Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398269.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1571.0, 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: 4473
ACGTcount: A:0.29, C:0.09, G:0.10, T:0.26
Warning! 1159 characters in sequence are not A, C, G, or T
Found at i:309 original size:170 final size:169
Alignment explanation
Indices: 6--495 Score: 603
Period size: 170 Copynumber: 2.9 Consensus size: 169
1 TTCTT
* * * * * *
6 CACGTGTCTCAAGGTAGACATTCAATTATAGTATGTTTTAATAAAAAATATAAAGAA-AATCAAC
1 CACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACAAAAAATGTAAA-AACATTCAAC
* * *
70 TTAAAA-CTAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGCCTTTTGAAGGAATGGG
65 TTAAAATC-AATTATGAGATTATAAAAC-GTTTAAAGCGAGTAATAAGCCTTTTGAAAGAATGGG
*
134 TGACTATAAATAGACTTTTCTTCTTAATGAATAAC-TTTTTTA
128 TGACTATAAAT-GACTTTTCTTCTCAATGAATAACTTTTTTTA
* * * *
176 CATGTTTCTCGAGGTAGACATTCAATTATAATCTATTATAACAAAAAATGTAAAAACATTCAACT
1 CACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACAAAAAATGTAAAAACATTCAACT
* * * * *
241 TAAAATCAATTATAAGATTATAAAATCGTTAAAAGCGGGTAATAATCCTTTTGAAAGAATGAGTG
66 TAAAATCAATTATGAGATTATAAAA-CGTTTAAAGCGAGTAATAAGCCTTTTGAAAGAATGGGTG
* ** *
306 ACTATAAATGAACTTTT-TTCTCAATGATTGGCTTTTTTTG
130 ACTATAAATG-ACTTTTCTTCTCAATGAATAACTTTTTTTA
* * *
346 CACGTTT-TCTAAGGTAGACAATCAATTATAGTCTATTTTAACAAAAGATGTAAAAACATTTAAC
1 CACGTTTCTC-AAGGTAGACATTCAATTATAGTCTATTTTAACAAAAAATGTAAAAACATTCAAC
* *
410 TTAAAATCAATTATGAGATTATAAAACCGTTTAAAGCGTGTAATAAGCTTTTTGAAAGAATGGGT
65 TTAAAATCAATTATGAGATTATAAAA-CGTTTAAAGCGAGTAATAAGCCTTTTGAAAGAATGGGT
*
475 GACTTTAAATGGACTTTTCTT
129 GACTATAAAT-GACTTTTCTT
496 GCCAAATGGA
Statistics
Matches: 274, Mismatches: 38, Indels: 15
0.84 0.12 0.05
Matches are distributed among these distances:
169 16 0.06
170 253 0.92
171 5 0.02
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (169 bp):
CACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACAAAAAATGTAAAAACATTCAACT
TAAAATCAATTATGAGATTATAAAACGTTTAAAGCGAGTAATAAGCCTTTTGAAAGAATGGGTGA
CTATAAATGACTTTTCTTCTCAATGAATAACTTTTTTTA
Found at i:791 original size:171 final size:171
Alignment explanation
Indices: 506--947 Score: 563
Period size: 171 Copynumber: 2.6 Consensus size: 171
496 GCCAAATGGA
* * * * * *
506 TGACTATAAATGGACTTTTCTCCTCAATCAATGACTTTTTCTACACCTTTCCTGAGGCA-AGCTT
1 TGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTACACATTTCCCGAGGCAGA-CAT
*
570 TCAATTATAGTATGTTTTAA-AGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAAATTA
65 TCAATTATAGTATGTTTTAATA-AAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAAATTA
** *
634 TAAAGTCATTTAAAGTGGGTAATAAGATTTTTG-AAGCAATGAG
129 TAAAAACATTTAAAGTGAGTAATAAGATTTTTGAAAG-AATGAG
677 TGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTACACATTTCCCGAGGCAGACATT
1 TGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTACACATTTCCCGAGGCAGACATT
* * * *
742 -AACTTATAATCTGTTTTAATAAAAAATATAAAATAATTCAACTTAAAATCAATTACGAAATTAT
66 CAA-TTATAGTATGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAAATTAT
* * *
806 AAAAACGTTTAAAGTGAGTAATAAGCTTTTTGAAAGAATGGG
130 AAAAACATTTAAAGTGAGTAATAAGATTTTTGAAAGAATGAG
* * * ** * **
848 TGACTCTCAATGGAC-TTTCTTGTCAATGAAT-GCTTTTTTCTTTACATTTCTCGAGTTAGACAT
1 TGACTATAAATGGACTTTTCTTCTCAATGAATGGC-TTTTTCTACACATTTCCCGAGGCAGACAT
*
911 TCAATTATAGTATGTTTTAATCAAAAATGTAAAAAAA
65 TCAATTATAGTATGTTTTAATAAAAAATGTAAAAAAA
948 NNNNNNNNNN
Statistics
Matches: 235, Mismatches: 30, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
169 2 0.01
170 70 0.30
171 158 0.67
172 5 0.02
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (171 bp):
TGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTACACATTTCCCGAGGCAGACATT
CAATTATAGTATGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAAATTATA
AAAACATTTAAAGTGAGTAATAAGATTTTTGAAAGAATGAG
Found at i:2175 original size:172 final size:172
Alignment explanation
Indices: 1881--2302 Score: 544
Period size: 172 Copynumber: 2.4 Consensus size: 172
1871 NNNNNNNNCT
* *
1881 AGGTAGACATTCAATTATACTCTATTTTAACAAAAAATGTAAAAAAAATTCAATTTGAAAA-CAA
1 AGGTAGACATTCAATTATAATCTATTTTAACAAAAAATGT-AAAAAAATTCAACTT-AAAATCAA
* *
1945 TTATGAGATTATAAAACCATTAAAAGCGGGTAATAAGCCTTTTGAAAGAATGGGTGACTATAAAT
64 TTATGAGATTATAAAACCATTAAAAGCGAGTAATAAGCCTTTTGAAAGAATAGGTGACTATAAAT
*
2010 GAACCTTTCTTCTCAATGAATGGTTTTTTTTTTCATGTTTCCCA
129 GAACCTTTCTTCTCAATGAATGGTTTTTTTTTTCATGTTTCACA
* * * * *
2054 AGGTAGATAGTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTTAACTTAAAATCAATT
1 AGGTAGACATTCAATTATAATCTATTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATT
* * * * *
2119 ATGAGATTATAAATCCGTTTAAAGCGAGTAATAAG-CTTTTTAAAGGAATAGGTGACTCTAAATG
66 ATGAGATTATAAAACCATTAAAAGCGAGTAATAAGCCTTTTGAAA-GAATAGGTGACTATAAATG
* * * * *
2183 GACTTTTCTTGTTAATGAATGGTTTTTTTTTTTATGTTTCACA
130 AACCTTTCTTCTCAATGAATGGTTTTTTTTTTCATGTTTCACA
** * * * * *
2226 AGACAAACATTCAATTATAATATATTTTAATC-AAAAAGGTAAAAAAAATCAACTTAAGATCAAT
1 AGGTAGACATTCAATTATAATCTATTTTAA-CAAAAAATGTAAAAAAATTCAACTTAAAATCAAT
2290 TATGAGATTATAA
65 TATGAGATTATAA
2303 TAAGCCTTTT
Statistics
Matches: 215, Mismatches: 31, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
171 12 0.06
172 166 0.77
173 37 0.17
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (172 bp):
AGGTAGACATTCAATTATAATCTATTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATT
ATGAGATTATAAAACCATTAAAAGCGAGTAATAAGCCTTTTGAAAGAATAGGTGACTATAAATGA
ACCTTTCTTCTCAATGAATGGTTTTTTTTTTCATGTTTCACA
Found at i:2431 original size:153 final size:153
Alignment explanation
Indices: 2147--2455 Score: 381
Period size: 153 Copynumber: 2.0 Consensus size: 153
2137 TTAAAGCGAG
* * * * * *
2147 TAATAAGCTTTTTAAAGGAATAGGTGACTCTAAATGGACTTTTCTTGTTAATGAATGGTTTTTTT
1 TAATAAGCTTTTGAAAGGAATAGGTGACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTTT
* * *
2212 TTTTATGTTTCACAAGACAAACATTCAATTATAATATATTTTAATCAAAAAGGTAAAAAAAATCA
66 TTTCATGTTTCACAAGACAAACATTCAATTATAATATATTTTAACCAAAAACGTAAAAAAAATCA
*
2277 ACTTAAGATCAATTATGAGATTA
131 ACTTAAAATCAATTATGAGATTA
* *
2300 TAATAAGCCTTTTGAAA-GAAT-GAGTGACTATAAATGGATTTTTTTTCTCAATGAATAGCTTTT
1 TAATAAG-CTTTTGAAAGGAATAG-GTGACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTT
* * * * * * * * *
2363 TTTTTCATGTTTCTCAA-AGCAAGCATTTAATTATAGTTTGTTTTGACCAAAAACGTAAAACAAT
64 TTTTTCATGTTTCACAAGA-CAAACATTCAATTATAATATATTTTAACCAAAAACGTAAAAAAAA
2427 TCAACTTAAAATCAATTATGAGATTA
128 TCAACTTAAAATCAATTATGAGATTA
2453 TAA
1 TAA
2456 AACAAAGTAA
Statistics
Matches: 132, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
152 2 0.02
153 122 0.92
154 8 0.06
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (153 bp):
TAATAAGCTTTTGAAAGGAATAGGTGACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTTT
TTTCATGTTTCACAAGACAAACATTCAATTATAATATATTTTAACCAAAAACGTAAAAAAAATCA
ACTTAAAATCAATTATGAGATTA
Found at i:2795 original size:171 final size:170
Alignment explanation
Indices: 2300--3691 Score: 1519
Period size: 171 Copynumber: 8.1 Consensus size: 170
2290 TATGAGATTA
* * * *
2300 TAATAAGCCTTTTGAAAGAATGAGTGACTATAAATGGATTTTTTTTCTCAATGAATAGCTTTTTT
1 TAATAAGCCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGGC-TTTTT
* * * * * * * *
2365 TTTCATGTTTCTCAAAGCA-AGCATTTAATTATAGTTTGTTTTGACCAAAAACGTAAAACAATTC
65 TTGCATGTTTCTCAAGGTAGA-CATTCAATTATAGTCTGTTTT-AACAAAAATGTAAAAAAATTC
* ** *
2429 AACTTAAAATCAATTATGAGATTATAAAACAAAGTAAACCGAG
128 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAG
* * * * *
2472 TAATAAGGCTTTTGAAGGAATG-GATGACTATAAATAGACTTTTGTTCTCAATGAAAAGACTTTT
1 TAATAAGCCTTTTGAAGGAATGAG-TGACTATAAATGGACTTTTCTTCTCAATG-AATGGCTTTT
* * ** ** * * * *
2536 TCTACATGTTTC-CTAAGACAGGTATTCAATTATAGTTTGTTTTAATAAAAACTGCAAAAAACTT
64 TTTGCATGTTTCTC-AAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAA-TGTAAAAAAATT
* * *
2600 CAACTTAAAATCAATTACGAGATTATAAAACCATTAAAAGCGGG
127 CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAG
* * *
2644 TAATAAGCCTTTCGAAGGAATAAGTGACTATAAATGGACTTTTCTTCTCAACGAATGGCTTTTTT
1 TAATAAGCCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTT
*
2709 TGTATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAGAAATGTAAAAAAATTCAA
66 TGCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAA-AAATGTAAAAAAATTCAA
*
2774 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAG
130 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAG
* * *
2815 TAATAAGCCTTTTGAAGAAATGAGTGACTCTAAATGGACTTTTCTTGTCAATGAAT-GCTTCTTT
1 TAATAAGCCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTT-TTT
* * ** * *
2879 CTT-CACGTTCCTTGAGGTAGACATTCAATTATATTTTGTTTTAATCAAAAATGTAAAAAAATTC
65 -TTGCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAA-CAAAAATGTAAAAAAATTC
*
2943 AACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGCGAG
128 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAG
* * * ** *
2986 TAATAAGCTTTTTGAAGGAATGGGTGACTCTAAATGGGTTTTTCTTGTCAATGAAT-GCTTGTTT
1 TAATAAGCCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTT-TTT
* ** *
3050 CTT-CATGTGTCTTGAGGTAGACATTCAATTATAGTATGTTTTAATCAAAAATGTAAAAAAATTC
65 -TTGCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAA-CAAAAATGTAAAAAAATTC
*
3114 AACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAG
128 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAG
* * * * * *
3157 TAATAAGCCTTTTGAACGAATGGGTGACTATAAATGAATTTTTCTTCTCAATCAATGGCTTTTTC
1 TAATAAGCCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTT
* * * * * *
3222 TGTACGTTTCTCATGTTAGACATTCAATTATTGTCTGTTTTTAAGAAAAATGTAAAAAAATTCAA
66 TGCATGTTTCTCAAGGTAGACATTCAATTATAGTCTG-TTTTAACAAAAATGTAAAAAAATTCAA
* * *
3287 CTTAAAATGAATTATGAGATTATAAAATCATTTAAACCGAG
130 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAG
* * * * * * *
3328 TAATAAGACTTTGGAAAGAATGGGTGACTAAAAATGGATTTTTCTTCTCAATGAATGGCTTTTTC
1 TAATAAGCCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTT
* * * * * * * *
3393 TAC-TCCTTTC-CTAAGGCAGGCTTTCAATTATAGTCTTTTTTAAAGAAAAATATAAAAAAATTC
66 TGCAT-GTTTCTC-AAGGTAGACATTCAATTATAGTCTGTTTT-AACAAAAATGTAAAAAAATTC
* *
3456 AACTTAAAATCAATCATAAGATTATAAAACCATTTAAAGC-AGG
128 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGA-G
* * * * *
3499 TAATCAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTTTCAATGAATGACTTTTTC
1 TAATAAGCCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTT
* * ** * * * *
3564 TGCATGTTT-TCCGAGGTAAACAACCACTTATAGTCTGTTTTAATAAAAAATATAAAATAATTCA
66 TGCATGTTTCT-CAAGGTAGACATTCAATTATAGTCTGTTTTAA-CAAAAATGTAAAAAAATTCA
* * * * *
3628 AATTAAAATCATTTACGAGATTATAAAATCGTTTAAAGCGAG
129 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAG
*
3670 TAATAAGCTTTTTGAAGGAATG
1 TAATAAGCCTTTTGAAGGAATG
3692 GGNNNNNNNN
Statistics
Matches: 1041, Mismatches: 156, Indels: 47
0.84 0.13 0.04
Matches are distributed among these distances:
170 13 0.01
171 829 0.80
172 195 0.19
173 4 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
TAATAAGCCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTT
TGCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAATGTAAAAAAATTCAAC
TTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAG
Found at i:3070 original size:342 final size:339
Alignment explanation
Indices: 1881--3693 Score: 1611
Period size: 342 Copynumber: 5.3 Consensus size: 339
1871 NNNNNNNNCT
* * * *
1881 AGGTAGACATTCAATTATACTCTATTTTAACAAAAAATGTAAAAAAAATTCAATTTGAAAA-CAA
1 AGGTAGACATTCAATTATAGTCTGTTTTAA-TAAAAATGT-AAAAAAATTCAACTT-AAAATCAA
* * * *
1945 TTATGAGATTATAAAACCATTAAAAGCGGGTAATAAGCCTTTTGAAAGAATGGGTGACTATAAAT
63 TTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAAT
* ** * * * * * *
2010 GAACCTTTCTTCTCAATGAATGGTTTTTTTTTTCATGTTTCCCAAGGTAGATAGTCAATTATAGT
128 GGATTTTTCTTCTCAATGAATGG-CTTTTTCTTCATGTTTCTCAAGGCAGACATTCAATTATAGT
* * **
2075 CTGTTTTAACAAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAATCCGTTTA
192 CTGTTTTAAC-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTA
* * * * *
2140 AAGCGAGTAATAAGCTTTTTAAAGGAAT-AGGTGACTCTAAATGGACTTTTCTTGTTAATGAATG
256 AAGCGAGTAATAAGCCTTTTGAAGGAATGA-GTGACTATAAATGGACTTTTCTTCTCAATGAAT-
** * * * *
2204 GTTTTTTTTTTTATGTTTCAC-A
319 GACTTTTTCTTCACG-TTC-CTG
** * * * * * * *
2226 AGACAAACATTCAATTATAATATATTTTAATCAAAAAGGTAAAAAAAATCAACTTAAGATCAATT
1 AGGTAGACATTCAATTATAGTCTGTTTTAAT-AAAAATGTAAAAAAATTCAACTTAAAATCAATT
* * *
2291 ATGAG-----------A-TT------A-TAATAAGCCTTTTGAAAGAATGAGTGACTATAAATGG
65 ACGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGG
** * * *** * * * * * *
2337 ATTTTTTTTCTCAATGAAT-AGCTTTTTTTTTCAT-GTTTCTCAAAGCAA-GCATTTA-ATT-AT
130 A---TTTTTCT-TCTCAATGA-ATGGCTTTTTCTTCATGTTTC---TCAAGGCA--GACATTCA-
* * * *
2397 AGTT-T-G--T-TTTGACCAAAAACGTAAAACAATTCAACTTAAAATCAATTATGAGATTATAAA
184 A-TTATAGTCTGTTTTAACAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* ** * * * *
2457 ACAAAGTAAACCGAGTAATAAGGCTTTTGAAGGAATG-GATGACTATAAATAGACTTTTGTTCTC
248 ACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAG-TGACTATAAATGGACTTTTCTTCTC
* * * *
2521 AATGAAAAGACTTTTTCTACATGTTTCCTA
312 AATG-AATGACTTTTTCTTCACG-TTCCTG
** ** * * *
2551 AGACAGGTATTCAATTATAGTTTGTTTTAATAAAAACTGCAAAAAACTTCAACTTAAAATCAATT
1 AGGTAGACATTCAATTATAGTCTGTTTTAATAAAAA-TGTAAAAAAATTCAACTTAAAATCAATT
* * * **
2616 ACGAGATTATAAAACCATTAAAAGCGGGTAATAAGCCTTTCGAAGGAATAAGTGACTATAAATGG
65 ACGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGG
* * * *
2681 ACTTTTCTTCTCAACGAATGGCTTTTT-TTGTATGTTTCTCAAGGTAGACATTCAATTATAGTCT
130 ATTTTTCTTCTCAATGAATGGCTTTTTCTT-CATGTTTCTCAAGGCAGACATTCAATTATAGTCT
2745 GTTTTAACAAGAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA
194 GTTTTAACAA-AAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA
* * *
2810 GCGAGTAATAAGCCTTTTGAAGAAATGAGTGACTCTAAATGGACTTTTCTTGTCAATGAATG-CT
258 GCGAGTAATAAGCCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGACT
2874 TCTTTCTTCACGTTCCTTG
323 T-TTTCTTCACGTTCC-TG
* *
2893 AGGTAGACATTCAATTATATTTTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATT
1 AGGTAGACATTCAATTATAGTCTGTTTTAAT-AAAAATGTAAAAAAATTCAACTTAAAATCAATT
* * * *
2958 ATGAAATTATAAAACCATTTAAAGCGAGTAATAAGCTTTTTGAAGGAATGGGTGACTCTAAATGG
65 ACGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGG
* * * ** * *
3023 GTTTTTCTTGTCAATGAAT-GCTTGTTTCTTCATGTGTCTTGAGGTAGACATTCAATTATAGTAT
130 ATTTTTCTTCTCAATGAATGGCTT-TTTCTTCATGTTTCTCAAGGCAGACATTCAATTATAGTCT
3087 GTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA
194 GTTTTAA-CAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA
* * * * * *
3152 GCGAGTAATAAGCCTTTTGAACGAATGGGTGACTATAAATGAATTTTTCTTCTCAATCAATGGCT
258 GCGAGTAATAAGCCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGACT
* *
3217 TTTTCTGT-ACGTTTCTC
323 TTTTCT-TCACGTTCCTG
* * * *
3234 ATGTTAGACATTCAATTATTGTCTGTTTTTAAGAAAAATGTAAAAAAATTCAACTTAAAATGAAT
1 A-GGTAGACATTCAATTATAGTCTG-TTTTAATAAAAATGTAAAAAAATTCAACTTAAAATCAAT
* * * * * * *
3299 TATGAGATTATAAAATCATTTAAACCGAGTAATAAGACTTTGGAAAGAATGGGTGACTAAAAATG
64 TACGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATG
* * * *
3364 GATTTTTCTTCTCAATGAATGGCTTTTTCTAC-TCCTTTC-CTAAGGCAGGCTTTCAATTATAGT
129 GATTTTTCTTCTCAATGAATGGCTTTTTCTTCAT-GTTTCTC-AAGGCAGACATTCAATTATAGT
* * * * * *
3427 CTTTTTTAAAGAAAAATATAAAAAAATTCAACTTAAAATCAATCATAAGATTATAAAACCATTTA
192 CTGTTTT-AACAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTA
* * *
3492 AAGC-AGGTAATCAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTTTCAATGAATG
256 AAGCGA-GTAATAAGCCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATG
* *
3556 ACTTTTTCTGCATGTTTTCC-G
320 ACTTTTTCTTCACG--TTCCTG
* ** * * * * *
3577 AGGTAAACAACCACTTATAGTCTGTTTTAATAAAAAATATAAAATAATTCAAATTAAAATCATTT
1 AGGTAGACATTCAATTATAGTCTGTTTTAAT-AAAAATGTAAAAAAATTCAACTTAAAATCAATT
* * *
3642 ACGAGATTATAAAATCGTTTAAAGCGAGTAATAAGCTTTTTGAAGGAATGGG
65 ACGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGG
3694 NNNNNNNNNN
Statistics
Matches: 1192, Mismatches: 206, Indels: 143
0.77 0.13 0.09
Matches are distributed among these distances:
324 7 0.01
325 197 0.17
326 7 0.01
327 5 0.00
328 13 0.01
329 9 0.01
330 7 0.01
331 3 0.00
332 1 0.00
333 1 0.00
336 1 0.00
337 4 0.00
338 8 0.01
339 5 0.00
340 9 0.01
341 33 0.03
342 660 0.55
343 128 0.11
344 62 0.05
345 32 0.03
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (339 bp):
AGGTAGACATTCAATTATAGTCTGTTTTAATAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
CGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGA
TTTTTCTTCTCAATGAATGGCTTTTTCTTCATGTTTCTCAAGGCAGACATTCAATTATAGTCTGT
TTTAACAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCG
AGTAATAAGCCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGACTTTT
TCTTCACGTTCCTG
Found at i:3365 original size:513 final size:510
Alignment explanation
Indices: 2300--3693 Score: 1691
Period size: 513 Copynumber: 2.7 Consensus size: 510
2290 TATGAGATTA
*
2300 TAATAAGCCTTTTGAAAGAATGAGTGACTATAAATGGATTTTTTTTCTCAATGAATAGCTTTTTT
1 TAATAAGCCTTTTGAAAGAATGAGTGACTATAAATGGATTTTTCTTCTCAATGAATAGC-TTTTT
* * * * * * * * * * *
2365 TTTCATGTTTCTCAAAGCA-AGCATTTAATTATAGTTTGTTTTGACCAAAAACGTAAAACAATTC
65 CTTCACGTTCCTTAAGGCAGA-CATTCAATTATATTTTGTTTTAAACAAAAATGTAAAAAAATTC
* * ** *
2429 AACTTAAAATCAATTATGAGATTATAAAACAAAGTAAACCGAGTAATAAGGCTTTTGAAGGAATG
129 AACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGCGAGTAATAA-GCTTTTGAAGGAATG
* * * * * * ** **
2494 GATGACTATAAATAGACTTTTGTTCTCAATGAAAAGACTTTTTCTACATGTTTCCTAAGACAGGT
193 GGTGACTATAAATGGACTTTTCTTCTCAATG-AATGACTTTTTCTACATG-TTCTTGAGGTAGAC
* * *
2559 ATTCAATTATAGTTTGTTTTAATAAAAACTGCAAAAAACTTCAACTTAAAATCAATTACGAGATT
256 ATTCAATTATAGTATGTTTTAATAAAAA-TGTAAAAAAATTCAACTTAAAATCAATTACGAGATT
* * * * ** *
2624 ATAAAACCATTAAAAGCGGGTAATAAGCCTTTCGAAGGAATAAGTGACTATAAATGGACTTTTCT
320 ATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCT
* *
2689 TCTCAACGAATGGCTTTTTTTGTATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACA
385 TCTCAACGAATGGCTTTTTCTGTACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACA
*
2754 AGAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAG
450 AGAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAACCGAG
* * *
2815 TAATAAGCCTTTTG-AAGAAATGAGTGACTCTAAATGGACTTTTCTTGTCAATGAAT-GCTTCTT
1 TAATAAGCCTTTTGAAAG-AATGAGTGACTATAAATGGATTTTTCTTCTCAATGAATAGCTT-TT
* * *
2878 TCTTCACGTTCCTTGAGGTAGACATTCAATTATATTTTGTTTTAATCAAAAATGTAAAAAAATTC
64 TCTTCACGTTCCTTAAGGCAGACATTCAATTATATTTTGTTTTAAACAAAAATGTAAAAAAATTC
2943 AACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGCGAGTAATAAGCTTTTTGAAGGAATG
129 AACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGCGAGTAATAAGC-TTTTGAAGGAATG
* ** * *
3008 GGTGACTCTAAATGGGTTTTTCTTGTCAATGAATG-CTTGTTTCTTCATGTGTCTTGAGGTAGAC
193 GGTGACTATAAATGGACTTTTCTTCTCAATGAATGACTT-TTTCTACATGT-TCTTGAGGTAGAC
*
3072 ATTCAATTATAGTATGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATT
256 ATTCAATTATAGTATGTTTTAAT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAGATT
* *
3137 ATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAACGAATGGGTGACTATAAATGAATTTTTCT
320 ATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCT
* * *
3202 TCTCAATC-AATGGCTTTTTCTGTACGTTTCTCATGTTAGACATTCAATTATTGTCTGTTTTTAA
385 TCTCAA-CGAATGGCTTTTTCTGTACGTTTCTCAAGGTAGACATTCAATTATAGTCTG-TTTTAA
* *
3266 GAA-AAATGTAAAAAAATTCAACTTAAAATGAATTATGAGATTATAAAA-TCATTTAAACCGAG
448 CAAGAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACT-ATTTAAACCGAG
* * * * *
3328 TAATAAGACTTTGGAAAGAATGGGTGACTAAAAATGGATTTTTCTTCTCAATGAATGGCTTTTTC
1 TAATAAGCCTTTTGAAAGAATGAGTGACTATAAATGGATTTTTCTTCTCAATGAATAGCTTTTTC
* * * * * *
3393 TACTC-CTTTCC-TAAGGCAGGCTTTCAATTATAGTCTT-TTTTAAAGAAAAATATAAAAAAATT
66 T--TCACGTTCCTTAAGGCAGACATTCAATTATA-TTTTGTTTTAAACAAAAATGTAAAAAAATT
* *
3455 CAACTTAAAATCAATCAT-AAGATTATAAAACCATTTAAAGC-AGGTAATCAGGCTTTTGAAGGA
128 CAACTTAAAATCAATTATGAA-ATTATAAAACCATTTAAAGCGA-GTAAT-AAGCTTTTGAAGGA
* * *
3518 ATGAGTGACTATAAATGGACTTTTCTTTTCAATGAATGACTTTTTCTGCATGTT-TTCCGAGGTA
190 ATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATGACTTTTTCTACATGTTCTT--GAGGTA
* ** * * * * * *
3582 AACAACCACTTATAGTCTGTTTTAATAAAAAATATAAAATAATTCAAATTAAAATCATTTACGAG
253 GACATTCAATTATAGTATGTTTTAAT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAG
* *
3647 ATTATAAAA-TCGTTTAAAGCGAGTAATAAGCTTTTTGAAGGAATGGG
317 ATTATAAAACT-ATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGG
3694 NNNNNNNNNN
Statistics
Matches: 761, Mismatches: 96, Indels: 46
0.84 0.11 0.05
Matches are distributed among these distances:
511 2 0.00
512 10 0.01
513 525 0.69
514 173 0.23
515 51 0.07
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (510 bp):
TAATAAGCCTTTTGAAAGAATGAGTGACTATAAATGGATTTTTCTTCTCAATGAATAGCTTTTTC
TTCACGTTCCTTAAGGCAGACATTCAATTATATTTTGTTTTAAACAAAAATGTAAAAAAATTCAA
CTTAAAATCAATTATGAAATTATAAAACCATTTAAAGCGAGTAATAAGCTTTTGAAGGAATGGGT
GACTATAAATGGACTTTTCTTCTCAATGAATGACTTTTTCTACATGTTCTTGAGGTAGACATTCA
ATTATAGTATGTTTTAATAAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAGATTATAAAA
CTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTCTCAA
CGAATGGCTTTTTCTGTACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAGAAAT
GTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAACCGAG
Done.