Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000353.1 Kokia drynarioides strain JFW-HI SEQ_111136, 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: 3911
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:66 original size:10 final size:10
Alignment explanation
Indices: 51--117 Score: 55
Period size: 10 Copynumber: 6.4 Consensus size: 10
41 TAATATTTTT
51 TATTTTTATA
1 TATTTTTATA
61 TATTTTT-TA
1 TATTTTTATA
*
70 AATTTATTATTA
1 TATTT-TTA-TA
*
82 TATTTTTTTGA
1 TATTTTTAT-A
* *
93 AATTATTTATG
1 TATT-TTTATA
104 TATTTTTATA
1 TATTTTTATA
114 TATT
1 TATT
118 CCTTTTAGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
9 6 0.14
10 19 0.43
11 9 0.20
12 10 0.23
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (10 bp):
TATTTTTATA
Found at i:74 original size:19 final size:19
Alignment explanation
Indices: 43--110 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 19
33 CTTGTCAATA
43 ATATTTTTT--ATTTTTAT
1 ATATTTTTTAAATTTTTAT
60 ATATTTTTTAAATTTATTATT
1 ATATTTTTTAAATTT-TTA-T
81 ATATTTTTTTGAAATTATTTAT
1 ATA-TTTTTT-AAATT-TTTAT
*
103 GTATTTTT
1 ATATTTTT
111 ATATATTCCT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
17 9 0.21
19 4 0.09
20 3 0.07
21 9 0.21
22 9 0.21
23 8 0.19
24 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
ATATTTTTTAAATTTTTAT
Found at i:99 original size:22 final size:23
Alignment explanation
Indices: 49--96 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
39 AATAATATTT
*
49 TTTATTTTTATATATTTTTTAAA
1 TTTATTATTATATATTTTTTAAA
72 TTTATTATTATAT-TTTTTTGAAA
1 TTTATTATTATATATTTTTT-AAA
95 TT
1 TT
97 ATTTATGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTATTATTATATATTTTTTAAA
Found at i:102 original size:23 final size:22
Alignment explanation
Indices: 50--110 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
40 ATAATATTTT
50 TTATTT-TTATATATTTTTTAAA
1 TTATTTATTATAT-TTTTTTAAA
72 TT-TATTATTATATTTTTTTGAAA
1 TTAT-TTATTATATTTTTTT-AAA
*
95 TTATTTA-TGTATTTTT
1 TTATTTATTATATTTTT
111 ATATATTCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 1 0.03
22 18 0.53
23 14 0.41
24 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (22 bp):
TTATTTATTATATTTTTTTAAA
Found at i:2092 original size:326 final size:326
Alignment explanation
Indices: 1499--2139 Score: 1237
Period size: 326 Copynumber: 2.0 Consensus size: 326
1489 AAAACAAATA
1499 TGTTGTGGGATTTTTTTTATATCGAGGATTATCTATTTTCTATTCAATATAGGTTAAAATTTTTG
1 TGTTGTGGGATTTTTTTTATATCGAGGATTATCTATTTTCTATTCAATATAGGTTAAAATTTTTG
*
1564 GGATTAATATAAAAACTTTGTATTTTAACAGTAAAAGAAAAGAAAAGAAAAGAAAATTGGGTTTT
66 GGATTAATATAAAAACTTTGTATTTTAACAGTAAAAGAAAAGAAAAGAAAAGAAAATTGGGTTTA
* *
1629 GGCTTTTTTTTTTTGGCGGAAATAGAAATTAATTAACCGGAACTAATTACATAGTAGTGTTCTAG
131 GGCTTTTTTTTTTTGGCGGAAATAGAAATTAATTAACCAGAACTAATTACATAGTAGTATTCTAG
1694 AAGGGTGGTACATCCCTATCTTTACCTAAATCAAATATAGATCGAACCACTGAAGGTGGGTCTTC
196 AAGGGTGGTACATCCCTATCTTTACCTAAATCAAATATAGATCGAACCACTGAAGGTGGGTCTTC
*
1759 AAATACTTGCAAATCATCTTCCCCGAGTAAGGCTTGCTTGGCCAATAACTTAGCAATAACTTAGC
261 AAATACTTGCAAATCATCTTCCCCGAGTAAGGCTAGCTTGGCCAATAACTTAGCAATAACTTAGC
1824 T
326 T
1825 TGTTGTGGGATTTTTTTTATATCGAGGATTATCTATTTTCTATTCAATATAGGTTAAAATTTTTG
1 TGTTGTGGGATTTTTTTTATATCGAGGATTATCTATTTTCTATTCAATATAGGTTAAAATTTTTG
1890 GGATTAATATAAAAACTTTGTATTTTAACAGTAAAAGAAAAGAAAAGAAAAGAAAATTGGGTTTA
66 GGATTAATATAAAAACTTTGTATTTTAACAGTAAAAGAAAAGAAAAGAAAAGAAAATTGGGTTTA
1955 GGCTTTTTTTTTTTGGCGGAAATAGAAATTAATTAACCAGAACTAATTACATAGTAGTATTCTAG
131 GGCTTTTTTTTTTTGGCGGAAATAGAAATTAATTAACCAGAACTAATTACATAGTAGTATTCTAG
*
2020 AAGGGTGGTACATCCCTATCTTTACCTAAATCAAATATAGATCGAACCATTGAAGGTGGGTCTTC
196 AAGGGTGGTACATCCCTATCTTTACCTAAATCAAATATAGATCGAACCACTGAAGGTGGGTCTTC
2085 AAATACTTGCAAATCATCTTCCCCGAGTAAGGCTAGCTTGGCCAATAACTTAGCA
261 AAATACTTGCAAATCATCTTCCCCGAGTAAGGCTAGCTTGGCCAATAACTTAGCA
2140 TTAAAAATTG
Statistics
Matches: 310, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
326 310 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (326 bp):
TGTTGTGGGATTTTTTTTATATCGAGGATTATCTATTTTCTATTCAATATAGGTTAAAATTTTTG
GGATTAATATAAAAACTTTGTATTTTAACAGTAAAAGAAAAGAAAAGAAAAGAAAATTGGGTTTA
GGCTTTTTTTTTTTGGCGGAAATAGAAATTAATTAACCAGAACTAATTACATAGTAGTATTCTAG
AAGGGTGGTACATCCCTATCTTTACCTAAATCAAATATAGATCGAACCACTGAAGGTGGGTCTTC
AAATACTTGCAAATCATCTTCCCCGAGTAAGGCTAGCTTGGCCAATAACTTAGCAATAACTTAGC
T
Done.