Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005760.1 Kokia drynarioides strain JFW-HI SEQ_120018, 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: 11580
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Found at i:462 original size:215 final size:216
Alignment explanation
Indices: 77--7904 Score: 6144
Period size: 216 Copynumber: 36.5 Consensus size: 216
67 CCGAGCATCC
* * * * *
77 AATGTTCGGAAAATTGCTCAAAGGAACGAAAT-GCCTTGAATACTTTAAGGAACTGAAGTTATAA
1 AATGTTCGAAAAATTGCTCGAAGGAATG-GATCGCCTTGAATACTTTAAGGAACCGAAGTTATAA
* * * * *
141 AGGAACGAATAAGAGCTTGACAAGTTCAAAAGTTCATCCTAA-AACCAAGAGAGAAACAATTCTC
65 AAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCC-AAGAACCAAGAGAGAAACAATTCTC
* * * ** * * **
205 ATGTAAATAAGATTTTAATTCAAAGATGAAAAGCTATTTACAAAATGATGAACTATTTAGACC-A
129 ACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAA
* *
269 ATGATGCGATTTCCTGAGCATCG
194 ATGATACGATTTCCTGAGCATGG
* * * * * *
292 AATATTCGAAAAATTGCTCGGAGAAATGGATCGCCTTGAATACTTTAAGGAGCCAAAGTTTTAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
*
357 AGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCAAAGAACCAAGAGAGAAACAATTCTCAC
66 AGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAC
* * * * *
422 GTGAATAAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATAATAAACAATTTAGACCGAAT
131 GTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAAT
* ** *
487 GATACAATTTCCCAAGCATTG
196 GATACGATTTCCTGAGCATGG
* * * * * * * *
508 AATGTTCGAATAATAGCTCGAAGGAATTGATTGTCTTGAATAGTTTAAGGAACTGAAGTTATGAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * * * *
573 AGAACTC-GTAAAAGTTTGACAAGTTTTG-ATGTTCG-GCAAGAACCAAGAGAGAAACAATTCTT
66 AGAAC-CAATAAGAGTTTGACAAG-TTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTC
* * * * * * *
635 GCATAAATAACTTTTTAATTCAAAGACCAAAAATTATTTACAAAATGACAAAATATTTAGACCAA
129 ACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAA
*
700 ATGATACTATTTCCTGAGCATGG
194 ATGATACGATTTCCTGAGCATGG
* * *
723 AATGTTC-AGAAAATTGCTCAAAGGAACT-GATCGCCTTTAATACTTTAAGGAACCGAAGGTATA
1 AATGTTCGA-AAAATTGCTCGAAGGAA-TGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATA
* * * * *
786 AAAGAACCAATAAGAGTATGACAAGTTCGGAAGTTTGTCCAAGAACCAAGA-AAAAATTAATTCT
64 AAAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAA-CAATTCT
* * *
850 CATGTGAATAAGTTTTTAATTCAAAAACCAAAAGTTTGTTTACAATATGACAAACTATTTAGACC
128 CACGTGAATAAGTTTTTAATTCAAAGACCAAAAG-TTGTTTACAAAATGACAAACTATTTAGACC
* *
915 AAAAGATACGATTT-TTCGAGCATGG
192 AAATGATACGATTTCCT-GAGCATGG
* * ** *
940 AATGTTCGAAAAATTGCTTGAAAGAACAGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * ** * * * *
1005 AGAACCAATAAGAGCTTGATAGGTTCTTAAGTACATCCTAA-AACCAATAGAGAAACAAATCTCA
66 AGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCC-AAGAACCAAGAGAGAAACAATTCTCA
* * * *
1069 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATAACAAACAATTTCGGCCAAA
130 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAA
*
1134 TGATACAATTT-CTCGAGCATGG
195 TGATACGATTTCCT-GAGCATGG
* * ** * **
1156 AATGTT-TAGAAAATTGCTCGAAGGAATTGA-CTATCTTGAATAGTTTAAGGAACTAAAGTTATA
1 AATGTTCGA-AAAATTGCTCGAAGGAATGGATC-GCCTTGAATACTTTAAGGAACCGAAGTTATA
* * ** * *
1219 AAAGAACTC-GTAAAAGTTTGACAAGTTTTAAAGTTCG-ACTAGAACCAAGAGAGAAACAATTCA
64 AAAGAAC-CAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTC-
* * * * * * * * *
1282 T-ATGTAAATAACTTTTTAATTCAAAAACCAGAAGTTTTTTTTACAGAATGAAAAACTATTTGGA
127 TCACGTGAATAAGTTTTTAATTCAAAGACCAAAAG--TTGTTTACAAAATGACAAACTATTTAGA
*
1346 CCAAATGATACTATTTCCTGAGCATGG
190 CCAAATGATACGATTTCCTGAGCATGG
1373 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
* *
1438 AGAACCAATAAGAGTTTGACAAGTTCTG-AAGTTTGTCCAAGAACCAAGAGAAAAACAATTCTCA
66 AGAACCAATAAGAGTTTGACAAGTTC-GAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
* * **
1502 CTTGAATAAGTTTTTATTTCAAAGACCAAAAGTT-TCTTACAAAATGACAAACTATTTAGATTAA
130 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGT-TTACAAAATGACAAACTATTTAGACCAA
* *
1566 ATGATAAGATTTCTTGAGCATGG
194 ATGATACGATTTCCTGAGCATGG
* * * * *
1589 AATGTTTGAAAAATTGCTCGAAAGAACGGATCGCCTTGAACACTTTAAGGAACCAAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * ** *
1654 AGAACCAATAAGAGTTTGACAAGTTCGGATGTTCGACCAAGAAATAAGAGAG-AAC--TTGT---
66 AGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAC
* * * * **** * ** *
1713 TTG-ACAAG---TT-A-TAAAAGAACTCGTAAAAG-T-TTGACTTGTTCG-GAAGTTTTTCTAAG
131 GTGAATAAGTTTTTAATTCAAAG-AC-C--AAAAGTTGTTTACAAAAT-GACAAACTATT-T-AG
* * * * *
1769 AACCAAGA-GAGA-AATAATT-CT-AACGT-A
189 -ACCAA-ATGATACGAT--TTCCTGAGCATGG
*** * * *** ** *** * *
1796 AATAAGTT-TTTAAA----T--AA-AAAAGGA-AAACTTGTTTACAAAAAGGCAAAC-TA-TT-T
1 AAT--GTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGG-AACCGAAGTTAT
* * ** * * * * * *** *** *
1849 ---AG-ACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGGAAAATTGCTTAA-AG-GAATA-
63 AAAAGAACC-AAT-AAGAG-TTTGACAAG-TTCGAAAGTTCGTCCAAGAAC-CAAGAGAGAA-AC
** * * * * * * ** ****
1907 GGTTGT--CTTTAAT-A-CTTTTAGGAATCGAAGTAATAAAA-AAACTT-C----T-A-AAA--A
122 AATTCTCACGTGAATAAGTTTTTA--ATTCAAAG-ACCAAAAGTTGTTTACAAAATGACAAACTA
* * * * ** ***
1958 TTT-G-CCAACTTCAAAAG-TTTGCCCAAG-AACC
184 TTTAGACCAA-ATGATACGATTT-CCTGAGCATGG
*** * * * * * * * * *
1989 AA-GAGAGAAACAATT-CTC-ATGTAA---ATAAGTCTT---TAATTCAAAG-ACCAAATTTTTT
1 AATGTTCGAAA-AATTGCTCGAAGGAATGGAT-CGCCTTGAATACTTTAAGGAACCGAA---GTT
* ** * ** * * * **
2044 TTAATAA-ATGA-CAA-ACTA-TTTAGACCAAATAAT-GCTATTTC-TCGAGCATGGAA-TATTA
61 ATAA-AAGA--ACCAATAAGAGTTT-GA-CAAGT--TCGAAAGTTCGTC---CA-AGAACCAAGA
* * * ** * * * * * *
2102 G-GAAA-ATTTCTAGAAG-GAATGGATCA-TCATGAATACTTTAAAGAACACAAA-TT-ATAAAA
115 GAGAAACAATTCT-CACGTGAAT--A--AGT--T-TTTAATTCAAAGACCA-AAAGTTGTTTACA
* * * * * * * **
2161 GAACACGTA-AAAGT-TTGATA-ATTTCGAAAGTTCATCCAATACCATTCC-CAGCATCC
171 -AA-ATG-ACAAACTATT--TAGA---CCAAA--TGATACGAT----TTCCTGAGCATGG
* * * * **
2217 AAT-TTCGGAATATTGCTCGAAGGAATGGAACGCCTTGAATACTTTAACGAATTGAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
* ** * * * *
2281 TGAATGAAAAAGAGTTTGACAAGTTCGGATGTTCATCCCAA-AACCAAGAGAGAAACAATTCTCA
66 AGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGT-CCAAGAACCAAGAGAGAAACAATTCTCA
* * * * ** *
2345 TGTAAATAAGATTCTAATTCAAAGATGAAAAGTTGTTTACAAAATGATAAACTATTTAGACCAAA
130 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAA
*
2410 TGATGCGATTTCCTGAGCATGG
195 TGATACGATTTCCTGAGCATGG
* * *
2432 AATGTTCAAAAAATTGCTTGAAGGAATGGATCGCCTTGGATACTTTAAGGAACCGAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * * * *
2497 GGAAACAATAAGAGGTTGACAAGTTCGGAAGTTCGTCAAAGAACCAAGAGAGAAACAATTCTCAT
66 AGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAC
* * * * *
2562 GTGAATAAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATAATAAACAATTTAGACCGAAT
131 GTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAAT
* * *
2627 GATACAATTTCCCGAGTATGG
196 GATACGATTTCCTGAGCATGG
* * * * * * * * **
2648 AATGTTCAAAAAATAGCTC-AACGGAATTGATTGTCTTGAAAAGTTTAAGTAACTAAAGTTATAA
1 AATGTTCGAAAAATTGCTCGAA-GGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAA
* * * * ** *
2712 AAGAACTC-GTAAAAGTTTGTCAAGTTTTG-AAGTTC-AACAAGAACCAAGAGAGAAATAATTCT
65 AAGAAC-CAATAAGAGTTTGACAAG-TTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCT
* * * *
2774 TACGTAAATAAGTTTTTAACTCAAACACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCA
128 CACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCA
* * *
2839 AAAGATACGATTTCCCGATCATGG
193 AATGATACGATTTCCTGAGCATGG
* * * * *
2863 AATGTTC-AGAAAATTGCTCGAAGGAACGAATCACCTTGAATACTTTAAGGAATCAAAGTTAT-A
1 AATGTTCGA-AAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAA
* * * * * *
2926 AAGAACCAATCAGAGTTTGACAAGCTC-AGAAGTTCATCCAACAACCAATAGAAAAACAATTCTC
65 AAGAACCAATAAGAGTTTGACAAGTTCGA-AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTC
* * * *
2990 ACGTGAATAAGTATTTAATTCAAAGACCAAAAGTTTTTTACAAAATGACAAACAATTTAGACTAA
129 ACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAA
* * *
3055 ATGATACGATTTCCCGGGCAAGG
194 ATGATACGATTTCCTGAGCATGG
** * * * *
3078 AATGTTCTTAAAATTGCTCGAAGGAACGGATCGGCTTGAGTACTTTAAGGAATCGAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * * *
3143 AGAACCAAAAAGAGTTTCACAAGTTCGGAAGTTCATCCAAGAA-CAAGGAGAGAAGCAATTCTCA
66 AGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAA-GAGAGAAACAATTCTCA
* * * * *
3207 CATAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTAAGACCAAA
130 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAA
* * * *
3272 TAATTCAATTTCTTGAGCATGG
195 TGATACGATTTCCTGAGCATGG
* * * * * *
3294 AAAGTTCGTAAAATTACTCGAAGGAAGGGATTGCCTTGAATACTTTAAGGAACTGAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * * *
3359 AGAACTC-ATAAAAGTTTCAAAAGTTCAAAAGTTCGGT-CAAGAA-CAAGTTGAGAAACAATTCT
66 AGAAC-CAATAAGAGTTTGACAAGTTCGAAAGTTC-GTCCAAGAACCAAG-AGAGAAACAATTCT
* * * *
3421 CACGTAAATAGGTTTTTAATTTAAAGACCAAAAGTTGTTTACAATATGACAAACTATTTAGACCA
128 CACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCA
*** *
3486 AATGATGTTATTT-CTCAAGCATGG
193 AATGATACGATTTCCT-GAGCATGG
* * * * * *
3510 AATGTTC-AGAATATTGTTCGAAGGAATGGCTCGTCTTGAATACTTAAAGGAACTGAAGTTATAA
1 AATGTTCGA-AAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAA
* * * *
3574 AAGAA-C--T---CG--T-A-AA-TTCGAAAGTTCTTCTAAGAACCAAGTGAGAAACAATTCTCA
65 AAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
* ** * ** * * *
3628 CATGAATAAGTTTTTGTTTTAAAGACCAAAAGTTGTTTACAAAAAAAAAAAAAAAACAATTTATA
130 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAC-----AAAATGACAAACTATTTAGA
*
3693 CCAAATGATACGATTT-CTCGAGCAT-T
190 CCAAATGATACGATTTCCT-GAGCATGG
* * * *
3719 AACTATTCGAAAAATTGCTCGAAGGAATTGATTGCCTTGAATACTTT-AGGAAACCCAAGTTATA
1 AA-TGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGG-AACCGAAGTTATA
* * * *
3783 AAAGAACCAATAAGAGTATGACAAGTTCGGAAGTTTGTCCAAGAACCAAGAGAAAAACAATTCTC
64 AAAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTC
* *
3848 ATGTGAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTA-AAAATGACAAACTATTTAGACCAA
129 ACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAA
* * *
3912 AAGATACGATTTCCCGATCATGG
194 ATGATACGATTTCCTGAGCATGG
* * * *
3935 AATGTTTGGAAAATTGCTCGAAGGAACGGATCGCCTTGAATACTTTAAGGAATCGAAGTTAT-AA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * * * *
3999 AGAACCAATCAGAGTTTGACAAGCTC-AGAAGTTCATCCAACAACCAATAGAAAAACAATTCTCA
66 AGAACCAATAAGAGTTTGACAAGTTCGA-AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
* * *
4063 CGTGAATAAGTATTTAATTCAAAGACCAAAAGATT-TTTACAAAATGACAAACAATTTAGACTAA
130 CGTGAATAAGTTTTTAATTCAAAGACCAAAAG-TTGTTTACAAAATGACAAACTATTTAGACCAA
* * *
4127 ATGATACGATTT-ATCGAGAAAGG
194 ATGATACGATTTCCT-GAGCATGG
** * * *
4150 AATGTTCTTAAAATTGCTCGAAGGAATGGATCGGCTTGAGTACTTTAAGGAATCGAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * *
4215 AGAACCAAAAAGAGTTTGACAAGTTCGAAAGTTCATCCAAGAA-CAAGGAGAGAAGCAATTCTCA
66 AGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAA-GAGAGAAACAATTCTCA
* * * * *
4279 CATAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTAAGACCAAA
130 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAA
* *
4344 TGATTCGATTTCTTGAGCATGG
195 TGATACGATTTCCTGAGCATGG
* * * ** *
4366 AAAGTTC-ATAAAATTACTCGAAGGAAGGGATTACCTTGAATACTTTAAGGAATCGAAGTTATAA
1 AATGTTCGA-AAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAA
* * * * *
4430 AAGAACTC-ATAAAAGTTTCAAAAGTTCGAAAGTTCGGT-CAAGAA-TAAGTTGAGAAACAATTC
65 AAGAAC-CAATAAGAGTTTGACAAGTTCGAAAGTTC-GTCCAAGAACCAAG-AGAGAAACAATTC
* * * * *
4492 TCACGTAAATAGGTTTTTAATTTAATGACCAAAAGTTGTTTACAATATGACAAACTATTTAGACC
127 TCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACC
* ***
4557 AAATTATGTTATTT-CTCGAGCATGG
192 AAATGATACGATTTCCT-GAGCATGG
* * * *
4582 AATGTTC-AGAAAATTGCTCGAAGGAATGGTTCGTCTTGAATACTTAAAGGAACTGAAGTTATAA
1 AATGTTCGA-AAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAA
* * * * *
4646 AAGAACTC-GTAAAAGTTTGACAAGTTCGAAAGTTCTTCTAAGAACCAAGTGAGAAACAATTCTC
65 AAGAAC-CAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTC
* * * ** * *
4710 ACATGAATAAGTTTTTGATTTAAAGACCAAAAGTTGTTTACAAAAAAAAAACAAACAATTTATAC
129 ACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAC---AAAATGACAAACTATTTAGAC
*
4775 CAAATGATACGATTT-CTCGAGCAT-T
191 CAAATGATACGATTTCCT-GAGCATGG
* * * * *
4800 AACTGTTCGAAAAATTGCTCGAAGGAATTGATTGTCTTGAATAGTTTAAGGAACTGAAGTTATAA
1 AA-TGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAA
*** * * * * *
4865 AAGAACTTGTAAAAGTTTGACAGGTTTTG-AAGTTCG-GCAAGAACCAAGAGAGAAACAATTCTT
65 AAGAACCAATAAGAGTTTGACAAG-TTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTC
* * * *
4928 ACATAAATAACTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCTA
129 ACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAA
** *
4993 ATGATATTATTTCCCGAGCATGG
194 ATGATACGATTTCCTGAGCATGG
* * * * * *
5016 AACGTTC-AGAAATTTGCTTGAAGGAACGGAT-GACCTTGAATACTCT-AGGAAACCCAAGTTAT
1 AATGTTCGA-AAAATTGCTCGAAGGAATGGATCG-CCTTGAATACTTTAAGG-AACCGAAGTTAT
* *
5078 AAAAGAACCAATAAGAGTATGACAAGTTCGAAAGTTTGTCCAAGAACCAAGAGA-AAATCAATTC
63 AAAAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAA-CAATTC
* * * *
5142 TCATGTGAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTA-AAAATGACAAACTATTTGGTCC
127 TCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACC
* * * * *
5206 AAAAGATACAATTTCCCGATCATGA
192 AAATGATACGATTTCCTGAGCATGG
* * * * * * *
5231 AATGTTTGGAAAAA-TGCTCGAAGGAACGGATTGCCTTCAATACTTTAAGGAAACAAAATTATAA
1 AATG-TTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAA
* * * * * * * * * *
5295 AAGAACCAATAAGAG--TCATAGGTTCGGAAGTACATCCTAA-AACTAGGAAACAAACAATTCTC
65 AAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCC-AAGAACCAAGAGAGAAACAATTCTC
* * * *
5357 AAC-TGAATAAGTTTTTAATTCAAAGACTAAAAGGTT-TTTACAAAATAACAAACAATTTAAACC
129 -ACGTGAATAAGTTTTTAATTCAAAGACCAAAA-GTTGTTTACAAAATGACAAACTATTTAGACC
* *
5420 AAATGATATGATTTCCCGAGCATGG
192 AAATGATACGATTTCCTGAGCATGG
* * * * * *
5445 AATGTTC-AGAAAATTGCTCGAATGAATTGA-CTGTCTTGAATAGTTTAAGGAGCTGAAGTTATA
1 AATGTTCGA-AAAATTGCTCGAAGGAATGGATC-GCCTTGAATACTTTAAGGAACCGAAGTTATA
* * * * *
5508 AAAGAACTC-ATAAAAGTTTGAGAAGTTATG-AAGTTCG-GCAAGAACCAAGAGAGTAACAATTC
64 AAAGAAC-CAATAAGAGTTTGACAAGTT-CGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTC
* * * *
5570 TTACGTAAATAACTTTTTAATTCAAAGAACAAAAGTTGTTTACAAAATGACAAACTATTTAGACC
127 TCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACC
** * *
5635 AAATGATACCTTTTCCCGAGAATGG
192 AAATGATACGATTTCCTGAGCATGG
* * *
5660 AATGTTCAAAAAATTGCTCGAAGGAA-CGATCGCCTTGAATTCTTTAAGGAACCGAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * * * * ** *
5724 AGAACCAATAAGAGTTCGAGAGGATCGTAAGTACGTCC-AGAAAGTAAGGGAGAAACAATTCTCA
66 AGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAG-AACCAAGAGAGAAACAATTCTCA
* * *
5788 CGTAAATAAGTTTTTAATTCAAAGATCAAAAGTTATTTACAAAATGACAAACTATTTAGACCAAA
130 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAA
* * **
5853 TAATGCGATTTCCCAAGCATGG
195 TGATACGATTTCCTGAGCATGG
* * * * * * *
5875 AATGCTCGAAAAATTGCTCGAAGGAACGAATCGCCATGAATAATTTAAGAAACCAAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
* *
5940 AGAACC----A-AGTTTGACAAGTTC-AGAAGTTCATCCAAGAACCAACAGAGAAACAATTCTCA
66 AGAACCAATAAGAGTTTGACAAGTTCGA-AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
* *
5999 CGTGAATAAGCTTTTAATTCAAAGACCAAAAGTTGTCTACAAAATGACAAACTATTTAGACCAAA
130 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAA
6064 TGATACGATTTCCTGAGCATGG
195 TGATACGATTTCCTGAGCATGG
* * * * * * * * * * *
6086 ACTGTTCGAAAAGTTTCTCGAAAGAACGGATCACCTTGAATACTATAAGGAGCTGAAGTAATTAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * * *
6151 AGAACCAATAAGAGTTTGAAAAGTTTGGAAGTTCGTCCAAGAACCAAGATAGAAATAATTCTCAC
66 AGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAC
* * *
6216 GTGAATAAGTTTTTAATTCAAAGACCAAAA-TCTGTTTCCAAAATGAAAAACTATTAAGACCAAA
131 GTGAATAAGTTTTTAATTCAAAGACCAAAAGT-TGTTTACAAAATGACAAACTATTTAGACCAAA
*
6280 TGATTCGATTT-CTCGAGCATGG
195 TGATACGATTTCCT-GAGCATGG
* * * *** ** *
6302 -A-GATCGTAAAATTGCTCGAAGGAAGGGATCGCCTTGAATACTTTATTAAACTAAAGTTATTAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
*** * * * * * ** *
6365 AGAACTTGTAAAAGTTTGACAAGTTTTGAAACTTCGGT-CAAGAA-CATGTAAAGAATTAGTTCT
66 AGAACCAATAAGAGTTTGACAAG-TTCGAAAGTTC-GTCCAAGAACCAAG-AGAGAAACAATTCT
* * * * * ** *
6428 CACATAAATAAGTTTTTAATTAAAAGA-CAAAAGTTGTTTACAATATGAAAAACTATGGACACCA
128 CACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCA
* *
6492 TATTATACGATTTCCTGAGCATGG
193 AATGATACGATTTCCTGAGCATGG
* * *** *
6516 AATGTTCGAAAAATTTCTTGAAGGAATGGATCATTTTGAATACTTTTAGGAACTC-AAGTTATAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAAC-CGAAGTTATAA
*** * * * * * * *
6580 AAGAACTTGTAAAAGTTTGACAAGTTTGGAAGTTTG-GCAAGTACCAAGAGAGAAACAATTCTTA
65 AAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
* * * *
6644 TGTAAATAACTTTTTAATTCAAAGACCAAAAGTTG---------T----AACTATTTTGACCAAA
130 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAA
* * *
6696 TGATACAATTTCCCGAGCATCG
195 TGATACGATTTCCTGAGCATGG
* * * * * * *
6718 AATG-TCCAGAAAATTGCTCAAAGGAACGGATCACCATGAATACTTTAAGGAACAGAAGTTAGAA
1 AATGTTCGA-AAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAA
6782 AAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
65 AAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
* *
6847 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACAATTTAAACCAAA
130 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAA
* *
6912 TGATACGATTTCCCGAGCAAGG
195 TGATACGATTTCCTGAGCATGG
** * *
6934 AATGTTCTTAAAATTGCTCGAAGGAACGGATCAG-CTT-AAGTACTTTAAGGAATCGAAGTTATA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATC-GCCTTGAA-TACTTTAAGGAACCGAAGTTATA
* * * *
6997 AAAGAACCAAAAAGAGTTTGACAAGTTTGGAAGTTCATCCCAA-AACCAAGAGAGAAACAATTCT
64 AAAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGT-CCAAGAACCAAGAGAGAAACAATTCT
* * *** *
7061 CACGTAAATAAGCTTTTAATTCAAAGATGGAAAGTTGTTTACAAAATGAAAAACTATTTAGACCA
128 CACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCA
* ** *
7126 AATGAAATTATTT-CTCGAACATGG
193 AATGATACGATTTCCT-GAGCATGG
* * * * *
7150 AATGTTCGAAAAATTTCTCAAAGGAACT-GATCGCCTTGAATACTTTAAAGAACCAAAGTTATTA
1 AATGTTCGAAAAATTGCTCGAAGGAA-TGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAA
* * ** * *
7214 AAGAACCAATAAAAATTTGACAAGTTTTAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTGA
65 AAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
* * * *
7279 CGTGAATAAATTTTTAATTCAAAGACCAATAGTTGTTTACAGAATGACAAACTATTTAGACTAAA
130 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAA
* * *
7344 TTATAAGATTTCCTGAGTATGG
195 TGATACGATTTCCTGAGCATGG
* * *
7366 AATGTTCAAAAAATTGTTCGAAGGAATGGATCACCTTGAATACTTTAAGGAACCGAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * * * * *
7431 ATAACCAATAAGAGTTTGACAAGTTTGGAAGTTTGTCTAAGAACCAAGAGAGAAA-ACATTATCC
66 AGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACA-ATTCTCA
* * * *
7495 CGTGAATAAGTTTTTAA-T-----ACAAAAAGTTGTTTACAAAATAACAAATTATTTAGACCGAA
130 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAA
* * *
7554 TAATACTATTTCCCGAGCATGG
195 TGATACGATTTCCTGAGCATGG
** * * * * *
7576 TGTGTT-TAGGAAATTACTCAAAGGAATGGATCGCCATGAATACTTTAAGGAACCGAAGTTATAA
1 AATGTTCGA-AAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAA
* * * * *
7640 AAGAACCAATAAAAGTTTGACAAGTTCGGAAGTTCGTCAAAGAACCATGAAAGAAACAATTCTCA
65 AAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
* * * * * ** *
7705 CGTGACTAGGTTTTTAATTCAAACACCAAAAGTTGTTTACAAATTGACAACCTATTTAGATTACA
130 CGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAA
* *
7770 TGATAAGATTT-CTCGAGCAGGG
195 TGATACGATTTCCT-GAGCATGG
** * * *
7792 AATGTTC-AGAAAATTGCTCGAAGGAATGGATCATCATGAATACTTCAAGGAACCAAAGTTATAA
1 AATGTTCGA-AAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAA
*
7856 AAGAACCAATAAGAGTTTGACATGTTCGAAAGTTCGTCCGAA-AACCAAG
65 AAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCC-AAGAACCAAG
7905 TACTAATTAC
Statistics
Matches: 6084, Mismatches: 1197, Indels: 663
0.77 0.15 0.08
Matches are distributed among these distances:
190 3 0.00
191 7 0.00
192 7 0.00
193 9 0.00
194 4 0.00
195 7 0.00
196 12 0.00
197 13 0.00
198 16 0.00
199 12 0.00
200 23 0.00
201 23 0.00
202 113 0.02
203 60 0.01
204 12 0.00
205 69 0.01
206 20 0.00
207 18 0.00
208 23 0.00
209 21 0.00
210 268 0.04
211 174 0.03
212 5 0.00
213 76 0.01
214 457 0.08
215 1410 0.23
216 2431 0.40
217 335 0.06
218 128 0.02
219 120 0.02
220 10 0.00
221 68 0.01
222 3 0.00
223 13 0.00
224 19 0.00
225 5 0.00
226 1 0.00
227 7 0.00
228 17 0.00
229 15 0.00
230 13 0.00
231 12 0.00
232 12 0.00
233 3 0.00
234 7 0.00
235 3 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (216 bp):
AATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCGAAGTTATAAA
AGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAC
GTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAAT
GATACGATTTCCTGAGCATGG
Found at i:1205 original size:433 final size:433
Alignment explanation
Indices: 67--1707 Score: 1809
Period size: 433 Copynumber: 3.8 Consensus size: 433
57 AAGACCATTC
** * *
67 CCGAGCATCCAATGTTCGGAAAATTGCTC-AAAGGAACGAAAT-GCCTTGAATACTTTAAGGAAC
1 CCGAGCATGGAATGTTCGAAAAATTGCTCGAAA-GAAC-AGATCGCCTTGAATACTTTAAGGAAC
* * * **
130 TGAAGTTATAAAGGAACGAATAAGAGCTTGACAAGTTCAAAAGTTCATCCTAA-AACCAAGAGAG
64 CGAAGTTATAAAAGAACCAATAAGAGCTTGACAAGTTCTTAAGTTCATCC-AAGAACCAAGAGAG
* * ** * ** *
194 AAACAATTCTCATGTAAATAAGATTTTAATTCAAAGATGAAAAGCTATTTACAAAATGATGAACT
128 AAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTATTTACAAAATGACAAACA
* * * * * * * *
259 ATTTAGACC-AATGATGCGATTTCCTGAGCATCGAAT-ATTCGAAAAATTGCTCGGAGAAATGGA
193 ATTTAGACCAAATGATACAATTTCCTGAGCATGGAATGTTTAGAAAAATTGCTCGAAGGAACGGA
* *
322 TCGCCTTGAATACTTTAAGGAGCCAAAGTTTTAAAAGAACCAATAAGAGTTTGACAAGTTCGAAA
258 TCGCCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTCGAAA
* * * *
387 GTTCGTCAAAGAACCAAGAGAGAAACAATTCTCACGTGAATAAGTTTTTAATTTAAAGACCAAAA
323 GTTCGTCCAAGAACCAAGAGAGAAACAATTCTCATGTGAATAAGTTTTTAATTCAAAAACCAAAA
* * *
452 G-TTGTTTACAAAAT-AATAAACAATTTAGACCGAATGATACAATTTC
388 GTTTGTTTAC-AAATGAA-AAACTATTTAGACCAAATGATACAATTTT
* * * * * ** * * * *
498 CCAAGCATTGAATGTTCGAATAATAGCTCGAAGGAATTGATTGTCTTGAATAGTTTAAGGAACTG
1 CCGAGCATGGAATGTTCGAAAAATTGCTCGAAAGAACAGATCGCCTTGAATACTTTAAGGAACCG
* * * * * **
563 AAGTTATGAAAGAACTC-GTAAAAGTTTGACAAGTT-TTGATGTTC-GGCAAGAACCAAGAGAGA
66 AAGTTATAAAAGAAC-CAATAAGAGCTTGACAAGTTCTT-AAGTTCATCCAAGAACCAAGAGAGA
** * * *
625 AACAATTCTTGCATAAATAACTTTTTAATTCAAAGACCAAAAATTATTTACAAAATGACAAA-AT
129 AACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTATTTACAAAATGACAAACA-
* * * *
689 ATTTAGACCAAATGATACTATTTCCTGAGCATGGAATGTTCAG-AAAATTGCTCAAAGGAACTGA
193 ATTTAGACCAAATGATACAATTTCCTGAGCATGGAATGTTTAGAAAAATTGCTCGAAGGAACGGA
* * * * *
753 TCGCCTTTAATACTTTAAGGAACCGAAGGTATAAAAGAACCAATAAGAGTATGACAAGTTCGGAA
258 TCGCCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTCGAAA
* * *
818 GTTTGTCCAAGAACCAAGA-AAAAATTAATTCTCATGTGAATAAGTTTTTAATTCAAAAACCAAA
323 GTTCGTCCAAGAACCAAGAGAGAAA-CAATTCTCATGTGAATAAGTTTTTAATTCAAAAACCAAA
* * *
882 AGTTTGTTTACAATATGACAAACTATTTAGACCAAAAGATACGATTTT
387 AGTTTGTTTACAA-ATGAAAAACTATTTAGACCAAATGATACAATTTT
* * *
930 TCGAGCATGGAATGTTCGAAAAATTGCTTGAAAGAACAGATCGTCTTGAATACTTTAAGGAACCG
1 CCGAGCATGGAATGTTCGAAAAATTGCTCGAAAGAACAGATCGCCTTGAATACTTTAAGGAACCG
* * * *
995 AAGTTATAAAAGAACCAATAAGAGCTTGATAGGTTCTTAAGTACATCCTAA-AACCAATAGAGAA
66 AAGTTATAAAAGAACCAATAAGAGCTTGACAAGTTCTTAAGTTCATCC-AAGAACCAAGAGAGAA
* * * *
1059 ACAAATCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATAACAAACAAT
130 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTATTTACAAAATGACAAACAAT
* * **
1124 TTCGGCCAAATGATACAATTT-CTCGAGCATGGAATGTTTAG-AAAATTGCTCGAAGGAATTGA-
195 TTAGACCAAATGATACAATTTCCT-GAGCATGGAATGTTTAGAAAAATTGCTCGAAGGAACGGAT
** * * * * **
1186 CTATCTTGAATAGTTTAAGGAACTAAAGTTATAAAAGAACTC-GTAAAAGTTTGACAAGTTTTAA
259 C-GCCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAAC-CAATAAGAGTTTGACAAGTTCGAA
* * * * *
1250 AGTTCG-ACTAGAACCAAGAGAGAAACAATTCAT-ATGTAAATAACTTTTTAATTCAAAAACCAG
322 AGTTCGTCCAAGAACCAAGAGAGAAACAATTC-TCATGTGAATAAGTTTTTAATTCAAAAACCAA
* * *
1313 AAGTTTTTTTTACAGAATGAAAAACTATTTGGACCAAATGATACTA-TTT
386 AAG-TTTGTTTACA-AATGAAAAACTATTTAGACCAAATGATACAATTTT
* **
1362 CCTGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACC
1 CC-GAGCATGGAATGTTCGAAAAATTGCTCGAAAGAACAGATCGCCTTGAATACTTTAAGGAACC
* * ** *
1427 GAAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTCTGAAGTTTGTCCAAGAACCAAGAGAAAA
65 GAAGTTATAAAAGAACCAATAAGAGCTTGACAAGTTCTTAAGTTCATCCAAGAACCAAGAGAGAA
* * * *
1492 ACAATTCTCACTTGAATAAGTTTTTATTTCAAAGACCAAAAGTT-TCTTACAAAATGACAAACTA
130 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTAT-TTACAAAATGACAAACAA
** * *
1556 TTTAGATTAAATGATA-AGATTTCTTGAGCATGGAATGTTT-GAAAAATTGCTCGAAAGAACGGA
194 TTTAGACCAAATGATACA-ATTTCCTGAGCATGGAATGTTTAGAAAAATTGCTCGAAGGAACGGA
* * *
1619 TCGCCTTGAACACTTTAAGGAACCAAAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTCGGAT
258 TCGCCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTCGAAA
* **
1684 GTTCGACCAAGAAATAAGAGAGAA
323 GTTCGTCCAAGAACCAAGAGAGAA
1708 CTTGTTTGAC
Statistics
Matches: 1003, Mismatches: 174, Indels: 63
0.81 0.14 0.05
Matches are distributed among these distances:
429 2 0.00
430 78 0.08
431 235 0.23
432 181 0.18
433 486 0.48
434 21 0.02
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (433 bp):
CCGAGCATGGAATGTTCGAAAAATTGCTCGAAAGAACAGATCGCCTTGAATACTTTAAGGAACCG
AAGTTATAAAAGAACCAATAAGAGCTTGACAAGTTCTTAAGTTCATCCAAGAACCAAGAGAGAAA
CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTATTTACAAAATGACAAACAATT
TAGACCAAATGATACAATTTCCTGAGCATGGAATGTTTAGAAAAATTGCTCGAAGGAACGGATCG
CCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTCGAAAGTT
CGTCCAAGAACCAAGAGAGAAACAATTCTCATGTGAATAAGTTTTTAATTCAAAAACCAAAAGTT
TGTTTACAAATGAAAAACTATTTAGACCAAATGATACAATTTT
Found at i:1217 original size:216 final size:215
Alignment explanation
Indices: 67--1679 Score: 1707
Period size: 215 Copynumber: 7.5 Consensus size: 215
57 AAGACCATTC
** * * * * *
67 CCGAGCATCCAATGTTCGGAAAATTGCTCAAAGGAACGAAAT-GCCTTGAATACTTTAAGGAACT
1 CCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATG-GATCGCCTTGAATACTTTAAGGAACC
* * * **
131 GAAGTTATAAAGGAACGAATAAGAGCTTGACAAGTTCAAAAGTTCATCCTAA-AACCAAGAGAGA
65 GAAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTCTTAAGTTCATCC-AAGAACCAAGAGAGA
* * * ** * * **
195 AACAATTCTCATGTAAATAAGATTTTAATTCAAAGATGAAAAGCTATTTACAAAATGATGAACTA
129 AACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTA
* *
260 TTTAGACC-AATGATGCGATTT
194 TTTAGACCAAATGATACAATTT
* * * * *
281 CCTGAGCATCGAATATTCGAAAAATTGCTCGGAGAAATGGATCGCCTTGAATACTTTAAGGAGCC
1 CC-GAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACC
* * ** * *
346 AAAGTTTTAAAAGAACCAATAAGAGTTTGACAAGTTCGAAAGTTCGTCAAAGAACCAAGAGAGAA
65 GAAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTCTTAAGTTCATCCAAGAACCAAGAGAGAA
* * * *
411 ACAATTCTCACGTGAATAAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATAATAAACAAT
130 ACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTAT
*
476 TTAGACCGAATGATACAATTT
195 TTAGACCAAATGATACAATTT
* * * * * * * * *
497 CCCAAGCATTGAATGTTCGAATAATAGCTCGAAGGAATTGATTGTCTTGAATAGTTTAAGGAACT
1 -CCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACC
* * * * **
562 GAAGTTATGAAAGAACTC-GTAAAAGTTTGACAAGTT-TTGATGTTC-GGCAAGAACCAAGAGAG
65 GAAGTTATAAAAGAAC-CAATAAGAGTTTGACAAGTTCTT-AAGTTCATCCAAGAACCAAGAGAG
** * * * * * *
624 AAACAATTCTTGCATAAATAACTTTTTAATTCAAAGACCAAAAATTATTTACAAAATGACAAAAT
128 AAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACT
*
689 ATTTAGACCAAATGATACTATTT
193 ATTTAGACCAAATGATACAATTT
* *
712 CCTGAGCATGGAATGTTC-AGAAAATTGCTCAAAGGAACT-GATCGCCTTTAATACTTTAAGGAA
1 CC-GAGCATGGAATGTTCGA-AAAATTGCTCGAAGGAA-TGGATCGCCTTGAATACTTTAAGGAA
* * ** ** *
775 CCGAAGGTATAAAAGAACCAATAAGAGTATGACAAGTTCGGAAGTTTGTCCAAGAACCAAGA-AA
63 CCGAAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTCTTAAGTTCATCCAAGAACCAAGAGAG
* * * *
839 AAATTAATTCTCATGTGAATAAGTTTTTAATTCAAAAACCAAAAGTTTGTTTACAATATGACAAA
128 AAA-CAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAG-TTGTTTACAAAATGACAAA
* *
904 CTATTTAGACCAAAAGATACGATTTT
191 CTATTTAGACCAAATGATAC-AATTT
* * * ** *
930 TCGAGCATGGAATGTTCGAAAAATTGCTTGAAAGAACAGATCGTCTTGAATACTTTAAGGAACCG
1 CCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCG
* * * * *
995 AAGTTATAAAAGAACCAATAAGAGCTTGATAGGTTCTTAAGTACATCCTAA-AACCAATAGAGAA
66 AAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTCTTAAGTTCATCC-AAGAACCAAGAGAGAA
* * *
1059 ACAAATCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATAACAAACAAT
130 ACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTAT
* *
1124 TTCGGCCAAATGATACAATTT
195 TTAGACCAAATGATACAATTT
* * ** *
1145 CTCGAGCATGGAATGTT-TAGAAAATTGCTCGAAGGAATTGA-CTATCTTGAATAGTTTAAGGAA
1 C-CGAGCATGGAATGTTCGA-AAAATTGCTCGAAGGAATGGATC-GCCTTGAATACTTTAAGGAA
** * * *
1208 CTAAAGTTATAAAAGAACTC-GTAAAAGTTTGACAAGTT-TTAAAGTTCGA--CTAGAACCAAGA
63 CCGAAGTTATAAAAGAAC-CAATAAGAGTTTGACAAGTTCTT-AAGTTC-ATCCAAGAACCAAGA
* * * * * * *
1269 GAGAAACAATTCAT-ATGTAAATAACTTTTTAATTCAAAAACCAGAAGTTTTTTTTACAGAATGA
125 GAGAAACAATTC-TCACGTGAATAAGTTTTTAATTCAAAGACCAAAAG--TTGTTTACAAAATGA
* * *
1333 AAAACTATTTGGACCAAATGATACTATTT
187 CAAACTATTTAGACCAAATGATACAATTT
1362 CCTGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACC
1 CC-GAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACC
* ** *
1427 GAAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTCTGAAGTTTGTCCAAGAACCAAGAGAAAA
65 GAAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTCTTAAGTTCATCCAAGAACCAAGAGAGAA
* *
1492 ACAATTCTCACTTGAATAAGTTTTTATTTCAAAGACCAAAAGTT-TCTTACAAAATGACAAACTA
130 ACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGT-TTACAAAATGACAAACTA
**
1556 TTTAGATTAAATGATA-AGATTT
194 TTTAGACCAAATGATACA-ATTT
* * * * *
1578 CTTGAGCATGGAATGTTTGAAAAATTGCTCGAAAGAACGGATCGCCTTGAACACTTTAAGGAACC
1 C-CGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACC
*
1643 AAAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTC
65 GAAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTC
1680 GGATGTTCGA
Statistics
Matches: 1157, Mismatches: 201, Indels: 80
0.80 0.14 0.06
Matches are distributed among these distances:
214 11 0.01
215 393 0.34
216 389 0.34
217 302 0.26
218 62 0.05
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (215 bp):
CCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAAGGAACCG
AAGTTATAAAAGAACCAATAAGAGTTTGACAAGTTCTTAAGTTCATCCAAGAACCAAGAGAGAAA
CAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATT
TAGACCAAATGATACAATTT
Found at i:1849 original size:19 final size:20
Alignment explanation
Indices: 1812--1849 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1802 TTTTTAAATA
*
1812 AAAAAGGAAAACTTGTTTAC
1 AAAAAGGAAAACTTATTTAC
*
1832 AAAAAGGCAAAC-TATTTA
1 AAAAAGGAAAACTTATTTA
1850 GACCAAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.53, C:0.11, G:0.13, T:0.24
Consensus pattern (20 bp):
AAAAAGGAAAACTTATTTAC
Found at i:1983 original size:18 final size:18
Alignment explanation
Indices: 1946--1980 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1936 GTAATAAAAA
1946 AACTTCTAAAAATTTGCC
1 AACTTCTAAAAATTTGCC
*
1964 AACTTC-AAAAGTTTGCC
1 AACTTCTAAAAATTTGCC
1981 CAAGAACCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.31
Consensus pattern (18 bp):
AACTTCTAAAAATTTGCC
Found at i:10561 original size:20 final size:20
Alignment explanation
Indices: 10536--10574 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
10526 TATAGTTAGA
10536 ATGAAATTAT-TTGTGTATTG
1 ATGAAA-TATGTTGTGTATTG
10556 ATGAAATATGTTGTGTATT
1 ATGAAATATGTTGTGTATT
10575 CAATTCAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (20 bp):
ATGAAATATGTTGTGTATTG
Done.