Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008574.1 Kokia drynarioides strain JFW-HI SEQ_123252, 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: 18474
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:5773 original size:6 final size:6
Alignment explanation
Indices: 5743--5833 Score: 80
Period size: 6 Copynumber: 15.5 Consensus size: 6
5733 TAAAATTTAT
* * * *
5743 TTTAAA ATTAAA TTT-AT TTTGAA TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * *
5789 TTT-GT TTTAAAA TTTAAA TTTAGA TTTATA TTTAAA TTTAAA TTT
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
5834 TATTGTAAAT
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
5 11 0.16
6 53 0.79
7 3 0.04
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:5804 original size:24 final size:24
Alignment explanation
Indices: 5735--5843 Score: 77
Period size: 24 Copynumber: 4.7 Consensus size: 24
5725 ACCCATTTTA
*
5735 AAATTTAT-TTTAAAATTAAATTT
1 AAATTTATATTTAAATTTAAATTT
* *
5758 -ATTTTGA-ATTTAAATTT-ATTTT
1 AAATTT-ATATTTAAATTTAAATTT
* **
5780 AAATTTAAATTT-GTTTTAAAATTT
1 AAATTTATATTTAAATTT-AAATTT
* *
5804 AAATTTAGATTTATATTTAAATTT
1 AAATTTATATTTAAATTTAAATTT
5828 AAATTT-TATTGTAAAT
1 AAATTTATATT-TAAAT
5844 ATTGAAAGTC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
22 12 0.18
23 20 0.30
24 31 0.47
25 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
AAATTTATATTTAAATTTAAATTT
Found at i:5833 original size:18 final size:17
Alignment explanation
Indices: 5735--5828 Score: 125
Period size: 17 Copynumber: 5.4 Consensus size: 17
5725 ACCCATTTTA
*
5735 AAATTTATTTTAAAATT
1 AAATTTATTTTAAATTT
*
5752 AAATTTATTTTGAATTT
1 AAATTTATTTTAAATTT
5769 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
*
5786 AAATTTGTTTTAAAATTT
1 AAATTTATTTT-AAATTT
* *
5804 AAATTTAGATTTATATTT
1 AAATTTA-TTTTAAATTT
5822 AAATTTA
1 AAATTTA
5829 AATTTTATTG
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
17 41 0.60
18 24 0.35
19 3 0.04
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:5842 original size:18 final size:18
Alignment explanation
Indices: 5731--5843 Score: 97
Period size: 17 Copynumber: 6.1 Consensus size: 18
5721 CTAAACCCAT
*
5731 TTTAAAATTTATTTTAAA
1 TTTAAATTTTATTTTAAA
* *
5749 ATTAAA-TTTATTTTGAA
1 TTTAAATTTTATTTTAAA
5766 TTTAAA-TTTATTTTAAA
1 TTTAAATTTTATTTTAAA
*
5783 TTTAAATTTGT-TTTAAAA
1 TTTAAATTT-TATTTTAAA
5801 TTTAAATTTAGATTTATATTTAAA
1 TTTAAA--T---TTTAT-TTTAAA
*
5825 TTTAAATTTTATTGTAAA
1 TTTAAATTTTATTTTAAA
5843 T
1 T
5844 ATTGAAAGTC
Statistics
Matches: 79, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
17 31 0.39
18 25 0.32
19 6 0.08
20 1 0.01
22 2 0.03
23 3 0.04
24 11 0.14
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
TTTAAATTTTATTTTAAA
Found at i:7749 original size:30 final size:29
Alignment explanation
Indices: 7713--8042 Score: 212
Period size: 30 Copynumber: 11.2 Consensus size: 29
7703 TAGAAATCAT
7713 ATTTTGACCCCTCGAACTTTCCAAAATTCC
1 ATTTTGA-CCCTCGAACTTTCCAAAATTCC
** * **
7743 ATTTTGA-CCTCGATTTTTTTCAAAAATTAT
1 ATTTTGACCCTCGA--ACTTTCCAAAATTCC
7773 ATTTT-ACCCTCGAACTTTCCAAAATTCC
1 ATTTTGACCCTCGAACTTTCCAAAATTCC
* * ** **
7801 ATTTTTAATCCT-GATTTTTCCAAAAATTAT
1 A-TTTTGACCCTCGAACTTTCC-AAAATTCC
* *
7831 ATTTTTACCCTCAAACTTTCCAAAATTCC
1 ATTTTGACCCTCGAACTTTCCAAAATTCC
*
7860 ATTTTTGA-CCTCG-ATTTTCCAAAATTACC
1 A-TTTTGACCCTCGAACTTTCCAAAATT-CC
* *
7889 ATTTT-ACCCCCGAAC-TTCCAAAAAATACC
1 ATTTTGACCCTCGAACTTTCC--AAAATTCC
* * ** **
7918 ATTTTTAACCTCGATTTTTCCAAAAATTAT
1 ATTTTGACCCTCGAACTTTCC-AAAATTCC
* * *
7948 ATTTTTACCCTCGAATTTTTCAAAAATTCC
1 ATTTTGACCCTCGAA-CTTTCCAAAATTCC
7978 ATTTTTGA-CCTCGAACTTTCCCAAAATTACC
1 A-TTTTGACCCTCGAACTTT-CCAAAATT-CC
* *
8009 ATTTT-ACCCTCGAA-TATCCAAAATTATC
1 ATTTTGACCCTCGAACTTTCCAAAATT-CC
8037 ATTTTG
1 ATTTTG
8043 GCCCCGGATA
Statistics
Matches: 234, Mismatches: 45, Indels: 43
0.73 0.14 0.13
Matches are distributed among these distances:
27 1 0.00
28 56 0.24
29 48 0.21
30 112 0.48
31 17 0.07
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.40
Consensus pattern (29 bp):
ATTTTGACCCTCGAACTTTCCAAAATTCC
Found at i:7973 original size:60 final size:58
Alignment explanation
Indices: 7706--8033 Score: 380
Period size: 58 Copynumber: 5.6 Consensus size: 58
7696 AACTGTCTAG
* *
7706 AAATCATATTTTGACCCCTCGAACTTTCCAAAATTCCA-TTTTGACCTCGATTTTTTTCAA
1 AAATTATATTTT-A-CCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGA-TTTTTCCAA
*
7766 AAATTATATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAATCCT-GATTTTTCCAA
1 AAATTATATTTTACCCTCGAACTTTCCAAAATTCCATTTTTGA-CCTCGATTTTTCCAA
*
7824 AAATTATATTTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCTCGA-TTTTCC-A
1 AAATTATA-TTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTCCAA
* * * *
7881 AAATTACCATTTTACCCCCGAAC-TTCCAAAAAATACCATTTTTAACCTCGATTTTTCCAA
1 AAATTA-TATTTTACCCTCGAACTTTCC--AAAATTCCATTTTTGACCTCGATTTTTCCAA
* * ** *
7941 AAATTATATTTTTACCCTCGAATTTTTCAAAAATTCCATTTTTGACCTCGAACTTTCCCA
1 AAATTATA-TTTTACCCTCGAA-CTTTCCAAAATTCCATTTTTGACCTCGATTTTTCCAA
* *
8001 AAATTACCATTTTACCCTCGAA-TATCCAAAATT
1 AAATTA-TATTTTACCCTCGAACTTTCCAAAATT
8034 ATCATTTTGG
Statistics
Matches: 233, Mismatches: 22, Indels: 28
0.82 0.08 0.10
Matches are distributed among these distances:
56 4 0.02
57 19 0.08
58 78 0.33
59 50 0.21
60 78 0.33
61 1 0.00
62 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (58 bp):
AAATTATATTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTCCAA
Found at i:8060 original size:117 final size:115
Alignment explanation
Indices: 7706--8041 Score: 394
Period size: 117 Copynumber: 2.9 Consensus size: 115
7696 AACTGTCTAG
* * * *
7706 AAATCATATTTTGACCCCTCGAACTTTCCAAAATTCCA-TTTTGACCTCGATTTTTTTCAAAAAT
1 AAATTATATTTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGA--ATTTTCCAAAAT
* * *
7770 TA-TATTTTACCCTCGAACTTTCCAAAATT-CCATTTTTAATCCTGATTTTTCCAA
63 TACCATTTTACCCTCGAAC-TTCCAAAATTACCA-TTTTAACCCCGA-TTTTCCAA
*
7824 AAATTATATTTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCTCG-ATTTTCCAAAATTAC
1 AAATTATATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGAATTTTCCAAAATTAC
* * *
7888 CATTTTACCCCCGAACTTCCAAAAAATACCATTTTTAACCTCGATTTTTCCAA
66 CATTTTACCCTCGAACTTCC-AAAATTACCA-TTTTAACCCCGA-TTTTCCAA
* * *
7941 AAATTATATTTTTACCCTCGAATTTTTCAAAAATTCCATTTTTGACCTCGAACTTTCCCAAAATT
1 AAATTATATTTTTACCCTCGAA-CTTTCCAAAATTCCATTTTTGACCTCGAA-TTTTCCAAAATT
*
8006 ACCATTTTACCCTCGAA-TATCCAAAATTATCATTTT
64 ACCATTTTACCCTCGAACT-TCCAAAATTACCATTTT
8042 GGCCCCGGAT
Statistics
Matches: 192, Mismatches: 18, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
115 16 0.08
116 19 0.10
117 65 0.34
118 52 0.27
119 10 0.05
120 30 0.16
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (115 bp):
AAATTATATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGAATTTTCCAAAATTAC
CATTTTACCCTCGAACTTCCAAAATTACCATTTTAACCCCGATTTTCCAA
Found at i:8445 original size:98 final size:98
Alignment explanation
Indices: 8272--8461 Score: 267
Period size: 98 Copynumber: 1.9 Consensus size: 98
8262 AAAAAATTTA
* * *
8272 AAATCGAGGCAATATTATTTTATTTCGAGTTTTAAAAATTTGTGCCTTAACTTACTAGGTGCAAT
1 AAATCGAGGCAATATTATTTTATCTCGAATTTTAAAAATTCGTGCCTTAACTTACTAGGTGCAAT
*
8337 TTTTCCTCAAATCGATATAATCAAATACCCTCT
66 TTTTCCTCAAATCGAGATAATCAAATACCCTCT
* * *
8370 AAATCGAGGCAATGTT-TCTTTATCTCTAATTTTGAAAATTCGTGCCTTAACTTACTAGGTGCGA
1 AAATCGAGGCAATATTAT-TTTATCTCGAATTTTAAAAATTCGTGCCTTAACTTACTAGGTGC-A
* *
8434 A-TTTTCTTCAAATCGAGATAATCGAATA
64 ATTTTTCCTCAAATCGAGATAATCAAATA
8462 TCCTTTTCCA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
97 1 0.01
98 78 0.96
99 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (98 bp):
AAATCGAGGCAATATTATTTTATCTCGAATTTTAAAAATTCGTGCCTTAACTTACTAGGTGCAAT
TTTTCCTCAAATCGAGATAATCAAATACCCTCT
Found at i:14722 original size:35 final size:36
Alignment explanation
Indices: 14683--14756 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 36
14673 CTAAACCCAT
*
14683 TTTAAAATTTATTTT-GAATTTAAACTT-ATCTTAAA
1 TTTAAAATTTATTTTAAAATTTAAACTTAAT-TTAAA
* *
14718 TTT-AAATTTGTTTTAAAATTTAAATTTAATTTAAA
1 TTTAAAATTTATTTTAAAATTTAAACTTAATTTAAA
14753 TTTA
1 TTTA
14757 GATTTAGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
34 10 0.30
35 21 0.64
36 2 0.06
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (36 bp):
TTTAAAATTTATTTTAAAATTTAAACTTAATTTAAA
Found at i:14724 original size:6 final size:6
Alignment explanation
Indices: 14713--14781 Score: 70
Period size: 6 Copynumber: 11.5 Consensus size: 6
14703 TAAACTTATC
** *
14713 TTAAAT TTAAAT TT-GTT TTAAAAT TTAAAT TT-AAT TTAAAT TTAGAT
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
14760 TTAGAT TTAAAT TTAAAAT TTA
1 TTAAAT TTAAAT TT-AAAT TTA
14782 TTATAAATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
5 8 0.15
6 36 0.68
7 9 0.17
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:14749 original size:29 final size:29
Alignment explanation
Indices: 14716--14775 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
14706 ACTTATCTTA
*
14716 AATTTAAATTT-GTTTTAAAATTTAAATTT
1 AATTTAAATTTAGATTT-AAATTTAAATTT
*
14745 AATTTAAATTTAGATTTAGATTTAAATTT
1 AATTTAAATTTAGATTTAAATTTAAATTT
14774 AA
1 AA
14776 AATTTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (29 bp):
AATTTAAATTTAGATTTAAATTTAAATTT
Found at i:14772 original size:35 final size:34
Alignment explanation
Indices: 14699--14789 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 34
14689 ATTTATTTTG
* *
14699 AATTTAAACTTATCTTAAATTTAAATTTGTTTTAA
1 AATTTAAATTTAT-TTAAATTTAAATTTGATTTAA
*
14734 AATTTAAATTTAATTTAAATTTAGATTTAGATTT-A
1 AATTTAAATTT-ATTTAAATTTAAATTT-GATTTAA
14769 AATTTAAAATTTATTATAAAT
1 AATTT-AAATTTATT-TAAAT
14790 ATTGAAAGTC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
35 32 0.65
36 17 0.35
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (34 bp):
AATTTAAATTTATTTAAATTTAAATTTGATTTAA
Found at i:14788 original size:18 final size:16
Alignment explanation
Indices: 14687--14789 Score: 89
Period size: 17 Copynumber: 5.9 Consensus size: 16
14677 ACCCATTTTA
*
14687 AAATTTATTTTGAATTT
1 AAATTTA-TTTAAATTT
*
14704 AAACTTATCTTAAATTT
1 AAATTTAT-TTAAATTT
*
14721 AAATTTGTTTTAAAATTT
1 AAATTT-ATTT-AAATTT
14739 AAATTTAATTTAAATTT
1 AAATTT-ATTTAAATTT
*
14756 AGATTTAGATTTAAATTT
1 AAATTT--ATTTAAATTT
14774 AAAATTTATTATAAAT
1 -AAATTTATT-TAAAT
14790 ATTGAAAGTC
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
16 1 0.01
17 34 0.48
18 31 0.44
19 5 0.07
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (16 bp):
AAATTTATTTAAATTT
Found at i:16709 original size:30 final size:29
Alignment explanation
Indices: 16673--16831 Score: 117
Period size: 30 Copynumber: 5.4 Consensus size: 29
16663 CATCAATCAT
*
16673 ATTTTGACCCATTGAACTTTCCAAAATTCC
1 ATTTTGACCC-TCGAACTTTCCAAAATTCC
* *
16703 ATTTTGACCCT-G-ATTTTCCAAAAATTAC
1 ATTTTGACCCTCGAACTTTCC-AAAATTCC
* * * * *
16731 ATTTTTACACGCAAACTTTCTAAAATTCC
1 ATTTTGACCCTCGAACTTTCCAAAATTCC
** *
16760 ATTTTTGA-CCTCGATTTTTCCAAAAATTAC
1 A-TTTTGACCCTCGAACTTTCC-AAAATTCC
* **
16790 ATTTTTACCCTCGAATCTTCTAAAAAATTCC
1 ATTTTGACCCTCGAA-CTT-TCCAAAATTCC
16821 ATTTTGACCCT
1 ATTTTGACCCT
16832 GATTTTTCAA
Statistics
Matches: 97, Mismatches: 24, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
27 6 0.06
28 16 0.16
29 21 0.22
30 34 0.35
31 19 0.20
32 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.40
Consensus pattern (29 bp):
ATTTTGACCCTCGAACTTTCCAAAATTCC
Found at i:16779 original size:29 final size:28
Alignment explanation
Indices: 16690--16897 Score: 138
Period size: 29 Copynumber: 7.1 Consensus size: 28
16680 CCCATTGAAC
*
16690 TTTCCAAAATTCCA-TTTTGACCCTGATT
1 TTTCAAAAATTCCATTTTTGACCC-GATT
* * * **
16718 TTCCAAAAATTACATTTTT-ACACGCAAAC
1 TTTCAAAAATTCCATTTTTGAC-C-CGATT
*
16747 TTTCTAAAATTCCATTTTTGACCTCGATT
1 TTTCAAAAATTCCATTTTTGACC-CGATT
*
16776 TTTCCAAAAATTACATTTTT-ACCCTCGAATCT
1 TTT-CAAAAATTCCATTTTTGA-CC-CG-AT-T
* *
16808 TCTAAAAAATTCCA-TTTTGACCCTGATT
1 TTTCAAAAATTCCATTTTTGACCC-GATT
* *
16836 TTTCAAAAAATTACCATTTTT-ACCCCATA
1 TTTC-AAAAATT-CCATTTTTGACCCGATT
*
16865 TGTCTAAAAATTCCATTTTTGACCCTGATT
1 TTTC-AAAAATTCCATTTTTGACCC-GATT
16895 TTT
1 TTT
16898 TTTTAAAAAT
Statistics
Matches: 138, Mismatches: 27, Indels: 28
0.72 0.14 0.15
Matches are distributed among these distances:
28 24 0.17
29 55 0.40
30 40 0.29
31 16 0.12
32 3 0.02
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (28 bp):
TTTCAAAAATTCCATTTTTGACCCGATT
Found at i:16794 original size:59 final size:57
Alignment explanation
Indices: 16695--16897 Score: 259
Period size: 59 Copynumber: 3.5 Consensus size: 57
16685 TGAACTTTCC
*
16695 AAAATTCCATTTTGACCCTGA-TTTTCCAAAAATTACATTTTTACACGCAAACTTTCT-
1 AAAATTCCATTTTGACCCTGATTTTTCCAAAAATTACATTTTTAC-CCCAAA-TTTCTA
*
16752 AAAATTCCATTTTTGA-CCTCGATTTTTCCAAAAATTACATTTTTACCCTCGAATCTTCTAA
1 AAAATTCCA-TTTTGACCCT-GATTTTTCCAAAAATTACATTTTTACCC-CAAAT-TTCT-A
* * *
16813 AAAATTCCATTTTGACCCTGATTTTTCAAAAAATTACCATTTTTACCCCATATGTCTA
1 AAAATTCCATTTTGACCCTGATTTTTCCAAAAATTA-CATTTTTACCCCAAATTTCTA
16871 AAAATTCCATTTTTGACCCTGATTTTT
1 AAAATTCCA-TTTTGACCCTGATTTTT
16898 TTTTAAAAAT
Statistics
Matches: 130, Mismatches: 6, Indels: 18
0.84 0.04 0.12
Matches are distributed among these distances:
57 12 0.09
58 20 0.15
59 50 0.38
60 25 0.19
61 23 0.18
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (57 bp):
AAAATTCCATTTTGACCCTGATTTTTCCAAAAATTACATTTTTACCCCAAATTTCTA
Found at i:16853 original size:30 final size:29
Alignment explanation
Indices: 16695--16897 Score: 146
Period size: 30 Copynumber: 6.9 Consensus size: 29
16685 TGAACTTTCC
*
16695 AAAATTCCATTTTGACCCTGA-TTTTCCA
1 AAAATTCCATTTTGACCCTGATTTTTCAA
* * * ** *
16723 AAAATTACATTTTTACACGC-AAACTTTC-T
1 AAAATTCCATTTTGAC-C-CTGATTTTTCAA
*
16752 AAAATTCCATTTTTGA-CCTCGATTTTTCCA
1 AAAATTCCA-TTTTGACCCT-GATTTTTCAA
* * * *
16782 AAAATTACATTTTTACCCTCGAATCTTCTAA
1 AAAATTCCATTTTGACCCT-GATTTTTC-AA
16813 AAAATTCCATTTTGACCCTGATTTTTCAA
1 AAAATTCCATTTTGACCCTGATTTTTCAA
* * * * *
16842 AAAATTACCATTTTTACCC-CATATGTCTA
1 AAAATT-CCATTTTGACCCTGATTTTTCAA
16871 AAAATTCCATTTTTGACCCTGATTTTT
1 AAAATTCCA-TTTTGACCCTGATTTTT
16898 TTTTAAAAAT
Statistics
Matches: 134, Mismatches: 29, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
27 1 0.01
28 18 0.13
29 48 0.36
30 49 0.37
31 18 0.13
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (29 bp):
AAAATTCCATTTTGACCCTGATTTTTCAA
Found at i:16929 original size:61 final size:59
Alignment explanation
Indices: 16695--17002 Score: 271
Period size: 61 Copynumber: 5.2 Consensus size: 59
16685 TGAACTTTCC
* * * *
16695 AAAATTCCA-TTTTGACCCTGA-TTTTCCAAAAATTA-CATTTTTACACGCAAACTTTCT-
1 AAAATTCCATTTTTGACCCTGATTTTTCAAAAAATTACCATTTTTAC-CCCGAA-TGTCTA
* *
16752 AAAATTCCATTTTTGA-CCTCGATTTTTCCAAAAATTA-CATTTTTACCCTCGAATCTTCTAA
1 AAAATTCCATTTTTGACCCT-GATTTTTCAAAAAATTACCATTTTTACCC-CGAAT-GTCT-A
16813 AAAATTCCA-TTTTGACCCTGATTTTTCAAAAAATTACCATTTTTACCCC-ATATGTCTA
1 AAAATTCCATTTTTGACCCTGATTTTTCAAAAAATTACCATTTTTACCCCGA-ATGTCTA
** *
16871 AAAATTCCATTTTTGACCCTGATTTTTTTTTAAAAATTACCA-TTTTACCTCCGGATGTCTA
1 AAAATTCCATTTTTGACCCTGA--TTTTTCAAAAAATTACCATTTTTACC-CCGAATGTCTA
* ** ** * *
16932 AAAATTCAATTTTTGA-CCTCGA-ACTTCCCAAAATTACCA-TTTTACCCTCGGATATCTA
1 AAAATTCCATTTTTGACCCT-GATTTTTCAAAAAATTACCATTTTTACCC-CGAATGTCTA
*
16990 AAAATTTCATTTT
1 AAAATTCCATTTT
17003 CAACTCCGAT
Statistics
Matches: 218, Mismatches: 16, Indels: 33
0.82 0.06 0.12
Matches are distributed among these distances:
57 13 0.06
58 59 0.27
59 46 0.21
60 35 0.16
61 65 0.30
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (59 bp):
AAAATTCCATTTTTGACCCTGATTTTTCAAAAAATTACCATTTTTACCCCGAATGTCTA
Found at i:16937 original size:29 final size:28
Alignment explanation
Indices: 16901--16995 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 28
16891 GATTTTTTTT
16901 TAAAAATTACCATTTTACCTCCGGATGTC
1 TAAAAATTACCATTTTACCTCCGGAT-TC
* *
16930 TAAAAATT-CAATTTTTGACCT-CGAACTTC
1 TAAAAATTACCA-TTTT-ACCTCCGGA-TTC
**
16959 CCAAAATTACCATTTTACC-CTCGGATATC
1 TAAAAATTACCATTTTACCTC-CGGAT-TC
16988 TAAAAATT
1 TAAAAATT
16996 TCATTTTCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
28 6 0.12
29 38 0.75
30 7 0.14
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (28 bp):
TAAAAATTACCATTTTACCTCCGGATTC
Done.