Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397733.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1031.0, 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: 39197
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.26
Warning! 11505 characters in sequence are not A, C, G, or T
Found at i:10844 original size:171 final size:169
Alignment explanation
Indices: 10529--11066 Score: 552
Period size: 170 Copynumber: 3.2 Consensus size: 169
10519 NNNNNNNNNN
* * * * * * *
10529 TACTCGTTTTAAATTATTTTATAATCTTATAATTGATTTTAAGTTAAATTTTTTCACTTTTTTTG
1 TACTCGCTTTAAATTGTTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTT-ACATTTTTTA
** * *
10594 TTAAAACAGACAATAATTGAATGTGTACCTCAGGAAA-GATG-AAGAAAAGGCATTCATTG-GCA
65 TTAAAACAGACAATAATTGAATGCCTACCTCAGAAAACG-TGTAA-AAAAGCCATTCATTGAG-A
*
10656 AGAAAAG-TCTATTTATAGTCACCCATTCCTTTAAAAGCCTTAT
127 AGAAAAGTTC-ATTTATAGTCACCCATTCCTTTAAAAGCCCTAT
* * *
10699 TACTCGCTTTATA-TGCTTTTATAAACTCATAATTAATTTTAAGTTGAATTGTTTTACATTTTTC
1 TACTCGCTTTAAATTG-TTTTATAATCTCATAATTAATTTTAAGTTGAATT-TTTTACATTTTTT
* * * *
10763 ATTAAAATAGACTATAATTCAATGCCTATCTCAGAAAACGTGTCAAAAAAGCCATTCATTGAGAA
64 ATTAAAACAGACAATAATTGAATGCCTACCTCAGAAAACGTGT-AAAAAAGCCATTCATTGAGAA
* * **********
10828 GAAAAGTTCGTTTATAGTCACCCATTCCTTCANNNNNNNNNN
128 GAAAAGTTCATTTATAGTCACCCATTCCTTTAAAAGCCCTAT
*
10870 TACTCACTTTAAATTGTTTTATAATCTCATAATTAATTTTAAGTTGAATTTCTTTACATTTTTTA
1 TACTCGCTTTAAATTGTTTTATAATCTCATAATTAATTTTAAGTTGAATTT-TTTACATTTTTTA
* * * * * * *
10935 -TAACACAAACAATAATTGAATGCTTGCCT-TGAGAAACGTGTAAAAAAAACTATTCATTGAGAA
65 TTAAAACAGACAATAATTGAATGCCTACCTCAGA-AAACGTGT-AAAAAAGCCATTCATTGAGAA
* *
10998 -AAAAGTCCACTTATAGTCACCCATTCCTTTAAAAGCCCTAT
128 GAAAAGTTCATTTATAGTCACCCATTCCTTTAAAAGCCCTAT
11039 TACTCGCTTTAAATTGTTTTATAATCTC
1 TACTCGCTTTAAATTGTTTTATAATCTC
11067 NNNNNNNNNN
Statistics
Matches: 297, Mismatches: 61, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
169 57 0.19
170 129 0.43
171 104 0.35
172 7 0.02
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.38
Consensus pattern (169 bp):
TACTCGCTTTAAATTGTTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTACATTTTTTAT
TAAAACAGACAATAATTGAATGCCTACCTCAGAAAACGTGTAAAAAAGCCATTCATTGAGAAGAA
AAGTTCATTTATAGTCACCCATTCCTTTAAAAGCCCTAT
Found at i:13646 original size:170 final size:160
Alignment explanation
Indices: 13470--13782 Score: 326
Period size: 170 Copynumber: 1.9 Consensus size: 160
13460 NNNNNNNNNN
* * * *
13470 TTTTATAATCTCAAAATTTATTTTAAGTTGAATTTTTTTACATGTCTACTTAAAA-AGAATATAA
1 TTTTATAATATCAAAATTGATTTTAAGTAGAA-TTCTTTACATGTCTACTTAAAACAGAATATAA
* *
13534 TTGAATGCCCGCCTTGAGAAACATGTAAAAAAAATC-ATTCATTGAGGAA-AAAAGTCCATTTAT
65 TTGAATGCCCGCCTTGAAAAACATG-AAAAAAAAGCTATTCATT-AGGAATAAAAGTCCATTTAT
13597 AGTCACCCATTCCNNNNNNNNNNTTATTACTCACTTTAAATTG
128 AGTCACCCATTCC----------TTATTACTCACTTTAAATTG
* * * ** *
13640 TTTTATAATATCATAATTGATTTTAAGTAGAATTCTTTACATTTTTTGTTAAAACAGATTATAAT
1 TTTTATAATATCAAAATTGATTTTAAGTAGAATTCTTTACATGTCTACTTAAAACAGAATATAAT
* * * ** *
13705 TGAATGTCTGCCTTGAAAAACATGCAAAAAAAGCTATTCATTTTGAATAAAATTCCATTTATAGT
66 TGAATGCCCGCCTTGAAAAACATGAAAAAAAAGCTATTCATTAGGAATAAAAGTCCATTTATAGT
13770 CACCCATTCCTTA
131 CACCCATTCCTTA
13783 AAAAGCCNNN
Statistics
Matches: 122, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
160 3 0.02
169 28 0.23
170 91 0.75
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.38
Consensus pattern (160 bp):
TTTTATAATATCAAAATTGATTTTAAGTAGAATTCTTTACATGTCTACTTAAAACAGAATATAAT
TGAATGCCCGCCTTGAAAAACATGAAAAAAAAGCTATTCATTAGGAATAAAAGTCCATTTATAGT
CACCCATTCCTTATTACTCACTTTAAATTG
Found at i:15387 original size:170 final size:160
Alignment explanation
Indices: 15157--15477 Score: 342
Period size: 170 Copynumber: 1.9 Consensus size: 160
15147 AAGCGTTATT
* *
15157 ACTCACTTTAAATTGTTTTATAATCTCATAATTAATTTTAAGTTGAAATTTTTTACATTTTTT-A
1 ACTCACTTTAAATGGTTTTATAAACTCATAATTAATTTTAAGTTGAAATTTTTTACATTTTTTGA
** * * * *
15221 TAACGCAAACAATAATTTAATGCCTACCTTGAGAAACGTGCAAAAAAAGCTATTCATTCAG-AAG
66 TAAAACAAACAATAATTGAATACCTACCTTGAGAAACATGAAAAAAAAGC-ATTCATT-AGCAAG
15285 AAAAGTCCATTTATAGTCACCCATTCCTTCAA
129 AAAAGTCCATTTATAGTCACCCATTCCTTCAA
* *
15317 NNNNNNNNNNACTCGCTTTTAATGGTTTTATAAACTCATAATTAATTTTAAGTT-AAATTTTTTA
1 ----------ACTCACTTTAAATGGTTTTATAAACTCATAATTAATTTTAAGTTGAAATTTTTT-
* * * * ** *
15381 ACATTTTTTGTTAAAATAGATAATAATTGAATATTTACCTTGAGAAATATGAAAAAAAAGCATTC
55 ACATTTTTTGATAAAACAAACAATAATTGAATACCTACCTTGAGAAACATGAAAAAAAAGCATTC
*
15446 ATTGGCAAGAAAAGTCCATTTATAGTCACCCA
120 ATTAGCAAGAAAAGTCCATTTATAGTCACCCA
15478 NNNNNNNNNN
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
169 10 0.08
170 82 0.63
171 38 0.29
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.36
Consensus pattern (160 bp):
ACTCACTTTAAATGGTTTTATAAACTCATAATTAATTTTAAGTTGAAATTTTTTACATTTTTTGA
TAAAACAAACAATAATTGAATACCTACCTTGAGAAACATGAAAAAAAAGCATTCATTAGCAAGAA
AAGTCCATTTATAGTCACCCATTCCTTCAA
Found at i:20060 original size:170 final size:154
Alignment explanation
Indices: 19864--20174 Score: 286
Period size: 170 Copynumber: 1.9 Consensus size: 154
19854 NNNNNNNGCG
*
19864 AGTAATAAGGCTTTTTAAGAAATGGGTGACTATAAATGGA-CTATTCTTCACAATGAATAACTTT
1 AGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGATCTATTCTTCACAATGAAT-ACTTT
* * * * *
19928 TTTTGCACGTTTTTCGAGG-TAGATATTCAATTATAATCTCTTTTAACAAAAAATGTAAAAAATT
65 TTTTACACGTTTCTCAAGGCAAG-CATTCAATTATAATCT-TTTTAACAAAAAATGTAAAAAATT
19992 CAACTTAAAANNNNNNNNNNNNNNNTAAAACAATTTAAAGTA
128 CAACTTAAAA---------------TAAAACAATTTAAAGTA
* * * * * **
20034 AGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGATGTTTTTTTCTCAATGAATGGTTTT
1 AGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGATCTATTCTTCACAATGAATACTTTT
* ***
20099 TTTACACGTTTCTCAAGGCAAGCATTCAATTATAGTCTTTTTAACCCTAAATGTAAAAAATTCAA
66 TTTACACGTTTCTCAAGGCAAGCATTCAATTATAATCTTTTTAACAAAAAATGTAAAAAATTCAA
20164 CTTAAAA-AAAA
131 CTTAAAATAAAA
20175 TTTTGATATT
Statistics
Matches: 122, Mismatches: 17, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
153 4 0.03
169 31 0.25
170 71 0.58
171 16 0.13
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.34
Consensus pattern (154 bp):
AGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGATCTATTCTTCACAATGAATACTTTT
TTTACACGTTTCTCAAGGCAAGCATTCAATTATAATCTTTTTAACAAAAAATGTAAAAAATTCAA
CTTAAAATAAAACAATTTAAAGTA
Found at i:23887 original size:170 final size:171
Alignment explanation
Indices: 23308--23925 Score: 483
Period size: 174 Copynumber: 3.6 Consensus size: 171
23298 NNNNNNNNNN
** * * * * * *
23308 GGTAGACATTCAATTATAGTC-ACTTTTAATGAAAAATGT-AAAACATATCAACTTACAGTCAAT
1 GGTAGACATTCAATTATAGTCTA-TTTTAACCAAAAATATAAAAAAAT-TAAACCTAAAATCAAT
* * * * **********
23371 TATGAGATCATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAANNNNNNNNNNACTATAAATG
64 TATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTAAAAGAATGAGAGACTATAAATG
**
23436 GACTTTTCTTGCCAATGAATGCATTTTTCTTCACCTTTCT-T-
129 GACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTCTA
* * * *
23477 GCGATAGACATTTAATTATTATGGTCTATTTAAACCAAAAATATAAAAAAATTCAACTTAAAATC
1 G-G-TAGACATTCAATTA-TA--GTCTATTTTAACCAAAAATATAAAAAAATTAAACCTAAAATC
* * * * **********
23542 AATTTTGTGATTATAAAACCATTTAAAGTTAGTAATAAGNNNNNNNNNNGAATGAGAGACTATAA
61 AATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTAAAAGAATGAGAGACTATAA
* * *
23607 ATGGACTTTTCTTGTCAACGAATGCATTTTTCTTCATGTTCCTCTA
126 ATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTCTA
* * * * * **********
23653 AGTAAAAATTCAATTATAGTCTATTTTAGCCAAAAATGTAAAAAANNNNNNNNNNAAATCAATTA
1 GGTAGACATTCAATTATAGTCTATTTTAACCAAAAATATAAAAAAATTAAACCTAAAATCAATTA
* * * * *
23718 TAAGATTATAAAACAATTTAAAGCGAATAATAAGGCTTTTAAAAGAATGGGTGACTATAAATGGA
66 TGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTAAAAGAATGAGAGACTATAAATGGA
*
23783 TCTTTT-TTGCCAATGAATGC-TTTTTTTTCATGTTTCTCTA
131 -CTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTCTA
* * *
23823 GGTAGACATTCGATTATAGTCTCTTTTATCCAAAAATATAAAAAAATTAAACCTAAAATCAATTA
1 GGTAGACATTCAATTATAGTCTATTTTAACCAAAAATATAAAAAAATTAAACCTAAAATCAATTA
* *
23888 TGAGGTTATAAAGCAATTTAAAGTGAGTAATAAGGCTT
66 TGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTT
23926 NNNNNNNNNN
Statistics
Matches: 341, Mismatches: 98, Indels: 19
0.74 0.21 0.04
Matches are distributed among these distances:
169 1 0.00
170 100 0.29
171 105 0.31
172 7 0.02
173 2 0.01
174 117 0.34
175 9 0.03
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.33
Consensus pattern (171 bp):
GGTAGACATTCAATTATAGTCTATTTTAACCAAAAATATAAAAAAATTAAACCTAAAATCAATTA
TGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTAAAAGAATGAGAGACTATAAATGGA
CTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTCTA
Found at i:26169 original size:170 final size:171
Alignment explanation
Indices: 25424--27246 Score: 1766
Period size: 171 Copynumber: 10.7 Consensus size: 171
25414 NNNNNNNNNN
* *
25424 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCAAGTAATACGGCTTTTGAA
1 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAA
** * * * **
25489 GGAATATGTGACTATAAATGGACTTTT-TTCCTCAATGAATG-GTTTTTTTTACATGTTTCTTAA
66 GGAATGGGTGACTATAAATGGACTTTTCTTGC-CAATGAATGCATTTTTCTT-CATGTTTCTCGA
* * * * *
25552 GGCAGGCATTCAATAATAGTGT-TTTTAACCATAAATGTAAAAAAA
129 GGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT---AAAA
* * * * *
25597 AAAGTCAACTTAAAATAAATTTTG-GTATTATAAAACAATTTCAAA-CGAGTAATAAGGTTTTTA
1 AAATTCAACTTAAAATCAATTATGAG-ATTATAAAACAATTT-AAAGCGAGTAATAAGGCTTTTG
* ** * ** * *
25660 AAGGAATGGGTGATTATAAATAAACTTTTCTTTCCAATGAAT--ACCTTTCTTCATATTTC-CTA
64 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTC-G
* * * *
25722 AGGTAGACATTCAATTATTGTGTGTTTTAACTAGAAATGTAAAA
128 AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAA
* * **********
25766 AAATTTAACTTAAAATCAATTATAAGATTATAAAACAANNNNNNNNNNGTAATAAGGCTTTTGAA
1 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAA
* * * * * *
25831 GGAATGGGTGACTATAAATGAACTTTTCTT-CTCGATG-ATGGC-TTTTTCAAT-ACGTTTTTTG
66 GGAATGGGTGACTATAAATGGACTTTTCTTGC-CAATGAAT-GCATTTTTC-TTCATGTTTCTCG
** * * * * *
25892 AGACAGGCATTGAATTATAGTCTG--TTGACTGAAAAAGGTAAAA
128 AGGTAGACATTCAATTATAGTCTGTTTTAAC-CAAAAATGTAAAA
* * ********* * *
25935 AAATTCAACTGAAAATTAATTATGAG-TNNNNNNNNNNATTTAAAGTGAGTAATAAGTCTTTTGA
1 AAATTCAACTTAAAATCAATTATGAGAT-TATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGA
** * *
25999 AGGAAAAGGTGACTATAAATAGACTTTTCTTACCAAT-AGATGCATTTTT-TTCATGTTTCTCGA
65 AGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGA-ATGCATTTTTCTTCATGTTTCTCGA
* **
26062 GGTAGACATTCAATTATAGCCTGTTTTAATGAAAAATGTAAAA
129 GGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAA
* * * * * *
26105 TAATTTAACTTACAATGAATTATGAGATCATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA
1 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAA
* * ** * *
26170 GGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCACATTTCTTGAGA
66 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTCGAGG
* *
26235 TAGACATTCAATTATTATAGTCTATTTTAACCAAAAATATAAAA
131 TAGACATTC-A--ATTATAGTCTGTTTTAACCAAAAATGTAAAA
* * * ***
26279 AAATTCAACTTAAAATCAATTTTGGGATTATAAAACCATTTAAAGTTTGTAATAAGGCTTTTGAA
1 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAA
* * * * * *
26344 GGAATGGGTGACTATAAATGGACTTTTCTTGTCAACGAATGCATTTTTCGTCACGTTTCTCCAAG
66 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTCGAGG
* *
26409 TAGAAATTCAATTATAGTCTGTTTTAGCCAAAAATGTAAAAA
131 TAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT-AAAA
* *
26451 AAATT-AACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTAAA
1 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAA
* * * * *
26515 AGAATGAGTGACTATAAATGGACCTTTCTTGCCAATGAATGCTTTTTTTTTCATGTTTCTCGAGG
66 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTCGAGG
* * *
26580 TAGACATTCGATTATAGTCTTTTTTACCCAAAAATGTAAAA
131 TAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAA
26621 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAA
1 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAA
* * * * * * * ** * *
26686 GGACTGGGTGACTACAAATGGATTTTTTTTACCGACGAATGTGTTTTTCTTCACGTTTCTC-AAG
66 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTCGAGG
* * * ** *
26750 TAAAAATTCAATTATAGTTTGTTTT-AGTAAAAAGTGTAAAT
131 TAGACATTCAATTATAGTCTGTTTTAACCAAAAA-TGTAAAA
* * *
26791 AAATTCAACTTAGAATCAATTATGAGATTATAAAACAATTTAAAACGAGTAATAGGGCTTTTGAA
1 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAA
* * * * * * * *
26856 TGAATGGGTGACTATAAATTGACTTTTTTTTGTCAACGAATGTATTTTTCTTCATGTTTCTCTAA
66 GGAATGGGTGACTATAAATGGAC-TTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTCGAG
* * *
26921 GTAGAAATTCAATTATAGTATGTTTTAGCCAAAAATGTAAAA
130 GTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAA
* * * * * *
26963 AATTTCAACCTAATATCAATTATGAGATTATAAAATAA-TTAAAGCGAGAAATAGGGCTTTTGAA
1 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAA
* * * * * *
27027 GGAATTGGTGACTATAAATGGACTATTCTTTCCAATCAATGCCTTTTTCTTCACT-TTTCTTGAG
66 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCA-TGTTTCTCGAG
* *
27091 GTAGGCATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAA
130 GTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAA
* * * * * *
27133 AAATTCAACTTAAAATTAATTATAAGTTTATAAAACCATATAAAGTGAGTAATAAGGCTTTTGAA
1 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAA
* * *
27198 GTAATTGGTGACTATAAATGGACTTTTCTT-CTCAATGAATAGCTTTTTT
66 GGAATGGGTGACTATAAATGGACTTTTCTTGC-CAATGAAT-GCATTTTT
27247 TGCACGTTTC
Statistics
Matches: 1346, Mismatches: 266, Indels: 77
0.80 0.16 0.05
Matches are distributed among these distances:
168 9 0.01
169 193 0.14
170 347 0.26
171 455 0.34
172 102 0.08
173 88 0.07
174 152 0.11
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (171 bp):
AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAA
GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTCGAGG
TAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAA
Found at i:31808 original size:51 final size:51
Alignment explanation
Indices: 31745--31892 Score: 206
Period size: 51 Copynumber: 2.9 Consensus size: 51
31735 CATTGGCAAC
* * * *
31745 AAAAGTCTATTTATAGTCACCCGTTCCTTTAAAAGGCTTATTACTCACAAG
1 AAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACTCACAAA
* * *
31796 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAACCTTATTACTCATAAA
1 AAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACTCACAAA
** *
31847 AAAAGTCCATTTATAGTCATTCATTCTTTTAAAAGCCTTATTACTC
1 AAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACTC
31893 GCTTTAAATT
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 85 1.00
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.35
Consensus pattern (51 bp):
AAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACTCACAAA
Found at i:33328 original size:170 final size:170
Alignment explanation
Indices: 33073--33720 Score: 396
Period size: 170 Copynumber: 3.8 Consensus size: 170
33063 TAGACATTTG
* * * * ** * * * * *
33073 ATTATAGTCTATTTGACCCAAAAATATAAGAAAATTCTACTTTGAATCAATTATGAGATAATAAA
1 ATTATAGTCTATTTTAACCAAAAATATAAAAAAATTCAACTTAAAATTAATTTTAAAATTATAAA
** ** * * ** *
33138 AGGATTTAAAGTGAGTAATAAGGTTTTTGAAGGAATGGGTGACCATAAACGG-GTTGTT-TT-CT
66 ATAATTTAAAGCAAGTAATAAGGCTTTTAAAAAAATGGGTGACCATAAACGGACTT-TTCTTGCT
* *
33200 CAATGAATGATTTTTTTTGCATGTTTTTCAAGGCAAACATTCA
130 -AATGAATGATTTTTTTT-CATGTTTCTCAAGGCAAACATACA
*
33243 ATTATAGTCTATTTTAACTAAAAAT-TGAAAAAAAATT-AACTTAAAATTAATTTTAAAATTATA
1 ATTATAGTCTATTTTAACCAAAAATAT--AAAAAAATTCAACTTAAAATTAATTTTAAAATTATA
* *
33306 AAATAATTTAAAGCAAGTAATAAGGCTTTTAAAAAAATGGGTGACTATAAATGGACTTTTCTTGC
64 AAATAATTTAAAGCAAGTAATAAGGCTTTTAAAAAAATGGGTGACCATAAACGGACTTTTCTTGC
* * * * *
33371 TAATGAATGCTTTTTTTTCTTGTTTCTCAAGGTAGACATACG
129 TAATGAATGATTTTTTTTCATGTTTCTCAAGGCAAACATACA
* * * * ***********
33413 ATTATATTTTGTTTTAGCCAAAAATATAAAAAAATTCAACTTAAAATCNNNNNNNNNNTTATAAA
1 ATTATAGTCTATTTTAACCAAAAATATAAAAAAATTCAACTTAAAATTAATTTTAAAATTATAAA
** * * * * * * * **
33478 ATAATTTAAAGTGAGTAATAAGCCTTTTGAAGAAATAGGAGACTATAAATGGACTTTT-TCCCTC
66 ATAATTTAAAGCAAGTAATAAGGCTTTTAAAAAAATGGGTGACCATAAACGGACTTTTCTTGCT-
* * ** *
33542 AATGAATGGCTTTTTTTATACA--TTTCTCAAGGTAGGCATTCA
130 AATGAAT-GATTTTTTT-T-CATGTTTCTCAAGGCAAACATACA
* * * * **********
33584 ATTATAGTCT-TTTTATCCATATATATAAAAAAATTCAACTTAAAATAAANNNNNNNNNNATAAA
1 ATTATAGTCTATTTTAACCAAAAATATAAAAAAATTCAACTTAAAATTAATTTTAAAATTATAAA
* * * * ** * *
33648 ATAATTTAAAGCGAGTAAATAAGCCTTTTAAAAGAATGGGTGACTATAAATAGACTTTTCTTACC
66 ATAATTTAAAGCAAGT-AATAAGGCTTTTAAAAAAATGGGTGACCATAAACGGACTTTTCTTGCT
33713 AATGAATG
130 AATGAATG
33721 CCTTTCTCTT
Statistics
Matches: 386, Mismatches: 79, Indels: 26
0.79 0.16 0.05
Matches are distributed among these distances:
169 13 0.03
170 261 0.68
171 106 0.27
172 5 0.01
173 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.35
Consensus pattern (170 bp):
ATTATAGTCTATTTTAACCAAAAATATAAAAAAATTCAACTTAAAATTAATTTTAAAATTATAAA
ATAATTTAAAGCAAGTAATAAGGCTTTTAAAAAAATGGGTGACCATAAACGGACTTTTCTTGCTA
ATGAATGATTTTTTTTCATGTTTCTCAAGGCAAACATACA
Found at i:34355 original size:170 final size:166
Alignment explanation
Indices: 33832--34606 Score: 640
Period size: 171 Copynumber: 4.5 Consensus size: 166
33822 NNNNNNNNNN
* * * *
33832 AAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAACGAATGCGTTTTTCTTCATGTTTCTCCT
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAACTAATG-TTTTTTCTTCATGTTTCT-CA
*
33897 AGTAGAAATTCAATTATAGTATGTTTTAGCCAAAAATGTAAAAATATTTAACTTAAAATCAATTA
64 AGTAGAAATTCAATTATAGTATATTTTAG-CAAAAATGTAAAAA-ATTTAACTTAAAATCAATTA
********** * *
33962 TGAGATTATANNNNNNNNNNNAGCGAGTAATAAGGCTTTTA
127 TGAGATTATA-AAAAAATTAAAGCGAGTAATAGGGCTTTTG
* * * *
34003 AAAGAATGGGTGACTATAAATGGACCTTTCTTGCTAA-TGAATGCTTTTTTTTTCATGTTTCTCG
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAACT-AATG-TTTTTTCTTCATGTTTCTC-
* * * * *
34067 AGGTA-AACATTCGATTATTGTGTCTTTTAGCAAAAAATGTAAAACAATTTAACTTAAAATCAAT
63 AAGTAGAA-ATTCAATTATAGTATATTTTAGC-AAAAATGTAAAA-AATTTAACTTAAAATCAAT
* * **********
34131 AATGAGATTATAAAACAATTTAAAGCNNNNNNNNNNGCTTTTG
125 TATGAGATTATAAAA-AAATTAAAGCGAGTAATAGGGCTTTTG
34174 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAACTAATGTGTTTTTCTTCATGTTTCTCAA
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAACTAATGT-TTTTTCTTCATGTTTCTCAA
* * * * * * *
34239 GTAAAAATTTAATTATAATCTATTTTAGTAAAAAGTGTAAATAAATTCAAGTTAAAATCAATTAT
65 GTAGAAATTCAATTATAGTATATTTTAGCAAAAA-TGTAAA-AAATTTAACTTAAAATCAATTAT
*********
34304 GAGATTATAANNNNNNNNNNAGCGAGTAATAGGGCTTTTG
128 GAGATTATAA-AAAAATTAAAGCGAGTAATAGGGCTTTTG
* * * * * * *
34344 AAGGAATGGGTGGCTATAAATGGACTTTTCTTACCGACGAATGCATTTTTCTTCACGTTACTCCA
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAACTAATG-TTTTTTCTTCATGTTTCT-CA
* * *
34409 AGTAGAAATTCAATTATAGTATGTTTTAGCCAAAAATGTAAATAAATTTGACCTAAAATCAATTA
64 AGTAGAAATTCAATTATAGTATATTTTAG-CAAAAATGTAAA-AAATTTAACTTAAAATCAATTA
* * *
34474 TGAGATTATAAAATAATTAAAGTGAGAAATAGGGCTTTTG
127 TGAGATTATAAAAAAATTAAAGCGAGTAATAGGGCTTTTG
* * * * *
34514 AAGGAATTGGTGACTATAAATGGACTATTCTTACC-AGTGAATGCTTTTTTCTTCACT-TTTCTT
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAACT-AATG-TTTTTTCTTCA-TGTTTCTC
* *
34577 AAGGTAGACATTCAATTATAGTCTATTTTA
63 AA-GTAGAAATTCAATTATAGTATATTTTA
34607 ATAAAAAATA
Statistics
Matches: 477, Mismatches: 109, Indels: 37
0.77 0.17 0.06
Matches are distributed among these distances:
169 8 0.02
170 217 0.45
171 245 0.51
172 7 0.01
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.35
Consensus pattern (166 bp):
AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAACTAATGTTTTTTCTTCATGTTTCTCAAG
TAGAAATTCAATTATAGTATATTTTAGCAAAAATGTAAAAAATTTAACTTAAAATCAATTATGAG
ATTATAAAAAAATTAAAGCGAGTAATAGGGCTTTTG
Found at i:34596 original size:341 final size:331
Alignment explanation
Indices: 33832--34613 Score: 707
Period size: 341 Copynumber: 2.3 Consensus size: 331
33822 NNNNNNNNNN
* ** * * *
33832 AAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAACGAATGCGTTTTTCTTCATGTTTCTCCT
1 AAGGAATGGGTGACTATAAATGGACTATTCTTACCAACTAATGTGTTTTTCTTCATGTTTCT-CA
* * * * ** * *
33897 AGTAGAAATTCAATTATAGTATGTTTTAGCCAAAAA-TGTAAA-AATATTTAACTTAAAATCAAT
65 AGTAAAAATTCAATTATAATCTATTTTA-ATAAAAAGTGTAAATAA-ATTCAAGTTAAAATCAAT
*
33960 TATGAGATTATANNNNNNNNNNNAGCGAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATG
128 TATGAGATTATA----------AAGCGAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATG
* * * * * * * * * * * *
34025 GACCTTTCTTGCTAATGAATGCTTTTTTTTTCATGTTTCTCGAGGTAAACATTCGATTATTGTGT
183 GACCTTTCTTACCAACGAATGCATTTTTCTTCACGTTACTCCAAGTAAACATTCAATTATAGTAT
*
34090 CTTTTAGCAAAAAATGTAAAACAATTTAACTTAAAATCAATAATGAGATTATAAAACAATTTAAA
248 CTTTTAGCAAAAAATGTAAAACAATTTAACCTAAAATCAATAATGAGATTATAAAACAATTTAAA
**********
34155 GCNNNNNNNNNNGCTTTTG
313 GCGAGAAATAGGGCTTTTG
* *
34174 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAACTAATGTGTTTTTCTTCATGTTTCTCAA
1 AAGGAATGGGTGACTATAAATGGACTATTCTTACCAACTAATGTGTTTTTCTTCATGTTTCTCAA
* *
34239 GTAAAAATTTAATTATAATCTATTTTAGTAAAAAGTGTAAATAAATTCAAGTTAAAATCAATTAT
66 GTAAAAATTCAATTATAATCTATTTTAATAAAAAGTGTAAATAAATTCAAGTTAAAATCAATTAT
* * * *
34304 GAGATTATAANNNNNNNNNNAGCGAGTAATAGGGCTTTTGAAGGAATGGGTGGCTATAAATGGAC
131 GAGATTATAA----------AGCGAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATGGAC
* * *
34369 TTTTCTTACCGACGAATGCATTTTTCTTCACGTTACTCCAAGTAGAA-ATTCAATTATAGTATGT
186 CTTTCTTACCAACGAATGCATTTTTCTTCACGTTACTCCAAGTA-AACATTCAATTATAGTATCT
* * * *
34433 TTTAGCCAAAAATGTAAATA-AATTTGACCTAAAATCAATTATGAGATTATAAAATAA-TTAAAG
250 TTTAGCAAAAAATGTAAA-ACAATTTAACCTAAAATCAATAATGAGATTATAAAACAATTTAAAG
*
34496 TGAGAAATAGGGCTTTTG
314 CGAGAAATAGGGCTTTTG
* *
34514 AAGGAATTGGTGACTATAAATGGACTATTCTTACC-AGTGAATGCT-TTTTTCTTCACT-TTTCT
1 AAGGAATGGGTGACTATAAATGGACTATTCTTACCAACT-AATG-TGTTTTTCTTCA-TGTTTCT
* * * *
34576 TAAGGTAGACATTCAATTATAGTCTATTTTAATAAAAA
63 CAA-GTAAAAATTCAATTATAATCTATTTTAATAAAAA
34614 ATATAAAAAA
Statistics
Matches: 363, Mismatches: 59, Indels: 37
0.79 0.13 0.08
Matches are distributed among these distances:
339 2 0.01
340 71 0.20
341 226 0.62
342 64 0.18
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.35
Consensus pattern (331 bp):
AAGGAATGGGTGACTATAAATGGACTATTCTTACCAACTAATGTGTTTTTCTTCATGTTTCTCAA
GTAAAAATTCAATTATAATCTATTTTAATAAAAAGTGTAAATAAATTCAAGTTAAAATCAATTAT
GAGATTATAAAGCGAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATGGACCTTTCTTACC
AACGAATGCATTTTTCTTCACGTTACTCCAAGTAAACATTCAATTATAGTATCTTTTAGCAAAAA
ATGTAAAACAATTTAACCTAAAATCAATAATGAGATTATAAAACAATTTAAAGCGAGAAATAGGG
CTTTTG
Found at i:39178 original size:170 final size:171
Alignment explanation
Indices: 38807--39197 Score: 437
Period size: 170 Copynumber: 2.3 Consensus size: 171
38797 NNNNNNNNNN
* * * ** * * *
38807 AAATCAATTTTGGGATTATAAAACGATTTAAAGTTAGTAATAAGGCTTTTGAAGGAATGGGTGAC
1 AAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGAA
**
38872 TATAAATGGATTTTTCTTGTCAACGAATGCATTTTTCTTCACGTTTCTCCAAGTAGAAATTCAAT
66 TATAAATGGACCTTTCTTGTCAACGAATGCATTTTTCTTCACGTTTCTCCAAGTAGAAATTCAAT
* * * *
38937 TATAGCCTGTTTTAGCCAAAAAGGTAAAAAAATTTAACTTA
131 TATAGACTCTTTTACCCAAAAAGGTAAAAAAATTCAACTTA
********* *
38978 AAATCAATTATNNNNNNNNNNAAA-AATTTAAAGCGAGTAATAAGGCTTTTTAAAGAATGAGTGA
1 AAATCAATTAT-GAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGA
* * * * * * * *
39042 ATTTAAATGGACCTTTCTTGTCAATGAATGC-TTTTTTTTCATGTTTCTCGAGGTAGACATTCGA
65 ATATAAATGGACCTTTCTTGTCAACGAATGCATTTTTCTTCACGTTTCTCCAAGTAGAAATTCAA
* *
39106 TTATAGACTCTTTTACCCAAAAATGTAAAAAAATTC-AGTCTA
130 TTATAGACTCTTTTACCCAAAAAGGTAAAAAAATTCAACT-TA
39148 AAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTT
1 AAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTT
Statistics
Matches: 175, Mismatches: 42, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
169 5 0.03
170 97 0.55
171 70 0.40
172 3 0.02
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.35
Consensus pattern (171 bp):
AAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGAA
TATAAATGGACCTTTCTTGTCAACGAATGCATTTTTCTTCACGTTTCTCCAAGTAGAAATTCAAT
TATAGACTCTTTTACCCAAAAAGGTAAAAAAATTCAACTTA
Done.