Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009288.1 Kokia drynarioides strain JFW-HI SEQ_123994, 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: 12934
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--29 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30 AATTACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1166 original size:19 final size:19
Alignment explanation
Indices: 1126--1186 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1116 TTTTTTAATC
*
1126 TTTT-ATAATTTT-TGCACT
1 TTTTAATAATTTTATGTA-T
* *
1144 TTTTTATATTTTTATAGTAT
1 TTTTAATAATTTTAT-GTAT
*
1164 TTTTAATAATTTTCTGTAT
1 TTTTAATAATTTTATGTAT
1183 TTTT
1 TTTT
1187 TAAATGTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 4 0.11
19 15 0.43
20 14 0.40
21 2 0.06
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTAATAATTTTATGTAT
Found at i:1264 original size:12 final size:13
Alignment explanation
Indices: 1240--1265 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1230 ATTTACATAA
1240 TTTTTCAATTTTT
1 TTTTTCAATTTTT
1253 TTTTTCAATTTTT
1 TTTTTCAATTTTT
1266 ATACTTTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTCAATTTTT
Found at i:1418 original size:78 final size:80
Alignment explanation
Indices: 1270--1421 Score: 184
Period size: 78 Copynumber: 1.9 Consensus size: 80
1260 ATTTTTATAC
* *
1270 TTTATATATTTTTTTGTCATTTATAATAATCTTATAACTTTCTATATTTTTATAATTTTTCTGCA
1 TTTATATATTTTTTTGTCATTTATAATAATCTTATAACTTTATATATTTTTATAATTTTTCTACA
1335 CTTTTTTATATATGT
66 CTTTTTTATATATGT
* * * ** * *
1350 TTTATA-ATTTTTTT-TCATTTTTAATACTTTTATAGTTTTATATATTTCTTAT-GTTTTTCTAT
1 TTTATATATTTTTTTGTCATTTATAATAATCTTATAACTTTATATATTT-TTATAATTTTTCTAC
*
1412 ATTTTTTTAT
65 ACTTTTTTAT
1422 GATTTTTTAC
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
78 43 0.70
79 12 0.20
80 6 0.10
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.65
Consensus pattern (80 bp):
TTTATATATTTTTTTGTCATTTATAATAATCTTATAACTTTATATATTTTTATAATTTTTCTACA
CTTTTTTATATATGT
Found at i:1427 original size:21 final size:21
Alignment explanation
Indices: 1388--1428 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1378 TTTATAGTTT
1388 TATATATTTCTTATGTTTTTC
1 TATATATTTCTTATGTTTTTC
*
1409 TATAT-TTTTTTATGATTTTT
1 TATATATTTCTTATG-TTTTT
1429 TACTGATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.71
Consensus pattern (21 bp):
TATATATTTCTTATGTTTTTC
Found at i:1897 original size:3 final size:3
Alignment explanation
Indices: 1889--1913 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1879 GTAAAATATG
1889 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1914 TTGTGAGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2945 original size:18 final size:18
Alignment explanation
Indices: 2922--2956 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2912 TTTTGTTCTA
* *
2922 TTTATGTCAATTAATTTT
1 TTTATGTAAAATAATTTT
2940 TTTATGTAAAATAATTT
1 TTTATGTAAAATAATTT
2957 AAGTTTAGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTATGTAAAATAATTTT
Found at i:5520 original size:30 final size:30
Alignment explanation
Indices: 5485--5570 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 30
5475 AATTTGACAT
* *
5485 TTTTTTTAATTTGATACTCAAACTTAATAA
1 TTTTTTTAATTTGGTACTCAAACTTAACAA
* *
5515 TTTTTTCTAATTTGGTAC-CTAAACTTGACAC
1 TTTTTT-TAATTTGGTACTC-AAACTTAACAA
* *
5546 TTTTTTTAAGTTGGTACTTAAACTT
1 TTTTTTTAATTTGGTACTCAAACTT
5571 TTTGGGATCC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 23 0.49
31 24 0.51
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (30 bp):
TTTTTTTAATTTGGTACTCAAACTTAACAA
Found at i:5539 original size:31 final size:30
Alignment explanation
Indices: 5485--5570 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
5475 AATTTGACAT
* *
5485 TTTTTTTAATTTGATA-CTCAAACTTAATAA
1 TTTTTTTAATTTGGTACCT-AAACTTAACAA
* *
5515 TTTTTTCTAATTTGGTACCTAAACTTGACAC
1 TTTTTT-TAATTTGGTACCTAAACTTAACAA
* *
5546 TTTTTTTAAGTTGGTACTTAAACTT
1 TTTTTTTAATTTGGTACCTAAACTT
5571 TTTGGGATCC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.48
31 23 0.48
32 2 0.04
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (30 bp):
TTTTTTTAATTTGGTACCTAAACTTAACAA
Found at i:5808 original size:28 final size:28
Alignment explanation
Indices: 5760--5814 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
5750 TATGATATTT
*
5760 TTTTATTTTATATATTCAATTACTTTTAG
1 TTTTATTTAATATATTCAATTA-TTTTAG
5789 TTTTATTTAAT-TAATT-AATTATTTTA
1 TTTTATTTAATAT-ATTCAATTATTTTA
5815 TTAATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.21
28 6 0.25
29 13 0.54
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTTATTTAATATATTCAATTATTTTAG
Found at i:5812 original size:16 final size:16
Alignment explanation
Indices: 5791--5822 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5781 ACTTTTAGTT
5791 TTATTTAATTAATTAA
1 TTATTTAATTAATTAA
*
5807 TTATTTTATTAATTAA
1 TTATTTAATTAATTAA
5823 AAATAATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTTAATTAATTAA
Found at i:6101 original size:60 final size:60
Alignment explanation
Indices: 5993--6105 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
5983 AATATTTAAT
* *
5993 AAATTAGGTACCAAATTGAACCTAAAAAAAAGTTTATGTACCAAATTAAAAAAAAATATC
1 AAATTAGGTACCAAATTGAACCCAAAAAAAAGTTTAAGTACCAAATTAAAAAAAAATATC
* * *
6053 AAATTCGGATACCAAATTGAACCCAAAAAAAA-TTTAAGTGCTAAATTAAAAAA
1 AAATTAGG-TACCAAATTGAACCCAAAAAAAAGTTTAAGTACCAAATTAAAAAA
6106 TATATTAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 25 0.53
61 22 0.47
ACGTcount: A:0.55, C:0.12, G:0.09, T:0.24
Consensus pattern (60 bp):
AAATTAGGTACCAAATTGAACCCAAAAAAAAGTTTAAGTACCAAATTAAAAAAAAATATC
Found at i:6124 original size:59 final size:61
Alignment explanation
Indices: 6001--6129 Score: 163
Period size: 59 Copynumber: 2.1 Consensus size: 61
5991 ATAAATTAGG
* * **
6001 TACCAAATTGAACCTAAAAAAAAGTTTATGTACCAAATTAAAAAAAAATATCAAATTCGGA
1 TACCAAATTGAACCCAAAAAAAAGTTTAAGTACCAAATTAAAAAAAAATATCAAATTCAAA
* * * * *
6062 TACCAAATTGAACCCAAAAAAAA-TTTAAGTGCTAAATT-AAAAAATATATTAAATTTAAA
1 TACCAAATTGAACCCAAAAAAAAGTTTAAGTACCAAATTAAAAAAAAATATCAAATTCAAA
6121 TACCAAATT
1 TACCAAATT
6130 AAAAAAAATA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 25 0.42
60 12 0.20
61 22 0.37
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.27
Consensus pattern (61 bp):
TACCAAATTGAACCCAAAAAAAAGTTTAAGTACCAAATTAAAAAAAAATATCAAATTCAAA
Done.