Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007806.1 Kokia drynarioides strain JFW-HI SEQ_122441, 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, 965
Length: 1609
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.36
Found at i:570 original size:221 final size:221
Alignment explanation
Indices: 1--1609 Score: 2197
Period size: 221 Copynumber: 7.2 Consensus size: 221
* * * *
1 ATAATATCCTTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTGAACGAAAAAGTGA
1 ATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGA
* * * *
66 CACAACTTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCGCATCAGTATTTTTATTCTTAATTT
66 CACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTTCATTCTTAATTT
* * * * *
131 CATCCTTTTCATCCTGAAAATATCAAATTCAAATTAAAATCCTGAAATTTAGGATGAAATTGTTG
131 CAACATTTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTG
196 GTGTGGCATAAAACTATTGGAAAGGG
196 GTGTGGCATAAAACTATTGGAAAGGG
* * *
222 ATAATATCCCTGTTTTATACAATCC-TT-TCTTCTTCAATGGAAACA-GATTGAATGAAATACTG
1 ATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAA-AGGATTGAATGAAACAGTG
** * *
284 ACACCACGTCATTTGTGTCCCTTTTCTTATAGTTTTACGCCACATCATTTTTTTCATTCTTAATT
65 ACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTTCATTCTTAATT
* * *
349 TTAACATTTTCATCCTGAAAAAATAAAAATAAAATTAAAATCCTGAAATTCAGGATGAAATTGTT
130 TCAACATTTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTT
* * * *
414 GATGAGGCATAAAACTATTGCAAAGTG
195 GGTGTGGCATAAAACTATTGGAAAGGG
* * * * *
441 ATAATTTCACTGTTTAATACAGTCCTTTCTCTTCTTCAACGGAAAAGGATTGAATGAAACAGTGA
1 ATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGA
* * * * *
506 CACCACGTCATCTGTATCCCTTTTCTAATAATTTTACGCCATATCAGTATTTTCATTCTTAATTT
66 CACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTTCATTCTTAATTT
* * *
571 CAACATTTTCATCCTGAAAAAAAT-AAATTAAAATTAAAATCCAGAAATACAGGTTGAAATTGTT
131 CAACATTTTCATCCTG-AAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTT
635 GGTGTGGCATAAAACTATTGGAAAGGG
195 GGTGTGGCATAAAACTATTGGAAAGGG
*
662 ATAATATCCCTCTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGA
1 ATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGA
* * *
727 CACAACGTCATTTGTGTCCCTTTTCCAATAGTTTTACTCCACATCAGTATTTTGATTCTTAATTT
66 CACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTTCATTCTTAATTT
* **
792 CAACATTTTCATCCTGAAAAAATAAAATTAAAATTAAAATCCTGAAATTCAAAATGAAATTGTTG
131 CAACATTTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTG
*
857 CTGTGGCATAAAACTATTGGAAAGGG
196 GTGTGGCATAAAACTATTGGAAAGGG
* * **
883 ATAATATCCTTGTTTCATACAATCCATTCTCTTCTTCAATGGAAAAGGATTGAATGAAACACCGA
1 ATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGA
* ** * *
948 CACCACGTTA-TTGTGTCTTTTTTCCAATTGTTTTACGCCACATCAGTAGTTTCATTCTTAATTT
66 CACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTTCATTCTTAATTT
* *
1012 AAACATTTTCATCCTGAAAAAATCAAATTAAAATTAAAATCTTGAAATTCAGGATGAAATTGTTG
131 CAACATTTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTG
* *
1077 GTGTGGCATAAAACTGTAGGAAAGGG
196 GTGTGGCATAAAACTATTGGAAAGGG
*
1103 ATAATATCCCTGTTTCATACAATTCTTTCTCTTCTTCAATGGAAAATGATTCAATAAAATGGAAA
1 ATAATATCCCTGTTTCATACAA-TC---CT-TTC-TC--T------T-CTTC-----AATGGAAA
* *
1168 AGGATTGAATAAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATTGTTTTACGCCACATC
46 AGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATC
* *
1233 AGTATTTTCATTCTTAATTTTAACATTTTCATCCTTAAAAAATCAAATTAAAATTAAAATCCTGA
111 AGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGA
* * **
1298 AATTTAGGATGAAATTGATGACGTGGCATAAAACTATTGGAAAGGG
176 AATTCAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGG
* * * * *
1344 AAAATATCCCTCTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAAGATTGAATGAAACAATAA
1 ATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGA
* * ** *
1409 CACCATGTTA-TTGTGTCTTTTTTCCAATTA-TTTTACGCCACATCTGTATTTTCATTCTTAATT
66 CACCACGTCATTTGTGTCCCTTTTCCAA-TAGTTTTACGCCACATCAGTATTTTCATTCTTAATT
* *
1472 TAAACATTTTCATCCTGAGAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTT
130 TCAACATTTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTT
**
1537 GGTGTGGCATAAAACTATAAGAAAGGG
195 GGTGTGGCATAAAACTATTGGAAAGGG
*
1564 ATAATATCCCTGTTTCATACAATTCTTTCTCTTCTTCAATGGAAAA
1 ATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAA
Statistics
Matches: 1227, Mismatches: 133, Indels: 57
0.87 0.09 0.04
Matches are distributed among these distances:
219 188 0.15
220 338 0.28
221 482 0.39
222 7 0.01
224 1 0.00
225 3 0.00
226 5 0.00
227 1 0.00
228 1 0.00
233 1 0.00
234 1 0.00
235 5 0.00
236 3 0.00
237 2 0.00
240 36 0.03
241 153 0.12
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.36
Consensus pattern (221 bp):
ATAATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGA
CACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTACGCCACATCAGTATTTTCATTCTTAATTT
CAACATTTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTG
GTGTGGCATAAAACTATTGGAAAGGG
Found at i:1165 original size:20 final size:20
Alignment explanation
Indices: 1140--1181 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1130 TCTCTTCTTC
*
1140 AATGGAAAATGATTCAATAA
1 AATGGAAAAGGATTCAATAA
*
1160 AATGGAAAAGGATTGAATAA
1 AATGGAAAAGGATTCAATAA
1180 AA
1 AA
1182 CAGTGACACC
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:0.02, G:0.19, T:0.21
Consensus pattern (20 bp):
AATGGAAAAGGATTCAATAA
Found at i:1563 original size:461 final size:455
Alignment explanation
Indices: 254--1609 Score: 1972
Period size: 461 Copynumber: 3.0 Consensus size: 455
244 TCCTTTCTTC
* * **
254 TTCAATGGAAACA-GATTGAATGAAATACTGACACCACGTCATTTGTGTCCCTTTTCTTATAGTT
1 TTCAATGGAAA-AGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTT
* * *
318 TTACGCCACATCATTTTTTTCATTCTTAATTTTAACATTTTCATCCTGAAAAAATAAAAATAAAA
65 TTACGCCACATCAGTATTTTCATTCTTAATTTTAACATTTTCATCCTGAAAAAATAAAATTAAAA
* * * * *
383 TTAAAATCCTGAAATTCAGGATGAAATTGTTGATGAGGCATAAAACTATTGCAAAGTGATAATTT
130 TTAAAATCCTGAAATTCAGGATGAAATTGTTGACGTGGCATAAAACTATTGGAAAGGGATAATAT
* * * * *
448 CACTGTTTAATACAGTCCTTTCTCTTCTTCAACGGAAAAGGATTGAATGAAACAGTGACACCACG
195 CCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAATGACACCACG
* * ** * * * *
513 TCATCTGTATCCCTTTTCTAATAATTTTACGCCATATCAGTATTTTCATTCTTAATTTCAACATT
260 TTAT-TGTGTCTTTTTTCCAATTATTTTACGCCACATCAGTATTTTCATTCTTAATTTAAACATT
* * *
578 TTCATCCTGAAAAAAAT-AAATTAAAATTAAAATCCAGAAATACAGGTTGAAATTGTTGGTGTGG
324 TTCATCCTG-AAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGGTGTGG
* *
642 CATAAAACTATTGGAAAGGGATAATATCCCTCTTTCATACAA-TC---CT-TTC-TC--T-----
388 CATAAAACTATAGGAAAGGGATAATATCCCTGTTTCATACAATTCTTTCTCTTCTTCAATGGAAA
*
694 -TC
453 ATA
*
696 TTCAATGGAAAAGGATTGAATGAAACAGTGACACAACGTCATTTGTGTCCCTTTTCCAATAGTTT
1 TTCAATGGAAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTT
* * *
761 TACTCCACATCAGTATTTTGATTCTTAATTTCAACATTTTCATCCTGAAAAAATAAAATTAAAAT
66 TACGCCACATCAGTATTTTCATTCTTAATTTTAACATTTTCATCCTGAAAAAATAAAATTAAAAT
**
826 TAAAATCCTGAAATTCAAAATGAAATTGTTG-CTGTGGCATAAAACTATTGGAAAGGGATAATAT
131 TAAAATCCTGAAATTCAGGATGAAATTGTTGAC-GTGGCATAAAACTATTGGAAAGGGATAATAT
* * **
890 CCTTGTTTCATACAATCCATTCTCTTCTTCAATGGAAAAGGATTGAATGAAACACCGACACCACG
195 CCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAATGACACCACG
* *
955 TTATTGTGTCTTTTTTCCAATTGTTTTACGCCACATCAGTAGTTTCATTCTTAATTTAAACATTT
260 TTATTGTGTCTTTTTTCCAATTATTTTACGCCACATCAGTATTTTCATTCTTAATTTAAACATTT
*
1020 TCATCCTGAAAAAATCAAATTAAAATTAAAATCTTGAAATTCAGGATGAAATTGTTGGTGTGGCA
325 TCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGGTGTGGCA
*
1085 TAAAACTGTAGGAAAGGGATAATATCCCTGTTTCATACAATTCTTTCTCTTCTTCAATGGAAAAT
390 TAAAACTATAGGAAAGGGATAATATCCCTGTTTCATACAATTCTTTCTCTTCTTCAATGGAAAAT
1150 GA
455 -A
*
1152 TTCAATAAAATGGAAAAGGATTGAATAAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAAT
1 TTC-----AATGGAAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAAT
* * *
1217 TGTTTTACGCCACATCAGTATTTTCATTCTTAATTTTAACATTTTCATCCTTAAAAAATCAAATT
61 AGTTTTACGCCACATCAGTATTTTCATTCTTAATTTTAACATTTTCATCCTGAAAAAATAAAATT
* * *
1282 AAAATTAAAATCCTGAAATTTAGGATGAAATTGATGACGTGGCATAAAACTATTGGAAAGGGAAA
126 AAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGACGTGGCATAAAACTATTGGAAAGGGATA
* * *
1347 ATATCCCTCTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAAGATTGAATGAAACAATAACAC
191 ATATCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAATGACAC
* *
1412 CATGTTATTGTGTCTTTTTTCCAATTATTTTACGCCACATCTGTATTTTCATTCTTAATTTAAAC
256 CACGTTATTGTGTCTTTTTTCCAATTATTTTACGCCACATCAGTATTTTCATTCTTAATTTAAAC
*
1477 ATTTTCATCCTGAGAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGGTGT
321 ATTTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGGTGT
*
1542 GGCATAAAACTATAAGAAAGGGATAATATCCCTGTTTCATACAATTCTTTCTCTTCTTCAATGGA
386 GGCATAAAACTATAGGAAAGGGATAATATCCCTGTTTCATACAATTCTTTCTCTTCTTCAATGGA
1607 AAA
451 AAA
Statistics
Matches: 818, Mismatches: 72, Indels: 29
0.89 0.08 0.03
Matches are distributed among these distances:
440 7 0.01
441 143 0.17
442 235 0.29
445 2 0.00
446 3 0.00
447 2 0.00
449 1 0.00
455 1 0.00
456 3 0.00
461 420 0.51
462 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (455 bp):
TTCAATGGAAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTT
TACGCCACATCAGTATTTTCATTCTTAATTTTAACATTTTCATCCTGAAAAAATAAAATTAAAAT
TAAAATCCTGAAATTCAGGATGAAATTGTTGACGTGGCATAAAACTATTGGAAAGGGATAATATC
CCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAATGACACCACGT
TATTGTGTCTTTTTTCCAATTATTTTACGCCACATCAGTATTTTCATTCTTAATTTAAACATTTT
CATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGGTGTGGCAT
AAAACTATAGGAAAGGGATAATATCCCTGTTTCATACAATTCTTTCTCTTCTTCAATGGAAAATA
Done.