Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401647.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4764.0, 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: 5092
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.30
Warning! 925 characters in sequence are not A, C, G, or T
Found at i:315 original size:172 final size:171
Alignment explanation
Indices: 1--1659 Score: 1493
Period size: 172 Copynumber: 9.7 Consensus size: 171
* * * * *
1 AAGGCATTCATTGACAAGAAAAGTCCATTTATATTCACCCATTACTTTAAAAGCCTTATTACTAA
1 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCA
* * * ********** *
66 CTTTCAAT-GATTTTATAATTTCAAAATTNNNNNNNNNNTGAATTCTTTGTACATTTTTTA-TTA
66 CTTTAAATAG-TTTTATAATCTCATAATTGATTTAAAGTTGAATTTTTTG-ACA-TTTTTAGTTA
* ** *
129 AAATAGATTATAATTGAATGTCAACCTCGAGAAACGTGAAGAAA
128 AAACAGATTATAATTGAATGTCAACCTTAAGAAACATGAAGAAA
* ** * * * * *
173 AATGCATTCATTGATAATAAAAGTCCATTTATGGTCACCCATACTTTCAAAAAGCATTATTACTC
1 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTC-AAAAGCCTTATTACTC
* * * *
238 GCTTTAAATAGTTTTATAATGC-CATAATTGATTTCAAGTTGAATTTTTTGACACTTTTACTTAA
65 ACTTTAAATAGTTTTATAAT-CTCATAATTGATTTAAAGTTGAATTTTTTGACATTTTTAGTTAA
* * * * *
302 AACCGACTATAATTAAATGTCTACCTTGAGAAAC--GAA-AAGA
129 AACAGATTATAATTGAATGTCAACCTTAAGAAACATGAAGAA-A
*
343 AATGGCATTCATTGGCAAG-AAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTC
1 AA-GGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTC
* * * * * * *
407 GCTTTAAATAGTTTTATAATCTCAAAATTTATTTACATTTGAATTCTTTGTATATTTTTAGTTAA
65 ACTTTAAATAGTTTTATAATCTCATAATTGATTTAAAGTTGAATTTTTTG-ACATTTTTAGTTAA
* * * *
472 AACAGATTATAATTGAGTATCAATCTCAAGAAACATGAAGAAA
129 AACAGATTATAATTGAATGTCAACCTTAAGAAACATGAAGAAA
*
515 AAGGCATTCATTGGCAAG-AAAGCTCCATTTATAGTCACCCATTCCTTCAAAAGCTTTATTACTC
1 AAGGCATTCATTGGCAAGAAAAG-TCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTC
* * * * * * * * *
579 ACTTTAAATATTTTTTATAACCTCATAATTGATTTTAGGTTGTATATTTTGATATTTTTTGATTT
65 ACTTTAAATA-GTTTTATAATCTCATAATTGATTTAAAGTTGAATTTTTTGACATTTTTAG-TTA
* * *** *
644 GAACATATTATAATTGAATGTTTGCCTT-GGAAA-ATGTGAAGAAA
128 AAACAGATTATAATTGAATGTCAACCTTAAGAAACA--TGAAGAAA
688 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCA
1 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCA
* * * * ** * *
753 CTTTAAATGGTTTTATCATCTCATAATTAATTTTAAGTACAAATTCTTTT-ACATTTTTGGCT-A
66 CTTTAAATAGTTTTATAATCTCATAATTGATTTAAAGT-TGAATT-TTTTGACATTTTTAGTTAA
* * * * *
816 AA-AGATTGTATAAGTCAATGTCTAGCTTAAGAAATATGAAGAAA
129 AACAGA-T-TATAATTGAATGTCAACCTTAAGAAACATGAAGAAA
** ** * * * *
860 AAGGCAACCATTGGCACCAAAAGTCTATTTATAGTCACCCATTCCTTTAAAAGCCTTGTTACTTA
1 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCA
* * * * *
925 CTTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTAAATTTTTTTGTTAA
66 CTTTAAATAGTTTTATAATCTCATAATTGATTTAAAGTTGAATTTTTTG-ACA-TTTTTAGTTAA
* * * * * * *
990 GACAGACTAGAATTGATTGTCTAGCTTAAGAAACATGAATAAA
129 AACAGATTATAATTGAATGTCAACCTTAAGAAACATGAAGAAA
* * * * * * * *
1033 AAAGTATTCATTGGCAATAAAAGTCCACTTATAGTCACCCATACCTTTAAAAGCCTCATTACTTA
1 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCA
* * ** * * * * * **
1098 CTTTACATGGTTTTATTTTGTCATACTTGACTTT-TAGTTGAATTTTTTTACATTTTTGGGAAAA
66 CTTTAAATAGTTTTATAATCTCATAATTGA-TTTAAAGTTGAATTTTTTGACATTTTTAGTTAAA
* * * ** *
1162 ACAGACTATAATTGAATGTCCACCTAAAGAAATGTAAAGAAA
130 ACAGATTATAATTGAATGTCAACCTTAAGAAACATGAAGAAA
* * * * * *
1204 AAGGTATTCATTAGAAAAAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGTCTTATTACTCA
1 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCA
* * * *
1269 CTTTAAAT-GATTTTATAATATCAAAATTGATTTAAATTTGAATTTTTTATACATTTTTAGTTAA
66 CTTTAAATAG-TTTTATAATCTCATAATTGATTTAAAGTTGAATTTTTT-GACATTTTTAGTTAA
* *
1333 AACAGATTATAATTGAATATCAACCTTAAGAAACATGAACAAA
129 AACAGATTATAATTGAATGTCAACCTTAAGAAACATGAAGAAA
* * *
1376 AAGGCATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCTTTATTACTCA
1 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCA
* * * * * * ** *
1441 CTTTAAATAATTTTATAATCTTATAACTGATTTTAAGTTCAAATTGTTTT-ACATCTTCGGTTTA
66 CTTTAAATAGTTTTATAATCTCATAATTGATTTAAAGTT-GAATT-TTTTGACATTTTTAGTTAA
* * * **
1505 AACATATTATAATTGAATGTCTAA-CTCAACAAATGTGAAG--A
129 AACAGATTATAATTGAATGTC-AACCTTAAGAAACATGAAGAAA
* * * *
1546 GAGGCATTCATTGGCAAGAAAAGTTCATTTATATTCACCCATTCCTTTAAAAGCCTTATTACTCA
1 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCA
* * * *
1611 CTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTGTTTG
66 CTTTAAATAGTTTTATAATCTCATAATTGATTTAAAGTTGAATTTTTTG
1660 CAAAGAAAAA
Statistics
Matches: 1205, Mismatches: 245, Indels: 77
0.79 0.16 0.05
Matches are distributed among these distances:
168 4 0.00
169 63 0.05
170 167 0.14
171 174 0.14
172 457 0.38
173 318 0.26
174 19 0.02
175 3 0.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (171 bp):
AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCA
CTTTAAATAGTTTTATAATCTCATAATTGATTTAAAGTTGAATTTTTTGACATTTTTAGTTAAAA
CAGATTATAATTGAATGTCAACCTTAAGAAACATGAAGAAA
Found at i:857 original size:345 final size:341
Alignment explanation
Indices: 1--1659 Score: 1497
Period size: 345 Copynumber: 4.8 Consensus size: 341
* * * *
1 AAGGCATTCATTGACAAGAAAAGTCCATTTATATTCACCCATTA-CTTTAAAAGCCTTATTACTA
1 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCA-TACCTTCAAAAGCCTTATTACTC
* * * ********** * **
65 ACTTTCAAT-GATTTTATAATTTCAAAATTNNNNNNNNNNT-GAATTCTTTGTACATTTTTTATT
65 ACTTTAAATAG-TTTTATAATCTCATAATTAATTTTAAGTTCAAATTCTTT-TACATTTTTGGTT
* * * ** * **
128 AAAATAGATTATAATTGAATGTC-AACCTCGAGAAACGTGAAGAAAAATGCATTCATTGATAATA
128 AAAACA-TTTATAATTGAATGTCTAA-CTCAAGAAATATGAAGAAAAAGGCATTCATTGGCAA-A
* * * * *
192 AAAGTCCATTTATGGTCACCCATACTTTCAAAAAGCATTATTACTCGCTTTAAATAGTTTTATAA
190 AAAGTCCATTTATAGTCACCCATTCCTTC-AAAAGCCTTATTACTCACTTTAAATAGTTTTATAA
* * * * * *
257 TGC-CATAATTGATTTCAAGTTGAATTTTTTGACA-CTTTTACTTAAAACCGACTATAATTAAAT
254 T-CTCAAAATTGATTTAAAGTTGAA-TTTTTGATATTTTTTACTTAAAACAGACTATAATTGAAT
* *
320 GTCTACCTTGAGAAAC--GAA-AAGA
317 GTCAACCTTAAGAAACATGAAGAA-A
* *
343 AATGGCATTCATTGGCAAG-AAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTC
1 AA-GGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTC
* * * ** * *
407 GCTTTAAATAGTTTTATAATCTCAAAATTTA-TTTACA-TTTGAATTCTTTGTATATTTTTAGTT
65 ACTTTAAATAGTTTTATAATCTCATAATTAATTTTA-AGTTCAAATTCTTT-TACATTTTTGGTT
* * * * *
470 AAAACAGATTATAATTGAGTATC-AATCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGA
128 AAAACA-TTTATAATTGAATGTCTAA-CTCAAGAAATATGAAGAAAAAGGCATTCATTGGCAAAA
* *
534 AAGCTCCATTTATAGTCACCCATTCCTTCAAAAGCTTTATTACTCACTTTAAATATTTTTTATAA
191 AAG-TCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATA-GTTTTATAA
* * * * * ** * *
599 CCTCATAATTGATTTTAGGTTGTATATTTTGATATTTTTTGA-TTTGAACATATTATAATTGAAT
254 TCTCAAAATTGATTTAAAGTTGAAT-TTTTGATATTTTTT-ACTTAAAACAGACTATAATTGAAT
*** *
663 GTTTGCCTT-GGAAA-ATGTGAAGAAA
317 GTCAACCTTAAGAAACA--TGAAGAAA
*
688 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCA
1 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCA
* * * *
753 CTTTAAATGGTTTTATCATCTCATAATTAATTTTAAGTACAAATTCTTTTACATTTTTGGCTAAA
66 CTTTAAATAGTTTTATAATCTCATAATTAATTTTAAGTTCAAATTCTTTTACATTTTTGGTTAAA
* * * * * ** *
818 AGATTGTATAAGTCAATGTCTAGCTTAAGAAATATGAAGAAAAAGGCAACCATTGGCACCAAAAG
131 ACATT-TATAATTGAATGTCTAACTCAAGAAATATGAAGAAAAAGGCATTCATTGGCA-AAAAAG
* * * *
883 TCTATTTATAGTCACCCATTCCTTTAAAAGCCTTGTTACTTACTTTAAATAGTTTTATAATCTCA
194 TCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCA
* * ** * * * *
948 AAATTGATTTAAATTTGAATTCTTTGTAAATTTTTTTGTTAAGACAGACTAGAATTGATTGTCTA
259 AAATTGATTTAAAGTTGAATT-TTTG-ATATTTTTTACTTAAAACAGACTATAATTGAATGTCAA
* *
1013 GCTTAAGAAACATGAATAAA
322 CCTTAAGAAACATGAAGAAA
* * * * * * *
1033 AAAGTATTCATTGGCAATAAAAGTCCACTTATAGTCACCCATACCTTTAAAAGCCTCATTACTTA
1 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCA
* * ** * * * * * **
1098 CTTTACATGGTTTTATTTTGTCATACTTGACTTTT-AGTT-GAATTTTTTTACATTTTTGGGAAA
66 CTTTAAATAGTTTTATAATCTCATAATT-AATTTTAAGTTCAAATTCTTTTACATTTTTGGTTAA
** * * * * * * **
1161 AACAGACTATAATTGAATGTCCACCTAAAGAAATGTAAAGAAAAAGGTATTCATTAGAAAAAAAA
130 AACA-TTTATAATTGAATGTCTAACTCAAGAAATATGAAGAAAAAGGCATTCATT-GGCAAAAAA
* * *
1226 GTCCATTTATAGTCACCTATTCCTTCAAAAGTCTTATTACTCACTTTAAAT-GATTTTATAATAT
193 GTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAG-TTTTATAATCT
* * * * * *
1290 CAAAATTGATTTAAATTTGAATTTTTTATACATTTTTAGTTAAAACAGATTATAATTGAATATCA
257 CAAAATTGATTTAAAGTTGAATTTTTGATA-TTTTTTACTTAAAACAGACTATAATTGAATGTCA
*
1355 ACCTTAAGAAACATGAACAAA
321 ACCTTAAGAAACATGAAGAAA
* *
1376 AAGGCATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCTTTATTACTCA
1 AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCA
* * * * * * * *
1441 CTTTAAATAATTTTATAATCTTATAACTGATTTTAAGTTCAAATTGTTTTACATCTTCGGTTTAA
66 CTTTAAATAGTTTTATAATCTCATAATTAATTTTAAGTTCAAATTCTTTTACATTTTTGGTTAAA
* * *
1506 ACATATTATAATTGAATGTCTAACTCAACAAATGTGAAG--AGAGGCATTCATTGGCAAGAAAAG
131 ACAT-TTATAATTGAATGTCTAACTCAAGAAATATGAAGAAAAAGGCATTCATTGGCAA-AAAAG
* * * *
1569 TTCATTTATATTCACCCATTCCTTTAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCA
194 TCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCA
*
1634 AAATTGATTTAAATTTGAATTGTTTG
259 AAATTGATTTAAAGTTGAATT-TTTG
1660 CAAAGAAAAA
Statistics
Matches: 1078, Mismatches: 201, Indels: 75
0.80 0.15 0.06
Matches are distributed among these distances:
341 35 0.03
342 296 0.27
343 176 0.16
344 241 0.22
345 300 0.28
346 29 0.03
347 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (341 bp):
AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCA
CTTTAAATAGTTTTATAATCTCATAATTAATTTTAAGTTCAAATTCTTTTACATTTTTGGTTAAA
ACATTTATAATTGAATGTCTAACTCAAGAAATATGAAGAAAAAGGCATTCATTGGCAAAAAAGTC
CATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAA
ATTGATTTAAAGTTGAATTTTTGATATTTTTTACTTAAAACAGACTATAATTGAATGTCAACCTT
AAGAAACATGAAGAAA
Found at i:1764 original size:122 final size:122
Alignment explanation
Indices: 1547--1781 Score: 393
Period size: 122 Copynumber: 1.9 Consensus size: 122
1537 ATGTGAAGAG
*
1547 AGGCATTCATTGGCAAGAAAAGTTCATTTATATTCACCCATTCCTTTAAAAGCCTTATTACTCAC
1 AGGCATTCATTGGCAAGAAAAGTTCATTTATATTCACCCATTACTTTAAAAGCCTTATTACTCAC
1612 TTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTGTTTGCAAAGAAAA
66 TTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTGTTTGCAAAGAAAA
1669 AGGCATTCATTGGCAAGAAAAG-TCTATTTATATTCACCCATTACTTTAACAA-CCTTATTACTC
1 AGGCATTCATTGGCAAGAAAAGTTC-ATTTATATTCACCCATTACTTTAA-AAGCCTTATTACTC
* * * *
1732 GCTTTAACTGGTTTTATAATCTCAAAATTGATTTGAATTTGAATTTTTTG
64 ACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTGTTTG
1782 TACAATTTTG
Statistics
Matches: 106, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
121 2 0.02
122 102 0.96
123 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (122 bp):
AGGCATTCATTGGCAAGAAAAGTTCATTTATATTCACCCATTACTTTAAAAGCCTTATTACTCAC
TTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTGTTTGCAAAGAAAA
Found at i:1989 original size:172 final size:170
Alignment explanation
Indices: 1662--2436 Score: 876
Period size: 172 Copynumber: 4.5 Consensus size: 170
1652 ATTGTTTGCA
* * *
1662 AAGAAAAAGGCATTCATTGGCAAGAAAAGTCTATTTATATTCACCCATTACTTTAACAA-CCTTA
1 AAGAAAAAGGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAA-AAGCCTTA
* * * * *
1726 TTACTCGCTTTAACTGGTTTTATAATCTCAAAATTGATTTGAATTTGAATTTTTTGTACAATTTT
65 TTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTAAATTTTTT-TAC-ATTTT
* * * * **
1791 GATTAAAATAGATTATAATCGAATGTCAACCTTAAGAAACAAG
128 TATTAAAACATATTATAATTGAATGTCAACCTCGAGAAACAAG
* * * * * **
1834 AAGAAAAATGCATTCATTGGCAAGAAACGTATATTTATAGTCACCCATACCATCAAAAAGGATTA
1 AAGAAAAAGGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTC-AAAAGCCTTA
** * * * *
1899 TTACTCACTTTAAATAATTTTATAATGC-CATAATTGATTTCAAGTTGAATTTTTTTACACTTTT
65 TTACTCACTTTAAATGGTTTTATAAT-CTCAAAATTGATTTTAAGTTAAATTTTTTTACATTTTT
* * * * * * *
1963 ACTTAAAACGTACTATAGTTGAATGTCTACGTTGAGAAACAAA
129 A-TTAAAACATATTATAATTGAATGTCAACCTCGAGAAACAAG
* * *
2006 AAGAAAAAGGCATTCATTGGCAAGAAAACTCCATTTATAGTAACCCATTCCTTCAAAAGCCTTAT
1 AAGAAAAAGGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTAT
* *
2071 TACTCACTTTAAATGGTTTTAGAATCTCAAAATTGATTTTAAGTCAAATTTTTTTTACAATTTTT
66 TACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTAAA-TTTTTTTAC-ATTTTT
* * * *
2136 AATAAAACATATTATAATTGTATGTCTAA-CTCGAGAAGCATG
129 ATTAAAACATATTATAATTGAATGTC-AACCTCGAGAAACAAG
* * * * *
2178 AAGAAAAAGGCATTCATTGGCAAGAAAAGTCCAATTATTGTCACTCATTCTTTCAAAAGCCTTAT
1 AAGAAAAAGGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTAT
* *
2243 TACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTCAAATTTTTTTATATTTTTG
66 TACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTT-AAATTTTTTTACATTTTT-
* * ** * * *
2308 GTTAAGACATATTATAATTGAATGTTTAGCTCGACAAACGTA-
129 ATTAAAACATATTATAATTGAATGTCAACCTCGAGAAAC-AAG
*
2350 AAGAAAAAGGCATTCATTGGCAAGAAAAGTC-ATATTATAGTCACTCATTCCTTCAAAAGCCTTA
1 AAGAAAAAGGCATTCATTGGCAAGAAAAGTCTAT-TTATAGTCACCCATTCCTTCAAAAGCCTTA
2414 TTACTCACTTTAAATGGTTTTAT
65 TTACTCACTTTAAATGGTTTTAT
2437 NNNNNNNNNN
Statistics
Matches: 509, Mismatches: 81, Indels: 26
0.83 0.13 0.04
Matches are distributed among these distances:
170 1 0.00
171 61 0.12
172 385 0.76
173 61 0.12
174 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (170 bp):
AAGAAAAAGGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTAT
TACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTAAATTTTTTTACATTTTTAT
TAAAACATATTATAATTGAATGTCAACCTCGAGAAACAAG
Found at i:2296 original size:344 final size:344
Alignment explanation
Indices: 1661--2435 Score: 968
Period size: 344 Copynumber: 2.3 Consensus size: 344
1651 AATTGTTTGC
* * * *
1661 AAAGAAAAAGGCATTCATTGGCAAGAAAAGTCTATTTATATTCACCCATTACTTTAACAA-CCTT
1 AAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAA-AAGCCTT
* * * * **
1725 ATTACTCGCTTTAACTGGTTTTATAATCTCAAAATTGATTTGAATTTGAATTTTTTGTACAATTT
65 ATTACTCACTTTAAATGGTTTTAGAATCTCAAAATTGATTTGAAGTCAAATTTTTTGTACAATTT
* * * *
1790 TGATTAAAATAGATTATAATCGAATGTCAACCTTAAGAAACAAGAAGAAAAATGCATTCATTGGC
130 TGAATAAAACAGATTATAATCGAATGTCAACCTCAAGAAACAAGAAGAAAAAGGCATTCATTGGC
* * * *
1855 AAGAAACGTATATTTATAGTCACCCATACCATCAAAAAGGATTATTACTCACTTTAAATAATTTT
195 AAGAAAAGTACAATTATAGTCACCCATACCATCAAAAAGCATTATTACTCACTTTAAATAATTTT
* * *
1920 ATAATGCCATAATTGATTTCAAGTTGAATTTTTTTACACTTTTACTTAAAACGTACTATAGTTGA
260 ATAATGCCATAATTGATTTCAAGTTAAATTTTTTTACACTTTTACTTAAAACATACTATAATTGA
* *
1985 ATGTCTA-CGTTGAGAAACAA
325 ATGTCTAGC-TCGACAAACAA
* *
2005 AAAGAAAAAGGCATTCATTGGCAAGAAAACTCCATTTATAGTAACCCATTCCTTCAAAAGCCTTA
1 AAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTA
* *
2070 TTACTCACTTTAAATGGTTTTAGAATCTCAAAATTGATTTTAAGTCAAATTTTTTTTACAATTTT
66 TTACTCACTTTAAATGGTTTTAGAATCTCAAAATTGATTTGAAGTCAAATTTTTTGTACAATTTT
* * * * * * *
2135 TAATAAAACATATTATAATTGTATGTCTAA-CTCGAGAAGCATGAAGAAAAAGGCATTCATTGGC
131 GAATAAAACAGATTATAATCGAATGTC-AACCTCAAGAAACAAGAAGAAAAAGGCATTCATTGGC
* * * * ** * **
2199 AAGAAAAGTCCAATTATTGTCACTCATTCTTTC-AAAAGCCTTATTACTCACTTTAAATGGTTTT
195 AAGAAAAGTACAATTATAGTCACCCATACCATCAAAAAGCATTATTACTCACTTTAAATAATTTT
* * * ** * *
2263 ATAAT-CTCATAATTGATTTTAAGTTCAAATTTTTTTATATTTTTGGTTAAGACATATTATAATT
260 ATAATGC-CATAATTGATTTCAAGTT-AAATTTTTTTACACTTTTACTTAAAACATACTATAATT
* **
2327 GAATGTTTAGCTCGACAAACGT
323 GAATGTCTAGCTCGACAAACAA
*
2349 AAAGAAAAAGGCATTCATTGGCAAGAAAAGT-CATATTATAGTCACTCATTCCTTCAAAAGCCTT
1 AAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCAT-TTATAGTCACCCATTCCTTCAAAAGCCTT
2413 ATTACTCACTTTAAATGGTTTTA
65 ATTACTCACTTTAAATGGTTTTA
2436 TNNNNNNNNN
Statistics
Matches: 369, Mismatches: 56, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
342 1 0.00
343 54 0.15
344 311 0.84
345 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (344 bp):
AAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTA
TTACTCACTTTAAATGGTTTTAGAATCTCAAAATTGATTTGAAGTCAAATTTTTTGTACAATTTT
GAATAAAACAGATTATAATCGAATGTCAACCTCAAGAAACAAGAAGAAAAAGGCATTCATTGGCA
AGAAAAGTACAATTATAGTCACCCATACCATCAAAAAGCATTATTACTCACTTTAAATAATTTTA
TAATGCCATAATTGATTTCAAGTTAAATTTTTTTACACTTTTACTTAAAACATACTATAATTGAA
TGTCTAGCTCGACAAACAA
Done.