Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014709.1 Kokia drynarioides strain JFW-HI SEQ_129748, 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: 43035
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:933 original size:23 final size:24
Alignment explanation
Indices: 891--945 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
881 ATCACGTTTC
891 GTGCCCTCTGTTATTAGCACTTCAT
1 GTGCCCTCTG-TATTAGCACTTCAT
**
916 GTGCCCTCTG-ATTAGCACTTTGT
1 GTGCCCTCTGTATTAGCACTTCAT
939 GTGCCCT
1 GTGCCCT
946 TTGCTACCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 18 0.64
25 10 0.36
ACGTcount: A:0.13, C:0.29, G:0.20, T:0.38
Consensus pattern (24 bp):
GTGCCCTCTGTATTAGCACTTCAT
Found at i:7251 original size:140 final size:139
Alignment explanation
Indices: 6986--7264 Score: 468
Period size: 140 Copynumber: 2.0 Consensus size: 139
6976 GAGCAACACC
* *
6986 CCCAAGACTCGACCACAACCCTTTCCTCTTAATCCCATTCAGACTTCCATAGATCCCGAAGAAAA
1 CCCAAGACTCGACCACAACCCTTTCCTCTTAATCCCATTCAGACTTCCATAGAACCCGAAAAAAA
* * *
7051 AAACTCAGTCATTAAGATTAGGAAATTTAACTCGTAAATGAACAAACTGAAAGCTATTAATCTCA
66 AAACCCAGTAATTAAGATTAGGAAATTTAACTCATAAATGAACAAACTGAAAGCTATTAATCTCA
*
7116 ACAGCCACT
131 ACAACCACT
* * *
7125 CCCAAGACTCGACCACAACCCTTTCCTCTTAATCCCATTCGGACTTCTATAGAACACGGAAAAAA
1 CCCAAGACTCGACCACAACCCTTTCCTCTTAATCCCATTCAGACTTCCATAGAAC-CCGAAAAAA
7190 AAAACCCAGTAATTAAGATTAGGAAATTTAACTCATAAATGAACAAACTGAAAGCTATTAATCTC
65 AAAACCCAGTAATTAAGATTAGGAAATTTAACTCATAAATGAACAAACTGAAAGCTATTAATCTC
7255 AACAACCACT
130 AACAACCACT
7265 TCGACACAAT
Statistics
Matches: 130, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
139 52 0.40
140 78 0.60
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (139 bp):
CCCAAGACTCGACCACAACCCTTTCCTCTTAATCCCATTCAGACTTCCATAGAACCCGAAAAAAA
AAACCCAGTAATTAAGATTAGGAAATTTAACTCATAAATGAACAAACTGAAAGCTATTAATCTCA
ACAACCACT
Found at i:9819 original size:10 final size:10
Alignment explanation
Indices: 9799--9831 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
9789 CACAATTTAT
9799 TTTTTCT-TC
1 TTTTTCTCTC
9808 TTTTTCTCTC
1 TTTTTCTCTC
*
9818 TTTTTGTCTC
1 TTTTTCTCTC
9828 TTTT
1 TTTT
9832 CATTTTCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:15446 original size:29 final size:29
Alignment explanation
Indices: 15405--15468 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
15395 GATCGTACAT
* *
15405 ATTAA-TCTAAATTCCTGCAAAGATAAGA
1 ATTAATTCTAAATTCCCGCAAAGAAAAGA
*
15433 ATTAATTCTAAATTCCCGCAAAGAAAATA
1 ATTAATTCTAAATTCCCGCAAAGAAAAGA
15462 ATTAATT
1 ATTAATT
15469 AGTACTCTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 5 0.16
29 27 0.84
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (29 bp):
ATTAATTCTAAATTCCCGCAAAGAAAAGA
Found at i:17278 original size:19 final size:19
Alignment explanation
Indices: 17247--17284 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
17237 TTTTNTTTTA
*
17247 CATCTTCCTCATTTTCAAC
1 CATCTTCCTCATTTGCAAC
17266 CATCGTTCC-CATTTGCAAC
1 CATC-TTCCTCATTTGCAAC
17285 AGTTGTAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.21, C:0.37, G:0.05, T:0.37
Consensus pattern (19 bp):
CATCTTCCTCATTTGCAAC
Found at i:22696 original size:42 final size:42
Alignment explanation
Indices: 22648--22745 Score: 160
Period size: 42 Copynumber: 2.3 Consensus size: 42
22638 CATTCTGAGT
*
22648 CATGAGTCTTCCTTTAATCATATTCTCATTCTCATCCCGAGA
1 CATGAGTCTTCCTTTAATCATATTCTCATTCTCATCCCAAGA
** *
22690 CATGAGTCTTCCTTTAATCATATTCTCATTCTCATCTTAAGG
1 CATGAGTCTTCCTTTAATCATATTCTCATTCTCATCCCAAGA
22732 CATGAGTCTTCCTT
1 CATGAGTCTTCCTT
22746 AAATTTATCC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.41
Consensus pattern (42 bp):
CATGAGTCTTCCTTTAATCATATTCTCATTCTCATCCCAAGA
Found at i:29591 original size:7 final size:7
Alignment explanation
Indices: 29581--29607 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
29571 GACAAAATAT
29581 TATTTTC
1 TATTTTC
29588 TATTTTC
1 TATTTTC
29595 TATTTTC
1 TATTTTC
29602 TATTTT
1 TATTTT
29608 TTAAATTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (7 bp):
TATTTTC
Found at i:38875 original size:12 final size:12
Alignment explanation
Indices: 38858--38896 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
38848 GGTTTATCAA
*
38858 AAAATGGGAATG
1 AAAATGGAAATG
38870 AAAATGGAAATG
1 AAAATGGAAATG
38882 AAAAATGAGAAATG
1 -AAAATG-GAAATG
38896 A
1 A
38897 TCTATTTGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 11 0.46
13 7 0.29
14 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (12 bp):
AAAATGGAAATG
Done.