Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011308.1 Kokia drynarioides strain JFW-HI SEQ_126288, 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: 37875
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:23860 original size:40 final size:40
Alignment explanation
Indices: 23814--23893 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
23804 AAAAAAATCA
*
23814 ACAAATTTAGCCCTTAATGTTTTAGTTCTAATTCTAAGAT
1 ACAAATTTAACCCTTAATGTTTTAGTTCTAATTCTAAGAT
23854 ACAAATTTAACCCTTAATGTTTTAGTTCTAATTCTAAGAT
1 ACAAATTTAACCCTTAATGTTTTAGTTCTAATTCTAAGAT
23894 TTCAACAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (40 bp):
ACAAATTTAACCCTTAATGTTTTAGTTCTAATTCTAAGAT
Found at i:28007 original size:2 final size:2
Alignment explanation
Indices: 28000--28033 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
27990 AACTAAAATA
28000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28034 AATTTATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29562 original size:87 final size:87
Alignment explanation
Indices: 29416--29594 Score: 340
Period size: 87 Copynumber: 2.1 Consensus size: 87
29406 ACAAATTCAA
29416 TCTAATAGAATTTGATTCGATTAAAATGATAAAATATTTAAGATTGATAAATATTGAATTGGAAA
1 TCTAATAGAATTTGATTCGATTAAAATGATAAAATATTTAAGATTGATAAATATTGAATTGGAAA
29481 AGCTTGATTTTGGGTGAATTAC
66 AGCTTGATTTTGGGTGAATTAC
*
29503 TCTAATAGAATTTGATTCGATTAAAATGATAAAATATTTAATATTGATAAATATTGAATTGGAAA
1 TCTAATAGAATTTGATTCGATTAAAATGATAAAATATTTAAGATTGATAAATATTGAATTGGAAA
29568 AGCTTGATTTTGGGTGAATTAC
66 AGCTTGATTTTGGGTGAATTAC
*
29590 ACTAA
1 TCTAA
29595 GGTTATTAAT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 90 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (87 bp):
TCTAATAGAATTTGATTCGATTAAAATGATAAAATATTTAAGATTGATAAATATTGAATTGGAAA
AGCTTGATTTTGGGTGAATTAC
Found at i:36695 original size:15 final size:15
Alignment explanation
Indices: 36675--36704 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36665 AAGGGTATAA
*
36675 GAAATCTAGTTATGG
1 GAAATCGAGTTATGG
36690 GAAATCGAGTTATGG
1 GAAATCGAGTTATGG
36705 AAGATCAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (15 bp):
GAAATCGAGTTATGG
Found at i:36767 original size:39 final size:39
Alignment explanation
Indices: 36719--36855 Score: 121
Period size: 39 Copynumber: 3.4 Consensus size: 39
36709 TCAGATGAAA
36719 GAGAAGAAGGATATGGAGGTAGGAGGAAATCGGATGATG
1 GAGAAGAAGGATATGGAGGTAGGAGGAAATCGGATGATG
* * ** * * **
36758 GAGATGAAGGGTATGAGAAATCTAGTTATGGAAGATCAGATGAAA
1 GAGAAGAAGGATATG-G--AGGTAG-GA-GGAA-ATCGGATGATG
*
36803 GAGAAGAAGAATATGGAGGTAGGAGGAAATCGGATGATG
1 GAGAAGAAGGATATGGAGGTAGGAGGAAATCGGATGATG
* *
36842 AAGATGAAGGATAT
1 GAGAAGAAGGATAT
36856 AAGAAGTCGA
Statistics
Matches: 72, Mismatches: 20, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
39 32 0.44
40 5 0.07
41 1 0.01
42 8 0.11
43 1 0.01
44 5 0.07
45 20 0.28
ACGTcount: A:0.42, C:0.03, G:0.37, T:0.18
Consensus pattern (39 bp):
GAGAAGAAGGATATGGAGGTAGGAGGAAATCGGATGATG
Found at i:36831 original size:84 final size:84
Alignment explanation
Indices: 36685--36869 Score: 307
Period size: 84 Copynumber: 2.2 Consensus size: 84
36675 GAAATCTAGT
* *
36685 TATGGGAAATCGAGTTATGGAAGATCAGATGAAAGAGAAGAAGGATATGGAGGTAGGAGGAAATC
1 TATGAGAAATCGAGTTATGGAAGATCAGATGAAAGAGAAGAAGAATATGGAGGTAGGAGGAAATC
* *
36750 GGATGATGGAGATGAAGGG
66 GGATGATGAAGATGAAGGA
*
36769 TATGAGAAATCTAGTTATGGAAGATCAGATGAAAGAGAAGAAGAATATGGAGGTAGGAGGAAATC
1 TATGAGAAATCGAGTTATGGAAGATCAGATGAAAGAGAAGAAGAATATGGAGGTAGGAGGAAATC
36834 GGATGATGAAGATGAAGGA
66 GGATGATGAAGATGAAGGA
* *
36853 TATAAGAAGTCGAGTTA
1 TATGAGAAATCGAGTTA
36870 CAGAAGAAAT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 93 1.00
ACGTcount: A:0.42, C:0.04, G:0.35, T:0.19
Consensus pattern (84 bp):
TATGAGAAATCGAGTTATGGAAGATCAGATGAAAGAGAAGAAGAATATGGAGGTAGGAGGAAATC
GGATGATGAAGATGAAGGA
Found at i:37728 original size:2 final size:2
Alignment explanation
Indices: 37721--37746 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37711 TAATTTTCAT
37721 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
37747 AAAGCAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.