Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015007.1 Kokia drynarioides strain JFW-HI SEQ_130051, 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: 33252
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 78 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
*
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36 GTAAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1855 original size:2 final size:2
Alignment explanation
Indices: 1843--1893 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
1833 TTGTAATCTA
1843 AT AT A- 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 AT AT AT
1884 AT AT AT AT AT
1 AT AT AT AT AT
1894 TGAGTAGCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5825 original size:59 final size:58
Alignment explanation
Indices: 5764--6078 Score: 300
Period size: 59 Copynumber: 5.3 Consensus size: 58
5754 TTAAAACGTG
** *
5764 ATTTTAGAGAAGTTTAAGGGTCAAAATGTAATTTTGAATAAGTTTA-GGGTCAAAACATG
1 ATTTTAGAGAAGTTT-AGGGTCAAAATGTAATTTTGAA-AAGTTTAGGGGTCAAAATGTA
* * * * *
5823 ATTTTAGAGAAGTTTGGAGGTCAAAATATAGTTTTGGATAAGTTTAGGGGTTAAAATGTA
1 ATTTTAGAGAAGTTTAG-GGTCAAAATGTAATTTT-GAAAAGTTTAGGGGTCAAAATGTA
* * *
5883 ATCTT-GAATAAGTTTAGGATCAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGTA
1 ATTTTAG-AGAAGTTTAGGGTCAAAATGTAATTTT-GAAAAGTTTAGGGGTCAAAATGTA
* * * *
5942 ATTTTGGAAAATTTTAGTGGTC-AAATGTAATTTTTGAAAAGTTTAGGGGTC--AATATA
1 ATTTTAGAGAAGTTTAG-GGTCAAAATGTAA-TTTTGAAAAGTTTAGGGGTCAAAATGTA
* * * *
5999 ATTTTTGAAAAGTTTTAGGGGTCAAAATGTAATTTTTGAAAAGTTTAGAGGTCAAAATATA
1 ATTTTAGAGAAG-TTTA-GGGTCAAAATGTAA-TTTTGAAAAGTTTAGGGGTCAAAATGTA
*
6060 ATTTATGGA-AAGTTTAGGG
1 ATTT-TAGAGAAGTTTAGGG
6079 ACCTATTAGA
Statistics
Matches: 218, Mismatches: 25, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
57 15 0.07
58 9 0.04
59 143 0.66
60 35 0.16
61 13 0.06
62 3 0.01
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (58 bp):
ATTTTAGAGAAGTTTAGGGTCAAAATGTAATTTTGAAAAGTTTAGGGGTCAAAATGTA
Found at i:5906 original size:89 final size:89
Alignment explanation
Indices: 5764--6077 Score: 307
Period size: 89 Copynumber: 3.5 Consensus size: 89
5754 TTAAAACGTG
* * * * * *
5764 ATTTTAGAGAAGTTTAAGGGTCAAAATGTAATTTTGAATAAGTTTAGGGTCAAAACATGATTTTA
1 ATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTGAATAAGTTTAGGATCAAAACATAATTTTA
*
5829 GAGAAGTTT-GGAGGTCAAAATATA
66 GAAAAGTTTAGG-GGTCAAAATATA
* * * ** *
5853 GTTTTGGATAAGTTTAGGGGTTAAAATGTAATCTTGAATAAGTTTAGGATCAAAATGTAATTTTG
1 ATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTGAATAAGTTTAGGATCAAAACATAATTTTA
*
5918 GAAAAGTTTAGGGGTCAAAATGTA
66 GAAAAGTTTAGGGGTCAAAATATA
* * * * *
5942 ATTTTGGAAAATTTTAGTGG-TCAAATGTAATTTTTGAA-AAGTTTAGGGGTC--AATATAATTT
1 ATTTTGGAAAAGTTTAGGGGTTAAAATGTAA-TTTTGAATAAGTTTA-GGATCAAAACATAATTT
* *
6003 TTGAAAAGTTTTAGGGGTCAAAATGTA
64 TAGAAAAG-TTTAGGGGTCAAAATATA
* * * * *
6030 ATTTTTGAAAAGTTTAGAGGTCAAAATATAATTTATGGA-AAGTTTAGG
1 ATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTT-TGAATAAGTTTAGG
6078 GACCTATTAG
Statistics
Matches: 190, Mismatches: 29, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
87 16 0.08
88 56 0.29
89 116 0.61
90 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.37
Consensus pattern (89 bp):
ATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTGAATAAGTTTAGGATCAAAACATAATTTTA
GAAAAGTTTAGGGGTCAAAATATA
Found at i:6076 original size:30 final size:29
Alignment explanation
Indices: 5721--6078 Score: 309
Period size: 30 Copynumber: 12.1 Consensus size: 29
5711 GAAAAAAAAG
* *
5721 GGGGTCGAAAATG-AAGTTTTGAAAAATAT-
1 GGGGTC-AAAATGTAA-TTTTGAAAAGTTTA
* * * * *
5750 GAGGTTAAAACGTGATTTTAGAGAAGTTTA
1 GGGGTCAAAATGTAATTTT-GAAAAGTTTA
*
5780 AGGGTCAAAATGTAATTTTGAATAAGTTTA
1 GGGGTCAAAATGTAATTTTGAA-AAGTTTA
** * *
5810 -GGGTCAAAACATGATTTTAGAGAAGTTT-
1 GGGGTCAAAATGTAATTTT-GAAAAGTTTA
* * *
5838 GGAGGTCAAAATATAGTTTTGGATAAGTTTA
1 GG-GGTCAAAATGTAATTTT-GAAAAGTTTA
* *
5869 GGGGTTAAAATGTAATCTTGAATAAGTTTA
1 GGGGTCAAAATGTAATTTTGAA-AAGTTTA
*
5899 -GGATCAAAATGTAATTTTGGAAAAGTTTA
1 GGGGTCAAAATGTAATTTT-GAAAAGTTTA
*
5928 GGGGTCAAAATGTAATTTTGGAAAATTTTA
1 GGGGTCAAAATGTAATTTT-GAAAAGTTTA
*
5958 GTGGTC-AAATGTAATTTTTGAAAAGTTTA
1 GGGGTCAAAATGTAA-TTTTGAAAAGTTTA
*
5987 GGGGTC--AATATAATTTTTGAAAAGTTTTA
1 GGGGTCAAAATGTAA-TTTTGAAAAG-TTTA
6016 GGGGTCAAAATGTAATTTTTGAAAAGTTTA
1 GGGGTCAAAATGTAA-TTTTGAAAAGTTTA
* * *
6046 GAGGTCAAAATATAATTTATGGAAAGTTTA
1 GGGGTCAAAATGTAATTT-TGAAAAGTTTA
6076 GGG
1 GGG
6079 ACCTATTAGA
Statistics
Matches: 272, Mismatches: 41, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
28 26 0.10
29 94 0.35
30 133 0.49
31 19 0.07
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTGAAAAGTTTA
Found at i:9581 original size:39 final size:41
Alignment explanation
Indices: 9507--9592 Score: 110
Period size: 39 Copynumber: 2.2 Consensus size: 41
9497 AAATTTATAT
*
9507 ATATTT-TT-TAATATTTTAGGTTTTTCATATTTTTTAA-A
1 ATATTTATTATAATATTTTAGGTTTTTCATATGTTTTAATA
*
9545 A-ATTTATTATAATTTTTTAGGATTTTT-ATATGTTTTAATA
1 ATATTTATTATAATATTTTAGG-TTTTTCATATGTTTTAATA
9585 ATATTTAT
1 ATATTTAT
9593 AAGTTTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
37 4 0.10
38 3 0.07
39 21 0.51
40 7 0.17
41 6 0.15
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.62
Consensus pattern (41 bp):
ATATTTATTATAATATTTTAGGTTTTTCATATGTTTTAATA
Found at i:9631 original size:10 final size:10
Alignment explanation
Indices: 9537--9631 Score: 51
Period size: 10 Copynumber: 9.9 Consensus size: 10
9527 TTTTTCATAT
* *
9537 TTTTTAAAAA
1 TTTTTATAAG
9547 TTTATTATAA-
1 TTT-TTATAAG
*
9557 TTTTT-TAGG
1 TTTTTATAAG
*
9566 ATTTTTATATG
1 -TTTTTATAAG
*
9577 TTTTAATAA-
1 TTTTTATAAG
*
9586 TATTTATAAG
1 TTTTTATAAG
*
9596 -TTTTAT-TG
1 TTTTTATAAG
9604 TTTTT-TATA-
1 TTTTTATA-AG
9613 TTTTTATAAG
1 TTTTTATAAG
9623 TTTTTATAA
1 TTTTTATAA
9632 ATTTATCTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
8 4 0.06
9 24 0.37
10 29 0.45
11 8 0.12
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (10 bp):
TTTTTATAAG
Found at i:12035 original size:12 final size:12
Alignment explanation
Indices: 12018--12073 Score: 60
Period size: 13 Copynumber: 4.6 Consensus size: 12
12008 TCAGCTCTTC
*
12018 CTTTCTCTTTCT
1 CTTTCTCTTTTT
12030 CTTTCTCTATTTT
1 CTTTCTCT-TTTT
12043 CTTCTCTCTTTTT
1 CTT-TCTCTTTTT
*
12056 CTTGC-CTTTTT
1 CTTTCTCTTTTT
*
12067 CCTTCTC
1 CTTTCTC
12074 AAGACAGCAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
11 9 0.24
12 10 0.27
13 13 0.35
14 5 0.14
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.64
Consensus pattern (12 bp):
CTTTCTCTTTTT
Found at i:14919 original size:15 final size:17
Alignment explanation
Indices: 14891--14923 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
14881 TAAATAAATT
14891 ATTAACAAATTATAAAA
1 ATTAACAAATTATAAAA
14908 ATTAA-AAA-TATAAAA
1 ATTAACAAATTATAAAA
14923 A
1 A
14924 AAATTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
ATTAACAAATTATAAAA
Found at i:15238 original size:21 final size:22
Alignment explanation
Indices: 15214--15255 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
15204 TTCATTAGAG
15214 AATTAT-AAAA-AATATAAAAAA
1 AATTATCAAAATAA-ATAAAAAA
15235 AATTATCAAAATAAATAAAAA
1 AATTATCAAAATAAATAAAAA
15256 TTTATTAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 11 0.58
23 2 0.11
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (22 bp):
AATTATCAAAATAAATAAAAAA
Found at i:15309 original size:34 final size:36
Alignment explanation
Indices: 15232--15323 Score: 91
Period size: 34 Copynumber: 2.6 Consensus size: 36
15222 AAAATATAAA
* * * * *
15232 AAAAATTATCAAAATAAATAAAAATTTATTAACTATT
1 AAAAA-TATTAAAATTAATATAAACTTATTAAATATT
15269 AAAAATA-TAAAATTAATATAAACTTA-TAAATATT
1 AAAAATATTAAAATTAATATAAACTTATTAAATATT
* *
15303 ATAAATATTATAA-TAATATAA
1 AAAAATATTAAAATTAATATAA
15324 GATTCTAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
34 21 0.45
35 19 0.40
36 2 0.04
37 5 0.11
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (36 bp):
AAAAATATTAAAATTAATATAAACTTATTAAATATT
Found at i:20577 original size:6 final size:6
Alignment explanation
Indices: 20557--20629 Score: 64
Period size: 6 Copynumber: 12.7 Consensus size: 6
20547 TCGGGCCTTT
* * * *
20557 TTTAAA TTT-AT TTTAAA TTTAGA TTT-AT TTTAAA TTTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
20603 -TT-AA TTTTAA TGTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA T-TTAAA TTTAAA TTTA
20630 TTTTCCTATT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
4 2 0.04
5 11 0.21
6 35 0.66
7 5 0.09
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:20582 original size:17 final size:17
Alignment explanation
Indices: 20557--20600 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
20547 TCGGGCCTTT
20557 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
20574 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
20591 TTTGAATTTA
1 TTTAAATTTA
20601 AATTAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:20598 original size:23 final size:23
Alignment explanation
Indices: 20569--20633 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
20559 TAAATTTATT
*
20569 TTAAATTTAGATTTATTTTAAAT-
1 TTAAATTTAAATTTATTTT-AATG
* *
20592 TTGAATTTAAATTAATTTTAATG
1 TTAAATTTAAATTTATTTTAATG
20615 TTAAATTTAAATTTATTTT
1 TTAAATTTAAATTTATTTT
20634 CCTATTTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 3 0.08
23 33 0.92
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (23 bp):
TTAAATTTAAATTTATTTTAATG
Found at i:20672 original size:14 final size:15
Alignment explanation
Indices: 20655--20683 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20645 AAATTATTAT
20655 AAAGTCC-AATTACA
1 AAAGTCCAAATTACA
20669 AAAGTCCAAATTACA
1 AAAGTCCAAATTACA
20684 TGTCCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.21
Consensus pattern (15 bp):
AAAGTCCAAATTACA
Found at i:21350 original size:3 final size:3
Alignment explanation
Indices: 21342--21413 Score: 54
Period size: 3 Copynumber: 23.0 Consensus size: 3
21332 TAAATAGCCT
* * * * * *
21342 TAA TAA TAA TAT TAA TAA TAGGA TAA CAC TAA TGA CAT TAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TA--A TAA TAA TAA TAA TAA TAA -TAA TAA
*
21390 TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
21414 CAAAAAAGTA
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
3 46 0.88
4 3 0.06
5 3 0.06
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:22688 original size:89 final size:88
Alignment explanation
Indices: 22508--22787 Score: 266
Period size: 89 Copynumber: 3.2 Consensus size: 88
22498 AAGGTCCTTA
* * * *
22508 AACTGTCCGAAAATTACATTTTT-ACCCCCG-AACTTCCAAAAA-TCCATTTTTGA-CCTCGAAA
1 AACT-TCCAAAAATTCCATTTTTGA-CACCGAAACTTCCAAAAATTACATTTTT-ACCCTC-AAA
*** * *
22569 CTTTTGAAAATTACATTTTTACACC-CG
62 CTTCCAAAAAATACAATTTTA-ACCTCG
* **
22596 AACTTCCAAAAATTCCATTTTTGACCCCGAAACTTTTAAAAATTACATTTTTGACCCT-AAAGCT
1 AACTTCCAAAAATTCCATTTTTGACACCGAAACTTCCAAAAATTACATTTTT-ACCCTCAAA-CT
* *
22660 TCCAAAAAATACAATTTTACCCTTG
64 TCCAAAAAATACAATTTTAACCTCG
* *
22685 AACTTCCAAAAATTCCATTTTTGACATCGAAACTTCCAAAACTTACATTTTTACCCTCAAACTTC
1 AACTTCCAAAAATTCCATTTTTGACACCGAAACTTCCAAAAATTACATTTTTACCCTCAAACTTC
* * *
22750 CAAAAATTCCATTTTTAACCTCG
66 CAAAAAATACAATTTTAACCTCG
*
22773 AAACTTTCAAAAATT
1 -AACTTCCAAAAATT
22788 ACCCTTTTAC
Statistics
Matches: 161, Mismatches: 23, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
87 21 0.13
88 47 0.29
89 90 0.56
90 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (88 bp):
AACTTCCAAAAATTCCATTTTTGACACCGAAACTTCCAAAAATTACATTTTTACCCTCAAACTTC
CAAAAAATACAATTTTAACCTCG
Found at i:22796 original size:30 final size:30
Alignment explanation
Indices: 22507--22789 Score: 256
Period size: 30 Copynumber: 9.6 Consensus size: 30
22497 GAAGGTCCTT
* * *
22507 AAACTGTCCGAAAATTACATTTTTACCCCCG
1 AAACT-TCCAAAAATTACATTTTTAACCTCG
* *
22538 -AACTTCCAAAAA-TCCATTTTTGACCTCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
***
22566 AAACTTTTGAAAATTACATTTTTACACC-CG
1 AAACTTCCAAAAATTACATTTTTA-ACCTCG
* * *
22596 -AACTTCCAAAAATTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
** * *
22625 AAACTTTTAAAAATTACATTTTTGACC-CT
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* * * *
22654 AAAGCTTCCAAAAAATACAATTTTACCCTTG
1 AAA-CTTCCAAAAATTACATTTTTAACCTCG
* * *
22685 -AACTTCCAAAAATTCCATTTTTGACATCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* *
22714 AAACTTCCAAAACTTACATTTTTACCCTC-
1 AAACTTCCAAAAATTACATTTTTAACCTCG
*
22743 AAACTTCCAAAAATTCCATTTTTAACCTCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
*
22773 AAACTTTCAAAAATTAC
1 AAACTTCCAAAAATTAC
22790 CCTTTTACCA
Statistics
Matches: 199, Mismatches: 44, Indels: 19
0.76 0.17 0.07
Matches are distributed among these distances:
28 15 0.08
29 86 0.43
30 95 0.48
31 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.33
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTAACCTCG
Found at i:22796 original size:59 final size:58
Alignment explanation
Indices: 22507--22798 Score: 252
Period size: 59 Copynumber: 4.9 Consensus size: 58
22497 GAAGGTCCTT
* * *
22507 AAACTGTCCGAAAATTACATTTTTACCCCCG-AACTTCCAAAAA-TCCATTTTTGA-CCTC
1 AAACT-TCCAAAAATTACATTTTTA-ACCCGAAACTTCCAAAAATTACATTTTT-ACCCTC
*** *
22565 GAAACTTTTGAAAATTACATTTTTACACCCG-AACTTCCAAAAATTCCATTTTTGACCC-C
1 -AAACTTCCAAAAATTACATTTTTA-ACCCGAAACTTCCAAAAATTACATTTTT-ACCCTC
** * * * * *
22624 GAAACTTTTAAAAATTACATTTTTGACCCTAAAGCTTCCAAAAAATACAATTTTACCCTT
1 -AAACTTCCAAAAATTACATTTTTAACCCGAAA-CTTCCAAAAATTACATTTTTACCCTC
* * * * *
22684 GAACTTCCAAAAATTCCATTTTTGACATCGAAACTTCCAAAACTTACATTTTTACCCTC
1 AAACTTCCAAAAATTACATTTTTAAC-CCGAAACTTCCAAAAATTACATTTTTACCCTC
* * **
22743 AAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTACCCTTTTACC
1 AAACTTCCAAAAATTACATTTTTAACC-CGAAACTTCCAAAAATTACATTTTTACC
22799 ACGGATGTCC
Statistics
Matches: 199, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
58 38 0.19
59 138 0.69
60 23 0.12
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.34
Consensus pattern (58 bp):
AAACTTCCAAAAATTACATTTTTAACCCGAAACTTCCAAAAATTACATTTTTACCCTC
Found at i:22812 original size:59 final size:58
Alignment explanation
Indices: 22689--22913 Score: 165
Period size: 58 Copynumber: 3.9 Consensus size: 58
22679 CCCTTGAACT
* * * * * **
22689 TCCAAAAATTCCATTTTTGACATCGAAACTTCCAAAACTTA-CATTTTTACCCTCAAACT-
1 TCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTACCA-TTTTA-CCACGGA-TG
*
22748 TCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTACCCTTTTACCACGGATG
1 TCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTACCATTTTACCACGGATG
* * * ** *
22806 TCCCAAAATTCCATTTTTTATCTCG-ATTTTTCTAAAAATTACCATTTTACCCCTGGATG
1 TCCAAAAATTCCATTTTTAACCTCGAAACTTTC-AAAAATTACCATTTTACCAC-GGATG
** * ** * *
22865 T-TTAAAGTT-TTTTTTTAATCTCG-AACTTTCCTAAAATTACCATTTTACC
1 TCCAAAAATTCCATTTTTAACCTCGAAACTTT-CAAAAATTACCATTTTACC
22914 CCCCGAGTAT
Statistics
Matches: 137, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
57 38 0.28
58 50 0.36
59 48 0.35
60 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTACCATTTTACCACGGATG
Found at i:25400 original size:96 final size:96
Alignment explanation
Indices: 25231--25413 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 96
25221 GGGAAAAGGA
* ** *
25231 TATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCAAAATC
1 TATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCGCAATATTTCAAAATC
25296 GAAGAT-AAAGAAACATTGCCTCTATTAGGGG
66 GAAGATAAAAG-AACATTGCCTCTATTAGGGG
* * * * * *
25327 TATTCGATTATTTTGATTTGAAGAAAAATCGCACCTAGTAAGTTAATGCGCAAATTTTTGAAACT
1 TATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCGC-AATATTTCAAAAT
*
25392 CGAA-ATAAAAGAATATTGCCTC
65 CGAAGATAAAAGAACATTGCCTC
25414 AATTTTTTAA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
96 56 0.76
97 18 0.24
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (96 bp):
TATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCGCAATATTTCAAAATC
GAAGATAAAAGAACATTGCCTCTATTAGGGG
Found at i:25877 original size:29 final size:29
Alignment explanation
Indices: 25836--26137 Score: 360
Period size: 29 Copynumber: 10.4 Consensus size: 29
25826 TTGGAGTCGG
* **
25836 AAATGGAATTTTTGGAAGATCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTCAAGGGTAA
* *
25865 AAATGAAATTTTTGGAAGTTCAGGGGTAA
1 AAATGGAATTTTTGGAAGTTCAAGGGTAA
**
25894 AAATGGAATTTTT-GAAGTTTTAGGGTCAA
1 AAATGGAATTTTTGGAAGTTCAAGGGT-AA
*
25923 AAATGGAATTTTTGGAAGTTTAAGGGTAA
1 AAATGGAATTTTTGGAAGTTCAAGGGTAA
*
25952 AAATGGAATTTTTGGAAGTTTAAGGGTAA
1 AAATGGAATTTTTGGAAGTTCAAGGGTAA
* **
25981 AAATGGAATTTTTGGAAGATCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTCAAGGGTAA
***
26010 AAATGGAA-TTTTGGAAGTTTTGGGGTCAA
1 AAATGGAATTTTTGGAAGTTCAAGGGT-AA
*
26039 AAATGGAA-TTTTGGAAGTTCGAGGGTAA
1 AAATGGAATTTTTGGAAGTTCAAGGGTAA
* *
26067 AAATGGAATTTTTGAAAGTTTC-GGGGTCAA
1 AAATGGAATTTTTGGAAG-TTCAAGGGT-AA
*
26097 AAATGGAATTTTTGGAAGTTTAAGGGTAA
1 AAATGGAATTTTTGGAAGTTCAAGGGTAA
*
26126 AAATGTAATTTT
1 AAATGGAATTTT
26138 CTAACAGTCT
Statistics
Matches: 242, Mismatches: 24, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
28 35 0.14
29 169 0.70
30 38 0.16
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTCAAGGGTAA
Found at i:25950 original size:87 final size:87
Alignment explanation
Indices: 25804--26137 Score: 415
Period size: 87 Copynumber: 3.8 Consensus size: 87
25794 ATCCGGGGCA
* * * ** * ***
25804 AAAAATGGAATTTTGGGTAGTTTTGGAGTCGGAAATGGAATTTTTGGAAGATCGGGGGTAAAAAT
1 AAAAATGGAATTTT-TGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAAAT
*
25869 GAAATTTTTGGAAGTTCAGGGGT
65 GGAATTTTTGGAAGTTCAGGGGT
*
25892 AAAAATGGAATTTTTGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAAATG
1 AAAAATGGAATTTTTGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAAATG
* *
25957 GAATTTTTGGAAGTTTAAGGGT
66 GAATTTTTGGAAGTTCAGGGGT
* ** **
25979 AAAAATGGAATTTTTGGAAGATCGGGGGT-AAAAATGGAA-TTTTGGAAGTTTTGGGGTCAAAAA
1 AAAAATGGAATTTTT-GAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTAAGGGT-AAAAA
26042 TGGAA-TTTTGGAAGTTC-GAGGGT
64 TGGAATTTTTGGAAGTTCAG-GGGT
*
26065 AAAAATGGAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAAAT
1 AAAAATGGAATTTTTG-AAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAAAT
*
26130 GTAATTTT
65 GGAATTTT
26138 CTAACAGTCT
Statistics
Matches: 212, Mismatches: 27, Indels: 14
0.84 0.11 0.06
Matches are distributed among these distances:
85 1 0.00
86 55 0.26
87 114 0.54
88 42 0.20
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (87 bp):
AAAAATGGAATTTTTGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAAATG
GAATTTTTGGAAGTTCAGGGGT
Found at i:27368 original size:18 final size:18
Alignment explanation
Indices: 27329--27368 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
27319 ATCATTATTA
* *
27329 ATTAATGTTATTATTACC
1 ATTAATGTCATTATGACC
*
27347 ATTAATGTCATTATGACT
1 ATTAATGTCATTATGACC
27365 ATTA
1 ATTA
27369 TTAATATTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (18 bp):
ATTAATGTCATTATGACC
Found at i:28094 original size:17 final size:17
Alignment explanation
Indices: 28072--28151 Score: 117
Period size: 17 Copynumber: 4.7 Consensus size: 17
28062 CAAATAAATT
28072 TAAATTTAAATTT-ATAA
1 TAAATTTAAATTTCA-AA
28089 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
28106 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
* * *
28123 TAAAATTAATTTTAAAA
1 TAAATTTAAATTTCAAA
28140 TAAATTTAAATT
1 TAAATTTAAATT
28152 CTATTAGGCC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
17 56 0.98
18 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:28115 original size:23 final size:23
Alignment explanation
Indices: 28064--28123 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
28054 ACATTATTCA
**
28064 AATAAATTTAAATTTAAATTTAT
1 AATAAATTTAAATTTAAATAAAT
28087 AATAAATTTAAATTTCAAATAAAT
1 AATAAATTTAAATTT-AAATAAAT
*
28111 -TTAAATTTCAAAT
1 AATAAATTT-AAAT
28124 AAAATTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (23 bp):
AATAAATTTAAATTTAAATAAAT
Found at i:28123 original size:7 final size:6
Alignment explanation
Indices: 28066--28151 Score: 69
Period size: 6 Copynumber: 15.0 Consensus size: 6
28056 ATTATTCAAA
28066 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT TCAAA-- TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
* * *
28112 TAAATT TCAAA-- TAAAAT TAATTT TAAA-A TAAATT TAAATT
1 TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT TAAATT
28152 CTATTAGGCC
Statistics
Matches: 65, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
4 8 0.12
5 8 0.12
6 41 0.63
7 8 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:28126 original size:11 final size:10
Alignment explanation
Indices: 28063--28116 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
28053 GACATTATTC
28063 AAATAAATTT
1 AAATAAATTT
28073 AAATTTAAATTT
1 AAA--TAAATTT
28085 ATAATAAATTT
1 A-AATAAATTT
*
28096 AAAT---TTC
1 AAATAAATTT
28103 AAATAAATTT
1 AAATAAATTT
28113 AAAT
1 AAAT
28117 TTCAAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
7 6 0.17
10 12 0.33
11 8 0.22
12 8 0.22
13 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (10 bp):
AAATAAATTT
Found at i:31172 original size:14 final size:14
Alignment explanation
Indices: 31153--31189 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
31143 ATTTCTTACA
* *
31153 AATAAAATATTAGT
1 AATAAAATAATAAT
31167 AATAAAATAATAAT
1 AATAAAATAATAAT
31181 AATAAAATA
1 AATAAAATA
31190 GAGAAAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
AATAAAATAATAAT
Done.