Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402628.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_57.0, 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: 51493
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.22
Warning! 22308 characters in sequence are not A, C, G, or T
Found at i:1431 original size:172 final size:170
Alignment explanation
Indices: 1067--1545 Score: 572
Period size: 172 Copynumber: 2.8 Consensus size: 170
1057 NNNNNNNNNN
* * * * * *
1067 TATTTAAAGCGAGTAATAAGACTTTTGAAGGCATCGGTGTCTATAAATAGACCTTT-TTGCTAAT
1 TATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACCTTTCTTGCCAAT
* * * * *
1131 GGATATCTTTTTCTTCATGTTTCTCGAGGTAAACATGCAGTTATAATCTGTTTTAATAATAA-A-
66 GGATATCTTTTTCTTCATGTTTCTCTAGGTAGACATTCAATTATAATCTGTTTTAATAAAAATAT
1194 AAAAAAGTTCAACTTAAAGGTAATTATGAGATTAAAAAAC
131 AAAAAAGTTCAACTTAAAGGTAATTATGAGATTAAAAAAC
*
1234 TATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAAT
1 TATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACCTTTCTTGCCAAT
* *
1299 GGATATCTTTTTCTTCATGTTTCTCTAGGTAGAGATTCAATTGTAATCTGTTTTAATAGAAAAAT
66 GGATATCTTTTTCTTCATGTTTCTCTAGGTAGACATTCAATTATAATCTGTTTTAAT--AAAAAT
** **********
1364 ATAAAAAAGTTTTACTTAANNNNNNNNNNGAGATTAAAAAAC
129 ATAAAAAAGTTCAACTTAAAGGTAATTATGAGATTAAAAAAC
* * * * * * *
1406 TATTTAACGCGTGTAATAAGGCTTTCCAAGGCATGGATGACTATGAATGAACCTTTCTTACCAAT
1 TATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACCTTTCTTGCCAAT
* * *
1471 GGATATCATTTTT-TT-ACGTTTCTCTAGGTAGACATTTAATTATACTCTGTTTTAATAAAAATA
66 GGATATC-TTTTTCTTCATGTTTCTCTAGGTAGACATTCAATTATAATCTGTTTTAATAAAAATA
1534 TAAAAAAGTTCA
130 TAAAAAAGTTCA
1546 NNNNNNNNNN
Statistics
Matches: 265, Mismatches: 41, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
167 50 0.19
168 58 0.22
169 17 0.06
170 4 0.02
171 37 0.14
172 94 0.35
173 5 0.02
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.36
Consensus pattern (170 bp):
TATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACCTTTCTTGCCAAT
GGATATCTTTTTCTTCATGTTTCTCTAGGTAGACATTCAATTATAATCTGTTTTAATAAAAATAT
AAAAAAGTTCAACTTAAAGGTAATTATGAGATTAAAAAAC
Found at i:3154 original size:16 final size:17
Alignment explanation
Indices: 3135--3166 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3125 ATAAGCTCAT
3135 AATTTATTTTA-ATTTG
1 AATTTATTTTATATTTG
3151 AATTTATTTTATATTT
1 AATTTATTTTATATTT
3167 TTTTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
AATTTATTTTATATTTG
Found at i:11635 original size:172 final size:161
Alignment explanation
Indices: 11232--11720 Score: 423
Period size: 172 Copynumber: 2.9 Consensus size: 161
11222 NNNNNNNNAA
* * *
11232 AAAACTATTTAAAGCGAGTAATAAGGCTTTCAAAGGCATG-GATGACTATAAAAAAACTTTTCTT
1 AAAACTATTTAAAGCGAGTAATAAAGCTTTCAAAGGCATGAG-TGACTATAAATAGACTTTTCTT
* * *
11296 ACCAATGGAT-T-TTTTTTTTTATGTTTCTTAAGGCAGACATTCAATTATAATCTGTTTTAATAA
65 ACCAATGGATATCTTTTTCTTTAGGCTTCTTAAGGCAGACATTCAATTATAATCTGTTTT-ATAA
* * * * ** *
11359 AAAANNNNNNNNNNTTTAACTTAAAA-CT-AATTATGATATTAA
129 AAAA---------ATATAA--AAAAATTTAAATTATGAGGTTAT
* ** * * *
11401 AAAACTATTTAAAGTGAGTAATATGGCTTTCAAAGGCATGGGTTACTATAAATAGACTTTTCTTG
1 AAAACTATTTAAAGCGAGTAATAAAGCTTTCAAAGGCATGAGTGACTATAAATAGACTTTTCTTA
* * * *
11466 CCAATGGATATCTTTTTCTTTATGTTTC-TATAGGCAGACATTCAATTGTAATTTGTTTTAATAA
66 CCAATGGATATCTTTTTCTTTAGGCTTCTTA-AGGCAGACATTCAATTATAATCTGTTTT-ATAA
11530 AAAAATATAAAAAAATTTAANNNNNNNNNNATTATGAGGTTAT
129 AAAAATATAAAAAAATTTAA----------ATTATGAGGTTAT
* * * *
11573 AAAATTATTTAAAGCGAGTAATAAAGCTTTTAAAGTCATGAGTGACTATAAATGGACTTTTCTTA
1 AAAACTATTTAAAGCGAGTAATAAAGCTTTCAAAGGCATGAGTGACTATAAATAGACTTTTCTTA
* * * *
11638 CCAATGGATATCTTTTTCTTTAGGCTTCTTAAGGTAGAGATTTAATTATAATCTGTTTTATTAAA
66 CCAATGGATATCTTTTTCTTTAGGCTTCTTAAGGCAGACATTCAATTATAATCTGTTTTATAAAA
*
11703 AAATATAAAAAAGTTTAA
131 AAATATAAAAAAATTTAA
11721 CTTAAAACTA
Statistics
Matches: 268, Mismatches: 35, Indels: 32
0.80 0.10 0.10
Matches are distributed among these distances:
160 4 0.01
161 1 0.00
162 5 0.02
169 66 0.25
170 4 0.01
171 72 0.27
172 114 0.43
173 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.37
Consensus pattern (161 bp):
AAAACTATTTAAAGCGAGTAATAAAGCTTTCAAAGGCATGAGTGACTATAAATAGACTTTTCTTA
CCAATGGATATCTTTTTCTTTAGGCTTCTTAAGGCAGACATTCAATTATAATCTGTTTTATAAAA
AAATATAAAAAAATTTAAATTATGAGGTTAT
Found at i:13932 original size:169 final size:171
Alignment explanation
Indices: 13605--13935 Score: 429
Period size: 169 Copynumber: 1.9 Consensus size: 171
13595 NNNNAAATGT
* * *
13605 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTCTTATATTTTTTTTTAAAACAGATTATAA
1 TTTTATAACCCCATAATTGATTTTAAGTTGAATTTTCTTATATTTTTTATTAAAACAGATTATAA
* * ** *
13670 TTGAATGTTTACTTTGAGAAACATGCAGAAAAAAGTATCCATTGACAAAAAAAGTTCATTTATAG
66 TTGAATGTTTACCTCGAGAAACATAAAGAAAAAAGAATCCATTGACAAAAAAAGTTCATTTATAG
*
13735 TAACACATTCCTTTGAAAGCCTTATTACTCGCATTAAATAG
131 TAACACATTCCTTCGAAAGCCTTATTACTCGCATTAAATAG
* *
13776 TTTTATAACCCCATAATTGATTTTCATTTGAATTTT-TCTATA-TTTTTATTAAAACAGATTATA
1 TTTTATAACCCCATAATTGATTTTAAGTTGAATTTTCT-TATATTTTTTATTAAAACAGATTATA
* * ** * *
13839 ATTGAAT-TTCTGCCTCGAGAAACGTAAAGAAAAAA-AATCCATTGGTAAGAAAAGTTTATTTAT
65 ATTGAATGTT-TACCTCGAGAAACATAAAGAAAAAAGAATCCATTGACAAAAAAAGTTCATTTAT
* *
13902 AGTCACCCATGT-CTTCGAAAGCCTTATTACTCGC
129 AGTAACACAT-TCCTTCGAAAGCCTTATTACTCGC
13936 TTTNNNNNNN
Statistics
Matches: 138, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
169 54 0.39
170 48 0.35
171 36 0.26
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (171 bp):
TTTTATAACCCCATAATTGATTTTAAGTTGAATTTTCTTATATTTTTTATTAAAACAGATTATAA
TTGAATGTTTACCTCGAGAAACATAAAGAAAAAAGAATCCATTGACAAAAAAAGTTCATTTATAG
TAACACATTCCTTCGAAAGCCTTATTACTCGCATTAAATAG
Found at i:17462 original size:171 final size:170
Alignment explanation
Indices: 17033--17751 Score: 728
Period size: 171 Copynumber: 4.2 Consensus size: 170
17023 NNATAATATG
* * * * *
17033 TTTTAAT-AAAAATATAAAAAATTTTAAATTAAAATCAAGTATGAGGTTATAAAATCAGTTAAAG
1 TTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAACTATGAGGTTATAAAATCATTTAAAC
** * * * * * *
17097 ATAGTAATAAAGCTTTCGAAAGCATAGGTGACTATAAATGGACTTTTCTTACCGAA-GGATATCT
66 CGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCC-AATGGATATCT
* ** * *
17161 TTTTCTTCATGTTTCTCGAGCCAGATATTCAATTACAATCTA
130 ATTTCTTCATGTTTCTCGAGATA-ACATTCAATTATAATCTA
** * * ****
17203 TTTTAAGGAAAATTATAAAAAAATTCAAATTAAAATCAATTATGAGGTTATAAAATCATTTNNNN
1 TTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAACTATGAGGTTATAAAATCATTTAAAC
****** * * * *
17268 NNNNNNATAAAGCTTTTGAAGGTATGAGTGACTATAAATGGACTTTTCTTACCAATGGATATATA
66 CGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTA
* *
17333 TTTCTTCACGTTTCTCGAGATAGACATTTAATTATAATCTA
131 TTTCTTCATGTTTCTCGAGATA-ACATTCAATTATAATCTA
* * **********
17374 TTTTAATAAAAAATATAAAAAAATTAAAATTAAAATTANNNNNNNNNNTATAAAAAT-ATTTAAA
1 TTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAACTATGAGGTTAT-AAAATCATTTAAA
* * * *
17438 CCGAGTAATAAGGCTTTCGAAGGTATGGGTTACTACAAAAGGACTTTTCTTGCCAATGGATATCT
65 CCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCT
* * *
17503 -TTTCTTCATGTTTCTCAAGGAAAAGATTCAATTATAATCTA
130 ATTTCTTCATGTTTCTCGA-GATAACATTCAATTATAATCTA
* * *
17544 ATTTAATAAAAAATATAAAAAAATTCAAATCAAAATCAACTATGAGGTTATAAAATCATTTAAAG
1 TTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAACTATGAGGTTATAAAATCATTTAAAC
* * * *
17609 TGAGTAATAGAGG-TTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCGAATGGATATCG
66 CGAGTAATA-AGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCT
* * *
17673 ATTTCTTCATGTTTCCCGAGGTAAGCATTCAATTATAATCTG
130 ATTTCTTCATGTTTCTCGAGATAA-CATTCAATTATAATCTA
*
17715 TTTTAATAAAAAATATAAAAACATTCAAATTAAAATC
1 TTTTAATAAAAAATATAAAAAAATTCAAATTAAAATC
17752 NNNNNNNNNN
Statistics
Matches: 442, Mismatches: 99, Indels: 15
0.79 0.18 0.03
Matches are distributed among these distances:
169 5 0.01
170 139 0.31
171 293 0.66
172 5 0.01
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.34
Consensus pattern (170 bp):
TTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAACTATGAGGTTATAAAATCATTTAAAC
CGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTA
TTTCTTCATGTTTCTCGAGATAACATTCAATTATAATCTA
Found at i:17581 original size:341 final size:332
Alignment explanation
Indices: 17099--17750 Score: 770
Period size: 341 Copynumber: 1.9 Consensus size: 332
17089 AGTTAAAGAT
* *
17099 AGTAATAAAGCTTTCGAAAGCATAGGTGACTATAAATGGACTTTTCTTACCGAAGGATATCTTTT
1 AGTAATAAAGCTTTCGAAAGCATAGGTGACTACAAAAGGACTTTTCTTACCGAAGGATATCTTTT
* * * * * * *
17164 TCTTCATGTTTCTCGAGCCAGATATTCAATTACAATCTATTTTAAGGAAAATTATAAAAAAATTC
66 TCTTCATGTTTCTCAAGCAAAAGATTCAATTACAATCTAATTTAAGAAAAAATATAAAAAAATTC
* * ********** *
17229 AAATTAAAATCAATTATGAGGTTATAAAATCATTTNNNNNNNNNNATAAAGCTTTTGAAGGTATG
131 AAATCAAAATCAACTATGAGGTTATAAAATCATTTAAAGTGAGTAATAAAGCTTTTGAAGGCATG
* *
17294 AGTGACTATAAATGGACTTTTCTTACCAATGGATATATATTTCTTCACGTTTCTCGAGAT-AGAC
196 AGTGACTATAAATGGACTTTTCTTACCAATGGATATAGATTTCTTCACGTTTCCCGAGATAAG-C
*
17358 ATTTAATTATAATCTATTTTAATAAAAAATATAAAAAAATTAAAATTAAAATTANNNNNNNNNNT
260 ATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAATTAAAATTAAAATTA----------T
17423 ATAAAAATATTTAAACCG
315 ATAAAAATATTTAAACCG
* * * * * *
17441 AGTAATAAGGCTTTCGAAGGTATGGGTTACTACAAAAGGACTTTTCTTGCC-AATGGATATC-TT
1 AGTAATAAAGCTTTCGAAAGCATAGGTGACTACAAAAGGACTTTTCTTACCGAA-GGATATCTTT
* * *
17504 TTCTTCATGTTTCTCAAGGAAAAGATTCAATTATAATCTAATTTAATAAAAAATATAAAAAAATT
65 TTCTTCATGTTTCTCAAGCAAAAGATTCAATTACAATCTAATTTAAGAAAAAATATAAAAAAATT
* *
17569 CAAATCAAAATCAACTATGAGGTTATAAAATCATTTAAAGTGAGTAATAGAGGTTTTGAAGGCAT
130 CAAATCAAAATCAACTATGAGGTTATAAAATCATTTAAAGTGAGTAATAAAGCTTTTGAAGGCAT
* * * * * *
17634 GGGTGACTATAAATGGACTTTTCTTGCGAATGGATATCGATTTCTTCATGTTTCCCGAGGTAAGC
195 GAGTGACTATAAATGGACTTTTCTTACCAATGGATATAGATTTCTTCACGTTTCCCGAGATAAGC
* * *
17699 ATTCAATTATAATCTGTTTTAATAAAAAATATAAAAACATTCAAATTAAAAT
260 ATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAATTAAAATTAAAAT
17751 CNNNNNNNNN
Statistics
Matches: 263, Mismatches: 45, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
341 211 0.80
342 52 0.20
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.34
Consensus pattern (332 bp):
AGTAATAAAGCTTTCGAAAGCATAGGTGACTACAAAAGGACTTTTCTTACCGAAGGATATCTTTT
TCTTCATGTTTCTCAAGCAAAAGATTCAATTACAATCTAATTTAAGAAAAAATATAAAAAAATTC
AAATCAAAATCAACTATGAGGTTATAAAATCATTTAAAGTGAGTAATAAAGCTTTTGAAGGCATG
AGTGACTATAAATGGACTTTTCTTACCAATGGATATAGATTTCTTCACGTTTCCCGAGATAAGCA
TTCAATTATAATCTATTTTAATAAAAAATATAAAAAAATTAAAATTAAAATTATATAAAAATATT
TAAACCG
Found at i:19885 original size:170 final size:171
Alignment explanation
Indices: 19552--19886 Score: 415
Period size: 170 Copynumber: 2.0 Consensus size: 171
19542 NNNNNNTAAA
* *
19552 CTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTGCCATAAGAAACATAAAGAAAA
1 CTTTTTTATATTTTTTATTAAAACAGATTACAATTGAATGTCTACCATAAGAAACATAAAGAAAA
* * * * *
19617 AGATATCCATTGATAAGAAAAGTCTATTTATAGACACCGATACCTTTGAAAGCCTTATTACTCGC
66 AGAAATCCATGGATAAGAAAAGTCTATTTATAGACACCCATACCTTCGAAAGCCATATTACTCGC
**********
19682 TCTAAATAGTTTTTTNNNNNNNNNNTTAATTTTAAGTTGAT
131 TCTAAATAGTTTTTTAATCTCATAATTAATTTTAAGTTGAT
* * * *
19723 CTTTTTTATATTTTTTATTGAAACAGATTGCAATTGAATGTCTACCTTAAGAAACTTAAAGAAAA
1 CTTTTTTATATTTTTTATTAAAACAGATTACAATTGAATGTCTACCATAAGAAACATAAAGAAAA
* *
19788 A-AAATCCATGGATAAGAAAAGAT-TTTTTATAGTCACCCA-AGCCTTCGAAAGCCATATTACTC
66 AGAAATCCATGGATAAGAAAAG-TCTATTTATAGACACCCATA-CCTTCGAAAGCCATATTACTC
*
19850 GCTTTAAATAGTTTTTTAATCTCATAATTAATTTTAA
129 GCTCTAAATAGTTTTTTAATCTCATAATTAATTTTAA
19887 TTTAAAATTN
Statistics
Matches: 138, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
169 1 0.01
170 76 0.55
171 61 0.44
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.37
Consensus pattern (171 bp):
CTTTTTTATATTTTTTATTAAAACAGATTACAATTGAATGTCTACCATAAGAAACATAAAGAAAA
AGAAATCCATGGATAAGAAAAGTCTATTTATAGACACCCATACCTTCGAAAGCCATATTACTCGC
TCTAAATAGTTTTTTAATCTCATAATTAATTTTAAGTTGAT
Found at i:21501 original size:169 final size:161
Alignment explanation
Indices: 21195--21516 Score: 346
Period size: 169 Copynumber: 2.0 Consensus size: 161
21185 NNNNNNNAAC
* * * *
21195 TTTTTTATATTTTTTATTAAAATATATTATAATTGAATGTCTGTCTTGAGAAAAGTAAAGAAAAA
1 TTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTAAGAAAAGTAAAGAAAAA
* * ** * *
21260 GATATCTATTGGTAAGAAAAGTTCTTTTATAGTCATTCATACCTTCGAAACCTTTATAACTTGCT
66 GACATCCATTGGTAAGAAAAGTTCTTTTATAGTCACCCAGACCTTCGAAACCTTTATAACTCGCT
21325 GTAAATAGTTTTTTAATCTCATAANNNNNNNNNNTTTAAAA
131 GTAAATAGTTTTTTAATCTCATAA----------TTTAAAA
* *
21366 TTTTTTATATTTTTTATTAAAACAGATTATCATTGAATGTTTGCCTTAAGAAACA-TAAA-AAAA
1 TTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTAAGAAA-AGTAAAGAAAA
* * * * *
21429 A-ACATCCATTGGTAAGAAATGTTTTTTTATAGTTACCCAGGCCTTCGAAAGCC-TTATTACTCG
65 AGACATCCATTGGTAAGAAAAGTTCTTTTATAGTCACCCAGACCTTCGAAA-CCTTTATAACTCG
*
21492 CTTTAAATAGTTTTTTAATCTCATA
129 CTGTAAATAGTTTTTTAATCTCATA
21517 NNNNNNNNNN
Statistics
Matches: 131, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
169 72 0.55
170 7 0.05
171 51 0.39
172 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.41
Consensus pattern (161 bp):
TTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTGCCTTAAGAAAAGTAAAGAAAAA
GACATCCATTGGTAAGAAAAGTTCTTTTATAGTCACCCAGACCTTCGAAACCTTTATAACTCGCT
GTAAATAGTTTTTTAATCTCATAATTTAAAA
Found at i:28718 original size:171 final size:172
Alignment explanation
Indices: 28417--28834 Score: 482
Period size: 171 Copynumber: 2.4 Consensus size: 172
28407 NNNNNNNNNN
* * *
28417 AGATTATAATTAAATGTCTGCCTTAAGAAACATGAAGAAAAAGATATCCATTGGAAAGAAAAGTC
1 AGATTATAATTGAATGTCTGCCTTAAGAAACATAAAGAAAAAGATATCCATTGGCAAGAAAAGTC
* * * * * * *
28482 TATTTCTAGTCACCCATGCCTTCGAAAGCCATATTACTTCCTTTAAATAGTTTTTTAATCTCATA
66 CATTTCTAGTCACCCATGCCTTCAAAAGCCATATCACTTCCTCTAAATAATTTTATAACCTCATA
* *
28547 A-TTAGTTTTAAGTTAAATTTTTTTAT-CTTTTTTATTAAAAC
131 ACTGA-TTTTAAGTTAAATTTTTTTATACTTTTTTACTAAAAC
* * * *
28588 AGATTATAATTGAATGTCTACCTTAAGAAACGTTAAGAAGAAGATATCCATTGGCAAGAAAAGTC
1 AGATTATAATTGAATGTCTGCCTTAAGAAACATAAAGAAAAAGATATCCATTGGCAAGAAAAGTC
********** **
28653 CANNNNNNNNNNCCCATGCCTTCAAAAGCTTTATCAC-TCGCTCTAAATAATTTTATAACCTCAT
66 CATTTCTAGTCACCCATGCCTTCAAAAGCCATATCACTTC-CTCTAAATAATTTTATAACCTCAT
* * *
28717 AACTGATTTTAATTTAAATTTTTTTATATTTTTTTACTAAAAT
130 AACTGATTTTAAGTTAAATTTTTTTATACTTTTTTACTAAAAC
* * *
28760 AGATTACAATTGAATGTCTGCCTCAAGAAACATAAAGAAAAAGATATCTATTGGCAAGAAAAGTC
1 AGATTATAATTGAATGTCTGCCTTAAGAAACATAAAGAAAAAGATATCCATTGGCAAGAAAAGTC
*
28825 CATTTATAGT
66 CATTTCTAGT
28835 AACCNNNNNN
Statistics
Matches: 199, Mismatches: 45, Indels: 5
0.80 0.18 0.02
Matches are distributed among these distances:
170 2 0.01
171 123 0.62
172 74 0.37
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.35
Consensus pattern (172 bp):
AGATTATAATTGAATGTCTGCCTTAAGAAACATAAAGAAAAAGATATCCATTGGCAAGAAAAGTC
CATTTCTAGTCACCCATGCCTTCAAAAGCCATATCACTTCCTCTAAATAATTTTATAACCTCATA
ACTGATTTTAAGTTAAATTTTTTTATACTTTTTTACTAAAAC
Found at i:33472 original size:172 final size:168
Alignment explanation
Indices: 32982--33505 Score: 539
Period size: 171 Copynumber: 3.1 Consensus size: 168
32972 NNNNNNNAAT
* *
32982 AAATATAAAAAAGTTCAACTTAAAATTAATTATAAGATTAAAAAACTATTTCAAGCAAGTAATAA
1 AAATATAAAAAAATTCAACTTAAAATCAATTATAAGATTAAAAAACTATTT-AAGCAAGTAATAA
* * *
33047 GGCTTTCGAAGGCATGGGTGACTATAAATGCACTTTGTTTACCAATGGATATCTTTTTCTTTACG
65 GGCTTTCGAAGGCATGGGTGACTATAAATGGACTTT-CTTGCCAATGGATATC-TTTTCTTTACG
*
33112 TTTCTCAAAGCAGACATTCAATTATAATATGTTTTAATAAA
128 TTTCTCAAGGCAGACATTCAATTATAATATGTTTTAATAAA
********** * * * *
33153 AAANNNNNNNNNNTTTAACTTAAAA-CTAATTATGAGATTAAAAAACTATTTATAGCAAGGAGTA
1 AAATATAAAAAAATTCAACTTAAAATC-AATTATAAGATTAAAAAACTATTTA-AGCAAGTAATA
* * * *
33217 AGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCGATGGATATCTATTTCTTCAT
64 AGGCTTTCGAAGGCATGGGTGACTATAAATGGAC-TTTCTTGCCAATGGATATCT-TTTCTTTAC
** *
33282 GTTTCTCAAGATAGACATTCAATTATAATGTGTTTTAATAAA
127 GTTTCTCAAGGCAGACATTCAATTATAATATGTTTTAATAAA
* * * *
33324 AAATATAAAACAAAATCAACTTAAAATCAATTATAAGGTTATAAAAA-TATTTAAGGCGAGTTAT
1 AAATATAAAA-AAATTCAACTTAAAATCAATTATAAGATTA-AAAAACTATTTAA-GCAAGTAAT
* * ** *
33388 AAGGCTTTTGAAGGCATGGGTGATTATAAATGGACTTATCCCGCCAATGGATACCATTTTCTTTA
63 AAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTT-TCTTGCCAATGGATATC-TTTTCTTTA
* ** * * *
33453 CGTTTTTTGAGGCAGACATTTAATTATAATCTGTATTAATAAA
126 CGTTTCTCAAGGCAGACATTCAATTATAATATGTTTTAATAAA
*
33496 AAATGTAAAA
1 AAATATAAAA
33506 NNNNNNNNNN
Statistics
Matches: 281, Mismatches: 62, Indels: 19
0.78 0.17 0.05
Matches are distributed among these distances:
170 2 0.01
171 142 0.51
172 130 0.46
173 7 0.02
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.34
Consensus pattern (168 bp):
AAATATAAAAAAATTCAACTTAAAATCAATTATAAGATTAAAAAACTATTTAAGCAAGTAATAAG
GCTTTCGAAGGCATGGGTGACTATAAATGGACTTTCTTGCCAATGGATATCTTTTCTTTACGTTT
CTCAAGGCAGACATTCAATTATAATATGTTTTAATAAA
Found at i:37156 original size:171 final size:169
Alignment explanation
Indices: 36860--37378 Score: 628
Period size: 171 Copynumber: 3.0 Consensus size: 169
36850 NNNNNNNNNN
** * * * *
36860 TTAAATGATTTTATAAAGTCATAATTTATTTTAATTTGAATTTATTTTATATATATT-TTAAAAT
1 TTAAATGATTTTATAACCTCATAATTGATTTTAATTTGAATTT-TTTTATATTTTTTATTAAAAC
* * * *
36924 AGATTATAATTGAATGTCTGCCTTAAGAAATGTGAAGAAAAAGATATCCATTGATAAGAAAAGTC
65 AGATTATAATTGAATGTTTACCTTGAGAAATGTGAAG-AAAAGATATCCATTG-CAAGAAAAGTC
*
36989 CATTTATAGTCACCCATACCTTCAAAAGCTTTATTACTCGCT
128 CATTTATAGTCACCCATGCCTTCAAAAGCTTTATTACTCGCT
37031 TTAAATGATTTTATAACCTCATAATTGATTTTAATTTGAATTTTTTTATATTTTTTATTAAAACA
1 TTAAATGATTTTATAACCTCATAATTGATTTTAATTTGAATTTTTTTATATTTTTTATTAAAACA
* * * * *
37096 TATTATAATTGTATGTTTACCATGGGAAATGTGAAGAAATAGATATCCGTTCGCAAGAAAAGTCC
66 GATTATAATTGAATGTTTACCTTGAGAAATGTGAAGAAA-AGATATCCATT-GCAAGAAAAGTCC
* * *
37161 ATTTATAGTCACTCTTGCCTTTAAAAGCTTTATTACTCGCT
129 ATTTATAGTCACCCATGCCTTCAAAAGCTTTATTACTCGCT
********** *
37202 TTAAANNNNNNNNNNACCTCATAATTGATTTTAATTTGAATTTTTTTTGTATTTTTTATTAAAAC
1 TTAAATGATTTTATAACCTCATAATTGATTTTAATTTGAA-TTTTTTTATATTTTTTATTAAAAC
* * *
37267 AGATTATAATTAAATCTTTTCCTTGAGAAATGTGAAGAAAAGATATCCATTGGCAAGAAAAGTCC
65 AGATTATAATTGAATGTTTACCTTGAGAAATGTGAAGAAAAGATATCCATT-GCAAGAAAAGTCC
* * *
37332 ATTTATAGT-ACCCCATGCCTTCGAAAGCCTTATTACTCACT
129 ATTTATAGTCA-CCCATGCCTTCAAAAGCTTTATTACTCGCT
37373 TTAAAT
1 TTAAAT
37379 ACTNNNNNNN
Statistics
Matches: 297, Mismatches: 46, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
170 15 0.05
171 225 0.76
172 57 0.19
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.40
Consensus pattern (169 bp):
TTAAATGATTTTATAACCTCATAATTGATTTTAATTTGAATTTTTTTATATTTTTTATTAAAACA
GATTATAATTGAATGTTTACCTTGAGAAATGTGAAGAAAAGATATCCATTGCAAGAAAAGTCCAT
TTATAGTCACCCATGCCTTCAAAAGCTTTATTACTCGCT
Found at i:38249 original size:171 final size:158
Alignment explanation
Indices: 38067--38383 Score: 330
Period size: 170 Copynumber: 1.9 Consensus size: 158
38057 ATGCCTTCAA
**********
38067 AAGCCTTATTACTAGATTTAAATGATTTTATAA-CGTCATAATTGATTTTAATNNNNNNNNNNTT
1 AAGCCTTATTACTAGATTTAAATGATTTTATAAGC-TCATAATTGATTTTAATTTTAATTTTTTT
* * *
38131 ATATTTTTTATTAAAACAGATTATAATTGAATGTTAACCTTGGGAAACGTGAAGAAAAAGATATG
65 ATA-TTTTTATTAAAACAGATTATAATTGAATGTTAACCTCGGGAAACATGAAGAAAAAGATATC
38196 CATTGGCAAGAAAAGTCCATTTATAGTCAC
129 CATTGGCAAGAAAAGTCCATTTATAGTCAC
* * * *
38226 NNNNNNNNNNNNAAGCTTTATTACTCGCTTTAAATGATTTTATAAGCTCATAATTTATTTTAATT
1 ------------AAGCCTTATTACTAGATTTAAATGATTTTATAAGCTCATAATTGATTTTAATT
* *
38291 TTAATTTTTTTATATTTTTATTAAAACAGATTATAATTTAATGTTTACCTCGGGAAACATGAAGA
54 TTAATTTTTTTATATTTTTATTAAAACAGATTATAATTGAATGTTAACCTCGGGAAACATGAAGA
38356 AAAAGATATCCATTGGCAAGAAAAGTCC
119 AAAAGATATCCATTGGCAAGAAAAGTCC
38384 NNNNNNNNNN
Statistics
Matches: 126, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
170 74 0.59
171 51 0.40
172 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.36
Consensus pattern (158 bp):
AAGCCTTATTACTAGATTTAAATGATTTTATAAGCTCATAATTGATTTTAATTTTAATTTTTTTA
TATTTTTATTAAAACAGATTATAATTGAATGTTAACCTCGGGAAACATGAAGAAAAAGATATCCA
TTGGCAAGAAAAGTCCATTTATAGTCAC
Found at i:38295 original size:16 final size:16
Alignment explanation
Indices: 38276--38308 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
38266 TATAAGCTCA
38276 TAATTTATTTTA-ATTT
1 TAATTT-TTTTATATTT
38292 TAATTTTTTTATATTT
1 TAATTTTTTTATATTT
38308 T
1 T
38309 TATTAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TAATTTTTTTATATTT
Found at i:42114 original size:171 final size:171
Alignment explanation
Indices: 41930--42320 Score: 437
Period size: 171 Copynumber: 2.3 Consensus size: 171
41920 NNNNNNNNNN
* * * * * *
41930 ACCTTAAGAAACGTTAGGAAAAAGATATCCATTAGG-AAAAAAAGTCTATTTATACACACCGATG
1 ACCTTGAGAAACGTGAAGAAAAAGATATCCATT-GGCAAGAAAAGTCCATTTATACACACCCATG
* * *
41994 CCTTCAAAAGCCTTATTACTAGCTTCAAAAGATTTTATAACGTTATAATTTATTTTAATTTTAAT
65 CCTTCAAAAGCCTTATTACTAGCTTCAAAAGATTTTATAACGTCATAATTTATTTCAATTTGAAT
*
42059 GT-TTTTATATTTTTTATTAAAATAGATTATAATGGAATGGT-T
130 GTATTTTATATATTTT-TTAAAATAGATTATAATGGAAT-GTCT
* **********
42101 ACCTTGGGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCNNNNNNNNNNACCCATGC
1 ACCTTGAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATACACACCCATGC
* * * * * * *
42166 CTTTAAAAGCTTTATTACTCGCTTTAAATGATTTTATAAGGTCATAATTTATTTCAATTTGAATT
66 CTTCAAAAGCCTTATTACTAGCTTCAAAAGATTTTATAACGTCATAATTTATTTCAATTTGAATG
*
42231 TATTTTATATATTTTTTAAAATAGATTATAATTGAATGTCT
131 TATTTTATATATTTTTTAAAATAGATTATAATGGAATGTCT
** * *
42272 GTCTTGAGAAACGTGAAGAAAAATATATCCATTGGTAAGAAAAGTCCAT
1 ACCTTGAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCAT
42321 NNNNNNNNNN
Statistics
Matches: 181, Mismatches: 36, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
170 4 0.02
171 165 0.91
172 12 0.07
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.36
Consensus pattern (171 bp):
ACCTTGAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATACACACCCATGC
CTTCAAAAGCCTTATTACTAGCTTCAAAAGATTTTATAACGTCATAATTTATTTCAATTTGAATG
TATTTTATATATTTTTTAAAATAGATTATAATGGAATGTCT
Found at i:42354 original size:171 final size:159
Alignment explanation
Indices: 41994--42465 Score: 381
Period size: 171 Copynumber: 2.8 Consensus size: 159
41984 CACACCGATG
* * * * *
41994 CCTTCAAAAGCCTTATTACTAGCTTCAAAAGATTTTATAACGTTATAATTTATTTTAATTTTAAT
1 CCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTATAA-GTCATAATTTATTTTAATTTAAAT
* * * *
42059 GTTTTTATATTTTTTATTAAAATAGATTATAATGGAATGGTTACCTTGGGAAACGTGAAGAAAAA
65 TTTTTTATA-TTTTT-TTAAAATAGATTATAATTGAAT-GTTGCCTTGAGAAACGTGAAGAAAAA
** *
42124 GATATCCATTGGCAAGAAAAGTCCNNNNNNNNNNACCCATG
127 GATATCCATTGGCAAGAAAAGTCC--------ATACCCATA
* * * *
42165 CCTTTAAAAGCTTTATTACTCGCTTTAAATGATTTTATAAGGTCATAATTTATTTCAATTTGAAT
1 CCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTATAA-GTCATAATTTATTTTAATTTAAAT
*
42230 TTATTTTATATATTTTTTAAAATAGATTATAATTGAATGTCTGTCTTGAGAAACGTGAAGAAAAA
65 TT-TTTTATAT-TTTTTTAAAATAGATTATAATTGAATGT-TGCCTTGAGAAACGTGAAGAAAAA
* * **
42295 TATATCCATTGGTAAGAAAAGTCCATNNNNNNNNNNCCATA
127 GATATCCATTGGCAAGAAAAGTCCAT--------ACCCATA
* * * * * *
42336 CGTTCGAAAGCCTTATTACTCGCTTTAAAT-AGTTTTTTAA-TCCTATAGTTAGTTTTAAGTTAA
1 CCTTCAAAAGCCTTATTACTCGCTTTAAATGA-TTTTATAAGTCATA-ATTTA-TTTTAATTTAA
* * * *
42399 ACTTTTTTATATTTTTTAATAAAACAGATTATAATTGAATGTTTGCCTTGAGAAACATAAAGAAA
63 ATTTTTTTATATTTTTT--TAAAATAGATTATAATTGAATG-TTGCCTTGAGAAACGTGAAGAAA
42464 AA
125 AA
42466 NNNNNNNNNN
Statistics
Matches: 248, Mismatches: 36, Indels: 34
0.78 0.11 0.11
Matches are distributed among these distances:
169 9 0.04
170 15 0.06
171 212 0.85
172 12 0.05
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.38
Consensus pattern (159 bp):
CCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTATAAGTCATAATTTATTTTAATTTAAATT
TTTTTATATTTTTTTAAAATAGATTATAATTGAATGTTGCCTTGAGAAACGTGAAGAAAAAGATA
TCCATTGGCAAGAAAAGTCCATACCCATA
Found at i:43596 original size:171 final size:169
Alignment explanation
Indices: 43079--43766 Score: 662
Period size: 171 Copynumber: 4.0 Consensus size: 169
43069 AATAGAAAAA
* * * * * * * *
43079 AAAAGTCTATTTATAGACACCGATGCCTTCAAAACCCTTATTACTAGCTTTAAATGATTTTATAA
1 AAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCTTTATTACTCGCTTTAAAT-ATTTTTTAA
* ***********
43144 CCTCATAATTGATTTTAATTTCAANNNNNNNNNNNTTTTTATTAAAATAGATTATAATTGAATGT
65 CCTCATAATT-ATTTTAATTTGAATTTTTTTATAATTTTTATTAAAATAGATTATAATTGAATGT
* * *
43209 TTGCCTT-AGGAAACATGAAGAAAAGGATATCCATTGGCAAA
129 CTGCCTTGA-GAAACATGAAGAAAAAGATATCCATTGGCAAG
* * * *********
43250 AAAAGTCCAATTATAGTCACTCATGCCTTCAAAAGCTTTATTACTCGCTTTANNNNNNNNNNTAA
1 AAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCTTTATTACTCGCTTTA-AATATTTTTTAA
* * * *
43315 GCTCATAATTTATTTTAATTTGAATTTTGTTAT-ATTTTT-TTAAAATAAATTATAATTAAATGT
65 CCTCATAA-TTATTTTAATTTGAATTTTTTTATAATTTTTATTAAAATAGATTATAATTGAATGT
**********
43378 CTGCCTTGAGAAACATGAAGAAAAAGATNNNNNNNNNNAAG
129 CTGCCTTGAGAAACATGAAGAAAAAGATATCCATTGGCAAG
* *
43419 AAAAGTCCATTTATTGTCACCCATACCTTTAAAAGCTTTATTACTCGCTTTAAATGATTTTTTAA
1 AAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCTTTATTACTCGCTTTAAAT-ATTTTTTAA
* *
43484 CCTCATAATTGAATTTAATTTGAATTTTTTTATAATTTTTATTAAAATAGATTATAATTGAATAT
65 CCTCATAATT-ATTTTAATTTGAATTTTTTTATAATTTTTATTAAAATAGATTATAATTGAATGT
* *
43549 CTGGCTCGAGAAACATGAAGAAAAAGATATCCATTGGCAAG
129 CTGCCTTGAGAAACATGAAGAAAAAGATATCCATTGGCAAG
* * * * *
43590 AAAAGTCCATTTATAGTCACCCAAACGTTCGAAAGCCTTATTACTTGCTTTAAATAGTTTTTTAA
1 AAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCTTTATTACTCGCTTTAAATA-TTTTTTAA
* * * *
43655 TCTCATAATTAGTTTTAAGTTAAAATTTTTTATAATTTTTATTAAAATAGATTATAATTGAATGT
65 CCTCATAATTA-TTTTAATTTGAATTTTTTTATAATTTTTATTAAAATAGATTATAATTGAATGT
* * * *
43720 CTTCCTTGAGAAATATAAAGAAAAAGATATCCATTGGTAAG
129 CTGCCTTGAGAAACATGAAGAAAAAGATATCCATTGGCAAG
43761 AAAAGT
1 AAAAGT
43767 NNNNNNNNNN
Statistics
Matches: 413, Mismatches: 95, Indels: 18
0.79 0.18 0.03
Matches are distributed among these distances:
168 2 0.00
169 125 0.30
170 14 0.03
171 270 0.65
172 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.37
Consensus pattern (169 bp):
AAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCTTTATTACTCGCTTTAAATATTTTTTAAC
CTCATAATTATTTTAATTTGAATTTTTTTATAATTTTTATTAAAATAGATTATAATTGAATGTCT
GCCTTGAGAAACATGAAGAAAAAGATATCCATTGGCAAG
Found at i:44569 original size:171 final size:168
Alignment explanation
Indices: 44111--44577 Score: 415
Period size: 171 Copynumber: 2.7 Consensus size: 168
44101 NNNNNNTATA
* * * **
44111 TTTA-TTATTAAAATAGATTATAATT-ATATGTTTACCTCGAGAAATGTGAGA-AAAAAGATATC
1 TTTATTTATTAAAATAGATTATAATTGA-ATGTCTACCTTGAAAAACATGA-ACAAAAAGATATC
* * * * * * *
44173 CATTAGGAAAAAACGTCTATTTATAGACAACCATGCCTTTAAAAGCCTTATTACTAGCTTGAAAT
64 CATT-GGAGAAAA-GTCTATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAAT
*
44238 GATTTTATAACGTCATAATTGATTTTAATTTGAATGTTTTCAT
127 GATTTTATAACGTAATAATTGATTTTAATTTGAATGTTTT-AT
* * **
44281 TTTGTTTATTAAAATAGATTATAATTGAATGTTTACCTTGGGAAACATGAACAAAAAGATATCCA
1 TTTATTTATTAAAATAGATTATAATTGAATGTCTACCTTGAAAAACATGAACAAAAAGATATCCA
* ****************
44346 TTGGCAAGAAAAGTCCATTTATAGTCACCCNNNNNNNNNNNNNNNNTATTACTCGCTTTAAATGA
66 TTGG--AGAAAAGTCTATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGA
*
44411 TTTTATAA-GCTAATAATTTATTTTAATTTGAAT-TTATT-T
129 TTTTATAACG-TAATAATTGATTTTAATTTGAATGTT-TTAT
* ** *
44450 TCTATATTTTTTAAAATAGATTATAATTGAATGTCTGTCTTGAAAAACATGAAGAAAAAGATATC
1 T-T-TATTTATTAAAATAGATTATAATTGAATGTCTACCTTGAAAAACATGAACAAAAAGATATC
*
44515 CATTGGTAGGAAAAGTCTATTTATAGTCACCCATACCTTCAAAAGCTTTATTACTCGCTTTAA
64 CATTGG-A-GAAAAGTCTATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAA
44578 NNNNNNNNNN
Statistics
Matches: 232, Mismatches: 55, Indels: 19
0.76 0.18 0.06
Matches are distributed among these distances:
169 2 0.01
170 11 0.05
171 213 0.92
172 6 0.03
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.37
Consensus pattern (168 bp):
TTTATTTATTAAAATAGATTATAATTGAATGTCTACCTTGAAAAACATGAACAAAAAGATATCCA
TTGGAGAAAAGTCTATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGATT
TTATAACGTAATAATTGATTTTAATTTGAATGTTTTAT
Done.