Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009686.1 Kokia drynarioides strain JFW-HI SEQ_124404, 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: 93405
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:4284 original size:16 final size:17
Alignment explanation
Indices: 4232--4289 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 17
4222 AAATAATACA
4232 TAAA-AAATAACT-AAG
1 TAAATAAATAACTAAAG
*
4247 TAAA-AAATAAAGTGAAATG
1 TAAATAAAT-AACT-AAA-G
4266 TAAATAAATAA-TAAAG
1 TAAATAAATAACTAAAG
4282 TAAATAAA
1 TAAATAAA
4290 AGGAGTAATG
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
15 8 0.22
16 12 0.32
17 3 0.08
18 3 0.08
19 7 0.19
20 4 0.11
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22
Consensus pattern (17 bp):
TAAATAAATAACTAAAG
Found at i:6025 original size:45 final size:43
Alignment explanation
Indices: 5970--6292 Score: 256
Period size: 45 Copynumber: 7.4 Consensus size: 43
5960 CATGGTCAGC
* * *
5970 GTAAGAGATTGGATGGTGGCTTAAAATTTCCCCTCTTGACTAGAG
1 GTAAAAGATTGGATGGTGGCTT-CAATTTCCCCTCTTGATTAG-G
*
6015 GTAAAAGATTGGAAGGTGGCTTCAATTTGCCCCTCTTGATTAGGG
1 GTAAAAGATTGGATGGTGGCTTCAATTT-CCCCTCTTGATTA-GG
* * * * * *
6060 GTAAAAAATTGGACGATGGCTTCAATTGCCCCTCTTAACTAGG
1 GTAAAAGATTGGATGGTGGCTTCAATTTCCCCTCTTGATTAGG
*** * *
6103 AGTAAAAGATTGGACAATGGCTTCAATCTGCCCTCTTGATTAAGG
1 -GTAAAAGATTGGATGGTGGCTTCAATTTCCCCTCTTGATT-AGG
* * *
6148 GTAAAAGATTGGATGGAGGCTTCAATCTTCTCCTTTTGATTAGG
1 GTAAAAGATTGGATGGTGGCTTCAAT-TTCCCCTCTTGATTAGG
* * * * * *
6192 GATAAAAGATTGGATGATGTCTTCAATCTGCCCT-ATGA-TCGAG
1 G-TAAAAGATTGGATGGTGGCTTCAATTTCCCCTCTTGATTAG-G
* * * * * ** *
6235 GTAAGAGATTGGCTGATGTCTTCAATCTGTCCTCTAG-TTAGG
1 GTAAAAGATTGGATGGTGGCTTCAATTTCCCCTCTTGATTAGG
6277 GTAAAAGATTGGATGG
1 GTAAAAGATTGGATGG
6293 CTTCATTCTA
Statistics
Matches: 227, Mismatches: 42, Indels: 21
0.78 0.14 0.07
Matches are distributed among these distances:
42 45 0.20
43 10 0.04
44 79 0.35
45 92 0.41
46 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (43 bp):
GTAAAAGATTGGATGGTGGCTTCAATTTCCCCTCTTGATTAGG
Found at i:6101 original size:89 final size:88
Alignment explanation
Indices: 5994--6225 Score: 247
Period size: 89 Copynumber: 2.6 Consensus size: 88
5984 GGTGGCTTAA
* * * *
5994 AATTTCCCCTCTTGACTA-GAGGTAAAAGATTGGA-AGGTGGCTTCAATTTGCCCCTCTTGATTA
1 AATTGCCCCTCTTAACTAGGA-GTAAAAGATTGGACA-ATGGCTTCAATCTG-CCCTCTTGATTA
*
6057 GGGGTAAAAAATTGGA-CGATGGCTTC
63 AGGGTAAAAAATTGGATCGA-GGCTTC
6083 AATTGCCCCTCTTAACTAGGAGTAAAAGATTGGACAATGGCTTCAATCTGCCCTCTTGATTAAGG
1 AATTGCCCCTCTTAACTAGGAGTAAAAGATTGGACAATGGCTTCAATCTGCCCTCTTGATTAAGG
* *
6148 GTAAAAGATTGGATGGAGGCTTC
66 GTAAAAAATTGGATCGAGGCTTC
* * * * * ** *
6171 AATCTTCTCCTTTTGATTAGG-GATAAAAGATTGGATGATGTCTTCAATCTGCCCT
1 AAT-TGCCCCTCTTAACTAGGAG-TAAAAGATTGGACAATGGCTTCAATCTGCCCT
6226 ATGATCGAGG
Statistics
Matches: 123, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
88 36 0.29
89 84 0.68
90 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (88 bp):
AATTGCCCCTCTTAACTAGGAGTAAAAGATTGGACAATGGCTTCAATCTGCCCTCTTGATTAAGG
GTAAAAAATTGGATCGAGGCTTC
Found at i:6280 original size:42 final size:41
Alignment explanation
Indices: 6099--6426 Score: 178
Period size: 42 Copynumber: 7.9 Consensus size: 41
6089 CCCTCTTAAC
** * * *
6099 TAGGAGTAAAAGATTGGACAATGGCTTCAATCTGCCCTCTTGAT
1 TAGG-GTAAAAGATTGG-TGATGTCTTCAATCTGTCCTCTAG-T
* * * *
6143 TAAGGGTAAAAGATTGGATGGA-GGCTTCAATCTTCTCCTTTTGAT
1 T-AGGGTAAAAGATTGG-T-GATGTCTTCAATC-TGTCCTCTAG-T
*
6188 TAGGGATAAAAGATTGGATGATGTCTTCAATCTG-CC-CTATGA
1 TAGGG-TAAAAGATTGG-TGATGTCTTCAATCTGTCCTCTA-GT
* *
6230 TCGAGGTAAGAGATTGGCTGATGTCTTCAATCTGTCCTCTAGT
1 TAG-GGTAAAAGATTGG-TGATGTCTTCAATCTGTCCTCTAGT
* * * *
6273 TAGGGTAAAAGATT-G-GATGGCTTC-AT-TCTACTCTATGG
1 TAGGGTAAAAGATTGGTGATGTCTTCAATCTGTCCTCTA-GT
* * * * *
6311 TCGGCGTGATAGATTGGTG-TGTCTTCAATCTGCCCTCTAAT
1 TAGG-GTAAAAGATTGGTGATGTCTTCAATCTGTCCTCTAGT
* * *
6352 TAGGGTAATAGATT-G-GATG-CTTCAGTCTGTCC-CAAGAT
1 TAGGGTAAAAGATTGGTGATGTCTTCAATCTGTCCTCTAG-T
* * *
6390 TAGGGTAAAAGATTGGTG-TATCTTTAATTTGTCCTCT
1 TAGGGTAAAAGATTGGTGATGTCTTCAATCTGTCCTCT
6427 TTAGATGCTT
Statistics
Matches: 222, Mismatches: 41, Indels: 45
0.72 0.13 0.15
Matches are distributed among these distances:
37 9 0.04
38 32 0.14
39 21 0.09
40 27 0.12
41 8 0.04
42 45 0.20
43 10 0.05
44 34 0.15
45 36 0.16
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34
Consensus pattern (41 bp):
TAGGGTAAAAGATTGGTGATGTCTTCAATCTGTCCTCTAGT
Found at i:6348 original size:79 final size:81
Alignment explanation
Indices: 6074--6375 Score: 229
Period size: 79 Copynumber: 3.6 Consensus size: 81
6064 AAAATTGGAC
* * *
6074 GATGGCTTCAAT-TGCCCCTCTTAACTAGGAGTAAAAGATTGGACAATGGCTTCAATCTGCCCTC
1 GATGTCTTCAATCTG-CCCTC-TAATTAGG-GTAAAAGATTGG---ATGGCTTCAATCTACCCT-
* ** * *
6138 TTGATTAAGGGTAAAAGATTGGAT
59 ATGATCGA-GGTAAGAGATTGGCT
* * * * *
6162 GGA-GGCTTCAATCTTCTCCTTTTGATTAGGGATAAAAGATTGGATGATGTCTTCAATCTGCCCT
1 -GATGTCTTCAATCTGC-CC-TCTAATTAGGG-TAAAAGATTGGATG--G-CTTCAATCTACCCT
6226 ATGATCGAGGTAAGAGATTGGCT
59 ATGATCGAGGTAAGAGATTGGCT
* * * * *
6249 GATGTCTTCAATCTGTCCTCTAGTTAGGGTAAAAGATTGGATGGCTTCATTCTACTCTATGGTCG
1 GATGTCTTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATGGCTTCAATCTACCCTATGATCG
* *
6314 -GCGTGATAGATTGG-T
66 AG-GTAAGAGATTGGCT
*
6329 G-TGTCTTCAATCTGCCCTCTAATTAGGGTAATAGATTGGAT-GCTTCA
1 GATGTCTTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATGGCTTCA
6376 GTCTGTCCCA
Statistics
Matches: 180, Mismatches: 24, Indels: 29
0.77 0.10 0.12
Matches are distributed among these distances:
78 6 0.03
79 37 0.21
80 3 0.02
81 27 0.15
82 1 0.01
84 14 0.08
85 8 0.04
86 7 0.04
87 23 0.13
88 17 0.09
89 36 0.20
90 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (81 bp):
GATGTCTTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATGGCTTCAATCTACCCTATGATCG
AGGTAAGAGATTGGCT
Found at i:6500 original size:40 final size:40
Alignment explanation
Indices: 6456--7187 Score: 905
Period size: 40 Copynumber: 18.5 Consensus size: 40
6446 TCATGGTCGA
* * *
6456 GGTAAGAGATTGGTATGTCTTCAATCAGCCCTCTGATTAG
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
*
6496 GGTAAAAGATTGGTGTGTCTTCAATCTGCTCTCTGATTAG
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
* * * **
6536 GTTAAAAGATTAG-ATG-CTTCAATCTGTCCC-AAGATTAG
1 GGTAAAAGATTGGTGTGTCTTCAATCTG-CCCTCTGATTAG
6574 GGTAAAAGATTGGTGTGTCTTCAATCTGCCC-CTGATTAG
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
* * * * *
6613 GGTAAAAGATTGG-AT-TATTCAATCTGCCATATGATTGG
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
* * *
6651 GGTAAGAGATTGGTGTGTCTTCAATCAGCCCTCTAATTAG
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
6691 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
* * ** *
6731 GGTAAAAGATTGG-ATG-CTTCAATCCGCCCTAAGATTAA
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
* * *
6769 GTTAAAAGATTGGTGTGTCTTCAATATGCCCTCTAATTAG
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
* * * *
6809 GGTAAAAGATTAG-ATG-CTTCAATCTACCCTATGATT-G
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
* * *
6846 GGCTAAGAGATTAGTGTGTCTTCAATCTACCCTCTGATTAG
1 GG-TAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
6887 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
*
6927 GGTAACAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
* *
6967 GGTAACAGATTGGTGTGTCTTCAATCTACCCTCTGATTAG
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
*
7007 GGTAAAAGATTGGTGTGTCTTGAATCTGCCCTCTGATTAG
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
* *
7047 GGTAAAATATTGGTGTGTCTTTAATCTGCCCTCTGATTAG
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
* ** * *
7087 GGTAAAATATTAATGTGTCTTTAATCTGCTCTCTGATTAG
1 GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
* * *
7127 GG-AAAGAGATTGGTGTGTCTTCAATCTACCCTATGA-TCG
1 GGTAAA-AGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
* *
7166 AGGTAAGAGATTGGTATGTCTT
1 -GGTAAAAGATTGGTGTGTCTT
7188 TTCTTTGCTT
Statistics
Matches: 600, Mismatches: 77, Indels: 30
0.85 0.11 0.04
Matches are distributed among these distances:
37 15 0.03
38 102 0.17
39 42 0.07
40 436 0.73
41 5 0.01
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (40 bp):
GGTAAAAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
Found at i:8400 original size:8 final size:8
Alignment explanation
Indices: 8375--8431 Score: 59
Period size: 7 Copynumber: 7.6 Consensus size: 8
8365 CTCCCTTTTC
8375 TTTTT-CT
1 TTTTTCCT
*
8382 TTCTT-CT
1 TTTTTCCT
8389 TTTTTCC-
1 TTTTTCCT
*
8396 TTTTTCCA
1 TTTTTCCT
*
8404 TTTTTCCA
1 TTTTTCCT
8412 TTTTTCCT
1 TTTTTCCT
8420 TTTTT-CT
1 TTTTTCCT
8427 TTTTT
1 TTTTT
8432 ATTTTCTTCT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
7 24 0.53
8 21 0.47
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTCCT
Found at i:8430 original size:15 final size:15
Alignment explanation
Indices: 8370--8448 Score: 65
Period size: 15 Copynumber: 5.3 Consensus size: 15
8360 GACCTCTCCC
8370 TTTTC-TTTTT-CTT
1 TTTTCTTTTTTCCTT
*
8383 TCTTCTTTTTTCCTT
1 TTTTCTTTTTTCCTT
* *
8398 TTTCCATTTTTCCATT
1 TTTTCTTTTTTCC-TT
*
8414 TTTCCTTTTTT-CTT
1 TTTTCTTTTTTCCTT
*
8428 TTTTATTTTCTTCTCTT
1 TTTTCTTTT-TTC-CTT
8445 TTTT
1 TTTT
8449 TTGGGTGAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
13 4 0.08
14 14 0.26
15 16 0.30
16 12 0.23
17 7 0.13
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCTTTTTTCCTT
Found at i:9045 original size:13 final size:13
Alignment explanation
Indices: 9027--9053 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9017 TTGACGATGT
9027 TGCTGAGTCGTGG
1 TGCTGAGTCGTGG
9040 TGCTGAGTCGTGG
1 TGCTGAGTCGTGG
9053 T
1 T
9054 ACTTGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.15, G:0.44, T:0.33
Consensus pattern (13 bp):
TGCTGAGTCGTGG
Found at i:14656 original size:6 final size:6
Alignment explanation
Indices: 14645--14683 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
14635 TGATCAAAAT
* * *
14645 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
14684 TATGACTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:19188 original size:36 final size:36
Alignment explanation
Indices: 19114--19189 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
19104 CTGGGACTTC
* * * * * *
19114 GACCTCGTCTTCATGTGCACATCGGGGTTTATCTTT
1 GACCCCGTCCTCATGTGCACATCGAGGTTGACCGTT
*
19150 GACCCCGTCCTCATGTGCACGTCGAGGTTGACCGTT
1 GACCCCGTCCTCATGTGCACATCGAGGTTGACCGTT
19186 GACC
1 GACC
19190 GTTGATCGAG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.14, C:0.30, G:0.25, T:0.30
Consensus pattern (36 bp):
GACCCCGTCCTCATGTGCACATCGAGGTTGACCGTT
Found at i:21090 original size:52 final size:52
Alignment explanation
Indices: 21029--21133 Score: 158
Period size: 52 Copynumber: 2.0 Consensus size: 52
21019 TAATAATATG
* * *
21029 AACAACATAATAATTAAC-TATTTAAAATTAAATAATTTAATGATATTTTCTT
1 AACAACATAATAATTAACGGA-TTAAAATTAAATAATTAAATAATATTTTCTT
*
21081 AACATCATAATAATTAACGGATTAAAATTAAATAATTAAATAATATTTTCTT
1 AACAACATAATAATTAACGGATTAAAATTAAATAATTAAATAATATTTTCTT
21133 A
1 A
21134 CCATTTGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 47 0.98
53 1 0.02
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.40
Consensus pattern (52 bp):
AACAACATAATAATTAACGGATTAAAATTAAATAATTAAATAATATTTTCTT
Found at i:21331 original size:40 final size:40
Alignment explanation
Indices: 21271--21479 Score: 260
Period size: 40 Copynumber: 5.2 Consensus size: 40
21261 NNNNNNNNNN
*
21271 GTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATTG
1 GTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTG
* *
21311 GTGTGTCTTGAATCTGCCCTCTGATTAGGGTAAAATATTG
1 GTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTG
* * *
21351 GTGTGTCTTTAATCTGCCCTCTGATTAGGGTAAAATATTA
1 GTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTG
* * *
21391 ATGTGTCTTTAATCTGCTCTCTGATTAGGG-AAAGAGATTG
1 GTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAA-AGATTG
* * * *
21431 GTGTGTCTTCAATCTACCCTATGA-TCGAGGTAAGAGATTG
1 GTGTGTCTTCAATCTGCCCTCTGATTAG-GGTAAAAGATTG
*
21471 GTATGTCTT
1 GTGTGTCTT
21480 TTCTTTGCTT
Statistics
Matches: 149, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
39 5 0.03
40 142 0.95
41 2 0.01
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.37
Consensus pattern (40 bp):
GTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTG
Found at i:22692 original size:8 final size:8
Alignment explanation
Indices: 22667--22723 Score: 59
Period size: 7 Copynumber: 7.6 Consensus size: 8
22657 CTCCCTTTTC
22667 TTTTT-CT
1 TTTTTCCT
*
22674 TTCTT-CT
1 TTTTTCCT
22681 TTTTTCC-
1 TTTTTCCT
*
22688 TTTTTCCA
1 TTTTTCCT
*
22696 TTTTTCCA
1 TTTTTCCT
22704 TTTTTCCT
1 TTTTTCCT
22712 TTTTT-CT
1 TTTTTCCT
22719 TTTTT
1 TTTTT
22724 ATTTTCTTCT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
7 24 0.53
8 21 0.47
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTCCT
Found at i:22722 original size:15 final size:15
Alignment explanation
Indices: 22662--22740 Score: 65
Period size: 15 Copynumber: 5.3 Consensus size: 15
22652 GACCTCTCCC
22662 TTTTC-TTTTT-CTT
1 TTTTCTTTTTTCCTT
*
22675 TCTTCTTTTTTCCTT
1 TTTTCTTTTTTCCTT
* *
22690 TTTCCATTTTTCCATT
1 TTTTCTTTTTTCC-TT
*
22706 TTTCCTTTTTT-CTT
1 TTTTCTTTTTTCCTT
*
22720 TTTTATTTTCTTCTCTT
1 TTTTCTTTT-TTC-CTT
22737 TTTT
1 TTTT
22741 TTGGGTGAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
13 4 0.08
14 14 0.26
15 16 0.30
16 12 0.23
17 7 0.13
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCTTTTTTCCTT
Found at i:23337 original size:13 final size:13
Alignment explanation
Indices: 23319--23345 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23309 TTGACGATGT
23319 TGCTGAGTCGTGG
1 TGCTGAGTCGTGG
23332 TGCTGAGTCGTGG
1 TGCTGAGTCGTGG
23345 T
1 T
23346 ACTTGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.15, G:0.44, T:0.33
Consensus pattern (13 bp):
TGCTGAGTCGTGG
Found at i:28948 original size:6 final size:6
Alignment explanation
Indices: 28937--28975 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
28927 TGATCAAAAT
* * *
28937 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
28976 TATGACTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:33480 original size:36 final size:36
Alignment explanation
Indices: 33406--33481 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
33396 CTGGGACTTC
* * * * * *
33406 GACCTCGTCTTCATGTGCACATCGGGGTTTATCTTT
1 GACCCCGTCCTCATGTGCACATCGAGGTTGACCGTT
*
33442 GACCCCGTCCTCATGTGCACGTCGAGGTTGACCGTT
1 GACCCCGTCCTCATGTGCACATCGAGGTTGACCGTT
33478 GACC
1 GACC
33482 GTTGATCGAG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.14, C:0.30, G:0.25, T:0.30
Consensus pattern (36 bp):
GACCCCGTCCTCATGTGCACATCGAGGTTGACCGTT
Found at i:35382 original size:52 final size:52
Alignment explanation
Indices: 35321--35425 Score: 158
Period size: 52 Copynumber: 2.0 Consensus size: 52
35311 TAATAATATG
* * *
35321 AACAACATAATAATTAAC-TATTTAAAATTAAATAATTTAATGATATTTTCTT
1 AACAACATAATAATTAACGGA-TTAAAATTAAATAATTAAATAATATTTTCTT
*
35373 AACATCATAATAATTAACGGATTAAAATTAAATAATTAAATAATATTTTCTT
1 AACAACATAATAATTAACGGATTAAAATTAAATAATTAAATAATATTTTCTT
35425 A
1 A
35426 CCATTTGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 47 0.98
53 1 0.02
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.40
Consensus pattern (52 bp):
AACAACATAATAATTAACGGATTAAAATTAAATAATTAAATAATATTTTCTT
Found at i:35575 original size:28 final size:28
Alignment explanation
Indices: 35548--35602 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
35538 ACTTTGGAAT
*
35548 TTGA-AATTTAGAATAAAAAATCGAGAA
1 TTGACAATTGAGAATAAAAAATCGAGAA
*
35575 TTGACAATTGAGAATAACAAATCGAGAA
1 TTGACAATTGAGAATAAAAAATCGAGAA
35603 CAAGAAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.24
Consensus pattern (28 bp):
TTGACAATTGAGAATAAAAAATCGAGAA
Found at i:35611 original size:28 final size:27
Alignment explanation
Indices: 35550--35613 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
35540 TTTGGAATTT
* **
35550 GAAATTTAGAATAAAAAATCGAGAATT
1 GAAATTGAGAATAAAAAATCGAGAAAA
*
35577 GACAATTGAGAATAACAAATCGAGAACAA
1 GA-AATTGAGAATAAAAAATCGAGAA-AA
35606 GAAATTGA
1 GAAATTGA
35614 AAATCAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 2 0.06
28 27 0.87
29 2 0.06
ACGTcount: A:0.55, C:0.08, G:0.17, T:0.20
Consensus pattern (27 bp):
GAAATTGAGAATAAAAAATCGAGAAAA
Found at i:43259 original size:21 final size:19
Alignment explanation
Indices: 43217--43262 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
43207 ATTTGTTTTC
43217 AATTAATTTTTATTTATAA
1 AATTAATTTTTATTTATAA
*
43236 AATTATATTTTTATTTTTATA
1 AATTA-ATTTTTATTTATA-A
43257 AATTAA
1 AATTAA
43263 ATAAAACACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 5 0.21
20 13 0.54
21 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTAATTTTTATTTATAA
Found at i:46351 original size:22 final size:23
Alignment explanation
Indices: 46321--46381 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
46311 ATATTAAAAT
46321 AAAATTAAAATAACTAAACTTCC
1 AAAATTAAAATAACTAAACTTCC
* * * *
46344 ATAA-TAAAATACCAAAATTTCC
1 AAAATTAAAATAACTAAACTTCC
46366 AAAATTAAAATTAACT
1 AAAATTAAAA-TAACT
46382 TACAATCCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
22 18 0.62
23 8 0.28
24 3 0.10
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAATTAAAATAACTAAACTTCC
Found at i:47628 original size:23 final size:21
Alignment explanation
Indices: 47594--47654 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 21
47584 GTTTTGGGTC
47594 AAAAGGTTTGGGTTTTTATTT
1 AAAAGGTTTGGGTTTTTATTT
47615 AAAAAGGGTTTGGGTTTCTTTATTT
1 -AAAA-GGTTTGGG-TT-TTTATTT
47640 AAAAGGTTTGGGTTT
1 AAAAGGTTTGGGTTT
47655 GTGTTAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
21 1 0.03
22 6 0.17
23 16 0.44
24 6 0.17
25 7 0.19
ACGTcount: A:0.25, C:0.02, G:0.26, T:0.48
Consensus pattern (21 bp):
AAAAGGTTTGGGTTTTTATTT
Found at i:59294 original size:13 final size:13
Alignment explanation
Indices: 59276--59300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59266 CTAGCACATG
59276 GGGGTGTGTCTAA
1 GGGGTGTGTCTAA
59289 GGGGTGTGTCTA
1 GGGGTGTGTCTA
59301 TACTTTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.48, T:0.32
Consensus pattern (13 bp):
GGGGTGTGTCTAA
Found at i:59315 original size:56 final size:56
Alignment explanation
Indices: 59247--59377 Score: 165
Period size: 56 Copynumber: 2.3 Consensus size: 56
59237 CGGAATGGTG
* * * * * *
59247 CTTTTCGAAGGCACACGGGCTAGCACATGGGGGTGTGTCTAAGGG-GTGTGTCTATA
1 CTTTTTGAAGGCACACGGGCTAGCACACGGGAGTATGTC-AAGGGTATGTGTCCATA
*
59303 CTTTTTGAAGGCACACGGGCTAGCACACGGGAGTATGTCCAGGGTATGTGTCCATA
1 CTTTTTGAAGGCACACGGGCTAGCACACGGGAGTATGTCAAGGGTATGTGTCCATA
* *
59359 CTATTTGGAGGCACACGGG
1 CTTTTTGAAGGCACACGGG
59378 AGTGTGTCCA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
55 4 0.06
56 61 0.94
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (56 bp):
CTTTTTGAAGGCACACGGGCTAGCACACGGGAGTATGTCAAGGGTATGTGTCCATA
Found at i:59397 original size:44 final size:44
Alignment explanation
Indices: 59325--59421 Score: 158
Period size: 44 Copynumber: 2.2 Consensus size: 44
59315 ACACGGGCTA
*
59325 GCACACGGGAGTATGTCCAGGGTATGTGTCCATACTATTTGGAG
1 GCACACGGGAGTATGTCCAAGGTATGTGTCCATACTATTTGGAG
* * *
59369 GCACACGGGAGTGTGTCCAAGGTGTGTGTCCATACTGTTTGGAG
1 GCACACGGGAGTATGTCCAAGGTATGTGTCCATACTATTTGGAG
59413 GCACACGGG
1 GCACACGGG
59422 CTGGCATACG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.25
Consensus pattern (44 bp):
GCACACGGGAGTATGTCCAAGGTATGTGTCCATACTATTTGGAG
Found at i:59453 original size:100 final size:97
Alignment explanation
Indices: 59269--59513 Score: 255
Period size: 100 Copynumber: 2.5 Consensus size: 97
59259 ACACGGGCTA
* * * * *
59269 GCACATGGGGGTGTGTCTAAGGGGTGTGTCTATACTTTTTGAAGGCACACGGGCTAGCACACGGG
1 GCACATGGGAGTGTGTCCAAGGTGTGTGTC-ATACTGTTTGGAGGCACACGGGCTAGCACACGGG
* *
59334 AGTATGTCCAGGGTATGTGTCCATACTATTTGGAG
65 AGCATGTCCAAGGTATGTGT--ATACTATTTGGAG
* * *
59369 GCACACGGGAGTGTGTCCAAGGTGTGTGTCCATACTGTTTGGAGGCACACGGGCTGGCATACGGG
1 GCACATGGGAGTGTGTCCAAGGTGTGTGT-CATACTGTTTGGAGGCACACGGGCTAGCACACGGG
* * *
59434 -GCATGTGTCAAGGTGTGTGTATACTGTTTGGAG
65 AGCATGT-CCAAGGTATGTGTATACTATTTGGAG
* * * * *
59467 GCACATGGGCGTGGGT-CAA-GTGTATGT-ATACTGTTTTGAGACACACG
1 GCACATGGGAGTGTGTCCAAGGTGTGTGTCATACTGTTTGGAGGCACACG
59514 AGCGTGTGTC
Statistics
Matches: 124, Mismatches: 19, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
94 18 0.15
96 7 0.06
97 3 0.02
98 25 0.20
99 5 0.04
100 65 0.52
101 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.35, T:0.27
Consensus pattern (97 bp):
GCACATGGGAGTGTGTCCAAGGTGTGTGTCATACTGTTTGGAGGCACACGGGCTAGCACACGGGA
GCATGTCCAAGGTATGTGTATACTATTTGGAG
Found at i:59553 original size:41 final size:40
Alignment explanation
Indices: 59437--59557 Score: 127
Period size: 40 Copynumber: 3.0 Consensus size: 40
59427 ATACGGGGCA
* * *
59437 TGTGTCAAGGTGTGTGTATACTGTTTGGAGGCACATGGGCG
1 TGTGTC-AGGTGTGTGTATACTGTTTAGAGGCACACGAGCG
* * * * *
59478 TGGGTCAAGTGTATGTATACTGTTTTGAGACACACGAGCG
1 TGTGTCAGGTGTGTGTATACTGTTTAGAGGCACACGAGCG
*
59518 TGTGTCAGGGTGTGTGTATACTATTCTAG-GGCACACGAGC
1 TGTGTCA-GGTGTGTGTATACTGTT-TAGAGGCACACGAGC
59558 TGACACATGG
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
40 34 0.52
41 29 0.45
42 2 0.03
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.31
Consensus pattern (40 bp):
TGTGTCAGGTGTGTGTATACTGTTTAGAGGCACACGAGCG
Found at i:60116 original size:40 final size:40
Alignment explanation
Indices: 60043--60121 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
60033 TTGAGTTGGC
* * *
60043 AGTGACACTATAAACACTGTAATATTAGAACTGAACTAGT
1 AGTGACACTATAAACACTGCAAGATTACAACTGAACTAGT
* * *
60083 AGTGACACTGTAAACACTGCAAGGTTACCACTGAACTAG
1 AGTGACACTATAAACACTGCAAGATTACAACTGAACTAG
60122 CAGTCTGTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (40 bp):
AGTGACACTATAAACACTGCAAGATTACAACTGAACTAGT
Found at i:61468 original size:20 final size:20
Alignment explanation
Indices: 61432--61473 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
61422 ATTTAAATAC
*
61432 TTTTTTTTTATAATTTT-TA
1 TTTTTTTTTACAATTTTGTA
*
61451 TTTTATTTTTACATTTTTGTA
1 TTTT-TTTTTACAATTTTGTA
61472 TT
1 TT
61474 AATATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 11 0.58
21 4 0.21
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTTTTTTACAATTTTGTA
Found at i:72331 original size:41 final size:40
Alignment explanation
Indices: 72259--72337 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 40
72249 CTTATTGTAT
72259 TTTTTAATTTGTTTGTTGTTTTACAAATTGTTTTAATATCG
1 TTTTTAATTTGTTTGTTGTTTTACAAATTG-TTTAATATCG
*
72300 TTTTTAATTTGTTTGTTGTTTTA-ATATTTGTTTAATAT
1 TTTTTAATTTGTTTGTTGTTTTACA-AATTGTTTAATAT
72338 TTTTAAGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 9 0.25
41 27 0.75
ACGTcount: A:0.22, C:0.03, G:0.11, T:0.65
Consensus pattern (40 bp):
TTTTTAATTTGTTTGTTGTTTTACAAATTGTTTAATATCG
Found at i:74681 original size:21 final size:20
Alignment explanation
Indices: 74637--74683 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
74627 ATAATTAAGT
*
74637 TTATTTTTTTAAATTAAGAG
1 TTATTTTTTTAAATTAAGAA
* *
74657 TTATTTTTTTAACTTCATGAA
1 TTATTTTTTTAAATT-AAGAA
74678 TTATTT
1 TTATTT
74684 ATTTCTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (20 bp):
TTATTTTTTTAAATTAAGAA
Found at i:77383 original size:19 final size:19
Alignment explanation
Indices: 77359--77401 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
77349 TACTAACCCG
77359 AGGAAACAATGAGTTATTT
1 AGGAAACAATGAGTTATTT
77378 AGGAAACAATGAGTTATTT
1 AGGAAACAATGAGTTATTT
77397 AGGAA
1 AGGAA
77402 TCACTTCTAA
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:0.44, C:0.05, G:0.23, T:0.28
Consensus pattern (19 bp):
AGGAAACAATGAGTTATTT
Found at i:79865 original size:28 final size:28
Alignment explanation
Indices: 79834--79904 Score: 133
Period size: 28 Copynumber: 2.5 Consensus size: 28
79824 TTCCTAAATC
*
79834 TTAAAAAAAAAACAACCTATTTGATCAA
1 TTAAAAGAAAAACAACCTATTTGATCAA
79862 TTAAAAGAAAAACAACCTATTTGATCAA
1 TTAAAAGAAAAACAACCTATTTGATCAA
79890 TTAAAAGAAAAACAA
1 TTAAAAGAAAAACAA
79905 TACATATGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.59, C:0.13, G:0.06, T:0.23
Consensus pattern (28 bp):
TTAAAAGAAAAACAACCTATTTGATCAA
Found at i:79919 original size:28 final size:28
Alignment explanation
Indices: 79834--79913 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
79824 TTCCTAAATC
* * *
79834 TTAAAAAAAAAACAACCTATTTGATCAA
1 TTAAAAGAAAAACAAACTATATGATCAA
* *
79862 TTAAAAGAAAAACAACCTATTTGATCAA
1 TTAAAAGAAAAACAAACTATATGATCAA
79890 TTAAAAGAAAAACAATAC-ATATGA
1 TTAAAAGAAAAACAA-ACTATATGA
79914 CTAATTTAGC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
28 47 0.98
29 1 0.02
ACGTcount: A:0.57, C:0.12, G:0.06, T:0.24
Consensus pattern (28 bp):
TTAAAAGAAAAACAAACTATATGATCAA
Found at i:92657 original size:39 final size:39
Alignment explanation
Indices: 92613--92689 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
92603 TTGATACATC
92613 TGTTCTAAAATCAAGAAATATAACTAAAAACTTCAACTG
1 TGTTCTAAAATCAAGAAATATAACTAAAAACTTCAACTG
92652 TGTTCTAAAATCAAGAAATATAACTAAAAACTTCAACT
1 TGTTCTAAAATCAAGAAATATAACTAAAAACTTCAACT
92690 AATCCCTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.49, C:0.16, G:0.06, T:0.29
Consensus pattern (39 bp):
TGTTCTAAAATCAAGAAATATAACTAAAAACTTCAACTG
Done.