Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399906.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_314.0, 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: 23708
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.23
Warning! 8737 characters in sequence are not A, C, G, or T
Found at i:3552 original size:170 final size:170
Alignment explanation
Indices: 3230--3751 Score: 403
Period size: 170 Copynumber: 3.1 Consensus size: 170
3220 NNNNNNNNNN
* * * ** * * * **
3230 AAATGGCTTTTTCTACACGTTTCTTGAGACAAG-CATTCAATTATAGTCTATTTTAACAAAAAAT
1 AAATGCCTTTTTCTACATGTTTCTCGA-AGTAGACAATCAATTATAGCCTATTGTAAGTAAAAAT
* * * * * *
3294 GTAAAAAAA-TTCAGCTTAAAATAATTATGAGACTGTAAAACAATTTGAAGTGAGTAATAAGGCT
65 GTAAAAAAATTTCA-CTTAAAACAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCA
* * * ** * ** * **
3358 TTTGTAGGAATGGGTGATTATAAATGGATTTTTC-TGCTGTAT
129 GTTGAAAGAATAAGTGACTATAAATAAACTTTTCTTGC-AAAT
* * * * *
3400 GAATGGCTTTTTCTACATGTTTCTCG-AGATAGACACTCAATTGCA-ATCC-ATTGTAAG-CAAA
1 AAATGCCTTTTTCTACATGTTTCTCGAAG-TAGACAATCAATT--ATAGCCTATTGTAAGTAAAA
*
3461 ATGTAAAAAAATTTCACTTAAAACCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGG
63 ATGTAAAAAAATTTCACTTAAAA-CAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGG
3526 CAGTTGAAAGAATAAGTGACTATAAATAAACTTTTCTTGCAAAT
127 CAGTTGAAAGAATAAGTGACTATAAATAAACTTTTCTTGCAAAT
* * * * * *
3570 AAATGCCTTTTTCTTCATGTTTCTCTAAGTCGACAATCAATTATAGCCTGTTTTAAGTAAAAATA
1 AAATGCCTTTTTCTACATGTTTCTCGAAGTAGACAATCAATTATAGCCTATTGTAAGTAAAAATG
* ********** **
3635 TAAAAAAATTTAACTTAAAATCAATTATGAGATTATNNNNNNNNNNAAAGCGAGTAATAAGGCTT
66 TAAAAAAATTTCACTTAAAA-CAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCAG
* * *
3700 TTGAAGGAATGAGTGACTATAAATTAACTTTTCTTGGC-AAT
130 TTGAAAGAATAAGTGACTATAAATAAACTTTTCTT-GCAAAT
*
3741 GAATGCCTTTT
1 AAATGCCTTTT
3752 AACCCAAGAT
Statistics
Matches: 282, Mismatches: 58, Indels: 23
0.78 0.16 0.06
Matches are distributed among these distances:
168 2 0.01
169 26 0.09
170 143 0.51
171 108 0.38
172 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.34
Consensus pattern (170 bp):
AAATGCCTTTTTCTACATGTTTCTCGAAGTAGACAATCAATTATAGCCTATTGTAAGTAAAAATG
TAAAAAAATTTCACTTAAAACAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCAGT
TGAAAGAATAAGTGACTATAAATAAACTTTTCTTGCAAAT
Found at i:4566 original size:170 final size:169
Alignment explanation
Indices: 4201--6255 Score: 719
Period size: 171 Copynumber: 12.1 Consensus size: 169
4191 NNNNTTGAAA
* * * * * * *
4201 GAATGGGTGACTATAAATGGACTTTTCTT-CTCAATGAATAGCTTTTTCCTCAAGTTTCTCT-AG
1 GAATGAGTGACTATAAAAGGACTTTTCTTGC-CAACGAATCG-TTTTTCTTCATGTTTCT-TGAA
* * * * ** * * * * *
4264 GCA-AGCATTCAATTATGGTCTGTTTTGTCCAAAAATATTTAAAAATTTAACTTAAATTCAATTA
63 GTAGA-CATTGAATTATAGTATGTTTTAACCAAAAAT-GTAAAAAATTCAGCTTAAAATCAATTA
* * **********
4328 TGAGATTATAAAATAATTGAAAGCGAGTAATAANNNNNNNNNNG
126 TGAGATTATAAGATAATTTAAAGCGAGTAATAAGACTTTTAAAG
* * *
4372 GAATGGGTGACTATAAAGGGACTTTTCTTACCAACGAATACGTTTTTCTTCATGTTTCTTGAAGT
1 GAATGAGTGACTATAAAAGGACTTTTCTTGCCAACGAAT-CGTTTTTCTTCATGTTTCTTGAAGT
*
4437 AGACATTGAATTATAGTCTGTTTTAACCAAAAATGTAAAAAATTCAGCTTAAAATCAATTATGAG
65 AGACATTGAATTATAGTATGTTTTAACCAAAAATGTAAAAAATTCAGCTTAAAATCAATTATGAG
*************** *
4502 ATTATNNNNNNNNNNNNNNNGAGTAATAAGACTTTTGAAG
130 ATTATAAGATAATTTAAAGCGAGTAATAAGACTTTTAAAG
* * * * *
4542 GAATGAGTGACTATAAATGGACTTTTCTTGGCAATGAATGGCTTTTTCTTCACGTTTCTTG-AGA
1 GAATGAGTGACTATAAAAGGACTTTTCTTGCCAACGAATCG-TTTTTCTTCATGTTTCTTGAAG-
* * * * * *
4606 TATACATTCAATTATAGTATGTTTTAACTAAAAATATAAAAAATTCATCTTAAAATGAATTATGA
64 TAGACATTGAATTATAGTATGTTTTAACCAAAAATGTAAAAAATTCAGCTTAAAATCAATTATGA
*
4671 GATTATAAGATAATTTAAAGCGAGTAATAAGTCTTTTAAAG
129 GATTATAAGATAATTTAAAGCGAGTAATAAGACTTTTAAAG
* *
4712 GAATGAGTGACTATAAAAGGACTTTTCTTGTCAACGAATGTGTTTTTCTTCATGTTTCTCT-AAG
1 GAATGAGTGACTATAAAAGGACTTTTCTTGCCAACGAAT-CGTTTTTCTTCATGTTTCT-TGAAG
* * *********
4776 TAGACATTGAATTATATTATGTTTTAATCAAAAATGTAAAANNNNNNNNNNTAAAATCAATTATG
64 TAGACATTGAATTATAGTATGTTTTAACCAAAAATGTAAAA-AATTCAGCTTAAAATCAATTATG
* * * *
4841 AGATTATAAAATAATTTTAAGTGAGTAATAAGGCTTTTAAAG
128 AGATTATAAGATAATTTAAAGCGAGTAATAAGACTTTTAAAG
* * * * * * * *
4883 G-ATGGGTGGCTATTAACGGACTTCTCTT-CTTAATGAATGGCTTTTTCTTCATGTTTCTT-AAG
1 GAATGAGTGACTATAAAAGGACTTTTCTTGC-CAACGAATCG-TTTTTCTTCATGTTTCTTGAA-
* * ** * *
4945 GTAGACATTCAA-T-TA-TA-GTTTTAA-CAAACAATGTAAAAAAATTGAAATTAGAATCAGTTA
63 GTAGACATTGAATTATAGTATGTTTTAACCAAA-AATGT-AAAAAATTCAGCTTAAAATCAATTA
* * ********** * *
5005 TGAGATTATAAAACANNNNNNNNNNAGTAATAAGGCTTTTAAAA
126 TGAGATTATAAGATAATTTAAAGCGAGTAATAAGACTTTTAAAG
* * * * * *
5049 GAATTAGTGATTATAAATA-GAGTTTTCTTAG-CAATGAATGCCTTTTTCTTCATGTTTCTTGAG
1 GAATGAGTGACTATAAA-AGGACTTTTCTT-GCCAACGAAT-CGTTTTTCTTCATGTTTCTTGAA
********** * * * *
5112 GNNNNNNNNNNATTATAGTCTGTTTTAACTAAAAATGTAAAAACCTTCATCTTAAAATCAATTAT
63 GTAGACATTGAATTATAGTATGTTTTAACCAAAAATGTAAAAA-ATTCAGCTTAAAATCAATTAT
********** * * *
5177 GAGATTATANNNNNNNNNNAAGCGTGTAATAAGCCTTTTGAAG
127 GAGATTATAAGATAATTTAAAGCGAGTAATAAGACTTTTAAAG
* *
5220 GAATGAGTGACTAT-AAAGGTACTTTTCTTGCCAACGAACACATTTTTCCTT-ATGTTTCTCT-A
1 GAATGAGTGACTATAAAAGG-ACTTTTCTTGCCAACGAA-TCGTTTTT-CTTCATGTTTCT-TGA
* * * * ** *
5282 AGCAGATACTT-AATTATTGTCTGTTTTAATTAAAAATGTAAAAAATTCAACTTAAAATCAATTA
62 AGTAGACA-TTGAATTATAGTATGTTTTAACCAAAAATGTAAAAAATTCAGCTTAAAATCAATTA
********** * ** *
5346 TGNNNNNNNNNNATAATTTAAAGTGAGTAATAAGGGTTTGAAAG
126 TGAGATTATAAGATAATTTAAAGCGAGTAATAAGACTTTTAAAG
** *** ** * * *
5390 GAATTG-GTGACTATAAATCGACTTTTCTTATTAATAAATGGCTTTTTCTACATGTTTCTTGAGG
1 GAA-TGAGTGACTATAAAAGGACTTTTCTTGCCAACGAATCG-TTTTTCTTCATGTTTCTTGAAG
* * ********** * * *
5454 CA-AGCATTCAATNNNNNNNNNNTTTAACAAAAAATATAAAAACATTCAACTTAAAATCAATTAT
64 TAGA-CATTGAATTATAGTATGTTTTAACCAAAAATGTAAAAA-ATTCAGCTTAAAATCAATTAT
* * * * * * **
5518 GAGGTTGTAAAACAATTTGAAGCGAGTAATAAGGCTTTTTCAG
127 GAGATTATAAGATAATTTAAAGCGAGTAATAAGACTTTTAAAG
* * * * * * * *
5561 GAATGGGTGATTATAAATGGACTTCTCTT-CTCAATGAATAGCTTTTTCTTTATCTTTCTT-AAG
1 GAATGAGTGACTATAAAAGGACTTTTCTTGC-CAACGAATCG-TTTTTCTTCATGTTTCTTGAA-
* ********** *
5624 GTAGACATTCAATTATNNNNNNNNNNAACCAAAAATATAAAAAAATTCAAGC-TAAAATCAATTA
63 GTAGACATTGAATTATAGTATGTTTTAACCAAAAATGT-AAAAAATTC-AGCTTAAAATCAATTA
* * *
5688 TGAGATTATAAAATAATTTAAAGCTAGTAATAAGGCTTTTAAAG
126 TGAGATTATAAGATAATTTAAAGCGAGTAATAAGACTTTTAAAG
* ** * *
5732 GAATGAGTGACTATGAATA-GACTTTTCTTGTTAATGAAT-GACTTTTTCTAT-ATGTTTCTCGA
1 GAATGAGTGACTAT-AAAAGGACTTTTCTTGCCAACGAATCG--TTTTTCT-TCATGTTTCTTGA
* * * * * ** * * * *
5794 GGCA-AGCATTCAATTATAG-ACGGTTGTAATGAAAAATGCAAAAAAACTCAACTGAAAATCAAT
62 AGTAGA-CATTGAATTATAGTA-TGTTTTAACCAAAAATG-TAAAAAATTCAGCTTAAAATCAAT
* * * * * * *
5857 TATAAGATCATAAAACAATTTAAAGCAAGTAATAAGGCTTTTGAAG
124 TATGAGATTATAAGATAATTTAAAGCGAGTAATAAGACTTTTAAAG
********** * *
5903 GAATGNNNNNNNNNNAATGGACTTTTCTTGCCAATGAAT-GTTTTTTTCTTCATGTTTCTCT-AA
1 GAATGAGTGACTATAAAAGGACTTTTCTTGCCAACGAATCG--TTTTTCTTCATGTTTCT-TGAA
* * * * * * * ****
5966 GTAGATATTCAATTATAGTCTGTTTTAACTATAAATGTAAAAAAATTTAACTTAAAATCANNNNN
63 GTAGACATTGAATTATAGTATGTTTTAACCAAAAATGT-AAAAAATTCAGCTTAAAATCA-ATTA
********** * * * *
6031 NNNNNNNNNNA-ACAATTTAAAACGAGTAATAAGGCTTTTGAAG
126 TGAGATTATAAGATAATTTAAAGCGAGTAATAAGACTTTTAAAG
** * * *
6074 GAATTG-GTGACTATAAATA-GAAATTTCTTAG-CAATGAATACCTTTTTCTTCCTGTTTCTTGA
1 GAA-TGAGTGACTATAAA-AGGACTTTTCTT-GCCAACGAAT-CGTTTTTCTTCATGTTTCTTGA
* * * * ** *
6136 GGTAGACATTCAATTATAGTCTATTTTAAATAAAAATGTAAAAAATTTCAACTTAAAATCAATT-
62 AGTAGACATTGAATTATAGTATGTTTTAACCAAAAATGTAAAAAA-TTCAGCTTAAAATCAATTA
* * *
6200 TCGACATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAAA-
126 T-GAGATTATAAGATAATTTAAAGCGAGTAATAAGACTTTT-AAAG
*
6245 GAATGGGTGAC
1 GAATGAGTGAC
6256 NNNNNNNNNN
Statistics
Matches: 1409, Mismatches: 400, Indels: 150
0.72 0.20 0.08
Matches are distributed among these distances:
165 4 0.00
166 55 0.04
167 51 0.04
168 4 0.00
169 17 0.01
170 450 0.32
171 799 0.57
172 29 0.02
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.34
Consensus pattern (169 bp):
GAATGAGTGACTATAAAAGGACTTTTCTTGCCAACGAATCGTTTTTCTTCATGTTTCTTGAAGTA
GACATTGAATTATAGTATGTTTTAACCAAAAATGTAAAAAATTCAGCTTAAAATCAATTATGAGA
TTATAAGATAATTTAAAGCGAGTAATAAGACTTTTAAAG
Found at i:7660 original size:171 final size:171
Alignment explanation
Indices: 7362--7684 Score: 402
Period size: 171 Copynumber: 1.9 Consensus size: 171
7352 NNATAAAACA
*
7362 ATTTAAAGCGAGTAATAAGGCTTTTGAAGCAATGGGTGACTATAAAGGGAGTTTTCTTATCAACA
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGCAATGGATGACTATAAAGGGAGTTTTCTTATCAACA
* * * **
7427 AATGTGTTTTTTTTCATGTTTCTCTAAGTAGACATTTAATTATAAACTATTTTAGTCAAAAATGT
66 AATGTGTTTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATAAACTATTTTAACCAAAAATGT
7492 AAAAAATTTCAAATTAAAATCAATTTTGAGATTAAAAAATT
131 AAAAAATTTCAAATTAAAATCAATTTTGAGATTAAAAAATT
* * * * *
7533 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATGATTATAAA-TGATTTTTTCTTGGT-AA
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGCAATGGATGACTATAAAGGGA-GTTTTCTT-ATCAA
** * * *** *
7596 TGAATG-GCTTTTTCTTCATGTTTCAT-GAGGTAGATATTCAATTATAGTTTGTTTTAACCAAAA
64 CAAATGTG-TTTTTCTTCATGTTTC-TCGAAGTAGACATTCAATTATAAACTATTTTAACCAAAA
*
7659 ATGTAAAAAATTTCAACTTAAAATCA
127 ATGTAAAAAATTTCAAATTAAAATCA
7685 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
170 3 0.02
171 123 0.96
172 2 0.02
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (171 bp):
ATTTAAAGCGAGTAATAAGGCTTTTGAAGCAATGGATGACTATAAAGGGAGTTTTCTTATCAACA
AATGTGTTTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATAAACTATTTTAACCAAAAATGT
AAAAAATTTCAAATTAAAATCAATTTTGAGATTAAAAAATT
Found at i:8209 original size:21 final size:20
Alignment explanation
Indices: 8171--8209 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
8161 AACATGAAGA
*
8171 AAAAGCCATTCATTATCAAG
1 AAAAGCCATTCATAATCAAG
*
8191 AAAAGACCATTTATAATCA
1 AAAAG-CCATTCATAATCA
8210 CCCATTCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.26
Consensus pattern (20 bp):
AAAAGCCATTCATAATCAAG
Found at i:8902 original size:77 final size:77
Alignment explanation
Indices: 8764--8910 Score: 195
Period size: 77 Copynumber: 1.9 Consensus size: 77
8754 AAATTATTTT
* * * * *
8764 ATAATCTCATAATTGATTTTAAATTGAATATTTTTATAGTTTTGGTTAAAATAGACAATAATTGA
1 ATAATCTCATAATTGATTTTAAATTAAATATTTTTACAGTTTTAGTGAAAACAGACAATAATTGA
8829 ATGTCATAATTG
66 ATGTCATAATTG
* * * * *
8841 ATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTAGTGAAAACAGGCTATAATTGA
1 ATAATCTCATAATTGATTTTAAATTAAATATTTTTACAGTTTTAGTGAAAACAGACAATAATTGA
*
8906 TTGTC
66 ATGTC
8911 TACTTAGAGA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
77 59 1.00
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.45
Consensus pattern (77 bp):
ATAATCTCATAATTGATTTTAAATTAAATATTTTTACAGTTTTAGTGAAAACAGACAATAATTGA
ATGTCATAATTG
Found at i:15714 original size:169 final size:170
Alignment explanation
Indices: 15422--15971 Score: 546
Period size: 169 Copynumber: 3.2 Consensus size: 170
15412 NNNNNNNNNN
* * *
15422 AATTATGAGATTATAAAACAATTTAAAGT-GAGTAATAAGACTTTTGAATGAATGAGTGACTATA
1 AATTATGAGATTATAAAATAATTTAAA-TCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATA
* * * *
15486 AAGGGACTTTTCTTAC-CAACGAATGCATTTTCTTCATCTTTCTCTAAGTAGATATTCAATTATA
65 AATGGACTTTTCTT-CGCAATGAATGCATTTTCTTCATATTTCTCTAAGAAGATATTCAATTATA
* * **********
15550 GTCTGTTTTAACCAAAAANNNNNNNNNNTTTAACTT-AAAATC
129 GTCTATTTTAACAAAAAATATAAAAAAATTTAACTTCAAAA-C
*
15592 AATTATGAGATTATAAAATAATTTAAATCGAGT-ATAAGGCTTTTGAAGGAATGGGTGACTATAA
1 AATTATGAGATTATAAAATAATTTAAATCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAA
* *
15656 ATGGACTTTT-TTCGTCAATGAATAGTATTTT-TTCATATTTCTCGT-GGCAAGA-ATTCAATTA
66 ATGGACTTTTCTTCG-CAATGAAT-GCATTTTCTTCATATTTCTC-TAAG-AAGATATTCAATTA
*
15717 TAGTCTATTTTAATAAAAAATATAAAAAAATTTAACTTCAAAAC
127 TAGTCTATTTTAACAAAAAATATAAAAAAATTTAACTTCAAAAC
* * * *
15761 AATTATCAGATTATAAAACT-ATTTAAAACGAGTAATAAGGCTTTTGATGGAATGAGTGACTCTA
1 AATTATGAGATTATAAAA-TAATTTAAATCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATA
* * * * * *
15825 AATAGACTTTTCTT-GCCAATGAATGCCTTTTTCTTCATGTTT-TCTGATGTAGACATTCAATTA
65 AATGGACTTTTCTTCG-CAATGAATG-CATTTTCTTCATATTTCTCT-AAGAAGATATTCAATTA
** * * * *
15888 TAGTCTATTTTAAGTAAAAATTTAAAAAAAATCTAACTTTAAATC
127 TAGTCTATTTTAACAAAAAATAT-AAAAAAATTTAACTTCAAAAC
* *
15933 AATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAG
1 AATTATGAGATTATAAAATAATTTAAATCGAGTAATAAG
15972 NNNNNNNNNN
Statistics
Matches: 319, Mismatches: 44, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
167 1 0.00
168 2 0.01
169 123 0.39
170 100 0.31
171 40 0.13
172 53 0.17
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (170 bp):
AATTATGAGATTATAAAATAATTTAAATCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAA
ATGGACTTTTCTTCGCAATGAATGCATTTTCTTCATATTTCTCTAAGAAGATATTCAATTATAGT
CTATTTTAACAAAAAATATAAAAAAATTTAACTTCAAAAC
Found at i:17116 original size:169 final size:170
Alignment explanation
Indices: 16822--17170 Score: 449
Period size: 169 Copynumber: 2.1 Consensus size: 170
16812 NNNNNNNNNN
* *
16822 TGAGATTA-AAAAATCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAGATAACTATAAATGG
1 TGAGATTATAAAAA-CATTTAAAGAGAGTAACAAGGCTTTTAAAGGAATAGATAACTATAAATGG
* *
16886 ACTTTTGTTATCAATGAATGGCTTTTTCTATAGGTTTATTGAGGCAAGCAATCAATTATAGTCTG
65 ACTTCTCTTATCAATGAATGGCTTTTTCTATAGGTTTATTGAGGCAAGCAATCAATTATAGT-TG
* *
16951 TTTTAACTAAAAATATAAAAAAATTCAACTTAAAATC-GTTA
129 TTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTA
* * * * *
16992 TGAGATTATAAAAA-ATTTAAAGTA-TGTAACAAGGCTTTTAAAGGGATCGGTGACTATAAATGG
1 TGAGATTATAAAAACATTTAAAG-AGAGTAACAAGGCTTTTAAAGGAATAGATAACTATAAATGG
* * * *
17055 ACTTCTCTTCTCAATGATTGGCTTTTTCT-TCATGTTT-TTCGAGGCAAGCATTCAATTATAGTT
65 ACTTCTCTTATCAATGAATGGCTTTTTCTAT-AGGTTTATT-GAGGCAAGCAATCAATTATAGTT
* * *
17118 TTTTTATCAAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
128 GTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTA
17161 TGAGATTATA
1 TGAGATTATA
17171 GAACAATTNN
Statistics
Matches: 156, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
168 38 0.24
169 104 0.67
170 9 0.06
171 5 0.03
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (170 bp):
TGAGATTATAAAAACATTTAAAGAGAGTAACAAGGCTTTTAAAGGAATAGATAACTATAAATGGA
CTTCTCTTATCAATGAATGGCTTTTTCTATAGGTTTATTGAGGCAAGCAATCAATTATAGTTGTT
TTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTA
Found at i:17624 original size:170 final size:160
Alignment explanation
Indices: 17367--17697 Score: 360
Period size: 170 Copynumber: 2.0 Consensus size: 160
17357 AGCGAGTAAT
* * * *
17367 AAGGCTTTTGTAGGAATGAATGACTATAAATGGACTTTTCTTACCAATGAATGTATTTTTCTTCA
1 AAGGCTTTTGAAGGAATGAATGACTATAAATAGACTTTTCTTACCAATCAATGGATTTTTCTTCA
* **
17432 CATTTTTCAAGGTAGACATTCAATTATAGTCTATTTTAATTAAAAATAT-AAAAAATTTAACTTA
66 CATTTTTCAAGGCAGACATTCAATTATAGTCTATTTTAACCAAAAATATAAAAAAATTTAACTTA
17496 AAATCAATTATGAGAATATAAAACAATTTAA
131 AAATC-ATTATGAGAATATAAAACAATTTAA
** * ** *
17527 ANNNNNNNNNNAGGCTTTTGAAGGAATGGGTGGCTATAAATAGACTTTTCTTGTCAATCAATGGC
1 A----------AGGCTTTTGAAGGAATGAATGACTATAAATAGACTTTTCTTACCAATCAATGGA
** * * * *
17592 TTTTTCTATC-TGTTTTTTAAGGCAGGCATTCAATTATAGTCTGTTTTAACCAAACATATAAAAA
56 TTTTTCT-TCACATTTTTCAAGGCAGACATTCAATTATAGTCTATTTTAACCAAAAATATAAAAA
*
17656 AATTTAACTTAAAATCATTATGAGATTATAAAACAATTTAA
120 AATTTAACTTAAAATCATTATGAGAATATAAAACAATTTAA
17697 A
1 A
17698 GTGTGTAATA
Statistics
Matches: 139, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
160 1 0.01
170 116 0.83
171 22 0.16
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.37
Consensus pattern (160 bp):
AAGGCTTTTGAAGGAATGAATGACTATAAATAGACTTTTCTTACCAATCAATGGATTTTTCTTCA
CATTTTTCAAGGCAGACATTCAATTATAGTCTATTTTAACCAAAAATATAAAAAAATTTAACTTA
AAATCATTATGAGAATATAAAACAATTTAA
Found at i:17714 original size:170 final size:170
Alignment explanation
Indices: 17323--18523 Score: 885
Period size: 171 Copynumber: 7.0 Consensus size: 170
17313 NNNNNNNNNN
* * * *
17323 TTAAAATCAATTTTTAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGTAGGAATGAAT
1 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGT
* * * ** *
17388 GACTATAAATGGACTTTTCTTACCAATGAATGTATTTTTCTTCACATTT-TTCAAGGTAGACATT
66 GACTATAAATAGACTTTTCTTGCCAATGAATG-GTTTTTCTTCATGTTTCTTTAA-GTAGACATT
* ** * *
17452 CAATTATAGTCTATTTTAATTAAAAATAT-AAAAAATTTAAC
129 CAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAAC
* ********** *
17493 TTAAAATCAATTATGAGAATATAAAACAATTTAAANNNNNNNNNNAGGCTTTTGAAGGAATGGGT
1 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGT
* * * * *
17558 GGCTATAAATAGACTTTTCTTGTCAATCAATGGCTTTTTCTATC-TGTTT-TTTAAGGCAGGCAT
66 GACTATAAATAGACTTTTCTTGCCAATGAATGG-TTTTTCT-TCATGTTTCTTTAA-GTAGACAT
* * *
17621 TCAATTATAGTCTGTTTTAACCAAACATATAAAAAAATTTAAC
128 TCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAAC
* * * *
17664 TTAAAATC-ATTATGAGATTATAAAACAATTTAAAGTGTGTAATAAGGCTTTTGAAGGGATGGGT
1 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGT
* ********** **** * *
17728 GACTATAAATGGACTTTTNNNNNNNNNNAATGGCTTTTTCTTCATGTTTCTCGGGGTAGATATTT
66 GACTATAAATAGACTTTTCTTGCCAATGAATGG-TTTTTCTTCATGTTTCTTTAAGTAGACATTC
* * *******
17793 AATTATAGTCTATTTTATCCAAAAATGTAAAAAANNNNNNN
130 AATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAAC
*** * *
17834 NNNAAATCAATTATGAGACTATAAAACAATTTAAAGCGTGTAATAAGGCTTTTGAAGGAATGAGT
1 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGT
** * ** *
17899 GACTATAAACGGACTTTTCTTGCCCACAAAT-GTAGTTTTCTTCATGTTTCTCTAAGTAGACATT
66 GACTATAAATAGACTTTTCTTGCCAATGAATGGT--TTTTCTTCATGTTTCTTTAAGTAGACATT
* * * ********
17963 CAATTATTGTCTGTTTTAACCAAAAATGGAAATANNNNNNNN
129 CAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAAC
*** * * * *
18005 NNCAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGAAATAAGGCTTTTGAAAGAATGGGT
1 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGT
* ** * *****
18070 GACTATAAAGAGACTTTTCTTGATAATGAATGTGTTTTTCTTCATGTTTCTCTAAGTAGANNNNN
66 GACTATAAATAGACTTTTCTTGCCAATGAATG-GTTTTTCTTCATGTTTCTTTAAGTAGACATTC
*****
18135 NNNNNTAGTCTGTTTTAACCAAAAATGTAAAAACAATTCAAC
130 AATTATAGTCTGTTTTAACCAAAAATGTAAAAA-AATTCAAC
* * * * * * *
18177 TTAAAATCAGTTATGAGATTATTAAATAATTTAAAGCAAGTAATAAGGCTTTTAAAGGAATCAAT
1 TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGT
* ** * *
18242 GACTATAAAGAGACTTTTCTTGCCAATGAATGTGTTTTTCTTCACATTTCTTTAAGAAGACATTG
66 GACTATAAATAGACTTTTCTTGCCAATGAATG-GTTTTTCTTCATGTTTCTTTAAGTAGACATTC
*
18307 AATTATAGTCTGTTTTAACCAAAAATGTAAAGAAATTCAAC
130 AATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAAC
* * * * * **
18348 TAAAAAAT-AATTATAAGATTACAAAACAATTTAAAGTGAGTAATAAGGCTTTCGAAGGAATGNN
1 T-TAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAG
******** * ** * *
18412 NNNNNNNNAAT-GCACTTTTCTT-CTCAATGAATGATATTTTCTAAATGTTTCCTT-AGATAGGC
65 TGACTATAAATAG-ACTTTTCTTGC-CAATGAATGGT-TTTTCTTCATGTTTCTTTAAG-TAGAC
** *
18474 ATTCAATTATAGTCTGTTTTAATGAAAAATATAAAAAAATTCAAC
126 ATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAAC
18519 -TAAAA
1 TTAAAA
18524 NNNNNNNNNN
Statistics
Matches: 812, Mismatches: 203, Indels: 33
0.77 0.19 0.03
Matches are distributed among these distances:
169 7 0.01
170 248 0.31
171 416 0.51
172 139 0.17
173 2 0.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.34
Consensus pattern (170 bp):
TTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGT
GACTATAAATAGACTTTTCTTGCCAATGAATGGTTTTTCTTCATGTTTCTTTAAGTAGACATTCA
ATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAAC
Done.