Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397782.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1082.0, 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: 12074
ACGTcount: A:0.24, C:0.08, G:0.09, T:0.23
Warning! 4246 characters in sequence are not A, C, G, or T
Found at i:368 original size:171 final size:160
Alignment explanation
Indices: 143--457 Score: 281
Period size: 170 Copynumber: 1.9 Consensus size: 160
133 TACAATCACG
* * * * *
143 TAATTGATTTTAAGTTGAATATTTTAATATTTCTGGTTAGAACAACTCATAATTGAATATTTGTC
1 TAATTAATTTTAAGTTGAATATTTTAATATTTCTAGTTAAAACAACTCATAATTGAATAGTTGCC
* * * **
208 TCGAGAAAAAAAAAGAAAAAGGCATTAATTGATTAGACAAGTCTATTTATAGTCGCCTATTCCTT
66 TCGAGAAAAAAAAAG-AAAAGGCATTAATTGACTAGAAAAGTCTATTTATAGTCACCTAGACCTT
273 CAAAAGCCTTATTACTCATTTTANNNNNNNNNNTAATCTCA
130 CAAAAGCCTTATTACTCATTTTA----------TAATCTCA
* * ** * *
314 TAATTAATTTTAGGTTGAAT-TTTTATATATTTTTAGTTAAAACAGTTTATAATTGAATGGTTGC
1 TAATTAATTTTAAGTTGAATATTTTA-ATATTTCTAGTTAAAACAACTCATAATTGAATAGTTGC
***** * * *
378 CTCGAGAAGTGTGAAGAAAAGTCATTCATTGACTAGAAAAGTCTATTTATAGTTACCTAGACCTT
65 CTCGAGAAAAAAAAAGAAAAGGCATTAATTGACTAGAAAAGTCTATTTATAGTCACCTAGACCTT
* *
443 CGAAAGCCTTGTTAC
130 CAAAAGCCTTATTAC
458 CCACTTTAAA
Statistics
Matches: 117, Mismatches: 26, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
170 59 0.50
171 58 0.50
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.37
Consensus pattern (160 bp):
TAATTAATTTTAAGTTGAATATTTTAATATTTCTAGTTAAAACAACTCATAATTGAATAGTTGCC
TCGAGAAAAAAAAAGAAAAGGCATTAATTGACTAGAAAAGTCTATTTATAGTCACCTAGACCTTC
AAAAGCCTTATTACTCATTTTATAATCTCA
Found at i:5228 original size:341 final size:335
Alignment explanation
Indices: 4664--6090 Score: 1010
Period size: 341 Copynumber: 4.2 Consensus size: 335
4654 TCGAGGCAAC
* * * * *
4664 CATTCAATTATAAA-CTGTTTTAACTAAAAATGTATAAAAATTGAACCTAAAATTAATTATGAGA
1 CATTCAATTA-AAATCTGTTTTAGCTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
* *
4728 TTATAAAATTATTTAAAGTGAGTAATAAGGCTTTCGAAGGAATAGGCGACTATAAATGGACTTGT
65 TTATAAAA-TATTTAAAGTGAGTAATAAGGCTTTCGAAGGAATGGGTGACTATAAATGGACTT-T
* * * * * * *
4793 CTAATCAAT-TAATGCCTTTTTTTTT--TGTTTCTCGAGACAAATATTCAATTAAG-AGTTGTTC
128 TTAATCAATAT-ATG-CTTTTTTTTTCATATTTCTTGAGACAAACATTCAATT--GTAATTATTT
* * * * * * * * *
4854 TAACCAGAAATATT-AAAATATTCAACTTAAAATCAATTACGCGATTGTACAACAATTTAAAGTG
189 TAA-TAAAAAAATTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAAC-ATTTAAAGTG
* *
4918 AGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAGTAGACTTTTCTTACCAATGAATG-TTTCT
252 AGTAATAA-GCTTTTGAAGGAATGAGTGACTATAA-TAGACTTTTCTTACCAATGAATGCGTT-T
*
4982 TTCTTCACGTTTCTCAATGTAGA
314 TTC-TCACGTTTCTCAAGGTAGA
* * *
5005 CATTCAATTAAAATCTGTGTTAGCTATAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGAT
1 CATTCAATTAAAATCTGTTTTAGCTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * *
5070 TCTAAAATCATTTAAAGTGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAGT-GACTTTTT
66 TATAAAAT-ATTTAAAGTGAGTAATAAGGCTTTCGAAGGAATGGGTGACTATAAATGGACTTTTT
* * * * * *
5134 AGTCAATATATGATTTTTTTTTCACATTTTTTAAGGCAAACATTCAATTGTAATCTATTTTAATA
130 AATCAATATATGCTTTTTTTTTCATATTTCTTGAGACAAACATTCAATTGTAAT-TATTTTAATA
* * *
5199 AAAAAAGTTAAAAAAATTCAGCCTAAAATCAATTATGAGACTATAAAATCATTTAAAGTGTGTAA
194 AAAAAA-TTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAA-CATTTAAAGTGAGTAA
*
5264 TGAAGCTTTTGAAGGAATTG-GTGACTATATATAGACTTTTCTTGCCAATGAATGCGTTTTTCTC
257 T-AAGCTTTTGAAGGAA-TGAGTGACTATA-ATAGACTTTTCTTACCAATGAATGCGTTTTTCTC
* **
5328 ATGTTTCTTGAGGTAGA
319 ACGTTTCTCAAGGTAGA
* * * * ** * * *
5345 CATTCAATCATAATATATTTTAAGC-AAAAACATAAAAATATTCAACTTAAAATCATTTATGAAA
1 CATTCAATTAAAATCTGTTTT-AGCTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
* * **
5409 ATATAAAAGTATTTAAAGTGAGTAGTAAGGCTTTTAAAGGGAATGGGTGACTATAAATGGACTTT
65 TTATAAAA-TATTTAAAGTGAGTAATAAGGCTTTCGAA-GGAATGGGTGACTATAAATGGACTTT
* * * * * * * *
5474 TCT-TTTAATAAATGCCTTTTTCTTCATATTTCTTGAGACAGACATTTAATTATAATTTATTTTA
128 T-TAATCAATATATGCTTTTTTTTTCATATTTCTTGAGACAAACATTCAATTGTAA-TTATTTTA
* * *
5538 AT-TAAAAATATAAAAAAATT-AACCTAAAATCAATTATGAGTTTATAAAACCATTTAAAGCGAG
191 ATAAAAAAAT-TAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAA-CATTTAAAGTGAG
* * *
5601 TAATAACGCTTTTGAAGGAATGAGTGACAATAAATGGAC-TTT-TT--C--T---T-C--ATTT-
254 TAATAA-GCTTTTGAAGGAATGAGTGACTAT-AATAGACTTTTCTTACCAATGAATGCGTTTTTC
*
5653 TCA------T-GAGGTAGA
317 TCACGTTTCTCAAGGTAGA
* * ** * * * * * *
5665 AATTCAATTATAGCCTATTTTAACAAAAAAAAGT-GAAAAATTTAACTTAAAATCAATTATGAGA
1 CATTCAATTAAAATCTGTTTTAGC-TAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
* * * * * *
5729 TTATAAAACCATTTGAAGTGAGAAATAAGGCTTTTGAAGTAATGGCTGACTATAAATGGACTTTG
65 TTATAAAA-TATTTAAAGTGAGTAATAAGGCTTTCGAAGGAATGGGTGACTATAAATGGACTTT-
* * *** * ** ** * * * * *
5794 CTT--GC-ATATGACTGCCTTTCCCTTCATGTTTCTCAAGGTAGATATTTAATTATAATATGTTT
128 -TTAATCAATAT-A-TGCTTTTTTTTTCATATTTCTTGAGACAAACATTCAATTGTAAT-TATTT
* * * * * *
5856 TAATAAAAAATATAAAAAAAATTAAACTTAAAATCAATTACGATATTATAAAACTATTTAAAGCG
189 TAATAAAAAA-ATTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAAC-ATTTAAAGTG
** * ** * *
5921 AGTAATAAAGCTTTCAAAGGTACAAGTGACTATGAATGGACTTTTC-TAGTCAATGAA--CAGTT
252 AGTAAT-AAGCTTTTGAAGGAATGAGTGACTAT-AATAGACTTTTCTTA-CCAATGAATGC-GTT
* *
5983 TTCTCTTCATGTTTCTTAAGGTAGA
313 TT-TC-TCACGTTTCTCAAGGTAGA
* * * * * **
6008 CATTCAATTATAGT-TAGTTTTAACTAAAAATGAAAAAAAAATTCAATTTAAAATCAATTACAAG
1 CATTCAATTAAAATCT-GTTTTAGCTAAAAATG-TAAAAAAATTCAACTTAAAATCAATTATGAG
6072 ATTATAAAACTATTTAAAG
64 ATTATAAAA-TATTTAAAG
6091 CAANNNNNNN
Statistics
Matches: 876, Mismatches: 148, Indels: 121
0.77 0.13 0.11
Matches are distributed among these distances:
318 3 0.00
319 28 0.03
320 124 0.14
321 22 0.03
322 68 0.08
323 6 0.01
326 1 0.00
327 3 0.00
328 4 0.00
330 2 0.00
331 1 0.00
333 2 0.00
334 2 0.00
336 4 0.00
338 12 0.01
339 25 0.03
340 197 0.22
341 232 0.26
342 71 0.08
343 28 0.03
344 41 0.05
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (335 bp):
CATTCAATTAAAATCTGTTTTAGCTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
TATAAAATATTTAAAGTGAGTAATAAGGCTTTCGAAGGAATGGGTGACTATAAATGGACTTTTTA
ATCAATATATGCTTTTTTTTTCATATTTCTTGAGACAAACATTCAATTGTAATTATTTTAATAAA
AAAATTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACATTTAAAGTGAGTAATAAG
CTTTTGAAGGAATGAGTGACTATAATAGACTTTTCTTACCAATGAATGCGTTTTTCTCACGTTTC
TCAAGGTAGA
Found at i:5248 original size:170 final size:168
Alignment explanation
Indices: 4606--6090 Score: 868
Period size: 170 Copynumber: 8.8 Consensus size: 168
4596 NNNNTAGGTA
* * ** *
4606 ACTATAAATAGACTTTTCTAGTCAATGAATGAC-TTTTCTTCATGCTTCTCGAGGCA-ACCATTC
1 ACTATAAATGGACTTTTCT-GTCAAT-AATG-CTTTTTTTTCATATTTCTTGAGGCAGA-CATTC
* * * *
4669 AATTATAA-ACTGTTTTAACT--AAAAATGTATAAAAATTGAACCTAAAATTAATTATGAGATTA
62 AATTATAATA-TATTTTAA-TAAAAAAAT-TAAAAAAATTCAACCTAAAATCAATTATGAGATTA
* * * *
4731 TAAAATTATTTAAAGTGAGTAATAAGGCTTTCGAAGGAATAGGCG
124 TAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * * * *
4776 ACTATAAATGGACTTGTCTAATCAATTAATGCCTTTTTTTT-TTGTTTCTCGAGACAAATATTCA
1 ACTATAAATGGACTTTTCT-GTCAA-TAATG-CTTTTTTTTCATATTTCTTGAGGCAGACATTCA
* * * * * * * * * *
4840 ATTA-AGAGT-TGTTCTAACCAGAAATATT-AAAATATTCAACTTAAAATCAATTACGCGATTGT
63 ATTATA-A-TATATTTTAA-TAAAAAAATTAAAAAAATTCAACCTAAAATCAATTATGAGATTAT
* * *
4902 ACAA-CAATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTG
125 AAAATC-ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * ** ** * *
4946 ACTATAAGTAGACTTTTCT-TACCAATGAATG-TTTCTTTCTTCACGTTTCTCAATGTAGACATT
1 ACTATAAATGGACTTTTCTGT--CAAT-AATGCTTT-TTT-TTCATATTTCTTGAGGCAGACATT
* * * * * * * * *
5009 CAATTAAAATCTGTGTTAGCT--ATAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTC
61 CAATTATAATATATTTTA-ATAAAAAAAT-TAAAAAAATTCAACCTAAAATCAATTATGAGATTA
* *
5072 TAAAATCATTTAAAGTGAGTAATAAGGCTTTCGAAGGTATGGGTG
124 TAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * *
5117 ACTATAAGT-GACTTTT-TAGTCAATATATGATTTTTTTTTCACATTTTTTAAGGCAAACATTCA
1 ACTATAAATGGACTTTTCT-GTCAATA-ATG-CTTTTTTTTCATATTTCTTGAGGCAGACATTCA
* * * *
5180 ATTGTAATCTATTTTAATAAAAAAAGTTAAAAAAATTCAGCCTAAAATCAATTATGAGACTATAA
63 ATTATAATATATTTTAATAAAAAAA-TTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAA
* *
5245 AATCATTTAAAGTGTGTAATGAA-GCTTTTGAAGGAATTGGTG
127 AATCATTTAAAGTGAGTAAT-AAGGCTTTTGAAGGAATGGGTG
* * * * * * *
5287 ACTATATATAGACTTTTCTTGCCAATGAATGCGTTTTTCTCATGTTTCTTGAGGTAGACATTCAA
1 ACTATAAATGGACTTTTC-TGTCAAT-AATGCTTTTTTTTCATATTTCTTGAGGCAGACATTCAA
* * * * * * * *
5352 TCATAATATATTTTAAGCAAAAACA-TAAAAATATTCAACTTAAAATCATTTATGAAAATATAAA
64 TTATAATATATTTTAA-TAAAAAAATTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAA
* *
5416 AGT-ATTTAAAGTGAGTAGTAAGGCTTTTAAAGGGAATGGGTG
128 A-TCATTTAAAGTGAGTAATAAGGCTTTTGAA-GGAATGGGTG
* * * * *
5458 ACTATAAATGGACTTTTCTTTTAATAAATGCCTTTTTCTTCATATTTCTTGAGACAGACATTTAA
1 ACTATAAATGGACTTTTCTGTCAAT-AATG-CTTTTTTTTCATATTTCTTGAGGCAGACATTCAA
* * *
5523 TTATAATTTATTTTAAT-TAAAAATATAAAAAAATT-AACCTAAAATCAATTATGAGTTTATAAA
64 TTATAATATATTTTAATAAAAAAAT-TAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAA
* * * *
5586 ACCATTTAAAGCGAGTAATAACGCTTTTGAAGGAATGAGTG
128 ATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * *
5627 ACAATAAATGGAC---T-T-T---T--T-C------TTCAT-TTTCATGAGGTAGAAATTCAATT
1 ACTATAAATGGACTTTTCTGTCAATAATGCTTTTTTTTCATATTTCTTGAGGCAGACATTCAATT
*** * * * * * *
5674 ATAGCCTATTTTAACAAAAAAAAGT-GAAAAATTTAACTTAAAATCAATTATGAGATTATAAAAC
66 ATAATATATTTTAA-TAAAAAAATTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAAT
* * * *
5738 CATTTGAAGTGAGAAATAAGGCTTTTGAAGTAATGGCTG
130 CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * *** * ** * * *
5777 ACTATAAATGGACTTTGCT-TGCATATGACTGCCTTTCCCTTCATGTTTCTCAAGGTAGATATTT
1 ACTATAAATGGACTTTTCTGT-CA-AT-AATG-CTTTTTTTTCATATTTCTTGAGGCAGACATTC
* * * * * *
5841 AATTATAATATGTTTTAATAAAAAATATAAAAAAAATTAAACTTAAAATCAATTACGATATTATA
62 AATTATAATATATTTTAATAAAAAA-ATTAAAAAAATTCAACCTAAAATCAATTATGAGATTATA
* * ** * ***
5906 AAA-CTATTTAAAGCGAGTAATAAAGCTTTCAAAGGTACAAGTG
126 AAATC-ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * *
5949 ACTATGAATGGACTTTTCTAGTCAATGAACAG-TTTTCTCTTCATGTTTCTTAAGGTAGACATTC
1 ACTATAAATGGACTTTTCT-GTCAAT-AA-TGCTTTT-TTTTCATATTTCTTGAGGCAGACATTC
* ** **
6013 AATTATAGT-TAGTTTTAACTAAAAATGAA--AAAAAAATTCAATTTAAAATCAATTACAAGATT
62 AATTATAATATA-TTTTAA-TAAAAA--AATTAAAAAAATTCAACCTAAAATCAATTATGAGATT
6075 ATAAAA-CTATTTAAAG
123 ATAAAATC-ATTTAAAG
6091 CAANNNNNNN
Statistics
Matches: 1039, Mismatches: 199, Indels: 152
0.75 0.14 0.11
Matches are distributed among these distances:
149 36 0.03
150 78 0.08
151 5 0.00
154 2 0.00
156 1 0.00
158 1 0.00
159 1 0.00
161 1 0.00
162 1 0.00
164 2 0.00
165 1 0.00
166 1 0.00
168 6 0.01
169 76 0.07
170 358 0.34
171 271 0.26
172 184 0.18
173 11 0.01
174 2 0.00
175 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (168 bp):
ACTATAAATGGACTTTTCTGTCAATAATGCTTTTTTTTCATATTTCTTGAGGCAGACATTCAATT
ATAATATATTTTAATAAAAAAATTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAATC
ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
Found at i:5675 original size:149 final size:151
Alignment explanation
Indices: 5480--5792 Score: 391
Period size: 150 Copynumber: 2.1 Consensus size: 151
5470 CTTTTCTTTT
* * * * ** **
5480 AATAAAT-GCCTTTTTCTTCATATTTCTTGAGACAGACATTTAATTATAATTTATTTTAATTAAA
1 AATAAATGGACTTTTTCTTCATATTTCATGAGACAGAAATTCAATTATAACCTATTTTAACAAAA
* * *
5544 AATA-TAAAAAAATTAACCTAAAATCAATTATGAGTTTATAAAACCATTTAAAGCGAGTAATAAC
66 AAAAGTAAAAAAATTAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGAAATAAC
5608 GCTTTTGAAGGAATGAG-TGAC
131 GCTTTTGAAGGAATG-GCTGAC
** *
5629 AATAAATGGACTTTTTCTTCAT-TTTCATGAGGTAGAAATTCAATTATAGCCTATTTTAACAAAA
1 AATAAATGGACTTTTTCTTCATATTTCATGAGACAGAAATTCAATTATAACCTATTTTAACAAAA
* * * * * *
5693 AAAAGTGAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTGAAGTGAGAAATAAG
66 AAAAGTAAAAAAATTAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGAAATAAC
*
5758 GCTTTTGAAGTAATGGCTGAC
131 GCTTTTGAAGGAATGGCTGAC
*
5779 TATAAATGGACTTT
1 AATAAATGGACTTT
5793 GCTTGCATAT
Statistics
Matches: 139, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
149 43 0.31
150 96 0.69
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (151 bp):
AATAAATGGACTTTTTCTTCATATTTCATGAGACAGAAATTCAATTATAACCTATTTTAACAAAA
AAAAGTAAAAAAATTAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGAAATAAC
GCTTTTGAAGGAATGGCTGAC
Found at i:5953 original size:172 final size:172
Alignment explanation
Indices: 5700--6091 Score: 456
Period size: 172 Copynumber: 2.3 Consensus size: 172
5690 AAAAAAAGTG
* * * * * * **
5700 AAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTGAAGTGAGAAATAAGGCTTTTG
1 AAAAATTAAACTTAAAATCAATTACGAGATTATAAAACTATTTAAAGCGAGAAATAAAGCTTTCA
* * *
5765 AAGTAATGGCTGACTATAAATGGACTTTGCTTG-CATATG-ACTGCCTTTCCCTTCATGTTTCTC
66 AAGTAATAGCTGACTATAAATGGACTTTGCTAGTCA-ATGAACAG-CTTTCCCTTCATGTTTCTC
* *
5828 AAGGTAGATATTTAATTATAA-TATGTTTTAA-TAAAAAAT-ATAAA
129 AAGGTAGACATTCAATTATAATTA-GTTTTAACT-AAAAATGA-AAA
* *
5872 AAAAATTAAACTTAAAATCAATTACGATATTATAAAACTATTTAAAGCGAGTAATAAAGCTTTCA
1 AAAAATTAAACTTAAAATCAATTACGAGATTATAAAACTATTTAAAGCGAGAAATAAAGCTTTCA
* * * * *
5937 AAGGTACA-AG-TGACTATGAATGGACTTTTCTAGTCAATGAACAGTTTTCTCTTCATGTTTCTT
66 AA-GTA-ATAGCTGACTATAAATGGACTTTGCTAGTCAATGAACAGCTTTCCCTTCATGTTTCTC
*
6000 AAGGTAGACATTCAATTATAGTTAGTTTTAACTAAAAATGAAAA
129 AAGGTAGACATTCAATTATAATTAGTTTTAACTAAAAATGAAAA
* * *
6044 AAAAATTCAATTTAAAATCAATTACAAGATTATAAAACTATTTAAAGC
1 AAAAATTAAACTTAAAATCAATTACGAGATTATAAAACTATTTAAAGC
6092 AANNNNNNNN
Statistics
Matches: 188, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
172 174 0.93
173 13 0.07
174 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (172 bp):
AAAAATTAAACTTAAAATCAATTACGAGATTATAAAACTATTTAAAGCGAGAAATAAAGCTTTCA
AAGTAATAGCTGACTATAAATGGACTTTGCTAGTCAATGAACAGCTTTCCCTTCATGTTTCTCAA
GGTAGACATTCAATTATAATTAGTTTTAACTAAAAATGAAAA
Found at i:7365 original size:171 final size:170
Alignment explanation
Indices: 7008--7874 Score: 703
Period size: 171 Copynumber: 5.1 Consensus size: 170
6998 AAAAAAAGTG
* *
7008 AAAAATTTAACTTAAAATCAATTATC-AGATTATAAAA-TCATTTAAAGCGAGAAATAAGGCTTT
1 AAAAATTCAACTTAAAATCAATTA-CGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGGCTTT
* * * ** * * *
7071 TGAAGTAAT-GGTGACTGTAAATAGACTTTGCT--TGCATATG-ATTGCCTTTCCCTTCACGTTT
64 TGAAGGAATGGGTGACTATAAATAGACTTTTCTAAT-CA-ATGAACAG-TTTTCTCTTCATGTTT
* * * *
7132 CTCGAA-GTAGATATTTAATTATAATATGTTTTAA-TCAAAAATAAAA
126 CTC-AAGGTAGACATTCAATTATATTA-GTTTTAACT-AAAAATGAAA
* * **
7178 AAAAATTAAACTTAAAATCAATTACGATATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCA
1 AAAAATTCAACTTAAAATCAATTACGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTG
* * * * *
7243 AAGGTACGGGTGACTATGAATGGACTTTTCTAGTCAATGAACAGTTTTCTCTTCATGTTTCTCAA
66 AAGGAATGGGTGACTATAAATAGACTTTTCTAATCAATGAACAGTTTTCTCTTCATGTTTCTCAA
7308 GGTAGACATTCAATTATAGTTAGTTTTAACTAAAAATGAAA
131 GGTAGACATTCAATTATA-TTAGTTTTAACTAAAAATGAAA
* * *
7349 AAAAATTCAACTTAAAATCAATTACAAGATTATAAAACTATTTAAAACAAGTAATAAGGCTTTTG
1 AAAAATTCAACTTAAAATCAATTACGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTG
* * * * * * * *
7414 AAGGAATGGATGATTACAAATAGACTTCTCTTA-CAAATG-ACTACCTTTTC-CTTTATATTTCT
66 AAGGAATGGGTGACTATAAATAGACTTTTCTAATC-AATGAAC-A-GTTTTCTCTTCATGTTTCT
*
7476 CAAGATAGACATTCAATTATAATCT-GTTTTAACCT-AAAAT-AGAA
128 CAAGGTAGACATTCAATTAT-AT-TAGTTTTAA-CTAAAAATGA-AA
* * * * * * * *
7520 AAACATTCAACTTAAAATCGATTATGAGAATACAAAACCATTTAAAGTGAGTAACAAGGCTTTTG
1 AAAAATTCAACTTAAAATCAATTACGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTG
* * * * ** * * * *
7585 AAGGCATGCGTGACTATGAATGGACTTTTCTAATCAATGAATGGTTTTTTCTTGATGCTTCTCGA
66 AAGGAATGGGTGACTATAAATAGACTTTTCTAATCAATGAACAGTTTTCTCTTCATGTTTCTCAA
* * * * * * *
7650 TGCAGCCATTCAATTACAATATGTTTTAACAAAAAATCTAAA
131 GGTAGACATTCAATTATATTA-GTTTTAACTAAAAAT-GAAA
* * * *
7692 AAAAA-TCAA-TCGAAAATTAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTT
1 AAAAATTCAACT-TAAAATCAATTACGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTT
* * * * * *
7755 GACGGAATAGCTGACTATAAGTAGACTTTTTTAATCAATGAATGC-CTTTT-TCTTCATGTTT-T
65 GAAGGAATGGGTGACTATAAATAGACTTTTCTAATCAATGAA--CAGTTTTCTCTTCATGTTTCT
* * * *
7817 CTGAGGTAAACATTCAATTATAAGTT-GTTCTAACTAAAAATGTAA
128 C-AAGGTAGACATTCAATTAT-A-TTAGTTTTAACTAAAAATGAAA
*
7862 AAATATTCAACTT
1 AAAAATTCAACTT
7875 NNNNNNNNNN
Statistics
Matches: 555, Mismatches: 110, Indels: 63
0.76 0.15 0.09
Matches are distributed among these distances:
169 2 0.00
170 81 0.15
171 439 0.79
172 30 0.05
173 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (170 bp):
AAAAATTCAACTTAAAATCAATTACGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTG
AAGGAATGGGTGACTATAAATAGACTTTTCTAATCAATGAACAGTTTTCTCTTCATGTTTCTCAA
GGTAGACATTCAATTATATTAGTTTTAACTAAAAATGAAA
Found at i:7832 original size:342 final size:337
Alignment explanation
Indices: 7008--7874 Score: 900
Period size: 342 Copynumber: 2.5 Consensus size: 337
6998 AAAAAAAGTG
* * * *
7008 AAAAATTTAACTTAAAATCAATTATCAGATTATAAAA-TCATTTAAAGCGAGAAATAAGGCTTTT
1 AAAAATTCAACTGAAAATCAATTATAAGATTATAAAACT-ATTTAAAGCGAGTAATAAGGCTTTT
* * * * * * *
7072 GAAGTAATGGTGACTGTAAATAGACTTTGCTTGCATATGATTGCCTTTCCCTTCACGTTTCTCGA
65 GAAGGAATGATGACTATAAATAGACTTT-CTTACA-ATGAATGCCTTTTCCTTCATGTTTCTCGA
* * * * * *
7137 AGTAGATATTTAATTATAATATGTTTTAATCAAAAATAAAAAAAAATTAAACTTAAAATCAATTA
128 GGTAGACATTCAATTATAAT-TGTTTTAA-CTAAAATAGAAAAAAATTCAACTTAAAATCAATTA
* * * * * * *
7202 CGATATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCAAAGGTACGGGTGACTATGAATGGA
191 CGAGAATACAAAACCATTTAAAGCGAGTAACAAGGCTTTCAAAGGCACGCGTGACTATGAATGGA
* * * * *
7267 CTTTTCTAGTCAATGAACAGTTTTCTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTTAGT
256 CTTTTCTAATCAATGAACAGTTTTCTCTTCATGCTTCTCAAGGCAGACATTCAATTACAATTAGT
*
7332 TTTAACTAAAAATGAAA
321 TTTAACAAAAAATGAAA
* * * *
7349 AAAAATTCAACTTAAAATCAATTACAAGATTATAAAACTATTTAAAACAAGTAATAAGGCTTTTG
1 AAAAATTCAACTGAAAATCAATTATAAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTG
* * * * * * *
7414 AAGGAATGGATGATTACAAATAGACTTCTCTTACAAATGACTACCTTTTCCTTTATATTTCTCAA
66 AAGGAAT-GATGACTATAAATAGACTT-TCTTAC-AATGAATGCCTTTTCCTTCATGTTTCTCGA
* * *
7479 GATAGACATTCAATTATAATCTGTTTTAACCTAAAATAGAAAAACATTCAACTTAAAATCGATTA
128 GGTAGACATTCAATTATAAT-TGTTTTAA-CTAAAATAGAAAAAAATTCAACTTAAAATCAATTA
* * ** *
7544 TGAGAATACAAAACCATTTAAAGTGAGTAACAAGGCTTTTGAAGGCATGCGTGACTATGAATGGA
191 CGAGAATACAAAACCATTTAAAGCGAGTAACAAGGCTTTCAAAGGCACGCGTGACTATGAATGGA
** * * * * *
7609 CTTTTCTAATCAATGAATGGTTTTTTCTTGATGCTTCTCGATGCAGCCATTCAATTACAA-TATG
256 CTTTTCTAATCAATGAACAGTTTTCTCTTCATGCTTCTCAAGGCAGACATTCAATTACAATTA-G
*
7673 TTTTAACAAAAAATCTAAA
320 TTTTAACAAAAAAT-GAAA
* * *
7692 AAAAA-TCAA-TCGAAAATTAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTT
1 AAAAATTCAACT-GAAAATCAATTATAAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTT
* * * * *
7755 GACGGAATAGCTGACTATAAGTAGACTTTTTTAATCAATGAATGCCTTTTTCTTCATGTTT-TCT
65 GAAGGAAT-GATGACTATAAATAGACTTTCTT-A-CAATGAATGCCTTTTCCTTCATGTTTCTC-
* * *
7819 GAGGTAAACATTCAATTATAAGTTGTTCTAACTAAAA-ATGTAAAAATATTCAACTT
126 GAGGTAGACATTCAATTATAA-TTGTTTTAACTAAAATA-G-AAAAAAATTCAACTT
7875 NNNNNNNNNN
Statistics
Matches: 433, Mismatches: 80, Indels: 25
0.80 0.15 0.05
Matches are distributed among these distances:
340 1 0.00
341 78 0.18
342 342 0.79
343 12 0.03
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (337 bp):
AAAAATTCAACTGAAAATCAATTATAAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTG
AAGGAATGATGACTATAAATAGACTTTCTTACAATGAATGCCTTTTCCTTCATGTTTCTCGAGGT
AGACATTCAATTATAATTGTTTTAACTAAAATAGAAAAAAATTCAACTTAAAATCAATTACGAGA
ATACAAAACCATTTAAAGCGAGTAACAAGGCTTTCAAAGGCACGCGTGACTATGAATGGACTTTT
CTAATCAATGAACAGTTTTCTCTTCATGCTTCTCAAGGCAGACATTCAATTACAATTAGTTTTAA
CAAAAAATGAAA
Done.