Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012473.1 Kokia drynarioides strain JFW-HI SEQ_127477, 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: 34307
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 75 characters in sequence are not A, C, G, or T
Found at i:422 original size:6 final size:6
Alignment explanation
Indices: 413--459 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
403 CCCTGGTCTA
*
413 AGCCCT AGCCCT AGCCCT AGCCCT AGCCCT AGCCCT AGCCTT AGCCC
1 AGCCCT AGCCCT AGCCCT AGCCCT AGCCCT AGCCCT AGCCCT AGCCC
460 AACCCATACC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.17, C:0.49, G:0.17, T:0.17
Consensus pattern (6 bp):
AGCCCT
Found at i:2911 original size:17 final size:17
Alignment explanation
Indices: 2888--2950 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
2878 GCCCAACAGG
2888 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* * *
2905 GTTTAAATTTACTTAAA
1 ATTTAAATTTATTTTAA
*
2922 ATTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
2939 ATTTAAAGTTTA
1 ATTTAAA-TTTA
2951 AATCTATCTA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 34 0.89
18 4 0.11
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:2952 original size:7 final size:6
Alignment explanation
Indices: 2888--2953 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
2878 GCCCAACAGG
* * * *
2888 ATTTAA ATTT-A TTTTAA GTTTAA ATTT-A CTTAAA ATTTAA ATTT--
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
2932 ATTATAA ATTTAA AGTTTAA AT
1 ATT-TAA ATTTAA A-TTTAA AT
2954 CTATCTAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
4 3 0.06
5 8 0.17
6 27 0.57
7 9 0.19
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:4841 original size:29 final size:29
Alignment explanation
Indices: 4800--5049 Score: 249
Period size: 30 Copynumber: 8.5 Consensus size: 29
4790 AAACTGTTCG
* *
4800 AAAATTCTATTTTTACCCTCGAACTTCTA
1 AAAATTCCATTTTTACCCTCAAACTTCTA
* * *
4829 AAAATCCCATTTTTTACCCTAAAACTTTTA
1 AAAATTCCA-TTTTTACCCTCAAACTTCTA
4859 AAAATTCCATTTTTACCCTCAAACTT-TCA
1 AAAATTCCATTTTTACCCTCAAACTTCT-A
** * *
4888 AAAATTCCATTTTTAACCCAAAAACTTATG
1 AAAATTCCATTTTT-ACCCTCAAACTTCTA
*
4918 AAAATTCCATTTTTA-CCTCGAACTTCTA
1 AAAATTCCATTTTTACCCTCAAACTTCTA
** *
4946 AAAAACCCATTTTTGACCC-CAAAACTTCCA
1 AAAATTCCATTTTT-ACCCTC-AAACTTCTA
4976 AAAATTCCATTTTTTA-CCTCGAAACTT-TCA
1 AAAATTCCA-TTTTTACCCTC-AAACTTCT-A
* *
5006 AAAATTCCATTTTTACCCCTCGAACTTCCA
1 AAAATTCCATTTTTA-CCCTCAAACTTCTA
5036 AAAATTCCATTTTT
1 AAAATTCCATTTTT
5050 GACACCAAAA
Statistics
Matches: 183, Mismatches: 25, Indels: 25
0.79 0.11 0.11
Matches are distributed among these distances:
28 21 0.11
29 49 0.27
30 103 0.56
31 10 0.05
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCTCAAACTTCTA
Found at i:4884 original size:59 final size:58
Alignment explanation
Indices: 4800--5066 Score: 263
Period size: 59 Copynumber: 4.5 Consensus size: 58
4790 AAACTGTTCG
* * **
4800 AAAATTCTATTTTTACCCTCGAAC-TTCTAAAAATCCCATTTTTTACCCTAAAACTTTTA
1 AAAATTCCATTTTTA-CCTCAAACTTTC-AAAAATCCCATTTTTTACCCTAAAACTTCCA
* * * ***
4859 AAAATTCCATTTTTACCCTCAAACTTTCAAAAATTCCATTTTTAACCCAAAAACTTATG
1 AAAATTCCATTTTTA-CCTCAAACTTTCAAAAATCCCATTTTTTACCCTAAAACTTCCA
* * * *
4918 AAAATTCCATTTTTACCTCGAAC-TTCTAAAAAACCCATTTTTGACCCCAAAACTTCCA
1 AAAATTCCATTTTTACCTCAAACTTTC-AAAAATCCCATTTTTTACCCTAAAACTTCCA
* **
4976 AAAATTCCATTTTTTACCTCGAAACTTTCAAAAATTCCA-TTTTTACCCCTCGAACTTCCA
1 AAAATTCCA-TTTTTACCTC-AAACTTTCAAAAATCCCATTTTTTA-CCCTAAAACTTCCA
5036 AAAATTCCATTTTTGACAC-CAAAACTTTCAA
1 AAAATTCCATTTTT-AC-CTC-AAACTTTCAA
5067 CAATTACCAT
Statistics
Matches: 177, Mismatches: 23, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
57 3 0.02
58 40 0.23
59 83 0.47
60 47 0.27
61 4 0.02
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (58 bp):
AAAATTCCATTTTTACCTCAAACTTTCAAAAATCCCATTTTTTACCCTAAAACTTCCA
Found at i:5062 original size:30 final size:29
Alignment explanation
Indices: 4800--5079 Score: 233
Period size: 30 Copynumber: 9.4 Consensus size: 29
4790 AAACTGTTCG
* ** *
4800 AAAATTCTATTTTTACCCTCGAACTTCTA
1 AAAATTCCATTTTTACCCTAAAACTTCCA
* **
4829 AAAATCCCATTTTTTACCCTAAAACTTTTA
1 AAAATTCCA-TTTTTACCCTAAAACTTCCA
* *
4859 AAAATTCCATTTTTACCCTCAAACTTTCA
1 AAAATTCCATTTTTACCCTAAAACTTCCA
* ***
4888 AAAATTCCATTTTTAACCCAAAAACTTATG
1 AAAATTCCATTTTT-ACCCTAAAACTTCCA
** *
4918 AAAATTCCATTTTTA-CCTCGAACTTCTA
1 AAAATTCCATTTTTACCCTAAAACTTCCA
** *
4946 AAAAACCCATTTTTGACCCCAAAACTTCCA
1 AAAATTCCATTTTT-ACCCTAAAACTTCCA
* *
4976 AAAATTCCATTTTTTA-CCTCGAAACTTTCA
1 AAAATTCCA-TTTTTACCCT-AAAACTTCCA
**
5006 AAAATTCCATTTTTACCCCTCGAACTTCCA
1 AAAATTCCATTTTTA-CCCTAAAACTTCCA
*
5036 AAAATTCCATTTTTGACACC-AAAACTTTCA
1 AAAATTCCATTTTT-AC-CCTAAAACTTCCA
*
5066 ACAATTACCATTTT
1 AAAATT-CCATTTT
5080 GCCCCCGGAT
Statistics
Matches: 204, Mismatches: 36, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
28 20 0.10
29 49 0.24
30 117 0.57
31 18 0.09
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCTAAAACTTCCA
Found at i:5164 original size:28 final size:28
Alignment explanation
Indices: 5122--5226 Score: 81
Period size: 28 Copynumber: 3.7 Consensus size: 28
5112 CTCGAAACCC
*
5122 TCAAAAA-TACAATTTTACCCTCGAATA
1 TCAAAAATTACCATTTTACCCTCGAATA
* *
5149 TCTAAAAATT-CCATTTTTAATCCT-GAATTT
1 TC-AAAAATTACCA-TTTT-ACCCTCGAA-TA
* * *
5179 TCAAAAAATTACCATTTTGCCCCCGAAAA
1 TC-AAAAATTACCATTTTACCCTCGAATA
*
5208 TCCAAAATTACCATTTTAC
1 TCAAAAATTACCATTTTAC
5227 GTCTCGGGTA
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
27 2 0.03
28 22 0.37
29 12 0.20
30 21 0.35
31 3 0.05
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (28 bp):
TCAAAAATTACCATTTTACCCTCGAATA
Found at i:5166 original size:29 final size:29
Alignment explanation
Indices: 4800--5167 Score: 133
Period size: 30 Copynumber: 12.5 Consensus size: 29
4790 AAACTGTTCG
*
4800 AAAATTCTATTTTTACCCTCGAACT-TCTA
1 AAAATTCCATTTTTACCCTCGAA-TATCTA
* ** *
4829 AAAATCCCATTTTTTACCCTAAAACT-TTTA
1 AAAATTCCA-TTTTTACCCTCGAA-TATCTA
* *
4859 AAAATTCCATTTTTACCCTCAAACTTTC-A
1 AAAATTCCATTTTTACCCTCGAA-TATCTA
* * *
4888 AAAATTCCATTTTTAACC-C-AAAAACTTA
1 AAAATTCCATTTTTACCCTCGAATATC-TA
4916 TGAAAATTCCATTTTTA-CCTCGAACT-TCTA
1 --AAAATTCCATTTTTACCCTCGAA-TATCTA
** * *
4946 AAAAACCCATTTTTGACCC-C-AAAACTTCCA
1 AAAATTCCATTTTT-ACCCTCGAATA--TCTA
*
4976 AAAATTCCATTTTTTA-CCTCGAA-ACTTTCA
1 AAAATTCCA-TTTTTACCCTCGAATA-TCT-A
*
5006 AAAATTCCATTTTTACCCCTCGAACT-TCCA
1 AAAATTCCATTTTTA-CCCTCGAA-TATCTA
* * *
5036 AAAATTCCATTTTTGACAC-C-AAAACTTTCA
1 AAAATTCCATTTTT-ACCCTCGAATA-TCT-A
* * * * * *
5066 ACAATTACCA-TTTTGCCCCCGGATGTCCA
1 AAAATT-CCATTTTTACCCTCGAATATCTA
* * *
5095 AAAACTT-CATTTTCAGCCTCGAA-ACCCTCA
1 AAAA-TTCCATTTTTACCCTCGAATA-TCT-A
* *
5125 AAAA-TACAATTTTACCCTCGAATATCTA
1 AAAATTCCATTTTTACCCTCGAATATCTA
5153 AAAATTCCATTTTTA
1 AAAATTCCATTTTTA
5168 ATCCTGAATT
Statistics
Matches: 251, Mismatches: 52, Indels: 72
0.67 0.14 0.19
Matches are distributed among these distances:
26 1 0.00
27 2 0.01
28 26 0.10
29 93 0.37
30 106 0.42
31 23 0.09
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCTCGAATATCTA
Found at i:5212 original size:117 final size:119
Alignment explanation
Indices: 4992--5214 Score: 276
Period size: 117 Copynumber: 1.9 Consensus size: 119
4982 CCATTTTTTA
** * *
4992 CCTCGAAACTTTCAAAAATTCCATTTTTACCCCTCGAACTTCCAAAAATTCCATTTTTGACACCA
1 CCTCGAAACCCTCAAAAATTACAATTTTACCCCTCGAACTTCCAAAAATTCCATTTTTGACACCA
* * **
5057 AAACTTTCAACAATTACCATTTTGCCCCCGGATGTCCAAAAACTTCATTTTCAG
66 AAACTTTCAAAAATTACCATTTTGCCCCCGAAAATCCAAAAACTTCATTTTCAG
*
5111 CCTCGAAACCCTCAAAAA-TACAATTTTA-CCCTCGAA-TATCTAAAAATTCCATTTTT-A-ATC
1 CCTCGAAACCCTCAAAAATTACAATTTTACCCCTCGAACT-TCCAAAAATTCCATTTTTGACA-C
** *
5171 CTGAATTTTCAAAAAATTACCATTTTGCCCCCGAAAATCCAAAA
64 CAAAACTTTC-AAAAATTACCATTTTGCCCCCGAAAATCCAAAA
5215 TTACCATTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
115 1 0.01
116 10 0.11
117 54 0.61
118 8 0.09
119 16 0.18
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.31
Consensus pattern (119 bp):
CCTCGAAACCCTCAAAAATTACAATTTTACCCCTCGAACTTCCAAAAATTCCATTTTTGACACCA
AAACTTTCAAAAATTACCATTTTGCCCCCGAAAATCCAAAAACTTCATTTTCAG
Found at i:5223 original size:117 final size:118
Alignment explanation
Indices: 4976--5224 Score: 262
Period size: 117 Copynumber: 2.1 Consensus size: 118
4966 AAAACTTCCA
* ** * *
4976 AAAATT-CCATTTTTTACCTCGAAACTTTCAAAAATTCCATTTTTACCCCTCGAACTTCCAAAAA
1 AAAATTACCA-TTTTCACCTCGAAACCCTCAAAAATTACAATTTTACCCCTCGAACTTCCAAAAA
* * **
5040 TTCCATTTTTGACACCAAAACTTTCAACAATTACCATTTTGCCCCCGGATGTCC
65 TTCCATTTTTGACACCAAAACTTTCAAAAATTACCATTTTGCCCCCGAAAATCC
*
5094 AAAA--ACTTCATTTTCAGCCTCGAAACCCTCAAAAA-TACAATTTTA-CCCTCGAA-TATCTAA
1 AAAATTAC--CATTTTCA-CCTCGAAACCCTCAAAAATTACAATTTTACCCCTCGAACT-TCCAA
** *
5154 AAATTCCATTTTT-A-ATCCTGAATTTTCAAAAAATTACCATTTTGCCCCCGAAAATCC
62 AAATTCCATTTTTGACA-CCAAAACTTTC-AAAAATTACCATTTTGCCCCCGAAAATCC
5211 AAAATTACCATTTT
1 AAAATTACCATTTT
5225 ACGTCTCGGG
Statistics
Matches: 109, Mismatches: 13, Indels: 19
0.77 0.09 0.13
Matches are distributed among these distances:
115 1 0.01
116 10 0.09
117 61 0.56
118 17 0.16
119 20 0.18
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (118 bp):
AAAATTACCATTTTCACCTCGAAACCCTCAAAAATTACAATTTTACCCCTCGAACTTCCAAAAAT
TCCATTTTTGACACCAAAACTTTCAAAAATTACCATTTTGCCCCCGAAAATCC
Found at i:6295 original size:26 final size:26
Alignment explanation
Indices: 6246--6328 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 26
6236 CCTTGAACTC
* *
6246 TGAA-CCTAAGCTCGAACCCTAAACCT
1 TGAACCCTAAACTCAAACCC-AAACCT
* * *
6272 TGAACCTTAAATTTAAACCCAAA-CT
1 TGAACCCTAAACTCAAACCCAAACCT
6297 TGAAACCCTAAACTCAAACCCAAACCT
1 TG-AACCCTAAACTCAAACCCAAACCT
*
6324 CGAAC
1 TGAAC
6329 TCAAGTTTCA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
25 4 0.09
26 28 0.62
27 13 0.29
ACGTcount: A:0.41, C:0.33, G:0.07, T:0.19
Consensus pattern (26 bp):
TGAACCCTAAACTCAAACCCAAACCT
Found at i:6699 original size:14 final size:14
Alignment explanation
Indices: 6680--6715 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
6670 TAAATGATTA
6680 AAACATAACATTTC
1 AAACATAACATTTC
6694 AAACATAACATTTC
1 AAACATAACATTTC
6708 AAACATAA
1 AAACATAA
6716 GCGACTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (14 bp):
AAACATAACATTTC
Found at i:8184 original size:18 final size:20
Alignment explanation
Indices: 8163--8206 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
8153 AAATTTAAAT
8163 TTTTATAAA-TATTTT-TAA
1 TTTTATAAATTATTTTGTAA
* *
8181 TTTTAAAAATTATTTTGTAT
1 TTTTATAAATTATTTTGTAA
8201 TTTTAT
1 TTTTAT
8207 TGAAAGAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 8 0.38
19 6 0.29
20 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTATAAATTATTTTGTAA
Found at i:8184 original size:19 final size:21
Alignment explanation
Indices: 8160--8206 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
8150 ATAAAATTTA
8160 AATTTTTATAAA-TATTTT-T
1 AATTTTTATAAATTATTTTGT
*
8179 AA-TTTTAAAAATTATTTTGT
1 AATTTTTATAAATTATTTTGT
8199 -ATTTTTAT
1 AATTTTTAT
8207 TGAAAGAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 8 0.35
19 9 0.39
20 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
AATTTTTATAAATTATTTTGT
Found at i:13581 original size:3 final size:3
Alignment explanation
Indices: 13568--13613 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
13558 CCGAACATGC
*
13568 AAG ATG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
13614 TGATGATTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:16604 original size:26 final size:26
Alignment explanation
Indices: 16531--16593 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
16521 TTTTTTCGAA
* *
16531 TCGAGTCAAATGAAATGAAATTCAGG
1 TCGAGTCGAATGAAATAAAATTCAGG
* *
16557 TCGAGTTGAATGAAATAAAATTTAGG
1 TCGAGTCGAATGAAATAAAATTCAGG
16583 TCGAGTCGAAT
1 TCGAGTCGAAT
16594 CGAGTAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.27
Consensus pattern (26 bp):
TCGAGTCGAATGAAATAAAATTCAGG
Found at i:16850 original size:38 final size:39
Alignment explanation
Indices: 16780--16860 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
16770 ATTCCAAAAT
* * * *
16780 TATTGTTTTAATTTTTTAAAATTGAAACTTTTTTTTATA
1 TATTCTTTAAATTTTTTAAAATTGAAACTTTTTTATAAA
*
16819 TATTCTTTAAATTTTTTTAAATT-ATAA-TTTTTTATAAA
1 TATTCTTTAAATTTTTTAAAATTGA-AACTTTTTTATAAA
16857 TATT
1 TATT
16861 TTGAATTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 14 0.39
39 22 0.61
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (39 bp):
TATTCTTTAAATTTTTTAAAATTGAAACTTTTTTATAAA
Found at i:18081 original size:17 final size:17
Alignment explanation
Indices: 18059--18091 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
18049 ACTGGTGCCA
18059 CCACTCTTTTTTACCCT
1 CCACTCTTTTTTACCCT
18076 CCACTCTTTTTTACCC
1 CCACTCTTTTTTACCC
18092 GTATTTTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.42, G:0.00, T:0.45
Consensus pattern (17 bp):
CCACTCTTTTTTACCCT
Found at i:24146 original size:29 final size:28
Alignment explanation
Indices: 24087--24146 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
24077 TGTTTGGGTG
* *
24087 TTTGGTCACTTTGGCCCTTATCATTTTT
1 TTTGGTCACTTTGGCCCCTAACATTTTT
* *
24115 TTTGTTCACTTTGGCCCCTAACCTTTATT
1 TTTGGTCACTTTGGCCCCTAACATTT-TT
24144 TTT
1 TTT
24147 TGGGTCAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.12, C:0.23, G:0.12, T:0.53
Consensus pattern (28 bp):
TTTGGTCACTTTGGCCCCTAACATTTTT
Found at i:24316 original size:9 final size:9
Alignment explanation
Indices: 24302--24373 Score: 69
Period size: 9 Copynumber: 7.8 Consensus size: 9
24292 AGCAATGATT
24302 TTAAAATTA
1 TTAAAATTA
24311 TTAAAATTA
1 TTAAAATTA
*
24320 TTTTTAAAAATA
1 ---TTAAAATTA
24332 -TAAAATTA
1 TTAAAATTA
24340 TTAAAATTA
1 TTAAAATTA
24349 TTTTAAAA-TA
1 --TTAAAATTA
24359 -TAAAATTA
1 TTAAAATTA
24367 TTAAAAT
1 TTAAAAT
24374 AATCATCATT
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
7 5 0.09
8 9 0.17
9 23 0.43
10 2 0.04
11 6 0.11
12 8 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAAAATTA
Found at i:24335 original size:20 final size:21
Alignment explanation
Indices: 24300--24341 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
24290 TCAGCAATGA
*
24300 TTTTAAAATTATTAAAATTAT
1 TTTTAAAAATATTAAAATTAT
24321 TTTTAAAAATA-TAAAATTAT
1 TTTTAAAAATATTAAAATTAT
24341 T
1 T
24342 AAAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTAAAAATATTAAAATTAT
Found at i:24357 original size:20 final size:20
Alignment explanation
Indices: 24299--24350 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
24289 GTCAGCAATG
24299 ATTTTAAAATTATTAAAATT
1 ATTTTAAAATTATTAAAATT
*
24319 ATTTTTAAAAATA-TAAAATT
1 A-TTTTAAAATTATTAAAATT
24339 A--TTAAAATTATT
1 ATTTTAAAATTATT
24351 TTAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 8 0.29
18 1 0.04
20 9 0.32
21 10 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTTAAAATTATTAAAATT
Found at i:24364 original size:27 final size:29
Alignment explanation
Indices: 24303--24373 Score: 128
Period size: 27 Copynumber: 2.5 Consensus size: 29
24293 GCAATGATTT
24303 TAAAATTATTAAAATTATTTTTAAAAATA
1 TAAAATTATTAAAATTATTTTTAAAAATA
24332 TAAAATTATTAAAATTA-TTTT-AAAATA
1 TAAAATTATTAAAATTATTTTTAAAAATA
24359 TAAAATTATTAAAAT
1 TAAAATTATTAAAAT
24374 AATCATCATT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 21 0.50
28 4 0.10
29 17 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTAAAAATA
Found at i:24372 original size:16 final size:16
Alignment explanation
Indices: 24326--24374 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
24316 ATTATTTTTA
24326 AAAATATAAAATTATT
1 AAAATATAAAATTATT
24342 AAAAT-T---ATT-TT
1 AAAATATAAAATTATT
24353 AAAATATAAAATTATT
1 AAAATATAAAATTATT
24369 AAAATA
1 AAAATA
24375 ATCATCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
11 7 0.25
12 4 0.14
15 4 0.14
16 13 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATATAAAATTATT
Found at i:24471 original size:13 final size:13
Alignment explanation
Indices: 24455--24484 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
24445 CCCTTCCCCC
24455 TTCCTTGTCCCTT
1 TTCCTTGTCCCTT
*
24468 TTCCTTTTCCCTT
1 TTCCTTGTCCCTT
24481 TTCC
1 TTCC
24485 CTTTTGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.40, G:0.03, T:0.57
Consensus pattern (13 bp):
TTCCTTGTCCCTT
Found at i:24475 original size:6 final size:7
Alignment explanation
Indices: 24457--24489 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
24447 CTTCCCCCTT
*
24457 CCTTGTC
1 CCTTTTC
24464 CCTTTT-
1 CCTTTTC
24470 CCTTTTC
1 CCTTTTC
24477 CCTTTTC
1 CCTTTTC
24484 CCTTTT
1 CCTTTT
24490 GTTTAGGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.00, C:0.39, G:0.03, T:0.58
Consensus pattern (7 bp):
CCTTTTC
Found at i:25335 original size:19 final size:19
Alignment explanation
Indices: 25311--25373 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
25301 TGATGATTTT
25311 AATAATTTTATATTTAAAA
1 AATAATTTTATATTTAAAA
25330 AATAATTTTAAAGTATTT--AA
1 AATAATTTT--A-TATTTAAAA
*
25350 AA-AATTATAT-TTTAAAA
1 AATAATTTTATATTTAAAA
25367 AATAATT
1 AATAATT
25374 AATTTTTTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
15 3 0.08
16 1 0.03
17 5 0.14
18 4 0.11
19 14 0.38
20 4 0.11
21 1 0.03
22 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AATAATTTTATATTTAAAA
Found at i:25346 original size:22 final size:24
Alignment explanation
Indices: 25321--25365 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
25311 AATAATTTTA
25321 TATTTAAAAAA-TA-ATTTTAAAG
1 TATTTAAAAAATTATATTTTAAAG
25343 TATTTAAAAAATTATATTTTAAA
1 TATTTAAAAAATTATATTTTAAA
25366 AAATAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.52
23 2 0.10
24 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TATTTAAAAAATTATATTTTAAAG
Found at i:31274 original size:22 final size:22
Alignment explanation
Indices: 31228--31288 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
31218 CGATCTAAGG
31228 AAAAATAAAAGAAACA-A-AATA
1 AAAAATAAAAGAAA-ATAGAATA
31249 AAAAATAAAAGAAAATAGAATTA
1 AAAAATAAAAGAAAATAGAA-TA
* *
31272 AAAGA-AATAGAAAATAG
1 AAAAATAAAAGAAAATAG
31289 GGAAGTCGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 1 0.03
21 15 0.43
22 13 0.37
23 6 0.17
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.13
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATA
Found at i:31281 original size:15 final size:16
Alignment explanation
Indices: 31254--31283 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31244 AAATAAAAAA
31254 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
31270 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
31284 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:32446 original size:14 final size:14
Alignment explanation
Indices: 32423--32473 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
32413 CCAACCATAT
*
32423 ATTTTGATTTTGTA
1 ATTTTAATTTTGTA
*
32437 ATTTTAATTTAGT-
1 ATTTTAATTTTGTA
* *
32450 ATTTTGATTTTGCA
1 ATTTTAATTTTGTA
*
32464 TTTTTAATTT
1 ATTTTAATTT
32474 GAGAAGTTTG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.65
Consensus pattern (14 bp):
ATTTTAATTTTGTA
Found at i:32488 original size:28 final size:28
Alignment explanation
Indices: 32425--32529 Score: 113
Period size: 28 Copynumber: 3.8 Consensus size: 28
32415 AACCATATAT
* * *
32425 TTTGATTTTGTAATTTTAATTT-AGTAT
1 TTTGATTTTGCATTTTTAATTTGAGTAG
*
32452 TTTGATTTTGCATTTTTAATTTGAGAAG
1 TTTGATTTTGCATTTTTAATTTGAGTAG
* *
32480 TTTGATTTTCCATTTTTAGTTTGAGTAG
1 TTTGATTTTGCATTTTTAATTTGAGTAG
* * * *
32508 GTTCATTTTGCGTTTTTTATTT
1 TTTGATTTTGCATTTTTAATTT
32530 TGAATATTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
27 20 0.31
28 44 0.69
ACGTcount: A:0.20, C:0.05, G:0.15, T:0.60
Consensus pattern (28 bp):
TTTGATTTTGCATTTTTAATTTGAGTAG
Done.