Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006444.1 Kokia drynarioides strain JFW-HI SEQ_121027, 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: 2716
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Found at i:84 original size:49 final size:49
Alignment explanation
Indices: 27--465 Score: 281
Period size: 49 Copynumber: 8.9 Consensus size: 49
17 CAGAAGCATG
* * *
27 AAGGGAAAGATTTAAGCCGCAACAGCGAATCCAGTACCACGAAGATACA
1 AAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCACGAAGACACA
* * * **
76 AAGGGAAAGGTTTAAGTCGTAACGGCGAA-CCTTA-TACCTC-AGAGACATG
1 AAGGGAAAGATTTAAGTCGCAACGGCGAATCC--AGTACCACGA-AGACACA
* ** * * *
125 AAGGGAAAGATTTAAGCCATAACGGTGAATCTAATACCACGAAGACACAA
1 AAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCACGAAGACAC-A
* * * * * **
175 AAGTGAAAGGTTTAAGTCGCAACGGCGAA-CCTTGTACCTC-AAAAGCATG
1 AAGGGAAAGATTTAAGTCGCAACGGCGAATCC-AGTACCACGAAGA-CACA
* * *
224 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATACA
1 AAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCACGAAGACACA
* * * * * **
273 AAGCGAAAGGTTTAAGTTGTAACGGCGAA-CCATATACCTTA-G-AGACATG
1 AAGGGAAAGATTTAAGTCGCAACGGCGAATCCA-GTACC--ACGAAGACACA
* * *
322 AAGGGAAAGATTTAAGTCGCAATGGCAAATCTAGTACCACGAAGACACAA
1 AAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCACGAAGACAC-A
* * * * **
372 AAGGGAAAGGTTTAAGTCGAAATGGCGAA-CCTTA-TACCTCAGAAG-CATG
1 AAGGGAAAGATTTAAGTCGCAACGGCGAATCC--AGTACCAC-GAAGACACA
* * *
421 AAGGGAAAGATTTAAG-CGACAACGACGAATCTATTACCACGAAGA
1 AAGGGAAAGATTTAAGTCG-CAACGGCGAATCCAGTACCACGAAGA
466 TATGGAGGGA
Statistics
Matches: 293, Mismatches: 72, Indels: 50
0.71 0.17 0.12
Matches are distributed among these distances:
47 1 0.00
48 14 0.05
49 198 0.68
50 74 0.25
51 6 0.02
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.18
Consensus pattern (49 bp):
AAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCACGAAGACACA
Found at i:227 original size:99 final size:98
Alignment explanation
Indices: 3--465 Score: 617
Period size: 99 Copynumber: 4.7 Consensus size: 98
1 GA
* * * *
3 CGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAGTACCACG
1 CGAACCTTATACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACG
*
68 AAGATACAAAGGGAAAGGTTTAAGTCGTAACGG
66 AAGACACAAAGGGAAAGGTTTAAGTCGTAACGG
* ** * *
101 CGAACCTTATACCTC-AGAGACATGAAGGGAAAGATTTAAGCCATAACGGTGAATCTAATACCAC
1 CGAACCTTATACCTCAAAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAC
* *
165 GAAGACACAAAAGTGAAAGGTTTAAGTCGCAACGG
65 GAAGACAC-AAAGGGAAAGGTTTAAGTCGTAACGG
*
200 CGAACCTTGTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACG
1 CGAACCTTATACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACG
* * *
265 AAGATACAAAGCGAAAGGTTTAAGTTGTAACGG
66 AAGACACAAAGGGAAAGGTTTAAGTCGTAACGG
* * * * * *
298 CGAACCATATACCT-TAGAGACATGAAGGGAAAGATTTAAGTCGCAATGGCAAATCTAGTACCAC
1 CGAACCTTATACCTCAAAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAC
* *
362 GAAGACACAAAAGGGAAAGGTTTAAGTCGAAATGG
65 GAAGACAC-AAAGGGAAAGGTTTAAGTCGTAACGG
* * *
397 CGAACCTTATACCTCAGAAGCATGAAGGGAAAGATTTAAG-CGACAACGACGAATCTATTACCAC
1 CGAACCTTATACCTCAAAAGCATGAAGGGAAAGATTTAAGCCG-CAACGGCGAATCTAGTACCAC
461 GAAGA
65 GAAGA
466 TATGGAGGGA
Statistics
Matches: 316, Mismatches: 42, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
97 5 0.02
98 144 0.46
99 162 0.51
100 5 0.02
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.18
Consensus pattern (98 bp):
CGAACCTTATACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACG
AAGACACAAAGGGAAAGGTTTAAGTCGTAACGG
Found at i:362 original size:197 final size:197
Alignment explanation
Indices: 3--467 Score: 734
Period size: 197 Copynumber: 2.4 Consensus size: 197
1 GA
* *
3 CGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAGTACCACG
1 CGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACG
* *
68 AAGATACAAAGGGAAAGGTTTAAGTCGTAACGGCGAACCTTATACCTCAGAGACATGAAGGGAAA
66 AAGATACAAAGCGAAAGGTTTAAGTCGTAACGGCGAACCATATACCTCAGAGACATGAAGGGAAA
* ** * *
133 GATTTAAGCCATAACGGTGAATCTAATACCACGAAGACACAAAAGTGAAAGGTTTAAGTCGCAAC
131 GATTTAAGCCACAACGGCAAATCTAATACCACGAAGACACAAAAGGGAAAGGTTTAAGTCGAAAC
198 GG
196 GG
*
200 CGAACCTTGTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACG
1 CGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACG
* *
265 AAGATACAAAGCGAAAGGTTTAAGTTGTAACGGCGAACCATATACCTTAGAGACATGAAGGGAAA
66 AAGATACAAAGCGAAAGGTTTAAGTCGTAACGGCGAACCATATACCTCAGAGACATGAAGGGAAA
* * * * *
330 GATTTAAGTCGCAATGGCAAATCTAGTACCACGAAGACACAAAAGGGAAAGGTTTAAGTCGAAAT
131 GATTTAAGCCACAACGGCAAATCTAATACCACGAAGACACAAAAGGGAAAGGTTTAAGTCGAAAC
395 GG
196 GG
* * *
397 CGAACCTTATACCTCAGAAGCATGAAGGGAAAGATTTAAG-CGACAACGACGAATCTATTACCAC
1 CGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCG-CAACGGCGAATCTAGTACCAC
461 GAAGATA
65 GAAGATA
468 TGGAGGGAAA
Statistics
Matches: 246, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
196 2 0.01
197 244 0.99
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (197 bp):
CGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACG
AAGATACAAAGCGAAAGGTTTAAGTCGTAACGGCGAACCATATACCTCAGAGACATGAAGGGAAA
GATTTAAGCCACAACGGCAAATCTAATACCACGAAGACACAAAAGGGAAAGGTTTAAGTCGAAAC
GG
Found at i:828 original size:39 final size:39
Alignment explanation
Indices: 785--1048 Score: 219
Period size: 39 Copynumber: 6.8 Consensus size: 39
775 TTGCAACCGT
*
785 TCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAA
1 TCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAA
* * * * * *
824 TCGATCTCTTAACCCTAGCCTAGGGTAGATCACCATTAA
1 TCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAA
* * ** *
863 CCGATCTCTTACCCCGAGCTTGGGGTAGAT-TGCAGTCAG
1 TCGATCTCTTACCCCGAGCTTGGGGCAGATCACCA-TCAA
* * * * * * * *
902 CCAATCTTTTACCCGGAGCTTGGGGCATATTA-CAGCCA
1 TCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAA
* * * *
940 TCTGATCTTTTACCCCGTA-CCTGGGGCAAATCACAATCAA
1 TC-GATCTCTTACCCCG-AGCTTGGGGCAGATCACCATCAA
* *
980 TCAATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAA
1 TCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAA
* * *
1019 CCAATCTCTTACCCCGAGCCTGGGGCAGAT
1 TCGATCTCTTACCCCGAGCTTGGGGCAGAT
1049 TGCAGTTATC
Statistics
Matches: 180, Mismatches: 39, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
38 5 0.03
39 169 0.94
40 6 0.03
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (39 bp):
TCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAA
Found at i:1516 original size:17 final size:17
Alignment explanation
Indices: 1446--1519 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 17
1436 TTAAAACTTT
*
1446 AATTTATTTTAAGTTTA
1 AATTTATTTTAAATTTA
*
1463 AACTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* * * * *
1480 AACTTACTATGATTTTA
1 AATTTATTTTAAATTTA
*
1497 AATTTATTTTAAATTAA
1 AATTTATTTTAAATTTA
1514 AATTTA
1 AATTTA
1520 ATTAAAAGTG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:2245 original size:12 final size:12
Alignment explanation
Indices: 2226--2332 Score: 84
Period size: 12 Copynumber: 9.0 Consensus size: 12
2216 AAATAAAGTC
2226 ATAA-ATTAATA
1 ATAATATTAATA
* *
2237 ATGATATTAATG
1 ATAATATTAATA
2249 ATAATATTAATA
1 ATAATATTAATA
2261 ATAAATAATGGTAATAA
1 AT-AAT-AT--TAAT-A
*
2278 ATAACATTAAT-
1 ATAATATTAATA
2289 A-AATATTAATA
1 ATAATATTAATA
2300 A-AATA-T--TA
1 ATAATATTAATA
2308 ATAATATTAATA
1 ATAATATTAATA
2320 ATTAATATTAATA
1 A-TAATATTAATA
2333 TTAAATAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
8 3 0.04
9 4 0.05
10 10 0.13
11 9 0.12
12 21 0.27
13 18 0.23
14 2 0.03
15 2 0.03
16 6 0.08
17 3 0.04
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (12 bp):
ATAATATTAATA
Found at i:2264 original size:3 final size:3
Alignment explanation
Indices: 2232--2332 Score: 51
Period size: 3 Copynumber: 32.7 Consensus size: 3
2222 AGTCATAAAT
* * * * **
2232 TAA TAA TGA TAT TAA TGA TAA TAT TAA TAA TAAA TAA TGG TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA
* * * * *
2279 TAA CAT TAA TAAA TAT TAA TAA -AA TAT TAA TAA TAT TAA TAA TTAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
*
2325 TAT TAA TA
1 TAA TAA TA
2333 TTAAATAAAA
Statistics
Matches: 69, Mismatches: 24, Indels: 10
0.67 0.23 0.10
Matches are distributed among these distances:
2 2 0.03
3 55 0.80
4 12 0.17
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (3 bp):
TAA
Done.