Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003805.1 Kokia drynarioides strain JFW-HI SEQ_116797, 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: 2033
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.30
Found at i:1053 original size:70 final size:70
Alignment explanation
Indices: 977--1190 Score: 374
Period size: 70 Copynumber: 3.1 Consensus size: 70
967 TCTCCACACT
* * * * *
977 TGGGTCTCTAAATGCAATGAAAAGTAAATAGGCCTTCACACCTGAGCCTCCAAATGCAATAAAAA
1 TGGGTCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCAATGAAAA
1042 GTAAA
66 GTAAA
1047 TGGGTCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCAATGAAAA
1 TGGGTCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCAATGAAAA
1112 GTAAA
66 GTAAA
*
1117 TGGGTCTCTAAATGCAATGAAAAATAAATGGGCCTCCACACCTGGGCCTCTAAATGCAATGAAAA
1 TGGGTCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCAATGAAAA
1182 GTAAA
66 GTAAA
1187 TGGG
1 TGGG
1191 CCCCTACACC
Statistics
Matches: 138, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 138 1.00
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (70 bp):
TGGGTCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCAATGAAAA
GTAAA
Found at i:1125 original size:28 final size:28
Alignment explanation
Indices: 1089--1152 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
1079 CCTCCACACC
*
1089 TGGGCCTCTAAATGCAATGAAAAGTAAA
1 TGGGCCTCTAAATGCAATGAAAAATAAA
*
1117 TGGGTCTCTAAATGCAATGAAAAATAAA
1 TGGGCCTCTAAATGCAATGAAAAATAAA
1145 TGGGCCTC
1 TGGGCCTC
1153 CACACCTGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (28 bp):
TGGGCCTCTAAATGCAATGAAAAATAAA
Found at i:1169 original size:42 final size:42
Alignment explanation
Indices: 1117--1588 Score: 602
Period size: 42 Copynumber: 11.4 Consensus size: 42
1107 GAAAAGTAAA
* *
1117 TGGGTCTCTAAATGCAATGAAAAATAAATGGGCCTCCACACC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
1159 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCC-CCTACACC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCC-ACACC
* * *
1201 TAGGCCTCTAAATGTAATGAATAGTAAATGGGCCTCCACACC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
* * *
1243 TCGACCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
* * *
1285 TCGGCCTCTAAATGTAATGAAAAGTAAATGGGCCTCCACACT
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
1327 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
* * *
1369 TAGGCCTTTAAATGCAATGAAAAGTAAATGGACCTCCACACC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
** * * * *
1411 TAAGCCTTTAAATGTAATGAAAAGTAAATAGACCTCCACACC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
* *
1453 TAGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACG
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
* * * * **
1495 TGGGCCTCAAAATGCAGTAAAAAGTAAATGGACCTCCACAAG
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
**
1537 TGGG---C-----GCAATGAAAAGTAAATGAACCTCCACACC
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
1571 TGGGCCTCTAAATGCAAT
1 TGGGCCTCTAAATGCAAT
1589 AAATGCTTTC
Statistics
Matches: 380, Mismatches: 40, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
34 28 0.07
37 1 0.00
39 1 0.00
41 2 0.01
42 346 0.91
43 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
Found at i:2001 original size:7 final size:7
Alignment explanation
Indices: 1989--2030 Score: 50
Period size: 8 Copynumber: 5.9 Consensus size: 7
1979 TCTTTCTATT
1989 TTTTTTC
1 TTTTTTC
1996 TTTTTTTC
1 -TTTTTTC
2004 TTTTTTTC
1 -TTTTTTC
2012 TTTTTTC
1 TTTTTTC
*
2019 -TTCTTC
1 TTTTTTC
2025 TTTTTT
1 TTTTTT
2031 TTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
6 5 0.16
7 11 0.35
8 15 0.48
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:2001 original size:8 final size:8
Alignment explanation
Indices: 1988--2017 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
1978 CTCTTTCTAT
1988 TTTTTTTC
1 TTTTTTTC
1996 TTTTTTTC
1 TTTTTTTC
2004 TTTTTTTC
1 TTTTTTTC
2012 TTTTTT
1 TTTTTT
2018 CTTCTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTC
Found at i:2010 original size:18 final size:19
Alignment explanation
Indices: 1981--2033 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
1971 TTGCTCTCTC
1981 TTTCTATTTTTTTTCTTT-T
1 TTTCT-TTTTTTTTCTTTCT
*
2000 TTTCTTTTTTTCTTTTTTCT
1 TTTCTTTTTTT-TTCTTTCT
2020 TCTTCTTTTTTTTT
1 T-TTCTTTTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.20
19 10 0.33
20 4 0.13
21 10 0.33
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTCTTTTTTTTTCTTTCT
Done.