Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002808.1 Kokia drynarioides strain JFW-HI SEQ_115157, 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: 45089
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:7250 original size:21 final size:23
Alignment explanation
Indices: 7216--7277 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 23
7206 CTTAAAAATG
**
7216 ATAAAATTTTAATTTAATCT-TT
1 ATAAAATTACAATTTAATCTATT
*
7238 -TAAAATTACAATTTTA-CTATT
1 ATAAAATTACAATTTAATCTATT
7259 ATAAAAATTACAATTTAAT
1 AT-AAAATTACAATTTAAT
7278 TTCGTCCCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 2 0.06
21 15 0.47
22 1 0.03
23 14 0.44
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAAAATTACAATTTAATCTATT
Found at i:7413 original size:20 final size:19
Alignment explanation
Indices: 7363--7420 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
7353 ATAATAAAAA
7363 TAATTGAAATATTTTATAAT
1 TAATTGAAAT-TTTTATAAT
* *
7383 TAATT-AAATTTTTGTACTT
1 TAATTGAAATTTTTATA-AT
*
7402 TAATTGAAATTTTTTTAAT
1 TAATTGAAATTTTTATAAT
7421 ATAAAGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
20 15 0.47
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (19 bp):
TAATTGAAATTTTTATAAT
Found at i:13691 original size:21 final size:21
Alignment explanation
Indices: 13665--13705 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13655 TGACTAAAAC
* *
13665 GAAAACTTATTTATAATTTAA
1 GAAAACCTATCTATAATTTAA
13686 GAAAACCTATCTATAATTTA
1 GAAAACCTATCTATAATTTA
13706 GTGACTAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (21 bp):
GAAAACCTATCTATAATTTAA
Found at i:21519 original size:17 final size:17
Alignment explanation
Indices: 21497--21531 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21487 TCTTATATAT
21497 TTTACCAAAATTTCTCA
1 TTTACCAAAATTTCTCA
* *
21514 TTTACCATATTTTCTCA
1 TTTACCAAAATTTCTCA
21531 T
1 T
21532 ACACTTTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTACCAAAATTTCTCA
Found at i:26376 original size:21 final size:22
Alignment explanation
Indices: 26352--26392 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
26342 TCGAATCTAA
*
26352 TTGAAA-AAATGCATTAATTTC
1 TTGAAAGAAATACATTAATTTC
*
26373 TTGAAAGAAATACTTTAATT
1 TTGAAAGAAATACATTAATT
26393 ATATCCTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (22 bp):
TTGAAAGAAATACATTAATTTC
Found at i:32141 original size:15 final size:16
Alignment explanation
Indices: 32112--32141 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32102 TATATTTCAC
32112 AAATAAAGAATTAAAA
1 AAATAAAGAATTAAAA
32128 AAATAAAG-ATTAAA
1 AAATAAAGAATTAAA
32142 TCTATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (16 bp):
AAATAAAGAATTAAAA
Found at i:44012 original size:28 final size:28
Alignment explanation
Indices: 43980--44040 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
43970 TGTATAGCTG
43980 TTTGGTTTTAATTACTGTGGGATGAGAC
1 TTTGGTTTTAATTACTGTGGGATGAGAC
44008 TTTGGTTTTAATTACTGTGGGATGAGAC
1 TTTGGTTTTAATTACTGTGGGATGAGAC
44036 TTTGG
1 TTTGG
44041 CTCAACTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.20, C:0.07, G:0.30, T:0.44
Consensus pattern (28 bp):
TTTGGTTTTAATTACTGTGGGATGAGAC
Found at i:44870 original size:19 final size:19
Alignment explanation
Indices: 44846--44884 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
44836 AAGAGAAAGA
44846 AAGAAGAAGGAAGAAGGAG
1 AAGAAGAAGGAAGAAGGAG
**
44865 AAGAAGGGGGAAGAAGGAG
1 AAGAAGAAGGAAGAAGGAG
44884 A
1 A
44885 GGAAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (19 bp):
AAGAAGAAGGAAGAAGGAG
Done.