Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_pilon, 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: 4652821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 23
Found at i:1784643 original size:6 final size:6
Alignment explanation
Indices: 1784608--1784654 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
1784598 CACGTATTAC
* * * *
1784608 CACGAC CACGAC CACGAC CACGAG CACGAG CACGAG CGCGAG -ACGAG
1 CACGAG CACGAG CACGAG CACGAG CACGAG CACGAG CACGAG CACGAG
1784655 ACAGACGGCG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
5 4 0.11
6 34 0.89
ACGTcount: A:0.32, C:0.38, G:0.30, T:0.00
Consensus pattern (6 bp):
CACGAG
Found at i:1785231 original size:21 final size:21
Alignment explanation
Indices: 1785205--1785460 Score: 395
Period size: 21 Copynumber: 12.2 Consensus size: 21
1785195 CAAATGCAAT
*
1785205 AACGAACTTGGAGACTATCAC
1 AACGAACTTGGAGACTATCGC
*
1785226 AACGAAGTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
*
1785247 AACGAATTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
*
1785268 AACGAAGTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
*
1785289 AACGAAGTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
*
1785310 AACGAAGTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
1785331 AACGAACTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
*
1785352 AACGAACTTGGAGTCTATCGC
1 AACGAACTTGGAGACTATCGC
* * *
1785373 AATGCACTTGGAGACTATCGT
1 AACGAACTTGGAGACTATCGC
* *
1785394 AACGTACTTGGAGACTATTGC
1 AACGAACTTGGAGACTATCGC
*
1785415 AACGAATTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
1785436 AACGAACTTGGAGACTATCGC
1 AACGAACTTGGAGACTATCGC
1785457 AACG
1 AACG
1785461 CGAATATGTA
Statistics
Matches: 217, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 217 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (21 bp):
AACGAACTTGGAGACTATCGC
Found at i:1785503 original size:21 final size:21
Alignment explanation
Indices: 1785479--1785546 Score: 136
Period size: 21 Copynumber: 3.2 Consensus size: 21
1785469 TAAATCGCAA
1785479 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
1785500 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
1785521 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
1785542 TGCGA
1 TGCGA
1785547 ATCTGGAAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:1786948 original size:63 final size:63
Alignment explanation
Indices: 1786849--1786974 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
1786839 CTATAACGGC
1786849 GTCAAGCGTCACTAAAGTACACATCTATAACGGTGTTTTCTCAAAAACACCATTAAAGTAGTG
1 GTCAAGCGTCACTAAAGTACACATCTATAACGGTGTTTTCTCAAAAACACCATTAAAGTAGTG
1786912 GTCAAGCGTCACTAAAGTACACATCTATAACGGTGTTTTCTCAAAAACACCATTAAAGTAGTG
1 GTCAAGCGTCACTAAAGTACACATCTATAACGGTGTTTTCTCAAAAACACCATTAAAGTAGTG
1786975 TTATTACGAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (63 bp):
GTCAAGCGTCACTAAAGTACACATCTATAACGGTGTTTTCTCAAAAACACCATTAAAGTAGTG
Found at i:1787427 original size:14 final size:13
Alignment explanation
Indices: 1787401--1787435 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1787391 TAAATTATGA
1787401 TTTTT-AATTTTT
1 TTTTTAAATTTTT
*
1787413 TTTTGAAATTTTT
1 TTTTTAAATTTTT
1787426 TTTTTAAATT
1 TTTTTAAATT
1787436 ATTATTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTTAAATTTTT
Found at i:1788172 original size:21 final size:21
Alignment explanation
Indices: 1788129--1788174 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1788119 TCGGTAAAAA
* *
1788129 TTTATCTAAAATATTATTATT
1 TTTATCTAAAACATAATTATT
1788150 TTTATCTAAAACATCAATT-TT
1 TTTATCTAAAACAT-AATTATT
1788171 TTTA
1 TTTA
1788175 ACATTTCCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTATCTAAAACATAATTATT
Found at i:1788932 original size:251 final size:248
Alignment explanation
Indices: 1788533--1789014 Score: 813
Period size: 251 Copynumber: 1.9 Consensus size: 248
1788523 ATTCAATTTT
1788533 AATTTATAAAATATAATTATCAATATAAAAATTATTTATATTTTTTTAATAATTTAGAGTGATTA
1 AATTTATAAAATATAATTATCAATATAAAAATTATTTATATTTTTTTAATAATTTAGAGTGATTA
*
1788598 TAAAATAATAACTATTCAATTTTCTTAATTATTGACAAATAATTATCAAGATTCTACGACAAGAG
66 TAAAATAATAACTATTAAATTTTCTTAATTATTGACAAATAATTATCAAGATTCTACGACAAGAG
* * *
1788663 AAATACTGACAATCTTTCTCTCATCTAAATGAGTTAGTATATTCTCGCTACAGATTTGATCAA-T
131 AAATACTAACAATCTTTCTCTCATCTAAATGAGCTAGTAGATTCTCGCTACAGATTTGATCAATT
*
1788727 TTTTCTTCTTTAACTTTGTTTAATCTGCGGTAGCATCGATAATTATCAATACA
196 TTTTCTTCTTTAACCTTGTTTAATCTGCGGTAGCATCGATAATTATCAATACA
*
1788780 AATTTATAAAATATAATTATCAATATAAAAATTATTTATATATTTTTTAATAATTTAGAGTGGTT
1 AATTTATAAAATATAATTATCAATATAAAAATTATTTATAT-TTTTTTAATAATTTAGAGTGATT
* * *
1788845 ATAAAATAATAACTATTTAAAATTTTCTTAATTTATTGACAAATAATTATTAAGATTCTACTACC
65 ATAAAATAATAACTA-TT-AAATTTTCTTAA-TTATTGACAAATAATTATCAAGATTCTACGACA
* *
1788910 AGAGAAATACTAATAATCTTTCTCTCATCTAAATGGGCTAGTAGATTCTCGCTACAGATTTGATC
127 AGAGAAATACTAACAATCTTTCTCTCATCTAAATGAGCTAGTAGATTCTCGCTACAGATTTGATC
*
1788975 AATTTTTTCTTCTTTAACCTTGTTTAATCTGCGGTGGCAT
192 AATTTTTTCTTCTTTAACCTTGTTTAATCTGCGGTAGCAT
1789015 TGATTTTAAT
Statistics
Matches: 218, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
247 41 0.19
248 37 0.17
249 2 0.01
250 11 0.05
251 92 0.42
252 35 0.16
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (248 bp):
AATTTATAAAATATAATTATCAATATAAAAATTATTTATATTTTTTTAATAATTTAGAGTGATTA
TAAAATAATAACTATTAAATTTTCTTAATTATTGACAAATAATTATCAAGATTCTACGACAAGAG
AAATACTAACAATCTTTCTCTCATCTAAATGAGCTAGTAGATTCTCGCTACAGATTTGATCAATT
TTTTCTTCTTTAACCTTGTTTAATCTGCGGTAGCATCGATAATTATCAATACA
Found at i:1794985 original size:43 final size:43
Alignment explanation
Indices: 1794889--1795008 Score: 125
Period size: 43 Copynumber: 2.8 Consensus size: 43
1794879 TGATTTTTTG
* *
1794889 ACGCCACAGTAGGTGTTGATG-TTTAGCGACGTTTTTCCTAAAA
1 ACGCCACAGTAGGTGTTGA-GATTTAGCGGCGTTTTACCTAAAA
*** * * *
1794932 ATATCGCAGTAGGTGTTGAGATTTAGCGGCGTTTTACTTACAA
1 ACGCCACAGTAGGTGTTGAGATTTAGCGGCGTTTTACCTAAAA
* * *
1794975 ACGCCACAGTAGGTGTTGATATTTTGCGGGGTTT
1 ACGCCACAGTAGGTGTTGAGATTTAGCGGCGTTT
1795009 CCCACAAACG
Statistics
Matches: 61, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 1 0.02
43 60 0.98
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (43 bp):
ACGCCACAGTAGGTGTTGAGATTTAGCGGCGTTTTACCTAAAA
Found at i:1795027 original size:41 final size:43
Alignment explanation
Indices: 1794889--1795061 Score: 111
Period size: 43 Copynumber: 4.1 Consensus size: 43
1794879 TGATTTTTTG
* * * * *
1794889 ACGCCACAGTAGGTGTTGATG-TTTAGCGACGTTTTTCCTAAAA
1 ACGCCACAGTAGGTGTTGA-GATTTAGCGGCGGTTTACCCACAA
*** * * **
1794932 ATATCGCAGTAGGTGTTGAGATTTAGCGGCGTTTTACTTACAA
1 ACGCCACAGTAGGTGTTGAGATTTAGCGGCGGTTTACCCACAA
* *
1794975 ACGCCACAGTAGGTGTTGATATTTTGCGG-GGTTT-CCCACAA
1 ACGCCACAGTAGGTGTTGAGATTTAGCGGCGGTTTACCCACAA
** * * * * *
1795016 ACGCCGGAGTAGGCGTTCATG-TTTAGTGGCGTTTTGCCCACAA
1 ACGCCACAGTAGGTGTTGA-GATTTAGCGGCGGTTTACCCACAA
1795059 ACG
1 ACG
1795062 AGACTACAAT
Statistics
Matches: 101, Mismatches: 25, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
41 26 0.26
42 9 0.09
43 66 0.65
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.31
Consensus pattern (43 bp):
ACGCCACAGTAGGTGTTGAGATTTAGCGGCGGTTTACCCACAA
Found at i:1795182 original size:21 final size:21
Alignment explanation
Indices: 1795158--1795243 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
1795148 GCTTATATGT
1795158 TGCTTCTCTCTGTGCTGCCGC
1 TGCTTCTCTCTGTGCTGCCGC
* *
1795179 TGCTTCTCTTTGTGTTGCCGC
1 TGCTTCTCTCTGTGCTGCCGC
* * *
1795200 TGCTTCTTTCTCTGCTTCCGC
1 TGCTTCTCTCTGTGCTGCCGC
* * *
1795221 TGCTACTCTCTTTGCTTCCGC
1 TGCTTCTCTCTGTGCTGCCGC
1795242 TG
1 TG
1795244 TTGCTGCTCT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.01, C:0.35, G:0.20, T:0.44
Consensus pattern (21 bp):
TGCTTCTCTCTGTGCTGCCGC
Found at i:1798377 original size:36 final size:36
Alignment explanation
Indices: 1798332--1798402 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
1798322 AAAATATCGA
1798332 CATTAGTGTAGCTAATTATTCTAGGTAAACTATATT
1 CATTAGTGTAGCTAATTATTCTAGGTAAACTATATT
* *
1798368 CATTGGTGTAGTTAATTATTCTAGGTAAACTATAT
1 CATTAGTGTAGCTAATTATTCTAGGTAAACTATAT
1798403 ATAATAATCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (36 bp):
CATTAGTGTAGCTAATTATTCTAGGTAAACTATATT
Found at i:1800156 original size:42 final size:41
Alignment explanation
Indices: 1800086--1800167 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 41
1800076 TACGACATTA
* *
1800086 TAAAAAAATGCCTCTATAATGCCGATATATTGCGGCGTTTT
1 TAAAAAAATGCCTCTATAATGCAGATATATCGCGGCGTTTT
* *
1800127 TAAACAAAATGCCTCTATAGTGCATATATATCGCGGCGTTT
1 TAAA-AAAATGCCTCTATAATGCAGATATATCGCGGCGTTT
1800168 AGGTAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 4 0.11
42 32 0.89
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (41 bp):
TAAAAAAATGCCTCTATAATGCAGATATATCGCGGCGTTTT
Found at i:1800301 original size:41 final size:42
Alignment explanation
Indices: 1800241--1800334 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 42
1800231 TTCAACTCTA
* ** *
1800241 TTGTCGCGTTTGTACAAAAAACGCCGCTAATGTGTAAATA-T
1 TTGTAGCGTTTGTACAAAAAACGCCGCTAAAATATAAATATT
** * *
1800282 TTGTAGCGTTTGTTGAAAAAGCGTCGCTAAAATATAAATATT
1 TTGTAGCGTTTGTACAAAAAACGCCGCTAAAATATAAATATT
*
1800324 TTGTGGCGTTT
1 TTGTAGCGTTT
1800335 ATTAACCAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 32 0.74
42 11 0.26
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (42 bp):
TTGTAGCGTTTGTACAAAAAACGCCGCTAAAATATAAATATT
Found at i:1801489 original size:21 final size:22
Alignment explanation
Indices: 1801463--1801516 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1801453 AATTCACGTT
*
1801463 TTCAAAAGCTATTA-TTTTCTA
1 TTCAAAAGCAATTATTTTTCTA
1801484 TTCAAAAGCAATTATTTTTCTA
1 TTCAAAAGCAATTATTTTTCTA
*
1801506 TTCGAAAGCAA
1 TTCAAAAGCAA
1801517 AAAAACACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (22 bp):
TTCAAAAGCAATTATTTTTCTA
Found at i:1802040 original size:41 final size:40
Alignment explanation
Indices: 1801991--1802129 Score: 140
Period size: 41 Copynumber: 3.4 Consensus size: 40
1801981 GAAATTACTT
*
1801991 CTCTATAGCGTCGTTTGTTGAAAAAACGCCACTATAAACAA
1 CTCTATAGCGGCGTTTGTT-AAAAAACGCCACTATAAACAA
* * *
1802032 CACTATAGCGGCGTTTGTT-TAAAACGCCACTA-AATTACCA
1 CTCTATAGCGGCGTTTGTTAAAAAACGCCACTATAA--ACAA
** *
1802072 CTCTATTA-CGGCGTTTGTTAAAAAAACATCACTATAAACAT
1 CTCTA-TAGCGGCGTTTGTT-AAAAAACGCCACTATAAACAA
*
1802113 CTCTATTGCGGCGTTTG
1 CTCTATAGCGGCGTTTG
1802130 AGCTATAAAC
Statistics
Matches: 80, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
38 2 0.03
39 12 0.15
40 19 0.24
41 35 0.44
42 10 0.12
43 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (40 bp):
CTCTATAGCGGCGTTTGTTAAAAAACGCCACTATAAACAA
Found at i:1802088 original size:81 final size:81
Alignment explanation
Indices: 1801917--1802182 Score: 270
Period size: 81 Copynumber: 3.3 Consensus size: 81
1801907 CATATTTTTG
* * * * * *
1801917 CGGCGTTTTTTGCACAAACGCCACTATAAATAATACTATTGCGGCATTT-TTTATTAAACGCCGC
1 CGGCGTTTGTTGAAAAAACGCCACTATAAACAACACTATTGCGGCGTTTGTTTA-TAAACGCCGC
* *
1801981 GAAATTACTTCTCTA-TA
65 TAAATTAC-CCTCTATTA
* * *
1801998 GCGTCGTTTGTTGAAAAAACGCCACTATAAACAACACTATAGCGGCGTTTGTTTA-AAACGCCAC
1 -CGGCGTTTGTTGAAAAAACGCCACTATAAACAACACTATTGCGGCGTTTGTTTATAAACGCCGC
1802062 TAAATTACCACTCTATTA
65 TAAATTACC-CTCTATTA
* ** * * **
1802080 CGGCGTTTGTTAAAAAAACATCACTATAAACATCTCTATTGCGGCGTTTGAGCTATAAACGCCGC
1 CGGCGTTTGTTGAAAAAACGCCACTATAAACAACACTATTGCGGCGTTTG-TTTATAAACGCCGC
1802145 TAAATTACCCTCTATTA
65 TAAATTACCCTCTATTA
* * *
1802162 CAG-TTTTGTTTAAAAAACGCC
1 CGGCGTTTGTTGAAAAAACGCC
1802183 GCTAAAGTAT
Statistics
Matches: 153, Mismatches: 26, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
81 77 0.50
82 55 0.36
83 21 0.14
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (81 bp):
CGGCGTTTGTTGAAAAAACGCCACTATAAACAACACTATTGCGGCGTTTGTTTATAAACGCCGCT
AAATTACCCTCTATTA
Found at i:1803540 original size:18 final size:18
Alignment explanation
Indices: 1803494--1803541 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1803484 TCAAATTATT
* *
1803494 TATTTTCTCTCTCCTTAA
1 TATTTCCTCTTTCCTTAA
1803512 TATTTCCTCTTTCCTTAA
1 TATTTCCTCTTTCCTTAA
*
1803530 TATTTCTTCTTT
1 TATTTCCTCTTT
1803542 TAGAAACAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.25, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTCCTCTTTCCTTAA
Found at i:1804707 original size:39 final size:39
Alignment explanation
Indices: 1804664--1804812 Score: 156
Period size: 39 Copynumber: 3.8 Consensus size: 39
1804654 GACCTTAATG
*
1804664 CTTACTGCAGGCTCCTCGGCTTTGTGCTTAGGGTAAGTC
1 CTTACTGCAGGCTCCTCGGCTTTGTGCTCAGGGTAAGTC
** *
1804703 CTTACCT-CAGGCTCCTCGATTTTGTGCTCAGAGTAAGTC
1 CTTA-CTGCAGGCTCCTCGGCTTTGTGCTCAGGGTAAGTC
* * * * * *
1804742 CTTACTGCATGCTCCTCTGCTTTGTGCACATGATAAGAC
1 CTTACTGCAGGCTCCTCGGCTTTGTGCTCAGGGTAAGTC
* * * *
1804781 CTTACCGTAGGCTCCTCTGCTTTGTGCACAGG
1 CTTACTGCAGGCTCCTCGGCTTTGTGCTCAGG
1804813 TAGACCCTTA
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
38 2 0.02
39 87 0.96
40 2 0.02
ACGTcount: A:0.16, C:0.28, G:0.23, T:0.33
Consensus pattern (39 bp):
CTTACTGCAGGCTCCTCGGCTTTGTGCTCAGGGTAAGTC
Found at i:1804805 original size:78 final size:78
Alignment explanation
Indices: 1804664--1804807 Score: 184
Period size: 78 Copynumber: 1.8 Consensus size: 78
1804654 GACCTTAATG
** * * *
1804664 CTTACTGCAGGCTCCTCGGCTTTGTGCTTAGGGTAAGTCCTTACCTCAGGCTCCTCGATTTTGTG
1 CTTACTGCAGGCTCCTCGGCTTTGTGCACAGGATAAGACCTTACCTCAGGCTCCTCGACTTTGTG
1804729 CTCAGAGTAAGTC
66 CTCAGAGTAAGTC
* * *
1804742 CTTACTGCATGCTCCTCTGCTTTGTGCACATGATAAGACCTTACCGT-AGGCTCCTCTG-CTTTG
1 CTTACTGCAGGCTCCTCGGCTTTGTGCACAGGATAAGACCTTACC-TCAGGCTCCTC-GACTTTG
1804805 TGC
64 TGC
1804808 ACAGGTAGAC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
78 54 0.96
79 2 0.04
ACGTcount: A:0.15, C:0.28, G:0.22, T:0.34
Consensus pattern (78 bp):
CTTACTGCAGGCTCCTCGGCTTTGTGCACAGGATAAGACCTTACCTCAGGCTCCTCGACTTTGTG
CTCAGAGTAAGTC
Found at i:1806694 original size:25 final size:26
Alignment explanation
Indices: 1806660--1806712 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 26
1806650 TCAGCACAAA
1806660 CATGGATAATC-GTGTTTGAATCAAG
1 CATGGATAATCAGTGTTTGAATCAAG
1806685 CATGGATAATCGAGTGTTTGAATCAAG
1 CATGGATAATC-AGTGTTTGAATCAAG
1806712 C
1 C
1806713 GCGAGAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 11 0.42
27 15 0.58
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (26 bp):
CATGGATAATCAGTGTTTGAATCAAG
Found at i:1808782 original size:103 final size:103
Alignment explanation
Indices: 1808603--1808809 Score: 414
Period size: 103 Copynumber: 2.0 Consensus size: 103
1808593 CTACATTCTG
1808603 CAAATGGCAATGGCTGTTTGCAAACGTCTCTTGCTGTATCATAACACAGCGTCATTCAACTACAG
1 CAAATGGCAATGGCTGTTTGCAAACGTCTCTTGCTGTATCATAACACAGCGTCATTCAACTACAG
1808668 ACTTCTATATCTCAGTGGACTGGATTCACACTCAAATT
66 ACTTCTATATCTCAGTGGACTGGATTCACACTCAAATT
1808706 CAAATGGCAATGGCTGTTTGCAAACGTCTCTTGCTGTATCATAACACAGCGTCATTCAACTACAG
1 CAAATGGCAATGGCTGTTTGCAAACGTCTCTTGCTGTATCATAACACAGCGTCATTCAACTACAG
1808771 ACTTCTATATCTCAGTGGACTGGATTCACACTCAAATT
66 ACTTCTATATCTCAGTGGACTGGATTCACACTCAAATT
1808809 C
1 C
1808810 CATGAAACTA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (103 bp):
CAAATGGCAATGGCTGTTTGCAAACGTCTCTTGCTGTATCATAACACAGCGTCATTCAACTACAG
ACTTCTATATCTCAGTGGACTGGATTCACACTCAAATT
Found at i:1827531 original size:60 final size:60
Alignment explanation
Indices: 1827404--1827558 Score: 152
Period size: 60 Copynumber: 2.6 Consensus size: 60
1827394 CATATGTCCC
* * * * *
1827404 TCATTCTAAATTAGTCCCTAAACTTTTAAATATTTTAATTTCATCCATAAACTATTACTA
1 TCATTCTAAATTAGTCACTAAACTTTTAAACATTTAAATTTCATCCACAAACTATGACTA
* * * *
1827464 TCGTTCTAAATTAG-CACTCAAACTTTTGAACATTTAAATTTCATCCCCAAAGTATGACCT-
1 TCATTCTAAATTAGTCACT-AAACTTTTAAACATTTAAATTTCATCCACAAACTATGA-CTA
* * * *
1827524 TCATTCTAGATTGGTCCCCAAACTTTTTAAACATT
1 TCATTCTAAATTAGTCACTAAAC-TTTTAAACATT
1827559 CCAATTTTAT
Statistics
Matches: 76, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
59 3 0.04
60 59 0.78
61 14 0.18
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (60 bp):
TCATTCTAAATTAGTCACTAAACTTTTAAACATTTAAATTTCATCCACAAACTATGACTA
Found at i:1829939 original size:3 final size:3
Alignment explanation
Indices: 1829931--1829995 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
1829921 TTACGTGCAT
1829931 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1829979 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
1829996 CGACTATGAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1831590 original size:3 final size:3
Alignment explanation
Indices: 1831582--1831624 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
1831572 CTATATAATA
1831582 TAT TAT TAT TAT TAT TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1831625 AAATAATACA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1831609 original size:25 final size:25
Alignment explanation
Indices: 1831575--1831624 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1831565 TCCGAGCCTA
1831575 TATAATATATTATTATTATTATTAT
1 TATAATATATTATTATTATTATTAT
*
1831600 TATATTATATTATTATTATTATTAT
1 TATAATATATTATTATTATTATTAT
1831625 AAATAATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TATAATATATTATTATTATTATTAT
Found at i:1842422 original size:20 final size:21
Alignment explanation
Indices: 1842397--1842448 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1842387 TTTTCCCAAT
*
1842397 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1842417 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1842438 TCGCAATGCGA
1 TCGCAATGCGA
1842449 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1842462 original size:20 final size:20
Alignment explanation
Indices: 1842437--1842551 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
1842427 AATTGGGAAA
*
1842437 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1842457 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
1842477 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1842498 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1842518 TTCGCAACGCGATTCTGAAT
1 ATCGCAACGCGATACTGACT
*
1842538 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1842552 ATACATAATC
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1842499 original size:61 final size:61
Alignment explanation
Indices: 1842434--1842571 Score: 177
Period size: 61 Copynumber: 2.3 Consensus size: 61
1842424 GCGAATTGGG
* * * *
1842434 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGAATATCGCAACGCGATAATAC
* * * * *
1842495 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGAATTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGAATATCGCAACGCGATAATAC
* *
1842556 ATAATCGCAATACGAT
1 AAAATCGCAATGCGAT
1842572 TTTCAAAGCG
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGAATATCGCAACGCGATAATAC
Found at i:1843091 original size:20 final size:20
Alignment explanation
Indices: 1843037--1843095 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1843027 GCGATTCTCT
**
1843037 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1843057 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1843077 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1843096 AGAAACTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1843283 original size:25 final size:24
Alignment explanation
Indices: 1843229--1843283 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1843219 TGTTTATTAT
* *
1843229 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1843253 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1843279 TGTTT
1 TGTTT
1843284 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1844407 original size:18 final size:16
Alignment explanation
Indices: 1844386--1844428 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1844376 TCCACTTTGG
*
1844386 GAGCCATCACCTCGCCCA
1 GAGCCATCA-CTC-ACCA
*
1844404 GAGCTATCACTCACCA
1 GAGCCATCACTCACCA
1844420 GAGCCATCA
1 GAGCCATCA
1844429 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 11 0.50
17 3 0.14
18 8 0.36
ACGTcount: A:0.28, C:0.42, G:0.16, T:0.14
Consensus pattern (16 bp):
GAGCCATCACTCACCA
Found at i:1844926 original size:20 final size:20
Alignment explanation
Indices: 1844901--1844943 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1844891 TAGTTTACTT
1844901 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
1844921 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1844941 TCG
1 TCG
1844944 TAATGCGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1844995 original size:31 final size:32
Alignment explanation
Indices: 1844940--1845028 Score: 144
Period size: 31 Copynumber: 2.8 Consensus size: 32
1844930 GGAAATGGCT
* *
1844940 ATCGTAATGCGAATTGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAA
1844972 ATCGCAATGCGAAATG-AAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAA
*
1845003 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1845029 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
31 30 0.57
32 23 0.43
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.15
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAA
Found at i:1845017 original size:13 final size:14
Alignment explanation
Indices: 1844957--1845017 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 14
1844947 TGCGAATTGA
1844957 AAATCGCAACGAC-
1 AAATCGCAACGACG
*
1844970 AAATCGCAATGCGAAATG
1 AAATCGCAA--CG--ACG
1844988 AAATCGCAACGAC-
1 AAATCGCAACGACG
1845001 AAATCGCAACG-CG
1 AAATCGCAACGACG
1845014 AAAT
1 AAAT
1845018 GAAAATCGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
12 1 0.03
13 24 0.60
14 1 0.03
15 2 0.05
16 2 0.05
17 1 0.03
18 9 0.22
ACGTcount: A:0.46, C:0.25, G:0.18, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACG
Found at i:1845064 original size:14 final size:14
Alignment explanation
Indices: 1845045--1845135 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
1845035 TTGTGTTTCG
1845045 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1845059 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1845075 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1845091 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
1845108 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1845124 CATTGCGATTTT
1 CGTTGCGATTTT
1845136 CATTTCGCAT
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 27 0.43
15 3 0.05
16 11 0.17
17 4 0.06
18 12 0.19
19 6 0.10
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1845109 original size:33 final size:33
Alignment explanation
Indices: 1845040--1845151 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
1845030 GCGATTTGTG
*
1845040 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1845072 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
1845105 TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1845138 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1845152 AGCCATTTCC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 26 0.34
33 51 0.66
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1845170 original size:20 final size:19
Alignment explanation
Indices: 1845136--1845191 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1845126 TTGCGATTTT
*
1845136 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1845155 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1845175 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
1845192 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1845288 original size:27 final size:26
Alignment explanation
Indices: 1845226--1845290 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
1845216 AACTATTCTT
*
1845226 CTTCTGGAATGTTTATATATGTTGTC
1 CTTCTGGAATGTTTATATATGTTGTA
**
1845252 CTT-TTAAATGTTTATATAAGTGTT-TA
1 CTTCTGGAATGTTTATAT-A-TGTTGTA
1845278 CTTCTGGAATGTT
1 CTTCTGGAATGTT
1845291 ATCTGAGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 12 0.39
26 8 0.26
27 11 0.35
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.51
Consensus pattern (26 bp):
CTTCTGGAATGTTTATATATGTTGTA
Found at i:1847287 original size:20 final size:20
Alignment explanation
Indices: 1847209--1847295 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
1847199 GCGATTTCTA
1847209 GTTGCGATAGCCA-TTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
1847228 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
*
1847248 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*
1847268 GTTGCGGTAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
1847288 GTTGCGAT
1 GTTGCGAT
1847296 TTCCCCGTTG
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
19 10 0.19
20 44 0.81
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:1847533 original size:20 final size:20
Alignment explanation
Indices: 1847508--1847557 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1847498 TTGAAGATGA
1847508 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
**
1847528 TTGCGAAATTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
1847548 TTGCGATTTT
1 TTGCGATTTT
1847558 GTATTATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:1847628 original size:20 final size:21
Alignment explanation
Indices: 1847584--1847634 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1847574 ATAGTCAGTA
*
1847584 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1847605 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1847625 TCGCA-TGCGA
1 TCGCATTGCGA
1847635 ATTAGGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 5 0.19
20 11 0.41
21 11 0.41
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1847845 original size:12 final size:12
Alignment explanation
Indices: 1847826--1847859 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1847816 CTCTCCGGCG
1847826 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1847838 ATATCCGTTCCT
1 ACATCCGTTCCT
1847850 ACATCC-TTCC
1 ACATCCGTTCC
1847860 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1848430 original size:23 final size:24
Alignment explanation
Indices: 1848404--1848456 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1848394 GTATTCGAAA
1848404 TTTGAT-CTGGTCAATACCCGGAC
1 TTTGATACTGGTCAATACCCGGAC
* * *
1848427 TTTGATATTGGTCAATACTCGGAT
1 TTTGATACTGGTCAATACCCGGAC
1848451 TTTGAT
1 TTTGAT
1848457 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (24 bp):
TTTGATACTGGTCAATACCCGGAC
Found at i:1848440 original size:24 final size:24
Alignment explanation
Indices: 1848411--1848456 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1848401 AAATTTGATC
1848411 TGGTCAATACCCGGACTTTGATAT
1 TGGTCAATACCCGGACTTTGATAT
* *
1848435 TGGTCAATACTCGGATTTTGAT
1 TGGTCAATACCCGGACTTTGAT
1848457 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (24 bp):
TGGTCAATACCCGGACTTTGATAT
Found at i:1850915 original size:19 final size:20
Alignment explanation
Indices: 1850878--1850915 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1850868 ATCTTAATGT
1850878 CTATCGCAACGCGGAAATTA
1 CTATCGCAACGCGGAAATTA
*
1850898 CTATCGCAATGC-GAAATT
1 CTATCGCAACGCGGAAATT
1850916 TTGGGACTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
CTATCGCAACGCGGAAATTA
Found at i:1851123 original size:19 final size:18
Alignment explanation
Indices: 1851101--1851230 Score: 86
Period size: 19 Copynumber: 7.7 Consensus size: 18
1851091 GGAAATTACT
1851101 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
1851120 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
1851134 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
1851153 ATCGCAA-CG--CT-AAT
1 ATCGCAAGCGAAATGAAA
*
1851167 TTCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
1851186 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
1851200 ATCGCAAGCGAAATGAAA
1 ATCGCAAGCGAAATGAAA
1851218 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
1851231 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 12, Indels: 30
0.67 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 5 0.06
16 4 0.05
17 7 0.08
18 11 0.13
19 30 0.36
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:1851124 original size:39 final size:36
Alignment explanation
Indices: 1851081--1851228 Score: 145
Period size: 33 Copynumber: 4.3 Consensus size: 36
1851071 CTTAATGTCT
*
1851081 ATCGCAACGCGGAAATTACTATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAA-GA--ATCGCAATGCGAAATGAAA
*
1851120 ATCGCAA--C-GAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
* **
1851153 ATCGCAACGC--TAA-TTTCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
*
1851186 ATCGCAACGAGG---GAATCGCAA-GCGAAATGAAA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
1851218 ATCGCAACGCG
1 ATCGCAACGCG
1851229 AATTTAATTT
Statistics
Matches: 94, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
32 21 0.22
33 59 0.63
34 1 0.01
35 2 0.02
36 3 0.03
37 1 0.01
39 7 0.07
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (36 bp):
ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
Found at i:1851143 original size:33 final size:33
Alignment explanation
Indices: 1851101--1851226 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
1851091 GGAAATTACT
1851101 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1851134 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1851166 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1851200 ATCGCAA-GCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1851227 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
32 21 0.25
33 62 0.74
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1851278 original size:18 final size:18
Alignment explanation
Indices: 1851230--1851292 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
1851220 CGCAACGCGA
*
1851230 ATTTAATTTCGCGTTGCG
1 ATTTCATTTCGCGTTGCG
*
1851248 A-TTC---TCTCGTTGCG
1 ATTTCATTTCGCGTTGCG
1851262 ATTTCATTTCGCGTTGCG
1 ATTTCATTTCGCGTTGCG
1851280 ATTCTCATTTCGC
1 ATT-TCATTTCGC
1851293 ATGCGATAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 10 0.27
15 3 0.08
17 2 0.05
18 13 0.35
19 9 0.24
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (18 bp):
ATTTCATTTCGCGTTGCG
Found at i:1851289 original size:19 final size:19
Alignment explanation
Indices: 1851235--1851292 Score: 74
Period size: 14 Copynumber: 3.4 Consensus size: 19
1851225 CGCGAATTTA
1851235 ATTTCGCGTTGCGATTCTC
1 ATTTCGCGTTGCGATTCTC
1851254 ---T--CGTTGCGATT-TC
1 ATTTCGCGTTGCGATTCTC
1851267 ATTTCGCGTTGCGATTCTC
1 ATTTCGCGTTGCGATTCTC
1851286 ATTTCGC
1 ATTTCGC
1851293 ATGCGATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 2 0.06
14 10 0.30
16 2 0.06
18 10 0.30
19 9 0.27
ACGTcount: A:0.10, C:0.26, G:0.21, T:0.43
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTCTC
Found at i:1851297 original size:18 final size:18
Alignment explanation
Indices: 1851258--1851299 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1851248 ATTCTCTCGT
*
1851258 TGCGATTTCATTTCGCGT
1 TGCGATTTCATTTCGCGA
1851276 TGCGATTCTCATTTCGC-A
1 TGCGATT-TCATTTCGCGA
1851294 TGCGAT
1 TGCGAT
1851300 AGTACTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.40
Consensus pattern (18 bp):
TGCGATTTCATTTCGCGA
Found at i:1851425 original size:14 final size:14
Alignment explanation
Indices: 1851406--1851441 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1851396 CATCAATTAA
1851406 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1851420 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1851434 AC-AATCAA
1 ACAAATCAA
1851442 TTAAACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1852810 original size:42 final size:41
Alignment explanation
Indices: 1852751--1852955 Score: 164
Period size: 42 Copynumber: 4.9 Consensus size: 41
1852741 GTGAATCGGG
* *
1852751 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
1852793 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
1852835 CTCTT-CACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
1852876 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
1852918 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
1852956 GCGAGTCGGG
Statistics
Matches: 126, Mismatches: 28, Indels: 18
0.73 0.16 0.10
Matches are distributed among these distances:
40 1 0.01
41 35 0.28
42 82 0.65
43 8 0.06
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:1852817 original size:21 final size:21
Alignment explanation
Indices: 1852751--1852817 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1852741 GTGAATCGGG
*
1852751 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1852771 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1852793 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1852814 CTCT
1 CTCT
1852818 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1852911 original size:83 final size:84
Alignment explanation
Indices: 1852781--1852955 Score: 343
Period size: 83 Copynumber: 2.1 Consensus size: 84
1852771 CCTCTTCAAC
1852781 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTC-ACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1852845 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1852864 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1852929 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1852948 GATGACAG
1 GATGACAG
1852956 GCGAGTCGGG
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 60 0.66
84 31 0.34
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:1853344 original size:90 final size:89
Alignment explanation
Indices: 1853174--1853356 Score: 280
Period size: 90 Copynumber: 2.0 Consensus size: 89
1853164 ATTTCAAACT
*
1853174 TTCAACCAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCA
1 TTCAACCAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGCA
1853239 GAATTGGCAGCAACCGAATAAATTTAC
63 GAATTGGCAGCAACCGAATAAATTTAC
1853266 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTG-T-AATAAACAGTTTAGCA
1 TTCAACC-AAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
1853329 GTATTGGCAGCAACCGAATAAATTTAC
63 GAATTGGCAGCAACCGAATAAATTTAC
1853356 T
1 T
1853357 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
90 42 0.49
92 7 0.08
93 11 0.13
94 1 0.01
95 25 0.29
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (89 bp):
TTCAACCAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGAA
TTGGCAGCAACCGAATAAATTTAC
Found at i:1853765 original size:18 final size:18
Alignment explanation
Indices: 1853738--1853774 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1853728 AGGTGTGTAG
1853738 TGGGTCAGGTGATGGCTC
1 TGGGTCAGGTGATGGCTC
*
1853756 TGGGTGAGGTGATGGCTC
1 TGGGTCAGGTGATGGCTC
1853774 T
1 T
1853775 CGAAGTGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.14, G:0.46, T:0.30
Consensus pattern (18 bp):
TGGGTCAGGTGATGGCTC
Found at i:1854898 original size:33 final size:33
Alignment explanation
Indices: 1854841--1854928 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
1854831 ACGAGATAAT
1854841 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
1854875 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1854908 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
1854929 AAATCACAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 39 0.74
34 14 0.26
ACGTcount: A:0.39, C:0.23, G:0.27, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:1854933 original size:19 final size:19
Alignment explanation
Indices: 1854816--1854980 Score: 143
Period size: 19 Copynumber: 9.1 Consensus size: 19
1854806 TCTTTTGGTT
*
1854816 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1854835 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1854855 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1854873 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1854889 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
1854906 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1854922 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
1854941 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1854960 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1854979 GA
1 GA
1854981 TTTTGGTTTC
Statistics
Matches: 118, Mismatches: 16, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
14 17 0.14
15 2 0.02
16 4 0.03
17 3 0.03
18 3 0.03
19 60 0.51
20 27 0.23
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1855003 original size:19 final size:19
Alignment explanation
Indices: 1854976--1855041 Score: 80
Period size: 18 Copynumber: 3.5 Consensus size: 19
1854966 AAAATCGCAA
**
1854976 TGCGATTTTGGTTTCGCG-
1 TGCGATTTTTATTTCGCGT
1854994 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
1855013 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1855033 TGCGATTTT
1 TGCGATTTT
1855042 CATTCTCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
18 16 0.40
19 12 0.30
20 12 0.30
ACGTcount: A:0.11, C:0.17, G:0.26, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1855033 original size:20 final size:19
Alignment explanation
Indices: 1854987--1855038 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1854977 GCGATTTTGG
**
1854987 TTTCGCG-TGCGATTTTTA
1 TTTCGCGTTGCGATAGTTA
1855005 TTTCGCGTTGCGATAGTTA
1 TTTCGCGTTGCGATAGTTA
1855024 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
1855039 TTTCATTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 7 0.23
19 12 0.40
20 11 0.37
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTTA
Found at i:1855574 original size:20 final size:20
Alignment explanation
Indices: 1855549--1855601 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1855539 GCGCTATGTA
1855549 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1855569 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1855589 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1855602 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1855636 original size:17 final size:19
Alignment explanation
Indices: 1855614--1855659 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
1855604 TTGTATTACG
1855614 CATTGCGATA-TAAGTAT-
1 CATTGCGATAGTAAGTATC
*
1855631 CATTGCGATAGTCAGTATC
1 CATTGCGATAGTAAGTATC
1855650 GCATTGCGAT
1 -CATTGCGAT
1855660 TTTCCCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 10 0.40
18 6 0.24
20 9 0.36
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (19 bp):
CATTGCGATAGTAAGTATC
Found at i:1855656 original size:20 final size:20
Alignment explanation
Indices: 1855550--1855659 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 20
1855540 CGCTATGTAA
* * *
1855550 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
1855570 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * **
1855590 ATCTCGTTGCGAT--TTTGT
1 ATCGCATTGCGATAGTCAGT
*
1855608 ATTACGCATTGCGATA-TAAGT
1 A-T-CGCATTGCGATAGTCAGT
1855629 AT--CATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1855647 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1855660 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
17 10 0.14
18 10 0.14
19 1 0.01
20 49 0.66
21 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1855770 original size:21 final size:21
Alignment explanation
Indices: 1855730--1855770 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1855720 ACTGTAGACC
**
1855730 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1855751 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1855771 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1860490 original size:60 final size:60
Alignment explanation
Indices: 1860366--1860548 Score: 181
Period size: 60 Copynumber: 3.0 Consensus size: 60
1860356 ATATAGTTAG
* * * * * * **
1860366 GGATGCAATTGAAATGTTCAAAAAGTTTAGGGGCTAATTTAAAATGAAGGTCAT-ATTTTG
1 GGATGAAATTGAAATATTC-AAAAGTTTAGAGACTAATTTAGAATGAAGATCATAATTTAA
* * * * * * *
1860426 GGATGGAATTGCAATGTTCAAAAGTTT-GAGAATTAGTTTAGAATGACGATCATAGTTTAA
1 GGATGAAATTGAAATATTCAAAAGTTTAGAG-ACTAATTTAGAATGAAGATCATAATTTAA
* *
1860486 GGATGAAATTGAAATATTTAAAAGTTTAGAGACTAATTTAGAATGAAGATCATAATTTGA
1 GGATGAAATTGAAATATTCAAAAGTTTAGAGACTAATTTAGAATGAAGATCATAATTTAA
1860546 GGA
1 GGA
1860549 CATGAGATAC
Statistics
Matches: 99, Mismatches: 21, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
58 2 0.02
59 24 0.24
60 70 0.71
61 3 0.03
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.33
Consensus pattern (60 bp):
GGATGAAATTGAAATATTCAAAAGTTTAGAGACTAATTTAGAATGAAGATCATAATTTAA
Found at i:1861371 original size:20 final size:20
Alignment explanation
Indices: 1861335--1861372 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1861325 ATCCTATTAC
**
1861335 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1861355 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1861373 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1864186 original size:20 final size:21
Alignment explanation
Indices: 1864146--1864209 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 21
1864136 CTTTAAAACA
1864146 TATAATATTATAAATATATTT
1 TATAATATTATAAATATATTT
1864167 TATAAT-TT-TAAATAATATTT
1 TATAATATTATAAAT-ATATTT
**
1864187 TATTTTATTAT--AT-TATTT
1 TATAATATTATAAATATATTT
1864205 TATAA
1 TATAA
1864210 ATTTTACTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
18 8 0.22
19 5 0.14
20 14 0.39
21 8 0.22
22 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATAATATTATAAATATATTT
Found at i:1870240 original size:2 final size:2
Alignment explanation
Indices: 1870233--1870257 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1870223 AGCAAAATGA
1870233 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1870258 ATTTAGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1875535 original size:42 final size:42
Alignment explanation
Indices: 1875418--1875537 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
1875408 TTTCCCCGAA
* *
1875418 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1875460 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1875502 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1875538 TGTAATTCAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:1875771 original size:26 final size:24
Alignment explanation
Indices: 1875709--1875771 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
1875699 CATTTTCATC
1875709 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
1875733 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
1875756 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
1875772 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:1875773 original size:22 final size:23
Alignment explanation
Indices: 1875726--1875786 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
1875716 TAATTATTAA
* *
1875726 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
1875747 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
1875770 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
1875787 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:1875849 original size:54 final size:52
Alignment explanation
Indices: 1875752--1875854 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 52
1875742 TTATTAATAT
*
1875752 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATA
1 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
* *
1875804 TTATATTAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAATT
1 TTATAATAATAT-A-ATATTATATTTTTAATATTATATAA-A-ATAATAAATT
1875855 TTTTTTATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
52 15 0.34
53 7 0.16
54 22 0.50
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (52 bp):
TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
Found at i:1875859 original size:29 final size:30
Alignment explanation
Indices: 1875812--1875905 Score: 77
Period size: 31 Copynumber: 3.1 Consensus size: 30
1875802 TATTATATTA
* *
1875812 ATATAAGATATTATATTTTTATTTTAATAAT
1 ATATAATA-ATTATTTTTTTATTTTAATAAT
1875843 ATATAATAAATT-TTTTTTATATATTTAATAAT
1 ATATAAT-AATTATTTTTT-TAT-TTTAATAAT
* * *
1875875 GA-ATAATAA-TATTTATATATTTCAATAAT
1 -ATATAATAATTATTTTTTTATTTTAATAAT
1875904 AT
1 AT
1875906 TTTAGTAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
28 1 0.02
29 8 0.15
30 9 0.17
31 18 0.35
32 15 0.29
33 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (30 bp):
ATATAATAATTATTTTTTTATTTTAATAAT
Found at i:1875881 original size:32 final size:31
Alignment explanation
Indices: 1875827--1875888 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
1875817 AGATATTATA
1875827 TTTTTATTTTAATAATATATAATAA-ATTTT
1 TTTTTATTTTAATAATATATAATAATATTTT
1875857 TTTTATATATTTAATAATGA-ATAATAATATTT
1 TTTT-TAT-TTTAATAAT-ATATAATAATATTT
1875889 ATATATTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 4 0.14
31 3 0.11
32 16 0.57
33 5 0.18
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (31 bp):
TTTTTATTTTAATAATATATAATAATATTTT
Found at i:1876149 original size:20 final size:20
Alignment explanation
Indices: 1876071--1876140 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
1876061 TTTCCAGATG
*
1876071 TTTTTCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1876091 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
1876111 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1876131 TTTTCCAGAA
1 TTTTCCAGAA
1876141 TTCAAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:1876149 original size:40 final size:40
Alignment explanation
Indices: 1876071--1876149 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
1876061 TTTCCAGATG
* **
1876071 TTTTTCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
1876111 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
1876150 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:1876159 original size:15 final size:15
Alignment explanation
Indices: 1876123--1876204 Score: 94
Period size: 15 Copynumber: 5.5 Consensus size: 15
1876113 TTACAGAAAT
**
1876123 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1876138 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
** *
1876152 GTAATTCATTTTTCA
1 GTAATTCAAATTCCA
*
1876167 GTAATTCAAATTCTA
1 GTAATTCAAATTCCA
*
1876182 GTAATTCAAATTTCA
1 GTAATTCAAATTCCA
1876197 GTAATTCA
1 GTAATTCA
1876205 TTTTCTGGAA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
14 12 0.22
15 43 0.78
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.41
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:1876173 original size:30 final size:30
Alignment explanation
Indices: 1876123--1876204 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
1876113 TTACAGAAAT
*
1876123 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTTCAGTAATTCAAATTCCA
*
1876152 GTAATTCATTTTTCAGTAATTCAAATTCTA
1 GTAATTCATTTTTCAGTAATTCAAATTCCA
**
1876182 GTAATTCAAATTTCAGTAATTCA
1 GTAATTCATTTTTCAGTAATTCA
1876205 TTTTCTGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 15 0.31
30 33 0.69
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTTCAGTAATTCAAATTCCA
Found at i:1877360 original size:2 final size:2
Alignment explanation
Indices: 1877353--1877380 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1877343 AGGGTAAACC
1877353 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1877381 GATCGTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1877976 original size:2 final size:2
Alignment explanation
Indices: 1877969--1878019 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1877959 GTAATTTATC
1877969 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1878011 AT AT AT AT A
1 AT AT AT AT A
1878020 AAGCCGTGAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1878672 original size:18 final size:17
Alignment explanation
Indices: 1878645--1878686 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
1878635 TTTAAACTAA
1878645 TTTTTATCAAAATTTCAT
1 TTTTTATC-AAATTTCAT
*
1878663 TTTTTTTCAAATTTCAT
1 TTTTTATCAAATTTCAT
1878680 TTTTTAT
1 TTTTTAT
1878687 TATCAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTATCAAATTTCAT
Found at i:1879347 original size:27 final size:27
Alignment explanation
Indices: 1879317--1879374 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
1879307 AATTGTTCAA
* *
1879317 CTTCAGCATTCAATCATACTCTGGATT
1 CTTCAACATTCAATAATACTCTGGATT
*
1879344 CTTCAACATTCAATAATAGTCTGGATT
1 CTTCAACATTCAATAATACTCTGGATT
1879371 CTTC
1 CTTC
1879375 TTGATAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (27 bp):
CTTCAACATTCAATAATACTCTGGATT
Found at i:1881521 original size:20 final size:20
Alignment explanation
Indices: 1881469--1881522 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1881459 AATTTAATAT
*
1881469 TATTATTTTTAAAATATTAAAA
1 TATTATTTTT--ATTATTAAAA
*
1881491 TAATT-TATTTATTATTAAAA
1 T-ATTATTTTTATTATTAAAA
1881511 TATTATTTTTAT
1 TATTATTTTTAT
1881523 AATTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.11
20 16 0.59
22 5 0.19
23 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTTTATTATTAAAA
Found at i:1881587 original size:31 final size:29
Alignment explanation
Indices: 1881479--1881588 Score: 77
Period size: 28 Copynumber: 3.7 Consensus size: 29
1881469 TATTATTTTT
*
1881479 AAAATATTAAAATAATT-TA-TTTATT-ATT
1 AAAATATT--AATAATTATATTTTATTAATA
**
1881507 AAAATATT-ATTTTTATAATTTTATTAATA
1 AAAATATTAATAATTAT-ATTTTATTAATA
*
1881536 AAAATATTAATATTGGTATATTTTATTGAAATA
1 AAAATATTAATAAT--TATATTTTATT--AATA
1881569 AAAATATT-ATAAATTATATT
1 AAAATATTAAT-AATTATATT
1881589 AATTATTTAT
Statistics
Matches: 67, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
25 4 0.06
26 1 0.01
27 1 0.01
28 14 0.21
29 10 0.15
30 4 0.06
31 14 0.21
32 5 0.07
33 14 0.21
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
AAAATATTAATAATTATATTTTATTAATA
Found at i:1881646 original size:23 final size:23
Alignment explanation
Indices: 1881618--1881690 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
1881608 AGTGTTATAT
1881618 TATATTTTTAAATTATTTATTAA
1 TATATTTTTAAATTATTTATTAA
*
1881641 TATA-TTTTAAATATCTTTATTAA
1 TATATTTTTAAAT-TATTTATTAA
* * *
1881664 AATATTATTAGATTATTATATTAA
1 TATATTTTTAAATTATT-TATTAA
1881688 TAT
1 TAT
1881691 TAAATATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
22 8 0.20
23 19 0.46
24 14 0.34
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (23 bp):
TATATTTTTAAATTATTTATTAA
Found at i:1881877 original size:21 final size:23
Alignment explanation
Indices: 1881851--1881925 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 23
1881841 TTATTTTATT
1881851 ATATTA-TT-AAAATA-TAATATA
1 ATATTATTTAAAAATATTAATA-A
1881872 ATATTATTTAAAAATATTAATAA
1 ATATTATTTAAAAATATTAATAA
* * *
1881895 ATA-TATTTTAATATTTTAATAA
1 ATATTATTTAAAAATATTAATAA
* *
1881917 TTAATATTT
1 ATATTATTT
1881926 TGATTAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
21 6 0.13
22 20 0.43
23 15 0.33
24 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATTATTTAAAAATATTAATAA
Found at i:1881878 original size:34 final size:34
Alignment explanation
Indices: 1881785--1881880 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 34
1881775 TAATTTATTA
* * *
1881785 TATATTATTAAAATAAAAATATAATA-TCTTATAT
1 TATATTATTAAAAT-ATAATATAATATTATTTTAT
* *
1881819 TATATTATTATAATATAAT-T--GATTATTTTAT
1 TATATTATTAAAATATAATATAATATTATTTTAT
1881850 TATATTATTAAAATATAATATAATATTATTT
1 TATATTATTAAAATATAATATAATATTATTT
1881881 AAAAATATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
30 1 0.02
31 24 0.47
32 2 0.04
33 4 0.08
34 20 0.39
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (34 bp):
TATATTATTAAAATATAATATAATATTATTTTAT
Found at i:1884042 original size:37 final size:36
Alignment explanation
Indices: 1883967--1884044 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 36
1883957 AAAAAGGTTA
* * * *
1883967 AATATCTATTTTTTGTCTTGATTAGATATTTAATTT
1 AATATCTATTTTTTGTCATGATTAAATATTAAAATT
1884003 AATATCTATTTTTTGTCATGATTAAATATATAAAATT
1 AATATCTATTTTTTGTCATGATTAAATAT-TAAAATT
1884040 AATAT
1 AATAT
1884045 GTATATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 27 0.73
37 10 0.27
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.53
Consensus pattern (36 bp):
AATATCTATTTTTTGTCATGATTAAATATTAAAATT
Found at i:1887280 original size:17 final size:16
Alignment explanation
Indices: 1887254--1887287 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1887244 TCTTTAAAGG
*
1887254 AAGAAGATAAAATTAAA
1 AAGAAAATAAAA-TAAA
1887271 AAGAAAATAAAATAAA
1 AAGAAAATAAAATAAA
1887287 A
1 A
1887288 TAACGTGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAGAAAATAAAATAAA
Found at i:1888283 original size:31 final size:31
Alignment explanation
Indices: 1888245--1888304 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1888235 TACAAGATAT
*
1888245 TTGAGCGTTCATTGTTAAATGATTGAGAGTC
1 TTGAGCGTTCATTGTTAAATAATTGAGAGTC
1888276 TTGAGCGTTCATTGTTAAATAATTGAGAG
1 TTGAGCGTTCATTGTTAAATAATTGAGAG
1888305 GTTTTAGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.38
Consensus pattern (31 bp):
TTGAGCGTTCATTGTTAAATAATTGAGAGTC
Found at i:1889391 original size:42 final size:42
Alignment explanation
Indices: 1889329--1889414 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
1889319 CCACGACCCT
* *
1889329 AAGGTTAAGAACCTTGTATTCTACCAACTGAACTGGATGGTA
1 AAGGTTAAGAACCTTATATTCTACCAACTGAACTGGATAGTA
*
1889371 AAGGTTAAGAACCTTATATTCTACCAACTGAGCTGGATAGTA
1 AAGGTTAAGAACCTTATATTCTACCAACTGAACTGGATAGTA
1889413 AA
1 AA
1889415 AAGAAGAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (42 bp):
AAGGTTAAGAACCTTATATTCTACCAACTGAACTGGATAGTA
Found at i:1889442 original size:15 final size:15
Alignment explanation
Indices: 1889418--1889451 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1889408 TAGTAAAAAG
1889418 AAGAAAAAGAAGAAA
1 AAGAAAAAGAAGAAA
*
1889433 AAGAAGAAGAAGAAA
1 AAGAAAAAGAAGAAA
1889448 AAGA
1 AAGA
1889452 CTCATTTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAAGAAA
Found at i:1889451 original size:9 final size:9
Alignment explanation
Indices: 1889412--1889446 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
1889402 GCTGGATAGT
1889412 AAAAAGAAG
1 AAAAAGAAG
1889421 AAAAAGAAG
1 AAAAAGAAG
1889430 AAAAAGAAG
1 AAAAAGAAG
*
1889439 AAGAAGAA
1 AAAAAGAA
1889447 AAAGACTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:1890329 original size:22 final size:22
Alignment explanation
Indices: 1890278--1890335 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1890268 TCTTATTAAG
1890278 AGAGTAACTTTTTAGAAAGTAC
1 AGAGTAACTTTTTAGAAAGTAC
* * * * *
1890300 AAAATAACTTTTTAGGATGTAT
1 AGAGTAACTTTTTAGAAAGTAC
1890322 AGAGTAACTTTTTA
1 AGAGTAACTTTTTA
1890336 TGTTGGACAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.38
Consensus pattern (22 bp):
AGAGTAACTTTTTAGAAAGTAC
Found at i:1891361 original size:18 final size:20
Alignment explanation
Indices: 1891326--1891362 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1891316 CACGGAATGT
1891326 AAGATTATCAGTGGGAATAA
1 AAGATTATCAGTGGGAATAA
1891346 AAGATTAT-AG-GGGAATA
1 AAGATTATCAGTGGGAATA
1891363 GAATTACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 2 0.12
20 8 0.47
ACGTcount: A:0.46, C:0.03, G:0.27, T:0.24
Consensus pattern (20 bp):
AAGATTATCAGTGGGAATAA
Found at i:1893479 original size:22 final size:22
Alignment explanation
Indices: 1893451--1893505 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1893441 ACCATATACT
1893451 TCGTACCCTTTCGTTTCCAAGA
1 TCGTACCCTTTCGTTTCCAAGA
1893473 TCGTACCCTTTCGTTTCCAAGA
1 TCGTACCCTTTCGTTTCCAAGA
**
1893495 TCCAACCCTTT
1 TCGTACCCTTT
1893506 TTCTTTCTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.18, C:0.35, G:0.11, T:0.36
Consensus pattern (22 bp):
TCGTACCCTTTCGTTTCCAAGA
Found at i:1897362 original size:2 final size:2
Alignment explanation
Indices: 1897355--1897400 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1897345 TTAGTCCGTG
*
1897355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1897397 AT AT
1 AT AT
1897401 GCCATTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1900412 original size:13 final size:13
Alignment explanation
Indices: 1900394--1900418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1900384 TTTAAATAGG
1900394 TTTAATGAGATTT
1 TTTAATGAGATTT
1900407 TTTAATGAGATT
1 TTTAATGAGATT
1900419 CATGGGATGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TTTAATGAGATTT
Found at i:1908135 original size:21 final size:21
Alignment explanation
Indices: 1908110--1908149 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1908100 AAGACTCTAT
1908110 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
1908131 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
1908150 AAACATTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:1911996 original size:20 final size:21
Alignment explanation
Indices: 1911936--1911996 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1911926 AAATTTTAGT
*
1911936 GCAGGAGGAATCGATACCCCTT
1 GCAGG-GGAATCGATACCCCTC
* * *
1911958 GCAGGGGAACCGTTTCCCCTC
1 GCAGGGGAATCGATACCCCTC
*
1911979 GTA-GGGAATCGATACCCC
1 GCAGGGGAATCGATACCCC
1911997 CCACGGGCTC
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
20 12 0.39
21 14 0.45
22 5 0.16
ACGTcount: A:0.23, C:0.31, G:0.28, T:0.18
Consensus pattern (21 bp):
GCAGGGGAATCGATACCCCTC
Found at i:1912171 original size:19 final size:19
Alignment explanation
Indices: 1912149--1912196 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
1912139 ATCATCTACT
* * *
1912149 AAATCTGCTAGCATCATTA
1 AAATCTGCTAACAACATCA
*
1912168 AAATCGTGCAAACAACATCA
1 AAATC-TGCTAACAACATCA
1912188 AAATCTGCT
1 AAATCTGCT
1912197 CAATCTTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (19 bp):
AAATCTGCTAACAACATCA
Found at i:1912472 original size:13 final size:13
Alignment explanation
Indices: 1912454--1912487 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1912444 CGTATATTGA
1912454 TTTTCAAACCTT-G
1 TTTTCAAA-CTTAG
1912467 TTTTCAAACTTAG
1 TTTTCAAACTTAG
1912480 TTTTCAAA
1 TTTTCAAA
1912488 ATTTCCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 3 0.15
13 17 0.85
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (13 bp):
TTTTCAAACTTAG
Found at i:1917993 original size:2 final size:2
Alignment explanation
Indices: 1917988--1918013 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1917978 ACATGTAACC
1917988 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1918014 TCAGACATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1930304 original size:21 final size:21
Alignment explanation
Indices: 1930279--1930318 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1930269 CCGTTAGACA
1930279 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
*
1930300 GGGGGAATCTGTACCCCCT
1 GGGGGAATCGGTACCCCCT
1930319 AGACATTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.30, G:0.38, T:0.17
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:1931414 original size:21 final size:21
Alignment explanation
Indices: 1931298--1931414 Score: 62
Period size: 21 Copynumber: 5.7 Consensus size: 21
1931288 ACGCGAAATA
**
1931298 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
1931318 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
1931338 -AAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
1931358 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* * **
1931379 AAATTTGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
1931400 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1931415 ACACATAAAT
Statistics
Matches: 68, Mismatches: 24, Indels: 9
0.67 0.24 0.09
Matches are distributed among these distances:
19 10 0.15
20 16 0.24
21 42 0.62
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:1931426 original size:20 final size:20
Alignment explanation
Indices: 1931401--1931574 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
1931391 CGATTTTCCA
* *
1931401 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1931421 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1931441 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1931461 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1931481 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1931501 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1931521 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1931541 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1931562 AAATCGCAACGCG
1 AAATCGCAACGCG
1931575 ATATTTAAAG
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.01
20 113 0.86
21 17 0.13
22 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1931914 original size:10 final size:10
Alignment explanation
Indices: 1931899--1931942 Score: 72
Period size: 10 Copynumber: 4.5 Consensus size: 10
1931889 TTTTCATATT
1931899 GAAAACTTAA
1 GAAAACTTAA
1931909 GAAAACTTAA
1 GAAAACTTAA
*
1931919 GAAAA-ATAA
1 GAAAACTTAA
1931928 GAAAACTTAA
1 GAAAACTTAA
1931938 GAAAA
1 GAAAA
1931943 ATAAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 8 0.26
10 23 0.74
ACGTcount: A:0.66, C:0.07, G:0.11, T:0.16
Consensus pattern (10 bp):
GAAAACTTAA
Found at i:1931930 original size:19 final size:19
Alignment explanation
Indices: 1931906--1931946 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1931896 ATTGAAAACT
1931906 TAAGAAAACTTAAGAAAAA
1 TAAGAAAACTTAAGAAAAA
1931925 TAAGAAAACTTAAGAAAAA
1 TAAGAAAACTTAAGAAAAA
1931944 TAA
1 TAA
1931947 AAATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (19 bp):
TAAGAAAACTTAAGAAAAA
Found at i:1932906 original size:14 final size:14
Alignment explanation
Indices: 1932887--1932922 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1932877 ATTGTTTAAT
1932887 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1932901 TGATTTGTATAAGT
1 TGATTTGTAAAAGA
1932915 TGATTTGT
1 TGATTTGT
1932923 GTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1933045 original size:19 final size:19
Alignment explanation
Indices: 1933029--1933126 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1933019 AAAAATGACT
1933029 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1933048 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1933067 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
1933081 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1933100 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1933120 ATCGCAA
1 ATCGCAA
1933127 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1933158 original size:53 final size:53
Alignment explanation
Indices: 1933029--1933144 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
1933019 AAAAATGACT
*
1933029 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1933081 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1933134 ATCGCAATGCG
1 ATCGCAATGCG
1933145 TTTATAATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1933197 original size:19 final size:19
Alignment explanation
Indices: 1933173--1933336 Score: 187
Period size: 19 Copynumber: 9.4 Consensus size: 19
1933163 GATTCTCTCG
1933173 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1933192 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1933211 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1933225 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1933244 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1933263 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
1933277 TTGCGATTTTCATTCCGCA
1 TTGCGATTTTCATTTCGCA
1933296 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
1933310 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1933329 TTGCGATT
1 TTGCGATT
1933337 CTCTCGTTGC
Statistics
Matches: 122, Mismatches: 8, Indels: 30
0.76 0.05 0.19
Matches are distributed among these distances:
14 23 0.19
16 16 0.13
17 14 0.11
19 69 0.57
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1933336 original size:52 final size:52
Alignment explanation
Indices: 1933151--1933308 Score: 307
Period size: 52 Copynumber: 3.0 Consensus size: 52
1933141 TGCGTTTATA
1933151 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1933203 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1933255 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1933307 AT
1 AT
1933309 GTTGGGATTT
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 105 1.00
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1933358 original size:33 final size:33
Alignment explanation
Indices: 1933151--1933350 Score: 210
Period size: 33 Copynumber: 5.9 Consensus size: 33
1933141 TGCGTTTATA
1933151 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
1933184 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
1933224 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1933255 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* * *
1933288 ATTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTTCGCATTGCGATTCTC-TCGTTGCGATTTTC
1933321 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1933351 GTAATTTCCG
Statistics
Matches: 136, Mismatches: 18, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
31 9 0.07
32 6 0.04
33 89 0.65
34 1 0.01
35 5 0.04
36 4 0.03
37 2 0.01
38 8 0.06
39 3 0.02
40 9 0.07
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:1935647 original size:12 final size:12
Alignment explanation
Indices: 1935630--1935654 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1935620 TCTTCGGGGA
1935630 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1935642 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1935654 C
1 C
1935655 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1935863 original size:24 final size:24
Alignment explanation
Indices: 1935829--1935875 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1935819 CTGAAACATC
1935829 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1935853 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1935876 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1936787 original size:20 final size:20
Alignment explanation
Indices: 1936557--1936786 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
1936547 AAATTTCAGT
* * *
1936557 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* *
1936577 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* *
1936597 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1936617 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1936637 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1936657 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1936677 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
1936697 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1936717 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1936737 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1936757 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1936777 GTTGCGATTT
1 GTTGCGATTT
1936787 TGGAAAATCG
Statistics
Matches: 186, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 185 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1936803 original size:21 final size:21
Alignment explanation
Indices: 1936773--1936855 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1936763 ATTTTCATAT
*
1936773 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1936794 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1936815 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1936836 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1936856 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1936846 original size:42 final size:43
Alignment explanation
Indices: 1936753--1936851 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1936743 ATTTATGTGT
* *
1936753 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1936794 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1936836 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1936852 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Done.