Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013632.1 Kokia drynarioides strain JFW-HI SEQ_128660, 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: 2301
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.39
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:902 original size:215 final size:212
Alignment explanation
Indices: 1--1193 Score: 1123
Period size: 215 Copynumber: 5.6 Consensus size: 212
* * * *
1 TCTTGGTTCTGGGCCGAACTTTCAAAGTTGACAAACTTTTACGATTTCTTTTATAACTTTGGTTC
1 TCTTGGTTCTCGGCCGAAC-TTCAAACTTGACAAACTTTTACGAGTTCTTTTATAA-TTTTGTTC
* * * * *
66 CTTAAAGTATTTAAGACGACCCATTCCTTCGAGCAATTTTTAGAACTTTCCATGCT-TGGAAATC
64 ATTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCAGAACATTCCATGCTCTGGAAATC
* * * **
130 GCATCATTTGGTTTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTCG
129 ACATCATTAGGTCTAAATAGTTGTCA-TTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTAT
* *
195 TTAGGTGAGAGTTGTTTCTT
193 TTAGGTGAGAATTGTTTCTC
* * * * *
215 TCTTGGTTCTCGGCCAAACTTTAAACTTGACAAA-ATTTCCAAGTTCTTTTATAAATTTTGTTCA
1 TCTTGGTTCTCGGCCGAACTTCAAACTTGACAAACTTTTACGAGTTCTTTTAT-AATTTTGTTCA
* * * * *
279 TTAAAGTATTCAAGACGATTCATTCCTTC-AACAATATATT--GTACAGTCCGTGC-CTGGGAAA
65 TTAAAGTATTCAAGACGATCCATTCCTTCGAGCAAT-T-TTCAGAACATTCCATGCTCT-GGAAA
* * * * * * *
340 TCACATTATTAGGTCTAAATTA-CTGTCATTT-TATAACTACTTTCGGTTTTTCAATTAAAAACT
127 TCACATCATTAGGTCTAAA-TAGTTGTCATTTGTA-AACAACTTTTGGTCTTTGAATTAAAAAAT
*
403 TATTTAGGTAAGAATTGTTTCTC
190 TATTTAGGTGAGAATTGTTTCTC
* * * * * *
426 TATTCGTTCT----C--A-GTCGAACTTGACAAAGTTTTACGAGTACTTTTATAACTTTTGTTCA
1 TCTTGGTTCTCGGCCGAACTTCAAACTTGACAAACTTTTACGAGTTCTTTTATAA-TTTTGTTCA
* * * * *
484 TTAAAGTATTCAAGACGATCGATTCCTTCGAGTAATTTTCTGTACAGTCCATGCT-TGGGAAATC
65 TTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCAGAACATTCCATGCTCT-GGAAATC
* * * *
548 ACATCATTAGTTCTAAA-AGTTGTCATTTTTGAAACTA-TTTCTGGTCTTCT-AATTAAAAATTT
129 ACATCATTAGGTCTAAATAGTTGTCATTTGT-AAACAACTTT-TGGTCTT-TGAATTAAAAAATT
*
610 ATTTAGTTGAGAATTGTTTCTC
191 ATTTAGGTGAGAATTGTTTCTC
* ** * * *
632 TTTTGGTTCTCGATCGAACTTCCGAGCTTGAAAAACTTTTACGAGTTAC-TTTATAATTTTGATT
1 TCTTGGTTCTCGGCCGAACTT-CAAACTTGACAAACTTTTACGAGTT-CTTTTATAATTTTG-TT
* * * * * *
696 CCTTAAAGTATTCAAGACGATCCTTTCCTTCGAGCAATTTTAAGAAAATTCTATGCTCTAGAAAT
63 CATTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCAGAACATTCCATGCTCTGGAAAT
* * * * * * *
761 CGCATCATTAAGTGTAAATAATTGTCATTATGTAAACAACTTTTGGTCTCTGAATTAAAAACTTT
128 CACATCATTAGGTCTAAATAGTTGTCATT-TGTAAACAACTTTTGGTCTTTGAATTAAAAAATTA
* *
826 TTTAGGTGAGAGTAGTTTCTC
192 TTTAGGTGAGAATTGTTTCTC
* * * * * * **
847 TCTTGTTTCTAGGCCAAACTTCCGAAGTTGACAAACTTTTACGTGTTCTTTTATAACTTCAGTTC
1 TCTTGGTTCTCGGCCGAACTT-CAAACTTGACAAACTTTTACGAGTTCTTTTATAA-TTTTGTTC
* * * * * * * * * *
912 CTTACAGTAATCAAGACAAACCATTCCTTCGAGCAATTTTCTGAACATTCCAAGCACAGGGAATC
64 ATTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCAGAACATTCCATGCTCTGGAAATC
* *
977 TCATCATTTGGTCTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTAT
129 ACATCATTAGGTCTAAATAGTTGTCA-TTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTAT
** *
1042 TTATATGAGAATTGTTTCTT
193 TTAGGTGAGAATTGTTTCTC
* * * *
1062 TCTTGGTTCTCGACCGAACTTTAAACTTGACAAACATTTACGAGTTCTTCTATAACTTTTGTTCA
1 TCTTGGTTCTCGGCCGAACTTCAAACTTGACAAACTTTTACGAGTTCTTTTATAA-TTTTGTTCA
* * *
1127 TTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGTACAGTCCATGC-CTGGAAAATC
65 TTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCAGAACATTCCATGCTCTGG-AAATC
1191 ACA
129 ACA
1194 ACNNNNNNNN
Statistics
Matches: 794, Mismatches: 148, Indels: 74
0.78 0.15 0.07
Matches are distributed among these distances:
204 17 0.02
205 63 0.08
206 90 0.11
207 3 0.00
210 3 0.00
211 68 0.09
212 74 0.09
213 28 0.04
214 203 0.26
215 235 0.30
216 10 0.01
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (212 bp):
TCTTGGTTCTCGGCCGAACTTCAAACTTGACAAACTTTTACGAGTTCTTTTATAATTTTGTTCAT
TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCAGAACATTCCATGCTCTGGAAATCAC
ATCATTAGGTCTAAATAGTTGTCATTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTATTTA
GGTGAGAATTGTTTCTC
Found at i:2045 original size:214 final size:212
Alignment explanation
Indices: 1251--2128 Score: 1007
Period size: 215 Copynumber: 4.1 Consensus size: 212
1241 NNNNNCTTAC
* * * * * * *
1251 AGTAATCAAGACAAACCATTCCTTCGAGCAATTTTCTGAACATTCCAAGCACAGGGAATCTCATC
1 AGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGC-CTGGAAATCGCATC
* * *
1316 ATTTGGTCTAAATAATTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTATTTATG
65 ATTTGGTCTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTAGTTAGG
* * *
1381 TGAGAATTTTTCTTTCTTGGTTCTCGTCCGAACTTTAAACTTGACAAACATTTACGAGTTCTTTT
130 TGAGAATTTTTCTCTCTTGGTTCTCGGCCAAACTTTAAACTTGACAAACATTTACGAGTTCTTTT
*
1446 ATAACTTTTGTTCATTAA
195 ATAACTTTGGTTCATTAA
* * * *
1464 AGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGTACAGT-CATGCCTGGAAAATCACAAC
1 AGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCCTGG-AAATCGCATC
* ** * *
1528 ATTAGGTC-AAATAGTTGTCATTTTGTAAACAACTTTTATTTTTTGAATTAAAAACTT-GTTTAG
65 ATTTGGTCTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTAG-TTAG
** * * * * * *
1591 GTGAGAATTATTTCTCTCTTGGTTCTCGGCCAAACTTCCGAACCTAACTAACTTTTAAGACTTCT
129 GTGAGAATT-TTTCTCTCTTGGTTCTCGGCCAAACTT-TAAACTTGACAAACATTTACGAGTTCT
* * *
1656 TTTATAACTTCGATTCTTTAA
192 TTTATAACTTTGGTTCATTAA
* *
1677 AGTAATCAA-AGCGATCTATTCCTTCGAGCAA-TTTCTGGAACATTCCAT-CCTCGAGAAATCGC
1 AGTATTCAAGA-CGATCCATTCCTTCGAGCAATTTTCT-GAACATTCCATGCCT-G-GAAATCGC
* * * * * * * * *
1739 ACCATTTAGTCTAAATATTTGTCATTATGTAAACTATTTTTGATCTTTGAATTAAAAACTTATTT
62 ATCATTTGGTCTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTAGTT
* * * * * *
1804 AGGTGAGAATACTTTCTCTCTTGGTTCTGGGCCGAACTTTCAAAGTTGACAAACTTTTACGATTT
127 AGGTGAGAAT-TTTTCTCTCTTGGTTCTCGGCCAAACTTT-AAACTTGACAAACATTTACGAGTT
*
1869 CTTTTATAACTTTGGTTCCTTAA
190 CTTTTATAACTTTGGTTCATTAA
* * * *
1892 AGTATTTAAGACGATCCATTTCTTCGAGCAATTTT-TCGAACTTTCCATGCTTGGAAATCGCATC
1 AGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCT-GAACATTCCATGCCTGGAAATCGCATC
* *
1956 ATTTGGTTTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTCGTTAGG
65 ATTTGGTCTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTAGTTAGG
* * * *
2021 TGAGAGTTGTTTCTTTCTTGGTTCTCGGCCAAACTTTAAACTTGACAAA-ATTTCCAAGTTCTTT
130 TGAGAATT-TTTCTCTCTTGGTTCTCGGCCAAACTTTAAACTTGACAAACATTTACGAGTTCTTT
* *
2085 TATAAATTTTGTTCATTAA
194 TATAACTTTGGTTCATTAA
2104 AGTATTCAAGACGATCCATTCCTTC
1 AGTATTCAAGACGATCCATTCCTTC
2129 AACAATATAT
Statistics
Matches: 552, Mismatches: 96, Indels: 35
0.81 0.14 0.05
Matches are distributed among these distances:
211 59 0.11
212 98 0.18
213 121 0.22
214 114 0.21
215 154 0.28
216 6 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (212 bp):
AGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCCTGGAAATCGCATCA
TTTGGTCTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTAGTTAGGT
GAGAATTTTTCTCTCTTGGTTCTCGGCCAAACTTTAAACTTGACAAACATTTACGAGTTCTTTTA
TAACTTTGGTTCATTAA
Done.