Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008134.1 Kokia drynarioides strain JFW-HI SEQ_122792, 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: 39995
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Found at i:47 original size:6 final size:6
Alignment explanation
Indices: 38--128 Score: 80
Period size: 6 Copynumber: 14.7 Consensus size: 6
28 TTTGGACATT
*
38 AATTTA AATTTA AATTTA AACTTA AATTTA TAA--TA AATTTA AATTAATA
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATT--TA
* *
87 AATTTA AATTAAGTA AATTTA AACTTA AA-ATA AATTTA AATT
1 AATTTA AATT---TA AATTTA AATTTA AATTTA AATTTA AATT
129 ATGTTAGGCC
Statistics
Matches: 71, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
4 2 0.03
5 6 0.08
6 49 0.69
7 2 0.03
8 6 0.08
9 6 0.08
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:75 original size:29 final size:27
Alignment explanation
Indices: 42--127 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 27
32 GACATTAATT
42 TAAATTTAAATTTAAACTTAAATTTATAA
1 TAAATTTAAATTTAAA-TTAAATTTA-AA
*
71 TAAATTTAAATTAATAAATTTAAA-TTAAG
1 TAAATTTAAATT--TAAA-TTAAATTTAAA
* *
100 TAAATTTAAACTTAAAATAAATTTAAA
1 TAAATTTAAATTTAAATTAAATTTAAA
127 T
1 T
128 TATGTTAGGC
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
26 4 0.08
27 9 0.18
29 24 0.49
30 3 0.06
31 9 0.18
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (27 bp):
TAAATTTAAATTTAAATTAAATTTAAA
Found at i:121 original size:46 final size:43
Alignment explanation
Indices: 42--129 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 43
32 GACATTAATT
* *
42 TAAATTTAAATTTAAACTTAAATTTATAATAAATTTAAATTAA
1 TAAATTTAAATTTAAACTTAAACTTAAAATAAATTTAAATTAA
*
85 TAAATTTAAATTAAGTAAATTTAAACTTAAAATAAATTTAAATTA
1 TAAATTTAAATT---TAAACTTAAACTTAAAATAAATTTAAATTA
130 TGTTAGGCCC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 12 0.31
46 27 0.69
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (43 bp):
TAAATTTAAATTTAAACTTAAACTTAAAATAAATTTAAATTAA
Found at i:3728 original size:42 final size:42
Alignment explanation
Indices: 3669--3752 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
3659 GCTATGTTTA
3669 ATGCCTCTCATCAGTAAATCGACAACAGCTCACAGACATTGC
1 ATGCCTCTCATCAGTAAATCGACAACAGCTCACAGACATTGC
* * * *
3711 ATGCCTCTCATTAGTAAATCGACGACAGTTCACAGAGATTGC
1 ATGCCTCTCATCAGTAAATCGACAACAGCTCACAGACATTGC
3753 TTTATCCATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (42 bp):
ATGCCTCTCATCAGTAAATCGACAACAGCTCACAGACATTGC
Found at i:10305 original size:189 final size:187
Alignment explanation
Indices: 9939--10303 Score: 458
Period size: 189 Copynumber: 2.0 Consensus size: 187
9929 AAAAAAATAG
* * * * *
9939 TTGATGCTATGATATTCCTCTTTATTTTTTAAATAAATTTTTTTTTTTTGATTTAGTGGGTTTTT
1 TTGATACTATAATATTCCTCTTTATTTTTAAAATAAATTTTTTTTTTTTAATTTAGTGGGTTGTT
* * *
10004 ACTATTTATTCTGTGATAATTTAATAAGAATATGATTCACATGCTTTTATTCTTCTTTTACCTTT
66 ACTATTTATTCAGTGACAATTGAATAAGAATATGATTCACATGCTTTTATTCTTCTTTTACCTTT
*
10069 TGTCTTATTGATTTTTATTTTAAGTACTAATTTTAACTTGTTTTCATTTCAATGTAA
131 TGTCTTACTGATTTTTATTTTAAGTACTAATTTTAACTTGTTTTCATTTCAATGTAA
10126 TTGATACTATAATATTCC-CTTTATTTTTAAAATAAATTATATTTTTTTGGTTAATTTAGTGGGT
1 TTGATACTATAATATTCCTCTTTATTTTTAAAATAAATT-T-TTTTTTT--TTAATTTAGTGGGT
* * * * * *
10190 TGTTACTGTTTATTCAGTGGCAGTTGGA-AATAATATGATTCACATGCTTTTATTTTTCTTTTA-
62 TGTTACTATTTATTCAGTGACAATTGAATAAGAATATGATTCACATGCTTTTATTCTTCTTTTAC
* * * *
10253 CTTTT-TC-T-CT-CTTTTTA-TTTAATTATTAATTTTAACTAGTTTTCCATTTCA
127 CTTTTGTCTTACTGATTTTTATTTTAAGTACTAATTTTAACTTGTTTT-CATTTCA
10304 TTGTGCTTTT
Statistics
Matches: 154, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
183 23 0.15
184 13 0.08
185 1 0.01
186 20 0.13
187 19 0.12
188 12 0.08
189 33 0.21
190 33 0.21
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (187 bp):
TTGATACTATAATATTCCTCTTTATTTTTAAAATAAATTTTTTTTTTTTAATTTAGTGGGTTGTT
ACTATTTATTCAGTGACAATTGAATAAGAATATGATTCACATGCTTTTATTCTTCTTTTACCTTT
TGTCTTACTGATTTTTATTTTAAGTACTAATTTTAACTTGTTTTCATTTCAATGTAA
Found at i:14378 original size:15 final size:16
Alignment explanation
Indices: 14345--14389 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
14335 TCATGACAAA
*
14345 TTCTTCCTCTTTCTTGTC
1 TTCTTTCTCTTTC--GTC
14363 TTCTTT-TCTTTCGTC
1 TTCTTTCTCTTTCGTC
14378 TTCTTTCTCTTT
1 TTCTTTCTCTTT
14390 TACCTTTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 9 0.36
16 5 0.20
17 6 0.24
18 5 0.20
ACGTcount: A:0.00, C:0.29, G:0.04, T:0.67
Consensus pattern (16 bp):
TTCTTTCTCTTTCGTC
Found at i:20126 original size:23 final size:23
Alignment explanation
Indices: 20082--20169 Score: 79
Period size: 23 Copynumber: 3.8 Consensus size: 23
20072 TTAATGTTCA
**
20082 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-CGAACATTAAT
*
20105 CGAACATGTTCACGAACATTAAA
1 CGAACATGTTCACGAACATTAAT
* * *
20128 CGAGCATGTTCATGAATATATAAT
1 CGAACATGTTCACGAACAT-TAAT
* *
20152 TGAACATGTTCACAAACA
1 CGAACATGTTCACGAACA
20170 ATGTTAATGA
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
22 3 0.06
23 32 0.63
24 16 0.31
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (23 bp):
CGAACATGTTCACGAACATTAAT
Found at i:20278 original size:12 final size:12
Alignment explanation
Indices: 20259--20293 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
20249 ATTATTAATA
20259 AATAAACGAG-C
1 AATAAACGAGTC
20270 AATTAAACGAGTC
1 AA-TAAACGAGTC
20283 AATAAACGAGT
1 AATAAACGAGT
20294 TTGTTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.09
12 17 0.77
13 3 0.14
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.17
Consensus pattern (12 bp):
AATAAACGAGTC
Found at i:28420 original size:2 final size:2
Alignment explanation
Indices: 28413--28437 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28403 AGTTTACAAT
28413 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28438 TGCTTACCGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31609 original size:10 final size:10
Alignment explanation
Indices: 31596--31649 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
31586 AATCTTATAA
31596 ATTTTTTTAT
1 ATTTTTTTAT
*
31606 ATTTTTCTAT
1 ATTTTTTTAT
*
31616 A--TTTTTAA
1 ATTTTTTTAT
*
31624 AATTTTTTA-
1 ATTTTTTTAT
31633 ATTTTTTTAT
1 ATTTTTTTAT
31643 AATTTTT
1 -ATTTTT
31650 AATAAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
8 6 0.17
9 8 0.22
10 16 0.44
11 6 0.17
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (10 bp):
ATTTTTTTAT
Found at i:31628 original size:29 final size:29
Alignment explanation
Indices: 31594--31686 Score: 91
Period size: 28 Copynumber: 3.1 Consensus size: 29
31584 AAAATCTTAT
31594 AAATTTTTTTATATTTTTCTATATTTTTA
1 AAATTTTTTTATATTTTTCTATATTTTTA
*
31623 AAA-TTTTTTA-ATTTTTTTATAATTTTTA
1 AAATTTTTTTATATTTTTCTAT-ATTTTTA
* ** *
31651 ATAAATTTTAAATATTATTTCTATTTTTATTA
1 A-AATTTTTTTATATT-TTTCTATATTT-TTA
31683 AAAT
1 AAAT
31687 ATAATCATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
27 9 0.17
28 15 0.29
29 5 0.10
30 5 0.10
31 8 0.15
32 10 0.19
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (29 bp):
AAATTTTTTTATATTTTTCTATATTTTTA
Found at i:31635 original size:8 final size:9
Alignment explanation
Indices: 31598--31650 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
31588 TCTTATAAAT
31598 TTTTTTATA
1 TTTTTTATA
31607 TTTTTCTATA
1 TTTTT-TATA
* *
31617 TTTTTAAAA
1 TTTTTTATA
31626 TTTTTTA-A
1 TTTTTTATA
31634 TTTTTTTATA
1 -TTTTTTATA
*
31644 ATTTTTA
1 TTTTTTA
31651 ATAAATTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
8 1 0.03
9 26 0.70
10 10 0.27
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTTTATA
Found at i:32019 original size:86 final size:86
Alignment explanation
Indices: 31866--32034 Score: 209
Period size: 86 Copynumber: 2.0 Consensus size: 86
31856 AATTTTAGAG
* * * *
31866 TCTTTTTGATACATTTTGAAAGATCAAGTACCCAATTGAGTGCCAAAAAAGCAATAGCTTAACTA
1 TCTTTTTGATACATTGTGAAAGATCAAGTACCCAAATGAGTGCCAAAAAAGAAAAAGCTTAACTA
31931 TTTTTTTTTCTAGTTTGAGGA
66 TTTTTTTTTCTAGTTTGAGGA
* * * * *
31952 TCTTTTTGATTCATTGTGAAAGTTCAAGTATCCAAATGAGTG-CAAAAAA-AAAAAGTTTAA-TT
1 TCTTTTTGATACATTGTGAAAGATCAAGTACCCAAATGAGTGCCAAAAAAGAAAAAGCTTAACTA
* *
32014 TTATTTTTTTTTAATTTGAGG
66 TT-TTTTTTTCTAGTTTGAGG
32035 GTTTTTTAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
83 3 0.04
84 24 0.34
85 7 0.10
86 37 0.52
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.41
Consensus pattern (86 bp):
TCTTTTTGATACATTGTGAAAGATCAAGTACCCAAATGAGTGCCAAAAAAGAAAAAGCTTAACTA
TTTTTTTTTCTAGTTTGAGGA
Found at i:35099 original size:16 final size:17
Alignment explanation
Indices: 35058--35106 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
35048 ATTCCTAATC
35058 CTTTAAAGAATT-TTATA
1 CTTTAAAGAATTATT-TA
*
35075 CGTTGAAAGAATTATTT-
1 C-TTTAAAGAATTATTTA
35092 CTTTAAAG-ATTATTT
1 CTTTAAAGAATTATTT
35107 TGAGTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 7 0.25
16 6 0.21
17 2 0.07
18 11 0.39
19 2 0.07
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (17 bp):
CTTTAAAGAATTATTTA
Found at i:35982 original size:43 final size:43
Alignment explanation
Indices: 35934--36022 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 43
35924 AATTATGAAG
** *
35934 GATAAATTTGATCGTCGTTAAAAAGAACTATCACTTTCAGTAA
1 GATAAATTTGATCGTCAATAAAAAGAACTATCACTTTCAGCAA
* *
35977 GATAAATTTGATCGTTAATAAAAAGAACTATCACTTTGAGCAA
1 GATAAATTTGATCGTCAATAAAAAGAACTATCACTTTCAGCAA
36020 GAT
1 GAT
36023 CGTGCTATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (43 bp):
GATAAATTTGATCGTCAATAAAAAGAACTATCACTTTCAGCAA
Done.