Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 57 of 190
Found at i:16249486 original size:19 final size:20
Alignment explanation
Indices: 16249464--16249501 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
16249454 TCAAAAAAAG
*
16249464 TGATGAAAATG-AAAAATGA
1 TGATGAAAAAGTAAAAATGA
16249483 TGATGAAAAAGTAAAAATG
1 TGATGAAAAAGTAAAAATG
16249502 GAAAAGCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (20 bp):
TGATGAAAAAGTAAAAATGA
Found at i:16249492 original size:20 final size:19
Alignment explanation
Indices: 16249464--16249501 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
16249454 TCAAAAAAAG
16249464 TGATGAAAA-TGAAAAATGA
1 TGATGAAAAGT-AAAAATGA
16249483 TGATGAAAAAGTAAAAATG
1 TGATG-AAAAGTAAAAATG
16249502 GAAAAGCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 11 0.65
21 1 0.06
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (19 bp):
TGATGAAAAGTAAAAATGA
Found at i:16250907 original size:44 final size:44
Alignment explanation
Indices: 16250855--16251287 Score: 267
Period size: 44 Copynumber: 9.6 Consensus size: 44
16250845 GAAATTGCAG
*
16250855 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTA
* * ** *
16250899 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATAAAG-G
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCT--AGTA
* * * *
16250943 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATCAGATTGAAACCAGAA
1 ATCTTATCTCCCTGAGA-TTACAGT---G--GA--G---CAGATTGAAGCTAGTA
* ** * *
16250997 ATCTTATCTCCCTGAGATTGCAGCAGAGCAGATTGAAGCCAGAA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTA
* **
16251041 ATCTTATCTCCCTGAGATTGCAGCAGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTA
* ** *
16251085 ATCTTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATAAAG-G
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCT--AGTA
* * * * * *
16251129 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATC-AG--
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCTAGTA
* ** ** * *
16251170 GTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAG-AATTTCA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTA-GT-A
**
16251215 GATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCT-GATA
1 -ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAG-TA
*
16251260 ATCCTATCTCCCTGAGATTACAGTGGAG
1 ATCTTATCTCCCTGAGATTACAGTGGAG
16251288 TGGATTAAAA
Statistics
Matches: 306, Mismatches: 54, Indels: 58
0.73 0.13 0.14
Matches are distributed among these distances:
41 30 0.10
42 3 0.01
43 8 0.03
44 190 0.62
45 6 0.02
46 32 0.10
47 2 0.01
49 4 0.01
51 1 0.00
53 2 0.01
54 24 0.08
55 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTA
Found at i:16251191 original size:41 final size:41
Alignment explanation
Indices: 16250997--16251381 Score: 189
Period size: 44 Copynumber: 8.9 Consensus size: 41
16250987 GAAACCAGAA
* ** * * *
16250997 ATCTTATCTCCCTGAGATTGCAGCAGAGCAGATTGAAGCCAG
1 ATCTTATCTCCCTGAGATTACAGTGGAGTAGATCGAA-TCAG
* ** * * *
16251039 AAATCTTATCTCCCTGAGATTGCAGCAGAGCAGATTGAAGCTAG
1 --ATCTTATCTCCCTGAGATTACAGTGGAGTAGATCGAATC-AG
** ** *
16251083 TAATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGG
1 --ATCTTATCTCCCTGAGATTACAGTGGAGTAGA-TCGAAT-CA-G
* * *
16251129 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATCAG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGTAGATCGAATCAG
* * *
16251170 GTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAG
1 ATCTTATCTCCCTGAGATTACAGTGGAGTAGATC---GAA--TCAG
** * * * *
16251216 ATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCTGATA
1 ATCTTATCTCCCTGAGATTACAGTGGAGTAGATCGAA--TCA-G
* * ** *
16251260 ATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGTAGA-TCGAAT-CA-G
* * * *
16251304 ATCTTATCTCTCTG-GAGTTATAGTAGAGTAGATCGCATCAG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGTAGATCGAATCAG
* * *
16251345 ATCTTATCTCCTTGAGATTACAGTGGAATAGACCGAA
1 ATCTTATCTCCCTGAGATTACAGTGGAGTAGATCGAA
16251382 GAATTACAGA
Statistics
Matches: 264, Mismatches: 61, Indels: 35
0.73 0.17 0.10
Matches are distributed among these distances:
41 56 0.21
42 5 0.02
43 16 0.06
44 148 0.56
45 7 0.03
46 32 0.12
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (41 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGTAGATCGAATCAG
Found at i:16251191 original size:85 final size:84
Alignment explanation
Indices: 16251085--16251371 Score: 306
Period size: 85 Copynumber: 3.3 Consensus size: 84
16251075 GAAGCTAGTA
*
16251085 ATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
1 ATCTTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTG-AGTTAC
16251150 AGTAGAGTAGATCGCATCAG
65 AGTAGAGTAGATCGCATCAG
* * * ** ** *
16251170 GTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCA-GATCTTATCTCCCTGAGAT
1 ATCTTATCTCCCTGAGATTACAGTGGAGTGGA-TTAA-AA-TAAAGGATCTTATCTCTCTGAG-T
*** * * * * *
16251234 TACAACGGAGCAGATTGAAGCTGATA
62 TACAGTAGAGTAGATCGCA--TCA-G
* *
16251260 ATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGGAGTTAT
1 ATCTTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCT-GAGTTAC
16251325 AGTAGAGTAGATCGCATCAG
65 AGTAGAGTAGATCGCATCAG
*
16251345 ATCTTATCTCCTTGAGATTACAGTGGA
1 ATCTTATCTCCCTGAGATTACAGTGGA
16251372 ATAGACCGAA
Statistics
Matches: 156, Mismatches: 37, Indels: 18
0.74 0.18 0.09
Matches are distributed among these distances:
85 53 0.34
86 6 0.04
87 32 0.21
88 30 0.19
89 7 0.04
90 28 0.18
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (84 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAGTTACA
GTAGAGTAGATCGCATCAG
Found at i:16251287 original size:175 final size:175
Alignment explanation
Indices: 16250847--16251396 Score: 757
Period size: 175 Copynumber: 3.1 Consensus size: 175
16250837 ATAGGTTGGA
*
16250847 AATTGCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCT
1 AATTACAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCT
16250912 GAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC
66 GAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC
* ** ** **
16250977 GCATCAGATTGAAACCAGAAATCTTATCTCCCTGAGATTGCAGCAGAGCAGATTGAAG
131 GCATC--A--G------G---TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAG
* * * * *
16251035 CCA-GA-A-ATCTTATCTCCCTGAGATTGCAGCAGAGCAGATTGAAGCTAGTAATCTTATCTCCC
1 -AATTACAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCC
16251097 TGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
65 TGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
16251162 CGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAG
130 CGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAG
* *
16251208 AATTTCAGATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCT-GATAATCCTATCTCCC
1 AATTACAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAG-TAATCCTATCTCCC
* * *
16251272 TGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGGAGTTATAGTAGAGTAGAT
65 TGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
* *
16251337 CGCATCAGATCTTATCTCCTTGAGATTACAGTGGAATAGACCGAAG
130 CGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAG
16251383 AATTACAGATCTTA
1 AATTACAGATCTTA
16251397 CATTCCTAGG
Statistics
Matches: 331, Mismatches: 26, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
172 1 0.00
173 30 0.09
174 2 0.01
175 169 0.51
176 1 0.00
182 1 0.00
184 1 0.00
186 124 0.37
187 1 0.00
189 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (175 bp):
AATTACAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCT
GAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC
GCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAG
Found at i:16252327 original size:15 final size:15
Alignment explanation
Indices: 16252307--16252338 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16252297 TTCGACTTGG
*
16252307 TTTTATTTTTTTATT
1 TTTTATTTTCTTATT
16252322 TTTTATTTTCTTATT
1 TTTTATTTTCTTATT
16252337 TT
1 TT
16252339 CTTGCGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTATTTTCTTATT
Found at i:16252339 original size:8 final size:8
Alignment explanation
Indices: 16252309--16252341 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
16252299 CGACTTGGTT
*
16252309 TTATTTTT
1 TTATTTTC
16252317 TTATTTT-
1 TTATTTTC
16252324 TTATTTTC
1 TTATTTTC
16252332 TTATTTTC
1 TTATTTTC
16252340 TT
1 TT
16252342 GCGTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (8 bp):
TTATTTTC
Found at i:16257498 original size:40 final size:40
Alignment explanation
Indices: 16257358--16257498 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
16257348 AGCGGCGCTT
* *
16257358 TTAGCGGCGTTTGGAC-AAAAAACGCCACTAATAATCGAGCA
1 TTAGCGGCGTTT-TACAAAAAAACGCCGCTAA-AATCGAGCA
* * *
16257399 TTAGCGGCATTTTAC-GAAAAACGCCGCAAAATATCGAGCA
1 TTAGCGGCGTTTTACAAAAAAACGCCGCTAAA-ATCGAGCA
* ** * * *
16257439 TTAGCGGCGCTACATAAAAAAACGCCGCTAAAACCAAGCA
1 TTAGCGGCGTTTTACAAAAAAACGCCGCTAAAATCGAGCA
*
16257479 TTAGCAGCGTTTTACAAAAA
1 TTAGCGGCGTTTTACAAAAA
16257499 GCGCCGCAAT
Statistics
Matches: 79, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
39 1 0.01
40 53 0.67
41 25 0.32
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (40 bp):
TTAGCGGCGTTTTACAAAAAAACGCCGCTAAAATCGAGCA
Found at i:16257777 original size:118 final size:113
Alignment explanation
Indices: 16257485--16257812 Score: 467
Period size: 113 Copynumber: 2.8 Consensus size: 113
16257475 AGCATTAGCA
* *
16257485 GCGTTTTACAAAAAGCGCCGCAATAGAGTCACACAGAACGACGTCGTTTTCATATATTTGGGAAC
1 GCGTTTTACAAAAAGCGCCGCAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAAC
* * **
16257550 ATAAGTGGCGGTTTTTCCCAAGCGCCGCTAAAACTCTGTTCTTCAGCG
66 ATTAGTGGCGGTTTTGCCCAAGCGCCGCTAAAACTCCATTCTTCAGCG
* * *
16257598 GCGTTTTATAAAAAGCGCCGTAATGGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAAC
1 GCGTTTTACAAAAAGCGCCGCAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAAC
*
16257663 ATTAGTGGCGGTTTTGCCCAAGTCGACCGACTAATACTCCATTCTTCAGCG
66 ATTAGTGGCGGTTTTGCCCAAG-CG-CCG-CTAAAACTCCATTCTTCAGCG
* *
16257714 GCGTTTTACAAGAAAGCGTCGCAAATAGAGTAACACAAAACGACGCCGTTTTCATATATTTGGGA
1 GCGTTTTACAA-AAAGCGCCGC-AATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGA
* * *
16257779 ACACTAGTGGCGGTTTTTGCCCAAACGCCACTAA
64 ACATTAGTGGCGG-TTTTGCCCAAGCGCCGCTAA
16257813 TAATTTGTTC
Statistics
Matches: 191, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
113 80 0.42
114 2 0.01
115 3 0.02
116 32 0.17
117 10 0.05
118 54 0.28
119 10 0.05
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (113 bp):
GCGTTTTACAAAAAGCGCCGCAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAAC
ATTAGTGGCGGTTTTGCCCAAGCGCCGCTAAAACTCCATTCTTCAGCG
Found at i:16260533 original size:16 final size:16
Alignment explanation
Indices: 16260509--16260539 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16260499 ATTTTCCCTA
16260509 TTTTAAAATCCCTAAG
1 TTTTAAAATCCCTAAG
*
16260525 TTTTGAAATCCCTAA
1 TTTTAAAATCCCTAA
16260540 CTCATAAACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (16 bp):
TTTTAAAATCCCTAAG
Found at i:16263368 original size:21 final size:21
Alignment explanation
Indices: 16263353--16263392 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16263343 AGCAGATGTG
16263353 GCAGCGAGAGAAGCAGAGGCA
1 GCAGCGAGAGAAGCAGAGGCA
*
16263374 GCAGCGAGAGAAGCTGAGG
1 GCAGCGAGAGAAGCAGAGG
16263393 TTCAACGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.17, G:0.45, T:0.03
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAGAGGCA
Found at i:16263429 original size:87 final size:87
Alignment explanation
Indices: 16263281--16263473 Score: 239
Period size: 87 Copynumber: 2.2 Consensus size: 87
16263271 ACTTAAAGTG
* * *
16263281 GAGGCAACATCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGC
1 GAGGCAGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGA
*
16263346 AGATGTGGCAGCGAGAGAAGCA
66 AGATGCGGCAGCGAGAGAAGCA
* * *
16263368 GAGGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAG-TATG-AGCAACTGCAGC-AGCAGCTTAA
1 GAGGCAGCAGCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAG-AACTCCAGCTA-CAACTTAA
16263430 AGAAGATGCGGCAGCGAGAGAAGCA
63 AGAAGATGCGGCAGCGAGAGAAGCA
* ** *
16263455 GCGGTTGCAGCGAGGGAAG
1 GAGGCAGCAGCGAGAGAAG
16263474 TAGAGGCTAC
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
86 3 0.03
87 85 0.92
88 4 0.04
ACGTcount: A:0.37, C:0.18, G:0.33, T:0.12
Consensus pattern (87 bp):
GAGGCAGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGA
AGATGCGGCAGCGAGAGAAGCA
Found at i:16263840 original size:43 final size:43
Alignment explanation
Indices: 16263779--16264255 Score: 828
Period size: 43 Copynumber: 11.1 Consensus size: 43
16263769 AAATTAGCGC
*
16263779 CGTTTTTTGGATAAGCGCCGCTAAAGACCATGGTCTATAGTGG
1 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
*
16263822 CGTTTTTCGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
1 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
* *
16263865 CGTTTTTTGTCTAAGCGCCGCTACAGACCATGGTCTATAGTGG
1 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
16263908 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
1 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
* * *
16263951 CGTTTTGTGGCTAAGCGCCTCTAAAGACCATGATCTATAGTGG
1 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
16263994 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
1 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
* *
16264037 CGTTTTTTGTCTAAGCGCCGATAAAGACCATGGTCTATAGTGG
1 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
* *
16264080 CGTTTTTTGTCTAAGCGCCGATAAAGACCATGGTCTATAGTGG
1 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
16264123 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
1 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
* *
16264166 CGTTTTGTGGCTAAGCGCCGCTAAAGACCATGATCTATAGTGG
1 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
*
16264209 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGCGG
1 CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
16264252 CGTT
1 CGTT
16264256 GCAAAGAAAA
Statistics
Matches: 412, Mismatches: 22, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 412 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (43 bp):
CGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGG
Found at i:16265929 original size:11 final size:11
Alignment explanation
Indices: 16265915--16265939 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16265905 TTTTGTGAAA
16265915 AATGATGCACT
1 AATGATGCACT
16265926 AATGATGCACT
1 AATGATGCACT
16265937 AAT
1 AAT
16265940 TATAATACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (11 bp):
AATGATGCACT
Found at i:16268079 original size:18 final size:18
Alignment explanation
Indices: 16268030--16268081 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
16268020 GACACGTAGC
16268030 ATATATAAATTAA-AAAA
1 ATATATAAATTAATAAAA
***
16268047 ATA-A-AAATCCTTAAAA
1 ATATATAAATTAATAAAA
16268063 ATATATAAATTAATAAAA
1 ATATATAAATTAATAAAA
16268081 A
1 A
16268082 GTGTAAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
15 4 0.15
16 8 0.31
17 4 0.15
18 10 0.38
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (18 bp):
ATATATAAATTAATAAAA
Found at i:16268240 original size:17 final size:17
Alignment explanation
Indices: 16268218--16268254 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16268208 TATTATTATG
16268218 AAATTAAAAATAAATAA
1 AAATTAAAAATAAATAA
* *
16268235 AAATTATAAATTAATAA
1 AAATTAAAAATAAATAA
16268252 AAA
1 AAA
16268255 ATATAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATTAAAAATAAATAA
Found at i:16268259 original size:17 final size:17
Alignment explanation
Indices: 16268225--16268261 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16268215 ATGAAATTAA
*
16268225 AAATAAATAAAAATTAT
1 AAATAAATAAAAAATAT
*
16268242 AAATTAATAAAAAATAT
1 AAATAAATAAAAAATAT
16268259 AAA
1 AAA
16268262 GAAGTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:16268375 original size:8 final size:8
Alignment explanation
Indices: 16268362--16268427 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 8
16268352 AGTTCTTTTA
16268362 TATATATT
1 TATATATT
16268370 TATATATT
1 TATATATT
16268378 TATCAT-TT
1 TAT-ATATT
*
16268386 TAT-CATT
1 TATATATT
16268393 T-T-TATT
1 TATATATT
16268399 TATATA-T
1 TATATATT
16268406 TATATATT
1 TATATATT
* *
16268414 CTAAATTTT
1 -TATATATT
16268423 TATAT
1 TATAT
16268428 GTTTTTCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
6 5 0.11
7 11 0.23
8 23 0.49
9 8 0.17
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATATT
Found at i:16268423 original size:29 final size:29
Alignment explanation
Indices: 16268366--16268425 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
16268356 CTTTTATATA
* *
16268366 TATTTATATATTTATCATTTTATCATTTT
1 TATTTATATATTTATCATTCTATAATTTT
16268395 TATTTATATATTATAT-ATTCTA-AATTTT
1 TATTTATATATT-TATCATTCTATAATTTT
16268423 TAT
1 TAT
16268426 ATGTTTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 8 0.29
29 17 0.61
30 3 0.11
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (29 bp):
TATTTATATATTTATCATTCTATAATTTT
Found at i:16269047 original size:18 final size:20
Alignment explanation
Indices: 16269020--16269069 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 20
16269010 CAAATAATTT
*
16269020 TAAAATTATAAAAC-ATTCA
1 TAAAAATATAAAACAATTCA
**
16269039 -AAAAATATATGACAATTCA
1 TAAAAATATAAAACAATTCA
16269058 TAAAAATA-AAAA
1 TAAAAATATAAAA
16269070 AGATTAGCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
18 10 0.42
19 7 0.29
20 7 0.29
ACGTcount: A:0.64, C:0.08, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAAAATATAAAACAATTCA
Found at i:16276084 original size:6 final size:6
Alignment explanation
Indices: 16276073--16276115 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
16276063 CTTGATAGCA
16276073 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC C
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC C
16276116 TAATTGCACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CCTCTC
Found at i:16277976 original size:25 final size:25
Alignment explanation
Indices: 16277948--16278017 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
16277938 TAGGCCCATT
*
16277948 TTCACAGCTCATGTAAGCATTCTGA
1 TTCACAGCTCATGTGAGCATTCTGA
*
16277973 TTCATAGCTCATGTGAGCATTCTGA
1 TTCACAGCTCATGTGAGCATTCTGA
* *
16277998 GTCACAGCTCGTGTGAGCAT
1 TTCACAGCTCATGTGAGCAT
16278018 ACATGTACAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (25 bp):
TTCACAGCTCATGTGAGCATTCTGA
Found at i:16279174 original size:15 final size:16
Alignment explanation
Indices: 16279154--16279183 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16279144 TGGTGCCTTG
16279154 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
16279169 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
16279184 ATCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:16284986 original size:25 final size:25
Alignment explanation
Indices: 16284958--16285011 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
16284948 TGTAGTGGCA
16284958 AGGTGGCAACACAGGTGTGGCAAGG
1 AGGTGGCAACACAGGTGTGGCAAGG
*** * *
16284983 AGGTGGTGTCATAGGTGTGGTAAGG
1 AGGTGGCAACACAGGTGTGGCAAGG
16285008 AGGT
1 AGGT
16285012 CAGAGGTTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.09, G:0.46, T:0.20
Consensus pattern (25 bp):
AGGTGGCAACACAGGTGTGGCAAGG
Found at i:16285160 original size:24 final size:21
Alignment explanation
Indices: 16285127--16285173 Score: 58
Period size: 24 Copynumber: 2.1 Consensus size: 21
16285117 TCAAATGAGT
*
16285127 GATTTAAGGAGTGGATCATGGAG
1 GATTTAAGGAGAGGAT--TGGAG
16285150 GATTTCAAGGAGAGGATTGGAG
1 GATTT-AAGGAGAGGATTGGAG
16285172 GA
1 GA
16285174 GTGATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 5 0.23
24 10 0.45
ACGTcount: A:0.32, C:0.04, G:0.40, T:0.23
Consensus pattern (21 bp):
GATTTAAGGAGAGGATTGGAG
Found at i:16285187 original size:25 final size:24
Alignment explanation
Indices: 16285146--16285197 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
16285136 AGTGGATCAT
16285146 GGAGGATTTCAAGGAGAGGATTGGA
1 GGAGGATTTCAAGGAGA-GATTGGA
* *
16285171 GGAGTGATTTTAA-GAGAGATTTGA
1 GGAG-GATTTCAAGGAGAGATTGGA
16285195 GGA
1 GGA
16285198 ATTTGAGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.38
25 8 0.33
26 7 0.29
ACGTcount: A:0.33, C:0.02, G:0.40, T:0.25
Consensus pattern (24 bp):
GGAGGATTTCAAGGAGAGATTGGA
Found at i:16286531 original size:26 final size:26
Alignment explanation
Indices: 16286482--16286531 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
16286472 ACATATACTG
* **
16286482 TACTGGCAGCTCTGCTGCGTTATTAT
1 TACTGGCAGCTATGCTGCAATATTAT
16286508 TACTGGCAGCTATGCTGCAATATT
1 TACTGGCAGCTATGCTGCAATATT
16286532 GGTGTGTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (26 bp):
TACTGGCAGCTATGCTGCAATATTAT
Found at i:16287953 original size:19 final size:19
Alignment explanation
Indices: 16287929--16287976 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
16287919 TGATGAATGC
16287929 CCAGCAAAAGCCAAACACT
1 CCAGCAAAAGCCAAACACT
16287948 CCAGCAAAAGCCAAACACT
1 CCAGCAAAAGCCAAACACT
16287967 CCAGCAAAAG
1 CCAGCAAAAG
16287977 ATCATTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.48, C:0.35, G:0.12, T:0.04
Consensus pattern (19 bp):
CCAGCAAAAGCCAAACACT
Found at i:16291117 original size:56 final size:50
Alignment explanation
Indices: 16291051--16291187 Score: 157
Period size: 50 Copynumber: 2.6 Consensus size: 50
16291041 GGGATGAGAC
* ** *
16291051 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGG---TA-CCAAG--ATGAGAGGT
**
16291107 CCCACGTAAGACCATGTCTGGGACATGGCGCTGGTACCAAGATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCAAGATGAGAGGT
*
16291157 CCCTCGTAAGACCATGTCTGGGACATGGCAT
1 CCCACGTAAGACCATGTCTGGGACATGGCAT
16291188 AAGAACCGAT
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
50 37 0.51
52 2 0.03
53 2 0.03
56 31 0.43
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (50 bp):
CCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCAAGATGAGAGGT
Found at i:16291202 original size:50 final size:50
Alignment explanation
Indices: 16291097--16291203 Score: 144
Period size: 50 Copynumber: 2.1 Consensus size: 50
16291087 TTATTGAGGT
* * *
16291097 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGCTGGTACCAA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGATAGAACCAA
* * *
16291147 GATGAGAGGTCCCTCGTAAGACCATGTCTGGGACATGGC-ATAAGAACCGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGAT-AGAACCAA
16291197 TATGAGA
1 TATGAGA
16291204 ACTCTCATGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
49 1 0.02
50 48 0.98
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.20
Consensus pattern (50 bp):
TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGATAGAACCAA
Found at i:16293089 original size:41 final size:41
Alignment explanation
Indices: 16293021--16293203 Score: 267
Period size: 41 Copynumber: 4.5 Consensus size: 41
16293011 TGACCTTTCG
* ** *
16293021 GGGCTTTAGTGGCGTTTTTAAAAAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA
* * * *
16293062 GGGATTTAGCGGTGTTTTTGGAGAAGCGCCACTAATGCTTA
1 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA
* * *
16293103 GGGCTTTAACGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA
16293144 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA
16293185 GGGCTTTAGCGGCGTTTTT
1 GGGCTTTAGCGGCGTTTTT
16293204 AAAAAAGTGC
Statistics
Matches: 124, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 124 1.00
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA
Found at i:16293161 original size:82 final size:82
Alignment explanation
Indices: 16293021--16293210 Score: 317
Period size: 82 Copynumber: 2.3 Consensus size: 82
16293011 TGACCTTTCG
* *
16293021 GGGCTTTAGTGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGGGATTTAGCGGTGTTTTTGGAGA
1 GGGCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGAGA
*
16293086 AGCGCCACTAATGCTTA
66 AGCGCCACTAATGCTCA
* * *
16293103 GGGCTTTAACGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAGA
1 GGGCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGAGA
*
16293168 AGCGCCGCTAATGCTCA
66 AGCGCCACTAATGCTCA
16293185 GGGCTTTAGCGGCGTTTTTAAAAAAG
1 GGGCTTTAGCGGCGTTTTTAAAAAAG
16293211 TGCCACAAAA
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 99 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (82 bp):
GGGCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGAGA
AGCGCCACTAATGCTCA
Found at i:16293562 original size:14 final size:14
Alignment explanation
Indices: 16293545--16293578 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16293535 GGGTTTAATA
16293545 TATATGGTTTAGGG
1 TATATGGTTTAGGG
* *
16293559 TATATTGTTTGGGG
1 TATATGGTTTAGGG
16293573 TATATG
1 TATATG
16293579 ATTAATTTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (14 bp):
TATATGGTTTAGGG
Found at i:16293813 original size:14 final size:14
Alignment explanation
Indices: 16293794--16293827 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16293784 TATTAAATAA
*
16293794 GGTTTATGGGTTAG
1 GGTTTATAGGTTAG
*
16293808 GGTTTATAGTTTAG
1 GGTTTATAGGTTAG
16293822 GGTTTA
1 GGTTTA
16293828 GATTAATTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (14 bp):
GGTTTATAGGTTAG
Found at i:16293820 original size:68 final size:70
Alignment explanation
Indices: 16293748--16293877 Score: 219
Period size: 68 Copynumber: 1.9 Consensus size: 70
16293738 TTAGGTTAAG
* *
16293748 GTTTAGGGTTTAGATTAATTAGTGTATTTTAA-TT-TATATTAAATAAGGTTTATGGGTTAGGGT
1 GTTTAGGGTTTAGATTAATTAGTATATTTTAATTTATATATTAAATAAGGTTTAGGGGTTAGGGT
16293811 TTATA
66 TTATA
*
16293816 GTTTAGGGTTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAAGGTTTAGGGGTTAG
1 GTTTAGGGTTTAGATTAATTAGTATATTTTAATTTATATATTAAATAAGGTTTAGGGGTTAG
16293878 TAGTTAAGGG
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
68 30 0.53
69 2 0.04
70 25 0.44
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (70 bp):
GTTTAGGGTTTAGATTAATTAGTATATTTTAATTTATATATTAAATAAGGTTTAGGGGTTAGGGT
TTATA
Found at i:16293911 original size:21 final size:21
Alignment explanation
Indices: 16293867--16293911 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
16293857 TAAATAAGGT
**
16293867 TTAGGGGTTAGTAGTTAAGGG
1 TTAGGGGTTAGTAGTTAAAAG
16293888 TTAGGGGTTAG-AGGTTAAAAG
1 TTAGGGGTTAGTA-GTTAAAAG
16293909 TTA
1 TTA
16293912 CTGATTTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.33
Consensus pattern (21 bp):
TTAGGGGTTAGTAGTTAAAAG
Found at i:16294029 original size:7 final size:7
Alignment explanation
Indices: 16294017--16294065 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
16294007 ATTGTAAAAG
16294017 AGGGGTT
1 AGGGGTT
16294024 AGGGGTT
1 AGGGGTT
16294031 AGGGGTT
1 AGGGGTT
**
16294038 AGCAGTT
1 AGGGGTT
*
16294045 AGGTGTT
1 AGGGGTT
16294052 AGGGGTT
1 AGGGGTT
*
16294059 AGAGGTT
1 AGGGGTT
16294066 TAAGGTTTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.18, C:0.02, G:0.49, T:0.31
Consensus pattern (7 bp):
AGGGGTT
Found at i:16294047 original size:21 final size:21
Alignment explanation
Indices: 16294021--16294060 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16294011 TAAAAGAGGG
16294021 GTTAGGGGTTAGGGGTTAGCA
1 GTTAGGGGTTAGGGGTTAGCA
*
16294042 GTTAGGTGTTAGGGGTTAG
1 GTTAGGGGTTAGGGGTTAG
16294061 AGGTTTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (21 bp):
GTTAGGGGTTAGGGGTTAGCA
Found at i:16300388 original size:43 final size:42
Alignment explanation
Indices: 16300335--16300495 Score: 171
Period size: 43 Copynumber: 3.8 Consensus size: 42
16300325 GTCAATGTTA
* *
16300335 TAGCGGCGTTTTTAGTAGAAGCGCCGCTAAAGGTCATGAGCTT
1 TAGCGGCGTTTTTAGGAAAAGCGCCGCTAAAGGTCATG-GCTT
* * * * *
16300378 TAGCGACGTTTGTAGGAAAAGCGTCGCTAAAGGTCTTGTTCTT
1 TAGCGGCGTTTTTAGGAAAAGCGCCGCTAAAGGTCATG-GCTT
* * *
16300421 TAGCGGCATTTTTGGGAAAAGCGCCGTTAAAGGT-ATTGGTCTT
1 TAGCGGCGTTTTTAGGAAAAGCGCCGCTAAAGGTCA-TGG-CTT
* *
16300464 TAGCGGCGTTTCTGGGAAAAGCGCCGCTAAAG
1 TAGCGGCGTTTTTAGGAAAAGCGCCGCTAAAG
16300496 TTAGCGACGC
Statistics
Matches: 97, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
43 97 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (42 bp):
TAGCGGCGTTTTTAGGAAAAGCGCCGCTAAAGGTCATGGCTT
Found at i:16300443 original size:86 final size:86
Alignment explanation
Indices: 16300335--16300495 Score: 209
Period size: 86 Copynumber: 1.9 Consensus size: 86
16300325 GTCAATGTTA
* * * *
16300335 TAGCGGCGTTTTTAGTAGAAGCGCCGCTAAAGGTCA-TGAG-CTTTAGCGACGTTTGTAGGAAAA
1 TAGCGGCATTTTTAGGAAAAGCGCCGCTAAAGGT-ATTG-GTCTTTAGCGACGTTTCTAGGAAAA
*
16300398 GCGTCGCTAAAGGTCTTGTTCTT
64 GCGCCGCTAAAGGTCTTGTTCTT
* * * *
16300421 TAGCGGCATTTTTGGGAAAAGCGCCGTTAAAGGTATTGGTCTTTAGCGGCGTTTCTGGGAAAAGC
1 TAGCGGCATTTTTAGGAAAAGCGCCGCTAAAGGTATTGGTCTTTAGCGACGTTTCTAGGAAAAGC
16300486 GCCGCTAAAG
66 GCCGCTAAAG
16300496 TTAGCGACGC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
85 2 0.03
86 62 0.97
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (86 bp):
TAGCGGCATTTTTAGGAAAAGCGCCGCTAAAGGTATTGGTCTTTAGCGACGTTTCTAGGAAAAGC
GCCGCTAAAGGTCTTGTTCTT
Found at i:16307499 original size:37 final size:37
Alignment explanation
Indices: 16307457--16307531 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
16307447 TATACTTGTG
16307457 AAAACCACCTACTCTTATATTTGATTGTAGTATTCAC
1 AAAACCACCTACTCTTATATTTGATTGTAGTATTCAC
16307494 AAAACCACCTACTCTTATATTTGATTGTAGTATTCAC
1 AAAACCACCTACTCTTATATTTGATTGTAGTATTCAC
16307531 A
1 A
16307532 CTCTAAACGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.37
Consensus pattern (37 bp):
AAAACCACCTACTCTTATATTTGATTGTAGTATTCAC
Found at i:16308022 original size:15 final size:14
Alignment explanation
Indices: 16307992--16308034 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
16307982 TTAAAGTATT
16307992 TAAAAT-AATAAAA
1 TAAAATAAATAAAA
*
16308005 TAAAATAACATAACA
1 TAAAATAA-ATAAAA
*
16308020 TAACATAAATAAAA
1 TAAAATAAATAAAA
16308034 T
1 T
16308035 TCAGGAGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 6 0.24
14 7 0.28
15 12 0.48
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAAATAAATAAAA
Found at i:16314414 original size:15 final size:16
Alignment explanation
Indices: 16314394--16314427 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
16314384 AAAAGGTTGT
16314394 CTTTTATATTTT-TTG
1 CTTTTATATTTTCTTG
*
16314409 CTTTTATGTTTTCTTG
1 CTTTTATATTTTCTTG
16314425 CTT
1 CTT
16314428 GAGGACAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.09, C:0.12, G:0.09, T:0.71
Consensus pattern (16 bp):
CTTTTATATTTTCTTG
Found at i:16316992 original size:23 final size:23
Alignment explanation
Indices: 16316955--16317003 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
16316945 CTTGACAATA
*
16316955 AAGATTGACATAAAGAATAAATC
1 AAGATTGACAGAAAGAATAAATC
*
16316978 AAGATTGGCAGAAAGAATAAATC
1 AAGATTGACAGAAAGAATAAATC
16317001 AAG
1 AAG
16317004 TTTATGATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.55, C:0.08, G:0.18, T:0.18
Consensus pattern (23 bp):
AAGATTGACAGAAAGAATAAATC
Found at i:16318190 original size:55 final size:55
Alignment explanation
Indices: 16318118--16318229 Score: 170
Period size: 55 Copynumber: 2.0 Consensus size: 55
16318108 GTTTCTAGCT
* *
16318118 TTCCCACTTCTCCTAATTTAGGATACTAACTTGCAGTCTCTTTCAATTTTATCCC
1 TTCCCACTTCTCCTAATTTACGATACTAACTTGCAGTCTCTTTCAATTTAATCCC
* * * *
16318173 TTCCCGCTTCTCCTAATTTACGCTGCTAACTTGCGGTCTCTTTCAATTTAATCCC
1 TTCCCACTTCTCCTAATTTACGATACTAACTTGCAGTCTCTTTCAATTTAATCCC
16318228 TT
1 TT
16318230 ATTGTTTCGT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.19, C:0.30, G:0.09, T:0.42
Consensus pattern (55 bp):
TTCCCACTTCTCCTAATTTACGATACTAACTTGCAGTCTCTTTCAATTTAATCCC
Found at i:16320182 original size:25 final size:26
Alignment explanation
Indices: 16320154--16320229 Score: 102
Period size: 25 Copynumber: 3.0 Consensus size: 26
16320144 TTACTGATTC
*
16320154 TCAACTCATATGAGCTTACCGTTA-T
1 TCAACTCGTATGAGCTTACCGTTACT
*
16320179 TCAACTCGCATGAGCTTACCGTTACT
1 TCAACTCGTATGAGCTTACCGTTACT
*
16320205 T-AGCTCGTATGAGCTTACCGATTAC
1 TCAACTCGTATGAGCTTACCG-TTAC
16320230 AGCTAGTAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
25 39 0.87
26 6 0.13
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (26 bp):
TCAACTCGTATGAGCTTACCGTTACT
Found at i:16320242 original size:24 final size:25
Alignment explanation
Indices: 16320190--16320251 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
16320180 CAACTCGCAT
* *
16320190 GAGCTTACCG-TTACTTAGCTCGTAT
1 GAGCTTACCGATTAC-TAGCTAGTAA
16320215 GAGCTTACCGATTAC-AGCTAGTAA
1 GAGCTTACCGATTACTAGCTAGTAA
* *
16320239 GAGCATACAGATT
1 GAGCTTACCGATT
16320252 TAGAGCTCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 18 0.56
25 10 0.31
26 4 0.12
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (25 bp):
GAGCTTACCGATTACTAGCTAGTAA
Found at i:16320267 original size:25 final size:24
Alignment explanation
Indices: 16320206--16320272 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
16320196 ACCGTTACTT
* *
16320206 AGCTCGTATGAGCTTACCGATTAC
1 AGCTCGTATGAGCATACAGATTAC
* * *
16320230 AGCTAGTAAGAGCATACAGATTTAG
1 AGCTCGTATGAGCATACAGA-TTAC
16320255 AGCTCGTATGAGCATACA
1 AGCTCGTATGAGCATACA
16320273 TGTACATTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
24 16 0.46
25 19 0.54
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (24 bp):
AGCTCGTATGAGCATACAGATTAC
Found at i:16326088 original size:17 final size:17
Alignment explanation
Indices: 16326066--16326099 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16326056 TAAGGCTTTG
16326066 TATATTCGTAAATGTCA
1 TATATTCGTAAATGTCA
16326083 TATATTCGTAAATGTCA
1 TATATTCGTAAATGTCA
16326100 AACTCCGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
TATATTCGTAAATGTCA
Found at i:16327084 original size:15 final size:16
Alignment explanation
Indices: 16327064--16327094 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16327054 TGGAAATTAG
16327064 TAAAT-AAAAATTAAA
1 TAAATAAAAAATTAAA
16327079 TAAATAAAAAATTAAA
1 TAAATAAAAAATTAAA
16327095 GTTTTCATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAATAAAAAATTAAA
Found at i:16327983 original size:25 final size:25
Alignment explanation
Indices: 16327955--16328019 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
16327945 CAATTCTTAG
* * *
16327955 CTCGTATAAGCTTACCGTTATTCAT
1 CTCGTATGAGCTTACCGTTACTCAA
16327980 CTCGTATGAGCTTACCGTTACTCAA
1 CTCGTATGAGCTTACCGTTACTCAA
16328005 CTCGTATGAGCTTAC
1 CTCGTATGAGCTTAC
16328020 TGATTACAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.35
Consensus pattern (25 bp):
CTCGTATGAGCTTACCGTTACTCAA
Found at i:16328034 original size:24 final size:24
Alignment explanation
Indices: 16327955--16328034 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 24
16327945 CAATTCTTAG
* * *
16327955 CTCGTATAAGCTTACCGTTATTCAT
1 CTCGTATGAGCTTACCGTTA-CCAA
16327980 CTCGTATGAGCTTACCGTTACTCAA
1 CTCGTATGAGCTTACCGTTAC-CAA
*
16328005 CTCGTATGAGCTTACTGATTA-CAA
1 CTCGTATGAGCTTACCG-TTACCAA
16328029 CTCGTA
1 CTCGTA
16328035 AAAGCATACC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
24 9 0.18
25 37 0.76
26 3 0.06
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (24 bp):
CTCGTATGAGCTTACCGTTACCAA
Found at i:16328048 original size:24 final size:24
Alignment explanation
Indices: 16328002--16328048 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
16327992 TACCGTTACT
** * *
16328002 CAACTCGTATGAGCTTACTGATTA
1 CAACTCGTAAAAGCATACCGATTA
16328026 CAACTCGTAAAAGCATACCGATT
1 CAACTCGTAAAAGCATACCGATT
16328049 CAGAGCTCGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (24 bp):
CAACTCGTAAAAGCATACCGATTA
Found at i:16330320 original size:24 final size:26
Alignment explanation
Indices: 16330277--16330340 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 26
16330267 TCATACGAGT
16330277 TGTA-AACGGTAAGCTCCTT-CGAAA
1 TGTATAACGGTAAGCTCCTTCCGAAA
**
16330301 TGTATAACGGTAAGCT-CTTCCGAGT
1 TGTATAACGGTAAGCTCCTTCCGAAA
*
16330326 TGAATAACGGTAAGC
1 TGTATAACGGTAAGC
16330341 GCATAAGAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.20
25 28 0.80
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (26 bp):
TGTATAACGGTAAGCTCCTTCCGAAA
Found at i:16330350 original size:25 final size:25
Alignment explanation
Indices: 16330304--16330353 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
16330294 TTCGAAATGT
* * **
16330304 ATAACGGTAAGCTCTTCCGAGTTGA
1 ATAACGGTAAGCGCATAAGAGTTGA
16330329 ATAACGGTAAGCGCATAAGAGTTGA
1 ATAACGGTAAGCGCATAAGAGTTGA
16330354 GTATCAGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (25 bp):
ATAACGGTAAGCGCATAAGAGTTGA
Found at i:16337681 original size:50 final size:51
Alignment explanation
Indices: 16337564--16337696 Score: 171
Period size: 50 Copynumber: 2.6 Consensus size: 51
16337554 ACTACAATTT
* *
16337564 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAATTATCCGGTA
1 CACGTAGTAGCCTGCACATAGTACTACACACGCGATCGAAATCATCCGGTA
* * * * **
16337615 CGCATAGTATCCTGCACATAGTACTACACATGCGA-C-TTATCATTCCGGTA
1 CACGTAGTAGCCTGCACATAGTACTACACACGCGATCGAAATCA-TCCGGTA
16337665 CACGTAGTAGCCTGCACATAGTACTACACACG
1 CACGTAGTAGCCTGCACATAGTACTACACACG
16337697 TGACCATCAT
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 3 0.04
50 36 0.52
51 30 0.43
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (51 bp):
CACGTAGTAGCCTGCACATAGTACTACACACGCGATCGAAATCATCCGGTA
Found at i:16339356 original size:49 final size:50
Alignment explanation
Indices: 16339130--16339371 Score: 202
Period size: 50 Copynumber: 4.7 Consensus size: 50
16339120 GGGAATGAGA
** **
16339130 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA---A---TATGAGAAC
* * * * * * **
16339186 TCCCACGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGATAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAATATGAGAAC
** * *
16339236 TCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCAATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAATATGAGAAC
* * **
16339286 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACA-A-GA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-ATATGAGAAC
*
16339334 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16339372 TGTTATTATC
Statistics
Matches: 157, Mismatches: 27, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
48 3 0.02
49 36 0.23
50 82 0.52
51 1 0.01
53 1 0.01
56 34 0.22
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAATATGAGAAC
Found at i:16341783 original size:24 final size:23
Alignment explanation
Indices: 16341727--16341786 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
16341717 AAAACCCATA
16341727 TGCATTCCCCCAAACTTAAAGTT
1 TGCATTCCCCCAAACTTAAAGTT
16341750 TGCATTCCCCCAAACTTAAAGTT
1 TGCATTCCCCCAAACTTAAAGTT
*
16341773 TGTATTGCCCCCAA
1 TGCATT-CCCCCAA
16341787 TGCACTAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 28 0.80
24 7 0.20
ACGTcount: A:0.28, C:0.32, G:0.10, T:0.30
Consensus pattern (23 bp):
TGCATTCCCCCAAACTTAAAGTT
Found at i:16341825 original size:17 final size:17
Alignment explanation
Indices: 16341799--16341831 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16341789 CACTAACATT
*
16341799 AAAATTCAATGACAATA
1 AAAATGCAATGACAATA
16341816 AAAATGCAATGACAAT
1 AAAATGCAATGACAAT
16341832 GTGCACTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.12, G:0.09, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:16352513 original size:22 final size:23
Alignment explanation
Indices: 16352488--16352535 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
16352478 AAGTGATTTT
*
16352488 AAATTTTTTA-TTATTAGACTAA
1 AAATTTTTTATTTATTACACTAA
*
16352510 AAA-TTTTTATTTATTACACTAT
1 AAATTTTTTATTTATTACACTAA
16352532 AAAT
1 AAAT
16352536 AGGTATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (23 bp):
AAATTTTTTATTTATTACACTAA
Found at i:16361467 original size:25 final size:26
Alignment explanation
Indices: 16361414--16361467 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
16361404 TTCTCCTAAA
* *
16361414 TTTCAATTTTATTTAATTTTTTAATT
1 TTTCAATTTTATTGAATTTATTAATT
16361440 TTTCAA-TTTATTGAA-TTATTAATAT
1 TTTCAATTTTATTGAATTTATTAAT-T
16361465 TTT
1 TTT
16361468 ATACTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 12 0.48
26 6 0.24
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTCAATTTTATTGAATTTATTAATT
Found at i:16369011 original size:17 final size:17
Alignment explanation
Indices: 16368979--16369016 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
16368969 TTCAATTCTA
16368979 ATTTGACCCAAAATATTT
1 ATTTGACCCAAAATA-TT
*
16368997 ATTTTACCC-AAATATT
1 ATTTGACCCAAAATATT
16369013 ATTT
1 ATTT
16369017 AAAACTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 5 0.26
18 8 0.42
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTTGACCCAAAATATT
Found at i:16376134 original size:49 final size:49
Alignment explanation
Indices: 16376079--16376173 Score: 156
Period size: 49 Copynumber: 1.9 Consensus size: 49
16376069 ATCTATTTAT
* *
16376079 AGGTTGAAA-AACCTTATTCTAATTAATGTCAAATAGAAGTAGTGTAGTA
1 AGGTTGAAACAA-CTTATTCTAATTAATATCAAATAGAAGAAGTGTAGTA
16376128 AGGTTGAAACAACTTATTCTAATTAATATCAAATAGAAGAAGTGTA
1 AGGTTGAAACAACTTATTCTAATTAATATCAAATAGAAGAAGTGTA
16376174 CTTCTCTACG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
49 41 0.95
50 2 0.05
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (49 bp):
AGGTTGAAACAACTTATTCTAATTAATATCAAATAGAAGAAGTGTAGTA
Found at i:16377107 original size:10 final size:10
Alignment explanation
Indices: 16377092--16377120 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
16377082 GTACTTCCCC
16377092 TGTTTTGACT
1 TGTTTTGACT
16377102 TGTTTTGACT
1 TGTTTTGACT
16377112 TGTTTTGAC
1 TGTTTTGAC
16377121 CCCTGAGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.59
Consensus pattern (10 bp):
TGTTTTGACT
Found at i:16377885 original size:23 final size:22
Alignment explanation
Indices: 16377853--16377899 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
16377843 TTTAACATTA
16377853 TCTTTTATTTCCTTT-TAGGTTT
1 TCTTTTATTTCCTTTCTA-GTTT
*
16377875 TCTTTTCATTTTCTTTCTAGTTT
1 TCTTTT-ATTTCCTTTCTAGTTT
16377898 TC
1 TC
16377900 ACTCAAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 14 0.64
24 2 0.09
ACGTcount: A:0.09, C:0.17, G:0.06, T:0.68
Consensus pattern (22 bp):
TCTTTTATTTCCTTTCTAGTTT
Found at i:16379765 original size:14 final size:14
Alignment explanation
Indices: 16379746--16379772 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16379736 ATTAAATTTG
16379746 AGAAATAATCTCCC
1 AGAAATAATCTCCC
16379760 AGAAATAATCTCC
1 AGAAATAATCTCC
16379773 TAGTTAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.22
Consensus pattern (14 bp):
AGAAATAATCTCCC
Found at i:16382648 original size:12 final size:12
Alignment explanation
Indices: 16382631--16382656 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16382621 ATTGGGGCTG
16382631 ATTTAAAAACAC
1 ATTTAAAAACAC
16382643 ATTTAAAAACAC
1 ATTTAAAAACAC
16382655 AT
1 AT
16382657 GGAAGGCTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (12 bp):
ATTTAAAAACAC
Found at i:16384544 original size:23 final size:23
Alignment explanation
Indices: 16384518--16384616 Score: 144
Period size: 23 Copynumber: 4.3 Consensus size: 23
16384508 AGTGTTATTG
16384518 ATCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
16384541 ATCAGTTGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* * *
16384564 TTTAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTACGGCTACAT
*
16384587 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
16384610 ATCAGTG
1 ATCAGTG
16384617 TGGCACTTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:16384590 original size:46 final size:46
Alignment explanation
Indices: 16384521--16384609 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
16384511 GTTATTGATC
*
16384521 AGTGGTAGCTACGGCTACATATCAGTTGTAGCTTCGGCTACATTTT
1 AGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCTACATTTT
*
16384567 AGTGGTAGCTACGGCTACGTATCAGTGGTAGCTTCGGCTACAT
1 AGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCTACAT
16384610 ATCAGTGTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.31
Consensus pattern (46 bp):
AGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCTACATTTT
Found at i:16389486 original size:17 final size:18
Alignment explanation
Indices: 16389464--16389498 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
16389454 TTATTTGTGT
*
16389464 TATTTTTCTCT-TTTTTC
1 TATTTTTCCCTCTTTTTC
16389481 TATTTTTCCCTCTTTTTC
1 TATTTTTCCCTCTTTTTC
16389499 AGGTATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTTTTCCCTCTTTTTC
Found at i:16397276 original size:27 final size:27
Alignment explanation
Indices: 16397229--16397675 Score: 436
Period size: 27 Copynumber: 16.6 Consensus size: 27
16397219 ACTTATAGGC
* *
16397229 AAATGACTGAAATACCCTTGAAGAGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* *
16397256 AAACT-ACCGAAATACCTTTGAACGGTA
1 AAA-TGACCGAAATACCCTTGAAGGGTA
* *
16397283 AAATGACCAAAATACCCTCGAAGGGT-
1 AAATGACCGAAATACCCTTGAAGGGTA
*
16397309 AAATGACTGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* * *
16397336 AAATGATCGAAATGCCCTCGAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
*
16397363 AAATGATCGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* *
16397390 AAATGATCGAAAT-GCCTTCGAAGGGTA
1 AAATGACCGAAATACCCTT-GAAGGGTA
* * *
16397417 AAATGATCGAAATACCC-TAAAAGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* * *
16397443 AAATGACTGAAATAACCTTGAAGGGTC
1 AAATGACCGAAATACCCTTGAAGGGTA
* *
16397470 AAATGACCGAAATGCCCTCGAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* * * *
16397497 AAATAACTGAAATACCTTTAAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* * *
16397524 AAATGACCAAAATACCTTTAAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
** * *
16397551 AAATGACTAAAATGCCCTTGAAAGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* * * *
16397578 AAATGATCGAGATACCCCTGAACGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* *
16397605 AAATGATCGAAATACCC-TCATAGGGTA
1 AAATGACCGAAATACCCTTGA-AGGGTA
* * * * *
16397632 AAAGGAACGAAATACCCCTGAAGAGTG
1 AAATGACCGAAATACCCTTGAAGGGTA
*
16397659 AAATGACTGAAATACCC
1 AAATGACCGAAATACCC
16397676 CCATAAGTTA
Statistics
Matches: 348, Mismatches: 64, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
26 50 0.14
27 293 0.84
28 5 0.01
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (27 bp):
AAATGACCGAAATACCCTTGAAGGGTA
Found at i:16397474 original size:134 final size:134
Alignment explanation
Indices: 16397229--16397674 Score: 530
Period size: 134 Copynumber: 3.3 Consensus size: 134
16397219 ACTTATAGGC
*
16397229 AAATG-ACTGAAATACCCTTGAAGAGTAAAACT-ACCGAAATACCTTTGAACGGTAAAATGACCA
1 AAATGAACTGAAATACCCTTGAAGAGTAAAA-TGACCGAAATACCTTTGAAGGGTAAAATGA-CA
*
16397292 AAATACCCTCGAAGGGT-AAATGACTGAAATACCCTTGAAGGGTAAAATGATCGAAATGCCCTCG
64 AAATACCCT-GAAAGGTAAAATGACTGAAATACCCTTGAAGGGTAAAATGATCGAAATGCCCTCG
16397356 AAGGGTA
128 AAGGGTA
* * * * * *
16397363 AAATGATC-GAAATACCCTTGAAGGGTAAAATGATCGAAATGCCTTCGAAGGGTAAAATGATCGA
1 AAATGAACTGAAATACCCTTGAAGAGTAAAATGACCGAAATACCTTTGAAGGGTAAAATGA-CAA
* * * *
16397427 AATACCCTAAAAGGTAAAATGACTGAAATAACCTTGAAGGGTCAAATGACCGAAATGCCCTCGAA
65 AATACCCTGAAAGGTAAAATGACTGAAATACCCTTGAAGGGTAAAATGATCGAAATGCCCTCGAA
16397492 GGGTA
130 GGGTA
* * * * *
16397497 AAAT-AACTGAAATACCTTTAAAGGGTAAAATGACCAAAATACCTTTAAAGGGTAAAATGACTAA
1 AAATGAACTGAAATACCCTTGAAGAGTAAAATGACCGAAATACCTTTGAAGGGTAAAATGAC-AA
* * * * *
16397561 AATGCCCTTGAAAGGTAAAATGA-TCGAGATACCCCTGAACGGTAAAATGATCGAAATACCCTC-
65 AATACCC-TGAAAGGTAAAATGACT-GAAATACCCTTGAAGGGTAAAATGATCGAAATGCCCTCG
16397624 ATAGGGTA
128 A-AGGGTA
* * * *
16397632 AAAGGAAC-GAAATACCCCTGAAGAGTGAAATGACTGAAATACC
1 AAATGAACTGAAATACCCTTGAAGAGTAAAATGACCGAAATACC
16397675 CCCATAAGTT
Statistics
Matches: 264, Mismatches: 39, Indels: 17
0.82 0.12 0.05
Matches are distributed among these distances:
133 9 0.03
134 169 0.64
135 83 0.31
136 3 0.01
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (134 bp):
AAATGAACTGAAATACCCTTGAAGAGTAAAATGACCGAAATACCTTTGAAGGGTAAAATGACAAA
ATACCCTGAAAGGTAAAATGACTGAAATACCCTTGAAGGGTAAAATGATCGAAATGCCCTCGAAG
GGTA
Found at i:16397902 original size:26 final size:26
Alignment explanation
Indices: 16397867--16397942 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
16397857 TGCCACATAT
* * *
16397867 ACTACTACTGGCAGCTTTGCTGTGTT
1 ACTATTACTGGCAGCTTTGCTGCGTC
* *
16397893 ACTGTTACTGGTAGCTTTGCTGCGTC
1 ACTATTACTGGCAGCTTTGCTGCGTC
*
16397919 ACTATTACTGGCAGCTTGGCTGCG
1 ACTATTACTGGCAGCTTTGCTGCG
16397943 ATATTGGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.14, C:0.24, G:0.26, T:0.36
Consensus pattern (26 bp):
ACTATTACTGGCAGCTTTGCTGCGTC
Found at i:16398075 original size:30 final size:28
Alignment explanation
Indices: 16398010--16398102 Score: 123
Period size: 28 Copynumber: 3.2 Consensus size: 28
16398000 TACTGCATTG
*
16398010 CACTGATTACTATATTGGGCTAAGGCCCC
1 CACTG-TTACTATATTGGGCTAAGGCCCA
*
16398039 CACTGTTACTGTATTGGGCTAAGGCCTACA
1 CACTGTTACTATATTGGGCTAAGGCC--CA
* *
16398069 CACTGTTACTATAATGGGCTAAAGCCCA
1 CACTGTTACTATATTGGGCTAAGGCCCA
16398097 CACTGT
1 CACTGT
16398103 ACTGATACTA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
28 28 0.49
29 5 0.09
30 24 0.42
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (28 bp):
CACTGTTACTATATTGGGCTAAGGCCCA
Found at i:16405207 original size:54 final size:54
Alignment explanation
Indices: 16405122--16405516 Score: 397
Period size: 54 Copynumber: 7.3 Consensus size: 54
16405112 ACTCATGGGC
*
16405122 AAATGATCGAAATA-CCTTCGAAGGATAAAATGACCGAAATACCCTTGAAGGGTA
1 AAATGATCGAAATACCCTT-GAAGGGTAAAATGACCGAAATACCCTTGAAGGGTA
* * * *
16405176 AATTGATCAAAATACCCTTGAAGGGTAAAATGACCGAAA-A-CTTTCAAAGGGTA
1 AAATGATCGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCTT-GAAGGGTA
* ** * * * * *
16405229 AAATTATTAAAATGCCCTCGAAGGGTAAAATGACAGAAATACCCTTAAAGGTTA
1 AAATGATCGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCTTGAAGGGTA
* * * * * * * *
16405283 AAATGACCGAAATGCCCTCGAAGGCTAAAATGATCGAAATTCCCTCGAAGAGTA
1 AAATGATCGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCTTGAAGGGTA
* * ** *
16405337 AAATGATAGAAATACCCCTGAAGGGTAAAATGACAAAAATACCCTTGGAGGGTA
1 AAATGATCGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCTTGAAGGGTA
* * *
16405391 AAATGATCGAAATGA-CCTCGAAGGGTAAAATGACTGAAATACCCTTGAAAGGTA
1 AAATGATCGAAAT-ACCCTTGAAGGGTAAAATGACCGAAATACCCTTGAAGGGTA
* ** * *
16405445 AAATGA-CTGAAATACCCTTCAAGGGTAAAATGATTGAAATGCCCTCGAAGGGTA
1 AAATGATC-GAAATACCCTTGAAGGGTAAAATGACCGAAATACCCTTGAAGGGTA
16405499 AAATGAAT-GAAATACCCT
1 AAATG-ATCGAAATACCCT
16405517 CATAAGATAA
Statistics
Matches: 281, Mismatches: 51, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
52 3 0.01
53 43 0.15
54 226 0.80
55 9 0.03
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (54 bp):
AAATGATCGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCTTGAAGGGTA
Found at i:16405342 original size:81 final size:81
Alignment explanation
Indices: 16405122--16405516 Score: 449
Period size: 81 Copynumber: 4.9 Consensus size: 81
16405112 ACTCATGGGC
* * * * * * *
16405122 AAATGATCGAAATACCTTCGAAGGATAAAATGACCGAAATACCCTTGAAGGGTAAATTGATCA-A
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATGCCCTCGAAGGGTAAAATGA-CAGA
*
16405186 AATACCCTTGAAGGGTA
65 AATACCCTTAAAGGGTA
** * * **
16405203 AAATGACCGAAA-ACTTTCAAAGGGTAAAATTATTAAAATGCCCTCGAAGGGTAAAATGACAGAA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATGCCCTCGAAGGGTAAAATGACAGAA
*
16405267 ATACCCTTAAAGGTTA
66 ATACCCTTAAAGGGTA
* * * * *
16405283 AAATGACCGAAATGCCCTCGAAGGCTAAAATGATCGAAATTCCCTCGAAGAGTAAAATGATAGAA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATGCCCTCGAAGGGTAAAATGACAGAA
* *
16405348 ATACCCCTGAAGGGTA
66 ATACCCTTAAAGGGTA
** * * * *
16405364 AAATGACAAAAATACCCTTGGAGGGTAAAATGATCGAAATGACCTCGAAGGGTAAAATGACTGAA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATGCCCTCGAAGGGTAAAATGACAGAA
16405429 ATACCCTTGAAA-GGTA
66 ATACCCTT-AAAGGGTA
* *
16405445 AAATGACTGAAATACCCTTC-AAGGGTAAAATGATTGAAATGCCCTCGAAGGGTAAAATGA-ATG
1 AAATGACCGAAATACCC-TCGAAGGGTAAAATGATCGAAATGCCCTCGAAGGGTAAAATGACA-G
16405508 AAATACCCT
64 AAATACCCT
16405517 CATAAGATAA
Statistics
Matches: 262, Mismatches: 47, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
79 2 0.01
80 65 0.25
81 192 0.73
82 3 0.01
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (81 bp):
AAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATGCCCTCGAAGGGTAAAATGACAGAA
ATACCCTTAAAGGGTA
Found at i:16405516 original size:27 final size:27
Alignment explanation
Indices: 16405122--16405517 Score: 310
Period size: 27 Copynumber: 14.7 Consensus size: 27
16405112 ACTCATGGGC
* *
16405122 AAATG-ATCGAAATACCTTCGAAGGATA
1 AAATGAAT-GAAATACCCTCGAAGGGTA
** *
16405149 AAATGACCGAAATACCCTTGAAGGGTA
1 AAATGAATGAAATACCCTCGAAGGGTA
* * *
16405176 AATTG-ATCAAAATACCCTTGAAGGGTA
1 AAATGAAT-GAAATACCCTCGAAGGGTA
** ** *
16405203 AAATGACCGAAA-ACTTTCAAAGGGTA
1 AAATGAATGAAATACCCTCGAAGGGTA
* * * *
16405229 AAATTATTAAAATGCCCTCGAAGGGTA
1 AAATGAATGAAATACCCTCGAAGGGTA
** *
16405256 AAATGACA-GAAATACCCTTAAAGGTTA
1 AAATGA-ATGAAATACCCTCGAAGGGTA
** * *
16405283 AAATGACCGAAATGCCCTCGAAGGCTA
1 AAATGAATGAAATACCCTCGAAGGGTA
* *
16405310 AAATG-ATCGAAATTCCCTCGAAGAGTA
1 AAATGAAT-GAAATACCCTCGAAGGGTA
16405337 AAATG-ATAGAAATACCC-CTGAAGGGTA
1 AAATGAAT-GAAATACCCTC-GAAGGGTA
* * *
16405364 AAATGACA-AAAATACCCTTGGAGGGTA
1 AAATGA-ATGAAATACCCTCGAAGGGTA
16405391 AAATG-ATCGAAATGA-CCTCGAAGGGTA
1 AAATGAAT-GAAAT-ACCCTCGAAGGGTA
* * *
16405418 AAATGACTGAAATACCCTTGAAAGGTA
1 AAATGAATGAAATACCCTCGAAGGGTA
*
16405445 AAATGACTGAAATACCCTTC-AAGGGTA
1 AAATGAATGAAATACCC-TCGAAGGGTA
* *
16405472 AAATGATTGAAATGCCCTCGAAGGGTA
1 AAATGAATGAAATACCCTCGAAGGGTA
16405499 AAATGAATGAAATACCCTC
1 AAATGAATGAAATACCCTC
16405518 ATAAGATAAA
Statistics
Matches: 291, Mismatches: 60, Indels: 36
0.75 0.16 0.09
Matches are distributed among these distances:
25 1 0.00
26 22 0.08
27 264 0.91
28 3 0.01
29 1 0.00
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.21
Consensus pattern (27 bp):
AAATGAATGAAATACCCTCGAAGGGTA
Found at i:16405929 original size:27 final size:30
Alignment explanation
Indices: 16405886--16405980 Score: 105
Period size: 30 Copynumber: 3.3 Consensus size: 30
16405876 ACTGCATTGC
16405886 ACTGATTACTGTATTGGGCTAAGGGCCC-C-
1 ACTG-TTACTGTATTGGGCTAAGGGCCCACA
*
16405915 A-TGTTACTGTATTGGGC-AAAGGCCCACA
1 ACTGTTACTGTATTGGGCTAAGGGCCCACA
*
16405943 GACTGTTACTATATTGGGCTAA-GGCCCAC-
1 -ACTGTTACTGTATTGGGCTAAGGGCCCACA
16405972 ACTG-TACTG
1 ACTGTTACTG
16405981 ATACTGTATA
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
26 7 0.12
27 19 0.33
28 6 0.10
29 2 0.03
30 22 0.38
31 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.27
Consensus pattern (30 bp):
ACTGTTACTGTATTGGGCTAAGGGCCCACA
Found at i:16410092 original size:29 final size:28
Alignment explanation
Indices: 16410040--16410122 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 28
16410030 CACAGTTTCC
* *
16410040 ATAAGAAATCCTTGTGGCGGTCTCTATT
1 ATAAGAAATCTTTGTGGCGATCTCTATT
* *
16410068 ATAAGAAAGTCTTTCTGGCGATCTCTTTT
1 ATAAGAAA-TCTTTGTGGCGATCTCTATT
* *
16410097 ATAAGAAAATTTTTGTGGCTATCTCT
1 ATAAG-AAATCTTTGTGGCGATCTCT
16410123 CTTAAAGGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
28 8 0.17
29 35 0.76
30 3 0.07
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40
Consensus pattern (28 bp):
ATAAGAAATCTTTGTGGCGATCTCTATT
Found at i:16419525 original size:5 final size:5
Alignment explanation
Indices: 16419515--16419539 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
16419505 GGTAATTTGG
16419515 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
16419540 ACAAAAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:16426269 original size:20 final size:19
Alignment explanation
Indices: 16426240--16426338 Score: 74
Period size: 20 Copynumber: 5.0 Consensus size: 19
16426230 ACGGGATTTG
16426240 CACTTCGGTGCCCCTGTATA
1 CACTTCGGTGCCCCTGT-TA
* * * *
16426260 CACTTTGGTGCCTCTATTCG
1 CACTTCGGTGCCCCTGTT-A
* *
16426280 CACTACGGTGCCCCTGTTTG
1 CACTTCGGTGCCCCTG-TTA
*
16426300 CACATT-TGTGCCCCTGTCTA
1 CAC-TTCGGTGCCCCTGT-TA
*
16426320 CACATCGGTGCCCCTGTTA
1 CACTTCGGTGCCCCTGTTA
16426339 TGCATCTATG
Statistics
Matches: 61, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
19 5 0.08
20 53 0.87
21 3 0.05
ACGTcount: A:0.13, C:0.34, G:0.20, T:0.32
Consensus pattern (19 bp):
CACTTCGGTGCCCCTGTTA
Found at i:16426492 original size:7 final size:7
Alignment explanation
Indices: 16426482--16426506 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16426472 GCAATTATTA
16426482 AATGTTC
1 AATGTTC
16426489 AATGTTC
1 AATGTTC
16426496 AATGTTC
1 AATGTTC
16426503 AATG
1 AATG
16426507 AATTACTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (7 bp):
AATGTTC
Found at i:16429197 original size:34 final size:35
Alignment explanation
Indices: 16429159--16429241 Score: 132
Period size: 36 Copynumber: 2.4 Consensus size: 35
16429149 TAGGTACGTG
*
16429159 TATATATAATATAAATATGTGTGCATGGTTTTATTA
1 TATATATAATATAAATATGAGTGCAT-GTTTTATTA
*
16429195 TATATATAATATAAATATGAGTGCATTTTTTA-TA
1 TATATATAATATAAATATGAGTGCATGTTTTATTA
16429229 TATATATAATATA
1 TATATATAATATA
16429242 TAGGTGTGGC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
34 15 0.33
35 5 0.11
36 25 0.56
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (35 bp):
TATATATAATATAAATATGAGTGCATGTTTTATTA
Found at i:16432108 original size:38 final size:39
Alignment explanation
Indices: 16432066--16432142 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 39
16432056 TTACTTTTAG
* *
16432066 GCATATATCACATTACACATATAAT-ACATAACATTCAA
1 GCATATACCACAATACACATATAATCACATAACATTCAA
* *
16432104 GCATATACCATAATACTCATATAATCACATAACATTCAA
1 GCATATACCACAATACACATATAATCACATAACATTCAA
16432143 ACTAGCCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
38 21 0.62
39 13 0.38
ACGTcount: A:0.47, C:0.22, G:0.03, T:0.29
Consensus pattern (39 bp):
GCATATACCACAATACACATATAATCACATAACATTCAA
Found at i:16434715 original size:38 final size:38
Alignment explanation
Indices: 16434664--16434743 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
16434654 CCTTATTCCT
* *
16434664 AAAACATAATCAATTAACAAAAAAATCTACGAAATCAC
1 AAAACATAATCAATTAACAAAAAAACCTACAAAATCAC
* *
16434702 AAAACGTAATCAATTAACAACAAAACCTACAAAATCAC
1 AAAACATAATCAATTAACAAAAAAACCTACAAAATCAC
16434740 AAAA
1 AAAA
16434744 ATGGATTTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.61, C:0.20, G:0.03, T:0.16
Consensus pattern (38 bp):
AAAACATAATCAATTAACAAAAAAACCTACAAAATCAC
Found at i:16436323 original size:26 final size:24
Alignment explanation
Indices: 16436294--16436347 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 24
16436284 AATAATACTC
*
16436294 TTAATATATTATTGAAAAATATTATA
1 TTAATATATTACT-AAAAATA-TATA
*
16436320 TTAATATTTTACTAAAAATATATA
1 TTAATATATTACTAAAAATATATA
16436344 TTAA
1 TTAA
16436348 AATTTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 8 0.31
25 7 0.27
26 11 0.42
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TTAATATATTACTAAAAATATATA
Found at i:16442103 original size:24 final size:25
Alignment explanation
Indices: 16442048--16442105 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
16442038 AAGCTCAATC
16442048 ATTATTTTAAATTTATTATTAATTT
1 ATTATTTTAAATTTATTATTAATTT
* *
16442073 -TTTTTTTAAATTTA-TCTT-ATGTT
1 ATTATTTTAAATTTATTATTAAT-TT
16442096 ATTATTTTAA
1 ATTATTTTAA
16442106 TTTCCATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 2 0.07
23 5 0.18
24 21 0.75
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (25 bp):
ATTATTTTAAATTTATTATTAATTT
Found at i:16447128 original size:39 final size:39
Alignment explanation
Indices: 16447085--16447264 Score: 193
Period size: 39 Copynumber: 4.6 Consensus size: 39
16447075 AAGGTGTTTT
* *
16447085 TGAGTATTGTCATATATGCTTAAATGTTATGCGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
16447124 TGAGTATGGTGATATATGATTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * * * *
16447163 CGAGTATTCTAACATATACTTAAATGTTATGTGACTT-TA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGA-TTATA
** *
16447202 TGAGTATTGTGATATATGCTTGTATGTTAGGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
16447241 TGTGTAATT-TGGTATATGCTTAAA
1 TGAGT-ATTGTGATATATGCTTAAA
16447265 AGTGAATATG
Statistics
Matches: 113, Mismatches: 25, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
38 2 0.02
39 106 0.94
40 5 0.04
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.44
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:16447264 original size:78 final size:78
Alignment explanation
Indices: 16447086--16447240 Score: 213
Period size: 78 Copynumber: 2.0 Consensus size: 78
16447076 AGGTGTTTTT
* *
16447086 GAGTATTGTCATATATGCTTAAATGTTATGCGATTATATGAGTATGGTGATATATGATTGAATGT
1 GAGTATTCTAATATATGCTTAAATGTTATGCGATTATATGAGTATGGTGATATATGATTGAATGT
*
16447151 TATGTGATTATAC
66 TAGGTGATTATAC
* * * * * *
16447164 GAGTATTCTAACATATACTTAAATGTTATGTGACTT-TATGAGTATTGTGATATATGCTTGTATG
1 GAGTATTCTAATATATGCTTAAATGTTATGCGA-TTATATGAGTATGGTGATATATGATTGAATG
16447228 TTAGGTGATTATA
65 TTAGGTGATTATA
16447241 TGTGTAATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
78 65 0.97
79 2 0.03
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (78 bp):
GAGTATTCTAATATATGCTTAAATGTTATGCGATTATATGAGTATGGTGATATATGATTGAATGT
TAGGTGATTATAC
Found at i:16455801 original size:40 final size:40
Alignment explanation
Indices: 16455748--16455858 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
16455738 GTTTGGACAA
* * *
16455748 AAAACGTCACTAAAAATCGAGCATTAGCGGCGCCTTACGT-
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCG-CTTACCTG
* *
16455788 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTCCTG
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTACCTG
* *
16455828 GAAGCGCCGCTAAAAAT-GAGCATTAGCGGCG
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCG
16455859 TTTTTTGGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 19 0.31
40 43 0.69
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTACCTG
Found at i:16455996 original size:41 final size:41
Alignment explanation
Indices: 16455914--16456155 Score: 308
Period size: 41 Copynumber: 5.9 Consensus size: 41
16455904 TTTCTACCTT
* *
16455914 TCAGATCTTTAGCGGCG-TTTGGAAAAAAAAGCACCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTG---AAAAAGCGCCGCTAATGC
16455957 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* ** ** *
16455998 TCAGATCTTTCGCGGCGTTTTCCATGAAGCGCCACTAATGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
*
16456039 TCAGATCTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
** * *
16456080 TCAGATCTTTAGCGGCGTTTTCCATGAAA-CGCCGCTAAAGC
1 TCAGATCTTTAGCGGCGTTTTTGA-AAAAGCGCCGCTAATGC
*
16456121 TCAGATCTTTAGCGGCGTTTTTGAAGAAGCGCCGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGC
16456156 AAAAATATTT
Statistics
Matches: 172, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
40 2 0.01
41 146 0.85
42 3 0.02
43 17 0.10
44 4 0.02
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (41 bp):
TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:16456056 original size:82 final size:82
Alignment explanation
Indices: 16455950--16456155 Score: 358
Period size: 82 Copynumber: 2.5 Consensus size: 82
16455940 AAAAGCACCG
*
16455950 CTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGATCTTTCGCGGCG
1 CTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCG
*
16456015 TTTTCCATGAAGCGCCA
66 TTTTCCATGAAACGCCA
*
16456032 CTAATGCTCAGATCTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCG
1 CTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCG
*
16456097 TTTTCCATGAAACGCCG
66 TTTTCCATGAAACGCCA
* *
16456114 CTAAAGCTCAGATCTTTAGCGGCGTTTTTGAAGAAGCGCCGC
1 CTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGC
16456156 AAAAATATTT
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 117 1.00
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (82 bp):
CTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCG
TTTTCCATGAAACGCCA
Found at i:16456563 original size:14 final size:15
Alignment explanation
Indices: 16456532--16456564 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
16456522 AAGGTTTATA
16456532 GATTATGGAATTAAG
1 GATTATGGAATTAAG
*
16456547 GATTATGG-ATTAGG
1 GATTATGGAATTAAG
16456561 GATT
1 GATT
16456565 CAGATTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAAG
Found at i:16457263 original size:17 final size:16
Alignment explanation
Indices: 16457230--16457263 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16457220 ATATTAGATT
*
16457230 TAAAAAAATTAATAAA
1 TAAAAAAATTAACAAA
16457246 TAAAAAAATGTAACAAA
1 TAAAAAAAT-TAACAAA
16457263 T
1 T
16457264 TGATACGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAAAATTAACAAA
Found at i:16457411 original size:19 final size:19
Alignment explanation
Indices: 16457389--16457427 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
16457379 TTTAGTTAGG
16457389 AAGAAATATCTTTAATAAA
1 AAGAAATATCTTTAATAAA
16457408 AAGAAATATCTTTAATAAA
1 AAGAAATATCTTTAATAAA
16457427 A
1 A
16457428 TGGAGATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (19 bp):
AAGAAATATCTTTAATAAA
Found at i:16458034 original size:74 final size:75
Alignment explanation
Indices: 16457789--16458033 Score: 456
Period size: 75 Copynumber: 3.3 Consensus size: 75
16457779 AGGTAAGCAA
*
16457789 TAGCGGCGTTTTTATAAAAAACGTCACAAAAAATAATTTTACTTTAAAAATAGCCATTTTATATA
1 TAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAATAGCCATTTTATATA
16457854 GCAAAACATT
66 GCAAAACATT
16457864 TAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAACATAGCCATTTTATAT
1 TAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAA-ATAGCCATTTTATAT
16457929 AGCAAAACATT
65 AGCAAAACATT
*
16457940 TAGCAGCGTTTTTAT-AAAAACGCCACAAAAAATAATTTTACTTTAAAAATAGCCATTTTATATA
1 TAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAATAGCCATTTTATATA
16458004 GCAAAACATT
66 GCAAAACATT
16458014 TAGCGGCGTTTTTATAAAAA
1 TAGCGGCGTTTTTATAAAAA
16458034 CACCGCAAAG
Statistics
Matches: 165, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
74 40 0.24
75 85 0.52
76 40 0.24
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (75 bp):
TAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAATAGCCATTTTATATA
GCAAAACATT
Found at i:16458142 original size:113 final size:113
Alignment explanation
Indices: 16457940--16458263 Score: 544
Period size: 113 Copynumber: 2.8 Consensus size: 113
16457930 GCAAAACATT
*
16457940 TAGCAGCGTTTTTATAAAAACGCCACAAAAAATAATTTTACTTTAAAAATAGCCATTTTATATAG
1 TAGCGGCGTTTTTATAAAAACGCCACAAAAAATAATTTTACTTTAAAAATAGCCATTTTATATAG
16458005 CAAAACATTTAGCGGCGTTTTTATAAAAACACCGC-AAAGGTAAGCAA
66 CAAAACATTTAGCGGCGTTTTTATAAAAACACCGCAAAAGGTAAGCAA
16458052 TAGCGGCGTTTTTATAAAAACGCCACAAAAAAATAATTTTACTTTAAAAATAGCCATTTTATATA
1 TAGCGGCGTTTTTATAAAAACGCCAC-AAAAAATAATTTTACTTTAAAAATAGCCATTTTATATA
16458117 GCAAAACATTTAGCGGCGTTTTTATAAAAAAACACCGCAAAAGGTAAGCAA
65 GCAAAACATTTAGCGGCGTTTTTAT--AAAAACACCGCAAAAGGTAAGCAA
* *
16458168 TAGCGGC-ATTTTAGTAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGGCATTTTATA
1 TAGCGGCGTTTTTA-T-AAAAACGCCACAAAAAATAATTTTACTTT-AAAAATAGCCATTTTATA
*
16458232 TAACAAAACATTTAGCGGCGTTTTTATAAAAA
63 TAGCAAAACATTTAGCGGCGTTTTTATAAAAA
16458264 ACGCCACAAA
Statistics
Matches: 201, Mismatches: 4, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
112 25 0.12
113 63 0.31
115 21 0.10
116 38 0.19
117 54 0.27
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (113 bp):
TAGCGGCGTTTTTATAAAAACGCCACAAAAAATAATTTTACTTTAAAAATAGCCATTTTATATAG
CAAAACATTTAGCGGCGTTTTTATAAAAACACCGCAAAAGGTAAGCAA
Found at i:16458248 original size:76 final size:76
Alignment explanation
Indices: 16458168--16458383 Score: 279
Period size: 76 Copynumber: 2.9 Consensus size: 76
16458158 AGGTAAGCAA
*
16458168 TAGCGGC-ATTTTAGTAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGGCATTTTATA
1 TAGCGGCGTTTTTA-TAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGGCATTTTA-A
16458232 TAACAAAACA-TT
64 TAACAAAACATTT
* *
16458244 TAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAATAACTA--CTATTTTACA
1 TAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGGC-ATTTTA-A
16458307 T-ACAAAACATTT
64 TAACAAAACATTT
16458319 TAGCGGCGTTTTTATAAAAAAACGCCAC-AAAAATAATTTTA---TAAAAAATAGCGTCATTTTA
1 TAGCGGCGTTTTTAT-AAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAG-G-CATTTTA
16458380 ATAA
63 ATAA
16458384 AATCCCCTCC
Statistics
Matches: 125, Mismatches: 6, Indels: 19
0.83 0.04 0.13
Matches are distributed among these distances:
72 7 0.06
74 11 0.09
75 45 0.36
76 57 0.46
77 5 0.04
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (76 bp):
TAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGGCATTTTAATA
ACAAAACATTT
Found at i:16458415 original size:22 final size:22
Alignment explanation
Indices: 16458388--16458434 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
16458378 TAATAAAATC
*
16458388 CCCTCCCCAAATCCCCAACTTT
1 CCCTCCCAAAATCCCCAACTTT
* * *
16458410 CCCTCCTAAAATCCCTAATTTT
1 CCCTCCCAAAATCCCCAACTTT
16458432 CCC
1 CCC
16458435 CCCTTGAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.49, G:0.00, T:0.28
Consensus pattern (22 bp):
CCCTCCCAAAATCCCCAACTTT
Found at i:16459173 original size:2 final size:2
Alignment explanation
Indices: 16459166--16459191 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16459156 TTGGTATTTC
16459166 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
16459192 GTTTTGTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16462131 original size:5 final size:5
Alignment explanation
Indices: 16462121--16462146 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16462111 TCAAATTTAA
16462121 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
16462147 TTTATCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:16462250 original size:43 final size:43
Alignment explanation
Indices: 16462189--16462431 Score: 256
Period size: 43 Copynumber: 5.6 Consensus size: 43
16462179 TATATATTTT
* * * * * *
16462189 TAAAGGTTATGGTTTTTAGTGGCGTTTTTGTGAGAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
16462232 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG-AAAAGCGCCGC
* * * * *
16462276 TAAATGTCTTGGTCTTTAGTGGCGTTTTTGGGAAAAGCGTCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * **
16462319 TAAAGAT-ATTAGTCTTTAGCGGCGTTTGTGGGAGTAGCGCCGC
1 TAAAGGTCA-TGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * * * *
16462362 TAAAGAT-ATTGGTTTTTAGCGGCATTTGTGGTAAAAGCGCTGC
1 TAAAGGTCA-TGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
*
16462405 TAAAGGTCTTGGTCTTTAGCGGCGTTT
1 TAAAGGTCATGGTCTTTAGCGGCGTTT
16462432 TTTTCTAAAA
Statistics
Matches: 166, Mismatches: 31, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
43 128 0.77
44 38 0.23
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (43 bp):
TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
Found at i:16462349 original size:87 final size:85
Alignment explanation
Indices: 16462198--16462431 Score: 283
Period size: 86 Copynumber: 2.7 Consensus size: 85
16462188 TTAAAGGTTA
* *
16462198 TGGTTTTTAGTGGCGTTTTTGTGAGAAGCGCCGCTAAAGGTCA-TGGTCTTTAGCGGCGTTTGTG
1 TGGTTTTTAGTGGCGTTTTTGGGAAAAGCG-CGCTAAAGGT-ATTGGTCTTTAGCGGCGTTTGTG
*
16462262 GGAAAAAGCGCCGCTAAATG-TCT
64 GG-AAAAGCGCCGCTAAA-GATAT
* * *
16462285 TGGTCTTTAGTGGCGTTTTTGGGAAAAGCGTCGCTAAAGATATTAGTCTTTAGCGGCGTTTGTGG
1 TGGTTTTTAGTGGCGTTTTTGGGAAAAGCG-CGCTAAAGGTATTGGTCTTTAGCGGCGTTTGTGG
**
16462350 GAGTAGCGCCGCTAAAGATAT
65 GAAAAGCGCCGCTAAAGATAT
* * * * *
16462371 TGGTTTTTAGCGGCATTTGTGGTAAAAGCGCTGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1 TGGTTTTTAGTGGCGTTTTTGGGAAAAGCGC-GCTAAAGGTATTGGTCTTTAGCGGCGTTT
16462432 TTTTCTAAAA
Statistics
Matches: 127, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
85 2 0.02
86 67 0.53
87 58 0.46
ACGTcount: A:0.20, C:0.15, G:0.32, T:0.34
Consensus pattern (85 bp):
TGGTTTTTAGTGGCGTTTTTGGGAAAAGCGCGCTAAAGGTATTGGTCTTTAGCGGCGTTTGTGGG
AAAAGCGCCGCTAAAGATAT
Found at i:16462552 original size:22 final size:22
Alignment explanation
Indices: 16462524--16462567 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
16462514 TTAGCGGCGC
*
16462524 AAAAAAGCGCCGCTAAAGGCCT
1 AAAAAAGCGCCGCTAAAAGCCT
*
16462546 AAAAAAGTGCCGCTAAAAGCCT
1 AAAAAAGCGCCGCTAAAAGCCT
16462568 GTTTTGGTGT
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:0.43, C:0.25, G:0.20, T:0.11
Consensus pattern (22 bp):
AAAAAAGCGCCGCTAAAAGCCT
Found at i:16469399 original size:20 final size:20
Alignment explanation
Indices: 16469360--16469399 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
16469350 ACTAACTTTA
16469360 CTCTATTTTTAACCTTCAAAG
1 CTCTATTTTTAACC-TCAAAG
16469381 CTCTATTTTATAACC-CAAA
1 CTCTATTTT-TAACCTCAAA
16469400 ACAATATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.40
Consensus pattern (20 bp):
CTCTATTTTTAACCTCAAAG
Found at i:16476175 original size:20 final size:20
Alignment explanation
Indices: 16476150--16476189 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
16476140 AATTATGTGT
16476150 TAGTCGATAAAGCCTACAAA
1 TAGTCGATAAAGCCTACAAA
16476170 TAGTCGATAAAGCCTACAAA
1 TAGTCGATAAAGCCTACAAA
16476190 AATTATCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (20 bp):
TAGTCGATAAAGCCTACAAA
Found at i:16487509 original size:51 final size:51
Alignment explanation
Indices: 16487378--16487573 Score: 209
Period size: 51 Copynumber: 3.9 Consensus size: 51
16487368 AGTGAAACTG
* * * *
16487378 ATGGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACTGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * * *
16487427 ATAGGTCGCATGTCTAGTACTATGTGCAGGCTACTATGTGTACCAGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * * * * *
16487478 TTCGATCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* *
16487530 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCG
16487574 AACATCATTG
Statistics
Matches: 118, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
49 2 0.02
50 37 0.31
51 77 0.65
52 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.32
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
Found at i:16487510 original size:101 final size:102
Alignment explanation
Indices: 16487382--16487568 Score: 308
Period size: 101 Copynumber: 1.8 Consensus size: 102
16487372 AAACTGATGG
*
16487382 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTA-CTGGAATGAT-A-GGTCGCATGTCTAG
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATC-GG-ATGATAATGGTCACATGTCTAG
16487444 TACTATGTGCAGGCTACTATGTGTACCAGATAGTTTCGA
64 TACTATGTGCAGGCTACTATGTGTACCAGATAGTTTCGA
* *
16487483 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATGGTAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATGATAATGGTCACATGTCTAGTA
16487548 CTATGTGCAGGCTACTATGTG
66 CTATGTGCAGGCTACTATGTG
16487569 AACCGAACAT
Statistics
Matches: 80, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
100 4 0.05
101 40 0.50
102 36 0.45
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATGATAATGGTCACATGTCTAGTA
CTATGTGCAGGCTACTATGTGTACCAGATAGTTTCGA
Found at i:16487626 original size:45 final size:45
Alignment explanation
Indices: 16487570--16487664 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
16487560 TACTATGTGA
* *
16487570 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
*
16487615 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
16487660 ACCGA
1 ACCGA
16487665 GTATCTGTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:16495351 original size:18 final size:18
Alignment explanation
Indices: 16495330--16495369 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
16495320 ATTGGGTTTC
16495330 GGCTGCTCAGGTTCTCTA
1 GGCTGCTCAGGTTCTCTA
16495348 GGCTGCTCAGGTTCTCTA
1 GGCTGCTCAGGTTCTCTA
16495366 GGCT
1 GGCT
16495370 ATTCTTCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.28, G:0.30, T:0.33
Consensus pattern (18 bp):
GGCTGCTCAGGTTCTCTA
Found at i:16504154 original size:50 final size:50
Alignment explanation
Indices: 16504095--16504234 Score: 210
Period size: 50 Copynumber: 2.8 Consensus size: 50
16504085 TCCTTGAGAT
16504095 CATGAGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
1 CATGAGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
* *
16504145 GATGAGAGGTCCTCC-GTAAGACCATGTTTGGGACATGGCATGGGCACCGA
1 CATGAGAGGTCC-CCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
** *
16504195 CATGAGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 CATGAG-AGGTCCCCTGTAAGACCATGTCTGGGACATGGC
16504235 TTTGGCATGT
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
50 51 0.64
51 29 0.36
ACGTcount: A:0.26, C:0.24, G:0.31, T:0.19
Consensus pattern (50 bp):
CATGAGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
Found at i:16510886 original size:39 final size:40
Alignment explanation
Indices: 16510798--16510875 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
16510788 GCGTTTGAAT
*
16510798 AAAAAACGCCACTAAAAATCAAGCATTAGTAGCGCTTTTC
1 AAAAAATGCCACTAAAAATCAAGCATTAGTAGCGCTTTTC
* * * *
16510838 AAAAAATGCCGCTAAAGATCGAGCATTAG-CGCGCTTTT
1 AAAAAATGCCACTAAAAATCAAGCATTAGTAGCGCTTTT
16510876 AGGAAAATGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 8 0.24
40 25 0.76
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (40 bp):
AAAAAATGCCACTAAAAATCAAGCATTAGTAGCGCTTTTC
Found at i:16511032 original size:14 final size:14
Alignment explanation
Indices: 16511010--16511040 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
16511000 TTAATTATCA
16511010 TTATAGTTTAGGGT
1 TTATAGTTTAGGGT
*
16511024 TTATGGTTTAGGGT
1 TTATAGTTTAGGGT
16511038 TTA
1 TTA
16511041 AGATTTAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (14 bp):
TTATAGTTTAGGGT
Found at i:16511140 original size:14 final size:14
Alignment explanation
Indices: 16511121--16511167 Score: 85
Period size: 14 Copynumber: 3.4 Consensus size: 14
16511111 TAAGGTTTAA
16511121 GGGTTATGGGTTTG
1 GGGTTATGGGTTTG
16511135 GGGTTATGGGTTTG
1 GGGTTATGGGTTTG
*
16511149 GGGTTATGGGTTTA
1 GGGTTATGGGTTTG
16511163 GGGTT
1 GGGTT
16511168 TAGATTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.09, C:0.00, G:0.49, T:0.43
Consensus pattern (14 bp):
GGGTTATGGGTTTG
Found at i:16511168 original size:21 final size:19
Alignment explanation
Indices: 16511114--16511168 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 19
16511104 GATCGTTTAA
16511114 GGTTTAAGGGTTATGGGTTTG
1 GGTTT-AGGGTT-TGGGTTTG
*
16511135 GGGTTATGGGTTTGGGGTTATG
1 GGTTTA-GGGTTT-GGGTT-TG
16511157 GGTTTAGGGTTT
1 GGTTTAGGGTTT
16511169 AGATTAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 2 0.07
21 20 0.69
22 7 0.24
ACGTcount: A:0.11, C:0.00, G:0.45, T:0.44
Consensus pattern (19 bp):
GGTTTAGGGTTTGGGTTTG
Found at i:16512921 original size:7 final size:7
Alignment explanation
Indices: 16512909--16512947 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
16512899 ACCCTTCTTC
16512909 TCCCCTT
1 TCCCCTT
16512916 TCCCCTT
1 TCCCCTT
16512923 TCCCC-T
1 TCCCCTT
16512929 T-CCCTT
1 TCCCCTT
16512935 TCCCC-T
1 TCCCCTT
16512941 TCCCCTT
1 TCCCCTT
16512948 GGGTTGCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 3 0.10
6 10 0.34
7 16 0.55
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (7 bp):
TCCCCTT
Found at i:16512945 original size:6 final size:6
Alignment explanation
Indices: 16512909--16512947 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
16512899 ACCCTTCTTC
*
16512909 TCCCCTT TCCCCTT TCCCCT TCCCTT TCCCCT TCCCCT T
1 TCCCC-T TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT T
16512948 GGGTTGCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 18 0.60
7 12 0.40
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (6 bp):
TCCCCT
Found at i:16513035 original size:25 final size:25
Alignment explanation
Indices: 16513007--16513056 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
16512997 CAGGTAAGGC
16513007 TCCTTCTCCTTCTTCCGTTCTTCAT
1 TCCTTCTCCTTCTTCCGTTCTTCAT
* *
16513032 TCCTTTTTCTTCTTCCGTTCTTCAT
1 TCCTTCTCCTTCTTCCGTTCTTCAT
16513057 CTTCTCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.04, C:0.36, G:0.04, T:0.56
Consensus pattern (25 bp):
TCCTTCTCCTTCTTCCGTTCTTCAT
Found at i:16515872 original size:19 final size:19
Alignment explanation
Indices: 16515848--16515901 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
16515838 AAAAATAAAT
16515848 ATAATTGTAATAATTTT-TA
1 ATAATT-TAATAATTTTGTA
*
16515867 ATAATTTATTAATTTTGTA
1 ATAATTTAATAATTTTGTA
** *
16515886 ATTGTTAAATAATTTT
1 ATAATTTAATAATTTT
16515902 AAAAACTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 9 0.31
19 20 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
ATAATTTAATAATTTTGTA
Done.