Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397538.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3371.0, 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: 9253
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.31
Warning! 1492 characters in sequence are not A, C, G, or T
Found at i:739 original size:169 final size:170
Alignment explanation
Indices: 1--2855 Score: 1744
Period size: 172 Copynumber: 16.7 Consensus size: 170
* * * * *
1 AAACTATTTAAAGTGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGG-CATTTCTTGC
1 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGC
** * * * ** ** * *
65 CAATGAATATCTTTTTTTTCACGTTTTTTGAGACAGACATTCAATTATAAT-TTTTTGTAACCAA
66 CAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTT-TAACTAA
* * *
129 AAATGTGAAAAAAATCAACCTAAAATTAATTATGAGATGATA
130 AAATGT-AAAAAATTCAACCTAAAATCAATTATGAGATTATA
** * ********** * * * *
171 AAATAATTTAAAGCGAGTANNNNNNNNNNTGAAGGGATGGGTGACTATAAATGGACTTTTCTTGT
1 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGC
* * * * * *
236 CAA-G---G--TTCTTCTTCATGTTTCCCAAGGTCA-ACACTCAATTAGAAT-TCGTTTGAACAA
66 CAATGAATGCCTTTTTCTTCATGTTTCTCAAGGT-AGACATTCAATTATAATCT-GTTTTAACTA
* ** * * *
293 AAAATGTGCAAAGAATTCAAATTAAAATTAATTTTGAGATTAGA
129 AAAATGT--AAAAAATTCAACCTAAAATCAATTATGAGATTATA
* * * * **********
337 AAACCATTTAGAGCGAGAAATAAGGCTTTTAAAGAAATGANNNNNNNNNNATGGACTTTTCTTGC
1 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGC
** * * * * * * *
402 CAATGAATATCGTTTTCTTCATGTTTCT-TAGGACAGACATTCAATTACAATTTATTCTAA-TCA
66 CAATGAATGCCTTTTTCTTCATGTTTCTCAAGG-TAGACATTCAATTATAATCTGTTTTAACT-A
* * * *
465 AAAATATTAAAAAAATTCAATCTAAAATCAATTATGAGATTGTG
129 AAAAT-GT-AAAAAATTCAACCTAAAATCAATTATGAGATTATA
* * * * * ** *
509 AAACCATTTAATGTCAATAATAGGGCTTTTGAAGGAACAAGCGACTATAAAT-GAGCTTTTCTTG
1 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGA-CTTTTCTTG
* * * * *
573 TCAATGAATACCTTTTTCTTCACGTTTTTCAAGGCAGACATTCAATTATAATCTGTTTTAACTAA
65 CCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTAA
* *
638 AAATGT-AAAATTTGAACCTAAAATCAATTATGAGATTATA
130 AAATGTAAAAAATTCAACCTAAAATCAATTATGAGATTATA
********** *
678 AAACCNNNNNNNNNNAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGACTTTTCTTGC
1 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGC
* * * * * * * * *
743 CATTAAAGGCTTTTTTTTTCATGTTTCTCAA-GTAGACATTCAATAATAATCT-ATTCAACAAAA
66 CAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTAAA
* *
806 AATGTAACAAAATTCAACCTAAAATCAATAATGAGATTATG
131 AATGTAA-AAAATTCAACCTAAAATCAATTATGAGATTATA
* * * * * *
847 AAATCATTTAAAGCGAGTAATACGGCTTTTAAAGGAATGCGTGACTATAAATAGACTTTTCTTAC
1 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGC
* * *
912 CAATGAATGTCTTTTT-TTCATGTTTCTCAAGGTAGACATTCAAATATTATCTGTTTTAACTAAA
66 CAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTAAA
* *
976 AATGTACAAAGAATTCAAACTAAAATCAATTTTGAGATTATA
131 AATGTA-AAA-AATTCAACCTAAAATCAATTATGAGATTATA
1018 AAACCATTTAAAGTGAGTAATAAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTG
1 AAACCATTTAAAGTGAGTAAT-AAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTG
* * ** * *
1083 CCAATGAATGCATTTCTT-TTCAAGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTCAACCA
65 CCAATGAATGCCTTT-TTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTA
** * * *
1147 AAAATGTAAAAAAAATT-AAATTAAAATCAATTAAGGGATTACA
129 AAAATGT--AAAAAATTCAACCTAAAATCAATTATGAGATTATA
* * * * * * * *
1190 AAGCCATTTAATGTGAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGGCTTTCCTTAC
1 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGC
* * * * * *
1255 CCATGAATAG-CTTCTCCTTTACAT-TTT-TCAAGGTAGACATTTAATTATAATCTATTCTAA-T
66 CAATGAAT-GCCTTTTTC-TT-CATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACT
* *
1316 AAAATATGTAAAAAAATTTAAACCTAAAATCAATTATGAGAATATA
128 AAAA-ATGT-AAAAAA-TTCAACCTAAAATCAATTATGAGATTATA
* * * *
1362 AAACCATTTAAATTTAGTAATAAGGCTTTTAAAGGAATGGGTGATTATAAATGGACTTTTCTTGC
1 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGC
* * * * * * *
1427 CTATGAATGTCTTTTTTCTT-ATGTTTCTCGAGGTAGATATTTAATTATAGTCTGTTTTAACCAA
66 CAATGAATG-CCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTAA
1491 AAATGTATAAAGAATTCGAA-CTAAAATCAAATT-TGAGATTATA
130 AAATGTA-AAA-AATTC-AACCTAAAATC-AATTATGAGATTATA
* * ********* * *
1534 AAACCATTTGAAGCGAGTAATAAGGCTTTTAAAGGAAT-ANNNNNNNNNNAATAGACTTTTTTTG
1 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGA-GTGACTATAAATGGACTTTTCTTG
* * * * * *
1598 CTAATGAATGCATTTTGT-TTCACGTTTCTCAAGGTAAACATTCAATTGTAATCTGTTTTAGCTA
65 CCAATGAATGCCTTTT-TCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTA
* ** *
1662 AAAAAGTATAAAGAATTCAAATTAAAATCAATTCTGAGATTATA
129 AAAATGTA-AAA-AATTCAACCTAAAATCAATTATGAGATTATA
* * * * * * * * *
1706 AAACCTTTTAAAGTAAGTGATAAGGATTTTGAAA-GAATTAATGAGTATAAATGGCCTTTTTTTG
1 AAACCATTTAAAGTGAGTAATAAGGCTTTT-AAAGGAATGAGTGACTATAAATGGACTTTTCTTG
* * * ** ** * * *
1770 GCAATGAATGCCTTTTTTTTCATATTTCTTGAGGTAGACACCCAATTAGAATTTGTTTTAACCAA
65 CCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTAA
* * * * *
1835 AAATATAAAAAAAATTTGAACTTAAAATCAACGT-TGAGCTTATA
130 AAATGT--AAAAAA-TTCAACCTAAAATCAA-TTATGAGATTATA
********** * *
1879 AAACCATTTAAAGTGAGTAATAAGGNNNNNNNNNNAATGGGTGAATATAAATGGACTTTTCTTGC
1 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGC
** * * * * * * *
1944 TGATGAATACCTATTTCTTCATGTTTC-CTAAGGCAAAGATGCAATTATAATCTGTTCTAACTAA
66 CAATGAATGCCTTTTTCTTCATGTTTCTC-AAGGTAGACATTCAATTATAATCTGTTTTAACTAA
* * **
2008 AAATGTAAAATAATTCAACTTAAAATCAATTATTAGGGTATA
130 AAATGTAAAA-AATTCAACCTAAAATCAATTATGAGATTATA
** * * * ** * *
2050 AAACC-TGTTAAA-CAAGTAATAACGCATTCAAAGGTTTGAGTGACTATAAATGGACTTTTCATA
1 AAACCAT-TTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTG
* * * * * * **
2113 CCAATGGATGGCTTTAATT-TT-ATGTTCCCCAAGGCAGAGATTCAATTATAGCCT-TTTTGAAC
65 CCAATGAATGCCTTT--TTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTT-AAC
* * **********
2175 TAAAAATATAAAAAAATTCAACTTAANNNNNNNNNNGAGATTATA
127 TAAAAATGT-AAAAAATTCAACCTAAAATCAATTATGAGATTATA
* *** * * * *
2220 AAATCATTTAAACCAAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATAGG-CTTTTATTG
1 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAAT-GGACTTTTCTTG
** * * ** **
2284 CTGATGAATGTCTTTTTCTTCATATTTCTTGAGGTAGACATTCAATTATAATAAGTTTTAACTAA
65 CCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTAA
* * * * *
2349 AATTGTAAAAAAAATTGAACTTAAAATCAATTATCAGACTATA
130 AAATGT--AAAAAATTCAACCTAAAATCAATTATGAGATTATA
********** * * * * *
2392 AAANNNNNNNNNNTGAGTAATAAGGCTTTTGAAGGAATGAGTAACTATAAATGCATTTTTCTTAC
1 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGC
** ** * * * * ** * *
2457 CAATGAATATCTTTTTCTTCACATTTTTGAAGGCAGAGATTCAATTATAAAATGTTCTAACCAAA
66 CAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTAAA
* *
2522 AATGTAAAAAAATTCAGCTTAAAATCAATTATGAGATTAT-
131 AATGT-AAAAAATTCAACCTAAAATCAATTATGAGATTATA
************************* *
2562 -AANNNNNNNNNNNNNNNNNNNNNNNNNTTAAAGGAATGTGTGACTATAAATGGACTTTTCTTGC
1 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGC
* * * ** * * *
2626 CAATGAGTGTCTTTTTCTTCACT-TTTTTTGAGGTCGACATTCAGTTATAATCTGTTTTGACTAA
66 CAATGAATGCCTTTTTCTTCA-TGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTAA
* * * *
2690 AAATGTACAAAGAATTCAAACTAAAATCAATTTTGGGATTAGA
130 AAATGTA-AAA-AATTCAACCTAAAATCAATTATGAGATTATA
* * *
2733 AAACCATTTAAAGTGAGTAATAAGGC-TTTAAAAGAATAAGTGACTATAAATGGACTTTTCTTAC
1 AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGC
* * *
2797 CCATGAATG-GTTTTTCTTCATGTTTCTCAAGGTAGACATTCAACTATAATCTGTTTTAA
66 CAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAA
2856 TCATAAATGT
Statistics
Matches: 2033, Mismatches: 571, Indels: 162
0.73 0.21 0.06
Matches are distributed among these distances:
165 39 0.02
166 71 0.03
167 14 0.01
168 35 0.02
169 313 0.15
170 246 0.12
171 360 0.18
172 747 0.37
173 202 0.10
174 5 0.00
175 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (170 bp):
AAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGC
CAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTAAA
AATGTAAAAAATTCAACCTAAAATCAATTATGAGATTATA
Found at i:5870 original size:171 final size:171
Alignment explanation
Indices: 5154--5851 Score: 625
Period size: 171 Copynumber: 4.1 Consensus size: 171
5144 NNNNNNNNNA
* * * * *
5154 GACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTT-CTCAAGGTAAACATTGAATTATAAGC
1 GACTTTTCTTGCCAATGAATACCTTTTTCTTCATCTTTCCT-AAGGAAAACATTCAATTATAATC
* * * * * * * ********** *
5218 TGTTTTAACTAAAAATGTACAAAGAATTCAAACTAAAATCNNNNNNNNNNTTATAAAACCATTTA
65 TGTTCTAACCACAAATTTA-AAAAAATTCAATCAAAAATCAATTATTAGATTATAAAGCCATTTA
* * * * * * * *
5283 AAGTGAGTAATAAGGCTTTTAAAAGAAAGGGTAACTGTTAATG
129 ATGTGAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATG
* * ** ** * * *** *
5326 GACTTTTCTTGCAAATAAATATATTTTTCTTTTTCTTTCTTGAGGTGGACAGTCAATTATAATCT
1 GACTTTTCTTGCCAATGAATACCTTTTTCTTCATCTTTCCTAAGGAAAACATTCAATTATAATCT
* ** * * * *
5391 GTTTTAATAAAAAATTTACAAAGAATTCAA-AATAAAATCAATT-TTGAGATTATAAAACCATTT
66 GTTCTAACCACAAATTTA-AAAAAATTCAATCA-AAAATCAATTATT-AGATTATAAAGCCATTT
* *
5454 GAA-GTGAGTAATATGGCTTTTGAAGGAATGGGTGA-TGATAAATG
128 -AATGTGAGTAATAAGACTTTTGAAGGAATGGGTGACT-ATAAATG
* * * * * * *
5498 GATTTTTTTTGCCAATTAATACCTTTTTCCTCATCTTTCCTAGGGCAGACATTCAATTATAATCT
1 GACTTTTCTTGCCAATGAATACCTTTTTCTTCATCTTTCCTAAGGAAAACATTCAATTATAATCT
* * * * * *
5563 GTTCTAACCACAGATTTAAAAAAATTCAGTCTAAAATTAATTATTAGATTATGAAGCCACTTAAT
66 GTTCTAACCACAAATTTAAAAAAATTCAATCAAAAATCAATTATTAGATTATAAAGCCATTTAAT
*
5628 GTGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATG
131 GTGAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATG
* * * * *
5669 GGCTTTTCTTACCAATGAATACCTTTTTCTTTATTTTTTCC-AAGGAAAATATTCAATTATAATC
1 GACTTTTCTTGCCAATGAATACCTTTTTCTTCA-TCTTTCCTAAGGAAAACATTCAATTATAATC
*
5733 TGTTCTAACCACAAATGTAAAAAAATTCAATCAAAAATCAATTATTAGATTATAAAGCCATTTAA
65 TGTTCTAACCACAAATTTAAAAAAATTCAATCAAAAATCAATTATTAGATTATAAAGCCATTTAA
*
5798 TGTGAGTAATAAGACTTTTGAAGGATTGGGTGACTATAAATG
130 TGTGAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATG
5840 GACTTTTCTTGC
1 GACTTTTCTTGC
5852 TAGTGAATGT
Statistics
Matches: 426, Mismatches: 90, Indels: 21
0.79 0.17 0.04
Matches are distributed among these distances:
170 2 0.00
171 222 0.52
172 199 0.47
173 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
GACTTTTCTTGCCAATGAATACCTTTTTCTTCATCTTTCCTAAGGAAAACATTCAATTATAATCT
GTTCTAACCACAAATTTAAAAAAATTCAATCAAAAATCAATTATTAGATTATAAAGCCATTTAAT
GTGAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATG
Found at i:5928 original size:171 final size:171
Alignment explanation
Indices: 5378--5964 Score: 506
Period size: 171 Copynumber: 3.4 Consensus size: 171
5368 AGGTGGACAG
* * * ** *
5378 TCAATTATAATCTGTTTTAATAAAAAATTTAC-AAAGAATTCAAAATAAAATCAATT-TTGAGAT
1 TCAATTATAATCTGTTCTAACAAAAAA--TACAAAAAAATTCAATCTAAAATTAATTATT-AGAT
* * * * *
5441 TATAAAACCATTTGAA-GTGAGTAATATGGCTTTTGAAGGAATGGGTGA-TGATAAATGGATTTT
63 TATAAAGCCATTT-AATGTGAGTAATAAGACTTTTGAAGGAATGAGTGACT-ATAAATGGACTTT
* * * * * * *
5504 TTTTGCCAATTAATACCTTTTTCCTCA--TCTTTCCTAGGGCAGACAT
126 TCTTACCAATGAATACCTTTTTCTTCACGT-TTTCC-AAGGAAAACAT
* * * ** *
5550 TCAATTATAATCTGTTCTAACCACAGATTTAAAAAAATTCAGTCTAAAATTAATTATTAGATTAT
1 TCAATTATAATCTGTTCTAACAAAAAATACAAAAAAATTCAATCTAAAATTAATTATTAGATTAT
* * *
5615 GAAGCCACTTAATGTGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATGGGCTTTTCTTA
66 AAAGCCATTTAATGTGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTA
* ** *
5680 CCAATGAATACCTTTTTCTTTATTTTTTCCAAGGAAAATAT
131 CCAATGAATACCTTTTTCTTCACGTTTTCCAAGGAAAACAT
* * ** * *
5721 TCAATTATAATCTGTTCTAACCACAAATGTAAAAAAATTCAATCAAAAATCAATTATTAGATTAT
1 TCAATTATAATCTGTTCTAACAAAAAATACAAAAAAATTCAATCTAAAATTAATTATTAGATTAT
* * *
5786 AAAGCCATTTAATGTGAGTAATAAGACTTTTGAAGGATTGGGTGACTATAAATGGACTTTTCTTG
66 AAAGCCATTTAATGTGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTA
* * *** ********** *
5851 CTAGTGAATGTGTTTTTCTTCACGTNNNNNNNNNNAGACAT
131 CCAATGAATACCTTTTTCTTCACGTTTTCCAAGGAAAACAT
* *
5892 TCAATTATAGTCTGTT-TCAATAAAAAATACAAAAAAATTCAA-CTTAAAATTAATTATTAGATT
1 TCAATTATAATCTGTTCT-AACAAAAAATACAAAAAAATTCAATC-TAAAATTAATTATTAGATT
*
5955 ATAAAACCAT
64 ATAAAGCCAT
5965 NNNNNNNNNN
Statistics
Matches: 338, Mismatches: 69, Indels: 17
0.80 0.16 0.04
Matches are distributed among these distances:
170 5 0.01
171 302 0.89
172 30 0.09
173 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (171 bp):
TCAATTATAATCTGTTCTAACAAAAAATACAAAAAAATTCAATCTAAAATTAATTATTAGATTAT
AAAGCCATTTAATGTGAGTAATAAGACTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTA
CCAATGAATACCTTTTTCTTCACGTTTTCCAAGGAAAACAT
Found at i:7376 original size:171 final size:168
Alignment explanation
Indices: 6382--7504 Score: 667
Period size: 172 Copynumber: 6.5 Consensus size: 168
6372 NNNNNNNNNT
* ** *
6382 TATTACTCACTTCAAATGGTTTTATAATCTCAAAATTGATTTTATTTTAAATTTTTTGTACATTT
1 TATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGA-TTTAGATTAAATATTTT-TACATTT
** * * * * * * ** * *
6447 TTTATTAAAATAGATTATAATTGACTGTCTACCTAAAGAAACAG-AAAGAAAAATACATTTATTT
64 TTGGTTAAAACAGATTATAATTGAATGTTTCCCT-AGGAAAC-GTGAAGAAAAAGGCATTCATTG
* * * * * * *
6511 GCAAGAAAAGTCCATTAACAATCACCCATTCTTTTAAAAGCC
127 GCAAGAAAAGACCATTTATAGTCACTCATTCCTTCAAAAGCC
* ** * * *
6553 TTATTACTCCCTTTAAATAATTTTATAATCTCAAAATTGATTTTAGTTTGAATTTTTTGTACATT
1 -TATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGA-TTTAGATTAAATATTTT-TACATT
* * * * * * *
6618 TGTT-GTTAAAGCAGCTTATAATTGAATGTTTATCTTAAGAAATGTAAAGAAAAAGGCATTCATT
63 T-TTGGTTAAAACAGATTATAATTGAATGTTT-CCCTAGGAAACGTGAAGAAAAAGGCATTCATT
* * * * * * *
6682 GACAAAAAAAAGTCTATTTATAGTCAC-CTATTTCTTTAATAGCC
126 GGC-AAGAAAAGACCATTTATAGTCACTC-ATTCCTTCAAAAGCC
* ********** * * *
6726 TTATTACTCGCTTTAAATGGTTTTNNNNNNNNNNAATTGATTTTAGGTTGAATTTTTTTACATTT
1 -TATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGA-TTTAGATTAAATATTTTTACATTT
* * * * * * **********
6791 TTGGTTAGTAA-AGATTATAATTGAATGTCTACCTTGGGATATGTGAANNNNNNNNNNTTCATTG
64 TTGGTTA-AAACAGATTATAATTGAATGT-TTCCCTAGGAAACGTGAAGAAAAAGGCATTCATTG
* * * *
6855 ACAA-AAAAG-CCTGTTTATAGTTACCCATTCCTTCAAAAGCC
127 GCAAGAAAAGACC-ATTTATAGTCACTCATTCCTTCAAAAGCC
* * * * * * * *
6896 ATATTTCTCACATTAAATGGCTTTATAATCTCATAATTTATTTGAGATTAAATTTTTTTATAGTT
1 -TATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTT-AGATTAAATATTTTTACATTT
* * * * *
6961 TTGGTTAGAACAAATTATAATTGAATATTTTCCCTAAGAAACGTGAAGAAAAAGGTATTCATTGG
64 TTGGTTAAAACAGATTATAATTGAAT-GTTTCCCTAGGAAACGTGAAGAAAAAGGCATTCATTGG
*
7026 CAAGAAAAGACCATTTATAGTCACTCATTCCTTCAAAAGACT
128 CAAGAAAAGACCATTTATAGTCACTCATTCCTTCAAAAG-CC
** * * * * *
7068 TATTACTCACTTTAAAATTATTTTATACTCTCAAAATTGATTTTAGTTTGAA-ATCTTTGCATAT
1 TATTACTCACTTT-AAATGGTTTTATAATCTCAAAATTGA-TTTAGATTAAATATTTTTACAT-T
* * * * * **
7132 GTTTAGTTAAAACAGATTACAACTGAACGTCTAGCTAGAGAAACGTGAAGAAAAAGGCATTCATT
63 -TTTGGTTAAAACAGATTATAATTGAATGTTTCCCTAG-GAAACGTGAAGAAAAAGGCATTCATT
* ********** *
7197 GGCAAGAAAAGTCCATTTANNNNNNNNNNTTCCTTTAAAAGCC
126 GGCAAGAAAAGACCATTTATAGTCACTCATTCCTTCAAAAGCC
* *
7240 TCATTACTCACTTTATATGGTTTTATAATCTCAAAATTGACTTTAGGTTAAATATTTTTACATTT
1 T-ATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGA-TTTAGATTAAATATTTTTACATTT
* *
7305 TTGGTTAAAACAGATTATAATTGAATGTTTCCCTTAGGAAACTTGAAGAAAAAGGCATTCATTGC
64 TTGGTTAAAACAGATTATAATTGAATGTTTCCC-TAGGAAACGTGAAGAAAAAGGCATTCATTGG
* * * *
7370 CAAGAAAAGCCCATTTATAGCCACCCATTCCTTTAAAAGCC
128 CAAGAAAAGACCATTTATAGTCACTCATTCCTTCAAAAGCC
** ** * * * * * *
7411 TTATTACTTGCTTTAAATGGTTTTCCAATCCCAAAATTGTTTTTAGTTTGAATGCTTTGTACATT
1 -TATTACTCACTTTAAATGGTTTTATAATCTCAAAATTG-ATTTAGATTAAAT-ATTTTTACATT
* * * *
7476 TTTAGTCAAAACATATTAGAATTGAATGT
63 TTTGGTTAAAACAGATTATAATTGAATGT
7505 CGACCTCAAG
Statistics
Matches: 729, Mismatches: 195, Indels: 54
0.75 0.20 0.06
Matches are distributed among these distances:
169 6 0.01
170 111 0.15
171 176 0.24
172 258 0.35
173 178 0.24
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.38
Consensus pattern (168 bp):
TATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAGATTAAATATTTTTACATTTTT
GGTTAAAACAGATTATAATTGAATGTTTCCCTAGGAAACGTGAAGAAAAAGGCATTCATTGGCAA
GAAAAGACCATTTATAGTCACTCATTCCTTCAAAAGCC
Found at i:8039 original size:171 final size:168
Alignment explanation
Indices: 7560--8226 Score: 540
Period size: 171 Copynumber: 3.9 Consensus size: 168
7550 NNNNNNNNTT
* * * **
7560 CTCGCTTTAAATTGTTTTATAATCACATAATTGATTTTAGGTTGAA-TTTTTTACATTTTTGGTT
1 CTCG-TTTAAATGGTTTTATAATCTCATAATTGATTTTA-GTTGAATTTTTTTATATTTTTTATT
* * * *
7624 AGAACATATTATAATTGAAT-CTCTGCCTTTGAAAACGTAAAGAAAAAGGTATTCATTGGCAAGA
64 AAAACAGATTATAATTGAATGC-CTGCCTTGGAAAACGTAAAGAAAAAGGCATTCATTGGCAAGA
* * * *
7688 AAAGCGTATTTATAGTTACTCATTCCTTTAAAAGCCTTATTA
128 AAAGC-CATTTATAGTCACCCATTCCTTCAAAAGCCTTATTA
* * * * *
7730 CAC-TTTAAATGGTTTTATAGTCTGATAATTGATTTTAAGTTTAATTTTTTT-TATATTTTAGTT
1 CTCGTTTAAATGGTTTTATAATCTCATAATTGATTTT-AGTTGAATTTTTTTATATTTTTTA-TT
* * * * * * *
7793 AAAACAGATTACAATTGAATGTCTACCTTGAAAAACGTGAAGAAAAAGGCATTCATTGACAAGGA
64 AAAACAGATTATAATTGAATGCCTGCCTTGGAAAACGTAAAGAAAAAGGCATTCATTGGCAAGAA
* *
7858 AAGCCCATTTATTGTCACCCATTCCTTCAAAAGTCTTATTA
129 AAG-CCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTA
*
7899 CTCGGTTTAAATGGATTTATAATCTCATAATTGATTTTGAGTTGAATTTTTTTATATTTTTTATT
1 CTC-GTTTAAATGGTTTTATAATCTCATAATTGATTTT-AGTTGAATTTTTTTATATTTTTTATT
* ** ** * * * * * *
7964 AAAAAAGGCTATAATTGAATGCCTGCCTTGGGGAACATAAAGCAAAAGCCATCCATTGGTATGAA
64 AAAACAGATTATAATTGAATGCCTGCCTTGGAAAACGTAAAGAAAAAGGCATTCATTGGCAAGAA
* * ** *
8029 AAGTCCATTTATATTCACTCA-AACTTTAAAATGCCTTATTA
129 AAG-CCATTTATAGTCACCCATTCCTTCAAAA-GCCTTATTA
* ** * * * ** *
8070 CTTGCTTTAACA-GGTTTTATACCCTAATAATTGATTTTAAGTTGAAGTATTTTACCTTTTTTGT
1 CTCG-TTTAA-ATGGTTTTATAATCTCATAATTGATTTT-AGTTGAATTTTTTTATATTTTTTAT
** * * * * * * * * *
8134 TGGAATAGATTATAATTG-CTTCTCTACCTAAGG-AAACATGAATAAAAAGACATTCATTGGCAA
63 TAAAACAGATTATAATTGAATGC-CTGCCT-TGGAAAACGTAAAGAAAAAGGCATTCATTGGCAA
*
8197 GAAAAGTCCATTTATAGCCACCCATTCCTT
126 GAAAAG-CCATTTATAGTCACCCATTCCTT
8227 TANNNNNNNN
Statistics
Matches: 390, Mismatches: 93, Indels: 26
0.77 0.18 0.05
Matches are distributed among these distances:
168 39 0.10
169 97 0.25
170 13 0.03
171 227 0.58
172 14 0.04
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (168 bp):
CTCGTTTAAATGGTTTTATAATCTCATAATTGATTTTAGTTGAATTTTTTTATATTTTTTATTAA
AACAGATTATAATTGAATGCCTGCCTTGGAAAACGTAAAGAAAAAGGCATTCATTGGCAAGAAAA
GCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTA
Found at i:8755 original size:172 final size:170
Alignment explanation
Indices: 8337--8984 Score: 554
Period size: 172 Copynumber: 3.8 Consensus size: 170
8327 TAATTGGGTG
* * * *
8337 TCTATCTTGAGAAACATGAAGAAAGAAGCATTCATTGGCAAGAAAAGTCCATTTATACTCACTCA
1 TCTACCTTGAGAAACATG-AGAAAAAAGCATTCATAGGCAAGAAAAGTCCATTTATAGTCACTCA
* * * *
8402 TTCCTTCAAAATCCTTATCACTCACTTTAAATAGTTTTATAATCTCAGAATTGATTTTAATTTGA
65 TTCCTTTAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAATTTGA
* * *
8467 ATTCATTGTACATTGTTAGCTAAACAGATTACAATTGAATG
130 ATTCATTGTACATTGTTAGCTAAACAGACTACAATTAAATA
*
8508 TCTACCTTGAGAAACATGA-AAAGAAATGCATTCATTA-GCAAGAAAAGTCTATTTATAGTCACT
1 TCTACCTTGAGAAACATGAGAAA-AAA-GCATTCA-TAGGCAAGAAAAGTCCATTTATAGTCACT
* * * * *******
8571 CATTCTTTTAAAAGCTTTATTACTCACTTCAAATGGTTTTATAATCTCAAAATTGATTNNNNNNN
63 CATTCCTTTAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAATTT
*** * * * * *
8636 NNNTTCTTTGTACATTTTTAGTTAAAACATACTATAATTAAATA
128 GAATTCATTGTACATTGTTAGCT-AAACAGACTACAATTAAATA
* * * *
8680 TTTACCTTGAGAAACATGAGAAAAAAGGCATTCATAGGCAAGGAAAGTCCATTTATAGTTACCCA
1 TCTACCTTGAGAAACATGAGAAAAAA-GCATTCATAGGCAAGAAAAGTCCATTTATAGTCACTCA
* * * * **
8745 TTCCTTTAAAAGCCTTATTACTAAATTTAAATAGTTTTATAATCTCATAATTGATTTTAGGTTCA
65 TTCCTTTAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTA-ATTTG
* * * * * * * *
8810 AATT-TTTTTACATT-TTTGATTAGAACAGATTATAATTGAATG
129 AATTCATTGTACATTGTTAG-CTA-AACAGACTACAATTAAATA
* * * * * * * *
8852 TCTACCTT-AGAAAATATGA-AGAAAAAGATATTCATTGGTAAGGAAAGCCCATTTATAGTCTCC
1 TCTACCTTGAG-AAACATGAGA-AAAAAG-CATTCATAGGCAAGAAAAGTCCATTTATAGTCACT
* * * * * **
8915 CATTCCTTCAAAAGCCTTATTACTCACATTAAATGGCTTTGTAATCTCTTAATTGATTTTAGA-T
63 CATTCCTTTAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTA-ATT
8979 TGAATT
127 TGAATT
8985 TTTTNNNNNN
Statistics
Matches: 386, Mismatches: 79, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
169 3 0.01
170 3 0.01
171 130 0.34
172 245 0.63
173 5 0.01
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (170 bp):
TCTACCTTGAGAAACATGAGAAAAAAGCATTCATAGGCAAGAAAAGTCCATTTATAGTCACTCAT
TCCTTTAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAATTTGAA
TTCATTGTACATTGTTAGCTAAACAGACTACAATTAAATA
Done.