Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012579.1 Kokia drynarioides strain JFW-HI SEQ_127588, 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: 24656
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--26 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
27 TAATCCATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:488 original size:25 final size:26
Alignment explanation
Indices: 456--507 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
446 AAATTTTAAC
**
456 AGCAAA-TTTTTGAAGAATGAAAGGA
1 AGCAAATTTTTTGAAGAAAAAAAGGA
481 AGCAAATTTTTTGAAGAAAAAAAGGA
1 AGCAAATTTTTTGAAGAAAAAAAGGA
507 A
1 A
508 ACAGAAGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.52, C:0.04, G:0.21, T:0.23
Consensus pattern (26 bp):
AGCAAATTTTTTGAAGAAAAAAAGGA
Found at i:7160 original size:17 final size:17
Alignment explanation
Indices: 7138--7170 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
7128 TAAAATTAAG
7138 TAAATAAAATTTAAATT
1 TAAATAAAATTTAAATT
*
7155 TAAATAACATTTAAAT
1 TAAATAAAATTTAAAT
7171 AATAATCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATAAAATTTAAATT
Found at i:13178 original size:20 final size:21
Alignment explanation
Indices: 13135--13178 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
13125 TTATTCTATC
* *
13135 TTTTAGTTTTTGTTGGTTTGA
1 TTTTAGTTTATGTTGGTTTAA
*
13156 TTTT-GTTTATGTTGTTTTAA
1 TTTTAGTTTATGTTGGTTTAA
13176 TTT
1 TTT
13179 CCCTTTCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.11, C:0.00, G:0.18, T:0.70
Consensus pattern (21 bp):
TTTTAGTTTATGTTGGTTTAA
Found at i:13473 original size:17 final size:18
Alignment explanation
Indices: 13428--13465 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 18
13418 CATCTTAAAA
13428 ATAATAAAATAATAAAATT
1 ATAAT-AAATAATAAAATT
13447 ATAATAAATAA-AAAATT
1 ATAATAAATAATAAAATT
13464 AT
1 AT
13466 TATGAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAATAAATAATAAAATT
Found at i:16659 original size:6 final size:6
Alignment explanation
Indices: 16650--16702 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
16640 ACCAAACATG
* * *
16650 TTGACT TTGACT ATTGACCG TTGACT TTAACT TTGACT TTGATCA TTGACT
1 TTGACT TTGACT -TTGA-CT TTGACT TTGACT TTGACT TTGA-CT TTGACT
16701 TT
1 TT
16703 TTTTTACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 24 0.63
7 13 0.34
8 1 0.03
ACGTcount: A:0.21, C:0.17, G:0.15, T:0.47
Consensus pattern (6 bp):
TTGACT
Found at i:16674 original size:20 final size:19
Alignment explanation
Indices: 16649--16686 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
16639 GACCAAACAT
*
16649 GTTGACTTTGACTATTGACC
1 GTTGACTTTAACT-TTGACC
16669 GTTGACTTTAACTTTGAC
1 GTTGACTTTAACTTTGAC
16687 TTTGATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (19 bp):
GTTGACTTTAACTTTGACC
Found at i:17885 original size:19 final size:19
Alignment explanation
Indices: 17861--17897 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
17851 AAATTATGAG
17861 AAATTAA-TTATTTTACAAT
1 AAATTAATTTA-TTTACAAT
17880 AAATTAATTTATTTACAA
1 AAATTAATTTATTTACAA
17898 ATTAAAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATTAATTTATTTACAAT
Found at i:20287 original size:5 final size:6
Alignment explanation
Indices: 20257--20290 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
20247 TTTAAAAATC
*
20257 ATAAAA ATTATAA ATAAAA ATAAAA ATAAAA ATA
1 ATAAAA A-TAAAA ATAAAA ATAAAA ATAAAA ATA
20291 TATTAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
ATAAAA
Found at i:20817 original size:2 final size:2
Alignment explanation
Indices: 20810--20840 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20800 AATTTAACCG
20810 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20841 TATTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22239 original size:10 final size:11
Alignment explanation
Indices: 22208--22252 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 11
22198 TCTTCAATTT
22208 ATATATTAT-A
1 ATATATTATAA
* *
22218 ATAAAATATAA
1 ATATATTATAA
22229 ATATATT-TAA
1 ATATATTATAA
22239 ATA-ATTATAA
1 ATATATTATAA
22249 ATAT
1 ATAT
22253 TAAATATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
9 3 0.11
10 19 0.68
11 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATATTATAA
Done.