Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005465.1 Kokia drynarioides strain JFW-HI SEQ_119512, 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: 8166
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:70 original size:29 final size:30
Alignment explanation
Indices: 11--233 Score: 150
Period size: 29 Copynumber: 7.7 Consensus size: 30
1 TTTAGAAAAA
* * * *
11 TCGAGGTTAAAAATGGAGTTTTTGG-AGGT
1 TCGAGGGTAAAAATGTAATTTTTGGAAAGT
40 TCGAGGGT-AAAATGTAATTTTTGGAAAGT
1 TCGAGGGTAAAAATGTAATTTTTGGAAAGT
* *
69 TC-ATGGTCAAAAATGGAA-TTTTGGAAAGT
1 TCGAGGGT-AAAAATGTAATTTTTGGAAAGT
* * *
98 T-TAGGTGTAAAAATGTACTTTTTGGAAAAT
1 TCGAGG-GTAAAAATGTAATTTTTGGAAAGT
* * * *
128 TTG-GGGTCAAAAATGGAA-ATTTGTAAAGT
1 TCGAGGGT-AAAAATGTAATTTTTGGAAAGT
* * *
157 T-TAGGGGT-AAAATGTAAATTTTGGAAAAT
1 TCGA-GGGTAAAAATGTAATTTTTGGAAAGT
186 T--AGGGTCAAAAATAG-AA-TTTTGGAAAGT
1 TCGAGGGT-AAAAAT-GTAATTTTTGGAAAGT
214 TCGA-GGTAAAAATGTAATTT
1 TCGAGGGTAAAAATGTAATTT
234 ATAGATAATT
Statistics
Matches: 154, Mismatches: 22, Indels: 36
0.73 0.10 0.17
Matches are distributed among these distances:
27 5 0.03
28 46 0.30
29 66 0.43
30 37 0.24
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.34
Consensus pattern (30 bp):
TCGAGGGTAAAAATGTAATTTTTGGAAAGT
Found at i:122 original size:59 final size:57
Alignment explanation
Indices: 44--233 Score: 238
Period size: 59 Copynumber: 3.3 Consensus size: 57
34 GGAGGTTCGA
* *
44 GGGTAAAATGTAATTTTTGGAAAGTTCATGGTCAAAAATGGAATTTTGGAAAGTTTAG
1 GGGTAAAATGTAATTTTTGGAAAATT-AGGGTCAAAAATGGAATTTTGGAAAGTTTAG
* * * * *
102 GTGTAAAAATGTACTTTTTGGAAAATTTGGGGTCAAAAATGGAAATTTGTAAAGTTTAG
1 GGGT-AAAATGTAATTTTTGGAAAA-TTAGGGTCAAAAATGGAATTTTGGAAAGTTTAG
* * *
161 GGGTAAAATGTAAATTTTGGAAAATTAGGGTCAAAAATAGAATTTTGGAAAG-TTCG
1 GGGTAAAATGTAATTTTTGGAAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTTAG
*
217 AGGTAAAAATGTAATTT
1 GGGT-AAAATGTAATTT
234 ATAGATAATT
Statistics
Matches: 112, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
56 6 0.05
57 35 0.31
58 21 0.19
59 48 0.43
60 2 0.02
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (57 bp):
GGGTAAAATGTAATTTTTGGAAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTTAG
Found at i:924 original size:21 final size:21
Alignment explanation
Indices: 900--940 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
890 TATTTTTTAA
*
900 AACG-GATCTAGGTCTAGATCG
1 AACGCGATCTA-GCCTAGATCG
921 AACGCGATCTAGCCTAGATC
1 AACGCGATCTAGCCTAGATC
941 TAAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (21 bp):
AACGCGATCTAGCCTAGATCG
Found at i:1321 original size:3 final size:3
Alignment explanation
Indices: 1313--1345 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1303 CTTTTTTCGG
1313 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1346 CCGTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2066 original size:17 final size:17
Alignment explanation
Indices: 2051--2111 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
2041 TTAAAATTTT
2051 ATTTCAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
2069 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
* * *
2086 ACTTAAAATGAATTAAA
1 ATTTAAAATAAATTTAA
*
2103 AATTAAAAT
1 ATTTAAAAT
2112 CTAAAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 35 0.90
18 4 0.10
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:4266 original size:36 final size:36
Alignment explanation
Indices: 4226--4295 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
4216 ATAGAAGTAA
*
4226 ATTTGATAAATTGAGTAA-TTTAAATACAGGATAATT
1 ATTTGATAAATT-AGGAATTTTAAATACAGGATAATT
*
4262 ATTTGATAAATTAGGAATTTTATATACAGGATAA
1 ATTTGATAAATTAGGAATTTTAAATACAGGATAA
4296 ATTGAGTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 4 0.13
36 27 0.87
ACGTcount: A:0.44, C:0.03, G:0.14, T:0.39
Consensus pattern (36 bp):
ATTTGATAAATTAGGAATTTTAAATACAGGATAATT
Found at i:6263 original size:26 final size:26
Alignment explanation
Indices: 6234--6284 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
6224 CGTGGTGTAG
* *
6234 TTAATGGACGCATTTGTGGCTATCTC
1 TTAATAGACGCATTTGTGACTATCTC
*
6260 TTAATAGACGCCTTTGTGACTATCT
1 TTAATAGACGCATTTGTGACTATCT
6285 ATGTGAATGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (26 bp):
TTAATAGACGCATTTGTGACTATCTC
Done.