Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009998.1 Kokia drynarioides strain JFW-HI SEQ_124754, 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: 34075
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:2956 original size:4 final size:4
Alignment explanation
Indices: 2947--3010 Score: 67
Period size: 4 Copynumber: 15.8 Consensus size: 4
2937 ACACATTACT
* * * *
2947 TTTC TTTC TTT- ATTC TTTC TTTCC TCTC CTTC TTCC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC
2995 TTTTC TTTC TTTC TTT
1 -TTTC TTTC TTTC TTT
3011 TCTCGTTTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
3 2 0.04
4 40 0.82
5 7 0.14
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:2999 original size:13 final size:13
Alignment explanation
Indices: 2947--3013 Score: 73
Period size: 13 Copynumber: 5.1 Consensus size: 13
2937 ACACATTACT
2947 TTTCTTTCTTTATTC
1 TTTCTTTC-TT-TTC
* *
2962 TTTCTTTCCTCTC
1 TTTCTTTCTTTTC
* *
2975 CTTC-TTCCTTTC
1 TTTCTTTCTTTTC
2987 TTTCTTTCTTTTC
1 TTTCTTTCTTTTC
3000 TTTCTTTCTTTTC
1 TTTCTTTCTTTTC
3013 T
1 T
3014 CGTTTATTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
12 10 0.22
13 26 0.58
14 1 0.02
15 8 0.18
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTCTTTCTTTTC
Found at i:3004 original size:25 final size:24
Alignment explanation
Indices: 2945--3010 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
2935 GAACACATTA
2945 CTTTTCTTTCTT-TATTCTTTCTTT
1 CTTTTCTTTCTTCT-TTCTTTCTTT
* * *
2969 CCTCTCCTTCTTCCTTTCTTTCTTT
1 CTTTTCTTTCTT-CTTTCTTTCTTT
2994 CTTTTCTTTCTTTCTTT
1 CTTTTCTTTC-TTCTTT
3011 TCTCGTTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
24 9 0.27
25 21 0.64
26 3 0.09
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.70
Consensus pattern (24 bp):
CTTTTCTTTCTTCTTTCTTTCTTT
Found at i:13089 original size:19 final size:18
Alignment explanation
Indices: 13048--13090 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
13038 ATTTATTTGT
13048 AAAAAAAAGGAAAGAAAA
1 AAAAAAAAGGAAAGAAAA
* *
13066 GAAAATAAATGAAAGAAAA
1 -AAAAAAAAGGAAAGAAAA
13085 AAAAAA
1 AAAAAA
13091 CTAAAGGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAAAAAAGGAAAGAAAA
Found at i:13404 original size:24 final size:24
Alignment explanation
Indices: 13376--13435 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
13366 TGTGTGTAAC
13376 GTTGGTATGTTTATTTAAAAACGT
1 GTTGGTATGTTTATTTAAAAACGT
13400 GTTGGTATGTTTATTTAAAAACGT
1 GTTGGTATGTTTATTTAAAAACGT
13424 GTTGGTATGTTT
1 GTTGGTATGTTT
13436 GTTCTGGGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.25, C:0.03, G:0.23, T:0.48
Consensus pattern (24 bp):
GTTGGTATGTTTATTTAAAAACGT
Found at i:16872 original size:136 final size:136
Alignment explanation
Indices: 16628--16902 Score: 550
Period size: 136 Copynumber: 2.0 Consensus size: 136
16618 AGGCCTATTA
16628 CAATCAGGTATTAATACTTGCAGTTGCTTAGAACCAATCATTGGTCCTTTCATTAAGAGCTTTCC
1 CAATCAGGTATTAATACTTGCAGTTGCTTAGAACCAATCATTGGTCCTTTCATTAAGAGCTTTCC
16693 CTCCATCCTCAACAGAGTGTAAAGCTTCACATAGGTAACAATAAAGTTCCACAATTTAATCTTAT
66 CTCCATCCTCAACAGAGTGTAAAGCTTCACATAGGTAACAATAAAGTTCCACAATTTAATCTTAT
16758 AGCTAG
131 AGCTAG
16764 CAATCAGGTATTAATACTTGCAGTTGCTTAGAACCAATCATTGGTCCTTTCATTAAGAGCTTTCC
1 CAATCAGGTATTAATACTTGCAGTTGCTTAGAACCAATCATTGGTCCTTTCATTAAGAGCTTTCC
16829 CTCCATCCTCAACAGAGTGTAAAGCTTCACATAGGTAACAATAAAGTTCCACAATTTAATCTTAT
66 CTCCATCCTCAACAGAGTGTAAAGCTTCACATAGGTAACAATAAAGTTCCACAATTTAATCTTAT
16894 AGCTAG
131 AGCTAG
16900 CAA
1 CAA
16903 ACCTCAAGCT
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 139 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (136 bp):
CAATCAGGTATTAATACTTGCAGTTGCTTAGAACCAATCATTGGTCCTTTCATTAAGAGCTTTCC
CTCCATCCTCAACAGAGTGTAAAGCTTCACATAGGTAACAATAAAGTTCCACAATTTAATCTTAT
AGCTAG
Found at i:33971 original size:2 final size:2
Alignment explanation
Indices: 33964--34004 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
33954 GTAATTAAGG
33964 TA TA TA 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 TA TA TA T
34005 TGAAATATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.