Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008511.1 Hibiscus syriacus cultivar Beakdansim tig00111366_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: 2221980
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 9
Found at i:237426 original size:66 final size:63
Alignment explanation
Indices: 237237--237419 Score: 161
Period size: 66 Copynumber: 2.8 Consensus size: 63
237227 TTTCAAAAGC
* ** * *
237237 AACTGTCTCGAAAGAGACAAAATTCGTTTCAAATGAAAC-AACTCAAAAGATGACGTTTAAAGGG
1 AACTGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACGATCTC-AAAGATGATGTTTAAAGGG
* * ** * * * * * *
237301 AATTGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAACGTTCTCAAATATCGGTGTTTCATGG
1 AACTGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGAT-GATGTTTAAAGG
237366 G
63 G
237367 AAACTGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 -AACTGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
237420 TTTGTTTTGT
Statistics
Matches: 92, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
63 2 0.02
64 17 0.18
65 18 0.20
66 36 0.39
67 19 0.21
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (63 bp):
AACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGATGTTTAAAGGG
Found at i:237653 original size:31 final size:30
Alignment explanation
Indices: 237589--237663 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
237579 ATAGAAAATG
*
237589 TTTCAAGTGAAACGACTCAAAAATGGTTTTA
1 TTTCAAGTGAAACAACTCAAAAAT-GTTTTA
*
237620 TTTCAAGTGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGTGAAAC-AACTCAAAAATGTTT-TA
* *
237651 TTTCTAGAGAAAC
1 TTTCAAGTGAAAC
237664 TGCCTCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.68
32 9 0.24
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTCAAGTGAAACAACTCAAAAATGTTTTA
Found at i:237756 original size:40 final size:40
Alignment explanation
Indices: 237696--237775 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
237686 GTTTTAATAA
237696 AAACAATCTCAAAGGTGGGTAGTTTT-AAAAGAAATTGTCT
1 AAACAATCTCAAAGGTGGGTA-TTTTCAAAAGAAATTGTCT
* * * *
237736 AAACGATCTCAAATGTGGGTATTTTCAGAAGAAGTTGTCT
1 AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
237776 CGAGAGACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (40 bp):
AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
Found at i:237831 original size:63 final size:64
Alignment explanation
Indices: 237757--237881 Score: 180
Period size: 64 Copynumber: 2.0 Consensus size: 64
237747 AATGTGGGTA
* * * *
237757 TTTTCAGAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
* * *
237820 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
237882 GGATCACATC
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
63 16 0.30
64 38 0.70
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.31
Consensus pattern (64 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
Found at i:237994 original size:120 final size:119
Alignment explanation
Indices: 237779--238002 Score: 276
Period size: 120 Copynumber: 1.9 Consensus size: 119
237769 GTTGTCTCGA
* *
237779 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAG
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAG
*
237844 AGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
66 AGAGAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
* * * **
237898 GAGACCAAA-TTTGTTTCAAATGAAACAATCTCAAA-AGTTAGTTTTTCATTAGAAACTGTC-TC
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGA-TT--TTTTTCAAAAGAAACTGTCTTC
** *
237960 AAGAGAGACAACA-TTTGTTTTTAAAGAAATAGACTCAAAGATG
63 AAGAGAGA-AA-ATTTTGTTTCAAAAGAAACAGACTCAAAGATG
238003 ATTTTGTTAA
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
117 1 0.01
118 26 0.29
119 16 0.18
120 45 0.51
121 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (119 bp):
GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAG
AGAGAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
Found at i:238153 original size:64 final size:64
Alignment explanation
Indices: 238048--238272 Score: 256
Period size: 67 Copynumber: 3.5 Consensus size: 64
238038 ATGAACATAT
** * * * * * * *
238048 TCAAAGATTTACTTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT-AAGAGAAATAGA
1 TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATT-TTGTTTCAA-AGAAACAAA
*
238111 T
64 C
* *
238112 TCAAAGATTTTTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAAC
1 TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT-CAAAGAAACAAAC
*
238177 TCAAAGATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1 TCAAAGA-TTTT-TTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT-CAAAGAAACAA
238242 AC
63 AC
*
238244 TCAAAGATTTTTTTCAAAAGAAACAATCT
1 TCAAAGATTTTTTTCAAAAGAAACTATCT
238273 CAAAGATTTT
Statistics
Matches: 139, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
63 1 0.01
64 40 0.29
65 30 0.22
66 10 0.07
67 58 0.42
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (64 bp):
TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCAAAGAAACAAAC
Found at i:238169 original size:37 final size:37
Alignment explanation
Indices: 238113--238239 Score: 108
Period size: 37 Copynumber: 3.6 Consensus size: 37
238103 GAAATAGATT
*
238113 CAAAGATTTT-TTTCAAAAGAAATTATCTTAAAAGAGA
1 CAAA-ATTTTGTTTCAAAAGAAACTATCTTAAAAGAGA
* * * *
238150 CAAAATTTTGTTTCCAAAGAAACAAAC-T-CAA-AG-
1 CAAAATTTTGTTTCAAAAGAAACTATCTTAAAAGAGA
* * *
238183 ---ATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGA
1 CAAAATTTTGTTTCAAAAGAAACTATCTTAAAAGAGA
*
238217 CAAAATTTTGTTTCCAAAGAAAC
1 CAAAATTTTGTTTCAAAAGAAAC
238240 AAACTCAAAG
Statistics
Matches: 67, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
30 19 0.28
31 1 0.01
32 1 0.01
33 2 0.03
34 2 0.03
35 2 0.03
36 6 0.09
37 34 0.51
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAAAGAAACTATCTTAAAAGAGA
Found at i:238218 original size:67 final size:65
Alignment explanation
Indices: 238112--238272 Score: 268
Period size: 67 Copynumber: 2.4 Consensus size: 65
238102 AGAAATAGAT
*
238112 TCAAAGATTTTTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAAC
1 TCAAAGATTTTTTTCAAAAGAAACTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAAC
* *
238177 TCAAAGATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1 TCAAAGA-TTTT-TTTCAAAAGAAACTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAA
238242 AC
64 AC
*
238244 TCAAAGATTTTTTTCAAAAGAAACAATCT
1 TCAAAGATTTTTTTCAAAAGAAACTATCT
238273 CAAAGATTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
65 23 0.26
66 8 0.09
67 58 0.65
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (65 bp):
TCAAAGATTTTTTTCAAAAGAAACTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAAC
Found at i:238264 original size:95 final size:93
Alignment explanation
Indices: 238150--238323 Score: 242
Period size: 95 Copynumber: 1.8 Consensus size: 93
238140 TTAAAAGAGA
* *
238150 CAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTTAAAAGAAACTATCTTAAGAGA
1 CAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT-TTTTAAAA-AAACTATCTCAAGAGA
*
238215 GACAAAATTTTGTTTCCAAAGAAACAAACT
64 GACAAAACTTTGTTTCCAAAGAAACAAACT
* * * * *
238245 CAAAGATTTT-TTTCAAAAGAAACAATCTCAAAGATTTTTTTTTCACAAAATTGTCTCAAGAGAG
1 CAAA-ATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTTTAAAAAAACTATCTCAAGAGAG
238309 ACAAAACTTTGTTTC
65 ACAAAACTTTGTTTC
238324 AGCTCAAAGA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
93 28 0.40
94 6 0.09
95 31 0.44
96 5 0.07
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (93 bp):
CAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTTTAAAAAAACTATCTCAAGAGAGA
CAAAACTTTGTTTCCAAAGAAACAAACT
Found at i:238282 original size:27 final size:28
Alignment explanation
Indices: 238217--238285 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
238207 TTAAGAGAGA
*
238217 CAAA-ATTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
*
238245 CAAAGATTTTTTTCAAAAGAAACAATCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
238273 CAAAGATTTTTTT
1 CAAAGATTTTTTT
238286 TTCACAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.35
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:238454 original size:29 final size:29
Alignment explanation
Indices: 238372--238643 Score: 213
Period size: 29 Copynumber: 9.4 Consensus size: 29
238362 AAAACTTTGT
* * *
238372 TTCAAAATAAATAGACTCAAAGA--TTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
238398 TTCAAAAGAAAC-AACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
238426 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
238455 TTCAAAAGGAACAAACTCAAAGATTTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *** *
238483 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGT-
1 TTCAAAAGAAACAAACTC-A-A-AG-----A-TTTTTA
* * *
238520 TTCAAAATAAATAGACTCAAAGA-TTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
238547 TTCAAAAGAAAC-AACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
238575 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
238604 TTCAAAAGGAACAAACTCAAAGATTTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
238632 TTCAAGAGAAAC
1 TTCAAAAGAAAC
238644 TGTCTCAAGA
Statistics
Matches: 201, Mismatches: 29, Indels: 30
0.77 0.11 0.12
Matches are distributed among these distances:
25 9 0.04
26 19 0.09
27 19 0.09
28 45 0.22
29 84 0.42
30 1 0.00
31 2 0.01
34 2 0.01
35 1 0.00
36 2 0.01
37 17 0.08
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (29 bp):
TTCAAAAGAAACAAACTCAAAGATTTTTA
Found at i:238521 original size:148 final size:149
Alignment explanation
Indices: 238342--238662 Score: 626
Period size: 149 Copynumber: 2.2 Consensus size: 149
238332 GATTTTTCAC
*
238342 GAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTCAAAGA-TTTTTCAAAAG
1 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTCAAAGATTTTTTCAAAAG
238406 AAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAAAC
66 AAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAAAC
238471 TCAAAGATTTTTTTCAAGA
131 TCAAAGATTTTTTTCAAGA
238490 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTCAAAGATTTTTTCAAAAG
1 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTCAAAGATTTTTTCAAAAG
238555 AAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAAAC
66 AAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAAAC
238620 TCAAAGATTTTTTTCAAGA
131 TCAAAGATTTTTTTCAAGA
238639 GAAACTGTCTCAAGAGAGACAAAA
1 GAAACTGTCTCAAGAGAGACAAAA
238663 AAAATCGTTT
Statistics
Matches: 171, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
148 52 0.30
149 119 0.70
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (149 bp):
GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTCAAAGATTTTTTCAAAAG
AAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAAAC
TCAAAGATTTTTTTCAAGA
Found at i:238968 original size:36 final size:36
Alignment explanation
Indices: 238861--238981 Score: 122
Period size: 36 Copynumber: 3.3 Consensus size: 36
238851 AACAACCTTG
*
238861 AAATTTGTATTATGAGAGAAATGATGTCTCAAGCGAGAC-
1 AAATTTGT-TT-TTAGAGAAAT--TGTCTCAAGCGAGACA
* * * **
238900 AAATTTG-CTTTA-AGATATAGTCTCAAATGAGACA
1 AAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACA
238934 AAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACA
1 AAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACA
*
238970 AAGTTTGTTTTT
1 AAATTTGTTTTT
238982 GAGGAAACGA
Statistics
Matches: 67, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
33 12 0.18
34 7 0.10
35 9 0.13
36 31 0.46
37 1 0.01
39 7 0.10
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (36 bp):
AAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACA
Found at i:238996 original size:36 final size:36
Alignment explanation
Indices: 238886--239003 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
238876 GAGAAATGAT
* * *
238886 GTCTCAAGCGAGAC-AAATTTG-CTTTA-AGATATA
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
** *
238919 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
*
238955 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGGAAA-C
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGA-GAAATC
*
238990 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
239004 TCAACTTTGT
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
33 12 0.17
34 7 0.10
35 7 0.10
36 44 0.63
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
Found at i:239079 original size:102 final size:103
Alignment explanation
Indices: 238955--239185 Score: 294
Period size: 103 Copynumber: 2.3 Consensus size: 103
238945 TAGAGAAATT
*
238955 GTCTCAAGCGAGAC-AAAGTTTGTTTTTG-AGGAAAC-G-ATCTCAA-GTGAGATCAACTTTGTT
1 GTCTCAAGCGAGACGAAA-TTTGTTTTTGAAAGAAACAGAATCT-AAGGTGAGATCAA-TTTGTT
* *
239015 TAATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
63 TAA-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
239057 GTCTCAAGCGAGACGAAATTTG-TTTTGAAAGAAACAAGAATCTAAGGTGAGATTAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTTGAAAGAAAC-AGAATCTAAGGTGAGATCAATTTGTTTA
* * *
239121 AGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
65 AGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
239160 GTCTCAAGCGAGACGAAGTTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
239186 AAGAGAATTT
Statistics
Matches: 113, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
101 5 0.04
102 24 0.21
103 57 0.50
104 14 0.12
105 13 0.12
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (103 bp):
GTCTCAAGCGAGACGAAATTTGTTTTTGAAAGAAACAGAATCTAAGGTGAGATCAATTTGTTTAA
GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:239199 original size:36 final size:36
Alignment explanation
Indices: 239159--239240 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
239149 AAAGGAAAAA
* * *
239159 TGTCTCAAGCGAGACGAAGTTTG-TTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAA-AGAAAT
* * *
239195 TGTCTTAAGTGATACAAACTTTGTTTTTAAAGAAAT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
239231 TGTCTCAAGC
1 TGTCTCAAGC
239241 AAAACAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 31 0.84
37 6 0.16
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
Found at i:239248 original size:36 final size:36
Alignment explanation
Indices: 239159--239253 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 36
239149 AAAGGAAAAA
* * * *
239159 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
* * * *
239195 TGTCTTAAGTGATACAAACTTTGTTTTTAA-AGAAAT
1 TGTCTCAAGCGAAACAAAATTTG-TTTTAAGAGAAAT
*
239231 TGTCTCAAGCAAAACAAAATTTG
1 TGTCTCAAGCGAAACAAAATTTG
239254 AGAAAACGAT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
36 41 0.87
37 6 0.13
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.35
Consensus pattern (36 bp):
TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
Found at i:239351 original size:167 final size:165
Alignment explanation
Indices: 239103--239420 Score: 385
Period size: 167 Copynumber: 1.9 Consensus size: 165
239093 AGAATCTAAG
* * *
239103 GTGAGATTAATTTGTTTTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAG
1 GTGAGATCAATTTGTTTAAGTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAG
* ** * *
239168 CGAGACGAAGTTTG-TTTT-AAGAGAATTTGTCTTAAGTGATACAAACTTTGTTTTTAAAGAAA-
66 CGAGACGAAGTTTGTTTTTCAAGA-AA-TTGTCTCAAACGAGACAAAATTTGTTTTT--AGAAAG
*
239230 TTGTCTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
127 CTGTCTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
* * *
239269 GTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATCTC-AATGAAAAATGTCTCC
1 GTGAGATCAA-TTTGTTTAA-GTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCA
* *
239333 AGTGAGGCGGAA-TTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAGAAAGC
64 AGCGAGAC-GAAGTTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAGAAAGC
* * *
239397 TGTCTCAATCGAGACAAAATTTGA
128 TGTCTCAAGCAAAACAAAATTTGA
239421 TTTGAAAGAA
Statistics
Matches: 129, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
165 5 0.04
166 30 0.23
167 56 0.43
168 34 0.26
169 4 0.03
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (165 bp):
GTGAGATCAATTTGTTTAAGTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAG
CGAGACGAAGTTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAGAAAGCTGT
CTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
Found at i:239383 original size:36 final size:35
Alignment explanation
Indices: 239343--239460 Score: 139
Period size: 36 Copynumber: 3.3 Consensus size: 35
239333 AGTGAGGCGG
239343 AATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAA
1 AATTTGTTTTT-AAGAAATTGTCTCAAACGAGACAA
* *
239379 AATTTGTTTTT-AGAAAGCTGTCTCAATCGAGACAA
1 AATTTGTTTTTAAGAAA-TTGTCTCAAACGAGACAA
** *
239414 AATTTGATTTGAAAGAAATTGTCTCAAGCGAGACAAA
1 AATTTG-TTTTTAAGAAATTGTCTCAAACGAGAC-AA
*
239451 AAATTGTTTT
1 AATTTGTTTT
239461 AAAATTCTCA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
34 5 0.07
35 22 0.31
36 31 0.44
37 12 0.17
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (35 bp):
AATTTGTTTTTAAGAAATTGTCTCAAACGAGACAA
Found at i:241256 original size:16 final size:16
Alignment explanation
Indices: 241208--241263 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 16
241198 TCTTTGTCCA
241208 CTTTCTCTTCT-TTTTT
1 CTTTCTCTT-TGTTTTT
* *
241224 TTTTCACTTTG--TTT
1 CTTTCTCTTTGTTTTT
241238 CTTTCTCTTTGTTTTT
1 CTTTCTCTTTGTTTTT
241254 CTTTTCTCTT
1 C-TTTCTCTT
241264 CGCTTTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
14 12 0.38
15 1 0.03
16 11 0.34
17 8 0.25
ACGTcount: A:0.02, C:0.21, G:0.04, T:0.73
Consensus pattern (16 bp):
CTTTCTCTTTGTTTTT
Found at i:243130 original size:31 final size:32
Alignment explanation
Indices: 243074--243135 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
243064 TGACAAAATG
243074 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
243106 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
243136 CATGTAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:246879 original size:9 final size:8
Alignment explanation
Indices: 246865--246924 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 8
246855 AATATGTAAT
246865 TAATAAACA
1 TAATAAA-A
246874 TAATAATAA
1 TAATAA-AA
246883 TAAATAATAA
1 T-AATAA-AA
246893 TAATAATAA
1 TAATAA-AA
246902 TAAT-AAA
1 TAATAAAA
246909 TATATATAAA
1 TA-ATA-AAA
246919 TAATAA
1 TAATAA
246925 TAAAAAAGAC
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
7 4 0.09
8 4 0.09
9 23 0.50
10 15 0.33
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (8 bp):
TAATAAAA
Found at i:246881 original size:3 final size:3
Alignment explanation
Indices: 246873--246927 Score: 67
Period size: 3 Copynumber: 17.3 Consensus size: 3
246863 ATTAATAAAC
246873 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA A-A TATA TATAA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A ATA
246921 ATA ATA A
1 ATA ATA A
246928 AAAAGACCCG
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 1 0.02
3 37 0.77
4 9 0.19
5 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:246888 original size:19 final size:17
Alignment explanation
Indices: 246865--246929 Score: 76
Period size: 19 Copynumber: 3.5 Consensus size: 17
246855 AATATGTAAT
246865 TAATAAACATAATAATAA
1 TAATAAA-ATAATAATAA
246883 TAAATAATAATAATAATAA
1 T-AATAA-AATAATAATAA
246902 TAATAAATATATATAAATAA
1 TAATAAA-ATA-AT-AATAA
246922 TAATAAAA
1 TAATAAAA
246930 AAGACCCGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.02
18 9 0.21
19 19 0.45
20 13 0.31
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATAAAATAATAATAA
Found at i:246890 original size:10 final size:10
Alignment explanation
Indices: 246875--246928 Score: 74
Period size: 10 Copynumber: 5.2 Consensus size: 10
246865 TAATAAACAT
246875 AATAATAATA
1 AATAATAATA
246885 AATAATAATAA
1 AATAATAAT-A
246896 TAATAATAATA
1 -AATAATAATA
246907 AAT-ATATATA
1 AATAATA-ATA
246917 AATAATAATA
1 AATAATAATA
246927 AA
1 AA
246929 AAAGACCCGG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
9 3 0.08
10 23 0.57
11 5 0.12
12 9 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATAATAATA
Found at i:246892 original size:16 final size:16
Alignment explanation
Indices: 246873--246927 Score: 78
Period size: 16 Copynumber: 3.4 Consensus size: 16
246863 ATTAATAAAC
246873 ATAATAATAATAAATA
1 ATAATAATAATAAATA
246889 ATAATAATAAT-AATA
1 ATAATAATAATAAATA
246904 ATAA-ATATATATAAATA
1 ATAATA-ATA-ATAAATA
246921 ATAATAA
1 ATAATAA
246928 AAAAGACCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.03
15 11 0.31
16 13 0.37
17 9 0.26
18 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATAATAATAAATA
Found at i:250104 original size:16 final size:16
Alignment explanation
Indices: 250083--250118 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
250073 TAACAAGTCA
250083 ACGATACATGAGAAAG
1 ACGATACATGAGAAAG
250099 ACGATACATGAGAAAG
1 ACGATACATGAGAAAG
250115 ACGA
1 ACGA
250119 GAGAGAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.14, G:0.25, T:0.11
Consensus pattern (16 bp):
ACGATACATGAGAAAG
Found at i:254297 original size:132 final size:132
Alignment explanation
Indices: 254060--254325 Score: 469
Period size: 132 Copynumber: 2.0 Consensus size: 132
254050 CATCTGATTT
* * * *
254060 TAGTGATTAAGTCTCCTAGCAGGAATTTTTTACCTACACAAGGATTTCAACTCGAGATATACTTA
1 TAGTGATTAAGTCTCCTAGCAAGAATTTTCTACATACACAAGGATTCCAACTCGAGATATACTTA
254125 AGAGATATTAAGTTATTTATCATTTGAACCAACCCTGTTGGTCATGTTAACATAAATTTAAACAA
66 AGAGATATTAAGTTATTTATCATTTGAACCAACCCTGTTGGTCATGTTAACATAAATTTAAACAA
254190 CA
131 CA
* *
254192 TAGTGATTAAGTCTCCTAGTAAGAATTTTCTACATACACAAGGATTCCAACTCGAGATCTACTTA
1 TAGTGATTAAGTCTCCTAGCAAGAATTTTCTACATACACAAGGATTCCAACTCGAGATATACTTA
*
254257 AGAGATATTAAGTTATTTATCATTTGAACCAACCCTGTTGGTCATGTTAACATAAATTTAAACCA
66 AGAGATATTAAGTTATTTATCATTTGAACCAACCCTGTTGGTCATGTTAACATAAATTTAAACAA
254322 CA
131 CA
254324 TA
1 TA
254326 AATTGCATTT
Statistics
Matches: 127, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 127 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (132 bp):
TAGTGATTAAGTCTCCTAGCAAGAATTTTCTACATACACAAGGATTCCAACTCGAGATATACTTA
AGAGATATTAAGTTATTTATCATTTGAACCAACCCTGTTGGTCATGTTAACATAAATTTAAACAA
CA
Found at i:254585 original size:32 final size:32
Alignment explanation
Indices: 254544--254615 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
254534 ATGTATTCAT
* *
254544 AGTGATGATGTGGCACAAATCACATATACATA
1 AGTGATGATGTGACACAAACCACATATACATA
* * * *
254576 AGTGATGATGTGACAGATACCACGTGTACATA
1 AGTGATGATGTGACACAAACCACATATACATA
254608 AGTGATGA
1 AGTGATGA
254616 CACAACACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (32 bp):
AGTGATGATGTGACACAAACCACATATACATA
Found at i:264692 original size:3 final size:3
Alignment explanation
Indices: 264686--264729 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
264676 TTAGTTTTTT
*
264686 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
264730 TCATTATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:269413 original size:69 final size:70
Alignment explanation
Indices: 269329--269466 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 70
269319 ATGTACGTAC
*
269329 GTATGCATGTATGACATTAGAATCTCCAT-AAATAGGATAATGCTACCTTGCCAATATGGAGA-T
1 GTATGCATGTATGACATTAGAATCTCCATGAAA-AGGATAACGCTACCTTGCCAATATGGAGATT
269392 AATTAT
65 AATTAT
* * * *
269398 GTATGTATGTGTGACATTAGAATCTCCATGACAAGGATAACGTTACCTTGCCAATATGGAGATTA
1 GTATGCATGTATGACATTAGAATCTCCATGAAAAGGATAACGCTACCTTGCCAATATGGAGATTA
269463 ATTA
66 ATTA
269467 ATTATTTGAC
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
69 54 0.87
70 8 0.13
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (70 bp):
GTATGCATGTATGACATTAGAATCTCCATGAAAAGGATAACGCTACCTTGCCAATATGGAGATTA
ATTAT
Found at i:270647 original size:33 final size:33
Alignment explanation
Indices: 270605--270670 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
270595 ATAAAATGAC
270605 ACGTTTTATTTTTATTTTGATGTTCGATATTTT
1 ACGTTTTATTTTTATTTTGATGTTCGATATTTT
270638 ACGTTTTATTTTTATTTTGATGTTCGATATTTT
1 ACGTTTTATTTTTATTTTGATGTTCGATATTTT
270671 TTCGTATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.18, C:0.06, G:0.12, T:0.64
Consensus pattern (33 bp):
ACGTTTTATTTTTATTTTGATGTTCGATATTTT
Found at i:272951 original size:30 final size:30
Alignment explanation
Indices: 272915--272991 Score: 154
Period size: 30 Copynumber: 2.6 Consensus size: 30
272905 TTGGGTATTC
272915 GTTTTAAATATAATTATTATTGAATTAATT
1 GTTTTAAATATAATTATTATTGAATTAATT
272945 GTTTTAAATATAATTATTATTGAATTAATT
1 GTTTTAAATATAATTATTATTGAATTAATT
272975 GTTTTAAATATAATTAT
1 GTTTTAAATATAATTAT
272992 ACCATGAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (30 bp):
GTTTTAAATATAATTATTATTGAATTAATT
Found at i:272958 original size:15 final size:15
Alignment explanation
Indices: 272915--272989 Score: 82
Period size: 15 Copynumber: 5.0 Consensus size: 15
272905 TTGGGTATTC
272915 GTTTTAAATATAATT
1 GTTTTAAATATAATT
* *
272930 ATTATTGAAT-TAATT
1 GTT-TTAAATATAATT
272945 GTTTTAAATATAATT
1 GTTTTAAATATAATT
* *
272960 ATTATTGAAT-TAATT
1 GTT-TTAAATATAATT
272975 GTTTTAAATATAATT
1 GTTTTAAATATAATT
272990 ATACCATGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
14 10 0.21
15 28 0.58
16 10 0.21
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
GTTTTAAATATAATT
Found at i:281896 original size:13 final size:13
Alignment explanation
Indices: 281878--281906 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
281868 TAATCATCGA
281878 ATTTTTAACTTGT
1 ATTTTTAACTTGT
281891 ATTTTTAACTTGT
1 ATTTTTAACTTGT
281904 ATT
1 ATT
281907 ATAATCGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (13 bp):
ATTTTTAACTTGT
Found at i:282696 original size:26 final size:26
Alignment explanation
Indices: 282667--282719 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
282657 TAAACCACAC
282667 ATTTAATA-TCTAAATTATT-TATTTTA
1 ATTTAATACT-TAAATT-TTATATTTTA
282693 ATTTAATACTTAAATTTTATATTTTA
1 ATTTAATACTTAAATTTTATATTTTA
282719 A
1 A
282720 AAATATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 2 0.08
26 22 0.88
27 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTAATACTTAAATTTTATATTTTA
Found at i:285434 original size:6 final size:6
Alignment explanation
Indices: 285423--285449 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
285413 GACACGTATT
285423 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
285450 CGGGACGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:286099 original size:19 final size:19
Alignment explanation
Indices: 286077--286276 Score: 112
Period size: 21 Copynumber: 9.8 Consensus size: 19
286067 TCGTTGCGAT
*
286077 TTTGGACTATCGTAACGAA
1 TTTGGACTATCGCAACGAA
*
286096 TTTGGAATAAATCGCAACACGAA
1 TTTGGACT--ATCGC-A-ACGAA
* *
286119 CTTCGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
**
286138 TTTGGAAAATCGCAACGCGAA
1 TTTGGACTATCGCAA--CGAA
* *
286159 CTTCGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
286178 TTTGGAATAAATCGCAACGCAAA
1 TTTGGACT--ATCGCAACG--AA
* * * *
286201 CTTCGACTATCTCAACTAA
1 TTTGGACTATCGCAACGAA
**
286220 TTTGGAAAATCGCAACGCGAA
1 TTTGGACTATCGCAA--CGAA
* *
286241 CTTAGACTATCGCAACGCGAA
1 TTTGGACTATCGCAA--CGAA
*
286262 CTTGGACTATCGCAA
1 TTTGGACTATCGCAA
286277 TGCGAATATG
Statistics
Matches: 137, Mismatches: 32, Indels: 22
0.72 0.17 0.12
Matches are distributed among these distances:
19 44 0.32
20 1 0.01
21 74 0.54
22 1 0.01
23 17 0.12
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:286159 original size:40 final size:42
Alignment explanation
Indices: 286081--286257 Score: 272
Period size: 40 Copynumber: 4.3 Consensus size: 42
286071 TGCGATTTTG
* *
286081 GACTATCGTAACGAATTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
286123 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
286163 GACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
286205 GACTATCTCAACTAATTTGG-A-AAATCGCAACGCGAACTTA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
286245 GACTATCGCAACG
1 GACTATCGCAACG
286258 CGAACTTGGA
Statistics
Matches: 124, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
40 66 0.53
41 3 0.02
42 55 0.44
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:286222 original size:82 final size:82
Alignment explanation
Indices: 286081--286257 Score: 300
Period size: 82 Copynumber: 2.2 Consensus size: 82
286071 TGCGATTTTG
* *
286081 GACTATCGTAACGAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAACGAATTTGGAAA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACACAAACTTCGACTATCGCAACGAATTTGGAAA
*
286146 ATCGCAACGCGAACTTC
66 ATCGCAACGCGAACTTA
* * *
286163 GACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTCGACTATCTCAACTAATTTGGAAA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACACAAACTTCGACTATCGCAACGAATTTGGAAA
286228 ATCGCAACGCGAACTTA
66 ATCGCAACGCGAACTTA
286245 GACTATCGCAACG
1 GACTATCGCAACG
286258 CGAACTTGGA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 89 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (82 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACACAAACTTCGACTATCGCAACGAATTTGGAAA
ATCGCAACGCGAACTTA
Found at i:286281 original size:21 final size:21
Alignment explanation
Indices: 286106--286282 Score: 141
Period size: 21 Copynumber: 8.6 Consensus size: 21
286096 TTTGGAATAA
* *
286106 ATCGCAACACGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* **
286127 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
*
286146 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* *
286167 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
* *
286186 AAATCGCAACGCAAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
* * * **
286209 ATCTCAA--CTAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
*
286228 ATCGCAACGCGAACTTAGACT
1 ATCGCAACGCGAACTTGGACT
286249 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
286270 ATCGCAATGCGAA
1 ATCGCAACGCGAA
286283 TATGTAAATC
Statistics
Matches: 119, Mismatches: 29, Indels: 16
0.73 0.18 0.10
Matches are distributed among these distances:
19 37 0.31
21 74 0.62
23 8 0.07
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:286320 original size:21 final size:21
Alignment explanation
Indices: 286291--286383 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
286281 AATATGTAAA
* *
286291 TCGCATTGCGATAGTCTAAGT
1 TCGCGTTGCGATAGTCGAAGT
286312 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
* * ** * *
286333 TCGCATTACGATTTTCCAAAT
1 TCGCGTTGCGATAGTCGAAGT
286354 T--CGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
286373 TCGCGTTGCGA
1 TCGCGTTGCGA
286384 ATTATCGATC
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
19 13 0.23
21 43 0.77
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:294731 original size:3 final size:3
Alignment explanation
Indices: 294723--294759 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
294713 TTGTGTATAG
294723 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
294760 TTTATCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:307446 original size:21 final size:22
Alignment explanation
Indices: 307402--307465 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
307392 AAAGTTTAGG
*
307402 TTTTTTACAAATAAATTAAGTT
1 TTTTTTACAAATAAATTAAATT
307424 TTTTTTA-AAATAAA-TAATATT
1 TTTTTTACAAATAAATTAA-ATT
* * *
307445 TTTATTATTAAAAAAATTAAA
1 TTTTTTA-CAAATAAATTAAA
307466 AAAATATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 3 0.09
21 15 0.43
22 7 0.20
23 7 0.20
24 3 0.09
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTTACAAATAAATTAAATT
Found at i:310796 original size:29 final size:30
Alignment explanation
Indices: 310745--310801 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
310735 TATTTTAAGT
* *
310745 AACGAAATGAAATATTAGGCACTAAACTAA
1 AACGAAATGAAACATTAGACACTAAACTAA
310775 AACGAAAT-AAACATTAGACACTAAACT
1 AACGAAATGAAACATTAGACACTAAACT
310802 GTAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.19
Consensus pattern (30 bp):
AACGAAATGAAACATTAGACACTAAACTAA
Found at i:316023 original size:44 final size:45
Alignment explanation
Indices: 315932--316034 Score: 172
Period size: 44 Copynumber: 2.3 Consensus size: 45
315922 GCTCAATGAC
315932 TAATGATGTAATTTATAGAAAAGAAAGTGTCACATTATCATGTCTT
1 TAATGATGTAATTTATAGAAAAGAAAG-GTCACATTATCATGTCTT
315978 TAATGATGTAATTTATAGAAAAGAAA-GTCACATTATCATGTCTT
1 TAATGATGTAATTTATAGAAAAGAAAGGTCACATTATCATGTCTT
* *
316022 TAAAGATTTAATT
1 TAATGATGTAATT
316035 GTCAAGTGAC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
44 29 0.53
46 26 0.47
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (45 bp):
TAATGATGTAATTTATAGAAAAGAAAGGTCACATTATCATGTCTT
Found at i:323491 original size:23 final size:23
Alignment explanation
Indices: 323465--323508 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
323455 GTTATCTCCG
*
323465 TTAACTTTCTTCTTCCTCTTCCA
1 TTAACCTTCTTCTTCCTCTTCCA
323488 TTAACCTTCTTCTTCCTCTTC
1 TTAACCTTCTTCTTCCTCTTC
323509 TTCTTACTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.36, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAACCTTCTTCTTCCTCTTCCA
Found at i:327442 original size:18 final size:18
Alignment explanation
Indices: 327419--327455 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
327409 TTAACGATCA
*
327419 ACATTTAAAACTCATGTG
1 ACATTTAAAAATCATGTG
327437 ACATTTAAAAATCATGTG
1 ACATTTAAAAATCATGTG
327455 A
1 A
327456 TATATTATGT
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:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (18 bp):
ACATTTAAAAATCATGTG
Found at i:333085 original size:30 final size:27
Alignment explanation
Indices: 333045--333099 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 27
333035 TAATGTATGT
333045 ATTTTATATCTGTGTAATGATGTATTTTA
1 ATTTTATATC--TGTAATGATGTATTTTA
*
333074 ATTTATATATCTGTAGTGATGTATTT
1 ATTT-TATATCTGTAATGATGTATTT
333100 ATTTTTGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 14 0.58
29 4 0.17
30 6 0.25
ACGTcount: A:0.27, C:0.04, G:0.15, T:0.55
Consensus pattern (27 bp):
ATTTTATATCTGTAATGATGTATTTTA
Found at i:333712 original size:3 final size:3
Alignment explanation
Indices: 333704--333735 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
333694 ATTAAAGTTT
333704 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
333736 GTTGCTCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:349779 original size:2 final size:2
Alignment explanation
Indices: 349772--349811 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
349762 AAGTGGAAGA
349772 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
349812 CCTAACATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:351533 original size:9 final size:9
Alignment explanation
Indices: 351519--351583 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 9
351509 GGCTGCTGGA
351519 AACCGGTTT
1 AACCGGTTT
351528 AACCGGTTTT
1 AACCGG-TTT
351538 CAACCGGTTCT
1 -AACCGGTT-T
*
351549 GACCGGTTT
1 AACCGGTTT
* *
351558 GACCGGTTCG
1 AACCGGTT-T
351568 AACCGGTTT
1 AACCGGTTT
*
351577 GACCGGT
1 AACCGGT
351584 CTGACCCGAC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
9 21 0.45
10 19 0.40
11 7 0.15
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:351544 original size:20 final size:21
Alignment explanation
Indices: 351519--351576 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 21
351509 GGCTGCTGGA
351519 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
351539 AACCGGTTCTGACCGG-TTT-
1 AACCGGTTCTAACCGGTTTTC
* *
351558 GACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
351577 GACCGGTCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 13 0.41
20 13 0.41
21 6 0.19
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:351555 original size:10 final size:10
Alignment explanation
Indices: 351540--351589 Score: 63
Period size: 9 Copynumber: 5.3 Consensus size: 10
351530 CCGGTTTTCA
351540 ACCGGTTCTG
1 ACCGGTTCTG
351550 ACCGGTT-TG
1 ACCGGTTCTG
351559 ACCGGTTC-G
1 ACCGGTTCTG
351568 AACCGGTT-TG
1 -ACCGGTTCTG
351578 ACCGG-TCTG
1 ACCGGTTCTG
351587 ACC
1 ACC
351590 CGACCCGACC
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 1 0.03
9 20 0.56
10 15 0.42
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.26
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:351564 original size:19 final size:19
Alignment explanation
Indices: 351540--351589 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
351530 CCGGTTTTCA
351540 ACCGGTTCTGACCGGTTTG
1 ACCGGTTCTGACCGGTTTG
351559 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTG-ACCGGTTTG
351578 ACCGG-TCTGACC
1 ACCGGTTCTGACC
351590 CGACCCGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.21
19 23 0.79
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.26
Consensus pattern (19 bp):
ACCGGTTCTGACCGGTTTG
Found at i:351607 original size:17 final size:17
Alignment explanation
Indices: 351585--351640 Score: 112
Period size: 17 Copynumber: 3.3 Consensus size: 17
351575 TTGACCGGTC
351585 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
351602 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
351619 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
351636 TGACC
1 TGACC
351641 GTTGACTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:366584 original size:25 final size:25
Alignment explanation
Indices: 366555--366603 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
366545 ATATTAATAA
366555 ATTTAATTTAAATAAAAATATATAT
1 ATTTAATTTAAATAAAAATATATAT
* *
366580 ATTTAATTTAAATATATATATATA
1 ATTTAATTTAAATAAAAATATATA
366604 CCCGACCCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTTAATTTAAATAAAAATATATAT
Found at i:366645 original size:12 final size:12
Alignment explanation
Indices: 366601--366666 Score: 73
Period size: 12 Copynumber: 5.6 Consensus size: 12
366591 ATATATATAT
*
366601 ATACCCGACCCG
1 ATACCCGACCCA
*
366613 ATTCCC-AGCCCA
1 ATACCCGA-CCCA
366625 ATA-CCGACCCA
1 ATACCCGACCCA
366636 ATACCCGACCCA
1 ATACCCGACCCA
* *
366648 ATACCTGGCCCA
1 ATACCCGACCCA
366660 ATACCCG
1 ATACCCG
366667 TTTAAATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
11 10 0.22
12 35 0.78
ACGTcount: A:0.29, C:0.47, G:0.12, T:0.12
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:369494 original size:31 final size:32
Alignment explanation
Indices: 369422--369494 Score: 85
Period size: 33 Copynumber: 2.3 Consensus size: 32
369412 CGAAGAAAAA
* **
369422 AAATATTAAATTTAGATACTAAATTAATCTAAG
1 AAATTTTAAATTTAGATACTAAA-TAAAATAAG
*
369455 AAATTTTAAATTTAGATACTAAA-AAAATAAT
1 AAATTTTAAATTTAGATACTAAATAAAATAAG
*
369486 TAATTTTAA
1 AAATTTTAA
369495 TTAATATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 13 0.37
33 22 0.63
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (32 bp):
AAATTTTAAATTTAGATACTAAATAAAATAAG
Found at i:370958 original size:22 final size:20
Alignment explanation
Indices: 370912--370951 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
370902 CAGTGTTTAA
370912 TTTAAAAATTATATTAAAAT
1 TTTAAAAATTATATTAAAAT
370932 TTTAAAAATTCA-ATTAAAAT
1 TTTAAAAATT-ATATTAAAAT
370952 ATTTTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTAAAAATTATATTAAAAT
Found at i:375084 original size:6 final size:6
Alignment explanation
Indices: 375073--375107 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
375063 CAAATAAAGG
375073 TATAGA TATAGA TATAGA TATAGA TATAGA TATAG
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAG
375108 CTGTATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (6 bp):
TATAGA
Found at i:377405 original size:2 final size:2
Alignment explanation
Indices: 377400--377453 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
377390 TGTGTGTGTG
377400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
377442 TA TA TA TA TA TA
1 TA TA TA TA TA TA
377454 ACTTTTGGGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:377960 original size:24 final size:25
Alignment explanation
Indices: 377913--377961 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
377903 ATGAATTATT
*
377913 TAATTTCGTATTTCATATGATTTTA
1 TAATTTCGTATATCATATGATTTTA
*
377938 TAATTTCGTATATC-TATGTTTTTA
1 TAATTTCGTATATCATATGATTTTA
377962 ATATAATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (25 bp):
TAATTTCGTATATCATATGATTTTA
Found at i:378385 original size:29 final size:29
Alignment explanation
Indices: 378348--378414 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
378338 AAAAAAGGCT
* ** *
378348 AAAAA-ATTATTAGACGTTAAAAATGATC
1 AAAAATATTACTAGACACTAAAAATAATC
*
378376 AAAAATATTACTAGACACTACAAATAATC
1 AAAAATATTACTAGACACTAAAAATAATC
*
378405 GAAAATATTA
1 AAAAATATTA
378415 AAAAATAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.16
29 27 0.84
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.27
Consensus pattern (29 bp):
AAAAATATTACTAGACACTAAAAATAATC
Found at i:379062 original size:17 final size:18
Alignment explanation
Indices: 379035--379068 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
379025 ATATTAATAA
*
379035 TTATGTAAATATTATTTT
1 TTATGTAAATAATATTTT
379053 TTAT-TAAATAATATTT
1 TTATGTAAATAATATTT
379069 ATATAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTATGTAAATAATATTTT
Found at i:379077 original size:29 final size:28
Alignment explanation
Indices: 379015--379095 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
379005 TTTAAATTGT
379015 TATTATTTTTATATTAATAATTATGTAAA
1 TATTATTTTT-TATTAATAATTATGTAAA
* *
379044 TATTATTTTTTATTAAATAA-TATTTATA
1 TATTATTTTTTATT-AATAATTATGTAAA
* * *
379072 TAATTATTATTTATTTAGAATTAT
1 T-ATTATTTTTTATTAATAATTAT
379096 TAATTTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 14 0.32
29 30 0.68
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TATTATTTTTTATTAATAATTATGTAAA
Found at i:380641 original size:19 final size:21
Alignment explanation
Indices: 380603--380641 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
380593 TAAATTATTA
*
380603 TATATTATTTTTACTGAAATC
1 TATATTATTTTTACTAAAATC
380624 TATATT-TTTTT-CTAAAAT
1 TATATTATTTTTACTAAAAT
380642 TTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (21 bp):
TATATTATTTTTACTAAAATC
Found at i:388447 original size:17 final size:17
Alignment explanation
Indices: 388425--388474 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
388415 TTAATAGTTT
388425 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
*
388442 GTATTTAATTTATTTGA
1 GTATTTAATTTATTTAA
* *
388459 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
388475 TTTTTTTGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:409868 original size:27 final size:27
Alignment explanation
Indices: 409809--409875 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
409799 AAAAACGATG
409809 GTAAT-AATAATAAAGATATATACAATA
1 GTAATAAATAA-AAAGATATATACAATA
** *
409836 AAAATAAATAAAAAGATATATATAATA
1 GTAATAAATAAAAAGATATATACAATA
*
409863 GTAATAAGTAAAA
1 GTAATAAATAAAA
409876 TAAAAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 28 0.85
28 5 0.15
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.27
Consensus pattern (27 bp):
GTAATAAATAAAAAGATATATACAATA
Found at i:411426 original size:15 final size:15
Alignment explanation
Indices: 411406--411438 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
411396 TGGAAACATG
411406 AAATAA-AAAATAAAT
1 AAATAATAAAAT-AAT
411421 AAATAATAAAATAAT
1 AAATAATAAAATAAT
411436 AAA
1 AAA
411439 ATATGTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATAATAAAATAAT
Found at i:412106 original size:106 final size:106
Alignment explanation
Indices: 411939--413034 Score: 1779
Period size: 106 Copynumber: 10.4 Consensus size: 106
411929 GTATTGCTCC
* *** * * * * * *
411939 GAGTCCAATATCCTCCACCGTGGAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
412004 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
412045 GAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAGTTGCTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
412110 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
412151 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTACTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
412216 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
412257 GAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAGTTGCTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
412322 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
412363 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTACTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
412428 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
412469 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG-TCCTGAAATTGAGAAGTTGCTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT-CTGAAATTGAGAAGTTGTTTATTGACA
412533 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
412575 GAGTCCAATATCCTCCATTGTGAAGTTGAAATTGGCTCTGAATTTGAGAA-ATATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
412639 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
412680 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAA-ATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
412744 CCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
412785 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAA-ATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
412849 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
412890 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAA-ATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
412954 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTCGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
412995 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
413035 GGTAAATCCT
Statistics
Matches: 941, Mismatches: 47, Indels: 5
0.95 0.05 0.01
Matches are distributed among these distances:
105 401 0.43
106 539 0.57
107 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:413258 original size:1 final size:1
Alignment explanation
Indices: 413252--413280 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
413242 CACATTCTGG
413252 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
413281 GGAAATGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:413883 original size:55 final size:56
Alignment explanation
Indices: 413810--413917 Score: 164
Period size: 55 Copynumber: 1.9 Consensus size: 56
413800 TTTTCTCTTC
* * *
413810 TTTTTTCTTTTTCTTTTTTCAATTTAGGACGCCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTTCTTTTTCTTTTTTCAACTTAGAACGCCCTCTCGGGTTTTCACCCTAAACG
* *
413866 TTTTTT-TTTTTTTTTTTTCAACTTAGAACGCCCTCTCGGGTTTTCATCCTAA
1 TTTTTTCTTTTTCTTTTTTCAACTTAGAACGCCCTCTCGGGTTTTCACCCTAA
413918 GCGAAGTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 41 0.87
56 6 0.13
ACGTcount: A:0.15, C:0.22, G:0.11, T:0.52
Consensus pattern (56 bp):
TTTTTTCTTTTTCTTTTTTCAACTTAGAACGCCCTCTCGGGTTTTCACCCTAAACG
Found at i:423342 original size:20 final size:20
Alignment explanation
Indices: 423303--423347 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
423293 AAATGGTTAG
*
423303 TAAATAAAAATAAATGGAAA
1 TAAATAAAAATAAATAGAAA
423323 TAAATAAAAATAACA-AGAAA
1 TAAATAAAAATAA-ATAGAAA
423343 TAAAT
1 TAAAT
423348 GGCAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (20 bp):
TAAATAAAAATAAATAGAAA
Found at i:424391 original size:27 final size:27
Alignment explanation
Indices: 424332--424398 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
424322 AAAAACGATG
424332 GTAAT-AATAATAAAGATATATACAATA
1 GTAATAAATAA-AAAGATATATACAATA
** *
424359 AAAATAAATAAAAAGATATATATAATA
1 GTAATAAATAAAAAGATATATACAATA
*
424386 GTAATAAGTAAAA
1 GTAATAAATAAAA
424399 TAAAAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 28 0.85
28 5 0.15
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.27
Consensus pattern (27 bp):
GTAATAAATAAAAAGATATATACAATA
Found at i:425953 original size:15 final size:15
Alignment explanation
Indices: 425933--425965 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
425923 TGGAAACATG
425933 AAATAA-AAAATAAAT
1 AAATAATAAAAT-AAT
425948 AAATAATAAAATAAT
1 AAATAATAAAATAAT
425963 AAA
1 AAA
425966 ATATGTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATAATAAAATAAT
Found at i:426665 original size:25 final size:26
Alignment explanation
Indices: 426615--426665 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
426605 AGGGGCGAAC
* *
426615 TTATAAAATTTTAAGTAGATGAAAAT
1 TTATAAAATTTTAAGAAGATAAAAAT
426641 TTATAAAATTTT-AGAAGATAAAAAT
1 TTATAAAATTTTAAGAAGATAAAAAT
426666 ATATTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (26 bp):
TTATAAAATTTTAAGAAGATAAAAAT
Found at i:435165 original size:2 final size:2
Alignment explanation
Indices: 435158--435182 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
435148 TAACTGAATT
435158 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
435183 TAGTTGGATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:438587 original size:18 final size:16
Alignment explanation
Indices: 438564--438598 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
438554 TGTTTTATTA
438564 AATAAAAATCATATTTTT
1 AATAAAAAT-AT-TTTTT
438582 AATAAAAATATTTTTT
1 AATAAAAATATTTTTT
438598 A
1 A
438599 GATCGAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 9 0.53
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AATAAAAATATTTTTT
Found at i:443914 original size:59 final size:59
Alignment explanation
Indices: 443836--443977 Score: 166
Period size: 59 Copynumber: 2.4 Consensus size: 59
443826 TTGGGAACCA
*
443836 ATTTAGAATGAATATCATAGTTTGGGGATGAAATT-AGAATGTTAAAAAGTTTAAGGACT
1 ATTTAGAATGAAGATCATAGTTTGGGGATGAAATTGA-AATGTTAAAAAGTTTAAGGACT
* * *
443895 ATTTAGAAT-AAGAGTCATAGTTTGGGTATGAAGTTGAAATGTTTAAAAGTTTAAGGA-T
1 ATTTAGAATGAAGA-TCATAGTTTGGGGATGAAATTGAAATGTTAAAAAGTTTAAGGACT
* *
443953 CATTTTGAATTGAGGA-CATAGTTTG
1 -ATTTAGAA-TGAAGATCATAGTTTG
443978 AGGACATATA
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
58 4 0.06
59 63 0.88
60 2 0.03
61 3 0.04
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (59 bp):
ATTTAGAATGAAGATCATAGTTTGGGGATGAAATTGAAATGTTAAAAAGTTTAAGGACT
Found at i:445611 original size:18 final size:17
Alignment explanation
Indices: 445579--445612 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
445569 ACAAATTTAA
445579 ATAATATATTCATATTC
1 ATAATATATTCATATTC
*
445596 ATAATATTTATCATATT
1 ATAATATAT-TCATATT
445613 TAAGGTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAATATATTCATATTC
Found at i:445736 original size:24 final size:23
Alignment explanation
Indices: 445708--445781 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 23
445698 TATTTTTATT
445708 AATTTTTTAATAATAAATAATTAA
1 AATTTTTTAA-AATAAATAATTAA
* *
445732 AATTTAATCAAAATATAAT-ATTAA
1 AATTT-TTTAAAATA-AATAATTAA
*
445756 ATATATTTTTAAAAATAATTAATTAA
1 A-AT-TTTTT-AAAATAAATAATTAA
445782 GTGACTAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
24 15 0.38
25 11 0.28
26 13 0.33
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTTTTTAAAATAAATAATTAA
Found at i:446111 original size:21 final size:21
Alignment explanation
Indices: 446087--446131 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
446077 GACAATTTAC
* * *
446087 TAAATATATTAATATTTTAGA
1 TAAAAATAATAATATTTTAAA
446108 TAAAAATAATAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
446129 TAA
1 TAA
446132 TTTTTTATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAA
Found at i:455477 original size:21 final size:21
Alignment explanation
Indices: 455426--455478 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
455416 ATTATGACTA
455426 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
455447 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
455468 TCGCAATGCGA
1 TCGCAATGCGA
455479 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:455511 original size:21 final size:21
Alignment explanation
Indices: 455468--455535 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
455458 TTTTCCCAAT
** *
455468 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
455488 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
455509 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
455530 TTGCAA
1 TCGCAA
455536 CGCGGTACTG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 12 0.28
21 31 0.72
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:455571 original size:41 final size:41
Alignment explanation
Indices: 455526--455663 Score: 134
Period size: 41 Copynumber: 3.4 Consensus size: 41
455516 GCGAATTTGG
* *
455526 AAAATTGCAACGCGGTACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * *
455567 AAAATCGCAACGCGATACTGACTTTCGTAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
** * * * *
455607 AATTTCGCAACTCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
455648 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
455664 TTTCAAAGCG
Statistics
Matches: 74, Mismatches: 22, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
40 31 0.42
41 43 0.58
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.25
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:455604 original size:20 final size:20
Alignment explanation
Indices: 455571--455637 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
455561 TAATACAAAA
*
455571 TCGCAACGCGATACTGACTT
1 TCGCAACTCGATACTGACTT
* * *
455591 TCGTAACTCGATACTTAATT
1 TCGCAACTCGATACTGACTT
*
455611 TCGCAACTCAATACTGACTT
1 TCGCAACTCGATACTGACTT
455631 TCGCAAC
1 TCGCAAC
455638 GAGATAATAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (20 bp):
TCGCAACTCGATACTGACTT
Found at i:455858 original size:22 final size:22
Alignment explanation
Indices: 455830--455873 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
455820 CACTCTCTCA
455830 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
455852 CCCATCTCGGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
455874 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:0.20, C:0.43, G:0.18, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:456175 original size:20 final size:20
Alignment explanation
Indices: 456152--456194 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
456142 GATAGTCAAA
*
456152 TTCGCGTTGCGATTGTCATT
1 TTCGCGTTACGATTGTCATT
* *
456172 TTCGTGTTACGATTTTCATT
1 TTCGCGTTACGATTGTCATT
456192 TTC
1 TTC
456195 AGAAACTATT
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:0.12, C:0.19, G:0.19, T:0.51
Consensus pattern (20 bp):
TTCGCGTTACGATTGTCATT
Found at i:456385 original size:25 final size:24
Alignment explanation
Indices: 456331--456385 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
456321 TGTTTATTAT
* *
456331 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
456355 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
456381 TGTTT
1 TGTTT
456386 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:457534 original size:18 final size:18
Alignment explanation
Indices: 457513--457560 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
457503 TCCACTTCGG
457513 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
457531 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
457549 GAGCCATCACCT
1 GAGCCATCACCT
457561 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:458118 original size:20 final size:20
Alignment explanation
Indices: 458093--458138 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
458083 TAGTTTACTT
458093 TCGCAACAC-GAAAATGACTA
1 TCGCAACACAG-AAATGACTA
* *
458113 TCGCAACGCAGAAATGGCTA
1 TCGCAACACAGAAATGACTA
458133 TCGCAA
1 TCGCAA
458139 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACAGAAATGACTA
Found at i:458147 original size:19 final size:20
Alignment explanation
Indices: 458104--458159 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
458094 CGCAACACGA
458104 AAATGACTATCGCAACGCAG
1 AAATGACTATCGCAACGCAG
* *
458124 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCAG
**
458143 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
458160 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCAG
Found at i:458186 original size:19 final size:19
Alignment explanation
Indices: 458093--458195 Score: 72
Period size: 19 Copynumber: 5.6 Consensus size: 19
458083 TAGTTTACTT
* **
458093 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
458113 TCGCAACGCAGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
458133 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
458152 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
458166 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
458185 TCGCAATGCGA
1 TCGCAACGCGA
458196 TTTGTGTTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 27 0.40
20 24 0.35
21 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:458267 original size:20 final size:20
Alignment explanation
Indices: 458233--458287 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
458223 TTGCGATTTT
*
458233 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
458252 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
458272 CATTTCCGCGTTGCGA
1 CATTTCCGCGTTGCGA
458288 AAGTAAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 5 0.15
20 28 0.85
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:458764 original size:42 final size:42
Alignment explanation
Indices: 458655--458743 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
458645 GACTCACCTG
* * * * *
458655 TCATTCCTCAAGAGTCCCCTCCAATCATTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCCCCCACCATTCAAGAGGCCACTA
* *
458697 TCATCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCCACCATTCAAGAGGCCACTA
458739 TCATC
1 TCATC
458744 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.24, C:0.42, G:0.13, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCCCCCACCATTCAAGAGGCCACTA
Found at i:460123 original size:14 final size:14
Alignment explanation
Indices: 460089--460127 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
460079 TTGATTGTTT
460089 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
460103 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
460117 TGTTGATTTGT
1 AATTGATTTGT
460128 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:460273 original size:14 final size:14
Alignment explanation
Indices: 460254--460307 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
460244 GAAACTGACT
460254 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
460268 ATCGCAATGTGAAATGAAA
1 ATCGCAA--CG--A-GAAA
460287 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
460301 ATCGCAA
1 ATCGCAA
460308 TGCGATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 18 0.55
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.33
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:460300 original size:19 final size:19
Alignment explanation
Indices: 460264--460300 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
460254 ATCGCAACGA
* *
460264 GAAAATCGCAATGTGAAAT
1 GAAAATCGCAACGAGAAAT
460283 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
460301 ATCGCAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.14, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:460356 original size:20 final size:20
Alignment explanation
Indices: 460331--460426 Score: 97
Period size: 20 Copynumber: 4.8 Consensus size: 20
460321 TCGCATTGCG
*
460331 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
460351 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
460372 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
460391 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
460411 ATTTTC-ACGTTGCGAT
1 ATTTTCGA-GTTGCGAT
460427 TTCCCCGTTG
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.05
20 54 0.90
21 3 0.05
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:460364 original size:34 final size:36
Alignment explanation
Indices: 460319--460406 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 36
460309 GCGATTTTCA
* *
460319 TTTCGCATTGCGATTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
460353 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCAT
460393 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
460407 AGCCATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
34 12 0.26
35 5 0.11
38 1 0.02
39 1 0.02
40 27 0.59
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
Found at i:460424 original size:40 final size:41
Alignment explanation
Indices: 460331--460426 Score: 117
Period size: 40 Copynumber: 2.4 Consensus size: 41
460321 TCGCATTGCG
* ***
460331 ATTTTCTAGTTGCGATAGCCATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGATAGCCATTTTCGCGTTGCGATTAGCC
*
460372 A-TTTCGAATTGCGATAGCCATTTTCGCGTTGCGA-TAGCC
1 ATTTTCGAGTTGCGATAGCCATTTTCGCGTTGCGATTAGCC
460411 ATTTTC-ACGTTGCGAT
1 ATTTTCGA-GTTGCGAT
460427 TTCCCCGTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
39 4 0.09
40 42 0.89
41 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (41 bp):
ATTTTCGAGTTGCGATAGCCATTTTCGCGTTGCGATTAGCC
Found at i:460665 original size:20 final size:20
Alignment explanation
Indices: 460640--460731 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
460630 TTGAAGATGA
460640 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
460660 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
460680 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
460701 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
460721 TTGCGATTTTC
1 TTGCGATTTTC
460732 CAAATTCGCA
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:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:461765 original size:12 final size:12
Alignment explanation
Indices: 461748--461784 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
461738 ATATAATCCT
461748 GAAGAAGAAAAA
1 GAAGAAGAAAAA
461760 GAAGAAGAAAAA
1 GAAGAAGAAAAA
461772 GAAGAAGAAAAA
1 GAAGAAGAAAAA
461784 G
1 G
461785 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:464334 original size:21 final size:21
Alignment explanation
Indices: 464288--464365 Score: 124
Period size: 21 Copynumber: 3.8 Consensus size: 21
464278 TGATAGTAAG
*
464288 ATTCGCATTGCGA-TTTACGT-
1 ATTCGCATTGCGATTTTTC-TA
464308 ATTCGCATTGCGATTTTTCTA
1 ATTCGCATTGCGATTTTTCTA
464329 ATTCGCATTGCGATTTTTCTA
1 ATTCGCATTGCGATTTTTCTA
464350 ATTCGCATTGCGATTT
1 ATTCGCATTGCGATTT
464366 ACTTAATCGC
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
20 14 0.25
21 41 0.75
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (21 bp):
ATTCGCATTGCGATTTTTCTA
Found at i:464336 original size:41 final size:41
Alignment explanation
Indices: 464288--464525 Score: 159
Period size: 41 Copynumber: 5.8 Consensus size: 41
464278 TGATAGTAAG
*
464288 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTTCTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTTCAA
*
464329 ATTCGCATTGCGATTTTTC-TAATTCGCATTGCGATTTACTT--A
1 ATTCGCATTGCGA-TTTACGT-ATTCGCATTGCGATTT--TTCAA
* * * * *
464371 A-TCGCGTTGCGATTTACGTATTCACATTGCGAATTATGAA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTTCAA
* ** * * * ****
464411 AATCGCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGAAA
1 ATTCGCATTGCGATTTACGT-ATTCGCATTGCG-ATTTTTCAA
* *
464453 ATT-GCATTGCGATAGT-CAGTA-TCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGAT-TTAC-GTATTCGCATTGCGATTTTTCAA
* *
464493 ATTCGCATTTCGATTTACTTATTCGCATTGCGA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA
464526 ATTGGGAAAA
Statistics
Matches: 151, Mismatches: 30, Indels: 32
0.71 0.14 0.15
Matches are distributed among these distances:
38 1 0.01
40 36 0.24
41 79 0.52
42 30 0.20
43 3 0.02
44 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36
Consensus pattern (41 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTTCAA
Found at i:464372 original size:21 final size:21
Alignment explanation
Indices: 464288--464402 Score: 123
Period size: 20 Copynumber: 5.6 Consensus size: 21
464278 TGATAGTAAG
*
464288 ATTCGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTACTTA
*
464308 ATTCGCATTGCGATTT-TTCTA
1 ATTCGCATTGCGATTTACT-TA
*
464329 ATTCGCATTGCGATTT-TTCTA
1 ATTCGCATTGCGATTTACT-TA
464350 ATTCGCATTGCGATTTACTTA
1 ATTCGCATTGCGATTTACTTA
* *
464371 A-TCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGATTTACTTA
*
464390 ATTCACATTGCGA
1 ATTCGCATTGCGA
464403 ATTATGAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
19 1 0.01
20 42 0.50
21 40 0.48
22 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (21 bp):
ATTCGCATTGCGATTTACTTA
Found at i:464425 original size:21 final size:21
Alignment explanation
Indices: 464399--464454 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
464389 TATTCACATT
*
464399 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
464420 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
464440 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
464455 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:464463 original size:21 final size:21
Alignment explanation
Indices: 464398--464464 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
464388 GTATTCACAT
*
464398 TGCGAATTATGAAAATCGCAA
1 TGCGAATTACGAAAATCGCAA
* *
464419 CGCGAA-TACGTAAATCGCAA
1 TGCGAATTACGAAAATCGCAA
* * *
464439 TGCGAATTAGGAAAATTGCAT
1 TGCGAATTACGAAAATCGCAA
464460 TGCGA
1 TGCGA
464465 TAGTCAGTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
TGCGAATTACGAAAATCGCAA
Found at i:464500 original size:21 final size:20
Alignment explanation
Indices: 464474--464525 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
464464 ATAGTCAGTA
*
464474 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
* **
464495 TCGCATTTCGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
464515 TCGCATTGCGA
1 TCGCATTGCGA
464526 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:464567 original size:21 final size:22
Alignment explanation
Indices: 464515--464567 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
464505 ATTTACTTAT
464515 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
464536 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
*
464557 TCGTATTGCGA
1 TCGCATTGCGA
464568 TAGTTATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:464861 original size:2 final size:2
Alignment explanation
Indices: 464854--464880 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
464844 ATTAATAAAA
464854 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
464881 GGTTACCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:467892 original size:17 final size:18
Alignment explanation
Indices: 467853--467894 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
467843 AACACAAGGC
* *
467853 TAACTTGTTTTTTTGTTC
1 TAACTTGTTTATTTGTTA
467871 T-ACTT-TTTATTTGTTA
1 TAACTTGTTTATTTGTTA
467887 TAACTTGT
1 TAACTTGT
467895 GGCATTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.50
17 8 0.40
18 2 0.10
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.64
Consensus pattern (18 bp):
TAACTTGTTTATTTGTTA
Found at i:470878 original size:149 final size:149
Alignment explanation
Indices: 470604--470896 Score: 514
Period size: 149 Copynumber: 2.0 Consensus size: 149
470594 CAATGAAATC
* * *
470604 GAAAGTGTTGGCAGTGCTTATCAAATGTGAAGCTTTGTTACTTTTATTTGACATCGAAGCGCCCC
1 GAAAGTGTTGGCAATGCTTATCAAATGTGAAGCTTTGTTACTTTTATTTGACACCGAAGCACCCC
*
470669 ACTTCAGTTACTTTGACAAATAGAATCCAGAAAGCTTTGTTACTTTAGGTAGAGACGGATGAAAG
66 ACTTCAGTTACTTTGACAAATAGAATCCAGAAAGCTTTGTTACTTTAGGAAGAGACGGATGAAAG
470734 AAGGTTTTCCTCCTATCCA
131 AAGGTTTTCCTCCTATCCA
*
470753 GAAAGTGTTGGCAATGCTTATCAAATGTGAAGTTTTGTTACTTTTATTTGACACCGAAGCACCCC
1 GAAAGTGTTGGCAATGCTTATCAAATGTGAAGCTTTGTTACTTTTATTTGACACCGAAGCACCCC
* *
470818 AGTTCAGTTACTTTGACAAATAGAATCCAGAAAGCTTTGTTACTTTAGGAAGAGATGGATGAAAG
66 ACTTCAGTTACTTTGACAAATAGAATCCAGAAAGCTTTGTTACTTTAGGAAGAGACGGATGAAAG
*
470883 AGGGTTTTCCTCCT
131 AAGGTTTTCCTCCT
470897 CCTGGCCCGT
Statistics
Matches: 136, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
149 136 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (149 bp):
GAAAGTGTTGGCAATGCTTATCAAATGTGAAGCTTTGTTACTTTTATTTGACACCGAAGCACCCC
ACTTCAGTTACTTTGACAAATAGAATCCAGAAAGCTTTGTTACTTTAGGAAGAGACGGATGAAAG
AAGGTTTTCCTCCTATCCA
Found at i:472493 original size:3 final size:3
Alignment explanation
Indices: 472478--472545 Score: 64
Period size: 3 Copynumber: 21.7 Consensus size: 3
472468 CTTCATTATA
* *
472478 ATC ATC CTC ATC ATC ATCC ATC AAGTC ATC ATC ATC ATC ATC GTC ATC
1 ATC ATC ATC ATC ATC AT-C ATC -A-TC ATC ATC ATC ATC ATC ATC ATC
** *
472526 ATC GCC ATC ATC ATT ATC AT
1 ATC ATC ATC ATC ATC ATC AT
472546 TCACACCTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
3 45 0.87
4 5 0.10
5 2 0.04
ACGTcount: A:0.29, C:0.34, G:0.04, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:501043 original size:4 final size:4
Alignment explanation
Indices: 501034--501060 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
501024 GCTGTCCTTG
501034 TTCA TTCA TTCA TTCA TTCA TTCA TTC
1 TTCA TTCA TTCA TTCA TTCA TTCA TTC
501061 TAAACCCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.26, G:0.00, T:0.52
Consensus pattern (4 bp):
TTCA
Found at i:503014 original size:2 final size:2
Alignment explanation
Indices: 503007--503050 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
502997 TTTCTAAATT
503007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
503047 TA TA
1 TA TA
503051 AATTTTATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:503234 original size:2 final size:2
Alignment explanation
Indices: 503222--503266 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
503212 TATCAATAAA
503222 AT AT A- 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
503263 AT AT
1 AT AT
503267 TAAAATATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:503545 original size:17 final size:17
Alignment explanation
Indices: 503523--503557 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
503513 TTTAAGAGAA
503523 CGATTAACCTTACCTAT
1 CGATTAACCTTACCTAT
503540 CGATTAACCTTACCTAT
1 CGATTAACCTTACCTAT
503557 C
1 C
503558 TCCTTCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (17 bp):
CGATTAACCTTACCTAT
Found at i:506831 original size:2 final size:2
Alignment explanation
Indices: 506824--506855 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
506814 TGATATTTTA
506824 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
506856 TATGAAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.