Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005415.1 Kokia drynarioides strain JFW-HI SEQ_119435, 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, 972
Length: 1620
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Found at i:678 original size:216 final size:216
Alignment explanation
Indices: 1--1620 Score: 1583
Period size: 216 Copynumber: 7.4 Consensus size: 216
* * * * * *
1 ATGCGATTTCCCGAGCATGGAATGTTAGGAATATTGCTCGAAGGATTGGATCATCTTGGATAGTT
1 ATGCGATTTCTCGAGCATGGAATGTTCGGAATATTGCTCGAAGGAATGGATCGTCTTGAATACTT
* * * **
66 TAAGGAACCGAAGTTATCATAGAAGAAATAGTAAAAGCTTGACAAGTTCAGAAGTTTGTCTAAGA
66 TAAGGAACCGAAGTTAT-A-A-AAGAACTCGTAAAAGCTTTACAAGTTCAGAAGTTCATCTAAGA
* * * * * *
131 ATCATA-AGAGAAATAATTTT-TCATAAATATA-TTTTTAATTCAAGGACCAAAAAGTTGTGTGC
128 ACCA-AGAGAGAAACAATTTTCACATAAATA-AGTTTTTAATTCAAAGACC-AAAAGTTGTTTAC
*
193 AAAATGACAAACTATTTAGACCGGATG
190 AAAATGACAAACTATTTAGACCGAATG
* * *
220 ATGCTATTTCCCGAGCATGGAATGTTCGGAATATTGATCGAAGGAATGGATCGTCTTGAATACTT
1 ATGCGATTTCTCGAGCATGGAATGTTCGGAATATTGCTCGAAGGAATGGATCGTCTTGAATACTT
* * * * *
285 TAATGAACCAAAGTTATAAAAGAACTCGTAAAAAG-TTTGACTAGTTCAGAAGGTT-GTCAAAGA
66 TAAGGAACCGAAGTTATAAAAGAACTCGT-AAAAGCTTT-ACAAGTTCAGAA-GTTCATCTAAGA
* * * * ** * *
348 ACCAA-AGGAGTAACAATTCTCACGTAAATAAGTTTTTAGTTTGAAGACCAAAACTTGATTTTCA
128 ACCAAGA-GAGAAACAATTTTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTG-TTTACA
* * *
412 AAATGGC-AACTATTTAGACCAAAAG
191 AAATGACAAACTATTTAGACCGAATG
* * * * * * * *
437 ATGCAATTTCTCGGGCACGGAATGTTCGGAAAATTTCTC-ATAGAAACGGATGGTCTTGAATACT
1 ATGCGATTTCTCGAGCATGGAATGTTCGGAATATTGCTCGA-AGGAATGGATCGTCTTGAATACT
* * * *
501 TTAAGGAACCGAAGTTATAAAATAACTCATAAAAGCTTTACAAGTTC-GATAGGTCATCCAAGAA
65 TTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGCTTTACAAGTTCAGA-AGTTCATCTAAGAA
* *
565 CCAAGAGAGAGAA-AATTTTCACATAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTCACAAA
129 CCAAGAGAGA-AACAATTTTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAA
* *
629 ATGACAAACTATTTAGATCAAATG
193 ATGACAAACTATTTAGACCGAATG
* * * * * * *
653 ATGCGATTT-TCTAGACATTGAATGTTCGAAAAATTTG-TAGAAGGAATGGATCG-CATAGAATG
1 ATGCGATTTCTCGAG-CATGGAATGTTCGGAATA-TTGCTCGAAGGAATGGATCGTC-TTGAATA
* * * *
715 CTTTGAGGAACCTAATGTT-TCAAATGAACTCGTAAAAG-TTTGACAAGTTCGGAAGTTCATCTA
63 CTTTAAGGAACCGAA-GTTAT-AAAAGAACTCGTAAAAGCTTT-ACAAGTTCAGAAGTTCATCTA
** * * * *
778 AGAACTTAGAGAGAAACAATTATCATAAAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAG
125 AGAACCAAGAGAGAAACAATTTTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAC
*
843 AAAATGACAAAATATTTAGACCGAATG
190 AAAATGACAAACTATTTAGACCGAATG
* * * * **
870 ATGCGATTTCTCGAGCATGGAATGTTTGGAATATTGGTTGAAAGAATGGATCACCTTGAATACTT
1 ATGCGATTTCTCGAGCATGGAATGTTCGGAATATTGCTCGAAGGAATGGATCGTCTTGAATACTT
*** * *
935 TAAGGAACC-AATGCCGTAAAAGAACTCGTAAAAGCTTGAAAAGTTCAGAAGTTCATCTAAGAAC
66 TAAGGAACCGAA-GTTATAAAAGAACTCGTAAAAGCTTTACAAGTTCAGAAGTTCATCTAAGAAC
* *
999 CAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACGAAAT
130 CAAGAGAGAAACAATTTTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAT
*
1064 GAAAAACTATTTAGACC-AAGTG
195 GACAAACTATTTAGACCGAA-TG
* ** * * *
1086 ATGCAATTTCTCGAGCATGGAATGTTCATAA-AGTTGCTCGAAGAAATGGATCATGTTGAATACT
1 ATGCGATTTCTCGAGCATGGAATGTTCGGAATA-TTGCTCGAAGGAATGGATCGTCTTGAATACT
* * ** * * * * *
1150 TTAAGGAACCGAAGTTATAACAGAAATAATAAAAGTTTTCCTAGTTC-GAAAGTTCGTCCAAGAA
65 TTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGCTTTACAAGTTCAG-AAGTTCATCTAAGAA
* * * * ** * *
1214 TCAAGAGAGAAACAATTTACAAATAAATAAGTATTTAATTCAGTGACCAAAAGTTTTTTTTACGA
129 CCAAGAGAGAAACAATTTTCACATAAATAAGTTTTTAATTCAAAGACCAAAAG--TTGTTTACAA
*
1279 AATGGA-AAACTATTTTGACCGAATG
192 AAT-GACAAACTATTTAGACCGAATG
* * * * * *
1304 ATGCGATTTCCCGAGCATGGAATGTTAGGAATATTGCTCGAAGGATTGGATCATCTTGGATAGTT
1 ATGCGATTTCTCGAGCATGGAATGTTCGGAATATTGCTCGAAGGAATGGATCGTCTTGAATACTT
* * * * **
1369 TAAGGAACCGAAGTTACCATAGAAGAAATAGTAAAAGCTTGACAAGTTCAGAAGTTTGTCTAAGA
66 TAAGGAACCGAAGTT---ATAAAAGAACTCGTAAAAGCTTTACAAGTTCAGAAGTTCATCTAAGA
* * * * * *
1434 ATCAAAAGAGAAATAATTCTT-TCATAAATATA-TTTTTAATTCAAGGACCAAAAAGTTGTTTGC
128 ACCAAGAGAGAAACAATT-TTCACATAAATA-AGTTTTTAATTCAAAGACC-AAAAGTTGTTTAC
*
1497 AAAATGACAAACTATTTAGACCGGATG
190 AAAATGACAAACTATTTAGACCGAATG
* * * *
1524 ATGCTATTTCCCAAGCATGGAATGTTCGGAATATTGATCGAAGGAATGGATCGTCTTGAATACTT
1 ATGCGATTTCTCGAGCATGGAATGTTCGGAATATTGCTCGAAGGAATGGATCGTCTTGAATACTT
* *
1589 TAATGAACCAAAGTTATAAAAGAACTCGTAAA
66 TAAGGAACCGAAGTTATAAAAGAACTCGTAAA
Statistics
Matches: 1159, Mismatches: 197, Indels: 92
0.80 0.14 0.06
Matches are distributed among these distances:
215 22 0.02
216 414 0.36
217 329 0.28
218 136 0.12
219 80 0.07
220 97 0.08
221 73 0.06
222 8 0.01
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (216 bp):
ATGCGATTTCTCGAGCATGGAATGTTCGGAATATTGCTCGAAGGAATGGATCGTCTTGAATACTT
TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGCTTTACAAGTTCAGAAGTTCATCTAAGAACC
AAGAGAGAAACAATTTTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATG
ACAAACTATTTAGACCGAATG
Found at i:930 original size:433 final size:426
Alignment explanation
Indices: 1--1620 Score: 1617
Period size: 433 Copynumber: 3.7 Consensus size: 426
* * * *
1 ATGCGATTTCCCGAGCATGGAATGTTAGGAATATTGCTCGAAGGATTGGATCATCTTGGATAGTT
1 ATGCGATTTCCCGAGCATGGAATGTTAGGAATATTGCTCGAAAGAATGGATCATCTTGAATACTT
**
66 TAAGGAACCGAAGTTATCATAGAAGAAATAGTAAAAGCTTGACAAGTTCAGAAGTTTGTCTAAGA
66 TAAGGAACCGAAGTTAT-A-A-AAGAAATAGTAAAAGCTTGACAAGTTCAGAAGTTCATCTAAGA
* * * * *
131 ATCATA-AGAGAAATAATTTTTCATAAATATATTTTTAATTCAAGGACCAAAAAGTTGTGTGCAA
128 ACCA-AGAGAGAAATAATTTTACATAAATATATTTTTAATTCAAAGACCAAAAAGTTGTTTACAA
** * * *
195 AATGACAAACTATTTAGACCGGATGATGCTATTTCCCGAGCATGGAATGTTCGGAATATTGATCG
192 AATGACAAACTATTTAGACCAAATGATGC-ATTTCTCGAGCATGGAATGTTCGAAAAATTGATCG
*
260 AAGGAATGGATCGTCTTGAATACTTTAATGAACCAAAGTTATAAAAGAACTCGTAAAAAGTTTGA
256 AAGGAATGGATCG-CTTGAATACTTTAAGGAACC-AAGTTAT-AAAGAACTCGT-AAAAGTTTGA
* * * ** *
325 CTAGTTCAGAAGGTT-GTCAAAGAACCAA-AGGAGTAACAATTCTCACGTAAATAAGTTTTTAGT
317 CTAGTTCGGAA-GTTCGTCAAAGAACTAAGA-GAGAAACAATT-TCA-AAAAATAAGTTTTTAAT
** * ** * * *
388 TTGAAGACCAAAACTTGATTTTCAAAATGGC-AACTATTTAGACCAAAAG
378 TCAAAGACCAAAAGTTG-TTTAGAAAATGACAAACTATTTAGACCGAATG
* * * * * * * * * **
437 ATGCAATTTCTCGGGCACGGAATGTTCGGAAAATTTCTC-ATAGAAACGGATGGTCTTGAATACT
1 ATGCGATTTCCCGAGCATGGAATGTTAGGAATATTGCTCGAAAG-AATGGATCATCTTGAATACT
* * * * *
501 TTAAGGAACCGAAGTTATAAAATAACTCA-TAAAAGCTTTACAAGTTC-GATAGGTCATCCAAGA
65 TTAAGGAACCGAAGTTATAAAAGAAAT-AGTAAAAGCTTGACAAGTTCAGA-AGTTCATCTAAGA
*
564 ACCAAGAGAGAGAA-AATTTTCACATAAATA-AGTTTTTAATTCAAAGA-CAAAAAGTTGTTCAC
128 ACCAAGAGAGA-AATAATTTT-ACATAAATATA-TTTTTAATTCAAAGACCAAAAAGTTGTTTAC
* * *
626 AAAATGACAAACTATTTAGATCAAATGATGCGATTT-TCTAGACATTGAATGTTCGAAAAATTTG
190 AAAATGACAAACTATTTAGACCAAATGATGC-ATTTCTCGAG-CATGGAATGTTCGAAAAA-TTG
* * * *
690 -TAGAAGGAATGGATCGCATAGAATGCTTTGAGGAACCTAATGTT-TCAAATGAACTCGTAAAAG
252 ATCGAAGGAATGGATCGC-TTGAATACTTTAAGGAACC-AA-GTTAT-AAA-GAACTCGTAAAAG
* * * *
753 TTTGACAAGTTCGGAAGTTCATCTAAGAACTTAGAGAGAAACAATTATCATAAAAATAAGTTTTT
312 TTTGACTAGTTCGGAAGTTCGTCAAAGAACTAAGAGAGAAACAATT-TCA-AAAAATAAGTTTTT
*
818 AATTCAAAGACCAAAAGTTGTTTAGAAAATGACAAAATATTTAGACCGAATG
375 AATTCAAAGACCAAAAGTTGTTTAGAAAATGACAAACTATTTAGACCGAATG
* * * * *
870 ATGCGATTTCTCGAGCATGGAATGTTTGGAATATTGGTTGAAAGAATGGATCACCTTGAATACTT
1 ATGCGATTTCCCGAGCATGGAATGTTAGGAATATTGCTCGAAAGAATGGATCATCTTGAATACTT
*** * * *
935 TAAGGAACC-AATGCCGTAAAAGAACTCGTAAAAGCTTGAAAAGTTCAGAAGTTCATCTAAGAAC
66 TAAGGAACCGAA-GTTATAAAAGAAATAGTAAAAGCTTGACAAGTTCAGAAGTTCATCTAAGAAC
* * *
999 CAAGAGAGAAACAATTCTCACATAAATA-AGTTTTTAATTCAAAGACC-AAAAGTTGTTTACGAA
130 CAAGAGAGAAATAATT-TTACATAAATATA-TTTTTAATTCAAAGACCAAAAAGTTGTTTACAAA
* * * *
1062 ATGAAAAACTATTTAGACCAAGTGATGCAATTTCTCGAGCATGGAATGTTC-ATAAAGTTGCTCG
193 ATGACAAACTATTTAGACCAAATGATGC-ATTTCTCGAGCATGGAATGTTCGA-AAAATTGATCG
* * ** **
1126 AAGAAATGGATCATG-TTGAATACTTTAAGGAACCGAAGTTATAACAGAAATAATAAAAGTTTTC
256 AAGGAATGGATC--GCTTGAATACTTTAAGGAACC-AAGTTATAA-AGAACTCGTAAAAGTTTGA
* * *
1190 CTAGTTCGAAAGTTCGTCCAAGAA-TCAAGAGAGAAACAATTTACAAATAAATAAGTATTTAATT
317 CTAGTTCGGAAGTTCGTCAAAGAACT-AAGAGAGAAACAATTT-CAAA-AAATAAGTTTTTAATT
** * *
1254 CAGTGACCAAAAGTTTTTTTTACG-AAATGGA-AAACTATTTTGACCGAATG
379 CAAAGACCAAAAG--TTGTTTA-GAAAAT-GACAAACTATTTAGACCGAATG
* * * *
1304 ATGCGATTTCCCGAGCATGGAATGTTAGGAATATTGCTCGAAGGATTGGATCATCTTGGATAGTT
1 ATGCGATTTCCCGAGCATGGAATGTTAGGAATATTGCTCGAAAGAATGGATCATCTTGAATACTT
* **
1369 TAAGGAACCGAAGTTACCATAGAAGAAATAGTAAAAGCTTGACAAGTTCAGAAGTTTGTCTAAGA
66 TAAGGAACCGAAGTT---ATAAAAGAAATAGTAAAAGCTTGACAAGTTCAGAAGTTCATCTAAGA
* * * * *
1434 ATCAAAAGAGAAATAATTCTTTCATAAATATATTTTTAATTCAAGGACCAAAAAGTTGTTTGCAA
128 ACCAAGAGAGAAATAATT-TTACATAAATATATTTTTAATTCAAAGACCAAAAAGTTGTTTACAA
** * * * *
1499 AATGACAAACTATTTAGACCGGATGATGCTATTTCCCAAGCATGGAATGTTCGGAATATTGATCG
192 AATGACAAACTATTTAGACCAAATGATGC-ATTTCTCGAGCATGGAATGTTCGAAAAATTGATCG
*
1564 AAGGAATGGATCGTCTTGAATACTTTAATGAACCAAAGTTATAAAAGAACTCGTAAA
256 AAGGAATGGATCG-CTTGAATACTTTAAGGAACC-AAGTTAT-AAAGAACTCGTAAA
Statistics
Matches: 976, Mismatches: 162, Indels: 90
0.79 0.13 0.07
Matches are distributed among these distances:
431 4 0.00
432 108 0.11
433 450 0.46
434 145 0.15
435 9 0.01
436 65 0.07
437 81 0.08
438 112 0.11
439 2 0.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (426 bp):
ATGCGATTTCCCGAGCATGGAATGTTAGGAATATTGCTCGAAAGAATGGATCATCTTGAATACTT
TAAGGAACCGAAGTTATAAAAGAAATAGTAAAAGCTTGACAAGTTCAGAAGTTCATCTAAGAACC
AAGAGAGAAATAATTTTACATAAATATATTTTTAATTCAAAGACCAAAAAGTTGTTTACAAAATG
ACAAACTATTTAGACCAAATGATGCATTTCTCGAGCATGGAATGTTCGAAAAATTGATCGAAGGA
ATGGATCGCTTGAATACTTTAAGGAACCAAGTTATAAAGAACTCGTAAAAGTTTGACTAGTTCGG
AAGTTCGTCAAAGAACTAAGAGAGAAACAATTTCAAAAAATAAGTTTTTAATTCAAAGACCAAAA
GTTGTTTAGAAAATGACAAACTATTTAGACCGAATG
Done.