Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009868.1 Kokia drynarioides strain JFW-HI SEQ_124602, 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: 2721
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Found at i:500 original size:38 final size:38
Alignment explanation
Indices: 472--586 Score: 230
Period size: 38 Copynumber: 3.0 Consensus size: 38
462 AAGAGTTAAA
472 AATGAAATTGCCATGCCTTTTTAACTACATCAGATCCT
1 AATGAAATTGCCATGCCTTTTTAACTACATCAGATCCT
510 AATGAAATTGCCATGCCTTTTTAACTACATCAGATCCT
1 AATGAAATTGCCATGCCTTTTTAACTACATCAGATCCT
548 AATGAAATTGCCATGCCTTTTTAACTACATCAGATCCT
1 AATGAAATTGCCATGCCTTTTTAACTACATCAGATCCT
586 A
1 A
587 CAATAGTTAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 77 1.00
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.34
Consensus pattern (38 bp):
AATGAAATTGCCATGCCTTTTTAACTACATCAGATCCT
Found at i:1433 original size:216 final size:215
Alignment explanation
Indices: 1060--1990 Score: 1056
Period size: 216 Copynumber: 4.3 Consensus size: 215
1050 CTCATATCAG
* ** * * * *
1060 AACTTGTCGAACATTTTTTGAGTTCTTTTATAACTTTGGTTTCTGAGAGTATTCAAGATGATCCA
1 AACTTGTCAAACATTTACT-AGTTCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGATGATCCA
* * * *
1125 TTCTTTCGACCAATTTTT-GAACATTCCAT-CTCGGGAAATCACGTCATTTGGTCTAAAA-ATTT
65 TTCCTTCGACC-ATTTTTCGAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAAATAGTT
*
1187 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTATCT
129 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCT
*
1252 CTCGGTTCTTGGACGAAGTGT-CG
194 CTCGGTTCTTGGA-GAAGT-TACA
* * *
1275 AACTTGTCAAACATATACTAGTTCTTTTATAACTTCAGTTCCTGATAGTAGTAAAGATGATCCAT
1 AACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGATGATCCAT
* * *
1340 TCCTTCGACCGATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAAAT-GTTT
66 TCCTTCGACC-ATTTTTCGAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAAATAGTTT
*
1404 GTCATTTTGTAAACAACTTTTGATCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTC
130 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTC
* * * *
1469 TCAGTTCTTGGATGACGTTCCT
195 TCGGTTCTTGGA-GAAGTTACA
* * *
1491 AACTT-TCAAACATTTACTAGTTCTTTGATAACTTCGATTCCTAATAGTAGTCAAGATGATCCAT
1 AACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGATGATCCAT
* * *
1555 TCCTTCGACTAATTTTTCGAACATTCCATGATCGAGAAATCGCATCATTTGGTC-AAAATAGTTT
66 TCCTTCGAC-CATTTTTCGAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAAATAGTTT
* * * *
1619 GTCATTTTTGTAAACAACTTTT-GTGCTTTGAATTAAACACTTTTTTATGAGAGAATTGTTTCCC
130 GTCA-TTTTGTAAACAACTTTTGGT-CTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTC
* * **
1683 TTTTGGTTCTTGGAGAAACATACA
193 TCTCGGTTCTTGGAG-AAGTTACA
* * * * * * *
1707 AACTAGT-AAAAATTTTACAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCA
1 AACTTGTCAAACA-TTTACTAGTTCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGATGATCCA
* * * * *
1771 ATCATTTGAGCATTTTTCGAACATTCTATGCT-GAGAAATCACATCATTTGGTCT-AAATAGTTT
65 TTCCTTCGACCATTTTTCGAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAAATAGTTT
** * ** *
1834 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAATGCTTATTTACGTGAGAATTGTAACTCGC
130 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTC
* * **
1899 TTGGTTATTGGATGAACATACA
195 TCGGTTCTTGGA-GAAGTTACA
* * * * * * * * *
1921 AACTAGTCAAACTTTTACAAGTCCTTTTATAACTTCGGTTCTTGAGAGTATTTAAGACGATCCAT
1 AACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGATGATCCAT
1986 TCCTT
66 TCCTT
1991 TGACTTATTT
Statistics
Matches: 620, Mismatches: 81, Indels: 31
0.85 0.11 0.04
Matches are distributed among these distances:
214 184 0.30
215 178 0.29
216 207 0.33
217 51 0.08
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (215 bp):
AACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGATGATCCAT
TCCTTCGACCATTTTTCGAACATTCCATGCTCGAGAAATCACATCATTTGGTCTAAAATAGTTTG
TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCT
CGGTTCTTGGAGAAGTTACA
Found at i:2025 original size:25 final size:25
Alignment explanation
Indices: 1979--2027 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1969 TATTTAAGAC
* **
1979 GATCCATTCCTTTGACTTATTTTTT
1 GATCCATTCCTTCGACCAATTTTTT
*
2004 GATCCATTTCTTCGACCAATTTTT
1 GATCCATTCCTTCGACCAATTTTT
2028 CGAACATTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.18, C:0.22, G:0.08, T:0.51
Consensus pattern (25 bp):
GATCCATTCCTTCGACCAATTTTTT
Found at i:2635 original size:215 final size:214
Alignment explanation
Indices: 2003--2709 Score: 749
Period size: 216 Copynumber: 3.3 Consensus size: 214
1993 ACTTATTTTT
* * **
2003 TGATCCATTTCTTCGACCAATTTTTCGAACATTCCATGATCGGGAAATCGCATCATTTGGTCAAA
1 TGATCCATTCCTTCAACCAATTTTTCGAACATTCCATGATCGGGAAATCGCATCATTTGGTCTTA
* * * * * * * *
2068 ATAATTTGTCATTTTGTAAACTACTTTCGGTCTTTGAATTAAAAACTTTTTTACATAAGATTTTT
66 ATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTTTTTACGTGAGAATTGT
* * * * * * * *
2133 TTGTCTATTGGCTCTTTGATGAAATTTCGAACCTATCAAACATTTATGAGTTCTTTTATAACTTT
131 TTCTCCATT-GTTCTTAGATGAAATTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAAC-TT
* * *
2198 GATTCCTTTAAAGTATTCAAGA
194 GGTTCCTGT-GAGTATTCAAGA
** * * * * * *
2220 CAACCCCTTCCTTCAAGC-ATTCTTTCGAACATTCCATGCTTCGGG-TATCACATCATTT-GT-T
1 TGATCCATTCCTTCAACCAATT-TTTCGAACATTCCATG-ATCGGGAAATCGCATCATTTGGTCT
* * * * **
2281 TAAAAAGTTTGTCATTTCGTAAAGAACTTTTGGTCTTTAAATTAAAAACTTGTTTACGTGAGAGC
64 T-AATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTTTTTACGTGAGAAT
* * * * * * *
2346 TGTTTCTCTCTTTCTTCTTGGATGAAATTCTGAACTTGTCAAACATTCACGAGTTCCTCTATAAC
128 TGTTTCTC-CATTGTTCTTAGATGAAATTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAAC
2411 ATTGGTTCCTGTGAGTATTCAAGA
192 -TTGGTTCCTGTGAGTATTCAAGA
* * *
2435 TGATTCATTCCTTCAACCAATTTCTCGTAA-ATTCCATGATCGAGAAATCGCATCATTTGGTCTT
1 TGATCCATTCCTTCAACCAATTTTTCG-AACATTCCATGATCGGGAAATCGCATCATTTGGTCTT
* * * *
2499 AATAGTTTGTCATTTTGGAAACAACTTTTGGTCTTTCAATTAAAAACTTTTTTATGTGTGAATTG
65 AATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTTTTTACGTGAGAATTG
* * * ** *
2564 TTTCTCCCTTGTTCTTAGACGAACTTCCGAACTTGTCAAATTTTTACGAGTACTTTTATAACTTC
130 TTTCTCCATTGTTCTTAGATGAAATTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAACTT-
*
2629 GGTTCCTGAGAGTATTCAAGA
194 GGTTCCTGTGAGTATTCAAGA
* *
2650 TGATCCATTCCTTCAACCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGG
1 TGATCCATTCCTTCAACCAATTTTTCGAACATTCCATGATCGGGAAATCGCATCATTTGG
2710 ACTAAAAAGT
Statistics
Matches: 397, Mismatches: 82, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
214 8 0.02
215 162 0.41
216 180 0.45
217 42 0.11
218 5 0.01
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (214 bp):
TGATCCATTCCTTCAACCAATTTTTCGAACATTCCATGATCGGGAAATCGCATCATTTGGTCTTA
ATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAAACTTTTTTACGTGAGAATTGT
TTCTCCATTGTTCTTAGATGAAATTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAACTTGG
TTCCTGTGAGTATTCAAGA
Done.