Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014044.1 Kokia drynarioides strain JFW-HI SEQ_129075, 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: 110638
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 17 characters in sequence are not A, C, G, or T
Found at i:5096 original size:2 final size:2
Alignment explanation
Indices: 5091--5116 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5081 TCCGTACATA
5091 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
5117 ATTTTGAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:7686 original size:72 final size:72
Alignment explanation
Indices: 7569--7778 Score: 330
Period size: 72 Copynumber: 2.9 Consensus size: 72
7559 TGCCTTTCAG
* * *
7569 TCTTCGGGTTCTACATTGGGTAACGGGCTCTTCGGAACCTGTAGCAGCTCTTACCCTAGTCTGAA
1 TCTTCGGGTTCTACACTGGGTAACGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
7634 TAGCAGC
66 TAGCAGC
* * * * * * *
7641 TCTTCGGGTTCTACAGTGGTTAATGCGCTCTTCGGAAGCAGTAGCAGCTATTACCCTAGTTTCAA
1 TCTTCGGGTTCTACACTGGGTAACGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
7706 TAGCAGC
66 TAGCAGC
7713 TCTTCGGGTTCTACACTGGGTAACGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
1 TCTTCGGGTTCTACACTGGGTAACGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
7778 T
66 T
7779 CCTGGTTACA
Statistics
Matches: 122, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 122 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (72 bp):
TCTTCGGGTTCTACACTGGGTAACGGGCTCTTCGGAAGCAGTAGCAGCTCTTACCCTAGTCTGAA
TAGCAGC
Found at i:8767 original size:6 final size:6
Alignment explanation
Indices: 8747--8808 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
8737 GTTTACTACC
** * * *
8747 CCAGCT CCCTCT CCAGTT CCAGTT CCAGCT CCAGCT CCAGCT CCCGCT
1 CCAGCT CCAGCT CCAGCT CCAGCT CCAGCT CCAGCT CCAGCT CCAGCT
* *
8795 CCCGTT CCAGCT CC
1 CCAGCT CCAGCT CC
8809 CAATGTCACT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.11, C:0.52, G:0.15, T:0.23
Consensus pattern (6 bp):
CCAGCT
Found at i:8809 original size:18 final size:18
Alignment explanation
Indices: 8747--8809 Score: 81
Period size: 18 Copynumber: 3.5 Consensus size: 18
8737 GTTTACTACC
*
8747 CCAGCTCCCTCTCCAGTT
1 CCAGCTCCCGCTCCAGTT
* * *
8765 CCAGTTCCAGCTCCAGCT
1 CCAGCTCCCGCTCCAGTT
*
8783 CCAGCTCCCGCTCCCGTT
1 CCAGCTCCCGCTCCAGTT
8801 CCAGCTCCC
1 CCAGCTCCC
8810 AATGTCACTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.11, C:0.52, G:0.14, T:0.22
Consensus pattern (18 bp):
CCAGCTCCCGCTCCAGTT
Found at i:8893 original size:108 final size:111
Alignment explanation
Indices: 8704--8976 Score: 435
Period size: 108 Copynumber: 2.5 Consensus size: 111
8694 AACAAGTGAC
*
8704 TGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTACCCCAGCTCCCTCTCCAGTTCCAG
1 TGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTACCCCAGCTCCCTCTCCAATTCCAG
* *
8769 TTCCAGCTCCAGCTCCAGCT-C-CC-GCTCCCGTTCCAGCTCCCAA
66 TTCCAGCTCCAGCTCCAGCTCCTCCAGCTCCAGCTCCAGCTCCCAA
8812 TGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTACCCCAGCTCCCTCTCCAATTCCAG
1 TGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTACCCCAGCTCCCTCTCCAATTCCAG
* *
8877 TTCCAGTTCCAGCTCCAGCTCCAGCTCCAGCTCCAGCTCCCGCTCCCAA
66 TTCCAGCTCCAGCTCCAGCT-C--CTCCAGCTCCAGCTCCAGCTCCCAA
* *
8926 TGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGCTCCAGCTCC
1 TGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTACCCCAGCTCC
8977 AGCTCCCGCT
Statistics
Matches: 152, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
108 83 0.55
112 1 0.01
113 2 0.01
114 66 0.43
ACGTcount: A:0.19, C:0.42, G:0.15, T:0.25
Consensus pattern (111 bp):
TGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTACCCCAGCTCCCTCTCCAATTCCAG
TTCCAGCTCCAGCTCCAGCTCCTCCAGCTCCAGCTCCAGCTCCCAA
Found at i:8923 original size:6 final size:6
Alignment explanation
Indices: 8872--8922 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
8862 CCTCTCCAAT
* * *
8872 TCCAGT TCCAGT TCCAGC TCCAGC TCCAGC TCCAGC TCCAGC TCCCGC
1 TCCAGC TCCAGC TCCAGC TCCAGC TCCAGC TCCAGC TCCAGC TCCAGC
8920 TCC
1 TCC
8923 CAATGTCACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.14, C:0.49, G:0.16, T:0.22
Consensus pattern (6 bp):
TCCAGC
Found at i:8958 original size:114 final size:109
Alignment explanation
Indices: 8704--8976 Score: 440
Period size: 114 Copynumber: 2.5 Consensus size: 109
8694 AACAAGTGAC
8704 TGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTACCCCAGCT-CCCTCTCCAGTTCCA
1 TGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTACCCCAGCTCCCCTCTCCAGTTCCA
* * *
8768 GTTCCAGCTCCAGCTCCAGCTCCCGCTCCCGTTCCAGCTCCCAA
66 GTTCCAGCTCCAGCTCCAGCTCCAGCTCCAGCTCCAGCTCCCAA
8812 TGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTACCCCAGCTCCCTCTCCAATTCCAG
1 TGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTACCCCAGCTCCC-CT-C---TCCAG
*
8877 TTCCAGTTCCAGCTCCAGCTCCAGCTCCAGCTCCAGCTCCCGCTCCCAA
61 TTCCAGTTCCAGCTCCAGCTCCAGCTCCAGCTCCAGCTCCAGCTCCCAA
* *
8926 TGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGCTCCAGCTCC
1 TGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTACCCCAGCTCC
8977 AGCTCCCGCT
Statistics
Matches: 153, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
108 49 0.32
109 2 0.01
110 2 0.01
111 1 0.01
114 99 0.65
ACGTcount: A:0.19, C:0.42, G:0.15, T:0.25
Consensus pattern (109 bp):
TGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTACCCCAGCTCCCCTCTCCAGTTCCA
GTTCCAGCTCCAGCTCCAGCTCCAGCTCCAGCTCCAGCTCCCAA
Found at i:8978 original size:90 final size:89
Alignment explanation
Indices: 8878--9250 Score: 218
Period size: 90 Copynumber: 4.3 Consensus size: 89
8868 CAATTCCAGT
*
8878 TCCAGTTCCAGCTCCAGCTCCAGCTCCAGCTCCAGCTCCCGCTCCCAATGTCACTGACCCACTCA
1 TCCAGCTCCAGCTCCAGCTCCAGCTCCAGCTCCA-CTCCCGCTCCCAATGTCACTGACCCACTCA
8943 GCGATGTACTCCGAATGTTTACTGC
65 GCGATGTACTCCGAATGTTTACTGC
* * * * * *
8968 TCCAGCTCCAGCTCCCGCTCCCGTTGTCA-CTGACCCACTCAGCGACGTACTCCGAATGTTTACT
1 TCCAGCTCCAGCTCCAGCTCCAGCT-CCAGCT---CCACTC--C--CG--CTCCCAATG-TCACT
* *
9032 G-CTCCAGCTC-GC---G--CTCC--A-G-TTCCAGC
55 GAC-CCA-CTCAGCGATGTACTCCGAATGTTTACTGC
* * *
9058 TCCCGCTCTC-GTTCCAGCTCCAGCTCCAGCTCCA-----------ACTGTCACTGACCCACTCA
1 TCCAGCTC-CAGCTCCAGCTCCAGCTCCAGCTCCACTCCCGCTCCCAATGTCACTGACCCACTCA
9111 GCGATGTACTCCGAATGTTTACTGC
65 GCGATGTACTCCGAATGTTTACTGC
* * * * ** * **
9136 TCCAGCTCCCGCTCCCGCTCCAGTTCCAGTTCCAGCTCCAACGCCCGCTGTCACTGACCCACTCA
1 TCCAGCTCCAGCTCCAGCTCCAGCTCCAGCTCCA-CTCCCGCTCCCAATGTCACTGACCCACTCA
9201 GCGATGTACTCCGAATGTTTACTGC
65 GCGATGTACTCCGAATGTTTACTGC
* * *
9226 TCCCGCTCCCGTTCCAGCTCCAGCT
1 TCCAGCTCCAGCTCCAGCTCCAGCT
9251 GTATATAACT
Statistics
Matches: 215, Mismatches: 29, Indels: 78
0.67 0.09 0.24
Matches are distributed among these distances:
68 3 0.01
69 10 0.05
70 4 0.02
72 1 0.00
74 4 0.02
76 1 0.00
77 2 0.01
78 32 0.15
87 3 0.01
89 2 0.01
90 112 0.52
91 4 0.02
92 4 0.02
93 3 0.01
94 5 0.02
96 3 0.01
98 9 0.04
99 10 0.05
100 3 0.01
ACGTcount: A:0.17, C:0.42, G:0.17, T:0.24
Consensus pattern (89 bp):
TCCAGCTCCAGCTCCAGCTCCAGCTCCAGCTCCACTCCCGCTCCCAATGTCACTGACCCACTCAG
CGATGTACTCCGAATGTTTACTGC
Found at i:9048 original size:66 final size:66
Alignment explanation
Indices: 8900--9041 Score: 257
Period size: 66 Copynumber: 2.2 Consensus size: 66
8890 TCCAGCTCCA
*
8900 GCTCCAGCTCCAGCTCCCGCTCCCAATGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTAC
1 GCTCCAGCTCCAGCTCCCGCTCCCAATGTCACTGACCCACTCAGCGACGTACTCCGAATGTTTAC
8965 T
66 T
**
8966 GCTCCAGCTCCAGCTCCCGCTCCCGTTGTCACTGACCCACTCAGCGACGTACTCCGAATGTTTAC
1 GCTCCAGCTCCAGCTCCCGCTCCCAATGTCACTGACCCACTCAGCGACGTACTCCGAATGTTTAC
9031 T
66 T
9032 GCTCCAGCTC
1 GCTCCAGCTC
9042 GCGCTCCAGT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 73 1.00
ACGTcount: A:0.18, C:0.41, G:0.18, T:0.24
Consensus pattern (66 bp):
GCTCCAGCTCCAGCTCCCGCTCCCAATGTCACTGACCCACTCAGCGACGTACTCCGAATGTTTAC
T
Found at i:9065 original size:6 final size:6
Alignment explanation
Indices: 9032--9091 Score: 61
Period size: 6 Copynumber: 10.0 Consensus size: 6
9022 AATGTTTACT
* * *
9032 GCTCCA GCTCGC- GCTCCA GTTCCA GCTCCC GCTCTC- GTTCCA GCTCCA
1 GCTCCA GCTC-CA GCTCCA GCTCCA GCTCCA GCTC-CA GCTCCA GCTCCA
9080 GCTCCA GCTCCA
1 GCTCCA GCTCCA
9092 ACTGTCACTG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
5 2 0.04
6 41 0.91
7 2 0.04
ACGTcount: A:0.12, C:0.48, G:0.18, T:0.22
Consensus pattern (6 bp):
GCTCCA
Found at i:9065 original size:24 final size:24
Alignment explanation
Indices: 9032--9089 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
9022 AATGTTTACT
*
9032 GCTCCAGCTCGCGCTCCAGTTCCA
1 GCTCCAGCTCGCGCTCCAGCTCCA
* * *
9056 GCTCCCGCTCTCGTTCCAGCTCCA
1 GCTCCAGCTCGCGCTCCAGCTCCA
9080 GCTCCAGCTC
1 GCTCCAGCTC
9090 CAACTGTCAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.10, C:0.48, G:0.19, T:0.22
Consensus pattern (24 bp):
GCTCCAGCTCGCGCTCCAGCTCCA
Found at i:9138 original size:78 final size:81
Alignment explanation
Indices: 9056--9250 Score: 252
Period size: 84 Copynumber: 2.3 Consensus size: 81
9046 TCCAGTTCCA
*
9056 GCTCCCGCTCTCGTTCCAGCTCCAGCTCCAGCTCCAA-CTGTCACTGACCCACTCAGCGATGTAC
1 GCTCCCGCTCCCGTTCCAGCTCCAGCTCCAGCTCCAACCTGTCACTGACCCACTCAGCGATGTAC
9120 TCCGAATGTTTACTGCTCC
66 TCCGAATGTTTAC--CT-C
* * *
9139 AGCTCCCGCTCCCGCTCCAGTTCCAGTTCCAGCTCCAACGCCCGCTGTCACTGACCCACTCAGCG
1 -GCTCCCGCTCCCGTTCCAGCTCCAGCTCCAGCTCCAA----C-CTGTCACTGACCCACTCAGCG
9204 ATGTACTCCGAATGTTTA-CT-
60 ATGTACTCCGAATGTTTACCTC
9224 GCTCCCGCTCCCGTTCCAGCTCCAGCT
1 GCTCCCGCTCCCGTTCCAGCTCCAGCT
9251 GTATATAACT
Statistics
Matches: 98, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
84 57 0.58
87 2 0.02
90 39 0.40
ACGTcount: A:0.16, C:0.43, G:0.17, T:0.24
Consensus pattern (81 bp):
GCTCCCGCTCCCGTTCCAGCTCCAGCTCCAGCTCCAACCTGTCACTGACCCACTCAGCGATGTAC
TCCGAATGTTTACCTC
Found at i:9149 original size:102 final size:99
Alignment explanation
Indices: 8968--9250 Score: 352
Period size: 102 Copynumber: 2.9 Consensus size: 99
8958 TGTTTACTGC
* *
8968 TCCAGCTCCAGCTCCCGCTCCCGTTGTCACTGACCCACTCAGCGACGTACTCCGAATGTTTACTG
1 TCCAGCTCCAGCT-CCGCT-CCGCTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTG
* *
9033 CTCCAGCTCGCGCTCCAGTTCCAGCTCCCGCTCTC-GT
64 CTCCAGCTCCCGCTCCAG-TCCAGCTCCAGCTC-CAGT
*
9070 TCCAGCTCCAGCTCCAGCTCCAACTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTG
1 TCCAGCTCCAGCTCC-GCTCC-GCTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTG
*
9135 CTCCAGCTCCCGCT-C---CC-GCTCCAGTTCCAGT
64 CTCCAGCTCCCGCTCCAGTCCAGCTCCAGCTCCAGT
*
9166 TCCAGCTCCA---ACGC-CCGCTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGCT
1 TCCAGCTCCAGCTCCGCTCCGCTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGCT
* *
9227 CCCGCTCCCGTTCCAGCTCCAGCT
66 CCAGCTCCCGCTCCAG-TCCAGCT
9251 GTATATAACT
Statistics
Matches: 162, Mismatches: 10, Indels: 24
0.83 0.05 0.12
Matches are distributed among these distances:
90 54 0.33
91 3 0.02
92 2 0.01
93 1 0.01
95 3 0.02
96 23 0.14
97 2 0.01
101 5 0.03
102 69 0.43
ACGTcount: A:0.16, C:0.42, G:0.18, T:0.24
Consensus pattern (99 bp):
TCCAGCTCCAGCTCCGCTCCGCTGTCACTGACCCACTCAGCGATGTACTCCGAATGTTTACTGCT
CCAGCTCCCGCTCCAGTCCAGCTCCAGCTCCAGT
Found at i:12645 original size:18 final size:18
Alignment explanation
Indices: 12622--12660 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
12612 TTAATAATGC
12622 TTTTATCTCAAAAATATT
1 TTTTATCTCAAAAATATT
12640 TTTTATCTCAAAAATATT
1 TTTTATCTCAAAAATATT
12658 TTT
1 TTT
12661 AGAAACAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTATCTCAAAAATATT
Found at i:19626 original size:26 final size:25
Alignment explanation
Indices: 19575--19632 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
19565 CACCATAAAT
* * *
19575 AAATAAAATAATAATTTAAGTATCA
1 AAATAAAATAAAAAATTAAATATCA
19600 AAATAAAATAAAAAAATTAAATATCA
1 AAATAAAAT-AAAAAATTAAATATCA
*
19626 AAGTAAA
1 AAATAAA
19633 TTCAAGTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (25 bp):
AAATAAAATAAAAAATTAAATATCA
Found at i:25966 original size:17 final size:16
Alignment explanation
Indices: 25944--25975 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
25934 CGCTAGCGTA
25944 TCTTTTTTCTTTTTTTT
1 TCTTTTTT-TTTTTTTT
25961 TCTTTTTTTTTTTTT
1 TCTTTTTTTTTTTTT
25976 AAGTTGTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
TCTTTTTTTTTTTTTT
Found at i:25967 original size:11 final size:10
Alignment explanation
Indices: 25946--25975 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
25936 CTAGCGTATC
25946 TTTTTTCTTT
1 TTTTTTCTTT
25956 TTTTTTCTTT
1 TTTTTTCTTT
25966 TTTTTT-TTT
1 TTTTTTCTTT
25975 T
1 T
25976 AAGTTGTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.20
10 16 0.80
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:29207 original size:4 final size:4
Alignment explanation
Indices: 29200--29230 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
29190 TATATATATA
29200 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
29231 GATGATCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:49618 original size:6 final size:6
Alignment explanation
Indices: 49607--49645 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
49597 TTCATATCAC
* * *
49607 TTTCAA TTTCAA TTTCAC TTTCAC TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTT
49646 TGATCACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTCAA
Found at i:49626 original size:18 final size:18
Alignment explanation
Indices: 49603--49641 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
49593 ACAATTCATA
49603 TCACTTTCAATTTCAATT
1 TCACTTTCAATTTCAATT
* *
49621 TCACTTTCACTTTCACTT
1 TCACTTTCAATTTCAATT
49639 TCA
1 TCA
49642 ATTTTGATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTTCAATT
Found at i:49628 original size:12 final size:12
Alignment explanation
Indices: 49607--49645 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
49597 TTCATATCAC
*
49607 TTTCAATTTCAA
1 TTTCACTTTCAA
*
49619 TTTCACTTTCAC
1 TTTCACTTTCAA
49631 TTTCACTTTCAA
1 TTTCACTTTCAA
49643 TTT
1 TTT
49646 TGATCACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTCACTTTCAA
Found at i:56756 original size:45 final size:45
Alignment explanation
Indices: 56705--56850 Score: 129
Period size: 45 Copynumber: 3.2 Consensus size: 45
56695 ATTTTCGTTG
* *
56705 ATTTTCATTGGTATCTCATTCACATTTCTGTGATTATGGAAGATC
1 ATTTTCATTTGTATCTCATTCACATTTCTGTGATTATAGAAGATC
* * * *** * *
56750 ATTTTCATTTGTATCTGCAGT-AAATTTAT-T-ACTTTATTTTCA-TTG
1 ATTTTCATTTGTATCT-CATTCACATTTCTGTGA--TTA-TAGAAGATC
56795 ATTTTCATTTGTATCTCATTCACATTTCTGTGATTATAGAAGATC
1 ATTTTCATTTGTATCTCATTCACATTTCTGTGATTATAGAAGATC
56840 ATTTTCTATTT
1 ATTTTC-ATTT
56851 CTCTATTTAT
Statistics
Matches: 75, Mismatches: 17, Indels: 17
0.69 0.16 0.16
Matches are distributed among these distances:
43 1 0.01
44 6 0.08
45 57 0.76
46 10 0.13
47 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.51
Consensus pattern (45 bp):
ATTTTCATTTGTATCTCATTCACATTTCTGTGATTATAGAAGATC
Found at i:56824 original size:90 final size:91
Alignment explanation
Indices: 56671--56850 Score: 317
Period size: 90 Copynumber: 2.0 Consensus size: 91
56661 TATATAATGT
*
56671 TATCTGCAGTAAATTCATTACTTTATTTTCGTTGATTTTCATTGGTATCTCATTCACATTTCTGT
1 TATCTGCAGTAAATTCATTACTTTATTTTCATTGATTTTCATTGGTATCTCATTCACATTTCTGT
*
56736 GATTATGGAAGATCATTTTC-ATTTG
66 GATTATAGAAGATCATTTTCTATTTG
* *
56761 TATCTGCAGTAAATTTATTACTTTATTTTCATTGATTTTCATTTGTATCTCATTCACATTTCTGT
1 TATCTGCAGTAAATTCATTACTTTATTTTCATTGATTTTCATTGGTATCTCATTCACATTTCTGT
56826 GATTATAGAAGATCATTTTCTATTT
66 GATTATAGAAGATCATTTTCTATTT
56851 CTCTATTTAT
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
90 81 0.95
91 4 0.05
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (91 bp):
TATCTGCAGTAAATTCATTACTTTATTTTCATTGATTTTCATTGGTATCTCATTCACATTTCTGT
GATTATAGAAGATCATTTTCTATTTG
Found at i:61126 original size:28 final size:28
Alignment explanation
Indices: 61095--61152 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
61085 TTTTTGTACT
61095 ATTAAAAAATGATATGATTAATGAAATA
1 ATTAAAAAATGATATGATTAATGAAATA
61123 ATTAAAAAATGATATGATTAATGAAATA
1 ATTAAAAAATGATATGATTAATGAAATA
61151 AT
1 AT
61153 CAGACATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (28 bp):
ATTAAAAAATGATATGATTAATGAAATA
Found at i:61142 original size:16 final size:16
Alignment explanation
Indices: 61095--61143 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
61085 TTTTTGTACT
61095 ATTAAAAAATGATATG
1 ATTAAAAAATGATATG
* *
61111 ATT----AATGAAATA
1 ATTAAAAAATGATATG
61123 ATTAAAAAATGATATG
1 ATTAAAAAATGATATG
61139 ATTAA
1 ATTAA
61144 TGAAATAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
12 10 0.40
16 15 0.60
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (16 bp):
ATTAAAAAATGATATG
Found at i:86796 original size:76 final size:76
Alignment explanation
Indices: 86670--86812 Score: 243
Period size: 76 Copynumber: 1.9 Consensus size: 76
86660 TAAAAAGCTG
*
86670 AAAATCAGGAGGACAAATCTGATTTGTCATTCTCTTATTGGAAAAGGATAGGGATGACATGAAAT
1 AAAATCAGGAGGAAAAATCTGATTTGTCATTCTCTTATTGGAAAAGGATAGGGATGACATGAAAT
86735 CAAGGTTTCAT
66 CAAGGTTTCAT
* *
86746 AAAATCAGGAGGAAAAATCTGATTTGTCATTCAT-TTATTGGAAAGGGATAGGGATGACATGGAA
1 AAAATCAGGAGGAAAAATCTGATTTGTCATTC-TCTTATTGGAAAAGGATAGGGATGACATGAAA
86810 TCA
65 TCA
86813 CAATCTCATA
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
76 62 0.98
77 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (76 bp):
AAAATCAGGAGGAAAAATCTGATTTGTCATTCTCTTATTGGAAAAGGATAGGGATGACATGAAAT
CAAGGTTTCAT
Found at i:88447 original size:3 final size:3
Alignment explanation
Indices: 88439--88468 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
88429 TCCCCATACT
88439 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
88469 AGAACACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:97369 original size:29 final size:30
Alignment explanation
Indices: 97327--97404 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
97317 GAATTGCATC
*
97327 AAATCAAGATTTCATGTATAAAATTACACA-
1 AAATCAA-AGTTCATGTATAAAATTACACAT
* * * * *
97357 AAATCAAAGTTCATATATACAGTTGCATATT
1 AAATCAAAGTTCATGTATAAAATTACACA-T
97388 AAATCAAAGTTCATGTA
1 AAATCAAAGTTCATGTA
97405 CAGTTTTGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 16 0.41
30 7 0.18
31 16 0.41
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.32
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTACACAT
Found at i:97822 original size:31 final size:31
Alignment explanation
Indices: 97755--97822 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
97745 ATTTAATAGA
* *
97755 GAGTGATCAAAATAAAATTCATCTAAAATGT
1 GAGTGATCAAAATAAAATTCACCTAAAACGT
* *
97786 GAGTGATCAAAATAGACATT-ACCTAAGACGT
1 GAGTGATCAAAATA-AAATTCACCTAAAACGT
*
97817 TAGTGA
1 GAGTGA
97823 CTAAATTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (31 bp):
GAGTGATCAAAATAAAATTCACCTAAAACGT
Found at i:98983 original size:26 final size:26
Alignment explanation
Indices: 98948--98997 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
98938 ATGAACAACA
*
98948 ACGAGAAAAGATCGTATGAAATAATG
1 ACGAAAAAAGATCGTATGAAATAATG
*
98974 ACGAAAAAAGATTGTATGAAATAA
1 ACGAAAAAAGATCGTATGAAATAA
98998 ATATATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (26 bp):
ACGAAAAAAGATCGTATGAAATAATG
Found at i:99733 original size:18 final size:18
Alignment explanation
Indices: 99686--99733 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
99676 GAACATGAAC
* *
99686 CATAAAATAAACATGAAT
1 CATAAAATAAAAAAGAAT
*
99704 AATATAAA-AAAAAAGAAT
1 CATA-AAATAAAAAAGAAT
99722 CATAAAATAAAA
1 CATAAAATAAAA
99734 TCGATTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.19
Consensus pattern (18 bp):
CATAAAATAAAAAAGAAT
Found at i:100243 original size:15 final size:17
Alignment explanation
Indices: 100222--100262 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
100212 TAATTTTTTA
100222 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
100238 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
100254 AAAATTATA
1 AAAATTATA
100263 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:103042 original size:20 final size:19
Alignment explanation
Indices: 103017--103065 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
103007 AATTATTTAG
103017 TAATTTTTTTCATTTTGTTT
1 TAATTTTTTTCATTTT-TTT
103037 TAATTTTCTTT-ATTTTTTT
1 TAATTTT-TTTCATTTTTTT
*
103056 T-CTTTTTTTC
1 TAATTTTTTTC
103066 GAGTCACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 3 0.12
18 4 0.15
19 4 0.15
20 12 0.46
21 3 0.12
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (19 bp):
TAATTTTTTTCATTTTTTT
Found at i:103133 original size:43 final size:42
Alignment explanation
Indices: 103085--103247 Score: 122
Period size: 43 Copynumber: 4.0 Consensus size: 42
103075 TCGTCGTTAT
* * * *
103085 TTCCAATCTCTACCGTCATTATCTTTCCTCTCACTCCTCACCA
1 TTCCAAGCTCCACCATCATTCTCTTTCCTCTCACTCCTCA-CA
* ** * **
103128 TTCCAAGCTCCACCATCATTCTCTTT--TCT--GTTGTTATG
1 TTCCAAGCTCCACCATCATTCTCTTTCCTCTCACTCCTCACA
** * *
103166 TT-CAATTTCTACCGTCATTGC-CTTTCCTCTCACTCCTCAACA
1 TTCCAAGCTCCACCATCATT-CTCTTTCCTCTCACTCCTC-ACA
*
103208 TTCCAAGCTCCACCATCATTCTCTTTCCTGTCACTCCTCA
1 TTCCAAGCTCCACCATCATTCTCTTTCCTCTCACTCCTCA
103248 TCGTTGATCT
Statistics
Matches: 87, Mismatches: 25, Indels: 17
0.67 0.19 0.13
Matches are distributed among these distances:
37 17 0.20
38 3 0.03
39 6 0.07
41 5 0.06
42 5 0.06
43 51 0.59
ACGTcount: A:0.18, C:0.38, G:0.06, T:0.39
Consensus pattern (42 bp):
TTCCAAGCTCCACCATCATTCTCTTTCCTCTCACTCCTCACA
Found at i:103213 original size:80 final size:80
Alignment explanation
Indices: 103080--103238 Score: 257
Period size: 80 Copynumber: 2.0 Consensus size: 80
103070 CACTATCGTC
* *
103080 GTTATTTCCAATCTCTACCGTCATTATCTTTCCTCTCACTCCTCACCATTCCAAGCTCCACCATC
1 GTTATTTCCAATCTCTACCGTCATTACCTTTCCTCTCACTCCTCAACATTCCAAGCTCCACCATC
*
103145 ATTCTCTTTTCTGTT
66 ATTCTCTTTCCTGTT
* *
103160 GTTATGTT-CAATTTCTACCGTCATTGCCTTTCCTCTCACTCCTCAACATTCCAAGCTCCACCAT
1 GTTAT-TTCCAATCTCTACCGTCATTACCTTTCCTCTCACTCCTCAACATTCCAAGCTCCACCAT
103224 CATTCTCTTTCCTGT
65 CATTCTCTTTCCTGT
103239 CACTCCTCAT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
80 71 0.97
81 2 0.03
ACGTcount: A:0.18, C:0.36, G:0.06, T:0.40
Consensus pattern (80 bp):
GTTATTTCCAATCTCTACCGTCATTACCTTTCCTCTCACTCCTCAACATTCCAAGCTCCACCATC
ATTCTCTTTCCTGTT
Found at i:107253 original size:82 final size:82
Alignment explanation
Indices: 107116--107348 Score: 466
Period size: 82 Copynumber: 2.8 Consensus size: 82
107106 AGGTTATTAA
107116 TGCTACATATGAAACCAAAATTACGTTGAAGAATCAACAACAGGCAACGTCAACGTCATGGCCAT
1 TGCTACATATGAAACCAAAATTACGTTGAAGAATCAACAACAGGCAACGTCAACGTCATGGCCAT
107181 CGGCGGGCAGGGTCATC
66 CGGCGGGCAGGGTCATC
107198 TGCTACATATGAAACCAAAATTACGTTGAAGAATCAACAACAGGCAACGTCAACGTCATGGCCAT
1 TGCTACATATGAAACCAAAATTACGTTGAAGAATCAACAACAGGCAACGTCAACGTCATGGCCAT
107263 CGGCGGGCAGGGTCATC
66 CGGCGGGCAGGGTCATC
107280 TGCTACATATGAAACCAAAATTACGTTGAAGAATCAACAACAGGCAACGTCAACGTCATGGCCAT
1 TGCTACATATGAAACCAAAATTACGTTGAAGAATCAACAACAGGCAACGTCAACGTCATGGCCAT
107345 CGGC
66 CGGC
107349 CGCCGGCTGT
Statistics
Matches: 151, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 151 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.18
Consensus pattern (82 bp):
TGCTACATATGAAACCAAAATTACGTTGAAGAATCAACAACAGGCAACGTCAACGTCATGGCCAT
CGGCGGGCAGGGTCATC
Found at i:107612 original size:23 final size:22
Alignment explanation
Indices: 107581--107628 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
107571 ATAAATGAAT
107581 TTTAATTTTATAT-AATTAAATA
1 TTTAATTTTAT-TCAATTAAATA
*
107603 TTTAATTTTTATTCAATTATATA
1 TTTAA-TTTTATTCAATTAAATA
107626 TTT
1 TTT
107629 TTAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTAATTTTATTCAATTAAATA
Done.