Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014371.1 Kokia drynarioides strain JFW-HI SEQ_129408, 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: 56070
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:18589 original size:33 final size:33
Alignment explanation
Indices: 18545--18610 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
18535 ATCATTAAAG
*
18545 TCTTATTTATCAAACACTACATCTTATCTGTCA
1 TCTTATATATCAAACACTACATCTTATCTGTCA
*
18578 TCTTATATATCAAGCACTACATCTTATCTGTCA
1 TCTTATATATCAAACACTACATCTTATCTGTCA
18611 AGTACTACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (33 bp):
TCTTATATATCAAACACTACATCTTATCTGTCA
Found at i:18602 original size:21 final size:21
Alignment explanation
Indices: 18576--18618 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18566 TCTTATCTGT
18576 CATCTTATATATCAAGCACTA
1 CATCTTATATATCAAGCACTA
* * *
18597 CATCTTATCTGTCAAGTACTA
1 CATCTTATATATCAAGCACTA
18618 C
1 C
18619 TTGCCTAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.35
Consensus pattern (21 bp):
CATCTTATATATCAAGCACTA
Found at i:21761 original size:31 final size:30
Alignment explanation
Indices: 21701--21783 Score: 78
Period size: 30 Copynumber: 2.7 Consensus size: 30
21691 AAAAGAGGAA
* *
21701 AAGCGTTGGACAAAAATATAATCTCAAAAAAT
1 AAGC-TTGAACAAAAATATAAGCTC-AAAAAT
** * *
21733 AATTTTGAACAAAAATATAGGCTTAAAAAT
1 AAGCTTGAACAAAAATATAAGCTCAAAAAT
*
21763 GAGCTTGAACAAAAATA-AAGC
1 AAGCTTGAACAAAAATATAAGC
21784 CTTTTTTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
29 3 0.07
30 20 0.49
31 16 0.39
32 2 0.05
ACGTcount: A:0.53, C:0.11, G:0.13, T:0.23
Consensus pattern (30 bp):
AAGCTTGAACAAAAATATAAGCTCAAAAAT
Found at i:22477 original size:15 final size:15
Alignment explanation
Indices: 22457--22486 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
22447 CAAGAATGGC
22457 AGTCTGGCTATGGTA
1 AGTCTGGCTATGGTA
22472 AGTCTGGCTATGGTA
1 AGTCTGGCTATGGTA
22487 CATGGGGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.33, T:0.33
Consensus pattern (15 bp):
AGTCTGGCTATGGTA
Found at i:23849 original size:25 final size:26
Alignment explanation
Indices: 23802--23852 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
23792 AGATATTTTT
23802 ATTCCTTTTCACAAAATATGCCTAGA
1 ATTCCTTTTCACAAAATATGCCTAGA
23828 ATTCCTTTTCAC-AAATATGCCTAGA
1 ATTCCTTTTCACAAAATATGCCTAGA
23853 GACTATCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (26 bp):
ATTCCTTTTCACAAAATATGCCTAGA
Found at i:28594 original size:22 final size:22
Alignment explanation
Indices: 28552--28592 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
28542 TCAGAGATCT
28552 CACTAAATGTAATCCCCTTTAC
1 CACTAAATGTAATCCCCTTTAC
28574 CACTAAATGTAA-CCCCTTT
1 CACTAAATGTAATCCCCTTT
28593 TATCCGGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32
Consensus pattern (22 bp):
CACTAAATGTAATCCCCTTTAC
Found at i:28725 original size:19 final size:19
Alignment explanation
Indices: 28683--28729 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
28673 ATTTATAAAA
*
28683 ATAATTATAAATATAAATAT
1 ATAATTA-AAATATAAATAC
28703 ATAATTAAAATA-AAATAGC
1 ATAATTAAAATATAAATA-C
28722 ATAATTAA
1 ATAATTAA
28730 TATCTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 5 0.20
19 13 0.52
20 7 0.28
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAATTAAAATATAAATAC
Found at i:48344 original size:57 final size:50
Alignment explanation
Indices: 48242--48354 Score: 118
Period size: 50 Copynumber: 2.1 Consensus size: 50
48232 TTTAAAGTCC
* * *
48242 TAAAAATACATATGCAATATTAATATTTAAAAAGATATTAACGTTTAATT
1 TAAAAATACATATGCAATATTAATATTAAAAAAGAAATAAACGTTTAATT
*
48292 TAAAAATACATATGCAATATTTAATAGTTGAAAAAAAGGAAAATAATACGTTTAGTT
1 TAAAAATACATATGCAATA-TTAATA-TT--AAAAAA-G-AAATAA-ACGTTTAATT
*
48349 CAAAAA
1 TAAAAA
48355 AAGTTTATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
50 19 0.37
51 6 0.12
52 2 0.04
54 5 0.10
55 1 0.02
56 4 0.08
57 14 0.27
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (50 bp):
TAAAAATACATATGCAATATTAATATTAAAAAAGAAATAAACGTTTAATT
Found at i:51098 original size:18 final size:18
Alignment explanation
Indices: 51064--51102 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
51054 TGATTTTAAA
*
51064 TAATATTAAAATTATATT
1 TAATATTAAAATAATATT
51082 TAATATT-AAATCAATATT
1 TAATATTAAAAT-AATATT
51100 TAA
1 TAA
51103 ATGTTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATTAAAATAATATT
Done.