Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011318.1 Kokia drynarioides strain JFW-HI SEQ_126298, 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: 17497
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:1262 original size:15 final size:15
Alignment explanation
Indices: 1218--1264 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
1208 AAAAAGTTAT
1218 TTTAGTGTTTTATTTAA
1 TTTA-TGTTTT-TTTAA
*
1235 TTT-TTTGTTTTTTAA
1 TTTATGT-TTTTTTAA
1250 TTTATGTTTTTTTAA
1 TTTATGTTTTTTTAA
1265 CAAATCACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 18 0.69
16 5 0.19
17 3 0.12
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (15 bp):
TTTATGTTTTTTTAA
Found at i:3829 original size:2 final size:2
Alignment explanation
Indices: 3822--3846 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3812 ATCAGACTAG
3822 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3847 AAGGGGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10247 original size:44 final size:44
Alignment explanation
Indices: 10180--10272 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
10170 TTGTCATTTT
* * *
10180 GGCTTGCAACCACTCGATCTTGCATTTAGACTGTCCGCCGCTTC
1 GGCTTGCAACCACTCGATCTTGCATTTAGACCGTCCGCCACCTC
* * *
10224 GGCTTGCACCCACTCGGGT-TTGCATTTAGACCGTCTGCCACCTC
1 GGCTTGCAACCACTC-GATCTTGCATTTAGACCGTCCGCCACCTC
10268 GGCTT
1 GGCTT
10273 ACAATTCGAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 40 0.95
45 2 0.05
ACGTcount: A:0.14, C:0.34, G:0.23, T:0.29
Consensus pattern (44 bp):
GGCTTGCAACCACTCGATCTTGCATTTAGACCGTCCGCCACCTC
Found at i:10334 original size:29 final size:30
Alignment explanation
Indices: 10292--10354 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
10282 CAGGCTCACA
* * *
10292 CTTTGACAGACTCGTAATTT-GCTTGCTGT
1 CTTTAACAGACTCGCAATTTGGCTTACTGT
* *
10321 CTTTAACAGGCTCGCACTTTGGCTTACTGT
1 CTTTAACAGACTCGCAATTTGGCTTACTGT
10351 CTTT
1 CTTT
10355 GACACTGTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (30 bp):
CTTTAACAGACTCGCAATTTGGCTTACTGT
Found at i:10373 original size:42 final size:42
Alignment explanation
Indices: 10317--10398 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
10307 AATTTGCTTG
*
10317 CTGTCTTTAACAGGCTCGCACTTTGGCTTACTGTCTTTGACA
1 CTGTCTTTAACAGGCTCGCACTTTGGCTTACTATCTTTGACA
*
10359 CTGTCTTTAACAGGCTCGCTCTTTGGCTTACTATCTTTGA
1 CTGTCTTTAACAGGCTCGCACTTTGGCTTACTATCTTTGA
10399 TAGGCTTGCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (42 bp):
CTGTCTTTAACAGGCTCGCACTTTGGCTTACTATCTTTGACA
Found at i:10404 original size:30 final size:30
Alignment explanation
Indices: 10370--10426 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
10360 TGTCTTTAAC
* *
10370 AGGCTCGCTCTTTGGCTTACTATCTTTGAT
1 AGGCTCGCGCTTTAGCTTACTATCTTTGAT
* *
10400 AGGCTTGCGCTTTAGCTTACTGTCTTT
1 AGGCTCGCGCTTTAGCTTACTATCTTT
10427 AACACGCTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (30 bp):
AGGCTCGCGCTTTAGCTTACTATCTTTGAT
Found at i:11539 original size:44 final size:44
Alignment explanation
Indices: 11449--11544 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
11439 TTGCCATTTT
** * * *
11449 GGCTTGCACCCACTCGATCTTGCATTTAGACTGTCCGTCGCTTC
1 GGCTTGCACCCACTCGATCTTGCATTTAGACCATCCGCCACCTC
*
11493 GGCTTGCACCCACTCGGGT-TTGCATTTAGACCATCCGCCACCTC
1 GGCTTGCACCCACTC-GATCTTGCATTTAGACCATCCGCCACCTC
11537 GGCTTGCA
1 GGCTTGCA
11545 ATTCGACGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 43 0.96
45 2 0.04
ACGTcount: A:0.15, C:0.35, G:0.22, T:0.28
Consensus pattern (44 bp):
GGCTTGCACCCACTCGATCTTGCATTTAGACCATCCGCCACCTC
Found at i:11622 original size:30 final size:30
Alignment explanation
Indices: 11581--11729 Score: 199
Period size: 30 Copynumber: 5.0 Consensus size: 30
11571 CTCGTAATTT
* * *
11581 GCTTGCTGTCTTCAATAGGCTCGCACTTTG
1 GCTTACTGTCTTTAACAGGCTCGCACTTTG
* *
11611 GCTTACTGTCTTTGACAAGCTCGCACTTTG
1 GCTTACTGTCTTTAACAGGCTCGCACTTTG
* **
11641 GCTTACTATCTTTAACAGGCTCGCTTTTTG
1 GCTTACTGTCTTTAACAGGCTCGCACTTTG
* *
11671 GCTTACTGTCTTTGACAGGCTCGCACTTTA
1 GCTTACTGTCTTTAACAGGCTCGCACTTTG
*
11701 GCTTACTGTCTTTAACAGGCTCACACTTT
1 GCTTACTGTCTTTAACAGGCTCGCACTTT
11730 TGATGGCTCG
Statistics
Matches: 102, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 102 1.00
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (30 bp):
GCTTACTGTCTTTAACAGGCTCGCACTTTG
Found at i:11754 original size:16 final size:16
Alignment explanation
Indices: 11735--11789 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
11725 ACTTTTGATG
11735 GCTCGCACCTTGTTGA
1 GCTCGCACCTTGTTGA
* *
11751 GCTCGCATTCTTTTTGCTGA
1 GCTCGCA--C--CTTGTTGA
11771 GCTCGCACCTTGTTGA
1 GCTCGCACCTTGTTGA
11787 GCT
1 GCT
11790 TACAGGTCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 16 0.52
18 2 0.06
20 13 0.42
ACGTcount: A:0.11, C:0.29, G:0.24, T:0.36
Consensus pattern (16 bp):
GCTCGCACCTTGTTGA
Found at i:12923 original size:30 final size:30
Alignment explanation
Indices: 12887--12999 Score: 172
Period size: 30 Copynumber: 3.8 Consensus size: 30
12877 ATTTGCTTGT
*
12887 TGTCTTTAACAGGCTCGCACTTTGGCTTAC
1 TGTCTTTAACAGGCTCACACTTTGGCTTAC
*
12917 TGTCTTTGACAGGCTCACACTTTGGCTTAC
1 TGTCTTTAACAGGCTCACACTTTGGCTTAC
* *
12947 TGTCTTTGACAGGCTCACACTTTAGCTTAC
1 TGTCTTTAACAGGCTCACACTTTGGCTTAC
* *
12977 TATCTTTAACAGGCTCGCACTTT
1 TGTCTTTAACAGGCTCACACTTT
13000 TGATGGCTCG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.37
Consensus pattern (30 bp):
TGTCTTTAACAGGCTCACACTTTGGCTTAC
Found at i:12959 original size:60 final size:59
Alignment explanation
Indices: 12861--12999 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 59
12851 CAGGCTCACA
* * * ** * * *
12861 CTTTGACAGACTCATAATTTGCTTGTTGTCTTTAACAGGCTCGCACTTTGGCTTACTGT
1 CTTTGACAGGCTCACACTTTGCTTACTGTCTTTAACAGGCTCACACTTTAGCTTACTAT
*
12920 CTTTGACAGGCTCACACTTTGGCTTACTGTCTTTGACAGGCTCACACTTTAGCTTACTAT
1 CTTTGACAGGCTCACACTTT-GCTTACTGTCTTTAACAGGCTCACACTTTAGCTTACTAT
* *
12980 CTTTAACAGGCTCGCACTTT
1 CTTTGACAGGCTCACACTTT
13000 TGATGGCTCG
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 17 0.25
60 51 0.75
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (59 bp):
CTTTGACAGGCTCACACTTTGCTTACTGTCTTTAACAGGCTCACACTTTAGCTTACTAT
Found at i:13024 original size:16 final size:16
Alignment explanation
Indices: 13005--13059 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
12995 ACTTTTGATG
13005 GCTCGCACCTTGTTGA
1 GCTCGCACCTTGTTGA
* *
13021 GCTCGCATTCTTTTTGCTGA
1 GCTCGCA--C--CTTGTTGA
13041 GCTCGCACCTTGTTGA
1 GCTCGCACCTTGTTGA
13057 GCT
1 GCT
13060 TACAGCTCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 16 0.52
18 2 0.06
20 13 0.42
ACGTcount: A:0.11, C:0.29, G:0.24, T:0.36
Consensus pattern (16 bp):
GCTCGCACCTTGTTGA
Done.