Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009414.1 Kokia drynarioides strain JFW-HI SEQ_124121, 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: 234809
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 55 characters in sequence are not A, C, G, or T
Found at i:631 original size:23 final size:22
Alignment explanation
Indices: 601--678 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 22
591 AGCGCGTTTC
* *
601 GTGCCCTCTGCTCAGCACTGTGT
1 GTGCCCTCTGATTAGCACT-TGT
624 GTGCCCTCTGTTATTAGCACTTCGT
1 GTGCCCTCTG--ATTAGCACTT-GT
*
649 GTGCCCTCTGATTAGCACTTTTT
1 GTGCCCTCTGATTAGCAC-TTGT
672 GTGCCCT
1 GTGCCCT
679 TTGTTACCCA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
23 26 0.54
24 3 0.06
25 19 0.40
ACGTcount: A:0.10, C:0.31, G:0.22, T:0.37
Consensus pattern (22 bp):
GTGCCCTCTGATTAGCACTTGT
Found at i:650 original size:25 final size:24
Alignment explanation
Indices: 614--709 Score: 88
Period size: 25 Copynumber: 3.9 Consensus size: 24
604 CCCTCTGCTC
614 AGCACTGTGTGTGCCCTCTGTTATT
1 AGCACT-TGTGTGCCCTCTGTTATT
639 AGCACTTCGTGTGCCCTCTG--ATT
1 AGCACTT-GTGTGCCCTCTGTTATT
* * **
662 AGCACTTTTTGTGCCCTTTGTTACCC
1 AGCAC-TTGTGTGCCCTCTGTTA-TT
* *
688 AGCACTTATGTGCCTTCTGTTA
1 AGCACTTGTGTGCCCTCTGTTA
710 AGTACTTCGG
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
23 18 0.31
24 3 0.05
25 33 0.56
26 5 0.08
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.40
Consensus pattern (24 bp):
AGCACTTGTGTGCCCTCTGTTATT
Found at i:700 original size:48 final size:48
Alignment explanation
Indices: 601--706 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 48
591 AGCGCGTTTC
* ** *
601 GTGCCCTCTGCTCAGCACTGTGTGTGCCCTCTGTTATTAGCACTTCGT
1 GTGCCCTCTGATCAGCACTGTGTGTGCCCTCTGTTACCAGCACTTCAT
* * * *
649 GTGCCCTCTGATTAGCACTTTTTGTGCCCTTTGTTACCCAGCACTT-AT
1 GTGCCCTCTGATCAGCACTGTGTGTGCCCTCTGTTA-CCAGCACTTCAT
*
697 GTGCCTTCTG
1 GTGCCCTCTG
707 TTAAGTACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
48 41 0.85
49 7 0.15
ACGTcount: A:0.11, C:0.30, G:0.21, T:0.38
Consensus pattern (48 bp):
GTGCCCTCTGATCAGCACTGTGTGTGCCCTCTGTTACCAGCACTTCAT
Found at i:3332 original size:37 final size:37
Alignment explanation
Indices: 3268--3343 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
3258 CCGTATTTAA
3268 GTATGAATTTATGTTTTATATATTTCATGATATGCTT
1 GTATGAATTTATGTTTTATATATTTCATGATATGCTT
*
3305 GTATGAATTTATGTTTTATATATTTCATGGTATGCTT
1 GTATGAATTTATGTTTTATATATTTCATGATATGCTT
3342 GT
1 GT
3344 TTATGATCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.54
Consensus pattern (37 bp):
GTATGAATTTATGTTTTATATATTTCATGATATGCTT
Found at i:10075 original size:17 final size:17
Alignment explanation
Indices: 10053--10093 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
10043 TCTCTTGATA
*
10053 TTTAACCTTTCATCTTC
1 TTTAACCTTTCATATTC
10070 TTTAACCTTTCATATTC
1 TTTAACCTTTCATATTC
10087 TTATAAC
1 TT-TAAC
10094 TATTTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAACCTTTCATATTC
Found at i:18957 original size:23 final size:23
Alignment explanation
Indices: 18925--19048 Score: 106
Period size: 23 Copynumber: 5.3 Consensus size: 23
18915 ACACTAGCGC
18925 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTCT-GT
* *
18948 GCTCTTTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTCTGT
* * *
18973 GCTCTCTGATTAGCACTTTATGT
1 GCTCTCTGTTTAGCACTGTCTGT
* * * *
18996 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
* * *
19019 ACTCTCTGTTTAGCATTGTGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
19042 GCTCTCT
1 GCTCTCT
19049 ATTGCCCAGC
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
23 64 0.76
24 1 0.01
25 16 0.19
26 3 0.04
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTCTGT
Found at i:19017 original size:21 final size:22
Alignment explanation
Indices: 18925--19083 Score: 99
Period size: 23 Copynumber: 6.8 Consensus size: 22
18915 ACACTAGCGC
* * *
18925 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACTTAT-GT
* *
18948 GCTCTTTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACT-TATGT
18973 GCTCTCTGATTAGCACTTTATGT
1 GCTCTCTGATTAGCAC-TTATGT
*
18996 GCTCTCTGATTAGTACTT-TGT
1 GCTCTCTGATTAGCACTTATGT
* * *
19017 GTACTCTCTGTTTAGCATTGTGTGT
1 G--CTCTCTGATTAGCACT-TATGT
19042 GCTCTCT-ATTGCCCAGCACTTATGT
1 GCTCTCTGATT----AGCACTTATGT
*
19067 GCTCTCTG-TTAGTACTT
1 GCTCTCTGATTAGCACTT
19084 TGATACTCTC
Statistics
Matches: 109, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
21 10 0.09
22 4 0.04
23 53 0.49
24 2 0.02
25 33 0.30
26 7 0.06
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTTATGT
Found at i:19025 original size:46 final size:46
Alignment explanation
Indices: 18958--19048 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
18948 GCTCTTTGTT
*
18958 ATTAGCACTGTGTGTGCTCTCTGATTAGCACTT-TATGTGCTCTCTG
1 ATTAGCACTGTGTGTACTCTCTGATTAGCA-TTGTATGTGCTCTCTG
* * * *
19004 ATTAGTACTTTGTGTACTCTCTGTTTAGCATTGTGTGTGCTCTCT
1 ATTAGCACTGTGTGTACTCTCTGATTAGCATTGTATGTGCTCTCT
19049 ATTGCCCAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 2 0.05
46 37 0.95
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.45
Consensus pattern (46 bp):
ATTAGCACTGTGTGTACTCTCTGATTAGCATTGTATGTGCTCTCTG
Found at i:19039 original size:69 final size:66
Alignment explanation
Indices: 18959--19098 Score: 192
Period size: 69 Copynumber: 2.0 Consensus size: 66
18949 CTCTTTGTTA
*
18959 TTAGCACTGTGTGTGCTCTCTGATT-AGCACTTTATGTGCTCTCTGATTAGTACTTTGTGTACTC
1 TTAGCACTGTGTGTGCTCTCT-ATTCAGCAC-TTATGTGCTCTCTG-TTAGTACTTTG-ATACTC
19023 TCTGT
62 TCTGT
*
19028 TTAGCATTGTGTGTGCTCTCTATTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTTGATACTCT
1 TTAGCACTGTGTGTGCTCTCTATT---CAGCACTTATGTGCTCTCTGTTAGTACTTTGATACTCT
19093 CTGT
63 CTGT
19097 TT
1 TT
19099 GTTCCGTATA
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
68 3 0.05
69 32 0.49
70 11 0.17
71 14 0.22
72 5 0.08
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.45
Consensus pattern (66 bp):
TTAGCACTGTGTGTGCTCTCTATTCAGCACTTATGTGCTCTCTGTTAGTACTTTGATACTCTCTG
T
Found at i:27485 original size:21 final size:22
Alignment explanation
Indices: 27461--27510 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
27451 AGTTTGATTC
*
27461 GATTTATTTTTATAT-TTTTGT
1 GATTTATTTTTATATATTATGT
27482 GATTTATTTTTATATATTATGT
1 GATTTATTTTTATATATTATGT
*
27504 AATTTAT
1 GATTTAT
27511 ATCCAGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (22 bp):
GATTTATTTTTATATATTATGT
Found at i:33843 original size:31 final size:31
Alignment explanation
Indices: 33787--33855 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
33777 AAAAAAAATT
** *
33787 AATAATTTAGTGACTTACATAAAAACTTTCTA
1 AATAATTTAGTGACGCAAATAAAAACTTTC-A
*
33819 AA-AATTTAGTGACGCAAATGAAAACTTTCA
1 AATAATTTAGTGACGCAAATAAAAACTTTCA
33849 AATAATT
1 AATAATT
33856 CAATAATCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 3 0.09
31 27 0.84
32 2 0.06
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (31 bp):
AATAATTTAGTGACGCAAATAAAAACTTTCA
Found at i:38797 original size:181 final size:180
Alignment explanation
Indices: 38493--38988 Score: 607
Period size: 181 Copynumber: 2.7 Consensus size: 180
38483 CCGAGGTGAT
** * * **
38493 AAATATGAGTTAGAAACTTCGAGCCATATGAATCAGCACTATATCAACTTGCAAAACAAGTTATG
1 AAATATGAGTTAGAAACTTCGAGTGATATGAATCAGCACTATACCAACTTGCAACACAAG-TACA
** * * * * *
38558 TAAGTACGCCATACATCTAGGAAGCAAATCATATTACCATACCGATATGTTAAAGCCTCCGTCCT
65 TAAGTACGCCATATGTCAAAGAAGCAAATCACATTACCATACCGGTATGTTAAAGCCTCTGTCCT
** * *
38623 AATAGCAAACTGAAATATGCGACTCACTGATGATGATAATATTTTGAGTTG
130 AATAGCAAACTGAAATACACAACTCACTGATGATGATAATATTTTGAGGTG
* * * * *
38674 AAATATGAGTTGGAAACATCGAGTGATATGAATCAGCACTATACCAACATGCAACCCGAGCTACA
1 AAATATGAGTTAGAAACTTCGAGTGATATGAATCAGCACTATACCAACTTGCAACACAAG-TACA
* *
38739 TAAGTACACCATATGTCAAAGAAGCAAAACACATTACCATACCGGTATGTTAAAGCCTCTGTCCT
65 TAAGTACGCCATATGTCAAAGAAGCAAATCACATTACCATACCGGTATGTTAAAGCCTCTGTCCT
* * * *
38804 AATAGCAAACTGAAATACATAACTCCCTGATGATGATGATGTTTTGAGGTG
130 AATAGCAAACTGAAATACACAACTCACTGATGATGATAATATTTTGAGGTG
* * * * * * *
38855 AATTTTGAGTTAGAAACTTTGAGTGACATGAATCCGCACTATACCAACTTGCAACATAAGTTCAA
1 AAATATGAGTTAGAAACTTCGAGTGATATGAATCAGCACTATACCAACTTGCAACACAAGTAC-A
* * * *
38920 TAAGCATGCCATATGTCAAAGAAGCAAATCACATTGCCATACCGGTATG-TAAAACCTCTGTCCT
65 TAAGTACGCCATATGTCAAAGAAGCAAATCACATTACCATACCGGTATGTTAAAGCCTCTGTCCT
38984 AATAG
130 AATAG
38989 AAATTTTCGA
Statistics
Matches: 267, Mismatches: 47, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
180 21 0.08
181 246 0.92
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (180 bp):
AAATATGAGTTAGAAACTTCGAGTGATATGAATCAGCACTATACCAACTTGCAACACAAGTACAT
AAGTACGCCATATGTCAAAGAAGCAAATCACATTACCATACCGGTATGTTAAAGCCTCTGTCCTA
ATAGCAAACTGAAATACACAACTCACTGATGATGATAATATTTTGAGGTG
Found at i:40599 original size:118 final size:118
Alignment explanation
Indices: 40390--40626 Score: 447
Period size: 118 Copynumber: 2.0 Consensus size: 118
40380 TTATAGTAGG
*
40390 TCTCTTTTATGTCATTCTAAATTTATATAGGGGAAATTTTAAGGACCATTAAATAGGCCAGACAT
1 TCTCTTTTATGTCATTCTAAAATTATATAGGGGAAATTTTAAGGACCATTAAATAGGCCAGACAT
40455 AACTACATGCTAGCAGGCTTTATCTGGAAATAAATGTCCACCAAGCCTAATAT
66 AACTACATGCTAGCAGGCTTTATCTGGAAATAAATGTCCACCAAGCCTAATAT
*
40508 TCTCTTTTATGTCATTCTAAAATTATATAGGGGCAATTTTAAGGACCATTAAATAGGCCAGACAT
1 TCTCTTTTATGTCATTCTAAAATTATATAGGGGAAATTTTAAGGACCATTAAATAGGCCAGACAT
*
40573 AACTACATGCTAGCAGGCTTTGTCTGGAAATAAATGTCCACCAAGCCTAATAT
66 AACTACATGCTAGCAGGCTTTATCTGGAAATAAATGTCCACCAAGCCTAATAT
40626 T
1 T
40627 TGTATCCGAT
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 116 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (118 bp):
TCTCTTTTATGTCATTCTAAAATTATATAGGGGAAATTTTAAGGACCATTAAATAGGCCAGACAT
AACTACATGCTAGCAGGCTTTATCTGGAAATAAATGTCCACCAAGCCTAATAT
Found at i:46419 original size:19 final size:20
Alignment explanation
Indices: 46384--46423 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
46374 TTTAAGTCTA
46384 ATTTTAAAAAAATTAAAAAT
1 ATTTTAAAAAAATTAAAAAT
*
46404 ATTTTAGAAAAA-TAAAAAT
1 ATTTTAAAAAAATTAAAAAT
46423 A
1 A
46424 ATTATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
ATTTTAAAAAAATTAAAAAT
Found at i:46503 original size:18 final size:18
Alignment explanation
Indices: 46476--46511 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
46466 TAATGATTTT
* *
46476 TAATTTAAAGATATAATA
1 TAATTAAAAGATAAAATA
46494 TAATTAAAAGATAAAATA
1 TAATTAAAAGATAAAATA
46512 AATAATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
TAATTAAAAGATAAAATA
Found at i:47231 original size:15 final size:15
Alignment explanation
Indices: 47211--47240 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47201 AAAGATTAAA
*
47211 AATATTTTTTATATT
1 AATATTTTATATATT
47226 AATATTTTATATATT
1 AATATTTTATATATT
47241 TTGTAATTAA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATATTTTATATATT
Found at i:47242 original size:22 final size:20
Alignment explanation
Indices: 47211--47269 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 20
47201 AAAGATTAAA
*
47211 AATATTTTTTATATTAATATTT
1 AATATATTTT-TATTAA-ATTT
*
47233 TATATATTTTGTAATTAAATTT
1 AATATATTTT-T-ATTAAATTT
*
47255 AAAATATTTTTATTA
1 AATATATTTTTATTA
47270 TTTAAAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 4 0.13
21 1 0.03
22 21 0.68
23 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
AATATATTTTTATTAAATTT
Found at i:49433 original size:49 final size:49
Alignment explanation
Indices: 49361--49459 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
49351 AAGGTACAGT
49361 ATGTGCTAATTATTTATCTATGGAAGTTTTATGACATTTGATCTTTTAA
1 ATGTGCTAATTATTTATCTATGGAAGTTTTATGACATTTGATCTTTTAA
49410 ATGTGCTAATTATTTATCTATGGAAGTTTTATGACATTTGATCTTTTAA
1 ATGTGCTAATTATTTATCTATGGAAGTTTTATGACATTTGATCTTTTAA
49459 A
1 A
49460 CCTTTTTTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.48
Consensus pattern (49 bp):
ATGTGCTAATTATTTATCTATGGAAGTTTTATGACATTTGATCTTTTAA
Found at i:57500 original size:12 final size:13
Alignment explanation
Indices: 57458--57500 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
57448 TAACTGAAAC
*
57458 TAAAATAATAGTT
1 TAAAATAAAAGTT
*
57471 TAAGTATAAAAGTT
1 TAA-AATAAAAGTT
57485 TAAAATAAAA-TT
1 TAAAATAAAAGTT
57497 TAAA
1 TAAA
57501 TATCAAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 6 0.23
13 9 0.35
14 11 0.42
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (13 bp):
TAAAATAAAAGTT
Found at i:64259 original size:31 final size:31
Alignment explanation
Indices: 64222--64290 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
64212 ATAAATAAAT
64222 AAATAAAAGCAAAGAAGAAGGGAAAAATGGG
1 AAATAAAAGCAAAGAAGAAGGGAAAAATGGG
*
64253 AAATAAAAGCAAAGAAGAAGGGCAAAATGGG
1 AAATAAAAGCAAAGAAGAAGGGAAAAATGGG
64284 AAATAAA
1 AAATAAA
64291 TAAAATAGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.62, C:0.04, G:0.26, T:0.07
Consensus pattern (31 bp):
AAATAAAAGCAAAGAAGAAGGGAAAAATGGG
Found at i:64513 original size:6 final size:6
Alignment explanation
Indices: 64495--64534 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
64485 TATACTTTTT
* *
64495 TATTAA TAATAA TAGTAA TTATTAA TATTAA TATTAA TAT
1 TATTAA TATTAA TATTAA -TATTAA TATTAA TATTAA TAT
64535 ACTATTCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
TATTAA
Found at i:64518 original size:19 final size:19
Alignment explanation
Indices: 64494--64532 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
64484 ATATACTTTT
64494 TTATTAATAATAATAGTAA
1 TTATTAATAATAATAGTAA
* *
64513 TTATTAATATTAATATTAA
1 TTATTAATAATAATAGTAA
64532 T
1 T
64533 ATACTATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TTATTAATAATAATAGTAA
Found at i:64965 original size:6 final size:6
Alignment explanation
Indices: 64956--64993 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
64946 TTTTAAAGGT
64956 GCTGCC GCTGCC GCTGCC GCTGCC GCTGCC GCTGCC GC
1 GCTGCC GCTGCC GCTGCC GCTGCC GCTGCC GCTGCC GC
64994 CCCTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.34, T:0.16
Consensus pattern (6 bp):
GCTGCC
Found at i:70337 original size:15 final size:14
Alignment explanation
Indices: 70309--70346 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
70299 TTCTAAATAT
70309 AAAAAAAA-ATTAA
1 AAAAAAAATATTAA
70322 AAAAATAAATATTAA
1 AAAAA-AAATATTAA
*
70337 ATAAAAAATA
1 AAAAAAAATA
70347 AAATTTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 8 0.36
15 9 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAAAAATATTAA
Found at i:73845 original size:51 final size:51
Alignment explanation
Indices: 73789--73893 Score: 167
Period size: 51 Copynumber: 2.1 Consensus size: 51
73779 ATGTTGTTGA
* *
73789 AACCAGACCAGACTAGCCT-GTTCAACCAGGAACCGATTGGTCTAATGGTTC
1 AACCAGACCAGACTAG-CTGGTTCAACCAGGAACCAATTGGTCTAACGGTTC
*
73840 AACCAGACCGGACTAGCTGGTTCAACCAGGAACCAATTGGTCTAACGGTTC
1 AACCAGACCAGACTAGCTGGTTCAACCAGGAACCAATTGGTCTAACGGTTC
73891 AAC
1 AAC
73894 ATGGTATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
50 2 0.04
51 48 0.96
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (51 bp):
AACCAGACCAGACTAGCTGGTTCAACCAGGAACCAATTGGTCTAACGGTTC
Found at i:86239 original size:3 final size:3
Alignment explanation
Indices: 86233--86280 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
86223 GTCAGCAAAC
86233 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
86281 AAATGGAGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:90082 original size:68 final size:68
Alignment explanation
Indices: 90010--90158 Score: 280
Period size: 68 Copynumber: 2.2 Consensus size: 68
90000 TTAATACATT
90010 AATTAAAGATGCTCCGTTAGGACATGTTTTAAATTAAATAAATATAAATATACTTTTTTATAAAT
1 AATTAAAGATGCTCCGTTAGGACATGTTTTAAATTAAATAAATATAAATATACTTTTTTATAAAT
90075 ATA
66 ATA
**
90078 AATTAAAGATGCTCTTTTAGGACATGTTTTAAATTAAATAAATATAAATATACTTTTTTATAAAT
1 AATTAAAGATGCTCCGTTAGGACATGTTTTAAATTAAATAAATATAAATATACTTTTTTATAAAT
90143 ATA
66 ATA
90146 AATTAAAGATGCT
1 AATTAAAGATGCT
90159 TTTTTTAACA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 79 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (68 bp):
AATTAAAGATGCTCCGTTAGGACATGTTTTAAATTAAATAAATATAAATATACTTTTTTATAAAT
ATA
Found at i:90387 original size:56 final size:56
Alignment explanation
Indices: 90301--90412 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
90291 TTTAACTCGA
90301 TACAATGTTAATTCACTTTACAAACCAACAATGGAGGAGGGAATAATCTGTGGATC
1 TACAATGTTAATTCACTTTACAAACCAACAATGGAGGAGGGAATAATCTGTGGATC
*
90357 TACAATGTTAATTCACTTTACAAACCAACAATGGAGGAGGGAATAATCTTTGGATC
1 TACAATGTTAATTCACTTTACAAACCAACAATGGAGGAGGGAATAATCTGTGGATC
90413 AGGCTGCAGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (56 bp):
TACAATGTTAATTCACTTTACAAACCAACAATGGAGGAGGGAATAATCTGTGGATC
Found at i:93940 original size:30 final size:30
Alignment explanation
Indices: 93875--93951 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
93865 AAATTTTAAA
* *
93875 TTAATAATGATAAAATTGTATTTTAATCCC
1 TTAAAAATGATAAAATTGTAATTTAATCCC
* **
93905 CTAAAAATGATATAAATT-TAATTTAATCTT
1 TTAAAAATGATA-AAATTGTAATTTAATCCC
*
93935 TTAAAAATTACTAAAAT
1 TTAAAAATGA-TAAAAT
93952 ATAAATTATT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 31 0.82
31 7 0.18
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.42
Consensus pattern (30 bp):
TTAAAAATGATAAAATTGTAATTTAATCCC
Found at i:93959 original size:15 final size:16
Alignment explanation
Indices: 93939--93972 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
93929 AATCTTTTAA
93939 AAATTACTAAAAT-AT
1 AAATTACTAAAATGAT
*
93954 AAATTATTAAAATGAT
1 AAATTACTAAAATGAT
93970 AAA
1 AAA
93973 ATTATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTACTAAAATGAT
Found at i:101278 original size:11 final size:11
Alignment explanation
Indices: 101264--101288 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
101254 TTGTGCTCTT
101264 TACCCCCTTCA
1 TACCCCCTTCA
101275 TACCCCCTTCA
1 TACCCCCTTCA
101286 TAC
1 TAC
101289 AAGTCTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.52, G:0.00, T:0.28
Consensus pattern (11 bp):
TACCCCCTTCA
Found at i:102378 original size:24 final size:24
Alignment explanation
Indices: 102349--102399 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
102339 AGAAATAATC
* *
102349 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTAGTTG
102373 TTTCAATTAAACTCTATTTAGTTG
1 TTTCAATTAAACTCTATTTAGTTG
102397 TTT
1 TTT
102400 GAGTCAAATT
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:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAGTTG
Found at i:103656 original size:25 final size:23
Alignment explanation
Indices: 103628--103673 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
103618 GTTGGATCCA
103628 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
103653 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
103674 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:112084 original size:35 final size:35
Alignment explanation
Indices: 112038--112108 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
112028 ACTCTTTTAA
112038 GTCTTTTGGGGACAACGGGTTCGAATGGGAATTGT
1 GTCTTTTGGGGACAACGGGTTCGAATGGGAATTGT
112073 GTCTTTTGGGGACAACGGGTTCGAATGGGAATTGT
1 GTCTTTTGGGGACAACGGGTTCGAATGGGAATTGT
112108 G
1 G
112109 GATGTGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.20, C:0.11, G:0.38, T:0.31
Consensus pattern (35 bp):
GTCTTTTGGGGACAACGGGTTCGAATGGGAATTGT
Found at i:117243 original size:2 final size:2
Alignment explanation
Indices: 117236--117270 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
117226 TGAAATCATG
117236 TA 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 TA T
117271 GAATTTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:121623 original size:3 final size:3
Alignment explanation
Indices: 121615--121655 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
121605 TCTCATTGAT
121615 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
121656 GTATCCTACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:124901 original size:164 final size:164
Alignment explanation
Indices: 124709--125199 Score: 982
Period size: 164 Copynumber: 3.0 Consensus size: 164
124699 TTAAACTTTA
124709 AATATAAAAATTATTAAAAACACAATCTTAGCTGGATTCATTTCTTTGTTCATGGAAACAAAATC
1 AATATAAAAATTATTAAAAACACAATCTTAGCTGGATTCATTTCTTTGTTCATGGAAACAAAATC
124774 ATTTCAATTATAAGTTGCTCATTTATTAAAAATATTTACATTTAATTTGATTATTGCTTTTTACA
66 ATTTCAATTATAAGTTGCTCATTTATTAAAAATATTTACATTTAATTTGATTATTGCTTTTTACA
124839 TCAATTAATTATTGTCGAATTTAAGACAATGTTG
131 TCAATTAATTATTGTCGAATTTAAGACAATGTTG
124873 AATATAAAAATTATTAAAAACACAATCTTAGCTGGATTCATTTCTTTGTTCATGGAAACAAAATC
1 AATATAAAAATTATTAAAAACACAATCTTAGCTGGATTCATTTCTTTGTTCATGGAAACAAAATC
124938 ATTTCAATTATAAGTTGCTCATTTATTAAAAATATTTACATTTAATTTGATTATTGCTTTTTACA
66 ATTTCAATTATAAGTTGCTCATTTATTAAAAATATTTACATTTAATTTGATTATTGCTTTTTACA
125003 TCAATTAATTATTGTCGAATTTAAGACAATGTTG
131 TCAATTAATTATTGTCGAATTTAAGACAATGTTG
125037 AATATAAAAATTATTAAAAACACAATCTTAGCTGGATTCATTTCTTTGTTCATGGAAACAAAATC
1 AATATAAAAATTATTAAAAACACAATCTTAGCTGGATTCATTTCTTTGTTCATGGAAACAAAATC
125102 ATTTCAATTATAAGTTGCTCATTTATTAAAAATATTTACATTTAATTTGATTATTGCTTTTTACA
66 ATTTCAATTATAAGTTGCTCATTTATTAAAAATATTTACATTTAATTTGATTATTGCTTTTTACA
125167 TCAATTAATTATTGTCGAATTTAAGACAATGTT
131 TCAATTAATTATTGTCGAATTTAAGACAATGTT
125200 TATGTTTAGG
Statistics
Matches: 327, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 327 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (164 bp):
AATATAAAAATTATTAAAAACACAATCTTAGCTGGATTCATTTCTTTGTTCATGGAAACAAAATC
ATTTCAATTATAAGTTGCTCATTTATTAAAAATATTTACATTTAATTTGATTATTGCTTTTTACA
TCAATTAATTATTGTCGAATTTAAGACAATGTTG
Found at i:126949 original size:9 final size:9
Alignment explanation
Indices: 126935--126966 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
126925 TATCTTATCT
126935 CCTCCGCCA
1 CCTCCGCCA
126944 CCTCCGCCA
1 CCTCCGCCA
126953 CCTCCGCCA
1 CCTCCGCCA
126962 CCTCC
1 CCTCC
126967 AAAGCAACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.09, C:0.69, G:0.09, T:0.12
Consensus pattern (9 bp):
CCTCCGCCA
Found at i:129651 original size:11 final size:11
Alignment explanation
Indices: 129635--129659 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
129625 AAATGAAAAT
129635 TTTGATTAAGC
1 TTTGATTAAGC
129646 TTTGATTAAGC
1 TTTGATTAAGC
129657 TTT
1 TTT
129660 TGAGCCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (11 bp):
TTTGATTAAGC
Found at i:135194 original size:31 final size:33
Alignment explanation
Indices: 135159--135226 Score: 106
Period size: 31 Copynumber: 2.1 Consensus size: 33
135149 TTTTTGAACT
135159 AAATTTGACCCA-CAATCTTTTG-AAAAGAGTC-
1 AAATTTGA-CCATCAATCTTTTGAAAAAGAGTCG
135190 AAATTTGACCATCAATCTTTTGAAAAAGAGTCG
1 AAATTTGACCATCAATCTTTTGAAAAAGAGTCG
135223 AAAT
1 AAAT
135227 GATGTTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 3 0.09
31 18 0.53
32 9 0.26
33 4 0.12
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.29
Consensus pattern (33 bp):
AAATTTGACCATCAATCTTTTGAAAAAGAGTCG
Found at i:140584 original size:21 final size:21
Alignment explanation
Indices: 140542--140602 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
140532 CCACGTCAAC
*
140542 AAATAATTTAAAAATTATAAA
1 AAATAATTTATAAATTATAAA
140563 AAATAATTTATAAATTCA-AAA
1 AAATAATTTATAAATT-ATAAA
* *
140584 AGA-AATTTATTAATTATAA
1 AAATAATTTATAAATTATAA
140603 TTTTATTTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 1 0.03
20 13 0.37
21 20 0.57
22 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATAATTTATAAATTATAAA
Found at i:141056 original size:7 final size:7
Alignment explanation
Indices: 141044--141069 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
141034 TGAAAATTAA
141044 ATATTTT
1 ATATTTT
141051 ATATTTT
1 ATATTTT
141058 ATATTTT
1 ATATTTT
141065 ATATT
1 ATATT
141070 GTAAGGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATATTTT
Found at i:141364 original size:2 final size:2
Alignment explanation
Indices: 141357--141391 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
141347 CTTTTAAACC
141357 TA 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 TA T
141392 TCCTCATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:152381 original size:4 final size:4
Alignment explanation
Indices: 152372--152396 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
152362 CTTAACTGTT
152372 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
152397 ATTTTAAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:154922 original size:22 final size:22
Alignment explanation
Indices: 154888--154950 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
154878 TAAAAATAAT
* * *
154888 AAAATTTTGATTTAATTCTTTTA
1 AAAATTAT-ATTTAATTATTGTA
*
154911 AAAATTATATTTTTATTATTGTA
1 AAAATTATA-TTTAATTATTGTA
*
154934 AAAATTACAATTTAATT
1 AAAATTA-TATTTAATT
154951 TCGACCCCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
22 1 0.03
23 30 0.94
24 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (22 bp):
AAAATTATATTTAATTATTGTA
Found at i:156047 original size:29 final size:30
Alignment explanation
Indices: 156004--156062 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
155994 GAATTCGATC
156004 AAATCAAAATTTTATGTATAAAATTGCACA
1 AAATCAAAATTTTATGTATAAAATTGCACA
*
156034 AAATCAAAA-TTTATGTATACAATTGCACA
1 AAATCAAAATTTTATGTATAAAATTGCACA
156063 TTAAATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTTATGTATAAAATTGCACA
Found at i:159962 original size:29 final size:29
Alignment explanation
Indices: 159920--159978 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
159910 TTATTTCAGA
*
159920 GAAGGGATTGTATGAAACTGTAATTCCAC
1 GAAGGGATTGTATGAAACTATAATTCCAC
159949 GAAGGGATTGTATGAAACTATAATTCCAC
1 GAAGGGATTGTATGAAACTATAATTCCAC
159978 G
1 G
159979 TCATCCTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.27
Consensus pattern (29 bp):
GAAGGGATTGTATGAAACTATAATTCCAC
Found at i:168128 original size:17 final size:17
Alignment explanation
Indices: 168106--168142 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
168096 AGGTGGAGAA
* *
168106 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
168123 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
168140 CTT
1 CTT
168143 ATCAAGGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.14, G:0.24, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:183745 original size:20 final size:20
Alignment explanation
Indices: 183720--183759 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
183710 TTACCTTAGG
183720 CACCACGAAAACAAAACTGA
1 CACCACGAAAACAAAACTGA
183740 CACCACGAAAACAAAACTGA
1 CACCACGAAAACAAAACTGA
183760 TGGTCTAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.30, G:0.10, T:0.05
Consensus pattern (20 bp):
CACCACGAAAACAAAACTGA
Found at i:185171 original size:23 final size:23
Alignment explanation
Indices: 185144--185190 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
185134 AATTTGGGAG
185144 ATAAAAATTAGAATCAACATACT
1 ATAAAAATTAGAATCAACATACT
185167 ATAAAAATTAGAATCAACATACT
1 ATAAAAATTAGAATCAACATACT
185190 A
1 A
185191 AACATTCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.13, G:0.04, T:0.26
Consensus pattern (23 bp):
ATAAAAATTAGAATCAACATACT
Found at i:191487 original size:16 final size:16
Alignment explanation
Indices: 191466--191498 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
191456 GTTTAAATTG
*
191466 AATTTTTAATTTTTTT
1 AATTTTTAAATTTTTT
191482 AATTTTTAAATTTTTT
1 AATTTTTAAATTTTTT
191498 A
1 A
191499 GTAATTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
AATTTTTAAATTTTTT
Found at i:192178 original size:13 final size:13
Alignment explanation
Indices: 192160--192190 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
192150 CGATTCGACC
*
192160 TATATTATTTTTT
1 TATATTATTTTAT
192173 TATATTATTTTAT
1 TATATTATTTTAT
192186 TATAT
1 TATAT
192191 ACAACAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TATATTATTTTAT
Found at i:192398 original size:24 final size:23
Alignment explanation
Indices: 192354--192398 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
192344 TACAATATTC
*
192354 AAATAATATTAAAAAAGACAACG
1 AAATAATATTAAAAAACACAACG
192377 AAATAAT-TGTAAAAACACACAA
1 AAATAATAT-TAAAAA-ACACAA
192399 AAAAATAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 1 0.05
23 13 0.68
24 5 0.26
ACGTcount: A:0.64, C:0.11, G:0.07, T:0.18
Consensus pattern (23 bp):
AAATAATATTAAAAAACACAACG
Found at i:192455 original size:12 final size:12
Alignment explanation
Indices: 192455--192556 Score: 77
Period size: 12 Copynumber: 8.8 Consensus size: 12
192445 ATAATAGCAA
*
192455 AACAACAAAAAT
1 AACAGCAAAAAT
*
192467 AGCAGCAAAAAT
1 AACAGCAAAAAT
* *
192479 AATAGC-AAAAC
1 AACAGCAAAAAT
192490 AACAGC--AAA-
1 AACAGCAAAAAT
**
192499 AACAATAAAAAT
1 AACAGCAAAAAT
192511 AACAGCAAAAAT
1 AACAGCAAAAAT
**
192523 AACAATAAAAAT
1 AACAGCAAAAAT
* *
192535 AACAACAAAAAC
1 AACAGCAAAAAT
*
192547 AACACCAAAA
1 AACAGCAAAA
192557 CGTAAAAAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
9 4 0.06
10 3 0.04
11 12 0.17
12 53 0.74
ACGTcount: A:0.70, C:0.18, G:0.05, T:0.08
Consensus pattern (12 bp):
AACAGCAAAAAT
Found at i:192470 original size:32 final size:34
Alignment explanation
Indices: 192418--192498 Score: 130
Period size: 32 Copynumber: 2.4 Consensus size: 34
192408 ATCCAAACAA
192418 AAAACAACAATCAAAGTAGCAGCAAAAATAATAGC
1 AAAACAACAA-CAAAGTAGCAGCAAAAATAATAGC
192453 AAAACAACAA-AAA-TAGCAGCAAAAATAATAGC
1 AAAACAACAACAAAGTAGCAGCAAAAATAATAGC
*
192485 AAAACAACAGCAAA
1 AAAACAACAACAAA
192499 AACAATAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
32 28 0.64
33 6 0.14
35 10 0.23
ACGTcount: A:0.64, C:0.17, G:0.10, T:0.09
Consensus pattern (34 bp):
AAAACAACAACAAAGTAGCAGCAAAAATAATAGC
Found at i:192509 original size:32 final size:32
Alignment explanation
Indices: 192418--192520 Score: 111
Period size: 32 Copynumber: 3.1 Consensus size: 32
192408 ATCCAAACAA
*
192418 AAAACAACAATCAAAGTAGCAGCAAAAATAATAGC
1 AAAACAACAA--AAA-TAGCAACAAAAATAATAGC
*
192453 AAAACAACAAAAATAGCAGCAAAAATAATAGC
1 AAAACAACAAAAATAGCAACAAAAATAATAGC
* *
192485 AAAACAACAGCAAAA-A-CAATAAAAATAACAGC
1 AAAACAACA--AAAATAGCAACAAAAATAATAGC
192517 AAAA
1 AAAA
192521 ATAACAATAA
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
32 45 0.71
33 4 0.06
34 4 0.06
35 10 0.16
ACGTcount: A:0.66, C:0.17, G:0.09, T:0.09
Consensus pattern (32 bp):
AAAACAACAAAAATAGCAACAAAAATAATAGC
Found at i:192526 original size:24 final size:24
Alignment explanation
Indices: 192455--192550 Score: 92
Period size: 24 Copynumber: 4.2 Consensus size: 24
192445 ATAATAGCAA
* *
192455 AACAACAAAAATAGCAGCAAAAAT
1 AACAATAAAAATAACAGCAAAAAT
* ** *
192479 AA-TAGCAAAACAACAGC--AAA-
1 AACAATAAAAATAACAGCAAAAAT
192499 AACAATAAAAATAACAGCAAAAAT
1 AACAATAAAAATAACAGCAAAAAT
* *
192523 AACAATAAAAATAACAACAAAAAC
1 AACAATAAAAATAACAGCAAAAAT
192547 AACA
1 AACA
192551 CCAAAACGTA
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
20 2 0.04
21 14 0.25
23 13 0.23
24 28 0.49
ACGTcount: A:0.70, C:0.17, G:0.05, T:0.08
Consensus pattern (24 bp):
AACAATAAAAATAACAGCAAAAAT
Found at i:192565 original size:21 final size:22
Alignment explanation
Indices: 192541--192588 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
192531 AAATAACAAC
192541 AAAAACAACACCAAAAC-GTAA
1 AAAAACAACACCAAAACAGTAA
* *
192562 AAAAACAGCACTAAAACAGTAA
1 AAAAACAACACCAAAACAGTAA
192584 AAAAA
1 AAAAA
192589 TACAGAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.69, C:0.19, G:0.06, T:0.06
Consensus pattern (22 bp):
AAAAACAACACCAAAACAGTAA
Found at i:199650 original size:19 final size:19
Alignment explanation
Indices: 199628--199664 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
199618 ACTGTCATCT
199628 ACCGTAATCAAATTTGTTC
1 ACCGTAATCAAATTTGTTC
199647 ACCGTAATCAAATTTGTT
1 ACCGTAATCAAATTTGTT
199665 ATTAATTTTC
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:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (19 bp):
ACCGTAATCAAATTTGTTC
Found at i:204567 original size:96 final size:92
Alignment explanation
Indices: 204461--204683 Score: 288
Period size: 95 Copynumber: 2.4 Consensus size: 92
204451 TTTAACACTG
* * *
204461 AATTGAGTACTTGAACTGTCAAAATACATAAAAAAAAACCCTCAATTTT-TGTTAAAAAAAATAA
1 AATTGAGTACTTGAACTGTCAAAATGCATAAAAAAAAACCCTCAATTTTCT-TCAAAAAAAACAA
*
204525 TTAAACCCCTGCCTTTTTTTTTTTCTGTACTC
65 TTAAACCCCTACC---TTTTTTTT-TGTACTC
* * * *
204557 AATTGAGTACTTGAACTGTCAAAATGCAT-AAAAAAATCCCTTAATTTTCTTCATAAAAAGCAAT
1 AATTGAGTACTTGAACTGTCAAAATGCATAAAAAAAAACCCTCAATTTTCTTCAAAAAAAACAAT
*
204621 TAAGCCCCTACCTTTTTTTTTGTACTC
66 TAAACCCCTACCTTTTTTTTTGTACTC
* *
204648 AATTGGGTACTTGAACTTTCAAAATGCATAAAAAAA
1 AATTGAGTACTTGAACTGTCAAAATGCATAAAAAAA
204684 CATTTTACCC
Statistics
Matches: 114, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
91 34 0.30
92 14 0.12
95 37 0.32
96 29 0.25
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (92 bp):
AATTGAGTACTTGAACTGTCAAAATGCATAAAAAAAAACCCTCAATTTTCTTCAAAAAAAACAAT
TAAACCCCTACCTTTTTTTTTGTACTC
Found at i:204677 original size:91 final size:93
Alignment explanation
Indices: 204461--204683 Score: 290
Period size: 91 Copynumber: 2.4 Consensus size: 93
204451 TTTAACACTG
* * *
204461 AATTGAGTACTTGAACTGTCAAAATACATAAAAAAAAACCCTCAATTTTTGTTAAAAAAAATAAT
1 AATTGAGTACTTGAACTGTCAAAATGCAT-AAAAAAAACCCTCAATTTTTGTCAAAAAAAACAAT
*
204526 TAAACCCCTGCCTTTTTTTTTTTCTGTACTC
65 TAAACCCCTACC--TTTTTTTTTCTGTACTC
* * * *
204557 AATTGAGTACTTGAACTGTCAAAATGCATAAAAAAATCCCTTAATTTTCT-TCATAAAAAGCAAT
1 AATTGAGTACTTGAACTGTCAAAATGCATAAAAAAAACCCTCAATTTT-TGTCAAAAAAAACAAT
*
204621 TAAGCCCCTACC-TTTTTTTT-TGTACTC
65 TAAACCCCTACCTTTTTTTTTCTGTACTC
* *
204648 AATTGGGTACTTGAACTTTCAAAATGCATAAAAAAA
1 AATTGAGTACTTGAACTGTCAAAATGCATAAAAAAA
204684 CATTTTACCC
Statistics
Matches: 115, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
91 41 0.36
92 8 0.07
95 37 0.32
96 29 0.25
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (93 bp):
AATTGAGTACTTGAACTGTCAAAATGCATAAAAAAAACCCTCAATTTTTGTCAAAAAAAACAATT
AAACCCCTACCTTTTTTTTTCTGTACTC
Found at i:204825 original size:21 final size:19
Alignment explanation
Indices: 204799--204847 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
204789 ACTATAAAAA
204799 TAAAAATTAT-TAAATTTTAAT
1 TAAAAATTATAT-AA-TTT-AT
*
204820 TAAAAAATATATAATTTAT
1 TAAAAATTATATAATTTAT
204839 TAAAAATTA
1 TAAAAATTA
204848 GAAAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 10 0.40
20 3 0.12
21 11 0.44
22 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAAAATTATATAATTTAT
Found at i:205144 original size:40 final size:41
Alignment explanation
Indices: 205061--205149 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 41
205051 AGTACGATAA
* * **
205061 TTTT-TATAATTTTTTTACGAATTTTATATTTTTTTTACAT
1 TTTTCTATAATTTTCTTACGAACTTTATAAATTTTTTACAT
205101 TTTTCTATAATTTTCTTACG-ACTTTATAAATTTTTTA-ATT
1 TTTTCTATAATTTTCTTACGAACTTTATAAATTTTTTACA-T
205141 TTTTCTATA
1 TTTTCTATA
205150 TTTCTATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 1 0.02
40 28 0.65
41 14 0.33
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (41 bp):
TTTTCTATAATTTTCTTACGAACTTTATAAATTTTTTACAT
Found at i:205157 original size:29 final size:28
Alignment explanation
Indices: 205108--205203 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 28
205098 CATTTTTCTA
*
205108 TAATTTTCTTACGA-CTTTATAAATTTTT
1 TAATTTT-TTACGATTTTTATAAATTTTT
* * *
205136 TAATTTTTT-CTATATTTCTATATATTTTA
1 TAATTTTTTACGAT-TTT-TATAAATTTTT
205165 TAATTTTTTACGATTTTTATAATATTTTTTT
1 TAATTTTTTACGATTTTTATAA-A--TTTTT
205196 TAATTTTT
1 TAATTTTT
205204 AATAAAATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
26 2 0.04
27 2 0.04
28 13 0.24
29 22 0.41
30 3 0.06
31 12 0.22
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (28 bp):
TAATTTTTTACGATTTTTATAAATTTTT
Found at i:205182 original size:19 final size:19
Alignment explanation
Indices: 205060--205193 Score: 82
Period size: 20 Copynumber: 6.8 Consensus size: 19
205050 TAGTACGATA
205060 ATTTTTATAATTTTTTTACG
1 ATTTTTATAA-TTTTTTACG
* *
205080 AATTTTATATTTTTTTTAC-
1 ATTTTTATA-ATTTTTTACG
205099 ATTTTTCTATAATTTTCTTACG
1 A-TTTT-TATAATTTT-TTACG
*
205121 A-CTTTATAAATTTTTTA--
1 ATTTTTAT-AATTTTTTACG
* * *
205138 ATTTTT-TCTATATTTCTA-T
1 ATTTTTAT-AAT-TTTTTACG
205157 ATATTTTATAATTTTTTACG
1 AT-TTTTATAATTTTTTACG
205177 ATTTTTATAATATTTTT
1 ATTTTTATAAT-TTTTT
205194 TTTAATTTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 26
0.70 0.09 0.20
Matches are distributed among these distances:
17 4 0.04
18 8 0.09
19 23 0.26
20 44 0.49
21 9 0.10
22 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTATAATTTTTTACG
Found at i:205201 original size:21 final size:23
Alignment explanation
Indices: 205168--205213 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
205158 TATTTTATAA
*
205168 TTTTTTACGATTTTT-ATAATATT
1 TTTTTTAC-ATTTTTAATAAAATT
205191 TTTTTTA-ATTTTTAATAAAATT
1 TTTTTTACATTTTTAATAAAATT
205213 T
1 T
205214 AAATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 8 0.38
23 7 0.33
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTTTACATTTTTAATAAAATT
Found at i:205224 original size:31 final size:31
Alignment explanation
Indices: 205180--205239 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
205170 TTTTACGATT
* **
205180 TTTATAATATTTTTTTTAATTTTTAATAAAA
1 TTTATAATATTTTTATTAAAATTTAATAAAA
205211 TTTA-AATATTTTTTATTAAAATTTAATAA
1 TTTATAATA-TTTTTATTAAAATTTAATAA
205240 TTTCTATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTATAATATTTTTATTAAAATTTAATAAAA
Found at i:208483 original size:33 final size:33
Alignment explanation
Indices: 208446--208508 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
208436 AATCTTCAAT
208446 ATTACACATTCATAATGGAATAAAGAAGATTGA
1 ATTACACATTCATAATGGAATAAAGAAGATTGA
*
208479 ATTACACTTTCATAATGGAATAAAGAAGAT
1 ATTACACATTCATAATGGAATAAAGAAGAT
208509 GGTAAGGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (33 bp):
ATTACACATTCATAATGGAATAAAGAAGATTGA
Found at i:221818 original size:27 final size:26
Alignment explanation
Indices: 221769--221819 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
221759 TTCTTGTGAA
* * *
221769 TTTATTAAAAATTAACAAGTATTTTT
1 TTTATAAAAAATTAAAAAATATTTTT
221795 TTTATAAAAAATCTAAAAAATATTT
1 TTTATAAAAAAT-TAAAAAATATTT
221820 ACACATGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (26 bp):
TTTATAAAAAATTAAAAAATATTTTT
Found at i:222565 original size:24 final size:22
Alignment explanation
Indices: 222517--222565 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
222507 TTTTAATTTA
* *
222517 ATATTTTAAATTTTATAAAATT
1 ATATATTAAATTTCATAAAATT
*
222539 ATATATTAACTTTCATAAAATT
1 ATATATTAAATTTCATAAAATT
*
222561 CTATA
1 ATATA
222566 ATTCAATTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATATTAAATTTCATAAAATT
Done.