Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003095.1 Kokia drynarioides strain JFW-HI SEQ_115657, 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: 60905
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:1159 original size:4 final size:4
Alignment explanation
Indices: 1139--1230 Score: 78
Period size: 4 Copynumber: 22.5 Consensus size: 4
1129 AACACATTAC
* * * * * *
1139 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTC CTTC CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
* *
1187 CTTT CTTT CTTTT CTTT CTTT CTTT CTTTT CTTT ATTT ATTT CT
1 CTTT CTTT C-TTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CT
1231 CGTTTATTTG
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
3 3 0.04
4 61 0.81
5 11 0.15
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:1202 original size:13 final size:12
Alignment explanation
Indices: 1139--1230 Score: 78
Period size: 13 Copynumber: 7.5 Consensus size: 12
1129 AACACATTAC
*
1139 CTTTCTTTCCTT
1 CTTTCTTTCTTT
1151 C-TTCTTTCTTT
1 CTTTCTTTCTTT
* * *
1162 CCTCTCCTTCTTC
1 -CTTTCTTTCTTT
* *
1175 CTTCCTTCCTTT
1 CTTTCTTTCTTT
1187 CTTTCTTTCTTTT
1 CTTTCTTTC-TTT
1200 CTTTCTTTCTTT
1 CTTTCTTTCTTT
*
1212 CTTTTCTTTATTT
1 C-TTTCTTTCTTT
*
1225 ATTTCT
1 CTTTCT
1231 CGTTTATTTG
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
11 9 0.14
12 25 0.40
13 29 0.46
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (12 bp):
CTTTCTTTCTTT
Found at i:1213 original size:17 final size:17
Alignment explanation
Indices: 1139--1230 Score: 82
Period size: 17 Copynumber: 5.6 Consensus size: 17
1129 AACACATTAC
*
1139 CTTTCTTTC-CTTC-TT
1 CTTTCTTTCTTTTCTTT
* * *
1154 CTTTCTTTCCTCTCCTT
1 CTTTCTTTCTTTTCTTT
* * *
1171 C-TTCCTTCCTTCCTTT
1 CTTTCTTTCTTTTCTTT
1187 CTTTCTTTCTTTTCTTT
1 CTTTCTTTCTTTTCTTT
1204 CTTTCTTTCTTTTCTTT
1 CTTTCTTTCTTTTCTTT
* *
1221 ATTTATTTCT
1 CTTTCTTTCT
1231 CGTTTATTTG
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
15 9 0.14
16 14 0.22
17 40 0.63
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (17 bp):
CTTTCTTTCTTTTCTTT
Found at i:16451 original size:6 final size:7
Alignment explanation
Indices: 16435--16459 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16425 ATACAAACTT
16435 AAAAAGA
1 AAAAAGA
16442 AAAAAGA
1 AAAAAGA
16449 AAAAAGA
1 AAAAAGA
16456 AAAA
1 AAAA
16460 TTATGTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:17197 original size:122 final size:124
Alignment explanation
Indices: 17034--17260 Score: 298
Period size: 123 Copynumber: 1.8 Consensus size: 124
17024 TTAGTTTTTC
* * * * *
17034 TCTTTAAGCGTCTTTGTGTTTTTTGAGTTTGATAGTTTATTAAAATTTGGTGTGTAATGTCAAAA
1 TCTTTAAGCGTCTTTGTGCTTCTTGAGTTTGATAGTTTATTAAAACTTGCTGTATAATGTCAAAA
* *
17099 -GGCAATCAA-CTAGCATAGTTTTAGAGTAAATTGGATTGTTTTTTAAAATTGTTCATAT
66 CGGCAATCAATC-AGCATAGTTCTAGAGTAAATTGCATTGTTTTTTAAAATTGTTCATAT
* * * *
17157 TCTTTAAGCTTTTTTGTGCTTCTT-AGTTTGGTAGTTTATTAAAACTTGCTTTATAATGTCAAAA
1 TCTTTAAGCGTCTTTGTGCTTCTTGAGTTTGATAGTTTATTAAAACTTGCTGTATAATGTCAAAA
* * *
17221 CGGTAATCAATCAGCGTAGTTCTAGAGTAATTTGCATTGT
66 CGGCAATCAATCAGCATAGTTCTAGAGTAAATTGCATTGT
17261 AAGTGGCTAA
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
122 35 0.40
123 52 0.59
124 1 0.01
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (124 bp):
TCTTTAAGCGTCTTTGTGCTTCTTGAGTTTGATAGTTTATTAAAACTTGCTGTATAATGTCAAAA
CGGCAATCAATCAGCATAGTTCTAGAGTAAATTGCATTGTTTTTTAAAATTGTTCATAT
Found at i:18619 original size:23 final size:23
Alignment explanation
Indices: 18589--18634 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
18579 GCAATTCACA
18589 TTGTGGGAGTGTGAAGAGACACG
1 TTGTGGGAGTGTGAAGAGACACG
18612 TTGTGGGAGTGTGAAGAGACACG
1 TTGTGGGAGTGTGAAGAGACACG
18635 AAGATGAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.43, T:0.22
Consensus pattern (23 bp):
TTGTGGGAGTGTGAAGAGACACG
Found at i:21226 original size:15 final size:15
Alignment explanation
Indices: 21191--21223 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
21181 TAAAGACAAG
21191 TAATAATTTTTTTGAA
1 TAAT-ATTTTTTTGAA
21207 TAATATTTTTTT-AA
1 TAATATTTTTTTGAA
21221 TAA
1 TAA
21224 ATAAAGACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 8 0.47
16 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TAATATTTTTTTGAA
Found at i:29964 original size:129 final size:129
Alignment explanation
Indices: 29766--30250 Score: 751
Period size: 129 Copynumber: 3.8 Consensus size: 129
29756 TAAAAAGTAA
*
29766 ATTTCATTAAATATTATAAGTTTATTTTAAAAAAAATTTATTTCATAAAAGGAAAGAAAATTAAT
1 ATTTCATTAAATATTATAAGTTTATTTT-AAAAAAATTTATATCATAAAAGGAAAGAAAATTAAT
*
29831 ATATTCAAGTTTATTAAATATAAATAATTGATAAAAAATTTCTCCGAATATCATATGGATATTTG
65 ATATTCAAGTTTATTAAATATAAATAATTGATAAAAAATTTCTCCGAATATCATATGAATATTTG
* **
29896 ATTTCATTAAATATTATAAGTTTATTTTAGAAATTTTTATATCATAAAAGGAAAGAAAATTAATA
1 ATTTCATTAAATATTATAAGTTTATTTTAAAAAAATTTATATCATAAAAGGAAAGAAAATTAATA
* *
29961 TATTTAAGTTTATTAAATATAAATAATT-AAAAAAAGATTTCTCCGAATATCATATGAATATTTG
66 TATTCAAGTTTATTAAATATAAATAATTGATAAAAA-ATTTCTCCGAATATCATATGAATATTTG
* * *
30025 ATTTTATTAAATATTATAAATTTA-TTTAAAAAAATTTATATCATAAAA-GAAAAAAAATTAATA
1 ATTTCATTAAATATTATAAGTTTATTTTAAAAAAATTTATATCATAAAAGGAAAGAAAATTAATA
* *
30088 TATTCAAGTTTATTAAATATATAAATAATTGATAAAAGATTTCTCCGAATGTCATATGAATATTT
66 TATTCAAGTTTATT-AA-ATATAAATAATTGATAAAAAATTTCTCCGAATATCATATGAATATTT
30153 G
129 G
* ** * *
30154 ATTTCATTAAATATTATAAGTTTATTTTAGAAATTTTTATATCATAAAATGAAAGAAAACTAATA
1 ATTTCATTAAATATTATAAGTTTATTTTAAAAAAATTTATATCATAAAAGGAAAGAAAATTAATA
*
30219 TAATCAAGTTTATTAAATATAAATAATTGATA
66 TATTCAAGTTTATTAAATATAAATAATTGATA
30251 GAACACTTTT
Statistics
Matches: 324, Mismatches: 25, Indels: 13
0.90 0.07 0.04
Matches are distributed among these distances:
127 27 0.08
128 29 0.09
129 186 0.57
130 56 0.17
131 26 0.08
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (129 bp):
ATTTCATTAAATATTATAAGTTTATTTTAAAAAAATTTATATCATAAAAGGAAAGAAAATTAATA
TATTCAAGTTTATTAAATATAAATAATTGATAAAAAATTTCTCCGAATATCATATGAATATTTG
Found at i:37919 original size:30 final size:29
Alignment explanation
Indices: 37883--37939 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
37873 TTGTATAAAT
*
37883 AAATTTTGATTTTATGCAATTCTATATATG
1 AAATTTTGATTTGATGCAATTCT-TATATG
*
37913 AAATTTTGATTTGATTCAATTCTTATA
1 AAATTTTGATTTGATGCAATTCTTATA
37940 AATTAATAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (29 bp):
AAATTTTGATTTGATGCAATTCTTATATG
Found at i:38140 original size:29 final size:31
Alignment explanation
Indices: 38067--38151 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 31
38057 ATTAAATCAA
* *
38067 AATTA-AAGTTTCAAGTATACATTTGA-ACCAC
1 AATTAGAAG-TTCATGTATACAATT-ACACCAC
* * *
38098 AATTAGAATTTCATGTCTATAATTACACCA-
1 AATTAGAAGTTCATGTATACAATTACACCAC
38128 AATTA-AAGTTCATGTATACAATTA
1 AATTAGAAGTTCATGTATACAATTA
38152 TACGTTAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 16 0.36
30 6 0.14
31 20 0.45
32 2 0.05
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.35
Consensus pattern (31 bp):
AATTAGAAGTTCATGTATACAATTACACCAC
Found at i:43718 original size:76 final size:76
Alignment explanation
Indices: 43587--43734 Score: 242
Period size: 76 Copynumber: 1.9 Consensus size: 76
43577 TGCTTCCGCC
* * * *
43587 AATACATATACAAATTTTGTGTCATGTCAACTATATTTTGATTATTCTAACATCGTGTAATAGGA
1 AATACATATACAAATCTTATGTCATGTCAACTATACTCTGATTATTCTAACATCGTGTAATAGGA
43652 CGAGTTCCACT
66 CGAGTTCCACT
* *
43663 AATATATATACAAATCTTATGTCATGTCAACTATACTCTGATTATTCTAACATCGTGTAATGGGA
1 AATACATATACAAATCTTATGTCATGTCAACTATACTCTGATTATTCTAACATCGTGTAATAGGA
43728 CGAGTTC
66 CGAGTTC
43735 ACAATTTAAC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 66 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (76 bp):
AATACATATACAAATCTTATGTCATGTCAACTATACTCTGATTATTCTAACATCGTGTAATAGGA
CGAGTTCCACT
Found at i:44040 original size:13 final size:13
Alignment explanation
Indices: 44022--44086 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 13
44012 AGTTTAGTAT
*
44022 TGCTTTTGAAAGA
1 TGCTTTTGAAAAA
*
44035 TGCTTTTAAAAAA
1 TGCTTTTGAAAAA
44048 TG-TTTTGAAAAAAA
1 TGCTTTTG--AAAAA
* *
44062 TGATTTTGAAAAG
1 TGCTTTTGAAAAA
*
44075 TACTTTT-AAAAA
1 TGCTTTTGAAAAA
44087 GTTTGATTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
12 8 0.19
13 22 0.52
14 7 0.17
15 5 0.12
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAA
Found at i:44061 original size:14 final size:15
Alignment explanation
Indices: 44042--44073 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
44032 AGATGCTTTT
44042 AAAAAATG-TTTTGA
1 AAAAAATGATTTTGA
44056 AAAAAATGATTTTGA
1 AAAAAATGATTTTGA
44071 AAA
1 AAA
44074 GTACTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (15 bp):
AAAAAATGATTTTGA
Done.