Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399093.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2369.0, 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: 14416
ACGTcount: A:0.25, C:0.09, G:0.08, T:0.25
Warning! 4737 characters in sequence are not A, C, G, or T
Found at i:318 original size:172 final size:172
Alignment explanation
Indices: 4--628 Score: 392
Period size: 171 Copynumber: 3.7 Consensus size: 172
1 GCA
* * * *
4 TTTCTCGAGACA-AGCATTCAATTATATTCTGTTTTATCTAAAAATGT--AAAAAAATTCACCTA
1 TTTCTCAAGACAGA-CATTCAACTATAGTCTGTTTTATCAAAAAATGTAAAAAAAAATTCACCTA
* ********** **
66 AAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTANNNNNNNNNNTAAAGAAATGGGTGA
65 AAAATCAATTATGAGATTATAAAACAACTTAAAGCGAGTAATAAGGCTTTTAAAGAAATGGACGA
* *
131 CTATAAATGGACTTTTGTTGC-CAATGAAT-GCATTTTTCTTCATG
130 CCATAAATGGACTTTT-TT-CTCAATGAATGGC-TTTTTCTACATG
* * * *
175 TTTCTCAAGACAGATATTCAACTATTGTCTGTTTTATCAAAAAATGTAAAAAAAAATT-AGCTTA
1 TTTCTCAAGACAGACATTCAACTATAGTCTGTTTTATCAAAAAATGTAAAAAAAAATTCACCTAA
* * *
239 AAATCGATTATGAGATTATAAAACAACTTAAAGCGAGTAATAAGGCTTTTTAAGGAATGGACGAC
66 AAATCAATTATGAGATTATAAAACAACTTAAAGCGAGTAATAAGGCTTTTAAAGAAATGGACGAC
* *
304 CATAAATTGACTTTTTTCTTAATGAATGGCTTTTTCTACATG
131 CATAAATGGACTTTTTTCTCAATGAATGGCTTTTTCTACATG
* ** * * * * * *******
346 TTTGTCAAGGTAGGCATTCAATTATAGTCTGTTTTAACCAAAAA--TATAAAAAAATTNNNNNNN
1 TTTCTCAAGACAGACATTCAACTATAGTCTGTTTTATCAAAAAATGTAAAAAAAAATTCACCTAA
*** * * * * * **
409 NNNTCAATTTTGAGATTATAAAACTATTTAAAGTGAGTAATAAGGGTTTTGAAAG-AATGGGTGA
66 AAATCAATTATGAGATTATAAAACAACTTAAAGCGAGTAATAAGGCTTTT-AAAGAAATGGACGA
** ********** *
473 ATATAAATGGACTTTTCTTCTCAANNNNNNNNNNTTTCTACACG
130 CCATAAATGGACTTTT-TTCTCAATGAATGGCTTTTTCTACATG
** * * * * * * *
517 TTTCTTGAGACAGGCATTTAATTATAGTCTGTTTTAACTAAAAATGT--AAAAAAATTTACCTTA
1 TTTCTCAAGACAGACATTCAACTATAGTCTGTTTTATCAAAAAATGTAAAAAAAAATTCACCTAA
* * * * *
580 AAATCGATTAT-TGATTATAAAATAATTTCAAGCGAGTAATAAGGCTTTT
66 AAATCAATTATGAGATTATAAAACAACTTAAAGCGAGTAATAAGGCTTTT
629 CTCAAAATTG
Statistics
Matches: 348, Mismatches: 96, Indels: 21
0.75 0.21 0.05
Matches are distributed among these distances:
169 11 0.03
170 94 0.27
171 164 0.47
172 69 0.20
173 10 0.03
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.34
Consensus pattern (172 bp):
TTTCTCAAGACAGACATTCAACTATAGTCTGTTTTATCAAAAAATGTAAAAAAAAATTCACCTAA
AAATCAATTATGAGATTATAAAACAACTTAAAGCGAGTAATAAGGCTTTTAAAGAAATGGACGAC
CATAAATGGACTTTTTTCTCAATGAATGGCTTTTTCTACATG
Found at i:1345 original size:172 final size:161
Alignment explanation
Indices: 1129--1454 Score: 332
Period size: 172 Copynumber: 2.0 Consensus size: 161
1119 TAAAATAAAT
* * * ** * *
1129 TAAAGCGAGTAACGAGACTTTTGAAAGAATGGGTAACTATAAATGGACTTTTCTTGTTAATGACT
1 TAAAGCGAGTAACAAGACTTTTGAAAGAATAGGTAACCATAAATGGACTTTTCTTGCCAACGAAT
* *
1194 ACATTTTTCTTCATATTTCAT-GAAGTAAACATTCAATTATTATCTGTTTTAACCAAAAATGTAA
66 ACATTTTTCCTCATATTT-ATCGAAGTAAACATTCAATTATTATCTATTTTAACCAAAAATGT-A
* *
1258 AAAAAATTCACCTTAAAATTAATTATGAGATTA
129 AAAAAATTCAACTTAAAATCAATTATGAGATTA
* *
1291 NNNNNNNNNNTAAAGCGAGTAATAAGGCTTTTG-AAGAAATAGGTAACCATAAATGGACTTTTCT
1 ----------TAAAGCGAGTAACAAGACTTTTGAAAG-AATAGGTAACCATAAATGGACTTTTCT
* * * * * *
1355 TGCCAACGAATGCATTTTTCCTCATGTTTATCGAGGTAAACATTCAATTATTGTTTATTTTATCC
55 TGCCAACGAATACATTTTTCCTCATATTTATCGAAGTAAACATTCAATTATTATCTATTTTAACC
* *
1420 ATAATTGTAAAAAAATTCAACTTAAAATCAATTAT
120 AAAAATGTAAAAAAATTCAACTTAAAATCAATTAT
1455 NNNNNNNNNN
Statistics
Matches: 131, Mismatches: 21, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
171 30 0.23
172 101 0.77
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.35
Consensus pattern (161 bp):
TAAAGCGAGTAACAAGACTTTTGAAAGAATAGGTAACCATAAATGGACTTTTCTTGCCAACGAAT
ACATTTTTCCTCATATTTATCGAAGTAAACATTCAATTATTATCTATTTTAACCAAAAATGTAAA
AAAATTCAACTTAAAATCAATTATGAGATTA
Found at i:3956 original size:171 final size:171
Alignment explanation
Indices: 3773--4092 Score: 365
Period size: 171 Copynumber: 1.9 Consensus size: 171
3763 NACATGAAGA
* * * * *
3773 AAAAGGCATTCATT-TGCAAGAAAAGTTCTTTTATAGTCACTCATTCCTTCAAAAGTCTCATTAC
1 AAAAGCCATTCATTAAG-AAGAAAAGTTCTTTTACAGTCACCCATTCCTTCAAAAGCCTCATTAC
** * * * * *
3837 TCGTTTTAAATGGTTTTATAAACTTATAATTGATTTTCAGCTGAATTTTTTTATA-TTTTTCATT
65 TCGCGTTAAATGATTTTATAAACTCATAATTAATTTTCAGCTAAATTTTTTTACATTTTTTCA-T
*
3901 AAAACAGACTATAATTGAATGTTAACCTCAAGAAACATTTGGG
129 AAAACAGAATATAATTGAATGTTAACCTCAAGAAACATTTGGG
**********
3944 AAAAGCCATTCATTAAGAAGAAANNNNNNNNNNCAGTCACCCATTCCTTCAAAAGCCTCATTACT
1 AAAAGCCATTCATTAAGAAGAAAAGTTCTTTTACAGTCACCCATTCCTTCAAAAGCCTCATTACT
* * * *
4009 CGCGTTAAATTATTTTATAATCTCATAATTAATTTTCAGTTAAATTTTTTTACATTTTTTGATAA
66 CGCGTTAAATGATTTTATAAACTCATAATTAATTTTCAGCTAAATTTTTTTACATTTTTTCATAA
4074 AACAGAATATAATTGAATG
131 AACAGAATATAATTGAATG
4093 CTTGCCTGGA
Statistics
Matches: 120, Mismatches: 27, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
171 113 0.94
172 7 0.06
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.38
Consensus pattern (171 bp):
AAAAGCCATTCATTAAGAAGAAAAGTTCTTTTACAGTCACCCATTCCTTCAAAAGCCTCATTACT
CGCGTTAAATGATTTTATAAACTCATAATTAATTTTCAGCTAAATTTTTTTACATTTTTTCATAA
AACAGAATATAATTGAATGTTAACCTCAAGAAACATTTGGG
Found at i:5460 original size:171 final size:168
Alignment explanation
Indices: 5278--7005 Score: 806
Period size: 171 Copynumber: 10.0 Consensus size: 168
5268 NNNNNNNNNN
* * * *
5278 AAAAACCTTATTACTCACTTTAAATAGTTTTATAATCTTATAATTGATTTTAAGCAGAATTTTTT
1 AAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTAGAATTTTTT
* * * **
5343 TACATTTTTAGATAAAACAGAATCTAATTGAATTTTTGTCTTAAGAAACATGTAGAAAAAGTCAT
66 TACATTTTT-GATAAAACAGAATATAATTGAATGTCTACCTTAAGAAACATG-AGAAAAAGTCAT
* * *
5408 TCGTTGAGAAGAAAAGTCTATTTATAGTCACTCATTCTTTT
129 TCATTG-GAAGAAAAGTCCATTTATAGTCACCCATTCTTTT
* ** * ********** * *
5449 GAAAGCCTTATTACTCATTTTAAATTGTTTTANNNNNNNNNNATTGATTTTAAGTTGAATTTCTT
1 AAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTAGAATTTTTT
* *
5514 TATATTTTTGAATAAAACAGATTATAATTGAATGTCTACCTCT-AGAAACATGAAGAAAAAGGT-
66 TACATTTTTG-ATAAAACAGAATATAATTGAATGTCTACCT-TAAGAAACATG-AGAAAAA-GTC
* * * * * *
5577 ATTTATTTGCAAGAAAAGTCCTTTTATAGTCACTCATTCCTTC
127 ATTCA-TTGGAAGAAAAGTCCATTTATAGTCACCCATTCTTTT
********** * * *
5620 AAANNNNNNNNNNCTCGCTTTAAATGGTTTTATAAACTCATAATTGATTTTCAA-TTGAA-TTTT
1 AAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTT-AAGTAGAATTTTT
* * * * * *
5683 TTATATTTTTCGTTAAAGCA-AACTATAATTGAATGTCTACCTTAGGAAACATGTGAAAAAAGCC
65 TTACATTTTT-GATAAAACAGAA-TATAATTGAATGTCTACCTTAAGAAACATGAG-AAAAAGTC
********* *
5747 ATTCNNNNNNNNNNAAAGTCCATTTATAGTCACCCATTCCATTT
127 ATTC-ATTGGAAGAAAAGTCCATTTATAGTCACCCATT-CTTTT
* * *
5791 -AAAGCCATATTACTCGCTTTAAATTA-TTTTATAATGTCGTAATTGATTTTAAGTTA-AATTTT
1 AAAAGCCTTATTACTCGCTTTAAA-TAGTTTTATAATCTCATAATTGATTTTAAG-TAGAATTTT
* * * * *
5853 TTTACATTTTTTGATAAAACAGAATATAATTGAATG-CTTGCCTTGACAAACATGAAAAAAAATG
64 TTTACA-TTTTTGATAAAACAGAATATAATTGAATGTC-TACCTTAAGAAACATGAGAAAAAGT-
* ********** *
5917 CATTCATTGGCAAGAAAAGTCTATTTATANNNNNNNNNNCTTTC
126 CATTCATTGG-AAGAAAAGTCCATTTATAGTCACCCATTCTTTT
* * *
5961 AAAAGCCTTATTACTCGCTTTAAAT--TATTTATAATCTAATAATTGATTTTAAGTTGAATTTAT
1 AAAAGCCTTATTACTCGCTTTAAATAGT-TTTATAATCTCATAATTGATTTTAAGTAGAATTTTT
** * * *
6024 TTACATTTTTTCCTTAAAACAGACTATAATTGAATGTCTA-CTTAGAGAAACATGAAAAAAAATG
65 TTACA-TTTTT-GATAAAACAGAATATAATTGAATGTCTACCTTA-AGAAACATGAGAAAAAGT-
* * * * *
6088 CATTCGTTGGCAAGAAAAGTCCCTTTATATTCGCCCATTCTTTC
126 CATTCATTGG-AAGAAAAGTCCATTTATAGTCACCCATTCTTTT
* * ** *
6132 AAAAGCCTAATTGCTTACTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTA-AATTTTT
1 AAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAG-TAGAATTTTT
********* * ** * *
6196 NNNNNNNNNNTGTTAAAACAGGCTATAATTCAATGTCTA-CTTAGAGAAACGTGAAGAAAAA-TA
65 -TTACATTTTTGATAAAACAGAATATAATTGAATGTCTACCTTA-AGAAACATG-AGAAAAAGT-
* ** * * * *
6259 CATTCGTTAATAAGAAAAGTCCCTTTATAGTCACCCACTCCTTC
126 CATTCATT-GGAAGAAAAGTCCATTTATAGTCACCCATTCTTTT
* * * * *
6303 AGAAGCATTATTATTCGCTTTAAATTA-TTTTATAATCTTATAGTTGATTTTAAGTTA-AATTTT
1 AAAAGCCTTATTACTCGCTTTAAA-TAGTTTTATAATCTCATAATTGATTTTAAG-TAGAATTTT
* * * * * * *
6366 TTTACATTTTTAGTTATAACAGACTATAATTGAATGTTTATCTCAAAAAACATGAAGAAACAAG-
64 TTTACATTTTT-GATAAAACAGAATATAATTGAATGTCTACCTTAAGAAACATG-AGAAA-AAGT
* * * ** * *
6430 CTTTCATTGCCAAGAAAAGTCCATTTATAGCCACATATTCCTTC
126 CATTCATTG-GAAGAAAAGTCCATTTATAGTCACCCATTCTTTT
* ********** * *
6474 AAAAGCCTTGTTACTCNNNNNNNNNNGTTTTATAATCTCATAATTGATTGTAAGTTGAATTTTTT
1 AAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTAGAATTTTTT
* ** *
6539 TACATTTTTTGATAAAACAAAATATAATTGAATG-CTTGTCTTGAGAAACATGAGGAAAAACG-C
66 TACA-TTTTTGATAAAACAGAATATAATTGAATGTC-TACCTTAAGAAACATGA-GAAAAA-GTC
* * * * *
6602 ATTCATCGGCAAGATAAGTCTATTTATAGCCACCCATTCCTTT
127 ATTCATTGG-AAGAAAAGTCCATTTATAGTCACCCATTCTTTT
* * * * * *
6645 AAAAGCCTTATTACTTTTC-CTTTGAA-AGTCTTATTAGTCGCTTTAAAT-AGTTTTNNNNNNNN
1 AAAAGCCTTATTAC---TCGCTTTAAATAGTTTTA-TAATCTC-ATAATTGA-TTTT--------
* * **
6707 NNAATTGTTTTTAAGTTGAAATTTTTTACATTTTTGGATAAAACAGACTATAATTGAATGTCTGT
52 --AA--G----T-A---GAATTTTTTTACATTTTT-GATAAAACAGAATATAATTGAATGTCTAC
* * * * * **
6772 C-TCAGAGAACGTGTAGAAAAAG-CCTTCCATTGAGAAAAAAAGTCAATTTATAGTCGTCCATTC
104 CTTAAGA-AACATG-AGAAAAAGTCATT-CATTG-GAAGAAAAGTCCATTTATAGTCACCCATTC
* *
6835 CTTC
165 TTTT
* * * * * * **
6839 AAAAGTCTTATTACCCGCTTTAAATGGTTTTATAACCTCATAAATGATTTTAAGTTGAATTCCTT
1 AAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTAGAATTTTTT
* * * * *
6904 TACATTTTTGGATAAAACAGACTATAATTGAATGTCTACCATGAGAAACATGAAGTAAAAGACAT
66 TACATTTTT-GATAAAACAGAATATAATTGAATGTCTACCTTAAGAAACATG-AGAAAAAGTCAT
*
6969 TCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTC
129 TCATTGG-AAGAAAAGTCCATTTATAGTCACCCATTC
7006 CTTCAAANNN
Statistics
Matches: 1171, Mismatches: 302, Indels: 168
0.71 0.18 0.10
Matches are distributed among these distances:
169 8 0.01
170 172 0.15
171 755 0.64
172 77 0.07
173 8 0.01
174 9 0.01
175 1 0.00
179 1 0.00
181 2 0.00
184 2 0.00
186 1 0.00
190 1 0.00
191 10 0.01
192 11 0.01
193 18 0.02
194 92 0.08
195 3 0.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.37
Consensus pattern (168 bp):
AAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTAGAATTTTTT
TACATTTTTGATAAAACAGAATATAATTGAATGTCTACCTTAAGAAACATGAGAAAAAGTCATTC
ATTGGAAGAAAAGTCCATTTATAGTCACCCATTCTTTT
Found at i:6178 original size:342 final size:342
Alignment explanation
Indices: 5285--7012 Score: 988
Period size: 342 Copynumber: 5.0 Consensus size: 342
5275 NNNAAAAACC
* * * *
5285 TTATTACTCACTTTAAA-TAGTTTTATAATCTTATAATTGATTTTAAG-CAGAATTTTTTTACAT
1 TTATTACTCGCTTTAAATTA-TTTTATAATCTAATAATTGATTTTAAGTTA-AATTTATTTACAT
** * * * * * * * * *
5348 TTTTAGATAAAACAGAATCTAATTGAATTTTTGTCTTAAGAAACATGTAG-AAAAAGTCATTCGT
64 TTTTACTTAAAACAGACTATAATTGAATGTCTATCTCAAAAAACATGAAGAAAAAAG-CATTCAT
** * * * * ** * *
5412 TGAGAAGAAAAGTCTATTTATAGTCACTCATTCTTTTGAAAGCCTTATTACTCATTTTAAATTGT
128 TGCCAAGAAAAGTCCATTTATAGCCACACATTCCTTCAAAAGCCTAATTACTCACTTTAAATTGT
********** * * * *
5477 TTTANNNNNNNNNNATTGATTTTAAGTTGAATTTCTTTATA-TTTTTGAATAAAACAGATTATAA
193 TTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTG-ATAAAACAGAATATAA
* * * *
5541 TTGAATG-TCT-ACCTCT-AGAAACATGAAGAAAAAGGTATTTATTTGCAAGAAAAGTCCT-TTT
257 TTGAATGCT-TGA-CT-TGAGAAACATGAAGAAAAATGCATTCATTGGCAAGAAAAGT-CTATTT
* * ****
5602 ATAGTCACTCATTCCTTCAAANNNN
318 ATAGTCACCCACTCCTTCAAAAGCA
****** ** * * * *
5627 NNNNNNCTCGCTTTAAATGGTTTTATAAACTCATAATTGATTTTCAA-TTGAATTT-TTTATATT
1 TTATTACTCGCTTTAAATTATTTTATAATCTAATAATTGATTTT-AAGTTAAATTTATTTACATT
* * * * ** * **
5690 TTT-CGTTAAAGCAAACTATAATTGAATGTCTACCTTAGGAAACATG-TGAAAAAAGCCATTCNN
65 TTTAC-TTAAAACAGACTATAATTGAATGTCTATCTCAAAAAACATGAAGAAAAAAG-CATTCAT
******** * * * *
5753 NNNNNNNNAAAGTCCATTTATAGTCACCCATTCCATT-TAAAGCC-ATATTACTCGCTTTAAATT
128 TGCCAAGAAAAGTCCATTTATAGCCACACATTCC-TTCAAAAGCCTA-ATTACTCACTTTAAATT
* * *
5816 ATTTTATAATGTCGTAATTGATTTTAAGTTAAATTTTTTTACATTTTTTGATAAAACAGAATATA
191 GTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTGATAAAACAGAATATA
* * *
5881 ATTGAATGCTTGCCTTGACAAACATGAAAAAAAATGCATTCATTGGCAAGAAAAGTCTATTTATA
256 ATTGAATGCTTGACTTGAGAAACATGAAGAAAAATGCATTCATTGGCAAGAAAAGTCTATTTATA
********** * *
5946 NNNNNNNNNNCTTTCAAAAGCC
321 GTCACCCACTCCTTCAAAAGCA
*
5968 TTATTACTCGCTTTAAATTA-TTTATAATCTAATAATTGATTTTAAGTTGAATTTATTTACATTT
1 TTATTACTCGCTTTAAATTATTTTATAATCTAATAATTGATTTTAAGTTAAATTTATTTACA-TT
* * * *
6032 TTTCCTTAAAACAGACTATAATTGAATGTCTA-CTTAGAGAAACATGAA-AAAAAATGCATTCGT
65 TTTACTTAAAACAGACTATAATTGAATGTCTATCTCA-AAAAACATGAAGAAAAAA-GCATTCAT
* * ** * * * * *
6095 TGGCAAGAAAAGTCCCTTTATATTCGCCCATTCTTTCAAAAGCCTAATTGCTTACTTTAAATTGT
128 TGCCAAGAAAAGTCCATTTATAGCCACACATTCCTTCAAAAGCCTAATTACTCACTTTAAATTGT
********** * **
6160 TTTATAATCTCATAATTGATTTTAAGTTAAATTTTTNNNNNNNNNNTGTTAAAACAGGCTATAAT
193 TTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTGATAAAACAGAATATAAT
* * * * *** **
6225 TCAATG-TCT-ACTTAGAGAAACGTGAAGAAAAATACATTCGTTAATAAGAAAAGTCCCTTTATA
258 TGAATGCT-TGACTT-GAGAAACATGAAGAAAAATGCATTCATTGGCAAGAAAAGTCTATTTATA
*
6288 GTCACCCACTCCTTCAGAAGCA
321 GTCACCCACTCCTTCAAAAGCA
* * * *
6310 TTATTATTCGCTTTAAATTATTTTATAATCTTATAGTTGATTTTAAGTTAAATTTTTTTACATTT
1 TTATTACTCGCTTTAAATTATTTTATAATCTAATAATTGATTTTAAGTTAAATTTATTTACATTT
* * * * *
6375 TTAGTTATAACAGACTATAATTGAATGTTTATCTCAAAAAACATGAAGAAACAAGCTTTCATTGC
66 TTACTTAAAACAGACTATAATTGAATGTCTATCTCAAAAAACATGAAGAAAAAAGCATTCATTGC
* ** **********
6440 CAAGAAAAGTCCATTTATAGCCACATATTCCTTCAAAAGCCTTGTTACTCNNNNNNNNNNGTTTT
131 CAAGAAAAGTCCATTTATAGCCACACATTCCTTCAAAAGCCTAATTACTCACTTTAAATTGTTTT
* * *
6505 ATAATCTCATAATTGATTGTAAGTTGAATTTTTTTACATTTTTTGATAAAACAAAATATAATTGA
196 ATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTGATAAAACAGAATATAATTGA
* * * * * *
6570 ATGCTTGTCTTGAGAAACATGAGGAAAAACGCATTCATCGGCAAGATAAGTCTATTTATAGCCAC
261 ATGCTTGACTTGAGAAACATGAAGAAAAATGCATTCATTGGCAAGAAAAGTCTATTTATAGTCAC
* * *
6635 CCATTCCTTTAAAAGCC
326 CCACTCCTTCAAAAGCA
* * ** *
6652 TTATTACTTTTC-CTTTGAAAGTCTTATTAGTCGCTTTAAATAGTTTTNNNNNNNNNNAATTGTT
1 TTATTAC---TCGCTTT-AAA---TTATT--T---TAT-AAT-CTAAT----------AATTGAT
*** * * *
6716 TTTAAGTTGAAATTT-TTTACATTTTTGGATAAAACAGACTATAATTGAATGTCTGTCTCAGAGA
42 TTTAAGTT-AAATTTATTTACATTTTTACTTAAAACAGACTATAATTGAATGTCTATCTCAAAAA
* * * ** * * **
6780 ACGTGTAG-AAAAAGCCTTCCATTGAGAAAAAAAGTCAATTTATAGTCGTC-CATTCCTTCAAAA
106 ACATGAAGAAAAAAGCATT-CATTGCCAAGAAAAGTCCATTTATAG-CCACACATTCCTTCAAAA
* * * * * * * * **
6843 GTCTTATTACCCGCTTTAAATGGTTTTATAACCTCATAAATGATTTTAAGTTGAATTCCTTTACA
169 GCCTAATTACTCACTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACA
* * * *
6908 TTTTTGGATAAAACAGACTATAATTGAATG-TCT-ACCATGAGAAACATGAAGTAAAA-GACATT
234 TTTTTTGATAAAACAGAATATAATTGAATGCT-TGA-CTTGAGAAACATGAAGAAAAATG-CATT
*
6970 CATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAA
296 CATTGGCAAGAAAAGTCTATTTATAGTCACCCACTCCTTCAAA
7013 NNNNNNNNNN
Statistics
Matches: 1049, Mismatches: 279, Indels: 93
0.74 0.20 0.07
Matches are distributed among these distances:
339 2 0.00
340 33 0.03
341 223 0.21
342 465 0.44
343 54 0.05
344 4 0.00
345 5 0.00
348 5 0.00
350 1 0.00
353 2 0.00
354 3 0.00
355 3 0.00
364 10 0.01
365 231 0.22
366 8 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.37
Consensus pattern (342 bp):
TTATTACTCGCTTTAAATTATTTTATAATCTAATAATTGATTTTAAGTTAAATTTATTTACATTT
TTACTTAAAACAGACTATAATTGAATGTCTATCTCAAAAAACATGAAGAAAAAAGCATTCATTGC
CAAGAAAAGTCCATTTATAGCCACACATTCCTTCAAAAGCCTAATTACTCACTTTAAATTGTTTT
ATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTGATAAAACAGAATATAATTGA
ATGCTTGACTTGAGAAACATGAAGAAAAATGCATTCATTGGCAAGAAAAGTCTATTTATAGTCAC
CCACTCCTTCAAAAGCA
Found at i:8394 original size:171 final size:162
Alignment explanation
Indices: 8045--8463 Score: 385
Period size: 171 Copynumber: 2.5 Consensus size: 162
8035 TTAAAATTAA
* * * * ***
8045 TTATAAGATTATAAAATAATTTAAAGTGAGTAATAATGCTTATGAAAGAATGGGTAACTATAAAG
1 TTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGACGACTATAAAG
* ** * * *
8110 TGACTTTTCTTATCAACGAATGCATTTTTCTTCACGTTTTTCTAAGTAGACATCGAATTATAGCC
66 GGACTTTTCTTGCCAACAAATGCATTTTTCTACACGTTTCTCTAAGTAGACATCGAATTATAGCC
* ***
8175 TGTTTTAACAAAAAATATAAAAAAATTCANNNNNNNNNNNN
131 TATTTTAACAAAAAATATAAAAAAATTCA---------ACT
*
8216 TTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGACGACTATAAAG
1 TTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGACGACTATAAAG
* *
8281 GGACTTTTCTTGCCAACAAATGTATTTTTCTACACGTTTCTCTAAGTAGACATTC-AATTATAGT
66 GGACTTTTCTTGCCAACAAATGCATTTTTCTACACGTTTCTCTAAGTAGACA-TCGAATTATAGC
** *
8345 CTATTTTAATGAAAAATATAAATAAATTCAACT
130 CTATTTTAACAAAAAATATAAAAAAATTCAACT
* * *
8378 NNNNNNNNNNTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT--TCG
1 ---------TTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGACG
*
8441 TAACTATAAATGGACTTTTCTTG
57 --ACTATAAAGGGACTTTTCTTG
8464 TCGATAATTA
Statistics
Matches: 208, Mismatches: 28, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
169 2 0.01
171 204 0.98
172 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.33
Consensus pattern (162 bp):
TTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGACGACTATAAAG
GGACTTTTCTTGCCAACAAATGCATTTTTCTACACGTTTCTCTAAGTAGACATCGAATTATAGCC
TATTTTAACAAAAAATATAAAAAAATTCAACT
Found at i:8481 original size:171 final size:159
Alignment explanation
Indices: 8045--8608 Score: 378
Period size: 171 Copynumber: 3.3 Consensus size: 159
8035 TTAAAATTAA
* * * * *
8045 TTATAAGATTATAAAATAATTTAAAGTGAGTAATAATGCTTATGAAAGAATGGGTAACTATAAAG
1 TTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAAT-TGTAACTATAAAG
* * *
8110 TGACTTTTCTTATCAACGAATGCATTTTTCTTCACGTTTTTCTAAGTAGACATCGAATTATAGCC
65 -GACTTTTCTTGTCAAC-AATGCATTTTTCTACACGTTTCTCTAAGTAGACATCGAATTATAGCC
* ***
8175 TGTTTTAACAAAAAATATAAAAAAATTCANNNNNNNNNNNN
128 TATTTTAACAAAAAATATAAAAAAATTCA---------ACT
* *
8216 TTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAA-TGGACGACTATAAA
1 TTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATTGTA--ACTATAAA
* *
8280 GGGACTTTTCTTGCCAACAAATGTATTTTTCTACACGTTTCTCTAAGTAGACATTC-AATTATAG
64 -GGACTTTTCTTGTCAAC-AATGCATTTTTCTACACGTTTCTCTAAGTAGACA-TCGAATTATAG
* ** *
8344 TCTATTTTAATGAAAAATATAAATAAATTCAACT
126 CCTATTTTAACAAAAAATATAAAAAAATTCAACT
* *
8378 NNNNNNNNNNTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATTCGTA
1 ---------TTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATT-GTA
* * * * * * * * **
8443 ACTATAAATGGACTTTTCTTGTCGATAATTACATTTTTCTTCATGTTTGTCTAGGAAAGATTTC-
56 ACTATAAA-GGACTTTTCTTGTCAACAA-TGCATTTTTCTACACGTTTCTCTAAG-TAGACATCG
** * * * * *
8507 AATTATATTCTGTTTTATCAAAAAATGTAAAAAAATTTAATTAAAAATT
118 AATTATAGCCTATTTTAACAAAAAA--TATAAAAA---AATT--CAACT
* * *
8556 AATTATGAGATTATAAAATAATTTAACGCGAGGAATAAGGCTTTTGAAGGAAT
1 --TTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAAT
8609 GGGTGANNNN
Statistics
Matches: 317, Mismatches: 52, Indels: 48
0.76 0.12 0.12
Matches are distributed among these distances:
169 2 0.01
170 2 0.01
171 291 0.92
172 7 0.02
173 8 0.03
176 4 0.01
178 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.35
Consensus pattern (159 bp):
TTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATTGTAACTATAAAGG
ACTTTTCTTGTCAACAATGCATTTTTCTACACGTTTCTCTAAGTAGACATCGAATTATAGCCTAT
TTTAACAAAAAATATAAAAAAATTCAACT
Found at i:11963 original size:171 final size:173
Alignment explanation
Indices: 11629--11998 Score: 416
Period size: 171 Copynumber: 2.2 Consensus size: 173
11619 NNNNNNNNNN
*
11629 TTCCTTCAAAAGCCTTATTAC-TCGCTTTAAAGTATTTTATAATCTTATAATTGATTTTAAGTTG
1 TTCCTTCAAAAGCCTTATTACTTCGCTTTAAAGTATTTTATAATCTCATAATTGATTTTAAGTTG
* * * * * * *
11693 AATTGTTTTGCACTTTTTTGTTAAAACAAATTATAATTGAATGTCTACTTAGAGAAACGTGAAGA
66 AATTGTTTTGCACTGTTTTGCTAAAACAAACTACAATTGAATGCCTACTCAGAGAAAAGTGAAGA
11758 AAAACACATTCATTGACAAAAAAAGCCCATTTATAGTCACCCA
131 AAAACACATTCATTGACAAAAAAAGCCCATTTATAGTCACCCA
* * * * * * *
11801 TTTCTTCAGAAGCCTTTTTACTTTG-TTTAAATTGTTTTATAATGTCATAATTGATTTTAAGTTG
1 TTCCTTCAAAAGCCTTATTACTTCGCTTTAAAGTATTTTATAATCTCATAATTGATTTTAAGTTG
* * * *
11865 AATT-TTTT-TA-TAGTTTTGCCTAAAACAAACTACAATTGAATGCCTGCCTCA-AGAAAATTGT
66 AATTGTTTTGCACT-GTTTTG-CTAAAACAAACTACAATTGAATGCCT-ACTCAGAGAAAAGTGA
* * * *
11926 AGAAAAAGC-CATTCATAT-ATAAGAAAAGTCTATTTATAGTCACCCA
128 AGAAAAA-CACATTCAT-TGACAAAAAAAGCCCATTTATAGTCACCCA
*
11972 TTCCTTCAAAAACCTTATTAC-TCGCTT
1 TTCCTTCAAAAGCCTTATTACTTCGCTT
11999 NNNNNNNNNN
Statistics
Matches: 163, Mismatches: 28, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
169 1 0.01
170 8 0.05
171 90 0.55
172 62 0.38
173 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (173 bp):
TTCCTTCAAAAGCCTTATTACTTCGCTTTAAAGTATTTTATAATCTCATAATTGATTTTAAGTTG
AATTGTTTTGCACTGTTTTGCTAAAACAAACTACAATTGAATGCCTACTCAGAGAAAAGTGAAGA
AAAACACATTCATTGACAAAAAAAGCCCATTTATAGTCACCCA
Found at i:13397 original size:21 final size:22
Alignment explanation
Indices: 13373--13420 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
13363 TATAAAACTA
*
13373 TTTAAA-GCGACTAATAAGGCT
1 TTTAAAGGCAACTAATAAGGCT
*
13394 TTTAAAGGGCAAGTAATAAGGCT
1 TTTAAA-GGCAACTAATAAGGCT
13417 TTTA
1 TTTA
13421 CAAGAATGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
23 17 0.74
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (22 bp):
TTTAAAGGCAACTAATAAGGCT
Done.