Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008589.1 Kokia drynarioides strain JFW-HI SEQ_123267, 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: 15464
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Found at i:8479 original size:105 final size:104
Alignment explanation
Indices: 8320--8542 Score: 266
Period size: 105 Copynumber: 2.1 Consensus size: 104
8310 ATTCCATGTG
* * * * * * *
8320 TTTCATCTTCTACGTAAAGAAACGACGATACTATTAGAAGATATAGTGTCACTGATAAAGTTTAG
1 TTTCATCTTCTATGTAAAGAAACAACAATAATATTAGAAGATATACTATCACTGATAAAGCTTAG
* * * *
8385 TCAAATTGGGAGATTTACTTTCTTGCCATCACTCCGTGCA
66 TCAAAATGGGAGAATTACGTTCTTGCCATCA-TCCATGCA
* * * **
8425 TTTCATCTCCTATGTAAAGAAGCAACAATAATATTAGAAGATATACTATTACTGATAGGGCTTAG
1 TTTCATCTTCTATGTAAAGAAACAACAATAATATTAGAAGATATACTATCACTGATAAAGCTTAG
** *
8490 TCAAAATGGGAGAATTACGTTCTTGTTATCATTCATGCA
66 TCAAAATGGGAGAATTACGTTCTTGCCATCATCCATGCA
8529 TTTCATCTTCTATG
1 TTTCATCTTCTATG
8543 CGGAAAAGCG
Statistics
Matches: 98, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
104 19 0.19
105 79 0.81
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (104 bp):
TTTCATCTTCTATGTAAAGAAACAACAATAATATTAGAAGATATACTATCACTGATAAAGCTTAG
TCAAAATGGGAGAATTACGTTCTTGCCATCATCCATGCA
Found at i:12121 original size:128 final size:128
Alignment explanation
Indices: 11966--12220 Score: 465
Period size: 128 Copynumber: 2.0 Consensus size: 128
11956 GTGTGTTCAA
*
11966 ACCGTGTAACTCACTGTTTTCATCTCCAAAAAACACAGAGTGGTCACACAGTCTAGCACACGCCC
1 ACCGTGTAACTCACTGTTTCCATCTCCAAAAAACACAGAGTGGTCACACAGTCTAGCACACGCCC
*
12031 GTGTGCCCAGACCGTGTAACTCACTATTTCTGGTTCACAACTTAGAATATCCACACGATCTAG
66 ATGTGCCCAGACCGTGTAACTCACTATTTCTGGTTCACAACTTAGAATATCCACACGATCTAG
12094 ACCGTGTAACTCACTGTTTCCATCTCCAAAAAACACAGAGTGGTCACACAGTCTAGCACACGCCC
1 ACCGTGTAACTCACTGTTTCCATCTCCAAAAAACACAGAGTGGTCACACAGTCTAGCACACGCCC
* * *
12159 ATGTGCCTAGATCGTGTAACTCACTCTTTCTGGTTCACAACTTAGAATATCCACACGATCTA
66 ATGTGCCCAGACCGTGTAACTCACTATTTCTGGTTCACAACTTAGAATATCCACACGATCTA
12221 CAACACGCCC
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 122 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (128 bp):
ACCGTGTAACTCACTGTTTCCATCTCCAAAAAACACAGAGTGGTCACACAGTCTAGCACACGCCC
ATGTGCCCAGACCGTGTAACTCACTATTTCTGGTTCACAACTTAGAATATCCACACGATCTAG
Found at i:12517 original size:15 final size:15
Alignment explanation
Indices: 12497--12545 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
12487 ATATCTAAAT
12497 CAACATTCATTTCAA
1 CAACATTCATTTCAA
* *
12512 CAACA-T-ATCTAAA
1 CAACATTCATTTCAA
12525 TCAACATTCATTTCAA
1 -CAACATTCATTTCAA
12541 CAACA
1 CAACA
12546 AGTCTTAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 5 0.19
14 6 0.22
15 11 0.41
16 5 0.19
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
CAACATTCATTTCAA
Found at i:12528 original size:29 final size:29
Alignment explanation
Indices: 12486--12545 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
12476 GTACGCTTTC
12486 CATATCTAAATCAACATTCATTTCAACAA
1 CATATCTAAATCAACATTCATTTCAACAA
12515 CATATCTAAATCAACATTCATTTCAACAA
1 CATATCTAAATCAACATTCATTTCAACAA
12544 CA
1 CA
12546 AGTCTTAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (29 bp):
CATATCTAAATCAACATTCATTTCAACAA
Found at i:13810 original size:21 final size:22
Alignment explanation
Indices: 13773--13828 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
13763 TTCATTTGTA
*
13773 TATAAATTCACATTCCTCTAATT
1 TATAAATTTA-ATTCCTCTAATT
*
13796 T-TAAATTTAATTCCTCTACTT
1 TATAAATTTAATTCCTCTAATT
13817 TATAATATTTAA
1 TATAA-ATTTAA
13829 AAAGTTGTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 12 0.41
22 10 0.34
23 7 0.24
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (22 bp):
TATAAATTTAATTCCTCTAATT
Found at i:13900 original size:27 final size:28
Alignment explanation
Indices: 13862--13932 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 28
13852 TAATTCACAG
*
13862 TTTGGT-TCTTAAAATATTTTT-ATTTAT
1 TTTGGTAT-TTAAAATATTTTTGATTTAA
*
13889 TTTGGTATTT-AAAT-TTTTTGTTTTAA
1 TTTGGTATTTAAAATATTTTTGATTTAA
*
13915 TTTGATATTTAAAATATT
1 TTTGGTATTTAAAATATT
13933 AATTTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 5 0.14
26 17 0.46
27 12 0.32
28 3 0.08
ACGTcount: A:0.28, C:0.01, G:0.08, T:0.62
Consensus pattern (28 bp):
TTTGGTATTTAAAATATTTTTGATTTAA
Done.