Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012050.1 Kokia drynarioides strain JFW-HI SEQ_127048, 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: 2197
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.27
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:2013 original size:219 final size:218
Alignment explanation
Indices: 1155--2193 Score: 997
Period size: 220 Copynumber: 4.7 Consensus size: 218
1145 ATTTAAACCG
*
1155 AAAGTTTTTTTGAGAAATGGA-AAACTATTTTGACCGAATGATGCGATTTCCCGAGCATGGAATG
1 AAAGTTTTTTTGA-AAAT-GACAAACTATTTAGACCGAATGATGCGATTTCCCGAGCATGGAATG
* * * * * *
1219 TCCGGAATATTGCTCGAAGGATTGGATCATCTTGAATACTTTACGGAACCAAAGTTATTGTAGAA
64 TTCGGAATATTGCTCGAAGAAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTA-T-TAAAA
* * * *
1284 GAAATAGTAAAACCTGGACAAGTTCAGAAGTTTGTCTAAGAA-TCAAAAGAGAAATAATTCT-CA
127 GAAACAGTAAAAGCTTGACAAGTTCAGAAGTTTGTCTAAGAACT-AAAAGAGAAACAATTCTACA
* *
1347 CATAATTATATTTTTAATTCAAACACCAA
191 CATAAATAGATTTTTAATTCAAACACC-A
* * *
1376 AAAG-TTGTTTGCAAAATGACAAACTATTTAGACCGAATGATGCTATTTCCTGAGCATGGAATGT
1 AAAGTTTTTTTG-AAAATGACAAACTATTTAGACCGAATGATGCGATTTCCCGAGCATGGAATGT
* *
1440 TCGGAATATTGATCGAAGAAATGCATCGTCTTGAATACTTTAAGGAACCAAAGTTA-TAAAAG-A
65 TCGGAATATTGCTCGAAGAAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATTAAAAGAA
* * * *
1503 ACTCGTAAAAGGCTTGGCTAGTTCAGAAGTTTGTCTGAA-AACTAAAGGAGAAACAATTC-ACAC
130 AC-AGTAAAA-GCTTGACAAGTTCAGAAGTTTGTCT-AAGAACTAAAAGAGAAACAATTCTACAC
* * * *
1566 GTAAATA-AGCTTTTAGTTTGAAGACCAAGACCA
192 ATAAATAGA-TTTTTA-ATTCAA-A-C---ACCA
* * * * * * * * *
1599 AAACTTGGTTTTCAAAAT-ATAAAACTATTTAGACCTAAAGATGCAATTTCTCGATCATGGAATG
1 AAAGTT-TTTTTGAAAATGA-CAAACTATTTAGACCGAATGATGCGATTTCCCGAGCATGGAATG
* * * ** * *
1663 TTTGGAAAATTGCTCGTAGAAGCGGATGGTCTTGAATACTTTAAGGAACCGAAA-TTA-TAATAG
64 TTCGGAATATTGCTCGAAGAAATGGATCGTCTTGAATACTTTAAGGAACC-AAAGTTATTAAAAG
* * ** ** * * **
1726 AAATAGTAAAAGATTTCCTCGTTC-GAAAGTTCGTCCAAGAACTAGGAGAGAAACAATT-TACAC
128 AAACAGTAAAAGCTTGACAAGTTCAG-AAGTTTGTCTAAGAACTAAAAGAGAAACAATTCTACAC
* * *** *
1789 ATAAATAGGTATTTAATTCAGTGACCG
192 ATAAATAGATTTTTAATTCAAACACCA
*
1816 AAAGTTTTTTTGAGAAATGACAAACTATTTTGACCGAATGATGCGATTTCCCGAGCATGGAATGT
1 AAAGTTTTTTTGA-AAATGACAAACTATTTAGACCGAATGATGCGATTTCCCGAGCATGGAATGT
* * * *
1881 TCGG-ATATTGCTCGAAGGATTGGATCATCTTGAATACTTTACGGAACCAAAGTTATTATAGAAG
65 TCGGAATATTGCTCGAAGAAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATTA-A-AAG
*
1945 AAACAGTAAAAGCTTGACAAGTTCAGAAGTTTGTCTAAGAA-TCAAAAGAGAAATAATTCTA-AC
128 AAACAGTAAAAGCTTGACAAGTTCAGAAGTTTGTCTAAGAACT-AAAAGAGAAACAATTCTACAC
*
2008 ATAAATATATTTTTAATTCAAACACCAA
192 ATAAATAGATTTTTAATTCAAACACC-A
* * *
2036 AAAG-TTGTTTGCAAAATGACAAAGTATTTAGACCGAATGATGCTG-TTTCCCGAGCATGAAATG
1 AAAGTTTTTTTG-AAAATGACAAACTATTTAGACCGAATGATGC-GATTTCCCGAGCATGGAATG
* *
2099 TTCGGAATATTGATTGAAGAAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTA-TAAAAG-
64 TTCGGAATATTGCTCGAAGAAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATTAAAAGA
* *
2162 AACTCGTAAAAAGCTTGA-ATAGTTCAAAAGTT
129 AAC-AGT-AAAAGCTTGACA-AGTTCAGAAGTT
2194 CGTC
Statistics
Matches: 663, Mismatches: 116, Indels: 81
0.77 0.13 0.09
Matches are distributed among these distances:
215 3 0.00
216 49 0.07
217 73 0.11
218 75 0.11
219 134 0.20
220 155 0.23
221 6 0.01
222 6 0.01
223 52 0.08
224 102 0.15
225 8 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (218 bp):
AAAGTTTTTTTGAAAATGACAAACTATTTAGACCGAATGATGCGATTTCCCGAGCATGGAATGTT
CGGAATATTGCTCGAAGAAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATTAAAAGAAA
CAGTAAAAGCTTGACAAGTTCAGAAGTTTGTCTAAGAACTAAAAGAGAAACAATTCTACACATAA
ATAGATTTTTAATTCAAACACCA
Done.