Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010031.1 Kokia drynarioides strain JFW-HI SEQ_124799, 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: 2554
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Found at i:1329 original size:96 final size:96
Alignment explanation
Indices: 1158--1331 Score: 219
Period size: 96 Copynumber: 1.8 Consensus size: 96
1148 TTTGATTATC
** * *
1158 TCGATTTGAAGAAAGGTCGCACCTAGTAAGTTAAGGCGCAATATTTCGAAATCGAAGATAAGAAA
1 TCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCGAAATATTTCGAAACCGAAGATAAGAAA
*
1223 ACATTTCCTCGATTAACGGTATTCGATTACT
66 ACATTGCCTCGATTAACGGTATTCGATTACT
* * *
1254 TCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGTAAAT-TTTCGGAACCCGAA-ATAA-A
1 TCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCG-AAATATTTC-GAAACCGAAGATAAGA
*
1316 AGAATATTGCCTCGAT
64 A-AACATTGCCTCGAT
1332 ATTAAAGATT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
95 2 0.03
96 54 0.82
97 10 0.15
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (96 bp):
TCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCGAAATATTTCGAAACCGAAGATAAGAAA
ACATTGCCTCGATTAACGGTATTCGATTACT
Found at i:1686 original size:59 final size:59
Alignment explanation
Indices: 1597--2117 Score: 570
Period size: 59 Copynumber: 8.9 Consensus size: 59
1587 ATGTTCGGAA
* * * * *
1597 TCAAAAAT-AGGA-TTTTGGAAGTTCGAGGGTAAAATGGTAATTTTCAAAAGGTCCGAGG
1 TCAAAAATGA-GATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
* *
1655 TCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAAAAGATCCGAGG
1 TCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
* * * * * * *
1714 TCAAAAATGGGAATTTTGGAAGTTCAGGGGTAAAATGGTAA-TTATAAAAAAGTTCGGGG
1 TCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGA-TTCGAGG
* * * *
1773 TCAAAAATGAGATTTTTGGAAGTTTGAGGGTAAAAAGGTAATTTTTAGAAGATTCAAGG
1 TCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
* * * *
1832 TCAAAAATGAGATTTTTGGGAGTACGAGGGTAAAATGGTAATTTTTAGAAGGTTCG-GG
1 TCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
* * ** * * *
1890 -CTAAAAATGGGAATTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGATTTGGGG
1 TC-AAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
* * * * *
1949 TCAAAAATGGGATTTTTGGGAGTGT-GAGGGTAAAATGGTCATTTTTAGAAGGTTCG-GG
1 TCAAAAATGAGATTTTTGGAAGT-TCGGGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
* * * *
2007 GCTAAAAATGAGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTTGAAGATTCGTGG
1 TC-AAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
* * * *
2067 TAAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATTGTAATTTTTGGAAG
1 TCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAG
2118 GTTTAGGGAC
Statistics
Matches: 393, Mismatches: 59, Indels: 21
0.83 0.12 0.04
Matches are distributed among these distances:
57 1 0.00
58 68 0.17
59 313 0.80
60 11 0.03
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (59 bp):
TCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
Found at i:1847 original size:30 final size:30
Alignment explanation
Indices: 1771--1848 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
1761 AAAAGTTCGG
* * * *
1771 GGTCAAAAATGAGATTTTTGGAAGTTTGAG
1 GGTCAAAAATGAGATTTTTAGAAGATTCAA
*
1801 GGT-AAAAAGGTA-ATTTTTAGAAGATTCAA
1 GGTCAAAAATG-AGATTTTTAGAAGATTCAA
1830 GGTCAAAAATGAGATTTTT
1 GGTCAAAAATGAGATTTTT
1849 GGGAGTACGA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 23 0.59
30 16 0.41
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.33
Consensus pattern (30 bp):
GGTCAAAAATGAGATTTTTAGAAGATTCAA
Found at i:1982 original size:235 final size:236
Alignment explanation
Indices: 1597--2120 Score: 666
Period size: 235 Copynumber: 2.2 Consensus size: 236
1587 ATGTTCGGAA
* * *
1597 TCAAAAAT-AGGA-TTTTGGAAGTTCGAGGGTAAAATGGTAATTTTCAAAAGGTCCGAGGTCAAA
1 TCAAAAATGA-GATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAA
* *
1660 AATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAAAAGATCCGAGGTCAAAAATGGG
65 AATGAGAATTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTAAAAGATCCGAGGTCAAAAATGGG
1725 AATTTTGGAAGTTCAGGGGTAAAATGGTAATTATAAAAAAGTTCGGGG-TCAAAAATGAGATTTT
130 AATTTTGGAAGTTCAGGGGTAAAATGGTAATTATAAAAAAGTTCGGGGCT-AAAAATGAGATTTT
*
1789 TGGAAGTT-TGAGGGTAAAAAGGTAATTTTTAGAAGATTCAAGG
194 TGGAAGTTCAG-GGGTAAAAAGGTAATTTTTAGAAGATTCAAGG
* *
1832 TCAAAAATGAGATTTTTGGGAGTACGAGGGTAAAATGGTAATTTTTAGAAGGTTCG-GG-CTAAA
1 TCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTC-AAA
* * ** ** *
1895 AATGGGAATTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGATTTGGGGTCAAAAATGGG
65 AATGAGAATTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTAAAAGATCCGAGGTCAAAAATGGG
* * * * * * * *
1960 ATTTTTGGGAGTGTGA-GGGTAAAATGGTCATTTTTAGAAGGTTCGGGGCTAAAAATGAGATTTT
130 AATTTTGGAAGT-TCAGGGGTAAAATGGTAATTATAAAAAAGTTCGGGGCTAAAAATGAGATTTT
* * **
2024 TGGAAGTTCAGGGGTAAAATGGTAATTTTTTGAAGATTCGTGG
194 TGGAAGTTCAGGGGTAAAAAGGTAATTTTTAGAAGATTCAAGG
* * * * *
2067 TAAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATTGTAATTTTTGGAAGGTT
1 TCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTT
2121 TAGGGACCTC
Statistics
Matches: 249, Mismatches: 34, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
234 1 0.00
235 205 0.82
236 43 0.17
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (236 bp):
TCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAA
ATGAGAATTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTAAAAGATCCGAGGTCAAAAATGGGA
ATTTTGGAAGTTCAGGGGTAAAATGGTAATTATAAAAAAGTTCGGGGCTAAAAATGAGATTTTTG
GAAGTTCAGGGGTAAAAAGGTAATTTTTAGAAGATTCAAGG
Found at i:2118 original size:118 final size:118
Alignment explanation
Indices: 1597--2120 Score: 664
Period size: 118 Copynumber: 4.5 Consensus size: 118
1587 ATGTTCGGAA
* * * * *
1597 TCAAAAATAGGA-TTTTGGAAGTTCGAGGGTAAAATGGTAATTTTCAAAAGGTCCGAGGTCAAAA
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAA
* * *
1661 ATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAAAAGATCCGAGG
66 ATGAGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
* * * * *
1714 TCAAAAATGGGAATTTTGGAAGTTC-AGGGGTAAAATGGTAATTATAAAAAAGTTCGGGGTCAAA
1 TCAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAA
* * *
1778 AATGAGATTTTTGGAAGTT-TGAGGGTAAAAAGGTAATTTTTAGAAGATTCAAGG
65 AATGAGATTTTTGGAAGTTCAG-GGGTAAAATGGTAATTTTTAGAAGATTCGAGG
* * * *
1832 TCAAAAATGAGATTTTTGGGAGTACGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGCT-AAAA
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAA
* * * * * *
1896 ATGGGAATTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGATTTGGGG
66 ATGAGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
* *
1949 TCAAAAATGGGATTTTTGGGAGTGT-GAGGGTAAAATGGTCATTTTTAGAAGGTTCGGGG-CTAA
1 TCAAAAATGGGATTTTTGGAAGT-TCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTC-AA
* *
2012 AAATGAGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTTGAAGATTCGTGG
64 AAATGAGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
* * * *
2067 TAAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATTGTAATTTTTGGAAGGTT
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTT
2121 TAGGGACCTC
Statistics
Matches: 354, Mismatches: 44, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
117 115 0.32
118 238 0.67
119 1 0.00
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (118 bp):
TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAA
ATGAGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
Done.