Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015114.1 Kokia drynarioides strain JFW-HI SEQ_130158, 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: 40916
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:3547 original size:13 final size:13
Alignment explanation
Indices: 3529--3563 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
3519 CTTTATCTCA
3529 TTTTCTCTTTAGC
1 TTTTCTCTTTAGC
3542 TTTTCTCTTTAGC
1 TTTTCTCTTTAGC
3555 TTTTCTCTT
1 TTTTCTCTT
3564 CCATTTCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.06, C:0.23, G:0.06, T:0.66
Consensus pattern (13 bp):
TTTTCTCTTTAGC
Found at i:5629 original size:37 final size:37
Alignment explanation
Indices: 5579--5652 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
5569 TGCTTTGAGC
5579 ATAGAGTATGAGTCAGTGTCAGATAAAGGCCAAAAGT
1 ATAGAGTATGAGTCAGTGTCAGATAAAGGCCAAAAGT
5616 ATAGAGTATGAGTCAGTGTCAGATAAAGGCCAAAAGT
1 ATAGAGTATGAGTCAGTGTCAGATAAAGGCCAAAAGT
5653 TAGCATGTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.27, T:0.22
Consensus pattern (37 bp):
ATAGAGTATGAGTCAGTGTCAGATAAAGGCCAAAAGT
Found at i:5831 original size:31 final size:31
Alignment explanation
Indices: 5796--5867 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
5786 TGCATATGCA
*
5796 TTCATGCATTTATAAAATTTCGCATCGCATT
1 TTCATGCATTCATAAAATTTCGCATCGCATT
* *
5827 TTCATGCATTCATAAAGTTTTGCATCGCATT
1 TTCATGCATTCATAAAATTTCGCATCGCATT
5858 TTCATGCATT
1 TTCATGCATT
5868 AAAAGTTTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.43
Consensus pattern (31 bp):
TTCATGCATTCATAAAATTTCGCATCGCATT
Found at i:10762 original size:50 final size:50
Alignment explanation
Indices: 10708--10816 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
10698 AGAGAAACAA
* * *
10708 ATTGAAGCCACGATGGCAAATCTCATAT-ACCTAAAGCTGTAGAGGGGCAG
1 ATTGAAGCCACAATGGCAAATCTCAT-TCACCTAAAGCTATAGAGAGGCAG
* ** * *
10758 ATTGAAGTCGTAATGGTAAATCTTATTCACCTAAAGCTATAGAGAGGCAG
1 ATTGAAGCCACAATGGCAAATCTCATTCACCTAAAGCTATAGAGAGGCAG
10808 ATTGAAGCC
1 ATTGAAGCC
10817 GAAAGAATGA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 1 0.02
50 48 0.98
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (50 bp):
ATTGAAGCCACAATGGCAAATCTCATTCACCTAAAGCTATAGAGAGGCAG
Found at i:10830 original size:50 final size:50
Alignment explanation
Indices: 10736--10832 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 50
10726 AATCTCATAT
* * * * *
10736 ACCTAAAGCTGTAGAGGGGCAGATTGAAGTCGTAATGGTAAATCTTATTC
1 ACCTAAAGCTATAGAGAGGCAGATTGAAGCCGTAAAGATAAATCTTATTC
*
10786 ACCTAAAGCTATAGAGAGGCAGATTGAAGCCG-AAAGAATGAATCTTA
1 ACCTAAAGCTATAGAGAGGCAGATTGAAGCCGTAAAG-ATAAATCTTA
10833 CACTCTTGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
49 3 0.08
50 37 0.93
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (50 bp):
ACCTAAAGCTATAGAGAGGCAGATTGAAGCCGTAAAGATAAATCTTATTC
Found at i:10966 original size:40 final size:40
Alignment explanation
Indices: 10894--11121 Score: 219
Period size: 40 Copynumber: 5.7 Consensus size: 40
10884 CGCCCATAGG
* * * *
10894 GCAGATTGAAGA-AATCCAATCTTTTACTCTAATTAGAGA
1 GCAGATTAAAGACTATCCAATCTTTTACCCTAATCAGAGA
* * *
10933 ACATATTAAAGACTATCCAATCTTTTACCCTAATCAAAGA
1 GCAGATTAAAGACTATCCAATCTTTTACCCTAATCAGAGA
* * * * *
10973 GCAGATTGAAGATTATCAAATCTTTTACCCTAATTAGAGG
1 GCAGATTAAAGACTATCCAATCTTTTACCCTAATCAGAGA
* *
11013 GCAGATTAAAGACTATCAAATATTTTACCCTAATCAGAGA
1 GCAGATTAAAGACTATCCAATCTTTTACCCTAATCAGAGA
* * * * *
11053 GCAGATTGAAGACCATCCAATCTCTTACCCCTACT-ATG-GG
1 GCAGATTAAAGACTATCCAATCTTTTA-CCCTAATCA-GAGA
* * *
11093 GCAGATTGAAGACCATCCAATCTCTTACC
1 GCAGATTAAAGACTATCCAATCTTTTACC
11122 TCGACCATGG
Statistics
Matches: 159, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
39 11 0.07
40 141 0.89
41 7 0.04
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (40 bp):
GCAGATTAAAGACTATCCAATCTTTTACCCTAATCAGAGA
Found at i:11010 original size:80 final size:79
Alignment explanation
Indices: 10894--11082 Score: 261
Period size: 80 Copynumber: 2.4 Consensus size: 79
10884 CGCCCATAGG
* * * *
10894 GCAGATTGAAGAAATCCAATCTTTTACTCTAATTAGAGAACATATTAAAGACTATCCAATCTTTT
1 GCAGATTGAAGAAATCCAATCTTTTACCCTAATTAGAGAACAGATTAAAGACTATCAAATATTTT
10959 ACCCTAATCAAAGA
66 ACCCTAATCAAAGA
* * **
10973 GCAGATTGAAGATTATCAAATCTTTTACCCTAATTAGAGGGCAGATTAAAGACTATCAAATATTT
1 GCAGATTGAAGA-AATCCAATCTTTTACCCTAATTAGAGAACAGATTAAAGACTATCAAATATTT
*
11038 TACCCTAATCAGAGA
65 TACCCTAATCAAAGA
* *
11053 GCAGATTGAAGACCATCCAATCTCTTACCC
1 GCAGATTGAAGA-AATCCAATCTTTTACCC
11083 CTACTATGGG
Statistics
Matches: 96, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 12 0.12
80 84 0.88
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (79 bp):
GCAGATTGAAGAAATCCAATCTTTTACCCTAATTAGAGAACAGATTAAAGACTATCAAATATTTT
ACCCTAATCAAAGA
Found at i:11095 original size:80 final size:80
Alignment explanation
Indices: 10937--11201 Score: 279
Period size: 80 Copynumber: 3.3 Consensus size: 80
10927 TAGAGAACAT
* ** * *
10937 ATTAAAGACTATCCAATCTTTTACCCTAATCAAAGAGCAGATTGAAGATTATCAAATCTTTTA-C
1 ATTAAAGACTATCCAATCTTTTACCCTAATCAGAGAGCAGATTGAAGACCATCCAATCTCTTACC
*
11001 CCTAAT-TAGAGGGCAG
66 CCTACTAT-G-GGGCAG
* *
11017 ATTAAAGACTATCAAATATTTTACCCTAATCAGAGAGCAGATTGAAGACCATCCAATCTCTTACC
1 ATTAAAGACTATCCAATCTTTTACCCTAATCAGAGAGCAGATTGAAGACCATCCAATCTCTTACC
11082 CCTACTATGGGGCAG
66 CCTACTATGGGGCAG
* * * * * *
11097 ATTGAAGACCATCCAATCTCTTA-CCTCGACCATG-GGGCAGATTGAAGACCATCCAATCTCTTA
1 ATTAAAGACTATCCAATCTTTTACCCT-AATCA-GAGAGCAGATTGAAGACCATCCAATCTCTTA
* * *
11160 CCTCGACCATGGGGCAG
64 CCCCTACTATGGGGCAG
* *
11177 ATTGAAGACCATCCAAT-TTCTTACC
1 ATTAAAGACTATCCAATCTT-TTACC
11202 ACAACTATGG
Statistics
Matches: 159, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
79 4 0.03
80 145 0.91
81 9 0.06
82 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (80 bp):
ATTAAAGACTATCCAATCTTTTACCCTAATCAGAGAGCAGATTGAAGACCATCCAATCTCTTACC
CCTACTATGGGGCAG
Found at i:11097 original size:120 final size:120
Alignment explanation
Indices: 10873--11477 Score: 314
Period size: 120 Copynumber: 5.1 Consensus size: 120
10863 CAACCATCTG
* * * *
10873 ATCTCTTACCTCGCCCAT-AGGGCAGATTGAAGA-AATCCAATCTTTTACTCTAATTAGAGAACA
1 ATCTCTTACCTCG-ACATGAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAATCAGAGAGCA
* * * * * ** * **
10936 TATTAAAGACTATCCAATCTTTTA-CCCTAATCAAAGAGCAGATTGAAGATTATCAA
65 GATTGAAGACCATCCAATCTCTTACCCCTACT-ATGGGGCAGATTGAAGACCATCAA
* * * * * *
10992 ATCTTTTACC-CTA-ATTAGAGGGCAGATTAAAGACTATCAAATATTTTACCCTAATCAGAGAGC
1 ATCTCTTACCTCGACA-T-GAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAATCAGAGAGC
*
11055 AGATTGAAGACCATCCAATCTCTTACCCCTACTATGGGGCAGATTGAAGACCATCCA
64 AGATTGAAGACCATCCAATCTCTTACCCCTACTATGGGGCAGATTGAAGACCATCAA
* * * * *
11112 ATCTCTTACCTCGACCATG-GGGCAGATTGAAGACCATCCAATCTCTTA-CCTCGACCATG-GGG
1 ATCTCTTACCTCGA-CATGAGGGCAGATTGAAGACAATCCAATCTTTTACCCT-AATCA-GAGAG
* * * * * *
11174 CAGATTGAAGACCATCCAATTTCTTACCACAACTATGGGGCATATTGAAG-CAATCCA
63 CAGATTGAAGACCATCCAATCTCTTACCCCTACTATGGGGCAGATTGAAGACCATCAA
* * * * ** * * * ** * ** * *
11231 CTGTTTTACC-CTAACCA-GAGGGCAGGCTAAAAACCATCCGGTCTATTACCCCGACCATG-GGG
1 ATCTCTTACCTC-GA-CATGAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAATCA-GAGAG
* * * * * * * * **
11293 TAGATTGAA-ACAATTCAATCTTTTA-TCCTAACGA-GAGGGCAGATTAAATACCATCCG
63 CAGATTGAAGACCATCCAATCTCTTACCCCT-ACTATG-GGGCAGATTGAAGACCATCAA
* * * * *
11350 ATCTCTTACC-CTGACCATG-GGGTAGATTGAAG-CAATCTAATATTTTACCCTAACCA-AAAGG
1 ATCTCTTACCTC-GA-CATGAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAATCAGAGA-G
* * * * *
11411 CAGATTGAAGACCATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAG-CAATCCA
63 CAGATTGAAGACCATCCAATCTCTTACCCCTACTATGGGGCAGATTGAAGACCATCAA
*
11468 ATCTTTTACC
1 ATCTCTTACC
11478 ATAATCAAAA
Statistics
Matches: 370, Mismatches: 94, Indels: 45
0.73 0.18 0.09
Matches are distributed among these distances:
116 1 0.00
117 3 0.01
118 67 0.18
119 135 0.36
120 152 0.41
121 10 0.03
122 1 0.00
123 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (120 bp):
ATCTCTTACCTCGACATGAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAATCAGAGAGCAG
ATTGAAGACCATCCAATCTCTTACCCCTACTATGGGGCAGATTGAAGACCATCAA
Found at i:11132 original size:40 final size:40
Alignment explanation
Indices: 11053--11558 Score: 425
Period size: 40 Copynumber: 12.8 Consensus size: 40
11043 TAATCAGAGA
* *
11053 GCAGATTGAAGACCATCCAATCTCTTACCCCTACTATGGG
1 GCAGATTGAAGACCATCCAATCTCTTACCCCAACCATGGG
* *
11093 GCAGATTGAAGACCATCCAATCTCTTACCTCGACCATGGG
1 GCAGATTGAAGACCATCCAATCTCTTACCCCAACCATGGG
* *
11133 GCAGATTGAAGACCATCCAATCTCTTACCTCGACCATGGG
1 GCAGATTGAAGACCATCCAATCTCTTACCCCAACCATGGG
* * *
11173 GCAGATTGAAGACCATCCAATTTCTTACCACAACTATGGG
1 GCAGATTGAAGACCATCCAATCTCTTACCCCAACCATGGG
* * * * * *
11213 GCATATTGAAG-CAATCCACTGTTTTACCCTAACCA-GAGG
1 GCAGATTGAAGACCATCCAATCTCTTACCCCAACCATG-GG
** * * ** * *
11252 GCAGGCTAAAAACCATCCGGTCTATTACCCCGACCATGGG
1 GCAGATTGAAGACCATCCAATCTCTTACCCCAACCATGGG
* * * * * * *
11292 GTAGATTGAA-ACAATTCAATCTTTTATCCTAACGA-GAGG
1 GCAGATTGAAGACCATCCAATCTCTTACCCCAACCATG-GG
* * * **
11331 GCAGATTAAATACCATCCGATCTCTTACCCTGACCATGGG
1 GCAGATTGAAGACCATCCAATCTCTTACCCCAACCATGGG
* * * * * * ***
11371 GTAGATTGAAG-CAATCTAATATTTTACCCTAACCAAAAG
1 GCAGATTGAAGACCATCCAATCTCTTACCCCAACCATGGG
*
11410 GCAGATTGAAGACCATCCGATCTCTTACCCCAACCATGGG
1 GCAGATTGAAGACCATCCAATCTCTTACCCCAACCATGGG
* * ** * ***
11450 GCAGATTGAAG-CAATCCAATCTTTTACCATAATCAAAAG
1 GCAGATTGAAGACCATCCAATCTCTTACCCCAACCATGGG
*
11489 GCAGATTGAAGACCAT-CAGATCTCTTACCCCGACCATGGG
1 GCAGATTGAAGACCATCCA-ATCTCTTACCCCAACCATGGG
* *
11529 GCAGATTGAA-ACAATCCAATCTTTTACCCC
1 GCAGATTGAAGACCATCCAATCTCTTACCCC
11559 TAAAACTATA
Statistics
Matches: 365, Mismatches: 91, Indels: 21
0.77 0.19 0.04
Matches are distributed among these distances:
38 2 0.01
39 127 0.35
40 234 0.64
41 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (40 bp):
GCAGATTGAAGACCATCCAATCTCTTACCCCAACCATGGG
Found at i:11280 original size:79 final size:79
Alignment explanation
Indices: 10864--11557 Score: 527
Period size: 79 Copynumber: 8.7 Consensus size: 79
10854 GCACAGTTAC
* * ** * * * **
10864 AACCATCTGATCTCTTACCTCGCCCATAGGGCAGATTGAAGAAATCCAATCTTTTACTCTAATTA
1 AACCATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCA
** *
10929 GAGAACATATTAAA
66 GAGGGCAGATTAAA
* * * * * * ** * * *
10943 GACTATCCAATCTTTTACCCTAATCAAAGAGCAGATTGAAG-ATTATCAAATCTTTTACCCTAAT
1 AACCATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAGCA--ATCCAATCTTTTACCCTAAC
*
11007 TAGAGGGCAGATTAAA
64 CAGAGGGCAGATTAAA
* * ** * * * * * * *
11023 GACTATCAAATATTTTACCCTAATCA-GAGAGCAGATTGAAGACCATCCAATCTCTTACCCCT-A
1 AACCATCCGATCTCTTACCCCAACCATG-GGGCAGATTGAAG-CAATCCAATCTTTTA-CCCTAA
* *
11086 CTATG-GGGCAGATTGAA
63 CCA-GAGGGCAGATTAAA
* * * * * * *
11103 GACCATCCAATCTCTTACCTCGACCATGGGGCAGATTGAAGACCATCCAATCTCTTA-CCTCGAC
1 AACCATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAG-CAATCCAATCTTTTACCCT-AAC
*
11167 CATG-GGGCAGATTGAA
64 CA-GAGGGCAGATTAAA
* * * * * * * *
11183 GACCATCCAATTTCTTACCACAACTATGGGGCATATTGAAGCAATCCACTGTTTTACCCTAACCA
1 AACCATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCA
**
11248 GAGGGCAGGCTAAA
66 GAGGGCAGATTAAA
* * * * * * * *
11262 AACCATCCGGTCTATTACCCCGACCATGGGGTAGATTGAAACAATTCAATCTTTTATCCTAACGA
1 AACCATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCA
11327 GAGGGCAGATTAAA
66 GAGGGCAGATTAAA
* ** * * *
11341 TACCATCCGATCTCTTACCCTGACCATGGGGTAGATTGAAGCAATCTAATATTTTACCCTAACCA
1 AACCATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCA
* * *
11406 AAAGGCAGATTGAA
66 GAGGGCAGATTAAA
* * *
11420 GACCATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCATAATCA
1 AACCATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCA
* * *
11485 AAAGGCAGATTGAA
66 GAGGGCAGATTAAA
* * * *
11499 GACCATCAGATCTCTTACCCCGACCATGGGGCAGATTGAAACAATCCAATCTTTTACCC
1 AACCATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCC
11558 CTAAAACTAT
Statistics
Matches: 512, Mismatches: 91, Indels: 24
0.82 0.15 0.04
Matches are distributed among these distances:
78 5 0.01
79 306 0.60
80 195 0.38
81 6 0.01
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (79 bp):
AACCATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCA
GAGGGCAGATTAAA
Found at i:11300 original size:119 final size:120
Alignment explanation
Indices: 11053--11556 Score: 366
Period size: 119 Copynumber: 4.2 Consensus size: 120
11043 TAATCAGAGA
* * *
11053 GCAGATTGAAGACCATCCAATCTCTTACCCCTACTATGGGGCAGATTGAAGACCATCCAATCTCT
1 GCAGATTGAAGACCATCCAATCTCTTACCACAACTATGGGGCAGATTGAAGACAATCCAATCTCT
* * * * * *
11118 TACCTCGACCATGGGGCAGATTGAAGACCATCCAATCTCTTACCTCGACCATGGG
66 TACCTCAACCATGGGGCAGACTAAAAACCATCCAATCTATTACCCCGACCATGGG
* * * * *
11173 GCAGATTGAAGACCATCCAATTTCTTACCACAACTATGGGGCATATTGAAG-CAATCCACTGTTT
1 GCAGATTGAAGACCATCCAATCTCTTACCACAACTATGGGGCAGATTGAAGACAATCCAATCTCT
* **
11237 TACC-CTAACCA-GAGGGCAGGCTAAAAACCATCCGGTCTATTACCCCGACCATGGG
66 TACCTC-AACCATG-GGGCAGACTAAAAACCATCCAATCTATTACCCCGACCATGGG
* * * * * * * * * *
11292 GTAGATTGAA-ACAATTCAATCTTTTATCC-TAACGA-GAGGGCAGATTAAATACCATCCGATCT
1 GCAGATTGAAGACCATCCAATCTCTTA-CCACAACTATG-GGGCAGATTGAAGACAATCCAATCT
* * ** * * * * * ** ***
11354 CTTACC-CTGACCATGGGGTAGA-TTGAAGCAATCTAATATTTTACCCTAACCAAAAG
64 CTTACCTC-AACCATGGGGCAGACTAAAAACCATCCAATCTATTACCCCGACCATGGG
* * * *
11410 GCAGATTGAAGACCATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAG-CAATCCAATCTTT
1 GCAGATTGAAGACCATCCAATCTCTTACCACAACTATGGGGCAGATTGAAGACAATCCAATCTCT
* *** * * * *
11474 TACCAT-AATCAAAAGGCAGATTGAAGACCAT-CAGATCTCTTACCCCGACCATGGG
66 TACC-TCAACCATGGGGCAGACTAAAAACCATCCA-ATCTATTACCCCGACCATGGG
* *
11529 GCAGATTGAA-ACAATCCAATCTTTTACC
1 GCAGATTGAAGACCATCCAATCTCTTACC
11557 CCTAAAACTA
Statistics
Matches: 288, Mismatches: 83, Indels: 28
0.72 0.21 0.07
Matches are distributed among these distances:
117 1 0.00
118 97 0.34
119 141 0.49
120 49 0.17
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (120 bp):
GCAGATTGAAGACCATCCAATCTCTTACCACAACTATGGGGCAGATTGAAGACAATCCAATCTCT
TACCTCAACCATGGGGCAGACTAAAAACCATCCAATCTATTACCCCGACCATGGG
Found at i:11416 original size:39 final size:39
Alignment explanation
Indices: 10893--11557 Score: 191
Period size: 40 Copynumber: 16.8 Consensus size: 39
10883 TCGCCCATAG
* * **
10893 GGCAGATTGAAGAAATCCAATCTTTTACTCTAATTAGAGAA
1 GGCAGATTGAAGCAATCCAATCTTTTACCCTAACCA-A-AA
* * * *
10934 --CATATTAAAGACTATCCAATCTTTTACCCTAATC-AAA
1 GGCAGATTGAAG-CAATCCAATCTTTTACCCTAACCAAAA
* ** * *
10971 GAGCAGATTGAAG-ATTATCAAATCTTTTACCCTAATTAGAG
1 G-GCAGATTGAAGCA--ATCCAATCTTTTACCCTAACCAAAA
* * * * * *
11012 GGCAGATTAAAGACTATCAAATATTTTACCCTAATC-AGA
1 GGCAGATTGAAG-CAATCCAATCTTTTACCCTAACCAAAA
* * * ***
11051 GAGCAGATTGAAGACCATCCAATCTCTTACCCCT-ACTATGG
1 G-GCAGATTGAAG-CAATCCAATCTTTTA-CCCTAACCAAAA
* * * ***
11092 GGCAGATTGAAGACCATCCAATCTCTTA-CCTCGACCATGG
1 GGCAGATTGAAG-CAATCCAATCTTTTACCCT-AACCAAAA
* * * ***
11132 GGCAGATTGAAGACCATCCAATCTCTTA-CCTCGACCATGG
1 GGCAGATTGAAG-CAATCCAATCTTTTACCCT-AACCAAAA
* * ***
11172 GGCAGATTGAAGACCATCCAAT-TTCTTACCAC-AACTATGG
1 GGCAGATTGAAG-CAATCCAATCTT-TTACC-CTAACCAAAA
* * * * *
11212 GGCATATTGAAGCAATCCACTGTTTTACCCTAACCAGAG
1 GGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAAAA
* ** * * ** * ** ***
11251 GGCAGGCTAAAAACCATCCGGTCTATTACCCCGACCATGG
1 GGCA-GATTGAAGCAATCCAATCTTTTACCCTAACCAAAA
* * * * * * *
11291 GGTAGATTGAAACAATTCAATCTTTTATCCTAACGAGAG
1 GGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAAAA
* * * * * * ***
11330 GGCAGATTAAATACCATCCGATCTCTTACCCTGACCATGG
1 GGCAGATTGAA-GCAATCCAATCTTTTACCCTAACCAAAA
* * *
11370 GGTAGATTGAAGCAATCTAATATTTTACCCTAACCAAAA
1 GGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAAAA
* * * * ***
11409 GGCAGATTGAAGACCATCCGATCTCTTACCCCAACCATGG
1 GGCAGATTGAAG-CAATCCAATCTTTTACCCTAACCAAAA
* *
11449 GGCAGATTGAAGCAATCCAATCTTTTACCATAATCAAAA
1 GGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAAAA
* * ** ***
11488 GGCAGATTGAAGACCAT-CAGATCTCTTACCCCGACCATGG
1 GGCAGATTGAAG-CAATCCA-ATCTTTTACCCTAACCAAAA
*
11528 GGCAGATTGAAACAATCCAATCTTTTACCC
1 GGCAGATTGAAGCAATCCAATCTTTTACCC
11558 CTAAAACTAT
Statistics
Matches: 477, Mismatches: 122, Indels: 52
0.73 0.19 0.08
Matches are distributed among these distances:
37 2 0.00
38 5 0.01
39 135 0.28
40 325 0.68
41 9 0.02
42 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (39 bp):
GGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAAAA
Found at i:12071 original size:63 final size:63
Alignment explanation
Indices: 11933--12109 Score: 263
Period size: 59 Copynumber: 2.8 Consensus size: 63
11923 TTCTTATTAT
11933 TTTTATTTATTTATTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTG
1 TTTTA-TTATTTATTTATTA-TTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTG
* *
11998 --TT-TTA-TTATTTATTATTCTATGAATATAAATAAATAAATGTAAAATAATATTAATTTTG
1 TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTG
* *
12057 TTTTATTATTTATTTATTATTTTATGAATATATATAAATAAATAAATAAATAA
1 TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATATA-AAATAA
12110 CAAACCCAAT
Statistics
Matches: 101, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
59 42 0.42
60 10 0.10
61 5 0.05
62 3 0.03
63 35 0.35
64 6 0.06
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (63 bp):
TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTG
Found at i:25960 original size:16 final size:16
Alignment explanation
Indices: 25939--25972 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25929 AAAGGATTTT
* *
25939 TTTAGTTATTTTTTAA
1 TTTAGTTAGTGTTTAA
25955 TTTAGTTAGTGTTTAA
1 TTTAGTTAGTGTTTAA
25971 TT
1 TT
25973 GACTCGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (16 bp):
TTTAGTTAGTGTTTAA
Found at i:27378 original size:2 final size:2
Alignment explanation
Indices: 27371--27403 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27361 CATCATTTAT
27371 TA TA 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 TA TA T
27404 TTAATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27759 original size:44 final size:46
Alignment explanation
Indices: 27666--27759 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 46
27656 GGTTCGCTGT
*
27666 AATGGAATAGAGTTGTAATCAGTAATTCAGTTGTTTGGTTGAATAG
1 AATGGAATAGAGCTGTAATCAGTAATTCAGTTGTTTGGTTGAATAG
* *
27712 AATGGAATAGAGCTGTAAT-AGT-ATT-ATTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCAGT-TGTTTGGTTGAATAG
27756 AATG
1 AATG
27760 ATATTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 2 0.05
44 21 0.48
45 3 0.07
46 18 0.41
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATCAGTAATTCAGTTGTTTGGTTGAATAG
Found at i:27933 original size:37 final size:39
Alignment explanation
Indices: 27891--27973 Score: 116
Period size: 38 Copynumber: 2.2 Consensus size: 39
27881 AAAATAATAA
*
27891 ATAATTTAATTACA-TTTTAACATAATTATTATTAA-AT
1 ATAATTTAATAACATTTTTAACATAATTATTATTAAGAT
* *
27928 ATAATTTAATAATATTTTTAATATAATTATTATTAAGAT
1 ATAATTTAATAACATTTTTAACATAATTATTATTAAGAT
27967 ATGAATT
1 AT-AATT
27974 AGTAAAAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
37 12 0.30
38 20 0.50
39 4 0.10
40 4 0.10
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (39 bp):
ATAATTTAATAACATTTTTAACATAATTATTATTAAGAT
Found at i:36980 original size:85 final size:84
Alignment explanation
Indices: 36836--36990 Score: 192
Period size: 84 Copynumber: 1.8 Consensus size: 84
36826 AATAGTCCTT
* * * *
36836 AAAATGATAAAATTTTAATTTAAACCCTTTATAATTTTTAAAATTTTAAATTTATAATAAAAAAA
1 AAAATAATAAAATTTTAATTTAAACCCTTTATAATTTATAAAATTATAAATTTAAAAT-AAAAAA
36901 ATTACACTTTAACTACCTCA
65 ATTACACTTTAACTACCTCA
*
36921 AAAATAATAATAA-TTTAATTT-AACCCTTTA-AATATTAT-AAATTATAAATTATTAAAATAAT
1 AAAATAATAA-AATTTTAATTTAAACCCTTTATAAT-TTATAAAATTATAAA-T-TTAAAATAAA
36982 AAAATTACA
62 AAAATTACA
36991 TTTTTACGCT
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
83 12 0.20
84 24 0.39
85 23 0.38
86 2 0.03
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (84 bp):
AAAATAATAAAATTTTAATTTAAACCCTTTATAATTTATAAAATTATAAATTTAAAATAAAAAAA
TTACACTTTAACTACCTCA
Found at i:37085 original size:14 final size:13
Alignment explanation
Indices: 37066--37102 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
37056 ACCATCCTTG
37066 CAAATAAAACAAGA
1 CAAATAAAACAA-A
37080 CAAATAATAACAAA
1 CAAATAA-AACAAA
37094 CAAATAAAA
1 CAAATAAAA
37103 ACCAGTAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 15 0.68
15 5 0.23
ACGTcount: A:0.73, C:0.14, G:0.03, T:0.11
Consensus pattern (13 bp):
CAAATAAAACAAA
Found at i:38311 original size:22 final size:21
Alignment explanation
Indices: 38273--38355 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 21
38263 ATTATATTGT
*
38273 TGTTTTGGTGCTATTTTTTAT
1 TGTTTTGGTGCTATTTTTTAC
* *
38294 TGTTTTGGTTGCTTTTTTTTGC
1 TGTTTTGG-TGCTATTTTTTAC
* * *
38316 TATTTTGGTGTTGTTTTTTTAC
1 TGTTTTGGTGCT-ATTTTTTAC
*
38338 TGTTTTAGTTGCTATTTT
1 TGTTTT-GGTGCTATTTT
38356 GGTATTTTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
21 11 0.22
22 34 0.69
23 4 0.08
ACGTcount: A:0.07, C:0.06, G:0.19, T:0.67
Consensus pattern (21 bp):
TGTTTTGGTGCTATTTTTTAC
Found at i:38444 original size:12 final size:12
Alignment explanation
Indices: 38376--38430 Score: 101
Period size: 12 Copynumber: 4.6 Consensus size: 12
38366 ATTGTTTTGA
38376 TGTTGTTATTTT
1 TGTTGTTATTTT
38388 TGTTGTTATTTT
1 TGTTGTTATTTT
*
38400 TGTTATTATTTT
1 TGTTGTTATTTT
38412 TGTTGTTATTTT
1 TGTTGTTATTTT
38424 TGTTGTT
1 TGTTGTT
38431 TTGCTGTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.09, C:0.00, G:0.16, T:0.75
Consensus pattern (12 bp):
TGTTGTTATTTT
Done.