Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013489.1 Kokia drynarioides strain JFW-HI SEQ_128515, 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: 3423
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:315 original size:3 final size:3
Alignment explanation
Indices: 307--398 Score: 67
Period size: 3 Copynumber: 30.3 Consensus size: 3
297 ATTTCCTTTT
* * * * *
307 TTA TTA TTA TTA TTA TTTA TTA CTA TTA TTA CTG TCA TTA GTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
353 CTA ATG TCA TTA GTA ATA TTA TTG TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
399 GACTAAAGGT
Statistics
Matches: 66, Mismatches: 22, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
3 63 0.95
4 3 0.05
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1079 original size:6 final size:6
Alignment explanation
Indices: 1070--1146 Score: 70
Period size: 6 Copynumber: 12.7 Consensus size: 6
1060 TTTGGACATT
*
1070 AATTTA AATTTA AATTTA AACTTA AATTTA TAA--TA AATTTA AATTAAGTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATT---TA
* *
1120 AATTTA AACTTA AA-ATA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATT
1147 CTGTTAGGCC
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
4 2 0.03
5 6 0.10
6 43 0.73
7 2 0.03
9 6 0.10
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:1834 original size:206 final size:206
Alignment explanation
Indices: 1470--2405 Score: 1218
Period size: 206 Copynumber: 4.6 Consensus size: 206
1460 TCTGGTCTCA
* ** ** ** *
1470 TTGATTTGGTCTTCTTCTCGGTATCTCATCAGGAAGATGATTGCATCACTTGTTTTGATCCTCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* * * * *
1535 CTCTTTGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCCA-TATCTCATCAGGAAGCTAACCA
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCT-CAGTATCTCATCAGGAAGCTAACCA
* * * * *
1599 CTTTATTGCTTCGACCTACTNCACAGTATCTCATCAGGAAGCTAAGG-TTTGAAGATTTGCTCAC
130 CTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGATTCGAAGATTTGCTCAC
1663 ATCGAGCGTGGGT
194 ATCGAGCGTGGGT
* *
1676 TTGATTTGGTCTTCTTCTCAGTATCTCATCACGAAGATGACCGCTTCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* * * * *
1741 ATTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATGACCGC
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAC
* * * *
1806 GTTATTGCTTCGACCTGTTTCTCAGTATCTCATCAAGAAGCTGGGATTCGAAGATTTGCTCACCT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACAT
1871 CGAGCGTGGGT
196 CGAGCGTGGGT
* * *
1882 TTGATTTGGTCTTCTTTTCAGTATATCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* *
1947 CTCTGTATCTCATCAGGAAGACTAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAC
* *
2012 TTTATTTCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACCT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACAT
2077 CGAGCGTGGGT
196 CGAGCGTGGGT
* * *
2088 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCGTTTGTTTCAATCTGTTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* * *
2153 CTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAC
* * **
2218 TTTATTTCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGG-TTCGAAGATTTTTTCACA
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGATTCGAAGATTTGCTCACA
* *
2282 TTGA--GTTGG-
195 TCGAGCGTGGGT
* * *** * *
2291 -T-A--T--ACTTC-TCT--GTATCTCATCAGGAAGATGACCGCCTTACTTGTTTTAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* * *
2347 CTCTGTACCTCATCAGGAAGACGAATTTGGTCCGCTTCTTAGTATCTCATCAGGAAGCT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCT
2406 GGGGTTCTAT
Statistics
Matches: 653, Mismatches: 74, Indels: 18
0.88 0.10 0.02
Matches are distributed among these distances:
194 90 0.14
196 3 0.00
197 4 0.01
199 1 0.00
201 1 0.00
202 1 0.00
204 4 0.01
205 4 0.01
206 542 0.83
207 3 0.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAC
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACAT
CGAGCGTGGGT
Done.