Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011497.1 Kokia drynarioides strain JFW-HI SEQ_126482, 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: 35184
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:471 original size:59 final size:57
Alignment explanation
Indices: 372--547 Score: 149
Period size: 59 Copynumber: 3.0 Consensus size: 57
362 GGTAAAAACG
* * * *
372 GTAATTTT-GAGAGTTTGGAGGTCGAAAAATGGAGTCTTTGGACA-TCCGGGAGTAAGATA
1 GTAATTTTAGA-AGGTTCGAGGTC-AAAAATGGA-TTTTTGGA-AGTCCGGGAGTAAAATA
* * * * * * *
431 GTAATTTTTGGATGTTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATG
1 GTAA-TTTTAGAAGGTTCGAGGTCAAAAATG-GATTTTTGGAAGTCCGGGAGTAAAATA
* *
490 GTAATTTTAGAAGGTTCGAGGTCAGAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAT
1 GTAATTTTAGAAGGTTCGAGGTCA-AAAAT-GGATTTTTGGAAGTCCGGGAGTAAAAT
548 GGGATTTTTG
Statistics
Matches: 99, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
58 17 0.17
59 64 0.65
60 16 0.16
61 2 0.02
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (57 bp):
GTAATTTTAGAAGGTTCGAGGTCAAAAATGGATTTTTGGAAGTCCGGGAGTAAAATA
Found at i:487 original size:29 final size:28
Alignment explanation
Indices: 434--839 Score: 349
Period size: 29 Copynumber: 13.8 Consensus size: 28
424 TAAGATAGTA
* *
434 ATTTTTGGATGTTTCGGGGTCAAAAATGAG
1 ATTTTTGGAAG-TTCGGGGT-AAAAATGGG
*
464 ATTTTTGGAAGTTCGGGGGT-AAAATGGT
1 ATTTTTGGAAGTTC-GGGGTAAAAATGGG
* * *
492 AATTTTAGAAGGTTCGAGGTCAGAAAATGGG
1 ATTTTTGGAA-GTTCGGGGT-A-AAAATGGG
523 ATTTTTGGAAGTTCGGGGGT-AAAATGGG
1 ATTTTTGGAAGTTC-GGGGTAAAAATGGG
*
551 ATTTTTGGAAGTTCGAGGGT-AAAATGGTA
1 ATTTTTGGAAGTTCG-GGGTAAAAATGG-G
* * *
580 ATTTCTAGAAGGTTCGAGGTCAAAAATGGG
1 ATTTTTGGAA-GTTCGGGGT-AAAAATGGG
* *
610 ATTTTTGGAAGTTTTGGGGT-AAAATGGTA
1 ATTTTTGGAAG-TTCGGGGTAAAAATGG-G
*
639 ATTTTTGGAAGGTTTGGGGTAAAAAATGGG
1 ATTTTTGGAA-GTTCGGGGT-AAAAATGGG
*
669 ATTTTTGGAAG-TCTGAGGGT-AAAATGGTA
1 ATTTTTGGAAGTTC-G-GGGTAAAAATGG-G
* *
698 ATTTTTAGAAGGTTCAGGGTCAAAAATGGG
1 ATTTTTGGAA-GTTCGGGGT-AAAAATGGG
*
728 ATTTTTGGAAGTTTAGGGGTAAAAATGGG
1 ATTTTTGGAAG-TTCGGGGTAAAAATGGG
* *
757 ATTTTTGGAAGTTTAGGGGT-AAAATGGTA
1 ATTTTTGGAAG-TTCGGGGTAAAAATGG-G
786 ATTTTTGGAAGGTTCGGGGTCAAAAATGGG
1 ATTTTTGGAA-GTTCGGGGT-AAAAATGGG
*
816 ATTTTTGGATGTTCGAGGGTAAAA
1 ATTTTTGGAAGTTCG-GGGTAAAA
840 TGGTAATTTT
Statistics
Matches: 314, Mismatches: 33, Indels: 59
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.00
28 73 0.23
29 108 0.34
30 83 0.26
31 49 0.16
ACGTcount: A:0.30, C:0.04, G:0.33, T:0.33
Consensus pattern (28 bp):
ATTTTTGGAAGTTCGGGGTAAAAATGGG
Found at i:548 original size:59 final size:57
Alignment explanation
Indices: 434--842 Score: 350
Period size: 59 Copynumber: 7.0 Consensus size: 57
424 TAAGATAGTA
* * * *
434 ATTTTTGGATGTTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGT
1 ATTTTTGGAAGGTTCGGGGT-AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGG
* * *
492 AATTTTAGAAGGTTCGAGGTCAGAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGG
1 ATTTTTGGAAGGTTCGGGGT-A-AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGG
* * * *
551 ATTTTTGGAA-GTTCGAGGGT-AAAATGGTAATTTCTAGAAGGTTC-GAGGTCAAAAATGGG
1 ATTTTTGGAAGGTTCG-GGGTAAAAATGG-GATTTTTGGAA-GTTCGGGGGT--AAAATGGG
* * * *
610 ATTTTTGGAAGTTTTGGGGT-AAAATGGTAATTTTTGGAAGGTT-TGGGGTAAAAAATGGG
1 ATTTTTGGAAGGTTCGGGGTAAAAATGG-GATTTTTGGAA-GTTCGGGGGT--AAAATGGG
* * *
669 ATTTTTGGAA-G-TCTGAGGGT-AAAATGGTAATTTTTAGAAGGTTC-AGGGTCAAAAATGGG
1 ATTTTTGGAAGGTTC-G-GGGTAAAAATGG-GATTTTTGGAA-GTTCGGGGGT--AAAATGGG
* * ** *
728 ATTTTTGGAAGTTTAGGGGTAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGGTA
1 ATTTTTGGAAGGTTCGGGGTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGG-G
* *
786 ATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGATGTTCGAGGGTAAAATGG
1 ATTTTTGGAAGGTTCGGGGT-AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGG
843 TAATTTTTTG
Statistics
Matches: 296, Mismatches: 38, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
56 7 0.02
57 20 0.07
58 48 0.16
59 209 0.71
60 11 0.04
61 1 0.00
ACGTcount: A:0.30, C:0.04, G:0.33, T:0.33
Consensus pattern (57 bp):
ATTTTTGGAAGGTTCGGGGTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGG
Found at i:606 original size:118 final size:115
Alignment explanation
Indices: 515--810 Score: 411
Period size: 118 Copynumber: 2.5 Consensus size: 115
505 TCGAGGTCAG
*
515 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTA
1 AAAATGGGATTTTTGGAAGTT-AGGGGTAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTA
*
580 ATTTCTAGAAGGTTC-GAGGTCAAAAATGGGATTTTTGGAAGTTTTGGGGT-
65 ATTTCTAGAAGGTTCAG-GGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTA
* *
630 AAAATGGTAATTTTTGGAAGGTTTGGGGTAAAAAATGGGATTTTTGGAAG-TCTGAGGGTAAAAT
1 AAAATGG-GATTTTTGGAA-GTTAGGGGT--AAAATGGGATTTTTGGAAGTTC-GAGGGTAAAAT
*
694 GGTAATTTTTAGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTA
61 GGTAATTTCTAGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTA
*
749 AAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGGTTCG-GGGTCAAAA
1 AAAATGGGATTTTTGGAAG-TTAGGGGTAAAATGG-GATTTTTGGAA-GTTCGAGGGT-AAAA
811 ATGGGATTTT
Statistics
Matches: 162, Mismatches: 7, Indels: 21
0.85 0.04 0.11
Matches are distributed among these distances:
115 7 0.04
116 22 0.14
117 20 0.12
118 103 0.64
119 10 0.06
ACGTcount: A:0.31, C:0.03, G:0.33, T:0.33
Consensus pattern (115 bp):
AAAATGGGATTTTTGGAAGTTAGGGGTAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAA
TTTCTAGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTA
Found at i:836 original size:88 final size:88
Alignment explanation
Indices: 431--863 Score: 397
Period size: 88 Copynumber: 4.9 Consensus size: 88
421 GAGTAAGATA
* * * *
431 GTAATTTTTGGATGTTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAA-T
1 GTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGG-AATT
* * *
495 TTTAGAAGGTTCGAGGTCAGAAAATG
65 TTTAGAAGTTTAGGGGT-A-AAAATG
*
521 G-GATTTTTGGAA-GTTCGGGGGT--AAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
1 GTAATTTTTGGAAGGTTC-GGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGG-AAT
* * * *
582 TTCTAGAAGGTTCGAGGTCAAAAATG
64 TTTTAGAAGTTTAGGGGT-AAAAATG
* * * * * *
608 G-GATTTTTGGAAGTTTTGGGGT--AAAATGGTAATTTTTGGAAGGTTTG-GGGTAAAAAATGGG
1 GTAATTTTTGGAAGGTTCGGGGTCAAAAATGG-GATTTTTGGAA-GTTCGAGGGT--AAAATGGA
* *
669 ATTTTTGGAAGTCT-GAGGGT-AAAATG
62 ATTTTTAGAAGTTTAG-GGGTAAAAATG
* * * *
695 GTAATTTTTAGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAAGTT-TAGGGGTAAAAATGGGAT
1 GTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGT-AAAATGGAAT
*
759 TTTTGGAAGTTTAGGGGT-AAAATG
64 TTTTAGAAGTTTAGGGGTAAAAATG
*
783 GTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGATGTTCGAGGGTAAAATGGTAATT
1 GTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGG-AATT
*
848 TTTTGATAGTTTAGGG
65 TTTAGA-AGTTTAGGG
864 ACCTTCGAGG
Statistics
Matches: 296, Mismatches: 30, Indels: 35
0.82 0.08 0.10
Matches are distributed among these distances:
87 80 0.27
88 145 0.49
89 56 0.19
90 15 0.05
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (88 bp):
GTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGAATTT
TTAGAAGTTTAGGGGTAAAAATG
Found at i:2617 original size:17 final size:17
Alignment explanation
Indices: 2597--2660 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 17
2587 AAATAAATTT
* *
2597 TAAATTCAAATTTATAA
1 TAAATTTAAATTTAAAA
* *
2614 TAAATTTAAATTCAGAA
1 TAAATTTAAATTTAAAA
*
2631 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
2648 TAAATTTAAATTT
1 TAAATTTAAATTT
2661 GTTGGGCCTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:2621 original size:23 final size:23
Alignment explanation
Indices: 2583--2658 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
2573 TCTGGACATT
2583 ATTTAAATAAATTTTAAATTCAA
1 ATTTAAATAAATTTTAAATTCAA
2606 ATTTATAATAAA-TTTAAATTCAGA
1 ATTTA-AATAAATTTTAAATTCA-A
* *
2630 A--TAAATTTAATTTTAAAAT-AA
1 ATTTAAA-TAAATTTTAAATTCAA
2651 ATTTAAAT
1 ATTTAAAT
2659 TTGTTGGGCC
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
21 4 0.09
22 7 0.16
23 26 0.58
24 8 0.18
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (23 bp):
ATTTAAATAAATTTTAAATTCAA
Found at i:5318 original size:42 final size:42
Alignment explanation
Indices: 5195--5348 Score: 118
Period size: 42 Copynumber: 3.7 Consensus size: 42
5185 CCAATATGAT
* * * *
5195 ATGATTCACT-AAGGTGCCAGATATATTGCTTCGGACTTTCCG
1 ATGATGCACTGAA-GTGCAAGATATATTACTTCGGACTTTTCG
* * * *
5237 ATGATGCACTGAAGTGCTAGATATATTTCTTTGGGCTTTTCG
1 ATGATGCACTGAAGTGCAAGATATATTACTTCGGACTTTTCG
* * * ** **
5279 ATGATGCATTGAGGTGGAAGATATATTACTTCAAACTTTTTT
1 ATGATGCACTGAAGTGCAAGATATATTACTTCGGACTTTTCG
* *
5321 ATGATGCA---ATGTGCTAGATATATTACTT
1 ATGATGCACTGAAGTGCAAGATATATTACTT
5349 TGGTTATATT
Statistics
Matches: 91, Mismatches: 20, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
39 17 0.19
42 72 0.79
43 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (42 bp):
ATGATGCACTGAAGTGCAAGATATATTACTTCGGACTTTTCG
Found at i:13984 original size:15 final size:16
Alignment explanation
Indices: 13963--14003 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
13953 ATTAGACATG
13963 AAAATAAAT-AACAAA
1 AAAATAAATAAACAAA
*
13978 TAAATAAATAAACAAA
1 AAAATAAATAAACAAA
13994 AAAATTAAAT
1 AAAA-TAAAT
14004 GTCAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 8 0.36
16 9 0.41
17 5 0.23
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAATAAATAAACAAA
Found at i:15196 original size:46 final size:45
Alignment explanation
Indices: 14831--15474 Score: 580
Period size: 45 Copynumber: 14.0 Consensus size: 45
14821 GCTTTCTATA
* * * *
14831 GCTTCAATTTACCCCTCTGGATTTAAGGGGTATAAGATTGGATGTGGTA
1 GCTTCAATCTACCCCTCTAGATTT-A-GGGTAAAAGATTGGA--TGGTG
** * * *
14880 GCTTCAATCTGTCCCTCTAGATTTAGGAGTATAAGATTAGATGTGGTA
1 GCTTCAATCTACCCCTCTAGATTTAGG-GTAAAAGATTGGA--TGGTG
* * * * * *
14928 GCTTAAATCTGCCTCTATGGATTTAAGGGTAAAAGATTGGATGATG
1 GCTTCAATCTACCCCTCTAGATTT-AGGGTAAAAGATTGGATGGTG
* * * * *
14974 GCTTTAATCTACCCCTCTAGCTTAAGGGCAAAAGATTGGATGGTA
1 GCTTCAATCTACCCCTCTAGATTTAGGGTAAAAGATTGGATGGTG
* *
15019 GCTTCAATCTGCCCCTCTAGATTAAGGGTAAAAGATTGGATGGTG
1 GCTTCAATCTACCCCTCTAGATTTAGGGTAAAAGATTGGATGGTG
* *
15064 GTTTCAATCTGCCCCTCTAGA-TTAGAGGTAAAAGATTGGATGGTG
1 GCTTCAATCTACCCCTCTAGATTTAG-GGTAAAAGATTGGATGGTG
* * *
15109 GCTTCAATCTACCCCTCT-GAATTAGGGGTAAAATATTGGATGGGG
1 GCTTCAATCTACCCCTCTAGATTTA-GGGTAAAAGATTGGATGGTG
* * * *
15154 GCTTCAATCTACCCTTTTGGATTTAGGGATAAAAGGTTGGATGGTG
1 GCTTCAATCTACCCCTCTAGATTTAGGG-TAAAAGATTGGATGGTG
** * * * *
15200 GCTTTGATCTACCTCTTTAGATTTAGGGGTAAAATATTGAATGGTG
1 GCTTCAATCTACCCCTCTAGATTTA-GGGTAAAAGATTGGATGGTG
* * * * *
15246 GCTTCAATTTGCCCATCTAGATTAAGGGTAAAAGATTGAATGGTG
1 GCTTCAATCTACCCCTCTAGATTTAGGGTAAAAGATTGGATGGTG
* *
15291 GCTTCAATTTA-TCCT-TATGCATTTAGGGGTAAAAGATTGGATGGTG
1 GCTTCAATCTACCCCTCTA-G-ATTTA-GGGTAAAAGATTGGATGGTG
* * *
15337 ACTTCAATCTATCCTTCT-GTATTTAGGGGTAAAAGATTGGATGGTG
1 GCTTCAATCTACCCCTCTAG-ATTTA-GGGTAAAAGATTGGATGGTG
* * *
15383 GCTTTAATCTACCCCTCTGGATTTAGGGAGTAAAAGATTAGATGGTG
1 GCTTCAATCTACCCCTCTAGATTTA-GG-GTAAAAGATTGGATGGTG
* * * *
15430 GTTTCAATCTGCCTCTCTAGA-TTAGGGGTAAAAGATTGGGTGGTG
1 GCTTCAATCTACCCCTCTAGATTTA-GGGTAAAAGATTGGATGGTG
15475 TAGCTTCACT
Statistics
Matches: 500, Mismatches: 80, Indels: 34
0.81 0.13 0.06
Matches are distributed among these distances:
43 2 0.00
44 8 0.02
45 201 0.40
46 174 0.35
47 41 0.08
48 51 0.10
49 23 0.05
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (45 bp):
GCTTCAATCTACCCCTCTAGATTTAGGGTAAAAGATTGGATGGTG
Found at i:15275 original size:137 final size:136
Alignment explanation
Indices: 14831--15474 Score: 579
Period size: 137 Copynumber: 4.7 Consensus size: 136
14821 GCTTTCTATA
* * * * *
14831 GCTTCAATTTACCCCTCTGGATTTAAGGGGTATAAGATTGGATGTGGTAGCTTCAATCTGTCCCT
1 GCTTCAATCTACCCCTCTAGA-TTAA-GGGTAAAAGATTGGA--TGGTGGCTTCAATCT-ACCCT
* * * * * * * *
14896 CTA--GATTTAGGAGTATAAGATTAGATGTGGTAGCTTAAATCTGCCTCTATGGATTTAAGGGTA
61 -TATGGATTTAGG-GTAAAAGATTGGA--TGGTGGCTTTAATCTACCTCTCTAGATTTAGGGGTA
*
14959 AAAGATTGGATGATG
122 AAAGATTGGATGGTG
* * * * * * * *
14974 GCTTTAATCTACCCCTCTAGCTTAAGGGCAAAAGATTGGATGGTAGCTTCAATCTGCCCCTCTAG
1 GCTTCAATCTACCCCTCTAGATTAAGGGTAAAAGATTGGATGGTGGCTTCAATCTACCCTTATGG
* * * *
15039 ATTAAGGGTAAAAGATTGGATGGTGG-TTTCAATCTGCCCCTCTAGA-TTAGAGGTAAAAGATTG
66 ATTTAGGGTAAAAGATTGGATGGTGGCTTT-AATCTACCTCTCTAGATTTAGGGGTAAAAGATTG
15102 GATGGTG
130 GATGGTG
* * * *
15109 GCTTCAATCTACCCCTCT-GAATTAGGGGTAAAATATTGGATGGGGGCTTCAATCTACCCTTTTG
1 GCTTCAATCTACCCCTCTAG-ATTAAGGGTAAAAGATTGGATGGTGGCTTCAATCTACCCTTATG
* * * *
15173 GATTTAGGGATAAAAGGTTGGATGGTGGCTTTGATCTACCTCTTTAGATTTAGGGGTAAAATATT
65 GATTTAGGG-TAAAAGATTGGATGGTGGCTTTAATCTACCTCTCTAGATTTAGGGGTAAAAGATT
*
15238 GAATGGTG
129 GGATGGTG
* * * * * * *
15246 GCTTCAATTTGCCCATCTAGATTAAGGGTAAAAGATTGAATGGTGGCTTCAATTTATCCTTATGC
1 GCTTCAATCTACCCCTCTAGATTAAGGGTAAAAGATTGGATGGTGGCTTCAATCTACCCTTATGG
* *
15311 ATTTAGGGGTAAAAGATTGGATGGTGACTTCAATCTATCCT-TCT-GTATTTAGGGGTAAAAGAT
66 ATTTA-GGGTAAAAGATTGGATGGTGGCTTTAATCTA-CCTCTCTAG-ATTTAGGGGTAAAAGAT
15374 TGGATGGTG
128 TGGATGGTG
* * * * * *
15383 GCTTTAATCTACCCCTCTGGATTTAGGGAGTAAAAGATTAGATGGTGGTTTCAATCTGCCTCTCT
1 GCTTCAATCTACCCCTCTAGA-TTAAGG-GTAAAAGATTGGATGGTGGCTTCAATCTACC-CT-T
*
15448 A--GA-TTAGGGGTAAAAGATTGGGTGGTG
62 ATGGATTTA-GGGTAAAAGATTGGATGGTG
15475 TAGCTTCACT
Statistics
Matches: 414, Mismatches: 72, Indels: 35
0.79 0.14 0.07
Matches are distributed among these distances:
134 1 0.00
135 82 0.20
136 48 0.12
137 148 0.36
138 49 0.12
139 48 0.12
140 2 0.00
141 15 0.04
142 4 0.01
143 17 0.04
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (136 bp):
GCTTCAATCTACCCCTCTAGATTAAGGGTAAAAGATTGGATGGTGGCTTCAATCTACCCTTATGG
ATTTAGGGTAAAAGATTGGATGGTGGCTTTAATCTACCTCTCTAGATTTAGGGGTAAAAGATTGG
ATGGTG
Found at i:16202 original size:20 final size:20
Alignment explanation
Indices: 16165--16202 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16155 GCCAAAGATT
*
16165 ACAAATATTGGTCAAAAATA
1 ACAAATATTGGTAAAAAATA
*
16185 ACAAATGTTGGTAAAAAA
1 ACAAATATTGGTAAAAAA
16203 ATGGCTAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.08, G:0.13, T:0.24
Consensus pattern (20 bp):
ACAAATATTGGTAAAAAATA
Found at i:23381 original size:14 final size:14
Alignment explanation
Indices: 23362--23396 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
23352 GAAAAGTAAT
*
23362 TCATTTTCCTGAAA
1 TCATTTTCCGGAAA
23376 TCATTTTCCGGAAA
1 TCATTTTCCGGAAA
*
23390 CCATTTT
1 TCATTTT
23397 TAGTCAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.43
Consensus pattern (14 bp):
TCATTTTCCGGAAA
Found at i:24380 original size:23 final size:22
Alignment explanation
Indices: 24344--24387 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
24334 TAAATATTTC
*
24344 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
24367 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
24388 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Done.