Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003048.1 Kokia drynarioides strain JFW-HI SEQ_115574, 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: 58422
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:152 original size:86 final size:86
Alignment explanation
Indices: 3--236 Score: 414
Period size: 86 Copynumber: 2.7 Consensus size: 86
1 AT
3 ATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAAT
1 ATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAAT
* *
68 AATGTGTTGATTTGACAGTAC
66 AATATGTTGATTTGACAATAC
* * *
89 ATTATTTATTAATTTTAAATATTTAAATAAAATTTATTATTATAATATTACAATTTTTTTCAAAT
1 ATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAAT
154 AATATGTTGATTTGACAATAC
66 AATATGTTGATTTGACAATAC
*
175 ATTATTTATTAATTTTATATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCA
1 ATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCA
237 TATTTTAAAT
Statistics
Matches: 139, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 139 1.00
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.51
Consensus pattern (86 bp):
ATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAAT
AATATGTTGATTTGACAATAC
Found at i:3574 original size:61 final size:60
Alignment explanation
Indices: 3489--3955 Score: 494
Period size: 61 Copynumber: 7.8 Consensus size: 60
3479 AGGGAAGTTA
* * **
3489 GTGTCGGCCATTACATGGTTAACA-CAAAAAAATTTGCAATTTTTTTATCCAAGAAAAGGG
1 GTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCAATTTTTTT-TCCAAGAAAAGGG
*
3549 AGTGTCGACAATTGCATGGCCAACA-CAAAAAAATTTGCAATTTTTTTATCCAAGAAAAAGGG
1 -GTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCAATTTTTTT-TCCAAG-AAAAGGG
*
3611 GTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCAATTTTTTTATCCGAGAACAAGGG
1 GTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCAATTTTTTT-TCCAAGAA-AAGGG
* * * * * *
3673 GTGTCGGCCATTACATGGCCTACACTAAAAAATTTTG-AATTTTTTTTCTC-A-AAAAGAGA
1 GTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCAATTTTTTTTC-CAAGAAAAG-GG
* * *
3732 GTGTCGGCCATTGCATGGCCTACACCAAAAAAATTTGCAA--TTTTTT-CAAAAAAAGGGG
1 GTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCAATTTTTTTTCCAAGAAAA-GGG
* * * *
3790 GTGTCGGCCATTTG-ATGGCCAACACCAAAAAATTTTG-AAATTTTTTTCTCGAGAAAAGGG
1 GTGTCGACCA-TTGCATGGCCAACACCAAAAAAATTTGCAATTTTTTTTC-CAAGAAAAGGG
*
3850 AGTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGC-ATTTTTTTT--TAGAACAAGGG
1 -GTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCAATTTTTTTTCCAAGAA-AAGGG
* * **
3909 GTGTCGACCATTTG-ATGGACAACACCAAAAAATTTTAAAATTTTTTT
1 GTGTCGACCA-TTGCATGGCCAACACCAAAAAAATTTGCAATTTTTTT
3956 CTCGAGCATG
Statistics
Matches: 357, Mismatches: 29, Indels: 42
0.83 0.07 0.10
Matches are distributed among these distances:
56 1 0.00
57 3 0.01
58 79 0.22
59 63 0.18
60 11 0.03
61 128 0.36
62 72 0.20
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (60 bp):
GTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCAATTTTTTTTCCAAGAAAAGGG
Found at i:3876 original size:119 final size:121
Alignment explanation
Indices: 3488--3961 Score: 547
Period size: 119 Copynumber: 3.9 Consensus size: 121
3478 AAGGGAAGTT
* * ** *
3488 AGTGTCGGCCATTACATGGTTAACA-CAAAAAAATTTGCAATTTTTTTATCCAAGAAAAGGGAGT
1 AGTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCAA-TTTTTTATCCAAAAAAAGGG-GT
* * * * * *
3552 GTC-GACAATTGCATGGCCAACA-CAAAAAAATTTGCAATTTTTTTATCCAAGAAAAAGGG
64 GTCGGCCATTTG-ATGGCCAACACCAAAAAATTTTGAAATTTTTTTCT-CGAG-AAAAGGG
* *
3611 -GTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCAATTTTTTTATCCGAGAACAAGGGGT
1 AGTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCAA-TTTTTTATCC-AAAAAAAGGGGT
** * * * *
3675 GTCGGCCATTACATGGCCTACACTAAAAAATTTTGAATTTTTTTTCTC-A-AAAAGAG
64 GTCGGCCATTTGATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGG
* *
3731 AGTGTCGGCCATTGCATGGCCTACACCAAAAAAATTTGCAA-TTTTT-T-CAAAAAAAGGGGGTG
1 AGTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCAATTTTTTATCCAAAAAAA-GGGGTG
3793 TCGGCCATTTGATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGG
65 TCGGCCATTTGATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGG
** * *
3850 AGTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGC-ATTTTTT-TTTAGAACAAGGGGTGT
1 AGTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCAATTTTTTATCCAAAAAAAGGGGTGT
* * *
3913 CGACCATTTGATGGACAACACCAAAAAATTTTAAAATTTTTTTCTCGAG
66 CGGCCATTTGATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTCGAG
3962 CATGGCCGAC
Statistics
Matches: 305, Mismatches: 36, Indels: 24
0.84 0.10 0.07
Matches are distributed among these distances:
116 5 0.02
117 49 0.16
118 3 0.01
119 107 0.35
120 11 0.04
121 38 0.12
122 21 0.07
123 41 0.13
124 30 0.10
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (121 bp):
AGTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCAATTTTTTATCCAAAAAAAGGGGTGT
CGGCCATTTGATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGG
Found at i:4017 original size:97 final size:97
Alignment explanation
Indices: 3863--4058 Score: 263
Period size: 97 Copynumber: 2.0 Consensus size: 97
3853 GTCGACCATT
*
3863 GCATGGCCAACACCAAAAAAATTTGCATTTTTTTTTAGAACAAGGGGTGTCGACCATTTGATGGA
1 GCATGGCCAACACCAAAAAAA-TTGCATTTTTTTTGAGAACAAGGGGTGTCGACCATTTGATGGA
*
3928 CAACACCAAAAAATTTTAAAATTTTTTTCTCGA
65 CAACACAAAAAAATTTTAAAATTTTTTTCTCGA
* * *
3961 GCATGGCCGACACC-CAAAAA-TGCAATTTTTTTTCGAGAA-AAGAGGGTGTCGGCCATTTGATG
1 GCATGGCCAACACCAAAAAAATTGC-ATTTTTTTT-GAGAACAAG-GGGTGTCGACCATTTGATG
* * *
4023 GACAACATAAAAAAATTTTGAATTTTTTTTCTCGA
63 GACAACACAAAAAAATTTTAAAATTTTTTTCTCGA
4058 G
1 G
4059 AAAGAGGGTG
Statistics
Matches: 87, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
95 3 0.03
96 12 0.14
97 59 0.68
98 13 0.15
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (97 bp):
GCATGGCCAACACCAAAAAAATTGCATTTTTTTTGAGAACAAGGGGTGTCGACCATTTGATGGAC
AACACAAAAAAATTTTAAAATTTTTTTCTCGA
Found at i:4108 original size:155 final size:154
Alignment explanation
Indices: 3828--4114 Score: 345
Period size: 155 Copynumber: 1.9 Consensus size: 154
3818 AAAATTTTGA
* *
3828 AATTTTTTTCTCGAGAAAAGGGAGTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGCATTT
1 AATTTTTTTCTCGAGAAAAGGGAGTGTCGACCATTGCATGGACAACACCAAAAAAATTTGAATTT
***
3893 TTTTTTAGAACAAGGGGTGTCGACCATTTGATGGACAACACCAAAAAATTTTAAAATTTTTTTCT
66 TTTTTTAGAACAAGGGGTGTCGACCATGCAATGGACAACACCAAAAAA--TTAAAATTTTTTTCT
3958 CGAGCATGGCCGACACCCAAAAATGC
129 CGAGCATGGCCGACACCCAAAAATGC
* *
3984 AATTTTTTT-TCGAGAAAAGAGG-GTGTCGGCCATTTG-ATGGACAACA-TAAAAAAATTTTGAA
1 AATTTTTTTCTCGAGAAAAG-GGAGTGTCGACCA-TTGCATGGACAACACCAAAAAAA-TTTGAA
* * * * *
4045 TTTTTTTTCTCGAGA-AAGAGGGTGTCGGCCATGCAATGGCCAACACCCAAAAA-TACAATTTTT
63 TTTTTTTT-TAGA-ACAAG-GGGTGTCGACCATGCAATGGACAACACCAAAAAATTAAAATTTTT
4108 TT-TCGAG
125 TTCTCGAG
4115 AAAAGGGGGT
Statistics
Matches: 113, Mismatches: 12, Indels: 15
0.81 0.09 0.11
Matches are distributed among these distances:
153 5 0.04
154 18 0.16
155 41 0.36
156 20 0.18
157 29 0.26
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (154 bp):
AATTTTTTTCTCGAGAAAAGGGAGTGTCGACCATTGCATGGACAACACCAAAAAAATTTGAATTT
TTTTTTAGAACAAGGGGTGTCGACCATGCAATGGACAACACCAAAAAATTAAAATTTTTTTCTCG
AGCATGGCCGACACCCAAAAATGC
Found at i:4111 original size:333 final size:336
Alignment explanation
Indices: 3623--4230 Score: 842
Period size: 333 Copynumber: 1.8 Consensus size: 336
3613 GTCGACCATT
3623 GCATGGCCAACACCAAAAAAATTTGCAATTTTTTTATCCGAGAACAAGGGGTGTCGGCCATTACA
1 GCATGGCCAACACCAAAAAAA-TTGCAATTTTTTTATCCGAGAACAAGGGGTGTCGGCCATTACA
* * *
3688 TGGCCTACACTAAAAAATTTTGAATTTTTTTTCTCAAAAAGAGAGTGTCGGCCATTGCATGGCCT
65 TGGACAACACTAAAAAATTTTGAATTTTTTTTCTCAAAAAGAGAGTGTCGGCCATTGCATGGCCA
* ** * *
3753 ACACCAAAAAAATTTGCAATTTTTTCAAAAAAAGGGGGTGTCGGCCATTTGATGGCCAACACCAA
130 ACACCAAAAAAA-TTACAATTTTTTCAAAAAAAGGGGGTGTCAACCATTTGATAGCCAACACAAA
*
3818 AAAATTTTGAAATTTTTTTCTCGAGAAAA-GGGAGTGTCGACCA-TTGCATGGCCAACACCAAAA
194 AAAATTTTGAAATTTTTTTCTCGAGAAAAGGGGA-TGTCGACCATTTG-ATGGACAACACCAAAA
* *
3881 AAATTTGCATTTTTTTTTAGAACAAGGGGTGTCGACCATTTGATGGACAACACCAAAAAATTTTA
257 AAATTTGAAATTTTTTTTAGAACAAGGGGTGTCGACCATTTGATGGACAACACCAAAAAATTTTA
3946 AAATTTTTTTCTCGA
322 AAATTTTTTTCTCGA
* * **
3961 GCATGGCCGACACC-CAAAAA-TGCAATTTTTTT-T-CGAGAA-AAGAGGGTGTCGGCCATTTGA
1 GCATGGCCAACACCAAAAAAATTGCAATTTTTTTATCCGAGAACAAG-GGGTGTCGGCCATTACA
* *
4021 TGGACAACA-TAAAAAAATTTTGAATTTTTTTTCTCGAGAAAGAGGGTGTCGGCCA-TGCAATGG
65 TGGACAACACT-AAAAAATTTTGAATTTTTTTTCTC-AAAAAGAGAGTGTCGGCCATTGC-ATGG
* * *
4084 CCAACACC-CAAAAA-TACAATTTTTTTTCGAGAAAAGGGGGTGTCAACCATTTGATAGCCAACA
127 CCAACACCAAAAAAATTACAA--TTTTTTCAAAAAAAGGGGGTGTCAACCATTTGATAGCCAACA
* *
4147 CAAAAAAATTTTTAAATTTTTTTCTCGAGAAAAGGGGATGTCGGCCATTTGATGGACAACACCAA
190 CAAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGGGATGTCGACCATTTGATGGACAACACCAA
*
4212 AAAATTTTGAAATTTTTTT
255 AAAAATTTGAAATTTTTTT
4231 CTCGAGAAAA
Statistics
Matches: 239, Mismatches: 23, Indels: 21
0.84 0.08 0.07
Matches are distributed among these distances:
331 4 0.02
332 4 0.02
333 165 0.69
334 36 0.15
335 12 0.05
337 5 0.02
338 13 0.05
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (336 bp):
GCATGGCCAACACCAAAAAAATTGCAATTTTTTTATCCGAGAACAAGGGGTGTCGGCCATTACAT
GGACAACACTAAAAAATTTTGAATTTTTTTTCTCAAAAAGAGAGTGTCGGCCATTGCATGGCCAA
CACCAAAAAAATTACAATTTTTTCAAAAAAAGGGGGTGTCAACCATTTGATAGCCAACACAAAAA
AATTTTGAAATTTTTTTCTCGAGAAAAGGGGATGTCGACCATTTGATGGACAACACCAAAAAAAT
TTGAAATTTTTTTTAGAACAAGGGGTGTCGACCATTTGATGGACAACACCAAAAAATTTTAAAAT
TTTTTTCTCGA
Found at i:4169 original size:117 final size:118
Alignment explanation
Indices: 3963--4244 Score: 354
Period size: 117 Copynumber: 2.4 Consensus size: 118
3953 TTTCTCGAGC
* * ** *
3963 ATGGCCGACACCCAAAAATGCAATTTTTTTTCGAGAAAAGAGGGTGTCGGCCATTTGATGGACAA
1 ATGGCCAACACCCAAAAATACAATTTTTTTTCGAGAAAAGAGGGTGTCAACCATTTGATAGACAA
* *
4028 CATAAAAAAATTTTGAATTTTTTTTCTCGAG-AAAGAGGG-TGTCGGCCATGCA
66 CACAAAAAAATTTTGAAATTTTTTTCTCGAGAAAAG-GGGATGTCGGCCATGCA
* *
4080 ATGGCCAACACCCAAAAATACAATTTTTTTTCGAGAAAAGGGGGTGTCAACCATTTGATAGCCAA
1 ATGGCCAACACCCAAAAATACAATTTTTTTTCGAGAAAAGAGGGTGTCAACCATTTGATAGACAA
* ***
4145 CACAAAAAAATTTTTAAATTTTTTTCTCGAGAAAAGGGGATGTCGGCCATTTG
66 CACAAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGGGATGTCGGCCATGCA
* *
4198 ATGGACAACACCAAAAAATTTTGA-AATTTTTTTCTCGAGAAAAGAGG
1 ATGGCCAACACCCAAAAA---T-ACAATTTTTTT-TCGAGAAAAGAGG
4245 CATGGCCAAC
Statistics
Matches: 142, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
117 89 0.63
118 30 0.21
121 10 0.07
122 13 0.09
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (118 bp):
ATGGCCAACACCCAAAAATACAATTTTTTTTCGAGAAAAGAGGGTGTCAACCATTTGATAGACAA
CACAAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGGGATGTCGGCCATGCA
Found at i:4293 original size:283 final size:272
Alignment explanation
Indices: 3782--4477 Score: 916
Period size: 283 Copynumber: 2.5 Consensus size: 272
3772 TTTTTTCAAA
* * * *
3782 AAAAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAA
1 AAAAGAGGGTGTCGGCCATGTAATGGCCAACACCCAAAAA---T-AAATTTTTTT-TCGAGAAAA
* ** *
3847 GGGAGTGTCGACCA-TTGCATGGCCAACACCAAAAAAA--TTTGCATTTTTTTTTAGAACAAGGG
61 GGGGGTGTCGACCATTTG-ATGGCCAACA-CAAAAAAATTTTTAAATTTTTTTTCAGAA-AAGGG
* *
3909 GTGTCGACCATTTGATGGACAACACCAAAAAATTTTAAAATTTTTTTCTCGAGCATGGCCGACAC
123 GTGTCGGCCATTTGATGGACAACACCAAAAAATTTTAAAATTTTTTTCTCGAGCATGGCCAACAC
* ** *
3974 CCAAAAATGCAATTTTTTTTCGAGAAAAGAGGGTGTCGGCCATTTGATGGACAACATAAAAAAAT
188 CCAAAAATACAATTTTTTTTCGAGAAAAGAGGGTGTCAACCATTTGATGGACAACACAAAAAAAT
*
4039 TTTGAATTTTTTTTCTCGAG
253 TTTGAAATTTTTTTCTCGAG
*
4059 -AAAGAGGGTGTCGGCCATGCAATGGCCAACACCCAAAAATACAATTTTTTTTCGAGAAAAGGGG
1 AAAAGAGGGTGTCGGCCATGTAATGGCCAACACCCAAAAATA-AATTTTTTTTCGAGAAAAGGGG
* *
4123 GTGTCAACCATTTGATAGCCAACACAAAAAAATTTTTAAATTTTTTTCTCGAGAAAAGGGGATGT
65 GTGTCGACCATTTGATGGCCAACACAAAAAAATTTTTAAATTTTTTT-TC-AGAAAAGGGG-TGT
*
4188 CGGCCATTTGATGGACAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGAGGCATGGCCA
127 CGGCCATTTGATGGACAACACCAAAAAATTTTAAAATTTTTTTCTC-------GA-GCATGGCCA
* *
4253 ACACCCAAAAATACAATTTTTTTTCGAGAAAAGGGGGTGTCAACCATTTGATGGCCAACACAAAA
184 ACACCCAAAAATACAATTTTTTTTCGAGAAAAGAGGGTGTCAACCATTTGATGGACAACACAAAA
4318 AAATTTTGAAATTTTTTTCTCGAG
249 AAATTTTGAAATTTTTTTCTCGAG
* * *
4342 AAAAGAGGGTGTCGACCATGTAATGGCCAACAACCAAAAATGTAATTTTTTTTCGAGAAAAGGGG
1 AAAAGAGGGTGTCGGCCATGTAATGGCCAACACCCAAAAAT-AAATTTTTTTTCGAGAAAAGGGG
*
4407 GTGTCGACCATTTGATGGCCAACACAAAAAAAATTTTGAAATTTTTTTATCA-AAAAGAGGGTGT
65 GTGTCGACCATTTGATGGCCAACAC-AAAAAAATTTTTAAATTTTTTT-TCAGAAAAG-GGGTGT
4471 CGGCCAT
127 CGGCCAT
4478 GCAATGACCA
Statistics
Matches: 371, Mismatches: 29, Indels: 32
0.86 0.07 0.07
Matches are distributed among these distances:
271 8 0.02
272 31 0.08
273 24 0.06
274 7 0.02
275 51 0.14
276 34 0.09
282 2 0.01
283 105 0.28
284 86 0.23
285 23 0.06
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (272 bp):
AAAAGAGGGTGTCGGCCATGTAATGGCCAACACCCAAAAATAAATTTTTTTTCGAGAAAAGGGGG
TGTCGACCATTTGATGGCCAACACAAAAAAATTTTTAAATTTTTTTTCAGAAAAGGGGTGTCGGC
CATTTGATGGACAACACCAAAAAATTTTAAAATTTTTTTCTCGAGCATGGCCAACACCCAAAAAT
ACAATTTTTTTTCGAGAAAAGAGGGTGTCAACCATTTGATGGACAACACAAAAAAATTTTGAAAT
TTTTTTCTCGAG
Found at i:4373 original size:118 final size:116
Alignment explanation
Indices: 4246--4555 Score: 467
Period size: 117 Copynumber: 2.6 Consensus size: 116
4236 GAAAAGAGGC
**
4246 ATGGCCAACACCCAAAAATACAATTTTTTTTCGAGAAAAGGGGGTGTCAACCATTTGATGGCCAA
1 ATGGCCAACACCCAAAAATGTAATTTTTTTTCGAGAAAAGGGGGTGTCAACCATTTGATGGCCAA
* *
4311 CACAAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGAGGGTGTCGACCATGTA
66 CACAAAAAAATTTTGAAATTTTTTTATC-A-AAAAGAGGGTGTCGACCATGCA
* *
4364 ATGGCCAACAACCAAAAATGTAATTTTTTTTCGAGAAAAGGGGGTGTCGACCATTTGATGGCCAA
1 ATGGCCAACACCCAAAAATGTAATTTTTTTTCGAGAAAAGGGGGTGTCAACCATTTGATGGCCAA
*
4429 CACAAAAAAAATTTTGAAATTTTTTTATCAAAAAGAGGGTGTCGGCCATGCA
66 CAC-AAAAAAATTTTGAAATTTTTTTATCAAAAAGAGGGTGTCGACCATGCA
* * * * * *
4481 ATGACCAACACACAAAAATGTAAATTTTTTTCGAGAAAAGGAGGTGTCTACCATTTGATGGCAAA
1 ATGGCCAACACCCAAAAATGTAATTTTTTTTCGAGAAAAGGGGGTGTCAACCATTTGATGGCCAA
*
4546 CAAAAAAAAA
66 CACAAAAAAA
4556 AAAATTTTAT
Statistics
Matches: 176, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
116 7 0.04
117 80 0.45
118 65 0.37
119 24 0.14
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (116 bp):
ATGGCCAACACCCAAAAATGTAATTTTTTTTCGAGAAAAGGGGGTGTCAACCATTTGATGGCCAA
CACAAAAAAATTTTGAAATTTTTTTATCAAAAAGAGGGTGTCGACCATGCA
Found at i:4489 original size:60 final size:61
Alignment explanation
Indices: 4267--4556 Score: 289
Period size: 57 Copynumber: 4.9 Consensus size: 61
4257 CCAAAAATAC
* * * *
4267 AATTTTTTTTCGAGAAAAGGGGGTGTCAACCATTTGATGGCCAACAC-AAAAAAATTTTGA
1 AATTTTTTTTCGAGAAAAGAGGGTGTCGACCATGTAATGGCCAACACAAAAAAAATTTTGA
** *
4327 AATTTTTTTCTCGAGAAAAGAGGGTGTCGACCATGTAATGGCCAACA-ACCAAAAA---TGT
1 AATTTTTTT-TCGAGAAAAGAGGGTGTCGACCATGTAATGGCCAACACAAAAAAAATTTTGA
* * *
4385 AATTTTTTTTCGAGAAAAGGGGGTGTCGACCATTTGATGGCCAACACAAAAAAAATTTTGA
1 AATTTTTTTTCGAGAAAAGAGGGTGTCGACCATGTAATGGCCAACACAAAAAAAATTTTGA
* * * * *
4446 AATTTTTTTATC-A-AAAAGAGGGTGTCGGCCATGCAATGACCAACAC-ACAAAAA-TGT-A
1 AATTTTTTT-TCGAGAAAAGAGGGTGTCGACCATGTAATGGCCAACACAAAAAAAATTTTGA
* * * * *
4503 AA-TTTTTTTCGAGAAAAG-GAGGTGTCTACCATTTGATGGCAAACAAAAAAAAAA
1 AATTTTTTTTCGAGAAAAGAG-GGTGTCGACCATGTAATGGCCAACACAAAAAAAA
4557 AAATTTTATC
Statistics
Matches: 189, Mismatches: 30, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
55 2 0.01
56 8 0.04
57 60 0.32
58 25 0.13
59 6 0.03
60 36 0.19
61 50 0.26
62 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (61 bp):
AATTTTTTTTCGAGAAAAGAGGGTGTCGACCATGTAATGGCCAACACAAAAAAAATTTTGA
Found at i:5374 original size:15 final size:15
Alignment explanation
Indices: 5356--5391 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5346 CCCACTTCTA
*
5356 ATATTATATATATAT
1 ATATAATATATATAT
5371 ATATAATATATATAT
1 ATATAATATATATAT
*
5386 AAATAA
1 ATATAA
5392 ATTGATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATAATATATATAT
Found at i:11195 original size:3 final size:3
Alignment explanation
Indices: 11187--11231 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
11177 TCGCAACATC
* *
11187 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11232 TTTTGGGACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:16115 original size:20 final size:19
Alignment explanation
Indices: 16065--16116 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
16055 CTACAAAATA
16065 AATATTAAATT-A-ACTTT
1 AATATTAAATTAATACTTT
16082 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-ACTTT
16102 AATATTAAATTAATA
1 AATATTAAATTAATA
16117 AAAAACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 9 0.30
18 2 0.07
19 2 0.07
20 17 0.57
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (19 bp):
AATATTAAATTAATACTTT
Found at i:16556 original size:19 final size:19
Alignment explanation
Indices: 16529--16568 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
16519 CTAACAAATC
16529 TAAAAGTAATGCGTACAAA
1 TAAAAGTAATGCGTACAAA
*
16548 TAAAGGTAATGCGTACAAA
1 TAAAAGTAATGCGTACAAA
16567 TA
1 TA
16569 CATACTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (19 bp):
TAAAAGTAATGCGTACAAA
Found at i:25511 original size:20 final size:21
Alignment explanation
Indices: 25478--25522 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
25468 TTTGCCTTTA
25478 TAATGTAAACTTTAAAATAAT
1 TAATGTAAACTTTAAAATAAT
* **
25499 TAAT-TAAATTTTAATTTAAT
1 TAATGTAAACTTTAAAATAAT
25519 TAAT
1 TAAT
25523 ATTAATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TAATGTAAACTTTAAAATAAT
Found at i:28278 original size:2 final size:2
Alignment explanation
Indices: 28271--28323 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
28261 TGAACAGGTT
*
28271 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28313 TC TC TC TC TC T
1 TC TC TC TC TC T
28324 GACTTATCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:29194 original size:176 final size:176
Alignment explanation
Indices: 28900--29253 Score: 699
Period size: 176 Copynumber: 2.0 Consensus size: 176
28890 GTAGTAGCTA
28900 AAACAATTTTTTTGAAATTTCATTTGAACCTGCCTTCTGCTTTCTGGAATAAAGAAGGTGAATCA
1 AAACAATTTTTTTGAAATTTCATTTGAACCTGCCTTCTGCTTTCTGGAATAAAGAAGGTGAATCA
28965 AAATGTAGATGGAACTTGATTATAATATGATGCCTTTTCGGGTTTTGTCGAATTTCTTGAAATGG
66 AAATGTAGATGGAACTTGATTATAATATGATGCCTTTTCGGGTTTTGTCGAATTTCTTGAAATGG
29030 TGACACGGTTTTTTGGTTTCTTACTTGAACTTCACTTTCTACATAG
131 TGACACGGTTTTTTGGTTTCTTACTTGAACTTCACTTTCTACATAG
29076 AAACAATTTTTTTGAAATTTCATTTGAACCTGCCTTCTGCTTTCTGGAATAAAGAAGGTGAATCA
1 AAACAATTTTTTTGAAATTTCATTTGAACCTGCCTTCTGCTTTCTGGAATAAAGAAGGTGAATCA
*
29141 AAATGTAGATGGAACTTGATTATAATATGATGCCTTTTTGGGTTTTGTCGAATTTCTTGAAATGG
66 AAATGTAGATGGAACTTGATTATAATATGATGCCTTTTCGGGTTTTGTCGAATTTCTTGAAATGG
29206 TGACACGGTTTTTTGGTTTCTTACTTGAACTTCACTTTCTACATAG
131 TGACACGGTTTTTTGGTTTCTTACTTGAACTTCACTTTCTACATAG
29252 AA
1 AA
29254 TCACAGTGCG
Statistics
Matches: 177, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 177 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (176 bp):
AAACAATTTTTTTGAAATTTCATTTGAACCTGCCTTCTGCTTTCTGGAATAAAGAAGGTGAATCA
AAATGTAGATGGAACTTGATTATAATATGATGCCTTTTCGGGTTTTGTCGAATTTCTTGAAATGG
TGACACGGTTTTTTGGTTTCTTACTTGAACTTCACTTTCTACATAG
Found at i:39844 original size:6 final size:6
Alignment explanation
Indices: 39833--39860 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39823 GCTTTAAAGG
39833 AACCCC AACCCC AACCCC AACCCC AACC
1 AACCCC AACCCC AACCCC AACCCC AACC
39861 AAATCTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (6 bp):
AACCCC
Found at i:47028 original size:2 final size:2
Alignment explanation
Indices: 46978--47011 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
46968 AAGGATGACG
*
46978 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47012 TGTCAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47035 original size:23 final size:21
Alignment explanation
Indices: 46999--47044 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
46989 TGTATATATA
46999 TATATATATATATTGTCAAATTT
1 TATATATATATATTG--AAATTT
* *
47022 TATATATTTTTATTGAAATTT
1 TATATATATATATTGAAATTT
47043 TA
1 TA
47045 AACATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
23 13 0.62
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (21 bp):
TATATATATATATTGAAATTT
Found at i:49631 original size:19 final size:19
Alignment explanation
Indices: 49607--49648 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
49597 TATTTTCGGA
49607 ATGGCTTGGAGGCTCGAGT
1 ATGGCTTGGAGGCTCGAGT
49626 ATGGCTTGGAGGCTCGAGT
1 ATGGCTTGGAGGCTCGAGT
49645 ATGG
1 ATGG
49649 ATACATTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.17, C:0.14, G:0.43, T:0.26
Consensus pattern (19 bp):
ATGGCTTGGAGGCTCGAGT
Done.