Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014127.1 Kokia drynarioides strain JFW-HI SEQ_129160, 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, 957
Length: 1596
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Found at i:890 original size:437 final size:431
Alignment explanation
Indices: 1--1331 Score: 1109
Period size: 437 Copynumber: 3.1 Consensus size: 431
* * * * * *
1 ACATAAATATA-TTTTTAATTCAAACACCAAAAAGTTGTTTGCAAAATGACAAAGTATTTAGACC
1 ACATAAATA-AGTTTTAAATTCAAAGACC-AAAAGCTGTTTACAAAATGACAAAATATTTAAACC
* * * * * * * *
65 -GAATGATGTTG-TTTCCCGAGTATGGAATG-TTCGGAATATTGATCGAAGGAATGGATCGTCTT
64 TGAA-GA-CTCGATTTCCAGAGAATGGAATGTTTC-GAAAATTGCTCGAAAGAATGGATCGCCTT
* * * ** **
127 GAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAATGCTTGACTAGTTCAA-AAGTTTG
126 GAATACTTCAAGGAACCAATGTTATAAAAAAACTCGTAAAA-GCTTGAAAAG-TCAAGAAGTTCA
** * * * *
191 TCTGAGAACCAA-AGGAGAAACAATTCACACGTAAATAAGCTTTTAGTTTGAAGACCAAGACCAA
189 TCCAAGAACCAAGA-GAGAAACAAATCCCACGTAAATAAG-TTTTA-ATT-----CAAAGACCAA
* ** * ** * *
255 AACTTGGTTTTCAAAATGACAAACTATTTAGACCAAAACATACAATTTCTCGAGCATGGAATGTT
246 AAGTT-GTTCACAAAATGAAAAACTATTTAGACCAAATGATGCAATTTCTCGAACATGGAATGTT
* * * * * ** * *
320 TGGAAAA-TTGCTCGCAGAAATGGAGGGTC-TTGAATACTTTAAGGAACCGAAGTTATAAAATAA
310 CGAAAAATTTG-TAGAAGGAATGGATCG-CATAGAATACTTTAAGGAACCGAAGTTATAAAAGAA
* * * * * * * *
383 CTCGTAAAAGTTTTACAAGTTCGGTAGTTCGTCCAAGAAACAAGATAGAGATAATTGTC
373 CTCGTAAAAGTTTGACAACTTCGGAAGTTCATCCAAGAAACAAGAGAGAAACAATTCTC
* *
442 ACATCAATAAGTTTTAAATTCAAAGACCAAAAGCTGTTTACAAAATGACAAACTATTTAAACC-G
1 ACATAAATAAGTTTTAAATTCAAAGACCAAAAGCTGTTTACAAAATGACAAAATATTTAAACCTG
* ** * * *
506 AAAGACTCGATTTCCGGAGAATGGAATG-TTCGAAAATTGCTCGATTGAGTTGATCG-TTTACGT
66 -AAGACTCGATTTCCAGAGAATGGAATGTTTCGAAAATTGCTCGAAAGAATGGATCGCCTT--G-
* * * * * ** *
569 ATAATACACTTCAAGGAACCGAA-GTTTTAAAAAAAGTTGTAAAAGTTTGACAAGTCCGGAGGTT
127 --AAT--ACTTCAAGGAACC-AATGTTATAAAAAAACTCGTAAAAGCTTGAAAAGTCAAGAAGTT
** *
633 TGTCCAAGAACCAAGAGAGAAACAAATCCCACGTCAATAAGTTTTTAATTCAAAGACCAAAAGTT
187 CATCCAAGAACCAAGAGAGAAACAAATCCCACGTAAATAAG-TTTTAATTCAAAGACCAAAAGTT
* * * *
698 GTTCACAAAATGAAAAACTATTTAGATCAAATGATGCGATTTTTCGAACATTGAATGTTCGAAAA
251 GTTCACAAAATGAAAAACTATTTAGACCAAATGATGCAATTTCTCGAACATGGAATGTTCGAAAA
* * * *
763 ATTTGTAGAAGGAATGGATCGCATAGAATGCTTTAAGGAACCTAGGTTGTAAAAGAACTCGTAAA
316 ATTTGTAGAAGGAATGGATCGCATAGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAA
*
828 AGTTTGACAAC-TCTGGAAGTTCATCCATG-AACTAAGAGAGAAACAATTCTC
381 AGTTTGACAACTTC-GGAAGTTCATCCAAGAAAC-AAGAGAGAAACAATTCTC
* * * * *
879 ACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAGAATGACAAAATATTTAGACCTG
1 ACATAAATAAGTTTTAAATTCAAAGACCAAAAGCTGTTTACAAAATGACAAAATATTTAAACCTG
* * * * * * *
944 ATGATTCGATTTCTAGAGCATGGAATGTTTGGAATATTGCTTGAAAGAATGGATCGCCTTGAATA
66 AAGACTCGATTTCCAGAGAATGGAATGTTTCGAAAATTGCTCGAAAGAATGGATCGCCTTGAATA
* * * *
1009 CTTTAAGGAACCAATGTTATAAAAGAACTCGTAAAAGCTTGAAAAGTTAAGAAGTTCATCTAAGA
131 CTTCAAGGAACCAATGTTATAAAAAAACTCGTAAAAGCTTGAAAAGTCAAGAAGTTCATCCAAGA
* * * *
1074 ACCAGGAGAGAAACAATTCTCACGTAAATAAGTTTTAATTCAAAGACCAAAAGTTGTTTACAAAA
196 ACCAAGAGAGAAACAAATCCCACGTAAATAAGTTTTAATTCAAAGACCAAAAGTTGTTCACAAAA
* * * ** *
1139 TGACAAACTATTTAGACCAAGTGATGCAATTTCTCGAGCATGGAATGTTCTCAAAA-TTGCTCGA
261 TGAAAAACTATTTAGACCAAATGATGCAATTTCTCGAACATGGAATGTTCGAAAAATTTG-TAGA
* * * * * * *** *
1203 AGAAATGGATCATC-TTGAATAGTTTAAGGAACCAAAGTTATAATAGAAAGAGTAAAAGTTT-TC
325 AGGAATGGATC-GCATAGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAC
** * * *
1266 CTCGTTCGAAAGTT-AGTCCAAGAACCAGGAGAGAAACAATT-TAC
389 AAC-TTCGGAAGTTCA-TCCAAGAAACAAGAGAGAAACAATTCT-C
1310 ACATAAATAAGTATTT-AATTCA
1 ACATAAATAAGT-TTTAAATTCA
1332 GTGACCGAAA
Statistics
Matches: 722, Mismatches: 139, Indels: 68
0.78 0.15 0.07
Matches are distributed among these distances:
430 7 0.01
431 174 0.24
432 85 0.12
434 3 0.00
436 6 0.01
437 214 0.30
438 40 0.06
439 23 0.03
440 55 0.08
441 25 0.03
443 7 0.01
444 51 0.07
445 30 0.04
446 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (431 bp):
ACATAAATAAGTTTTAAATTCAAAGACCAAAAGCTGTTTACAAAATGACAAAATATTTAAACCTG
AAGACTCGATTTCCAGAGAATGGAATGTTTCGAAAATTGCTCGAAAGAATGGATCGCCTTGAATA
CTTCAAGGAACCAATGTTATAAAAAAACTCGTAAAAGCTTGAAAAGTCAAGAAGTTCATCCAAGA
ACCAAGAGAGAAACAAATCCCACGTAAATAAGTTTTAATTCAAAGACCAAAAGTTGTTCACAAAA
TGAAAAACTATTTAGACCAAATGATGCAATTTCTCGAACATGGAATGTTCGAAAAATTTGTAGAA
GGAATGGATCGCATAGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAA
CTTCGGAAGTTCATCCAAGAAACAAGAGAGAAACAATTCTC
Found at i:898 original size:216 final size:216
Alignment explanation
Indices: 4--1594 Score: 1089
Period size: 216 Copynumber: 7.3 Consensus size: 216
1 ACA
* * * * *
4 TAAATATA-TTTTTAATTCAAACACCAAAAAGTTGTTTGCAAAATGACAAAGTATTTAGACCGAA
1 TAAATA-AGTTTTTAATTCAAAGACC-AAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAA
* * * * * * * * *
68 TGATGTTG-TTTCCCGAGTATGGAATGTTCGGAATATTGATCGAAGGAATGGATCGTC-TTGAAT
64 TGATG-CGATTTCTCGAGCATGGAATGTTCGAAAAATTGCTAGAAAGAATGGATCG-CATAGAAT
* * * ** ** **
131 ACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAATGCTTGACTAGT-TCAAAAGTTTGTCTG
127 ACTTTAAGGAACCAAGGTTATAAAAGAACTCGTAAAA-GTTTGACAAGTCT-GGAAGTTCATCCA
*
195 AGAACCAA-AGGAGAAACAATTCACACG
190 AGAACCAAGA-GAGAAACAATTCTCACG
** * * * *
222 TAAATAAGCTTTTAGTTTGAAGACCAAGACCAAAACTTGGTTTTCAAAATGACAAACTATTTAGA
1 TAAATAAG---TT--TTT-AATTCAAAGACCAAAAGTT-GTTTACAAAATGAAAAACTATTTAGA
** * * * * * * **
287 CCAAAACATACAATTTCTCGAGCATGGAATGTTTGGAAAATTGCTCG-CAGAAATGGAGGGTC-T
59 CCAAATGATGCGATTTCTCGAGCATGGAATGTTCGAAAAATTGCTAGAAAG-AATGGATCG-CAT
* * * *
350 TGAATACTTTAAGGAACCGAA-GTTATAAAATAACTCGTAAAAGTTTTACAAGT-TCGGTAGTTC
122 AGAATACTTTAAGGAACC-AAGGTTATAAAAGAACTCGTAAAAGTTTGACAAGTCT-GGAAGTTC
* * * * * * *
413 GTCCAAGAAACAAGATAGAGATAATTGTCACA
185 ATCCAAGAACCAAGAGAGAAACAATTCTCACG
* * * * *
445 TCAATAAGTTTTAAATTCAAAGACCAAAAGCTGTTTACAAAATGACAAACTATTTAAACCGAAA-
1 TAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACC-AAAT
* * ** * * * *
509 GACT-CGATTTC-CGGAGAATGGAATGTTCG-AAAATTGCTCGATTGAGTTGATCGTTTACGTAT
65 GA-TGCGATTTCTC-GAGCATGGAATGTTCGAAAAATTGCTAGAAAGAATGGATCG----CATAG
* * * * * * * **
571 AATACACTTCAAGGAACCGAA-GTTTTAAAAAAAGTTGTAAAAGTTTGACAAGTCCGGAGGTTTG
124 AAT--ACTTTAAGGAACC-AAGGTTATAAAAGAACTCGTAAAAGTTTGACAAGTCTGGAAGTTCA
* *
635 TCCAAGAACCAAGAGAGAAACAAATCCCACG
186 TCCAAGAACCAAGAGAGAAACAATTCTCACG
* * *
666 TCAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTCACAAAATGAAAAACTATTTAGATCAAATG
1 TAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATG
* * * * *
731 ATGCGATTTTTCGAACATTGAATGTTCGAAAAATTTG-TAGAAGGAATGGATCGCATAGAATGCT
66 ATGCGATTTCTCGAGCATGGAATGTTCGAAAAA-TTGCTAGAAAGAATGGATCGCATAGAATACT
* * * *
795 TTAAGGAACCTAGGTTGTAAAAGAACTCGTAAAAGTTTGACAACTCTGGAAGTTCATCCATGAAC
130 TTAAGGAACCAAGGTTATAAAAGAACTCGTAAAAGTTTGACAAGTCTGGAAGTTCATCCAAGAAC
*
860 TAAGAGAGAAACAATTCTCACG
195 CAAGAGAGAAACAATTCTCACG
* **
882 TAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAGAATGACAAAA-TATTTAGACCTGAT
1 TAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGA-AAAACTATTTAGACCAAAT
* * * * * * * *
946 GATTCGATTTCTAGAGCATGGAATGTTTGGAATATTGCTTGAAAGAATGGATCGCCTTGAATACT
65 GATGCGATTTCTCGAGCATGGAATGTTCGAAAAATTGCTAGAAAGAATGGATCGCATAGAATACT
* * * * *
1011 TTAAGGAACCAATGTTATAAAAGAACTCGTAAAAGCTTGAAAAGT-TAAGAAGTTCATCTAAGAA
130 TTAAGGAACCAAGGTTATAAAAGAACTCGTAAAAGTTTGACAAGTCT-GGAAGTTCATCCAAGAA
*
1075 CCAGGAGAGAAACAATTCTCACG
194 CCAAGAGAGAAACAATTCTCACG
* *
1098 TAAATAAG-TTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAGTG
1 TAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATG
* ** * * * *
1162 ATGCAATTTCTCGAGCATGGAATGTTCTCAAAATTGCTCG-AAGAAATGGATCATC-TTGAATAG
66 ATGCGATTTCTCGAGCATGGAATGTTCGAAAAATTGCTAGAAAG-AATGGATC-GCATAGAATAC
* * *** ** ** *
1225 TTTAAGGAACCAAAGTTATAATAGAAAGAGTAAAAGTTTTCCTCGT-TCGAAAGTT-AGTCCAAG
129 TTTAAGGAACCAAGGTTATAAAAGAACTCGTAAAAGTTTGACAAGTCT-GGAAGTTCA-TCCAAG
* *
1288 AACCAGGAGAGAAACAATT-TACACA
192 AACCAAGAGAGAAACAATTCT-CACG
* ** * * ** ** *
1313 TAAATAAGTATTTAATTCAGTGACCGAAAGTTTTTTTGAGAAATGGCAAACTACTTT-GACCGAA
1 TAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACA-AAATGAAAAACTA-TTTAGACCAAA
* ** * * * * *
1377 TGATGCGATTTC-CAGAGCATGGAATGTTCGGAATCTTGCTTGAAGGATTGGATCATC-TTGAAT
64 TGATGCGATTTCTC-GAGCATGGAATGTTCGAAAAATTGCTAGAAAGAATGGATC-GCATAGAAT
* * * * * * **
1440 ACTTTACGGAACCAAAGTTATTATAGAAGAAATAGTAAAA-TATTGACAA-TTTCAGAAGTTTGT
127 ACTTTAAGGAACCAAGGTTA-TA-A-AAGAACTCGTAAAAGT-TTGACAAGTCT-GGAAGTTCAT
* * * * * *
1503 CAAAGAATCAAAAAGAGAAATAATTCTAACA
187 CCAAGAA-CCAAGAGAGAAACAATTCTCACG
* * * *
1534 TAAATATA-TTTTTAATTCAAACACCAAAAAGTTGTTTGCAAAATGACAAAGTATTTAGACC
1 TAAATA-AGTTTTTAATTCAAAGACC-AAAAGTTGTTTACAAAATGAAAAACTATTTAGACC
1595 GA
Statistics
Matches: 1102, Mismatches: 218, Indels: 103
0.77 0.15 0.07
Matches are distributed among these distances:
214 8 0.01
215 192 0.17
216 328 0.30
217 108 0.10
218 22 0.02
219 7 0.01
220 38 0.03
221 198 0.18
222 28 0.03
223 55 0.05
224 116 0.11
225 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (216 bp):
TAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATG
ATGCGATTTCTCGAGCATGGAATGTTCGAAAAATTGCTAGAAAGAATGGATCGCATAGAATACTT
TAAGGAACCAAGGTTATAAAAGAACTCGTAAAAGTTTGACAAGTCTGGAAGTTCATCCAAGAACC
AAGAGAGAAACAATTCTCACG
Done.