Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399477.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_274.0, 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: 14981
ACGTcount: A:0.22, C:0.08, G:0.09, T:0.22
Warning! 5760 characters in sequence are not A, C, G, or T
Found at i:2030 original size:172 final size:171
Alignment explanation
Indices: 1715--3738 Score: 1910
Period size: 172 Copynumber: 11.8 Consensus size: 171
1705 NNNNNNAGAG
* ** * *
1715 AAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCACTTTTTATGGTCTTATAATC
1 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATC
* *
1780 TCAAAATTGATTTAAATTTCAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGCC
66 TCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGTC
* * * * *
1845 TACTTTAAGAAACATGATGAAAAAAGTATTCATTGGAAAAAA
131 TAC-TTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAA
* * * *
1887 AAGTTCATTTATAGTCACCCATTCCTTCAAAAGCCCTATTCCTCACTTTATATAGTTTTATAATC
1 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATC
* * * * *
1952 TCAAAATTGATTTAAATTTGACTTCTTTGTACATTTTTCGTTAAAACAAACTAGGATTGAAAGTC
66 TCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGTC
* *
2017 TTCATTCAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAA
131 TAC-TTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAA
* * * ** * * * * **
2059 AATTCTATTTATAATCACTTATTCCTTCTAGAGCCTTATTACTCAGTTTAAATGGTTTTATAAGA
1 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATC
* * * * *
2124 TCAAAATTGATTTTAATTTGACTGT-TTTATACATTTTTAGTTAAAATAGACTAGAATTGAATGT
66 TCAAAATTGATTTAAATTTGAAT-TCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGT
* * * *
2188 CTACCATGATAAACAT-AA-AAAAAAGTATTCATTGGCAAGAA
130 CTA-CTTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAA
** * * * *
2229 AAGTTTATTTATAGTCACCTATTGCTTCAAAAGCCTTATTAATCACTTTAAATAGTTTTAAAATC
1 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATC
* * * * * * * * *
2294 TCAAAATTTATTTTAAGTTT-AATTTTTTTTTGC-TTTTCTGGTTAAAACATATTATAGTTGAAT
66 TCAAAATTGA-TTTAAATTTGAA-TTCTTTGTACATTTT-TGGTTAAAACAGACTAGAATTGAAT
** * * *
2357 GTCTACCCCAAGAAACATAAAGAAGAGAA-CATTCATTGCCAAGAA
128 GTCTACTTC-AGAAACATGAAGAA-AAAAGCATTCATTGGCAAGAA
* *
2402 AAGTCCATTTATAGTCACTCATTCCTTCAGAAGCCTTATTACTCACTTTAAAT-GTTTTTATAAT
1 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAG-TTTTATAAT
* * *
2466 CTTAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTAGTTAAAACAGACTATAATTGAATGT
65 CTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGT
** * *
2531 CTACCTTGGGAAATATGAAGAAAAAAGCATTCATTGGGAAGAA
130 CTA-CTTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAA
* * * * * * *
2574 AAGTCCACTTATAGTCACCCATACCTTCAAAAGCCTTATTACCCGCTTTAAATGGGTTTGTAATG
1 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAAT-
** * * * * * * *
2639 C-CGTAATTGATTTTAAGTTGAATTTTTATTTTATATTTTTTGTT-AAACAGACTATAATTGAAT
65 CTCAAAATTGATTTAAATTTGAA-TTCT-TTGTACATTTTTGGTTAAAACAGACTAGAATTGAAT
* * *
2702 GTCTACCTCGAGAAATAT-AACGAAAAAGGCATTCATTGGCACA-AA
128 GTCTACTTC-AGAAACATGAA-GAAAAAAGCATTCATTGGCA-AGAA
* * * * * *
2747 AAGTCCACTTATAGCCGCCCATTCCTTTAAGAGCCTTATTACTCAGTTTAAATAGTTTTATAATC
1 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATC
* ** * *
2812 TCAAAATTCATTTAAATTTGAATGT-TTTGGGCATTTTTGGTTAAAATAAACTAGAATTGAATGT
66 TCAAAATTGATTTAAATTTGAAT-TCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGT
* * * *
2876 CTACCATGAGAAACATGAAGAAAAATGTATTCATTGGCAAGAA
130 CTA-CTTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAA
* * * *
2919 AAGTCTATCTATAGTCACCCATTGCTTCAAAAGCCTTATTAATCACTTTAAATAGTTTTATAATC
1 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATC
* * * * * * * * * *
2984 TCAAAATTGATTTTAAGTTCAATTTTTTTTTGC-TTTTCTAGTTAAAACATATTATAATTGAATG
66 TCAAAATTGATTTAAATTTGAA-TTCTTTGTACATTTT-TGGTTAAAACAGACTAGAATTGAATG
** * *
3048 TCTACCCCAAGAAACATAAAGAAGAGAA-CATTCATTGGCAAGAA
129 TCTACTTC-AGAAACATGAAGAA-AAAAGCATTCATTGGCAAGAA
* * * *
3092 AAGTCCATTTATAGTCATCCATTCCTTCAAAAGCCTTATTACTCACTTTATATGGTTTTGTAATC
1 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATC
* * * *
3157 TCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTTAATCAGGCTAGAATTGAATATC
66 TCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGTC
* * * *
3222 TACCATGAGAAACATGATGAAAAAAGAATTCATTGGCAAGAA
131 TA-CTTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAA
* * * * * * *
3264 AAATCCATTTATAGTGACTCATACTTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTGTAATG
1 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAAT-
** * * * * * * * * *
3329 CTGTATA-TAATTT-AAGTTGAATTTTTTTTTATATCTTTT-GTT-AAACAGACTATAATTAAAA
65 CTCAAAATTGATTTAAATTTGAA-TTCTTTGTACAT-TTTTGGTTAAAACAGACTAGAATTGAAT
* * ** * * * ** *
3390 GTCTAGCTTGACAAATGTAAAGAAAAAGGCATTCATCGATAAGAG
128 GTCTA-CTTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAA
* * * * *
3435 AAGTCCATTTATAGCCACCTATTCCTTCAAAAGCCTTATTACTCACTTTATATGGTTTTATAATA
1 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATC
* *
3500 TCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGGATTGAAAGTC
66 TCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGTC
* * ** * *
3565 TTCCTTCAGAAATATGGGGAAAAAAGTATTCAATGGCAAGAA
131 -TACTTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAA
* * * * *
3607 AAGTCTATCTATAGTCACCCATTGCTTCAAAAGCCTTATTAATCAATTTAAATAGTTTTATAATC
1 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATC
* * * * * ** * *
3672 TCAAGATTGATTTTAAGTTCAATTGTTT-T-CACTTTTCTACTTAAAACATACTACAATTGAATG
66 TCAAAATTGATTTAAATTTGAATTCTTTGTACA-TTTT-TGGTTAAAACAGACTAGAATTGAATG
3735 TCTA
129 TCTA
3739 TCCCAAGAAA
Statistics
Matches: 1498, Mismatches: 308, Indels: 93
0.79 0.16 0.05
Matches are distributed among these distances:
170 100 0.07
171 192 0.13
172 820 0.55
173 367 0.24
174 19 0.01
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (171 bp):
AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATC
TCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGTC
TACTTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAA
Found at i:2751 original size:345 final size:344
Alignment explanation
Indices: 1715--3776 Score: 2251
Period size: 345 Copynumber: 6.0 Consensus size: 344
1705 NNNNNNAGAG
** *
1715 AAGTCCATTTATAGTCAC-CTATTCCTTCAAAAGCCTTATTACTCACTTTTTATGGTCTTATAAT
1 AAGTCCATTTATAGTCACTC-ATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAAT
* *
1779 CTCAAAATTGATTTAAATTTCAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGC
65 CTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGT
** * * * * *
1844 CTACTTTAAGAAACATGATGAAAAAAGTATTCATTGGAAAAAAAAGTTCATTTATAGTCACCCAT
130 CTACCATGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAT
* * * * *
1909 TCCTTCAAAAGCCCTATTCCTCACTTTATATAGTTTTATAATCTCAAAATTGATTTAAATTTG-A
195 TCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAA
* * * * * * ** * * * *
1973 CTTCTTTGTACATTTTTCGTTAAAACAAACTAGGATTGAAAGTCTTCATTC-AGAAACATGAAGA
260 TTTTTTTTTATATTTTTTGTTAAAACAGACTATAATTGAATGTCTAC-CTCAAGAAACATAAAG-
*
2037 AAAAAGTATTCATTGGCAAGAA
323 AAAAAGCATTCATTGGCAAGAA
* * * * * * * **
2059 AATTCTATTTATAATCACTTATTCCTTCTAGAGCCTTATTACTCAGTTTAAATGGTTTTATAAGA
1 AAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATC
* * * * *
2124 TCAAAATTGATTTTAATTTGACTGT-TTTATACATTTTTAGTTAAAATAGACTAGAATTGAATGT
66 TCAAAATTGATTTAAATTTGAAT-TCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGT
* ** *
2188 CTACCATGATAAACAT-AA-AAAAAAGTATTCATTGGCAAGAAAAGTTTATTTATAGTCACCTAT
130 CTACCATGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAT
* * * * *
2251 TGCTTCAAAAGCCTTATTAATCACTTTAAATAGTTTTAAAATCTCAAAATTTATTTTAAGTTTAA
195 TCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAA
* * * * * * *
2316 TTTTTTTTTGCT-TTTCTGGTTAAAACATATTATAGTTGAATGTCTACCCCAAGAAACATAAAGA
260 TTTTTTTTT-ATATTTTTTGTTAAAACAGACTATAATTGAATGTCTACCTCAAGAAACATAAAGA
*
2380 AGAGAA-CATTCATTGCCAAGAA
324 A-A-AAGCATTCATTGGCAAGAA
* *
2402 AAGTCCATTTATAGTCACTCATTCCTTCAGAAGCCTTATTACTCACTTTAAATGTTTTTATAATC
1 AAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATC
* * *
2467 TTAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTAGTTAAAACAGACTATAATTGAATGTC
66 TCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGTC
* * * * * * *
2532 TACCTTGGGAAATATGAAGAAAAAAGCATTCATTGGGAAGAAAAGTCCACTTATAGTCACCCATA
131 TACCATGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATT
* * * * * **
2597 CCTTCAAAAGCCTTATTACCCGCTTTAAATGGGTTTGTAATGC-CGTAATTGATTTTAAGTTGAA
196 CCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAAT-CTCAAAATTGATTTTAAGTTGAA
* * *
2661 TTTTTATTTTATATTTTTTGTT-AAACAGACTATAATTGAATGTCTACCTCGAGAAATATAACGA
260 TTTTT-TTTTATATTTTTTGTTAAAACAGACTATAATTGAATGTCTACCTCAAGAAACATAAAGA
2725 AAAAGGCATTCATTGGCACA-AA
324 AAAA-GCATTCATTGGCA-AGAA
* * * * * * * *
2747 AAGTCCACTTATAGCCGCCCATTCCTTTAAGAGCCTTATTACTCAGTTTAAATAGTTTTATAATC
1 AAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATC
* ** * *
2812 TCAAAATTCATTTAAATTTGAATGT-TTTGGGCATTTTTGGTTAAAATAAACTAGAATTGAATGT
66 TCAAAATTGATTTAAATTTGAAT-TCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGT
* * *
2876 CTACCATGAGAAACATGAAGAAAAATGTATTCATTGGCAAGAAAAGTCTATCTATAGTCACCCAT
130 CTACCATGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAT
* * *
2941 TGCTTCAAAAGCCTTATTAATCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAA
195 TCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAA
* * * * * *
3006 TTTTTTTTTGCT-TTTCTAGTTAAAACATATTATAATTGAATGTCTACCCCAAGAAACATAAAGA
260 TTTTTTTTT-ATATTTTTTGTTAAAACAGACTATAATTGAATGTCTACCTCAAGAAACATAAAGA
3070 AGAGAA-CATTCATTGGCAAGAA
324 A-A-AAGCATTCATTGGCAAGAA
* *
3092 AAGTCCATTTATAGTCA-TCCATTCCTTCAAAAGCCTTATTACTCACTTTATATGGTTTTGTAAT
1 AAGTCCATTTATAGTCACT-CATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAAT
* * * *
3156 CTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTTAATCAGGCTAGAATTGAATAT
65 CTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGT
* * * * *
3221 CTACCATGAGAAACATGATGAAAAAAGAATTCATTGGCAAGAAAAATCCATTTATAGTGACTCAT
130 CTACCATGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAT
* * * * ** * *
3286 ACTTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTGTAATGCTGTATA-T-AATTTAAGTTGA
195 TCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAAT-CTCAAAATTGATTTTAAGTTGA
* * * * ** * **
3349 ATTTTTTTTTATATCTTTTGTT-AAACAGACTATAATTAAAAGTCTAGCTTGACAAATGTAAAGA
259 ATTTTTTTTTATATTTTTTGTTAAAACAGACTATAATTGAATGTCTACCTCAAGAAACATAAAGA
* ** *
3413 AAAAGGCATTCATCGATAAGAG
324 AAAA-GCATTCATTGGCAAGAA
* *
3435 AAGTCCATTTATAGCCAC-CTATTCCTTCAAAAGCCTTATTACTCACTTTATATGGTTTTATAAT
1 AAGTCCATTTATAGTCACTC-ATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAAT
* * *
3499 ATCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGGATTGAAAGT
65 CTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGT
* * * * ** * * *
3564 CTTCCTTCAGAAATATGGGGAAAAAAGTATTCAATGGCAAGAAAAGTCTATCTATAGTCACCCAT
130 CTACCATGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAT
* * * * *
3629 TGCTTCAAAAGCCTTATTAATCAATTTAAATAGTTTTATAATCTCAAGATTGATTTTAAGTTCAA
195 TCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAA
* * * ** * *
3694 -TTGTTTTCACT-TTTCTACTTAAAACATACTACAATTGAATGTCTATCC-CAAGAAACATAAAG
260 TTTTTTTTTA-TATTTTTTGTTAAAACAGACTATAATTGAATGTCTA-CCTCAAGAAACATAAAG
* **
3756 AAGAGAGCATGAATTGGCAAG
323 AA-AAAGCATTCATTGGCAAG
3777 NNNNNNNNNN
Statistics
Matches: 1413, Mismatches: 268, Indels: 74
0.81 0.15 0.04
Matches are distributed among these distances:
341 2 0.00
342 104 0.07
343 446 0.32
344 217 0.15
345 623 0.44
346 19 0.01
347 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (344 bp):
AAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATC
TCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAATTGAATGTC
TACCATGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATT
CCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAAT
TTTTTTTTATATTTTTTGTTAAAACAGACTATAATTGAATGTCTACCTCAAGAAACATAAAGAAA
AAGCATTCATTGGCAAGAA
Found at i:4573 original size:172 final size:169
Alignment explanation
Indices: 3942--4574 Score: 623
Period size: 172 Copynumber: 3.7 Consensus size: 169
3932 AAAAAAATAA
* * * * * * * * *
3942 AACTTAAAATTAATGTTGAGATTATAAAACTATTTAAATTGATTAATAAGGCTTTTGAAGCAATG
1 AACTTTAAATCAATTTTGAGATTATAAAACCATATAAAGTGAGTAATAAAGCTTTTGAAGGAATG
* * * * * * * *
4007 GGTGACTATATATAGACTTTTCTTGCCAATGAATACTTTTTTCCTCATGTTTTTGAAGGAAGACT
66 GGTGACTATAAATGGACTTTTCTTGCCAATGAAT-GTTTTTTCTTCATGTTTCTCAAGGTAGACA
*
4072 TTC-AATCCTAGTCTCTTTTAACCAAAAATGTACAAAGAATTC
130 TTCAAAT-CTAGTCT-TTTTAACCAAAAATATACAAA-AATTC
* *
4114 AAATTTAAATCAATTTTGAGATTATAAAACCATATAAAGTGAGTAATAAGGCTTTTGAAGGAATG
1 AACTTTAAATCAATTTTGAGATTATAAAACCATATAAAGTGAGTAATAAAGCTTTTGAAGGAATG
* * * * * *
4179 GGT-AGCTATAAATGGACTTCTCTTGCGAATGAATGCCTTTTTCATT-ACGTTTGTCAAGCTAGA
66 GGTGA-CTATAAATGGACTTTTCTTGCCAATGAATG-TTTTTTC-TTCATGTTTCTCAAGGTAGA
* * * *
4242 CATTTAATTATAGTCTTTTTAA-CAAAAGATATAAAAAAAATTC
128 CATTCAAATCTAGTCTTTTTAACCAAAA-ATAT-ACAAAAATTC
** ** * * * * * *
4285 AAC-TTAAATTTA-TTACAGCATTACAAAACTATTTAAAGCGAATAATAAAGCTTTTGAAGGTAT
1 AACTTTAAATCAATTTTGAG-ATTATAAAACCATATAAAGTGAGTAATAAAGCTTTTGAAGGAAT
* * *
4348 GGGTGACTATAAATGGATTTTTCTTGCCAATGAAT-TCCTGTTTCTTCATGTTTCTCATGGTAGA
65 GGGTGACTATAAATGGACTTTTCTTGCCAATGAATGT--TTTTTCTTCATGTTTCTCAAGGTAGA
* *
4412 CATTCAAATCTAGCCTGTTTTAACCAAAAATTTACAACAAATTC
128 CATTCAAATCTAGTCT-TTTTAACCAAAAATATACAA-AAATTC
*
4456 AACTTTAAATCAATTTTGGGATTATAAAACCATATAAAGTGAGTAATAAAGCTTTTGAAGGAATG
1 AACTTTAAATCAATTTTGAGATTATAAAACCATATAAAGTGAGTAATAAAGCTTTTGAAGGAATG
* * * * *
4521 CGTGACTATAAATGGACTTTTCTTACTAATGAATGTTCTCTTCTTTATGTTTCT
66 GGTGACTATAAATGGACTTTTCTTGCCAATGAATGTT-TTTTCTTCATGTTTCT
4575 TGGAGTAGAC
Statistics
Matches: 371, Mismatches: 72, Indels: 36
0.77 0.15 0.08
Matches are distributed among these distances:
169 6 0.02
170 112 0.30
171 37 0.10
172 209 0.56
173 7 0.02
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (169 bp):
AACTTTAAATCAATTTTGAGATTATAAAACCATATAAAGTGAGTAATAAAGCTTTTGAAGGAATG
GGTGACTATAAATGGACTTTTCTTGCCAATGAATGTTTTTTCTTCATGTTTCTCAAGGTAGACAT
TCAAATCTAGTCTTTTTAACCAAAAATATACAAAAATTC
Found at i:4688 original size:104 final size:104
Alignment explanation
Indices: 4492--4698 Score: 242
Period size: 104 Copynumber: 2.0 Consensus size: 104
4482 AAACCATATA
* *
4492 AAGTGAGTAATAAAGCTTTTGAAGGAATGCGTGACTATAAATGGACTTTTCTTACTAATGAATGT
1 AAGTGAGTAATAAAGCTTTTGAAGGAATGCGTGACTATAAATGGACTTCTCTTACCAATGAATGT
* * * **
4557 TCTCTTCTTTATGTTTCTTGGAGTAGACATGTAATTATG
66 TCTCTTCATTACGTTTCGTCAAGTAGACATGTAATTATG
* * * *
4596 AAGTGAGTAATAAGGCTTTTGAAGGGATGGGT-AGCTATAAATGGACTTCTCTTGCCAATGAATG
1 AAGTGAGTAATAAAGCTTTTGAAGGAATGCGTGA-CTATAAATGGACTTCTCTTACCAATGAATG
*
4660 CCTT-T-TTCATTACGTTT-GTCAAGCTAGACATTTAATTAT
65 --TTCTCTTCATTACGTTTCGTCAAG-TAGACATGTAATTAT
4699 AGTCTGTTTA
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
103 4 0.05
104 80 0.92
105 1 0.01
106 2 0.02
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (104 bp):
AAGTGAGTAATAAAGCTTTTGAAGGAATGCGTGACTATAAATGGACTTCTCTTACCAATGAATGT
TCTCTTCATTACGTTTCGTCAAGTAGACATGTAATTATG
Found at i:4828 original size:274 final size:276
Alignment explanation
Indices: 4327--4828 Score: 636
Period size: 276 Copynumber: 1.8 Consensus size: 276
4317 TTAAAGCGAA
* * * *
4327 TAATAAAGCTTTTGAAGGTATGGGTGACTATAAATGGATTTTTCTTGCCAATGAATTCCTGTTTC
1 TAATAAAGCTTTTGAAGGGATGGGTGACTATAAATGGACTTCTCTTGCCAATGAATGCCTGTTTC
* * * * * * *
4392 TTCATGTTTCTCATGGTAGACATTCAAATCTAGCCTGTTTTAACCAAAAATTTACAACAAATTCA
66 TTCACGTTTCTCAAGCTAGACATTCAAATATAGCCTGTTTTAACCAAAAATATAAAAAAAATTCA
* *** * * * *
4457 ACTTTAAATCAATTTTGGGATTATAAAACCATATAAAGTGAGTAATAAAGCTTTTGAAGGAATGC
131 ACTTTAAATCAAATACAGCATTACAAAACCATATAAAGCGAATAATAAAGCTTTTGAAGGAATGC
*
4522 GTGACTATAAATGGACTTTTCTTACTAATGAATGTTCTCTTCTTTATGTTTCTTGGAGTAGACAT
196 GTGACTATAAATGGACTTTTCTTACCAATGAATGTTCTCTTCTTTATGTTTCTTGGAGTAGACAT
4587 GTAATTATGAAGTGAG
261 GTAATTATGAAGTGAG
* *
4603 TAATAAGGCTTTTGAAGGGATGGGT-AGCTATAAATGGACTTCTCTTGCCAATGAATGCCTTTTT
1 TAATAAAGCTTTTGAAGGGATGGGTGA-CTATAAATGGACTTCTCTTGCCAATGAATGCCTGTTT
* * * * *
4667 CATT-ACGTTTGTCAAGCTAGACATTTAATTATAGTCTG-TTTAA-CAGAAGATATAAAAAAAAT
65 C-TTCACGTTTCTCAAGCTAGACATTCAAATATAGCCTGTTTTAACCA-AAAATATAAAAAAAAT
* * * *
4729 TCAAC-TTAAATTAAATACAGCATTACAAAACTATTTAAAGCGAATAATAAAGCTTTTGAAGGTA
128 TCAACTTTAAATCAAATACAGCATTACAAAACCATATAAAGCGAATAATAAAGCTTTTGAAGGAA
* * *
4793 TGGGTGACTATAAATGGATTTTTCTTGCCAATGAAT
193 TGCGTGACTATAAATGGACTTTTCTTACCAATGAAT
4829 TCCTTTTTCT
Statistics
Matches: 189, Mismatches: 34, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
274 81 0.43
275 23 0.12
276 83 0.44
277 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (276 bp):
TAATAAAGCTTTTGAAGGGATGGGTGACTATAAATGGACTTCTCTTGCCAATGAATGCCTGTTTC
TTCACGTTTCTCAAGCTAGACATTCAAATATAGCCTGTTTTAACCAAAAATATAAAAAAAATTCA
ACTTTAAATCAAATACAGCATTACAAAACCATATAAAGCGAATAATAAAGCTTTTGAAGGAATGC
GTGACTATAAATGGACTTTTCTTACCAATGAATGTTCTCTTCTTTATGTTTCTTGGAGTAGACAT
GTAATTATGAAGTGAG
Found at i:4860 original size:274 final size:276
Alignment explanation
Indices: 4327--4848 Score: 633
Period size: 274 Copynumber: 1.9 Consensus size: 276
4317 TTAAAGCGAA
* * * *
4327 TAATAAAGCTTTTGAAGGTATGGGTGACTATAAATGGATTTTTCTTGCCAATGAATTCCTGTTTC
1 TAATAAAGCTTTTGAAGGGATGGGTGACTATAAATGGACTTCTCTTGCCAATGAATGCCTGTTTC
* * * * * * *
4392 TTCATGTTTCTCATGGTAGACATTCAAATCTAGCCTGTTTTAACCAAAAATTTACAACAAATTCA
66 TTCACGTTTCTCAAGCTAGACATTCAAATATAGCCTGTTTTAACCAAAAATATAAAAAAAATTCA
* *** * * * *
4457 ACTTTAAATCAATTTTGGGATTATAAAACCATATAAAGTGAGTAATAAAGCTTTTGAAGGAATGC
131 ACTTTAAATCAAATACAGCATTACAAAACCATATAAAGCGAATAATAAAGCTTTTGAAGGAATGC
* * *
4522 GTGACTATAAATGGACTTTTCTTACTAATGAATGTTCTCTTCTTTATGTTTCTTGGAGTAGACAT
196 GTGACTATAAATGGACTTTTCTTACCAATGAATGTCCTCTTCTTCATGTTTCTTGGAGTAGACAT
4587 GTAATTATGAAGTGAG
261 GTAATTATGAAGTGAG
* *
4603 TAATAAGGCTTTTGAAGGGATGGGT-AGCTATAAATGGACTTCTCTTGCCAATGAATGCCTTTTT
1 TAATAAAGCTTTTGAAGGGATGGGTGA-CTATAAATGGACTTCTCTTGCCAATGAATGCCTGTTT
* * * * *
4667 CATT-ACGTTTGTCAAGCTAGACATTTAATTATAGTCTG-TTTAA-CAGAAGATATAAAAAAAAT
65 C-TTCACGTTTCTCAAGCTAGACATTCAAATATAGCCTGTTTTAACCA-AAAATATAAAAAAAAT
* * * *
4729 TCAAC-TTAAATTAAATACAGCATTACAAAACTATTTAAAGCGAATAATAAAGCTTTTGAAGGTA
128 TCAACTTTAAATCAAATACAGCATTACAAAACCATATAAAGCGAATAATAAAGCTTTTGAAGGAA
* * * *
4793 TGGGTGACTATAAATGGATTTTTCTTGCCAATGAAT-TCCTTTTTCTTCATGTTTCT
193 TGCGTGACTATAAATGGACTTTTCTTACCAATGAATGTCC-TCTTCTTCATGTTTCT
4849 CATGGTAGAC
Statistics
Matches: 205, Mismatches: 37, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
273 2 0.01
274 95 0.46
275 23 0.11
276 83 0.40
277 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (276 bp):
TAATAAAGCTTTTGAAGGGATGGGTGACTATAAATGGACTTCTCTTGCCAATGAATGCCTGTTTC
TTCACGTTTCTCAAGCTAGACATTCAAATATAGCCTGTTTTAACCAAAAATATAAAAAAAATTCA
ACTTTAAATCAAATACAGCATTACAAAACCATATAAAGCGAATAATAAAGCTTTTGAAGGAATGC
GTGACTATAAATGGACTTTTCTTACCAATGAATGTCCTCTTCTTCATGTTTCTTGGAGTAGACAT
GTAATTATGAAGTGAG
Found at i:4980 original size:172 final size:173
Alignment explanation
Indices: 4596--5354 Score: 745
Period size: 172 Copynumber: 4.4 Consensus size: 173
4586 TGTAATTATG
* * *
4596 AAGTGAGTAATAAGGCTTTTGAAGGGATGGGT-AGCTATAAATGGACTTCTCTTGCCAATGAATG
1 AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGA-CTATAAATGGACTTTTCTTGCCAATGAATA
* * * * * * *
4660 CCTTTTTCATT-ACGTTTGTCAAGCTAGACATTTAATTATAGTCT-GTTT-AACAGAAGATATAA
65 CCTTTTTC-TTCATGTTTCTCATGGTAGACATTCAATTATAGTCTATTTTAAACAGAAAATATAA
* * ** * *
4722 AAAAAATTCAAC-TTAAATTAA-ATACAGCATTACAAAACTATTTA
129 AAAAAATTCAACTTTAAATCAATTTTGAG-ATTATAAAACCATTTA
* * * * * *
4766 AAGCGAATAATAAAGCTTTTGAAGGTATGGGTGACTATAAATGGATTTTTCTTGCCAATGAATTC
1 AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATAC
* * *
4831 CTTTTTCTTCATGTTTCTCATGGTAGACATTCAAATT-TAGCCTATTTTAAACA-AAAATTTACA
66 CTTTTTCTTCATGTTTCTCATGGTAGACATTC-AATTATAGTCTATTTTAAACAGAAAATATAAA
* *
4894 AAGAATTCAACTTTAAATCAATTTTGAGATTATAAAACCATATA
130 AAAAATTCAACTTTAAATCAATTTTGAGATTATAAAACCATTTA
* *
4938 AAGTGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCAATGAAT--
1 AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATAC
* * *** * * * * * * **
5001 GTTCTCTTCTTTATGTTTCTTGGGGTAGGCAATCAATTATAATATGTTTT-CACTAGAAAA-GCA
66 CTT-T-TTCTTCATGTTTCTCATGGTAGACATTCAATTATAGTCTATTTTAAAC-AGAAAATATA
* ** *
5064 AAAAAAATTGAACTCAAAATCAATTTTGAGATTATAAAACTATTTA
128 AAAAAAATTCAACTTTAAATCAATTTTGAGATTATAAAACCATTTA
* * * *
5110 AAGTGATTAGTAAGGCTTTTGAAGCAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATAC
1 AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATAC
* * * * * * *
5175 TTTTTTTTTCATGTTTCACGTGGTAGACATTCAATTCTAGTCTATTTTAACCA-AAAA-ACTACA
66 CTTTTTCTTCATGTTTCTCATGGTAGACATTCAATTATAGTCTATTTTAAACAGAAAATA-TAAA
* * * *
5238 AAACATTCAAATTCAAATCAATTTTGGGATTATAAAACCATTTA
130 AAAAATTCAACTTTAAATCAATTTTGAGATTATAAAACCATTTA
* * * * *
5282 AACTGAGTAATAAGGCTCTTGAAGGAATGAGTGACTAGAAATAGACTTTTCTTGCCAATGAATAC
1 AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATAC
*
5347 TTTTTTCT
66 CTTTTTCT
5355 NNNNNNNNNN
Statistics
Matches: 484, Mismatches: 89, Indels: 30
0.80 0.15 0.05
Matches are distributed among these distances:
169 2 0.00
170 87 0.18
171 36 0.07
172 348 0.72
173 9 0.02
174 2 0.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (173 bp):
AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATAC
CTTTTTCTTCATGTTTCTCATGGTAGACATTCAATTATAGTCTATTTTAAACAGAAAATATAAAA
AAAATTCAACTTTAAATCAATTTTGAGATTATAAAACCATTTA
Found at i:4983 original size:446 final size:446
Alignment explanation
Indices: 4150--5028 Score: 1616
Period size: 446 Copynumber: 2.0 Consensus size: 446
4140 AAACCATATA
*
4150 AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTAGCTATAAATGGACTTCTCTTGCGAATGAATGC
1 AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTAGCTATAAATGGACTTCTCTTGCCAATGAATGC
*
4215 CTTTTTCATTACGTTTGTCAAGCTAGACATTTAATTATAGTCTTTTTAACAAAAGATATAAAAAA
66 CTTTTTCATTACGTTTGTCAAGCTAGACATTTAATTATAGTCTGTTTAACAAAAGATATAAAAAA
* *
4280 AATTCAACTTAAATTTATTACAGCATTACAAAACTATTTAAAGCGAATAATAAAGCTTTTGAAGG
131 AATTCAACTTAAATTAAATACAGCATTACAAAACTATTTAAAGCGAATAATAAAGCTTTTGAAGG
4345 TATGGGTGACTATAAATGGATTTTTCTTGCCAATGAATTCCTGTTTCTTCATGTTTCTCATGGTA
196 TATGGGTGACTATAAATGGATTTTTCTTGCCAATGAATTCCTGTTTCTTCATGTTTCTCATGGTA
* * *
4410 GACATTCAAATCTAGCCTGTTTTAACCAAAAATTTACAACAAATTCAACTTTAAATCAATTTTGG
261 GACATTCAAATCTAGCCTATTTTAAACAAAAATTTACAACAAATTCAACTTTAAATCAATTTTGA
4475 GATTATAAAACCATATAAAGTGAGTAATAAAGCTTTTGAAGGAATGCGTGACTATAAATGGACTT
326 GATTATAAAACCATATAAAGTGAGTAATAAAGCTTTTGAAGGAATGCGTGACTATAAATGGACTT
*
4540 TTCTTACTAATGAATGTTCTCTTCTTTATGTTTCTTGGAGTAGACATGTAATTATG
391 TTCTTACCAATGAATGTTCTCTTCTTTATGTTTCTTGGAGTAGACATGTAATTATG
*
4596 AAGTGAGTAATAAGGCTTTTGAAGGGATGGGTAGCTATAAATGGACTTCTCTTGCCAATGAATGC
1 AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTAGCTATAAATGGACTTCTCTTGCCAATGAATGC
*
4661 CTTTTTCATTACGTTTGTCAAGCTAGACATTTAATTATAGTCTGTTTAACAGAAGATATAAAAAA
66 CTTTTTCATTACGTTTGTCAAGCTAGACATTTAATTATAGTCTGTTTAACAAAAGATATAAAAAA
4726 AATTCAACTTAAATTAAATACAGCATTACAAAACTATTTAAAGCGAATAATAAAGCTTTTGAAGG
131 AATTCAACTTAAATTAAATACAGCATTACAAAACTATTTAAAGCGAATAATAAAGCTTTTGAAGG
*
4791 TATGGGTGACTATAAATGGATTTTTCTTGCCAATGAATTCCTTTTTCTTCATGTTTCTCATGGTA
196 TATGGGTGACTATAAATGGATTTTTCTTGCCAATGAATTCCTGTTTCTTCATGTTTCTCATGGTA
*
4856 GACATTCAAATTTAGCCTATTTTAAACAAAAATTTACAA-AGAATTCAACTTTAAATCAATTTTG
261 GACATTCAAATCTAGCCTATTTTAAACAAAAATTTACAACA-AATTCAACTTTAAATCAATTTTG
*
4920 AGATTATAAAACCATATAAAGTGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACT
325 AGATTATAAAACCATATAAAGTGAGTAATAAAGCTTTTGAAGGAATGCGTGACTATAAATGGACT
*
4985 TTTCTTACCAATGAATGTTCTCTTCTTTATGTTTCTTGGGGTAG
390 TTTCTTACCAATGAATGTTCTCTTCTTTATGTTTCTTGGAGTAG
5029 GCAATCAATT
Statistics
Matches: 418, Mismatches: 14, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
445 1 0.00
446 417 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (446 bp):
AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTAGCTATAAATGGACTTCTCTTGCCAATGAATGC
CTTTTTCATTACGTTTGTCAAGCTAGACATTTAATTATAGTCTGTTTAACAAAAGATATAAAAAA
AATTCAACTTAAATTAAATACAGCATTACAAAACTATTTAAAGCGAATAATAAAGCTTTTGAAGG
TATGGGTGACTATAAATGGATTTTTCTTGCCAATGAATTCCTGTTTCTTCATGTTTCTCATGGTA
GACATTCAAATCTAGCCTATTTTAAACAAAAATTTACAACAAATTCAACTTTAAATCAATTTTGA
GATTATAAAACCATATAAAGTGAGTAATAAAGCTTTTGAAGGAATGCGTGACTATAAATGGACTT
TTCTTACCAATGAATGTTCTCTTCTTTATGTTTCTTGGAGTAGACATGTAATTATG
Done.