Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010652.1 Kokia drynarioides strain JFW-HI SEQ_125595, 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: 1884
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.38
Warning! 134 characters in sequence are not A, C, G, or T
Found at i:1030 original size:343 final size:340
Alignment explanation
Indices: 408--1095 Score: 1121
Period size: 343 Copynumber: 2.0 Consensus size: 340
398 TCCTTCTAGC
408 AACTTTCTTAACATTCTATGCAAGAAAAACGCATCATTTTTCTAAATTGTTTGTCATTTTGTAAA
1 AACTTTCTTAACATTCTATGCAAGAAAAACGCATCATTTTTCTAAATTGTTTGTCATTTTGTAAA
*
473 CAAGTTATGGTATTTTTAAAACTTATTTACGTGAGAATTGTTTCTCTCTCTTTGTTCTTGGATGA
66 CAAGTTATGGTATTTTTAAAACTTATTTACGTGACAATTGTTTCTCTCTCTTTGTTCTTGGATGA
* * *
538 ACTTCCAGACTTTTCAAACTTTTACGAGTTCATTTATAGCTCCGGTTCCTTAAAGTATTCAAGAC
131 ACTTCCAAACTTGTCAAACTTTTACGAGTTCATTTATAACTCCGGTTCCTTAAAGTATTCAAGAC
*
603 GATCCATTCCTTTGAAGAGTTTTTGAACATTCCATTCTCGGGAAATCGCATCATTTAGTCTAAAT
196 GATCCATTCCTTTGAAGAATTTTTGAACATTCCATTCTCGGGAAATCGCATCATTTAGTCTAAAT
668 AGGTCTTAATTTTGTAAACGAGTTTTGATCATTAAAACAAGAACATATTTTCCTGAGGA-TTTTT
261 AGGTCTTAATTTTGTAAACGAGTTTTGATCATTAAAACAAGAACATATTTTCCTGAGGATTTTTT
*
732 CTTTGCTATTGGACG
326 CTTGGCTATTGGACG
**
747 AACTTTCTTAACATTCTATGCTCGAAAAATCGCATCATTTTTCTAAA-TGTTTGTCATTTTGTAA
1 AACTTTCTTAACATTCTATGCAAGAAAAA-CGCATCATTTTTCTAAATTGTTTGTCATTTTGTAA
* * *
811 ACAAGTTTTGGTCTTTAAATTTAAAACTTATTTACGTGACAATTGTTTCTCTCTCTTTGTTCTTT
65 ACAAGTTATGGT-ATT---TTTAAAACTTATTTACGTGACAATTGTTTCTCTCTCTTTGTTCTTG
*
876 GATGAACTTCCAAACTTGTCAAACTTTTACGAGTTC-TTTAATAACTTCGGTTCCTTAAAGTATT
126 GATGAACTTCCAAACTTGTCAAACTTTTACGAGTTCATTT-ATAACTCCGGTTCCTTAAAGTATT
* * * * *
940 CAAGACGTTCCATTCCTTTGAGGAATTTTTGATCATTCCGTTCTCGTGAAATCGCATCATTTAGT
190 CAAGACGATCCATTCCTTTGAAGAATTTTTGAACATTCCATTCTCGGGAAATCGCATCATTTAGT
*
1005 CTAAATAGGTCTTAATTTTGTAAACGAGTTTTGATCATTAAAACATGAACATATTTTCCTGAGGA
255 CTAAATAGGTCTTAATTTTGTAAACGAGTTTTGATCATTAAAACAAGAACATATTTTCCTGAGGA
* *
1070 TTTTTTCTTGGCTGTTGGATG
320 TTTTTTCTTGGCTATTGGACG
1091 AACTT
1 AACTT
1096 CGAAACATTT
Statistics
Matches: 322, Mismatches: 20, Indels: 9
0.92 0.06 0.03
Matches are distributed among these distances:
339 55 0.17
340 19 0.06
342 3 0.01
343 223 0.69
344 22 0.07
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (340 bp):
AACTTTCTTAACATTCTATGCAAGAAAAACGCATCATTTTTCTAAATTGTTTGTCATTTTGTAAA
CAAGTTATGGTATTTTTAAAACTTATTTACGTGACAATTGTTTCTCTCTCTTTGTTCTTGGATGA
ACTTCCAAACTTGTCAAACTTTTACGAGTTCATTTATAACTCCGGTTCCTTAAAGTATTCAAGAC
GATCCATTCCTTTGAAGAATTTTTGAACATTCCATTCTCGGGAAATCGCATCATTTAGTCTAAAT
AGGTCTTAATTTTGTAAACGAGTTTTGATCATTAAAACAAGAACATATTTTCCTGAGGATTTTTT
CTTGGCTATTGGACG
Found at i:1415 original size:216 final size:213
Alignment explanation
Indices: 756--1884 Score: 1147
Period size: 216 Copynumber: 5.3 Consensus size: 213
746 GAACTTTCTT
* * * *
756 AACATTCTATGCTCGAAAAATCGCATCATTTTTCTAAAT-GTTTGTCATTTTGTAAACAAGTTTT
1 AACATTCCATGCTCGAGAAATCGCATCATTTGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTT
* * * * * * *
820 GGTCTTTAAATTTAAAACTTATTTACGTGACAATTGTTTCTCTCTCTTTGTTCTTTGATGAACTT
66 GGTATTTGAATTGAAAACTTATTTACGTGAGAATTG-TT-TCTCT-TTGGTTCTTGGACGAACTT
* * * *
885 CCAAACTTGTCAAACTTTTACGAGTTCTTTAATAACTTCGGTTCCTTAAAGTATTCAAGACGTTC
128 CCGAACTTATCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATC
* *
950 CATTCCTTTGAGGAATTTTTG
193 CATTCCTTCGAGCAATTTTTG
* * * * * * **
971 ATCATTCCGTTCTCGTGAAATCGCATCATTTAGTCTAAATAGGTCT-TAATTTTGTAAACGAGTT
1 AACATTCCATGCTCGAGAAATCGCATCATTT-GTCTAAATA-GTTTGTCATTTTGTAAAAAAGTT
* ** * * * * * * * *
1035 TTGATCATTAAAACATG--AACATATTTTCCTGAGGATT-TTT-TC-TTGGCTGTTGGATGAACT
64 TTGGT-ATTTGAA-TTGAAAACTTATTTACGTGAGAATTGTTTCTCTTTGGTTCTTGGACGAACT
* **
1095 T-CGAAACATT-TCAAACTTTTACGAGTTCTTTTATAAC-TCTGTTCCTTGCAGTATTCAAGACG
127 TCCG-AAC-TTATCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACG
* * *
1157 ATCCCTTCCATCAAGCAATTTTTTG
190 ATCCATTCCTTCGAGCAA-TTTTTG
* * *
1182 AACATTCCATCCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAACTTT
1 AACATTCCATGCTCGAGAAATCGCATCATTT-GTCTAAATAGTTTGTCATTTTGTAAAAAAGTTT
*
1247 TGGTATTTGAATTGAATACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTC
65 TGGTATTTGAATTGAAAACTTATTTACGTGAGAATTGTTTCTC-TTTGGTTCTTGGACGAACTTC
* * * * *
1312 CGAACTTATCAAACTTTTACGAGTTCTTTTATAATTTCAGTTCCATAAAGAATTCAGGACGATCC
129 CGAACTTATCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCC
1377 ATTCCTTCGAGCAATTTTTCG
194 ATTCCTTCGAGCAATTTTT-G
* * * * *
1398 AACATTCCATGCTCGGGAAATCGTATCAATTTGTCTAAATAATTTGTCATTTTGTTAAAAGGTTT
1 AACATTCCATGCTCGAGAAATCGCATC-ATTTGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTT
* * *
1463 TGTTGTTTGAATT-ATAAACTTATTTACGTGAGAATTGCTTCTCTCTTGGTTCTTGGACGAACTT
65 TGGTATTTGAATTGA-AAACTTATTTACGTGAGAATTGTTTCTCT-TTGGTTCTTGGACGAACTT
* * * * *
1527 CCGAAC-TAGTCAAACTTTTACAAGTTCTCTCATATCTTTGGTTCCTTAAAGTATTCAAGACGAT
128 CCGAACTTA-TCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGAT
*
1591 CCATTCCTTCGAGCAATTTTCTA
192 CCATTCCTTCGAGCAATTTT-TG
* * * * * * * * *
1614 AATATTCAATTCTTGAGAAATGGCAGCATTTGGTCTCAAGAGTTTGTCATTTT-AAAAACAAGTT
1 AACATTCCATGCTCGAGAAATCGCATCATTT-GTCTAAATAGTTTGTCATTTTGTAAAA-AAGTT
* ** *
1678 TTGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTGTTT-TGC-TTGGTTCTTGGACAAACTT
64 TTGGTATTTGAATTGAAAACTTATTTACGTGAGAATTGTTTCT-CTTTGGTTCTTGGACGAACTT
* * * * *
1741 TCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTACAGTATTCAAGGCGATA
128 CCGAACTTATCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATC
*
1806 CATTCCTTCTAGCAACTTTCTT-
193 CATTCCTTCGAGCAA-TTT-TTG
* * * *
1828 AACATTCTATGCTCGAAAAATCGCATCATTTTTCTAAATTGTTTGTCATTTTGTAAA
1 AACATTCCATGCTCGAGAAATCGCATCATTTGTCTAAATAGTTTGTCATTTTGTAAA
Statistics
Matches: 752, Mismatches: 130, Indels: 65
0.79 0.14 0.07
Matches are distributed among these distances:
209 2 0.00
210 43 0.06
211 119 0.16
212 5 0.01
213 21 0.03
214 115 0.15
215 94 0.12
216 303 0.40
217 41 0.05
218 8 0.01
219 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (213 bp):
AACATTCCATGCTCGAGAAATCGCATCATTTGTCTAAATAGTTTGTCATTTTGTAAAAAAGTTTT
GGTATTTGAATTGAAAACTTATTTACGTGAGAATTGTTTCTCTTTGGTTCTTGGACGAACTTCCG
AACTTATCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAT
TCCTTCGAGCAATTTTTG
Done.