Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011384.1 Kokia drynarioides strain JFW-HI SEQ_126366, 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: 2819
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Found at i:147 original size:13 final size:12
Alignment explanation
Indices: 138--190 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
128 GAAAAAAGAC
138 AAAAAAAAAAAG
1 AAAAAAAAAAAG
*
150 AAAAAAAAGAA-
1 AAAAAAAAAAAG
*
161 AAAAGAAAAAAG
1 AAAAAAAAAAAG
*
173 AAATAGAAAAAAG
1 AAA-AAAAAAAAG
186 AAAAA
1 AAAAA
191 TGAGAGGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
11 9 0.26
12 14 0.40
13 12 0.34
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:152 original size:29 final size:27
Alignment explanation
Indices: 111--190 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 27
101 AAATTTCACC
*
111 AAAAAAAGAGAAAAAGAGAAAAAAGACAA
1 AAAAAAAAAGAAAAA-AGAAAAAAGA-AA
140 AAAAAAAAAGAAAAAAAAGAAAAAAGAAA
1 AAAAAAAAAG--AAAAAAGAAAAAAGAAA
* *
169 AAAGAAATAGAAAAAAGAAAAA
1 AAAAAAAAAGAAAAAAGAAAAA
191 TGAGAGGTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
27 12 0.26
29 19 0.41
30 10 0.22
31 5 0.11
ACGTcount: A:0.84, C:0.01, G:0.14, T:0.01
Consensus pattern (27 bp):
AAAAAAAAAGAAAAAAGAAAAAAGAAA
Found at i:155 original size:23 final size:23
Alignment explanation
Indices: 112--190 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
102 AATTTCACCA
*
112 AAAAAAGAGAAAAAGAGAAAAAAG
1 AAAAAAGA-AAAAAGAAAAAAAAG
136 ACAAAAA-AAAAAAGAAAAAAAAG
1 A-AAAAAGAAAAAAGAAAAAAAAG
*
159 AAAAAAGAAAAAAG---AAATAG
1 AAAAAAGAAAAAAGAAAAAAAAG
179 AAAAAAGAAAAA
1 AAAAAAGAAAAA
191 TGAGAGGTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
20 17 0.33
22 5 0.10
23 22 0.43
24 2 0.04
25 5 0.10
ACGTcount: A:0.84, C:0.01, G:0.14, T:0.01
Consensus pattern (23 bp):
AAAAAAGAAAAAAGAAAAAAAAG
Found at i:1608 original size:49 final size:48
Alignment explanation
Indices: 1133--1877 Score: 431
Period size: 49 Copynumber: 15.3 Consensus size: 48
1123 AAAAAACATT
* * *
1133 GAATC-TATACCCTAGAGATGTGAAGGGAGAGATTGAAG-TGGCAATGAC
1 GAATCTTATACCTTAGAGATGTG-AGGGAAAGATTGAAGCT-GCAACGAC
* * * * *
1181 GAATCTTATGCCCTAGAGATGTGAAGGGAAA-ATTTTAAG-T-CATAATGGC
1 GAATCTTATACCTTAGAGATGTG-AGGGAAAGA-TTGAAGCTGC--AACGAC
* * * * * *
1230 GAATCTCATGCCCTAGAGATGTGAAGGGAAAGATTGAAGCGGCAAAGGC
1 GAATCTTATACCTTAGAGATGTG-AGGGAAAGATTGAAGCTGCAACGAC
* * * * * *
1279 GAATCTTATACATTGGGGATGTGAGGGAAAGGTTGAAACCGCAACCG-C
1 GAATCTTATACCTTAGAGATGTGAGGGAAAGATTGAAGCTGCAA-CGAC
* * * * *
1327 GAACCTTGTACCTT--AGATATGATGGGAAAGACTGAAG-TCACAACGAC
1 GAATCTTATACCTTAGAGATGTGA-GGGAAAGATTGAAGCT-GCAACGAC
* * * * * * * * * *
1374 GAATCTTGTACCCTAAATATATGGAAGGAAAGGTTGAAAC-CCAAACGAT
1 GAATCTTATACCTTAGAGATGT-GAGGGAAAGATTGAAGCTGC-AACGAC
* * * * * *
1423 GAACCTTATACCCTAGAGATATGGAGGGAAAGGTTGAA-C-CCATTACGAT
1 GAATCTTATACCTTAGAGATGT-GAGGGAAAGATTGAAGCTGCA--ACGAC
* * * * * *
1472 GAACCTTATACCTTAGAGATGTGATGAGAAAGATTGAATCCGTAATGAC
1 GAATCTTATACCTTAGAGATGTGA-GGGAAAGATTGAAGCTGCAACGAC
* * * *
1521 GAATCTTATACCCTAGAGATGTAAAGGGAAAGGTTGAAGCTGCAACGGC
1 GAATCTTATACCTTAGAGATGT-GAGGGAAAGATTGAAGCTGCAACGAC
* * * **
1570 GAACCTTATACCCTAGAGATGTAGAGGGAAAGGTTGAAG-TCGCAACGGT
1 GAATCTTATACCTTAGAGATGT-GAGGGAAAGATTGAAGCT-GCAACGAC
* * * * *
1619 GAACCTTATACGTTAGAAATGTGATGGGAAAGATTGAAGCTACAAC-AGT
1 GAATCTTATACCTTAGAGATGTGA-GGGAAAGATTGAAGCTGCAACGA-C
* * * * *
1668 GAATCTTATACTTTAGAGATGTAGAGGGAAAGGTTGAAGCCGTATCGAC
1 GAATCTTATACCTTAGAGATGT-GAGGGAAAGATTGAAGCTGCAACGAC
* * * * * **
1717 GAACCTTATACCTTAAAGATGTGAGTAGAAAGATTGAAG-TCGTAATGGT
1 GAATCTTATACCTTAGAGATGTGAG-GGAAAGATTGAAGCT-GCAACGAC
* * *
1766 GAATCTTATACCTTAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGAT
1 GAATCTTATACCTTAGAGATGT-GAGGGAAAGATTGAAGCTGCAACGAC
* * *
1815 GAATCTTATACCTTAGAGATATGAAAGGAAAGATTGAAGCTGTAACGAC
1 GAATCTTATACCTTAGAGATGTG-AGGGAAAGATTGAAGCTGCAACGAC
*
1864 AAATCTTATACCTT
1 GAATCTTATACCTT
1878 GAAGATAAGG
Statistics
Matches: 561, Mismatches: 103, Indels: 65
0.77 0.14 0.09
Matches are distributed among these distances:
46 8 0.01
47 29 0.05
48 49 0.09
49 461 0.82
50 12 0.02
51 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (48 bp):
GAATCTTATACCTTAGAGATGTGAGGGAAAGATTGAAGCTGCAACGAC
Found at i:1853 original size:98 final size:96
Alignment explanation
Indices: 1138--1877 Score: 547
Period size: 98 Copynumber: 7.6 Consensus size: 96
1128 ACATTGAATC
* * * * * *
1138 TATACCCTAGAGATGTGAAGGGAGAGATTGAAGTGGCAATGACGAATCTTATGCCCTAGAGATGT
1 TATACCCTAGAGATGTGAAGGGAAAGATTGAAG-CGCAACGGCGAATCTTATACCTTAGAGATGT
** * * ** * * *
1203 GAAGGGAAAATTTTAAGTCATAATGGCGAATCT
65 G-AGGGAAAGGTTGAAGCCGCAACGACGAACCT
* * * * * *
1236 CATGCCCTAGAGATGTGAAGGGAAAGATTGAAGCGGCAAAGGCGAATCTTATACATTGGGGATGT
1 TATACCCTAGAGATGTGAAGGGAAAGATTGAAGC-GCAACGGCGAATCTTATACCTTAGAGATGT
*
1301 GAGGGAAAGGTTGAAACCGCAACCG-CGAACCT
65 GAGGGAAAGGTTGAAGCCGCAA-CGACGAACCT
* * * * * * * * * * * *
1333 TGTA-CCT-TAGATATGATGGGAAAGACTGAAGTCACAACGACGAATCTTGTACCCTAAATATAT
1 TATACCCTAGAGATGTGAAGGGAAAGATTGAAG-CGCAACGGCGAATCTTATACCTTAGAGATGT
* * *
1396 GGAAGGAAAGGTTGAAACC-CAAACGATGAACCT
65 -GAGGGAAAGGTTGAAGCCGC-AACGACGAACCT
* * * * ** *
1429 TATACCCTAGAGATATGGAGGGAAAGGTTGAA-CCCATTACGATGAACCTTATACCTTAGAGATG
1 TATACCCTAGAGATGTGAAGGGAAAGATTGAAGCGCA--ACGGCGAATCTTATACCTTAGAGATG
* * * * * *
1493 TGATGAGAAAGATTGAATCCGTAATGACGAATCT
64 TGA-GGGAAAGGTTGAAGCCGCAACGACGAACCT
* * * *
1527 TATACCCTAGAGATGTAAAGGGAAAGGTTGAAGCTGCAACGGCGAACCTTATACCCTAGAGATGT
1 TATACCCTAGAGATGTGAAGGGAAAGATTGAAGC-GCAACGGCGAATCTTATACCTTAGAGATGT
* **
1592 AGAGGGAAAGGTTGAAGTCGCAACGGTGAACCT
65 -GAGGGAAAGGTTGAAGCCGCAACGACGAACCT
** * * * * * *
1625 TATACGTTAGAAATGTGATGGGAAAGATTGAAGCTACAACAGTGAATCTTATACTTTAGAGATGT
1 TATACCCTAGAGATGTGAAGGGAAAGATTGAAGC-GCAACGGCGAATCTTATACCTTAGAGATGT
* *
1690 AGAGGGAAAGGTTGAAGCCGTATCGACGAACCT
65 -GAGGGAAAGGTTGAAGCCGCAACGACGAACCT
* * * * * *
1723 TATACCTTAAAGATGTG-AGTAGAAAGATTGAAGTCGTAATGGTGAATCTTATACCTTAGAGATG
1 TATACCCTAGAGATGTGAAG-GGAAAGATTGAAG-CGCAACGGCGAATCTTATACCTTAGAGATG
* *
1787 TAGAGGGAAAGGTTGAAGCCGCAACGATGAATCT
64 T-GAGGGAAAGGTTGAAGCCGCAACGACGAACCT
* * * * * *
1821 TATACCTTAGAGATATGAAAGGAAAGATTGAAGCTGTAACGACAAATCTTATACCTT
1 TATACCCTAGAGATGTGAAGGGAAAGATTGAAGC-GCAACGGCGAATCTTATACCTT
1878 GAAGATAAGG
Statistics
Matches: 506, Mismatches: 117, Indels: 38
0.77 0.18 0.06
Matches are distributed among these distances:
95 42 0.08
96 35 0.07
97 28 0.06
98 394 0.78
99 5 0.01
100 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.24
Consensus pattern (96 bp):
TATACCCTAGAGATGTGAAGGGAAAGATTGAAGCGCAACGGCGAATCTTATACCTTAGAGATGTG
AGGGAAAGGTTGAAGCCGCAACGACGAACCT
Found at i:1872 original size:147 final size:146
Alignment explanation
Indices: 1296--1883 Score: 499
Period size: 147 Copynumber: 4.0 Consensus size: 146
1286 ATACATTGGG
* * ** * * * *
1296 GATGT-GAGGGAAAGGTTGAAACCGCAACCGCGAACCTTGTACCTT--AGATATGATGGGAAAGA
1 GATGTAGAGAGAAAGATTGAAGTCGCAACGGTGAACCTTATACCTTAGAGATGTGATGGGAAAGA
* * * * * * * * * * * *** *
1358 CTGAAGTCACAACGACGAATCTTGTACCCTAAATATATGGAAGGAAAGGTTGAAACCCAAACGAT
66 TTGAAGCCGCAACGATGAATCTTATACCTTAGAGATGT-AAAGGAAAGGTTGAAGCTGTAACGAC
* *
1423 GAACCTTATACCCTAGA
130 GAACCTTATACCTTAAA
* * * * * * *
1440 GATATGGAGGGAAAGGTTGAA--CCCATTACGATGAACCTTATACCTTAGAGATGTGATGAGAAA
1 GATGTAGAGAGAAAGATTGAAGTCGCA--ACGGTGAACCTTATACCTTAGAGATGTGATGGGAAA
* * * * * *
1503 GATTGAATCCGTAATGACGAATCTTATACCCTAGAGATGTAAAGGGAAAGGTTGAAGCTGCAACG
64 GATTGAAGCCGCAACGATGAATCTTATACCTTAGAGATGTAAA-GGAAAGGTTGAAGCTGTAACG
* * *
1568 GCGAACCTTATACCCTAGA
128 ACGAACCTTATACCTTAAA
* * * *
1587 GATGTAGAGGGAAAGGTTGAAGTCGCAACGGTGAACCTTATACGTTAGAAATGTGATGGGAAAGA
1 GATGTAGAGAGAAAGATTGAAGTCGCAACGGTGAACCTTATACCTTAGAGATGTGATGGGAAAGA
** * * * *
1652 TTGAAGCTACAAC-AGTGAATCTTATACTTTAGAGATGTAGAGGGAAAGGTTGAAGCCGTATCGA
66 TTGAAGCCGCAACGA-TGAATCTTATACCTTAGAGATGTA-AAGGAAAGGTTGAAGCTGTAACGA
1716 CGAACCTTATACCTTAAA
129 CGAACCTTATACCTTAAA
* * *
1734 GATGT-GAGTAGAAAGATTGAAGTCGTAATGGTGAATCTTATACCTTAGAGATGTAGA-GGGAAA
1 GATGTAGAG-AGAAAGATTGAAGTCGCAACGGTGAACCTTATACCTTAGAGATGT-GATGGGAAA
* * *
1797 GGTTGAAGCCGCAACGATGAATCTTATACCTTAGAGATATGAAAGGAAAGATTGAAGCTGTAACG
64 GATTGAAGCCGCAACGATGAATCTTATACCTTAGAGATGT-AAAGGAAAGGTTGAAGCTGTAACG
* * *
1862 ACAAATCTTATACCTTGAA
128 ACGAACCTTATACCTTAAA
1881 GAT
1 GAT
1884 AAGGAGAAGC
Statistics
Matches: 364, Mismatches: 66, Indels: 25
0.80 0.15 0.05
Matches are distributed among these distances:
143 3 0.01
144 4 0.01
145 30 0.08
146 6 0.02
147 313 0.86
148 5 0.01
149 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.23
Consensus pattern (146 bp):
GATGTAGAGAGAAAGATTGAAGTCGCAACGGTGAACCTTATACCTTAGAGATGTGATGGGAAAGA
TTGAAGCCGCAACGATGAATCTTATACCTTAGAGATGTAAAGGAAAGGTTGAAGCTGTAACGACG
AACCTTATACCTTAAA
Found at i:2292 original size:93 final size:94
Alignment explanation
Indices: 2195--2433 Score: 254
Period size: 93 Copynumber: 2.5 Consensus size: 94
2185 ATGAAGTGCG
*
2195 TCAAAACAGGTAGCAGATCTCAATGTCTCTAAGGTTACAATGGAATGGAATGAAG-CACCAGATC
1 TCAAAACAGGTAGCAGATCTCAATGTCTCTAAGGTTACAATGGAATGGAATGAAGACACCAAATC
2259 CTATATCC-CTGAAGTTGCAGTGGATCAGA
66 CTATA-CCTCTGAAGTTGCAGTGGATCAGA
* * * *
2288 TCAAAA-TGAGTAACAGATCTCAATGTC-CTTGAGGTTACAATGGAATGGAGTGAAGTTAAAACA
1 TCAAAACAG-GTAGCAGATCTCAATGTCTC-TAAGGTTACAATGGAATGGAATGAAG-----ACA
* *
2351 CCAAATCCTATACCTCTGAAGTTGTAGTGGGTCAGA
59 CCAAATCCTATACCTCTGAAGTTGCAGTGGATCAGA
* * * *
2387 TTAAAACAATGAAGCAGATCTCAATGT-TCCTAAGGTTACAGTGGAAT
1 TCAAAAC-AGGTAGCAGATCTCAATGTCT-CTAAGGTTACAATGGAAT
2434 AGAGAGAAGC
Statistics
Matches: 119, Mismatches: 14, Indels: 19
0.78 0.09 0.12
Matches are distributed among these distances:
92 2 0.02
93 47 0.39
98 2 0.02
99 37 0.31
100 30 0.25
101 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.26
Consensus pattern (94 bp):
TCAAAACAGGTAGCAGATCTCAATGTCTCTAAGGTTACAATGGAATGGAATGAAGACACCAAATC
CTATACCTCTGAAGTTGCAGTGGATCAGA
Found at i:2452 original size:100 final size:99
Alignment explanation
Indices: 2195--2456 Score: 258
Period size: 100 Copynumber: 2.7 Consensus size: 99
2185 ATGAAGTGCG
* * * *
2195 TCAAAACAGGTAGCAGATCTCAATGT-CTCTAAGGTTACAATGGAAT---G-GAA--TGAAGCAC
1 TCAAAACAAGTAACAGATCTCAATGTCCT-TAAGGTTACAATGGAATAGAGAGAAGTTAAAACAC
*
2253 CAGATCCTATATCCCTGAAGTTGCAGTGGATCAGA
65 CAAATCCTATATCCCTGAAGTTGCAGTGGATCAGA
** * * *
2288 TCAAAATGAGTAACAGATCTCAATGTCCTTGAGGTTACAATGGAATGGAGTGAAGTTAAAACACC
1 TCAAAACAAGTAACAGATCTCAATGTCCTTAAGGTTACAATGGAATAGAGAGAAGTTAAAACACC
* *
2353 AAATCCTATA-CCTCTGAAGTTGTAGTGGGTCAGA
66 AAATCCTATATCC-CTGAAGTTGCAGTGGATCAGA
* * *
2387 TTAAAACAA-TGAAGCAGATCTCAATGTTCC-TAAGGTTACAGTGGAATAGAGAGAAGCTT-CAA
1 TCAAAACAAGT-AA-CAGATCTCAATG-TCCTTAAGGTTACAATGGAATAGAGAGAAG-TTAAAA
2449 CACCAAAT
62 CACCAAAT
2457 TCCATTTTCT
Statistics
Matches: 139, Mismatches: 18, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
93 38 0.27
94 2 0.01
96 1 0.01
97 3 0.02
98 3 0.02
99 43 0.31
100 44 0.32
101 5 0.04
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (99 bp):
TCAAAACAAGTAACAGATCTCAATGTCCTTAAGGTTACAATGGAATAGAGAGAAGTTAAAACACC
AAATCCTATATCCCTGAAGTTGCAGTGGATCAGA
Done.