Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008453.1 Kokia drynarioides strain JFW-HI SEQ_123128, 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: 11165
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:651 original size:31 final size:31
Alignment explanation
Indices: 608--666 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
598 CACAAGTACG
608 TAACATTCTCAAGAGTGCCATTTGTTCAACA
1 TAACATTCTCAAGAGTGCCATTTGTTCAACA
* *
639 TAACTTTCTCAAGAGTGCCATTTTTTCA
1 TAACATTCTCAAGAGTGCCATTTGTTCA
667 TGGAAATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (31 bp):
TAACATTCTCAAGAGTGCCATTTGTTCAACA
Found at i:4473 original size:4 final size:4
Alignment explanation
Indices: 4458--4514 Score: 78
Period size: 4 Copynumber: 14.2 Consensus size: 4
4448 TTACAAGAAT
* * *
4458 TGTA TTTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTG CGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
4506 TGCA TGTA T
1 TGTA TGTA T
4515 TAAGCCCCTG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.23, C:0.04, G:0.25, T:0.49
Consensus pattern (4 bp):
TGTA
Found at i:6817 original size:30 final size:30
Alignment explanation
Indices: 6783--6855 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
6773 CAAATTTGAT
*
6783 TTTTTGGAAACTTCACGGGTCAAATCAAAA
1 TTTTTGGAAACTTAACGGGTCAAATCAAAA
* * * * * *
6813 TTTTTAGAAAATTAAGGGGTGAAATTAGAA
1 TTTTTGGAAACTTAACGGGTCAAATCAAAA
6843 TTTTTGGAAACTT
1 TTTTTGGAAACTT
6856 TGGGGGCCTA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (30 bp):
TTTTTGGAAACTTAACGGGTCAAATCAAAA
Found at i:6934 original size:29 final size:30
Alignment explanation
Indices: 6871--6930 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
6861 GCCTAATTGG
** *
6871 AATTTTTAGAAAATTTGGATGTCATATTAG
1 AATTTTTAGAAAATTTGGATGTCATAAAAA
6901 AATTTTTAGAAAATTTGGA-GTC-TAAAAA
1 AATTTTTAGAAAATTTGGATGTCATAAAAA
6929 AA
1 AA
6931 ATTTAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 5 0.19
29 3 0.11
30 19 0.70
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.38
Consensus pattern (30 bp):
AATTTTTAGAAAATTTGGATGTCATAAAAA
Found at i:8643 original size:40 final size:40
Alignment explanation
Indices: 8599--8744 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
8589 ATTGGATTGT
* *
8599 TTCAATCTGCCCTATGGTTAGGGTAAGAGATCTGATGGTC
1 TTCAATCTGCCCTCTAGTTAGGGTAAGAGATCTGATGGTC
* * *
8639 TTCAATCTGCCCTCTTGTTAGGGTAAAAGATCTGATAGTC
1 TTCAATCTGCCCTCTAGTTAGGGTAAGAGATCTGATGGTC
* * *
8679 TTCAATCTGCCCTCTAGTTAGGGAAAGAGATCAGATGATC
1 TTCAATCTGCCCTCTAGTTAGGGTAAGAGATCTGATGGTC
* * *
8719 TTTAATTTGCCATCTAGTTAGGGTAA
1 TTCAATCTGCCCTCTAGTTAGGGTAA
8745 AATATTGGAT
Statistics
Matches: 92, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 92 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (40 bp):
TTCAATCTGCCCTCTAGTTAGGGTAAGAGATCTGATGGTC
Found at i:8691 original size:80 final size:79
Alignment explanation
Indices: 8580--8763 Score: 226
Period size: 80 Copynumber: 2.3 Consensus size: 79
8570 ATAGATTTAG
* * * * *
8580 GGGTAAAAGATTGGATTGTTTCAATCTGCCCTATGGTTAGGGTAAGAGATCTGATGGTCTTCAAT
1 GGGTAAAAGATTGGATAGTTTCAATCTGCCCTATAGTTAGGGAAAGAGATCAGATGATCTTCAAT
* *
8645 CTGCCCTCTTGTTA
66 CTGCCATCTAGTTA
* *
8659 GGGTAAAAGATCT-GATAGTCTTCAATCTGCCCTCTAGTTAGGGAAAGAGATCAGATGATCTTTA
1 GGGTAAAAGAT-TGGATAGT-TTCAATCTGCCCTATAGTTAGGGAAAGAGATCAGATGATCTTCA
*
8723 ATTTGCCATCTAGTTA
64 ATCTGCCATCTAGTTA
* * *
8739 GGGTAAAATATTGGATTGCTTCAAT
1 GGGTAAAAGATTGGATAGTTTCAAT
8764 TTTCCCCATG
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
79 23 0.26
80 66 0.74
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (79 bp):
GGGTAAAAGATTGGATAGTTTCAATCTGCCCTATAGTTAGGGAAAGAGATCAGATGATCTTCAAT
CTGCCATCTAGTTA
Found at i:8913 original size:50 final size:50
Alignment explanation
Indices: 8840--8934 Score: 145
Period size: 50 Copynumber: 1.9 Consensus size: 50
8830 AGATTCATCC
* *
8840 TTATGACTTCAATATGCCTCTCTACAGCTTTAGGTAAATGAGATTCGCCA
1 TTATGACTTCAATATACCCCTCTACAGCTTTAGGTAAATGAGATTCGCCA
* **
8890 TTATGACTTCAATCTACCCCTCTACAGCTTTAGGTGTATGAGATT
1 TTATGACTTCAATATACCCCTCTACAGCTTTAGGTAAATGAGATT
8935 TGTCATTCCG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (50 bp):
TTATGACTTCAATATACCCCTCTACAGCTTTAGGTAAATGAGATTCGCCA
Found at i:8950 original size:50 final size:50
Alignment explanation
Indices: 8844--8972 Score: 132
Period size: 50 Copynumber: 2.6 Consensus size: 50
8834 TCATCCTTAT
* * * *
8844 GACTTCAATATGCCTCTCTACAGCTTTAGGTAAATGAGATTCGCCATTAT
1 GACTTCAATCTACCCCTCTACAGCTTTAGGTAAATGAGATTCGCCATTAC
** * * *
8894 GACTTCAATCTACCCCTCTACAGCTTTAGGTGTATGAGATTTGTCATTCC
1 GACTTCAATCTACCCCTCTACAGCTTTAGGTAAATGAGATTCGCCATTAC
* *** *
8944 GGCTTCAATCTGTTCCTCTACAACTTTAG
1 GACTTCAATCTACCCCTCTACAGCTTTAG
8973 AGGTATAGGA
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.36
Consensus pattern (50 bp):
GACTTCAATCTACCCCTCTACAGCTTTAGGTAAATGAGATTCGCCATTAC
Found at i:10039 original size:29 final size:29
Alignment explanation
Indices: 9979--10039 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
9969 GAATACTCGA
* *
9979 GGGCAAAATGGTAAATTTTAGACACTTGG
1 GGGCAAAATGGTAAATTTTAGAAACTTCG
* *
10008 GGGCAAAATGGT-AATTTTGGGAAAGTTCG
1 GGGCAAAATGGTAAATTTT-AGAAACTTCG
10037 GGG
1 GGG
10040 TTAAAACTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.31, C:0.08, G:0.34, T:0.26
Consensus pattern (29 bp):
GGGCAAAATGGTAAATTTTAGAAACTTCG
Found at i:10144 original size:29 final size:31
Alignment explanation
Indices: 10112--10224 Score: 87
Period size: 29 Copynumber: 3.8 Consensus size: 31
10102 AAAATGAAAA
10112 TTTT-GAAAGTTCGGGGGT-AAAATGGTAAT
1 TTTTAGAAAGTTCGGGGGTAAAAATGGTAAT
** *
10141 TTTTAGAAAAATC-GAGGTCAAAAATGG-AAT
1 TTTTAGAAAGTTCGGGGGT-AAAAATGGTAAT
* * *
10171 TTTT-GGAAGTTCGGGTGTAAAAAT-ATAAT
1 TTTTAGAAAGTTCGGGGGTAAAAATGGTAAT
* *
10200 TTTTGGAAAGTT-TGGGGTCAAAAAT
1 TTTTAGAAAGTTCGGGGGT-AAAAAT
10225 ATGATTTTTG
Statistics
Matches: 65, Mismatches: 12, Indels: 13
0.72 0.13 0.14
Matches are distributed among these distances:
29 30 0.46
30 28 0.43
31 7 0.11
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (31 bp):
TTTTAGAAAGTTCGGGGGTAAAAATGGTAAT
Found at i:10200 original size:59 final size:60
Alignment explanation
Indices: 10079--10209 Score: 167
Period size: 59 Copynumber: 2.2 Consensus size: 60
10069 TAAAATGGGG
* *
10079 ATTTTTGGAAAGAATCGAGATTAAAAATGAAAATTTTGAAAGTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAAGAATCGAGATCAAAAATGAAAATTTTGAAAGTTCGGGGGTAAAATGATA
* * * * * *
10139 ATTTTTAGAAA-AATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGTGTAAAAAT-ATA
1 ATTTTTGGAAAGAATCGAGATCAAAAATGAAAATTTTGAAAGTTCGGGGGT-AAAATGATA
10198 ATTTTTGGAAAG
1 ATTTTTGGAAAG
10210 TTTGGGGTCA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
59 45 0.75
60 15 0.25
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (60 bp):
ATTTTTGGAAAGAATCGAGATCAAAAATGAAAATTTTGAAAGTTCGGGGGTAAAATGATA
Found at i:10223 original size:30 final size:30
Alignment explanation
Indices: 10156--10242 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 30
10146 GAAAAATCGA
** *
10156 GGTCAAAAATGGAATTTTTGG-AAGTTCGG
1 GGTCAAAAATATAATTTTTGGAAAGTTTGG
10185 GTGT-AAAAATATAATTTTTGGAAAGTTTGG
1 G-GTCAAAAATATAATTTTTGGAAAGTTTGG
* *
10215 GGTCAAAAATATGATTTTTGGATAGTTT
1 GGTCAAAAATATAATTTTTGGAAAGTTT
10243 ACAGACCTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
29 18 0.36
30 32 0.64
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.38
Consensus pattern (30 bp):
GGTCAAAAATATAATTTTTGGAAAGTTTGG
Done.