Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013337.1 Kokia drynarioides strain JFW-HI SEQ_128359, 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, 760
Length: 1268
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Found at i:1012 original size:426 final size:430
Alignment explanation
Indices: 89--1268 Score: 1251
Period size: 426 Copynumber: 2.8 Consensus size: 430
79 AGGAACATAT
* *
89 CGTCTTGAATACTGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAATGTGACAAGTTCGGAAG
1 CGTCTTGAATACTGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAG
* * * *
154 TTTGTCCAAGAACC--AAGCGAAACAATTCTCACATAAATAAGTTTTTGATTCAAAGACCAAAAC
66 TTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAG-TTTTAATTCAAAGACCAAAA-
* * * * * * *
217 TTGTTTTT--AAAATGACAAACTCTTGAGACCAAATGCTGCCATTTCTCAAGAATTGAATGTTTA
129 TT-TTTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCAAGCATAGAATGTTAA
* * * * * * * *
280 GAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTATGGAACCGAAGATATGAAAGTACTTG
193 GAAAATTGCTAGAAGGAATGAATCGTCTTGAATACTATAAGGAACCGAAGTTATAAAAGAACTCG
* * * *
345 TAAAAGTTTGACTAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAGCAATTCTCACGTAAATAA
258 TAAAAGTTTGAATAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAA-CAATCCTCACGAAAATAA
* *
410 GTTTATAATTCAAACAACAAAACCTTTTAACAAAATGACAAATTATTTAGACCAAATGATACGAT
322 GTTTATAATTCAAACAACAAAACCGTTTAACAAAATGACAAACTATTTAGACCAAATGATACGAT
** * * * *
475 TTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGAT
387 TTCCCGAAAATGGAATGTTCGAAAAATTCCTCAAAAGAATGGAA
* ** * * * * * *
519 CATCAAGAATACTTTATGGAACTGAAATTATAAAAGAACTCGTAAAAGTTTGATAAGTTCAGAAG
1 CGTCTTGAATACTGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAG
*
584 TTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAAAAAGTATTTAATTCAAAGACCAAAAG
66 TTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGT-TTTAATTCAAAGACCAAAA-
* * * *
649 TTTTTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAG
129 TTTTTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCAAGCATAGAATGTTAAG
* * * * * *
714 AAACTTGCTTGATGGAACGAATCGTCTTGAATACTACAAGGAA-CGGAGTTATAAAAGAACTCGT
194 AAAATTGCTAGAAGGAATGAATCGTCTTGAATACTATAAGGAACCGAAGTTATAAAAGAACTCGT
* * * * *
778 AAAAGTTTGAA-ATGTTTTG-AAGTTTGTCCAACAGCCAAGA-A-AA-AATCCTCAGGAAAATAT
259 AAAAGTTTGAATA-G-TTCGAAAGTTCGTCCAACAACCAAGAGAGAACAATCCTCACGAAAATAA
** * ** * * * * **
838 GTTCT-TGTTTTAATGATCAAAACTCGTTT-ACAAAATTA-AGACCTATTTAGACTAAATGATGT
322 GTT-TATAATTCAAACAACAAAAC-CGTTTAACAAAATGACA-AACTATTTAGACCAAATGATAC
* *
900 GATTTCCCGAAAATTGAAT-TT-TAAAAATTCCTCAAAAGAATGGAA
384 GATTTCCCGAAAATGGAATGTTCGAAAAATTCCTCAAAAGAATGGAA
* * *
945 CGTCTTGAATACTGTAAGGAACCGAAGTTATAAATGAACTGGTAAAAGTTTGACAAGTTTGGAAG
1 CGTCTTGAATACTGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAG
* * * * *
1010 TTCATCAAAGAACAAAGAGAGAGAAACAATTCTCACGTAAATAAGTTTTAAATTTAAAGACTAAA
66 TTCGTCCAAGAACCAA-A-AGAGAAACAATTCTCACGTAAATAAGTTTT-AATTCAAAGACCAAA
* * * * * *
1075 ACTTGTTTACAAAATGACAAACAATTTAGA-AAAATGATGCGATTTTTCTAGCATAGAATGTTAA
128 ATTTTTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCAAGCATAGAATGTTAA
* * *
1139 GAAAGTTGCTAGAAGGATTGCATCGTCTTGAATACTATAAGGAACCGAAGTTATAAAAGAACTCG
193 GAAAATTGCTAGAAGGAATGAATCGTCTTGAATACTATAAGGAACCGAAGTTATAAAAGAACTCG
* * * * * * * *
1204 TAAAAGTGTGACTAGTTCGGAAGTTTGTCCAAGAACCAAGCGA-AACAATTCTCACGTAAATAAG
258 TAAAAGTTTGAATAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAACAATCCTCACGAAAATAAG
1268 T
323 T
Statistics
Matches: 618, Mismatches: 114, Indels: 37
0.80 0.15 0.05
Matches are distributed among these distances:
426 153 0.25
427 81 0.13
428 113 0.18
429 20 0.03
430 69 0.11
431 8 0.01
432 89 0.14
433 85 0.14
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (430 bp):
CGTCTTGAATACTGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAG
TTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTAATTCAAAGACCAAAATT
TTTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCAAGCATAGAATGTTAAGAA
AATTGCTAGAAGGAATGAATCGTCTTGAATACTATAAGGAACCGAAGTTATAAAAGAACTCGTAA
AAGTTTGAATAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAACAATCCTCACGAAAATAAGTTT
ATAATTCAAACAACAAAACCGTTTAACAAAATGACAAACTATTTAGACCAAATGATACGATTTCC
CGAAAATGGAATGTTCGAAAAATTCCTCAAAAGAATGGAA
Found at i:1192 original size:217 final size:212
Alignment explanation
Indices: 1--1268 Score: 1253
Period size: 216 Copynumber: 5.9 Consensus size: 212
* * **
1 AACTTGTTTACAAAATGACAAACAATTTAGA-AAAATGATGCGATTTTTCGAGCATAGAATGTTA
1 AACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATAGAATGTTA
*** *
65 AGAAAGTTGCTAGAAGGAACATATCGTCTTGAATACTGTAAGGAACCGAAGTTATAAAAGAACTC
66 AGAAA-TTGCTAGAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTATAAAAGAACTC
* * * * * *
130 GTAAAAATGTGACAAGTTCGGAAGTTTGTCCAAGAACCAAGCGAAACAATTCTCACATAAATAAG
130 GTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAAACAATTCTCACGTAAATAAG
*
195 TTTTTGATTCAAAGACCAA
195 -TTTTAATTCAAAGACCAA
** * * * * * * * * *
214 AACTTGTTTTTAAAATGACAAACTCTTGAGACCAAATGCTGCCATTTCTCAAGAATTGAATGTTT
1 AACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATAGAATGTTA
* * * * * * *
279 AGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTATGGAACCGAAGATATGAAAGTACTT
66 AG-AAATTGCTAGAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTATAAAAGAACTC
* * *
344 GTAAAAGTTTGACTAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAGCAATTCTCACGTAAATA
130 GTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA-CAA-AGAGAAACAATTCTCACGTAAATA
* *
409 AGTTTATAATTCAAACAACAA
193 AGTTT-TAATTCAAAGACCAA
* * * *
430 AACCTT-TTAACAAAATGACAAATTATTTAGACCAAATGATACGATTTCCCGAGCATGGAATGTT
1 AA-CTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATAGAATGTT
* * ** * * * *
494 CGAA-AAATTGCTCGAAGGAATGGATCATCAAGAATACTTTATGGAACTGAAATTATAAAAGAAC
65 --AAGAAATTGCTAGAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTATAAAAGAAC
* *
558 TCGTAAAAGTTTGATAAGTTCAGAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAA
128 TCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA-C-AAAGAGAAACAATTCTCACGTAAA
*
623 AAAGTATTTAATTCAAAGACCAA
191 TAAGT-TTTAATTCAAAGACCAA
* * *
646 AAGTTTTTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTT
1 AA-CTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATAGAATGTT
* * * * * * *
711 CAGAAACTTGCTTGATGGAACGAATCGTCTTGAATACTACAAGGAA-CGGAGTTATAAAAGAACT
65 AAGAAA-TTGCTAGAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTATAAAAGAACT
** * * * * * * *
775 CGTAAAAGTTTGA-AATGTTTTGAAGTTTGTCCAACAGCCAAGA-AAA-AATCCTCAGGAAAATA
129 CGTAAAAGTTTGACAA-GTTCGGAAGTTCGTCCAAGAACAAAGAGAAACAATTCTCACGTAAATA
* ** * * *
837 TGTTCTTGTTTTAATGATCAA
193 AGTT-TTAATTCAAAGACCAA
* * * * * ** * *
858 AACTCGTTTACAAAATTA-AGACCTATTTAGACTAAATGATGTGATTTCCCGAAAATTGAATTTT
1 AACTTGTTTACAAAATGACA-AACTATTTAGACCAAATGATGCGATTTCCCGAGCATAGAATGTT
* * * * *
922 AA-AAATTCCTCA-AAAGAATGGAACGTCTTGAATACTGTAAGGAACCGAAGTTATAAATGAACT
65 AAGAAATTGCT-AGAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTATAAAAGAACT
* * * *
985 GGTAAAAGTTTGACAAGTTTGGAAGTTCATCAAAGAACAAAGAGAGAGAAACAATTCTCACGTAA
129 CGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAAC--A-A-AGAGAAACAATTCTCACGTAA
* *
1050 ATAAGTTTTAAATTTAAAGACTAA
190 ATAAGTTTT-AATTCAAAGACCAA
* * ** *
1074 AACTTGTTTACAAAATGACAAACAATTTAGA-AAAATGATGCGATTTTTCTAGCATAGAATGTTA
1 AACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATAGAATGTTA
* *
1138 AGAAAGTTGCTAGAAGGATTGCATCGTCTTGAATACTATAAGGAACCGAAGTTATAAAAGAACTC
66 AGAAA-TTGCTAGAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTATAAAAGAACTC
* * * * *
1203 GTAAAAGTGTGACTAGTTCGGAAGTTTGTCCAAGAACCAAGCGAAACAATTCTCACGTAAATAAG
130 GTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAAACAATTCTCACGTAAATAAG
1268 T
195 T
Statistics
Matches: 855, Mismatches: 170, Indels: 60
0.79 0.16 0.06
Matches are distributed among these distances:
209 29 0.03
210 48 0.06
211 53 0.06
212 27 0.03
213 56 0.07
214 115 0.13
215 42 0.05
216 312 0.36
217 172 0.20
218 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (212 bp):
AACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATAGAATGTTA
AGAAATTGCTAGAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTATAAAAGAACTCG
TAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAAACAATTCTCACGTAAATAAGT
TTTAATTCAAAGACCAA
Done.