Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398990.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2270.0, 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: 12283
ACGTcount: A:0.25, C:0.10, G:0.09, T:0.27
Warning! 3647 characters in sequence are not A, C, G, or T
Found at i:1005 original size:173 final size:172
Alignment explanation
Indices: 645--1030 Score: 440
Period size: 173 Copynumber: 2.2 Consensus size: 172
635 NNNNNNNNNN
** * * *
645 AGAAAAGTCCATTTATAGAATCCTATT-ATGTAAAAAGCCTTATTACTTGCTTTAAATAGTTTTA
1 AGAAAAGTCCATTTATAGTCTCCTATTCCT-TTAAAAGCCTTATTACTTGCTTAAAATAGTTTTA
* *
709 TAACCTCAAAATTATTTTTCAGTTCAATTCTTTTTACATTTTTAGTTAAAACAGAAAATAATTGA
65 TAACCTCAAAATTATTTTTCAGTTCAATTCTTTTTAAATTTTTAGATAAAACAGAAAATAATTGA
* * * *
774 ATGTCTACCTCGAGAAACATGAAGAAAAAGGGATTCATTGGCN
130 ATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTGACA
********* *
817 NNNNNNNNNCATTTATAGTCTCTTATTCCTTTAAAAGCCTTATTACTTGCTTAAAAT-GATTTTA
1 AGAAAAGTCCATTTATAGTCTCCTATTCCTTTAAAAGCCTTATTACTTGCTTAAAATAG-TTTTA
*
881 TAACCTCAAAATTGA-TTTT-AGGTTCAATT-TTTTTAAAATTTTTTAGATAAAACAGATAATAA
65 TAACCTCAAAATT-ATTTTTCA-GTTCAATTCTTTTT-AAA-TTTTTAGATAAAACAGAAAATAA
* * *
943 TTGAATGTCTACCTCAAGAAACATGAAGTAAAATGCATTTATTGACA
126 TTGAATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTGACA
* *
990 AGAAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTT
1 AGAAAAGTCCATTTATAGTCTCCTATTCCTTTAAAAGCCTT
1031 NNNNNNNNNN
Statistics
Matches: 171, Mismatches: 37, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
171 7 0.04
172 72 0.42
173 92 0.54
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.37
Consensus pattern (172 bp):
AGAAAAGTCCATTTATAGTCTCCTATTCCTTTAAAAGCCTTATTACTTGCTTAAAATAGTTTTAT
AACCTCAAAATTATTTTTCAGTTCAATTCTTTTTAAATTTTTAGATAAAACAGAAAATAATTGAA
TGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTGACA
Found at i:1747 original size:172 final size:170
Alignment explanation
Indices: 1441--1944 Score: 494
Period size: 172 Copynumber: 2.9 Consensus size: 170
1431 NNNNNNNNNT
* * * * *
1441 AATTGATTTTAAGTT-AAATTTTTTTACATTTTTGGGTAAAACAGACTATAATTGAATGACTACC
1 AATTGATTTTAAGTTCAATTTTTTTTACATTTTTGGTTAAAATAGAATATAATTGAATGTCTACC
* * * * * *
1505 TC-AGAAAACGTTAAGAAACGAGCATTCATTGGCAAGAAAAGTTTATTTATAGTCTACTATTCCG
66 TCGAG-AAACATGAAGAAA-AAGCATTCATTGGCAAGAAAAGTCTATTGATAGTC-ACTATTCCT
1569 TCAAAAGCCTTATTACTCGCTCTAAATGGTTTTATAACCTCAA
128 TCAAAAGCCTTATTACTCGCTCTAAATGGTTTTATAACCTCAA
* * * * *
1612 AATT-ATTTTTCAGTTCAATTTTTTTTACATTTTTTGTTAAAATGGAAAATAATTGGATGTCTAC
1 AATTGA-TTTTAAGTTCAATTTTTTTTACATTTTTGGTTAAAATAGAATATAATTGAATGTCTAC
*
1676 CTCGAGAAACATGAAGAAAAATGCATTCATTGGCAAGAAAAGTCTACTGATAGTCACCTATTCCT
65 CTCGAGAAACATGAAGAAAAA-GCATTCATTGGCAAGAAAAGTCTATTGATAGTCA-CTATTCCT
* ********** *
1741 TCAAAAGCCTTATTAATNNNNNNNNNNGGTTTTATAATCTCAA
128 TCAAAAGCCTTATTACTCGCTCTAAATGGTTTTATAACCTCAA
* * * * *
1784 AATTGATTTTAATTTCAATTTGTTTTACATTTTTGGTCAAAATAGATTTTAATTGAATGTCTACC
1 AATTGATTTTAAGTTCAATTTTTTTTACATTTTTGGTTAAAATAGAATATAATTGAATGTCTACC
* * * * * * * * **
1849 TTGAGAAATATGAAGAAAAAGGTATTTATTGACAAGAAATGCCCATTTG-TAGTGGCTCATTCCT
66 TCGAGAAACATGAAGAAAAA-GCATTCATTGGCAAGAAAAGTCTA-TTGATAGTCACT-ATTCCT
*
1913 TCAAAAGCCTTATTACTCGCTTTAAATGGTTT
128 TCAAAAGCCTTATTACTCGCTCTAAATGGTTT
1945 NNNNNNNNNN
Statistics
Matches: 263, Mismatches: 62, Indels: 15
0.77 0.18 0.04
Matches are distributed among these distances:
170 1 0.00
171 16 0.06
172 241 0.92
173 5 0.02
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.37
Consensus pattern (170 bp):
AATTGATTTTAAGTTCAATTTTTTTTACATTTTTGGTTAAAATAGAATATAATTGAATGTCTACC
TCGAGAAACATGAAGAAAAAGCATTCATTGGCAAGAAAAGTCTATTGATAGTCACTATTCCTTCA
AAAGCCTTATTACTCGCTCTAAATGGTTTTATAACCTCAA
Found at i:3090 original size:342 final size:331
Alignment explanation
Indices: 2467--3094 Score: 706
Period size: 342 Copynumber: 1.9 Consensus size: 331
2457 AACTTATATT
* * * * *
2467 TTTTTTTATTTTTTTGCTTAAAAAGACTATAATTGAGTGTCTACCTCAAGAAACATAGAGAAAAA
1 TTTTTTTATATTATTGATTAAAAAGACTATAATTGAATGTATACCTCAAGAAACATAGAGAAAAA
* *
2532 TACATCCATTGGTAAGAAAAGTCTATTATAATTACCCATTCCTTTAAAAGTCTTATTACTAACTT
66 GACATCCATTGGTAAGAAAAGTCTATTATAAGTACCCATTCCTTTAAAAGTCTTATTACTAACTT
* *
2597 TAAATAGTTTTATAACCTCAAAATTGATTTTAAATTGAATTTTTTTTACAAAGTTGGTCAAAATA
131 TAAATAGTTTTATAACCTCAAAATTGATTTTAAATTGAATTTTTTTTACAAAGTGGGTCAAAACA
* * ** * * * * *
2662 GATTATAATTGATTGTCTACCTTAGGAAACATGAAGAAAAAGGTAGTCATTGGCAAGAAAAGTCC
196 GACTATAATTGAATGTCTACCTTAACAAACATAAAGAAAAAAGCAGTCATTAGCAAGAAAACTCC
2727 ATATATAGTCACCCATTCCTTCAAAAACCTTCTTATTCACTTTAAATGATTTTATAATCTCNNNN
261 ATATATAGTCACCCATTCCTTCAAAAACCTTCTTATTCACTTTAAATGATTTTATAATCTC----
2792 NNNNNNTTAAGTTAAA
322 ------TTAAGTTAAA
*
2808 TTTTTTTATATTATTGATTAACATAGACTATAATTGAATGTATACCTCAAGAAACAT-GAAGAAA
1 TTTTTTTATATTATTGATTAA-AAAGACTATAATTGAATGTATACCTCAAGAAACATAG-AGAAA
* ** * *
2872 AAGGCATTTATTGGTAAGAAAAGTCTATT-TACAGT-CTCATATTCTTTCAAAAGTCTTATTACT
64 AAGACATCCATTGGTAAGAAAAGTCTATTATA-AGTACCCAT-TCCTTT-AAAAGTCTTATTACT
** ** * * * * ** *
2935 CGCTTTAAATTTTTTTATAATCTTAAAATTGATTTTAAGTTGAA-TTTTTTTATATTGTGGGTTA
126 AACTTTAAATAGTTTTATAACCTCAAAATTGATTTTAAATTGAATTTTTTTTACAAAGTGGGTCA
* * *
2999 AAGCAGACTATAATTGAATGTCTACCTTAACAAACATAAAGAAAAAAGCATTCATTAGTAAGAAA
191 AAACAGACTATAATTGAATGTCTACCTTAACAAACATAAAGAAAAAAGCAGTCATTAGCAAGAAA
* * * **
3064 ACTCTATTTATAGTCTCTTATTCCTTCAAAA
256 ACTCCATATATAGTCACCCATTCCTTCAAAA
3095 GCCTNNNNNN
Statistics
Matches: 239, Mismatches: 43, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
341 25 0.10
342 162 0.68
343 52 0.22
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (331 bp):
TTTTTTTATATTATTGATTAAAAAGACTATAATTGAATGTATACCTCAAGAAACATAGAGAAAAA
GACATCCATTGGTAAGAAAAGTCTATTATAAGTACCCATTCCTTTAAAAGTCTTATTACTAACTT
TAAATAGTTTTATAACCTCAAAATTGATTTTAAATTGAATTTTTTTTACAAAGTGGGTCAAAACA
GACTATAATTGAATGTCTACCTTAACAAACATAAAGAAAAAAGCAGTCATTAGCAAGAAAACTCC
ATATATAGTCACCCATTCCTTCAAAAACCTTCTTATTCACTTTAAATGATTTTATAATCTCTTAA
GTTAAA
Found at i:3095 original size:171 final size:170
Alignment explanation
Indices: 2467--3095 Score: 580
Period size: 171 Copynumber: 3.7 Consensus size: 170
2457 AACTTATATT
* * * * * *
2467 TTTTTTTATTTTTTTGCTTAAAAAGACTATAATTGAGTGTCTACCTCAAGAAACATAGAGAAAAA
1 TTTTTTTATATTGTTGGTTAAATAGACTATAATTGAATGTCTACCTCAAGAAACATAAAGAAAAA
* * * *
2532 TA-CATCCATTGGTAAGAAAAGTCTA-TTATAAT-TACCCATTCCTTTAAAAGTCTTATTACTAA
66 -AGCATTCATTGGTAAGAAAAGTCTATTTATAGTCT-CCCATTCCTTCAAAAGTCTTATTACTCA
* * *
2594 CTTTAAATAGTTTTATAACCTCAAAATTGATTTTAAATTGAA
129 CTTTAAATAATTTTATAATCTCAAAATTGATTTTAAGTTGAA
* ** * * * * * *
2636 TTTTTTTTACAAAGTTGGTCAAAATAGATTATAATTGATTGTCTACCTTAGGAAACATGAAGAAA
1 -TTTTTTTATATTGTTGGT-TAAATAGACTATAATTGAATGTCTACCTCAAGAAACATAAAGAAA
* * * * * * * ** * *
2701 AAGGTAGTCATTGGCAAGAAAAGTCCATATATAGTCACCCATTCCTTCAAAAACCTTCTTATTCA
64 AAAGCATTCATTGGTAAGAAAAGTCTATTTATAGTCTCCCATTCCTTCAAAAGTCTTATTACTCA
* ********** *
2766 CTTTAAATGATTTTATAATCTCNNNNNNNNNNTTAAGTTAAA
129 CTTTAAATAATTTTATAATCTCAAAATTGATTTTAAGTTGAA
* * * *
2808 TTTTTTTATATTATTGATTAACATAGACTATAATTGAATGTATACCTCAAGAAACATGAAGAAAA
1 TTTTTTTATATTGTTGGTTAA-ATAGACTATAATTGAATGTCTACCTCAAGAAACATAAAGAAAA
* * * ** * *
2873 AGGCATTTATTGGTAAGAAAAGTCTATTTACAGTCTCATATTCTTTCAAAAGTCTTATTACTCGC
65 AAGCATTCATTGGTAAGAAAAGTCTATTTATAGTCTCCCATTCCTTCAAAAGTCTTATTACTCAC
** *
2938 TTTAAATTTTTTTATAATCTTAAAATTGATTTTAAGTTGAA
130 TTTAAATAATTTTATAATCTCAAAATTGATTTTAAGTTGAA
* * * *
2979 TTTTTTTATATTGTGGGTTAAAGCAGACTATAATTGAATGTCTACCTTAACAAACATAAAGAAAA
1 TTTTTTTATATTGTTGGTTAAA-TAGACTATAATTGAATGTCTACCTCAAGAAACATAAAGAAAA
* * **
3044 AAGCATTCATTAGTAAGAAAACTCTATTTATAGTCTCTTATTCCTTCAAAAG
65 AAGCATTCATTGGTAAGAAAAGTCTATTTATAGTCTCCCATTCCTTCAAAAG
3096 CCTNNNNNNN
Statistics
Matches: 353, Mismatches: 100, Indels: 11
0.76 0.22 0.02
Matches are distributed among these distances:
170 15 0.04
171 284 0.80
172 54 0.15
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (170 bp):
TTTTTTTATATTGTTGGTTAAATAGACTATAATTGAATGTCTACCTCAAGAAACATAAAGAAAAA
AGCATTCATTGGTAAGAAAAGTCTATTTATAGTCTCCCATTCCTTCAAAAGTCTTATTACTCACT
TTAAATAATTTTATAATCTCAAAATTGATTTTAAGTTGAA
Found at i:7787 original size:170 final size:168
Alignment explanation
Indices: 7610--8185 Score: 583
Period size: 170 Copynumber: 3.4 Consensus size: 168
7600 NNNNNNNNNN
* * * *
7610 ATTTTTTTACATTTTTAGTTAAAACGGACTATAGTTGAATGTCTACCTAGAGACACATGAAGCAA
1 ATTTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGACTACCTAGAGAAACATGAAG-AA
* * *
7675 AAGTCATTCATTAGCAGGAAAAGTCCATTTATGACACCCAGTCTTTCAAAAGCATTTTTTCTTGC
65 AAGTCATTCATTAGCAAGAAAAGTCCATTTATGTCACCCA-TCTTTCAAAAGCCTTTTTTCTTGC
*
7740 TTTAAATGGTTTTATAATCTCATAATTGATTTTTAGTTGA
129 TTTAAATGGTTTTATAATCTCATAATTGATTTTTAGTTAA
* * * * * *
7780 CTTTTTTTACATTGTTGGTTAAAACATACTATAATTGAATGACTACCTTAGA-ATACGTGAAGAA
1 ATTTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGACTACC-TAGAGAAACATGAAGAA
* * * * *
7844 ACGAG-CATTCATTAACAAGAAAAGTCCATTTATAGTCTCCTAT-TTCGTCAAAAGCCTTATTAC
65 A--AGTCATTCATTAGCAAGAAAAGTCCATTTAT-GTCACCCATCTT--TCAAAAGCCTTTTTTC
** * * * * *
7907 TCT-CTTTAAATGGTTTTGCAACCACAAAATTGCTTTTTAGTTTTA
125 T-TGCTTTAAATGGTTTTATAATCTCATAATTGATTTTTAG-TTAA
* * * *
7952 TTTTTTTTACATTTTTAGTTAAAACAGA-TAATAATTGGATGTCTACCTCGAGAAACATGAA-AA
1 ATTTTTTTACATTTTTAGTTAAAACAGACT-ATAATTGAATGACTACCTAGAGAAACATGAAGAA
* * * * *
8015 AAATGCATTCATTGGCAAGAAAAGTTCATTTATGTCACCCATTCCTTT-AAAATCCTTTTTTCTC
65 AAGT-CATTCATTAGCAAGAAAAGTCCATTTATGTCACCCA-T-CTTTCAAAAGCCTTTTTTCTT
* ** *
8079 GTTTTAAACAGTTTTATAATCTCATAATTGATTTTAAGTTAA
127 GCTTTAAATGGTTTTATAATCTCATAATTGATTTTTAGTTAA
* * *
8121 ATTGTTTTACAGTTTTAGTTAAAACAGACTATAATTGAATGACTACCTTAG-GAAACGTGAAGAA
1 ATTTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGACTACC-TAGAGAAACATGAAGAA
8185 A
65 A
8186 CGAGCANNNN
Statistics
Matches: 326, Mismatches: 61, Indels: 38
0.77 0.14 0.09
Matches are distributed among these distances:
169 58 0.18
170 126 0.39
171 90 0.28
172 50 0.15
173 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (168 bp):
ATTTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGACTACCTAGAGAAACATGAAGAAA
AGTCATTCATTAGCAAGAAAAGTCCATTTATGTCACCCATCTTTCAAAAGCCTTTTTTCTTGCTT
TAAATGGTTTTATAATCTCATAATTGATTTTTAGTTAA
Found at i:7873 original size:341 final size:340
Alignment explanation
Indices: 7424--8191 Score: 849
Period size: 341 Copynumber: 2.3 Consensus size: 340
7414 NNNNNNNNNN
* * *
7424 ATTGATTTTAAGTTGAATTATTTTATATTTTTTA-TTAAAACATACTATAATTGATTG-CTTGCC
1 ATTGATTTTAAGTTGAATTATTTTACA--TTTTAGTTAAAACATACTATAATTGAATGAC-TACC
* * * * * *
7487 TTAAAAATATGTAGAA-AAA-GA-AATTCATTGAGAAGAAATGTCCATTTATAG-C-CACTCATT
63 TT-AGAATACGT-GAAGAAACGAGCATTCATTAACAAGAAAAGTCCATTTATAGTCTC-CT-ATT
* * * * * **********
7547 CCTTCAAAGGCCTTATTACTCGCTTTAAATAGTTTTATAACCTCATAATTGATNNNNNNNNNNA-
124 CCGTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTACAACCACAAAATTGATTTTTAGTTTTAT
* * * *
7611 TTTTTTTACATTTTTAGTTAAAACGGACT-ATAGTTGAATGTCTACCTAGAGACACATGAAGCAA
189 TTTTTTTACATTTTTAGTTAAAACAGA-TAATAATTGAATGTCTACCTAGAGAAACATGAA-AAA
* *
7675 AA-GTCATTCATTAGCAGGAAAAGTCCATTTATGACACCCAGT-CTTTCAAAAGCATTTTTTCTT
252 AATG-CATTCATTAGCAAGAAAAGTCCATTTATGACACCCAGTCCTTT-AAAAGCATTTTTTCTC
**
7738 GCTTTAAATGGTTTTATAATCTCATA
315 GCTTTAAACAGTTTTATAATCTCATA
* * * *
7764 ATTGATTTTTAGTTGACTTTTTTTACATTGTTGGTTAAAACATACTATAATTGAATGACTACCTT
1 ATTGATTTTAAGTTGAATTATTTTACATT-TTAGTTAAAACATACTATAATTGAATGACTACCTT
*
7829 AGAATACGTGAAGAAACGAGCATTCATTAACAAGAAAAGTCCATTTATAGTCTCCTATTTCGTCA
65 AGAATACGTGAAGAAACGAGCATTCATTAACAAGAAAAGTCCATTTATAGTCTCCTATTCCGTCA
* * * *
7894 AAAGCCTTATTACTCTCTTTAAATGGTTTTGCAACCACAAAATTGCTTTTTAGTTTTATTTTTTT
130 AAAGCCTTATTACTCGCTTTAAATAGTTTTACAACCACAAAATTGATTTTTAGTTTTATTTTTTT
* *
7959 TACATTTTTAGTTAAAACAGATAATAATTGGATGTCTACCTCGAGAAACATGAAAAAAATGCATT
195 TACATTTTTAGTTAAAACAGATAATAATTGAATGTCTACCTAGAGAAACATGAAAAAAATGCATT
* * * * * * *
8024 CATTGGCAAGAAAAGTTCATTTATGTCACCCATTCCTTTAAAATCCTTTTTTCTCGTTTTAAACA
260 CATTAGCAAGAAAAGTCCATTTATGACACCCAGTCCTTTAAAAGCATTTTTTCTCGCTTTAAACA
8089 GTTTTATAATCTCATA
325 GTTTTATAATCTCATA
* * *
8105 ATTGATTTTAAGTTAAATTGTTTTACAGTTTTAGTTAAAACAGACTATAATTGAATGACTACCTT
1 ATTGATTTTAAGTTGAATTATTTTACA-TTTTAGTTAAAACATACTATAATTGAATGACTACCTT
8170 AGGAA-ACGTGAAGAAACGAGCA
65 A-GAATACGTGAAGAAACGAGCA
8192 NNNNNNNNNN
Statistics
Matches: 358, Mismatches: 56, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
338 5 0.01
339 12 0.03
340 52 0.15
341 222 0.62
342 66 0.18
343 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.38
Consensus pattern (340 bp):
ATTGATTTTAAGTTGAATTATTTTACATTTTAGTTAAAACATACTATAATTGAATGACTACCTTA
GAATACGTGAAGAAACGAGCATTCATTAACAAGAAAAGTCCATTTATAGTCTCCTATTCCGTCAA
AAGCCTTATTACTCGCTTTAAATAGTTTTACAACCACAAAATTGATTTTTAGTTTTATTTTTTTT
ACATTTTTAGTTAAAACAGATAATAATTGAATGTCTACCTAGAGAAACATGAAAAAAATGCATTC
ATTAGCAAGAAAAGTCCATTTATGACACCCAGTCCTTTAAAAGCATTTTTTCTCGCTTTAAACAG
TTTTATAATCTCATA
Found at i:9489 original size:172 final size:162
Alignment explanation
Indices: 9224--9558 Score: 287
Period size: 172 Copynumber: 2.0 Consensus size: 162
9214 ACTCGCTTTA
* * * *
9224 AATGGTTTTGTAACCTCAAAATTATTTTTTAGTTCAATTGTTTTTACATTTTTGGTTAAAACAGA
1 AATGGTTTTATAACCTCAAAATTATTTTTAAGTTCAATTGTTTTTACATTTTTGATCAAAACAGA
* * * * * * * *
9289 CAATGATTGGATCTCTACCTCAAGAAACATGAAGAAAAATACATTAATTGGCAAGAGAAGTCTAT
66 CAATAATTGAATCTCTACCTCAAGAAACATAAAGAAAAAGACATTAATTGACAAGAAAAGCCCAT
* *
9354 TTATAGTCACCT-ATTCCTTCAAAAGCCTTATT
131 TTATAAT-ACCTCATTCCTTCAAAAGCATTATT
** *
9386 ANNNNNNNNNNATGGTTTTATAATTTCAAAATTGA-TTTTAAGTTCAATTTTTTTTACATTTTTG
1 A----------ATGGTTTTATAACCTCAAAATT-ATTTTTAAGTTCAATTGTTTTTACATTTTTG
* *** * * ** * *
9450 ATCAAAATAGATTTTAATTGAATGTTTACCTTGAGAAACATAAAGAAAAAGGCATTTATTGACAA
55 ATCAAAACAGACAATAATTGAATCTCTACCTCAAGAAACATAAAGAAAAAGACATTAATTGACAA
**
9515 GAAAAGCCCATTTATAATGGCTCATTCCTTCAAAAGCATTATT
120 GAAAAGCCCATTTATAATACCTCATTCCTTCAAAAGCATTATT
9558 A
1 A
9559 CTCGCTTTAA
Statistics
Matches: 132, Mismatches: 29, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
162 1 0.01
171 2 0.02
172 128 0.97
173 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.37
Consensus pattern (162 bp):
AATGGTTTTATAACCTCAAAATTATTTTTAAGTTCAATTGTTTTTACATTTTTGATCAAAACAGA
CAATAATTGAATCTCTACCTCAAGAAACATAAAGAAAAAGACATTAATTGACAAGAAAAGCCCAT
TTATAATACCTCATTCCTTCAAAAGCATTATT
Found at i:10346 original size:172 final size:162
Alignment explanation
Indices: 10144--10481 Score: 308
Period size: 172 Copynumber: 2.0 Consensus size: 162
10134 GTTAAATGGT
* *
10144 TTTATAACCACAAAATTATTTTTTAGTTCAAT-TTTTTTTTCATTTT-TTGCTAAAACAGACAAT
1 TTTATAACCACAAAATTATTTTTAAGTTCAATATTTTTTTACATTTTATT-C-AAAACAGACAAT
* * * * * *
10207 AATTGGATGTCTACC-TAGAGAAACATGAAGAAAAATGCATTAATTGGCAAGAAAAGTCTATTTA
64 AATTGAATGTCTACCAT-GAGAAACATGAAGAAAAACGCATTAATTGACAACAAAAGCCCATTTA
*
10271 TAGTTACCT-ATTCCTTTAAAAGCCTTATTGCTCAC
128 TAG-TACCTCATTCCTTCAAAAGCCTTATTGCTCAC
* *
10306 TNNNNNNNNNNTTATAATCTCAAAATTGA-TTTTAAGTTCAATATTTTTTTACATTTTATTCAAA
1 T----------TTATAACCACAAAATT-ATTTTTAAGTTCAATATTTTTTTACATTTTATTCAAA
* *** * * *
10370 ATAGATTTTAATTGAATGTCTACCATGAGAAACATGAAGGAAAACGTATTTATTGACAACAAAAG
55 ACAGACAATAATTGAATGTCTACCATGAGAAACATGAAGAAAAACGCATTAATTGACAACAAAAG
** * *
10435 CCCATTTATAGTGGCTCATTCCTTCAAAAGCCTTATTACTCGC
120 CCCATTTATAGTACCTCATTCCTTCAAAAGCCTTATTGCTCAC
10478 TTTA
1 TTTA
10482 NNNNNNNNNN
Statistics
Matches: 139, Mismatches: 22, Indels: 30
0.73 0.12 0.16
Matches are distributed among these distances:
162 4 0.03
171 3 0.02
172 114 0.82
173 16 0.12
174 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (162 bp):
TTTATAACCACAAAATTATTTTTAAGTTCAATATTTTTTTACATTTTATTCAAAACAGACAATAA
TTGAATGTCTACCATGAGAAACATGAAGAAAAACGCATTAATTGACAACAAAAGCCCATTTATAG
TACCTCATTCCTTCAAAAGCCTTATTGCTCAC
Done.