Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015328.1 Kokia drynarioides strain JFW-HI SEQ_130374, 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: 430948
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 584 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:366253 original size:2 final size:2
Alignment explanation
Indices: 366246--366273 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
366236 CTAAGAAAAT
366246 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
366274 TTAAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:371078 original size:29 final size:28
Alignment explanation
Indices: 371051--371151 Score: 100
Period size: 30 Copynumber: 3.5 Consensus size: 28
371041 ATTTGGGGTT
371051 TAAAATGG-AATTTTAGACATTCGAGGG
1 TAAAATGGTAATTTTAGACATTCGAGGG
**
371078 TAAAATGGTAATTTTTGAGAGTTTCG-GGG
1 TAAAATGGTAA-TTTT-AGACATTCGAGGG
* *
371107 TCAAAAATGG-AGTTTTTGGACATTCGAGGG
1 T--AAAATGGTA-ATTTTAGACATTCGAGGG
371137 TAAAATGGTAATTTT
1 TAAAATGGTAATTTT
371152 TGAAAGTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
27 8 0.14
28 13 0.22
29 15 0.25
30 16 0.27
31 7 0.12
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.35
Consensus pattern (28 bp):
TAAAATGGTAATTTTAGACATTCGAGGG
Found at i:371142 original size:59 final size:60
Alignment explanation
Indices: 371022--371302 Score: 287
Period size: 59 Copynumber: 4.8 Consensus size: 60
371012 ACCTGGGGGC
* ** *
371022 AAAATGGTAA-TTTTGCAAA-ATTTGGGGTTTAAAATGGAA-TTTTAGACATTC-GAGGGT-
1 AAAATGGTAATTTTTG-AAAGTTTTGGGGTCAAAAATGGAATTTTTGGACATTCGGA-GGTA
* * *
371079 AAAATGGTAATTTTTGAGAGTTTCGGGGTCAAAAATGGAGTTTTTGGACATTC-GAGGGT-
1 AAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGACATTCGGA-GGTA
* ** *
371138 AAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAAATGGAATTTTTGGAGGTTTGGAGGTA
1 AAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGACATTCGGAGGTA
** * * *
371198 AAAAT-GTAATTTTTGAAAGTTTTACGGTCAAAAATGAAATTGTTGGA-AGTTCGGCGGTA
1 AAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGACA-TTCGGAGGTA
* *
371257 AAAAT-ATAATTTTTGAAAGTTTTGAGGTC-AAAATGGAATTTTTGGA
1 AAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGA
371303 AGTTTTAAGG
Statistics
Matches: 191, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
57 12 0.06
58 35 0.18
59 137 0.72
60 7 0.04
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (60 bp):
AAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGACATTCGGAGGTA
Found at i:371152 original size:29 final size:28
Alignment explanation
Indices: 371051--371153 Score: 111
Period size: 29 Copynumber: 3.6 Consensus size: 28
371041 ATTTGGGGTT
*
371051 TAAAATGGAA-TTTTAGACATTCGAGGG
1 TAAAATGGAATTTTTGGACATTCGAGGG
**
371078 TAAAATGGTAATTTTTGAGAGTTTCG-GGG
1 TAAAATGG-AATTTTTG-GACATTCGAGGG
*
371107 TCAAAAATGGAGTTTTTGGACATTCGAGGG
1 T--AAAATGGAATTTTTGGACATTCGAGGG
371137 TAAAATGGTAATTTTTG
1 TAAAATGG-AATTTTTG
371154 AAAGTTTTGG
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
27 8 0.13
28 9 0.15
29 21 0.34
30 17 0.27
31 7 0.11
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.35
Consensus pattern (28 bp):
TAAAATGGAATTTTTGGACATTCGAGGG
Found at i:371166 original size:29 final size:30
Alignment explanation
Indices: 371075--371337 Score: 174
Period size: 29 Copynumber: 8.9 Consensus size: 30
371065 AGACATTCGA
* *
371075 GGGT-AAAATGGTAATTTTTGAGAGTTTCG
1 GGGTAAAAATGGTAATTTTTGAAAGTTTTG
* * *
371104 GGGTCAAAAATGG-AGTTTTTGGACA--TTCG
1 GGGT-AAAAATGGTAATTTTT-GAAAGTTTTG
371133 AGGGT-AAAATGGTAATTTTTGAAAGTTTTG
1 -GGGTAAAAATGGTAATTTTTGAAAGTTTTG
* *
371163 GGGTTAAAAATGG-AATTTTTG-GAGGTTTG
1 GGG-TAAAAATGGTAATTTTTGAAAGTTTTG
*
371192 GAGGTAAAAAT-GTAATTTTTGAAAGTTTTA
1 G-GGTAAAAATGGTAATTTTTGAAAGTTTTG
* * * * *
371222 CGGTCAAAAAT-GAAATTGTTGGAAG-TTCG
1 GGGT-AAAAATGGTAATTTTTGAAAGTTTTG
*
371251 GCGGTAAAAAT-ATAATTTTTGAAAGTTTTG
1 G-GGTAAAAATGGTAATTTTTGAAAGTTTTG
* * * *
371281 AGGTCAAAATGG-AATTTTTGGAAGTTTTA
1 GGGTAAAAATGGTAATTTTTGAAAGTTTTG
* * *
371310 AGGAAAAAAT-GTAATTTTCGAACAGTTT
1 GGGTAAAAATGGTAATTTTTGAA-AGTTT
371338 AGGGACCTCC
Statistics
Matches: 185, Mismatches: 31, Indels: 35
0.74 0.12 0.14
Matches are distributed among these distances:
28 12 0.06
29 99 0.54
30 57 0.31
31 17 0.09
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (30 bp):
GGGTAAAAATGGTAATTTTTGAAAGTTTTG
Found at i:371337 original size:59 final size:58
Alignment explanation
Indices: 371079--371337 Score: 256
Period size: 59 Copynumber: 4.4 Consensus size: 58
371069 ATTCGAGGGT
* * * * *
371079 AAAATGGTAATTTTTGAGAGTTTCGGGGTCAAAAATGGAGTTTTTGGACA--TTCGAGGGT-
1 AAAAT-GTAATTTTTGAAAGTTTTGAGGTC-AAAATGGAATTTTTGGA-AGTTTGGA-GGTA
* * *
371138 AAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAAATGGAATTTTTGGAGGTTTGGAGGTA
1 AAAAT-GTAATTTTTGAAAGTTTTGAGG-TCAAAATGGAATTTTTGGAAGTTTGGAGGTA
* * * *
371198 AAAATGTAATTTTTGAAAGTTTT-ACGGTCAAAAATGAAATTGTTGGAAGTTCGGCGGTA
1 AAAATGTAATTTTTGAAAGTTTTGA-GGTC-AAAATGGAATTTTTGGAAGTTTGGAGGTA
* ** *
371257 AAAATATAATTTTTGAAAGTTTTGAGGTCAAAATGGAATTTTTGGAAGTTTTAAGGAA
1 AAAATGTAATTTTTGAAAGTTTTGAGGTCAAAATGGAATTTTTGGAAGTTTGGAGGTA
*
371315 AAAATGTAATTTTCGAACAGTTT
1 AAAATGTAATTTTTGAA-AGTTT
371338 AGGGACCTCC
Statistics
Matches: 169, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
58 38 0.22
59 120 0.71
60 11 0.07
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.36
Consensus pattern (58 bp):
AAAATGTAATTTTTGAAAGTTTTGAGGTCAAAATGGAATTTTTGGAAGTTTGGAGGTA
Found at i:373115 original size:18 final size:18
Alignment explanation
Indices: 373054--373117 Score: 85
Period size: 19 Copynumber: 3.6 Consensus size: 18
373044 ATTAAGTTTT
*
373054 AAATCAATTTAAATTT-A
1 AAATAAATTTAAATTTAA
**
373071 AAGCAAATTTAAATTTAA
1 AAATAAATTTAAATTTAA
373089 AAGATAAATTTAAATTTAA
1 AA-ATAAATTTAAATTTAA
373108 AAATAAATTT
1 AAATAAATTT
373118 GAATCAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
17 13 0.32
18 11 0.28
19 16 0.40
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
AAATAAATTTAAATTTAA
Found at i:373299 original size:21 final size:22
Alignment explanation
Indices: 373275--373328 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
373265 AAAAAATTGT
*
373275 ATAAAATTATTAA-ATATTAAA
1 ATAAAATTATAAAGATATTAAA
* *
373296 ATAAAATAATAAAGATATTTAA
1 ATAAAATTATAAAGATATTAAA
373318 A-AAAATT-TAAA
1 ATAAAATTATAAA
373329 TAATATGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 4 0.14
21 16 0.57
22 8 0.29
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
ATAAAATTATAAAGATATTAAA
Found at i:376929 original size:24 final size:23
Alignment explanation
Indices: 376870--376942 Score: 67
Period size: 26 Copynumber: 3.0 Consensus size: 23
376860 ATATAAACTT
* * *
376870 AAAAATTATAAGTATTATAAAAT
1 AAAATTTATAAGAATTATAAAAC
376893 ATATAATTTATAATGAATTATAAAAC
1 A-A-AATTTATAA-GAATTATAAAAC
*
376919 AAAATTTATAA-AATCAATAAAAC
1 AAAATTTATAAGAAT-TATAAAAC
376942 A
1 A
376943 TATTAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
22 3 0.07
23 9 0.21
24 10 0.24
25 9 0.21
26 11 0.26
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (23 bp):
AAAATTTATAAGAATTATAAAAC
Found at i:376978 original size:21 final size:21
Alignment explanation
Indices: 376954--376993 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
376944 ATTAAAAATA
* *
376954 TTTAATATTTTATAAAAAAGT
1 TTTAAGATTCTATAAAAAAGT
376975 TTTAAGATTCTATAAAAAA
1 TTTAAGATTCTATAAAAAA
376994 TCATAAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (21 bp):
TTTAAGATTCTATAAAAAAGT
Found at i:377016 original size:9 final size:9
Alignment explanation
Indices: 376989--377058 Score: 77
Period size: 9 Copynumber: 7.4 Consensus size: 9
376979 AGATTCTATA
*
376989 AAAAATCAT
1 AAAAATTAT
376998 AAACAATTAT
1 AAA-AATTAT
377008 AAAAATTAT
1 AAAAATTAT
377017 AAAAATTAT
1 AAAAATTAT
*
377026 TAAAATTAAT
1 AAAAATT-AT
* *
377036 ATAAACTTAC
1 A-AAAATTAT
377046 AAAAATTAT
1 AAAAATTAT
377055 AAAA
1 AAAA
377059 CATCCTAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
9 34 0.67
10 12 0.24
11 5 0.10
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:377068 original size:19 final size:19
Alignment explanation
Indices: 377007--377071 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 19
376997 TAAACAATTA
377007 TAAAAATTATAAAA-ATTA-
1 TAAAAATTATAAAACA-TAC
* *
377025 TTAAAATTAATATAAACTTAC
1 TAAAAATT-ATA-AAACATAC
*
377046 -AAAAATTATAAAACATCC
1 TAAAAATTATAAAACATAC
377064 TAAAAATT
1 TAAAAATT
377072 TGAAATGGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
18 13 0.35
19 13 0.35
20 11 0.30
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATTATAAAACATAC
Found at i:377468 original size:29 final size:29
Alignment explanation
Indices: 377427--377496 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
377417 TTTTACAATT
* * * *
377427 TTTTTTATTATTTTTAAGAATTCTAATATG
1 TTTTTTA-AATTTTAAAGAATTCAAATAAG
* *
377457 TTTTTTAAATTTTAAATATTTCAAATAAG
1 TTTTTTAAATTTTAAAGAATTCAAATAAG
377486 TTTTATTAAAT
1 TTTT-TTAAAT
377497 AAGTTTATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 20 0.61
30 13 0.39
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (29 bp):
TTTTTTAAATTTTAAAGAATTCAAATAAG
Found at i:377536 original size:19 final size:19
Alignment explanation
Indices: 377514--377558 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
377504 TATCATAGAA
* *
377514 ATAATAAAATCTTATAATC
1 ATAATAAAATCATAAAATC
*
377533 ATAAAAAAATCATAAAATC
1 ATAATAAAATCATAAAATC
377552 -TAATAAA
1 ATAATAAA
377559 TATAAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAATAAAATCATAAAATC
Found at i:377747 original size:8 final size:9
Alignment explanation
Indices: 377709--377746 Score: 51
Period size: 8 Copynumber: 4.1 Consensus size: 9
377699 AAGTTGTTAC
377709 AATTTTAAT
1 AATTTTAAT
377718 AATTTTATAT
1 AATTTTA-AT
377728 CAATTTTAAT
1 -AATTTTAAT
377738 -ATTTTAAT
1 AATTTTAAT
377746 A
1 A
377747 TATATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 8 0.31
9 7 0.27
10 4 0.15
11 7 0.27
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (9 bp):
AATTTTAAT
Found at i:385903 original size:37 final size:37
Alignment explanation
Indices: 385853--385930 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 37
385843 TTTTCCTAGG
*
385853 ATTTGTATCAATACTTTAGAGGACTGGTATCGTAACA
1 ATTTGTATCAATACTTCAGAGGACTGGTATCGTAACA
*
385890 ATTTGTATCAATACTTCAGAGGATTGGTATCGTAACA
1 ATTTGTATCAATACTTCAGAGGACTGGTATCGTAACA
385927 ATTT
1 ATTT
385931 TTCATTAGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (37 bp):
ATTTGTATCAATACTTCAGAGGACTGGTATCGTAACA
Found at i:386754 original size:27 final size:29
Alignment explanation
Indices: 386724--386778 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
386714 TATATTTATA
386724 TTGTTTT-TATAGAT-TATAAATTTTTAG
1 TTGTTTTATATAGATATATAAATTTTTAG
**
386751 TTGTTTTATATATTTATATAAATTTTTA
1 TTGTTTTATATAGATATATAAATTTTTA
386779 ATTTTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.29
28 5 0.21
29 12 0.50
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (29 bp):
TTGTTTTATATAGATATATAAATTTTTAG
Found at i:390948 original size:14 final size:14
Alignment explanation
Indices: 390890--390954 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
390880 GTCTTTTTTC
390890 AGAAAAAAAG-AGA
1 AGAAAAAAAGAAGA
**
390903 AGAAAGGAAGTAAGA
1 AGAAAAAAAG-AAGA
* * * *
390918 TGAAGAACAGAACA
1 AGAAAAAAAGAAGA
390932 AGAAAAAAAGAAGA
1 AGAAAAAAAGAAGA
390946 AGAAAAAAA
1 AGAAAAAAA
390955 CAAACCTTGG
Statistics
Matches: 38, Mismatches: 12, Indels: 3
0.72 0.23 0.06
Matches are distributed among these distances:
13 8 0.21
14 22 0.58
15 8 0.21
ACGTcount: A:0.71, C:0.03, G:0.23, T:0.03
Consensus pattern (14 bp):
AGAAAAAAAGAAGA
Found at i:392658 original size:30 final size:30
Alignment explanation
Indices: 392624--392680 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
392614 TTTAAAATTT
392624 TAAAAATCA-AGATTAAATTTATAGAATGTG
1 TAAAAATCATAG-TTAAATTTATAGAATGTG
* * *
392654 TAAAATTGATAGTTAAATTTATTGAAT
1 TAAAAATCATAGTTAAATTTATAGAAT
392681 TTTTTAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 21 0.91
31 2 0.09
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39
Consensus pattern (30 bp):
TAAAAATCATAGTTAAATTTATAGAATGTG
Found at i:393999 original size:23 final size:24
Alignment explanation
Indices: 393949--394005 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
393939 TTTAAATTTA
**
393949 TTAATGATCAAAATTAT-AAATTTTT
1 TTAAT-AT-AAAATTATAAAATAATT
*
393974 TTTATATAAAATTATAAAATAATT
1 TTAATATAAAATTATAAAATAATT
393998 TTAATATA
1 TTAATATA
394006 TTTTAATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 8 0.30
24 15 0.56
25 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
TTAATATAAAATTATAAAATAATT
Found at i:396491 original size:53 final size:52
Alignment explanation
Indices: 396411--396539 Score: 222
Period size: 53 Copynumber: 2.5 Consensus size: 52
396401 TTACAATTTC
* *
396411 TTTATATAATATAACGGCGTACAATTACGGGTAACTTCGCACTTGTGGTTTTT
1 TTTATGTAATATAATGGCGTACAATTACGGGTAACTTCGCACTTGTGG-TTTT
*
396464 TTTATGTAATATAATGGCGTACGATTACGGGTAACTTCGCACTTGTGGTTTT
1 TTTATGTAATATAATGGCGTACAATTACGGGTAACTTCGCACTTGTGGTTTT
396516 TTTATGTAATATAATGGCGTACAA
1 TTTATGTAATATAATGGCGTACAA
396540 ATTTTAGAAC
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
52 27 0.38
53 45 0.62
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (52 bp):
TTTATGTAATATAATGGCGTACAATTACGGGTAACTTCGCACTTGTGGTTTT
Found at i:398283 original size:13 final size:13
Alignment explanation
Indices: 398265--398301 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
398255 GATAGAGTTG
*
398265 AAAAATAAAATAA
1 AAAAATAAAAGAA
398278 AAAAATAAAAGAA
1 AAAAATAAAAGAA
398291 AGAAAATAAAA
1 A-AAAATAAAA
398302 CATTTGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (13 bp):
AAAAATAAAAGAA
Found at i:399994 original size:29 final size:30
Alignment explanation
Indices: 399921--399987 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
399911 AATGTTCAAT
* *
399921 GTTCAATATTGTACTTATACTTTCATAAAAT
1 GTTCAATATTGTACTTATACTTT-AGAAAAC
399952 GTTCAATATTGTACTTATACTTT-GAAAAC
1 GTTCAATATTGTACTTATACTTTAGAAAAC
399981 GTTCAAT
1 GTTCAAT
399988 GTGGTACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 11 0.32
31 23 0.68
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (30 bp):
GTTCAATATTGTACTTATACTTTAGAAAAC
Found at i:418267 original size:22 final size:21
Alignment explanation
Indices: 418218--418267 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 21
418208 TTAAAATTAA
*
418218 AAAAAAAATTATTTTATTTTC
1 AAAAAAAATTATATTATTTTC
418239 AATAAAAAATTAATATTATTTTTC
1 AA-AAAAAATT-ATATTA-TTTTC
418263 AAAAA
1 AAAAA
418268 CCAAACCCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 8 0.32
23 8 0.32
24 7 0.28
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAAAAAATTATATTATTTTC
Found at i:420234 original size:19 final size:20
Alignment explanation
Indices: 420196--420238 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
420186 AAAAATATAA
*
420196 ATTTTGAAATTTTTATAATT
1 ATTTTGAAATTTTTAAAATT
420216 ATTTTGAAA-TTTTAAAATT
1 ATTTTGAAATTTTTAAAATT
420235 ATTT
1 ATTT
420239 AGAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
ATTTTGAAATTTTTAAAATT
Found at i:420255 original size:29 final size:28
Alignment explanation
Indices: 420194--420257 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 28
420184 AAAAAAATAT
* *
420194 AAATTTTGAAATTTTTATAATTATTTTG
1 AAATTTTAAAATTTTTAGAATTATTTTG
420222 AAATTTTAAAATTATTTAGAATTATTTTG
1 AAATTTTAAAATT-TTTAGAATTATTTTG
*
420251 TAATTTT
1 AAATTTT
420258 TGTTGAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 12 0.38
29 20 0.62
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (28 bp):
AAATTTTAAAATTTTTAGAATTATTTTG
Found at i:423342 original size:23 final size:24
Alignment explanation
Indices: 423299--423343 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
423289 TAAAAATATA
*
423299 TTTTTATATTATTTTAATTTTAAT
1 TTTTTATATTATTTAAATTTTAAT
423323 TTTTTAT-TTA-TTAAACTTTTA
1 TTTTTATATTATTTAAA-TTTTA
423344 TGTATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTTATATTATTTAAATTTTAAT
Found at i:429165 original size:60 final size:60
Alignment explanation
Indices: 429101--429234 Score: 171
Period size: 60 Copynumber: 2.2 Consensus size: 60
429091 ACCTCAAGCT
* * * * * *
429101 ACATTTTAATCACTTATGTTTAAAAT-TATATGTTTTAGTTACTTACGTTATCATGTTGTA
1 ACATTTTAGTCACTTATATTTAAAATAT-TACGCTTCAGTTACTTACGTTATCACGTTGTA
* * *
429161 ACATTTTAGTTACTTGTATTTAAAATATTACGCTTCAGTTATTTACGTTATCACGTTGTA
1 ACATTTTAGTCACTTATATTTAAAATATTACGCTTCAGTTACTTACGTTATCACGTTGTA
429221 ACATTTTAGTCACT
1 ACATTTTAGTCACT
429235 GAACAATTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 62 0.98
61 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (60 bp):
ACATTTTAGTCACTTATATTTAAAATATTACGCTTCAGTTACTTACGTTATCACGTTGTA
Found at i:430534 original size:11 final size:11
Alignment explanation
Indices: 430518--430572 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
430508 GGGGATCAAC
* *
430518 GAAAAATGAAG
1 GAAAAAAGAAA
430529 GAAAAAAGAAA
1 GAAAAAAGAAA
430540 GAAAAAAG--A
1 GAAAAAAGAAA
430549 GAAAGAAAGAAA
1 GAAA-AAAGAAA
430561 GAAAGAAAGAAA
1 GAAA-AAAGAAA
430573 AAAGGAAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
9 5 0.13
10 4 0.10
11 17 0.44
12 13 0.33
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:430542 original size:4 final size:4
Alignment explanation
Indices: 430529--430582 Score: 67
Period size: 4 Copynumber: 13.8 Consensus size: 4
430519 AAAAATGAAG
*
430529 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAAA -AAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA
*
430576 GGAA GAA
1 GAAA GAA
430583 GGAGAAGAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
3 6 0.14
4 34 0.79
5 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
GAAA
Done.