Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008209.1 Kokia drynarioides strain JFW-HI SEQ_122871, 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: 27350
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1465 original size:23 final size:25
Alignment explanation
Indices: 1418--1470 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 25
1408 AAATTAATCC
*
1418 AAATATAAATAGGAGTGTTGAATTT
1 AAATAGAAATAGGAGTGTTGAATTT
1443 AAATAGAAATAGGA-T-TTGAATTT
1 AAATAGAAATAGGAGTGTTGAATTT
1466 AAATA
1 AAATA
1471 CAAAATAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 13 0.48
24 1 0.04
25 13 0.48
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (25 bp):
AAATAGAAATAGGAGTGTTGAATTT
Found at i:1483 original size:24 final size:23
Alignment explanation
Indices: 1435--1483 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1425 AATAGGAGTG
* *
1435 TTGAATTTAAATAGAAATAGGAT
1 TTGAATTTAAATAAAAATAGCAT
1458 TTGAATTTAAATACAAAATAGCAT
1 TTGAATTTAAATA-AAAATAGCAT
1482 TT
1 TT
1484 ATTGGGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (23 bp):
TTGAATTTAAATAAAAATAGCAT
Found at i:1662 original size:7 final size:7
Alignment explanation
Indices: 1650--1685 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
1640 CGTGGGAATT
1650 TCCAGTC
1 TCCAGTC
1657 TCCAGTC
1 TCCAGTC
1664 TCCAGTC
1 TCCAGTC
1671 TCCAGTC
1 TCCAGTC
1678 TCCAGTC
1 TCCAGTC
1685 T
1 T
1686 TCCTTAAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.42, G:0.14, T:0.31
Consensus pattern (7 bp):
TCCAGTC
Found at i:7032 original size:21 final size:22
Alignment explanation
Indices: 6977--7032 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
6967 ATTATGTGTC
*
6977 AATGACCTATAAAAATTTGCTAA
1 AATGACC-ATAAAAATTTGCAAA
* *
7000 AAT-ATCATTAAAATTTTG-AAA
1 AATGACCA-TAAAAATTTGCAAA
7021 AATGACCATAAA
1 AATGACCATAAA
7033 TGATACGGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
21 10 0.37
22 14 0.52
23 3 0.11
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (22 bp):
AATGACCATAAAAATTTGCAAA
Found at i:8370 original size:24 final size:24
Alignment explanation
Indices: 8340--8422 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 24
8330 TTTATTTTTT
*
8340 GGGAAAATACTTTGTTTGTTTCTG
1 GGGAAAATACTTTGTTTGTTTCTC
*
8364 GGGAAAATACTTTGTTTGTTTTTC
1 GGGAAAATACTTTGTTTGTTTCTC
* * * *
8388 AGGAAAATACTCTATTTGTTTCAC
1 GGGAAAATACTTTGTTTGTTTCTC
*
8412 GAGAAAATACT
1 GGGAAAATACT
8423 AAACCCATCT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (24 bp):
GGGAAAATACTTTGTTTGTTTCTC
Found at i:8708 original size:6 final size:6
Alignment explanation
Indices: 8697--8746 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
8687 ATAAGGAGGA
* *
8697 GGGAAG GGGAAG GGGAAG AGGAAG AGGAAG GGGAA- GGG-A- GGGAAG
1 GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG
8742 GGGAA
1 GGGAA
8747 CAGAAAAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 4 0.10
5 4 0.10
6 32 0.80
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (6 bp):
GGGAAG
Found at i:8725 original size:18 final size:16
Alignment explanation
Indices: 8696--8746 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 16
8686 AATAAGGAGG
8696 AGGGAAGGGGAAGGGGA
1 AGGGAA-GGGAAGGGGA
8713 AGAGGAAGAGGAAGGGGA
1 AG-GGAAG-GGAAGGGGA
8731 AGGG-AGGGAAGGGGA
1 AGGGAAGGGAAGGGGA
8746 A
1 A
8747 CAGAAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 10 0.31
16 2 0.06
17 5 0.16
18 15 0.47
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (16 bp):
AGGGAAGGGAAGGGGA
Found at i:8828 original size:11 final size:10
Alignment explanation
Indices: 8812--8850 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
8802 TTTTAAAAAA
8812 TAATTTTACAT
1 TAATTTTA-AT
8823 TAATTTTAAAT
1 TAATTTT-AAT
8834 TAATTTTAA-
1 TAATTTTAAT
8843 TAATTTTA
1 TAATTTTA
8851 TATTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.30
10 2 0.07
11 16 0.59
12 1 0.04
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (10 bp):
TAATTTTAAT
Found at i:8841 original size:51 final size:50
Alignment explanation
Indices: 8785--8882 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 50
8775 GATAGTGATG
*
8785 ATTTTAATAATTATATATTTT-AAAAAATAATTTTACATTAATTTTAAATTA
1 ATTTTAATAATTATATATTTTAAAAAAATAAATTTA-A-TAATTTTAAATTA
*
8836 ATTTTAATAATTTTATATTTTAAAAAAATAAATTTAATAATTTTAAA
1 ATTTTAATAATTATATATTTTAAAAAAATAAATTTAATAATTTTAAA
8883 ATCATTTGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 10 0.23
51 21 0.48
52 13 0.30
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (50 bp):
ATTTTAATAATTATATATTTTAAAAAAATAAATTTAATAATTTTAAATTA
Found at i:13966 original size:3 final size:3
Alignment explanation
Indices: 13958--13996 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
13948 TGGGTGTGAT
13958 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
13997 AGAATCGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:15334 original size:16 final size:17
Alignment explanation
Indices: 15299--15337 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
15289 TTAAAATTTG
* *
15299 TATTTTATTTTTATTTT
1 TATTTTATTGTTATTAT
15316 TATTTT-TTGTTATTAT
1 TATTTTATTGTTATTAT
15332 TATTTT
1 TATTTT
15338 GCAATCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (17 bp):
TATTTTATTGTTATTAT
Found at i:26874 original size:20 final size:20
Alignment explanation
Indices: 26846--26908 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 20
26836 ACCCGGCATA
*
26846 AGAGTATTACATACAATGTC
1 AGAGAATTACATACAATGTC
*
26866 AGAGAATTA-A-A-AA---A
1 AGAGAATTACATACAATGTC
*
26880 AGAGTATTACATACAATGTC
1 AGAGAATTACATACAATGTC
26900 AGAGAATTA
1 AGAGAATTA
26909 AAAACGAGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 12
0.65 0.10 0.24
Matches are distributed among these distances:
14 8 0.25
15 1 0.03
16 1 0.03
17 4 0.12
18 1 0.03
19 1 0.03
20 16 0.50
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (20 bp):
AGAGAATTACATACAATGTC
Found at i:26919 original size:33 final size:34
Alignment explanation
Indices: 26845--26912 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
26835 AACCCGGCAT
26845 AAGAGTATTACATACAATGTCAGAGAATTAAAAA
1 AAGAGTATTACATACAATGTCAGAGAATTAAAAA
26879 AAGAGTATTACATACAATGTCAGAGAATTAAAAA
1 AAGAGTATTACATACAATGTCAGAGAATTAAAAA
26913 CGAGTATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.24
Consensus pattern (34 bp):
AAGAGTATTACATACAATGTCAGAGAATTAAAAA
Done.