Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008723.1 Kokia drynarioides strain JFW-HI SEQ_123405, 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: 2250
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Found at i:1760 original size:217 final size:216
Alignment explanation
Indices: 874--1785 Score: 995
Period size: 216 Copynumber: 4.2 Consensus size: 216
864 GCTATCACCA
* * * *
874 AACTTCCGCACTTGTT-AAACATTTTTGAGTTCTTTTAAAACTTCGGTTCCTTAAAGTATTCAAG
1 AACTTCCGAACTT-TTCAAACTTTTTTGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAG
* * * * *
938 AGGATCGATTCCTTCGAGCAATTTTCTG-AACATTCCATGCTCGGGAAATTC-CATCATTTGGAC
65 ACGATCCATTCCTTCGAGCAATTTTC-GAAACATTCCATTCTC-GGAAAATCACATCATTTGGTC
* * * * * *
1001 CAAATAGTTTGTCCTTTTGAAAAAAACTTTCAATCTTTGAATTAAAAACTTATTTACGTGAGAA-
128 AAAATAATTTGTCATTTTGTAAAAAACTTTCGATCTTTGAATTAAAAACTTATTTATGTGAGAAT
1065 TGATTTCTCTCTTGGTTCTTGGCCG
193 TG-TTTCTCTCTTGGTTCTTGGCCG
* *** * * *
1090 AATTTTTTAACTTTTCAAACTTTTTCGAGTTCCTTTATAACTTCGATTTCTTAAAGTATTCAAGA
1 AACTTCCGAACTTTTCAAACTTTTTTGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGA
** * * *
1155 CGATCCATTCCTTCGAGCAATTTTTTAAACATTCCGTTCTCGGGAAATCACAT--TTATGGTCCA
66 CGATCCATTCCTTCGAGCAATTTTCGAAACATTCCATTCTCGGAAAATCACATCATT-TGGTCAA
* * *
1218 AATAA--TGTCATTTTGTAAAGAACTGTT-GATCTTTGGATTAAAAACTTATTTATTTGAGAATT
130 AATAATTTGTCATTTTGTAAAAAACT-TTCGATCTTTGAATTAAAAACTTATTTATGTGAGAATT
* *
1280 -TTT-TCTCTTCGTTCTTGGCCA
194 GTTTCTCTCTTGGTTCTTGGCCG
* * *
1301 AACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTATAACTTCGATTCCTTAAAGTAATCAAGA
1 AACTTCCGAACTTTTCAAACTTTTTTGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGA
* * * * * ** * ** *
1366 TGATCGATTCCTCCGGGCAATTTTCCAAACATTCCAGCCTCGGGAAATGGCACCATTTGGTCAAA
66 CGATCCATTCCTTCGAGCAATTTTCGAAACATTCCATTCTCGGAAAATCACATCATTTGGTCAAA
* * * * * *
1431 ACAGTTTGTCCTTTTGTAAAAAACATTCGATCTTTGAATTAAAAGCTTATTTATGTAAGAATTGT
131 ATAATTTGTCATTTTGTAAAAAACTTTCGATCTTTGAATTAAAAACTTATTTATGTGAGAATTGT
*
1496 TTCTCTCTTTGTTCTTGGCCG
196 TTCTCTCTTGGTTCTTGGCCG
* * *
1517 AACTTTCGAACTTTTTAAACTTTTTTGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTTAAGA
1 AACTTCCGAACTTTTCAAACTTTTTTGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGA
** ** * *
1582 CGATCCATTATTTCGAATAATTTTTCGAAA-ATTCCATTATCGAAAAATCACATCATTTGGTCTA
66 CGATCCATTCCTTCGAGCAA-TTTTCGAAACATTCCATTCTCGGAAAATCACATCATTTGGTC-A
* * * * * *
1646 AAATAATCTGTCATTTTCTAAACAACTTTTGGTCATT-AGATTAAAAACTTATTTATGTGAGAAT
129 AAATAATTTGTCATTTTGTAAAAAACTTTCGATCTTTGA-ATTAAAAACTTATTTATGTGAGAAT
1710 TGTTTCTCTCTTGGTTCTTGGCCG
193 TGTTTCTCTCTTGGTTCTTGGCCG
* * * * *
1734 AACTTCCGAAATTTTCAAAATTTTTTGAGTTCTTTCACAACTTCGGTTCCTT
1 AACTTCCGAACTTTTCAAACTTTTTTGAGTTCTTTTATAACTTCGATTCCTT
1786 TCCTTCAAGC
Statistics
Matches: 575, Mismatches: 105, Indels: 31
0.81 0.15 0.04
Matches are distributed among these distances:
211 114 0.20
212 12 0.02
213 49 0.09
214 52 0.09
215 21 0.04
216 200 0.35
217 127 0.22
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (216 bp):
AACTTCCGAACTTTTCAAACTTTTTTGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGA
CGATCCATTCCTTCGAGCAATTTTCGAAACATTCCATTCTCGGAAAATCACATCATTTGGTCAAA
ATAATTTGTCATTTTGTAAAAAACTTTCGATCTTTGAATTAAAAACTTATTTATGTGAGAATTGT
TTCTCTCTTGGTTCTTGGCCG
Found at i:1933 original size:195 final size:196
Alignment explanation
Indices: 1600--1980 Score: 534
Period size: 195 Copynumber: 1.9 Consensus size: 196
1590 TATTTCGAAT
*
1600 AATTTTTCGAAAATTCCATTATCGAAAAATCACATCATTTGGTCTAAAATAATCTGTCATTTTCT
1 AATTTTTCGAAAATTCCATTATCGAAAAATCACATCATTTGGTCCAAAATAATCTGTCATTTTCT
* * *
1665 AAACAACTTTTGGTCATTAGATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTG
66 AAACAACTTTTAGTCATTAGATTAAAAACTAAATTATGTGAGAATTGTTTCTCTCTTGGTTCTTG
* * * * *
1730 GCCGAACTTCCGAAATTTTCAAAATTTTTTGAGTTCTTTCACAACTTCGGTTCCTTTCCTTCAAG
131 GACGAACTTCCGAAATTATCAAAATTTTTCGAGTTCTTTCAAAACTTCGATTCCTTTCCTTCAAG
1795 C
196 C
* * * * *
1796 AATTTTTTGAACATTCCATTATCGAGAAAT-AGCATCATTTGGTCC-AAATAAAT-TTTCCTTTT
1 AATTTTTCGAAAATTCCATTATCGAAAAATCA-CATCATTTGGTCCAAAAT-AATCTGTCATTTT
* * *
1858 GTAAACAACTTTTAGTCTTTGGATTAAAAACTAAATTATGTGAGAATTGTTTCTCTCTTGGTTCT
64 CTAAACAACTTTTAGTCATTAGATTAAAAACTAAATTATGTGAGAATTGTTTCTCTCTTGGTTCT
* ** *
1923 TGGACGAACTTCCGAACTTATCAAGCTTTTTCGAGTTCTTTTAAAACTTCGATTCCTT
129 TGGACGAACTTCCGAAATTATCAAAATTTTTCGAGTTCTTTCAAAACTTCGATTCCTT
1981 AAAGTATTCA
Statistics
Matches: 162, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
195 120 0.74
196 42 0.26
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (196 bp):
AATTTTTCGAAAATTCCATTATCGAAAAATCACATCATTTGGTCCAAAATAATCTGTCATTTTCT
AAACAACTTTTAGTCATTAGATTAAAAACTAAATTATGTGAGAATTGTTTCTCTCTTGGTTCTTG
GACGAACTTCCGAAATTATCAAAATTTTTCGAGTTCTTTCAAAACTTCGATTCCTTTCCTTCAAG
C
Done.