Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004269.1 Kokia drynarioides strain JFW-HI SEQ_117557, 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: 26599
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:7194 original size:26 final size:27
Alignment explanation
Indices: 7163--7218 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
7153 AATTAGTAAT
*
7163 AATAAAA-TTATATTTTATTTTCTAAA
1 AATAAAATTTATAATTTATTTTCTAAA
* *
7189 AATAAAATTTTTAATTTATTTTTTAAA
1 AATAAAATTTATAATTTATTTTCTAAA
7216 AAT
1 AAT
7219 TTATAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
AATAAAATTTATAATTTATTTTCTAAA
Found at i:7355 original size:6 final size:6
Alignment explanation
Indices: 7344--7390 Score: 51
Period size: 6 Copynumber: 7.3 Consensus size: 6
7334 TATTGTTTAG
7344 AAGAAA AAGAAA AAGAAA ATA-AAA AAGAGAA AATGAAGA AAGAAA AA
1 AAGAAA AAGAAA AAGAAA A-AGAAA AAGA-AA AA-GAA-A AAGAAA AA
7391 TATAGCGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
5 1 0.03
6 21 0.58
7 9 0.25
8 5 0.14
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (6 bp):
AAGAAA
Found at i:9163 original size:29 final size:29
Alignment explanation
Indices: 9087--9163 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
9077 CTCTTTGAGC
* * * *
9087 GTAAATTTATTGATATTTCAGTGATTATTTT
1 GTAAATTTATTAATA-TT-AGTGATCAATGT
* *
9118 GT-AATTTTTTAAAATTAGTGATCAATGT
1 GTAAATTTATTAATATTAGTGATCAATGT
9146 GTAAATTTATTAATATTA
1 GTAAATTTATTAATATTA
9164 CAGTGACCTT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
28 11 0.30
29 15 0.41
30 9 0.24
31 2 0.05
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.51
Consensus pattern (29 bp):
GTAAATTTATTAATATTAGTGATCAATGT
Found at i:13353 original size:16 final size:16
Alignment explanation
Indices: 13332--13365 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
13322 TTTTTTAGAT
13332 TAATTTTTATTAAAAA
1 TAATTTTTATTAAAAA
*
13348 TAATTTTTTTTAAAAA
1 TAATTTTTATTAAAAA
13364 TA
1 TA
13366 TATAATACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATTTTTATTAAAAA
Found at i:16329 original size:22 final size:22
Alignment explanation
Indices: 16299--16372 Score: 55
Period size: 22 Copynumber: 3.3 Consensus size: 22
16289 ATTTATATTG
16299 TTTTA-ATTAAATATTTAATAA
1 TTTTATATTAAATATTTAATAA
** *
16320 TTTTATATTATTTATTTACTGAAA
1 TTTTATATTAAATATTTAAT--AA
16344 TTTT-TA-TAACATATTTAATATA
1 TTTTATATTAA-ATATTTAATA-A
16366 TCTTTAT
1 T-TTTAT
16373 TTTTTTAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
21 6 0.15
22 15 0.38
23 12 0.30
24 7 0.17
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (22 bp):
TTTTATATTAAATATTTAATAA
Found at i:20328 original size:2 final size:2
Alignment explanation
Indices: 20321--20351 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20311 GTAGCTTTTA
20321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20352 CTTATAATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23883 original size:23 final size:23
Alignment explanation
Indices: 23856--23901 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
23846 TTGAATTGTC
23856 AAACTATGAAGCAAACACAACAA
1 AAACTATGAAGCAAACACAACAA
23879 AAACTATGAAGCAAACACAACAA
1 AAACTATGAAGCAAACACAACAA
23902 GAAAGACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.61, C:0.22, G:0.09, T:0.09
Consensus pattern (23 bp):
AAACTATGAAGCAAACACAACAA
Found at i:25754 original size:16 final size:16
Alignment explanation
Indices: 25733--25766 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
25723 ATTTTTCATA
*
25733 TTTTTAGAATTTTATT
1 TTTTTAGAATTATATT
25749 TTTTTAGAATTATATT
1 TTTTTAGAATTATATT
25765 TT
1 TT
25767 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TTTTTAGAATTATATT
Done.