Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000319.1 Kokia drynarioides strain JFW-HI SEQ_111083, 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: 3555
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.37
Found at i:1275 original size:6 final size:6
Alignment explanation
Indices: 1264--1346 Score: 79
Period size: 6 Copynumber: 14.7 Consensus size: 6
1254 ATTTTGAAAA
1264 TAAATT TAAATT TAAA-T TAAATT TAAATT TAAGA-T T-AATT T-AATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAA-ATT TAAATT TAAATT
* * * *
1309 CAAATT TAAA-A TAAATC TAAATT TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
1347 AGGGGCCCGA
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
4 1 0.02
5 20 0.31
6 42 0.66
7 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:1285 original size:11 final size:11
Alignment explanation
Indices: 1264--1346 Score: 64
Period size: 11 Copynumber: 7.4 Consensus size: 11
1254 ATTTTGAAAA
1264 TAAATTTAAATT
1 TAAA-TTAAATT
1276 TAAATTAAATT
1 TAAATTAAATT
1287 TAAATTTAAGA-T
1 TAAA-TTAA-ATT
*
1299 T-AATTTAATT
1 TAAATTAAATT
* *
1309 CAAATTTAAA-A
1 TAAA-TTAAATT
1320 TAAATCTAAATT
1 TAAAT-TAAATT
*
1332 TAAAATAAATT
1 TAAATTAAATT
1343 TAAA
1 TAAA
1347 AGGGGCCCGA
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
9 1 0.02
10 5 0.09
11 32 0.56
12 18 0.32
13 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (11 bp):
TAAATTAAATT
Found at i:1286 original size:17 final size:17
Alignment explanation
Indices: 1260--1346 Score: 93
Period size: 17 Copynumber: 4.8 Consensus size: 17
1250 TGTTATTTTG
1260 AAAATAAATTTAAATTT
1 AAAATAAATTTAAATTT
*
1277 AAATTAAATTTAAATTT
1 AAAATAAATTTAAATTT
* *
1294 AAGATTAATTTAATTCAAATTT
1 -A-A--AA-TAAATTTAAATTT
*
1316 AAAATAAATCTAAATTT
1 AAAATAAATTTAAATTT
1333 AAAATAAATTTAAA
1 AAAATAAATTTAAA
1347 AGGGGCCCGA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
17 39 0.68
18 3 0.05
19 1 0.02
20 1 0.02
21 2 0.04
22 11 0.19
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (17 bp):
AAAATAAATTTAAATTT
Found at i:1303 original size:28 final size:28
Alignment explanation
Indices: 1260--1347 Score: 101
Period size: 28 Copynumber: 3.1 Consensus size: 28
1250 TGTTATTTTG
*
1260 AAAATAAATTTAAATTTAAATTAAATTT
1 AAAATAAATCTAAATTTAAATTAAATTT
*
1288 AAATTTAAGAT-T-AATTT-AATTCAAATTT
1 AAA-ATAA-ATCTAAATTTAAATT-AAATTT
*
1316 AAAATAAATCTAAATTTAAAATAAATTT
1 AAAATAAATCTAAATTTAAATTAAATTT
1344 AAAA
1 AAAA
1348 GGGGCCCGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
26 2 0.04
27 8 0.16
28 32 0.63
29 7 0.14
30 2 0.04
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (28 bp):
AAAATAAATCTAAATTTAAATTAAATTT
Found at i:2050 original size:205 final size:206
Alignment explanation
Indices: 1668--2258 Score: 745
Period size: 205 Copynumber: 2.9 Consensus size: 206
1658 TTGACTTGAC
* * * ** ** * * * *
1668 CTTCTTCTCAATATCTCATCAGGAAGACGACCATATCACTTGTTTTGATCCACTTCTCTATGTTT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCGTTTGTTTCAATTCACTTCTCTGTATCT
* * ** * * *
1733 CATCAAGAAGATGGTTTTGGTTCACTTCCCCGTATTTCATCAGGAAGCTAACCATTTTATTACTT
66 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTT
* * * * *
1798 CGACCTGCTGCTCAATATCTCATCAGGAAATTGGGATTCGAAGATTTGCTAACATCAAGCGTGGG
131 CGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTAACATCAAGCATGGG
*
1863 TTTGATTCGGT
196 TTTGATTCAGT
* *
1874 CTTCTTCTCAGTATCTCATCAGGGAGATGACCACATCGTTTGTTTCAATTCACCTCTCTGTATCT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCGTTTGTTTCAATTCACTTCTCTGTATCT
1939 CATCAGGAAGACGAATTT-GTTCCACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTACT
66 CATCAGGAAGACGAATTTGGTT-CACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACT
* * * * * *
2002 TTGACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCATGG
130 TCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTAACATCAAGCATGG
* *
2067 GTTTGATTTATT
195 GTTTGATTCAGT
* * * ** * *
2079 CTTCTTCTCAGTATCTCATCAGGAAAATGACCGCGTCGTTTGTTTCAATTTTCTTTTTTGTATCT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCGTTTGTTTCAATTCACTTCTCTGTATCT
* * * * *
2144 CATCCGAAAAACGAATTTGGTTCACTTCTCAGTATCTTATCAGGAAGCTAACCATTTTATTGCTT
66 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTT
2209 CGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCT
131 CGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCT
2259 CGCATCGAGC
Statistics
Matches: 330, Mismatches: 52, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
205 177 0.54
206 153 0.46
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (206 bp):
CTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCGTTTGTTTCAATTCACTTCTCTGTATCT
CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTT
CGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTAACATCAAGCATGGG
TTTGATTCAGT
Found at i:2381 original size:116 final size:117
Alignment explanation
Indices: 2213--2488 Score: 297
Period size: 116 Copynumber: 2.4 Consensus size: 117
2203 TTGCTTCGAC
* * * * * * * *
2213 CTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCGCATCGAGCCCTGAATTT
1 CTGCATCTCAGTATCTCATCAAGAAGCTAGGATTCGAAGATTTGATCACATCGAGCCCTGAATTG
* *
2278 GTATTC-TTCTCTGTGTCTCATCAGGAAGATGACCGCCTTACTTGTTTGAAT
66 GTATACTTTCTCTGTATCTCATCAGGAAGATGACCGCCTTACTTGTTTGAAT
* * *
2329 CTGCATCTCTGTATCTCATCAAGAAGCTAGGATTCGAAGATTTGATCACATCGAGCGCTGAGTTG
1 CTGCATCTCAGTATCTCATCAAGAAGCTAGGATTCGAAGATTTGATCACATCGAGCCCTGAATTG
* * * *** * *
2394 GTATACTTTCTCTGTATCTCATCAGGAAGCTAATCATTTTA-TTATTTTG-AC
66 GTATACTTTCTCTGTATCTCATCAGGAAGATGACCGCCTTACTT-GTTTGAAT
* * * *
2445 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTG
1 CTGCATCTCAGTATCTCATCAAGAAGCTAGGATTCGAAGATTTG
2489 CTTGCTTTGA
Statistics
Matches: 132, Mismatches: 26, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
116 101 0.77
117 31 0.23
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (117 bp):
CTGCATCTCAGTATCTCATCAAGAAGCTAGGATTCGAAGATTTGATCACATCGAGCCCTGAATTG
GTATACTTTCTCTGTATCTCATCAGGAAGATGACCGCCTTACTTGTTTGAAT
Found at i:3183 original size:45 final size:45
Alignment explanation
Indices: 3132--3221 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
3122 GTTGCCCCGG
*
3132 ATATCGCAAAATGAGCTATTCTACGCTGAATTGTTTGAGAATCAT
1 ATATCGCAAAATGAGCTATTCTACGCCGAATTGTTTGAGAATCAT
3177 ATATCGCAAAATGAGCTATTCTACGCCGAATTGTTTGAGAATCAT
1 ATATCGCAAAATGAGCTATTCTACGCCGAATTGTTTGAGAATCAT
3222 TCCTAGCTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (45 bp):
ATATCGCAAAATGAGCTATTCTACGCCGAATTGTTTGAGAATCAT
Done.