Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012132.1 Kokia drynarioides strain JFW-HI SEQ_127131, 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: 13575
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Found at i:35 original size:16 final size:16
Alignment explanation
Indices: 14--44 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4 ATTAAATAGT
*
14 TATTATTATTATTAAC
1 TATTATTACTATTAAC
30 TATTATTACTATTAA
1 TATTATTACTATTAA
45 TGTTACTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTATTACTATTAAC
Found at i:2396 original size:18 final size:18
Alignment explanation
Indices: 2350--2396 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
2340 TAAAATGTCA
* *
2350 AAAC-TAAAAACCAAATC
1 AAACATAAAAATCAAACC
* *
2367 AAATATATAAATCAAACC
1 AAACATAAAAATCAAACC
2385 AAACATAAAAAT
1 AAACATAAAAAT
2397 AGATTGAACT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (18 bp):
AAACATAAAAATCAAACC
Found at i:7333 original size:14 final size:13
Alignment explanation
Indices: 7314--7370 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
7304 ATCCAAAGAG
7314 TTAAATTTAAAAA
1 TTAAATTTAAAAA
*
7327 TTGAAATTAAAAAA
1 TT-AAATTTAAAAA
7341 TTAAAAGTTTTAAAAA
1 TT-AAA--TTTAAAAA
* *
7357 GTAAAGTTAAAAA
1 TTAAATTTAAAAA
7370 T
1 T
7371 ATTTTAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 9 0.26
14 15 0.43
15 3 0.09
16 8 0.23
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (13 bp):
TTAAATTTAAAAA
Found at i:7386 original size:31 final size:28
Alignment explanation
Indices: 7316--7388 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 28
7306 CCAAAGAGTT
*
7316 AAATTTAAAAATTGAAATTAAAAAATTA
1 AAATTTAAAAAGTGAAATTAAAAAATTA
7344 AAAGTTTTAAAAAGT-AAAGTTAAAAATATTTTA
1 AAA--TTTAAAAAGTGAAA-TTAAAAA-A--TTA
7377 AAATTTAAAAAG
1 AAATTTAAAAAG
7389 AATTTTTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
28 3 0.08
29 3 0.08
30 16 0.42
31 10 0.26
33 6 0.16
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (28 bp):
AAATTTAAAAAGTGAAATTAAAAAATTA
Found at i:8999 original size:17 final size:17
Alignment explanation
Indices: 8977--9009 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
8967 TTTTTATAAT
8977 ATTTAATAATT-TTTAGA
1 ATTTAA-AATTATTTAGA
8994 ATTTAAAATTATTTAG
1 ATTTAAAATTATTTAG
9010 TTATGTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
ATTTAAAATTATTTAGA
Found at i:9830 original size:62 final size:61
Alignment explanation
Indices: 9673--10059 Score: 484
Period size: 61 Copynumber: 6.4 Consensus size: 61
9663 AATTTGGGTT
* * *
9673 TTGGCCATGCAATGGCCGACACCCTCTTTTTCAGATAAAAAAAATTCAAATTTTTTTTGTG
1 TTGGCCATGCAATGGCCGACACCCTCTTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTG
*
9734 TCGGCCATGCAATGGCCGACACCCTCTTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTG
1 TTGGCCATGCAATGGCCGACACCCTCTTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTG
* * * *
9795 TAGGCCATGCAATGGCGGACACCCTCTTTTCTCAGATAAAAAATTTTCAAAATTTTTTAGTG
1 TTGGCCATGCAATGGCCGACACCCTCTTTT-TCAGATAAAAAAATTTCAAAATTTTTTGGTG
* * * *
9857 TTGACCATACAATGGTCGACACCCCCTTTTCTCAGAT-AAAAAATTTC-AAATTTTTTGGTG
1 TTGGCCATGCAATGGCCGACACCCTCTTTT-TCAGATAAAAAAATTTCAAAATTTTTTGGTG
*
9917 TTGGCCATGCAATGGCCGACA-CCTCCTTTTTCAGATAAAAAAATTTCAAAATTTTTTGATG
1 TTGGCCATGCAATGGCCGACACCCT-CTTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTG
** * *
9978 TTGGCCATGCAATGATCGACACTCTCTTTTT-ATTTGGT-AAAAAA-TT--AAATTTTTTGGTG
1 TTGGCCATGCAATGGCCGACACCCTCTTTTTCA---GATAAAAAAATTTCAAAATTTTTTGGTG
* * *
10037 TTGGTCATGTAATAGCCGACACC
1 TTGGCCATGCAATGGCCGACACC
10060 AACTTCTCCT
Statistics
Matches: 286, Mismatches: 32, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
59 37 0.13
60 46 0.16
61 133 0.47
62 68 0.24
63 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (61 bp):
TTGGCCATGCAATGGCCGACACCCTCTTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTG
Found at i:11928 original size:83 final size:84
Alignment explanation
Indices: 11790--12012 Score: 317
Period size: 83 Copynumber: 2.6 Consensus size: 84
11780 TACATTTAAA
*
11790 ATTAA-TTTAACATTATTTAAATAAAAAATATTATTATTATATTACAATTTATATCAAAT-ATCG
1 ATTAATTTTAA-A-TATTTAAATAAAAAA-A-TATTATTATATTACAATTTTTATCAAATAAT-G
*
11853 TGTTCATTTGATAATACATTATTT
61 TGTTCATTTGACAATACATTATTT
*
11877 ATTAATTTTAAATATTTAAAT-AAAAAATATTATTATATTACAATTTTTATCAAATAATGTGTTG
1 ATTAATTTTAAATATTTAAATAAAAAAATATTATTATATTACAATTTTTATCAAATAATGTGTTC
11941 ATTTGACAATACATTATTT
66 ATTTGACAATACATTATTT
* * * *
11960 ATTAATTTTAAATATTTAAATCAACAATTATTATTATATTATAATTTTTATCA
1 ATTAATTTTAAATATTTAAATAAAAAAATATTATTATATTACAATTTTTATCA
12013 TATTTTAAAT
Statistics
Matches: 127, Mismatches: 6, Indels: 9
0.89 0.04 0.06
Matches are distributed among these distances:
83 71 0.56
84 31 0.24
85 5 0.04
86 9 0.07
87 6 0.05
88 5 0.04
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (84 bp):
ATTAATTTTAAATATTTAAATAAAAAAATATTATTATATTACAATTTTTATCAAATAATGTGTTC
ATTTGACAATACATTATTT
Found at i:12164 original size:22 final size:22
Alignment explanation
Indices: 12114--12168 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
12104 ACCCAATTTT
* *
12114 CAGCTCACCTAAACCGATATTC
1 CAGCTCACCAAAACCGAAATTC
* * *
12136 TAACTCAGCAAAACCGAAATTC
1 CAGCTCACCAAAACCGAAATTC
12158 CAGCTCACCAA
1 CAGCTCACCAA
12169 CACCTCAAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.35, G:0.09, T:0.18
Consensus pattern (22 bp):
CAGCTCACCAAAACCGAAATTC
Done.