Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013680.1 Kokia drynarioides strain JFW-HI SEQ_128708, 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: 4868
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.34
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:538 original size:40 final size:41
Alignment explanation
Indices: 463--547 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 41
453 TGATGCTGAT
*
463 AACATTAATAACCTTAATAATTGTTTTTAATAATAATAAAAATA
1 AACATTAATAA-CTTAAT-ATTGTTTTTAAAAATAAT-AAAATA
* *
507 AACATTAATAA-TTAAT-TTTTTTTTAAAAATAATGAAATA
1 AACATTAATAACTTAATATTGTTTTTAAAAATAATAAAATA
546 AA
1 AA
548 AGTTGAAAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
39 7 0.18
40 15 0.39
42 5 0.13
44 11 0.29
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (41 bp):
AACATTAATAACTTAATATTGTTTTTAAAAATAATAAAATA
Found at i:1891 original size:30 final size:29
Alignment explanation
Indices: 1855--2206 Score: 243
Period size: 30 Copynumber: 12.2 Consensus size: 29
1845 AAACTATGCG
*
1855 AAAATTCCATTTTTACCCTCGAACTTCCAA
1 AAAATTCCATTTTTACCCTCAAACTTCC-A
*
1885 AAAATTCCATTTTTGGTCCCT-AAACTTCCA
1 AAAATTCCATTTTT--ACCCTCAAACTTCCA
1915 AAAATTCCATTTTTGACCC-CGAAACTTCC-
1 AAAATTCCATTTTT-ACCCTC-AAACTTCCA
* *
1944 AAAATTCCATTTTTACCCTCGAACCTCCA
1 AAAATTCCATTTTTACCCTCAAACTTCCA
* *
1973 AAAATTCCATTTTAACCC-CAAAACTTCTA
1 AAAATTCCATTTTTACCCTC-AAACTTCCA
** *
2002 AAAATTATAATTTTACCC-CTAAACTT-CA
1 AAAATTCCATTTTTACCCTC-AAACTTCCA
*
2030 AAATATTCAATTTTTTA--C-C---C-T--A
1 AAA-ATTCCA-TTTTTACCCTCAAACTTCCA
* *
2052 AAAATTCCATTTTTACCCCT-AAACCTCTA
1 AAAATTCCATTTTTA-CCCTCAAACTTCCA
* *
2081 AAAATTCCTTTTTTGACCC-CAAAACTTCCT
1 AAAATTCCATTTTT-ACCCTC-AAACTTCCA
*
2111 AAAATTCCATTTTTGACCCTAAAACTTCCA
1 AAAATTCCATTTTT-ACCCTCAAACTTCCA
* ** * * *
2141 AATATTAAAATTTTACCCTCGAACCTCCAA
1 AAAATTCCATTTTTACCCTCAAACTTCC-A
* *
2171 AAAATTCCATTTTTAACCTCGAAACTTTCA
1 AAAATTCCATTTTTACCCTC-AAACTTCCA
2201 AAAATT
1 AAAATT
2207 ACTATTTCAC
Statistics
Matches: 256, Mismatches: 41, Indels: 50
0.74 0.12 0.14
Matches are distributed among these distances:
20 6 0.02
21 5 0.02
22 4 0.02
23 2 0.01
24 1 0.00
26 1 0.00
27 1 0.00
28 17 0.07
29 95 0.37
30 108 0.42
31 12 0.05
32 4 0.02
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCTCAAACTTCCA
Found at i:2063 original size:21 final size:22
Alignment explanation
Indices: 2029--2074 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
2019 CCTAAACTTC
2029 AAAATATTCAATTTTTTA-CCCT
1 AAAATATTCAA-TTTTTACCCCT
*
2051 AAAA-ATTCCATTTTTACCCCT
1 AAAATATTCAATTTTTACCCCT
2072 AAA
1 AAA
2075 CCTCTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 12 0.55
22 4 0.18
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATATTCAATTTTTACCCCT
Found at i:2074 original size:50 final size:50
Alignment explanation
Indices: 2012--2109 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
2002 AAAATTATAA
* *
2012 TTTTACCCCTAAACTTC-AAAATATTCAATTTTTT-ACCCTAAAAATTCCAT
1 TTTTACCCCTAAACCTCTAAAA-ATTC-ATTTTTTGACCCCAAAAATTCCAT
* *
2062 TTTTACCCCTAAACCTCTAAAAATTCCTTTTTTGACCCCAAAACTTCC
1 TTTTACCCCTAAACCTCTAAAAATTCATTTTTTGACCCCAAAAATTCC
2110 TAAAATTCCA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 6 0.14
50 32 0.76
51 4 0.10
ACGTcount: A:0.33, C:0.29, G:0.01, T:0.38
Consensus pattern (50 bp):
TTTTACCCCTAAACCTCTAAAAATTCATTTTTTGACCCCAAAAATTCCAT
Found at i:2131 original size:80 final size:79
Alignment explanation
Indices: 1972--2140 Score: 207
Period size: 79 Copynumber: 2.1 Consensus size: 79
1962 TCGAACCTCC
* *
1972 AAAAATTCCATTTTAACCCCAAAACTTCTAAAAATTATAATTTTACCCCTAAACTTCAAAATATT
1 AAAAATTCCATTTTAACCCCAAAACCTCTAAAAATTATAATTTTACCCCAAAACTTCAAAATATT
*
2037 CAATTTTTTACCCT
66 CAATTTTTGACCCT
* * * * *
2051 AAAAATTCCATTTTTACCCCTAAACCTCTAAAAATTCCT-TTTTTGACCCCAAAACTTCCTAAA-
1 AAAAATTCCATTTTAACCCCAAAACCTCTAAAAATT-ATAATTTT-ACCCCAAAACTT-CAAAAT
*
2114 ATTCCATTTTTGACCCT
63 ATTCAATTTTTGACCCT
*
2131 AAAACTTCCA
1 AAAAATTCCA
2141 AATATTAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
79 37 0.48
80 36 0.47
81 4 0.05
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (79 bp):
AAAAATTCCATTTTAACCCCAAAACCTCTAAAAATTATAATTTTACCCCAAAACTTCAAAATATT
CAATTTTTGACCCT
Found at i:2374 original size:59 final size:59
Alignment explanation
Indices: 2200--2412 Score: 166
Period size: 59 Copynumber: 3.6 Consensus size: 59
2190 CGAAACTTTC
* * * * * * * * *
2200 AAAAATTACTATTTCACTCCCGGATGTCTAAAAATTCTTTTTTTGATCC-CAATTTTCCT
1 AAAAATTACCATTTTACCCCCGAATGTCCAAAAATTC-ATTCTTAATCCTCATTTTTCCT
* * * *
2259 AAAAATTACTATTTCACCCCTGAATGTCCAAAAATTTCATTCTTAATCCTGATTTTTCCT
1 AAAAATTACCATTTTACCCCCGAATGTCCAAAAA-TTCATTCTTAATCCTCATTTTTCCT
* * * *
2319 -AAAATTACCATTTTACCCCCGAATATCCAAAAATTCAATTTTTTATCCTC-TTTTT-TT
1 AAAAATTACCATTTTACCCCCGAATGTCCAAAAATTC-ATTCTTAATCCTCATTTTTCCT
* * * *
2376 GAAAGA-TACCATTTTACCCTCGAGTGTCTAAAAATTC
1 -AAAAATTACCATTTTACCCCCGAATGTCCAAAAATTC
2413 CTTTAACCCC
Statistics
Matches: 127, Mismatches: 22, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
57 1 0.01
58 35 0.28
59 80 0.63
60 11 0.09
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCATTCTTAATCCTCATTTTTCCT
Found at i:3502 original size:22 final size:23
Alignment explanation
Indices: 3484--3534 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
3474 ATAGTGGTGT
3484 TGGTGCAGAGGGG-TGGTGGCGC
1 TGGTGCAGAGGGGCTGGTGGCGC
3506 TGGTGCAGAGGGGCTGGTGAGCTGC
1 TGGTGCAGAGGGGCTGGTG-GC-GC
3531 TGGT
1 TGGT
3535 TATGCTGACG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.50
23 5 0.19
24 2 0.08
25 6 0.23
ACGTcount: A:0.10, C:0.14, G:0.55, T:0.22
Consensus pattern (23 bp):
TGGTGCAGAGGGGCTGGTGGCGC
Found at i:3682 original size:13 final size:13
Alignment explanation
Indices: 3658--3699 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
3648 CCTGTTAAAA
3658 TGGACATTTGTATT
1 TGGAC-TTTGTATT
3672 TGGACTTTGTAATT
1 TGGACTTTGT-ATT
*
3686 TGGGCTTTGTATT
1 TGGACTTTGTATT
3699 T
1 T
3700 AAAACACACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.17, C:0.07, G:0.24, T:0.52
Consensus pattern (13 bp):
TGGACTTTGTATT
Found at i:4672 original size:3 final size:3
Alignment explanation
Indices: 4664--4692 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4654 CCCCCTTTTG
4664 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4693 CATTTAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.