Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005884.1 Kokia drynarioides strain JFW-HI SEQ_120215, 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: 33168
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3574 original size:20 final size:19
Alignment explanation
Indices: 3536--3573 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3526 TAAAATGGTA
3536 CTTAAACTATACTATTTTT
1 CTTAAACTATACTATTTTT
*
3555 CTTAAATTAGTACT-TTTTT
1 CTTAAACTA-TACTATTTTT
3574 TTTTTGTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.29, C:0.13, G:0.03, T:0.55
Consensus pattern (19 bp):
CTTAAACTATACTATTTTT
Found at i:4896 original size:17 final size:18
Alignment explanation
Indices: 4874--4921 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
4864 AAAGTGTGTA
*
4874 ATTTAAATATTTTAAA-T
1 ATTTAAATATTATAAATT
4891 ATTTAAA-ATTATAAATT
1 ATTTAAATATTATAAATT
* *
4908 ATTCAAATAATATA
1 ATTTAAATATTATA
4922 TTATAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 7 0.27
17 14 0.54
18 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTAAATATTATAAATT
Found at i:4941 original size:21 final size:23
Alignment explanation
Indices: 4898--4941 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
4888 AATATTTAAA
*
4898 ATTATAAATTATTCAAATAATAT
1 ATTATAAATTATTAAAATAATAT
*
4921 ATTAT-AATT-TTAAAATTATAT
1 ATTATAAATTATTAAAATAATAT
4942 TCTATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 4 0.21
23 5 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTATAAATTATTAAAATAATAT
Found at i:4942 original size:19 final size:18
Alignment explanation
Indices: 4918--4954 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4908 ATTCAAATAA
4918 TATATTATAATTTTAAAAT
1 TATATTAT-ATTTTAAAAT
*
4937 TATATTCTATTTTAAAAT
1 TATATTATATTTTAAAAT
4955 AACAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATTATATTTTAAAAT
Found at i:11834 original size:3 final size:3
Alignment explanation
Indices: 11826--11894 Score: 120
Period size: 3 Copynumber: 23.0 Consensus size: 3
11816 GTTCGGGCTC
* *
11826 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA TTA CTA CTA TTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
11874 CTA CTA CTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA
11895 TTATTATTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (3 bp):
CTA
Found at i:13063 original size:19 final size:20
Alignment explanation
Indices: 13034--13081 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
13024 TTGCTCCCAC
*
13034 TTATATATTTTATTTAATTT
1 TTATATATTTTAATTAATTT
*
13054 TTAT-TATTTTAATTATTTT
1 TTATATATTTTAATTAATTT
*
13073 TTATCTATT
1 TTATATATT
13082 ATTTATTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATATATTTTAATTAATTT
Found at i:13117 original size:18 final size:17
Alignment explanation
Indices: 13066--13109 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
13056 ATTATTTTAA
* *
13066 TTATTTTTTATCTATTAT
1 TTATTTGTTA-CTATTTT
13084 TTATTTGTTACTATTTT
1 TTATTTGTTACTATTTT
13101 TTATATTGT
1 TTAT-TTGT
13110 CTACATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (17 bp):
TTATTTGTTACTATTTT
Found at i:13142 original size:14 final size:15
Alignment explanation
Indices: 13123--13157 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
13113 CATTTATGCC
13123 TTATTTAATTTT-AT
1 TTATTTAATTTTCAT
*
13137 TTATTTATTTTTCAT
1 TTATTTAATTTTCAT
13152 TTATTT
1 TTATTT
13158 TTTATGTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTAATTTTCAT
Found at i:23536 original size:49 final size:49
Alignment explanation
Indices: 23462--24049 Score: 355
Period size: 49 Copynumber: 12.0 Consensus size: 49
23452 CACACCAAAT
* * * *
23462 CCTAAAGTTGAAGAGGGACATATTAAAGCTGTAACGATGAATCTTACAA
1 CCTAAAATCGAAGAGGGACAGATTAAAGCTGTAACGATGAATCTTACAC
*
23511 CCTAAAATCGAAGAGGGACAAATTAAAG-TCGTAACGATGAATCTTACAC
1 CCTAAAATCGAAGAGGGACAGATTAAAGCT-GTAACGATGAATCTTACAC
* * *
23560 CCTAAAATTGAATAGCGACAGATTAAAG-TCGTAACGA-G--TCTTACAC
1 CCTAAAATCGAAGAGGGACAGATTAAAGCT-GTAACGATGAATCTTACAC
* * * * *
23606 CCTAAAATCAAAGAGGGATAGATTAAAACTGCAACGATTAATCTTACAC
1 CCTAAAATCGAAGAGGGACAGATTAAAGCTGTAACGATGAATCTTACAC
* ** * ** * * *
23655 CCTAAAA-CAAAAGAAAGACATATTAAAGCTACAATGGTAAATCTTACAC
1 CCTAAAATC-GAAGAGGGACAGATTAAAGCTGTAACGATGAATCTTACAC
* * * * * * * *
23704 CCCAAAACCAAAAAGGGATAGATTAAAGTTGCAACGGTGAATCTTACAC
1 CCTAAAATCGAAGAGGGACAGATTAAAGCTGTAACGATGAATCTTACAC
* * * *
23753 CCTAAAAATTGAAGAAGGACAGATTAAAGCCGTAACGAAGAATCTTACATC
1 CCT-AAAATCGAAGAGGGACAGATTAAAGCTGTAACGATGAATCTTACA-C
* * * **
23804 GC-AAAA-CTGAAGAGTGACAAATTAAAG-TCGTAATAATGAATCTTACA-
1 CCTAAAATC-GAAGAGGGACAGATTAAAGCT-GTAACGATGAATCTTACAC
* * * * ** * *
23851 CCAAAAAACTAAAAAGGGATGGATTAAAG-TCATAACAGA-AAATCTTACAC
1 CCTAAAATC-GAAGAGGGACAGATTAAAGCT-GTAAC-GATGAATCTTACAC
* * * * * *
23901 CCCAAAATTGAAGAGGGATAGATTAAAG-TCATAA-TAGTGAATCTTATAC
1 CCTAAAATCGAAGAGGGACAGATTAAAGCT-GTAACGA-TGAATCTTACAC
* * * * **
23950 CGC-AAAATTGAAGAGGAACAGATTAAAG-TCGCAATGACAAATCTTACACC
1 C-CTAAAATCGAAGAGGGACAGATTAAAGCT-GTAACGATGAATCTTACA-C
* * *
24000 CCTAAAA-CTAAAGAGGGACAGATTAAAGCTGCAACGGTGAATCTTACAC
1 CCTAAAATC-GAAGAGGGACAGATTAAAGCTGTAACGATGAATCTTACAC
24049 C
1 C
24050 TTTAAACCCG
Statistics
Matches: 425, Mismatches: 91, Indels: 46
0.76 0.16 0.08
Matches are distributed among these distances:
46 36 0.08
47 3 0.01
48 7 0.02
49 295 0.69
50 81 0.19
51 3 0.01
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (49 bp):
CCTAAAATCGAAGAGGGACAGATTAAAGCTGTAACGATGAATCTTACAC
Found at i:23946 original size:246 final size:241
Alignment explanation
Indices: 23483--24049 Score: 541
Period size: 246 Copynumber: 2.3 Consensus size: 241
23473 AGAGGGACAT
* * * * * *
23483 ATTAAAGCTGTAACGATGAATCTTACAACCTAAAATCGAAGAGGGACAAATTAAAGTCGTAACGA
1 ATTAAAGTTGCAACGATGAATCTTACACCCTAAAATTGAAGAGGGACAGATTAAAGCCGTAACGA
* * * * **
23548 TGAATCTTACACCCTAAAATTGAATAGCGACAGATTAAAGTCGTAACGAGTCTTACACCCTAAAA
66 TGAATCTTACACCCTAAAACTGAAGAGCGACAAATTAAAGTCGTAACGAATCTTACACCAAAAAA
* * * *
23613 TCAAAGAGGGATAGATTAAAACTGCAACGATTAATCTTACACCCTAAAACAAAAGAAAGACATAT
131 TCAAAAAGGGATAGATTAAAACT-CAACGATAAATCTTACACCCCAAAACAAAAGAAAGACAGAT
* * *
23678 TAAAGCTACAATGGTAAATCTTACACCCCAAAACCAAAAAGGGATAG
195 TAAAGCTACAATAGTAAATCTTACACCCCAAAACCAAAAAGGAACAG
* *
23725 ATTAAAGTTGCAACGGTGAATCTTACACCCTAAAAATTGAAGAAGGACAGATTAAAGCCGTAACG
1 ATTAAAGTTGCAACGATGAATCTTACACCCT-AAAATTGAAGAGGGACAGATTAAAGCCGTAACG
* * * *
23790 AAGAATCTTACATCGC-AAAACTGAAGAGTGACAAATTAAAGTCGTAATAATGAATCTTACACCA
65 ATGAATCTTACA-CCCTAAAACTGAAGAGCGACAAATTAAAGTCG---TAACGAATCTTACACCA
* * *** *
23854 AAAAA-CTAAAAAGGGATGGATT-AAAGTCATAACAGA-AAATCTTACACCCCAAAATTGAAGAG
126 AAAAATC-AAAAAGGGATAGATTAAAACTC--AAC-GATAAATCTTACACCCCAAAACAAAAGAA
* * * * * * *** *
23916 GGATAGATTAAAG-TCATAATAGTGAATCTTATACCGCAAAATTGAAGAGGAACAG
187 AGACAGATTAAAGCT-ACAATAGTAAATCTTACACCCCAAAACCAAAAAGGAACAG
* * ** * * * *
23971 ATTAAAGTCGCAATGACAAATCTTACACCCCTAAAACTAAAGAGGGACAGATTAAAGCTGCAACG
1 ATTAAAGTTGCAACGATGAATCTTACA-CCCTAAAATTGAAGAGGGACAGATTAAAGCCGTAACG
*
24036 GTGAATCTTACACC
65 ATGAATCTTACACC
24050 TTTAAACCCG
Statistics
Matches: 260, Mismatches: 54, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
242 27 0.10
243 64 0.25
244 3 0.01
245 7 0.03
246 153 0.59
247 6 0.02
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.21
Consensus pattern (241 bp):
ATTAAAGTTGCAACGATGAATCTTACACCCTAAAATTGAAGAGGGACAGATTAAAGCCGTAACGA
TGAATCTTACACCCTAAAACTGAAGAGCGACAAATTAAAGTCGTAACGAATCTTACACCAAAAAA
TCAAAAAGGGATAGATTAAAACTCAACGATAAATCTTACACCCCAAAACAAAAGAAAGACAGATT
AAAGCTACAATAGTAAATCTTACACCCCAAAACCAAAAAGGAACAG
Found at i:24122 original size:50 final size:50
Alignment explanation
Indices: 23891--24143 Score: 192
Period size: 50 Copynumber: 5.1 Consensus size: 50
23881 CATAACAGAA
* * * * *
23891 AATCTTACACCCC-AAAATTGAAGAGGGATAGATTAAAG-T-CATAATAGTG
1 AATCTTACACCCCTAAAACTGAAGAGGGACAGATTGAAGCTGCA-AA-GGCG
* * * * * * * *
23940 AATCTTATACCGC-AAAATTGAAGAGGAACAGATTAAAG-TCGCAATGACA
1 AATCTTACACCCCTAAAACTGAAGAGGGACAGATTGAAGCT-GCAAAGGCG
* * * *
23989 AATCTTACACCCCTAAAACTAAAGAGGGACAGATTAAAGCTGCAACGGTG
1 AATCTTACACCCCTAAAACTGAAGAGGGACAGATTGAAGCTGCAAAGGCG
** * * * * *
24039 AATCTTACACCTTTAAACCCGAATAGAGACAGATTGAAGCTACAAAGGCG
1 AATCTTACACCCCTAAAACTGAAGAGGGACAGATTGAAGCTGCAAAGGCG
* * * *
24089 AATCGTACACCCCTAAAACTGTAGAGGGGCAGATTGAAGCCGCAAAGGCG
1 AATCTTACACCCCTAAAACTGAAGAGGGACAGATTGAAGCTGCAAAGGCG
24139 AATCT
1 AATCT
24144 CATATCTCCG
Statistics
Matches: 159, Mismatches: 41, Indels: 7
0.77 0.20 0.03
Matches are distributed among these distances:
49 46 0.29
50 110 0.69
51 3 0.02
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (50 bp):
AATCTTACACCCCTAAAACTGAAGAGGGACAGATTGAAGCTGCAAAGGCG
Found at i:24442 original size:3 final size:3
Alignment explanation
Indices: 24434--24488 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
24424 GGCTCCTACA
*
24434 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
24480 ATT ATT ATT
1 ATT ATT ATT
24489 TATTTATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:25465 original size:58 final size:58
Alignment explanation
Indices: 25375--25489 Score: 221
Period size: 58 Copynumber: 2.0 Consensus size: 58
25365 CCTAACTCAA
*
25375 TAGGCTCTAAAACGATATCGTTTTGACCATGACCCGACAATCCTATCCGACCCAGGTT
1 TAGGCTCTAAAACGACATCGTTTTGACCATGACCCGACAATCCTATCCGACCCAGGTT
25433 TAGGCTCTAAAACGACATCGTTTTGACCATGACCCGACAATCCTATCCGACCCAGGT
1 TAGGCTCTAAAACGACATCGTTTTGACCATGACCCGACAATCCTATCCGACCCAGGT
25490 AAGATCAATG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (58 bp):
TAGGCTCTAAAACGACATCGTTTTGACCATGACCCGACAATCCTATCCGACCCAGGTT
Found at i:25814 original size:11 final size:11
Alignment explanation
Indices: 25790--25828 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
25780 CATTTATGCC
25790 TTATTTAATT-
1 TTATTTAATTA
25800 TTATTTAATTA
1 TTATTTAATTA
*
25811 TTATTTATTTA
1 TTATTTAATTA
*
25822 TTTTTTA
1 TTATTTA
25829 TATGTTGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTTAATTA
Found at i:28811 original size:19 final size:18
Alignment explanation
Indices: 28761--28823 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
28751 ATTTTAAATA
28761 TTTAAAATTATAATT-TA-
1 TTTAAAATTAT-ATTATAT
* *
28778 TTCAAATAATATATTATAAT
1 TTTAAA-ATTATATTAT-AT
*
28798 TTTAAAATTATATTCTAT
1 TTTAAAATTATATTATAT
28816 TTTAAAAT
1 TTTAAAAT
28824 AAAAAATTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 8 0.22
18 15 0.41
19 9 0.24
20 5 0.14
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAAATTATATTATAT
Done.