Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005673.1 Kokia drynarioides strain JFW-HI SEQ_119854, 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: 25823
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Found at i:9823 original size:44 final size:43
Alignment explanation
Indices: 9735--9867 Score: 105
Period size: 44 Copynumber: 3.1 Consensus size: 43
9725 AATCTAATAT
** *
9735 TTAAAA-AAATA-AAAA-T-AAAA-ATTATAATTTATCAAAAA
1 TTAAAATAAATAGAAAATTAAAAATATTATAAAATATTAAAAA
* *
9773 TAAAAATAAATAGAAAATTAAAAATATTATTAAATATTGAAAAA
1 TTAAAATAAATAGAAAATTAAAAATATTATAAAATATT-AAAAA
** * * * *
9817 TTAAAATTGATATAAACTTATAAATCTTATAAAATATTATAAATA
1 TTAAAATAAATAGAAAATTAAAAATATTATAAAATATTA-AAA-A
9862 TTAAAA
1 TTAAAA
9868 AATATAAAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
38 5 0.07
39 5 0.07
40 4 0.05
41 1 0.01
42 4 0.05
43 10 0.14
44 38 0.51
45 7 0.09
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (43 bp):
TTAAAATAAATAGAAAATTAAAAATATTATAAAATATTAAAAA
Found at i:9856 original size:19 final size:19
Alignment explanation
Indices: 9834--9872 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
9824 TGATATAAAC
* *
9834 TTATAAATCTTATAAAATA
1 TTATAAATATTAAAAAATA
9853 TTATAAATATTAAAAAATA
1 TTATAAATATTAAAAAATA
9872 T
1 T
9873 AAAAAACCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
TTATAAATATTAAAAAATA
Found at i:10560 original size:22 final size:22
Alignment explanation
Indices: 10532--10616 Score: 93
Period size: 22 Copynumber: 3.9 Consensus size: 22
10522 GATTATATTG
*
10532 TTATTTTAGTGCTGTTTTTTTA
1 TTATTTTGGTGCTGTTTTTTTA
* *
10554 TTATTTTGGTTGTTG-TTTTTTG
1 TTATTTTGG-TGCTGTTTTTTTA
* *
10576 TTGTTTTGGTGTTGTTTTTTTA
1 TTATTTTGGTGCTGTTTTTTTA
*
10598 TTATTTTTGTGCT-TTTTTT
1 TTATTTTGGTGCTGTTTTTT
10617 CAATTTTTGA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 11 0.21
22 38 0.72
23 4 0.08
ACGTcount: A:0.07, C:0.02, G:0.18, T:0.73
Consensus pattern (22 bp):
TTATTTTGGTGCTGTTTTTTTA
Found at i:10659 original size:3 final size:3
Alignment explanation
Indices: 10649--10724 Score: 52
Period size: 3 Copynumber: 26.3 Consensus size: 3
10639 TGTTTTTTAC
* * * *
10649 TGT T-T TGT TGT TAT TTT TGT TGT TGT TGT TGT T-T TGC TGT TAT T-T
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * *
10694 TTT CTGT TGT T-T GGT TGT TTT TGT TGT TGT T
1 TGT -TGT TGT TGT TGT TGT TGT TGT TGT TGT T
10725 TTGATGTTAT
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
2 7 0.12
3 48 0.84
4 2 0.04
ACGTcount: A:0.03, C:0.03, G:0.24, T:0.71
Consensus pattern (3 bp):
TGT
Found at i:10659 original size:18 final size:19
Alignment explanation
Indices: 10636--10689 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
10626 ATTTTTTTTG
10636 TGTTGTT-TTTTACTGTT-T
1 TGTTGTTATTTT-CTGTTGT
10654 TGTTGTTATTTT-TGTTGT
1 TGTTGTTATTTTCTGTTGT
*
10672 TGTTGTTGTTTTGCTGTT
1 TGTTGTTATTTT-CTGTT
10690 ATTTTTTCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 4 0.13
18 19 0.61
19 4 0.13
20 4 0.13
ACGTcount: A:0.04, C:0.04, G:0.22, T:0.70
Consensus pattern (19 bp):
TGTTGTTATTTTCTGTTGT
Found at i:10680 original size:12 final size:11
Alignment explanation
Indices: 10631--10737 Score: 68
Period size: 11 Copynumber: 10.4 Consensus size: 11
10621 TTTTGATTTT
10631 TTTTG-TGTTG
1 TTTTGTTGTTG
**
10641 TTTT-TTACTG
1 TTTTGTTGTTG
10651 TTTTGTTGTT-
1 TTTTGTTGTTG
*
10661 ATTT-TTGTTG
1 TTTTGTTGTTG
10671 --TTGTTGTTG
1 TTTTGTTGTTG
* *
10680 TTTTGCTGTTA
1 TTTTGTTGTTG
*
10691 TTTTTTCTGTTG
1 TTTTGT-TGTTG
*
10703 TTTGGTTG-T-
1 TTTTGTTGTTG
10712 TTTTGTTGTTG
1 TTTTGTTGTTG
* *
10723 TTTTGATGTTA
1 TTTTGTTGTTG
10734 TTTT
1 TTTT
10738 TATGCGTTTT
Statistics
Matches: 73, Mismatches: 15, Indels: 17
0.70 0.14 0.16
Matches are distributed among these distances:
8 2 0.03
9 18 0.25
10 16 0.22
11 29 0.40
12 8 0.11
ACGTcount: A:0.05, C:0.03, G:0.21, T:0.71
Consensus pattern (11 bp):
TTTTGTTGTTG
Found at i:10684 original size:49 final size:49
Alignment explanation
Indices: 10631--10724 Score: 129
Period size: 49 Copynumber: 1.9 Consensus size: 49
10621 TTTTGATTTT
* *
10631 TTTTG-TGTTGTTTTTTACTGTT-TTGTTGTTATTTTTGTTGTTGTTGTTG
1 TTTTGCTGTTATTTTTT-CTGTTGTT-TGGTTATTTTTGTTGTTGTTGTTG
*
10680 TTTTGCTGTTATTTTTTCTGTTGTTTGGTTGTTTTTGTTGTTGTT
1 TTTTGCTGTTATTTTTTCTGTTGTTTGGTTATTTTTGTTGTTGTT
10725 TTGATGTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
49 28 0.70
50 12 0.30
ACGTcount: A:0.03, C:0.03, G:0.22, T:0.71
Consensus pattern (49 bp):
TTTTGCTGTTATTTTTTCTGTTGTTTGGTTATTTTTGTTGTTGTTGTTG
Found at i:10689 original size:29 final size:31
Alignment explanation
Indices: 10649--10714 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
10639 TGTTTTTTAC
*
10649 TGTTTTGTTGTTATTTTTGT-TGTTG-TT-GT
1 TGTTTTGCTGTTATTTTT-TCTGTTGTTTGGT
10678 TGTTTTGCTGTTATTTTTTCTGTTGTTTGGT
1 TGTTTTGCTGTTATTTTTTCTGTTGTTTGGT
10709 TGTTTT
1 TGTTTT
10715 TGTTGTTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 1 0.03
29 22 0.67
30 2 0.06
31 8 0.24
ACGTcount: A:0.03, C:0.03, G:0.23, T:0.71
Consensus pattern (31 bp):
TGTTTTGCTGTTATTTTTTCTGTTGTTTGGT
Done.