Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000747.1 Kokia drynarioides strain JFW-HI SEQ_111784, 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: 3618
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Found at i:2303 original size:14 final size:15
Alignment explanation
Indices: 2279--2307 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2269 AACATATATA
2279 CAATAAAATGCAAAG
1 CAATAAAATGCAAAG
2294 CAAT-AAATGCAAAG
1 CAATAAAATGCAAAG
2308 GATCACAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
CAATAAAATGCAAAG
Found at i:2492 original size:925 final size:925
Alignment explanation
Indices: 841--3556 Score: 4026
Period size: 926 Copynumber: 2.9 Consensus size: 925
831 ATTTGTACAT
* * * * * *
841 AAAGCTCGTTATTTCGAACTAATCGAGAAAAA-ACTCATATCCTGTAAGTTACGACATAACAATT
1 AAAGCTCGTTATTTCTAATTAATCGAGAAAAACAATCACATCATGTAAGTTAGGACATAACAATT
* * *
905 CGAATTTTCGAAAATAGCAAGCATTCCTAATTATTATCCTAAAGTCTCGTATTTTAACA-TTAAA
66 TGAATTTTCGAAAATAGCAAGCATTCCTAATTATTATCCCAAAATCTCGTATTTTAA-ATTTAAA
* * *
969 AAGGGTACTCAAAACAAAGAACCTACTCATCTATTTCGGGTAATCACTAAAAGTTCGGCATGGCT
130 AAGGATACTCAAAACAAAGAACCTACGCATCTATTTCGGGTAATCACTAAAAGTTCAGCATGGCT
* * *
1034 CTATCTAGAATAGGCACCTAAGGTTCACTATATGTAGTTTGAGTTCTAGAGT-AAAGGTACCCAA
195 CTACCTAGGATAGGCACCTAAGGTTCACTATATGTTGTTTGAGTTCTAGAGTAAAAGGTACCCAA
** * * * * *
1098 ACCAACAGATTCCTCAATCCTCACCCATTATAGGCTCTTTTA-GG-CGAGCTCGATTTAGGGAGA
260 ACCTGCAGATTCCTCAATCCTCACCCATTATAGGCTC--ATACGGATGAGTTCGGTTCAGGGAGA
* * * * * *
1161 AATATTTCCCATATGTTTGCAC-AAAATTGAAAACCTCACGAAAACATAGGTACAGATATATCTC
323 CATATTTCCCATACGTTTGCACGAAAGTT-AAAACCTCACGAAAACACAAGTACGGATATATCTC
* **
1225 GAAAGCAATCAACTATCCTGCACGAAGGCGAAAACCTCA-AGAAGAAGTAGCTTCTTACTTCCAC
387 GAAAGCAATCCACTATCCTGCACGGTGGCGAAAACCTCACA-AAGAAGTAGCTTCTTACTTCCAC
* *
1289 TTAGAAAGTATAATCACACATGCAAATGTATGCGAAAACATTACAAATTAAATACAACATATATA
451 TTAGAAAGTATAGTAACACATGCAAATGTATGCGAAAACATTACAAATTAAATACAACATATATA
* * * **
1354 CTATAAAATGCAGAGCAATAAATGCAAAGGATCACAACTTAAATTAAATCAAATTTTAAA-TTAA
516 CAATAAAATGCAAAGCAATAAATGCAAAGGATCACAACTTAAATTAAATCGAATTTTAAATTTTC
* *
1418 AAAAAAAAACCAAAAATAATCGACTTTTGGCCTGACTCACTACAAAAAAGTCCCTAGTGGAGTCG
581 AACAAAAAACCAAAAATAATCGACTTTTGGCCTGACTCACTAAAAAAAAGTCCCTAGTGGAGTCG
* * * * *
1483 CCAAGCTTTCGAAACCATTTTTTTTTAAAACAATTCTCTATTATATTTTGGAAAACACGAAAATG
646 CCTAGCTATCGAAACCA--TTTTTTGAAAAAAATTCTCGATTATATTTTGGAAAACACGAAAATG
* *
1548 GACTCATCACTAATTTTTTTTTAAAAATAGGTGTGATTGGGTCACCTTTTAAAAAGTTTTAAAAT
709 GAGTCACCACTAATTTTTTTTTAAAAATAGGTGTGATTGGGTCACCTTTTAAAAAGTTTTAAAAT
* *
1613 CATTAAAAACAAATTTTGGTCTCTTTAACCACAAAAAGGGTTCAGGAGTCAGTTACGAGTAAGGA
774 CATTAAAAACAAATTTTGGTCTCTGTAACCATAAAAAGGGTTCAGGAGTCAGTTACGAGTAAGGA
*
1678 AGGATTAACACCCTTACACGCCCAAAAATTGGTACCTAATCCATGCATGTCATAATTATTTATTT
839 AGGATTAACACCCTTACACGCCCAAAAATTGGTACCTAAACCATGCATGTCATAATTATTTATTT
*
1743 TGAAAAAAAAAATTTAT-GAAG
904 TGAAAAAAAAAATTTATAGAAA
*
1764 AAAGCTCGTTATTTCTAATTAATTGAGAAAAACAATCACATCATGTAAGTTAGGACATAACAATT
1 AAAGCTCGTTATTTCTAATTAATCGAGAAAAACAATCACATCATGTAAGTTAGGACATAACAATT
* *
1829 TGAATTTTCGAAAAAAGCAAGTA-TCCATAATTATTATCCCAAAATCTCGTATTTTAAATTTAAA
66 TGAATTTTCGAAAATAGCAAGCATTCC-TAATTATTATCCCAAAATCTCGTATTTTAAATTTAAA
* * *
1893 AAGGATACTCTAAACAAAGAACCTACGCATCTATTTCGGGTAATCACTAAAAGTTCAGCCTTGCT
130 AAGGATACTCAAAACAAAGAACCTACGCATCTATTTCGGGTAATCACTAAAAGTTCAGCATGGCT
*
1958 CTACCTAGGATTGGCACCTAAGGTTCACTATATGTTGTTTGAGTTCTAGAGTAAAAGGTACCCAA
195 CTACCTAGGATAGGCACCTAAGGTTCACTATATGTTGTTTGAGTTCTAGAGTAAAAGGTACCCAA
* *
2023 ACCTGTAGGTTCCTCAATCCTCACCCATTATAGGCTCATACGGATGAGTTCGGTTCAGGGAGACA
260 ACCTGCAGATTCCTCAATCCTCACCCATTATAGGCTCATACGGATGAGTTCGGTTCAGGGAGACA
*
2088 TATTTCTCATACGTTTGCACGAAAGTTAAAACCTCACGAAAACACAAGTACGGATATATCTCGAA
325 TATTTCCCATACGTTTGCACGAAAGTTAAAACCTCACGAAAACACAAGTACGGATATATCTCGAA
* * *
2153 AGCAATCCACTATCCTGCATGGTGGCGATAACCTCACAAAGAAGTAGATTCTTACTTCCACTTAG
390 AGCAATCCACTATCCTGCACGGTGGCGAAAACCTCACAAAGAAGTAGCTTCTTACTTCCACTTAG
* * *
2218 AAACTATAGTAACACATGCAAATGTATGTGAAAACATTACAAATTAAGTACAACATATATACAAT
455 AAAGTATAGTAACACATGCAAATGTATGCGAAAACATTACAAATTAAATACAACATATATACAAT
2283 AAAATGCAAAGCAATAAATGCAAAGGATCACAACTTAAATTAAATCGAATTTTAAATTTTCAACA
520 AAAATGCAAAGCAATAAATGCAAAGGATCACAACTTAAATTAAATCGAATTTTAAATTTTCAACA
* * *
2348 AAAAACCAAAAATAATCGACTTTTGGCCGGACTCCCTAAAAAAAAGTCCCTAGTAGAGTCGCCTA
585 AAAAACCAAAAATAATCGACTTTTGGCCTGACTCACTAAAAAAAAGTCCCTAGTGGAGTCGCCTA
* *
2413 GCTATCGAAACCATTTTTTGAAAAAAATTCTCGATTATATTTTAGAAAACACGAAAATGGAGTCG
650 GCTATCGAAACCATTTTTTGAAAAAAATTCTCGATTATATTTTGGAAAACACGAAAATGGAGTCA
* * *
2478 CCACTAATTTTTTTTAAAAAATAGGTGTGATTGGGTCACTTTTTAAAAAGTCTTAAAATCATTAA
715 CCACTAATTTTTTTTTAAAAATAGGTGTGATTGGGTCACCTTTTAAAAAGTTTTAAAATCATTAA
2543 AAACAAATTTTGGTCTCTGTAACCATAAAAAGGGTTCAGGAGTCAGTTACGAGTAAGGAAGGATT
780 AAACAAATTTTGGTCTCTGTAACCATAAAAAGGGTTCAGGAGTCAGTTACGAGTAAGGAAGGATT
* * *
2608 AACACCCTTAAACGCCCAAAAATTGGTACCTAAAGCATGCATGTCATATTTATTTATTTTGAAAA
845 AACACCCTTACACGCCCAAAAATTGGTACCTAAACCATGCATGTCATAATTATTTATTTTGAAAA
** **
2673 ATTATTTTTATACGAAA
910 AAAAAATTTATA-GAAA
2690 AAAGCTCGTTATTT-TGAATTAATCGAGAAAAACAATCACATCATGTAAGTTAGGACATAACAAT
1 AAAGCTCGTTATTTCT-AATTAATCGAGAAAAACAATCACATCATGTAAGTTAGGACATAACAAT
* *
2754 TTGAATTTTCGAAAATAGCAAGCATTCCTAATTATTATTCCAAAATCTCGTATTTTAACTTTAAA
65 TTGAATTTTCGAAAATAGCAAGCATTCCTAATTATTATCCCAAAATCTCGTATTTTAAATTTAAA
* *
2819 AAGGATACTCAAAACAAAGAACCTACGCATCTATTACGGGTAATCACTAAAAGTTCAGCATGGGT
130 AAGGATACTCAAAACAAAGAACCTACGCATCTATTTCGGGTAATCACTAAAAGTTCAGCATGGCT
* * *
2884 CTACCTAGGATAGGCACCTAAGATTCACTATATGTTGTTAGAGTTCTAGAGTAAAAGGTACTCAA
195 CTACCTAGGATAGGCACCTAAGGTTCACTATATGTTGTTTGAGTTCTAGAGTAAAAGGTACCCAA
*
2949 ACCTGCAGATTTCTCAATCCTCACCCATTATAGGCTCATACGGATGAGTTCGGTTCAGGGAGACA
260 ACCTGCAGATTCCTCAATCCTCACCCATTATAGGCTCATACGGATGAGTTCGGTTCAGGGAGACA
* * *
3014 TATTTCCCATACGTTTTCAAGAAAGTGAAAACCTCACGAAAACACAAGTACGGATATATCTCGAA
325 TATTTCCCATACGTTTGCACGAAAGTTAAAACCTCACGAAAACACAAGTACGGATATATCTCGAA
*
3079 AGCAATCCACTATCCTGCACGGTGGCGAAAACCTCACAAAGAAGTAGCTTCTTGCTTCCACTTAG
390 AGCAATCCACTATCCTGCACGGTGGCGAAAACCTCACAAAGAAGTAGCTTCTTACTTCCACTTAG
*
3144 AAAGTATAGTAACACATGCAAATGTATGCGAAAACATTACAAATTAAATACAACATATATAGAAT
455 AAAGTATAGTAACACATGCAAATGTATGCGAAAACATTACAAATTAAATACAACATATATACAAT
* * *
3209 AAAATGCAAAGCAATAAAATGTAAAGGATCAAAACTTAAATTAAACCGAATTTTAAATTTTTC-A
520 AAAATGCAAAGCAAT-AAATGCAAAGGATCACAACTTAAATTAAATCGAATTTTAAA-TTTTCAA
* * *
3273 CAAAAAAACCAAAAATAATCGACTTGTGGCCTGACTCTCTAAAAAAAAGTGCAC-AGTGGA-TAC
583 C-AAAAAACCAAAAATAATCGACTTTTGGCCTGACTCACTAAAAAAAAGT-CCCTAGTGGAGT-C
* * *
3336 G-CTAAGCTGTCGAAACCCTTTTTTTTGGAAGAAAAAAAAAGTCTCGATTATATTTTGGAAAACA
645 GCCT-AGCTATCGAAA-CC-ATTTTTT----G--AAAAAAATTCTCGATTATATTTTGGAAAACA
* * * *
3400 CGAAAATGGAGTCACCACTAACTTTTTTTTTTAAAAAATAGTTGTGATT-TGTCATCTTTTAGAA
701 CGAAAATGGAGTCACCACTAA--TTTTTTTTT-AAAAATAGGTGTGATTGGGTCACCTTTTAAAA
* * * ** *
3464 AGTTTTAAAATCATTAAAAAAAAATTTT-GTCTCTGAAACCATAAAATGGGTTCACAAGTCCGTT
763 AGTTTTAAAATCATTAAAAACAAATTTTGGTCTCTGTAACCATAAAAAGGGTTCAGGAGTCAGTT
* *
3528 ACGAGTAAGGAAGAATTAGCACCCTTACA
828 ACGAGTAAGGAAGGATTAACACCCTTACA
3557 AACCAAAAAA
Statistics
Matches: 1623, Mismatches: 140, Indels: 46
0.90 0.08 0.03
Matches are distributed among these distances:
923 35 0.02
924 428 0.26
925 285 0.18
926 585 0.36
927 46 0.03
928 67 0.04
929 4 0.00
930 6 0.00
934 1 0.00
936 49 0.03
937 57 0.04
938 45 0.03
939 15 0.01
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.29
Consensus pattern (925 bp):
AAAGCTCGTTATTTCTAATTAATCGAGAAAAACAATCACATCATGTAAGTTAGGACATAACAATT
TGAATTTTCGAAAATAGCAAGCATTCCTAATTATTATCCCAAAATCTCGTATTTTAAATTTAAAA
AGGATACTCAAAACAAAGAACCTACGCATCTATTTCGGGTAATCACTAAAAGTTCAGCATGGCTC
TACCTAGGATAGGCACCTAAGGTTCACTATATGTTGTTTGAGTTCTAGAGTAAAAGGTACCCAAA
CCTGCAGATTCCTCAATCCTCACCCATTATAGGCTCATACGGATGAGTTCGGTTCAGGGAGACAT
ATTTCCCATACGTTTGCACGAAAGTTAAAACCTCACGAAAACACAAGTACGGATATATCTCGAAA
GCAATCCACTATCCTGCACGGTGGCGAAAACCTCACAAAGAAGTAGCTTCTTACTTCCACTTAGA
AAGTATAGTAACACATGCAAATGTATGCGAAAACATTACAAATTAAATACAACATATATACAATA
AAATGCAAAGCAATAAATGCAAAGGATCACAACTTAAATTAAATCGAATTTTAAATTTTCAACAA
AAAACCAAAAATAATCGACTTTTGGCCTGACTCACTAAAAAAAAGTCCCTAGTGGAGTCGCCTAG
CTATCGAAACCATTTTTTGAAAAAAATTCTCGATTATATTTTGGAAAACACGAAAATGGAGTCAC
CACTAATTTTTTTTTAAAAATAGGTGTGATTGGGTCACCTTTTAAAAAGTTTTAAAATCATTAAA
AACAAATTTTGGTCTCTGTAACCATAAAAAGGGTTCAGGAGTCAGTTACGAGTAAGGAAGGATTA
ACACCCTTACACGCCCAAAAATTGGTACCTAAACCATGCATGTCATAATTATTTATTTTGAAAAA
AAAAATTTATAGAAA
Done.