Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007735.1 Kokia drynarioides strain JFW-HI SEQ_122368, 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: 8785
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:369 original size:47 final size:47
Alignment explanation
Indices: 300--395 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
290 AATTTAAAAT
*
300 TATCCGAATTCAAATTTTATATGAAATAATGAACACCATAATTATCA
1 TATCCAAATTCAAATTTTATATGAAATAATGAACACCATAATTATCA
* *
347 TATCCAAATTCAAATTTTATATGAGATAATGAACACCATATTTATCA
1 TATCCAAATTCAAATTTTATATGAAATAATGAACACCATAATTATCA
394 TA
1 TA
396 GTTTGACATG
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:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (47 bp):
TATCCAAATTCAAATTTTATATGAAATAATGAACACCATAATTATCA
Found at i:2463 original size:14 final size:16
Alignment explanation
Indices: 2444--2476 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2434 TTTTAGACTA
2444 AAATA-TTAAAA-AAT
1 AAATATTTAAAATAAT
2458 AAATATTTAAAATAAT
1 AAATATTTAAAATAAT
2474 AAA
1 AAA
2477 GAATTCAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 6 0.35
16 6 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATATTTAAAATAAT
Found at i:4643 original size:161 final size:161
Alignment explanation
Indices: 4368--4826 Score: 618
Period size: 161 Copynumber: 2.9 Consensus size: 161
4358 AGGGAGTTCG
* ** * *
4368 TCATCATGATGTGACATCA-CGACTTGGTCTCGTTGTGATGACAGGATTCCTCGCCACGCTATTG
1 TCATCATGATGTGACAT-ATTGACTTGGTCTCGTTGTGATGACAGGATTCCTCATCACGCCATTT
* * ** * *
4432 CTTGAAGTTTAGAGCTCGTCATGAC-AACAATTGCCCGACATCGCGACATGGACTTTGTTTTGGG
65 CTTGAAGTCTAGAGCTCGTCGTGACGAAC-ATCACCAGACATTGCGACATGGACTTTGTTTTGGG
4496 TACATTTTAGAAATCACTACGTGATAAAGCTCC
129 TACATTTTAGAAATCACTACGTGATAAAGCTCC
* *
4529 TCATCACGATGTGACATATTGACTTGGTCTTGTTGTGATGACAGGATTCCTCATCACGCCATTTC
1 TCATCATGATGTGACATATTGACTTGGTCTCGTTGTGATGACAGGATTCCTCATCACGCCATTTC
* * * * *
4594 TTGAAGTCTAGAGCTCGTTGTGACGATCATCACTAGACATTGTGACATGGACTTTGTTTTAGGTA
66 TTGAAGTCTAGAGCTCGTCGTGACGAACATCACCAGACATTGCGACATGGACTTTGTTTTGGGTA
*
4659 CATTTTAGAAATCACTACGTGATGAAGCTCC
131 CATTTTAGAAATCACTACGTGATAAAGCTCC
* *
4690 TCATCGTGATGTGACATATTGATTTGGTCTCGTTGTGATGACAGGATTCCTCATCACGCCATTTC
1 TCATCATGATGTGACATATTGACTTGGTCTCGTTGTGATGACAGGATTCCTCATCACGCCATTTC
* * * * * * *
4755 CTGAAGTCCAGAGATCATCGTGACGACCATCACCCA-ACATTGCGACATGGACTCTGTTTTGGAT
66 TTGAAGTCTAGAGCTCGTCGTGACGAACATCA-CCAGACATTGCGACATGGACTTTGTTTTGGGT
4819 ACATTTTA
130 ACATTTTA
4827 AACCATTTGA
Statistics
Matches: 261, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
160 1 0.00
161 256 0.98
162 4 0.02
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (161 bp):
TCATCATGATGTGACATATTGACTTGGTCTCGTTGTGATGACAGGATTCCTCATCACGCCATTTC
TTGAAGTCTAGAGCTCGTCGTGACGAACATCACCAGACATTGCGACATGGACTTTGTTTTGGGTA
CATTTTAGAAATCACTACGTGATAAAGCTCC
Found at i:6333 original size:14 final size:14
Alignment explanation
Indices: 6314--6340 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6304 ACTTCTTTTA
6314 ATAATTAATTAATC
1 ATAATTAATTAATC
6328 ATAATTAATTAAT
1 ATAATTAATTAAT
6341 TAAATCTTAA
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:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAATTAATTAATC
Found at i:6334 original size:10 final size:9
Alignment explanation
Indices: 6315--6360 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 9
6305 CTTCTTTTAA
6315 TAAT-TAAT
1 TAATCTAAT
6323 TAATCATAAT
1 TAATC-TAAT
6333 TAAT-TAAT
1 TAATCTAAT
6341 TAAATCTTAAT
1 T-AATC-TAAT
6352 TAATCTAAT
1 TAATCTAAT
6361 GTTAAGCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 9 0.27
9 7 0.21
10 12 0.36
11 5 0.15
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (9 bp):
TAATCTAAT
Found at i:6375 original size:10 final size:10
Alignment explanation
Indices: 6318--6375 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
6308 CTTTTAATAA
6318 TTAATTAATC
1 TTAATTAATC
*
6328 ATAATTAA--
1 TTAATTAATC
6336 TTAATTAAATC
1 TTAATT-AATC
6347 TTAATTAATC
1 TTAATTAATC
*
6357 -TAATGTTAAGC
1 TTAA--TTAATC
6368 TTAATTAA
1 TTAATTAA
6376 AAAAGTTAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
8 5 0.13
9 5 0.13
10 15 0.38
11 11 0.28
12 3 0.08
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (10 bp):
TTAATTAATC
Found at i:7953 original size:22 final size:22
Alignment explanation
Indices: 7925--7968 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
7915 TATACAGTTT
*
7925 CAATTTTCAAAAATATCAGAGG
1 CAATTTTAAAAAATATCAGAGG
7947 CAATTTTAAAAAATATCAGAGG
1 CAATTTTAAAAAATATCAGAGG
7969 ATTTTTCTTA
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:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (22 bp):
CAATTTTAAAAAATATCAGAGG
Done.