Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015092.1 Kokia drynarioides strain JFW-HI SEQ_130136, 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: 93561
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 184 characters in sequence are not A, C, G, or T
Found at i:7153 original size:36 final size:36
Alignment explanation
Indices: 7106--7180 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
7096 CACACCTTGC
7106 ACACATAGGCGCTCAAACCCAGGACCCTTAGGATGA
1 ACACATAGGCGCTCAAACCCAGGACCCTTAGGATGA
* *
7142 ACACATAGGCGCTCGAACCCAGGACTCTTAGGATGA
1 ACACATAGGCGCTCAAACCCAGGACCCTTAGGATGA
7178 ACA
1 ACA
7181 ACATCCTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.23, T:0.15
Consensus pattern (36 bp):
ACACATAGGCGCTCAAACCCAGGACCCTTAGGATGA
Found at i:7939 original size:29 final size:28
Alignment explanation
Indices: 7889--8171 Score: 214
Period size: 29 Copynumber: 9.8 Consensus size: 28
7879 AGGTCCCAAA
* * **
7889 AACTTCTAAAAAATCCATTTTTGACCTTG
1 AACTTCCAAAAATTCCA-TTTTGACCCCG
* * * **
7918 AAACATCCAAAAATTACATTTTTTACCCTAA
1 -AACTTCCAAAAATTCCA-TTTTGACCC-CG
*
7949 AACTTCCAAAAATCCCATTTT-ACCCCCG
1 AACTTCCAAAAATTCCATTTTGA-CCCCG
* *
7977 AACTTCCAAAAAATCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTGA-CCCCG
* **
8006 AACTTCTAAAAATTCCATTTTTCCCCCCG
1 AACTTCCAAAAATTCCA-TTTTGACCCCG
8035 AACTTCCAAAAATTCCATTTTGACCCCG
1 AACTTCCAAAAATTCCATTTTGACCCCG
* *
8063 AAACTTCCAAAAATTCCATTTTTACCCTTG
1 -AACTTCCAAAAATTCCATTTTGACCC-CG
** **
8093 AACTTTTAAAAATTCCATTTTTGACCTTG
1 AACTTCCAAAAATTCCA-TTTTGACCCCG
8122 AAACTTCCAAAAATTTCC-TTTT-ACCCCCG
1 -AACTTCCAAAAA-TTCCATTTTGA-CCCCG
*
8151 AA-TGTCTAAAAATTCCATTTT
1 AACT-TCCAAAAATTCCATTTT
8172 TAACTCTGAA
Statistics
Matches: 208, Mismatches: 33, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
27 5 0.02
28 43 0.21
29 99 0.48
30 57 0.27
31 4 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTGACCCCG
Found at i:8033 original size:58 final size:58
Alignment explanation
Indices: 7888--8173 Score: 287
Period size: 58 Copynumber: 4.9 Consensus size: 58
7878 GAGGTCCCAA
* * ** * * **
7888 AAACTTCTAAAAAATCCATTTTTGA-CCTTGAAACATCCAAAAATTACATTTTTTACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCCG-AACTTCCAAAAATTCCA-TTTTTACCCCG
* *
7948 AAACTTCCAAAAATCCCA-TTTTACCCCCGAACTTCCAAAAAATCCATTTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTA-CCCCG
* * *
8006 -AACTTCTAAAAATTCCATTTTTCCCCCCGAACTTCCAAAAATTCCATTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTACCCCG
** ** **
8063 AAACTTCCAAAAATTCCATTTTTACCCTTGAACTTTTAAAAATTCCATTTTTGACCTTG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTT-ACCCCG
*
8122 AAACTTCCAAAAATTTCC--TTTTACCCCCGAA-TGTCTAAAAATTCCATTTTTA
1 AAACTTCCAAAAA-TTCCATTTTTACCCCCGAACT-TCCAAAAATTCCATTTTTA
8174 ACTCTGAATT
Statistics
Matches: 192, Mismatches: 27, Indels: 17
0.81 0.11 0.07
Matches are distributed among these distances:
57 28 0.15
58 121 0.63
59 24 0.12
60 19 0.10
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:8071 original size:87 final size:87
Alignment explanation
Indices: 7926--8173 Score: 306
Period size: 87 Copynumber: 2.9 Consensus size: 87
7916 TGAAACATCC
* * ** * *
7926 AAAAATTACATTTTTTACCCTAAAACTTCCAAAAATCCCATTTTACCCCCGAACTTCCAAAAAAT
1 AAAAATTCCATTTTTCACCCCGAAACTTCCAAAAATTCCATTTTACCCCCGAACTTCCAAAAATT
7991 CCATTTTTACCCCCGAACTTCT
66 CCATTTTTACCCCCGAACTTCT
*
8013 AAAAATTCCATTTTTCCCCCCG-AACTTCCAAAAATTCCATTTTGA-CCCCGAAACTTCCAAAAA
1 AAAAATTCCATTTTTCACCCCGAAACTTCCAAAAATTCCATTTT-ACCCCCG-AACTTCCAAAAA
** *
8076 TTCCATTTTTACCCTTGAACTTTT
64 TTCCATTTTTACCCCCGAACTTCT
* ** *
8100 AAAAATTCCATTTTTGACCTTGAAACTTCCAAAAATTTCC-TTTTACCCCCGAA-TGTCTAAAAA
1 AAAAATTCCATTTTTCACCCCGAAACTTCCAAAAA-TTCCATTTTACCCCCGAACT-TCCAAAAA
8163 TTCCATTTTTA
64 TTCCATTTTTA
8174 ACTCTGAATT
Statistics
Matches: 140, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
86 26 0.19
87 89 0.64
88 21 0.15
89 4 0.03
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.34
Consensus pattern (87 bp):
AAAAATTCCATTTTTCACCCCGAAACTTCCAAAAATTCCATTTTACCCCCGAACTTCCAAAAATT
CCATTTTTACCCCCGAACTTCT
Found at i:8173 original size:29 final size:29
Alignment explanation
Indices: 7923--8173 Score: 262
Period size: 29 Copynumber: 8.7 Consensus size: 29
7913 CCTTGAAACA
* ***
7923 TCCAAAAATTACATTTTTTACCCTAAAACT
1 TCCAAAAATTCCA-TTTTTACCCCCGAACT
*
7953 TCCAAAAATCCCA-TTTTACCCCCGAACT
1 TCCAAAAATTCCATTTTTACCCCCGAACT
*
7981 TCCAAAAAATCCATTTTTACCCCCGAACT
1 TCCAAAAATTCCATTTTTACCCCCGAACT
* *
8010 TCTAAAAATTCCATTTTTCCCCCCGAACT
1 TCCAAAAATTCCATTTTTACCCCCGAACT
*
8039 TCCAAAAATTCCATTTTGA-CCCCGAAACT
1 TCCAAAAATTCCATTTTTACCCCCG-AACT
**
8068 TCCAAAAATTCCATTTTTACCCTTGAACT
1 TCCAAAAATTCCATTTTTACCCCCGAACT
** **
8097 TTTAAAAATTCCATTTTTGA-CCTTGAAACT
1 TCCAAAAATTCCATTTTT-ACCCCCG-AACT
8127 TCCAAAAATTTCC--TTTTACCCCCGAA-T
1 TCCAAAAA-TTCCATTTTTACCCCCGAACT
*
8154 GTCTAAAAATTCCATTTTTA
1 -TCCAAAAATTCCATTTTTA
8174 ACTCTGAATT
Statistics
Matches: 188, Mismatches: 23, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
27 5 0.03
28 38 0.20
29 116 0.62
30 25 0.13
31 4 0.02
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCCCCGAACT
Found at i:8193 original size:87 final size:87
Alignment explanation
Indices: 7889--8186 Score: 286
Period size: 87 Copynumber: 3.4 Consensus size: 87
7879 AGGTCCCAAA
* * * * ** * * * *
7889 AACTTCTAAAAAATCCATTTTTGACCTTGAAACATCCAAAAATTACATTTTTTACCCTAAAACTT
1 AACTTCCAAAAATTCCATTTTTAACCCTG-AATTTTCAAAAATTCCATTTTTCACCCTGAAACTT
*
7954 CCAAAAATCCCATTTTACCCCCG
65 CCAAAAATTCCATTTTACCCCCG
* * * * * *
7977 AACTTCCAAAAAATCCATTTTTACCCCCGAA-CTTCTAAAAATTCCATTTTTCCCCCCG-AACTT
1 AACTTCCAAAAATTCCATTTTTAACCCTGAATTTTC-AAAAATTCCATTTTTCACCCTGAAACTT
8040 CCAAAAATTCCATTTTGA-CCCCG
65 CCAAAAATTCCATTTT-ACCCCCG
* *
8063 AAACTTCCAAAAATTCCATTTTT-ACCCTTGAACTTTT-AAAAATTCCATTTTTGACCTTGAAAC
1 -AACTTCCAAAAATTCCATTTTTAACCC-TGAA-TTTTCAAAAATTCCATTTTTCACCCTGAAAC
8126 TTCCAAAAATTTCC-TTTTACCCCCG
63 TTCCAAAAA-TTCCATTTTACCCCCG
* *
8151 AA-TGTCTAAAAATTCCATTTTTAACTCTGAATTTTC
1 AACT-TCCAAAAATTCCATTTTTAACCCTGAATTTTC
8187 CCAAATTTAC
Statistics
Matches: 175, Mismatches: 23, Indels: 25
0.78 0.10 0.11
Matches are distributed among these distances:
86 35 0.20
87 86 0.49
88 48 0.27
89 6 0.03
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.35
Consensus pattern (87 bp):
AACTTCCAAAAATTCCATTTTTAACCCTGAATTTTCAAAAATTCCATTTTTCACCCTGAAACTTC
CAAAAATTCCATTTTACCCCCG
Found at i:20916 original size:17 final size:17
Alignment explanation
Indices: 20894--20959 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
20884 GTCATATTGG
*
20894 GTTTAAATTTGATTTAA
1 GTTTAAATTTAATTTAA
**
20911 GTTTAAACTTTTCTTTTAAA
1 GTTTAAA--TTTAATTT-AA
* *
20931 GCTTAAATTTAAATTAA
1 GTTTAAATTTAATTTAA
20948 GTTTAAATTTAA
1 GTTTAAATTTAA
20960 ATATAAATTG
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
17 20 0.51
18 5 0.13
19 6 0.15
20 8 0.21
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.50
Consensus pattern (17 bp):
GTTTAAATTTAATTTAA
Found at i:22965 original size:23 final size:23
Alignment explanation
Indices: 22935--22980 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
22925 GAGGTCCCCC
*
22935 AAAACTTCCAAAAATTCCATTTT
1 AAAACTTCCAAAAATTACATTTT
22958 AAAACTTCCAAAAATTACATTTT
1 AAAACTTCCAAAAATTACATTTT
22981 TGACACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAACTTCCAAAAATTACATTTT
Found at i:23022 original size:29 final size:28
Alignment explanation
Indices: 22937--23334 Score: 400
Period size: 29 Copynumber: 13.8 Consensus size: 28
22927 GGTCCCCCAA
*
22937 AACTTCCAAAAATTCCA-TTTTA----A
1 AACTTCCAAAAATTCCATTTTTACCCCG
* **
22960 AACTTCCAAAAATTACATTTTTGACACCAA
1 AACTTCCAAAAATTCCATTTTT-AC-CCCG
22990 AACTTCCAAAAA-TCTCATTTTTACCCTCG
1 AACTTCCAAAAATTC-CATTTTTACCC-CG
*
23019 AACTTCCAAAAATTCCATTTTTACACTCG
1 AACTTCCAAAAATTCCATTTTTAC-CCCG
*
23048 AACTTCCAAAAATTCCATTTTTGACCCCA
1 AACTTCCAAAAATTCCATTTTT-ACCCCG
* *
23077 AATCTTCCAAAAATTCTATTTTTACCCTCA
1 AA-CTTCCAAAAATTCCATTTTTACCC-CG
*
23107 AACTTCCAAAAATTCCATTTTTACCCCCAA
1 AACTTCCAAAAATTCCATTTTTA-CCCC-G
23137 AACTTCCAAAAATTCCATTTTTACTCCCG
1 AACTTCCAAAAATTCCATTTTTAC-CCCG
*
23166 AACTTCCAAAAA-TCTCATTTTTGGCCCCG
1 AACTTCCAAAAATTC-CATTTTT-ACCCCG
*
23195 AAACTTCCAAAAATTCCATTTTTATCTCCG
1 -AACTTCCAAAAATTCCATTTTTA-CCCCG
23225 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCC-CG
** * *
23254 AACTTTTAAAAATTTCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCC-G
23284 AACTTCCAAAAATTCC-TTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTA-CCCCG
**
23312 AA-TGTTTAAAAATTCCATTTTTA
1 AACT-TCCAAAAATTCCATTTTTA
23335 ATTCCGAATT
Statistics
Matches: 323, Mismatches: 24, Indels: 50
0.81 0.06 0.13
Matches are distributed among these distances:
23 16 0.05
24 4 0.01
25 1 0.00
27 1 0.00
28 19 0.06
29 161 0.50
30 119 0.37
31 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.35
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTTACCCCG
Found at i:23031 original size:59 final size:56
Alignment explanation
Indices: 22936--23334 Score: 393
Period size: 59 Copynumber: 6.9 Consensus size: 56
22926 AGGTCCCCCA
* *
22936 AAACTTCCAAAAATTCCA-TTTTA----AAACTTCCAAAAATTACATTTTTGACACC
1 AAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTT-ACACC
22988 AAAACTTCCAAAAA-TCTCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTACACTC
1 -AAACTTCCAAAAATTC-CATTTTTACCC-CGAACTTCCAAAAATTCCATTTTTACAC-C
* * * *
23047 GAACTTCCAAAAATTCCATTTTTGACCCCAAATCTTCCAAAAATTCTATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTT-ACCCCGAA-CTTCCAAAAATTCCATTTTTACAC-C
* *
23106 AAACTTCCAAAAATTCCATTTTTACCCCCAAAACTTCCAAAAATTCCATTTTTACTCCC
1 AAACTTCCAAAAATTCCATTTTTA-CCCC-GAACTTCCAAAAATTCCATTTTTAC-ACC
* * *
23165 GAACTTCCAAAAA-TCTCATTTTTGGCCCCGAAACTTCCAAAAATTCCATTTTTATCTCC
1 AAACTTCCAAAAATTC-CATTTTT-ACCCCG-AACTTCCAAAAATTCCATTTTTA-CACC
* ** * *
23224 GAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTTAAAAATTTCATTTTTGACCCC
1 AAACTTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATTCCATTTTT-ACACC
**
23282 AAAACTTCCAAAAATTCC-TTTTTACCCCCGAA-TGTTTAAAAATTCCATTTTTA
1 -AAACTTCCAAAAATTCCATTTTTA-CCCCGAACT-TCCAAAAATTCCATTTTTA
23335 ATTCCGAATT
Statistics
Matches: 303, Mismatches: 19, Indels: 44
0.83 0.05 0.12
Matches are distributed among these distances:
52 2 0.01
53 15 0.05
54 5 0.02
57 2 0.01
58 81 0.27
59 190 0.63
60 8 0.03
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (56 bp):
AAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTTACACC
Found at i:23084 original size:88 final size:86
Alignment explanation
Indices: 22931--23334 Score: 445
Period size: 88 Copynumber: 4.7 Consensus size: 86
22921 CCTGGAGGTC
* *
22931 CCCCAAAACTTCCAAAAATTCCA-TTTTA-A----AACTTCCAAAAATTACATTTTTGACACCAA
1 CCCC-AAACTTCCAAAAATTCCATTTTTACACCCGAACTTCCAAAAATTCCATTTTT-AC-CCCA
22990 AACTTCCAAAAATCTCATTTTT-A
63 AACTTCCAAAAATCTCATTTTTGA
* *
23013 CCCTCGAACTTCCAAAAATTCCATTTTTACACTCGAACTTCCAAAAATTCCATTTTTGACCCCAA
1 CCC-CAAACTTCCAAAAATTCCATTTTTACACCCGAACTTCCAAAAATTCCATTTTT-ACCCCAA
23078 ATCTTCCAAAAAT-TCTATTTTT-A
64 A-CTTCCAAAAATCTC-ATTTTTGA
* * *
23101 CCCTCAAACTTCCAAAAATTCCATTTTTACCCCCAAAACTTCCAAAAATTCCATTTTTACTCCCG
1 CCC-CAAACTTCCAAAAATTCCATTTTTACACCC-GAACTTCCAAAAATTCCATTTTTAC-CCCA
*
23166 AACTTCCAAAAATCTCATTTTTGG
63 AACTTCCAAAAATCTCATTTTTGA
* *
23190 CCCCGAAACTTCCAAAAATTCCATTTTTATC-TCCGAACTTCCAAAAATTCCATTTTTACCCTCG
1 CCCC-AAACTTCCAAAAATTCCATTTTTA-CACCCGAACTTCCAAAAATTCCATTTTTACCC-CA
** *
23254 AACTTTTAAAAATTTCATTTTTGA
63 AACTTCCAAAAATCTCATTTTTGA
* **
23278 CCCCAAAACTTCCAAAAATTCC-TTTTTACCCCCGAA-TGTTTAAAAATTCCATTTTTA
1 CCCC-AAACTTCCAAAAATTCCATTTTTACACCCGAACT-TCCAAAAATTCCATTTTTA
23335 ATTCCGAATT
Statistics
Matches: 285, Mismatches: 19, Indels: 31
0.85 0.06 0.09
Matches are distributed among these distances:
82 20 0.07
83 6 0.02
84 1 0.00
86 2 0.01
87 37 0.13
88 160 0.56
89 58 0.20
90 1 0.00
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (86 bp):
CCCCAAACTTCCAAAAATTCCATTTTTACACCCGAACTTCCAAAAATTCCATTTTTACCCCAAAC
TTCCAAAAATCTCATTTTTGA
Found at i:28309 original size:11 final size:11
Alignment explanation
Indices: 28286--28323 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
28276 AAATCTCAAT
*
28286 TATAAACATAA
1 TATAAATATAA
28297 TAT-AATATAAA
1 TATAAATAT-AA
28308 TATAAATATAA
1 TATAAATATAA
28319 TATAA
1 TATAA
28324 TCAAATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 4 0.17
11 15 0.62
12 5 0.21
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (11 bp):
TATAAATATAA
Found at i:28337 original size:17 final size:17
Alignment explanation
Indices: 28286--28323 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28276 AAATCTCAAT
*
28286 TATAAACAT-AATATAA
1 TATAAATATAAATATAA
28302 TATAAATATAAATATAA
1 TATAAATATAAATATAA
28319 TATAA
1 TATAA
28324 TCAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
TATAAATATAAATATAA
Found at i:28337 original size:22 final size:22
Alignment explanation
Indices: 28286--28346 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
28276 AAATCTCAAT
* *
28286 TATAAACATAATATAATATAAA
1 TATAAATATAATATAATACAAA
28308 TATAAATATAATATAAT-CAAA
1 TATAAATATAATATAATACAAA
*
28329 TATATAATACAATTATAA
1 TATA-AATATAA-TATAA
28347 ACACACATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.21
22 22 0.65
23 5 0.15
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (22 bp):
TATAAATATAATATAATACAAA
Found at i:31559 original size:12 final size:10
Alignment explanation
Indices: 31526--31558 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
31516 AAAATTATTA
*
31526 TTTTATA-AA
1 TTTTATATAT
31535 TTTTATATAT
1 TTTTATATAT
31545 TTTTATATAT
1 TTTTATATAT
31555 TTTT
1 TTTT
31559 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTATATAT
Found at i:31638 original size:19 final size:20
Alignment explanation
Indices: 31614--31658 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
31604 TTTTTATAAA
*
31614 TATTTTGAA-ATTTAAAAAT
1 TATTTTCAATATTTAAAAAT
* *
31633 TATTTTCAATTTTTTAAAAT
1 TATTTTCAATATTTAAAAAT
31653 TATTTT
1 TATTTT
31659 AATTTTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TATTTTCAATATTTAAAAAT
Found at i:31673 original size:20 final size:20
Alignment explanation
Indices: 31628--31666 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31618 TTGAAATTTA
31628 AAAATTATTTTCAATTTTTT
1 AAAATTATTTTCAATTTTTT
31648 AAAATTATTTT-AATTTTTT
1 AAAATTATTTTCAATTTTTT
31667 TGTAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
AAAATTATTTTCAATTTTTT
Found at i:34064 original size:22 final size:24
Alignment explanation
Indices: 34039--34091 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
34029 TTTTACGATA
*
34039 TTAAAAATTTA-A-TTTTATTATT
1 TTAAAAATTTATATTTTTATAATT
*
34061 TTAATAATTTATATTTTTATAATT
1 TTAAAAATTTATATTTTTATAATT
*
34085 TTTAAAA
1 TTAAAAA
34092 GATAAAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 10 0.40
23 1 0.04
24 14 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTAAAAATTTATATTTTTATAATT
Found at i:34077 original size:15 final size:16
Alignment explanation
Indices: 34052--34085 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
34042 AAAATTTAAT
34052 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
34068 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
34083 TTT
1 TTT
34086 TTAAAAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:34139 original size:30 final size:29
Alignment explanation
Indices: 34070--34139 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 29
34060 TTTAATAATT
*
34070 TATATTTTTATAATTTTTAAAAGATAAAA
1 TATAATTTTATAATTTTTAAAAGATAAAA
* * *
34099 T-TAAATTTTTATTATTTTTAATAGGTCAAAA
1 TAT-AA-TTTTATAATTTTTAAAAGAT-AAAA
34130 TATAATTTTA
1 TATAATTTTA
34140 CTTTTATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
28 1 0.03
29 2 0.06
30 22 0.67
31 7 0.21
32 1 0.03
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (29 bp):
TATAATTTTATAATTTTTAAAAGATAAAA
Found at i:35164 original size:2 final size:2
Alignment explanation
Indices: 35157--35185 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35147 TCATTGGAAC
35157 TA 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 TA T
35186 GCATGTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37661 original size:18 final size:19
Alignment explanation
Indices: 37640--37678 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
37630 TTTTATATGA
37640 TATAAATAAT-TTAAAA-TT
1 TATAAA-AATATTAAAACTT
37658 TATAAAAATATTAAAACTT
1 TATAAAAATATTAAAACTT
37677 TA
1 TA
37679 AATTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 12 0.63
19 4 0.21
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
TATAAAAATATTAAAACTT
Found at i:39385 original size:46 final size:46
Alignment explanation
Indices: 39316--39423 Score: 148
Period size: 46 Copynumber: 2.3 Consensus size: 46
39306 TCCAGAGTGT
39316 ATATAAATTGAATTGAACGTTATAAGGAAATAGG-TGTTTGTTTGCC
1 ATATAAATTGAATTGAACGTTATAAGGAAATAGGAT-TTTGTTTGCC
* * *
39362 ATATAAATTGAATTGAATC-TTATAAGGGAATGGGATTTTGTTTGCT
1 ATATAAATTGAATTGAA-CGTTATAAGGAAATAGGATTTTGTTTGCC
*
39408 ATATAAATGGAATTGA
1 ATATAAATTGAATTGA
39424 TTTTGTGTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
46 54 0.96
47 2 0.04
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (46 bp):
ATATAAATTGAATTGAACGTTATAAGGAAATAGGATTTTGTTTGCC
Found at i:50692 original size:17 final size:15
Alignment explanation
Indices: 50660--50704 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 15
50650 AACATTATTT
50660 TAATATTTATTTTAG
1 TAATATTTATTTTAG
50675 TAATATTATATATTTAG
1 TAATATT-TAT-TTTAG
*
50692 TATAAATTTATTT
1 TA-ATATTTATTT
50705 AGTTTAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 7 0.27
16 5 0.19
17 10 0.38
18 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (15 bp):
TAATATTTATTTTAG
Found at i:56242 original size:15 final size:16
Alignment explanation
Indices: 56216--56245 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56206 GAAAGGGAAG
56216 AAAAGCAATATATATC
1 AAAAGCAATATATATC
56232 AAAAG-AATATATAT
1 AAAAGCAATATATAT
56246 AATAATGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (16 bp):
AAAAGCAATATATATC
Found at i:59385 original size:18 final size:18
Alignment explanation
Indices: 59337--59390 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
59327 ATATGTTACG
59337 TAATAATCGATTTAAA-A
1 TAATAATCGATTTAAATA
*
59354 AAAGTAAT--ATTTAAATA
1 TAA-TAATCGATTTAAATA
59371 TAATAATCGATTTAAATA
1 TAATAATCGATTTAAATA
59389 TA
1 TA
59391 TAAATAATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 11 0.35
17 5 0.16
18 15 0.48
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (18 bp):
TAATAATCGATTTAAATA
Found at i:59398 original size:21 final size:20
Alignment explanation
Indices: 59337--59407 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 20
59327 ATATGTTACG
59337 TAATAATCGATTTAAA-A-A
1 TAATAATCGATTTAAATATA
59355 -AAGTAAT--ATTT-AA-ATA
1 TAA-TAATCGATTTAAATATA
59371 TAATAATCGATTTAAATATA
1 TAATAATCGATTTAAATATA
*
59391 TAAATAATTGATTTAAA
1 T-AATAATCGATTTAAA
59408 AGAAAAAGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
15 3 0.07
16 9 0.20
17 4 0.09
18 8 0.18
19 2 0.05
20 4 0.09
21 14 0.32
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.38
Consensus pattern (20 bp):
TAATAATCGATTTAAATATA
Found at i:61576 original size:204 final size:204
Alignment explanation
Indices: 61226--61634 Score: 818
Period size: 204 Copynumber: 2.0 Consensus size: 204
61216 CAGCGGAGAT
61226 AGGGCGAGTAACCCCAGTTGGAGAAGGGGAGCACGTGCAACAACGCACATATATATGGGGAATAA
1 AGGGCGAGTAACCCCAGTTGGAGAAGGGGAGCACGTGCAACAACGCACATATATATGGGGAATAA
61291 GGCACTCATTTGCACGTGCCCTGCTTCTCCAACAAGACCTATTCACCCCTTTAAAACATCCACGC
66 GGCACTCATTTGCACGTGCCCTGCTTCTCCAACAAGACCTATTCACCCCTTTAAAACATCCACGC
61356 CATGAACGAGGTTTACAAAGCTCCTAAGTTGAGATGTTGAAGACAACACTAGTATTTATAAGTGT
131 CATGAACGAGGTTTACAAAGCTCCTAAGTTGAGATGTTGAAGACAACACTAGTATTTATAAGTGT
61421 AAGAGAAAG
196 AAGAGAAAG
61430 AGGGCGAGTAACCCCAGTTGGAGAAGGGGAGCACGTGCAACAACGCACATATATATGGGGAATAA
1 AGGGCGAGTAACCCCAGTTGGAGAAGGGGAGCACGTGCAACAACGCACATATATATGGGGAATAA
61495 GGCACTCATTTGCACGTGCCCTGCTTCTCCAACAAGACCTATTCACCCCTTTAAAACATCCACGC
66 GGCACTCATTTGCACGTGCCCTGCTTCTCCAACAAGACCTATTCACCCCTTTAAAACATCCACGC
61560 CATGAACGAGGTTTACAAAGCTCCTAAGTTGAGATGTTGAAGACAACACTAGTATTTATAAGTGT
131 CATGAACGAGGTTTACAAAGCTCCTAAGTTGAGATGTTGAAGACAACACTAGTATTTATAAGTGT
61625 AAGAGAAAG
196 AAGAGAAAG
61634 A
1 A
61635 TATGGTGACA
Statistics
Matches: 205, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
204 205 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (204 bp):
AGGGCGAGTAACCCCAGTTGGAGAAGGGGAGCACGTGCAACAACGCACATATATATGGGGAATAA
GGCACTCATTTGCACGTGCCCTGCTTCTCCAACAAGACCTATTCACCCCTTTAAAACATCCACGC
CATGAACGAGGTTTACAAAGCTCCTAAGTTGAGATGTTGAAGACAACACTAGTATTTATAAGTGT
AAGAGAAAG
Found at i:64204 original size:57 final size:56
Alignment explanation
Indices: 64100--64210 Score: 134
Period size: 57 Copynumber: 2.0 Consensus size: 56
64090 ACATGTTCTT
* *
64100 TTATATAAAAATGGTCAAATTTCAAGTTTAGTCCCTATACTATACTCAAATCTAAGA
1 TTATATAAAAATGGTCAAATTTCAAGTTTAGTCCCTACACTACACTC-AATCTAAGA
* * ** *
64157 TTATATAATAATGGTCAAATTTCAA-TTTTGATCTTTACACTGCACTCAATCTAA
1 TTATATAAAAATGGTCAAATTTCAAGTTTAG-TCCCTACACTACACTCAATCTAA
64211 AATTTAATCT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
56 11 0.24
57 35 0.76
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (56 bp):
TTATATAAAAATGGTCAAATTTCAAGTTTAGTCCCTACACTACACTCAATCTAAGA
Found at i:67980 original size:20 final size:20
Alignment explanation
Indices: 67947--68000 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
67937 AAAAATATCA
*
67947 ATTTACCAATATTTCTAAGC
1 ATTTATCAATATTTCTAAGC
*
67967 ATTTATCAAAATTTCTAAGC
1 ATTTATCAATATTTCTAAGC
67987 ATTTATCAATATTT
1 ATTTATCAATATTT
68001 ACGAGACTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (20 bp):
ATTTATCAATATTTCTAAGC
Found at i:68177 original size:20 final size:20
Alignment explanation
Indices: 68154--68216 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
68144 ATTTCTATCG
* *
68154 TTTTATTAATATTTACGAGA
1 TTTTATAAATATTTACAAGA
* *
68174 TTTTACCAAA-ATTTATAAGA
1 TTTTA-TAAATATTTACAAGA
*
68194 TTTTATAAATATTTTCAA-A
1 TTTTATAAATATTTACAAGA
68213 TTTT
1 TTTT
68217 CCAATCCCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 8 0.24
20 24 0.71
21 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTTATAAATATTTACAAGA
Found at i:68294 original size:20 final size:20
Alignment explanation
Indices: 68271--68326 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
68261 CTTTACCATA
*
68271 ATATTTAATGATTTATTAAT
1 ATATTTAACGATTTATTAAT
* * *
68291 ATATCTAACGACTTACTAAT
1 ATATTTAACGATTTATTAAT
* *
68311 ATTTTTAAGGATTTAT
1 ATATTTAACGATTTAT
68327 CAAAATATCT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (20 bp):
ATATTTAACGATTTATTAAT
Found at i:68376 original size:20 final size:20
Alignment explanation
Indices: 68320--68509 Score: 104
Period size: 20 Copynumber: 9.5 Consensus size: 20
68310 TATTTTTAAG
*
68320 GATTTATCAAAATATCTATC
1 GATTTACCAAAATATCTATC
*
68340 GATTT-CTGAATAA-ATCTATC
1 GATTTAC-CAA-AATATCTATC
* *
68360 GGTTTACCAAAATATCTAAC
1 GATTTACCAAAATATCTATC
* * **
68380 GATTTATCAAAAT-TTTAAAA
1 GATTTACCAAAATATCT-ATC
68400 GATTTACCAAAATATCTAAT-
1 GATTTACCAAAATATCT-ATC
* * *
68420 AATTTACCAAAATTTTTAAT-
1 GATTTACCAAAATATCT-ATC
* *
68440 GTTTTACCAAAATATCTAAC
1 GATTTACCAAAATATCTATC
* * *
68460 AATTTATCAAAATTTCTAAT-
1 GATTTACCAAAATATCT-ATC
* * * *
68480 GTTTTACTAAAATTTTTATC
1 GATTTACCAAAATATCTATC
68500 GATTTACCAA
1 GATTTACCAA
68510 TATTTATGAG
Statistics
Matches: 129, Mismatches: 32, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
19 7 0.05
20 114 0.88
21 8 0.06
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (20 bp):
GATTTACCAAAATATCTATC
Found at i:68451 original size:60 final size:59
Alignment explanation
Indices: 68362--68514 Score: 155
Period size: 60 Copynumber: 2.6 Consensus size: 59
68352 AATCTATCGG
* * * *
68362 TTTACCAAAATATCTAACGATTTATCAAAATTTTAAAAGATTTACCAAAATATCTAATAA
1 TTTACCAAAATTTTTAATGATTTACCAAAATTTTAAAA-ATTTACCAAAATATCTAATAA
* * * * * **
68422 TTTACCAAAATTTTTAATGTTTTACCAAAATATCTAACAATTTATCAAAATTTCTAATGT
1 TTTACCAAAATTTTTAATGATTTACCAAAAT-TTTAAAAATTTACCAAAATATCTAATAA
* *
68482 TTTACTAAAATTTTT-ATCGATTTACCAATATTT
1 TTTACCAAAATTTTTAAT-GATTTACCAAAATTT
68515 ATGAGACTTT
Statistics
Matches: 76, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
59 3 0.04
60 68 0.89
61 5 0.07
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (59 bp):
TTTACCAAAATTTTTAATGATTTACCAAAATTTTAAAAATTTACCAAAATATCTAATAA
Found at i:68480 original size:40 final size:39
Alignment explanation
Indices: 68362--68492 Score: 181
Period size: 40 Copynumber: 3.3 Consensus size: 39
68352 AATCTATCGG
* * *
68362 TTTACCAAAATATCTAACGATTTATCAAAATTTTAAAAGA
1 TTTACCAAAATATCTAACAATTTATCAAAATTTT-AATGT
* *
68402 TTTACCAAAATATCTAATAATTTACCAAAATTTTTAATGT
1 TTTACCAAAATATCTAACAATTTATCAAAA-TTTTAATGT
68442 TTTACCAAAATATCTAACAATTTATCAAAATTTCTAATGT
1 TTTACCAAAATATCTAACAATTTATCAAAATTT-TAATGT
*
68482 TTTACTAAAAT
1 TTTACCAAAAT
68493 TTTTATCGAT
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.91
41 4 0.05
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (39 bp):
TTTACCAAAATATCTAACAATTTATCAAAATTTTAATGT
Found at i:68636 original size:20 final size:20
Alignment explanation
Indices: 68623--68664 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
68613 ATTTTCCAAT
68623 ATATCTAATTATTTATCAAA
1 ATATCTAATTATTTATCAAA
**
68643 ATATCTAACGATTTATCAAA
1 ATATCTAATTATTTATCAAA
68663 AT
1 AT
68665 TTCCATCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATCTAATTATTTATCAAA
Found at i:70097 original size:21 final size:21
Alignment explanation
Indices: 70071--70112 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
70061 GTAACTGCAG
70071 AAAGCTCAATTGACACAATCC
1 AAAGCTCAATTGACACAATCC
70092 AAAGCTCAATTGACACAATCC
1 AAAGCTCAATTGACACAATCC
70113 TTCAGTATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.10, T:0.19
Consensus pattern (21 bp):
AAAGCTCAATTGACACAATCC
Found at i:71294 original size:149 final size:149
Alignment explanation
Indices: 71024--71325 Score: 604
Period size: 149 Copynumber: 2.0 Consensus size: 149
71014 ATACAGGCTT
71024 AACCTTAACAAAAGGACCAGTTTCATTCAATTACAATTAAAAAGTATCTAATCTTTGACCATCAT
1 AACCTTAACAAAAGGACCAGTTTCATTCAATTACAATTAAAAAGTATCTAATCTTTGACCATCAT
71089 GTTGTGGACCACCACGACAAATTCCATGTTGTATCAACAAAAGATGCTCTCGCCAACTCTCTCGA
66 GTTGTGGACCACCACGACAAATTCCATGTTGTATCAACAAAAGATGCTCTCGCCAACTCTCTCGA
71154 CTAGCATAAGGTTTACATC
131 CTAGCATAAGGTTTACATC
71173 AACCTTAACAAAAGGACCAGTTTCATTCAATTACAATTAAAAAGTATCTAATCTTTGACCATCAT
1 AACCTTAACAAAAGGACCAGTTTCATTCAATTACAATTAAAAAGTATCTAATCTTTGACCATCAT
71238 GTTGTGGACCACCACGACAAATTCCATGTTGTATCAACAAAAGATGCTCTCGCCAACTCTCTCGA
66 GTTGTGGACCACCACGACAAATTCCATGTTGTATCAACAAAAGATGCTCTCGCCAACTCTCTCGA
71303 CTAGCATAAGGTTTACATC
131 CTAGCATAAGGTTTACATC
71322 AACC
1 AACC
71326 AGATTTAAGC
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.28
Consensus pattern (149 bp):
AACCTTAACAAAAGGACCAGTTTCATTCAATTACAATTAAAAAGTATCTAATCTTTGACCATCAT
GTTGTGGACCACCACGACAAATTCCATGTTGTATCAACAAAAGATGCTCTCGCCAACTCTCTCGA
CTAGCATAAGGTTTACATC
Found at i:75963 original size:128 final size:128
Alignment explanation
Indices: 75730--75986 Score: 478
Period size: 128 Copynumber: 2.0 Consensus size: 128
75720 TTTTACTGCC
* *
75730 CCTCTCAACAATGATGTATCCAAAGTTTGGGCTCGAGTCTCCCCTTGAGAGTGCAATGCCTTACC
1 CCTCCCAACAATGATGTATCCAAAGTTTGAGCTCGAGTCTCCCCTTGAGAGTGCAATGCCTTACC
*
75795 ATTCCACCTCACACTTGTTGGTCCTTTCCACCACTTTCTATTCACTCAATAGTTGCTTAATAG
66 ATTCCACCTAACACTTGTTGGTCCTTTCCACCACTTTCTATTCACTCAATAGTTGCTTAATAG
75858 CCTCCCAACAATGATGTATCCAAAGTTTGAGCTCGAGTCTCCCCTTGAGAGTGCAATGCCTTACC
1 CCTCCCAACAATGATGTATCCAAAGTTTGAGCTCGAGTCTCCCCTTGAGAGTGCAATGCCTTACC
*
75923 ATTCCACCTAACACTTGTTGGTCCTTTCCATCACTTTCTATTCACTCAATAGTTGCTTAATAG
66 ATTCCACCTAACACTTGTTGGTCCTTTCCACCACTTTCTATTCACTCAATAGTTGCTTAATAG
75986 C
1 C
75987 AACATAAATT
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 125 1.00
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (128 bp):
CCTCCCAACAATGATGTATCCAAAGTTTGAGCTCGAGTCTCCCCTTGAGAGTGCAATGCCTTACC
ATTCCACCTAACACTTGTTGGTCCTTTCCACCACTTTCTATTCACTCAATAGTTGCTTAATAG
Found at i:80183 original size:24 final size:24
Alignment explanation
Indices: 80155--80217 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
80145 AGAAATAATC
80155 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
*
80179 TTTCAATTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
80203 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
80218 TATTAGTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTG
Found at i:82206 original size:24 final size:24
Alignment explanation
Indices: 82155--82209 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
82145 TCTTTTAGTT
* *
82155 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTATTTATTTGTTTCAATC
* *
82179 AAACTCTATTTATTTGTTTGAGTC
1 AAACTCTATTTATTTGTTTCAATC
82203 AAACTCT
1 AAACTCT
82210 TATTAGTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (24 bp):
AAACTCTATTTATTTGTTTCAATC
Found at i:82304 original size:13 final size:13
Alignment explanation
Indices: 82286--82310 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
82276 ACCTTAAAAA
82286 ATATACTCATTAG
1 ATATACTCATTAG
82299 ATATACTCATTA
1 ATATACTCATTA
82311 AAGTTAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (13 bp):
ATATACTCATTAG
Found at i:84906 original size:69 final size:69
Alignment explanation
Indices: 84795--84933 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
84785 CGGAGGGACC
*
84795 AATCAGACATATACAATTAGACTCTAGTAATTACAATTATGTCCAGAAGCATCATTCTGATAATT
1 AATCAGACATATACAACTAGACTCTAGTAATTACAATTATGTCCAGAAGCATCATTCTGATAATT
84860 CGCA
66 CGCA
*
84864 AATCAGACATATACAACTAGGCTCTAGTAATTACAATTATGTCCAGAAGCATCATTCTGATAATT
1 AATCAGACATATACAACTAGACTCTAGTAATTACAATTATGTCCAGAAGCATCATTCTGATAATT
84929 CGCA
66 CGCA
84933 A
1 A
84934 TTACTTAATC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.29
Consensus pattern (69 bp):
AATCAGACATATACAACTAGACTCTAGTAATTACAATTATGTCCAGAAGCATCATTCTGATAATT
CGCA
Found at i:85977 original size:15 final size:15
Alignment explanation
Indices: 85957--85986 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
85947 CACAAAAAAT
*
85957 GCCGCTAAAGATAAC
1 GCCGCTAAAAATAAC
85972 GCCGCTAAAAATAAC
1 GCCGCTAAAAATAAC
85987 AACGTTTATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.17, T:0.13
Consensus pattern (15 bp):
GCCGCTAAAAATAAC
Found at i:86111 original size:43 final size:43
Alignment explanation
Indices: 86002--86278 Score: 299
Period size: 43 Copynumber: 6.5 Consensus size: 43
85992 TTATGAGGAA
* * *
86002 AAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTT-TACCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCCACCAC
*
86044 AAACGCCGCTAAAGAATATGGTCTTTAGCGGCGCTTTCCA-CAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGC-TTCCACCAC
* *
86087 AAACGCCGCTAAAGAACATAGTCTTTAGCGGCGCTTCTACCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCCACCAC
* * *
86130 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTACTACCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCCACCAC
* * * * * * *
86173 AAACGCTGTTAAAGAACATGGTCTTTAGTGACACTTCTACCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCCACCAC
* ** * * * *
86216 AAATGCCATTAAAGAACAAGGTTTTTAGCGACGCTT-TACCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCCA-CCAC
*
86259 AAACACCGCTAAAGAACATG
1 AAACGCCGCTAAAGAACATG
86279 ATTTACCACA
Statistics
Matches: 202, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
42 38 0.19
43 163 0.81
44 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCCACCAC
Found at i:86155 original size:86 final size:86
Alignment explanation
Indices: 86002--86278 Score: 344
Period size: 86 Copynumber: 3.2 Consensus size: 86
85992 TTATGAGGAA
*
86002 AAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTT-TACCATAAACGCCGCTAAAGAATATGGT
1 AAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTCTACCATAAACGCCGCTAAAGAACATGGT
86066 CTTTAGCGGCGCTTTCCACAC
66 CTTTAGCGGCGCTTTCCACAC
* * *
86087 AAACGCCGCTAAAGAACATAGTCTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGAACATGGT
1 AAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTCTACCATAAACGCCGCTAAAGAACATGGT
* * *
86152 CTTTAGCGGCGC-TACTACCAT
66 CTTTAGCGGCGCTTTCCA-CAC
* * * * * * * ** *
86173 AAACGCTGTTAAAGAACATGGTCTTTAGTGACACTTCTACCATAAATGCCATTAAAGAACAAGGT
1 AAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTCTACCATAAACGCCGCTAAAGAACATGGT
* *
86238 TTTTAGCGACGCTTTACC-CAC
66 CTTTAGCGGCGCTTT-CCACAC
86259 AAACACCGCTAAAGAACATG
1 AAACACCGCTAAAGAACATG
86279 ATTTACCACA
Statistics
Matches: 162, Mismatches: 26, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
85 37 0.23
86 123 0.76
87 1 0.01
88 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (86 bp):
AAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTCTACCATAAACGCCGCTAAAGAACATGGT
CTTTAGCGGCGCTTTCCACAC
Found at i:86200 original size:129 final size:128
Alignment explanation
Indices: 86002--86278 Score: 362
Period size: 129 Copynumber: 2.2 Consensus size: 128
85992 TTATGAGGAA
* *
86002 AAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTTACCATAAACGCCGCTAAAGAATATGGTC
1 AAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTCTACCATAAACGCCGCTAAAGAACATGGTC
* * * *
86067 TTTAGCGGCGCTTTCCA-CACAAACGCCGCTAAAGAACATA-GTCTTTAGCGGCGCTTCTA-CCA
66 TTTAGCGACAC-TTCCACCACAAACGCCACTAAAGAACA-AGGTCTTTAGCGACGCTT-TACCCA
86129 C
128 C
* * *
86130 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTACTACCATAAACGCTGTTAAAGAACATGGT
1 AAACACCGCTAAAGAACATGGTCTTTAGCGGCGCT-CTACCATAAACGCCGCTAAAGAACATGGT
* * * * * *
86195 CTTTAGTGACACTTCTACCATAAATGCCATTAAAGAACAAGGTTTTTAGCGACGCTTTACCCAC
65 CTTTAGCGACACTTCCACCACAAACGCCACTAAAGAACAAGGTCTTTAGCGACGCTTTACCCAC
86259 AAACACCGCTAAAGAACATG
1 AAACACCGCTAAAGAACATG
86279 ATTTACCACA
Statistics
Matches: 129, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
128 41 0.32
129 88 0.68
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (128 bp):
AAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTCTACCATAAACGCCGCTAAAGAACATGGTC
TTTAGCGACACTTCCACCACAAACGCCACTAAAGAACAAGGTCTTTAGCGACGCTTTACCCAC
Found at i:86296 original size:29 final size:30
Alignment explanation
Indices: 86250--86309 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
86240 TTAGCGACGC
86250 TTTACCCACAAACACCGCTAAAGAACATGA
1 TTTACCCACAAACACCGCTAAAGAACATGA
*
86280 TTTA-CCACAAACGCCGCTAAAGAACATGA
1 TTTACCCACAAACACCGCTAAAGAACATGA
86309 T
1 T
86310 CTTTAGCGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.18
Consensus pattern (30 bp):
TTTACCCACAAACACCGCTAAAGAACATGA
Found at i:88499 original size:17 final size:17
Alignment explanation
Indices: 88477--88512 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
88467 TTTCCCTCAA
88477 CAGGATTACTGTCATAG
1 CAGGATTACTGTCATAG
88494 CAGGATTACTGTCATAG
1 CAGGATTACTGTCATAG
88511 CA
1 CA
88513 CTAGCATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (17 bp):
CAGGATTACTGTCATAG
Found at i:90324 original size:11 final size:11
Alignment explanation
Indices: 90308--90338 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
90298 TTCTGACTTT
90308 GAAAAATTATA
1 GAAAAATTATA
90319 GAAAAA-TATA
1 GAAAAATTATA
90329 GAAAAATTAT
1 GAAAAATTAT
90339 TAGAGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (11 bp):
GAAAAATTATA
Found at i:90999 original size:6 final size:6
Alignment explanation
Indices: 90988--91026 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
90978 TGATCAAAAT
* * *
90988 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
91027 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:93028 original size:24 final size:24
Alignment explanation
Indices: 92997--93043 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
92987 GGATTGCTAG
92997 AGAAGAAGACAAGGGCGTGCGTGA
1 AGAAGAAGACAAGGGCGTGCGTGA
**
93021 AGAAGAAGGGAAGGGCGTGCGTG
1 AGAAGAAGACAAGGGCGTGCGTG
93044 CGTGAAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.11, G:0.47, T:0.09
Consensus pattern (24 bp):
AGAAGAAGACAAGGGCGTGCGTGA
Found at i:93495 original size:21 final size:20
Alignment explanation
Indices: 93469--93513 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
93459 ATTATTAATG
*
93469 ATATTTTAGTAAATGAAAATA
1 ATATTTTAATAAAT-AAAATA
*
93490 ATA-TTTAATAAATAAAATT
1 ATATTTTAATAAATAAAATA
93509 ATATT
1 ATATT
93514 ATAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 8 0.38
20 10 0.48
21 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
ATATTTTAATAAATAAAATA
Found at i:93512 original size:19 final size:20
Alignment explanation
Indices: 93473--93513 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
93463 TTAATGATAT
*
93473 TTTAGTAAATGAAAATAATA
1 TTTAATAAATGAAAATAATA
*
93493 TTTAATAAAT-AAAATTATA
1 TTTAATAAATGAAAATAATA
93512 TT
1 TT
93514 ATAAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
TTTAATAAATGAAAATAATA
Done.