Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005350.1 Kokia drynarioides strain JFW-HI SEQ_119320, 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: 19057
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Found at i:5940 original size:18 final size:18
Alignment explanation
Indices: 5917--5976 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
5907 CATTTTATTT
*
5917 ATGTTTTTATTTATCTAA
1 ATGTTTTTATTTATCAAA
5935 ATGTTTTTAAGTTAATATCAAA
1 ATGTTTTT-A-TT--TATCAAA
* *
5957 ATGTTTTTGTTTATCCAA
1 ATGTTTTTATTTATCAAA
5975 AT
1 AT
5977 CTATGTTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 16 0.46
19 1 0.03
20 4 0.11
22 14 0.40
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.53
Consensus pattern (18 bp):
ATGTTTTTATTTATCAAA
Found at i:6585 original size:22 final size:23
Alignment explanation
Indices: 6543--6590 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
6533 TTTTATTGTT
6543 TTGCTATCATTTTGCTATTA-TA
1 TTGCTATCATTTTGCTATTATTA
* *
6565 TTGCTA-CTATTTTGTTGTTATTA
1 TTGCTATC-ATTTTGCTATTATTA
6588 TTG
1 TTG
6591 GGATATTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 1 0.05
22 16 0.73
23 5 0.23
ACGTcount: A:0.19, C:0.10, G:0.12, T:0.58
Consensus pattern (23 bp):
TTGCTATCATTTTGCTATTATTA
Found at i:8286 original size:7 final size:7
Alignment explanation
Indices: 8276--8304 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
8266 TTTTAAACCT
8276 TATACTA
1 TATACTA
8283 TATACTA
1 TATACTA
8290 TATACTA
1 TATACTA
8297 TATA-TA
1 TATACTA
8303 TA
1 TA
8305 ATATGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (7 bp):
TATACTA
Found at i:8320 original size:21 final size:21
Alignment explanation
Indices: 8296--8338 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
8286 ACTATATACT
8296 ATATATATAATATGTAATATA
1 ATATATATAATATGTAATATA
* *
8317 ATATATCTAATATGTATTATA
1 ATATATATAATATGTAATATA
8338 A
1 A
8339 ATGATAGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (21 bp):
ATATATATAATATGTAATATA
Found at i:12335 original size:70 final size:70
Alignment explanation
Indices: 12222--12361 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
12212 TCCTGACATA
12222 TTAGGATTTAACTCTGTTACTCAGATGTACCATATTGATCAACGGTGTTAAAGTTTAAGTACCAA
1 TTAGGATTTAACTCTGTTACTCAGATGTACCATATTGATCAACGGTGTTAAAGTTTAAGTACCAA
12287 AATTG
66 AATTG
12292 TTAGGATTTAACTCTGTTACTCAGATGTACCATATTGATCAACGGTGTTAAAGTTTAAGTACCAA
1 TTAGGATTTAACTCTGTTACTCAGATGTACCATATTGATCAACGGTGTTAAAGTTTAAGTACCAA
12357 AATTG
66 AATTG
12362 ATATTTTAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (70 bp):
TTAGGATTTAACTCTGTTACTCAGATGTACCATATTGATCAACGGTGTTAAAGTTTAAGTACCAA
AATTG
Found at i:15364 original size:67 final size:66
Alignment explanation
Indices: 15246--15377 Score: 174
Period size: 67 Copynumber: 2.0 Consensus size: 66
15236 GTTAGCCAAA
* * ** * *
15246 GACGGAAATGAATTAATGCATGCGTCTCGTTTGACATGATGGTCCCTTCAAAGTTCCAAACCAGT
1 GACGGAAATGAATTAATGCATGCCTCTCGTATGACATGATCATCCCTTCAAAATTCAAAACCAGT
15311 T
66 T
* * *
15312 GACGTAAATGAAATTACTGCATGCCTCTCGTATGACATGATCATTCCTTCAAAATTCAAAACCAG
1 GACGGAAATG-AATTAATGCATGCCTCTCGTATGACATGATCATCCCTTCAAAATTCAAAACCAG
15377 T
65 T
15378 AGATAATTGG
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
66 9 0.16
67 47 0.84
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (66 bp):
GACGGAAATGAATTAATGCATGCCTCTCGTATGACATGATCATCCCTTCAAAATTCAAAACCAGT
T
Found at i:15531 original size:63 final size:63
Alignment explanation
Indices: 15431--15555 Score: 223
Period size: 63 Copynumber: 2.0 Consensus size: 63
15421 AACAGATAAG
* *
15431 GTAGATTTTAGGATGAGGATAACTCCACAAGCGTCATCCTTCTCTATTCATATTTGGATTCAC
1 GTAGATTTCAGGATGAGGATAACTCCACAAGCATCATCCTTCTCTATTCATATTTGGATTCAC
*
15494 GTAGATTTCAGGATGAGGATAACTCCACAAGCATCATCCTTGTCTATTCATATTTGGATTCA
1 GTAGATTTCAGGATGAGGATAACTCCACAAGCATCATCCTTCTCTATTCATATTTGGATTCA
15556 GTTATATTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (63 bp):
GTAGATTTCAGGATGAGGATAACTCCACAAGCATCATCCTTCTCTATTCATATTTGGATTCAC
Done.