Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397420.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_151.0, 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: 21009
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.22
Warning! 8988 characters in sequence are not A, C, G, or T
Found at i:1769 original size:174 final size:171
Alignment explanation
Indices: 1--2598 Score: 836
Period size: 171 Copynumber: 15.2 Consensus size: 171
* ** * * * * *
1 AAAGCGAGTAATAAGGCTTTCGAAGGCATGAATTACAATAAGTGGACTTTTCTTGCCAATGGATA
1 AAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGGATA
* * * * * * * * * * *
66 TCTTTTCCTTCACGTTTCACAATGTAGACATTCAATTATAATATGTTTTAATAAAAAATATAAAA
66 TCTTTTTCTTCACATTTCTCGAGGCAGACGTTCAATTATAATCTGATGTAATAAAAAAAAT-AAA
* * * **********
131 AAAATACAAACTAAAATCAATTATGAGGNNNNNNNNNNATTT
130 AAAATTCAAATTAAAACCAATTATGAGGTTATAAAATCATTT
** ** *
173 AAAGCGAGTAATAAGGCTTTTTAAGGCGTGGGTGACTATAAATGGACTTTTCTCT-CCAATGGAT
1 AAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCT-TACCAATGGAT
* ** * * * * * * **
237 ATATTTTT-TTCATGTTTCTCAAGGTAGACTTTAAATTATAATCTGTTTTAATAAAAAGTATAAA
65 ATCTTTTTCTTCACATTTCTCGAGGCAGACGTTCAATTATAATCTGATGTAATAAAAAAAATAAA
* **********
301 AAAATTCAAATCANNNNNNNNNNTGAGGTTATAAAATCATTT
130 AAAATTCAAATTAAAACCAATTATGAGGTTATAAAATCATTT
* * * * * * * * *
343 AAACCGAGTAATAATGCTTTTGAAGGAATGGGTGATTGTAAATGGACTTCTCTTATCAATGGATA
1 AAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGGATA
* ** * * * * * *
408 TCATTTTCGTT-ATGTTTTTTGAGGCAGGA-ATTCAATTATAATCTGTTTTAAT-AAAAATAT-A
66 TCTTTTTC-TTCACATTTCTCGAGGCA-GACGTTCAATTATAATCTGATGTAATAAAAAAAATAA
* * * * * * * *
469 CAAAATTTAACTTAAAACTAATTATAAGATTAAAAAAGCATTT
129 AAAAATTCAAATTAAAACCAATTATGAGGTTATAAAATCATTT
* * * * ********** * *
512 AAAGCAAGTAATAAAGTTTTCGAAGGCATGGGNNNNNNNNNNTGGACTTTTCTTCCCAATGGATA
1 AAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGGATA
* ** * ** * * * * * * *
577 TATTTTTCTTCATGTTTATTAAAGTAGACATTCAATTATAAT-TTATTTTCATAAAAAATATAAA
66 TCTTTTTCTTCACATTTCTCGAGGCAGACGTTCAATTATAATCTGA-TGTAATAAAAAAAATAAA
********** *
641 AAAATTCAAATTAAAANNNNNNNNNNGGTTATAAAATTATTT
130 AAAATTCAAATTAAAACCAATTATGAGGTTATAAAATCATTT
* * ** * * * *
683 AATGCGAGTAATAAGGCTTTCGAAAGTATGGGTGACTCCAACTGGACTTTTTTTGCCAATGGATA
1 AAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGGATA
* * * ********** * * *
748 TCTTTTCCTTCACGTTTCTCAAGGNNNNNNNNNNATTATAATCTGTTTTAATAAAAAATATAAAA
66 TCTTTTTCTTCACATTTCTCGAGGCAGACGTTCAATTATAATCTGATGTAATAAAAAAAATAAAA
** * *
813 AAATTCAAATTAAAATGAATTATGGGGTTATAAAATTATTT
131 AAATTCAAATTAAAACCAATTATGAGGTTATAAAATCATTT
* * * ** *
854 AATA-CGAGTAATAAGGCTTCCGAAGGTATGGGTGACTCTAAAT-AGACTTTTGTTGTCAATAGA
1 AA-AGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGA-ACTTTTCTTACCAATGGA
* * * ** * * * **********
917 TATCCTTTTCTTCACGTTTCTC-AAGCTAGATATTCAATTATAATATGTTTTAATNNNNNNNNNN
64 TATCTTTTTCTTCACATTTCTCGAGGC-AGACGTTCAATTATAATCTGATGTAATAAAAAAAATA
* * *
981 AAAAAATTCAACTTAAAATCAATTATGAGGTTATAAAAACATTT
128 AAAAAATTCAAATTAAAACCAATTATGAGGTTATAAAATCATTT
** * * * * * *
1025 AAAGTAAGTAATAAAGCTTTTGAAGGCATAGGTGCCTATAAAT-AGACTTTTCTTGCCAATGGAT
1 AAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGA-ACTTTTCTTACCAATGGAT
** * * * * * *
1089 ATCTTTTTCTTCATGTTTCTCGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAA
65 ATCTTTTTCTTCACATTTCTCGAGGCAGACGTTCAATTATAATCTGATGTAATAAAAAAAATAAA
* *
1154 AAATTTCAAAATTAAAATTCAATTATTGAGGTTAATAAAATCACTTT
130 AAAATTC-AAATTAAAA-CCAATTA-TGAGGTT-ATAAAATCA-TTT
** * ** * ** *
1201 AAAGCGAGTAATAAGGCTTTTAAAGGCATCAGTGACTATAAATGGACTTTTCTGGCTAATGGATA
1 AAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGGATA
* * * * * * * * *
1266 CCTTATTT-TT-A-AGTTTCTCGAGGTAAACATAT-AATTATAATTTTATTTAATAATAAATATA
66 TCTT-TTTCTTCACA-TTTCTCGAGGCAGACGT-TCAATTATAATCTGATGTAATAAAAAAAATA
* * * * ******
1327 AAAAAGTTCAACTT-AAACCTAATTATGAGATTAAAAAANNNNNN
128 AAAAAATTCAAATTAAAACC-AATTATGAGGTTATAAAATCATTT
****************** * *
1371 NNNNNNNNNNNNNNNNNNTTCGAAGGCATGGGTGACTATAAAT-AGACTTTTCTTACCAATGTAT
1 AAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGA-ACTTTTCTTACCAATGGAT
* * * * * * * * **
1435 ATCTTTTT-TGTTACGTTTATCAAGGTAGACATTCAAATTTATAATCTGTTTTAATAAAAAATTT
65 ATCTTTTTCT-TCACATTTCTCGAGGCAGACGTTC-AA-TTATAATCTGATGTAATAAAAAAAAT
* * *********** * *
1499 AAAAAAGTTCAACTTAAAACNNNNNNNNNNATTAAAAAAGCATTT
127 AAAAAAATTCAAATTAAAACCAATTATGAGGTTATAAAATCATTT
* ** * *
1544 AAAGCGAGTAATATA-CCTTTCGAAGCCATGGGTGACTATAAATGGACTTTTCTTACGAATGGAT
1 AAAGCGAGTAATA-AGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGGAT
*
1608 ATC-TTTTCTTCACATTTCTCGAGGCAGACATTTCAATTAATTAAAT-TGATGTAATAAGAAAAA
65 ATCTTTTTCTTCACATTTCTCGAGGCAGAC-GTTCAATT-A-T-AATCTGATGTAATAA-AAAAA
* * *
1671 ATATAAACAATTTAAATTAAAATC-ATTATGAGGTTATAAAATCATTT
125 ATA-AAAAAATTCAAATTAAAACCAATTATGAGGTTATAAAATCATTT
** * *
1718 AAAGCGAGTAATAAGGCTTTTAAAGGTATGGGTGATTGTAAATGAACTTTTCTTACCAATGGATA
1 AAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGGATA
* * * * * * ***
1783 TCTTTTTGTTCAGATTTCTTGAGGCAGACGTTCAATTATAATCTGTTTTTATAAAAATGGTAAAA
66 TCTTTTTCTTCACATTTCTCGAGGCAGACGTTCAATTATAATCTGATGTAATAAAAAAAATAAAA
* * *
1848 AAATTCAACTTAAAACCAATTATGAGGTTATACAGTCATTT
131 AAATTCAAATTAAAACCAATTATGAGGTTATAAAATCATTT
* * ********** **
1889 AAAGTGAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAANNNNNNNNNNCTTGTCAATGGATA
1 AAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGGATA
* * * * * ** * * * * *
1954 TCTTTTTCTTCACGTTTCCCAAAGTAGATATTTAATTATAATCTGTTTTAATAAAAAACATAAAG
66 TCTTTTTCTTCACATTTCTCGAGGCAGACGTTCAATTATAATCTGATGTAATAAAAAAAATAAAA
* * * * * *
2019 AAATTTAACA-TAAAATCAATTATGAGATAACAAAAGCATTT
131 AAATTCAA-ATTAAAACCAATTATGAGGTTATAAAATCATTT
* ********** * * ** *
2060 AAAGTGAGTAATAAGGCTTTCGANNNNNNNNNNGACAATAAATGGACTTTTCTTGTCAATAGATA
1 AAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGGATA
** * * ** * * * *
2125 TCTTTTTCTTCATGTTTCCCGAAGCAGAAATTTAATTATAATCTGTTTTAATAAAAAATATAAAA
66 TCTTTTTCTTCACATTTCTCGAGGCAGACGTTCAATTATAATCTGATGTAATAAAAAAAATAAAA
* * ********** * * *
2190 AAGTTCAACTTAAANNNNNNNNNNAGATTAAAAAAGCATTT
131 AAATTCAAATTAAAACCAATTATGAGGTTATAAAATCATTT
* ** * * * * * * * *
2231 AAAGTGAGTAATAATCCTTTCAAAAGCATGGGAGAGTCTAAATGGACTTTTCTTGA-CAATAGAT
1 AAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTT-ACCAATGGAT
** * ** * ** * * * * *
2295 ATCTTTTTCTTCATGTTTCTCAAGATACATATTTAATTATAATCTGTTGTAGTAAAGAATATAAA
65 ATCTTTTTCTTCACATTTCTCGAGGCAGACGTTCAATTATAATCTGATGTAATAAAAAAAATAAA
* * *
2360 AAGATTCAAATTAAAATCAATTATGAGGTTCTAAAAAT-ATTT
130 AAAATTCAAATTAAAACCAATTATGAGGTTAT-AAAATCATTT
* ********** * *
2402 AATGCGAGTNNNNNNNNNNTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATGGATA
1 AAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGGATA
* * * * * * * * * ********
2467 CCCTTTTCTTCACATTTCTCAAAGTAGACATTCAATTAAAATCTGTTTTAATAAAAANNNNNNNN
66 TCTTTTTCTTCACATTTCTCGAGGCAGACGTTCAATTATAATCTGATGTAATAAAAAAAATAAAA
** * * * *
2532 NNATTCAACTTAAAATCAATTATGAGGTTACAAAAACATTT
131 AAATTCAAATTAAAACCAATTATGAGGTTATAAAATCATTT
*
2573 AAAACGAGTAATAAGGCTTTCGAAGG
1 AAAGCGAGTAATAAGGCTTTCGAAGG
2599 CATGAGTTAN
Statistics
Matches: 1795, Mismatches: 578, Indels: 107
0.72 0.23 0.04
Matches are distributed among these distances:
168 5 0.00
169 112 0.06
170 162 0.09
171 1015 0.57
172 119 0.07
173 121 0.07
174 99 0.06
175 96 0.05
176 63 0.04
177 3 0.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.34
Consensus pattern (171 bp):
AAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGGATA
TCTTTTTCTTCACATTTCTCGAGGCAGACGTTCAATTATAATCTGATGTAATAAAAAAAATAAAA
AAATTCAAATTAAAACCAATTATGAGGTTATAAAATCATTT
Found at i:1917 original size:171 final size:174
Alignment explanation
Indices: 1534--1929 Score: 455
Period size: 174 Copynumber: 2.3 Consensus size: 174
1524 NNNNNATTAA
* * ** *
1534 AAAAGCATTTAAAGCGAGTAATATA-CCTTTCGAAGCCATGGGTGACTATAAATGGACTTTTCTT
1 AAAATCATTTAAAGCGAGTAATA-AGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTT
* *
1598 ACGAATGGATATCTTTTCTTCACATTTCTCGAGGCAGACATTTCAATTAATTAAATTGATGTAAT
65 ACCAATGGATATCTTTTCTTCACATTTCTCGAGGCAGACAGTTCAATTAATTAAATTGATGTAAT
* * *
1663 AAGAAAAAATATAAACAATTTAAATTAAAATCATTATGAGGTTAT
130 AAGAAAAAATATAAAAAATTCAAATTAAAACCATTATGAGGTTAT
** * *
1708 AAAATCATTTAAAGCGAGTAATAAGGCTTTTAAAGGTATGGGTGATTGTAAATGAACTTTTCTTA
1 AAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTTA
* * * * * *
1773 CCAATGGATATCTTTTTGTTCAGATTTCTTGAGGCAGAC-GTTCAATT-A-T-AATCTGTTTTTA
66 CCAATGGATATC-TTTTCTTCACATTTCTCGAGGCAGACAGTTCAATTAATTAAAT-TGATGTAA
*** *
1834 TAA-AAATGGTA-AAAAAATTCAACTTAAAACCAATTATGAGGTTAT
129 TAAGAAAAAATATAAAAAATTCAAATTAAAACC-ATTATGAGGTTAT
* * * *
1879 ACAGTCATTTAAAGTGAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAA
1 AAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAA
1930 NNNNNNNNNN
Statistics
Matches: 186, Mismatches: 32, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
170 16 0.09
171 64 0.34
172 9 0.05
173 2 0.01
174 72 0.39
175 23 0.12
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (174 bp):
AAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGAACTTTTCTTA
CCAATGGATATCTTTTCTTCACATTTCTCGAGGCAGACAGTTCAATTAATTAAATTGATGTAATA
AGAAAAAATATAAAAAATTCAAATTAAAACCATTATGAGGTTAT
Found at i:3142 original size:171 final size:170
Alignment explanation
Indices: 2840--3216 Score: 450
Period size: 171 Copynumber: 2.2 Consensus size: 170
2830 CTTGAGGCAG
*
2840 ACATTCAATTATAATATGTTTTAATAAAAATATTACAAAGTTCAACTTAAAACTAATTATGAGAT
1 ACATTCAATTATAATATGTTTTAATAAAAATATAACAAAGTTCAACTTAAAACTAATTATGAGAT
* **********
2905 TAAAAAAAAATTTAAAACGAGGAATAAGGCTTTCGAAGGCATGGGTGANNNNNNNNNNACTTTTC
66 TAAAAAAAAATTTAAAACGAGGAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTTTC
* * *
2970 TTACTAATGGATATCTTTCTGTTCGCATTTCTC-ATGGTAA
131 TTACCAATGGATATCTTTCTCTTCACATTTCTCAAT-GTAA
* * *
3010 ACATACAATTATAATTTGTTTTAATAATAAATATAACAAAGTTCAACTTAAAACTCATTATGAGA
1 ACATTCAATTATAATATGTTTTAATAA-AAATATAACAAAGTTCAACTTAAAACTAATTATGAGA
* * * * * *
3075 TTAAAAAATAATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATGAGTTACTATAAATGGATTTTT
65 TTAAAAAAAAATTTAAAACGAGGAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTTT
* * * * *
3140 CTTGCCAATGGATATCTTTTTCTTTACGTTTCTCAATGTAG
130 CTTACCAATGGATATCTTTCTCTTCACATTTCTCAATGTAA
*
3181 ACATTCAATTATAATCTGTTTTAATAAAAAATATAA
1 ACATTCAATTATAATATGTTTTAAT-AAAAATATAA
3217 AACANNNNNN
Statistics
Matches: 173, Mismatches: 31, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
170 25 0.14
171 144 0.83
172 4 0.02
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.36
Consensus pattern (170 bp):
ACATTCAATTATAATATGTTTTAATAAAAATATAACAAAGTTCAACTTAAAACTAATTATGAGAT
TAAAAAAAAATTTAAAACGAGGAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTTTC
TTACCAATGGATATCTTTCTCTTCACATTTCTCAATGTAA
Found at i:13456 original size:171 final size:171
Alignment explanation
Indices: 13148--13536 Score: 415
Period size: 171 Copynumber: 2.3 Consensus size: 171
13138 NNNNNNNTGG
* * * * *
13148 TTTTAAGTTGAATTTTTTTACAATTTTTATAAAAACAGATTATAATTGAACATCTGCCTCAAGAA
1 TTTTAAGTTTAATTTTTTTATATTTTTTATTAAAACAGATTATAATTAAACATCTGCCTCAAGAA
* ** * * * * *
13213 ACCTGAATAAAAAGATATCCATTGGCAAGAAAAGTCTATTTATAGTCACCTATATTTTCTAAAGC
66 ACCTGAAGAAAAAGATATCCATTAACAACAAAAGTCCATTTATAGTCACCCATACTTTCGAAAGC
* * * ********
13278 ATTATTACTCGCTTTAAATACTTTTT-TAATCTCNNNNNNNN
131 ATTATTACACACTTTAAATA-TTTTTGTAACCTCATTATTGA
** * ** * *
13319 NNTTAAGTTTAACTTTTTTATATTTTTTATTAAAACAGATTATAATTAAATGTTTGCTTC-AGAA
1 TTTTAAGTTTAATTTTTTTATATTTTTTATTAAAACAGATTATAATTAAACATCTGCCTCAAG-A
* * *
13383 AACGTGAAGAAAAAGATATCCATTAATAACAAAAGTCCATTTATAGT-AGCCCATGCTTTCGAAA
65 AACCTGAAGAAAAAGATATCCATTAACAACAAAAGTCCATTTATAGTCA-CCCATACTTTCGAAA
*
13447 GCCTTATTACACACTTTAAATATTTTTGTAACCTCATTATTGA
129 GCATTATTACACACTTTAAATATTTTTGTAACCTCATTATTGA
13490 TTTTAAGTTTAATTTTTTTATATTTTTTATTAAAACAGATTATAATT
1 TTTTAAGTTTAATTTTTTTATATTTTTTATTAAAACAGATTATAATT
13537 GANNNNNNNN
Statistics
Matches: 177, Mismatches: 38, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
170 8 0.05
171 169 0.95
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.41
Consensus pattern (171 bp):
TTTTAAGTTTAATTTTTTTATATTTTTTATTAAAACAGATTATAATTAAACATCTGCCTCAAGAA
ACCTGAAGAAAAAGATATCCATTAACAACAAAAGTCCATTTATAGTCACCCATACTTTCGAAAGC
ATTATTACACACTTTAAATATTTTTGTAACCTCATTATTGA
Found at i:15656 original size:170 final size:170
Alignment explanation
Indices: 15327--15722 Score: 429
Period size: 170 Copynumber: 2.3 Consensus size: 170
15317 NNNNNNNNNN
* *
15327 ATAATTGATTTTAA-TTTAAATTTTTGTATATTTTTATTAAAACAGATTATAATTCAATGTTTAC
1 ATAATTGATTTTAATTTTAAATTTTT-TATATTTTTATTAAAACAGATTATAATTAAATGTCTAC
*******
15391 CTTGAGAAACATCAAGAAAAAGATATGCATTGGCAAGAAAAGTCCATTTATAGTCACCNNNNNNN
65 CTTGAGAAACATCAAGAAAAAGATATGCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCG
**** * *
15456 NNNNAAGCCTTATCACTCGCGTTTAATGATTTTATAAACTC
130 TACAAAGCCATATCACTCACGTTTAATGATTTTATAAACTC
15497 ATAATTGATTTTAATTTTAACA-TTTTTATATTTTTATTAAAACAGATTATAATTAAATGTCTAC
1 ATAATTGATTTTAATTTTAA-ATTTTTTATATTTTTATTAAAACAGATTATAATTAAATGTCTAC
* **********
15561 CTTGAGAAACGTCAAGAAAAAGNNNNNNNNNNGCAAGAAAAGTCCATTTATAGTCACCCATTCCG
65 CTTGAGAAACATCAAGAAAAAGATATGCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCG
* * * * *
15626 TACAAAGTCATATTACTCAC-TTTAAATGATTTTATGACCTT
130 TACAAAGCCATATCACTCACGTTT-AATGATTTTATAAACTC
* *
15667 ATATTTGATTTTAATTTTAAATTTTTTTATATTTTTTATTAAAATAGATTATAATT
1 ATAATTGATTTTAATTTTAAA-TTTTTTATA-TTTTTATTAAAACAGATTATAATT
15723 GANNNNNNNN
Statistics
Matches: 187, Mismatches: 33, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
169 4 0.02
170 142 0.76
171 17 0.09
172 24 0.13
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.39
Consensus pattern (170 bp):
ATAATTGATTTTAATTTTAAATTTTTTATATTTTTATTAAAACAGATTATAATTAAATGTCTACC
TTGAGAAACATCAAGAAAAAGATATGCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCGT
ACAAAGCCATATCACTCACGTTTAATGATTTTATAAACTC
Found at i:19122 original size:171 final size:170
Alignment explanation
Indices: 18715--19976 Score: 633
Period size: 171 Copynumber: 7.4 Consensus size: 170
18705 NNNNNNNNAG
* * *
18715 TTTTAAGTTT-AACTTTTTTATATTTTTTATTAAAACAGATTATATTT-AATATTTGCTTCGGGA
1 TTTTAA-TTTGAATTTTTTTATATTTTTTATTAAAACAGATTATATTTGAATATTTACTTCGAGA
* * * * * *
18778 AACATGAATAAAAAGATATCTATTGATAAAAAAAGTCCATTTATAGTAACTCATGCCTCCGAAAG
65 AACATGAAGAAAAAGATATCCA-TGGTAAGAAAAGTCCATTTATAGTAACCCATGCCTTCGAAAG
* *
18843 CCTTATTACTCGCTTTAAAGGTTTTTGTAACCTCATTATTGA
129 CCTTATTACTCGCTTTAAAGATTTTTATAACCTCATTATTGA
* * ********** * * * *
18885 ATTTAAGTTGAATTTTTTTATATTTTTTATTAANNNNNNNNNNAATTGAATGTCTACTTTGAGAA
1 TTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAGATTATATTTGAATATTTACTTCGAGAA
* * *
18950 ACATGAAGAAAAAGGTATCCACTGGTAAGAAAAGTCCATTTATAGTTACCCACGCCTTCGAAAGC
66 ACATGAAGAAAAAGATATCCA-TGGTAAGAAAAGTCCATTTATAGTAACCCATGCCTTCGAAAGC
* **********
19015 CTTATTACTCG-TATTAAATATTTTTATAACCNNNNNNNNNN
130 CTTATTACTCGCT-TTAAAGATTTTTATAACCTCATTATTGA
* *
19056 TTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAGATTATGTTTGAATATTTACCTCGAGAA
1 TTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAGATTATATTTGAATATTTACTTCGAGAA
* * * * * * * * **
19121 ACATGGAGAAAAAGATATCCATTGCAAGAAAAGTCTATTTAGAGTCACCCATGCTTTTGAAAGGA
66 ACATGAAGAAAAAGATATCCATGGTAAGAAAAGTCCATTTATAGTAACCCATGCCTTCGAAAGCC
********* * *
19186 TTATTACTCGCTTTNNNNNNNNNNT-TAATCTCATAATT-A
131 TTATTACTCGCTTT-AAAGATTTTTATAACCTCATTATTGA
* * * * * * * *
19225 GTTTTAAATTGAACTTTTTTATATTTTTGATTAAAACAGATTATAATTAAATGTCTGCTTC-AGG
1 -TTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAGATTATATTTGAATATTTACTTCGA-G
* * * * * * * *
19289 AAACGTGAAGAAAAAGATATCTAGTGGCAAGAAAAGTCCATTAATAATCACCCATACCTTCAAAA
64 AAACATGAAGAAAAAGATATCCA-TGGTAAGAAAAGTCCATTTATAGTAACCCATGCCTTCGAAA
* ***********
19354 GCCTTATTACTCGCTTGAAATGA-TTTTATAACNNNNNNNNNNN
128 GCCTTATTACTCGCTTTAAA-GATTTTTATAACCTCATTATTGA
**** * * * **
19397 NNNNAATTTTAAATTTTTTTATATTTTTTATTAAAACA-ATTTATAATTGAATGTCTGCCTT-GA
1 TTTTAA-TTTGAATTTTTTTATATTTTTTATTAAAACAGA-TTATATTTGAATAT-TTACTTCGA
* * * * * * * *
19460 GAAACGTGAAGAAAAAGATATTCATTGGCATGAAAAGTCTATTTAGAGTCACCCATGCTTTCGAA
63 GAAACATGAAGAAAAAGATATCCA-TGGTAAGAAAAGTCCATTTATAGTAACCCATGCCTTCGAA
* *********** * *
19525 AGTCTTATTACNNNNNNNNNNTAATTTTATAACCTCATAATTGA
127 AGCCTTATTACTCGCTTTAAAGATTTTTATAACCTCATTATTGA
* * * * * * **
19569 TTTTAGTTTGAATTTTTTTATATTTTCTATTAAAATAAATTATAATTT-AATGTCTACTTTAAGA
1 TTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAGATTAT-ATTTGAATATTTACTTCGAGA
* * * * ** * * * *
19633 AACGTGAAGAAACATAGATCCATTGACAAGAAAAGTCAATTTATAGTCACCTATGCTTTCGAAAG
65 AACATGAAGAAAAAGATATCCA-TGGTAAGAAAAGTCCATTTATAGTAACCCATGCCTTCGAAAG
** * * *
19698 CCTTATTACTTACATTAAATG-TTTTTATAACCTTATAATTGA
129 CCTTATTACTCGCTTTAAA-GATTTTTATAACCTCATTATTGA
********** * * * * **
19740 TTTTAATTTGAA-TTTTTNNNNNNNNNNATTAAAATAGATTTTAATTGAATGACTGCCTT-GAGA
1 TTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAGATTATATTTGAAT-ATTTACTTCGAGA
* * * ** * * * **
19803 AACGTAAAGAAAATGATATCCATTGACAAGAAAAGTCCATTTAGAGTCACCAATGGTTTCGAAAG
65 AACATGAAGAAAAAGATATCCA-TGGTAAGAAAAGTCCATTTATAGTAACCCATGCCTTCGAAAG
* * * * *
19868 ACTTATTACTCGCATTAAATAATTTTATAACCTCATAATTGA
129 CCTTATTACTCGCTTTAAAGATTTTTATAACCTCATTATTGA
* * * * *
19910 TTTTGATTCGAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACTTCGAGAA
1 TTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAGATTATATTTGAATATTTACTTCGAGAA
19975 AC
66 AC
19977 NNNNNNNNNN
Statistics
Matches: 796, Mismatches: 271, Indels: 49
0.71 0.24 0.04
Matches are distributed among these distances:
169 6 0.01
170 284 0.36
171 384 0.48
172 118 0.15
173 4 0.01
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.37
Consensus pattern (170 bp):
TTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAGATTATATTTGAATATTTACTTCGAGAA
ACATGAAGAAAAAGATATCCATGGTAAGAAAAGTCCATTTATAGTAACCCATGCCTTCGAAAGCC
TTATTACTCGCTTTAAAGATTTTTATAACCTCATTATTGA
Done.