Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009871.1 Kokia drynarioides strain JFW-HI SEQ_124606, 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: 17690
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:1036 original size:23 final size:22
Alignment explanation
Indices: 981--1030 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
971 AAATTTTAGC
* *
981 TTTAA-ATTTTATATTTTAATC
1 TTTAATATATTATATTTTAATA
*
1002 TTTAATATATTATATTTTTATAA
1 TTTAATATATTATATTTTAAT-A
1025 TTTAAT
1 TTTAAT
1031 TAATTACTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.21
22 13 0.54
23 6 0.25
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTAATATATTATATTTTAATA
Found at i:1137 original size:20 final size:21
Alignment explanation
Indices: 1091--1137 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1081 ATAAATTTTA
1091 TTTAA-AAAAAAAAATACTAT
1 TTTAACAAAAAAAAATACTAT
**
1111 TCGAACAAAAAAAAAT-CTAT
1 TTTAACAAAAAAAAATACTAT
1131 TTTAACA
1 TTTAACA
1138 TGATGAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.28
Consensus pattern (21 bp):
TTTAACAAAAAAAAATACTAT
Found at i:3908 original size:18 final size:18
Alignment explanation
Indices: 3885--3919 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3875 AATTTTACCA
*
3885 AAAGGACTAGATTGTGTT
1 AAAGGAATAGATTGTGTT
*
3903 AAAGGAATTGATTGTGT
1 AAAGGAATAGATTGTGT
3920 GATTTAATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (18 bp):
AAAGGAATAGATTGTGTT
Found at i:4262 original size:52 final size:52
Alignment explanation
Indices: 4182--4301 Score: 177
Period size: 52 Copynumber: 2.3 Consensus size: 52
4172 GTAAATGTAA
* * * *
4182 AAGGTCCGATGATTACGTGTCATTGTGAGTATATGGATCCTTTACGAATTAT
1 AAGGTCCGATGACTACGTGTCATCGTGAGTATACGAATCCTTTACGAATTAT
* *
4234 AAGGTCCGATAACTACGTGTCATCGTGAGTATACGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTACGTGTCATCGTGAGTATACGAATCCTTTACGAATTAT
*
4286 AAGGTTCGATGACTAC
1 AAGGTCCGATGACTAC
4302 ATAGATTATA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (52 bp):
AAGGTCCGATGACTACGTGTCATCGTGAGTATACGAATCCTTTACGAATTAT
Found at i:5685 original size:43 final size:42
Alignment explanation
Indices: 5575--5856 Score: 273
Period size: 43 Copynumber: 6.6 Consensus size: 42
5565 TTATGTGAGA
* *
5575 AAACGCCGCTATAAAACATGATCTTTAGCGACGCTTTTCCAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTTCCCAC
* * * *
5617 AAACACCGCTATAAAACATGATCTTTAACGACGCTTTCCTCAT
1 AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTTCC-CAC
* * * *
5660 AAACGCCACTATAGAACATGATCTTTAACGGCGCTTTCTCAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTTCCCAC
* * ***
5702 AAACGTCGCTATAGAACATTATCTTTAGCGGTACTTTACCCAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTT-CCCAC
* * * *
5745 AAACGCCACTATAGAGCATGGTTTTTAGC-A-GCATTTTTCCCAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGACGC---TTTCCCAC
* * * *
5788 AAACACCGCTGTAGAACATGATCTTTAGCGACACTTTTTCCAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGACGC-TTTCCCAC
*
5831 AAACGCC-CTATAAAACATGATCTTTA
1 AAACGCCGCTATAGAACATGATCTTTA
5857 ATGACGTTTT
Statistics
Matches: 197, Mismatches: 36, Indels: 14
0.80 0.15 0.06
Matches are distributed among these distances:
41 1 0.01
42 86 0.44
43 105 0.53
44 4 0.02
45 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (42 bp):
AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTTCCCAC
Found at i:5720 original size:85 final size:85
Alignment explanation
Indices: 5575--5857 Score: 286
Period size: 85 Copynumber: 3.3 Consensus size: 85
5565 TTATGTGAGA
* * * *
5575 AAACGCCGCTATAAAACATGATCTTTAGCGACGCTTT-TCCACAAACACCGCTATAAAACATGAT
1 AAACGCCACTATAAAACATGATCTTTAACGGCGCTTTCT-CACAAACACCGCTATAGAACATGAT
* * *
5639 CTTTAACGACGCTTTCCTCAT
65 CTTTAGCGACACTTTCCTCAC
* ** *
5660 AAACGCCACTATAGAACATGATCTTTAACGGCGCTTTCTCACAAACGTCGCTATAGAACATTATC
1 AAACGCCACTATAAAACATGATCTTTAACGGCGCTTTCTCACAAACACCGCTATAGAACATGATC
**
5725 TTTAGCGGTACTTTACC-CAC
66 TTTAGCGACACTTT-CCTCAC
* * * * * * ** * *
5745 AAACGCCACTATAGAGCATGGTTTTTAGCAGCATTTTTCCCACAAACACCGCTGTAGAACATGAT
1 AAACGCCACTATAAAACATGATCTTTAACGGC-GCTTTCTCACAAACACCGCTATAGAACATGAT
*
5810 CTTTAGCGACACTTT-TTCCAC
65 CTTTAGCGACACTTTCCT-CAC
5831 AAACGCC-CTATAAAACATGATCTTTAA
1 AAACGCCACTATAAAACATGATCTTTAA
5858 TGACGTTTTT
Statistics
Matches: 160, Mismatches: 33, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
85 109 0.68
86 51 0.32
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (85 bp):
AAACGCCACTATAAAACATGATCTTTAACGGCGCTTTCTCACAAACACCGCTATAGAACATGATC
TTTAGCGACACTTTCCTCAC
Found at i:14549 original size:23 final size:21
Alignment explanation
Indices: 14511--14554 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
14501 TGAGTAAATT
14511 ATTTTTTTTTTATATTCTTTTA
1 ATTTTTTTTTTATATT-TTTTA
*
14533 ATTTTTTTTTCTGTATTTTTTA
1 ATTTTTTTTT-TATATTTTTTA
14555 TTCCCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (21 bp):
ATTTTTTTTTTATATTTTTTA
Found at i:14679 original size:18 final size:19
Alignment explanation
Indices: 14639--14681 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
14629 GAGAAGAGAG
*
14639 AAAAATGAATTGAAAGAAA
1 AAAAAGGAATTGAAAGAAA
14658 AAAAAGGAATT-AAA-AAA
1 AAAAAGGAATTGAAAGAAA
14675 TAAAAAG
1 -AAAAAG
14682 ATAAAAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 9 0.41
19 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (19 bp):
AAAAAGGAATTGAAAGAAA
Found at i:15036 original size:19 final size:19
Alignment explanation
Indices: 15014--15050 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
15004 CCACTGTCAT
15014 CCACCATAATCAAATTTGG
1 CCACCATAATCAAATTTGG
*
15033 CCACTATAATCAAATTTG
1 CCACCATAATCAAATTTG
15051 TTATTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (19 bp):
CCACCATAATCAAATTTGG
Found at i:15888 original size:18 final size:18
Alignment explanation
Indices: 15846--15891 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
15836 GATTTTTGGT
* *
15846 TTATTCAAATTATTCGAG
1 TTATTCGAATTATTCAAG
15864 TTATTCGAATTATTCAAG
1 TTATTCGAATTATTCAAG
15882 TTATTCGAAT
1 TTATTCGAAT
15892 AAACTCAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
TTATTCGAATTATTCAAG
Found at i:16493 original size:24 final size:24
Alignment explanation
Indices: 16461--16509 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
16451 ATTCTAAAAG
16461 TTCAACAAATTTAGTCTCAACATT
1 TTCAACAAATTTAGTCTCAACATT
16485 TTCAACAAATTTAGTCTCAACATT
1 TTCAACAAATTTAGTCTCAACATT
16509 T
1 T
16510 ACACATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (24 bp):
TTCAACAAATTTAGTCTCAACATT
Found at i:16677 original size:6 final size:6
Alignment explanation
Indices: 16666--16744 Score: 76
Period size: 6 Copynumber: 13.7 Consensus size: 6
16656 GGCCCAACAG
* * * *
16666 AATTTA AATTT- ATTTTA AGTTTA AATTT- ACTTAA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
16711 -ATTATA AATTTA AGTTTA AATTTA AATTTA AATT
1 AATT-TA AATTTA AATTTA AATTTA AATTTA AATT
16745 AATGTCCAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
4 3 0.05
5 8 0.14
6 45 0.76
7 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:16690 original size:17 final size:17
Alignment explanation
Indices: 16666--16744 Score: 95
Period size: 17 Copynumber: 4.6 Consensus size: 17
16656 GGCCCAACAG
16666 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* * *
16683 AGTTTAAATTTACTTAA
1 AATTTAAATTTATTTTA
*
16700 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
* *
16717 AATTTAAGTTTAAATTTA
1 AATTTAAATTT-ATTTTA
16735 AATTTAAATT
1 AATTTAAATT
16745 AATGTCCAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
17 37 0.74
18 13 0.26
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:16704 original size:34 final size:35
Alignment explanation
Indices: 16666--16744 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 35
16656 GGCCCAACAG
* * *
16666 AATTTAAATTTATTTTAAGTTTAAATTT-ACTTAA
1 AATTTAAATTTATTATAAATTTAAATTTAAATTAA
* *
16700 AATTTAAATTTATTATAAATTTAAGTTTAAATTTA
1 AATTTAAATTTATTATAAATTTAAATTTAAATTAA
16735 AATTTAAATT
1 AATTTAAATT
16745 AATGTCCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 25 0.64
35 14 0.36
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (35 bp):
AATTTAAATTTATTATAAATTTAAATTTAAATTAA
Found at i:16732 original size:12 final size:11
Alignment explanation
Indices: 16666--16744 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
16656 GGCCCAACAG
16666 AATTTAAATTT
1 AATTTAAATTT
* *
16677 ATTTTAAGTTT
1 AATTTAAATTT
* *
16688 AAATTT-ACTTAA
1 -AATTTAAATT-T
16700 AATTTAAATTT
1 AATTTAAATTT
16711 -ATTATAAATTT
1 AATT-TAAATTT
16722 AAGTTTAAATTT
1 AA-TTTAAATTT
16734 AAATTTAAATT
1 -AATTTAAATT
16745 AATGTCCAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
10 3 0.06
11 24 0.44
12 23 0.43
13 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (11 bp):
AATTTAAATTT
Done.