Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001871.1 Kokia drynarioides strain JFW-HI SEQ_113636, 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: 69444
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 36 characters in sequence are not A, C, G, or T
Found at i:6236 original size:19 final size:18
Alignment explanation
Indices: 6212--6255 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
6202 TTTTCAGAAA
*
6212 AAAAAAATTAATATAGTTT
1 AAAAAAATGAAT-TAGTTT
*
6231 AAAAAAATGAATTATTTT
1 AAAAAAATGAATTAGTTT
6249 AAAAAAA
1 AAAAAAA
6256 ATTCTGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
AAAAAAATGAATTAGTTT
Found at i:6256 original size:19 final size:20
Alignment explanation
Indices: 6211--6257 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
6201 CTTTTCAGAA
*
6211 AAAAAAAATTAATATAGTTT
1 AAAAAAAATGAATATAGTTT
*
6231 -AAAAAAATGAAT-TATTTT
1 AAAAAAAATGAATATAGTTT
6249 AAAAAAAAT
1 AAAAAAAAT
6258 TCTGATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (20 bp):
AAAAAAAATGAATATAGTTT
Found at i:6688 original size:24 final size:25
Alignment explanation
Indices: 6654--6704 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
6644 TAAAATTTTA
6654 TTATAAATTCTTATAATAT-ATATTT
1 TTATAAATTCTTATAAT-TCATATTT
*
6679 TTAT-AATTCTTCTAATTCATATTT
1 TTATAAATTCTTATAATTCATATTT
6703 TT
1 TT
6705 TATATTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 1 0.04
24 19 0.79
25 4 0.17
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATAAATTCTTATAATTCATATTT
Found at i:6705 original size:25 final size:23
Alignment explanation
Indices: 6648--6708 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 23
6638 ATTTTTTAAA
6648 ATTTTATTATAAATTCTTATAATAT
1 ATTTT-TTAT-AATTCTTATAATAT
*
6673 ATATTTTTATAATTCTTCTAATTCAT
1 AT-TTTTTATAATTCTTATAA-T-AT
6699 ATTTTTTATA
1 ATTTTTTATA
6709 TTAATAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 10 0.31
25 15 0.47
26 7 0.22
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (23 bp):
ATTTTTTATAATTCTTATAATAT
Found at i:6853 original size:7 final size:7
Alignment explanation
Indices: 6819--6853 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
6809 TGGGCCATTC
*
6819 CAGCAGC
1 CAGCAGT
*
6826 CAGCAGC
1 CAGCAGT
6833 CAGCAGT
1 CAGCAGT
6840 CAGCAGT
1 CAGCAGT
6847 CAGCAGT
1 CAGCAGT
6854 GAAGTCTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.34, G:0.29, T:0.09
Consensus pattern (7 bp):
CAGCAGT
Found at i:11255 original size:16 final size:16
Alignment explanation
Indices: 11236--11266 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11226 TAAAAATGTA
*
11236 TTATTAATTAAATTTG
1 TTATTAATAAAATTTG
11252 TTATTAATAAAATTT
1 TTATTAATAAAATTT
11267 TAATATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTATTAATAAAATTTG
Found at i:18707 original size:21 final size:21
Alignment explanation
Indices: 18683--18733 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
18673 GATTTGTATC
*
18683 GATATAAGTGAC-AATTTTACT
1 GATACAAGTGACTAA-TTTACT
*
18704 GATACAAGTGACTCATTTACT
1 GATACAAGTGACTAATTTACT
18725 GATACAAGT
1 GATACAAGT
18734 CTTATCTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (21 bp):
GATACAAGTGACTAATTTACT
Found at i:25151 original size:18 final size:18
Alignment explanation
Indices: 25123--25163 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
25113 CTTTAATATT
25123 AAAATCAATAATAGAACAA
1 AAAATCAATAA-AGAACAA
*
25142 AAAATC-ATAAGGAACAA
1 AAAATCAATAAAGAACAA
25159 AAAAT
1 AAAAT
25164 AGTATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.52
18 4 0.19
19 6 0.29
ACGTcount: A:0.68, C:0.10, G:0.07, T:0.15
Consensus pattern (18 bp):
AAAATCAATAAAGAACAA
Found at i:36612 original size:6 final size:6
Alignment explanation
Indices: 36596--36626 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
36586 GGGAGGAAAT
*
36596 GAAAAA AAAAAA GAAAAA GAAAAA GAAAAA G
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G
36627 TAAAGTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:48424 original size:30 final size:30
Alignment explanation
Indices: 48388--48446 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
48378 GCCACCGGGT
48388 CAGTCTGGATAATAATAGAATTTCAGCCAA
1 CAGTCTGGATAATAATAGAATTTCAGCCAA
48418 CAGTCTGGATAATAATAGAATTTCAGCCA
1 CAGTCTGGATAATAATAGAATTTCAGCCA
48447 TTAACACTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (30 bp):
CAGTCTGGATAATAATAGAATTTCAGCCAA
Found at i:56578 original size:27 final size:27
Alignment explanation
Indices: 56525--56578 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
56515 AAAAAAGGTA
* * **
56525 AATTTAAGGATTAAAATATATTTTTAT
1 AATTTAAGAATTAAAAAATATCATTAT
56552 AATTTAAGAATTAAAAAATATCATTAT
1 AATTTAAGAATTAAAAAATATCATTAT
56579 GCTATTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (27 bp):
AATTTAAGAATTAAAAAATATCATTAT
Found at i:58293 original size:31 final size:30
Alignment explanation
Indices: 58227--58304 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 30
58217 CTTAATAAAA
* * * * *
58227 AAAAGTTATAATTTGATTATTGAATTATTT
1 AAAAGTTTTAATTTAATCATTAAATTATTC
*
58257 GAAAGTTTTAATTTAACTCATTAAATTATTC
1 AAAAGTTTTAATTTAA-TCATTAAATTATTC
*
58288 AAAAGTTTTCATTTAAT
1 AAAAGTTTTAATTTAAT
58305 TCAATGAGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 14 0.36
31 25 0.64
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (30 bp):
AAAAGTTTTAATTTAATCATTAAATTATTC
Found at i:62039 original size:19 final size:19
Alignment explanation
Indices: 62003--62042 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
61993 CCAAAACTCT
** *
62003 CAAAACTTTTTTTTTCTCC
1 CAAAACTTTTACTCTCTCC
62022 CAAAACTTTTACTCTCTCC
1 CAAAACTTTTACTCTCTCC
62041 CA
1 CA
62043 TTATATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.42
Consensus pattern (19 bp):
CAAAACTTTTACTCTCTCC
Found at i:62067 original size:17 final size:17
Alignment explanation
Indices: 62042--62133 Score: 72
Period size: 17 Copynumber: 5.8 Consensus size: 17
62032 ACTCTCTCCC
*
62042 ATTATATTATTTATATT
1 ATTAAATTATTTATATT
62059 ATTAAATTATTTATATT
1 ATTAAATTATTTATATT
*
62076 ATTTATATT-TTTA-A--
1 A-TTAAATTATTTATATT
* *
62090 ATTAAA-T-TTCACATT
1 ATTAAATTATTTATATT
*
62105 -TTATATTATTTATATT
1 ATTAAATTATTTATATT
*
62121 ATTGAATTATTTA
1 ATTAAATTATTTA
62134 ATCATAACGA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
12 4 0.07
13 5 0.08
14 5 0.08
15 1 0.02
16 7 0.12
17 31 0.53
18 6 0.10
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (17 bp):
ATTAAATTATTTATATT
Found at i:62079 original size:26 final size:26
Alignment explanation
Indices: 62043--62093 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
62033 CTCTCTCCCA
62043 TTATATTATTTATATTATTAAATTAT
1 TTATATTATTTATATTATTAAATTAT
*
62069 TTATATTATTTATATTTTTAAATTA
1 TTATATTATTTATATTATTAAATTA
62094 AATTTCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
TTATATTATTTATATTATTAAATTAT
Found at i:64653 original size:30 final size:30
Alignment explanation
Indices: 64619--64681 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
64609 AAATAACACG
*
64619 AAATAGGATAATTAGGTAGATAAGTGATAT
1 AAATAGGATAATTAGGCAGATAAGTGATAT
*
64649 AAATAGGGTAATTAGGCAGATAAGTGATAT
1 AAATAGGATAATTAGGCAGATAAGTGATAT
64679 AAA
1 AAA
64682 AAATAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.27
Consensus pattern (30 bp):
AAATAGGATAATTAGGCAGATAAGTGATAT
Found at i:64810 original size:28 final size:28
Alignment explanation
Indices: 64787--64851 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
64777 ATTTTTGGGT
* *
64787 AATCGGGGGCAAAATGATAATTTTAGAC
1 AATCGAGGGCAAAATGATAATTTTGGAC
* * *
64815 ACTCGAGGGCAAAATGGTAATTTTGGAAA
1 AATCGAGGGCAAAATGATAATTTTGG-AC
64844 AATCGAGG
1 AATCGAGG
64852 TAAAAAATGG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 22 0.73
29 8 0.27
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.23
Consensus pattern (28 bp):
AATCGAGGGCAAAATGATAATTTTGGAC
Found at i:64892 original size:28 final size:29
Alignment explanation
Indices: 64854--65184 Score: 118
Period size: 28 Copynumber: 11.5 Consensus size: 29
64844 AATCGAGGTA
64854 AAAAATGGAATTTTAGGAAGTTCAGGGGT
1 AAAAATGGAATTTTAGGAAGTTCAGGGGT
* * *
64883 -AAAATGGAATTTT-TGAATGTTTAGGGGG
1 AAAAATGGAATTTTAGGAA-GTTCAGGGGT
* * *
64911 AAAAATGATAATTTTTGGTGAA-ATC-GGGGT
1 AAAAATG-GAA-TTTTAG-GAAGTTCAGGGGT
* ** *
64941 CAAAAATGGGATTTTAAAAAGTTCA-AGGT
1 -AAAAATGGAATTTTAGGAAGTTCAGGGGT
* * * *
64970 AAAAATGTAATTTTTGAAAGTTCAAGGGT
1 AAAAATGGAATTTTAGGAAGTTCAGGGGT
* * *
64999 -ATAATGGTAATTTTTGGTAAAATTC--GGGT
1 AAAAATGG-AATTTTAGG--AAGTTCAGGGGT
* * * *
65028 CAAAATGGGA-TTTATGAAAGTTCGGGGGT
1 AAAAATGGAATTTTA-GGAAGTTCAGGGGT
* * *
65057 AAAAATGTAATTTTTGAAAGTTC-GAGGGT
1 AAAAATGGAATTTTAGGAAGTTCAG-GGGT
* * *
65086 -AAAATGTAATTTTTAGTAAAATT-A-GGGT
1 AAAAATGGAA-TTTTAG-GAAGTTCAGGGGT
* * *
65114 CAAAATGGGATTTT-GGAAAGTTTAGGGGT
1 AAAAATGGAATTTTAGG-AAGTTCAGGGGT
* * * *
65143 AAAAATGTAATTTT-TGAAATTTAGGGGT
1 AAAAATGGAATTTTAGGAAGTTCAGGGGT
65171 -AAAATGGTAATTTT
1 AAAAATGG-AATTTT
65185 TGGTGAAATC
Statistics
Matches: 230, Mismatches: 45, Indels: 55
0.70 0.14 0.17
Matches are distributed among these distances:
27 19 0.08
28 87 0.38
29 83 0.36
30 21 0.09
31 17 0.07
33 3 0.01
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAAATGGAATTTTAGGAAGTTCAGGGGT
Found at i:65105 original size:86 final size:87
Alignment explanation
Indices: 64819--65252 Score: 476
Period size: 87 Copynumber: 5.0 Consensus size: 87
64809 TTAGACACTC
* * * *
64819 GAGGGCAAAATGGTAA-TTTTGGAAAAATCGAGGTAAAAAATGGAATTTTAGG-AAGTTCAGGGG
1 GAGGGTAAAATGGTAATTTTTGGTAAAATCG-GGTCAAAAATGGGATTTT-GGAAAGTTCAGGGG
* *
64882 T-AAAATGGAATTTTTGAATGTTTA
64 TAAAAATGTAATTTTTGAAAG-TTA
* * * * ** *
64906 GGGGGAAAAATGATAATTTTTGGTGAAATCGGGGTCAAAAATGGGATTTTAAAAAGTTCA-AGGT
1 GAGGGTAAAATGGTAATTTTTGGTAAAATC-GGGTCAAAAATGGGATTTTGGAAAGTTCAGGGGT
64970 AAAAATGTAATTTTTGAAAGTTCA
65 AAAAATGTAATTTTTGAAAGTT-A
* *
64994 -AGGGTATAATGGTAATTTTTGGTAAAATTCGGGTC-AAAATGGGATTTAT-GAAAGTTCGGGGG
1 GAGGGTAAAATGGTAATTTTTGGTAAAA-TCGGGTCAAAAATGGGATTT-TGGAAAGTTCAGGGG
*
65056 TAAAAATGTAATTTTTGAAAGTTC
64 TAAAAATGTAATTTTTGAAAGTTA
* * *
65080 GAGGGTAAAAT-GTAATTTTTAGTAAAATTAGGGTC-AAAATGGGATTTTGGAAAGTTTAGGGGT
1 GAGGGTAAAATGGTAATTTTTGGTAAAA-TCGGGTCAAAAATGGGATTTTGGAAAGTTCAGGGGT
*
65143 AAAAATGTAATTTTTGAAATTTA
65 AAAAATGTAATTTTTGAAAGTTA
* * * *
65166 G-GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTAAGGGT
1 GAGGGTAAAATGGTAATTTTTGGTAAAATCG-GGTCAAAAATGGGATTTTGGAAAGTTCAGGGGT
65230 -AAAATGTTAATTTTTGGAAAGTT
65 AAAAATG-TAATTTTT-GAAAGTT
65253 TGGGGGTCAT
Statistics
Matches: 298, Mismatches: 34, Indels: 29
0.83 0.09 0.08
Matches are distributed among these distances:
85 12 0.04
86 111 0.37
87 114 0.38
88 60 0.20
89 1 0.00
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (87 bp):
GAGGGTAAAATGGTAATTTTTGGTAAAATCGGGTCAAAAATGGGATTTTGGAAAGTTCAGGGGTA
AAAATGTAATTTTTGAAAGTTA
Found at i:65119 original size:57 final size:56
Alignment explanation
Indices: 64854--65252 Score: 179
Period size: 58 Copynumber: 6.9 Consensus size: 56
64844 AATCGAGGTA
* * * * * * * *
64854 AAAAATGGAATTTTAGGAAGTTCAGGGGTAAAATGGAATTTTTGAATGTTTAGGGGG
1 AAAAATGTAATTTTTGAAAATT-AGGGGTAAAATGTAATTTTTGAAAGTTGAGGGGT
* * ** ** * *
64911 AAAAATGATAATTTTTGGTGAAA-TCGGGGTCAAAAATGGGATTTTAAAAAGTTCA-AGGT
1 AAAAATG-TAATTTTT-G-AAAATTAGGGGT--AAAATGTAATTTTTGAAAGTTGAGGGGT
* * * * *
64970 AAAAATGTAATTTTTGAAAGTTCAAGGGTATAATGGTAATTTTTGGTAAAATT--CGGGT
1 AAAAATGTAATTTTTGAAAATT-AGGGGTAAAAT-GTAATTTTT-G-AAAGTTGAGGGGT
* ** * * *
65028 CAAAATGGGATTTATGAAAGTTCGGGGGTAAAAATGTAATTTTTGAAAGTTCGA-GGGT
1 AAAAATGTAATTTTTGAAAATT-AGGGGT-AAAATGTAATTTTTGAAAGTT-GAGGGGT
** * *
65086 -AAAATGTAATTTTTAGTAAAATTA-GGGTCAAAATGGGATTTTGGAAAGTTTAGGGGT
1 AAAAATGTAATTTTT-G-AAAATTAGGGGT-AAAATGTAATTTTTGAAAGTTGAGGGGT
* *
65143 AAAAATGTAATTTTTGAAATTTAGGGGTAAAATGGTAATTTTTGGTGAAA-TCGA--GGT
1 AAAAATGTAATTTTTGAAAATTAGGGGTAAAAT-GTAA-TTTT--TGAAAGTTGAGGGGT
* * * *
65200 CAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGTTAATTTTTGGAAAGTT
1 -AAAAATGTAATTTTTGAAA-ATTAGGGGTAAAATG-TAATTTTT-GAAAGTT
65253 TGGGGGTCAT
Statistics
Matches: 263, Mismatches: 50, Indels: 57
0.71 0.14 0.15
Matches are distributed among these distances:
56 24 0.09
57 67 0.25
58 104 0.40
59 43 0.16
60 25 0.10
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (56 bp):
AAAAATGTAATTTTTGAAAATTAGGGGTAAAATGTAATTTTTGAAAGTTGAGGGGT
Found at i:65233 original size:29 final size:29
Alignment explanation
Indices: 64854--65253 Score: 136
Period size: 29 Copynumber: 13.8 Consensus size: 29
64844 AATCGAGGTA
* *
64854 AAAAATGGAATTTTAGG-AAGTTCAGGGGT
1 AAAAATGGAATTTT-GGAAAGTTTAAGGGT
* * * *
64883 -AAAATGGAATTTTTGAATGTTTAGGGGG
1 AAAAATGGAATTTTGGAAAGTTTAAGGGT
* **
64911 AAAAATGATAATTTTTGGTGAAA---TCGGGGT
1 AAAAATG-GAA-TTTT-G-GAAAGTTTAAGGGT
* ** *
64941 CAAAAATGGGATTTTAAAAAGTTCAA-GGT
1 -AAAAATGGAATTTTGGAAAGTTTAAGGGT
* * *
64970 AAAAATGTAATTTTTGAAAGTTCAAGGGT
1 AAAAATGGAATTTTGGAAAGTTTAAGGGT
* * *
64999 -ATAATGGTAATTTTTGGTAAA-ATT-CGGGT
1 AAAAATGG-AA-TTTTGG-AAAGTTTAAGGGT
* * ***
65028 CAAAATGGGATTTAT-GAAAGTTCGGGGGT
1 AAAAATGGAATTT-TGGAAAGTTTAAGGGT
* * **
65057 AAAAATGTAATTTTTGAAAGTTCGAGGGT
1 AAAAATGGAATTTTGGAAAGTTTAAGGGT
* * *
65086 -AAAATGTAATTTTTAGTAAA-ATT-AGGGT
1 AAAAATGGAA-TTTT-GGAAAGTTTAAGGGT
* * *
65114 CAAAATGGGATTTTGGAAAGTTTAGGGGT
1 AAAAATGGAATTTTGGAAAGTTTAAGGGT
* * *
65143 AAAAATGTAATTTTTGAAA-TTTAGGGGT
1 AAAAATGGAATTTTGGAAAGTTTAAGGGT
**
65171 -AAAATGGTAATTTTTGGTGAAA--TCGA-GGT
1 AAAAATGG-AA-TTTT-G-GAAAGTTTAAGGGT
65200 CAAAAATGGAATTTTGGAAAGTTTAAGGGT
1 -AAAAATGGAATTTTGGAAAGTTTAAGGGT
*
65230 -AAAATGTTAATTTTTGGAAAGTTT
1 AAAAATG-GAA-TTTTGGAAAGTTT
65254 GGGGGTCATA
Statistics
Matches: 280, Mismatches: 56, Indels: 69
0.69 0.14 0.17
Matches are distributed among these distances:
27 21 0.08
28 92 0.33
29 97 0.35
30 42 0.15
31 25 0.09
33 3 0.01
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAAATGGAATTTTGGAAAGTTTAAGGGT
Found at i:65272 original size:59 final size:57
Alignment explanation
Indices: 65053--65272 Score: 134
Period size: 57 Copynumber: 3.8 Consensus size: 57
65043 GAAAGTTCGG
* * * * *
65053 GGGTAAAAAT-GTAATTTTT-GAAAG-TTCGAGGGTAAAATGTAATTTTTAGTAAAATT-A
1 GGGT-AAAATGGTAATTTTTGGAAAGTTTAG-GGGTCAAATATAA-TTTT-GGAAATTTAA
* * * * *
65110 GGGTCAAAATGG-GA-TTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAATTTAG
1 GGGT-AAAATGGTAATTTTTGGAAAGTTTAGGGGT-CAAATATAATTTTGGAAATTTAA
* * *
65167 GGGTAAAATGGTAATTTTTGGTGAAA---TCGAGGTCAAAAATGGAATTTTGGAAAGTTTAA
1 GGGTAAAATGGTAATTTTT-G-GAAAGTTTAGGGGTCAAATAT--AATTTTGGAAA-TTTAA
* *
65226 GGGTAAAATGTTAATTTTTGGAAAGTTTGGGGGTCATAATATAATTT
1 GGGTAAAATGGTAATTTTTGGAAAGTTTAGGGGTCA-AATATAATTT
65273 CTGGTCAGTT
Statistics
Matches: 128, Mismatches: 19, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
56 20 0.16
57 37 0.29
58 28 0.22
59 28 0.22
60 11 0.09
61 4 0.03
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTTAGGGGTCAAATATAATTTTGGAAATTTAA
Found at i:66504 original size:13 final size:13
Alignment explanation
Indices: 66488--66526 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
66478 TTCTTTTTAT
*
66488 TAATAATTAATAC
1 TAATTATTAATAC
*
66501 TAATTATTAATAA
1 TAATTATTAATAC
*
66514 TTATTATTAATAC
1 TAATTATTAATAC
66527 AGTTATCAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATTATTAATAC
Found at i:66517 original size:10 final size:10
Alignment explanation
Indices: 66484--66524 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
66474 CTTTTTCTTT
66484 TTATTAATAA
1 TTATTAATAA
* *
66494 TTAATACTAA
1 TTATTAATAA
66504 TTATTAATAA
1 TTATTAATAA
*
66514 TTATTATTAA
1 TTATTAATAA
66524 T
1 T
66525 ACAGTTATCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (10 bp):
TTATTAATAA
Found at i:66918 original size:22 final size:22
Alignment explanation
Indices: 66890--66934 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
66880 GAAATTGTAT
66890 ATTGATTTCTTTTGAATGTTCC
1 ATTGATTTCTTTTGAATGTTCC
66912 ATTGATTTCTTTTGAATGTTCC
1 ATTGATTTCTTTTGAATGTTCC
66934 A
1 A
66935 AAAGGTTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (22 bp):
ATTGATTTCTTTTGAATGTTCC
Found at i:67356 original size:12 final size:12
Alignment explanation
Indices: 67339--67392 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 12
67329 ATATTTTTTG
67339 AATTTAAATATA
1 AATTTAAATATA
67351 AATTTAAACT-TA
1 AATTTAAA-TATA
*
67363 AA-TTAAATTTA
1 AATTTAAATATA
* *
67374 AA-ATAAAAATA
1 AATTTAAATATA
67385 AATTTAAA
1 AATTTAAA
67393 ATGAGTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 1 0.03
11 17 0.49
12 16 0.46
13 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
AATTTAAATATA
Found at i:67371 original size:17 final size:17
Alignment explanation
Indices: 67342--67394 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
67332 TTTTTTGAAT
*
67342 TTAAATATAAATTTAAAC
1 TTAAAT-TAAATTTAAAA
67360 TTAAATTAAATTTAAAA
1 TTAAATTAAATTTAAAA
* *
67377 TAAAAATAAATTTAAAA
1 TTAAATTAAATTTAAAA
67394 T
1 T
67395 GAGTTAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 26 0.81
18 6 0.19
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAATTAAATTTAAAA
Found at i:69058 original size:17 final size:17
Alignment explanation
Indices: 69021--69109 Score: 88
Period size: 17 Copynumber: 5.1 Consensus size: 17
69011 CCAAACTCCC
* *
69021 TTTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
*
69039 TTTGAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
69056 TTTAAATTTGTCTTGAA
1 TTTAAATTTATTTTAAA
* *
69073 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
69090 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
69108 TT
1 TT
69110 AAAAAAAATT
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
17 41 0.73
18 15 0.27
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:69064 original size:23 final size:23
Alignment explanation
Indices: 69036--69083 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
69026 ATTTGTTTAA
* *
69036 AAATTTGAATTTATTTTAAATTT
1 AAATTTGAATTGAATTTAAATTT
**
69059 AAATTTGTCTTGAATTTAAATTT
1 AAATTTGAATTGAATTTAAATTT
69082 AA
1 AA
69084 TTTAAGTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (23 bp):
AAATTTGAATTGAATTTAAATTT
Found at i:69097 original size:23 final size:23
Alignment explanation
Indices: 69050--69099 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
69040 TTGAATTTAT
*
69050 TTTAAATTTAAATTTGTCTTGAA
1 TTTAAATTTAAATTTGTCTTAAA
69073 TTTAAATTT-AATTTAAGT-TTAAA
1 TTTAAATTTAAATTT--GTCTTAAA
69096 TTTA
1 TTTA
69100 TTTTCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.21
23 17 0.71
24 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (23 bp):
TTTAAATTTAAATTTGTCTTAAA
Done.