Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009381.1 Kokia drynarioides strain JFW-HI SEQ_124088, 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: 39307
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Found at i:794 original size:69 final size:66
Alignment explanation
Indices: 709--856 Score: 192
Period size: 69 Copynumber: 2.2 Consensus size: 66
699 ATCTCGTGCT
*
709 CTCTGT-TATTAGCACTGTGTGTGCTCTCTGATT-AGCATTTTGTGTGCTCTCTGATTAGTACTT
1 CTCTGTGT-TTAGCACTGTGTGTGCTCTCTG-TTCAGCA-TTTATGTGCTCTCTG-TTAGTACTT
772 TGTGTA
62 TG-GTA
778 CTCTGTGTTTAGCACTGTGTGTGCTCTCTGTTGCCCAGCATTTATGTGCTCTCTGTTAGTACTTT
1 CTCTGTGTTTAGCACTGTGTGTGCTCTCTGTT---CAGCATTTATGTGCTCTCTGTTAGTACTTT
843 GGTA
63 GGTA
*
847 CTCTCTGTTT
1 CTCTGTGTTT
857 GTTCCGTATA
Statistics
Matches: 72, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
68 2 0.03
69 40 0.56
70 12 0.17
71 14 0.19
72 4 0.06
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (66 bp):
CTCTGTGTTTAGCACTGTGTGTGCTCTCTGTTCAGCATTTATGTGCTCTCTGTTAGTACTTTGGT
A
Found at i:809 original size:23 final size:23
Alignment explanation
Indices: 681--809 Score: 134
Period size: 23 Copynumber: 5.5 Consensus size: 23
671 GAACACTAGC
* *
681 GTGCTCTCTGTTTAGCACATCT-C
1 GTGCTCTCTGTTTAGCAC-TGTGT
704 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTG-T-TTAGCACTGTGT
* * *
729 GTGCTCTCTGATTAGCATTTTGT
1 GTGCTCTCTGTTTAGCACTGTGT
* * *
752 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGTTTAGCACTGTGT
* *
775 GTACTCTGTGTTTAGCACTGTGT
1 GTGCTCTCTGTTTAGCACTGTGT
798 GTGCTCTCTGTT
1 GTGCTCTCTGTT
810 GCCCAGCATT
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
23 69 0.78
24 3 0.03
25 17 0.19
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (23 bp):
GTGCTCTCTGTTTAGCACTGTGT
Found at i:1847 original size:70 final size:70
Alignment explanation
Indices: 1763--1902 Score: 226
Period size: 70 Copynumber: 2.0 Consensus size: 70
1753 ATTCCATTTA
* * ** *
1763 TTTAATATCACATAAAAAACAGAATTATCTTTTTAGAGAAACATATGGAAAGTATTAAAACATCG
1 TTTAATATAACATAAAAAACAGAATAATCCCTTTAGAGAAACATATGGAAAATATTAAAACATCG
1828 AATCC
66 AATCC
*
1833 TTTAATATAACATAAAAAATAGAATAATCCCTTTAGAGAAACATATGGAAAATATTAAAACATCG
1 TTTAATATAACATAAAAAACAGAATAATCCCTTTAGAGAAACATATGGAAAATATTAAAACATCG
1898 AATCC
66 AATCC
1903 AGAAGAATAT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29
Consensus pattern (70 bp):
TTTAATATAACATAAAAAACAGAATAATCCCTTTAGAGAAACATATGGAAAATATTAAAACATCG
AATCC
Found at i:8462 original size:18 final size:18
Alignment explanation
Indices: 8424--8465 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
8414 AGTTCTTTTT
*
8424 AAAAGCACTTTTGACATA
1 AAAAGCACTTTTGACACA
*
8442 AAAAGCACTTTTGA-ACC
1 AAAAGCACTTTTGACACA
8459 AAAAGCA
1 AAAAGCA
8466 ATGCTAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (18 bp):
AAAAGCACTTTTGACACA
Found at i:8887 original size:13 final size:13
Alignment explanation
Indices: 8851--8902 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
8841 TTAAATCAAG
*
8851 CTTTTCAAAACCA
1 CTTTTCAAAAGCA
*
8864 CTTTTCCAAAGCA
1 CTTTTCAAAAGCA
* *
8877 CTTTTTAAAAGTA
1 CTTTTCAAAAGCA
*
8890 CTTCTCAAAAGCA
1 CTTTTCAAAAGCA
8903 ATGCTAAACT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.33
Consensus pattern (13 bp):
CTTTTCAAAAGCA
Found at i:13753 original size:13 final size:13
Alignment explanation
Indices: 13737--13762 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13727 TTTAGAATGG
13737 ATTTTTATTTTTT
1 ATTTTTATTTTTT
13750 ATTTTTATTTTTT
1 ATTTTTATTTTTT
13763 CTCGTTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:16448 original size:18 final size:18
Alignment explanation
Indices: 16421--16455 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16411 GTGTGTGGAA
*
16421 TAAAAACATGGTTAGTGT
1 TAAAAACATGGTGAGTGT
*
16439 TAAAAGCATGGTGAGTG
1 TAAAAACATGGTGAGTG
16456 AAAGAGTGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (18 bp):
TAAAAACATGGTGAGTGT
Found at i:16719 original size:22 final size:21
Alignment explanation
Indices: 16670--16719 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
16660 AAAATTATTG
* * *
16670 TTTTCTTGTTTTTTTTTACTG
1 TTTTGTTGTTTTTTCTTACTA
*
16691 TTATGTTGTTATTTTCTTACTA
1 TTTTGTTGTT-TTTTCTTACTA
16713 TTTTGTT
1 TTTTGTT
16720 ACAATTTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.10, C:0.08, G:0.10, T:0.72
Consensus pattern (21 bp):
TTTTGTTGTTTTTTCTTACTA
Found at i:16958 original size:14 final size:14
Alignment explanation
Indices: 16938--16976 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
16928 AGGATTAATA
16938 TATTATAACATTG-
1 TATTATAACATTGC
*
16951 TGATTATAACACTGC
1 T-ATTATAACATTGC
16966 TATTATAACAT
1 TATTATAACAT
16977 GTTATTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (14 bp):
TATTATAACATTGC
Found at i:20229 original size:27 final size:27
Alignment explanation
Indices: 20195--20261 Score: 91
Period size: 28 Copynumber: 2.5 Consensus size: 27
20185 TCACAAAGCT
*
20195 CATT-CTTTCAGAATATGCCACTAAGG
1 CATTCCTTTCAGAATACGCCACTAAGG
* *
20221 CATTCCTTTCCATATTACGCCACTAAGG
1 CATTCCTTT-CAGAATACGCCACTAAGG
20249 CATTCCTTTCAGA
1 CATTCCTTTCAGA
20262 GTTCGTTACA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.11
27 7 0.20
28 24 0.69
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.33
Consensus pattern (27 bp):
CATTCCTTTCAGAATACGCCACTAAGG
Found at i:24312 original size:48 final size:48
Alignment explanation
Indices: 24257--24400 Score: 137
Period size: 48 Copynumber: 3.0 Consensus size: 48
24247 GTAGTTTAAT
* *
24257 TGCGATTATGTGGCAATTATTGGCAAATATGTGGTGGGTTATCCACAA
1 TGCGATTATGTGGCAATTATCGGCAAATATGTGGTGGCTTATCCACAA
** * * * *
24305 TGCGATTATGTGGCCGTTATCGGTAATTATGTGGTGGCTTGTCCACGA
1 TGCGATTATGTGGCAATTATCGGCAAATATGTGGTGGCTTATCCACAA
** * * ** *
24353 TTTG-TTATGTGGTCATTTATCAGCATTTATGTGGTGGCTTGTCCACAA
1 TGCGATTATGTGG-CAATTATCGGCAAATATGTGGTGGCTTATCCACAA
24401 ATGGTGTGTT
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
47 8 0.10
48 71 0.90
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.38
Consensus pattern (48 bp):
TGCGATTATGTGGCAATTATCGGCAAATATGTGGTGGCTTATCCACAA
Found at i:28354 original size:16 final size:16
Alignment explanation
Indices: 28333--28363 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28323 ATAATGTGAA
28333 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
28349 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
28364 AGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:29091 original size:26 final size:26
Alignment explanation
Indices: 29055--29109 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
29045 GGCATAATTC
29055 TGGACACGTTCATGCAGCGACAATCT
1 TGGACACGTTCATGCAGCGACAATCT
* * * *
29081 TGGACATGTTCATGTAGCGAGATTCT
1 TGGACACGTTCATGCAGCGACAATCT
29107 TGG
1 TGG
29110 GTGCAATTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (26 bp):
TGGACACGTTCATGCAGCGACAATCT
Found at i:36034 original size:40 final size:40
Alignment explanation
Indices: 35979--36060 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
35969 ATATCCAAAT
35979 ATTTTGTTTTTGTTAATATTCTTTGAGAAAGGATATTAGA
1 ATTTTGTTTTTGTTAATATTCTTTGAGAAAGGATATTAGA
36019 ATTTTGTTTTTGTTAATATTCTTTGAGAAAGGATATTAGA
1 ATTTTGTTTTTGTTAATATTCTTTGAGAAAGGATATTAGA
36059 AT
1 AT
36061 GTAGTAATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.50
Consensus pattern (40 bp):
ATTTTGTTTTTGTTAATATTCTTTGAGAAAGGATATTAGA
Found at i:38849 original size:39 final size:39
Alignment explanation
Indices: 38795--38913 Score: 238
Period size: 39 Copynumber: 3.1 Consensus size: 39
38785 GAGAACTAAT
38795 AACTTGTAATGAGTTAAGGGGGAGAGTAATTTGAACCAG
1 AACTTGTAATGAGTTAAGGGGGAGAGTAATTTGAACCAG
38834 AACTTGTAATGAGTTAAGGGGGAGAGTAATTTGAACCAG
1 AACTTGTAATGAGTTAAGGGGGAGAGTAATTTGAACCAG
38873 AACTTGTAATGAGTTAAGGGGGAGAGTAATTTGAACCAG
1 AACTTGTAATGAGTTAAGGGGGAGAGTAATTTGAACCAG
38912 AA
1 AA
38914 GTTCAACAAG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.37, C:0.08, G:0.30, T:0.25
Consensus pattern (39 bp):
AACTTGTAATGAGTTAAGGGGGAGAGTAATTTGAACCAG
Done.