Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011708.1 Kokia drynarioides strain JFW-HI SEQ_126702, 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: 13199
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Found at i:1088 original size:19 final size:20
Alignment explanation
Indices: 1066--1112 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1056 TTTTTTACAT
1066 ATATTTTTATA-TTTTCGAA
1 ATATTTTTATACTTTTCGAA
1085 ATATTTTT-TAGCTTTTCGAA
1 ATATTTTTATA-CTTTTCGAA
1105 AT-TTTTTA
1 ATATTTTTA
1113 AAATTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 13 0.52
20 10 0.40
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (20 bp):
ATATTTTTATACTTTTCGAA
Found at i:1092 original size:20 final size:20
Alignment explanation
Indices: 1064--1111 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1054 ATTTTTTTAC
*
1064 ATATATTTTTATATTTTCGAA
1 ATAT-TTTTTAGATTTTCGAA
*
1085 ATATTTTTTAGCTTTTCGAA
1 ATATTTTTTAGATTTTCGAA
1105 AT-TTTTT
1 ATATTTTT
1112 AAAATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.20
20 16 0.64
21 4 0.16
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.60
Consensus pattern (20 bp):
ATATTTTTTAGATTTTCGAA
Found at i:2224 original size:30 final size:30
Alignment explanation
Indices: 2131--2246 Score: 157
Period size: 30 Copynumber: 3.9 Consensus size: 30
2121 GATTTTATCG
* * *
2131 TTTATTTTTTAAAATTTAATTTGTAATTTCG
1 TTTATATTTT-AAATTTAATTTTTAATTTCT
*
2162 TTTATA-TTTAAATTT-ATTTCTAATTT-T
1 TTTATATTTTAAATTTAATTTTTAATTTCT
2189 ATTTATATTTTAAATTTAATTTTTAATTTCT
1 -TTTATATTTTAAATTTAATTTTTAATTTCT
2220 TTTATATTTTAAATTTAATTTTTAATT
1 TTTATATTTTAAATTTAATTTTTAATT
2247 ATTATTTTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
28 16 0.21
29 15 0.19
30 40 0.52
31 6 0.08
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (30 bp):
TTTATATTTTAAATTTAATTTTTAATTTCT
Found at i:2253 original size:13 final size:12
Alignment explanation
Indices: 2162--2255 Score: 50
Period size: 12 Copynumber: 7.8 Consensus size: 12
2152 TGTAATTTCG
* *
2162 TTTATATTTAAA
1 TTTATTTTTAAT
*
2174 TTTATTTCTAAT
1 TTTATTTTTAAT
*
2186 TTTATTTAT-AT
1 TTTATTTTTAAT
**
2197 TTTAAATTTAATT
1 TTTATTTTTAA-T
2210 TTTAATTTCTT--T
1 TTT-ATTT-TTAAT
* *
2222 TATATTTTAAAT
1 TTTATTTTTAAT
*
2234 TTAATTTTTAAT
1 TTTATTTTTAAT
2246 TATTATTTTT
1 T-TTATTTTT
2256 TTTCAAAATT
Statistics
Matches: 60, Mismatches: 15, Indels: 13
0.68 0.17 0.15
Matches are distributed among these distances:
10 1 0.02
11 12 0.20
12 32 0.53
13 11 0.18
14 2 0.03
15 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTATTTTTAAT
Found at i:2502 original size:17 final size:17
Alignment explanation
Indices: 2466--2516 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
2456 GAATAACAAT
*
2466 AATACAAA-ATAAATTAA
1 AATACAAATATATA-TAA
*
2483 AATTACAGATATA-ATAA
1 AA-TACAAATATATATAA
2500 AATACAAATATATATAA
1 AATACAAATATATATAA
2517 TGTCCATCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 9 0.31
17 11 0.38
18 6 0.21
19 3 0.10
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (17 bp):
AATACAAATATATATAA
Found at i:3436 original size:13 final size:13
Alignment explanation
Indices: 3420--3445 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3410 ATTTAGAATC
3420 ATTATTGTTCATT
1 ATTATTGTTCATT
3433 ATTATTGTTCATT
1 ATTATTGTTCATT
3446 TTAAGTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (13 bp):
ATTATTGTTCATT
Found at i:8858 original size:44 final size:44
Alignment explanation
Indices: 8808--8919 Score: 188
Period size: 44 Copynumber: 2.5 Consensus size: 44
8798 CATATGTATA
* *
8808 ACAAGCATTTAAATAATTAACTCATTTAATGCCTTCTGCATATT
1 ACAAGCAATTAAATAATTAACTCATTTAATCCCTTCTGCATATT
*
8852 ACAAGCACTTAAATAATTAACTCATTTAATCCCTTCTGCATATT
1 ACAAGCAATTAAATAATTAACTCATTTAATCCCTTCTGCATATT
*
8896 ACAAGTAATTAAATAATTAACTCA
1 ACAAGCAATTAAATAATTAACTCA
8920 AATTTTAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 64 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (44 bp):
ACAAGCAATTAAATAATTAACTCATTTAATCCCTTCTGCATATT
Found at i:12144 original size:22 final size:23
Alignment explanation
Indices: 12119--12176 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
12109 GCTGGGAAAA
*
12119 CAGTAAGCACACACAGAGC-AAT
1 CAGTAGGCACACACAGAGCAAAT
* * *
12141 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGAGCAAAT
12164 CAGTAGGCACACA
1 CAGTAGGCACACA
12177 AGGTGTGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 15 0.50
23 15 0.50
ACGTcount: A:0.40, C:0.28, G:0.22, T:0.10
Consensus pattern (23 bp):
CAGTAGGCACACACAGAGCAAAT
Found at i:12190 original size:23 final size:23
Alignment explanation
Indices: 12091--12240 Score: 99
Period size: 23 Copynumber: 6.4 Consensus size: 23
12081 CGAAGTACTT
12091 AACAGTAAGCACAC-AAGTGCTGGGAA
1 AACAGTAAGCACACAAAGTGC---G-A
* *
12117 AACAGTAAGCACACACAGAGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * * *
12139 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * *
12161 AATCAGTAGGCACACAAGGTGTGA
1 AA-CAGTAAGCACACAAAGTGCGA
12185 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
* * * *
12208 AACAATAAGGACACGAAGTGCAA
1 AACAGTAAGCACACAAAGTGCGA
*
12231 AACAGCAAGC
1 AACAGTAAGC
12241 GCACTAGCGT
Statistics
Matches: 98, Mismatches: 23, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
22 19 0.19
23 58 0.59
24 3 0.03
26 14 0.14
27 4 0.04
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Done.