Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014782.1 Kokia drynarioides strain JFW-HI SEQ_129824, 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: 24511
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:2813 original size:24 final size:24
Alignment explanation
Indices: 2785--2847 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
2775 AGAAATAATC
*
2785 TTTCAGTTAAATTCTGTTTATTTG
1 TTTCAGTTAAATTCTGTTTAGTTG
* *
2809 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAGTTAAATTCTGTTTAGTTG
* *
2833 TTTGAGTCAAATTCT
1 TTTCAGTTAAATTCT
2848 TATTAGTCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.52
Consensus pattern (24 bp):
TTTCAGTTAAATTCTGTTTAGTTG
Found at i:4807 original size:24 final size:24
Alignment explanation
Indices: 4774--4824 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
4764 AGAAATAATC
*
4774 TTTCAGTTAAACTTTGTTT-GTTTG
1 TTTCAATTAAACTTTGTTTAG-TTG
4798 TTTCAATTAAACTTTGTTTAGTTG
1 TTTCAATTAAACTTTGTTTAGTTG
4822 TTT
1 TTT
4825 GAGTCAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.20, C:0.08, G:0.14, T:0.59
Consensus pattern (24 bp):
TTTCAATTAAACTTTGTTTAGTTG
Found at i:7642 original size:24 final size:23
Alignment explanation
Indices: 7597--7642 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
7587 CAAGATAGTA
*
7597 AAGTAAAAAAAAATTTTGAATAT
1 AAGTAAAAAAAAATTTTAAATAT
7620 AAGTAAAGTAAAAAA-TTTAAATA
1 AAGTAAA--AAAAAATTTTAAATA
7643 GTATGGTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 7 0.35
25 6 0.30
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (23 bp):
AAGTAAAAAAAAATTTTAAATAT
Found at i:9004 original size:12 final size:12
Alignment explanation
Indices: 8982--9041 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
8972 TTCATTTAAC
8982 TTAATTGAACATG
1 TTAA-TGAACATG
*
8995 TTCATGAACAT-
1 TTAATGAACATG
*
9006 ATAATTGAACATG
1 TTAA-TGAACATG
* *
9019 TTCACGAACAATG
1 TTAATGAAC-ATG
9032 TTAATGAACA
1 TTAATGAACA
9042 ATAAACAAAC
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
11 2 0.06
12 19 0.53
13 15 0.42
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (12 bp):
TTAATGAACATG
Found at i:9015 original size:24 final size:23
Alignment explanation
Indices: 8965--9028 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 23
8955 TAATGTTCAC
*
8965 GAACATGTTCATTTAAC-TTAATT
1 GAACATGTTCA-TGAACATTAATT
8988 GAACATGTTCATGAACATATAATT
1 GAACATGTTCATGAACAT-TAATT
*
9012 GAACATGTTCACGAACA
1 GAACATGTTCATGAACA
9029 ATGTTAATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 21 0.57
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (23 bp):
GAACATGTTCATGAACATTAATT
Found at i:9870 original size:61 final size:60
Alignment explanation
Indices: 9805--9931 Score: 184
Period size: 59 Copynumber: 2.1 Consensus size: 60
9795 ATATAATAGG
* * *
9805 ATTATTATTAAATGTAATTTAATAAAAATGATAATAAATAATTTAATTATATT-TTAATATA
1 ATTATTATTAAATATAATTTAAT--AAATAATAATAAATAATTTAATAATATTATTAATATA
* *
9866 ATTATTATTAAATATAATTTAATGAATAATAATATATAATTTAATAATATTATTAATATA
1 ATTATTATTAAATATAATTTAATAAATAATAATAAATAATTTAATAATATTATTAATATA
9926 ATTATT
1 ATTATT
9932 TTTATATTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
59 24 0.40
60 14 0.23
61 22 0.37
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.47
Consensus pattern (60 bp):
ATTATTATTAAATATAATTTAATAAATAATAATAAATAATTTAATAATATTATTAATATA
Found at i:9904 original size:22 final size:22
Alignment explanation
Indices: 9876--9928 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
9866 ATTATTATTA
9876 AATATAATTTAATGAATAATAAT
1 AATATAATTTAAT-AATAATAAT
* *
9899 -ATATAATTTAATAATATTATT
1 AATATAATTTAATAATAATAAT
9920 AATATAATT
1 AATATAATT
9929 ATTTTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AATATAATTTAATAATAATAAT
Found at i:9987 original size:32 final size:30
Alignment explanation
Indices: 9949--10012 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 30
9939 TAAATTATAT
* *
9949 TAAAATACTTTATTTTAAATTATATTTTCAAA
1 TAAAATACTTTATATTAAA-AATA-TTTCAAA
*
9981 TAAAATATTTTATATTAAAAATATTTCAAA
1 TAAAATACTTTATATTAAAAATATTTCAAA
10011 TA
1 TA
10013 TTTTATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 9 0.31
31 3 0.10
32 17 0.59
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (30 bp):
TAAAATACTTTATATTAAAAATATTTCAAA
Found at i:14194 original size:35 final size:37
Alignment explanation
Indices: 14126--14194 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 37
14116 ACCAGACAAT
* *
14126 TTTATAATTATTAAAATTGATTAAATGATCTTTTATC
1 TTTATAATTATTAAAATGGATTAAATGAACTTTTATC
* *
14163 TTTATAATT-TTTAAA-GGATTAAATTAACTTTT
1 TTTATAATTATTAAAATGGATTAAATGAACTTTT
14195 TATTATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 14 0.50
36 5 0.18
37 9 0.32
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (37 bp):
TTTATAATTATTAAAATGGATTAAATGAACTTTTATC
Found at i:19749 original size:24 final size:23
Alignment explanation
Indices: 19717--19795 Score: 67
Period size: 22 Copynumber: 3.5 Consensus size: 23
19707 ATTTTTTTAA
*
19717 AATATTTATTTTATTTTAATATTT
1 AATAATTA-TTTATTTTAATATTT
*
19741 AATAATTATATATTTT--TATTT
1 AATAATTATTTATTTTAATATTT
* *
19762 ATTAAATTATTTA-TATAATCATTT
1 AAT-AATTATTTATTTTAAT-ATTT
19786 AAT-ATTATTT
1 AATAATTATTT
19796 TAATATTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
21 9 0.20
22 15 0.33
23 8 0.18
24 13 0.29
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (23 bp):
AATAATTATTTATTTTAATATTT
Found at i:21513 original size:15 final size:16
Alignment explanation
Indices: 21479--21516 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
21469 TTACTAAAAG
*
21479 AAATTTTTTTATATAT
1 AAATATTTTTATATAT
*
21495 AAATATTTTTATGTA-
1 AAATATTTTTATATAT
21510 AAATATT
1 AAATATT
21517 CTTTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
AAATATTTTTATATAT
Found at i:24476 original size:2 final size:2
Alignment explanation
Indices: 24469--24498 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24459 ATAACACAAA
24469 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
24499 TTTTGAGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.