Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003241.1 Kokia drynarioides strain JFW-HI SEQ_115889, 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: 18523
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Found at i:2180 original size:24 final size:23
Alignment explanation
Indices: 2144--2191 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
2134 TCTTTCCTTC
*
2144 AAAATTGGAATCTTTATTCGTTTT
1 AAAATTGGAATCTTCATTC-TTTT
2168 AAAATT-GAGATCTTCATTCTTTT
1 AAAATTGGA-ATCTTCATTCTTTT
2191 A
1 A
2192 TTTTTACGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (23 bp):
AAAATTGGAATCTTCATTCTTTT
Found at i:2308 original size:3 final size:3
Alignment explanation
Indices: 2300--2325 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2290 ATCTTTTTAA
2300 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2326 CAACACCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:14048 original size:48 final size:47
Alignment explanation
Indices: 13978--14242 Score: 255
Period size: 49 Copynumber: 5.5 Consensus size: 47
13968 CAGGTCTCAT
* * * *
13978 TACCACAAAAACAAGAAGGGAAAGGTTTAAGCCGCAACGGTGAACCTTG
1 TACCTCAAAAA-ATGAAGGGAAAGGTTTAAGCCGTAACGGCGAACC-TG
* * *
14027 TACCTCAAAAAATGAGGGGAAAGATTTAAGCCGTAACGGCGAATCCAG
1 TACCTCAAAAAATGAAGGGAAAGGTTTAAGCCGTAACGGCGAA-CCTG
* * * *
14075 TACCAC-GAAGATGCAAAGGGAAAGGTTTAAGCCGCAACGGCGAACCGTG
1 TACCTCAAAAAATG--AAGGGAAAGGTTTAAGCCGTAACGGCGAACC-TG
* *
14124 TACCTCAAAAAATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAG
1 TACCTCAAAAAATGAAGGGAAAGGTTTAAGCCGTAACGGCGAA-CCTG
* * * * * *
14172 TACCAC-GAAGATGCAAAGGGAAAGGTTTAAGTCGTAACGACGAACTGTG
1 TACCTCAAAAAATG--AAGGGAAAGGTTTAAGCCGTAACGGCGAAC-CTG
14221 TACCTCAAAAAATGAAGGGAAA
1 TACCTCAAAAAATGAAGGGAAA
14243 ATGAAGGGAA
Statistics
Matches: 175, Mismatches: 31, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
47 10 0.06
48 77 0.44
49 78 0.45
50 10 0.06
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (47 bp):
TACCTCAAAAAATGAAGGGAAAGGTTTAAGCCGTAACGGCGAACCTG
Found at i:14144 original size:97 final size:97
Alignment explanation
Indices: 13993--14432 Score: 495
Period size: 97 Copynumber: 4.4 Consensus size: 97
13983 CAAAAACAAG
* * * *
13993 AAGGGAAAGGTTTAAGCCGCAACGGTGAACCTTGTACCTCAAAAAATGAGGGGAAAGATTTAAGC
1 AAGGGAAAGGTTTAAGTCGCAACGGCGAACCGTGTACCTCAAAAAATGAAGGGAAAGATTTAAGC
*
14058 CGTAACGGCGAATCCAGTACCACGAAGATGCA
66 CGCAACGGCGAATCCAGTACCACGAAGATGCA
*
14090 AAGGGAAAGGTTTAAGCCGCAACGGCGAACCGTGTACCTCAAAAAATGAAGGGAAAGATTTAAGC
1 AAGGGAAAGGTTTAAGTCGCAACGGCGAACCGTGTACCTCAAAAAATGAAGGGAAAGATTTAAGC
*
14155 CGTAACGGCGAATCCAGTACCACGAAGATGCA
66 CGCAACGGCGAATCCAGTACCACGAAGATGCA
* * *
14187 AAGGGAAAGGTTTAAGTCGTAACGACGAACTGTGTACCTCAAAAAATGAAGGGAAAATGAAGGGA
1 AAGGGAAAGGTTTAAGTCGCAACGGCGAACCGTGTACCTC--------AA---AAAATGAAGGGA
* *
14252 AAGATTTAAGCCGCAATGGCGAATCCAGTACCATGAAGATGCA
55 AAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATGCA
* * * ** *** *
14295 AAGGGAACGGTTTAAGTCGCAATGGTGAACTTTGTACCTCAGAAGCGTAAAGGGAAAGATTTAAG
1 AAGGGAAAGGTTTAAGTCGCAACGGCGAACCGTGTACCTCA-AAAAATGAAGGGAAAGATTTAAG
* * * * *
14360 CTGCAACGACGAATCTAGTACCA-TAGAGATACA
65 CCGCAACGGCGAATCCAGTACCACGA-AGATGCA
* * *
14393 AAGGGAAAGGTTTAAGTCACAACGACGAACCCTGTACCTC
1 AAGGGAAAGGTTTAAGTCGCAACGGCGAACCGTGTACCTC
14433 GAAAGCGTGA
Statistics
Matches: 297, Mismatches: 33, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
97 131 0.44
98 76 0.26
100 1 0.00
101 1 0.00
105 2 0.01
108 86 0.29
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.17
Consensus pattern (97 bp):
AAGGGAAAGGTTTAAGTCGCAACGGCGAACCGTGTACCTCAAAAAATGAAGGGAAAGATTTAAGC
CGCAACGGCGAATCCAGTACCACGAAGATGCA
Found at i:14245 original size:11 final size:11
Alignment explanation
Indices: 14229--14253 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
14219 TGTACCTCAA
14229 AAAATGAAGGG
1 AAAATGAAGGG
14240 AAAATGAAGGG
1 AAAATGAAGGG
14251 AAA
1 AAA
14254 GATTTAAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.32, T:0.08
Consensus pattern (11 bp):
AAAATGAAGGG
Found at i:14325 original size:108 final size:108
Alignment explanation
Indices: 14132--14432 Score: 345
Period size: 108 Copynumber: 2.9 Consensus size: 108
14122 TGTACCTCAA
*
14132 AAAATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGATGCAAAGGGAAAGG
1 AAAATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATGCAAAGGGAAAGG
*
14197 TTTAAGTCGTAACGACGAACTGTGTACCTCAAAAAATGAAGGG
66 TTTAAGTCGCAACGACGAACTGTGTACCTCAAAAAATGAAGGG
* * *
14240 AAAATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCATGAAGATGCAAAGGGAACGG
1 AAAATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATGCAAAGGGAAAGG
* ** * *
14305 TTTAAGTCGCAATGGTGAACTTTGTACCTC-----A-GAAGCG
66 TTTAAGTCGCAACGACGAACTGTGTACCTCAAAAAATGAAGGG
* * * * * *
14342 ----TAAAGGGAAAGATTTAAGCTGCAACGACGAATCTAGTACCA-TAGAGATACAAAGGGAAAG
1 AAAATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGA-AGATGCAAAGGGAAAG
* **
14402 GTTTAAGTCACAACGACGAACCCTGTACCTC
65 GTTTAAGTCGCAACGACGAACTGTGTACCTC
14433 GAAAGCGTGA
Statistics
Matches: 168, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
97 1 0.01
98 75 0.45
102 5 0.03
103 1 0.01
108 86 0.51
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.18
Consensus pattern (108 bp):
AAAATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATGCAAAGGGAAAGG
TTTAAGTCGCAACGACGAACTGTGTACCTCAAAAAATGAAGGG
Found at i:14429 original size:98 final size:98
Alignment explanation
Indices: 14246--14440 Score: 250
Period size: 98 Copynumber: 2.0 Consensus size: 98
14236 AGGGAAAATG
* * * *
14246 AAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCATGAAGATGCAAAGGGAACGGTTTAAG
1 AAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCATGAAGATACAAAGGGAAAGGTTTAAG
* * ** **
14311 TCGCAATGGTGAACTTTGTACCTC-AGAAGCGTA
66 TCACAACGACGAACCCTGTACCTCGA-AAGCGTA
* *
14344 AAGGGAAAGATTTAAGCTGCAACGACGAATCTAGTACCAT-AGAGATACAAAGGGAAAGGTTTAA
1 AAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCATGA-AGATACAAAGGGAAAGGTTTAA
14408 GTCACAACGACGAACCCTGTACCTCGAAAGCGT
65 GTCACAACGACGAACCCTGTACCTCGAAAGCGT
14441 GAATCTAGTA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
97 1 0.01
98 81 0.98
99 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (98 bp):
AAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCATGAAGATACAAAGGGAAAGGTTTAAG
TCACAACGACGAACCCTGTACCTCGAAAGCGTA
Found at i:14486 original size:71 final size:71
Alignment explanation
Indices: 14370--14503 Score: 207
Period size: 71 Copynumber: 1.9 Consensus size: 71
14360 CTGCAACGAC
* *
14370 GAATCTAGTACCATAGAGATACAAAGGGAAAGGTTTAAGTCACAACGACGAACCCTGTACCTCGA
1 GAATCTAGTACCATAGAGATACAAAGGGAAAAGTTTAAGTCACAACGACAAACCCTGTACCTCGA
14435 AAGCGT
66 AAGCGT
* * *
14441 GAATCTAGTACC-TCGAAGATACAAAGGGAAAAGTTTAAGTCACAACGGCAAACCTTGTACCTC
1 GAATCTAGTACCATAG-AGATACAAAGGGAAAAGTTTAAGTCACAACGACAAACCCTGTACCTC
14504 AGAGACATGG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 2 0.04
71 55 0.96
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (71 bp):
GAATCTAGTACCATAGAGATACAAAGGGAAAAGTTTAAGTCACAACGACAAACCCTGTACCTCGA
AAGCGT
Found at i:16648 original size:24 final size:23
Alignment explanation
Indices: 16612--16659 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
16602 TTTTTCCTTC
*
16612 AAAATTGGAATCTTTATTCGTTTT
1 AAAATTGGAATCTTCATTC-TTTT
16636 AAAATT-GAGATCTTCATTCTTTT
1 AAAATTGGA-ATCTTCATTCTTTT
16659 A
1 A
16660 TTTTCACGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (23 bp):
AAAATTGGAATCTTCATTCTTTT
Done.