Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002174.1 Kokia drynarioides strain JFW-HI SEQ_114137, 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: 2020
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Found at i:412 original size:214 final size:215
Alignment explanation
Indices: 1--1559 Score: 1699
Period size: 214 Copynumber: 7.3 Consensus size: 215
* * * *
1 AACTTTTGGTCTATGAATTAAAAACTTATTCAGGTGAGAATAGTTTCTCTCTTGGTTCTAGGCCG
1 AACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGGTTCTCGGCCG
* * * * *
66 AACATTCGAAGTTGACAAACTTTTACGAGTTCTTTTAAAACTTCGGTTCCTTAAAGTATTCAAGA
66 AACTTTCGAACTTGACAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGA
* * * * * * * *
131 CGAACCATTTCTTCAAGCAATTTTCTGAACATTCCACGCTTAGGAAATCTCATCTTTTGGTCTAA
131 CGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTAGAAAATCACATCATTAGGTCTAA
196 ATAGTTGTCATTTTGTAAAC
196 ATAGTTGTCATTTTGTAAAC
* * * *
216 AACTTTTGGTCTTTGAATTAAAAAATTATTTATGTGAGAATTGTTTCTTTCTTGGTTCTCGGCGG
1 AACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGGTTCTCGGCCG
* * * * ** *
281 AACGTT-AAACTTGGA-AAACTTTTATAAGTTCATTTATAACTTTTTTTCATTAAAGTATTCAAG
66 AACTTTCGAACTT-GACAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAG
* * * * *
344 ATGATCCATTCCTTCGAGTAATTTTCTGTACAGTCCATGCTTAGAAAATCACATCATTAGTTCTA
130 ACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTAGAAAATCACATCATTAGGTCTA
* *
409 AATAGTTGACATTTCGTAAAC
195 AATAGTTGTCATTTTGTAAAC
* * * * *
430 TACTTTTGGTTTTTCAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTATTCGTTCT----C-
1 AACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGGTTCTCGGCCG
* * * * * *
490 -A--GTCGAACTTGACAAAGTTTTACGAGTACTTTTATAACTTTTGTTCATTAAAGTATTCAAGA
66 AACTTTCGAACTTGACAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGA
* * * * *
552 CGATCCATTCCTTCGAGCAATATTCTGTACAGTCCATGCTTGGAAAATCACAACATTAGGTCTAA
131 CGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTAGAAAATCACATCATTAGGTCTAA
617 ATAGTTGTCA-TTTGTAAAC
196 ATAGTTGTCATTTTGTAAAC
** * * * *
636 AACTTTTATTTTTTGAGTTAAAAACTTATTTACGTGAGAATTATTTCTCTCTTGGTTCTCGGCCG
1 AACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGGTTCTCGGCCG
* * * * *
701 AACTTCCGAACCTGACTAACTTTTA-AGAGTTCTTTTATAACTTCGGTTCCTTAAAGTAATCAAG
66 AACTTTCGAACTTGACAAACTTTTACA-AGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAG
* * * *
765 ACGATCTATTCCTTCGAGCAATTTT-TGGAACATTCCATGC-TCGAGAAATCGCACCAATT-GGT
130 ACGATCCATTCCTTCGAGCAATTTTCT-GAACATTCCATGCTTAGA-AAATCACATC-ATTAGGT
* *
827 CTAAATAGTTGTTATTATGTAAAC
192 CTAAATAGTTGTCATTTTGTAAAC
** * ** *
851 AACTTTTTATCATTGAATTAAAAACTTATTTAGGTGAGAATAATTTCTCTCTTGGTTCTGGGCCG
1 AACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGGTTCTCGGCCG
* * * * * *
916 AACTTTCGAAGTTGACAAACTTTCACGATTTCTTTTATAACTTTGGTTCCTTAAACTATTTAAGA
66 AACTTTCGAACTTGACAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGA
* * * * *
981 CGATCCATTCCTTCGAGCAATTTTCCGAACTTTCCATGCTT-GGAAATCACATCATTTGGTTTAA
131 CGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTAGAAAATCACATCATTAGGTCTAA
1045 ATAGTTGTCATTTTGTAAAC
196 ATAGTTGTCATTTTGTAAAC
* * *
1065 AACTTTTGGTCTCTGAATTAAGAAA-TTCTTTAGGTGAGAATTGTTTCTTTCTTGGTTCTCGGCC
1 AACTTTTGGTCTTTGAATTAA-AAACTTATTTAGGTGAGAATTGTTTCTCTCTTGGTTCTCGGCC
* * * * * * *
1129 AAACTTT-AAACTTGACAAAATTTT-CAAGTTCGTTTATAAATTTTGTTCATTAAAGTATTCAAG
65 GAACTTTCGAACTTGACAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAG
* * * * * * * * *
1192 ATGATCCATTCCTTC-AGCAATATAT-TGTACAGTCCGTGCTTGGGAAATCACATTATTAGTTCT
130 ACGATCCATTCCTTCGAGCAAT-TTTCTGAACATTCCATGCTTAGAAAATCACATCATTAGGTCT
* *
1255 AAATTGTTGTCATTCTGTAAAC
194 AAATAGTTGTCATTTTGTAAAC
* * * * * * *
1277 TACTTTTGGTTTTTCAATTAAAAACTTATTTAGGTGAGAATTGTTTCTATTTTGGTTCTCAGTCG
1 AACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGGTTCTCGGCCG
* * *
1342 AACTTTCGAACTTGAAAAACTTTTACAAGTTAC-TTTATAACTTTGATTCCTTAAAATATTCAAG
66 AACTTTCGAACTTGACAAACTTTTACAAGTT-CTTTTATAACTTTGGTTCCTTAAAGTATTCAAG
* ** * *
1406 ACGATCCCTTCCTTCGAGCAATTTTAAGAACATTCCCTGCTCTAG-AAATCGCATCATTTA-GTC
130 ACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCT-TAGAAAATCACATCA-TTAGGTC
* *
1469 TAAATAGTTGCCATTATGTAAAC
193 TAAATAGTTGTCATTTTGTAAAC
* * * * * *
1492 AACTTTTTGTCTTTAAATTAAAAACTTATTCATGTGAGAATAGTTTCTCTCTTGGTTCTAGGCCG
1 AACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGGTTCTCGGCCG
1557 AAC
66 AAC
1560 ATCCGAAGAT
Statistics
Matches: 1118, Mismatches: 195, Indels: 62
0.81 0.14 0.05
Matches are distributed among these distances:
206 61 0.05
207 116 0.10
208 1 0.00
210 1 0.00
211 20 0.02
212 142 0.13
213 34 0.03
214 408 0.36
215 329 0.29
216 6 0.01
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (215 bp):
AACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGGTTCTCGGCCG
AACTTTCGAACTTGACAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGA
CGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTTAGAAAATCACATCATTAGGTCTAA
ATAGTTGTCATTTTGTAAAC
Found at i:1793 original size:275 final size:275
Alignment explanation
Indices: 1302--1842 Score: 769
Period size: 275 Copynumber: 2.0 Consensus size: 275
1292 AATTAAAAAC
* *
1302 TTATTTAGGTGAGAATTGTTTCTATTTTGGTTCTCAGTCGAACTTTCGAACTTGAAAAACTTTTA
1 TTATTTAGGTGAGAATTGTTTCTATTTTGGTTCCCAGTCGAACTTCCGAACTTGAAAAACTTTTA
*
1367 CAAGTTACTTTATAACTTTGATTCCTTAAAATATTCAAGACGATCCCTTCCTTCGAGCAATTTTA
66 CAAGTTACTTTATAACTTTGATTCCTTAAAATATTCAAGACGATCCATTCCTTCGAGCAATTTTA
* * * * *
1432 AGAACATTCCCTGCTCTAGAAATCGCATCATTTAGTCTAAATAGTTGCCATTATGTAAACAACTT
131 AGAAAATTCCATGCTCTAGAAATCGCATCATTAAGTCTAAATAATTGCCATTATGTAAACAAATT
** * * * *
1497 TTTGTCTTTAAATTAAAAACTTATTCATGTGAGAATAGTTTCTCTCTTGGTTCTAGGCCGAACAT
196 TCGGTCTCTAAATTAAAAACTTATTCAGGTGAGAATAGTTTCTCTCTTGGTTCTAGGACAAACAT
1562 CCGAAGATAACAAAT
261 CCGAAGATAACAAAT
* * * *
1577 TTATTTAGTTGAGAATTGTTTCTCTTTTTGTTCCC-GATCGAACTTCCGAGCTTGAAAAACTTTT
1 TTATTTAGGTGAGAATTGTTTCTATTTTGGTTCCCAG-TCGAACTTCCGAACTTGAAAAACTTTT
* * * *
1641 ACGAGTTACTTTATAATTTTGATTCCTTAAACTATTCAAGACGATCCATTCGTTCGAGCAATTTT
65 ACAAGTTACTTTATAACTTTGATTCCTTAAAATATTCAAGACGATCCATTCCTTCGAGCAATTTT
* * * * *
1706 AAGAAAATTCTATGGTCTAGAAATTGCATCATTAAGTGTAAATAATTTCCATTATGTAAACAAAT
130 AAGAAAATTCCATGCTCTAGAAATCGCATCATTAAGTCTAAATAATTGCCATTATGTAAACAAAT
* * * * * *
1771 TTCGGTCTCTGAATTAAAAACTTTTTTAGGTGAGAGTAGTTTCTCTCTTGTTTCTAGGACAAACT
195 TTCGGTCTCTAAATTAAAAACTTATTCAGGTGAGAATAGTTTCTCTCTTGGTTCTAGGACAAACA
1836 TCCGAAG
260 TCCGAAG
1843 TTGACAAACT
Statistics
Matches: 232, Mismatches: 33, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
274 1 0.00
275 231 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (275 bp):
TTATTTAGGTGAGAATTGTTTCTATTTTGGTTCCCAGTCGAACTTCCGAACTTGAAAAACTTTTA
CAAGTTACTTTATAACTTTGATTCCTTAAAATATTCAAGACGATCCATTCCTTCGAGCAATTTTA
AGAAAATTCCATGCTCTAGAAATCGCATCATTAAGTCTAAATAATTGCCATTATGTAAACAAATT
TCGGTCTCTAAATTAAAAACTTATTCAGGTGAGAATAGTTTCTCTCTTGGTTCTAGGACAAACAT
CCGAAGATAACAAAT
Done.