Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008667.1 Kokia drynarioides strain JFW-HI SEQ_123349, 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: 43267
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Found at i:10707 original size:31 final size:30
Alignment explanation
Indices: 10661--10759 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 30
10651 TTTGGAATCC
*
10661 AAACTTGATATTTTTTACTAATTTGGTACTT
1 AAACTTGACATTTTTT-CTAATTTGGTACTT
* * *
10692 AAATTTGACACTTTTTTTTAATTTGGTACCT
1 AAACTTGACA-TTTTTTCTAATTTGGTACTT
* *
10723 AAACTTGACATTTTTTCTTAAGTTGATACTT
1 AAACTTGACATTTTTTC-TAATTTGGTACTT
10754 AAACTT
1 AAACTT
10760 TTTGGGAGTC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
30 6 0.11
31 45 0.79
32 6 0.11
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.49
Consensus pattern (30 bp):
AAACTTGACATTTTTTCTAATTTGGTACTT
Found at i:11342 original size:60 final size:60
Alignment explanation
Indices: 11204--11365 Score: 154
Period size: 62 Copynumber: 2.7 Consensus size: 60
11194 TAAATTTAGG
* * * * * *
11204 TATCAAATTGAACATAAAAAATCTTAGGTATCAAA-T-T--AAAAAATATATCAAGTTTAGA
1 TATCAAATTGAAC-CAAAAAAT-TTAAGTATCAAATTATAAAAAAAAAATATCAAATTCAAA
* *
11262 TATCAAATTGGATCCAAAAAAATTTAAGTATCAAATTATAAAAAAAAAATGTCAAATTCAAA
1 TATCAAATT-GAACC-AAAAAATTTAAGTATCAAATTATAAAAAAAAAATATCAAATTCAAA
* * *
11324 TATCAAATTGAACCAAAAAATTTAAATACCAAATCA-AAAAAA
1 TATCAAATTGAACCAAAAAATTTAAGTATCAAATTATAAAAAA
11366 TATTAAACTC
Statistics
Matches: 86, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
58 20 0.23
59 17 0.20
60 20 0.23
61 4 0.05
62 25 0.29
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.27
Consensus pattern (60 bp):
TATCAAATTGAACCAAAAAATTTAAGTATCAAATTATAAAAAAAAAATATCAAATTCAAA
Found at i:20545 original size:26 final size:27
Alignment explanation
Indices: 20516--20576 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
20506 TATTATTTTT
20516 TTATTTTTTTAAATATTT-AT-ATTATA
1 TTATTTTTTT-AATATTTAATAATTATA
*
20542 TTA-TTTTTTAATATTTAATAATTTTA
1 TTATTTTTTTAATATTTAATAATTATA
20568 -TATTTTTTT
1 TTATTTTTTT
20577 TATTGAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 7 0.23
25 10 0.32
26 14 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (27 bp):
TTATTTTTTTAATATTTAATAATTATA
Found at i:27865 original size:7 final size:7
Alignment explanation
Indices: 27853--27902 Score: 61
Period size: 7 Copynumber: 7.3 Consensus size: 7
27843 AGGTAGATTT
27853 ATTTATA
1 ATTTATA
27860 ATTTATA
1 ATTTATA
27867 ATTTATA
1 ATTTATA
27874 ATTTAT-
1 ATTTATA
27880 ATTTATTA
1 ATTTA-TA
27888 A-TTAT-
1 ATTTATA
27893 ATTTCATA
1 ATTT-ATA
27901 AT
1 AT
27903 CAATTTGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
5 1 0.03
6 8 0.21
7 26 0.68
8 3 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTATA
Found at i:27872 original size:14 final size:13
Alignment explanation
Indices: 27852--27902 Score: 68
Period size: 13 Copynumber: 3.8 Consensus size: 13
27842 AAGGTAGATT
27852 TATTTATAATTTA
1 TATTTATAATTTA
27865 TAATTTATAATTTA
1 T-ATTTATAATTTA
27879 TATTTATTAA-TTA
1 TATTTA-TAATTTA
27892 TATTTCATAAT
1 TATTT-ATAAT
27903 CAATTTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
13 17 0.50
14 17 0.50
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (13 bp):
TATTTATAATTTA
Found at i:28337 original size:17 final size:17
Alignment explanation
Indices: 28310--28349 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
28300 CGCTCTTGAA
28310 TTTGGTAATTAGATTTAT
1 TTTGGTAATTAGATTT-T
*
28328 TTTGGT-ATTATATTTT
1 TTTGGTAATTAGATTTT
28344 TTTGGT
1 TTTGGT
28350 CTATTTTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 8 0.38
18 6 0.29
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.62
Consensus pattern (17 bp):
TTTGGTAATTAGATTTT
Found at i:29375 original size:18 final size:19
Alignment explanation
Indices: 29341--29376 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29331 TTTTATAAGT
*
29341 TTTTAATAATTTTTTTAAC
1 TTTTAATAATTTATTTAAC
29360 TTTTAAT-ATTTATTTAA
1 TTTTAATAATTTATTTAA
29377 TTTGAGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTAATAATTTATTTAAC
Found at i:30734 original size:21 final size:22
Alignment explanation
Indices: 30696--30740 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
30686 TATTTACATC
*
30696 AAATTTTTTAATTAATAATGAT
1 AAATTTTATAATTAATAATGAT
*
30718 AAATTTTATAATT-ATAATTAT
1 AAATTTTATAATTAATAATGAT
30739 AA
1 AA
30741 TTATCACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
AAATTTTATAATTAATAATGAT
Found at i:30849 original size:18 final size:18
Alignment explanation
Indices: 30828--30870 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
30818 TTTTAATCAA
30828 TAATTATAATTTAAAT-TC
1 TAATTAT-ATTTAAATGTC
* *
30846 TAATTATTTTTAAATGTG
1 TAATTATATTTAAATGTC
30864 TAATTAT
1 TAATTAT
30871 CACAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (18 bp):
TAATTATATTTAAATGTC
Found at i:34426 original size:16 final size:16
Alignment explanation
Indices: 34389--34442 Score: 72
Period size: 16 Copynumber: 3.2 Consensus size: 16
34379 GAATTCTTGT
*
34389 TAAAATAAAATACAGTAG
1 TAAAATAAAATA-A-AAG
34407 TAAAATAAAATAAAAG
1 TAAAATAAAATAAAAG
*
34423 TAAAGTAAAATAAAAG
1 TAAAATAAAATAAAAG
34439 TAAA
1 TAAA
34443 GTCCAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
16 21 0.62
17 1 0.03
18 12 0.35
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.20
Consensus pattern (16 bp):
TAAAATAAAATAAAAG
Found at i:34443 original size:21 final size:18
Alignment explanation
Indices: 34389--34444 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 18
34379 GAATTCTTGT
*
34389 TAAAATAAAATACAGTAG
1 TAAAATAAAATAAAGTAG
34407 TAAAATAAAATAAAAGTAAAG
1 TAAAATAAAAT-AAAGT--AG
34428 TAAAATAAAAGTAAAGT
1 TAAAATAAAA-TAAAGT
34445 CCAAATAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 11 0.33
19 4 0.12
21 17 0.52
22 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.11, T:0.21
Consensus pattern (18 bp):
TAAAATAAAATAAAGTAG
Found at i:38015 original size:22 final size:23
Alignment explanation
Indices: 37970--38015 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
37960 TTTAATCCTT
* *
37970 TAAAAATTACACTTTTACTATCG
1 TAAAAATTACAATTTAACTATCG
*
37993 TAAAAATTATAATTTAACT-TCG
1 TAAAAATTACAATTTAACTATCG
38015 T
1 T
38016 CCCCCCTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.41
Consensus pattern (23 bp):
TAAAAATTACAATTTAACTATCG
Found at i:42833 original size:45 final size:45
Alignment explanation
Indices: 42783--42868 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
42773 ATTTTTTTTA
42783 TAAATAAATAAAACCTAAAA-AAACCTAAGTAAATAAATAAACTTG
1 TAAATAAATAAAACCTAAAATAAACCTAA-TAAATAAATAAACTTG
* *
42828 TAAATAAATAAACCCTAAAATAACCCTAATAAATAAATAAA
1 TAAATAAATAAAACCTAAAATAAACCTAATAAATAAATAAA
42869 TAAATAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
45 31 0.82
46 7 0.18
ACGTcount: A:0.63, C:0.13, G:0.02, T:0.22
Consensus pattern (45 bp):
TAAATAAATAAAACCTAAAATAAACCTAATAAATAAATAAACTTG
Found at i:43259 original size:30 final size:30
Alignment explanation
Indices: 43190--43263 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
43180 ACAGGCCCAT
*
43190 TTTTTGACCCCGAACCTTCTAAAAATTACCA
1 TTTTTGACCCCGAA-CTTCCAAAAATTACCA
43221 -TTTT-ACCCCCGAACTTCCAAAAA-T-CCAA
1 TTTTTGA-CCCCGAACTTCCAAAAATTACC-A
43249 TTTTTGACCCCGAAC
1 TTTTTGACCCCGAAC
43264 CTCC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
27 2 0.05
28 2 0.05
29 22 0.58
30 12 0.32
ACGTcount: A:0.31, C:0.32, G:0.07, T:0.30
Consensus pattern (30 bp):
TTTTTGACCCCGAACTTCCAAAAATTACCA
Done.