Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400425.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3622.0, 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: 11233
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.24
Warning! 3562 characters in sequence are not A, C, G, or T
Found at i:722 original size:18 final size:18
Alignment explanation
Indices: 674--722 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
664 GTCAAAAATG
674 TAAAACAATTT-AACTTA
1 TAAAACAATTTAAACTTA
*
691 -AAATCAATTATAAACTTA
1 TAAAACAATT-TAAACTTA
*
709 TAAAACCATTTAAA
1 TAAAACAATTTAAA
723 GCGAGTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 8 0.31
17 1 0.04
18 10 0.38
19 7 0.27
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAACAATTTAAACTTA
Found at i:886 original size:171 final size:170
Alignment explanation
Indices: 541--870 Score: 380
Period size: 171 Copynumber: 1.9 Consensus size: 170
531 NNNNNNNNNN
* * * * * *
541 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATTAGTGACTATAAATAGAATTTTCTTGCT
1 AACCATTTAAAGCGAGTAATAAAGCTTCTGAACGAATGAGTGACCATAAATAGAATTTTCTTGCT
* * ** * *
606 AATGAATGTCTTTTTTTCCTTGTTTCTCGAGGTAAACATTCAATTATAGTCTAATTTAGTCAAAA
66 AATGAATGCCTTTTTTT-CATGTTTCTCGAGGTAAACATTCAACAATAATCTAATTTACTCAAAA
* *
671 ATGTAAAACAATTTAACTTAAAATCAATTATAAACTTATAA
130 ATGTAAAAAAATATAACTTAAAATCAATTATAAACTTATAA
* *
712 AACCATTTAAAGCGAGTAATAAAGCTTCTGAACGAATGGGTGACCATAAAT-GGATATTTCTTGG
1 AACCATTTAAAGCGAGTAATAAAGCTTCTGAACGAATGAGTGACCATAAATAGAAT-TTTCTT-G
* * * **
776 C-AATGAATGCCTTGTTCTTT-ATGTTTCTTGAGGTAGATATTCAACAATAATCTGTTTTAACT-
64 CTAATGAATGCCTT-TT-TTTCATGTTTCTCGAGGTAAACATTCAACAATAATCTAATTT-ACTC
*
838 AAAAATGTAAAAAAATATAGCTTAAAATCAATT
126 AAAAATGTAAAAAAATATAACTTAAAATCAATT
871 TTGAGATTAT
Statistics
Matches: 132, Mismatches: 22, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
170 3 0.02
171 120 0.91
172 6 0.05
173 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
AACCATTTAAAGCGAGTAATAAAGCTTCTGAACGAATGAGTGACCATAAATAGAATTTTCTTGCT
AATGAATGCCTTTTTTTCATGTTTCTCGAGGTAAACATTCAACAATAATCTAATTTACTCAAAAA
TGTAAAAAAATATAACTTAAAATCAATTATAAACTTATAA
Found at i:924 original size:171 final size:159
Alignment explanation
Indices: 729--1056 Score: 295
Period size: 171 Copynumber: 2.0 Consensus size: 159
719 TAAAGCGAGT
* *
729 AATAAAGCTTCTGAACGAATGGGTGACCATAAATGGA-TATTTC-TTGGCAATGAATGCCTTGTT
1 AATAAAGCTTCTGAACGAATGGGTGACCATAAATGGACT-TTTCATT-CCAATAAATGCCTTGTT
* ** * **
792 CTT-TATGTTTCTTGAGGTAGATATTCAACAATAATCTGTTTTAACTAAAAATGTAAAAAAAT-A
64 CTTCT-CGTTTCTCAAGGTAGACATTCAACAATAATCTGTTTTAAC-AAAAAAATAAAAAAATCA
*
855 TAGCTTAAAATCAATTTTGAGATTATAAAACCNNNNNNNNNNAGC
127 -A-CTTAAAATCAAATTTGAGATTATAAAACC----------AGC
* * * * ** * *
900 AATAAGGCTTTTGAATGTATGGGTGACTGTAAATGGACTTTTCATTCCAATAAATGTCTTTTTCT
1 AATAAAGCTTCTGAACGAATGGGTGACCATAAATGGACTTTTCATTCCAATAAATGCCTTGTTCT
** *
965 TCTCGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACAAAAAAATAAGAAAATCAACTT
66 TCTCGTTTCTCAAGGTAGACATTCAACAATAATCTGTTTTAACAAAAAAATAAAAAAATCAACTT
*
1030 AAAATCAAATTTGATATTATAAAACCA
131 AAAATCAAATTTGAGATTATAAAACCA
1057 TTTAAAGTGN
Statistics
Matches: 132, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
159 1 0.01
169 27 0.20
170 14 0.11
171 86 0.65
172 4 0.03
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Consensus pattern (159 bp):
AATAAAGCTTCTGAACGAATGGGTGACCATAAATGGACTTTTCATTCCAATAAATGCCTTGTTCT
TCTCGTTTCTCAAGGTAGACATTCAACAATAATCTGTTTTAACAAAAAAATAAAAAAATCAACTT
AAAATCAAATTTGAGATTATAAAACCAGC
Found at i:3262 original size:170 final size:170
Alignment explanation
Indices: 2965--3400 Score: 423
Period size: 170 Copynumber: 2.6 Consensus size: 170
2955 NNNNNNNNNN
* * * *
2965 ATTATGAGATTATAAAAGCATTCATAGCGAGTAATAAGGCTTTTGAA-GAAATAGGAGACCATAA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT-AATGGAATAGGAGACCATAA
* * ********** * *
3029 ATGGACTTTTCTTCCTAATTAATGGTTTTTTCTACACATNNNNNNNNNNAGACATTCAATTATAG
65 ATGGACTTTTCTTCC-AATGAATGGCTTTTTCTACACATTTCCCTAGCAAGACACTAAATTATAG
** *
3094 TCTACTTTAACAAAAAATAT-AAAAAAATTCAAC-TTTAATTA
129 TCTACTTTAACAAAAAAT-TGAAAAAAATTCAACATAAAATCA
* * *
3135 ATTATGAGATTATAATACCATTTAAAGCGAGTAATAAGGCTTTTAATGGAATAAGAGACCATAGA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAATGGAATAGGAGACCATAAA
** *
3200 TGGACTTTTCTTCCAAATGAATGGCTTTTTCTACATGTTTCCCTAGCAAGGCACTAAATTATAGT
66 TGGACTTTTCTTCC-AATGAATGGCTTTTTCTACACATTTCCCTAGCAAGACACTAAATTATAGT
** * *
3265 CTGTTTTGATAAAAAATTGGAAAAAAATTCAACATAAAATCA
130 CTACTTTAACAAAAAATT-GAAAAAAATTCAACATAAAATCA
* ** * * **
3307 ATTATGAGATTACAAAACCATTTAAAATGAGTAATGAGGTTTTTAATGGAAT-GGATGATTATAA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAATGGAATAGGA-GACCATAA
*
3371 ATAGACTTTTCTTGCCAATGAAT-GCTTTTT
65 ATGGACTTTTCTT-CCAATGAATGGCTTTTT
3401 TCTTCCTATT
Statistics
Matches: 217, Mismatches: 43, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
169 3 0.01
170 115 0.53
171 22 0.10
172 75 0.35
173 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.34
Consensus pattern (170 bp):
ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAATGGAATAGGAGACCATAAA
TGGACTTTTCTTCCAATGAATGGCTTTTTCTACACATTTCCCTAGCAAGACACTAAATTATAGTC
TACTTTAACAAAAAATTGAAAAAAATTCAACATAAAATCA
Found at i:4622 original size:171 final size:171
Alignment explanation
Indices: 4299--6852 Score: 1948
Period size: 171 Copynumber: 14.9 Consensus size: 171
4289 NNNNNNNNNN
* * * * * **
4299 TGAAGGAATAGGAGACCATAAATGGACTTTTCTTCCTAATTAATGGC-TTTTTCACACATTTGCT
1 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTCCTAATGAATGCCTTTTTTTTCACATTT-CT
* * * * * *
4363 -AAGATAGACATTTAATTATAATCTGTTTTAACTAAAAATAGAAAAAAAGTTGAACTTAAAATCA
65 CGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAAAA-TTCAACTTAAAATCA
* * * *
4427 ATTTTGACATAATAAAATCATTTAAAGTGAGTAATAAGGCTTT
129 ATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* ** * * * * *
4470 TGAAGGCATGGAAGACTAGAGATGGACTTTTTTTCCAAATGAATGGCTTTTTTTTCACATTTC-C
1 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTCCTAATGAATGCCTTTTTTTTCACATTTCTC
* * * * * * ** *
4534 TAAGGAAAACATTAAATTATAGTCTGTTTTGAGGAAAAATATAAAAACATTCAACTTAAAATCAA
66 -GAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAA
* * * * *
4599 TTATGAGATTACAAAACCATTTAAAACAAGTAATAAGGTTTT
130 TTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * *
4641 TAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCC-AATGAATGCC-CTTTCTTCATATTTCT
1 TGAAGGAATGGGTGACTATAAATGGACTTTTCTT-CCTAATGAATGCCTTTTTTTTCACATTTCT
* * * *
4704 CGAGGTAGACAATCAATTATAATCTGTTTTAACCAAAACTGTATAAAGAATTCAACTTAAAATCA
65 CGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATA-AAAAAATTCAACTTAAAATCA
* ** * *
4769 ATTTTCAGATTATAAAATTATTTAAAGTGAGTAATAAGGCTTC
129 ATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * *
4812 TGAAGGAATGGGTGACTATAAATGGAATTTTCTTGCTAATGAATGCCTTTTTTCT-ACGTTTCTC
1 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTCCTAATGAATGCCTTTTTTTTCACATTTCTC
* * * * *
4876 GAGGTAGACATTCAATTATAGTCTGTTTTAGCTAAAAATTTAATAAAATTCAACTTAAAATCAAT
66 GAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAAT
* * * *
4941 TATGAAATTATAGAACCATTTAAAGCGAGTAATACGGCTTT
131 TTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * * * * **
4982 TGAAGGAATGGCTGAGTATAAAAGAACATTTTATGCC-AATGAATGCCTTTTTCTTT-ATGTTTC
1 TGAAGGAATGGGTGACTATAAATGGAC-TTTTCTTCCTAATGAATGCCTTTTT-TTTCACATTTC
* * ** ** *
5045 TTGAGGCAGACATTCAAAAATAATCTGTTTTAAATAAAAATGTAAAAAAAAATTCAACTTAAAAT
64 TCGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAA--TATAAAAAAATTCAACTTAAAAT
* * * * *
5110 CAATTATGAGATTACAAAACCATTTAAAACGACTAATAAGGTTTT
127 CAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * * **
5155 TAAAGGAATGGATGACTATAAATAGACTTTTCTTACC-AATGAATGCCTTTTTCTTCATGTTTCT
1 TGAAGGAATGGGTGACTATAAATGGACTTTTCTT-CCTAATGAATGCCTTTTTTTTCACATTTCT
* * * * * * *
5219 TGAGGTAGACATTAAATTATAATATGTTTTAATCAAAACTATACAAAGAATTCAACTTAAAATTA
65 CGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATA-AAAAAATTCAACTTAAAATCA
* * * *
5284 ATTTTGACATTATAAAACCATTTAAAGTGAGCAATAAAGCTTT
129 ATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * *
5327 TGAAGGAATGGGTGACTATAAATGGAATTTTCTTGCTAATGAATGCCTTTTTTTCCACGTTTCTC
1 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTCCTAATGAATGCCTTTTTTTTCACATTTCTC
* * * * * *
5392 GAGGTAGATATTCAATGATAGTCTGTTTTAGCCAAAAATGTAAAAAAATTTAACTTAAAATCAAT
66 GAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAAT
* * * * *
5457 TATGAAATTATAAAACAATTTAGAGCGAGTAAAAAGGCTTT
131 TTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * *
5498 TGAAGGAATGGGTGACTATAAATAGACATTTCATTCC-AATGAATGCCTTTTTCATT-ACGTTTC
1 TGAAGGAATGGGTGACTATAAATGGACTTTTC-TTCCTAATGAATGCCTTTTT-TTTCACATTTC
* * * ** * * * * *
5561 TCAAGGCAAACATTCAACAATAATCAGTTTTAACCAAAAATGTAAAAAAATTTAATTTAAAATCG
64 TCGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCA
* *
5626 ATTTTCGA-ATTATAAAACCATTTCATGCGAGTAATAAGGCTTT
129 ATTTT-GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * * * * * *
5669 TGAAGGTATGGGTGACTGTAAATGGAATTTTCTTGCTGATAAATGCCTTTTTCTTCTCATTTCTC
1 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTCCTAATGAATGCCTTTTTTTTCACATTTCTC
* * * *
5734 GAGGTAGACATTCAATTATAATATGTTTTAACAAAAAATGTAAAAAAAATT----TTAAAATCAG
66 GAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATAT-AAAAAAATTCAACTTAAAATCAA
*
5795 TTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
130 TTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * ** * * *
5837 TAAAGGAATGAGTGACTATAAATGGA-TATTTATTGTTAATGAATGCCTTCTTCTTCATATTTCT
1 TGAAGGAATGGGTGACTATAAATGGACT-TTTCTTCCTAATGAATGCCTTTTTTTTCACATTTCT
* * * * * * * * * * * *
5901 CGAGGAATACATTAAATTACAATATTTTTTAACCAAAACTTTTAAAAAACT-ATATTTAGAATCA
65 CGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCA-ACTTAAAATCA
* *
5965 ATTTTGAGATTATAAAACCATTTAAAGCAAGTAATAAGGTTTT
129 ATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * * * **
6008 TGACGTAAT-GGTAGGCTATAAATGGACTTTTTTTCCAAATGAATAG--TTTTTTCTAT-ATGTT
1 TGAAGGAATGGGT-GACTATAAATGGACTTTTCTTCCTAATGAAT-GCCTTTTTT-T-TCACATT
* ** * * ** * *
6069 TCTTGAGACAGGCATTCAATAATAGCCTGTTTTAACAAAAAATATAAAAAAATTCTACTTAAAAT
62 TCTCGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAAT
* * *
6134 CAATTATGAGATTATAAAAGCATTCATAA-CGAGTAATAAGGCTTT
127 CAATTTTGAGATTATAAAACCATTTA-AAGCGAGTAATAAGGCTTT
* ** * * * * * *
6179 TAAAGGAATAAGAGACCATAAATGGACTTTTCTTCCTAATTAATAG-CTTTTTCTACAC-TTTTT
1 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTCCTAATGAAT-GCCTTTTTTTTCACATTTCT
* ** ** * * *
6242 CCAAGCCA-AGCATTCAATTATAATAGGTTTTAACAAAAAATAGAAAAAAAATTAAACTTAAAAT
65 -CGAGGTAGA-CATTCAATTATAATCTGTTTTAACCAAAAATA-TAAAAAAATTCAACTTAAAAT
* * * * *
6306 TAATTTTGACATAATATAACCATTTAAAGTGAGTAATAAGGCTTT
127 CAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * * * * * **
6351 TGAAGGAATTGATGATTATAAATAGACTTTTGTTGCC-AATGAATG--TAATTTTTTAATGTTTC
1 TGAAGGAATGGGTGACTATAAATGGACTTTTCTT-CCTAATGAATGCCT-TTTTTTTCACATTTC
* * ** ** *
6413 TCAAGGTAGACATTCAATTATAGTCTACTTTAATGAAAAATATAAAAAAATTCAACTT-AAATTA
64 TCGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCA
* **********
6477 ATTATGAGATTATANNNNNNNNNNAAGCGAGTAATAAGGCTTT
129 ATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * ** * * * *
6520 TGAAGGAATGGGAGACTATAGATGGACTTTTCTTCCAAATGAATTACTTTTTCTACATATTTCCC
1 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTCCTAATGAATGCCTTTTTTTTCACATTTCTC
* * * * * * * ** ** ***
6585 AAGGAAGGCATTAAATTATAGTCTATTTTGATAAAAAATGCAAAAAAATTCAACTTAAAATCNNN
66 GAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAAT
******* * ** **
6650 NNNNNNNTTACAAAACCATTTAAAATGAGTAATAAGATTTT
131 TTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * ********** * * ** *
6691 TAAAGGAATGGATGAATATAAANNNNNNNNNNTTACC-AATGAATGCATTTTTCTTCATGTTTGT
1 TGAAGGAATGGGTGACTATAAATGGACTTTTCTT-CCTAATGAATGCCTTTTTTTTCACATTTCT
* * * * * * *
6755 TGAGGTAAATATTCAATTATAATATGTTTTAACCAAAACTATACAAAGAATTGAACTTAAAATCA
65 CGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATA-AAAAAATTCAACTTAAAATCA
*
6820 ATTTTGAGATTATAAAACCATTTAAAGTGAGTA
129 ATTTTGAGATTATAAAACCATTTAAAGCGAGTA
6853 NNNNNNNNNN
Statistics
Matches: 1871, Mismatches: 460, Indels: 103
0.77 0.19 0.04
Matches are distributed among these distances:
167 10 0.01
168 131 0.07
169 69 0.04
170 223 0.12
171 942 0.50
172 359 0.19
173 137 0.07
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (171 bp):
TGAAGGAATGGGTGACTATAAATGGACTTTTCTTCCTAATGAATGCCTTTTTTTTCACATTTCTC
GAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAAT
TTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
Found at i:6029 original size:510 final size:506
Alignment explanation
Indices: 4299--6852 Score: 2106
Period size: 512 Copynumber: 5.0 Consensus size: 506
4289 NNNNNNNNNN
* * * * * * * *
4299 TGAAGGAAT-AGGAGACCATAAATGGACTTTTCTTCCTAATTAATGGCTTTTTCACACATTTGCT
1 TGAAGGAATGA-GTGACTATAAATGGAATTTTCTTGCTAATGAATGCCTTTTT-TCATATTT-CT
* * * * * * **
4363 -AAGATAGACATTTAATTATAATCTGTTTTAACTAAAAATAGAAAAAAAGT-TGAACTTAAAATC
63 CGAGGTAGACATTCAATTATAGTCTGTTTTAGCCAAAAATTTAAAAAAA-TAT--ACTTAAAATC
* * * * * * * * * *
4426 AATTTTGACATAATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCATGGAAGACTAGAG
125 AATTATGAAATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGG-TGGCTATAA
* * * * ** * * * * *
4491 ATGGAC-TTTTTTTCCAAATGAATGGCTTTTTTTTCACATTTCCTAAGGAAAACATT-AAATTAT
189 ATAGACATTTTATTCC-AATGAATGCCTTTTTCTT-ATGTTTCTTGAGGCAGACATTCAAA-AAT
* * ** *
4554 AGTCTGTTTTGAGGAAAAATATAAAAACATTCAACTTAAAATCAATTATGAGATTACAAAACCAT
251 AATCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAACCAT
* *
4619 TTAAAACAAGTAATAAGGTTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAA
316 TTAAAACGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAA
* * * * * *
4684 TGCC-CTTTCTTCATATTTCTCGAGGTAGACAATCAATTATAATCTGTTTTAACCAAAACTGTAT
381 TGCCTTTTTCTTCATATTTCTCGAGGTAGACATTCAATTATAATATGTTTTAACAAAAAATGTAA
* * * ** *
4748 AAAGAATTCAACTTAAAATCAATTTTCAGATTATAAAATTATTTAAAGTGAGTAATAAGGCTTC
446 AAAAAATT--A-TTAAAATCAATTTTGACATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
*
4812 TGAAGGAATGGGTGACTATAAATGGAATTTTCTTGCTAATGAATGCCTTTTTTC-TACGTTTCTC
1 TGAAGGAATGAGTGACTATAAATGGAATTTTCTTGCTAATGAATGCCTTTTTTCATA--TTTCTC
* *
4876 GAGGTAGACATTCAATTATAGTCTGTTTTAGCTAAAAATTTAATAAAAT-TCAACTTAAAATCAA
64 GAGGTAGACATTCAATTATAGTCTGTTTTAGCCAAAAATTTAAAAAAATAT--ACTTAAAATCAA
* *
4940 TTATGAAATTATAGAACCATTTAAAGCGAGTAATACGGCTTTTGAAGGAATGGCTGAG-TATAAA
127 TTATGAAATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGG-TG-GCTATAAA
*
5004 -AGAACATTTTATGCCAATGAATGCCTTTTTCTTTATGTTTCTTGAGGCAGACATTCAAAAATAA
190 TAG-ACATTTTATTCCAATGAATGCCTTTTTC-TTATGTTTCTTGAGGCAGACATTCAAAAATAA
*
5068 TCTGTTTTAA-ATAAAAATGTAAAAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAACCA
253 TCTGTTTTAACA-AAAAA--TATAAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAACCA
* * * * *
5132 TTTAAAACGACTAATAAGGTTTTTAAAGGAATGGATGACTATAAATAGACTTTTCTTACCAATGA
315 TTTAAAACGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGA
* * * * *
5197 ATGCCTTTTTCTTCATGTTTCTTGAGGTAGACATTAAATTATAATATGTTTTAATC-AAAACTAT
380 ATGCCTTTTTCTTCATATTTCTCGAGGTAGACATTCAATTATAATATGTTTTAA-CAAAAAATGT
* * * * *
5261 ACAAAGAATTCAACTTAAAATTAATTTTGACATTATAAAACCATTTAAAGTGAGCAATAAAGCTT
444 AAAAAAAATT--A-TTAAAATCAATTTTGACATTATAAAACCATTTAAAGTGAGTAATAAGGCTT
5326 T
506 T
* **
5327 TGAAGGAATGGGTGACTATAAATGGAATTTTCTTGCTAATGAATGCCTTTTTTTCCACGTTTCTC
1 TGAAGGAATGAGTGACTATAAATGGAATTTTCTTGCTAATGAATGCC-TTTTTT-CATATTTCTC
* * * *
5392 GAGGTAGATATTCAATGATAGTCTGTTTTAGCCAAAAATGTAAAAAAATTTAACTTAAAATCAAT
64 GAGGTAGACATTCAATTATAGTCTGTTTTAGCCAAAAATTTAAAAAAATAT-ACTTAAAATCAAT
* * * *
5457 TATGAAATTATAAAACAATTTAGAGCGAGTAAAAAGGCTTTTGAAGGAATGGGTGACTATAAATA
128 TATGAAATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGTGGCTATAAATA
* * ** * * *
5522 GACATTTCATTCCAATGAATGCCTTTTTCATTACGTTTCTCAAGGCAAACATTCAACAATAATCA
192 GACATTTTATTCCAATGAATGCCTTTTTC-TTATGTTTCTTGAGGCAGACATTCAAAAATAATCT
* * * * * * * *
5587 GTTTTAACCAAAAATGTAAAAAAATTTAATTTAAAATCGATTTTCGA-ATTATAAAACCATTTCA
256 GTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTAT-GAGATTACAAAACCATTTAA
** * * * * ** *
5651 TGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTGTAAATGGAATTTTCTTGCTGATAAATGCC
320 AACGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCC
5716 TTTTTCTTC-TCATTTCTCGAGGTAGACATTCAATTATAATATGTTTTAACAAAAAATGTAAAAA
385 TTTTTCTTCAT-ATTTCTCGAGGTAGACATTCAATTATAATATGTTTTAACAAAAAATGTAAAAA
* *
5780 AAATT-TTAAAATCAGTTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
449 AAATTATTAAAATCAATTTTGACATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
* * *
5837 TAAAGGAATGAGTGACTATAAATGG-ATATTTATTGTTAATGAATGCCTTCTTCTTCATATTTCT
1 TGAAGGAATGAGTGACTATAAATGGAAT-TTTCTTGCTAATGAATGCCTT-TT-TTCATATTTCT
* * * * * * * * * * * *
5901 CGAGGAATACATTAAATTACAATATTTTTTAACCAAAACTTTTAAAAAACTATATTTAGAATCAA
63 CGAGGTAGACATTCAATTATAGTCTGTTTTAGCCAAAA-ATTTAAAAAAATATACTTAAAATCAA
* * * * * *
5966 TTTTGAGATTATAAAACCATTTAAAGCAAGTAATAAGGTTTTTGACGTAATGGTAGGCTATAAAT
127 TTATGAAATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGT-GGCTATAAAT
* * * * * * *
6031 GGAC-TTTTTTTCCAAATGAATAG-TTTTTTCTATATGTTTCTTGAGACAGGCATTCAATAATAG
191 AGACATTTTATTCC-AATGAAT-GCCTTTTTCT-TATGTTTCTTGAGGCAGACATTCAAAAATAA
* * * * *
6094 CCTGTTTTAACAAAAAATATAAAAAAATTCTACTTAAAATCAATTATGAGATTATAAAAGCATTC
253 TCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAACCATTT
* ** * * *
6159 ATAACGAGTAATAAGGCTTTTAAAGGAATAAGAGACCATAAATGGACTTTTCTT-CCTAATTAAT
318 AAAACGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCC-AATGAAT
* * * ** *
6223 AG-CTTTTTCTACACTTTTTC-CAAGCCA-AGCATTCAATTATAATAGGTTTTAACAAAAAATAG
382 -GCCTTTTTCTTCA-TATTTCTCGAGGTAGA-CATTCAATTATAATATGTTTTAACAAAAAAT-G
* * *
6285 -AAAAAAAATTAAACTTAAAATTAATTTTGACATAATATAACCATTTAAAGTGAGTAATAAGGCT
443 TAAAAAAAATT--A-TTAAAATCAATTTTGACATTATAAAACCATTTAAAGTGAGTAATAAGGCT
6349 TT
505 TT
* * * * * ** * *
6351 TGAAGGAATTGA-TGATTATAAATAGACTTTTGTTGCCAATGAATGTAATTTTTTAATGTTTCTC
1 TGAAGGAA-TGAGTGACTATAAATGGAATTTTCTTGCTAATGAATG-CCTTTTTTCATATTTCTC
* ** *** * *
6415 AAGGTAGACATTCAATTATAGTCTACTTTAATGAAAAATATAAAAAAAT-TCAACTT-AAATTAA
64 GAGGTAGACATTCAATTATAGTCTGTTTTAGCCAAAAATTTAAAAAAATAT--ACTTAAAATCAA
* ********** *
6478 TTATGAGATTATANNNNNNNNNNAAGCGAGTAATAAGGCTTTTGAAGGAATGG-GAGACTATAGA
127 TTATGAAATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGTG-G-CTATAAA
* * ** * * *** * * *
6542 TGGAC-TTTTCTTCCAAATGAATTACTTTTTCTACATATTTCCCAAGGAAGGCATT-AAATTATA
190 TAGACATTTTATTCC-AATGAATGCCTTTTTCT-TATGTTTCTTGAGGCAGACATTCAAA-AATA
* * * * ** **********
6605 GTCTATTTTGATAAAAAATGCAAAAAAATTCAACTTAAAATCNNNNNNNNNNTTACAAAACCATT
252 ATCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAACCATT
* ** * * ********** *
6670 TAAAATGAGTAATAAGATTTTTAAAGGAATGGATGAATATAAANNNNNNNNNNTTACCAATGAAT
317 TAAAACGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * * * * * * * *
6735 GCATTTTTCTTCATGTTTGTTGAGGTAAATATTCAATTATAATATGTTTTAACCAAAACTATACA
382 GCCTTTTTCTTCATATTTCTCGAGGTAGACATTCAATTATAATATGTTTTAACAAAAAATGTAAA
* *
6800 AAGAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTA
447 AAAAATT--A-TTAAAATCAATTTTGACATTATAAAACCATTTAAAGTGAGTA
6853 NNNNNNNNNN
Statistics
Matches: 1659, Mismatches: 324, Indels: 117
0.79 0.15 0.06
Matches are distributed among these distances:
509 19 0.01
510 376 0.23
511 30 0.02
512 396 0.24
513 143 0.09
514 337 0.20
515 161 0.10
516 191 0.12
517 6 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (506 bp):
TGAAGGAATGAGTGACTATAAATGGAATTTTCTTGCTAATGAATGCCTTTTTTCATATTTCTCGA
GGTAGACATTCAATTATAGTCTGTTTTAGCCAAAAATTTAAAAAAATATACTTAAAATCAATTAT
GAAATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGTGGCTATAAATAGACA
TTTTATTCCAATGAATGCCTTTTTCTTATGTTTCTTGAGGCAGACATTCAAAAATAATCTGTTTT
AACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAACCATTTAAAACGAG
TAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTC
TTCATATTTCTCGAGGTAGACATTCAATTATAATATGTTTTAACAAAAAATGTAAAAAAAATTAT
TAAAATCAATTTTGACATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
Found at i:9308 original size:171 final size:160
Alignment explanation
Indices: 9126--9438 Score: 297
Period size: 171 Copynumber: 1.9 Consensus size: 160
9116 NNNNNNNNNN
* * * * *
9126 ATAAAGCTTTTGAAGGAATGGGTGACTATAAAAGAACATTTCATGCCAATGAATGCCTTTTTCTT
1 ATAAAGCTTTTGAACGAATGAGTAACTATAAAAGAACATTTCATACCAATAAATGCCTTTTTCTT
* * * *
9191 -TATGTTTCTCTAGGTAGACATTCAACGATAATCTGTTTTAATC-AAAATGTAAAAAAAATTCAA
66 CT-CGTTTCTCGAGGTAGACATTCAACGATAATCTATTTTAACCAAAAATGT--AAAAAATTCAA
* *
9254 CTTAAAATTAATTTTNNNNNNNNNNAACCATTTAAAGTGAGTA
128 CTGAAAATCAATTTT----------AACCATTTAAAGTGAGTA
* * * * * * **
9297 ATAAGGCTTTTGAACGTATGAGTAACTGTAAATGGACTTTTGTTACCAATAAATGCCTTTTTCTT
1 ATAAAGCTTTTGAACGAATGAGTAACTATAAAAGAACATTTCATACCAATAAATGCCTTTTTCTT
* **
9362 CTCGTTTCTCGAGGTAGACGTTCAATTATAATCTATTTTAACCAAAAATGTAAAAAATTCAACTG
66 CTCGTTTCTCGAGGTAGACATTCAACGATAATCTATTTTAACCAAAAATGTAAAAAATTCAACTG
9427 AAAATCAATTTT
131 AAAATCAATTTT
9439 GAGATTATAA
Statistics
Matches: 118, Mismatches: 22, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
170 24 0.20
171 86 0.73
172 8 0.07
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.35
Consensus pattern (160 bp):
ATAAAGCTTTTGAACGAATGAGTAACTATAAAAGAACATTTCATACCAATAAATGCCTTTTTCTT
CTCGTTTCTCGAGGTAGACATTCAACGATAATCTATTTTAACCAAAAATGTAAAAAATTCAACTG
AAAATCAATTTTAACCATTTAAAGTGAGTA
Found at i:10790 original size:170 final size:162
Alignment explanation
Indices: 10544--10859 Score: 318
Period size: 170 Copynumber: 1.9 Consensus size: 162
10534 ATTTAGAGTG
* * ** * *
10544 AGTAATAAAGTTTTGGAAGGAATGGGAGGCTATAAATTTACTTTTCTTCCAAATGAATTGCTTTT
1 AGTAATAAAGTTTTGGAAGGAATGGGAGACCATAAATGGACTGTTCTTCCAAATGAATAGCTTTT
* * * * * *
10609 TCTATATGTTTCTCGAG-GCAAGCATTCATTTATAGTCTGTTTTAAC-AAAAA-ATG-TAAAAAA
66 TCTACATGTTTCCCAAGAG-AAGCATTCAATTATAATCTGTTTTAACTAAAAACA-GAAAAAAAA
*
10670 TTCAACTTAAAATCAATTATAAGATTATANNNNNNNNNNTAGCA
129 TTAAACTTAAAATCAATTATAAGATTATA----------TAGCA
* * *
10714 AGTAATAAGGCTTTT-GAAGGAATGGGAGACCATAAATGGACTGTTCTTCCTAATTAATAGCTTT
1 AGTAATAAAG-TTTTGGAAGGAATGGGAGACCATAAATGGACTGTTCTTCCAAATGAATAGCTTT
* *
10778 TTCTACATGTTTCCCAAGAGAGGCATTGAATTATAATCTGTTTTAACTAAAAACAGAAAAAAAAT
65 TTCTACATGTTTCCCAAGAGAAGCATTCAATTATAATCTGTTTTAACTAAAAACAGAAAAAAAAT
10843 TAAACTTAAAATCAATT
130 TAAACTTAAAATCAATT
10860 TTGGCATAAT
Statistics
Matches: 123, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
170 88 0.72
171 11 0.09
172 24 0.20
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (162 bp):
AGTAATAAAGTTTTGGAAGGAATGGGAGACCATAAATGGACTGTTCTTCCAAATGAATAGCTTTT
TCTACATGTTTCCCAAGAGAAGCATTCAATTATAATCTGTTTTAACTAAAAACAGAAAAAAAATT
AAACTTAAAATCAATTATAAGATTATATAGCA
Done.