Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009065.1 Hibiscus syriacus cultivar Beakdansim tig00112488_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: 1198333
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:410152 original size:88 final size:88
Alignment explanation
Indices: 410048--410222 Score: 350
Period size: 88 Copynumber: 2.0 Consensus size: 88
410038 GTATGGTACC
410048 TATGGATTTAGACGGATACCGTTTAGACTGTGTAATGCTCCAGCTACATTCCAAATATGCATGAT
1 TATGGATTTAGACGGATACCGTTTAGACTGTGTAATGCTCCAGCTACATTCCAAATATGCATGAT
410113 GGCAATCTTTTCAGATATGATGG
66 GGCAATCTTTTCAGATATGATGG
410136 TATGGATTTAGACGGATACCGTTTAGACTGTGTAATGCTCCAGCTACATTCCAAATATGCATGAT
1 TATGGATTTAGACGGATACCGTTTAGACTGTGTAATGCTCCAGCTACATTCCAAATATGCATGAT
410201 GGCAATCTTTTCAGATATGATG
66 GGCAATCTTTTCAGATATGATG
410223 AAAGAATGCA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (88 bp):
TATGGATTTAGACGGATACCGTTTAGACTGTGTAATGCTCCAGCTACATTCCAAATATGCATGAT
GGCAATCTTTTCAGATATGATGG
Found at i:419339 original size:36 final size:34
Alignment explanation
Indices: 419272--419388 Score: 162
Period size: 36 Copynumber: 3.2 Consensus size: 34
419262 GTTGTCGCCT
419272 TTGAGACAATTTCTTTTAAAAACAAATTTTGTCTCAC
1 TTGAGACAATTTC--TT-AAAACAAATTTTGTCTCAC
*
419309 TTGAGACAGATTTCTTAATAACAAATTTTGTCTCGC
1 TTGAGACA-ATTTCTTAA-AACAAATTTTGTCTCAC
419345 TTGAGACAATTTCTCTCAAAACAAATTTTGTCTCAC
1 TTGAGACAATTTCT-T-AAAACAAATTTTGTCTCAC
419381 TTGAGACA
1 TTGAGACA
419389 GTTTTTCTCG
Statistics
Matches: 74, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
35 8 0.11
36 51 0.69
37 10 0.14
38 5 0.07
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (34 bp):
TTGAGACAATTTCTTAAAACAAATTTTGTCTCAC
Found at i:419407 original size:38 final size:36
Alignment explanation
Indices: 419293--419410 Score: 148
Period size: 36 Copynumber: 3.2 Consensus size: 36
419283 TCTTTTAAAA
* *
419293 ACAAATTTTGTCTCACTTGAGACAG-ATTTCTTAAT
1 ACAAATTTTGTCTCACTTGAGACAGTTTTTCTCAAT
* * * *
419328 AACAAATTTTGTCTCGCTTGAGACAATTTCTCTCAAA
1 -ACAAATTTTGTCTCACTTGAGACAGTTTTTCTCAAT
419365 ACAAATTTTGTCTCACTTGAGACAGTTTTTCTCGGAAT
1 ACAAATTTTGTCTCACTTGAGACAGTTTTTCTC--AAT
419403 ACAAATTT
1 ACAAATTT
419411 CAAAATTATT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
36 53 0.77
37 6 0.09
38 10 0.14
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (36 bp):
ACAAATTTTGTCTCACTTGAGACAGTTTTTCTCAAT
Found at i:419619 original size:66 final size:66
Alignment explanation
Indices: 419537--419827 Score: 297
Period size: 66 Copynumber: 4.4 Consensus size: 66
419527 CAAAAGTTAT
*
419537 AATCTTTGAGTCTGTTTCTCTTGAAAGAAATTTTGTCTCCCTTGAGACCCTTTCTCATGAAACAC
1 AATCTTTGAGTCTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACCCTTTCTCATGAAACAC
419602 C
66 C
* *
419603 AATCTTTGAGTCTGTTTCT-TTCGAAACAAATTTTGTCTCCCTTGAGATCGTTTCTCATGAAACA
1 AATCTTTGAGTCTGTTTCTCTT-GAAACAAATTTTGTCTCCCTTGAGACCCTTTCTCATGAAACA
419667 CC
65 CC
* * * *** * * *
419669 AATCTTTGAGTCTATTTCTCTTGAAACAAATTTTGTATCTCTTGAGATAGTTTATCTTCAAACAC
1 AATCTTTGAGTCTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACCCTTTCTCATGAAACAC
419734 TC
66 -C
* * * * * * * *
419736 -ATCTTTGAGATC-ATTTCCCTTGAAACAAATTTTTGTCTCTCGTGATACAGC-TTCTCTTGAAG
1 AATCTTTGAG-TCTGTTTCTCTTGAAACAAA-TTTTGTCTCCCTTGAGAC-CCTTTCTCATGAAA
*
419798 CATC
63 CACC
419802 -ATCTTTGAGTC-GCTTTCTCTTGAAAC
1 AATCTTTGAGTCTG-TTTCTCTTGAAAC
419828 CATTATCCCT
Statistics
Matches: 195, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
65 4 0.02
66 162 0.83
67 29 0.15
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (66 bp):
AATCTTTGAGTCTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACCCTTTCTCATGAAACAC
C
Found at i:419621 original size:30 final size:30
Alignment explanation
Indices: 419587--419696 Score: 75
Period size: 30 Copynumber: 3.5 Consensus size: 30
419577 CTTGAGACCC
419587 TTTCTCATGAAACACCAATCTTTGAGTCTG
1 TTTCTCATGAAACACCAATCTTTGAGTCTG
*
419617 TTTCT-TTCGAAACA--AATTTTGTCTCCCTTGAGATC-G
1 TTTCTCAT-GAAACACCAA-----TCT---TTGAG-TCTG
*
419653 TTTCTCATGAAACACCAATCTTTGAGTCTA
1 TTTCTCATGAAACACCAATCTTTGAGTCTG
*
419683 TTTCTCTTGAAACA
1 TTTCTCATGAAACA
419697 AATTTTGTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 28
0.66 0.04 0.30
Matches are distributed among these distances:
28 2 0.03
29 3 0.05
30 29 0.47
33 6 0.10
36 17 0.27
37 3 0.05
38 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (30 bp):
TTTCTCATGAAACACCAATCTTTGAGTCTG
Found at i:420125 original size:91 final size:88
Alignment explanation
Indices: 419937--420131 Score: 248
Period size: 91 Copynumber: 2.2 Consensus size: 88
419927 TAACCGGTCA
* * * * * *
419937 TCCTCATCAGGTAGTAACTGTGTTATCATCCCTAAAGATGGCCTGCCATCTTCATTGCGTAAGAA
1 TCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGCCTACCATCCTCATTGCATAAGAA
420002 CAGTGTCATCCCCTGACCAGACC
66 CAGTGTCATCCCCTGACCAGACC
* * *
420025 TCCTTATCACGTAGGAACCGTGTTATCACCCTCTCTAAAGATGGCCTACCATCCTCATTGCATAG
1 TCCTCATCACGTAGGAACCGTGTTATCA---TCCCTAAAGATGGCCTACCATCCTCATTGCATAA
* *
420090 GAACTGTGTCATCCACC-GACCAGATC
63 GAACAGTGTCATCC-CCTGACCAGACC
420116 TCCTCATCACGTAGGA
1 TCCTCATCACGTAGGA
420132 GCTATGTCAT
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
88 24 0.26
91 65 0.71
92 2 0.02
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (88 bp):
TCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGCCTACCATCCTCATTGCATAAGAA
CAGTGTCATCCCCTGACCAGACC
Found at i:428217 original size:39 final size:40
Alignment explanation
Indices: 428173--428278 Score: 151
Period size: 40 Copynumber: 2.7 Consensus size: 40
428163 ATACCTAAAG
* * *
428173 TTTAATTTTTGTTTTATTTTAGTATCC-GCCATTAAAAAC
1 TTTAATTTTTGTTTCATTTTAGTACCCTACCATTAAAAAC
* *
428212 TTTAATCTTTGTTTCATTTTAGTACCCTACCGTTAAAAAC
1 TTTAATTTTTGTTTCATTTTAGTACCCTACCATTAAAAAC
*
428252 TTTAGTTTTTGTTTCATTTTAGTACCC
1 TTTAATTTTTGTTTCATTTTAGTACCC
428279 GTTCAAAATT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
39 24 0.41
40 35 0.59
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.51
Consensus pattern (40 bp):
TTTAATTTTTGTTTCATTTTAGTACCCTACCATTAAAAAC
Found at i:430718 original size:18 final size:18
Alignment explanation
Indices: 430678--430712 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
430668 TGTTTTTAAA
*
430678 ATAAAAGATAAGAATTAG
1 ATAAAAGAAAAGAATTAG
*
430696 ATAAAAGAAAATAATTA
1 ATAAAAGAAAAGAATTA
430713 ATTAAATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (18 bp):
ATAAAAGAAAAGAATTAG
Found at i:434303 original size:21 final size:21
Alignment explanation
Indices: 434279--434338 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
434269 ATTCCCCGTG
434279 AAAAAGGATCGATCCCTTTCA
1 AAAAAGGATCGATCCCTTTCA
* * *
434300 AAAAAAGATCGATCTCTTTTA
1 AAAAAGGATCGATCCCTTTCA
* *
434321 AAAGAGGATTGATCCCTT
1 AAAAAGGATCGATCCCTT
434339 CACTATTGAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (21 bp):
AAAAAGGATCGATCCCTTTCA
Found at i:443141 original size:46 final size:46
Alignment explanation
Indices: 443058--443558 Score: 538
Period size: 46 Copynumber: 11.0 Consensus size: 46
443048 TATATGTCGT
* * * **
443058 TAATATACCATTATGTATTTTCATTGGTGGCATCATTTCATGCC-A
1 TAATGTACCGTTATGCATTTTCATTTATGGCATCATTTCATGCCTA
* *
443103 -ACTGGTTACCGTTAAGCATTTTCATTTATGGCATCATTTCATGCCTA
1 TAAT-G-TACCGTTATGCATTTTCATTTATGGCATCATTTCATGCCTA
* * *
443150 TAATGTACCTTTATGCATTTTCATTTGTGGCATCATTTCATGCCGA
1 TAATGTACCGTTATGCATTTTCATTTATGGCATCATTTCATGCCTA
* ** *
443196 TAATGCATTGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTA
1 TAATGTACCGTTATGCATTTTCATTTATGGCATCATTTCATGCCTA
*
443242 TAATG-ACTG-TATGCATTTTCATTTATGGCATCATTTCATGCCTA
1 TAATGTACCGTTATGCATTTTCATTTATGGCATCATTTCATGCCTA
* * * * *
443286 TAA-GCACCATTATGCATTTTCATTCATGGCATCCTTTCATGCCGA
1 TAATGTACCGTTATGCATTTTCATTTATGGCATCATTTCATGCCTA
* * * *
443331 TAATGCACCATTATGCATTTTCATTTATGGCATCCTTCCATGCC--
1 TAATGTACCGTTATGCATTTTCATTTATGGCATCATTTCATGCCTA
* *
443375 TAA-G--GC-TTATGCATTTTCATTTATGGCATCCTTTCATGCCTA
1 TAATGTACCGTTATGCATTTTCATTTATGGCATCATTTCATGCCTA
* *
443417 TAATGAACTGTTATGCATTTTCATTTATGGCATCATTTCATGCCTA
1 TAATGTACCGTTATGCATTTTCATTTATGGCATCATTTCATGCCTA
* * * * *
443463 TAATGCACCATTATGTATTCATTTTCATTCATGGCATCCTTTCATGCCGA
1 TAATGTACCGTTATG----CATTTTCATTTATGGCATCATTTCATGCCTA
* * * *
443513 TAATGCACCATTATGCATTTTCATTTATGGCATCCTTCCATGCCTA
1 TAATGTACCGTTATGCATTTTCATTTATGGCATCATTTCATGCCTA
443559 AGGCATTTCA
Statistics
Matches: 397, Mismatches: 42, Indels: 33
0.84 0.09 0.07
Matches are distributed among these distances:
40 33 0.08
41 1 0.00
42 3 0.01
43 3 0.01
44 44 0.11
45 38 0.10
46 228 0.57
47 2 0.01
48 2 0.01
50 43 0.11
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (46 bp):
TAATGTACCGTTATGCATTTTCATTTATGGCATCATTTCATGCCTA
Found at i:443488 original size:227 final size:226
Alignment explanation
Indices: 443064--443556 Score: 640
Period size: 227 Copynumber: 2.2 Consensus size: 226
443054 TCGTTAATAT
* ** * * * *
443064 ACCATTATGTATTTTCATTGGTGGCATCATTTCATGCCAACTGGTTACCGTTAAGCATTTTCATT
1 ACCATTATGCATTTTCATTCATGGCATCCTTTCATGCCAAATGGTCACCATTAAGCATTTTCATT
* *
443129 TATGGCATCATTTCATGCCTATAATGTACCTTTATGCATTTTCATTTGTGGCATCATTTCATGCC
66 TATGGCATCATTCCATGCC-ATAATG-ACCTTTATGCATTTTCATTTATGGCATCATTTCATGCC
* * *
443194 GATAATGCATTGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGACTGTATGCATT
129 GATAATGAACTGTTATGCATTTTCATTTATGGCATCATTTCATGCCTATAATGACTGTATGCATT
* *
443259 TTCATTTATGGCATCATTTCATGCCTATAA-GC
194 TTCATTCATGGCATCATTTCATGCCGATAATGC
*
443291 ACCATTATGCATTTTCATTCATGGCATCCTTTCATGCCGATAAT-G-CACCATTATGCATTTTCA
1 ACCATTATGCATTTTCATTCATGGCATCCTTTCATGCC-A-AATGGTCACCATTAAGCATTTTCA
* * *
443354 TTTATGGCATCCTTCCATGCC-TAA-G-GC-TTATGCATTTTCATTTATGGCATCCTTTCATGCC
64 TTTATGGCATCATTCCATGCCATAATGACCTTTATGCATTTTCATTTATGGCATCATTTCATGCC
*
443415 TATAATGAACTGTTATGCATTTTCATTTATGGCATCATTTCATGCCTATAATGCACCATTATGTA
129 GATAATGAACTGTTATGCATTTTCATTTATGGCATCATTTCATGCCTATAATG-A-C----TGTA
* *
443480 TTCATTTTCATTCATGGCATCCTTTCATGCCGATAATGC
188 TGCATTTTCATTCATGGCATCATTTCATGCCGATAATGC
* *
443519 ACCATTATGCATTTTCATTTATGGCATCCTTCCATGCC
1 ACCATTATGCATTTTCATTCATGGCATCCTTTCATGCC
443557 TAAGGCATTT
Statistics
Matches: 234, Mismatches: 23, Indels: 17
0.85 0.08 0.06
Matches are distributed among these distances:
221 81 0.35
222 2 0.01
223 1 0.00
224 1 0.00
225 3 0.01
227 104 0.44
228 40 0.17
229 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.41
Consensus pattern (226 bp):
ACCATTATGCATTTTCATTCATGGCATCCTTTCATGCCAAATGGTCACCATTAAGCATTTTCATT
TATGGCATCATTCCATGCCATAATGACCTTTATGCATTTTCATTTATGGCATCATTTCATGCCGA
TAATGAACTGTTATGCATTTTCATTTATGGCATCATTTCATGCCTATAATGACTGTATGCATTTT
CATTCATGGCATCATTTCATGCCGATAATGC
Found at i:443523 original size:182 final size:176
Alignment explanation
Indices: 443069--443562 Score: 695
Period size: 182 Copynumber: 2.7 Consensus size: 176
443059 AATATACCAT
* ** * * * * * *
443069 TATGTATTTTCATTGGTGGCATCATTTCATGCCAACT-GGTTACCGTTAAGCATTTTCATTTATG
1 TATGCATTTTCATTTATGGCATCATTTCATGCCTA-TAAG-CACCATTATGCATTTTCATTCATG
* * * * * * *
443133 GCATCATTTCATGCCTATAATGTACCTTTATGCATTTTCATTTGTGGCATCATTTCATGCCGATA
64 GCATCCTTTCATGCCGATAATGCACCATTATGCATTTTCATTTATGGCATCCTTCCATGCC--TA
*
443198 ATGCATTGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGACTG
127 AGGC--T-TTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGACTG
443251 TATGCATTTTCATTTATGGCATCATTTCATGCCTATAAGCACCATTATGCATTTTCATTCATGGC
1 TATGCATTTTCATTTATGGCATCATTTCATGCCTATAAGCACCATTATGCATTTTCATTCATGGC
443316 ATCCTTTCATGCCGATAATGCACCATTATGCATTTTCATTTATGGCATCCTTCCATGCCTAAGGC
66 ATCCTTTCATGCCGATAATGCACCATTATGCATTTTCATTTATGGCATCCTTCCATGCCTAAGGC
443381 -TTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGAACTG
131 TTTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATG-ACTG
443427 TTATGCATTTTCATTTATGGCATCATTTCATGCCTATAATGCACCATTATGTATTCATTTTCATT
1 -TATGCATTTTCATTTATGGCATCATTTCATGCCTATAA-GCACCATTATG----CATTTTCATT
443492 CATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTCATTTATGGCATCCTTCCATGCC
60 CATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTCATTTATGGCATCCTTCCATGCC
443557 TAAGGC
125 TAAGGC
443563 ATTTCACCTT
Statistics
Matches: 287, Mismatches: 17, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
175 41 0.14
176 4 0.01
177 38 0.13
178 11 0.04
179 5 0.02
181 75 0.26
182 113 0.39
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (176 bp):
TATGCATTTTCATTTATGGCATCATTTCATGCCTATAAGCACCATTATGCATTTTCATTCATGGC
ATCCTTTCATGCCGATAATGCACCATTATGCATTTTCATTTATGGCATCCTTCCATGCCTAAGGC
TTTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGACTG
Found at i:443706 original size:81 final size:81
Alignment explanation
Indices: 443558--444201 Score: 892
Period size: 81 Copynumber: 8.0 Consensus size: 81
443548 TTCCATGCCT
* * * * * ** * *
443558 AAGGCATTTCACCTTTCATCTAACTTGCATTATTGGCATATTTCTGCCAAATGCACAGTTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCA
*
443623 ATTAATTTTTTACTCA
66 ATTAATCTTTTACTCA
* * * * *
443639 AAGATATTTAACATTTCATCTAACTGGCATGATTGATACCTTTCTGTCAAATGCATAGTTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCA
443704 ATTAATCTTTTACTCA
66 ATTAATCTTTTACTCA
* * * **
443720 AAGGTATTTAACCCTTCAACTAACTTGCATGATTGACATATTTCTGTCAAATGCACAGCTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCA
443785 ATTAATCTTTTACTCA
66 ATTAATCTTTTACTCA
* * * * *
443801 AAGTTATTTAACCTTTCATCAAACTAGCATGATTGACACCTTTCTGTCAAATGCACAGATAGACA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCA
*
443866 ATTAATCTTTAACTCA
66 ATTAATCTTTTACTCA
* * *
443882 AAGGTATTTAACCTTTCATCTAACTTGCATGATTGACGCCTTTCTGTCAAATGCACAACTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCA
443947 ATTAATCTTTTACTCA
66 ATTAATCTTTTACTCA
** * *
443963 AAGGTATGCAACCTTTCATCTAACTGTCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCA
*
444028 ATAAATCTTTTACTCA
66 ATTAATCTTTTACTCA
* * * * * *
444044 AAGGTCTTTAACTTTTCATCTACCTAGCATGATTGACACCATTCTGTCAAATGCACAACTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCA
444109 ATTAATCTTTTACTCA
66 ATTAATCTTTTACTCA
* * * *
444125 AAGGTATTTAACCTTTCATCTTACTGGTATGATTGACACATTTATGTCAAATGCACAGCTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCA
444190 ATTAATCTTTTA
66 ATTAATCTTTTA
444202 TTTTAAAACG
Statistics
Matches: 493, Mismatches: 70, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 493 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (81 bp):
AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCA
ATTAATCTTTTACTCA
Found at i:453092 original size:9 final size:9
Alignment explanation
Indices: 453070--453157 Score: 95
Period size: 9 Copynumber: 9.3 Consensus size: 9
453060 GCTGCTAGAA
453070 ACCGGTTCTG
1 ACCGGTT-TG
453080 ACCGGTTTG
1 ACCGGTTTG
*
453089 ACCGGTTTCA
1 ACCGGTTT-G
*
453099 ACCGGTTCG
1 ACCGGTTTG
*
453108 AACCAGTTTG
1 -ACCGGTTTG
*
453118 ACCGGTCTG
1 ACCGGTTTG
453127 AACCGGTTTG
1 -ACCGGTTTG
453137 ACCGGTTTG
1 ACCGGTTTG
*
453146 ACCGGTCTG
1 ACCGGTTTG
453155 ACC
1 ACC
453158 CGACCCGACC
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
9 37 0.56
10 29 0.44
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:453094 original size:19 final size:19
Alignment explanation
Indices: 453069--453157 Score: 101
Period size: 19 Copynumber: 4.7 Consensus size: 19
453059 GGCTGCTAGA
453069 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTTTG
* *
453089 -ACCGGTTTCAACCGGTTCG
1 AACCGGTTT-GACCGGTTTG
* *
453108 AACCAGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTTTG
453127 AACCGGTTTGACCGGTTTG
1 AACCGGTTTGACCGGTTTG
*
453146 -ACCGGTCTGACC
1 AACCGGTTTGACC
453158 CGACCCGACC
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
18 12 0.21
19 39 0.67
20 7 0.12
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTTG
Found at i:453116 original size:29 final size:28
Alignment explanation
Indices: 453069--453153 Score: 116
Period size: 29 Copynumber: 3.0 Consensus size: 28
453059 GGCTGCTAGA
*
453069 AACCGGTTCTGACCGGTTTGACCGGTTTC
1 AACCGGTTC-GACCGGTTTGACCGGTCTC
* *
453098 AACCGGTTCGAACCAGTTTGACCGGTCTG
1 AACCGGTTCG-ACCGGTTTGACCGGTCTC
*
453127 AACCGGTTTGACCGGTTTGACCGGTCT
1 AACCGGTTCGACCGGTTTGACCGGTCT
453154 GACCCGACCC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 17 0.34
29 33 0.66
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.28
Consensus pattern (28 bp):
AACCGGTTCGACCGGTTTGACCGGTCTC
Found at i:453167 original size:28 final size:28
Alignment explanation
Indices: 453079--453168 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 28
453069 AACCGGTTCT
* * ***
453079 GACCGGTTTGACCGGTTTCAACCGGTTC
1 GACCGGTTTGACCGGTCTGAACCGACCC
* ****
453107 GAACCAGTTTGACCGGTCTGAACCGGTTT
1 G-ACCGGTTTGACCGGTCTGAACCGACCC
*
453136 GACCGGTTTGACCGGTCTGACCCGACCC
1 GACCGGTTTGACCGGTCTGAACCGACCC
453164 GACCG
1 GACCG
453169 TGACCCGACA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 27 0.53
29 24 0.47
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.23
Consensus pattern (28 bp):
GACCGGTTTGACCGGTCTGAACCGACCC
Found at i:453204 original size:13 final size:14
Alignment explanation
Indices: 453186--453215 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
453176 ACACCCGACC
453186 GACCGTTGA-CGTT
1 GACCGTTGACCGTT
453199 GACCGTTGACCGTT
1 GACCGTTGACCGTT
453213 GAC
1 GAC
453216 TTTCTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.27
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:453207 original size:7 final size:7
Alignment explanation
Indices: 453186--453215 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
453176 ACACCCGACC
453186 GACCGTT
1 GACCGTT
453193 GA-CGTT
1 GACCGTT
453199 GACCGTT
1 GACCGTT
453206 GACCGTT
1 GACCGTT
453213 GAC
1 GAC
453216 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:456976 original size:17 final size:17
Alignment explanation
Indices: 456930--456979 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 17
456920 ACTCAATTTA
*
456930 TTTTTACTTATTCTT--
1 TTTTTTCTTATTCTTCC
*
456945 TTTTATCTT-TT-TTCC
1 TTTTTTCTTATTCTTCC
456960 TTTTTTCTTATTCTTCC
1 TTTTTTCTTATTCTTCC
456977 TTT
1 TTT
456980 ATTTTCTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 2 0.07
14 2 0.07
15 15 0.54
16 2 0.07
17 7 0.25
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTCTTATTCTTCC
Found at i:469661 original size:99 final size:99
Alignment explanation
Indices: 469455--469705 Score: 346
Period size: 99 Copynumber: 2.5 Consensus size: 99
469445 CACAAAGCTG
* * * * * *
469455 GGGCGTTTAACAAATTACTCTAGAGGGACATCTCAA--TATCATTTTATAGATATTATAATCACC
1 GGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCT-TTATTGTATAGATATTAAAATCACC
*
469518 TTTATCAAGCTAGCTGAATATTATCCATAAAGTCG
65 TTTATCAAGCTAGCTGAATATTATCCATAAAGTCC
*
469553 GGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAGATATTAAAATCACCT
1 GGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAGATATTAAAATCACCT
** *
469618 TTATCTGGCTTAGCTGAATCTTATCCATAAAG-CC
66 TTATCAAGC-TAGCTGAATATTATCCATAAAGTCC
* *
469652 GGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTGTATATATAT
1 GGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAGATAT
469706 AATATTATAA
Statistics
Matches: 136, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
98 32 0.24
99 82 0.60
100 22 0.16
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (99 bp):
GGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAGATATTAAAATCACCT
TTATCAAGCTAGCTGAATATTATCCATAAAGTCC
Found at i:472226 original size:8 final size:8
Alignment explanation
Indices: 472186--472237 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
472176 GTTAAATAGA
472186 AAAATAAT
1 AAAATAAT
472194 -AAATAACT
1 AAAATAA-T
472202 ATTAAATAA-
1 A--AAATAAT
472211 AAAATAAT
1 AAAATAAT
*
472219 AGAATAAT
1 AAAATAAT
472227 AAAATAAT
1 AAAATAAT
472235 AAA
1 AAA
472238 TCAAAAGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 12 0.32
8 18 0.49
9 1 0.03
11 6 0.16
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (8 bp):
AAAATAAT
Found at i:472266 original size:15 final size:14
Alignment explanation
Indices: 472205--472300 Score: 61
Period size: 15 Copynumber: 6.3 Consensus size: 14
472195 AATAACTATT
472205 AAATAAAAAATAATA
1 AAATAAAAAA-AATA
*
472220 GAATAATAAAATAATA
1 AAATAA-AAAA-AATA
*
472236 AATCAAAAGGAAAAAATA
1 AA--ATAA--AAAAAATA
472254 ATAATAAAAAAAATAA
1 A-AATAAAAAAAAT-A
*
472270 AAATATAAAAATATA
1 AAATA-AAAAAAATA
472285 AAA-AAAAAAAA-A
1 AAATAAAAAAAATA
472297 AAAT
1 AAAT
472301 TAACAAACAA
Statistics
Matches: 66, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
12 4 0.06
13 6 0.09
14 1 0.02
15 20 0.30
16 19 0.29
17 3 0.05
18 8 0.12
19 5 0.08
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (14 bp):
AAATAAAAAAAATA
Found at i:472267 original size:29 final size:28
Alignment explanation
Indices: 472205--472299 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 28
472195 AATAACTATT
*
472205 AAATAAAAA-ATAATAGAATAATAAAATAAT
1 AAATAAAAAGATAA-A-AATAATAAAA-AAA
*
472235 AAATCAAAAGGA-AAAAATAATAATAAAAA
1 AAAT-AAAAAGATAAAAATAATAA-AAAAA
*
472264 AAATAAAAATATAAAAAT-ATAAAAAAA
1 AAATAAAAAGATAAAAATAATAAAAAAA
*
472291 AAAAAAAAA
1 AAATAAAAA
472300 TTAACAAACA
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
27 13 0.23
28 9 0.16
29 20 0.36
30 7 0.12
31 6 0.11
32 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.03, T:0.17
Consensus pattern (28 bp):
AAATAAAAAGATAAAAATAATAAAAAAA
Found at i:472277 original size:8 final size:8
Alignment explanation
Indices: 472246--472288 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
472236 AATCAAAAGG
472246 AAAAA-AT
1 AAAAATAT
*
472253 AATAATA-
1 AAAAATAT
*
472260 AAAAAAAT
1 AAAAATAT
472268 AAAAATAT
1 AAAAATAT
472276 AAAAATAT
1 AAAAATAT
472284 AAAAA
1 AAAAA
472289 AAAAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 9 0.30
8 21 0.70
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (8 bp):
AAAAATAT
Found at i:472312 original size:12 final size:13
Alignment explanation
Indices: 472297--472326 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
472287 AAAAAAAAAA
472297 AAATT-AACAAAC
1 AAATTAAACAAAC
472309 AAATTAAACAAAC
1 AAATTAAACAAAC
472322 AAATT
1 AAATT
472327 GGAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATTAAACAAAC
Found at i:472688 original size:3 final size:3
Alignment explanation
Indices: 472682--472801 Score: 97
Period size: 3 Copynumber: 40.7 Consensus size: 3
472672 TTAGAAAAAA
* * * * *
472682 AAT AAT AAT AAT AAA AAG AAA AAT AGT AA- AA- AAT -AT AAA AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * * *
472728 AAA AAT AAT -AT ATAT ATAT AAT AGT AAT AAT AAT AAC AAT AAT CAT
1 AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
472774 AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
472802 AGAAATATAT
Statistics
Matches: 95, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
2 10 0.11
3 75 0.79
4 10 0.11
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:472706 original size:18 final size:16
Alignment explanation
Indices: 472676--472732 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 16
472666 AAACGTTTAG
*
472676 AAAAAAAATAATAATA
1 AAAAAAAAAAATAATA
*
472692 ATAAAAAGAAAAATAGTA
1 A-AAAAA-AAAAATAATA
472710 AAAAATATAAAAATAAATA
1 AAAAA-A-AAAAAT-AATA
472729 AAAA
1 AAAA
472733 TAATATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
16 1 0.03
17 9 0.27
18 16 0.48
19 7 0.21
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.18
Consensus pattern (16 bp):
AAAAAAAAAAATAATA
Found at i:472747 original size:29 final size:26
Alignment explanation
Indices: 472676--472802 Score: 91
Period size: 26 Copynumber: 4.8 Consensus size: 26
472666 AAACGTTTAG
* *
472676 AAAAAAAATAATAATAATAAAAAGAA-
1 AAAAATAATAATAAT-ATAAAAATAAT
*
472702 AAATAGTAA-AA-AATATAAAAATAAAT
1 AAA-AATAATAATAATATAAAAAT-AAT
* *
472728 AAAAATAATATATATATATAATAGTAAT
1 AAAAATAATA-ATA-ATATAAAAATAAT
* *
472756 AATAATAACAATAATCAT-AAAATAAT
1 AAAAATAATAATAAT-ATAAAAATAAT
*
472782 AATAATAATAATAATAATAAA
1 AAAAATAATAATAAT-ATAAA
472803 GAAATATATA
Statistics
Matches: 80, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
24 7 0.09
25 9 0.11
26 33 0.41
27 11 0.14
28 12 0.15
29 8 0.10
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (26 bp):
AAAAATAATAATAATATAAAAATAAT
Found at i:472813 original size:2 final size:2
Alignment explanation
Indices: 472806--472850 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
472796 TAATAAAGAA
472806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
472846 AT AT A
1 AT AT A
472851 ACAAAATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:472851 original size:10 final size:11
Alignment explanation
Indices: 472737--472851 Score: 74
Period size: 12 Copynumber: 11.1 Consensus size: 11
472727 TAAAAATAAT
472737 ATATATATATA
1 ATATATATATA
472748 ATAGTA-ATAATA
1 ATA-TATAT-ATA
*
472760 ATA-ACA-ATA
1 ATATATATATA
*
472769 ATCATA-AAATA
1 AT-ATATATATA
472780 ATA-ATA-ATA
1 ATATATATATA
472789 ATA-ATA-ATA
1 ATATATATATA
*
472798 ATA-A-AGA-A
1 ATATATATATA
472806 ATATATATATA
1 ATATATATATA
472817 TATATATATATA
1 -ATATATATATA
472829 TATATATATATA
1 -ATATATATATA
472841 ATAT-TATATA
1 ATATATATATA
472851 A
1 A
472852 CAAAATATTA
Statistics
Matches: 91, Mismatches: 1, Indels: 25
0.78 0.01 0.21
Matches are distributed among these distances:
8 5 0.05
9 24 0.26
10 14 0.15
11 17 0.19
12 31 0.34
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (11 bp):
ATATATATATA
Found at i:472872 original size:14 final size:15
Alignment explanation
Indices: 472840--472872 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
472830 ATATATATAT
*
472840 AATATTATATAACAA
1 AATATTAGATAACAA
472855 AATATTAGATAA-AA
1 AATATTAGATAACAA
472869 AATA
1 AATA
472873 ATAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (15 bp):
AATATTAGATAACAA
Found at i:472886 original size:17 final size:17
Alignment explanation
Indices: 472866--472911 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
472856 ATATTAGATA
472866 AAAAATAATAAA-TAATT
1 AAAAATAATAAATTAA-T
472883 AAAAATAATAAATTAAT
1 AAAAATAATAAATTAAT
*
472900 AAAATTAATAAA
1 AAAAATAATAAA
472912 AGGACTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 24 0.89
18 3 0.11
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAAATAATAAATTAAT
Found at i:473414 original size:16 final size:15
Alignment explanation
Indices: 473388--473418 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
473378 TTCCCCAGAT
473388 CTGGTTTTATCTTTC
1 CTGGTTTTATCTTTC
473403 CTGGTATTTATCTTTC
1 CTGGT-TTTATCTTTC
473419 GAAAACCGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.10, C:0.19, G:0.13, T:0.58
Consensus pattern (15 bp):
CTGGTTTTATCTTTC
Found at i:477312 original size:21 final size:21
Alignment explanation
Indices: 477252--477309 Score: 107
Period size: 21 Copynumber: 2.7 Consensus size: 21
477242 ACTATCGCAA
477252 TGCGATTTTCCAATTTCGCGT
1 TGCGATTTTCCAATTTCGCGT
477273 TGCGATTTTCCAATTTCGCGT
1 TGCGATTTTCCAATTTCGCGT
477294 TGCGATTTTCCCAATT
1 TGCGATTTT-CCAATT
477310 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 30 0.83
22 6 0.17
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (21 bp):
TGCGATTTTCCAATTTCGCGT
Found at i:477318 original size:21 final size:21
Alignment explanation
Indices: 477246--477319 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
477236 ATTATGACTA
477246 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
477267 TCGCGTTGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
477288 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
477309 TCGCAATGCGA
1 TCGCAATGCGA
477320 ATAAGTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 44 0.92
22 4 0.08
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:477334 original size:20 final size:21
Alignment explanation
Indices: 477309--477360 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
477299 TTTTCCCAAT
*
477309 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
477329 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
477350 TCGCAATGCGA
1 TCGCAATGCGA
477361 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:477373 original size:41 final size:39
Alignment explanation
Indices: 477328--477449 Score: 112
Period size: 41 Copynumber: 3.2 Consensus size: 39
477318 GAATAAGTAA
*
477328 ATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACT
1 ATCGCAA-GCGAA-TTGGAAAATCGCAACGCGATACTGACT
*
477369 AT--C--GC-AA-TGGAAAATCGCAACGCGGTACTGACT
1 ATCGCAAGCGAATTGGAAAATCGCAACGCGATACTGACT
* **
477402 ATCGCAACGCGATAATACAAAATCGCAACGCGATACTGACT
1 ATCGCAA-GCGA-ATTGGAAAATCGCAACGCGATACTGACT
*
477443 TTCGCAA
1 ATCGCAA
477450 CTCGATACTT
Statistics
Matches: 67, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
33 26 0.39
35 3 0.04
36 2 0.03
38 2 0.03
39 2 0.03
40 1 0.01
41 31 0.46
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (39 bp):
ATCGCAAGCGAATTGGAAAATCGCAACGCGATACTGACT
Found at i:477374 original size:20 final size:20
Alignment explanation
Indices: 477349--477516 Score: 70
Period size: 20 Copynumber: 8.7 Consensus size: 20
477339 AATTTGGAAA
477349 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
477369 ATCGCAATG-GA-A---A--
1 ATCGCAATGCGATACTGACT
* *
477382 ATCGCAACGCGGTACTGACT
1 ATCGCAATGCGATACTGACT
* * *
477402 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
*
477423 ATCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
477443 TTCGCAACT-CGATACTTAAT
1 ATCGCAA-TGCGATACTGACT
* *
477463 TTCGCAACT-CAATACTGACT
1 ATCGCAA-TGCGATACTGACT
* * * *
477483 TTCGCAACGAGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
477503 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
477517 TTTCAAAGCG
Statistics
Matches: 113, Mismatches: 21, Indels: 27
0.70 0.13 0.17
Matches are distributed among these distances:
13 8 0.07
14 1 0.01
15 2 0.02
18 2 0.02
19 6 0.05
20 67 0.59
21 25 0.22
22 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:477385 original size:33 final size:33
Alignment explanation
Indices: 477343--477408 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
477333 AATGCGAATT
*
477343 TGGAAAATCGCAATGCGATACTGACTATCGCAA
1 TGGAAAATCGCAACGCGATACTGACTATCGCAA
*
477376 TGGAAAATCGCAACGCGGTACTGACTATCGCAA
1 TGGAAAATCGCAACGCGATACTGACTATCGCAA
477409 CGCGATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (33 bp):
TGGAAAATCGCAACGCGATACTGACTATCGCAA
Found at i:477450 original size:41 final size:41
Alignment explanation
Indices: 477379--477516 Score: 161
Period size: 41 Copynumber: 3.4 Consensus size: 41
477369 ATCGCAATGG
* *
477379 AAAATCGCAACGCGGTACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
477420 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
** * * *
477460 AATTTCGCAACTCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
477501 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
477517 TTTCAAAGCG
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 32 0.42
41 45 0.58
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:477701 original size:22 final size:22
Alignment explanation
Indices: 477673--477716 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
477663 CCATCTCTCA
*
477673 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
*
477695 CCCATCTCCGGCAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
477717 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:478020 original size:20 final size:20
Alignment explanation
Indices: 477966--478039 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
477956 AAATCGTAAC
* *
477966 GCGATTTT-ATTCTCTCGTT
1 GCGATTTTCATTTTCGCGTT
** **
477985 GCGATAGTCAAATTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
478005 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
478025 GCGATTTTCATTTTC
1 GCGATTTTCATTTTC
478040 AGAAACTATT
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 6 0.14
20 37 0.86
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:479959 original size:93 final size:91
Alignment explanation
Indices: 479790--479976 Score: 254
Period size: 93 Copynumber: 2.0 Consensus size: 91
479780 TAGATTGCTT
* *
479790 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGCTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTACCAATACTGCTAAACTGCTTATTAACACTATGAAGTTAGTATTT
479855 GTCTCTTTTTGTTTTGTCTTTTGGTTGA
66 G-CTC-TTTTGTTTTGTCTTTTGGTTGA
* *
479883 AGTAAATTTATTCGGTTGCTACCAATTCTGCTAATCTG-TGTATTCTTTAACACTATGAAGTTAG
1 AGTAAATTTATTCGGTTGCTACCAATACTGCTAAACTGCT-TA----TTAACACTATGAAGTTAG
479947 TATTTG-TC-TTTGTTTTGTCTTTTGGTTGA
61 TATTTGCTCTTTTGTTTTGTCTTTTGGTTGA
479976 A
1 A
479977 AGTTTGAAAT
Statistics
Matches: 85, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
92 1 0.01
93 59 0.69
95 2 0.02
97 23 0.27
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (91 bp):
AGTAAATTTATTCGGTTGCTACCAATACTGCTAAACTGCTTATTAACACTATGAAGTTAGTATTT
GCTCTTTTGTTTTGTCTTTTGGTTGA
Found at i:480231 original size:19 final size:20
Alignment explanation
Indices: 480177--480243 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
480167 TAGTTTACTT
* *
480177 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
* *
480197 TCGTAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
480217 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
480236 TCGCAACG
1 TCGCAACG
480244 ACAAAATCAC
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 14 0.38
20 23 0.62
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:480251 original size:14 final size:14
Alignment explanation
Indices: 480232--480290 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
480222 ATGCGAAATG
480232 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
480246 AAAATCACAATGCGAAATG
1 AAAATCGCAA--CG--A-C
480265 AAAATCGCAACGAC
1 AAAATCGCAACGAC
480279 AAAATCGCAACG
1 AAAATCGCAACG
480291 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.25
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:480262 original size:33 final size:33
Alignment explanation
Indices: 480220--480307 Score: 158
Period size: 33 Copynumber: 2.7 Consensus size: 33
480210 ATGGCTATCG
480220 CAATGCGAAATGAAAATCGCAACGACAAAATCA
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
*
480253 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
*
480286 CAACGCGAAATGAAAATCGCAA
1 CAATGCGAAATGAAAATCGCAA
480308 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCA
Found at i:480270 original size:19 final size:19
Alignment explanation
Indices: 480216--480312 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
480206 GGAAATGGCT
480216 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
480235 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
480249 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
480268 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
480282 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
480301 ATCGCAATGCGA
1 ATCGCAATGCGA
480313 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.49
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:480343 original size:14 final size:14
Alignment explanation
Indices: 480324--480382 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
480314 TTGTGTTTCG
480324 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
480338 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
*
480355 CGCATTACGATTTTGT
1 CG--TTGCGATTTTGT
480371 CGTTGCGATTTT
1 CGTTGCGATTTT
480383 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 17 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 5 0.14
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:480356 original size:33 final size:33
Alignment explanation
Indices: 480319--480398 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
480309 GCGATTTGTG
*
480319 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
480352 TTTCGCATTACGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
480385 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
480399 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:480397 original size:19 final size:19
Alignment explanation
Indices: 480340--480398 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
480330 GATTTTGTCG
480340 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
480359 TTACGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
480373 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
480392 TTGCGAT
1 TTGCGAT
480399 AGCCATTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 5 0.16
15 3 0.10
16 4 0.13
17 4 0.13
18 3 0.10
19 12 0.39
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:480417 original size:20 final size:20
Alignment explanation
Indices: 480383--480477 Score: 129
Period size: 20 Copynumber: 4.8 Consensus size: 20
480373 TTGCGATTTT
*
480383 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
480402 CATTTCCGCGTTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
* *
480422 CATTTACGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
*
480442 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
* *
480462 CATTTTCGCGTCGCGA
1 CATTTCCGCGTTGCGA
480478 AAGTAAGTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
19 5 0.07
20 64 0.93
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:480488 original size:20 final size:20
Alignment explanation
Indices: 480465--480503 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
480455 CGATAGTCAT
480465 TTTCGCGTCGCGAAAGTAAG
1 TTTCGCGTCGCGAAAGTAAG
* *
480485 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTCGCGAAAGTAA
480504 ACTATTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (20 bp):
TTTCGCGTCGCGAAAGTAAG
Found at i:480495 original size:40 final size:40
Alignment explanation
Indices: 480403--480497 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
480393 TGCGATAGCC
* * *
480403 ATTTCCGCGTTGCGATAGCCATTTACGCGTTGCGATAGTC
1 ATTTCCGCGTTGCGATAGCCATTTACGCGTCGCGAAAGTA
* *
480443 ATTTCCGCGTTGCGATAGTCATTTTCGCGTCGCGAAAGTA
1 ATTTCCGCGTTGCGATAGCCATTTACGCGTCGCGAAAGTA
*
480483 AGTTT-CGTGTTGCGA
1 A-TTTCCGCGTTGCGA
480498 AAGTAAACTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
40 45 0.94
41 3 0.06
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (40 bp):
ATTTCCGCGTTGCGATAGCCATTTACGCGTCGCGAAAGTA
Found at i:480495 original size:60 final size:59
Alignment explanation
Indices: 480371--480497 Score: 139
Period size: 60 Copynumber: 2.1 Consensus size: 59
480361 ACGATTTTGT
** * * *
480371 CGTTGCGATTTTCATTTCGCATTGCGATAGCCATTTCCGCGTTGCGATAGCCATTTACG
1 CGTTGCGATAGTCATTTCGCATTGCGATAGCCATTTCCGCGTCGCGAAAGCAATTTACG
* * * *
480430 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATTTTCGCGTCGCGAAAGTAAGTTT-CG
1 CGTTGCGATAGTCATTT-CGCATTGCGATAGCCATTTCCGCGTCGCGAAAGCAA-TTTACG
*
480490 TGTTGCGA
1 CGTTGCGA
480498 AAGTAAACTA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
59 15 0.27
60 38 0.68
61 3 0.05
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (59 bp):
CGTTGCGATAGTCATTTCGCATTGCGATAGCCATTTCCGCGTCGCGAAAGCAATTTACG
Found at i:480879 original size:21 final size:20
Alignment explanation
Indices: 480853--480921 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
480843 CTGTCATTCC
480853 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
480874 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
480895 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
480915 TCAAGAG
1 TCAAGAG
480922 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:480933 original size:41 final size:42
Alignment explanation
Indices: 480843--480933 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
480833 CCCGACTCAC
* * *
480843 CTGTCATTCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
480885 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
480926 CTGTCATC
1 CTGTCATC
480934 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 23 0.53
42 20 0.47
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:482375 original size:14 final size:14
Alignment explanation
Indices: 482341--482379 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
482331 TTGATTGTTT
482341 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
482355 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
482369 TGTTGATTTGT
1 AATTGATTTGT
482380 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:482542 original size:20 final size:20
Alignment explanation
Indices: 482517--482578 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
482507 TCGTAACGAG
*
482517 AAAATCGTAATGCGAAATGA
1 AAAATCGCAATGCGAAATGA
482537 AAAATCGCAATGCGAAATG-
1 AAAATCGCAATGCGAAATGA
*
482556 AAAATCACAATGCGAAATGA
1 AAAATCGCAATGCGAAATGA
482576 AAA
1 AAA
482579 TAGCAACGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 18 0.46
20 21 0.54
ACGTcount: A:0.53, C:0.13, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAATGCGAAATGA
Found at i:482561 original size:19 final size:19
Alignment explanation
Indices: 482516--482584 Score: 102
Period size: 19 Copynumber: 3.6 Consensus size: 19
482506 ATCGTAACGA
*
482516 GAAAATCGTAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
482535 GAAAAATCGCAATGCGAAAT
1 G-AAAATCGCAATGCGAAAT
*
482555 GAAAATCACAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
482574 GAAAATAGCAA
1 GAAAATCGCAA
482585 CGAGAAAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 27 0.60
20 18 0.40
ACGTcount: A:0.52, C:0.13, G:0.19, T:0.16
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:482647 original size:20 final size:20
Alignment explanation
Indices: 482622--482717 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
482612 TCGCATTGCG
*
482622 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
***
482642 ATTTTCGCA-TTGCGATTTTTC
1 ATTTTCG-AGTTGCGA-TAGCC
* *
482663 A-TTTCGAATTGTGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
482682 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
482702 ATTTTC-ACGTTGCGAT
1 ATTTTCGA-GTTGCGAT
482718 TTCCCCGTTG
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
19 4 0.07
20 51 0.86
21 4 0.07
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:482956 original size:20 final size:20
Alignment explanation
Indices: 482931--482980 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
482921 TTGAAGATGA
482931 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
482951 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
482971 TTGCGATTTT
1 TTGCGATTTT
482981 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:483895 original size:24 final size:24
Alignment explanation
Indices: 483844--483897 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
483834 GTATTCGAAA
* *
483844 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCAGGAC
* *
483868 TTTGATATTGGTCAATACTAGGAT
1 TTTGATATTGGTCAATACCAGGAC
483892 TTTGAT
1 TTTGAT
483898 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCAGGAC
Found at i:486386 original size:19 final size:19
Alignment explanation
Indices: 486364--486494 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
486354 GGAAATTACT
486364 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
486383 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
486397 ATCGAAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
486416 ATCGCAA--C--TA-GAAT
1 ATCGCAATGCGAAATGAAA
*
486430 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
486449 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
486463 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
486482 ATCGCAACGCGAA
1 ATCGCAATGCGAA
486495 TTTAGTTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 27 0.33
15 3 0.04
16 5 0.06
17 5 0.06
18 3 0.04
19 39 0.48
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:486411 original size:33 final size:33
Alignment explanation
Indices: 486364--486490 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
486354 GGAAATTACT
486364 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
486397 ATCGAAATGCGAAATGAAAATCGCAACTAGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
486429 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
486463 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
486491 CGAATTTAGT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:486472 original size:66 final size:66
Alignment explanation
Indices: 486365--486489 Score: 232
Period size: 66 Copynumber: 1.9 Consensus size: 66
486355 GAAATTACTA
486365 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAATGAAAATCGCAACTAGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAATGAAAATCGCAACTAGAAT
486430 T
66 T
* *
486431 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAAC
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAATGAAAATCGCAAC
486490 GCGAATTTAG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.15
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAATGAAAATCGCAACTAGAAT
T
Found at i:486517 original size:19 final size:19
Alignment explanation
Indices: 486490--486535 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
486480 AAATCGCAAC
* *
486490 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCATT
*
486509 GGGATTTTAGTTTCGCATT
1 GCGATTTTAGTTTCGCATT
486528 GCGATTTT
1 GCGATTTT
486536 GTGGTTGCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCATT
Found at i:486563 original size:33 final size:33
Alignment explanation
Indices: 486505--486626 Score: 165
Period size: 33 Copynumber: 3.7 Consensus size: 33
486495 TTTAGTTTCG
* * *
486505 CGTTGGGATTTT-AGTTTCGCATTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
* * *
486538 GGTTGCGATTTTCATTTTGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
486571 CGTTACGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
486604 CGTTGCGATTTTCATTTCGCATT
1 CGTTGCGATTTTCATTTCGCATT
486627 ATGATAGTAC
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
33 76 0.99
34 1 0.01
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:486574 original size:14 final size:14
Alignment explanation
Indices: 486557--486613 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
486547 TTTCATTTTG
486557 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
486571 CGTTACGATTTTCATTT
1 CGTTGCGA--TTC-TCT
486588 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
486604 CGTTGCGATT
1 CGTTGCGATT
486614 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 15 0.44
16 7 0.21
17 7 0.21
19 5 0.15
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:486763 original size:14 final size:14
Alignment explanation
Indices: 486737--486773 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
486727 CATCAATTAA
486737 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
486751 ACAGATCACCTTTT
1 ACAAATCAACTTTT
486765 ACAAATCAA
1 ACAAATCAA
486774 TTAAACAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:488186 original size:21 final size:21
Alignment explanation
Indices: 488120--488186 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
488110 GTGAATCGGG
*
488120 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
488140 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
488162 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
488183 CTCT
1 CTCT
488187 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:488569 original size:93 final size:89
Alignment explanation
Indices: 488460--488642 Score: 271
Period size: 91 Copynumber: 2.0 Consensus size: 89
488450 ATTTCAAACT
* *
488460 TTCAACCAAAAGACAAAAC-AA-AGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 TTCAACCAAAAGACAAAACAAAGAGACAAATACTAACTTCACAATGTT----AATAAACAGTTTA
488523 GCAGAATTGGCAGCAACCGAATAAATTTAC
62 GCAGAATTGGCAGCAA-CGAAT-AATTTAC
488553 TTCAACCAAAAGACAAAACAAAGAGACAAATACTAACTTCACAATGTTAATAAACAGTTTAGCAG
1 TTCAACCAAAAGACAAAACAAAGAGACAAATACTAACTTCACAATGTTAATAAACAGTTTAGCAG
*
488618 TATTGGCAGCAACGAATAATTTAC
66 AATTGGCAGCAACGAATAATTTAC
488642 T
1 T
488643 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
89 8 0.09
90 5 0.06
91 27 0.32
93 19 0.22
94 2 0.02
95 24 0.28
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (89 bp):
TTCAACCAAAAGACAAAACAAAGAGACAAATACTAACTTCACAATGTTAATAAACAGTTTAGCAG
AATTGGCAGCAACGAATAATTTAC
Found at i:490355 original size:20 final size:19
Alignment explanation
Indices: 490324--490445 Score: 102
Period size: 20 Copynumber: 6.8 Consensus size: 19
490314 TCTTTTGGTT
490324 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
490343 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
490364 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
490383 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
490397 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
490416 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
490430 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
490446 TGCGATTTTG
Statistics
Matches: 82, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
14 21 0.26
16 4 0.05
17 4 0.05
19 22 0.27
20 29 0.35
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:490392 original size:14 final size:14
Alignment explanation
Indices: 490373--490428 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
490363 GGAAATGACT
490373 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
490387 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
490406 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
490420 ATCGCAACG
1 ATCGCAACG
490429 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:490410 original size:33 final size:33
Alignment explanation
Indices: 490349--490445 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 33
490339 ACGAGATAAT
**
490349 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAAAATCGCAACGA
490383 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
490416 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
490446 TGCGATTTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:490472 original size:19 final size:19
Alignment explanation
Indices: 490448--490492 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
490438 AATCGCAATG
* *
490448 CGATTTTGGTTTCGTGTTA
1 CGATTTTGATTTCGCGTTA
* *
490467 CGATTTTTATTTCGCGTTG
1 CGATTTTGATTTCGCGTTA
490486 CGATTTT
1 CGATTTT
490493 CTCGTTGCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.11, C:0.13, G:0.22, T:0.53
Consensus pattern (19 bp):
CGATTTTGATTTCGCGTTA
Found at i:491070 original size:20 final size:20
Alignment explanation
Indices: 491045--491156 Score: 82
Period size: 20 Copynumber: 5.5 Consensus size: 20
491035 GCTATGTAAA
491045 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* *
491065 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ***
491085 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATGTAAGT-AT
* ** *
491106 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATGTAAGTAT
* * *
491126 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
491146 TCGCATTGCGA
1 TCGCATTGCGA
491157 ATTATGAAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.04
20 58 0.73
21 18 0.23
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:491115 original size:41 final size:40
Alignment explanation
Indices: 491063--491156 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
491053 CGATAGTAAG
* *
491063 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
491103 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
491144 ATTCGCATTGCGA
1 ATTCGCATTGCGA
491157 ATTATGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 13 0.27
41 35 0.73
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:491169 original size:41 final size:41
Alignment explanation
Indices: 491037--491219 Score: 126
Period size: 41 Copynumber: 4.5 Consensus size: 41
491027 CGAATGGCGC
*
491037 TATGTAAATCGCATTGCGA--TA-GTAAGATTCGCATTGCGATT
1 TATG-AAATCGCATTGCGATTTACGT-A-ATTCGCATTGCGAAT
* * * * * *
491078 TACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATT
1 TATGAAATCGCATTGCGATTTACGTAATTCGCATTGCGAAT
* *
491119 TACT-TAATCGCGTTGCGATTTACGT-ATTCGCATTGCGAAT
1 TA-TGAAATCGCATTGCGATTTACGTAATTCGCATTGCGAAT
** * * *
491159 TATGAAAATCGCAACGCGA-ATACGTAAATCGCAATGCGAAT
1 TATG-AAATCGCATTGCGATTTACGTAATTCGCATTGCGAAT
* *
491200 TAGGAAAATTGCATTGCGAT
1 TATG-AAATCGCATTGCGAT
491220 AGTCAGAATC
Statistics
Matches: 112, Mismatches: 22, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
39 1 0.01
40 33 0.29
41 75 0.67
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (41 bp):
TATGAAATCGCATTGCGATTTACGTAATTCGCATTGCGAAT
Found at i:491177 original size:21 final size:21
Alignment explanation
Indices: 491153--491208 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
491143 TATTCGCATT
*
491153 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
491174 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
491194 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
491209 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:491189 original size:61 final size:61
Alignment explanation
Indices: 491065--491197 Score: 144
Period size: 61 Copynumber: 2.2 Consensus size: 61
491055 ATAGTAAGAT
* * * ** * *
491065 TCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATACTAAA
* *
491126 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTAT-GAAAATCGCAACGCGA-ATACGTAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCG-ATTATCCAAAATCGCAACGCGATATAC-TAAA
*
491187 TCGCAATGCGA
1 TCGCATTGCGA
491198 ATTAGGAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
60 3 0.05
61 52 0.88
62 4 0.07
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (61 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATACTAAA
Found at i:491217 original size:21 final size:21
Alignment explanation
Indices: 491146--491218 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
491136 ATTTACGTAT
* *
491146 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
491167 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
491187 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
491208 TTGCATTGCGA
1 TCGCAATGCGA
491219 TAGTCAGAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:491241 original size:20 final size:20
Alignment explanation
Indices: 491210--491256 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
491200 TAGGAAAATT
*
491210 GCATTGCGATAGTCAGAATC
1 GCATTGCAATAGTCAGAATC
*
491230 GTATTGCAATAGTCAGAATC
1 GCATTGCAATAGTCAGAATC
491250 GCATTGC
1 GCATTGC
491257 GATTTTCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (20 bp):
GCATTGCAATAGTCAGAATC
Found at i:491292 original size:20 final size:21
Alignment explanation
Indices: 491248--491297 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
491238 ATAGTCAGAA
*
491248 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
491269 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
491289 TCGCATTGC
1 TCGCATTGC
491298 AAATTGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:491341 original size:21 final size:22
Alignment explanation
Indices: 491289--491341 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
491279 ATTTACTTAT
491289 TCGCATTGC-AAATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
491310 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
491331 TCGCATTGCGA
1 TCGCATTGCGA
491342 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:491820 original size:22 final size:22
Alignment explanation
Indices: 491795--491852 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
491785 TATTATTTAT
* *
491795 TTATTTATTATTATTAGTATTA
1 TTATTTATTATTATTACTAATA
*
491817 TTATTTAGTATTATTACTAATA
1 TTATTTATTATTATTACTAATA
*
491839 ATATTT-TTATTATT
1 TTATTTATTATTATT
491853 TTGCAGAGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 7 0.23
22 24 0.77
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (22 bp):
TTATTTATTATTATTACTAATA
Found at i:495956 original size:84 final size:84
Alignment explanation
Indices: 495830--496664 Score: 733
Period size: 84 Copynumber: 10.0 Consensus size: 84
495820 TCTGTTAGCC
* * * * *
495830 AAGACCTTCGAGTTCGACTACGCTAAGCTCCAAGGCACATCATTTGCAGCATAGCTAAAGGCTAT
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCGAG
*
495895 AAGGGTTATCTGTCACCAA
66 AAGGGTTATCTGCCACCAA
* * * *
495914 AAGTCCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCGAG
* *
495979 AAGGGTTATCTACCAACAA
66 AAGGGTTATCTGCCACCAA
* * * * * *
495998 AAGACCTTCGAGTTCGACCATGCTCAACTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCGAG
* *
496063 AA-GTTCTATCTGTCATCC-A
66 AAGGGT-TATCTGCCA-CCAA
* * * ** ** * *
496082 AATACCTTCGAGTTTGACTATGCTTGGCTCCAAGGCACATCATTTGCATTATAACTGAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCGAG
* *
496147 AAGGGTTATCTGCCAACTA
66 AAGGGTTATCTGCCACCAA
* * * * * * * * * **
496166 ATGACCTTCGGGTTCGATTATGCTCAACTCTAAGGCACATCATTTGCAACATTATTTAAGTTGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCGAG
* *
496231 AAGGGCTATCTG----CGA
66 AAGGGTTATCTGCCACCAA
* * * * * *
496246 AAGACCCTCGAGTTCGATTACACTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCGAG
* *
496311 AAGGGTTATCTGCCAACTA
66 AAGGGTTATCTGCCACCAA
* * * * **
496330 AAGACCTTCGAGTTCAACTACACTCAACTCCAAGGCACATCATTT-CAGCATAGCTTAAGTTGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCGAG
*
496394 AAGGGCTATCTG---CC-A
66 AAGGGTTATCTGCCACCAA
* * * * * * * * *
496409 AAGACGC-TCTAGTTCGATTTCACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCT
1 AAGAC-CTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGGCG
**
496473 AGAAGGGTTATCTGTGACCAA
64 AGAAGGGTTATCTGCCACCAA
* * * * *
496494 AAGACCTTTGAGTTCGATTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCGAG
* * *
496559 AAGGGCTATATGCCAGCC-G
66 AAGGGTTATCTGCCA-CCAA
** * * * * *
496578 AAGACCTTTTAGTTCGACTACACTCAGCTCAAAGGCACCAACATTTGCAGCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTGCAGCATAACTTAAGGCGA
* * *
496643 GAAGAGTTATCTGTCAACAA
65 GAAGGGTTATCTGCCACCAA
496663 AA
1 AA
496665 TTATCGAGTT
Statistics
Matches: 608, Mismatches: 124, Indels: 37
0.79 0.16 0.05
Matches are distributed among these distances:
79 22 0.04
80 82 0.13
81 25 0.04
83 30 0.05
84 386 0.63
85 63 0.10
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (84 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCGAG
AAGGGTTATCTGCCACCAA
Found at i:496114 original size:168 final size:164
Alignment explanation
Indices: 495830--496664 Score: 877
Period size: 168 Copynumber: 5.0 Consensus size: 164
495820 TCTGTTAGCC
* * *
495830 AAGACCTTCGAGTTCGACTACGCT-AAGCTCCAAGGCACATCATTTGCAGCATAGCTAAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAA-CTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
* * * * * *
495894 TAAGGGTTATCTGTCACCAAAAGTCCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTT
65 GAAGGGCTATCTG---CC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTT
*
495959 GCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACAA
126 GCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAA
* * *
495998 AAGACCTTCGAGTTCGACCATGCTCAACTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
** * * ** **
496063 AAGTTCTATCTGTCATCCAAATACCTTCGAGTTTGACTATGCTTGGCTCCAAGGCACATCATTTG
66 AAGGGCTATCTG----CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTG
** * *
496128 CATTATAACTGAAGTCGAGAAGGGTTATCTGCCAACTA
127 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAA
* * * * * * * *
496166 ATGACCTTCGGGTTCGATTATGCTCAACTCTAAGGCACATCATTTGCAACATTA-TTTAAGTTGA
1 AAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCA-TAGCTTAAGTCGA
* * * * *
496230 GAAGGGCTATCTGCGAAAGACCCTCGAGTTCGATTACACTCAGCTCCAAGGCATATCATTTGTAG
65 GAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAG
*
496295 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACTA
130 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACAA
* * *
496330 AAGACCTTCGAGTTCAACTACACTCAACTCCAAGGCACATCATTT-CAGCATAGCTTAAGTTGAG
1 AAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
* * * * * *
496394 AAGGGCTATCTGCCAAAGACGC-TCTAGTTCGATTTCACTCAGCTTCGAGGGCACATCATTTACA
66 AAGGGCTATCTGCCAAAGAC-CTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCA
* * * ** *
496458 GCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
129 GCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAA
* * * *
496494 AAGACCTTTGAGTTCGATTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAA
1 AAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
* ** * *
496559 AAGGGCTATATGCCAGCCGAAGACCTTTTAGTTCGACTACACTCAGCTCAAAGGCACCAACATTT
66 AAGGGCTATCTGCCA----AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCA-CATCATTT
* * * * *
496624 GCAGCATAACTCAAGGCTAGAAGAGTTATCTGTCAACAA
126 GCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAA
496663 AA
1 AA
496665 TTATCGAGTT
Statistics
Matches: 563, Mismatches: 91, Indels: 25
0.83 0.13 0.04
Matches are distributed among these distances:
162 2 0.00
163 52 0.09
164 196 0.35
165 31 0.06
168 209 0.37
169 73 0.13
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (164 bp):
AAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGC
ATAACTTAAGTCGAGAAGGGTTATCTGCCAACAA
Found at i:496363 original size:248 final size:246
Alignment explanation
Indices: 495830--496679 Score: 784
Period size: 248 Copynumber: 3.4 Consensus size: 246
495820 TCTGTTAGCC
* * *
495830 AAGACCTTCGAGTTCGACTACGCT-AAGCTCCAAGGCACATCATTTGCAGCATAGCTAAAGGCTA
1 AAGACCTTCGAGTTCGACTACACTCAA-CTCCAAGGCACATCATTTGCAGCATAACTAAAGGCGA
* * * * * *
495894 TAAGGGTTATCTGTCACCAA-AAGTCCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATT
65 GAAGGGTTATCTG---CCAACAAGACCTTCGAGTTCGATTATGCTCAGCTCCAAGGCACATCATT
* * ** *
495958 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACCATGCTC
127 TGCAGCATAACTTAAGTTGAGAAGGGTTATCT----GCAAAAGACCTTCGAGTTCGATTACGCTC
* * * *
496023 AACTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAA-GTTCTATCTGTCATCCA
188 AGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGT-TATCTGCCAACCA
* * ** *** ** * *
496082 AATACCTTCGAGTTTGACTATGCTTGGCTCCAAGGCACATCATTTGCATTATAACTGAAGTCGAG
1 AAGACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTGCAGCATAACTAAAGGCGAG
* * *
496147 AAGGGTTATCTGCCAACTAATGACCTTCGGGTTCGATTATGCTCAACTCTAAGGCACATCATTTG
66 AAGGGTTATCTGCCAAC-AA-GACCTTCGAGTTCGATTATGCTCAGCTCCAAGGCACATCATTTG
* * * * * * *
496212 CAACATTATTTAAGTTGAGAAGGGCTATCTGCGAAAGACCCTCGAGTTCGATTACACTCAGCTCC
129 CAGCATAACTTAAGTTGAGAAGGGTTATCTGCAAAAGACCTTCGAGTTCGATTACGCTCAGCTCC
* * *
496277 AAGGCATATCATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACTA
194 AAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCA
* * * **
496330 AAGACCTTCGAGTTCAACTACACTCAACTCCAAGGCACATCATTT-CAGCATAGCTTAAGTTGAG
1 AAGACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTGCAGCATAACTAAAGGCGAG
* * * * *
496394 AAGGGCTATCTGCC-A-AAGACGC-TCTAGTTCGATT-TCACTCAGCTTCGAGGGCACATCATTT
66 AAGGGTTATCTGCCAACAAGAC-CTTCGAGTTCGATTAT-GCTCAGC-TCCAAGGCACATCATTT
* * * *
496455 ACAGCATAACTCAAGGCT-AGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGATTACGCTC
128 GCAGCATAACTTAA-GTTGAGAAGGGTTATC--TG--CAAAAGACCTTCGAGTTCGATTACGCTC
* * * * * *
496519 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATATGCCAGCCG
188 AGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCA
** * * * * *
496578 AAGACCTTTTAGTTCGACTACACTCAGCTCAAAGGCACCAACATTTGCAGCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACACTCAACTCCAAGGCA-CATCATTTGCAGCATAACTAAAGGCGA
* * **
496643 GAAGAGTTATCTGTCAACAA-AATTATCGAGTTCGATT
65 GAAGGGTTATCTGCCAACAAGACCT-TCGAGTTCGATT
496680 CCATTTAGCT
Statistics
Matches: 483, Mismatches: 96, Indels: 38
0.78 0.16 0.06
Matches are distributed among these distances:
242 1 0.00
243 18 0.04
244 38 0.08
245 2 0.00
246 3 0.01
247 27 0.06
248 214 0.44
249 13 0.03
250 25 0.05
251 4 0.01
252 138 0.29
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (246 bp):
AAGACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATCATTTGCAGCATAACTAAAGGCGAG
AAGGGTTATCTGCCAACAAGACCTTCGAGTTCGATTATGCTCAGCTCCAAGGCACATCATTTGCA
GCATAACTTAAGTTGAGAAGGGTTATCTGCAAAAGACCTTCGAGTTCGATTACGCTCAGCTCCAA
GGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCA
Found at i:496926 original size:13 final size:13
Alignment explanation
Indices: 496888--496935 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
496878 TTTTAAAAAA
*
496888 TATTATTTATTTATT
1 TATTA-TTATTTA-G
496903 TATTATT-TTTAG
1 TATTATTATTTAG
496915 TATTATTATTTAG
1 TATTATTATTTAG
496928 TATTATTA
1 TATTATTA
496936 CTAATAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 7 0.23
13 17 0.55
14 2 0.06
15 5 0.16
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (13 bp):
TATTATTATTTAG
Found at i:500192 original size:19 final size:19
Alignment explanation
Indices: 500160--500206 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
500150 TGTTTAATTT
*
500160 TTTTTATTATAATT-ATAAA
1 TTTTTATTACAATTCA-AAA
*
500179 TTTTTATTGCAATTCAAAA
1 TTTTTATTACAATTCAAAA
500198 TATTTTATT
1 T-TTTTATT
500207 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTTATTACAATTCAAAA
Found at i:500454 original size:21 final size:21
Alignment explanation
Indices: 500403--500455 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
500393 ATTATGACTA
500403 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
500424 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
500445 TCGCAATGCGA
1 TCGCAATGCGA
500456 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:500488 original size:21 final size:21
Alignment explanation
Indices: 500445--500519 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
500435 TTTTCCCAAT
** *
500445 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
*
500465 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
500486 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
500507 TCGCAATGCGAAT
1 TCGCAATGCGAAT
500520 ACGTAAATCG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 11 0.22
21 38 0.78
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:501137 original size:19 final size:19
Alignment explanation
Indices: 501113--501157 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
501103 GCAATGAGAG
*
501113 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
501132 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
501151 AATCGCA
1 AATCGCA
501158 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:501194 original size:14 final size:14
Alignment explanation
Indices: 501175--501211 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
501165 TTTCATTTCG
501175 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
501189 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
501203 CGTTGCGAT
1 CGTTGCGAT
501212 AGTCATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.08, C:0.27, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:501237 original size:20 final size:20
Alignment explanation
Indices: 501203--501259 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
501193 GCGATTCTCT
**
501203 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTCTCATTTTCG
* *
501223 CGTTGCGATTCTCATTATCT
1 CGTTGCGATTCTCATTTTCG
* *
501243 CATTGCGATTTTCATTT
1 CGTTGCGATTCTCATTT
501260 CAACCAAAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTTCG
Found at i:501378 original size:25 final size:26
Alignment explanation
Indices: 501324--501378 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
501314 TTATGTTTAT
*
501324 TGTTTTTGGTATATCTTGACAGTGTA
1 TGTTTTTGGTATATCTTAACAGTGTA
501350 -GTTTTTGGTATATC-TAACA-TGGTA
1 TGTTTTTGGTATATCTTAACAGT-GTA
501374 TGTTT
1 TGTTT
501379 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 1 0.04
24 7 0.27
25 18 0.69
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.51
Consensus pattern (26 bp):
TGTTTTTGGTATATCTTAACAGTGTA
Found at i:503427 original size:21 final size:21
Alignment explanation
Indices: 503403--503469 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
503393 TCATTCCTCG
503403 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
503424 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
503445 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
503466 AGAG
1 AGAG
503470 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:503430 original size:42 final size:42
Alignment explanation
Indices: 503384--503469 Score: 95
Period size: 42 Copynumber: 2.0 Consensus size: 42
503374 ATCATTGAAA
* *
503384 AGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAG
1 AGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTCAAG
* * *
503426 AGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTCAAG
1 AGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTCAAG
503468 AG
1 AG
503470 CCCGATTCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
41 4 0.11
42 31 0.84
43 2 0.05
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.21
Consensus pattern (42 bp):
AGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTCAAG
Found at i:504840 original size:14 final size:14
Alignment explanation
Indices: 504821--504856 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
504811 ATTGTTTAAT
504821 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
504835 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
504849 TGATTTGT
1 TGATTTGT
504857 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:504947 original size:19 final size:19
Alignment explanation
Indices: 504923--504972 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
504913 AAAAAGTACT
* * *
504923 ATCGCAATGCGAAATGAAG
1 ATCGCAACGAGAAATGAAA
504942 ATCGCAACGAGAAATGAAA
1 ATCGCAACGAGAAATGAAA
504961 ATCGCAACGAGA
1 ATCGCAACGAGA
504973 GAATCGCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAACGAGAAATGAAA
Found at i:505040 original size:33 final size:32
Alignment explanation
Indices: 504998--505125 Score: 150
Period size: 33 Copynumber: 3.9 Consensus size: 32
504988 ATTAAATTCG
*
504998 CGTTGCGATTTCCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
505031 CGTTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
505064 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
** *
505097 CGTTGCGATAGTAATTTCCGCATTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
505126 AGACATTAAG
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
31 3 0.04
33 66 0.80
34 10 0.12
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:505057 original size:19 final size:19
Alignment explanation
Indices: 504994--505092 Score: 65
Period size: 19 Copynumber: 5.7 Consensus size: 19
504984 CGAAATTAAA
* *
504994 TTCGCGTTGCGATTTCCAT
1 TTCGCATTGCGATTTTCAT
*
505013 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
505029 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
505046 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
*
505060 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
505079 TTCGTATTGCGATT
1 TTCGCATTGCGATT
505093 CTCTCGTTGC
Statistics
Matches: 59, Mismatches: 11, Indels: 20
0.66 0.12 0.22
Matches are distributed among these distances:
14 18 0.31
16 6 0.10
17 5 0.08
19 30 0.51
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:505080 original size:66 final size:67
Alignment explanation
Indices: 504991--505124 Score: 207
Period size: 66 Copynumber: 2.0 Consensus size: 67
504981 ACGCGAAATT
** *
504991 AAATTCGCGTTGCGATTTCCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTT-CGCATTG
1 AAATTCGCGTTGCGATTTCCATTTCGCATTGCGATTCCCTCGTTGCGATAGTAATTTCCGCATTG
505055 CG
66 CG
* * *
505057 AAATTCGCGTTGCGATTTTCATTTCGTATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCATTG
1 AAATTCGCGTTGCGATTTCCATTTCGCATTGCGATTCCCTCGTTGCGATAGTAATTTCCGCATTG
505122 CG
66 CG
505124 A
1 A
505125 TAGACATTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
66 51 0.84
67 10 0.16
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (67 bp):
AAATTCGCGTTGCGATTTCCATTTCGCATTGCGATTCCCTCGTTGCGATAGTAATTTCCGCATTG
CG
Found at i:507604 original size:24 final size:24
Alignment explanation
Indices: 507577--507630 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
507567 TTGAAACATC
*
507577 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
507601 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
507625 ATCAAA
1 ATCAAA
507631 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:508536 original size:20 final size:20
Alignment explanation
Indices: 508447--508538 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
508437 TGCGATTTTG
* *
508447 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
508467 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
508487 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
508508 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
508528 GAAAATCGCAA
1 GAAAATCGCAA
508539 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:508847 original size:20 final size:20
Alignment explanation
Indices: 508752--508839 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
508742 CAACGGGGAA
508752 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
508772 ATTGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
508792 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
508812 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
508832 ATCGCAAC
1 ATCGCAAC
508840 TAGAAAATCG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 5 0.09
20 44 0.81
21 5 0.09
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:510970 original size:20 final size:20
Alignment explanation
Indices: 510947--511000 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
510937 AAAACTTAAA
510947 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
510967 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
* *
510987 ATCACAATGCGAAA
1 ATCGCAACGCGAAA
511001 TGTAAATCGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:511023 original size:14 final size:14
Alignment explanation
Indices: 511004--511093 Score: 81
Period size: 14 Copynumber: 5.8 Consensus size: 14
510994 TGCGAAATGT
511004 AAATCGCAACGACA
1 AAATCGCAACGACA
*
511018 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
511037 AAATCGCAACGACA
1 AAATCGCAACGACA
*
511051 AAATCGCAATGCGAAA
1 AAATCGCAA--CGACA
511067 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
511083 AAATCGCAACG
1 AAATCGCAACG
511094 CGAAACACAA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 10 0.16
19 10 0.16
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:511078 original size:32 final size:33
Alignment explanation
Indices: 510991--511098 Score: 191
Period size: 33 Copynumber: 3.3 Consensus size: 33
510981 ATGGCTATCA
*
510991 CAATGCGAAATGTAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
511024 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
511057 CAATGCGAAATG-AAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
*
511089 CAACGCGAAA
1 CAATGCGAAA
511099 CACAAATCGC
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 29 0.40
33 44 0.60
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCG
Found at i:511127 original size:19 final size:19
Alignment explanation
Indices: 511105--511154 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
511095 GAAACACAAA
511105 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
511124 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
511143 TCGCATTGCGAT
1 TCGCATTGCGAT
511155 AGCCATTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:511173 original size:20 final size:19
Alignment explanation
Indices: 511105--511193 Score: 88
Period size: 19 Copynumber: 4.6 Consensus size: 19
511095 GAAACACAAA
* **
511105 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
**
511124 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
* *
511143 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATAGTCATT
511162 TCCGCGTTGCGATAGTCATTT
1 T-CGCGTTGCGATAGTCA-TT
*
511183 TCGTGTTGCGA
1 TCGCGTTGCGA
511194 AAGTAAACTA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
19 34 0.57
20 23 0.38
21 3 0.05
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCATT
Found at i:511701 original size:18 final size:18
Alignment explanation
Indices: 511675--511719 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
511665 GTCGATCAGA
511675 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
*
511693 TGATAGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
511711 TGATGGCTC
1 TGATGGCTC
511720 CCGAAGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.44, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTGGGTGAGG
Found at i:513082 original size:20 final size:20
Alignment explanation
Indices: 513034--513092 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
513024 AATAGTTTCT
** *
513034 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
513054 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
513074 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
513093 AGAGAATCGC
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:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:513383 original size:22 final size:22
Alignment explanation
Indices: 513356--513399 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
513346 GATGGAGATA
513356 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
513378 GACGGATTTTGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
513400 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:513613 original size:20 final size:20
Alignment explanation
Indices: 513588--513639 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
513578 ATTATGTATT
513588 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
513608 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
513628 ATCTCGTTGCGA
1 ATCGCGTTGCGA
513640 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:513700 original size:41 final size:41
Alignment explanation
Indices: 513608--513702 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
513598 GAAAGTCAGA
* * * * ** *
513608 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
513649 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
513691 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
513703 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:513792 original size:21 final size:21
Alignment explanation
Indices: 513752--513792 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
513742 ACTGTAGACC
** *
513752 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
513773 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
513793 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:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:514541 original size:20 final size:20
Alignment explanation
Indices: 514496--514685 Score: 206
Period size: 20 Copynumber: 9.5 Consensus size: 20
514486 CGATTTTCCA
* *
514496 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
514516 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
514536 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
514556 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
514576 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
514596 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
*
514616 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* *
514636 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
514656 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
514676 AAATCACAAC
1 AAATCGCAAC
514686 ACTGAAATTT
Statistics
Matches: 152, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
19 1 0.01
20 149 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:515406 original size:24 final size:24
Alignment explanation
Indices: 515367--515413 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
515357 AAATTTGGTC
515367 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
515391 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
515414 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Done.