Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000071.1 Kokia drynarioides strain JFW-HI SEQ_110646, 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: 6284
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Found at i:72 original size:48 final size:48
Alignment explanation
Indices: 1--226 Score: 245
Period size: 48 Copynumber: 4.7 Consensus size: 48
* * * *
1 ATGGAGGAGGTGGGGACTTGTAGTAGTATGGAGGAGGTGGGGAAGGAG
1 ATGGAGGTGGTGGAGACTTGTAGTAGTATGGAGGAGGTGGGGATGGGG
* * * * * * *
49 ATGGAGGTGGTGGGGATTTGTAGTTGTAAGGAGGAGGTGGTGACGGTG
1 ATGGAGGTGGTGGAGACTTGTAGTAGTATGGAGGAGGTGGGGATGGGG
* * *
97 ACGGAGGTGGTGGAGACTTATAGTAATATGGAGGAGGTGGGGATGGGG
1 ATGGAGGTGGTGGAGACTTGTAGTAGTATGGAGGAGGTGGGGATGGGG
* * * * *
145 ACGGAGGTGGTGGAGACCTGTAGTAGTACGGGGGAGGTGGTGATGGGG
1 ATGGAGGTGGTGGAGACTTGTAGTAGTATGGAGGAGGTGGGGATGGGG
* * * *
193 ATGGTGGTGGTGGAGATTTATAGTGGTATGGAGG
1 ATGGAGGTGGTGGAGACTTGTAGTAGTATGGAGG
227 GTCCACTTCA
Statistics
Matches: 147, Mismatches: 31, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 147 1.00
ACGTcount: A:0.22, C:0.04, G:0.52, T:0.23
Consensus pattern (48 bp):
ATGGAGGTGGTGGAGACTTGTAGTAGTATGGAGGAGGTGGGGATGGGG
Found at i:167 original size:96 final size:96
Alignment explanation
Indices: 3--226 Score: 277
Period size: 96 Copynumber: 2.3 Consensus size: 96
1 AT
* * * * * **
3 GGAGGAGGTGGGGACTTGTAGTAGTATGGAGGAGGTGGGGAAGGAGATGGAGGTGGTGGGGATTT
1 GGAGGTGGTGGAGACTTATAGTAGTATGGAGGAGGTGGGGAAGGAGACGGAGGTGGTGGAGACCT
* *
68 GTAGTTGTAAGGAGGAGGTGGTGACGGTGAC
66 GTAGTAGTAAGGAGGAGGTGGTGACGGGGAC
* * *
99 GGAGGTGGTGGAGACTTATAGTAATATGGAGGAGGTGGGGATGGGGACGGAGGTGGTGGAGACCT
1 GGAGGTGGTGGAGACTTATAGTAGTATGGAGGAGGTGGGGAAGGAGACGGAGGTGGTGGAGACCT
* * * *
164 GTAGTAGTACGGGGGAGGTGGTGATGGGGAT
66 GTAGTAGTAAGGAGGAGGTGGTGACGGGGAC
* * *
195 GGTGGTGGTGGAGATTTATAGTGGTATGGAGG
1 GGAGGTGGTGGAGACTTATAGTAGTATGGAGG
227 GTCCACTTCA
Statistics
Matches: 108, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
96 108 1.00
ACGTcount: A:0.21, C:0.04, G:0.52, T:0.23
Consensus pattern (96 bp):
GGAGGTGGTGGAGACTTATAGTAGTATGGAGGAGGTGGGGAAGGAGACGGAGGTGGTGGAGACCT
GTAGTAGTAAGGAGGAGGTGGTGACGGGGAC
Found at i:298 original size:48 final size:48
Alignment explanation
Indices: 246--381 Score: 155
Period size: 48 Copynumber: 2.8 Consensus size: 48
236 ATGTTTCGGT
* * *
246 GGAGGTGGTGGTGACTTGTACTCATAAGGTGGTGGTGGAGAAGGTGAA
1 GGAGGTGGTGGTGACTTATACTCATAAGGTGGTGGAGGAGAAGGAGAA
* * * * * * *
294 GGAGGTGGTGGAGATTTATACACGTATGGTGGTGGGGGAGATGGAGAA
1 GGAGGTGGTGGTGACTTATACTCATAAGGTGGTGGAGGAGAAGGAGAA
** *
342 GCTGGTGGAGGTGACTTATACTCATAAGGTGGTGGAGGAG
1 GGAGGTGGTGGTGACTTATACTCATAAGGTGGTGGAGGAG
382 GTGAAGAGTA
Statistics
Matches: 70, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.24, C:0.07, G:0.46, T:0.24
Consensus pattern (48 bp):
GGAGGTGGTGGTGACTTATACTCATAAGGTGGTGGAGGAGAAGGAGAA
Found at i:775 original size:25 final size:25
Alignment explanation
Indices: 746--808 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
736 AGCTGGCTTC
*
746 TTAAAATAATTTTTTTTTTGAA-ATA
1 TTAAAATAATTATTTTTTT-AATATA
*
771 TTAAAATAAATATTTTTTTAATATA
1 TTAAAATAATTATTTTTTTAATATA
*
796 TTAATATAATTAT
1 TTAAAATAATTAT
809 ATGGTAACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 2 0.06
25 31 0.94
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TTAAAATAATTATTTTTTTAATATA
Found at i:1630 original size:20 final size:20
Alignment explanation
Indices: 1602--1645 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1592 AATCGAATAA
**
1602 TTATAAAATTATTTTATTTG
1 TTATAAAATTATTAAATTTG
*
1622 TTATTAAATTATTAAATTTG
1 TTATAAAATTATTAAATTTG
1642 TTAT
1 TTAT
1646 GTTTTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTATAAAATTATTAAATTTG
Found at i:2291 original size:3 final size:3
Alignment explanation
Indices: 2278--2315 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
2268 AAGTATCTTA
2278 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2316 TATGGAGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3486 original size:20 final size:21
Alignment explanation
Indices: 3456--3504 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
3446 ATGAGATAAT
3456 TAAAGAATATATATAAA-A-AAA
1 TAAA-AATATAT-TAAAGACAAA
3477 TAAAAATATATTAAAGACAAA
1 TAAAAATATATTAAAGACAAA
3498 -AAAAATA
1 TAAAAATA
3505 ATTGTTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.15
20 15 0.58
21 7 0.27
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (21 bp):
TAAAAATATATTAAAGACAAA
Done.