Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014737.1 Kokia drynarioides strain JFW-HI SEQ_129776, 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: 4991
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:665 original size:216 final size:215
Alignment explanation
Indices: 1--966 Score: 1102
Period size: 216 Copynumber: 4.5 Consensus size: 215
* **
1 TTTAGAAAATGACAAAGTATTTAGACCAAATGATGCGCCTTCCCGAGCATGGAATGTTCAAAAAA
1 TTTAGAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAAAAAA
* * * * * * *
66 CTGCTCT-AAGGAATGGATTATCCTGAATACTTTAAGAAACCAAAGTTATTGAAGAACTCATAAA
66 TTACT-TGAAGGAATGGATTGTCATGAATACTTTAAGGAACCAAAGTTATAGAAGAACTCGTAAA
* * * * *
130 AGTTCGTCAAGTTTGGAAGTTCGTCTAAGAACCAAAAGAAAAACAACTCTCACGTAAATAGGTTT
130 AGTT-GTCAAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAACTCTCACGTAAATAAGATT
*
195 TTAATTCAAAGACCAAAATTTG
194 TTAATTCAAAGACCAAAAGTTG
* * ***
217 TTTAG-AAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGTGCATGGAATGTTTGGAAAA
1 TTTAGAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAAAAAA
* * * * * * * * * *
281 TTGCTAGAAGGAATTGATCGTTATGAATACTTTATGGAACTGAAGGTT-TAAAAGAACTTG-AGA
66 TTACTTGAAGGAATGGATTGTCATGAATACTTTAAGGAAC-CAAAGTTATAGAAGAACTCGTA-A
* * * * * *
344 AACTTCATCAAGTTCGGAAG-T--T-C----A--AAGAGAGAAACAATTCTTAAGTAAATAAGAT
129 AAGTT-GTCAAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAACTCTCACGTAAATAAGAT
*
399 TTTAATTTAAAGACCAAAAGTTG
193 TTTAATTCAAAGACCAAAAGTTG
* * * * *
422 TTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCTGAGCATGGAACGTTCAGAAAA
1 TTTAGAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAAAAAA
* * * *
487 TTACTTGAAGGAATGGATTGTCATGAATACTTTGAGGAACAAAAGTTATAGATGAACTGGTAAAA
66 TTACTTGAAGGAATGGATTGTCATGAATACTTTAAGGAACCAAAGTTATAGAAGAACTCGTAAAA
* * **
552 GTTTTACAAGTTCAGAAGTTCGTCCAAGAACCAGGAGAGAAACAACTCTCACGTAAATAAG-TTT
131 GTTGT-CAAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAACTCTCACGTAAATAAGATTT
*
616 TACATTCAAAGACCAAAAGTCG
195 TA-ATTCAAAGACCAAAAGTTG
* * *
638 TTTAGAAAATGACAAAGTATTTAGACCAAATGATGAGATTTCTCGAGCATGGAATGTTCAAAAAA
1 TTTAGAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAAAAAA
* * * *
703 TTCCTCT-AAGGAATGGATTGTCTTGAATACTTTAAGAAATCAAAGTTATAGAAGAACTCGTAAA
66 TTACT-TGAAGGAATGGATTGTCATGAATACTTTAAGGAACCAAAGTTATAGAAGAACTCGTAAA
* * * * * *
767 AGTATGTCTAGTTTGGAAGTTCGTCTAAGAGCCAAAAGAGAAACAACTCTCACATAAAT-AGGTT
130 AGT-TGTCAAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAACTCTCACGTAAATAAGATT
*
831 TTAAATTCAAGGACCAAAAGTTG
194 TT-AATTCAAAGACCAAAAGTTG
854 TTTAGAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAAAAAA
1 TTTAGAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAAAAAA
* * *
919 TTACTCGAAGGAGTGGATTGTCATGAATACTTTAATGAACCAAAGTTA
66 TTACTTGAAGGAATGGATTGTCATGAATACTTTAAGGAACCAAAGTTA
967 CAAAACAACT
Statistics
Matches: 626, Mismatches: 101, Indels: 46
0.81 0.13 0.06
Matches are distributed among these distances:
205 55 0.09
206 110 0.18
207 3 0.00
209 1 0.00
210 1 0.00
212 1 0.00
214 3 0.00
215 114 0.18
216 334 0.53
217 4 0.01
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (215 bp):
TTTAGAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAAAAAA
TTACTTGAAGGAATGGATTGTCATGAATACTTTAAGGAACCAAAGTTATAGAAGAACTCGTAAAA
GTTGTCAAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAACTCTCACGTAAATAAGATTTT
AATTCAAAGACCAAAAGTTG
Found at i:1412 original size:218 final size:212
Alignment explanation
Indices: 1009--1709 Score: 687
Period size: 218 Copynumber: 3.2 Consensus size: 212
999 AAAATTAAAT
* * * ** * * *
1009 GACCAAAAGTTCTATACCAAATGACAAACTAAGTAGACAAAACGATGTC-ATTTCCCTAGCATGG
1 GACCAAAAGTTGTTTAACAAATGACAAACTATTTAGACAAAATGATG-CGATTTCCCAAGCATGT
* * * *
1073 AATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCATGAAAACTTTAAAGAACTGAAGTTATAGA
65 AATCTTC-GAAAATTTCTCG-AGGAATGGATCGTCATGTATACTTT-AAGAACTGAAGTTATAGA
* * * * * * * * *
1138 AGAAGTCGTCAAAGTTTATCAAGTTTAGAAGTTTATCCAATATCCAAGAGAGAAACAATTCTCAT
127 AGAACTCGTAAAAG-TTGTCAAGTTTGGAAGTTCATCCAAGAACCAAGAGAGAAACAACTCTCAC
1203 GTAAATAAGTTTTTCATTCAAA
191 GTAAATAAGTTTTTCATTCAAA
** * *
1225 CCCCAAAAGTTGCTTAACAAATGACAAA-TAGTTTAGAAAAAAAATGATGCGATTTCCCAAGCAT
1 GACCAAAAGTTGTTTAACAAATGACAAACTA-TTTAG--ACAAAATGATGCGATTTCCCAAGCAT
* * * *
1289 -TAAATTTTTGAAAGATTTCTCGACGGAATGGATCGTCATGTATACTTTATTGAACTGAGGTTAT
63 GT-AATCTTCGAAA-ATTTCTCGA-GGAATGGATCGTCATGTATACTTTA-AGAACTGAAGTTAT
* * * * *
1353 AAAAGAACTCGTAAAAGCTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGATAGAAACAACTCT
124 AGAAGAACTCGTAAAAG-TTGTCAAGTTTGGAAGTTCATCCAAGAACCAAGAGAGAAACAACTCT
1418 CACGTAAGA-AAGTTTTTCATTCAAA
188 CACGTAA-ATAAGTTTTTCATTCAAA
* * * * * * *
1443 GACAAAAAGTAGTTTAGA-AAATGACAAAGTATTTAGACCAAATGATGTGATTTCCCGAGTATGT
1 GACCAAAAGTTGTTTA-ACAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCAAGCATGT
* * * * * * * *
1507 AATCTTCAAAAAATTTCTCTAAGAATGGGTTGTCCT-TAATACTTTAAGAAACCGAAGTTATTGA
65 AATCTTC-GAAAATTTCTCGAGGAATGGATCGTCATGT-ATACTTTAAG-AACTGAAGTTATAGA
* * *
1571 AGAACTCGTAAAAGTTCGTCAAGTTTGGAAGTTCATCTAAGAACCAAGAGA-AAAAAACTCTTAC
127 AGAACTCGTAAAAGTT-GTCAAGTTTGGAAGTTCATCCAAGAACCAAGAGAGAAACAACTCTCAC
* *
1635 GTAAATAGGGTTTTCATTCAAA
191 GTAAATAAGTTTTTCATTCAAA
*
1657 GACCAAAAGTTGTTTACCAAATGACAAACTATTTAGACAAAATGATGCGATTT
1 GACCAAAAGTTGTTTAACAAATGACAAACTATTTAGACAAAATGATGCGATTT
1710 ACTGTGCNNN
Statistics
Matches: 395, Mismatches: 72, Indels: 38
0.78 0.14 0.08
Matches are distributed among these distances:
213 1 0.00
214 79 0.20
215 75 0.19
216 59 0.15
217 11 0.03
218 166 0.42
219 4 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (212 bp):
GACCAAAAGTTGTTTAACAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCAAGCATGTA
ATCTTCGAAAATTTCTCGAGGAATGGATCGTCATGTATACTTTAAGAACTGAAGTTATAGAAGAA
CTCGTAAAAGTTGTCAAGTTTGGAAGTTCATCCAAGAACCAAGAGAGAAACAACTCTCACGTAAA
TAAGTTTTTCATTCAAA
Found at i:2145 original size:216 final size:216
Alignment explanation
Indices: 1778--4808 Score: 2776
Period size: 216 Copynumber: 14.1 Consensus size: 216
1768 GAATGTTGGG
** * *
1778 AAAATTGCTCGAAGGAATGGATCT-TCATGAATACTTTAAGGAATTGAAGTTTTAAAAGAACTCG
1 AAAATTGCTCGAAGGAATGGAT-TGTCATGAATACTTTAAGGAACCGAAGTTATAGAAGAACTCG
* ** * * * *
1842 TAAAACTTCATCAAGTTTGAAAGTTCGTCCAAG-ACCAAAGAGAGAAAAAACTCTCACATAAATA
65 TAAAAGTTTGTCAAGTTAGGAAGTTCGTCCAAGAACC-AAGAGAGAAACAACTCTCACGTAAATA
* * *
1906 ACTTTTTAATTTATAA-ACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCA
129 AGTTTTTAATTCA-AAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCG
*
1970 ATTTCCCGAGCATAGAATGTTCAA
193 ATTTCCCGAGCATGGAATGTTCAA
* * * * * * * * *
1994 AAAATTACTCGAAGGAGTGGATTGTCATAAATACTTTAATGAACCAAAGTTAGAGAACAACTGGC
1 AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACCGAAGTTATAGAAGAACTCGT
* * * * * *
2059 AAAAGTTTGTGAAGTTAGGAAGTTTGTCCATGATCCAAGAGATAATA-AATTCTCACGTAAATAA
66 AAAAGTTTGTCAAGTTAGGAAGTTCGTCCAAGAACCAAGAGAGAA-ACAACTCTCACGTAAATAA
* * ** * * *
2123 GTTTTTAATT-AAATGACCAAAAGTTGTATACCAAATGACAAACTAAGTAGACAAAACGATGTGA
130 GTTTTTAATTCAAA-GACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
* *
2187 TTTCCCTAGCATGGAATGTTCAG
194 TTTCCCGAGCATGGAATGTTCAA
* ** * * ** *
2210 AAAATTGCTTGAAGGAATGGATCATCATGAAAACTTTAAAGAACAAAAGTTATAGAAGAAGTCGT
1 AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACCGAAGTTATAGAAGAACTCGT
* * * * * * *
2275 CAAAGTTTATCAAGTTTA-GAAGTTCATCCAATATCCAAGAGAGAAACAATTCTCATGTAAATAA
66 AAAAGTTTGTCAAG-TTAGGAAGTTCGTCCAAGAACCAAGAGAGAAACAACTCTCACGTAAATAA
* * * * **
2339 GTTTTTCATTCAAAGCCCAAAAGTTGCTTACCAAATGACAAA-TAGTTTAGAAAAAAATGATGCG
130 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTA-TTTAG-ACCAAATGATGCG
* ** * *
2403 ATTTCCCAAGCATTAAATTTTCGA
193 ATTTCCCGAGCATGGAATGTTCAA
* * * * ** * *
2427 AAAATTTCTCAAAGGAAT-GA--ATCAT-CA-A-TTTATTGAACTGAAGTTATAAAAGAACTCGT
1 AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACCGAAGTTATAGAAGAACTCGT
** * * ** *
2486 -AAA--TTGT----TTA-GAAAAT-G-AC-A-AACTATTTAGAAAATGACAACTCTCACGTAAAT
66 AAAAGTTTGTCAAGTTAGGAAGTTCGTCCAAGAACCA-AGAGAGAA--ACAACTCTCACGTAAAT
* * * * * * *
2539 AAGATTTTAATTTATAGACCCAAAGTTGTTTAGAAAATGACAAACTATTTAGATCAAACGATGCG
128 AAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCG
* * *
2604 TTTTCCCGAGCATGGAATGCTCGA
193 ATTTCCCGAGCATGGAATGTTCAA
* * *
2628 AAAATTGTTTGAAGGAATGGATTGTCATGAATACTTTAAGGAA-CGAATGTTATAGATGAACT-G
1 AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACCGAA-GTTATAGAAGAACTCG
* * * * *
2691 GAAAAGTTT-TCCAAGTTCA-AAAGTTCATCCAAGAACTAAGAGAGAAACTACTCTCACGTAAAT
65 TAAAAGTTTGT-CAAGTT-AGGAAGTTCGTCCAAGAACCAAGAGAGAAACAACTCTCACGTAAAT
* * * * * * *
2754 AAGTTTTTCATTCAAAGACCAAAAGTCGTTTAGAAAATCACAAAGTATTTAAACCAAATAATGCG
128 AAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCG
**
2819 ATTTCTGGAGCATGGAATGTTCAA
193 ATTTCCCGAGCATGGAATGTTCAA
* * * * * * * *
2843 AAAATTGTTCTAAGGAATGGATTGTCTTGAATACTTGAAGAAATCAAAGTTATAGAAGAACTCAT
1 AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACCGAAGTTATAGAAGAACTCGT
* * * * * * * * *
2908 AAAAGTATGTCTAGTTTGGAAGTTCGTCTAAGAGCCAAAAGAGAAACAATTCTCACATAAATAGG
66 AAAAGTTTGTCAAGTTAGGAAGTTCGTCCAAGAACCAAGAGAGAAACAACTCTCACGTAAATAAG
* * * *
2973 TTTTAAATTCAAGGATCAAAAGTTGTTTAGAAAATGACAAACTATTTAGA-CATAATGATGCGAT
131 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCA-AATGATGCGAT
* ***
3037 TTCCC-ATGCTTGGAATGTTGGG
195 TTCCCGA-GCATGGAATGTTCAA
* * *
3059 AAAATTGCTCGAAGGAATGGATCT-TCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCG
1 AAAATTGCTCGAAGGAATGGAT-TGTCATGAATACTTTAAGGAACCGAAGTTATAGAAGAACTCG
* * * *
3123 TAAAACTTCGTCAAGTTCGGAAGTTCGTCCAAG-ACCAAAGAGAGAGAA-AACTCTCACATAAAT
65 TAAAAGTTTGTCAAGTTAGGAAGTTCGTCCAAGAACC-AAGAGAGA-AACAACTCTCACGTAAAT
* * *
3186 AACTTTTTAATTTATAA-ACCAAAAGTTGTTTACAAAATAACAAACTATTTAGACCAAATGATGC
128 AAGTTTTTAATTCA-AAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGC
* * *
3250 GATTTCCCAAGCATGAAATGTTAAA
192 GATTTCCCGAGCATGGAATGTTCAA
* ** * * * * *
3275 AAAATTACTCGAAGGAGGGGATTGTCATGAATACTTTAATGAACCAAAGTTATGGAACAACTGGT
1 AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACCGAAGTTATAGAAGAACTCGT
* * * * * * * *
3340 AAAATTTTGTGAAGTTAGGAAGTTTGTCCATGATCCAAGAGATAATA-AATTTTCACGTAAATAA
66 AAAAGTTTGTCAAGTTAGGAAGTTCGTCCAAGAACCAAGAGAGAA-ACAACTCTCACGTAAATAA
* * ** *
3404 GTTTTTAATT-AAATGACCAAAAGTTGTATACCAAATGACAAACTAAGTAGA-CAAGATGATGTG
130 GTTTTTAATTCAAA-GACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAA-ATGATGCG
* * *
3467 ATTTCCCTAGCATTGAATGTTCAG
193 ATTTCCCGAGCATGGAATGTTCAA
* * * * * * *
3491 AAAATTGCTCGAAGGAATGGATCGTCGTGAAAACTTTAAAGAACGGAAGTTATAGAAGAAGTCAT
1 AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACCGAAGTTATAGAAGAACTCGT
* * * * * * *
3556 CAAAGTTTATCAAGTTTA-GAAGTTCATCCAATATCCAAGAGAGAAACAATTCTCATGTAAATAA
66 AAAAGTTTGTCAAG-TTAGGAAGTTCGTCCAAGAACCAAGAGAGAAACAACTCTCACGTAAATAA
* * * * **
3620 GTTTTTCATTCAAAGCCCAAAAGTTGCTTACCAAATGACAAA-TAGTTTAGAAAAAAAATGATGC
130 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTA-TTTAG--ACCAAATGATGC
** * *
3684 GATTTCCC-ACGCATTAAATTTTCGA
192 GATTTCCCGA-GCATGGAATGTTCAA
* ** * ** * *
3709 AAAATTTCTTTAAGGAATGGATCGTCATGAATACTTTATTGAACTGAAGTTATAAAAGAACTCGT
1 AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACCGAAGTTATAGAAGAACTCGT
* * * * *
3774 AAAAGCTTGCCAAGTTCGGAAGTTTGTCCAAGAACCAAGATAGAAACAACTCTCACGTAAGA-AA
66 AAAAGTTTGTCAAGTTAGGAAGTTCGTCCAAGAACCAAGAGAGAAACAACTCTCACGTAA-ATAA
* * * * *
3838 GTTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGTGAT
130 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* *
3903 TTCCCGAGTATGTAATGTTCAA
195 TTCCCGAGCATGGAATGTTCAA
* * * *
3925 AAAATTGCTCTAA-GAATGGGTTGTCCAT-AATACTTTAAGAAACCGAAGTTATTGAAGAACTCG
1 AAAATTGCTCGAAGGAATGGATTGT-CATGAATACTTTAAGGAACCGAAGTTATAGAAGAACTCG
* * * * * * *
3988 TAAAAGTTCGTCAAGTTTGGAAGTTCATCTAAGAACGAAGAGAAAAAAAAACTCTCACGTAAATA
65 TAAAAGTTTGTCAAGTTAGGAAGTTCGTCCAAGAACCAAGAG-AGAAACAACTCTCACGTAAATA
* * * **
4053 GGTTTTTAATTCAAAGACCAAAAGTTGTTTACCAAATGCCAAACTATTTAGATAAAATGATGCGA
129 AGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
*** * * **
4118 TTTGTTGTGCATGGAATGCTCGG
194 TTTCCCGAGCATGGAATGTTCAA
* * * * *
4141 AAAATTGCTCGAAGGAATGGATTGTCATGAATATTTTAAGGAACTGAAGTTTTAAAAGAACTTG-
1 AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACCGAAGTTATAGAAGAACTCGT
* ** * * * * * * *
4205 AAAACTTCATCAAGTTTGAAAGTTTGTCCAAGAACAAAGAGAGGAACAATTCTCACGTCAATAAG
66 AAAAGTTTGTCAAGTTAGGAAGTTCGTCCAAGAACCAAGAGAGAAACAACTCTCACGTAAATAAG
* * * *
4270 ATTTTAATTTAAAGACCAAAAGTTATTTACAAAATGACAAACTATTTAGACCAAATGATGTGATT
131 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
**
4335 TCCCGAGCATGGAATGTTCGG
196 TCCCGAGCATGGAATGTTCAA
* * * * *
4356 AAAATTGCTTGAAGGAATGGATTGTCATGGATACTTTAAGGAA-CGAAAGTGATAGATGAACTGG
1 AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACCG-AAGTTATAGAAGAACTCG
*
4420 TAAAAGTTT-TCCAAGTTCA-GAAGTTTGTCCAAGAACCAAGAGAGAAACAACTCTCACGTAAAT
65 TAAAAGTTTGT-CAAGTT-AGGAAGTTCGTCCAAGAACCAAGAGAGAAACAACTCTCACGTAAAT
* * * * * *
4483 AAGTATTTCATTCAGAGACCAAAAGTCGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
128 AAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCG
* *
4548 ATTTCTCGAGCATGAAATGTTCAA
193 ATTTCCCGAGCATGGAATGTTCAA
* * * * * * * * *
4572 AAAATTACTCTAAGGAATGGATTATCTTGAATACATTAAGAAATCGAAGTTATAGAAGTACTCAT
1 AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACCGAAGTTATAGAAGAACTCGT
* * * * *
4637 AAAAGTATGTCAAGTTTGGAAGTTCGTCTAAGAGCCAAGAGAGAAA-AACCTCTCACGTAAATAG
66 AAAAGTTTGTCAAGTTAGGAAGTTCGTCCAAGAACCAAGAGAGAAACAA-CTCTCACGTAAATAA
* * * *
4701 GTTTTTAATTCAAAGACCAAAAGTTGTTCACAAAATGACAAACTATTTAGACTAAATTATGCAAT
130 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
**
4766 TTCCCGAGCATGGAATGTTCGT
195 TTCCCGAGCATGGAATGTTCAA
*
4788 AAAATTACTCGAAGGAATGGA
1 AAAATTGCTCGAAGGAATGGA
4809 GCAAAGTTAT
Statistics
Matches: 2268, Mismatches: 470, Indels: 154
0.78 0.16 0.05
Matches are distributed among these distances:
199 3 0.00
200 6 0.00
201 43 0.02
202 57 0.03
203 9 0.00
204 4 0.00
205 1 0.00
206 5 0.00
207 22 0.01
208 4 0.00
209 2 0.00
210 3 0.00
211 25 0.01
212 1 0.00
213 3 0.00
214 14 0.01
215 377 0.17
216 1391 0.61
217 119 0.05
218 174 0.08
219 5 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (216 bp):
AAAATTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAACCGAAGTTATAGAAGAACTCGT
AAAAGTTTGTCAAGTTAGGAAGTTCGTCCAAGAACCAAGAGAGAAACAACTCTCACGTAAATAAG
TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
TCCCGAGCATGGAATGTTCAA
Found at i:4516 original size:647 final size:643
Alignment explanation
Indices: 1767--4808 Score: 3047
Period size: 647 Copynumber: 4.7 Consensus size: 643
1757 NNNNNNNNNN
* * *
1767 GGAATGTTGGGAAAATTGCTCGAAGGAATGGATCTTCATGAATACTTTAAGGAATTGAAGTTTTA
1 GGAATGTTCGGAAAATTGCTCGAAGGAATGGAT-TTCATGAATACTTTAAGGAACTGAAGTTATA
* * * *
1832 AAAGAACTCGTAAAACTTCATCAAGTT-TGAAAGTTCGTCCAAG-ACCAAAGAGAGAAAAAACTC
65 AAAGAACTCGTAAAACTT-TTCAAGTTCAG-AAGTTTGTCCAAGAACC-AAGAGAGAAACAACTC
* * * *
1895 TCACATAAATAACTTTTTAATTTATAAACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACC
127 TCACGTAAATAAGTTTTTAATTTATAGACCAAAAGTTGTTTAGAAAATGACAAACTATTTAGACC
* * * *
1960 AAATGATGCAATTTCCCGAGCAT-AGAATGTTCAAAAAATTACTCGAAGGAGTGGATTGTCATAA
192 AAATGATGCGATTTCCCGAGCATGA-AATGTTCAAAAAATTACTCTAAGGAATGGATTGTCATGA
* * * * * * *
2024 ATACTTTAATGAACCAAAGTTAGAGAACAACTGGCAAAAGTTTGTGAAGTTAGGAAGTTTGTCCA
256 ATACTTTAA-GAACCGAAGTTATAGAAGAACTCGTAAAAG-TTGTCAAGTTAGGAAGTTCGTCCA
* * * * * *
2089 TGATCCAAGAGATAATAAATTCTCACGTAAATAAGTTTTTAATT-AAATGACCAAAAGTTGTATA
319 AGAACCAAGAGAGAAAAAACTCTCACGTAAATAAGTTTTTAATTCAAA-GACCAAAAGTTGTTTA
** * *
2153 CCAAATGACAAACTAAGTAGACAAAACGATGTGATTTCCCT-AGCATGGAATGTTCAGAAAATTG
383 CCAAATGACAAACTATTTAGACAAAATGATGCGATTT-CCTGAGCATGGAATGTTCAGAAAATTG
* * * * *
2217 CTTGAAGGAATGGATCATCATGAAAACTTTAAAGAACAAAAGTTATAGAAGAAGTCGTCAAAGTT
447 CTCGAAGGAATGGATCGTCATGAAAACTTTAAAGAACTAAAGTTATAGAAGAA--CTTAAAAGTT
* * * *
2282 TATCAAGTTTAGAAGTTCATCCAATATCCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTCA
510 TATCAAGTTTAGAAGTTCATCCAAGATCAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAA
* * *
2347 TTCAAAGCCCAAAAGTTGCTTACCAAATGACAAATAGTTTAGAAAAAAATGATGCGATTTCCCAA
575 TTCAAAGACCAAAAGTTGCTTACAAAATGACAAATAGTTTAGAAAAAAATGATGCGATTTCCCAC
2412 GCAT
640 GCAT
** * * * * * * **
2416 TAAATTTTCGAAAAATTTCTCAAAGGAAT-GA-ATCAT-CA-A-TTTATTGAACTGAAGTTATAA
1 GGAATGTTCGGAAAATTGCTCGAAGGAATGGATTTCATGAATACTTTAAGGAACTGAAGTTATAA
* ** * * ** *
2476 AAGAACTCGT-AAA---TT---GTTTAGAA-AATG-AC-A-AACTATTTAGAAAATGACAACTCT
66 AAGAACTCGTAAAACTTTTCAAGTTCAGAAGTTTGTCCAAGAACCA-AGAGAGAA--ACAACTCT
* * *
2530 CACGTAAATAAGATTTTAATTTATAGACCCAAAGTTGTTTAGAAAATGACAAACTATTTAGATCA
128 CACGTAAATAAGTTTTTAATTTATAGACCAAAAGTTGTTTAGAAAATGACAAACTATTTAGACCA
* * * * * * *
2595 AACGATGCGTTTTCCCGAGCATGGAATGCTCGAAAAATT-GTTTGAAGGAATGGATTGTCATGAA
193 AATGATGCGATTTCCCGAGCATGAAATGTTCAAAAAATTACTCT-AAGGAATGGATTGTCATGAA
* * * * *
2659 TACTTTAAGGAA-CGAATGTTATAGATGAACT-GGAAAAGTTTTCCAAGTTCA-AAAGTTCATCC
257 TACTTTAA-GAACCGAA-GTTATAGAAGAACTCGTAAAAGTTGT-CAAGTT-AGGAAGTTCGTCC
* ** * *
2721 AAGAACTAAGAGAGAAACTACTCTCACGTAAATAAGTTTTTCATTCAAAGACCAAAAGTCGTTTA
318 AAGAACCAAGAGAGAAAAAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTA
** * * * * * *
2786 GAAAATCACAAAGTATTTAAACCAAATAATGCGATTT-CTGGAGCATGGAATGTTCAAAAAATTG
383 CCAAATGACAAACTATTTAGACAAAATGATGCGATTTCCT-GAGCATGGAATGTTCAGAAAATTG
* * * * * * *
2850 TTCTAAGGAATGGATTGTCTTGAATAC-TTGAAGAAATCAAAGTTATAGAAGAACTCATAAAAGT
447 CTCGAAGGAATGGATCGTCATGAAAACTTTAAAGAACT-AAAGTTATAGAAGAACT--TAAAAGT
* * * * * * * * * *
2914 ATGTCTAGTTTGGAAGTTCGTCTAAGAGCCAAA-AGAGAAACAATTCTCACATAAATAGGTTTTA
509 TTATCAAGTTTAGAAGTTCATCCAAGA-TCAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * * * * *
2978 AATTCAAGGATCAAAAGTTGTTTAGAAAATGACAAACTA-TTTAG-ACATAATGATGCGATTTCC
573 AATTCAAAGACCAAAAGTTGCTTACAAAATGACAAA-TAGTTTAGAAAAAAATGATGCGATTTCC
* *
3041 CATGCTT
637 CACGCAT
* *
3048 GGAATGTTGGGAAAATTGCTCGAAGGAATGGATCTTCATGAATACTTTAAGGAACTGAAGTTTTA
1 GGAATGTTCGGAAAATTGCTCGAAGGAATGGAT-TTCATGAATACTTTAAGGAACTGAAGTTATA
* * *
3113 AAAGAACTCGTAAAACTTCGTCAAGTTCGGAAGTTCGTCCAAG-ACCAAAGAGAGAGAA-AACTC
65 AAAGAACTCGTAAAACTT-TTCAAGTTCAGAAGTTTGTCCAAGAACC-AAGAGAGA-AACAACTC
* * * * *
3176 TCACATAAATAACTTTTTAATTTATAAACCAAAAGTTGTTTACAAAATAACAAACTATTTAGACC
127 TCACGTAAATAAGTTTTTAATTTATAGACCAAAAGTTGTTTAGAAAATGACAAACTATTTAGACC
* * * **
3241 AAATGATGCGATTTCCCAAGCATGAAATGTTAAAAAAATTACTCGAAGGAGGGGATTGTCATGAA
192 AAATGATGCGATTTCCCGAGCATGAAATGTTCAAAAAATTACTCTAAGGAATGGATTGTCATGAA
* * * * * * * *
3306 TACTTTAATGAACCAAAGTTATGGAACAACTGGTAAAATTTTGTGAAGTTAGGAAGTTTGTCCAT
257 TACTTTAA-GAACCGAAGTTATAGAAGAACTCGTAAAA-GTTGTCAAGTTAGGAAGTTCGTCCAA
* * * * * *
3371 GATCCAAGAGATAATAAATTTTCACGTAAATAAGTTTTTAATT-AAATGACCAAAAGTTGTATAC
320 GAACCAAGAGAGAAAAAACTCTCACGTAAATAAGTTTTTAATTCAAA-GACCAAAAGTTGTTTAC
** * * *
3435 CAAATGACAAACTAAGTAGACAAGATGATGTGATTTCCCT-AGCATTGAATGTTCAGAAAATTGC
384 CAAATGACAAACTATTTAGACAAAATGATGCGATTT-CCTGAGCATGGAATGTTCAGAAAATTGC
* ** * *
3499 TCGAAGGAATGGATCGTCGTGAAAACTTTAAAGAACGGAAGTTATAGAAGAAGTCATCAAAGTTT
448 TCGAAGGAATGGATCGTCATGAAAACTTTAAAGAACTAAAGTTATAGAAGAA--CTTAAAAGTTT
* * * *
3564 ATCAAGTTTAGAAGTTCATCCAATATCCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTCAT
511 ATCAAGTTTAGAAGTTCATCCAAGATCAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAAT
* *
3629 TCAAAGCCCAAAAGTTGCTTACCAAATGACAAATAGTTTAGAAAAAAAATGATGCGATTTCCCAC
576 TCAAAGACCAAAAGTTGCTTACAAAATGACAAATAGTTTAG-AAAAAAATGATGCGATTTCCCAC
3694 GCAT
640 GCAT
** * * * ** * **
3698 TAAATTTTCGAAAAATTTCTTTAAGGAATGGATCGTCATGAATACTTTATTGAACTGAAGTTATA
1 GGAATGTTCGGAAAATTGCTCGAAGGAATGGAT-TTCATGAATACTTTAAGGAACTGAAGTTATA
** * *
3763 AAAGAACTCGTAAAAGCTTGCCAAGTTCGGAAGTTTGTCCAAGAACCAAGATAGAAACAACTCTC
65 AAAGAACTCGTAAAA-CTTTTCAAGTTCAGAAGTTTGTCCAAGAACCAAGAGAGAAACAACTCTC
* * * * *
3828 ACGTAAGA-AAGTTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCA
129 ACGTAA-ATAAGTTTTTAATTTATAGACCAAAAGTTGTTTAGAAAATGACAAACTATTTAGACCA
* * * * *
3892 AATGATGTGATTTCCCGAGTATGTAATGTTCAAAAAATTGCTCTAA-GAATGGGTTGTCCAT-AA
193 AATGATGCGATTTCCCGAGCATGAAATGTTCAAAAAATTACTCTAAGGAATGGATTGT-CATGAA
* * * *
3955 TACTTTAAGAAACCGAAGTTATTGAAGAACTCGTAAAAGTTCGTCAAGTTTGGAAGTTCATCTAA
257 TACTTTAAG-AACCGAAGTTATAGAAGAACTCGTAAAAGTT-GTCAAGTTAGGAAGTTCGTCCAA
* * *
4020 GAACGAAGAGAAAAAAAAACTCTCACGTAAATAGGTTTTTAATTCAAAGACCAAAAGTTGTTTAC
320 GAACCAAGAG-AGAAAAAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAC
* * ** * * *
4085 CAAATGCCAAACTATTTAGATAAAATGATGCGATTTGTTGTGCATGGAATGCTCGGAAAATTGCT
384 CAAATGACAAACTATTTAGACAAAATGATGCGATTTCCTGAGCATGGAATGTTCAGAAAATTGCT
* * * * * * * * *
4150 CGAAGGAATGGATTGTCATGAATATTTTAAGGAACTGAAGTTTTAAAAGAACTTGAAAACTTCAT
449 CGAAGGAATGGATCGTCATGAAAACTTTAAAGAACTAAAGTTATAGAAGAACTT-AAAAGTTTAT
** * * * *
4215 CAAGTTT-GAAAGTTTGTCCAAGAACAAAGAGAGGAACAATTCTCACGTCAATAAGATTTTAATT
513 CAAGTTTAG-AAGTTCATCCAAGATCAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATT
* ** ** *
4279 TAAAGACCAAAAGTTATTTACAAAATGACAAACTA-TTTAG-ACCAAATGATGTGATTTCCCGA-
577 CAAAGACCAAAAGTTGCTTACAAAATGACAAA-TAGTTTAGAAAAAAATGATGCGATTTCCC-AC
4341 GCAT
640 GCAT
* * *
4345 GGAATGTTCGGAAAATTGCTTGAAGGAATGGATTGTCATGGATACTTTAAGGAAC-GAAAGTGAT
1 GGAATGTTCGGAAAATTGCTCGAAGGAATGGATT-TCATGAATACTTTAAGGAACTG-AAGTTAT
* * * *
4409 AGATGAACTGGTAAAAGTTTTCCAAGTTCAGAAGTTTGTCCAAGAACCAAGAGAGAAACAACTCT
64 AAAAGAACTCGTAAAACTTTT-CAAGTTCAGAAGTTTGTCCAAGAACCAAGAGAGAAACAACTCT
* * * * * *
4474 CACGTAAATAAGTATTTCATTCAGAGACCAAAAGTCGTTTAGAAAATGACAAAGTATTTAGACCA
128 CACGTAAATAAGTTTTTAATTTATAGACCAAAAGTTGTTTAGAAAATGACAAACTATTTAGACCA
* * *
4539 AATGATGCGATTTCTCGAGCATGAAATGTTCAAAAAATTACTCTAAGGAATGGATTATCTTGAAT
193 AATGATGCGATTTCCCGAGCATGAAATGTTCAAAAAATTACTCTAAGGAATGGATTGTCATGAAT
* * * * * *
4604 ACATTAAGAAATCGAAGTTATAGAAGTACTCATAAAAGTATGTCAAGTTTGGAAGTTCGTCTAAG
258 ACTTTAAG-AACCGAAGTTATAGAAGAACTCGTAAAAGT-TGTCAAGTTAGGAAGTTCGTCCAAG
* * * * *
4669 AGCCAAGAGAGAAAAACCTCTCACGTAAATAGGTTTTTAATTCAAAGACCAAAAGTTGTTCACAA
321 AACCAAGAGAGAAAAAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACCA
* * * * *
4734 AATGACAAACTATTTAGACTAAATTATGCAATTTCCCGAGCATGGAATGTTC-GTAAAATTACTC
386 AATGACAAACTATTTAGACAAAATGATGCGATTTCCTGAGCATGGAATGTTCAG-AAAATTGCTC
4798 GAAGGAATGGA
450 GAAGGAATGGA
4809 GCAAAGTTAT
Statistics
Matches: 1942, Mismatches: 376, Indels: 152
0.79 0.15 0.06
Matches are distributed among these distances:
631 4 0.00
632 62 0.03
633 246 0.13
634 147 0.08
635 9 0.00
636 2 0.00
637 1 0.00
638 29 0.01
639 3 0.00
642 3 0.00
643 28 0.01
644 1 0.00
645 1 0.00
646 15 0.01
647 487 0.25
648 328 0.17
649 201 0.10
650 365 0.19
651 10 0.01
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (643 bp):
GGAATGTTCGGAAAATTGCTCGAAGGAATGGATTTCATGAATACTTTAAGGAACTGAAGTTATAA
AAGAACTCGTAAAACTTTTCAAGTTCAGAAGTTTGTCCAAGAACCAAGAGAGAAACAACTCTCAC
GTAAATAAGTTTTTAATTTATAGACCAAAAGTTGTTTAGAAAATGACAAACTATTTAGACCAAAT
GATGCGATTTCCCGAGCATGAAATGTTCAAAAAATTACTCTAAGGAATGGATTGTCATGAATACT
TTAAGAACCGAAGTTATAGAAGAACTCGTAAAAGTTGTCAAGTTAGGAAGTTCGTCCAAGAACCA
AGAGAGAAAAAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACCAAATGA
CAAACTATTTAGACAAAATGATGCGATTTCCTGAGCATGGAATGTTCAGAAAATTGCTCGAAGGA
ATGGATCGTCATGAAAACTTTAAAGAACTAAAGTTATAGAAGAACTTAAAAGTTTATCAAGTTTA
GAAGTTCATCCAAGATCAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
AAAGTTGCTTACAAAATGACAAATAGTTTAGAAAAAAATGATGCGATTTCCCACGCAT
Found at i:4964 original size:194 final size:194
Alignment explanation
Indices: 4636--4987 Score: 469
Period size: 194 Copynumber: 1.8 Consensus size: 194
4626 GAAGTACTCA
* * * *
4636 TAAAAGTATGTCAAGTTTGGAAGTTCGTCTAAGAGCCAAGAGAGAAAAACCTCTCACGTAAATAG
1 TAAAAGTATGTCAAGTTAGGAAGTTCGTCCAAGAGCCAAGAGAGAAAAACCTCTCACATAAATAA
* * *
4701 GTTTTTAATTCAAAGACCAAAAGTTGTTCACAAAATGACAAACTATTTAGACTAAATTATGCAAT
66 GTTTTTAATTCAAAGACCAAAAGTTGTTCACAAAATGACAAACTATGTAGACAAAATGATGCAAT
*
4766 TTCCCGAGCATGGAATGTTC-GTAAAATTACTCGAAGGAATGGAGCAAAGTTATTGAACAACTGG
131 TTCCCAAGCATGGAATGTTCAG-AAAATTACTCGAAGGAATGGAGCAAAGTTATTGAACAACTGG
* * * * * * *
4830 TAAAAGTTTGTGAAGTTAGGAAGTTTGTCCATGATCCAAGAGATAATAAA-TTCTCACATAAATA
1 TAAAAGTATGTCAAGTTAGGAAGTTCGTCCAAGAGCCAAGAGAGAA-AAACCTCTCACATAAATA
* *
4894 AGTTTTTAATT-AAATGACCAAAAGTTGTAT-ACCAAATGACAAACTATGTAGACAAAATGATGT
65 AGTTTTTAATTCAAA-GACCAAAAGTTGT-TCACAAAATGACAAACTATGTAGACAAAATGATGC
* *
4957 GATTTCCCAAGCATTGAATGTTCAGAAAATT
128 AATTTCCCAAGCATGGAATGTTCAGAAAATT
4988 GCTC
Statistics
Matches: 135, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
193 3 0.02
194 127 0.94
195 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (194 bp):
TAAAAGTATGTCAAGTTAGGAAGTTCGTCCAAGAGCCAAGAGAGAAAAACCTCTCACATAAATAA
GTTTTTAATTCAAAGACCAAAAGTTGTTCACAAAATGACAAACTATGTAGACAAAATGATGCAAT
TTCCCAAGCATGGAATGTTCAGAAAATTACTCGAAGGAATGGAGCAAAGTTATTGAACAACTGG
Done.