Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398140.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1443.0, 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: 8638
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.29
Warning! 1691 characters in sequence are not A, C, G, or T
Found at i:453 original size:171 final size:170
Alignment explanation
Indices: 56--885 Score: 636
Period size: 171 Copynumber: 4.8 Consensus size: 170
46 ACTGACAGTC
*
56 GACATTC-ATATATAGTCTGTTTTAACCAAAAATGTAAAAAAAGAAATTGAACATAAAATCAATT
1 GACATTCAAT-TATAGTCTGTTTTAACC-AAAA---AAGAAAA-AAATTGAACATAAAATCAATT
* * * *
120 TTGAGATAATAAAA-TCATGTGAAGTGGGTAATAAGGCTTTTGAAGGAACGAGTGACTATAAATG
60 TTGAGATTATAAAACT-ATGTGAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATA
* * * * * *
184 GACTTTTCATGCCAATGAATACCATTTTCTTTATATTTCTTGATGTA
124 GACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGGTA
* * * ********* *
231 GAAATTCAATTATAATATGTTTTAACC-AAAAAGTANNNNNNNNNNAACTTAAAATCAATTTTGA
1 GACATTCAATTATAGTCTGTTTTAACCAAAAAAG-A-AAAAAATTGAACATAAAATCAATTTTGA
* * * *
295 GATTATAAAACTATTTGAAGTGATTAATAAGGCTTTTGAAGGACTGAGTGATTATAAATAGACTT
64 GATTATAAAACTATGTGAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTT
* * *
360 TTCTTGCCAATGAATGCCTTTTTCTTCATTTTTCTTGACGTG
129 TTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGGTA
* * * * *
402 GACATTTAATTATAATCTGTTTTAACCAAAAAAGAAAATAAATAGAACTTAAAATCAATTTGGAG
1 GACATTCAATTATAGTCTGTTTTAACCAAAAAAGAAAA-AAATTGAACATAAAATCAATTTTGAG
* * * * * ********* *
467 ATTAAAAAACCA-ATAAAGTGAGTAGTAAGGCTTTNNNNNNNNNNG-GTGACTAT-AATAGTCTT
65 ATTATAAAACTATGTGAAGTGAGTAATAAGGCTTT-TGAAGGAATGAGTGACTATAAATAGACTT
** * * *
529 TTCTTGCCAATGAATGTATTTTCCTTAATGTTTCTTAAGGTA
129 TTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGGTA
* * * * ********** *
571 AACATTCAATTATTGTCTATTTTAACCAAAAATATAAAAANNNNNNNNNNAAAATAAATTTTGAG
1 GACATTCAATTATAGTCTGTTTTAACCAAAAA-AGAAAAAAATTGAACATAAAATCAATTTTGAG
* * * ** ** * * *
636 ATTATAAAACAATTTAAAACGAGTAATAAAACTTTTGAAAGAATGAGAGACTATAAATTGACTTT
65 ATTATAAAACTATGTGAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTT
701 TCTTGCCAATGAATG-CTCTTTTCTTCATGTTTC-TGAAGGTA
130 TCTTGCCAATGAATGCCT-TTTTCTTCATGTTTCTTG-AGGTA
* * *
742 GACATTCAATTACAGTCTGTTTTAACTAAAAATGTAAAAACAAAATTGAACATAAAATCAATTTT
1 GACATTCAATTATAGTCTGTTTTAACCAAAAA---AGAAA-AAAATTGAACATAAAATCAATTTT
* *
807 GAGA-TATAAAA-TCATGTGAAGTGGGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGA
62 GAGATTATAAAACT-ATGTGAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGA
*
870 CTTTTCATGCCAATGA
126 CTTTTCTTGCCAATGA
886 NNNNNNNNNN
Statistics
Matches: 500, Mismatches: 138, Indels: 36
0.74 0.20 0.05
Matches are distributed among these distances:
169 94 0.19
170 57 0.11
171 232 0.46
172 7 0.01
173 70 0.14
174 17 0.03
175 21 0.04
176 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.34
Consensus pattern (170 bp):
GACATTCAATTATAGTCTGTTTTAACCAAAAAAGAAAAAAATTGAACATAAAATCAATTTTGAGA
TTATAAAACTATGTGAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTT
CTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGGTA
Found at i:2357 original size:173 final size:172
Alignment explanation
Indices: 1183--2402 Score: 780
Period size: 172 Copynumber: 7.1 Consensus size: 172
1173 NNNNNNNNNN
* * * * * *
1183 AAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACGATTTAAAGCGAGTGATAAAGCTTT
1 AAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATGTAAAGTGAGTAATAAGGCTTT
* * * * * **********
1248 TGAAAGAATGAGAGACTATAAATAGACTTTTCTTGCCAGTGAATGCCTTTTTCTTNNNNNNNNNN
66 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTC
* * * *
1313 AATGTAGACATTCAATTATAGTCTGTTTTAAACAAAAAT-TAA
131 GATGTAAACATTCAATTATAATCTGTTTTAACCAAAAATGT-A
* ********** * *
1355 AAAAAAATTGAACATAAAATCAATTTTNNNNNNNNNNAACCATGTGAAGTGGGTAATAAGGCTTT
1 AAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATGTAAAGTGAGTAATAAGGCTTT
* * * * * *
1420 TGAAGGAATGAGTAACTATAAATGGACTTTTCATGCCAATGAATGCCTTTTTCTTTATATTTCTT
66 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTC
* *
1485 GATGTAGAA-ATTCAATTCTAATCTGTTTTAACCAAAAAAGTA
131 GATGTA-AACATTCAATTATAATCTGTTTTAACCAAAAATGTA
* * * ********* *
1527 TAAAAAATTAAACTGAAAAATCAATTTTGAGATTATAANNNNNNNNNNAA-TGAGTAGTAAGGCT
1 AAAAAAATTGAACT-TAAAATCAATTTTGAGATTATAA-AACCATGTAAAGTGAGTAATAAGGCT
* * ***
1591 TTTGAAGGAATGGGTGGCTATAAATGGAC-TTTCTTGCCAATGAATGCTTTTTTCTTCATGTNNN
64 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTC
******* *
1655 NNNNNNNAAACATTCAATTATAA-CATGTTTTAAGCAAAAAAT-TA
129 TCGATGTAAACATTCAATTATAATC-TGTTTTAA-CCAAAAATGTA
* * * * * * * *
1699 AAAAAAATTGAACTTAAAATTAGTTTTTAGTTTATAAAACTATTTAAAGTTAGTAATAGGGCTTT
1 AAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATGTAAAGTGAGTAATAAGGCTTT
* * *
1764 CTGAAGGAACGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGTC-TTTTCTTCACGTTTCT
66 -TGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCT
* * * * *********** *
1828 TGATGTAGACATTTAATTGTAATNNNNNNNNNNAAAAAAAGT-
130 CGATGTAAACATTCAATTATAATCTGTTTTAACCAAAAATGTA
* * * * * *
1870 AAATAAATTGAACTTAAAATTAATTTTGA-ATTTATAAAACTA-ATAAAGTGAGTAGTAAGACTT
1 AAAAAAATTGAACTTAAAATCAATTTTGAGA-TTATAAAACCATGTAAAGTGAGTAATAAGGCTT
* * * * *
1933 TTGAAGTAATGGGTGACTAT-AATAGCCTTTTCTTGCCAATGAATGCATTTTTCTTAATGTTTCT
65 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCT
* * * ** * * * * *
1997 -TAAGATAACCATTCAATTATTGTTTATGTCAACCAAAAAGGT-
130 CGATG-TAAACATTCAATTATAATCTGTTTTAACCAAAAATGTA
* ** * ** *
2039 AAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAAAGATTTAAAGCAAGTAATAAAGCTTT
1 AAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATGTAAAGTGAGTAATAAGGCTTT
* * * ********** *
2104 TGAAAGAATGAGAGACTATAAATGGACTTTTNNNNNNNNNNAATGCTTTTTTCTTCATGTTTCTC
66 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTC
* * * * * *
2169 AAAGTAGACATTCAATTGTAGTCTGTTTTAACTAAAAATGTAA
131 GATGTAAACATTCAATTATAATCTGTTTTAACCAAAAATGT-A
* * *
2212 AAAAAAATTGAACATAAAATCAATTTTGACATTATAAAACCATGTGAAGTG-GATAATAAGGCTT
1 AAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATGTAAAGTGAG-TAATAAGGCTT
* * * * * *
2276 TCGAAGGAA-GGAGCGACTATAAATGGACTTTTCATGCCAATGAATGCCTTCTTCTTTATATTTC
65 TTGAAGGAATGG-GTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTC
* *
2340 TCGATGTAAAAATTCAATTATAATATGTTTTAACCAAAAA-GTA
129 TCGATGTAAACATTCAATTATAATCTGTTTTAACCAAAAATGTA
* *
2383 TAAAAAATTAAACTTAAAAT
1 AAAAAAATTGAACTTAAAAT
2403 NNNNNNNNNN
Statistics
Matches: 775, Mismatches: 250, Indels: 47
0.72 0.23 0.04
Matches are distributed among these distances:
168 25 0.03
169 85 0.11
170 51 0.07
171 152 0.20
172 257 0.33
173 203 0.26
174 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.34
Consensus pattern (172 bp):
AAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATGTAAAGTGAGTAATAAGGCTTT
TGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTC
GATGTAAACATTCAATTATAATCTGTTTTAACCAAAAATGTA
Found at i:3590 original size:172 final size:171
Alignment explanation
Indices: 2805--3952 Score: 883
Period size: 171 Copynumber: 6.7 Consensus size: 171
2795 NNNNNNNNAA
* * * *
2805 AAAAAAATTGAACATAAAATCAATTTTGAGATAATAAAACCATTTAAAGTGGAA--AACAAGGCT
1 AAAAAAATTGAACTTAAAATCAATTTTGTGATTATAAAACCATTTAAAGT--AAGTAATAAGGCT
* * * * *
2868 TTTGAAGGAATGAGTGACTATAAATAGACTTTTGTTGCTAATGAATGTCTTTTTCTTCACGTTTC
64 TTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTC
* * * *
2933 TCGATGTAAATATTCAATTATAATATGTTTTAAGC-AAAAAAGT
129 TTGAGGTAAACATTCAATTATAATCTGTTTTAA-CTAAAAAAGT
* * * * *
2976 AAAAACAAATTTGAACTTAAAATCAATATTGAGATTATGAAACCATTTAAAGTGAGTAATAAGCC
1 -AAAA-AAA-TTGAACTTAAAATCAATTTTGTGATTATAAAACCATTTAAAGTAAGTAATAAGGC
* ** *
3041 TTTTGAAGGAATTGGTGACTAT-AATAGACTTTTCTTGCCAATGAATGTGTTTTTCTTCACGTTT
63 TTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTT
* ********** *
3105 CTTAAGGTAAACATTNNNNNNNNNNCTGTTTTAACTAAAAATGT
128 CTTGAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAAAGT
* * * * *** *
3149 AAAAAAATTCAACTTAAAATTAATTTTGAGATTATAAAACCATTTGAACCGAGTAATAAAGCTTT
1 AAAAAAATTGAACTTAAAATCAATTTTGTGATTATAAAACCATTTAAAGTAAGTAATAAGGCTTT
* * * * * ** ** * *
3214 TAGAA-GAATGGGAGGCTCTAAATGGACTTTTCTTACCAACAAATGAGTTTTTCTACATGTTTCC
66 T-GAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCT
** ** * * * * *
3278 CAAGGTAGGCATTCAATTACAATATGTTTTAACCAGAAATGT
130 TGAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAAAGT
* * * * * * * *
3320 AAAAAACTTCAGCTTAAAATCAATTATGAGATTCTAAAACCATTTAAAGCAAGTAATAAGCCTTT
1 AAAAAAATTGAACTTAAAATCAATTTTGTGATTATAAAACCATTTAAAGTAAGTAATAAGGCTTT
* * * * * * *
3385 TGAAGGAATGGGAGAGTGTAAATGGATTTTTCTTGCCAATAAATGCCTTTTTCTTCATGTTTGTT
66 TGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTT
3450 GAGGTAAACATTCAATTATAA-CATGTTTTAAGC-AAAAAAGT
131 GAGGTAAACATTCAATTATAATC-TGTTTTAA-CTAAAAAAGT
*********** * * *
3491 AAAAAAAATTGAANNNNNNNNNNGTTTT-TAGTTTATAAAACCATTTAAAGTTAGTAATAGGGCT
1 -AAAAAAATTGAACTTAAAATCAATTTTGT-GATTATAAAACCATTTAAAGTAAGTAATAAGGCT
* * * **
3555 TCTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAACGAATACCTTTTTCTTCACATTTC
64 TTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTC
* *
3620 TTGACGTAAACATTTAATTATAATCTGTTTTAACTAAAAAAGT
129 TTGAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAAAGT
* * * *
3663 AAATAAATTGAACTTAAAATCAATTTTGTGATTATAAAACTATTTAAAGTGAGTAGTAAGGCTTT
1 AAAAAAATTGAACTTAAAATCAATTTTGTGATTATAAAACCATTTAAAGTAAGTAATAAGGCTTT
* * * * * *
3728 TGAAGTAAAGGGTGACTAT-AATAGTCTTTTCTTGCCAATGAATGCATTTTTGTTAATGTTTCTT
66 TGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTT
* ** * **********
3792 AAGGTAAACATTCAATTATTGTCTATTTTNNNNNNNNNNGT
131 GAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAAAGT
* * ** * ** ** * *
3833 AAAAAAATTCAACTTAAAAGCAATTTTAAGTTTATAAAATGATTTAAAGCGAGTGATAAAGCTTT
1 AAAAAAATTGAACTTAAAATCAATTTTGTGATTATAAAACCATTTAAAGTAAGTAATAAGGCTTT
* * * * * *
3898 CGAAAGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTT
66 TGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTT
3953 NNNNNNNNNN
Statistics
Matches: 764, Mismatches: 196, Indels: 33
0.77 0.20 0.03
Matches are distributed among these distances:
170 191 0.25
171 297 0.39
172 142 0.19
173 69 0.09
174 65 0.09
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.35
Consensus pattern (171 bp):
AAAAAAATTGAACTTAAAATCAATTTTGTGATTATAAAACCATTTAAAGTAAGTAATAAGGCTTT
TGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTT
GAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAAAGT
Found at i:4940 original size:172 final size:158
Alignment explanation
Indices: 4809--5117 Score: 164
Period size: 170 Copynumber: 1.9 Consensus size: 158
4799 NNNNNNNNNN
* * * * *
4809 ATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTGTAGTCTGTTTTAAACAAAAATGTA
1 ATGCTTTTTTCTTCATGTTTCTCAAGATAGACATTCAATTATAGTCTATGTTAAACAAAAAGGT-
* * * *
4874 AAAAAAATTGAA-TATAAAATTAATTTTGAGA-TAGTAAAATC-TTGTGAAGTG-GATAATAAGG
65 AAAAAAATTCAACT-TAAAATCAATTTTGAGATTA-TAAAA-CATT-TAAAGTGAG-TAATAAAG
* * *
4935 CTTTTGAAGGACTAAGTGACTATAAATGGACTTTT
125 CTTTTGAAAGAATAAGAGACTATAAATGGAC-TTT
* * * * * * *
4970 CATGCCAATGAAAGCCTTTTCTTTATATTTCTCGATG-TAGAAATTCAATTATAATCTATTTTAA
1 -ATG-C--T------TTTTTCTTCATGTTTCTC-AAGATAGACATTCAATTATAGTCTATGTTAA
* *
5034 CCAAAAA-GTATAAAAAATTAAACTTAAAATC-ATGTTTGAGATTATAAAACTATTTAAAGTGAG
55 ACAAAAAGGTA-AAAAAATTCAACTTAAAATCAAT-TTTGAGATTATAAAAC-ATTTAAAGTGAG
* * *
5097 TAGTAAGGCTTTTGAAGGAAT
117 TAATAAAGCTTTTGAAAGAAT
5118 GGGTNNNNNN
Statistics
Matches: 116, Mismatches: 14, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
162 3 0.03
163 1 0.01
165 1 0.01
169 4 0.03
170 55 0.47
171 50 0.43
172 2 0.02
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (158 bp):
ATGCTTTTTTCTTCATGTTTCTCAAGATAGACATTCAATTATAGTCTATGTTAAACAAAAAGGTA
AAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACATTTAAAGTGAGTAATAAAGCTTTTG
AAAGAATAAGAGACTATAAATGGACTTT
Found at i:5114 original size:170 final size:170
Alignment explanation
Indices: 4499--5118 Score: 538
Period size: 171 Copynumber: 3.6 Consensus size: 170
4489 NNNNNNNNNN
* * * * * * *
4499 ACATTTAATTGTAATCTGTTTTAACAAAAAAAGTAAATAAATTGAACTTAAAATCAATTTTGAGT
1 ACATTCAATTATAATCTATTTTAACCAAAAAGGTAAAAAAATTGAACTTAAAATCAATTTTGAGA
* * * * * * * *
4564 TTATAAAACTA-ATAAAGTGAGTAGTAAGACTTTTGAAGTAATGGGTAACTAT-AATAGCCTTTT
66 TTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTT
* * *
4627 CTTGCCAATGAATGCATATTTCGTAATGTTTCT-TAAGATAG
131 CATGCCAATGAATGCAT-TTTCTTAATGTTTCTCAAAG-TAG
* ** * *
4668 CCATTCAATTATTGTCTATGTTAACCAAAAAGGTAAAAAAATTCAACTTAAAATCAATTTTGAGA
1 ACATTCAATTATAATCTATTTTAACCAAAAAGGTAAAAAAATTGAACTTAAAATCAATTTTGAGA
* * * * *
4733 TTATAAAACGATTTAAAGTGAGTAATAAAGCTTTTGAAAGAATGAGAGACTATAAATGGACTTTN
66 TTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTT
*********** * * *
4798 NNNNNNNNNNNATGCTTTTTTCTTCATGTTTCTCAAGGTAG
131 CATGCCAATGAATGC-ATTTTCTTAATGTTTCTCAAAGTAG
* * * * * *
4839 ACATTCAATTGTAGTCTGTTTTAAACAAAAATGTAAAAAAAATTGAA-TATAAAATTAATTTTGA
1 ACATTCAATTATAATCTATTTTAACCAAAAAGGT-AAAAAAATTGAACT-TAAAATCAATTTTGA
* * * *
4903 GA-TAGTAAAATCT-TGTGAAGTG-GATAATAAGGCTTTTGAAGGACTAAGTGACTATAAATGGA
64 GATTA-TAAAA-CTATTTAAAGTGAG-TAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGA
* * * * * *
4965 CTTTTCATGCCAATGAAAGCCTTTTCTTTATATTTCTCGATGTAG
126 CTTTTCATGCCAATGAATGCATTTTCTTAATGTTTCTCAAAGTAG
* *
5010 AAATTCAATTATAATCTATTTTAACCAAAAA-GTATAAAAAATTAAACTTAAAATC-ATGTTTGA
1 ACATTCAATTATAATCTATTTTAACCAAAAAGGTA-AAAAAATTGAACTTAAAATCAAT-TTTGA
*
5073 GATTATAAAACTATTTAAAGTGAGTAGTAAGGCTTTTGAAGGAATG
64 GATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATG
5119 GGTNNNNNNN
Statistics
Matches: 348, Mismatches: 88, Indels: 29
0.75 0.19 0.06
Matches are distributed among these distances:
169 68 0.20
170 88 0.25
171 109 0.31
172 82 0.24
173 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.35
Consensus pattern (170 bp):
ACATTCAATTATAATCTATTTTAACCAAAAAGGTAAAAAAATTGAACTTAAAATCAATTTTGAGA
TTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTT
CATGCCAATGAATGCATTTTCTTAATGTTTCTCAAAGTAG
Found at i:7233 original size:343 final size:334
Alignment explanation
Indices: 6884--7509 Score: 670
Period size: 343 Copynumber: 1.8 Consensus size: 334
6874 NNNNNNATTT
* *
6884 AATTATAATCTGTTTTAA-CCAAAAAGTATAAAAAATAAAACTTAAAATCAATTTTGAGATTATA
1 AATTATAATCTATTTTAAGCCAAAAAGTA-AAAAAATAAAACTTAAAATCAATTTTGAGACTATA
********** *
6948 NNNNNNNNNNAAGTGAGTGATAAGGCTTTTGAAGGAAAT-GATAACTATAAATGGGCTTTTCTTA
65 AAACCATTTAAAGTGAGTGATAAGGCTTTTGAA-GAAATGGATAACTAT-AATAGGCTTTTCTTA
* * * **
7012 CCAATGAATGCCTTTTTCTTTATGTTTCTCATTATAGACATTCAATTACAATCTGTTGTAAGCAA
128 CCAATGAATGCATTTTTCTTCATGTCTCTCAAGATAGACATTCAATTACAATCTGTTGTAAGCAA
* * * * *
7077 AAAAATAAAAAAA-AATTGAACTTAAAACCAATT-TTAAGATTATAAAACCATTTAAAGT-GAGT
193 AAAAACAAAAAAACAATTCAAATTAAAACCAATTACT-AGATTATAAAACCATTTAAA-TCGACT
7139 AAAAAGGCTTTTGAAGGAAT-GGTGACTATAAATGGNNNNNNNNNNCTAATGAATGTCTTTTTCT
256 AAAAAGGCTTTTGAAGGAATGGGTGACTATAAATGG----------CTAATGAATGTCTTTTTCT
7203 TCACATTTCTAGATGTAGATATTC
311 TCACATTTCTAGATGTAGATATTC
* * ** *
7227 AATTATAATCTATTTTAAGCTAAAAAGTAAAAAATTTGAACTTAAAATCATTTTTGAGACTATAA
1 AATTATAATCTATTTTAAGCCAAAAAGTAAAAAAATAAAACTTAAAATCAATTTTGAGACTATAA
* * * * *
7292 AACCATTTAAAGTGAGTGATAAGGCTTTTGAATAAATGGGTGATTATAATAGGCTTTTCTTGCCA
66 AACCATTTAAAGTGAGTGATAAGGCTTTTGAAGAAATGGATAACTATAATAGGCTTTTCTTACCA
* * * *** * *
7357 GTGAATGCATTTTTCTTCATGTCTCTCAAGGTTGACATTCAATTATTGTCTGTTTTAATCAAAAA
131 ATGAATGCATTTTTCTTCATGTCTCTCAAGATAGACATTCAATTACAATCTGTTGTAAGCAAAAA
** * *
7422 TGCAAAAAAACAATTCAAATTAAAATCAATTACTAGATTATAAAACCATTTAAATCGACTAATAA
196 AACAAAAAAACAATTCAAATTAAAACCAATTACTAGATTATAAAACCATTTAAATCGACTAAAAA
7487 GGCTTTTGAAGGAATGGGTGACT
261 GGCTTTTGAAGGAATGGGTGACT
7510 NNNNNNNNNN
Statistics
Matches: 232, Mismatches: 45, Indels: 11
0.81 0.16 0.04
Matches are distributed among these distances:
342 80 0.34
343 135 0.58
344 17 0.07
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.34
Consensus pattern (334 bp):
AATTATAATCTATTTTAAGCCAAAAAGTAAAAAAATAAAACTTAAAATCAATTTTGAGACTATAA
AACCATTTAAAGTGAGTGATAAGGCTTTTGAAGAAATGGATAACTATAATAGGCTTTTCTTACCA
ATGAATGCATTTTTCTTCATGTCTCTCAAGATAGACATTCAATTACAATCTGTTGTAAGCAAAAA
AACAAAAAAACAATTCAAATTAAAACCAATTACTAGATTATAAAACCATTTAAATCGACTAAAAA
GGCTTTTGAAGGAATGGGTGACTATAAATGGCTAATGAATGTCTTTTTCTTCACATTTCTAGATG
TAGATATTC
Found at i:7298 original size:20 final size:18
Alignment explanation
Indices: 7261--7299 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
7251 AAGTAAAAAA
*
7261 TTTGAACTTAAAATCATT
1 TTTGAACTTAAAACCATT
7279 TTTGAGACTATAAAACCATT
1 TTTGA-ACT-TAAAACCATT
7299 T
1 T
7300 AAAGTGAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 3 0.17
20 10 0.56
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (18 bp):
TTTGAACTTAAAACCATT
Found at i:7372 original size:170 final size:169
Alignment explanation
Indices: 6958--7509 Score: 405
Period size: 170 Copynumber: 3.2 Consensus size: 169
6948 NNNNNNNNNN
* * *
6958 AAGTGAGTGATAAGGCTTTTGAAGGAAATGATAACTATAAATGGGCTTTTCTTACCAATGAATGC
1 AAGTGAGTGATAAGGCTTTTGAA-GAAATGGTGACTAT-AATAGGCTTTTCTTACCAATGAATG-
* ** * *
7023 CTTTTTCTTTATGTTTCTCATTATAGACATTCAATTACAATCTGTTGTAAGCAAAAAAATAAAAA
63 CTTTTTCTTCACATTTCTCAATATAGACATTCAATTACAATCTATTGTAAGCAAAAAAAT-AAAA
*
7088 AAAATTGAACTTAAAACCAATTTTAAGATTATAAAACCATTTA
127 AAAATTGAACTTAAAACCAATTTTAAGACTATAAAACCATTTA
* * * ********* *
7131 AAGTGAGTAAAAAGGCTTTTGAAGGAATGGTGACTATAA-ATGGNNNNNNNNNNCTAATGAATGT
1 AAGTGAGTGATAAGGCTTTTGAAGAAATGGTGACTATAATA-GG-CTTTTCTTACCAATGAATG-
* * * * * *
7195 CTTTTTCTTCACATTTCT-AGATGTAGATATTCAATTATAATCTATTTTAAGCTAAAAAGT-AAA
63 CTTTTTCTTCACATTTCTCA-ATATAGACATTCAATTACAATCTATTGTAAGCAAAAAAATAAAA
* * * *
7258 AAATTTGAACTTAAAATCATTTTTGAGACTATAAAACCATTTA
127 AAAATTGAACTTAAAACCAATTTTAAGACTATAAAACCATTTA
* * * *
7301 AAGTGAGTGATAAGGCTTTTGAATAAATGGGTGATTATAATAGGCTTTTCTTGCCAGTGAATGCA
1 AAGTGAGTGATAAGGCTTTTGAAGAAAT-GGTGACTATAATAGGCTTTTCTTACCAATGAATGC-
** * ** * *** * * *
7366 TTTTTCTTCATGTCTCTCAAGGTTGACATTCAATTATTGTCTGTTTTAATCAAAAATGCAA-AAA
64 TTTTTCTTCACATTTCTCAATATAGACATTCAATTACAATCTATTGTAAGCAAAAA---AATAAA
* * * * * *
7430 AACAATTCAAATTAAAATCAATTACT-AGATTATAAAACCATTTA
126 AAAAATTGAACTTAAAACCAATT-TTAAGACTATAAAACCATTTA
* * *
7474 AA-TCGACTAATAAGGCTTTTGAAGGAATGGGTGACT
1 AAGT-GAGTGATAAGGCTTTTGAAGAAAT-GGTGACT
7510 NNNNNNNNNN
Statistics
Matches: 293, Mismatches: 73, Indels: 26
0.75 0.19 0.07
Matches are distributed among these distances:
169 1 0.00
170 116 0.40
171 18 0.06
172 69 0.24
173 88 0.30
174 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.35
Consensus pattern (169 bp):
AAGTGAGTGATAAGGCTTTTGAAGAAATGGTGACTATAATAGGCTTTTCTTACCAATGAATGCTT
TTTCTTCACATTTCTCAATATAGACATTCAATTACAATCTATTGTAAGCAAAAAAATAAAAAAAA
TTGAACTTAAAACCAATTTTAAGACTATAAAACCATTTA
Done.