Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012694.1 Kokia drynarioides strain JFW-HI SEQ_127705, 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: 25548
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 102 characters in sequence are not A, C, G, or T
Found at i:1121 original size:51 final size:49
Alignment explanation
Indices: 1066--1345 Score: 199
Period size: 50 Copynumber: 5.6 Consensus size: 49
1056 CGAATTAAAC
*
1066 CTTTCCTTTTTGTATCTTTGTGGTACTAGATCTGCCGTTGCGATATTAGAT
1 CTTTCC-TTTTGTATCTTTGTGGTACTAGATCTGCCGTTGCGA-CTTAGAT
** * ** * * *
1117 CTTTCCTTTCATGTCTTCATGGTACTAGAT-TCGCCGTTACGGCTTAAAT
1 CTTTCCTTTTGTATCTTTGTGGTACTAGATCT-GCCGTTGCGACTTAGAT
* * * * * *
1166 CTTTCCCTTCGTGTCTTCTGAGGTAC-ACGGTCTTGCCGTTGCGACTTAGAC
1 CTTTCCTTTTGTATCTT-TGTGGTACTA-GATC-TGCCGTTGCGACTTAGAT
* * * * *
1217 CTTTCCCTTTTGTATCTTTGTGGTATTGGAT-TCGTCGTTGCAACTTAAAT
1 CTTT-CCTTTTGTATCTTTGTGGTACTAGATCT-GCCGTTGCGACTTAGAT
* * * * *
1267 CTTTCCCTTCGTGTCTTCTGAGGTAC-ACGATCCTGCCGTTGCGACTTAGAC
1 CTTTCCTTTTGTATCTT-TGTGGTACTA-GAT-CTGCCGTTGCGACTTAGAT
1318 CTTTCCCTTTTGTATCTTTGTGGTACTA
1 CTTT-CCTTTTGTATCTTTGTGGTACTA
1346 AAACCTGTAG
Statistics
Matches: 171, Mismatches: 44, Indels: 27
0.71 0.18 0.11
Matches are distributed among these distances:
49 33 0.19
50 60 0.35
51 55 0.32
52 23 0.13
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (49 bp):
CTTTCCTTTTGTATCTTTGTGGTACTAGATCTGCCGTTGCGACTTAGAT
Found at i:1191 original size:50 final size:50
Alignment explanation
Indices: 989--1326 Score: 197
Period size: 50 Copynumber: 6.7 Consensus size: 50
979 ATATTCGTGT
* * * * *
989 TACTAGATTCGCCATTGCGGCTTAAATCTTTACCTTCTTGTCTTTTGAGG
1 TACTAGATTCGCCGTTGCGACTTAAATCTTTCCCTTCGTGTCTTCTGAGG
* * *** * * * * * * *
1039 TAC-ATGGTCCGTAATTACGAATTAAACCTTTCCTTTTTGTATCTT-TGTGG
1 TACTA-GATTCGCCGTTGCGACTTAAATCTTTCC-CTTCGTGTCTTCTGAGG
* * * *
1089 TACTAGA-TCTGCCGTTGCGATATTAGATCTTTCCTTTCATGTCTTC--ATGG
1 TACTAGATTC-GCCGTTGCGA-CTTAAATCTTTCCCTTCGTGTCTTCTGA-GG
* *
1139 TACTAGATTCGCCGTTACGGCTTAAATCTTTCCCTTCGTGTCTTCTGAGG
1 TACTAGATTCGCCGTTGCGACTTAAATCTTTCCCTTCGTGTCTTCTGAGG
* * * * * * *
1189 TAC-ACGGTCTTGCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTT-TGTGG
1 TACTA-GAT-TCGCCGTTGCGACTTAAATCTTTCCC-TTCGTGTCTTCTGAGG
* * * *
1240 TATTGGATTCGTCGTTGCAACTTAAATCTTTCCCTTCGTGTCTTCTGAGG
1 TACTAGATTCGCCGTTGCGACTTAAATCTTTCCCTTCGTGTCTTCTGAGG
* * *
1290 TAC-ACGATCCTGCCGTTGCGACTTAGACCTTTCCCTT
1 TACTA-GATTC-GCCGTTGCGACTTAAATCTTTCCCTT
1327 TTGTATCTTT
Statistics
Matches: 212, Mismatches: 59, Indels: 33
0.70 0.19 0.11
Matches are distributed among these distances:
49 32 0.15
50 99 0.47
51 73 0.34
52 8 0.04
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.41
Consensus pattern (50 bp):
TACTAGATTCGCCGTTGCGACTTAAATCTTTCCCTTCGTGTCTTCTGAGG
Found at i:1264 original size:101 final size:101
Alignment explanation
Indices: 1159--1342 Score: 350
Period size: 101 Copynumber: 1.8 Consensus size: 101
1149 GCCGTTACGG
* *
1159 CTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCTTGCCGTTGCGACTTAGACCTTTCCC
1 CTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGATCCTGCCGTTGCGACTTAGACCTTTCCC
1224 TTTTGTATCTTTGTGGTATTGGATTCGTCGTTGCAA
66 TTTTGTATCTTTGTGGTATTGGATTCGTCGTTGCAA
1260 CTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGATCCTGCCGTTGCGACTTAGACCTTTCCC
1 CTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGATCCTGCCGTTGCGACTTAGACCTTTCCC
1325 TTTTGTATCTTTGTGGTA
66 TTTTGTATCTTTGTGGTA
1343 CTAAAACCTG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 81 1.00
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (101 bp):
CTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGATCCTGCCGTTGCGACTTAGACCTTTCCC
TTTTGTATCTTTGTGGTATTGGATTCGTCGTTGCAA
Found at i:1269 original size:150 final size:150
Alignment explanation
Indices: 989--1284 Score: 364
Period size: 150 Copynumber: 2.0 Consensus size: 150
979 ATATTCGTGT
* * * * *
989 TACTAGATTCGCCATTGCGGCTTAAATCTTTACCTTCTTGTCTTTTGAGGTACATGGTCCGTAAT
1 TACTAGATTCGCCATTACGGCTTAAATCTTTACCTTCGTGTCTTCTGAGGTACACGGTCCGCAAT
* *
1054 TACGAATTAAACCTTTCCTTTTTGTATCTTTGTGGTACTAGATCTGCCGTTGCGATATTAGATCT
66 TACGAATTAAACCTTTCCCTTTTGTATCTTTGTGGTACTAGATCTGCCGTTGCGATATTAAATCT
*
1119 TTCCTTTCATGTCTTCATGG
131 TTCCCTTCATGTCTTCATGG
* * * **
1139 TACTAGATTCGCCGTTACGGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCTTGCCG
1 TACTAGATTCGCCATTACGGCTTAAATCTTTACCTTCGTGTCTTCTGAGGTACACGGTC-CGCAA
* * * * * *
1204 TTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTATTGGAT-TCGTCGTTGC-A-ACTTAAA
65 TTACGAATTAAACCTTTCCCTTTTGTATCTTTGTGGTACTAGATCT-GCCGTTGCGATA-TTAAA
*
1266 TCTTTCCCTTCGTGTCTTC
128 TCTTTCCCTTCATGTCTTC
1285 TGAGGTACAC
Statistics
Matches: 123, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
149 1 0.01
150 76 0.62
151 46 0.37
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (150 bp):
TACTAGATTCGCCATTACGGCTTAAATCTTTACCTTCGTGTCTTCTGAGGTACACGGTCCGCAAT
TACGAATTAAACCTTTCCCTTTTGTATCTTTGTGGTACTAGATCTGCCGTTGCGATATTAAATCT
TTCCCTTCATGTCTTCATGG
Found at i:2396 original size:9 final size:10
Alignment explanation
Indices: 2374--2405 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
2364 TTTGCTTTCC
2374 CTTT-TTCTT
1 CTTTCTTCTT
2383 CTTTCTTCTT
1 CTTTCTTCTT
2393 -TTTCTTCTT
1 CTTTCTTCTT
2402 CTTT
1 CTTT
2406 TTTTTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (10 bp):
CTTTCTTCTT
Found at i:2411 original size:16 final size:16
Alignment explanation
Indices: 2374--2409 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2364 TTTGCTTTCC
2374 CTTTTTCTTCTTTCTT
1 CTTTTTCTTCTTTCTT
2390 CTTTTTCTTC-TTCTT
1 CTTTTTCTTCTTTCTT
2405 -TTTTT
1 CTTTTT
2410 TTTTTGTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.25
15 5 0.25
16 10 0.50
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
CTTTTTCTTCTTTCTT
Found at i:5376 original size:3 final size:3
Alignment explanation
Indices: 5324--5362 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5314 TTAAACCCAT
5324 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5363 ATGAATTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6113 original size:17 final size:17
Alignment explanation
Indices: 6084--6149 Score: 78
Period size: 17 Copynumber: 3.9 Consensus size: 17
6074 ATTAATTTTT
*
6084 AATTGAAAATAAATTTA
1 AATTTAAAATAAATTTA
* *
6101 AATTTAAAGTAAATTCA
1 AATTTAAAATAAATTTA
* * *
6118 AACTCAAAATAAATTTG
1 AATTTAAAATAAATTTA
6135 AATTTAAAATAAATT
1 AATTTAAAATAAATT
6150 CAAACTTATT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:6173 original size:34 final size:34
Alignment explanation
Indices: 6089--6155 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
6079 TTTTTAATTG
*
6089 AAAATAAATTTAAATTTAAAGTAAATTCAAACTC
1 AAAATAAATTTAAATTTAAAATAAATTCAAACTC
*
6123 AAAATAAATTTGAATTTAAAATAAATTCAAACT
1 AAAATAAATTTAAATTTAAAATAAATTCAAACT
6156 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAAAATAAATTCAAACTC
Found at i:16531 original size:14 final size:14
Alignment explanation
Indices: 16512--16541 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
16502 GATATCAAAT
16512 CATGGATTACTGTA
1 CATGGATTACTGTA
16526 CATGGATTACTGTA
1 CATGGATTACTGTA
16540 CA
1 CA
16542 AACCTAGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (14 bp):
CATGGATTACTGTA
Found at i:21540 original size:34 final size:34
Alignment explanation
Indices: 21497--21562 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
21487 CTTTGTATTC
* **
21497 ACTTAGATTCTATGTTAGCAAATTGAAATTGAGT
1 ACTTAGATTCTATGTCAGCAAACCGAAATTGAGT
21531 ACTTAGATTCTATGTCAGCAAACCGAAATTGA
1 ACTTAGATTCTATGTCAGCAAACCGAAATTGA
21563 ATATATGCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (34 bp):
ACTTAGATTCTATGTCAGCAAACCGAAATTGAGT
Done.