Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014350.1 Kokia drynarioides strain JFW-HI SEQ_129387, 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: 2150
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.35
Warning! 347 characters in sequence are not A, C, G, or T
Found at i:558 original size:216 final size:215
Alignment explanation
Indices: 21--643 Score: 682
Period size: 214 Copynumber: 2.9 Consensus size: 215
11 CGTTCCTCAC
* * * * * * * *
21 AGTATTCATGATGATCCATTCATTCCAGCAATTTTTCGAATATTCCATGGTCAGGAAAACGCATC
1 AGTATTCAAGACGATCCATTCCTTTCAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATC
* * * * *
86 ATTTGGT-TCAAATAGTTTTTCATTTTGTAAACAAAATTTT-GTGTTTGAAATAAAATTTTATTT
66 ATTTGGTCT-AAATTGTTTGTCATTTTGTAAAC-AACTTTTGGTCTTTG-AATAAAATCTTATTT
* * * * *
149 ACGTGAGTATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCGAACTTTTACGGGTT
128 ACGTGAGAATTGTTTCTCTCTTGATTCTTGGACGAACTTCCGAACTTATCAAACTTTTACGAGTT
* * *
214 CTTTTATAACTTCTGCTCGTTAA
193 CTTTTATAACTTCGGATCATTAA
** *
237 AGTA-T-AAGACGATCCATTCC-TTCAGGCAATTTTTCGAACATTTGATGCTCGAGAAATCGCAT
1 AGTATTCAAGACGATCCATTCCTTTCA-GCAATTTTTCGAACATTCCATGCTCGGGAAATCGCAT
* * *
299 CATTTCGTCTAAATCT-TTTGTCATTTTGTAAACAGCATTTGGTCTTTGAATTAAAATCTTATTT
65 CATTTGGTCTAAAT-TGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAA-TAAAATCTTATTT
* * * * * ** * *
363 ATGTGACAATTATTTATCTCTTGAATCTTGGACGAACTTTTGATCTTATCAAACTTTTATGAGTT
128 ACGTGAGAATTGTTTCTCTCTTGATTCTTGGACGAACTTCCGAACTTATCAAACTTTTACGAGTT
428 CTTTTATAACTTCGGATCATTAA
193 CTTTTATAACTTCGGATCATTAA
* * *
451 AGTATTCAAGACGATCCATTCCTTTCAGCAATTTTTTGAACATTCCACGCTCGGGAAATCACATC
1 AGTATTCAAGACGATCCATTCCTTTCAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATC
* * *
516 ATTTGGTCTAAGTTGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGGAATAAAAACTTGTTTAC
66 ATTTGGTCTAAATTGTTTGTCATTTTGTAAACAACTTTTGGTCTTT-GAATAAAATCTTATTTAC
* ** * * * * * *
581 ATGAGAATTGTTTCTCTCTTGATTCTTTTATGAACATCCAAACTTGTCAAGCTTTTACAAGTT
130 GTGAGAATTGTTTCTCTCTTGATTCTTGGACGAACTTCCGAACTTATCAAACTTTTACGAGTT
644 NNNNNNNNNN
Statistics
Matches: 331, Mismatches: 66, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
213 9 0.03
214 162 0.49
215 4 0.01
216 149 0.45
217 7 0.02
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (215 bp):
AGTATTCAAGACGATCCATTCCTTTCAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATC
ATTTGGTCTAAATTGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATAAAATCTTATTTACG
TGAGAATTGTTTCTCTCTTGATTCTTGGACGAACTTCCGAACTTATCAAACTTTTACGAGTTCTT
TTATAACTTCGGATCATTAA
Found at i:1109 original size:215 final size:215
Alignment explanation
Indices: 787--1195 Score: 550
Period size: 215 Copynumber: 1.9 Consensus size: 215
777 TATTAAAGAC
* * * * * * *
787 GATCCATTCCTTTCAGCAATTTTTTGAACATTCCACGCTCGGGAAATCACATCATTTGGTCTAAG
1 GATCCATTCATTCCAGCAATTTTTCGAACATTCCACGATCAGGAAAACACATCATTTGGTCTAAA
* * * *
852 TTGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGGAATAAAAACTTGTTTACGTGAGAATTGTT
66 TAGTTTGTCAATTTGTAAACAACTTTTGGTCTTTGAAATAAAAACTTATTTACGTGAGAATTGTT
* *
917 TCTCTCTTGATTCTTTGATGAACTTCCAAACTTGTC-AAGCTTTTACAAGTTCTTTAATAACTTC
131 TCTCTCTAGATTCTTGGATGAACTTCCAAACTTGTCGAA-CTTTTACAAGTTCTTTAATAACTTC
981 GTTCCTCACAGTATTCATGAT
195 GTTCCTCACAGTATTCATGAT
* * * *
1002 GATCCATTCATTCCAGCAATTTTTCGAATATTCCATGATCAGGAAAACGCATCATTTGGTTTAAA
1 GATCCATTCATTCCAGCAATTTTTCGAACATTCCACGATCAGGAAAACACATCATTTGGTCTAAA
* * * * * *
1067 TAGTTTTTCAATTTGTGAACAAGTTTTTGTGTTTGAAATAAAAACTTATTTACGTGAGTATTGTT
66 TAGTTTGTCAATTTGTAAACAACTTTTGGTCTTTGAAATAAAAACTTATTTACGTGAGAATTGTT
* * ** *
1132 TCTCTCTAGGTTCTTGGATGAACTTCCGAACTTGTCGAACTTTTACGGGTTCTTTTATAACTTC
131 TCTCTCTAGATTCTTGGATGAACTTCCAAACTTGTCGAACTTTTACAAGTTCTTTAATAACTTC
1196 TGCTCNNNNN
Statistics
Matches: 165, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
215 163 0.99
216 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (215 bp):
GATCCATTCATTCCAGCAATTTTTCGAACATTCCACGATCAGGAAAACACATCATTTGGTCTAAA
TAGTTTGTCAATTTGTAAACAACTTTTGGTCTTTGAAATAAAAACTTATTTACGTGAGAATTGTT
TCTCTCTAGATTCTTGGATGAACTTCCAAACTTGTCGAACTTTTACAAGTTCTTTAATAACTTCG
TTCCTCACAGTATTCATGAT
Found at i:1833 original size:216 final size:214
Alignment explanation
Indices: 1481--1873 Score: 556
Period size: 216 Copynumber: 1.8 Consensus size: 214
1471 CGGGAAATCA
* * *
1481 CATCATTTGGTCTAAGTTGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGGAATAAAAACTTGT
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGGAATAAAAACTTAT
* * *
1546 TTACGTGAGAATTGTTTCTCTCTTGATTCTTTGATGAACATCCAAACTTGTCAAGCTTTTACAAT
66 TTACGTGAGAATTGTTTCTCTCTTGATTCTTGGACGAACATCCAAACTTGTCAAGCTTTTACAAG
* *
1611 TTCTTTTATAACTTCGGTTCCG-TAAAGTATTCAAGACGATCTATTCCTTTGAGAAAATTTTCAA
131 TTCTTTTATAACTTCGGCT-CGTTAAAGTA-T-AAGACGATCCATTCCTTTGAGAAAATTTTCAA
1675 ACATTCCATGATCAGGAAAATG
193 ACATTCCATGATCAGGAAAATG
* * * * *
1697 CATCATTTGGTTTAAATAGTTTTTCATTTTGTAAACAAGTTTTTGTGTTTGGAATAAAAACTTAT
1 CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGGAATAAAAACTTAT
* * * * **
1762 TTACGTGAGTATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCCAA-CTTTTACGG
66 TTACGTGAGAATTGTTTCTCTCTTGATTCTTGGACGAACATCCAAACTTGT-CAAGCTTTTACAA
*
1826 GTTCTTTTATAACTTCTGCTCGTTAAAGTATAAGACGATCCATTCCTT
130 GTTCTTTTATAACTTCGGCTCGTTAAAGTATAAGACGATCCATTCCTT
1874 CAATCAATTT
Statistics
Matches: 155, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
214 16 0.10
215 3 0.02
216 133 0.86
217 3 0.02
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (214 bp):
CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGGAATAAAAACTTAT
TTACGTGAGAATTGTTTCTCTCTTGATTCTTGGACGAACATCCAAACTTGTCAAGCTTTTACAAG
TTCTTTTATAACTTCGGCTCGTTAAAGTATAAGACGATCCATTCCTTTGAGAAAATTTTCAAACA
TTCCATGATCAGGAAAATG
Done.