Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009127.1 Kokia drynarioides strain JFW-HI SEQ_123831, 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: 8252
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:970 original size:22 final size:22
Alignment explanation
Indices: 944--992 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
934 GTTGATCTGA
* *
944 AATTTCGATTTTGATGAGTTGG
1 AATTTCGATTTTGATGAGCTAG
* *
966 AATTTCGGTTTTGGTGAGCTAG
1 AATTTCGATTTTGATGAGCTAG
988 AATTT
1 AATTT
993 GGGTGGTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.06, G:0.27, T:0.45
Consensus pattern (22 bp):
AATTTCGATTTTGATGAGCTAG
Found at i:1184 original size:83 final size:84
Alignment explanation
Indices: 1089--1391 Score: 484
Period size: 84 Copynumber: 3.6 Consensus size: 84
1079 TTTAAAATTG
*
1089 GATAAAAATTGTAATATATTAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTG
1 GATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTG
1154 TCAAATCAACACATT-TTT
66 TCAAATCAACACATTATTT
* *
1172 GATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTAGTAAATAATGTGTTG
1 GATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTG
1237 TCAAATCAACACATTATTT
66 TCAAATCAACACATTATTT
* *
1256 GATAAAAATTGTAATATAATAATAATTTTTAATTTAAATATTAAAATTT-GATAAATAATGTATT
1 GATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAG-TAAATAATGTATT
1320 GTCAAATCAACACATTATTT
65 GTCAAATCAACACATTATTT
* *
1340 GATATAAATTGAAATATAATAATAATCTTTTTTATTTAAATAATGTTAAATT
1 GATAAAAATTGTAATATAATAATAA--TTTTTTATTTAAAT-AT-TTAAATT
1392 AATTTTAAAT
Statistics
Matches: 204, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
83 78 0.38
84 105 0.51
86 13 0.06
87 2 0.01
88 6 0.03
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (84 bp):
GATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTG
TCAAATCAACACATTATTT
Found at i:1517 original size:11 final size:12
Alignment explanation
Indices: 1495--1543 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
1485 AAACATATAC
1495 ATTAATTTTCAA
1 ATTAATTTTCAA
*
1507 ATTAATTTCAACTTAA
1 ATTAATTT----TCAA
1523 ATTAATTTTCAA
1 ATTAATTTTCAA
1535 ATTAATTTT
1 ATTAATTTT
1544 TACACAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 20 0.65
16 11 0.35
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTAATTTTCAA
Found at i:1541 original size:16 final size:16
Alignment explanation
Indices: 1505--1539 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1495 ATTAATTTTC
*
1505 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
1521 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
1538 AA
1 AA
1540 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:1552 original size:28 final size:28
Alignment explanation
Indices: 1495--1552 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
1485 AAACATATAC
**
1495 ATTAATTTTCAAATTAATTTCAACTTAA
1 ATTAATTTTCAAATTAATTTCAACACAA
**
1523 ATTAATTTTCAAATTAATTTTTACACAA
1 ATTAATTTTCAAATTAATTTCAACACAA
1551 AT
1 AT
1553 ATTCTTCATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTAATTTTCAAATTAATTTCAACACAA
Found at i:5185 original size:17 final size:17
Alignment explanation
Indices: 5134--5185 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
5124 AATTTTTTAT
5134 TTGATATTTTTAGATTA
1 TTGATATTTTTAGATTA
*
5151 TT--T-TTTTT-GATAA
1 TTGATATTTTTAGATTA
*
5164 GTGATATTTTTAGATTA
1 TTGATATTTTTAGATTA
5181 TTGAT
1 TTGAT
5186 TCATATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
13 5 0.19
14 5 0.19
15 2 0.07
16 5 0.19
17 10 0.37
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (17 bp):
TTGATATTTTTAGATTA
Found at i:7157 original size:3 final size:3
Alignment explanation
Indices: 7151--7178 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
7141 GGACTTGACC
7151 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
7179 CCTCCTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Done.