Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402320.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5400.0, 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: 3451
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.30
Warning! 369 characters in sequence are not A, C, G, or T
Found at i:911 original size:171 final size:171
Alignment explanation
Indices: 583--2680 Score: 1943
Period size: 171 Copynumber: 12.2 Consensus size: 171
573 NNNNNNNNNN
583 TAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGG-CTTTTCT-TACCAATGGA
1 TAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCT-CCAATGGA
* * * *
646 TGGCTTTTGCTTCATGTTTCCCAAGGTAGGCATTCAATTATAACATATTTCAACTAAAAATGTAA
65 TGGCTTTTGCTTCATGTTTCCGAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATGT-A
* ********** *
711 AAAAAATCCAACTNNNNNNNNNNTATGAGAATATAAAACTATT
129 AAAAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATT
* ** * * *
754 TAAAGTGAGTGATATTGCTTTCGAAGGCTTGAGTGACTATAAATGGACTTTTCTCTCAAATGCAT
1 TAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTCCAATGGAT
* * * * *
819 GGCTTTTGCTTTACGCTTCCGAAGATAGACATTCAATTATAGCATATTTTAACCAAAAATGTAAA
66 GGCTTTTGCTTCATGTTTCCGAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATGTAAA
* * * *
884 AACATCCAACTTAAAATCAATTATGAGAATCTAAAACCCTT
131 AAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATT
* ** * * * * * * * * * * *
925 TAATGCAAGTAACAAGGCTTCCGATGACTTGAGTTACTATAAATAGATTTTTTTTCTCTAATGTA
1 TAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGA-CTTTTCTCTCCAATGGA
* * * * * *
990 TGGCTTTTGATTCACGTTTCTCG-AGGCAGACATTCAATTATAGCATATTTTAACCCAAAATATA
65 TGGCTTTTGCTTCATGTTTC-CGAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATGTA
* *
1054 AAAAAATCCAACTTAAAATCCATTATGAGAATATAAAACCATT
129 AAAAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATT
** * *** *
1097 TAAAGCCAGTAATAAGGCTTTTAAAGGCTTGAGTGACTATAAACAAACTTTT-TCCTCCAATAGA
1 TAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCT-CTCCAATGGA
* * * * *
1161 TGGCTTTTACTTCACGTTT-CGCAAGGTAGATATTCAATTATAATATATTTCAACCAAAAA--T-
65 TGGCTTTTGCTTCATGTTTCCG-AAGGTAGACATTCAATTATAACATATTTTAACCAAAAATGTA
* * *
1222 AAAAAATCTAACTTAAAATCAATTATGAGTATACAAAAGCATT
129 AAAAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATT
** * * * * *
1265 CGAAGTGAGTAATTAGGCTTTCAAAGGCTTGAGTGACTATAAATGCATTTTTCTCTCAAATGCAT
1 TAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTCCAATGGAT
*** * *
1330 GGCTTTTGCTTCATGTTTTTTAAGGTAGACATTCAATTATAGCATATTTTAATCAAAAATGTAAA
66 GGCTTTTGCTTCATGTTTCCGAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATGTAAA
* * * * *
1395 AACATCTAATTTAAAATAAATTATGAGAATCTAAAACCCTT
131 AAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATT
* ** *
1436 TAAAGTGAGTAACAAGGCTTTC-AAGGACCAGAGTGACTATAAATGGACTTTTCTCTCTAATGGA
1 TAAAGTGAGTAATAAGGCTTTCAAAGG-CTTGAGTGACTATAAATGGACTTTTCTCTCCAATGGA
* * * * * *
1500 TGGCTTTTGCTTAACAT-TTT-TGAAGGCAAACATTCAATTAT-AGATATTTTAACTAAAAAAGT
65 TGGCTTTTGCTT--CATGTTTCCGAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATGT
* * * * *
1562 AAAAAAATCCAACTTAAAACCAATTATGAGGATATAAAACTATC
128 AAAAAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATT
* * * * **
1606 TAAAGCGTGTAATAAAGCTTTTAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTTAAATGGAT
1 TAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTCCAATGGAT
* * * *
1671 GGCTTTTGCTTCATATTTCCTAAGGCAGACATTCAATTATAACATATTTTAACCAAAAATATAAA
66 GGCTTTTGCTTCATGTTTCCGAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATGTAAA
* * *
1736 AAAATCTGACTTAGAATCAATTATGAGAATATAAAACTATT
131 AAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATT
* * *
1777 TAAAGTGAGTAATAAGGCTTTCGAAGGCTAT-AGTGACTATAAAAGG-CTTTTCT-TATCAATGG
1 TAAAGTGAGTAATAAGGCTTTCAAAGGCT-TGAGTGACTATAAATGGACTTTTCTCT-CCAATGG
* * * * * * *
1839 ATGGCTTTTGCATCATGTTTTCC-AAGGCA-AGCATTTAATTATAACAAATTTGAACGAAAAATA
64 ATGGCTTTTGCTTCATG-TTTCCGAAGGTAGA-CATTCAATTATAACATATTTTAACCAAAAATG
** *
1902 TAAAAAAATCTAACTTAAAAAGAATTATGAGAATACAAAACCATT
127 TAAAAAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATT
*** * * * ** **
1947 TAAAACAAGTAATAAGGCCTTCAAAGGCTTGAGTGACTATAAATGGACATTTCTTTTTAATCAAT
1 TAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTCCAATGGAT
** * * * * *
2012 GATTTTTTGCTTCATGTTTGCC-AAAGAAAACATTTAATTATAACATATTTTTAACTAAAAATGT
66 G-GCTTTTGCTTCATGTTT-CCGAAGGTAGACATTCAATTATAACATA-TTTTAACCAAAAATGT
* * *
2076 AAAAGAATAC-AACTTAAAATTAATTATGAGAATATAAAACTATT
128 AAAAAAAT-CTAACTTAAAATCAATTATGAGAATATAAAACCATT
* * * *
2120 TAAAGCT-TGTAATAAGGCTTTTAAAGGCTTGAGTGACTATAAATGGACTTTTGTCTCCAACGGA
1 TAAAG-TGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTCCAATGGA
* * *
2184 TGGCTTTTGCCTCATGTTTTCC-AAGATAGACA-TCTAATTATAACATATTTTAATCAAAAATGT
65 TGGCTTTTGCTTCATG-TTTCCGAAGGTAGACATTC-AATTATAACATATTTTAACCAAAAATGT
* * * *
2247 AAAAAATTCTACCATAAAATCAATTATAAGAATATAAAACCATT
128 AAAAAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATT
* ** * *
2291 GAAAACGAGCAATAAGGCTTTCAAAGGCTTGCA-TGACTGTAAATGG-CTTTTCT-TGCCAATGG
1 TAAAGTGAGTAATAAGGCTTTCAAAGGCTTG-AGTGACTATAAATGGACTTTTCTCT-CCAATGG
* * *
2353 ATGGCTTTTGCTTCATGTTTCCTAAGGCAGACATTCAATTATAACATATTTTAACCATAAATGTA
64 ATGGCTTTTGCTTCATGTTTCCGAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATGTA
*
2418 AAAAAATGTAACTTAAAATCAATTATGAGAATATAAAACCATT
129 AAAAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATT
* ** * * * * *
2461 TCAAGCAAGTAAT-AGGCCTTTCAAAAGCTTGCGTGATTATAAATAG-CTTTCCT-TACCAATGG
1 TAAAGTGAGTAATAAGG-CTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCT-CCAATGG
* * * * * * *
2523 ATAGCTTTTTCTTCATGTGTCCTG-AGGCAGACATTGAATTATAATATTTTTTTTACGTTTTAAT
64 ATGGCTTTTGCTTCATGTTTCC-GAAGGTAGACATTCAATTATAACA-------TA--TTTTAAC
* * * * * *
2587 GAAACATG-AAAAAATATCCAACTTAAAATGAATTATGTGAATCTAAAACCATT
119 CAAAAATGTAAAAAA-ATCTAACTTAAAATCAATTATGAGAATATAAAACCATT
* * * * *
2640 TGAAGCGAGTAACAAGGCTTTCAAAGGCTTAAGTCACTATA
1 TAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATA
2681 TATTTTAACC
Statistics
Matches: 1582, Mismatches: 291, Indels: 100
0.80 0.15 0.05
Matches are distributed among these distances:
168 140 0.09
169 19 0.01
170 461 0.29
171 486 0.31
172 279 0.18
173 112 0.07
174 1 0.00
177 2 0.00
178 6 0.00
179 73 0.05
180 3 0.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (171 bp):
TAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTCCAATGGAT
GGCTTTTGCTTCATGTTTCCGAAGGTAGACATTCAATTATAACATATTTTAACCAAAAATGTAAA
AAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATT
Found at i:1720 original size:341 final size:339
Alignment explanation
Indices: 583--2680 Score: 1811
Period size: 341 Copynumber: 6.1 Consensus size: 339
573 NNNNNNNNNN
*
583 TAAAGTGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGG-C-TTT-TCTTACCAATGG
1 TAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTTA--AATGG
* * * * *
645 ATGGCTTTTGCTTCATGTTTCCCAAGGTAGGCATTCAATTATAACATATTTCAACTAAAAATGTA
64 ATGGCTTTTGCTTCATGTTTCCTAAGGCAGACATTCAATTATAACATATTTTAACCAAAAATGT-
* ********** * * **
710 AAAAAAATCCAACTNNNNNNNNNNTATGAGAATATAAAACTATTTAAAGTGAGTGATATTGCTTT
128 AAAAAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGTGAGTAATAAGGCTTT
* * * ** **
775 CGAAGGCTTGAGTGACTATAAATGGACTTTTCTCTCAAATGCATGGCTTTTGCTTTACGCTTCCG
193 C-AAGGCTTGAGTGACTATAAATGGACTTTTCTCTCCAATGGATGGCTTTTGCTTAACATTTTTG
* * * * *
840 AAGATAGACATTCAATTATAGCATATTTTAACCAAAAATGTAAAAACATCCAACTTAAAATCAAT
257 AAGGTAGACATTCAATTATA-CATATTTTAACTAAAAAAGTAAAAAAATCTAACTTAAAATCAAT
* *
905 TATGAGAATCTAAAACCCTT
321 TATGAGAATATAAAA-CCAT
* * * * * * * * * * * *
925 TAATGCAAGTAACAAGGCTTCCGATGACTTGAGTTACTATAAATAGATTTTTTTTCTCT-AATGT
1 TAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGA-CTTTTCTCT-TAAATGG
* * * * * *
989 ATGGCTTTTGATTCACGTTT-CTCGAGGCAGACATTCAATTATAGCATATTTTAACCCAAAATAT
64 ATGGCTTTTGCTTCATGTTTCCT-AAGGCAGACATTCAATTATAACATATTTTAACCAAAAATGT
* * **
1053 AAAAAAATCCAACTTAAAATCCATTATGAGAATATAAAACCATTTAAAGCCAGTAATAAGGCTTT
128 AAAAAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGTGAGTAATAAGGC-TT
* *** * * * * *
1118 TAAAGGCTTGAGTGACTATAAACAAACTTTT-TCCTCCAATAGATGGCTTTTACTTCAC-GTTTC
192 TCAAGGCTTGAGTGACTATAAATGGACTTTTCT-CTCCAATGGATGGCTTTTGCTTAACATTTTT
* *
1181 GCAAGGTAGATATTCAATTATA-ATATATTTCAAC-CAAAAA-T-AAAAAATCTAACTTAAAATC
256 G-AAGGTAGACATTCAATTATACATAT-TTT-AACTAAAAAAGTAAAAAAATCTAACTTAAAATC
* * *
1242 AATTATGAGTATACAAAAGCAT
318 AATTATGAGAATATAAAACCAT
* * * * * * *
1264 TCGAAGTGAGTAATTAGGCTTTCAAAGGCTTGAGTGACTATAAATGCATTTTTCTCTCAAATGCA
1 T-AAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTTAAATGGA
** * * *
1329 TGGCTTTTGCTTCATGTTTTTTAAGGTAGACATTCAATTATAGCATATTTTAATCAAAAATGTAA
65 TGGCTTTTGCTTCATGTTTCCTAAGGCAGACATTCAATTATAACATATTTTAACCAAAAATGTAA
* * * * * *
1394 AAACATCTAATTTAAAATAAATTATGAGAATCTAAAACCCTTTAAAGTGAGTAACAAGGCTTTCA
130 AAAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGTGAGTAATAAGGCTTTCA
** *
1459 AGGACCAGAGTGACTATAAATGGACTTTTCTCTCTAATGGATGGCTTTTGCTTAACATTTTTGAA
195 AGG-CTTGAGTGACTATAAATGGACTTTTCTCTCCAATGGATGGCTTTTGCTTAACATTTTTGAA
* * * * *
1524 GGCAAACATTCAATTATAGATATTTTAACTAAAAAAGTAAAAAAATCCAACTTAAAACCAATTAT
259 GGTAGACATTCAATTATACATATTTTAACTAAAAAAGTAAAAAAATCTAACTTAAAATCAATTAT
* *
1589 GAGGATATAAAACTAT
324 GAGAATATAAAACCAT
* * *
1605 CTAAAGCGTGTAATAAAGCTTTTAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTTAAATGGA
1 -TAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTTAAATGGA
* *
1670 TGGCTTTTGCTTCATATTTCCTAAGGCAGACATTCAATTATAACATATTTTAACCAAAAATATAA
65 TGGCTTTTGCTTCATGTTTCCTAAGGCAGACATTCAATTATAACATATTTTAACCAAAAATGTAA
* * *
1735 AAAAATCTGACTTAGAATCAATTATGAGAATATAAAACTATTTAAAGTGAGTAATAAGGCTTTCG
130 AAAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGTGAGTAATAAGGCTTTC-
* * *
1800 AAGGCTAT-AGTGACTATAAAAGG-CTTTTCT-TATCAATGGATGGCTTTTGC--ATCATGTTTT
194 AAGGCT-TGAGTGACTATAAATGGACTTTTCTCT-CCAATGGATGGCTTTTGCTTAACAT-TTTT
* * * * * * *
1860 CCAAGGCA-AGCATTTAATTATAACAAATTTGAACGAAAAATA-TAAAAAAATCTAACTTAAAAA
256 -GAAGGTAGA-CATTCAATTAT-ACATATTTTAACTAAAAA-AGTAAAAAAATCTAACTTAAAAT
* *
1923 GAATTATGAGAATACAAAACCATT
317 CAATTATGAGAATATAAAACCA-T
* * * * * * **
1947 TAAAACAAGTAATAAGGCCTTCAAAGGCTTGAGTGACTATAAATGGACATTTCTTTTTAATCAAT
1 TAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTTAAATGGAT
** * * * * *
2012 GATTTTTTGCTTCATGTTTGCC-AAAGAAAACATTTAATTATAACATATTTTTAACTAAAAATGT
66 G-GCTTTTGCTTCATGTTT-CCTAAGGCAGACATTCAATTATAACATA-TTTTAACCAAAAATGT
* * * *
2076 AAAAGAATAC-AACTTAAAATTAATTATGAGAATATAAAACTATTTAAAGCT-TGTAATAAGGCT
128 AAAAAAAT-CTAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAG-TGAGTAATAAGGC-
* * * *
2139 TTTAAAGGCTTGAGTGACTATAAATGGACTTTTGTCTCCAACGGATGGCTTTTGCCT--CATGTT
190 TTTCAAGGCTTGAGTGACTATAAATGGACTTTTCTCTCCAATGGATGGCTTTTGCTTAACAT-TT
* * * * * *
2202 TTCCAAGATAGACA-TCTAATTATAACATATTTTAA-TCAAAAATGTAAAAAATTCTACCATAAA
254 TT-GAAGGTAGACATTC-AATTAT-ACATATTTTAACT-AAAAAAGTAAAAAAATCTAACTTAAA
*
2265 ATCAATTATAAGAATATAAAACCAT
315 ATCAATTATGAGAATATAAAACCAT
* * * **
2290 TGAAAACGAGCAATAAGGCTTTCAAAGGCTTGCA-TGACTGTAAATGG-CTTTTCT-TGCCAATG
1 T-AAAGCGAGTAATAAGGCTTTCAAAGGCTTG-AGTGACTATAAATGGACTTTTCTCT-TAAATG
*
2352 GATGGCTTTTGCTTCATGTTTCCTAAGGCAGACATTCAATTATAACATATTTTAACCATAAATGT
63 GATGGCTTTTGCTTCATGTTTCCTAAGGCAGACATTCAATTATAACATATTTTAACCAAAAATGT
* * **
2417 AAAAAAATGTAACTTAAAATCAATTATGAGAATATAAAACCATTTCAAGCAAGTAAT-AGGCCTT
128 AAAAAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGTGAGTAATAAGG-CTT
* * * * * * *
2481 TCAAAAGCTTGCGTGATTATAAATAG-CTTTCCT-TACCAATGGATAGCTTTTTCTT--CATGTG
192 TC-AAGGCTTGAGTGACTATAAATGGACTTTTCTCT-CCAATGGATGGCTTTTGCTTAACAT-T-
* * * *
2542 TCCTG-AGGCAGACATTGAATTATA-ATATTTTTTTTACGTTTTAATGAAACA-TGAAAAAATAT
253 T-TTGAAGGTAGACATTCAATTATACATA---TTTTAAC----TAA--AAA-AGT-AAAAAA-AT
* * * *
2604 CCAACTTAAAATGAATTATGTGAATCTAAAACCATT
305 CTAACTTAAAATCAATTATGAGAATATAAAACCA-T
* * * *
2640 TGAAGCGAGTAACAAGGCTTTCAAAGGCTTAAGTCACTATA
1 TAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATA
2681 TATTTTAACC
Statistics
Matches: 1421, Mismatches: 262, Indels: 139
0.78 0.14 0.08
Matches are distributed among these distances:
338 17 0.01
339 195 0.14
340 161 0.11
341 419 0.29
342 129 0.09
343 218 0.15
344 197 0.14
345 8 0.01
346 4 0.00
347 5 0.00
348 7 0.00
349 59 0.04
350 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (339 bp):
TAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTTAAATGGAT
GGCTTTTGCTTCATGTTTCCTAAGGCAGACATTCAATTATAACATATTTTAACCAAAAATGTAAA
AAAATCTAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGTGAGTAATAAGGCTTTCAA
GGCTTGAGTGACTATAAATGGACTTTTCTCTCCAATGGATGGCTTTTGCTTAACATTTTTGAAGG
TAGACATTCAATTATACATATTTTAACTAAAAAAGTAAAAAAATCTAACTTAAAATCAATTATGA
GAATATAAAACCAT
Found at i:3243 original size:171 final size:171
Alignment explanation
Indices: 2680--3451 Score: 730
Period size: 171 Copynumber: 4.5 Consensus size: 171
2670 AAGTCACTAT
* * * * * *
2680 ATATTTTAACC-AAAAT-CTAAAATAT-TCCAACATAAAATCATTTATTAAAATATAAAACCATT
1 ATATTTTAACCAAAAATGTTAAAACATCT-CAACTTAAAATCAATTATGAGAATATAAAACCATT
* * * *
2742 TAAAGCGAGTAATAAGGCTTTCAAAGGCTTACGTGACTATAAATGGACTTTTCACTCCGATGGAT
65 TAAAGCGAGTAATAAGGCTTTCAAAGGCTTAAGTGACTATAAAAGG-CTTTTCTCTCCAATGGAT
* * * * *
2807 GACTTTTGCTTCAGGTTTCCCCAAGA-AAATATTTAATTATAAC
129 GACTTTTGCTTCATGTTT-CCTAAGACAAACATTCAACTATAAC
* * * * *
2850 ATATTTTACCCAAAAATATTAAAAAATC-CAACTTAAAATTAATTTTGAGAATATAAAACCATTC
1 ATATTTTAACCAAAAATGTTAAAACATCTCAACTTAAAATCAATTATGAGAATATAAAACCA-T-
* ** ** * *
2914 ATTAAAAGTGAGTAATAATTCTTTTGAAGGCTTAAGTAACTATAAGAGGCTTTTCGTGCT--AAT
64 -TT-AAAGCGAGTAATAAGGCTTTCAAAGGCTTAAGTGACTATAAAAGGCTTTTC-T-CTCCAAT
* * * * *
2977 GGATGGCTTTTGCTTCATATTACCTAAGGCAGACATTCAACTATAAC
125 GGATGACTTTTGCTTCATGTTTCCTAAGACAAACATTCAACTATAAC
* * * *
3024 ATATTTTAACCAAAAAT-CTAAAATAT-TCCAACATAAAATCATTTATGAGAATATAAAACCATT
1 ATATTTTAACCAAAAATGTTAAAACATCT-CAACTTAAAATCAATTATGAGAATATAAAACCATT
** ** *
3087 TAAAGCGAGTAATAAGGCTTTCAAATTCTTGCGTGACTATAAAAGGACTTTTCTCTTCAATGGAT
65 TAAAGCGAGTAATAAGGCTTTCAAAGGCTTAAGTGACTATAAAAGG-CTTTTCTCTCCAATGGAT
* * * *
3152 GACTTTTGCATCACGTTTCCTAAGATAAACATTCAATTATAAC
129 GACTTTTGCTTCATGTTTCCTAAGACAAACATTCAACTATAAC
* * *
3195 ATATTTTAGCTAAAAATGTTGAAAA-ATCTC-ACTTAAAATTAATTATGAGAATATAAAACCATT
1 ATATTTTAACCAAAAATGTT-AAAACATCTCAACTTAAAATCAATTATGAGAATATAAAACCATT
* * ** * * *
3258 TAAAGTGACTAATAATTCTTTCAAAGGCTTGAGTGACTATAAATGGCTTTTCT-TGCCAATAGAT
65 TAAAGCGAGTAATAAGGCTTTCAAAGGCTTAAGTGACTATAAAAGGCTTTTCTCT-CCAATGGAT
* * * *
3322 -AGCTTTTGCTTAATGTTTCCTAAGGCACACATTCAACTATAAT
129 GA-CTTTTGCTTCATGTTTCCTAAGACAAACATTCAACTATAAC
* *
3365 ATATTTTAACC--AAAGGTATAAAACATTTCAA-TATAAAATCAATTATGAGAATATAAAACCAT
1 ATATTTTAACCAAAAATGT-TAAAACATCTCAACT-TAAAATCAATTATGAGAATATAAAACCAT
*
3427 TGAAAGCGAGTAATAAGGCTTTCAA
64 TTAAAGCGAGTAATAAGGCTTTCAA
Statistics
Matches: 487, Mismatches: 91, Indels: 48
0.78 0.15 0.08
Matches are distributed among these distances:
168 9 0.02
169 10 0.02
170 150 0.31
171 164 0.34
172 12 0.02
173 18 0.04
174 86 0.18
175 36 0.07
176 2 0.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (171 bp):
ATATTTTAACCAAAAATGTTAAAACATCTCAACTTAAAATCAATTATGAGAATATAAAACCATTT
AAAGCGAGTAATAAGGCTTTCAAAGGCTTAAGTGACTATAAAAGGCTTTTCTCTCCAATGGATGA
CTTTTGCTTCATGTTTCCTAAGACAAACATTCAACTATAAC
Found at i:3441 original size:341 final size:343
Alignment explanation
Indices: 2678--3451 Score: 1092
Period size: 345 Copynumber: 2.3 Consensus size: 343
2668 TTAAGTCACT
* *
2678 ATATATTTTAACCAAAATCTAAAATATTCCAACATAAAATCATTTATTAAAATATAAAACCATTT
1 ATATATTTTAACCAAAATCTAAAATATTCCAACATAAAATCATTTATGAGAATATAAAACCATTT
* *
2743 AAAGCGAGTAATAAGGCTTTCAAAGGCTTACGTGACTATAAATGGACTTTTCACTCCGATGGATG
66 AAAGCGAGTAATAAGGCTTTCAAAGGCTTACGTGACTATAAAAGGACTTTTCACTCCAATGGATG
* * * *
2808 ACTTTTGCTTCAGGTTTCCCCAAGAAAATATTTAATTATAACATATTTTACCCAAAAATATTAAA
131 ACTTTTGCATCACGTTTCCCCAAGAAAACATTCAATTATAACATATTTTACCCAAAAATATTAAA
* *
2873 AAATCCAACTTAAAATTAATTTTGAGAATATAAAACCATTCATTAAAAGTGAGTAATAATTCTTT
196 AAATCCAACTTAAAATTAATTATGAGAATATAAAACCATT-ATTAAAAGTGACTAATAATTCTTT
** * * * *
2938 TGAAGGCTTAAGTAACTATAAGAGGCTTTTCGTGCTAATGGATGGCTTTTGCTTCATATTACCTA
260 CAAAGGCTTAAGTAACTATAAGAGGCTTTTCGTGCCAATAGATAGCTTTTGCTTAATATTACCTA
*
3003 AGGCAGACATTCAACTATA
325 AGGCACACATTCAACTATA
*
3022 ACATATTTTAACCAAAAATCTAAAATATTCCAACATAAAATCATTTATGAGAATATAAAACCATT
1 ATATATTTTAACC-AAAATCTAAAATATTCCAACATAAAATCATTTATGAGAATATAAAACCATT
** * * *
3087 TAAAGCGAGTAATAAGGCTTTCAAATTCTTGCGTGACTATAAAAGGACTTTTCTCTTCAATGGAT
65 TAAAGCGAGTAATAAGGCTTTCAAAGGCTTACGTGACTATAAAAGGACTTTTCACTCCAATGGAT
* * * * *
3152 GACTTTTGCATCACGTTT-CCTAAGATAAACATTCAATTATAACATATTTTAGCTAAAAATGTTG
130 GACTTTTGCATCACGTTTCCCCAAGA-AAACATTCAATTATAACATATTTTACCCAAAAATATTA
3216 AAAAATCTC-ACTTAAAATTAATTATGAGAATATAAAACCA-T-TT-AAAGTGACTAATAATTCT
194 AAAAATC-CAACTTAAAATTAATTATGAGAATATAAAACCATTATTAAAAGTGACTAATAATTCT
* * * * *
3277 TTCAAAGGCTTGAGTGACTATAA-ATGGCTTTTCTTGCCAATAGATAGCTTTTGCTTAATGTTTC
258 TTCAAAGGCTTAAGTAACTATAAGA-GGCTTTTCGTGCCAATAGATAGCTTTTGCTTAATATTAC
3341 CTAAGGCACACATTCAACTATA
322 CTAAGGCACACATTCAACTATA
* * * * * *
3363 ATATATTTTAACCAAAGGTATAAAACATTTCAATATAAAATCAATTATGAGAATATAAAACCATT
1 ATATATTTTAACCAAA-ATCTAAAATATTCCAACATAAAATCATTTATGAGAATATAAAACCATT
*
3428 GAAAGCGAGTAATAAGGCTTTCAA
65 TAAAGCGAGTAATAAGGCTTTCAA
Statistics
Matches: 384, Mismatches: 41, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
340 4 0.01
341 166 0.43
342 2 0.01
344 19 0.05
345 192 0.50
346 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (343 bp):
ATATATTTTAACCAAAATCTAAAATATTCCAACATAAAATCATTTATGAGAATATAAAACCATTT
AAAGCGAGTAATAAGGCTTTCAAAGGCTTACGTGACTATAAAAGGACTTTTCACTCCAATGGATG
ACTTTTGCATCACGTTTCCCCAAGAAAACATTCAATTATAACATATTTTACCCAAAAATATTAAA
AAATCCAACTTAAAATTAATTATGAGAATATAAAACCATTATTAAAAGTGACTAATAATTCTTTC
AAAGGCTTAAGTAACTATAAGAGGCTTTTCGTGCCAATAGATAGCTTTTGCTTAATATTACCTAA
GGCACACATTCAACTATA
Done.