Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003109.1 Kokia drynarioides strain JFW-HI SEQ_115679, 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: 34787
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Warning! 72 characters in sequence are not A, C, G, or T
Found at i:1893 original size:29 final size:28
Alignment explanation
Indices: 1860--2201 Score: 157
Period size: 29 Copynumber: 11.8 Consensus size: 28
1850 AAGTATGCTT
*
1860 GAGGGCAAAATGGTAATTTTGTGATGATC
1 GAGGGTAAAATGGTAATTTT-TGATGATC
* * *
1889 GAGGGTAAAACGGTAATTTTGGA-CATC
1 GAGGGTAAAATGGTAATTTTTGATGATC
*
1916 TAAGGGGTAAAATGGTAATTTTTGGAT-ACTC
1 -GA-GGGTAAAATGGTAATTTTT-GATGA-TC
* * *
1947 GTGGGCT-AAATGGTAATTTTTGAAAAGTTC
1 GAGGG-TAAAATGGTAATTTTTG--ATGATC
* *
1977 GA-GATCAAAAAT-GTAATTTTTGGATGTTC
1 GAGGGT--AAAATGGTAATTTTT-GATGATC
* *
2006 GGGGGTAAAATGGTAATTTTTTGATGTTC
1 GAGGGTAAAATGGTAA-TTTTTGATGATC
* * *
2035 GAGGGTAAAATGATAATTTTTGGA-AAGTT
1 GAGGGTAAAATGGTAATTTTT-GATGA-TC
* * * * *
2064 TAGAGTTAAAATGGAAATTTTTAGAAGTTC
1 GAG-GGTAAAATGGTAATTTTT-GATGATC
*
2094 G-GGGTCAAAAAT-GTACTTTTTGGAT-ATCC
1 GAGGGT--AAAATGGTAATTTTT-GATGAT-C
* *
2123 GA-GGTAAAATGGTAATTTTTGGAAGTTC
1 GAGGGTAAAATGGTAATTTTT-GATGATC
* * * *
2151 GAGGGTAAAATGATAATTTTTGAAAGTTT
1 GAGGGTAAAATGGTAATTTTTG-ATGATC
2180 GAGGGTAAAAAT-GTAATTTTTG
1 GAGGGT-AAAATGGTAATTTTTG
2202 GAAGTTTAAG
Statistics
Matches: 242, Mismatches: 42, Indels: 58
0.71 0.12 0.17
Matches are distributed among these distances:
27 8 0.03
28 33 0.14
29 142 0.59
30 52 0.21
31 7 0.03
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (28 bp):
GAGGGTAAAATGGTAATTTTTGATGATC
Found at i:2015 original size:88 final size:83
Alignment explanation
Indices: 1919--2203 Score: 254
Period size: 88 Copynumber: 3.3 Consensus size: 83
1909 GGACATCTAA
1919 GGGGT-AAAATGGTAATTTTTGGATACTCGTGGGCT-AAATGGTAATTTTTGAAAAGTTCGAGAT
1 GGGGTAAAAAT-GTAATTTTTGGATA-TCG-GGG-TAAAATGGTAATTTTTG-AAAGTTCGAGAT
*
1982 CAAAAATGTAATTTTTGGATGTTCG
61 --AAAATGTAATTTTTGGAAGTTCG
* * * * *
2007 GGGGT-AAAATGGTAATTTTTTGATGTTCGAGGGTAAAATGATAATTTTTGGAAAGTTTAGAGTT
1 GGGGTAAAAAT-GTAATTTTTGGAT-ATCG-GGGTAAAATGGTAATTTTT-GAAAG-TTCGAGAT
* *
2071 AAAATGGAAATTTTTAGAAGTTC-
61 AAAAT-GTAATTTTTGGAAGTTCG
* * * *
2094 GGGGTCAAAAATGTACTTTTTGGATATCCGAGGTAAAATGGTAATTTTTGGAAGTTCGAGGGTAA
1 GGGGT-AAAAATGTAATTTTTGGATAT-CGGGGTAAAATGGTAATTTTTGAAAGTTCGA-GATAA
* *
2159 AATGATAATTTTTGAAAGTTTG
63 AATG-TAATTTTTGGAAGTTCG
*
2181 AGGGTAAAAATGTAATTTTTGGA
1 GGGGTAAAAATGTAATTTTTGGA
2204 AGTTTAAGGG
Statistics
Matches: 163, Mismatches: 23, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
85 5 0.03
86 40 0.25
87 33 0.20
88 73 0.45
89 12 0.07
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (83 bp):
GGGGTAAAAATGTAATTTTTGGATATCGGGGTAAAATGGTAATTTTTGAAAGTTCGAGATAAAAT
GTAATTTTTGGAAGTTCG
Found at i:2074 original size:59 final size:59
Alignment explanation
Indices: 1954--2259 Score: 272
Period size: 59 Copynumber: 5.2 Consensus size: 59
1944 CTCGTGGGCT
* * * ** * *
1954 AAATGGTAATTTTTGAAAAGTTCGA-GATCAAAAATGTAATTTTTGG-ATGTTCGGGGGTA
1 AAATGGTAATTTTTG-GAAGTTCGAGGGT-AAAAATGTAATTTTTGGAAAGTTTAGAGTTA
* *
2013 AAATGGTAATTTTTTGATGTTCGAGGGT-AAAATGATAATTTTTGGAAAGTTTAGAGTTA
1 AAATGGTAATTTTTGGAAGTTCGAGGGTAAAAATG-TAATTTTTGGAAAGTTTAGAGTTA
* * * * ** *
2072 AAATGGAAATTTTTAGAAGTTCG-GGGTCAAAAATGTACTTTTTGGATA--TCCGAGGTA
1 AAATGGTAATTTTTGGAAGTTCGAGGGT-AAAAATGTAATTTTTGGAAAGTTTAGAGTTA
* *
2129 AAATGGTAATTTTTGGAAGTTCGAGGGT-AAAATGATAATTTTT-GAAAGTTTGAGGGTAA
1 AAATGGTAATTTTTGGAAGTTCGAGGGTAAAAATG-TAATTTTTGGAAAGTTT-AGAGTTA
** * * *
2188 AAAT-GTAATTTTTGGAAGTTTAAGGGTAAAAATGTAATTTTTGAAAAGTTTATGGGTCA
1 AAATGGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTA-GAGTTA
2247 AAAT-GTAATTTTT
1 AAATGGTAATTTTT
2260 CGAAAGTTTG
Statistics
Matches: 204, Mismatches: 30, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
56 9 0.04
57 40 0.20
58 56 0.27
59 93 0.46
60 6 0.03
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.38
Consensus pattern (59 bp):
AAATGGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTAGAGTTA
Found at i:2206 original size:29 final size:28
Alignment explanation
Indices: 1920--2259 Score: 246
Period size: 29 Copynumber: 11.6 Consensus size: 28
1910 GACATCTAAG
* *
1920 GGGTAAAATGGTAATTTTTGGATA-CTCGT
1 GGGTAAAAT-GTAATTTTTGGA-AGTTCGA
*
1949 GGGCT-AAATGGTAATTTTTGAAAAGTTCGA
1 GGG-TAAAAT-GTAATTTTTG-GAAGTTCGA
* * *
1979 -GATCAAAAATGTAATTTTTGGATGTTCGG
1 GGGT--AAAATGTAATTTTTGGAAGTTCGA
* *
2008 GGGTAAAATGGTAATTTTTTGATGTTCGA
1 GGGTAAAAT-GTAATTTTTGGAAGTTCGA
*
2037 GGGTAAAATGATAATTTTTGGAAAGTT-TA
1 GGGTAAAATG-TAATTTTTGG-AAGTTCGA
* * *
2066 GAGTTAAAATGGAAATTTTTAGAAGTTCG-
1 G-GGTAAAAT-GTAATTTTTGGAAGTTCGA
* *
2095 GGGTCAAAAATGTACTTTTTGGATA-TCCGA
1 GGGT--AAAATGTAATTTTTGGA-AGTTCGA
2125 -GGTAAAATGGTAATTTTTGGAAGTTCGA
1 GGGTAAAAT-GTAATTTTTGGAAGTTCGA
* *
2153 GGGTAAAATGATAATTTTTGAAAGTTTGA
1 GGGTAAAATG-TAATTTTTGGAAGTTCGA
**
2182 GGGTAAAAATGTAATTTTTGGAAGTTTAA
1 GGGT-AAAATGTAATTTTTGGAAGTTCGA
* *
2211 GGGTAAAAATGTAATTTTTGAAAAGTT-TA
1 GGGT-AAAATGTAATTTTTG-GAAGTTCGA
2240 TGGGTCAAAATGTAATTTTT
1 -GGGT-AAAATGTAATTTTT
2260 CGAAAGTTTG
Statistics
Matches: 256, Mismatches: 31, Indels: 47
0.77 0.09 0.14
Matches are distributed among these distances:
27 6 0.02
28 25 0.10
29 149 0.58
30 71 0.28
31 5 0.02
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (28 bp):
GGGTAAAATGTAATTTTTGGAAGTTCGA
Found at i:2250 original size:145 final size:144
Alignment explanation
Indices: 1984--2259 Score: 355
Period size: 145 Copynumber: 1.9 Consensus size: 144
1974 TTCGAGATCA
* * * *
1984 AAAATGTAATTTTTGGATGTTCGGGGGTAAAATGGTAATTTTTTGATGTTCGAGGGTAAAATGAT
1 AAAATGTAATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTTGAAGTTCGAGGGTAAAATGAT
* * * *
2049 AATTTTTGGAAAGTTTAGAGTTAAAATGGAAATTTTTAGAAGTTCGGGGTCAAAAATGTACTTTT
66 AATTTTTGGAAAGTTTAGAGTAAAAATGGAAATTTTTAAAAGTTAGGGGTCAAAAATGTAATTTT
2114 TGGATATCCGAGGT
131 TGGATATCCGAGGT
*
2128 AAAATGGTAATTTTTGGAAGTTCGAGGGTAAAATGATAA-TTTTTGAAAGTTTGAGGGTAAAAAT
1 AAAAT-GTAATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTTG-AAGTTCGAGGGT-AAAAT
* * *
2192 G-TAATTTTTGG-AAGTTTAAGGGTAAAAAT-GTAATTTTTGAAAAGTTTATGGGTC-AAAATGT
63 GATAATTTTTGGAAAGTTT-AGAGTAAAAATGGAAATTTTT-AAAAG-TTAGGGGTCAAAAATGT
2253 AATTTTT
125 AATTTTT
2260 CGAAAGTTTG
Statistics
Matches: 114, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
144 25 0.22
145 76 0.67
146 13 0.11
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (144 bp):
AAAATGTAATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTTGAAGTTCGAGGGTAAAATGAT
AATTTTTGGAAAGTTTAGAGTAAAAATGGAAATTTTTAAAAGTTAGGGGTCAAAAATGTAATTTT
TGGATATCCGAGGT
Found at i:3892 original size:17 final size:17
Alignment explanation
Indices: 3870--3938 Score: 102
Period size: 17 Copynumber: 4.1 Consensus size: 17
3860 CATTTTTAAT
*
3870 TAAATTCAAATTTAAAA
1 TAAATTTAAATTTAAAA
3887 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
3904 TAAATTTGAACTTAAAA
1 TAAATTTAAATTTAAAA
*
3921 TAAATTAAAATTTAAAA
1 TAAATTTAAATTTAAAA
3938 T
1 T
3939 TAAACTTGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:3896 original size:6 final size:6
Alignment explanation
Indices: 3869--3942 Score: 55
Period size: 6 Copynumber: 12.8 Consensus size: 6
3859 ACATTTTTAA
* * * * *
3869 TTAAAT TCAAAT TTAAA- ATAAAT TTAAAT TTAAA- ATAAAT TTGAAC
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * *
3915 TTAAA- ATAAAT TAAAAT TTAAAA TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
3943 CTTGATTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
5 12 0.24
6 39 0.76
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:4187 original size:4 final size:5
Alignment explanation
Indices: 4164--4192 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
4154 TGCTTTGGTA
4164 TTATT TTATT TTATT TTA-T TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT
4193 ATTACTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:8622 original size:66 final size:66
Alignment explanation
Indices: 8540--8665 Score: 243
Period size: 66 Copynumber: 1.9 Consensus size: 66
8530 TAACCTAAAT
*
8540 ATATGGGGTATGAGTATAAGATTAGGGTCATGAAAGGTCAATTTAGTGTAGAGGGGTAAAGACAA
1 ATATGGGGTATGAGTATAAGATTAGGGTCATGAAAGGTCAATTTAGTGTAGAGAGGTAAAGACAA
8605 C
66 C
8606 ATATGGGGTATGAGTATAAGATTAGGGTCATGAAAGGTCAATTTAGTGTAGAGAGGTAAA
1 ATATGGGGTATGAGTATAAGATTAGGGTCATGAAAGGTCAATTTAGTGTAGAGAGGTAAA
8666 AATTTTACTA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.27
Consensus pattern (66 bp):
ATATGGGGTATGAGTATAAGATTAGGGTCATGAAAGGTCAATTTAGTGTAGAGAGGTAAAGACAA
C
Found at i:15733 original size:42 final size:42
Alignment explanation
Indices: 15679--15772 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 42
15669 AATAAAAATT
*
15679 TTATTTAAATTATCATTTGGATTGAAATAATGTTATTTTTTA
1 TTATTTAAATTATCATTTGAATTGAAATAATGTTATTTTTTA
*
15721 TTATTTATATTATCATTTGAATTGAAATAATGTTATTTTTTA
1 TTATTTAAATTATCATTTGAATTGAAATAATGTTATTTTTTA
15763 TTATTTAAAT
1 TTATTTAAAT
15773 AATTTTAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.56
Consensus pattern (42 bp):
TTATTTAAATTATCATTTGAATTGAAATAATGTTATTTTTTA
Found at i:15903 original size:22 final size:22
Alignment explanation
Indices: 15871--15914 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
15861 GATTAATAAA
*
15871 ATTGTAAAAAT-ATTAATTTTT
1 ATTGTAAAAATAAGTAATTTTT
15892 ATTGTTAAAAATAAGTAATTTTT
1 ATTG-TAAAAATAAGTAATTTTT
15915 TATTATTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (22 bp):
ATTGTAAAAATAAGTAATTTTT
Found at i:19925 original size:23 final size:23
Alignment explanation
Indices: 19893--19996 Score: 77
Period size: 23 Copynumber: 4.4 Consensus size: 23
19883 ACACTAGCGA
* *
19893 GCTCTTTGTTTAGCAC-GTCTTGT
1 GCTCTCTGTTTAGCACTGT-GTGT
* *
19916 GCTTTCTGTTATTAGCACTGTTTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* * *
19941 GTTATCTGATTAGCACT-TCGTGT
1 GCTCTCTGTTTAGCACTGT-GTGT
* *
19964 ACTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
19987 GCTCTCTGTT
1 GCTCTCTGTT
19997 GCCCAGGAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
22 1 0.02
23 43 0.66
24 2 0.03
25 17 0.26
26 2 0.03
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.46
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:23233 original size:77 final size:79
Alignment explanation
Indices: 23091--23245 Score: 260
Period size: 78 Copynumber: 2.0 Consensus size: 79
23081 ATTTTCAACT
* * *
23091 ACTCTTCCATTTTGATTTATTGTTTATAGGATAGTATATTTTGGTGCCTTAATCTGACTGTATAG
1 ACTCTCCCATTTAGATTTATTGTTTATAGGATAGTATATTTTGGTGCCTTAATCTGACTGCATAG
*
23156 C-CTAAATTCATTC
66 CAATAAATTCATTC
23169 ACTCTCCCATTTAGATTTATTGTTTATAGGATA-TATATTTTGGTGCCTTAATCTGACTGCATAG
1 ACTCTCCCATTTAGATTTATTGTTTATAGGATAGTATATTTTGGTGCCTTAATCTGACTGCATAG
23233 CAATAAATTCATT
66 CAATAAATTCATT
23246 GATGAATGAA
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
77 31 0.43
78 41 0.57
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (79 bp):
ACTCTCCCATTTAGATTTATTGTTTATAGGATAGTATATTTTGGTGCCTTAATCTGACTGCATAG
CAATAAATTCATTC
Found at i:26252 original size:31 final size:31
Alignment explanation
Indices: 26209--26296 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
26199 TTAGATGGGG
* * *
26209 GCTAGTAAATTTAGAGTTTGATCACTTAA-GA
1 GCTAATAAATTTATA-TTTGATCACTCAACGA
* *
26240 GCTAATAAATTTATATTTAATCACTCAACTA
1 GCTAATAAATTTATATTTGATCACTCAACGA
*
26271 -TTAATAAATTTATAATTTGATCACTC
1 GCTAATAAATTTAT-ATTTGATCACTC
26297 CCAATGTAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 23 0.48
31 25 0.52
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (31 bp):
GCTAATAAATTTATATTTGATCACTCAACGA
Found at i:28324 original size:26 final size:27
Alignment explanation
Indices: 28276--28326 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
28266 TTGCAGTCTA
*
28276 GTGATGAAGAAGAGATAGGAGAAGATG
1 GTGATGAAGAAGAGATAGAAGAAGATG
28303 GTGA-GAAGAAGAGGA-AGAAGAAGA
1 GTGATGAAGAAGA-GATAGAAGAAGA
28327 AGGAGAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.41, T:0.10
Consensus pattern (27 bp):
GTGATGAAGAAGAGATAGAAGAAGATG
Found at i:30242 original size:91 final size:91
Alignment explanation
Indices: 30131--30325 Score: 227
Period size: 91 Copynumber: 2.1 Consensus size: 91
30121 AAAAAAAGAG
* * **
30131 TAGGTGCCAAATTAGAAAAAAAAGGGTCAAGTTCATG-TA-CGAAATTGGACCCCAAAA-AATTT
1 TAGGTACCAAATTAGAAAAAAAAAGGTCAAGTT--TGATATC-AAATTGGACCAAAAAATAATTT
*
30193 AAGTACCAACTTA-AAAAAAGTGTCAAGTT
63 AAGTACCAAATTAGAAAAAA-TGTCAAGTT
* **
30222 TAGGTACCAAATTAGGAAAAAAAATTTCAAGTTTGACTATCAAATTGGACCAAAAAATAATTTAA
1 TAGGTACCAAATTAGAAAAAAAAAGGTCAAGTTTGA-TATCAAATTGGACCAAAAAATAATTTAA
*
30287 GTACCAAATTAGGAAAAATGTCAAGTT
65 GTACCAAATTAGAAAAAATGTCAAGTT
*
30314 CAGGTACCAAAT
1 TAGGTACCAAAT
30326 GTTATATTAA
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
89 2 0.02
91 44 0.49
92 38 0.43
93 5 0.06
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (91 bp):
TAGGTACCAAATTAGAAAAAAAAAGGTCAAGTTTGATATCAAATTGGACCAAAAAATAATTTAAG
TACCAAATTAGAAAAAATGTCAAGTT
Found at i:30244 original size:33 final size:32
Alignment explanation
Indices: 30205--30325 Score: 96
Period size: 33 Copynumber: 3.9 Consensus size: 32
30195 GTACCAACTT
30205 AAAAAAAGTGTCAAGTTTAGGTACCAAATTAGG
1 AAAAAAA-TGTCAAGTTTAGGTACCAAATTAGG
* * *
30238 AAAAAAAATTTCAAGTTT-GACTATCAAATT-GG
1 -AAAAAAATGTCAAGTTTAG-GTACCAAATTAGG
*
30270 ACCAAAAAA--T-AA-TTTAAGTACCAAATTAGG
1 A--AAAAAATGTCAAGTTTAGGTACCAAATTAGG
*
30300 --AAAAATGTCAAGTTCAGGTACCAAAT
1 AAAAAAATGTCAAGTTTAGGTACCAAAT
30326 GTTATATTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
26 5 0.07
28 1 0.01
29 13 0.19
30 16 0.23
31 2 0.03
32 3 0.04
33 23 0.33
34 7 0.10
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.26
Consensus pattern (32 bp):
AAAAAAATGTCAAGTTTAGGTACCAAATTAGG
Found at i:30609 original size:32 final size:32
Alignment explanation
Indices: 30563--30625 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
30553 TTAGTACACG
*
30563 TAAGAGAATGCTGGCGTGGCATATATGCCACA
1 TAAGAGAATGCTGGCATGGCATATATGCCACA
*
30595 TAAGTGAATGCTGGCATGGCATATATGCCAC
1 TAAGAGAATGCTGGCATGGCATATATGCCAC
30626 GTCAGCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (32 bp):
TAAGAGAATGCTGGCATGGCATATATGCCACA
Found at i:31726 original size:18 final size:17
Alignment explanation
Indices: 31701--31734 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31691 AAAAATTATA
31701 TTATTTTTAAATTTAAT
1 TTATTTTTAAATTTAAT
*
31718 TTATATTTTAAGTTTAA
1 TTAT-TTTTAAATTTAA
31735 AATTTTTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTATTTTTAAATTTAAT
Found at i:32896 original size:16 final size:17
Alignment explanation
Indices: 32870--32901 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
32860 TTAAAATTAT
32870 ATTTTTGTTATTATATG
1 ATTTTTGTTATTATATG
32887 ATTTTT-TTATTATAT
1 ATTTTTGTTATTATAT
32902 TAATAACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (17 bp):
ATTTTTGTTATTATATG
Found at i:34059 original size:20 final size:20
Alignment explanation
Indices: 34034--34077 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
34024 TTTTTCAAAT
34034 AATTATAAAACA-ATATTAAA
1 AATTATAAAA-ATATATTAAA
*
34054 AATTATAAAAATATTTTAAA
1 AATTATAAAAATATATTAAA
34074 AATT
1 AATT
34078 GAAAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTATAAAAATATATTAAA
Found at i:34068 original size:18 final size:18
Alignment explanation
Indices: 34034--34094 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 18
34024 TTTTTCAAAT
34034 AATTATAAAACAATATTAAA
1 AATTAT-AAA-AATATTAAA
34054 AATTATAAAAATATTTTAAA
1 AATTATAAAAATA--TTAAA
* *
34074 AA-T-TGAAAATATTTAA
1 AATTATAAAAATATTAAA
34090 AATTA
1 AATTA
34095 ATCTTAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
16 6 0.17
17 1 0.03
18 11 0.31
19 4 0.11
20 13 0.37
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
AATTATAAAAATATTAAA
Done.