Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398952.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2234.0, 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: 8726
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.23
Warning! 3358 characters in sequence are not A, C, G, or T
Found at i:2710 original size:165 final size:167
Alignment explanation
Indices: 2533--2909 Score: 431
Period size: 165 Copynumber: 2.3 Consensus size: 167
2523 NNNGTCTACC
* * * *
2533 AATGGACTTTTCTTGCCAAAGAATATCTTTTTCTTCGTGTTTCCCAACTTAGACATTCAATTATA
1 AATGGACTTTTCTTGCCAAAGAATATCTTTTTCTTCATGTTTCCCAACATAAACATTAAATTATA
* * *
2598 ATTT-TTTTAATAAAAAATATAAAAAAATCAACTTCAAATCAATTATGTGATTATAAAAAAATTT
66 ATTTGTTTTAACAAAAAATATAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAAAAATTT
*
2662 AA-AGTAATAAGGCTTTGGAA-GGCATGTGTAACCATA
131 AAGAGTAATAAGGCTTTGGAATGG-ATGGGTAACCATA
* * * * * *
2698 AATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTTCTAAGATAAACATTAAATTATT
1 AATGGACTTTTCTTGCCAAAGAATATCTTTTTCTTCATGTTTCCCAACATAAACATTAAATTATA
* * * * *
2763 ATTTGTTTTAACCAAAAATATAAAAAAATTAACTTAAAATTAATTATGAGATTATGAAAACATTT
66 ATTTGTTTTAACAAAAAATATAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAAAAATTT
* * *
2828 AAGGCGAGTAATAAGGCTTTTGAATGGATGGGTGACTATA
131 AA---GAGTAATAAGGCTTTGGAATGGATGGGTAACCATA
* * * *
2868 AATCGA-TATTTCTTG-CAAATAGATATCTTCTTCTTCACGTTT
1 AATGGACT-TTTCTTGCCAAAGA-ATATCTTTTTCTTCATGTTT
2910 TCTGAGGTAG
Statistics
Matches: 176, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
165 59 0.34
166 54 0.31
169 4 0.02
170 57 0.32
171 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (167 bp):
AATGGACTTTTCTTGCCAAAGAATATCTTTTTCTTCATGTTTCCCAACATAAACATTAAATTATA
ATTTGTTTTAACAAAAAATATAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAAAAATTT
AAGAGTAATAAGGCTTTGGAATGGATGGGTAACCATA
Found at i:2895 original size:170 final size:165
Alignment explanation
Indices: 2537--2951 Score: 476
Period size: 170 Copynumber: 2.5 Consensus size: 165
2527 TCTACCAATG
* * * ** *
2537 GACTTTTCTTGCCAA-AGAATATCTTTTTCTTCGTGTTTCCCAACTTAGACATTCAATTATAATT
1 GACTTTTCTTGCCAATAG-ATATCTTTTTCTTCATGTTTTCTAAGATAGACATTCAATTATTATT
** * *
2601 TTTTTAATAAAAAATATAAAAAAATCAACTTCAAATCAATTATGTGATTATAAAAAAATTTAAAG
65 TTTTTAACCAAAAATATAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAAAAATTTAAAG
* *
2666 TAATAAGGCTTTGGAAGGCATGTGTAACCATAAATG
130 TAATAAGGCTTTGGAAGGCATGGGTAACCATAAATC
* * *
2702 GACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTTCTAAGATAAACATTAAATTATTATTT
1 GACTTTTCTTGCCAATAGATATCTTTTTCTTCATGTTTTCTAAGATAGACATTCAATTATTATTT
* * * *
2767 GTTTTAACCAAAAATATAAAAAAATTAACTTAAAATTAATTATGAGATTATGAAAACATTTAAGG
66 -TTTTAACCAAAAATATAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAAAAATTTAA--
* * *
2832 CGAGTAATAAGGCTTTTGAATGG-ATGGGTGACTATAAATC
128 --AGTAATAAGGCTTTGGAA-GGCATGGGTAACCATAAATC
* * * * *
2872 GA-TATTTCTTGCAAATAGATATCTTCTTCTTCACGTTTTCTGAGGTAGACATTCAATTATTATC
1 GACT-TTTCTTGCCAATAGATATCTTTTTCTTCATGTTTTCTAAGATAGACATTCAATTATTAT-
*
2936 TATTTTAACCAAAAAT
64 TTTTTTAACCAAAAAT
2952 NNNNNNNNNN
Statistics
Matches: 210, Mismatches: 31, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
165 54 0.26
166 55 0.26
169 1 0.00
170 97 0.46
171 3 0.01
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (165 bp):
GACTTTTCTTGCCAATAGATATCTTTTTCTTCATGTTTTCTAAGATAGACATTCAATTATTATTT
TTTTAACCAAAAATATAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAAAAATTTAAAGT
AATAAGGCTTTGGAAGGCATGGGTAACCATAAATC
Found at i:3395 original size:171 final size:173
Alignment explanation
Indices: 2975--3395 Score: 476
Period size: 173 Copynumber: 2.4 Consensus size: 173
2965 NNNNNNNNNN
* *
2975 AATTATGAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTCGAAGGCATGTGTGACTATAA
1 AATTATGAGATTATAAAAACATTT-AAACGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAA
* ** *
3040 ATGGACTTTT-TCTTACCAATAGATACCTTCTTCTTCACATTTCTTAAGGTAGATATTCAATTAC
65 ATGGACTTTTCTCTTACCAATAGAAACCTTCTTCTTCACATTTCTTAAGACAGACATTCAATTAC
* ** * *
3104 AATCTGTTTTAAGAAGAAATGTAAAAGTATTCAAGTTTAAAATT
130 AATCTGTTTTAACAAGAAATGTAAAAAAATTCAAGTTGAAAATC
* * * *
3148 AACTATGAGATT-TTAAAACTATTTAAACAGAGTAATAAGGCTTTCGAAGGCGTGGGTGACTATA
1 AATTATGAGATTATAAAAAC-ATTTAAAC-GAGTAATAAGGCTTTCGAAGGCATGAGTGACTATA
* ** * * * * *
3212 AAGGGACTTTTCT-TTTTCAGTGGAAATCTTTTTCTTCACATTT-TCTGAGACAGACATTCAATT
64 AATGGACTTTTCTCTTACCAATAGAAACCTTCTTCTTCACATTTCT-TAAGACAGACATTCAATT
** *
3275 ATTATCTGTTTTAACTA-AAATGTAAAAAAATTCAA-TTGAAAATC
128 ACAATCTGTTTTAACAAGAAATGTAAAAAAATTCAAGTTGAAAATC
* * * * *
3319 AATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGCCTTCCAAAGGCATAAGTGACTCTAA
1 AATTATGAGATTATAAAAACATTTAAA-CGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAA
3384 ATGGACTTTTCT
65 ATGGACTTTTCT
3396 NNNNNNNNNN
Statistics
Matches: 207, Mismatches: 35, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
171 65 0.31
172 33 0.16
173 108 0.52
174 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (173 bp):
AATTATGAGATTATAAAAACATTTAAACGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAA
TGGACTTTTCTCTTACCAATAGAAACCTTCTTCTTCACATTTCTTAAGACAGACATTCAATTACA
ATCTGTTTTAACAAGAAATGTAAAAAAATTCAAGTTGAAAATC
Found at i:3794 original size:171 final size:169
Alignment explanation
Indices: 3497--3978 Score: 483
Period size: 171 Copynumber: 2.8 Consensus size: 169
3487 CGAAGCCGTT
* ** *
3497 GGTGACTATAAATGGACTTTTCTTTTCATTGAATATCTTTTTCTTCATGTTTCTCAAGGTAGACA
1 GGTGACAATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCTCAAGGTAGACA
* * * * * ***********
3562 TTCAACTCTAATCAATTCTAATAAAAATGTAAAAAAAATTCAACANNNNNNNNNNTATGAGATTA
66 TTCAATTTTAATCTATTTTAATAAAAATGT-AAAAAAATTTAACTTAAAATCAATTATGAGATTA
* * *
3627 TAAAACCATTTAAACCGAATAATAAGGGTTTCGAAGGTATG
130 TAAAA-AATTTAAACCGAATAATAAGGGTTTCGAAAGAATG
** * *
3668 GGTTTCTACT-AATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCTCAAGTTAGAC
1 GGTGAC-AATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCTCAAGGTAGAC
* * *
3732 ATTCAATTTTAATTTATTTTAATAAAATATATAAAAAAATTTAACTTCAAATCAATTATGAGATT
65 ATTCAATTTTAATCTATTTTAATAAAA-ATGTAAAAAAATTTAACTTAAAATCAATTATGAGATT
* * * *
3797 ATTAAAAAATTTAAAGCGAGTAATAAGGTTTTTGAAAGAATG
129 A-TAAAAAATTTAAACCGAATAATAAGGGTTTCGAAAGAATG
* *
3839 GGTGACAATAAATGGACTTTTCTTGCCAATGAAT-T-TTTTT-TTCATGTTTC-CTGAGGTAAAC
1 GGTGACAATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCTC-AAGGTAGAC
* * *
3900 ATTCAATTATT-ATCTA-TTTAACCAAAAATGTAAAAAAATTTAACTTAAAATTAATTGTGAGAT
65 ATTCAATT-TTAATCTATTTTAA-TAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGAT
3963 TATAAAAATATTTAAA
128 TATAAAAA-ATTTAAA
3979 GCGANNNNNN
Statistics
Matches: 258, Mismatches: 45, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
166 6 0.02
167 47 0.18
168 32 0.12
169 7 0.03
170 3 0.01
171 154 0.60
172 9 0.03
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.38
Consensus pattern (169 bp):
GGTGACAATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCTCAAGGTAGACA
TTCAATTTTAATCTATTTTAATAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTAT
AAAAAATTTAAACCGAATAATAAGGGTTTCGAAAGAATG
Found at i:5078 original size:149 final size:149
Alignment explanation
Indices: 4808--5087 Score: 373
Period size: 149 Copynumber: 1.9 Consensus size: 149
4798 NNNNNNNNNN
* * * * * *
4808 TAAGAAAAGTCTATTTACAGTTACCCATACCGTCAAAAGCCTTATTTCGTGCTTAAAATGTTTTT
1 TAAGAAAAGACCATTTACAGTCACCCATACCGTCAAAAGCCTTATTACGTACTTAAAATGATTTT
* * *
4873 AGAATCTCGTAATTGATTTTAACTTAAATTTTTATATATTTTTTATTAAAATAGATAATAATTGA
66 AGAATCTCATAATTGATTTTAACTTAAATTTTTATATATTTTTGATTAAAACAGATAATAATTGA
4938 AGAAAAAGATAGCCATTGG
131 AGAAAAAGATAGCCATTGG
* * * * *
4957 TAAGAAAAGACCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTAC-TCACTTTAAATGATTT
1 TAAGAAAAGACCATTTACAGTCACCCATACCGTCAAAAGCCTTATTACGT-ACTTAAAATGATTT
* * * * *
5021 TATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTGGTTAAAACAGATAATAATTG
65 TAGAATCTCATAATTGATTTTAACTTAAATTTTTATATATTTTTGATTAAAACAGATAATAATTG
5086 AA
130 AA
5088 TGTCGACCTT
Statistics
Matches: 111, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
148 1 0.01
149 110 0.99
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (149 bp):
TAAGAAAAGACCATTTACAGTCACCCATACCGTCAAAAGCCTTATTACGTACTTAAAATGATTTT
AGAATCTCATAATTGATTTTAACTTAAATTTTTATATATTTTTGATTAAAACAGATAATAATTGA
AGAAAAAGATAGCCATTGG
Found at i:5225 original size:171 final size:171
Alignment explanation
Indices: 4935--5573 Score: 781
Period size: 171 Copynumber: 3.7 Consensus size: 171
4925 AGATAATAAT
* * * * *
4935 TGAAGAAAAAGATAGCCATTGGTAAGAAAAGACCATTTATAGTCACCCATGCCTTCGAAAGCCTT
1 TGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTT
* *
5000 ATTACTCACTTTAAATGA-TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTT
66 ATTACTCGCTTTAAAT-ATTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTT
5064 TGGTTAAAACAGATAATAATTGAATGTCGACCTTAGGAAACA
130 TGGTTAAAACAGATAATAATTGAATGTCGACCTTAGGAAACA
* * * *
5106 TGAAGAAAAAGATATCTATTCGCAAGAAAAGTTCATTTATAGTCACCCATCCCTTCAAAAGCCTT
1 TGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTT
* * *
5171 ATTACTCGCTTTAAATATTTTTATAATCTCACAATTAATTTTAAGTT-AAATTTTTTACATTTTT
66 ATTACTCGCTTTAAATATTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTT
* *
5235 GGTT-AAACAGATAATAATTGAATGTTTG-CCTCAGGAAACA
131 GGTTAAAACAGATAATAATTGAATG-TCGACCTTAGGAAACA
* * * *
5275 TGAAAAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATGGTCACCCATTCTTTCAAAAGCCTT
1 TGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTT
* * * *
5340 ATTACTCGCTCTAAAT-TTTTTAATAATCTCATAATTGATTTGAAGTTGAACTTTTTTATATATT
66 ATTACTCGCTTTAAATATTTTT-ATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACAT-TT
* * * * * * *
5404 TT-ATTAAAATAAATTATAATTTAATGTCTAACTT-GAGAAACA
129 TTGGTTAAAACAGATAATAATTGAATGTCGACCTTAG-GAAACA
* * ** ** *
5446 TGAAGAAAAAGATATTCATTGGCAAAAAAAGTCCATTGGTAGAAACCCATACCTTCGAAA-CCTT
1 TGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCC-T
* ** **
5510 TATTACTCGTTTTAAATGGTTTTATAATCTCATAATTGATTTTGTGTTGAATTTTTTTACATTT
65 TATTACTCGCTTTAAATATTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTT
5574 NNNNNNNNNN
Statistics
Matches: 402, Mismatches: 56, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
168 5 0.01
169 126 0.31
170 41 0.10
171 226 0.56
172 4 0.01
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (171 bp):
TGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTT
ATTACTCGCTTTAAATATTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTT
GGTTAAAACAGATAATAATTGAATGTCGACCTTAGGAAACA
Found at i:6386 original size:171 final size:171
Alignment explanation
Indices: 5974--6402 Score: 452
Period size: 172 Copynumber: 2.5 Consensus size: 171
5964 NNNGAAAAAG
* * *
5974 AAAAGTCCCTTTATAGTCACCCA-CACCTTCGAAAGCCTTATTACTCTG-TTTAAATGGTTTTAA
1 AAAAGTCCATTTATAGTCA-CCATC-CCTTCGAAAGCCTTATTACTC-GCTTTAAATAGTTTTAT
* * * ** *
6037 AATCTCATAGTTAATTTTAAACTTGAATATTTTTATATTTCTTCTTAAAACAGATTGTAATTGTA
63 AATCTCATAATTGATTTT-AAGTTGAATATTTTTATATTTCTTCTTAAAACAGATAATAATTGAA
* * * * * *
6102 TGTATACCTTGAGAAACGTGAAGAAGAAGGTATCTATTGGTAAGA
127 TGTATACCTCGAAAAACGTGAAGAAAAAGATATCTATTAGCAAGA
* **********
6147 AAAAGTCCATTTATAGTCACCTATGCCTTCGAAAGCCTTATTACTCGCTTTANNNNNNNNNNTAA
1 AAAAGTCCATTTATAGTCACC-ATCCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTATAA
* *
6212 TCTCATAATTGATTTTAAGTTGAAT-TTTTTCATATTTTTTGTTAAAACAGATAATAATTGAATG
65 TCTCATAATTGATTTTAAGTTGAATATTTTT-ATATTTCTTCTTAAAACAGATAATAATTGAATG
* *
6276 TTTACCTCGAAAAATGTGAAGAAAAAGATATCTATTAGCAAG-
129 TATACCTCGAAAAACGTGAAGAAAAAGATATCTATTAGCAAGA
* * * * *
6318 AAATGTCGATTTATAGTCACTCATCCCTTCAAAAGCCTTATTACTCGCATTAAATATTTTTATAA
1 AAAAGTCCATTTATAGTCAC-CATCCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTATAA
6383 TCTCATAATTGATTTTAAGT
65 TCTCATAATTGATTTTAAGT
6403 NNNNNNNNNN
Statistics
Matches: 207, Mismatches: 44, Indels: 12
0.79 0.17 0.05
Matches are distributed among these distances:
171 73 0.35
172 74 0.36
173 60 0.29
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.38
Consensus pattern (171 bp):
AAAAGTCCATTTATAGTCACCATCCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTATAAT
CTCATAATTGATTTTAAGTTGAATATTTTTATATTTCTTCTTAAAACAGATAATAATTGAATGTA
TACCTCGAAAAACGTGAAGAAAAAGATATCTATTAGCAAGA
Found at i:7401 original size:170 final size:171
Alignment explanation
Indices: 7115--7545 Score: 537
Period size: 170 Copynumber: 2.5 Consensus size: 171
7105 AAGCAGATTG
* * * * ** * *
7115 TAATTGAATGTCTACATCAGGAAACGTGAAGAAAAAGATATCTGTTAGCAAGAAAAGTTCATTTA
1 TAATTGAATGTCTACCTCGGGAAACATGAAGAAAAATATATCAATTGGCAAGAAAAGTCCATTTA
* * **
7180 TAGTCACCTATGCCTTCGAAAGCCTTATTACTCACTTTAAATGTTTTTATAATCTCATAATTGAC
66 TAGTCACCCATGCCTTCGAAAGCCTTATTACACACTTTAAATGGCTTTATAATCTCATAATTGAC
* * * *
7245 TTTCAGTTGAATTTTTTTACAT-TTTGGTTAAAATAG-ATAA
131 TTTAAGTTGAATTGTTTTACATCTTTGATTAAAACAGAAT-A
*
7285 TAATTGAATGTCTACCTCGGGAAACATGAAGAAAAATATATCAATTGGCAATAAAAGTCCATTTA
1 TAATTGAATGTCTACCTCGGGAAACATGAAGAAAAATATATCAATTGGCAAGAAAAGTCCATTTA
* * *
7350 TAATCACCCATGTC-TCTGAAAGCCTTATTACACATTTTAAATGGCTTTATAATCTCATAATTGA
66 TAGTCACCCATGCCTTC-GAAAGCCTTATTACACACTTTAAATGGCTTTATAATCTCATAATTGA
* *
7414 TTTTAAGTTGAATTGTTTTACATCTTTTATTAAAACAGAATA
130 CTTTAAGTTGAATTGTTTTACATCTTTGATTAAAACAGAATA
* * * * * * *
7456 TAATTGAATGTTTACCTTGAGAAAAATGGAAG-AAAATACATCCACTGGCAAGAAAAGTCCATTT
1 TAATTGAATGTCTACCTCGGGAAACAT-GAAGAAAAATATATCAATTGGCAAGAAAAGTCCATTT
*
7520 GTAGTCACCCATGCCTTCGAAAGCCT
65 ATAGTCACCCATGCCTTCGAAAGCCT
7546 CTTTACTCGN
Statistics
Matches: 223, Mismatches: 33, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
169 2 0.01
170 130 0.58
171 83 0.37
172 8 0.04
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (171 bp):
TAATTGAATGTCTACCTCGGGAAACATGAAGAAAAATATATCAATTGGCAAGAAAAGTCCATTTA
TAGTCACCCATGCCTTCGAAAGCCTTATTACACACTTTAAATGGCTTTATAATCTCATAATTGAC
TTTAAGTTGAATTGTTTTACATCTTTGATTAAAACAGAATA
Found at i:8041 original size:171 final size:171
Alignment explanation
Indices: 7776--8088 Score: 416
Period size: 171 Copynumber: 1.8 Consensus size: 171
7766 TATAGTAATC
* * *
7776 CATGCCTTGAAAAGCCTTATTACTCTCTTTAAATAGTTTTATTATCTCATAATTGATTTTAAGTC
1 CATGCCTTGAAAAGCCTTATTACTCACTTTAAATAGTTTTATAACCTCATAATTGATTTTAAGTC
* * * * **
7841 AATTTTTTTTATATTTTTTATTAAAATAGATTATAATTAAATGTC-GACCTTGGGAAACGTGAAG
66 AATGTTTTTTACATTTTTGATTAAAATAGATAATAATTAAATGTCTG-CCTCAGGAAACGTGAAG
7905 AAAAAGATATCCATTTTTAAAAAAATTTTATTTATAGTCGCT
130 AAAAAGATATCCATTTTTAAAAAAATTTTATTTATAGTCGCT
* * * * * *
7947 CATGCCTTCG-AAAGTCTTGTTAGTCACTTTACATGGTTTTATAACCTCATAATTGATTTTATGT
1 CATGCCTT-GAAAAGCCTTATTACTCACTTTAAATAGTTTTATAACCTCATAATTGATTTTAAG-
* * *
8011 TGAATGTTTTTT-CATTTTTGATTCAAATAGATAATAATTGAATGTCTGCCTCAGGAAACGTGAA
64 TCAATGTTTTTTACATTTTTGATTAAAATAGATAATAATTAAATGTCTGCCTCAGGAAACGTGAA
8075 GAAAAAGATATCCA
129 GAAAAAGATATCCA
8089 CTAGCAACAA
Statistics
Matches: 121, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
171 109 0.90
172 12 0.10
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (171 bp):
CATGCCTTGAAAAGCCTTATTACTCACTTTAAATAGTTTTATAACCTCATAATTGATTTTAAGTC
AATGTTTTTTACATTTTTGATTAAAATAGATAATAATTAAATGTCTGCCTCAGGAAACGTGAAGA
AAAAGATATCCATTTTTAAAAAAATTTTATTTATAGTCGCT
Found at i:8111 original size:171 final size:171
Alignment explanation
Indices: 7724--8111 Score: 415
Period size: 171 Copynumber: 2.3 Consensus size: 171
7714 NNNNCTTAGA
* * * * *
7724 AAACATGAGGAAAAAGATATCTACTGGTAAGAAAAGTCCATTTATAGTAATCCATGCCTTGAAAA
1 AAACGTGAAGAAAAAGATATCCACTAGTAAAAAAAGTCCATTTATAGTAATCCATGCCTTGAAAA
* * * * *
7789 GCCTTATTACTCTCTTTAAATAGTTTTATTATCTCATAATTGATTTTAAGTCAATTTTTTTTATA
66 GCCTTATTACTCACTTTAAATAGTTTTATAACCTCATAATTGATTTTAAGTCAATGTTTTTTACA
* * **
7854 TTTTTTATTAAAATAGATTATAATTAAATGTCGACCTTGGG
131 TTTTTGATTAAAATAGATAATAATTAAATGTCGACCTCAGG
* ** * ** **
7895 AAACGTGAAGAAAAAGATATCCATTTTTAAAAAAATTTTATTTATAGT-CGCTCATGCCTTCG-A
1 AAACGTGAAGAAAAAGATATCCACTAGTAAAAAAAGTCCATTTATAGTAATC-CATGCCTT-GAA
* * * * * * *
7958 AAGTCTTGTTAGTCACTTTACATGGTTTTATAACCTCATAATTGATTTTATGTTGAATGTTTTTT
64 AAGCCTTATTACTCACTTTAAATAGTTTTATAACCTCATAATTGATTTTAAG-TCAATGTTTTTT
* *
8023 -CATTTTTGATTCAAATAGATAATAATTGAATGTCTG-CCTCAGG
128 ACATTTTTGATTAAAATAGATAATAATTAAATGTC-GACCTCAGG
* *
8066 AAACGTGAAGAAAAAGATATCCACTAGCAACAAAAGTCCATTTATA
1 AAACGTGAAGAAAAAGATATCCACTAGTAAAAAAAGTCCATTTATA
8112 NNNNNNNNNN
Statistics
Matches: 175, Mismatches: 38, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
170 1 0.01
171 162 0.93
172 12 0.07
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (171 bp):
AAACGTGAAGAAAAAGATATCCACTAGTAAAAAAAGTCCATTTATAGTAATCCATGCCTTGAAAA
GCCTTATTACTCACTTTAAATAGTTTTATAACCTCATAATTGATTTTAAGTCAATGTTTTTTACA
TTTTTGATTAAAATAGATAATAATTAAATGTCGACCTCAGG
Done.