Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009580.1 Kokia drynarioides strain JFW-HI SEQ_124294, 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: 2292
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.27
Warning! 84 characters in sequence are not A, C, G, or T
Found at i:1293 original size:215 final size:216
Alignment explanation
Indices: 269--1687 Score: 1384
Period size: 216 Copynumber: 6.6 Consensus size: 216
259 NNNNNNNNNN
* * * * * * *
269 CCAAAAGTTGTTTAGAAATTGACAAATTATTTAGACATAATGATGCGATTTCCTGTGCTTGGAAT
1 CCAAAAGTTGTTTACAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAAT
* * **
334 GTTTGAAAAATTACTCGAA-GAAGTGGATCGTCATGAATACTTTAAGGAATTGAAGTT-TTAAAA
66 GTTCGAAAAATTGCTCGAAGGAA-TGGATCGTCATGAATACTTTAAGGAACCGAAGTTATT-AAA
* * * * * *
397 GAACTCGTAACACTTCGTCAAGTTCGAAAGTTCGTCCAAGAA-CAAGGAGAGAAACAAATCTCAT
129 GAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCATCCAAGAACCAA-GAGAGAAACAATTCTCAC
** *
461 GTAAATAACTTTTTAATTTATAA-A
193 GTAAATAAGATTTTAATTCA-AAGA
* * * *
485 CCAAAAGTCGTTTACAAAATGACAAACTATTTAGACTAAATTATGCAATTTCCCGAGCATGGAAT
1 CCAAAAGTTGTTTACAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAAT
* * * * * *
550 GTTCGAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAATGG-AGCAAAGTTATTGAAC
66 GTTCGAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAA-GGAACCGAAGTTATTAAAG
* * ** * ** * * * *
614 AACTGGTAAAAGTTTGTGGAGTTAGGAAGTTTGTCCATGATCCAAGAGATAGTA-AATTCTCACG
130 AACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGA-AACAATTCTCACG
* *
678 AAAATAAGCTTTTAATT-AAATGA
194 TAAATAAGATTTTAATTCAAA-GA
* * *** * *
701 CCAAAAGTTGTATACCAAATGACAAACTAAGCAGACAAAATGATGTGATTTCCCAAGCATGGAAT
1 CCAAAAGTTGTTTACAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAAT
* *
766 GTTC-AGAAAATTGCTCGAAGGAATGGAACGTCATGAATACTTTATA-GAACCGAAGTTA-CAGA
66 GTTCGA-AAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTA-AGGAACCGAAGTTATTA-A
* * * ** * * *
828 TGAACTCGTCAAAGTTTGTCAAGTTTAGAAGTTCATCCAATATCCAAGAGAGAAACAATTCTCAT
128 AGAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCAC
* *
893 GTAAATAAGTTTTTCATTCAAAGA
193 GTAAATAAGATTTTAATTCAAAGA
* * * * ** * * *
917 GCAAAAGTTGTTTACCAAATGACAAA-TAGTTTAGAAAAAAATGATGCTATTTTACAATCATGAA
1 CCAAAAGTTGTTTACAAAATGACAAACTA-TTTAG-ACAAAATGATGCGATTTCCCGAGCATGGA
* * * *
981 ATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTATGGAACTGATGTTATAAAA
64 ATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCGAAGTTATTAAA
* * * * *
1046 GAACTCGTAAAAGTT-TTCCAAGTTCAGAAGTTCGTCCAAGAACCAAGATAGAAACAACTCTCAC
129 GAACTCGTAAAAGTTCGT-CAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCAC
*
1110 GTAAGA-AAG-TTTTACATTGAAAGA
193 GTAA-ATAAGATTTTA-ATTCAAAGA
* * * * * * * * *
1134 CGAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCGATTTCCCGAGTAAGTAAA
1 CCAAAAGTTGTTTACAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAAT
* * * * * * *
1199 GTTCAAAAAATTGCTCTAA-GAATGGGTTGTCCTGAATACTTTAAGAAACCGAAGTTATTGAAGA
66 GTTCGAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCGAAGTTATTAAAGA
* * * * * * *
1263 ACTCATAAAAGTTCGTAAAGTTTGGAAGTTCATCTAAGAACCAAGAGAAAAACAACTCTCACGGA
131 ACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTA
* *
1328 AATAGGTTTTTAATTCAAAGA
196 AATAAGATTTTAATTCAAAGA
* ** * *
1349 CCAAAAGTTGTTTAGAAAATGACAAACTATTTAGACAAAATGATGTAATTTCCTGTGCATGGAAT
1 CCAAAAGTTGTTTACAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAAT
* * *
1414 GCTCGAAAAATTGCTCGAAGAAATGGATCGTCATGAATA-TTTAAGGAACTGAAGTT-TTAAAAG
66 GTTCGAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCGAAGTTATT-AAAG
* * * * **
1477 AACTTGCAAAACTTCATCAAGTTCGGAAGTTCATCCAAGAAGAAAGAGAGAAACAATTCTCACGT
130 AACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGT
*
1542 AAATAAGATTTTAATTTAAAGA
195 AAATAAGATTTTAATTCAAAGA
* * * *
1564 CCAGAAGTTGTTTACAAAATGGCAAACTATTTAGACCAAATGGTGCGATTTCCCGAGCATGGAAT
1 CCAAAAGTTGTTTACAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAAT
* *
1629 GTTCAGAAAATATT--TTGAAGGAATGGATTGTCATGAATACTTTAAGGAA-CGAAAGTTAT
66 GTTC-GAAAA-ATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCG-AAGTTAT
1688 AGATGAAATA
Statistics
Matches: 979, Mismatches: 192, Indels: 63
0.79 0.16 0.05
Matches are distributed among these distances:
214 5 0.01
215 346 0.35
216 434 0.44
217 189 0.19
218 5 0.01
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (216 bp):
CCAAAAGTTGTTTACAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAAT
GTTCGAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCGAAGTTATTAAAGA
ACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTA
AATAAGATTTTAATTCAAAGA
Found at i:1828 original size:158 final size:158
Alignment explanation
Indices: 1540--1846 Score: 422
Period size: 158 Copynumber: 1.9 Consensus size: 158
1530 CAATTCTCAC
* * *
1540 GTAAATAAGATTTTAATTTAAAGACCAGAAGTTGTTTACAAAATGGCAAACTATTTAGACCAAAT
1 GTAAATAAGATTTTAATTCAAAGACCAGAAGTCGTTTACAAAATGACAAACTATTTAGACCAAAT
** * * * * *
1605 GGTGCGATTTCCCGAGCATGGAATGTTCAGAAAATATTTTGAAGGAATGGATTGTCATGAATACT
66 AATGCGATTTCCCGAGCATGAAATGTTCAAAAAATACTCTGAAGGAATGGATTATCATGAATACT
*
1670 TTAAGGAA-CGAAAGTTATAGATGAAATA
131 TTAAGAAATCG-AAGTTATAGATGAAATA
* * * *
1698 GTAAATAAGTTTTTCATTCAAAGACCA-AAGGTCGTTTAGAAAATGACAAAGTATTTAGACCAAA
1 GTAAATAAGATTTTAATTCAAAGACCAGAA-GTCGTTTACAAAATGACAAACTATTTAGACCAAA
*
1762 TAATGCGATTTCCCGAGCATGAAATGTTCAAAAAATTACTCT-AAGGAATGGATTATCTTGAATA
65 TAATGCGATTTCCCGAGCATGAAATGTTCAAAAAA-TACTCTGAAGGAATGGATTATCATGAATA
1826 CTTTAAGAAATCGAAGTTATA
129 CTTTAAGAAATCGAAGTTATA
1847 AAAGAACTCG
Statistics
Matches: 130, Mismatches: 16, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
157 2 0.02
158 122 0.94
159 6 0.05
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.30
Consensus pattern (158 bp):
GTAAATAAGATTTTAATTCAAAGACCAGAAGTCGTTTACAAAATGACAAACTATTTAGACCAAAT
AATGCGATTTCCCGAGCATGAAATGTTCAAAAAATACTCTGAAGGAATGGATTATCATGAATACT
TTAAGAAATCGAAGTTATAGATGAAATA
Found at i:2028 original size:374 final size:372
Alignment explanation
Indices: 1327--2051 Score: 899
Period size: 374 Copynumber: 1.9 Consensus size: 372
1317 ACTCTCACGG
* * *
1327 AAATAGGTTTTTAATTCAAAGACCAAAAGTTGTTTAGAAAATGACAAACTATTTAGACAAAATGA
1 AAATAAGTTTTTAATTCAAAGACCAAAAGTCGTTTAGAAAATGACAAACTATTTAGACAAAATAA
* * * * * * *
1392 TGTAATTTCCTGTGCATGGAATGCTCGAAAAATTGCTCGAAGAAATGGATCGTCATGAATATTTA
66 TGCAATTTCCCGAGCATGAAATGCTCAAAAAATTACTCGAAGAAATGGATCATCATGAATATTTA
* * *
1457 AGGAACTGAAGTTTTAAAAGAACTTGCAAAACTTCATCAAGTTCGGAAGTTCATCCAAGAAGAAA
131 AGAAACTGAAGTTATAAAAGAACTCGCAAAACTTCATCAAGTTCGGAAGTTCATCCAAGAAGAAA
* * * *
1522 GAGAGAAACAATTCTCACGTAAATAAGATTTTAATTTAAAGACCAGAAGTTGTTTACAAAATGGC
196 GAGAGAAACAACTCTCACGCAAATAAGATTTTAATTCAAAGACCAGAAGTTGTTTACAAAATGAC
* * * *
1587 AAACTATTTAGACCAAATGGTGCGATTTCCCGAGCATGGAATGTTCAGAAAATATTTTGAAGGAA
261 AAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAATGCTCAGAAAATATTTCGAAGGAA
**
1652 TGGATTGTCATGAATACTTTAAGGAACGAAAGTTATAGATGAAATAGT
326 TGGATCATCATGAATA-TTTAAGGAACGAAAGTTATAGATGAAATAGT
* * * *
1700 AAATAAGTTTTTCATTCAAAGACCAAAGGTCGTTTAGAAAATGACAAAGTATTTAGACCAAATAA
1 AAATAAGTTTTTAATTCAAAGACCAAAAGTCGTTTAGAAAATGACAAACTATTTAGACAAAATAA
* * * * * *
1765 TGCGATTTCCCGAGCATGAAATGTTCAAAAAATTACTCTAAGGAATGGATTATCTTGAATACTTT
66 TGCAATTTCCCGAGCATGAAATGCTCAAAAAATTACTCGAAGAAATGGATCATCATGAATA-TTT
* * * * *
1830 AAGAAA-TCGAAGTTATAAAAGAACTCGTAAAAGTAT-GTCAAGCTT-GGAAGTTCGTCTAAG-A
130 AAGAAACT-GAAGTTATAAAAGAACTCGCAAAACT-TCATCAAG-TTCGGAAGTTCATCCAAGAA
* * * * *
1891 GCCAAGAGAGAAA-AACCTCTCACGCAAATAGGTTTTTAATTCGAAGACCA-AAGGTTGTTTAGA
192 G-AAAGAGAGAAACAA-CTCTCACGCAAATAAGATTTTAATTCAAAGACCAGAA-GTTGTTTACA
* *
1954 AAATGACAAACTATTTAGACAAAATGATGCGATTTCCTGTGCATGGAATGCTC-GAAAA-ATTGC
254 AAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAATGCTCAGAAAATATT--
2017 TCGAAGGAATGGATCATCATGAATATTTAAGGAAC
317 TCGAAGGAATGGATCATCATGAATATTTAAGGAAC
2052 TGAAGTTTTA
Statistics
Matches: 298, Mismatches: 45, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
372 3 0.01
373 128 0.43
374 164 0.55
375 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (372 bp):
AAATAAGTTTTTAATTCAAAGACCAAAAGTCGTTTAGAAAATGACAAACTATTTAGACAAAATAA
TGCAATTTCCCGAGCATGAAATGCTCAAAAAATTACTCGAAGAAATGGATCATCATGAATATTTA
AGAAACTGAAGTTATAAAAGAACTCGCAAAACTTCATCAAGTTCGGAAGTTCATCCAAGAAGAAA
GAGAGAAACAACTCTCACGCAAATAAGATTTTAATTCAAAGACCAGAAGTTGTTTACAAAATGAC
AAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAATGCTCAGAAAATATTTCGAAGGAA
TGGATCATCATGAATATTTAAGGAACGAAAGTTATAGATGAAATAGT
Found at i:2165 original size:215 final size:214
Alignment explanation
Indices: 1698--2276 Score: 736
Period size: 215 Copynumber: 2.7 Consensus size: 214
1688 AGATGAAATA
* * *
1698 GTAAATAAGTTTTTCATTCAAAGACCAAAGGTCGTTTAGAAAATGACAAAGTATTTAGACCAAAT
1 GTAAATAAGTTTTTAATTCAAAGACCAAAGGTTGTTTAGAAAATGACAAACTATTTAGACCAAAT
* * * * * *
1763 AATGCGATTTCCCGAGCATGAAATGTTCAAAAAATTACTCTAAGGAATGGATTATCTTGAATACT
66 GATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTATCATGAATACT
* * * * * *
1828 TTAAGAAATCGAAGTTATAAAAGAACTCGTAAAAGTATGTCAAGCTTGGAAGTTCGTCTAAGAGC
131 TTAAGGAAT-GAAGTTATAAAAGAACTCGCAAAACTATATCAAGCTTGGAAGTTCGTCCAAGAAC
*
1893 CAAGAGAGAAAAACCTCTCAC
195 AAAGAGAGAAAAA-CTCTCAC
* * * *
1914 GCAAATAGGTTTTTAATTCGAAGACCAAAGGTTGTTTAGAAAATGACAAACTATTTAGACAAAAT
1 GTAAATAAGTTTTTAATTCAAAGACCAAAGGTTGTTTAGAAAATGACAAACTATTTAGACCAAAT
* * * *
1979 GATGCGATTTCCTGTGCATGGAATGCTCGAAAAATTGCTCGAAGGAATGGATCATCATGAATA-T
66 GATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTATCATGAATACT
* *
2043 TTAAGGAACTGAAGTTTTAAAAGAACTTGCAAAACT-TCATCAAG-TTCGGAAGTTCGTCCAAGA
131 TTAAGGAA-TGAAGTTATAAAAGAACTCGCAAAACTAT-ATCAAGCTT-GGAAGTTCGTCCAAGA
*
2106 ATAAAGAGAGAAACAA-TACTCAC
193 ACAAAGAGAGAAA-AACT-CTCAC
* * * * *
2129 GTAAATAAGATTTTAATTTAAAGACCAAAAGTTGTTTACAAAATGGCAAACTATTTAGACCAAAT
1 GTAAATAAGTTTTTAATTCAAAGACCAAAGGTTGTTTAGAAAATGACAAACTATTTAGACCAAAT
* * *
2194 GATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTTGAAGG-ATGGATTGTCATGAATACT
66 GATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTATCATGAATACT
2258 TTAAGGAATGAAAGTTATA
131 TTAAGGAATG-AAGTTATA
2277 GATGAAATAG
Statistics
Matches: 312, Mismatches: 44, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
214 21 0.07
215 177 0.57
216 114 0.37
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (214 bp):
GTAAATAAGTTTTTAATTCAAAGACCAAAGGTTGTTTAGAAAATGACAAACTATTTAGACCAAAT
GATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTATCATGAATACT
TTAAGGAATGAAGTTATAAAAGAACTCGCAAAACTATATCAAGCTTGGAAGTTCGTCCAAGAACA
AAGAGAGAAAAACTCTCAC
Done.