Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398935.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2218.0, 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: 2923
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.32
Warning! 279 characters in sequence are not A, C, G, or T
Found at i:298 original size:172 final size:170
Alignment explanation
Indices: 1--991 Score: 870
Period size: 171 Copynumber: 5.8 Consensus size: 170
* * * *
1 CTTGTCAATGAATGCCTTTTTCTTCACGTTTCTCAAGCTAGACATTCAGTTAT-ATTATGTTTTA
1 CTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATT-TGTTTTA
* * * *
65 A-CAAAAA-AGTAAAACAGTTTGAACTTAAAATCAATCTTGAGATTATAAAAGCATTTAAAGTGA
65 ACCAAAAATA-TAAAACA-ATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGA
* *
128 GTAATAAGGCTTTTGAAGCAATGAGTGACTGTAAATAGACTTTT
128 GTAATAAGGCTTTTGAAGC-ATGAGTGACTATAAATGGACTTTT
* * * * *
172 CTTGTCAATGAATGCTTTTTTCTTTACATTTCTCGAGGTAGACATTCAATCATAATTTGTTTTAA
1 CTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATTTGTTTTAA
* * * * *
237 CCAAAAATACAAAAAAATTTGAACTTAGAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGC
66 CCAAAAATATAAAACAA-TTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGT
* * *
302 AATAAGGCTTTTGAAGGAACGGGTGACTATAAATGGACTTTT
130 AATAAGGCTTTTGAA-GCATGAGTGACTATAAATGGACTTTT
* * * * * ** *
344 CTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGTAGACATTTAATTATAGTCTACTTTAG
1 CTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATTTGTTTTAA
* * * *** *
409 CCAAAAATATAAAACAATTCAACTTAAAATCAATTATG-GCAATATAAAACCACTTAAAACAACT
66 CCAAAAATATAAAACAATTCAACTTAAAATCAATTTTGAG-ATTATAAAACCATTTAAAGTGAGT
* * * * * *
473 AAAAAGGCTTTTTGAAGGTATAAGTGACTATAAGTGGGCCTTT
130 AATAAGGC-TTTTGAA-GCATGAGTGACTATAAATGGACTTTT
* * * * * *
516 CTTGCGAATGAATGCTTTTCTCTTCACGTTTCTTAAGGTAGACATTCAAGTCTAGTCTT-TTTTA
1 CTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAAT-TTGTTTTA
** * * **
580 ATGAAAAATGA-AAAACAATTCAACTTAAAATCAATTATT-AGTTTATAAAACCATTTAATGCAA
65 ACCAAAAAT-ATAAAACAATTCAACTTAAAATCAATT-TTGAGATTATAAAACCATTTAAAGTGA
* ** * *
643 GAAATAAGGCTTCCGAAGGCTTGAGTGACTGTAAATGGACTTTT
128 GTAATAAGGCTTTTGAA-GCATGAGTGACTATAAATGGACTTTT
** ** * * * * * * * * **
687 -TGTGCCAATGGTTGGATTTTGCTTTATGTTCCCCATGGCAGGA-ACTCAATTATAGCCTT-TTT
1 CT-TGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTA-GACATTCAATTATA-ATTTGTTT
* * * * *
749 TAACCAAAAATCTAAAAAAATTCAACATAAAATCAATTTTGAGATTATAAAGCCATTTAAAGTGG
63 TAACCAAAAATATAAAACAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGA
* * **
814 GTAGTAAGGCTTTTGAAGGCTTGAGCAACTATAAATGGACTTTT
128 GTAATAAGGCTTTTGAA-GCATGAGTGACTATAAATGGACTTTT
* * * * * * ** *
858 CTTGCCAATGAGTGCTTTTTTCCTCATGTTTGCT-AAGGAAAACATTCAATTATACTCAGTTCTA
1 CTTGCCAATGAATGCTTTTTTCTTCACGTTT-CTCAAGGTAGACATTCAATTATAATTTGTTTTA
* * * *
922 ACCAAAAATGTAAAACAATTCAATTTAAAATCAATTATGAGGTTATAAAACCATTTAAAGTGAGT
65 ACCAAAAATATAAAACAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGT
987 AATAA
130 AATAA
992 NNNNNNNNNN
Statistics
Matches: 656, Mismatches: 144, Indels: 40
0.78 0.17 0.05
Matches are distributed among these distances:
170 6 0.01
171 345 0.53
172 299 0.46
173 6 0.01
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (170 bp):
CTTGCCAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATTTGTTTTAA
CCAAAAATATAAAACAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTA
ATAAGGCTTTTGAAGCATGAGTGACTATAAATGGACTTTT
Found at i:632 original size:343 final size:338
Alignment explanation
Indices: 1--991 Score: 931
Period size: 343 Copynumber: 2.9 Consensus size: 338
* * * * * * * *
1 CTTGTCAATGAATGCCTTTTTCTTCACGTTTCTCAAGCTAGACATTCAGTTATATTATGTTTTAA
1 CTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAC
* * *
66 CAAAAA-AGTAAAACAGTTTGAACTTAAAATCAATCTTGAGATTATAAAAGCATTTAAAGTGAGT
66 CAAAAATA-TAAAACA-ATTCAACTTAAAATCAAT-TTGAGATTATAAAACCATTTAAAGTGAGT
** * *
130 AATAAGGCTTTTGAAGCAATGAGTGACTGTAAATAGACTTTTCTTGTCAATGAATGCTTTTTTCT
128 AATAAGGCTTTTGAAGGTATGAGTGACTATAAATGGACTTTTCTTG-CAATGAATGCTTTTTTCT
* * ** * *
195 TTACATTTCTCGAGGTAGACATTCAATCATAAT-TTGTTTTAACCAAAAAT-ACAAAAAAATTTG
192 TCACGTTTCTTAAGGTAGACATTCAATC-TAATCTT-TTTTAACCAAAAATGA-AAAACAA-TTC
* * **
258 AACTTAGAATCAATT-TTGAGATTATAAAACCATTTAAAGTGAGCAATAAGGCTTTTGAAGGAAC
253 AACTTAAAATCAATTATT-AGATTATAAAACCATTTAAAGTGAGAAATAAGGCTTCCGAAGGAAC
*
322 GGGTGACTATAAATGGACTTTT
317 GAGTGACTATAAATGGACTTTT
* *
344 CTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGTAGACATTTAATTATAGTCTACTTTAG
1 CTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTA-
* * *** *
409 CCAAAAATATAAAACAATTCAACTTAAAATCAATTATG-GCAATATAAAACCACTTAAAACAACT
65 CCAAAAATATAAAACAATTCAACTTAAAATCAATT-TGAG-ATTATAAAACCATTTAAAGTGAGT
* * * * * *
473 AAAAAGGCTTTTTGAAGGTATAAGTGACTATAAGTGGGCCTTTCTTGCGAATGAATGCTTTTCTC
128 AATAAGGC-TTTTGAAGGTATGAGTGACTATAAATGGACTTTTCTTGC-AATGAATGCTTTTTTC
* **
538 TTCACGTTTCTTAAGGTAGACATTCAAGTCTAGTCTTTTTTAATGAAAAATGAAAAACAATTCAA
191 TTCACGTTTCTTAAGGTAGACATTCAA-TCTAATCTTTTTTAACCAAAAATGAAAAACAATTCAA
* * ** ***
603 CTTAAAATCAATTATTAGTTTATAAAACCATTTAATGCAAGAAATAAGGCTTCCGAAGGCTTGAG
255 CTTAAAATCAATTATTAGATTATAAAACCATTTAAAGTGAGAAATAAGGCTTCCGAAGGAACGAG
*
668 TGACTGTAAATGGACTTTT
320 TGACTATAAATGGACTTTT
** ** * * * * * * * * *
687 -TGTGCCAATGGTTGGATTTTGCTTTATGTTCCCCATGGCAGGA-ACTCAATTATAGCCTTTTTT
1 CT-TGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGTA-GACATTCAATTATAGTCTATTTT
* * * * *
750 AACCAAAAATCTAAAAAAATTCAACATAAAATCAATTTTGAGATTATAAAGCCATTTAAAGTGGG
64 -ACCAAAAATATAAAACAATTCAACTTAAAATCAA-TTTGAGATTATAAAACCATTTAAAGTGAG
* ** *
815 TAGTAAGGCTTTTGAAGGCT-TGAGCAACTATAAATGGACTTTTCTTGCCAATGAGTGCTTTTTT
127 TAATAAGGCTTTTGAAGG-TATGAGTGACTATAAATGGACTTTTCTTG-CAATGAATGCTTTTTT
* * * * ** * *
879 CCTCATGTTTGC-TAAGGAAAACATTCAAT-TATACTCAGTTCTAACCAAAAATGTAAAACAATT
190 CTTCACGTTT-CTTAAGGTAGACATTCAATCTA-A-TCTTTTTTAACCAAAAATGAAAAACAATT
* * * *
942 CAATTTAAAATCAATTATGAGGTTATAAAACCATTTAAAGTGAGTAATAA
252 CAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGTGAGAAATAA
992 NNNNNNNNNN
Statistics
Matches: 523, Mismatches: 105, Indels: 41
0.78 0.16 0.06
Matches are distributed among these distances:
340 2 0.00
341 1 0.00
342 134 0.26
343 270 0.52
344 110 0.21
345 6 0.01
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (338 bp):
CTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAC
CAAAAATATAAAACAATTCAACTTAAAATCAATTTGAGATTATAAAACCATTTAAAGTGAGTAAT
AAGGCTTTTGAAGGTATGAGTGACTATAAATGGACTTTTCTTGCAATGAATGCTTTTTTCTTCAC
GTTTCTTAAGGTAGACATTCAATCTAATCTTTTTTAACCAAAAATGAAAAACAATTCAACTTAAA
ATCAATTATTAGATTATAAAACCATTTAAAGTGAGAAATAAGGCTTCCGAAGGAACGAGTGACTA
TAAATGGACTTTT
Found at i:1759 original size:171 final size:171
Alignment explanation
Indices: 1276--2923 Score: 1638
Period size: 171 Copynumber: 9.6 Consensus size: 171
1266 NNNNNGGAAT
* * **
1276 ACATTCAATTATAGTCTGTTTTAACCTAAAATGTAAAAAAAAATTCAATCTTAAAATCAATCCTG
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGT--AAAACAATTCAA-CTTAAAATCAATTATG
* * * * * * *
1341 -GCATTACAAAACTATTTAAAGCAAGTAATAAAGCTTTTGAAGGTATGGGTGGCTATAAATAGAC
63 AG-ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGAGTGACTATAAATGGAC
** * * *
1405 TTTTCTTGGAAATTAATGCTTTTTTCTTCT-TTTTTCTCAAGGTAG
127 TTTTCTTGCCAATGAATGCCTTTTTCTT-TATGTTTCTCAAGGTAG
* * * * * *
1450 GCATTCAATTATAGTCTGTTTTAACCAAAAATGATAGAAGAATTCAAATTTAAATCAATTTTGAG
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATG-TAAAACAATTCAACTTAAAATCAATTATGAG
* * * * * * * * * *
1515 ATTACAAAGCCATTTAAAGTGAGTAATAATGCCTTTAAAAGAATGGGTGACTATAAATTGACTTT
65 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGAGTGACTATAAATGGACTTT
*
1580 TTTTGCCAATGAATGCCTTTTTCTTTATGTTTCTCAAGGTAG
130 TCTTGCCAATGAATGCCTTTTTCTTTATGTTTCTCAAGGTAG
* **
1622 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAA-ATATTTAACTTAAAATCAATTATGCC
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACA-ATTCAACTTAAAATCAATTATGAG
* * *
1686 ATTATAAAACCATTTAAAGCGAGTAATGAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTT
65 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGAGTGACTATAAATGGACTTT
* * *
1751 TCTTGCCAATGAATGCTTTTTTCTATATGTTTCTAAAGGTAG
130 TCTTGCCAATGAATGCCTTTTTCTTTATGTTTCTCAAGGTAG
* * * * * * * * * *
1793 GCATTCAATTCTAGTCTGTTTTAATCAAAAATGATAGAAGAGTTCAAATTTAAATCGATTTTGAG
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATG-TAAAACAATTCAACTTAAAATCAATTATGAG
** * * * *
1858 ATTGCAAAACCATTTAAA-CTGAGTAATGAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTT
65 ATTATAAAACCATTTAAAGC-GAGTAATAAGGCTTTTGAAGGTATGAGTGACTATAAATGGACTT
* * * *
1922 TTCTTGCGAATGAATGCCTTTTTCTTCATGTTTCTCGAGCTAG
129 TTCTTGCCAATGAATGCCTTTTTCTTTATGTTTCTCAAGGTAG
* * * * *
1965 ACATTCAGTTATATTATGTTTTAACAAAAAATGTAAAACAATTTGAACTTAAAATCAATCT-TGA
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACAA-TTCAACTTAAAATCAAT-TATGA
* * * ** * *
2029 -ACTTATAAAATCATTTAAAGTGAGTAATAAGGCTATTGAAGCAATGAGTGACTGTAAATAGACT
64 GA-TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGAGTGACTATAAATGGACT
* * ** * * *
2093 TTTCTTGCCAATGATTGCCCTTTTCTTTACATTTCTAAAAGTTG
128 TTTCTTGCCAATGAATGCCTTTTTCTTTATGTTTCTCAAGGTAG
* * * *
2137 ACATTCAATTCTAATTTGTTTTAACCAAAAATGTAAAACAAATCAACTTAAAATCAATTATG-GC
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACTTAAAATCAATTATGAG-
* * * * *
2201 AATATAAAACCACTAAAAGCAAGTAATAAGGCTTTTTGAAGGTATGAGTGACTATAAATGGGCTT
65 ATTATAAAACCATTTAAAGCGAGTAATAAGGC-TTTTGAAGGTATGAGTGACTATAAATGGACTT
2266 TTCTTGCCAATGAATGCCTTTTTCTTTATGTTTCTCAAGGTAG
129 TTCTTGCCAATGAATGCCTTTTTCTTTATGTTTCTCAAGGTAG
* ** * *
2309 ACATTCAATTTTAGTCT-ACTTAGCCACAAATGTAAAACAATTCAACTTAAAATCAATTATG-GC
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACTTAAAATCAATTATGAG-
* * * * *
2372 AATATAAAACCACTTAAAGCAAGTAATAAGGCTTTTTCAAGATATGAGTGACTATAAATGGACTT
65 ATTATAAAACCATTTAAAGCGAGTAATAAGGC-TTTTGAAGGTATGAGTGACTATAAATGGACTT
* * * * * *
2437 TTCTTGCTAATCAATGCTTTTTTCTTCACGTTTCTTAAGGTAG
129 TTCTTGCCAATGAATGCCTTTTTCTTTATGTTTCTCAAGGTAG
* * * * * *
2480 ACATTCAATTCTAGTCTGTTTTAACTAAAACTGTAAAACAATTCAACTCAAAATCAATTATTAGT
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACTTAAAATCAATTATGAGA
* * *
2545 TTATAAAACCATTTAAAGCAAGAAATAAGGCTTTCGAAGGCT-TGAGTGACTATAAATGGACTTT
66 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGG-TATGAGTGACTATAAATGGACTTT
** ** * * * * * *
2609 T-TGTGCCAATGGTTGGATTTTGCTTTACGTTCCCCATGGCAGG
130 TCT-TGCCAATGAATGCCTTTTTCTTTATGTTTCTCAAGGTA-G
* * * * *
2652 A-ACTCAATTATAGCCTTTTTTAACCAAAAATGTAAAACAATTCAACATAAAATCAATTTTGAGA
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACTTAAAATCAATTATGAGA
* * **
2716 TTATAAAGCTATTTAACATG-G-GTAATAAGGCTTTTGAAGGCT-TGAGCAACTATAAATGGACT
66 TTATAAAACCATTTAA-A-GCGAGTAATAAGGCTTTTGAAGG-TATGAGTGACTATAAATGGACT
* * * *
2778 TTTCTTGCCAATGAGTGCTTTTTTCTTCATGTTTGC-CAAGGTAA
128 TTTCTTGCCAATGAATGCCTTTTTCTTTATGTTT-CTCAAGGTAG
* ** * ** * *
2822 ACATTCAATTATAATGAGTTCTAATAAAAAATGTAAAAAAATTCAA-TCTAAAATCAATTATGTG
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACT-TAAAATCAATTATGAG
*
2886 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGA
65 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGA
Statistics
Matches: 1222, Mismatches: 224, Indels: 59
0.81 0.15 0.04
Matches are distributed among these distances:
169 1 0.00
170 6 0.00
171 615 0.50
172 553 0.45
173 15 0.01
174 31 0.03
175 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (171 bp):
ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACTTAAAATCAATTATGAGA
TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGAGTGACTATAAATGGACTTTT
CTTGCCAATGAATGCCTTTTTCTTTATGTTTCTCAAGGTAG
Found at i:1955 original size:343 final size:342
Alignment explanation
Indices: 1276--2921 Score: 1688
Period size: 343 Copynumber: 4.8 Consensus size: 342
1266 NNNNNGGAAT
* * **
1276 ACATTCAATTATAGTCTGTTTTAACCTAAAATGTAAAAAAAAATTCAATCTTAAAATCAATCCTG
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGT--AAAACAATTCAA-CTTAAAATCAATTATG
* * * * * *
1341 GCATTACAAAACTATTTAAAGCAAGTAATAAAGCTTTTGAAGGTATGGGTGGCTATAAATAGACT
63 GCATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGAGTGACTATAAATAGACT
** * * * * * *
1406 TTTCTTGGAAATTAATGCTTTTTTCTTCTTTTTTCTCAAGGTAGGCATTCAATTATAGTCTGTTT
128 TTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTAAAGGTAGACATTCAATTCTAGTCTGTTT
* * * * * *
1471 TAACCAAAAATGATAGAAGAATTCAAATTTAAATCAATTTTGAGATTACAAAGCCATTTAAAGTG
193 TAACCAAAAATG-TAAAACAATTCAAATTAAAATCAATTTTGAGATTATAAAACCATTTAAACTG
* * * * * *
1536 AGTAATAATGCCTTTAAAAGAATGGGTGACTATAAATTGACTTTTTTTGCCAATGAATGCCTTTT
257 AGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTT
1601 TCTTTATGTTTCTCAAGGTAG
322 TCTTTATGTTTCTCAAGGTAG
* *
1622 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAA-ATATTTAACTTAAAATCAATTATGCC
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACA-ATTCAACTTAAAATCAATTATGGC
* *
1686 ATTATAAAACCATTTAAAGCGAGTAATGAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTT
65 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGAGTGACTATAAATAGACTTT
*
1751 TCTTGCCAATGAATGCTTTTTTCTAT-ATGTTTCTAAAGGTAGGCATTCAATTCTAGTCTGTTTT
130 TCTTGCCAATGAATGCTTTTTTCT-TCATGTTTCTAAAGGTAGACATTCAATTCTAGTCTGTTTT
* * * * * * **
1815 AATCAAAAATGATAGAAGAGTTCAAATTTAAATCGATTTTGAGATTGCAAAACCATTTAAACTGA
194 AACCAAAAATG-TAAAACAATTCAAATTAAAATCAATTTTGAGATTATAAAACCATTTAAACTGA
* * *
1880 GTAATGAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCGAATGAATGCCTTTTT
258 GTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTT
* * *
1945 CTTCATGTTTCTCGAGCTAG
323 CTTTATGTTTCTCAAGGTAG
* * * * *
1965 ACATTCAGTTATATTATGTTTTAACAAAAAATGTAAAACAATTTGAACTTAAAATCAATCT-T-G
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACAA-TTCAACTTAAAATCAAT-TATGG
* * * * ** *
2028 AACTTATAAAATCATTTAAAGTGAGTAATAAGGCTATTGAAGCAATGAGTGACTGTAAATAGACT
64 CA-TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGAGTGACTATAAATAGACT
* ** * ** * * * *
2093 TTTCTTGCCAATGATTGCCCTTTTCTTTACATTTCTAAAAGTTGACATTCAATTCTAATTTGTTT
128 TTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTAAAGGTAGACATTCAATTCTAGTCTGTTT
* * * * * *
2158 TAACCAAAAATGTAAAACAAATCAACTTAAAATCAATTATG-GCAATATAAAACCACTAAAAGC-
193 TAACCAAAAATGTAAAACAATTCAAATTAAAATCAATTTTGAG-ATTATAAAACCATTTAAA-CT
* * * *
2221 AAGTAATAAGGCTTTTTGAAGGTATGAGTGACTATAAATGGGCTTTTCTTGCCAATGAATGCCTT
256 GAGTAATAAGGC-TTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTT
2286 TTTCTTTATGTTTCTCAAGGTAG
320 TTTCTTTATGTTTCTCAAGGTAG
* ** * *
2309 ACATTCAATTTTAGTCT-ACTTAGCCACAAATGTAAAACAATTCAACTTAAAATCAATTATGGCA
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACTTAAAATCAATTATGGCA
* * * * * *
2373 ATATAAAACCACTTAAAGCAAGTAATAAGGCTTTTTCAAGATATGAGTGACTATAAATGGACTTT
66 TTATAAAACCATTTAAAGCGAGTAATAAGGC-TTTTGAAGGTATGAGTGACTATAAATAGACTTT
* * * *
2438 TCTTGCTAATCAATGCTTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTCTAGTCTGTTTTA
130 TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTAAAGGTAGACATTCAATTCTAGTCTGTTTTA
* * * * * *
2503 ACTAAAACTGTAAAACAATTCAACTCAAAATCAATTATT-AGTTTATAAAACCATTTAAAGC-AA
195 ACCAAAAATGTAAAACAATTCAAATTAAAATCAATT-TTGAGATTATAAAACCATTTAAA-CTGA
* ** ** ** **
2566 GAAATAAGGCTTTCGAAGGCTTGAGTGACTATAAATGGACTTTT-TGTGCCAATGGTTGGATTTT
258 GTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCT-TGCCAATGAATGCCTTTT
* * * * * *
2630 GCTTTACGTTCCCCATGGCAGG
322 TCTTTATGTTTCTCAAGGTA-G
* * * * *
2652 A-ACTCAATTATAGCCTTTTTTAACCAAAAATGTAAAACAATTCAACATAAAATCAATTTTGAG-
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACTTAAAATCAATTATG-GC
* * ** *
2715 ATTATAAAGCTATTTAACATG-G-GTAATAAGGCTTTTGAAGGCT-TGAGCAACTATAAATGGAC
65 ATTATAAAACCATTTAA-A-GCGAGTAATAAGGCTTTTGAAGG-TATGAGTGACTATAAATAGAC
* * * * * **
2777 TTTTCTTGCCAATGAGTGCTTTTTTCTTCATGTTTGC-CAAGGTAAACATTCAATTATAATGAGT
127 TTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTT-CTAAAGGTAGACATTCAATTCTAGTCTGT
* ** * * * *
2841 TCTAATAAAAAATGTAAAAAAATTC-AATCTAAAATCAATTATGTGATTATAAAACCATTTAAAG
191 TTTAACCAAAAATGTAAAACAATTCAAAT-TAAAATCAATTTTGAGATTATAAAACCATTTAAAC
2905 TGAGTAATAAGGCTTTT
255 TGAGTAATAAGGCTTTT
2922 GA
Statistics
Matches: 1091, Mismatches: 183, Indels: 56
0.82 0.14 0.04
Matches are distributed among these distances:
341 5 0.00
342 251 0.23
343 569 0.52
344 231 0.21
345 2 0.00
346 33 0.03
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (342 bp):
ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACTTAAAATCAATTATGGCA
TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGAGTGACTATAAATAGACTTTT
CTTGCCAATGAATGCTTTTTTCTTCATGTTTCTAAAGGTAGACATTCAATTCTAGTCTGTTTTAA
CCAAAAATGTAAAACAATTCAAATTAAAATCAATTTTGAGATTATAAAACCATTTAAACTGAGTA
ATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTT
TATGTTTCTCAAGGTAG
Found at i:2041 original size:20 final size:17
Alignment explanation
Indices: 1998--2033 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1988 ACAAAAAATG
1998 TAAAA-CAATTTGAACT
1 TAAAATCAATTTGAACT
2014 TAAAATCAATCTTGAACT
1 TAAAATCAAT-TTGAACT
2032 TA
1 TA
2034 TAAAATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 4 0.22
18 9 0.50
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (17 bp):
TAAAATCAATTTGAACT
Done.