Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011661.1 Kokia drynarioides strain JFW-HI SEQ_126653, 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: 31801
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 126 characters in sequence are not A, C, G, or T
Found at i:8327 original size:6 final size:6
Alignment explanation
Indices: 8316--8347 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
8306 GTGCCTGTCT
*
8316 TGCACA TGCACA TGCACA TGCACA TCCACA TG
1 TGCACA TGCACA TGCACA TGCACA TGCACA TG
8348 GTTAATGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.19
Consensus pattern (6 bp):
TGCACA
Found at i:13333 original size:7 final size:7
Alignment explanation
Indices: 13321--13384 Score: 60
Period size: 7 Copynumber: 8.7 Consensus size: 7
13311 AATGAAATTC
13321 AATTTTA
1 AATTTTA
13328 AATTTTA
1 AATTTTA
13335 AATTTTA
1 AATTTTA
*
13342 AATTTCAA
1 AATTT-TA
13350 ATTATTTTA
1 A--ATTTTA
13359 AA-TTTA
1 AATTTTA
13365 AATTTATTA
1 AA-TT-TTA
13374 AA-TTTA
1 AATTTTA
13380 AATTT
1 AATTT
13385 AAGTTTAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
6 11 0.23
7 23 0.48
8 3 0.06
9 7 0.15
10 4 0.08
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (7 bp):
AATTTTA
Found at i:13358 original size:17 final size:16
Alignment explanation
Indices: 13322--13383 Score: 76
Period size: 15 Copynumber: 4.0 Consensus size: 16
13312 ATGAAATTCA
*
13322 ATTTTAAATTTTAA--
1 ATTTTAAATTTAAATT
13336 ATTTTAAATTTCAAATT
1 ATTTTAAATTT-AAATT
13353 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
*
13369 -TATTAAATTTAAATT
1 ATTTTAAATTTAAATT
13384 TAAGTTTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
14 11 0.26
15 16 0.37
16 5 0.12
17 11 0.26
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTAAATTTAAATT
Found at i:13360 original size:31 final size:31
Alignment explanation
Indices: 13322--13383 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
13312 ATGAAATTCA
13322 ATTTTAAATTTTAAA-TT-TTAAATTTCAAATT
1 ATTTTAAA-TTTAAATTTATTAAATTT-AAATT
13353 ATTTTAAATTTAAATTTATTAAATTTAAATT
1 ATTTTAAATTTAAATTTATTAAATTTAAATT
13384 TAAGTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 6 0.21
31 15 0.52
32 8 0.28
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (31 bp):
ATTTTAAATTTAAATTTATTAAATTTAAATT
Found at i:13366 original size:6 final size:6
Alignment explanation
Indices: 13324--13393 Score: 60
Period size: 6 Copynumber: 12.0 Consensus size: 6
13314 GAAATTCAAT
*
13324 TTTAAA TTTTAAA TTTTAAA TTTCAAA -TT-AT TTTAAA TTTAAA TTT--A
1 TTTAAA -TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
*
13371 -TTAAA TTTAAA TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
13394 ATGTTCAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 3 0.06
6 30 0.57
7 16 0.30
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:13403 original size:21 final size:20
Alignment explanation
Indices: 13324--13395 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 20
13314 GAAATTCAAT
13324 TTTAAATTT-TAAATTTTAAA
1 TTTAAATTTATAAA-TTTAAA
13344 TTTCAAA-TTAT---TTTAAA
1 TTT-AAATTTATAAATTTAAA
13361 TTTAAATTTATTAAATTTAAA
1 TTTAAATTTA-TAAATTTAAA
*
13382 TTTAAGTTTA-AAAT
1 TTTAAATTTATAAAT
13396 GTTCAAATAC
Statistics
Matches: 44, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
16 3 0.07
17 12 0.27
18 1 0.02
19 4 0.09
20 5 0.11
21 19 0.43
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (20 bp):
TTTAAATTTATAAATTTAAA
Found at i:14342 original size:26 final size:28
Alignment explanation
Indices: 14300--14353 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
14290 TGGTTTGAGA
14300 GAAAAGAGAAGAAAG-AAATG-TTTTTT
1 GAAAAGAGAAGAAAGAAAATGATTTTTT
*
14326 GAAAAGA-AATGACAGAAAATGATTTTTT
1 GAAAAGAGAA-GAAAGAAAATGATTTTTT
14354 TTCCTGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 2 0.08
26 11 0.46
27 5 0.21
28 6 0.25
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.28
Consensus pattern (28 bp):
GAAAAGAGAAGAAAGAAAATGATTTTTT
Found at i:14774 original size:29 final size:29
Alignment explanation
Indices: 14742--14937 Score: 177
Period size: 29 Copynumber: 6.8 Consensus size: 29
14732 TCACACTTCA
* * *
14742 CAAAAATCATCATTTTGCCCTTGAACATC
1 CAAAAATTACCATTTTGCCCTCGAACATC
*
14771 CAAAAATTACCATTTTGCTCC-CGAGCATC
1 CAAAAATTACCATTTTGC-CCTCGAACATC
* * *
14800 CAAAAATTACTATTTTACCCCCGAACAT-
1 CAAAAATTACCATTTTGCCCTCGAACATC
* *
14828 CTAAAATTACCATTTTGACCC-CGAACTTTTC
1 CAAAAATTACCATTTTG-CCCTCGAAC--ATC
* * *
14859 C-AAAATTATCATTTTACCCTTGAACATC
1 CAAAAATTACCATTTTGCCCTCGAACATC
* *
14887 CAAAAATTACCATTTTACCC-CTGAGCATC
1 CAAAAATTACCATTTTGCCCTC-GAACATC
*
14916 CAAAAATTACCTTTTTGCCCTC
1 CAAAAATTACCATTTTGCCCTC
14938 AAATTTTCCA
Statistics
Matches: 137, Mismatches: 20, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
28 24 0.18
29 91 0.66
30 21 0.15
31 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (29 bp):
CAAAAATTACCATTTTGCCCTCGAACATC
Found at i:14805 original size:58 final size:57
Alignment explanation
Indices: 14742--14924 Score: 219
Period size: 58 Copynumber: 3.2 Consensus size: 57
14732 TCACACTTCA
* *
14742 CAAAAATCATCATTTTGCCCTTGAACATCCAAAAATTACCATTTTGCTCCCGAGCATC
1 CAAAAATTATCATTTTACCCTTGAACATCCAAAAATTACCATTTTGC-CCCGAGCATC
** * * *
14800 CAAAAATTA-CTATTTTACCCCCGAACAT-CTAAAATTACCATTTTGACCCCGAACTTTTC
1 CAAAAATTATC-ATTTTACCCTTGAACATCCAAAAATTACCATTTTG-CCCCGAGC--ATC
*
14859 C-AAAATTATCATTTTACCCTTGAACATCCAAAAATTACCATTTTACCCCTGAGCATC
1 CAAAAATTATCATTTTACCCTTGAACATCCAAAAATTACCATTTTGCCCC-GAGCATC
14916 CAAAAATTA
1 CAAAAATTA
14925 CCTTTTTGCC
Statistics
Matches: 104, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
57 26 0.25
58 56 0.54
59 22 0.21
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.31
Consensus pattern (57 bp):
CAAAAATTATCATTTTACCCTTGAACATCCAAAAATTACCATTTTGCCCCGAGCATC
Found at i:14865 original size:87 final size:87
Alignment explanation
Indices: 14773--14950 Score: 218
Period size: 87 Copynumber: 2.0 Consensus size: 87
14763 TGAACATCCA
* * * *
14773 AAAATTACCATTTTGCTCC-CGAGCATCCAAAAATTACTATTTTACCCCCGAACAT-CTAAAATT
1 AAAATTACCATTTTAC-CCTCGAACATCCAAAAATTACCATTTTACCCCCGAACATCCAAAAATT
*
14836 ACCATTTTGACCC-CGAACTTTTCC
65 ACCATTTTG-CCCTC-AAATTTTCC
* * * *
14860 AAAATTATCATTTTACCCTTGAACATCCAAAAATTACCATTTTACCCCTGAGCATCCAAAAATTA
1 AAAATTACCATTTTACCCTCGAACATCCAAAAATTACCATTTTACCCCCGAACATCCAAAAATTA
*
14925 CCTTTTTGCCCTCAAATTTTCC
66 CCATTTTGCCCTCAAATTTTCC
14947 AAAA
1 AAAA
14951 GTTCAATTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
86 2 0.03
87 60 0.77
88 16 0.21
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (87 bp):
AAAATTACCATTTTACCCTCGAACATCCAAAAATTACCATTTTACCCCCGAACATCCAAAAATTA
CCATTTTGCCCTCAAATTTTCC
Found at i:14960 original size:29 final size:29
Alignment explanation
Indices: 14928--15002 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
14918 AAAATTACCT
14928 TTTTGCCCTCAAATTTTCCAAAA-GTTCAA
1 TTTTGCCC-CAAATTTTCCAAAATGTTCAA
** *
14957 TTTTAATCCCAAATTTTCCAAAATTTTCAA
1 TTTT-GCCCCAAATTTTCCAAAATGTTCAA
14987 TTTTGATCCCCAAATT
1 TTTTG--CCCCAAATT
15003 CCTCAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
29 18 0.49
30 11 0.30
31 8 0.22
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (29 bp):
TTTTGCCCCAAATTTTCCAAAATGTTCAA
Found at i:14960 original size:87 final size:87
Alignment explanation
Indices: 14796--14961 Score: 221
Period size: 87 Copynumber: 1.9 Consensus size: 87
14786 TGCTCCCGAG
* * *
14796 CATCCAAAAATTACTATTTTACCCCCGAACATCTAAAATTACCATTTTGACCCCGAACTTTTCCA
1 CATCCAAAAATTACCATTTTACCCCCGAACATCAAAAATTACCATTTTGACCCCGAAATTTTCCA
*
14861 AAATTATCATTTTACCCTTGAA
66 AAAGTATCATTTTACCCTTGAA
* * *
14883 CATCCAAAAATTACCATTTTACCCCTGAGCATCCAAAAATTACCTTTTTG-CCCTC-AAATTTTC
1 CATCCAAAAATTACCATTTTACCCCCGAACAT-CAAAAATTACCATTTTGACCC-CGAAATTTTC
14946 CAAAAGT-TCAATTTTA
64 CAAAAGTATC-ATTTTA
14962 ATCCCAAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
86 2 0.03
87 51 0.74
88 16 0.23
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (87 bp):
CATCCAAAAATTACCATTTTACCCCCGAACATCAAAAATTACCATTTTGACCCCGAAATTTTCCA
AAAGTATCATTTTACCCTTGAA
Found at i:14974 original size:116 final size:116
Alignment explanation
Indices: 14744--14990 Score: 295
Period size: 116 Copynumber: 2.1 Consensus size: 116
14734 ACACTTCACA
* * *
14744 AAAATCATCATTTTGCCCTTGAACATCCAAAAATTACCATTTTGCTCCCGAGCATCCAAAAATTA
1 AAAATTATCATTTTACCCTTGAACATCCAAAAATTACCATTTTACTCCCGAGCATCCAAAAATTA
* * * * *
14809 CTATTTTACCCCCGAACATCTAAAATTACCATTTTGACCCCGAACTTTTCC
66 CTATTTTACCCCCAAACATCCAAAATTACAATTTTAACCCCGAAATTTTCC
14860 AAAATTATCATTTTACCCTTGAACATCCAAAAATTACCATTTTAC-CCCTGAGCATCCAAAAATT
1 AAAATTATCATTTTACCCTTGAACATCCAAAAATTACCATTTTACTCCC-GAGCATCCAAAAATT
* * ** *
14924 ACCT-TTTTGCCCTCAAATTTTCCAAAAGTT-CAATTTTAATCCC-AAATTTTCC
65 A-CTATTTTACCCCCAAA-CATCCAAAA-TTACAATTTTAACCCCGAAATTTTCC
*
14976 AAAATTTTCAATTTT
1 AAAATTATC-ATTTT
14991 GATCCCCAAA
Statistics
Matches: 112, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
115 3 0.03
116 84 0.75
117 23 0.21
118 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (116 bp):
AAAATTATCATTTTACCCTTGAACATCCAAAAATTACCATTTTACTCCCGAGCATCCAAAAATTA
CTATTTTACCCCCAAACATCCAAAATTACAATTTTAACCCCGAAATTTTCC
Found at i:14988 original size:30 final size:30
Alignment explanation
Indices: 14937--15002 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
14927 TTTTTGCCCT
14937 CAAATTTTCCAAAAGTTCAATTTTAAT-CC
1 CAAATTTTCCAAAAGTTCAATTTTAATCCC
* *
14966 CAAATTTTCCAAAATTTTCAATTTTGATCCC
1 CAAATTTTCCAAAA-GTTCAATTTTAATCCC
14997 CAAATT
1 CAAATT
15003 CCTCAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.42
30 11 0.33
31 8 0.24
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (30 bp):
CAAATTTTCCAAAAGTTCAATTTTAATCCC
Found at i:16485 original size:29 final size:30
Alignment explanation
Indices: 16442--16522 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 30
16432 AAATCAGATC
*
16442 AAATCGAAATTTCATGTATAAAATTACACA-
1 AAATC-AAAGTTCATGTATAAAATTACACAT
* *
16472 AAATCAAAGTTCATGTATATAATTGCACATT
1 AAATCAAAGTTCATGTATAAAATTACACA-T
16503 AAA-CAATAGTTCATGTATAA
1 AAATCAA-AGTTCATGTATAA
16523 TTTTGATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 21 0.48
30 8 0.18
31 15 0.34
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTACACAT
Found at i:20069 original size:3 final size:3
Alignment explanation
Indices: 20061--20085 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20051 TGATTGTCAT
20061 AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC A
20086 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:22185 original size:2 final size:2
Alignment explanation
Indices: 22178--22217 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
22168 TTTTGATGAT
* * *
22178 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22218 GGGATATCTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22571 original size:14 final size:15
Alignment explanation
Indices: 22548--22578 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
22538 AGCAAATCTC
22548 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
22563 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
22578 T
1 T
22579 GTTATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:23226 original size:2 final size:2
Alignment explanation
Indices: 23219--23247 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23209 CGCCCCAAGT
23219 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
23248 TGCAGAAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28963 original size:15 final size:16
Alignment explanation
Indices: 28943--28980 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
28933 AACAGCACGC
* *
28943 TTTGCTTTGTTTTG-T
1 TTTGCTTTGCTCTGCT
28958 TTTGCTTTGCTCTGCT
1 TTTGCTTTGCTCTGCT
28974 TTTGCTT
1 TTTGCTT
28981 CCTGAGATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.00, C:0.16, G:0.18, T:0.66
Consensus pattern (16 bp):
TTTGCTTTGCTCTGCT
Done.