Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012474.1 Kokia drynarioides strain JFW-HI SEQ_127478, 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: 393988
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 69 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:367793 original size:22 final size:25
Alignment explanation
Indices: 367759--367807 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 25
367749 TCTAATTCCA
*
367759 TTTTACTTATAATTTAAT-C-TATT
1 TTTTACTTATAATATAATACATATT
*
367782 TTTTA-TTTTAATATAATACATATT
1 TTTTACTTATAATATAATACATATT
367806 TT
1 TT
367808 ATGTGTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 10 0.45
23 6 0.27
24 6 0.27
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTTACTTATAATATAATACATATT
Found at i:368644 original size:21 final size:21
Alignment explanation
Indices: 368605--368644 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
368595 TAAAATGAAA
**
368605 AATTTTTTATTTAGGTTTTTG
1 AATTTTTTATTTAAATTTTTG
*
368626 AATTTTTTTTTTAAATTTT
1 AATTTTTTATTTAAATTTT
368645 AAATTAATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (21 bp):
AATTTTTTATTTAAATTTTTG
Found at i:369530 original size:59 final size:58
Alignment explanation
Indices: 369404--369550 Score: 172
Period size: 59 Copynumber: 2.6 Consensus size: 58
369394 TTTTAAATAT
* * * * *
369404 TTAATTTTTTTTCTAATTTGGTATCTAAA--TTTTTTAACCCAATTTGGTACTTAAAC
1 TTAACTTTTTTCCTAATTTGGTACCTAAACTTTTTTTAACCCAAATTGGTACCTAAAC
** ** *
369460 TTAACACTTTTCCTAATTTGGTGGCTAAACTTTTTTTAGATCCAAATTGGTACCTAAAC
1 TTAACTTTTTTCCTAATTTGGTACCTAAACTTTTTTTA-ACCCAAATTGGTACCTAAAC
*
369519 TTGACTTTTTTCCTAATTTGGTACCTAAACTT
1 TTAACTTTTTTCCTAATTTGGTACCTAAACTT
369551 GACTTTTTTT
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
56 23 0.31
58 7 0.09
59 44 0.59
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (58 bp):
TTAACTTTTTTCCTAATTTGGTACCTAAACTTTTTTTAACCCAAATTGGTACCTAAAC
Found at i:369562 original size:31 final size:30
Alignment explanation
Indices: 369444--369578 Score: 143
Period size: 30 Copynumber: 4.5 Consensus size: 30
369434 TTTTTAACCC
* * **
369444 AATTTGGTACTTAAACTTAACACTTTTCCT
1 AATTTGGTACCTAAACTTGACTTTTTTCCT
**
369474 AATTTGGTGGCTAAACTT---TTTTTAGATCC-
1 AATTTGGTACCTAAACTTGACTTTTT---TCCT
*
369503 AAATTGGTACCTAAACTTGACTTTTTTCCT
1 AATTTGGTACCTAAACTTGACTTTTTTCCT
369533 AATTTGGTACCTAAACTTGACTTTTTTTCCT
1 AATTTGGTACCTAAACTTGAC-TTTTTTCCT
369564 AATTTGGTACCTAAA
1 AATTTGGTACCTAAA
369579 TTTATTAAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.03
29 18 0.20
30 38 0.43
31 24 0.27
32 5 0.06
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (30 bp):
AATTTGGTACCTAAACTTGACTTTTTTCCT
Found at i:378713 original size:2 final size:2
Alignment explanation
Indices: 378706--378740 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
378696 TCTGTAATCT
378706 TA TA 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 TA TA T
378741 TTTATAATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:378790 original size:16 final size:17
Alignment explanation
Indices: 378750--378790 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
378740 TTTTATAATC
378750 TATATTATAATGATAGG
1 TATATTATAATGATAGG
* *
378767 TTTA-TATAATGGTA-G
1 TATATTATAATGATAGG
378782 TATATTATA
1 TATATTATA
378791 TATTATTGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 4 0.20
16 13 0.65
17 3 0.15
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (17 bp):
TATATTATAATGATAGG
Found at i:384758 original size:17 final size:18
Alignment explanation
Indices: 384733--384767 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
384723 AAATTTTCAT
*
384733 TTTTGTAATTTTTTTAAA
1 TTTTGTAATTTCTTTAAA
384751 TTTT-TAATTTCTTTAAA
1 TTTTGTAATTTCTTTAAA
384768 ATTCATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTGTAATTTCTTTAAA
Found at i:385129 original size:23 final size:21
Alignment explanation
Indices: 385101--385146 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
385091 ATTTTTTTAA
385101 TAAAAGGGAAAAAACTGGAGTTT
1 TAAAA-GGAAAAAACTGG-GTTT
**
385124 TAAAAGGAATTAACTGGGTTT
1 TAAAAGGAAAAAACTGGGTTT
385145 TA
1 TA
385147 TATGAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 10 0.48
23 5 0.24
ACGTcount: A:0.43, C:0.04, G:0.24, T:0.28
Consensus pattern (21 bp):
TAAAAGGAAAAAACTGGGTTT
Found at i:390995 original size:26 final size:26
Alignment explanation
Indices: 390966--391027 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
390956 AATTTTAAAA
*
390966 ATTATATTTAATACAATAAAATATTT
1 ATTATATTTAAAACAATAAAATATTT
* *
390992 ATTATTTTTAAAATAATAAAATATTT
1 ATTATATTTAAAACAATAAAATATTT
391018 ATTATATTTA
1 ATTATATTTA
391028 TGGTATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTATATTTAAAACAATAAAATATTT
Found at i:393894 original size:21 final size:21
Alignment explanation
Indices: 393870--393979 Score: 166
Period size: 21 Copynumber: 5.2 Consensus size: 21
393860 AGGGACAGGA
393870 GGAGGAGAATGCACTGGTGGT
1 GGAGGAGAATGCACTGGTGGT
393891 GGAGGAGAATGCACTGGTGGT
1 GGAGGAGAATGCACTGGTGGT
393912 GGAGGAGAATGCACTGGTGGT
1 GGAGGAGAATGCACTGGTGGT
* * *
393933 GGTGGAGAGTGGACTGGTGGT
1 GGAGGAGAATGCACTGGTGGT
* * *
393954 GGTGGAGAGTGGACTGGTGGT
1 GGAGGAGAATGCACTGGTGGT
393975 GGAGG
1 GGAGG
393980 TGGTGGAGA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 85 1.00
ACGTcount: A:0.20, C:0.07, G:0.53, T:0.20
Consensus pattern (21 bp):
GGAGGAGAATGCACTGGTGGT
Done.