Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006310.1 Kokia drynarioides strain JFW-HI SEQ_120885, 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: 52130
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:4832 original size:20 final size:18
Alignment explanation
Indices: 4793--4828 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4783 CCATCAAAAA
4793 TAAAATATATATTTAAAT
1 TAAAATATATATTTAAAT
*
4811 TAAACTATATATTTAAAT
1 TAAAATATATATTTAAAT
4829 ATTATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATATATATTTAAAT
Found at i:5528 original size:43 final size:43
Alignment explanation
Indices: 5465--5572 Score: 171
Period size: 43 Copynumber: 2.5 Consensus size: 43
5455 AAAAAAAAGG
*
5465 GAGAATATGCCTATTCAGAAAACTACTATCTAATTGTCCTAGA
1 GAGAATATGCCTGTTCAGAAAACTACTATCTAATTGTCCTAGA
* *
5508 GAGAATATGCCTGTTTAGAAAGCTACTATCTAATTGTCCTAGA
1 GAGAATATGCCTGTTCAGAAAACTACTATCTAATTGTCCTAGA
* *
5551 GAGAATCTGTCTGTTCAGAAAA
1 GAGAATATGCCTGTTCAGAAAA
5573 TGATTTGAGC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (43 bp):
GAGAATATGCCTGTTCAGAAAACTACTATCTAATTGTCCTAGA
Found at i:7524 original size:7 final size:7
Alignment explanation
Indices: 7509--7544 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
7499 AAATTTCATG
*
7509 TATACAT
1 TATAAAT
7516 TATAAAT
1 TATAAAT
7523 TATAAAT
1 TATAAAT
7530 TATAAAT
1 TATAAAT
7537 TATCAAAT
1 TAT-AAAT
7545 AGTTTCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
7 23 0.85
8 4 0.15
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (7 bp):
TATAAAT
Found at i:10101 original size:44 final size:44
Alignment explanation
Indices: 10026--10125 Score: 120
Period size: 44 Copynumber: 2.3 Consensus size: 44
10016 CTAAGTCCCG
10026 AAAATCTCC-AAATTTTTAACCTTAAATCAAAA-TCTCCAAACCCC
1 AAAATC-CCTAAATTTTTAACCTTAAATCAAAATTCTCCAAA-CCC
10070 AAAATCCCTAAATTTCTTAAACC-TAAA-CAAAATTCTCCAAACCC
1 AAAATCCCTAAATTT-TT-AACCTTAAATCAAAATTCTCCAAACCC
10114 AACAA-CCCTAAA
1 AA-AATCCCTAAA
10126 AATCCCAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
43 2 0.04
44 29 0.57
45 16 0.31
46 4 0.08
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (44 bp):
AAAATCCCTAAATTTTTAACCTTAAATCAAAATTCTCCAAACCC
Found at i:10498 original size:17 final size:18
Alignment explanation
Indices: 10473--10506 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
10463 AAAAATTATA
*
10473 TTATTTTTTAA-TTTAAT
1 TTATATTTTAAGTTTAAT
10490 TTATATTTTAAGTTTAA
1 TTATATTTTAAGTTTAA
10507 AATTTTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTATATTTTAAGTTTAAT
Found at i:19162 original size:35 final size:34
Alignment explanation
Indices: 19114--19182 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 34
19104 CCTTCCTCAC
19114 CCCTGCCCTAAAATCATATTATTATAATAAGTCA
1 CCCTGCCCTAAAATCATATTATTATAATAAGTCA
* **
19148 CCCTTCCCTAAAAATTTTATTATTATAATAAGTCA
1 CCCTGCCCT-AAAATCATATTATTATAATAAGTCA
19183 AGTTTCATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 8 0.26
35 23 0.74
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (34 bp):
CCCTGCCCTAAAATCATATTATTATAATAAGTCA
Found at i:26597 original size:2 final size:2
Alignment explanation
Indices: 26590--26624 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
26580 ACTTCCACAA
26590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26625 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31829 original size:24 final size:25
Alignment explanation
Indices: 31783--31830 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
31773 TTGAAAATAT
* *
31783 TTGAGAAAGTAATTCAATCTTTAGG
1 TTGAGAAAGTAATCCAATATTTAGG
*
31808 TTGAGCAAGTAA-CCAATATTTAG
1 TTGAGAAAGTAATCCAATATTTAG
31831 ACAAACCTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (25 bp):
TTGAGAAAGTAATCCAATATTTAGG
Found at i:35110 original size:33 final size:32
Alignment explanation
Indices: 35035--35143 Score: 103
Period size: 33 Copynumber: 3.3 Consensus size: 32
35025 GGTGTGTTAG
* * * *
35035 TTTGATAGCTTTTACGAGCATATCGTGTAATGA
1 TTTGATAGCTTTTTCGAGCATACCATGTACT-A
*
35068 TTGGATAGCTTTTTCGAGCATACCATGTACTA
1 TTTGATAGCTTTTTCGAGCATACCATGTACTA
* *
35100 TTTGATTAGCTCTTAT-AAGCATACCATGTACTA
1 TTTGA-TAGCT-TTTTCGAGCATACCATGTACTA
*
35133 ATTGATTAGCT
1 TTTGA-TAGCT
35144 CTTACAGGCA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 5 0.08
33 57 0.88
34 3 0.05
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (32 bp):
TTTGATAGCTTTTTCGAGCATACCATGTACTA
Found at i:35144 original size:33 final size:33
Alignment explanation
Indices: 35084--35223 Score: 147
Period size: 33 Copynumber: 4.2 Consensus size: 33
35074 AGCTTTTTCG
*
35084 AGCATACCATGTACTATTTGATTAGCTCTTATA
1 AGCATACCATGTACTAATTGATTAGCTCTTATA
*
35117 AGCATACCATGTACTAATTGATTAGCTCTTACA
1 AGCATACCATGTACTAATTGATTAGCTCTTATA
* * * **
35150 GGCATA-CAGTGTATTGATTGATTAGCTCTTAGG
1 AGCATACCA-TGTACTAATTGATTAGCTCTTATA
** * * *
35183 AGCATACTGTGTATTGAATTGATGAGCTCTTATG
1 AGCATACCATGTACT-AATTGATTAGCTCTTATA
35217 AGCATAC
1 AGCATAC
35224 TGTGAATTTA
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
32 2 0.02
33 67 0.74
34 22 0.24
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (33 bp):
AGCATACCATGTACTAATTGATTAGCTCTTATA
Found at i:35211 original size:34 final size:34
Alignment explanation
Indices: 35101--35227 Score: 152
Period size: 33 Copynumber: 3.8 Consensus size: 34
35091 CATGTACTAT
* ** *
35101 TTGATTAGCTCTTATAAGCATACCATGTACT-AA
1 TTGATTAGCTCTTATGAGCATACTGTGTATTGAA
* *
35134 TTGATTAGCTCTTA-CAGGCATACAGTGTATTG-A
1 TTGATTAGCTCTTATGA-GCATACTGTGTATTGAA
*
35167 TTGATTAGCTCTTAGGAGCATACTGTGTATTGAA
1 TTGATTAGCTCTTATGAGCATACTGTGTATTGAA
*
35201 TTGATGAGCTCTTATGAGCATACTGTG
1 TTGATTAGCTCTTATGAGCATACTGTG
35228 AATTTACATG
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
32 1 0.01
33 54 0.66
34 27 0.33
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (34 bp):
TTGATTAGCTCTTATGAGCATACTGTGTATTGAA
Found at i:36156 original size:21 final size:21
Alignment explanation
Indices: 36130--36169 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
36120 CGGAGATATA
36130 GGTGTGT-GAGAGAGCCACATG
1 GGTGTGTAG-GAGAGCCACATG
36151 GGTGTGTAGGAGAGCCACA
1 GGTGTGTAGGAGAGCCACA
36170 CGGTCGTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.15, G:0.42, T:0.17
Consensus pattern (21 bp):
GGTGTGTAGGAGAGCCACATG
Found at i:36178 original size:23 final size:21
Alignment explanation
Indices: 36130--36180 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
36120 CGGAGATATA
*
36130 GGTGTGTGAGAGAGCCACATG
1 GGTGTGTGAGAGAGCCACACG
36151 GGTGTGT-AGGAGAGCCACAC-
1 GGTGTGTGA-GAGAGCCACACG
36171 GGTCGTGTGA
1 GGT-GTGTGA
36181 CCCCTGTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.15
21 21 0.81
22 1 0.04
ACGTcount: A:0.22, C:0.16, G:0.43, T:0.20
Consensus pattern (21 bp):
GGTGTGTGAGAGAGCCACACG
Found at i:40918 original size:22 final size:23
Alignment explanation
Indices: 40857--40932 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
40847 GCTGGGAAAT
* *
40857 AGAGAGTACACAAAGTGCTAATC
1 AGAGAGCACACGAAGTGCTAATC
40880 AGAGAGCACACGAAGTGCTAATC
1 AGAGAGCACACGAAGTGCTAATC
40903 AGAGAGCAC-CGAAGTGCTAATAAC
1 AGAGAGCACACGAAGTGCTAAT--C
40927 AGAGAG
1 AGAGAG
40933 ACGTGCTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
22 12 0.24
23 30 0.61
24 7 0.14
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.13
Consensus pattern (23 bp):
AGAGAGCACACGAAGTGCTAATC
Found at i:40980 original size:23 final size:23
Alignment explanation
Indices: 40938--40994 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
40928 GAGAGACGTG
*
40938 CTAAACAAAGAG--CACACAATA
1 CTAAACAGAGAGCACACACAATA
* *
40959 CTGAACAGAGAGCACACACAATG
1 CTAAACAGAGAGCACACACAATA
40982 CTAAACAGAGAGC
1 CTAAACAGAGAGC
40995 GCACTAGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 10 0.33
23 20 0.67
ACGTcount: A:0.49, C:0.25, G:0.18, T:0.09
Consensus pattern (23 bp):
CTAAACAGAGAGCACACACAATA
Found at i:44896 original size:23 final size:23
Alignment explanation
Indices: 44869--44968 Score: 164
Period size: 23 Copynumber: 4.3 Consensus size: 23
44859 ATCTTAATTC
* *
44869 TTTAAGCACAAATCAAATTAATA
1 TTTAAGCATAAATCATATTAATA
*
44892 TTTAATCATAAATCATATTAATA
1 TTTAAGCATAAATCATATTAATA
*
44915 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCATATTAATA
44938 TTTAAGCATAAATCATATTAATA
1 TTTAAGCATAAATCATATTAATA
44961 TTTAAGCA
1 TTTAAGCA
44969 CAGATATAAG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (23 bp):
TTTAAGCATAAATCATATTAATA
Done.