Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011622.1 Kokia drynarioides strain JFW-HI SEQ_126613, 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: 2132
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.23
Found at i:1520 original size:205 final size:205
Alignment explanation
Indices: 1164--1686 Score: 904
Period size: 205 Copynumber: 2.6 Consensus size: 205
1154 GATTATCCAT
1164 AAAC-AACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC
1 AAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC
* *
1228 GATGTGAGCAAATCTTCGAACCCCGGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAA
66 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAA
* * *
1293 AAGGTTAGCTTCCTTATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAG
131 AAGGTTAGCTTCCTGATGAGATACTAAGAAATGAACCAAATTCGTCTTCCTGATGAGATACAGAG
1358 AAGAGAAATG
196 AAGAGAAATG
* *
1368 AAACAAACGACGTAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACTCACGCTC
1 AAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC
*
1433 GATGTGAGCAAATCTTCGAACCCCAGTTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAA
66 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAA
* *
1498 AAGGTTAGCTTCCTGATGAGATACTGAGAAATGAACCAAATTCGTCTTCCTGATGAGATATAGAG
131 AAGGTTAGCTTCCTGATGAGATACTAAGAAATGAACCAAATTCGTCTTCCTGATGAGATACAGAG
* *
1563 AAGCGAATTG
196 AAGAGAAATG
* *
1573 AAACAAACGACACAGTCATCTTCCTGATGAGATACTGAGAAGAAGACTAAATCAAACTCACGCTC
1 AAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC
*
1638 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGATATACTGAGAAG
66 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAG
1687 TGGACCAAAT
Statistics
Matches: 300, Mismatches: 18, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
204 4 0.01
205 296 0.99
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (205 bp):
AAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTC
GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAA
AAGGTTAGCTTCCTGATGAGATACTAAGAAATGAACCAAATTCGTCTTCCTGATGAGATACAGAG
AAGAGAAATG
Found at i:1844 original size:158 final size:158
Alignment explanation
Indices: 1504--1844 Score: 529
Period size: 158 Copynumber: 2.2 Consensus size: 158
1494 ATAAAAGGTT
* * *
1504 AGCTTCCTGATGAGATACTGAGAAATGAACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGA
1 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGA
* *
1569 ATTGAAACAAACGACACAGTCATCTTCCTGATGAGATACTGAGAAGAAGACTAAATCAAACTCAC
66 ATTGAAACAAACGACACAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
1634 GCTCGATGTGAGCAAATCTTCGAACCCC
131 GCTCGATGTGAGCAAATCTTCGAACCCC
* * * * * *
1662 AGCTTCCTGATGATATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGGTACAAAGAAGTGG
1 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGA
* * * *
1727 ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTGAAACCCAC
66 ATTGAAACAAACGACACAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
1792 GCTCGATGTGAGCAAATCTTCGAACCCC
131 GCTCGATGTGAGCAAATCTTCGAACCCC
* *
1820 AGCTTCCTGATGAGACACCGAGAAG
1 AGCTTCCTGATGAGATACTGAGAAG
1845 CAGGTCGATG
Statistics
Matches: 165, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
158 165 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (158 bp):
AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGA
ATTGAAACAAACGACACAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
GCTCGATGTGAGCAAATCTTCGAACCCC
Found at i:1945 original size:208 final size:206
Alignment explanation
Indices: 1662--2094 Score: 543
Period size: 208 Copynumber: 2.1 Consensus size: 206
1652 TTCGAACCCC
* * * * *
1662 AGCTTCCTGATGATATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGGTACAAAGAAGTGG
1 AGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTGA
* * * * * *
1727 ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTGAAACCCAC
66 ACTAAAACAAACGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATCAAACCC-C
* *
1792 -GCTCGATGT-GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGATG
130 TGCTCAAT-TCGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACCGAGAAGCAGGTCGA--
*
1855 TGAGAATAAAATG-TT
192 -AAGAATAAAATGATT
*
1870 AGCTTCTTGATGAGATA-TGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCT
1 AGCTTCTTGATGAGATACT-GAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAG-T
*
1934 -AACTAAAACAAATGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATCAAACCC
64 GAACTAAAACAAACGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATCAAACCC
* * ****
1998 CTTCTCAATTCGAGCGAATCTTCGAACCCCAACTTCCTGATGAGATGTTGAGAAGCAGGTCGAAA
129 CTGCTCAATTCGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACCGAGAAGCAGGTCGAAA
*
2063 TAATAAAATGAATT
194 GAATAAAATG-ATT
*
2077 AGCTTCTTGATGAAATAC
1 AGCTTCTTGATGAGATAC
2095 GGGGAAGTAA
Statistics
Matches: 194, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
205 10 0.05
207 21 0.11
208 162 0.84
209 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (206 bp):
AGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTGA
ACTAAAACAAACGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATCAAACCCCT
GCTCAATTCGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACCGAGAAGCAGGTCGAAAGA
ATAAAATGATT
Found at i:2052 original size:366 final size:363
Alignment explanation
Indices: 1301--2052 Score: 1062
Period size: 363 Copynumber: 2.1 Consensus size: 363
1291 AAAAGGTTAG
* * *
1301 CTTCCTTATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGAGAAA
1 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGAGAAA
* *
1366 TGAAACAAACGACGTAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACTCACGC
66 TGAAACAAACGACGCAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCCACGC
* * *
1431 TCGATGTGAGCAAATCTTCGAACCCCAGTTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAAT
131 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGGCAAAGCAAT
*
1496 AAAAGGTTAGCTTCCTGATGAGATACTGAGAAATGAACCAAATTCGTCTTCCTGATGAGATATAG
196 AAAAGGTTAGCTTCCTGATGAGATACTGAGAAATGAACCAAATTCGTCTTCCTGATGAGATACAG
* * * *
1561 AGAAGCGAATTGAAACAAACGACACAGTCATCTTCCTGATGAGATACTGAGAAGAAGACTAAATC
261 AGAAGCGAACTAAAACAAACGACACAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATC
* *
1626 AAACTCACGCTCGATGTGAGCAAATCTTCGAACCCCAG
326 AAACTCACGCTCAATGTGAGCAAATCTTCGAACCCCAA
* * * * * *
1664 CTTCCTGATGATATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGGTACAAAGAAGTGGAT
1 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGAGAAA
* * * *
1729 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTGAAACCCACGC
66 TGAAACAAACGACGCAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCCACGC
* *
1794 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGATGTGAG
131 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGGC-A---AAG
* * * *
1859 -AATAAAATGTTAGCTTCTTGATGAGATA-TGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
192 CAATAAAAGGTTAGCTTCCTGATGAGATACT-GAGAAATGAACCAAATTCGTCTTCCTGATGAGA
* * *
1922 TACAGAGAAGCTAACTAAAACAAATGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACC
256 TACAGAGAAGCGAACTAAAACAAACGACACAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACC
* * *
1987 AAATCAAAC-CCCTTCTCAAT-TCGAGCGAATCTTCGAACCCCAA
321 AAATCAAACTCAC-GCTCAATGT-GAGCAAATCTTCGAACCCCAA
**
2030 CTTCCTGATGAGATGTTGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
2053 CAGGTCGAAA
Statistics
Matches: 342, Mismatches: 40, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
363 168 0.49
364 1 0.00
365 4 0.01
366 167 0.49
367 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (363 bp):
CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGAGAAA
TGAAACAAACGACGCAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCCACGC
TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGGCAAAGCAAT
AAAAGGTTAGCTTCCTGATGAGATACTGAGAAATGAACCAAATTCGTCTTCCTGATGAGATACAG
AGAAGCGAACTAAAACAAACGACACAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATC
AAACTCACGCTCAATGTGAGCAAATCTTCGAACCCCAA
Found at i:2119 original size:366 final size:356
Alignment explanation
Indices: 1301--2052 Score: 927
Period size: 366 Copynumber: 2.1 Consensus size: 356
1291 AAAAGGTTAG
* * * * * * *
1301 CTTCCTTATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGAGAAA
1 CTTCCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCTTGATGAAATACAAAGAAGTG--A
* *
1366 TGAAACAAACGACGTAGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACTCACGC
64 T-AAACAAAC-AC--CG-CATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCCACGC
* * *
1431 TCGATGTGAGCAAATCTTCGAACCCCAGTTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAAT
124 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGGCAAAGCAAT
*
1496 AAAAGGTTAGCTTCCTGATGAGATACTGAGAAATGAACCAAATTCGTCTTCCTGATGAGATATAG
189 AAAAGGTTAGCTTCCTGATGAGATACTGAGAAATGAACCAAATTCGTCTTCCTGATGAGATACAG
* * * *
1561 AGAAGCGAATTGAAACAAACGACACAGTCATCTTCCTGATGAGATACTGAGAAGAAGACTAAATC
254 AGAAGCGAACTAAAACAAACGACACAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATC
* *
1626 AAACTCACGCTCGATGTGAGCAAATCTTCGAACCCCAG
319 AAACTCACGCTCAATGTGAGCAAATCTTCGAACCCCAA
* * **
1664 CTTCCTGATGATATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGGTACAAAGAAGTGGAT
1 CTTCCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCTTGATGAAATACAAAGAAGT-GA-
* * *
1729 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTGAAACCCACGC
64 T-AAACAAAC-AC-C-G-CATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCCACGC
* *
1794 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGATGTGAG
124 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGGC-A---AAG
* * * *
1859 -AATAAAATGTTAGCTTCTTGATGAGATA-TGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
185 CAATAAAAGGTTAGCTTCCTGATGAGATACT-GAGAAATGAACCAAATTCGTCTTCCTGATGAGA
* * *
1922 TACAGAGAAGCTAACTAAAACAAATGACGCAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACC
249 TACAGAGAAGCGAACTAAAACAAACGACACAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACC
* * *
1987 AAATCAAAC-CCCTTCTCAAT-TCGAGCGAATCTTCGAACCCCAA
314 AAATCAAACTCAC-GCTCAATGT-GAGCAAATCTTCGAACCCCAA
**
2030 CTTCCTGATGAGATGTTGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
2053 CAGGTCGAAA
Statistics
Matches: 341, Mismatches: 38, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
362 1 0.00
363 165 0.48
364 2 0.01
365 4 0.01
366 167 0.49
367 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (356 bp):
CTTCCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCTTGATGAAATACAAAGAAGTGATA
AACAAACACCGCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAAACCCACGCTCGATGT
GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGGCAAAGCAATAAAAGGT
TAGCTTCCTGATGAGATACTGAGAAATGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
AACTAAAACAAACGACACAGTCATCTTCCTGAAGAGATACTGAGAAGAAGACCAAATCAAACTCA
CGCTCAATGTGAGCAAATCTTCGAACCCCAA
Done.