Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012286.1 Kokia drynarioides strain JFW-HI SEQ_127287, 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: 3224
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.35
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:52 original size:29 final size:29
Alignment explanation
Indices: 4--146 Score: 130
Period size: 30 Copynumber: 4.8 Consensus size: 29
1 AAT
*
4 CTTCCAAGAATTACCA-TTTTACCCCTAAA
1 CTTCCAA-AAATACCATTTTTACCCCTAAA
* **
33 CTTCCAAAAATCCCATTTTTGGTCCCTAAA
1 CTTCCAAAAATACCATTTTT-ACCCCTAAA
*
63 CCTTCCAAAAATTACCA-TTTTACCCCCAAA
1 -CTTCCAAAAA-TACCATTTTTACCCCTAAA
* * *
93 CTTCCAAAAATCCCATTTTTGACCTCAAAA
1 CTTCCAAAAATACCATTTTT-ACCCCTAAA
*
123 C-TCTCAAAATTACCATTTTTACCC
1 CTTC-CAAAAATACCATTTTTACCC
147 TCGAACGTTT
Statistics
Matches: 93, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
28 10 0.11
29 30 0.32
30 35 0.38
31 14 0.15
32 4 0.04
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (29 bp):
CTTCCAAAAATACCATTTTTACCCCTAAA
Found at i:926 original size:29 final size:29
Alignment explanation
Indices: 878--1020 Score: 130
Period size: 30 Copynumber: 4.8 Consensus size: 29
868 NNNNNNNAAT
*
878 CTTCCAAGAATTACCA-TTTTACCCCTAAA
1 CTTCCAA-AAATACCATTTTTACCCCTAAA
* **
907 CTTCCAAAAATCCCATTTTTGGTCCCTAAA
1 CTTCCAAAAATACCATTTTT-ACCCCTAAA
*
937 CCTTCCAAAAATTACCA-TTTTACCCCCAAA
1 -CTTCCAAAAA-TACCATTTTTACCCCTAAA
* * *
967 CTTCCAAAAATCCCATTTTTAACCTCAAAA
1 CTTCCAAAAATACCATTTTT-ACCCCTAAA
*
997 C-TCTCAAAATTACCATTTTTACCC
1 CTTC-CAAAAATACCATTTTTACCC
1021 TCGAACATTT
Statistics
Matches: 93, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
28 10 0.11
29 30 0.32
30 35 0.38
31 14 0.15
32 4 0.04
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.31
Consensus pattern (29 bp):
CTTCCAAAAATACCATTTTTACCCCTAAA
Found at i:1687 original size:874 final size:824
Alignment explanation
Indices: 1--1699 Score: 2669
Period size: 874 Copynumber: 2.0 Consensus size: 824
1 AATCTTCCAAGAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGGTCCCTAAACCT
1 AATCTTCCAAGAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGGTCCCTAAACCT
*
66 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTCTCAAA
66 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCTCAAAACTCTCAAA
* *
131 ATTACCATTTTTACCCTCGAACGTTTTAAATTCCAGTTTTTTAAAAAAAAACACGCATTTTCATG
131 ATTACCATTTTTACCCTCGAACATTTTAAATTCCAGTTTTTTAAAAAAAAACACGCATTTTCACG
*
196 AAACTACCATGTTGCCCCTGTGCATCCGAAAGGTCTCGTTTTGAACTCCGATTGCATCATTCTCC
196 AAACTACCATGTTGCCCCTGTGCATCCGAAAGGTCACGTTTTGAACTCCGATTGCATCATTCTCC
*
261 TTTCTCATCAACATTTATATATTTTTTATACGCTCGCATTTTGCATTTTGATTTCTCGTGGATAA
261 TTTCTCATCAACATTTATATATTTTTTATACGCTCGCATTTTACATTTTGATTTCTCGTGGATAA
326 TTTATCTTCTTGTTTATCTTACTTTGCATTATATATCCACTATTAGCTACACATTCATCTTCAAC
326 TTTATCTTCTTGTTTATCTTACTTTGCATTATATATCCACTATTAGCTACACATTCATCTTCAAC
391 TCACAACGCTTGTTTTCAAAATTGTTTTTTTATAAAAGTTTCAAAAATCGAGGCAATATTCTTTT
391 TCACAACGCTTGTTTTCAAAATTGTTTTTTTATAAAAGTTTCAAAAATCGAGGCAATATTCTTTT
*
456 GTTTTGAGTTTCAAAAATTTGTGCCTTAACTCATTAGGTACAATTTTCCTTCAAATTGAAATAAT
456 GTTTTGAGATTCAAAAATTTGTGCCTTAACTCATTAGGTACAATTTTCCTTCAAATTGAAATAAT
*
521 CGAATACCCTTAATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAATATTGCACCTTAACTTAC
521 CGAATACCCTTAATCGAGGCAATGTTTCCTTATCTTCAATTCTGAAATATTGCACCTTAACTTAC
* *
586 TAGGTGCAACCTTTCTTCAAATCGAGATAATCGGATATCCTTTTGTAAAAATAAAAAAAAGGTTC
586 TAGGTGCAACCTTTCTTCAAATCGAGATAATCAGATATCCTTTTGCAAAAATAAAAAAAAGGTTC
651 TATAAAGGAAAACTCGTTATTTATAGATCTTGATATGTCATGTCCTAACTCACTGGACGTAATTT
651 TATAAAGGAAAACTCGTTATTTATAGATCTTGATATGTCATGTCCTAACTCACTGGACGTAATTT
716 TCTTCCTCGATCACTTTGAGATAGCAAGATTTCCAAACAAACCCCCATTTCTTTTAAACTCAACT
716 TCTTCCTCGATCACTTTGAGATAGCAAGATTTCCAAACAAACCCCCATTTCTTTTAAACTCAACT
781 CATGCATTCACGGATCATATTTTAAACTTTATTCAAGCTTTTAA
781 CATGCATTCACGGATCATATTTTAAACTTTATTCAAGCTTTTAA
*********** *
825 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAATCTTCCAAGAATT
1 ---------------------------------------AATCTTCCAAGAAT-TACCA------
890 ACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGGTCCCTAAACCTTCCAAAAATTACCAT
20 ----TTTTACCCCTAAACTTCCAAAAATCCCATTTTTGGTCCCTAAACCTTCCAAAAATTACCAT
955 TTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCTCAAAACTCTCAAAATTACCATTTTTACC
81 TTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCTCAAAACTCTCAAAATTACCATTTTTACC
* *
1020 CTCGAACATTTTAAATTCCAGTTTTTTTAAAAAAAACACGTATTTTCACGAAACTACCATGTTGC
146 CTCGAACATTTTAAATTCCAGTTTTTTAAAAAAAAACACGCATTTTCACGAAACTACCATGTTGC
1085 CCCTGTGCATCCGAAAGGTCACGTTTTGAACTCCGATTGCATCATTCTCCTTTCTCATCAACATT
211 CCCTGTGCATCCGAAAGGTCACGTTTTGAACTCCGATTGCATCATTCTCCTTTCTCATCAACATT
* *
1150 TTTATATTTTTTATGCGCTCGCATTTTACATTTTGATTTCTCGTGGATAATTTATCTTCTTGTTT
276 TATATATTTTTTATACGCTCGCATTTTACATTTTGATTTCTCGTGGATAATTTATCTTCTTGTTT
1215 ATCTTACTTTGCATTATATATCCACTATTAGCTACACATTCATCTTCAACTCACAACGCTTGTTT
341 ATCTTACTTTGCATTATATATCCACTATTAGCTACACATTCATCTTCAACTCACAACGCTTGTTT
1280 TCAAAATTGTTTTTTTATAAAAGTTTCAAAAATCGAGGCAATATTCTTTTGTTTTGAGATTCAAA
406 TCAAAATTGTTTTTTTATAAAAGTTTCAAAAATCGAGGCAATATTCTTTTGTTTTGAGATTCAAA
1345 AATTTGTGCCTTAACTCATTAGGTACAATTTTCCTTCAAATTGAAATAATCGAATACCCTTAATC
471 AATTTGTGCCTTAACTCATTAGGTACAATTTTCCTTCAAATTGAAATAATCGAATACCCTTAATC
**
1410 GAGGCAATGTTTCCTTATCTTCAATTCTGAAATATTGTGCCTTAACTTACTAGGTGCAACCTTTC
536 GAGGCAATGTTTCCTTATCTTCAATTCTGAAATATTGCACCTTAACTTACTAGGTGCAACCTTTC
*
1475 TTCAAATCGAGATAATCAGATATCCTTTTGCAAAAATAAAAAAAAGGTTCTATAAAGGAAAGCTC
601 TTCAAATCGAGATAATCAGATATCCTTTTGCAAAAATAAAAAAAAGGTTCTATAAAGGAAAACTC
* *
1540 GTTATTTCTAGATCTTGATATGTCATGTCCTAACTCATTGGACGTAATTTTCTTCCTCGATCACT
666 GTTATTTATAGATCTTGATATGTCATGTCCTAACTCACTGGACGTAATTTTCTTCCTCGATCACT
*
1605 TTGAGATAGGAAGATTTCCAAACAAACCCCCATTTCTTTTAAACTCAACTCATGCATTCACGGAT
731 TTGAGATAGCAAGATTTCCAAACAAACCCCCATTTCTTTTAAACTCAACTCATGCATTCACGGAT
1670 CATATTTTAAACTTTATTCAAGCTTTTAA
796 CATATTTTAAACTTTATTCAAGCTTTTAA
1699 A
1 A
1700 TGTTACAAAT
Statistics
Matches: 793, Mismatches: 32, Indels: 50
0.91 0.04 0.06
Matches are distributed among these distances:
863 3 0.00
864 4 0.01
874 786 0.99
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.36
Consensus pattern (824 bp):
AATCTTCCAAGAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGGTCCCTAAACCT
TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCTCAAAACTCTCAAA
ATTACCATTTTTACCCTCGAACATTTTAAATTCCAGTTTTTTAAAAAAAAACACGCATTTTCACG
AAACTACCATGTTGCCCCTGTGCATCCGAAAGGTCACGTTTTGAACTCCGATTGCATCATTCTCC
TTTCTCATCAACATTTATATATTTTTTATACGCTCGCATTTTACATTTTGATTTCTCGTGGATAA
TTTATCTTCTTGTTTATCTTACTTTGCATTATATATCCACTATTAGCTACACATTCATCTTCAAC
TCACAACGCTTGTTTTCAAAATTGTTTTTTTATAAAAGTTTCAAAAATCGAGGCAATATTCTTTT
GTTTTGAGATTCAAAAATTTGTGCCTTAACTCATTAGGTACAATTTTCCTTCAAATTGAAATAAT
CGAATACCCTTAATCGAGGCAATGTTTCCTTATCTTCAATTCTGAAATATTGCACCTTAACTTAC
TAGGTGCAACCTTTCTTCAAATCGAGATAATCAGATATCCTTTTGCAAAAATAAAAAAAAGGTTC
TATAAAGGAAAACTCGTTATTTATAGATCTTGATATGTCATGTCCTAACTCACTGGACGTAATTT
TCTTCCTCGATCACTTTGAGATAGCAAGATTTCCAAACAAACCCCCATTTCTTTTAAACTCAACT
CATGCATTCACGGATCATATTTTAAACTTTATTCAAGCTTTTAA
Done.