Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398000.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1306.0, 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: 13493
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.27
Warning! 3448 characters in sequence are not A, C, G, or T
Found at i:4631 original size:170 final size:170
Alignment explanation
Indices: 3695--4973 Score: 954
Period size: 171 Copynumber: 7.5 Consensus size: 170
3685 TCTCAAAATT
* * * * * * *
3695 AACGTGAAGAAAAAGACATTCATTGGCAACAAAAGTCCATTTATAGTCACTCATTCCTTTAAAAA
1 AACGAGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG
* * * ********** *
3760 CTTTATTACTCATTTTAAATGGTTTTGTNNNNNNNNNNTTGATTTTAAGTTGAATTTTTTTGCAT
66 CCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTT-AATTTTTTTACAT
* ** * * * * * *
3825 CTTTCCTCAAAACAGACTATAATTTAATGCCTTCCT-TAGGA
130 TTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCGA-GA
* * ** * *** *
3866 AACGTGTAGAAAAACCCATTCATTTGA-AAGAAAAGTCCATCTATAGTCTTTCACTCCTTCAAAA
1 AACGAGAAGAAAAAGGCATTCA-TTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
* ** * *
3930 GCCTTATTACTCACTTTAAATGGTTCTATTGTGTCAAAAATGATTTTAAGTTCAATTTTTTT-C-
65 GCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTT-AATTTTTTTACA
******** * *
3993 TNNNNNNNNNNAAAACAGATTATAATTGAATGT-TCATCTTGAGA
129 T--TTTTGGTTAAAACAGATTATAATTGAATGTCT-ACCTCGAGA
* * ** * * * * * * *
4037 AATGTGTAA-AAAAAGTTATTAATT-AGGAAGAAAAGTCCATTTCTGGTCTCTCATTCCTACAAA
1 AACGAG-AAGAAAAAGGCATTCATTGA-CAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* * * *********** *
4100 AGCCTTATTACTCGCTATGAATGGTTTTATAATCTCATNNNNNNNNNNAAGTTGAATTTTTTTAT
64 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTT-AATTTTTTTAC
** * * * * * *
4165 ATTTTTTATTAAAATAGACTATAAATGAATGCCTGCCTCAAGA
128 ATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCGAGA
* * * * *** * *
4208 AACGTA-TAGAAAAAGCCATTCATT-AGGAAGAAAAGTCCATTTATAGCCTTTCATTCTTTAAAA
1 AACG-AGAAGAAAAAGGCATTCATTGA-CAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* * * *
4271 AACCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATATAGTTTTTTTTA
64 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGT-TA-ATTTTTTTA
* *
4336 AATTTTTGGTATAAAA-A-ATTATAATTGAATGTCTACCTCGAAA
127 CATTTTTGGT-TAAAACAGATTATAATTGAATGTCTACCTCGAGA
* * * * * * *
4379 AATGGGAAGAAGAAGGCATTCATTGACATGAAATGTCCATTTATAGTCACCTATTCCTTTAAAAG
1 AACGAGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG
4444 CCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGATTAATTTTTTTACAT
66 CCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAG-TTAATTTTTTTACAT
* * *
4509 TTTTGGTTAAAATAGATTATAATTAAATGTCCACCTCGAGA
130 TTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCGAGA
* * * * * * *
4550 AACGAGAA-AAAAATGTATTTATTGGCAAGAAAAGTCCATTTACAATCACCCATACCTTCAAAAG
1 AACGAGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG
*
4614 CCTTATTAC-CTACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTGACTTTTTTTACA
66 CCTTATTACTC-ACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTT-AATTTTTTTACA
** *
4678 TTTTTGGTTAAAACAGATTATTGTTGAATGTCTGCCTCGAGA
129 TTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCGAGA
** *
4720 AACGTA-AAGAAAAAGGCATTCATTGACAAGAATGGTCCATTTTTAGTCACCCATTCCTTCAAAA
1 AACG-AGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
* * * * *
4784 GCCTTATTACTAACTTTAAATGGTTTTATAATTTCATAATTTATTTTAAGTTGATTTTTTTGACA
65 GCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTAATTTTTTT-ACA
* * *
4849 TTGTTGGCTAAAACAGACTATAATTGAATGTCTACCTCGAG-
129 TTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCGAGA
* * * * * *
4890 AACCATAAAAAAAAGGCATTCATTTGTA-AA-AAAATTACATTTATAGTTACCCATTCCTTCAAA
1 AACGAGAAGAAAAAGGCATTCA-TTG-ACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* *
4953 AGCCGTATTACTTACTTTAAA
64 AGCCTTATTACTCACTTTAAA
4974 NNNNNNNNNN
Statistics
Matches: 875, Mismatches: 203, Indels: 61
0.77 0.18 0.05
Matches are distributed among these distances:
169 11 0.01
170 238 0.27
171 594 0.68
172 26 0.03
173 6 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.37
Consensus pattern (170 bp):
AACGAGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG
CCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTAATTTTTTTACATT
TTTGGTTAAAACAGATTATAATTGAATGTCTACCTCGAGA
Found at i:4709 original size:341 final size:341
Alignment explanation
Indices: 4268--4973 Score: 904
Period size: 341 Copynumber: 2.1 Consensus size: 341
4258 TCATTCTTTA
* * *
4268 AAAAACCTTATTA-CTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATATAGTTTTT
1 AAAAGCCTTATTACCT-ACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATATAGCTTTT
* * *
4332 TTTAAATTTTTGGTATAAAAAATTATAATTGAATGTCTACCTCGAAAAATGGGAAGAAGAAGGCA
65 TTTAAATTTTTGGTATAAAAAATTATAATTGAATGTCTACCTCGAAAAACGGAAAGAAAAAGGCA
* * * *
4397 TTCATTGACATGAAAT-GTCCATTTATAGTCACCTATTCCTTTAAAAGCCTTATTACTCACTTTA
130 TTCATTGACAAG-AATGGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTAACTTTA
* * *
4461 AATGGTTTTATAATCTCAAAATTGATTTTAAGATTAATTTTTTT-ACATTTTTGGTTAAAATAGA
194 AATGGTTTTATAATCTCAAAATTGATTTTAAG-TTAATTTTTTTGACATTGTTGGCTAAAACAGA
* * * * * * * *
4525 TTATAATTAAATGTCCACCTCGAGAAACGA-GAAAAAAATGTATTTATTGGCAAGAAAAGTCCAT
258 CTATAATTAAATGTCCACCTCGAG-AACCATAAAAAAAAGGCATTCATTGGCAAAAAAAGTACAT
4589 TTACAATCACCCATACCTTC
322 TTACAATCACCCATACCTTC
*
4609 AAAAGCCTTATTACCTACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGT-T-GACTTTT
1 AAAAGCCTTATTACCTACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATATAG-CTTTT
* ** * * *
4672 TTTACATTTTTGGT-TAAAACAGATTATTGTTGAATGTCTGCCTCGAGAAACGTAAAGAAAAAGG
65 TTTAAATTTTTGGTATAAAA-A-ATTATAATTGAATGTCTACCTCGAAAAACGGAAAGAAAAAGG
*
4736 CATTCATTGACAAGAATGGTCCATTTTTAGTCACCCATTCCTTCAAAAGCCTTATTACTAACTTT
128 CATTCATTGACAAGAATGGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTAACTTT
* * * *
4801 AAATGGTTTTATAATTTCATAATTTATTTTAAGTTGATTTTTTTGACATTGTTGGCTAAAACAGA
193 AAATGGTTTTATAATCTCAAAATTGATTTTAAGTTAATTTTTTTGACATTGTTGGCTAAAACAGA
* * * * *
4866 CTATAATTGAATGTCTACCTCGAGAACCATAAAAAAAAGGCATTCATTTGTAAAAAAATTACATT
258 CTATAATTAAATGTCCACCTCGAGAACCATAAAAAAAAGGCATTCATTGGCAAAAAAAGTACATT
* * * *
4931 TATAGTTACCCATTCCTTC
323 TACAATCACCCATACCTTC
* *
4950 AAAAGCCGTATTACTTACTTTAAA
1 AAAAGCCTTATTACCTACTTTAAA
4974 NNNNNNNNNN
Statistics
Matches: 314, Mismatches: 44, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
339 6 0.02
340 36 0.11
341 270 0.86
342 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (341 bp):
AAAAGCCTTATTACCTACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATATAGCTTTTT
TTAAATTTTTGGTATAAAAAATTATAATTGAATGTCTACCTCGAAAAACGGAAAGAAAAAGGCAT
TCATTGACAAGAATGGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTAACTTTAAA
TGGTTTTATAATCTCAAAATTGATTTTAAGTTAATTTTTTTGACATTGTTGGCTAAAACAGACTA
TAATTAAATGTCCACCTCGAGAACCATAAAAAAAAGGCATTCATTGGCAAAAAAAGTACATTTAC
AATCACCCATACCTTC
Found at i:5395 original size:172 final size:170
Alignment explanation
Indices: 5074--5440 Score: 407
Period size: 172 Copynumber: 2.1 Consensus size: 170
5064 NNNNNNNNNN
* * *** * *
5074 CTATAAATGGACTTTTCTTCCAAATGAATGGCTTTTTCTATATGTTTCTTGAGGCAGACATTCAA
1 CTAT-AATGGACTTTTCTTCCAAATGAATGGATTTTTCTACATGTTTCCCAAGGAAGACATTAAA
* ** * ** *
5139 TTATCATCTGTTTTAACAAAAGATGTAAAAAAATTGAACTTAAAATCAATTTTGACATAATAAAA
65 TTATCATCTATTTTAACAAAAGATCAAAAAAAATTCAACTTAAAATCAATGATGACATAACAAAA
*
5204 CCATTTAAACTGAGTAATAAGACTTTT-AAAGGAATGGAAGA
130 CCATTTAAACTGAGTAATAAG-CTTTTCAAAAGAATGGAAGA
* * *
5245 CTATAGATGGACTTTTCTTTCAAATGAATGTATTTTTCTACATGTTTCCCAAGGAAGGCATTAAA
1 CTATA-ATGGACTTTTCTTCCAAATGAATGGATTTTTCTACATGTTTCCCAAGGAAGACATTAAA
* * * * *
5310 TTAT-AGTCTATTTTGAGAAAATATACAAAAAAAATTCAACTTAAAATCAATGATGAGATTACAA
65 TTATCA-TCTATTTTAACAAAAGAT-CAAAAAAAATTCAACTTAAAATCAATGATGACATAACAA
* **
5374 AACCATTTAAAAC-GAGTAATAAGGTTTTCAAAAGAATGGGTGA
128 AACCATTT-AAACTGAGTAATAAGCTTTTCAAAAGAATGGAAGA
5417 CTATAACTGGACTTTTCTTGCCAA
1 CTATAA-TGGACTTTTCTT-CCAA
5441 TAAATGCCTC
Statistics
Matches: 162, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
170 2 0.01
171 76 0.47
172 77 0.48
173 7 0.04
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (170 bp):
CTATAATGGACTTTTCTTCCAAATGAATGGATTTTTCTACATGTTTCCCAAGGAAGACATTAAAT
TATCATCTATTTTAACAAAAGATCAAAAAAAATTCAACTTAAAATCAATGATGACATAACAAAAC
CATTTAAACTGAGTAATAAGCTTTTCAAAAGAATGGAAGA
Found at i:5554 original size:30 final size:31
Alignment explanation
Indices: 5504--5567 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
5494 TTAATAAGGC
*
5504 TTTTAAAGAAATGAGTGACTATAAATGGA-A
1 TTTTAAAGAAATGAGTGACTAAAAATGGACA
*
5534 TTTTGAAAG-AATGGGTGACTAAAAATGGACA
1 TTTT-AAAGAAATGAGTGACTAAAAATGGACA
5565 TTT
1 TTT
5568 CTTGCCAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.31
Consensus pattern (31 bp):
TTTTAAAGAAATGAGTGACTAAAAATGGACA
Found at i:5819 original size:171 final size:171
Alignment explanation
Indices: 5534--6543 Score: 1006
Period size: 171 Copynumber: 5.9 Consensus size: 171
5524 ATAAATGGAA
* * * *
5534 TTTTGAAAGAATGGGTGACTAAAAATGGACATTTCTTGCCAATGAATGCCTTTTTCTT-TACGTT
1 TTTTGAAGGAATGGATGACTATAAATGGACATTTCTTGCCAATGAATACCTTTTTCTTCT-CGTT
* * * ** * *
5598 TCTCAAGGCAGACATTCAACAATAATCTATTCTAACCAAAAATGTAAAAAAATTAAACTTAAAAT
65 TTTCGAGGTAGACATTCAATTATAATCTATTTTAACTAAAAATGTAAAAAAATTAAACTTAAAAT
* * *
5663 CAATTTTAAGATTATAAAGCCATTTAAAGCGAGTAATATGGC
130 CAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGC
* ** * *
5705 TTTTGAAGGTATGGATGACTATAAATGGAGTTTTCTTGCCAGTAAATACCTTTTTCTTCTCGTTT
1 TTTTGAAGGAATGGATGACTATAAATGGACATTTCTTGCCAATGAATACCTTTTTCTTCTCGTTT
* * *
5770 TTCTAGGTACACATTCAATTATAATCTATTTTAACTAAAAATGTAAAAAAATTAATCTTAAAATC
66 TTCGAGGTAGACATTCAATTATAATCTATTTTAACTAAAAATGTAAAAAAATTAAACTTAAAATC
* *
5835 AATTTTGAGATTATAAAACCATTTAAAGTGAGTTATAAGGC
131 AATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGC
* * * * * * *
5876 TTTTGAAGGAATGGGTGACTATAAATGGACATTTCATGTCAATGAATTCCTTCTTCTTCACATTT
1 TTTTGAAGGAATGGATGACTATAAATGGACATTTCTTGCCAATGAATACCTTTTTCTTCTCGTTT
* * * * * *
5941 TTCGAGGTAGACATTCAATTATAAT-TTTTTTTA-TGAAAAATTTTAAAAAAACTATATTTAAAA
66 TTCGAGGTAGACATTCAATTATAATCTATTTTAACT-AAAAA-TGTAAAAAAATTAAACTTAAAA
* *
6004 TCAATTTTGAGATTATAAAACC-TGTTAAAGCGAGTAATTAGGT
129 TCAATTTTGAGATTATAAAACCAT-TTAAAGCGAGTAATAAGGC
* ** * * * *
6047 TTTTTAAGGAATGTGA-GGTTATAAATGGACTTTTCTT-CAAAATGAATAGCTTTTT-TTACACG
1 TTTTGAAGGAATG-GATGACTATAAATGGACATTTCTTGC-CAATGAATACCTTTTTCTT-CTCG
* * * * * * * * *
6109 -TTTCCTAAGGCAGGCATTCAATTATATTCTATTTTAGCAAAAAATAGAAAAAAAATTCAACTTA
63 TTTTTC-GAGGTAGACATTCAATTATAATCTATTTTAACTAAAAAT-GTAAAAAAATTAAACTTA
* * * *
6173 AAATCAATTATGCA-ATTATAAAAGCATTCAAAGTGAGTAATAAGGC
126 AAATCAATTTTG-AGATTATAAAACCATTTAAAGCGAGTAATAAGGC
* * * * * *
6219 TTTTGAA-GATATGGGTTACTATAAATGAACATTTCTTACCAATGAATGCCCTTTTCTT-TACGT
1 TTTTGAAGGA-ATGGATGACTATAAATGGACATTTCTTGCCAATGAATACCTTTTTCTTCT-CGT
* ** * * * *
6282 TTCTT-GAGGTAAACATTCAAAAATAATATGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAC
64 TT-TTCGAGGTAGACATTCAATTATAATCTATTTTAACTAAAAATGTAAAAAAATTAAACTTAAA
* *
6346 ATCAATTTTGAGGTTATAAAACTATTTAAAGCGAGTAATAAGGC
128 ATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGC
* * * * * *
6390 TTCTGAAGGTAT-GAGTGACTGTAAA-GGAC-TTTGCTTGTCAATAAATACCTTTTTCTTTTCGT
1 TTTTGAAGGAATGGA-TGACTATAAATGGACATTT-CTTGCCAATGAATACCTTTTTCTTCTCGT
* * * ** *
6452 TTCTCGAGGTAGACATTCAATTATAATCTGTTTTAACAAAAAACATAAAAAAATTCAACTTAAAA
64 TTTTCGAGGTAGACATTCAATTATAATCTATTTTAACTAAAAATGTAAAAAAATTAAACTTAAAA
6517 TCAATTTTGAGATTATAAAACCATTTA
129 TCAATTTTGAGATTATAAAACCATTTA
6544 NNNNNNNNNN
Statistics
Matches: 678, Mismatches: 135, Indels: 53
0.78 0.16 0.06
Matches are distributed among these distances:
169 5 0.01
170 124 0.18
171 413 0.61
172 128 0.19
173 7 0.01
174 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (171 bp):
TTTTGAAGGAATGGATGACTATAAATGGACATTTCTTGCCAATGAATACCTTTTTCTTCTCGTTT
TTCGAGGTAGACATTCAATTATAATCTATTTTAACTAAAAATGTAAAAAAATTAAACTTAAAATC
AATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGC
Found at i:7072 original size:171 final size:172
Alignment explanation
Indices: 6787--7125 Score: 411
Period size: 171 Copynumber: 2.0 Consensus size: 172
6777 NNNTTTTGAG
* * * * * * *
6787 ATTATAAAATCATTTAGAGCGAGTAATAAGGTTTTTGAAGGAATAGGAGGCTATAAGTGGACTTT
1 ATTATAAAAGCATTCAGAGCGAGTAATAAGGCTTGTGAAGGAATAGGAGACCATAAATGGACTTT
* * * * * **
6852 TCTTCCAAATGAATGGCTTTTTCTATATGTTTCTTGAGGCAAACATTCAATTATAGTCTTTTTTA
66 TCTTCCAAATGAATGGC-ATTTCTATATGTTTCCTAAGACAAACATTCAATTATAATCCGTTTTA
*
6917 AC-AAAAGAT-G-TAAAAAAATTCAACTTAAAATCAATTATGAT
130 ACTAAAA-ATAGAAAAAAAAATTCAACTTAAAATCAATTATGAT
*
6958 ATTATAAAAGCATTCATAGCGAGTAATAAGGCTTGTGACA-GAAT-GAGAGACCATAAATGGACT
1 ATTATAAAAGCATTCAGAGCGAGTAATAAGGCTTGTGA-AGGAATAG-GAGACCATAAATGGACT
* *
7021 TTTCTTCCAAATTAATGG-ATTTCTATGCATGTTTCCTAAGACAAGCATTCAATTATAATCCGTT
64 TTTCTTCCAAATGAATGGCATTTCTAT--ATGTTTCCTAAGACAAACATTCAATTATAATCCGTT
*
7085 TTAACTAAAAATAGAAAAAAAAATTGAACTTAAAATCAATT
127 TTAACTAAAAATAGAAAAAAAAATTCAACTTAAAATCAATT
7126 TTGACATAAT
Statistics
Matches: 142, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
169 7 0.05
170 1 0.01
171 104 0.73
172 6 0.04
173 24 0.17
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.34
Consensus pattern (172 bp):
ATTATAAAAGCATTCAGAGCGAGTAATAAGGCTTGTGAAGGAATAGGAGACCATAAATGGACTTT
TCTTCCAAATGAATGGCATTTCTATATGTTTCCTAAGACAAACATTCAATTATAATCCGTTTTAA
CTAAAAATAGAAAAAAAAATTCAACTTAAAATCAATTATGAT
Found at i:8146 original size:171 final size:171
Alignment explanation
Indices: 7851--8162 Score: 398
Period size: 171 Copynumber: 1.8 Consensus size: 171
7841 NNNNNNNNNN
* * * * *
7851 AATCAATTTTGAAATTATAAAACCATTTAAAGCGAGTAATTAGGTTTTTGAAGGAATAGGAGACT
1 AATCAATATTGAAATAAAAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACT
* * ** ** * *
7916 ATAAATGGACTTTTCTTCCAAATGAATGACTTTTTCTATATGTTTCTTGAGGCAGGCATTCAATT
66 ATAAATGGACTTTTCTTCCAAATCAATGACTTTTTCTACACATTTCTCCAAGCAGGCATTAAATT
*
7981 ATCGTCTATTTTAACAAAAGATGTAAAAAAATTGAACTTAA
131 ATAGTCTATTTTAACAAAAGATGTAAAAAAATTGAACTTAA
* * *
8022 AATCAATATTGACATAAAAAAACTATTTAAAGTGTA-TAATAAGGCTTTTGAAGGAAT-GGAAGA
1 AATCAATATTGAAATAAAAAAACCATTTAAAGCG-AGTAATAAGGCTTTTGAAGGAATAGG-AGA
*
8085 CTATAGATGGACTTTTCTTCCAAATCAATG-CATTTTTCTACACATTTC-CCAAGCAAGGCATTA
64 CTATAAATGGACTTTTCTTCCAAATCAATGAC-TTTTTCTACACATTTCTCCAAGC-AGGCATTA
8148 AATTATAGTCTATTT
127 AATTATAGTCTATTT
8163 GAGGATGAGA
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
170 6 0.05
171 112 0.94
172 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (171 bp):
AATCAATATTGAAATAAAAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACT
ATAAATGGACTTTTCTTCCAAATCAATGACTTTTTCTACACATTTCTCCAAGCAGGCATTAAATT
ATAGTCTATTTTAACAAAAGATGTAAAAAAATTGAACTTAA
Found at i:8858 original size:171 final size:171
Alignment explanation
Indices: 8271--8879 Score: 572
Period size: 171 Copynumber: 3.6 Consensus size: 171
8261 TCACGTTAAT
* * * *
8271 TTTGAGATTATAAAATCATTTAAAATGATTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
1 TTTGAAATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
* * * * *
8336 GA-AGTTTTTTG-CTAATGAATGCCTATTT-TTCTACGTTTCTCAAGGTAGCCATTCAATTATAG
66 GATA-TTTCTTGTC-AATGAATGCCTTTTTCTTCTACGTTTCTCAAGGTAGACATTCAATCATAA
* * **********
8398 TCTGTTTTAGCCAAAAACGTAAAAAAANNNNNNNNNNAATC-AA
129 TCTGTTTTAACCAAAAATGT-AAAAAATTAAACTTAAAATCAAA
*
8441 TTATGAAATTATAAAACCATTTAAAGTGAGGAATAAGGCTTTTGAAGGAATGGGTGACTA-AAAT
1 TT-TGAAATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT
* * * * *
8505 GGACATTTCTTGCCAATGAATACCTTTTTCTT-TACATTTCTCAAGGCAGACATTCAA-CAATAA
65 GGATATTTCTTGTCAATGAATGCCTTTTTCTTCTACGTTTCTCAAGGTAGACATTCAATC-ATAA
* * *
8568 TCTGTTTTAACTAAAAATGTAAAACAATTCAACTTAAAATCAAT
129 TCTGTTTTAACCAAAAATGTAAAA-AATTAAACTTAAAATCAAA
* * * *********
8612 TTTGAAATTATAGAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTNNNNNNNNNNT
1 TTTGAAATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT-GACTATAAAT
* * * *
8677 -GACT-TTTCTTGTCAATAAATGCCTTTTTCTTCT-CGTTTCTCGAGGTAGATATTTAATCATAA
65 GGA-TATTTCTTGTCAATGAATGCCTTTTTCTTCTACGTTTCTCAAGGTAGACATTCAATCATAA
* *
8739 TATATTTTAACCAAAAATGTGAAAAAATTAAACTTAAAATCAAA
129 TCTGTTTTAACCAAAAATGT-AAAAAATTAAACTTAAAATCAAA
* * * * *
8783 TTTGAGATTATAAAACTATTTAAAGTTAGTAATAAGGCTTTTAAAGGAATGTGTGACTATAAATG
1 TTTGAAATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
* *
8848 GATATTTCTTGTCAATGACTGCCTTCTTCTTC
66 GATATTTCTTGTCAATGAATGCCTTTTTCTTC
8880 AAATTTTTTG
Statistics
Matches: 351, Mismatches: 73, Indels: 29
0.77 0.16 0.06
Matches are distributed among these distances:
169 4 0.01
170 126 0.36
171 214 0.61
172 7 0.02
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (171 bp):
TTTGAAATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
GATATTTCTTGTCAATGAATGCCTTTTTCTTCTACGTTTCTCAAGGTAGACATTCAATCATAATC
TGTTTTAACCAAAAATGTAAAAAATTAAACTTAAAATCAAA
Found at i:9666 original size:171 final size:161
Alignment explanation
Indices: 9440--9766 Score: 275
Period size: 171 Copynumber: 2.0 Consensus size: 161
9430 ATAATAAAAT
* * * *
9440 CATTTAGAGTGAGTAACAAGGCTTTTGAAGGAATGAAAGACTATAGATGGACTTTT-TT-TCCAA
1 CATTTAAAATGAGTAACAAGGCTTTTAAAGGAATGAAAGACTATAAATGGACTTTTCTTGT-CAA
* * * * * * **
9503 GTGAATGGCTTTTTCTACATGTTTCCCAAGGAAGACATTA-AATTTTAGTCTGTTTTGAGGAAAA
65 -TGAATGCCTTTTGCTACAAGTTTCCCAAGGAAGACA-TACAATTATAATCTGTTTTAACCAAAA
9567 -ATACAAAAACATTCAACTTAAAATCAATTATGNNNNNNNNNNAC
128 CATACAAAAA-ATTCAACTTAAAATCAATTATG----------AC
* * *** *
9611 CATTTAAAATGAGTAATAAGGTTTTTAAAGGAATGGGTGACTATAAATTGACTTTTCTTGTCAAT
1 CATTTAAAATGAGTAACAAGGCTTTTAAAGGAATGAAAGACTATAAATGGACTTTTCTTGTCAAT
** ** * *
9676 GAATGCCTTTTGCTTTAAGTTTCTTAAGGGAGACATACAATTATAATCTGTTTTAACCAAAACTG
66 GAATGCCTTTTGCTACAAGTTTCCCAAGGAAGACATACAATTATAATCTGTTTTAACCAAAAC-A
9741 TACAAAAAATTCAACTTAAAATCAAT
130 TACAAAAAATTCAACTTAAAATCAAT
9767 NNNNNNNNNN
Statistics
Matches: 127, Mismatches: 24, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
170 2 0.02
171 93 0.73
172 23 0.18
173 9 0.07
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.33
Consensus pattern (161 bp):
CATTTAAAATGAGTAACAAGGCTTTTAAAGGAATGAAAGACTATAAATGGACTTTTCTTGTCAAT
GAATGCCTTTTGCTACAAGTTTCCCAAGGAAGACATACAATTATAATCTGTTTTAACCAAAACAT
ACAAAAAATTCAACTTAAAATCAATTATGAC
Found at i:12555 original size:171 final size:169
Alignment explanation
Indices: 12346--12994 Score: 633
Period size: 171 Copynumber: 3.8 Consensus size: 169
12336 TCGAGGTAAA
* * * * * * * *
12346 CATTCAATTATAAT-TTTTTTGACCAAAAATTTTAAAAAAACT-ATATTTAAAATCAATTTTTAG
1 CATTCAATTATAATCTGTTTT-AACAAAAAATGTAAAAAAATTCA-ACTTAAAATCAATTATGAG
* * * * * * *
12409 ATTATAAAACTATTTAAAGCGAGTAATAAAGTTTTTTAAGGAATGGGAGGCTATAAAAAGACTTC
64 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGAGACTATAAATAGACTTT
* * * **
12474 TC-TCCAAATGAATGGCTTTTTTCTAAATGTTTCTTGCGGTAGG
129 TCTTCCAAATGAATGG-ATTTCTCTAAA-GTTTCCTAAGG-AGG
* * *
12517 CATTCAATTATAGTCTATTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGAT
1 CATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * * * * * * *
12582 TATAAAA-GATTCAAAGCGTGTAATAAGGCTTTTGAAGGAATAGGAGACCACAAATGGACTTTTC
66 TATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGAGACTATAAATAGACTTTTC
* * *
12646 TTCCCAATTAATGGATTTCTCTACAAGTTTCCCAAGAGAGG
131 TTCCAAATGAATGGATTTCTCTA-AAGTTTCCTAAG-GAGG
* * * * * *
12687 CATTCAATTATAATCTGTTATAACTAAAAATAGAAAAAAAATTGAACTT-AAATCAATTTTGACA
1 CATTCAATTATAATCTGTTTTAACAAAAAAT-GTAAAAAAATTCAACTTAAAATCAATTATGAGA
* * * * *
12751 TAATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGAAGACTATAGATGGACTTTT
65 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGAGACTATAAATAGACTTTT
* *
12816 CTTCCAAATGAATGGGTTTCTCTACACGTTTCCTAAGGAAGG
130 CTTCCAAATGAATGGATTTCTCTA-AAGTTTCCTAAGG-AGG
* * * * * ** *
12858 AATTAAATTATAGTCTGTTTTGAGAAAAAATACAAAAAAATTCAACTTAAAATCAATTACGAGAT
1 CATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * * *
12923 TACAAAACCATTTAAAACGAGTAATAAGGTTTTTAAAGGAATGGGTGACTATAAATAGACTTTTC
66 TATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGAGACTATAAATAGACTTTTC
12988 TTACCAA
131 TT-CCAA
12995 TAAATGCCTT
Statistics
Matches: 391, Mismatches: 77, Indels: 19
0.80 0.16 0.04
Matches are distributed among these distances:
170 121 0.31
171 260 0.66
172 10 0.03
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (169 bp):
CATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
TATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGAGACTATAAATAGACTTTTC
TTCCAAATGAATGGATTTCTCTAAAGTTTCCTAAGGAGG
Found at i:13253 original size:277 final size:275
Alignment explanation
Indices: 12741--13284 Score: 668
Period size: 277 Copynumber: 2.0 Consensus size: 275
12731 AACTTAAATC
* * * *
12741 AATTTTGACATAATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGAAGACTATAG
1 AATTTTGACATAATAAAACCACTTAAAGTGAGTAATAAGACTTTTAAAGGAATGGAAGACTACAA
* *
12806 ATGGACTTTTCTTCCAAATGAATGGGTTTCTCTACACGTTTCCTAAGGAAGGAATTAAATTATAG
66 ATGGAATTTTCTTCCAAATGAATGAGTTTCTCTACACGTTTCCTAAGGAAGGAATTAAATTATAG
* *
12871 TCTGTTTTGAGAAAAAATACAAAAAAATTCAACTTAAAATCAATTACGAGATTACAAAACCATTT
131 TCTGTTTTGAGAAAAAATA-AAAAAAATTCAACTTAAAATCAATTACGAAATTACAAAACCATTC
* *
12936 AAAACGAGTAATAAGGTTTTTAAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATAAATG
195 AAAACGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATAGACATTTCTTACCAATAAATG
13001 CCTTTTTCTTCACGTT
260 CCTTTTTCTTCACGTT
* * * **
13017 AATTTTGAGATTATAAAACCACTTAAAGTGAGTAATAAGACTTTTTAAGGAATGGGTGACTACAA
1 AATTTTGACATAATAAAACCACTTAAAGTGAGTAATAAGACTTTTAAAGGAATGGAAGACTACAA
* * * * * * *
13082 ATGGAATTTTCTTGCTAATGAATGCAGTTT-TTTTCTACGTTT-CTCGAGGTA-GATATTCAATT
66 ATGGAATTTTCTTCCAAATGAATG-AGTTTCTCTAC-ACGTTTCCT-AAGGAAGGA-ATTAAATT
** *
13144 ATAGTCTGTTTT-AGCCAAAAAAGT-AAAAAAATTCAACTTAAAATCAATTATTAAATTATAAAA
127 ATAGTCTGTTTTGAG--AAAAAA-TAAAAAAAATTCAACTTAAAATCAATTACGAAATTACAAAA
** * * * *
13207 CCATTCAAGGCGAGTAATAAGGCTTTTGAA-GATATGGGTTACTATAAATGGACATTTCTTGCCA
189 CCATTCAAAACGAGTAATAAGGCTTTTAAAGGA-ATGGGTGACTATAAATAGACATTTCTTACCA
* *
13271 ATGAATTCCTTTTT
253 ATAAATGCCTTTTT
13285 ATTTATGTTT
Statistics
Matches: 227, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
276 88 0.39
277 132 0.58
278 6 0.03
279 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (275 bp):
AATTTTGACATAATAAAACCACTTAAAGTGAGTAATAAGACTTTTAAAGGAATGGAAGACTACAA
ATGGAATTTTCTTCCAAATGAATGAGTTTCTCTACACGTTTCCTAAGGAAGGAATTAAATTATAG
TCTGTTTTGAGAAAAAATAAAAAAAATTCAACTTAAAATCAATTACGAAATTACAAAACCATTCA
AAACGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATAGACATTTCTTACCAATAAATGC
CTTTTTCTTCACGTT
Found at i:13376 original size:171 final size:171
Alignment explanation
Indices: 13017--13483 Score: 439
Period size: 171 Copynumber: 2.7 Consensus size: 171
13007 TCTTCACGTT
* * * *
13017 AATTTTGAGATTATAAAACCACTTAAAGTGAGTAATAAGACTTTTTAAGGA-ATGGGTGACTACA
1 AATTTTAAGATTATAAAACCA-TTAAAGCGAGTAATAAGACTTTTGAA-GATATGGGTGACTATA
* * * * * **
13081 AATGGA-ATTTTCTTGCTAATGAATGCAGTTTTTTTCTACGTTTCTCGAGGTAGATATTCAATTA
64 AATGGACA-TTTCTTGCCAATGAATGCACTTTTTTTCTACGTTTCTCGAGGTAAACAATCAACAA
* * * * *
13145 TAGTCTGTTTTAGCCAAAAAAGTAAAAAAATTCAACTTAAAATC
128 CAATATGTTTTACCCAAAAAAGTAAAAAAATACAACTTAAAATC
* * *
13189 AATTATTAA-ATTATAAAACCATTCAAGGCGAGTAATAAGGCTTTTGAAGATATGGGTTACTATA
1 AATT-TTAAGATTATAAAACCATT-AAAGCGAGTAATAAGACTTTTGAAGATATGGGTGACTATA
* * *
13253 AATGGACATTTCTTGCCAATGAATTC-CTTTTTATT-TATGTTTCTTGAGGTAAACAATCAACAA
64 AATGGACATTTCTTGCCAATGAATGCACTTTTT-TTCTACGTTTCTCGAGGTAAACAATCAACAA
*
13316 CAATATGTTTTACCCAAAAATA-TAAAAAAATACAACTTAACATC
128 CAATATGTTTTACCCAAAAA-AGTAAAAAAATACAACTTAAAATC
* * * * * * * **
13360 AATTTTAAGGTTATAAAACTATTTAAAACAAGGAATAAGCCTTTTGAAGGTATGGGTGACGGTAA
1 AATTTTAAGATTATAAAACCA-TTAAAGCGAGTAATAAGACTTTTGAAGATATGGGTGACTATAA
* * * * * *
13425 ATGGAC-TTTGCTTGTCAATAAATAC-CATTTTCTTCT-CGTTTCTCGAGGTATACATTCAA
65 ATGGACATTT-CTTGCCAATGAATGCAC-TTTTTTTCTACGTTTCTCGAGGTAAACAATCAA
13484 TTATAATCTG
Statistics
Matches: 242, Mismatches: 42, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
170 7 0.03
171 152 0.63
172 79 0.33
173 4 0.02
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (171 bp):
AATTTTAAGATTATAAAACCATTAAAGCGAGTAATAAGACTTTTGAAGATATGGGTGACTATAAA
TGGACATTTCTTGCCAATGAATGCACTTTTTTTCTACGTTTCTCGAGGTAAACAATCAACAACAA
TATGTTTTACCCAAAAAAGTAAAAAAATACAACTTAAAATC
Done.