Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012934.1 Kokia drynarioides strain JFW-HI SEQ_127952, 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: 46947
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:16983 original size:3 final size:3
Alignment explanation
Indices: 16975--17008 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
16965 TTGATTGTTT
*
16975 GAA GAA GAA GAC GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
17009 CGTAAACGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:17904 original size:23 final size:24
Alignment explanation
Indices: 17852--17904 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
17842 TAAAAAGTCG
* *
17852 AAATT-AAATTATAATTTTTACGA
1 AAATTAAAAATATAATTTTTACAA
*
17875 TAA-TAAAAATATAATTTTTA-AA
1 AAATTAAAAATATAATTTTTACAA
17897 AAATTAAA
1 AAATTAAA
17905 TAAAAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
AAATTAAAAATATAATTTTTACAA
Found at i:26357 original size:62 final size:58
Alignment explanation
Indices: 26273--26389 Score: 155
Period size: 59 Copynumber: 1.9 Consensus size: 58
26263 TGTCCTCCCC
* * *
26273 AAAATTTTGATTTTTCCTTTGAAATTTTTAGAGAATTTTAGTTAGGTCTCCT-AAATTTTTT
1 AAAATTTTCATTTTTCCCTTGAAA-TTTTAGA-AA-TTTAATTAGGTC-CCTCAAATTTTTT
26334 AAAATGTTTCATTTTTCCCTTGAAATTTTAGAAATTTAATTAGGTCCCTCAAATTT
1 AAAAT-TTTCATTTTTCCCTTGAAATTTTAGAAATTTAATTAGGTCCCTCAAATTT
26390 CTAGAAATTC
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
58 3 0.06
59 17 0.33
60 2 0.04
61 12 0.24
62 17 0.33
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (58 bp):
AAAATTTTCATTTTTCCCTTGAAATTTTAGAAATTTAATTAGGTCCCTCAAATTTTTT
Found at i:26516 original size:26 final size:26
Alignment explanation
Indices: 26486--26537 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
26476 CAAAAATTTT
*
26486 AATTAAACT-CTCAATATTTTTAAAAA
1 AATTAAACTCCT-AAAATTTTTAAAAA
26512 AATTAAACTCCTAAAATTTTTAAAAA
1 AATTAAACTCCTAAAATTTTTAAAAA
26538 TTTACTAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.37
Consensus pattern (26 bp):
AATTAAACTCCTAAAATTTTTAAAAA
Found at i:33524 original size:30 final size:31
Alignment explanation
Indices: 33466--33524 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
33456 AACATAACAA
*
33466 TTTAGTGACTTAAATAAAAACTTTCAAATTG
1 TTTAATGACTTAAATAAAAACTTTCAAATTG
*
33497 TTTAATGACTTAAATGAAAAC-TTCAAAT
1 TTTAATGACTTAAATAAAAACTTTCAAAT
33525 AATTTAGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.37
Consensus pattern (31 bp):
TTTAATGACTTAAATAAAAACTTTCAAATTG
Found at i:36035 original size:31 final size:30
Alignment explanation
Indices: 35990--36062 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 30
35980 AAGTGCTAAC
35990 TTAAAAAAAATGTCAAGTTTAAATACCAAA
1 TTAAAAAAAATGTCAAGTTTAAATACCAAA
* *
36020 TTAAGAAAAAGTGTCAAGTTTAAATATCAAA
1 TTAA-AAAAAATGTCAAGTTTAAATACCAAA
36051 TTAGACAAAAAA
1 TTA-A-AAAAAA
36063 AATTAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 4 0.11
31 27 0.73
32 6 0.16
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (30 bp):
TTAAAAAAAATGTCAAGTTTAAATACCAAA
Found at i:39087 original size:7 final size:7
Alignment explanation
Indices: 39075--39111 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
39065 GTCGCATAAC
39075 ATTTAAA
1 ATTTAAA
39082 ATTTAAA
1 ATTTAAA
39089 ATTTAAA
1 ATTTAAA
39096 ATTTAAA
1 ATTTAAA
39103 ATTTAAA
1 ATTTAAA
39110 AT
1 AT
39112 ACATTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATTTAAA
Found at i:41027 original size:27 final size:26
Alignment explanation
Indices: 40962--41027 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
40952 CTAGAAATCT
*
40962 TAATTTTTTAATTTTTTTAATTTTAAA
1 TAATTTTTT-ATTTTTTTAAATTTAAA
*
40989 T-ATTATTTTATTTTTTCTAAATTTATA
1 TAATT-TTTTATTTTTT-TAAATTTAAA
*
41016 TAATTTTGTATT
1 TAATTTTTTATT
41028 ATAAGAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 10 0.30
27 20 0.61
28 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (26 bp):
TAATTTTTTATTTTTTTAAATTTAAA
Found at i:41320 original size:30 final size:31
Alignment explanation
Indices: 41277--41337 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
41267 ATACTAACCC
*
41277 TATAATTATATTATTTTTATAATATAAAAAT
1 TATAAATATATTATTTTTATAATATAAAAAT
*
41308 TATAAATA-ATTATTTTTATATTATAAAAAT
1 TATAAATATATTATTTTTATAATATAAAAAT
41338 AAATTTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TATAAATATATTATTTTTATAATATAAAAAT
Found at i:41795 original size:23 final size:23
Alignment explanation
Indices: 41769--41813 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
41759 CAAAGCTAGT
*
41769 ATTTAATTTTAAAATATATATAA
1 ATTTAATATTAAAATATATATAA
* * *
41792 ATTTTATATTAATATTTATATA
1 ATTTAATATTAAAATATATATA
41814 TTTTCATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTAATATTAAAATATATATAA
Done.