Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1720
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: 2790
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:918 original size:474 final size:474
Alignment explanation
Indices: 1--2790 Score: 5263
Period size: 474 Copynumber: 5.9 Consensus size: 474
1 AATAAGGCAAGCATTGATTCTCATAACAATCTTCACTCTTTTTGAGTTTGGGAACCAAAAACGCA
1 AATAAGGCAAGCATTGATTCTCATAACAATCTTCACTCTTTTTGAGTTTGGGAACCAAAAACGCA
66 TTCCTTTCAATAGGATACACGACATTGACGC-TTAATGTCGCAAGAAAAGCATTTCTTTCAACCG
66 TTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTCAACCG
130 TTTTTGACAGAATCAAAGTTTGTCTCTTAAATAAGAAAAACATGAATAGACGCACAAATCCTCAT
131 TTTTTGACAGAATCAAAGTTTGTCTCTTAAATAAGAAAAACATGAATAGACGCACAAATCCTCAT
195 TC-TTTTTAGATTAGGGCACCATAAACTTAGTCTTCTCATAAGCGTACACGATATTGATGGTTAA
196 TCTTTTTTAGATTA-GGCACCATAAACTTAGTCTTCTCATAAGCGTACACGATATTGATGGTTAA
259 GTTTCATAAGAAAGCTTTCTT-CCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAATGTGCC
260 GTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAATGTGCC
*
323 AAACATGGATTTTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTCTCCTCC
325 AAACATGGATTGTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTCTCCTCC
388 TTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTA
390 TTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTA
453 AAGTCAAAGTTCCTTCCTTA
455 AAGTCAAAGTTCCTTCCTTA
473 AATAAGGCAAGCATTGATTCTCATAACAATCTTCACTCTTTTTGAGTTTGGGAACCAAAAACGCA
1 AATAAGGCAAGCATTGATTCTCATAACAATCTTCACTCTTTTTGAGTTTGGGAACCAAAAACGCA
538 TTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTCAACCG
66 TTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTCAACCG
603 TTTTTGACAGAATCAAAGTTTGTCTCTTAAATAAGAAAAACATGAATAGACGCACAAATCCTCAT
131 TTTTTGACAGAATCAAAGTTTGTCTCTTAAATAAGAAAAACATGAATAGACGCACAAATCCTCAT
*
668 TCTTTTTTAGATTAGGCACCATAAACTTAGTCTCCTCATAAGCGTACACGATATTGATGGTTAAG
196 TCTTTTTTAGATTAGGCACCATAAACTTAGTCTTCTCATAAGCGTACACGATATTGATGGTTAAG
733 TTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAATGTGCCA
261 TTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAATGTGCCA
798 AACATGGATTGTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTCTCCTCCT
326 AACATGGATTGTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTCTCCTCCT
863 TAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAA
391 TAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAA
928 AGTCAAAGTTCCTTCCTTA
456 AGTCAAAGTTCCTTCCTTA
*
947 AATCAGGCAAGCATTGATTCTCATAACAATCTTCACTCTTTTTGAGTTTGGGAACCAAAAACGCA
1 AATAAGGCAAGCATTGATTCTCATAACAATCTTCACTCTTTTTGAGTTTGGGAACCAAAAACGCA
1012 TTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTCAACCG
66 TTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTCAACCG
1077 TTTTTGACAGAATCAAAGTTTGTCTCTTAAATAAGAAAAACATGAATAGACGCACAAATCCTCAT
131 TTTTTGACAGAATCAAAGTTTGTCTCTTAAATAAGAAAAACATGAATAGACGCACAAATCCTCAT
1142 TCTTTTTTAGATTAGGCACCATAAACTTAGTCTTCTCATAAGCGTACACGATATTGATGGTTAAG
196 TCTTTTTTAGATTAGGCACCATAAACTTAGTCTTCTCATAAGCGTACACGATATTGATGGTTAAG
1207 TTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAATGTGCCA
261 TTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAATGTGCCA
1272 AACATGGATTGTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTCTCCTCCT
326 AACATGGATTGTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTCTCCTCCT
1337 TAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAA
391 TAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAA
1402 AGTCAAAGTTCCTTCCTTA
456 AGTCAAAGTTCCTTCCTTA
*
1421 AATCAGGCAAGCATTGATTCTCATAACAATCTTCACTCTTTTTGAGTTTGGGAACCAAAAACGCA
1 AATAAGGCAAGCATTGATTCTCATAACAATCTTCACTCTTTTTGAGTTTGGGAACCAAAAACGCA
1486 TTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTCAACCG
66 TTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTCAACCG
1551 TTTTTGACAGAATCAAAGTTTGTCTCTTAAATAAGAAAAACATGAATAGACGCACAAATCCTCAT
131 TTTTTGACAGAATCAAAGTTTGTCTCTTAAATAAGAAAAACATGAATAGACGCACAAATCCTCAT
1616 TCTTTTTTAGATTAGGCACCATAAACTTAGTCTTCTCATAAGCGTACACGATATTGATGGTTAAG
196 TCTTTTTTAGATTAGGCACCATAAACTTAGTCTTCTCATAAGCGTACACGATATTGATGGTTAAG
1681 TTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAATGTGCCA
261 TTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAATGTGCCA
1746 AACATGGATTGTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTCTCCTCCT
326 AACATGGATTGTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTCTCCTCCT
1811 TAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAA
391 TAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAA
1876 AGTCAAAGTTCCTTCCTTA
456 AGTCAAAGTTCCTTCCTTA
*
1895 AATCAGGCAAGCATTGATTCTCATAAC-ATCCTTCACTCTTTTTGAGTTTGGGAACCAAAAACGC
1 AATAAGGCAAGCATTGATTCTCATAACAAT-CTTCACTCTTTTTGAGTTTGGGAACCAAAAACGC
1959 ATTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTCAACC
65 ATTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTCAACC
2024 GTTTTTGACAGAATCAAAGTTTGTCTCTTAAATAAGAAAAACATGAATAGACGCACAAATCCTCA
130 GTTTTTGACAGAATCAAAGTTTGTCTCTTAAATAAGAAAAACATGAATAGACGCACAAATCCTCA
2089 TTCTTTTTTAGATTAGGCACCATAAACTTAGTCTTCTCATAAGCGTACACGATATTGATGGTTAA
195 TTCTTTTTTAGATTAGGCACCATAAACTTAGTCTTCTCATAAGCGTACACGATATTGATGGTTAA
2154 GTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAATGTGCC
260 GTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAATGTGCC
*
2219 AAACATGGATTGTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTTTCCTCC
325 AAACATGGATTGTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTCTCCTCC
2284 TTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTTTG-CCTATTTTCCTTA
390 TTAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTA
2348 AAGTCAAAGTTCCTTCCTTA
455 AAGTCAAAGTTCCTTCCTTA
* * *
2368 AATAAGGCAAGCATTTGATTCTCATAACAAATCTCCACTCTTTTCGATGATTGGGAACCAAAAAA
1 AATAAGGCAAGCA-TTGATTCTCATAAC-AATCTTCACTCTTTTTGA-GTTTGGGAACC-AAAAA
* * *
2433 CACAGTCC-TTC-ATAGGATACACGACATTGACGCTTTAAATGTCGCAAGAAAAGGCATGTCTTT
62 CGCATTCCTTTCAATAGGATACACGACATTGACGCTTT-AATGTCGCAAGAAAA-GCATTTCTTT
* * * * * **
2496 GAACCATTTTTCGAGAGAATCAAAGTTTATCTCTTAAATCAGAAAAACATGAATAGACATTACAA
125 CAACCGTTTTT-GACAGAATCAAAGTTTGTCTCTTAAATAAGAAAAACATGAATAGAC-GCACAA
2561 ATCCTCATTCTTTTTTAGATTAGGCACCATAAACTTAGTC-TCTCATAAGCGTACACGATATTGA
188 ATCCTCATTCTTTTTTAGATTAGGCACCATAAACTTAGTCTTCTCATAAGCGTACACGATATTGA
2625 TGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAA
253 TGGTTAAGTTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAA
2690 ATGTGCCAAACATGGATTGTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATT
318 ATGTGCCAAACATGGATTGTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATT
2755 CTCCTCCTTAGGATAAAGGATATGGATGGTTTTCTT
383 CTCCTCCTTAGGATAAAGGATATGGATGGTTTTCTT
Statistics
Matches: 2285, Mismatches: 20, Indels: 20
0.98 0.01 0.01
Matches are distributed among these distances:
472 96 0.04
473 217 0.09
474 1599 0.70
475 38 0.02
476 30 0.01
477 29 0.01
478 232 0.10
479 44 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (474 bp):
AATAAGGCAAGCATTGATTCTCATAACAATCTTCACTCTTTTTGAGTTTGGGAACCAAAAACGCA
TTCCTTTCAATAGGATACACGACATTGACGCTTTAATGTCGCAAGAAAAGCATTTCTTTCAACCG
TTTTTGACAGAATCAAAGTTTGTCTCTTAAATAAGAAAAACATGAATAGACGCACAAATCCTCAT
TCTTTTTTAGATTAGGCACCATAAACTTAGTCTTCTCATAAGCGTACACGATATTGATGGTTAAG
TTTCATAAGAAAGCTTTCTTCCCACCAATTTTGCTAAAGTCTATGTTCGTGCCTCAAATGTGCCA
AACATGGATTGTAGTAATGATCTACTTCACGTTGTGATTAGGCAGTATAAACTTATTCTCCTCCT
TAGGATAAAGGATATGGATGGTTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAA
AGTCAAAGTTCCTTCCTTA
Done.