Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015193.1 Kokia drynarioides strain JFW-HI SEQ_130237, 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: 594178
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 490 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:482399 original size:57 final size:57
Alignment explanation
Indices: 482247--482401 Score: 163
Period size: 57 Copynumber: 2.7 Consensus size: 57
482237 TATATTATGA
* * *
482247 TTTTTATT-AATTCATATTTTAATAATAAT-TATATTAAGAATGTTATTAAATTATATACT
1 TTTTTATTAAATT-ATA-TTTAATAATAATCT-TATTAA-AATATGATTAAAATATATACT
* * * * * *
482306 ATTTTATTAAATTGTATTTAATAATAATC-AAGTTAAAATATGATTAAAATGTTTATT
1 TTTTTATTAAATTATATTTAATAATAATCTTA-TTAAAATATGATTAAAATATATACT
482363 TTTTTATTAAATTATATTTAATAATAATCTTATTAAAAT
1 TTTTTATTAAATTATATTTAATAATAATCTTATTAAAAT
482402 TTAACAACAC
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
57 50 0.62
58 17 0.21
59 9 0.11
60 4 0.05
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
TTTTTATTAAATTATATTTAATAATAATCTTATTAAAATATGATTAAAATATATACT
Found at i:482613 original size:16 final size:16
Alignment explanation
Indices: 482594--482635 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
482584 ATTATAGCTC
* *
482594 TATTACATTACAGTTT
1 TATTCCATTACAGATT
482610 TATTCCATTACAGATT
1 TATTCCATTACAGATT
482626 TATTCCATTA
1 TATTCCATTA
482636 TAGCGAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.48
Consensus pattern (16 bp):
TATTCCATTACAGATT
Found at i:486864 original size:14 final size:16
Alignment explanation
Indices: 486845--486879 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
486835 TACTCTGTTT
486845 TTGTTATTTG-TCA-A
1 TTGTTATTTGATCAGA
486859 TTGTTATTTGATCAGA
1 TTGTTATTTGATCAGA
486875 TTGTT
1 TTGTT
486880 GTTTAATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
15 3 0.16
16 6 0.32
ACGTcount: A:0.20, C:0.06, G:0.17, T:0.57
Consensus pattern (16 bp):
TTGTTATTTGATCAGA
Found at i:494413 original size:17 final size:16
Alignment explanation
Indices: 494378--494425 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
494368 AGATTTCAAG
*
494378 TTTATATTTTTGATTAA
1 TTTA-ATTTTTAATTAA
*
494395 TTTGATTTTTAATTAAA
1 TTTAATTTTTAATT-AA
*
494412 TTTAACTTTTAATT
1 TTTAATTTTTAATT
494426 TTTTAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (16 bp):
TTTAATTTTTAATTAA
Found at i:497107 original size:9 final size:9
Alignment explanation
Indices: 497093--497142 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
497083 AAGCTATTAC
497093 TAATTCGGT
1 TAATTCGGT
497102 TAATTCGGT
1 TAATTCGGT
*
497111 TAATTCAGT
1 TAATTCGGT
*
497120 TAATTCGAT
1 TAATTCGGT
*
497129 TAATTTGGT
1 TAATTCGGT
497138 TAATT
1 TAATT
497143 ATATTAAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (9 bp):
TAATTCGGT
Found at i:502715 original size:24 final size:24
Alignment explanation
Indices: 502687--502733 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
502677 TTAATTTTTA
502687 ATGTTTATATTTTTTATCAATTTG
1 ATGTTTATATTTTTTATCAATTTG
*
502711 ATGTTTATATTTTTTGTCAATTT
1 ATGTTTATATTTTTTATCAATTT
502734 AATTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.04, G:0.09, T:0.64
Consensus pattern (24 bp):
ATGTTTATATTTTTTATCAATTTG
Found at i:502926 original size:22 final size:22
Alignment explanation
Indices: 502901--502961 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
502891 TTATGCTGTT
502901 TTTTTTTTTTTTTTAATTATGA
1 TTTTTTTTTTTTTTAATTATGA
* * *
502923 TTTTTTATATTTTTAATTTTGA
1 TTTTTTTTTTTTTTAATTATGA
502945 TTTGATTTTTTTATTTT
1 TTT--TTTTTTT-TTTT
502962 TTATTTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 22 0.71
24 5 0.16
25 4 0.13
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (22 bp):
TTTTTTTTTTTTTTAATTATGA
Found at i:502969 original size:27 final size:27
Alignment explanation
Indices: 502899--502976 Score: 90
Period size: 27 Copynumber: 2.9 Consensus size: 27
502889 TTTTATGCTG
502899 TTTTT-TTTTTT-TTTTTAATTATGAT
1 TTTTTATTTTTTATTTTTAATTATGAT
* *
502924 TTTTTATATTTTTAATTTTGATT-TGATT
1 TTTTTAT-TTTTTATTTTTAATTATGA-T
502952 TTTTTATTTTTTATTTTTAAATTAT
1 TTTTTATTTTTTATTTTT-AATTAT
502977 TGAAATATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
25 5 0.12
26 1 0.02
27 18 0.42
28 18 0.42
29 1 0.02
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.76
Consensus pattern (27 bp):
TTTTTATTTTTTATTTTTAATTATGAT
Found at i:514999 original size:22 final size:22
Alignment explanation
Indices: 514974--515015 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
514964 TAATAATTTT
514974 ATTTGGAATT-TTGAATTAAAGA
1 ATTT-GAATTATTGAATTAAAGA
*
514996 ATTTTAATTATTGAATTAAA
1 ATTTGAATTATTGAATTAAA
515016 ATTTAGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (22 bp):
ATTTGAATTATTGAATTAAAGA
Found at i:524381 original size:24 final size:23
Alignment explanation
Indices: 524323--524381 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
524313 ATTAAAAAAG
* *
524323 AAATAATAAAGATTTTATATTAAT
1 AAAT-ATAAATATATTATATTAAT
*
524347 AAATATCAAATATATTATGTTAAT
1 AAATAT-AAATATATTATATTAAT
524371 AAATACTAAAT
1 AAATA-TAAAT
524382 CTTTTAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 2 0.07
24 27 0.90
25 1 0.03
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (23 bp):
AAATATAAATATATTATATTAAT
Found at i:529819 original size:29 final size:25
Alignment explanation
Indices: 529771--529832 Score: 63
Period size: 28 Copynumber: 2.4 Consensus size: 25
529761 ATCTATATCC
*
529771 ATAATAAAAAAAATTAAATTGTTTTT
1 ATAATAAAAAAAATTAAATT-ATTTT
*
529797 ATAATTAATAAAAAATTCGAATTATTTT
1 ATAA-TAA-AAAAAATT-AAATTATTTT
529825 ATAA-AAAA
1 ATAATAAAA
529833 CCCATTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
25 2 0.06
26 6 0.19
27 3 0.10
28 16 0.52
29 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (25 bp):
ATAATAAAAAAAATTAAATTATTTT
Found at i:534141 original size:6 final size:6
Alignment explanation
Indices: 534130--534160 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
534120 GCCCTAACAA
534130 CGCCAC CGCCAC CGCCAC CGCCAC CGCCAC C
1 CGCCAC CGCCAC CGCCAC CGCCAC CGCCAC C
534161 AATAACGCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.68, G:0.16, T:0.00
Consensus pattern (6 bp):
CGCCAC
Found at i:534169 original size:18 final size:18
Alignment explanation
Indices: 534125--534169 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
534115 TCAACGCCCT
534125 AACAACGCCACCGCCACC
1 AACAACGCCACCGCCACC
** *
534143 GCCACCGCCACCGCCACC
1 AACAACGCCACCGCCACC
*
534161 AATAACGCC
1 AACAACGCC
534170 GTCTATTAGT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.56, G:0.13, T:0.02
Consensus pattern (18 bp):
AACAACGCCACCGCCACC
Found at i:535785 original size:120 final size:120
Alignment explanation
Indices: 535542--535778 Score: 316
Period size: 120 Copynumber: 2.0 Consensus size: 120
535532 GATTTTTCCA
* * * ** *
535542 TGTGTTCCACGAACGGGTTAGTTCAAGTGAATTAAATGAGTCTCATCTAATTGATTAACCTCCAT
1 TGTGTTCCACGAACGAGTCAGTTAAAGTGAATTAAATGAACCCCATCTAATTGATTAACCTCCAT
* * * *
535607 AAGATACTCTTTGCGTGTCAAGGATTTTGATTTGCTACTCGTTACACTTACACTT
66 AAGATACTCTTTGCATGTCAAGAATTTTGATTCGCTACCCGTTACACTTACACTT
* * *
535662 TGTGTTCCACGAACGAGTCAGTTAAAGTGAGTTAAATGAACCCCAGT-TAATTGATTGACTTCCA
1 TGTGTTCCACGAACGAGTCAGTTAAAGTGAATTAAATGAACCCCA-TCTAATTGATTAACCTCCA
*
535726 TGAGATACTCTTTGCATGTCAAGAATTTTG-TTCCGCTACCCGTTACACTTACA
65 TAAGATACTCTTTGCATGTCAAGAATTTTGATT-CGCTACCCGTTACACTTACA
535779 TCTTGTGGTA
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
119 2 0.02
120 98 0.97
121 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (120 bp):
TGTGTTCCACGAACGAGTCAGTTAAAGTGAATTAAATGAACCCCATCTAATTGATTAACCTCCAT
AAGATACTCTTTGCATGTCAAGAATTTTGATTCGCTACCCGTTACACTTACACTT
Found at i:538546 original size:22 final size:22
Alignment explanation
Indices: 538506--538566 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
538496 CGATTTGAGG
*
538506 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
538527 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
538549 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
538567 GGAAGTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 11 0.31
22 24 0.67
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:538557 original size:15 final size:16
Alignment explanation
Indices: 538532--538561 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
538522 GAATTAAAAA
538532 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
538548 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
538562 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:541504 original size:21 final size:24
Alignment explanation
Indices: 541480--541534 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 24
541470 CCTGCAACTT
*
541480 CTACCGATACAAGCAT-C-C-TAA
1 CTACCGATACAAGCATACACAGAA
541501 CTACCGATACAAGCATACACAGAA
1 CTACCGATACAAGCATACACAGAA
541525 CTACCGATAC
1 CTACCGATAC
541535 CTACTATTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 16 0.53
22 1 0.03
23 1 0.03
24 12 0.40
ACGTcount: A:0.40, C:0.33, G:0.11, T:0.16
Consensus pattern (24 bp):
CTACCGATACAAGCATACACAGAA
Found at i:548225 original size:14 final size:13
Alignment explanation
Indices: 548199--548239 Score: 64
Period size: 14 Copynumber: 3.0 Consensus size: 13
548189 ATTTGTTTGC
548199 TTGAAAATGATTT
1 TTGAAAATGATTT
548212 TTGAAAATTGATTT
1 TTGAAAA-TGATTT
548226 TTGGAAAATGATTT
1 TT-GAAAATGATTT
548240 ACTTTTCTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.27
14 14 0.54
15 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (13 bp):
TTGAAAATGATTT
Found at i:548537 original size:17 final size:17
Alignment explanation
Indices: 548482--548547 Score: 82
Period size: 17 Copynumber: 3.8 Consensus size: 17
548472 CATCAAATTA
548482 AATATATAATAGTACTC
1 AATATATAATAGTACTC
*
548499 AAT-TATTGCAATAG-AATC
1 AATATA-T--AATAGTACTC
548517 AATATATAATAGTACTC
1 AATATATAATAGTACTC
548534 AATATATAATAGTA
1 AATATATAATAGTA
548548 TTTAATTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
16 7 0.17
17 21 0.50
18 7 0.17
19 7 0.17
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.35
Consensus pattern (17 bp):
AATATATAATAGTACTC
Found at i:551482 original size:22 final size:22
Alignment explanation
Indices: 551454--551496 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
551444 ATTTTAACAA
*
551454 TTTTTAATAATTTTATTTTTAG
1 TTTTTAATAATTTTAATTTTAG
*
551476 TTTTTAATATTTTTAATTTTA
1 TTTTTAATAATTTTAATTTTA
551497 TTTAACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTTAATAATTTTAATTTTAG
Found at i:559704 original size:20 final size:19
Alignment explanation
Indices: 559662--559706 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
559652 TTTTTTTTAT
*
559662 TAATTTAATATTTTAAAAA
1 TAATTTAAAATTTTAAAAA
559681 -AATTTAAAATTTTAAAAAA
1 TAATTTAAAATTTT-AAAAA
559700 TAATTTA
1 TAATTTA
559707 TCGAGCCGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 12 0.52
19 5 0.22
20 6 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATTTAAAATTTTAAAAA
Found at i:564833 original size:17 final size:17
Alignment explanation
Indices: 564811--564844 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
564801 GTAACAACCC
564811 GATTATAGTTTAATTAA
1 GATTATAGTTTAATTAA
564828 GATTATAGTTTAATTAA
1 GATTATAGTTTAATTAA
564845 TCAACATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
GATTATAGTTTAATTAA
Found at i:566555 original size:30 final size:30
Alignment explanation
Indices: 566490--566555 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 30
566480 TATAAAATAT
* * *
566490 TTAATTTATTTTTAATAAAATTTTATGATTT
1 TTAATTTATTTCTAAT-AAATTTTATGAATG
*
566521 TTAATTTATTTCTAAT-CATTATTATGAATG
1 TTAATTTATTTCTAATAAATT-TTATGAATG
566551 TTAAT
1 TTAAT
566556 GATCTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 3 0.10
30 12 0.40
31 15 0.50
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.58
Consensus pattern (30 bp):
TTAATTTATTTCTAATAAATTTTATGAATG
Found at i:568105 original size:35 final size:35
Alignment explanation
Indices: 568066--568132 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
568056 TTTACCACCC
* *
568066 AATTATAAAAAATTATAAAATAATCATTTTACACT
1 AATTATAAAAAATTACAAAATAATCATCTTACACT
*
568101 AATTATAAAAAATTACAAAATGATCATCTTAC
1 AATTATAAAAAATTACAAAATAATCATCTTAC
568133 TATTTAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (35 bp):
AATTATAAAAAATTACAAAATAATCATCTTACACT
Found at i:568949 original size:30 final size:28
Alignment explanation
Indices: 568904--568969 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 28
568894 TTGTTTTAGA
*
568904 AATTTTTT-A-ATTTTTAACTTTTTTAT
1 AATTTTTTAATATTTTTAAATTTTTTAT
568930 ATATTCTTTTAATATTTTTAAATTTTTTAT
1 A-ATT-TTTTAATATTTTTAAATTTTTTAT
568960 AATTTTTTAA
1 AATTTTTTAA
568970 AATAATATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
26 1 0.03
27 3 0.09
28 10 0.29
29 4 0.11
30 17 0.49
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (28 bp):
AATTTTTTAATATTTTTAAATTTTTTAT
Found at i:568968 original size:10 final size:10
Alignment explanation
Indices: 568906--568968 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
568896 GTTTTAGAAA
568906 TTTTT-TAA-
1 TTTTTATAAT
*
568914 TTTTTA-ACT
1 TTTTTATAAT
568923 TTTTTATATAT
1 TTTTTATA-AT
*
568934 TCTTT-TAAT
1 TTTTTATAAT
568943 ATTTTTA-AAT
1 -TTTTTATAAT
568953 TTTTTATAAT
1 TTTTTATAAT
568963 TTTTTA
1 TTTTTA
568969 AAATAATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
8 6 0.14
9 14 0.32
10 19 0.43
11 5 0.11
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:568996 original size:18 final size:17
Alignment explanation
Indices: 568975--569018 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
568965 TTTAAAATAA
568975 TATAAATTTTAGAACTTT
1 TATAAATTTTAGAA-TTT
*
568993 TATAAATATTTTGAATTT
1 TATAAAT-TTTAGAATTT
*
569011 TAAAAATT
1 TATAAATT
569019 ATTTTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
19 6 0.26
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (17 bp):
TATAAATTTTAGAATTT
Found at i:569030 original size:19 final size:18
Alignment explanation
Indices: 568980--569029 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
568970 AATAATATAA
*
568980 ATTTTAGAACTTTTATAAAT
1 ATTTT-GAA-TTTTAAAAAT
569000 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAA-T
569019 ATTTT-AATTTT
1 ATTTTGAATTTT
569030 TTTGTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 14 0.50
19 9 0.32
20 5 0.18
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (18 bp):
ATTTTGAATTTTAAAAAT
Found at i:577261 original size:31 final size:32
Alignment explanation
Indices: 577220--577287 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
577210 TATTATTCAA
* *
577220 ATATTTAAAATTATA-AAAAATTACTAAA-AAT
1 ATATTGAAAATAATATAAAAATT-CTAAATAAT
* *
577251 ATATTGAAAATAATATAACAATTCTAAATTAT
1 ATATTGAAAATAATATAAAAATTCTAAATAAT
577283 ATATT
1 ATATT
577288 TTTAAAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (32 bp):
ATATTGAAAATAATATAAAAATTCTAAATAAT
Found at i:578353 original size:24 final size:25
Alignment explanation
Indices: 578323--578370 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
578313 AAACTTGATA
578323 TTTTTTA-TTAATTTAATATTTAAT
1 TTTTTTATTTAATTTAATATTTAAT
* *
578347 TTTTTTATTTAGTTTGATATTTAA
1 TTTTTTATTTAATTTAATATTTAA
578371 ATTTAATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTTTTATTTAATTTAATATTTAAT
Found at i:580578 original size:102 final size:102
Alignment explanation
Indices: 580468--580661 Score: 264
Period size: 102 Copynumber: 1.9 Consensus size: 102
580458 AGCTTATTCT
* * * *
580468 TTTTTTAATCACTGGTCTAATGTGACAAATTTGAG-TGCTCCTATAATTAGTGCATGTTGCAGAT
1 TTTTTTAATCACTGGTCTAATGTGACAAATTTGAGTTGCCCCTATAATCAGTACA-GATGCAGAT
*
580532 CAAGATTATGAAGTTGCAAGGAAATGAAAGGATTGTTC
65 CAAGATTATAAAGTTGCAAGGAAATGAAAGGATTGTTC
* ** * *
580570 TTTTTTAATCACTGGTTTGTTGTGGCAAATTTGAGTTGCCCCTATAATCATTACAGATGCAGATC
1 TTTTTTAATCACTGGTCTAATGTGACAAATTTGAGTTGCCCCTATAATCAGTACAGATGCAGATC
* *
580635 AAGATTTTAAAGTTGCAAGGAGATGAA
66 AAGATTATAAAGTTGCAAGGAAATGAA
580662 TGAACTGCTC
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
102 64 0.81
103 15 0.19
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (102 bp):
TTTTTTAATCACTGGTCTAATGTGACAAATTTGAGTTGCCCCTATAATCAGTACAGATGCAGATC
AAGATTATAAAGTTGCAAGGAAATGAAAGGATTGTTC
Found at i:580954 original size:88 final size:88
Alignment explanation
Indices: 580805--580973 Score: 239
Period size: 88 Copynumber: 1.9 Consensus size: 88
580795 TATTCGATGC
* * * * *
580805 TAAGTCGTTATGTCCGTTGCTTTCGTCATTCTAAGCTCAAACAAACCAGGGCGTAACTATAGATG
1 TAAGTCATTATGTCCGTTGCTTTCGTCATTCCAAGCTCAAACAAACAAGGACATAACTATAGATG
*
580870 GAAACATGGCGGATATGATTTGT
66 GAAACATGGCAGATATGATTTGT
* * * * *
580893 TAAGTCATTATGTCTGTTGTTTTCGTCATTCCGAGCTCAAAGAAACAAGGACATAACTATAGCTG
1 TAAGTCATTATGTCCGTTGCTTTCGTCATTCCAAGCTCAAACAAACAAGGACATAACTATAGATG
580958 GAAACATGGCAGATAT
66 GAAACATGGCAGATAT
580974 AATTCTTGTT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
88 70 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (88 bp):
TAAGTCATTATGTCCGTTGCTTTCGTCATTCCAAGCTCAAACAAACAAGGACATAACTATAGATG
GAAACATGGCAGATATGATTTGT
Found at i:588674 original size:30 final size:30
Alignment explanation
Indices: 588604--588911 Score: 275
Period size: 30 Copynumber: 10.4 Consensus size: 30
588594 CAAACTTCTA
* *
588604 AAAAATTACA-TTTT-ACCCCCAAATTTTCC
1 AAAAATTACATTTTTGA-CCCTAAACTTTCC
* *
588633 -AAAATTCCATTTTTGACCCTAGACTTTCC
1 AAAAATTACATTTTTGACCCTAAACTTTCC
588662 AAAAATTACATTTTT-ACACCTAAACTTTCC
1 AAAAATTACATTTTTGAC-CCTAAACTTTCC
*
588692 AAAAATTCCATTTTTGACCCTAAACTTTCC
1 AAAAATTACATTTTTGACCCTAAACTTTCC
*
588722 -AAAATTACATTTTT-ACATCC-AAACTTT-T
1 AAAAATTACATTTTTGAC--CCTAAACTTTCC
* * * *
588750 TAAAATTTCATTTTTGGCCCCAAACTTTCC
1 AAAAATTACATTTTTGACCCTAAACTTTCC
588780 AAAAATTACATTTTT-ACCCTTAAACTTTCC
1 AAAAATTACATTTTTGACCC-TAAACTTTCC
* * *
588810 -AAAATTCCATTTTTGACCTTAAAGTTTCC
1 AAAAATTACATTTTTGACCCTAAACTTTCC
* *
588839 AAAAAATTACATTTTT-ATCCC-AGA-TGTCC
1 -AAAAATTACATTTTTGA-CCCTAAACTTTCC
* * *
588868 CAAAATTACATTTTTGACCTCGAAA-TTTTC
1 AAAAATTACATTTTTGACC-CTAAACTTTCC
588898 AAAAATTACTATTT
1 AAAAATTAC-ATTT
588912 CACCCTTGGA
Statistics
Matches: 231, Mismatches: 28, Indels: 38
0.78 0.09 0.13
Matches are distributed among these distances:
28 28 0.12
29 87 0.38
30 95 0.41
31 21 0.09
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.39
Consensus pattern (30 bp):
AAAAATTACATTTTTGACCCTAAACTTTCC
Found at i:588695 original size:59 final size:59
Alignment explanation
Indices: 588604--588911 Score: 344
Period size: 59 Copynumber: 5.2 Consensus size: 59
588594 CAAACTTCTA
* * * *
588604 AAAAATTACA-TTTTACCCCCAAATTTTCCAAAATTCCATTTTTGACCCTAGACTTTCC
1 AAAAATTACATTTTTACACCTAAACTTTCCAAAATTCCATTTTTGACCCTAAACTTTCC
588662 AAAAATTACATTTTTACACCTAAACTTTCCAAAAATTCCATTTTTGACCCTAAACTTTCC
1 AAAAATTACATTTTTACACCTAAACTTTCC-AAAATTCCATTTTTGACCCTAAACTTTCC
** * * *
588722 -AAAATTACATTTTTACATCC-AAACTTTTTAAAATTTCATTTTTGGCCCCAAACTTTCC
1 AAAAATTACATTTTTACA-CCTAAACTTTCCAAAATTCCATTTTTGACCCTAAACTTTCC
* *
588780 AAAAATTACATTTTTAC-CCTTAAACTTTCCAAAATTCCATTTTTGACCTTAAAGTTTCC
1 AAAAATTACATTTTTACACC-TAAACTTTCCAAAATTCCATTTTTGACCCTAAACTTTCC
* * * * *
588839 AAAAAATTACATTTTTATC-CC-AGA-TGTCCCAAAATTACATTTTTGACCTCGAAA-TTTTC
1 -AAAAATTACATTTTTA-CACCTAAACT-TTCCAAAATTCCATTTTTGACC-CTAAACTTTCC
588898 AAAAATTACTATTT
1 AAAAATTAC-ATTT
588912 CACCCTTGGA
Statistics
Matches: 217, Mismatches: 22, Indels: 21
0.83 0.08 0.08
Matches are distributed among these distances:
57 2 0.01
58 46 0.21
59 117 0.54
60 49 0.23
61 3 0.01
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.39
Consensus pattern (59 bp):
AAAAATTACATTTTTACACCTAAACTTTCCAAAATTCCATTTTTGACCCTAAACTTTCC
Found at i:588873 original size:118 final size:117
Alignment explanation
Indices: 588580--588946 Score: 374
Period size: 118 Copynumber: 3.1 Consensus size: 117
588570 TATCTAAAAA
** * *
588580 CCATATTTTGACCACAAAC-TTCTAAAAAATTACA-TTTTACCCCCAAATTTTCCAAAATTCCAT
1 CCAT-TTTTGACCTTAAACTTTCCAAAAAATTACATTTTTA--CCCAAA-TTTCCAAAATTACAT
* *
588643 TTTTGACCCTAGACTTTCCAAAAATTACATTTTTACACC-TAAACTTTCCAAAAATT
62 TTTTGACCCCAAACTTTCCAAAAATTACATTTTTAC-CCTTAAACTTTCCAAAAATT
* ** *
588699 CCATTTTTGACCCTAAACTTTCC--AAAATTACATTTTTACATCCAAACTTTTTAAAATTTCATT
1 CCATTTTTGACCTTAAACTTTCCAAAAAATTACATTTTTAC--CCAAA-TTTCCAAAATTACATT
*
588762 TTTGGCCCCAAACTTTCCAAAAATTACATTTTTACCCTTAAACTTTCC-AAAATT
63 TTTGACCCCAAACTTTCCAAAAATTACATTTTTACCCTTAAACTTTCCAAAAATT
* * *
588816 CCATTTTTGACCTTAAAGTTTCCAAAAAATTACATTTTTATCCCAGATGTCCCAAAATTACATTT
1 CCATTTTTGACCTTAAACTTTCCAAAAAATTACATTTTTA-CCCAAAT-TTCCAAAATTACATTT
* * * ** *
588881 TTGACCTCGAAA-TTTTCAAAAATTAC-TATTTCACCCTTGGA-TGTCCAAAAATT
64 TTGACC-CCAAACTTTCCAAAAATTACAT-TTTTACCCTTAAACTTTCCAAAAATT
*
588934 CTATTTTTGACCT
1 CCATTTTTGACCT
588947 CGAACCTCTA
Statistics
Matches: 211, Mismatches: 25, Indels: 25
0.81 0.10 0.10
Matches are distributed among these distances:
116 1 0.00
117 44 0.21
118 139 0.66
119 26 0.12
120 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.38
Consensus pattern (117 bp):
CCATTTTTGACCTTAAACTTTCCAAAAAATTACATTTTTACCCAAATTTCCAAAATTACATTTTT
GACCCCAAACTTTCCAAAAATTACATTTTTACCCTTAAACTTTCCAAAAATT
Found at i:588901 original size:88 final size:86
Alignment explanation
Indices: 588604--588882 Score: 296
Period size: 88 Copynumber: 3.2 Consensus size: 86
588594 CAAACTTCTA
* * * *
588604 AAAAATTACA-TTTTACCCCCAAATTTTCCAAAATTCCATTTTTGACCCTAGACTTTCCAAAAAT
1 AAAAATTACATTTTTA-CCCTAAACTTTCCAAAATTCCATTTTTGACCTTAAACTTTCCAAAAAT
588668 TACATTTTTACACCTAAACTTTCC
65 TACATTTTTAC-CC-AAACTTTCC
* * * * **
588692 AAAAATTCCATTTTTGACCCTAAACTTTCCAAAATTACATTTTT-ACATCCAAACTTT-TTAAAA
1 AAAAATTACATTTTT-ACCCTAAACTTTCCAAAATTCCATTTTTGACCT-TAAACTTTCCAAAAA
* *
588755 TTTCATTTTTGGCCCCAAACTTTCC
64 TTACATTTTT--ACCCAAACTTTCC
*
588780 AAAAATTACATTTTTACCCTTAAACTTTCCAAAATTCCATTTTTGACCTTAAAGTTTCCAAAAAA
1 AAAAATTACATTTTTACCC-TAAACTTTCCAAAATTCCATTTTTGACCTTAAACTTTCC-AAAAA
* *
588845 TTACATTTTTATCCCAGA-TGTCC
64 TTACATTTTTA-CCCAAACTTTCC
*
588868 CAAAATTACATTTTT
1 AAAAATTACATTTTT
588883 GACCTCGAAA
Statistics
Matches: 157, Mismatches: 24, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
87 4 0.03
88 94 0.60
89 44 0.28
90 15 0.10
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (86 bp):
AAAAATTACATTTTTACCCTAAACTTTCCAAAATTCCATTTTTGACCTTAAACTTTCCAAAAATT
ACATTTTTACCCAAACTTTCC
Found at i:588990 original size:58 final size:59
Alignment explanation
Indices: 588862--588993 Score: 153
Period size: 59 Copynumber: 2.3 Consensus size: 59
588852 TTTATCCCAG
* * * *
588862 ATGTCCCAAAATTACATTTTTGACCTCGAAATTTTCAAAAATTACTATTTCACCCTTGG
1 ATGTCCAAAAATTACATTTTTGACCTCGAAACTCTCAAAAATTACTATTTCACCCTTGA
* **
588921 ATGTCCAAAAATT-CTATTTTTGACCTCGAACCTCT-AAAAATTACTATTTTGCCCTTGA
1 ATGTCCAAAAATTAC-ATTTTTGACCTCGAAACTCTCAAAAATTACTATTTCACCCTTGA
*
588979 AGTGT-CGAAAATTAC
1 A-TGTCCAAAAATTAC
588994 CGTTTTACCC
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
58 29 0.47
59 33 0.53
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (59 bp):
ATGTCCAAAAATTACATTTTTGACCTCGAAACTCTCAAAAATTACTATTTCACCCTTGA
Found at i:591885 original size:23 final size:23
Alignment explanation
Indices: 591844--591887 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
591834 TGTAAAAAAT
* * *
591844 TAAAAGTATATATTTAAAATTAA
1 TAAAAGTAAACATTCAAAATTAA
591867 TAAAAGTAAACATTCAAAATT
1 TAAAAGTAAACATTCAAAATT
591888 TTAACGTGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.34
Consensus pattern (23 bp):
TAAAAGTAAACATTCAAAATTAA
Done.