Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011546.1 Kokia drynarioides strain JFW-HI SEQ_126532, 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: 39406
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:1197 original size:21 final size:21
Alignment explanation
Indices: 1173--1218 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1163 AAGCAGACGC
*
1173 AGCAATGAGAGAAGCAAAGGA
1 AGCAACGAGAGAAGCAAAGGA
* *
1194 AGCAGCGAGAGAAGCGAAGGA
1 AGCAACGAGAGAAGCAAAGGA
1215 AGCA
1 AGCA
1219 GAGGCAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.13, G:0.37, T:0.02
Consensus pattern (21 bp):
AGCAACGAGAGAAGCAAAGGA
Found at i:1219 original size:21 final size:21
Alignment explanation
Indices: 1179--1219 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1169 ACGCAGCAAT
1179 GAGAGAAGCAAAGGAAGCAGC
1 GAGAGAAGCAAAGGAAGCAGC
*
1200 GAGAGAAGCGAAGGAAGCAG
1 GAGAGAAGCAAAGGAAGCAG
1220 AGGCAACAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.41, T:0.00
Consensus pattern (21 bp):
GAGAGAAGCAAAGGAAGCAGC
Found at i:1761 original size:43 final size:43
Alignment explanation
Indices: 1596--1873 Score: 189
Period size: 43 Copynumber: 6.5 Consensus size: 43
1586 AAAGCACTGT
* * * * * * *
1596 TAAAGATCATGTTTTTTAGTGGCGTTTGGGGCAAAAGCGTTGC
1 TAAAGACCATGTTCTTTAGCGACGTTTGTGGAAAAAGCGTCGC
** ** * ** *
1639 TAAAGATTATGTTCTTTAGCGGTGTTTGT-GAGGAAAGCCCCGA
1 TAAAGACCATGTTCTTTAGCGACGTTTGTGGA-AAAAGCGTCGC
* ** * * * * * ** *
1682 TAAAGACCATGTGCAATAGCGGCATTAGTTGCAAAAGCCCCGT
1 TAAAGACCATGTTCTTTAGCGACGTTTGTGGAAAAAGCGTCGC
* *
1725 TAAAGACCATGTTCTTTAACGACGTTTGTGAAAAAAGCGTCGC
1 TAAAGACCATGTTCTTTAGCGACGTTTGTGGAAAAAGCGTCGC
* * * * ** *
1768 TAAAAACCATGTTCTTTGGCGGCATTTGTGGGGAAAGCGTTGC
1 TAAAGACCATGTTCTTTAGCGACGTTTGTGGAAAAAGCGTCGC
* * *
1811 GAAAGACCATGTTCTTTAGCGACGTTTGTGGACAAAGCATCGC
1 TAAAGACCATGTTCTTTAGCGACGTTTGTGGAAAAAGCGTCGC
*
1854 TAAAGATCATGTTCTTTAGC
1 TAAAGACCATGTTCTTTAGC
1874 AGCATTTATT
Statistics
Matches: 178, Mismatches: 55, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
42 1 0.01
43 176 0.99
44 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (43 bp):
TAAAGACCATGTTCTTTAGCGACGTTTGTGGAAAAAGCGTCGC
Found at i:9626 original size:31 final size:31
Alignment explanation
Indices: 9583--9650 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
9573 TTGCAAAATG
9583 ATCACTGAACTATTCAAAAGTTTTCATTTAA
1 ATCACTGAACTATTCAAAAGTTTTCATTTAA
* * *
9614 ATCATTGAACTATTTAAAAGTTTTTATTTAA
1 ATCACTGAACTATTCAAAAGTTTTCATTTAA
9645 ATCACT
1 ATCACT
9651 AAATTATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (31 bp):
ATCACTGAACTATTCAAAAGTTTTCATTTAA
Found at i:17511 original size:5 final size:5
Alignment explanation
Indices: 17501--17526 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17491 AGGGTGCTAC
17501 TGTTT TGTTT TGTTT TGTTT TGTTT T
1 TGTTT TGTTT TGTTT TGTTT TGTTT T
17527 TAATCCTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TGTTT
Found at i:20227 original size:6 final size:6
Alignment explanation
Indices: 20218--20243 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20208 AGGTAAAGGT
20218 AAAGCA AAAGCA AAAGCA AAAGCA AA
1 AAAGCA AAAGCA AAAGCA AAAGCA AA
20244 CCACGCCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGCA
Found at i:34426 original size:17 final size:18
Alignment explanation
Indices: 34404--34439 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
34394 TAAATGAGTT
34404 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
34421 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
34439 A
1 A
34440 TAAAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:34759 original size:18 final size:18
Alignment explanation
Indices: 34736--34772 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
34726 TTTGTAATCA
34736 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
34754 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
34772 A
1 A
34773 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Done.