Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399044.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_232.1, 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: 5446
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.32
Warning! 793 characters in sequence are not A, C, G, or T
Found at i:458 original size:43 final size:43
Alignment explanation
Indices: 392--478 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
382 AGCCTTCGAA
392 AGCCCTATTACTAGCTTTAAATGGTTTTATAATCTCATAATTG
1 AGCCCTATTACTAGCTTTAAATGGTTTTATAATCTCATAATTG
* * * *
435 AGCCTTATTACTCA-CTTTAAATGGTTTTTTAATCTGATAGTTG
1 AGCCCTATTACT-AGCTTTAAATGGTTTTATAATCTCATAATTG
478 A
1 A
479 TTTTAAGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 38 0.97
44 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.44
Consensus pattern (43 bp):
AGCCCTATTACTAGCTTTAAATGGTTTTATAATCTCATAATTG
Found at i:725 original size:170 final size:168
Alignment explanation
Indices: 435--847 Score: 444
Period size: 171 Copynumber: 2.4 Consensus size: 168
425 CTCATAATTG
** * * * *
435 AGCCTTATTACTCACTTTAAATGGTTTTTTAATCTGATAGTTGATTTTAAGTTAAATTCTTTTAT
1 AGCCTTATTACTCGTTTTAAAT-GTTTTATAATCTCATAATTGA-TTTAAGTTAAATT-TTTTTT
* * * * *
500 AC-TTTTTTTCAAAGAAATTATAATTGAATGTTTACTTTGAGAAACGTGAAAGAAAAGA-TATTC
63 ACATTTTTTTAAAAGAAATTATAATTGAATGCTGACTTAGAGAAACGTGAAAGAAAA-ACCATTC
* *
563 ATTGGTAAAAAAATTCCATTGATAGTCACTCATACCTTCG-A
127 ATTGGCAAAAAAAGTCCATTGATAGTCACTCATACCTTCGTA
604 AGGCCTTATTACTCGTTTTAAATAGTTTTATAATCTCATAATTGATTTCAAGTT-AATTTTTTTT
1 A-GCCTTATTACTCGTTTTAAAT-GTTTTATAATCTCATAATTGATTT-AAGTTAAATTTTTTTT
* * *
668 ACATTTTCTATTAAAATAGATTATAATTGAATGGCTGCCTTAG-GAAACGTG-AAGAAAAACCCA
63 ACATTTT-T-TTAAAAGAAATTATAATTGAAT-GCTGACTTAGAGAAACGTGAAAGAAAAA-CCA
* * * *
731 TTTATTGGCAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGTA
124 TTCATTGGCAAAAAAAGTCCATTGATAGTCACTCATACCTTCGTA
* ** *
776 AGCCTAATTACTCGTTCCAAATGATTTTATAATCTCATAATTGACTTTAAGTTGAATTTTTTTT-
1 AGCCTTATTACTCGTTTTAAATG-TTTTATAATCTCATAATTGA-TTTAAGTTAAATTTTTTTTA
840 CATTTTTT
64 CATTTTTT
848 GTTAAANNNN
Statistics
Matches: 208, Mismatches: 24, Indels: 24
0.81 0.09 0.09
Matches are distributed among these distances:
168 7 0.03
169 14 0.07
170 52 0.25
171 114 0.55
172 21 0.10
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (168 bp):
AGCCTTATTACTCGTTTTAAATGTTTTATAATCTCATAATTGATTTAAGTTAAATTTTTTTTACA
TTTTTTTAAAAGAAATTATAATTGAATGCTGACTTAGAGAAACGTGAAAGAAAAACCATTCATTG
GCAAAAAAAGTCCATTGATAGTCACTCATACCTTCGTA
Found at i:2428 original size:171 final size:161
Alignment explanation
Indices: 2186--2501 Score: 323
Period size: 171 Copynumber: 1.9 Consensus size: 161
2176 ATCTTAAGAG
* * * *
2186 ACATGAAGAAAAAGCCATTTATTGACAAAAAAAGCCTATTTGTAGTCACTCAAACCTTCCAAAGC
1 ACATGAAGAAAAAGACATTAATTGACAAAAAAAGCCTATTTATAGTCACTCAAACCTTCAAAAGC
* ** *
2251 CTTATTACTCGCTTTAAATGGTTAT-ATAATCTTATAATTGGTTGGAAGTTAAACTTTTTTATAT
66 CTTATTACTCGCTTTAAATGGTT-TCATAATCTCATAATTGGTTCAAAGTTAAACTTTTTTACAT
*
2315 TTTTTATTAAAACAGATTATNNNNNNNNNNCTACATCGAGAA
130 TTTTTACTAAAACAGATTAT----------CTACATCGAGAA
* * * **
2357 ACATGAAGAAAAAGATATTAATTGCCAAGAAAAGTCC-ATTTATAGTCAC-CTATGCCTTCAAAA
1 ACATGAAGAAAAAGACATTAATTGACAAAAAAAG-CCTATTTATAGTCACTC-AAACCTTCAAAA
* * * * *
2420 GTCTTATTATTCGCTTTAAATGGTTTCATAATCTCATAATTGTTTCAAAGTTGAATTTTTTTACA
64 GCCTTATTACTCGCTTTAAATGGTTTCATAATCTCATAATTGGTTCAAAGTTAAACTTTTTTACA
2485 TTTTTTACTAAAACAGA
129 TTTTTTACTAAAACAGA
2502 ATATAATAGA
Statistics
Matches: 123, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
170 2 0.02
171 119 0.97
172 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.36
Consensus pattern (161 bp):
ACATGAAGAAAAAGACATTAATTGACAAAAAAAGCCTATTTATAGTCACTCAAACCTTCAAAAGC
CTTATTACTCGCTTTAAATGGTTTCATAATCTCATAATTGGTTCAAAGTTAAACTTTTTTACATT
TTTTACTAAAACAGATTATCTACATCGAGAA
Found at i:2529 original size:171 final size:171
Alignment explanation
Indices: 2012--3316 Score: 933
Period size: 170 Copynumber: 7.7 Consensus size: 171
2002 TGTCTGTCTA
** * * * * **
2012 AGAAAGCATGAAG-AAAAGCCATTTATTGTCAAAAAAAGTCTATTTATAGTCACCCAAGCCTTTG
1 AGAAA-CATGAAGAAAAAGATATTTATTGACAAGAAAAGTCCATTTATAGTCACCTAAGCCTTCA
* * ** * *
2076 GAAGCCTTATTGCTTACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTT-AATATTTTT
65 AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTGAAGTTGAATTTTTTT
* * * * *
2140 AGAATTTTGATTAAAACAGACA-ATAATTGAATGTCTATCTTA
130 ATATTTTTTATTAAAACAGA-ATATAATTGAATGTCTACCTTG
* ** * * *
2182 AGAGACATGAAGAAAAAGCCATTTATTGACAAAAAAAG-CCTATTTGTAGTCA-CTCAAACCTTC
1 AGAAACATGAAGAAAAAGATATTTATTGACAAGAAAAGTCC-ATTTATAGTCACCT-AAGCCTTC
* * * * * * *
2245 CAAAGCCTTATTACTCGCTTTAAATGGTTATATAATCTTATAATTGGTTGGAAGTTAAACTTTTT
64 AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTGAAGTTGAATTTTTT
* ********** * *
2310 TATATTTTTTATTAAAACAGATTATNNNNNNNNNNCTACATCG
129 TATATTTTTTATTAAAACAGAATATAATTGAATGTCTACCTTG
* * *
2353 AGAAACATGAAGAAAAAGATATTAATTGCCAAGAAAAGTCCATTTATAGTCACCTATGCCTTCAA
1 AGAAACATGAAGAAAAAGATATTTATTGACAAGAAAAGTCCATTTATAGTCACCTAAGCCTTCAA
* * * *
2418 AAGTCTTATTATTCGCTTTAAATGGTTTCATAATCTCATAATTG-TTTCAAAGTTGAATTTTTTT
66 AAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT-GAAGTTGAATTTTTTT
* * *
2482 ACATTTTTTACTAAAACAGAATATAATAGAATGTCTACCTTG
130 ATATTTTTTATTAAAACAGAATATAATTGAATGTCTACCTTG
* * * * * * * *
2524 AGAAACAAGAAGAAAAAGATATTCATT-AGTAAGAAAAGTCTAATTATATTCACCTATGGCTTCA
1 AGAAACATGAAGAAAAAGATATTTATTGA-CAAGAAAAGTCCATTTATAGTCACCTAAGCCTTCA
* * * *
2588 AAAGCCTTATTAC-CTGCTTTAAGTGGCTTTCTAATCTCATAAGTGACTTT-AAGTTGAATTTTT
65 AAAGCCTTATTACTC-GCTTTAAATGGTTTTATAATCTCATAATTGA-TTTGAAGTTGAATTTTT
*** ** * * * * * ** *
2651 TT-TAATTTTTGGCTAAATTATATTACAGTTGACTGTCTGTC-TA
128 TTAT-ATTTTTTATTAAAACAGAATATAATTGAATGTCTACCTTG
* * * * * * * * *
2694 AGGCAAGACG-AGAAAAAAGTTAGTCATTGGCAAGAAAAG-CCTATTTATAGTTACCCAAGCCTT
1 A-GAAACATGAAG-AAAAAGATATTTATTGACAAGAAAAGTCC-ATTTATAGTCACCTAAGCCTT
* * *
2757 CGAAAGCCTTATTACTCTCTTTAAATGGTTTTAGAATCTCATAATTGATTTGAAGTTG-ATTTTT
63 CAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTGAAGTTGAATTTTT
*
2821 TTATATTTTTTATTAAAACATAATATAATTGAATGTCTACCTTG
128 TTATATTTTTTATTAAAACAGAATATAATTGAATGTCTACCTTG
* * * * * * * *
2865 GGAAACGTGAAGAAAAATATATTTATTGGCAAGAAAAGTCCATTTATTGTCACTTATGCCTTGAA
1 AGAAACATGAAGAAAAAGATATTTATTGACAAGAAAAGTCCATTTATAGTCACCTAAGCCTTCAA
********** *
2930 AAGCCTTANNNNNNNNNNTAAATGGTTTTATAATCTCATAATTGGCTTT-AAGTTG-ATTGTTTT
66 AAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATT-GATTTGAAGTTGAATT-TTTT
* * * **********
2993 T-TATTTTTTGTTAAAACATATTATAANNNNNNNNNNACCTTG
129 TATATTTTTTATTAAAACAGAATATAATTGAATGTCTACCTTG
* ** * * *
3035 AAAAACATGAAGAAAAAG-TCATTCCTTGACAAGAAAAGTCCATTTATAGGCACCTAAGTCTTCG
1 AGAAACATGAAGAAAAAGAT-ATTTATTGACAAGAAAAGTCCATTTATAGTCACCTAAGCCTTCA
********** *
3099 AAAGCCTTATTACTCGCTTTAAANNNNNNNNNNATCTCATAATTGATTTGAAGTTGAATATTTTT
65 AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTGAAGTTGAATTTTTTT
* * *
3164 ACA-TTTTTATTAAAATAG-ATCATGATTGAATGTCTACCTTG
130 ATATTTTTTATTAAAACAGAAT-ATAATTGAATGTCTACCTTG
* * ** * * *
3205 AGAAACGTGAAAAAAAAGCCATTTATTGATAAGAAAAGTCCATGTATAGTCACCTATA-CTTTCA
1 AGAAACATGAAGAAAAAGATATTTATTGACAAGAAAAGTCCATTTATAGTCACCTA-AGCCTTCA
*
3269 AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAGTTGATT
65 AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATT
3317 NNNNNNNNNN
Statistics
Matches: 855, Mismatches: 248, Indels: 64
0.73 0.21 0.05
Matches are distributed among these distances:
169 15 0.02
170 438 0.51
171 394 0.46
172 5 0.01
173 3 0.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.36
Consensus pattern (171 bp):
AGAAACATGAAGAAAAAGATATTTATTGACAAGAAAAGTCCATTTATAGTCACCTAAGCCTTCAA
AAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTGAAGTTGAATTTTTTTA
TATTTTTTATTAAAACAGAATATAATTGAATGTCTACCTTG
Found at i:3939 original size:171 final size:168
Alignment explanation
Indices: 3420--3974 Score: 476
Period size: 171 Copynumber: 3.2 Consensus size: 168
3410 NNNNNNNTAG
* * *
3420 AAGCCTTATTACTCACTTTAAATGGTTTTATGATCTCATAATTGATTTTAAATTAAATTTTTTTA
1 AAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTG-TTTCAAATTAAATTTTTTTA
* * * * * * * * * **
3485 CAATTTTGGTTACAATAGACA-ATAATTGAATGTCTGCCTTGAGAGACATGAAGAACAAGCCATT
65 CATTTTTTGCTAAAACAGA-ATATAATTGAATGT-TTCCTCGAGAAACATGAAGAAAAAGATATT
* * * *
3549 TATTGGCAAGAAAAGCCTATTTATAGTGA-CTCAAGCCTTTCG-
128 AATTGGCAAGAAAAGCC-AATTATAGTCACCT-ATGCC-TTCGA
* ** *
3591 AAGCCTTATTACTCGA-TTTAAAT-GATTATATAATCTCATAATTGATTGAAAATTAATTTTTTT
1 AAGCCTTATTACTC-ACTTTAAATAG-TTTTATAATCTCATAATTG-TTTCAAATTAA-ATTTTT
* * * * *
3654 TTATATTTTTTACTAAAACAGATTATAATTGAATGTCTTCATCAAGAAACATGAAGAAAAAGATA
62 TTACATTTTTTGCTAAAACAGAATATAATTGAATGT-TTCCTCGAGAAACATGAAGAAAAAGATA
********* * *
3719 TTAATTGGCAAGAANNNNNNNNNNATAGTCACCTTTGCCTTCAA
126 TTAATTGGCAAGAA-AAGCCAATTATAGTCACCTATGCCTTCGA
3763 AAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGTTTCAAAGTTAAATTTTTTTA
1 AAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGTTTCAAA-TTAAATTTTTTTA
*
3828 CATTTTTTGCTAAAACAGAATATAA-TAAATTGTTTACCTCGAGAAACGA-GAAGAAAAAGATAT
65 CATTTTTTGCTAAAACAGAATATAATTGAA-TGTTT-CCTCGAGAAAC-ATGAAGAAAAAGATAT
* * * * * *
3891 TCATTAGTAAGAAAAGTTCAATTATATTCACCTATGACTTCGA
127 TAATTGGCAAGAAAAG-CCAATTATAGTCACCTATGCCTTCGA
** *
3934 AAGCCTTATTACTTGCTTTAAATAGCTTTATAATCTCATAA
1 AAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAA
3975 GTGACTTTAA
Statistics
Matches: 306, Mismatches: 64, Indels: 28
0.77 0.16 0.07
Matches are distributed among these distances:
170 6 0.02
171 177 0.58
172 120 0.39
173 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.37
Consensus pattern (168 bp):
AAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGTTTCAAATTAAATTTTTTTAC
ATTTTTTGCTAAAACAGAATATAATTGAATGTTTCCTCGAGAAACATGAAGAAAAAGATATTAAT
TGGCAAGAAAAGCCAATTATAGTCACCTATGCCTTCGA
Found at i:4110 original size:343 final size:343
Alignment explanation
Indices: 3755--4385 Score: 815
Period size: 343 Copynumber: 1.8 Consensus size: 343
3745 AGTCACCTTT
* * *
3755 GCCTTCAAAAGCCTTATTACTCACTTT-AAATAGTTTTATAATCTCATAATTGTTTCAAAGTTAA
1 GCCTTCAAAAGCCTTATGACTC-CTTTCAAATAGTTTTATAATATCATAATTGATTCAAAGTTAA
* * * *
3819 ATTTTTTTACATTTTTTGCTAAAACAGAATATAA-TAAATTGTTTACCTCGAG-AAACGAGAAGA
65 ATTGTTTTACATTTCTTACTAAAACAGAATATAATTAAA-TGTCTACCT-GAGAAAACGAGAAGA
* * * * *
3882 AAAAGATATTCATTAGTAAGAAAAGTTCAATTATATTCACCTATGACTTCGAAAGCCTTATTACT
128 AAAAGATATTCATTAGTAAGAAAAGTCCAATTATAGTCACCCATGACTTCAAAAGCCGTATTA--
* *
3947 TGC-TTTAAATAGCTTT-ATAATCTCATAAGTGACTTTAAGTAGAA-TTGTTTTTCATTTTTGGT
191 TCCATTTAAATAGCTTTCA-AATCTCATAAGTGACTTTAAGTAGAATTTGTTTTTCATTTTTAGT
* * *
4009 TAAAATATATTACAGTTTACTGTCTGCCTAAGGCAAGACAAAAAAACAGCCAATCATTGGCAAAA
255 TAAAATAGATTACAGTTAAATGTCTGCCTAAGGCAAGACAAAAAAACAGCCAATCATTGGCAAAA
4074 AAAAGCCTATTTACAATCAGTCAA
320 AAAAGCCTATTTACAATCAGTCAA
* * * * * *
4098 GCCTTTAAAAGCCTTATGACTCGTTTCAAATGGTTTTATAATATCATAATTGATTCGAGGTTGAA
1 GCCTTCAAAAGCCTTATGACTCCTTTCAAATAGTTTTATAATATCATAATTGATTCAAAGTTAAA
* * * * *
4163 TTGTTTTACATTTCTTATTAAAACAGGATATAATTGAATGTCTAGCTTAGAAAACGAGAAGAAAA
66 TTGTTTTACATTTCTTACTAAAACAGAATATAATTAAATGTCTACCTGAGAAAACGAGAAGAAAA
* * * *
4228 AGATATTCATTGGTAGGAAAAGTCCATTTATAGTCACCCATGGCTTCAAAAGCCGTATTATCCAT
131 AGATATTCATTAGTAAGAAAAGTCCAATTATAGTCACCCATGACTTCAAAAGCCGTATTATCCA-
* * * * *
4293 TTTAAATGGTTTTCAAATCTTATAAGTGACTTTAAGTAGAATTTTTTTTTCATTTTTAGTTACAA
195 TTTAAATAGCTTTCAAATCTCATAAGTGACTTTAAGTAGAATTTGTTTTTCATTTTTAGTTAAAA
*
4358 TAGATTACAGTTAAATGTTTGCCTAAGG
260 TAGATTACAGTTAAATGTCTGCCTAAGG
4386 AAACATGAAG
Statistics
Matches: 243, Mismatches: 38, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
341 2 0.01
342 5 0.02
343 188 0.77
344 48 0.20
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (343 bp):
GCCTTCAAAAGCCTTATGACTCCTTTCAAATAGTTTTATAATATCATAATTGATTCAAAGTTAAA
TTGTTTTACATTTCTTACTAAAACAGAATATAATTAAATGTCTACCTGAGAAAACGAGAAGAAAA
AGATATTCATTAGTAAGAAAAGTCCAATTATAGTCACCCATGACTTCAAAAGCCGTATTATCCAT
TTAAATAGCTTTCAAATCTCATAAGTGACTTTAAGTAGAATTTGTTTTTCATTTTTAGTTAAAAT
AGATTACAGTTAAATGTCTGCCTAAGGCAAGACAAAAAAACAGCCAATCATTGGCAAAAAAAAGC
CTATTTACAATCAGTCAA
Found at i:4444 original size:343 final size:341
Alignment explanation
Indices: 3755--4477 Score: 814
Period size: 343 Copynumber: 2.1 Consensus size: 341
3745 AGTCACCTTT
* * * *
3755 GCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGTTTCAAAGTTAAA
1 GCCTTCAAAAGCCTTATTACTC-GTTTAAATGGTTTTATAATATCATAATTGATTCAAAGTTAAA
* * * * *
3820 TTTTTTTACATTTTTTGCTAAAACAGAATATAATAAATTGTTTACCTCGAGAAACGAGAAGAAAA
65 TTGTTTTACATTTCTTACTAAAACAGAATATAATAAATTGTCTACCTAGAGAAACGAGAAGAAAA
* * * * * *
3885 AGATATTCATTAGTAAGAAAAGTTCAATTATATTCACCTATGACTTCGAAAGCCTTATTACTTGC
130 AGATATTCATTAGTAAGAAAAGTCCAATTATAGTCACCCATGACTTCAAAAGCCGTATTACAT-C
*
3950 TTTAAATAGCTTTATAATCTCATAAGTGACTTTAAGTAGAATTGTTTTTCATTTTTGGTTAAAAT
194 TTTAAATAGCTTTATAATCTCATAAGTGACTTTAAGTAGAATTGTTTTTCATTTTTAGTTAAAAT
* * * *
4015 ATATTACAGTTTACTGTCTGCCTAAGGCAAGACAAAAAAACAGCCAATCATTGGCAAAAAAAAGC
259 AGATTACAGTTAAATGTCTGCCTAAGGCAAGACAAAAAAACAGCCAATCATTGACAAAAAAAAGC
**
4080 CTATTTACAATCAGTCAA
324 CTATTTACAATCACCCAA
* * * * *
4098 GCCTTTAAAAGCCTTATGACTCGTTTCAAATGGTTTTATAATATCATAATTGATTCGAGGTTGAA
1 GCCTTCAAAAGCCTTATTACTCGTTT-AAATGGTTTTATAATATCATAATTGATTCAAAGTTAAA
* * * *
4163 TTGTTTTACATTTCTTATTAAAACAGGATATAATTGAA-TGTCTAGCTTAGA-AAACGAGAAGAA
65 TTGTTTTACATTTCTTACTAAAACAGAATATAA-TAAATTGTCTA-CCTAGAGAAACGAGAAGAA
* * * *
4226 AAAGATATTCATTGGTAGGAAAAGTCCATTTATAGTCACCCATGGCTTCAAAAGCCGTATTATCC
128 AAAGATATTCATTAGTAAGAAAAGTCCAATTATAGTCACCCATGACTTCAAAAGCCGTATTA--C
* * * *
4291 AT-TTTAAATGGTTTTCA-AATCTTATAAGTGACTTTAAGTAGAATTTTTTTTTCATTTTTAGTT
191 ATCTTTAAATAGCTTT-ATAATCTCATAAGTGACTTTAAGTAGAA-TTGTTTTTCATTTTTAGTT
* * * * *
4354 ACAATAGATTACAGTTAAATGTTTGCCTAAGG-AA-ACATGAAGAAAA-AGCCATTTATTGATAA
254 AAAATAGATTACAGTTAAATGTCTGCCTAAGGCAAGACA--AA-AAAACAGCCAATCATTGACAA
* * * *
4416 GAAAAA-CTTATTTATAGTCACCCAA
316 AAAAAAGCCTATTTACAATCACCCAA
* * *
4441 GCCTTCGAAAGCCCTATTACTAGCTTTAAATGGTTTT
1 GCCTTCAAAAGCCTTATTACTCG-TTTAAATGGTTTT
4478 NNNNNNNNNN
Statistics
Matches: 316, Mismatches: 53, Indels: 22
0.81 0.14 0.06
Matches are distributed among these distances:
342 6 0.02
343 230 0.73
344 74 0.23
345 6 0.02
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (341 bp):
GCCTTCAAAAGCCTTATTACTCGTTTAAATGGTTTTATAATATCATAATTGATTCAAAGTTAAAT
TGTTTTACATTTCTTACTAAAACAGAATATAATAAATTGTCTACCTAGAGAAACGAGAAGAAAAA
GATATTCATTAGTAAGAAAAGTCCAATTATAGTCACCCATGACTTCAAAAGCCGTATTACATCTT
TAAATAGCTTTATAATCTCATAAGTGACTTTAAGTAGAATTGTTTTTCATTTTTAGTTAAAATAG
ATTACAGTTAAATGTCTGCCTAAGGCAAGACAAAAAAACAGCCAATCATTGACAAAAAAAAGCCT
ATTTACAATCACCCAA
Found at i:4834 original size:171 final size:171
Alignment explanation
Indices: 4541--5442 Score: 805
Period size: 171 Copynumber: 5.3 Consensus size: 171
4531 CTCATAATTG
* * * *
4541 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTGATAGTTGATATTAAGTTAAATTTTTTTAT
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
* * * * *
4606 ACTTTTTGTTCAAAGAGATTATAATTGAATGTTTACCTTGAGAAACAT-AAGGAAAAAGATATTC
66 ATTTTTTGTTAAAACAGATTATAATTGAATGTCTACCTAGAGAAACATGAA-GAAAAAGATATTC
* *
4670 ATTGCCAAGAAAAGTCCATTGATAGTCACTCATACCTTCGAA
130 ATTGGCAAGAAAAGTCCATTTATAGTCACTCATACCTTCGAA
* * * * *
4712 GGCCTTATTACTCATTTTAAATGGTTTTATAAACTCATAATTGATTTTAAATTGAATTCTTTTAT
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
* * ** *
4777 ATTTTTTGTTAAAACAGATTATAATTGAATGTCTGCCTCAG-GAAACGTGAAGAAAAAGCCATTG
66 ATTTTTTGTTAAAACAGATTATAATTGAATGTCTACCT-AGAGAAACATGAAGAAAAAGATATTC
* * * *
4841 ATTGG-AAAAACAATTCCATTTATAGTCACTTATGCCTTCGAA
130 ATTGGCAAGAA-AAGTCCATTTATAGTCACTCATACCTTCGAA
* * ** * *
4883 AGCCTAATTACTCGCTCCAAATGGTTTTATAATCTCATAATTAACTTTAAGTTGAAATTTTTTT-
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTG-AATTTTTTTA
* * * * * * * *
4947 TATTTTTGGTTAAAACATATTATAATTAAATGCCTTCCTCA-AAAAATATGAAGAAAAAGCTATT
65 TATTTTTTGTTAAAACAGATTATAATTGAATGTCTACCT-AGAGAAACATGAAGAAAAAGATATT
* *
5011 CATTGGCAAGAAAAGTCCATTTATAGTCA-TCCACACCTTCAAA
129 CATTGGCAAGAAAAGTCCATTTATAGTCACT-CATACCTTCGAA
*** * **
5054 ATTTTTATTACTCACTTTAAATGGTTTTATAATCTGATAGCTGATTTTAAGTTGAATTTTTTTAT
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
********** * * *
5119 NNNNNNNNNNAAAACAGATTATAATTGAATGTTTACCTAGAGAAACATGAAGTACAAGATATTCA
66 ATTTTTTGTTAAAACAGATTATAATTGAATGTCTACCTAGAGAAACATGAAGAAAAAGATATTCA
* * *
5184 TTGGCAAGAAAAGTCCATTTATAGTCAC-CTATACTTTAGCA
131 TTGGCAAGAAAAGTCCATTTATAGTCACTC-ATACCTTCGAA
*** * * * * *
5225 AGCCTTATTACTTGTTTTAAATAGTTTTATAATCTCATAATTGATTTCAAATTAAATTTTTTTAC
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
** * * * ********* **
5290 ATTTTTACTTAAAACAGATTATGATTGAATGTCTATCTCGAGAAACANNNNNNNNNNA-CCATTC
66 ATTTTTTGTTAAAACAGATTATAATTGAATGTCTACCTAGAGAAACA-TGAAGAAAAAGATATTC
* * * **
5354 ATTGGTAAGAAAAGTCTATTTATAGTCAC-CTATGCCTTTAAA
130 ATTGGCAAGAAAAGTCCATTTATAGTCACTC-ATACCTTCGAA
** *
5396 AGCCTTATTACTTGCTTTAAATGGTTTTATAATCTCATAGTTGATTT
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTT
5443 AAAG
Statistics
Matches: 581, Mismatches: 138, Indels: 24
0.78 0.19 0.03
Matches are distributed among these distances:
170 16 0.03
171 549 0.94
172 16 0.03
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.38
Consensus pattern (171 bp):
AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
ATTTTTTGTTAAAACAGATTATAATTGAATGTCTACCTAGAGAAACATGAAGAAAAAGATATTCA
TTGGCAAGAAAAGTCCATTTATAGTCACTCATACCTTCGAA
Done.