Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011179.1 Kokia drynarioides strain JFW-HI SEQ_126155, 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: 50819
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:8998 original size:18 final size:18
Alignment explanation
Indices: 8977--9023 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
8967 TGATATAATT
*
8977 AATTAAAATTTCAAAATA
1 AATTAAAATTTAAAAATA
* *
8995 AATTATAAAATGAAAAATA
1 AATTA-AAATTTAAAAATA
9014 AA-TAAAATTT
1 AATTAAAATTT
9024 TATATTTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
17 4 0.17
18 7 0.30
19 12 0.52
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
AATTAAAATTTAAAAATA
Found at i:12943 original size:38 final size:37
Alignment explanation
Indices: 12826--12962 Score: 177
Period size: 37 Copynumber: 3.7 Consensus size: 37
12816 GTAATTTTAA
*
12826 TCTAGAATTGCGCCCAAACATGTCGCTACATGAGCACT
1 TCTAG-ATTGCGCCCAAACATGTCGCCACATGAGCACT
* *
12864 TCTAGATTGCGCCCAAACATGTCGCCACATGAGTACC
1 TCTAGATTGCGCCCAAACATGTCGCCACATGAGCACT
* * *
12901 TCTAGATTACGCCCAAAAACTGTCTCCACATGAGCACT
1 TCTAGATTGCGCCCAAACA-TGTCGCCACATGAGCACT
* *
12939 TCTAGATTGCACCAAAAC-TGTCGC
1 TCTAGATTGCGCCCAAACATGTCGC
12963 TGCATAAATA
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
36 5 0.06
37 46 0.54
38 34 0.40
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (37 bp):
TCTAGATTGCGCCCAAACATGTCGCCACATGAGCACT
Found at i:13078 original size:26 final size:26
Alignment explanation
Indices: 13029--13081 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
13019 CACCCAGGAA
**
13029 TGTCGCTGCATGAACATGTACAGAAT
1 TGTCGCTGCATGAACACATACAGAAT
* *
13055 TGTCGCTGCATGAACGCATCCAGAAT
1 TGTCGCTGCATGAACACATACAGAAT
13081 T
1 T
13082 ACGCCCAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (26 bp):
TGTCGCTGCATGAACACATACAGAAT
Found at i:17403 original size:12 final size:12
Alignment explanation
Indices: 17382--17423 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
17372 AGGGTCCTTC
*
17382 TCTTCATTCTCT
1 TCTTCCTTCTCT
17394 TCTTCCTTCTCT
1 TCTTCCTTCTCT
17406 TCTT-CTTC-CT
1 TCTTCCTTCTCT
17416 T-TTCCTTC
1 TCTTCCTTC
17424 AACTGGTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 2 0.07
10 7 0.25
11 4 0.14
12 15 0.54
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (12 bp):
TCTTCCTTCTCT
Found at i:22984 original size:12 final size:12
Alignment explanation
Indices: 22967--22998 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
22957 TGAGTATCTG
22967 TACAAGAGCATC
1 TACAAGAGCATC
22979 TACAAGAGCATC
1 TACAAGAGCATC
22991 TACAAGAG
1 TACAAGAG
22999 GTATGTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.16
Consensus pattern (12 bp):
TACAAGAGCATC
Found at i:26020 original size:7 final size:7
Alignment explanation
Indices: 26008--26034 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
25998 TCTTGATGAT
26008 TTCTTCA
1 TTCTTCA
26015 TTCTTCA
1 TTCTTCA
26022 TTCTTCA
1 TTCTTCA
26029 TTCTTC
1 TTCTTC
26035 TAGTTATAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.30, G:0.00, T:0.59
Consensus pattern (7 bp):
TTCTTCA
Found at i:27803 original size:356 final size:357
Alignment explanation
Indices: 27243--27993 Score: 980
Period size: 356 Copynumber: 2.1 Consensus size: 357
27233 GTCGAAAAAC
* *
27243 ATCAAGGATCCACTTATCCAAAAACAAAGGTAC-AGTTTTGGTATAAGGTTAATTGGTATAAATA
1 ATCAAGGATTCGCTTATCCAAAAACAAAGGTACGA-TTTT-G-AT----TT-ATTGGTATAAATA
* * * *
27307 TCACAAATCTGGTCGATTTTCAAAATTTTAATTTTCTACTATGCAAGAAAATTATTTTCAAATCG
58 TCACAAATCTGGTCGATTTTCAAAATTTTAATGTCCTACTATGCAAGAAAATCATTTTCAAACCG
* *
27372 GATTTTTTTTCCAACATGTCAGAGTTGAAAGATTATCTCAAGAGGGCATCAACAACCTTATTAGC
123 GATCTTTTTTCCAACATGTCAGAGTTGAAAGATTATCTCAAGAGGGCATAAACAACCTTATTAGC
* * * *
27437 ACTGCCTTTCCTATAAATCACCTCAAATTCATAACCTAGCATTTTCGCCACCCACCTCTACTT-G
188 ACTACCTTTCCTATAAACCACCTCAAATTCATAACCAAGCATTTGCGCCACCCACCTCTA-TTCG
* * * * ** *
27501 AAGGGAGTGATGATCTGTTGGTC-ATAGAGAAACGTTAAACTCTGGTGGGCAGTCCGAATGCAGA
252 AA-GGAGTGATGATCTGCTGGTCGA-AAAGAAACCTCAAACTCAAGTGGGCAATCCGAATGCAGA
* * *
27565 AGTGGTGGTTAATCAAGTAATGATGCCACTTTTTGA-ATATAAAT
315 ACTGGCGGTCAATCAAGTAATGATGCCAC-TTTT-ACATATAAAT
*
27609 ATCAATGATTCGCTTATCCAAAAACAAAGGTACGATTTTGATTTATTGGTATAAATATCACAAAT
1 ATCAAGGATTCGCTTATCCAAAAACAAAGGTACGATTTTGATTTATTGGTATAAATATCACAAAT
*
27674 -TGGGTCGGTTTTCAAAATTTTAATGTCCT-CTATGCAAGAAAATCATTTTCAAACCGGA-CTTT
66 CT-GGTCGATTTTCAAAATTTTAATGTCCTACTATGCAAGAAAATCATTTTCAAACCGGATCTTT
* ** *
27736 TTTCCATA-A-GTTAGAGTTGAAAGATTATCTTGAGAGGGTATAAACAACCTTATTAGCACTACC
130 TTTCCA-ACATGTCAGAGTTGAAAGATTATCTCAAGAGGGCATAAACAACCTTATTAGCACTACC
* *
27799 TTTCCTATAAACCACCTTAAATTCATAACCAAGCATTTGCGCTACCCACCTCTATTGCGAAGGAG
194 TTTCCTATAAACCACCTCAAATTCATAACCAAGCATTTGCGCCACCCACCTCTATT-CGAAGGAG
* *
27864 TGATGATCTGCTGGTCGAAAAGAAACCTCAAACTCAAGTGGTCAATCCGATTGCAGAACTGGCGG
258 TGATGATCTGCTGGTCGAAAAGAAACCTCAAACTCAAGTGGGCAATCCGAATGCAGAACTGGCGG
* *
27929 TCAATCAGGTAATGATGCCACTTTTACCTATAAAT
323 TCAATCAAGTAATGATGCCACTTTTACATATAAAT
*
27964 ATCAAGGATTCGCTTATCCATAAACAAAGG
1 ATCAAGGATTCGCTTATCCAAAAACAAAGG
27994 AACGGTTTCA
Statistics
Matches: 342, Mismatches: 36, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
354 1 0.00
355 41 0.12
356 172 0.50
357 14 0.04
358 29 0.08
359 45 0.13
360 2 0.01
364 2 0.01
365 1 0.00
366 34 0.10
367 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (357 bp):
ATCAAGGATTCGCTTATCCAAAAACAAAGGTACGATTTTGATTTATTGGTATAAATATCACAAAT
CTGGTCGATTTTCAAAATTTTAATGTCCTACTATGCAAGAAAATCATTTTCAAACCGGATCTTTT
TTCCAACATGTCAGAGTTGAAAGATTATCTCAAGAGGGCATAAACAACCTTATTAGCACTACCTT
TCCTATAAACCACCTCAAATTCATAACCAAGCATTTGCGCCACCCACCTCTATTCGAAGGAGTGA
TGATCTGCTGGTCGAAAAGAAACCTCAAACTCAAGTGGGCAATCCGAATGCAGAACTGGCGGTCA
ATCAAGTAATGATGCCACTTTTACATATAAAT
Found at i:28599 original size:45 final size:45
Alignment explanation
Indices: 28560--28664 Score: 165
Period size: 45 Copynumber: 2.3 Consensus size: 45
28550 TCTTTTAGCC
28560 ATGGTCTTACTCATTTCCATCATGATGCCATAACATCTTTCAACT
1 ATGGTCTTACTCATTTCCATCATGATGCCATAACATCTTTCAACT
* ** * *
28605 ATGGTCTTACTCTTTTTTATCCTGATGTCATAACATCTTTCAACT
1 ATGGTCTTACTCATTTCCATCATGATGCCATAACATCTTTCAACT
28650 ATGGTCTTACTCATT
1 ATGGTCTTACTCATT
28665 CTAGGCGTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.43
Consensus pattern (45 bp):
ATGGTCTTACTCATTTCCATCATGATGCCATAACATCTTTCAACT
Found at i:32185 original size:28 final size:28
Alignment explanation
Indices: 32152--32208 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
32142 ATTAAGTAAA
32152 ACATGCAATGTACTAATCATATTAAACT
1 ACATGCAATGTACTAATCATATTAAACT
32180 ACATGCAATGTACTAATCATATTAAACT
1 ACATGCAATGTACTAATCATATTAAACT
32208 A
1 A
32209 AGGGTTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.32
Consensus pattern (28 bp):
ACATGCAATGTACTAATCATATTAAACT
Found at i:42065 original size:20 final size:20
Alignment explanation
Indices: 42040--42077 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42030 GTTTTTCGAA
42040 AAAAAGACAAAGATCAACCT
1 AAAAAGACAAAGATCAACCT
* *
42060 AAAAAGTCAACGATCAAC
1 AAAAAGACAAAGATCAAC
42078 TGTCAATGGT
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:0.58, C:0.21, G:0.11, T:0.11
Consensus pattern (20 bp):
AAAAAGACAAAGATCAACCT
Found at i:42091 original size:21 final size:21
Alignment explanation
Indices: 42065--42111 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
42055 AACCTAAAAA
* * *
42065 GTCAACGATCAACTGTCAATG
1 GTCAACGATAAACTATCAACG
42086 GTCAACGATAAACTATCAACG
1 GTCAACGATAAACTATCAACG
42107 GTCAA
1 GTCAA
42112 TGGTTGGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (21 bp):
GTCAACGATAAACTATCAACG
Found at i:45756 original size:3 final size:3
Alignment explanation
Indices: 45748--45787 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
45738 CCCACAAGTT
45748 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
45788 ATTTTTTCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:48151 original size:21 final size:21
Alignment explanation
Indices: 48126--48165 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
48116 AACCCAAAAA
*
48126 GTCAAAAGTCAACTGTCAATT
1 GTCAAAAGTCAACGGTCAATT
**
48147 GTCAATGGTCAACGGTCAA
1 GTCAAAAGTCAACGGTCAA
48166 CGGTCAATGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (21 bp):
GTCAAAAGTCAACGGTCAATT
Found at i:48171 original size:21 final size:21
Alignment explanation
Indices: 48133--48177 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
48123 AAAGTCAAAA
* **
48133 GTCAACTGTCAATTGTCAATG
1 GTCAACGGTCAACGGTCAATG
48154 GTCAACGGTCAACGGTCAATG
1 GTCAACGGTCAACGGTCAATG
48175 GTC
1 GTC
48178 GGGTTCGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (21 bp):
GTCAACGGTCAACGGTCAATG
Found at i:48246 original size:22 final size:22
Alignment explanation
Indices: 48221--48271 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
48211 TGGATCTAGA
*
48221 GTTTTGGTGATTTGGTTTT-AGG
1 GTTTTGGT-ATTGGGTTTTCAGG
* *
48243 GTTTGGGTATTGGGTTTTCATG
1 GTTTTGGTATTGGGTTTTCAGG
48265 GTTTTGG
1 GTTTTGG
48272 GTTTACACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.08, C:0.02, G:0.37, T:0.53
Consensus pattern (22 bp):
GTTTTGGTATTGGGTTTTCAGG
Found at i:50665 original size:43 final size:43
Alignment explanation
Indices: 50617--50713 Score: 140
Period size: 43 Copynumber: 2.3 Consensus size: 43
50607 TACTAGAAGA
* * * *
50617 AAGACTCATGTCTTGGATAGAGCATGAGATTATTTATAAATGG
1 AAGACTTATGTCTCGGATAGAGCATAAGATTATTTATAAAAGG
* *
50660 AAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATAAAAGG
1 AAGACTTATGTCTCGGATAGAGCATAAGATTATTTATAAAAGG
50703 AAGACTTATGT
1 AAGACTTATGT
50714 GTAACACCCT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (43 bp):
AAGACTTATGTCTCGGATAGAGCATAAGATTATTTATAAAAGG
Done.