Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013703.1 Kokia drynarioides strain JFW-HI SEQ_128731, 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: 82223
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1330 original size:43 final size:43
Alignment explanation
Indices: 1248--1332 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
1238 ATTAACATGT
* *
1248 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
1291 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
1333 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:1963 original size:45 final size:45
Alignment explanation
Indices: 1899--2035 Score: 202
Period size: 45 Copynumber: 3.0 Consensus size: 45
1889 GGATAGCTCA
*
1899 TCAAGCCAAGGATATCAGCCTTAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* * *
1944 TCAAGCCATGGATATCAGCCTCAATTTGACGACCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
** * *
1989 TCAAGGGAAGGATATCAGTCTGAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
2034 TC
1 TC
2036 TATTCCTCCC
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 81 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:5849 original size:4 final size:4
Alignment explanation
Indices: 5840--5912 Score: 71
Period size: 4 Copynumber: 18.2 Consensus size: 4
5830 AACGCATTAC
* * *
5840 CTTT CTTT CTTT C-TT CTTT CTTT CCTCT CTTT C-TT CCTT CATTC CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT C-TTT CTTT
5888 CTTT CTTT CTTTT CTTT CTTT -TTT C
1 CTTT CTTT C-TTT CTTT CTTT CTTT C
5913 CCCGTTTATT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
3 9 0.16
4 40 0.69
5 9 0.16
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:5853 original size:8 final size:8
Alignment explanation
Indices: 5840--5912 Score: 71
Period size: 9 Copynumber: 9.1 Consensus size: 8
5830 AACGCATTAC
5840 CTTTCTTT
1 CTTTCTTT
5848 CTTTC-TT
1 CTTTCTTT
5855 CTTTCTTT
1 CTTTCTTT
*
5863 CCTCTCTTT
1 -CTTTCTTT
*
5872 C-TTCCTT
1 CTTTCTTT
*
5879 CATTCCTTT
1 C-TTTCTTT
5888 CTTTCTTT
1 CTTTCTTT
5896 CTTTTCTTT
1 C-TTTCTTT
5905 CTTT-TTT
1 CTTTCTTT
5912 C
1 C
5913 CCCGTTTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
7 16 0.30
8 18 0.33
9 20 0.37
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.68
Consensus pattern (8 bp):
CTTTCTTT
Found at i:5912 original size:20 final size:20
Alignment explanation
Indices: 5840--5905 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
5830 AACGCATTAC
5840 CTTT-CTTTCTTTCTTCTTT
1 CTTTCCTTTCTTTCTTCTTT
* *
5859 CTTTCCTCTCTTTCTTCCTT
1 CTTTCCTTTCTTTCTTCTTT
*
5879 CATTCCTTTCTTTCTTTCTTTT
1 CTTTCCTTTCTTTC-TTC-TTT
5901 CTTTC
1 CTTTC
5906 TTTTTTCCCC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 4 0.11
20 25 0.66
21 3 0.08
22 6 0.16
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.67
Consensus pattern (20 bp):
CTTTCCTTTCTTTCTTCTTT
Found at i:7085 original size:26 final size:26
Alignment explanation
Indices: 7056--7117 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
7046 GATGCTGCTT
*
7056 TTGCTTTTTTTTTTGTTATTGTTTTG
1 TTGCTATTTTTTTTGTTATTGTTTTG
7082 TTGCTATTTTTTTTGTTATTGTTTTG
1 TTGCTATTTTTTTTGTTATTGTTTTG
* *
7108 CTGCTGTTTT
1 TTGCTATTTT
7118 AGTTGTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.05, C:0.06, G:0.16, T:0.73
Consensus pattern (26 bp):
TTGCTATTTTTTTTGTTATTGTTTTG
Found at i:7123 original size:26 final size:26
Alignment explanation
Indices: 7068--7124 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
7058 GCTTTTTTTT
* **
7068 TTGTTATTGTTTTGTTGCTATTTTTT
1 TTGTTATTGTTTTGCTGCTATTTTAG
*
7094 TTGTTATTGTTTTGCTGCTGTTTTAG
1 TTGTTATTGTTTTGCTGCTATTTTAG
7120 TTGTT
1 TTGTT
7125 TTTTTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.07, C:0.05, G:0.19, T:0.68
Consensus pattern (26 bp):
TTGTTATTGTTTTGCTGCTATTTTAG
Found at i:7141 original size:17 final size:17
Alignment explanation
Indices: 7115--7149 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
7105 TTGCTGCTGT
* *
7115 TTTAGTTGTTTTTTTTA
1 TTTAGATGTTATTTTTA
7132 TTTAGATGTTATTTTTA
1 TTTAGATGTTATTTTTA
7149 T
1 T
7150 GTGTTTTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.71
Consensus pattern (17 bp):
TTTAGATGTTATTTTTA
Found at i:8183 original size:14 final size:14
Alignment explanation
Indices: 8150--8213 Score: 57
Period size: 13 Copynumber: 4.9 Consensus size: 14
8140 TTAACTCAAG
*
8150 TTTTTCAAAAGTAC
1 TTTTTCAAAAGCAC
*
8164 --TTTCAAAATCAC
1 TTTTTCAAAAGCAC
8176 TTTTTC-AAAGCAC
1 TTTTTCAAAAGCAC
*
8189 TTTTT-AAAAGTAC
1 TTTTTCAAAAGCAC
*
8202 -ATTTCAAAAGCA
1 TTTTTCAAAAGCA
8214 ATACTAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
12 13 0.32
13 23 0.57
14 4 0.10
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (14 bp):
TTTTTCAAAAGCAC
Found at i:11887 original size:81 final size:81
Alignment explanation
Indices: 11752--11914 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
11742 CAGTCACTGC
11752 ATCTATTCAGGAAGGGATACTGGGTAGGGGGCAAAGCGCTTGTAGAATACCAAATGTACTACTAT
1 ATCTATTCAGGAAGGGATACTGGGTAGGGGGCAAAGCGCTTGTAGAATACCAAATGTACTACTAT
11817 GATGCTGTTCTTCGCT
66 GATGCTGTTCTTCGCT
11833 ATCTATTCAGGAAGGGATACTGGGTAGGGGGCAAAGCGCTTGTAGAATACCAAATGTACTACTAT
1 ATCTATTCAGGAAGGGATACTGGGTAGGGGGCAAAGCGCTTGTAGAATACCAAATGTACTACTAT
11898 GATGCTGTTCTTCGCT
66 GATGCTGTTCTTCGCT
11914 A
1 A
11915 ATACTTTACT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (81 bp):
ATCTATTCAGGAAGGGATACTGGGTAGGGGGCAAAGCGCTTGTAGAATACCAAATGTACTACTAT
GATGCTGTTCTTCGCT
Found at i:15271 original size:4 final size:4
Alignment explanation
Indices: 15262--15294 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
15252 AATTGAATAT
15262 ATTA ATTA ATTA ATTA ATTA ATTA ATT- ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
15295 AATATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:20533 original size:16 final size:16
Alignment explanation
Indices: 20505--20537 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20495 AAATGAAAAT
20505 AGAAAATATGAGAGAAG
1 AGAAAATATGAGA-AAG
20522 AGAAAA-ATGAGAAAG
1 AGAAAATATGAGAAAG
20537 A
1 A
20538 TGTGTATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 6 0.38
17 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (16 bp):
AGAAAATATGAGAAAG
Found at i:25070 original size:23 final size:23
Alignment explanation
Indices: 25038--25091 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
25028 ACGCTAGCGC
*
25038 GCTTATTGTTTCGCA-CTTCGTGT
1 GCTTACTGTTTCGCACCTT-GTGT
25061 GCTTACTGTTTCGCACCTTGTGT
1 GCTTACTGTTTCGCACCTTGTGT
*
25084 GCCTACTG
1 GCTTACTG
25092 ATTTGCGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 25 0.89
24 3 0.11
ACGTcount: A:0.09, C:0.26, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTTACTGTTTCGCACCTTGTGT
Found at i:25141 original size:23 final size:23
Alignment explanation
Indices: 25114--25159 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
25104 TGCGCCTACT
25114 GATTGCACTGCGTGTGCTTATTG
1 GATTGCACTGCGTGTGCTTATTG
*
25137 GATTGCACTGTGTGTGCTTATTG
1 GATTGCACTGCGTGTGCTTATTG
25160 TTTCCCTAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.15, G:0.30, T:0.41
Consensus pattern (23 bp):
GATTGCACTGCGTGTGCTTATTG
Found at i:48069 original size:52 final size:52
Alignment explanation
Indices: 47986--48097 Score: 188
Period size: 52 Copynumber: 2.2 Consensus size: 52
47976 GTAAATAAAG
* * *
47986 AAAAGGTCCGATGATTATGTATCATCGTGAGTATATGAATCCTTTATGGATT
1 AAAAGGTCCGATGACTATGTATCATCATGAGTATATGAATCATTTATGGATT
*
48038 AAAAGGTCCGATGACTATGTGTCATCATGAGTATATGAATCATTTATGGATT
1 AAAAGGTCCGATGACTATGTATCATCATGAGTATATGAATCATTTATGGATT
48090 AAAAGGTC
1 AAAAGGTC
48098 TGAGGATTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (52 bp):
AAAAGGTCCGATGACTATGTATCATCATGAGTATATGAATCATTTATGGATT
Found at i:48121 original size:16 final size:16
Alignment explanation
Indices: 48085--48122 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
48075 AATCATTTAT
*
48085 GGATTAAAAGGTCTGA
1 GGATTAAAAGGTCCGA
48101 GGATTAAAAGGTCCGA
1 GGATTAAAAGGTCCGA
*
48117 TGATTA
1 GGATTA
48123 TGTGTCATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.08, G:0.29, T:0.26
Consensus pattern (16 bp):
GGATTAAAAGGTCCGA
Found at i:48142 original size:68 final size:68
Alignment explanation
Indices: 48033--48168 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 68
48023 AATCCTTTAT
48033 GGATTAAAAGGTCCGATGACTATGTGTCATCATGAGTATATGAATCATTTATGGATTAAAAGGTC
1 GGATTAAAAGGTCCGATGACTATGTGTCATCATGAGTATATGAATCATTTATGGATTAAAAGGTC
48098 TGA
66 TGA
* *
48101 GGATTAAAAGGTCCGATGATTATGTGTCATCGTGAGTATATGAATCATTTATGGATTAAAAGGTC
1 GGATTAAAAGGTCCGATGACTATGTGTCATCATGAGTATATGAATCATTTATGGATTAAAAGGTC
48166 TGA
66 TGA
48169 TGACTATGTG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (68 bp):
GGATTAAAAGGTCCGATGACTATGTGTCATCATGAGTATATGAATCATTTATGGATTAAAAGGTC
TGA
Found at i:48179 original size:52 final size:52
Alignment explanation
Indices: 48101--48243 Score: 189
Period size: 52 Copynumber: 2.8 Consensus size: 52
48091 AAAGGTCTGA
* * * *
48101 GGATTAAAAGGTCCGATGATTATGTGTCATCGTGAGTATATGAATCATTTAT
1 GGATTAAAAGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCATTCAC
* *
48153 GGATTAAAAGGTCTGATGACTATGTGTCATCGTGAGTATATGATTCCTTCAC
1 GGATTAAAAGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCATTCAC
* * *
48205 GGATTAAGAGGT-TCGATGACCATGTGTCATCATGAGTAT
1 GGATTAAAAGGTCT-GATGACTATGTGTCATCGTGAGTAT
48244 TAAATGGAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 1 0.01
52 80 0.99
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (52 bp):
GGATTAAAAGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCATTCAC
Found at i:48209 original size:120 final size:120
Alignment explanation
Indices: 47986--48216 Score: 381
Period size: 120 Copynumber: 1.9 Consensus size: 120
47976 GTAAATAAAG
*
47986 AAAAGGTCCGATGATTATGTATCATCGTGAGTATATGAATCCTTTATGGATTAAAAGGTCCGATG
1 AAAAGGTCCGATGATTATGTATCATCGTGAGTATATGAATCATTTATGGATTAAAAGGTCCGATG
* *
48051 ACTATGTGTCATCATGAGTATATGAATCATTTATGGATTAAAAGGTCTGAGGATT
66 ACTATGTGTCATCATGAGTATATGAATCATTCACGGATTAAAAGGTCTGAGGATT
* *
48106 AAAAGGTCCGATGATTATGTGTCATCGTGAGTATATGAATCATTTATGGATTAAAAGGTCTGATG
1 AAAAGGTCCGATGATTATGTATCATCGTGAGTATATGAATCATTTATGGATTAAAAGGTCCGATG
* * * *
48171 ACTATGTGTCATCGTGAGTATATGATTCCTTCACGGATTAAGAGGT
66 ACTATGTGTCATCATGAGTATATGAATCATTCACGGATTAAAAGGT
48217 TCGATGACCA
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
120 102 1.00
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (120 bp):
AAAAGGTCCGATGATTATGTATCATCGTGAGTATATGAATCATTTATGGATTAAAAGGTCCGATG
ACTATGTGTCATCATGAGTATATGAATCATTCACGGATTAAAAGGTCTGAGGATT
Found at i:48479 original size:21 final size:22
Alignment explanation
Indices: 48439--48479 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
48429 TACCTGTGAA
* *
48439 AACTGTTGTTGTTTGTAGATTT
1 AACTGTTGTTGTTCGAAGATTT
48461 AACT-TTGTTGTTCGAAGAT
1 AACTGTTGTTGTTCGAAGAT
48480 CGGATCATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.49
Consensus pattern (22 bp):
AACTGTTGTTGTTCGAAGATTT
Found at i:50457 original size:115 final size:115
Alignment explanation
Indices: 50255--50476 Score: 363
Period size: 115 Copynumber: 1.9 Consensus size: 115
50245 TAGGCCATTG
* * * * *
50255 GGTTTCAGATGATGGGGACCTTGTCTAATTAGCCACATTGTACTTTTAGGGGCTTTTCAGTTCTT
1 GGTTTCAAATGATGGAGACCTTGTCCAATTAGCCACATCGTACTTTTAGGGGCTTTTCACTTCTT
*
50320 GTGATGGTAATGACACAGATAGGGTCTTGGATATCGTTGATCAGCTTTTA
66 GTGATGGTAATGACACAGATAGGGTCTTAGATATCGTTGATCAGCTTTTA
*
50370 GGTTTCAAATGATGGAGACCTTGTCCAATTAGCCATATCGTACTTTTAGGGGCTTTTCACTTCTT
1 GGTTTCAAATGATGGAGACCTTGTCCAATTAGCCACATCGTACTTTTAGGGGCTTTTCACTTCTT
* *
50435 GTTATGGTAGTGACACAGATAGGGTCTTAGATATCGTTGATC
66 GTGATGGTAATGACACAGATAGGGTCTTAGATATCGTTGATC
50477 GGTGTATTTT
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
115 98 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.37
Consensus pattern (115 bp):
GGTTTCAAATGATGGAGACCTTGTCCAATTAGCCACATCGTACTTTTAGGGGCTTTTCACTTCTT
GTGATGGTAATGACACAGATAGGGTCTTAGATATCGTTGATCAGCTTTTA
Found at i:50801 original size:15 final size:15
Alignment explanation
Indices: 50781--50811 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
50771 TACTGTACAA
50781 GATCATTGCAAATGT
1 GATCATTGCAAATGT
50796 GATCATTGCAAATGT
1 GATCATTGCAAATGT
50811 G
1 G
50812 TTAATGAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (15 bp):
GATCATTGCAAATGT
Found at i:53125 original size:11 final size:11
Alignment explanation
Indices: 53109--53147 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
53099 AGTCAAACCA
*
53109 TTGACCGACTG
1 TTGACCGACCG
53120 TTGACC-AGCCG
1 TTGACCGA-CCG
53131 TTGACCGACCG
1 TTGACCGACCG
53142 TTGACC
1 TTGACC
53148 ATTGACTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 1 0.04
11 23 0.92
12 1 0.04
ACGTcount: A:0.18, C:0.33, G:0.26, T:0.23
Consensus pattern (11 bp):
TTGACCGACCG
Found at i:54265 original size:3 final size:3
Alignment explanation
Indices: 54257--54291 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
54247 ATTTATTTAT
54257 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54292 TTGATTTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:55299 original size:110 final size:110
Alignment explanation
Indices: 55106--55325 Score: 422
Period size: 110 Copynumber: 2.0 Consensus size: 110
55096 AAGGACTAAG
55106 TAGAAATTTAGTTAAAATGAATTAGGAGTCGTCATGGGAATTATAGAGATTAAGGAAGGGCAAGT
1 TAGAAATTTAGTTAAAATGAATTAGGAGTCGTCATGGGAATTATAGAGATTAAGGAAGGGCAAGT
*
55171 GAGTAATTAGCATCGGTGATATTTTTGGAGGGAATGATTTTGGGC
66 GAGTAATTAGCATCGGTGATATTTTTGGAGGCAATGATTTTGGGC
55216 TAGAAATTTAGTTAAAATGAATTAGGAGTCGTCATGGGAATTATAGAGATTAAGGAAGGGCAAGT
1 TAGAAATTTAGTTAAAATGAATTAGGAGTCGTCATGGGAATTATAGAGATTAAGGAAGGGCAAGT
*
55281 GAGTAATTAGCATGGGTGATATTTTTGGAGGCAATGATTTTGGGC
66 GAGTAATTAGCATCGGTGATATTTTTGGAGGCAATGATTTTGGGC
55326 CAAAGTGTAA
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 108 1.00
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.31
Consensus pattern (110 bp):
TAGAAATTTAGTTAAAATGAATTAGGAGTCGTCATGGGAATTATAGAGATTAAGGAAGGGCAAGT
GAGTAATTAGCATCGGTGATATTTTTGGAGGCAATGATTTTGGGC
Found at i:56816 original size:19 final size:22
Alignment explanation
Indices: 56765--56844 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 22
56755 CATTAAGGAA
56765 CACTTGTGTGCCTGCTGTTCAG
1 CACTTGTGTGCCTGCTGTTCAG
*
56787 CACTGTGTGTG-CTTCTGTT-AG
1 CACT-TGTGTGCCTGCTGTTCAG
* *
56808 CACTTTGTGTGTCTACTGTTGCCAG
1 CAC-TTGTGTGCCTGCTGTT--CAG
*
56833 CACTTATGTGCC
1 CACTTGTGTGCC
56845 CTCTGTTAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
21 11 0.23
22 19 0.40
23 6 0.12
24 7 0.15
25 5 0.10
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (22 bp):
CACTTGTGTGCCTGCTGTTCAG
Found at i:58826 original size:19 final size:20
Alignment explanation
Indices: 58786--58831 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
58776 TTAATACTTA
58786 TTATTAAATAAATTACATAAT
1 TTATT-AATAAATTACATAAT
*
58807 TTATTAATATATTA-ATAAT
1 TTATTAATAAATTACATAAT
58826 TTATTA
1 TTATTA
58832 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 11 0.46
20 8 0.33
21 5 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTAATAAATTACATAAT
Found at i:58842 original size:19 final size:20
Alignment explanation
Indices: 58786--58842 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
58776 TTAATACTTA
* *
58786 TTATTAAATAAATTACATAAT
1 TTATT-AATATATTAAATAAT
58807 TTATTAATATATT-AATAAT
1 TTATTAATATATTAAATAAT
*
58826 TTATT-ATTTATTAAATA
1 TTATTAATATATTAAATA
58843 TAAATACTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 6 0.19
19 14 0.44
20 7 0.22
21 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTAATATATTAAATAAT
Found at i:59377 original size:16 final size:17
Alignment explanation
Indices: 59343--59380 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
59333 AAAGAAAATT
* *
59343 GAAAAATTGAAGAGGTA
1 GAAAAATAGAAGAGATA
59360 GAAAAATAGAA-AGATA
1 GAAAAATAGAAGAGATA
59376 GAAAA
1 GAAAA
59381 TATAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.13
Consensus pattern (17 bp):
GAAAAATAGAAGAGATA
Found at i:64046 original size:17 final size:17
Alignment explanation
Indices: 64024--64059 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
64014 CATTTTATCT
64024 TTGCTTTCTCAAAAAAA
1 TTGCTTTCTCAAAAAAA
*
64041 TTGCTTTCTCAAAACAA
1 TTGCTTTCTCAAAAAAA
64058 TT
1 TT
64060 ATTTTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (17 bp):
TTGCTTTCTCAAAAAAA
Found at i:64065 original size:17 final size:17
Alignment explanation
Indices: 64027--64066 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
64017 TTTATCTTTG
*
64027 CTTTCTCAAAAAAATTG
1 CTTTCTCAAAAAAATTA
*
64044 CTTTCTCAAAACAATTA
1 CTTTCTCAAAAAAATTA
*
64061 TTTTCT
1 CTTTCT
64067 TTTTCTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (17 bp):
CTTTCTCAAAAAAATTA
Found at i:69323 original size:31 final size:31
Alignment explanation
Indices: 69279--69339 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
69269 TTCAATTTCT
*
69279 TCACTAACGTTTTAGATCATTTCTATTTTGA
1 TCACTAACATTTTAGATCATTTCTATTTTGA
* * *
69310 TCACTCACATTTTAGATCGTTTCTGTTTTG
1 TCACTAACATTTTAGATCATTTCTATTTTG
69340 GTCAATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.49
Consensus pattern (31 bp):
TCACTAACATTTTAGATCATTTCTATTTTGA
Found at i:76050 original size:16 final size:17
Alignment explanation
Indices: 76009--76052 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
75999 AAATCATTTG
*
76009 TTATAGATTAATTATTA
1 TTATTGATTAATTATTA
*
76026 TTATT-ATTAGTTATTA
1 TTATTGATTAATTATTA
76042 TT-TTGATTAAT
1 TTATTGATTAAT
76053 GTGGCTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 2 0.09
16 17 0.74
17 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (17 bp):
TTATTGATTAATTATTA
Found at i:77836 original size:18 final size:18
Alignment explanation
Indices: 77796--77838 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
77786 GTTCAAGGTG
77796 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
77814 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
77832 TAATTAA
1 TAATTAA
77839 AAACATATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:79261 original size:31 final size:31
Alignment explanation
Indices: 79223--79281 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
79213 GTAACAACAG
79223 TGACTTAAAAAAAAACTTTCAAATAATTTAA
1 TGACTTAAAAAAAAACTTTCAAATAATTTAA
**
79254 TGACTTAAATGAAAACTTTCAAATAATT
1 TGACTTAAAAAAAAACTTTCAAATAATT
79282 AAATAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (31 bp):
TGACTTAAAAAAAAACTTTCAAATAATTTAA
Found at i:82196 original size:2 final size:2
Alignment explanation
Indices: 82189--82223 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
82179 TGAATAATAC
82189 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.