Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399648.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2897.0, 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: 11655
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.27
Warning! 3137 characters in sequence are not A, C, G, or T
Found at i:1255 original size:172 final size:172
Alignment explanation
Indices: 1--1937 Score: 1165
Period size: 171 Copynumber: 11.3 Consensus size: 172
* *
1 CATTCTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATATTCTCAAAATCT-ATTTTAAGT
1 CATTCTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAAT-TGATTTTAAGT
* * * * * *
65 TCAATTTTTTTTACATTTTTGTGTAAAACAGATTATAATTGACTGTCTACC-TCATGAAATGTAA
65 TTAATTTTTTTTACATTTTTTTTTAAAACAGATTATAATTGAATGTCTACCTTGA-GAAACGTAA
* * *
129 AGAAAAAGGCAATCATTGGA-AAGAAAAGTCCATTTATAGTTACC
129 AGAAAAAGACATTCATT-GATAAGAAAAGTCCATTTATAGTCACC
* * **
173 CATTCCATT-AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCGA-AATAAATTTTAA-
1 CATT-CTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTC-ATAATTGATTTTAAG
* * * ** * * * *
235 TTTGAATTCTTTGTATATTTTTGGTTAAAATAGATTATAATTGAATCTTTGCCTCT-AGAAACGT
64 TTT-AATTTTTTTTACATTTTTTTTTAAAACAGATTATAATTGAATGTCTACCT-TGAGAAACGT
* * * * *
299 AAAGAAAAAGGCATTCATTAATAAAAAAAGTCAATTTATAGTCTCC
127 AAAGAAAAAGACATTCATTGATAAGAAAAGTCCATTTATAGTCACC
* ********** *
345 CATTCTTTCAAAAACCTTATTACTCGCTTTAANNNNNNNNNNAATCTCATAATTAATTTTAAGTT
1 CATTCTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAATTGATTTTAAGTT
* * * * * * *
410 GAA-TTTTTTTATATTTTTTATTATAACATG-TTATAATTAAATGTCTACCTTGAGAGACATCAA
66 TAATTTTTTTTACATTTTTTTTTAAAACA-GATTATAATTGAATGTCTACCTTGAGAAACGT-AA
*
473 A-AAAAAGATATTCATTGATAAGAAAAGTCCATTTATAGTCACC
129 AGAAAAAGACATTCATTGATAAGAAAAGTCCATTTATAGTCACC
* * * * * * *
516 CATT-TCTTCAAAAGCCCTACTACTTGCTTTAAAAGTTTTTATATTCTCAAAATTGATTTTAACT
1 CATTCT-TTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAATTGATTTTAAGT
* * * ** * * * *
580 TCAATGTTTTTTATATTTTCATGTAAAATAAATTATAATT-AACTGTCTACCTTGAGAAACAT-A
65 TTAATTTTTTTTACATTTTTTTTTAAAACAGATTATAATTGAA-TGTCTACCTTGAGAAACGTAA
* * * * * *
643 AGAAAAAGGCATTCATTGACAAGAAAAGTTCATTTATAATAACT
129 AGAAAAAGACATTCATTGATAAGAAAAGTCCATTTATAGTCACC
** * ********** * * *
687 CATTCCCTCAAAAGCTTTANNNNNNNNNNTAAAAGGTTTTATATTCTCAAAATTAATTTTAAG-T
1 CATTCTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAATTGATTTTAAGTT
* ** * * * * *
751 TAAATTTTTTTACATTTTCCTGTAAAACAGATTATAATT-AACTGTTTATCTAGAGAAATGTAAA
66 TAATTTTTTTTACATTTTTTTTTAAAACAGATTATAATTGAA-TGTCTACCTTGAGAAACGTAAA
* * * *
815 GAAAAAGATATTTATTGACAAGAAAAGTCAATTTATAGTCACC
130 GAAAAAGACATTCATTGATAAGAAAAGTCCATTTATAGTCACC
* * * * *
858 TATTCTTTTAAAAGCCTTATTATTTGCTTTAAAAAGTTTTATAA-CTCATAATTGA-TTTAAGTT
1 CATTCTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAATTGATTTTAAGTT
* * * * * * * **
921 GAA-TTTTTTTATATTTTTTGTTAGAACGGATTATAATTGAATATCTACCTT-AGTAAGCGCGAA
66 TAATTTTTTTTACATTTTTTTTTAAAACAGATTATAATTGAATGTCTACCTTGAG-AAACGTAAA
* *** * * **
984 GGAAAAGGTGTTCATTGATAATAAAAGTCAATTTATAGTCANN
130 GAAAAAGACATTCATTGATAAGAAAAGTCCATTTATAGTCACC
***************************** * * * *
1027 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAAATGATTTTATATTCTCAAAATTGATTTTAAGTT
1 CATTCTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAATTGATTTTAAGTT
* * *
1092 TAATTTTTTTTACATTTTTTTTTAAAACAGATTATAATTGACTATGTACCTTGAGAAACGTAAAG
66 TAATTTTTTTTACATTTTTTTTTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACGTAAAG
** * *
1157 AAAAAGACATTCATTGGCAAGAAAATTCTATTTATAGTCACC
131 AAAAAGACATTCATTGATAAGAAAAGTCCATTTATAGTCACC
* * ** *
1199 CATTCTTTCAAAAGCCTTGTTACTTGCTTTAAAACTTTTTAAAATCTCATAATTGATTTTAAG-T
1 CATTCTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAATTGATTTTAAGTT
* ** * * *
1263 TATTTTTTTTTACATTTTTAGTTAAAGA-AGGTTATAATTGAATGTCTACCTTGAAAAACATAAA
66 TAATTTTTTTTACATTTTTTTTTAAA-ACAGATTATAATTGAATGTCTACCTTGAGAAACGTAAA
* * * ***
1327 GTGACAAGA-ATTTATTGGA-AAGAAAAGTCCATTTATAGTTGTC
130 G-AAAAAGACATTCATT-GATAAGAAAAGTCCATTTATAGTCACC
* * * * *
1370 TATTCCTTT-AAAAGGCTTATTA-T-GCTTTAAAAGATTTTATATTCTCAAAATT-ATTTTTAAG
1 CATT-CTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAATTGA-TTTTAAG
* * ** *
1431 TTGT-A-TTTTTTTACATTTTTTTGTTAAAACAGATTATATTTGAATAT-TAGCCTCCAGAAATG
64 TT-TAATTTTTTTTACATTTTTTT-TTAAAACAGATTATAATTGAATGTCTA-CCTTGAGAAACG
* * * * *
1493 TGAAGAAAAA-AGTATTGATTGGTAAGAAAAATCCATTTATAGTCACC
126 TAAAGAAAAAGA-CATTCATTGATAAGAAAAGTCCATTTATAGTCACC
* * * * ** * ****
1540 TATTCTTTCAAAATCCTTATTACTAGTTTTAAAAATTTTTATAATCTCATAATTCATTTT-NNNN
1 CATTCTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAATTGATTTTAAGTT
****** * * * *
1604 NNNNNNTTTTTATATTTTTTATTAAAACAGATTATAATTGAGTATCTACCTTGAGAAACGTGAAA
66 TAATTTTTTTTACATTTTTTTTTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACGT-AAA
* * *
1669 AAAAAAGAATATTCATTGATAAGAAAAGTCCATTTATAGTCACT
130 GAAAAAG-ACATTCATTGATAAGAAAAGTCCATTTATAGTCACC
********** * *
1713 CNNNNNNNNNNAAGCCTTATTACTCGCTTTAAATGGTTTTAT-AT-TCATAAAAGTGATTTTAAG
1 CATTCTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTCAT--AATTGATTTTAAG
* * * ** * * *
1776 CTAAATTTGTTTTACATTTTCATTTAAAACATATTATAATTGACTGTCTATCTTGAGAAACGTGA
64 TTTAATTTTTTTTACATTTTTTTTTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACGT-A
* * * * * *
1841 AAAAAAAATG-CATTTATTGACAAGAAAAGTCCATTTATAGGCGCT
128 AAGAAAAA-GACATTCATTGATAAGAAAAGTCCATTTATAGTCACC
*
1886 TATTCCTTT-AAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAA
1 CATT-CTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAA
1938 NNNNNNNNNN
Statistics
Matches: 1321, Mismatches: 387, Indels: 113
0.73 0.21 0.06
Matches are distributed among these distances:
168 4 0.00
169 148 0.11
170 151 0.11
171 419 0.32
172 398 0.30
173 136 0.10
174 60 0.05
175 5 0.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.39
Consensus pattern (172 bp):
CATTCTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAATCTCATAATTGATTTTAAGTT
TAATTTTTTTTACATTTTTTTTTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACGTAAAG
AAAAAGACATTCATTGATAAGAAAAGTCCATTTATAGTCACC
Found at i:3621 original size:172 final size:167
Alignment explanation
Indices: 3323--4176 Score: 633
Period size: 171 Copynumber: 5.0 Consensus size: 167
3313 NNNNNNNTCG
* *
3323 CTTTAAAAGGTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTATTTTTTTTCTAAAA
1 CTTT-AAAGTTTTTATAATCTCATAATTGATTTTAAGTT-AATTTTTTTTA-ATTTTTT-TAAAA
* * * *** **
3387 TAGATTATAATTGAATGTCTACCTTGAGAAATGTAAAGAAAAAGGTATTCGTTGACAAGAAAAGT
62 TAGATTATAATTGACTGTCTACCTTGAGAAACGTGAAGAAAAATACATTTATTGACAAGAAAAGT
* * *
3452 CTATTTATAGTCACCTATTCCTTCAAAAGCCTAATTATTCA
127 CCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCA
* * * *
3493 CTTTAAATTATTTTATATTCTCAAAATTGATTTGAAGTTAAATTTTTTTTAACTTTTCATTTAAA
1 CTTTAAAGT-TTTTATAATCTCATAATTGATTTTAAGTT-AATTTTTTTTAA-TTTT--TTTAAA
* * * ** *
3558 ACAGATTATAATTGACTATCTACCATGAGAAACGTGAAGAAAAATACATTTATTGGTAAGAAAAT
61 ATAGATTATAATTGACTGTCTACCTTGAGAAACGTGAAGAAAAATACATTTATTGACAAGAAAAG
* * * * *
3623 TCCATTTATAGGCACTTATTCTTTTAAAAGACTTATTACT-A
126 TCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCA
* * *
3664 GCTTTAAAAGTTTTTATAATGTCATAATTAATTTTAAGTTGATTTTTTTTACAATTTTTGTTAAA
1 -CTTT-AAAGTTTTTATAATCTCATAATTGATTTTAAGTTAATTTTTTTT--AATTTTT-TTAAA
* * ***
3729 ATAGATTATAATTGACTGTTTA-CTTAGAGAAACGTG-AGGAAAATTGTTTTCATTGACAAGAAA
61 ATAGATTATAATTGACTGTCTACCTT-GAGAAACGTGAAGAAAAATACATTT-ATTGACAAGAAA
* * * *
3792 AGTCCATATATAGTAACCCATTCCTTCAAAAGCCTTATTACTCG
124 AGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCA
* ************* * *
3836 CTTTAAAAGGTTTTATAATCTCATANNNNNNNNNNNNNTGATTTTTCTTATATTTTTTGTTGAAA
1 CTTT-AAAGTTTTTATAATCTCATAATTGATTTTAAGTTAATTTTT-TT-TAATTTTT-TT-AAA
* * * * * * * * **
3901 A-AGGTGATCATTGAATGTCTGCCTTGGGAAACATAAAGAAAAAGGCATTTATTTG-CAAGAAAA
61 ATAGATTATAATTGACTGTCTACCTTGAGAAACGTGAAGAAAAATACATTTA-TTGACAAGAAAA
* * * *
3964 GTCCAGTTACAGTCACTTATTCCTTTAAAAGCCTTATTACTCA
125 GTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCA
* * * * * *
4007 CTTTCAAAGGTTTTATAATCTTAAAATTGATTTTAATTTGAATTCTTTATATATTTTTGGTTAAA
1 CTTT-AAAGTTTTTATAATCTCATAATTGATTTTAAGTT-AATTTTTTTTA-ATTTTT--TTAAA
* * ** * * * *
4072 ATAGATTATAATTGAATGTCTAGCTCAAGAAACCTAAAGAAAAA-GCTATTTATTGGCAAGAAAA
61 ATAGATTATAATTGACTGTCTACCTTGAGAAACGTGAAGAAAAATAC-ATTTATTGACAAGAAAA
* *
4136 GTCCATTTATAGTCACCCATTCCTTCAAAAGCTTTATTACT
125 GTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACT
4177 NNNNNNNNNN
Statistics
Matches: 530, Mismatches: 129, Indels: 48
0.75 0.18 0.07
Matches are distributed among these distances:
169 3 0.01
170 47 0.09
171 242 0.46
172 229 0.43
173 9 0.02
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (167 bp):
CTTTAAAGTTTTTATAATCTCATAATTGATTTTAAGTTAATTTTTTTTAATTTTTTTAAAATAGA
TTATAATTGACTGTCTACCTTGAGAAACGTGAAGAAAAATACATTTATTGACAAGAAAAGTCCAT
TTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCA
Found at i:4929 original size:171 final size:170
Alignment explanation
Indices: 4602--5018 Score: 426
Period size: 171 Copynumber: 2.4 Consensus size: 170
4592 NNNNNNNNCA
* * * * *
4602 AAAAATGTAAAACAATTCAACTTAAAAGCAATTATAACATTATAAAACTGTTTAAAGCAAGTAAT
1 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGACATTATAAAACTATTTAAAGC-GGTAAT
* * * ** *
4667 AAAGCTTTTAAAAGAATAAATGTCTATAAATGGACTTTTCTTTTCAATAAATGCATTTTTCTTTA
65 AAGGCTTTTAAAAGAATAAATGCCTATAAATGGAATTTTCTTACCAATAAATGCATTTTTCTTCA
** * *
4732 TGTTCCCCAAGGCAGACATGCAATTATAGCCTT-CTTTAACT
130 CATTCCCCAAGGCAGACATGCAATTATA-ACTTGCTTTAAAT
* *
4773 AAAAATGTAAAAAAAATCAACTTAAAATCAATTATGACATTATAAAACTTTTTAAAGCTGGTAAT
1 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGACATTATAAAACTATTTAAAGC-GGTAAT
* * * *
4838 AAGGCTTTTAAAGGAATTAGTGCCTATAAATGGAATTTTCTTACCAATAAATGTATTTTTCTTCA
65 AAGGCTTTTAAAAGAATAAATGCCTATAAATGGAATTTTCTTACCAATAAATGCATTTTTCTTCA
* *** ** * * *
4903 CATTTCTTGAGGTTGATA-GTCAATTATAATTTGTTTTAAAT
130 CATTCCCCAAGGCAGACATG-CAATTATAACTTGCTTTAAAT
* * * * * *
4944 GAAAATGTAAAACAAATTTAACTTCAAATCAATTTTGAGAATATAAAA-TAATTTAAAGCGAGTA
1 AAAAATGTAAAA-AAATTCAACTTAAAATCAATTATGACATTATAAAACT-ATTTAAAGCG-GTA
5008 ATAAGGCTTTT
63 ATAAGGCTTTT
5019 GAANNNNNNN
Statistics
Matches: 203, Mismatches: 38, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
170 3 0.01
171 149 0.73
172 51 0.25
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.36
Consensus pattern (170 bp):
AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGACATTATAAAACTATTTAAAGCGGTAATA
AGGCTTTTAAAAGAATAAATGCCTATAAATGGAATTTTCTTACCAATAAATGCATTTTTCTTCAC
ATTCCCCAAGGCAGACATGCAATTATAACTTGCTTTAAAT
Found at i:5757 original size:172 final size:171
Alignment explanation
Indices: 5482--5794 Score: 373
Period size: 172 Copynumber: 1.8 Consensus size: 171
5472 TCTTTCACCA
* *
5482 AAAATGTAAAAAAAATTAACTTAAAATAAATTAGGAGATTATAAAACCTTTTAAAGCGAGTAGTA
1 AAAATGTAAAAAAAATTAACTTAAAATAAATTAGGAGAATATAAAACCTTTTAAAGCGAGTACTA
* * * * *
5547 AGGCTTTTACAGGAATAGGTACCTATAAATGAACTTTTCTTGCCAATAAATGTATTTTTCTTAAT
66 AGGCTTTTACACGAATAGGTACCTACAAATGAACTTTTCGTACCAATAAATATATTTTTCTTAAT
5612 GTTTCTCGAGGTAAATAAGCAATTATAATCTGTTTTGAATG
131 GTTTCTCGAGGTAAATAAGCAATTATAATCTGTTTTGAATG
* * * * ** *
5653 AAAATTTAAAAACAATTTGACTTAAAATCAATTTTGAGAATATAAAA-CTATTTAAAGTGAGTAC
1 AAAATGTAAAAA-AAATTAACTTAAAATAAATTAGGAGAATATAAAACCT-TTTAAAGCGAGTAC
* * * * *
5717 TAAGGCTTTTGA-ACGAGT-GAGTGA-CTACAAATGGACTTTTCGTATCAATGAATATCTTTTTC
64 TAAGGCTTTT-ACACGAATAG-GT-ACCTACAAATGAACTTTTCGTACCAATAAATATATTTTTC
*
5779 TTCATGTTTCTCGAGG
126 TTAATGTTTCTCGAGG
5795 CAGACATTCA
Statistics
Matches: 117, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
171 14 0.12
172 101 0.86
173 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (171 bp):
AAAATGTAAAAAAAATTAACTTAAAATAAATTAGGAGAATATAAAACCTTTTAAAGCGAGTACTA
AGGCTTTTACACGAATAGGTACCTACAAATGAACTTTTCGTACCAATAAATATATTTTTCTTAAT
GTTTCTCGAGGTAAATAAGCAATTATAATCTGTTTTGAATG
Found at i:5809 original size:172 final size:169
Alignment explanation
Indices: 5164--6205 Score: 658
Period size: 170 Copynumber: 6.1 Consensus size: 169
5154 NNNNNNNNNN
* *
5164 AAATCAATTATGAGATTATAAAACTTTTTAAAGCGAGTAATAAGGCTTTTGAAGAAATCG-GTGA
1 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GAGTGA
* * * * * * *
5228 CTATAAATAGACTTTT-TT-CTTCAATGAATATTTTTTTATTCA-GGTTCTTGAGGTAGACATTC
65 CTATAAATGGACTTTTCTTGC--CAATAAATATCTTTTTCTTCATGTTTCTCGAGGCAGACATTC
*
5290 AATTATAATCTGTTTTAACAAAAAATACAAAAAAATTTAACTTA
128 AATTATAATCTGTTTT-A-AAAAAATATAAAAAAATTTAACTTA
* * * * * **********
5334 AAATCAATTATGACATTACAAAACTATTTGAAGCAAGTAATAAGGCTTTTAAAGGNNNNNNNNNN
1 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGAC
* * * * * * *
5399 TATAAAAGTACTTTTCTTGCCAATAAATGTCTTTTTCTTCATCTTCCCCAAGGCAGACATTCAAT
66 TATAAATGGACTTTTCTTGCCAATAAATATCTTTTTCTTCATGTTTCTCGAGGCAGACATTCAAT
** * * *
5464 TATAGCCT-TCTTTCACCAAAAATGTAAAAAAAATTAACTTA
131 TATAATCTGT-TTT-A-AAAAAATATAAAAAAATTTAACTTA
* * *
5505 AAATAAATTAGGAGATTATAAAACCT-TTTAAAGCGAGTAGTAAGGCTTTT-ACAGGAAT-AG-G
1 AAATCAATTATGAGATTATAAAA-CTATTTAAAGCGAGTAATAAGGCTTTTGA-AGGAATGAGTG
* * * * * * * **
5566 TACCTATAAATGAACTTTTCTTGCCAATAAATGTATTTTTCTTAATGTTTCTCGAGGTAAATAAG
64 -A-CTATAAATGGACTTTTCTTGCCAATAAATATCTTTTTCTTCATGTTTCTCGAGGCAGACATT
* * *
5631 CAATTATAATCTGTTTTGAATGAAAATTTAAAAACAATTTGACTTA
127 CAATTATAATCTGTTTT-AA-AAAAATATAAAAA-AATTTAACTTA
* * * * * *
5677 AAATCAATTTTGAGAATATAAAACTATTTAAAGTGAGTACTAAGGCTTTTGAACGAGTGAGTGAC
1 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGAC
* * ** *
5742 TACAAATGGACTTTTCGTATCAATGAATATCTTTTTCTTCATGTTTCTCGAGGCAGACATTCAAT
66 TATAAATGGACTTTTCTTGCCAATAAATATCTTTTTCTTCATGTTTCTCGAGGCAGACATTCAAT
************ * *
5807 TATAATCTNNNNNNNNNNNNTGTAAAAAAATTCAACTTA
131 TATAATCTGTTTTAAAAAAATATAAAAAAATTTAACTTA
* * *
5846 AAATCAATTATGAGATTATAAAATCT-TTTAAAGCGGGTAATAAGGCTTTTGAAGAAAT-AGGTA
1 AAATCAATTATGAGATTATAAAA-CTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA-GTG
* ** * * * * *
5909 ACTAAAAATAAACTTTTTTTGCCAATGAATATCTTTTTCTTCATG-TTCACCAAGCCAGACATTC
64 ACTATAAATGGACTTTTCTTGCCAATAAATATCTTTTTCTTCATGTTTC-TCGAGGCAGACATTC
* **
5973 AATCATAGCCT-TCTTTAACTAAAAATATAAAAAAA-TTAACTTA
128 AATTATAATCTGT-TTTAA--AAAAATATAAAAAAATTTAACTTA
********** * *
6016 AAATCANNNNNNNNNNTATAAAACCT-TTTAAAGCGAGTAATAAGGCCTTTAAAGGAAT-AGGTG
1 AAATCAATTATGAGATTATAAAA-CTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA-GTG
* * * ** * * * * * *
6079 CCCATAAATGGAATTTTCTTATCAATAAATGTCATTTTCTTCACGTTTCTCAAAGTAGACATTCA
64 ACTATAAATGGACTTTTCTTGCCAATAAATATCTTTTTCTTCATGTTTCTCGAGGCAGACATTCA
* * * * *
6144 ATTATAATCTATTTTATCTAAAAATATACAAAGAATTCAAATTA
129 ATTATAATCTGTTTTA--AAAAAATATA-AAAAAATTTAACTTA
*
6188 AAATCAATTTTGAGATTA
1 AAATCAATTATGAGATTA
6206 NNNNNNNNNN
Statistics
Matches: 649, Mismatches: 195, Indels: 54
0.72 0.22 0.06
Matches are distributed among these distances:
168 4 0.01
169 116 0.18
170 206 0.32
171 186 0.29
172 132 0.20
173 4 0.01
174 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.34
Consensus pattern (169 bp):
AAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGAC
TATAAATGGACTTTTCTTGCCAATAAATATCTTTTTCTTCATGTTTCTCGAGGCAGACATTCAAT
TATAATCTGTTTTAAAAAAATATAAAAAAATTTAACTTA
Found at i:7391 original size:171 final size:171
Alignment explanation
Indices: 6615--7543 Score: 459
Period size: 171 Copynumber: 5.4 Consensus size: 171
6605 NNNNNNNNNN
* * * **
6615 ATAAGGCTTTT-GAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAGTGAATATTTTTTTCT
1 ATAAGG-TTTTAGAAGGAATGGG-CACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCT
* * * * ** * * * *
6679 TCATGTTTCTTAAGGTAAACACACAAGTATAAGCTTTTTGAACAAAAAATGT-AAAAAAATTCAA
64 TCAAGTTTCTTGAGGCAGACATTCAATTATAATCTTCTTCAACAAAAAATGTAAAAAAAATTCAA
* * **
6743 ATTAAATTCAATTATGAGATTATAAAACCTTTTAAAGCGAGNN
129 CTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGCGAGTA
***************** * * *
6786 NNNNNNNNNNNNNNNNNATGGGTGACTATAAATGGACTTTTTTTGTCAATGAATACCTTTTTCTT
1 ATAAGGTTTTAGAAGGAATGGG-CACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTT
* ** * * * **********
6851 CATG-TTCTCAAGGCAAACATTCAATTATAATCTGT-TTTAA-GANNNNNNNNNNAAAAATTCAA
65 CAAGTTTCTTGAGGCAGACATTCAATTATAATCT-TCTTCAACAAAAAATGTAAAAAAAATTCAA
* *
6913 CTTAAAATCAATTATAAGGTTATAAAACCTTTTAAAGCGAGTA
129 CTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGCGAGTA
* * * * * * * *
6956 ATAAAGCTTTTAAAAGGATAT-GTCACTATAAATGGATTTTTCTTACCAATAAATGCTTTTTTCT
1 AT-AAGGTTTTAGAAGGA-ATGGGCACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCT
* * * * * ** * * *
7020 TC-ACTTTCCCTAAGGCAGACATTTAATTCTAGCCTTCTTTAACCAAAAATGTAAAAAAAAAATC
64 TCAAGTTT-CTTGAGGCAGACATTCAATTATAATCTTCTTCAACAAAAAATGT-AAAAAAAATTC
*
7084 AACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGGGAGTA
127 AACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGCGAGTA
* * * ********** * *
7129 TTAAGGCTTTCGAAGG-ATGGTG-ACNNNNNNNNNNCTTTTATTGTCAATGAATACCTTTTTCTT
1 ATAAGGTTTTAGAAGGAATGG-GCACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTT
* * *
7192 CATGTGTCTCGAGGCA-AGCATTCAATTATAATCTAT-TTCAACAAAAAATGT-AAAAAAATTCA
65 CAAGTTTCTTGAGGCAGA-CATTCAATTATAATCT-TCTTCAACAAAAAATGTAAAAAAAATTCA
* * *
7254 ACTTAAAGTCATTTATGAGATTATAAAATCTTTTAAAGCGAGTA
128 ACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGCGAGTA
* * *
7298 ATAAGGTTTTTGAAGGAATGGGCAACTATAAATGGACTTCTCTTGCCAATGAATACCTTTTTGTT
1 ATAAGGTTTTAGAAGGAATGGGC-ACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTT
* * ********** * * *
7363 CAAGTTTCTTGAGGTAGACATTCAATTATAATATGT-TNNNNNNNNNNATATATAAAGAATTCAA
65 CAAGTTTCTTGAGGCAGACATTCAATTATAATCT-TCTTCAACAAAAAATGTAAAAAAAATTCAA
* * * * * *
7427 ATTAAAATCAATTTTAAGATTATAAAA-CTATTGAAAGTGTGTA
129 CTTAAAATCAATTATGAGATTATAAAACCT-TTTAAAGCGAGTA
* ** *
7470 ATAAGGCTTTT-GAAGGAATGAGTG-ACTATAAATGGATTTTTCTTATCAATGAATATCTTTTTC
1 ATAAGG-TTTTAGAAGGAATG-G-GCACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTC
*
7533 TTCACGTTTCT
63 TTCAAGTTTCT
7544 NNNNNNNNNN
Statistics
Matches: 550, Mismatches: 184, Indels: 47
0.70 0.24 0.06
Matches are distributed among these distances:
169 65 0.12
170 119 0.22
171 193 0.35
172 117 0.21
173 55 0.10
174 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.35
Consensus pattern (171 bp):
ATAAGGTTTTAGAAGGAATGGGCACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTC
AAGTTTCTTGAGGCAGACATTCAATTATAATCTTCTTCAACAAAAAATGTAAAAAAAATTCAACT
TAAAATCAATTATGAGATTATAAAACCTTTTAAAGCGAGTA
Found at i:9596 original size:172 final size:171
Alignment explanation
Indices: 9321--9743 Score: 525
Period size: 172 Copynumber: 2.5 Consensus size: 171
9311 TATAGCCTTC
* *
9321 TTTAACTAAAAATGTAAAAATAAA-TTAACTTAAAATCAATTATGAGATTATAAAACGTTTTAAA
1 TTTAAATAAAAATGTAAAAA-AAATTTAACTT-AAATCAATTATGAGATTATAAAACATTTTAAA
* * *
9385 GCGAGTAATAAAGCTTTTAAATAAATGGGTAACTATAAATAAACTTTTCTTTTCAATGAATGTCT
64 GCGAGTAATAAAGCTTTTAAAGAAATGGGTAACTATAAATAAACTTTTCTTGTCAATGAATATCT
*
9450 TTTTCTTCA-CATT-TCATGACGTAGACAGTCAATTATAATCTGT
129 TTTTCTTCATCATTCTCATGAC-AAG-CAGTCAATTATAATCTGT
* *
9493 TTTAAATAAAAATGTAAAAAAAATTTAACTTCAAATCAATT-TGGAGAATATAAAACAATTTAAA
1 TTTAAATAAAAATGTAAAAAAAATTTAACTT-AAATCAATTAT-GAGATTATAAAACATTTTAAA
* * * * * * *
9557 GCGAGTAGTAAAGCTTTTGAAGGAATGGGTGATTATAAATAGACTTTTCTTGTCAATGAATATTT
64 GCGAGTAATAAAGCTTTTAAAGAAATGGGTAACTATAAATAAACTTTTCTTGTCAATGAATATCT
** * *
9622 TTTTCTTCATGTTTCTCATGGCAAGCATTCAATTATAATCTGT
129 TTTTCTTCATCATTCTCATGACAAGCAGTCAATTATAATCTGT
* * *
9665 TTTAAA-AAGAATAT-AAAAAAATTTAACTTAAAGTCAATTATGAGATTATAAAACCTTTTAAAG
1 TTTAAATAAAAATGTAAAAAAAATTTAACTTAAA-TCAATTATGAGATTATAAAACATTTTAAAG
* *
9728 CAAGTAATAAGGCTTT
65 CGAGTAATAAAGCTTT
9744 NNNNNNNNNN
Statistics
Matches: 217, Mismatches: 28, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
169 3 0.01
170 53 0.24
171 11 0.05
172 140 0.65
173 4 0.02
174 6 0.03
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (171 bp):
TTTAAATAAAAATGTAAAAAAAATTTAACTTAAATCAATTATGAGATTATAAAACATTTTAAAGC
GAGTAATAAAGCTTTTAAAGAAATGGGTAACTATAAATAAACTTTTCTTGTCAATGAATATCTTT
TTCTTCATCATTCTCATGACAAGCAGTCAATTATAATCTGT
Done.