Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006051.1 Kokia drynarioides strain JFW-HI SEQ_120521, 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: 28387
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:861 original size:216 final size:215
Alignment explanation
Indices: 15--2252 Score: 2321
Period size: 216 Copynumber: 10.4 Consensus size: 215
5 AATTTTATGA
** * * *
15 GTTCTTTTATAACTTAAGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCTATTTTTTGA
1 GTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAATTTTCTGA
* * * * *
80 ACATTCCATGCTCGGGAAATCGCATCATCTAGTCTAAACAATTTGACATTTTGTAAACAACTTTT
66 ACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTT
* * * * *
145 GGTCTTTGAATTAAAAACTTATTTACATGAGAATTTTTTTCTCTCTTGTTTCTTGGTCGAACATC
131 GGTCTTTGAATTAAAAACTTATTTACGTGAGAA-TTGTTTCTCTCTTGGTT-TTGGACGAACTTC
* * *
210 CGAACTTGT-TAACTATT-TGCG
194 CGAACTTGTCAAACTCTTAT-TG
* * * *
231 AGTTCTTTTATAACTTCGTTTCCTTAAAGTATTCAACGTGATCCAATCCTTCGAGCAATTTT-TC
1 -GTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAATTTTCT-
* * * * * * **
295 AAACATTCCATGATCGTGAAATTGCATTATTTGGTCTAAATAGCTTGTCATTTTGTAAACAAGAT
64 GAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTT
** * * * * * *
360 TTCATCTATGAATTAAAAA-TGCATTTACGTGAGAATTTTTTCTCTCTTTGTTCTTGGTCGATCT
129 TTGGTCTTTGAATTAAAAACT-TATTTACGTGAGAATTGTTTCTCTCTTGGTT-TTGGACGAACT
** * * ***
424 TTTGAACTAGTCAAACTTTTACAA
192 TCCGAACTTGTCAAACTCTTATTG
* * * * * ** * * * *
448 GTTCATTATT-T-ACTTCAGTTTCATAAAGTTTTCAAGGTGATTGATTCCTTCAATCAGTTTTCC
1 GTTC-TT-TTATAACTTCGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAATTTTCT
* *
511 GAACATTCCATGCTCGGGAAATC-CATCATTTGGTCTAAATAGTTTGTCAATTTGTAAATAACTT
64 GAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTT
* * *
575 TTGGTCTTTAAATTAAAAACTTATTTACGTGAGAATTGTTTCCCTCTTGGTTTTGGGGCGAACTT
129 TTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTTT-GGACGAACTT
* *
640 CCAAACTTGTTAAACTCTTATTG
193 CCGAACTTGTCAAACTCTTATTG
* * * *
663 GTTCTTTTATAACTTCGGTTCCTTAAATTATTCAAGGCAATCCGTTCCTTTGAGCAATTTTCTGA
1 GTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAATTTTCTGA
* * *
728 ACATTCCATGCTCGGGAAATCGCATCATTTGGTTTAAATAGTATGTCATTTTGTAAAACAACTGT
66 ACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGT-AAACAACTTT
* * * * *
793 TGGTCTTTGAATTTAAAACTTATTTACATGATAATTCTTTCTCTCTTGGTTTGGGGACGAAC-TC
130 TGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTT-TGGACGAACTTC
* *
857 CAAACTCGTCAAACTCTTATTG
194 CGAACTTGTCAAACTCTTATTG
* *
879 GTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAATGCGATCCATTCCTTCGATCAAATTTTC-G
1 GTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGC-AATTTTCTG
* * * * *
943 AACATTCTATGCTTGGGAAATCGTATTATTTGGTCTAAATGGTTTGTCATTTTGTAAACAACTTT
65 AACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTT
* * * * * *
1008 TGGTCTTTGAATTAAAAACTTATTCACGTGAGACTTGTTTCTCTCTGGGTTCTTTGACAAACTTT
130 TGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTT-TTGGACGAACTTC
1073 CGAACTTGTCAAACTCTTATTG
194 CGAACTTGTCAAACTCTTATTG
** * * * *
1095 GTTCTTTTATAACTTCAATTCCTTAAAGTATTCAAGGCAATCCGTTCTTTCGAGCAATTTTTTGA
1 GTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAATTTTCTGA
* * * ** ** *
1160 ACATTCTATGCTCCGAAAATCTTATCATTTAATCTAAATAGTTTTTCATTTTGTAAACAACTTTT
66 ACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTT
* * * * * *
1225 GGTCTTTGAATTAAAAACTAATTCACATGAGAATTGTTTCTCTCTTGGGTCTTAGACGAACCTCC
131 GGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT-GGTTTTGGACGAACTTCC
*
1290 GAACTTGTCAAACTTTTATTG
195 GAACTTGTCAAACTCTTATTG
* * **
1311 GTTCTTTTATTACTTCGGTTCCTTAAAGTATTCAAGGCGATCCATTCATTCGAGCAATTTTCCAA
1 GTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAATTTTCTGA
* * * *
1376 ACATTCCATGCTCGGGAAATCACGTTC-TTTGGTTTAAATAGTTTGTCATTTTG-AAAGCATCTT
66 ACATTCCATGCTCGGGAAATCGC-ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-CAACTT
* * * * * *
1439 TTTGTCTTTAAATAAAAAACTTATTTACATG-GAAATTATTTCTCTCTTGGTTTTGGGATGAACT
129 TTGGTCTTTGAATTAAAAACTTATTTACGTGAG-AATTGTTTCTCTCTTGGTTTT-GGACGAACT
*
1503 TCTGAACTTGTCAAACTCTTATTG
192 TCCGAACTTGTCAAACTCTTATTG
* * * * * * *
1527 GTTCTTTTATAACTTCGGTTTCGTAAAGTATTCAAGGTGATTCGTTCCTTCGAGTAAATTTTC-A
1 GTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAG-CAATTTTCTG
* * * *
1591 AACATTCCATGCTTGGGAAATCGTATCCTTTGGTCTAAATTGTTTGTCATTTTGTAAACAACTTT
65 AACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTT
* * *
1656 TGGTCTTTGAATTAAAAACTTATTCACGTGAGAATTGTTTCTCTCTTGATTCTTGGACAAACTTC
130 TGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTT-TTGGACGAACTTC
*
1721 CGAACTTGTCAAACTTTTA-TG
194 CGAACTTGTCAAACTCTTATTG
* * * ** **
1742 AGTTCTTTTATAACTTCGATTCCTTAAACTATTCAATGTAATCCATTGATTCGAGCAA-TTTCTC
1 -GTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAATTTTCT-
* ** * * **
1806 GAACATTCCATGCTCGAGAAATTACATCATTAGGTCTAAATAGTTTGTGATTTTGTAAACAAGAT
64 GAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTT
* * *
1871 TTGGTCTTTGAATTAAAAA-TGTATTTACGTGAGAATTATTTCTCTCTTGGTTTTTGGTCGATCT
129 TTGGTCTTTGAATTAAAAACT-TATTTACGTGAGAATTGTTTCTCTCTTGG-TTTTGGACGAACT
* *
1935 TCCGAACTTGTCAAACTTTTA-CG
192 TCCGAACTTGTCAAACTCTTATTG
** * * * * *
1958 AGTTCATTATT-T-ACTTTAGTTTCATAAAGTTTTCAAGGCGGTCCATTCCTTCGAGCAGTTTT-
1 -GTTC-TT-TTATAACTTCGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAATTTTC
* * * * *
2020 TCGAACATTACATGCTCAGGAAATTGCATCATTTGGTCTAAATAGTTTTTCATTTTGTAAATAAC
63 T-GAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAC
* * * *
2085 TTTTGGTCTTTGAAATAAAAACTTATTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGTCGATC
127 TTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTT-TTGGACGAAC
*
2150 TTCCGAACTTGTGAAACT-TT-TTCG
191 TTCCGAACTTGTCAAACTCTTATT-G
* ** * * * *
2174 AATTCTTCATT-T-ACTTCAATTTCATAAAGTTTTCAAGGCGATCCAATCCATT-GAGCAATTTT
1 -GTTCTT--TTATAACTTCGGTTCCTTAAAGTATTCAAGGCGATCCATTCC-TTCGAGCAATTTT
*
2236 CTAAACATTCCATGCTC
62 CTGAACATTCCATGCTC
2253 AGAAAGGCGA
Statistics
Matches: 1691, Mismatches: 287, Indels: 87
0.82 0.14 0.04
Matches are distributed among these distances:
213 2 0.00
214 9 0.01
215 250 0.15
216 1186 0.70
217 240 0.14
218 4 0.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (215 bp):
GTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAATTTTCTGA
ACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTT
GGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTTTGGACGAACTTCCG
AACTTGTCAAACTCTTATTG
Found at i:2419 original size:175 final size:174
Alignment explanation
Indices: 2103--2433 Score: 420
Period size: 175 Copynumber: 1.9 Consensus size: 174
2093 TTTGAAATAA
* * * *
2103 AAACTTATTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGTCGATCTTCCGAACTTGTGAAACT
1 AAACTTATTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGTCAAACT
* * *
2168 TTTTCGAATTCTTCATTTACTTCAATTTCATAAAGTTTTCAAGGCGATCCAATCCATTGAGCAAT
66 TTTTCG-ATTCTT-ATTTACTTCAATTCCATAAAGTATTCAAGACGATCCAATCCATTGAGCAAT
2233 TTTCTAAACATTCCATGCTC-AGAAAGGCGATCCAATCCAATCCAT
129 TTTCTAAACATTCCATGCTCGAGAAAGGCGATCCAATCCAATCCAT
2278 AAACTTATTTACGTGAGAATTATTTCTCTCTTGGTT-TTGGAACGAACTTCCAAACTTGTCAAAC
1 AAACTTATTTACGTGAGAATTATTTCTCTCTTGGTTCTTGG-ACGAACTTCCAAACTTGTCAAAC
* * * ** * *
2342 TCTTGTTTG-TTCTT-TTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCGTTCCTTTGAGT
65 T-TT-TTCGATTCTTATT-T-ACTTCAATTCCATAAAGTATTCAAGACGATCCAATCCATTGAGC
*
2405 AATTTT-TCAAACATTCCATGGTCGAGAAA
126 AATTTTCT-AAACATTCCATGCTCGAGAAA
2434 TCGCATCATT
Statistics
Matches: 134, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
173 2 0.01
174 6 0.04
175 116 0.87
176 7 0.05
177 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (174 bp):
AAACTTATTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGTCAAACT
TTTTCGATTCTTATTTACTTCAATTCCATAAAGTATTCAAGACGATCCAATCCATTGAGCAATTT
TCTAAACATTCCATGCTCGAGAAAGGCGATCCAATCCAATCCAT
Found at i:2821 original size:216 final size:216
Alignment explanation
Indices: 2278--6570 Score: 4314
Period size: 216 Copynumber: 19.9 Consensus size: 216
2268 TCCAATCCAT
* * *
2278 AAACTTATTTACGTGAGAATTATTTCTCTCTTGGTT-TTGGAACGAACTTCCAAACTTGTCAAAC
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGG-CCGAACTTCCGAACTTGTCAAAC
* **** * * * *
2342 TCTTGTTTGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCGTTCCTTTGAGTAA
65 TTTTACGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAA
* * * *
2407 TTTTTCAAACATTCCATGGTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
130 TTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
* *
2472 CAACTTTTGTTCTTTGAATTTA
195 CAACTTTTGGTCTTTGAATTAA
* * ** *
2494 AAACTTATTTA-ATGAGAATT-TTTCTCTCTTGGTTTTTGGGTGAACTTCCAAACTTGTCAAACT
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACT
* *** ** *
2557 CTTATTTGTTCTTTTATAACTTC-AGTTCCTTAAAGTATTCAAGGCGATCCGCTCCTTCGATCAA
66 TTTACGAGTTCTTTTATAACTTCGA-TTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAA
* * * * ** *
2621 TTCTCCGAACATTCCAAGCTTAGGAAATCATATTATTTGGTCTAAA-AGGTTTGTCATTTTGTAA
130 TTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATA-GTTTGTCATTTTGTAA
2685 ACAACTTTTGGTCTTTGAATTAA
194 ACAACTTTTGGTCTTTGAATTAA
* * * * *
2708 AAACTTATTCACGTGAGAATTGTTTCTTTCTTGGTTCTTTGACGAACTTCCGAACATGTCAAACT
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACT
* * * * *
2773 CTTATTG-GTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGGCGATCCGTTCTTTCAAGCAA
66 TTTA-CGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAA
** * * ** **
2837 TTTTTTTAACATTCCATGCTCGAGAAATCTTATCATTTAATCTAAATAGTTTGTCATTTTGTAAA
130 TTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
2902 CAACTTTTGGTCTTTGAATTAA
195 CAACTTTTGGTCTTTGAATTAA
* * * *
2924 AAACTTATTAACGTGAGAATTGTTTCTCTCTTGGGTCTTGGACGAACCTCCGAACTTGTCAAACT
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACT
* * * * * * *
2989 TTTATTG-GTTCTTTTATTACTTTGGTTCCTTAAAGTATTCAAGGCGAACCATTTCTTTGAGCAA
66 TTTA-CGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAA
* * * * *
3053 TTTTCCCAACATTCCATGCTCGGGAAATCGCGTTATTTGGTCTAAATAGTTTGTCATTTTGTAAA
130 TTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
*
3118 CAACTTTTGGTATTTGAATTAA
195 CAACTTTTGGTCTTTGAATTAA
* * * ** * ** * *
3140 AAACATATTTACGTAAGAATTGATTCTCTCTTCATTCTTAGCCGAGTTTCCAAACTTATCAAACT
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACT
* * * * **
3205 TTTACCAGTTCTTTTATAACTTTCG-TTCCTTAAACTATTCAACGTGATCTGTTCCTTCGAGCAA
66 TTTACGAGTTCTTTTATAAC-TTCGATTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAA
* * ** * * *
3269 -TTTTCGAACATTCCATGC-TCGAAATATTTCATTATTTGGTCTTAATAGTTTGTCATATTGTAA
130 TTTTTCGAACATTCCATGCTTGGGAA-ATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAA
** * *
3332 ACAAGATTCGATCTTTGAATTAA
194 ACAACTTTTGGTCTTTGAATTAA
* * * * *
3355 AAA-TGTATTTACGTGAGAATTATTTCTCTCTTGGTTCTTCGCCGATCTTTCGAATTTGTCAAAC
1 AAACT-TATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAAC
* * * * * *
3419 TTTTACGAGTTC-TTTATTTACTTC-AGTTTCATAAAGTTTTCAAGACGATCCATTCCTTTGAGC
65 TTTTACGAGTTCTTTTA-TAACTTCGA-TTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGC
* * * *** *
3482 AGTTTTCCAAACATTCCATGCTCAAGAAATCGCATCATTTGCTCTAAATAGTTTGTCATTTTGTA
128 AATTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTA
3547 AACAACTTTTGGTCTTTGAATTAA
193 AACAACTTTTGGTCTTTGAATTAA
* *
3571 AAACTTATTTACGTGAGAATTG-TT-TCTCTTGGTGCTTGGCCGATCTTCCGAACTTGTCAAACT
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACT
* * * **
3634 TTTACGAGTTC-TTTATTAACTTC-AGTTTCTTAAAGTATTCAAGGTGATCCATTCCTTCAAAAA
66 TTTACGAGTTCTTTTA-TAACTTCGA-TTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCA
* * * * *
3697 ATTTTCCAAACATTCCATCCTCGGGAAATCGCATCATTT-GTCTAAATAGTTTGTCATTTTGTGA
129 ATTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAA
* *
3761 ACAACTTTTGGTTTTTGATTTAA
194 ACAACTTTTGGTCTTTGAATTAA
* * * *
3784 AAACTTATTTTCGTGAGAATTGTTTCACTCTTGGTTCTTGGCCGATCTTTCGAACTTGTCAAACT
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACT
* * ** *
3849 TTTACAAGTTC-TTTATTAACTTC-AGTTTCTTCCAGTATTCAAGACGATCCATTCCTTCGAGCA
66 TTTACGAGTTCTTTTA-TAACTTCGA-TTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCA
* * * ** * * * *
3912 AATTTTCGAAAATTCCATGCTCGAAAAATCGCATCATTTGATTTAAATAGTTTGTCATTTTCTGA
129 ATTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAA
* *
3977 CCAACTTTTGGTCTTCGAATTAA
194 ACAACTTTTGGTCTTTGAATTAA
** * * * *
4000 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGATCGATCTTTCGAACTTTTTAAACT
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACT
* * * * * * * *
4065 TTTACGAGTT-GTTTATTAACTCCAATTTCTTAAAGTATTCAAGGTGATCCATTCCATCTAGCAG
66 TTTACGAGTTCTTTTA-TAACTTCGATTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAA
* * * * *
4129 TTTTCCAAAAATTTCATGCTTGGGAAATCACATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
130 TTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
4194 CAACTTTTGGTCTTTGAATTAA
195 CAACTTTTGGTCTTTGAATTAA
* * * * ** ** * * *
4216 AAACTTATTTATGTGACAATTGTTTCTATTTTATTTCTTGGTTGAACATCCGAACTTATTAAA-T
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACT
** * * *
4280 GTTTGTGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAATCCTTCGAGCAA
66 -TTTACGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAA
** ** * *
4345 TTTTTCGAACATTCCATGCTTAAGAAATATCATTATTTGGTCTAAATAGTTTGTCTTTTTGTAAA
130 TTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
*
4410 CAACTTTTGGTCTTTGATTTAA
195 CAACTTTTGGTCTTTGAATTAA
* * * ** **
4432 AGACATATCTGTA--TGAGAATTGTTTCTCTCTTGGTTCTTAGAAGAACTTCCGAACAAGTCAAA
1 AAACTTAT-T-TACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAA
*** *
4495 CTTTTACGAGTTCTTTTATAACTTC-ATGTCCTTAAAGTATTCAAGATAATTCATTCCTTCGAGC
64 CTTTTACGAGTTCTTTTATAACTTCGAT-TCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGC
* * * * ** *
4559 TA-TTTTCTAAACATTCCATGCTCGAGAAATCTTATCATTTGGTCTAAACAGTTTGTCATTTTGT
128 AATTTTTC-GAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGT
* *
4623 -AACAACTTTTAGTCTTTGAATTTA
192 AAACAACTTTTGGTCTTTGAATTAA
* ** * *
4647 AAACTTATTTACATGAGAATTGTTTCTCTCTTATTTCTTGGCCGAACATCTGAACTTGGT-AAAC
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTT-GTCAAAC
* * * * * * * * *
4711 GTTTGCAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAATGTGATCCAATCCTTCGATCAA
65 TTTTACGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAA
* * * *
4776 TTTTTCAAACATTCCATGATCGGGAAATTGCATCATTTGGT-TAAATAGTTTGTCATTTTGTAAA
130 TTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
*
4840 CAATTTTTGGTCTTTGAATTAA
195 CAACTTTTGGTCTTTGAATTAA
* ** * * * **
4862 AAAGTTATTTATATAAGAATTTTTTCTCTCTTGGTTCTT-GCCGAACATCAAAACTTGTCAAACT
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACT
* * *
4926 TTTACGAGTTCTTTTATAACTTC-AGTTCCTTAAAGTATTCAAGACGATTCATTCCTTTGA-CAA
66 TTTACGAGTTCTTTTATAACTTCGA-TTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAA
* * * *
4989 ATTTTCTGAACATTCCACGCTTGGGAAATCACATCATTTGGTCTAAATAGTTTGTCACTTTGTAA
130 TTTTTC-GAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAA
* *
5054 ACAACTTTTGGTATATGAATTAA
194 ACAACTTTTGGTCTTTGAATTAA
* * * * * * *
5077 AAACATT-TTTAAGTAAGAATTGTTTCTCTCTTCGTTCTTGGCCAAATTTCCAAACTTTTCAAAC
1 AAAC-TTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAAC
* * * ** *
5141 TTTTACGAGTTCTTTTATAACTTCCG-TTCCTTAAACTATTCAACGTGATCTGTTCCTTTGAGCA
65 TTTTACGAGTTCTTTTATAACTT-CGATTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCA
** * *** * *
5205 ATTTTT-GAACATTCCATGCTCAGAAAATTTTATCATTTGGTCAAAATATTTTGTCATTTTGTAA
129 ATTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAA
* *
5269 ACAAAATTTT-GTCTTTAAATTAA
194 AC-AACTTTTGGTCTTTGAATTAA
* * * * * *
5292 AAA-TGTATTTACATGAGAATTATTTCTCTCTTGCTTCTTGGTCGATCTTCTGAACTTGTCAAAC
1 AAACT-TATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAAC
* * * ** * * * * * **
5356 TTTTACGAG-CCCTTTATTTACTTTTTAGTTTCATAAAGTTTTCAAGGTGATCCACTCCTTTAAG
65 TTTTACGAGTTCTTTTA-TAAC-TTCGA-TTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAG
* * * * *
5420 CAGTTTTTCGAACATTCCATGCTCGAGAGATCGCAAT-ATTTGGTCTAAATAGTTTGTTATTTTG
127 CAATTTTTCGAACATTCCATGCTTGGGAAATCGC-ATCATTTGGTCTAAATAGTTTGTCATTTTG
* * *
5484 TAGATAACTTTTGGTCTTGGAATTAA
191 TAAACAACTTTTGGTCTTTGAATTAA
* **
5510 AAACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGGCC-AATCTTCTAAACTTGTCAAAC
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAA-CTTCCGAACTTGTCAAAC
* * * *
5574 TTTTACGAGTTC-TTTATTAACTT-TAGTTTCTTAAAGTATTCAA-G-G-T--GTTCCTTTGAG-
65 TTTTACGAGTTCTTTTA-TAACTTCGA-TTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGC
* * * * *
5631 AAATTTTCTAACCATTCTATGCTTGGGAAATCGCATCTTTTGGTCTAAATAGTTTATCATTTTGT
128 AATTTTTCGAA-CATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGT
* * **
5696 GAACAACTTTTGCT-TTTGAATTGT
192 AAACAACTTTTGGTCTTTGAATTAA
* * *
5720 AAACTTATTTACGTGAGAATTGTTTCTCTATTGGTTCTTGGTCGATCTTCCGAACTTGTCAAACT
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACT
* * * *
5785 TTTACGAGTT-TTTTTTAACTACAGATT-TTTAAAGTATTCAAGGCGAGCCATTCCTTCGAGCAA
66 TTTACGAGTTCTTTTATAACTTC-GATTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAA
* * * *
5848 TTTTTTGAACATTCCATGCTCGGGAAATCGCGTCATTTGGTCTAAATAGTTTGTCATTTTGTGAA
130 TTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
* *
5913 CAAC-TATGGTCTTCGAATTAA
195 CAACTTTTGGTCTTTGAATTAA
* *
5934 AAACTTATTTACGTGA-AATTGTTTCTGTCTTGGTTCTTGGCCGATCTTCCGAACTTGTCAAACT
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACT
* * * *
5998 TTTACAAGTTC-TTTATTAACTTC-AGTTTCTTAAAGTATTCAAGGCAATCCATTCCATCG-GTC
66 TTTACGAGTTCTTTTA-TAACTTCGA-TTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAG-C
** * * *
6060 AATTTTTTAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAATTAGTTTGTCCTTTTGTA
128 AATTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTA
* **
6125 AACAACTTTTGGTGTTCAAATTAA
193 AACAACTTTTGGTCTTTGAATTAA
* * * * * * *
6149 AAACTTATATACGTGAGAATTGTTTCTCTCTTGTTTCTTGGGCAAACATCCTAACTTGTTAAA-T
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACT
* * * * ** * *
6213 GTTTGCAAGTTCTTTTATAAATTTGATTCCTTAAAGTATTCAACACGTTCCAATCCTTCGAGCAA
66 -TTTACGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAA
* ** *
6278 TTTTTCGAACATTCCATACTCAGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGCAAA
130 TTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
* * * *
6343 CAACATTTAGTCTTTAAATTTA
195 CAACTTTTGGTCTTTGAATTAA
* * * * * *
6365 AAACTTATTTACATGAGAGTTTTTTCTCTCTTTGTT-TTAGGATGAACTTCTGAACTTGTCAAAC
1 AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTT--G--G--C--C-GAACTT-CCGAAC
* *
6429 TTGTCAAACTTTTACGAGTTCTTTTATAACTTC-ACTTCCTTAAAGTATTCAACGCGATCCACTC
56 TTGTCAAACTTTTACGAGTTCTTTTATAACTTCGA-TTCCTTAAAGTATTCAAGGCGATCCATTC
* * * *
6493 CTTCGAGCAATTTATCGATA-ATTCCATGGTCGTGAAATCGCATCATTTGGTCTAAATAGTTTGT
120 CTTCGAGCAATTTTTCGA-ACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGT
6557 CATTTTGTAAACAA
184 CATTTTGTAAACAA
6571 GTGATGGTAT
Statistics
Matches: 3411, Mismatches: 571, Indels: 181
0.82 0.14 0.04
Matches are distributed among these distances:
209 18 0.01
210 90 0.03
211 64 0.02
212 1 0.00
213 145 0.04
214 621 0.18
215 744 0.22
216 1385 0.41
217 74 0.02
218 130 0.04
219 5 0.00
223 1 0.00
224 5 0.00
225 126 0.04
226 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (216 bp):
AAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACT
TTTACGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGGCGATCCATTCCTTCGAGCAAT
TTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAC
AACTTTTGGTCTTTGAATTAA
Found at i:4014 original size:645 final size:645
Alignment explanation
Indices: 2278--6570 Score: 4447
Period size: 645 Copynumber: 6.6 Consensus size: 645
2268 TCCAATCCAT
* * *
2278 AAACTTATTTACGTGAGAATTATTTCTCTCTTGGTT-TTGGAACGAACTTCCAAACTTGTCAAAC
1 AAACTTATTTACGTGAGAATT-GTTCTCTCTTGGTTCTTGG-CCGAACATCCAAACTTGTCAAAC
* **** * *
2342 TCTTGTTTGTTCTTT-TATAACTTC-GATTCCTTAAAGTATTCAAGACGATCCGTTCCTTTGAGT
64 TTTTACGAGTTCTTTAT-TAACTTCAG-TTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGA
* * *
2405 AATTTTTCAAACATTCCATGGTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTA
127 AATTTTCCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTA
* *
2470 AACAACTTTT-GTTCTTTGAATTT-AAAACTTATTTA-ATGAGAATT-TTTCTCTCTTGGTTTTT
192 AACAACTTTTGGTT-TTTG-ATTTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTT
** * * ***
2531 GGGTGAACTTCCAAACTTGTCAAACTCTTATTTGTTCTTTTATAACTTCAGTTCCTTAAAGTATT
255 GGCCGATCTTCCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTAAAGTATT
** * * * * ** *
2596 CAAGGCGATCCGCTCCTTCGATCAATTCTCCGAACATTCCAAGCT-TAGGAAATCATATTATTTG
320 CAA-GCGATCCATTCCTTCGAGCAATT-TTCGAACATTCCATGCTCGA-GAAATCGCATCATTTG
*
2660 GTCTAAA-AGGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTCACGTGA
382 GTCTAAATA-GTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGA
* * * * * * * *
2724 GAATTGTTTCTTTCTTGGTTCTTTGACGAACTTCCGAACATGTCAAACTCTTATTG-GTTCTTT-
446 GAATTGTTTCTCTCTTGGTTCTTGGCCGATCTTTCGAACTTGTCAAACTTTTA-CGAGTTCTTTA
* * * **
2787 TATAACTTC-GATTCCTTAAAGTATTCAAGGCGATCCGTT-CTTTCAAGCAATTTTTTTAACATT
510 T-TAACTTCAG-TTTCTTAAAGTATTCAAGGCGATCCATTCCTTT-GAGCAATTTTTCAAACATT
** **
2850 CCATGCTCGAGAAATCTTATCATTTAATCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCT
572 CCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCT
2915 TTGAATTAA
637 TTGAATTAA
* * * * *
2924 AAACTTATTAACGTGAGAATTGTTTCTCTCTTGGGTCTTGGACGAACCTCCGAACTTGTCAAACT
1 AAACTTATTTACGTGAGAATTG-TTCTCTCTTGGTTCTTGGCCGAACATCCAAACTTGTCAAACT
* ** * * * *
2989 TTTATTG-GTTCTTTTATT-ACTTTGGTTCCTTAAAGTATTCAAGGCGAACCATTTCTTTGAGCA
65 TTTA-CGAGTTC-TTTATTAACTTCAGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGAA
* * *
3052 ATTTTCCCAACATTCCATGCTCGGGAAATCGCGTTATTTGGTCTAAATAGTTTGTCATTTTGTAA
128 ATTTTCCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAA
* * * * * ** *
3117 ACAACTTTTGGTATTTGAATTAAAAACATATTTACGTAAGAATTGATTCTCTCTTCATTCTTAGC
193 ACAACTTTTGGTTTTTGATTTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGC
* * *
3182 CGAGT-TTCCAAACTTATCAAACTTTTACCAGTTCTTTTATAACTTTC-GTTCCTTAAACTATTC
258 CGA-TCTTCCAAACTTGTCAAACTTTTACGAGTTCTTTTATAAC-TTCAGTTCCTTAAAGTATTC
* ** ** *
3245 AACGTGATCTGTTCCTTCGAGCAATTTTCGAACATTCCATGCTCGA-AATATTTCATTATTTGGT
321 AA-GCGATCCATTCCTTCGAGCAATTTTCGAACATTCCATGCTCGAGAA-ATCGCATCATTTGGT
* * ** * *
3309 CTTAATAGTTTGTCATATTGTAAACAAGATTCGATCTTTGAATTAAAAA-TGTATTTACGTGAGA
384 CTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACT-TATTTACGTGAGA
* * * *
3373 ATTATTTCTCTCTTGGTTCTTCGCCGATCTTTCGAATTTGTCAAACTTTTACGAGTTCTTTATTT
448 ATTGTTTCTCTCTTGGTTCTTGGCCGATCTTTCGAACTTGTCAAACTTTTACGAGTTCTTTATTA
* * * * *
3438 ACTTCAGTTTCATAAAGTTTTCAAGACGATCCATTCCTTTGAGCAGTTTTCCAAACATTCCATGC
513 ACTTCAGTTTCTTAAAGTATTCAAGGCGATCCATTCCTTTGAGCAATTTTTCAAACATTCCATGC
* *
3503 TCAAGAAATCGCATCATTTGCTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAAT
578 TCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAAT
3568 TAA
643 TAA
* * * *
3571 AAACTTATTTACGTGAGAATTGTT-TCTCTTGGTGCTTGGCCGATCTTCCGAACTTGTCAAACTT
1 AAACTTATTTACGTGAGAATTGTTCTCTCTTGGTTCTTGGCCGAACATCCAAACTTGTCAAACTT
* ** ** *
3635 TTACGAGTTCTTTATTAACTTCAGTTTCTTAAAGTATTCAAGGTGATCCATTCCTTCAAAAAATT
66 TTACGAGTTCTTTATTAACTTCAGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGAAATT
* *
3700 TTCCAAACATTCCATCCTCGGGAAATCGCATCATTT-GTCTAAATAGTTTGTCATTTTGTGAACA
131 TTCCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACA
* *
3764 ACTTTTGGTTTTTGATTTAAAAACTTATTTTCGTGAGAATTGTTTCACTCTTGGTTCTTGGCCGA
196 ACTTTTGGTTTTTGATTTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGA
* * * * **
3829 TCTTTCGAACTTGTCAAACTTTTACAAGTTC-TTTATTAACTTCAGTTTCTTCCAGTATTCAAGA
261 TCTTCCAAACTTGTCAAACTTTTACGAGTTCTTTTA-TAACTTCAGTTCCTTAAAGTATTCAAG-
* * * *
3893 CGATCCATTCCTTCGAGCAAATTTTCGAAAATTCCATGCTCGAAAAATCGCATCATTTGATTTAA
324 CGATCCATTCCTTCGAGC-AATTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAA
* * * *
3958 ATAGTTTGTCATTTTCTGACCAACTTTTGGTCTTCGAATTAAAAACTTATTTACGTGAGAATTGT
388 ATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
** * * * *
4023 TTCTCTCTTGGTTCTTGATCGATCTTTCGAACTTTTTAAACTTTTACGAGTTGTTTATTAACTCC
453 TTCTCTCTTGGTTCTTGGCCGATCTTTCGAACTTGTCAAACTTTTACGAGTTCTTTATTAACTTC
* * * * * * * * *
4088 AATTTCTTAAAGTATTCAAGGTGATCCATTCCATCT-AGCAGTTTTCCAAAAATTTCATGCTTGG
518 AGTTTCTTAAAGTATTCAAGGCGATCCATTCC-TTTGAGCAATTTTTCAAACATTCCATGCTCGA
*
4152 GAAATCACATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAA
582 GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAA
* * * * ** ** * * *
4216 AAACTTATTTATGTGACAATTGTTTCTATTTTATTTCTTGGTTGAACATCCGAACTTATTAAA-T
1 AAACTTATTTACGTGAGAATTG-TTCTCTCTTGGTTCTTGGCCGAACATCCAAACTTGTCAAACT
** * * * *
4280 GTTTGTGAGTTCTTT-TATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCAATCCTTCGAGCA
65 -TTTACGAGTTCTTTAT-TAACTTCAGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGAA
* * *** ** * *
4344 ATTTTTCGAACATTCCATGCTTAAGAAATATCATTATTTGGTCTAAATAGTTTGTCTTTTTGTAA
128 ATTTTCCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAA
* * * *
4409 ACAACTTTTGGTCTTTGATTTAAAGACATATCTGTA--TGAGAATTGTTTCTCTCTTGGTTCTTA
193 ACAACTTTTGGTTTTTGATTTAAAAACTTAT-T-TACGTGAGAATTGTTTCTCTCTTGGTTCTTG
** * * **
4472 GAAGAACTTCCGAACAAGTCAAACTTTTACGAGTTCTTTTATAACTTCA-TGTCCTTAAAGTATT
256 GCCGATCTTCCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGT-TCCTTAAAGTATT
** * * * **
4536 CAAGATAATTCATTCCTTCGAGCTATTTTCTAAACATTCCATGCTCGAGAAATCTTATCATTTGG
320 CAAG-CGATCCATTCCTTCGAGCAATTTTC-GAACATTCCATGCTCGAGAAATCGCATCATTTGG
* * * *
4601 TCTAAACAGTTTGTCATTTTGT-AACAACTTTTAGTCTTTGAATTTAAAACTTATTTACATGAGA
383 TCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGA
** * * * * *
4665 ATTGTTTCTCTCTTATTTCTTGGCCGAAC-ATCTGAACTTGGT-AAACGTTTGCAAGTTCTTT-T
448 ATTGTTTCTCTCTTGGTTCTTGGCCGATCTTTC-GAACTT-GTCAAACTTTTACGAGTTCTTTAT
** * * * * * *
4727 ATAACTTTGGTTCCTTAAAGTATTCAATGTGATCCAATCCTTCGATCAATTTTTCAAACATTCCA
511 -TAACTTCAGTTTCTTAAAGTATTCAAGGCGATCCATTCCTTTGAGCAATTTTTCAAACATTCCA
* * * *
4792 TGATCGGGAAATTGCATCATTTGGT-TAAATAGTTTGTCATTTTGTAAACAATTTTTGGTCTTTG
575 TGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTG
4856 AATTAA
640 AATTAA
* ** * * *
4862 AAAGTTATTTATATAAGAATTTTTTCTCTCTTGGTTCTT-GCCGAACATCAAAACTTGTCAAACT
1 AAACTTATTTACGTGAGAA-TTGTTCTCTCTTGGTTCTTGGCCGAACATCCAAACTTGTCAAACT
* *
4926 TTTACGAGTTCTTT-TATAACTTCAGTTCCTTAAAGTATTCAAGACGATTCATTCCTTTGACAAA
65 TTTACGAGTTCTTTAT-TAACTTCAGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGAAA
** * * * *
4990 TTTTCTGAACATTCCACGCTTGGGAAATCACATCATTTGGTCTAAATAGTTTGTCACTTTGTAAA
129 TTTTCCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
* * * * * *
5055 CAACTTTTGGTATATGAATTAAAAACATT-TTTAAGTAAGAATTGTTTCTCTCTTCGTTCTTGGC
194 CAACTTTTGGTTTTTGATTTAAAAAC-TTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGC
* * * *
5119 CAAAT-TTCCAAACTTTTCAAACTTTTACGAGTTCTTTTATAACTTCCGTTCCTTAAACTATTCA
258 C-GATCTTCCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTAAAGTATTCA
* ** * * ***
5183 ACGTGATCTGTTCCTTTGAGCAATTTTTGAACATTCCATGCTC-AGAAAATTTTATCATTTGGTC
322 A-GCGATCCATTCCTTCGAGCAATTTTCGAACATTCCATGCTCGAG-AAATCGCATCATTTGGTC
* * * * *
5247 AAAATATTTTGTCATTTTGTAAACAAAATTTT-GTCTTTAAATTAAAAA-TGTATTTACATGAGA
385 TAAATAGTTTGTCATTTTGTAAAC-AACTTTTGGTCTTTGAATTAAAAACT-TATTTACGTGAGA
* * * **
5310 ATTATTTCTCTCTTGCTTCTTGGTCGATC-TTCTGAACTTGTCAAACTTTTACGAGCCCTTTATT
448 ATTGTTTCTCTCTTGGTTCTTGGCCGATCTTTC-GAACTTGTCAAACTTTTACGAGTTCTTTATT
* * * * * * * * *
5374 TACTTTTTAGTTTCATAAAGTTTTCAAGGTGATCCACTCCTTTAAGCAGTTTTTCGAACATTCCA
512 AAC--TTCAGTTTCTTAAAGTATTCAAGGCGATCCATTCCTTTGAGCAATTTTTCAAACATTCCA
* * * * *
5439 TGCTCGAGAGATCGCAAT-ATTTGGTCTAAATAGTTTGTTATTTTGTAGATAACTTTTGGTCTTG
575 TGCTCGAGAAATCGC-ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTT
5503 GAATTAA
639 GAATTAA
* * *
5510 AAACTTATTTACATGAGAATTGTTTCTCTCTTGGTTCTTGGCC-AATCTTCTAAACTTGTCAAAC
1 AAACTTATTTACGTGAGAATTG-TTCTCTCTTGGTTCTTGGCCGAA-CATCCAAACTTGTCAAAC
* * *
5574 TTTTACGAGTTCTTTATTAACTTTAGTTTCTTAAAGTATTCAAG--G-T--GTTCCTTTGAGAAA
64 TTTTACGAGTTCTTTATTAACTTCAGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGAAA
* * * * * * *
5634 TTTTCTAACCATTCTATGCTTGGGAAATCGCATCTTTTGGTCTAAATAGTTTATCATTTTGTGAA
129 TTTTCCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
* * ** * *
5699 CAACTTTT-GCTTTTGAATTGTAAACTTATTTACGTGAGAATTGTTTCTCTATTGGTTCTTGGTC
194 CAACTTTTGGTTTTTGATTTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCC
* * * *
5763 GATCTTCCGAACTTGTCAAACTTTTACGAGTT-TTTTTTAACTACAGATT-TTTAAAGTATTCAA
259 GATCTTCCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAG-TTCCTTAAAGTATTCAA
* * * *
5826 GGCGAGCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCGTCATTTGGTCT
323 -GCGATCCATTCCTTCGAGCAA-TTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCT
* * *
5891 AAATAGTTTGTCATTTTGTGAACAAC-TATGGTCTTCGAATTAAAAACTTATTTACGTGA-AATT
386 AAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATT
* * *
5954 GTTTCTGTCTTGGTTCTTGGCCGATCTTCCGAACTTGTCAAACTTTTACAAGTTCTTTATTAACT
451 GTTTCTCTCTTGGTTCTTGGCCGATCTTTCGAACTTGTCAAACTTTTACGAGTTCTTTATTAACT
* * * *
6019 TCAGTTTCTTAAAGTATTCAAGGCAATCCATTCCATCG-GTCAATTTTTTAAACATTCCATGCTC
516 TCAGTTTCTTAAAGTATTCAAGGCGATCCATTCCTTTGAG-CAATTTTTCAAACATTCCATGCTC
* * * * **
6083 GGGAAATCGCATCATTTGGTCTAATTAGTTTGTCCTTTTGTAAACAACTTTTGGTGTTCAAATTA
580 GAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTA
6148 A
645 A
* * * * * *
6149 AAACTTATATACGTGAGAATTGTTTCTCTCTTGTTTCTTGGGCAAACATCCTAACTTGTTAAA-T
1 AAACTTATTTACGTGAGAATTG-TTCTCTCTTGGTTCTTGGCCGAACATCCAAACTTGTCAAACT
* * * * * * * * * *
6213 GTTTGCAAGTTCTTTTATAAATTTGA-TTCCTTAAAGTATTCAACACGTTCCAATCCTTCGAGCA
65 -TTTACGAGTTC-TTTATTAACTTCAGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGAA
* * * * *
6277 ATTTTTCGAACATTCCATACTCAGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGCAA
128 ATTTTCCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAA
* * ** * * * *
6342 ACAACATTTAGTCTTTAAATTT-AAAACTTATTTACATGAGAGTTTTTTCTCTCTTTGTT-TTAG
193 ACAACTTTTGGT-TTTTGATTTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTT--
* * *
6405 GATGAACTTCTGAACTTGTCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCACTTCCTT
255 G--G--C--C-GATCTT-CCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTT
* * *
6470 AAAGTATTCAACGCGATCCACTCCTTCGAGCAATTTATCGATA-ATTCCATGGTCGTGAAATCGC
312 AAAGTATTCAA-GCGATCCATTCCTTCGAGCAATTT-TCGA-ACATTCCATGCTCGAGAAATCGC
6534 ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAA
374 ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAA
6571 GTGATGGTAT
Statistics
Matches: 3041, Mismatches: 506, Indels: 191
0.81 0.14 0.05
Matches are distributed among these distances:
638 4 0.00
639 181 0.06
640 12 0.00
641 59 0.02
642 72 0.02
643 140 0.05
644 348 0.11
645 750 0.25
646 290 0.10
647 618 0.20
648 362 0.12
649 67 0.02
650 2 0.00
652 1 0.00
653 5 0.00
654 29 0.01
655 100 0.03
656 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (645 bp):
AAACTTATTTACGTGAGAATTGTTCTCTCTTGGTTCTTGGCCGAACATCCAAACTTGTCAAACTT
TTACGAGTTCTTTATTAACTTCAGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGAAATT
TTCCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACA
ACTTTTGGTTTTTGATTTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGA
TCTTCCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGTTCCTTAAAGTATTCAAGCG
ATCCATTCCTTCGAGCAATTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATA
GTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
TCTCTTGGTTCTTGGCCGATCTTTCGAACTTGTCAAACTTTTACGAGTTCTTTATTAACTTCAGT
TTCTTAAAGTATTCAAGGCGATCCATTCCTTTGAGCAATTTTTCAAACATTCCATGCTCGAGAAA
TCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAA
Found at i:5277 original size:22 final size:21
Alignment explanation
Indices: 5228--5281 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
5218 CCATGCTCAG
* *
5228 AAAATTTTATCATTTGGTCAA
1 AAAATTTTGTCATTTGGTAAA
* *
5249 AATATTTTGTCATTTTGTAAA
1 AAAATTTTGTCATTTGGTAAA
5270 CAAAATTTTGTC
1 -AAAATTTTGTC
5282 TTTAAATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.46
Consensus pattern (21 bp):
AAAATTTTGTCATTTGGTAAA
Found at i:11477 original size:5 final size:6
Alignment explanation
Indices: 11464--11492 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
11454 ATGTTGAATG
11464 AGAAAA AG-AAA AGAAAA AGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
11493 TTTTCTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:14084 original size:21 final size:23
Alignment explanation
Indices: 14043--14090 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
14033 CTAAAAATGA
14043 AGAAATAAGGAAGGTGAGAGAAGG
1 AGAAATAAGGAAGGT-AGAGAAGG
*
14067 AGAAATAAGG-AGGT-GAGATGG
1 AGAAATAAGGAAGGTAGAGAAGG
14088 AGA
1 AGA
14091 GCGACAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
23 4 0.17
24 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.42, T:0.10
Consensus pattern (23 bp):
AGAAATAAGGAAGGTAGAGAAGG
Found at i:15168 original size:14 final size:14
Alignment explanation
Indices: 15149--15180 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
15139 AAAATCTTAT
15149 AAGTGGCTTTGGGG
1 AAGTGGCTTTGGGG
15163 AAGTGGCTTTGGGG
1 AAGTGGCTTTGGGG
15177 AAGT
1 AAGT
15181 TAGGTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.19, C:0.06, G:0.47, T:0.28
Consensus pattern (14 bp):
AAGTGGCTTTGGGG
Found at i:22218 original size:20 final size:20
Alignment explanation
Indices: 22193--22230 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22183 GTTTCACAAC
*
22193 TTGAAAAGTAAAACCTAAAA
1 TTGAAAACTAAAACCTAAAA
*
22213 TTGAAAACTAAAATCTAA
1 TTGAAAACTAAAACCTAA
22231 GTAATGGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.24
Consensus pattern (20 bp):
TTGAAAACTAAAACCTAAAA
Found at i:22902 original size:14 final size:14
Alignment explanation
Indices: 22883--22909 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22873 GTTTCAAAGC
22883 ATAAAAATAAAATG
1 ATAAAAATAAAATG
22897 ATAAAAATAAAAT
1 ATAAAAATAAAAT
22910 AAAGAAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
ATAAAAATAAAATG
Found at i:24175 original size:125 final size:125
Alignment explanation
Indices: 23946--24195 Score: 419
Period size: 125 Copynumber: 2.0 Consensus size: 125
23936 AACACATAGG
* * * *
23946 TTACACAATTTATTTAATTAAGAAATCTAAACTAAATCCTATGAAAACATAACAAAAATACTTGA
1 TTACACAATTTATTCAAATAAGAAATCTAAACTAAATCCTACGAAAAAATAACAAAAATACTTGA
*
24011 TTTCAAGCTCTTCAAGTGTGAAAAATAGTTCAATTTGCTAGGTATGAAACCAACAAATCA
66 TTTCAAGCTCTTCAAGTGTGAAAAATAGTTCAATCTGCTAGGTATGAAACCAACAAATCA
*
24071 TTACACAATTTATTCAAATAAGAAATCTAAACTAAATCCTACGAAAAAATAAGAAAAATACTTGA
1 TTACACAATTTATTCAAATAAGAAATCTAAACTAAATCCTACGAAAAAATAACAAAAATACTTGA
* * *
24136 TTTCAAGCTCTTCAAGTGTGAAAAATAGTTTAATCTGCTAGGTATGAAACCGACAGATCA
66 TTTCAAGCTCTTCAAGTGTGAAAAATAGTTCAATCTGCTAGGTATGAAACCAACAAATCA
24196 CTAACCTACT
Statistics
Matches: 116, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
125 116 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (125 bp):
TTACACAATTTATTCAAATAAGAAATCTAAACTAAATCCTACGAAAAAATAACAAAAATACTTGA
TTTCAAGCTCTTCAAGTGTGAAAAATAGTTCAATCTGCTAGGTATGAAACCAACAAATCA
Found at i:28257 original size:46 final size:46
Alignment explanation
Indices: 28185--28289 Score: 156
Period size: 46 Copynumber: 2.3 Consensus size: 46
28175 AAAGAACAGG
* * *
28185 TTTCAAAAACCCAAGTTTCTAAGTTTGATTTTTAAAAAAATTTAGA
1 TTTCAAAAACCCAAGTTTCTAAGTTTGATTTTAAAAAAAATTCAAA
* *
28231 TTTCAAAAACCCAAGTTTTTAGGTTTGATTTTAAAAAAAATTCAAA
1 TTTCAAAAACCCAAGTTTCTAAGTTTGATTTTAAAAAAAATTCAAA
*
28277 TTTCAGAAACCCA
1 TTTCAAAAACCCA
28290 TATTTCATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (46 bp):
TTTCAAAAACCCAAGTTTCTAAGTTTGATTTTAAAAAAAATTCAAA
Done.