Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010833.1 Kokia drynarioides strain JFW-HI SEQ_125800, 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: 2078
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Found at i:413 original size:215 final size:215
Alignment explanation
Indices: 5--2078 Score: 2114
Period size: 216 Copynumber: 9.7 Consensus size: 215
1 CATT
* * * * * * * *
5 CTCGAGAATTCGCATCATTTAGTCTAAATAGTTTTTTAATTTTGTAAACGAGTTTTGATCATTAA
1 CTCGAGAAATCGCATCATTTGGTCTAAATAG-TTTGTCATTTTGTAAA-AAGTTTTGGTCTTTGA
** * * * * * * *
70 AACAAAGAACATATTTTCCTGAGGATT-TTT-TC--TTGGCTGTTGGACGAACTTCTGAA--T-T
64 ATTAAA-AACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTAT
** * * *
128 CAAACTTTTACGAGTTCTTTTATAACTT-GGTTCCTTGCAGTATTCAAGAAGATCCATTCCATCA
128 CAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
192 AGCAATTTTCTGAACATTCCATG
193 AGCAATTTTCTGAACATTCCATG
* * * **
215 CTCGTGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTGTGTAAAAAATTTTGGTCACTGAAT
1 CTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAGTTTTGGTCTTTGAAT
* ** *
280 TAAATACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTTTGAGCTTATCAA
66 TAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTATCAA
* * * * * *
345 ATTTTTACGAGTTCTTTTATAATTTCAGTTTCATAAAGCATTCAAGACGATCCATTCCTTCGAGC
131 ACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGC
**
410 AATTTTCCAAACATTCCATG
196 AATTTTCTGAACATTCCATG
* * * * * *
430 CTCGGGAAATCGCATCATTTGGTCTAAATATTTTGTCATTTTGTTAAAAGGTTTCGTTGTTTGAA
1 CTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG-TAAAAAGTTTTGGTCTTTGAA
* * * *
495 TTAAAAGCTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCGTGCACGAACTTCCGAAC-TAGTC
65 TTAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTA-TC
* *
559 AAACTTTTACGAGTTCTTTCATATCTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGA
129 AAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGA
* *
624 GCAATTTTCTGAACATTCAATT
194 GCAATTTTCTGAACATTCCATG
* * * * ** *
646 CTTGAGAAATGGCAGCATTTGGTCTAAAGAGTTTGTCATTTTAAAAACAAGTTTTGGTCTTTGCA
1 CTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AAGTTTTGGTCTTTGAA
* * * * * * *
711 TCAAAAACTTATTTAC----G---TG-TTCGC--TTGGTTCTTGGACAAACTTTCAAACTTGTTA
65 TTAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTATCA
* ** * * *
766 AACTTTTAGGAGTTCTTTTATAACTTCAATTCCTTACAGTAATCAAGACGATACATTCCTTCGAG
130 AACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAG
* * * *
831 CAACTTTCTTAACATTCTAAG
195 CAATTTTCTGAACATTCCATG
* * * *
852 CTCGAAAAATCGCATCATTT-TTCTAAATTGTTTGTCATTTTGTAAACAAGTTTT-GTCTTTAAA
1 CTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AAGTTTTGGTCTTTGAA
* * * *
915 TTAAAAACTTATTTACGTGAGAATTATTTCTCTCTCTTTGTTCTTGGACGAACTTCCAAACTTTT
65 TTAAAAACTTATTTACGTGAGAATTGTTTCTCT-T-TTGGTTCTTGGACGAACTTCCGAACTTAT
* * *
980 CAAACCTTTACGAGTTCTTTTATAACTCCGGTTCCTTAAA-TATTCAACAAC-ATCCATTCCTTT
128 CAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAA-GACGATCCATTCC-TT
*
1043 C-AGCAA-TTT-TGAACATTCCATT
191 CGAGCAATTTTCTGAACATTCCATG
* * * * * *
1065 CTTGGGTAATCGCATCATTTAGTCTAAATAGTTT-TCGTTTTGTAAACAAGTTTTTGGTCTTTAA
1 CTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AAG-TTTTGGTCTTTGA
*** * * * * * * *
1129 AGCGAAAACTTATTAACGTGAGAATTGTTTCTC--TTGGCTGTTGGATGAACTTCTGAACTTTTT
64 ATTAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTATC
* * *
1192 AAACTTTTACCAGTTCTTTTATAACTT-GGTTCCCTACAA-TATTCAAGATGATCCATTCCTTCG
129 AAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTA-AAGTATTCAAGACGATCCATTCCTTCG
*
1255 AGCTATTTTCTGAACATTCCATG
193 AGCAATTTTCTGAACATTCCATG
* * * * *
1278 CTCGGGAAATCGCATAATTTTGTCTAAATAGTTTGTCATTTTGTGAACAACTTTTGGTCTTTGAA
1 CTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGT-AAAAAGTTTTGGTCTTTGAA
* * * *
1343 TTAAATACTTATTTACGCGAGAATTGTTTCTCTTTTAGTTCTTGGACGAACTTCTGAACTTATCA
65 TTAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTATCA
* * * * * * *
1408 AACTTTTATGAGTACTTCTATAATTTCAGTTCCATAAAGCATTCAAGACGATCCATTCCTTCGAG
130 AACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAG
*
1473 CAATTTTCCGAACATTCCATG
195 CAATTTTCTGAACATTCCATG
* * * * * * *
1494 CTCGGGAAATCGCATCATTTGGTCTAAATATTTTTTCATTTTGTTAAAAGGTTTCGTTGTTTGAA
1 CTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG-TAAAAAGTTTTGGTCTTTGAA
* ** * *
1559 TTAAAAGCTTATTTACGTGAGAATTGTTTCTCTCATGGTTCGTGGACGAACTTTCGAAC-TAGTC
65 TTAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTA-TC
* *
1623 AAACTTTTACGAGTTCTTTCATATCTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGA
129 AAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGA
* *
1688 GCAATTTTCTGAACATTCAATT
194 GCAATTTTCTGAACATTCCATG
* * * * ** *
1710 CTTGAGAAATGGCAGCATTTGGTCTAAAGAGTTTGTCATTTTAAAAACAAGTTTTGGTCTTTGCA
1 CTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AAGTTTTGGTCTTTGAA
* * * * * *
1775 TCAAAAACTTATTTACGTGAGAATTGTTTCGC--TTGGTTCTTGGACAAACTTTCGAACTTGTTA
65 TTAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTATCA
* ** * * *
1838 AACTTTTATGAGTTCTTTTATAACTTCAATTCCTTACAGTAATCAAGACGATACATTCCTTCGAG
130 AACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAG
* * * * *
1903 CAACTTTCTTAACTTTCTAAG
195 CAATTTTCTGAACATTCCATG
* * * * *
1924 CTCGAAAAATCCCATCATTT-TTCTAAATTGTTTGTCATTTTGTAAACAAGTTTT-GTCTTTAAA
1 CTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AAGTTTTGGTCTTTGAA
* * * * *
1987 TTAAAAAATTATTTACGTGAGAATTATTTCTCTCTCTTTGTTCTTGGACGAACTTCCAAACTTTT
65 TTAAAAACTTATTTACGTGAGAATTGTTTCTCT-T-TTGGTTCTTGGACGAACTTCCGAACTTAT
*
2052 CAAACCTTTACGAGTTCTTTTATAACT
128 CAAACTTTTACGAGTTCTTTTATAACT
Statistics
Matches: 1534, Mismatches: 282, Indels: 90
0.80 0.15 0.05
Matches are distributed among these distances:
204 22 0.01
205 29 0.02
206 111 0.07
207 16 0.01
208 23 0.01
209 17 0.01
210 40 0.03
211 90 0.06
212 43 0.03
213 151 0.10
214 166 0.11
215 204 0.13
216 621 0.40
217 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (215 bp):
CTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAGTTTTGGTCTTTGAAT
TAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGACGAACTTCCGAACTTATCAA
ACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGC
AATTTTCTGAACATTCCATG
Done.