Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002550.1 Kokia drynarioides strain JFW-HI SEQ_114739, 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: 29021
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2467 original size:21 final size:20
Alignment explanation
Indices: 2418--2467 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2408 TTAGTTAAAA
* * *
2418 TAAGTATAAATAGGTTTAAT
1 TAAGTTTAAAAAGGGTTAAT
*
2438 TAAGATTAAAAAGGGTTAAT
1 TAAGTTTAAAAAGGGTTAAT
2458 TAAAGTTTAA
1 T-AAGTTTAA
2468 TGATGAAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (20 bp):
TAAGTTTAAAAAGGGTTAAT
Found at i:3422 original size:52 final size:53
Alignment explanation
Indices: 3317--3456 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 53
3307 GTACCAAAGA
* * * *
3317 ATTAAA-GTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATGG
1 ATTAAAGGTCCGATGACTTTGTGTCATCGTGAGTTACACGAATCCTATCATGG
*
3369 ATTAAAGGTCCGATGACTTTGTGTCATCATGAGTTACACGAATCC-ATCATGG
1 ATTAAAGGTCCGATGACTTTGTGTCATCGTGAGTTACACGAATCCTATCATGG
*
3421 ATTAAAGGTTCGATGACTTTGTGTCATCGTGAGTTA
1 ATTAAAGGTCCGATGACTTTGTGTCATCGTGAGTTA
3457 TCAAATGCGA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
52 47 0.59
53 33 0.41
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (53 bp):
ATTAAAGGTCCGATGACTTTGTGTCATCGTGAGTTACACGAATCCTATCATGG
Found at i:4079 original size:21 final size:21
Alignment explanation
Indices: 4053--4098 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
4043 GTGTTTAGAA
4053 GTATTGGTAGTTTGTATACTT
1 GTATTGGTAGTTTGTATACTT
*
4074 GTATTGGTAGTTTGTGTACTT
1 GTATTGGTAGTTTGTATACTT
4095 GTAT
1 GTAT
4099 CAGTAAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.04, G:0.26, T:0.52
Consensus pattern (21 bp):
GTATTGGTAGTTTGTATACTT
Found at i:4528 original size:24 final size:24
Alignment explanation
Indices: 4496--4541 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
4486 TGTGGGACGT
4496 GAAGGTGCCATTGGTAGTGCACGC
1 GAAGGTGCCATTGGTAGTGCACGC
*
4520 GAAGGTGCCGTTGGTAGTGCAC
1 GAAGGTGCCATTGGTAGTGCAC
4542 ACGACGGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.39, T:0.22
Consensus pattern (24 bp):
GAAGGTGCCATTGGTAGTGCACGC
Found at i:5718 original size:11 final size:11
Alignment explanation
Indices: 5704--5732 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
5694 ATTTTATAAA
5704 TAAATAAAACC
1 TAAATAAAACC
5715 TAAA-AAAACC
1 TAAATAAAACC
5725 TAAATAAA
1 TAAATAAA
5733 TAAATAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (11 bp):
TAAATAAAACC
Found at i:5754 original size:28 final size:29
Alignment explanation
Indices: 5699--5767 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 29
5689 AAAATATTTT
5699 ATAAATAAATAAAACCTAAAAAAACCTAA
1 ATAAATAAATAAAACCTAAAAAAACCTAA
* *
5728 ATAAATAAATAAACCCT-AAAAATCCTAA
1 ATAAATAAATAAAACCTAAAAAAACCTAA
*
5756 ACAAATAAATAA
1 ATAAATAAATAA
5768 CTAAACCCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 21 0.57
29 16 0.43
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (29 bp):
ATAAATAAATAAAACCTAAAAAAACCTAA
Found at i:5767 original size:32 final size:34
Alignment explanation
Indices: 5726--5788 Score: 103
Period size: 32 Copynumber: 1.9 Consensus size: 34
5716 AAAAAAACCT
5726 AAATAAATAAATAAACCCTAAA-AA-TCCTAAAC
1 AAATAAATAAATAAACCCTAAATAAGTCCTAAAC
*
5758 AAATAAATAACTAAACCCTAAATAAGTCCTA
1 AAATAAATAAATAAACCCTAAATAAGTCCTA
5789 GAATGTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 21 0.75
33 2 0.07
34 5 0.18
ACGTcount: A:0.59, C:0.19, G:0.02, T:0.21
Consensus pattern (34 bp):
AAATAAATAAATAAACCCTAAATAAGTCCTAAAC
Found at i:6059 original size:20 final size:20
Alignment explanation
Indices: 5971--6064 Score: 59
Period size: 20 Copynumber: 4.7 Consensus size: 20
5961 GTGTGAGTGA
*
5971 AATTAACTATTATTTAAAAT
1 AATTAATTATTATTTAAAAT
* ** * *
5991 AATTAAATAAAAAATT-AATT
1 AATT-AATTATTATTTAAAAT
* *
6011 AATTAATTAATTATTCTTACA-
1 AATTAATT-ATTATT-TAAAAT
*
6032 AATGAATTATTATTTAAAAT
1 AATTAATTATTATTTAAAAT
6052 AATTAATT-TTATT
1 AATTAATTATTATT
6065 CAATCCAATT
Statistics
Matches: 53, Mismatches: 16, Indels: 11
0.66 0.20 0.14
Matches are distributed among these distances:
19 11 0.21
20 27 0.51
21 14 0.26
22 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (20 bp):
AATTAATTATTATTTAAAAT
Found at i:9261 original size:20 final size:20
Alignment explanation
Indices: 9224--9262 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9214 TTCTGAATTA
* * *
9224 TTTATATTTATTTTCATTTT
1 TTTATATGTATATACATTTT
9244 TTTATATGTATATACATTT
1 TTTATATGTATATACATTT
9263 AATAATATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTATATGTATATACATTTT
Found at i:11379 original size:40 final size:41
Alignment explanation
Indices: 11311--11387 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
11301 GTAGAAGCAA
* *
11311 ATTGAATAGATTGGTATCTTTTTCATGAAGTAAATTAATAG
1 ATTGAATAGATTGATATCTTTTTCATGAAGCAAATTAATAG
11352 ATTG-ATAGATTGATATCCTTTTT-ATGAAGCAAATTA
1 ATTGAATAGATTGATAT-CTTTTTCATGAAGCAAATTA
11388 GAAAGAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 23 0.70
41 10 0.30
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (41 bp):
ATTGAATAGATTGATATCTTTTTCATGAAGCAAATTAATAG
Found at i:13765 original size:3 final size:3
Alignment explanation
Indices: 13757--13802 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
13747 TGGATTGGTT
13757 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
13803 CCACATTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:22049 original size:19 final size:22
Alignment explanation
Indices: 22005--22057 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
21995 TACAAACAAT
22005 AACAACAAAATAGTAGCAATAC
1 AACAACAAAATAGTAGCAATAC
*
22027 AACAACAAAAT-GATAGCAAAAC
1 AACAACAAAATAG-TAGCAATAC
*
22049 AACATCAAA
1 AACAACAAA
22058 CAGTAGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.62, C:0.19, G:0.08, T:0.11
Consensus pattern (22 bp):
AACAACAAAATAGTAGCAATAC
Found at i:22317 original size:30 final size:26
Alignment explanation
Indices: 22279--22338 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 26
22269 AATGTTGAAT
22279 TTTG-GATTTGGTCCTTCTATTATTTTAGA
1 TTTGAGATTTGGT-CTT-TA-TATTTTA-A
22308 TTTGAGATTTGGTCTTTATATTTTAA
1 TTTGAGATTTGGTCTTTATATTTTAA
22334 TTTGA
1 TTTGA
22339 CATAATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 6 0.20
27 7 0.23
28 2 0.07
29 7 0.23
30 8 0.27
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.57
Consensus pattern (26 bp):
TTTGAGATTTGGTCTTTATATTTTAA
Done.