Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011845.1 Kokia drynarioides strain JFW-HI SEQ_126841, 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: 11793
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1293 original size:93 final size:92
Alignment explanation
Indices: 1175--1450 Score: 426
Period size: 93 Copynumber: 3.0 Consensus size: 92
1165 ATCATGGTCG
* *
1175 GCAGAAGAAATCATTTCATAAGCAACCAGGCCCTCACCACTGGGCTCTGTTTCTTTAGCTTGCAT
1 GCAGAAGAAATCATTTCAGAAGCAACCTGGCCCTCACCACTGGGCTC-GTTTCTTTAGCTTGCAT
*
1240 AAAATGTTCGGCATGAGTTGTAACATCT
65 AAAATGTTCAGCATGAGTTGTAACATCT
* *
1268 GCAGAAGAAATCATTTGAGAAGCAACCTGGCCCTCACCACTGGGCTCAGCTTCTTTAGCTTGCAT
1 GCAGAAGAAATCATTTCAGAAGCAACCTGGCCCTCACCACTGGGCTC-GTTTCTTTAGCTTGCAT
1333 AAAATGTTCAGCATGAGTTGTAACATCT
65 AAAATGTTCAGCATGAGTTGTAACATCT
* ** * *
1361 GCAGAAGAAATCATTTTAGAAGCAACCTGGGACTCAACACTGGCCTCGATTTCTTTAGCTTGCAT
1 GCAGAAGAAATCATTTCAGAAGCAACCTGGCCCTCACCACTGGGCTCG-TTTCTTTAGCTTGCAT
*
1426 AAAATGTTCCGCATGAGTTGTAACA
65 AAAATGTTCAGCATGAGTTGTAACA
1451 CCACCATGTA
Statistics
Matches: 169, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
92 1 0.01
93 168 0.99
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (92 bp):
GCAGAAGAAATCATTTCAGAAGCAACCTGGCCCTCACCACTGGGCTCGTTTCTTTAGCTTGCATA
AAATGTTCAGCATGAGTTGTAACATCT
Found at i:3852 original size:22 final size:22
Alignment explanation
Indices: 3826--3869 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3816 TAAGAAAAAT
*
3826 CCTCTGATATTTTTTAAAATTG
1 CCTCTGATATTTTTGAAAATTG
3848 CCTCTGATATTTTTGAAAATTG
1 CCTCTGATATTTTTGAAAATTG
3870 AAACTGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (22 bp):
CCTCTGATATTTTTGAAAATTG
Found at i:4527 original size:10 final size:10
Alignment explanation
Indices: 4487--4540 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
4477 AACATAAAAG
4487 AAATGTTATAA
1 AAAT-TTATAA
* *
4498 AAATTAATTA
1 AAATTTATAA
*
4508 AAATTCATAA
1 AAATTTATAA
*
4518 AATTTTATAA
1 AAATTTATAA
*
4528 AAAATTATAA
1 AAATTTATAA
4538 AAA
1 AAA
4541 ACCATAAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
10 31 0.89
11 4 0.11
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (10 bp):
AAATTTATAA
Found at i:4547 original size:30 final size:30
Alignment explanation
Indices: 4487--4548 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
4477 AACATAAAAG
* **
4487 AAATGTTATAAAAATTAATTAAAATTCATA
1 AAATGTTATAAAAATTAATAAAAAACCATA
*
4517 AAATTTTATAAAAAATT-ATAAAAAACCATA
1 AAATGTTAT-AAAAATTAATAAAAAACCATA
4547 AA
1 AA
4549 TTGATGATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (30 bp):
AAATGTTATAAAAATTAATAAAAAACCATA
Found at i:5450 original size:10 final size:10
Alignment explanation
Indices: 5419--5476 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
5409 ACTAACTTTT
*
5419 TTAATTAAGC
1 TTAATTAAGA
5429 TTAACATT-AGA
1 TT-A-ATTAAGA
5440 TTAATTAAGA
1 TTAATTAAGA
5450 TTTAATT-A-A
1 -TTAATTAAGA
*
5459 TTAATTATGA
1 TTAATTAAGA
5469 TTAATTAA
1 TTAATTAA
5477 TTATTAAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
8 6 0.15
9 4 0.10
10 15 0.38
11 11 0.28
12 3 0.08
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (10 bp):
TTAATTAAGA
Found at i:5473 original size:14 final size:14
Alignment explanation
Indices: 5454--5480 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5444 TTAAGATTTA
5454 ATTAATTAATTATG
1 ATTAATTAATTATG
5468 ATTAATTAATTAT
1 ATTAATTAATTAT
5481 TAAAAGAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
ATTAATTAATTATG
Found at i:7233 original size:161 final size:159
Alignment explanation
Indices: 6968--7426 Score: 607
Period size: 161 Copynumber: 2.8 Consensus size: 159
6958 TCAAATGGTT
* * * *
6968 TAAAATGTATCCAAAACAGAGTCCATGTCGCAATGT-TGGGTGATGGTCGTCACGATGATCTCTG
1 TAAAATGTA-CCAAAACAAAGTCCATGTCGCAATGTCT-GGTGAT-GTCGTCACGACGAGCTCTA
* *
7032 GACTTCAGGAAATGGCGTGATGAGGAATCCTGTCATCACAACGAGACCAAATCAATATGTCACAT
63 GACTTCAAGAAATGGCGTGATGAGGAATCCTGTCATCACAACGAGACCAAGTCAATATGTCACAT
*
7097 CACGATGAGGAGCTTCATCACGTAGTGATTTC
128 CATGATGAGGAGCTTCATCACGTAGTGATTTC
* * *
7129 TAAAATGTACCTAAAACAAAGTCCATGTCACAATGTCTAGTGATGATCGTCACAACGAGCTCTAG
1 TAAAATGTACC-AAAACAAAGTCCATGTCGCAATGTCTGGTGATG-TCGTCACGACGAGCTCTAG
*
7194 ACTTCAAGAAATGGCGTGATGAGGAATCCTGTCATCACAACAAGACCAAGTCAATATGTCACATC
64 ACTTCAAGAAATGGCGTGATGAGGAATCCTGTCATCACAACGAGACCAAGTCAATATGTCACATC
* *
7259 GTGATGAGGAGCTTTATCACGTAGTGATTTC
129 ATGATGAGGAGCTTCATCACGTAGTGATTTC
* * ** * * *
7290 TAAAATGTACCCAAAACAAAGTCCATGTCGCGATGTCGGGCAATTGTTGTCATGACGAGCTCTAA
1 TAAAATGTA-CCAAAACAAAGTCCATGTCGCAATGTCTGGTGA-TGTCGTCACGACGAGCTCTAG
* * ** *
7355 ACTTCAAGCAATAGCGTGGCGAGGAATCCTGTCATCACAACGAGACCAAGTC-GTGATGTCACAT
64 ACTTCAAGAAATGGCGTGATGAGGAATCCTGTCATCACAACGAGACCAAGTCAAT-ATGTCACAT
7419 CATGATGA
128 CATGATGA
7427 CGAACTCCCT
Statistics
Matches: 262, Mismatches: 30, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
160 4 0.02
161 253 0.97
162 5 0.02
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (159 bp):
TAAAATGTACCAAAACAAAGTCCATGTCGCAATGTCTGGTGATGTCGTCACGACGAGCTCTAGAC
TTCAAGAAATGGCGTGATGAGGAATCCTGTCATCACAACGAGACCAAGTCAATATGTCACATCAT
GATGAGGAGCTTCATCACGTAGTGATTTC
Found at i:9347 original size:14 final size:16
Alignment explanation
Indices: 9318--9350 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
9308 GCTTGAATTC
9318 TTTATTATTTTAAATA
1 TTTATTATTTTAAATA
9334 TTTATT-TTTT-AATA
1 TTTATTATTTTAAATA
9348 TTT
1 TTT
9351 TAGTCTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 4 0.24
16 6 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATTATTTTAAATA
Found at i:11468 original size:47 final size:47
Alignment explanation
Indices: 11399--11494 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
11389 CATGTCAAAC
*
11399 TATGATAAATATGGTGTTCATTATCTCATATAAAATTTGAATTTGGA
1 TATGATAAATATGGTGTTCATTATCTCATATAAAATTTGAATTCGGA
* *
11446 TATGATAATTATGGTGTTCATTATTTCATATAAAATTTGAATTCGGA
1 TATGATAAATATGGTGTTCATTATCTCATATAAAATTTGAATTCGGA
11493 TA
1 TA
11495 ATTTTAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (47 bp):
TATGATAAATATGGTGTTCATTATCTCATATAAAATTTGAATTCGGA
Done.