Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009392.1 Kokia drynarioides strain JFW-HI SEQ_124099, 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: 143751
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 359 characters in sequence are not A, C, G, or T
Found at i:903 original size:23 final size:22
Alignment explanation
Indices: 873--999 Score: 105
Period size: 23 Copynumber: 5.6 Consensus size: 22
863 GAACGCTAGC
873 GTGCTTACTGTTTCGCACTTTGT
1 GTGCTTACTGTTT-GCACTTTGT
896 GTGCTTACTGTTTCGCACTTCT-T
1 GTGCTTACTGTTT-GCACTT-TGT
* * *
919 GTGCTTAATGATTTGCGCTATGT
1 GTGCTTACTG-TTTGCACTTTGT
* * *
942 GCGCCTACTGATTGCA-TTGTGT
1 GTGCTTACTGTTTGCACTT-TGT
* * *
964 GTGCCTACTGGATTGCACTGTGT
1 GTGCTTACT-GTTTGCACTTTGT
987 GTGCTTACTGTTT
1 GTGCTTACTGTTT
1000 TCCCAGCACT
Statistics
Matches: 85, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
21 1 0.01
22 19 0.22
23 60 0.71
24 5 0.06
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.43
Consensus pattern (22 bp):
GTGCTTACTGTTTGCACTTTGT
Found at i:11712 original size:2 final size:2
Alignment explanation
Indices: 11705--11744 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
11695 AAATTTTTGT
11705 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
11745 ACCCCAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12819 original size:29 final size:30
Alignment explanation
Indices: 12778--12835 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
12768 TTAATTTATA
* *
12778 ATTTGATTCTTAAAGTGTATTTATTTTTTT
1 ATTTGATTATTAAAGTATATTTATTTTTTT
12808 ATTTGA-TATTAAAGTATATTTATTTTTT
1 ATTTGATTATTAAAGTATATTTATTTTTT
12836 GTCTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.62
Consensus pattern (30 bp):
ATTTGATTATTAAAGTATATTTATTTTTTT
Found at i:13301 original size:20 final size:20
Alignment explanation
Indices: 13271--13313 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
13261 CAAATATATA
13271 TTTTTAATTTTA-ATATCAT
1 TTTTTAATTTTATATATCAT
*
13290 TTTTTAATTTTTATATATTAT
1 TTTTTAA-TTTTATATATCAT
13311 TTT
1 TTT
13314 GACTTTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTAATTTTATATATCAT
Found at i:14504 original size:2 final size:2
Alignment explanation
Indices: 14497--14526 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14487 CTTCAAACTG
14497 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
14527 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:15505 original size:2 final size:2
Alignment explanation
Indices: 15498--15527 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15488 TATGAAAGTA
15498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15528 GGGGGTACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18950 original size:23 final size:22
Alignment explanation
Indices: 18915--18975 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
18905 TTAAATTAAA
* *
18915 TAATTTAAAAATATTTAAATTT
1 TAATATAAAAATATTTAAATAT
18937 TAATGATAAAAATA--TAAATAT
1 TAAT-ATAAAAATATTTAAATAT
*
18958 TGATATAAAAA-ATTTAAA
1 TAATATAAAAATATTTAAA
18976 AATTTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 1 0.03
20 7 0.21
21 13 0.39
22 4 0.12
23 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (22 bp):
TAATATAAAAATATTTAAATAT
Found at i:30488 original size:5 final size:6
Alignment explanation
Indices: 30476--30501 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
30466 CGTCTCCTTT
30476 CCTCCC CCTCCC CCTCCC CCTCCC CC
1 CCTCCC CCTCCC CCTCCC CCTCCC CC
30502 ACCTTTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.85, G:0.00, T:0.15
Consensus pattern (6 bp):
CCTCCC
Found at i:40036 original size:12 final size:12
Alignment explanation
Indices: 40019--40057 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40009 GGTACCATAC
40019 ACATACATGCAT
1 ACATACATGCAT
*
40031 ACATACATACAT
1 ACATACATGCAT
* *
40043 ACATATATGTAT
1 ACATACATGCAT
40055 ACA
1 ACA
40058 GAGCATGCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.46, C:0.21, G:0.05, T:0.28
Consensus pattern (12 bp):
ACATACATGCAT
Found at i:41574 original size:19 final size:18
Alignment explanation
Indices: 41529--41574 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
41519 GAGTTAAACA
* *
41529 AATCAATTTATTCGAGTT
1 AATCAAATTATTCGAGTC
*
41547 AATCGAATTATTCGAGTC
1 AATCAAATTATTCGAGTC
41565 AATTCAAATT
1 AA-TCAAATT
41575 TTTTTCGAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (18 bp):
AATCAAATTATTCGAGTC
Found at i:41748 original size:30 final size:29
Alignment explanation
Indices: 41691--41749 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
41681 TCTTTTTACT
* * *
41691 TTTCTCCCAAAATTTTTACTCATTCCCAC
1 TTTCCCCCAAAACTTTTACTCACTCCCAC
*
41720 TTTCCCCCAAAACTTTTACTCCCCTCCCAC
1 TTTCCCCCAAAACTTTTACT-CACTCCCAC
41750 CNCCCATCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.22, C:0.42, G:0.00, T:0.36
Consensus pattern (29 bp):
TTTCCCCCAAAACTTTTACTCACTCCCAC
Found at i:41886 original size:29 final size:29
Alignment explanation
Indices: 41854--41909 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
41844 AACTCTTTAT
41854 TTTCCCAC-AAAACATTTACTCTCTCTCAC
1 TTTCCCACTAAAACATTTACTC-CTCTCAC
* *
41883 TTTCCCCCTAAAACTTTTACTCCTCTC
1 TTTCCCACTAAAACATTTACTCCTCTC
41910 CCATCTAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.23, C:0.39, G:0.00, T:0.38
Consensus pattern (29 bp):
TTTCCCACTAAAACATTTACTCCTCTCAC
Found at i:42475 original size:19 final size:19
Alignment explanation
Indices: 42447--42483 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
42437 GAAAATTAAT
*
42447 AATAATTTTGATTACGATA
1 AATAAATTTGATTACGATA
42466 AATAAATTTGATTACGAT
1 AATAAATTTGATTACGAT
42484 GAATGACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (19 bp):
AATAAATTTGATTACGATA
Found at i:53712 original size:23 final size:22
Alignment explanation
Indices: 53686--53755 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 22
53676 TTCATTTAAC
53686 TTAATCGAACATGTTCACGAACA
1 TTAAT-GAACATGTTCACGAACA
*
53709 TTAAATGAACATGTTCATGAACA
1 TT-AATGAACATGTTCACGAACA
*
53732 TATAATTGAACATATTCACGAACA
1 T-TAA-TGAACATGTTCACGAACA
53756 ATGTTAATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 21 0.51
24 20 0.49
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (22 bp):
TTAATGAACATGTTCACGAACA
Found at i:57743 original size:19 final size:19
Alignment explanation
Indices: 57708--57745 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
57698 ACATAAAATG
*
57708 ATTTGATTTTAATTTTTTT
1 ATTTGATTTAAATTTTTTT
57727 ATTTG-TTTAAATCTTTTTT
1 ATTTGATTTAAAT-TTTTTT
57746 TCTCAAGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (19 bp):
ATTTGATTTAAATTTTTTT
Found at i:57997 original size:2 final size:2
Alignment explanation
Indices: 57992--58025 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
57982 ACACTGTTAA
*
57992 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58026 TTTTAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:64861 original size:25 final size:25
Alignment explanation
Indices: 64827--64874 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
64817 TCGCTTATGT
*
64827 CATGACCGACACCTAAAAAATACAA
1 CATGACCGACACCCAAAAAATACAA
64852 CATGACCGACACCCAAAAAATAC
1 CATGACCGACACCCAAAAAATAC
64875 GGATAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.50, C:0.31, G:0.08, T:0.10
Consensus pattern (25 bp):
CATGACCGACACCCAAAAAATACAA
Found at i:65161 original size:23 final size:24
Alignment explanation
Indices: 65118--65164 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
65108 TTCAAATGTA
*
65118 AAAATATAAATTTTCAATTTAAAT
1 AAAATATAAATTTTAAATTTAAAT
65142 AAAAT-TAAA-TTTAAACTTTAAAT
1 AAAATATAAATTTTAAA-TTTAAAT
65165 TAATCTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 11 0.52
24 5 0.24
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAATATAAATTTTAAATTTAAAT
Found at i:65286 original size:28 final size:28
Alignment explanation
Indices: 65246--65338 Score: 106
Period size: 28 Copynumber: 3.5 Consensus size: 28
65236 AAATTAAAAC
65246 AATTATAATTAAAATAATATTTATTTCA
1 AATTATAATTAAAATAATATTTATTTCA
* * * **
65274 AATTAAAAATAAAA-AA-ATATAACT-A
1 AATTATAATTAAAATAATATTTATTTCA
65299 AA--ATAATTAAAATAATATTTATTTCA
1 AATTATAATTAAAATAATATTTATTTCA
65325 AATTATAATTAAAA
1 AATTATAATTAAAA
65339 ATTATAACTA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
23 8 0.16
24 2 0.04
25 8 0.16
26 8 0.16
27 2 0.04
28 22 0.44
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (28 bp):
AATTATAATTAAAATAATATTTATTTCA
Found at i:65311 original size:51 final size:49
Alignment explanation
Indices: 65250--65376 Score: 168
Period size: 51 Copynumber: 2.6 Consensus size: 49
65240 TAAAACAATT
65250 ATAATTAAAATAATATTTATTTCAAATTAAAAATAAAAAAATATAACTAAA
1 ATAATTAAAATAATATTTATTTCAAATT-AAAATAAAAAAATATAACT-AA
* * *
65301 ATAATTAAAATAATATTTATTTCAAATTATAATTAAAAATTATAACTAA
1 ATAATTAAAATAATATTTATTTCAAATTAAAATAAAAAAATATAACTAA
* *
65350 A-AA-TAAAATTAATGTTAATTTCAAATT
1 ATAATTAAAA-TAATATTTATTTCAAATT
65377 GTTTTTGAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
47 5 0.07
48 18 0.26
49 3 0.04
50 16 0.23
51 28 0.40
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (49 bp):
ATAATTAAAATAATATTTATTTCAAATTAAAATAAAAAAATATAACTAA
Found at i:65342 original size:13 final size:13
Alignment explanation
Indices: 65324--65353 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
65314 TATTTATTTC
*
65324 AAATTATAATTAA
1 AAATTATAACTAA
65337 AAATTATAACTAA
1 AAATTATAACTAA
65350 AAAT
1 AAAT
65354 AAAATTAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATTATAACTAA
Found at i:67222 original size:16 final size:16
Alignment explanation
Indices: 67201--67231 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
67191 AATTATGTGT
*
67201 TCAAATTTTATTTTAC
1 TCAAATTTTAATTTAC
67217 TCAAATTTTAATTTA
1 TCAAATTTTAATTTA
67232 ATTTTTCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TCAAATTTTAATTTAC
Found at i:71795 original size:42 final size:42
Alignment explanation
Indices: 71732--71816 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
71722 TGAAGAAAGG
*
71732 TCGAAACTGTCAGGCAGCAGCAAAGGGGTAAATTGAATGAAT
1 TCGAAACTGTCAGGCAACAGCAAAGGGGTAAATTGAATGAAT
71774 TCGAAACTGTCAGGCAACAGCAAAGGGGTAAATTGAATGAAT
1 TCGAAACTGTCAGGCAACAGCAAAGGGGTAAATTGAATGAAT
71816 T
1 T
71817 TACTGTACAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (42 bp):
TCGAAACTGTCAGGCAACAGCAAAGGGGTAAATTGAATGAAT
Found at i:72145 original size:23 final size:23
Alignment explanation
Indices: 72114--72238 Score: 92
Period size: 23 Copynumber: 5.4 Consensus size: 23
72104 CACTAGCGCA
72114 CTCTCTGTTTAGCAC-GTCTCGTG
1 CTCTCTGTTTAGCACTGTCT-GTG
* *
72137 CTCTTTGTTATTAGCACTGTGTGTG
1 CTCTCTG-T-TTAGCACTGTCTGTG
* * *
72162 CTCTCTGATTAGCACTTTGTGTG
1 CTCTCTGTTTAGCACTGTCTGTG
* * * * *
72185 CTCT-TGATTAGTACTTTGTGTA
1 CTCTCTGTTTAGCACTGTCTGTG
* *
72207 CTCTCTGTTTAGCACTATGTGTG
1 CTCTCTGTTTAGCACTGTCTGTG
*
72230 TTCTCTGTT
1 CTCTCTGTT
72239 AGTACTTTGG
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
22 20 0.23
23 46 0.53
24 1 0.01
25 16 0.19
26 3 0.03
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (23 bp):
CTCTCTGTTTAGCACTGTCTGTG
Found at i:72211 original size:45 final size:46
Alignment explanation
Indices: 72146--72254 Score: 143
Period size: 45 Copynumber: 2.4 Consensus size: 46
72136 GCTCTTTGTT
* * * *
72146 ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCT-TG
1 ATTAGTACTTTGTGTACTCTCTGATTAGCACTATGTGTGCTCTCTG
* *
72191 ATTAGTACTTTGTGTACTCTCTGTTTAGCACTATGTGTGTTCTCTG
1 ATTAGTACTTTGTGTACTCTCTGATTAGCACTATGTGTGCTCTCTG
72237 -TTAGTACTTTG-GTACTCT
1 ATTAGTACTTTGTGTACTCT
72255 TTGTTTCTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 7 0.12
45 48 0.84
46 2 0.04
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (46 bp):
ATTAGTACTTTGTGTACTCTCTGATTAGCACTATGTGTGCTCTCTG
Found at i:95776 original size:25 final size:25
Alignment explanation
Indices: 95737--95841 Score: 112
Period size: 25 Copynumber: 4.4 Consensus size: 25
95727 ACTAGCGTGT
*
95737 CCTCTG-T-TTAGCACTGTGTGTGC
1 CCTCTGTTATTAGCACTTTGTGTGC
95760 CCTCTGTTATTAGCACTTTGTGTGC
1 CCTCTGTTATTAGCACTTTGTGTGC
* * *
95785 CCT-T-TGATTAACACTTTGCGTGC
1 CCTCTGTTATTAGCACTTTGTGTGC
* *
95808 CCTCTGTTATCAAGCAC-TTATGTGC
1 CCTCTGTTAT-TAGCACTTTGTGTGC
95833 CCTCTGTTA
1 CCTCTGTTA
95842 AGTACTTTGG
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
23 25 0.37
24 3 0.04
25 36 0.53
26 4 0.06
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.40
Consensus pattern (25 bp):
CCTCTGTTATTAGCACTTTGTGTGC
Found at i:95849 original size:48 final size:48
Alignment explanation
Indices: 95737--95850 Score: 133
Period size: 48 Copynumber: 2.4 Consensus size: 48
95727 ACTAGCGTGT
* * * * *
95737 CCTCTGTTTAGCACTGTGTGTGCCCTCTGTTATTAGCACTTTGTGTGC
1 CCTCTGTTAAGCACTTTGCGTGCCCTCTGTTATAAGCACTTTATGTGC
*
95785 CCTTTGATTAA-CACTTTGCGTGCCCTCTGTTATCAAGCAC-TTATGTGC
1 CCTCTG-TTAAGCACTTTGCGTGCCCTCTGTTAT-AAGCACTTTATGTGC
*
95833 CCTCTGTTAAGTACTTTG
1 CCTCTGTTAAGCACTTTG
95851 GTACTTTCTG
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
47 4 0.07
48 43 0.78
49 8 0.15
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.40
Consensus pattern (48 bp):
CCTCTGTTAAGCACTTTGCGTGCCCTCTGTTATAAGCACTTTATGTGC
Found at i:97160 original size:27 final size:28
Alignment explanation
Indices: 97122--97174 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
97112 ACAGTTACGG
* *
97122 TAAAAAGTAAAA-CTTTAAAAATGAAAA
1 TAAAAAGAAAAACCTTAAAAAATGAAAA
97149 TAAAAAGAAAAACCTTAAAAAATGAA
1 TAAAAAGAAAAACCTTAAAAAATGAA
97175 TCCGATCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.68, C:0.06, G:0.08, T:0.19
Consensus pattern (28 bp):
TAAAAAGAAAAACCTTAAAAAATGAAAA
Found at i:97477 original size:1 final size:1
Alignment explanation
Indices: 97471--97504 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
97461 TACAATACAC
97471 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
97505 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:97519 original size:1 final size:1
Alignment explanation
Indices: 97515--97549 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
97505 NNNNNNNNNN
97515 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
97550 CTCTTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:107206 original size:21 final size:20
Alignment explanation
Indices: 107173--107223 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 20
107163 GTTAAAACTG
107173 TTTTTTAATATTTAAATATTTAA
1 TTTTTT-ATATTT-AA-ATTTAA
107196 TTTTTTA-ATTTAAATTTAA
1 TTTTTTATATTTAAATTTAA
107215 TGTTTTTAT
1 T-TTTTTAT
107224 TTTTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 7 0.27
20 8 0.31
21 4 0.15
22 1 0.04
23 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTTATATTTAAATTTAA
Found at i:107237 original size:27 final size:27
Alignment explanation
Indices: 107173--107237 Score: 62
Period size: 27 Copynumber: 2.4 Consensus size: 27
107163 GTTAAAACTG
*
107173 TTTTTTAATATTTAAATATTTAATTTT
1 TTTTTTAAAATTTAAATATTTAATTTT
* * *
107200 TTAATTT-AAATTT-AATGTTTTTATTTT
1 TT-TTTTAAAATTTAAAT-ATTTAATTTT
107227 TTTTTTAAAAT
1 TTTTTTAAAAT
107238 AAATATCAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
26 6 0.20
27 21 0.70
28 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
TTTTTTAAAATTTAAATATTTAATTTT
Found at i:110127 original size:17 final size:17
Alignment explanation
Indices: 110095--110128 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
110085 AAATTTTCTT
**
110095 TTTCTTTCCTTGCTTTC
1 TTTCTTTCCTCCCTTTC
110112 TTTCTTTCCTCCCTTTC
1 TTTCTTTCCTCCCTTTC
110129 CTTACTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.35, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTCTTTCCTCCCTTTC
Found at i:113584 original size:6 final size:6
Alignment explanation
Indices: 113573--113598 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
113563 GATTGGTACC
113573 TTGCAT TTGCAT TTGCAT TTGCAT TT
1 TTGCAT TTGCAT TTGCAT TTGCAT TT
113599 ACCTACCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (6 bp):
TTGCAT
Found at i:114230 original size:24 final size:25
Alignment explanation
Indices: 114197--114247 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
114187 AACCCTATTC
*
114197 TAATCAATGTCAAATAGAAGAAGTG
1 TAATCAATGTCAAATAGAAGAAATG
*
114222 TAAT-AATGTCAAATAGGAGAAATG
1 TAATCAATGTCAAATAGAAGAAATG
114246 TA
1 TA
114248 GTTTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.25
Consensus pattern (25 bp):
TAATCAATGTCAAATAGAAGAAATG
Found at i:120289 original size:28 final size:28
Alignment explanation
Indices: 120249--120304 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
120239 AGACCAGTGT
120249 TCCACATGGGTCCCTTATGAACAACGAA
1 TCCACATGGGTCCCTTATGAACAACGAA
120277 TCCACATGGGTCCCTTATGAACAACGAA
1 TCCACATGGGTCCCTTATGAACAACGAA
120305 AACTAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (28 bp):
TCCACATGGGTCCCTTATGAACAACGAA
Found at i:123968 original size:19 final size:19
Alignment explanation
Indices: 123944--123986 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
123934 ATGATGCATT
123944 TGACTAGCCAAAGGCAGAA
1 TGACTAGCCAAAGGCAGAA
123963 TGACTAGCCAAAGGCAGAA
1 TGACTAGCCAAAGGCAGAA
123982 TGACT
1 TGACT
123987 TTGTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.14
Consensus pattern (19 bp):
TGACTAGCCAAAGGCAGAA
Found at i:134358 original size:29 final size:30
Alignment explanation
Indices: 134303--134372 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
134293 ATCTTAAAAT
*
134303 TATACATGAACTATGGTTTAATGTGTAATTA
1 TATACATGAACTATGATTT-ATGTGTAATTA
* * *
134334 TATACATGAACTTTGATTT-TTTGTAATTT
1 TATACATGAACTATGATTTATGTGTAATTA
*
134363 TATATATGAA
1 TATACATGAA
134373 TTTTTTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 17 0.50
31 17 0.50
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (30 bp):
TATACATGAACTATGATTTATGTGTAATTA
Found at i:134413 original size:12 final size:12
Alignment explanation
Indices: 134398--134423 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
134388 AATCTTTATA
134398 AATTATTAACAT
1 AATTATTAACAT
134410 AATTATTAACAT
1 AATTATTAACAT
134422 AA
1 AA
134424 CATCATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTATTAACAT
Found at i:137363 original size:16 final size:16
Alignment explanation
Indices: 137342--137377 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
137332 AATGGTAAGA
*
137342 ACAGATAGAAGTGGAG
1 ACAGATAGAAATGGAG
*
137358 ACAGATGGAAATGGAG
1 ACAGATAGAAATGGAG
137374 ACAG
1 ACAG
137378 CAAAAATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.08, G:0.36, T:0.11
Consensus pattern (16 bp):
ACAGATAGAAATGGAG
Found at i:137815 original size:19 final size:19
Alignment explanation
Indices: 137776--137815 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
137766 TCAACTAATT
**
137776 AAATTAAAAAAATAATTAA
1 AAATTAAAAAAATAAAGAA
*
137795 AAATTATAAAAATAAAGAA
1 AAATTAAAAAAATAAAGAA
137814 AA
1 AA
137816 TAGAAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (19 bp):
AAATTAAAAAAATAAAGAA
Found at i:138257 original size:22 final size:25
Alignment explanation
Indices: 138215--138265 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 25
138205 TTCAGTTAGA
*
138215 AAAATAATAAAAATAATATTTTT-T
1 AAAACAATAAAAATAATATTTTTAT
138239 AAAACAAT-AAAA-AATATTTTTAT
1 AAAACAATAAAAATAATATTTTTAT
138262 AAAA
1 AAAA
138266 ATATTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 9 0.36
23 9 0.36
24 7 0.28
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
AAAACAATAAAAATAATATTTTTAT
Found at i:138266 original size:24 final size:25
Alignment explanation
Indices: 138214--138266 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
138204 ATTCAGTTAG
*
138214 AAAAATAATAAAAATAATATTTTTT
1 AAAAACAATAAAAATAATATTTTTT
138239 -AAAACAAT-AAAA-AATATTTTTAT
1 AAAAACAATAAAAATAATATTTTT-T
138262 AAAAA
1 AAAAA
138267 TATTTATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 9 0.36
23 5 0.20
24 11 0.44
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
AAAAACAATAAAAATAATATTTTTT
Done.