Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398671.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1957.0, 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: 8479
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.31
Warning! 1508 characters in sequence are not A, C, G, or T
Found at i:1334 original size:171 final size:171
Alignment explanation
Indices: 982--1341 Score: 425
Period size: 171 Copynumber: 2.1 Consensus size: 171
972 NNNNTCTCAT
982 AATTCATTTTAAGTTGAA-TTTTTTACATTTCTGATTAAAATAGATAATAATTGAATGTTTACCT
1 AATTCATTTTAAGTTGAATTTTTTTACATTTCTGATTAAAATAGATAATAATTGAATGTTTACCT
* *
1046 TGTGAAACGTGAGAAAAAAGGCATTGATGTGTAAGAAAAGTTCATTTATAGTTACCCATTCCTTT
66 TGTGAAACGTGAGAAAAAAGGCATTCATGTGTAAGAAAAGTTCATTTATAGTCACCCATTCCTTT
* *****
1111 AAAAGCTTTATTACTCGCTTTAAATTGTTTTATAATNNNNN
131 AAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATACTAA
***** * * * *
1152 NNNNNATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAATAGATAATAATTTATTGTTTACCT
1 AATTCATTTTAAGTTGAATTTTTTTACATTTCTGATTAAAATAGATAATAATTGAATGTTTACCT
* * * *******
1217 TGTGAAACGTGAGGAAAAAGGTATTCATGTGTAAGAAAAGTTTATTTATAGTCACCCANNNNNNN
66 TGTGAAACGTGAGAAAAAAGGCATTCATGTGTAAGAAAAGTTCATTTATAGTCACCCATTCCTTT
*** *
1282 NNNAGCCTTATTACTCGCTTTAAATTGTTTTCTAATACTAA
131 AAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATACTAA
*
1323 AATTTATTTTAAGTTGAAT
1 AATTCATTTTAAGTTGAAT
1342 NNNNNNNNNN
Statistics
Matches: 153, Mismatches: 36, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
170 13 0.08
171 140 0.92
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.40
Consensus pattern (171 bp):
AATTCATTTTAAGTTGAATTTTTTTACATTTCTGATTAAAATAGATAATAATTGAATGTTTACCT
TGTGAAACGTGAGAAAAAAGGCATTCATGTGTAAGAAAAGTTCATTTATAGTCACCCATTCCTTT
AAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATACTAA
Found at i:1611 original size:170 final size:168
Alignment explanation
Indices: 1358--1818 Score: 494
Period size: 170 Copynumber: 2.7 Consensus size: 168
1348 NNNNTTATTG
* *
1358 TTAAAAAGACTATAATCAAATGCTTGCCTCGAGAAACGTGTAAAAAAAACCATACATTGAGGAAA
1 TTAAAAAGACTATAAT-AAATGCTTGCCTTGAGAAACGTGTAAAAAAAGCCAT-CATTGA-GAAA
* * *
1423 AAA-TCCATTTATAGTCACCCATTCCTTCAAAAGTCTTATTACTCAGTTTAAATTATTTTATAAT
63 AAAGTCCATTTATAGTCACCCAATCCTTCAAAAGCCTTATTACTCACTTTAAATTATTTTATAAT
* * * *
1487 CTAATAATTAATTTTAAGTTTAATTTTTTTTTA-GTTTTTA
128 CTAATAATTAATTTTAAGCTGAATTGTTTTATATGTTTTTA
* * * * *
1527 TTAAAACAGACTATAACTGAATGCTTGCCTTGAGAAACATATACAAAAAGCTACTCATTGAGAAA
1 TTAAAA-AGACTATAA-TAAATGCTTGCCTTGAGAAACGTGTAAAAAAAGCCA-TCATTGAGAAA
********** *
1592 AAAGTCCATTTATAGTCACCCNNNNNNNNNNAAGCCTTATTACTCATTTTAAATTATTTTATAAT
63 AAAGTCCATTTATAGTCACCCAATCCTTCAAAAGCCTTATTACTCACTTTAAATTATTTTATAAT
* *
1657 CTTATAATTAATTTTAAGCTGAATTGTTTTATATTTTTTTA
128 CTAATAATTAATTTTAAGCTGAATTGTTTTATATGTTTTTA
* * * * * * *
1698 TTAAAAGAGGCTATAATTAAATACCTACTTTGAGAAACGTGCAAAAAAAGCGATTCATTGAGAAG
1 TTAAAA-AGACTATAA-TAAATGCTTGCCTTGAGAAACGTGTAAAAAAAGCCA-TCATTGAGAA-
* *
1763 TAAAGTCTATTTATAGTCACCCAATCCTTCAAAAGCCTTATTACTCACTTTAAATT
62 AAAAGTCCATTTATAGTCACCCAATCCTTCAAAAGCCTTATTACTCACTTTAAATT
1819 GTTTNNNNNN
Statistics
Matches: 234, Mismatches: 52, Indels: 9
0.79 0.18 0.03
Matches are distributed among these distances:
169 13 0.06
170 120 0.51
171 58 0.25
172 43 0.18
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (168 bp):
TTAAAAAGACTATAATAAATGCTTGCCTTGAGAAACGTGTAAAAAAAGCCATCATTGAGAAAAAA
GTCCATTTATAGTCACCCAATCCTTCAAAAGCCTTATTACTCACTTTAAATTATTTTATAATCTA
ATAATTAATTTTAAGCTGAATTGTTTTATATGTTTTTA
Found at i:4146 original size:171 final size:169
Alignment explanation
Indices: 3862--4179 Score: 431
Period size: 171 Copynumber: 1.9 Consensus size: 169
3852 NNNNNNNNNN
* *
3862 ATGCACAAAAAGCTACTCATTGAGAAAAAAGTCCATTATAGTCACCAATTCCTTCGAAAGCCTTA
1 ATGCAAAAAAAGCTACTCATTGAGAAAAAAGTCCATTATAGTCACCAAGTCCTTCGAAAGCCTTA
** *
3927 TTACTCGCTTGAAATTATTTTATAATTTCATAATTGATTTTAAGTTGAATTGGTTTACATTTTTT
66 TTACTCGCTTGAAATTATTTTATAATCGCATAATTAATTTTAAGTTGAATTGGTTTACATTTTTT
*
3992 GCTAAAAAAGACTATAAGTGAATGCTTACCTTGAAAAAT
131 CCTAAAAAAGACTATAAGTGAATGCTTACCTTGAAAAAT
* ** * *
4031 ATGCAAAAAAAGCTATTCATTGAGAAGAATTGTCCATTTCTAGTCACCTAGTCCTTC-AGAAGCC
1 ATGCAAAAAAAGCTACTCATTGAGAA-AAAAGTCCA-TTATAGTCACCAAGTCCTTCGA-AAGCC
* ** * * ** *
4095 TTATTACTTGCTTTCAATTGTTTTATAATCGCATAATTAATTTTGAGTTGAATTTTTTTACCTTT
63 TTATTACTCGCTTGAAATTATTTTATAATCGCATAATTAATTTTAAGTTGAATTGGTTTACATTT
4160 TTTCCTAAAAAAGACTATAA
128 TTTCCTAAAAAAGACTATAA
4180 TCGAATGTCT
Statistics
Matches: 127, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
169 24 0.19
170 8 0.06
171 95 0.75
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (169 bp):
ATGCAAAAAAAGCTACTCATTGAGAAAAAAGTCCATTATAGTCACCAAGTCCTTCGAAAGCCTTA
TTACTCGCTTGAAATTATTTTATAATCGCATAATTAATTTTAAGTTGAATTGGTTTACATTTTTT
CCTAAAAAAGACTATAAGTGAATGCTTACCTTGAAAAAT
Found at i:4212 original size:171 final size:170
Alignment explanation
Indices: 3533--4691 Score: 805
Period size: 172 Copynumber: 6.8 Consensus size: 170
3523 NNNNNNAGAC
* * * * * * * **
3533 ATTCATT-AGCAAGAAAAATCTATTTATAGTCACCCATTCCTTTAATAGACATATTACTCACTTT
1 ATTCATTGAG-AAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTTGCTTT
* * * * * * * *
3597 AAATTATTTTATAATCCCAAAATTGATTTTAAGTTAAATTTTTTTGCATTTATTGTTAAAACAGA
65 AAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGCTAAAAAAGA
* * * * **
3662 CTATAATTGAATGCCTGCCTTCAGATATGTGTAAAAAAA-CAT
130 CTATAATTGAATGTCTACCTTAAGAAACATG-AAAAAAAGC-T
* * * * *****
3704 CATTCATTGAGAAAAAAAGTTCATTTATAGTC-GCTCATTTCTTCAAAAGCCTTATTACTNNNNN
1 -ATTCATTGAGAAGAAAAGTCCATTTATAGTCACCT-ATTCCTTCAAAAGCCTTATTACTTGCTT
***** * ** *
3768 NNNNNTGTTTTATAATATCATAATTGATTTTAAGTTGAATTTCTTTT-CATTTTTTATTAAAACA
64 TAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTT-TTTTACATTTTTTGCTAAAAAA
* * ********** *
3832 GACTATAATTGAATGCCTGCNNNNNNNNNNATGCACAAAAAGCT
128 GACTATAATTGAATGTCTACCTTAAGAAACATG-AAAAAAAGCT
* * * * *
3876 ACTCATTGAGAA-AAAAGTCCA-TTATAGTCACCAATTCCTTCGAAAGCCTTATTACTCGCTTGA
1 ATTCATTGAGAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTTGCTTTA
* * **
3939 AATTATTTTATAATTTCATAATTGATTTTAAGTTGAATTGGTTTACATTTTTTGCTAAAAAAGAC
66 AATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGCTAAAAAAGAC
* *
4004 TATAAGTGAATG-CTTACCTTGAA-AAATATGCAAAAAAAGCT
131 TATAATTGAATGTC-TACCTT-AAGAAACATG-AAAAAAAGCT
** * * * *
4045 ATTCATTGAGAAGAATTGTCCATTTCTAGTCACCTAGTCCTTCAGAAGCCTTATTACTTGCTTTC
1 ATTCATTGAGAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTTGCTTTA
* * * * *
4110 AATTGTTTTATAATCGCATAATTAATTTTGAGTTGAATTTTTTTACCTTTTTTCCTAAAAAAGAC
66 AATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGCTAAAAAAGAC
* * * **
4175 TATAATCGAATGTCTACCTCAAGAAACGTGAAAAAAAAAAT
131 TATAATTGAATGTCTACCTTAAGAAACATG-AAAAAAAGCT
* * **********
4216 CATTCATTGACAATAAAAGTCCATTTATAGTCACCTATTCCTTNNNNNNNNNNATTACTTGCTTT
1 -ATTCATTGAGAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTTGCTTT
* * * * * * * * * * *
4281 AAATTATTTTATAATCCCAAAATTGATTTTAAATTAAATATTTTTAAAATTTTGGTTAAAATAGA
65 AAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGCTAAAAAAGA
* * * *
4346 CTATAATTGAACGTCTACCTTGAGAAACGTGTAAAAAAATCT
130 CTATAATTGAATGTCTACCTTAAGAAACATG-AAAAAAAGCT
******** *
4388 ATTCATTGAGAAGAAAAGTCCATNNNNNNNNNNA-C-ATTCCTTCAAAAGCCTTATTGCTTGCTT
1 ATTCATTGAGAAGAAAAGTCCAT--TTATAGTCACCTATTCCTTCAAAAGCCTTATTACTTGCTT
* * * * * * *
4451 TAAATGGTTTTATAAACTCATAATAGATTTTGAGTTGAATTTTTTTACATTTTTAGTTAAAACAG
64 TAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGCTAAAAAAG
* * * *
4516 ACAATAATTGATTGTTTACCTTAAGAAACATGTAAAAAAGAC-
129 ACTATAATTGAATGTCTACCTTAAGAAACATGAAAAAAAG-CT
* * * *
4558 ATTCATT-AGTAAGAAAAGTCTATTTATAGTCATCTATTCCTTTAAAAGCCTTATTACTCGCTTT
1 ATTCATTGAG-AAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTTGCTTT
* * * * * * * *
4622 GAATTGTTTTATAATC-CAAAAATTGATTTTAAGTTAAATGTTTTTACATTTATAGTTAAAACAG
65 AAATTGTTTTATAATCTC-ATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGCTAAAAAAG
4686 ACTATA
129 ACTATA
4692 NNNNNNNNNN
Statistics
Matches: 759, Mismatches: 208, Indels: 42
0.75 0.21 0.04
Matches are distributed among these distances:
168 5 0.01
169 121 0.16
170 127 0.17
171 246 0.32
172 252 0.33
173 8 0.01
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.38
Consensus pattern (170 bp):
ATTCATTGAGAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTTGCTTTA
AATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGCTAAAAAAGAC
TATAATTGAATGTCTACCTTAAGAAACATGAAAAAAAGCT
Found at i:4384 original size:343 final size:330
Alignment explanation
Indices: 3922--4599 Score: 655
Period size: 343 Copynumber: 2.0 Consensus size: 330
3912 CCTTCGAAAG
** * * * * *
3922 CCTTATTACTCGCTTGAAATTATTTTATAATTTCATAATTGATTTTAAGTTGAATTGGTTTACAT
1 CCTTATTACTCGCTTGAAATTATTTTATAATCCCAAAATTGATTTTAAATTAAATTGGTTTAAAA
* * *
3987 TTTTTGCTAAAAAAGACTATAAGTGAATGCTTACCTTGAAAAATATGCAAAAAAAGCTATTCATT
66 TTTTGGCTAAAAAAGACTATAAGTGAACGCTTACCTTGAAAAACATGCAAAAAAAGCTATTCATT
** * * *
4052 GAGAAGAATTGTCCAT-TTCTAGTCACCTAGTCCTTCAGAAGCCTTATTACTTGCTTTCAATTGT
131 GAGAAGAAAAGTCCATATTCTAGTCA-C-AGTCCTTCAAAAGCCTTATTACTTGCTTTAAATGGT
* * * *
4116 TTTATAATCGCATAATTA-ATTTTGAGTTGAATTTTTTTACCTTTTTTCCTAAAAAAGACTATAA
194 TTTATAAACGCATAA-TAGATTTTGAGTTGAATTTTTTTACATTTTTACCTAAAAAAGACAATAA
* *
4180 TCGAATGTCTACCTCAAGAAACGTGAAAAAAAAAATCATTCATT-GACAATAAAAGTCCATTTAT
258 TCGAATGTCTACCTCAAGAAACATG-AAAAAAAAA-CATTCATTAG-CAAGAAAAGTCCATTTAT
4244 AGTCACCTATT
320 AGTCACCTATT
* *
4255 CCTTNNNNNNNNNNATTACTTGCTTTAAATTATTTTATAATCCCAAAATTGATTTTAAATTAAAT
1 CCTT----------ATTACTCGCTTGAAATTATTTTATAATCCCAAAATTGATTTTAAATTAAAT
* * * * * * *
4320 AT-TTTTAAAATTTTGGTTAAAATAGACTATAATTGAACG-TCTACCTTGAGAAACGTGTAAAAA
56 -TGGTTTAAAATTTTGGCTAAAAAAGACTATAAGTGAACGCT-TACCTTGAAAAACATGCAAAAA
* ********* * *
4383 AATCTATTCATTGAGAAGAAAAGTCCATNNNNNNNNNNACATTCCTTCAAAAGCCTTATTGCTTG
119 AAGCTATTCATTGAGAAGAAAAGTCCAT-ATTCTAGTCACAGTCCTTCAAAAGCCTTATTACTTG
* **
4448 CTTTAAATGGTTTTATAAACTCATAATAGATTTTGAGTTGAATTTTTTTACATTTTTAGTTAAAA
183 CTTTAAATGGTTTTATAAACGCATAATAGATTTTGAGTTGAATTTTTTTACATTTTTACCTAAAA
* * * * * * * *
4513 CAGACAATAATTGATTGTTTACCTTAAGAAACATGTAAAAAAGACATTCATTAGTAAGAAAAGTC
248 AAGACAATAATCGAATGTCTACCTCAAGAAACATGAAAAAAAAACATTCATTAGCAAGAAAAGTC
* *
4578 TATTTATAGTCATCTATT
313 CATTTATAGTCACCTATT
4596 CCTT
1 CCTT
4600 TAAAAGCCTT
Statistics
Matches: 275, Mismatches: 54, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
333 4 0.01
341 37 0.13
342 11 0.04
343 220 0.80
344 2 0.01
345 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.38
Consensus pattern (330 bp):
CCTTATTACTCGCTTGAAATTATTTTATAATCCCAAAATTGATTTTAAATTAAATTGGTTTAAAA
TTTTGGCTAAAAAAGACTATAAGTGAACGCTTACCTTGAAAAACATGCAAAAAAAGCTATTCATT
GAGAAGAAAAGTCCATATTCTAGTCACAGTCCTTCAAAAGCCTTATTACTTGCTTTAAATGGTTT
TATAAACGCATAATAGATTTTGAGTTGAATTTTTTTACATTTTTACCTAAAAAAGACAATAATCG
AATGTCTACCTCAAGAAACATGAAAAAAAAACATTCATTAGCAAGAAAAGTCCATTTATAGTCAC
CTATT
Found at i:6333 original size:171 final size:161
Alignment explanation
Indices: 6134--6466 Score: 292
Period size: 171 Copynumber: 2.0 Consensus size: 161
6124 AAAGCGAGTA
* ** * * ***
6134 ATAAGGCTTTTGAAGAAATAGATGACTATAAATGGATTTTTCTTGCCAACAAATGTGTTTTTCTT
1 ATAAGGATTTTGAAGAAATAGATGACTATAAAAAGACTTTTCCTGCCAACAAATACATTTTTCTT
* ********** * *
6199 CACGTTTCTCCAAGTNNNNNNNNNNTTATAGTCTGTTTTA-GCAAAAAGTGTAAAACAATTTAAC
66 CACGTTTCCCCAAGTGCAAATTCAATTATAGTCTGTTTTATGCAAAAA-TGTAAAAAAATTCAAC
* *
6263 TTAAAATCAATTATGAGATTATAAAACATTTT
130 CTAAAATCAATTATAAGATTATAAAACATTTT
* * *
6295 NNNNNNNNNNATAAGGATTTTGAA-AGAATGGGTGACTATAAAAAGACTTTTCCTGCCAACGAAT
1 ----------ATAAGGATTTTGAAGA-AATAGATGACTATAAAAAGACTTTTCCTGCCAACAAAT
*
6359 ACATTTTTCTTCACGTTTCCCCAAGTGCAAATTCAATTATAGTCTGTTTTATTCAAAAATGTAAA
55 ACATTTTTCTTCACGTTTCCCCAAGTGCAAATTCAATTATAGTCTGTTTTATGCAAAAATGTAAA
*
6424 AAAATTCAACCTAAAATCAATTATAAGATTATAAAACAATTT
120 AAAATTCAACCTAAAATCAATTATAAGATTATAAAACATTTT
6466 A
1 A
6467 AAGNNNNNNN
Statistics
Matches: 132, Mismatches: 28, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
161 1 0.01
170 1 0.01
171 124 0.94
172 6 0.05
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.34
Consensus pattern (161 bp):
ATAAGGATTTTGAAGAAATAGATGACTATAAAAAGACTTTTCCTGCCAACAAATACATTTTTCTT
CACGTTTCCCCAAGTGCAAATTCAATTATAGTCTGTTTTATGCAAAAATGTAAAAAAATTCAACC
TAAAATCAATTATAAGATTATAAAACATTTT
Found at i:6516 original size:171 final size:159
Alignment explanation
Indices: 6312--6635 Score: 291
Period size: 170 Copynumber: 2.0 Consensus size: 159
6302 NNNATAAGGA
*
6312 TTTTGAAAGAATGGGTGACTATAAAAAGACTTTTCCTGC-CAACGAATA-CATTTTTCTTCACGT
1 TTTTGAAAGAATGGGTGACTATAAAAAGACTTTT--TGCTCAACGAATAGC-TTTTTCTGCA-GT
* *
6375 TTCCCCAAGTGCAA-ATTCAATTATAGTCTGTTTTATTC-AAAAATGTAAAAA-AATTCAACCTA
62 TTCCCCAAG-GCAACATTCAATTATAGTATGTTTTA-ACAAAAAAT-TAAAAACAATTCAACCTA
6437 AAATCAATTAT-AAGATTATAAAACAATTTAAAGNNNNNNNNNNGGC
124 AAATCAATTATGAA-ATTATAAAACAATTTAAAG----------GGC
* * ** * * * * * *
6483 TTTTGAAGGAATTGGTGACTATAAATGGACTTTTTTCTCAATGAGTAGCTTTTTGTGCATTTTTC
1 TTTTGAAAGAATGGGTGACTATAAAAAGACTTTTTGCTCAACGAATAGCTTTTTCTGCAGTTTCC
* * *
6548 TCAAGGCAAGCATTCAATTATTGTATGTTTTAACAAAAAATTAAAAACAATTCAACTTAAAATCA
66 CCAAGGCAA-CATTCAATTATAGTATGTTTTAACAAAAAATTAAAAACAATTCAACCTAAAATCA
6613 ATTATGAAATTATAAAACAATTT
130 ATTATGAAATTATAAAACAATTT
6636 CAAGTAAGTA
Statistics
Matches: 130, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
168 4 0.03
169 17 0.13
170 76 0.58
171 33 0.25
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.35
Consensus pattern (159 bp):
TTTTGAAAGAATGGGTGACTATAAAAAGACTTTTTGCTCAACGAATAGCTTTTTCTGCAGTTTCC
CCAAGGCAACATTCAATTATAGTATGTTTTAACAAAAAATTAAAAACAATTCAACCTAAAATCAA
TTATGAAATTATAAAACAATTTAAAGGGC
Found at i:7405 original size:21 final size:21
Alignment explanation
Indices: 7379--7428 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
7369 TAAATAGACT
*
7379 TTTCTTCGCAAAGAATGCATG
1 TTTCTTCACAAAGAATGCATG
* *
7400 TTTCTTCACGAAGAATGCGTG
1 TTTCTTCACAAAGAATGCATG
7421 TTTCTTCA
1 TTTCTTCA
7429 TGTTTCTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (21 bp):
TTTCTTCACAAAGAATGCATG
Found at i:8066 original size:170 final size:171
Alignment explanation
Indices: 7681--8066 Score: 438
Period size: 170 Copynumber: 2.3 Consensus size: 171
7671 NCAATTTTAG
* * *
7681 GATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATTCGTGACTATAAATGAACTT
1 GATTATAAAACAATTTAAAACGAGTAATAAGGCTTTTAAAGGAATGCGCGACTATAAATGAACTT
* * * * ** * * * * *
7746 TTCTTGTCAATGAATGCCTTTTTCTTCATGTTTCCTTAGGTAGACATTCACTTTTTGTCTGTTTT
66 TTCTTGCCAACGAATGCCGTTTTCTTCACGTTTCCCGAGGTAGAAATTCAATTATAGTCTGTCTT
*
7811 AACTAAAAATATAAAAAAATTAAACTTAAAATCAAGTATGA
131 AACCAAAAATATAAAAAAATTAAACTTAAAATCAAGTATGA
* * * * * * *
7852 GGTTATAAAACAATTTATAATGAATAATAAAGCTTTTAAAGGAATGGGCGACTATAAATGGACTT
1 GATTATAAAACAATTTAAAACGAGTAATAAGGCTTTTAAAGGAATGCGCGACTATAAATGAACTT
* ** *
7917 TTTTTGCCAACGAATGTGGTTTT-TTCACGTTTCTCCGA-GTAGAAATTTAATTATAG-CATGTC
66 TTCTTGCCAACGAATGCCGTTTTCTTCACGTTTC-CCGAGGTAGAAATTCAATTATAGTC-TGTC
* * *
7979 TTAGCCAAAAATGTAAAAAAATTCAACTTAAAATTCAA-TATGA
129 TTAACCAAAAATATAAAAAAATTAAACTTAAAA-TCAAGTATGA
* *
8022 GATTATAAAATAATTTAAAACGAGTAATAAGGCTTTTGAAGGAAT
1 GATTATAAAACAATTTAAAACGAGTAATAAGGCTTTTAAAGGAAT
8067 AAGTGATTAT
Statistics
Matches: 176, Mismatches: 36, Indels: 7
0.80 0.16 0.03
Matches are distributed among these distances:
169 1 0.01
170 97 0.55
171 78 0.44
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (171 bp):
GATTATAAAACAATTTAAAACGAGTAATAAGGCTTTTAAAGGAATGCGCGACTATAAATGAACTT
TTCTTGCCAACGAATGCCGTTTTCTTCACGTTTCCCGAGGTAGAAATTCAATTATAGTCTGTCTT
AACCAAAAATATAAAAAAATTAAACTTAAAATCAAGTATGA
Done.