Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001233.1 Kokia drynarioides strain JFW-HI SEQ_112595, 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, 970
Length: 1617
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Found at i:664 original size:216 final size:216
Alignment explanation
Indices: 1--679 Score: 797
Period size: 216 Copynumber: 3.1 Consensus size: 216
* * *
1 GTCTTTGAATTAAAAACTTATTCACCTGAGAATTGTTTCTCTGTTGGTTCTTGGACGAACTTCCG
1 GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTATTGGTTCTTGGACGAACTTCCG
* * *
66 AACTTGTCAAACATTTACAAGTTATTCGATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCAT
66 AACTTGTCAAACTTTTACAAGTTCTTCAATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCAT
* * * * *
131 TCCTTCCAGCTA-TTTTCGAACATTTAATGTTCAGGTAATCGCATCTTTTCGTCCAAATAGTTTG
131 TCCTTCAAGCAATTTTTCGAACATTTAATGCTCGGGAAATCGCATCTTTTCGTCCAAATAGTTTG
*
195 TCATTTTGTAAATAACTTTTG
196 TCATTTTGTAAAAAACTTTTG
* * * * * * * * * *
216 GTCTTTGAATTAAAAAGTTATCTACATGAGATTTGATTCTCTCTCGGTTTTTGGACAAACTTCCA
1 GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTATTGGTTCTTGGACGAACTTCCG
* **
281 AACTTGTCAAACTTGTACGAA-TTCTGGAATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCA
66 AACTTGTCAAACTTTTAC-AAGTTCTTCAATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCA
* * ** * * * * *
345 TTCCTTCAAGCAATTTTCCAAACATTCCATGCTCGGGGAATCGCATCATCTGGTCTAAATAGTTT
130 TTCCTTCAAGCAATTTTTCGAACATTTAATGCTCGGGAAATCGCATCTTTTCGTCCAAATAGTTT
* * *
410 ATGATATTTGTAAACAACTTTTG
195 GTCAT-TTTGTAAAAAACTTTTG
* * * * * *
433 GTCTTTCAATTAAAAACTTATTTATGTGAGAATCGTTTGTGTATTGGTTCTTGGATGAACTTCCG
1 GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTATTGGTTCTTGGACGAACTTCCG
** * * * *
498 AACTTGTCAAACTTTTACAAGTTCTTTTATAACTTCGATACCTTAAAGTA-TCATGACGATCCAT
66 AACTTGTCAAACTTTTACAAGTTCTTCAATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCAT
* * * *
562 TCCTTCGAGCAATTTTTTGAACATTTTATACTCGGGAAATCGCATCTTTTCGTCCAAATAGTTTG
131 TCCTTCAAGCAATTTTTCGAACATTTAATGCTCGGGAAATCGCATCTTTTCGTCCAAATAGTTTG
* *
627 TCATTTTGAAAAAAAACTATTG
196 TCATTTTG-TAAAAAACTTTTG
* *
649 GTCTTTGATTTAAAAACTTATTTATGTGAGA
1 GTCTTTGAATTAAAAACTTATTTACGTGAGA
680 TTTACTTCCG
Statistics
Matches: 383, Mismatches: 76, Indels: 9
0.82 0.16 0.02
Matches are distributed among these distances:
215 124 0.32
216 153 0.40
217 106 0.28
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (216 bp):
GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTATTGGTTCTTGGACGAACTTCCG
AACTTGTCAAACTTTTACAAGTTCTTCAATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCAT
TCCTTCAAGCAATTTTTCGAACATTTAATGCTCGGGAAATCGCATCTTTTCGTCCAAATAGTTTG
TCATTTTGTAAAAAACTTTTG
Found at i:1195 original size:216 final size:215
Alignment explanation
Indices: 794--1196 Score: 508
Period size: 216 Copynumber: 1.9 Consensus size: 215
784 TATTCTGGTC
* * * * * *
794 CAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTTAAAACTTATTACGTGAGAATT
1 CAAATAGTTAGTCATTTTGTAAAAAACTTTTAGTCTTCGAATTTAAAACTCATTACGTAAGAATT
** * * *
859 ATTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCCAACTTTTACGAGTTCTTAAATAACT
66 ATTTCTAGCTTGGTTCTTGGACCAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTAAATAACA
* * * * *
924 TTGGTTCCTTAAAGTATTCAAGACAATCCATTCCTTCGAGTAATTTCCCGAACATTCCATGCTCG
131 TCGGTCCCTTAAAGCATTCAAGACAATCCATTCCTTCGAGCAATTTCCAGAACATTCCATGCTCG
989 AGAAATCGTATCATTTTGTT
196 AGAAATCGTATCATTTTGTT
* *
1009 CAAATAGTTAGTCGTTTTGTAAAAAACTTTTAGTCTTCG-ATTTAAAAAGTCATTTACGTAAGAA
1 CAAATAGTTAGTCATTTTGTAAAAAACTTTTAGTCTTCGAATTT-AAAACTCA-TTACGTAAGAA
* **
1073 TTGTTTCTAGCTTGGTTCTTGG-CTCAA-TTTCCGAACTTGTCAAACTTTTACGAGTTCTTCTAT
64 TTATTTCTAGCTTGGTTCTTGGAC-CAACTTT-CGAACTTGTCAAACTTTTACGAGTTCTTAAAT
* * **
1136 AACATCGGTCCCTTAAAGCATTCAAGACGATCCATT-TTATCGAGCAATTTTTAGAACATTC
127 AACATCGGTCCCTTAAAGCATTCAAGACAATCCATTCCT-TCGAGCAATTTCCAGAACATTC
1197 GCATAATTTG
Statistics
Matches: 158, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
214 4 0.03
215 45 0.28
216 109 0.69
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (215 bp):
CAAATAGTTAGTCATTTTGTAAAAAACTTTTAGTCTTCGAATTTAAAACTCATTACGTAAGAATT
ATTTCTAGCTTGGTTCTTGGACCAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTAAATAACA
TCGGTCCCTTAAAGCATTCAAGACAATCCATTCCTTCGAGCAATTTCCAGAACATTCCATGCTCG
AGAAATCGTATCATTTTGTT
Found at i:1363 original size:202 final size:206
Alignment explanation
Indices: 683--1603 Score: 727
Period size: 215 Copynumber: 4.4 Consensus size: 206
673 TGTGAGATTT
* * * * *
683 ACTTCCGAACTTGTCAAACTTTTACAATTTCTTTTATAACGTCGATTTCTTAAAGTATTCAAGAT
1 ACTTCCGAACTTGTCAAAC-TTTACAAGTT-TTTGATAACTTCGGTTCCTTAAAGTATTCAAGAT
*
748 GATCCATTCCTT-CATGCAATTTTCAGAACA-TTA-G-CA-T-AT-TCTGGTC-C-AAATAGTTT
64 GATCCATTCCTTCCA-GCAATTTT-AGAACATTTACGTCAGTAATCTCTGATCGCAAAATAGTTT
* * * * * * *
804 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTTAAAACTTA-TTACGTGAGAATTATTTCTCTC
127 GTCATTTTGTAAAAAACTTTTAGTCTTTGAATTAAAAAGTTATTTACATGAGAATTGTTTCTCTG
*
868 TTGGTTCTTGGACGA
192 TTGGTTCTTGGACAA
* * * ** * *
883 ACTTTCGAACTTGTCCAACTTTTACGAGTTCTTAAATAACTTTGGTTCCTTAAAGTATTCAAGAC
1 ACTTCCGAACTTGTCAAAC-TTTACAAGTT-TTTGATAACTTCGGTTCCTTAAAGTATTCAAGAT
* * * ** * * * * * *
948 AATCCATTCCTTCGAGTAATTTCCCGAACATTCCATGCTCGAGAAATCGTATCATTTTGTTC-AA
64 GATCCATTCCTTCCAGCAATTT-TAGAACATT-TACG-TC-AGTAATC-TCTGA--TCG--CAAA
* * * * * * *
1012 ATAGTTAGTCGTTTTGTAAAAAACTTTTAGTCTTCGATTTAAAAAGTCATTTACGTAAGAATTGT
120 ATAGTTTGTCATTTTGTAAAAAACTTTTAGTCTTTGAATTAAAAAGTTATTTACATGAGAATTGT
* *
1077 TTCT-AGCTTGGTTCTTGG-CTCA
185 TTCTCTG-TTGGTTCTTGGAC-AA
* * * * *
1099 ATTTCCGAACTTGTCAAACTTTTACGAGTTCTTCT-ATAACATCGGTCCCTTAAAGCATTCAAGA
1 ACTTCCGAACTTGTCAAAC-TTTACAAGTT-TT-TGATAACTTCGGTTCCTTAAAGTATTCAAGA
* * *
1163 CGATCCATT-TTATCGAGCAATTTTTAGAACA-TT-CG-CA-TAAT-T-TGATC-CAAAATAGTT
63 TGATCCATTCCT-TCCAGCAA-TTTTAGAACATTTACGTCAGTAATCTCTGATCGCAAAATAGTT
* * * *
1220 TGTCATTTTGTAAACAACTTTTAGTCTTTGAATTAAAAACTTATTCACCTGAGAATTGTTTCTCT
126 TGTCATTTTGTAAAAAACTTTTAGTCTTTGAATTAAAAAGTTATTTACATGAGAATTGTTTCTCT
*
1285 GTTGGTTCTTGGACGA
191 GTTGGTTCTTGGACAA
1301 ACTTCCGAACTTGTCAAACATTTACAAGTTATTTGATAACTTCGGTTCCTTAAAGTATTCAAGAT
1 ACTTCCGAACTTGTCAAAC-TTTACAAGTT-TTTGATAACTTCGGTTCCTTAAAGTATTCAAGAT
* * * ** *
1366 GATCCATTCCTTCCAGCTATTTTCGAACATTTAATGTTCAGGTAATCGCATCTTTTCGTCCAAAT
64 GATCCATTCCTTCCAGCAATTTTAGAACATTT-ACG-TCA-GTAAT--C-TCTGATCG-CAAAAT
* * * *
1431 AGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAAGTTATTTACATGAGATTTGATT
122 AGTTTGTCATTTTGTAAAAAACTTTTAGTCTTTGAATTAAAAAGTTATTTACATGAGAATTGTTT
* * * *
1496 CTCTCTCGATTTTTGGACAA
187 CTCTGTTGGTTCTTGGACAA
* * *
1516 ACTTCCAAACTTGTCAAACTTGTACGAA-TTCTGGAATAACTTCGGTTCCTTAAAGTATTCAAGA
1 ACTTCCGAACTTGTCAAACTT-TAC-AAGTTTTTG-ATAACTTCGGTTCCTTAAAGTATTCAAGA
*
1580 TGATCCATTCCTTCAAGCAATTTT
63 TGATCCATTCCTTCCAGCAATTTT
1604 CCAAACATTC
Statistics
Matches: 577, Mismatches: 99, Indels: 75
0.77 0.13 0.10
Matches are distributed among these distances:
200 76 0.13
201 13 0.02
202 145 0.25
203 4 0.01
204 2 0.00
205 1 0.00
206 5 0.01
207 1 0.00
208 6 0.01
209 3 0.01
210 3 0.01
211 1 0.00
212 2 0.00
213 4 0.01
214 4 0.01
215 198 0.34
216 106 0.18
217 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (206 bp):
ACTTCCGAACTTGTCAAACTTTACAAGTTTTTGATAACTTCGGTTCCTTAAAGTATTCAAGATGA
TCCATTCCTTCCAGCAATTTTAGAACATTTACGTCAGTAATCTCTGATCGCAAAATAGTTTGTCA
TTTTGTAAAAAACTTTTAGTCTTTGAATTAAAAAGTTATTTACATGAGAATTGTTTCTCTGTTGG
TTCTTGGACAA
Found at i:1613 original size:417 final size:416
Alignment explanation
Indices: 683--1613 Score: 1160
Period size: 417 Copynumber: 2.2 Consensus size: 416
673 TGTGAGATTT
* * * *
683 ACTTCCGAACTTGTCAAACTTTTAC-AATTTCTTTTATAACGTCGATTTCTTAAAGTATTCAAGA
1 ACTTCCGAACTTGTCAAACTTTTACGAA-TTCTTCTATAACATCGGTTCCTTAAAGTATTCAAGA
* * *
747 TGATCCATTCCTTCATGCAATTTTCAGAACATTAGCATATTCTGGTCCAAATAGTTTGTCATTTT
65 TGATCCATTCCTTCAAGCAATTTTCAGAACATTCGCATATTCTGATCCAAATAGTTTGTCATTTT
* * *
812 GTAAACAACTTTTGGTCTTTGAATTTAAAACTTATTACGTGAGAATTATTTCTCTCTTGGTTCTT
130 GTAAACAACTTTTAGTCTTTGAATTAAAAACTTATTACCTGAGAATTATTTCTCTCTTGGTTCTT
* * * * * *
877 GGACGAACTTTCGAACTTGTCCAACTTTTACGAGTTCTTAAATAACTTTGGTTCCTTAAAGTATT
195 GGACGAACTTCCGAACTTGTCAAACATTTACAAGTTATTAAATAACTTCGGTTCCTTAAAGTATT
* * *
942 CAAGACAATCCATTCCTTCGAGTAATTTCCCGAACATTCCATGCTCGAGAAATCGTATCATTTTG
260 CAAGACAATCCATTCCTTCCAGTAATTTCCCGAACATTCAATGCTCGAGAAATCGCATCATTTTG
* * * *
1007 TTCAAATAGTTAGTCGTTTTGTAAAAAACTTTTAGTCTTCGATTTAAAAAGTCATTTACGTAAGA
325 TCCAAATAGTTAGTCATTTTGTAAAAAACTTTTAGTCTTCGAATTAAAAAGTCATTTACATAAGA
* * * *
1072 ATTGTTTCTAGCTTGGTTCTTGGCTCA
390 ATTGATTCTAGCTCGATTCTTGGCTAA
* * * * *
1099 ATTTCCGAACTTGTCAAACTTTTACGAGTTCTTCTATAACATCGGTCCCTTAAAGCATTCAAGAC
1 ACTTCCGAACTTGTCAAACTTTTACGAATTCTTCTATAACATCGGTTCCTTAAAGTATTCAAGAT
* * *
1164 GATCCATT-TTATCGAGCAATTTTTAGAACATTCGCATAATT-TGATCCAAAATAGTTTGTCATT
66 GATCCATTCCT-TCAAGCAATTTTCAGAACATTCGCAT-ATTCTGATCC-AAATAGTTTGTCATT
* *
1227 TTGTAAACAACTTTTAGTCTTTGAATTAAAAACTTATTCACCTGAGAATTGTTTCTCTGTTGGTT
128 TTGTAAACAACTTTTAGTCTTTGAATTAAAAACTTATT-ACCTGAGAATTATTTCTCTCTTGGTT
**
1292 CTTGGACGAACTTCCGAACTTGTCAAACATTTACAAGTTATTTGATAACTTCGGTTCCTTAAAGT
192 CTTGGACGAACTTCCGAACTTGTCAAACATTTACAAGTTATTAAATAACTTCGGTTCCTTAAAGT
** * * * *
1357 ATTCAAGATGATCCATTCCTTCCAGCT-ATTT-TCGAACATTTAATGTTC-AGGTAATCGCATC-
257 ATTCAAGACAATCCATTCCTTCCAG-TAATTTCCCGAACATTCAATGCTCGA-GAAATCGCATCA
* * * * *
1418 TTTTCGTCCAAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAAGTTATTTAC
320 TTTT-GTCCAAATAGTTAGTCATTTTGTAAAAAACTTTTAGTCTTCGAATTAAAAAGTCATTTAC
* * ** *
1483 ATGAGATTTGATTCTCTCTCGATTTTTGGAC-AA
384 ATAAGAATTGATTCTAGCTCGATTCTTGG-CTAA
* * *** *
1516 ACTTCCAAACTTGTCAAACTTGTACGAATTCTGGAATAACTTCGGTTCCTTAAAGTATTCAAGAT
1 ACTTCCGAACTTGTCAAACTTTTACGAATTCTTCTATAACATCGGTTCCTTAAAGTATTCAAGAT
1581 GATCCATTCCTTCAAGCAATTTTCCA-AACATTC
66 GATCCATTCCTTCAAGCAATTTT-CAGAACATTC
1614 CATG
Statistics
Matches: 435, Mismatches: 69, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
415 1 0.00
416 94 0.22
417 230 0.53
418 109 0.25
419 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (416 bp):
ACTTCCGAACTTGTCAAACTTTTACGAATTCTTCTATAACATCGGTTCCTTAAAGTATTCAAGAT
GATCCATTCCTTCAAGCAATTTTCAGAACATTCGCATATTCTGATCCAAATAGTTTGTCATTTTG
TAAACAACTTTTAGTCTTTGAATTAAAAACTTATTACCTGAGAATTATTTCTCTCTTGGTTCTTG
GACGAACTTCCGAACTTGTCAAACATTTACAAGTTATTAAATAACTTCGGTTCCTTAAAGTATTC
AAGACAATCCATTCCTTCCAGTAATTTCCCGAACATTCAATGCTCGAGAAATCGCATCATTTTGT
CCAAATAGTTAGTCATTTTGTAAAAAACTTTTAGTCTTCGAATTAAAAAGTCATTTACATAAGAA
TTGATTCTAGCTCGATTCTTGGCTAA
Done.