Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000173.1 Kokia drynarioides strain JFW-HI SEQ_110845, 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: 44524
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:600 original size:15 final size:16
Alignment explanation
Indices: 558--597 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
548 TTTGGGCCTT
558 TTTGTAATTTGGGTCA
1 TTTGTAATTTGGGTCA
*
574 TCTG-AATTTGGGTCA
1 TTTGTAATTTGGGTCA
589 TTTGTAATT
1 TTTGTAATT
598 GGGCCGTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.20, C:0.07, G:0.23, T:0.50
Consensus pattern (16 bp):
TTTGTAATTTGGGTCA
Found at i:671 original size:17 final size:17
Alignment explanation
Indices: 649--704 Score: 85
Period size: 17 Copynumber: 3.3 Consensus size: 17
639 GGACTTTTCA
* *
649 AAATTTAATTTTATAAT
1 AAATTTAAATTTAAAAT
666 AAATTTAAATTTAAAAT
1 AAATTTAAATTTAAAAT
*
683 AAACTTAAATTTAAAAT
1 AAATTTAAATTTAAAAT
700 AAATT
1 AAATT
705 CAATTTCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTTAAATTTAAAAT
Found at i:1031 original size:8 final size:7
Alignment explanation
Indices: 997--1027 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
987 TAGAAAGATG
997 CCCTTCC
1 CCCTTCC
1004 CCCTTCC
1 CCCTTCC
1011 CCCTTCC
1 CCCTTCC
1018 CCCTTCC
1 CCCTTCC
1025 CCC
1 CCC
1028 CTTCAACTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.74, G:0.00, T:0.26
Consensus pattern (7 bp):
CCCTTCC
Found at i:2651 original size:6 final size:6
Alignment explanation
Indices: 2642--2669 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2632 GCTGTTTAGG
2642 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
2670 ATTAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:6396 original size:21 final size:21
Alignment explanation
Indices: 6376--6414 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6366 TTAAAATTTA
6376 AGTTTA-AATTAATTATTTTT
1 AGTTTATAATTAATTATTTTT
* *
6396 ATTTTATATTTAATTATTT
1 AGTTTATAATTAATTATTT
6415 CAACACAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (21 bp):
AGTTTATAATTAATTATTTTT
Found at i:6410 original size:25 final size:25
Alignment explanation
Indices: 6319--6411 Score: 62
Period size: 27 Copynumber: 3.4 Consensus size: 25
6309 ACTATTTGAA
6319 ATATTTATATTAATTATTTTTTATTTT
1 ATATTTA-ATTAATTA-TTTTTATTTT
* * * * *
6346 ATGTATAGTTATTTTAATTTTTAAAATTT
1 ATATTTAATTA-ATT-ATTTTT--ATTTT
6375 A-AGTTTAAATTAATTATTTTTATTTT
1 ATA-TTT-AATTAATTATTTTTATTTT
6401 ATATTTAATTA
1 ATATTTAATTA
6412 TTTCAACACA
Statistics
Matches: 49, Mismatches: 10, Indels: 16
0.65 0.13 0.21
Matches are distributed among these distances:
25 5 0.10
26 11 0.22
27 13 0.27
28 7 0.14
29 9 0.18
30 4 0.08
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (25 bp):
ATATTTAATTAATTATTTTTATTTT
Found at i:8795 original size:19 final size:20
Alignment explanation
Indices: 8764--8801 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
8754 GTATAAAAAA
8764 ATGTACTAAATTA-AAATTG
1 ATGTACTAAATTATAAATTG
8783 ATGTA-TAACATTATAAATT
1 ATGTACTAA-ATTATAAATT
8802 ATATCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 9 0.53
20 5 0.29
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (20 bp):
ATGTACTAAATTATAAATTG
Found at i:10773 original size:24 final size:25
Alignment explanation
Indices: 10746--10792 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
10736 CAAAAAGTAA
10746 ATTAATTCTT-TTATTAAAAATTCT
1 ATTAATTCTTATTATTAAAAATTCT
* *
10770 ATTAATTTTTATTGTTAAAAATT
1 ATTAATTCTTATTATTAAAAATT
10793 GATTTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (25 bp):
ATTAATTCTTATTATTAAAAATTCT
Found at i:12406 original size:14 final size:14
Alignment explanation
Indices: 12384--12422 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
12374 TTATTTGAAA
*
12384 AAAAAATATTTTTT
1 AAAAAATATTTTAT
*
12398 AAGAAATA-TTTAT
1 AAAAAATATTTTAT
12411 AAAAAATATTTT
1 AAAAAATATTTT
12423 GAAATTTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
AAAAAATATTTTAT
Found at i:17573 original size:90 final size:92
Alignment explanation
Indices: 17410--17620 Score: 220
Period size: 90 Copynumber: 2.3 Consensus size: 92
17400 TTCTCGTCAA
* *
17410 CTTAGTGTGAGCAGCATCGT-TA--GAG-AACAGTTATATGTACAGATACCGTATCAATGGCTGA
1 CTTAGTGTGAGCAGCATCATATACCG-GTAACAGTTATATGAACAGATACCGTATCAATGGCTGA
**
17471 GGCACCGTATATGATGC-G-CTCGTTAG
65 GGCACCACATATGATGCAGCCTCGTTAG
* * * *
17497 CTTAGTGTGAGTAGCATCATATACTGGTAACAGTTATATGAACAGATATCGTATCGATGG-TCGA
1 CTTAGTGTGAGCAGCATCATATACCGGTAACAGTTATATGAACAGATACCGTATCAATGGCT-GA
* * *
17561 GGTATCACATATGTTGCTAGTCCTCGTTAG
65 GGCACCACATATGATGC-AG-CCTCGTTAG
* *
17591 CTTAGTGTGAGCAGTATCGTATACCGGTAA
1 CTTAGTGTGAGCAGCATCATATACCGGTAA
17621 TAGAAATGAC
Statistics
Matches: 101, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
87 18 0.18
88 2 0.02
89 2 0.02
90 44 0.44
92 1 0.01
94 34 0.34
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (92 bp):
CTTAGTGTGAGCAGCATCATATACCGGTAACAGTTATATGAACAGATACCGTATCAATGGCTGAG
GCACCACATATGATGCAGCCTCGTTAG
Found at i:31887 original size:14 final size:13
Alignment explanation
Indices: 31866--31900 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
31856 AATAAATATT
31866 AATTAATTAATCTA
1 AATTAATTAATC-A
*
31880 ATTTAATTAATCA
1 AATTAATTAATCA
31893 AATTAATT
1 AATTAATT
31901 TCTCAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTAATTAATCA
Found at i:31899 original size:18 final size:18
Alignment explanation
Indices: 31864--31901 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
31854 AAAATAAATA
*
31864 TTAATTAATTAATCTAAT
1 TTAATTAATAAATCTAAT
31882 TTAATTAATCAAAT-TAAT
1 TTAATTAAT-AAATCTAAT
31900 TT
1 TT
31902 CTCAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATTAATAAATCTAAT
Done.