Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007204.1 Kokia drynarioides strain JFW-HI SEQ_121818, 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: 50605
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 77 characters in sequence are not A, C, G, or T
Found at i:2373 original size:30 final size:31
Alignment explanation
Indices: 2315--2373 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2305 ATTTTAAGGA
* **
2315 TTAAATTTAAATTTTAGTGAGTTTTAGGGGG
1 TTAAATCTAAATTTTAGTGAAATTTAGGGGG
2346 TTAAATCTAAATTTTA-TGAAATTTAGGG
1 TTAAATCTAAATTTTAGTGAAATTTAGGG
2374 TTTAATTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (31 bp):
TTAAATCTAAATTTTAGTGAAATTTAGGGGG
Found at i:6628 original size:9 final size:9
Alignment explanation
Indices: 6616--6640 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6606 ATTCAAATAG
6616 ACCAAATTC
1 ACCAAATTC
6625 ACCAAATTC
1 ACCAAATTC
6634 ACCAAAT
1 ACCAAAT
6641 CCAACTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (9 bp):
ACCAAATTC
Found at i:8726 original size:16 final size:17
Alignment explanation
Indices: 8705--8738 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
8695 GCTTTCTTAT
8705 TGAAATA-CCAAAAAGA
1 TGAAATAGCCAAAAAGA
8721 TGAAATATGCCAAAAAGA
1 TGAAATA-GCCAAAAAGA
8739 AATTGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (17 bp):
TGAAATAGCCAAAAAGA
Found at i:16375 original size:27 final size:30
Alignment explanation
Indices: 16338--16399 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
16328 TTCAGTATAT
* *
16338 ATATTAAAAATTGA-TATTTT-TTAATTTA
1 ATATTTAAATTTGACTATTTTATTAATTTA
*
16366 ATATTTAAATTTGACTTTTTTATTAATTTA
1 ATATTTAAATTTGACTATTTTATTAATTTA
16396 ATAT
1 ATAT
16400 ATATTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 12 0.41
29 5 0.17
30 12 0.41
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (30 bp):
ATATTTAAATTTGACTATTTTATTAATTTA
Found at i:16427 original size:20 final size:21
Alignment explanation
Indices: 16383--16430 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
16373 AATTTGACTT
*
16383 TTTTATTAATTTAATATAT-A
1 TTTTATTAATTTAATACATAA
* *
16403 TTTTTTTAATTTAATACCTAA
1 TTTTATTAATTTAATACATAA
16424 TTTTATT
1 TTTTATT
16431 TTTTTAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTATTAATTTAATACATAA
Found at i:16437 original size:26 final size:26
Alignment explanation
Indices: 16401--16460 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
16391 ATTTAATATA
* *
16401 TATTTTTTTAATTTAATACCTAATTT
1 TATTTTTTTAATTTAATACCCAATTG
*
16427 TATTTTTTTAATTTGATACCCAATTG
1 TATTTTTTTAATTTAATACCCAATTG
16453 T-TTTTTTT
1 TATTTTTTT
16461 GTTGGATTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 7 0.23
26 24 0.77
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.63
Consensus pattern (26 bp):
TATTTTTTTAATTTAATACCCAATTG
Found at i:20417 original size:13 final size:13
Alignment explanation
Indices: 20378--20418 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
20368 CGACTGCTTT
20378 AAACAAACA-ATC
1 AAACAAACATATC
*
20390 AAACAAACATGTC
1 AAACAAACATATC
20403 AAACCAAA-ATATC
1 AAA-CAAACATATC
20416 AAA
1 AAA
20419 TCAGATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 9 0.36
13 12 0.48
14 4 0.16
ACGTcount: A:0.63, C:0.22, G:0.02, T:0.12
Consensus pattern (13 bp):
AAACAAACATATC
Found at i:32790 original size:17 final size:17
Alignment explanation
Indices: 32746--32791 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
32736 GTAGCATGCG
*
32746 TTATCTTAAGTAATTTTA
1 TTAT-TTAAATAATTTTA
*
32764 -TATTTCAATAATTTTA
1 TTATTTAAATAATTTTA
32780 TTATTTAAATAA
1 TTATTTAAATAA
32792 ACAGTATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.54
Consensus pattern (17 bp):
TTATTTAAATAATTTTA
Found at i:34153 original size:17 final size:17
Alignment explanation
Indices: 34111--34158 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
34101 AATTCAATTT
*
34111 TAATATAAAT-ATTTAA
1 TAATATAAATAATTCAA
34127 T-ATGATTAAATAATTCAA
1 TAAT-A-TAAATAATTCAA
34145 TAATATAAATAATT
1 TAATATAAATAATT
34159 AAAAATGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 2 0.07
16 2 0.07
17 14 0.52
18 7 0.26
19 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:34483 original size:18 final size:19
Alignment explanation
Indices: 34456--34493 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
34446 GTGGAAAGTG
*
34456 GGAGGGAAT-AAAAGTTTT
1 GGAGGAAATAAAAAGTTTT
34474 GGAGGAAATAAAAAGTTTT
1 GGAGGAAATAAAAAGTTTT
34493 G
1 G
34494 AGGGTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (19 bp):
GGAGGAAATAAAAAGTTTT
Found at i:38068 original size:2 final size:2
Alignment explanation
Indices: 38063--38109 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
38053 GTGTTTAATC
*
38063 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38105 TA TA T
1 TA TA T
38110 TGTCAATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:41276 original size:4 final size:4
Alignment explanation
Indices: 41269--41299 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
41259 TACGTACGTT
41269 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
41300 TAAACTATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:44894 original size:5 final size:5
Alignment explanation
Indices: 44880--44909 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
44870 CTTATTGTAG
44880 TTTTC TTTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTT
44910 TTTCAGGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Done.