Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399291.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_256.0, 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: 9324
ACGTcount: A:0.29, C:0.09, G:0.10, T:0.27
Warning! 2330 characters in sequence are not A, C, G, or T
Found at i:1275 original size:171 final size:171
Alignment explanation
Indices: 1080--1394 Score: 395
Period size: 170 Copynumber: 1.8 Consensus size: 171
1070 NNTAAGACTT
* * * **
1080 TTGAAGGAATGGGTGAAGATAAATA-AGCTTTT-TTTTACCAATGAATGCCTTTTTCTTCACGGT
1 TTGAAGGAATGGGAGAAGATAAATAGA-CTTTTCATGT--CAATGAATGCCTTTTTCTTCAAAGT
* *
1143 TCTCG-AGATAGACATTCAATTATAGTTTGTTTTAACCAAAAATATAAAATAATTC-ACTTAAAA
63 TCTCGAAG-TAGACATTCAATTATAGTATGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAA
* * *
1206 TCATTTATGAGATTATAAAACCATTTAAAGCGGTTAATAAGGCTA
127 TCAATGATGAGAATATAAAACCATTTAAAGCGGTTAATAAGGCTA
** * * *
1251 TTGAAGGAATGGGAGACTATAAATAGACTTTTCATGTCAATGAATGCTTTTTTTTTCAAATTTCT
1 TTGAAGGAATGGGAGAAGATAAATAGACTTTTCATGTCAATGAATGCCTTTTTCTTCAAAGTTCT
* * * *
1316 CGAAGTAGACATTTAATTTTCGTATGTTTTAACGAAAAATATAAAAAAATTCAACTTAAAATCAA
66 CGAAGTAGACATTCAATTATAGTATGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAA
1381 TGATGAGAATATAA
131 TGATGAGAATATAA
1395 NNNNNNNNNN
Statistics
Matches: 121, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
170 66 0.55
171 52 0.43
172 3 0.02
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (171 bp):
TTGAAGGAATGGGAGAAGATAAATAGACTTTTCATGTCAATGAATGCCTTTTTCTTCAAAGTTCT
CGAAGTAGACATTCAATTATAGTATGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAA
TGATGAGAATATAAAACCATTTAAAGCGGTTAATAAGGCTA
Found at i:1738 original size:170 final size:171
Alignment explanation
Indices: 1456--1874 Score: 473
Period size: 170 Copynumber: 2.5 Consensus size: 171
1446 NNNNNNNNNN
* ** *
1456 GGAATGGGTGACTATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTCTTTACATTTCTCAAGG
1 GGAATGGGGGACTATAAATGGACTTTCCTTGCCAACGAATGCCTTTTTCTTTACATTTCTCAAGG
* * * * * ** *
1521 TAGACATTCAATTATTGTCTATTTTAACGAAAAATTTAAAAATAATCAACTT-GGATCATTTATG
66 TAGACATTCAATTATTATCTACTTTAACAAAAAATGTAAAAATAATCAAATTAAAATCAATTATG
*
1585 AGATTATAAAACCATTTAAAGCGAGCAATAAGGCTTTTGAA
131 AGATTATAAAACCATTTAAAGCGAGCAATAAGCCTTTTGAA
* **
1626 GGAATGGGGGACTATAAATTGACTTTCCTTGCCAACGAATGCCTTTTTCTTTATGTTTCTCAAGG
1 GGAATGGGGGACTATAAATGGACTTTCCTTGCCAACGAATGCCTTTTTCTTTACATTTCTCAAGG
* * * *
1691 TAGATATTCAATTATTATCTGCTTTAATAAAAAATGTAAAAATAATCAAATTAAAATTAATTATG
66 TAGACATTCAATTATTATCTACTTTAACAAAAAATGTAAAAATAATCAAATTAAAATCAATTATG
* * * *
1756 AGATTGTAAAACTATTTAAAGTGAGTAATAAGCCTTTTGAA
131 AGATTATAAAACCATTTAAAGCGAGCAATAAGCCTTTTGAA
* *** * * * ** * * * *
1797 AGAACAAGTGACTATAAATGGACCTTT-CTTACTAGTGAATGTCTTTCTCTTCACGTTTCTCAAG
1 GGAATGGGGGACTATAAATGGA-CTTTCCTTGCCAACGAATGCCTTTTTCTTTACATTTCTCAAG
*
1861 GTAAACATTCAATT
65 GTAGACATTCAATT
1875 GCAATATGTT
Statistics
Matches: 207, Mismatches: 40, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
170 102 0.49
171 101 0.49
172 4 0.02
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (171 bp):
GGAATGGGGGACTATAAATGGACTTTCCTTGCCAACGAATGCCTTTTTCTTTACATTTCTCAAGG
TAGACATTCAATTATTATCTACTTTAACAAAAAATGTAAAAATAATCAAATTAAAATCAATTATG
AGATTATAAAACCATTTAAAGCGAGCAATAAGCCTTTTGAA
Found at i:1857 original size:171 final size:170
Alignment explanation
Indices: 1463--1874 Score: 484
Period size: 171 Copynumber: 2.4 Consensus size: 170
1453 NNNGGAATGG
* * *
1463 GTGACTATAAATGGACTTTTGTTGCCAATGAATGCCTTTTTCTTTACATTTCTCAAGGTAGACAT
1 GTGACTATAAATGGACCTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGTAGACAT
* * * * * ** *
1528 TCAATTATTGTCTATTTTAACGAAAAATTTAAAAATAATCAACTTGGATCATTTATGAGATTATA
66 TCAATTATTATCTACTTTAACAAAAAATGTAAAAATAATCAAATTAAATCAATTATGAGATTATA
* * ***
1593 AAACCATTTAAAGCGAGCAATAAGGCTTTTGAAGGAATGG
131 AAACCATTTAAAGCGAGCAATAAGCCTTTTGAAAGAACAA
* * * * *
1633 GGGACTATAAATTGA-CTTTCCTTGCCAACGAATGCCTTTTTCTTTATGTTTCTCAAGGTAGATA
1 GTGACTATAAATGGACCTTT-CTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGTAGACA
* * * *
1697 TTCAATTATTATCTGCTTTAATAAAAAATGTAAAAATAATCAAATTAAAATTAATTATGAGATTG
65 TTCAATTATTATCTACTTTAACAAAAAATGTAAAAATAATCAAATT-AAATCAATTATGAGATTA
* * *
1762 TAAAACTATTTAAAGTGAGTAATAAGCCTTTTGAAAGAACAA
129 TAAAACCATTTAAAGCGAGCAATAAGCCTTTTGAAAGAACAA
* * * * * * *
1804 GTGACTATAAATGGACCTTTCTTACTAGTGAATGTCTTTCTCTTCACGTTTCTCAAGGTAAACAT
1 GTGACTATAAATGGACCTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGTAGACAT
1869 TCAATT
66 TCAATT
1875 GCAATATGTT
Statistics
Matches: 199, Mismatches: 40, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
169 3 0.02
170 91 0.46
171 101 0.51
172 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (170 bp):
GTGACTATAAATGGACCTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGTAGACAT
TCAATTATTATCTACTTTAACAAAAAATGTAAAAATAATCAAATTAAATCAATTATGAGATTATA
AAACCATTTAAAGCGAGCAATAAGCCTTTTGAAAGAACAA
Found at i:2757 original size:172 final size:172
Alignment explanation
Indices: 2317--3095 Score: 670
Period size: 171 Copynumber: 4.5 Consensus size: 172
2307 NNNNNNCTTG
* * * * * *
2317 AGGTAGACATTCAATTATAGTTTTTTTTAACT-AAAAGTA-AAAAACAATTC-ACTTAAAATCAT
1 AGGTAGACATTCAATTATTGTCTATTTTAA-TGAAAAATATAAAAATAA-TCAACTTAAAATCAA
* * * *
2379 TTATGAGATTATAAAACTATTTAAAGCGGGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAAA
64 TTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT
* ** * ** *
2444 AGA-TTTTTCATGTCAATGAATGCTTTTTTCTTCACGTTTCTTTATGTTTCTCA
129 GGACTTTTTTTTGCCAAAAAATGCCTTTTTCTTCA---------A-GTTTCTCA
* * * * * *
2497 AGGTAGACATTCAATT-TTAGTGTGTTTTAACGAAAAATGTAAAACA-ATTTAACTTAAAATCAA
1 AGGTAGACATTCAATTATT-GTCTATTTTAATGAAAAATATAAAA-ATAATCAACTTAAAATCAA
* * * * *
2560 TGATGAGAATATAAAACTATTTAAAGTGAATAATAAGGCTTTTGAAGGAATGGGTGACCATAAAT
64 TTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT
* **
2625 GGACTTTTTTTTGTCAAAAAATGCCTTTTTCATT-ACA-TTTCTTG
129 GGACTTTTTTTTGCCAAAAAATGCCTTTTTC-TTCA-AGTTTCTCA
* * * *
2669 AGGTAGACATTCAATTATTGTCTATTTTCATGAAAAATTTAAAAATAATCAACTTGAAATCATTT
1 AGGTAGACATTCAATTATTGTCTATTTTAATGAAAAATATAAAAATAATCAACTTAAAATCAATT
* * * * *
2734 ATGAGATTATAAAACCATTTAAAGCGAGCAATAAGGCTTTTGAAGAAATGGATGACTATAAATTG
66 ATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
**
2799 A-TTTTTTTTGCCAAGGAATGCCTTTTTCTTCAAGTTTCTCA
131 ACTTTTTTTTGCCAAAAAATGCCTTTTTCTTCAAGTTTCTCA
* *
2840 AGGTAGACATTCAATTATTATCTATTTTAATAAAAAATATAAAAATAATCAACTTAAAATCAATT
1 AGGTAGACATTCAATTATTGTCTATTTTAATGAAAAATATAAAAATAATCAACTTAAAATCAATT
* * * * *
2905 ATGAGATTGTAAAACTATTGAAAGCGAGTAATAAGCCTTTTGAAAGAATAGGTGACTATAAATGG
66 ATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
* * * ** *
2970 AC-CTTTCTT-ACAAGTGAATGTCTTTTTCTTCACA-TTTCTCA
131 ACTTTTTTTTGCCAA-AAAATGCCTTTTTCTTCA-AGTTTCTCA
* * **** * * * * *
3011 AGGTAAACATTCCATTGCAATCTGTTTTCAA--AAAAAGTATAAAGA-AATTAAATTTAAATCAA
1 AGGTAGACATTCAATTATTGTCTATTTT-AATGAAAAA-TATAAAAATAATCAACTTAAAATCAA
*
3073 TTTTGAGATTATAAAACTATTTA
64 TTATGAGATTATAAAACTATTTA
3096 NNNNNNNNNN
Statistics
Matches: 498, Mismatches: 85, Indels: 42
0.80 0.14 0.07
Matches are distributed among these distances:
170 45 0.09
171 203 0.41
172 115 0.23
173 2 0.00
174 1 0.00
179 1 0.00
180 31 0.06
181 74 0.15
182 24 0.05
183 2 0.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (172 bp):
AGGTAGACATTCAATTATTGTCTATTTTAATGAAAAATATAAAAATAATCAACTTAAAATCAATT
ATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
ACTTTTTTTTGCCAAAAAATGCCTTTTTCTTCAAGTTTCTCA
Found at i:3644 original size:170 final size:170
Alignment explanation
Indices: 3297--3712 Score: 450
Period size: 171 Copynumber: 2.4 Consensus size: 170
3287 NNNNNNGGGT
* * * *
3297 AACTAGAAATGAACTTTTCTTGCCAATGAAAGCCTTTTCTTTACATTTCTGTAGGTAGACATTCA
1 AACTATAAATGGACTTTTCTTGCCAATGAAAGCCTTTTCGTCACATTTCTGTAGGTAGACATTCA
* * *
3362 ATTATAATCTGTTTTAACCAATAATGTAAAAAAAATTGAACCTAAAATCAATTTTGAGATTATAA
66 ATTATAATCTGTTTTAACCAATAATATAAAAAAAATTCAACCTAAAATCAATTATGAGATTATAA
* *
3427 AACCATTTAAAGTGAGCAATAAGGCTTTTGAAGGATGGAA
131 AACCATTTAAAGTGAGCAATAAGCCTTTTAAAGGATGGAA
** * *
3467 AACTATAAATGGACTTTTCTTGCCAATGAATTCTTTTTTCGTCACATTTCTCG-AGGTAGATATT
1 AACTATAAATGGACTTTTCTTGCCAATGAAAGC-CTTTTCGTCACATTTCT-GTAGGTAGACATT
* * * * *
3531 CAATTATAGTTTG-TTTAACCAA-AA-ATATAAAAAATTCAGCTTAAAATCAATTATGAGATTAT
64 CAATTATAATCTGTTTTAACCAATAATATAAAAAAAATTCAACCTAAAATCAATTATGAGATTAT
* * * * *
3593 AAAACTATTTAATGTGGGTAATAAGACCTTTTAAAGGAAT-GAGT
129 AAAACCATTTAAAGTGAGCAATAAG-CCTTTTAAAGG-ATGGA-A
* * * * *
3637 GACTATAAATGGACTTTTTTTTTACCAATGAATGCCTTTTCTTCA-AGTTTCT-TAAGGTAGACA
1 AACTATAAATGGAC--TTTTCTTGCCAATGAAAGCCTTTTCGTCACA-TTTCTGT-AGGTAGACA
3700 TTCAATTATAATC
62 TTCAATTATAATC
3713 NNNNNNNNNN
Statistics
Matches: 204, Mismatches: 32, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
168 53 0.26
169 13 0.06
170 54 0.26
171 67 0.33
172 17 0.08
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (170 bp):
AACTATAAATGGACTTTTCTTGCCAATGAAAGCCTTTTCGTCACATTTCTGTAGGTAGACATTCA
ATTATAATCTGTTTTAACCAATAATATAAAAAAAATTCAACCTAAAATCAATTATGAGATTATAA
AACCATTTAAAGTGAGCAATAAGCCTTTTAAAGGATGGAA
Found at i:5375 original size:171 final size:169
Alignment explanation
Indices: 4835--5646 Score: 714
Period size: 171 Copynumber: 4.8 Consensus size: 169
4825 NNNNNNNNNN
* * * * * *
4835 GATTATAAAACTATTTAATGTGGGTAATAAGGCCTTTGAAGGAATGAGTGACTATAAATGGATTT
1 GATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGAGTGACTATAAATGGACTT
* ** *
4900 TTTTTATCAATGAATGTC-TTTTCTTTA-AGTTTCTCAAGGTAGACATTCAATTATAATCTGTTT
66 TTCTTGCCAATGAATATCTTTTTC-TTACA-TTTCTCAAGGTAGACATTCAATTATAATCTGTTT
* *
4963 TAA-CTAGAAATA-AAAAAAATTAACTTAAAATCAATTCTGA
129 TAATC-AAAAATATAAAAAAATTAACTTAAAATCAATTATGA
* * * * * * *
5003 GATTATAAAATTATTTAAAGCGAGCAATAAGGTTTTTGAA-ACTATAAATGACCATAAATGGACT
1 GATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGA-AATGAGTGACTATAAATGGACT
* * ** ** * * *
5067 TTTTTTGCTAGCGAATGCCTTTTGCTTCACATTTCTCAAGGTA-AGCATTCAATTATGATTTGTT
65 TTTCTTGCCAATGAATATCTTTTTCTT-ACATTTCTCAAGGTAGA-CATTCAATTATAATCTGTT
**
5131 TTAGCCAAAAATATTAAAAAAATTGAACTTAAAATCAAATT-TGA
128 TTAATCAAAAATA-TAAAAAAATT-AACTTAAAATC-AATTATGA
* * * ** *
5175 TATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTCCAAGAAATGAGTGACTATAAATAGACTT
1 GATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGAGTGACTATAAATGGACTT
* * * * * ** *
5240 TGCTTGCCAATGAATATGTTTTTTTTCACGTTTTTCAAGGTAGACATTCAATTATTCTCCGTTTT
66 TTCTTGCCAATGAATATCTTTTTCTT-ACATTTCTCAAGGTAGACATTCAATTATAATCTGTTTT
* *
5305 AATCAAAAATATAAAATAATTTGACTTAAAATCAATTATGA
130 AATCAAAAATATAAAA-AAATTAACTTAAAATCAATTATGA
* * * *
5346 GATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAA-AGAATGAGAGACTATAAATGAACT
1 GATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGA-AATGAGTGACTATAAATGGACT
* * * * * *
5410 TTTCTTGCCAATGAATA-GTTTTTCCTACATGTT-TCCTGAGGCAAACATTCAATTATAGTCTGT
65 TTTCTTGCCAATGAATATCTTTTTCTTACAT-TTCT-C-AAGGTAGACATTCAATTATAATCTGT
* * *
5473 TTTAAT-GAAAATGTAAAAAAATTCAACTTAAAATCAATTATCA
127 TTTAATCAAAAATATAAAAAAATT-AACTTAAAATCAATTATGA
* * * * * *
5516 GATTATAAAACTATTTAAAGCAAGTAATAAAGTTTTTGAGGGAATGAGTGACTATAAATGGATTT
1 GATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGAGTGACTATAAATGGACTT
* * * * * * *
5581 GTTTTTG-CAATGAATACCTTTATCTTCATATTTTTCTAA-GTCGACATTCAATTATAGTCTGTT
66 -TTCTTGCCAATGAATATCTTTTTCTT-ACATTTCTC-AAGGTAGACATTCAATTATAATCTGTT
5644 TTA
128 TTA
5647 GCTAAAAATG
Statistics
Matches: 523, Mismatches: 97, Indels: 46
0.79 0.15 0.07
Matches are distributed among these distances:
168 66 0.13
169 51 0.10
170 133 0.25
171 139 0.27
172 128 0.24
173 6 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.37
Consensus pattern (169 bp):
GATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGAGTGACTATAAATGGACTT
TTCTTGCCAATGAATATCTTTTTCTTACATTTCTCAAGGTAGACATTCAATTATAATCTGTTTTA
ATCAAAAATATAAAAAAATTAACTTAAAATCAATTATGA
Found at i:5565 original size:341 final size:340
Alignment explanation
Indices: 4835--5655 Score: 800
Period size: 341 Copynumber: 2.4 Consensus size: 340
4825 NNNNNNNNNN
* * * * * *
4835 GATTATAAAACTATTTAATGTGGGTAATAAGGCCTTTGAAGGAATGAGTGACTATAAATGGATTT
1 GATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTT
** * * *
4900 TTTTTATCAATGAATGTCTTTTCTTTAAGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTA
66 TGCTTACCAATGAATATCTTTTCTTTAAGTTTCTCAAGGTAGACATTCAATTATAATCCGTTTTA
* * ** *
4965 ACTAGAAATAAAAAAAATTAACTTAAAATCAATTCTGAGATTATAAAATTATTTAAAGCGAGCAA
131 ACTAAAAATAAAAAAAATTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGCAA
* * * * * * * *
5030 TAAGGTTTTTGAAACTATAAATGACCATAAATGGACTTTTTTTGCTAGCGAATGCCTTTTGCTTC
196 TAAGGCTTTTGAAACAATAAATGACCATAAATGAACTTTTCTTGCCAACGAATGCCTTTTCCTAC
* * * * * *
5095 ACATTTCTCAAGGTAAGCATTCAATTATGATTTGTTTTAGCCAAAAATATTAAAAAAATTGAACT
261 ACATTTCTCAAGGCAAACATTCAATTATGATCTGTTTTAGACAAAAATAGTAAAAAAATTCAACT
*
5160 TAAAATCAAATTTGA
326 TAAAATCAAATTTCA
* * * ** *
5175 TATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTCCAAGAAATGAGTGACTATAAATAGACTT
1 GATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTT
* * * * * **
5240 TGCTTGCCAATGAATATGTTTTTTTTCACGTTTTTCAAGGTAGACATTCAATTATTCTCCGTTTT
66 TGCTTACCAATGAATATCTTTTCTTT-AAGTTTCTCAAGGTAGACATTCAATTATAATCCGTTTT
* *
5305 AA-TCAAAAATATAAAATAATTTGACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAA
130 AACT-AAAAATA-AAAA-AAATTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAA
* * * * * *
5369 GTAATAAGGCTTTTGAAAGAATGAGA-GACTATAAATGAACTTTTCTTGCCAATGAATAG-TTTT
192 GCAATAAGGCTTTTGAAACAAT-AAATGACCATAAATGAACTTTTCTTGCCAACGAAT-GCCTTT
** * **
5432 TCCTACATGTTTC-CTGAGGCAAACATTCAATTAT-AGTCTGTTTTA-ATGAAAAT-GTAAAAAA
255 TCCTACACATTTCTC-AAGGCAAACATTCAATTATGA-TCTGTTTTAGACAAAAATAGTAAAAAA
5493 ATTCAACTTAAAATC-AATTATCA
318 ATTCAACTTAAAATCAAATT-TCA
* * * * *
5516 GATTATAAAACTATTTAAAGCAAGTAATAAAGTTTTTGAGGGAATGAGTGACTATAAATGGA-TT
1 GATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTT
* ** * * * * * *
5580 TGTTTTTGCAATGAATACCTTTATCTTCATA-TTTTTCTAA-GTCGACATTCAATTATAGTCTGT
66 TG-CTTACCAATGAATATCTTT-TCTTTA-AGTTTCTC-AAGGTAGACATTCAATTATAATCCGT
*
5643 TTTAGCTAAAAAT
127 TTTAACTAAAAAT
5656 GTAAANNNNN
Statistics
Matches: 386, Mismatches: 81, Indels: 27
0.78 0.16 0.05
Matches are distributed among these distances:
340 81 0.21
341 165 0.43
342 17 0.04
343 120 0.31
344 3 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.37
Consensus pattern (340 bp):
GATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTT
TGCTTACCAATGAATATCTTTTCTTTAAGTTTCTCAAGGTAGACATTCAATTATAATCCGTTTTA
ACTAAAAATAAAAAAAATTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGCAA
TAAGGCTTTTGAAACAATAAATGACCATAAATGAACTTTTCTTGCCAACGAATGCCTTTTCCTAC
ACATTTCTCAAGGCAAACATTCAATTATGATCTGTTTTAGACAAAAATAGTAAAAAAATTCAACT
TAAAATCAAATTTCA
Found at i:6559 original size:27 final size:27
Alignment explanation
Indices: 6529--6582 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
6519 ATTATAATAT
6529 GCTTTAACTAGAAATGAAAAAAAATTA
1 GCTTTAACTAGAAATGAAAAAAAATTA
6556 GCTTTAACTAGAAATGAAAAAAAATTA
1 GCTTTAACTAGAAATGAAAAAAAATTA
6583 ACTTAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.26
Consensus pattern (27 bp):
GCTTTAACTAGAAATGAAAAAAAATTA
Found at i:6716 original size:197 final size:198
Alignment explanation
Indices: 6360--6723 Score: 477
Period size: 197 Copynumber: 1.8 Consensus size: 198
6350 TTATAGTCTG
* *
6360 TTTAACTAAAAATATAAAAAAATTCAAATTAAAATTAATTATGAGATTATAAAACTATTTAAAGT
1 TTTAACTAAAAATATAAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACCATTTAAAGT
* * * * ** *
6425 GAGTAATAAGGTCTTTGAAGGAATGTGTAACTATAAATAGACTTTTTTTGTCAATGAATGCCTTT
66 GAGCAATAAGGTCTTTGAAAGAATGGGTAACTATAAATAGACTTTCTTACTCAACGAATGCCTTT
* * *
6490 TTCTTCACATTTCTTAATGTAGACATTCAATTATAATATGCTTTAACTAGAAATGAAAAAAAATT
131 TACTTCACATTTCTCAAGGTAGACATTCAATTATAATATGCTTTAACTAGAAATGAAAAAAAATT
6555 AGC
196 AGC
* *
6558 TTTAACTAGAAATGA-AAAAAAATT-AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
1 TTTAACTAAAAAT-ATAAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * *
6621 TGAGCAATAAGG-CTTTTGAAAGAATGGGTGACTATAAATGGACTTCTCTTACT-AGCGAATGCC
65 TGAGCAATAAGGTC-TTTGAAAGAATGGGTAACTATAAATAGACTT-TCTTACTCAACGAATGCC
* **
6684 TTTTACTTTATGTTTCTCAAGGTA-AGCATTCAATTATAAT
128 TTTTACTTCACATTTCTCAAGGTAGA-CATTCAATTATAAT
6724 TTGTTTTAGC
Statistics
Matches: 142, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
196 2 0.01
197 114 0.80
198 25 0.18
199 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (198 bp):
TTTAACTAAAAATATAAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACCATTTAAAGT
GAGCAATAAGGTCTTTGAAAGAATGGGTAACTATAAATAGACTTTCTTACTCAACGAATGCCTTT
TACTTCACATTTCTCAAGGTAGACATTCAATTATAATATGCTTTAACTAGAAATGAAAAAAAATT
AGC
Found at i:7018 original size:171 final size:169
Alignment explanation
Indices: 6556--7099 Score: 524
Period size: 171 Copynumber: 3.2 Consensus size: 169
6546 AAAAAAATTA
* *
6556 GCTTTAACTAGAAATG-AAAAAAAATTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
1 GCTTTAACTAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * * * * * ** *
6620 GTGAGCAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTCTCTTACTAGCGAATGCCT
66 GCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGAACTTTTCTTGCCAATGAAT--AT
* * *
6685 TTTACTTT-ATGTTTCTCAAGGTAAGCATTCAATTATAATTT
129 TTT-TTTTCACGTTTCTCAAGGTAAGCATTCAATTATAATCT
* * * * ** * **
6726 GTTTTAGCTAAAAATATTAAAAAAATTAAACTTAAAATTTATTTTGACTTTATAAAACCATTTAA
1 GCTTTAACTAAAAAT-GTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAA
* * * * *
6791 ACCGAGTAATAATGCTTTTCAAAGAAAGGGTGACTATAAATAAACTTTGT-TTGCCAATGAATAT
65 AGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGAACTTT-TCTTGCCAATGAATAT
* *
6855 GTTTTTTTCCACGTTTCTCAAGGT-AGATATTCAATTACT-CTCT
129 -TTTTTTT-CACGTTTCTCAAGGTAAG-CATTCAATTA-TAATCT
* * * * *
6898 GCTTTAACCAAAAATGTAAAAAAATTTGACTTACAATCAATTATGAGATTATAGAACTATTTAAA
1 GCTTTAACTAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * *
6963 GCAAGTAATAAGGCTTTTGAAAGAATGAGAGACTATAAATGAACTTTTCTTGCCAATGAATGATT
66 GCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGAACTTTTCTTGCCAATGAAT-ATT
* * * * *
7028 TTTTCTACACGTTTCTCGAGGCAAGCATTCAATTATAGTTT
130 TTTT-TTCACGTTTCTCAAGGTAAGCATTCAATTATAATCT
* * *
7069 GTTTTAA-TGAAATATGTAAAAAAATTCAACT
1 GCTTTAACT-AAAAATGTAAAAAAATTTAACT
7100 NNNNNNNNNN
Statistics
Matches: 297, Mismatches: 63, Indels: 27
0.77 0.16 0.07
Matches are distributed among these distances:
170 18 0.06
171 149 0.50
172 128 0.43
173 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (169 bp):
GCTTTAACTAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
GCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATATTT
TTTTTCACGTTTCTCAAGGTAAGCATTCAATTATAATCT
Found at i:8914 original size:171 final size:170
Alignment explanation
Indices: 8140--9165 Score: 480
Period size: 171 Copynumber: 6.0 Consensus size: 170
8130 NNNNNNNNNN
* * * * * *
8140 TAAAACTATTTAAAGTGAGTAATA-AGGCTTTTGAAAGAATAAGAGACTATAAATGAATTTTTCT
1 TAAAACCATTTAAAGTGAGTAATAGA-GCTTTTGAAAAAATAGGTGACTATAAATAAACTTTTCT
* * ** * * * * * ** *
8204 TACCAATAAAT-GGTTTTTCATACACGTTTCTCGAGGCA-AGCATTTAATTATTGTTTGTTTTAA
65 TACTAATGAATACCTTCTTCAT-TACGTTTCTTGAGGTAGA-CATTCAATTATAATCTGTTTTAA
* * * * * *
8267 TGAACAATGTAAAAAAATTTAACTTAAAATTAATTATCAAATTA
128 TCAAAAATATAAAAAAA-TTAACTTAAAATCAATTATGAGATTA
* *** * * * *
8311 TAAAACTATTTAAAGTGAGTAATA-AGGCTTTTGAGGGAATGGGTGACGACAAATGAACTTTT-T
1 TAAAACCATTTAAAGTGAGTAATAGA-GCTTTTGAAAAAATAGGTGACTATAAATAAACTTTTCT
* * * ********** ** *
8374 TGC-AATGAATATCTTTTTCNNNNNNNNNNTCAAGGTAGACATTCAATTATAGTCTGTTTTAA-C
65 TACTAATGAATACCTTCTTCATTACGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAATC
* *
8437 TAAAAATATAAAACAATTAAACTTTAAATCAATTATGAGATTA
130 -AAAAATATAAAAAAATT-AACTTAAAATCAATTATGAGATTA
** * * * * **
8480 TAAAACCATTTAAAACGAGCAATA-AGGCTTTT-AAGAGAAT-GAGAGACTACAAATGCACTTTT
1 TAAAACCATTTAAAGTGAGTAATAGA-GCTTTTGAA-AAAATAG-GTGACTATAAATAAACTTTT
* * * * * * *
8542 CTTGCCAATGAATGCCTT-TTCCTTTATGTTTCTTGAGGTAGACATTCAATTATAGTCTCTTTTA
63 CTTACTAATGAATACCTTCTT-CATTACGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTA
********** *
8606 NNNNNNNNNNTAAAAAAATTCAAGTTAAAATCAATTATGAG---A
127 ATCAAAAATATAAAAAAATT-AACTTAAAATCAATTATGAGATTA
* * ** ** ** *
8648 TAAAACCTTTTAAA-TCGAGTAATAAAATTTTTGAAGGAATATTTGACTATAAATAGACTTTTCT
1 TAAAACCATTTAAAGT-GAGTAATAGAGCTTTTGAAAAAATAGGTGACTATAAATAAACTTTTCT
* * * ************ * * *
8712 TACCATTGAATGCANNNNNNNNNNTGTTTCTTGAGGTAGACATTCAATTATTATCTATTTTAATG
65 TACTAATGAATACCTTCTTCATTACGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAATC
*
8777 AAAAATATAAAAATAATTAACTTAAAATCAATTATGATATTA
130 AAAAATATAAAAA-AATTAACTTAAAATCAATTATGAGATTA
********** ** * *
8819 TAAAACCATTTAAAGTNNNNNNNNNNGCTTTTGAAGGAATATGTGACTATAAATAGACTTTTCTT
1 TAAAACCATTTAAAGTGAGTAATAGAGCTTTTGAAAAAATAGGTGACTATAAATAAACTTTTCTT
* * * ** * * * *
8884 ACTAATGAATACCTTTTTCTTTACGTTTCTTAAAATAGACATTTAATTATAATCTGTGTTGACCA
66 ACTAATGAATACCTTCTTCATTACGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAATCA
** ** * * *
8949 AGCAGGTAACAAAATTAACTTTAAAATCAATTTTGAGATAA
131 AAAATATAAAAAAATTAAC-TTAAAATCAATTATGAGATTA
* * *
8990 TAAAACCATTTAAAGTGAGTAATAGAGCTTTTGAAAAAATGGGTGACTTTAAATAAACTTTTTTT
1 TAAAACCATTTAAAGTGAGTAATAGAGCTTTTGAAAAAATAGGTGACTATAAATAAACTTTTCTT
* * * * * * * *
9055 GCTAATGAATGCCTTCTTCATTACATTTCTCGAGGTACATATTCAATTATAATTTGTTTTAATTA
66 ACTAATGAATACCTTCTTCATTACGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAATCA
* *
9120 AAAATATAAAACAATTCAACTTAAAATCAATTATAAGATTA
131 AAAATATAAAAAAATT-AACTTAAAATCAATTATGAGATTA
9161 TAAAA
1 TAAAA
9166 ATATTAAAAA
Statistics
Matches: 632, Mismatches: 201, Indels: 44
0.72 0.23 0.05
Matches are distributed among these distances:
168 120 0.19
169 120 0.19
170 23 0.04
171 365 0.58
172 4 0.01
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.35
Consensus pattern (170 bp):
TAAAACCATTTAAAGTGAGTAATAGAGCTTTTGAAAAAATAGGTGACTATAAATAAACTTTTCTT
ACTAATGAATACCTTCTTCATTACGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAATCA
AAAATATAAAAAAATTAACTTAAAATCAATTATGAGATTA
Done.