTTCTATGAACTCACATGTATGAG
**
37233 CCTGT
130 CCCAT
* * *
37238 CATATCTACGAATCCTCTTTTATGAATCCGTATGTATGAGTTTGTCATATCTACGAATCTTCTTC
1 CATATCTACGAATCCTCTTTTATGAATCCGCATGTATGAGTCTGCCATATCTACGAATCTTCTTC
*
37303 TACGAGTTCGCATGTATGAGT
66 TACGAATTCGCATGTATGAGT
37324 TCTAATATAA
Statistics
Matches: 186, Mismatches: 30, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
133 42 0.23
134 113 0.61
135 31 0.17
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (134 bp):
CATATCTACGAATCCTCTTTTATGAATCCGCATGTATGAGTCTGCCATATCTACGAATCTTCTTC
TACGAATTCGCATGTATGAGTCTGCCATATCACGAATCCTCTTCTATGAACTCACATGTATGAGC
CCAT
Found at i:37324 original size:45 final size:45
Alignment explanation
Indices: 36962--37323 Score: 370
Period size: 45 Copynumber: 8.1 Consensus size: 45
36952 TTTAGAGAAT
* * * * * * *
36962 TGAGTCAGCCATATC-ATGAATCTTCTTTTATGAATTCACATATA
1 TGAGTCTGTCATATCTACGAATCCTCTTCTATGAATTCGCATGTA
*** *
37006 TGAGTCCACCATATCTACGAATCCTCTTCTATGAATCCGCATGTA
1 TGAGTCTGTCATATCTACGAATCCTCTTCTATGAATTCGCATGTA
* * * * *
37051 AGAGTCTGCCATATC-ATGAATCTTCTTCTATGAACTCGCATGTA
1 TGAGTCTGTCATATCTACGAATCCTCTTCTATGAATTCGCATGTA
* ** * * *
37095 TGACTCCATCATATCTACGAATCCTCTTTTATGAATCCGCATGCA
1 TGAGTCTGTCATATCTACGAATCCTCTTCTATGAATTCGCATGTA
* * * * * *
37140 TGAGTCTGCCATATC-ATGAATCTTCTTCTACGAATTCACTTGTA
1 TGAGTCTGTCATATCTACGAATCCTCTTCTATGAATTCGCATGTA
*
37184 TGAGTCTGTCATATCTACGAATCCTCTTCTATGAATTCACATGTA
1 TGAGTCTGTCATATCTACGAATCCTCTTCTATGAATTCGCATGTA
* * * *
37229 TGAGCCTGTCATATCTACGAATCCTCTTTTATGAATCCGTATGTA
1 TGAGTCTGTCATATCTACGAATCCTCTTCTATGAATTCGCATGTA
* * * *
37274 TGAGTTTGTCATATCTACGAATCTTCTTCTACGAGTTCGCATGTA
1 TGAGTCTGTCATATCTACGAATCCTCTTCTATGAATTCGCATGTA
37319 TGAGT
1 TGAGT
37324 TCTAATATAA
Statistics
Matches: 259, Mismatches: 56, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
44 83 0.32
45 176 0.68
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.36
Consensus pattern (45 bp):
TGAGTCTGTCATATCTACGAATCCTCTTCTATGAATTCGCATGTA
Found at i:38887 original size:27 final size:27
Alignment explanation
Indices: 38839--38890 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
38829 AGTTAGTCCA
* **
38839 TCAGGATACTAAATGCGAGGAAGTCTG
1 TCAGGACACTAAAAACGAGGAAGTCTG
*
38866 TCAGGACACTAAAAACGGGGAAGTC
1 TCAGGACACTAAAAACGAGGAAGTC
38891 CGCCAGGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (27 bp):
TCAGGACACTAAAAACGAGGAAGTCTG
Found at i:40717 original size:13 final size:13
Alignment explanation
Indices: 40699--40728 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
40689 TACCACTTAA
40699 CGTATTTACTCAG
1 CGTATTTACTCAG
40712 CGTATTTACTCAG
1 CGTATTTACTCAG
40725 CGTA
1 CGTA
40729 CGATTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (13 bp):
CGTATTTACTCAG
Found at i:44083 original size:37 final size:34
Alignment explanation
Indices: 43996--44075 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
43986 TTATATTCAA
* *
43996 TAAT-TTAAATAAAAAATATTATTTTAAATTAAT
1 TAATATTAAATAAAAAATAATATTTTAAAATAAT
* *
44029 TATTA-TAATTAAAAAAATAATATTTTAAAATAAT
1 TAATATTAAAT-AAAAAATAATATTTTAAAATAAT
44063 TAAATATTAAATA
1 T-AATATTAAATA
44076 CATAAAATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
33 7 0.19
34 22 0.59
35 4 0.11
36 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
TAATATTAAATAAAAAATAATATTTTAAAATAAT
Found at i:45562 original size:18 final size:18
Alignment explanation
Indices: 45539--45583 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
45529 TAAAAATAAT
* *
45539 TATTTAAACATATTTTAA-
1 TATTTAAAC-TAATTAAAG
45557 TATTTAAACTAATTAAAG
1 TATTTAAACTAATTAAAG
45575 TATTTAAAC
1 TATTTAAAC
45584 CCTAAAACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (18 bp):
TATTTAAACTAATTAAAG
Found at i:48110 original size:19 final size:20
Alignment explanation
Indices: 48077--48115 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
48067 GTTAACCAAT
*
48077 AACTACTCAATTAACTAATC
1 AACTACTCAACTAACTAATC
48097 AACTAC-CAACTAACTAATC
1 AACTACTCAACTAACTAATC
48116 TGTAGTTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (20 bp):
AACTACTCAACTAACTAATC
Found at i:50455 original size:20 final size:20
Alignment explanation
Indices: 50430--50469 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
50420 TTTCTTTTTG
50430 CAACCCCATTCTACTAAGAA
1 CAACCCCATTCTACTAAGAA
*
50450 CAACCCCATTCTACTGAGAA
1 CAACCCCATTCTACTAAGAA
50470 GTGGAGACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.35, G:0.07, T:0.20
Consensus pattern (20 bp):
CAACCCCATTCTACTAAGAA
Found at i:53414 original size:59 final size:59
Alignment explanation
Indices: 53342--53472 Score: 185
Period size: 59 Copynumber: 2.2 Consensus size: 59
53332 ACGGGCTAAG
* * * *
53342 CACACAGGTGTGGGTCAGACCGTGTATGCGTACTATTTTGAAAAGT-GCCATACAAGGGA
1 CACACGGGCGTGGGTCAGACAGTGTATGCATACTATTTTGAAAAGTAG-CATACAAGGGA
* *
53401 CACACGGGCGTGGGTCAGACAGTGTGTGCATACTATTTTGGAAAGTAGCATACAAGGGA
1 CACACGGGCGTGGGTCAGACAGTGTATGCATACTATTTTGAAAAGTAGCATACAAGGGA
53460 CACACGGGC-TGGG
1 CACACGGGCGTGGG
53473 CGTACGGGCA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
58 4 0.06
59 60 0.92
60 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.21
Consensus pattern (59 bp):
CACACGGGCGTGGGTCAGACAGTGTATGCATACTATTTTGAAAAGTAGCATACAAGGGA
Found at i:57995 original size:30 final size:30
Alignment explanation
Indices: 57959--58103 Score: 190
Period size: 29 Copynumber: 4.9 Consensus size: 30
57949 AAAAAATAAT
*
57959 AATTAGAAATGAAATTTAAAATATAAATGA
1 AATTAGAAATGAAATTTAAAATATAAACGA
*
57989 AATTAGAAATGAAATTTAAAATATAAACAA
1 AATTAGAAATGAAATTTAAAATATAAACGA
58019 AATTAGAAATTG-AA-TTAAAATATAAACGA
1 AATTAGAAA-TGAAATTTAAAATATAAACGA
* * *
58048 AATTACAAGTTAAA-TTAAAATATAAACGA
1 AATTAGAAATGAAATTTAAAATATAAACGA
* *
58077 AATTACAAATTAAATTTAAAA-ATAAAC
1 AATTAGAAATGAAATTTAAAATATAAAC
58104 AAAAAATCAG
Statistics
Matches: 105, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
28 1 0.01
29 57 0.54
30 45 0.43
31 2 0.02
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (30 bp):
AATTAGAAATGAAATTTAAAATATAAACGA
Found at i:58565 original size:12 final size:12
Alignment explanation
Indices: 58544--58596 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
58534 GTTATTGCTT
*
58544 GGGCTAGTACTC
1 GGGCTGGTACTC
*
58556 GGGCTGGTACTT
1 GGGCTGGTACTC
* * *
58568 GAGCTCGTACTA
1 GGGCTGGTACTC
*
58580 GGGCTGATACTC
1 GGGCTGGTACTC
58592 GGGCT
1 GGGCT
58597 CGCCTTCGAG
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.15, C:0.23, G:0.36, T:0.26
Consensus pattern (12 bp):
GGGCTGGTACTC
Found at i:58568 original size:24 final size:24
Alignment explanation
Indices: 58541--58596 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
58531 CGGGTTATTG
* *
58541 CTTGGGCTAGTACTCGGGCTGGTA
1 CTTGGGCTAGTACTAGGGCTGATA
* *
58565 CTTGAGCTCGTACTAGGGCTGATA
1 CTTGGGCTAGTACTAGGGCTGATA
*
58589 CTCGGGCT
1 CTTGGGCT
58597 CGCCTTCGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (24 bp):
CTTGGGCTAGTACTAGGGCTGATA
Found at i:58608 original size:36 final size:36
Alignment explanation
Indices: 58551--58620 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
58541 CTTGGGCTAG
*
58551 TACTCGGGCTGGTACTTGAGCTCGTACTAGGGCTGA
1 TACTCGGGCTCGTACTTGAGCTCGTACTAGGGCTGA
* * *
58587 TACTCGGGCTCG-CCTTCGAGCTCGTCCTCGGGCT
1 TACTCGGGCTCGTACTT-GAGCTCGTACTAGGGCT
58621 TGGATTCTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 3 0.10
36 26 0.90
ACGTcount: A:0.11, C:0.30, G:0.31, T:0.27
Consensus pattern (36 bp):
TACTCGGGCTCGTACTTGAGCTCGTACTAGGGCTGA
Found at i:59383 original size:21 final size:21
Alignment explanation
Indices: 59335--59383 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
59325 TTTAAAAAAA
59335 TCAAAAATATAAAAAAACATT
1 TCAAAAATATAAAAAAACATT
* * *
59356 TCGAAAATATTAAAAAATATT
1 TCAAAAATATAAAAAAACATT
*
59377 TTAAAAA
1 TCAAAAA
59384 ATTTGAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (21 bp):
TCAAAAATATAAAAAAACATT
Found at i:59676 original size:49 final size:49
Alignment explanation
Indices: 59604--59714 Score: 204
Period size: 49 Copynumber: 2.3 Consensus size: 49
59594 GTCTTGGACA
*
59604 TTCGCGATAGAAGGCAGTCGGTATAATTACCACGATTGGAGCAAATACG
1 TTCGCGATAGAAGGCAGTCGGTATAATTACCACAATTGGAGCAAATACG
59653 TTCGCGATAGAAGGCAGTCGGTATAATTACCACAATTGGAGCAAATACG
1 TTCGCGATAGAAGGCAGTCGGTATAATTACCACAATTGGAGCAAATACG
*
59702 TTCGTGATAGAAG
1 TTCGCGATAGAAG
59715 TCCAGTACAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.23
Consensus pattern (49 bp):
TTCGCGATAGAAGGCAGTCGGTATAATTACCACAATTGGAGCAAATACG
Done.