Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004253.1 Kokia drynarioides strain JFW-HI SEQ_117537, 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: 1797
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:703 original size:221 final size:221
Alignment explanation
Indices: 1--1797 Score: 2499
Period size: 221 Copynumber: 8.0 Consensus size: 221
** *
1 TGAAATTGTTGATGTGGCATAAAACTATTGGAAAGGGATAATATCTTTGTGTCATACAATCCTTT
1 TGAAATTGTTGATGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTT
* * ** *
66 CTCTTCTTCAATGGAAAAGAATTGAATGAAACAGTGGCACCACGTCATTTGTGTTTCTTTTCCAA
66 CTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAT
* *
131 TAGTTTTACGCCACATCAGTATTTTGATTCTTAATTTTAACATTTTCATCCTGAAAAAATCAAAT
131 TAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAAT
* *
196 TAAAATTAAAATCCTGAAATACAGGA
196 TAAAATTAAAATCCTAAAATTCAGGA
* *
222 TGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTTATACAATCCTTT
1 TGAAATTGTTGATGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTT
* **
287 CTCCTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCAC-TCATTTGTGTATCTTTTCCAT
66 CTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAT
* *
351 TAGTTTTACGCCACATCCGTATTTTCATTCTTAATTTCAACATTTACATCCTGAAAAAATCAAAT
131 TAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAAT
* * *
416 TAAAATCAAAATCCAAAAATACAGGA
196 TAAAATTAAAATCCTAAAATTCAGGA
* *
442 TGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTTATGA-AATCCTT
1 TGAAATTGTTGATGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTCAT-ACAATCCTT
* * * *
506 TCTCCTCTTCAATGGAAATGAATTGAATGAAATAGTGACACCACGTCATTTGTGTCCCTTTTCCA
65 TCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCA
* * * * *
571 TTAGTTTTACGGCACATCAGTATTTTCATTCTTAATTTTAACATTTTCGTCCTGTAAAAATTAAA
130 TTAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAA
**
636 TTAAAATTAAAATCCTAAAATTCAAAA
195 TTAAAATTAAAATCCTAAAATTCAGGA
* *
663 TGAAATTGTTGATGTGGCATAAAACAATTGGAAAGGGATAATATCCCTGTTTCAGACAATCCTTT
1 TGAAATTGTTGATGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTT
* * * * *
728 CTCTTCTTCAATGGAAAATGATTGAATGAAACAGCGACACAACGTCATTTGAGTCCCTTTTCCAA
66 CTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAT
* * *
793 AAATTTTACGCCACATCAGTATTTTCATTCTTAAATTT-AACATTTTCATCCTGTAAAAATCAAA
131 TAGTTTTACGCCACATCAGTATTTTCATTCTT-AATTTCAACATTTTCATCCTGAAAAAATCAAA
*
857 TTAAAATTAAAATCCTGAAATTCAGGA
195 TTAAAATTAAAATCCTAAAATTCAGGA
* *
884 TGAAATTATTGATGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTTATACAATCCTTT
1 TGAAATTGTTGATGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTT
* * * * *
949 CTCTTCTTCAATGGGAAAGGATTGAATGAAAAAGTGACACCAAGTCATTTGTGTCCCTTTTCTAA
66 CTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAT
*
1014 TAGTTTTACGCCATATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAAT
131 TAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAAT
*
1079 TAAAATTAAAATCC-AGAAATACAGGA
196 TAAAATTAAAATCCTA-AAATTCAGGA
* *
1105 TGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTTATACAATCCTTT
1 TGAAATTGTTGATGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTT
* *
1170 CTCCTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTACCTTTTCCAT
66 CTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAT
* * * *
1235 TAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTTATCCTGAAAAATTAAAAT
131 TAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAAT
* * **
1300 TAAAATTAAAATCCTGAAATTGAAAA
196 TAAAATTAAAATCCTAAAATTCAGGA
1326 TGAAATTGTTGATGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTT
1 TGAAATTGTTGATGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTT
* *
1391 CTCTTCTTCAATGGAAAATGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCTAT
66 CTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAT
* * * * *
1456 T-GTTTTTATGCCACATCAATATATTCATTCTTAATGTCAACATTTTCATCCTGAGAAAATCAAA
131 TAG-TTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAA
*
1520 TTAAAATTAAAATCCTAAAATTTAGGA
195 TTAAAATTAAAATCCTAAAATTCAGGA
* * *
1547 TGAAATTGTTGGTGTGGCATAAAGCTATTGGAAAGGGATAATATCCTTGTTTCATACAATCCTTT
1 TGAAATTGTTGATGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTCATACAATCC-TT
* * * *
1612 CTCATCTTCAATGGAAAATGATTTAATAAAATGGAAAAGGATTGAATAAAAAAGTGAAACCACGT
65 -TC-TCTTC--------------T--T-CAATGGAAAAGGATTGAATGAAACAGTGACACCACGT
* * * * *
1677 CATTTGTGTCCCTTTGT-TAATAATTTTACGCTACATAAGTATTTTCATTCTTAATTTCAACATT
111 CATTTGTGTCCCTTT-TCCATTAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACATT
* * * *
1741 TACATCCTGAAAAGAAACAAATTAAAATTAAAATCCTGAAATTCAAGA
175 TTCATCCTGAAAA-AATCAAATTAAAATTAAAATCCTAAAATTCAGGA
1789 TGAAATTGT
1 TGAAATTGT
Statistics
Matches: 1414, Mismatches: 131, Indels: 41
0.89 0.08 0.03
Matches are distributed among these distances:
220 213 0.15
221 1049 0.74
222 7 0.00
223 2 0.00
224 5 0.00
238 1 0.00
240 1 0.00
241 96 0.07
242 40 0.03
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (221 bp):
TGAAATTGTTGATGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTT
CTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAT
TAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAAT
TAAAATTAAAATCCTAAAATTCAGGA
Found at i:1646 original size:20 final size:20
Alignment explanation
Indices: 1621--1662 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1611 TCTCATCTTC
* *
1621 AATGGAAAATGATTTAATAA
1 AATGGAAAAGGATTGAATAA
1641 AATGGAAAAGGATTGAATAA
1 AATGGAAAAGGATTGAATAA
1661 AA
1 AA
1663 AAGTGAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.24
Consensus pattern (20 bp):
AATGGAAAAGGATTGAATAA
Done.