Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401534.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_466.0, 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: 6565
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.25
Warning! 2100 characters in sequence are not A, C, G, or T
Found at i:2473 original size:172 final size:171
Alignment explanation
Indices: 2176--3402 Score: 1295
Period size: 172 Copynumber: 7.2 Consensus size: 171
2166 NNNNNNNNNA
* * * * * *
2176 CTTTTTTCTTCATGTTTCTTACGATAGACATTCAATCCTAGTCTGTTTTAACCAAAAATGAACAA
1 CTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTATTTTAA-CAAAAATGTACAA
** * * *
2241 AGCATTCAAATTTAAATCAATTTTCAGATTATAAAACCATTTAAAGTGAGTAAGAAGGCTTTTGA
65 AAAATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGA
* *
2306 AGGAATGGGTCACTGTAAATGGACTTCTCTTGCCAATGAATG
130 AGGAATGGGTGACTATAAATGGACTTCTCTTGCCAATGAATG
* * * * * * * * * * * * * *
2348 CTCTCTTCTTTATGTTTCTTAGGGTAAACGTTCAATTATAATATGTTTTAACCGGAACAT-CA-A
1 CTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTATTTTAA-C-AAAAATGTACA
* * *
2411 AAAAATTTGAACTTAAAATCAATTTTGAG-TTAATAAAACCATTTAAAGTGATTAATAAGGCTTT
64 AAAAATTT-AAATTTAAATCAATTTTGAGATT-ATAAAACCATTTAAAGTGAGTAATAAGGCTTT
* * * * * * * * *
2475 TGAAGCAGTTGCTGACAATAAATAGAATTTTCTTGCCAATGAATC
127 TGAAGGAATGGGTGACTATAAATGGACTTCTCTTGCCAATGAATG
* * *
2520 CTTTTTTCTTCATGTTTCTCATGGTATAGATTCAATTCTAGTCTATTTTAACCAAAAATGTAC-A
1 CTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTATTTTAA-CAAAAATGTACAA
* * * **
2584 AACATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTCAACTGAGTAATAAGGCACTTGA
65 AAAATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGA
* *
2649 AGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATA
130 AGGAATGGGTGACTATAAATGGACTTCTCTTGCCAATGAATG
* * *
2691 CTTTTTTCTTCATGTTTTTGAAGGTAGACATTCAATCCTAGTCTATTTTAACTAAAAATGTACAA
1 CTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTATTTTAAC-AAAAATGTACAA
* * * *
2756 AGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGCGTAATAAGGCTTTTAA
65 AAAATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGA
* * *
2821 AGGAGTGGGTGACTGTGAATGGACTTCTCTTGCCAATGAATG
130 AGGAATGGGTGACTATAAATGGACTTCTCTTGCCAATGAATG
* * * * * * ** *
2863 CCTTCTTCTTTACGTTTCTCAAAGTAGGCATTCAATTAGAGT-T-TCTTTAACTAAAAATGTAAA
1 CTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTAT-TTTAAC-AAAAATGTACA
* * * * * *
2926 AAAAATTTAACTTCAAATCAATTATG-GCATTACAAAACCATTGAAAGCGAGTAATAAGGCTTTT
64 AAAAATTTAAATTTAAATCAATTTTGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTT
* * * * *
2990 GAA--ATATGGGTAACTATAAATAGACTTTTCTTACCAATGATTG
128 GAAGGA-ATGGGTGACTATAAATGGACTTCTCTTGCCAATGAATG
* * * *
3033 CTTTTTTCTTCATGTTTCTCAAGGTCGACATTCAATTCTAGTCTGTTTTAATAAAAAATGCACAA
1 CTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTATTTTAA-CAAAAATGTACAA
* * * *
3098 AGAATTCAAATCTAAATCAATTTTGAGATTATGAAACCATTTAAAGTGAGTAATAAGGCTTTTGA
65 AAAATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGA
* * *
3163 AGGAATGGGTGACTATAAATGAACTAT-TATTGCCAATGAATA
130 AGGAATGGGTGACTATAAATGGACT-TCTCTTGCCAATGAATG
* * * * * *
3205 CTTTTTTCTTCATGTTTCTGAGGGTAGACATTCAATCCTAGTTTCTTTTAACCAAAAATGTATAA
1 CTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTATTTTAA-CAAAAATGTACAA
* * * *
3270 AGAATTTAAATTTAAATCAATTTTGAGATTATAAAACTATTTAAAGTGCGTAATAAGGCTTTCGA
65 AAAATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGA
* * * *
3335 AGGAGTGGATGACTATAAATAGACTTCTCTGGCCAATGAATG
130 AGGAATGGGTGACTATAAATGGACTTCTCTTGCCAATGAATG
* * *
3377 CCTTTTTCTTTATGTTTCTCAGGGTA
1 CTTTTTTCTTCATGTTTCTCAAGGTA
3403 AACGNNNNNN
Statistics
Matches: 867, Mismatches: 169, Indels: 38
0.81 0.16 0.04
Matches are distributed among these distances:
169 1 0.00
170 66 0.08
171 293 0.34
172 501 0.58
173 6 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (171 bp):
CTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTATTTTAACAAAAATGTACAAA
AAATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAA
GGAATGGGTGACTATAAATGGACTTCTCTTGCCAATGAATG
Found at i:2803 original size:343 final size:341
Alignment explanation
Indices: 2176--3393 Score: 1351
Period size: 343 Copynumber: 3.6 Consensus size: 341
2166 NNNNNNNNNA
* * * *
2176 CTTTTTTCTTCATGTTTCTTACGATAGACATTCAATCCTAGTCTGTTTTAACCAAAAATGAACAA
1 CTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATCCTAGTCT-TTTTAACCAAAAATGTACAA
* * * * *
2241 AGCATTCAAATTTAAATCAATTTTCAGATTATAAAACCATTTAAAGTGAGTAAGAAGGCTTTTGA
65 AGAATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAACTGAGTAATAAGGCTTTTGA
* * * * * * *
2306 AGGAATGGGTCACTGTAAATGGACTTCTCTTGCCAATGAATGCTCTCTTCTTTATGTTTCTTAGG
130 AGGAATGGGTGACTATAAATAGACTTCTCTTGCCAATGAATGCTTTTTTCTTCATGTTT-TTAAG
* * * * * ** * * * * *
2371 GTAAACGTTCAATTATAATATGTTTTAACCGGAACAT-CA-AAAAAATTTGAACTTAAAATCAAT
194 GTAGACATTCAATTCTAGTCTGTTTTAA-CTAAAAATGCACAAAGAA-TTCAAATTTAAATCAAT
* * * * *
2434 TTTGAG-TTAATAAAACCATTTAAAGTGATTAATAAGGCTTTTGAAGCAGTTGCTGACAATAAAT
257 TTTGAGATT-ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAGTGGGTGACTATAAAT
2498 AGAATTTTCTTGCCAATGAATC
321 -GAATTTTCTTGCCAATGAATC
* * * *
2520 CTTTTTTCTTCATGTTTCTCATGGTATAGATTCAATTCTAGTCTATTTTAACCAAAAATGTACAA
1 CTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATCCTAGTCT-TTTTAACCAAAAATGTACAA
* * **
2585 A-CATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTCAACTGAGTAATAAGGCACTTGA
65 AGAATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAACTGAGTAATAAGGCTTTTGA
* * *
2649 AGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTTTGAAG
130 AGGAATGGGTGACTATAAATAGACTTCTCTTGCCAATGAATGCTTTTTTCTTCATGTTTTT-AAG
* * *
2714 GTAGACATTCAATCCTAGTCTATTTTAACTAAAAATGTACAAAGAATTCAAATTTAAATCAATTT
194 GTAGACATTCAATTCTAGTCTGTTTTAACTAAAAATGCACAAAGAATTCAAATTTAAATCAATTT
* * * *
2779 TGAGATTATAAAACCATTTAAAGTGCGTAATAAGGCTTTTAAAGGAGTGGGTGACTGTGAATGGA
259 TGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAGTGGGTGACTATAAAT-GA
* *
2844 CTTCTCTTGCCAATGAATGC
323 ATTTTCTTGCCAATGAAT-C
* * * * * *** * *
2864 C-TTCTTCTTTACGTTTCTCAAAGTAGGCATTCAATTAGAGT-TTCTTTAACTAAAAATGTAAAA
1 CTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATCCTAGTCTT-TTTAACCAAAAATGTACAA
* * * * * *
2927 AAAATTTAACTTCAAATCAATTATG-GCATTACAAAACCATTGAAAGC-GAGTAATAAGGCTTTT
65 AGAATTTAAATTTAAATCAATTTTGAG-ATTATAAAACCATTTAAA-CTGAGTAATAAGGCTTTT
* * * * *
2990 GAA--ATATGGGTAACTATAAATAGACTTTTCTTACCAATGATTGCTTTTTTCTTCATGTTTCTC
128 GAAGGA-ATGGGTGACTATAAATAGACTTCTCTTGCCAATGAATGCTTTTTTCTTCATGTTT-TT
* *
3053 AAGGTCGACATTCAATTCTAGTCTGTTTTAA-TAAAAAATGCACAAAGAATTCAAATCTAAATCA
191 AAGGTAGACATTCAATTCTAGTCTGTTTTAACT-AAAAATGCACAAAGAATTCAAATTTAAATCA
* *
3117 ATTTTGAGATTATGAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAA
255 ATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAGTGGGTGACTATAAA
* * *
3182 TGAACTATTATTGCCAATGAATA
320 TGAA-TTTTCTTGCCAATGAATC
* * * *
3205 CTTTTTTCTTCATGTTTCTGAGGGTAGACATTCAATCCTAGTTTCTTTTAACCAAAAATGTATAA
1 CTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATCCTAGTCT-TTTTAACCAAAAATGTACAA
* * * *
3270 AGAATTTAAATTTAAATCAATTTTGAGATTATAAAACTATTTAAAGTGCGTAATAAGGCTTTCGA
65 AGAATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAACTGAGTAATAAGGCTTTTGA
* * * * *
3335 AGGAGTGGATGACTATAAATAGACTTCTCTGGCCAATGAATGCCTTTTTCTTTATGTTT
130 AGGAATGGGTGACTATAAATAGACTTCTCTTGCCAATGAATGCTTTTTTCTTCATGTTT
3394 CTCAGGGTAA
Statistics
Matches: 730, Mismatches: 124, Indels: 40
0.82 0.14 0.04
Matches are distributed among these distances:
341 6 0.01
342 238 0.33
343 369 0.51
344 116 0.16
345 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Consensus pattern (341 bp):
CTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATCCTAGTCTTTTTAACCAAAAATGTACAAA
GAATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAACTGAGTAATAAGGCTTTTGAA
GGAATGGGTGACTATAAATAGACTTCTCTTGCCAATGAATGCTTTTTTCTTCATGTTTTTAAGGT
AGACATTCAATTCTAGTCTGTTTTAACTAAAAATGCACAAAGAATTCAAATTTAAATCAATTTTG
AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAGTGGGTGACTATAAATGAATT
TTCTTGCCAATGAATC
Found at i:3233 original size:514 final size:515
Alignment explanation
Indices: 2175--3397 Score: 1652
Period size: 514 Copynumber: 2.4 Consensus size: 515
2165 NNNNNNNNNN
* * * * *
2175 ACTTTTTTCTTCATGTTTCTTACGATAGACATTCAATCCTAGTCTGTTTTAACCAAAAATGAACA
1 ACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATCCTAGTCTATTTTAACCAAAAATGTACA
* * * *
2240 AAGCATTCAAATTTAAATCAATTTTCAGATTATAAAACCATTTAAAGTGAGTAAGAAGGCTTTTG
66 AAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGCGTAATAAGGCTTTTG
* * *
2305 AAGGAATGGGTCACTGTAAATGGACTTCTCTTGCCAATGAATG-CTCTCTTCTTTATGTTTCTTA
131 AAGGAGTGGGTGACTGTAAATGGACTTCTCTTGCCAATGAATGCCT-TCTTCTTTATGTTTCTCA
** * * * * *
2369 GGGTAAACGTTCAATTATAATATGTTTTAACCGGAACATCAAAAAAATTTGAACTTAAAATCAAT
195 AAGTAAACATTCAATTAGAATATGTTTTAACCGAAAAATAAAAAAAATTTGAACTTAAAATCAAT
* * * * * * * *
2434 TTTGAGTTAATAAAACCATTTAAAGTGATTAATAAGGCTTTTGAAGCAGTTGCTGACAATAAATA
260 TTGGAGTTAACAAAACCATTGAAAGCGAGTAATAAGGCTTTTGAAACAGTGGCTAACAATAAATA
* * * *
2499 GAATTTTCTTGCCAATGAATCCTTTTTTCTTCATGTTTCTCATGGTATAGATTCAATTCTAGTCT
325 GAATTTTCTTACCAATGAATCCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCT
* * * * * *
2564 ATTTTAACCAAAAATGTACAAACATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTCAA
390 ATTTTAACAAAAAATGCACAAAAATTCAAATCTAAATCAATTTTGAGATTATAAAACCATTTAAA
* * *
2629 CTGAGTAATAAGGCACTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
455 CTGAGTAATAAGGCACTTGAAGGAATGGGTGACTATAAATGAACTATTATTGCCAATGAAT
* *
2690 ACTTTTTTCTTCATGTTTTTGAAGGTAGACATTCAATCCTAGTCTATTTTAACTAAAAATGTACA
1 ACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATCCTAGTCTATTTTAACCAAAAATGTACA
*
2755 AAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGCGTAATAAGGCTTTTA
66 AAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGCGTAATAAGGCTTTTG
* *
2820 AAGGAGTGGGTGACTGTGAATGGACTTCTCTTGCCAATGAATGCCTTCTTCTTTACGTTTCTCAA
131 AAGGAGTGGGTGACTGTAAATGGACTTCTCTTGCCAATGAATGCCTTCTTCTTTATGTTTCTCAA
** * * *
2885 AGTAGGCATTCAATTAGAGT-T-TCTTTAA-CTAAAAATGTAAAAAAAATTT-AACTTCAAATCA
196 AGTAAACATTCAATTAGAATATGT-TTTAACCGAAAAA--TAAAAAAAATTTGAACTTAAAATCA
* * *
2946 ATTATGGCA-TT-ACAAAACCATTGAAAGCGAGTAATAAGGCTTTTGAAATA-TGGGTAACTATA
258 ATT-TGG-AGTTAACAAAACCATTGAAAGCGAGTAATAAGGCTTTTGAAACAGTGGCTAACAATA
* * * *
3008 AATAGACTTTTCTTACCAATGATTGCTTTTTTCTTCATGTTTCTCAAGGTCGACATTCAATTCTA
321 AATAGAATTTTCTTACCAATGAATCCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTA
* * *
3073 GTCTGTTTTAATAAAAAATGCACAAAGAATTCAAATCTAAATCAATTTTGAGATTATGAAACCAT
386 GTCTATTTTAACAAAAAATGCACAAA-AATTCAAATCTAAATCAATTTTGAGATTATAAAACCAT
* **
3138 TTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACTATTATTGCCAATGAA
450 TTAAACTGAGTAATAAGGCACTTGAAGGAATGGGTGACTATAAATGAACTATTATTGCCAATGAA
3203 T
515 T
* * * *
3204 ACTTTTTTCTTCATGTTTCTGAGGGTAGACATTCAATCCTAGTTTCTTTTAACCAAAAATGTATA
1 ACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATCCTAGTCTATTTTAACCAAAAATGTACA
* * *
3269 AAGAATTTAAATTTAAATCAATTTTGAGATTATAAAACTATTTAAAGTGCGTAATAAGGCTTTCG
66 AAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGCGTAATAAGGCTTTTG
* * * * *
3334 AAGGAGTGGATGACTATAAATAGACTTCTCTGGCCAATGAATGCCTTTTTCTTTATGTTTCTCA
131 AAGGAGTGGGTGACTGTAAATGGACTTCTCTTGCCAATGAATGCCTTCTTCTTTATGTTTCTCA
3398 GGGTAAACGN
Statistics
Matches: 621, Mismatches: 80, Indels: 15
0.87 0.11 0.02
Matches are distributed among these distances:
513 92 0.15
514 323 0.52
515 203 0.33
516 3 0.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (515 bp):
ACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATCCTAGTCTATTTTAACCAAAAATGTACA
AAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGCGTAATAAGGCTTTTG
AAGGAGTGGGTGACTGTAAATGGACTTCTCTTGCCAATGAATGCCTTCTTCTTTATGTTTCTCAA
AGTAAACATTCAATTAGAATATGTTTTAACCGAAAAATAAAAAAAATTTGAACTTAAAATCAATT
TGGAGTTAACAAAACCATTGAAAGCGAGTAATAAGGCTTTTGAAACAGTGGCTAACAATAAATAG
AATTTTCTTACCAATGAATCCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTA
TTTTAACAAAAAATGCACAAAAATTCAAATCTAAATCAATTTTGAGATTATAAAACCATTTAAAC
TGAGTAATAAGGCACTTGAAGGAATGGGTGACTATAAATGAACTATTATTGCCAATGAAT
Found at i:4724 original size:171 final size:170
Alignment explanation
Indices: 4206--5087 Score: 724
Period size: 171 Copynumber: 5.2 Consensus size: 170
4196 NNNNNNNTTC
* * *
4206 AAAAGCCTTATTACTCGCTTTAAATGGTTTCATAATCTCAAAATTGATTGAAATTTGAAT-TCTT
1 AAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATGT-TT
* * * *
4270 TGTACATTTTTTGTTGAAAAAGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGCA
65 TGTACATTTTTCGTT-AAAAAGACTAGAATTGAATCTCTACCATGAGAAACATGAAGAAAAAGTA
* *
4335 TTCATTGGCCAGAAAAGTCTATTTATAGTCACCCATACCTTT
129 TTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTT
* * * * ********* * *
4377 AAAAACCTTATTTCTCTCTTTAAATGGTTTTGTAATGC-CANNNNNNNNNNT-AAGTTAAAT-TT
1 AAAAGCCTTATTACTCACTTTAAATGGTTTTATAAT-CTCA-AAATTGATTTAAATTTGAATGTT
* * ** * * *
4439 TTTTATA-TTTTCGTTAAACAA-ACTCTAATTGAATGC-CTACCTTGAGAAACGTAAAGAAAAAA
64 TTGTACATTTTTCGTTAAA-AAGACTAGAATTGAAT-CTCTACCATGAGAAACATGAAG-AAAAA
** * * *
4501 CAATTCATTGGCAAGAGAAGTCCATTTATAGTCACCCACTCCTTGT
126 GTATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTT-T
* * * *
4547 -AGAGCCTTATTACGCATTTTAAATGGTTTTATAATCTCAAAATTGATTTAAAATTGAATGTTTT
1 AAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATGTTTT
* * * *
4611 GTACATTTTTAGTTAAAATAGACTAGAATTGAAACTATACCATGAGAAACATGAATAAAAAGTAT
66 GTACATTTTTCGTTAAAA-AGACTAGAATTGAATCTCTACCATGAGAAACATGAAGAAAAAGTAT
* * *
4676 TCATTGGGAAGAAAAGTCTATTTATAGTCACTCATTTCTTT
130 TCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTT
* * ********** *
4717 AAGAGCCTTATTACTCAGTTTAAANNNNNNNNNNATCTCAAAATTGATTTAAATTTCAATGTTTT
1 AAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATGTTTT
* * *
4782 GCACATTTTTCGTTAAAATATACTAGAATTGAATCTATACCATGAGAAACATGAAGAAAAATGTA
66 GTACATTTTTCGTTAAAA-AGACTAGAATTGAATCTCTACCATGAGAAACATGAAGAAAAA-GTA
* *
4847 TTCATTGGCAAAAAAAGTCTATTTATAGTCACCCATTGCTTT
129 TTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTT
********** * *
4889 AAAAGCCTNNNNNNNNNNTTTAAATGGTTTTATAATCTCAAAATTGATTTTAACTTGAAATGTTT
1 AAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTG-AATGTTT
* * *** * * * *
4954 T-TGC-TTTTCTGGTTAAAACATTTTAGAATTGAATGTCTACCCTGAGAAACATAAAGAAGAGCA
65 TGTACATTTT-TCGTTAAAA-AGACTAGAATTGAATCTCTACCATGAGAAACATGAAGAA-A-AA
** * **
5017 GT-TTCATTGGCAAGAGCAGTCCATTTATAGTCACCCATTCCTCC
126 GTATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTT
5061 AAAAGCCTTATTACTCACTTTAAATGG
1 AAAAGCCTTATTACTCACTTTAAATGG
5088 NNNNNNNNNN
Statistics
Matches: 548, Mismatches: 144, Indels: 37
0.75 0.20 0.05
Matches are distributed among these distances:
168 34 0.06
169 88 0.16
170 16 0.03
171 204 0.37
172 194 0.35
173 11 0.02
174 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.35
Consensus pattern (170 bp):
AAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATGTTTT
GTACATTTTTCGTTAAAAAGACTAGAATTGAATCTCTACCATGAGAAACATGAAGAAAAAGTATT
CATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTT
Found at i:4971 original size:172 final size:170
Alignment explanation
Indices: 4206--5087 Score: 624
Period size: 172 Copynumber: 5.2 Consensus size: 170
4196 NNNNNNNTTC
* *
4206 AAAAGCCTTATTACTC-GCTTTAAATGGTTTCATAATCTCAAAATTGA-TTGAAATTTGAAT-TC
1 AAAAGCCTTATTACTCAG-TTTAAATGGTTTTATAATCTCAAAATTGATTTTAAA-TTGAATGT-
* * * * * *
4268 TTTGTACATTTTTTGTTGAAAA-AGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAA
63 TTT-TGCATTTTTAGTT-AAAATATACTAGAATTGAATCTATACCATGAGAAACATGAAGAAAAA
* * **
4332 GCATTCATTGGCCAGAAAAGTCTATTTATAGTCACCCATACCTTT
126 GTATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTGCTTT
* * ** * ********** * *
4377 AAAAACCTTATTTCTCTCTTTAAATGGTTTTGTAATGC-CANNNNNNNNNNTAAGTTAAAT-TTT
1 AAAAGCCTTATTACTCAGTTTAAATGGTTTTATAAT-CTCAAAATTGATTTTAAATTGAATGTTT
* * ** * * * *
4440 TT-TATATTTTCGTTAAACA-A-ACTCTAATTGAATGC-CTACCTTGAGAAACGTAAAGAAAAAA
65 TTGCAT-TTTTAGTTAAA-ATATACTAGAATTGAAT-CTATACCATGAGAAACATGAAG-AAAAA
** * * * *
4501 CAATTCATTGGCAAGAGAAGTCCATTTATAGTCACCCACTCCTTGT
126 GTATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTGCTT-T
* * * *
4547 -AGAGCCTTATTACGCATTTTAAATGGTTTTATAATCTCAAAATTGATTTAAAATTGAATGTTTT
1 AAAAGCCTTATTACTCAGTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATTGAATGTTTT
* * * *
4611 GTACATTTTTAGTTAAAATAGACTAGAATTGAAACTATACCATGAGAAACATGAATAAAAAGTAT
66 -TGCATTTTTAGTTAAAATATACTAGAATTGAATCTATACCATGAGAAACATGAAGAAAAAGTAT
* * *
4676 TCATTGGGAAGAAAAGTCTATTTATAGTCACTCATTTCTTT
130 TCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTGCTTT
* ********** *
4717 AAGAGCCTTATTACTCAGTTTAAANNNNNNNNNNATCTCAAAATTGA-TTTAAATTTCAATG-TT
1 AAAAGCCTTATTACTCAGTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAA-TTGAATGTTT
*
4780 TTGCACATTTTTCGTTAAAATATACTAGAATTGAATCTATACCATGAGAAACATGAAGAAAAATG
65 TTG--CATTTTTAGTTAAAATATACTAGAATTGAATCTATACCATGAGAAACATGAAGAAAAA-G
*
4845 TATTCATTGGCAAAAAAAGTCTATTTATAGTCACCCATTGCTTT
127 TATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTGCTTT
********** *
4889 AAAAGCCTNNNNNNNNNNTTTAAATGGTTTTATAATCTCAAAATTGATTTTAACTTGAAATGTTT
1 AAAAGCCTTATTACTCAGTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATTG-AATGTTT
* * ** * * * * *
4954 TTGC-TTTTCTGGTTAAAACATTTTAGAATTGAATGTCTACCCTGAGAAACATAAAGAAGAGCAG
65 TTGCATTTT-TAGTTAAAATATACTAGAATTGAATCTATACCATGAGAAACATGAAGAA-A-AAG
** * * **
5018 T-TTCATTGGCAAGAGCAGTCCATTTATAGTCACCCATTCCTCC
127 TATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTGCTTT
*
5061 AAAAGCCTTATTACTCACTTTAAATGG
1 AAAAGCCTTATTACTCAGTTTAAATGG
5088 NNNNNNNNNN
Statistics
Matches: 544, Mismatches: 141, Indels: 51
0.74 0.19 0.07
Matches are distributed among these distances:
168 35 0.06
169 90 0.17
170 18 0.03
171 190 0.35
172 193 0.35
173 12 0.02
174 6 0.01
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.35
Consensus pattern (170 bp):
AAAAGCCTTATTACTCAGTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAATTGAATGTTTT
TGCATTTTTAGTTAAAATATACTAGAATTGAATCTATACCATGAGAAACATGAAGAAAAAGTATT
CATTGGCAAGAAAAGTCTATTTATAGTCACCCATTGCTTT
Done.