Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011936.1 Kokia drynarioides strain JFW-HI SEQ_126934, 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: 9866
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Found at i:887 original size:31 final size:31
Alignment explanation
Indices: 847--905 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
837 TTTAAATGTG
* *
847 TATAGTTGAATCGCAATCAAAATTTCATTTA
1 TATAGTTGAACCACAATCAAAATTTCATTTA
* * *
878 TATATTTGAACCATAATTAAAATTTCAT
1 TATAGTTGAACCACAATCAAAATTTCAT
906 GTGTATAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.41
Consensus pattern (31 bp):
TATAGTTGAACCACAATCAAAATTTCATTTA
Found at i:946 original size:30 final size:31
Alignment explanation
Indices: 865--939 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
855 AATCGCAATC
* *
865 AAAATTTCATTTATATATTTGA-ACCATAATT
1 AAAATTTCATGTATATAATT-ACACCATAATT
*
896 AAAATTTCATGTGTATAATTACACCA-AATT
1 AAAATTTCATGTATATAATTACACCATAATT
926 AAAA-TTCATAGTAT
1 AAAATTTCAT-GTAT
940 CAAATTATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 5 0.13
30 12 0.32
31 21 0.55
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (31 bp):
AAAATTTCATGTATATAATTACACCATAATT
Found at i:1795 original size:17 final size:18
Alignment explanation
Indices: 1773--1830 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 18
1763 TTTATTTACT
1773 TAAATTTAATT-TAAAAA
1 TAAATTTAATTATAAAAA
* * *
1790 TAAATTTCATTATTAAAT
1 TAAATTTAATTATAAAAA
1808 TAAA-TTAATTATAAAAA
1 TAAATTTAATTATAAAAA
*
1825 GAAATT
1 TAAATT
1831 GCAAATCCCC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
17 23 0.72
18 9 0.28
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
TAAATTTAATTATAAAAA
Found at i:3529 original size:31 final size:31
Alignment explanation
Indices: 3494--3552 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
3484 ATAGTTATTG
*
3494 AACTATTCAAAAGTTTTTATTTAAGTCATTA
1 AACTATTCAAAAGTTTTCATTTAAGTCATTA
3525 AACTATTCAAAAGTTTTCATTTAAGTCA
1 AACTATTCAAAAGTTTTCATTTAAGTCA
3553 CCAGGTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTCATTTAAGTCATTA
Found at i:5222 original size:15 final size:15
Alignment explanation
Indices: 5202--5230 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5192 TTCTTAACGT
5202 ATATAATTTTTTTTA
1 ATATAATTTTTTTTA
5217 ATATAATTTTTTTT
1 ATATAATTTTTTTT
5231 GTTCATATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATAATTTTTTTTA
Found at i:8549 original size:96 final size:96
Alignment explanation
Indices: 8375--8556 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 96
8365 AAGGATATTT
** * *
8375 GATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCGGAATCAAAGA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACCAAAGA
*
8440 TAAGGAAACATTGCCTCGATTAAGGGTATCC
66 TAAAGAAACATTGCCTCGATTAAGGGTATCC
* * *
8471 GATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTCGAAACCCGAA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATA-TTTCGAAA-CCAAA
*
8535 -ATAAA-AGAATATTGCCTCGATT
64 GATAAAGA-AACATTGCCTCGATT
8557 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 2 0.03
96 69 0.93
97 3 0.04
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACCAAAGA
TAAAGAAACATTGCCTCGATTAAGGGTATCC
Found at i:8998 original size:59 final size:58
Alignment explanation
Indices: 8866--9118 Score: 332
Period size: 58 Copynumber: 4.3 Consensus size: 58
8856 AAAAGGGGAT
* * * *
8866 TTTTTGGAAGGTTCAAGGTC-AAAATGGGATTTTTAGAAGTTCGGAGTGGGGGTAAAATGATAA
1 TTTTTGGAAGGTTCGAGGTCAAAAAT-GGACTTTTGGAAGTTC-----GGGGGTAAAATGGTAA
8929 TTTTTGGAAGGTTCGAGGTCAAAAATGAGACTTTTGGAAGTTCGGGGGTAAAATGGTAA
1 TTTTTGGAAGGTTCGAGGTCAAAAATG-GACTTTTGGAAGTTCGGGGGTAAAATGGTAA
* * *
8988 TTTTTAGAAGGTTC-AGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAA
1 TTTTTGGAAGGTTCGAGGTCAAAAAT-GGACTTTTGGAAGTTCGGGGGTAAAATGGTAA
*
9046 TTTTTGGAAGGTTCGAGGTAAAAAATGGAACTTTTGGAAGTTC-GGGGTAAAATGGTAA
1 TTTTTGGAAGGTTCGAGGTCAAAAATGG-ACTTTTGGAAGTTCGGGGGTAAAATGGTAA
9104 TTTTTGGAAGGTTCG
1 TTTTTGGAAGGTTCG
9119 GGGGGTAAAA
Statistics
Matches: 174, Mismatches: 11, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
58 84 0.48
59 52 0.30
63 20 0.11
64 18 0.10
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.32
Consensus pattern (58 bp):
TTTTTGGAAGGTTCGAGGTCAAAAATGGACTTTTGGAAGTTCGGGGGTAAAATGGTAA
Found at i:9335 original size:206 final size:206
Alignment explanation
Indices: 8866--9404 Score: 721
Period size: 206 Copynumber: 2.6 Consensus size: 206
8856 AAAAGGGGAT
*
8866 TTTTTGGAAGGTTCAA-GGTCAAAATGG-GATTTTTAGAAGTTCGGAGTGGGGGTAAAATGATAA
1 TTTTTGGAA-GTTCAAGGGT-AAAATGGTAATTTTTAGAAGTTC-GA---GGGGTAAAATGATAA
* * * *
8929 TTTTTGGAAGGTTCGAGGTCAAAAATGAGACTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTA
60 TTTTTAGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTA
* *
8994 GAAGGTTCAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTT
125 GAAGGTTCAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTAGAAGGTT
9059 CGAGGTAAAAAATGGAA
190 CGAGGTAAAAAATGGAA
* * * * *
9076 CTTTTGGAAGTTC-GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGGGTAAAATGGTAATTTTT
1 TTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTAGAA-GTTCGAGGGGTAAAATGATAATTTTT
** *
9140 AGAAGGTTCGGGGTTTAAAATGAGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTAGAAGG
65 AGAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGG
* * *
9205 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGATAATTTTTAGAAGGTTCGAG
130 TTC-AGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTAGAAGGTTCGAG
*
9270 GTTAAAAAT-GATA
194 GTAAAAAATGGA-A
*
9283 TTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTAGAAGTTC-AGGAGTAAAATGATAATTTTTA
1 TTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTAGAAGTTCGAGGGGTAAAATGATAATTTTTA
* * ** *
9347 AAAGGTTCGGGGTCAAAAAT-ATAATTTTTAAAAGTTCGAGGGTAAAACGGTAATTTTT
66 GAAGGTTCGGGGTCAAAAATGA-GATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTT
9405 GGAAAGTTTA
Statistics
Matches: 289, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
205 1 0.00
206 149 0.52
207 81 0.28
208 29 0.10
209 17 0.06
210 12 0.04
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (206 bp):
TTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTAGAAGTTCGAGGGGTAAAATGATAATTTTTA
GAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGT
TCAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTAGAAGGTTCGAGGT
AAAAAATGGAA
Found at i:9341 original size:29 final size:30
Alignment explanation
Indices: 8914--9417 Score: 327
Period size: 29 Copynumber: 17.1 Consensus size: 30
8904 GTTCGGAGTG
8914 GGGGTAAAATGATAATTTTTGGAAGGTTC-
1 GGGGTAAAATGATAATTTTTGGAAGGTTCA
* * * *
8943 GAGGTCAAAAATGA-GACTTTTGGAA-GTTCG
1 GGGGT--AAAATGATAATTTTTGGAAGGTTCA
* *
8973 GGGGTAAAATGGTAATTTTTAGAAGGTTCA
1 GGGGTAAAATGATAATTTTTGGAAGGTTCA
*** **
9003 GGTCAAAAATG-GGATTTTTGGAA-GTTC-
1 GGGGTAAAATGATAATTTTTGGAAGGTTCA
*
9030 GAGGGTAAAATGGTAATTTTTGGAAGGTTC-
1 G-GGGTAAAATGATAATTTTTGGAAGGTTCA
* * *
9060 GAGGTAAAAAATG-GAACTTTTGGAA-GTTC-
1 GGGGT--AAAATGATAATTTTTGGAAGGTTCA
* *
9089 GGGGTAAAATGGTAATTTTTGGAAGGTTCGG
1 GGGGTAAAATGATAATTTTTGGAAGGTTC-A
* *
9120 GGGGTAAAATGGTAATTTTTAGAAGGTTC-
1 GGGGTAAAATGATAATTTTTGGAAGGTTCA
* * *
9149 GGGGTTTAAAATGA-GATTTTTGGAAGTTTGA
1 GGGG--TAAAATGATAATTTTTGGAAGGTTCA
* *
9180 -GGGTAAAATGGTAATTTTTAGAAGGTTC-
1 GGGGTAAAATGATAATTTTTGGAAGGTTCA
** **
9208 GGGGTCAAAAATG-GGATTTTTGGAA-GTTTG
1 GGGGT--AAAATGATAATTTTTGGAAGGTTCA
*
9238 GGGGTAAAATGATAATTTTTAGAAGGTTC-
1 GGGGTAAAATGATAATTTTTGGAAGGTTCA
*
9267 GAGGTTAAAAATGAT-ATTTTTGGAA-GTTCA
1 G-GGGT-AAAATGATAATTTTTGGAAGGTTCA
* * *
9297 AGGGTAAAATGGTAATTTTTAGAA-GTTCA
1 GGGGTAAAATGATAATTTTTGGAAGGTTCA
* **
9326 GGAGTAAAATGATAATTTTTAAAAGGTTC-
1 GGGGTAAAATGATAATTTTTGGAAGGTTCA
* *
9355 GGGGTCAAAAAT-ATAATTTTT-AAAAGTTC-
1 GGGGT--AAAATGATAATTTTTGGAAGGTTCA
* * * *
9384 GAGGGTAAAACGGTAATTTTTGGAAAGTTTA
1 G-GGGTAAAATGATAATTTTTGGAAGGTTCA
9415 GGG
1 GGG
9418 ACCTCCGAGG
Statistics
Matches: 379, Mismatches: 61, Indels: 69
0.74 0.12 0.14
Matches are distributed among these distances:
27 7 0.02
28 51 0.13
29 144 0.38
30 109 0.29
31 68 0.18
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.33
Consensus pattern (30 bp):
GGGGTAAAATGATAATTTTTGGAAGGTTCA
Found at i:9372 original size:59 final size:59
Alignment explanation
Indices: 8866--9408 Score: 401
Period size: 59 Copynumber: 9.2 Consensus size: 59
8856 AAAAGGGGAT
** * *
8866 TTTTTGGAAGGTTCAAGGTCAAAATGG-GATTTTTAGAAGTTCGGAGTGGGGGTAAAATGATAA
1 TTTTTGGAAGGTTCGGGGTAAAAATGGTAATTTTTAGAAGTTC--A---GGGGTAAAATGATAA
* * * * *
8929 TTTTTGGAAGGTTCGAGGTCAAAAAT-G-AGACTTTTGGAAGTTCGGGGGTAAAATGGTAA
1 TTTTTGGAAGGTTCGGGGT-AAAAATGGTA-ATTTTTAGAAGTTCAGGGGTAAAATGATAA
* * * * *
8988 TTTTTAGAAGGTTC-AGGTCAAAAATGG-GATTTTTGGAAGTTC-GAGGGTAAAATGGTAA
1 TTTTTGGAAGGTTCGGGGT-AAAAATGGTAATTTTTAGAAGTTCAG-GGGTAAAATGATAA
* * * *
9046 TTTTTGGAAGGTTCGAGGTAAAAAATGG-AACTTTTGGAAGTTC-GGGGTAAAATGGTAA
1 TTTTTGGAAGGTTCGGGGT-AAAAATGGTAATTTTTAGAAGTTCAGGGGTAAAATGATAA
*
9104 TTTTTGGAAGGTTCGGGGGGT-AAAATGGTAATTTTTAGAAGGTTC-GGGGTTTAAAATGA-GA
1 TTTTTGGAAGGTTC--GGGGTAAAAATGGTAATTTTTAGAA-GTTCAGGGG--TAAAATGATAA
* **
9165 TTTTTGGAA-GTTTGAGGGT-AAAATGGTAATTTTTAGAAGGTTC-GGGGTCAAAAATG-GGA
1 TTTTTGGAAGGTTCG-GGGTAAAAATGGTAATTTTTAGAA-GTTCAGGGGT--AAAATGATAA
* * * *
9224 TTTTTGGAAGTTTGGGGGT-AAAATGATAATTTTTAGAAGGTTC-GAGGTTAAAAATGAT-A
1 TTTTTGGAAGGTTCGGGGTAAAAATGGTAATTTTTAGAA-GTTCAG-GGGT-AAAATGATAA
* *
9283 TTTTTGGAA-GTTCAAGGGT-AAAATGGTAATTTTTAGAAGTTCAGGAGTAAAATGATAA
1 TTTTTGGAAGGTTC-GGGGTAAAAATGGTAATTTTTAGAAGTTCAGGGGTAAAATGATAA
** * * * *
9341 TTTTTAAAAGGTTCGGGGTCAAAAAT-ATAATTTTTAAAAGTTC-GAGGGTAAAACGGTAA
1 TTTTTGGAAGGTTCGGGGT-AAAAATGGTAATTTTTAGAAGTTCAG-GGGTAAAATGATAA
9400 TTTTTGGAA
1 TTTTTGGAA
9409 AGTTTAGGGA
Statistics
Matches: 414, Mismatches: 41, Indels: 54
0.81 0.08 0.11
Matches are distributed among these distances:
57 10 0.02
58 108 0.26
59 217 0.52
60 26 0.06
61 10 0.02
62 7 0.02
63 19 0.05
64 17 0.04
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (59 bp):
TTTTTGGAAGGTTCGGGGTAAAAATGGTAATTTTTAGAAGTTCAGGGGTAAAATGATAA
Done.