Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003526.1 Kokia drynarioides strain JFW-HI SEQ_116369, 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: 84075
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1663 original size:21 final size:21
Alignment explanation
Indices: 1639--1680 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1629 TTTAGGTACA
*
1639 AAGGTGATATTTTTATACTTG
1 AAGGTGATATCTTTATACTTG
1660 AAGGTGATATCTTTATACTTG
1 AAGGTGATATCTTTATACTTG
1681 GGGAGTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.45
Consensus pattern (21 bp):
AAGGTGATATCTTTATACTTG
Found at i:5986 original size:2 final size:2
Alignment explanation
Indices: 5979--6006 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5969 ATTACTTTTA
5979 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
6007 TTAACATGAT
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:8607 original size:21 final size:21
Alignment explanation
Indices: 8558--8600 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
8548 GAATGAGTGT
*
8558 TTTGAA-TAAATTTTAAAGAC
1 TTTGAATTTAATTTTAAAGAC
*
8578 TTTGAATTTAATTTTTAAGAC
1 TTTGAATTTAATTTTAAAGAC
8599 TT
1 TT
8601 GTAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (21 bp):
TTTGAATTTAATTTTAAAGAC
Found at i:11533 original size:3 final size:3
Alignment explanation
Indices: 11502--11561 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
11492 TCACTACAAA
* * * *
11502 TTC TTC TTA TTT TTC CTC TTC TCC TTC TTC TTC TCTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TTC TTC
*
11547 TTC CTC TTC TTC TTC
1 TTC TTC TTC TTC TTC
11562 AACACCCACA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:14983 original size:51 final size:50
Alignment explanation
Indices: 14906--15092 Score: 169
Period size: 51 Copynumber: 3.6 Consensus size: 50
14896 GCTATAAACG
* *
14906 AAAGGATCCGATGACTAAGTGCCATCATGAGTAAATGAATCCTTTACGGATT
1 AAAGG-TCTGATGACTAA-TGTCATCATGAGTAAATGAATCCTTTACGGATT
* * * * *
14958 AAAGGTCTGATGACTAAGTGTCATCATGAGTAAATAAATCCATGATGCATT
1 AAAGGTCTGATGACTAA-TGTCATCATGAGTAAATGAATCCTTTACGGATT
* * * * * **
15009 AAAGGTCTGATGACTCAATGTTATCGTGAGTATATGAGTTCCTATACGGAAC
1 AAAGGTCTGATGACT-AATGTCATCATGAGTAAATGA-ATCCTTTACGGATT
*
15061 AAGAGGTCTGA-GACTATATGTCATCGTGAGTA
1 AA-AGGTCTGATGACTA-ATGTCATCATGAGTA
15093 TAAAATGAAA
Statistics
Matches: 111, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
51 70 0.63
52 33 0.30
53 8 0.07
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (50 bp):
AAAGGTCTGATGACTAATGTCATCATGAGTAAATGAATCCTTTACGGATT
Found at i:15181 original size:60 final size:61
Alignment explanation
Indices: 15042--15217 Score: 241
Period size: 61 Copynumber: 2.9 Consensus size: 61
15032 TCGTGAGTAT
*
15042 ATGAGTTCCTATACGGAACAAGAGGTCTGA-GACTATATGTCATCGTGAGTATAAAATGAA
1 ATGAGTTCCTATACGGAACAAGAGGTCTAATGACTATATGTCATCGTGAGTATAAAATGAA
* * *
15102 ATGAGTTCTTATACGGAACAAGAGGTCCAATGACTATATGTCATCGTGAGTATCAAATGAA
1 ATGAGTTCCTATACGGAACAAGAGGTCTAATGACTATATGTCATCGTGAGTATAAAATGAA
* * * * *
15163 ATGAGTTCCAATGC-GAACAAG-GGTCTAATGACTTTGTGTTATCGTGAGTAATAAA
1 ATGAGTTCCTATACGGAACAAGAGGTCTAATGACTATATGTCATCGTGAGT-ATAAA
15218 TGTGAGTGAA
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
59 24 0.24
60 38 0.37
61 40 0.39
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (61 bp):
ATGAGTTCCTATACGGAACAAGAGGTCTAATGACTATATGTCATCGTGAGTATAAAATGAA
Found at i:22163 original size:51 final size:50
Alignment explanation
Indices: 22087--22265 Score: 205
Period size: 51 Copynumber: 3.5 Consensus size: 50
22077 GAAAAGATCT
* *
22087 GATGACTAAGTGCCATTGTGAGTAAATGAATCCTTTACGGATTAAAGGTCC
1 GATGACTAA-TGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCC
* * **
22138 GATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATAGATTAAAGGTCC
1 GATGACTAA-TGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCC
* * * **
22189 GATGACTCAATGTCATCGTGAGTATATGAGTTCCTATACGGAACAAGAGGTCC
1 GATGACT-AATGTCATCGTGAGTAAATGA-ATCCTTTACGGATTAA-AGGTCC
22242 GATGACTATATGTCATCGTGAGTA
1 GATGACTA-ATGTCATCGTGAGTA
22266 TTAAATGAAA
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
51 70 0.64
52 11 0.10
53 28 0.26
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (50 bp):
GATGACTAATGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCC
Found at i:22315 original size:61 final size:60
Alignment explanation
Indices: 22214--22392 Score: 234
Period size: 61 Copynumber: 3.0 Consensus size: 60
22204 TCGTGAGTAT
*
22214 ATGAGTTCCTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAA
1 ATGAGTTCCTATAC-GAACAAGAGGTTCGATGACTATATGTCATCGTGAGTATTAAATGAA
* * * *
22275 ATGAGTTCCTATACAGAACAAGAGGTTTGATAACTGTATGTCATCGTGAGTATTAAATGAG
1 ATGAGTTCCTATAC-GAACAAGAGGTTCGATGACTATATGTCATCGTGAGTATTAAATGAA
* * * * * *
22336 ATGAGTTCCAATGCGAACAAG-GGTTCGATGACTTTGTGTTATCGTGAGTAATAAATG
1 ATGAGTTCCTATACGAACAAGAGGTTCGATGACTATATGTCATCGTGAGTATTAAATG
22393 CGAGTGAAAC
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
59 30 0.29
60 7 0.07
61 67 0.64
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (60 bp):
ATGAGTTCCTATACGAACAAGAGGTTCGATGACTATATGTCATCGTGAGTATTAAATGAA
Found at i:24999 original size:12 final size:12
Alignment explanation
Indices: 24982--25006 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24972 TGTTATCATG
24982 ATGAATGCTATT
1 ATGAATGCTATT
24994 ATGAATGCTATT
1 ATGAATGCTATT
25006 A
1 A
25007 ATTCTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:32936 original size:2 final size:2
Alignment explanation
Indices: 32931--32971 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
32921 ATATATAAGT
* *
32931 TA TA TA TA CA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32972 CCTTTTCTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:35163 original size:16 final size:15
Alignment explanation
Indices: 35129--35164 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
35119 ATATTTAAAG
35129 AAAAATGAATATTGT
1 AAAAATGAATATTGT
* *
35144 AAAAATGGATGTTGT
1 AAAAATGAATATTGT
35159 AAAAAT
1 AAAAAT
35165 ATTGATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:41609 original size:31 final size:31
Alignment explanation
Indices: 41571--41636 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
41561 CGTAACATTT
41571 CAAACATAAGAAACTAAAATGTAA-CTTGAGG
1 CAAACATAAGAAACTAAAATGTAATC-TGAGG
*
41602 CAAACATAAGAGACTAAAATGTAATCTGAGG
1 CAAACATAAGAAACTAAAATGTAATCTGAGG
41633 CAAA
1 CAAA
41637 TAAAAGTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.18
Consensus pattern (31 bp):
CAAACATAAGAAACTAAAATGTAATCTGAGG
Found at i:45460 original size:28 final size:28
Alignment explanation
Indices: 45417--45597 Score: 186
Period size: 28 Copynumber: 6.5 Consensus size: 28
45407 AAGACTTAAG
45417 AGAGCGTTATTCTGTAATATGGCTCGAA
1 AGAGCGTTATTCTGTAATATGGCTCGAA
* * *
45445 AGAGCGTTATTTTGTATTCTGGCTCGAA
1 AGAGCGTTATTCTGTAATATGGCTCGAA
45473 AGAGCGTTATTCTGTAATATGGCTCGAA
1 AGAGCGTTATTCTGTAATATGGCTCGAA
* * * *
45501 AGAGTGTTATTTTGTATTCTGGCTCGAA
1 AGAGCGTTATTCTGTAATATGGCTCGAA
* * * * * *
45529 AGAGTGCTACTCTGTATTCTGGCT-TAA
1 AGAGCGTTATTCTGTAATATGGCTCGAA
* * *
45556 ATGAGCGTTACTCTG-AATCTAGCTCGAA
1 A-GAGCGTTATTCTGTAATATGGCTCGAA
*
45584 AGAGCATTATTCTG
1 AGAGCGTTATTCTG
45598 GGTTGGTTCG
Statistics
Matches: 130, Mismatches: 21, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
27 21 0.16
28 109 0.84
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (28 bp):
AGAGCGTTATTCTGTAATATGGCTCGAA
Found at i:45502 original size:56 final size:56
Alignment explanation
Indices: 45417--45597 Score: 231
Period size: 56 Copynumber: 3.2 Consensus size: 56
45407 AAGACTTAAG
45417 AGAGCGTTATTCTGTAATATGGCTCGAAAGAGCGTTATTTTGTATTCTGGCTCGAA
1 AGAGCGTTATTCTGTAATATGGCTCGAAAGAGCGTTATTTTGTATTCTGGCTCGAA
*
45473 AGAGCGTTATTCTGTAATATGGCTCGAAAGAGTGTTATTTTGTATTCTGGCTCGAA
1 AGAGCGTTATTCTGTAATATGGCTCGAAAGAGCGTTATTTTGTATTCTGGCTCGAA
* * * * * * * * * *
45529 AGAGTGCTACTCTGTATTCTGGCT-TAAATGAGCGTTACTCTG-AATCTAGCTCGAA
1 AGAGCGTTATTCTGTAATATGGCTCGAAA-GAGCGTTATTTTGTATTCTGGCTCGAA
*
45584 AGAGCATTATTCTG
1 AGAGCGTTATTCTG
45598 GGTTGGTTCG
Statistics
Matches: 108, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
55 24 0.22
56 84 0.78
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (56 bp):
AGAGCGTTATTCTGTAATATGGCTCGAAAGAGCGTTATTTTGTATTCTGGCTCGAA
Found at i:45563 original size:84 final size:83
Alignment explanation
Indices: 45417--45597 Score: 220
Period size: 84 Copynumber: 2.2 Consensus size: 83
45407 AAGACTTAAG
* * *
45417 AGAGCGTTATTCTGTAATATGGCTCGAAAGAGCGTTATTTTGTATTCTGGCTCGAAAGAGCGTTA
1 AGAGCGTTATTCTGTAATATGGCTCGAAAGAGCGCTACTCTGTATTCTGGCTCGAAAGAGCGTTA
* *
45482 TTCTGTAATATGGCTCGAA
66 CTCTG-AATATAGCTCGAA
* * * * * *
45501 AGAGTGTTATTTTGTATTCTGGCTCGAAAGAGTGCTACTCTGTATTCTGGCT-TAAATGAGCGTT
1 AGAGCGTTATTCTGTAATATGGCTCGAAAGAGCGCTACTCTGTATTCTGGCTCGAAA-GAGCGTT
*
45565 ACTCTGAATCTAGCTCGAA
65 ACTCTGAATATAGCTCGAA
*
45584 AGAGCATTATTCTG
1 AGAGCGTTATTCTG
45598 GGTTGGTTCG
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
83 25 0.31
84 56 0.69
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (83 bp):
AGAGCGTTATTCTGTAATATGGCTCGAAAGAGCGCTACTCTGTATTCTGGCTCGAAAGAGCGTTA
CTCTGAATATAGCTCGAA
Found at i:45991 original size:20 final size:19
Alignment explanation
Indices: 45963--46006 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
45953 ATTATTTTGT
* *
45963 TACACTCTTATGTTGATTGA
1 TACATTCTTATG-TGAATGA
*
45983 TACATTCTTGTGTGAATGA
1 TACATTCTTATGTGAATGA
46002 TACAT
1 TACAT
46007 GATAGTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (19 bp):
TACATTCTTATGTGAATGA
Found at i:46458 original size:22 final size:22
Alignment explanation
Indices: 46433--46508 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
46423 GGTTGGAGGT
46433 ACGGGCGTGTGTGTAGGGACAC
1 ACGGGCGTGTGTGTAGGGACAC
46455 ACGGGCGTGTGTGTAGGGACAC
1 ACGGGCGTGTGTGTAGGGACAC
* *
46477 ACGGGCGTGTGTTTA-AGACAC
1 ACGGGCGTGTGTGTAGGGACAC
46498 AC-GGC-TGTGTG
1 ACGGGCGTGTGTG
46509 ACCCCTGTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.10
20 3 0.06
21 7 0.14
22 36 0.71
ACGTcount: A:0.18, C:0.18, G:0.42, T:0.21
Consensus pattern (22 bp):
ACGGGCGTGTGTGTAGGGACAC
Found at i:52869 original size:34 final size:34
Alignment explanation
Indices: 52770--52869 Score: 102
Period size: 34 Copynumber: 3.1 Consensus size: 34
52760 GAAATATATA
*
52770 AATTAAATACATGATATGATGCATGATGAATTTT
1 AATTAAATACATGATATGATGCACGATGAATTTT
*** * *
52804 AA-GGCATTCAT-ATAT--TAC-CGATTGAATTTT
1 AATTAAATACATGATATGATGCACGA-TGAATTTT
52834 AATTAAATACATGATATGATGCACGATGAATTTT
1 AATTAAATACATGATATGATGCACGATGAATTTT
52868 AA
1 AA
52870 GGAATTTAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
29 2 0.04
30 12 0.24
31 5 0.10
32 8 0.16
33 5 0.10
34 14 0.29
35 3 0.06
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (34 bp):
AATTAAATACATGATATGATGCACGATGAATTTT
Found at i:53265 original size:19 final size:20
Alignment explanation
Indices: 53221--53265 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
53211 TAAAAAAATA
*
53221 AACAA-AAGTTCAAGTAAAC
1 AACAATAAGTCCAAGTAAAC
53240 AAC-ATAAGTCCAAGT-AAC
1 AACAATAAGTCCAAGTAAAC
53258 AACAATAA
1 AACAATAA
53266 CACAACAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.58, C:0.18, G:0.09, T:0.16
Consensus pattern (20 bp):
AACAATAAGTCCAAGTAAAC
Found at i:59041 original size:22 final size:22
Alignment explanation
Indices: 59014--59076 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
59004 GAATATTGCT
*
59014 AGAGAATCTCACTATTCATGCC
1 AGAGAATATCACTATTCATGCC
* * *
59036 ATAGAATATCACTGTTCATGTC
1 AGAGAATATCACTATTCATGCC
*
59058 AGAGAATTTCACTATTCAT
1 AGAGAATATCACTATTCAT
59077 TTTGTTTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (22 bp):
AGAGAATATCACTATTCATGCC
Found at i:59129 original size:22 final size:22
Alignment explanation
Indices: 59104--59167 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
59094 AGAATATTAT
59104 CAGAGAATCTCACTATTCATGC
1 CAGAGAATCTCACTATTCATGC
* *
59126 CAGAGAATATTACTATTCATGC
1 CAGAGAATCTCACTATTCATGC
* *
59148 TAGAGAATCTCACTGTTCAT
1 CAGAGAATCTCACTATTCAT
59168 TTTATTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (22 bp):
CAGAGAATCTCACTATTCATGC
Found at i:59161 original size:91 final size:91
Alignment explanation
Indices: 59014--59192 Score: 270
Period size: 91 Copynumber: 2.0 Consensus size: 91
59004 GAATATTGCT
* * *
59014 AGAGAATCTCACTATTCATGCCATAGAATATCACTGTTCATGTCAGAGAATTTCACTATTCATTT
1 AGAGAATCTCACTATTCATGCCAGAGAATATCACTATTCATGTCAGAGAATCTCACTATTCATTT
*
59079 TGTTTTTTCTTGCAAAGAATATTATC
66 TATTTTTTCTTGCAAAGAATATTATC
* *
59105 AGAGAATCTCACTATTCATGCCAGAGAATATTACTATTCATG-CTAGAGAATCTCACTGTTCATT
1 AGAGAATCTCACTATTCATGCCAGAGAATATCACTATTCATGTC-AGAGAATCTCACTATTCATT
**
59169 TTATTTTTTCTTGCAGGGAATATT
65 TTATTTTTTCTTGCAAAGAATATT
59193 TCCTGTTCAC
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
90 1 0.01
91 78 0.99
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (91 bp):
AGAGAATCTCACTATTCATGCCAGAGAATATCACTATTCATGTCAGAGAATCTCACTATTCATTT
TATTTTTTCTTGCAAAGAATATTATC
Found at i:62464 original size:4 final size:4
Alignment explanation
Indices: 62455--62563 Score: 57
Period size: 4 Copynumber: 26.2 Consensus size: 4
62445 AATTTTTATT
* *
62455 TTTA TTTA TTTA TTTA TTTA TCTT- GTTA -TTA TTTA TTTTCA TGCTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA -TTT-A T-TTA
* *
62501 TTTA TTTA TTTTA TTTAA TTTACA TTTA -TTA -TTA -TTA TCTTG TTTG
1 TTTA TTTA -TTTA TTT-A TTT--A TTTA TTTA TTTA TTTA T-TTA TTTA
*
62547 TTTA CTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA T
62564 CATTAAATTT
Statistics
Matches: 86, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
3 14 0.16
4 47 0.55
5 19 0.22
6 6 0.07
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:62471 original size:37 final size:37
Alignment explanation
Indices: 62406--62513 Score: 94
Period size: 37 Copynumber: 2.8 Consensus size: 37
62396 AATCCCAATT
* *
62406 ATTTTTATTGTTTATATTTGTTTGTTTATTTTAGCATT-TA
1 ATTTTTA-T-TTT-TATTTATTTATTTATTTTAGC-TTGTA
* *
62446 ATTTTTATTTTTATTTATTTATTTA-TTTATCTTGTT
1 ATTTTTATTTTTATTTATTTATTTATTTTAGCTTGTA
* *
62482 ATTATTTATTTTCATGCTATTTATTTATTTTA
1 ATT-TTTATTTTTAT-TTATTTATTTATTTTA
62514 TTTAATTTAC
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
35 2 0.03
36 9 0.16
37 22 0.38
38 13 0.22
39 5 0.09
40 7 0.12
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.69
Consensus pattern (37 bp):
ATTTTTATTTTTATTTATTTATTTATTTTAGCTTGTA
Found at i:62488 original size:19 final size:19
Alignment explanation
Indices: 62461--62512 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
62451 TATTTTTATT
* *
62461 TATTTATTTATTTATCTTGT
1 TATTTATTTATTT-TCATGC
62481 TA-TTATTTATTTTCATGC
1 TATTTATTTATTTTCATGC
62499 TATTTATTTATTTT
1 TATTTATTTATTTT
62513 ATTTAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 6 0.21
19 21 0.72
20 2 0.07
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (19 bp):
TATTTATTTATTTTCATGC
Found at i:62887 original size:23 final size:24
Alignment explanation
Indices: 62859--62913 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
62849 ATTTAATACC
* *
62859 TTAATTATATATTTATTGTGTT-A-
1 TTAATTATAT-TTGATTGTCTTCAT
*
62882 TTAATTGTATTTGATTGTCTTCAT
1 TTAATTATATTTGATTGTCTTCAT
62906 TTAATTAT
1 TTAATTAT
62914 TTATATTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 9 0.35
23 10 0.38
24 7 0.27
ACGTcount: A:0.27, C:0.04, G:0.09, T:0.60
Consensus pattern (24 bp):
TTAATTATATTTGATTGTCTTCAT
Found at i:71785 original size:95 final size:95
Alignment explanation
Indices: 71586--71942 Score: 437
Period size: 95 Copynumber: 3.7 Consensus size: 95
71576 GCAATAACGA
*
71586 ATCTTACACCTTAAAATTGAAGAGGGATAGGTTGAAGCCGTAACGACAGACCTAACACCCTAAAA
1 ATCTTACACCTTAAAATTGAAGAGGGATAGGTTGAAGCCGTAACGACA-ACCTAACACCTTAAAA
* * *
71651 TCGTAAGGAAAGATTGAAGTCGTAACAATAG
65 TCGTAGGGAAAGATTAAAGTCGCAACAATAG
* * *
71682 ATCTTACACCTTAAAATTGAAGAGGGATAGGTTGATGTCGTAACGACAAACTAACACCTTAAAAT
1 ATCTTACACCTTAAAATTGAAGAGGGATAGGTTGAAGCCGTAACGACAACCTAACACCTTAAAAT
* *
71747 TGTAGGGAAAGATTAAAGTCACAACAATAG
66 CGTAGGGAAAGATTAAAGTCGCAACAATAG
* * **
71777 ATCTTACACCTTAAAACTGAAGAGGGATAGGTTGAAGCCGCAACGGAGGACCTAACACCTTAAAA
1 ATCTTACACCTTAAAATTGAAGAGGGATAGGTTGAAGCCGTAAC-GACAACCTAACACCTTAAAA
* * ** *
71842 CCGAATAGGGAAGGATTAAAGTCGCAATGA-CG
65 TCG--TAGGGAAAGATTAAAGTCGCAACAATAG
* * ** * *
71874 AATCTTACACCTTAAACTTGAAGAGGGATAGATTGAAGCCGTAACGGTAGACCTAACACCCTGAA
1 -ATCTTACACCTTAAAATTGAAGAGGGATAGGTTGAAGCCGTAACGACA-ACCTAACACCTTAAA
71939 ATCG
64 ATCG
71943 AAGAGGGATA
Statistics
Matches: 223, Mismatches: 33, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
95 80 0.36
96 64 0.29
97 2 0.01
98 77 0.35
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (95 bp):
ATCTTACACCTTAAAATTGAAGAGGGATAGGTTGAAGCCGTAACGACAACCTAACACCTTAAAAT
CGTAGGGAAAGATTAAAGTCGCAACAATAG
Found at i:71950 original size:98 final size:97
Alignment explanation
Indices: 71511--71956 Score: 446
Period size: 98 Copynumber: 4.6 Consensus size: 97
71501 AAAACCAAAA
* * ** * * *
71511 AGGGATA-GATGAAGCCGTAATGGTGGATCTAACACCTTAAAA-CTGAAGAGGGAAAGATTGAA-
1 AGGGATAGGTTGAAGCCGTAACGGCAGACCTAACACCCTAAAATC-GAAGAGGGAAAGATTAAAG
71573 TCCGCAATAACGAATCTTACACCTTAAAATTGAAG
65 T-CGCAAT-ACGAATCTTACACCTTAAAATTGAAG
* * *
71608 AGGGATAGGTTGAAGCCGTAACGACAGACCTAACACCCTAAAATCGTA-A-GGAAAGATTGAAGT
1 AGGGATAGGTTGAAGCCGTAACGGCAGACCTAACACCCTAAAATCGAAGAGGGAAAGATTAAAGT
71671 CGTAACAATA-G-ATCTTACACCTTAAAATTGAAG
66 CG---CAATACGAATCTTACACCTTAAAATTGAAG
* * * * * * *
71704 AGGGATAGGTTGATGTCGTAACGACA-AACTAACACCTTAAAATTG--TAGGGAAAGATTAAAGT
1 AGGGATAGGTTGAAGCCGTAACGGCAGACCTAACACCCTAAAATCGAAGAGGGAAAGATTAAAGT
* * ** *
71766 CACAACAATAGATCTTACACCTTAAAACTGAAG
66 CGCAATACGA-ATCTTACACCTTAAAATTGAAG
* * * * *
71799 AGGGATAGGTTGAAGCCGCAACGG-AGGACCTAACACCTTAAAACCGAATAGGGAAGGATTAAAG
1 AGGGATAGGTTGAAGCCGTAACGGCA-GACCTAACACCCTAAAATCGAAGAGGGAAAGATTAAAG
*
71863 TCGCAATGACGAATCTTACACCTTAAACTTGAAG
65 TCGCAAT-ACGAATCTTACACCTTAAAATTGAAG
* * * *
71897 AGGGATAGATTGAAGCCGTAACGGTAGACCTAACACCCTGAAATCGAAGAGGGATAGATT
1 AGGGATAGGTTGAAGCCGTAACGGCAGACCTAACACCCTAAAATCGAAGAGGGAAAGATT
71957 GAAGCCATAA
Statistics
Matches: 292, Mismatches: 40, Indels: 33
0.80 0.11 0.09
Matches are distributed among these distances:
92 4 0.01
94 2 0.01
95 71 0.24
96 76 0.26
97 10 0.03
98 121 0.41
99 8 0.03
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.21
Consensus pattern (97 bp):
AGGGATAGGTTGAAGCCGTAACGGCAGACCTAACACCCTAAAATCGAAGAGGGAAAGATTAAAGT
CGCAATACGAATCTTACACCTTAAAATTGAAG
Found at i:71990 original size:49 final size:49
Alignment explanation
Indices: 71458--71993 Score: 349
Period size: 49 Copynumber: 11.1 Consensus size: 49
71448 TCCTAGAGTT
* ** * * * * *
71458 GAAGAGGGATAGGTTGAAGCTATAACGGCAAACCTAACACCCTAAAACC
1 GAAGAGGGATAGATTGAAGCCGTAACGACAGATCTAACACCTTAAAATC
* * * ***
71507 AAAAAGGGATAGA-TGAAGCCGTAATGGTGGATCTAACACCTTAAAA-C
1 GAAGAGGGATAGATTGAAGCCGTAACGACAGATCTAACACCTTAAAATC
* * * ** * *
71554 TGAAGAGGGAAAGATTGAATCCGCAATAAC-GAATCTTACACCTTAAAATT
1 -GAAGAGGGATAGATTGAAGCCGTAACGACAG-ATCTAACACCTTAAAATC
* * *
71604 GAAGAGGGATAGGTTGAAGCCGTAACGACAGACCTAACACCCTAAAATC
1 GAAGAGGGATAGATTGAAGCCGTAACGACAGATCTAACACCTTAAAATC
* * * * * * *
71653 GTA-A-GGAAAGATTGAAGTCGTAACAATAGATCTTACACCTTAAAATT
1 GAAGAGGGATAGATTGAAGCCGTAACGACAGATCTAACACCTTAAAATC
* * * * *
71700 GAAGAGGGATAGGTTGATGTCGTAACGACA-AACTAACACCTTAAAATT
1 GAAGAGGGATAGATTGAAGCCGTAACGACAGATCTAACACCTTAAAATC
* * * * ** * * *
71748 G--TAGGGAAAGATTAAAGTCACAACAATAGATCTTACACCTTAAAA-C
1 GAAGAGGGATAGATTGAAGCCGTAACGACAGATCTAACACCTTAAAATC
* * * * *
71794 TGAAGAGGGATAGGTTGAAGCCGCAACGGA-GGACCTAACACCTTAAAACC
1 -GAAGAGGGATAGATTGAAGCCGTAAC-GACAGATCTAACACCTTAAAATC
* * * * * * * *
71844 GAATAGGGA-AGGATTAAAGTCGCAATGAC-GAATCTTACACCTTAAACTT
1 GAAGAGGGATA-GATTGAAGCCGTAACGACAG-ATCTAACACCTTAAAATC
** * * *
71893 GAAGAGGGATAGATTGAAGCCGTAACGGTAGACCTAACACCCTGAAATC
1 GAAGAGGGATAGATTGAAGCCGTAACGACAGATCTAACACCTTAAAATC
* *
71942 GAAGAGGGATAGATTGAAGCCATAACGACGGATCTAACACCTTAAAATC
1 GAAGAGGGATAGATTGAAGCCGTAACGACAGATCTAACACCTTAAAATC
71991 GAA
1 GAA
71994 TATGGGAAGA
Statistics
Matches: 368, Mismatches: 101, Indels: 36
0.73 0.20 0.07
Matches are distributed among these distances:
46 18 0.05
47 52 0.14
48 59 0.16
49 234 0.64
50 5 0.01
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (49 bp):
GAAGAGGGATAGATTGAAGCCGTAACGACAGATCTAACACCTTAAAATC
Found at i:72074 original size:70 final size:70
Alignment explanation
Indices: 71942--72075 Score: 171
Period size: 70 Copynumber: 1.9 Consensus size: 70
71932 CCCTGAAATC
* * * * *
71942 GAAGAGGGATAGATTGAAGCCATAACGACGGATCTAACACCTTAAAATCGAATATGGGAAGATTA
1 GAAGAGGGATAGATTGAACCCACAACGACGGACCTAACACCTTAAAATCGAAGATGGAAAGATTA
72007 AAACT
66 AAACT
* * **
72012 GAAGAGGGATAGGTTGAACCCACAATGGTGGACCTAACACCTTAAAATCGAAGA-GAGAAAGATT
1 GAAGAGGGATAGATTGAACCCACAACGACGGACCTAACACCTTAAAATCGAAGATG-GAAAGATT
72076 GAAGTCGTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
69 1 0.02
70 53 0.98
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.19
Consensus pattern (70 bp):
GAAGAGGGATAGATTGAACCCACAACGACGGACCTAACACCTTAAAATCGAAGATGGAAAGATTA
AAACT
Found at i:72248 original size:50 final size:49
Alignment explanation
Indices: 72142--72248 Score: 117
Period size: 49 Copynumber: 2.2 Consensus size: 49
72132 AACGATGAAC
* * * ** *
72142 CTAACACTCGAAAACTAAAGAGGGATAGATTGAAGCCACGAAGGCGGAT
1 CTAACACCCTAAAACTAAAGAGGGACAGATTGAAGCCACGAAAACGAAT
*
72191 CTAACACCCTAAAACTAAAGAGGGAACATATTGAAGCCAC-AATAACGAAT
1 CTAACACCCTAAAACTAAAGAGGG-ACAGATTGAAGCCACGAA-AACGAAT
*
72241 CTCACACC
1 CTAACACC
72249 TTTTGAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
49 24 0.50
50 24 0.50
ACGTcount: A:0.43, C:0.23, G:0.19, T:0.15
Consensus pattern (49 bp):
CTAACACCCTAAAACTAAAGAGGGACAGATTGAAGCCACGAAAACGAAT
Found at i:72921 original size:25 final size:24
Alignment explanation
Indices: 72864--72908 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
72854 TTGGAATAAA
*
72864 ATTCAGAG-ATTTTTTTATACAAC
1 ATTCAGAGAATTTTTTTAGACAAC
72887 ATTCAGAGAATTTTTTTAGACA
1 ATTCAGAGAATTTTTTTAGACA
72909 TATATTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (24 bp):
ATTCAGAGAATTTTTTTAGACAAC
Found at i:73261 original size:4 final size:4
Alignment explanation
Indices: 73243--73361 Score: 58
Period size: 4 Copynumber: 29.8 Consensus size: 4
73233 TTTATTTTAG
* *
73243 TATT TAAT T-TT TATT TATT TATT TATT T-TT TGTT TATT T-TT CT-TGT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT -TAT-T
* *
73289 TA-T TATT TA-T T-TT TATGC CATT TA-T TATT TA-T TATT TAATT TACATT
1 TATT TATT TATT TATT TAT-T TATT TATT TATT TATT TATT T-ATT T--ATT
73336 TATTGT TATTT TATT TATT TATT TAT
1 TA-T-T TA-TT TATT TATT TATT TAT
73362 CATTAAATTT
Statistics
Matches: 92, Mismatches: 8, Indels: 30
0.71 0.06 0.23
Matches are distributed among these distances:
3 20 0.22
4 52 0.57
5 11 0.12
6 9 0.10
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:73263 original size:15 final size:14
Alignment explanation
Indices: 73207--73359 Score: 82
Period size: 15 Copynumber: 10.4 Consensus size: 14
73197 CTAATCCCAA
73207 TTATTTTTA-TTAT
1 TTATTTTTATTTAT
* * *
73220 TTATATTTGTTTGT
1 TTATTTTTATTTAT
73234 TTATTTTAGTATTTAAT
1 TTATTTT--TATTT-AT
73251 TT-TTATTTATTTAT
1 TTATT-TTTATTTAT
*
73265 TTATTTTTTGTTTAT
1 TTA-TTTTTATTTAT
*
73280 TTTTCTTGTTA-TTAT
1 TTAT-TT-TTATTTAT
**
73295 TTATTTTTATGCCAT
1 TTATTTTTAT-TTAT
73310 TTATTATTTA-TTAT
1 TTATT-TTTATTTAT
**
73324 TTAATTTACATTTAT
1 TT-ATTTTTATTTAT
73339 TGT-TATTTTATTTAT
1 T-TAT-TTTTATTTAT
73354 TTATTT
1 TTATTT
73360 ATCATTAAAT
Statistics
Matches: 105, Mismatches: 18, Indels: 33
0.67 0.12 0.21
Matches are distributed among these distances:
13 10 0.10
14 26 0.25
15 49 0.47
16 15 0.14
17 5 0.05
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.71
Consensus pattern (14 bp):
TTATTTTTATTTAT
Found at i:73265 original size:19 final size:19
Alignment explanation
Indices: 73243--73360 Score: 61
Period size: 19 Copynumber: 6.3 Consensus size: 19
73233 TTTATTTTAG
73243 TATTTAATTTTTATTTATT
1 TATTTAATTTTTATTTATT
* *
73262 TATTTATTTTTTGTTTATT
1 TATTTAATTTTTATTTATT
** *
73281 T-TTCTTGTTATTATTTATT
1 TATT-TAATTTTTATTTATT
*
73300 T-TTATGCCATTTATTATTTA-T
1 TATT-T--AATTT-TTATTTATT
**
73321 TATTTAATTTACATTTA-T
1 TATTTAATTTTTATTTATT
*
73339 T-GTT-A-TTTTATTTATT
1 TATTTAATTTTTATTTATT
73355 TATTTA
1 TATTTA
73361 TCATTAAATT
Statistics
Matches: 74, Mismatches: 17, Indels: 17
0.69 0.16 0.16
Matches are distributed among these distances:
15 7 0.09
16 3 0.04
17 4 0.05
18 9 0.12
19 37 0.50
21 5 0.07
22 9 0.12
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.70
Consensus pattern (19 bp):
TATTTAATTTTTATTTATT
Found at i:73335 original size:25 final size:25
Alignment explanation
Indices: 73307--73356 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
73297 ATTTTTATGC
73307 CATTTATTATT-TATTATTTAATTTA
1 CATTTATTATTATATTATTT-ATTTA
* *
73332 CATTTATTGTTATTTTATTTATTTA
1 CATTTATTATTATATTATTTATTTA
73357 TTTATCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (25 bp):
CATTTATTATTATATTATTTATTTA
Found at i:73337 original size:40 final size:41
Alignment explanation
Indices: 73293--73371 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 41
73283 TCTTGTTATT
* * *
73293 ATTTATTTTTATGCCATTTA-TTATTTATTATTTAATTTAC
1 ATTTATTGTTATGCCATTTATTTATTTATCATTAAATTTAC
***
73333 ATTTATTGTTATTTTATTTATTTATTTATCATTAAATTT
1 ATTTATTGTTATGCCATTTATTTATTTATCATTAAATTT
73372 TATGTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
40 16 0.50
41 16 0.50
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (41 bp):
ATTTATTGTTATGCCATTTATTTATTTATCATTAAATTTAC
Found at i:84053 original size:2 final size:2
Alignment explanation
Indices: 84046--84075 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
84036 GAATATCATG
84046 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
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.