Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011733.1 Kokia drynarioides strain JFW-HI SEQ_126727, 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: 7879
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:4605 original size:631 final size:625
Alignment explanation
Indices: 3140--4672 Score: 1969
Period size: 631 Copynumber: 2.4 Consensus size: 625
3130 CATGAGCTGG
* * * ** * * ** * * * *
3140 ACCATTCCTCATGGCCAGACCACACGGCTCTGTGACCCACACAACCACGTGATAGGCCAAACCGA
1 ACCATTCCACACGACCAGACCACACGATTGTGTGACCCACACGACCATATGGTAAGCCATATCGA
* * * * * * *
3205 TTTCACGGAATTGCATACCAAACAACGAAAAATCAA-AATTTTTAGGTTTTCCGAGCATTCTAAG
66 TATCACGAAATTACACACCAAACAATGGAAAAT-AACAAATTTTAGGTTTT-CGAGCATTCTAAG
* ** * *
3269 ATGTATATATGACAAAAATAAGAAACTTA-GAGGGAGAAATCAGAGAACATTCAAGAAAATAACT
129 ACGTATATATGACAAAAATAAGAAAC-TAGGAGGGAGCCATCAGAGAATATTCAAGAAAACAAC-
* * *
3333 TGAAAAACACCATTGAAGCCGACTTTGAAGCATATTT-GAGTCAAGATTGAAGATTCTCATTTGA
192 TCAAAAACACCATTGAAGCCGACTTTGAAGCAAATTTCCA-TCAAGATTGAAGATTCTCATTTGA
*
3397 TTTGATAGCAGATTATCATGAGTTTCTTTATTTTTTCGGTTATATTGTCTCTTGGATGTTTTTAC
256 TTTGATAGGAGATTATCATGAGTTTCTTTATTTTTTCGGTTATATTGTCTCTTGGATGTTTTTAC
* * *
3462 TTTCAAGAATGAACTAATTTTCTAAATACCTAGGGGAGATGAAACCTATGATGGATTATGATGTT
321 TTTCAAGAATGAACCAATTTCCTAAATACCTAGGGGAGATGAAACCTATGATAGATTATGATGTT
* *
3527 TGATTTTTATTATGCGCAACAAATACTTAGTTTTTCTCTCAATTATGTGTTCTTAAATCGTGAAT
386 TGATTTTTATTATGCGCAAAAAATACTTAGTTTTTCTCTCAATTATGTGTACTTAAATCGTGAAT
* * * * *
3592 ATTCGATGTTCATTGTAAATGTTATGCTCCTAATCCTTTCAATTCATGTTTTTATGCTTAATATA
451 ATTCAATGTTCATTCTAAATGTTATGCTCCTAATCCTTTCAATACATGATTTTATGCCTAATATA
*
3657 GCACTAGAAATCAAAAGGAGAGAAAAATGAGTGAAAAAAAAATCGGAGCAAGCTACAGGAGCCAC
516 GCACTAGAAATCAAAAGGAGAGAAAAATGAGCGAAAAAAAAATCGGAGCAAGCTACAGGAGCCAC
* * *
3722 ACGGGTTGAACCATTCCACTTGACCATATGATCCGCACGAGCAAA
581 ACGGGCTGAACCATTCCACATGACCATATGATCCGCACAAGCAAA
* *
3767 ACCATTCCACACGGCCAGACCACACGGTTGTGTGACCCACACGACCATATGGTAAGCCATATCGA
1 ACCATTCCACACGACCAGACCACACGATTGTGTGACCCACACGACCATATGGTAAGCCATATCGA
* * * *
3832 TATCATGTAATTGCACACCAAACAATGGAAAATCACAAATTTTAGGTTTTTCGAGCATTCTAAGA
66 TATCACGAAATTACACACCAAACAATGGAAAATAACAAATTTTAGG-TTTTCGAGCATTCTAAGA
* * *
3897 CGTACATATGAC-AAAATAAGAAACTAGGAGTGAGCCAAT-AGAGAATATTCAAGAAAACAAATC
130 CGTATATATGACAAAAATAAGAAACTAGGAGGGAGCC-ATCAGAGAATATTCAAGAAAACAACTC
* * *
3960 GAAAAACACCATTGAAGCCGACTTTGAAGCAAATTTCCATTAAGATTGAATATTCTGATTTGATT
194 -AAAAACACCATTGAAGCCGACTTTGAAGCAAATTTCCATCAAGATTGAAGATTCTCATTTGATT
*
4025 TGATAGGAGATTATCATGAGTTTCTTTATTTCTTTCGGTTATATTGTCTCCTT-GATGTTTTTTC
258 TGATAGGAGATTATCATGAGTTTCTTTATTT-TTTCGGTTATATTGTCT-CTTGGATG-TTTTTA
* *
4089 CTTTCAAGAATGAACCAATTTCCTAAATACCTAGGGGAGATG-AACCATGTGATAGATTATGTTG
320 CTTTCAAGAATGAACCAATTTCCTAAATACCTAGGGGAGATGAAACC-TATGATAGATTATGATG
* * *
4153 TTTGATTTTTATTTTGCGCAAAAAATGCTTAGTTTTTTCTCTCAATTATGAT-TACTTAAATTGT
384 TTTGATTTTTATTATGCGCAAAAAATACTTAG-TTTTTCTCTCAATTATG-TGTACTTAAATCGT
* * * * *
4217 GATTATTCAATGTTCATTCTGAATTTTATGCTCTTAATCTTTTCAATACAT-ATTTTATGCCTAA
447 GAATATTCAATGTTCATTCTAAATGTTATGCTCCTAATCCTTTCAATACATGATTTTATGCCTAA
* * *
4281 TA-AGGCACTTGAAATCAAAAGGAGTGAAAAATGAGCGAAAATCGAAAAATTGGAGCAAGCTACA
512 TATA-GCACTAGAAATCAAAAGGAGAGAAAAATGAGCGAAAA---AAAAATCGGAGCAAGCTAC-
* * * *
4345 AGG-GCCACATGGGCTGGACCATTCCACATGGCCATATGATCCGCACAAGCTAA
572 AGGAGCCACACGGGCTGAACCATTCCACATGACCATATGATCCGCACAAGCAAA
* * * * *
4398 AGCATTCCACACGACCTA-ACCACATGATTGTGTGA-CCGCACGACCATGTGGTAGGCCATATCG
1 ACCATTCCACACGACC-AGACCACACGATTGTGTGACCCACACGACCATATGGTAAGCCATATCG
* * * *
4461 ATGTCACGAAATTACACACCAAACAGTGGAAAATAACAAATTTTAGGCTTTTCGGGCATTTTAAG
65 ATATCACGAAATTACACACCAAACAATGGAAAATAACAAATTTTAGG-TTTTCGAGCATTCTAAG
* *
4526 ACATATATATGACAAAAATAAGAAACTAGGAGGGAGCCATCAAAGAATATTCAAGAAAACAACTC
129 ACGTATATATGACAAAAATAAGAAACTAGGAGGGAGCCATCAGAGAATATTCAAGAAAACAACTC
* * *
4591 AAAAAAATCCATTGAAGCCGACTTTGAAGCAAATTTCCGTCAAGATT-ATAGATTCTTATTTGAT
194 AAAAACA-CCATTGAAGCCGACTTTGAAGCAAATTTCCATCAAGATTGA-AGATTCTCATTTGAT
*
4655 TTAATAGGAGATTATCAT
257 TTGATAGGAGATTATCAT
4673 ATACCTAGGG
Statistics
Matches: 791, Mismatches: 93, Indels: 40
0.86 0.10 0.04
Matches are distributed among these distances:
625 3 0.00
626 125 0.16
627 143 0.18
628 142 0.18
629 70 0.09
630 102 0.13
631 202 0.26
632 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (625 bp):
ACCATTCCACACGACCAGACCACACGATTGTGTGACCCACACGACCATATGGTAAGCCATATCGA
TATCACGAAATTACACACCAAACAATGGAAAATAACAAATTTTAGGTTTTCGAGCATTCTAAGAC
GTATATATGACAAAAATAAGAAACTAGGAGGGAGCCATCAGAGAATATTCAAGAAAACAACTCAA
AAACACCATTGAAGCCGACTTTGAAGCAAATTTCCATCAAGATTGAAGATTCTCATTTGATTTGA
TAGGAGATTATCATGAGTTTCTTTATTTTTTCGGTTATATTGTCTCTTGGATGTTTTTACTTTCA
AGAATGAACCAATTTCCTAAATACCTAGGGGAGATGAAACCTATGATAGATTATGATGTTTGATT
TTTATTATGCGCAAAAAATACTTAGTTTTTCTCTCAATTATGTGTACTTAAATCGTGAATATTCA
ATGTTCATTCTAAATGTTATGCTCCTAATCCTTTCAATACATGATTTTATGCCTAATATAGCACT
AGAAATCAAAAGGAGAGAAAAATGAGCGAAAAAAAAATCGGAGCAAGCTACAGGAGCCACACGGG
CTGAACCATTCCACATGACCATATGATCCGCACAAGCAAA
Found at i:5080 original size:498 final size:498
Alignment explanation
Indices: 4341--5338 Score: 1854
Period size: 498 Copynumber: 2.0 Consensus size: 498
4331 TGGAGCAAGC
4341 TACAAGGGCCACATGGGCTGGACCATTCCACATGGCCATATGATCCGCACAAGCTAAAGCATTCC
1 TACAAGGGCCACATGGGCTGGACCATTCCACATGGCCATATGATCCGCACAAGCTAAAGCATTCC
* * *
4406 ACACGACCTAACCACATGATTGTGTGACCGCACGACCATGTGGTAGGCCATATCGATGTCACGAA
66 ACACGACCTAACCACATGATTATGTGACCACACGACCATGTGGTAGGCCATATCGATATCACGAA
4471 ATTACACACCAAACAGTGGAAAATAACAAATTTTAGGCTTTTCGGGCATTTTAAGACATATATAT
131 ATTACACACCAAACAGTGGAAAATAACAAATTTTAGGCTTTTCGGGCATTTTAAGACATATATAT
*
4536 GACAAAAATAAGAAACTAGGAGGGAGCCATCAAAGAATATTCAAGAAAACAACTCAAAAAAATCC
196 GACAAAAATAAGAAACTAGGAGGGAGCCATCAAAGAATACTCAAGAAAACAACTCAAAAAAATCC
*
4601 ATTGAAGCCGACTTTGAAGCAAATTTCCGTCAAGATTATAGATTCTTATTTGATTTAATAGGAGA
261 ATTGAAGCCGACTTTGAAGCAAATTTCCGTCAAGATTATAGATTATTATTTGATTTAATAGGAGA
*
4666 TTATCATATACCTAGGGGATATGAACCCTATGATAGAATGTGTCGTTCGATTTTTATTTGTGCAA
326 TTATCATATACCTAGGGGATATGAACCCTATGATAGAATATGTCGTTCGATTTTTATTTGTGCAA
*
4731 CAAAGACTTAGTTTT-TTATCTCAATTATATGTGCTTAAATTGTGATTATTCGATGTTCATTGTG
391 CAAAGACTTAGTTTTCTT-TCTAAATTATATGTGCTTAAATTGTGATTATTCGATGTTCATTGTG
4795 AATTTTATACTCCTAATTCTTTCAATTCATTTTTTTATGCTTAA
455 AATTTTATACTCCTAATTCTTTCAATTCATTTTTTTATGCTTAA
*
4839 TACAGGGGCCACATGGGCTGGACCATTCCACATGGCCATATGATCCGCACAAGCTAAAGCATTCC
1 TACAAGGGCCACATGGGCTGGACCATTCCACATGGCCATATGATCCGCACAAGCTAAAGCATTCC
*
4904 ACACGACCTAACCACATGATTATGTGACCACACGACCATGTGGTAGGCCATATCGATATCACGGA
66 ACACGACCTAACCACATGATTATGTGACCACACGACCATGTGGTAGGCCATATCGATATCACGAA
* *
4969 ATTGCACACCAAACAGTGGAAAATCACAAATTTTAGGCTTTTCGGGCATTTTAAGACATATATAT
131 ATTACACACCAAACAGTGGAAAATAACAAATTTTAGGCTTTTCGGGCATTTTAAGACATATATAT
5034 GACAAAAATAAGAAACTAGGAGGGAGCCATCAAAGAATACTCAAGAAAACAACTCAAAAAAATCC
196 GACAAAAATAAGAAACTAGGAGGGAGCCATCAAAGAATACTCAAGAAAACAACTCAAAAAAATCC
* *
5099 ATTGAAGCCGACTTTGAAGCAGATTTCCGTCAAGATTATAGATTATTATTTGATTTGATAGGAGA
261 ATTGAAGCCGACTTTGAAGCAAATTTCCGTCAAGATTATAGATTATTATTTGATTTAATAGGAGA
5164 TTATCATATACCTAGGGGATATGAACCCTATGATAGAATATGTCGTTCGATTTTTATTTGTGCAA
326 TTATCATATACCTAGGGGATATGAACCCTATGATAGAATATGTCGTTCGATTTTTATTTGTGCAA
5229 CAAAGACTTAGTTTTCTTTCTAAATTATATGTGCTTAAATTGTGATTATTCGATGTTCATTGTGA
391 CAAAGACTTAGTTTTCTTTCTAAATTATATGTGCTTAAATTGTGATTATTCGATGTTCATTGTGA
*
5294 ATTTTATGCTCCTAATTCTTTCAATTCATTTTTTTATGCTTAA
456 ATTTTATACTCCTAATTCTTTCAATTCATTTTTTTATGCTTAA
5337 TA
1 TA
5339 GAGAACTTGA
Statistics
Matches: 485, Mismatches: 14, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
498 483 1.00
499 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (498 bp):
TACAAGGGCCACATGGGCTGGACCATTCCACATGGCCATATGATCCGCACAAGCTAAAGCATTCC
ACACGACCTAACCACATGATTATGTGACCACACGACCATGTGGTAGGCCATATCGATATCACGAA
ATTACACACCAAACAGTGGAAAATAACAAATTTTAGGCTTTTCGGGCATTTTAAGACATATATAT
GACAAAAATAAGAAACTAGGAGGGAGCCATCAAAGAATACTCAAGAAAACAACTCAAAAAAATCC
ATTGAAGCCGACTTTGAAGCAAATTTCCGTCAAGATTATAGATTATTATTTGATTTAATAGGAGA
TTATCATATACCTAGGGGATATGAACCCTATGATAGAATATGTCGTTCGATTTTTATTTGTGCAA
CAAAGACTTAGTTTTCTTTCTAAATTATATGTGCTTAAATTGTGATTATTCGATGTTCATTGTGA
ATTTTATACTCCTAATTCTTTCAATTCATTTTTTTATGCTTAA
Done.