Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011600.1 Kokia drynarioides strain JFW-HI SEQ_126590, 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: 270200
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4806 original size:17 final size:17
Alignment explanation
Indices: 4773--4821 Score: 80
Period size: 17 Copynumber: 2.8 Consensus size: 17
4763 AGGAGAAGGG
4773 AGAAGAAGGAAAGAAAGAA
1 AGAAGAAGG--AGAAAGAA
4792 AGAAGAAGGAGAAAGAA
1 AGAAGAAGGAGAAAGAA
4809 AGAAGAAGGAGAA
1 AGAAGAAGGAGAA
4822 GAATGTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 21 0.70
19 9 0.30
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (17 bp):
AGAAGAAGGAGAAAGAA
Found at i:5157 original size:71 final size:71
Alignment explanation
Indices: 5082--5216 Score: 270
Period size: 71 Copynumber: 1.9 Consensus size: 71
5072 TTTTGTTTAA
5082 TTTAATTTTTATTTGATTTGTTATTAATTTTTTTATTTGGTAGAGTAGATTAAGAAGAGAGGAAG
1 TTTAATTTTTATTTGATTTGTTATTAATTTTTTTATTTGGTAGAGTAGATTAAGAAGAGAGGAAG
5147 AAAGAG
66 AAAGAG
5153 TTTAATTTTTATTTGATTTGTTATTAATTTTTTTATTTGGTAGAGTAGATTAAGAAGAGAGGAA
1 TTTAATTTTTATTTGATTTGTTATTAATTTTTTTATTTGGTAGAGTAGATTAAGAAGAGAGGAA
5217 AGAAGGTAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (71 bp):
TTTAATTTTTATTTGATTTGTTATTAATTTTTTTATTTGGTAGAGTAGATTAAGAAGAGAGGAAG
AAAGAG
Found at i:17800 original size:26 final size:26
Alignment explanation
Indices: 17771--17825 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
17761 GATACCGAAG
* *
17771 CTTCAATGAGATCACAATATCCTAAC
1 CTTCAATGAAATCACAATACCCTAAC
* *
17797 CTTCGATGAAATCACAGTACCCTAAC
1 CTTCAATGAAATCACAATACCCTAAC
17823 CTT
1 CTT
17826 TTCACTGGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.27
Consensus pattern (26 bp):
CTTCAATGAAATCACAATACCCTAAC
Found at i:22804 original size:15 final size:16
Alignment explanation
Indices: 22756--22805 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
22746 TAAATAAAAA
*
22756 AAAAATAAAAATAGCAT
1 AAAAATAAAAACA-CAT
* *
22773 AAAAAT-ATAACATAT
1 AAAAATAAAAACACAT
22788 AAAAATAAAAACA-AT
1 AAAAATAAAAACACAT
22803 AAA
1 AAA
22806 TAAGGCAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 13 0.46
16 9 0.32
17 6 0.21
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.18
Consensus pattern (16 bp):
AAAAATAAAAACACAT
Found at i:24578 original size:50 final size:50
Alignment explanation
Indices: 24500--24821 Score: 222
Period size: 50 Copynumber: 6.5 Consensus size: 50
24490 TTTGCTATTA
* * * *
24500 CGGCTTTGATCTGTCCCTCTTC-GATTTTAAAGGTGTAAGATTCACCTTTA
1 CGGCTTTAATCTGTCCCTCTTCAG-TTTTAAGGGTGTAAGATTCACCGTTG
* * * * *
24550 CGACTTTAATTTGTCCCTCTTCAGTTTT-AGAGGTATAAGATTTATCGTTG
1 CGGCTTTAATCTGTCCCTCTTCAGTTTTAAG-GGTGTAAGATTCACCGTTG
* * * * **
24600 TGGTTTTAATCTGTCCATCTTCAATTTTAAGGGTGTAAGATT-AGTTGTTG
1 CGGCTTTAATCTGTCCCTCTTCAGTTTTAAGGGTGTAAGATTCA-CCGTTG
* * * * * *
24650 TGGCTTTAATATGTCCTTCTTC-GATTTTAGGGGTATAAGATTCATCGTTG
1 CGGCTTTAATCTGTCCCTCTTCAG-TTTTAAGGGTGTAAGATTCACCGTTG
* * * *
24700 CGACTTTAATCTGTCCCTTTTTAGTTTTAAGGGTGTAAGATTCACTGTTG
1 CGGCTTTAATCTGTCCCTCTTCAGTTTTAAGGGTGTAAGATTCACCGTTG
** * ** * * * * *
24750 CAACTTTTATCTAACCCTCTTCAGCTTT-AGGGTATACGATTCGCCTTTG
1 CGGCTTTAATCTGTCCCTCTTCAGTTTTAAGGGTGTAAGATTCACCGTTG
* * * *
24799 TGGCTTCAATCTGCCCCTATTCA
1 CGGCTTTAATCTGTCCCTCTTCA
24822 ACTTTAGGAT
Statistics
Matches: 211, Mismatches: 54, Indels: 15
0.75 0.19 0.05
Matches are distributed among these distances:
49 33 0.16
50 173 0.82
51 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (50 bp):
CGGCTTTAATCTGTCCCTCTTCAGTTTTAAGGGTGTAAGATTCACCGTTG
Found at i:24749 original size:100 final size:101
Alignment explanation
Indices: 24503--24791 Score: 291
Period size: 100 Copynumber: 2.9 Consensus size: 101
24493 GCTATTACGG
* * * * * *
24503 CTTTGATCTGTCCCTCTTCGATTTTAAAGGTGTAAGATTCACCT-TTACGACTTTAATTTGTCCC
1 CTTTAATCTGTCCATCTTCAATTTTAAGGGTGTAAGATTCACCTGTTGCGACTTTAATATGTCCC
* * *
24567 TCTTCAGTTTTAGAGGTATAAGATTTATCGTTGTGG
66 TCTTCAGTTTTAGAGGTATAAGATTCATCGTTGCGA
* ** * * *
24603 TTTTAATCTGTCCATCTTCAATTTTAAGGGTGTAAGATT-AGTTGTTGTGGCTTTAATATGTCCT
1 CTTTAATCTGTCCATCTTCAATTTTAAGGGTGTAAGATTCACCTGTTGCGACTTTAATATGTCCC
*
24667 TCTTC-GATTTTAGGGGTATAAGATTCATCGTTGCGA
66 TCTTCAG-TTTTAGAGGTATAAGATTCATCGTTGCGA
* * * * * * * **
24703 CTTTAATCTGTCCCTTTTTAGTTTTAAGGGTGTAAGATTCA-CTGTTGCAACTTTTATCTAACCC
1 CTTTAATCTGTCCATCTTCAATTTTAAGGGTGTAAGATTCACCTGTTGCGACTTTAATATGTCCC
* *
24767 TCTTCAGCTTTAG-GGTATACGATTC
66 TCTTCAGTTTTAGAGGTATAAGATTC
24792 GCCTTTGTGG
Statistics
Matches: 153, Mismatches: 32, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
99 14 0.09
100 137 0.90
101 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.43
Consensus pattern (101 bp):
CTTTAATCTGTCCATCTTCAATTTTAAGGGTGTAAGATTCACCTGTTGCGACTTTAATATGTCCC
TCTTCAGTTTTAGAGGTATAAGATTCATCGTTGCGA
Found at i:24772 original size:150 final size:150
Alignment explanation
Indices: 24501--24772 Score: 316
Period size: 150 Copynumber: 1.8 Consensus size: 150
24491 TTGCTATTAC
* * * * *
24501 GGCTTTGATCTGTCCCTCTTCGATTTTAAAGGTGTAAGATTCACCTTTACGACTTTAATTTGTCC
1 GGCTTTAATATGTCCCTCTTCGATTTTAAAGGTATAAGATTCACCGTTACGACTTTAATCTGTCC
* *** **
24566 CTCTTCAGTTTTAGAGGTATAAGATTTATCGTTGTGGTTTTAATCTGTCCATCTTCAATTTTAAG
66 CTCTTCAGTTTTAGAGGTATAAGATTCATCGTTGAACTTTTAATCTAACCATCTTCAATTTTAAG
24631 GGTGTAAGATTAGTTGTTGT
131 GGTGTAAGATTAGTTGTTGT
* ** * *
24651 GGCTTTAATATGTCCTTCTTCGATTTTAGGGGTATAAGATTCATCGTTGCGACTTTAATCTGTCC
1 GGCTTTAATATGTCCCTCTTCGATTTTAAAGGTATAAGATTCACCGTTACGACTTTAATCTGTCC
* * * *
24716 CTTTTTAGTTTTA-AGGGTGTAAGATTCA-CTGTTGCAACTTTT-ATCTAACCCTCTTCA
66 CTCTTCAGTTTTAGA-GGTATAAGATTCATC-GTTG-AACTTTTAATCTAACCATCTTCA
24773 GCTTTAGGGT
Statistics
Matches: 99, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
149 2 0.02
150 93 0.94
151 4 0.04
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.43
Consensus pattern (150 bp):
GGCTTTAATATGTCCCTCTTCGATTTTAAAGGTATAAGATTCACCGTTACGACTTTAATCTGTCC
CTCTTCAGTTTTAGAGGTATAAGATTCATCGTTGAACTTTTAATCTAACCATCTTCAATTTTAAG
GGTGTAAGATTAGTTGTTGT
Found at i:28310 original size:82 final size:82
Alignment explanation
Indices: 28173--28332 Score: 241
Period size: 82 Copynumber: 2.0 Consensus size: 82
28163 CCCACACTCT
* * *
28173 CGGGTTATGCTTCTTGAGAAGACGTAAGATACAATCACATTTCTCATTTAGTTGTGAGATGAATC
1 CGGGTTATGCTTCTTGAGAAGACGGAAGATACAATCACATTTCTCATTTAGTTGTGACATGAACC
28238 G-GTCGATGTAATTCAGA
66 GAG-CGATGTAATTCAGA
** * *
28255 CGGGTTATGCTTCTTGAGAAGACGGAAGATAGGATCACATTTTTCGTTTAGTTGTGACATGAACC
1 CGGGTTATGCTTCTTGAGAAGACGGAAGATACAATCACATTTCTCATTTAGTTGTGACATGAACC
28320 GAGCGATGTAATT
66 GAGCGATGTAATT
28333 TAGTCTCCCT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
82 69 0.99
83 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (82 bp):
CGGGTTATGCTTCTTGAGAAGACGGAAGATACAATCACATTTCTCATTTAGTTGTGACATGAACC
GAGCGATGTAATTCAGA
Found at i:46924 original size:11 final size:11
Alignment explanation
Indices: 46908--46934 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
46898 ATAAATACAA
46908 TAAATAAAAAT
1 TAAATAAAAAT
46919 TAAATAAAAAT
1 TAAATAAAAAT
46930 TAAAT
1 TAAAT
46935 GCTAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAATAAAAAT
Found at i:55524 original size:28 final size:28
Alignment explanation
Indices: 55484--55554 Score: 142
Period size: 28 Copynumber: 2.5 Consensus size: 28
55474 AATAGGCATA
55484 ACCTTTGGGTTAACAGGGACTAACCATG
1 ACCTTTGGGTTAACAGGGACTAACCATG
55512 ACCTTTGGGTTAACAGGGACTAACCATG
1 ACCTTTGGGTTAACAGGGACTAACCATG
55540 ACCTTTGGGTTAACA
1 ACCTTTGGGTTAACA
55555 AGGAGTAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (28 bp):
ACCTTTGGGTTAACAGGGACTAACCATG
Found at i:56300 original size:21 final size:21
Alignment explanation
Indices: 56274--56313 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
56264 TTTTTAATAC
*
56274 CGATAGAAGCATTATTTGTTT
1 CGATAGAAGCATTACTTGTTT
*
56295 CGATAGAAGCTTTACTTGT
1 CGATAGAAGCATTACTTGT
56314 ATCGGTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (21 bp):
CGATAGAAGCATTACTTGTTT
Found at i:59850 original size:7 final size:7
Alignment explanation
Indices: 59838--59871 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
59828 TAAGATCTCG
59838 TTAGGGT
1 TTAGGGT
59845 TTAGGGT
1 TTAGGGT
59852 TTAGGGT
1 TTAGGGT
*
59859 TTAGGAT
1 TTAGGGT
59866 TTAGGG
1 TTAGGG
59872 CTTAATTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (7 bp):
TTAGGGT
Found at i:61329 original size:16 final size:17
Alignment explanation
Indices: 61299--61340 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
61289 TGCATGTGGA
61299 AAATAATAAAATAAA-T
1 AAATAATAAAATAAACT
* *
61315 AAATAATACATTAAACT
1 AAATAATAAAATAAACT
*
61332 AAAAAATAA
1 AAATAATAA
61341 CTCTTAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAATAAAATAAACT
Found at i:64458 original size:46 final size:46
Alignment explanation
Indices: 64359--64468 Score: 130
Period size: 46 Copynumber: 2.4 Consensus size: 46
64349 TTAGTCTAGT
** * * *
64359 CAATTGTCTTCCACAATTTTAGAGGTTTATTTGATTAAATTATAGG
1 CAATTGTCTTCCACAATTGCAGAGATTTATTTGACTAAATTATAAG
* * * * *
64405 CATTTGTCTTCCACAATTGCAGAGATTTGTTTGGCTAATTTGTAAG
1 CAATTGTCTTCCACAATTGCAGAGATTTATTTGACTAAATTATAAG
64451 CAATTGTCTTCCACAATT
1 CAATTGTCTTCCACAATT
64469 TCAAGGATTA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (46 bp):
CAATTGTCTTCCACAATTGCAGAGATTTATTTGACTAAATTATAAG
Found at i:67555 original size:26 final size:26
Alignment explanation
Indices: 67525--67602 Score: 147
Period size: 26 Copynumber: 3.0 Consensus size: 26
67515 AATAGTAATA
*
67525 ACTGCCAGTCAGGTGTCTTATAATGT
1 ACTGCCAGCCAGGTGTCTTATAATGT
67551 ACTGCCAGCCAGGTGTCTTATAATGT
1 ACTGCCAGCCAGGTGTCTTATAATGT
67577 ACTGCCAGCCAGGTGTCTTATAATGT
1 ACTGCCAGCCAGGTGTCTTATAATGT
67603 GCAGGATATC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (26 bp):
ACTGCCAGCCAGGTGTCTTATAATGT
Found at i:68086 original size:21 final size:21
Alignment explanation
Indices: 68047--68086 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
68037 TTTTATATGA
*
68047 AATTTTGAATTGAAGAGTTTT
1 AATTTTGAATTGAAAAGTTTT
68068 AATTATTGAATT-AAAAGTT
1 AATT-TTGAATTGAAAAGTT
68087 AGTGTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (21 bp):
AATTTTGAATTGAAAAGTTTT
Found at i:71297 original size:24 final size:24
Alignment explanation
Indices: 71261--71769 Score: 525
Period size: 24 Copynumber: 21.2 Consensus size: 24
71251 ACAAGTTGAT
* *
71261 TACGTTTACGCTCGTCACCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * * *
71285 TACGTTTAAGCTCGTCAACTTGAA
1 TACGTTTACGCTCGCCAGCATGAA
* *
71309 TACGTTTACACTCACCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
71333 TATGTTTATGCTCACCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
71357 TACGTTCACGCTCGTCAGCATTAA
1 TACGTTTACGCTCGCCAGCATGAA
* *
71381 TACGTTTACACTCGTCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
*
71405 TACGTTTACGCTTGCCAG-ATTGAA
1 TACGTTTACGCTCGCCAGCA-TGAA
*
71429 TACGTTTACGCTCGCCAACATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* *
71453 TACATTTACGCTCGTCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* *
71477 TACGTTTACGCTCACTAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
71501 TACGTTTACGCTTGCTAGCGTGAA
1 TACGTTTACGCTCGCCAGCATGAA
* ** *
71525 TACGTTTATGCTCGTTAGAATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* *
71549 TATGTTTACGCTCGCCAACATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* *
71573 TACTTTTACGCTCGCCAACATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
71597 TACGTTTGCACTCGCCTGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
71621 TACGTTTATGCTCGACGGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
71645 TACATTTATGCTCGCCAACATGAA
1 TACGTTTACGCTCGCCAGCATGAA
*
71669 TACATTTACGCTCGCCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * * *
71693 TATGTTTATGCTCGTCAACATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
71717 TATGTTTACGCTTGCCAGCATAAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
71741 TACGTTGATGCTCGTCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
71765 TACGT
1 TACGT
71770 GAAACATTGT
Statistics
Matches: 402, Mismatches: 81, Indels: 4
0.83 0.17 0.01
Matches are distributed among these distances:
23 1 0.00
24 400 1.00
25 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (24 bp):
TACGTTTACGCTCGCCAGCATGAA
Found at i:74054 original size:38 final size:37
Alignment explanation
Indices: 74012--74088 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
74002 TAATCACCGA
* ** *
74012 CACAAAGGCTTGCTAGACTTATAGCCCGATTACACTGG
1 CACAAA-GCCTGCTAGACACATAGCCCGAATACACTGG
*
74050 CACAAAGCCTGCTAGGCACATAGCCCGAATACACTGG
1 CACAAAGCCTGCTAGACACATAGCCCGAATACACTGG
74087 CA
1 CA
74089 TGAAGCCTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
37 28 0.82
38 6 0.18
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.18
Consensus pattern (37 bp):
CACAAAGCCTGCTAGACACATAGCCCGAATACACTGG
Found at i:79890 original size:24 final size:24
Alignment explanation
Indices: 79854--80108 Score: 223
Period size: 24 Copynumber: 10.5 Consensus size: 24
79844 GCAAGTTCAT
* *
79854 TACGTTTGCGCTCGTCAGCATTAA
1 TACGTTTACGCTCGTCAGCATGAA
* *
79878 TACATTTACGCTCGCCAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
*
79902 TACGTTTACACTCGTCAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
79926 TACGTTTACGCACGCTCGTCAGCATGAA
1 TACGTTT----ACGCTCGTCAGCATGAA
** *
79954 TATATTTACGCTC-TCCAGGATGAA
1 TACGTTTACGCTCGT-CAGCATGAA
* *
79978 TAC-TTTATGCTTGTCAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
* *
80001 TATGTTTACGCTC-TCCAACATGAA
1 TACGTTTACGCTCGT-CAGCATGAA
* *
80025 TATGTTTACGCTCGCCAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
* **
80049 TAC-TTTACACTCACCAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
* * *
80072 TATGTTTACACTC-TCCAACATGAA
1 TACGTTTACGCTCGT-CAGCATGAA
*
80096 AACGTTTACGCTC
1 TACGTTTACGCTC
80109 ACCAACATGA
Statistics
Matches: 190, Mismatches: 30, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
23 39 0.21
24 130 0.68
28 21 0.11
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (24 bp):
TACGTTTACGCTCGTCAGCATGAA
Found at i:80012 original size:47 final size:48
Alignment explanation
Indices: 79869--80122 Score: 187
Period size: 47 Copynumber: 5.2 Consensus size: 48
79859 TTGCGCTCGT
* * ** *
79869 CAGCATTAATA-CATTTACGCTCGCCAGCATGAATACGTTTACACTCGT-
1 CAGCATGAATATC-TTTACGCTCGTCAGCATGAATATATTTACGCTC-TC
79917 CAGCATGAATA-CGTTTACGCACGCTCGTCAGCATGAATATATTTACGCTCTC
1 CAGCATGAATATC-TTT----ACGCTCGTCAGCATGAATATATTTACGCTCTC
* * * *
79969 CAGGATGAATA-CTTTATGCTTGTCAGCATGAATATGTTTACGCTCTC
1 CAGCATGAATATCTTTACGCTCGTCAGCATGAATATATTTACGCTCTC
* * * * * *
80016 CAACATGAATATGTTTACGCTCGCCAGCATGAATA-CTTTACACTCAC
1 CAGCATGAATATCTTTACGCTCGTCAGCATGAATATATTTACGCTCTC
* * * * ** *
80063 CAGCATGAATATGTTTACACTC-TCCAACATGAAAACGTTTACGCTCAC
1 CAGCATGAATATCTTTACGCTCGT-CAGCATGAATATATTTACGCTCTC
*
80111 CAACATGAATAT
1 CAGCATGAATAT
80123 GTGAAACATT
Statistics
Matches: 171, Mismatches: 27, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
47 76 0.44
48 54 0.32
51 4 0.02
52 37 0.22
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (48 bp):
CAGCATGAATATCTTTACGCTCGTCAGCATGAATATATTTACGCTCTC
Found at i:80034 original size:71 final size:71
Alignment explanation
Indices: 79882--80121 Score: 291
Period size: 71 Copynumber: 3.3 Consensus size: 71
79872 CATTAATACA
* *
79882 TTTACGCTCGCCAGCATGAATACGTTTACACTCGTCAGCATGAATACGTTTACGCACGCTCGTCA
1 TTTACGCTCGCCAGCATGAATAC-TTTACACTCGTCAGCATGAATATGTTTACG--CTCTC--CA
* *
79947 GCATGAATATA
61 ACATGAATATG
* * ** *
79958 TTTACGCTCTCCAGGATGAATACTTTATGCTTGTCAGCATGAATATGTTTACGCTCTCCAACATG
1 TTTACGCTCGCCAGCATGAATACTTTACACTCGTCAGCATGAATATGTTTACGCTCTCCAACATG
80023 AATATG
66 AATATG
** *
80029 TTTACGCTCGCCAGCATGAATACTTTACACTCACCAGCATGAATATGTTTACACTCTCCAACATG
1 TTTACGCTCGCCAGCATGAATACTTTACACTCGTCAGCATGAATATGTTTACGCTCTCCAACATG
* *
80094 AAAACG
66 AATATG
* *
80100 TTTACGCTCACCAACATGAATA
1 TTTACGCTCGCCAGCATGAATA
80122 TGTGAAACAT
Statistics
Matches: 143, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
71 92 0.64
73 4 0.03
75 26 0.18
76 21 0.15
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (71 bp):
TTTACGCTCGCCAGCATGAATACTTTACACTCGTCAGCATGAATATGTTTACGCTCTCCAACATG
AATATG
Found at i:80113 original size:24 final size:24
Alignment explanation
Indices: 79995--80124 Score: 163
Period size: 24 Copynumber: 5.5 Consensus size: 24
79985 TGCTTGTCAG
*
79995 CATGAATATGTTTACGCTCTCCAA
1 CATGAATATGTTTACGCTCACCAA
* *
80019 CATGAATATGTTTACGCTCGCCAG
1 CATGAATATGTTTACGCTCACCAA
* * *
80043 CATGAATA-CTTTACACTCACCAG
1 CATGAATATGTTTACGCTCACCAA
* *
80066 CATGAATATGTTTACACTCTCCAA
1 CATGAATATGTTTACGCTCACCAA
* *
80090 CATGAAAACGTTTACGCTCACCAA
1 CATGAATATGTTTACGCTCACCAA
80114 CATGAATATGT
1 CATGAATATGT
80125 GAAACATTAT
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
23 20 0.22
24 71 0.78
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (24 bp):
CATGAATATGTTTACGCTCACCAA
Found at i:81400 original size:80 final size:80
Alignment explanation
Indices: 81263--81495 Score: 272
Period size: 80 Copynumber: 2.9 Consensus size: 80
81253 GGATATTGAC
* * * * *
81263 TATAAGGACCCTCTGATGGCTAAGATTCTGCATATGTT-ACGGATTCTTGATAGCTTGTGTGAGC
1 TATAAGGACCCTCCGATGGTTGAGATTCTGCATATGTTGA-AGATTCTTGACAGCTTGTGTGAGC
81327 AACATCGTGAGTGGAT
65 AACATCGTGAGTGGAT
* *
81343 TATAAGGACCCTCCGATGATTGAGATTCTGCATATGTTGAAGATTCTTGACAACTTGTGTGAG-A
1 TATAAGGACCCTCCGATGGTTGAGATTCTGCATATGTTGAAGATTCTTGACAGCTTGTGTGAGCA
81407 AGCATCGTGAGTGGAT
66 A-CATCGTGAGTGGAT
* * * * * * * * *
81423 TATATGGACCGTATCGATGGTTGGGATCCTACATATGTTGCAGTTTCCTGACAGCTTGTGTGAGC
1 TATAAGGACCCT-CCGATGGTTGAGATTCTGCATATGTTGAAGATTCTTGACAGCTTGTGTGAGC
*
81488 AGCATCGT
65 AACATCGT
81496 ATAGTGGTTA
Statistics
Matches: 130, Mismatches: 19, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
79 2 0.02
80 78 0.60
81 49 0.38
82 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (80 bp):
TATAAGGACCCTCCGATGGTTGAGATTCTGCATATGTTGAAGATTCTTGACAGCTTGTGTGAGCA
ACATCGTGAGTGGAT
Found at i:81546 original size:25 final size:25
Alignment explanation
Indices: 81517--81577 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
81507 ATTCTATTTG
*
81517 GGCTCGTAAGAGCGATATACTGTCT
1 GGCTCGTAAGAGCGATATACTATCT
*
81542 GGCTCGTAAGAGCGATATTCTATCT
1 GGCTCGTAAGAGCGATATACTATCT
*
81567 AGCTCGTAAGA
1 GGCTCGTAAGA
81578 TAATTATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (25 bp):
GGCTCGTAAGAGCGATATACTATCT
Found at i:85912 original size:16 final size:15
Alignment explanation
Indices: 85881--85923 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
85871 TTTATTTTAC
85881 AATTAAATTAAATTT
1 AATTAAATTAAATTT
*
85896 AATTAATATTTAATTT
1 AATTAA-ATTAAATTT
*
85912 AACTCAAATTAA
1 AA-TTAAATTAA
85924 CCCCTAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 6 0.26
16 14 0.61
17 3 0.13
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATTAAATTT
Found at i:86912 original size:17 final size:17
Alignment explanation
Indices: 86890--86922 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
86880 ATCATTGAAA
86890 GGGTATT-TGTCACAAAG
1 GGGTATTGT-TCACAAAG
86907 GGGTATTGTTCACAAA
1 GGGTATTGTTCACAAA
86923 CTTACATGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (17 bp):
GGGTATTGTTCACAAAG
Found at i:89476 original size:17 final size:16
Alignment explanation
Indices: 89456--89493 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
89446 TAGAACAAAT
89456 AAAATGCAGA-GATAATA
1 AAAATGCA-ATGATAA-A
89473 AAAATGCAATGATAAA
1 AAAATGCAATGATAAA
89489 AAAAT
1 AAAAT
89494 ATGCATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.63, C:0.05, G:0.13, T:0.18
Consensus pattern (16 bp):
AAAATGCAATGATAAA
Found at i:110998 original size:57 final size:57
Alignment explanation
Indices: 110905--111062 Score: 214
Period size: 57 Copynumber: 2.8 Consensus size: 57
110895 ATATTATAAT
*
110905 TTTTATT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATTATAT-TTA
1 TTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTATATATTA
* * *
110963 TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTATTTATTA
1 TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTATATATTA
*
111020 TTTTATTAAATTATATTTAATAATAATCT-TATTAAAATTTAAT
1 TTTTATTAAATTATATTTAATAATAAT-TATATTAAAATATAAT
111063 AACAATAATC
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
56 18 0.20
57 58 0.64
58 10 0.11
59 4 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (57 bp):
TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTATATATTA
Found at i:111250 original size:16 final size:16
Alignment explanation
Indices: 111229--111273 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
111219 ATTGAAGCCT
111229 TATTTCATTACAGTTC
1 TATTTCATTACAGTTC
* *
111245 TATTTCATTGCAGTTT
1 TATTTCATTACAGTTC
*
111261 TATTCCATTACAG
1 TATTTCATTACAG
111274 CGAACCAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.49
Consensus pattern (16 bp):
TATTTCATTACAGTTC
Found at i:112939 original size:18 final size:18
Alignment explanation
Indices: 112896--112932 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
112886 AACACTCTGC
112896 CTGACAACATATATGAAA
1 CTGACAACATATATGAAA
112914 CTGACAACATATATGAAA
1 CTGACAACATATATGAAA
112932 C
1 C
112933 ATTCAACGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.22
Consensus pattern (18 bp):
CTGACAACATATATGAAA
Found at i:117529 original size:30 final size:31
Alignment explanation
Indices: 117471--117535 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
117461 TACGACCACC
*
117471 ACCTCCAATTATTACTTGTGATTTTAGTGAA
1 ACCTCCAATTATAACTTGTGATTTTAGTGAA
117502 ACCTCCAATTATAACTTGTGA-TTTAGTGAA
1 ACCTCCAATTATAACTTGTGATTTTAGTGAA
117532 ACCT
1 ACCT
117536 GACTCTAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 13 0.39
31 20 0.61
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (31 bp):
ACCTCCAATTATAACTTGTGATTTTAGTGAA
Found at i:118925 original size:28 final size:26
Alignment explanation
Indices: 118893--118958 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 26
118883 CATAAAATGA
*
118893 AAATAAAATAAAAAG--AATGAAAAT
1 AAATAAAATAAAAAGAAAAAGAAAAT
118917 AAATAAATAATAAAAAGAAAAAGAAAAT
1 AAAT-AA-AATAAAAAGAAAAAGAAAAT
118945 AAATAAAAATAAAA
1 AAAT-AAAATAAAA
118959 TTGGGTTGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
24 4 0.11
25 2 0.05
26 9 0.24
27 7 0.19
28 15 0.41
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (26 bp):
AAATAAAATAAAAAGAAAAAGAAAAT
Found at i:147625 original size:17 final size:17
Alignment explanation
Indices: 147608--147640 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
147598 ATAATATTAT
147608 TTTAA-TAAATTTAATA
1 TTTAATTAAATTTAATA
*
147624 TTTAATTTAATTTAATA
1 TTTAATTAAATTTAATA
147641 CTTATCTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTAAATTTAATA
Found at i:147813 original size:58 final size:59
Alignment explanation
Indices: 147686--147813 Score: 140
Period size: 58 Copynumber: 2.2 Consensus size: 59
147676 AGTGATTATC
* * *
147686 TTAAT-ATT-AAATTAATTTAATATTTATCTTGAAGATAAATATTCTATTAATTTAATAGA
1 TTAATGATTAAAATTAATCTAATACTTATCTTG-AGATAAATATTATATTAATTTAATA-A
* *
147745 TTTATTATTAAAATTAATCTAATACTTATCTTG-G-TAAATATTATATTAATTTAAT-A
1 TTAATGATTAAAATTAATCTAATACTTATCTTGAGATAAATATTATATTAATTTAATAA
147801 TTAAAGTGATTAA
1 TT-AA-TGATTAA
147814 GTTTGATCAT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
56 3 0.05
57 1 0.02
58 26 0.44
59 5 0.08
60 3 0.05
61 21 0.36
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (59 bp):
TTAATGATTAAAATTAATCTAATACTTATCTTGAGATAAATATTATATTAATTTAATAA
Found at i:153024 original size:31 final size:31
Alignment explanation
Indices: 152982--153070 Score: 133
Period size: 31 Copynumber: 2.9 Consensus size: 31
152972 GGCCCATTTC
152982 ACAACTCATGTGAGCATACATGATTACAATT
1 ACAACTCATGTGAGCATACATGATTACAATT
* * *
153013 ACAACTTATGTGAGCAAACATGATTACAGTT
1 ACAACTCATGTGAGCATACATGATTACAATT
* *
153044 ACAACTCGTGTAAGCATACATGATTAC
1 ACAACTCATGTGAGCATACATGATTAC
153071 GTATATGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (31 bp):
ACAACTCATGTGAGCATACATGATTACAATT
Found at i:154951 original size:38 final size:38
Alignment explanation
Indices: 154898--155097 Score: 222
Period size: 38 Copynumber: 5.3 Consensus size: 38
154888 TAGTTGTACG
* *
154898 CGGTGTTTATTGGGCTTAATTCCTAGCAAGCTTCGTGC
1 CGGTGTTTATAGGGCTTAATGCCTAGCAAGCTTCGTGC
*
154936 CGGTGTTTATAGGGCTTAATGCCTAGCAGGCTTCGTGC
1 CGGTGTTTATAGGGCTTAATGCCTAGCAAGCTTCGTGC
* * *
154974 TGGTGTTTATCA-GGCTTAATGCCTAGCAAGCTTCATGT
1 CGGTGTTTAT-AGGGCTTAATGCCTAGCAAGCTTCGTGC
* * * * * * * * *
155012 CGATGATAATCGAGCTTAGTTCCTAGCAGGCTTCGTGT
1 CGGTGTTTATAGGGCTTAATGCCTAGCAAGCTTCGTGC
* * *
155050 CAGTGTTTATCGGGCTTAGTGCCTAGCAAGCTTCGTGC
1 CGGTGTTTATAGGGCTTAATGCCTAGCAAGCTTCGTGC
155088 CGGTGTTTAT
1 CGGTGTTTAT
155098 TATTAGGCTT
Statistics
Matches: 134, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
38 133 0.99
39 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.34
Consensus pattern (38 bp):
CGGTGTTTATAGGGCTTAATGCCTAGCAAGCTTCGTGC
Found at i:163460 original size:21 final size:18
Alignment explanation
Indices: 163413--163468 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 18
163403 TTTATCAAAA
163413 TTTTCTTTCTTTTCTTTTT
1 TTTTC-TTCTTTTCTTTTT
*
163432 CTTT-TTCTTATTACTTTGTT
1 TTTTCTTCTT-TT-CTTT-TT
163452 TTTTCTTCTTTT-TTTTT
1 TTTTCTTCTTTTCTTTTT
163469 CAAATGACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
17 7 0.23
18 5 0.16
19 7 0.23
20 7 0.23
21 5 0.16
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTCTTCTTTTCTTTTT
Found at i:164197 original size:3 final size:3
Alignment explanation
Indices: 164189--164223 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
164179 CTCGTCATGA
164189 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
164224 ATCCTTGCGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:168676 original size:23 final size:22
Alignment explanation
Indices: 168640--168683 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
168630 TAAATATTTC
*
168640 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
168663 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
168684 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:174803 original size:22 final size:22
Alignment explanation
Indices: 174767--174827 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
174757 TGACCAGCCA
* *
174767 TTGACCGACCGTTGACTGACTG
1 TTGACCGATCATTGACTGACTG
*
174789 TTGACC-AGTCATTGACCGACTG
1 TTGACCGA-TCATTGACTGACTG
*
174811 TTGATCGATCATTGACT
1 TTGACCGATCATTGACT
174828 AGCCATTGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (22 bp):
TTGACCGATCATTGACTGACTG
Found at i:174826 original size:33 final size:33
Alignment explanation
Indices: 174756--174839 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
174746 AGTCAAACCG
*
174756 TTGACCAGCCATTGACCGACCGTTGACTGACTG
1 TTGACCAGCCATTGACCGACCGTTGACTGACTA
* *
174789 TTGACCAGTCATTGACCGACTGTTGA-TCGA-TCA
1 TTGACCAGCCATTGACCGACCGTTGACT-GACT-A
*
174822 TTGACTAGCCATTGACCG
1 TTGACCAGCCATTGACCG
174840 TTGACCGGCC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
32 2 0.05
33 42 0.95
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (33 bp):
TTGACCAGCCATTGACCGACCGTTGACTGACTA
Found at i:174843 original size:18 final size:18
Alignment explanation
Indices: 174820--174863 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
174810 GTTGATCGAT
*
174820 CATTGACTAGCCATTGAC
1 CATTGACCAGCCATTGAC
* *
174838 CGTTGACCGGCCATTGAC
1 CATTGACCAGCCATTGAC
174856 CATTGACC
1 CATTGACC
174864 GTTGACCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (18 bp):
CATTGACCAGCCATTGAC
Found at i:174864 original size:18 final size:18
Alignment explanation
Indices: 174829--174864 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
174819 TCATTGACTA
*
174829 GCCATTGACCGTTGACCG
1 GCCATTGACCATTGACCG
174847 GCCATTGACCATTGACCG
1 GCCATTGACCATTGACCG
174865 TTGACCATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.33, G:0.25, T:0.22
Consensus pattern (18 bp):
GCCATTGACCATTGACCG
Found at i:174870 original size:14 final size:14
Alignment explanation
Indices: 174830--174883 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
174820 CATTGACTAG
174830 CCATTGACCGTTGA
1 CCATTGACCGTTGA
* *
174844 CC---GGCCATTGA
1 CCATTGACCGTTGA
174855 CCATTGACCGTTGA
1 CCATTGACCGTTGA
*
174869 CCATTGACTGTTGA
1 CCATTGACCGTTGA
174883 C
1 C
174884 TTTTTTTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
11 9 0.28
14 23 0.72
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (14 bp):
CCATTGACCGTTGA
Found at i:180898 original size:19 final size:19
Alignment explanation
Indices: 180876--180912 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
180866 TACCCATGCT
180876 TTGCCGCCACTCCCATTAC
1 TTGCCGCCACTCCCATTAC
180895 TTGCCGCCACTCCCATTA
1 TTGCCGCCACTCCCATTA
180913 ACCCTAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.46, G:0.11, T:0.27
Consensus pattern (19 bp):
TTGCCGCCACTCCCATTAC
Found at i:188426 original size:52 final size:52
Alignment explanation
Indices: 188308--188633 Score: 445
Period size: 52 Copynumber: 6.2 Consensus size: 52
188298 CAACGACATA
* * ** * * *
188308 TAGTCGTCGGACCTCTTGTTCCATAAAGGAATTCATGTACTAACGATGACACT
1 TAGTCATCGGACCTCATAATCCGTAAAGG-ATTCATTTACTCACGATGACACT
* * * ** * * * *
188361 TAGCCATCAGACCTTACCATCCATAAAGGATTTATATACTCACGATTACACT
1 TAGTCATCGGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGACACT
*
188413 TAGTCATCGGACCTCATAATCCGTAAAGGATTTATTTACTCACGATGACACT
1 TAGTCATCGGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGACACT
188465 TAGTCATCGGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGACACT
1 TAGTCATCGGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGACACT
* * *
188517 TAGTCATTGGACCTCATAATCCGTGAAGGATTCATTTACGCACGATGACACT
1 TAGTCATCGGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGACACT
188569 TAGTCATCGGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGACACT
1 TAGTCATCGGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGACACT
* *
188621 TAATCATCAGACC
1 TAGTCATCGGACC
188634 CTTTTCATTT
Statistics
Matches: 244, Mismatches: 29, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
52 223 0.91
53 21 0.09
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (52 bp):
TAGTCATCGGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGACACT
Found at i:189547 original size:24 final size:20
Alignment explanation
Indices: 189495--189536 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
189485 GCTTTTATAA
189495 TTAACC-TAATTAATCCACT
1 TTAACCTTAATTAATCCACT
189514 TTAACCTTAATTAATCTCACT
1 TTAACCTTAATTAATC-CACT
189535 TT
1 TT
189537 TAAGCACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.29
20 9 0.43
21 6 0.29
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAACCTTAATTAATCCACT
Found at i:195858 original size:52 final size:52
Alignment explanation
Indices: 195781--196124 Score: 356
Period size: 52 Copynumber: 6.7 Consensus size: 52
195771 AAAAGGGCTT
* * * *
195781 GATGATTAAGTGTTATCGTGAGTAAATGAATCCTTTATAGATTATGAGGTCT
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATTATGAGGTCC
* * *
195833 GATGTCTAAGTGTCATCGTAAGTAAATGAATCCTTTACAGATTATGAGGCCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATTATGAGGTCC
* * * * * * *
195885 GATGACTAAGTGCCATCATGAATACACGAATCTTTTACGGA-T-TGAGGTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATTATGAGGTCC
* * *
195935 GATGACTAAGTGTCATCGTGAGTACATGAATCTTTTAC-GAAT-TGAGGTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATTATGAGGTCC
* * * * *
195985 AATGACTAAGTCTCATCGTGAGTAAATGAATTCTTTACGGATTATAAGGTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATTATGAGGTCC
* * * ** ** *
196037 GATGGCTAAGTTTAATCGTGAGTATAA-GAATCCTTTATGGATGGTGAGGTTC
1 GATGACTAAGTGTCATCGTGAGTA-AATGAATCCTTTACAGATTATGAGGTCC
*
196089 GATGACTAAGTGTCATCGTGAGTACATGAATTCCTT
1 GATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTT
196125 ATGGAACAAG
Statistics
Matches: 244, Mismatches: 42, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.01
50 83 0.34
51 5 0.02
52 147 0.60
53 7 0.03
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (52 bp):
GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATTATGAGGTCC
Found at i:196139 original size:104 final size:103
Alignment explanation
Indices: 195795--196139 Score: 251
Period size: 102 Copynumber: 3.4 Consensus size: 103
195785 ATTAAGTGTT
** ** * * * *
195795 ATCGTGAGTAAATGAA-TCCTTTATAGATTAT-GAGGTCTGATGTCTAAGTGTCATCGTAAGTA-
1 ATCGTGAGTAAATGAATTCC-TTACGGAACATAGAGGTCCGATGACTAAGTGTAATCGTGAGTAC
* * *
195857 AATGAATCCTTTACAGATTATGAGGCCCGATGACTAAGTGC-C
65 AA-GAATCCTTTAC-GAAT-TGAGGTCCAATGACTAAGT-CTC
* * * * * * *
195899 ATCATGAATACACGAA-TCTTTTACGG---ATTGAGGTCCGATGACTAAGTGTCATCGTGAGTAC
1 ATCGTGAGTAAATGAATTC-CTTACGGAACATAGAGGTCCGATGACTAAGTGTAATCGTGAGTAC
* *
195960 ATGAATCTTTTACGAATTGAGGTCCAATGACTAAGTCTC
65 AAGAATCCTTTACGAATTGAGGTCCAATGACTAAGTCTC
* ** * * *
195999 ATCGTGAGTAAATGAATTCTTTACGGATTATA-AGGTCCGATGGCTAAGTTTAATCGTGAGTATA
1 ATCGTGAGTAAATGAATTCCTTACGGAACATAGAGGTCCGATGACTAAGTGTAATCGTGAGTACA
* * * * *
196063 AGAATCCTTTATGGATGGTGAGGTTCGATGACTAAGTGTC
66 AGAATCCTTTACGAAT--TGAGGTCCAATGACTAAGTCTC
* *
196103 ATCGTGAGTACATGAATTCCTTATGGAACA-AGAGGTC
1 ATCGTGAGTAAATGAATTCCTTACGGAACATAGAGGTC
196140 TAAGGACTAT
Statistics
Matches: 194, Mismatches: 36, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
99 1 0.01
100 37 0.19
101 7 0.04
102 78 0.40
103 4 0.02
104 67 0.35
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (103 bp):
ATCGTGAGTAAATGAATTCCTTACGGAACATAGAGGTCCGATGACTAAGTGTAATCGTGAGTACA
AGAATCCTTTACGAATTGAGGTCCAATGACTAAGTCTC
Found at i:201002 original size:26 final size:25
Alignment explanation
Indices: 200973--201029 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
200963 TGAAGGGACG
200973 ATTTGAGAAGT-AGGGTTGA-AGGTTCA
1 ATTT-AGAAGTGA-GGTTGAGAGGTT-A
*
200999 ATTTATAAGTGAGGTTGAGAGGTTA
1 ATTTAGAAGTGAGGTTGAGAGGTTA
201024 ATTTAG
1 ATTTAG
201030 TAAAATTAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.32, C:0.02, G:0.32, T:0.35
Consensus pattern (25 bp):
ATTTAGAAGTGAGGTTGAGAGGTTA
Found at i:201573 original size:12 final size:12
Alignment explanation
Indices: 201556--201596 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
201546 TTTTGAGAGC
201556 ATAAAATAAAAG
1 ATAAAATAAAAG
*
201568 ATAAAATAAAAT
1 ATAAAATAAAAG
*
201580 AGAAAATAAAAG
1 ATAAAATAAAAG
201592 -TAAAA
1 ATAAAA
201597 GTTTGAGATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:201578 original size:17 final size:17
Alignment explanation
Indices: 201556--201596 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
201546 TTTTGAGAGC
201556 ATAAAATA-AAAGATAAA
1 ATAAAATAGAAA-ATAAA
201573 ATAAAATAGAAAATAAA
1 ATAAAATAGAAAATAAA
201590 AGTAAAA
1 A-TAAAA
201597 GTTTGAGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (17 bp):
ATAAAATAGAAAATAAA
Found at i:204007 original size:55 final size:55
Alignment explanation
Indices: 203917--204033 Score: 180
Period size: 55 Copynumber: 2.1 Consensus size: 55
203907 AATCTGAGTT
* * *
203917 CAGAGTAATGCTCTTACGAGTCAGAGTCCAAAATAACACTCTTTTGAGCCAAAAA
1 CAGAGTAATGCTCTTACGAGCCAAAGTCCAAAATAACACTCTTTCGAGCCAAAAA
* * *
203972 CAGAGTAATGCTCTTACGAGCCAAAGTCTAGAATAACGCTCTTTCGAGCCAAAAA
1 CAGAGTAATGCTCTTACGAGCCAAAGTCCAAAATAACACTCTTTCGAGCCAAAAA
204027 CAGAGTA
1 CAGAGTA
204034 TCACTCTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (55 bp):
CAGAGTAATGCTCTTACGAGCCAAAGTCCAAAATAACACTCTTTCGAGCCAAAAA
Found at i:204019 original size:28 final size:27
Alignment explanation
Indices: 203948--204061 Score: 111
Period size: 27 Copynumber: 4.2 Consensus size: 27
203938 CAGAGTCCAA
* *
203948 AATAACACTCTTTTGAGCCAAAAACAG
1 AATAACGCTCTTTCGAGCCAAAAACAG
* * * **
203975 AGTAATGCTCTTACGAGCCAAAGTCTAG
1 AATAACGCTCTTTCGAGCCAAAAAC-AG
204003 AATAACGCTCTTTCGAGCCAAAAACAG
1 AATAACGCTCTTTCGAGCCAAAAACAG
* * * * *
204030 AGTATCACTCTTTTGAGCCAGAAACAG
1 AATAACGCTCTTTCGAGCCAAAAACAG
204057 AATAA
1 AATAA
204062 TTATTATGCC
Statistics
Matches: 67, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
27 45 0.67
28 22 0.33
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (27 bp):
AATAACGCTCTTTCGAGCCAAAAACAG
Found at i:208288 original size:7 final size:7
Alignment explanation
Indices: 208276--208303 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
208266 AATAAATTTA
208276 ATTTCAC
1 ATTTCAC
208283 ATTTCAC
1 ATTTCAC
208290 ATTTCAC
1 ATTTCAC
208297 ATTTCAC
1 ATTTCAC
208304 TGTTATACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (7 bp):
ATTTCAC
Found at i:210815 original size:24 final size:24
Alignment explanation
Indices: 210788--210862 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
210778 AATTTGACTC
*
210788 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
210812 AAACAAATGAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
210836 AAACAAATAAATAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
210860 AAA
1 AAA
210863 GATTATTTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:212830 original size:24 final size:24
Alignment explanation
Indices: 212803--212853 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
212793 AATTTGACTC
* *
212803 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
212827 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
212851 AAA
1 AAA
212854 TATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:216947 original size:14 final size:14
Alignment explanation
Indices: 216928--216968 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
216918 ACTTGGACCA
216928 TATATACATATATG
1 TATATACATATATG
216942 TATATACATATATG
1 TATATACATATATG
*
216956 TATATATATATAT
1 TATATACATATAT
216969 TAATTACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (14 bp):
TATATACATATATG
Found at i:228160 original size:18 final size:18
Alignment explanation
Indices: 228137--228175 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
228127 ATATCAAAAT
*
228137 ATTT-AATTAATAATTGTA
1 ATTTAAATT-ATAATTATA
228155 ATTTAAATTATAATTATA
1 ATTTAAATTATAATTATA
228173 ATT
1 ATT
228176 ATATTATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTTAAATTATAATTATA
Found at i:228301 original size:18 final size:17
Alignment explanation
Indices: 228275--228308 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
228265 TAATTGTAAA
228275 TTAAAATATAACTATTT
1 TTAAAATATAACTATTT
*
228292 TTAAATATATAATTATT
1 TTAAA-ATATAACTATT
228309 GCAACTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAATATAACTATTT
Found at i:229902 original size:21 final size:21
Alignment explanation
Indices: 229860--229900 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
229850 CCTTTTAATT
229860 TTAAATATAATTATAGAAAAA
1 TTAAATATAATTATAGAAAAA
229881 TTAAA-ATAATTA-AGATAAAA
1 TTAAATATAATTATAGA-AAAA
229901 ATATTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 11 0.58
21 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (21 bp):
TTAAATATAATTATAGAAAAA
Found at i:229912 original size:21 final size:20
Alignment explanation
Indices: 229888--229929 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
229878 AAATTAAAAT
229888 AATTAAGATAAAAATATTAAA
1 AATT-AGATAAAAATATTAAA
* *
229909 AATTAGTTTAAAATATTAAA
1 AATTAGATAAAAATATTAAA
229929 A
1 A
229930 TTTTATACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AATTAGATAAAAATATTAAA
Found at i:253400 original size:18 final size:19
Alignment explanation
Indices: 253355--253401 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
253345 TGATAAAGAT
253355 AATAATATAAAAGAAAGAAC
1 AATAATA-AAAAGAAAGAAC
*
253375 AA-ATATAAAAAGAAATAA-
1 AATA-ATAAAAAGAAAGAAC
253393 AATAATAAA
1 AATAATAAA
253402 TTGAGTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 7 0.29
19 12 0.50
20 5 0.21
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.17
Consensus pattern (19 bp):
AATAATAAAAAGAAAGAAC
Found at i:254319 original size:17 final size:17
Alignment explanation
Indices: 254282--254332 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
254272 AGAGAGATTC
* *
254282 ATTTATTTATATAACATA
1 ATTTATTT-TAGAAAATA
254300 ATTTATTTTAGAAAATA
1 ATTTATTTTAGAAAATA
*
254317 ATTCT-TTTTCGAAAAT
1 ATT-TATTTTAGAAAAT
254333 TTTGATGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 20 0.69
18 9 0.31
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (17 bp):
ATTTATTTTAGAAAATA
Done.