Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011918.1 Kokia drynarioides strain JFW-HI SEQ_126916, 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: 6701
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Found at i:775 original size:41 final size:41
Alignment explanation
Indices: 730--807 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
720 CCTCTCACAC
730 AGATTGTTAGAATTGGGTGACTAGAATTCTTGTTAAAGTGG
1 AGATTGTTAGAATTGGGTGACTAGAATTCTTGTTAAAGTGG
771 AGATTGTTAGAATTGGGTGACTAGAATTCTTGTTAAA
1 AGATTGTTAGAATTGGGTGACTAGAATTCTTGTTAAA
808 ATAAAATTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (41 bp):
AGATTGTTAGAATTGGGTGACTAGAATTCTTGTTAAAGTGG
Found at i:5134 original size:17 final size:17
Alignment explanation
Indices: 5112--5150 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
5102 AGGTGGAGAA
* *
5112 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
5129 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
5146 CTTGT
1 CTTGT
5151 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:5197 original size:41 final size:41
Alignment explanation
Indices: 5140--5235 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
5130 TTGTTCGTAG
* *
5140 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGATGACT
1 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGATGACT
*
5181 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGATGACT
5222 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
5236 AATAAAATTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.36
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGATGACT
Found at i:5983 original size:251 final size:244
Alignment explanation
Indices: 5546--6056 Score: 711
Period size: 251 Copynumber: 2.1 Consensus size: 244
5536 TAATTTTATC
* * *
5546 AAAAGGAAAATTAAGTTATGAGGTTGCCGCCAAACCTTCAGATAAACCTTTATATATTTATATTG
1 AAAAGGAAAAGTGAGTAATGAGGTTGCCGCCAAACCTTCAGATAAACCTTTATATATTTATATTG
* * * *
5611 ACATCATCTTAGCATTATATATATTTATATTTTCCATTACTCAATGTCAAAGTGAACCTGTATAT
66 ACATCATCTTAGAATTATATATATTTATATTTGCCATTACTCAATGTCAAAATGAACCTATATAT
* * *
5676 ATTCTCTCTTCTCACTTAGATAAACTGAATTCTTTTGCCATTCAAACTTATTTCTTCTCTTCTCT
131 ATTCTCTCTTCTCACTAAGATAAACTGAATTCTTCTCCCATTCAAACTTATTTCTTCTCTTCTCT
* * *
5741 CAGTTT-TTCATCTTTTTCTCTTTGTTAGTTTATGTTAAGATGATTAAAGG
196 CA-TTTCATCATCTTTTTCTCTTTGTTAGTTGATGTTAAGATGATGAAA-G
**
5791 AAAAGGAAAAGTGAGTAATGAGGTTGTTGCCAAACCTTCAGATAAACCTATATATATATATATAT
1 AAAAGGAAAAGTGAGTAATGAGGTTGCCGCCAAACCTTCAGATAAACC--T-T-TATATAT-T-T
* *
5856 ATATTGACATCATCTTAGAATTATATATATTTATATTTGCTATTACTCAATGTCAAAATGACCCT
60 ATATTGACATCATCTTAGAATTATATATATTTATATTTGCCATTACTCAATGTCAAAATGAACCT
* * * * *
5921 ATATATTTTCTTTGTTCTCACTAAGATAAGCTTAATTCTTCTCCCATTCAAACTTATTTCTTCTC
125 ATATATATTCTCTCTTCTCACTAAGATAAACTGAATTCTTCTCCCATTCAAACTTATTTCTTCTC
* *
5986 TTCTCTCATTTCATCATCTTTTTCTTTTTGTTAGTTGATGTTAATATGATGAAAG
190 TTCTCTCATTTCATCATCTTTTTCTCTTTGTTAGTTGATGTTAAGATGATGAAAG
*
6041 AAAA-AAAAAGTGAGTA
1 AAAAGGAAAAGTGAGTA
6057 TAGAGGCTGC
Statistics
Matches: 234, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
245 43 0.18
247 1 0.00
248 1 0.00
249 18 0.08
250 9 0.04
251 162 0.69
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (244 bp):
AAAAGGAAAAGTGAGTAATGAGGTTGCCGCCAAACCTTCAGATAAACCTTTATATATTTATATTG
ACATCATCTTAGAATTATATATATTTATATTTGCCATTACTCAATGTCAAAATGAACCTATATAT
ATTCTCTCTTCTCACTAAGATAAACTGAATTCTTCTCCCATTCAAACTTATTTCTTCTCTTCTCT
CATTTCATCATCTTTTTCTCTTTGTTAGTTGATGTTAAGATGATGAAAG
Found at i:6595 original size:359 final size:359
Alignment explanation
Indices: 5936--6701 Score: 1166
Period size: 359 Copynumber: 2.1 Consensus size: 359
5926 TTTTCTTTGT
5936 TCTCACT-AAGATAAGCTTAATTCTTCTCCCATTCAAACTTATTTCTTCTCTTCTCTCATTTCAT
1 TCTCACTCAA-ATAAGCTTAATTCTTCTCCCATTCAAACTTATTTCTTCTCTTCTCTCATTTCAT
* * ** * *
6000 CATCTTTTTCTTTTTGTTAGTTGATGTTAATATGATGAAAGAAAAAAAAAGTGAGTATAGAGGCT
65 CATCTATTCCTTTTTGTTAGTCAATGTTAATATGATGAAAGAAAAAAAAAGTGAGTAAAGAGACT
* * * *
6065 GCTACAAAGTCTTCAATTGTCTATATTACCCAATCTCCATCATTTACAATCCTACCACCAAGAAA
130 ACTACAAAGCCTTCAATTGTCTATAGTACCCAATCTCCATCATTTACAAGCCTACCACCAAGAAA
6130 TATGTTTAAATTTATAAGGAAAACCATCCAAAATTCTTTCTTAGTTCATGTTTATAACAAAGATG
195 TATGTTTAAATTTATAAGGAAAACCATCCAAAATTCTTTCTTAGTTCATGTTTATAACAAAGATG
* *
6195 GATTTTAATTATATTTTTCTAATCTGCGTTTTTAAGTTCAACATGATTTATAGATCTTTTGGTGA
260 GATTTTAATTATATGTTTCAAATCTGCGTTTTTAAGTTCAACATGATTTATAGATCTTTTGGTGA
* *
6260 TAATGAATCATAATTGACCTTTATATATCCTCTCC
325 CAACGAATCATAATTGACCTTTATATATCCTCTCC
* *
6295 TCTCACTCAAATAAGCTTAATTCTTCTCCCATT-AAACTTATTTCTTCTCTTCTCTTATTTCTTC
1 TCTCACTCAAATAAGCTTAATTCTTCTCCCATTCAAACTTATTTCTTCTCTTCTCTCATTTCATC
* *
6359 ATCTATTCCTTTTTGTTGGTCAATGTTGATATGATGAAAGAAAAAGTAAAAGTGAGTAAAGAGAC
66 ATCTATTCCTTTTTGTTAGTCAATGTTAATATGATGAAAGAAAAA--AAAAGTGAGTAAAGAGAC
* * *
6424 TACTATAAAGCCTTCAGTTGTCTATAGTACCCAATCTCCATCATTTCCAAGCCTACCACCAAGAA
129 TACTACAAAGCCTTCAATTGTCTATAGTACCCAATCTCCATCATTTACAAGCCTACCACCAAGAA
* **
6489 TTAAT-TTTAAATTTATGAA-G-AAATTATCCAAAATTCTTTCTTAGTTCATGTTTATAACAAAG
194 AT-ATGTTTAAATTTAT-AAGGAAAACCATCCAAAATTCTTTCTTAGTTCATGTTTATAACAAAG
* *
6551 ATGGATTTTAATTATATGTTTCAAATCTGCGTTTTTAGGTTCAACATGATTTTTAGATCTTTTGG
257 ATGGATTTTAATTATATGTTTCAAATCTGCGTTTTTAAGTTCAACATGATTTATAGATCTTTTGG
6616 TGACAACGAATCATAATTGACCTTTATATATCCTCTCC
322 TGACAACGAATCATAATTGACCTTTATATATCCTCTCC
* * * *
6654 ACTCACTCAGATTAA-CTTAATTTTTCTCCTATTCAAACTTATTTCTTC
1 TCTCACTCA-AATAAGCTTAATTCTTCTCCCATTCAAACTTATTTCTTC
Statistics
Matches: 370, Mismatches: 30, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
358 68 0.18
359 191 0.52
360 107 0.29
361 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (359 bp):
TCTCACTCAAATAAGCTTAATTCTTCTCCCATTCAAACTTATTTCTTCTCTTCTCTCATTTCATC
ATCTATTCCTTTTTGTTAGTCAATGTTAATATGATGAAAGAAAAAAAAAGTGAGTAAAGAGACTA
CTACAAAGCCTTCAATTGTCTATAGTACCCAATCTCCATCATTTACAAGCCTACCACCAAGAAAT
ATGTTTAAATTTATAAGGAAAACCATCCAAAATTCTTTCTTAGTTCATGTTTATAACAAAGATGG
ATTTTAATTATATGTTTCAAATCTGCGTTTTTAAGTTCAACATGATTTATAGATCTTTTGGTGAC
AACGAATCATAATTGACCTTTATATATCCTCTCC
Done.