Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011199.1 Kokia drynarioides strain JFW-HI SEQ_126176, 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: 54674
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:9196 original size:17 final size:18
Alignment explanation
Indices: 9173--9214 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
9163 TATAAGAATA
9173 GAAATGCAACT-AC-AAT
1 GAAATGCAACTAACAAAT
9189 GCAAATGC-ACTAACAAAT
1 G-AAATGCAACTAACAAAT
9207 GAAATGCA
1 GAAATGCA
9215 GTGACAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (18 bp):
GAAATGCAACTAACAAAT
Found at i:10300 original size:20 final size:23
Alignment explanation
Indices: 10275--10320 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
10265 ATGGGCGTAT
10275 TTTCC-TGC-TTT-TCCTTCTTC
1 TTTCCTTGCATTTATCCTTCTTC
*
10295 TTTCCTTTCATTTATCCTTCTTC
1 TTTCCTTGCATTTATCCTTCTTC
10318 TTT
1 TTT
10321 AGTGCCTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 2 0.09
22 3 0.14
23 12 0.55
ACGTcount: A:0.04, C:0.30, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTCCTTGCATTTATCCTTCTTC
Found at i:11588 original size:20 final size:20
Alignment explanation
Indices: 11563--11606 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
11553 CATAAGATTT
11563 AAAAGAAAAAAGTAAATGTA
1 AAAAGAAAAAAGTAAATGTA
*
11583 AAAAGATAAAAGTAAATGTA
1 AAAAGAAAAAAGTAAATGTA
11603 AAAA
1 AAAA
11607 TGCGTTGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (20 bp):
AAAAGAAAAAAGTAAATGTA
Found at i:23751 original size:17 final size:17
Alignment explanation
Indices: 23731--23840 Score: 57
Period size: 17 Copynumber: 6.4 Consensus size: 17
23721 GCTATCATCA
23731 CATTTCGTTTGTCATTG
1 CATTTCGTTTGTCATTG
*
23748 CATTTAGTTT-TCA-TG
1 CATTTCGTTTGTCATTG
* * * **
23763 CATATCATGTAGCTATCATCA
1 CATTTC--GT--TTGTCATTG
23784 CATTTCGTTTGTCATTG
1 CATTTCGTTTGTCATTG
* *
23801 CATTT-TTCTTGTCACTG
1 CATTTCGT-TTGTCATTG
*
23818 CATCTTC-ATTGTCATTG
1 CAT-TTCGTTTGTCATTG
23835 CATTTC
1 CATTTC
23841 TATATATATT
Statistics
Matches: 69, Mismatches: 15, Indels: 19
0.67 0.15 0.18
Matches are distributed among these distances:
15 6 0.09
16 7 0.10
17 43 0.62
18 2 0.03
19 3 0.04
20 3 0.04
21 5 0.07
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.48
Consensus pattern (17 bp):
CATTTCGTTTGTCATTG
Found at i:23756 original size:53 final size:53
Alignment explanation
Indices: 23697--23805 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
23687 CGATACTTAG
23697 TTTAGTTTTCATGCATATCATGTAGCTATCATCACATTTCGTTTGTCATTGCA
1 TTTAGTTTTCATGCATATCATGTAGCTATCATCACATTTCGTTTGTCATTGCA
23750 TTTAGTTTTCATGCATATCATGTAGCTATCATCACATTTCGTTTGTCATTGCA
1 TTTAGTTTTCATGCATATCATGTAGCTATCATCACATTTCGTTTGTCATTGCA
23803 TTT
1 TTT
23806 TTCTTGTCAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (53 bp):
TTTAGTTTTCATGCATATCATGTAGCTATCATCACATTTCGTTTGTCATTGCA
Found at i:23918 original size:50 final size:50
Alignment explanation
Indices: 23860--23962 Score: 197
Period size: 50 Copynumber: 2.1 Consensus size: 50
23850 TTGTAAATTA
*
23860 ATGATAATGCATTGTGGACAAAGCAGACTTTAAGTTTGGGGGGAATGTAT
1 ATGATAATGCATTGTGGACAAAGCAGACTTTAAGTTTAGGGGGAATGTAT
23910 ATGATAATGCATTGTGGACAAAGCAGACTTTAAGTTTAGGGGGAATGTAT
1 ATGATAATGCATTGTGGACAAAGCAGACTTTAAGTTTAGGGGGAATGTAT
23960 ATG
1 ATG
23963 GGTTGGAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (50 bp):
ATGATAATGCATTGTGGACAAAGCAGACTTTAAGTTTAGGGGGAATGTAT
Found at i:28486 original size:16 final size:16
Alignment explanation
Indices: 28465--28497 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28455 ATCGACAGCT
28465 CGAATATAACCTATTC
1 CGAATATAACCTATTC
28481 CGAATATAACCTATTC
1 CGAATATAACCTATTC
28497 C
1 C
28498 AAAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.30
Consensus pattern (16 bp):
CGAATATAACCTATTC
Found at i:28683 original size:22 final size:22
Alignment explanation
Indices: 28626--28686 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
28616 CGATCTAAGG
28626 AAAAATAAAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
28647 AAAAATAAAATAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
28669 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
28687 GGAAGTAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.29
22 24 0.69
23 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:29469 original size:14 final size:14
Alignment explanation
Indices: 29452--29492 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
29442 TTTAAACTCT
29452 AAAAGATAAATACA
1 AAAAGATAAATACA
29466 AAAAGAT-AA-ACA
1 AAAAGATAAATACA
*
29478 TAAA-ATAAATACA
1 AAAAGATAAATACA
29491 AA
1 AA
29493 TTTAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 2 0.09
12 8 0.35
13 6 0.26
14 7 0.30
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAAGATAAATACA
Found at i:29505 original size:19 final size:19
Alignment explanation
Indices: 29481--29525 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29471 ATAAACATAA
29481 AATAAATACAAAT-TTAAAT
1 AATAAATA-AAATCTTAAAT
*
29500 AATAAATAATATCTTAAAT
1 AATAAATAAAATCTTAAAT
*
29519 ATTAAAT
1 AATAAAT
29526 CCTAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAAATAAAATCTTAAAT
Found at i:43415 original size:18 final size:18
Alignment explanation
Indices: 43392--43434 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
43382 GTTCAATGTG
43392 TAATTAATTTAAATTT-TT
1 TAATTAA-TTAAATTTATT
43410 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
43428 TAATTAA
1 TAATTAA
43435 AAATCTATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:44888 original size:17 final size:17
Alignment explanation
Indices: 44845--44888 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
44835 TTCAAACTAT
*
44845 ATAATTTATGGAATAAA
1 ATAAATTATGGAATAAA
*
44862 ATAAACTATGGAATAAA
1 ATAAATTATGGAATAAA
*
44879 ATGAATTATG
1 ATAAATTATG
44889 ACACAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.32
Consensus pattern (17 bp):
ATAAATTATGGAATAAA
Found at i:50730 original size:36 final size:36
Alignment explanation
Indices: 50678--50772 Score: 109
Period size: 36 Copynumber: 2.6 Consensus size: 36
50668 TCAAAGGAAA
* * ** *
50678 GCATATATCTCGGTTAGAATGTATTGTTATGATGTT
1 GCATACATCTCAGTTAGAACATATTGCTATGATGTT
* *
50714 GCATACGTCTCAGTTAGAGCATATTGCTATGATGTT
1 GCATACATCTCAGTTAGAACATATTGCTATGATGTT
* *
50750 GCATACACCTCAGTTAGAGCATA
1 GCATACATCTCAGTTAGAACATA
50773 AGGCCATTCT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (36 bp):
GCATACATCTCAGTTAGAACATATTGCTATGATGTT
Done.