Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014965.1 Kokia drynarioides strain JFW-HI SEQ_130009, 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: 38912
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:628 original size:153 final size:152
Alignment explanation
Indices: 411--804 Score: 535
Period size: 153 Copynumber: 2.6 Consensus size: 152
401 AAAGGAATGG
* * *
411 TGATGAAATTCTTACCACTAAGATCAAGACGTATCAAAGAGGATAGACCTGAAATTTCACTATGA
1 TGATGAAATTGTTACCACTAAGATCAAGACGTATCAAAGAGGATAGACCAGAAATATCACTATGA
*
476 ATATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGACAAGTA-AAGAAAC-TGAAGCTTGGAG
66 ATATCT-CTTCACCAAGAGTGCACATGTTGCAATTTGACAA-TATAAG-AACTTCAAGCTTGGAG
*
539 AGTCGAGTAAGAGATGCAGGTATGC
128 AGTCGAGTAAGAGATGCAGGCATGC
**
564 TGATGAAATTGTTACCACTAAGATCAAGACACCA-CAAAGAGGATAGACCAGAAATATCACTATG
1 TGATGAAATTGTTACCACTAAGATCAAGAC-GTATCAAAGAGGATAGACCAGAAATATCACTATG
* * *
628 AGTATCCTCTTCACCAAGAGTGCACATTTTGCAATTTGACAATATAAGATCTTCAAGCTTGGAGA
65 AATAT-CTCTTCACCAAGAGTGCACATGTTGCAATTTGACAATATAAGAACTTCAAGCTTGGAGA
*
693 GTCGAGTAAGAGATGCGGGCATGC
129 GTCGAGTAAGAGATGCAGGCATGC
* * * * *
717 TGATGAAATTGTTACCACTAAGTTCGAGACGTATCAAAGAGGGTCGACCAGAAATATCACGT-GG
1 TGATGAAATTGTTACCACTAAGATCAAGACGTATCAAAGAGGATAGACCAGAAATATCAC-TATG
* *
781 AATATCTCCTTCACAAAGATTGCA
65 AATATCT-CTTCACCAAGAGTGCA
805 GTCCCTTAGT
Statistics
Matches: 213, Mismatches: 21, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
152 7 0.03
153 202 0.95
154 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (152 bp):
TGATGAAATTGTTACCACTAAGATCAAGACGTATCAAAGAGGATAGACCAGAAATATCACTATGA
ATATCTCTTCACCAAGAGTGCACATGTTGCAATTTGACAATATAAGAACTTCAAGCTTGGAGAGT
CGAGTAAGAGATGCAGGCATGC
Found at i:9840 original size:30 final size:28
Alignment explanation
Indices: 9781--9858 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 28
9771 AAAATAATAA
** *
9781 ATTATTTTTATAAATTTTAATTAATTTCT
1 ATTATTTTTAT-AATTTTTTTTAAATTCT
9810 ATTACTTTTTATAATTTTTTTTAGAATTCT
1 ATTA-TTTTTATAATTTTTTTTA-AATTCT
9840 A--ATTTTTATATATTTTTTT
1 ATTATTTTTATA-ATTTTTTT
9859 ATATTTTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 8 0.19
28 9 0.21
29 13 0.30
30 13 0.30
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (28 bp):
ATTATTTTTATAATTTTTTTTAAATTCT
Found at i:11468 original size:2 final size:2
Alignment explanation
Indices: 11461--11490 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11451 TTACAAAGAG
11461 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11491 TTGAAGGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20428 original size:3 final size:3
Alignment explanation
Indices: 20422--20459 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
20412 CATCGATATG
20422 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
20460 GGACAAGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:26243 original size:25 final size:23
Alignment explanation
Indices: 26202--26247 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
26192 TCAATTAGGG
26202 AATTATTGTTTAGATTTAATTCT
1 AATTATTGTTTAGATTTAATTCT
*
26225 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
26248 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCT
Found at i:27081 original size:35 final size:35
Alignment explanation
Indices: 27042--27139 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 35
27032 ATTTCTTATT
27042 TTAATATTTGTTGCACTTTTAGTTTTTTAATTTAG
1 TTAATATTTGTTGCACTTTTAGTTTTTTAATTTAG
*
27077 TTAAT-TTT-TTG-----TTA-TTTCTT-ATTT--
1 TTAATATTTGTTGCACTTTTAGTTTTTTAATTTAG
*
27101 TA-ATATTTGTTGCACTTTTAGTTTTTTAATTTAG
1 TTAATATTTGTTGCACTTTTAGTTTTTTAATTTAG
27135 TTAAT
1 TTAAT
27140 TTTAATTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 24
0.63 0.05 0.32
Matches are distributed among these distances:
23 2 0.04
24 4 0.09
25 3 0.06
26 4 0.09
27 5 0.11
28 3 0.06
30 3 0.06
31 5 0.11
32 4 0.09
33 3 0.06
34 4 0.09
35 7 0.15
ACGTcount: A:0.22, C:0.05, G:0.09, T:0.63
Consensus pattern (35 bp):
TTAATATTTGTTGCACTTTTAGTTTTTTAATTTAG
Found at i:27117 original size:58 final size:58
Alignment explanation
Indices: 27027--27142 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
27017 ATTAAAACAC
27027 TTGTTATTTCTTATTTTAATATTTGTTGCACTTTTAGTTTTTTAATTTAGTTAATTTT
1 TTGTTATTTCTTATTTTAATATTTGTTGCACTTTTAGTTTTTTAATTTAGTTAATTTT
27085 TTGTTATTTCTTATTTTAATATTTGTTGCACTTTTAGTTTTTTAATTTAGTTAATTTT
1 TTGTTATTTCTTATTTTAATATTTGTTGCACTTTTAGTTTTTTAATTTAGTTAATTTT
27143 AATTTAAAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.21, C:0.05, G:0.09, T:0.66
Consensus pattern (58 bp):
TTGTTATTTCTTATTTTAATATTTGTTGCACTTTTAGTTTTTTAATTTAGTTAATTTT
Found at i:27870 original size:36 final size:36
Alignment explanation
Indices: 27830--27902 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
27820 TGATGAATGT
27830 CATATCATTTTGTCTCTTTGGCTCAACAACCTCTGA
1 CATATCATTTTGTCTCTTTGGCTCAACAACCTCTGA
27866 CATATCATTTTGTCTCTTTGGCTCAACAACCTCTGA
1 CATATCATTTTGTCTCTTTGGCTCAACAACCTCTGA
27902 C
1 C
27903 GCAGTAAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.29, G:0.11, T:0.38
Consensus pattern (36 bp):
CATATCATTTTGTCTCTTTGGCTCAACAACCTCTGA
Found at i:30548 original size:21 final size:22
Alignment explanation
Indices: 30497--30548 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
30487 TTTTCAAGTT
*
30497 TATCATATATTATTTTTCATTTA
1 TATCATATATTA-TTATCATTTA
* * *
30520 TTTTATATATTA-TATGATTTA
1 TATCATATATTATTATCATTTA
30541 TATCATAT
1 TATCATAT
30549 GAAGAAAAGT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 13 0.57
23 10 0.43
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.60
Consensus pattern (22 bp):
TATCATATATTATTATCATTTA
Found at i:31295 original size:29 final size:29
Alignment explanation
Indices: 31238--31294 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
31228 CGATCTAATG
* *
31238 TGTAATTTTATACATGGATTTTGATTTTA
1 TGTAATTTTATAAATGAATTTTGATTTTA
31267 TGTAATTTTATAAATGAAATTTTGATTT
1 TGTAATTTTATAAATG-AATTTTGATTT
31295 AATCCAATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (29 bp):
TGTAATTTTATAAATGAATTTTGATTTTA
Done.