Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010558.1 Kokia drynarioides strain JFW-HI SEQ_125479, 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: 25769
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:5924 original size:8 final size:8
Alignment explanation
Indices: 5911--5935 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5901 TCACACAAGA
5911 TTTCAATT
1 TTTCAATT
5919 TTTCAATT
1 TTTCAATT
5927 TTTCAATT
1 TTTCAATT
5935 T
1 T
5936 CATCATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTCAATT
Found at i:11125 original size:31 final size:30
Alignment explanation
Indices: 11088--11145 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
11078 ATCGGAGTTC
*
11088 AAAATGA-GAATTTTCGGATTCTCGGGGGGCA
1 AAAATGATG-ATTTT-GGATTCTCAGGGGGCA
11119 AAAATGATGATTTTGGATTCTCAGGGG
1 AAAATGATGATTTTGGATTCTCAGGGG
11146 TGAAACGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 12 0.48
31 12 0.48
32 1 0.04
ACGTcount: A:0.29, C:0.10, G:0.31, T:0.29
Consensus pattern (30 bp):
AAAATGATGATTTTGGATTCTCAGGGGGCA
Found at i:11218 original size:59 final size:59
Alignment explanation
Indices: 11171--11524 Score: 503
Period size: 59 Copynumber: 6.0 Consensus size: 59
11161 GGGAAAATTC
* * **
11171 GGGGTCAAAAATTGGATTTTTGAAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTT
* * *
11230 AGGGTC-AAAATGGTATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTTGGAAGTTTT
1 GGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAA-TTTTTGGAAGTTTT
* **
11289 GAGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTT
* * * *
11348 AGGGTTAAGAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTT
1 GGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTT
* * * *
11407 GGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATTGATTTTTTGGAAGTTTC
1 GGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTT
* *
11466 GAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGATTTTTTGGATAGTTT
1 GGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA-AGTTT
11525 AGGGACCTTC
Statistics
Matches: 261, Mismatches: 31, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
58 32 0.12
59 190 0.73
60 39 0.15
ACGTcount: A:0.30, C:0.03, G:0.31, T:0.36
Consensus pattern (59 bp):
GGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTT
Found at i:11515 original size:29 final size:29
Alignment explanation
Indices: 11171--11524 Score: 379
Period size: 29 Copynumber: 12.0 Consensus size: 29
11161 GGGAAAATTC
* * *
11171 GGGGTCAAAAATTGGATTTTTGAAAGTTTA
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTG
* *
11201 GGGGTAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGGATTTTTGGAAGTTTG
* * * *
11230 AGGGTCAAAATGGTATTTTTGGAAGTTCG
1 GGGGTAAAAATGGGATTTTTGGAAGTTTG
* * *
11259 GGGGTAAAAATAGAATTTTTTGGAAGTTTT
1 GGGGTAAAAATGGGA-TTTTTGGAAGTTTG
* *
11289 GAGGTCAAAAATGGGATTTTTGGAAGTTTA
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTG
* *
11319 GGGGTAAAAATGGAATTTTTGGAAGTTTTA
1 GGGGTAAAAATGGGATTTTTGGAAG-TTTG
* * *
11349 GGGTTAAGAATGGGATTTTTGGAAGTTCG
1 GGGGTAAAAATGGGATTTTTGGAAGTTTG
*
11378 GGGGTAAAAATGGGATTTTTGGAAGTTTT
1 GGGGTAAAAATGGGATTTTTGGAAGTTTG
*
11407 GGGGTCAAAAATGGGATTTTTGGAAGTTCG
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTG
* * *
11437 AGGGTAAAAAT-TGATTTTTTGGAAGTTTC
1 GGGGTAAAAATGGGA-TTTTTGGAAGTTTG
* *
11466 GAGGTCAAAAATGGGATTTTTGGAAGTTCG
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTG
11496 GGGGTAAAAAT-GGATTTTTTGGATAGTTT
1 GGGGTAAAAATGGGA-TTTTTGGA-AGTTT
11525 AGGGACCTTC
Statistics
Matches: 272, Mismatches: 43, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
28 5 0.02
29 141 0.52
30 116 0.43
31 10 0.04
ACGTcount: A:0.30, C:0.03, G:0.31, T:0.36
Consensus pattern (29 bp):
GGGGTAAAAATGGGATTTTTGGAAGTTTG
Found at i:12641 original size:15 final size:15
Alignment explanation
Indices: 12621--12649 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12611 TTTATTTGTC
12621 ATTAATATTATTAAT
1 ATTAATATTATTAAT
12636 ATTAATATTATTAA
1 ATTAATATTATTAA
12650 GAAAATATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTAATATTATTAAT
Found at i:13460 original size:6 final size:6
Alignment explanation
Indices: 13446--13509 Score: 71
Period size: 6 Copynumber: 11.2 Consensus size: 6
13436 ATTTGGAAAA
* * *
13446 TAAATT TAAACT TAAA-T TAAATT TAAATT CAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
13492 T-AATA TAAATT TAAATT T
1 TAAATT TAAATT TAAATT T
13510 CTAAACAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
5 12 0.25
6 36 0.75
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:13471 original size:11 final size:11
Alignment explanation
Indices: 13446--13508 Score: 58
Period size: 11 Copynumber: 5.5 Consensus size: 11
13436 ATTTGGAAAA
*
13446 TAAATTTAAACT
1 TAAA-TTAAATT
13458 TAAATTAAATT
1 TAAATTAAATT
*
13469 TAAATTCAAA-A
1 TAAATT-AAATT
13480 TAAATTTAAATT
1 TAAA-TTAAATT
13492 T-AATATAAATT
1 TAAAT-TAAATT
13503 TAAATT
1 TAAATT
13509 TCTAAACAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
10 1 0.02
11 29 0.67
12 13 0.30
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (11 bp):
TAAATTAAATT
Found at i:13509 original size:17 final size:17
Alignment explanation
Indices: 13414--13541 Score: 125
Period size: 17 Copynumber: 7.4 Consensus size: 17
13404 CCTTATTTAT
*
13414 TTTAAATTTATAAT-AA
1 TTTAAATTTAAAATAAA
13430 TCTTAAATTTGGAAAATAAA
1 T-TTAAATTT--AAAATAAA
* *
13450 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
*
13467 TTTAAATTCAAAATAAA
1 TTTAAATTTAAAATAAA
*
13484 TTTAAATTTAATATAAA
1 TTTAAATTTAAAATAAA
* *
13501 TTTAAATTTCTAAACAAA
1 TTTAAATTT-AAAATAAA
*
13519 TTT-ATTCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
13536 TTTAAA
1 TTTAAA
13542 GGGAGTTTGG
Statistics
Matches: 90, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
16 1 0.01
17 64 0.71
18 11 0.12
19 11 0.12
20 3 0.03
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:14269 original size:206 final size:203
Alignment explanation
Indices: 13851--14652 Score: 987
Period size: 206 Copynumber: 3.9 Consensus size: 203
13841 TCTGGTTTTA
* * * * * **
13851 TTGACTTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGGCCGCATCACTTGTTTTGATC-CATT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCGCTTGTTTCAATCGC--T
* * * * * *
13915 TCTCTGTGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGGAGTTAACCA
64 TCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACC-
* * * * *
13980 CTTTATTGCTTCGACCTGTTTCTCAGTGTCTCATCAAGAAGCTGAGATTCGAAGA-TTTGCTCAC
128 TTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCAC
* * * *
14044 ATCGGGCATGAGT
193 TTTGAGC-TG-GC
*
14057 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTTGTTTCAACTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCGCTTGTTTCAA-TCGCTT
* * *
14122 CTCTATACCTCATCAGGAAGGC-AGATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCT
65 CTCTGTATCTCATCAGGAAGACGA-ATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCT
* * * *
14186 TTTATTGCTTCGACCTGCTTCTCAGTGTCTTATCAGGAAGTTGGGGTTCGAAGATTTTGTTCGCT
129 TTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACT
14251 TTGAGCGTGGGC
194 TTGAGC-T-GGC
* *
14263 TTGATTTGGTCTTCTTATCAGTATCTCATCAGGGAGATGA-TCGCATCGCTTGTTTCAATCCGCT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACT-GCATCGCTTGTTTCAAT-CGCT
*
14327 TCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTTTCAGTATCTCATCAGGAAGCTAACCT
64 TCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCT
* *
14392 TTTATCGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGTTGGGGTTCGAAGATTTTGCTCACT
129 TTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACT
14457 TTGAGC---C
194 TTGAGCTGGC
* * * * *
14464 TCG-TTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACTGCGTTGTTTGTTTCAACTCGCT
1 TTGATTT-GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCGCTTGTTTCAA-TCGCT
* * *
14528 TCTCTGTATCTCATCAGGAAGGCGAATTTGGTTGAC-TCATCAGTATCTCATTAGGAAGCTAACC
64 TCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTC-TCAGTATCTCATCAGGAAGCTAACC
* *
14592 -TTTATTGCTTCGACCTGCTTCTCAATGTCTCATCAAGG-AGCTGGGGTTCGAAGGTTTTGCT
128 TTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATC-AGGAAGCTGGGGTTCGAAGATTTTGCT
14653 TGCTTTGTGG
Statistics
Matches: 526, Mismatches: 57, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
200 57 0.11
201 111 0.21
202 2 0.00
205 50 0.10
206 301 0.57
207 4 0.01
208 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.36
Consensus pattern (203 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCGCTTGTTTCAATCGCTTC
TCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTT
TATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTT
GAGCTGGC
Done.