Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013930.1 Kokia drynarioides strain JFW-HI SEQ_128960, 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: 3318
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.32
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:695 original size:17 final size:17
Alignment explanation
Indices: 673--707 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
663 ACCCTAAACC
673 CTAAGCAATGAAACTTA
1 CTAAGCAATGAAACTTA
* *
690 CTAAGCTATGAAGCTTA
1 CTAAGCAATGAAACTTA
707 C
1 C
708 CAAATATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (17 bp):
CTAAGCAATGAAACTTA
Found at i:1619 original size:17 final size:17
Alignment explanation
Indices: 1597--1631 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1587 ACCCTAAACC
1597 CTAAGCAATGAAACTTA
1 CTAAGCAATGAAACTTA
* *
1614 CTAAGCTATGAAGCTTA
1 CTAAGCAATGAAACTTA
1631 C
1 C
1632 CAAATATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (17 bp):
CTAAGCAATGAAACTTA
Found at i:1788 original size:924 final size:874
Alignment explanation
Indices: 1--1798 Score: 2501
Period size: 924 Copynumber: 2.0 Consensus size: 874
1 AAAAAGGAATAACTTGTGTTGAATGACTCAATTATGTGATGTAATGTGAGAATTGGATGATTTTT
1 AAAAAGGAATAACTTGTGTTGAATGACTCAATTATGTGATGTAATGTGAGAATTGGATGATTTTT
66 GGATGTAGACAAATCGTGCTTTAGATCGCGGAAAAGGGAAATTAGCGGAGTAGTCCCTGAAGTCT
66 GGATGTAGACAAATCGTGCTTTAGATCGCGGAAAAGGGAAATTAGCGGAGTAGTCCCTGAAGTCT
*
131 AATCGTAACTGCAAGTTAGTCCGGTAAGTTCGTAATGTAAATTTTACTTAATATTTCTTGTATGT
131 AATCGTAACTGCAAGTTAGTCCGGTAAGTTCGTAATGTAAATTTTACTTAATATTTCTTGTAAGT
*
196 ATATTGTCAATGTTAAGCAATTGGAAGCACTTGGAATTGAAGAGGTCGAGGAAATGAAACAAAAG
196 ATATTGTCAATGTTAAGCAATTGAAAGCACTTGGAATTGAAGAGGTCGAGGAAATGAAACAAAAG
*
261 AGATAGTGCGCTTTATGCCATTGAAAAAGCATTAACGCGATGGTTGGGGTTTCGCATATGTTACG
261 AGATAGTGCGCTTTATGCCATTGAAAAAGCATTAACGCGATGGTTGGGGTATCGCATATGTTACG
326 AGTCGTTGATAGCTCGTGTGAGCAGCATCATGATTCGAAAAAGAGATATGTTCCTAAATGGATTA
326 AGTCGTTGATAGCTCGTGTGAGCAGCATCATGATTCGAAAAAGAGATATGTTCCTAAATGGATTA
391 AAGGCCTTTCAATGGTTGGGAATTATGCTGTATGCATACTTCCGATAGCTCGTGTGAGCAGTATC
391 AAGGCCTTTCAATGGTTGGGAATTATGCTGTATGCATACTTCCGATAGCTCGTGTGAGCAGTATC
456 ATTTGGGAACAATTTACAAACATACATCATACCGATGGCTGGGGTACTGCATATGTTGCGAGTCC
456 ATTTGGGAACAATTTACAAACATACATCATACCGATGGCTGGGGTACTGCATATGTTGCGAGTCC
521 TCAATAGCTTGTGTGAGCAACATCAAGTACTGGTAACAAAAAACTTATAGAAAAGAAAGTGAAAG
521 TCAATAGCTTGTGTGAGCAACATCAAGTACTGGTAACAAAAAACTTATAGAAAAGAAAGTGAAAG
*
586 ATTATAATTGACTCGAGGAAGCAATAGAACTATCCTAGCTCGGTTGAGTTATAGCTGCTTTATAG
586 ATTATAATTGACTCAAGGAAGCAATAGAACTATCCTAGCTCGGTTGAGTTATAGCTGCTTTATAG
651 ATCATTTACCAAACCCTAAACCCTAAGCAATGAAACTTACTAAGCTATGAAGCTTACCAAATATG
651 ATCATTTACCAAACCCTAAACCCTAAGCAATGAAACTTACTAAGCTATGAAGCTTACCAAATATG
*
716 TTGTTGCTATTTTTTAGATCGTTTTGTTGATTGAAGATCGGATCATCACCATCTCTTCGAAGTCA
716 TTGTTGCTATTTTGTAGATCGTTTTGTTGATTGAAGATCGGATCATCACCATCTCTTCGAAGTCA
* *
781 CATTATCGCAGAGCTTGTTGGTAGGTTTTGCATCACTCGATCTCATGCATGTACTAGGATGATGT
781 CATTATCACAGAGCTCGTTGGTAGGTTTTGCATCACTCGATCTCATGCATGTACTAGGATGATGT
846 TATCTTTTGCTTTATGTATTTGAACTTGT
846 TATCTTTTGCTTTATGTATTTGAACTTGT
***************************** * * *
875 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAA-AAAG-GA-ATAA
1 ---------------------AAAAAGGAATAACTTGTGTTGAATGACTCAATTATGTGATGTAA
* * * * * * * * * **
937 CTTGTGTTGAA-T-GACTCAATTATGTGATGTAATGTGAGAATTGGATGATTTTTGGAT-GTAGA
45 --TGTG-AGAATTGGA-TGATTTTTG-GATGT-A---GACAAATCG-TG--CTTTAGATCGCGGA
* ***
999 CAAATCGTGCTTTTGATCGCGGAAAAGGGAAATTAGCGGAGTAGTCCCTGAAGTCTAATCGTAAC
98 -AAA--GGGAAATT-A--GCGG---A--G----TAG--------TCCCTGAAGTCTAATCGTAAC
1064 TGCAAGTTAGTCCGGTAAGTTCGTAATGTAAATTTTACTTAATATTTCTTGTAAGTATATTGTCA
140 TGCAAGTTAGTCCGGTAAGTTCGTAATGTAAATTTTACTTAATATTTCTTGTAAGTATATTGTCA
1129 ATGTTAAGCAATTGAAAGCACTTGGAATTGAAGAGGTCGAGGAAATGAAACAAAAGAGATAGTGC
205 ATGTTAAGCAATTGAAAGCACTTGGAATTGAAGAGGTCGAGGAAATGAAACAAAAGAGATAGTGC
*
1194 GCTTTATGCCATTGAAAAAGCATTAACGCGATGGTTGGGGTATCGCATATGTTGCGAGTCGTTGA
270 GCTTTATGCCATTGAAAAAGCATTAACGCGATGGTTGGGGTATCGCATATGTTACGAGTCGTTGA
1259 TAGCTCGTGTGAGCAGCATCATGATTCGAAAAAGAGATATGTTCCTAAATGGATTAAAGGCCTTT
335 TAGCTCGTGTGAGCAGCATCATGATTCGAAAAAGAGATATGTTCCTAAATGGATTAAAGGCCTTT
*
1324 CAATGGTTGGGAATTATGTTGTATGCATACTTCCGATAGCTCGTGTGAGCAGTATCATTTGGGAA
400 CAATGGTTGGGAATTATGCTGTATGCATACTTCCGATAGCTCGTGTGAGCAGTATCATTTGGGAA
1389 CAATTTACAAACATACATCATACCGATGGCTGGGGTACTGCATATGTTGCGAGTCCTCAATAGCT
465 CAATTTACAAACATACATCATACCGATGGCTGGGGTACTGCATATGTTGCGAGTCCTCAATAGCT
1454 TGTGTGAGCAACATCAAGTACTGGTAACAAAAAACTTATAGAAAAGAAAGTGAAAGATTATAATT
530 TGTGTGAGCAACATCAAGTACTGGTAACAAAAAACTTATAGAAAAGAAAGTGAAAGATTATAATT
* *
1519 GACTCAAGGAAGCAATAGAACTATCCTAGCTCGGTTGAGTTATAGTTGCTTTATAGATCGTTTAC
595 GACTCAAGGAAGCAATAGAACTATCCTAGCTCGGTTGAGTTATAGCTGCTTTATAGATCATTTAC
*
1584 CAAACCCTAAACCCTAAGCAATGAAACTTACTAAGCTATGAAGCTTACCAAATATGTTTTTGCTA
660 CAAACCCTAAACCCTAAGCAATGAAACTTACTAAGCTATGAAGCTTACCAAATATGTTGTTGCTA
*
1649 TTTTGTAGATCGTTTTTTTGATTGAAGATCGGATCATCACCATCTCTTCGAAGTCACATTATCAC
725 TTTTGTAGATCGTTTTGTTGATTGAAGATCGGATCATCACCATCTCTTCGAAGTCACATTATCAC
*
1714 AGAGCTCGTTGGTAGGTTTTGCATCACTCGATCTCATGCGTGTACTAGGATGATGTTATCTTTTG
790 AGAGCTCGTTGGTAGGTTTTGCATCACTCGATCTCATGCATGTACTAGGATGATGTTATCTTTTG
1779 CTTTATGTATTTGAACTTGT
855 CTTTATGTATTTGAACTTGT
1799 GGAAACCTTG
Statistics
Matches: 807, Mismatches: 61, Indels: 41
0.89 0.07 0.05
Matches are distributed among these distances:
892 3 0.00
893 4 0.00
894 13 0.02
895 10 0.01
896 1 0.00
899 6 0.01
900 2 0.00
901 3 0.00
902 9 0.01
904 4 0.00
905 1 0.00
907 4 0.00
910 1 0.00
912 1 0.00
916 3 0.00
924 742 0.92
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.31
Consensus pattern (874 bp):
AAAAAGGAATAACTTGTGTTGAATGACTCAATTATGTGATGTAATGTGAGAATTGGATGATTTTT
GGATGTAGACAAATCGTGCTTTAGATCGCGGAAAAGGGAAATTAGCGGAGTAGTCCCTGAAGTCT
AATCGTAACTGCAAGTTAGTCCGGTAAGTTCGTAATGTAAATTTTACTTAATATTTCTTGTAAGT
ATATTGTCAATGTTAAGCAATTGAAAGCACTTGGAATTGAAGAGGTCGAGGAAATGAAACAAAAG
AGATAGTGCGCTTTATGCCATTGAAAAAGCATTAACGCGATGGTTGGGGTATCGCATATGTTACG
AGTCGTTGATAGCTCGTGTGAGCAGCATCATGATTCGAAAAAGAGATATGTTCCTAAATGGATTA
AAGGCCTTTCAATGGTTGGGAATTATGCTGTATGCATACTTCCGATAGCTCGTGTGAGCAGTATC
ATTTGGGAACAATTTACAAACATACATCATACCGATGGCTGGGGTACTGCATATGTTGCGAGTCC
TCAATAGCTTGTGTGAGCAACATCAAGTACTGGTAACAAAAAACTTATAGAAAAGAAAGTGAAAG
ATTATAATTGACTCAAGGAAGCAATAGAACTATCCTAGCTCGGTTGAGTTATAGCTGCTTTATAG
ATCATTTACCAAACCCTAAACCCTAAGCAATGAAACTTACTAAGCTATGAAGCTTACCAAATATG
TTGTTGCTATTTTGTAGATCGTTTTGTTGATTGAAGATCGGATCATCACCATCTCTTCGAAGTCA
CATTATCACAGAGCTCGTTGGTAGGTTTTGCATCACTCGATCTCATGCATGTACTAGGATGATGT
TATCTTTTGCTTTATGTATTTGAACTTGT
Found at i:2203 original size:21 final size:21
Alignment explanation
Indices: 2174--2214 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2164 TTTTAGTATC
*
2174 GGTAGAAGTAAGACTTATATT
1 GGTAAAAGTAAGACTTATATT
2195 GGTAAAAGTAAGACTTATAT
1 GGTAAAAGTAAGACTTATAT
2215 CGATAGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GGTAAAAGTAAGACTTATATT
Found at i:2231 original size:21 final size:21
Alignment explanation
Indices: 2207--2258 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
2197 TAAAAGTAAG
* *
2207 ACTTATATCGATAGAAGAGTC
1 ACTTGTATCGATAGAACAGTC
*
2228 ACTTGTATCGATAGAACTGTC
1 ACTTGTATCGATAGAACAGTC
2249 ACTTGTATCG
1 ACTTGTATCG
2259 GTAGGAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGATAGAACAGTC
Done.