Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398724.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2008.0, 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: 9558
ACGTcount: A:0.21, C:0.08, G:0.07, T:0.21
Warning! 4136 characters in sequence are not A, C, G, or T
Found at i:3427 original size:173 final size:171
Alignment explanation
Indices: 2877--3644 Score: 469
Period size: 171 Copynumber: 4.5 Consensus size: 171
2867 NNNNNNNNNN
* * * * * *
2877 TCCATTTATAGTCACCCA-TATCTTCAAAAGCCTTATTACTCGCTTTAAATGATTGTGTAATGTC
1 TCCATTTATAGTCACCCATTA-CTTCAAAAGCCTTATCACTCACTTTAAATGGTTTTATAATCTC
* * * * * * ** *
2941 ATAATTGAATTTAAGTTGAATTTTTCTTATATTTTTGGTT-AAACAGACTATAATTAAATGTCTA
65 AAAATTGATTTTAAGTTCAATGTTT-TTATACTTTTGGTTAAAATAGACTATAATGGAACGTCTA
************ * *
3005 NNNNNNNNNNTGTAAAGAAAAAGGCATTCATTGGA-AAGAGAAG
129 CCTCGAGAAACATAAAGAAAAAAGCATTCA-TGGACAAGAAAAG
********** * *
3048 TCCATTTATAGTCACCCA-TACCTTCAAAAGCCTNNNNNNNNNNTTTAAATGATTTTGTAATGC-
1 TCCATTTATAGTCACCCATTA-CTTCAAAAGCCTTATCACTCACTTTAAATGGTTTTATAAT-CT
* * *
3111 CATAATTGATTTTAAGTTGAATGTTTTTATACTTTTGGTTAAAATAGACTATAATGGAATGTCTA
64 CAAAATTGATTTTAAGTTCAATGTTTTTATACTTTTGGTTAAAATAGACTATAATGGAACGTCTA
* * * *
3176 CCTCGATAAACATAAATAAAAAAGCATTCATTGATAAGAAAAG
129 CCTCGAGAAACATAAAGAAAAAAGCATTCATGGACAAGAAAAG
* ** * *
3219 TTCATTTATAGTCACCCATTACTTCAAAAGCCTTATCGGTCGCTTTGAATGGTTTTATAATCTCA
1 TCCATTTATAGTCACCCATTACTTCAAAAGCCTTATCACTCACTTTAAATGGTTTTATAATCTCA
* * * * *
3284 AAATTGATTTTAAGTTCAATTTTTTTTTGCTTTTTCGGTTAAAATATATTATAACT-GAACGTCT
66 AAATTGATTTTAAGTTCAATGTTTTTATAC-TTTT-GGTTAAAATAGACTATAA-TGGAACGTCT
* * * *
3348 ATCC-CGAGAAACATAAAGAAGAGAGGATTCATGGGCAA-AAGAAG
128 A-CCTCGAGAAACATAAAGAAAAAAGCATTCATGGACAAGAA-AAG
* * * * * *
3392 TCCATTTATAGTCAGCTATTCCTTTAAATGCCTTATTACTCACTTTAAATGGTTTTATAATCTCA
1 TCCATTTATAGTCACCCATTACTTCAAAAGCCTTATCACTCACTTTAAATGGTTTTATAATCTCA
* * * * ** * * ***********
3457 AAATT-AATTCAAATTCGAAATCTTTGCATA-TTTATGGTTAAAACAGAGTAGNNNNNNNNNNCT
66 AAATTGATTTTAAGTTC--AATGTTTTTATACTTT-TGGTTAAAATAGACTATAATGGAACGTCT
* * * *
3520 ACCTTGAGAAACATAAAGGAAAAAGTATTCATTGACAAGAAAAG
128 ACCTCGAGAAACATAAAGAAAAAAGCATTCATGGACAAGAAAAG
* * * * *
3564 TCTATTTATAGTCACCCATTACTTTAAAAG-CTTAATTAATCACTTTAAATGGTTTTATATTCTC
1 TCCATTTATAGTCACCCATTACTTCAAAAGCCTT-ATCACTCACTTTAAATGGTTTTATAATCTC
3628 AAAATTGATTTTAAGTT
65 AAAATTGATTTTAAGTT
3645 GAATTNNNNN
Statistics
Matches: 465, Mismatches: 114, Indels: 34
0.76 0.19 0.06
Matches are distributed among these distances:
170 17 0.04
171 193 0.42
172 123 0.26
173 122 0.26
174 10 0.02
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.36
Consensus pattern (171 bp):
TCCATTTATAGTCACCCATTACTTCAAAAGCCTTATCACTCACTTTAAATGGTTTTATAATCTCA
AAATTGATTTTAAGTTCAATGTTTTTATACTTTTGGTTAAAATAGACTATAATGGAACGTCTACC
TCGAGAAACATAAAGAAAAAAGCATTCATGGACAAGAAAAG
Found at i:4700 original size:170 final size:171
Alignment explanation
Indices: 4412--5141 Score: 695
Period size: 172 Copynumber: 4.3 Consensus size: 171
4402 NNNNNNNNNT
* * * * * * *
4412 AAGAAGAGTCCATTTATAGTCACCCATACCCTCAAAAGCCTTATTACCCGCTTTAAATAGTTTTT
1 AAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTA
* * * * * * *
4477 TAAT-TCCATAATTGGTTTTGAA-TT-AAATTTTTTTAAATTTTGGTTGAAACAGACTATAATTA
66 TAATCT-CAAAATT-GATTTGAATTTGAAATCTTTTCACATTTTGGTTAAAACAGACTATAATTG
* * *
4539 AATGTCTACCTAGAGAAACAT-AAAGAAAAAGGGATTCATTTGC
129 AATATCTACCTAGAGAAACATCAAAGAAAAA-GCATTCATTGGC
* * *
4582 AAGAAAAGTCCATTTATAGTCACCTATTGCTTCAAGAGGCTTATTACTCACTTTAAATAG-TTTA
1 AAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTA
* * * *
4646 TAATCTCAAAATTGATTTAAATTTGAATTCTTTGCACATTTTAGTTAAAACAGACT-TGAATTGA
66 TAATCTCAAAATTGATTTGAATTTGAAATCTTTTCACATTTTGGTTAAAACAGACTAT-AATTGA
* * * * * * *
4710 ATGTCTACTTTGATAAACATCAAGGAAAAAGTATTCATTGGG
130 ATATCTACCTAGAGAAACATCAAAGAAAAAGCATTCATTGGC
* * * * *
4752 AAGAAAAGTCTATTTATAGTCACCCATTGCTTCAAAAGCCTTATTAATCACTTTAAATGGTTTTA
1 AAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTA
* * * * * * * * * *
4817 TAATCTCCAAATTGATTTTAAGTTCAAATGTTTTTACTTTTCTTGTTAAAACATATTATAATTGA
66 TAATCTCAAAATTGATTTGAATTTGAAATCTTTTCACATTT-TGGTTAAAACAGACTATAATTGA
* * * *
4882 ACATCTAGCTCGAGAAACAT-AAAGTAGAAAGCATTCATTGGC
130 ATATCTACCTAGAGAAACATCAAAG-AAAAAGCATTCATTGGC
* * * * * * *
4924 AAGAGAAGTCCATTTATAGCCA-CTCATTCCTTTAAAGGTCTTATTACTTACTTTAAATGGTTTT
1 AAGAAAAGTCCATTTATAGTCACCT-ATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTT
* * * * *
4988 AAAATCTCAAAATTGATTTGGATTTGAAATCTTTACACATTTTTGGTTAAAACAGAGTAGAATTG
65 ATAATCTCAAAATTGATTTGAATTTGAAATCTTTTCACA-TTTTGGTTAAAACAGACTATAATTG
* * *
5053 AATATCTACCTTA-AGAAAGATGAAAAAAAAAGCATTCATTGGC
129 AATATCTACC-TAGAGAAACATCAAAGAAAAAGCATTCATTGGC
** * *
5096 AAGAAAAGTCCATTTATAGTCACCTATAACTACAAAAGCCTAATTA
1 AAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTA
5142 ATNNNNNNNN
Statistics
Matches: 451, Mismatches: 95, Indels: 26
0.79 0.17 0.05
Matches are distributed among these distances:
168 6 0.01
169 16 0.04
170 161 0.36
171 48 0.11
172 210 0.47
173 10 0.02
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (171 bp):
AAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTA
TAATCTCAAAATTGATTTGAATTTGAAATCTTTTCACATTTTGGTTAAAACAGACTATAATTGAA
TATCTACCTAGAGAAACATCAAAGAAAAAGCATTCATTGGC
Found at i:5134 original size:344 final size:339
Alignment explanation
Indices: 4412--5143 Score: 853
Period size: 344 Copynumber: 2.1 Consensus size: 339
4402 NNNNNNNNNT
* * ** * *
4412 AAGAAGAGTCCATTTATAGTCACCCATACCCTCAAAAGCCTTATTACCCGCTTTAAATAGTTTTT
1 AAGAAAAGTCCATTTATAGTCACCCATA-ACTCAAAAGCCTTATTAATCACTTTAAATAGTTTTA
* * * *
4477 TAATTCCATAATTGGTTTTGAATTAAATTTTTTTAAATTTTGGTTGAAACAGACTATAATTAAAT
65 TAATTCCATAATTGATTTTGAATTAAATGTTTTTAAATTTTGGTTAAAACAGACTATAATTAAAC
* * * *
4542 GTCTACCTAGAGAAACATAAAGAAAAAGGGATTCATTTGCAAGAAAAGTCCATTTATAGTCACCT
130 ATCTACCTAGAGAAACATAAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGCCACCT
* *
4607 ATTGCTTCAAGAGGCTTATTACTCACTTTAAATAGTTTATAATCTCAAAATTGATTTAAATTTGA
195 ATTCCTTCAAGAGGCTTATTACTCACTTTAAATAGTTTAAAATCTCAAAATTGATTTAAATTTGA
* * * * * * * **
4672 ATTCTTTGCACATTTTAGTTAAAACAGACTTGAATTGAATGTCTACTTTGATAAACATCAAGGAA
260 AATCTTTACACATTTTAGTTAAAACAGACTAGAATTGAATATCTACCTTAAGAAACATCAAAAAA
* *
4737 AAAGTATTCATTGGG
325 AAAGCATTCATTGGC
* ** *
4752 AAGAAAAGTCTATTTATAGTCACCCATTGCTTCAAAAGCCTTATTAATCACTTTAAATGGTTTTA
1 AAGAAAAGTCCATTTATAGTCACCCATAAC-TCAAAAGCCTTATTAATCACTTTAAATAGTTTTA
** * * *
4817 TAATCTCCA-AATTGATTTT-AAGTTCAAATGTTTTTACTTTTCTTGTTAAAACATATTATAATT
65 TAAT-TCCATAATTGATTTTGAA-TT-AAATGTTTTTAAATTT-TGGTTAAAACAGACTATAATT
* * * * *
4880 GAACATCTAGCTCGAGAAACATAAAGTAGAAA-GCATTCATTGGCAAGAGAAGTCCATTTATAGC
126 AAACATCTACCTAGAGAAACATAAAG-AAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGC
* * *
4944 CA-CTCATTCCTTTAA-AGGTCTTATTACTTACTTTAAATGGTTTTAAAATCTCAAAATTGATTT
190 CACCT-ATTCCTTCAAGAGG-CTTATTACTCACTTTAAATAG-TTTAAAATCTCAAAATTGATTT
** * * *
5007 GGATTTGAAATCTTTACACATTTTTGGTTAAAACAGAGTAGAATTGAATATCTACCTTAAGAAAG
252 AAATTTGAAATCTTTACACA-TTTTAGTTAAAACAGACTAGAATTGAATATCTACCTTAAGAAAC
*
5072 ATGAAAAAAAAAGCATTCATTGGC
316 ATCAAAAAAAAAGCATTCATTGGC
* *
5096 AAGAAAAGTCCATTTATAGTCACCTATAACTACAAAAGCCTAATTAAT
1 AAGAAAAGTCCATTTATAGTCACCCATAACT-CAAAAGCCTTATTAAT
5144 NNNNNNNNNN
Statistics
Matches: 327, Mismatches: 54, Indels: 18
0.82 0.14 0.05
Matches are distributed among these distances:
339 3 0.01
340 69 0.21
341 22 0.07
342 95 0.29
343 42 0.13
344 96 0.29
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (339 bp):
AAGAAAAGTCCATTTATAGTCACCCATAACTCAAAAGCCTTATTAATCACTTTAAATAGTTTTAT
AATTCCATAATTGATTTTGAATTAAATGTTTTTAAATTTTGGTTAAAACAGACTATAATTAAACA
TCTACCTAGAGAAACATAAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGCCACCTA
TTCCTTCAAGAGGCTTATTACTCACTTTAAATAGTTTAAAATCTCAAAATTGATTTAAATTTGAA
ATCTTTACACATTTTAGTTAAAACAGACTAGAATTGAATATCTACCTTAAGAAACATCAAAAAAA
AAGCATTCATTGGC
Found at i:7858 original size:171 final size:172
Alignment explanation
Indices: 7567--7882 Score: 399
Period size: 171 Copynumber: 1.8 Consensus size: 172
7557 NNAATCTCAA
* *
7567 AATTGATTTAAATTTGAATTCTTCGTACATTTTTGGTTAAAATAGACTAAGATTGAATGTCTACC
1 AATTGATTTAAAGTTGAATTCTTCGTACATTTTTGGTTAAAACAGACTAAGATTGAATGTCTACC
* * * * * * *
7632 TTGAGAATGATGAAGAAAAATGCATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACTTT
66 TTGAGAACGATAAAAAAAAAGGCATCCATTAGCAAGAAAAATCCATTTATAGTCACCCATACCTT
*
7697 CAAAAGTCGTATTACTCGCTTTAAATGGTTTTGTAATGCAAT
131 CAAAAGCCGTATTACTCGCTTTAAATGGTTTTGTAATGCAAT
* * *
7739 AATTTATTTAAAGTTGAATTTTTC-TACATTTTTGGTTTAAACAGACTATA-ATTGAATGTCTAC
1 AATTGATTTAAAGTTGAATTCTTCGTACATTTTTGGTTAAAACAGACTA-AGATTGAATGTCTAC
* * * *
7802 AC-TGAGAAACG-TAAAAAAAAAGGCATTCTTTAGCAA-AACAAATGCATTTATAGTCACCCATT
65 -CTTGAG-AACGATAAAAAAAAAGGCATCCATTAGCAAGAA-AAATCCATTTATAGTCACCCATA
*
7864 CCTTCAAAAGCCTTATTAC
127 CCTTCAAAAGCCGTATTAC
7883 NNNNNNNNNN
Statistics
Matches: 122, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
170 2 0.02
171 94 0.77
172 26 0.21
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (172 bp):
AATTGATTTAAAGTTGAATTCTTCGTACATTTTTGGTTAAAACAGACTAAGATTGAATGTCTACC
TTGAGAACGATAAAAAAAAAGGCATCCATTAGCAAGAAAAATCCATTTATAGTCACCCATACCTT
CAAAAGCCGTATTACTCGCTTTAAATGGTTTTGTAATGCAAT
Found at i:8439 original size:343 final size:341
Alignment explanation
Indices: 7956--9558 Score: 1266
Period size: 343 Copynumber: 4.7 Consensus size: 341
7946 NNNNNNNNNN
* * **
7956 TAAAACAGACTAGAATTGAATGTCTACCATGAGAAACATGAAGAAAAAAACATTTATTGATGAGA
1 TAAAACAAACTAGAATTGAATGTCTACCATCAGAAACATGAAG-AAAAAAGTTTTATTGATGAGA
* *
8021 AAAGTCCACTTATATTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAACGGTTTTGTAAT
65 AAAGTCCACTTATACTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAATGGTTTTGTAAT
********* *
8086 GCCATAATTGATTTTAAGTNNNNNNNNNNTTATATTTTTAGTTAAACAGACTATTATTGGATGTC
130 GCCATAATTGATTTTAAGT-GAATTTTTCTTATATTTTTAGTTAAACAGACTATTATTGAATGTC
*
8151 TACCTTGAGAAATGTAAAGAAAAAGTAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATT
194 TACCTTGAGAAATGTAAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATT
**********
8216 CCTTCAAAAGCCNNNNNNNNNNCTTTAAATAGTTTTATAACCTCAAAATTCATTTAAATTTGAAT
259 CCTTCAAAAGCCTTATCACTCACTTTAAATAGTTTTATAACCTCAAAATTCATTTAAATTTGAAT
8281 TCTTTATACATTTTTTCT
324 TCTTTATACATTTTTTCT
* * * * * ***
8299 TAAAGCAAACTAGGATTGATTGTCTACCTTCAGAAATATGAAGAAAAAAGTTTTCATTGGCAAGA
1 TAAAACAAACTAGAATTGAATGTCTACCATCAGAAACATGAAGAAAAAAGTTTT-ATTGATGAGA
* * * * * * *
8364 AAATTCCATTTATAGTCACCCATATCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAAT
65 AAAGTCCACTTATACTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAATGGTTTTGTAAT
* * * *
8429 GTCATAATTGATTTTAAGCTGAATTTTTCTTACATTTTTGGTTAAACAGACTATAATTGAATGTC
130 GCCATAATTGATTTTAAG-TGAATTTTTCTTATATTTTTAGTTAAACAGACTATTATTGAATGTC
* ** * * * *
8494 TACCTCGAGAAACATAAAGAAAAAGGCATTCATTGGCAAGAGAAGTCCATTTATAGTCGCCAATT
194 TACCTTGAGAAATGTAAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATT
* ********** *
8559 CCTTCAAAAGCCTTATCACTCACTTTAAATGGTTTTATNNNNNNNNNNTTGATTTAAATTTGAAT
259 CCTTCAAAAGCCTTATCACTCACTTTAAATAGTTTTATAACCTCAAAATTCATTTAAATTTGAAT
* * *
8624 TCTTTGTATATTTTTTGT
324 TCTTTATACATTTTTTCT
* * *
8642 TAAAACATACTAGAATTGAATGTCTACCATGAGAAACATGAAAAAAAAAGTATTTATTGATGAGA
1 TAAAACAAACTAGAATTGAATGTCTACCATCAGAAACATGAAGAAAAAAGT-TTTATTGATGAGA
* *********
8707 AAAGTCCACTTACACTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAATGGNNNNNNNNN
65 AAAGTCCACTTATACTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAATGGTTTTGTAAT
* * * * * *
8772 NCCATAATTGATTTTAAGTTGAATTTTTTTTATATTTTTACTTAAACAGACTATTATCGAATATT
130 GCCATAATTGATTTTAAG-TGAATTTTTCTTATATTTTTAGTTAAACAGACTATTATTGAATGTC
**********
8837 TACCTTGAGAAATGTAAAGAAAAAGGAATTCATTGGCAAGAAAAGTNNNNNNNNNNTCACCCATT
194 TACCTTGAGAAATGTAAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATT
* * *
8902 CCTTCAAAAGCCTTATTACTCATTTTAAATAGTTTTATAACCTCAAAGTTCATTTAAATTTGAAT
259 CCTTCAAAAGCCTTATCACTCACTTTAAATAGTTTTATAACCTCAAAATTCATTTAAATTTGAAT
* * *
8967 TGTTTCTACATTGTTTCT
324 TCTTTATACATTTTTTCT
* * * * * ***************
8985 TAAAACAGACTAGGATTGATTGTCTACCTTCAGAAATATGAAGAAAAAANNNNNNNNNNNNNNNN
1 TAAAACAAACTAGAATTGAATGTCTACCATCAGAAACATGAAGAAAAAA-GTTTTATTGATGAGA
********** * * * * *
9050 NNNNNNNNNNTATAGTCACCCATATCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAA-
65 AAAGTCCACTTATACTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAATGGTTTTGTAAT
* * ********** *
9114 GATCATAATTGATTTTAAGCTGAATTTTTCTTACATTTTNNNNNNNNNNGACTATAATTGAATGT
130 G-CCATAATTGATTTTAAG-TGAATTTTTCTTATATTTTTAGTTAAACAGACTATTATTGAATGT
** * * * * *
9179 CTACCTCAAGAAACGTAAAGAGAAAGGCATTCATTTGCAAGAGAAGTCCATTTATAGTCACCCAT
193 CTACCTTGAGAAATGTAAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAT
******************** * *
9244 TCCTTCAAAAGCCTTNNNNNNNNNNNNNNNNNNNNTTATAATCTCAAAATTGATTTAAATTTGAA
258 TCCTTCAAAAGCCTTATCACTCACTTTAAATAGTTTTATAACCTCAAAATTCATTTAAATTTGAA
* *
9309 TTCTTTGTACATTTTTTGT
323 TTCTTTATACATTTTTTCT
* * * * *
9328 TGAAATAGACTAGAATTGAATGTCTACCATGAGAAACATAAAGAAAAAAGTATTTATTGATGAGA
1 TAAAACAAACTAGAATTGAATGTCTACCATCAGAAACATGAAGAAAAAAGT-TTTATTGATGAGA
* * **********
9393 AATGTCCACTTATATTCA-CCCTACCTTCAAAAGCCTTATTACTCGCTTTCANNNNNNNNNNAAT
65 AAAGTCCACTTATACTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAATGGTTTTGTAAT
* *
9457 GCCATAATTGATTTTAAGTTGAATTGTTTTTTATATTTTTAGTTAAATAGACTATTATTGAATGT
130 GCCATAATTGATTTTAAG-TGAATT-TTTCTTATATTTTTAGTTAAACAGACTATTATTGAATGT
*
9522 TTACCTTGAGAAATGTAAAGAAAAAGGAATTCATTGG
193 CTACCTTGAGAAATGTAAAGAAAAAGGAATTCATTGG
Statistics
Matches: 932, Mismatches: 320, Indels: 16
0.74 0.25 0.01
Matches are distributed among these distances:
342 63 0.07
343 865 0.93
344 4 0.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.34
Consensus pattern (341 bp):
TAAAACAAACTAGAATTGAATGTCTACCATCAGAAACATGAAGAAAAAAGTTTTATTGATGAGAA
AAGTCCACTTATACTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAATGGTTTTGTAATG
CCATAATTGATTTTAAGTGAATTTTTCTTATATTTTTAGTTAAACAGACTATTATTGAATGTCTA
CCTTGAGAAATGTAAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCC
TTCAAAAGCCTTATCACTCACTTTAAATAGTTTTATAACCTCAAAATTCATTTAAATTTGAATTC
TTTATACATTTTTTCT
Found at i:8465 original size:172 final size:169
Alignment explanation
Indices: 7958--9033 Score: 575
Period size: 171 Copynumber: 6.3 Consensus size: 169
7948 NNNNNNNNTA
* * * ** * ***
7958 AAACAGACTAGAATTGAATGTCTACCATGAGAAACATGAAGAAAAAAACATTTATTGATGAGAAA
1 AAACAGACTAGAATTGAATGTCTACCTTCAGAAACATAAAGAAAAAAGTATTCATTGGCAAGAAA
* * * * * * * *
8023 AGTCCACTTATATTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAACGGTTTTGTAATGC
66 AGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAATGT
******** *
8088 CATAATTGATTTTAAGTNNNNNNNNNNTTATATTTTTAGTT
131 CATAATTGATTTTAAGT--GAATTTTTTTACATTTTTAGTT
** * * **
8129 AAACAGACTATTATTGGATGTCTACCTTGAGAAATGTAAAG-AAAAAGTAATTCATTGGCAAGAA
1 AAACAGACTAGAATTGAATGTCTACCTTCAGAAACATAAAGAAAAAAGT-ATTCATTGGCAAGAA
********** * *
8193 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCNNNNNNNNNNCTTTAAAT-AGTTTTATAAC
65 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGA-TTTTGTAAT
* * * * * * **
8257 CTCAAAATTCATTTAAATTTGAATTCTTTATACATTTTTTCTT
129 GTCATAATTGATTTTAA-GTGAATT-TTTTTACATTTTTAGTT
* * * * * *
8300 AAAGCAAACTAGGATTGATTGTCTACCTTCAGAAATATGAAGAAAAAAGTTTTCATTGGCAAGAA
1 AAA-CAGACTAGAATTGAATGTCTACCTTCAGAAACATAAAGAAAAAAGTATTCATTGGCAAGAA
*
8365 AATTCCATTTATAGTCACCCATAT-CTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAAT
65 AAGTCCATTTATAGTCACCCAT-TCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAAT
*
8429 GTCATAATTGATTTTAAGCTGAATTTTTCTTACATTTTTGGTT
129 GTCATAATTGATTTTAAG-TGAATTTTT-TTACATTTTTAGTT
* * * *
8472 AAACAGACTATAATTGAATGTCTACC-TCGAGAAACATAAAGAAAAAGGCATTCATTGGCAAGAG
1 AAACAGACTAGAATTGAATGTCTACCTTC-AGAAACATAAAGAAAAAAGTATTCATTGGCAAGAA
* * * * * * ****
8536 AAGTCCATTTATAGTCGCCAATTCCTTCAAAAGCCTTATCACTCACTTTAAATGGTTTTATNNNN
65 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAATG
****** * * * * *
8601 NNNNNNTTGATTTAAATTTGAATTCTTTGTATATTTTTTGTT
130 TCATAATTGATTTTAA-GTGAATT-TTTTTACATTTTTAGTT
* * * * ***
8643 AAAACATACTAGAATTGAATGTCTACCATGAGAAACATGAAA-AAAAAAGTATTTATTGATGAGA
1 -AAACAGACTAGAATTGAATGTCTACCTTCAGAAACAT-AAAGAAAAAAGTATTCATTGGCAAGA
* * * * * * **********
8707 AAAGTCCACTTACACTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAATGGNNNNNNNNN
64 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAAT
** * *
8772 NCCATAATTGATTTTAAGTTGAATTTTTTTTATATTTTTACTT
129 GTCATAATTGATTTTAAG-TGAA-TTTTTTTACATTTTTAGTT
** * * * * ** * *
8815 AAACAGACTATTATCGAATATTTACCTTGAGAAATGTAAAGAAAAAGGAATTCATTGGCAAGAAA
1 AAACAGACTAGAATTGAATGTCTACCTTCAGAAACATAAAGAAAAAAGTATTCATTGGCAAGAAA
********** ** * **
8880 AGTNNNNNNNNNNTCACCCATTCCTTCAAAAGCCTTATTACTCATTTTAAAT-AGTTTTATAACC
66 AGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGA-TTTTGTAATG
* * * * *
8944 TCA-AAGTTCATTTAAATTTGAATTGTTTCTACATTGTTT-CTT
130 TCATAA-TTGATTTTAA-GTGAATT-TTTTTACATT-TTTAGTT
* * * *
8986 AAAACAGACTAGGATTGATTGTCTACCTTCAGAAATATGAAGAAAAAA
1 -AAACAGACTAGAATTGAATGTCTACCTTCAGAAACATAAAGAAAAAA
9034 NNNNNNNNNN
Statistics
Matches: 673, Mismatches: 206, Indels: 51
0.72 0.22 0.05
Matches are distributed among these distances:
170 15 0.02
171 351 0.52
172 292 0.43
173 15 0.02
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.34
Consensus pattern (169 bp):
AAACAGACTAGAATTGAATGTCTACCTTCAGAAACATAAAGAAAAAAGTATTCATTGGCAAGAAA
AGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAATGT
CATAATTGATTTTAAGTGAATTTTTTTACATTTTTAGTT
Found at i:8566 original size:171 final size:170
Alignment explanation
Indices: 7958--9258 Score: 557
Period size: 171 Copynumber: 7.6 Consensus size: 170
7948 NNNNNNNNTA
* * * ***
7958 AAACAGACTAGAATTGAATGTCTACCAT-GAGAAACATGAAGAAAAAAACATTTATTGATGAGAA
1 AAACAGACTAGAATTGAATGTCTACCATCGAGAAACATAAAGAAAAAAGCATTCATTGGCAAGAA
* * * * * * *
8022 AAGTCCACTTATATTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAACGGTTTTGTAATG
66 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAATG
* ******** *
8087 CCATAATTGATTTTAAGTNNNNNNNNNNTTATATTTTTAGTT
131 TCATAATTGATTTTAAGT--GAATTTTTTTACATTTTTAGTT
** * * ** *
8129 AAACAGACTATTATTGGATGTCTACC-TTGAGAAATGTAAAG-AAAAAGTAATTCATTGGCAAGA
1 AAACAGACTAGAATTGAATGTCTACCATCGAGAAACATAAAGAAAAAAG-CATTCATTGGCAAGA
********** *
8192 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCNNNNNNNNNNCTTTAAAT-AGTTTTATAA
65 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGA-TTTTGTAA
** * * * * * **
8256 CCTCAAAATTCATTTAAATTTGAATTCTTTATACATTTTTTCTT
129 TGTCATAATTGATTTTAA-GTGAATT-TTTTTACATTTTTAGTT
* * * * * * **
8300 AAAGCAAACTAGGATTGATTGTCTACCTTC-AGAAATATGAAGAAAAAAGTTTTCATTGGCAAGA
1 AAA-CAGACTAGAATTGAATGTCTACCATCGAGAAACATAAAGAAAAAAGCATTCATTGGCAAGA
*
8364 AAATTCCATTTATAGTCACCCATAT-CTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAA
65 AAAGTCCATTTATAGTCACCCAT-TCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAA
*
8428 TGTCATAATTGATTTTAAGCTGAATTTTTCTTACATTTTTGGTT
129 TGTCATAATTGATTTTAAG-TGAATTTTT-TTACATTTTTAGTT
* * *
8472 AAACAGACTATAATTGAATGTCTACC-TCGAGAAACATAAAGAAAAAGGCATTCATTGGCAAGAG
1 AAACAGACTAGAATTGAATGTCTACCATCGAGAAACATAAAGAAAAAAGCATTCATTGGCAAGAA
* * * * * * ****
8536 AAGTCCATTTATAGTCGCCAATTCCTTCAAAAGCCTTATCACTCACTTTAAATGGTTTTATNNNN
66 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAATG
****** * * * * *
8601 NNNNNNTTGATTTAAATTTGAATTCTTTGTATATTTTTTGTT
131 TCATAATTGATTTTAA-GTGAATT-TTTTTACATTTTTAGTT
* * * ***
8643 AAAACATACTAGAATTGAATGTCTACCAT-GAGAAACATGAAA-AAAAAAGTATTTATTGATGAG
1 -AAACAGACTAGAATTGAATGTCTACCATCGAGAAACAT-AAAGAAAAAAGCATTCATTGGCAAG
* * * * * * *********
8706 AAAAGTCCACTTACACTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAATGGNNNNNNNN
64 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAA
*** * *
8771 NNCCATAATTGATTTTAAGTTGAATTTTTTTTATATTTTTACTT
129 TGTCATAATTGATTTTAAG-TGAA-TTTTTTTACATTTTTAGTT
** * * * * ** * *
8815 AAACAGACTATTATCGAATATTTACC-TTGAGAAATGTAAAGAAAAAGGAATTCATTGGCAAGAA
1 AAACAGACTAGAATTGAATGTCTACCATCGAGAAACATAAAGAAAAAAGCATTCATTGGCAAGAA
********** ** * *
8879 AAGTNNNNNNNNNNTCACCCATTCCTTCAAAAGCCTTATTACTCATTTTAAAT-AGTTTTATAAC
66 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGA-TTTTGTAAT
* * * * * *
8943 CTCA-AAGTTCATTTAAATTTGAATTGTTTCTACATTGTTT-CTT
130 GTCATAA-TTGATTTTAA-GTGAATT-TTTTTACATT-TTTAGTT
* * * * * ****************
8986 AAAACAGACTAGGATTGATTGTCTACCTTC-AGAAATATGAAGAAAAAANNNNNNNNNNNNNNNN
1 -AAACAGACTAGAATTGAATGTCTACCATCGAGAAACATAAAGAAAAAAGCATTCATTGGCAAGA
**********
9050 NNNNNNNNNNTATAGTCACCCATAT-CTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAA
65 AAAGTCCATTTATAGTCACCCAT-TCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAA
*****
9114 -GATCATAATTGATTTTAAGCTGAATTTTTCTTACATTTTNNNNN
129 TG-TCATAATTGATTTTAAG-TGAATTTTT-TTACATTTTTAGTT
***** * * * * * * *
9158 NNNNNGACTATAATTGAATGTCTACC-TCAAGAAACGTAAAGAGAAAGGCATTCATTTGCAAGAG
1 AAACAGACTAGAATTGAATGTCTACCATCGAGAAACATAAAGAAAAAAGCATTCATTGGCAAGAA
9222 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTT
66 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTT
9259 NNNNNNNNNN
Statistics
Matches: 810, Mismatches: 281, Indels: 78
0.69 0.24 0.07
Matches are distributed among these distances:
170 20 0.02
171 411 0.51
172 359 0.44
173 20 0.02
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.33
Consensus pattern (170 bp):
AAACAGACTAGAATTGAATGTCTACCATCGAGAAACATAAAGAAAAAAGCATTCATTGGCAAGAA
AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTGTAATG
TCATAATTGATTTTAAGTGAATTTTTTTACATTTTTAGTT
Found at i:8911 original size:686 final size:686
Alignment explanation
Indices: 7956--9558 Score: 1837
Period size: 686 Copynumber: 2.3 Consensus size: 686
7946 NNNNNNNNNN
*
7956 TAAAACAGACTAGAATTGAATGTCTACCATGAGAAACATGAAGAAAAAAA-CATTTATTGATGAG
1 TAAAACAGACTAGAATTGAATGTCTACCATGAGAAACATGAA-AAAAAAAGTATTTATTGATGAG
8020 AAAAGTCCACTTATATTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAACGGTTTTGTAA
65 AAAAGTCCACTTATATTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAACGGTTTTGTAA
********** *
8085 TGCCATAATTGATTTTAAGTNNNNNNNNNNTTATATTTTTAGTTAAACAGACTATTATTGGATGT
130 TGCCATAATTGATTTTAAGTTGAATTTTTTTTATATTTTTAGTTAAACAGACTATTATTGAATGT
* *
8150 CTACCTTGAGAAATGTAAAGAAAAAGTAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAT
195 TTACCTTGAGAAATGTAAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAT
**********
8215 TCCTTCAAAAGCCNNNNNNNNNNCTTTAAATAGTTTTATAACCTCAAAATTCATTTAAATTTGAA
260 TCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAACCTCAAAATTCATTTAAATTTGAA
* *
8280 TTCTTTATACATTTTTTCTTAAAGCAAACTAGGATTGATTGTCTACCTTCAGAAATATGAAGAAA
325 TTCTTTATACATTGTTTCTTAAAACAAACTAGGATTGATTGTCTACCTTCAGAAATATGAAGAAA
8345 AAAGTTTTCATTGGCAAGAAAATTCCATTTATAGTCACCCATATCTTCAAAAGCCTTATTACTCG
390 AAAGTTTTCATTGGCAAGAAAATTCCATTTATAGTCACCCATATCTTCAAAAGCCTTATTACTCG
8410 CTTTAAATGATTTTGTAATG-TCATAATTGATTTTAAGCTGAATTTTTCTTACATTTTTGGTTAA
455 CTTTAAATGATTTTGTAA-GATCATAATTGATTTTAAGCTGAATTTTTCTTACATTTTTGGTTAA
*
8474 ACAGACTATAATTGAATGTCTACCTCGAGAAACATAAAGAAAAAGGCATTCATTGGCAAGAGAAG
519 ACAGACTATAATTGAATGTCTACCTCAAGAAACATAAAGAAAAAGGCATTCATTGGCAAGAGAAG
* *******
8539 TCCATTTATAGTCGCCAATTCCTTCAAAAGCCTTATCACTCACTTTAAATGGTTTTATNNNNNNN
584 TCCATTTATAGTCACCAATTCCTTCAAAAGCCTTATCACTCACTTTAAATGGTTTTATAATCTCA
*** *
8604 NNNTTGATTTAAATTTGAATTCTTTGTATATTTTTTGT
649 AAATTGATTTAAATTTGAATTCTTTGTACATTTTTTGT
*
8642 TAAAACATACTAGAATTGAATGTCTACCATGAGAAACATGAAAAAAAAAGTATTTATTGATGAGA
1 TAAAACAGACTAGAATTGAATGTCTACCATGAGAAACATGAAAAAAAAAGTATTTATTGATGAGA
* * * *********
8707 AAAGTCCACTTACACTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAATGGNNNNNNNNN
66 AAAGTCCACTTATATTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAACGGTTTTGTAAT
* * * *
8772 NCCATAATTGATTTTAAGTTGAATTTTTTTTATATTTTTACTTAAACAGACTATTATCGAATATT
131 GCCATAATTGATTTTAAGTTGAATTTTTTTTATATTTTTAGTTAAACAGACTATTATTGAATGTT
**********
8837 TACCTTGAGAAATGTAAAGAAAAAGGAATTCATTGGCAAGAAAAGTNNNNNNNNNNTCACCCATT
196 TACCTTGAGAAATGTAAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATT
* *
8902 CCTTCAAAAGCCTTATTACTCATTTTAAATAGTTTTATAACCTCAAAGTTCATTTAAATTTGAAT
261 CCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAACCTCAAAATTCATTTAAATTTGAAT
* * *
8967 TGTTTCTACATTGTTTCTTAAAACAGACTAGGATTGATTGTCTACCTTCAGAAATATGAAGAAAA
326 TCTTTATACATTGTTTCTTAAAACAAACTAGGATTGATTGTCTACCTTCAGAAATATGAAGAAAA
**************************
9032 AANNNNNNNNNNNNNNNNNNNNNNNNNNTATAGTCACCCATATCTTCAAAAGCCTTATTACTCGC
391 AAGTTTTCATTGGCAAGAAAATTCCATTTATAGTCACCCATATCTTCAAAAGCCTTATTACTCGC
*********
9097 TTTAAATGATTTTGTAAGATCATAATTGATTTTAAGCTGAATTTTTCTTACATTTTNNNNNNNNN
456 TTTAAATGATTTTGTAAGATCATAATTGATTTTAAGCTGAATTTTTCTTACATTTTTGGTTAAAC
* * * *
9162 NGACTATAATTGAATGTCTACCTCAAGAAACGTAAAGAGAAAGGCATTCATTTGCAAGAGAAGTC
521 AGACTATAATTGAATGTCTACCTCAAGAAACATAAAGAAAAAGGCATTCATTGGCAAGAGAAGTC
* ********************
9227 CATTTATAGTCACCCATTCCTTCAAAAGCCTTNNNNNNNNNNNNNNNNNNNNTTATAATCTCAAA
586 CATTTATAGTCACCAATTCCTTCAAAAGCCTTATCACTCACTTTAAATGGTTTTATAATCTCAAA
9292 ATTGATTTAAATTTGAATTCTTTGTACATTTTTTGT
651 ATTGATTTAAATTTGAATTCTTTGTACATTTTTTGT
* *
9328 TGAAATAGACTAGAATTGAATGTCTACCATGAGAAACAT-AAAGAAAAAAGTATTTATTGATGAG
1 TAAAACAGACTAGAATTGAATGTCTACCATGAGAAACATGAAA-AAAAAAGTATTTATTGATGAG
* **********
9392 AAATGTCCACTTATATTCA-CCCTACCTTCAAAAGCCTTATTACTCGCTTTCANNNNNNNNNNAA
65 AAAAGTCCACTTATATTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAACGGTTTTGTAA
*
9456 TGCCATAATTGATTTTAAGTTGAATTGTTTTTTATATTTTTAGTTAAATAGACTATTATTGAATG
130 TGCCATAATTGATTTTAAGTTGAATT-TTTTTTATATTTTTAGTTAAACAGACTATTATTGAATG
9521 TTTACCTTGAGAAATGTAAAGAAAAAGGAATTCATTGG
194 TTTACCTTGAGAAATGTAAAGAAAAAGGAATTCATTGG
Statistics
Matches: 764, Mismatches: 149, Indels: 8
0.83 0.16 0.01
Matches are distributed among these distances:
685 74 0.10
686 690 0.90
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.34
Consensus pattern (686 bp):
TAAAACAGACTAGAATTGAATGTCTACCATGAGAAACATGAAAAAAAAAGTATTTATTGATGAGA
AAAGTCCACTTATATTCACCCCTACCTTCAAAAGCCTTATTACTCGCTTTCAACGGTTTTGTAAT
GCCATAATTGATTTTAAGTTGAATTTTTTTTATATTTTTAGTTAAACAGACTATTATTGAATGTT
TACCTTGAGAAATGTAAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATT
CCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAACCTCAAAATTCATTTAAATTTGAAT
TCTTTATACATTGTTTCTTAAAACAAACTAGGATTGATTGTCTACCTTCAGAAATATGAAGAAAA
AAGTTTTCATTGGCAAGAAAATTCCATTTATAGTCACCCATATCTTCAAAAGCCTTATTACTCGC
TTTAAATGATTTTGTAAGATCATAATTGATTTTAAGCTGAATTTTTCTTACATTTTTGGTTAAAC
AGACTATAATTGAATGTCTACCTCAAGAAACATAAAGAAAAAGGCATTCATTGGCAAGAGAAGTC
CATTTATAGTCACCAATTCCTTCAAAAGCCTTATCACTCACTTTAAATGGTTTTATAATCTCAAA
ATTGATTTAAATTTGAATTCTTTGTACATTTTTTGT
Done.