Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002290.1 Kokia drynarioides strain JFW-HI SEQ_114322, 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: 3329
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Found at i:392 original size:215 final size:216
Alignment explanation
Indices: 1--2693 Score: 1949
Period size: 215 Copynumber: 12.5 Consensus size: 216
*
1 GAAATCGCATCATTTGGTCTAAATAGTTTGTG-ATTTTATAAACAACTTTTGGTCTTTGAATTAA
1 GAAATCGCATCATTTGGTCTAAATAGTTT-TGCATTTTGTAAACAACTTTTGGTCTTTGAATTAA
* * * * * *
65 ATACTTATTTACGTGAGAATTGTTTCTCTTTTGGTTCTTGGATGAACTTCCCAACTTGTCAAAAT
65 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACT
* * ** * * * * *
130 TTTATGAGTTCTTTTATAATTTTTGTTCCATAAGGTGTTCTAGACGATCCATTCCTTTGAGCAAT
130 TTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAAT
* *
195 TTCTCGAACTTTCCATGCTCGG
195 TTTTCGAACATTCCATGCTCGG
** * *
217 GAAATCGCATCATTTGGTCTAAATAGTTTTGCATTTTGT-AA-AAGGTTTGGTTGTTTGTATTAA
1 GAAATCGCATCATTTGGTCTAAATAGTTTTGCATTTTGTAAACAACTTTTGG-TCTTTGAATTAA
280 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACT
65 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACT
* * * * *
345 TTTACGAGTTCTTTCATAACATCAGTTCCTTAAAGTATTCAAGACGATTCATTCCTTCGAGTAAT
130 TTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAAT
* *
410 TTTCCGAACATTCTATGCTCGG
195 TTTTCGAACATTCCATGCTCGG
* * * * * * *
432 GATATCGCATCATTTGGTCTAAATAGTTTTTCATTTTATAAAAAAAATTTTGTTGTTTGAATTAA
1 GAAATCGCATCATTTGGTCTAAATAGTTTTGCATTTTGT-AAACAACTTTTGGTCTTTGAATTAA
* * * * *
497 AAACTTATTTACGTGAGAATTG-TT-TGTCTTGGTTCTTGGATGAACTTTCAAACTTTTCCAACT
65 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACT
* * * * * * * ** *
560 TTTATGAGTTCTTTTATAACTGCGATTCCATAAAGTATTCAGGATGATCCTTTAATTCAAGCAA-
130 TTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAAT
* *
624 ATTTCTAAACATTCCATGCTCGG
195 TTTTC-GAACATTCCATGCTCGG
* * ** * * *
647 GAAATCGTATCATTTGGTCTAAATTG-TTTGTCACATTGTAAACAAGTTTTGCTCTTTGGATTAA
1 GAAATCGCATCATTTGGTCTAAATAGTTTTG-CATTTTGTAAACAACTTTTGGTCTTTGAATTAA
* * * * * *
711 AAACTTA-TTCCGTGAGAATTGTTACTCTCTCGGTTCTCGGACGAACTTCCAAACTTGTCAAACT
65 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACT
*
775 TTTACGAATTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCATT-GAGCAA
130 TTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCC-TTCGAGCAA
* * **
839 TTTTT-GAACATTCCCTTCTCCA
194 TTTTTCGAACATTCCATGCTCGG
* * * * * * ***
861 AAAATCGCATCATTTAGTCTAAATAGTTTTTCATATTGTAAACAAGTTTTGGTCTTTAAAACGAA
1 GAAATCGCATCATTTGGTCTAAATAGTTTTGCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
* ** * * * * *
926 ATCTTATTTACGTGAGAATTG-TT-TCTCTAAGCTCTTAGATGAACTTTCGAACTTTTCAAACTC
66 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTT
* *
989 TTACGAGTTCTTTTATAACTT-GGTTCCTTACAGTATTCAAGACGATCCATTCCTTCGAGTAATT
131 TTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATT
*
1053 TTTCGAACATTCCATGCTCGA
196 TTTCGAACATTCCATGCTCGG
* * ** * * *
1074 GAAATCGCATCATTTGCTCTAAATCG-CAT-CATTTGCTCTAAA-TA-GTTT-GTCATTT---TG
1 GAAATCGCATCATTTGGTCTAAATAGTTTTGCATTT--TGTAAACAACTTTTGGTC-TTTGAAT-
* * * * * * *** * *
1131 TAAACAACTTTTGGTCTAAGAATTAAACACTTATTTAAGTGAGGATTGTTCTCCCTTGGTTCTTG
62 TAAA-AACTTAT--T-TACG--TGAGA-A-TTGTTT--CT--CTCTTGGT-T--CTTGG-AC--G
* ** * * * * * * *
1196 GACGAACTTTCGAAATAGTCAAACTTTTACGACTTATTTTACAACTTCGGTTCCTTAAAGTGTTC
109 AAC--TTTC--GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTC
* * * * * ** *
1261 AAGACAATCCACTCATTCGAGTAATTTTTCGAACATTCCTTTTTCGA
170 AAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGG
* * * * * *
1308 AAAATCGAAACATTTGGTATAAATA-TTTTGTCATTTTGTAAACAACTTTTCGTGTTTGAATTAA
1 GAAATCGCATCATTTGGTCTAAATAGTTTTG-CATTTTGTAAACAACTTTTGGTCTTTGAATT-A
* * * * * *
1372 AAGAAGTT-TTCTACATGGGAATTGTTTCTCTCTTAGTTCTTGGACGAACTTTTGAAGTTGTCAA
64 AA-AACTTATT-TACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAA
* * *
1436 AATTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTTCTTCAAGC
127 ACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGC
* *
1501 AATTTTTCGATCATTCCATTCTCGG
192 AATTTTTCGAACATTCCATGCTCGG
* * * *
1526 GAAATCGCATCATTCGATCTAAATTG-TTTGACATTTTGTAAACAACTTTTGGTCTTTGAGTTAA
1 GAAATCGCATCATTTGGTCTAAATAGTTTTG-CATTTTGTAAACAACTTTTGGTCTTTGAATTAA
** **
1590 AAACTTATTTACGTGAGAATTGTTTCTCTCTTCTTTCTTGGACGAACTTTTATAAGTTCTT-TCA
65 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAAC-TTTCGAA---CTTGTCA
* * * * * * * *
1654 TAACTTTGGTACCA-TAAAGCATTCA-AAATGATC-ATTCATTTGAGCAA-TTTTCCAA-AC-AT
126 -AACTTT--TACGAGT---TCTTTTATAACT--TCGGTTC-CTT-A--AAGTATT-CAAGACGA-
* * * ** * *
1713 TCCA-TGC-TCG-G-GATATAGC-ATCATT---TGGTC--
177 TCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGG
* * ** * * * *
1743 TAAATAGTTTTTCATTT--TGTAAACA-----AC-TTTTG----G---------TCTTTGAATTA
1 GAAATCG--CATCATTTGGTCTAAATAGTTTTGCATTTTGTAAACAACTTTTGGTCTTTGAATTA
* * * * *
1787 AAATCTTATTTTCCTGAGCAA-CGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAA
64 AAAACTTATTTACGTGAG-AATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAA
** **
1851 CTTTTACGAGTTCTTTTATAACTTCGGTTCCTTATCGTATTCAAGACGATCCGCTCCTTCGAGCA
128 CTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCA
* * *
1916 ATTTCTCGAACTTTCCATGCTCGA
193 ATTTTTCGAACATTCCATGCTCGG
* * * * * * * * *
1940 AAAATCGCGTTATTTGGACTAAATAG-TTTGTAATTTTGCAAAAAAGTTTTGTTGC-TTGAATTA
1 GAAATCGCATCATTTGGTCTAAATAGTTTTG-CATTTTGTAAACAACTTTTGGT-CTTTGAATTA
* ** *
2003 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACAAACTTTAAAACTTGTTAAAC
64 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAAC
* ** * * *
2068 TATTACTCGTTCTTTCATAACTTCAGTTCCTTAAAGTATTAAAGACGATCCATTCCTTCGAGCAA
129 TTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAA
* *
2133 TTTTTTGAACATTCCATTCTCGG
194 TTTTTCGAACATTCCATGCTCGG
* ** * *
2156 GAAATAGCAGT-ATTTGGTCTAAATAGTTCTT-C-TTATTGGGAACAAGTTTTTGTCTTTGAA-T
1 GAAATCGCA-TCATTTGGTCTAAATAGTT-TTGCATT-TTGTAAACAACTTTTGGTCTTTGAATT
* * * *
2217 AAACAACTTATTTATGTGAAAATTG-TT-TCTCTTGGTTCTTGGACAAACTTTCGAACTCGTCAA
63 AAA-AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAA
* * * * *
2280 ACTATTACGAGTTCTTTTATAACTTCGGTTCCTTACATTATTCTAGACGATCCATTCCTTAGAGC
127 ACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGC
* * *
2345 AA-TTTTCTAAACATTACATGCTCAG
192 AATTTTTC-GAACATTCCATGCTCGG
** * * * *
2370 GAAAT-GACATCATTTAATATAAATAG-TGTGTCATTTTGTAAAAAACTTTTGGTCTTTGGATTA
1 GAAATCG-CATCATTTGGTCTAAATAGTTTTG-CATTTTGTAAACAACTTTTGGTCTTTGAATTA
* * * *
2433 AACAC-TATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTTGATGAATTTTCGAACTTGTCAAAC
64 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAAC
* * *** * *
2497 TTTCATGAGTTCTTTTATAACTTTAATTTCTTAGAGTATTCAAGACGATCCATTCCTTCGAGCAA
129 TTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAA
* *
2562 -TTTTCCAATCATTCCATGCTCCG
194 TTTTTCGAA-CATTCCATGCTCGG
* * * * * * *
2585 GATATCGCATCATTCGGTCTAAATTG-TTTGACATTTTGTAAACAAGTTTTGTTCTTTGAAATAG
1 GAAATCGCATCATTTGGTCTAAATAGTTTTG-CATTTTGTAAACAACTTTTGGTCTTTGAATTAA
* *
2649 AAACTTATTTACGTGAGAATTGTTACTCTCTTTGTTCTTGGACGA
65 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGA
2694 GGTTTTACGA
Statistics
Matches: 1928, Mismatches: 414, Indels: 270
0.74 0.16 0.10
Matches are distributed among these distances:
186 3 0.00
187 8 0.00
188 4 0.00
189 7 0.00
190 8 0.00
191 7 0.00
192 8 0.00
193 1 0.00
194 9 0.00
195 12 0.01
197 14 0.01
198 49 0.03
199 2 0.00
203 5 0.00
209 2 0.00
210 8 0.00
211 17 0.01
212 46 0.02
213 129 0.07
214 256 0.13
215 578 0.30
216 310 0.16
217 60 0.03
218 144 0.07
219 11 0.01
220 9 0.00
221 2 0.00
222 13 0.01
223 8 0.00
224 10 0.01
225 11 0.01
226 8 0.00
227 10 0.01
228 8 0.00
229 3 0.00
230 1 0.00
231 1 0.00
232 5 0.00
233 30 0.02
234 83 0.04
235 1 0.00
236 15 0.01
237 2 0.00
238 2 0.00
239 8 0.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (216 bp):
GAAATCGCATCATTTGGTCTAAATAGTTTTGCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTT
TTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATT
TTTCGAACATTCCATGCTCGG
Found at i:1099 original size:19 final size:19
Alignment explanation
Indices: 1075--1116 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1065 CATGCTCGAG
1075 AAATCGCATCATTTGCTCT
1 AAATCGCATCATTTGCTCT
1094 AAATCGCATCATTTGCTCT
1 AAATCGCATCATTTGCTCT
1113 AAAT
1 AAAT
1117 AGTTTGTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.36
Consensus pattern (19 bp):
AAATCGCATCATTTGCTCT
Found at i:1836 original size:198 final size:199
Alignment explanation
Indices: 1445--1836 Score: 502
Period size: 198 Copynumber: 2.0 Consensus size: 199
1435 AAATTTTACG
* * * * * * *
1445 AGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTTCTTCAAGCAATTTTTCG
1 AGTTCTTTCATAACTTCGGTACCATAAAGCATTCAAAACGATCCATTTCTTCAAGCAATTTTCCA
* * * *
1510 ATCATTCCATTCTCGGGAAATCGCATCATTCGATCTAAATTGTTTGACATTTTGTAAACAACTTT
66 AACATTCCATGCTCGGGAAATAGCATCATTCGATCTAAATAGTTTGACATTTTGTAAACAACTTT
* * * *
1575 TGGTCTTTGAGTTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTCTTTCTTGGACGAACTTT
131 TGGTCTTTGAATTAAAAACTTATTTACCTGAGAATCGTTTCTCTCTTCGTTCTTGGACGAACTTT
1640 TATA
196 TATA
* * **
1644 AGTTCTTTCATAACTTTGGTACCATAAAGCATTCAAAATGAT-CA-TTCATTTGAGCAATTTTCC
1 AGTTCTTTCATAACTTCGGTACCATAAAGCATTCAAAACGATCCATTTC-TTCAAGCAATTTTCC
* * * **
1707 AAACATTCCATGCTCGGGATATAGCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAACAACTT
65 AAACATTCCATGCTCGGGAAATAGCATCATTCGATCTAAATAGTTTGACATTTTGTAAACAACTT
* * *
1772 TTGGTCTTTGAATTAAAATCTTATTTTCCTGAGCAA-CGTTTCTCTCTTGGTTCTTGGACGAACT
130 TTGGTCTTTGAATTAAAAACTTATTTACCTGAG-AATCGTTTCTCTCTTCGTTCTTGGACGAACT
1836 T
194 T
1837 CCGAACTTGT
Statistics
Matches: 164, Mismatches: 27, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
197 3 0.02
198 124 0.76
199 37 0.23
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (199 bp):
AGTTCTTTCATAACTTCGGTACCATAAAGCATTCAAAACGATCCATTTCTTCAAGCAATTTTCCA
AACATTCCATGCTCGGGAAATAGCATCATTCGATCTAAATAGTTTGACATTTTGTAAACAACTTT
TGGTCTTTGAATTAAAAACTTATTTACCTGAGAATCGTTTCTCTCTTCGTTCTTGGACGAACTTT
TATA
Found at i:2082 original size:216 final size:214
Alignment explanation
Indices: 1644--3329 Score: 1560
Period size: 216 Copynumber: 7.9 Consensus size: 214
1634 AACTTTTATA
* * * * * * * * * *
1644 AGTTCTTTCATAACTTTGGTACCATAAAGCATTCAAAATGAT-CATTCATTTGAGCAATTTTCCA
1 AGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTT-CG
* * * * *
1708 AACATTCCATGCTCGGGATATAGCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAACAACTTT
65 AACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTT
* * * *
1773 TGGTCTTTGAATTAAAATCTTATTTTCCTGAGCAA-CGTTTCTCTCTTGGTTCTTGGACGAACTT
130 TGGTCTTTGAATTAAAAACTTATTTACGTGAG-AATTGTTTCTCTCTTGGTTCTTGGACGAACTT
*
1837 CCGAACTTGTCAAACTTTTACG
194 TCGAACTTGTCAAAC-TTTACG
** **
1859 AGTTCTTTTATAACTTCGGTTCCTTATCGTATTCAAGACGATCCGCTCCTTCGAGCAATTTCTCG
1 AGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTT-TCG
* * * * * * * *
1924 AACTTTCCATGCTCGAAAAATCGCGTTATTTGGACTAAATAGTTTGTAATTTTGCAAAAAAGTTT
65 AACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTT
* *
1989 TGTTGC-TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACAAACTT
130 TGGT-CTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTT
** * *
2053 TAAAACTTGTTAAACTATTACT
194 TCGAACTTGTCAAACT-TTACG
* * * * *
2075 CGTTCTTTCATAACTTCAGTTCCTTAAAGTATTAAAGACGATCCATTCCTTCGAGCAATTTTTTG
1 AGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAA-TTTTCG
* * * **
2140 AACATTCCATTCTCGGGAAATAGCAGT-ATTTGGTCTAAATAGTTCT-TC-TTATTGGGAACAAG
65 AACATTCCATGCTCGAGAAATCGCA-TCATTTGGTCTAAATAGTT-TGTCATT-TTGTAAACAAG
* * * *
2202 TTTTTGTCTTTGAA-TAAACAACTTATTTATGTGAAAATTG-TT-TCTCTTGGTTCTTGGACAAA
127 TTTTGGTCTTTGAATTAAA-AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAA
*
2264 CTTTCGAACTCGTCAAACTATTACG
191 CTTTCGAACTTGTCAAACT-TTACG
* * * * *
2289 AGTTCTTTTATAACTTCGGTTCCTTACATTATTCTAGACGATCCATTCCTTAGAGCAATTTTCTA
1 AGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTC-G
* ** * * * *
2354 AACATTACATGCTC-AGGAAAT-GACATCATTTAATATAAATAGTGTGTCATTTTGTAAAAAACT
65 AACATTCCATGCTCGA-GAAATCG-CATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGT
* * * * *
2417 TTTGGTCTTTGGATTAAACAC-TATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTTGATGAATT
128 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACT
*
2481 TTCGAACTTGTCAAACTTTCATG
193 TTCGAACTTGTCAAACTTT-ACG
*** * * *
2504 AGTTCTTTTATAACTTTAATTTCTTAGAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCA
1 AGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCGA
* * * *
2569 ATCATTCCATGCTCCG-GATATCGCATCATTCGGTCTAAATTGTTTGACATTTTGTAAACAAGTT
66 A-CATTCCATGCT-CGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTT
* * * * *
2633 TTGTTCTTTGAAATAGAAACTTATTTACGTGAGAATTGTTACTCTCTTTGTTCTTGGACG-A---
129 TTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTT
2694 --G-----GT-----TTTACG
194 TCGAACTTGTCAAACTTTACG
* * * ** * * *
2703 AGTTCTTTCATAA-TTCGGTTACTTAAAGTATTAAAGTTGATCCATTCGTTCGAGCTATTTTCCA
1 AGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTT-CG
* * * * * *
2767 AACATTCCAAGCTCGTGAGATCGCATCATTTGGTCTAAGTAGTTTTTCATTTTGTAAACAACTTT
65 AACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTT
* * * * * * *
2832 TGGTCTTTGAGTTAAAAACTTATTTATGTGAGAATTATTTGTCTTTTGGTTCTTGGATGAACTTC
130 TGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTT
*
2897 CGAACTTGTCAATCTCTTACG
195 CGAACTTGTCAAACT-TTACG
* * *** * *
2918 AGTTCTTTTATAACTTTGGTTCCATAAAGTATTCAAGACGATCCCCACCTTCTAGCATTTTTTCG
1 AGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCA-ATTTTCG
* * ** * *
2983 AACAGTCCGTGCTC-AGGAAATCGTGTCATTTGGTCTAAATAGTTTGTAATTTCGTAAA-ATAGT
65 AACATTCCATGCTCGA-GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACA-AGT
** * *
3046 TTT-GTAGATTGAATTAAAAACTTATTTA-ATAGAGAATTGTTTCTCTATCT-GTTCTTGGACGA
128 TTTGGT-CTTTGAATTAAAAACTTATTTACGT-GAGAATTGTTTCTCTCT-TGGTTCTTGGACGA
*
3108 ACTTTCGAACTTGTCAAACTTTTATG
190 ACTTTCGAACTTGTCAAAC-TTTACG
* * * * * * *
3134 AGTTCTTTCACAAGTTTGGTTCCTTAAAGTATTCAAAACTACCCATTCCTTCGAGCAATTTTCTG
1 AGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTC-G
* * * * * * *
3199 AACATTCCATTCTCGGGAAATAGCAACATTTGATCAAAATAGTTCT-TCATTTTG-GAACAAGTT
65 AACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTT-TGTCATTTTGTAAACAAGTT
* *
3262 TTGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTG-TT-TCTCTTGGTTCTAGGACGAACTT
129 TTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTT
3325 TCGAA
194 TCGAA
Statistics
Matches: 1182, Mismatches: 229, Indels: 122
0.77 0.15 0.08
Matches are distributed among these distances:
197 2 0.00
198 138 0.12
199 18 0.02
200 3 0.00
204 1 0.00
205 2 0.00
209 2 0.00
210 1 0.00
212 1 0.00
213 46 0.04
214 154 0.13
215 265 0.22
216 535 0.45
217 14 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (214 bp):
AGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCGA
ACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTT
GGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTC
GAACTTGTCAAACTTTACG
Found at i:3069 original size:414 final size:414
Alignment explanation
Indices: 2284--3107 Score: 955
Period size: 414 Copynumber: 2.0 Consensus size: 414
2274 CGTCAAACTA
* * * * **
2284 TTACGAGTTCTTTTATAACTTCGGTTCCTTACATTATTCTAGACGATCCATTCCTTAGAGCAATT
1 TTACGAGTTCTTTCATAACTTCGGTTACTTAAAGTATTAAAGACGATCCATTCCTTAGAGCAATT
* *
2349 TTCTAAACATTACATGCTCAGGAAATGACATCATTTAATATAAATAGTGTGTCATTTTGTAAAAA
66 TTCCAAACATTACAAGCTCAGGAAATGACATCATTTAATATAAATAGTGTGTCATTTTGTAAAAA
* * *
2414 ACTTTTGGTCTTTGGATTAAACACTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTTGATGAA
131 ACTTTTGGTCTTTGGATTAAAAACTATTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGATGAA
* * * * * *
2479 TTTTCGAACTTGTCAAACTTTCATGAGTTCTTTTATAACTTTAATTTCTTAGAGTATTCAAGACG
196 CTTCCGAACTTGTCAAACTTTCACGAGTTCTTTTATAACTTTAATTCCATAAAGTATTCAAGACG
** * * *
2544 ATCCATTCCTTCGAGCAATTTTCCAATCATTCCATGCTCCGGATATCGCATCATTCGGTCTAAAT
261 ATCCACACCTTCGAGCAATTTTCCAATCAGTCCATGCTCAGGAAATCGCATCATTCGGTCTAAAT
* * * * * *
2609 TGTTTGACATTTTGTAAACAAGTTTTGTTCTTTGAAATAGAAACTTATTTACGT-GAGAATTGTT
326 AGTTTGACATTTCGTAAACAAGTTTTGTACATTGAAATAAAAACTTATTTA-ATAGAGAATTGTT
* *
2673 ACTCTCTTTGTTCTTGGACGAGGTT
390 ACTCTATCTGTTCTTGGACGAGGTT
** * * *
2698 TTACGAGTTCTTTCATAA-TTCGGTTACTTAAAGTATTAAAGTTGATCCATTCGTTCGAGCTATT
1 TTACGAGTTCTTTCATAACTTCGGTTACTTAAAGTATTAAAGACGATCCATTCCTTAGAGCAATT
* * ** * * * *
2762 TTCCAAACATTCCAAGCTC-GTGAGATCG-CATCATTTGGTCTAAGTAGTTTTTCATTTTGTAAA
66 TTCCAAACATTACAAGCTCAG-GAAAT-GACATCATTTAATATAAATAGTGTGTCATTTTGTAAA
* * * *
2825 CAACTTTTGGTCTTT-GAGTTAAAAACTTATTTATGTGAGAATTATTTGTCTTTTGGTTCTTGGA
129 AAACTTTTGGTCTTTGGA-TTAAAAAC-TATTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGA
* **
2889 TGAACTTCCGAACTTGTCAATCTCTT-ACGAGTTCTTTTATAACTTTGGTTCCATAAAGTATTCA
192 TGAACTTCCGAACTTGTCAAACT-TTCACGAGTTCTTTTATAACTTTAATTCCATAAAGTATTCA
* * * * * ** *
2953 AGACGATCCCCACCTTCTAGCATTTTTTCGAA-CAGTCCGTGCTCAGGAAATCGTGTCATTTGGT
256 AGACGATCCACACCTTCGAGCA-ATTTTCCAATCAGTCCATGCTCAGGAAATCGCATCATTCGGT
* *
3017 CTAAATAGTTTGTA-ATTTCGTAAA-ATAGTTTTGTAGATTGAATTAAAAACTTATTTAATAGAG
320 CTAAATAGTTTG-ACATTTCGTAAACA-AGTTTTGTACATTGAAATAAAAACTTATTTAATAGAG
*
3080 AATTGTTTCTCTATCTGTTCTTGGACGA
383 AATTGTTACTCTATCTGTTCTTGGACGA
3108 ACTTTCGAAC
Statistics
Matches: 340, Mismatches: 61, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
412 3 0.01
413 108 0.32
414 219 0.64
415 10 0.03
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.41
Consensus pattern (414 bp):
TTACGAGTTCTTTCATAACTTCGGTTACTTAAAGTATTAAAGACGATCCATTCCTTAGAGCAATT
TTCCAAACATTACAAGCTCAGGAAATGACATCATTTAATATAAATAGTGTGTCATTTTGTAAAAA
ACTTTTGGTCTTTGGATTAAAAACTATTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGATGAA
CTTCCGAACTTGTCAAACTTTCACGAGTTCTTTTATAACTTTAATTCCATAAAGTATTCAAGACG
ATCCACACCTTCGAGCAATTTTCCAATCAGTCCATGCTCAGGAAATCGCATCATTCGGTCTAAAT
AGTTTGACATTTCGTAAACAAGTTTTGTACATTGAAATAAAAACTTATTTAATAGAGAATTGTTA
CTCTATCTGTTCTTGGACGAGGTT
Done.