Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006289.1 Kokia drynarioides strain JFW-HI SEQ_120861, 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: 27297
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Found at i:2033 original size:15 final size:15
Alignment explanation
Indices: 2013--2044 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2003 TCAATTGGGC
2013 GGGGCGGGTGCGGGG
1 GGGGCGGGTGCGGGG
2028 GGGGCGGGTGCGGGG
1 GGGGCGGGTGCGGGG
2043 GG
1 GG
2045 AAACTCACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.81, T:0.06
Consensus pattern (15 bp):
GGGGCGGGTGCGGGG
Found at i:2534 original size:16 final size:16
Alignment explanation
Indices: 2513--2561 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2503 ATTATTAAAC
*
2513 TTAATTAATTTAATAT
1 TTAATTAATATAATAT
*
2529 TTAATTAATATAATAC
1 TTAATTAATATAATAT
*
2545 TT-ATTAAGATAAATAT
1 TTAATTAATAT-AATAT
2561 T
1 T
2562 AGATTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
TTAATTAATATAATAT
Found at i:2649 original size:11 final size:11
Alignment explanation
Indices: 2633--2657 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2623 TTAATGTTAA
2633 ATTATTAAAAT
1 ATTATTAAAAT
2644 ATTATTAAAAT
1 ATTATTAAAAT
2655 ATT
1 ATT
2658 TATTCAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTATTAAAAT
Found at i:2734 original size:20 final size:20
Alignment explanation
Indices: 2709--2760 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2699 TTATTATATT
* *
2709 ATGCGGGGCGGGCGGGGATG
1 ATGCGGGGCGAGCGAGGATG
*
2729 ATGCGGGGCGAGTGAGGATG
1 ATGCGGGGCGAGCGAGGATG
*
2749 GTGCGGGGCGAG
1 ATGCGGGGCGAG
2761 TGGTGATGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.13, C:0.13, G:0.62, T:0.12
Consensus pattern (20 bp):
ATGCGGGGCGAGCGAGGATG
Found at i:2761 original size:20 final size:19
Alignment explanation
Indices: 2723--2774 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
2713 GGGGCGGGCG
*
2723 GGGATGATGCGGGGCGAGT
1 GGGATGGTGCGGGGCGAGT
2742 GAGGATGGTGCGGGGCGAGT
1 G-GGATGGTGCGGGGCGAGT
2762 GGTGATGG-GCGGG
1 GG-GATGGTGCGGG
2775 TACAAGGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 7 0.23
20 23 0.77
ACGTcount: A:0.13, C:0.10, G:0.62, T:0.15
Consensus pattern (19 bp):
GGGATGGTGCGGGGCGAGT
Found at i:3061 original size:17 final size:17
Alignment explanation
Indices: 3039--3075 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3029 TTTGATTGCT
*
3039 GTTTTTTTATTGTTTTG
1 GTTTTTTTATTATTTTG
3056 GTTTTTTTATTATTTTG
1 GTTTTTTTATTATTTTG
3073 GTT
1 GTT
3076 GCTGTTTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.08, C:0.00, G:0.16, T:0.76
Consensus pattern (17 bp):
GTTTTTTTATTATTTTG
Found at i:3092 original size:40 final size:40
Alignment explanation
Indices: 3017--3094 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
3007 TTGTTCTTTT
* **
3017 TTTTTTTACTGTTTTGATTGCTGTTTTTTTATTGTTTTGG
1 TTTTTTTACTATTTTGATTGCTGTTTTGGTATTGTTTTGG
* * *
3057 TTTTTTTATTATTTTGGTTGCTGTTTTGGTGTTGTTTT
1 TTTTTTTACTATTTTGATTGCTGTTTTGGTATTGTTTT
3095 TTTACTGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.06, C:0.04, G:0.19, T:0.71
Consensus pattern (40 bp):
TTTTTTTACTATTTTGATTGCTGTTTTGGTATTGTTTTGG
Found at i:3094 original size:11 final size:11
Alignment explanation
Indices: 3068--3154 Score: 66
Period size: 11 Copynumber: 7.6 Consensus size: 11
3058 TTTTTTATTA
*
3068 TTTTGGTTGCTG
1 TTTTGG-TGTTG
3080 TTTTGGTGTTG
1 TTTTGGTGTTG
** **
3091 TTTTTTTACTG
1 TTTTGGTGTTG
3102 TTTTGGTGTTG
1 TTTTGGTGTTG
* *
3113 TTTTTGCTGTTAT
1 -TTTTGGTGTT-G
*
3126 TTTTGTTGTTG
1 TTTTGGTGTTG
*
3137 TTTTGCTGTTG
1 TTTTGGTGTTG
3148 TTTTGGT
1 TTTTGGT
3155 TTTTTTTTGT
Statistics
Matches: 58, Mismatches: 15, Indels: 5
0.74 0.19 0.06
Matches are distributed among these distances:
11 34 0.59
12 24 0.41
ACGTcount: A:0.02, C:0.05, G:0.26, T:0.67
Consensus pattern (11 bp):
TTTTGGTGTTG
Found at i:3118 original size:34 final size:33
Alignment explanation
Indices: 3056--3162 Score: 110
Period size: 34 Copynumber: 3.2 Consensus size: 33
3046 TATTGTTTTG
* *
3056 GTTTTTTTATTATTTTGGTTGCTGTTTTGGTGTT
1 GTTTTTTTATTGTTTTGG-TGTTGTTTTGGTGTT
* *
3090 GTTTTTTTACTGTTTTGGTGTTGTTTTTGCTGTT
1 GTTTTTTTATTGTTTTGGTGTTG-TTTTGGTGTT
* * *
3124 ATTTTTGTTGTTGTTTTGCTGTTGTTTTGGT-TT
1 GTTTTT-TTATTGTTTTGGTGTTGTTTTGGTGTT
3157 -TTTTTT
1 GTTTTTT
3163 GTTTGGATGT
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
31 1 0.02
32 5 0.08
33 6 0.10
34 36 0.58
35 14 0.23
ACGTcount: A:0.04, C:0.04, G:0.22, T:0.70
Consensus pattern (33 bp):
GTTTTTTTATTGTTTTGGTGTTGTTTTGGTGTT
Found at i:3123 original size:12 final size:12
Alignment explanation
Indices: 3102--3151 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
3092 TTTTTTACTG
*
3102 TTTTGGTGTTGT
1 TTTTGCTGTTGT
*
3114 TTTTGCTGTTAT
1 TTTTGCTGTTGT
*
3126 TTTTGTTGTTG-
1 TTTTGCTGTTGT
3137 TTTTGCTGTTGT
1 TTTTGCTGTTGT
3149 TTT
1 TTT
3152 GGTTTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 10 0.31
12 22 0.69
ACGTcount: A:0.02, C:0.04, G:0.24, T:0.70
Consensus pattern (12 bp):
TTTTGCTGTTGT
Found at i:3780 original size:9 final size:9
Alignment explanation
Indices: 3766--3794 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
3756 AAAACATTTA
3766 TTTTAATAT
1 TTTTAATAT
3775 TTTTAATAT
1 TTTTAATAT
3784 TTTTAATAT
1 TTTTAATAT
3793 TT
1 TT
3795 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTAATAT
Found at i:4246 original size:26 final size:26
Alignment explanation
Indices: 4213--4268 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
4203 GCGAAGCAGG
* * *
4213 GATCACCAATGGGCTTGGCGAGCTCT
1 GATCACCAATGAGCCTGACGAGCTCT
*
4239 GATCACCAATGAGCCTGACGAGCTGT
1 GATCACCAATGAGCCTGACGAGCTCT
4265 GATC
1 GATC
4269 GCTCTTTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.29, T:0.21
Consensus pattern (26 bp):
GATCACCAATGAGCCTGACGAGCTCT
Found at i:6154 original size:234 final size:234
Alignment explanation
Indices: 5740--6211 Score: 872
Period size: 234 Copynumber: 2.0 Consensus size: 234
5730 AACAAATATG
*
5740 AATTTCAAGTCTACGCATATAGTTCAAGTTTGATTGATGTTTCTTAAATTACAAGTTCATACCTA
1 AATTACAAGTCTACGCATATAGTTCAAGTTTGATTGATGTTTCTTAAATTACAAGTTCATACCTA
5805 AGTAATTAAAATTTGAACATAGTGTTTGCCCTAAGCAATATAATAAAACATATCAAGTGACTAAC
66 AGTAATTAAAATTTGAACATAGTGTTTGCCCTAAGCAATATAATAAAACATATCAAGTGACTAAC
5870 TTATATAGAGTTCGCCAAGGTTGCTACGAAGTAACAAGATTGGTAAACTGTGCAATAGTGCGAAC
131 TTATATAGAGTTCGCCAAGGTTGCTACGAAGTAACAAGATTGGTAAACTGTGCAATAGTGCGAAC
* *
5935 CCAAACATGTGGCACATTGGTATCTATGAACCCTTAATA
196 CCAAACATGTGGCAAATTGGTATCTACGAACCCTTAATA
5974 AATTACAAGTCTACGCATATAGTTCAAGTTTGATTGATGTTTCTTAAATTACAAGTTCATACCTA
1 AATTACAAGTCTACGCATATAGTTCAAGTTTGATTGATGTTTCTTAAATTACAAGTTCATACCTA
*
6039 AGTAATTAAATTTTGAACATAGTGTTTGCCCTAAGCAATATAATAAAACATATCAAGTGACTAAC
66 AGTAATTAAAATTTGAACATAGTGTTTGCCCTAAGCAATATAATAAAACATATCAAGTGACTAAC
* ***
6104 TTATATAGAGTTCGCCAAGGTTGTTACTTCGTAACAAGATTGGTAAACTGTGCAATAGTGCGAAC
131 TTATATAGAGTTCGCCAAGGTTGCTACGAAGTAACAAGATTGGTAAACTGTGCAATAGTGCGAAC
6169 CCAAACATGTGGCAAATTGGTATCTACGAACCCTTAATA
196 CCAAACATGTGGCAAATTGGTATCTACGAACCCTTAATA
6208 AATT
1 AATT
6212 TTGAAATACT
Statistics
Matches: 230, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
234 230 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (234 bp):
AATTACAAGTCTACGCATATAGTTCAAGTTTGATTGATGTTTCTTAAATTACAAGTTCATACCTA
AGTAATTAAAATTTGAACATAGTGTTTGCCCTAAGCAATATAATAAAACATATCAAGTGACTAAC
TTATATAGAGTTCGCCAAGGTTGCTACGAAGTAACAAGATTGGTAAACTGTGCAATAGTGCGAAC
CCAAACATGTGGCAAATTGGTATCTACGAACCCTTAATA
Found at i:7789 original size:16 final size:15
Alignment explanation
Indices: 7762--7804 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
7752 TATATATATA
*
7762 TATATATTAAAAGAAC
1 TATATA-TAAAAAAAC
*
7778 TATATATAAAAAAAT
1 TATATATAAAAAAAC
7793 TA-ATATAAAAAA
1 TATATATAAAAAA
7805 TTAATATGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 10 0.40
15 9 0.36
16 6 0.24
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (15 bp):
TATATATAAAAAAAC
Found at i:7804 original size:13 final size:14
Alignment explanation
Indices: 7781--7811 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
7771 AAAGAACTAT
7781 ATATAAAAAAATTA
1 ATATAAAAAAATTA
7795 ATAT-AAAAAATTA
1 ATATAAAAAAATTA
7808 ATAT
1 ATAT
7812 GGGGGTCGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATATAAAAAAATTA
Found at i:8542 original size:20 final size:20
Alignment explanation
Indices: 8472--8552 Score: 90
Period size: 20 Copynumber: 3.9 Consensus size: 20
8462 TTTGGAGCTA
*
8472 TTTTTTTACTATTTTGGTTGT
1 TTTTTTTACTGTTTTGG-TGT
* * * *
8493 TATTTTTGCTGCTTTGTTGT
1 TTTTTTTACTGTTTTGGTGT
8513 TGTATTTTTACTGTTTTGGTGT
1 T-T-TTTTTACTGTTTTGGTGT
8535 TTTTTTTACTGTTTTGGT
1 TTTTTTTACTGTTTTGGT
8553 TACTGCTTTG
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 20 0.41
21 13 0.27
22 16 0.33
ACGTcount: A:0.07, C:0.06, G:0.19, T:0.68
Consensus pattern (20 bp):
TTTTTTTACTGTTTTGGTGT
Found at i:8556 original size:32 final size:34
Alignment explanation
Indices: 8520--8586 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
8510 TGTTGTATTT
* *
8520 TTACTGTTTTGGTG-T-TTTTTTTACTGTTTTGG
1 TTACTGCTTTGGTGATATTTTTTTACTATTTTGG
8552 TTACTGCTTTGGTGATATTTTTTTACTATTTTGG
1 TTACTGCTTTGGTGATATTTTTTTACTATTTTGG
8586 T
1 T
8587 GTTGCTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 13 0.42
33 1 0.03
34 17 0.55
ACGTcount: A:0.10, C:0.07, G:0.19, T:0.63
Consensus pattern (34 bp):
TTACTGCTTTGGTGATATTTTTTTACTATTTTGG
Found at i:8607 original size:12 final size:12
Alignment explanation
Indices: 8592--8661 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
8582 TTGGTGTTGC
8592 TTTTATTGTTAT
1 TTTTATTGTTAT
* *
8604 TTTTGTTGCTAT
1 TTTTATTGTTAT
* *
8616 TTTTTTTATTAT
1 TTTTATTGTTAT
** * *
8628 TTTTGCTGCTGT
1 TTTTATTGTTAT
*
8640 TTTGATTGTTAT
1 TTTTATTGTTAT
*
8652 TTTGATTGTT
1 TTTTATTGTT
8662 TGGATGTTAT
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.11, C:0.04, G:0.14, T:0.70
Consensus pattern (12 bp):
TTTTATTGTTAT
Found at i:8619 original size:24 final size:24
Alignment explanation
Indices: 8592--8654 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
8582 TTGGTGTTGC
*
8592 TTTTATTGTTATTTTTGTTGCTAT
1 TTTTATTGTTATTTTTGCTGCTAT
* * *
8616 TTTTTTTATTATTTTTGCTGCTGT
1 TTTTATTGTTATTTTTGCTGCTAT
*
8640 TTTGATTGTTATTTT
1 TTTTATTGTTATTTT
8655 GATTGTTTGG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.11, C:0.05, G:0.13, T:0.71
Consensus pattern (24 bp):
TTTTATTGTTATTTTTGCTGCTAT
Found at i:8842 original size:28 final size:27
Alignment explanation
Indices: 8791--8844 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
8781 ATATAAAGAA
**
8791 TTTTTAATGTATTTTTAATTTTTTTAT
1 TTTTTAATGTATTTTTAAAGTTTTTAT
*
8818 TTTTTAATGTTTGTTTTAAAGTTTTTA
1 TTTTTAATGTAT-TTTTAAAGTTTTTA
8845 AGCGTATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (27 bp):
TTTTTAATGTATTTTTAAAGTTTTTAT
Found at i:10642 original size:72 final size:72
Alignment explanation
Indices: 10547--10817 Score: 263
Period size: 73 Copynumber: 3.7 Consensus size: 72
10537 TTTTATCTAA
* * *
10547 AACCTTTAAAAAAAAATTAAAATAAACCCGTCTAAAATAACCTTAAAAAAATTGAAATAAACCTT
1 AACCTTT--AAAAAAGTTGAAATAAACCCGTCTAAAATAACCTTAAAAAAATTGAAATAAACATT
*
10612 ATTTAAAAC
64 ATCTAAAAC
* * * ** * *
10621 AACCTTTAAAAACGTTGAAATAAACCCGTCTGAGATAATATTAAAAAAAATTGAAGTAAACATTG
1 AACCTTTAAAAAAGTTGAAATAAACCCGTCTAAAATAACCTT-AAAAAAATTGAAATAAACATTA
*
10686 TCTAAAAT
65 TCTAAAAC
* * * * * * * * * *
10694 AACCTTTAAAAAAATTGAGATAAACTCATTTAAAGTAACTTTAAAAAGATTAAAATAAATATTAT
1 AACCTTTAAAAAAGTTGAAATAAACCCGTCTAAAATAACCTTAAAAAAATTGAAATAAACATTAT
10759 CTAAAAC
66 CTAAAAC
* * ** *
10766 AACTTTTAAAAAAGATTAAAATAAACCCGTCTAAAGCAATCTTAAAAAAATT
1 AACCTTTAAAAAAG-TTGAAATAAACCCGTCTAAAATAACCTTAAAAAAATT
10818 AGGATATGCA
Statistics
Matches: 155, Mismatches: 40, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
72 64 0.41
73 84 0.54
74 7 0.05
ACGTcount: A:0.54, C:0.13, G:0.06, T:0.28
Consensus pattern (72 bp):
AACCTTTAAAAAAGTTGAAATAAACCCGTCTAAAATAACCTTAAAAAAATTGAAATAAACATTAT
CTAAAAC
Found at i:10799 original size:37 final size:36
Alignment explanation
Indices: 10556--10818 Score: 147
Period size: 37 Copynumber: 7.3 Consensus size: 36
10546 AAACCTTTAA
* *
10556 AAAAAAATTAAAATAAACCCGTCTAAAATAAC-CTT
1 AAAAAAATTAAAATAAACCCGTCTAAAACAACTTTT
* ** * *
10591 AAAAAAATTGAAATAAACCTTATTTAAAACAACCTTT
1 AAAAAAATTAAAATAAACC-CGTCTAAAACAACTTTT
** * * * * *
10628 AAAAACGTTGAAATAAACCCGTCTGAGATAA-TATTA
1 AAAAAAATTAAAATAAACCCGTCTAAAACAACT-TTT
* * ** * *
10664 AAAAAAATTGAAGTAAACATTGTCTAAAATAACCTTT
1 AAAAAAATTAAAATAAAC-CCGTCTAAAACAACTTTT
* * * * * **
10701 AAAAAAATTGAGATAAACTCATTTAAAGTAAC-TTT
1 AAAAAAATTAAAATAAACCCGTCTAAAACAACTTTT
* ****
10736 AAAAAGATTAAAATAAATATTATCTAAAACAACTTTT
1 AAAAAAATTAAAATAAA-CCCGTCTAAAACAACTTTT
* *
10773 AAAAAAGATTAAAATAAACCCGTCTAAAGCAA-TCTT
1 AAAAAA-ATTAAAATAAACCCGTCTAAAACAACTTTT
10809 AAAAAAATTA
1 AAAAAAATTA
10819 GGATATGCAG
Statistics
Matches: 174, Mismatches: 46, Indels: 16
0.74 0.19 0.07
Matches are distributed among these distances:
35 39 0.22
36 61 0.35
37 63 0.36
38 11 0.06
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.27
Consensus pattern (36 bp):
AAAAAAATTAAAATAAACCCGTCTAAAACAACTTTT
Found at i:10941 original size:22 final size:23
Alignment explanation
Indices: 10915--10957 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
10905 ATTGTGCTTT
*
10915 AAATACAACTAAAA-AAAAATAA
1 AAATAAAACTAAAATAAAAATAA
*
10937 AAATAAAATTAAAATAAAAAT
1 AAATAAAACTAAAATAAAAAT
10958 TGAATATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (23 bp):
AAATAAAACTAAAATAAAAATAA
Found at i:11211 original size:31 final size:31
Alignment explanation
Indices: 11173--11258 Score: 163
Period size: 31 Copynumber: 2.8 Consensus size: 31
11163 CTCCTTCCTC
*
11173 CTTCATGATACTAAACTTCTTTTCGAAGGTG
1 CTTCATGATACTAAACTTTTTTTCGAAGGTG
11204 CTTCATGATACTAAACTTTTTTTCGAAGGTG
1 CTTCATGATACTAAACTTTTTTTCGAAGGTG
11235 CTTCATGATACTAAACTTTTTTTC
1 CTTCATGATACTAAACTTTTTTTC
11259 AAATGCACCT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (31 bp):
CTTCATGATACTAAACTTTTTTTCGAAGGTG
Found at i:19598 original size:17 final size:17
Alignment explanation
Indices: 19572--19606 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
19562 GAAGAACTTA
* *
19572 TTTGTTGAGAGTTCTTG
1 TTTGTAGAGAATTCTTG
19589 TTTGTAGAGAATTCTTG
1 TTTGTAGAGAATTCTTG
19606 T
1 T
19607 CAATGTGGAG
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:0.06, G:0.26, T:0.51
Consensus pattern (17 bp):
TTTGTAGAGAATTCTTG
Found at i:21988 original size:57 final size:57
Alignment explanation
Indices: 21896--22006 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
21886 TATTATCTGT
*
21896 TCAATCCTCCCACCACCGAACAAGTAGGAGGCTCTACCTCTGTTCCCACAGATCCCG
1 TCAATCCTCCCACCACCGAACAAGTAGGAGACTCTACCTCTGTTCCCACAGATCCCG
* * * *
21953 TCAATCCTCCCACCATCGAACAAGTCGGAGACTCTACCTTTGTTCCCATAGATC
1 TCAATCCTCCCACCACCGAACAAGTAGGAGACTCTACCTCTGTTCCCACAGATC
22007 GTAGCGCCAC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.23
Consensus pattern (57 bp):
TCAATCCTCCCACCACCGAACAAGTAGGAGACTCTACCTCTGTTCCCACAGATCCCG
Found at i:25023 original size:20 final size:21
Alignment explanation
Indices: 24992--25031 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
24982 AAAAATAAAA
24992 TTTAATTAATTATAAAATTAT
1 TTTAATTAATTATAAAATTAT
*
25013 TTTAATT-ATTATTAAATTA
1 TTTAATTAATTATAAAATTA
25032 AATTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAATTAATTATAAAATTAT
Done.