Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402319.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_540.0, 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: 8219
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.31
Warning! 1393 characters in sequence are not A, C, G, or T
Found at i:1127 original size:171 final size:170
Alignment explanation
Indices: 276--1140 Score: 587
Period size: 171 Copynumber: 5.1 Consensus size: 170
266 NNNNNNNNNN
* * * * *
276 AAGTTGAATTTTTTTATATTTTTGGTTAAGACAAACTATAATTGAATGTCTACCATGAGAAATGT
1 AAGTTGAATTTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACGT
* * * * * * * *
341 GAAGAAAAAGGCATTCATTAGTAAGAGAAGTCCGTTTATAGTCAGTCATTCTTTCAAAAGCTTTA
66 GAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTCACT-ATTCCTTCAAAAGCCTTA
* *
406 TTACTCACTTTAAATGGTCTTATAATCTCAGAATTGAATTT
130 TTACTCACTTTAAATGGTCTTATAATCTCAAAATTGATTTT
* * ** * * *
447 AAGTAGAATTCTTTTACATTTTTGGTTAAAACAGACTATAATTTG-ATGTCTACCTCAACAATCA
1 AAGTTGAATTTTTTTACATTTTTGGTTAAAACAGACTATAA-TTGAATGTCTACCTTGAGAAACG
* * * * * * *
511 TAAAGAAAAAGGTATTCATTGGCAAGAGAAG-TCTATTTATGGTCACCCATTGCATCAAAAGCCT
65 TGAAGAAAAAGGCATTCATTGGCAAGAAAAGTTC-ATTTATAGTCA-CTATTCCTTCAAAAGCCT
* **********
575 TATTACTCTCTTTAAATGNNNNNNNNNNCTCAAAATTGATTTT
128 TATTACTCACTTTAAATGGTCTTATAATCTCAAAATTGATTTT
* * * * * * * *
618 AATTTGAATTTTTTGTACATTTTTTGTTAAAACAGATTATAATTGAATGTTTGCATCGAGAAACA
1 AAGTTGAATTTTTT-TACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACG
* * * * *
683 TAAAGAAAAATGCATTCATTGACAAGAAAAGTCCATTTATAGTCA-TGCATTCCTTTAAAAGCCT
65 TGAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTCACT--ATTCCTTCAAAAGCCT
* ********** *
747 TATTACTCTCTTNNNNNNNNNNTATAATCTCATAATTGATTTT
128 TATTACTCACTTTAAATGGTCTTATAATCTCAAAATTGATTTT
* * * * * *
790 AAGTT-CATTTTTTTGCATATTTGGTTAAAAAATACTATAATTGAATGTCTACCTTGGGAAACGT
1 AAGTTGAATTTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACGT
* * ** * ** *
854 GAAGCAAAAA-CCATCCATTGATACGAAAAG-TCTATTTATAGTCACTCAAGCTTTCGAAAA-CC
66 GAAG-AAAAAGGCATTCATTGGCAAGAAAAGTTC-ATTTATAGTCACT-ATTCCTTC-AAAAGCC
* ** * *********
916 TTACTACTTGCTTTCAATNNNNNNNNNNA-CT-AATAATTGATTTT
127 TTATTACTCACTTTAAAT-GGTCTTATAATCTCAA-AATTGATTTT
* * * * * * *
960 AAGTTGAACTTGTTTATATTTTTGGTTAAAACAGATTATAATTGAATGTTTATCTTAAGAAACGT
1 AAGTTGAATTTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACGT
* * * *
1025 GAAGAAAAAGGCATTCATAGGCAAGAAAAGTTCGTTTATAGTCACCTATTCCTTCGAAAGCTTTA
66 GAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTCA-CTATTCCTTCAAAAGCCTTA
* *
1090 TTACTCACTTTCAATGGTTTTATAATCTCAAAATTGATTTT
130 TTACTCACTTTAAATGGTCTTATAATCTCAAAATTGATTTT
*
1131 AATTTGAATT
1 AAGTTGAATT
1141 NNNNNNNNNN
Statistics
Matches: 525, Mismatches: 148, Indels: 42
0.73 0.21 0.06
Matches are distributed among these distances:
169 2 0.00
170 113 0.22
171 278 0.53
172 131 0.25
173 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.37
Consensus pattern (170 bp):
AAGTTGAATTTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACGT
GAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTCACTATTCCTTCAAAAGCCTTAT
TACTCACTTTAAATGGTCTTATAATCTCAAAATTGATTTT
Found at i:1746 original size:171 final size:169
Alignment explanation
Indices: 1293--2830 Score: 1319
Period size: 171 Copynumber: 9.0 Consensus size: 169
1283 GCAGGCTTTG
* * * * *
1293 AATTCTAGTCTGTTTGAA-TGAAAAATGTAAAAAAAATCAACTTAAAATCAGTTACGAG-TTATA
1 AATTATAGTCTGTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
* * *
1356 AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTTCTCA
65 AAACCATTTAAAGCGAGTAATAAGG-TTTTGAAGGAATGAGTGACTATAAATGGAC-TTTTCTTA
* * *
1421 CCAATGAGTCCCTTTTTCTTCATGTTTCTTGAGGTAGACATTC
128 CCAATGAATGCCTTTTTCTTCACGTTTCTT-AGGTAGACATTC
* * * * * * *
1464 AATTATAATCTCTTTTAA-TAAAAACTGTACAAAGAATTCAAATTAAAATTAATTTTGAAATTAT
1 AATTATAGTCTGTTTTAACTAAAAA-TGTA-AAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * *
1528 AAAATCATTGAAAGTGAGTAATAAGGCTTTCGAAGGAAT-AGGTGACTATAAACGGACTTTTCTT
64 AAAACCATTTAAAGCGAGTAATAAGG-TTTTGAAGGAATGA-GTGACTATAAATGGACTTTTCTT
* * * *
1592 GCCTATGAATGCCTTTTTCTTAACGTTTCTTAGGATAAACATTC
127 ACCAATGAATGCCTTTTTCTTCACGTTTCTTAGG-TAGACATTC
* * * *
1636 AATTATAATCTGTTTTAACTAAAAATGTAAAAAAGTTCAACTTAAAATCAATTATTAGTTTATAA
1 AATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * ** *
1701 AACCATTGAAAGCAAGTAGTAAGGTTTTCGAAGGCTTGAGTGACTATAAATGGACTTTT-TGTAT
66 AACCATTTAAAGCGAGTAATAAGGTTTT-GAAGGAATGAGTGACTATAAATGGACTTTTCT-TAC
* * * ** * * *
1765 CAATGGATG-GTTTTTGCTTCATGTTTCCCAAGGAAAACATTT
129 CAATGAATGCCTTTTT-CTTCACGTTT-CTTAGGTAGACATTC
* * * * * * * * *
1807 AATTATTGCCTTTTTTAACCAAATATGCAAAAAAAATAAACTTAATATCAATTATGAGATTATAA
1 AATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
** * *
1872 AACCATTTAAAAAGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCCTACC
66 AACCATTTAAAGCGAGTAATAAGG-TTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTACC
* * * **
1937 AATGAATGCATTTTTCTTTATGTTTCTTGATGCCA-ACATTC
130 AATGAATGCCTTTTTCTTCACGTTTCTT-A-GGTAGACATTC
* * **** *
1978 AATTATAATCTTTTTTAACTAAAAATGTATAAATGGGT-GAC-TATAAAT---TT-TGAGATTAT
1 AATTATAGTCTGTTTTAACTAAAAATGTA-AAAAAATTCAACTTA-AAATCAATTATGAGATTAT
* * * * * * * *
2037 GAAACCATTTAAAGCGAGCAATAAGACTTTCGATGCAATGGGTGACTATAAATGGACTTCTCTTA
64 AAAACCATTTAAAGCGAGTAATAAG-GTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTA
* * * * *
2102 CCAATAAATACCTTTTTCTTTACGTTTGTTGAGTTAGACATTC
128 CCAATGAATGCCTTTTTCTTCACGTTTCTT-AGGTAGACATTC
* * * * * * *
2145 AATTATAGTCTATTTTAACCAAAAATATAAAAGAATTCTACTTAAATTTAATTATGAGATTATAA
1 AATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * ** * * * * *
2210 GACCATTCAAAGTGAGTAATAAAACTTTTGAAAGAATGACTGACTATAAATGGACTTCTCTTGCT
66 AACCATTTAAAGCGAGTAAT-AAGGTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTACC
* * *
2275 AATGAATGCTTTTTTCTTCACATTTCTCACGGTAGACATTC
130 AATGAATGCCTTTTTCTTCACGTTTCTTA-GGTAGACATTC
* * * * * *
2316 AATTATAGTTTGTCTTAACCAAAAATATAAAAAAATTCAACTTAAATTTAATTATGAGATTATAA
1 AATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * * * * * * *
2381 GACCATTTAAAGTGAGTAACAAAGCTTTTGAAAGAATGACTGACTATAAATGGACTTCTCTTGCT
66 AACCATTTAAAGCGAGTAA-TAAGGTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTACC
* * *
2446 AATGAATGCTTTTTTCTTCACATTTCTCACGGTAGACATTC
130 AATGAATGCCTTTTTCTTCACGTTTCTTA-GGTAGACATTC
* * * * * *
2487 AATTATAGTTTGTCTTAAC-CAAAATATAAAAAAATTCAACTTAAAATCAATTATTAGTTTATAA
1 AATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * *
2551 AACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTT-TTTCT
66 AACCATTTAAAGCGAGTAATAAGG-TTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTAC-
* * * * * * *
2615 CAATGAATGGCTTTTTCTACAAGTTTCTCAAGGCAGGCATTT
129 CAATGAATGCCTTTTTCTTCACGTTTCT-TAGGTAGACATTC
** * * *
2657 AATTATAGTCTGTTTTAA-TGAAAAATGTAAAAACCTTCAGCTTAAAATCAGTTACGAGATTATA
1 AATTATAGTCTGTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
* ** * *
2721 AAACTATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTGA-TCATAAATGAACTTTTTCTT
65 AAACCATTTAAAGCGAGTAATAAGG-TTTTGAAGGAATGAGTGACT-ATAAATGGAC-TTTTCTT
* * *
2785 GCCAATGAATACCTTTTTCTTCATGTTTCTTGAGGTAGACATTC
127 ACCAATGAATGCCTTTTTCTTCACGTTTCTT-AGGTAGACATTC
2829 AA
1 AA
2831 NNNNNNNNNN
Statistics
Matches: 1120, Mismatches: 209, Indels: 75
0.80 0.15 0.05
Matches are distributed among these distances:
166 6 0.01
167 124 0.11
168 4 0.00
169 6 0.01
170 153 0.14
171 623 0.56
172 142 0.13
173 62 0.06
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (169 bp):
AATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
AACCATTTAAAGCGAGTAATAAGGTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTACCA
ATGAATGCCTTTTTCTTCACGTTTCTTAGGTAGACATTC
Found at i:2106 original size:167 final size:167
Alignment explanation
Indices: 1856--2170 Score: 407
Period size: 167 Copynumber: 1.9 Consensus size: 167
1846 ACTTAATATC
* * * *
1856 AATTATGAGATTATAAAACCATTTAAAAAGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAA
1 AATTATGAGATTATAAAACCATTTAAAAAGAGCAATAAGACTTTCAAAGCAATGAGTGACTATAA
* * * *
1921 ATGGACTTTTCCTACCAATGAATGCATTTTTCTTTATGTTTCTTGATGCCA-ACATTCAATTATA
66 ATGGACTTCTCCTACCAATAAATACATTTTTCTTTACGTTTCTTGA-GCCAGACATTCAATTATA
* *
1985 ATCTTTTTTAACTAAAAATGTATAAATGGGTGACTATA
130 ATCTATTTTAACCAAAAATGTATAAATGGGTGACTATA
* * ** * * *
2023 AATTTTGAGATTATGAAACCATTTAAAGCGAGCAATAAGACTTTCGATGCAATGGGTGACTATAA
1 AATTATGAGATTATAAAACCATTTAAAAAGAGCAATAAGACTTTCAAAGCAATGAGTGACTATAA
* * * ** *
2088 ATGGACTTCTCTTACCAATAAATACCTTTTTCTTTACGTTTGTTGAGTTAGACATTCAATTATAG
66 ATGGACTTCTCCTACCAATAAATACATTTTTCTTTACGTTTCTTGAGCCAGACATTCAATTATAA
2153 TCTATTTTAACCAAAAAT
131 TCTATTTTAACCAAAAAT
2171 ATAAAAGAAT
Statistics
Matches: 124, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
166 2 0.02
167 122 0.98
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (167 bp):
AATTATGAGATTATAAAACCATTTAAAAAGAGCAATAAGACTTTCAAAGCAATGAGTGACTATAA
ATGGACTTCTCCTACCAATAAATACATTTTTCTTTACGTTTCTTGAGCCAGACATTCAATTATAA
TCTATTTTAACCAAAAATGTATAAATGGGTGACTATA
Found at i:2487 original size:509 final size:510
Alignment explanation
Indices: 1313--2493 Score: 1258
Period size: 509 Copynumber: 2.3 Consensus size: 510
1303 TGTTTGAATG
* * * *
1313 AAAAATGTAAAAAAAATCAACTTAAAATCAGTTACGAG-TTATAAAACCATTTAAAGCGAGTAAT
1 AAAAATGTAAAAAAAATCAACTTAAATTCAATTATGAGATTATAAAACCATTTAAAGAGAGTAAT
* * * * * * *
1377 AAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTTCTCACCAATGAGTCCCTTTTTCTTC
66 AAGGCTTTTGAAAGAATGAGTGACTATAAATGGAC-TTTTCTTACCAATGAATGCATTTTTCTTC
* *
1442 ATGTTTCTTGAGGTAGACATTCAATTATAATCTCTTTTAATAAAAACTGTACAAAGAATTCAAAT
130 ATGTTTCTTGAGGTAGACATTCAATTATAATCTCTTTTAATAAAAACTGTACAAAGAAGT-AAAC
* * * * * *
1507 TAAAATTAATTTTGAAATTATAAAATCATTGAAAGTGAGTAATAAGGCTTTCGAAGGAATAGGTG
194 T--AATAAATTTTGAAATTATAAAACCATTGAAAGCGAGCAATAAGACTTTCGAAGCAATAGGTG
* * * * *
1572 ACTATAAACGGACTTTTCTTGCCTATGAATGCCTTTTTCTTAACGTTTCTTAGGATAAACATTCA
257 ACTATAAACGGACTTCTCTTACCAATAAATACCTTTTTCTTAACGTTTCTTAGGATAAACATTCA
* * * * *
1637 ATTATAATCTGTTTTAACTAAAAATGTAAAAAAGTTCAACTTAAAATCAATTATTAGTTTATAAA
322 ATTATAATCTATTTTAACCAAAAATATAAAAAAGTTCAACTTAAAATCAATTATGAGATTATAAA
* * ** * ** *
1702 ACCATTGAAAGCAAGTAGTAAGGTTTTCGAAGGCTTGAGTGACTATAAATGGACTTTTTGTATCA
387 ACCATTCAAAGCAAGTAATAAACTTTTCGAAAGAATGACTGACTATAAATGGACTTTTTGTATCA
* * ** * *
1767 ATGGATGGTTTTTGCTTCATGTTTCCCAAGGAAAACATTTAATTATTGCCTTTTTTAACC
452 ATGAATGCTTTTTGCTTCACATTTCCCAAGGAAAACATTCAATTATAG-CTTTTTTAACC
* * * *
1827 AAATATGCAAAAAAAATAAACTT-AATATCAATTATGAGATTATAAAACCATTTAAAAAGAGTAA
1 AAAAATGTAAAAAAAATCAACTTAAAT-TCAATTATGAGATTATAAAACCATTTAAAGAGAGTAA
*
1891 TAAGGCTTTT-AAAGGAATGAGTGACTATAAATGGACTTTTCCTACCAATGAATGCATTTTTCTT
65 TAAGGCTTTTGAAA-GAATGAGTGACTATAAATGGACTTTTCTTACCAATGAATGCATTTTTCTT
* ** * * *
1955 TATGTTTCTTGATGCCA-ACATTCAATTATAATCTTTTTTAACTAAAAA-TGTATAAATG-GGT-
129 CATGTTTCTTGA-GGTAGACATTCAATTATAATCTCTTTTAA-TAAAAACTGTACAAA-GAAGTA
* * * * * *
2016 GACT-ATAAATTTTGAGATTATGAAACCATTTAAAGCGAGCAATAAGACTTTCGATGCAATGGGT
191 AACTAATAAATTTTGAAATTATAAAACCATTGAAAGCGAGCAATAAGACTTTCGAAGCAATAGGT
* * * * *
2080 GACTATAAATGGACTTCTCTTACCAATAAATACCTTTTTCTTTACGTTTGTT-GAGTTAGACATT
256 GACTATAAACGGACTTCTCTTACCAATAAATACCTTTTTCTTAACGTTTCTTAG-GATAAACATT
* * * *
2144 CAATTATAGTCTATTTTAACCAAAAATATAAAAGAA-TTCTACTTAAATTTAATTATGAGATTAT
320 CAATTATAATCTATTTTAACCAAAAATATAAAA-AAGTTCAACTTAAAATCAATTATGAGATTAT
* **
2208 AAGACCATTCAAAGTGAGTAATAAAACTTTT-GAAAGAATGACTGACTATAAATGGACTTCTCTT
384 AAAACCATTCAAAGCAAGTAAT-AAACTTTTCGAAAGAATGACTGACTATAAATGGACTT-T-TT
* * * * * *
2272 G-CT-AATGAATGCTTTTTTCTTCACATTTCTCACGGTAGACATTCAATTATAG-TTTGTCTTAA
446 GTATCAATGAATGCTTTTTGCTTCACATTTCCCAAGGAAAACATTCAATTATAGCTTT-T-TTAA
2334 CC
509 CC
* * * * * *
2336 AAAAATATAAAAAAATTCAACTTAAATTTAATTATGAGATTATAAGACCATTTAAAGTGAGTAAC
1 AAAAATGTAAAAAAAATCAACTTAAATTCAATTATGAGATTATAAAACCATTTAAAGAGAGTAAT
* * * * * *
2401 AAAGCTTTTGAAAGAATGACTGACTATAAATGGACTTCTCTTGCTAATGAATGCTTTTTTCTTCA
66 AAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTACCAATGAATGCATTTTTCTTCA
** *
2466 CATTTC-TCACGGTAGACATTCAATTATA
131 TGTTTCTTGA-GGTAGACATTCAATTATA
2494 GTTTGTCTTA
Statistics
Matches: 549, Mismatches: 102, Indels: 37
0.80 0.15 0.05
Matches are distributed among these distances:
507 3 0.01
508 6 0.01
509 359 0.65
510 16 0.03
511 3 0.01
512 2 0.00
513 2 0.00
514 96 0.17
515 62 0.11
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (510 bp):
AAAAATGTAAAAAAAATCAACTTAAATTCAATTATGAGATTATAAAACCATTTAAAGAGAGTAAT
AAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTACCAATGAATGCATTTTTCTTCA
TGTTTCTTGAGGTAGACATTCAATTATAATCTCTTTTAATAAAAACTGTACAAAGAAGTAAACTA
ATAAATTTTGAAATTATAAAACCATTGAAAGCGAGCAATAAGACTTTCGAAGCAATAGGTGACTA
TAAACGGACTTCTCTTACCAATAAATACCTTTTTCTTAACGTTTCTTAGGATAAACATTCAATTA
TAATCTATTTTAACCAAAAATATAAAAAAGTTCAACTTAAAATCAATTATGAGATTATAAAACCA
TTCAAAGCAAGTAATAAACTTTTCGAAAGAATGACTGACTATAAATGGACTTTTTGTATCAATGA
ATGCTTTTTGCTTCACATTTCCCAAGGAAAACATTCAATTATAGCTTTTTTAACC
Found at i:5669 original size:171 final size:169
Alignment explanation
Indices: 5312--6462 Score: 1112
Period size: 171 Copynumber: 6.7 Consensus size: 169
5302 NNNNNNNNAG
* * * * *
5312 CCTTATTACTCGCTTTAAATGGTTTTATAA-CTCGTAACTGATTTTAAGTTGACTTTTCTTACAT
1 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACAT
** * * * * * *
5376 TTTTCATTAAAACAGACTATAATTCAATGCCTGCCTTGAGAAACTTG-AGAACAAGCCATTCATT
66 TTTTGGTTAAAACAGATTATAATTGAATGTC-G-CTTGAGAAACATGAAGAAAAACCCATTCATT
* *
5440 GAG-AAGAAAAGTCCATTTATAGTCCCCCATTCTTTCAAAAA
129 G-GCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAA
* * * *
5481 CGTTATTACTAGCTTTAAATGGTTTTATAAACTAATAATTGATTTTAAGTTAAATTTTTTTACAT
1 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACAT
* ** * * * * **
5546 TTTTGGTTAAAACAGACTATAATTGAATGTCGATCTCAATAAACGTAAACAAAAAGGCATTCATT
66 TTTTGGTTAAAACAGATTATAATTGAATGTCG--CTTGAGAAACATGAAGAAAAACCCATTCATT
* * * *
5611 GGCAAGAGAAGTCCATTTATAGTCACCCATTACATCAAAAT
129 GGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAA
* * * * *
5652 CCTTATTACTCGCTTTAAATGGTTTCATAATCTCAAAATTGATTTTAATTTGAATTCTTTGTACA
1 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATT-TTTTTACA
* * * ** * **
5717 GTTTTGGTTAAAATAGATTATAATTGAATGTCTACATAAAAAAACATGAAGAAAAATGCATTCAT
65 TTTTTGGTTAAAACAGATTATAATTGAATGTC-GC-TTGAGAAACATGAAGAAAAACCCATTCAT
* * * *
5782 TGGCAAGAAAAGTCCATTTATAGTCGCACATTCCTTTAAAAG
128 TGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAA
* * * **
5824 CCTTATTACTCTCTTTAAATAGTTTTATAATCTCACAATTGATTTTAAGTTAAATTTTTTTGTAT
1 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACAT
* * * **
5889 TTTTGGTTAAAACAGACTATAATTGAATGTTTGCCTTGGGAAACATGAAGAAAAACTAATTCATT
66 TTTTGGTTAAAACAGATTATAATTGAATG-TCG-CTTGAGAAACATGAAGAAAAACCCATTCATT
* *
5954 GGCAAGAAAAGTCCAATTATAGTCATCCATTCCTTCAAAAA
129 GGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAA
* * * * *
5995 CCTTACTACTCCCTTTAAATAGTTTCGA-AATCCCATAATTGATTTTAAGTTAAATGTTTTTTAC
1 CCTTATTACTCGCTTTAAATGGTTT-TATAATCTCATAATTGATTTTAAGTTAAAT-TTTTTTAC
* *
6059 A-TTTTGGTTAAAACAGATTATAATTGAATGTTTGGCTTTG-GAAACATGAAGAAAAACACATTC
64 ATTTTTGGTTAAAACAGATTATAATTGAATG--TCGC-TTGAGAAACATGAAGAAAAACCCATTC
* ** * *
6122 ATTGGCAAGAAAAG-CCAATTTATAGTTACCCAAGCCTTTAAAAG
126 ATTGGCAAGAAAAGTCC-ATTTATAGTCACCCATTCCTTCAAAAA
* * * * * * * ***
6166 CCTTATTACTCTCTATAAACGGTTTTATAACCTAAAAATTGATTTTAAGTTAATTTTTTTTTTGT
1 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACAT
* * * * * * *
6231 TTTTGGCTAAAGCAGATTATAATTGAATATTTGACTTGAGAACCATGAAGAAATACCAATTCATT
66 TTTTGGTTAAAACAGATTATAATTGAAT-GTCG-CTTGAGAAACATGAAGAAAAACCCATTCATT
* * * ** * *
6296 GTCAAGAAAAGCCCATTTACAGTCACCCAAGCCTTCGAAAG
129 GGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAA
* * *
6337 TCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGA-TTTGAGTTAAGTTTTTTTTACA
1 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAA-ATTTTTTTACA
* * * * *
6401 TTTTTAGTTAAAATAGATTATAATTGAATGTTTGCCTTAAGAAACATGAAGAAAAAGCCATT
65 TTTTTGGTTAAAACAGATTATAATTGAATG-TCG-CTTGAGAAACATGAAGAAAAACCCATT
6463 NNNNNNNNNN
Statistics
Matches: 813, Mismatches: 147, Indels: 42
0.81 0.15 0.04
Matches are distributed among these distances:
169 29 0.04
170 87 0.11
171 535 0.66
172 162 0.20
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (169 bp):
CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACAT
TTTTGGTTAAAACAGATTATAATTGAATGTCGCTTGAGAAACATGAAGAAAAACCCATTCATTGG
CAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAA
Found at i:6208 original size:342 final size:340
Alignment explanation
Indices: 5312--6462 Score: 1242
Period size: 342 Copynumber: 3.4 Consensus size: 340
5302 NNNNNNNNAG
* * * * * *
5312 CCTTATTACTCGCTTTAAATGGTTTTATAA-CTCGTAACTGATTTTAAGTTGACTTTTCTTACAT
1 CCTTATTACTCGCTTTAAATGGTTTCATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACAT
** * * * * * *
5376 TTTTCATTAAAACAGACTATAATTCAATGCCTGCCTTGAGAAACTTG-AGAACAAGCCATTCATT
66 TTTTGGTTAAAACAGATTATAATTGAATGTCTG-CTTAAGAAACATGAAGAA-AAACCATTCATT
* * * * * **
5440 GAG-AAGAAAAGTCCATTTATAG-TCCCCCATTCTTTCAAAAACGTTATTACTAGCTTTAAATGG
129 G-GCAAGAAAAGTCCATTTATAGTTACCCAATCCTTT-AAAAGCCTTATTACTCTCTTTAAATGG
* *
5503 TTTTATAAACTAATAATTGATTTTAAGTTAAATTTTTTTACATTTTTGGTTAAAACAGACTATAA
192 TTTTATAAACTAAAAATTGATTTTAAGTTAAATTTTTTTATATTTTTGGTTAAAACAGACTATAA
* ** * * * * * *
5568 TTGAATG-TCGATCTCAATAAACGTAAACAAAAAGGC-ATTCATTGGCAAGAGAAGTCCATTTAT
257 TTGAATGTTTGA-CTTGAGAAACATGAAGAAAAA-CCAATTCATTGGCAAGAAAAGTCCATTTAT
* * *
5631 AGTCACCCATTACATCAAAAT
320 AGTCACCCATTCCTTCAAAAA
* * * *
5652 CCTTATTACTCGCTTTAAATGGTTTCATAATCTCAAAATTGATTTTAATTTGAATTCTTTGTACA
1 CCTTATTACTCGCTTTAAATGGTTTCATAATCTCATAATTGATTTTAAGTTAAATT-TTTTTACA
* * * * * *
5717 GTTTTGGTTAAAATAGATTATAATTGAATGTCTACATAAAAAAACATGAAGAAAAATGCATTCAT
65 TTTTTGGTTAAAACAGATTATAATTGAATGTCTGC-TTAAGAAACATGAAGAAAAA-CCATTCAT
** * * *
5782 TGGCAAGAAAAGTCCATTTATAGTCGCACATTCCTTTAAAAGCCTTATTACTCTCTTTAAATAGT
128 TGGCAAGAAAAGTCCATTTATAGTTACCCAATCCTTTAAAAGCCTTATTACTCTCTTTAAATGGT
* * * *
5847 TTTATAATCTCACAATTGATTTTAAGTTAAATTTTTTTGTATTTTTGGTTAAAACAGACTATAAT
193 TTTATAAACTAAAAATTGATTTTAAGTTAAATTTTTTTATATTTTTGGTTAAAACAGACTATAAT
* * * *
5912 TGAATGTTTGCCTTGGGAAACATGAAGAAAAACTAATTCATTGGCAAGAAAAGTCCAATTATAGT
258 TGAATGTTTGACTTGAGAAACATGAAGAAAAACCAATTCATTGGCAAGAAAAGTCCATTTATAGT
*
5977 CATCCATTCCTTCAAAAA
323 CACCCATTCCTTCAAAAA
* * * *
5995 CCTTACTACTCCCTTTAAATAGTTTCGA-AATCCCATAATTGATTTTAAGTTAAATGTTTTTTAC
1 CCTTATTACTCGCTTTAAATGGTTTC-ATAATCTCATAATTGATTTTAAGTTAAAT-TTTTTTAC
* **
6059 A-TTTTGGTTAAAACAGATTATAATTGAATGTTTGGCTTTGGAAACATGAAGAAAAACACATTCA
64 ATTTTTGGTTAAAACAGATTATAATTGAATGTCT-GCTTAAGAAACATGAAGAAAAAC-CATTCA
* * *
6123 TTGGCAAGAAAAG-CCAATTTATAGTTACCCAAGCCTTTAAAAGCCTTATTACTCTCTATAAACG
127 TTGGCAAGAAAAGTCC-ATTTATAGTTACCCAATCCTTTAAAAGCCTTATTACTCTCTTTAAATG
* * * * * * *
6187 GTTTTATAACCTAAAAATTGATTTTAAGTTAATTTTTTTTTTGTTTTTGGCTAAAGCAGATTATA
191 GTTTTATAAACTAAAAATTGATTTTAAGTTAAATTTTTTTATATTTTTGGTTAAAACAGACTATA
* * * * * *
6252 ATTGAATATTTGACTTGAGAACCATGAAGAAATACCAATTCATTGTCAAGAAAAGCCCATTTACA
256 ATTGAATGTTTGACTTGAGAAACATGAAGAAAAACCAATTCATTGGCAAGAAAAGTCCATTTATA
** * *
6317 GTCACCCAAGCCTTCGAAAG
321 GTCACCCATTCCTTCAAAAA
* * * *
6337 TCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGA-TTTGAGTTAAGTTTTTTTTACA
1 CCTTATTACTCGCTTTAAATGGTTTCATAATCTCATAATTGATTTTAAGTTAA-ATTTTTTTACA
* * *
6401 TTTTTAGTTAAAATAGATTATAATTGAATGTTTGCCTTAAGAAACATGAAGAAAAAGCCATT
65 TTTTTGGTTAAAACAGATTATAATTGAATGTCTG-CTTAAGAAACATGAAGAAAAA-CCATT
6463 NNNNNNNNNN
Statistics
Matches: 677, Mismatches: 115, Indels: 36
0.82 0.14 0.04
Matches are distributed among these distances:
340 29 0.04
341 43 0.06
342 362 0.53
343 232 0.34
344 11 0.02
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (340 bp):
CCTTATTACTCGCTTTAAATGGTTTCATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACAT
TTTTGGTTAAAACAGATTATAATTGAATGTCTGCTTAAGAAACATGAAGAAAAACCATTCATTGG
CAAGAAAAGTCCATTTATAGTTACCCAATCCTTTAAAAGCCTTATTACTCTCTTTAAATGGTTTT
ATAAACTAAAAATTGATTTTAAGTTAAATTTTTTTATATTTTTGGTTAAAACAGACTATAATTGA
ATGTTTGACTTGAGAAACATGAAGAAAAACCAATTCATTGGCAAGAAAAGTCCATTTATAGTCAC
CCATTCCTTCAAAAA
Found at i:6877 original size:171 final size:161
Alignment explanation
Indices: 6631--6951 Score: 301
Period size: 171 Copynumber: 1.9 Consensus size: 161
6621 AAGAAAATTC
* * **
6631 AACTTAAAATCAATTATAAGATGACAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGTCCTA
1 AACTTAAAATCAATTATAAGATGACAAAAACATTTAAAACGAGTAATAAGGCTTTCGAAGTAATA
* * *
6696 GGTGACTATAAAT-GAGTTTTCT-TGCCAATGAATTGGTTTTC-CTTCATGATTT-TCAAGGCAA
66 GGTGACTATAAATGGACTTTT-TGTGCCAATGAA-TGGCTTTCTCTTCAAG-TTTCTCAAGG-AA
*
6757 ACATTTAATTATAATCTATTTTAAGANNNNNNNNNNAAAGCATTG
127 ACATTCAATTATAATCTATTTTAAGA----------AAAGCATTG
* * * * * * * *
6802 AACTTAAAATCAATTATGAGTTTACAAAAATATTTAAAATGAGTAGTAAGGTTTTTGAAAG-AAT
1 AACTTAAAATCAATTATAAGATGACAAAAACATTTAAAACGAGTAATAAGGCTTTCG-AAGTAAT
* *
6866 AGGTGACTATAAATGGACTTTTTGTGCCAATGAATGGCTTTCTCTTCAAGTTTCTTAAGGAAAGA
65 AGGTGACTATAAATGGACTTTTTGTGCCAATGAATGGCTTTCTCTTCAAGTTTCTCAAGGAAACA
*
6931 TTCAATTATAATCTGTTTTAA
130 TTCAATTATAATCTATTTTAA
6952 CCAAAAATAT
Statistics
Matches: 126, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
171 96 0.76
172 30 0.24
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.35
Consensus pattern (161 bp):
AACTTAAAATCAATTATAAGATGACAAAAACATTTAAAACGAGTAATAAGGCTTTCGAAGTAATA
GGTGACTATAAATGGACTTTTTGTGCCAATGAATGGCTTTCTCTTCAAGTTTCTCAAGGAAACAT
TCAATTATAATCTATTTTAAGAAAAGCATTG
Found at i:7613 original size:21 final size:21
Alignment explanation
Indices: 7584--7623 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
7574 GCTTGGGTAA
7584 CAATAAATGGGCTTTTCTTGC
1 CAATAAATGGGCTTTTCTTGC
* * *
7605 CAATGAATGTGTTTTTCTT
1 CAATAAATGGGCTTTTCTT
7624 CATGTTTCCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (21 bp):
CAATAAATGGGCTTTTCTTGC
Found at i:7737 original size:171 final size:168
Alignment explanation
Indices: 7428--7972 Score: 526
Period size: 171 Copynumber: 3.2 Consensus size: 168
7418 NNNNNNNNNN
* * ** *
7428 CTTGACAATGAATTGGTATTTT-TTCATGTTT-CTCAAGTCAAACATTCAATTACGATCTGCTTT
1 CTTGCCAATGAATTGGT-TTTTCTTCATGTTTCCT-AAGCCAAACATTCAATTATAATCTGTTTT
* * * * *
7491 AGCTAAAAACGGAAAAAAAATTCAACTTAAAATCAATTTTAGGTTATTAAAACCATTTATAGAGA
64 AAC-AAAAAC-GCAAAAAAATTCAACTTAAAATCAATTAT-GG-GATTAAAACCATTTAAAGAGA
** * * * *
7556 ATAATAAGGCTTTTAAAGGCTTGGGTAACAATAAATGGGCTTTT
125 ATAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTT
7600 CTTGCCAATGAA-TGTGTTTTTCTTCATGTTTCCTAAGCCAAACATTCAATTATAATCTGTTTTA
1 CTTGCCAATGAATTG-GTTTTTCTTCATGTTTCCTAAGCCAAACATTCAATTATAATCTGTTTTA
* * * *
7664 ACAAAAATGTAAAAAACATTCAACTTAAAATCAATTATGGGATTACCAAACCATTTAAAGGGAGT
65 ACAAAAACGCAAAAAA-ATTCAACTTAAAATCAATTATGGGATTA--AAACCATTTAAAGAGAAT
* * *
7729 AGTAAGGCTTTTGAAA-GAATGAATGACTATAATTGGACTTTT
127 AATAAGGCTTTT-AAAGGAATGAGTGACTATAAATGGACTTTT
* ** *
7771 CTTGCCAATGAATTGGTTTTTCTTCATGTTTCCCAAGGTAAACATTCAATTATAGTCTGTTTTAN
1 CTTGCCAATGAATTGGTTTTTCTTCATGTTTCCTAAGCCAAACATTCAATTATAATCTGTTTTA-
********* * * *
7836 NNNNNNNNNCAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA-ACAAAT
65 ACAAAAACGCAAAAAAATTCAACTTAAAATCAATTATGGGA-T-TAAAACCATTTAAAGA-GAAT
*
7900 AATAAGGCTTTTAAAGGAATGTGTGACTATAAATGGACTTTT
127 AATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTT
* *
7942 TTTGCCAATGAA-TGCTTTTTTCTTCATGTTT
1 CTTGCCAATGAATTG-GTTTTTCTTCATGTTT
7973 TTTGATGTAG
Statistics
Matches: 312, Mismatches: 47, Indels: 29
0.80 0.12 0.07
Matches are distributed among these distances:
169 4 0.01
170 14 0.04
171 229 0.73
172 61 0.20
173 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.36
Consensus pattern (168 bp):
CTTGCCAATGAATTGGTTTTTCTTCATGTTTCCTAAGCCAAACATTCAATTATAATCTGTTTTAA
CAAAAACGCAAAAAAATTCAACTTAAAATCAATTATGGGATTAAAACCATTTAAAGAGAATAATA
AGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTT
Done.