Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400458.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3655.0, 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: 4650
ACGTcount: A:0.21, C:0.09, G:0.07, T:0.20
Warning! 2005 characters in sequence are not A, C, G, or T
Found at i:1819 original size:172 final size:170
Alignment explanation
Indices: 1359--2726 Score: 1042
Period size: 172 Copynumber: 8.0 Consensus size: 170
1349 NGTAATCTCA
* * * * * * *
1359 AAATTGATTGAAATTTGAATTCTTTGTACATTTTTGATTAAAAAATATTATAATTCAATGTCTAC
1 AAATTGATTTAAATTTGAATTCTTTGTACATTTTTTAATAAAACAGATTATAATTGAATGTCAAC
*** ** * * *
1424 CTCAAGAATTGTGAAGGTAAAGGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCAATTCCT
66 CTCAAGAA-ACAGAAGAAAAAGGCATACATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCT
* * *
1489 TCGAAAAGCCTTATTACTCGCTTTACATGGTTTTATAATAC-C
130 TC-AAAAGCCTTATTACTCACTTTAAATGATTTTATAA-ACTC
* * * * * * * *
1531 ATAATTGATTTGAAGTTGAA--CGTTTTTACA-TTTTTAGTTAAAAAAGAATAGAATTG-TTGTC
1 A-AATTGATTTAAATTTGAATTC-TTTGTACATTTTTTA-ATAAAACAGATTATAATTGAATGTC
* ** * * * * * *
1592 TACCTTGAGAAAC-GTAATGAAAAAGGCATTCGTTTGTAAAAAAAGTCTATTTATAGTCACCCAT
63 AACCTCAAGAAACAG-AA-GAAAAAGGCATACATTGGCAAGAAAAGTCCATTTATAGTCACCCAT
* * * * *
1656 TTCTTTAAAAGCATTTTTACTCACTTTAAATGATTTTATAACCTC
126 TCCTTCAAAAGCCTTATTACTCACTTTAAATGATTTTATAAACTC
* * *
1701 AACATTGATTTAAATTTTAATTCTTTGTACATTTTTTAATAAAACAGATTATAATTGAATGACAG
1 AA-ATTGATTTAAATTTGAATTCTTTGTACATTTTTTAATAAAACAGATTATAATTGAATGTCAA
* * * * *
1766 CCTGAAGAAACGAGAAGAAAAAGGCATACATTGCCAAGAAAAATTCGTTTATAGTCACCCATTCC
65 CCTCAAGAAAC-AGAAGAAAAAGGCATACATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCC
* * * *
1831 TTCAAAAGCCTCATTACTCGCTTTAAATGGTTTTATAATGC-C
129 TTCAAAAGCCTTATTACTCACTTTAAATGATTTTATAA-ACTC
* ** * * * ** *
1873 ATAATTAATTTTTAGTTGAAGTATTT-TACATTTTTTGTTAAAACAGACTATAATTGAATGTCAA
1 A-AATTGATTTAAATTTGAATTCTTTGTACATTTTTTAATAAAACAGATTATAATTGAATGTCAA
* * * ** *** * * *
1937 TCTCGAGAAACACAAAGAAAAAGATATTTGTTCGTAATAAAAGTCCATTTATAGTCACCCATTCC
65 CCTCAAGAAACA-GAAGAAAAAGGCATACATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCC
* * * * ** *
2002 TTCAAAAACCTTAGTACTCTCTTTAAATGGTTTTGCAATCTCC
129 TTCAAAAGCCTTATTACTCACTTTAAATGATTTTATAAACT-C
* * * *
2045 AAATTGATTAAAATTTGATTTCTTTGTAAATTTTTGGTAA-AAAA-AGATTATAATTGAACGTCA
1 AAATTGATTTAAATTTGAATTCTTTGTACATTTTT--TAATAAAACAGATTATAATTGAATGTCA
** * ** *
2108 ATGTCAAGAAACATGAAGAAAAAGTCATTTATTGGCAAGAGAAGTCCATTTATAGTCACCCATTC
64 ACCTCAAGAAACA-GAAGAAAAAGGCATACATTGGCAAGAAAAGTCCATTTATAGTCACCCATTC
* * * * * *
2173 CTCCCAAAGCCTTATAATTGACTTTAAATGATTTTGTAATA-TC
128 CTTCAAAAGCCTTATTACTCACTTTAAATGATTTTATAA-ACTC
** * * * * *
2216 AAAATTGATTGCAATTTGAATTCTTTGTATA-TTGTTCATCAAAAAAGATTATAATTCAATGTCA
1 -AAATTGATTTAAATTTGAATTCTTTGTACATTTTTTAAT-AAAACAGATTATAATTGAATGTCA
* * ** * * *
2280 ACCTCCAGAAACGTGAAGGTAAAGGCATTCATTGGCAAGAAAAGTCCATTAATAGTCAACCATTC
64 ACCTCAAGAAAC-AGAAGAAAAAGGCATACATTGGCAAGAAAAGTCCATTTATAGTCACCCATTC
* * *
2345 CTTCAAAAAACCTTATTACTCGCTTTACATGATTTTATAATAC-C
128 CTTC-AAAAGCCTTATTACTCACTTTAAATGATTTTATAA-ACTC
* * * * * ** *
2389 ATAATTGATTTTAAGTTGAA--CATTTTTACA-TTTTTAGTTAAAACGGACAAGAATTG-ATGTC
1 A-AATTGATTTAAATTTGAATTC-TTTGTACATTTTTTA-ATAAAACAGATTATAATTGAATGTC
* * * * *
2450 TACCTCGAGAAACATAATGAAAAAGGCATTCGTTGGCAAGAAAAGTCCATTTATAGTCACCCATT
63 AACCTCAAGAAACAGAA-GAAAAAGGCATACATTGGCAAGAAAAGTCCATTTATAGTCACCCATT
** *
2515 CCTTCAAAAGTATTTTTACTCACTTTAAATGATTTTATAAACTC
127 CCTTCAAAAGCCTTATTACTCACTTTAAATGATTTTATAAACTC
* * ** * * * *
2559 AAAACTGATATAAATTTGAATTCTTTGTACATTTTTTGTTCAAACAGATTTTCATTAAATGTCAA
1 -AAATTGATTTAAATTTGAATTCTTTGTACATTTTTTAATAAAACAGATTATAATTGAATGTCAA
* * * * **
2624 CCTCAAGAAACGTGAAGAAAAAGACATACATTGGCAAGAAAAATCCGTTTATAGTCACCCATTTT
65 CCTCAAGAAAC-AGAAGAAAAAGGCATACATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCC
* * * *
2689 TTCCAAAGTCTTATTACTCATTTTAAATGGTTTTATAA
129 TTCAAAAGCCTTATTACTCACTTTAAATGATTTTATAA
2727 TGCCATAATT
Statistics
Matches: 936, Mismatches: 220, Indels: 80
0.76 0.18 0.06
Matches are distributed among these distances:
169 7 0.01
170 96 0.10
171 301 0.32
172 459 0.49
173 71 0.08
174 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (170 bp):
AAATTGATTTAAATTTGAATTCTTTGTACATTTTTTAATAAAACAGATTATAATTGAATGTCAAC
CTCAAGAAACAGAAGAAAAAGGCATACATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTT
CAAAAGCCTTATTACTCACTTTAAATGATTTTATAAACTC
Found at i:1989 original size:343 final size:339
Alignment explanation
Indices: 1359--2554 Score: 996
Period size: 343 Copynumber: 3.5 Consensus size: 339
1349 NGTAATCTCA
* * * * *
1359 AAATTGATTGAAATTTGAATTCTTTGTACATTTTTGATTAAAAAATATTATAATTCAATGTCTAC
1 AAATTGATTAAAATTTGAATTCTTTGTACATTTTTTAAT-AAAAAGATTATAATTGAATGTC-AC
** * ** * *
1424 CTCAAGAATTGTGAAGGTAAAGGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCAATTCCT
64 CTCAAGAAACGAGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCT
* * *
1489 TCGAAAAGCCTTATTACTCGCTTTACATGGTTTTATAATACCATAATTGATTTGAAGTTGAACGT
129 TC-AAAAGCCTCATTACTCGCTTTAAATGGTTTTATAATACCATAATTAATTTGAAGTTGAACGT
* * * ** * *
1554 TTTTACATTTTTAGTTAAAAAAGAATAGAATTGTTGTCTACCTTGAGAAACGTAATGAAAAAGGC
193 TTTTACATTTTTAGTTAAAAAAGAATAGAATTGATGTCAACCTCGAGAAACACAAAGAAAAAGAC
* * * * * **
1619 ATTCGTTTGTAAAAAAAGTCTATTTATAGTCACCCATTTCTTTAAAAGCATTTTTACTCACTTTA
258 ATTCGTTCGTAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAACATTAGTACTCACTTTA
*
1684 AATGATTTTATAACCTC
323 AATGATTTTACAACCTC
* * *
1701 AACATTGATTTAAATTTTAATTCTTTGTACATTTTTTAATAAAACAGATTATAATTGAATGACAG
1 AA-ATTGATTAAAATTTGAATTCTTTGTACATTTTTTAATAAAA-AGATTATAATTGAATGTCA-
* * * * * *
1766 CCTGAAGAAACGAGAAGAAAAAGGCATACATTGCCAAGAAAAATTCGTTTATAGTCACCCATTCC
63 CCTCAAGAAACGAGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCC
* **
1831 TTCAAAAGCCTCATTACTCGCTTTAAATGGTTTTATAATGCCATAATTAATTTTTAGTTGAA-GT
128 TTCAAAAGCCTCATTACTCGCTTTAAATGGTTTTATAATACCATAATTAATTTGAAGTTGAACGT
* * * * *
1895 ATTTTACATTTTTTGTTAAAACAGACTATAATTGAATGTCAATCTCGAGAAACACAAAGAAAAAG
193 -TTTTACATTTTTAGTTAAAAAAGAATAGAATTG-ATGTCAACCTCGAGAAACACAAAGAAAAAG
* * * * *
1960 ATATTTGTTCGTAATAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAACCTTAGTACTCTCTT
256 ACATTCGTTCGTAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAACATTAGTACTCACTT
* * *
2025 TAAATGGTTTTGCAATCTCC
321 TAAATGATTTTACAACCT-C
* * *
2045 AAATTGATTAAAATTTGATTTCTTTGTAAATTTTTGGTAA-AAAAAGATTATAATTGAACGTCAA
1 AAATTGATTAAAATTTGAATTCTTTGTACATTTTT--TAATAAAAAGATTATAATTGAATGTC-A
** * * *
2109 TGTCAAGAAAC-ATGAAGAAAAAGTCATTTATTGGCAAGAGAAGTCCATTTATAGTCACCCATTC
63 CCTCAAGAAACGA-GAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTC
* * * * * * * * * * *
2173 CTCCCAAAGCCTTA-TAATTGACTTTAAATGATTTTGTAATATCAAAATTGA-TTGCAATTTGAA
127 CTTCAAAAGCCTCATTACTCG-CTTTAAATGGTTTTATAATACCATAATTAATTTG-AAGTTGAA
* * * * * * * * *** *
2236 TTC-TTTGTATATTGTTCA-TCAAAAAAGATTATAATTCAATGTCAACCTCCAGAAACGTGAAGG
190 --CGTTTTTACATT-TTTAGTTAAAAAAGAATAGAATT-GATGTCAACCTCGAGAAACACAAAGA
* * * * * * * * * *
2299 TAAAGGCATTCATTGGCAAGAAAAGTCCATTAATAGTCAACCATTCCTTCAAAAAACCTTATTAC
251 AAAAGACATTCGTTCGTAAAAAAAGTCCATTTATAGTCACCCATTCCTTC-AAAAACATTAGTAC
* * * *
2364 TCGCTTTACATGATTTTATAATAC-C
315 TCACTTTAAATGATTTTACAA-CCTC
** * * * * ** *
2389 ATAATTGATTTTAAGTTGAA--CATTTTTACA-TTTTTAGTTAAAACGGACAAGAATTG-ATGTC
1 A-AATTGATTAAAATTTGAATTC-TTTGTACATTTTTTA-ATAAAA-AGATTATAATTGAATGTC
* * *
2450 TACCTCGAGAAAC-ATAATGAAAAAGGCATTCGTTGGCAAGAAAAGTCCATTTATAGTCACCCAT
62 -ACCTCAAGAAACGAGAA-GAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAT
** ** * *
2514 TCCTTCAAAAGTATTTTTACTCACTTTAAATGATTTTATAA
125 TCCTTCAAAAGCCTCATTACTCGCTTTAAATGGTTTTATAA
2555 ACTCAAAACT
Statistics
Matches: 682, Mismatches: 146, Indels: 51
0.78 0.17 0.06
Matches are distributed among these distances:
341 4 0.01
342 98 0.14
343 422 0.62
344 108 0.16
345 49 0.07
346 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (339 bp):
AAATTGATTAAAATTTGAATTCTTTGTACATTTTTTAATAAAAAGATTATAATTGAATGTCACCT
CAAGAAACGAGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTC
AAAAGCCTCATTACTCGCTTTAAATGGTTTTATAATACCATAATTAATTTGAAGTTGAACGTTTT
TACATTTTTAGTTAAAAAAGAATAGAATTGATGTCAACCTCGAGAAACACAAAGAAAAAGACATT
CGTTCGTAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAACATTAGTACTCACTTTAAAT
GATTTTACAACCTC
Found at i:2577 original size:343 final size:343
Alignment explanation
Indices: 1442--2744 Score: 813
Period size: 343 Copynumber: 3.8 Consensus size: 343
1432 TTGTGAAGGT
* * * * *
1442 AAAGGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCAATTCCTTCGAAAAGCCTTATTACT
1 AAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCC-TCCAAAAGCATTATAACT
* * * * * * * *
1507 CGCTTTACATGGTTTTATAATACCATAATTGATTTG-AAGTTGAA--CGTTTTTACATTT-TT-A
65 CACTTTAAATGATTTTATAATATCAAAACTGA-TTGAAATTTGAATTC-TTTGTACATTTGTTCA
* * * ** * ** * * * * *
1567 GTTAAAAAAGAATAGAATT-GTTGTCTACCTTGAGAAACGT-AATGAAAAAGGCATTCGTTTGTA
128 --TCAAAAAGATTATAATTAAATGTCAACCTCAAGAAACGTGAA-GAAAAAGACATACATTGGCA
* * * * * * * *
1630 A-AAAAAGTCTATTTATAGTCACCCATTTCTTTAAAAGCATTTTTACTCACTTTAAATGATTTTA
190 AGAAAAA-TCCATTAATAGTCAACCATTCCTTCAAAAACCTTATTACTCACTTTAAATGATTTTA
* * * * * * * ** *
1694 TAA-CCTCA-ACATTGA-TTTAAATTTTAATTC-TTTGTACATTTTTTA-ATAAAACAGATTATA
254 TAATAC-CATA-ATTGACTTTTAAGTTGAA--CATTTTTACA-TTTTTAGTTAAAACGGACAAGA
*
1754 ATTGAATGAC-AGCCT-GAAGAAACGA-GAAGAA
314 ATTG-ATGTCTA-CCTCG-AGAAAC-ATGAAGAA
* * * * * * * * *
1785 AAAGGCATACATTGCCAAGAAAAATTCGTTTATAGTCACCCATTCCTTCAAAAGCCTCATTACTC
1 AAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTCCAAAAGCATTATAACTC
* * ** * * * *** * * * ** *
1850 GCTTTAAATGGTTTTATAATGCCATAATTAATTTTTAGTTGAAGTATTT-TACATTT-TTTGTTA
66 ACTTTAAATGATTTTATAATATCAAAACTGATTGAAATTTGAATTCTTTGTACATTTGTTCATCA
* * * * *** * *** * * *
1913 AAACAGACTATAATTGAATGTCAATCTCGAGAAACACAAAGAAAAAGATATTTGTTCGTAATAAA
131 AAA-AGATTATAATTAAATGTCAACCTCAAGAAACGTGAAGAAAAAGACATACATTGGCAAGAAA
* * * * * * ** *
1978 AGTCCATTTATAGTCACCCATTCCTTCAAAAACCTTAGTACTCTCTTTAAATGGTTTTGCAATCT
195 AATCCATTAATAGTCAACCATTCCTTCAAAAACCTTATTACTCACTTTAAATGATTTTATAAT-A
** * * * * * * ** ** * *
2043 CCA-AATTGA-TTAAAATTTGATTTC-TTTGTAAATTTTTGGTAAAAAAAGATTATAATTGAACG
259 CCATAATTGACTTTTAAGTTGA--ACATTTTTACATTTTTAGTTAAAACGGACAAGAATTG-ATG
* ** *
2105 TCAATGTCAAGAAACATGAAGAA
321 TCTACCTCGAGAAACATGAAGAA
* * * * * * *
2128 AAAGTCATTTATTGGCAAGAGAAGTCCATTTATAGTCACCCATTCCTCCCAAAGCCTTATAATTG
1 AAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTCCAAAAGCATTATAACTC
* * * *
2193 ACTTTAAATGATTTTGTAATATCAAAATTGATTGCAATTTGAATTCTTTGTATA-TTGTTCATCA
66 ACTTTAAATGATTTTATAATATCAAAACTGATTGAAATTTGAATTCTTTGTACATTTGTTCATC-
* * ** * *
2257 AAAAAGATTATAATTCAATGTCAACCTCCAGAAACGTGAAGGTAAAGGCATTCATTGGCAAGAAA
130 AAAAAGATTATAATTAAATGTCAACCTCAAGAAACGTGAAGAAAAAGACATACATTGGCAAGAAA
* * *
2322 AGTCCATTAATAGTCAACCATTCCTTCAAAAAACCTTATTACTCGCTTTACATGATTTTATAATA
195 AATCCATTAATAGTCAACCATTCCTTC-AAAAACCTTATTACTCACTTTAAATGATTTTATAATA
2387 CCATAATTGA-TTTTAAGTTGAACATTTTTACATTTTTAGTTAAAACGGACAAGAATTGATGTCT
259 CCATAATTGACTTTTAAGTTGAACATTTTTACATTTTTAGTTAAAACGGACAAGAATTGATGTCT
2451 ACCTCGAGAAACAT-AATGAA
324 ACCTCGAGAAACATGAA-GAA
* * * * *
2471 AAAGGCATTCGTTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGTATTTTTACTC
1 AAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTCCAAAAGCATTATAACTC
* **
2536 ACTTTAAATGATTTTATAA-ACTCAAAACTGATAT-AAATTTGAATTCTTTGTACATTTTTTGTT
66 ACTTTAAATGATTTTATAATA-TCAAAACTGAT-TGAAATTTGAATTCTTTGTACATTTGTTCAT
* * *
2599 CAAACAGATTTTCATTAAATGTCAACCTCAAGAAACGTGAAGAAAAAGACATACATTGGCAAGAA
129 CAAAAAGATTATAATTAAATGTCAACCTCAAGAAACGTGAAGAAAAAGACATACATTGGCAAGAA
* * * ** * ** * * *
2664 AAATCCGTTTATAGTCACCCATTTTTTCCAAAGTCTTATTACTCATTTTAAATGGTTTTATAATG
194 AAATCCATTAATAGTCAACCATTCCTTCAAAAACCTTATTACTCACTTTAAATGATTTTATAATA
2729 CCATAATTGACTTTTA
259 CCATAATTGACTTTTA
2745 GTNNNNNNNN
Statistics
Matches: 760, Mismatches: 173, Indels: 54
0.77 0.18 0.05
Matches are distributed among these distances:
341 7 0.01
342 117 0.15
343 466 0.61
344 121 0.16
345 49 0.06
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (343 bp):
AAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTCCAAAAGCATTATAACTC
ACTTTAAATGATTTTATAATATCAAAACTGATTGAAATTTGAATTCTTTGTACATTTGTTCATCA
AAAAGATTATAATTAAATGTCAACCTCAAGAAACGTGAAGAAAAAGACATACATTGGCAAGAAAA
ATCCATTAATAGTCAACCATTCCTTCAAAAACCTTATTACTCACTTTAAATGATTTTATAATACC
ATAATTGACTTTTAAGTTGAACATTTTTACATTTTTAGTTAAAACGGACAAGAATTGATGTCTAC
CTCGAGAAACATGAAGAA
Found at i:2716 original size:515 final size:512
Alignment explanation
Indices: 1442--2727 Score: 1366
Period size: 515 Copynumber: 2.5 Consensus size: 512
1432 TTGTGAAGGT
* * *
1442 AAAGGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCAATTCCTTCGAAAAGCCTTATTACT
1 AAAGGCATTCGTTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTC-AAAAGCCTTATTACT
* * * * * *
1507 CGCTTTACATGGTTTTATAATAC-CATAATTGATTTGAAGTTGAA--CGTTTTTACATTTTTAGT
65 CACTTTAAATGGTTTTATAA-ACTCAAAATTGA-TTAAATTTGAATTC-TTTGTACATTTTTAGT
* * ** * ** * * * *
1569 TAAAAAAGAATAGAATTGTTGTCTACCTTGAGAAACGT-AATGAAAAAGGCATTCGTTTGTAA-A
127 TAAAAAAGATTATAATTAATGTCAACCTCAAGAAACGTGAA-GAAAAAGACATTCATTGGCAAGA
* * *
1632 AAAAGTCTATTTATAGTCACCCATTTCTTT-AAAAGCATTTTTACTCACTTTAAATGATTTTATA
191 AAAA-TCCATTTATAGTCACCCATTT-TTTCCAAAGC-TTATTACTCACTTTAAATGATTTTATA
** * * * * * *
1696 ACCTCAACATTGATTTAAATTTTAATTCTTTGTACATTTTTTAATAAAACAGATTATAATTGAAT
253 ATATCAAAATTGATTGAAATTTGAATTCTTTGTACATTTGTTAATAAAAAAGATTATAATTCAAT
* * * * * *
1761 GACAGCCTGAAGAAACGAGAAGAAAAAGGCATACATTGCCAAGAAAAATTCGTTTATAGTCACCC
318 GACAACCTCAAGAAACGAGAAGAAAAAGGCATACATTGCCAAGAAAAATCCATTAATAGTCAACC
* * * *
1826 ATTCCTTCAAAAGCCTCATTACTCGCTTTAAATGGTTTTATAATGCCATAATTAATTTTTAGTTG
383 ATTCCTTCAAAAACCTCATTACTCGCTTTAAATGATTTTATAATACCATAATTAATTTTAAGTTG
* * * * *
1891 AAGTATTTTACATTTTTTGTTAAAACAGACTATAATTGAATGTCAATCTCGAGAAACACAAAGAA
448 AAATATTTTACATTTTTAGTTAAAACAGACAAGAATTGAATGTCAACCTCGAGAAACACAAAGAA
** * * * * * *
1956 AAAGATATTTGTTCGTAATAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAACCTTAGTACTC
1 AAAGGCATTCGTTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTC
* ** * * * * * *
2021 TCTTTAAATGGTTTTGCAATCTCCAAATTGATTAAAATTTGATTTCTTTGTAAATTTTTGGTAAA
66 ACTTTAAATGGTTTTATAAACTCAAAATTGATT-AAATTTGAATTCTTTGTACATTTTTAGTTAA
* ** * * * *
2086 AAAAGATTATAATTGAACGTCAATGTCAAGAAACATGAAGAAAAAGTCATTTATTGGCAAGAGAA
130 AAAAGATTATAATT-AATGTCAACCTCAAGAAACGTGAAGAAAAAGACATTCATTGGCAAGAAAA
* ** * * * * *
2151 GTCCATTTATAGTCACCCATTCCTCCCAAAGCCTTATAATTGACTTTAAATGATTTTGTAATATC
194 ATCCATTTATAGTCACCCATTTTTTCCAAAG-CTTATTACTCACTTTAAATGATTTTATAATATC
* * * *
2216 AAAATTGATTGCAATTTGAATTCTTTGTATA-TTGTTCATCAAAAAAGATTATAATTCAATGTCA
258 AAAATTGATTGAAATTTGAATTCTTTGTACATTTGTTAAT-AAAAAAGATTATAATTCAATGACA
* * ** * * *
2280 ACCTCCAGAAACGTGAAGGTAAAGGCATTCATTGGCAAGAAAAGTCCATTAATAGTCAACCATTC
322 ACCTCAAGAAACGAGAAGAAAAAGGCATACATTGCCAAGAAAAATCCATTAATAGTCAACCATTC
* * *
2345 CTTCAAAAAACCTTATTACTCGCTTTACATGATTTTATAATACCATAATTGATTTTAAGTTGAAC
387 CTTC-AAAAACCTCATTACTCGCTTTAAATGATTTTATAATACCATAATTAATTTTAAGTTGAA-
* * * *
2410 AT-TTTTACATTTTTAGTTAAAACGGACAAGAATTG-ATGTCTACCTCGAGAAACATAATGAA
450 ATATTTTACATTTTTAGTTAAAACAGACAAGAATTGAATGTCAACCTCGAGAAACACAAAGAA
** *
2471 AAAGGCATTCGTTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGTATTTTTACTC
1 AAAGGCATTCGTTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTC
* * * *
2536 ACTTTAAATGATTTTATAAACTCAAAACTGATATAAATTTGAATTCTTTGTACATTTTTTGTTCA
66 ACTTTAAATGGTTTTATAAACTCAAAATTGAT-TAAATTTGAATTCTTTGTACATTTTTAGTTAA
* * * *
2601 AACAGATTTTCATTAAATGTCAACCTCAAGAAACGTGAAGAAAAAGACATACATTGGCAAGAAAA
130 AAAAGATTATAATT-AATGTCAACCTCAAGAAACGTGAAGAAAAAGACATTCATTGGCAAGAAAA
* * *
2666 ATCCGTTTATAGTCACCCATTTTTTCCAAAGTCTTATTACTCATTTTAAATGGTTTTATAAT
194 ATCCATTTATAGTCACCCATTTTTTCCAAAG-CTTATTACTCACTTTAAATGATTTTATAAT
2728 GCCATAATTG
Statistics
Matches: 618, Mismatches: 141, Indels: 25
0.79 0.18 0.03
Matches are distributed among these distances:
512 3 0.00
513 42 0.07
514 74 0.12
515 410 0.66
516 88 0.14
517 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (512 bp):
AAAGGCATTCGTTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTC
ACTTTAAATGGTTTTATAAACTCAAAATTGATTAAATTTGAATTCTTTGTACATTTTTAGTTAAA
AAAGATTATAATTAATGTCAACCTCAAGAAACGTGAAGAAAAAGACATTCATTGGCAAGAAAAAT
CCATTTATAGTCACCCATTTTTTCCAAAGCTTATTACTCACTTTAAATGATTTTATAATATCAAA
ATTGATTGAAATTTGAATTCTTTGTACATTTGTTAATAAAAAAGATTATAATTCAATGACAACCT
CAAGAAACGAGAAGAAAAAGGCATACATTGCCAAGAAAAATCCATTAATAGTCAACCATTCCTTC
AAAAACCTCATTACTCGCTTTAAATGATTTTATAATACCATAATTAATTTTAAGTTGAAATATTT
TACATTTTTAGTTAAAACAGACAAGAATTGAATGTCAACCTCGAGAAACACAAAGAA
Found at i:3149 original size:170 final size:160
Alignment explanation
Indices: 2861--3175 Score: 312
Period size: 170 Copynumber: 1.9 Consensus size: 160
2851 CAAGAGAAGT
* * * * *
2861 CCATTAATAGTCACCCATTCCTTCAAAAGCCTTATTACACCATTTAAATGGTTTTATAATCTCAA
1 CCATTAATAGTCACCCATTCCTCCAAAAGCCTTATAACACCATTTAAATGATTTTACAATATCAA
* * * * * * *
2926 AATTGATTTAAATTTGAACTCTTTGTACGTTTTTGGTTAAAACAGATTATAATTGAATGTCAACC
66 AATTGATTGAAATTTGAACTCTTTGTACATTGTTCGTCAAAACAGAATATAATTCAATGTCAACC
*
2991 TCAATAAACATGAAGAAAAAAGTTCATTGG
131 TCAAGAAACATGAAGAAAAAAGTTCATTGG
* * *
3021 NNNNNNNNNNCCATTTATAGTCACCCATTCCTCCCAAAGGCTTATAACTGA-C-TTTAAATGATT
1 ----------CCATTAATAGTCACCCATTCCTCCAAAAGCCTTATAAC--ACCATTTAAATGATT
* * *
3084 TTACAATATCAAAATTGATTGCAATTTGAATTCTTTGTATATTGTTCGTCAAAA-AGGAATATAA
54 TTACAATATCAAAATTGATTGAAATTTGAACTCTTTGTACATTGTTCGTCAAAACA-GAATATAA
*
3148 TTCAATGTCAACCTCCAGAAACATGAAG
118 TTCAATGTCAACCTCAAGAAACATGAAG
3176 GTAAAGGCAT
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
169 1 0.01
170 119 0.98
171 1 0.01
172 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.34
Consensus pattern (160 bp):
CCATTAATAGTCACCCATTCCTCCAAAAGCCTTATAACACCATTTAAATGATTTTACAATATCAA
AATTGATTGAAATTTGAACTCTTTGTACATTGTTCGTCAAAACAGAATATAATTCAATGTCAACC
TCAAGAAACATGAAGAAAAAAGTTCATTGG
Done.