Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008139.1 Kokia drynarioides strain JFW-HI SEQ_122797, 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: 47228
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Warning! 58 characters in sequence are not A, C, G, or T
Found at i:2637 original size:13 final size:13
Alignment explanation
Indices: 2619--2643 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2609 CAAAAAGGAT
2619 ACAAAGGGTAGCA
1 ACAAAGGGTAGCA
2632 ACAAAGGGTAGC
1 ACAAAGGGTAGC
2644 TATGCCTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.32, T:0.08
Consensus pattern (13 bp):
ACAAAGGGTAGCA
Found at i:4792 original size:13 final size:13
Alignment explanation
Indices: 4776--4800 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4766 TATAAAAAAA
4776 ATTTATTTATTTT
1 ATTTATTTATTTT
4789 ATTTATTTATTT
1 ATTTATTTATTT
4801 AAAAATTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTATTTATTTT
Found at i:4967 original size:9 final size:8
Alignment explanation
Indices: 4939--4970 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
4929 AATTAATTAA
4939 ATTTTTAT
1 ATTTTTAT
4947 ATTTTTAT
1 ATTTTTAT
4955 ATTTTTAT
1 ATTTTTAT
*
4963 AATTTTAT
1 ATTTTTAT
4971 GCTTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
ATTTTTAT
Found at i:8463 original size:133 final size:133
Alignment explanation
Indices: 8225--8474 Score: 367
Period size: 133 Copynumber: 1.9 Consensus size: 133
8215 ATGAATTCGA
*
8225 GTGTTGTGATCAGGGATTAATACAATGGCTTGAAATCCAAAATATGTTGCGGATTCTCTTAAGCT
1 GTGTTGTGATCAGGGATTAATACAATGGCTTGAAATCCAAAATATGTTGCGGATTCTCTGAAGCT
* * *
8290 AGTGTTAGCAACCCTAATCTGAAGCCAGTGTTAGTAGCCCGA-ATATGTCAACTTGTATAAACAA
66 AATGTTAGCAACCCTAATCCGAAGCCAGTGTTAGCAGCCCGATA-ATGTCAACTTGTATAAACAA
8354 ACGG
130 ACGG
* * * * * *
8358 GTGTTGTGATCAGGGATTAATTCGATGGCTTGAGATTCAATATATGTTGTGGATTCTCTGAAGCT
1 GTGTTGTGATCAGGGATTAATACAATGGCTTGAAATCCAAAATATGTTGCGGATTCTCTGAAGCT
* * *
8423 AATGTTAGCAATCCTGATCCGAAGCTAGTGTTAGCAGCCCGATAATGTCAAC
66 AATGTTAGCAACCCTAATCCGAAGCCAGTGTTAGCAGCCCGATAATGTCAAC
8475 ATATGTAATC
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
133 102 0.99
134 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (133 bp):
GTGTTGTGATCAGGGATTAATACAATGGCTTGAAATCCAAAATATGTTGCGGATTCTCTGAAGCT
AATGTTAGCAACCCTAATCCGAAGCCAGTGTTAGCAGCCCGATAATGTCAACTTGTATAAACAAA
CGG
Found at i:10469 original size:82 final size:82
Alignment explanation
Indices: 10363--10529 Score: 316
Period size: 82 Copynumber: 2.0 Consensus size: 82
10353 CCATCCCCGC
* *
10363 CCCGTGATTCGCAAGACTAAAACCATCCCCGCCCCACCACCCACATGGATCACCAGATCCACCTA
1 CCCGCGATTCACAAGACTAAAACCATCCCCGCCCCACCACCCACATGGATCACCAGATCCACCTA
10428 ATCCCCGCTATATTCGT
66 ATCCCCGCTATATTCGT
10445 CCCGCGATTCACAAGACTAAAACCATCCCCGCCCCACCACCCACATGGATCACCAGATCCACCTA
1 CCCGCGATTCACAAGACTAAAACCATCCCCGCCCCACCACCCACATGGATCACCAGATCCACCTA
10510 ATCCCCGCTATATTCGT
66 ATCCCCGCTATATTCGT
10527 CCC
1 CCC
10530 ACGACCCACT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.27, C:0.44, G:0.11, T:0.17
Consensus pattern (82 bp):
CCCGCGATTCACAAGACTAAAACCATCCCCGCCCCACCACCCACATGGATCACCAGATCCACCTA
ATCCCCGCTATATTCGT
Found at i:11819 original size:18 final size:18
Alignment explanation
Indices: 11798--11841 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
11788 TTAATTAAAA
*
11798 AATAAATAAATATAATAC-
1 AATAAA-AAACATAATACT
*
11816 AATAAAAAGCATAATACT
1 AATAAAAAACATAATACT
11834 AATAAAAA
1 AATAAAAA
11842 TAAAGATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (18 bp):
AATAAAAAACATAATACT
Found at i:14343 original size:33 final size:34
Alignment explanation
Indices: 14259--14343 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 34
14249 TGTAAACACA
*
14259 GTATGGTCATAAGAGCT-ATCAAATCAAAACTCT
1 GTATGCTCATAAGAGCTAATCAAATCAAAACTCT
* *
14292 GTATGCTCATAAGAGCTAATC-AATCCATA-TACT
1 GTATGCTCATAAGAGCTAATCAAATCAAAACT-CT
14325 GTATGCTCATAAGAGCTAA
1 GTATGCTCATAAGAGCTAA
14344 CCAACCAACA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
32 1 0.02
33 43 0.91
34 3 0.06
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (34 bp):
GTATGCTCATAAGAGCTAATCAAATCAAAACTCT
Found at i:31674 original size:8 final size:8
Alignment explanation
Indices: 31661--31690 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
31651 AGAATGCTTT
31661 TTTTTTTC
1 TTTTTTTC
31669 TTTTTTTC
1 TTTTTTTC
31677 TTTTTTT-
1 TTTTTTTC
31684 TTTTTTT
1 TTTTTTT
31691 ACATTTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (8 bp):
TTTTTTTC
Found at i:31682 original size:16 final size:15
Alignment explanation
Indices: 31661--31690 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
31651 AGAATGCTTT
31661 TTTTTTTCTTTTTTTC
1 TTTTTTT-TTTTTTTC
31677 TTTTTTTTTTTTTT
1 TTTTTTTTTTTTTT
31691 ACATTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (15 bp):
TTTTTTTTTTTTTTC
Found at i:31697 original size:16 final size:17
Alignment explanation
Indices: 31661--31698 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
31651 AGAATGCTTT
*
31661 TTTTTTTCTTTTTTTC-
1 TTTTTTTCTTTTTTACA
*
31677 TTTTTTTTTTTTTTACA
1 TTTTTTTCTTTTTTACA
31694 TTTTT
1 TTTTT
31699 GGGCTTATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTTTTTCTTTTTTACA
Found at i:31885 original size:74 final size:75
Alignment explanation
Indices: 31731--31886 Score: 203
Period size: 74 Copynumber: 2.1 Consensus size: 75
31721 CGAATATGTT
*
31731 TTGAGACAAGATAGTCAAATTTAAATTGAGAATGCATTTTTGGGTGCATGTCTCGGGACATGAAT
1 TTGAGACAAGATAATCAAATTTAAATTGAGAATGCATTTTTGGGTGCATGTCTCGGGACATGAAT
*
31796 GGCAAAGGTC
66 GGCAAAAGTC
* * * *
31806 -CGAGACAAGATAATCAAATTTGAATTGA-ACATGCATTTATT-GGTGCATGTCTCTGGATATGA
1 TTGAGACAAGATAATCAAATTTAAATTGAGA-ATGCATTT-TTGGGTGCATGTCTCGGGACATGA
*
31868 A-GGGAAAAGTC
64 ATGGCAAAAGTC
31879 TTGAGACA
1 TTGAGACA
31887 TTCGAAGTCA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
73 9 0.13
74 59 0.84
75 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (75 bp):
TTGAGACAAGATAATCAAATTTAAATTGAGAATGCATTTTTGGGTGCATGTCTCGGGACATGAAT
GGCAAAAGTC
Found at i:36172 original size:16 final size:18
Alignment explanation
Indices: 36146--36178 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
36136 GAGTTATTTA
36146 AATATTTAATT-AAGAAC
1 AATATTTAATTGAAGAAC
36163 AATA-TTAATTGAAGAA
1 AATATTTAATTGAAGAA
36179 TTAAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (18 bp):
AATATTTAATTGAAGAAC
Done.