Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403325.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_997.0, 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: 17932
ACGTcount: A:0.29, C:0.09, G:0.10, T:0.28
Warning! 4429 characters in sequence are not A, C, G, or T
Found at i:3178 original size:171 final size:171
Alignment explanation
Indices: 2132--3195 Score: 587
Period size: 171 Copynumber: 6.2 Consensus size: 171
2122 NNNNNNNNNN
* * * *
2132 CATTCCTTTAAAAGCCTTATTACTCGCTTTAAATTATTTTATAATC-CTAAAATTAATTTTAAAT
1 CATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTC-AAAATTGATTTTAAGT
* * * * ** * * * *
2196 TAAATTTTTTTA-ATTTTTTGGTTAAAAGAGACTATAATTGGGTGTC-TGCCTTGATAAACATGT
65 TAAATTTTTTTACA-TTTATAGTCAAAACAGACTATAATTGAAT-TCTTACCTTTAAAAACGTGT
** * *
2259 -AAAAAAAGCTATTCATTGAGAGGAAAAGTCTATTTATGGTCACC
128 AAAAAAAAGC-ATTCATTGAGAAAAAAAGTCCATTTATAGTCACC
* * * *********** *
2303 TATTCCTTCAAAAGCCTTATTACTGGCTTTAAATGGTTTNNNNNNNNNNTAATTAATTTTAAGTT
1 CATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCAAAATTGATTTTAAGTT
* * * * * *** * * * * *
2368 TAATTTTTTTATATTTTTGGTTAAAACCCCCAATAATT-TATTGTTTACC-TCAACAAACAT-TA
66 AAATTTTTTTACATTTATAGTCAAAACAGACTATAATTGAATT-CTTACCTTTAA-AAACGTGTA
* * * *
2430 AACAAAAGGCATTCATT-AGGAAGAAAAA-TCTATTTATAATTACC
129 AA-AAAAAGCATTCATTGA-GAA-AAAAAGTCCATTTATAGTCACC
* **
2474 CATTCCATT-AAAAGACTTATTACTCGCTTTAAATTGTTTTATAATCTCAAAAAGGATTTTAAGT
1 CATTCC-TTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCAAAATTGATTTTAAGT
* * *
2538 TAAATTTTTTTAAATTTATGGTTC-AAACAGACTATAATTGAATGTC-T-GCTTTAAAAATC-TG
65 TAAATTTTTTTACATTTATAG-TCAAAACAGACTATAATTGAAT-TCTTACCTTTAAAAA-CGTG
* * * *
2599 TAAAAAAAAACATTCATTGAGAAAAAGAGTCCATTTATTGTCACT
127 TAAAAAAAAGCATTCATTGAGAAAAAAAGTCCATTTATAGTCACC
** * * *******
2644 CATTCCTTCAAAAGCCTTATTACTCATTTTAAATTCTTTTATAATCTCATAATTGATTNNNNNNN
1 CATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCAAAATTGATTTTAAGTT
*** * * * * * * * * *
2709 NNNTTTTTTTGCATTTTTGGTTATAACAGACTATAATTG-ATTATTTACGTTGAGAAACGTGTAA
66 AAATTTTTTTACATTTATAGTCAAAACAGACTATAATTGAATT-CTTACCTTTAAAAACGTGTAA
* * *
2773 AAAAAAGCTATTCATTGAGAAGAAAAGTCGATTTATGGTCACC
130 AAAAAAGC-ATTCATTGAGAAAAAAAGTCCATTTATAGTCACC
* * * * * * * **
2816 CATTCATTCTAAAGTCTTATTACTCGCTTTACATTATTTTATAATCACATAATTGATTTTAAAAT
1 CATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCAAAATTGATTTTAAGTT
* * * * * * ********** ** *
2881 GAA-TTTTTTATATTTTTAGTTAAAATAGACAATANNNNNNNNNNTACCTCAAAAAACATG-AAA
66 AAATTTTTTTACATTTATAGTCAAAACAGACTATAATTGAATTCTTACCTTTAAAAACGTGTAAA
* * * * *
2944 AAAAAGGCATTCATTAATAAGAAAAGTCTATTTATAGTCACN
131 AAAAA-GCATTCATTGAGAAAAAAAGTCCATTTATAGTCACC
********* * * * * *
2986 NNNNNNNNNAAAAGTCTTATTACTCGCTTTAAACTGTTTTATAATCGCAAAATTGATATTGAGTT
1 CATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCAAAATTGATTTTAAGTT
* * * * *
3051 AAATGTTTTTACATTTATAGTCAAAATAGACTATAATTGAATTCTTGCCTTTAGAAATGTGTAAA
66 AAATTTTTTTACATTTATAGTCAAAACAGACTATAATTGAATTCTTACCTTTAAAAACGTGTAAA
* *
3116 AAAAATCATTCATTGAGAAAAAAAGCCCATTTATAGTCACC
131 AAAAAGCATTCATTGAGAAAAAAAGTCCATTTATAGTCACC
* *
3157 CATTCCTTCAAAGGCCTTATTACTCACTTTAAATTGTTT
1 CATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTT
3196 NNNNNNNNNN
Statistics
Matches: 655, Mismatches: 209, Indels: 58
0.71 0.23 0.06
Matches are distributed among these distances:
168 1 0.00
169 10 0.02
170 200 0.31
171 340 0.52
172 103 0.16
173 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.38
Consensus pattern (171 bp):
CATTCCTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCAAAATTGATTTTAAGTT
AAATTTTTTTACATTTATAGTCAAAACAGACTATAATTGAATTCTTACCTTTAAAAACGTGTAAA
AAAAAGCATTCATTGAGAAAAAAAGTCCATTTATAGTCACC
Found at i:3886 original size:161 final size:161
Alignment explanation
Indices: 3599--3901 Score: 376
Period size: 161 Copynumber: 1.9 Consensus size: 161
3589 ATTTTTTTAC
* * *
3599 ATTTTTAGTTAAAATAGACTATAATTGAATGCCTGCCTCAAGAAACATACAAAAAATGATATTCA
1 ATTTTTAGTTAAAACAGACTATAATTGAATGCCTACCTCAAGAAACATACAAAAAATAATATTCA
********** *
3664 TTGAGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAANNNNNNNNNNTCACTTTAAATTG
66 TTGAGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAG
3729 TTTTATAATCTCATAATTGATTTTGAGTTGA
131 TTTTATAATCTCATAATTGATTTTGAGTTGA
** * * *
3760 ATTTTTAGTTAAAACAGACTATAATTGAATGCCTACCTTGAGAAATATGCAAAAAA-AATTATTT
1 ATTTTTAGTTAAAACAGACTATAATTGAATGCCTACCTCAAGAAACATACAAAAAATAA-TATTC
* *
3824 ATTGAGAAGAAAAGTCCATTTATAGTCATCCATTTCC-TCAAAAGCCTTATTACTCGCTTTAAAT
65 ATTGAGAAGAAAAGTCCATTTATAGTCACCCA-TTCCTTCAAAAGCCTTATTACTCACTTTAAAT
*
3888 AGTTTTATAGTCTC
129 AGTTTTATAATCTC
3902 NNNNNNNNNN
Statistics
Matches: 118, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
160 1 0.01
161 113 0.96
162 4 0.03
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.35
Consensus pattern (161 bp):
ATTTTTAGTTAAAACAGACTATAATTGAATGCCTACCTCAAGAAACATACAAAAAATAATATTCA
TTGAGAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAG
TTTTATAATCTCATAATTGATTTTGAGTTGA
Found at i:6065 original size:170 final size:169
Alignment explanation
Indices: 5650--6709 Score: 671
Period size: 170 Copynumber: 6.3 Consensus size: 169
5640 NNNNNNNNNN
* *
5650 AATTATTGTCTATTTTAACTAAAAATGTAAAAAATTCAAATTAAAATCAATTATAAGATTATAAA
1 AATTATTGTCTATTTTAACTAAAAATGTAAAAAATTCAACTTAAAATCAATTATTAGATTATAAA
* * * * *
5715 ACAATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGGGTTACTATAAATGGACTTTTTTCTCAA
66 ACAATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTCACTATAAATAGACTTTTTTCTCAA
**
5780 TGAGCGATTTTTTTTACACATTTCTAAAGGCAGGCATTC
131 TGAGCGATTTTTTTTACACATTTCTAAAGGCAAACATTC
* * ** * * *
5819 AATTATAGTCTATTTTAACTATAAACATAAAATAATTTAACTCAAAATCAATT-TTAGGATTTTA
1 AATTATTGTCTATTTTAACTAAAAATGTAAAA-AATTCAACTTAAAATCAATTATTA-GATTATA
* ****
5883 AAACAGTTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTCACTATAAATAGACTTTTNNNNN
64 AAACAATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTCACTATAAATAGACTTTT-TTCT
******** ** ** ** *
5948 NNNNNNNTG-TCTTTTTTTTGATGTTTCTTGAGGTAAACATTC
128 CAATGAGCGAT-TTTTTTTACACATTTCTAAAGGCAAACATTC
*
5990 AATTATTGTCTATTTTAACAAAAAATGTAAAAAATTCAACTTAAAA-CTAATTATGTA-ATTATA
1 AATTATTGTCTATTTTAACTAAAAATGTAAAAAATTCAACTTAAAATC-AATTAT-TAGATTATA
* ********** *
6053 AAATAATTTAAAGCGAGTAATAAGGC-TTTAGAAGNNNNNNNNNNCTATAAATGGACTTTTCTTC
64 AAACAATTTAAAGCGAGTAATAAGGCTTTTA-AAGGAATGGGTCACTATAAATAGACTTTT-TTC
** * * * **
6117 TCAATGA---A---TAGTTGCACATTTCTCAAGGTAGGCATTC
127 TCAATGAGCGATTTTTTTTACACATTTCTAAAGGCAAACATTC
* * * * * *
6154 AATTATTGTCTGTTTTAACAAAAAATTTTAAAAAATTTAACTCAAAATCAATTATGAGATTATAA
1 AATTATTGTCTATTTTAACTAAAAA-TGTAAAAAATTCAACTTAAAATCAATTATTAGATTATAA
* ** *********** * *
6219 AATAATTTAAATTGAGTAATAAGGCTTTTGNNNNNNNNNNTGACTATAAATGGACTTTTCTTCTC
65 AACAATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTCACTATAAATAGACTTTT-TTCTC
** ** * ** ** *
6284 AATGA-ATAGCTTTTTTGCATGTTTCTTGAGGCAGACATTC
129 AATGAGCGATTTTTTTTACACATTTCTAAAGGCAAACATTC
* * ** * *
6324 AATTATAGTCTATTTTAACCAAAAATGTAAAAAAATTTGATTTAAAATCAATTATGAGATTATAA
1 AATTATTGTCTATTTTAACTAAAAATGT-AAAAAATTCAACTTAAAATCAATTATTAGATTATAA
* * * * *
6389 AATAATTTAAAGTGAGTAATAAGGGCTTTGAAA-GAATAGGTAACTATAAATAGACTTTTCTTCT
65 AACAATTTAAAGCGAGTAATAA-GGCTTTTAAAGGAATGGGTCACTATAAATAGACTTTT-TTCT
* ** * **
6453 CAATTAATGATTTTTTTTACACGTTTCTAACA-GCAGGCATTC
128 CAATGAGCGATTTTTTTTACACATTTCTAA-AGGCAAACATTC
* * * * * * *
6495 AATTATAGTCTGTTTTAACCATAAATGTAAAACAATTTAACTCAAAATAAATT-TTGAGATTATA
1 AATTATTGTCTATTTTAACTAAAAATGTAAAA-AATTCAACTTAAAATCAATTATT-AGATTATA
* * * * * *
6559 AAACAGTTTAAAGTGAGTAAAAAGACTTTTAAAGGAATGGGGTGACTATAAATAGACTTTTCTTG
64 AAACAATTTAAAGCGAGTAATAAGGCTTTTAAAGGAAT-GGGTCACTATAAATAGACTTTT-TTC
* * * * *** *
6624 TTAATGAATGC-CTTGTTTTT-C-CTGTTTCTTGGGGTAAACATTC
127 TCAATG-A-GCGATTTTTTTTACAC-ATTTCTAAAGGCAAACATTC
6667 AATTATTGTCTATTTTAACTAAAAATGTAAAAAATTCAACTTA
1 AATTATTGTCTATTTTAACTAAAAATGTAAAAAATTCAACTTA
6710 NNNNNNNNNN
Statistics
Matches: 697, Mismatches: 164, Indels: 58
0.76 0.18 0.06
Matches are distributed among these distances:
164 44 0.06
165 88 0.13
166 4 0.01
167 1 0.00
169 37 0.05
170 278 0.40
171 165 0.24
172 72 0.10
173 8 0.01
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.36
Consensus pattern (169 bp):
AATTATTGTCTATTTTAACTAAAAATGTAAAAAATTCAACTTAAAATCAATTATTAGATTATAAA
ACAATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTCACTATAAATAGACTTTTTTCTCAA
TGAGCGATTTTTTTTACACATTTCTAAAGGCAAACATTC
Found at i:7419 original size:170 final size:170
Alignment explanation
Indices: 6758--7442 Score: 508
Period size: 170 Copynumber: 4.0 Consensus size: 170
6748 NNNNNNATGA
* * * * * *
6758 GTGACTATAAATGGACTTTTTTTCTCAATGAATGATTTTTTTGACACATTTCTAAAAGCAGGCAT
1 GTGACTATAAATGGACTTTTCTTCTCAATGAATGCTTTTTTTG-CACGTTTCTCAAGGCAGACAT
* ** * * * * * *
6823 TCAATTATAGTTTGTTTTAACCATAAATGTAAAAATATTTAAGTCAAAATCAATTTTGGGATTAT
65 TCAATTATAGTCTGTTTTAATAAAAAATGTAAAAAAATTCAACTCAAAATCAATTATGAGATTAT
* ********
6888 AAAACTATTTAAAGTGAGTAATAAGGCTTTT-ANNNNNNNNN
130 AAAACAATTTAAAGTGAGTAATAAGGCTTTTGA-AGGAATAG
* * * * *
6929 NTGACTATAAATAGACTTTTCTTGCT-AATGAATGCCTTTTTTTTCATGTTTCTTC-AGGCAAAC
1 GTGACTATAAATGGACTTTTCTT-CTCAATGAATG-CTTTTTTTGCACGTTTC-TCAAGGCAGAC
* * * * *
6992 ATTCAATTATTGTCTATTTTAACT-AAAAATGT-AAAAAATTTAACTTAAAATCAATTATGTGAT
63 ATTCAATTATAGTCTGTTTTAA-TAAAAAATGTAAAAAAATTCAACTCAAAATCAATTATGAGAT
********** * *
7055 TATAAAACAATNNNNNNNNNNTAATAAGGCTTTAGAAGGAATGG
127 TATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAG
* * * * * *
7099 GTGACTATAAATGGACTTTACTTCTCAATGAATAG-TTTTTCTGCACGTTTTTGAAGGTACACAT
1 GTGACTATAAATGGACTTTTCTTCTCAATGAAT-GCTTTTTTTGCACGTTTCTCAAGGCAGACAT
* ** * * *
7163 TCAATTATAGTCTGTTTTAATATAAAA-GATAAAAAAACACAACTTAAAATCAATTATGAGAATN
65 TCAATTATAGTCTGTTTTAATAAAAAATG-TAAAAAAATTCAACTCAAAATCAATTATGAGATTA
********* * * *
7227 NNNNNNNNNTTAAAGCGAGTAATAACGCTTTTGAGGGAATAG
129 TAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAG
* * *
7269 TTGACTATAAATGGACTTTTCTTCTCAATAAATAG-TTTTTTTGCACGTTTCTCAAGGTAGGA-A
1 GTGACTATAAATGGACTTTTCTTCTCAATGAAT-GCTTTTTTTGCACGTTTCTCAAGGCA-GACA
7332 TTCAATTATAGTCTGTTTTAATAAAAAAT-TCAAAAAAATTCAACTCAAAATCAATTATGAGATT
64 TTCAATTATAGTCTGTTTTAATAAAAAATGT-AAAAAAATTCAACTCAAAATCAATTATGAGATT
* * * *
7396 GTAAAACAATTTAAAATGAGTAATAAGGCTTTTGAATGAATGG
128 ATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAG
7439 GTGA
1 GTGA
7443 TGTAATTGAG
Statistics
Matches: 388, Mismatches: 112, Indels: 29
0.73 0.21 0.05
Matches are distributed among these distances:
168 3 0.01
169 46 0.12
170 261 0.67
171 68 0.18
172 10 0.03
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.35
Consensus pattern (170 bp):
GTGACTATAAATGGACTTTTCTTCTCAATGAATGCTTTTTTTGCACGTTTCTCAAGGCAGACATT
CAATTATAGTCTGTTTTAATAAAAAATGTAAAAAAATTCAACTCAAAATCAATTATGAGATTATA
AAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAG
Found at i:8443 original size:171 final size:171
Alignment explanation
Indices: 7906--8484 Score: 617
Period size: 171 Copynumber: 3.4 Consensus size: 171
7896 NNNNNNNNNN
* * * **
7906 TTATAAAACCATTTAAAGTGAGTAATAAGTCTTTTGAATAAATGAGTGA-TCATAAATGGACTTT
1 TTATAAAACAATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGAGTGACT-ATAAATGGACTTT
* * * * *
7970 TCTTGTCAATCAATAGCTTTTTTTGCACGTTTCTCAAGGCATGTATTCAATTATAGTCTGTTTTA
65 TCTTCTCAATCAATAGCTTTTTTTGCACATTTCTAAAGGCAGGCATTCAATTATAGTCTGTTTTA
*
8035 ATAAAAAATTTAAAAAAATTCAACTCAAAATCAA-TGAGGAGA
130 ATCAAAAATTTAAAAAAATTCAACTCAAAATCAATTGAGG-GA
* *
8077 TTATAAAACAATTTAAAGTGAGTAATAAGGCATTTGAAGGAATAAGTGACTATAAATGGACTTTT
1 TTATAAAACAATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGAGTGACTATAAATGGACTTTT
* ** * ** * *
8142 CTTCTCAATTAATAGCTTTTTTTGCATGTTTTGTTGAGGCAGACATTGAATTATAGTCTGTTTTA
66 CTTCTCAATCAATAGCTTTTTTTGCA-CATTTCTAAAGGCAGGCATTCAATTATAGTCTGTTTTA
* * ******
8207 ATCAAAAATTTAAAAAAATTCAATTTAAAATCAATTNNNNNN
130 ATCAAAAATTTAAAAAAATTCAACTCAAAATCAATTGAGGGA
**** *
8249 NNNNAAAACAATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGAGTGACTATACATGGACTTTT
1 TTATAAAACAATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGAGTGACTATAAATGGACTTTT
* ** * * *
8314 TTTCTCAATGGAT-GATTTTTTTTACCCATTTCTAAAGGCAGGCATTCAATTATAGTCTGTTTTA
66 CTTCTCAATCAATAG-CTTTTTTTGCACATTTCTAAAGGCAGGCATTCAATTATAGTCTGTTTTA
* * * ** **
8378 ACCATAAATATAAAAAAATTTTACTCAAAATCAATTTTGGGA
130 ATCAAAAATTTAAAAAAATTCAACTCAAAATCAATTGAGGGA
* * * * *
8420 TTATAAAACAGTTTAAAGTGAGTAATAAGG-CTATTAAAAGAATGGGTGACTATAAATAGACTTT
1 TTATAAAACAATTTAAAGTGAGTAATAAGGCCT-TTGAAGGAATGAGTGACTATAAATGGACTTT
8484 T
65 T
8485 TTTTGCTAAT
Statistics
Matches: 334, Mismatches: 69, Indels: 10
0.81 0.17 0.02
Matches are distributed among these distances:
170 2 0.01
171 194 0.58
172 137 0.41
173 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.36
Consensus pattern (171 bp):
TTATAAAACAATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGAGTGACTATAAATGGACTTTT
CTTCTCAATCAATAGCTTTTTTTGCACATTTCTAAAGGCAGGCATTCAATTATAGTCTGTTTTAA
TCAAAAATTTAAAAAAATTCAACTCAAAATCAATTGAGGGA
Found at i:10706 original size:171 final size:171
Alignment explanation
Indices: 10470--10956 Score: 496
Period size: 171 Copynumber: 2.8 Consensus size: 171
10460 NNNNNNNNNN
* * * *
10470 AAATCAATTATGTGATTATAAAATAATTTAAAATGAGTAATAAGGCTTTAG-AGGAAATGGGTGA
1 AAATCAATTATGAGATTATAAAATAATTTAAAGTGAGTAATAAGGCTTTTGAAGG-AATAGGTGA
* * * * *
10534 CTATAAATGGACTTTTCTTCTTAATGAATAGTTTTTTTTGCACGTTTCTCAAGGTAGGCTTTCAA
65 CTATAAAAGAACTTTTCTTCTCAATGAATAGTTTTTTTTGCACGTTTCTAAAGGTAGGCATTCAA
10599 TTATAGTCTGTTTTAACAAAAAATTCAAAAAAATTCAACTCA
130 TTATAGTCTGTTTTAACAAAAAATTCAAAAAAATTCAACTCA
* *
10641 AAATGAATTATGAGATTATAAAATAATTTAAAGTGAGCAATAAGGCTTTTGAAGGAATAGGTGAC
1 AAATCAATTATGAGATTATAAAATAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
********** * ** *
10706 TNNNNNNNNNNTTTTCTTCTCAATGAATAGCTTTTTTTGCACGTTTCTTGAGGTAGGCATTGAAT
66 TATAAAAGAACTTTTCTTCTCAATGAATAGTTTTTTTTGCACGTTTCTAAAGGTAGGCATTCAAT
* * ********** *
10771 TATAGTCTATTTTAACCAAAAATNNNNNNNNNNTCAACTTA
131 TATAGTCTGTTTTAACAAAAAATTCAAAAAAATTCAACTCA
* * *
10812 AAATCAATTATGAGAGTATTAAATAATTTAAAGTGAGTAATAAGGCCTTTGAAGGAA-AGGGTGA
1 AAATCAATTATGAGATTATAAAATAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATA-GGTGA
* * * * *
10876 CTATAAAAGAACTTTT-TCTCTCAATAAAT-GATTTTTTTTACTCATTTCTAAAGGCAGGCATTC
65 CTATAAAAGAACTTTTCT-TCTCAATGAATAG-TTTTTTTTGCACGTTTCTAAAGGTAGGCATTC
10939 AATTATAGTCTGTTTTAA
128 AATTATAGTCTGTTTTAA
10957 TCATAAACGT
Statistics
Matches: 252, Mismatches: 60, Indels: 8
0.79 0.19 0.03
Matches are distributed among these distances:
170 3 0.01
171 246 0.98
172 3 0.01
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.36
Consensus pattern (171 bp):
AAATCAATTATGAGATTATAAAATAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
TATAAAAGAACTTTTCTTCTCAATGAATAGTTTTTTTTGCACGTTTCTAAAGGTAGGCATTCAAT
TATAGTCTGTTTTAACAAAAAATTCAAAAAAATTCAACTCA
Found at i:11993 original size:170 final size:170
Alignment explanation
Indices: 11695--12003 Score: 381
Period size: 170 Copynumber: 1.8 Consensus size: 170
11685 NNNNNNNNNT
* ** *
11695 GTCTATTTTAACTAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTGTAAAATAATAT
1 GTCTATTTTAACTAAAAATGTAAAAAATTCAACTAAAAATCAATTATGAGATTACAAAACAATAT
* * * * * *
11760 AAAGTAAGTAATAAGGCTTTTGAAGGAATGGGTTACTATAAATGGACTGTTTTCCTCAATGAATA
66 AAAGGAAGTAATAAGGCTTTTAAAGGAAAGGGTGACTATAAATAGACTGTTTTCATCAATGAATA
11825 -ATTTTTTTACACATTTATAAAGGCAGGAGTTCAATTATA
131 CATTTTTTTACACATTTATAAAGGCAGGAGTTCAATTATA
* * * * * *
11864 GTCTGTTTTAACTATAAATGTAAAACAATTTAACTAAAAAAT-AATTTTGGGATTACAAAACAGT
1 GTCTATTTTAACTAAAAATGTAAAA-AATTCAACT-AAAAATCAATTATGAGATTACAAAACAAT
* * * *
11928 TTAAAGGGAGTAATAAGGCTTTTAAAGGAAAGGGTGACTATAAATAGACTTTTCTTGAT-AATGA
64 ATAAAGGAAGTAATAAGGCTTTTAAAGGAAAGGGTGACTATAAATAGACTGTT-TTCATCAATGA
*
11992 ATACCTTTTTTT
128 ATACATTTTTTT
12004 TTATGTTTCT
Statistics
Matches: 115, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
169 23 0.20
170 77 0.67
171 15 0.13
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.36
Consensus pattern (170 bp):
GTCTATTTTAACTAAAAATGTAAAAAATTCAACTAAAAATCAATTATGAGATTACAAAACAATAT
AAAGGAAGTAATAAGGCTTTTAAAGGAAAGGGTGACTATAAATAGACTGTTTTCATCAATGAATA
CATTTTTTTACACATTTATAAAGGCAGGAGTTCAATTATA
Found at i:13213 original size:171 final size:167
Alignment explanation
Indices: 12860--13757 Score: 486
Period size: 171 Copynumber: 5.3 Consensus size: 167
12850 ACAATTTAAA
**
12860 GCGAGTAATAAGGCTTTAAAAAGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATAG--
1 GCGAGTAATAAGGCTTT-TGAAGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATAGCT
* * * * *
12923 TTTTTTGCATGTTTCTCAAGGTAGGCATTTAGTTATAGTCTGTTTTAAAATAAAATTAAAAAAAA
65 TTTTTTGCACGTTTCTCAAGGCAGGCATTCAATTATAGTCTATTTTAAAATAAAATTAAAAAAAA
* *******
12988 TTCAACTTAAAATCAATTATGAGATTATAAANNNNNNNNNN
130 TTCAACTCAAAATCAATTATGAGATTATAAA---ATAATTT
*
13029 GCGAGTAATAAGGCTTTTGACAGAATGGGTGACTATAAATCGACTTTTCTTCTCAATGAATAGCT
1 GCGAGTAATAAGGCTTTTGA-AGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATAGCT
* ** **
13094 TTTTTTGCACGTTTCTCAAGACAATCATTCAATTATAGTCTATTTTAACAA-AAAATTCGAAAAA
65 TTTTTTGCACGTTTCTCAAGGCAGGCATTCAATTATAGTCTATTTTAA-AATAAAATTAAAAAAA
13158 ATTCAACTCAAAATCAATTATGAGATTATAAAATAATTT
129 ATTCAACTCAAAATCAATTATGAGATTATAAAATAATTT
******* * *
13197 NNNNNNNNNNATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTAC-CTAATGAAT
1 ---GCGAGTAATAAGGCTTTTGAA-GAATGGGTGACTATAAATGGACTTTTCTTCTC-AATGAAT
** * **********
13261 AGCTTTTTTTGCACGTTTCTTGAGGCAGGCATTCAATTATAGTCTGTTNNNNNNNNNNA-TATAA
61 AGCTTTTTTTGCACGTTTCTCAAGGCAGGCATTCAATTATAGTCTATTTTAAAATAAAATTA-AA
* * * * *
13325 AAAAATTCAACTTAAAATCAATTACGAGAGTACAAAACAATTT
125 AAAAATTCAACTCAAAATCAATTATGAGATTATAAAATAATTT
* * ********** *
13368 AAAGTGAGTTATAAGGCANNNNNNNNNNTGGGTGACTATAAATGGACTTTTGTTCTCAATGAAT-
1 ---GCGAGTAATAAGGC-TTTTGAAGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATA
* * * * * * ***
13432 GATTTTTTTTACACATTTCTAAAGGCAGGCATTCAATTGTAGTCTTTTTGTGTCAT-AAATGT-A
62 G-CTTTTTTTGCACGTTTCTCAAGGCAGGCATTCAATTATAGTCTATTT-TAAAATAAAAT-TAA
* * * * * *
13495 AAAAAATTTAACTTAAAATCAATTTTGGGATTATAAAACAGTTT
124 AAAAAATTCAACTCAAAATCAATTATGAGATTATAAAATAATTT
* ** * * *
13539 AAAGCGAGTAATAGGGCTTTCAAAGGAATGGCTGACTATAAATAGACTTTTTTTACT-AATGAAT
1 ---GCGAGTAATAAGGCTTTTGAA-GAATGGGTGACTATAAATGGACTTTTCTT-CTCAATGAAT
* ** ********** * * * *
13603 -GCCTTTTTTTTCATATTTCTNNNNNNNNNNATTCAATTATTGTCTATTTT-AACTAAAAATATA
61 AG-CTTTTTTTGCACGTTTCTCAAGGCAGGCATTCAATTATAGTCTATTTTAAAATAAAATTAAA
* * * * *
13666 AAAAATTTAACTTAAAATCAATTATCATATTATAAAACAATTT
125 AAAAATTCAACTCAAAATCAATTATGAGATTATAAAATAATTT
* * * *
13709 AAAGTGAATAATAAGACCTTTGAAGGAATGGGTGACTATAAATGGACTT
1 ---GCGAGTAATAAGGCTTTTGAA-GAATGGGTGACTATAAATGGACTT
13758 NNNNNNNNNN
Statistics
Matches: 557, Mismatches: 151, Indels: 41
0.74 0.20 0.05
Matches are distributed among these distances:
168 1 0.00
169 60 0.11
170 87 0.16
171 403 0.72
172 5 0.01
173 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.34
Consensus pattern (167 bp):
GCGAGTAATAAGGCTTTTGAAGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATAGCTT
TTTTTGCACGTTTCTCAAGGCAGGCATTCAATTATAGTCTATTTTAAAATAAAATTAAAAAAAAT
TCAACTCAAAATCAATTATGAGATTATAAAATAATTT
Found at i:14800 original size:171 final size:159
Alignment explanation
Indices: 14485--14814 Score: 358
Period size: 171 Copynumber: 2.0 Consensus size: 159
14475 AGTAATAAGA
* * **
14485 CTTTAGAAGGAATGGGTGACTATAAATGGACTTTTCCTCTTAATGAATAGTTTTTTTGTATATTT
1 CTTTAGAAGGAATGAGTGACTATAAATGGACTTTTCCTCTCAATGAATAGTTTTTTTACATATTT
* **
14550 CTCAAGGCATGCATTCAATTATAGTCTGTTTTAACAAAAAATTTAAAAAAATTCAACTCAAAATC
66 CTCAAGGCAGGCATTCAATTATAGTCTGTTTTAACAAAAAATAAAAAAAAATTCAACTCAAAATC
14615 AATTATGAGATTATAAAACAATTTNNNNNNNNNNNTAAAG
131 AATTATGAGATTATAAAACAATTT-----------TAAAG
* **
14655 CTTTTGAAGGAATGAGTGACTATAAATGGACTTTTTTTCTCAATGAAT-GATGTTTTTTACATAT
1 CTTTAGAAGGAATGAGTGACTATAAATGGACTTTTCCTCTCAATGAATAG-T-TTTTTTACATAT
* * * * **
14719 TTCTTAAGGCAGGCATTCAATTATAGTCTGTTTTAACCAGAAATAAAAAAAAATTTAACTTGAAA
64 TTCTCAAGGCAGGCATTCAATTATAGTCTGTTTTAACAAAAAATAAAAAAAAATTCAACTCAAAA
* * *
14784 TTAATTTTGGGATTATAAAACAA-TTTAAAG
129 TCAATTATGAGATTATAAAACAATTTTAAAG
14814 C
1 C
14815 GAGTAATANN
Statistics
Matches: 139, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
159 6 0.04
169 1 0.01
170 46 0.33
171 86 0.62
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.36
Consensus pattern (159 bp):
CTTTAGAAGGAATGAGTGACTATAAATGGACTTTTCCTCTCAATGAATAGTTTTTTTACATATTT
CTCAAGGCAGGCATTCAATTATAGTCTGTTTTAACAAAAAATAAAAAAAAATTCAACTCAAAATC
AATTATGAGATTATAAAACAATTTTAAAG
Found at i:17374 original size:170 final size:169
Alignment explanation
Indices: 16987--17788 Score: 563
Period size: 170 Copynumber: 4.7 Consensus size: 169
16977 NNNNNNGCAT
* * * * * * *
16987 TCAATTATAGTCTGTTTTAACCATAAATGTAAAAAAATTTAACTCAAAATTAATTTTGAGATTAT
1 TCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAA-TTCACTTAAAATCAATTATGAGATTAT
** * * * * * * * *
17052 AAAACAGCTTAAAGCGAGTAACAAGGCTTTTAAAAGAATGGATGAATATAAATAGACTTTTCTTC
65 AAAACAATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTC
** ** ** **
17117 -CTAATGAATATTTTTTTTTTAATGTTTCTTGAGGTAAACA
130 TC-AATGAATAGCTTTTTTTGCATGTTTCTCAAGGTAGGCA
* * * * ********** *
17157 TTCAATTATTGTCTATTTTAACTAAAAATGTNNNNNNNNNNACTTAAAATCAATTATGTGATTAT
1 -TCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCACTTAAAATCAATTATGAGATTAT
* *
17222 AAAACAATTTAAAGTGAGTAATAAGGCCATAGAAGGAATGGGTGACTATAAATGGACTTTTCTTC
65 AAAACAATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTC
17287 TCAATGAATAG-TTTTTTTGCATGTTTCTCAAGGTAGGCA
130 TCAATGAATAGCTTTTTTTGCATGTTTCTCAAGGTAGGCA
* * *
17326 TTCAGTTATAGTTTGTTTTAACATAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTA
1 -TCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTC-ACTTAAAATCAATTATGAGATTA
********** * *
17391 TANNNNNNNNNNAAGCGAGTAATAAGGCTTTTGACA-GAATGGGTGACTATAAATGGACTTTTCT
64 TAAAACAATTTAAAGTGAGTAATAAGGCCTTTGA-AGGAATGGGTGACTATAAATGGACTTTTCT
* ******
17455 TCTCAATGAA-AGTTTTTTTTGCATGTTTCTCAAGGCNNNNNN
128 TCTCAATGAATAGCTTTTTTTGCATGTTTCTCAAGG-TAGGCA
****
17497 NNNNTTATAGTCTGTTTTAACAAAAAAT-TCAAAAAAATTC-CGTTCAAAATCAATTATGAGATT
1 TCAATTATAGTCTGTTTTAACAAAAAATAT-AAAAAAATTCAC-TT-AAAATCAATTATGAGATT
* * * ********** *
17560 ATAAAACAATGTAAAGTGAGTAATAAGACTTTTGAAGGAATGGGTNNNNNNNNNNGGACCTTTCT
63 ATAAAACAATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT
* * ** *
17625 TCTCAATGAATAGCTTTTTTTTCATATTTCTTGAGGTAGTTCA
128 TCTCAATGAATAGCTTTTTTTGCATGTTTCTCAAGGTAG-GCA
*********
17668 TCAATTATAGTCTGTTTTAACAAAAAATATAAANNNNNNNNNNTTAAAATCAATTATGAGATTAT
1 TCAATTATAGTCTGTTTTAACAAAAAATATAAA-AAAATTCACTTAAAATCAATTATGAGATTAT
* **
17733 AGAACAATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATAAGTGACTATAAATGGA
65 AAAACAATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAATGGA
17789 NNNNNNNNNN
Statistics
Matches: 474, Mismatches: 143, Indels: 28
0.73 0.22 0.04
Matches are distributed among these distances:
168 1 0.00
169 52 0.11
170 283 0.60
171 135 0.28
172 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.34
Consensus pattern (169 bp):
TCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCACTTAAAATCAATTATGAGATTATA
AAACAATTTAAAGTGAGTAATAAGGCCTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCT
CAATGAATAGCTTTTTTTGCATGTTTCTCAAGGTAGGCA
Done.