Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001524.1 Kokia drynarioides strain JFW-HI SEQ_113087, 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: 2171
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:872 original size:282 final size:280
Alignment explanation
Indices: 5--2168 Score: 2312
Period size: 282 Copynumber: 7.7 Consensus size: 280
1 AAAG
* *
5 TAAAAGAGAAAATATTTTCTTATATCAAGAACGCCGCGTGTCAAAATCCAGAGAAACAAATAGTA
1 TAAAAGAGAAAATATTTT-TTATATCAAGAACGCCGCGTGTCAAAATCCAAAGAAACAAATATTA
* * * * * * *
70 CTTTAGTTTAAATTTAAAAAATAGTCATTGTACTTGTTGATTTGTGCGGATTTAGTCCCACTATT
65 TTTTAGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGATTTGGTCCCACAATT
* *
135 TTTATTTACTCGTAGCATTCAAATTGGCATCTTATATTTGAGAAAAAAAATAGAAAATTGATGAA
130 TTTATTTACTCGTAGCATTCAAATTGGCGTCTTATGTTTGAG-AAAAAAATAGAAAATTGATGAA
** * *
200 ATCAACGAAGAATCTCCCTGCCAAATTTAAGCAGTTCAATCACATGCATTTAAATTGAAACCGCC
194 ATCAACGAAGAATCTCCCTGCCAAATACAAGCAGCTCAATCACATGCATTTAACTTGAAACCGCC
*
265 GCGTAAGATGGCTGTTTTAAAA
259 GCGTAAGATGGCAGTTTTAAAA
* * *
287 TAAAAGAGAAAATATTTTTTATATCAAGAACGTCGCATGT-AAGAATCCAAAGAAGCAAATATTA
1 TAAAAGAGAAAATATTTTTTATATCAAGAACGCCGCGTGTCAA-AATCCAAAGAAACAAATATTA
* * *
351 TTTTAGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGATTTTGTCCCTCATTT
65 TTTTAGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGATTTGGTCCCACAATT
* * * * *
416 TTTATTTACTCGTAGCATTGAAATTGGCCTCTTATGTTTGA-CAAAAAA-ACAAAATAGATGAAA
130 TTTATTTACTCGTAGCATTCAAATTGGCGTCTTATGTTTGAGAAAAAAATAGAAAATTGATGAAA
* * * * *
479 TCAAAGAAGAATCTCCCTGCCAAATACAATCAGCTCCATCACATGCATTTAACTTGAAACTGCCC
195 TCAACGAAGAATCTCCCTGCCAAATACAAGCAGCTCAATCACATGCATTTAACTTGAAACCGCCG
*
544 CGTAAGATGGCAGTTTTAAAG
260 CGTAAGATGGCAGTTTTAAAA
* * *
565 TAAAAGAGAAAATATTTTCTTATATCAAGAACGCCGCCTGTCAAAATCCATAGAAACAAATAGTA
1 TAAAAGAGAAAATATTTT-TTATATCAAGAACGCCGCGTGTCAAAATCCAAAGAAACAAATATTA
* * * *
630 CTCTAGTTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGATTTGGTCTCACAATT
65 TTTTAGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGATTTGGTCCCACAATT
* *
695 TTTATTTACTCGTAGCATTCAAATTGGCGTCTTATCTTTGAGAAAAATAATAGAAAATGGATGAA
130 TTTATTTACTCGTAGCATTCAAATTGGCGTCTTATGTTTGAGAAAAA-AATAGAAAATTGATGAA
* ** *
760 ATCAACAAAGAATCTCCCTGCCAAATTTAAGCCA-CTCAATCACATGCATTTAACTTGAATCCGC
194 ATCAACGAAGAATCTCCCTGCCAAATACAAG-CAGCTCAATCACATGCATTTAACTTGAAACCGC
* * *
824 CACGTAAGAAGTCAGTTTTAAAA
258 CGCGTAAGATGGCAGTTTTAAAA
* *
847 TAAAAGAGAAAATATATTTTTATATCAAGAATGCTGCGTGTCAAAATCCAAAGAAACAAATATTA
1 TAAAAGAGAAAATAT-TTTTTATATCAAGAACGCCGCGTGTCAAAATCCAAAGAAACAAATATTA
* * * * * *
912 TTTTAGCTTAAATTTTCAGATTAGTCCTTGTACGTGTTGATTTGTGCAGACTTGGTCCCACTATT
65 TTTTAGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGATTTGGTCCCACAATT
* * * * * *
977 TTTATTTACTCATAGCATTCAAATCGGGGTCTTATCTTTGAGAAAAAAAAAAAAGGAAATTGATG
130 TTTATTTACTCGTAGCATTCAAATTGGCGTCTTATGTTTGAG---AAAAAAATAGAAAATTGATG
* * * * * * * **
1042 AAATCAACGAAGAATCTTCCTACCAAACACAAGCAGCTCAGTCACATGAAATTATA-TTAAAATG
192 AAATCAACGAAGAATCTCCCTGCCAAATACAAGCAGCTCAATCACATGCATTTA-ACTTGAAACC
* * * **
1106 GCTC-CGTTAGATGACCGTTTTAGGA
256 GC-CGCGTAAGATGGCAGTTTTAAAA
* ** * * **** * * * * **
1131 TAAAAAAGAATTTATTATTTTTATATTAAAAATATTGCATGTCAGAGTCGAGTGAAACAAATATT
1 TAAAAGAGAAAATA-T-TTTTTATATCAAGAACGCCGCGTGTCAAAATCCAAAGAAACAAATATT
* * ** * * * * * * * * ***
1196 ATTCTAGGTTTGACTCTAAGAATAGTCCTTTTACTTATCGATTTGGGCAGATTTGCTCCCTTTAT
64 ATTTTAGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGATTTGGTCCCACAAT
* * * * * * * * *
1261 TTGTATTTACTCATAGAATTCAAATTGACATCTTAAGTTTGAGAAAACAA-ACAATATTGATGAA
129 TTTTATTTACTCGTAGCATTCAAATTGGCGTCTTATGTTTGAGAAAAAAATAGAAAATTGATGAA
* * ** * * * *
1325 ATCGACGAAGAATC-CGCCTACCAAATACAAGCAGCTCTGTCACATGCAATTATCTTAAAACCGT
194 ATCAACGAAGAATCTC-CCTGCCAAATACAAGCAGCTCAATCACATGCATTTAACTTGAAACCGC
* ** *
1389 CGCATAAGACAGCAGTCTTAAAA
258 CGCGTAAGATGGCAGTTTTAAAA
* * * ** * * * * * *
1412 TAAAAAAGAATTTATTATTTTTTATATCAAAAATTCCGTGTGTTAGAGT-GAAGTGAAACAAATA
1 TAAAAGAGAA---AATATTTTTTATATCAAGAACGCCGCGTGTCAAAATCCAA-AGAAACAAATA
* * * * ** * *
1476 TTATTTTAGCTTAAATTCTAAGAATAGTCCTAGTATTTCTTGATTTGCACAGATTTGGTCCCTCA
62 TTATTTTAGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGATTTGGTCCCACA
* * * * * * *
1541 TTTTTTATTTACTCGTAGCATTGAAAATAGCTTCTTAAGTTTGAGAAAAAAACT---AAATAGAT
127 ATTTTTATTTACTCGTAGCATTCAAATTGGCGTCTTATGTTTGAGAAAAAAA-TAGAAAATTGAT
* **
1603 GAAATCCAA-GAAGAATCT-CCTACCAAATACAA-CAGCTCCGTCACATGCATTTAACTTGAAAC
191 GAAAT-CAACGAAGAATCTCCCTGCCAAATACAAGCAGCTCAATCACATGCATTTAACTTGAAAC
*
1665 CGTCGCGTAAGATGGCAGTTTTAAAA
255 CGCCGCGTAAGATGGCAGTTTTAAAA
* * * * * *
1691 TAAAACAGAAAATATTTTTTTATATCAAGAACGTCGTGTGTCAGAATCTAAAGAAACAAATATAA
1 TAAAAGAGAAAATA-TTTTTTATATCAAGAACGCCGCGTGTCAAAATCCAAAGAAACAAATATTA
* * * * *
1756 CTTTAGTTTAAATTTTAAGAATAGTCCCTGTACTTGTTGATTTGTGCGGATTTCGTCCCACTATT
65 TTTTAGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGATTTGGTCCCACAATT
* *
1821 TTTATTTACTCGTAGCATTCAAATTGGCGTCTTATCTTTGAGAAAAAAAATAGAAAATTGATTAA
130 TTTATTTACTCGTAGCATTCAAATTGGCGTCTTATGTTTGAG-AAAAAAATAGAAAATTGATGAA
* *
1886 ATCAACGAAGAATCTCCCTGCCAAATTCAAGCAGCTCAATCACATGCATTTGACTTGAAACCGCC
194 ATCAACGAAGAATCTCCCTGCCAAATACAAGCAGCTCAATCACATGCATTTAACTTGAAACCGCC
*
1951 GCGTAAGATGGCAATTTTAAAA
259 GCGTAAGATGGCAGTTTTAAAA
* * *
1973 TAAAAGAGAAAATATTTTTTATATCAAGAACGTCGCGTGTCAGAATCCAAAGAAGCAAATATTAT
1 TAAAAGAGAAAATATTTTTTATATCAAGAACGCCGCGTGTCAAAATCCAAAGAAACAAATATTAT
* * * *
2038 TTTAGCTTAAATTTTAAGAATAGTCCTTGTATTTGTTTATTTGTGCGGACTTT-GTCCCTCATTT
66 TTTAGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGA-TTTGGTCCCACAATT
* * * * *
2102 TTTATTTACTCGTAGCATTGAAATTGGCCTCTTATGTTTGA-CAAAAAA-ACAAAATAGATGAAA
130 TTTATTTACTCGTAGCATTCAAATTGGCGTCTTATGTTTGAGAAAAAAATAGAAAATTGATGAAA
2165 TCAA
195 TCAA
2169 AGA
Statistics
Matches: 1580, Mismatches: 266, Indels: 76
0.82 0.14 0.04
Matches are distributed among these distances:
276 3 0.00
277 126 0.08
278 131 0.08
279 206 0.13
280 43 0.03
281 390 0.25
282 454 0.29
283 8 0.01
284 89 0.06
285 130 0.08
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (280 bp):
TAAAAGAGAAAATATTTTTTATATCAAGAACGCCGCGTGTCAAAATCCAAAGAAACAAATATTAT
TTTAGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGATTTGGTCCCACAATTT
TTATTTACTCGTAGCATTCAAATTGGCGTCTTATGTTTGAGAAAAAAATAGAAAATTGATGAAAT
CAACGAAGAATCTCCCTGCCAAATACAAGCAGCTCAATCACATGCATTTAACTTGAAACCGCCGC
GTAAGATGGCAGTTTTAAAA
Found at i:1719 original size:844 final size:838
Alignment explanation
Indices: 5--2171 Score: 2468
Period size: 844 Copynumber: 2.6 Consensus size: 838
1 AAAG
* * * *
5 TAAAAGAGAAAATATTTTCTTATATCAAGAACGCCGCGTGTCAAAATCCAGAGAAACAAATAGTA
1 TAAAAGAGAAAATATTTTTTTATATCAAGAACGCTGCGTGTCAAAATCCAAAGAAACAAATATTA
* * *
70 CTTTAGTTTAAATTTAAAAAATAGTCATTGTACTTGTTGATTTGTGCGGATTTAGTCCCACTATT
66 CTTTAGTTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGATTTAGTCCCACTATT
* *
135 TTTATTTACTCGTAGCATTCAAATTGGCATCTTATATTTGAGAAAAAAAATAGAAAATTGATGAA
131 TTTATTTACTCGTAGCATTCAAATTGGCGTCTTATCTTTGAGAAAAAAAATAGAAAATTGATGAA
* * * * *
200 ATCAACGAAGAATCTCCCTGCCAAATTTAAGCAGTTCAATCACATGCATTTAAATTGAAACCGCC
196 ATCAACGAAGAATCTCCCTGCCAAATTCAAGCAGCTCAATCACATGAAATTAAATTAAAACCGCC
* * * * *
265 GCGTAAGATGGCTGTTTTAAAATAAAAGAGAAAATATTTTTTATATCAAGAACGTCGCATGTAAG
261 GCGTAAGATGACCGTTTTAAAATAAAAAAGAAAATATTTTTTATATCAAAAACATCGCATGTAAG
* * * * * *
330 AATCCAAAGAAGCAAATATTATTTTAGCTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTG
326 AATCCAAAGAAACAAATATTATTCTAGCTTAAACTCTAAGAATAGTCCTTGTACTTATCGATTTG
* * * * * * * *
395 TGCGGATTTTGTCCCTCATTTTTTATTTACTCGTAGCATTGAAATTGGCCTCTTATGTTTGACAA
391 GGCAGATTTTGTCCCT-ATTTTTTATTTACTCATAGAATTCAAATTGACATCTTAAGTTTGACAA
* *
460 AAAAACAAAATAGATGAAATCAAAGAAGAATCTCCCTGCCAAATACAATCAGCTCCATCACATGC
455 AAAAACAAAATAGATGAAATCAAAGAAGAATCTCCCTACCAAATACAAGCAGCTCCATCACATGC
* * * * ** * * *
525 ATTTAACTTGAAACTGCCCCGTAAGATGGCAGTTTTAAAGTAAAAGAGAAAATATTTTCTTATAT
520 AATTAACTTAAAACCGCCCCATAAGACAGCAGTCTTAAAATAAAAAAGAAAATATTTTCTTATAT
* * * *
590 CAAGAACGCCGCCTGTCAAAATCCATAGAAACAAATAGTACTCTAGTTTAAATTTTAAGAATAGT
585 CAAAAACGCCGCCTGTCAAAATCAATAGAAACAAATAGTACTCTAGCTTAAATTCTAAGAATAGT
* * ** * * *
655 CCTTGTACTTGTTGATTTGTGCGGATTTGGTCTCACAATTTTTATTTACTCGTAGCATTCAAATT
650 CCTAGTACTTCTTGATTTGCACAGATTTGGTCCCACAATTTTTATTTACTCGTAGCATTCAAAAT
* * * *
720 GGCGTCTTATCTTTGAGAAAAATAATAGAAAATGGATGAAATCAACAAAGAATCTCCCTGCCAAA
715 AGCGTCTTAACTTTGAGAAAAATAAT--AAAATAGATGAAATCAACAAAGAATCTCCCTACCAAA
** * *
785 TTTAAGCCACTCAATCACATGCATTTAACTTGAATCCGCCACGTAAGAAGTCAGTTTTAAAA
778 TACAA-CCACTCAATCACATGCATTTAACTTGAAACCGCCACGTAAGAAGGCAGTTTTAAAA
* *
847 TAAAAGAGAAAATATATTTTTATATCAAGAATGCTGCGTGTCAAAATCCAAAGAAACAAATATTA
1 TAAAAGAGAAAATATTTTTTTATATCAAGAACGCTGCGTGTCAAAATCCAAAGAAACAAATATTA
* * * * * * * *
912 TTTTAGCTTAAATTTTCAGATTAGTCCTTGTACGTGTTGATTTGTGCAGACTTGGTCCCACTATT
66 CTTTAGTTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGATTTAGTCCCACTATT
* * * * *
977 TTTATTTACTCATAGCATTCAAATCGGGGTCTTATCTTTGAGAAAAAAAAAAAAGGAAATTGATG
131 TTTATTTACTCGTAGCATTCAAATTGGCGTCTTATCTTTGAG--AAAAAAAATAGAAAATTGATG
* * ** * * **
1042 AAATCAACGAAGAATCTTCCTACCAAACACAAGCAGCTCAGTCACATGAAATTATATTAAAATGG
194 AAATCAACGAAGAATCTCCCTGCCAAATTCAAGCAGCTCAATCACATGAAATTAAATTAAAACCG
* ** ** * * *
1107 CTC-CGTTAGATGACCGTTTTAGGATAAAAAAGAATTTATTATTTTTATATTAAAAATATTGCAT
259 C-CGCGTAAGATGACCGTTTTAAAATAAAAAAGAAAATA-T-TTTTTATATCAAAAACATCGCAT
* * * ** * ** *
1171 GTCAGAGTCGAGTGAAACAAATATTATTCTAGGTTTGACTCTAAGAATAGTCCTTTTACTTATCG
321 GTAAGAATCCAAAGAAACAAATATTATTCTAGCTTAAACTCTAAGAATAGTCCTTGTACTTATCG
1236 ATTTGGGCAGA-TTTGCTCCCT-TTATTTGTATTTACTCATAGAATTCAAATTGACATCTTAAGT
386 ATTTGGGCAGATTTTG-TCCCTATT-TTT-TATTTACTCATAGAATTCAAATTGACATCTTAAGT
* * * * * *
1299 TTGAGAAAACAAACAATATTGATGAAATCGACGAAGAATC-CGCCTACCAAATACAAGCAGCTCT
448 TTGACAAAA-AAACAAAATAGATGAAATCAAAGAAGAATCTC-CCTACCAAATACAAGCAGCTCC
* * * * *
1363 GTCACATGCAATTATCTTAAAACCGTCGCATAAGACAGCAGTCTTAAAATAAAAAAGAATTTATT
511 ATCACATGCAATTAACTTAAAACCGCCCCATAAGACAGCAGTCTTAAAATAAAAAAGAA---AAT
** ** * * * * * * *
1428 ATTTT-TTATATCAAAAATTCCGTGTGTTAGAGTGAAGT-GAAACAAATATTATTTTAGCTTAAA
573 ATTTTCTTATATCAAAAACGCCGCCTGTCAAAATCAA-TAGAAACAAATAGTACTCTAGCTTAAA
* * *
1491 TTCTAAGAATAGTCCTAGTATTTCTTGATTTGCACAGATTTGGTCCCTCATTTTTTATTTACTCG
637 TTCTAAGAATAGTCCTAGTACTTCTTGATTTGCACAGATTTGGTCCCACAATTTTTATTTACTCG
* * * *
1556 TAGCATTGAAAATAGCTTCTTAAGTTTGAGAAAAA-AACT-AAATAGATGAAATCCAA-GAAGAA
702 TAGCATTCAAAATAGCGTCTTAACTTTGAGAAAAATAA-TAAAATAGATGAAAT-CAACAAAGAA
** * * *
1618 TCT-CCTACCAAATACAA-CAGCTCCGTCACATGCATTTAACTTGAAACCGTCGCGTAAGATGGC
765 TCTCCCTACCAAATACAACCA-CTCAATCACATGCATTTAACTTGAAACCGCCACGTAAGAAGGC
1681 AGTTTTAAAA
829 AGTTTTAAAA
* * * * *
1691 TAAAACAGAAAATATTTTTTTATATCAAGAACG-TCGTGTGTCAGAATCTAAAGAAACAAATATA
1 TAAAAGAGAAAATATTTTTTTATATCAAGAACGCT-GCGTGTCAAAATCCAAAGAAACAAATATT
* *
1755 ACTTTAGTTTAAATTTTAAGAATAGTCCCTGTACTTGTTGATTTGTGCGGATTTCGTCCCACTAT
65 ACTTTAGTTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGATTTAGTCCCACTAT
*
1820 TTTTATTTACTCGTAGCATTCAAATTGGCGTCTTATCTTTGAGAAAAAAAATAGAAAATTGATTA
130 TTTTATTTACTCGTAGCATTCAAATTGGCGTCTTATCTTTGAGAAAAAAAATAGAAAATTGATGA
* * * * *
1885 AATCAACGAAGAATCTCCCTGCCAAATTCAAGCAGCTCAATCACATGCATTTGACTTGAAACCGC
195 AATCAACGAAGAATCTCCCTGCCAAATTCAAGCAGCTCAATCACATGAAATTAAATTAAAACCGC
* ** * * * * *
1950 CGCGTAAGATGGCAATTTTAAAATAAAAGAGAAAATATTTTTTATATCAAGAACGTCGCGTGTCA
260 CGCGTAAGATGACCGTTTTAAAATAAAAAAGAAAATATTTTTTATATCAAAAACATCGCATGTAA
* * * * * * **
2015 GAATCCAAAGAAGCAAATATTATTTTAGCTTAAATTTTAAGAATAGTCCTTGTATTTGTTTATTT
325 GAATCCAAAGAAACAAATATTATTCTAGCTTAAACTCTAAGAATAGTCCTTGTACTTATCGATTT
* * * * * * * * *
2080 GTGCGGACTTTGTCCCTCATTTTTTATTTACTCGTAGCATTGAAATTGGCCTCTTATGTTTGACA
390 GGGCAGATTTTGTCCCT-ATTTTTTATTTACTCATAGAATTCAAATTGACATCTTAAGTTTGACA
2145 AAAAAACAAAATAGATGAAATCAAAGA
454 AAAAAACAAAATAGATGAAATCAAAGA
Statistics
Matches: 1087, Mismatches: 216, Indels: 47
0.81 0.16 0.03
Matches are distributed among these distances:
839 20 0.02
840 117 0.11
841 9 0.01
842 249 0.23
843 3 0.00
844 298 0.27
845 20 0.02
846 140 0.13
847 94 0.09
848 2 0.00
849 127 0.12
850 8 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (838 bp):
TAAAAGAGAAAATATTTTTTTATATCAAGAACGCTGCGTGTCAAAATCCAAAGAAACAAATATTA
CTTTAGTTTAAATTTTAAGAATAGTCCTTGTACTTGTTGATTTGTGCGGATTTAGTCCCACTATT
TTTATTTACTCGTAGCATTCAAATTGGCGTCTTATCTTTGAGAAAAAAAATAGAAAATTGATGAA
ATCAACGAAGAATCTCCCTGCCAAATTCAAGCAGCTCAATCACATGAAATTAAATTAAAACCGCC
GCGTAAGATGACCGTTTTAAAATAAAAAAGAAAATATTTTTTATATCAAAAACATCGCATGTAAG
AATCCAAAGAAACAAATATTATTCTAGCTTAAACTCTAAGAATAGTCCTTGTACTTATCGATTTG
GGCAGATTTTGTCCCTATTTTTTATTTACTCATAGAATTCAAATTGACATCTTAAGTTTGACAAA
AAAACAAAATAGATGAAATCAAAGAAGAATCTCCCTACCAAATACAAGCAGCTCCATCACATGCA
ATTAACTTAAAACCGCCCCATAAGACAGCAGTCTTAAAATAAAAAAGAAAATATTTTCTTATATC
AAAAACGCCGCCTGTCAAAATCAATAGAAACAAATAGTACTCTAGCTTAAATTCTAAGAATAGTC
CTAGTACTTCTTGATTTGCACAGATTTGGTCCCACAATTTTTATTTACTCGTAGCATTCAAAATA
GCGTCTTAACTTTGAGAAAAATAATAAAATAGATGAAATCAACAAAGAATCTCCCTACCAAATAC
AACCACTCAATCACATGCATTTAACTTGAAACCGCCACGTAAGAAGGCAGTTTTAAAA
Done.