Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013919.1 Kokia drynarioides strain JFW-HI SEQ_128949, 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: 21735
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:907 original size:16 final size:16
Alignment explanation
Indices: 886--935 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
876 TGATGAAGAT
886 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
902 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
917 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
932 ATTA
1 ATTA
936 GTTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:1220 original size:20 final size:21
Alignment explanation
Indices: 1195--1237 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1185 TACTTACTAC
1195 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
1215 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
1236 TA
1 TA
1238 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:1412 original size:12 final size:12
Alignment explanation
Indices: 1395--1420 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1385 AAATTAAAAT
1395 ATTTTAAAATTA
1 ATTTTAAAATTA
1407 ATTTTAAAATTA
1 ATTTTAAAATTA
1419 AT
1 AT
1421 CATACTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:1611 original size:9 final size:9
Alignment explanation
Indices: 1597--1637 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
1587 TTTTTTTTTT
1597 TTCTTCTCC
1 TTCTTCTCC
*
1606 TTCTTCCCC
1 TTCTTCTCC
1615 TTCTTCTCC
1 TTCTTCTCC
1624 TTC-T-TCC
1 TTCTTCTCC
1631 TTCTTCT
1 TTCTTCT
1638 TTCTTTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 6 0.21
8 2 0.07
9 20 0.71
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (9 bp):
TTCTTCTCC
Found at i:1641 original size:4 final size:4
Alignment explanation
Indices: 1634--1684 Score: 77
Period size: 4 Copynumber: 12.8 Consensus size: 4
1624 TTCTTCCTTC
*
1634 TTCT TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT
1682 TTC
1 TTC
1685 AATTTTCGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 3 0.07
4 37 0.86
5 3 0.07
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:2893 original size:19 final size:19
Alignment explanation
Indices: 2866--2903 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2856 TACGCTAATC
*
2866 ATAAGAATATATATTTTAT
1 ATAAAAATATATATTTTAT
2885 ATAAAAATATATATTTTAT
1 ATAAAAATATATATTTTAT
2904 TATTATTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
ATAAAAATATATATTTTAT
Found at i:6434 original size:6 final size:6
Alignment explanation
Indices: 6423--6453 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
6413 AACAAGGGGG
6423 GAACAA GAACAA GAACAA GAACAA GAA-AA GA
1 GAACAA GAACAA GAACAA GAACAA GAACAA GA
6454 GAAAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.68, C:0.13, G:0.19, T:0.00
Consensus pattern (6 bp):
GAACAA
Found at i:8247 original size:13 final size:13
Alignment explanation
Indices: 8229--8256 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8219 CGCGCGACTA
8229 AGACAACAAGTTG
1 AGACAACAAGTTG
8242 AGACAACAAGTTG
1 AGACAACAAGTTG
8255 AG
1 AG
8257 GAGGTTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.25, T:0.14
Consensus pattern (13 bp):
AGACAACAAGTTG
Found at i:20413 original size:8 final size:8
Alignment explanation
Indices: 20377--20421 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
20367 TCAAAAATTG
*
20377 TTATTTTC
1 TTATTTTT
20385 TTATTTTT
1 TTATTTTT
*
20393 GTTTTTATTT
1 -TTATT-TTT
20403 TTATTTTT
1 TTATTTTT
20411 TTATTTTT
1 TTATTTTT
20419 TTA
1 TTA
20422 AGTTGTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 21 0.66
9 8 0.25
10 3 0.09
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.82
Consensus pattern (8 bp):
TTATTTTT
Found at i:20438 original size:26 final size:25
Alignment explanation
Indices: 20372--20438 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
20362 TTTAGTCAAA
20372 AATTGTTATTTTCTTATTTTTGTTTT
1 AATTGTTATTTTCTT-TTTTTGTTTT
* * *
20398 TATTTTTATTTT-TTTATTT-TTTT
1 AATTGTTATTTTCTTTTTTTGTTTT
20421 AAGTTGTTATTTTCTTTT
1 AA-TTGTTATTTTCTTTT
20439 GACTAAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
23 5 0.15
24 13 0.39
25 5 0.15
26 10 0.30
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (25 bp):
AATTGTTATTTTCTTTTTTTGTTTT
Done.