Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008918.1 Kokia drynarioides strain JFW-HI SEQ_123609, 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: 2235
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Found at i:399 original size:215 final size:214
Alignment explanation
Indices: 1--2235 Score: 1972
Period size: 216 Copynumber: 10.4 Consensus size: 214
* * **
1 AGAACCAAGAGAGAAACAATTC-ACATGTAAATAAGTTTTTAATTGAAA-ATTAAAACTTG-TTA
1 AGAACCAAGAGAGAAACAATTCTA-ACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
* * * *
63 CAAAATGACAAACTATTTAAACGAAATGATGCGATTTC-CAGAGCATGGTATGTTCAGAAAATTT
65 CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTC-GAGCATGGAATGTTCA-AAAATTG
* * * * *
127 CTCGAAGGAATGGATTGTCTTGAATACTTTACA-AAATCGAGGTTATAAAACAACTCGTAAAAGT
128 CTCAAAGGAATGGATTGTCTTGAATACTTTA-AGGACTCGAAGTTATAAAAGAACTCGTAAAAGT
*
191 TTGACATGTTTTGAAGTTCGTGC
192 TTGACATGTTTGGAAGTTCGTGC
* * * * * *
214 AGAACCAAGAGAGAAACAATTCTGACGTAAGTAAGTTTCTATTTCAAGGACCAAAACTTATTTAC
1 AGAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
** ** * * *
279 AAAATGGTAAACTATTTAGACCAAATGATGAAATTTCTCGAGCATGAAATGCTCTAAAAATTGGT
66 AAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTC-AAAAATTGCT
* * * * *
344 CAAAGGAATGGATTGTCTTGAATATTTTAAGGACTAGAAGTTGTGAAGGAACTCGTAAAAGTTTG
130 CAAAGGAATGGATTGTCTTGAATACTTTAAGGACTCGAAGTTATAAAAGAACTCGTAAAAGTTTG
409 AC-TAGTTTAGG-AGCTT-GTGC
195 ACAT-GTTT-GGAAG-TTCGTGC
* **
429 AAGAACCAAGAGAGAAACAATTCTAACGTAATTAAGTTTTTAATTCAAATG-CCAAATTTTGTTT
1 -AGAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAA-GACCAAAACTTGTTT
* * * * * ** * *
493 ACCAAATAACAAAATATTTAGACCAAATTATGCGATTTCTTGAATATGGTATGTTCAAAATATTC
64 ACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCAAAA-ATTG
* * * *
558 CTCGGAA-GATTGGATTAG-CTTGGATACTTTAAGGAAC-CGAAATTATAAAAGAACTCGTAAAA
128 CTC-AAAGGAATGGATT-GTCTTGAATACTTTAAGG-ACTCGAAGTTATAAAAGAACTCGTAAAA
*
620 GTTTGACATGTTTTGAAGTTCGTGC
190 GTTTGACATGTTTGGAAGTTCGTGC
** * *
645 AGAACCAAGAGAGAAACAATTCT--C--ATGTAAGTTTTTATTTTAAAGACCAAAACTTGTTTAC
1 AGAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
* * * *
706 AAAATCG-TAAACTATTTAGACCAAATGATGTGATTTCTCGAACATGAAATGTTCGAAAAATTGC
66 AAAAT-GACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTC-AAAAATTGC
** * * * *
770 TCAAAGGAATGGATTGTCTTGAATACTTTAAGGGAC-AAAAGTTATGAAGGCACTCGTAAAAGCT
129 TCAAAGGAATGGATTGTCTTGAATACTTTAA-GGACTCGAAGTTATAAAAGAACTCGTAAAAGTT
834 TGAC-TAGTTTGGAAGTTCGTGC
193 TGACAT-GTTTGGAAGTTCGTGC
* * * * *
856 AAGAACCAAAAGGGAAACAATTCAAACGTAATTAAGCTTTTAATTCAAAGACCAAAACTTGTTTA
1 -AGAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
** * * ** * *
921 CAAAAAAACAAAATATTTAGACCAAATTATAAGATTTC-CTGAGTATGGAATGTTCAGAATATTG
65 CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTC-GAGCATGGAATGTTCA-AAAATTG
** * *
985 CTCGAAA-GAATGGACCAG-CTTGAATACTTTAAGGAATCGAAGCTATAAAAGAACTCGTAAAAG
128 CTC-AAAGGAATGGA-TTGTCTTGAATACTTTAAGGACTCGAAGTTATAAAAGAACTCGTAAAAG
* * *
1048 TTTGACAAGTTCGGAAGTTCGTCC
191 TTTGACATGTTTGGAAGTTCGTGC
* * * * * *** * *
1072 A-ATAACTA-AGAGAAA-AATTGTAATGCAAATAAGTTCAAAATTCAAAAACCAAAACTTTTTTA
1 AGA-ACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
* * * * * *
1134 AAAAATGACAAAAT-TTTAGACGAAATGAAGCGATTTCTCGAGCATGAAATGTTCAAAAAATTTC
65 CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTC-AAAAATTGC
* * * * * * * **
1198 TCAAAGGAACGGATCGTCCTGAAAACATTAAGTACCCGAAGTCGTAAAAGAACTCGTAAAAGTTT
129 TCAAAGGAATGGATTGTCTTGAATACTTTAAGGACTCGAAGTTATAAAAGAACTCGTAAAAGTTT
* ** * *
1263 GACAAGTGCGGAAGTTAGTCC
194 GACATGTTTGGAAGTTCGTGC
* ** * * *
1284 ATGAACCAAAAGAGTGACAATTCTCAGGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTA
1 A-GAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
* * * * * *
1349 CAAACTGACAAACTATTTAAACCAAATGATGCGATTTACT-GAGTAAGGAATGTTCGGAAAATTT
65 CAAAATGACAAACTATTTAGACCAAATGATGCGATTT-CTCGAGCATGGAATGTTC-AAAAATTG
* * * * * * * *
1413 CTCGAAGGAATGGATCGTCTTAAACACTTTAAGGAAC-CAAAGTTTTAAAACATCTCGTAAAAGT
128 CTCAAAGGAATGGATTGTCTTGAATACTTTAAGG-ACTCGAAGTTATAAAAGAACTCGTAAAAGT
* * * * *
1477 TTCACCAAAG--AGGAAGTACAT-C
192 TTGA-C-ATGTTTGGAAGTTCGTGC
* * **
1499 TAAGAACCAAGAGAGAAACAATTC-ACATGTAAATAAGTTTTTAATTGAAA-ATTAAAACTTG-T
1 --AGAACCAAGAGAGAAACAATTCTA-ACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTT
* * *
1561 TACAAAATGACAAACTATTTAAACAAAATGATGCGATTTC-CAGAGCATGGTATGTTCAGAAAAT
63 TACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTC-GAGCATGGAATGTTCA-AAAAT
* * * * * *
1625 TTCTCGAAGGAATGGATTGTCTTCAATACTTTTCAA--AATCGAGGTTATAAAAGAACTTGTAAA
126 TGCTCAAAGGAATGGATTGTCTTGAATAC-TTT-AAGGACTCGAAGTTATAAAAGAACTCGTAAA
*
1688 AGTTTGACATGTTTTGAAGTTCGTGC
189 AGTTTGACATGTTTGGAAGTTCGTGC
* * * * *
1714 AGAACCAAGAGAGAAACAATTCTGACGTAAGTAAGTTTCTATTTCAAAGACCAAAACTTATTTAC
1 AGAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
** ** *
1779 AAAATGGTAAACTATTTAGACCAAATGATGAAATTTCTCGAGCATGAAATGTTCGAAAAATTGCT
66 AAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTC-AAAAATTGCT
* * * * * * * *
1844 CAAAGGAATGGATTGTCTTGAGTATTTTAAGGAATAGAAGTTGTGAAGGAACTCGTAAAAGTTTT
130 CAAAGGAATGGATTGTCTTGAATACTTTAAGGACTCGAAGTTATAAAAGAACTCGTAAAAGTTTG
* * *
1909 AC-TAGTTTGGGAGCTCGTAC
195 ACAT-GTTTGGAAGTTCGTGC
* * **
1929 AAGAACCAAGAGAGAAACAATTCTAACGTAATTAAGTTTTTAATTCAAAGGCCAAATTTTGTTTA
1 -AGAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
* * * * ** * *
1994 CCAAATAACAAAATATTTAGACCAAATTATGCGATTTC-CTGAAAATGGTATGTTCAGAATATTG
65 CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTC-GAGCATGGAATGTTCA-AAAATTG
** * *
2058 CTTGGAA-GAATGGATCAG-CTTGGATACTTTAAGGAAC-CGAAGTTATAAAAGAACTCGTAAAA
128 C-TCAAAGGAATGGAT-TGTCTTGAATACTTTAAGG-ACTCGAAGTTATAAAAGAACTCGTAAAA
*
2120 GTTTGACATGTTTCGAAGTTCGTGC
190 GTTTGACATGTTTGGAAGTTCGTGC
** *
2145 AGAACCAAGAGAGAAACAATTCT--C--ATGTAAGTTTTTATTTCAAAGACCAAAACTTGTTTAC
1 AGAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
*
2206 AAAATCG-TAAACTATTTAGACCAAATGATG
66 AAAAT-GACAAACTATTTAGACCAAATGATG
Statistics
Matches: 1625, Mismatches: 318, Indels: 160
0.77 0.15 0.08
Matches are distributed among these distances:
210 5 0.00
211 200 0.12
212 132 0.08
213 140 0.09
214 148 0.09
215 363 0.22
216 611 0.38
217 23 0.01
218 3 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (214 bp):
AGAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
AAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCAAAAATTGCTC
AAAGGAATGGATTGTCTTGAATACTTTAAGGACTCGAAGTTATAAAAGAACTCGTAAAAGTTTGA
CATGTTTGGAAGTTCGTGC
Found at i:890 original size:427 final size:423
Alignment explanation
Indices: 1--2235 Score: 1965
Period size: 427 Copynumber: 5.2 Consensus size: 423
* * **
1 AGAACCAAGAGAGAAACAATTC-ACATGTAAATAAGTTTTTAATTGAAA-ATTAAAACTTG-TTA
1 AGAACCAAGAGAGAAACAATTCTA-ACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
* * * * * *
63 CAAAATGACAAACTATTTAAACGAAATGATGCGATTTCCAGAGCATGGTATGTTCAGAAA-ATTT
65 CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGTATGGAATGTTCA-AAATATTG
* * *
127 CTCGAAGGAATGGATTGTCTTGAATACTTTACA-AAATCGAGGTTATAAAACAACTCGTAAAAGT
129 CTCGAAGGAATGGATTGTCTTGAATACTTTA-AGGAATCGAAGTTATAAAAGAACTCGTAAAAGT
* * * *
191 TTGACATGTTTTGAAGTTCGTGCAGAACCAAGAGAGAAACAATTCTGACGTAAGTAAGTTTCTAT
193 TTGACATGTTTGGAAGTTCGTGCAGAACCAAGAGAGAAACAATTCT--C--ATGTAAGTTTTTAA
* * * **
256 TTCAAGGACCAAAACTTATTTACAAAATGGTAAACTATTTAGACCAAATGATGAAATTTCTCGAG
254 TTCAAAGACCAAAACTTGTTTACAAAAT-GCAAACTATTTAGACCAAATGATGCGATTTCTCGAG
* * * *
321 CATGAAATGCTCTAAAAATTGGTCAAAGGAATGGATTGTCTTGAATATTTTAAGGACTAGAAGTT
318 CATGAAATGTTC-AAAAATTGCTCAAAGGAATGGATTGTCTTGAATACTTTAAGAAC-AGAAGTT
* * *
386 GTGAAGGAACTCGTAAAAGTTTGACTAGTTTAGG-AGCTT-GTGCA
381 ATAAAAGAACTCGTAAAAGTTTGAC-AGTTT-GGAAG-TTCGTGCA
* **
430 AGAACCAAGAGAGAAACAATTCTAACGTAATTAAGTTTTTAATTCAAATG-CCAAATTTTGTTTA
1 AGAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAA-GACCAAAACTTGTTTA
* * * * * * * *
494 CCAAATAACAAAATATTTAGACCAAATTATGCGATTTCTTGAATATGGTATGTTCAAAATATTCC
65 CAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGTATGGAATGTTCAAAATATTGC
* * * *
559 TCGGAA-GATTGGATTAG-CTTGGATACTTTAAGGAACCGAAATTATAAAAGAACTCGTAAAAGT
130 TC-GAAGGAATGGATT-GTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGT
* * *
622 TTGACATGTTTTGAAGTTCGTGCAGAACCAAGAGAGAAACAATTCTCATGTAAGTTTTTATTTTA
193 TTGACATGTTTGGAAGTTCGTGCAGAACCAAGAGAGAAACAATTCTCATGTAAGTTTTTAATTCA
* * *
687 AAGACCAAAACTTGTTTACAAAATCGTAAACTATTTAGACCAAATGATGTGATTTCTCGAACATG
258 AAGACCAAAACTTGTTTACAAAAT-GCAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATG
* * *
752 AAATGTTCGAAAAATTGCTCAAAGGAATGGATTGTCTTGAATACTTTAAGGGACAAAAGTTATGA
322 AAATGTTC-AAAAATTGCTCAAAGGAATGGATTGTCTTGAATACTTTAA-GAACAGAAGTTATAA
* * *
817 AGGCACTCGTAAAAGCTTGACTAGTTTGGAAGTTCGTGCA
385 AAGAACTCGTAAAAGTTTGAC-AGTTTGGAAGTTCGTGCA
* * * * *
857 AGAACCAAAAGGGAAACAATTCAAACGTAATTAAGCTTTTAATTCAAAGACCAAAACTTGTTTAC
1 AGAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
** * * ** *
922 AAAAAAACAAAATATTTAGACCAAATTATAAGATTTCCTGAGTATGGAATGTTCAGAATATTGCT
66 AAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGTATGGAATGTTCAAAATATTGCT
* ** *
987 CGAAAGAATGGACCAG-CTTGAATACTTTAAGGAATCGAAGCTATAAAAGAACTCGTAAAAGTTT
131 CGAAGGAATGGA-TTGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTTT
* * * * * * * ***
1051 GACAAGTTCGGAAGTTCGTCCA-ATAACTA-AGAGAAA-AATTGTAATGCAAATAAGTTCAAAAT
195 GACATGTTTGGAAGTTCGTGCAGA-ACCAAGAGAGAAACAATTCTCATG----TAAGTTTTTAAT
* * * * * *
1113 TCAAAAACCAAAACTTTTTTAAAAAATGACAAAAT-TTTAGACGAAATGAAGCGATTTCTCGAGC
255 TCAAAGACCAAAACTTGTTTACAAAATG-CAAACTATTTAGACCAAATGATGCGATTTCTCGAGC
* * * * * * * * **
1177 ATGAAATGTTCAAAAAATTTCTCAAAGGAACGGATCGTCCTGAAAACATTAAGTACCCGAAGTCG
319 ATGAAATGTTC-AAAAATTGCTCAAAGGAATGGATTGTCTTGAATACTTTAAG-AACAGAAGTTA
** * *
1242 TAAAAGAACTCGTAAAAGTTTGACAAGTGCGGAAGTTAGTCCA
382 TAAAAGAACTCGTAAAAGTTTGAC-AGTTTGGAAGTTCGTGCA
* * ** * * *
1285 TGAACCAAAAGAGTGACAATTCTCAGGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTAC
1 AGAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
* * * *
1350 AAACTGACAAACTATTTAAACCAAATGATGCGATTTACTGAGTAAGGAATGTTCGGAAAAT-TT-
66 AAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGTATGGAATGTTC--AAAATATTG
* * * * * * * *
1413 CTCGAAGGAATGGATCGTCTTAAACACTTTAAGGAACCAAAGTTTTAAAACATCTCGTAAAAGTT
129 CTCGAAGGAATGGATTGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTT
* * * * * *
1478 TCACCAAAG--AGGAAGTACAT-CTAAGAACCAAGAGAGAAACAATTCACATGTAAATAAGTTTT
194 TGA-C-ATGTTTGGAAGTTCGTGC--AGAACCAAGAGAGAAACAATTCTCATG----TAAGTTTT
* ** * *
1540 TAATTGAAA-ATTAAAACTTG-TTACAAAATGACAAACTATTTAAACAAAATGATGCGATTTC-C
251 TAATTCAAAGACCAAAACTTGTTTACAAAATG-CAAACTATTTAGACCAAATGATGCGATTTCTC
** * * *
1602 AGAGCATGGTATGTTCAGAAAATTTCTCGAAGGAATGGATTGTCTTCAATACTTTTCAA-AATC-
315 -GAGCATGAAATGTTCA-AAAATTGCTCAAAGGAATGGATTGTCTTGAATAC-TTT-AAGAA-CA
* * *
1665 GAGGTTATAAAAGAACTTGTAAAAGTTTGACATGTTTTGAAGTTCGTGC-
375 GAAGTTATAAAAGAACTCGTAAAAGTTTGACA-GTTTGGAAGTTCGTGCA
* * * * *
1714 AGAACCAAGAGAGAAACAATTCTGACGTAAGTAAGTTTCTATTTCAAAGACCAAAACTTATTTAC
1 AGAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
** ** * *
1779 AAAATGGTAAACTATTTAGACCAAATGATGAAATTT-CTCGAGCATGAAATGTTCGAAAA-ATTG
66 AAAATGACAAACTATTTAGACCAAATGATGCGATTTCCT-GAGTATGGAATGTTC-AAAATATTG
* * * * * * *
1842 CTCAAAGGAATGGATTGTCTTGAGTATTTTAAGGAATAGAAGTTGTGAAGGAACTCGTAAAAGTT
129 CTCGAAGGAATGGATTGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTT
* * * *
1907 TTAC-TAGTTTGGGAGCTCGTACAAGAACCAAGAGAGAAACAATTCTAACGTAAT-TAAGTTTTT
194 TGACAT-GTTTGGAAGTTCGTGC-AGAACCAAGAGAGAAACAATTCT--C---ATGTAAGTTTTT
* ** * * * *
1970 AATTCAAAGGCCAAATTTTGTTTACCAAATAACAAAATATTTAGACCAAATTATGCGATTTC-CT
252 AATTCAAAGACCAAAACTTGTTTACAAAAT-GCAAACTATTTAGACCAAATGATGCGATTTCTC-
** ** * ** * * *
2034 GAAAATGGTATGTTCAGAATATTGCTTGGAA-GAATGGATCAG-CTTGGATACTTTAAGGAACCG
315 GAGCATGAAATGTTCA-AAAATTGC-TCAAAGGAATGGAT-TGTCTTGAATACTTTAA-GAACAG
*
2097 AAGTTATAAAAGAACTCGTAAAAGTTTGACATGTTTCGAAGTTCGTGC-
376 AAGTTATAAAAGAACTCGTAAAAGTTTGACA-GTTTGGAAGTTCGTGCA
** *
2145 AGAACCAAGAGAGAAACAATTCT--C--ATGTAAGTTTTTATTTCAAAGACCAAAACTTGTTTAC
1 AGAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
*
2206 AAAATCG-TAAACTATTTAGACCAAATGATG
66 AAAAT-GACAAACTATTTAGACCAAATGATG
Statistics
Matches: 1497, Mismatches: 250, Indels: 120
0.80 0.13 0.06
Matches are distributed among these distances:
425 8 0.01
426 16 0.01
427 412 0.28
428 286 0.19
429 301 0.20
430 145 0.10
431 316 0.21
432 11 0.01
434 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (423 bp):
AGAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
AAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGTATGGAATGTTCAAAATATTGCT
CGAAGGAATGGATTGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTTTG
ACATGTTTGGAAGTTCGTGCAGAACCAAGAGAGAAACAATTCTCATGTAAGTTTTTAATTCAAAG
ACCAAAACTTGTTTACAAAATGCAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGAAAT
GTTCAAAAATTGCTCAAAGGAATGGATTGTCTTGAATACTTTAAGAACAGAAGTTATAAAAGAAC
TCGTAAAAGTTTGACAGTTTGGAAGTTCGTGCA
Done.