Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013443.1 Kokia drynarioides strain JFW-HI SEQ_128469, 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: 49250
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:236 original size:26 final size:29
Alignment explanation
Indices: 190--242 Score: 76
Period size: 26 Copynumber: 1.9 Consensus size: 29
180 AAAAAAAAAA
190 AAAAGTTTGAATTTTTAATAA-TTTTTCT
1 AAAAGTTTGAATTTTTAATAACTTTTTCT
*
218 AAAA-TTT-AATTTTTTATAACTTTTT
1 AAAAGTTTGAATTTTTAATAACTTTTT
243 TTGTCAACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 8 0.35
28 4 0.17
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (29 bp):
AAAAGTTTGAATTTTTAATAACTTTTTCT
Found at i:1672 original size:2 final size:2
Alignment explanation
Indices: 1665--1691 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1655 GCACTAAAAC
1665 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 T
1692 TTTTTAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15339 original size:81 final size:81
Alignment explanation
Indices: 15204--15368 Score: 321
Period size: 81 Copynumber: 2.0 Consensus size: 81
15194 GAGAACGGTT
15204 ATGACTTCGAACCAAGTCGTTCGAGCAACGGAAGAAGCAACTGAATAAGTTGATATCGAAAACCA
1 ATGACTTCGAACCAAGTCGTTCGAGCAACGGAAGAAGCAACTGAATAAGTTGATATCGAAAACCA
15269 GTCCACTAGTGTCCCA
66 GTCCACTAGTGTCCCA
*
15285 ATGACTTCGAACCAAGTGGTTCGAGCAACGGAAGAAGCAACTGAATAAGTTGATATCGAAAACCA
1 ATGACTTCGAACCAAGTCGTTCGAGCAACGGAAGAAGCAACTGAATAAGTTGATATCGAAAACCA
15350 GTCCACTAGTGTCCCA
66 GTCCACTAGTGTCCCA
15366 ATG
1 ATG
15369 GATTAAACTA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (81 bp):
ATGACTTCGAACCAAGTCGTTCGAGCAACGGAAGAAGCAACTGAATAAGTTGATATCGAAAACCA
GTCCACTAGTGTCCCA
Found at i:18490 original size:24 final size:26
Alignment explanation
Indices: 18458--18506 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
18448 AATTCAAAAT
*
18458 ATTTATAAAAAGTT-T-AAAATTTAC
1 ATTTATAAAAAATTATGAAAATTTAC
*
18482 ATTTTTAAAAAATTATGAAAATTTA
1 ATTTATAAAAAATTATGAAAATTTA
18507 AATATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
25 1 0.05
26 8 0.38
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (26 bp):
ATTTATAAAAAATTATGAAAATTTAC
Found at i:19513 original size:24 final size:24
Alignment explanation
Indices: 19486--19533 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
19476 CATCCCTCCT
*
19486 GATATTCCACCACCTAAAAGTCCA
1 GATATTCCACCACCGAAAAGTCCA
* *
19510 GATATTCCATCACCGAAAGGTCCA
1 GATATTCCACCACCGAAAAGTCCA
19534 TCCTTCGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.21
Consensus pattern (24 bp):
GATATTCCACCACCGAAAAGTCCA
Found at i:21334 original size:17 final size:17
Alignment explanation
Indices: 21312--21357 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
21302 ATTATTTCAA
21312 CTTTTTTATATTCATAT
1 CTTTTTTATATTCATAT
21329 CTTTTTTATATTCATAT
1 CTTTTTTATATTCATAT
*
21346 CTTTTATATATT
1 CTTTTTTATATT
21358 TGAATATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (17 bp):
CTTTTTTATATTCATAT
Found at i:21421 original size:16 final size:17
Alignment explanation
Indices: 21390--21422 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
21380 TTTAAAAATC
*
21390 TTTCAAATATATAATTT
1 TTTCAAATAAATAATTT
21407 TTTCAAA-AAATAATTT
1 TTTCAAATAAATAATTT
21423 CCAAATTCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTCAAATAAATAATTT
Found at i:22758 original size:97 final size:97
Alignment explanation
Indices: 22573--22766 Score: 239
Period size: 97 Copynumber: 2.0 Consensus size: 97
22563 CACTTTTGAA
* * *
22573 AAGGATGTTCGATTATCTCAATTTAAAGAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTTC
1 AAGGATATTCGATTATCTCAATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTC
* * * *
22638 AGAATCCGAGATGAGAAACATTGCCTCGATTT
66 AAAATCCGAAATAAAAAACATTGCCTCGATTT
* * **
22670 AAGGATATTCGATTAT-TCCGATTTGAAGAAAAA-TCGTGCCTAGTAAGTTAAGGCACAAATTTT
1 AAGGATATTCGATTATCT-CAATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTT
* *
22733 CAAAATTCGAAATAAAAGAATATTGCCTCGATTT
65 CAAAATCCGAAATAAAA-AACATTGCCTCGATTT
22767 TAAAGTTTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
96 39 0.48
97 43 0.52
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCAATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTC
AAAATCCGAAATAAAAAACATTGCCTCGATTT
Found at i:23155 original size:29 final size:29
Alignment explanation
Indices: 23123--23491 Score: 219
Period size: 30 Copynumber: 12.5 Consensus size: 29
23113 AATCGAGATA
23123 AAAAATGAAATTTTTGGACA-TTCGAGGGT
1 AAAAATGAAATTTTTGGA-AGTTCGAGGGT
** * * *
23152 AAAAGGGTAATTTTTGAAAGTTTC-TGGGT
1 AAAAATGAAATTTTTGGAAG-TTCGAGGGT
*
23181 CAAAAAT-AGAA-TTTTGGAAGTTTTG-GGGT
1 -AAAAATGA-AATTTTTGGAAG-TTCGAGGGT
* *
23210 -AAAATAGTAATTTTTGGAAGTTACG-GCGT
1 AAAAAT-GAAATTTTTGGAAGTT-CGAGGGT
* *
23239 CAAAAATGGAATTTTTGGAAGTTACG-GCGT
1 -AAAAATGAAATTTTTGGAAGTT-CGAGGGT
* * *
23269 CAAAAATGGAATTTTTGAAAGTT-TAGGGGT
1 -AAAAATGAAATTTTTGGAAGTTCGA-GGGT
* *
23299 AAAAATGTAATTTTTGGAAGTTTCGAGGTT
1 AAAAATGAAATTTTTGGAAG-TTCGAGGGT
* * *
23329 AAAAATGGAATTCTT-GAAGTTCGAGTGT
1 AAAAATGAAATTTTTGGAAGTTCGAGGGT
* *
23357 AAAAATGTAATTTTTGGAAGTTTCGAGGTT
1 AAAAATGAAATTTTTGGAAG-TTCGAGGGT
* *
23387 AAAAATGGAATTTTTTGGAAAGTTTG-GGGTT
1 AAAAAT-GAAATTTTTGG-AAGTTCGAGGG-T
* *
23418 AAAAATGAAATTTTTGGAAAGTTTGAGGTT
1 AAAAATGAAATTTTTGG-AAGTTCGAGGGT
*
23448 AAAAAT-ATAATTTTGGAGAAG-TCG-GGGTT
1 AAAAATGA-AATTTTTG-GAAGTTCGAGGG-T
23477 AAAAAT-ATAATTTTT
1 AAAAATGA-AATTTTT
23492 AGACAGTTTA
Statistics
Matches: 277, Mismatches: 39, Indels: 48
0.76 0.11 0.13
Matches are distributed among these distances:
27 5 0.02
28 27 0.10
29 90 0.32
30 124 0.45
31 28 0.10
32 3 0.01
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
AAAAATGAAATTTTTGGAAGTTCGAGGGT
Found at i:23194 original size:59 final size:57
Alignment explanation
Indices: 23123--23436 Score: 243
Period size: 58 Copynumber: 5.3 Consensus size: 57
23113 AATCGAGATA
*
23123 AAAAATGAAATTTTTGGACA-TTCGAGGGTAAAAGGGTAATTTTTGAAAGTTTCTGGGTC
1 AAAAATGAAATTTTTGGA-AGTTCG-GGGTAAAATGGTAATTTTTGAAAGTTTC-GGGTC
* * * *
23182 AAAAAT-AGAA-TTTTGGAAGTTTTGGGGTAAAATAGTAATTTTTGGAAGTTACGGCGTC
1 AAAAATGA-AATTTTTGGAAG-TTCGGGGTAAAATGGTAATTTTTGAAAGTTTCGG-GTC
* * *
23240 AAAAATGGAATTTTTGGAAGTTACGGCGTCAAAAATGG-AATTTTTGAAAGTTTAGGGGT-
1 AAAAATGAAATTTTTGGAAGTT-CGGGGT--AAAATGGTAATTTTTGAAAGTTT-CGGGTC
* * *
23299 AAAAATGTAATTTTTGGAAGTTTCGAGGTTAAAAATGG-AATTCTTG-AAG-TTCGAGTGT-
1 AAAAATGAAATTTTTGGAAG-TTCG-GGGT-AAAATGGTAATTTTTGAAAGTTTCG-G-GTC
* * * *
23357 AAAAATGTAATTTTTGGAAGTTTCGAGGTTAAAAATGG-AATTTTTTGGAAAGTTTGGGGTT
1 AAAAATGAAATTTTTGGAAG-TTCG-GGGT-AAAATGGTAA-TTTTT-GAAAGTTTCGGGTC
23418 AAAAATGAAATTTTTGGAA
1 AAAAATGAAATTTTTGGAA
23437 AGTTTGAGGT
Statistics
Matches: 216, Mismatches: 20, Indels: 36
0.79 0.07 0.13
Matches are distributed among these distances:
56 1 0.00
57 6 0.03
58 90 0.42
59 64 0.30
60 22 0.10
61 30 0.14
62 3 0.01
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.35
Consensus pattern (57 bp):
AAAAATGAAATTTTTGGAAGTTCGGGGTAAAATGGTAATTTTTGAAAGTTTCGGGTC
Found at i:23254 original size:30 final size:28
Alignment explanation
Indices: 23160--23441 Score: 248
Period size: 30 Copynumber: 9.5 Consensus size: 28
23150 GTAAAAGGGT
* *
23160 AATTTTTGAAAGTTTCTGGGTCAAAAATAG
1 AATTTTTGGAAGTTTC-GGGT-AAAAATGG
* *
23190 AA-TTTTGGAAGTTTTGGGGT-AAAATAGT
1 AATTTTTGGAAG-TTTCGGGTAAAAAT-GG
*
23218 AATTTTTGGAAGTTACGGCGTCAAAAATGG
1 AATTTTTGGAAGTTTCGG-GT-AAAAATGG
*
23248 AATTTTTGGAAGTTACGGCGTCAAAAATGG
1 AATTTTTGGAAGTTTCGG-GT-AAAAATGG
* * *
23278 AATTTTTGAAAGTTTAGGGGTAAAAATGT
1 AATTTTTGGAAGTTT-CGGGTAAAAATGG
23307 AATTTTTGGAAGTTTCGAGGTTAAAAATGG
1 AATTTTTGGAAGTTTCG-GG-TAAAAATGG
* *
23337 AATTCTT-GAAG-TTCGAGTGTAAAAATGT
1 AATTTTTGGAAGTTTCG-G-GTAAAAATGG
23365 AATTTTTGGAAGTTTCGAGGTTAAAAATGG
1 AATTTTTGGAAGTTTCG-GG-TAAAAATGG
* *
23395 AATTTTTTGGAAAGTTTGGGGTTAAAAATGA
1 AA-TTTTTGG-AAGTTTCGGG-TAAAAATGG
23426 AATTTTTGGAAAGTTT
1 AATTTTTGG-AAGTTT
23442 GAGGTTAAAA
Statistics
Matches: 217, Mismatches: 20, Indels: 30
0.81 0.07 0.11
Matches are distributed among these distances:
27 5 0.02
28 27 0.12
29 56 0.26
30 95 0.44
31 27 0.12
32 7 0.03
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (28 bp):
AATTTTTGGAAGTTTCGGGTAAAAATGG
Found at i:23313 original size:89 final size:85
Alignment explanation
Indices: 23123--23436 Score: 289
Period size: 89 Copynumber: 3.6 Consensus size: 85
23113 AATCGAGATA
* * * *
23123 AAAAATGAAATTTTTGGACA-TTCGAGGGT-AAAAGGGTAATTTTTGAAAGTTTCTGGGTCAAAA
1 AAAAATGTAATTTTTGGA-AGTTCG-GGTTAAAAATGG-AATTTTTGGAAG-TTC-GGGTCAAAA
* *
23186 ATAGAA-TTTTGGAAGTTTTGGGGT
61 ATGGAATTTTTGGAAGTTTAGGGGT
*
23210 -AAAATAGTAATTTTTGGAAGTTACGGCGTCAAAAATGGAATTTTTGGAAGTTACGGCGTCAAAA
1 AAAAAT-GTAATTTTTGGAAGTT-CGG-GTTAAAAATGGAATTTTTGGAAGTT-CGG-GTCAAAA
*
23274 ATGGAATTTTTGAAAGTTTAGGGGT
61 ATGGAATTTTTGGAAGTTTAGGGGT
*
23299 AAAAATGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTCTT-GAAGTTCGAGTGT-AAAAA
1 AAAAATGTAATTTTTGGAAG-TTCG-GGTTAAAAATGGAATTTTTGGAAGTTCG-G-GTCAAAAA
* * *
23362 TGTAATTTTTGGAAGTTTCGAGGTT
62 TGGAATTTTTGGAAGTTTAG-GGGT
* * *
23387 AAAAATGGAATTTTTTGGAAAGTTTGGGGTTAAAAATGAAATTTTTGGAA
1 AAAAATGTAA-TTTTTGG-AAG-TTCGGGTTAAAAATGGAATTTTTGGAA
23437 AGTTTGAGGT
Statistics
Matches: 192, Mismatches: 19, Indels: 29
0.80 0.08 0.12
Matches are distributed among these distances:
86 6 0.03
87 42 0.22
88 48 0.25
89 78 0.41
90 18 0.09
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.35
Consensus pattern (85 bp):
AAAAATGTAATTTTTGGAAGTTCGGGTTAAAAATGGAATTTTTGGAAGTTCGGGTCAAAAATGGA
ATTTTTGGAAGTTTAGGGGT
Found at i:23377 original size:58 final size:58
Alignment explanation
Indices: 23123--23500 Score: 287
Period size: 59 Copynumber: 6.4 Consensus size: 58
23113 AATCGAGATA
* * * **
23123 AAAAATGAAATTTTTGGACA--TTCGAGGGT-AAAAGGGTAATTTTTGAAAGTTTCTGGGT
1 AAAAATGTAATTTTTGGA-AGTTTCGAGGTTAAAAATGG-AATTTTTGAAAG-TTGAGGGT
* * * *
23181 CAAAAATAG-AA-TTTTGGAAGTTTTG-GGGT-AAAATAGTAATTTTTGGAAGTT-ACGGCGT
1 -AAAAAT-GTAATTTTTGGAAGTTTCGAGGTTAAAAAT-GGAATTTTTGAAAGTTGA-GG-GT
* * * *
23239 CAAAAATGGAATTTTTGGAAGTTACG-GCGTCAAAAATGGAATTTTTGAAAGTTTAGGGGT
1 -AAAAATGTAATTTTTGGAAGTTTCGAG-GTTAAAAATGGAATTTTTGAAAGTTGA-GGGT
* *
23299 AAAAATGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTCTTG-AAGTTCGAGTGT
1 AAAAATGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGAAAGTT-GAGGGT
23357 AAAAATGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTTGGAAAGTTTG-GGGTT
1 AAAAATGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGAA-TTTTT-GAAAG-TTGAGGG-T
* ** * *
23418 AAAAATGAAATTTTTGGAAAGTTT-GAGGTTAAAAATATAATTTTGGAGAAGTCG-GGGTT
1 AAAAATGTAATTTTTGG-AAGTTTCGAGGTTAAAAATGGAATTTTTGA-AAGTTGAGGG-T
* *
23477 AAAAATATAATTTTTAGACAGTTT
1 AAAAATGTAATTTTTGGA-AGTTT
23501 AAGGGCCTCC
Statistics
Matches: 270, Mismatches: 28, Indels: 42
0.79 0.08 0.12
Matches are distributed among these distances:
57 6 0.02
58 86 0.32
59 98 0.36
60 29 0.11
61 43 0.16
62 8 0.03
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (58 bp):
AAAAATGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGAAAGTTGAGGGT
Found at i:25142 original size:15 final size:15
Alignment explanation
Indices: 25124--25161 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
25114 GTTTGGGCCT
25124 ATTTGGGCCA-TTGTA
1 ATTTGGGCCATTTG-A
*
25139 ATTTGGGTCATTTGA
1 ATTTGGGCCATTTGA
25154 ATTTGGGC
1 ATTTGGGC
25162 TCAATTGGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.42
Consensus pattern (15 bp):
ATTTGGGCCATTTGA
Found at i:25247 original size:18 final size:17
Alignment explanation
Indices: 25209--25321 Score: 111
Period size: 17 Copynumber: 6.4 Consensus size: 17
25199 CTTTATTTAT
* *
25209 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
25226 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
25244 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
*
25261 TTTAAATTTTAAAACAAA
1 TTTAAA-TTTAAAATAAA
*
25279 TTTATAAATTTTAAAACAAA
1 -TT-TAAA-TTTAAAATAAA
25299 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
25316 TTTAAA
1 TTTAAA
25322 ATGAGTTTGA
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
16 1 0.01
17 36 0.44
18 25 0.30
19 4 0.05
20 16 0.20
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:25288 original size:20 final size:20
Alignment explanation
Indices: 25263--25302 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
25253 AAATTAAATT
25263 TAAATTTTAAAACAAATTTA
1 TAAATTTTAAAACAAATTTA
25283 TAAATTTTAAAACAAATTTA
1 TAAATTTTAAAACAAATTTA
25303 ATCTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATTTTAAAACAAATTTA
Found at i:27760 original size:21 final size:20
Alignment explanation
Indices: 27713--27764 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
27703 ATTTTTTCAG
*
27713 TTATTTAAATTAATAATTTT
1 TTATTTAAATTAATAATTAT
* *
27733 TTAATTTGAATTTAATTATTAT
1 TT-ATTT-AAATTAATAATTAT
27755 TTATTTAAAT
1 TTATTTAAAT
27765 AATTTATTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 5 0.19
21 8 0.31
22 13 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATTTAAATTAATAATTAT
Found at i:28968 original size:22 final size:21
Alignment explanation
Indices: 28943--28993 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
28933 TATTATAATA
* *
28943 ATTTAAGTTTAATATTGAATCT
1 ATTTAA-TTTAAAATTCAATCT
28965 ATTTAATTTAAAATTCAATC-
1 ATTTAATTTAAAATTCAATCT
28985 ATTATAATT
1 ATT-TAATT
28994 GTTTATGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.12
21 17 0.65
22 6 0.23
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (21 bp):
ATTTAATTTAAAATTCAATCT
Found at i:32064 original size:6 final size:6
Alignment explanation
Indices: 32039--32083 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
32029 ATAATTCATA
* * *
32039 TCACTT TCAATT ACAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
32084 ATTTTGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:46195 original size:14 final size:15
Alignment explanation
Indices: 46151--46210 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 15
46141 ATAATTTTTT
*
46151 TAAAAAAATT-AT-A
1 TAAAAATATTAATCA
* **
46164 TAAAAATATGAAAAA
1 TAAAAATATTAATCA
46179 TAAAAAT-TTAATCA
1 TAAAAATATTAATCA
*
46193 TAAAAATATTAATTA
1 TAAAAATATTAATCA
46208 TAA
1 TAA
46211 TTTTAAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 8 0.22
14 12 0.32
15 17 0.46
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
TAAAAATATTAATCA
Done.