Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015361.1 Kokia drynarioides strain JFW-HI SEQ_130408, 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: 183492
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 312 characters in sequence are not A, C, G, or T
Found at i:13168 original size:17 final size:18
Alignment explanation
Indices: 13138--13171 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13128 CTTGCTTAAG
*
13138 TTCAGATCAGTTTCAAGT
1 TTCAGATCAATTTCAAGT
13156 TTCAG-TCAATTTCAAG
1 TTCAGATCAATTTCAAG
13172 ATCGGGTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (18 bp):
TTCAGATCAATTTCAAGT
Found at i:22293 original size:21 final size:20
Alignment explanation
Indices: 22256--22294 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
22246 ACCATTGTCT
* *
22256 TTTTTTTTTTAAAAATATTA
1 TTTTATTTTGAAAAATATTA
22276 TTTTATTTTGAAATAATAT
1 TTTTATTTTGAAA-AATAT
22295 AATCAACCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTATTTTGAAAAATATTA
Found at i:22956 original size:40 final size:39
Alignment explanation
Indices: 22897--22975 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 39
22887 CACTCCATCT
22897 CATCACACGTCTTGCAACCCCAATAACTTAACATAGTTAA
1 CATCACACGTCTTGCAACCCCAATAACTT-ACATAGTTAA
* *
22937 CATCACACGTCTTGTAACCCCAATAACTTGCATAGTTAA
1 CATCACACGTCTTGCAACCCCAATAACTTACATAGTTAA
22976 TTTAACATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
39 9 0.24
40 28 0.76
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.27
Consensus pattern (39 bp):
CATCACACGTCTTGCAACCCCAATAACTTACATAGTTAA
Found at i:29993 original size:23 final size:23
Alignment explanation
Indices: 29967--30010 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
29957 AGGAAAGCCA
*
29967 AAATTTAAGAATTAATTTAAAAG
1 AAATTAAAGAATTAATTTAAAAG
**
29990 AAATTAAAGTTTTAATTTAAA
1 AAATTAAAGAATTAATTTAAA
30011 CATCGAAACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (23 bp):
AAATTAAAGAATTAATTTAAAAG
Found at i:30545 original size:22 final size:23
Alignment explanation
Indices: 30520--30565 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
30510 GTCTTTTGCA
* *
30520 TTTT-TACTTGATCAATTTTAGT
1 TTTTGTACTCGATAAATTTTAGT
*
30542 TTTTGTACTCGGTAAATTTTAGT
1 TTTTGTACTCGATAAATTTTAGT
30565 T
1 T
30566 CATGTACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.57
Consensus pattern (23 bp):
TTTTGTACTCGATAAATTTTAGT
Found at i:31828 original size:3 final size:3
Alignment explanation
Indices: 31814--31847 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
31804 TTAACACAAG
31814 CTT CTAT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT
31848 TCTTTCAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:33621 original size:5 final size:6
Alignment explanation
Indices: 33606--33631 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
33596 AAATTAGCTC
33606 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
33632 CAGAAATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:39155 original size:19 final size:19
Alignment explanation
Indices: 39115--39157 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
39105 ATATTATAAG
*
39115 AATTATTAAAATGGAAAGA
1 AATTATTAAAATAGAAAGA
*
39134 AATTATTAAACATATAAA-A
1 AATTATTAAA-ATAGAAAGA
39153 AATTA
1 AATTA
39158 GTTTTTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.30
Consensus pattern (19 bp):
AATTATTAAAATAGAAAGA
Found at i:40437 original size:22 final size:22
Alignment explanation
Indices: 40399--40445 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
40389 ATAAAAATAT
40399 TAAATATTAAAATAAAATAAAA
1 TAAATATTAAAATAAAATAAAA
* *
40421 TAAATACTTTAAA-AAAATAATA
1 TAAATA-TTAAAATAAAATAAAA
40443 TAA
1 TAA
40446 GCAGACTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAATATTAAAATAAAATAAAA
Found at i:41965 original size:22 final size:22
Alignment explanation
Indices: 41935--41977 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41925 AATTAAATCG
* *
41935 TATATTTTTATTATATTAAAAA
1 TATAATTTTATCATATTAAAAA
*
41957 TATAATTTTATCATTTTAAAA
1 TATAATTTTATCATATTAAAA
41978 TGATTAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATAATTTTATCATATTAAAAA
Found at i:44950 original size:106 final size:100
Alignment explanation
Indices: 44716--44966 Score: 297
Period size: 106 Copynumber: 2.5 Consensus size: 100
44706 TGTGTGTGTG
* * * *
44716 TGTATGGTCTTGAATTGGCC-TTTCAATATTCATAATTGATTGAAACAAAGGGACTTGACCTACC
1 TGTATGGTCTTGAGTTGGCCTTTTC-ACATTCATAATTGACTGAAAAAAAGGGACTTGACCTACC
44780 ATGTTTTCCTTATATCTGTGTGAATGCATGCATGTA
65 ATGTTTTCCTTATATCTGTGTGAATGCATGCATGTA
* * * * * *
44816 TTTAGGGTCTTGAGTTGGCATTTCCACATTCATAAGTGACTGAAAAAAAGGGACTTGAGCTACCA
1 TGTATGGTCTTGAGTTGGCCTTTTCACATTCATAATTGACTGAAAAAAAGGGACTTGACCTACCA
* * *
44881 TGTTTTCCTTGTATATATATGTGTGTGTATGGATGCATGTA
66 TGTTTTCC-----T-TATATCTGTGTGAATGCATGCATGTA
* *
44922 TGTATGGTCTTGAGGTGGCCTTTTCACATACATAATTGACTGAAA
1 TGTATGGTCTTGAGTTGGCCTTTTCACATTCATAATTGACTGAAA
44967 CTAAGGAGTC
Statistics
Matches: 124, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
100 59 0.48
101 3 0.02
105 1 0.01
106 61 0.49
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.37
Consensus pattern (100 bp):
TGTATGGTCTTGAGTTGGCCTTTTCACATTCATAATTGACTGAAAAAAAGGGACTTGACCTACCA
TGTTTTCCTTATATCTGTGTGAATGCATGCATGTA
Found at i:45277 original size:98 final size:98
Alignment explanation
Indices: 44990--45300 Score: 358
Period size: 100 Copynumber: 3.1 Consensus size: 98
44980 GTGCGTGCGC
* * * *
44990 GCATGCATGTAT-AGTCTTGAATTGGCCTTTTCGCATTCATAATTGACTGAAACAAAGGGACTTG
1 GCATGCATGCATGA-TCTTGAATTGGCTTTTTCACATTCATAATTGATTGAAACAAAGGGACTTG
* *
45054 AGCTACCATG-TTTCCTTTATATATGTATGTATGAAT
65 AGCTACCATGTTTTCC-TTATATGTGTAT-T-TGCAT
* * * ** * * *
45090 GTACGTATTTATGGTCTTCAATTGGCTTTTTCACATTCATAATTTTGACTT-AAACGAAGGGACT
1 GCATGCATGCATGATCTTGAATTGGCTTTTTCACATTCATAA--TTGA-TTGAAACAAAGGGACT
45154 TGAGCTACCATGTTTTCCTTATATGTGTATTTGCAT
63 TGAGCTACCATGTTTTCCTTATATGTGTATTTGCAT
45190 GCATGCATGCATGATCTTGAATTGGCTTTTTCACATTCATAATTGATTGAAACAAAGGGACTTGA
1 GCATGCATGCATGATCTTGAATTGGCTTTTTCACATTCATAATTGATTGAAACAAAGGGACTTGA
* * * * * *
45255 ACTACCGTGTTTTCCTTGTATGTATGTATGCAT
66 GCTACCATGTTTTCCTTATATGTGTATTTGCAT
45288 GCATGCATGCATG
1 GCATGCATGCATG
45301 CATGCATGTA
Statistics
Matches: 179, Mismatches: 26, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
97 2 0.01
98 59 0.33
100 72 0.40
101 1 0.01
102 39 0.22
103 6 0.03
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (98 bp):
GCATGCATGCATGATCTTGAATTGGCTTTTTCACATTCATAATTGATTGAAACAAAGGGACTTGA
GCTACCATGTTTTCCTTATATGTGTATTTGCAT
Found at i:45313 original size:4 final size:4
Alignment explanation
Indices: 45282--45308 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
45272 GTATGTATGT
45282 ATGC ATGC ATGC ATGC ATGC ATGC ATG
1 ATGC ATGC ATGC ATGC ATGC ATGC ATG
45309 TATGTTCATG
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:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (4 bp):
ATGC
Found at i:51179 original size:191 final size:192
Alignment explanation
Indices: 50681--51255 Score: 1055
Period size: 192 Copynumber: 3.0 Consensus size: 192
50671 AAACTGTAAT
*
50681 TAGTTATAGCCATTGAAAACACAATGTTCCCGCAAACAAATAACGGAAGCAGTTT-TGTTAAGAT
1 TAGTTATAGCCATTGAAAACACAATGTTCCCACAAACAAATAACGGAAGCAGTTTGT-TTAAGAT
*
50745 GTAAGCCTTTCTGCCCGGCCGGTGAAAACGAAACAAACAGTCAGGCCACTTCTAAGAAAATATGT
65 GTAAGCCTTTCTGCCCGGCCAGTGAAAACGAAACAAACAGTCAGGCCACTTCTAAGAAAATATGT
50810 TTATTCCTTTGTGTTAAACCAAACCTCAAAATACAACTTCCTTATTTAGTTTATGCCTTGTTC
130 TTATTCCTTTGTGTTAAACCAAACCTCAAAATACAACTTCCTTATTTAGTTTATGCCTTGTTC
*
50873 TAGTTATAGCCATTGAAAACACAATGTTCCCACAAACAAATAACGGAAGCAGTTTGTTTTAGATG
1 TAGTTATAGCCATTGAAAACACAATGTTCCCACAAACAAATAACGGAAGCAGTTTGTTTAAGATG
* * *
50938 TAAGCCTTTCTGCCAGGCCAGTGAAAACGAAACAAACATTCAGACCACTTCTAAGAAAATATGTT
66 TAAGCCTTTCTGCCCGGCCAGTGAAAACGAAACAAACAGTCAGGCCACTTCTAAGAAAATATGTT
*
51003 TATTCCTTTGTGTTAAACCAAACCTCAAAATACAACTTCTTTATTTAGTTTATGCCTTGTTC
131 TATTCCTTTGTGTTAAACCAAACCTCAAAATACAACTTCCTTATTTAGTTTATGCCTTGTTC
51065 TAG-TATAGCCATTGAAAACACAATGTTCCCACAAACAAATAACGGAAGCAGTTTGTTTAAGATG
1 TAGTTATAGCCATTGAAAACACAATGTTCCCACAAACAAATAACGGAAGCAGTTTGTTTAAGATG
*
51129 TAAGCCTTTCTGCCCGGCCAGTGAAAACAAAACAAACAGTCAGGCCACTTCTAAGAAAATATGTT
66 TAAGCCTTTCTGCCCGGCCAGTGAAAACGAAACAAACAGTCAGGCCACTTCTAAGAAAATATGTT
51194 TATTCCTTTGTGTTAAACCAAACCTCAAAATACAACTTCCTTATTTAGTTTATGCCTTGTTC
131 TATTCCTTTGTGTTAAACCAAACCTCAAAATACAACTTCCTTATTTAGTTTATGCCTTGTTC
51256 ATAGCATTGA
Statistics
Matches: 369, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
191 182 0.49
192 186 0.50
193 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (192 bp):
TAGTTATAGCCATTGAAAACACAATGTTCCCACAAACAAATAACGGAAGCAGTTTGTTTAAGATG
TAAGCCTTTCTGCCCGGCCAGTGAAAACGAAACAAACAGTCAGGCCACTTCTAAGAAAATATGTT
TATTCCTTTGTGTTAAACCAAACCTCAAAATACAACTTCCTTATTTAGTTTATGCCTTGTTC
Found at i:54438 original size:195 final size:187
Alignment explanation
Indices: 53900--54683 Score: 589
Period size: 195 Copynumber: 4.1 Consensus size: 187
53890 GCATCTGTCT
* * * *
53900 CTCATAAACAGGCTCACGAATT-CCA-AGCAAGAGAGAAAAAAGTTAATGAAAAAAGGTAATATT
1 CTCATAAACAGGATCAAGAATTACAAGAGCAAGAGAGAAAAAAATTAATG-AAAAA-GTAA-ATT
* ** * * *
53963 CTACTTATCTTAAAATACATAATTGCATGCACCTGTC--GTCTTCTTAGATTAAAAATTAATGAA
63 CTACTTATCTTACAATACATAATTGCATGCAATTATCTTTTCTTCTTAGATTAAAAATTAAT--T
* *
54026 AGGGAAAAAAGAAGAAGGTAAAATTCTACTTATCTTACAATAATAAAGGAAAATAAGAAATAGAA
126 A--CAAAAAAG-AG-A-GTAAAATTCTACTTATCTTACAATAATAAAGGAAAATAAAAAATAGAA
54091 AC
186 AC
* * * **
54093 CTCATAAACAGGCTCACGAATTATAAGA--AAGAGAGAAAAATAA-TAATGAAAAAAAAAAATTC
1 CTCATAAACAGGATCAAGAATTACAAGAGCAAGAGAGAAAAA-AATTAATG-AAAAAGTAAATTC
* *
54155 TACTTATCTTACAATACCTAATTGCATGCAACTGTCTTCTTCTTCTTCTTACTTCTTAGATTAAA
64 TACTTATCTTACAATACATAATTGCATGCAA--------TT-ATCTT-TT-CTTCTTAGATTAAA
** *
54220 AATTAATTTTAAAAAA-A-AGTAAAATTTTACTTATCTTACAATAATAAAGGAAAATAAAAAATA
118 AATTAATTACAAAAAAGAGAGTAAAATTCTACTTATCTTACAATAATAAAGGAAAATAAAAAATA
54283 GAAAC
183 GAAAC
54288 CTCA-AAACAGGATCAAGAATTCCCAGCAAGAGCAAGAGAGAAAAAAATTAATGAGAAAACGTAG
1 CTCATAAACAGGATCAAGAATT---A-CAAGAGCAAGAGAGAAAAAAATTAATGA-AAAA-GTA-
*
54352 AATTCTACTTATCTTACAATACATAATAGCATGCAATTATCTTATTCTTCTTAGATTAAAAATTA
59 AATTCTACTTATCTTACAATACATAATTGCATGCAATTATCTT-TTCTTCTTAGATTAAAAATT-
* * **
54417 AATTACAAAAAAGAGAGTAAAATTCTACTTATCCTAC----A-AAA-G-TAAT-AATCAT---AA
122 AATTACAAAAAAGAGAGTAAAATTCTACTTATCTTACAATAATAAAGGAAAATAAAAAATAGAAA
54471 C
187 C
* * * * * *
54472 CTCATAAACAAGCTCACGAATTAC-A-AGCAAGAGAGAATGAAGA-GAA--AAAAGAGTAAATTC
1 CTCATAAACAGGATCAAGAATTACAAGAGCAAGAGAGAA-AAAAATTAATGAAAA-AGTAAATTC
* * ** * * **
54532 TACTTATCTTACGATAAATAATTGTTTGCAACTATCTTCTTCTTCTTAGATTAAAATTTAACGA-
64 TACTTATCTTACAATACATAATTGCATGCAATTATCTT-TTCTTCTTAGATTAAAAATTAATTAC
* * * * * *
54596 AAAAAA-AAAGGAAAATTCTACTTATCCTACAATAATAAAGAAAAAGGTAAGAAATAAAAAC
128 AAAAAAGAGAGTAAAATTCTACTTATCTTACAATAATAAAGGAAAA--TAAAAAATAGAAAC
* * *
54657 CTCATAAACAGGCTCACGAATTCCAAG
1 CTCATAAACAGGATCAAGAATTACAAG
54684 CGAGAGTGAA
Statistics
Matches: 487, Mismatches: 57, Indels: 100
0.76 0.09 0.16
Matches are distributed among these distances:
172 22 0.05
173 6 0.01
174 3 0.01
175 56 0.11
176 7 0.01
177 5 0.01
179 16 0.03
180 4 0.01
181 2 0.00
182 4 0.01
184 7 0.01
185 39 0.08
186 1 0.00
187 4 0.01
188 3 0.01
189 1 0.00
190 3 0.01
191 33 0.07
192 20 0.04
193 61 0.13
194 20 0.04
195 73 0.15
196 1 0.00
197 1 0.00
198 5 0.01
199 4 0.01
200 29 0.06
201 1 0.00
202 34 0.07
203 1 0.00
204 21 0.04
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.27
Consensus pattern (187 bp):
CTCATAAACAGGATCAAGAATTACAAGAGCAAGAGAGAAAAAAATTAATGAAAAAGTAAATTCTA
CTTATCTTACAATACATAATTGCATGCAATTATCTTTTCTTCTTAGATTAAAAATTAATTACAAA
AAAGAGAGTAAAATTCTACTTATCTTACAATAATAAAGGAAAATAAAAAATAGAAAC
Found at i:64280 original size:75 final size:75
Alignment explanation
Indices: 64157--64309 Score: 306
Period size: 75 Copynumber: 2.0 Consensus size: 75
64147 ATTCTCTATA
64157 TATCGAGACGGTACTAAATTTATATGGACTGATATTATATTTTGGTCCTTCAAATTTGGAAAATT
1 TATCGAGACGGTACTAAATTTATATGGACTGATATTATATTTTGGTCCTTCAAATTTGGAAAATT
64222 ACAAAATATT
66 ACAAAATATT
64232 TATCGAGACGGTACTAAATTTATATGGACTGATATTATATTTTGGTCCTTCAAATTTGGAAAATT
1 TATCGAGACGGTACTAAATTTATATGGACTGATATTATATTTTGGTCCTTCAAATTTGGAAAATT
64297 ACAAAATATT
66 ACAAAATATT
64307 TAT
1 TAT
64310 TAGATAATTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.39
Consensus pattern (75 bp):
TATCGAGACGGTACTAAATTTATATGGACTGATATTATATTTTGGTCCTTCAAATTTGGAAAATT
ACAAAATATT
Found at i:79020 original size:39 final size:39
Alignment explanation
Indices: 78961--79040 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
78951 TCTATAAAAT
78961 ATATAAAAGGAAGGTCATAGGGCATTCGACAGTGAACAC
1 ATATAAAAGGAAGGTCATAGGGCATTCGACAGTGAACAC
*
79000 ATATAAAAGGAAGGTTATAGGGCATTCGACAGTGAACAC
1 ATATAAAAGGAAGGTCATAGGGCATTCGACAGTGAACAC
79039 AT
1 AT
79041 GAAAACATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (39 bp):
ATATAAAAGGAAGGTCATAGGGCATTCGACAGTGAACAC
Found at i:80914 original size:6 final size:6
Alignment explanation
Indices: 80900--80936 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
80890 GAAACAAATT
* *
80900 GAACCC GAACTC GAACTC GAACCC GAACCC GAACCC G
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC G
80937 TGGTCCGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.32, C:0.43, G:0.19, T:0.05
Consensus pattern (6 bp):
GAACCC
Found at i:85236 original size:77 final size:77
Alignment explanation
Indices: 85109--85262 Score: 299
Period size: 77 Copynumber: 2.0 Consensus size: 77
85099 ACATTCAGTA
*
85109 AAATTTGTGATACATGTATAGGGTGAACAGTAATACAAATGCATTTTGTACTCTATGTTAGAGCA
1 AAATTTGTGATACATGTATAGGGTGAACAGTAATACAAATGCATTTTGTACTCTATGTTAGAACA
85174 GATTCTTTGAAT
66 GATTCTTTGAAT
85186 AAATTTGTGATACATGTATAGGGTGAACAGTAATACAAATGCATTTTGTACTCTATGTTAGAACA
1 AAATTTGTGATACATGTATAGGGTGAACAGTAATACAAATGCATTTTGTACTCTATGTTAGAACA
85251 GATTCTTTGAAT
66 GATTCTTTGAAT
85263 GTTCTGTACC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.36
Consensus pattern (77 bp):
AAATTTGTGATACATGTATAGGGTGAACAGTAATACAAATGCATTTTGTACTCTATGTTAGAACA
GATTCTTTGAAT
Found at i:92324 original size:90 final size:90
Alignment explanation
Indices: 92171--92352 Score: 364
Period size: 90 Copynumber: 2.0 Consensus size: 90
92161 GGCATCTAAG
92171 AGTGATATACGTCTAGTAGGGTTTTAACCTTATGCTCCTTATATGACACCTAAGAGTATATACAA
1 AGTGATATACGTCTAGTAGGGTTTTAACCTTATGCTCCTTATATGACACCTAAGAGTATATACAA
92236 TTTTTCAAATCCTCGATAGGGTGAT
66 TTTTTCAAATCCTCGATAGGGTGAT
92261 AGTGATATACGTCTAGTAGGGTTTTAACCTTATGCTCCTTATATGACACCTAAGAGTATATACAA
1 AGTGATATACGTCTAGTAGGGTTTTAACCTTATGCTCCTTATATGACACCTAAGAGTATATACAA
92326 TTTTTCAAATCCTCGATAGGGTGAT
66 TTTTTCAAATCCTCGATAGGGTGAT
92351 AG
1 AG
92353 ATGGCTTACA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 92 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (90 bp):
AGTGATATACGTCTAGTAGGGTTTTAACCTTATGCTCCTTATATGACACCTAAGAGTATATACAA
TTTTTCAAATCCTCGATAGGGTGAT
Found at i:93791 original size:16 final size:17
Alignment explanation
Indices: 93759--93792 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
93749 ACTATCAAAC
93759 TTTTTAAAAGCATTTTT
1 TTTTTAAAAGCATTTTT
*
93776 TTTTTAACAGCATTTTT
1 TTTTTAAAAGCATTTTT
93793 CAAAAACACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (17 bp):
TTTTTAAAAGCATTTTT
Found at i:94707 original size:13 final size:13
Alignment explanation
Indices: 94686--94746 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
94676 ACTATCAAAC
94686 TTTTCAAAAGCAT
1 TTTTCAAAAGCAT
* *
94699 TTTTTAAAAGTATTT
1 TTTTCAAAAGCA--T
* *
94714 TTTTTAACAGCAT
1 TTTTCAAAAGCAT
* *
94727 TTTTCAAAAACAC
1 TTTTCAAAAGCAT
94740 TTTTCAA
1 TTTTCAA
94747 CCTCAATGGT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
13 27 0.71
15 11 0.29
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (13 bp):
TTTTCAAAAGCAT
Found at i:95355 original size:938 final size:917
Alignment explanation
Indices: 93287--96518 Score: 4226
Period size: 938 Copynumber: 3.5 Consensus size: 917
93277 TTTAAAGAAT
* * * * * * *
93287 GCTTTTGAAAAGTTTGATAGTATTTACCATTGCTGT-CAAAGTGATTTTGAGAAGATAAAATGTC
1 GCTTTTGAAAAATTTGATAGTGTTTATCATTACTGTAAAAAGTGCTTTTGAAAAGATAAAATGTC
* * * * * *
93351 AATTTTAGACATTATGTTATCAAGTGAAAGATATAATAGAGGATAAAAAAGTAACTTCATTGAAA
66 AATTTTA-A-A-CATGTTATTAAGTGAAAGATTTAATGGGGGATAAAAAAGTAAATTCATTGAAA
* *
93416 AACATTTTCCCAAAAG-CTGAAGGTT-AAAATTG--TTGGCTTGGGTTAGAATCGCAGTTTAAAA
128 AACATTTTTCCAAAAGTC-GAAGGTTAAAAATTGTTTTGGCTTGGGTTAGAATCGCAGTTTGAAA
*
93477 TCATGGTTTGGTTTGAAGAGCTCTTTGTTTACCAAATTTTTTGTTTACTATTGAGG-TGGGAAAG
192 TCATGCTTTGGTTTGAAGAGCTCTTTGTTTACCAAATTTTTTGTTTACTATTGAGGCT-GGAAAG
* ** * *
93541 CAGTAAACAAAAAAAATTTGGTAAGCAAGCAGCTTTTTAAACCGAACATGATTTTAAACTAGGAT
256 CAATAAACAAAAAAAAAATGGTAAGCAAGCAGCTTTTTAAATCGAACATGATTTTAAACTAAGAT
* ** *
93606 TTTAACCAAGCCAAAAAAATTGGAAAAGTATTTTTCAATGAAATTACTTTTTTATATCCCCATTA
321 TTTAACCAAGTCAAAAATTTTGGAAAAGTATTTTTCAATGAAACTACTTTTTTATATCCCCATTA
* *
93671 AATCTTTCACTTTATAACATCATGTCTAAAATTTACATTTTATTTTCTCAAAAACACTTTTTAAC
386 AATCTTTCACTTTATAACATCATGTCTAAAATTAACATTTTATCTTCTCAAAAACACTTTTTAAC
*
93736 AACAATGGTAAACACTATCAAACTTTTTAAAAGCAT-TTTTTTTTTAACAGCATTTTTCAAAAAC
451 AACAATGGTAAACACTATCAAACTTTTCAAAAGCATGTTTTTTTTTAACAGCATTTTTCAAAAAC
93800 ACTTTTCAACCTCAATGGTAAACTAGCCCTTAGGCAATTGTGTATGGTTCTAAATGGTAAACTAG
516 ACTTTTCAACCTCAATGGTAAACTAGCCCTTAGGCAATTGTGTATGGTTCTAAATGGTAAACTAG
* * *
93865 TCCTAAGTAGAGTTGTCCATAGATCATGTCGGATCCAGTCAAAAAAATGAGCCTAATTTTTTACC
581 TCCTAAGTAGAGTTGTCCATAGATCGTGTCGGATCCAGTCCAAAAAATGAGCCTAAATTTTTACC
* *
93930 CAAACTCGACCCAAATAAAAATAATAAAACTTTGTCCCGACCCAACCTAGCCCGTATTAATTTTA
646 CAAACTTGACCCAAATAAAAATGATAAAACTTTGTCCCGACCCAACCTAGCCCGTATTAATTTTA
* *
93995 TTTTTTATATATATATTTTTAAAAAATACAATACACACCAAATACATAGTTAGGGCTGGATCCAA
711 TTTTTTATATATATATTTTT-AAAAATACAATACACACCAAATACATAGTTAGGGTTGGATCTAA
*
94060 GCCTAAAATTTTGTAAGGGTCCGACACGACACATGGACAACTTTACTTAGGACTAGTTTACCATT
775 GCCTAAAATTTTGTAAGGGTCCGACACGACACATGGACAACTCTACTTAGGACTAGTTTACCATT
*
94125 TAGAACCATACATATTTATCTAAGGGCAAGTTTACTATTTAGATTGAAAAATGTTTTTGAAAACT
840 TAGAACCATACATATTTATCTAAGGGCAAGTTTACTATTGAGATTGAAAAATGTTTTTGAAAACT
*
94190 GCTGTGAAAAAGA
905 GCTGTGAAAAAAA
* *
94203 GCTTTTGAAAAATTTGATAGTGTTTATCATTACTGACAAAAAGTGCTTTTGAGAAGATAAAATGT
1 GCTTTTGAAAAATTTGATAGTGTTTATCATTACTG-TAAAAAGTGCTTTTGAAAAGATAAAATGT
*
94268 TAATTTTAAACATGTTATTAAGTGAAAGATTTAATGGGGGATAAAAAAGTAAATAT-ATTGAAAA
65 CAATTTTAAACATGTTATTAAGTGAAAGATTTAATGGGGGATAAAAAAGTAAAT-TCATTGAAAA
* *
94332 TCATTTTTCCAAAAGTCGAAGGTTAAAAATTTTGGTTTTTTTGGCTTGGGTTAGAACCGCAGTTT
129 ACATTTTTCCAAAAGTCGAAGGTTAAAAA--TT-G---TTTTGGCTTGGGTTAGAATCGCAGTTT
94397 GAAATCATGCTTTGGATTT-AAGAGCTCTTTGTTTACCAAATTTTTTGTTTACTATTGAGGCTGG
188 GAAATCATGCTTTGG-TTTGAAGAGCTCTTTGTTTACCAAATTTTTTGTTTACTATTGAGGCTGG
* *
94461 AAAGCAGTAAACAAAAAAAAAAAATGGTAAGCAAGCAGCTTTTTAAATTGAACATGATTTTAAAC
252 AAAGCAATAAAC--AAAAAAAAAATGGTAAGCAAGCAGCTTTTTAAATCGAACATGATTTTAAAC
* *
94526 TAAGATTTTAATCAAGTCAAAAATTTTGGAAAAGTATTTTTTCAATGAAATTACTTTTTTATATC
315 TAAGATTTTAACCAAGTCAAAAATTTTGGAAAAGTA-TTTTTCAATGAAACTACTTTTTTATATC
* * *
94591 CCCGTTAAATCTTTCACTTTATAACATCATGTCTAAAATTTACATTTTATTTTCTCAAAAACACT
379 CCCATTAAATCTTTCACTTTATAACATCATGTCTAAAATTAACATTTTATCTTCTCAAAAACACT
*
94656 TTTTAACAACAATGATAAACACTATCAAACTTTTCAAAAGCATTTTTTAAAAGTATTTTTTTTAA
444 TTTTAACAACAATGGTAAACACTATCAAACTTTTCAAAAGCA-----T----GT-TTTTTTTTAA
*
94721 CAGCATTTTTCAAAAACACTTTTCAACCTCAATGGTAAACTAGCCCTTAAGCAATTGTGTATGGT
499 CAGCATTTTTCAAAAACACTTTTCAACCTCAATGGTAAACTAGCCCTTAGGCAATTGTGTATGGT
* *
94786 TCTAAATGGTAAATTAGTCCTAAGTGGAGTTGTCCATAGATCGTGTCGGATCCAGTCCAAAAAAT
564 TCTAAATGGTAAACTAGTCCTAAGTAGAGTTGTCCATAGATCGTGTCGGATCCAGTCCAAAAAAT
94851 GAGCCTAAATTTTTACCCAAACTTGACCCAAATAAAAATGATAAAACTTTGTCCCTG-CCCAACC
629 GAGCCTAAATTTTTACCCAAACTTGACCCAAATAAAAATGATAAAACTTTGTCCC-GACCCAACC
*
94915 TAACCCGTATTAATTTTATTTTTTATATATATATTTTTAAAAGATACAATACACACCAAATACAT
693 TAGCCCGTATTAATTTTATTTTTTATATATATATTTTTAAAA-ATACAATACACACCAAATACAT
* *
94980 AGTTAGGGTTGGATCTAAGCTTAAAATTTTGTAAGGGTCCGACACGACACGTGGACAACTCTACT
757 AGTTAGGGTTGGATCTAAGCCTAAAATTTTGTAAGGGTCCGACACGACACATGGACAACTCTACT
95045 TAGGACTAGTTTACCATTTAGAACCATACATATTTATCTAAGGGCAAGTTTACTATTGAGATTGA
822 TAGGACTAGTTTACCATTTAGAACCATACATATTTATCTAAGGGCAAGTTTACTATTGAGATTGA
95110 AAAATGTTTTTGAAAACTGCTGTGAAAAAAA
887 AAAATGTTTTTGAAAACTGCTGTGAAAAAAA
*
95141 GCTTTTGAAAAATTTGACAGTGTTTATCATTACTGATAAAAAGTGCTTTTGAAAAGATAAAATGT
1 GCTTTTGAAAAATTTGATAGTGTTTATCATTACTG-TAAAAAGTGCTTTTGAAAAGATAAAATGT
*
95206 TAATTTTAAACATGTTATTAAGTGAAAGATTTAATGGGGGATAAAAAAGTAAATAT-ATTGAAAA
65 CAATTTTAAACATGTTATTAAGTGAAAGATTTAATGGGGGATAAAAAAGTAAAT-TCATTGAAAA
95270 ACATTTTTCCAAAAGTCGAAGGTTAAAAATTTTGGCTTTTTTGGCTTGGGTTAGAATCGCAGTTT
129 ACATTTTTCCAAAAGTCGAAGGTTAAAAA--TT-G---TTTTGGCTTGGGTTAGAATCGCAGTTT
*
95335 GAAATCATGCTTTGGATTT-AAGAGCTCTTTGTTTACTAAATTTTTTGTTTACTATTGAGGCTGG
188 GAAATCATGCTTTGG-TTTGAAGAGCTCTTTGTTTACCAAATTTTTTGTTTACTATTGAGGCTGG
* * * *
95399 AAAGCAATAAACAAAAAAAAAATGATACGCAAGTAGCTTTTTAAATTGAACATGATTTTAAACTA
252 AAAGCAATAAACAAAAAAAAAATGGTAAGCAAGCAGCTTTTTAAATCGAACATGATTTTAAACTA
* * * * *
95464 AGATTTTAATCAAGTCAAAAATTTTGGAAAAGTATTTTTTAATGAAGCTA-TCTTTTTATAACCA
317 AGATTTTAACCAAGTCAAAAATTTTGGAAAAGTATTTTTCAATGAAACTACT-TTTTTATATCCC
* * *
95528 CGTTAAATCTTTCACTTTATAA-ATC-TGTGTTAAATATTAACATTTTATCTTCTCAAAAACGCT
381 CATTAAATCTTTCACTTTATAACATCATGT-CTAAA-ATTAACATTTTATCTTCTCAAAAACACT
* * * * * *
95591 TTTTGACAACAATGGTAGATACTATCAAATTTTTCAAAAGC-TG----TTTTTCACATCATTTTT
444 TTTTAACAACAATGGTAAACACTATCAAACTTTTCAAAAGCATGTTTTTTTTTAACAGCATTTTT
* * * *
95651 CAAAGACACCTTTCAACCTCAATGGTAAACTAGCCTTTAGGCAACTGTGTATGGTTCTAAATGGT
509 CAAAAACACTTTTCAACCTCAATGGTAAACTAGCCCTTAGGCAATTGTGTATGGTTCTAAATGGT
* * ** *
95716 AAACTAGTCCTGAGTAGAGTTGTCCAT-GAATCGTATCGGATCCAACCCAAAAAATGAGTCTAAA
574 AAACTAGTCCTAAGTAGAGTTGTCCATAG-ATCGTGTCGGATCCAGTCCAAAAAATGAGCCTAAA
* * * * * * * *
95780 TTTTTATCCAAA-TTCGACCCGAATAAAAATGTTAAAACTCTGTCTCGACCCATCTTAGCTCGTA
638 TTTTTACCCAAACTT-GACCCAAATAAAAATGATAAAACTTTGTCCCGACCCAACCTAGCCCGTA
* *
95844 TTAATTTTATTTTATATATATATATTTTTTAAAAATATAATACACACCAAATACATAGTTAGGGT
702 TTAATTTTATTTTTTATATATATA-TTTTTAAAAATACAATACACACCAAATACATAGTTAGGGT
* * * * * *
95909 TGTG-TCTAGGCCTAAAATTTTGTTAGGGTCTGGCACGGCTCATGGACAACTCTACTTAGGACTA
766 TG-GATCTAAGCCTAAAATTTTGTAAGGGTCCGACACGACACATGGACAACTCTACTTAGGACT-
* * * * * *
95973 AGTTAACCATTTAAAACCATACATAGTTT-TTTAACGGCTAGTTTACTATTGAGATTGAAAAGTG
829 AGTTTACCATTTAGAACCATACATA-TTTATCTAAGGGCAAGTTTACTATTGAGATTGAAAAATG
* * * ** * *
96037 TTGTGTAAAAAATAAAT-T-TAAAAAT
893 TT-TTTGAAAACT-GCTGTGAAAAAAA
* * * *
96062 GCTTTTGAAAAGTTTAATAGTGTTTATCATTACTGTCAAAAAGTACTTTT-AAGAAGATAAAATA
1 GCTTTTGAAAAATTTGATAGTGTTTATCATTACTGT-AAAAAGTGCTTTTGAA-AAGATAAAATG
* *
96126 TCAATTTTAAACATGTTATAAAGTGAAAGATTTAATGGGGGATAAAAAAGTAAATTCATTAAAAA
64 TCAATTTTAAACATGTTATTAAGTGAAAGATTTAATGGGGGATAAAAAAGTAAATTCATTGAAAA
* * * * *
96191 ACATTTTTTCAAAAGTTGAAAGTTAAAAA---TTTTGGATTGGGTTAGAATTGCAGTTTGAAATC
129 ACATTTTTCCAAAAGTCGAAGGTTAAAAATTGTTTTGGCTTGGGTTAGAATCGCAGTTTGAAATC
** * * * * * *
96253 ATGGATTGGTTTGGAA-AGATCTTTGCTTA-CAATTTTTTTTGTTCACTATTAAGGTTGGTAAGC
194 ATGCTTTGGTTT-GAAGAGCTCTTTGTTTACCAA-ATTTTTTGTTTACTATTGAGGCTGG-AA--
* * * * *
96316 AACAAAANNNNNNNNNNNAAAAAAAAAAAAAAAAAATTTTGCAAGCAAGCAGCTTTTTAAATCGA
254 AGC----------------AATAAACAAAAAAAAAA--TGGTAAGCAAGCAGCTTTTTAAATCGA
* * *
96381 ACATGATTTTAAACTAAGATTTTAACCAAGTCAAAAATTTTGAAAAAGTATTTTTCAATTAAGCT
301 ACATGATTTTAAACTAAGATTTTAACCAAGTCAAAAATTTTGGAAAAGTATTTTTCAATGAAACT
* * * *
96446 ACCTTTTTT-TATACCCATTAAATCTTTCACTTTATAACACCGTGTCTAAAATTAAAATTTTATC
366 A-CTTTTTTATATCCCCATTAAATCTTTCACTTTATAACATCATGTCTAAAATTAACATTTTATC
96510 TTCTCAAAA
430 TTCTCAAAA
96519 GTATTTTTTG
Statistics
Matches: 2082, Mismatches: 160, Indels: 131
0.88 0.07 0.06
Matches are distributed among these distances:
911 5 0.00
912 70 0.03
913 4 0.00
915 68 0.03
916 38 0.02
917 1 0.00
918 34 0.02
919 5 0.00
920 290 0.14
921 211 0.10
922 11 0.01
923 1 0.00
924 92 0.04
925 5 0.00
926 78 0.04
927 132 0.06
929 1 0.00
931 15 0.01
932 1 0.00
933 132 0.06
934 19 0.01
935 110 0.05
936 84 0.04
937 5 0.00
938 669 0.32
939 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (917 bp):
GCTTTTGAAAAATTTGATAGTGTTTATCATTACTGTAAAAAGTGCTTTTGAAAAGATAAAATGTC
AATTTTAAACATGTTATTAAGTGAAAGATTTAATGGGGGATAAAAAAGTAAATTCATTGAAAAAC
ATTTTTCCAAAAGTCGAAGGTTAAAAATTGTTTTGGCTTGGGTTAGAATCGCAGTTTGAAATCAT
GCTTTGGTTTGAAGAGCTCTTTGTTTACCAAATTTTTTGTTTACTATTGAGGCTGGAAAGCAATA
AACAAAAAAAAAATGGTAAGCAAGCAGCTTTTTAAATCGAACATGATTTTAAACTAAGATTTTAA
CCAAGTCAAAAATTTTGGAAAAGTATTTTTCAATGAAACTACTTTTTTATATCCCCATTAAATCT
TTCACTTTATAACATCATGTCTAAAATTAACATTTTATCTTCTCAAAAACACTTTTTAACAACAA
TGGTAAACACTATCAAACTTTTCAAAAGCATGTTTTTTTTTAACAGCATTTTTCAAAAACACTTT
TCAACCTCAATGGTAAACTAGCCCTTAGGCAATTGTGTATGGTTCTAAATGGTAAACTAGTCCTA
AGTAGAGTTGTCCATAGATCGTGTCGGATCCAGTCCAAAAAATGAGCCTAAATTTTTACCCAAAC
TTGACCCAAATAAAAATGATAAAACTTTGTCCCGACCCAACCTAGCCCGTATTAATTTTATTTTT
TATATATATATTTTTAAAAATACAATACACACCAAATACATAGTTAGGGTTGGATCTAAGCCTAA
AATTTTGTAAGGGTCCGACACGACACATGGACAACTCTACTTAGGACTAGTTTACCATTTAGAAC
CATACATATTTATCTAAGGGCAAGTTTACTATTGAGATTGAAAAATGTTTTTGAAAACTGCTGTG
AAAAAAA
Found at i:109231 original size:98 final size:100
Alignment explanation
Indices: 109105--109286 Score: 260
Period size: 98 Copynumber: 1.8 Consensus size: 100
109095 TCGAGCACGT
* * *
109105 TGATGGAATACATGGTATCTTATTCTTAGTTCACCAGTGACATGTG-AG-TAATAGGAAATGGCT
1 TGATGGAATACATGGTATCTTATTCTTAGTTCACCAATGAAATATGAAGCTAATAGGAAATGGCT
**
109168 TAGGGTATACAGATAAATGATTGTTAATAGTAGGC
66 TAGCATATACAGATAAATGATTGTTAATAGTAGGC
* * * *
109203 TGATGGAATACATGGTATCTTGTTCTTAGTTCATCAATGAAATATGAAGCTACTAGGGAATGGCT
1 TGATGGAATACATGGTATCTTATTCTTAGTTCACCAATGAAATATGAAGCTAATAGGAAATGGCT
*
109268 TAGCATATATAGATAAATG
66 TAGCATATACAGATAAATG
109287 TATACAGATA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
98 41 0.57
99 2 0.03
100 29 0.40
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (100 bp):
TGATGGAATACATGGTATCTTATTCTTAGTTCACCAATGAAATATGAAGCTAATAGGAAATGGCT
TAGCATATACAGATAAATGATTGTTAATAGTAGGC
Found at i:110183 original size:19 final size:19
Alignment explanation
Indices: 110140--110183 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
110130 TAAATTTTTA
*
110140 CAAATATGGAAAGTCTATT
1 CAAATATAGAAAGTCTATT
110159 -AAATATAGAAAG-CTTATT
1 CAAATATAGAAAGTC-TATT
110177 CAAATAT
1 CAAATAT
110184 TGAATGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 15 0.68
19 6 0.27
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (19 bp):
CAAATATAGAAAGTCTATT
Found at i:110720 original size:59 final size:57
Alignment explanation
Indices: 110612--110781 Score: 200
Period size: 59 Copynumber: 2.9 Consensus size: 57
110602 TTAATATAAC
* *
110612 ATTTGGTACCTAAACTTGATACTTATTCTTAATTTGGTACCTAAATTTTTTTTGACCCA
1 ATTTGGTACCTAAACTTGACACTT-TTTTTAATTTGGTA-CTAAATTTTTTTTGACCCA
* * *
110671 ATTTGGTACCTAAACTTGACACTTTTTTTAATTTGGTACGTAAACTTTTTCTGGACGCA
1 ATTTGGTACCTAAACTTGACACTTTTTTTAATTTGGTAC-TAAA-TTTTTTTTGACCCA
* *
110730 ATTTGATACC-AGAACTTGACA-TTTTTCTTAATTTGGTGACTAAGTTTTTTTT
1 ATTTGGTACCTA-AACTTGACACTTTTT-TTAATTTGGT-ACTAAATTTTTTTT
110782 TAGATTCAAT
Statistics
Matches: 97, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
57 1 0.01
58 29 0.30
59 65 0.67
60 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (57 bp):
ATTTGGTACCTAAACTTGACACTTTTTTTAATTTGGTACTAAATTTTTTTTGACCCA
Found at i:111055 original size:31 final size:32
Alignment explanation
Indices: 111010--111073 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
111000 TCAACTTTAA
*
111010 AAAAAAATTATCAAGCTTAG-GTACCAAATTAG
1 AAAAAAATTATCAAG-TTAGAATACCAAATTAG
* *
111042 AAAAAAA-TGTCAAGTTTGAATACCAAATTAG
1 AAAAAAATTATCAAGTTAGAATACCAAATTAG
111073 A
1 A
111074 CCAAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 3 0.11
31 18 0.64
32 7 0.25
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.25
Consensus pattern (32 bp):
AAAAAAATTATCAAGTTAGAATACCAAATTAG
Found at i:113194 original size:111 final size:110
Alignment explanation
Indices: 113001--113221 Score: 298
Period size: 111 Copynumber: 2.0 Consensus size: 110
112991 GTCCCTTAGG
*** * **
113001 ATATACAGATAAATGTTTGTTAATGGTACAATTAAATTAGCTGACAGAATATGTGGTATCTTATT
1 ATATACAGATAAATGACCGTTAATCGTACAATTAAATTAGCTGACAGAATACATGGTATCTTATT
* * * *
113066 CTTTGTTCATCAATGACATATGAGGCTACTAGGGAATGGCCTAGA
66 CTTAGTTAATCAATGACATAGGAGGCTACTAGAGAATGGCCTAGA
* * *
113111 ATATACAGATAAATGACCGTTAATCGTACAATTCAATTTGGCTGATAGAATACATGGTATCTTAT
1 ATATACAGATAAATGACCGTTAATCGTACAATT-AAATTAGCTGACAGAATACATGGTATCTTAT
* *
113176 TCTTAGTTAATCTATGACATAGGAGGCTACTAGAGAATGGCTTAGA
65 TCTTAGTTAATCAATGACATAGGAGGCTACTAGAGAATGGCCTAGA
113222 GAACGGTAAT
Statistics
Matches: 95, Mismatches: 15, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
110 29 0.31
111 66 0.69
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (110 bp):
ATATACAGATAAATGACCGTTAATCGTACAATTAAATTAGCTGACAGAATACATGGTATCTTATT
CTTAGTTAATCAATGACATAGGAGGCTACTAGAGAATGGCCTAGA
Found at i:113804 original size:19 final size:19
Alignment explanation
Indices: 113782--113818 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
113772 TACAAATTTG
**
113782 GAAGGTATTTTCAAATATA
1 GAAGGTATAATCAAATATA
113801 GAAGGTATAATCAAATAT
1 GAAGGTATAATCAAATAT
113819 GGATACCTTC
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:0.46, C:0.05, G:0.16, T:0.32
Consensus pattern (19 bp):
GAAGGTATAATCAAATATA
Found at i:113994 original size:19 final size:19
Alignment explanation
Indices: 113970--114016 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
113960 CAATATGTCC
**
113970 ATATTTGATTATACCTTCT
1 ATATTTGAAAATACCTTCT
113989 ATATTTGAAAATACCTTCT
1 ATATTTGAAAATACCTTCT
114008 ATATTTGAA
1 ATATTTGAA
114017 TAATCAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (19 bp):
ATATTTGAAAATACCTTCT
Found at i:114310 original size:46 final size:49
Alignment explanation
Indices: 114215--114310 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 49
114205 ACATAAATGT
*
114215 TAGAATATGTAAATGTTGTAGGCTAAATTTGTTAAATTAGGACCAAATTGG
1 TAGAATATGTAAATGTTGTAGGCTAAA-TTGTT-AATTAAGACCAAATTGG
*
114266 TAGAATATGTAAATGTTG-CGTGCTAAA-T-TT-ATTAAGACCAAATTG
1 TAGAATATGTAAATGTTGTAG-GCTAAATTGTTAATTAAGACCAAATTG
114311 ACAAAATGCG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
46 14 0.33
48 2 0.05
49 1 0.02
50 1 0.02
51 24 0.57
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (49 bp):
TAGAATATGTAAATGTTGTAGGCTAAATTGTTAATTAAGACCAAATTGG
Found at i:120313 original size:3 final size:3
Alignment explanation
Indices: 120305--120339 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
120295 CCCCTAATGT
120305 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
120340 TAAAATATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:120487 original size:19 final size:21
Alignment explanation
Indices: 120448--120489 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
120438 GATAATGTAT
120448 TTAATATTATATATATTTAAA
1 TTAATATTATATATATTTAAA
*
120469 TTAATATT-TA-ATGTTTAAA
1 TTAATATTATATATATTTAAA
120488 TT
1 TT
120490 GGTAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 2 0.10
21 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTAATATTATATATATTTAAA
Found at i:135208 original size:21 final size:21
Alignment explanation
Indices: 135167--135208 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
135157 TTGTATAGTA
* *
135167 TTTTTTTTATAAATTTTAAAT
1 TTTTTTTTATAAATATAAAAT
*
135188 TTTTTTTTTTAAATATAAAAT
1 TTTTTTTTATAAATATAAAAT
135209 ATTTATCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTTTTATAAATATAAAAT
Found at i:143020 original size:14 final size:16
Alignment explanation
Indices: 142991--143023 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
142981 CATAATATTA
142991 ATAATATGTAAATTTT
1 ATAATATGTAAATTTT
143007 ATAATAT-T-AATTTT
1 ATAATATGTAAATTTT
143021 ATA
1 ATA
143024 GCAATTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
ATAATATGTAAATTTT
Found at i:145337 original size:204 final size:209
Alignment explanation
Indices: 144970--145353 Score: 523
Period size: 204 Copynumber: 1.9 Consensus size: 209
144960 TACTCAGAGC
**
144970 ATGTATGTATGACACCTATGTATGTATGTAATTAATGCCACTAGAATGGAAAATTCAGATAGCTA
1 ATGTATGTATGACACCTACCTATGTATGTAATTAATGCCACTAGAATGGAAAATTCAGATAGCTA
145035 ACCAGGAACAGAATGGTACACCAGAGAAATAGTATAAAAGCACCCACAGTTAGAACCTAAGAGTA
66 ACCAGGAACAGAATGGTACACCAGAG-AATAGTATAAAAGCACCCACAGTTAGAACCTAAGAGTA
*
145100 CTCAGAGCATGTATGAAGGTATGTATGACACCATCTATACATATATGTATGACACCATATATGTA
130 CTCAGAGCATGTATGAAGGTATGTATAACACCATCTATACATATATGTATGACACCATATATGTA
145165 TTTATGAAACTCTCT
195 TTTATGAAACTCTCT
* * *
145180 ATGTATGTCTGACACC-ACCTATGTATGT-ATTGAAAT-CCACTAGTA-GG-AAATTCAGATGGC
1 ATGTATGTATGACACCTACCTATGTATGTAATT--AATGCCACTAGAATGGAAAATTCAGATAGC
* * * * * * *
145240 TAA-CTGGGACTAGGATGGTACACCAGAG-ATATTATAAAAGCACCCATAG-TAGACCCTCAGAG
64 TAACCAGGAAC-AGAATGGTACACCAGAGAATAGTATAAAAGCACCCACAGTTAGAACCTAAGAG
* * * *
145302 TACTCAGAGCATTTATGAATGTATGTATAACACCATCTATATATGTATGTAT
128 TACTCAGAGCATGTATGAAGGTATGTATAACACCATCTATACATATATGTAT
145354 AATACTGTTT
Statistics
Matches: 154, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
204 58 0.38
205 19 0.12
206 5 0.03
207 31 0.20
208 5 0.03
209 18 0.12
210 18 0.12
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (209 bp):
ATGTATGTATGACACCTACCTATGTATGTAATTAATGCCACTAGAATGGAAAATTCAGATAGCTA
ACCAGGAACAGAATGGTACACCAGAGAATAGTATAAAAGCACCCACAGTTAGAACCTAAGAGTAC
TCAGAGCATGTATGAAGGTATGTATAACACCATCTATACATATATGTATGACACCATATATGTAT
TTATGAAACTCTCT
Found at i:150675 original size:72 final size:72
Alignment explanation
Indices: 150576--150864 Score: 371
Period size: 72 Copynumber: 3.8 Consensus size: 72
150566 TTAAAGTACA
*
150576 AATTATTATTATATTACAATTTTTATCAAATAATGTGTAGATTTGACAATACATTATTTACTAAA
1 AATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAA
150641 TTTAAAT
66 TTTAAAT
* *
150648 AATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGATAATACATTATTTACTAAA
1 AATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAA
150713 TTTAAAT
66 TTTAAAT
*
150720 AAAAAAATTTATTATAATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTT
1 -----AA-TTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTA--T
*
150785 ATTAATTTTAAATATTTAAATCAAT
58 -TT-A--CT-AA-ATTT--A--AAT
150810 AATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATT
1 AATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATT
150865 TAAATAAAAA
Statistics
Matches: 191, Mismatches: 8, Indels: 24
0.86 0.04 0.11
Matches are distributed among these distances:
72 69 0.36
77 2 0.01
78 51 0.27
80 1 0.01
81 2 0.01
82 1 0.01
84 53 0.28
85 4 0.02
86 4 0.02
88 1 0.01
90 3 0.02
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (72 bp):
AATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAA
TTTAAAT
Found at i:150757 original size:78 final size:77
Alignment explanation
Indices: 150515--150864 Score: 433
Period size: 84 Copynumber: 4.4 Consensus size: 77
150505 NNNNNNNNNA
* * *
150515 TATCAAATATTGTGTTCATTTGACAATACATTATTTA-TCAAATTTTCATATTTAAAGTACAAAT
1 TATCAAATAATGTGTTGATTTGACAATACATTATTTACT-AAA-TTT-A-A-ATAAA--A-AAAT
150579 TATTATTATATTACAATTTT
58 TATTATTATATTACAATTTT
*
150599 TATCAAATAATGTGTAGATTTGACAATACATTATTTACTAAATTTAAAT-----AATTATTATTA
1 TATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATAAAAAAATTATTATTA
150659 TATTACAATTTT
66 TATTACAATTTT
* * *
150671 TATCAAATAATATGTTGATTTGATAATACATTATTTACTAAATTTAAATAAAAAAATTTATTATA
1 TATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATAAAAAAA-TTATTATT
150736 ATATTACAATTTT
65 ATATTACAATTTT
* *
150749 TATCAAATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAAATATTTAAATCAATAATT
1 TATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTT-AA-A--TAAA--AA-AATT
150814 ATTATTATATTACAATTTT
59 ATTATTATATTACAATTTT
150833 TATCAAATAATGTGTTGATTTGACAATACATT
1 TATCAAATAATGTGTTGATTTGACAATACATT
150865 TAAATAAAAA
Statistics
Matches: 239, Mismatches: 13, Indels: 28
0.85 0.05 0.10
Matches are distributed among these distances:
72 69 0.29
77 2 0.01
78 61 0.26
79 2 0.01
80 2 0.01
81 1 0.00
82 5 0.02
83 3 0.01
84 91 0.38
85 3 0.01
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (77 bp):
TATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATAAAAAAATTATTATTA
TATTACAATTTT
Found at i:150795 original size:150 final size:158
Alignment explanation
Indices: 150515--150864 Score: 432
Period size: 162 Copynumber: 2.2 Consensus size: 158
150505 NNNNNNNNNA
* * * *
150515 TATCAAATATTGTGTTCATTTGACAATACATTATTTA-TCAAATTTTCATATTTAAAGTACAAA-
1 TATCAAATAATATGTTGATTTGACAATACATTATTTACT-AAA-TTT-A-A-ATAAA--A-AAAT
*
150578 TTATTATTATATTACAATTTTTATCAAATAATGTGTAGATTTGACAATACATTA-T-TT-A-CT-
58 TTATTATAATATTACAATTTTTATCAAATAATGTGTAGATTTGACAATACATTATTATTAATCTA
150638 -AAATTT-A-AATAATTATTATTATATTACAATTTT
123 AAAATTTAACAATAATTATTATTATATTACAATTTT
*
150671 TATCAAATAATATGTTGATTTGATAATACATTATTTACTAAATTTAAATAAAAAAATTTATTATA
1 TATCAAATAATATGTTGATTTGACAATACATTATTTACTAAATTTAAATAAAAAAATTTATTATA
* * *
150736 ATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAAATATT
66 ATATTACAATTTTTATCAAATAATGTGTAGATTTGACAATACATTA-TTATTAA-TCTAAAAATT
150801 TAAATCAATAATTATTATTATATTACAATTTT
129 T-AA-CAATAATTATTATTATATTACAATTTT
*
150833 TATCAAATAATGTGTTGATTTGACAATACATT
1 TATCAAATAATATGTTGATTTGACAATACATT
150865 TAAATAAAAA
Statistics
Matches: 169, Mismatches: 11, Indels: 22
0.84 0.05 0.11
Matches are distributed among these distances:
149 3 0.02
150 53 0.31
152 5 0.03
153 3 0.02
154 2 0.01
155 3 0.02
156 37 0.22
157 1 0.01
158 5 0.03
160 1 0.01
162 56 0.33
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (158 bp):
TATCAAATAATATGTTGATTTGACAATACATTATTTACTAAATTTAAATAAAAAAATTTATTATA
ATATTACAATTTTTATCAAATAATGTGTAGATTTGACAATACATTATTATTAATCTAAAAATTTA
ACAATAATTATTATTATATTACAATTTT
Found at i:150978 original size:62 final size:60
Alignment explanation
Indices: 150870--151069 Score: 228
Period size: 59 Copynumber: 3.4 Consensus size: 60
150860 ACATTTAAAT
* * * ** *
150870 AAAAAATTTAGAATTTTTTATCTGAGAAAGGGA-GTGTTGGCCATTGCATGGCCAACACCA
1 AAAAAATTTA-AAATTTTTATCAGATAAATAGAGGTGTCGGCCATTGCATGGCCAACACCA
*
150930 AAAAAATTTGAAAAATTTTTATCAGATAAATAGAGGTGTCGGTCATTGCATGGCCAACACC-
1 AAAAAATTT--AAAATTTTTATCAGATAAATAGAGGTGTCGGCCATTGCATGGCCAACACCA
* ** * *
150991 TAAAAATTTAATTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGCATGGCTAACA-CA
1 AAAAAATTTAAAATTTTTATCAGATAAATAGAGGTGTCGGCCATTGCATGGCCAACACCA
*
151050 AAAAAA-TTAAATTTTTTATC
1 AAAAAATTTAAAATTTTTATC
151070 TAATAAAACA
Statistics
Matches: 121, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
58 14 0.12
59 48 0.40
60 9 0.07
61 25 0.21
62 25 0.21
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (60 bp):
AAAAAATTTAAAATTTTTATCAGATAAATAGAGGTGTCGGCCATTGCATGGCCAACACCA
Found at i:151135 original size:147 final size:148
Alignment explanation
Indices: 150945--151216 Score: 361
Period size: 147 Copynumber: 1.8 Consensus size: 148
150935 ATTTGAAAAA
** * **
150945 TTTTTATCAGATAAATAGAGGTGTCGGTCATTGCATGGCCAACAC-CTAAAAATT-TAATTTTTT
1 TTTTTATCAGATAAATAGAGGTGTCGACCATTGCACGGCCAACACAAAAAAAATTGT-A-TTTTT
* * * *
151008 TATCAGATAAATAGGGGTGTCGGCCATTGCATGGCTAACA-CAAAAAAATTAAATTTTTTATCTA
64 TATCAGACAAAAAAGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTAAATTTTTTATCTA
151072 ATAAAACAAAAAATTTAATT
129 ATAAAACAAAAAATTTAATT
* *
151092 TTTTTATCAGATAAATAGGGGTGTCGACCATTGTACGGCCAACACAAAAAAAATTGTATTTTTTA
1 TTTTTATCAGATAAATAGAGGTGTCGACCATTGCACGGCCAACACAAAAAAAATTGTATTTTTTA
* * * * *
151157 TCTGACAAAAAAGGGTGTCGGCCATTGTATGGCCAACACCCAAAAAATTGATTTTTTTAT
66 TCAGACAAAAAAGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTAAATTTTTTAT
151217 AAGATTAAAA
Statistics
Matches: 106, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
147 79 0.75
148 26 0.25
149 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (148 bp):
TTTTTATCAGATAAATAGAGGTGTCGACCATTGCACGGCCAACACAAAAAAAATTGTATTTTTTA
TCAGACAAAAAAGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTAAATTTTTTATCTAAT
AAAACAAAAAATTTAATT
Found at i:151140 original size:88 final size:89
Alignment explanation
Indices: 150992--151159 Score: 275
Period size: 88 Copynumber: 1.9 Consensus size: 89
150982 GCCAACACCT
* * *
150992 AAAAATTTAATTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGCATGGCTAACAC-AAAAAAA
1 AAAAATTTAATTTTTTTATCAGATAAATAGGGGTGTCGACCATTGCACGGCCAACACAAAAAAAA
151056 TTAAATTTTTTATCTAATAAAACA
66 TTAAATTTTTTATCTAATAAAACA
*
151080 AAAAATTTAATTTTTTTATCAGATAAATAGGGGTGTCGACCATTGTACGGCCAACACAAAAAAAA
1 AAAAATTTAATTTTTTTATCAGATAAATAGGGGTGTCGACCATTGCACGGCCAACACAAAAAAAA
**
151145 TTGTATTTTTTATCT
66 TTAAATTTTTTATCT
151160 GACAAAAAAG
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
88 53 0.73
89 20 0.27
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (89 bp):
AAAAATTTAATTTTTTTATCAGATAAATAGGGGTGTCGACCATTGCACGGCCAACACAAAAAAAA
TTAAATTTTTTATCTAATAAAACA
Found at i:151233 original size:60 final size:59
Alignment explanation
Indices: 151077--151234 Score: 192
Period size: 59 Copynumber: 2.6 Consensus size: 59
151067 ATCTAATAAA
* *
151077 ACAAAAAATTTAATTTTTTTATCAGATAAATAGGGGTGTCGACCATTGTACGGCCAACAC
1 ACAAAAAA-TTGATTTTTTTATCAGATAAAAAGGGGTGTCGACCATTGTACGGCCAACAC
* * * * * *
151137 AAAAAAAATTG-TATTTTTTATCTGACAAAAAAGGGTGTCGGCCATTGTATGGCCAACAC
1 ACAAAAAATTGAT-TTTTTTATCAGATAAAAAGGGGTGTCGACCATTGTACGGCCAACAC
* *
151196 CCAAAAAATTGATTTTTTTATAAGATTAAAAAGGGGTGT
1 ACAAAAAATTGATTTTTTTATCAGA-TAAAAAGGGGTGT
151235 TGCCATATTT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
58 1 0.01
59 61 0.75
60 19 0.23
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (59 bp):
ACAAAAAATTGATTTTTTTATCAGATAAAAAGGGGTGTCGACCATTGTACGGCCAACAC
Found at i:151340 original size:105 final size:104
Alignment explanation
Indices: 151157--151366 Score: 402
Period size: 105 Copynumber: 2.0 Consensus size: 104
151147 GTATTTTTTA
*
151157 TCTGACAAAAAAGGGTGTCGGCCATTGTATGGCCAACACCCAAAAAATTGATTTTTTTATAAGAT
1 TCTGACAAAAAAGGGTGTCGGCCATTGTATGGCCAACACCAAAAAAATTGATTTTTTTATAAGAT
151222 TAAAAAGGGGTGTTGCCATATTTTTTTTTCAAATTCTCG
66 TAAAAAGGGGTGTTGCCATATTTTTTTTTCAAATTCTCG
151261 TNCTGACAAAAAAGGGTGTCGGCCATTGTATGGCCAACACCAAAAAAATTGATTTTTTTATAAGA
1 T-CTGACAAAAAAGGGTGTCGGCCATTGTATGGCCAACACCAAAAAAATTGATTTTTTTATAAGA
151326 TTAAAAAGGGGTGTTGCCATATTTTTTTTTCAAATTCTCG
65 TTAAAAAGGGGTGTTGCCATATTTTTTTTTCAAATTCTCG
151366 T
1 T
151367 ATTTTCATAT
Statistics
Matches: 104, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
104 1 0.01
105 103 0.99
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (104 bp):
TCTGACAAAAAAGGGTGTCGGCCATTGTATGGCCAACACCAAAAAAATTGATTTTTTTATAAGAT
TAAAAAGGGGTGTTGCCATATTTTTTTTTCAAATTCTCG
Found at i:154961 original size:20 final size:20
Alignment explanation
Indices: 154938--154991 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
154928 AAAAAAAAGT
*
154938 ATATAAAAATATATTAAAAA
1 ATATAAAAATAAATTAAAAA
* * *
154958 ATATAATAATAAATTTAAAT
1 ATATAAAAATAAATTAAAAA
*
154978 ATATATAAATAAAT
1 ATATAAAAATAAAT
154992 ATTTTTTATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATAAAAATAAATTAAAAA
Found at i:155068 original size:6 final size:6
Alignment explanation
Indices: 155029--155077 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
155019 TTAAAATTTC
* *
155029 TATTAA TATTAA TATTAA -ATAAA TATAAATA TATTAA TATTAA TATTAA
1 TATTAA TATTAA TATTAA TATTAA TAT-TA-A TATTAA TATTAA TATTAA
155078 GTTTTTTACT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 4 0.11
6 27 0.71
7 3 0.08
8 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TATTAA
Found at i:164933 original size:6 final size:6
Alignment explanation
Indices: 164922--164979 Score: 80
Period size: 6 Copynumber: 9.7 Consensus size: 6
164912 GAGGAAGGCT
* * *
164922 TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC TGGGAC TGGGAC TGGGAC
1 TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC
*
164970 TGGGAC TGGG
1 TGGGGC TGGG
164980 ACTCCTTTTG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.07, C:0.16, G:0.60, T:0.17
Consensus pattern (6 bp):
TGGGGC
Found at i:164945 original size:18 final size:18
Alignment explanation
Indices: 164922--164979 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
164912 GAGGAAGGCT
*
164922 TGGGGCTGGGGCTGGGGC
1 TGGGGCTGGGGCTGGGAC
164940 TGGGGCTGGGGCTGGGAC
1 TGGGGCTGGGGCTGGGAC
* *
164958 TGGGACTGGGACTGGGAC
1 TGGGGCTGGGGCTGGGAC
164976 TGGG
1 TGGG
164980 ACTCCTTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.07, C:0.16, G:0.60, T:0.17
Consensus pattern (18 bp):
TGGGGCTGGGGCTGGGAC
Found at i:180344 original size:13 final size:13
Alignment explanation
Indices: 180326--180352 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
180316 GATGGCATTC
180326 ACCTATTCTAAAA
1 ACCTATTCTAAAA
180339 ACCTATTCTAAAA
1 ACCTATTCTAAAA
180352 A
1 A
180353 AGAAATTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
ACCTATTCTAAAA
Found at i:180672 original size:27 final size:27
Alignment explanation
Indices: 180642--180695 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
180632 TATGGACAAT
180642 GATTAAGTAACAATGATATTCACTACC
1 GATTAAGTAACAATGATATTCACTACC
180669 GATTAAGTAACAATGATATTCACTACC
1 GATTAAGTAACAATGATATTCACTACC
180696 AAGATACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (27 bp):
GATTAAGTAACAATGATATTCACTACC
Found at i:181446 original size:18 final size:19
Alignment explanation
Indices: 181409--181446 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
181399 AAATTGTATC
* *
181409 ATTCAATCTGATACCAATA
1 ATTCAATCTAATAACAATA
181428 ATTCAAT-TAATAACAATA
1 ATTCAATCTAATAACAATA
181446 A
1 A
181447 AAAACAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.32
Consensus pattern (19 bp):
ATTCAATCTAATAACAATA
Found at i:181515 original size:65 final size:65
Alignment explanation
Indices: 181388--181515 Score: 211
Period size: 65 Copynumber: 2.0 Consensus size: 65
181378 ATCACTGTTG
*
181388 AAGAGAACATAAAATTGTATCATTCAATCTGATACCAATAATTCAATTAATAACAATAAAAAACA
1 AAGAGAACATAAAATTGTATCATTCAATCTGAAACCAATAATTCAATTAATAACAATAAAAAACA
* * *
181453 AAGATAACATAAAATTGTATCATTCTATCTGAAACCAAATAATTCAATTAATAACCATAAAAA
1 AAGAGAACATAAAATTGTATCATTCAATCTGAAACC-AATAATTCAATTAATAACAATAAAAA
181516 GCGTTGAGCA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
65 33 0.57
66 25 0.43
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.27
Consensus pattern (65 bp):
AAGAGAACATAAAATTGTATCATTCAATCTGAAACCAATAATTCAATTAATAACAATAAAAAACA
Done.