Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014757.1 Kokia drynarioides strain JFW-HI SEQ_129796, 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: 1948
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.40
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:384 original size:216 final size:216
Alignment explanation
Indices: 9--1174 Score: 1455
Period size: 216 Copynumber: 5.4 Consensus size: 216
1 TTTCCTAG
* * * *
9 TTCTTTTATAACTTCGGTTCCAGATAGTAGTCGAGATGATCCATTCCTTTGACCAATTTTTTGAA
1 TTCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGATGATCCATTCCTTCGACCAATTTTTCGAA
* * * * *
74 CATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAA-ACGTTTGTCATTTTGTAAGA-AGCATT
66 CATTCCATGATCGGGAAATCGCATCATTTGGTCCAAATA-GTTTGTCATTTTGTAA-ATAACTTT
* * *
137 TGGTCTTTGAATTAAAATCTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGAAGTTC
129 TGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTC
*
202 CAAACTTGTCAAACATTTACTAA
194 CGAACTTGTCAAACATTTACTAA
* * * * *
225 ATCTTTTATAACTTTGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTTGACCAATTTTTCGAA
1 TTCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGATGATCCATTCCTTCGACCAATTTTTCGAA
*** * *
290 CATTCCATGATATAGATATCGCATCATTTGGTCCAAATATTTTGTCATTTTGTAAATTAA-TTTT
66 CATTCCATGATCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAA-TAACTTTT
* * * * *
354 GGACTTTGAATTAAAAACTTTTTAACGTGAGACTTGTTTCTCTATTAGTTCTTGGACGAACTTCC
130 GGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCC
*
419 GAACTTGTTAAACATTTACTAA
195 GAACTTGTCAAACATTTACTAA
* ** * * * * *
441 TTCTTTTATAACATCATTTCCTAAGAGTATTCAAGATGATCCATTCCTTTGACCTATTTTTCGAA
1 TTCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGATGATCCATTCCTTCGACCAATTTTTCGAA
* * * *
506 TATTCCATGATCGGGAAATCACATCATTTAGTCAAAATAGTTTGTCATTTTGTAAATAACTTTTG
66 CATTCCATGATCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAATAACTTTTG
* * ** * * *
571 GTCTTCGATTTAAAAACTTTTTTACGTGAGAATTGGATCTCTCTTGGTTCTCGGACAAACTTTCG
131 GTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCG
* *
636 AACTTGTGAAACATTTA-TGAG
196 AACTTGTCAAACATTTACT-AA
* * * * * * *
657 TTCTTTTATAACTTTGGTTTCTAAGAGTATTCAATATGATCCATTTCTTCGACCAATTTTTCGAA
1 TTCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGATGATCCATTCCTTCGACCAATTTTTCGAA
* * * *
722 CATTCCATGATCGGGATATCGCATCATTTGGTCCAAATATTTTGTCTTTTTGTAAACAACTTTTG
66 CATTCCATGATCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAATAACTTTTG
* * * * *
787 GTCTTTAAATTAAAAACTTTTTTACGAGAGATTTATTTCTCTCTTGGTTCTTGGACGAACTTTCG
131 GTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCG
*
852 AACTTGTCAAACATTTACTAG
196 AACTTGTCAAACATTTACTAA
* * * *
873 TTCTTTTATAACTTCGGTTCCTGATAGTAGTCGAGATGATCTATTCCCTCGACCAAATTTTT-AA
1 TTCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGATGATCCATTCCTTCGACC-AATTTTTCGA
* * *
937 ACATTCCATGCTCGGGAAATCGCATCATTTAGTCTAAA-ACGTTTGTCATTTTGTAAA-AAGCTT
65 ACATTCCATGATCGGGAAATCGCATCATTTGGTCCAAATA-GTTTGTCATTTTGTAAATAA-CTT
* * * * * *
1000 TTGGTCTTTGAATTAAAATCTTTTTTACATGAGAGTTGTTTCTCTCCTGGTTCTTGGATGAAGTT
128 TTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTT
*
1065 CTGAACTTGTCAAACATTTACTAA
193 CCGAACTTGTCAAACATTTACTAA
* * * *
1089 ATCTTTTATAACTTCGATTCCTGATAGTAGTCAAGATGATCCATTTCTTCGACCAATTTTTTGAA
1 TTCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGATGATCCATTCCTTCGACCAATTTTTCGAA
1154 CATTCCATGATCGGGAAATCG
66 CATTCCATGATCGGGAAATCG
1175 TANNNNNNNN
Statistics
Matches: 815, Mismatches: 125, Indels: 20
0.85 0.13 0.02
Matches are distributed among these distances:
215 15 0.02
216 790 0.97
217 10 0.01
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (216 bp):
TTCTTTTATAACTTCGGTTCCTGATAGTAGTCAAGATGATCCATTCCTTCGACCAATTTTTCGAA
CATTCCATGATCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAATAACTTTTG
GTCTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCG
AACTTGTCAAACATTTACTAA
Found at i:1616 original size:216 final size:211
Alignment explanation
Indices: 1231--1944 Score: 840
Period size: 216 Copynumber: 3.3 Consensus size: 211
1221 NNNNNNACCT
* * *
1231 ATTTTTCGAATATTCCATGATCGGGAAATCACATCATTTAGTC-AAAATAGTTTGTCATTTTGTA
1 ATTTTT-GAACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAAA-AGTTTGTCATTTTGTA
* * *
1295 AATAACTTTTGGTCTTTGATTTAAAAACTTTTTTACATGAGAATTGGTTCTCTCTTGGTTCTCGG
64 AA-AACTTTTGGTCTTTGA-TTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGG
** * * * *
1360 ACAAACTTTCGAACTTGTCAAACATTTATGAGTTCTTTTATAACTTTC-GTTTCTAAGAGTATTC
127 ATGAA-GTTCGAACTTGTCAAACATTTCT-AGTTCTTTTATAAC-TTCAGTTTCTAATAGTAGTC
*
1424 AATACGATCCATTCCTTCGACCA
189 AAGACGATCCATTCCTTCGACCA
* * *
1447 ATTTCTTGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTATAA
1 ATTT-TTGAACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAA
* * * * *
1512 AGAACATTTAGTCTTTGGATTAAAAACTTTATTACGTGAGAATTGTTTCTCACTCGGTTCTTGGA
65 A-AACTTTTGGTCTTT-GATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGA
* *
1577 TGAAGTGTCGAACTTGTCAAACATTTCCTAGTTCTTTTATAACTTCAG-TTCCAGATAGTAGTCG
128 TGAAGT-TCGAACTTGTCAAACATTT-CTAGTTCTTTTATAACTTCAGTTTCTA-ATAGTAGTCA
* *
1641 AGATGATCCATTCCTTTGACCA
190 AGACGATCCATTCCTTCGACCA
* * * **
1663 ATTTTTTGAACTTTCTATGCTCGGGAAATCGCATCATTTGGTCTAAAACTTTTGTCATTTTGTAA
1 A-TTTTTGAACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAA
* *
1728 AAAGCTTTTGGTCTTTTAATTAAAATCTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGA
65 AAA-CTTTTGGTC-TTTGATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGA
* ** * * *
1793 TGAAGTTCCAAACTTGTCAAACATTTACTAAATCTTTTATAACTTCGGTTCCTGATAGTAGTCAA
128 TGAAGTT-CGAACTTGTCAAACATTT-CTAGTTCTTTTATAACTTCAGTTTCTAATAGTAGTCAA
* *
1858 GACGATTCATTTCTTCGACCA
191 GACGATCCATTCCTTCGACCA
* * * *
1879 ATTTTTCGAACATTCCATGATCGGGATATCGCATCATTTGGTCCAAATATTTTGTCATTTTGTAA
1 ATTTTT-GAACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAA
1944 A
65 A
1945 CAAC
Statistics
Matches: 426, Mismatches: 59, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
215 16 0.04
216 393 0.92
217 17 0.04
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (211 bp):
ATTTTTGAACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAAAAGTTTGTCATTTTGTAAA
AACTTTTGGTCTTTGATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGATGA
AGTTCGAACTTGTCAAACATTTCTAGTTCTTTTATAACTTCAGTTTCTAATAGTAGTCAAGACGA
TCCATTCCTTCGACCA
Done.