Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015090.1 Kokia drynarioides strain JFW-HI SEQ_130134, 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: 762378
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 242 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:617239 original size:15 final size:15
Alignment explanation
Indices: 617219--617248 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
617209 GATTTGAATC
*
617219 AATTGATAGTTTGAG
1 AATTGATAGTCTGAG
617234 AATTGATAGTCTGAG
1 AATTGATAGTCTGAG
617249 GATTAAATGC
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:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (15 bp):
AATTGATAGTCTGAG
Found at i:634915 original size:20 final size:20
Alignment explanation
Indices: 634877--634916 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
634867 TTCATATGAA
*
634877 TGAATCATACAATTACAATT
1 TGAATCATACAATAACAATT
634897 TGAA-CATACAATAATCAATT
1 TGAATCATACAATAA-CAATT
634917 AAAGATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (20 bp):
TGAATCATACAATAACAATT
Found at i:645884 original size:13 final size:13
Alignment explanation
Indices: 645868--645915 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
645858 TTAAAAGTTT
*
645868 TTTTCAAAATCAC
1 TTTTCAAAAGCAC
645881 TTTTTC-AAAGCAC
1 -TTTTCAAAAGCAC
*
645894 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
*
645907 TTCTCAAAA
1 TTTTCAAAA
645916 ATAATACTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 4 0.14
13 20 0.69
14 5 0.17
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:645886 original size:14 final size:14
Alignment explanation
Indices: 645867--645908 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
645857 TTTAAAAGTT
*
645867 TTTTTCAAAATCAC
1 TTTTTCAAAAGCAC
645881 TTTTTC-AAAGCAC
1 TTTTTCAAAAGCAC
645894 TTTTT-AAAAGCAC
1 TTTTTCAAAAGCAC
645907 TT
1 TT
645909 CTCAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (14 bp):
TTTTTCAAAAGCAC
Found at i:646103 original size:15 final size:15
Alignment explanation
Indices: 646083--646130 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
646073 CTGGTCCCCA
646083 GGGACCTCCAGGCCC
1 GGGACCTCCAGGCCC
*
646098 GGGACC-CCA--ACC
1 GGGACCTCCAGGCCC
*
646110 AGGACCTCCAGGCCC
1 GGGACCTCCAGGCCC
646125 GGGACC
1 GGGACC
646131 CCAACCAGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
12 7 0.27
13 3 0.12
14 3 0.12
15 13 0.50
ACGTcount: A:0.19, C:0.46, G:0.31, T:0.04
Consensus pattern (15 bp):
GGGACCTCCAGGCCC
Found at i:646119 original size:27 final size:27
Alignment explanation
Indices: 646055--646148 Score: 131
Period size: 27 Copynumber: 3.6 Consensus size: 27
646045 CCAGGCCAAA
* * *
646055 AACCAGGACCTCCAAGCCCTGGTCCCC
1 AACCAGGACCTCCAGGCCCGGGACCCC
*
646082 -A--GGGACCTCCAGGCCCGGGACCCC
1 AACCAGGACCTCCAGGCCCGGGACCCC
646106 AACCAGGACCTCCAGGCCCGGGACCCC
1 AACCAGGACCTCCAGGCCCGGGACCCC
646133 AACCAGGACCTCCAGG
1 AACCAGGACCTCCAGG
646149 TCCAAATCCG
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
24 19 0.32
25 1 0.02
26 1 0.02
27 38 0.64
ACGTcount: A:0.22, C:0.46, G:0.26, T:0.06
Consensus pattern (27 bp):
AACCAGGACCTCCAGGCCCGGGACCCC
Found at i:646220 original size:30 final size:29
Alignment explanation
Indices: 646186--646256 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
646176 GGGACCCCAA
*
646186 CCACCAGGTCCTCCTC-CCCATCCTCCCGGT
1 CCACCAGGTCCTCC-CGCCC-TCCTCCCGGG
*
646216 CCACCAGGTCCTCCCGGCCCTCCTCCTGGG
1 CCACCAGGTCCTCCC-GCCCTCCTCCCGGG
646246 CCACCAGGTCC
1 CCACCAGGTCC
646257 CATTTTGCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 1 0.03
30 33 0.89
31 3 0.08
ACGTcount: A:0.10, C:0.55, G:0.18, T:0.17
Consensus pattern (29 bp):
CCACCAGGTCCTCCCGCCCTCCTCCCGGG
Found at i:649194 original size:14 final size:14
Alignment explanation
Indices: 649175--649203 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
649165 ATTATTTAAC
649175 AATTTCCATTGTTA
1 AATTTCCATTGTTA
649189 AATTTCCATTGTTA
1 AATTTCCATTGTTA
649203 A
1 A
649204 GGGATTAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (14 bp):
AATTTCCATTGTTA
Found at i:658104 original size:19 final size:19
Alignment explanation
Indices: 658061--658104 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
658051 TTATAAAACT
658061 TTAAAATTTATTTAAAAAA
1 TTAAAATTTATTTAAAAAA
* *
658080 -TAAAAATTATTTAAATATA
1 TTAAAATTTATTTAAA-AAA
658099 TTAAAA
1 TTAAAA
658105 AGTTGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 14 0.67
19 2 0.10
20 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTAAAATTTATTTAAAAAA
Found at i:658114 original size:48 final size:50
Alignment explanation
Indices: 657999--658114 Score: 134
Period size: 49 Copynumber: 2.4 Consensus size: 50
657989 TTTTTAAAAA
* * *
657999 ATATTAAAAAGTTGTAAAGTTTCTTTAAAAATATAAAAATTAGTACAGGT
1 ATATTAAAAAGTTGTAAAATTTATTTAAAAATATAAAAATTAGTACAGAT
* *
658049 AT-TTATAAAACTT-TAAAATTTATTTAAAAA-ATAAAAATTATTTA-A-AT
1 ATATTA-AAAAGTTGTAAAATTTATTTAAAAATATAAAAATTA-GTACAGAT
658096 ATATTAAAAAGTTGTAAAA
1 ATATTAAAAAGTTGTAAAA
658115 GAATTGTTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
47 9 0.16
48 19 0.34
49 20 0.36
50 8 0.14
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (50 bp):
ATATTAAAAAGTTGTAAAATTTATTTAAAAATATAAAAATTAGTACAGAT
Found at i:664255 original size:2 final size:2
Alignment explanation
Indices: 664248--664275 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
664238 GATAACAAAC
664248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
664276 GCCTGACTCA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:665413 original size:24 final size:22
Alignment explanation
Indices: 665369--665413 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
665359 ACTATTAAAA
*
665369 AATTAATAAATTTGATTAATTC
1 AATTAATAAATTTGATAAATTC
*
665391 AATTAATATTAATTTGGTAAATT
1 AATTAATA--AATTTGATAAATT
665414 AATCGTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (22 bp):
AATTAATAAATTTGATAAATTC
Found at i:668091 original size:17 final size:18
Alignment explanation
Indices: 668069--668103 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
668059 ATAGAGAAAC
668069 TCAACT-ACAAATAACTT
1 TCAACTGACAAATAACTT
*
668086 TCAACTGTCAAATAACTT
1 TCAACTGACAAATAACTT
668104 GCTCTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.23, G:0.03, T:0.31
Consensus pattern (18 bp):
TCAACTGACAAATAACTT
Found at i:676317 original size:24 final size:26
Alignment explanation
Indices: 676290--676338 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
676280 TATATATTTC
*
676290 TTTATTTAATATG-A-AATAAAATTA
1 TTTATTTAACATGTATAATAAAATTA
*
676314 TTTATTTTACATGTATAATAAAATT
1 TTTATTTAACATGTATAATAAAATT
676339 TCTTGAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 1 0.05
26 9 0.43
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (26 bp):
TTTATTTAACATGTATAATAAAATTA
Found at i:678619 original size:24 final size:24
Alignment explanation
Indices: 678582--678636 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
678572 TGGTCCCCAT
*
678582 CAATAT-TCATTTCAAAATTCATG
1 CAATATATAATTTCAAAATTCATG
678605 CAATATATAATTTCAAAATTCATG
1 CAATATATAATTTCAAAATTCATG
678629 CAATATAT
1 CAATATAT
678637 GGAGTGTCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 6 0.20
24 24 0.80
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (24 bp):
CAATATATAATTTCAAAATTCATG
Found at i:687679 original size:31 final size:29
Alignment explanation
Indices: 687644--687714 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
687634 AATCTCAAAA
*
687644 TTATACATGAACTTTAGTCTATTGTGTAATT
1 TTATACATGAACTTTAAT-T-TTGTGTAATT
* *
687675 TTATACGTGTACTTTAATTTTGTGTAATT
1 TTATACATGAACTTTAATTTTGTGTAATT
*
687704 TTGTACATGAA
1 TTATACATGAA
687715 AATTTGACTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 18 0.53
30 1 0.03
31 15 0.44
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.49
Consensus pattern (29 bp):
TTATACATGAACTTTAATTTTGTGTAATT
Found at i:687801 original size:2 final size:2
Alignment explanation
Indices: 687796--687831 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
687786 TTACAAACAC
687796 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
687832 TTNNNNNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:688528 original size:15 final size:15
Alignment explanation
Indices: 688508--688551 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
688498 TTTATTTTGT
688508 TTTTATTTTAAAACA
1 TTTTATTTTAAAACA
**
688523 TTTTATTTTTTAAAATT
1 TTTTA--TTTTAAAACA
688540 TTTTATTTTAAA
1 TTTTATTTTAAA
688552 TTATGTCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 12 0.48
17 13 0.52
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTATTTTAAAACA
Found at i:688535 original size:17 final size:17
Alignment explanation
Indices: 688513--688548 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
688503 TTTGTTTTTA
688513 TTTTAAAACATTTTATT
1 TTTTAAAACATTTTATT
**
688530 TTTTAAAATTTTTTATT
1 TTTTAAAACATTTTATT
688547 TT
1 TT
688549 AAATTATGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTAAAACATTTTATT
Found at i:688917 original size:6 final size:6
Alignment explanation
Indices: 688906--688932 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
688896 GAAAATTCTA
688906 AAAATT AAAATT AAAATT AAAATT AAA
1 AAAATT AAAATT AAAATT AAAATT AAA
688933 TTTGAAGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:700583 original size:49 final size:47
Alignment explanation
Indices: 700489--700583 Score: 118
Period size: 49 Copynumber: 2.0 Consensus size: 47
700479 AATCTATATG
** * * *
700489 AAAGAATAATCTGGGAAAAAAGTAATGGACTAACTAATTGCAACAAT
1 AAAGAATAATCTGAAAAAAAAGTAATGAAATAACTAATTACAACAAT
*
700536 AAAGAATAATCTGTAAAAATAAAGTAATGAAATAACTAATTATAACAA
1 AAAGAATAATCTG-AAAAA-AAAGTAATGAAATAACTAATTACAACAA
700584 CTACCATACA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
47 13 0.32
48 3 0.08
49 24 0.60
ACGTcount: A:0.56, C:0.08, G:0.13, T:0.23
Consensus pattern (47 bp):
AAAGAATAATCTGAAAAAAAAGTAATGAAATAACTAATTACAACAAT
Found at i:711809 original size:33 final size:34
Alignment explanation
Indices: 711738--711820 Score: 123
Period size: 33 Copynumber: 2.4 Consensus size: 34
711728 AAAGTCCAAG
*
711738 TAAACAACATTTGGGTAAGGTAAAAGATAAAAAAT
1 TAAA-AACATTTGGGTAAGATAAAAGATAAAAAAT
* *
711773 TAAAAATATTTGGGTAAGATAAAAGGT-AAAAAT
1 TAAAAACATTTGGGTAAGATAAAAGATAAAAAAT
711806 TAAAAACATTTGGGT
1 TAAAAACATTTGGGT
711821 TTAGTTTATG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 20 0.45
34 20 0.45
35 4 0.09
ACGTcount: A:0.52, C:0.04, G:0.18, T:0.27
Consensus pattern (34 bp):
TAAAAACATTTGGGTAAGATAAAAGATAAAAAAT
Found at i:711988 original size:18 final size:18
Alignment explanation
Indices: 711961--711995 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
711951 TATAGTTTTG
*
711961 TTTGATTTATTCCAATTA
1 TTTGAGTTATTCCAATTA
*
711979 TTTGAGTTATTCGAATT
1 TTTGAGTTATTCCAATT
711996 CGAAAATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTGAGTTATTCCAATTA
Found at i:733256 original size:1 final size:1
Alignment explanation
Indices: 733252--733281 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
733242 NNNNNNNNNN
733252 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
733282 GAAGAAGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:734454 original size:19 final size:19
Alignment explanation
Indices: 734421--734521 Score: 78
Period size: 19 Copynumber: 5.1 Consensus size: 19
734411 AAATTTTACT
* *
734421 AAAAATTATTAAAAATTAA
1 AAAAAATATAAAAAATTAA
*
734440 AAAAAATATATAAAAATCATA
1 AAAAAATATA-AAAAATTA-A
* **
734461 AAATAATATAAAAAAATTGT
1 AAAAAATAT-AAAAAATTAA
* *
734481 AAAAATTATAAAAATAGT-A
1 AAAAAATATAAAAA-ATTAA
734500 AAAAAATATAAAAAATATAA
1 AAAAAATATAAAAAAT-TAA
734520 AA
1 AA
734522 TTTTATAAAG
Statistics
Matches: 63, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
18 1 0.02
19 27 0.43
20 19 0.30
21 15 0.24
22 1 0.02
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAAATATAAAAAATTAA
Found at i:734515 original size:9 final size:9
Alignment explanation
Indices: 734420--734521 Score: 80
Period size: 10 Copynumber: 10.6 Consensus size: 9
734410 TAAATTTTAC
*
734420 TAAAAATTA
1 TAAAAAATA
*
734429 TTAAAAATTA
1 -TAAAAAATA
*
734439 AAAAAAATA
1 TAAAAAATA
734448 TATAAAAATCA
1 TA-AAAAAT-A
734459 TAAAATAATA
1 TAAAA-AATA
*
734469 TAAAAAAATTG
1 T-AAAAAA-TA
*
734480 TAAAAATTA
1 TAAAAAATA
734489 T-AAAAATA
1 TAAAAAATA
734497 GTAAAAAAATA
1 -T-AAAAAATA
734508 TAAAAAATA
1 TAAAAAATA
734517 TAAAA
1 TAAAA
734522 TTTTATAAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
8 6 0.08
9 24 0.31
10 28 0.36
11 19 0.25
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.26
Consensus pattern (9 bp):
TAAAAAATA
Found at i:734894 original size:16 final size:16
Alignment explanation
Indices: 734862--734902 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
734852 TTTTAAAGTT
734862 TTTATATTTTTATTAAC
1 TTTAT-TTTTTATTAAC
734879 ATTTATTTTTTA-TAAC
1 -TTTATTTTTTATTAAC
734895 TTT-TTTTT
1 TTTATTTTT
734903 CTAATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.22
15 3 0.13
16 4 0.17
17 6 0.26
18 5 0.22
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATTTTTTATTAAC
Found at i:735016 original size:87 final size:82
Alignment explanation
Indices: 734924--735124 Score: 199
Period size: 87 Copynumber: 2.4 Consensus size: 82
734914 TAAGAGCAAG
** *
734924 AGCTTAATTGCTTTTTTGAAAAATTTTGAGGGTATTTTTTTTATGCATTTTGAAAGTTCAAGTAC
1 AGCTTAATTGCTTTTTTGAAAAATTTTGAGGG-ACCTTTTTTATGCATTTTGAAAATTCAAGTAC
*
734989 CCAATTGAGTGAGAAAAAA
65 CCAATTGAGT-ACAAAAAA
** * * *
735008 ATGGGCTTAATTGCTTTTTTTTTTAAAAGTTCGA-GGACCTTTTTTATGCCTTTTGAAAATTCAA
1 A---GCTTAATTGC--TTTTTTGAAAAATTTTGAGGGACCTTTTTTATGCATTTTGAAAATTCAA
* * *
735072 GTGCTCAATTGAGTCCAAAAAA
61 GTACCCAATTGAGTACAAAAAA
735094 AG-TTCAATTGCTTTTTATGAAAAATTTTGAG
1 AGCTT-AATTGCTTTTT-TGAAAAATTTTGAG
735125 AGCTTTTTAC
Statistics
Matches: 93, Mismatches: 16, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
81 5 0.05
82 11 0.12
83 7 0.08
84 1 0.01
86 7 0.08
87 46 0.49
88 2 0.02
89 14 0.15
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (82 bp):
AGCTTAATTGCTTTTTTGAAAAATTTTGAGGGACCTTTTTTATGCATTTTGAAAATTCAAGTACC
CAATTGAGTACAAAAAA
Found at i:735836 original size:15 final size:16
Alignment explanation
Indices: 735818--735847 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
735808 TTAACGATTA
735818 AATCGT-TAAAATATT
1 AATCGTATAAAATATT
735833 AATCGTATAAAATAT
1 AATCGTATAAAATAT
735848 ATTTAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (16 bp):
AATCGTATAAAATATT
Found at i:736864 original size:19 final size:19
Alignment explanation
Indices: 736837--736884 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
736827 TAAACAGATA
*
736837 TATTAAAAATCATAATAAT
1 TATTAAAAATCATAAAAAT
*
736856 TATTTAAAATCATAAAAAT
1 TATTAAAAATCATAAAAAT
*
736875 TATAAAAAAT
1 TATTAAAAAT
736885 TTTGTTGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
TATTAAAAATCATAAAAAT
Found at i:737491 original size:3 final size:3
Alignment explanation
Indices: 737483--737522 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
737473 TGGAGCACAC
737483 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
737523 TTAAACCAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:741337 original size:31 final size:32
Alignment explanation
Indices: 741302--741361 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
741292 ATTACCTAAC
*
741302 TGGTCACTTAA-TTCTTAGGGTGTT-TTCATTT
1 TGGTCACCTAACTTC-TAGGGTGTTGTTCATTT
*
741333 TGGTCACCTAACTTCTAGGTTGTTGTTCA
1 TGGTCACCTAACTTCTAGGGTGTTGTTCA
741362 CTAAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.47
Consensus pattern (32 bp):
TGGTCACCTAACTTCTAGGGTGTTGTTCATTT
Found at i:751661 original size:19 final size:20
Alignment explanation
Indices: 751619--751661 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
751609 ATAAACAACA
*
751619 ATAATACATAGATATAAATT
1 ATAATACATAGATATAAATG
* *
751639 ATAATAGAT-GATATAGATG
1 ATAATACATAGATATAAATG
751658 ATAA
1 ATAA
751662 ATAAAAACAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (20 bp):
ATAATACATAGATATAAATG
Found at i:754924 original size:25 final size:25
Alignment explanation
Indices: 754895--754947 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
754885 ATAAAATTGT
754895 AATCAATAATTTAATTGTTTGGTTG
1 AATCAATAATTTAATTGTTTGGTTG
* *
754920 AATCAGTAATTTAATTGTTTTGTTG
1 AATCAATAATTTAATTGTTTGGTTG
754945 AAT
1 AAT
754948 GTAATGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.49
Consensus pattern (25 bp):
AATCAATAATTTAATTGTTTGGTTG
Found at i:755135 original size:12 final size:12
Alignment explanation
Indices: 755112--755184 Score: 55
Period size: 11 Copynumber: 6.0 Consensus size: 12
755102 ATTATTAAAT
755112 ATAATTTAATAA
1 ATAATTTAATAA
755124 A-AATTATAATAA
1 ATAATT-TAATAA
*
755136 ATAATTTAAT-C
1 ATAATTTAATAA
*
755147 ATATTTTAAT--
1 ATAATTTAATAA
755157 ATAATTATAATTAAA
1 ATAATT-TAA-T-AA
755172 TATAATTTAATAA
1 -ATAATTTAATAA
755185 CATTTAATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
10 5 0.10
11 16 0.32
12 13 0.26
13 6 0.12
14 1 0.02
15 3 0.06
16 6 0.12
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (12 bp):
ATAATTTAATAA
Found at i:755173 original size:16 final size:16
Alignment explanation
Indices: 755093--755199 Score: 64
Period size: 16 Copynumber: 7.0 Consensus size: 16
755083 CATCAAATAT
* *
755093 AATATGATTATTATTA
1 AATATAATTATAATTA
755109 AATATAATT-TAA-TA
1 AATATAATTATAATTA
* * * *
755123 AAAATTATAATAAAT-
1 AATATAATTATAATTA
* * * *
755138 AATTTAATCATATTTT
1 AATATAATTATAATTA
755154 AATATAATTATAATTA
1 AATATAATTATAATTA
755170 AATATAATT-TAA-TA
1 AATATAATTATAATTA
*
755184 ACATTTAA-TATAATTA
1 A-ATATAATTATAATTA
755200 TTTTTATATT
Statistics
Matches: 69, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
14 12 0.17
15 25 0.36
16 32 0.46
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (16 bp):
AATATAATTATAATTA
Found at i:755196 original size:36 final size:33
Alignment explanation
Indices: 755115--755200 Score: 100
Period size: 36 Copynumber: 2.5 Consensus size: 33
755105 ATTAAATATA
* * *
755115 ATTTAATAAAAATTATAATAAATAATTTAATCAT
1 ATTTAAT-ATAATTATAATAAATAATTTAATAAC
755149 ATTTTAATATAATTATAATTAAATATAATTTAATAAC
1 A-TTTAATATAATTATAA-T-AA-ATAATTTAATAAC
755186 ATTTAATATAATTAT
1 ATTTAATATAATTAT
755201 TTTTATATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 10 0.22
35 7 0.16
36 16 0.36
37 12 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (33 bp):
ATTTAATATAATTATAATAAATAATTTAATAAC
Found at i:762037 original size:4 final size:4
Alignment explanation
Indices: 762018--762073 Score: 52
Period size: 4 Copynumber: 15.5 Consensus size: 4
762008 AGGAAAAAAA
* *
762018 AAAG AAA- AAA- AGAG AAAG AAAG AAA- AAA- AGAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
762062 -AAG -AAG AAAG AA
1 AAAG AAAG AAAG AA
762074 GGAGAACAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 16 0.36
4 29 0.64
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:762041 original size:18 final size:18
Alignment explanation
Indices: 762018--762101 Score: 89
Period size: 18 Copynumber: 4.6 Consensus size: 18
762008 AGGAAAAAAA
762018 AAAGAAAAAAAGAGAAAG
1 AAAGAAAAAAAGAGAAAG
762036 AAAGAAAAAAAGAGAAAG
1 AAAGAAAAAAAGAGAAAG
*
762054 AAAG-AAAGAAGAAGAAAG
1 AAAGAAAAAAAG-AGAAAG
* * * * *
762072 AAGGAGAACAAGGGGAAG
1 AAAGAAAAAAAGAGAAAG
762090 AAGAGAAAAAAA
1 AA-AGAAAAAAA
762102 AAGGTAATGT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
17 6 0.11
18 37 0.69
19 11 0.20
ACGTcount: A:0.71, C:0.01, G:0.27, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAAGAGAAAG
Found at i:762068 original size:14 final size:14
Alignment explanation
Indices: 762020--762079 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
762010 GAAAAAAAAA
*
762020 AGAAAAAAAGAGAA-
1 AGAAAGAAAGA-AAG
*
762034 AGAAAGAAAAAAAG
1 AGAAAGAAAGAAAG
762048 AGAAAGAAAGAAAG
1 AGAAAGAAAGAAAG
*
762062 A-AGAAGAAAGAAGG
1 AGA-AAGAAAGAAAG
762076 AGAA
1 AGAA
762080 CAAGGGGAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
13 3 0.08
14 35 0.90
15 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAGAAAG
Done.