Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004462.1 Kokia drynarioides strain JFW-HI SEQ_117874, 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, 780
Length: 1301
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Found at i:431 original size:216 final size:214
Alignment explanation
Indices: 8--1300 Score: 871
Period size: 216 Copynumber: 6.1 Consensus size: 214
1 TTACTAG
* ** * * * ** * * *
8 TTCTTTTATAACTTCAGATCCTTAAAGTATTCAAGACGATACATTGCATCGAGCAATTTTTCGAA
1 TTCTTTTATAACTTCAGTTCCCAAAAATATTCAACAAGACCCATTCCTTAGAGCAATTTTTCGAA
* * * * * * *
73 TATTCCATGCTCGGCAAATTGCATAATTTGGCCTAATTAGTTTGTCATTTTACAAACAAGTTTTG
66 CATTCCATGCTCGGAAAATTGTATCATTTGGTCTAAATAGTTTGTCATTTT-CGAACAAGTTTTG
* *
138 GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT-TCTCTCTTTGTCTTTGTATGAACTTTC
130 GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTCTCTCTCTTT-TC-TTGAACGAACTTTC
* *
202 GAGCTTGTCAAACTTTTACGAG
193 GAACTTGTCAAACTTTTACGAC
* * * *
224 TTATTTTTTAACTTCGGTTCCCAAAAATATTCAACAAGATCCATTCCTTAGAGCAATTTTTCGAA
1 TTCTTTTATAACTTCAGTTCCCAAAAATATTCAACAAGACCCATTCCTTAGAGCAATTTTTCGAA
* * * *
289 CATTCCATGCACGGAAAATTGTATCATTTGGTCTAAATAGTGTGTCATTTTCTGATCATGTTTTG
66 CATTCCATGCTCGGAAAATTGTATCATTTGGTCTAAATAGTTTGTCATTTTC-GAACAAGTTTTG
* * * * * * *
354 GTCTTTCAATTAAAAACTTATTTATGAGAGAATTGTATCACTCTCGTTTCATGAACGAACTCTCG
130 GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT-TCTCTCTCTTTTCTTGAACGAACTTTCG
* *
419 AACTTTTCAAACTTATT-GGAC
194 AACTTGTCAAACTT-TTACGAC
* * * ** * * * * * *
440 ATCTTTTATAACTTAACTTCCTTAAAGTATTGAAGACGACCCATTCCTTTGAGC-ATTTTCCTGA
1 TTCTTTTATAACTTCAGTTCCCAAAAATATTCAACAAGACCCATTCCTTAGAGCAATTTTTC-GA
*
504 ACATTCCATGCTC-GAGAAATT-TCATCATTTGGTCTAAAGAGTTTGTCA-TTTCGTACACAAGT
65 ACATTCCATGCTCGGA-AAATTGT-ATCATTTGGTCTAAATAGTTTGTCATTTTCG-A-ACAAGT
* *
566 TTTGGTCTTGGAATTAAAAACTTATTTACGTGAGAATTGTT-TCTCTCTTTCTTCTTGGACGAAC
126 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTCTCTCTC-TT-TTCTTGAACGAAC
*
630 TTTCGAACATGTCAAACTTTTACGAC
189 TTTCGAACTTGTCAAACTTTTACGAC
* ** ** **** * * * * * *
656 TTCTTTTATAACTTCCGTTCCTTAAAGCATTCAAGGTTATCCATTCCTTCGAGTAGTTTTCCAAA
1 TTCTTTTATAACTTCAGTTCCCAAAAATATTCAACAAGACCCATTCCTTAGAGCAATTTTTCGAA
* * * * * * * * ****
721 CATTCCTTGCTC-AAGAAATCGCATCATTTGGTCTGAATAGATTGTC--GTT-GAATTAAAAACT
66 CATTCCATGCTCGGA-AAATTGTATCATTTGGTCTAAATAGTTTGTCATTTTCGAA-CAAGTTTT
* ** * * * * * * *
782 --TATTT-ACGTGAGAA-TTGTTT-C------A--G-TCT-T-T-GTTT-TTGGACGAACTTCCA
129 GGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTCTCTCTCTTTTCTTGAACGAACTTTCG
* * *
829 AACTGGTCAAACTTCTACGAG
194 AACTTGTCAAACTTTTACGAC
* * * * ** * *
850 TTTTTTTTTAACTT-TGTTTCCCTAAAGCATTCAACAAAATCCATTCCTTAGAGCAATTTTTCGA
1 TTCTTTTATAACTTCAG-TTCCCAAAAATATTCAACAAGACCCATTCCTTAGAGCAATTTTTCGA
* * * * *
914 ACATTCCATGCTCGGGAAATCGCATCATTTGATC-AAA-A-TATGTCATTTT-GTAAACAAGTTT
65 ACATTCCATGCTCGGAAAATTGTATCATTTGGTCTAAATAGTTTGTCATTTTCG--AACAAGTTT
* * *
975 TGATCTTTGAATTAAAAACTTATCTACGTGAGAATTGTT-TCTCTCTTTGTCTTTGTACGAACTT
128 TGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTCTCTCTCTTT-TC-TTGAACGAACTT
* *
1039 TCGAACTTGTCAAAATTTTACGAG
191 TCGAACTTGTCAAACTTTTACGAC
* * ** ** * * * *
1063 TTATTTTTTTAACTT-TTTTTTCTAAAGTATTCAACAAGATCCATTCCTTAGAGCAATTTTTTGA
1 TT-CTTTTATAACTTCAGTTCCCAAAAATATTCAACAAGACCCATTCCTTAGAGCAATTTTTCGA
* * * * *
1127 ACATTCCATGCTC-GAGAGATCGCATCAATTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTT
65 ACATTCCATGCTCGGA-AAATTGTATCATTTGGTCTAAATAGTTTGTCATTTT-CGAACAAGTTT
* * *
1191 AGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT-TCTCTCTTTGCCTTTGTACGAACTT
128 TGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTCTCTCTCTTT-TC-TTGAACGAACTT
* * *
1255 CCGAACTTGTCAAACTGTTACGAG
191 TCGAACTTGTCAAACTTTTACGAC
* * *
1279 TTATTTTTTAACTTCGGTTCCC
1 TTCTTTTATAACTTCAGTTCCC
1301 T
Statistics
Matches: 853, Mismatches: 174, Indels: 100
0.76 0.15 0.09
Matches are distributed among these distances:
191 4 0.00
192 1 0.00
193 6 0.01
194 111 0.13
195 4 0.00
196 5 0.01
197 5 0.01
198 5 0.01
199 3 0.00
200 2 0.00
202 1 0.00
205 1 0.00
207 2 0.00
208 3 0.00
209 6 0.01
210 7 0.01
211 4 0.00
212 2 0.00
213 106 0.12
214 23 0.03
215 33 0.04
216 501 0.59
217 11 0.01
218 7 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (214 bp):
TTCTTTTATAACTTCAGTTCCCAAAAATATTCAACAAGACCCATTCCTTAGAGCAATTTTTCGAA
CATTCCATGCTCGGAAAATTGTATCATTTGGTCTAAATAGTTTGTCATTTTCGAACAAGTTTTGG
TCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTCTCTCTCTTTTCTTGAACGAACTTTCGAA
CTTGTCAAACTTTTACGAC
Found at i:919 original size:194 final size:193
Alignment explanation
Indices: 576--1173 Score: 615
Period size: 194 Copynumber: 3.0 Consensus size: 193
566 TTTGGTCTTG
* *
576 GAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTCTTCTTGGACGAACTTTCGAACATG
1 GAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTTTTGGACGAACTTTCGAAC-TG
* * * * * ****
641 TCAAACTTTTACGACTTCTTTTATAACTTCCG-TTCCTTAAAGCATTCAAGGTTATCCATTCCTT
65 TCAAACTTTTACGAGTTTTTTTTTAACTT-TGTTTCCCTAAAGCATTCAACAAAATCCATTCCTT
* * * * * * * *
705 CGAGTAGTTTTCCAAACATTCCTTGCTCAAGAAATCGCATCATTTGGTCTGAATAGATTGTCGTT
129 AGAGCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTGAATAGTTTGTCGTT
** * *
770 GAATTAAAAACTTATTTACGTGAGAATTGTTTCAGTCTTTGTTTTTGGACGAACTTCCAAACTGG
1 GAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTTTTGGACGAACTTTCGAACT-G
*
835 TCAAACTTCTACGAGTTTTTTTTTAACTTTGTTTCCCTAAAGCATTCAACAAAATCCATTCCTTA
65 TCAAACTTTTACGAGTTTTTTTTTAACTTTGTTTCCCTAAAGCATTCAACAAAATCCATTCCTTA
*
900 GAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGATCAAAATATGTCATTTTGT
130 GAGCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTG----------GTC----TG-
* *
965 AAACAAGTTTTGATCTTT
180 -AA-TAG-TTTG-TCGTT
* * *
983 GAATTAAAAACTTATCTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTACGAACTTTCGAACTTG
1 GAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTTTTGGACGAACTTTCGAAC-TG
* ** * *
1048 TCAAAATTTTACGAGTTATTTTTTTAACTTT-TTTTTCTAAAGTATTCAACAAGATCCATTCCTT
65 TCAAACTTTTACGAGTT-TTTTTTTAACTTTGTTTCCCTAAAGCATTCAACAAAATCCATTCCTT
* * * *
1112 AGAGCAATTTTTTGAACATTCCATGCTCGAGAGATCGCATCAATTGGTCTAAATAGTTTGTC
129 AGAGCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTGAATAGTTTGTC
1174 ATTTTGCAAA
Statistics
Matches: 335, Mismatches: 46, Indels: 46
0.78 0.11 0.11
Matches are distributed among these distances:
193 2 0.01
194 149 0.44
195 4 0.01
196 2 0.01
197 2 0.01
199 1 0.00
203 3 0.01
204 3 0.01
208 2 0.01
210 2 0.01
211 2 0.01
212 3 0.01
213 146 0.44
214 14 0.04
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (193 bp):
GAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTTTTGGACGAACTTTCGAACTGT
CAAACTTTTACGAGTTTTTTTTTAACTTTGTTTCCCTAAAGCATTCAACAAAATCCATTCCTTAG
AGCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTGAATAGTTTGTCGTT
Found at i:1135 original size:213 final size:217
Alignment explanation
Indices: 768--1301 Score: 783
Period size: 213 Copynumber: 2.5 Consensus size: 217
758 TAGATTGTCG
** * * *
768 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCAGTCTTTGTTTTTGGACGAACTTCCAAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTACGAACTTCCGAACT
* *
833 GGTCAAACTTCTACGAGTT-TTTTTTTAACTTTGTTTCCCTAAAGCATTCAACAAAATCCATTCC
66 TGTCAAACTTTTACGAGTTATTTTTTTAACTTTGTTTCCCTAAAGCATTCAACAAAATCCATTCC
* *
897 TTAGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGATC-AAA-A-TATGTCA
131 TTAGAGCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCAATTGATCTAAATAGTATGTCA
* *
959 TTTTGTAAACAAGTTTTGATCT
196 TTTTGCAAACAAGTTTAGATCT
* *
981 TTGAATTAAAAACTTATCTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTACGAACTTTCGAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTACGAACTTCCGAACT
* ** * *
1046 TGTCAAAATTTTACGAGTTATTTTTTTAACTTT-TTTTTCTAAAGTATTCAACAAGATCCATTCC
66 TGTCAAACTTTTACGAGTTATTTTTTTAACTTTGTTTCCCTAAAGCATTCAACAAAATCCATTCC
* * * *
1110 TTAGAGCAATTTTTTGAACATTCCATGCTCGAGAGATCGCATCAATTGGTCTAAATAGTTTGTCA
131 TTAGAGCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCAATTGATCTAAATAGTATGTCA
*
1175 TTTTGCAAACAAGTTTAGGTCT
196 TTTTGCAAACAAGTTTAGATCT
*
1197 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGCCTTTGTACGAACTTCCGAACT
1 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTACGAACTTCCGAACT
* * *
1262 TGTCAAACTGTTACGAGTTA-TTTTTTAACTTCGGTTCCCT
66 TGTCAAACTTTTACGAGTTATTTTTTTAACTTTGTTTCCCT
Statistics
Matches: 284, Mismatches: 32, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
213 147 0.52
214 16 0.06
215 12 0.04
216 109 0.38
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (217 bp):
TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTACGAACTTCCGAACT
TGTCAAACTTTTACGAGTTATTTTTTTAACTTTGTTTCCCTAAAGCATTCAACAAAATCCATTCC
TTAGAGCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCAATTGATCTAAATAGTATGTCA
TTTTGCAAACAAGTTTAGATCT
Done.