Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014061.1 Kokia drynarioides strain JFW-HI SEQ_129092, 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: 5316
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1883 original size:14 final size:14
Alignment explanation
Indices: 1841--1884 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1831 TTAACCAATC
1841 TAGTGTTTACGGTT
1 TAGTGTTTACGGTT
* *
1855 TAGAGTTT-CAAGTT
1 TAGTGTTTAC-GGTT
1869 TAGTGTTTACGGTT
1 TAGTGTTTACGGTT
1883 TA
1 TA
1885 AGGTTTTAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 1 0.04
14 22 0.92
15 1 0.04
ACGTcount: A:0.20, C:0.07, G:0.25, T:0.48
Consensus pattern (14 bp):
TAGTGTTTACGGTT
Found at i:1905 original size:28 final size:28
Alignment explanation
Indices: 1841--1898 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
1831 TTAACCAATC
1841 TAGTGTTTACGGTTTAGAGTTTCAAGTT
1 TAGTGTTTACGGTTTAGAGTTTCAAGTT
*
1869 TAGTGTTTACGGTTTA-AGGTTTTAAGTT
1 TAGTGTTTACGGTTTAGA-GTTTCAAGTT
1897 TA
1 TA
1899 AGGTTTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.48
Consensus pattern (28 bp):
TAGTGTTTACGGTTTAGAGTTTCAAGTT
Found at i:1915 original size:13 final size:14
Alignment explanation
Indices: 1880--1919 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1870 AGTGTTTACG
1880 GTTTAAGGTTTTAA
1 GTTTAAGGTTTTAA
1894 GTTTAAGGTTTATAA
1 GTTTAAGGTTT-TAA
1909 -TTT-AGGTTTTA
1 GTTTAAGGTTTTA
1920 GGGTTTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.08
13 6 0.24
14 14 0.56
15 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.53
Consensus pattern (14 bp):
GTTTAAGGTTTTAA
Found at i:2261 original size:45 final size:45
Alignment explanation
Indices: 2212--2319 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
2202 CAAAGTCAGC
* * *
2212 CTGATATCCTTTCCTTGAGTATTGCGGTAGCT-CATCAAATTGAGG
1 CTGATATCCTTGCCTTGAGTATTGCGGT-GCTCCATCAAACTAAGG
* * *
2257 CTGATATCCTTGGCTTGAGTATTGCGGTGGTCCGTCAAACTAAGG
1 CTGATATCCTTGCCTTGAGTATTGCGGTGCTCCATCAAACTAAGG
*
2302 CTGATATCCTTGGCTTGA
1 CTGATATCCTTGCCTTGA
2320 TGAGCTATGC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 2 0.04
45 54 0.96
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.34
Consensus pattern (45 bp):
CTGATATCCTTGCCTTGAGTATTGCGGTGCTCCATCAAACTAAGG
Found at i:4285 original size:16 final size:16
Alignment explanation
Indices: 4264--4312 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
4254 TGATGGGGAT
4264 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
4280 ATTATTTTTAT-ATT-
1 ATTATTTTGATAATTA
*
4294 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
4309 ATTA
1 ATTA
4313 GCTAAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
15 4 0.15
16 12 0.44
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:4788 original size:12 final size:12
Alignment explanation
Indices: 4773--4797 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4763 AAATTAAAAT
4773 ATTTTAAAATTA
1 ATTTTAAAATTA
4785 ATTTTAAAATTA
1 ATTTTAAAATTA
4797 A
1 A
4798 CCATACTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:4986 original size:4 final size:4
Alignment explanation
Indices: 4972--5029 Score: 61
Period size: 4 Copynumber: 15.0 Consensus size: 4
4962 TACCTTTTTT
*
4972 TTTC TTCTC TTTC TTTC -TTC -TTC -TTC TTTC TTTC TTTC TCTTT TTTC
1 TTTC TT-TC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC
5019 TTTC TTT- TTTC
1 TTTC TTTC TTTC
5030 CTTCAATTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
3 12 0.25
4 29 0.60
5 7 0.15
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:4990 original size:13 final size:13
Alignment explanation
Indices: 4972--5025 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
4962 TACCTTTTTT
4972 TTTCTTCTCTTTC
1 TTTCTTCTCTTTC
4985 TTTCTTCT-TCTTC
1 TTTCTTCTCT-TTC
4998 TTTCTT-TCTTTC
1 TTTCTTCTCTTTC
*
5010 TCTT-TTTTCTTTC
1 T-TTCTTCTCTTTC
5023 TTT
1 TTT
5026 TTTCCTTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 10 0.27
13 27 0.73
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCTTCTCTTTC
Found at i:5005 original size:21 final size:21
Alignment explanation
Indices: 4973--5029 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
4963 ACCTTTTTTT
4973 TTCTTCTCTTTCTTTCT-TCTTC
1 TTCTT-TCTTTCTTTCTCT-TTC
*
4995 TTCTTTCTTTCTTTCTCTTTT
1 TTCTTTCTTTCTTTCTCTTTC
5016 TTCTTTCTTT-TTTC
1 TTCTTTCTTTCTTTC
5030 CTTCAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 4 0.12
21 23 0.70
22 6 0.18
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (21 bp):
TTCTTTCTTTCTTTCTCTTTC
Found at i:5025 original size:17 final size:18
Alignment explanation
Indices: 4972--5025 Score: 78
Period size: 17 Copynumber: 3.2 Consensus size: 18
4962 TACCTTTTTT
4972 TTTCTTC-TCTTTCTTTC
1 TTTCTTCTTCTTTCTTTC
4989 -TTCTTCTTCTTTCTTTC
1 TTTCTTCTTCTTTCTTTC
*
5006 TTTC-TCTTTTTTCTTTC
1 TTTCTTCTTCTTTCTTTC
5023 TTT
1 TTT
5026 TTTCCTTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.18
17 25 0.74
18 3 0.09
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTCTTCTTCTTTCTTTC
Found at i:5028 original size:13 final size:13
Alignment explanation
Indices: 4967--5028 Score: 63
Period size: 14 Copynumber: 4.5 Consensus size: 13
4957 CATATTACCT
4967 TTTTTTTTCTTCTC
1 TTTTTTTTCTT-TC
4981 TTTCTTTCTTC-TTC
1 TTT-TTT-TTCTTTC
4995 TTCTTTCTTTCTTTC
1 TT-TTT-TTTCTTTC
*
5010 TCTTTTTTCTTTC
1 TTTTTTTTCTTTC
5023 TTTTTT
1 TTTTTT
5029 CCTTCAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
13 13 0.32
14 15 0.37
15 10 0.24
16 3 0.07
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTTTCTTTC
Done.