Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402588.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_566.0, 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: 26102
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.25
Warning! 8358 characters in sequence are not A, C, G, or T
Found at i:613 original size:171 final size:170
Alignment explanation
Indices: 49--1090 Score: 929
Period size: 172 Copynumber: 6.1 Consensus size: 170
39 ATTAGGAAGA
* * * * * *
49 AAAGTCTATTTATGGTCTCCCATTCCTTCAAAAGCCTTATT-C--GCTATGAATGCTTTTATAAT
1 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTAGCTTTAAATGGTTTTATAAT
*** * * * * *
111 CTTGTAATTGATTTTAAGTTGAATTTTTTTACATTTTTTTGTTAAAA-TAGACTATAATTGACTG
66 CTCAAAATTGATTTTAAGATGAA-TTTTTTACA-TTTTTGGTTAAAACAAGATTATAATTGAATG
* * * * * * * *
175 TTTGCCTCGAGACACATA-TAGAAAGAGCCATTCATTTGG-AGG
129 TCTACCTTGAGAAACA-AGAAGAAAAAGGCATTCA-TTGGCAAG
* * * * * * * **
217 AAAAGTCCATTTATAGCCTCTCATTTCGTCAAAAAG-CTTATTACTTGTTTTAAATTATTTTATA
1 -AAAGTCCATTTATAGTCACCCATTCCTTC-AAAAGCCTTATTACTAGCTTTAAATGGTTTTATA
* * *
281 ATCTCAAAATTGATTTTAA-AT-ATAGTTTTTTTAAAATTTTTGATGAAAA-AAGATTATAATTG
64 ATCTCAAAATTGATTTTAAGATGA-A--TTTTTT-ACATTTTTGGTTAAAACAAGATTATAATTG
* *** * *
343 AATGTCTACCTCGAGAAATGTGAAGAAGAAGGCATTCATTGACAAG
125 AATGTCTACCTTGAGAAACAAGAAGAAAAAGGCATTCATTGGCAAG
* * *
389 AAATGTTCATTTATAGTCATCCATTCCTTTAAAAGCCTTATTACTCA-CTTTAAATGGTTTTATA
1 AAA-GTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT-AGCTTTAAATGGTTTTATA
*
453 ATCTCAAAATTGATTTTAAGATGAATGTTTTTACATTTTTGGTTAAAACAAG-TTATAATTGAAC
64 ATCTCAAAATTGATTTTAAGATGAAT-TTTTTACATTTTTGGTTAAAACAAGATTATAATTGAAT
* * * * *
517 GTCTACCTTAAGAAACAAGAAGACAAAGTCATTTATTGGCAAC
128 GTCTACCTTGAGAAACAAGAAGAAAAAGGCATTCATTGGCAAG
* * * * *
560 AGAAGTCCATTTACATTCACCCATACGTTCAAAAGCCTTATTACTAGCTTTAAATGATTTTATAA
1 A-AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTAGCTTTAAATGGTTTTATAA
* * * **
625 TCTCAAAATTAATTTTAAG-TTAATTTTTTTTTACATTTTTAGTTAAAAC-AGATTATTGTTGAA
65 TCTCAAAATTGATTTTAAGATGAA---TTTTTTACATTTTTGGTTAAAACAAGATTATAATTGAA
* *
688 TGTCTATCTTGAAAAACACA-AAGAAAAAGGCATTCATTGGCATA-
127 TGTCTACCTTGAGAAACA-AGAAGAAAAAGGCATTCATTGGCA-AG
* * * * *
732 AAATGTTCTTTTATAGTCACCCATTCCTTTAAAAACCTTATTACTCGCTTTAAATGGTTTTATAA
1 AAA-GTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTAGCTTTAAATGGTTTTATAA
* * * * * * *
797 TTTCATAATTGATTTGAAGTTAAATTTTATTACATTTTTGGCTAAAAC-AGACTATAATTGAATG
65 TCTCAAAATTGATTTTAAGATGAATTTT-TTACATTTTTGGTTAAAACAAGATTATAATTGAATG
* * *
861 CCTACCTCGAGAAACATAGAA-AAAAA-GCATTCATTAGCAAG
129 TCTACCTTGAGAAACA-AGAAGAAAAAGGCATTCATTGGCAAG
* *
902 AAAATTCCATTTATAGTCACCCATTCCTTCAAAAGCCATATTACTCA-CTTTAAATGGTTTTATA
1 -AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT-AGCTTTAAATGGTTTTATA
* * * *
966 ATCTGAAAATTGATTTTAAGTTGAATTCTTTGTACATTTTTAGTTAAAACAA-ATTATAATTGAT
64 ATCTCAAAATTGATTTTAAGATGAATT-TTT-TACATTTTTGGTTAAAACAAGATTATAATTGAA
* * *
1030 TGTCTACCTTGAGAAACATGAAGAAAAAGGCATTTATTGGAAAG
127 TGTCTACCTTGAGAAACAAGAAGAAAAAGGCATTCATTGGCAAG
1074 AAAAGTCCATTTATAGT
1 -AAAGTCCATTTATAGT
1091 NNNNNNNNNN
Statistics
Matches: 707, Mismatches: 130, Indels: 69
0.78 0.14 0.08
Matches are distributed among these distances:
169 30 0.04
170 105 0.15
171 244 0.35
172 316 0.45
173 11 0.02
174 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (170 bp):
AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTAGCTTTAAATGGTTTTATAAT
CTCAAAATTGATTTTAAGATGAATTTTTTACATTTTTGGTTAAAACAAGATTATAATTGAATGTC
TACCTTGAGAAACAAGAAGAAAAAGGCATTCATTGGCAAG
Found at i:738 original size:343 final size:341
Alignment explanation
Indices: 248--1090 Score: 1034
Period size: 343 Copynumber: 2.5 Consensus size: 341
238 CATTTCGTCA
* * * * *
248 AAAAG-CTTATTACTTGTTTTAAATTATTTTATAATCTCAAAATTGATTTTAAATATAGTTTTTT
1 AAAAGCCTTATTACTAGCTTTAAATGATTTTATAATCTCAAAATTGATTTTAAGT-TAATTTTTT
* * * * * ** *
312 TAAAATTTTT-GATGAAAAAAGATTATAATTGAATGTCTACCTCGAGAAATGTGAAGAAGAAGGC
65 TTACATTTTTAG-TTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGC
* * *
376 ATTCATTGACAAGAAATGTTCATTTATAGTCATCCATTCCTTTAAAAGCCTTATTACTCACTTTA
129 ATTCATTGGCAAGAAATGTTCATTTATAGTCACCCATTCCTTTAAAAACCTTATTACTCACTTTA
* * *
441 AATGGTTTTATAATCTCAAAATTGATTTTAAGATGAATGTTT-TTACATTTTTGGTTAAAACA-A
194 AATGGTTTTATAATCTCAAAATTGATTTGAAGATAAAT-TTTATTACATTTTTGGCTAAAACAGA
* * * * * * *
504 GTTATAATTGAACGTCTACCTTAAGAAACA-AGAAGACAAAGTCATTTATTGGCAACAGAAGTCC
258 -CTATAATTGAACGCCTACCTCAAGAAACATAGAA-AAAAAG-CATTCATTAGCAACAAAAGTCC
* *
568 ATTTACATTCACCCATACGTTC
320 ATTTACAGTCACCCATACCTTC
*
590 AAAAGCCTTATTACTAGCTTTAAATGATTTTATAATCTCAAAATTAATTTTAAGTTAATTTTTTT
1 AAAAGCCTTATTACTAGCTTTAAATGATTTTATAATCTCAAAATTGATTTTAAGTTAA-TTTTTT
** * * **
655 TTACATTTTTAGTTAAAACAGATTATTGTTGAATGTCTATCTTGAAAAACACAAAGAAAAAGGCA
65 TTACATTTTTAGTTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGCA
* *
720 TTCATTGGCATA-AAATGTTCTTTTATAGTCACCCATTCCTTTAAAAACCTTATTACTCGCTTTA
130 TTCATTGGCA-AGAAATGTTCATTTATAGTCACCCATTCCTTTAAAAACCTTATTACTCACTTTA
* * *
784 AATGGTTTTATAATTTCATAATTGATTTGAAGTTAAATTTTATTACATTTTTGGCTAAAACAGAC
194 AATGGTTTTATAATCTCAAAATTGATTTGAAGATAAATTTTATTACATTTTTGGCTAAAACAGAC
* * * *
849 TATAATTGAATGCCTACCTCGAGAAACATAGAAAAAAAGCATTCATTAGCAAGAAAATTCCATTT
259 TATAATTGAACGCCTACCTCAAGAAACATAGAAAAAAAGCATTCATTAGCAACAAAAGTCCATTT
* *
914 ATAGTCACCCATTCCTTC
324 ACAGTCACCCATACCTTC
* * * *
932 AAAAGCCATATTACTCA-CTTTAAATGGTTTTATAATCTGAAAATTGATTTTAAGTTGAATTCTT
1 AAAAGCCTTATTACT-AGCTTTAAATGATTTTATAATCTCAAAATTGATTTTAAGTT-AATTTTT
* * *
996 TGTACATTTTTAGTTAAAACAAATTATAATTGATTGTCTACCTTGAGAAACATGAAGAAAAAGGC
64 TTTACATTTTTAGTTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGC
* * * *
1061 ATTTATTGGAAAGAAAAGTCCATTTATAGT
129 ATTCATTGGCAAGAAATGTTCATTTATAGT
1091 NNNNNNNNNN
Statistics
Matches: 426, Mismatches: 65, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
341 1 0.00
342 178 0.42
343 240 0.56
344 7 0.02
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (341 bp):
AAAAGCCTTATTACTAGCTTTAAATGATTTTATAATCTCAAAATTGATTTTAAGTTAATTTTTTT
TACATTTTTAGTTAAAACAGATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGCAT
TCATTGGCAAGAAATGTTCATTTATAGTCACCCATTCCTTTAAAAACCTTATTACTCACTTTAAA
TGGTTTTATAATCTCAAAATTGATTTGAAGATAAATTTTATTACATTTTTGGCTAAAACAGACTA
TAATTGAACGCCTACCTCAAGAAACATAGAAAAAAAGCATTCATTAGCAACAAAAGTCCATTTAC
AGTCACCCATACCTTC
Found at i:1843 original size:171 final size:168
Alignment explanation
Indices: 1558--2312 Score: 667
Period size: 171 Copynumber: 4.4 Consensus size: 168
1548 NNNNNNNNNN
* * * * * *
1558 ATAATTGATTTTAAGTTAAATTTTTTTACATTTTTAGTTAAAATAGATTATAATAGAATATCTAC
1 ATAATTGA-TTTAAGTTGAA-TTTTTTATATTTTTAGTTCAAA-AGACTATAATTGAATGTCTAC
*** * * * * **
1623 CTCAAGAATCGTGAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCT
63 CTTGGGAAACGTGAAGAAAAAGGTATTCATTGGCAACAAAAGTCCATTTATAGTCACTCAAGCCT
*
1688 TCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAACCTC
128 TCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAACCTC
* * ** * *
1729 ATAATTGATTATAAATTGAATTTTTTGATGTTTTTACCTCGAAAAGAATATAATTGAATGTTTAC
1 ATAATTGATT-TAAGTTGAATTTTTT-ATATTTTTAGTTC-AAAAGACTATAATTGAATGTCTAC
* **
1794 CTTGGGAAACATGAAGAAAAAGGTATTCATTGGCAACAAAAGTCCATTTATAGTTGCTCAAGCCT
63 CTTGGGAAACGTGAAGAAAAAGGTATTCATTGGCAACAAAAGTCCATTTATAGTCACTCAAGCCT
** * * *
1859 TCAAAAGCCTTATTACTCTTTTTAAATGGCTTTATAATCTT
128 TCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAACCTC
* * * * * *
1900 AAAATTGATTTTAAGTTGAAATTTTTTATATTTTTGGTTAAAAAAGGCTATAATGGAATG-CGTG
1 ATAATTGA-TTTAAGTTG-AATTTTTTATATTTTTAGTT-CAAAAGACTATAATTGAATGTC-TA
* * * * * *
1964 CACTAGGG-AACGTGAAGCAAAAGCTA-GCAATTGGC-ACAAAAAGTCCATTTATAGTTACTGAA
62 C-CTTGGGAAACGTGAAGAAAAAGGTATTC-ATTGGCAAC-AAAAGTCCATTTATAGTCACTCAA
* * *
2026 GCCTTCAAAAGCCTTATTACTTGCTTTAAATGGTTTTATAAACTA
124 GCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAACCTC
* * *
2071 ATAATTGATTTGAAGTTGAATTTTTTTTACATTTTAGGTTCAAACAGACTAGAATTGAATGTCTA
1 ATAATTGATTT-AAGTTGAATTTTTTATA-TTTTTA-GTTCAAA-AGACTATAATTGAATGTCTA
* * * * *
2136 TCTTGAGAAACGTGAAGAGAAAA-GCATTCATTGGCAAAAAGAAAATCCATTTATAGTCACTCAT
62 CCTTGGGAAACGTGAAGA-AAAAGGTATTCATTGGC-AACA-AAAGTCCATTTATAGTCACTCA-
* ** * *
2200 A-CCTTCTAAAAGCCTTATTACTTGCTCGAAATAGTTTTATAACATC
123 AGCCTTC-AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAACCTC
* * * * * *
2246 ATAATTAATTTTCAGTTGAATTGTTTTACATTTTTAGCTAAAATAGACTATAATTGAAAGTCTAC
1 ATAATTGA-TTTAAGTTGAATT-TTTTATATTTTTAGTTCAAA-AGACTATAATTGAATGTCTAC
2311 CT
63 CT
2313 NNNNNNNNNN
Statistics
Matches: 469, Mismatches: 90, Indels: 47
0.77 0.15 0.08
Matches are distributed among these distances:
170 24 0.05
171 274 0.58
172 51 0.11
173 7 0.01
174 50 0.11
175 55 0.12
176 8 0.02
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (168 bp):
ATAATTGATTTAAGTTGAATTTTTTATATTTTTAGTTCAAAAGACTATAATTGAATGTCTACCTT
GGGAAACGTGAAGAAAAAGGTATTCATTGGCAACAAAAGTCCATTTATAGTCACTCAAGCCTTCA
AAAGCCTTATTACTCGCTTTAAATGGTTTTATAACCTC
Found at i:4274 original size:171 final size:171
Alignment explanation
Indices: 3981--4580 Score: 659
Period size: 172 Copynumber: 3.5 Consensus size: 171
3971 NNNNNNNNNN
* * * *
3981 ATGCCTTTTTCTTTATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAAATCAAAAATGT
1 ATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACT-AAAAAAGT
* *
4046 AAAAAAATTCAATCGTAAAATCAATTATAGCATTACAAAACCATTTAAAGTGAGTAATAAGGCTT
65 AAAAAAATTCAA-CTTAAAATCAATTATGGCATTACAAAACCATTTAAAGTGAGTAATAAGGCTT
* *
4111 TTGAAAGAATGGGTGACTATATATGGACTTTTCTTGGCAATGA
129 TTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGA
* ** * *
4154 ATTCCTTTTTCTTCATGTTTCTTGAGGTAGACATTCTATTATAATCTGCTTTAACTAAAAAAGTA
1 ATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTA
* * *
4219 AAAAAATTCAACTTAAAATCAATTATGGCATTATAAAACCATTTAAAGCGAGTAATGAGGCTTTT
66 AAAAAATTCAACTTAAAATCAATTATGGCATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTT
* * ** * * *
4284 GAAGGTATGGGTGACTATAAATAAACTCTGCTTACCAATGA
131 GAAAGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGA
* * * * * ** *
4325 ATGCTTTTTTCCTCATGTTTCTCAAGGTAGGCATTCAATTCTAGTCTGTTTTAACCGAAAATG-A
1 ATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTA
* * * * * * *
4389 ATGAAGAATTCAAATTTAAATCAATTTTGAG-ATTACAAAATCGTTTAAAGTGAGTAATAAAGCT
66 A--AAAAATTCAACTTAAAATCAATTATG-GCATTACAAAACCATTTAAAGTGAGTAATAAGGCT
* *
4453 TTTAAAAGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGA
128 TTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGA
* ** * ** *
4497 ATGCCTTTTTCTTTACT-TTTCTTGAGCTAGACATTTGATTATAATATGTTTTAA-TAAAAAATG
1 ATGCCTTTTTCTTCA-TGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAA-G
* *
4560 TAAAACAATTTGAACTTAAAA
64 TAAAA-AAATTCAACTTAAAA
4581 ACCATTTGAA
Statistics
Matches: 345, Mismatches: 75, Indels: 15
0.79 0.17 0.03
Matches are distributed among these distances:
170 2 0.01
171 137 0.40
172 154 0.45
173 52 0.15
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.37
Consensus pattern (171 bp):
ATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAAAGTA
AAAAAATTCAACTTAAAATCAATTATGGCATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTT
GAAAGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGA
Found at i:4717 original size:153 final size:151
Alignment explanation
Indices: 4450--4731 Score: 352
Period size: 153 Copynumber: 1.9 Consensus size: 151
4440 GAGTAATAAA
* * *
4450 GCTTTTAAAAGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTTACTT
1 GCTTTTAAAAGAATGGGCGACTATAAATAGACTTTTCTTGTCAATGAATGCCTTTTTCTTTAATT
** ** * * * *
4515 TTCTTGAGCTAGACATTTGATTATAATATGTTTTAATAAAAAATGTAAAACAATTTGAACTTAAA
66 TTCTAAAGCTAGACATTCAATGATAATATATTTTAACAAAAAATCTAAAA-AATTT-AACTTAAA
4580 AACCATTTGAAGTGAGCAGTGAG
129 AACCATTTGAAGTGAGCAGTGAG
* *
4603 GCTTTTGAAGGAATGGGCGACTATAAATAGACTTTTCTTGTCAATGAATGCCTTTTTC-TTAATG
1 GCTTTTAAAAGAATGGGCGACTATAAATAGACTTTTCTTGTCAATGAATGCCTTTTTCTTTAAT-
* * * * *
4667 TTTCTCAAAG-TATACATTCAATGATAGTCTATTTTAGCCAAAAATCTAAAAAATTTAACTTAAA
65 TTTCT-AAAGCTAGACATTCAATGATAATATATTTTAACAAAAAATCTAAAAAATTTAACTTAAA
4731 A
129 A
4732 TCAATTATGG
Statistics
Matches: 109, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
151 9 0.08
152 9 0.08
153 89 0.82
154 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (151 bp):
GCTTTTAAAAGAATGGGCGACTATAAATAGACTTTTCTTGTCAATGAATGCCTTTTTCTTTAATT
TTCTAAAGCTAGACATTCAATGATAATATATTTTAACAAAAAATCTAAAAAATTTAACTTAAAAA
CCATTTGAAGTGAGCAGTGAG
Found at i:5055 original size:496 final size:494
Alignment explanation
Indices: 4082--5075 Score: 1093
Period size: 496 Copynumber: 2.0 Consensus size: 494
4072 ATAGCATTAC
* * * *
4082 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATATATGGACTTTTCTTG
1 AAAACCATTTAAAGTGAGCAATAAGGCTTTTGAAAGAATGGGCGACTATAAATAGACTTTTCTTG
* * ** * * * * *
4147 GCAATGAATTCCTTTTTCTTCATGTTTCTTGAGGTAGACATTCTATTATAATCTGCTTTAACTAA
66 GCAATGAATGCCTTTTTCTTAATGTTTCTCAAAGTAGACATTCAATGATAATCTACTTTAACCAA
* *
4212 AAAAGTAAAAAAATTCAACTTAAAATCAATTATGGCATTATAAAACCATTTAAAGCGAGTAATGA
131 AAAACTAAAAAAATTCAACTTAAAATCAATTATGGCATTATAAAACCATTTAAAGCGAGTAATAA
* * * * **
4277 GGCTTTTGAAGGTATGGGTGACTATAAATAAACTCTGCTTACCAATGAATGCTTTTTTCCTCATG
196 AGCTTTTGAAGGTATGAGTGACTATAAATAAACTCTGCTTACCAATGAATGATTTTCTCCTCACA
* * * *
4342 TTTCTCAAGGTAGGCATTCAATTCTAGTCTGTTTTAACCGAAAATGAATGAAGAATTCAAATTTA
261 TTTCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATG-ATGAAAAATTCAAATTAA
* * ** **
4407 AATCAATTTTGAGATTACAAAATCGTTTAAAGTGAGTAATAAAGCTTTTAAAAGAATGGGTGACT
325 AATCAATTTTGAGATTACAAAACCATTTAAAGCAAGTAATAAAGCTTTTAAAAGAATCAGTGACT
* * * ** * * **
4472 ATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTTACTTTTCTTGAGCTAGACATTTGATT
390 ATAAATGAACTTTTCTTGCCAATGAATGCCTTTTGCTTTACTTCCCTAGAGCAAGACATTCAATT
* * *
4537 ATAATATGTTTTAATAAAAAATGTAAAACAATTTGAACTTA
455 ATAACATGTTTTAACAAAAAATGTAAAA-AATTTCAACTTA
* * * *
4578 AAAACCATTTGAAGTGAGCAGTGAGGCTTTTGAAGGAATGGGCGACTATAAATAGACTTTTCTTG
1 AAAACCATTTAAAGTGAGCAATAAGGCTTTTGAAAGAATGGGCGACTATAAATAGACTTTTCTTG
* * * * *
4643 TCAATGAATGCCTTTTTCTTAATGTTTCTCAAAGTATACATTCAATGATAGTCTATTTTAGCCAA
66 GCAATGAATGCCTTTTTCTTAATGTTTCTCAAAGTAGACATTCAATGATAATCTACTTTAACCAA
* * * * **
4708 AAATCT-AAAAAATTTAACTTAAAATCAATTATGGCGTTATAAAACTATTTCGAGC-ACGTAATA
131 AAAACTAAAAAAATTCAACTTAAAATCAATTATGGCATTATAAAACCATTTAAAGCGA-GTAATA
* ** * ** * *
4771 AAGCTTTTTGAAGGTATGAGTGGCTATAAATGGACTTTTTTTCCCAATGAAT-ATTTTACTCTTC
195 AAGC-TTTTGAAGGTATGAGTGACTATAAATAAACTCTGCTTACCAATGAATGATTTT-CTCCTC
* * *
4835 ACATTTTTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACTAAAAATG-TGAAAACAGTTCAAC
258 ACATTTCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGATGAAAA-A-TTCAAA
* * * * * **
4899 TTAAAATCAATTATT-AGTTTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGCTTCAG
321 TTAAAATCAATT-TTGAGATTACAAAACCATTTAAAGCAAGTAATAAAGCTTTTAAAAGAATCAG
** * *
4963 TGACTATAAATGAACTTTT-TGTGCCAATGGCTGGCTTTTGCTTTACATTCCCTAGGGCAAG-CA
385 TGACTATAAATGAACTTTTCT-TGCCAATGAATGCCTTTTGCTTTAC-TTCCCTAGAGCAAGACA
* * * *
5026 TTCAATTATAGCCTTTTTTAACCAAAAATGTAAAAAATTTCAACTTA
448 TTCAATTATAACATGTTTTAACAAAAAATGTAAAAAATTTCAACTTA
5073 AAA
1 AAA
5076 TNNNNNNNNN
Statistics
Matches: 406, Mismatches: 84, Indels: 17
0.80 0.17 0.03
Matches are distributed among these distances:
494 6 0.01
495 72 0.18
496 317 0.78
497 11 0.03
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (494 bp):
AAAACCATTTAAAGTGAGCAATAAGGCTTTTGAAAGAATGGGCGACTATAAATAGACTTTTCTTG
GCAATGAATGCCTTTTTCTTAATGTTTCTCAAAGTAGACATTCAATGATAATCTACTTTAACCAA
AAAACTAAAAAAATTCAACTTAAAATCAATTATGGCATTATAAAACCATTTAAAGCGAGTAATAA
AGCTTTTGAAGGTATGAGTGACTATAAATAAACTCTGCTTACCAATGAATGATTTTCTCCTCACA
TTTCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGATGAAAAATTCAAATTAAA
ATCAATTTTGAGATTACAAAACCATTTAAAGCAAGTAATAAAGCTTTTAAAAGAATCAGTGACTA
TAAATGAACTTTTCTTGCCAATGAATGCCTTTTGCTTTACTTCCCTAGAGCAAGACATTCAATTA
TAACATGTTTTAACAAAAAATGTAAAAAATTTCAACTTA
Found at i:9903 original size:172 final size:171
Alignment explanation
Indices: 8980--10186 Score: 893
Period size: 171 Copynumber: 7.0 Consensus size: 171
8970 TTTCGAGCAC
* * * * * * * * *
8980 GTAATAAAGCTTTTTGAAGGTATGAGTGGCTATAAATGGA-TTTTTTTCCCAATGAATGCTTTTC
1 GTAATAAGGC-TTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTT
* * * * * * * * *
9044 TCTTCACGTTTGTCAAGGTAGACATTCAATTCTAGTTTGTTATAGCCTAAAATG-TAAAAATAAT
65 TCTTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGAT-AAAA-AAT
* * * * * **
9108 TCAACTTAAAATCAATTATTAGTTTATAAAACCATTTAAAGCAA
128 TCAAATTTAAATCAATTATGAGATTACAAAACCATTTAAAGTGA
* * *** * * **
9152 GTAATAAGGCTTTTGAA-GACTTCAATGACTATAAATGGACTTTT-TGTGCTAATGGCTGGC-TT
1 GTAATAAGGCTTTTAAAGGA-ATGGGTGACTATAAATGAACTTTTCT-TGCCAATGAAT-GCTTT
*** * * * * * ** *
9214 TCGGTTCACT-TTCCCTAGGGCAGGCATTCAATTATAGCCTTTTTTAACCAAAAATG-TAAAAAA
63 TTTCTTCA-TGTTTCTTAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGATAAAAAA
* * * * **
9277 TTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAAAGA
127 -TTCAAATTTAAATCAATTATGAGATTACAAAACCATTTAAAGTGA
* * * ** ** ** * * * *
9323 GTAATAAAGCTCTTGAAGGCTTAAGCAACTATAAATGGACTTTTTTTGCCAATGAATACCTTTTT
1 GTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTT
* * * * * *
9388 CTTCATGTTT-TCTAACGCAAACATTTAATTATAATCTGTTCTAACCAAAAA-CATCAAAAAATT
66 CTTCATGTTTCT-TAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGAT-AAAAAATT
* * *
9451 C-AATCTAAATTCAATTATGAGGTTATAAAACCATTTAAAGTGA
129 CAAATTTAAA-TCAATTATGAGATTACAAAACCATTTAAAGTGA
*
9494 GTAATAAGGCTTTTGAAA-GAATGGGT-AGCTATAAATGAACTTTTCTTGCCAATGAATTCTTTT
1 GTAATAAGGCTTTT-AAAGGAATGGGTGA-CTATAAATGAACTTTTCTTGCCAATGAATGCTTTT
* * * * *
9557 TTCTTCACGTTTCTTGAGGTAGACATTCTATTATAATCTTTTTTAACTAAAAATG-TAAAAAAAT
64 TTCTTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGAT-AAAAAAT
* * * *
9621 TCAACTTAAAATCAATTATG-GCATTATAAAACCATTTAAAATGA
128 TCAAATTTAAATCAATTATGAG-ATTACAAAACCATTTAAAGTGA
* * * * * * *
9665 GTAATGACGCTTTTAAAGGTATGGGGGACTATAAATTAACTTTGCTTGCCAAAGAATGCTTTTTT
1 GTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTT
* * * * * *
9730 CTTCATGTTTCTTAAGGTAGGCATTCAATTCTAGTATGTTTTAACCAAAAATGACTGAAGAATTC
66 CTTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGA-TAAAAAATTC
* * * *
9795 AAATTTAAATTAATTTTGAGATTACAAAATCGTTTAAAGTGA
130 AAATTTAAATCAATTATGAGATTACAAAACCATTTAAAGTGA
* * *
9837 GTAATAAGGCTTTTAAAGGAATGGATGACTATAAATGAACTTTTCTTGTCAATGAATGCCTTTTT
1 GTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTT
* * * * * *
9902 CTTTATATTTCTTAAAGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATAGA-AAAACATT-
66 CTTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAAT-GATAAAAAATTC
** * * * *
9965 TGATCCTAAAATCAATTATG-GCATTAC-AAACCTTTTGAAGTAA
130 AAAT--TTAAATCAATTATGAG-ATTACAAAACCATTTAAAGTGA
* * * * * *
10008 GTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTACAAATTAATGCTTTTTT
1 GTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTT
* * * * * * ****
10073 CTTCATTTTTCTCAAGGTACACATTCAATTCTAATATGTTTTAACCAAAAATAACTGTTGAATTC
66 CTTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGA-TAAAAAATTC
* * *
10138 AAATTTAAATCAATTTTGAGACTACAAAACTATTTAAAGTGA
130 AAATTTAAATCAATTATGAGATTACAAAACCATTTAAAGTGA
10180 GTAATAA
1 GTAATAA
10187 NNNNNNNNNN
Statistics
Matches: 817, Mismatches: 184, Indels: 68
0.76 0.17 0.06
Matches are distributed among these distances:
170 18 0.02
171 535 0.65
172 256 0.31
173 8 0.01
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (171 bp):
GTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTT
CTTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGATAAAAAATTCA
AATTTAAATCAATTATGAGATTACAAAACCATTTAAAGTGA
Found at i:10029 original size:343 final size:342
Alignment explanation
Indices: 9238--10186 Score: 1002
Period size: 343 Copynumber: 2.8 Consensus size: 342
9228 CTAGGGCAGG
** * * * * *
9238 CATTCAATTATAGCCTTTTTTAACCAAAAATGTAAAAAATTTCAACTTAAAATCAATTTTGAG-A
1 CATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAACCTAAAATCAATTATG-GCA
* * * ** ** *
9302 TTATAAAACCATTTAAAA-AGAGTAATAAAGCTCTTGAAGGCT-TAAGCAACTATAAATGGACTT
65 TTATAAAACCATTTAAAATA-AGTAATAACGCTTTTAAAGG-TATGGGGGACTATAAATGAACTT
** * * * * * * * * * * *
9365 TTTTTGCCAATGAATACCTTTTTCTTCATGTTT-TCTAACGCAAACATTTAATTATAATCTGTTC
128 TGCTTACAAATGAATGCTTTTTTCTTCATGTTTCTC-AAGGTACACATTCAATTCTAATATGTTT
* * * * * * * *
9429 TAACCAAAAACATC-AAAAAATTC-AATCTAAATTCAATTATGAGGTTATAAAACCATTTAAAGT
192 TAACCAAAAATAACTGAAGAATTCAAATTTAAATT-AATTTTGAGATTACAAAA-CATTTAAAGT
* * *
9492 GAGTAATAAGGCTTTTGAAAGAATGGGTAGCTATAAATGAACTTTTCTTGCCAATGAATTCTTTT
255 GAGTAATAAGGCTTTTGAAAGAATGGATAGCTATAAATGAACTTTTCTTGCCAATGAATGCCTTT
* * *
9557 TTCTTCACGTTTCTTGAGGTAGA
320 TTCTTCACATTTCTTAAAGTAGA
* * * *
9580 CATTCTATTATAATCTTTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGGCAT
1 CATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAACCTAAAATCAATTATGGCAT
* * *
9645 TATAAAACCATTTAAAATGAGTAATGACGCTTTTAAAGGTATGGGGGACTATAAATTAACTTTGC
66 TATAAAACCATTTAAAATAAGTAATAACGCTTTTAAAGGTATGGGGGACTATAAATGAACTTTGC
* * ** *
9710 TTGCCAAA-GAATGCTTTTTTCTTCATGTTTCTTAAGGTAGGCATTCAATTCTAGTATGTTTTAA
131 TT-ACAAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTACACATTCAATTCTAATATGTTTTAA
* *
9774 CCAAAAATGACTGAAGAATTCAAATTTAAATTAATTTTGAGATTACAAAATCGTTTAAAGTGAGT
195 CCAAAAATAACTGAAGAATTCAAATTTAAATTAATTTTGAGATTACAAAA-CATTTAAAGTGAGT
*
9839 AATAAGGCTTTT-AAAGGAATGGAT-GACTATAAATGAACTTTTCTTGTCAATGAATGCCTTTTT
259 AATAAGGCTTTTGAAA-GAATGGATAG-CTATAAATGAACTTTTCTTGCCAATGAATGCCTTTTT
* *
9902 CTTTATATTTCTTAAAGTAGA
322 CTTCACATTTCTTAAAGTAGA
* * * *
9923 CATTCAATTATAGTCTGTTTTAACAAAAAATAG-AAAAACATTTGATCCTAAAATCAATTATGGC
1 CATTCAATTATAATCTGTTTTAACAAAAAAT-GTAAAAA-AATTCAACCTAAAATCAATTATGGC
* * * * * * * *
9987 ATTA-CAAACCTTTTGAAGTAAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTT
64 ATTATAAAACCATTTAAAATAAGTAATAACGCTTTTAAAGGTATGGGGGACTATAAATGAACTTT
* * *
10051 TCTTACAAATTAATGCTTTTTTCTTCATTTTTCTCAAGGTACACATTCAATTCTAATATGTTTTA
129 GCTTACAAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTACACATTCAATTCTAATATGTTTTA
** * *
10116 ACCAAAAATAACTGTTGAATTCAAATTTAAATCAATTTTGAGACTACAAAACTATTTAAAGTGAG
194 ACCAAAAATAACTGAAGAATTCAAATTTAAATTAATTTTGAGATTACAAAAC-ATTTAAAGTGAG
10181 TAATAA
258 TAATAA
10187 NNNNNNNNNN
Statistics
Matches: 508, Mismatches: 86, Indels: 25
0.82 0.14 0.04
Matches are distributed among these distances:
341 2 0.00
342 167 0.33
343 304 0.60
344 35 0.07
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (342 bp):
CATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTCAACCTAAAATCAATTATGGCAT
TATAAAACCATTTAAAATAAGTAATAACGCTTTTAAAGGTATGGGGGACTATAAATGAACTTTGC
TTACAAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTACACATTCAATTCTAATATGTTTTAAC
CAAAAATAACTGAAGAATTCAAATTTAAATTAATTTTGAGATTACAAAACATTTAAAGTGAGTAA
TAAGGCTTTTGAAAGAATGGATAGCTATAAATGAACTTTTCTTGCCAATGAATGCCTTTTTCTTC
ACATTTCTTAAAGTAGA
Found at i:11415 original size:344 final size:342
Alignment explanation
Indices: 10720--12180 Score: 1346
Period size: 344 Copynumber: 4.3 Consensus size: 342
10710 NNNNNNNNCA
* * * * * * ** *
10720 AATTGTTTTACATTTTTTGTTAAAACATATTATAACT-GAATGTCTAGCTCAATAAA-AGTGAAG
1 AATTTTTTTACATTTTTGGTTAAAACAGACTATAA-TAGAATGTGTACCTTGAGAAACA-TGAAG
* * *
10783 AAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAATCACCTATTCCTTTAAAAGCCTTATTAC
64 AAAAAGGCATTCATTGACAAGAAAAGTTCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTAC
* *
10848 TTACTTTAAATGGTTTTGTAATCTCAAAATTGATTTAAATTTGAATTCTTT-AGTCATTTTTTGT
129 TCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTCA-TCATTTTTTGT
** * * * * *
10912 TAAAATGGACTAGATTTGAATGCCTACCCTGAGAAAAATGAAGAAAATAACATTAATTTGCAAGA
193 TAAAACAGACTAGAATTGAATGCCTA-CCTGAGAAACATGAAGAAAAAAACATTCATTGGCAAGA
* * * * *
10977 AAAGTCTATTTATAGTCACCAATACCTTCAAAAGCCTTATTAC-CTGCTTGAAAAGGTTTTGTAA
257 AAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTC-GCTTTAAATGGTTTTATAA
* * *
11041 TGCCATAATTGATTTTACGATC
321 TGCCATAATTGATTTTAAGTTG
* * *
11063 ATATTTTTTTATATTTTTTGTTAAAACAGACTATAATAGAATGTGTACTTTGAGAAACATGAAGA
1 A-ATTTTTTTACATTTTTGGTTAAAACAGACTATAATAGAATGTGTACCTTGAGAAACATGAAGA
* * *
11128 AAAAGGCATTTATTGACAAGAAAAGTTCATTTATAGTCACCCGTTCCTTTAAAATCCTTATTACT
65 AAAAGGCATTCATTGACAAGAAAAGTTCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACT
* * *
11193 CACTTTAAACGGTTTTGTTATCTCAAAATTGATTTAAATTTGAATT-TTTCAGTCA-TTTTTGAT
130 CACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTCA-TCATTTTTTG-T
11256 TAAAACAGACTAGAATTGAATGCCTACCATGAGAAACATGAAGAAAAAAAGCATTC-TTAGGCAA
193 TAAAACAGACTAGAATTGAATGCCTACC-TGAGAAACATGAAGAAAAAAA-CATTCATT-GGCAA
* * * *
11320 GCAAAGTCTATTCATAGTCACCCATACCTTCAAAAGCCTCATTACTCGCTTTAAATGGTTTTATA
255 GAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATA
11385 ATGCCATAATTGATTTTAAGTTG
320 ATGCCATAATTGATTTTAAGTTG
* * **
11408 AATTTTTTTTACATTTTTAGTTAAAACAGATTATAATAGAATGTCG-ACCTCAAGAAACATGAAG
1 AA-TTTTTTTACATTTTTGGTTAAAACAGACTATAATAGAATGT-GTACCTTGAGAAACATGAAG
* ** *
11472 AGAAAGAAATTCATTGGCAAGAAAAGTTCATTTATAGTCACCCATT-CTTTCAAAAGCCTTATTA
64 AAAAAGGCATTCATTGACAAGAAAAGTTCATTTATAGTCACCCATTCCTTT-AAAAGCCTTATTA
* * * * * * *
11536 CTCACTTTATATGGTTTTATAACCTCATAATTGATTTTAGA-TTGAATTGTTTGAT--GTTTTTG
128 CTCACTTTAAATGGTTTTATAATCTCAAAATTGA-TTTAAATTTGAATTCTTTCATCATTTTTTG
* * * * ** * * **
11598 CCTAGAACAGATTATAATTGAATGTTTGCCTTAGGAAACATGAA-AAAAAAGGTATTCATTGGCA
192 -TTAAAACAGACTAGAATTGAATGCCTACCTGA-GAAACATGAAGAAAAAA-ACATTCATTGGCA
** * ** * *
11662 AGAAAAGTCCATTTATAGTTGCTCA-AGCCTTCAAAAGCCTTATTACTCTTTTTAAGTGGCTTTA
254 AGAAAAGTCCATTTATAGTCACCCATA-CCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTA
* *
11726 T-ATTCTCAAAATTGATTTTAAGTTG
318 TAATGC-CATAATTGATTTTAAGTTG
* * * * * ** * * **
11751 AAATTTTTCACATTTTTGGTTAAAAAAGGCTATAATTGAATGCCTGCCCT-AGGGA-ATGTAA-A
1 AATTTTTTTACATTTTTGGTTAAAACAGACTATAATAGAATGTGTACCTTGAGAAACATG-AAGA
* ** * ** ** ** *
11813 CCAAAAGCCAGCCATTGGCACTAAAAGTTCATTTATAGTCACTGAAGCCTTCAAAAGCCTTATTA
65 --AAAAGGCATTCATTGACAAGAAAAGTTCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTA
** * * *
11878 CTTGCTTTAAATGGTTTTATAAACT-AATAATTGATTTTAAGTTGAACTAT-TTTCA-CATTTTT
128 CTCACTTTAAATGGTTTTATAATCTCAA-AATTGATTTAAATTTGAA-T-TCTTTCATCATTTTT
* * ** ** *
11940 TGTTAAAATAGACTAGAATTGAATGTCTACCTTGAGAAATGTGAAGAGTAAAACATTCATTGGGA
190 TGTTAAAACAGACTAGAATTGAATGCCTACC-TGAGAAACATGAAGAAAAAAACATTCATTGGCA
* * * * * * ** *
12005 AGAAAAGACCATTTATAGCCACTCATACATTCAAAAAGCTTTATTGCGT-GCTCAAAATAGTTTT
254 AGAAAAGTCCATTTATAGTCACCCATACCTTC-AAAAGCCTTATTAC-TCGCTTTAAATGGTTTT
* *
12069 ATAACGCCATAATTGATTTTAAGTTA
317 ATAATGCCATAATTGATTTTAAGTTG
* * * * * * * *
12095 AATTTTTTTACATTTTTGGCTAAAATAGACTATCATTGAATGTATACTTTGAGAAACGTTAAGAA
1 AATTTTTTTACATTTTTGGTTAAAACAGACTATAATAGAATGTGTACCTTGAGAAACATGAAGAA
12160 AAAGGCATTCATTGACAAGAA
66 AAAGGCATTCATTGACAAGAA
12181 NNNNNNNNNN
Statistics
Matches: 908, Mismatches: 170, Indels: 79
0.78 0.15 0.07
Matches are distributed among these distances:
340 4 0.00
341 10 0.01
342 118 0.13
343 174 0.19
344 354 0.39
345 235 0.26
346 13 0.01
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (342 bp):
AATTTTTTTACATTTTTGGTTAAAACAGACTATAATAGAATGTGTACCTTGAGAAACATGAAGAA
AAAGGCATTCATTGACAAGAAAAGTTCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACTC
ACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTCATCATTTTTTGTTAA
AACAGACTAGAATTGAATGCCTACCTGAGAAACATGAAGAAAAAAACATTCATTGGCAAGAAAAG
TCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATGCCA
TAATTGATTTTAAGTTG
Found at i:11697 original size:171 final size:169
Alignment explanation
Indices: 10778--12180 Score: 923
Period size: 172 Copynumber: 8.2 Consensus size: 169
10768 TCAATAAAAG
* * * * * ** *
10778 TGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAATCACCTATTCCTTTAAAAGCCTT
1 TGAAAAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTCACCCAAGCCTTCAAAAGCCTT
* * * * *
10843 ATTACTTACTTTAAATGGTTTTGTAATCTCAAAATTGATTTAAATTTGAATTCTTT-AGTCATTT
66 ATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATT-TTTCA--CA-TT
** * * * * *
10907 TTTGTTAAAATGGACTAGATTTGAATGCCTACCCT-GAGAAAAA
127 TTTGTTAAAACAGACTATAATTGAATGCCTGCCTTAG-GAAACA
* * *
10950 TGAAGAAAATAA--CATTAATTTGCAAGAAAAG-TCTATTTATAGTCA-CCAATACCTTCAAAAG
1 TGAA-AAAA-AAGGCATTCATTGGCAAGAAAAGTTC-ATTTATAGTCACCCAA-GCCTTCAAAAG
* * * * * * * *
11011 CCTTATTAC-CTGCTTGAAAAGGTTTTGTAATGC-CATAATTGATTTTACGATCATATTTTTTTA
62 CCTTATTACTC-ACTTTAAATGGTTTTATAAT-CTCATAATTGATTTTAAGTTGA-A-TTTTTCA
* * * *
11074 TATTTTTTGTTAAAACAGACTATAATAGAATG--TGTACTTTGAGAAACA
123 CA-TTTTTGTTAAAACAGACTATAATTGAATGCCTG-CCTTAG-GAAACA
* * * *** * *
11122 TGAAGAAAAAGGCATTTATTGACAAGAAAAGTTCATTTATAGTCACCCGTTCCTTTAAAATCCTT
1 TGAAAAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTCACCCAAGCCTTCAAAAGCCTT
* * * * * *
11187 ATTACTCACTTTAAACGGTTTTGTTATCTCAAAATTGATTTAAATTTGAATTTTTCAGTCATTTT
66 ATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTCA--CATTTT
* * *
11252 TGATTAAAACAGACTAGAATTGAATGCCTACCAT-GAGAAACA
129 TG-TTAAAACAGACTATAATTGAATGCCTGCCTTAG-GAAACA
* * *
11294 TGAAGAAAAAAAGCATTC-TTAGGCAAGCAAAG-TCTATTCATAGTCACCCATA-CCTTCAAAAG
1 TGAA-AAAAAAGGCATTCATT-GGCAAGAAAAGTTC-ATTTATAGTCACCCA-AGCCTTCAAAAG
* * *
11356 CCTCATTACTCGCTTTAAATGGTTTTATAATGC-CATAATTGATTTTAAGTTGAATTTTTTTTAC
62 CCTTATTACTCACTTTAAATGGTTTTATAAT-CTCATAATTGATTTTAAGTTGAA--TTTTTCAC
* * * * *
11420 ATTTTTAGTTAAAACAGATTATAATAGAATGTC-GACCTCAAGAAACA
124 ATTTTT-GTTAAAACAGACTATAATTGAATGCCTG-CCTTAGGAAACA
* * ** ** *
11467 TGAAGAGAAAGAAATTCATTGGCAAGAAAAGTTCATTTATAGTCACCCATTCTTTCAAAAGCCTT
1 TGAAAAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTCACCCAAGCCTTCAAAAGCCTT
* * * **
11532 ATTACTCACTTTATATGGTTTTATAACCTCATAATTGATTTT-AGATTGAATTGTTTGATGTTTT
66 ATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAG-TTGAATT-TTTCACATTTT
* * * **
11596 TGCCTAGAACAGATTATAATTGAATGTTTGCCTTAGGAAACA
129 TG-TTAAAACAGACTATAATTGAATGCCTGCCTTAGGAAACA
* * ** *
11638 TGAAAAAAAAGGTATTCATTGGCAAGAAAAGTCCATTTATAGTTGCTCAAGCCTTCAAAAGCCTT
1 TGAAAAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTCACCCAAGCCTTCAAAAGCCTT
** * * * *
11703 ATTACTCTTTTTAAGTGGCTTTATATTCTCAAAATTGATTTTAAGTTGAAATTTTTCACATTTTT
66 ATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTG-AATTTTTCACATTTTT
* * * *
11768 GGTTAAAAAAGGCTATAATTGAATGCCTGCCCTAGG-GA-A
130 -GTTAAAACAGACTATAATTGAATGCCTGCCTTAGGAAACA
* * ** ** **
11807 TGTAAACCAAAAGCCAGCCATTGGCACTAAAAGTTCATTTATAGTCACTGAAGCCTTCAAAAGCC
1 TG-AAA-AAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTCACCCAAGCCTTCAAAAGCC
** * *
11872 TTATTACTTGCTTTAAATGGTTTTATAAACTAATAATTGATTTTAAGTTGAACTATTTTCACATT
64 TTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAA-T-TTTTCACA-T
* * * * **
11937 TTTTGTTAAAATAGACTAGAATTGAATGTCTACCTT-GAGAAATG
126 TTTTGTTAAAACAGACTATAATTGAATGCCTGCCTTAG-GAAACA
* * ** * * *
11981 TGAAGAGTAAAA--CATTCATTGGGAAGAAAAGACCATTTATAGCCACTCATA-CATTCAAAAAG
1 TGAA-A-AAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTCACCCA-AGCCTTC-AAAAG
* * * ** * * * *
12043 CTTTATTGCGT-GCTCAAAATAGTTTTATAA-CGCCATAATTGATTTTAAGTTAAATTTTTTTAC
62 CCTTATTAC-TCACTTTAAATGGTTTTATAATC-TCATAATTGATTTTAAGTTGAA-TTTTTCAC
* * * ** * * *
12106 ATTTTTGGCTAAAATAGACTATCATTGAATGTAT-ACTTTGAGAAACG
124 ATTTTT-GTTAAAACAGACTATAATTGAATGCCTGCCTTAG-GAAACA
* * *
12153 TTAAGAAAAAGGCATTCATTGACAAGAA
1 TGAAAAAAAAGGCATTCATTGGCAAGAA
12181 NNNNNNNNNN
Statistics
Matches: 974, Mismatches: 197, Indels: 120
0.75 0.15 0.09
Matches are distributed among these distances:
169 3 0.00
170 22 0.02
171 283 0.29
172 444 0.46
173 200 0.21
174 16 0.02
175 6 0.01
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (169 bp):
TGAAAAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTCACCCAAGCCTTCAAAAGCCTT
ATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTCACATTTTTG
TTAAAACAGACTATAATTGAATGCCTGCCTTAGGAAACA
Found at i:13404 original size:18 final size:18
Alignment explanation
Indices: 13381--13428 Score: 80
Period size: 17 Copynumber: 2.7 Consensus size: 18
13371 TATTGCTCAC
*
13381 TTCAAATGGTTTTTTAAG
1 TTCAAATTGTTTTTTAAG
13399 TTCAAATTG-TTTTTAAG
1 TTCAAATTGTTTTTTAAG
13416 TTCAAATTGTTTT
1 TTCAAATTGTTTT
13429 ACATTTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 17 0.61
18 11 0.39
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.54
Consensus pattern (18 bp):
TTCAAATTGTTTTTTAAG
Found at i:14120 original size:172 final size:171
Alignment explanation
Indices: 13833--14145 Score: 398
Period size: 172 Copynumber: 1.8 Consensus size: 171
13823 NNTCATTGGC
* * * * *
13833 AAGAAAAGTCCATTTATAGTCACCTATTCCTTTAAAAGCCCTATTAGTCACTTTAAATGGTTTTG
1 AAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCCTATTACTCACTTTAAATAGTTTTG
* *
13898 TAATCTCAAAATTGATTTAAATTTGAATTTATAAGTCATTTTTGGTTAAAACATACTAGAATTGA
66 TAATCTCAAAATTGATTTAAATTTCAATTTATAAG-CATTTTTGGTTAAAACAGACTAGAATTGA
13963 ATGCCTACCTTGAGAAAAATGAAGACAAGAGCATTAATTTTA
130 ATGCCTACCTTGAGAAAAATGAAGACAAGAGCATTAATTTTA
* **
14005 AAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTTGCTTTAAATAGTTTTG
1 AAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCCTATTACTCACTTTAAATAGTTTTG
* * * * * * *
14070 TAATGC-CATAATTGATTTTACGA-TTCAATTTTTTTA-CATTTTTTGTTAAAATAGACTATAAT
66 TAAT-CTCAAAATTGA-TTTA-AATTTCAA-TTTATAAGCATTTTTGGTTAAAACAGACTAGAAT
*
14132 TGAATGTCTACCTT
127 TGAATGCCTACCTT
14146 AAGANNNNNN
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
172 104 0.87
173 9 0.08
174 6 0.05
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (171 bp):
AAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCCCTATTACTCACTTTAAATAGTTTTG
TAATCTCAAAATTGATTTAAATTTCAATTTATAAGCATTTTTGGTTAAAACAGACTAGAATTGAA
TGCCTACCTTGAGAAAAATGAAGACAAGAGCATTAATTTTA
Found at i:17662 original size:17 final size:18
Alignment explanation
Indices: 17640--17687 Score: 80
Period size: 17 Copynumber: 2.7 Consensus size: 18
17630 NNNNAAATGT
17640 AAAACAATTTGAACTT-A
1 AAAACAATTTGAACTTCA
17657 AAAACAATTTGAACTTCA
1 AAAACAATTTGAACTTCA
*
17675 AAAACCATTTGAA
1 AAAACAATTTGAA
17688 GTGAGCAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (18 bp):
AAAACAATTTGAACTTCA
Found at i:17811 original size:171 final size:162
Alignment explanation
Indices: 17634--17951 Score: 315
Period size: 172 Copynumber: 1.9 Consensus size: 162
17624 NNNNNNNNNN
**
17634 AAATGTAAAACAATTTGAACTTAAAAACAATT-TGA-ACTTCA-AAAACCATTT-GAAGTGAGCA
1 AAATGTAAAACAATTT-AACTTAAAAACAATTATGACA-TT-ATAAAACCATTTCG-AGCAAGCA
** * * *
17695 ATAAGGC-TTTTGAAGGAATGTGCGACTATAAATGGACTTTTCTTTCCAATGAATACCTTTT-TC
62 ATAAGGCTTTTTGAAGGAATGAACGACTATAAATGGACTTTTCTTCCCAAGGAAT-CCTTTTCCC
17758 TTGACGTTTCTCAAGGTAGACNNNNNNNNNNAGTCTATTTTAGCCAA
126 TTGACGTTTCTCAAGGTAGAC----------AGTCTATTTTAGCCAA
* * * *
17805 AAATGTAAAACAATTTAACTTAAAATCAATTATGGCATTATAAAACTATTTCGAGCAAGTAATAA
1 AAATGTAAAACAATTTAACTTAAAAACAATTATGACATTATAAAACCATTTCGAGCAAGCAATAA
* * * * *
17870 GGCTTTTTGATGGTATGAATGACTATAAATGGACTTTTCTTCCCAAGGAATGCTTTTCCCTTTAC
66 GGCTTTTTGAAGGAATGAACGACTATAAATGGACTTTTCTTCCCAAGGAATCCTTTTCCCTTGAC
17935 GTTTCTCAAGGTAGACA
131 GTTTCTCAAGGTAGACA
17952 TTCAATTCCA
Statistics
Matches: 125, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
162 1 0.01
170 15 0.12
171 46 0.37
172 63 0.50
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.33
Consensus pattern (162 bp):
AAATGTAAAACAATTTAACTTAAAAACAATTATGACATTATAAAACCATTTCGAGCAAGCAATAA
GGCTTTTTGAAGGAATGAACGACTATAAATGGACTTTTCTTCCCAAGGAATCCTTTTCCCTTGAC
GTTTCTCAAGGTAGACAGTCTATTTTAGCCAA
Found at i:19419 original size:172 final size:171
Alignment explanation
Indices: 19214--19628 Score: 430
Period size: 172 Copynumber: 2.4 Consensus size: 171
19204 NNNNNNNNNN
* * *
19214 AGTAATAAGGCTTTTTGACGGTATGAGTGACTATAAATGGACTTTTCTTCCCAATGAAT-GCTTT
1 AGTAATAA-GC-TTTTGAAGGTTTGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTT
* * * *
19278 TCTCTTCACTTTTCT-CAAGG-TAGACATTCAATTCTAGTC-TGTTTTAACCAAAAAAGTAAAAA
64 T-TCTTCAC-GTTCTGCAAGGCAAGA-ATTCAATTATAGCCTTGTTTTAACCAAAAAAGTAAAAA
* *
19340 CAATTCAACTTAAAATCAATTATT-AGTTTATAAAACCATTT-AAAGC
126 -AATTCAACTTAAAATCAATT-TTGAGATTATAAAACCATTTAAAAAC
* * * **
19386 AAGTAATAACGCTTTTGAAGGTTTCAATGACTATAAATGGACTTTT-TGTGTCAATGGCTGGCTT
1 -AGTAATAA-GCTTTTGAAGGTTTGAGTGACTATAAATGGACTTTTCT-TGCCAATGAATGGCTT
* * * * * *
19450 TTTCTTCACGTTCTGTAGGGCAAGAATTCAATTATAGCCTTTTTTTAATCAAAAATGTAAAAAAT
63 TTTCTTCACGTTCTGCAAGGCAAGAATTCAATTATAGCCTTGTTTTAACCAAAAAAGTAAAAAAA
* *
19515 TTCAACTTAAAATCAATTTTGAGATTATAAAGCTATTTAAAAAC
128 TTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAAAC
* * ** **
19559 AGTAATAAGTCTTTTAAAGGCTTGAGCAACTATAAATGGACTTTTCTTGCCAATGAATACCTTTT
1 AGTAATAAG-CTTTTGAAGGTTTGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTT
19624 TCTTC
65 TCTTC
19629 NNNNNNNNNN
Statistics
Matches: 199, Mismatches: 34, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
171 8 0.04
172 147 0.74
173 44 0.22
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Consensus pattern (171 bp):
AGTAATAAGCTTTTGAAGGTTTGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTT
CTTCACGTTCTGCAAGGCAAGAATTCAATTATAGCCTTGTTTTAACCAAAAAAGTAAAAAAATTC
AACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAAAC
Found at i:20307 original size:172 final size:171
Alignment explanation
Indices: 19954--20324 Score: 430
Period size: 172 Copynumber: 2.2 Consensus size: 171
19944 NNNNNNCAAC
* * ** * * *
19954 TTAAAATCAATTATTGCATTATAAAACCATATAAAGTGAGTAATAAGGCTTTTGAAGGTATGGGT
1 TTAAAATCAATTATGGCATTACAAAACGGTTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGT
*
20019 GACTACAAATAGACTTTGCTTGCCAATGAATGCTTTTTTCTTCATGGTTCTCAAGGTGAGCATTC
66 GACTACAAATAGACTTTGCTTGCCAATGAATGCCTTTTTCTTCATGGTTCTCAAGGTGAGCATTC
* * * * *
20084 AATTCTAGTCTATTTTATATAAAAATGACTGAAGAATTCAAA
131 AATTATAGTCTACTTTATACAAAAATGAC-AAAAAATTCAAA
* *
20126 TTTAAATCAATTTTGAG-ATTACAAAACGGTTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGG
1 TTAAAATCAATTATG-GCATTACAAAACGGTTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGG
* * * * *
20190 TGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTTA-GGTTTCTCAAGGT-AGACA
65 TGACTACAAATAGACTTTGCTTGCCAATGAATGCCTTTTTCTTCATGG-TTCTCAAGGTGAG-CA
* *
20253 TTCAATTATAGTTTGCTTTA-ACCAAAAATGTA-AAAAAATTC-AA
128 TTCAATTATAGTCTACTTTATA-CAAAAATG-ACAAAAAATTCAAA
20296 TCGTAAAATCAATTATGGCATTACAAAAC
1 T--TAAAATCAATTATGGCATTACAAAAC
20325 CATTNNNNNN
Statistics
Matches: 167, Mismatches: 24, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
170 3 0.02
171 13 0.08
172 149 0.89
173 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35
Consensus pattern (171 bp):
TTAAAATCAATTATGGCATTACAAAACGGTTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGT
GACTACAAATAGACTTTGCTTGCCAATGAATGCCTTTTTCTTCATGGTTCTCAAGGTGAGCATTC
AATTATAGTCTACTTTATACAAAAATGACAAAAAATTCAAA
Found at i:21345 original size:172 final size:171
Alignment explanation
Indices: 21109--21728 Score: 588
Period size: 172 Copynumber: 3.6 Consensus size: 171
21099 NNNNNNTTTA
* * * * * *
21109 AAGGAATGGGTGACTATAAATGGACTTTTCTTGTC-AATGAATGCCTTTTTATT--TTGGTTTCT
1 AAGGTATGGGTGACTATAAATAGATTTTTCTTG-CAAATTAATGCTTTTTTCTTCATT--TTTCT
* * *
21171 CAAGGTAGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAACAATTCAATCGTAAAATCA
63 CAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATG-AAAAAAATTCAATCGTAAAATCA
* * * *
21236 GTTACGACATTACAAAACCATTTAAAGCAAGTAGTAAGGCTTTTG
127 ATTATGACATTACAAAACTATTTAAAGTAAGTAGTAAGGCTTTTG
* * * ** *
21281 AAGGTATGGGTGACAATGAATGGACGTTTCTTGCAAATTAATACTTTTTTCTTCATTTTTCTCAA
1 AAGGTATGGGTGACTATAAATAGATTTTTCTTGCAAATTAATGCTTTTTTCTTCATTTTTCTCAA
* * * ** *
21346 GGTAGCCATTCAATTCTAGTCTGTTTTAACCAGAAATGACTGATGAATTCAAAT--TTAAATCAA
66 GGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGA--AAAAAATTC-AATCGTAAAATCAA
* * * * * * *
21409 TTTTGAGACTACAAAGCTATTTAAAGTGAGTAATAAGGCTTTTA
128 TTATGACATTACAAAACTATTTAAAGTAAGTAGTAAGGCTTTTG
** * * * * * *** **
21453 AAGAAATAGGTGACTATAAATAGATTTTTCTTGCCAATGAATGCCTTTTTCTTTACGGTTCTTGA
1 AAGGTATGGGTGACTATAAATAGATTTTTCTTGCAAATTAATGCTTTTTTCTTCATTTTTCTCAA
* * ** * * *
21518 GGTAGACATTTAATTTTAGTCTGTTTTAACTTAAAATGAAAAAAAAAGTCGA-CGTTAAAAACAA
66 GGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATG--AAAAAAATTCAATCG-TAAAATCAA
* *
21582 TTATGGCATTACAAAACTATTTAAAGTAAGCAGTAAGGCTTTTG
128 TTATGACATTACAAAACTATTTAAAGTAAGTAGTAAGGCTTTTG
*
21626 AAGGTATGGGTGACTATAAATCGATTTTTC-TGCAAATTAATGCTTTTTTCTTCATTTTTCTCAA
1 AAGGTATGGGTGACTATAAATAGATTTTTCTTGCAAATTAATGCTTTTTTCTTCATTTTTCTCAA
* * *
21690 GATAGGCATTTAATTCTAGTCTGTTTTAACCAAAAATGA
66 GGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGA
21729 CTGAATAATT
Statistics
Matches: 352, Mismatches: 85, Indels: 24
0.76 0.18 0.05
Matches are distributed among these distances:
170 1 0.00
171 3 0.01
172 268 0.76
173 74 0.21
174 6 0.02
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (171 bp):
AAGGTATGGGTGACTATAAATAGATTTTTCTTGCAAATTAATGCTTTTTTCTTCATTTTTCTCAA
GGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGAAAAAAATTCAATCGTAAAATCAATTA
TGACATTACAAAACTATTTAAAGTAAGTAGTAAGGCTTTTG
Found at i:21662 original size:344 final size:344
Alignment explanation
Indices: 21105--21799 Score: 957
Period size: 344 Copynumber: 2.0 Consensus size: 344
21095 NNNNNNNNNN
* * * * *
21105 TTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTATTTTGGTTTC
1 TTTAAAGAAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTATTTCGGTTTC
* * * * *
21170 TCAAGGTAGACATTCAATTATAGTTTGTTTTAACCAAAAATGTAAAACAATTCAATCGTAAAATC
66 TCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGAAAAAAAAGTCAATCGTAAAAAC
* * *
21235 AGTTACGACATTACAAAACCATTTAAAGCAAGTAGTAAGGCTTTTGAAGGTATGGGTGACAATGA
131 AATTACGACATTACAAAACCATTTAAAGCAAGCAGTAAGGCTTTTGAAGGTATGGGTGACAATAA
* *
21300 ATGGACGTTTCTTGCAAATTAATACTTTTTTCTTCATTTTTCTCAAGGTAGCCATTCAATTCTAG
196 ATCGACGTTTCTTGCAAATTAATACTTTTTTCTTCATTTTTCTCAAGATAGCCATTCAATTCTAG
* * *
21365 TCTGTTTTAACCAGAAATGACTG-ATGAATTCAAATTTAAATCAATTTTGAGACTACAAAGCTAT
261 TCTGTTTTAACCAAAAATGACTGAAT-AATTCAAATTTAAATCAATTTTGAGACTACAAAACCAT
21429 TTAAAGTGAGTAATAAGGCT
325 TTAAAGTGAGTAATAAGGCT
* *
21449 TTTAAAGAAATAGGTGACTATAAATAGATTTTTCTTGCCAATGAATGCCTTTTTCTTTACGG-TT
1 TTTAAAGAAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTATTT-CGGTTT
** * * ** *
21513 CTTGAGGTAGACATTTAATTTTAGTCTGTTTTAACTTAAAATGAAAAAAAAAGTCGA-CGTTAAA
65 CTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG-AAAAAAAAGTCAATCG-TAAA
* * * * *
21577 AACAATTATGGCATTACAAAACTATTTAAAGTAAGCAGTAAGGCTTTTGAAGGTATGGGTGACTA
128 AACAATTACGACATTACAAAACCATTTAAAGCAAGCAGTAAGGCTTTTGAAGGTATGGGTGACAA
** * * *
21642 TAAATCGATTTTTC-TGCAAATTAATGCTTTTTTCTTCATTTTTCTCAAGATAGGCATTTAATTC
193 TAAATCGACGTTTCTTGCAAATTAATACTTTTTTCTTCATTTTTCTCAAGATAGCCATTCAATTC
* * * *
21706 TAGTCTGTTTTAACCAAAAATGACTGAATAATTGAAATTTATATCAATTTTGAGATTGCAAAACC
258 TAGTCTGTTTTAACCAAAAATGACTGAATAATTCAAATTTAAATCAATTTTGAGACTACAAAACC
21771 ATTTAAAGTGAGTAATAAGGCT
323 ATTTAAAGTGAGTAATAAGGCT
21793 TTTAAAG
1 TTTAAAG
21800 GANNNNNNNN
Statistics
Matches: 306, Mismatches: 41, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
344 222 0.73
345 84 0.27
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (344 bp):
TTTAAAGAAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTATTTCGGTTTC
TCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGAAAAAAAAGTCAATCGTAAAAAC
AATTACGACATTACAAAACCATTTAAAGCAAGCAGTAAGGCTTTTGAAGGTATGGGTGACAATAA
ATCGACGTTTCTTGCAAATTAATACTTTTTTCTTCATTTTTCTCAAGATAGCCATTCAATTCTAG
TCTGTTTTAACCAAAAATGACTGAATAATTCAAATTTAAATCAATTTTGAGACTACAAAACCATT
TAAAGTGAGTAATAAGGCT
Found at i:22323 original size:172 final size:169
Alignment explanation
Indices: 21912--22791 Score: 569
Period size: 170 Copynumber: 5.2 Consensus size: 169
21902 NNNNNNNNNN
* * ** *
21912 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGCAATGGGTGACTACGAATAGACTT
1 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTT
* * * * *
21977 TTCTTGCCAATGAATGCCTTTTTCTTTATA-TTTGT-AGAGGTAGGCATTCAATTGTA-TT-TTT
66 TTCTTACCAATGAATG-TTTTTTCTTTA-AGTTTCTCA-AGGTAGACATTCAATTATAGTTATTT
* * *
22038 TCAACTAAAAATGTAAAAAAATTTAAACTTAGAATCAATTTTGA
128 T-AACTAAAAATGTAAAAAAA-TTCAACTTAAAATCAATTATGA
* * * *
22082 GATTATAAAATCATTTAAAGTGAGCAATAAGGCTTTTGTATGAAT-AGGTGACTATAAATGGACT
1 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGA-GTGACTATAAATGGACT
* **
22146 TTTCTTTCCAATGAATGTATTTTTCTTTGCGTTTCTCAAGGTAGACA-TCTAATTATAGTCTATT
65 TTTCTTACCAATGAATGT-TTTTTCTTTAAGTTTCTCAAGGTAGACATTC-AATTATAGT-TATT
* * *
22210 TTAGCCAAAAATGTAAAAAGATTCAACTTAAAATCAATTATG-
127 TTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA
* *** * *
22252 GCGTTATAAAACCATTTAAACCAAGTAATAAGGCTTTCTGAAGGTATGAGTGACTATAAATGGAA
1 G-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT-TGAAGGAATGAGTGACTATAAATGGAC
* * * *
22317 TTTTCTTACCAATGAATGCTTTTTTCTTCAAGTTTCTCTAGGTAGATATTCAATTCTAGTTTATT
64 TTTTCTTACCAATGAATG-TTTTTTCTTTAAGTTTCTCAAGGTAGACATTCAATTATAG-TTATT
********** *
22382 TTAACTAAAAATGTAAAAAAATTCAACTTANNNNNNNNNNTTA
127 TTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA
* ** * ** **
22425 GTTTATAAAACCATTTAAAGAAAGTAATACGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTT
1 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTT
********** ** * * * * * * * *
22490 NNNNNNNNNNTGGTTGGCTTTTGCTTCATG-TTCCCTAGGGTAGGCATTCAATTTTAGCCTT-TT
66 TTCTTACCAATGAAT-GTTTTTTCTTTAAGTTTCTC-AAGGTAGACATTCAATTATAG--TTATT
* * * * *
22553 TTCACCAAAAATGTAAAAAAATTCTACTT-AAATAAATTTTGA
127 TTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA
* * * * * ** **
22595 GATTATAAAGCCATTTAAAGTGGGCAATAAGGTTTTTAAAGGCTTGAGCAACTATAAATGGACTT
1 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTT
* * * * * ** * * **
22660 TTCTTATCAATGAATATATTTTTCTTCACGTTTCCCAAGACAAACATTCAATTATA-ATATGCAC
66 TTCTTACCAATGAATGT-TTTTTCTTTAAGTTTCTCAAGGTAGACATTCAATTATAGTTAT--TT
* * * *
22724 TAACCAGAAACGTAAAAAAATTCAA-TCTAAAATCAATTGTGA
128 TAACTAAAAATGTAAAAAAATTCAACT-TAAAATCAATTATGA
*
22766 GGTTATAAAACCATTTAAAGTGAGTA
1 GATTATAAAACCATTTAAAGTGAGTA
22792 NNNNNNNNNN
Statistics
Matches: 541, Mismatches: 144, Indels: 49
0.74 0.20 0.07
Matches are distributed among these distances:
167 1 0.00
168 1 0.00
169 3 0.01
170 207 0.38
171 168 0.31
172 151 0.28
173 10 0.02
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.35
Consensus pattern (169 bp):
GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTT
TTCTTACCAATGAATGTTTTTTCTTTAAGTTTCTCAAGGTAGACATTCAATTATAGTTATTTTAA
CTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA
Found at i:25239 original size:172 final size:171
Alignment explanation
Indices: 24567--25241 Score: 602
Period size: 172 Copynumber: 3.9 Consensus size: 171
24557 NNNNNNNNNN
* * * * * *
24567 AAAATGTAAAAAAAATTTAACCTAAAATCAATTATG-GCATTATAAAACTATTTAAAGTAGGTAA
1 AAAATG-ATAAAAAATTCAACCTAAAATCAATTTTGAG-ATTATAAAACCATTTAAAGCAAGTAA
* * * *
24631 TAAAGCTTTTTGAAGGTGTGGGTGACTATAATTAGACTTTTCTTGTCAATGAATGCTTTTTTCTT
64 TAAAGC-TTTTGAAGATATGAGTGACTATAATTAGACTTTTCTTGCCAATGAATGCTTTTTTCTT
** * * *
24696 CACGTTT-TTGAAGGTAGACATTCAACTATAGTCTGTTTTATCCA
128 CATATTTCTT-AAGGTAGACATTCAATTATAGTCTATTTTAACCA
* * **
24740 AAAAT-ATAAAAATATTCAACCTAAAATCAATTATGACATTATAAAATTATTTAAAGCAAGTAAT
1 AAAATGATAAAAA-ATTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAAAGCAAGTAAT
*
24804 AAGGCTCTTTGAA-AGTATGAGTGA-TGATAATTAGACTTTTCTT-CTCAATGAATGCTTTTTTC
65 AAAGCT-TTTGAAGA-TATGAGTGACT-ATAATTAGACTTTTCTTGC-CAATGAATGCTTTTTTC
* *
24866 TTC-TCATTTCTTAAGGTAGACATTCAATTCTAGTCTATTTTAACAAA
126 TTCAT-ATTTCTTAAGGTAGACATTCAATTATAGTCTATTTTAAC-CA
*
24913 AAAATGCA-AAAAAAATCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAAAGCAAGTAAT
1 AAAATG-ATAAAAAATTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAAAGCAAGTAAT
** * * * * * ** *
24977 AAAGCTTTCCAAGGCT-TGAGTCACTATAAATGGTCTTTT-TATGCCAATGGTTGGC-TTTTGCT
65 AAAGCTTTTGAA-GATATGAGTGACTATAATTAGACTTTTCT-TGCCAATGAAT-GCTTTTTTCT
* * * * *
25039 TCATGTTCCCTAAGGTAGACATTCAATTATAGCTTTTTTTTAACCA
127 TCATATTTCTTAAGGTAGACATTCAATTATAG-TCTATTTTAACCA
* * * * * * * * *
25085 AAAATGTTAAAAAATTCAACTTAAATTCATTTTTGAGGTTACATAGCCATTTAAAGTAAGTAATA
1 AAAATGATAAAAAATTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAAAGCAAGTAATA
* * * * *
25150 AGGCTTTTGAAGAAATGAGTGACTATAAAGT-GACTTTTCTTGCGAATGAAT-ATCTTTTTCTTC
66 AAGCTTTTGAAGATATGAGTGACTAT-AATTAGACTTTTCTTGCCAATGAATGCT-TTTTTCTTC
* * *
25213 ATATTTTTTAAGGCAGACACTCAATTATA
129 ATATTTCTTAAGGTAGACATTCAATTATA
25242 ANNNNNNNNN
Statistics
Matches: 407, Mismatches: 70, Indels: 51
0.77 0.13 0.10
Matches are distributed among these distances:
171 10 0.02
172 308 0.76
173 83 0.20
174 5 0.01
175 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (171 bp):
AAAATGATAAAAAATTCAACCTAAAATCAATTTTGAGATTATAAAACCATTTAAAGCAAGTAATA
AAGCTTTTGAAGATATGAGTGACTATAATTAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCAT
ATTTCTTAAGGTAGACATTCAATTATAGTCTATTTTAACCA
Done.