Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001121.1 Kokia drynarioides strain JFW-HI SEQ_112404, 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: 1846
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Found at i:438 original size:249 final size:247
Alignment explanation
Indices: 1--989 Score: 1306
Period size: 249 Copynumber: 4.1 Consensus size: 247
1 GAAAAGTGAGTAATGC-GGTCGCCGCCAAACCTTCAG-ATAAGCC--TT-TATATATATATTGAC
1 GAAAAGTGAGTAAT-CAGGTCGCCGCCAAACCTTCAGTATAAGCCTTTTATATATATATATTGAC
*
61 ATCATCTTAGCATTATATATATTTATATTTTCCATTACTCAATTTCAAAATGAACCTGTATATAT
65 ATCATCTTAGCATTATATATATTTATATTTTCCATTACTCAATGTCAAAATGAACCTGTATATAT
* *
126 TCTCTCTTCTCACTTAGATAAACTTAATTCTTCTCCTATTCAAACTTATTTCTTCTATTCTCTCA
130 TCTCTCTTCTCACTTAGATAAACTTAATTCTTCTCCCATTCAAACTTATTTCTTCTCTTCTCTCA
191 GTTCTTCATCTTTCTCTCTTTGTTAGTTTATGTTAAGATGATTAAAGGAAAAG
195 GTTCTTCATCTTTCTCTCTTTGTTAGTTTATGTTAAGATGATTAAAGGAAAAG
244 GAAAAGTGAGTAATCAGGTCGCCGCCAAACCTTC-GTATAAGCCTTTATATATATATATATATTG
1 GAAAAGTGAGTAATCAGGTCGCCGCCAAACCTTCAGTATAAGCC-TT-T-TATATATATATATTG
* *
308 ACATCATCTTAGCGTTATATATATTTATATTTTCCATTACTCAATGTCAAAATGAACCTTTATAT
63 ACATCATCTTAGCATTATATATATTTATATTTTCCATTACTCAATGTCAAAATGAACCTGTATAT
* *
373 ATTCTCTCTTCTCACATAGATAAACTTAATTCTTCTCCTATTCAAACTTATTTCTTCTCTTCTCT
128 ATTCTCTCTTCTCACTTAGATAAACTTAATTCTTCTCCCATTCAAACTTATTTCTTCTCTTCTCT
438 CAGTTCTTCATCTTTCTCTCTTTGTTAGTTTATGTTAAGATGATTAAAGGAAAAG
193 CAGTTCTTCATCTTTCTCTCTTTGTTAGTTTATGTTAAGATGATTAAAGGAAAAG
** *
493 GAAAAGTGAGTAATCA-G--GCCGGAAAACCTTCA-TATAAG-CGTTTATATATATATATTGACA
1 GAAAAGTGAGTAATCAGGTCGCCGCCAAACCTTCAGTATAAGCCTTTTATATATATATATTGACA
* *
553 TCATCTTAGCATTATATATATTTATATTTTCCATTACTTAATGTCAAAGTGAACCTGTATATATT
66 TCATCTTAGCATTATATATATTTATATTTTCCATTACTCAATGTCAAAATGAACCTGTATATATT
* *
618 CTCTCTTCTCACTCAG---------ATTCTTCTCCCATTCAAACTTATTTCTTCTCTTCTCTCAT
131 CTCTCTTCTCACTTAGATAAACTTAATTCTTCTCCCATTCAAACTTATTTCTTCTCTTCTCTCAG
* * *
674 TTCTTCATCTTTTTCTCTTTGCTAGTTTATGTTAAGACGATTAAAGGAAAAG
196 TTCTTCATCTTTCTCTCTTTGTTAGTTTATGTTAAGATGATTAAAGGAAAAG
* * *
726 GAAAAGTGAGTAATGAGGTTGCTGCCAAACCTTCAGGTA-AA-CCTTTATATATATGTATATAGA
1 GAAAAGTGAGTAATCAGGTCGCCGCCAAACCTTCA-GTATAAGCCTTT-TATATA--TATAT--A
* * * ** * ** * * *
789 TTGACAACATCTTAG-ATTTATATATATTGACATTTGGCTTTACAGAATGCCAAAATGAACTTAT
60 TTGACATCATCTTAGCA-TTATATATATTTATATTTTCCATTACTCAATGTCAAAATGAACCTGT
* * * *
853 ATATTTTCTCTCGTCTCACTTAGATAAACTTAATTCTTCTCCCATTAAAACTTATTTCTTCTTTT
124 ATATATTCTCTCTTCTCACTTAGATAAACTTAATTCTTCTCCCATTCAAACTTATTTCTTCTCTT
* * * * ** * *
918 CTCCCATTTCTTCATCTTT-TACTTTTTGTTAGTTGATGTTAATTTGCTGAAAGGAAAAG
189 CTCTCAGTTCTTCATCTTTCT-CTCTTTGTTAGTTTATGTTAAGATGATTAAAGGAAAAG
*
977 AAAAAGTGAGTAA
1 GAAAAGTGAGTAA
990 AGAGGTTGCT
Statistics
Matches: 664, Mismatches: 51, Indels: 54
0.86 0.07 0.07
Matches are distributed among these distances:
233 102 0.15
234 1 0.00
236 12 0.02
237 5 0.01
238 8 0.01
240 5 0.01
241 1 0.00
242 166 0.25
243 40 0.06
244 1 0.00
245 1 0.00
246 18 0.03
247 1 0.00
248 2 0.00
249 209 0.31
250 1 0.00
251 91 0.14
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (247 bp):
GAAAAGTGAGTAATCAGGTCGCCGCCAAACCTTCAGTATAAGCCTTTTATATATATATATTGACA
TCATCTTAGCATTATATATATTTATATTTTCCATTACTCAATGTCAAAATGAACCTGTATATATT
CTCTCTTCTCACTTAGATAAACTTAATTCTTCTCCCATTCAAACTTATTTCTTCTCTTCTCTCAG
TTCTTCATCTTTCTCTCTTTGTTAGTTTATGTTAAGATGATTAAAGGAAAAG
Found at i:984 original size:484 final size:481
Alignment explanation
Indices: 27--989 Score: 1369
Period size: 484 Copynumber: 2.0 Consensus size: 481
17 GGTCGCCGCC
27 AAACCTTCAGATAAGCCTTTATATATATATTGACATCATCTTAGCATTATATATATTTATATTTT
1 AAACCTTCAGATAAGCCTTTATATATATATTGACATCATCTTAGCATTATATATATTTATATTTT
* *
92 CCATTACTCAATTTCAAAATGAACCTGTATATATTCTCTCTTCTCACTTAGATAAACTTAATTCT
66 CCATTACTCAATGTCAAAATGAACCTGTATATATTCTCTCTTCTCACTCAG--------AATTCT
* *
157 TCTCCTATTCAAACTTATTTCTTCTATTCTCTCAGTTCTTCATCTTTCTCTCTTTGTTAGTTTAT
123 TCTCCCATTCAAACTTATTTCTTCTATTCTCTCAGTTCTTCATCTTTCTCTCTTTGCTAGTTTAT
*
222 GTTAAGATGATTAAAGGAAAAGGAAAAGTGAGTAATCAGGTCGCCGCCAAACCTTCGTATAAGCC
188 GTTAAGACGATTAAAGGAAAAGGAAAAGTGAGTAATCAGGTCGCCGCCAAACCTTCGTATAAGCC
* * * * * * *
287 TTTATATATATATATATATTGACATCATCTTAGCGTTATATATATTTATATTTTCCATTACTCAA
253 TTTATATATATATATAGATTGACAACATCTTAGAGTTATATATATTGACATTTGCCATTACACAA
* * * *
352 TGTCAAAATGAACCTTTATATATTCTCTCTTCTCACATAGATAAACTTAATTCTTCTCCTATTCA
318 TGCCAAAATGAACCTTTATATATTCTCTCGTCTCACATAGATAAACTTAATTCTTCTCCCATTAA
* *
417 AACTTATTTCTTCTCTTCTCTCAGTTCTTCATCTTTCTCTCTTTGTTAGTTTATGTTAAGATGAT
383 AACTTATTTCTTCTCTTCTCCCAGTTCTTCATCTTTCTCTCTTTGTTAGTTGATGTTAAGATGAT
* *
482 TAAAGGAAAAGGAAAAGTGAGTAATCAGGCCGGA
448 GAAAGGAAAAGAAAAAGTGAGTAATCAGGCCGGA
* *
516 AAACCTTCATATAAGCGTTTATATATATATATTGACATCATCTTAGCATTATATATATTTATATT
1 AAACCTTCAGATAAGC-CTT-TATATATATATTGACATCATCTTAGCATTATATATATTTATATT
* *
581 TTCCATTACTTAATGTCAAAGTGAACCTGTATATATTCTCTCTTCTCACTCAG-ATTCTTCTCCC
64 TTCCATTACTCAATGTCAAAATGAACCTGTATATATTCTCTCTTCTCACTCAGAATTCTTCTCCC
* * *
645 ATTCAAACTTATTTCTTCTCTTCTCTCATTTCTTCATCTTTTTCTCTTTGCTAGTTTATGTTAAG
129 ATTCAAACTTATTTCTTCTATTCTCTCAGTTCTTCATCTTTCTCTCTTTGCTAGTTTATGTTAAG
* * *
710 ACGATTAAAGGAAAAGGAAAAGTGAGTAATGAGGTTGCTGCCAAACCTTCAGGTA-AA-CCTTTA
194 ACGATTAAAGGAAAAGGAAAAGTGAGTAATCAGGTCGCCGCCAAACCTTC--GTATAAGCCTTTA
* * * *
773 TATATATGTATATAGATTGACAACATCTTAGATTTATATATATTGACATTTGGCTTTACAGAATG
257 TATATA--TATATAGATTGACAACATCTTAGAGTTATATATATTGACATTTGCCATTACACAATG
* *
838 CCAAAATGAA-CTTATATATTTTCTCTCGTCTCACTTAGATAAACTTAATTCTTCTCCCATTAAA
320 CCAAAATGAACCTT-TATATATTCTCTCGTCTCACATAGATAAACTTAATTCTTCTCCCATTAAA
* * * ** *
902 ACTTATTTCTTCTTTTCTCCCATTTCTTCATCTTT-TACTTTTTGTTAGTTGATGTTAATTTGCT
384 ACTTATTTCTTCTCTTCTCCCAGTTCTTCATCTTTCT-CTCTTTGTTAGTTGATGTTAAGATGAT
966 GAAAGGAAAAGAAAAAGTGAGTAA
448 GAAAGGAAAAGAAAAAGTGAGTAA
990 AGAGGTTGCT
Statistics
Matches: 424, Mismatches: 42, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
482 129 0.30
483 6 0.01
484 179 0.42
489 15 0.04
490 2 0.00
491 93 0.22
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.41
Consensus pattern (481 bp):
AAACCTTCAGATAAGCCTTTATATATATATTGACATCATCTTAGCATTATATATATTTATATTTT
CCATTACTCAATGTCAAAATGAACCTGTATATATTCTCTCTTCTCACTCAGAATTCTTCTCCCAT
TCAAACTTATTTCTTCTATTCTCTCAGTTCTTCATCTTTCTCTCTTTGCTAGTTTATGTTAAGAC
GATTAAAGGAAAAGGAAAAGTGAGTAATCAGGTCGCCGCCAAACCTTCGTATAAGCCTTTATATA
TATATATAGATTGACAACATCTTAGAGTTATATATATTGACATTTGCCATTACACAATGCCAAAA
TGAACCTTTATATATTCTCTCGTCTCACATAGATAAACTTAATTCTTCTCCCATTAAAACTTATT
TCTTCTCTTCTCCCAGTTCTTCATCTTTCTCTCTTTGTTAGTTGATGTTAAGATGATGAAAGGAA
AAGAAAAAGTGAGTAATCAGGCCGGA
Found at i:1755 original size:589 final size:587
Alignment explanation
Indices: 634--1846 Score: 1845
Period size: 589 Copynumber: 2.1 Consensus size: 587
624 TCTCACTCAG
* * **
634 ATTCTTCTCCCATTCAAACTTATTTCTTCTCTTCTCTCATTTCTTCATCTTTTTCTCTTTGCTAG
1 ATTCTTTTCCCATTCAAACTTATTTCTTCTTTTCTCTCATTTCTTCATCTTTTTCAATTTGCTAG
* * * *
699 TTTATGTTAAGACGATTAAAGGAAAAGGAAAAGTGAGTAATGAGGTTGCTGCCAAACCTTCAGGT
66 TTGATGTTAAGACGATGAAAGGAAAAGGAAAAGTGAGTAATGAGGTTGATGCCAAACCTTCAGAT
** * * *
764 AAACCTTTATATATATGTATATAGATTGACAACATCTTAGATTTATATATATTGACATTTGGCTT
131 AAACCTTTATATATATACATATAGATTGACAACATCATAGATTTATATATATTGACATTTGCCAT
* * * * *
829 TACAGAATGCCAAAATGAACTTATATATTTTCTCTCGTCTCACTTAGATAAACTTAATTCTTCTC
196 TACACAATGCCAAAATGAACCTACATATATTCTCTCGTCTCACTTACATAAACTTAATTCTTCTC
*
894 CCATTAAAACTTATTTCTTCTTTTCTCCCATTTCTTCATCTTTTACTTTTTGTTAGTTGATGTTA
261 CCATTAAAACTTATTTCTTCTTGTCTCCCATTTCTTCATCTTTTACTTTTTGTTAGTTGATGTTA
* *
959 ATTTGCTGAAAGGAAAAGAAAAAGTGAGTAAAGAGGTTGCTAAAAAACCTTCAGTTGCCTCCATT
326 ATTTGATGAAAGGAAAAGAAAAAGTGAGTAAAGAGGCTGCTAAAAAACCTTCAGTTGCCTCCATT
* * * *
1024 ACCCAATCTCTATCATTGCCAATCCTACCACCAAGAAATAGGTTTAAATCTATGACAAATATTAT
391 ACCCAATCTCCATCATTGCCAAGCCAACCACCAAGAAATAGGTTTAAATCTATGACAAATATGAT
1089 CCAAAATTCTTTCATAATTTATGTTTATAACAAAGACGGATTTTAATTATATGTTTCTAATCAGC
456 CCAAAATTCTTTCATAATTTATGTTTATAACAAAGACGGATTTTAATTATATGTTTCTAATCAGC
* *
1154 GTCTTTAGGTTCAACATGATTTAATCTTTTGGTGTATATATCCTCCCCTCCCACTCAGATAAACT
521 GTCTTTAGGTTCAACATGATTTAATCTTTTGGTGTATATATCCTCCCCGCCCACTCAAATAAACT
*
1219 TT
586 TA
* *
1221 ATTCTTTTCCCATTCAAACTTATTTCTTCTTTTCTCTCATTTCTTTATCTTTTTCAATTTGTTAG
1 ATTCTTTTCCCATTCAAACTTATTTCTTCTTTTCTCTCATTTCTTCATCTTTTTCAATTTGCTAG
* *
1286 TTGATGTTAAGA-GTATGAAAGTAAAAGGAAAAGTGAGTAATGAGGTTGATGCCAAACCTTTAGA
66 TTGATGTTAAGACG-ATGAAAGGAAAAGGAAAAGTGAGTAATGAGGTTGATGCCAAACCTTCAGA
* * * * *
1350 TAAACCTTTATTTATATATACATATATATTGACATCATCATAGCA-TTATATATATTTATATTTT
130 TAAACCTTTA--TATATATACATATAGATTGACAACATCATAG-ATTTATATATATTGACATTTG
* * * * *
1414 CCATTACTCAATGTCAAAATGAACCTGCATATATTCTCTCTTCTCACTTACATAAACTTTATTCT
192 CCATTACACAATGCCAAAATGAACCTACATATATTCTCTCGTCTCACTTACATAAACTTAATTCT
* * ** * *
1479 TCTCCTATTAAAACTTTTTTCTTCTTGTCTCTGATTTCTTCATCTTTTTCTTTTTGTTAGTTGTT
257 TCTCCCATTAAAACTTATTTCTTCTTGTCTCCCATTTCTTCATCTTTTACTTTTTGTTAGTTGAT
*
1544 GTTAATTTGATGAAAGGAAAAGAAAAAGTGAGTAAAGAGGCTGCTAAAAAACCTTCAGTTGTCTC
322 GTTAATTTGATGAAAGGAAAAGAAAAAGTGAGTAAAGAGGCTGCTAAAAAACCTTCAGTTGCCTC
* * * *
1609 CATTACCCGATCTCCATCATTGTCAAGCCAATCACCAAGAAATAGGTTTAAATTTATGACAAATA
387 CATTACCCAATCTCCATCATTGCCAAGCCAACCACCAAGAAATAGGTTTAAATCTATGACAAATA
*
1674 TGATCCAAAATTCTTTCTTAATTTATGTTTATAACAAAGACGGATTTTAATTATATGTTTCTAAT
452 TGATCCAAAATTCTTTCATAATTTATGTTTATAACAAAGACGGATTTTAATTATATGTTTCTAAT
* ** **
1739 CAGCGTCTTTAGGTTCAACATGGTTTAATCTTTTGGTGTATATATCCTCTTCGCCTTCTCAAATA
517 CAGCGTCTTTAGGTTCAACATGATTTAATCTTTTGGTGTATATATCCTCCCCGCCCACTCAAATA
1804 AACTTA
582 AACTTA
1810 ATTCTTTTCCCATTCAAACTTATTTCTTCTTTTCTCT
1 ATTCTTTTCCCATTCAAACTTATTTCTTCTTTTCTCT
Statistics
Matches: 563, Mismatches: 59, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
586 1 0.00
587 125 0.22
589 436 0.77
590 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (587 bp):
ATTCTTTTCCCATTCAAACTTATTTCTTCTTTTCTCTCATTTCTTCATCTTTTTCAATTTGCTAG
TTGATGTTAAGACGATGAAAGGAAAAGGAAAAGTGAGTAATGAGGTTGATGCCAAACCTTCAGAT
AAACCTTTATATATATACATATAGATTGACAACATCATAGATTTATATATATTGACATTTGCCAT
TACACAATGCCAAAATGAACCTACATATATTCTCTCGTCTCACTTACATAAACTTAATTCTTCTC
CCATTAAAACTTATTTCTTCTTGTCTCCCATTTCTTCATCTTTTACTTTTTGTTAGTTGATGTTA
ATTTGATGAAAGGAAAAGAAAAAGTGAGTAAAGAGGCTGCTAAAAAACCTTCAGTTGCCTCCATT
ACCCAATCTCCATCATTGCCAAGCCAACCACCAAGAAATAGGTTTAAATCTATGACAAATATGAT
CCAAAATTCTTTCATAATTTATGTTTATAACAAAGACGGATTTTAATTATATGTTTCTAATCAGC
GTCTTTAGGTTCAACATGATTTAATCTTTTGGTGTATATATCCTCCCCGCCCACTCAAATAAACT
TA
Done.