Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000529.1 Kokia drynarioides strain JFW-HI SEQ_111419, 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: 33315
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6416 original size:20 final size:20
Alignment explanation
Indices: 6378--6416 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
6368 TAAATTATAT
*
6378 ATAAATTAAAAATTCAAAAA
1 ATAAATTAAAAAATCAAAAA
6398 ATAATATTAAAAAAT-AAAA
1 ATAA-ATTAAAAAATCAAAA
6417 TTATATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
ATAAATTAAAAAATCAAAAA
Found at i:6427 original size:15 final size:13
Alignment explanation
Indices: 6386--6419 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
6376 ATATAAATTA
6386 AAAATTCAAAAAAT
1 AAAATT-AAAAAAT
*
6400 AATATTAAAAAAT
1 AAAATTAAAAAAT
6413 AAAATTA
1 AAAATTA
6420 TATAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAATTAAAAAAT
Found at i:10032 original size:87 final size:87
Alignment explanation
Indices: 9886--10060 Score: 350
Period size: 87 Copynumber: 2.0 Consensus size: 87
9876 ACCATACTGC
9886 ATACATAGATGACTATGTGCAGTCCAATACCATATCATTTATCATAGTTTTATATACAAAATCAT
1 ATACATAGATGACTATGTGCAGTCCAATACCATATCATTTATCATAGTTTTATATACAAAATCAT
9951 ATATGATTCCAAAATGATAGCT
66 ATATGATTCCAAAATGATAGCT
9973 ATACATAGATGACTATGTGCAGTCCAATACCATATCATTTATCATAGTTTTATATACAAAATCAT
1 ATACATAGATGACTATGTGCAGTCCAATACCATATCATTTATCATAGTTTTATATACAAAATCAT
10038 ATATGATTCCAAAATGATAGCT
66 ATATGATTCCAAAATGATAGCT
10060 A
1 A
10061 GAACTAGATT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.34
Consensus pattern (87 bp):
ATACATAGATGACTATGTGCAGTCCAATACCATATCATTTATCATAGTTTTATATACAAAATCAT
ATATGATTCCAAAATGATAGCT
Found at i:11088 original size:27 final size:26
Alignment explanation
Indices: 11057--11115 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
11047 ACAGATAATA
11057 TTTTTAATAA-AAAAAATTAATTTATT
1 TTTTTAA-AAGAAAAAATTAATTTATT
**
11083 TATTTTAAAAGAAATGATTAATTTATT
1 T-TTTTAAAAGAAAAAATTAATTTATT
11110 TTTTTA
1 TTTTTA
11116 TCAGATGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (26 bp):
TTTTTAAAAGAAAAAATTAATTTATT
Found at i:11556 original size:2 final size:2
Alignment explanation
Indices: 11549--11576 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11539 AAAATAGTAC
11549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11577 TATTTAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12948 original size:43 final size:43
Alignment explanation
Indices: 12754--12993 Score: 201
Period size: 43 Copynumber: 5.6 Consensus size: 43
12744 ATGCTACTAT
* * ** * * *
12754 AGAACATGGTCTTTAGCGGGGCTTTCCTCACAATCCCCGCTAA
1 AGAACACGATCTTTAGCGACGCTTTCCCCACAAACACCGCTAA
* * * ** ** **
12797 AAAACACGGTCTTTAACGGGGCTTTCCTTACAAATGCCGCTAA
1 AGAACACGATCTTTAGCGACGCTTTCCCCACAAACACCGCTAA
** * * *
12840 AGAACACGATCTTTAGCGGTGCTTTCCACAAAAACACTGCTAA
1 AGAACACGATCTTTAGCGACGCTTTCCCCACAAACACCGCTAA
*
12883 AGAACACGATCTTTAGCGACGCTTTCCCCACAAGCACCGCTAA
1 AGAACACGATCTTTAGCGACGCTTTCCCCACAAACACCGCTAA
* * * **
12926 AGAGCACGACCTTTAGCAACGCTTTTTCCACAAACACCGCTAA
1 AGAACACGATCTTTAGCGACGCTTTCCCCACAAACACCGCTAA
* * * *
12969 ATAACATGGTCTTTAACGACGCTTT
1 AGAACACGATCTTTAGCGACGCTTT
12994 TATCACAAAT
Statistics
Matches: 161, Mismatches: 36, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 161 1.00
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (43 bp):
AGAACACGATCTTTAGCGACGCTTTCCCCACAAACACCGCTAA
Found at i:19093 original size:34 final size:34
Alignment explanation
Indices: 19047--19292 Score: 233
Period size: 34 Copynumber: 7.4 Consensus size: 34
19037 TAAATATTTT
19047 TAATTAAATAATTAAATATTTGGGTTGTTTTTAA
1 TAATTAAATAATTAAATATTTGGGTTGTTTTTAA
* *
19081 TAATTAATTAATT--A-A-TTGGGTTGTTTTAAA
1 TAATTAAATAATTAAATATTTGGGTTGTTTTTAA
** *
19111 TAATTAAATAATTAAGCATTTAGGTTGTTTTTAA
1 TAATTAAATAATTAAATATTTGGGTTGTTTTTAA
*** *
19145 TAATTAAATAATTAAATA-TT---TAAATATT--
1 TAATTAAATAATTAAATATTTGGGTTGTTTTTAA
* *
19173 TAATTAAAAAATTAATTATTTGGGTTGTTTTTAA
1 TAATTAAATAATTAAATATTTGGGTTGTTTTTAA
** *
19207 TAATTAAATAATTAAATATTTGAATTATTTTTAA
1 TAATTAAATAATTAAATATTTGGGTTGTTTTTAA
* * *
19241 TAATTAATTAATTAATTAATTAATTGGGTTGTTTTAAA
1 TAATT-A--AA-TAATTAAATATTTGGGTTGTTTTTAA
19279 TAATTAAATAATTA
1 TAATTAAATAATTA
19293 GGTTGCCTTT
Statistics
Matches: 169, Mismatches: 29, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
28 16 0.09
29 2 0.01
30 30 0.18
31 1 0.01
32 5 0.03
33 3 0.02
34 81 0.48
35 3 0.02
37 3 0.02
38 25 0.15
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (34 bp):
TAATTAAATAATTAAATATTTGGGTTGTTTTTAA
Found at i:19122 original size:26 final size:27
Alignment explanation
Indices: 19050--19123 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 27
19040 ATATTTTTAA
*
19050 TTAAATAATTAAATATTTGGGTTGTTT
1 TTAAATAATTAAATAATTGGGTTGTTT
*
19077 TTAATAATTAATTAATTAATTGGGTTG-TT
1 TT-A-AA-TAATTAAATAATTGGGTTGTTT
19106 TTAAATAATTAAATAATT
1 TTAAATAATTAAATAATT
19124 AAGCATTTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 12 0.29
27 4 0.10
28 2 0.05
29 6 0.15
30 17 0.41
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (27 bp):
TTAAATAATTAAATAATTGGGTTGTTT
Found at i:19187 original size:20 final size:20
Alignment explanation
Indices: 19153--19193 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19143 AATAATTAAA
* *
19153 TAATTAAATATTTAAATATT
1 TAATTAAAAAATTAAATATT
*
19173 TAATTAAAAAATTAATTATT
1 TAATTAAAAAATTAAATATT
19193 T
1 T
19194 GGGTTGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATTAAAAAATTAAATATT
Found at i:19250 original size:4 final size:4
Alignment explanation
Indices: 19203--19265 Score: 53
Period size: 4 Copynumber: 16.5 Consensus size: 4
19193 TGGGTTGTTT
* * * *
19203 TTAA -TAA TTAA ATAA TTAA ATAT TTGAA TT-A TT-T TTAA -TAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TT-AA TTAA TTAA TTAA TTAA TTAA
19248 TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TT
19266 GGGTTGTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
3 11 0.23
4 33 0.70
5 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:19261 original size:72 final size:70
Alignment explanation
Indices: 19143--19292 Score: 210
Period size: 72 Copynumber: 2.1 Consensus size: 70
19133 GGTTGTTTTT
* * *
19143 AATAATTAAATAATTAAATATTTAAATATTTAATTAAAAAATTAATTATTTGGGTTGTTTTTAAT
1 AATAATTAAATAATTAAATATTTAAATAATTAATTAAAAAATTAATTAATTGGGTTGTTTTAAAT
19208 AATTA
66 AATTA
* * * **
19213 AATAATTAAATATTTGAATTATTTTTAATAATTAATTAATTAATTAATTAATTGGGTTGTTTTAA
1 AATAATTAAATAATT-AAATA-TTTAAATAATTAATTAAAAAATTAATTAATTGGGTTGTTTTAA
19278 ATAATTA
64 ATAATTA
19285 AATAATTA
1 AATAATTA
19293 GGTTGCCTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
70 14 0.20
71 4 0.06
72 52 0.74
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (70 bp):
AATAATTAAATAATTAAATATTTAAATAATTAATTAAAAAATTAATTAATTGGGTTGTTTTAAAT
AATTA
Found at i:19278 original size:126 final size:125
Alignment explanation
Indices: 19031--19288 Score: 281
Period size: 126 Copynumber: 2.0 Consensus size: 125
19021 GGTTGTTTTT
* *
19031 AATAGTTAAATATTTTTAATTAAATAATTAAATATTTGGGTTGTTTTTAATAATTAATTAATTAA
1 AATAGTTAAATA-TTTTAATTAAAAAATTAAATATTTGGGTTGTTTTTAATAATTAAATAATTAA
** * * * * *
19096 TTGGGTTGTTTTAAATAATTAAATAATTAAGCATTTAGGTTGTTTTTAATAATTAAATAATTA
65 TTGAATTATTTTAAATAATTAAATAATTAAGCAATTAGATTGGTTGT-AT-ATTAAATAATTA
* *
19159 AATATTTAAATA-TTTAATTAAAAAATTAATTATTTGGGTTGTTTTTAATAATTAAATAATTAAA
1 AATAGTTAAATATTTTAATTAAAAAATTAAATATTTGGGTTGTTTTTAATAATTAAATAATT--A
* * **
19223 TATTTGAATTATTTTTAATAATTAATTAATTAATTAATTA-ATTGGGTTGT-T-TTAAATAATTA
64 -A-TTGAATTATTTTAAATAATTAAATAATTAAGCAATTAGATT-GGTTGTATATTAAATAATTA
19285 AATA
1 AATA
19289 ATTAGGTTGC
Statistics
Matches: 110, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
126 61 0.55
128 13 0.12
129 3 0.03
130 33 0.30
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (125 bp):
AATAGTTAAATATTTTAATTAAAAAATTAAATATTTGGGTTGTTTTTAATAATTAAATAATTAAT
TGAATTATTTTAAATAATTAAATAATTAAGCAATTAGATTGGTTGTATATTAAATAATTA
Found at i:19282 original size:26 final size:27
Alignment explanation
Indices: 19248--19314 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 27
19238 TAATAATTAA
* * * *
19248 TTAATTAATTAATTAATTGGGTTG-TT
1 TTAAATAATTAAATAATTAGGTTGCCT
19274 TTAAATAATTAAATAATTAGGTTGCCT
1 TTAAATAATTAAATAATTAGGTTGCCT
19301 TT-AATAATTAAATA
1 TTAAATAATTAAATA
19315 TTATTTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 33 0.92
27 3 0.08
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.46
Consensus pattern (27 bp):
TTAAATAATTAAATAATTAGGTTGCCT
Found at i:24544 original size:41 final size:41
Alignment explanation
Indices: 24455--24771 Score: 313
Period size: 41 Copynumber: 7.8 Consensus size: 41
24445 TAACGGCGTT
* * *
24455 TTTCACATAAGCGTCGCTAATGCA-CTGACCTTT---GGCGC
1 TTTCCCATAAGCGCCGCTATTG-ATCTGACCTTTAGCGGCGC
** *
24493 TTTTACATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
1 TTTCCCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC
* * *
24534 TTTCCCATAAGCGTCGCTATTGATATGACCTTTAGCGACGC
1 TTTCCCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC
* *
24575 TTTCTCATAAGC-CCGCTATTGATCTGACCTTTAGCGACGC
1 TTTCCCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC
* * *
24615 -TTCCTCATAAGCACCGTTATTGCTCTGACCTTTAGCGGCGC
1 TTTCC-CATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC
*** * * *
24656 TTGATCATAAGCACCGCTATTGATCTGACCTTTAGTGGTGC
1 TTTCCCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC
* * * * * *
24697 TTGCCTATAAGCGTCGGTATTGATATGACCTTTAGCAGCGC
1 TTTCCCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC
* * *
24738 TTTCTCATAAGCGTCGCTATTGCTCTGACCTTTA
1 TTTCCCATAAGCGCCGCTATTGATCTGACCTTTA
24772 ACAGTGCTTA
Statistics
Matches: 232, Mismatches: 40, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
38 28 0.12
39 3 0.01
40 33 0.14
41 167 0.72
42 1 0.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (41 bp):
TTTCCCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC
Found at i:24718 original size:82 final size:81
Alignment explanation
Indices: 24488--24771 Score: 356
Period size: 82 Copynumber: 3.5 Consensus size: 81
24478 ACTGACCTTT
* *
24488 GGCGCTTT-TACATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGTCGCT
1 GGCGCTTTCT-CATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGC-TTCCTATAAGCGTCGCT
24552 ATTGATATGACCTTTAGC
64 ATTGATATGACCTTTAGC
* * ** *
24570 GACGCTTTCTCATAAGC-CCGCTATTGATCTGACCTTTAGCGACGCTTCCTCATAAGCACCGTTA
1 GGCGCTTTCTCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGCTTCCT-ATAAGCGTCGCTA
* *
24634 TTGCTCTGACCTTTAGC
65 TTGATATGACCTTTAGC
** * * * *
24651 GGCGCTTGATCATAAGCACCGCTATTGATCTGACCTTTAGTGGTGCTTGCCTATAAGCGTCGGTA
1 GGCGCTTTCTCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGCTT-CCTATAAGCGTCGCTA
24716 TTGATATGACCTTTAGC
65 TTGATATGACCTTTAGC
* * *
24733 AGCGCTTTCTCATAAGCGTCGCTATTGCTCTGACCTTTA
1 GGCGCTTTCTCATAAGCGCCGCTATTGATCTGACCTTTA
24772 ACAGTGCTTA
Statistics
Matches: 172, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 4 0.02
81 65 0.38
82 99 0.58
83 4 0.02
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (81 bp):
GGCGCTTTCTCATAAGCGCCGCTATTGATCTGACCTTTAGCGGCGCTTCCTATAAGCGTCGCTAT
TGATATGACCTTTAGC
Found at i:27686 original size:17 final size:18
Alignment explanation
Indices: 27665--27707 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
27655 TATAAGAATG
27665 GAAATGCAACT-AT-AAT
1 GAAATGCAACTAATAAAT
27681 GAAAATGC-ACTAATAAAT
1 G-AAATGCAACTAATAAAT
27699 GAAATGCAA
1 GAAATGCAA
27708 TGACAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.17
17 14 0.61
18 5 0.22
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21
Consensus pattern (18 bp):
GAAATGCAACTAATAAAT
Found at i:27721 original size:18 final size:18
Alignment explanation
Indices: 27700--27736 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27690 CTAATAAATG
27700 AAATGCAATGACAAATAA
1 AAATGCAATGACAAATAA
* *
27718 AAATGTAATGACAACTAA
1 AAATGCAATGACAAATAA
27736 A
1 A
27737 TAAGATGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (18 bp):
AAATGCAATGACAAATAA
Found at i:28227 original size:18 final size:16
Alignment explanation
Indices: 28204--28250 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
28194 CCCTTAATTC
28204 TCTTTCTCATGTCCTTCT
1 TCTTTCTCATG--CTTCT
28222 TCTTTCTC-TGCTTCT
1 TCTTTCTCATGCTTCT
* *
28237 TCTTCCTCAAGCTT
1 TCTTTCTCATGCTT
28251 GTCCTACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 12 0.46
16 4 0.15
17 2 0.08
18 8 0.31
ACGTcount: A:0.06, C:0.34, G:0.06, T:0.53
Consensus pattern (16 bp):
TCTTTCTCATGCTTCT
Done.