Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401596.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4717.0, 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: 6772
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.27
Warning! 1735 characters in sequence are not A, C, G, or T
Found at i:1005 original size:170 final size:170
Alignment explanation
Indices: 699--1118 Score: 488
Period size: 170 Copynumber: 2.5 Consensus size: 170
689 NNNNNNNNNN
*
699 AATCTCATAATTGATTTTAAATAGAATTTTTTTACATTTTTCATGAAAACAGACTATAATTGAAA
1 AATCTCATAATTGATTTTAAGTAGAATTTTTTTACATTTTTCATGAAAACAGACTATAATT-AAA
* *********
764 -GCTAGTCTCGAGAAACGGTAGAAAATGTCATTTATTGAGAAGAAAAGTCCATTTANNNNNNNNN
65 TGCTAGTCTCGAGAAACGGTAGAAAATGACATTTATTGAGAAGAAAAGTCCATTTATAGTCACCT
* *
828 NTTCTTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTAA
130 ATTCTTTCAAAAGCCTTATTACTCACTTTAAATTGTTTTAA
*
869 AATCTCATAACTGATTTTAAGTAGAATTTTTTTACATTTTTCATGAAAACAGACTATAATTAAAT
1 AATCTCATAATTGATTTTAAGTAGAATTTTTTTACATTTTTCATGAAAACAGACTATAATTAAAT
* *
934 GCTTGTCTCGAGAAACGGTAGAAAATGACATTTATTGAGAAGAAAAGTCTATTTATAGTCACCTA
66 GCTAGTCTCGAGAAACGGTAGAAAATGACATTTATTGAGAAGAAAAGTCCATTTATAGTCACCTA
********** * * *
999 TTCTTTCANNNNNNNNNNTGCTCATTTTAAATTGTTTTAT
131 TTCTTTCAAAAGCCTTATTACTCACTTTAAATTGTTTTAA
* * *
1039 AATCTCATAATTGATTTTAAGTTGAA-TTTCTTACATTTTT-ATTTAAAACAGACTATAATTAAA
1 AATCTCATAATTGATTTTAAGTAGAATTTTTTTACATTTTTCA-TGAAAACAGACTATAATTAAA
*
1102 TGTCTA-CCTCGAGAAAC
65 TG-CTAGTCTCGAGAAAC
1119 ATGANNNNNN
Statistics
Matches: 212, Mismatches: 35, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
168 1 0.00
169 48 0.23
170 163 0.77
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.37
Consensus pattern (170 bp):
AATCTCATAATTGATTTTAAGTAGAATTTTTTTACATTTTTCATGAAAACAGACTATAATTAAAT
GCTAGTCTCGAGAAACGGTAGAAAATGACATTTATTGAGAAGAAAAGTCCATTTATAGTCACCTA
TTCTTTCAAAAGCCTTATTACTCACTTTAAATTGTTTTAA
Found at i:1825 original size:171 final size:170
Alignment explanation
Indices: 1223--3311 Score: 1249
Period size: 171 Copynumber: 12.2 Consensus size: 170
1213 NNNNNNNNNN
** *
1223 ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAACAATAAGGCTTTTGAAAG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGG
* * * * * * * ** *
1288 AATGGGTGATTATATATGGACTTTTCTTCTCAATAAATGACATTTTCTACA-GTTTCTCAAGGCA
66 AATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTA
* *
1352 -AGCATTAAATTATTGTCTGTTTTAA-TGAAAAATGTAAAAAAAA
131 GA-CATTCAATTATAGTCTGTTTTAACT-AAAAATGT---AAAAA
* * * ** * *****
1395 AGCTCTACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTAAGTAATAAGACTTTNNNNN
1 A-TTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAG
********** * * **
1460 NNNNNNNNNNCTATAAATGGACTTTTCTTCTCAATGAATGAC-TTTT-TTCACATGTTTCTCAAG
65 GAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCAC--GTTTCTTGAG
* * *
1523 GTA-AGCATTTAATTATAGTCTATTTTAA-TGAAAAATATAAAAA
128 GTAGA-CATTCAATTATAGTCTGTTTTAACT-AAAAATGTAAAAA
* * * * *
1566 ACTTTAACTT-AAATCAATTATGAGATTACAAAACCATTTAAAGCGTGCAATAAGGCTTTTGAAG
1 A-TTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAG
********** * * * *
1630 GAATGGGTNNNNNNNNNNGGACTTTTTTTGTCAATGAATGCCTTGTTCTTTAGGTTTCTTGAGGT
65 GAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGT
** *
1695 AGACATTCAATTATAGTAAGTTTTAACTAAATATGTAAAATA
130 AGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAA-A
* * *
1737 ATTAAACTTAAAATCAATTATGAGATTATAAAACAATTTAATGCGAGGAATAAGGCTTTTGAAGG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGG
* * * * *
1802 AATAGGTAACTATAAATGGACTTTTCTTGCCAAGGAATACCTTTTTCTTCACGTTTCTTGAGGTA
66 AATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTA
********** *
1867 GACATTCNNNNNNNNNNTGTTTTAACCAAAAATGTAAAAAA
131 GACATTCAATTATAGTCTGTTTTAACTAAAAATGT-AAAAA
*** * * * **
1908 ACTT-AACTTAAAATTTTTTATGAGATTACAAAACAATTTAAAGCAAGCAATAAGGCTTCCGAAG
1 A-TTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAG
*********** * **
1972 GAATGGGTGACTATAAATGNNNNNNNNNNCTCAATGAATGAC-TTTT-TTCACATGTTTCTCAAG
65 GAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCAC--GTTTCTTGAG
* * * *
2035 G-AAATCATTCAATTATACTCTGTTTT-ATTGAAAAATATAAAAA
128 GTAGA-CATTCAATTATAGTCTGTTTTAACT-AAAAATGTAAAAA
********** * *
2078 TATTCAACTTAAAATCAATTATGAGANNNNNNNNNNATTTAAAGTGTGTAATAAGGCTTTTGAAG
1 -ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAG
* * * * * * *
2143 GAATGGGTGACTCTAAATGGACTTTTCTTGCCAATAAATGTCTTTTTCTTCTCATTTC-TCATGG
65 GAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCACGTTTCTTGA-GG
*
2207 TAGACATTCAATTATAGTCTGTTTTAACTAAAAATTTTAAAAA
129 TAGACATTCAATTATAGTCTGTTTTAACTAAAAA-TGTAAAAA
********** *
2250 ATTCAACTTAAAATCAATTATGAGATTANNNNNNNNNNTAAAGTGAGTAATAAGGCTTTTGAAGG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGG
* * *
2315 AATGGGTGACTAT-AATGGAC-TTTCTCG-CAAATGAATGCATTTTTCTTCACGTTTCTTGGGGT
66 AATGGGTGACTATAAATGGACTTTTCTTGTC-AATGAATGCCTTTTTCTTCACGTTTCTTGAGGT
* * *
2377 AGACATTCAATTAGAGTCTGTTTTAA-TCGAAATTGTAAAACA
130 AGACATTCAATTATAGTCTGTTTTAACT-AAAAATGTAAAA-A
*********************** * *
2419 ATTCAACTTAAAATCAATTATGAGATTNNNNNNNNNNNNNNNNNNNNNNNTAAGACTTTTGAAAG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGG
* * * * * ** *
2484 AATGAGTAACTATAAATGGACTTTTCTTCTCAATGAATGACTTTTTCTAT-AGGTTTCTCAAGGC
66 AATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCT-TCACGTTTCTTGAGGT
* * * **
2548 AGGCATTCAATTATGGTTTGTTTTAA-TGAAAAAAATAAAAAA
130 AGACATTCAATTATAGTCTGTTTTAACT-AAAAATGT-AAAAA
* * * * **
2590 ATTCAACTTAAAATCAATTATCAGATTATAGAACTATTTAAAGCGTGTAATAAGGCTTTTGAATA
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGG
* * * * * * **
2655 AATGGGTGACTATAGATGGACTTTTCTTGCCAATGAATGGCTTTTTATTCATGTATCTCAAGGTA
66 AATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTA
*
2720 GACATTCAATTATAGTCTGTTTTAAC-CAAAATGTAAAAAAA
131 GACATTCAATTATAGTCTGTTTTAACTAAAAATGT--AAAAA
* * * * *
2761 ATTCAGCTTGAAATCAATTACGAGATTATAAAACAATTTAAAGCGAGTAATCATGCTTTTGAAGG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGG
* * * ** *
2826 AATGGGTGACTATAAATAGACTTTTCTTCTCAGTGAATAACTTTTTCTAT-ACGTTTCTTGAGGC
66 AATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCT-TCACGTTTCTTGAGGT
* * *
2890 A-AGCATTCAATTATAG-CTTGTCTTAACCAAAACTGTTAAAAA
130 AGA-CATTCAATTATAGTC-TGTTTTAACTAAAAATG-TAAAAA
* ***********
2932 ATTCAACTTAAAATCAATTTTGAGATTATAAAACCNNNNNNNNNNAGTAATAAGGCTTTTGAAGG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGG
* * *
2997 AATGGGTGACTAT-AATGGAC-TTTCTTG-CAAATGAATGCATTTTTCTTCACGTTTATTGGGGT
66 AATGGGTGACTATAAATGGACTTTTCTTGTC-AATGAATGCCTTTTTCTTCACGTTTCTTGAGGT
* *
3059 AGACATTCAATTAGT-GTCTGTTTTAA-TCGAAATTGTAAAACA
130 AGACATTCAATTA-TAGTCTGTTTTAACT-AAAAATGTAAAA-A
*********** * *
3101 ATTCAACTTAAAATCAATTATGAGATTNNNNNNNNNNNTAAAGCAAGTAATAAGGCTTTTGAAAG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGG
* * ** * *
3166 AATGAGTGACTATAAATAGACTTTTCTCCT-AGATGAATAG-CTTTTTCTACATGTTT-TTAGAG
66 AATGGGTGACTATAAATGGACTTTTCTTGTCA-ATGAAT-GCCTTTTTCTTCACGTTTCTT-GAG
* * *
3228 GCA-ACCATTCAATTCTAGTCTGTTTTAA-TAAAAAATATAAAACA
128 GTAGA-CATTCAATTATAGTCTGTTTTAACT-AAAAATGTAAAA-A
* * *
3272 ATTTAACTTAAAATCAATTTTGAGATTATAAAACCATTTA
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTA
3312 NNNNNNNNNN
Statistics
Matches: 1463, Mismatches: 398, Indels: 113
0.74 0.20 0.06
Matches are distributed among these distances:
168 15 0.01
169 240 0.16
170 170 0.12
171 869 0.59
172 42 0.03
173 84 0.06
174 43 0.03
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.34
Consensus pattern (170 bp):
ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGG
AATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTA
GACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAA
Found at i:2572 original size:682 final size:656
Alignment explanation
Indices: 1884--3127 Score: 1275
Period size: 682 Copynumber: 1.9 Consensus size: 656
1874 NNNNNNNNNN
** *** *
1884 TGTTTTAACCAAAAATGTAAAAAAACTT-AACTTAAAATTTTTTATGAGATTACAAAACAATTTA
1 TGTTTTAACCAAAAAAATAAAAAAA-TTCAACTTAAAATCAATTATCAGATTACAAAACAATTTA
* **********
1948 AAGCAAGCAATAAGGCTTCCGAAGGAATGGGTGACTATAAAT-GNNNNNNNNNNCTCAATGAATG
65 AAGCAAGCAATAAGGCTTCCGAAGAAATGGGTGACTATAAATGGACTTTTCTTGC-CAATGAATG
* **
2012 ACTTTTT-TCACATGTTTCTCAAGG-AAATCATTCAATTATACTCTGTTTTATTGAAAAATAT-A
129 ACTTTTTAT-ACATGTATCTCAAGGTAAA-CATTCAATTATACTCTGTTTTA-ACAAAAATATAA
* * ********** * *
2074 AAAATATTCAACTTAAAATCAATTATGAGANNNNNNNNNNATTTAAAGTGTGTAATAAGGCTTTT
191 AAAAAATTCAACTTAAAATCAATTACGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTT
* * ** *
2139 GAAGGAATGGGTGACTCTAAATGGACTTTTCTTGC-CAATAAATGTCTTTTTCT-TCTCATTTC-
256 GAAGGAATGGGTGACTATAAATAGACTTTTCTT-CTCAATAAATAACTTTTTCTAT-ACATTTCT
* * * *
2201 TCATGG-TAGACATTCAATTATAG-TCTGTTTTAACTAAAAATTTTAAAAAATTCAACTTAAAAT
319 TCA-GGCAAG-CATTCAATTATAGCT-TGTCTTAACCAAAAATGTTAAAAAATTCAACTTAAAAT
*******
2264 CAATTATGAGATTANNNNNNNNNNTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATA
381 CAATTATGAGATTA---TAAAACCTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATA
*
2329 ATGGACTTTCTCGCAAATGAATGCATTTTTCTTCACGTTTCTTGGGGTAGACATTCAATTAGAGT
443 ATGGACTTTCTCGCAAATGAATGCATTTTTCTTCACGTTTATTGGGGTAGACATTCAATTAGAGT
2394 CTGTTTTAATCGAAATTGTAAAACAATTCAACTTAAAATCAATTATGAGATTNNNNNNNNNNNNN
508 CTGTTTTAATCGAAATTGTAAAACAATTCAACTTAAAATCAATTATGAGATT-------------
2459 NNNNNNNNNNTAAGACTTTTGAAAGAATGAGTAACTATAAATGGACTTTTCTTCTCAATGAATGA
560 ----------TAAGACTTTTGAAAGAATGAGTAACTATAAATGGACTTTTCTTCTCAATGAATGA
2524 CTTTTTCTATAGGTTTCTCAAGGCAGGCATTCAATTATGGTT
615 CTTTTTCTATAGGTTTCTCAAGGCAGGCATTCAATTATGGTT
** * * *
2566 TGTTTTAATGAAAAAAATAAAAAAATTCAACTTAAAATCAATTATCAGATTATAGAACTATTTAA
1 TGTTTTAACCAAAAAAATAAAAAAATTCAACTTAAAATCAATTATCAGATTACAAAACAATTTAA
** * ** * * *
2631 AGCGTGTAATAAGGCTTTTGAATAAATGGGTGACTATAGATGGACTTTTCTTGCCAATGAATGGC
66 AGCAAGCAATAAGGCTTCCGAAGAAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGAC
* * * * *
2696 TTTTTATTCATGTATCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAATGTAAAAAAA
131 TTTTTATACATGTATCTCAAGGTAAACATTCAATTATACTCTGTTTTAACAAAAATATAAAAAAA
* * * *
2761 ATTCAGCTTGAAATCAATTACGAGATTATAAAACAATTTAAAGCGAGTAATCATGCTTTTGAAGG
196 ATTCAACTTAAAATCAATTACGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGG
* * * *
2826 AATGGGTGACTATAAATAGACTTTTCTTCTCAGTGAATAACTTTTTCTATACGTTTCTTGAGGCA
261 AATGGGTGACTATAAATAGACTTTTCTTCTCAATAAATAACTTTTTCTATACATTTCTTCAGGCA
* *
2891 AGCATTCAATTATAGCTTGTCTTAACCAAAACTGTTAAAAAATTCAACTTAAAATCAATTTTGAG
326 AGCATTCAATTATAGCTTGTCTTAACCAAAAATGTTAAAAAATTCAACTTAAAATCAATTATGAG
*******
2956 ATTATAAAACCNNNNNNNNNNAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAATGGACTTTC
391 ATTATAAAACC---TAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAATGGACTTTC
* *
3021 TTGCAAATGAATGCATTTTTCTTCACGTTTATTGGGGTAGACATTCAATTAGTGTCTGTTTTAAT
453 TCGCAAATGAATGCATTTTTCTTCACGTTTATTGGGGTAGACATTCAATTAGAGTCTGTTTTAAT
3086 CGAAATTGTAAAACAATTCAACTTAAAATCAATTATGAGATT
518 CGAAATTGTAAAACAATTCAACTTAAAATCAATTATGAGATT
3128 NNNNNNNNNN
Statistics
Matches: 461, Mismatches: 88, Indels: 26
0.80 0.15 0.05
Matches are distributed among these distances:
681 9 0.02
682 441 0.96
683 11 0.02
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.34
Consensus pattern (656 bp):
TGTTTTAACCAAAAAAATAAAAAAATTCAACTTAAAATCAATTATCAGATTACAAAACAATTTAA
AGCAAGCAATAAGGCTTCCGAAGAAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGAC
TTTTTATACATGTATCTCAAGGTAAACATTCAATTATACTCTGTTTTAACAAAAATATAAAAAAA
ATTCAACTTAAAATCAATTACGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGG
AATGGGTGACTATAAATAGACTTTTCTTCTCAATAAATAACTTTTTCTATACATTTCTTCAGGCA
AGCATTCAATTATAGCTTGTCTTAACCAAAAATGTTAAAAAATTCAACTTAAAATCAATTATGAG
ATTATAAAACCTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAATGGACTTTCTCG
CAAATGAATGCATTTTTCTTCACGTTTATTGGGGTAGACATTCAATTAGAGTCTGTTTTAATCGA
AATTGTAAAACAATTCAACTTAAAATCAATTATGAGATTTAAGACTTTTGAAAGAATGAGTAACT
ATAAATGGACTTTTCTTCTCAATGAATGACTTTTTCTATAGGTTTCTCAAGGCAGGCATTCAATT
ATGGTT
Found at i:2598 original size:511 final size:490
Alignment explanation
Indices: 2001--2958 Score: 977
Period size: 511 Copynumber: 1.9 Consensus size: 490
1991 NNNNNNNNNN
* * *
2001 CTCAATGAATGACTTTTTTCACATGTTTCTCAAGGAAATCATTCAATTATACTCTGTTTTATTGA
1 CTCAATGAATGACTTTTTTCACAGGTTTCTCAAGGAAAGCATTCAATTATACTCTGTTTTAATGA
* * * ********** *
2066 AAAATATAAAAATATTCAACTTAAAATCAATTATGAGANNNNNNNNNNATTTAAAGTGTGTAATA
66 AAAAAATAAAAAAATTCAACTTAAAATCAATTATCAGATTATAGAACTATTTAAAGCGTGTAATA
* * * *
2131 AGGCTTTTGAAGGAATGGGTGACTCTAAATGGACTTTTCTTGCCAATAAATGTCTTTTTCTTCTC
131 AGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGGCTTTTT-AT-TC
* **
2196 AT-T-TCTCATGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAAT-TTTAAAAAATTCAACT
194 ATGTATCTCAAGGTAGACATTCAATTATAGTCTGTTTTAAC-AAAAATGTAAAAAAAATTCAACT
* ********** *
2258 TAAAATCAATTATGAGATTANNNNNNNNNNTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
258 TAAAATCAATTACGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * **
2323 ACTAT-AATGGAC-TTTC-TCGCAAATGAAT-GCATTTTTCT-TCACGTTTCTTG-GGGTAGACA
323 ACTATAAATAGACTTTTCTTCGC-AATGAATAAC-TTTTTCTAT-ACGTTTCTTGAGGCAAG-CA
* * * *
2382 TTCAATTAGAG-TCTGTTTTAATCGAAATTG-TAAAACAATTCAACTTAAAATCAATTATGAGAT
384 TTCAATTAGAGCT-TGTCTTAACCAAAACTGTTAAAA-AATTCAACTTAAAATCAATTATGAGAT
2445 TNNNNNNNNNNNNNNNNNNNNNNNTAAGACTTTTGAAAGAATGAGTAACTATAAATGGACTTTTC
447 T-----------------------TAAGACTTTTGAAAGAATGAGTAACTATAAATGGACTTTTC
2510 TT
489 TT
* * * ** *
2512 CTCAATGAATGAC-TTTTTCTATAGGTTTCTCAAGGCAGGCATTCAATTATGGTTTGTTTTAATG
1 CTCAATGAATGACTTTTTTC-ACAGGTTTCTCAAGGAAAGCATTCAATTATACTCTGTTTTAATG
2576 AAAAAAATAAAAAAATTCAACTTAAAATCAATTATCAGATTATAGAACTATTTAAAGCGTGTAAT
65 AAAAAAATAAAAAAATTCAACTTAAAATCAATTATCAGATTATAGAACTATTTAAAGCGTGTAAT
* * *
2641 AAGGCTTTTGAATAAATGGGTGACTATAGATGGACTTTTCTTGCCAATGAATGGCTTTTTATTCA
130 AAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGGCTTTTTATTCA
* * *
2706 TGTATCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAATGTAAAAAAAATTCAGCTTG
195 TGTATCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAATGTAAAAAAAATTCAACTTA
* *
2771 AAATCAATTACGAGATTATAAAACAATTTAAAGCGAGTAATCATGCTTTTGAAGGAATGGGTGAC
260 AAATCAATTACGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* *
2836 TATAAATAGACTTTTCTTCTCAGTGAATAACTTTTTCTATACGTTTCTTGAGGCAAGCATTCAAT
325 TATAAATAGACTTTTCTTCGCAATGAATAACTTTTTCTATACGTTTCTTGAGGCAAGCATTCAAT
* *
2901 TATAGCTTGTCTTAACCAAAACTGTTAAAAAATTCAACTTAAAATCAATTTTGAGATT
390 TAGAGCTTGTCTTAACCAAAACTGTTAAAAAATTCAACTTAAAATCAATTATGAGATT
2959 ATAAAACCNN
Statistics
Matches: 373, Mismatches: 62, Indels: 22
0.82 0.14 0.05
Matches are distributed among these distances:
509 4 0.01
510 13 0.03
511 256 0.69
512 6 0.02
513 79 0.21
514 15 0.04
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.35
Consensus pattern (490 bp):
CTCAATGAATGACTTTTTTCACAGGTTTCTCAAGGAAAGCATTCAATTATACTCTGTTTTAATGA
AAAAAATAAAAAAATTCAACTTAAAATCAATTATCAGATTATAGAACTATTTAAAGCGTGTAATA
AGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGGCTTTTTATTCAT
GTATCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAATGTAAAAAAAATTCAACTTAA
AATCAATTACGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACT
ATAAATAGACTTTTCTTCGCAATGAATAACTTTTTCTATACGTTTCTTGAGGCAAGCATTCAATT
AGAGCTTGTCTTAACCAAAACTGTTAAAAAATTCAACTTAAAATCAATTATGAGATTTAAGACTT
TTGAAAGAATGAGTAACTATAAATGGACTTTTCTT
Found at i:4055 original size:171 final size:169
Alignment explanation
Indices: 3756--5547 Score: 884
Period size: 171 Copynumber: 10.5 Consensus size: 169
3746 NNNNNNNNNT
* * * *
3756 TTTAAGTTGAATTTTTTTACATTTTAGATTAAAACA-AACTATAATTGAATGTATACCTCGAGAA
1 TTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAA-TATAATTGAATGTCTACCTCAAGAA
* * * **********
3820 ACATGAAGACAAAGGCATTCAATGGCAAGAAAAGTCCATTTATAGTCANNNNNNNNNNCAAAAGC
65 ACATGAAGAAAAAGGTATTCATTGGCAAGAAAAGT-CATTTATAGTCACCCATTCCTTCAAAAGC
*
3885 TTTATTACTCGCTTTAAATTGTTTTATAATCCCATAATTGA
129 TTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGA
* * * * **
3926 TATTAAGTTGAATTTTTTAACATTTTTGGTTAAAATAGAATATAATAGAATGTTTACCTTGAGAA
1 T-TTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAATATAATTGAATGTCTACCTCAAGAA
* *
3991 ACATGAAGAAAAAGGTATTCACTGGTAAGAAAAGTACATTTATAGTCACCCATTCCTTCAAAAGC
65 ACATGAAGAAAAAGGTATTCATTGGCAAGAAAAGT-CATTTATAGTCACCCATTCCTTCAAAAGC
* * * * *
4056 CTTACTGCTCGCTTGAAATTATTTTATAATCTCATAATTGA
129 TTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGA
********* * * ** * ** *
4097 TTTNNNNNNNNNNTGTTTTATATTTTTCATTAAAACAGATTATAATTGAATACCTGCC-CTAAGA
1 TTT-AAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAATATAATTGAATGTCTACCTC-AAGA
* * ********* *
4161 AACTTGTAGAAAAA-GTCATTCATTGAG-AAGNNNNNNNNNNTTATAGTCACCCATTTCTTCAAA
64 AACATGAAGAAAAAGGT-ATTCATTG-GCAAG-AAAAGTCATTTATAGTCACCCATTCCTTCAAA
* * * * *
4224 AG-TCTTATTTCTCGCGTTAAAGTATTTTATAATTTCATAATTGA
126 AGCT-TTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGA
* * * * * *
4268 TTTGAAGTTAAATTTTTTAACATTTTTGCTTAAAACAGACTATAATTGAATGTCTATCTCGAGAA
1 TTT-AAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAATATAATTGAATGTCTACCTCAAGAA
* * * * *
4333 ACGTAAAGAAAAA-TTCATTCATTTGCAAGAAAAGTCA-TTATAGTCACCCATTCCTTGAAAAAG
65 ACATGAAGAAAAAGGT-ATTCATTGGCAAGAAAAGTCATTTATAGTCACCCATTCCTT-CAAAAG
* * * * *
4396 AC-TTATTACTCACTATAAATGGTTTTATAATCTCAAAATTAA
128 -CTTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGA
* *******
4438 TTTCAAGTTGAATTTTTTTACATTTTTGGTTAAAACA-AACTATAATTGAATGCCTACANNNNNN
1 TTT-AAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAA-TATAATTGAATGTCTACCTCAAGA
**** * * ** * * * *
4502 NNNNTGTAGAAAAA-GTCATTCGTTGATAAGAAAAGTCCAGTTATAGTTACTCATTCCTTCAGAA
64 AACATGAAGAAAAAGGT-ATTCATTGGCAAGAAAAGT-CATTTATAGTCACCCATTCCTTCAAAA
* * * *
4566 GCCTTATTACTCGCTTAAAATTGTTTTATAATCTTAGAATTGA
127 GCTTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGA
* * * * *
4609 TTTTATA-TCT-AATTGTTTTATATTTTTGGTTAAAACAGACTATAATTGAGTGTTTACCTCAAG
1 -TTTA-AGT-TGAATTTTTTTACATTTTTGGTTAAAACAGAATATAATTGAATGTCTACCTCAAG
* * * ********* *
4672 AAACATAAAAAAAAAGGCATTCATTGGCAAGAAAAGNNNNNNNNNNGTCACTCATTCCTTCAAAA
63 AAACATGAAGAAAAAGGTATTCATTGGCAAGAAAAG-TCATTTATAGTCACCCATTCCTTCAAAA
* * *
4737 GCCTTATTACTCACTTTAAA-TATTTTATAATCTCATAATTGA
127 GCTTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGA
* ** * * **********
4779 TTTTAATTTGAATTTTTTTACATTTTCAGTTAAAACATACTATAATTGAATGTCNNNNNNNNNNA
1 -TTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAATATAATTGAATGTCTACCTCAAGAA
* * * * *
4844 ATATGAAGAAAAATGTATTCATTTGTAAGAAAAGTTCA-TTATAGTCACTCATTCCTTCAAAAG-
65 ACATGAAGAAAAAGGTATTCATTGGCAAGAAAAG-TCATTTATAGTCACCCATTCCTTCAAAAGC
* *
4907 TCTTATTACTCTCTTTAAA-TGATTTTATAATCTCAAAATTGA
129 T-TTATTACTCGCTTTAAATTG-TTTTATAATCTCATAATTGA
*********** * *
4949 TTCTAAGTTGAATTTTTTTATNNNNNNNNNNAACACA-AACTATAATTGAATGTCGACCTCAAGA
1 TT-TAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAA-TATAATTGAATGTCTACCTCAAGA
* * * *
5013 AACATGAAGAAAAAGGTATTCAATGGCAAGAAAAATCTATTTATAGAT-ACCTATTCGTTCAAAA
64 AACATGAAGAAAAAGGTATTCATTGGCAAGAAAAGTC-ATTTATAG-TCACCCATTCCTTCAAAA
* * **********
5077 GCTTTATTACTCGCATTAAATGGTTTTATAATNNNNNNNNNNA
127 GCTTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGA
* * * ** * * *
5120 TTTTAAGTTAAATTGTTTTATATTTTTTATTAATACA-AACTAGAATTGAATGGT-TGCCTCTAA
1 -TTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAA-TATAATTGAAT-GTCTACCTC-AA
* * * * * *
5183 -AAACATGTAGAAAAAGCTATTCATCT--AAGAGAAAAGTCTATTTGTAGTCACTCATTCTTTCA
62 GAAACATGAAGAAAAAGGTATTCAT-TGGCA-AGAAAAGTC-ATTTATAGTCACCCATTCCTTCA
* * **********
5245 AAAGCCTTATTACTTGCTTTNNNNNNNNNNATAATCTCATAATTGA
124 AAAGCTTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGA
* * * * * * *
5291 TTTTAAGTTGAATTGTTTTAAAATTTCGATTAAAACAGACTCTAATTGAATGTCTACC-CTAAGA
1 -TTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAATATAATTGAATGTCTACCTC-AAGA
* *** * *
5355 AACGTGAAGAAAAATACATTCATTTGCAAG-AAAGTCCA-TTATAGTCACCGATTCCTTCAAAAG
64 AACATGAAGAAAAAGGTATTCATTGGCAAGAAAAGT-CATTTATAGTCACCCATTCCTTCAAAAG
* * * ********** *
5418 CCTTATTACTCACTTTAAATGGNNNNNNNNNNTCAAAATTGA
128 CTTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGA
* * * * *
5460 TTTTAAGTT-AAATTTTTTACATTTTTGGTTAAAAAAGACTATAATCGAATGTCTACCTCGAGAA
1 -TTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAATATAATTGAATGTCTACCTCAAGAA
* * *
5524 ACCTAAAGAAAAAGGCATTCATTG
65 ACATGAAGAAAAAGGTATTCATTG
5548 ACAANNNNNN
Statistics
Matches: 1201, Mismatches: 374, Indels: 96
0.72 0.22 0.06
Matches are distributed among these distances:
168 62 0.05
169 121 0.10
170 304 0.25
171 674 0.56
172 40 0.03
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.35
Consensus pattern (169 bp):
TTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAATATAATTGAATGTCTACCTCAAGAAA
CATGAAGAAAAAGGTATTCATTGGCAAGAAAAGTCATTTATAGTCACCCATTCCTTCAAAAGCTT
TATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGA
Found at i:4595 original size:341 final size:330
Alignment explanation
Indices: 4201--4830 Score: 678
Period size: 341 Copynumber: 1.9 Consensus size: 330
4191 NNNNNNNNNN
* * * *
4201 TTATAGTCACCCATTTCTTCAAAAGTCTTATTTCTCGCGTTAAAGTATTTTATAAT-TTCATAAT
1 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCGTTAAAGTATTTTATAATCTT-AGAAT
*
4265 TGATTTGA-AGT-TAAATT-TTTTAACATTTTTGCTTAAAACAGACTATAATTGAATGTCTATCT
65 TGATTTGATA-TCT-AATTGTTTT-ACATTTTTGCTTAAAACAGACTATAATTGAATGTCTACCT
* * * ** *
4327 CGAGAAACGTAAAGAAAAATTCATTCATTTGCAAGAAAAG-TCATTATAGTCACCCATTCCTTGA
127 CAAGAAACATAAAAAAAAAGGCATTCATTGGCAAGAAAAGATCATTATAGTCACCCATTCCTT-A
*
4391 AAAAGACTTATTACTCACTATAAATGGTTTTATAATCTCAAAATTAATTTCAAGTTGAATTTTTT
191 AAAAGACTTATTACTCACTATAAAT-ATTTTATAATCTCAAAATTAATTTCAAGTTGAATTTTTT
**
4456 TACATTTTTGGTTAAAACAAACTATAATTGAATGCCTACANNNNNNNNNNTGTAGAAAAAGTCAT
255 TACATTTTCAGTTAAAACAAACTATAATTGAATGCCTACA----------TGTAGAAAAAGTCAT
4521 TCGTTGATAAGAAAAGTCCAG
310 TCGTTGATAAGAAAAGTCCAG
* * * * *
4542 TTATAGTTACTCATTCCTTCAGAAGCCTTATTACTCGC-TTAAAATTGTTTTATAATCTTAGAAT
1 TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCGTT-AAAGTATTTTATAATCTTAGAAT
* * * * *
4606 TGATTTTATATCTAATTGTTTTATATTTTTGGTTAAAACAGACTATAATTGAGTGTTTACCTCAA
65 TGATTTGATATCTAATTGTTTTACATTTTTGCTTAAAACAGACTATAATTGAATGTCTACCTCAA
********* * *
4671 GAAACATAAAAAAAAAGGCATTCATTGGCAAGAAAAGNNNNNNNNNNGTCACTCATTCCTTCAAA
130 GAAACATAAAAAAAAAGGCATTCATTGGCAAGAAAAG-ATCATTATAGTCACCCATTCCTTAAAA
* * * * * *
4736 AGCCTTATTACTCACTTTAAATATTTTATAATCTCATAATTGATTTTAATTTGAATTTTTTTACA
194 AGACTTATTACTCACTATAAATATTTTATAATCTCAAAATTAATTTCAAGTTGAATTTTTTTACA
*
4801 TTTTCAGTTAAAACATACTATAATTGAATG
259 TTTTCAGTTAAAACAAACTATAATTGAATG
4831 TCNNNNNNNN
Statistics
Matches: 241, Mismatches: 41, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
340 2 0.01
341 195 0.81
342 31 0.13
343 13 0.05
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.38
Consensus pattern (330 bp):
TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCGTTAAAGTATTTTATAATCTTAGAATT
GATTTGATATCTAATTGTTTTACATTTTTGCTTAAAACAGACTATAATTGAATGTCTACCTCAAG
AAACATAAAAAAAAAGGCATTCATTGGCAAGAAAAGATCATTATAGTCACCCATTCCTTAAAAAG
ACTTATTACTCACTATAAATATTTTATAATCTCAAAATTAATTTCAAGTTGAATTTTTTTACATT
TTCAGTTAAAACAAACTATAATTGAATGCCTACATGTAGAAAAAGTCATTCGTTGATAAGAAAAG
TCCAG
Found at i:4614 original size:20 final size:19
Alignment explanation
Indices: 4579--4630 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
4569 TTATTACTCG
4579 CTTAAAATTGTTTTATAAT
1 CTTAAAATTGTTTTATAAT
*
4598 CTTAGAATTGATTTTAT-AT
1 CTTAAAATTG-TTTTATAAT
4617 C-T--AATTGTTTTATA
1 CTTAAAATTGTTTTATA
4631 TTTTTGGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 6 0.20
16 5 0.17
18 1 0.03
19 12 0.40
20 6 0.20
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.54
Consensus pattern (19 bp):
CTTAAAATTGTTTTATAAT
Found at i:4629 original size:15 final size:17
Alignment explanation
Indices: 4583--4631 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 17
4573 TACTCGCTTA
4583 AAATTGTTTTATAATCTT
1 AAATTGTTTTAT-ATCTT
4601 AGAATTGATTTTATATC-T
1 A-AATTG-TTTTATATCTT
4619 -AATTGTTTTATAT
1 AAATTGTTTTATAT
4632 TTTTGGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.28
16 5 0.17
18 2 0.07
19 8 0.28
20 6 0.21
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (17 bp):
AAATTGTTTTATATCTT
Found at i:6496 original size:170 final size:169
Alignment explanation
Indices: 6214--6772 Score: 723
Period size: 170 Copynumber: 3.3 Consensus size: 169
6204 NNNNNNNNNN
* * *
6214 ACAGACTATAATTGAATGTCTACCTCATGAAACATGAAGAAAAATGCATTCATTTGCAAGAAAAG
1 ACAGACTATAATTGAATGTTTACCTCAAGAAACATGAAGAAAAATGCATTCATTGGCAAGAAAAG
* *
6279 TCCA-TTATAGTCACCCATTCCTTCAAAAGGCC-TATTGCTCGCTTTAAATTGTTTAATAATCTA
66 TCCATTTATAGTCA-CCATTCCTTCAAAA-GCCTTATTACTCGCTTTAAATTGTTTTATAATCTA
* *
6342 ATAATTAATTTTAAGTTAAATTTTTTTATATTTTTGGTTCAA
129 ATAATTGATTTTAAGTTAAA-TTTTTTATATTTTTGGTTAAA
*
6384 ACAGACTATAATTGAATGTTTACCTTAAGAAACATGAAG-AAAATGCATTCATTGGCAAGAAAAG
1 ACAGACTATAATTGAATGTTTACCTCAAGAAACATGAAGAAAAATGCATTCATTGGCAAGAAAAG
* * ** * *
6448 TTCATTTATACTCACTCATTCCTTCAAAAGCCTTATTTTTCGCTTTAAATTGTTTTGTAATCTTA
66 TCCATTTATAGTCAC-CATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTAA
* * * * **
6513 GAATTGATTTTAAGTTGAACTGTTTTACATTTTTTATTAAA
130 TAATTGATTTTAAGTT-AAATTTTTTATATTTTTGGTTAAA
* ** * * *
6554 ACAGACTATAATTGATTGTTTA-CTTGAGAAACTTGAAGAAAAAGGCATTCATTGACAAGAAAAG
1 ACAGACTATAATTGAATGTTTACCTCAAGAAACATGAAGAAAAATGCATTCATTGGCAAGAAAAG
* * ** *
6618 CCCATTTATAGTTACCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTCA
66 TCCATTTATAGTCACC-ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTAA
6683 TAATTGATTTTAAGTTAAATTTTTTATATTTTTAGG-TAAA
130 TAATTGATTTTAAGTTAAATTTTTTATATTTTT-GGTTAAA
* *
6723 ACAGACTATAATTGAATGTTTACCTCGAGAAACATGAAGAAAAAGGCATT
1 ACAGACTATAATTGAATGTTTACCTCAAGAAACATGAAGAAAAATGCATT
Statistics
Matches: 338, Mismatches: 43, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
169 85 0.25
170 251 0.74
171 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (169 bp):
ACAGACTATAATTGAATGTTTACCTCAAGAAACATGAAGAAAAATGCATTCATTGGCAAGAAAAG
TCCATTTATAGTCACCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTAAT
AATTGATTTTAAGTTAAATTTTTTATATTTTTGGTTAAA
Done.