Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399575.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2828.0, 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: 12237
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.26
Warning! 3029 characters in sequence are not A, C, G, or T
Found at i:909 original size:170 final size:170
Alignment explanation
Indices: 728--1197 Score: 701
Period size: 170 Copynumber: 2.8 Consensus size: 170
718 NNNNNNNNNN
* * *
728 AATCTCATAATTGATTTTAAGTTGAATTTGTTTACATTTTTAATTAAAACAGATTAAAACTAAAT
1 AATCTCATAATTGATTTTAAGTTGAATTTGTTTACATTTTTAGTTAAAACAGATTAAAATTGAAT
* *
793 GTCTGCCTTGAAAAATGTGAAGAAAAGGCATTCATTTATAAAAAAAGTCCAATTATAGTCACCTA
66 GTCTACCTTGAAAAATGTGAAGAAAAGGCATTCATTAATAAAAAAAGTCCAATTATAGTCACCTA
*
858 TTCCCTCAAAAGCCTTATCACTCGCTTAAAATAGTTTTGT
131 TTCCCTCAAAAGCCTTATCACTCGCTCAAAATAGTTTTGT
*
898 AATCTCATAATTGATTTTAAGTTGAATTTGTTTACATTTTTAGTTAAAAGAGATTAAAATTGAAT
1 AATCTCATAATTGATTTTAAGTTGAATTTGTTTACATTTTTAGTTAAAACAGATTAAAATTGAAT
* *
963 GTCTACCTT-AGAAAATGTGAAGAAAAGGCATTCATTGATAAGAAAAGTCCAATTATAGTCACCT
66 GTCTACCTTGA-AAAATGTGAAGAAAAGGCATTCATTAATAAAAAAAGTCCAATTATAGTCACCT
* *
1027 ATTCTCTCAAAAGCCTTATCACTCGCTCGAAATAGTTTTGT
130 ATTCCCTCAAAAGCCTTATCACTCGCTCAAAATAGTTTTGT
* * * *
1068 AACCTTATAGTTGATTTTAAGTTGAATATT-TTTATATTTTTAGTTAAAACAGATTAAAATTGAA
1 AATCTCATAATTGATTTTAAGTTGAAT-TTGTTTACATTTTTAGTTAAAACAGATTAAAATTGAA
* * * * ** *
1132 TGTCTACCTTGGAAAATATGAAGAAAAAGTCATTCATTAACAGTAAAAGTCCATTTATAGTCACC
65 TGTCTACCTTGAAAAATGTGAAG-AAAAGGCATTCATTAATAAAAAAAGTCCAATTATAGTCACC
1197 T
129 T
1198 TAGCCTTCGA
Statistics
Matches: 273, Mismatches: 23, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
169 1 0.00
170 234 0.86
171 38 0.14
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (170 bp):
AATCTCATAATTGATTTTAAGTTGAATTTGTTTACATTTTTAGTTAAAACAGATTAAAATTGAAT
GTCTACCTTGAAAAATGTGAAGAAAAGGCATTCATTAATAAAAAAAGTCCAATTATAGTCACCTA
TTCCCTCAAAAGCCTTATCACTCGCTCAAAATAGTTTTGT
Found at i:1947 original size:171 final size:170
Alignment explanation
Indices: 1649--2573 Score: 909
Period size: 171 Copynumber: 5.4 Consensus size: 170
1639 NNNNNNNTAT
* ** * * * *
1649 ATGGTTTTACAATCTCATAATTGATTTTAAGTCAAATTTTTTTACATTTTTTATTAAAATATACT
1 ATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGATT
* * * * * * ** *
1714 ATAATCGAATGCCTACCTTGACAAACATGAAGCAAAAGCCATCCATAGATATCAACAGTCCATTT
66 ATAATTGAATGTCTACCTCGAGAAACATGAAG-AAAAGCCATTCATTGATAAGAAAAGTCCATTT
** ** *
1779 ATAGTCACTTAAACC-TCTTAAAGCCTTATTACTCGCTTTAA
130 ATAGTCACCCATGCCTTC-AAAAGCCTTATTACTCGCTTTAA
* *
1820 ATGGTTTTATAATCTCATAATTGATTTTAAGTTGATTTTTTTTACATTTTTGATGAAAACAGATT
1 ATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGATT
* * * *
1885 ATAATTAAATGTCTACCTCAAAAAACATGAAGAAAAGGCCATTCATTGATAGGAAAAGTCCATTT
66 ATAATTGAATGTCTACCTCGAGAAACATGAAGAAAA-GCCATTCATTGATAAGAAAAGTCCATTT
* * * *
1950 ATAGTCACGCATTCCTTCAAAAGCCTTACTACTCACTTTAA
130 ATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTTTAA
* ** * * * *
1991 ATAGTTTTGGAATCTCATAATTAATTTTAAGTTCAATTTTTTTATATTTTTCG-TTAAAACAAAT
1 ATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTT-GATTAAAACAGAT
* * *
2055 TATAATTGAATGTCTACCTCGTGAAACCTGAAGAAAAAGCCATTCATTGACAAGAAAAGTCCATT
65 TATAATTGAATGTCTACCTCGAGAAACATGAAG-AAAAGCCATTCATTGATAAGAAAAGTCCATT
** *
2120 TATAGTCACCCATGCCTTTGAAAGCCTTATTACTCGCTTTAT
129 TATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTTTAA
* * * *
2162 ATGATTTTATAATCTCATAATTGATTTTAGGTTGAA-TTTTTTATATTTTTTATTAAAACAGATT
1 ATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGATT
** * * * * ** *
2226 ATAATTGTCTGTCTACCTTGAGAAATATGAAGACAAAGCCATTCA---AT--CACAAGTATACTT
66 ATAATTGAATGTCTACCTCGAGAAACATGAAGA-AAAGCCATTCATTGATAAGAAAAGTCCATTT
* **
2286 ATAGTCACCCATGCCTTCGAGAA-CCTTATTAC-CTATTTTAA
130 ATAGTCACCCATGCCTTC-AAAAGCCTTATTACTC-GCTTTAA
* * * * * *
2327 ATGGATTTATAATCTCATAATTAATTTTAGGTTTAATTGTTTTACATGTTTT-ATTAAAACATAT
1 ATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACAT-TTTTGATTAAAACAGAT
* * * * ** * ** * *
2391 TATAATTAAATATTTACCTCAAGAAATGTGAAGAAAAACCAATTCATTGGCAAGAAAAGTCTAGT
65 TATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAGCC-ATTCATTGATAAGAAAAGTCCATT
* *
2456 TATAGTCACCCAAGCCTTGAAAAGCCTTATTACTCGCTTTAA
129 TATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTTTAA
* * ** * *
2498 AGGGTTTTATAACCTCATAATTGATTTTATCTTGAATTTGTTTTCCATTTTTGGTTAAAACAGAT
1 ATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTT-TTTTACATTTTTGATTAAAACAGAT
2563 TATAATTGAAT
65 TATAATTGAAT
2574 NNNNNNNNNN
Statistics
Matches: 618, Mismatches: 116, Indels: 39
0.80 0.15 0.05
Matches are distributed among these distances:
164 1 0.00
165 75 0.12
166 52 0.08
167 5 0.01
169 1 0.00
170 69 0.11
171 380 0.61
172 35 0.06
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (170 bp):
ATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGATT
ATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAGCCATTCATTGATAAGAAAAGTCCATTTA
TAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTTTAA
Found at i:2439 original size:336 final size:338
Alignment explanation
Indices: 1654--2573 Score: 953
Period size: 336 Copynumber: 2.7 Consensus size: 338
1644 NNTATATGGT
* * * * * * *
1654 TTTACAATCTCATAATTGATTTTAAG-TCAAATTTTTTTACATTTTTTATTAAAATATACTATAA
1 TTTAGAATCTCATAATTAATTTTAAGTTC-AATTGTTTTACATTTTTCATTAAAACAAATTATAA
** ** ** * * * * * * ** *
1718 TCGAATGCCTACCTTGACAAACATGAAGCAAAAGCCATCCATAGATATCAACAGTCCATTTATAG
65 TTAAATATCTACCTCAAGAAACCTGAAGAAAAAGCCATTCATTGACAAGAAAAGTCCATTTATAG
** *
1783 TCACTTAAACCTCTT-AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
130 TCACCCAAGCCT-TTGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * *
1847 TAAGTTGATTTTTTTTACATTTTTGATGAAAACAGATTATAATTAAATGTCTACCTCAAAAAACA
194 TAAGTTGA-ATTTTTTATATTTTTGATTAAAACAGATTATAATTGAATGTCTACCTCAAAAAACA
* * * * *
1912 TGAAGAAAAGGCCATTCATTGATAGGAAAAGTCCATTTATAGTCACGCATTCCTTCAAAAGCCTT
258 TGAAGAAAAGGCCATTCA-T-ATA-CAAAAGTACACTTATAGTCACCCATGCCTTCAAAAGCCTT
*
1977 ACTACTCACTTTAAATAGT
320 ACTACTCACTTTAAATAGA
* * * *
1996 TTTGGAATCTCATAATTAATTTTAAGTTCAATTTTTTTATATTTTTCGTTAAAACAAATTATAAT
1 TTTAGAATCTCATAATTAATTTTAAGTTCAATTGTTTTACATTTTTCATTAAAACAAATTATAAT
* * **
2061 TGAATGTCTACCTCGTGAAACCTGAAGAAAAAGCCATTCATTGACAAGAAAAGTCCATTTATAGT
66 TAAATATCTACCTCAAGAAACCTGAAGAAAAAGCCATTCATTGACAAGAAAAGTCCATTTATAGT
* * *
2126 CACCCATGCCTTTGAAAGCCTTATTACTCGCTTTATATGATTTTATAATCTCATAATTGATTTTA
131 CACCCAAGCCTTTGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTA
* * ** ** * *
2191 GGTTGAATTTTTTATATTTTTTATTAAAACAGATTATAATTGTCTGTCTACCTTGAGAAATATGA
196 AGTTGAATTTTTTATATTTTTGATTAAAACAGATTATAATTGAATGTCTACCTCAAAAAACATGA
* * * *
2256 AGACAAA-GCCATTCA-AT-CACAAGTATACTTATAGTCACCCATGCCTTCGAGAA-CCTTATTA
261 AGA-AAAGGCCATTCATATACAAAAGTACACTTATAGTCACCCATGCCTTC-AAAAGCCTTACTA
* *
2317 C-CTATTTTAAATGGA
324 CTC-ACTTTAAATAGA
* * * *
2332 TTTATAATCTCATAATTAATTTTAGGTTTAATTGTTTTACATGTTTT-ATTAAAACATATTATAA
1 TTTAGAATCTCATAATTAATTTTAAGTTCAATTGTTTTACAT-TTTTCATTAAAACAAATTATAA
* ** * * *
2396 TTAAATATTTACCTCAAGAAATGTGAAGAAAAA-CCAATTCATTGGCAAGAAAAGTCTAGTTATA
65 TTAAATATCTACCTCAAGAAACCTGAAGAAAAAGCC-ATTCATTGACAAGAAAAGTCCATTTATA
* *
2460 GTCACCCAAGCC-TTGAAAAGCCTTATTACTCGCTTTAAAGGGTTTTATAACCTCATAATTGATT
129 GTCACCCAAGCCTTTG-AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATT
** *
2524 TTATCTTGAATTTGTTT-TCCATTTTTGGTTAAAACAGATTATAATTGAAT
193 TTAAGTTGAATTT-TTTAT--ATTTTTGATTAAAACAGATTATAATTGAAT
2574 NNNNNNNNNN
Statistics
Matches: 486, Mismatches: 81, Indels: 26
0.82 0.14 0.04
Matches are distributed among these distances:
335 6 0.01
336 210 0.43
337 10 0.02
338 28 0.06
341 61 0.13
342 169 0.35
343 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (338 bp):
TTTAGAATCTCATAATTAATTTTAAGTTCAATTGTTTTACATTTTTCATTAAAACAAATTATAAT
TAAATATCTACCTCAAGAAACCTGAAGAAAAAGCCATTCATTGACAAGAAAAGTCCATTTATAGT
CACCCAAGCCTTTGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTA
AGTTGAATTTTTTATATTTTTGATTAAAACAGATTATAATTGAATGTCTACCTCAAAAAACATGA
AGAAAAGGCCATTCATATACAAAAGTACACTTATAGTCACCCATGCCTTCAAAAGCCTTACTACT
CACTTTAAATAGA
Found at i:3016 original size:172 final size:161
Alignment explanation
Indices: 2828--3327 Score: 368
Period size: 171 Copynumber: 3.0 Consensus size: 161
2818 NNNNNATGGA
*
2828 TGACTATAGATAGACTTTTCTTACCAATGAAT-GGCCTTTTCTTAACATTTCCTAAGGTAGACAT
1 TGACTATAGATAGACTTTTCTTACCAATGAATAGG-CTTTTCTTAACATTTCCTAAGGTAAACAT
* * *
2892 TCAATTATAATCTATTTTAACT-AAAAATGGAAAACAAATTCAAGATAAAATCAATTATGAGGTT
65 TCAATTATAATATATTTTAA-TAAAAAATGGAAAAC-AATTCAACATAAAATCAATTATGAGATT
2956 ATAAAACCATTTAAAGCGAGTAANNNNNNNNNNCAAGGCTTGGG
128 ATAAAACCATTTAAAGCGAGTAA----------CAAGGCTTGGG
* * * * * *
3000 TGACTATA-ACTAGACTTTTCTTGCCAATGAATAGGTTTTTCTTCACGTTTCTTAAGGTAAATAT
1 TGACTATAGA-TAGACTTTTCTTACCAATGAATAGGCTTTTCTTAACATTTCCTAAGGTAAACAT
* * * *
3064 TTAATTATAATATATTTTAATAAAAAATGTAAAACAATTCAACCTAAAATTAATTATGAGATTAT
65 TCAATTATAATATATTTTAATAAAAAATGGAAAACAATTCAACATAAAATCAATTATGAGATTAT
* *** *
3129 AAATCCATTTAAAATAAGTAATAAGGTTCTCGAAGGTATGGG
130 AAAACCATTTAAAGCGAGTAACAAGG----C-----T-TGGG
* *** * * *
3171 TGACTATA-AGTATACTTTTCTTGTGATTGAAT-GGCTTTGTCTT--CATGTTTCTCAAGGTAGA
1 TGACTATAGA-TAGACTTTTCTTACCAATGAATAGGCTTT-TCTTAACAT-TTCCT-AAGGTAAA
** * ** * *
3232 CAGACAATTATAATCTATTTTAATAAAAAATATAAAA-AATTCAACCTAAAATCAATTAAGAGAT
62 CATTCAATTATAATATATTTTAATAAAAAATGGAAAACAATTCAACATAAAATCAATTATGAGAT
* * *
3296 TATAAAATCATATAAAGCGAGTAATAAGGCTT
127 TATAAAACCATTTAAAGCGAGTAACAAGGCTT
3328 TCAAAGGCAT
Statistics
Matches: 269, Mismatches: 43, Indels: 44
0.76 0.12 0.12
Matches are distributed among these distances:
160 1 0.00
161 5 0.02
165 1 0.00
166 1 0.00
169 2 0.01
170 57 0.21
171 118 0.44
172 82 0.30
173 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.34
Consensus pattern (161 bp):
TGACTATAGATAGACTTTTCTTACCAATGAATAGGCTTTTCTTAACATTTCCTAAGGTAAACATT
CAATTATAATATATTTTAATAAAAAATGGAAAACAATTCAACATAAAATCAATTATGAGATTATA
AAACCATTTAAAGCGAGTAACAAGGCTTGGG
Found at i:3193 original size:171 final size:170
Alignment explanation
Indices: 2990--3344 Score: 437
Period size: 171 Copynumber: 2.1 Consensus size: 170
2980 NNNNNNNNNC
* * *
2990 AAGGCTTGGGTGACTATAACTAGACTTTTCTTGCCAATGAATAGG-TTTTTCTTCACGTTTCTTA
1 AAGGCATGGGTGACTATAACTAGACTTTTCTTGCCAATGAAT-GGCTTTGTCTTCACGTTTCTCA
* *** * *
3054 AGGTAAATATTTAATTATAATATATTTTAATAAAAAATGTAAAACAATTCAACCTAAAATTAATT
65 AGGTAAACAGACAATTATAATATATTTTAATAAAAAATATAAAA-AATTCAACCTAAAATCAATT
* * * *
3119 ATGAGATTAT-AAATCCATTTAAAATAAGTAATAAGG-TTCTCG
129 AAGAGATTATAAAAT-CATATAAAACAAGTAATAAGGCTT-TCA
* * * ** * *
3161 AAGGTATGGGTGACTATAAGTATACTTTTCTTGTGATTGAATGGCTTTGTCTTCATGTTTCTCAA
1 AAGGCATGGGTGACTATAACTAGACTTTTCTTGCCAATGAATGGCTTTGTCTTCACGTTTCTCAA
* *
3226 GGTAGACAGACAATTATAATCTATTTTAATAAAAAATATAAAAAATTCAACCTAAAATCAATTAA
66 GGTAAACAGACAATTATAATATATTTTAATAAAAAATATAAAAAATTCAACCTAAAATCAATTAA
* *
3291 GAGATTATAAAATCATATAAAGCGAGTAATAAGGCTTTCA
131 GAGATTATAAAATCATATAAAACAAGTAATAAGGCTTTCA
3331 AAGGCATGGGTGAC
1 AAGGCATGGGTGAC
3345 NNNNNNNNNN
Statistics
Matches: 156, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
170 62 0.40
171 94 0.60
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (170 bp):
AAGGCATGGGTGACTATAACTAGACTTTTCTTGCCAATGAATGGCTTTGTCTTCACGTTTCTCAA
GGTAAACAGACAATTATAATATATTTTAATAAAAAATATAAAAAATTCAACCTAAAATCAATTAA
GAGATTATAAAATCATATAAAACAAGTAATAAGGCTTTCA
Found at i:4462 original size:170 final size:171
Alignment explanation
Indices: 4173--4572 Score: 500
Period size: 170 Copynumber: 2.3 Consensus size: 171
4163 NNNNNNNNAT
* * * * * * *
4173 CGAGTAATAAGGCTTTCGAAGG-CTAAGGTGACTATAAATGGACTTTTAC-TGTCAATGAATGAC
1 CGAGTGATAAGGCTTTTGAGGGAATAA-GTGACTATAATTGGA-TTTTTCTTATCAATGAATGAC
* **
4236 TTTTTCTTCATGTTTTCTAAGGCAGACATTCAATTTTAATCTATTTTAACTAAAAATATAAAAAT
64 CTTTTCTTCACATTTTCTAAGGCAGACATTCAATTTTAATCTATTTTAACTAAAAATATAAAAAT
* *
4301 ATTCAGCTTAAAATCAACTATAAGGTTACAAAACTATTTCAAG
129 ATTCAACTTAAAATCAACTATAAGATTACAAAACTATTTCAAG
4344 CGAGTGATAAGGCTTTTGAGGGAATAAGTGACTATAATTGGATTTTTCTTATCAATGAATG-CCT
1 CGAGTGATAAGGCTTTTGAGGGAATAAGTGACTATAATTGGATTTTTCTTATCAATGAATGACCT
* **********
4408 TTTCTTCACATTTTCTAAGGCAGACATTCAATTTTAATCTGTTTTAACTAAAAATGNNNNNNNNN
66 TTTCTTCACATTTTCTAAGGCAGACATTCAATTTTAATCTATTTTAACTAAAAATATAAAAATAT
* * *
4473 NCAACTTAAAATCAATTATGAGATTACAAAACTATTTCAAG
131 TCAACTTAAAATCAACTATAAGATTACAAAACTATTTCAAG
* * *
4514 CGAGTGATAAGGCTTTTGAGGGAATAGGTGACTATAATTGGACTTTTCTTATAAATGAA
1 CGAGTGATAAGGCTTTTGAGGGAATAAGTGACTATAATTGGATTTTTCTTATCAATGAA
4573 NNNNNNNNNN
Statistics
Matches: 198, Mismatches: 29, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
170 151 0.76
171 44 0.22
172 3 0.02
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.35
Consensus pattern (171 bp):
CGAGTGATAAGGCTTTTGAGGGAATAAGTGACTATAATTGGATTTTTCTTATCAATGAATGACCT
TTTCTTCACATTTTCTAAGGCAGACATTCAATTTTAATCTATTTTAACTAAAAATATAAAAATAT
TCAACTTAAAATCAACTATAAGATTACAAAACTATTTCAAG
Found at i:5076 original size:170 final size:171
Alignment explanation
Indices: 4730--5432 Score: 608
Period size: 170 Copynumber: 4.1 Consensus size: 171
4720 NNNNNNNNNN
* *
4730 AATCAATTATGAGATTATAAAACCATTTAAAGCCAGTAATAAGGCTTTCGAAGGCTT-GAGTGAC
1 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTAG-GTGAC
* ** * ** * * * *
4794 TATAAGTGAAAC-TTTGATACCACT-AGATAACTTTTGCTTCACGTTTCACAAGGTAGACATTTA
65 TATAAAT-AAACTTTTCTTACCAATGA-ATGGCTTTTTCTTCATGTTTCACAAGGCAGACATTCA
* ** * * *
4857 ATTATAATATATTTTATTTAAAAATGTAAAATAATTCAAGTTAA
128 ATTATAATCTATTTTAACTAAAAAAGTAAAAAAATTCAACTTAA
* * * *
4901 AATCAATTATGAGATTATAAAACTAATTTAAATCGAGTAACAAGGCTTTCAAAGGCTTAGGCGAC
1 AATCAATTATGAGATTATAAAAC-CATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTAGGTGAC
* * *
4966 TATAAATAAACTTTT-TTATCAATGAATGGCTTTTTCTTCA-GGTTC-CGAAGGTAGACATTCAA
65 TATAAATAAACTTTTCTTACCAATGAATGGCTTTTTCTTCATGTTTCAC-AAGGCAGACATTCAA
* * * *
5028 TTATAATTTGTTTTAACTAAAAAAGTAAAAAAATCCTACTTAA
129 TTATAATCTATTTTAACTAAAAAAGTAAAAAAATTCAACTTAA
* ** * ** * ** ** *
5071 AATCAATTATGA-AGTTACAAAACTGTTTAAAGTGAGCGATAAGGCTTTTAGGGGAATGGGTGA-
1 AATCAATTATGAGA-TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTAGGTGAC
* * * * *
5134 TAGTAATTAGATTTTTCTTGCCAATGAATGCCTTTTTC-TCATGTTT-ACCAAGGCA-AGCATTC
65 TA-TAAATAAACTTTTCTTACCAATGAATGGCTTTTTCTTCATGTTTCA-CAAGGCAGA-CATTC
* *
5196 AATTATAATCTATTTTAACTAAAAATGTAAAAAAATTCAACTTCA
127 AATTATAATCTATTTTAACTAAAAAAGTAAAAAAATTCAACTTAA
* * * *
5241 AATTAATTATGAAATTGTAAAACCATTTAAAGCGAGTAATAATGCTTTCGAAA-GCTTA-GTGAC
1 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTC-AAAGGCTTAGGTGAC
*** * * * * * *
5304 TATAAATGGGCTTTTCTTGCAAATGAATGGGC-TTTTCTTCATATTTCTCGAGGCAAACATTCAA
65 TATAAATAAACTTTTCTTACCAATGAAT-GGCTTTTTCTTCATGTTTCACAAGGCAGACATTCAA
* **
5368 GTATAATCTGCTTTAAC-AAAAAATGTAAAAAAAATTCAACTTAA
129 TTATAATCTATTTTAACTAAAAAA-GT-AAAAAAATTCAACTTAA
5412 AATCAATTATGAGATTATAAA
1 AATCAATTATGAGATTATAAA
5433 NNNNNNNNNN
Statistics
Matches: 426, Mismatches: 85, Indels: 42
0.77 0.15 0.08
Matches are distributed among these distances:
168 2 0.00
169 77 0.18
170 221 0.52
171 82 0.19
172 43 0.10
173 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (171 bp):
AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTAGGTGACT
ATAAATAAACTTTTCTTACCAATGAATGGCTTTTTCTTCATGTTTCACAAGGCAGACATTCAATT
ATAATCTATTTTAACTAAAAAAGTAAAAAAATTCAACTTAA
Found at i:6698 original size:172 final size:171
Alignment explanation
Indices: 6405--6848 Score: 543
Period size: 171 Copynumber: 2.6 Consensus size: 171
6395 NNNNNNNNNN
* * * *
6405 TTTAACCAAAAATATAAAAAA-ATTCAACTTAAAATCAATTACGAGATTATAAAGTCATTTAAAG
1 TTTAACCAAAAATATAAAAAACATTAAACTTAAAATCAATTATGAGATTACAAAATCATTTAAAG
* * ** *
6469 TGAGTAATAAGGCTTTCGAAGGCTTGGGTGACTATAAATGGGCCGTTCTTGCCAATGAACGGGTT
66 TGAGTAGTAAGGCTTTTGAAGGAATGGGTGACTATAAATGGGCCGTTCTTACCAATGAACGGGTT
*
6534 TTTCTTCATGTTTCCTAAGGTAAACATTCAATTACAAT-TGGT
131 TTTCATCATGTTTCCTAAGGTAAACA-TCAATTACAATGT-GT
* * * *
6576 TTTAACCAAATATGTAAAAAACATTTAACTTAAAATCAATTATGAGATTCCAAAATCATTTAAAG
1 TTTAACCAAAAATATAAAAAACATTAAACTTAAAATCAATTATGAGATTACAAAATCATTTAAAG
* ********** *
6641 TGAGTAGTAAGGCTTTTGAAGGAATGAGTGACTATANNNNNNNNNNTCTTACCAATGAATGGGTT
66 TGAGTAGTAAGGCTTTTGAAGGAATGGGTGACTATAAATGGGCCGTTCTTACCAATGAACGGGTT
* *
6706 TTTCATCATGTTTCCTAAGGTAAGCATCAATTATAATGTGT
131 TTTCATCATGTTTCCTAAGGTAAACATCAATTACAATGTGT
* * *
6747 TTTAACCAAAAATCTAAAAAACATTAAACTTAAAATTAATTATGAGATTACAAAA-CTATTGAAA
1 TTTAACCAAAAATATAAAAAACATTAAACTTAAAATCAATTATGAGATTACAAAATC-ATTTAAA
* *
6811 GTGAGTAGTAAGGCTTTTGAATGAATGGGTGATTATAA
65 GTGAGTAGTAAGGCTTTTGAAGGAATGGGTGACTATAA
6849 TTTAACGTTN
Statistics
Matches: 233, Mismatches: 37, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
170 1 0.00
171 121 0.52
172 111 0.48
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.32
Consensus pattern (171 bp):
TTTAACCAAAAATATAAAAAACATTAAACTTAAAATCAATTATGAGATTACAAAATCATTTAAAG
TGAGTAGTAAGGCTTTTGAAGGAATGGGTGACTATAAATGGGCCGTTCTTACCAATGAACGGGTT
TTTCATCATGTTTCCTAAGGTAAACATCAATTACAATGTGT
Found at i:10601 original size:171 final size:170
Alignment explanation
Indices: 10090--11408 Score: 1203
Period size: 171 Copynumber: 7.7 Consensus size: 170
10080 CTTGGGTCAT
* * **
10090 TATAAATGGGCTTTTCTTGCCAATGAACTGG-TTTTTCTTCACGTTTCTTAAAACAAACATTCAA
1 TATAAATGGACTTTTCTTGCCAATGAA-TGGCTTTTTCTTCATGTTTCTTAAGGCAAACATTCAA
* * * *
10154 TTATAATCTGTTTTAACAAAAAATATAAAAAACATTCAACGTAAAGTTAATTATGAGATTATAAA
65 TTATAATCTGTTTTAACTAAAAATAT-AAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAA
* *
10219 ATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGGGTGAC
128 ATCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGAC
* * * ** * *
10262 TATAAATGGGCTTTTTTTGCCAATAAATGAATTTTTCTTCATGTTT-TCCAATGCAAACATTCAA
1 TATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATGTTTCT-TAAGGCAAACATTCAA
* * * ** * *
10326 TTATAATCTGTTTTAACAAAAAATGTAAAAATTTCATTTTAAAATCAAATATGAGATTATAAAAC
65 TTATAATCTGTTTTAACTAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAT
* * ***
10391 CATTTAAAGTGAGTAATAAGGCTTTTGAAA-AAATGAGTGAC
130 CATTTAAAGCGAGTAATAAGGC-TTTCAAAGGCTTGAGTGAC
* * * * * *
10432 TATAAATAGACTTTTCTTACCAATGAATAGCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAAT
1 TATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGCAAACATTCAAT
* * *
10497 TATAATCCGTTTTAACTAAAAATATAAAAACCTTCAACTTAAAATCAATTATGAGATTATAAAAC
66 TATAATCTGTTTTAACTAAAAATATAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAAT
* *
10562 CCTTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGAT
130 CATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGAC
** * ** * * * *
10603 TATAAATATACTTTTCATATCAATAAATGGCTTTTGCTTCATGTTTCTTGAGGTAAACATTCAAT
1 TATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGCAAACATTCAAT
* * * * * * *
10668 TACAATATATTTT-AGTAAAAAAATAGAAAAATACAACTTAGAATCAATTATGAGATTATAAAAT
66 TATAATCTGTTTTAACTAAAAATATA-AAAAATTCAACTTAAAATCAATTATGAGATTATAAAAT
* * * * * *
10732 CATTTAAAACAAGCAATAAGGCTTGCAAAGGCTTGGGTAAC
130 CATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGAC
* * * * * * *
10773 TATGAAT-GAGCTTTTTTTCCCAATAAATGG-TATTTTTTTCATGTTTTCTCAA-GCAAACATTT
1 TATAAATGGA-CTTTTCTTGCCAATGAATGGCT-TTTTCTTCATG-TTTCTTAAGGCAAACATTC
* * * * * * * *
10835 AATTTTAATATGTTTCAACCAAAAATGTAAAAAAATTCAACTTAAAATCATTTATGAGAGTACAA
63 AATTATAATCTGTTTTAACTAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * *
10900 AATTATGTAAAGCGAGTAATAAGGCTTT-AGAAGGCTTGGGTGAC
127 AATCATTTAAAGCGAGTAATAAGGCTTTCA-AAGGCTTGAGTGAC
* * ** *
10944 TATAAAT-GAGCTTTTCTTGTCAATGAATGGGTTTTTCTTCACATTTC-TAGAGGCAAACGTTCA
1 TATAAATGGA-CTTTTCTTGCCAATGAATGGCTTTTTCTTCATGTTTCTTA-AGGCAAACATTCA
* * * * **
11007 ATTATAAT-TGATTTTAACTAAAAATGTAAAAAATATTGAACTTAAAATCAACTATAAGATTGCA
64 ATTATAATCTG-TTTTAACTAAAAATAT-AAAAA-ATTCAACTTAAAATCAATTATGAGATTATA
* * * *** *
11071 AAA-CTATTTAAAGTGAGTAGTAAGGCTTTTAAAGAAATGAGTGAT
126 AAATC-ATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGAC
* ** * *
11116 TATAATTGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATGTTTCCCAAGACAAACATTTAAT
1 TATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGCAAACATTCAAT
* * *
11181 TATAATCTGTTTTAACCAAAAA-AGTAAAACAATTCAACTTAAAATCAGTTATGAGATTGTAAAA
66 TATAATCTGTTTTAACTAAAAATA-TAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAA
* * ** * **
11245 TCATATAAAGTGAGTAATAAGGCTTTTGAAGGCATGAACGAC
129 TCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGAC
* * ** * * *
11287 TATAAATGGACTTTT-TTGGTCAATGAATGGCTGTTTCTTCACATTT-TCAAGGTAGACACTT-A
1 TATAAATGGACTTTTCTT-GCCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGCAAACA-TTCA
* * * *
11349 ATTATAATCTATTTTAACTAAAAATATTAGAAAATTTAAATTAAAATCAATTATGAGATT
64 ATTATAATCTGTTTTAACTAAAAATA-TAAAAAATTCAACTTAAAATCAATTATGAGATT
11409 NNNNNNNNNN
Statistics
Matches: 942, Mismatches: 176, Indels: 60
0.80 0.15 0.05
Matches are distributed among these distances:
169 3 0.00
170 327 0.35
171 398 0.42
172 208 0.22
173 6 0.01
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (170 bp):
TATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGCAAACATTCAAT
TATAATCTGTTTTAACTAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATC
ATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGAC
Found at i:10722 original size:341 final size:338
Alignment explanation
Indices: 10090--11408 Score: 1184
Period size: 341 Copynumber: 3.9 Consensus size: 338
10080 CTTGGGTCAT
* * *
10090 TATAAATGGGCTTTTCTTGCCAATGAACTGGTTTTTCTTCACGTTTCTTAAAACAAACATTCAAT
1 TATAAATGGACTTTTCTTGCCAATGAA-TGCTTTTTCTTCATGTTTCTTAAAACAAACATTCAAT
* * * *
10155 TATAATCTGTTTTAACAAAAAATATAAAAAACATTCAACGTAAAGTTAATTATGAGATTATAAAA
65 TATAATCTGTTTTAACCAAAAATAT-AAAAACATTCAACTTAAAATCAATTATGAGATTATAAAA
* * * *
10220 TCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGGGTGACTATAAATGGGCTTTTTTTGCCAA
129 TCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGGGTGACTATAAAT-AGCTTTTCTTGTCAA
* * * *
10285 TAAATGAATTTTTCTTCATGTTTTCCA-ATGCAAACATTCAATTATAATCTGTTTTA-ACAAAAA
193 TAAATGGATTTTTCTTCATG-TTTCTAGAGGCAAACATTCAATTATAAT-TATTTTATA-AAAAA
* **
10348 AT-GTAAAAATTTCATTTTAAAATCAAATATGAGATTATAAAACCATTTAAAGTGAGTAATAAGG
255 ATAG-AAAAA-TACAACTTAAAATCAAATATGAGATTATAAAACCATTTAAAGTGAGTAATAAGG
10412 CTTTTGAAA-AAATGAGTGAC
318 CTTTTGAAAGAAATGAGTGAC
* * * *** *
10432 TATAAATAGACTTTTCTTACCAATGAATAGCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAAT
1 TATAAATGGACTTTTCTTGCCAATGAAT-GCTTTTTCTTCATGTTTCTTAAAACAAACATTCAAT
* * * *
10497 TATAATCCGTTTTAACTAAAAATATAAAAACCTTCAACTTAAAATCAATTATGAGATTATAAAAC
65 TATAATCTGTTTTAACCAAAAATATAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAAT
* * * * * *
10562 CCTTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGATTATAAATATACTTTTCATATCAAT
130 CATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGGGTGACTATAAATA-GCTTTTCTTGTCAAT
* * * * *
10627 AAATGGCTTTTGCTTCATGTTTCTTGAGGTAAACATTCAATTACAATATATTTTAGTAAAAAAAT
194 AAATGGATTTTTCTTCATGTTTCTAGAGGCAAACATTCAATTATAAT-TATTTTA-TAAAAAAAT
* * * *** *
10692 AGAAAAATACAACTTAGAATCAATTATGAGATTATAAAATCATTTAAAACAAGCAATAAGGC--T
257 AGAAAAATACAACTTAAAATCAAATATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
*** * *
10755 TGCAAAGGCTTGGGTAAC
322 TG-AAAGAAATGAGTGAC
* * * * * * * * *
10773 TATGAAT-GAGCTTTTTTTCCCAATAAATGGTATTTTTTTCATGTTT-TCTCAAGCAAACATTTA
1 TATAAATGGA-CTTTTCTTGCCAATGAATGCT-TTTTCTTCATGTTTCT-TAAAACAAACATTCA
* * * * * * * *
10836 ATTTTAATATGTTTCAACCAAAAATGTAAAAAAATTCAACTTAAAATCATTTATGAGAGTACAAA
63 ATTATAATCTGTTTTAACCAAAAATATAAAAACATTCAACTTAAAATCAATTATGAGATTATAAA
* *
10901 ATTATGTAAAGCGAGTAATAAGGCTTT-AGAAGGCTTGGGTGACTATAAATGAGCTTTTCTTGTC
128 ATCATTTAAAGCGAGTAATAAGGCTTTCA-AAGGCTTGGGTGACTATAAAT-AGCTTTTCTTGTC
* * ** *
10965 AATGAATGGGTTTTTCTTCACATTTCTAGAGGCAAACGTTCAATTATAATTGATTTTAACTAAAA
191 AATAAATGGATTTTTCTTCATGTTTCTAGAGGCAAACATTCAATTATAATT-ATTTT-A-TAAAA
** * * * ** * *
11030 ATGTA-AAAAATATTGAACTTAAAATCAACTATAAGATTGCAAAACTATTTAAAGTGAGTAGTAA
253 AAATAGAAAAATA--CAACTTAAAATCAAATATGAGATTATAAAACCATTTAAAGTGAGTAATAA
*
11094 GGCTTTT-AAAGAAATGAGTGAT
316 GGCTTTTGAAAGAAATGAGTGAC
* ** * *
11116 TATAATTGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATGTTTCCCAAGACAAACATTTAAT
1 TATAAATGGACTTTTCTTGCCAATGAAT-GCTTTTTCTTCATGTTTCTTAAAACAAACATTCAAT
* *
11181 TATAATCTGTTTTAACCAAAAA-AGT-AAAACAATTCAACTTAAAATCAGTTATGAGATTGTAAA
65 TATAATCTGTTTTAACCAAAAATA-TAAAAAC-ATTCAACTTAAAATCAATTATGAGATTATAAA
* * ** * *** *
11244 ATCATATAAAGTGAGTAATAAGGCTTTTGAAGGCATGAACGACTATAAATGGACTTTT-TTGGTC
128 ATCATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGGGTGACTATAAATAG-CTTTTCTT-GTC
* * * * *
11308 AATGAATGGCTGTTTCTTCACAT-TTTC-A-AGGTAGACACTT-AATTATAATCTATTTTAACTA
191 AATAAATGGATTTTTCTT--CATGTTTCTAGAGGCAAACA-TTCAATTATAAT-TATTTT-A-TA
* * *
11369 AAAATATTAGAAAATTTA-AA-TTAAAATCAATTATGAGATT
250 AAAA-AATAGAAAA-ATACAACTTAAAATCAAATATGAGATT
11409 NNNNNNNNNN
Statistics
Matches: 788, Mismatches: 155, Indels: 69
0.78 0.15 0.07
Matches are distributed among these distances:
339 3 0.00
340 14 0.02
341 401 0.51
342 136 0.17
343 216 0.27
344 12 0.02
345 6 0.01
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (338 bp):
TATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTCATGTTTCTTAAAACAAACATTCAATT
ATAATCTGTTTTAACCAAAAATATAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAATC
ATTTAAAGCGAGTAATAAGGCTTTCAAAGGCTTGGGTGACTATAAATAGCTTTTCTTGTCAATAA
ATGGATTTTTCTTCATGTTTCTAGAGGCAAACATTCAATTATAATTATTTTATAAAAAAATAGAA
AAATACAACTTAAAATCAAATATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAA
AGAAATGAGTGAC
Done.