Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401043.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4202.0, 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: 4387
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.34
Warning! 221 characters in sequence are not A, C, G, or T
Found at i:1486 original size:343 final size:332
Alignment explanation
Indices: 903--2901 Score: 888
Period size: 340 Copynumber: 5.9 Consensus size: 332
893 NNNNNNNNNT
* * *
903 AATAAGGCTTTTGAAGACATGGGTGACTATAAATAGGTTTTTCTTGTGAATGAGTGGCTCCTTCT
1 AATAAGGCTTTTGAAGACATGGGTGACTATAAATAGGCTTTTATTGTGAATGAATGGCTCCTTCT
** * * * *
968 TCACGTTTCTCAAGGTAGACACTTAATTATTTTTTGTTTTAACCAAAAATGTCAGAAAATTTAAC
66 TCACGTTTCTCAAGGTAGACACTTAATTATAATCTATTTTAACCAAAAATGTAAAAAAATTTAAC
* * ********** * *
1033 TTAAAATCAATTATGAGGTTATAAAACCATTTANNNNNNNNNNTAAGGCTTTTGAAGGTATGGGT
131 TTAAAAGCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTGAAGGCATGGGT
* * *
1098 GACTATAAATAGACTTTTCTTACCTATGAATGGCTTTTTCTTCATGTTTCTCA-TGG-TAGACAT
196 GACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTACTTCATGTTT-TCAGAGGAT-GACAT
1161 AT-AATTATAATCTGTTGTAACCAAAAATGTAAAAAAATTCAACCTAANNNNNNNNNNGAGATTA
259 -TCAATTATAATCTGTTGTAACCAAAAATGTAAAAAAATTCAACCTAA----------GAGATTA
1225 TAAAAACATTTAAAGCGAGC
313 TAAAAACATTTAAAGCGAGC
**
1245 AATAAGGCTTTTGAAGACATGGGTGACTATAAAT-GGACTTTTATTGCT-AATGAATGGCTTTTT
1 AATAAGGCTTTTGAAGACATGGGTGACTATAAATAGG-CTTTTATTG-TGAATGAATGGCTCCTT
* ** * *
1308 CTTCATGTTTCTTGAGGTAGATATTTAATTATAATCTATTTTAACCAAAAATGATAAAAAAATTT
64 CTTCACGTTTCTCAAGGTAGACACTTAATTATAATCTATTTTAACCAAAAATG-TAAAAAAATTT
* * *
1373 AACTTAAAGGCAGTTATGAGATTATAAAACCATTTAAAGTGAGTAATATGACTTTTGAAGGCATG
128 AACTTAAAAGCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTGAAGGCATG
* * **
1438 GGTGACTATAAATAGGCTTTTTTTGTCAATGAATGGCTTTTACTTCATGTTTTCAGAGGATGACA
193 GGTGACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTACTTCATGTTTTCAGAGGATGACA
* * * * * * *
1503 TTCAATTATTATCTGTTTTAACCAAAAATGTAATACAATTCAACTTAAAATCAATTATNNNNNNN
258 TTCAATTATAATCTGTTGTAACCAAAAATGTAAAAAAATTCAACCTAAGA--GATTAT-------
** * *
1568 NNNAAACATTTAAAGCTAGT
314 -AAAAACATTTAAAGCGAGC
* * * ** * *
1588 AATAAGGATTTTGAAGGCATGGGTGACTATAAATAGACTTTTCCTATGAATGAATGGC-CTTTTC
1 AATAAGGCTTTTGAAGACATGGGTGACTATAAATAGGCTTTTATTGTGAATGAATGGCTC-CTTC
* * * * * *
1652 TTCATGTTTCTCAAGGCA-A-AC---ATT-CAA--T-TTTTACCCAAAAATATAAAAAAAATTCA
65 TTCACGTTTCTCAAGGTAGACACTTAATTATAATCTATTTTAACCAAAAATGT-AAAAAAATTTA
* * * * * * ** * **
1708 ATTTAAAATCAATTCTGAGCTTATAAAATCTTTTAAAGCAAGTAATAAGGCTTTCAAAGGCATGG
129 ACTTAAAAGCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTGAAGGCATGG
* * * ** ** *
1773 GTGACTATCAATAGACTTTTCTTGCCAATGCATATCTTTTTGTTCACG-TTTCTAGAGG-TAGAC
194 GTGACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTACTTCATGTTTTC-AGAGGAT-GAC
* * * * * * * *
1836 GTTCAATTATAATCTATTTTAA-TATAAAATATTAAAAAAGTCAACTTTAAATCATTTATGAGAT
257 ATTCAATTATAATCTGTTGTAACCA-AAAAT-GT-AAAAA---AA--TTCAA-C--CTAAGAGAT
* * * *
1900 TATAAAAATAATTAAAGCAAGT
311 TATAAAAACATTTAAAGCGAGC
********** * * * * **
1922 AATAAGGCTTNNNNNNNNNNGGGTGAGTATAAAT-GGACTTTTCTCGTTAATGAATGG-TTGTTC
1 AATAAGGCTTTTGAAGACATGGGTGACTATAAATAGG-CTTTTATTGTGAATGAATGGCTCCTTC
** * * * * * *
1985 TTCACAATTCTCAAGGTAGACA-TTCAGTTATAATATGTTTTCACCAAAAAT-AAAAAAAATTCA
65 TTCACGTTTCTCAAGGTAGACACTT-AATTATAATCTATTTTAACCAAAAATGTAAAAAAATTTA
* * * * * *
2048 ACTT-AAAGTTAATTATGAGATTATAAAACTATTTAAAATGAGTAATAAGGCTTATGAAGGCATA
129 ACTTAAAAG-CAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTGAAGGCATG
* ** * * * *
2112 CGTGACTATAAATAGACTTTTCTTACCAATGAATATCTTTTTCATC-TTTTTTCTTGAGG-TAGA
193 GGTGACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTACTTCATGTTTTC-AGAGGAT-GA
********** * * *
2175 CAATT-AATTATAATCNNNNNNNNNNAAAAATGTAAAAAAATTCAACTTCAAATCACTTATGTGA
256 C-ATTCAATTATAATCTGTTGTAACCAAAAATGTAAAAAAATTCAAC--CTAA-GA--GAT-T-A
*
2239 TTGAAAAACCATTTAAAGCGAGT
313 -T-AAAAA-CATTTAAAGCGAGC
* * * * * ** * ** *
2262 AATAAGGCTTTGGAAGGCTTGGGTGATTATAAATAGGCTTTTCTTGCCAATGAATGGGTTTTTTT
1 AATAAGGCTTTTGAAGACATGGGTGACTATAAATAGGCTTTTATTGTGAATGAATGGCTCCTTCT
* ** * ** ** * * *
2327 TCATGTTTCTTTAGG-CGAGCA-TTCACCTGGAATCTGTTTTAA-CTAAAATGTAAAAAAATTCA
66 TCACGTTTCTCAAGGTAGA-CACTT-AATTATAATCTATTTTAACCAAAAATGTAAAAAAATTTA
* *************** ** *
2389 ACTTAAAATCAATTATGAGATTNNNNNNNNNNNNNNNGCAAGTAATAAGGCTTTTGAAGGCATGG
129 ACTTAAAAGCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTGAAGGCATGG
* * * * * *
2454 GTGACTATAAATAGACTTTTCTTATCGATGAATGGCTTTTTCTTTATG-TTTCTTGAGG-TAACA
194 GTGACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTACTTCATGTTTTC-AGAGGATGACA
* * * * * * *
2517 TTTAATTATAATCTGTTTTAACTAAAAATATAAAAACGTTCAACTTAAAATCAATTATGAGATTA
258 TTCAATTATAATCTGTTGTAACCAAAAATGTAAAAA-----AA-TT-CAA-C--CTAAGAGATTA
* * *
2582 TGAAACCATTTAAAGCGAGT
313 TAAAAACATTTAAAGCGAGC
* ** ** * * * *
2602 AATAAGGCTTTTGTAGGTATAAGTGACTATAAATAGACTTTTCTTGCT-AATGAGTGACT--TTC
1 AATAAGGCTTTTGAAGACATGGGTGACTATAAATAGGCTTTTATTG-TGAATGAATGGCTCCTTC
* * * * * * * ***
2664 TCTACATGTTTCCCATGGTAGACA-TAAAATTATTATCTGTTTTAACGAAAAATGTAAAATCTTT
65 T-T-CACGTTTCTCAAGGTAGACACT-TAATTATAATCTATTTTAACCAAAAATGTAAAA-AAAT
* * ** * * * *
2728 TTTACTTAAAATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTCTTGAAAGCA
126 TTAACTTAAAAGCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTGAAGGCA
* * * * *
2793 TGGGTGACTATAAATAGACTTTTCTTGCTAATGAATGGCTTTTGCTTCATGTTTCCTA-AGCCA-
191 TGGGTGACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTACTTCATGTTTTC-AGAG-GAT
* * *
2856 GACATTCAATTATTATCTATTTTAACCAAAAAAT-TAAAAAAATTCA
254 GACATTCAATTATAATCTGTTGTAACC-AAAAATGTAAAAAAATTCA
2902 CCTTAAGGCT
Statistics
Matches: 1249, Mismatches: 325, Indels: 172
0.72 0.19 0.10
Matches are distributed among these distances:
332 3 0.00
333 31 0.02
334 197 0.16
335 12 0.01
336 5 0.00
337 5 0.00
338 16 0.01
339 17 0.01
340 294 0.24
341 160 0.13
342 219 0.18
343 266 0.21
344 13 0.01
345 4 0.00
346 2 0.00
347 3 0.00
348 2 0.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.35
Consensus pattern (332 bp):
AATAAGGCTTTTGAAGACATGGGTGACTATAAATAGGCTTTTATTGTGAATGAATGGCTCCTTCT
TCACGTTTCTCAAGGTAGACACTTAATTATAATCTATTTTAACCAAAAATGTAAAAAAATTTAAC
TTAAAAGCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTGAAGGCATGGGT
GACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTACTTCATGTTTTCAGAGGATGACATTC
AATTATAATCTGTTGTAACCAAAAATGTAAAAAAATTCAACCTAAGAGATTATAAAAACATTTAA
AGCGAGC
Found at i:2487 original size:170 final size:155
Alignment explanation
Indices: 2259--2580 Score: 306
Period size: 170 Copynumber: 2.0 Consensus size: 155
2249 ATTTAAAGCG
* * * * *
2259 AGTAATAAGGCTTTGGAAGGCTTGGGTGATTATAAATAGGCTTTTCTTGCCAATGAATGGGTTTT
1 AGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGGCTTTT
* * * * *
2324 T-TTTCATGTTTCTTTAGGCGAGCATTCACCTGGAATCTGTTTTAACT-AAAATGTAAAAAAATT
66 TCTTT-ATGTTTCTTGAGG-GAACATTCAACTAGAATCTGTTTTAACTAAAAATATAAAAAAATT
2387 CAACTTAAAATCAATTATGAGATTNNNNNNNNNNNNNNNGCA
129 CAACTTAAAATCAATTATGAGATT---------------GCA
* * *
2429 AGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTATCGATGAATGGCTTTT
1 AGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGGCTTTT
* * * * **
2494 TCTTTATGTTTCTTGAGGTAACATTTAATTATAATCTGTTTTAACTAAAAATATAAAAACGTTCA
66 TCTTTATGTTTCTTGAGGGAACATTCAACTAGAATCTGTTTTAACTAAAAATATAAAAAAATTCA
2559 ACTTAAAATCAATTATGAGATT
131 ACTTAAAATCAATTATGAGATT
2581 ATGAAACCAT
Statistics
Matches: 131, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
169 21 0.16
170 107 0.82
171 3 0.02
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.36
Consensus pattern (155 bp):
AGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGGCTTTT
TCTTTATGTTTCTTGAGGGAACATTCAACTAGAATCTGTTTTAACTAAAAATATAAAAAAATTCA
ACTTAAAATCAATTATGAGATTGCA
Found at i:2605 original size:170 final size:171
Alignment explanation
Indices: 724--2907 Score: 1506
Period size: 171 Copynumber: 12.8 Consensus size: 171
714 NNNNNNNNNN
* * * * *
724 AAAGTGAGTAATAAGGCTTTTAAAGGCATGTGTGACTATAAATAGACTTTTCTTGAT-GATGAAC
1 AAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTG-TCAATGAAT
* * ** *
788 GACTTTTTCTTCACGTTTCTTGACATAGACGTTTAATTATAATCTGTTTTAACC-AAAATGTAAA
65 GGCTTTTTCTTCATGTTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAACCAAAAATGTAAA
* ******************
852 AAAAATCAACTTAAAATCAATTATNNNNNNNNNNNNNNNNNN
130 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
******** * ** * *
894 NNNNNNNNTAATAAGGCTTTTGAAGACATGGGTGACTATAAATAGGTTTTTCTTGTGAATGAGTG
1 AAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTCAATGAATG
** * ** * ** * * *
959 GCTCCTTCTTCACGTTTCTCAAGGTAGACACTTAATTATTTTTTGTTTTAACCAAAAATGTCAGA
66 GCTTTTTCTTCATGTTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAACCAAAAATGTAAAA
* *
1024 AAATTTAACTTAAAATCAATTATGAGGTTATAAAACCATTT
131 AAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
********** * ** *
1065 ANNNNNNNNNNTAAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCTTACCTATGAATG
1 AAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTCAATGAATG
* * *
1130 GCTTTTTCTTCATGTTTC-TCATGGTAGACATATAATTATAATCTGTTGTAACCAAAAATGTAAA
66 GCTTTTTCTTCATGTTTCTTGA-GGTAGACATTTAATTATAATCTGTTTTAACCAAAAATGTAAA
* ********** *
1194 AAAATTCAACCTAANNNNNNNNNNGAGATTATAAAAACATTT
130 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * * *
1236 AAAGCGAGCAATAAGGCTTTTGAAGACATGGGTGACTATAAATGGACTTTTATTG-CTAATGAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTC-AATGAAT
* *
1300 GGCTTTTTCTTCATGTTTCTTGAGGTAGATATTTAATTATAATCTATTTTAACCAAAAATGATAA
65 GGCTTTTTCTTCATGTTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAACCAAAAATG-TAA
* ** *
1365 AAAAATTTAACTTAAAGGCAGTTATGAGATTATAAAACCATTT
129 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * * * *
1408 AAAGTGAGTAATATGACTTTTGAAGGCATGGGTGACTATAAATAGGCTTTTTTTGTCAATGAATG
1 AAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTCAATGAATG
* * * *
1473 GCTTTTACTTCATGTTT-TCAGAGG-ATGACATTCAATTATTATCTGTTTTAACCAAAAATGTAA
66 GCTTTTTCTTCATGTTTCT-TGAGGTA-GACATTTAATTATAATCTGTTTTAACCAAAAATGTAA
* * *********
1536 TACAATTCAACTTAAAATCAATTATNNNNNNNNNNAAA-CATTT
129 AAAAATTCAACTTAAAATCAATTAT-GAGATTATAAAACCATTT
* * * * *
1579 AAAGCTAGTAATAAGGATTTTGAAGGCATGGGTGACTATAAATAGACTTTTCCTATGAATGAATG
1 AAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTCAATGAATG
* ** * * * * *
1644 GCCTTTTCTTCATGTTTCTCAAGGCA-A-A---CATT-CAA--T-TTTTACCCAAAAATATAAAA
66 GCTTTTTCTTCATGTTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAACCAAAAATGT-AAA
* * * * *
1700 AAAATTCAATTTAAAATCAATTCTGAGCTTATAAAATCTTTT
130 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* ** * * * *
1742 AAAGCAAGTAATAAGGCTTTCAAAGGCATGGGTGACTATCAATAGACTTTTCTTGCCAATGCATA
1 AAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTCAATGAATG
* * * * * * * * * *
1807 TCTTTTTGTTCACGTTTCTAGAGGTAGACGTTCAATTATAATCTATTTTAA-TATAAAATATTAA
66 GCTTTTTCTTCATGTTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAACCA-AAAATGTAAA
* * * ** *
1871 AAAAGTCAACTTTAAATCATTTATGAGATTATAAAAATAATT
130 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* ********** * * * *
1913 AAAGCAAGTAATAAGGCTTNNNNNNNNNNGGGTGAGTATAAATGGACTTTTCTCGTTAATGAATG
1 AAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTCAATGAATG
* *** ** * * * * *
1978 G-TTGTTCTTCACAATTCTCAAGGTAGACATTCAGTTATAATATGTTTTCACCAAAAAT-AAAAA
66 GCTTTTTCTTCATGTTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAACCAAAAATGTAAAA
* * *
2041 AAATTCAACTTAAAGTTAATTATGAGATTATAAAACTATTT
131 AAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
** * ** ** *
2082 AAAATGAGTAATAAGGCTTATGAAGGCATACGTGACTATAAATAGACTTTTCTTACCAATGAATA
1 AAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTCAATGAATG
* * * * * **********
2147 TCTTTTTCATCTTTTTTCTTGAGGTAGACAATTAATTATAATCNNNNNNNNNNAAAAATGTAAAA
66 GCTTTTTCTTCATGTTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAACCAAAAATGTAAAA
* * *
2212 AAATTCAACTTCAAATCACTTATGTGATTGA-AAAACCATTT
131 AAATTCAACTTAAAATCAATTATGAGATT-ATAAAACCATTT
* * * * *
2253 AAAGCGAGTAATAAGGCTTTGGAAGGCTTGGGTGATTATAAATAGGCTTTTCTTGCCAATGAATG
1 AAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTCAATGAATG
* * * * * ** ** *
2318 GGTTTTTTTTCATGTTTCTTTAGG-CGAGCATTCACCTGGAATCTGTTTTAA-CTAAAATGTAAA
66 GCTTTTTCTTCATGTTTCTTGAGGTAGA-CATTTAATTATAATCTGTTTTAACCAAAAATGTAAA
************
2381 AAAATTCAACTTAAAATCAATTATGAGATTNNNNNNNNNNNN
130 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
*** * * *
2423 NNNGCAAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTATCGATGAATG
1 AAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTCAATGAATG
* * *
2488 GCTTTTTCTTTATGTTTCTTGAGGTA-ACATTTAATTATAATCTGTTTTAACTAAAAATATAAAA
66 GCTTTTTCTTCATGTTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAACCAAAAATGTAAAA
** *
2552 ACGTTCAACTTAAAATCAATTATGAGATTATGAAACCATTT
131 AAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * ** *
2593 AAAGCGAGTAATAAGGCTTTTGTAGGTATAAGTGACTATAAATAGACTTTTCTTG-CTAATGAGT
1 AAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTC-AATGAAT
* * * ** ** * *
2657 GACTTTCTCTACATGTTTC-CCATGGTAGACATAAAATTATTATCTGTTTTAACGAAAAATGTAA
65 GGCTTTTTCTTCATGTTTCTTGA-GGTAGACATTTAATTATAATCTGTTTTAACCAAAAATGTAA
*** ** **
2721 AATCTTTTTTACTTAAAATCAATTATGAGATTATAAAAATATTT
129 AA-AAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* *
2765 AAAGCGAGTAATAAGGCTCTTGAAAGCATGGGTGACTATAAATAGACTTTTCTTG-CTAATGAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTC-AATGAAT
* * * ** * * *
2829 GGCTTTTGCTTCATGTTTCCTAAGCCAGACATTCAATTATTATCTATTTTAACCAAAAAAT-TAA
65 GGCTTTTTCTTCATGTTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAACC-AAAAATGTAA
*
2893 AAAAATTCACCTTAA
129 AAAAATTCAACTTAA
2908 GGCTTTTGAA
Statistics
Matches: 1522, Mismatches: 454, Indels: 75
0.74 0.22 0.04
Matches are distributed among these distances:
162 17 0.01
163 101 0.07
164 1 0.00
165 1 0.00
166 3 0.00
168 3 0.00
169 104 0.07
170 390 0.26
171 601 0.39
172 293 0.19
173 8 0.01
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.35
Consensus pattern (171 bp):
AAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTCAATGAATG
GCTTTTTCTTCATGTTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAACCAAAAATGTAAAA
AAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
Found at i:2928 original size:129 final size:129
Alignment explanation
Indices: 2776--3030 Score: 316
Period size: 129 Copynumber: 2.0 Consensus size: 129
2766 AAGCGAGTAA
* * *
2776 TAAGGCTCTTGAAAGCATGGGTGACTATAAATAGACTTTTCTTGCTAATGAAT-GGCTTTTGCTT
1 TAAGGCTCTTGAAAGCATGGGTGACCATAAATAGACTTTTCTTGCCAATGAATAGCCTTTT-CTT
* * *
2840 CATGTTTCCTAAGCCAGACATTCAATTATTATCTATTTTAACCAAAAA-ATTAAAAAAATTCACC
65 CATGTTTCCTAAGCCAGACATTCAATTATAATCTATTATAACCAAAAATA-AAAAAAAATTCACC
2904 T
129 T
* * * * * * *
2905 TAAGGCTTTTGAAGGCTTGGGTGACCATGAATAGGCTTTTTTTGCCATTGAATAGCCTTTTCTTC
1 TAAGGCTCTTGAAAGCATGGGTGACCATAAATAGACTTTTCTTGCCAATGAATAGCCTTTTCTTC
* * * * *
2970 ATGTTTCCTTAGGCAGACATTCAATTGTAATTTGTTATAACCAAAAATAAAAAAAAATTCA
66 ATGTTTCCTAAGCCAGACATTCAATTATAATCTATTATAACCAAAAATAAAAAAAAATTCA
3031 ACTCAAAGTC
Statistics
Matches: 106, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
129 99 0.93
130 7 0.07
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (129 bp):
TAAGGCTCTTGAAAGCATGGGTGACCATAAATAGACTTTTCTTGCCAATGAATAGCCTTTTCTTC
ATGTTTCCTAAGCCAGACATTCAATTATAATCTATTATAACCAAAAATAAAAAAAAATTCACCT
Found at i:3669 original size:171 final size:170
Alignment explanation
Indices: 2905--4387 Score: 1397
Period size: 172 Copynumber: 8.7 Consensus size: 170
2895 AAATTCACCT
* * * * *
2905 TAAGGCTTTTGAAGGCTTGGGTGACCATGAATAGG-CTTTTTTTGCCATTGAATAGCCTTTTCTT
1 TAAGGCTTTTGAAGGCTTGGGTGACTATAAAT-GGACTTTTCTTGCCAATGAATAGCTTTTTCTT
* * * * **
2969 CATGTTTCCTTAGGCAGACATTCAATTGTAATTTGTTATAACCAAAAATAAAAAAAAATTCAACT
65 CATGTTTCCTTAGGTAGACATTCAATTATAATCTGTTTTAA-CAAAAATGTAAAAAAATTCAACT
* *
3034 CAAAGTCAATTATGAAATTATAAAACCATTTAAAGCGAGTAA
129 TAAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * * * *
3076 TAAGGCTTTTGAAGGCATAGGTGACTATGAATGGACTTTTCTTGCGCAATGAATATCTTTTACTT
1 TAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGC-CAATGAATAGCTTTTTCTT
* * * *
3141 C-TCTTTTCCTAAGGTAGACATTCAATTATATTCTGTTTTAACAACAAATGTAAAAAAAATCAAC
65 CAT-GTTTCCTTAGGTAGACATTCAATTATAATCTGTTTTAACAA-AAATGTAAAAAAATTCAAC
* * ** *
3205 TTCGAA-TCAATTATAAGATTATAAAACCATTTAAAATGGGTAA
128 TT-AAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * *
3248 TAAGGCTTTTGAAGGCTTGGGTGACTATAAATAGG-CTTTTCTTACCAATGAATGGCTTTTGCTT
1 TAAGGCTTTTGAAGGCTTGGGTGACTATAAAT-GGACTTTTCTTGCCAATGAATAGCTTTTTCTT
* * * * * * *
3312 TATGTTTCCTTAGG--CA-ATTTAACTGTAAT-AGATTTTAACCAAAAATG-AAAAAGCATTCAA
65 CATGTTTCCTTAGGTAGACATTCAATTATAATCTG-TTTTAA-CAAAAATGTAAAAA-AATTCAA
* * *
3372 CTTAAAGTCAATTATGAGACTATAAAACCA--T-GA-TG-GTAA
127 CTTAAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* ** * * *
3411 TAAGGCTTTTGAAGGCATAAGTGACTATAAATGGACTTTTCTTGTCAATAAATATCATTTATT-T
1 TAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGCCAATGAATAGC-TTT-TTCT
* * *
3475 CTCAT-TTT-CTAAGGTAAACATTCAATTATAATCTGTTTTAATAAGAAATGTAAAAAAATTCAA
64 -TCATGTTTCCTTAGGTAGACATTCAATTATAATCTGTTTTAACAA-AAATGTAAAAAAATTCAA
* * *
3538 CTTCAAA-TCAATTATGAGATTCTAAAGCCATTTTAAGCGAGTAA
127 CTT-AAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
** * * * *
3582 TAAACCTTTCGAAGGCTTGGGTGACTATAAATAGGA-TTTTTTTGCTAATGAATGGCTTTTTCTT
1 TAAGGCTTTTGAAGGCTTGGGTGACTATAAAT-GGACTTTTCTTGCCAATGAATAGCTTTTTCTT
* * *** * * *
3646 AATGTTTCCTTATGTAGACATTCAACCGTAATCGGTTTTAACCAAATATGTAAAAAACTTCAACT
65 CATGTTTCCTTAGGTAGACATTCAATTATAATCTGTTTTAA-CAAAAATGTAAAAAAATTCAACT
* *
3711 TAAAGTCAATTATGAGATTATGAAACCATTTAAAGCAAGTAA
129 TAAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * * **
3753 TAAGGC-TTTCAGAGGCATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATAATTTTTTCTT
1 TAAGGCTTTTGA-AGGCTTGGGTGACTATAAATGGACTTTTCTTGCCAATGAATAGCTTTTTCTT
* * *
3817 CATGTTT-CTCGAGGTAGACATTTAATTATAATCTGTTTTAACTAAAAATG-AAAGCCAAATTCA
65 CATGTTTCCT-TAGGTAGACATTCAATTATAATCTGTTTTAAC-AAAAATGTAAA--AAAATTCA
*
3880 ACTTAAAGTCAATTATGAGATTATAAAACCATTTGAAA-TGAGTAA
126 ACTTAAAGTCAATTATGAGATTATAAAACCATTT-AAAGCGAGTAA
* ** * ** * *
3925 TATGGCTTTTGAAGG-TACAGGTGATTGCAAATGGACTTTTCTTGTCAATGAATATCTTTTTCTT
1 TAAGGCTTTTGAAGGCT-TGGGTGACTATAAATGGACTTTTCTTGCCAATGAATAGCTTTTTCTT
** * * * *
3989 CACATTTCCTAAGGTAGACA-TCTAATTACAATTTGTTTTAAGAAAAAATGTAAAAAAATTCAAC
65 CATGTTTCCTTAGGTAGACATTC-AATTATAATCTGTTTTAA-CAAAAATGTAAAAAAATTCAAC
* *
4053 TTCAAA-TCAATTATGAGATTATAAAACCATTTAAAGCAAGGAA
128 TT-AAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * * * * *
4096 TAAGGC-TTTCAAGGGCTTGAGTGACTATAAATAGG-CATTTGTTGCCAATGAATGGTTTTTTCT
1 TAAGGCTTTTGAA-GGCTTGGGTGACTATAAAT-GGACTTTTCTTGCCAATGAATAGCTTTTTCT
* * * * * *
4159 TCATGTTTCCTTAGGCAAACATTCAACTGTAATCTGTTTTAGCCAAAAATGAAAAACAAATTCTA
64 TCATGTTTCCTTAGGTAGACATTCAATTATAATCTGTTTTA-ACAAAAATGTAAAA-AAATTC-A
* * *
4224 A-TTAAAGTCAAGTATGAGATTAGAAAACCATTTAAAGCAAGTAA
126 ACTTAAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * * * * *
4268 TAAGGCTTTTGAAGCCATGAGTGACAATAAATGGACTTTTCTTGCCAATAAATATCTTTTTCTTC
1 TAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGCCAATGAATAGCTTTTTCTTC
* * *
4333 -TCGTTTCCTGAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATGTAAAAA
66 AT-GTTTCCTTAGGTAGACATTCAATTATAATCTGTTTTAA-CAAAAATGTAAAAA
Statistics
Matches: 1058, Mismatches: 194, Indels: 120
0.77 0.14 0.09
Matches are distributed among these distances:
162 2 0.00
163 54 0.05
164 9 0.01
165 8 0.01
166 51 0.05
167 17 0.02
168 50 0.05
169 10 0.01
170 32 0.03
171 397 0.38
172 405 0.38
173 23 0.02
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (170 bp):
TAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGCCAATGAATAGCTTTTTCTTC
ATGTTTCCTTAGGTAGACATTCAATTATAATCTGTTTTAACAAAAATGTAAAAAAATTCAACTTA
AAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
Found at i:4008 original size:343 final size:344
Alignment explanation
Indices: 2905--4387 Score: 1394
Period size: 343 Copynumber: 4.4 Consensus size: 344
2895 AAATTCACCT
** * * * * *
2905 TAAGGCTTTTGAAGGCTTGGGTGACCATGAATAGG-CTTTTTTTGCCATTGAATAGCCTTTTCTT
1 TAAGGCTTTTGAAGGCTCAGGTGACTATAAATAGGACTTTTCTTGCCAATGAATAGCTTTTTCTT
* * * * **
2969 CATGTTTCCTTAGGCAGACATTCAATTGTAATTTGTTATAACCAAAAATAAAAAAAAATTCAACT
66 CATGTTTCCTTAGGTAGACATTCAACTGTAATTGGTTTTAACCAAAAATGTAAAAAAATTCAACT
* * * * *
3034 CAAAGTCAATTATGAAATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTG
131 TAAAGTCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTAGAAGGCATAAGTG
* * * * *
3099 ACTATGAATGGACTTTTCTTGCGCAATGAAT-ATCTTTTACTTC-TCTTT-TCCTAAGGTAGACA
196 ACTATAAATGAACTTTTCTTGC-CAATGAATAAT-TTTTTCTTCATGTTTCT-CTAAGGTAAACA
* * * *
3161 TTCAATTATATTCTGTTTTAAC-AACAAATGTAAAAAAAATCAACTTCGAATCAATTATAAGATT
258 TTCAATTATAATCTGTTTTAACTAACAAATGTAAAAAAATTCAACTTCAAATCAATTATGAGATT
*
3225 ATAAAACCATTTAAAATGGGTAA
323 ATAAAACCATTT-AAATGAGTAA
** * * *
3248 TAAGGCTTTTGAAGGCTTGGGTGACTATAAATAGG-CTTTTCTTACCAATGAATGGCTTTTGCTT
1 TAAGGCTTTTGAAGGCTCAGGTGACTATAAATAGGACTTTTCTTGCCAATGAATAGCTTTTTCTT
* * * * * *
3312 TATGTTTCCTTAGG--CA-ATTTAACTGTAATAGATTTTAACCAAAAATG-AAAAAGCATTCAAC
66 CATGTTTCCTTAGGTAGACATTCAACTGTAATTGGTTTTAACCAAAAATGTAAAAA-AATTCAAC
* * * *
3373 TTAAAGTCAATTATGAGACTATAAAACCA--TGATG---GTAATAAGGCTTTTGAAGGCATAAGT
130 TTAAAGTCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTAGAAGGCATAAGT
* * *
3433 GACTATAAATGGACTTTTCTTGTCAATAAATATCATTTATTTC-TCA--TTT-TCTAAGGTAAAC
195 GACTATAAATGAACTTTTCTTGCCAATGAATA--ATTT-TTTCTTCATGTTTCTCTAAGGTAAAC
*
3494 ATTCAATTATAATCTGTTTTAA-TAAGAAATGTAAAAAAATTCAACTTCAAATCAATTATGAGAT
257 ATTCAATTATAATCTGTTTTAACTAACAAATGTAAAAAAATTCAACTTCAAATCAATTATGAGAT
* * **
3558 TCTAAAGCCATTTTAAGCGAGTAA
322 TATAAAACCA-TTTAAATGAGTAA
** * ** * * *
3582 TAAACCTTTCGAAGGCTTGGGTGACTATAAATAGGA-TTTTTTTGCTAATGAATGGCTTTTTCTT
1 TAAGGCTTTTGAAGGCTCAGGTGACTATAAATAGGACTTTTCTTGCCAATGAATAGCTTTTTCTT
* * * * * *
3646 AATGTTTCCTTATGTAGACATTCAACCGTAATCGGTTTTAACCAAATATGTAAAAAACTTCAACT
66 CATGTTTCCTTAGGTAGACATTCAACTGTAATTGGTTTTAACCAAAAATGTAAAAAAATTCAACT
* **
3711 TAAAGTCAATTATGAGATTATGAAACCATTTAAAGCAAGTAATAAGGCTTTCAG-AGGCATGGGT
131 TAAAGTCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTT-AGAAGGCATAAGT
* *
3775 GACTATAAATGAACTTTTCTTGCCAATGAATAATTTTTTCTTCATGTTTCTC-GAGGTAGACATT
195 GACTATAAATGAACTTTTCTTGCCAATGAATAATTTTTTCTTCATGTTTCTCTAAGGTAAACATT
* *
3839 TAATTATAATCTGTTTTAACTAA-AAATG-AAAGCCAAATTCAACTT-AAAGTCAATTATGAGAT
260 CAATTATAATCTGTTTTAACTAACAAATGTAAA--AAAATTCAACTTCAAA-TCAATTATGAGAT
3901 TATAAAACCATTTGAAATGAGTAA
322 TATAAAACCATTT-AAATGAGTAA
* * ** * *
3925 TATGGCTTTTGAAGG-TACAGGTGATTGCAAAT-GGACTTTTCTTGTCAATGAATATCTTTTTCT
1 TAAGGCTTTTGAAGGCT-CAGGTGACTATAAATAGGACTTTTCTTGCCAATGAATAGCTTTTTCT
** * * ** * **
3988 TCACATTTCCTAAGGTAGACA-TCTAATTACAATTTGTTTTAAGAAAAAATGTAAAAAAATTCAA
65 TCATGTTTCCTTAGGTAGACATTC-AACTGTAATTGGTTTTAACCAAAAATGTAAAAAAATTCAA
* * * *
4052 CTTCAAA-TCAATTATGAGATTATAAAACCATTTAAAGCAAGGAATAAGGCTTTCA-AGGGCTTG
129 CTT-AAAGTCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTT-AGAAGGCATA
* * * ** * *
4115 AGTGACTATAAAT-AGGCATTTGTTGCCAATGAATGGTTTTTTCTTCATGTTTC-CTTAGGCAAA
192 AGTGACTATAAATGA-ACTTTTCTTGCCAATGAATAATTTTTTCTTCATGTTTCTCTAAGGTAAA
* * * * * *
4178 CATTCAACTGTAATCTGTTTTAGCCAA-AAATGAAAAACAAATTCTAA-TT-AAAGTCAAGTATG
256 CATTCAATTATAATCTGTTTTAACTAACAAATGTAAAA-AAATTC-AACTTCAAA-TCAATTATG
*
4240 AGATTAGAAAACCATTTAAA-GCAAGTAA
318 AGATTATAAAACCATTTAAATG--AGTAA
* * *
4268 TAAGGCTTTTGAA-GC-CATGAGTGACAATAAAT-GGACTTTTCTTGCCAATAAATATCTTTTTC
1 TAAGGCTTTTGAAGGCTCA-G-GTGACTATAAATAGGACTTTTCTTGCCAATGAATAGCTTTTTC
* * * * **
4330 TTC-TCGTTTCCTGAGGTAGACATTCAATTATAATCT-ATTTTAATAAAAAATGTAAAAA
64 TTCAT-GTTTCCTTAGGTAGACATTCAACTGTAAT-TGGTTTTAACCAAAAATGTAAAAA
Statistics
Matches: 957, Mismatches: 137, Indels: 92
0.81 0.12 0.08
Matches are distributed among these distances:
334 158 0.17
335 53 0.06
336 5 0.01
337 64 0.07
338 8 0.01
339 12 0.01
340 64 0.07
341 7 0.01
342 105 0.11
343 470 0.49
344 11 0.01
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (344 bp):
TAAGGCTTTTGAAGGCTCAGGTGACTATAAATAGGACTTTTCTTGCCAATGAATAGCTTTTTCTT
CATGTTTCCTTAGGTAGACATTCAACTGTAATTGGTTTTAACCAAAAATGTAAAAAAATTCAACT
TAAAGTCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTAGAAGGCATAAGTG
ACTATAAATGAACTTTTCTTGCCAATGAATAATTTTTTCTTCATGTTTCTCTAAGGTAAACATTC
AATTATAATCTGTTTTAACTAACAAATGTAAAAAAATTCAACTTCAAATCAATTATGAGATTATA
AAACCATTTAAATGAGTAA
Done.