Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007692.1 Kokia drynarioides strain JFW-HI SEQ_122323, 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: 6507
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Found at i:319 original size:18 final size:19
Alignment explanation
Indices: 285--322 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
275 AAATCATTGG
*
285 TTTAATTTAGTAATATTAT
1 TTTAATTGAGTAATATTAT
304 TTTAATTGAG-AATATTAT
1 TTTAATTGAGTAATATTAT
322 T
1 T
323 ATTTTTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (19 bp):
TTTAATTGAGTAATATTAT
Found at i:988 original size:30 final size:30
Alignment explanation
Indices: 954--1051 Score: 162
Period size: 30 Copynumber: 3.3 Consensus size: 30
944 TTTTGGGTCA
*
954 AATTTTGTACTCAAACTTGAAAATTTTCCT
1 AATTTGGTACTCAAACTTGAAAATTTTCCT
984 AATTTGGTACTCAAACTTGAAAATTTTCCT
1 AATTTGGTACTCAAACTTGAAAATTTTCCT
1014 AATTTGGTA-TCCAAACTTGAAAATTTTCCT
1 AATTTGGTACT-CAAACTTGAAAATTTTCCT
*
1044 ACTTTGGT
1 AATTTGGT
1052 CCCTAAACTT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 1 0.02
30 64 0.98
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (30 bp):
AATTTGGTACTCAAACTTGAAAATTTTCCT
Found at i:1060 original size:30 final size:29
Alignment explanation
Indices: 966--1063 Score: 135
Period size: 30 Copynumber: 3.3 Consensus size: 29
956 TTTTGTACTC
*
966 AAACTTGAAAATTTTCCTAATTTGGTACT
1 AAACTTGAAAATTTTCCTAATTTGGTCCT
995 CAAACTTGAAAATTTTCCTAATTTGGTATCC-
1 -AAACTTGAAAATTTTCCTAATTTGG--TCCT
*
1026 AAACTTGAAAATTTTCCTACTTTGGTCCCT
1 AAACTTGAAAATTTTCCTAATTTGGT-CCT
1056 AAACTTGA
1 AAACTTGA
1064 CACTTCATTT
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
28 1 0.02
29 2 0.03
30 57 0.92
32 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (29 bp):
AAACTTGAAAATTTTCCTAATTTGGTCCT
Found at i:1391 original size:29 final size:27
Alignment explanation
Indices: 1350--1455 Score: 95
Period size: 29 Copynumber: 3.7 Consensus size: 27
1340 GAAAAATGTC
1350 AAGTTCAGGTACCAAATTGGGTCCAAAA
1 AAGTTCAGGTACCAAATTGGG-CCAAAA
* ***
1378 GAAGTTTAGGTACCAAATTAGGAAAAAAA
1 -AAGTTCAGGTACCAAATT-GGGCCAAAA
* *
1407 TTCAAGTTGAGGTATCAAATTGGGCCAAAA
1 ---AAGTTCAGGTACCAAATTGGGCCAAAA
1437 AAGGTTCAGGTACCAAATT
1 AA-GTTCAGGTACCAAATT
1456 AGAAAAAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
27 2 0.03
28 14 0.23
29 21 0.34
30 8 0.13
31 16 0.26
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.24
Consensus pattern (27 bp):
AAGTTCAGGTACCAAATTGGGCCAAAA
Found at i:1414 original size:60 final size:60
Alignment explanation
Indices: 1324--1486 Score: 210
Period size: 59 Copynumber: 2.8 Consensus size: 60
1314 AAACAAAAGC
1324 TTAGGTACCAAATTAGG--AAAAATGTCAAGTTCAGGTACCAAATTGGGTCCAAAAGAA-GT
1 TTAGGTACCAAATTAGGAAAAAAATGTCAAGTTCAGGTACCAAATTGGG-CCAAAA-AAGGT
* *
1383 TTAGGTACCAAATTAGGAAAAAAAT-TCAAGTTGAGGTATCAAATTGGGCCAAAAAAGGT
1 TTAGGTACCAAATTAGGAAAAAAATGTCAAGTTCAGGTACCAAATTGGGCCAAAAAAGGT
* * * * *
1442 TCAGGTACCAAATTA-GAAAAAAATGTTAAATTTAAGTACCAAATT
1 TTAGGTACCAAATTAGGAAAAAAATGTCAAGTTCAGGTACCAAATT
1487 TTATATTAAG
Statistics
Matches: 92, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
58 11 0.12
59 54 0.59
60 21 0.23
61 6 0.07
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (60 bp):
TTAGGTACCAAATTAGGAAAAAAATGTCAAGTTCAGGTACCAAATTGGGCCAAAAAAGGT
Found at i:2991 original size:58 final size:59
Alignment explanation
Indices: 2927--3051 Score: 198
Period size: 58 Copynumber: 2.1 Consensus size: 59
2917 ACGGGCCAGG
* *
2927 CACACGGGCGTGTGCCAGACCGTGTGTGTATACT-GTTTGCAATTAGAGGTACAATGGT
1 CACACGGGCGTGTGCCAGACCGTGTGTGTATACTAGTTTACAATTAAAGGTACAATGGT
* * *
2985 CACACGGACGTGTGCCAGACTGTGTGTGTATACTATTTTACAATTAAAGGTACAATGGT
1 CACACGGGCGTGTGCCAGACCGTGTGTGTATACTAGTTTACAATTAAAGGTACAATGGT
3044 CACACGGG
1 CACACGGG
3052 TCAAACACAC
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
58 32 0.53
59 28 0.47
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (59 bp):
CACACGGGCGTGTGCCAGACCGTGTGTGTATACTAGTTTACAATTAAAGGTACAATGGT
Found at i:3068 original size:58 final size:57
Alignment explanation
Indices: 2948--3071 Score: 133
Period size: 59 Copynumber: 2.1 Consensus size: 57
2938 GTGCCAGACC
* * **** * *
2948 GTGTGTGTATACTGTTTGCAATTAGAGGTACAATGGTCACACGGACGTGTGCCAGACT
1 GTGTGTGTATACTGTTTACAATTAAAGGTACAATGGTCACACGGA-GTCAAACACACG
*
3006 GTGTGTGTATACTATTTTACAATTAAAGGTACAATGGTCACACGG-GTCAAACACACGG
1 GTGTGTGTATACT-GTTTACAATTAAAGGTACAATGGTCACACGGAGTCAAACACAC-G
3064 GTGTGTGT
1 GTGTGTGT
3072 CCAAACCGTG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
57 6 0.11
58 21 0.38
59 28 0.51
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (57 bp):
GTGTGTGTATACTGTTTACAATTAAAGGTACAATGGTCACACGGAGTCAAACACACG
Found at i:6266 original size:18 final size:19
Alignment explanation
Indices: 6233--6268 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6223 AATCATTGGT
*
6233 TTAATTTAGTAATATTATC
1 TTAATTGAGTAATATTATC
6252 TTAATTGAG-AATATTAT
1 TTAATTGAGTAATATTAT
6269 TATTTTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAATTGAGTAATATTATC
Done.