Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012658.1 Kokia drynarioides strain JFW-HI SEQ_127669, 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: 23800
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:3421 original size:96 final size:96
Alignment explanation
Indices: 3247--3428 Score: 221
Period size: 96 Copynumber: 1.9 Consensus size: 96
3237 AAGGATGTTT
* * *
3247 GATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCAGAATCGAAGA
1 GATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCACAATATTTCAGAACCGAAGA
*
3312 TAAGTAAACATTGCCTCGATTAAGTGTATTC
66 TAAGAAAACATTGCCTCGATTAAGTGTATTC
* *
3343 GATTATTTCGATTTGAAGGAAA-ATTGCACCTAGTGAGTTAAGGCACAA-ATTTTC-GAAACCCG
1 GATTATCTCGATTTGAA-GAAAGATTGCACCTAGTAAGTTAAGGCACAATA-TTTCAG-AA-CCG
*
3405 AA-ATAA-AAGAATATTGCCTCGATT
62 AAGATAAGAA-AACATTGCCTCGATT
3429 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
95 3 0.04
96 63 0.85
97 8 0.11
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.30
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCACAATATTTCAGAACCGAAGA
TAAGAAAACATTGCCTCGATTAAGTGTATTC
Found at i:3737 original size:29 final size:29
Alignment explanation
Indices: 3696--4131 Score: 359
Period size: 29 Copynumber: 14.8 Consensus size: 29
3686 GTTTGGAGTC
*
3696 AAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
3725 -AAAATGGTAATTTTTGGAAGGTTC-GGGGT
1 AAAAATGG-AATTTTTGGAA-GTTCGGGGGT
* ** *
3754 CAAAAATGGGACTTTTTGGAAGTTTAGGGTT
1 -AAAAAT-GGAATTTTTGGAAGTTCGGGGGT
* * ***
3785 AAAAATGGGATTTTTGGAATTTTAAGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
*
3814 -AAAATGGTAATTTTTAGAAGATTC-GGGGT
1 AAAAATGG-AATTTTTGGAAG-TTCGGGGGT
* *
3843 CAAAAATGGGACTTTTTGGAAGTT-TGGGGT
1 -AAAAAT-GGAATTTTTGGAAGTTCGGGGGT
* * * * * *
3873 TAAAATGGGATATTTGGAAGTTTGAGGTT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
*
3902 AAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
*
3931 -AAAATGGTAATTTTTGGAAGGTTCGGGGTT
1 AAAAATGG-AATTTTTGGAA-GTTCGGGGGT
*
3961 AAAAATGATAATTTTTGGAAGGTTC-GGGGT
1 AAAAATG-GAATTTTTGGAA-GTTCGGGGGT
* * *
3991 TAAAATGGGATTTTTGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
* *
4020 -AAAATGGTAATTTTTGGAAGGTTTGGGGTT
1 AAAAATGG-AATTTTTGGAA-GTTCGGGGGT
* * *
4050 AAAAATGGGATTTTTAGAAGTTCAGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
* *
4079 -AAAATGGTAATTTTTAGAAGGTTCGGGGTT
1 AAAAATGG-AATTTTTGGAA-GTTCGGGGGT
*
4109 AAAAATGGGATTTTTTGGAAGTT
1 AAAAAT-GGAATTTTTGGAAGTT
4132 TAGGGACCTC
Statistics
Matches: 334, Mismatches: 48, Indels: 49
0.77 0.11 0.11
Matches are distributed among these distances:
28 51 0.15
29 130 0.39
30 70 0.21
31 77 0.23
32 6 0.02
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGGT
Found at i:3760 original size:59 final size:59
Alignment explanation
Indices: 3658--4131 Score: 459
Period size: 59 Copynumber: 8.0 Consensus size: 59
3648 TCCGGATGCA
* * *
3658 CGGGGGT-AAAATGGT-AGTTTTGAAGAAGGTTTGGAGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAAATGGTAATTTTTG--GAAGGTTCGGGGT-AAAAATGGGATTTTTGGAAGTT
3718 CGGGGGT-AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGACTTTTTGGAAGTT
1 CGGGGGTAAAAATGGTAATTTTTGGAAGGTTCGGGGT-AAAAATGGGA-TTTTTGGAAGTT
** * * ** ** * *
3778 TAGGGTTAAAAATGG-GATTTTTGGAATTTTAAGGGT-AAAATGGTAATTTTTAGAAGATT
1 CGGGGGTAAAAATGGTAATTTTTGGAAGGTTCGGGGTAAAAATGG-GATTTTTGGAAG-TT
* * * * *
3837 C-GGGGTCAAAAATGGGACTTTTTGGAA-GTTTGGGGTTAAAATGGGATATTTGGAAGTT
1 CGGGGGT-AAAAATGGTAATTTTTGGAAGGTTCGGGGTAAAAATGGGATTTTTGGAAGTT
* * * * *
3895 TGAGGTTAAAAATGG-GATTTTTGGAA-GTTCGGGGGT-AAAATGGTAATTTTTGGAAGGTT
1 CGGGGGTAAAAATGGTAATTTTTGGAAGGTTC-GGGGTAAAAATGG-GATTTTTGGAA-GTT
* * *
3954 CGGGGTTAAAAATGATAATTTTTGGAAGGTTCGGGGTTAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAAATGGTAATTTTTGGAAGGTTCGGGGTAAAAATGGGATTTTTGGAAGTT
* * *
4013 TGGGGGT-AAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAAATGGGATTTTTAGAAGTT
1 CGGGGGTAAAAATGGTAATTTTTGGAAGGTTCGGGG-TAAAAATGGGATTTTTGGAAGTT
* *
4072 CAGGGGT-AAAATGGTAATTTTTAGAAGGTTCGGGGTTAAAAATGGGATTTTTTGGAAGTT
1 CGGGGGTAAAAATGGTAATTTTTGGAAGGTTCGGGG-TAAAAATGGGA-TTTTTGGAAGTT
4132 TAGGGACCTC
Statistics
Matches: 350, Mismatches: 47, Indels: 34
0.81 0.11 0.08
Matches are distributed among these distances:
57 19 0.05
58 70 0.20
59 138 0.39
60 99 0.28
61 24 0.07
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.35
Consensus pattern (59 bp):
CGGGGGTAAAAATGGTAATTTTTGGAAGGTTCGGGGTAAAAATGGGATTTTTGGAAGTT
Found at i:3789 original size:89 final size:88
Alignment explanation
Indices: 3686--4132 Score: 510
Period size: 89 Copynumber: 5.0 Consensus size: 88
3676 TTTGAAGAAG
* *
3686 GTTTGGAGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGG
1 GTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGG
*
3751 GGTCAAAAATGGGACTTTTTGGAA
66 GGT-AAAAATGGGAATTTTTGGAA
* * *** * *
3775 GTTTAGGGTTAAAAATGGGATTTTTGGAATTTTAAGGGTAAAATGGTAATTTTTAGAAGATTCGG
1 GTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGG
*
3840 GGTCAAAAATGGGACTTTTTGGAA
66 GGT-AAAAATGGGAATTTTTGGAA
* * * * *
3864 GTTTGGGGTT-AAAATGGGATATTTGGAAGTTTGAGGTTAAAAATGG-GATTTTTGGAA-GTTCG
1 GTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGT-AAAATGGTAATTTTTGGAAGGTTC-
*
3926 GGGGT-AAAATGGTAATTTTTGGAA
64 GGGGTAAAAATGGGAATTTTTGGAA
* ** * * *
3950 GGTTCGGGGTTAAAAATGATAATTTTTGGAAGGTTCGGGGTTAAAATGG-GATTTTTGGAAGTTT
1 -GTTTGGGGTTAAAAATG-GGATTTTTGGAA-GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTT
* *
4014 GGGGGT-AAAATGGTAATTTTTGGAA
63 CGGGGTAAAAATGGGAATTTTTGGAA
* * *
4039 GGTTTGGGGTTAAAAATGGGATTTTTAGAAGTTCAGGGGTAAAATGGTAATTTTTAGAAGGTTCG
1 -GTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCG
*
4104 GGGTTAAAAATGGGATTTTTTGGAA
65 GGG-TAAAAATGGGAATTTTTGGAA
4129 GTTT
1 GTTT
4133 AGGGACCTCC
Statistics
Matches: 309, Mismatches: 39, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
86 17 0.06
87 27 0.09
88 69 0.22
89 169 0.55
90 27 0.09
ACGTcount: A:0.29, C:0.03, G:0.32, T:0.36
Consensus pattern (88 bp):
GTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGG
GGTAAAAATGGGAATTTTTGGAA
Found at i:4056 original size:206 final size:207
Alignment explanation
Indices: 3660--4131 Score: 632
Period size: 206 Copynumber: 2.3 Consensus size: 207
3650 CGGATGCACG
* * *
3660 GGGGTAAAATGGTAGT-TTTGAAGAAGGTTTG-GAGTCAAAAATGGGATTTTTGGAAGTTCGGGG
1 GGGGTAAAATGGTAATATTT--AGAAGGTTCGAG-GTTAAAAATGGGATTTTTGGAAGTTCGGGG
* * *
3723 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGACTTTTTGGAAGTTTAGGGTTAAA
63 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAGAATTTTTGGAAGTTCAGGGTTAAA
*
3788 AATGGGATTTTTGGAATTTTAAGGGTAAAATGGTAATTTTTAGAAGATTCGGGGTCAAAAATGGG
128 AATGGGATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTAGAAGATTCGGGGTCAAAAATGGG
* *
3853 ACTTTTTGGAAGTT-T
193 A-TTTTTAGAAGTTCA
* * *
3868 GGGGTTAAAATGG-GATATTTGGAA-GTTTGAGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 GGGG-TAAAATGGTAATATTTAGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
3931 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGATAATTTTTGGAAGGTTCGGGGTT-AAA
65 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAGAATTTTTGGAA-GTTCAGGGTTAAAA
** * * * *
3995 ATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAAATGGGA
129 ATGGGATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTAGAAGATTCGGGGTCAAAAATGGGA
4060 TTTTTAGAAGTTCA
194 TTTTTAGAAGTTCA
* *
4074 GGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTTAAAAATGGGATTTTTTGGAAGTT
1 GGGGTAAAATGGTAATATTTAGAAGGTTCGAGGTTAAAAATGGGA-TTTTTGGAAGTT
4132 TAGGGACCTC
Statistics
Matches: 232, Mismatches: 24, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
205 19 0.08
206 155 0.67
207 30 0.13
208 17 0.07
209 11 0.05
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.35
Consensus pattern (207 bp):
GGGGTAAAATGGTAATATTTAGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTA
AAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGAGAATTTTTGGAAGTTCAGGGTTAAAAAT
GGGATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTAGAAGATTCGGGGTCAAAAATGGGATT
TTTAGAAGTTCA
Found at i:5004 original size:12 final size:12
Alignment explanation
Indices: 4987--5013 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4977 AGAAATGTAA
4987 TTTGGACTTTAT
1 TTTGGACTTTAT
4999 TTTGGACTTTAT
1 TTTGGACTTTAT
5011 TTT
1 TTT
5014 TTTTAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.63
Consensus pattern (12 bp):
TTTGGACTTTAT
Found at i:5045 original size:6 final size:6
Alignment explanation
Indices: 5036--5147 Score: 83
Period size: 6 Copynumber: 19.2 Consensus size: 6
5026 TTTTAGCTTC
* * *
5036 ATTTAA ATTTATA A--TAA TTTTAA ATTTGAA A-ATAA ATTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA
* * **
5083 A-TTAA ATTTAA ATTCAA A-ATAA ATTTAA ATTTAA AAATAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
5129 ATTTGAA A-ATAA ATTTAA A
1 ATTT-AA ATTTAA ATTTAA A
5148 GGAAATTTGG
Statistics
Matches: 82, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
4 1 0.01
5 16 0.20
6 57 0.70
7 8 0.10
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:5075 original size:18 final size:17
Alignment explanation
Indices: 5036--5147 Score: 152
Period size: 18 Copynumber: 6.4 Consensus size: 17
5026 TTTTAGCTTC
*
5036 ATTTAAATTTATAATAA
1 ATTTAAATTTAAAATAA
*
5053 TTTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
* *
5071 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
*
5088 ATTTAAATTCAAAATAA
1 ATTTAAATTTAAAATAA
5105 ATTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAATAA
5123 ATTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
5141 ATTTAAA
1 ATTTAAA
5148 GGAAATTTGG
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
17 38 0.46
18 45 0.54
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:8118 original size:28 final size:26
Alignment explanation
Indices: 8063--8160 Score: 81
Period size: 26 Copynumber: 3.6 Consensus size: 26
8053 AAAATAATTT
*
8063 TAAAATAAATATATAAAAATTTTCAA
1 TAAAATAAATATATAAAAATTTTAAA
* *
8089 TAAATTAAATATTTATAAAATTATTAAATA
1 TAAAATAAATATATA-AAAATT-TT-AA-A
*
8119 TTAAAATAAA-ATCATAAATATTTTAAA
1 -TAAAATAAATAT-ATAAAAATTTTAAA
* *
8146 AAAAATTAATATATA
1 TAAAATAAATATATA
8161 TATATGAACA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
26 23 0.40
27 9 0.16
28 4 0.07
29 3 0.05
30 8 0.14
31 10 0.18
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
TAAAATAAATATATAAAAATTTTAAA
Found at i:8129 original size:21 final size:21
Alignment explanation
Indices: 8103--8153 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
8093 TTAAATATTT
8103 ATAAAATTATTAAATA-TTAAA
1 ATAAAATTA-TAAATATTTAAA
*
8124 ATAAAATCATAAATATTTTAAA
1 ATAAAATTATAAATA-TTTAAA
8146 A-AAAATTA
1 ATAAAATTA
8154 ATATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 6 0.23
21 14 0.54
22 6 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAAATTATAAATATTTAAA
Found at i:8159 original size:20 final size:21
Alignment explanation
Indices: 8103--8161 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
8093 TTAAATATTT
* *
8103 ATAAAATTATTAAATATTAAA
1 ATAAAATTAATATATATTAAA
*
8124 ATAAAATCATAA-ATATTTTAAA
1 ATAAAAT--TAATATATATTAAA
8146 A-AAAATTAATATATAT
1 ATAAAATTAATATATAT
8162 ATATGAACAG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
19 3 0.10
20 5 0.16
21 12 0.39
22 9 0.29
23 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAAAATTAATATATATTAAA
Found at i:8161 original size:22 final size:22
Alignment explanation
Indices: 8103--8161 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 22
8093 TTAAATATTT
*
8103 ATAAAATTATTAAATA--TTAAA
1 ATAAAA-TAATAAATATTTTAAA
*
8124 ATAAAATCATAAATATTTTAAA
1 ATAAAATAATAAATATTTTAAA
*
8146 A-AAAATTAATATATAT
1 ATAAAA-TAATAAATAT
8162 ATATGAACAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 7 0.23
21 10 0.32
22 14 0.45
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAAAATAATAAATATTTTAAA
Found at i:16303 original size:20 final size:21
Alignment explanation
Indices: 16260--16303 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
16250 TTTGCATACC
* **
16260 TATAATTTTTAAAAATATTCT
1 TATAATTTTCAAAAATATGAT
16281 TATAATTTTCAAAAATA-GAT
1 TATAATTTTCAAAAATATGAT
16301 TAT
1 TAT
16304 GATATTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (21 bp):
TATAATTTTCAAAAATATGAT
Found at i:17832 original size:21 final size:21
Alignment explanation
Indices: 17794--17844 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
17784 AAAAAAAAAA
17794 CTTTTTTCTTTTGATTTTTATC
1 CTTTTTT-TTTTGATTTTTATC
* *
17816 CTTTTTTTTTT-ACTTTTTTTT
1 CTTTTTTTTTTGA-TTTTTATC
17837 CTTTTTTT
1 CTTTTTTT
17845 CCTTCTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.04
21 18 0.69
22 7 0.27
ACGTcount: A:0.06, C:0.12, G:0.02, T:0.80
Consensus pattern (21 bp):
CTTTTTTTTTTGATTTTTATC
Found at i:20075 original size:58 final size:58
Alignment explanation
Indices: 19880--20132 Score: 221
Period size: 59 Copynumber: 4.3 Consensus size: 58
19870 TGTCCGAGGC
* * * * * *
19880 TAAAATGGTAATTTTAAGGAAAAAAATCGGGATAAAAAATGAAATTTTTAGAAGTTTGGGGG
1 TAAAATGGTAATTTT-AGG--AAAATTAGGG-TCAAAAATGGAATTTTTGGAAGTTTAGGGG
* *
19942 TAAAATGGTAATTTTAGGAAAAAAATAGGGT-TAAAATGGAA-TTTTGGAAAGTTTAGGGG
1 TAAAATGGTAATTTTAGG--AAAATTAGGGTCAAAAATGGAATTTTTGG-AAGTTTAGGGG
*
20001 TAAAATTGTAATTTTTA-GAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTTTAAGGGG
1 TAAAATGGTAA-TTTTAGGAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTTT-AGGGG
* ** * * *
20060 TAAAATGGTTATTTTATAAAAATTAAGGTC-AAAATGGAA-TTTTGTAAAGTTTGGGGGG
1 TAAAATGGTAATTTTAGGAAAATTAGGGTCAAAAATGGAATTTTTG-GAAGTTT-AGGGG
20118 TAAAAAT-GTAATTTT
1 T-AAAATGGTAATTTT
20133 TACAAAGTTT
Statistics
Matches: 167, Mismatches: 16, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
57 15 0.09
58 52 0.31
59 65 0.39
60 6 0.04
61 14 0.08
62 15 0.09
ACGTcount: A:0.42, C:0.01, G:0.24, T:0.34
Consensus pattern (58 bp):
TAAAATGGTAATTTTAGGAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGG
Found at i:20131 original size:30 final size:30
Alignment explanation
Indices: 20097--20202 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 30
20087 GTCAAAATGG
*
20097 AATTTTGTAAAGTTTGGGGGGTAAAAATGT
1 AATTTTGTAAAGTTTGGGGGGTAAAAATAT
* *
20127 AATTTT-TACAAAGTTT-AGGGGTTAAAATAT
1 AATTTTGT--AAAGTTTGGGGGGTAAAAATAT
* *
20157 AATTTTGGAGAAGTTTGGGGGG-CAAAATAT
1 AATTTTGTA-AAGTTTGGGGGGTAAAAATAT
*
20187 AATTTTAGAAAAGTTT
1 AATTTT-GTAAAGTTT
20203 ATGTGCCAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
29 2 0.03
30 48 0.76
31 13 0.21
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
AATTTTGTAAAGTTTGGGGGGTAAAAATAT
Found at i:20134 original size:59 final size:56
Alignment explanation
Indices: 19915--20192 Score: 220
Period size: 59 Copynumber: 4.7 Consensus size: 56
19905 ATCGGGATAA
* * * *
19915 AAAATGAAATTTT-TAGAAGTTTGGGGGTAAAATGGTAATTTTAGGAAAAAAATAGGGTT
1 AAAATGGAATTTTGTA-AAGTTTGGGGGTAAAAT-GTAATTTT--TAAAAAATTAGGGTC
* * *
19974 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATTGTAATTTTTAGAAAATTAGGGTC
1 AAAATGGAATTTTGTAAAGTTTGGGGGTAAAA-TGTAATTTTTAAAAAATTAGGGTC
* * * *
20031 AAAAATGGAATTTT-TGGAAGTTTAAGGGGTAAAATGGTTA-TTTTATAAAAATTAAGGTC
1 -AAAATGGAATTTTGT-AAAGTTT-GGGGGTAAAAT-GTAATTTTTA-AAAAATTAGGGTC
** *
20090 AAAATGGAATTTTGTAAAGTTTGGGGGGTAAAAATGTAATTTTTACAAAGTTTAGGGGTT
1 AAAATGGAATTTTGTAAAGTTT-GGGGGT-AAAATGTAATTTTTA-AAAAATTA-GGGTC
** * * *
20150 AAAATATAATTTTGGAGAAGTTTGGGGGGCAAAATATAATTTT
1 AAAATGGAATTTTGTA-AAGTTT-GGGGGTAAAATGTAATTTT
20193 AGAAAAGTTT
Statistics
Matches: 181, Mismatches: 26, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
57 11 0.06
58 52 0.29
59 76 0.42
60 30 0.17
61 12 0.07
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.35
Consensus pattern (56 bp):
AAAATGGAATTTTGTAAAGTTTGGGGGTAAAATGTAATTTTTAAAAAATTAGGGTC
Found at i:20177 original size:60 final size:57
Alignment explanation
Indices: 19967--20296 Score: 222
Period size: 60 Copynumber: 5.6 Consensus size: 57
19957 AGGAAAAAAA
* ** * *
19967 TAGGGTTAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATTGTAATTTTTAGAAA-AT
1 TAGGGTCAAAATATAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTA-AAAGTT
* *
20024 TAGGGTCAAAA-ATGGAATTTTTGG-AAGTTTAAGGGGT-AAAATGGTTATTTTATAAAA-AT
1 TAGGGTCAAAATAT--AA-TTTTGGAAAGTTT-AGGGGTAAAAAT-GTAATTTT-TAAAAGTT
* ** * *
20083 TAAGGTCAAAATGGAATTTTGTAAAGTTTGGGGGGTAAAAATGTAATTTTTACAAAGTT
1 TAGGGTCAAAATATAATTTTGGAAAGTTT-AGGGGTAAAAATGTAATTTTTA-AAAGTT
* * ** * *
20142 TAGGGGTTAAAATATAATTTTGGAGAAGTTTGGGGGGCAAAATATAATTTTAGAAAAGTT
1 TA-GGGTCAAAATATAATTTTGGA-AAGTTTAGGGGTAAAAATGTAATTTT-TAAAAGTT
* * * * * *
20202 TATGTGCCAAAATGTAATTTTAGAAAAGTTTTA-TGGTAAAAATGTAATTTTGGAAAAGTT
1 TA-GGGTCAAAATATAATTTT-GGAAAG-TTTAGGGGTAAAAATGTAATTTT-TAAAAGTT
* *
20262 TAATGGTCAAAATATAATTTTTGGATAGTTTAGGG
1 T-AGGGTCAAAATATAA-TTTTGGAAAGTTTAGGG
20297 TCCTCCAAGG
Statistics
Matches: 213, Mismatches: 41, Indels: 35
0.74 0.14 0.12
Matches are distributed among these distances:
57 17 0.08
58 35 0.16
59 46 0.22
60 98 0.46
61 17 0.08
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.36
Consensus pattern (57 bp):
TAGGGTCAAAATATAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTAAAAGTT
Found at i:20293 original size:30 final size:30
Alignment explanation
Indices: 20136--20282 Score: 143
Period size: 30 Copynumber: 4.9 Consensus size: 30
20126 TAATTTTTAC
** * *
20136 AAAGTTTAGGGGTTAAAATATAATTTTGGA
1 AAAGTTTAATGGTCAAAATATAATTTTAGA
* *** *
20166 GAAGTTTGGGGGGCAAAATATAATTTTAGA
1 AAAGTTTAATGGTCAAAATATAATTTTAGA
* *
20196 AAAGTTT-ATGTGCCAAAATGTAATTTTAGA
1 AAAGTTTAATG-GTCAAAATATAATTTTAGA
* * * *
20226 AAAGTTTTATGGTAAAAATGTAATTTTGGA
1 AAAGTTTAATGGTCAAAATATAATTTTAGA
20256 AAAGTTTAATGGTCAAAATATAATTTT
1 AAAGTTTAATGGTCAAAATATAATTTT
20283 TGGATAGTTT
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
29 1 0.01
30 95 0.96
31 3 0.03
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (30 bp):
AAAGTTTAATGGTCAAAATATAATTTTAGA
Done.