Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398231.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1535.1, 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: 6710
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.34
Warning! 345 characters in sequence are not A, C, G, or T
Found at i:569 original size:171 final size:172
Alignment explanation
Indices: 1--4294 Score: 3366
Period size: 171 Copynumber: 25.2 Consensus size: 172
* * * * *
1 ATTTAAAGTGAGTAATAAGGCTTTAGAAGGCATGGGTGACTATAAAT-AGGCTTTTCTTGTCAAT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGA-ACTTTTCTTGCCAAT
* * * * * * * *
65 GAATGGT-TTTTTCTTCAGGTTTGT-TTAGGCAGACATTTAACTATAATCTATTTTAACCAAAAG
65 GAAT-GTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAA
* * *
128 TATAAAAAAATTTAAC-T-CAGTCAATTATGAGATTATAAATCC
129 TATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
*
170 ATTTAAAGCGAATAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGGAACTTTT-TTGCCAAT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAAT-GAACTTTTCTTGCCAAT
** * * *
234 GAACATCTTGTTCTTCACT-TTTTTC-GAGTTAGACATTCAATTATAATCTGTTTTAA-TAAAAT
65 GAATGTCTTTTTCTTCA-TGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACTAAAA-
* * *
296 ATTTTAAAAAAATTTAACTTCAAA-TCGATTATGAGATTATAAAACC
128 A-TATAAAAAAATTCAACTT-AAAGTCAATTATGAGATTATAAAACC
* ** * * * * * * *
342 ATTTAAAGTGAGTAATAACACTCTAGAAGGCTTGGGTGATTATAAAT-AGGCTTTTCTTGTCAAT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGA-ACTTTTCTTGCCAAT
* * * ** * * * * *
406 GAATGGCTTTATCTTCA-GATTCCCTTAGGCAAACATTCAACTGTAATCTGTTTTAACTAAAAAG
65 GAATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAT
* ** * *
470 GTAAAAAAATTCAACTTAAAGTTGATTGTGAGATTATAAAATC
130 ATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* * * *
513 AGTTAAAACGCA-TAATAAGTG-TTTTGAAGGTATAGGTGACTATAAATGAACTTTTCTTACCAA
1 ATTTAAAGCG-AGTAATAAG-GCTTTTGAAGGCATAGGTGACTATAAATGAACTTTTCTTGCCAA
* * * * *
576 TGAATATCTTTTTATTTATG--TTTCTAGAGGTAGACATTCAATTATAATCTATTTTAA-TAAAA
64 TGAATGTCTTTTTCTTCATGTTTTTCT-TAGGTAGACATTCAATTATAATCTGTTTTAACT-AAA
*
638 AATATAAAAAAATTCAACTTCAAA-TCAATTATGACATTATAAAACC
127 AATATAAAAAAATTCAACTT-AAAGTCAATTATGAGATTATAAAACC
* ** * *
684 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGTTTGGGTGACTATAAAT-AGTCTTTTCTTGCCAAT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGA-ACTTTTCTTGCCAAT
** * * * * * * * * * *
748 GAATGAATTTTTCTTTA-GATTTCCTTAGGCAGATATTCAACTGTATTATGTTTTAACCAAAAAT
65 GAATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAT
* * *
812 ATAAAAAAATT-AACTTAAAATCAATTATGAGATTAGAAAATC
130 ATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* * * * **
854 ATTTAAAGTGAGTAATGAGGCTTTTGAAGGCATAGG-GCACTATAACTGGA-TCTTTCTTTTCAA
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTG-ACTATAAATGAACT-TTTCTTGCCAA
* * * * * * * * * * *
917 TGAATGGCTGTTTCCTCA--CTTTTCTCAAGGCACACATTCAATTATTATCTCTTTCAACAAAAA
64 TGAATGTCTTTTTCTTCATGTTTTTCT-TAGGTAGACATTCAATTATAATCTGTTTTAACTAAAA
* * * * * *
980 ATGTAAAAAAATTCTACTTGATA-TCAATTATGAGATTCTGAAATC
128 ATATAAAAAAATTCAACTT-AAAGTCAATTATGAGATTATAAAACC
* * * * * * * *
1025 GTTTAAAGAGAGAAATGAGGCTTTCGAAGGCATAGGTGATTAAAAATGAACTTTTCTTGACAATG
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGAACTTTTCTTGCCAATG
* * *
1090 AATATCTTTTTCTTCACG--TTTCTT-GAGTAGACATTCAATTATAATCTGTTTTAA-TAAAAAA
66 AATGTCTTTTTCTTCATGTTTTTCTTAG-GTAGACATTCAATTATAATCTGTTTTAACTAAAAAT
* * * **
1151 AGTAAAAAAATTTAACTTAAAATCAATTATGATATTATAAAAAT
130 A-TAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
** * * * * * * * * **
1195 AAATAAAGCAAGTACTAGGGCTTTCGAAGGTATGGGTGACTATAAAT-AGTCATTTCTCACCAAT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGA-ACTTTTCTTGCCAAT
* * * * * * * *
1259 GAAAGGT-TTTTTTTTCACGTTTTTC-AAAGTAGACATTCAATTATAATCTGTTATAACCACAAA
65 G-AATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAA
* * *
1322 TGA-AGAAAATTTCAACTTAAGGTCAATTATGAGATTATAAAACC
129 T-ATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* * * *
1366 ATTTAAAGCGAGTAATAAGGC---TGAAGGCATAGGTGACTGTTAAT-AGACTTTTGTTACCAAT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGA-ACTTTTCTTGCCAAT
* * * * * * * *
1427 CAATATCTTTTTCTACACGTTTCTCAT-GTTAGACATTAAATTATAATCTGTTTTAA-TAAAAAA
65 GAATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACT-AAAAA
* *
1490 TATAAAAAAATTCAACTTCAAA-TCAACTATGAGAGTATAAAACC
129 TATAAAAAAATTCAACTT-AAAGTCAATTATGAGATTATAAAACC
* ** * * * * * * *
1534 ATTTAAAGCTAACAATAAGACTGTTGAAGGCTTTGGTTACTATAAAT-ACGCTTTTCTTGCTAAT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGA-ACTTTTCTTGCCAAT
* * * * * * * *
1598 GAATGACTTTTTCTTTAAGTGTGT-TTAGGCAGACATTCAACTGTAATCTGTTTTAACTAAAAAT
65 GAATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAT
* * * * * *
1662 GTAAAAACATTTAACTAAAAGTCAATTATGAGATTATAAATCT
130 ATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* * * * * * * *
1705 ATTTAAAGTGAGTAATAAGGTTTTTGAAGGTACATGTGATTATAAATGGACTTTTGTTGCCAATG
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGAACTTTTCTTGCCAATG
* ** * * *
1770 AATATCTTTTTCTT--TACTTTTCTCAAGTTAGACATTCAATTATAATCTGTTTTGA-TAAAGAA
66 AATGTCTTTTTCTTCATGTTTTTCT-TAGGTAGACATTCAATTATAATCTGTTTTAACT-AA-AA
* *
1832 ATATAAAAAAATTTAACTTTAAA-TCAATTATGAGACTATAAAACC
128 ATATAAAAAAATTCAAC-TTAAAGTCAATTATGAGATTATAAAACC
** * * * * * * * *
1877 ATTTAAAGCCTGTAATAAGAC-TTTGCTATGCTTGGGTGACTACAAAT-AGGCTTTTCTTACCAA
1 ATTTAAAGCGAGTAATAAGGCTTTTG-AAGGCATAGGTGACTATAAATGA-ACTTTTCTTGCCAA
* ** * * *
1940 TGAATGACTTTTTCTTC-TAGTTAAT-TTAGGCAGACATTCAACTGTAATCTGTTTTAA-TAAAA
64 TGAATGTCTTTTTCTTCAT-GTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACT-AAA
* * * *
2002 AATATATAAAAATTTAACTTAAAATCAATTATGAGAGTATAAAACC
127 AATATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* * * *
2048 ATTTAAAGCAAGTAATAAGGC-TTTGAAAGGCTTGGGTTACTATAAAT-ATACTTTTCTTGCCAA
1 ATTTAAAGCGAGTAATAAGGCTTTTG-AAGGCATAGGTGACTATAAATGA-ACTTTTCTTGCCAA
* * * * ** * *
2111 TGAATGGCTTTTTCTTCAGGTTTAT-TTAGGCAGACATTCAATTGCAATTTGTTTTAACCAAAAA
64 TGAATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAA
* * * *
2175 TGTAAAACAATTCAAGTTAAAGTCAATTATAAGATTATAAAACC
129 TATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* * * * *
2219 ATTTAAAGCGAGTTATAAGGCTTTTGAAGGCATAGGTGAGTATAAATGGACTTTTCCTACCAA-G
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGAACTTTTCTTGCCAATG
* * * * * *
2283 CAATATCTTTTTCTTTATG-TTTTCCTAGGCAGACATTTAATTATAATCTGTTTTAACAAAAAAT
66 -AATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAT
*
2347 ATAAAAAAATTCAACTTCAAGTC-ATGTATGAGATTATAAAACC
130 ATAAAAAAATTCAACTTAAAGTCAAT-TATGAGATTATAAAACC
* * * * * *
2390 ATTTAAAACGAGCAATAAGGCTTTCGAATGCGT-GAGTGACTATAAATGGACTTTTCTTGCCAAT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAG-GTGACTATAAATGAACTTTTCTTGCCAAT
* * ** * * * * * * *
2454 GACTATAATTTTCATCACG-TTTCCCTAGGTAAACATTCAATTATAATTTATTTTAAC-AAAAA-
65 GAATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAT
* * * *
2516 ATAAAAAAACTT-AACTTAAAATCAACTATGATATTATAAAACT
130 ATAAAAAAA-TTCAACTTAAAGTCAATTATGAGATTATAAAACC
* ** *
2559 ATTTAAAGCGAGTACTAAGGC-TTTGAAAGGC-TAGGATGACTATAAATGGGCTTTTCCTAG-CA
1 ATTTAAAGCGAGTAATAAGGCTTTTG-AAGGCATAGG-TGACTATAAATGAACTTTT-CTTGCCA
* * * * * *
2621 ATTAATGGCCTTTTC-TCAACG--TTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAACTAC
63 ATGAATGTCTTTTTCTTC-ATGTTTTTCTT-AGGTAGACATTCAATTATAATCTGTTTTAACTAA
** * *
2683 AAAT-GCAAAAAATTCAACTTAAAGTCAATTATGAGGTTATAAAACT
126 AAATATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* * * * *
2729 ATTCAAAGAGAGTAATAAGGCTTTCGAAGGCAT-GAGTGACTATAAATGAGCTTTTCTTGCCATT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAG-GTGACTATAAATGAACTTTTCTTGCCAAT
* * * * * * *
2793 GAATGGCTTTTTCTTTATGTTTCTC-AAGGTAGACATTCAATTATAGTCTGTTTTCACAAAAAAT
65 GAATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAT
* * *
2857 AAAAAAAAATTCATCTTAAAGTTC-ATTATGACATTATAAAACC
130 ATAAAAAAATTCAACTTAAAG-TCAATTATGAGATTATAAAACC
* * * * * * *
2900 ATTTAAAGCGAGTAATAAGGCTTTTGGAGGCATATGTGAGTATATATGGACTTTTCTTACCAATA
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGAACTTTTCTTGCCAATG
*
2965 AATGTC-TTTTCTTCATG--TTTCTTGAGGTAGACATTTAATTATAAT-TGATTTTAACT-AAAA
66 AATGTCTTTTTCTTCATGTTTTTCTT-AGGTAGACATTCAATTATAATCTG-TTTTAACTAAAAA
* ** * *
3025 -ATAAAAAAATT-GACTGGAAGTCAATTATGAGATTACAAAGCC
129 TATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* * * * * **
3067 ATTTAAAGCTAGTAATAAGTG-TTTGGAAAGCATAGGTGACTATACATGGACTTTTCTTATCAAT
1 ATTTAAAGCGAGTAATAAG-GCTTTTGAAGGCATAGGTGACTATAAATGAACTTTTCTTGCCAAT
* * * * ** * * *
3131 GAATATCATTTTCTTCACG-TTTCCCAAAGTAGACAGTCAATTATAATATGTTTTAA-TAAAAAA
65 GAATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACT-AAAAA
* *
3194 TATAAAAATATTCAACTTCAAA-TCAATTATGAGATTATAAAATC
129 TATAAAAAAATTCAACTT-AAAGTCAATTATGAGATTATAAAACC
* * * *
3238 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGTAT-GAGTGACAATAACTGAACTTTTCTTGCCAAT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAG-GTGACTATAAATGAACTTTTCTTGCCAAT
* * * * ** *
3302 GCATATCTTTTTCTTCATGTTTCTC-GAATTATACATTCAATTATAATCTGTTTTAA-TAAAAAA
65 GAATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACT-AAAAA
* * * **
3365 TGTAAAAATAATTCAACTTAAAATCAGTTATGAGATTATAAAAAT
129 TATAAAAA-AATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* * * * * *
3410 AATTAAAGCAAGTAATAAGGCTTTCGAAGGCAT-GTGTGAGTATAAATGGACTTTTCTTGCTAAT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAG-GTGACTATAAATGAACTTTTCTTGCCAAT
* * * * *
3474 GAATGGCTCTTTT-TTCATG--TTTCGTGAGATAGACATTCAATTATAGTCTGTTTTAACTGAAA
65 GAATGTCT-TTTTCTTCATGTTTTTC-TTAGGTAGACATTCAATTATAATCTGTTTTAACTAAAA
* * * *
3536 AT-GAAAACAATTCAACTTAAAGTCAATTATGATATTATAAAACT
128 ATATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* * * * *
3580 ATCTAAAGCGAGTAATAAGTGTTTTTTGAAGGCATGGGTGACTATAAATGAACTTTTCTTACGAA
1 ATTTAAAGCGAGTAATAAG-G-CTTTTGAAGGCATAGGTGACTATAAATGAACTTTTCTTGCCAA
** * * * * *
3645 TGAATACCTTTTTCTTCATG-TTTCCTAAGGTATAGATTCAATTATAATATGTTTTAA-TAAAAA
64 TGAATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACT-AAAA
* * * *
3708 ATGTAAAAAACTTCAACTTCAAA-TCAGTTATGAGATTATAAAACT
128 ATATAAAAAAATTCAACTT-AAAGTCAATTATGAGATTATAAAACC
* * * * * * * *
3753 ATTCAAAACGAGTAAT-AGGACTTTTGAAGGCTTGGGT-AGGTTTAAATTG-GCTTTCCTTGCCA
1 ATTTAAAGCGAGTAATAAGG-CTTTTGAAGGCATAGGTGA-CTATAAA-TGAACTTTTCTTGCCA
* * * * * * * * *
3815 ATAAATGCCTCTTTCTTCACG-TTTCCTTAGGTAGACATTCAATTGTTATATGTTTTAACAAAAA
63 ATGAATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACTAAAA
** * * **
3879 ATATAAAAAAATTCAAGGTAAAGTCAATTATGATATTACAAAAAT
128 ATATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* ** * * *
3924 ATTTAAAGTGAGTAATAAGGCTTTCAAAGACA-AGGGTGACTATAAATGGACTTTTCTTGTCAAT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATA-GGTGACTATAAATGAACTTTTCTTGCCAAT
* * * ** * *
3988 GAATATCTTTTTCTTTACG-TTTTCCAAGGTTGACATTCAATTACAATCTGTTTTGGAA--AAAA
65 GAATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTT--AACTAAAA
* *
4050 A-AGTAAAAAAATTCAACTTTAAA-TCAAATATGAGATTATAAAATC
128 ATA-TAAAAAAATTCAAC-TTAAAGTCAATTATGAGATTATAAAACC
* * * * *
4095 ATTTAAAGTGAGTAATAAGGCTTTTGAATGAATGGGTGACTATAAATGGACTTTTCTTGCCAATG
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGAACTTTTCTTGCCAATG
* * * ** * *
4160 AATATCTTTTTCTTTATATTTTTCCAAGGTAGACATTCAATTATAGTCTGTTTTGAC-ATAAAAT
66 AATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACTA-AAAAT
* *
4224 -TAGAAAAAATTCAACTTAAAGTTAATTATGATATTATAAAACC
130 ATA-AAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
4267 ATTTAAAGCGAGTAATAAGGCTTTTGAA
1 ATTTAAAGCGAGTAATAAGGCTTTTGAA
4295 AGTATTTAAC
Statistics
Matches: 3290, Mismatches: 684, Indels: 299
0.77 0.16 0.07
Matches are distributed among these distances:
166 2 0.00
167 85 0.03
168 190 0.06
169 249 0.08
170 529 0.16
171 1593 0.48
172 567 0.17
173 70 0.02
174 5 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (172 bp):
ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGAACTTTTCTTGCCAATG
AATGTCTTTTTCTTCATGTTTTTCTTAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATA
TAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
Found at i:5255 original size:20 final size:21
Alignment explanation
Indices: 5230--5272 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5220 AAGGCATGGG
5230 TTACT-ATGAATAAACTTTTC
1 TTACTAATGAATAAACTTTTC
* *
5250 TTACTAATGAATATATTTTTC
1 TTACTAATGAATAAACTTTTC
5271 TT
1 TT
5273 CATGTTTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.51
Consensus pattern (21 bp):
TTACTAATGAATAAACTTTTC
Found at i:5298 original size:169 final size:170
Alignment explanation
Indices: 4395--5318 Score: 843
Period size: 171 Copynumber: 5.4 Consensus size: 170
4385 TACAAAACTA
* * * * * ** *
4395 TTTCTTACCATTGTATATCATTTTCTTCATATTT-CTCAAAATAGACAATCAATTATAATATGTT
1 TTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCCT-AAGGTAGACATTCAATTATAATATGTT
*
4459 TTAA-TAAAAAATATAAAA-ATATTCAACTTCAAATCAATTATGAGA-TATAAAA-CATTTAAAG
65 TTAACT-AAAAATGTAAAACA-ATTCAACTT-AAATCAATTATGAGATTATAAAACCATTTAAAG
* * * * *
4520 CGAGTAATAAAGCTTTGGAAGGCTTAGCTGACTATAAATAGG-CT
127 CGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAAT-GGACT
* ** * * * ** *
4564 TTTCTCGCCAATGAATGCCTTTTTCTTCATGTTTCCTTAGGTAGACATTTAACTGCAATCTGTTT
1 TTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCCTAAGGTAGACATTCAATTATAATATGTTT
* * * * * ** *
4629 TAACAAAAAATGTAAAAAAAATCAAGTTAAAGTCAATTATGAGATTACAAAAATATTTAAAGCAA
66 TAACTAAAAATGTAAAACAATTCAACTTAAA-TCAATTATGAGATTATAAAACCATTTAAAGCGA
* * *
4694 GTAATAAGGCTTTCGAAGGCATTGGTGATTATAAACGGACT
130 GTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACT
* * * * * * * * *
4735 TTTCTTACGAATGAATATCTTTTTTTTCACGTTTCAC-GAGCTTGA-ACTTCAATTCTAAT-CGA
1 TTTCTTGCCAATGAATATCTTTTTCTTCATGTTTC-CTAAGGTAGACA-TTCAATTATAATATG-
* *
4797 TTTTAAC-AAAAACAGTAAAACAATTCCACTTCAAATCAATTATGAGATTATAAAACCATTTAAA
63 TTTTAACTAAAAA-TGTAAAACAATTCAACTT-AAATCAATTATGAGATTATAAAACCATTTAAA
* * ** *
4861 GCGAGTAATAAGGCTTTTGAAAGTGTGGGTGACTATAACTGGACT
126 GCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACT
* ** * * * *
4906 TTTCTTGCCAATGCATA-AATTTTCGTCATGTTTCTTGAA-TTAGACATTCAATTATAATCTGTT
1 TTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCCT-AAGGTAGACATTCAATTATAATATGTT
* * * * * **
4969 TTAACTACAAATGTAAAAACAATTGAACTAAAAATCAGTTATGAGATTATAAAAACACCTAAAGC
65 TTAACTAAAAATGT-AAAACAATTCAACT-TAAATCAATTATGAGATTATAAAACCATTTAAAGC
* * * *
5034 AAGTAATAAGGCTTTCAAAGGCATGTGTGAGTATAAATGGACT
128 GAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACT
* * * * *
5077 TTTCTTGCTAATGAATAGCTTTTTCTTCATATTTCTTAAGGTAGACATTCAATTATAGTATGTTT
1 TTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCCTAAGGTAGACATTCAATTATAATATGTTT
* *
5142 TAACTAAAAATG-AAAACAATTCAACTTAAAGTCAATTATGTGATTATAAAACCA-TAAAAGCGA
66 TAACTAAAAATGTAAAACAATTCAACTTAAA-TCAATTATGAGATTATAAAACCATTTAAAGCGA
* * * **
5205 GTAATAAGGCTTTTGAAGGCATGGGTTACTATGAATAAACT
130 GTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACT
* * * * *
5246 TTTCTTACTAATGAATATATTTTTCTTCATGTTTCCTAAGGTATAGATTCAATTATAATATGTTT
1 TTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCCTAAGGTAGACATTCAATTATAATATGTTT
5311 TAA-TAAAA
66 TAACTAAAA
5319 NNNNNNNNNN
Statistics
Matches: 604, Mismatches: 129, Indels: 45
0.78 0.17 0.06
Matches are distributed among these distances:
168 8 0.01
169 180 0.30
170 86 0.14
171 278 0.46
172 52 0.09
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (170 bp):
TTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCCTAAGGTAGACATTCAATTATAATATGTTT
TAACTAAAAATGTAAAACAATTCAACTTAAATCAATTATGAGATTATAAAACCATTTAAAGCGAG
TAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACT
Found at i:6490 original size:170 final size:160
Alignment explanation
Indices: 6208--6518 Score: 338
Period size: 170 Copynumber: 1.9 Consensus size: 160
6198 NNNNNNNNNN
*
6208 AAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGGTATGGGTGACTATAAATAAACTTTTCTTA
1 AAAACCATTTAAAACGAGTAATAAGACTTTTGAAGGTATGGGTGACTATAAATAAACTTTTCTTA
* * * * * *
6273 CCAATGAATACATTTTTCTTCATGTTTCCTAAGGTATAGATTCAATTAT-ATCTGTTTTAATAAA
66 CCAATGAATACATCTTTCTTCACGTTTCCTAAGGCAAACATTCAATTATAAT-TGTTTTAACAAA
6337 AAATGTAAAAAAANNNNNNNNNNAATCAATTATGAGATTAT
130 AAATGTAAAAAAA----------AATCAATTATGAGATTAT
* * * * ***
6378 AAAACCATTTAAAATGAGTAATAGGGCTTTTGAAGGCT-TGGGTGGCTATAAATTGGCTTTTCTT
1 AAAACCATTTAAAACGAGTAATAAGACTTTTGAAGG-TATGGGTGACTATAAATAAACTTTTCTT
* * *
6442 GCCAATGAATACCTCTTTCTTCACGTTTCCTTAGGCAAACATTCAATTATAAATTGTTTTAACAA
65 ACCAATGAATACATCTTTCTTCACGTTTCCTAAGGCAAACATTCAATTAT-AATTGTTTTAACAA
6507 AAAATGTAAAAA
129 AAAATGTAAAAA
6519 CAATTCAAGG
Statistics
Matches: 121, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
170 96 0.79
171 23 0.19
172 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (160 bp):
AAAACCATTTAAAACGAGTAATAAGACTTTTGAAGGTATGGGTGACTATAAATAAACTTTTCTTA
CCAATGAATACATCTTTCTTCACGTTTCCTAAGGCAAACATTCAATTATAATTGTTTTAACAAAA
AATGTAAAAAAAAATCAATTATGAGATTAT
Done.