Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 172 of 226
Found at i:54951526 original size:52 final size:53
Alignment explanation
Indices: 54951426--54951529 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 53
54951416 ATGTGCAGGA
* ** *
54951426 TGAACCACATGGTCTCATAGAGTTACATGACCTAGCGACACTGTCATGTGACT
1 TGAACCACATGGTCACATAGAGTTACATGACCTAGCGACAAGGCCATGTGACT
* * *
54951479 TGAACCACATGGTCACA-ATAGTTACATGGCCTGGCGACAAGGCCATGTGAC
1 TGAACCACATGGTCACATAGAGTTACATGACCTAGCGACAAGGCCATGTGAC
54951530 CAAACTTCGA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 28 0.64
53 16 0.36
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (53 bp):
TGAACCACATGGTCACATAGAGTTACATGACCTAGCGACAAGGCCATGTGACT
Found at i:54958879 original size:24 final size:23
Alignment explanation
Indices: 54958852--54958896 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
54958842 TGTGGTTGAA
54958852 TGGTATGCTATGGATA-AGGTTTCT
1 TGGTATG-TAT-GATATAGGTTTCT
*
54958876 TGGTTTGTATGATATAGGTTT
1 TGGTATGTATGATATAGGTTT
54958897 AAGGAATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 9 0.47
24 6 0.32
ACGTcount: A:0.20, C:0.04, G:0.29, T:0.47
Consensus pattern (23 bp):
TGGTATGTATGATATAGGTTTCT
Found at i:54965767 original size:20 final size:19
Alignment explanation
Indices: 54965731--54965769 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
54965721 GGCAATAGAT
*
54965731 AACAAAACAATCGATTGAA
1 AACAAAACAATCAATTGAA
54965750 AACAAAAGCAATCAATTGAA
1 AACAAAA-CAATCAATTGAA
54965770 CAAGAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.59, C:0.15, G:0.10, T:0.15
Consensus pattern (19 bp):
AACAAAACAATCAATTGAA
Found at i:54967958 original size:27 final size:26
Alignment explanation
Indices: 54967906--54967987 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 26
54967896 ACATAAGGCC
54967906 ATAACAGTCATTTTATCTCCTA-GGGGT
1 ATAACAGTCATTTTA-C-CCTATGGGGT
*
54967933 ATAACAGTTATTTTACCCTATGGGGGT
1 ATAACAGTCATTTTACCCTAT-GGGGT
* *
54967960 A-ATTCGGTCATTTTACCCTATAGGGGT
1 ATA-ACAGTCATTTTACCCTAT-GGGGT
54967987 A
1 A
54967988 ATTCGATCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
25 4 0.09
26 2 0.04
27 41 0.87
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (26 bp):
ATAACAGTCATTTTACCCTATGGGGT
Found at i:54967988 original size:27 final size:27
Alignment explanation
Indices: 54967942--54968026 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
54967932 TATAACAGTT
54967942 ATTTTACCCTATGGGGGTAATTCGGTC
1 ATTTTACCCTATGGGGGTAATTCGGTC
* *
54967969 ATTTTACCCTATAGGGGTAATTCGATC
1 ATTTTACCCTATGGGGGTAATTCGGTC
* *
54967996 ATTTTATCCTTTGGGGGTAATTCGGTC
1 ATTTTACCCTATGGGGGTAATTCGGTC
54968023 ATTT
1 ATTT
54968027 ATTGACCTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.41
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTAATTCGGTC
Found at i:54970279 original size:25 final size:27
Alignment explanation
Indices: 54970250--54970308 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 27
54970240 CATATCTATC
54970250 CATATAAACATTTC-ATATAAC-AAAT
1 CATATAAACATTTCGATATAACTAAAT
** * *
54970275 CATATAATTATTTCGATATACCTAATT
1 CATATAAACATTTCGATATAACTAAAT
54970302 CATATAA
1 CATATAA
54970309 TTATTTCGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 12 0.43
26 6 0.21
27 10 0.36
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (27 bp):
CATATAAACATTTCGATATAACTAAAT
Found at i:54970306 original size:27 final size:26
Alignment explanation
Indices: 54970274--54970335 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 26
54970264 ATATAACAAA
54970274 TCATATAATTATTTCGATATACCTAAT
1 TCATATAATTATTTCG-TATACCTAAT
* *
54970301 TCATATAATTATTTCGTTTACCTATT
1 TCATATAATTATTTCGTATACCTAAT
54970327 TCTATATAA
1 TC-ATATAA
54970336 CTGATTCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 10 0.31
27 22 0.69
ACGTcount: A:0.34, C:0.15, G:0.03, T:0.48
Consensus pattern (26 bp):
TCATATAATTATTTCGTATACCTAAT
Found at i:54970360 original size:26 final size:26
Alignment explanation
Indices: 54970251--54970436 Score: 84
Period size: 26 Copynumber: 6.9 Consensus size: 26
54970241 ATATCTATCC
* *
54970251 ATATAAAC-ATTTCATATAACAAATC-
1 ATAT-AACTATTTCATATAACCATTCT
*
54970276 ATATAATTATTTCGATAT-ACCTAATTC-
1 ATATAACTATTTC-ATATAACC--ATTCT
* * *
54970303 ATATAATTATTTCGT-TTACCTATTTCT
1 ATATAACTATTTCATATAACC-A-TTCT
54970330 ATATAACTGA-TTCATATAACCATTCTGT
1 ATATAACT-ATTTCATATAACCATTC--T
*
54970358 ATATGTATCTATTTCTATATAACCAATTCT
1 ATA--TAACTATTTC-ATATAACC-ATTCT
*
54970388 -TATAA-TCATTTCACATAACCATT-T
1 ATATAACT-ATTTCATATAACCATTCT
* *
54970412 CATATAACCAATTCATATAACCATT
1 -ATATAACTATTTCATATAACCATT
54970437 TTGTATAGCC
Statistics
Matches: 127, Mismatches: 14, Indels: 39
0.71 0.08 0.22
Matches are distributed among these distances:
24 3 0.02
25 16 0.13
26 41 0.32
27 35 0.28
28 9 0.07
29 3 0.02
30 8 0.06
31 8 0.06
32 4 0.03
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.42
Consensus pattern (26 bp):
ATATAACTATTTCATATAACCATTCT
Found at i:54970405 original size:13 final size:13
Alignment explanation
Indices: 54970368--54970452 Score: 89
Period size: 13 Copynumber: 6.5 Consensus size: 13
54970358 ATATGTATCT
54970368 ATTTCTATATAACC
1 ATTTC-ATATAACC
* * *
54970382 AATTCTTATAATC
1 ATTTCATATAACC
*
54970395 ATTTCACATAACC
1 ATTTCATATAACC
54970408 ATTTCATATAACC
1 ATTTCATATAACC
*
54970421 AATTCATATAACC
1 ATTTCATATAACC
** *
54970434 ATTTTGTATAGCC
1 ATTTCATATAACC
54970447 ATTTCA
1 ATTTCA
54970453 AAGTGTTAAC
Statistics
Matches: 56, Mismatches: 15, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
13 52 0.93
14 4 0.07
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.40
Consensus pattern (13 bp):
ATTTCATATAACC
Found at i:54972717 original size:4 final size:4
Alignment explanation
Indices: 54972701--54972753 Score: 63
Period size: 4 Copynumber: 13.2 Consensus size: 4
54972691 GCTACCTAGC
* **
54972701 AACT AACT -TCT AACT AACT AACT AACT AACT AACT ATTT CAACT AACT
1 AACT AACT AACT AACT AACT AACT AACT AACT AACT AACT -AACT AACT
54972749 AACT A
1 AACT A
54972754 CTAGCTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 2 0.05
4 37 0.90
5 2 0.05
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (4 bp):
AACT
Found at i:54972748 original size:25 final size:24
Alignment explanation
Indices: 54972716--54972762 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
54972706 ACTTCTAACT
54972716 AACTAACTAACTAACTAACTATTTC
1 AACTAACTAACT-ACTAACTATTTC
*
54972741 AACTAACTAACTACTAGCTATT
1 AACTAACTAACTACTAACTATT
54972763 AGTTATCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.32
Consensus pattern (24 bp):
AACTAACTAACTACTAACTATTTC
Found at i:54973829 original size:27 final size:27
Alignment explanation
Indices: 54973799--54973852 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
54973789 CCGACCCCTG
*
54973799 ACCGAATTAATTCGGTTAACCGAATTA
1 ACCGAATTAAGTCGGTTAACCGAATTA
**
54973826 ACCGAATTCGGTCGGTTAACCGAATTA
1 ACCGAATTAAGTCGGTTAACCGAATTA
54973853 CTTCGGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (27 bp):
ACCGAATTAAGTCGGTTAACCGAATTA
Found at i:54974326 original size:11 final size:11
Alignment explanation
Indices: 54974310--54974340 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
54974300 TTTTATTACA
54974310 TTCAGTTTGGT
1 TTCAGTTTGGT
54974321 TTCAGTTTGGT
1 TTCAGTTTGGT
*
54974332 TTCAATTTG
1 TTCAGTTTG
54974341 ATTGGGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.10, G:0.23, T:0.55
Consensus pattern (11 bp):
TTCAGTTTGGT
Found at i:54985178 original size:16 final size:16
Alignment explanation
Indices: 54985157--54985194 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
54985147 AAATTTTCGA
54985157 TTAATT-CTAGTTTAAT
1 TTAATTACTAGTTT-AT
*
54985173 TTAATTATTAGTTTAT
1 TTAATTACTAGTTTAT
54985189 TTAATT
1 TTAATT
54985195 TATTATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (16 bp):
TTAATTACTAGTTTAT
Found at i:54985186 original size:17 final size:18
Alignment explanation
Indices: 54985164--54985204 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
54985154 CGATTAATTC
54985164 TAGTTTAATTTAA-TTAT
1 TAGTTTAATTTAATTTAT
54985181 TAGTTT-ATTTAATTTAT
1 TAGTTTAATTTAATTTAT
54985198 TA-TTTAA
1 TAGTTTAA
54985205 ATAAGGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
TAGTTTAATTTAATTTAT
Found at i:54989984 original size:26 final size:26
Alignment explanation
Indices: 54989951--54990080 Score: 88
Period size: 26 Copynumber: 4.8 Consensus size: 26
54989941 TATTTTTTTT
54989951 AAATTTTACTAAGGATAAAATCGTTA
1 AAATTTTACTAAGGATAAAATCGTTA
* *
54989977 AAATTTTACTAAGG-TAAAATTGGAATGAGA
1 AAATTTTACTAAGGATAAAA-TCG--T--TA
* * * *
54990007 AAATTATT-TTATTGGAAAATTAAT-GTTT
1 AAATT-TTACTA-AGGATAA--AATCGTTA
*
54990035 ATATTTTACTAAGGATAAAATCGTTA
1 AAATTTTACTAAGGATAAAATCGTTA
54990061 AAATTTTACTAAGG-TAAAAT
1 AAATTTTACTAAGGATAAAAT
54990081 TGGAATGAGA
Statistics
Matches: 79, Mismatches: 13, Indels: 25
0.68 0.11 0.21
Matches are distributed among these distances:
25 14 0.18
26 32 0.41
27 7 0.09
28 7 0.09
30 9 0.11
31 4 0.05
32 3 0.04
33 1 0.01
34 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.38
Consensus pattern (26 bp):
AAATTTTACTAAGGATAAAATCGTTA
Found at i:54990094 original size:84 final size:84
Alignment explanation
Indices: 54989948--54990120 Score: 337
Period size: 84 Copynumber: 2.1 Consensus size: 84
54989938 ACATATTTTT
*
54989948 TTTAAATTTTACTAAGGATAAAATCGTTAAAATTTTACTAAGGTAAAATTGGAATGAGAAAATTA
1 TTTATATTTTACTAAGGATAAAATCGTTAAAATTTTACTAAGGTAAAATTGGAATGAGAAAATTA
54990013 TTTTATTGGAAAATTAATG
66 TTTTATTGGAAAATTAATG
54990032 TTTATATTTTACTAAGGATAAAATCGTTAAAATTTTACTAAGGTAAAATTGGAATGAGAAAATTA
1 TTTATATTTTACTAAGGATAAAATCGTTAAAATTTTACTAAGGTAAAATTGGAATGAGAAAATTA
54990097 TTTTATTGGAAAATTAATG
66 TTTTATTGGAAAATTAATG
54990116 TTTAT
1 TTTAT
54990121 TTTGGAAAAT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (84 bp):
TTTATATTTTACTAAGGATAAAATCGTTAAAATTTTACTAAGGTAAAATTGGAATGAGAAAATTA
TTTTATTGGAAAATTAATG
Found at i:54997030 original size:19 final size:19
Alignment explanation
Indices: 54997003--54997043 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
54996993 ATTAATAACC
54997003 AATTAATC-TTAATTAAATT
1 AATTAATCTTTAATT-AATT
*
54997022 AATTTATCTTTAATTAATT
1 AATTAATCTTTAATTAATT
54997041 AAT
1 AAT
54997044 ACTAAACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTAATCTTTAATTAATT
Found at i:55003716 original size:185 final size:185
Alignment explanation
Indices: 55003397--55003764 Score: 594
Period size: 185 Copynumber: 2.0 Consensus size: 185
55003387 GTGGATTGGA
* *
55003397 CAAGTGAATGTTTTCTTCCTGACATTTTTCCAATATTCTTAATTTGTTCCTTCATGAATTACAGT
1 CAAGTGAATGTTGTCTTCCTGACATTTTTCCAATATTCCTAATTTGTTCCTTCATGAATTACAGT
* * * * *
55003462 GATGAAAACGATGTTTGAGTAGAATTTTTTTTGCTAGCCTATGAGTTAAATCTCATAGGGTTGGG
66 GATGAAAACGATGTTTGAATAGAATTTTTTTTGCCAACCTATAAGTTAAATCTCATAGGGTTAGG
* *
55003527 ATTACTTTGATGAACTTTAACTGTCTTTAATGGTTGCAGCAATAATCAGAGTTGT
131 ATTACTTTGATGAACTTCAACTGTCTTTAATGGCTGCAGCAATAATCAGAGTTGT
*
55003582 CAAGTGAATGTTGTCTTTCTGACATTTTTCCAATATTCCTAATTTGTTCCTTCATGAATTACAGT
1 CAAGTGAATGTTGTCTTCCTGACATTTTTCCAATATTCCTAATTTGTTCCTTCATGAATTACAGT
*
55003647 GATGAAAACGATGTTTGAATTGAATTTTATTTT-CCAACCTATAAGTTAAATCTCATAGGGTTAG
66 GATGAAAACGATGTTTGAATAGAATTTT-TTTTGCCAACCTATAAGTTAAATCTCATAGGGTTAG
* * *
55003711 GATTACTTTTATGAACTTCAACTGTCTTTAATGGCTGTAGTAATAATCAGAGTT
130 GATTACTTTGATGAACTTCAACTGTCTTTAATGGCTGCAGCAATAATCAGAGTT
55003765 ATTTTACAGT
Statistics
Matches: 168, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
185 164 0.98
186 4 0.02
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (185 bp):
CAAGTGAATGTTGTCTTCCTGACATTTTTCCAATATTCCTAATTTGTTCCTTCATGAATTACAGT
GATGAAAACGATGTTTGAATAGAATTTTTTTTGCCAACCTATAAGTTAAATCTCATAGGGTTAGG
ATTACTTTGATGAACTTCAACTGTCTTTAATGGCTGCAGCAATAATCAGAGTTGT
Found at i:55009834 original size:45 final size:45
Alignment explanation
Indices: 55009765--55009987 Score: 272
Period size: 45 Copynumber: 5.0 Consensus size: 45
55009755 TACGTGTACT
55009765 GAGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
1 GAGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
* * *
55009810 GAGTACCATTGATTATAAATGTGGTTGCTATGTGTTGATTCCACC
1 GAGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
* * * *
55009855 GAGTACCAGTGATTATAAAGGTGGTTACTATGTGCTGACTCCACC
1 GAGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
* ** * ** * *
55009900 AAAAATTATTGAAAATAAAGGTGGTTGCTATATACTGATTCCACC
1 GAGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
* *
55009945 GAATATAATTGATTAT-AAGGTGG-TGCTATGTGCTGA-TCCACC
1 GAGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
55009987 G
1 G
55009988 TGTAACGATT
Statistics
Matches: 151, Mismatches: 27, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
42 7 0.05
43 11 0.07
44 7 0.05
45 126 0.83
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (45 bp):
GAGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
Found at i:55015168 original size:45 final size:45
Alignment explanation
Indices: 55015104--55015321 Score: 269
Period size: 45 Copynumber: 4.9 Consensus size: 45
55015094 TACTAAGTAT
* *
55015104 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACTGGGTAC
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATAC
* *
55015149 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCATCGGGTAC
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATAC
* * * *
55015194 CATTGATTATAAAGGTGGTTGCTATGTACTGACTCCACCGGAAAT
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATAC
** * * * * *
55015239 CATTGAAAATAAAGGTGGTTGTTATATGATGATTCCACCGAATAT
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATAC
* *
55015284 AATTGATTATAAGGGTGG-TGCTATGTGCTGA-TCCACCG
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCG
55015322 TGTAACGGTT
Statistics
Matches: 149, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
43 7 0.05
44 10 0.07
45 132 0.89
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (45 bp):
CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATAC
Found at i:55027194 original size:90 final size:90
Alignment explanation
Indices: 55027041--55027222 Score: 355
Period size: 90 Copynumber: 2.0 Consensus size: 90
55027031 TAGATAATTT
*
55027041 CATTCAATTAAGTACTTCAAGTATTCAATTTAATCCATAATTCGTATTTATGAAAAATTATGAAA
1 CATTCAATTAAGTACGTCAAGTATTCAATTTAATCCATAATTCGTATTTATGAAAAATTATGAAA
55027106 TTACCCCTAACATTTAAACTTTTTA
66 TTACCCCTAACATTTAAACTTTTTA
55027131 CATTCAATTAAGTACGTCAAGTATTCAATTTAATCCATAATTCGTATTTATGAAAAATTATGAAA
1 CATTCAATTAAGTACGTCAAGTATTCAATTTAATCCATAATTCGTATTTATGAAAAATTATGAAA
55027196 TTACCCCTAACATTTAAACTTTTTA
66 TTACCCCTAACATTTAAACTTTTTA
55027221 CA
1 CA
55027223 ATTTAGTCCT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (90 bp):
CATTCAATTAAGTACGTCAAGTATTCAATTTAATCCATAATTCGTATTTATGAAAAATTATGAAA
TTACCCCTAACATTTAAACTTTTTA
Found at i:55033285 original size:20 final size:20
Alignment explanation
Indices: 55033216--55033302 Score: 68
Period size: 20 Copynumber: 4.3 Consensus size: 20
55033206 GCATCATAGA
55033216 TGCATAACAGGGGCA-CAAATG
1 TGCA-AACAGGGGCACCAAA-G
* * * *
55033237 TACAAAGAGGGACACCGAAG
1 TGCAAACAGGGGCACCAAAG
* * *
55033257 TGTATACAGGGGCATCAAAG
1 TGCAAACAGGGGCACCAAAG
* *
55033277 TGCAAACAGAGGCACCGAAG
1 TGCAAACAGGGGCACCAAAG
55033297 TGCAAA
1 TGCAAA
55033303 TCCCATACAA
Statistics
Matches: 49, Mismatches: 16, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
20 43 0.88
21 6 0.12
ACGTcount: A:0.40, C:0.20, G:0.29, T:0.11
Consensus pattern (20 bp):
TGCAAACAGGGGCACCAAAG
Found at i:55033293 original size:40 final size:40
Alignment explanation
Indices: 55033222--55033298 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
55033212 TAGATGCATA
*
55033222 ACAGGGGCACAAATGTACAAAGAGGGACACCGAAGTGTAT
1 ACAGGGGCACAAATGTACAAACAGGGACACCGAAGTGTAT
*
55033262 ACAGGGGCATCAAA-GTGCAAACAGAGG-CACCGAAGTG
1 ACAGGGGCA-CAAATGTACAAACAG-GGACACCGAAGTG
55033299 CAAATCCCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 27 0.82
41 6 0.18
ACGTcount: A:0.39, C:0.19, G:0.31, T:0.10
Consensus pattern (40 bp):
ACAGGGGCACAAATGTACAAACAGGGACACCGAAGTGTAT
Found at i:55040670 original size:21 final size:21
Alignment explanation
Indices: 55040616--55040670 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
55040606 TGCATCCCAA
* *
55040616 ATATATATATCTAACTTATAC
1 ATATATACATATAACTTATAC
* *
55040637 ATATTTGAC-TATAACTTATCC
1 ATATAT-ACATATAACTTATAC
55040658 ATATATACATATA
1 ATATATACATATA
55040671 TAGTTTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 2 0.07
21 24 0.89
22 1 0.04
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.42
Consensus pattern (21 bp):
ATATATACATATAACTTATAC
Found at i:55041136 original size:15 final size:16
Alignment explanation
Indices: 55041107--55041136 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55041097 CAAACATGCT
55041107 TTAACACATTATCAAA
1 TTAACACATTATCAAA
55041123 TTAACACA-TATCAA
1 TTAACACATTATCAA
55041137 CAAAGCTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:55043349 original size:16 final size:17
Alignment explanation
Indices: 55043316--55043349 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
55043306 GGGGATGGCA
*
55043316 TTTGTTTGGTTTTTATT
1 TTTGTTTGGTTTTCATT
55043333 TTTGTTT-GTTTTCATT
1 TTTGTTTGGTTTTCATT
55043349 T
1 T
55043350 CATAATATTT
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:0.06, C:0.03, G:0.15, T:0.76
Consensus pattern (17 bp):
TTTGTTTGGTTTTCATT
Found at i:55055057 original size:32 final size:32
Alignment explanation
Indices: 55055016--55055084 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
55055006 TATAAGATCC
55055016 TTAAGTACGTCCTCACCCAAAAGAAGTTTAAT
1 TTAAGTACGTCCTCACCCAAAAGAAGTTTAAT
55055048 TTAAGTACGTCCTCACCCAAAAGAAGTTTAAT
1 TTAAGTACGTCCTCACCCAAAAGAAGTTTAAT
55055080 TTAAG
1 TTAAG
55055085 GCAAAGGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (32 bp):
TTAAGTACGTCCTCACCCAAAAGAAGTTTAAT
Found at i:55056788 original size:28 final size:28
Alignment explanation
Indices: 55056720--55056789 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 28
55056710 TAGCCCTTTC
*
55056720 CAGTATCAGTGTGGGCCTTAGCCCAATA
1 CAGTATCAGTGTGGGCCTAAGCCCAATA
* * * * ***
55056748 TAATAACAATGTGGGCCTAAGCCTGTTA
1 CAGTATCAGTGTGGGCCTAAGCCCAATA
55056776 CAGTATCAGTGTGG
1 CAGTATCAGTGTGG
55056790 TGCAAATATG
Statistics
Matches: 30, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (28 bp):
CAGTATCAGTGTGGGCCTAAGCCCAATA
Found at i:55057220 original size:26 final size:25
Alignment explanation
Indices: 55057126--55057372 Score: 210
Period size: 26 Copynumber: 9.4 Consensus size: 25
55057116 TCATCTACTA
* * *
55057126 GGGGTATATCAGTCAATCTACCCTTC
1 GGGGTATTTCAGT-AATTTACCCATC
*
55057152 TGGGGGTATTTCAGTAATTTTGCCCCA-C
1 --GGGGTATTTCAGTAA-TTT-ACCCATC
55057180 AGGGGTATTTCAGTAATTTACCCATC
1 -GGGGTATTTCAGTAATTTACCCATC
55057206 GGGAGTATTTCAGTAATTTACCCATC
1 GGG-GTATTTCAGTAATTTACCCATC
* *
55057232 GAAGGTATTTC-GATAATTTCCCCATC
1 G-GGGTATTTCAG-TAATTTACCCATC
* **
55057258 AAGGGTATTTTGGTAATTTACCCATC
1 -GGGGTATTTCAGTAATTTACCCATC
* *
55057284 GAGGGTATTTCAGTAATATACACATC
1 G-GGGTATTTCAGTAATTTACCCATC
* ** *
55057310 AAGGGTATTTTGGTAATTTACCTATC
1 -GGGGTATTTCAGTAATTTACCCATC
*
55057336 GAGGGTATTTCAATAATTTACCCATC
1 G-GGGTATTTCAGTAATTTACCCATC
55057362 GAGGGTATTTC
1 G-GGGTATTTC
55057373 GGTCAACACC
Statistics
Matches: 180, Mismatches: 28, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
25 8 0.04
26 135 0.75
27 19 0.11
28 15 0.08
29 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (25 bp):
GGGGTATTTCAGTAATTTACCCATC
Found at i:55057256 original size:52 final size:52
Alignment explanation
Indices: 55057182--55057375 Score: 257
Period size: 52 Copynumber: 3.7 Consensus size: 52
55057172 TGCCCCACAG
* *
55057182 GGGTATTTCAGTAATTTACCCATC-GGGAGTATTTCAGTAATTTACCCATCGA
1 GGGTATTTCAGTAATTTACCCATCAAGG-GTATTTCGGTAATTTACCCATCGA
* * *
55057234 AGGTATTTC-GATAATTTCCCCATCAAGGGTATTTTGGTAATTTACCCATCGA
1 GGGTATTTCAG-TAATTTACCCATCAAGGGTATTTCGGTAATTTACCCATCGA
* * * *
55057286 GGGTATTTCAGTAATATACACATCAAGGGTATTTTGGTAATTTACCTATCGA
1 GGGTATTTCAGTAATTTACCCATCAAGGGTATTTCGGTAATTTACCCATCGA
* *
55057338 GGGTATTTCAATAATTTACCCATCGAGGGTATTTCGGT
1 GGGTATTTCAGTAATTTACCCATCAAGGGTATTTCGGT
55057376 CAACACCGTG
Statistics
Matches: 124, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
51 1 0.01
52 120 0.97
53 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (52 bp):
GGGTATTTCAGTAATTTACCCATCAAGGGTATTTCGGTAATTTACCCATCGA
Found at i:55057275 original size:78 final size:78
Alignment explanation
Indices: 55057155--55057372 Score: 264
Period size: 78 Copynumber: 2.8 Consensus size: 78
55057145 ACCCTTCTGG
*
55057155 GGGTATTTC-AGTAATTTTGCCCCA-CAGGGGTATTTCAGTAATTTACCCATCG-GGAGTATTTC
1 GGGTATTTCGA-TAA-TTT-CCCCATCAAGGGTATTTCAGTAATTTACCCATCGAGG-GTATTTC
* *
55057217 AGTAATTTACCCATCGAA
62 AGTAATATACACATC-AA
**
55057235 -GGTATTTCGATAATTTCCCCATCAAGGGTATTTTGGTAATTTACCCATCGAGGGTATTTCAGTA
1 GGGTATTTCGATAATTTCCCCATCAAGGGTATTTCAGTAATTTACCCATCGAGGGTATTTCAGTA
55057299 ATATACACATCAA
66 ATATACACATCAA
* * * * * *
55057312 GGGTATTTTGGTAATTTACCTATCGAGGGTATTTCAATAATTTACCCATCGAGGGTATTTC
1 GGGTATTTCGATAATTTCCCCATCAAGGGTATTTCAGTAATTTACCCATCGAGGGTATTTC
55057373 GGTCAACACC
Statistics
Matches: 121, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
77 7 0.06
78 100 0.83
79 13 0.11
80 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (78 bp):
GGGTATTTCGATAATTTCCCCATCAAGGGTATTTCAGTAATTTACCCATCGAGGGTATTTCAGTA
ATATACACATCAA
Found at i:55065323 original size:21 final size:21
Alignment explanation
Indices: 55065297--55065345 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
55065287 AGCAATGTCA
* *
55065297 TGACACCGGGGTTTCGTGTTG
1 TGACACCGGGGTTCCATGTTG
55065318 TGACACCGGGGTTCCATGTTG
1 TGACACCGGGGTTCCATGTTG
*
55065339 CGACACC
1 TGACACC
55065346 CCTAGTAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.14, C:0.27, G:0.33, T:0.27
Consensus pattern (21 bp):
TGACACCGGGGTTCCATGTTG
Found at i:55069335 original size:22 final size:22
Alignment explanation
Indices: 55069289--55069329 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
55069279 TACAAAGGTG
*
55069289 ATGTCGCGACATACGAGGTCCT
1 ATGTCACGACATACGAGGTCCT
55069311 ATGTCACGACAT-CGAGGTC
1 ATGTCACGACATACGAGGTC
55069330 AGTATGGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (22 bp):
ATGTCACGACATACGAGGTCCT
Found at i:55071564 original size:42 final size:42
Alignment explanation
Indices: 55071460--55071573 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 42
55071450 ATATCCAGTG
* *
55071460 ATACGGGGAATCA-ACACATAGCAACCCCTTTCACAATCAAGG
1 ATACGGGGAATCAGA-ACTTAGCAACCCCTTTCACAATCAAGC
* *
55071502 ATACGGTGGAATCAGAACTTAGCAACCACCTTT-AGAATCAATC
1 ATACGG-GGAATCAGAACTTAGCAACC-CCTTTCACAATCAAGC
* *
55071545 ATTCGGGGAATCAGAACTTAGTAACCCCT
1 ATACGGGGAATCAGAACTTAGCAACCCCT
55071574 CGGGGAATCT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
41 3 0.05
42 25 0.40
43 29 0.46
44 6 0.10
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (42 bp):
ATACGGGGAATCAGAACTTAGCAACCCCTTTCACAATCAAGC
Found at i:55072765 original size:26 final size:26
Alignment explanation
Indices: 55072736--55072788 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
55072726 TAACCACATG
55072736 ATAAACCATTTTAATAAAGATTACAA
1 ATAAACCATTTTAATAAAGATTACAA
*
55072762 ATAAATCATTTTAATAAAGATTACAA
1 ATAAACCATTTTAATAAAGATTACAA
55072788 A
1 A
55072789 CTTTAAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (26 bp):
ATAAACCATTTTAATAAAGATTACAA
Found at i:55076388 original size:42 final size:42
Alignment explanation
Indices: 55076308--55076389 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
55076298 CTTTTTCTCT
* **
55076308 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
* *
55076350 ATGCCGTAGCCCAGCTATGGTCTTACACA-ATAGCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACATAT-GCACATAT
55076390 CACACCGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
Found at i:55079149 original size:51 final size:51
Alignment explanation
Indices: 55079091--55079277 Score: 224
Period size: 51 Copynumber: 3.7 Consensus size: 51
55079081 TCGATTCACA
55079091 TAGTAGCCTGCACATAGTACTACACATGTGACCATTATCATTCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTATCATTCGGTACACG
* * * *
55079142 TAGTAGCCTGCACATAGTACTACACACATGATCGA-AACTATC--T-GGTACGCA
1 TAGTAGCCTGCACATAGTACT--ACACATG-T-GACCATTATCATTCGGTACACG
**
55079193 TAGTAGCCTGCACATAGTACTACACATACGACC--TATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTATCATT-CGGTACACG
*
55079243 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
55079278 CACTTTCACT
Statistics
Matches: 113, Mismatches: 12, Indels: 21
0.77 0.08 0.14
Matches are distributed among these distances:
46 4 0.04
47 2 0.02
48 1 0.01
49 6 0.05
50 36 0.32
51 48 0.42
52 1 0.01
53 7 0.06
54 6 0.05
55 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATTATCATTCGGTACACG
Found at i:55079297 original size:101 final size:99
Alignment explanation
Indices: 55079088--55079269 Score: 294
Period size: 101 Copynumber: 1.8 Consensus size: 99
55079078 TGTTCGATTC
**
55079088 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATCATTCGGTACACGTAGTAGCCTGC
1 ACATAGTAGCCTGCACATAGTACTACACATACGACCA-TATCATTCGGTACACGTAGTAGCCTGC
*
55079153 ACATAGTACTACACACATGATCGAAACTATCTGGT
65 ACATAGTACTACACACATGATCCAAACTATCTGGT
55079188 ACGCATAGTAGCCTGCACATAGTACTACACATACGACC-TATCATTCCGGTACACGTAGTAGCCT
1 A--CATAGTAGCCTGCACATAGTACTACACATACGACCATATCATT-CGGTACACGTAGTAGCCT
55079252 GCACATAGTACTACACAC
63 GCACATAGTACTACACAC
55079270 GTGACCATCA
Statistics
Matches: 77, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
100 8 0.10
101 36 0.47
102 33 0.43
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (99 bp):
ACATAGTAGCCTGCACATAGTACTACACATACGACCATATCATTCGGTACACGTAGTAGCCTGCA
CATAGTACTACACACATGATCCAAACTATCTGGT
Found at i:55083899 original size:19 final size:19
Alignment explanation
Indices: 55083863--55083904 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
55083853 AGAAAGATTC
* *
55083863 ATTTATTTTTATATAAAATA
1 ATTTATTTTTAGA-AAAAAA
55083883 ATTTA-TTTTAGAAAAAAA
1 ATTTATTTTTAGAAAAAAA
55083901 ATTT
1 ATTT
55083905 CAAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 6 0.30
20 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
ATTTATTTTTAGAAAAAAA
Found at i:55083929 original size:17 final size:17
Alignment explanation
Indices: 55083907--55083941 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
55083897 AAAAATTTCA
55083907 AAATATTTTGTGAAGTC
1 AAATATTTTGTGAAGTC
*
55083924 AAATATTTTGTGGAGTC
1 AAATATTTTGTGAAGTC
55083941 A
1 A
55083942 TTGCCAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (17 bp):
AAATATTTTGTGAAGTC
Found at i:55089630 original size:94 final size:94
Alignment explanation
Indices: 55089518--55089690 Score: 276
Period size: 94 Copynumber: 1.8 Consensus size: 94
55089508 TAAAAAGGGA
* * * *
55089518 ATTTGATATATTCCTTATTAGATAAGGAAATAGAATTTAATTATTATTTAAAATA-TTTTAATAT
1 ATTTGATATATTCATTATTAGATAAGGAAATAAAATTTAATTATTATTTAAAAGAGTTTT-AGAT
55089582 AAATAACAATTAAAATTCAAAATCAAAAGG
65 AAATAACAATTAAAATTCAAAATCAAAAGG
*
55089612 ATTTGATATATTCATTATTAGATAAGGAAATAAAATTTAATTTTTATTTAAAAGAGTTTTAGATA
1 ATTTGATATATTCATTATTAGATAAGGAAATAAAATTTAATTATTATTTAAAAGAGTTTTAGATA
*
55089677 AATAATAATTAAAA
66 AATAACAATTAAAA
55089691 CAGAATTTAA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
94 68 0.94
95 4 0.06
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (94 bp):
ATTTGATATATTCATTATTAGATAAGGAAATAAAATTTAATTATTATTTAAAAGAGTTTTAGATA
AATAACAATTAAAATTCAAAATCAAAAGG
Found at i:55089709 original size:49 final size:48
Alignment explanation
Indices: 55089645--55089769 Score: 187
Period size: 49 Copynumber: 2.6 Consensus size: 48
55089635 AAGGAAATAA
* * *
55089645 AATTTAATTTTTATTTAAAAGAGTTTTAGATAAATAATAATTAAAACAG
1 AATTTAATTATTATTTAAAAGAGTTTTAAATAAAGAATAATT-AAACAG
* *
55089694 AATTTAATTATTATTTAAAAGAGTTTTAAATAAAGGATAATTAAATAG
1 AATTTAATTATTATTTAAAAGAGTTTTAAATAAAGAATAATTAAACAG
55089742 AATTTAGATTATTATTTAAAAGAGTTTT
1 AATTTA-ATTATTATTTAAAAGAGTTTT
55089770 TAAAATTCAA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 11 0.16
49 59 0.84
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.42
Consensus pattern (48 bp):
AATTTAATTATTATTTAAAAGAGTTTTAAATAAAGAATAATTAAACAG
Found at i:55091375 original size:41 final size:41
Alignment explanation
Indices: 55091330--55091432 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 41
55091320 TGATTCAGTA
*
55091330 CACCGGCACTT-AGCCTACTAGACATATAGTCTGAAATGTTT
1 CACCGGCA-TTAAGCCTACTAGACATAAAGTCTGAAATGTTT
* *
55091371 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAATTGTTT
1 CACCGGCATTAAGCCTACTAGACATAAAGTCTGAAATGTTT
* * *
55091412 CACTGGCAATAAGCCTGCTAG
1 CACCGGCATTAAGCCTACTAG
55091433 GTGCTAAGCC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 2 0.04
41 54 0.96
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (41 bp):
CACCGGCATTAAGCCTACTAGACATAAAGTCTGAAATGTTT
Found at i:55091446 original size:41 final size:41
Alignment explanation
Indices: 55091287--55091432 Score: 125
Period size: 41 Copynumber: 3.6 Consensus size: 41
55091277 TTTAAACAGA
* * * * *
55091287 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTG-ATTCAG-
1 TTCACCGGCAATAAGCCTGCTAGACATAAAGCCTGAAAT--GT
* * * * * *
55091328 TACACCGGCACTTAGCCTACTAGACATATAGTCTGAAATGT
1 TTCACCGGCAATAAGCCTGCTAGACATAAAGCCTGAAATGT
* * *
55091369 TTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAATTGT
1 TTCACCGGCAATAAGCCTGCTAGACATAAAGCCTGAAATGT
*
55091410 TTCACTGGCAATAAGCCTGCTAG
1 TTCACCGGCAATAAGCCTGCTAG
55091433 GTGCTAAGCC
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 1 0.01
41 85 0.97
42 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (41 bp):
TTCACCGGCAATAAGCCTGCTAGACATAAAGCCTGAAATGT
Found at i:55091843 original size:2 final size:2
Alignment explanation
Indices: 55091836--55091880 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
55091826 TTTATTCATG
55091836 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55091878 TA T
1 TA T
55091881 TCGGGCCTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55099984 original size:12 final size:12
Alignment explanation
Indices: 55099967--55100008 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
55099957 GGACACATGA
55099967 CCGTGTCCCAGC
1 CCGTGTCCCAGC
55099979 CCGTGTCCTCA-C
1 CCGTGTCC-CAGC
* *
55099991 CCGTGTACCAGG
1 CCGTGTCCCAGC
55100003 CCGTGT
1 CCGTGT
55100009 AACTCTCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.10, C:0.43, G:0.26, T:0.21
Consensus pattern (12 bp):
CCGTGTCCCAGC
Found at i:55102267 original size:50 final size:49
Alignment explanation
Indices: 55102213--55102333 Score: 129
Period size: 49 Copynumber: 2.4 Consensus size: 49
55102203 GAGGTCCCCC
* * *
55102213 GTAAGACCATGTTTGGGACATGACATGGGCACCG-ATATGAGAAC-TCCCAT
1 GTAAGACCATGTCTGGGACATGACATGGGCA--GTACAGGA-AACATCCCAT
* * * * *
55102263 GTAAGACCATATCTGGGATATGGCATTGGTAGTACAGGAAACATCCCAT
1 GTAAGACCATGTCTGGGACATGACATGGGCAGTACAGGAAACATCCCAT
55102312 GTAAGACCATGTCTGGGACATG
1 GTAAGACCATGTCTGGGACATG
55102334 GCTTTGGATT
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
48 4 0.07
49 30 0.51
50 25 0.42
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGACATGGGCAGTACAGGAAACATCCCAT
Found at i:55102569 original size:20 final size:20
Alignment explanation
Indices: 55102544--55102592 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
55102534 TGAGTTATTT
55102544 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
55102564 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
55102584 AA-TAAGCAA
1 AAGTAAGCAA
55102593 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.57, C:0.06, G:0.22, T:0.14
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:55108001 original size:17 final size:16
Alignment explanation
Indices: 55107951--55108002 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
55107941 AGAAATGTAA
55107951 TATATAATTATATTAAT
1 TATAT-ATTATATTAAT
* * *
55107968 TATAAAGTAATAATAAT
1 TATATA-TTATATTAAT
55107985 TAATATATTATATTAAT
1 T-ATATATTATATTAAT
55108002 T
1 T
55108003 TTTAATAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 1 0.04
17 22 0.81
18 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
TATATATTATATTAAT
Found at i:55108059 original size:16 final size:15
Alignment explanation
Indices: 55108027--55108065 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
55108017 TGATAATAAG
55108027 TAATATATAATTATAT
1 TAAT-TATAATTATAT
*
55108043 TTATTATAATGTATAT
1 TAATTATAAT-TATAT
55108059 TAATTAT
1 TAATTAT
55108066 TATCAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TAATTATAATTATAT
Found at i:55119914 original size:103 final size:104
Alignment explanation
Indices: 55119677--55119943 Score: 446
Period size: 103 Copynumber: 2.6 Consensus size: 104
55119667 TGTATATAAA
**
55119677 AGGGGTTGCTGTGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
*
55119742 TTGAAATGAAAAGGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
55119782 AGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
55119847 TGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* * **
55119885 AGGGGTTGCTAAGTGCTGATTCCCTGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
55119944 ATAACGGCTA
Statistics
Matches: 153, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
103 85 0.56
104 44 0.29
105 24 0.16
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:55122136 original size:13 final size:13
Alignment explanation
Indices: 55122118--55122147 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
55122108 TTTAACATTT
*
55122118 TTAATTTTCTTAG
1 TTAATTTACTTAG
55122131 TTAATTTACTTAG
1 TTAATTTACTTAG
55122144 TTAA
1 TTAA
55122148 AATATAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (13 bp):
TTAATTTACTTAG
Found at i:55122579 original size:16 final size:17
Alignment explanation
Indices: 55122542--55122580 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
55122532 TCATTTTTAC
*
55122542 TTTTTATTTTTTTCAAA
1 TTTTTATTTTTTGCAAA
*
55122559 TTTTTATTTTTTGCACA
1 TTTTTATTTTTTGCAAA
55122576 TTTTT
1 TTTTT
55122581 GTTGGACCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTTATTTTTTGCAAA
Found at i:55126594 original size:9 final size:9
Alignment explanation
Indices: 55126564--55126605 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
55126554 TGTTTACAAT
55126564 TTAAAA-AA
1 TTAAAATAA
*
55126572 TTCAAA-AA
1 TTAAAATAA
55126580 TATAAAATAA
1 T-TAAAATAA
55126590 TTAAAATAA
1 TTAAAATAA
55126599 TTAAAAT
1 TTAAAAT
55126606 TTATAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
8 8 0.27
9 19 0.63
10 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (9 bp):
TTAAAATAA
Found at i:55126618 original size:21 final size:20
Alignment explanation
Indices: 55126592--55126636 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
55126582 TAAAATAATT
55126592 AAAATAATTAAAATTTATAAA
1 AAAATAATTAAAATTT-TAAA
* *
55126613 AAAATATTTTTAAATTTTAAA
1 AAAATA-ATTAAAATTTTAAA
55126634 AAA
1 AAA
55126637 TTTAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATAATTAAAATTTTAAA
Found at i:55135214 original size:29 final size:30
Alignment explanation
Indices: 55135172--55135233 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
55135162 ATACACTTCA
55135172 TAATTTAATTTCTAT-TTTTTTCACAAATT
1 TAATTTAATTTCTATCTTTTTTCACAAATT
*
55135201 TAATTTAATTTCTATCTTTTTTTACAAATT
1 TAATTTAATTTCTATCTTTTTTCACAAATT
55135231 TAA
1 TAA
55135234 AGAATACCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (30 bp):
TAATTTAATTTCTATCTTTTTTCACAAATT
Found at i:55135905 original size:17 final size:16
Alignment explanation
Indices: 55135883--55135931 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
55135873 TTTACAAACT
55135883 TTTTTAAATTTTGTTAA
1 TTTTTAAATTTT-TTAA
*
55135900 TTTTTAAATATTTTTAT
1 TTTTTAAAT-TTTTTAA
*
55135917 TTTTTAAAATTTTTA
1 TTTTTAAATTTTTTA
55135932 TGATTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 6 0.21
17 20 0.69
18 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTTAAATTTTTTAA
Found at i:55137655 original size:18 final size:17
Alignment explanation
Indices: 55137619--55137663 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
55137609 ATGAGTGGTG
55137619 AATTATACTAATATCATA
1 AATTATA-TAATATCATA
55137637 AATTATATAATAT-ATA
1 AATTATATAATATCATA
*
55137653 TAAATATATAA
1 -AATTATATAA
55137664 GCCAGTCTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 3 0.12
17 15 0.60
18 7 0.28
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTATATAATATCATA
Found at i:55138223 original size:24 final size:24
Alignment explanation
Indices: 55138171--55138225 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
55138161 ATTTTTTAGA
* *
55138171 ATATTTAGTATTTATTAGTATAAT
1 ATATTTAGTATTTATTAGCACAAT
55138195 ATATTTA-TCATTTATTAGCACAAT
1 ATATTTAGT-ATTTATTAGCACAAT
*
55138219 TTATTTA
1 ATATTTA
55138226 ACTTACGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (24 bp):
ATATTTAGTATTTATTAGCACAAT
Found at i:55140185 original size:24 final size:24
Alignment explanation
Indices: 55140157--55140208 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
55140147 TTTGTAGAAG
* *
55140157 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
55140181 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
55140205 ATTT
1 ATTT
55140209 GACCTACGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:55146609 original size:19 final size:19
Alignment explanation
Indices: 55146507--55146609 Score: 57
Period size: 19 Copynumber: 5.3 Consensus size: 19
55146497 CACTAACGTG
55146507 CCCCTGTTGTACTTCGGTA
1 CCCCTGTTGTACTTCGGTA
* *** *
55146526 CCCCTAATCACACTTAC-GTG
1 CCCCT-GTTGTACTT-CGGTA
*
55146546 CTCCTGTTGTACTTCGGTA
1 CCCCTGTTGTACTTCGGTA
* * * *
55146565 CCCCTAATGGCACTTAC-GTG
1 CCCCT-GTTGTACTT-CGGTA
55146585 CCCCTGTTGTACTTCGGTA
1 CCCCTGTTGTACTTCGGTA
*
55146604 CTCCTG
1 CCCCTG
55146610 ATAGCACTTT
Statistics
Matches: 57, Mismatches: 21, Indels: 12
0.63 0.23 0.13
Matches are distributed among these distances:
18 2 0.04
19 29 0.51
20 24 0.42
21 2 0.04
ACGTcount: A:0.15, C:0.34, G:0.18, T:0.33
Consensus pattern (19 bp):
CCCCTGTTGTACTTCGGTA
Found at i:55146617 original size:39 final size:39
Alignment explanation
Indices: 55146496--55146624 Score: 188
Period size: 39 Copynumber: 3.3 Consensus size: 39
55146486 ACCTCTGATT
*
55146496 GCACTAACGTGCCCCTGTTGTACTTCGGTACCCCTAATCA
1 GCACTTACGTGCCCCTGTTGTACTTCGGTACCCCTAAT-A
* *
55146536 -CACTTACGTGCTCCTGTTGTACTTCGGTACCCCTAATG
1 GCACTTACGTGCCCCTGTTGTACTTCGGTACCCCTAATA
* *
55146574 GCACTTACGTGCCCCTGTTGTACTTCGGTACTCCTGATA
1 GCACTTACGTGCCCCTGTTGTACTTCGGTACCCCTAATA
*
55146613 GCACTTTCGTGC
1 GCACTTACGTGC
55146625 TGTGGTTATG
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.16, C:0.33, G:0.19, T:0.32
Consensus pattern (39 bp):
GCACTTACGTGCCCCTGTTGTACTTCGGTACCCCTAATA
Found at i:55150714 original size:23 final size:23
Alignment explanation
Indices: 55150681--55150724 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
55150671 ATCAAAATGC
*
55150681 GTAATATCCCGAAAATTACTATT
1 GTAATACCCCGAAAATTACTATT
55150704 GTAATACCCCGAAAATTACTA
1 GTAATACCCCGAAAATTACTA
55150725 CAGTAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (23 bp):
GTAATACCCCGAAAATTACTATT
Found at i:55150730 original size:23 final size:23
Alignment explanation
Indices: 55150681--55150730 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
55150671 ATCAAAATGC
* **
55150681 GTAATATCCCGAAAATTACTATT
1 GTAATACCCCGAAAATTACTACA
55150704 GTAATACCCCGAAAATTACTACA
1 GTAATACCCCGAAAATTACTACA
55150727 GTAA
1 GTAA
55150731 GAAAGTAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (23 bp):
GTAATACCCCGAAAATTACTACA
Found at i:55155939 original size:26 final size:27
Alignment explanation
Indices: 55155882--55155961 Score: 83
Period size: 26 Copynumber: 3.0 Consensus size: 27
55155872 ATAGAGGAAG
* **
55155882 TATACTG-TATTGGTGGCTTTGCCACA
1 TATACTGTTATTGGTAGCTTTGCTGCA
*
55155908 TATACTGTTGTTGGTAGCTTTGCTGCA
1 TATACTGTTATTGGTAGCTTTGCTGCA
* * *
55155935 T-TACTGTTACTGGCAGCTTAGCTGCA
1 TATACTGTTATTGGTAGCTTTGCTGCA
55155961 T
1 T
55155962 CACTATTACC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
26 29 0.64
27 16 0.36
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (27 bp):
TATACTGTTATTGGTAGCTTTGCTGCA
Found at i:55156124 original size:28 final size:28
Alignment explanation
Indices: 55156092--55156163 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
55156082 CATATTGCGT
*
55156092 TGTTACTGTTTTGGGCTAAGGCCCACAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
* *
55156120 TGTTACTGTATTGGGCTAAGTCCCACAT
1 TGTTACTGTATTGGGCTAAGGCCCACAC
* *
55156148 TGTTGCTGTATAGGGC
1 TGTTACTGTATTGGGC
55156164 CCAGACCCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (28 bp):
TGTTACTGTATTGGGCTAAGGCCCACAC
Found at i:55156172 original size:28 final size:28
Alignment explanation
Indices: 55156092--55156183 Score: 76
Period size: 28 Copynumber: 3.3 Consensus size: 28
55156082 CATATTGCGT
* * * *
55156092 TGTTACTGTTTTGGGCTAAGGCCCACAC
1 TGTTACTGTATAGGGCCAAGACCCACAC
* * * *
55156120 TGTTACTGTATTGGGCTAAGTCCCACAT
1 TGTTACTGTATAGGGCCAAGACCCACAC
* * *
55156148 TGTTGCTGTATAGGGCCCAGACCCAGAC
1 TGTTACTGTATAGGGCCAAGACCCACAC
*
55156176 TGCTACTG
1 TGTTACTG
55156184 CATGTTGTAT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (28 bp):
TGTTACTGTATAGGGCCAAGACCCACAC
Found at i:55162644 original size:27 final size:27
Alignment explanation
Indices: 55162605--55162907 Score: 342
Period size: 27 Copynumber: 11.3 Consensus size: 27
55162595 GTAATGGGCT
* **
55162605 TAAAATGATCGAAATACCCTAAAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* *
55162632 TAAAATGACCGAAATACTCTTGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * * *
55162659 TACAATGACCAAAATATCCTCGAATGG
1 TAAAATGACCGAAATACCCTCGAAGGG
*
55162686 TAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
** * **
55162713 TAACGTGACTGAAATACCCTTAAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * * *
55162740 TAAAATGTCTGAAATACCCTTGAAGTG
1 TAAAATGACCGAAATACCCTCGAAGGG
* *
55162767 TAAAATGACTG-TATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
55162793 TAAAATGACCGAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* *
55162820 TAAAATG-CTTGAAATACCCCCGAAGGG
1 TAAAATGAC-CGAAATACCCTCGAAGGG
*
55162847 TAAAATGACCAAAATATCCC-CGAAGGG
1 TAAAATGACCGAAATA-CCCTCGAAGGG
*
55162874 TAAAATGACCGAAATACCCTAGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
55162901 TAAAATG
1 TAAAATG
55162908 GCTATTGCAC
Statistics
Matches: 235, Mismatches: 36, Indels: 10
0.84 0.13 0.04
Matches are distributed among these distances:
26 26 0.11
27 205 0.87
28 4 0.02
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCTCGAAGGG
Found at i:55163129 original size:26 final size:27
Alignment explanation
Indices: 55163081--55163139 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 27
55163071 TATTGGTGGT
* *
55163081 TTTGCCACGTATATTGTTACTGGCAGC
1 TTTGCTACGTATACTGTTACTGGCAGC
55163108 TTTGCTACGT-TACTGTTACTGGCAGC
1 TTTGCTACGTATACTGTTACTGGCAGC
55163134 TTTGCT
1 TTTGCT
55163140 GCATCACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 21 0.70
27 9 0.30
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (27 bp):
TTTGCTACGTATACTGTTACTGGCAGC
Found at i:55163152 original size:26 final size:26
Alignment explanation
Indices: 55163097--55163163 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
55163087 ACGTATATTG
* * *
55163097 TTACTGGCAGCTTTGCTACGTTACTG
1 TTACTGGCAGCTTTGCTACATCACTA
*
55163123 TTACTGGCAGCTTTGCTGCATCACTA
1 TTACTGGCAGCTTTGCTACATCACTA
55163149 TTACAT-GCAGCTTTG
1 TTAC-TGGCAGCTTTG
55163164 TTGCGATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 35 0.97
27 1 0.03
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTACATCACTA
Found at i:55163308 original size:30 final size:30
Alignment explanation
Indices: 55163272--55163332 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
55163262 TATTGCATTG
* *
55163272 CACTGTTACTGTTTTGGGCTAAGGCCCACA
1 CACTGTTACTATATTGGGCTAAGGCCCACA
55163302 CACTGTTACTATATTGGGCTAAGGCCCACA
1 CACTGTTACTATATTGGGCTAAGGCCCACA
55163332 C
1 C
55163333 TGTTGCTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (30 bp):
CACTGTTACTATATTGGGCTAAGGCCCACA
Found at i:55163348 original size:28 final size:28
Alignment explanation
Indices: 55163272--55163368 Score: 104
Period size: 28 Copynumber: 3.4 Consensus size: 28
55163262 TATTGCATTG
*
55163272 CACTGTTACTGTTTTGGGCTAAGGCCCACA
1 CACTGTTACTGTATTGGGCTAAGG-CC-CA
*
55163302 CACTGTTACTATATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
* * **
55163330 CACTGTTGCTGTATAGGGCCCAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
* *
55163358 AACTGCTACTG
1 CACTGTTACTG
55163369 CATGTTGTAT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 33 0.58
29 2 0.04
30 22 0.39
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.27
Consensus pattern (28 bp):
CACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:55171279 original size:102 final size:110
Alignment explanation
Indices: 55171171--55171630 Score: 506
Period size: 120 Copynumber: 4.0 Consensus size: 110
55171161 TATATGTTTT
* *
55171171 TATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTT
1 TATTAAA-TATA-TTAAT-ATAATTA-TTTAAATTATATTTTATAGTATCATATATTATAATTTT
*
55171236 AGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAA-TA-A
62 AGTAAATTCATATAAGAATATTGAATATTAAGAATTTTATTAAATTATA
* *
55171283 TATT---TA-A-T-A-ATAATTATGTTAAATTATATTTTATACTATTATATATTATAATTTTAGT
1 TATTAAATATATTAATATAATTAT-TTAAATTATATTTTATAGTATCATATATTATAATTTTAGT
*
55171341 AAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATCATATA
65 AAATTCATATAAGAATATTGAATATTAAGAATTTTATTAAAT--TATA
55171389 TTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATAA
1 ---T-ATT-AAATATA-TTAAT-ATAATTATTT-AAATTATATTTTATAGTATCATATATTATAA
* * *
55171454 TTTTAGTAAATTCATATAAGCATATTGATTACTAAGAATTTTATTAAATCATATA
58 TTTTAGTAAATTCATATAAGAATATTGAATATTAAGAATTTTATTAAAT--TATA
*
55171509 TTTTAATTGAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGA
1 ---T-ATT-AAATATA-TTAAT-ATAATTAT-TTAAATTATATTTTATAGTATCATATATTATAA
* * * *
55171574 TTTGAGTAAAATAATATAAGAATATTGATTATTAAGAATTTTATTAAATTATA
58 TTTTAGTAAATTCATATAAGAATATTGAATATTAAGAATTTTATTAAATTATA
55171627 TATT
1 TATT
55171631 TTAATTAAAA
Statistics
Matches: 312, Mismatches: 15, Indels: 40
0.85 0.04 0.11
Matches are distributed among these distances:
101 1 0.00
102 86 0.28
104 1 0.00
105 3 0.01
106 1 0.00
107 1 0.00
108 2 0.01
109 1 0.00
110 3 0.01
112 4 0.01
114 5 0.02
115 2 0.01
117 1 0.00
118 5 0.02
119 2 0.01
120 192 0.62
121 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (110 bp):
TATTAAATATATTAATATAATTATTTAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
AATTCATATAAGAATATTGAATATTAAGAATTTTATTAAATTATA
Found at i:55171388 original size:61 final size:61
Alignment explanation
Indices: 55171323--55171636 Score: 234
Period size: 61 Copynumber: 5.2 Consensus size: 61
55171313 TTATACTATT
*
55171323 ATATATTATAATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATC
1 ATATATTATAATTTAAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATC
* * * * * * * *
55171384 ATATATTTTAATTAAAATATATTTA-ATAATAATTATTTCAA-ATT-A-TATTTTA-TAGTATC
1 ATATATTATAATTTAAGTAAATTCATATAAGAA-TATTT-AATATTAAGAATTTTATTA-AATC
* * * * *
55171443 ATATATTATAATTTTAGTAAATTCATATAAGCATATTGATTACTAAGAATTTTATTAAATC
1 ATATATTATAATTTAAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATC
* * * * * * * *
55171504 ATATATTTTAATTGAAATATATTTA-ATAATAATTATGTTAA-ATT-A-TATTTTA-TAGTATC
1 ATATATTATAATTTAAGTAAATTCATATAAGAA-TAT-TTAATATTAAGAATTTTATTA-AATC
* * * * * * *
55171563 ATATATTATGATTTGAGTAAAATAATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATAATTTAAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATC
*
55171624 ATATATTTTAATT
1 ATATATTATAATT
55171637 AAAATATATT
Statistics
Matches: 186, Mismatches: 51, Indels: 32
0.69 0.19 0.12
Matches are distributed among these distances:
58 7 0.04
59 66 0.35
60 26 0.14
61 79 0.42
62 8 0.04
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (61 bp):
ATATATTATAATTTAAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATC
Found at i:55171414 original size:120 final size:120
Alignment explanation
Indices: 55171269--55171665 Score: 647
Period size: 120 Copynumber: 3.3 Consensus size: 120
55171259 AATATTAAGA
* *
55171269 ATTTT-ATT-AAATAATATTTAATAATAATTATGTTAAATTATATTTTATACTATTATATATTAT
1 ATTTTAATTAAAAT-ATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTAT
* *
55171332 AATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATCATAT
65 AATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATAT
55171388 ATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTTTATAGTATCATATATTAT
1 ATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTTTATAGTATCATATATTAT
* *
55171452 AATTTTAGTAAATTCATATAAGCATATTGATTACTAAGAATTTTATTAAATCATAT
65 AATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATAT
* *
55171508 ATTTTAATTGAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATG
1 ATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATA
* * * *
55171573 ATTTGAGTAAAATAATATAAGAATATTGATTATTAAGAATTTTATTAAATTATAT
66 ATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATAT
55171628 ATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 ATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
55171666 ATATGATTAA
Statistics
Matches: 259, Mismatches: 15, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
119 7 0.03
120 246 0.95
121 6 0.02
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
ATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATA
ATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATAT
Found at i:55171639 original size:18 final size:17
Alignment explanation
Indices: 55171611--55171645 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55171601 ATTATTAAGA
*
55171611 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
55171628 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
55171646 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:55171865 original size:44 final size:45
Alignment explanation
Indices: 55171802--55171898 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
55171792 CTATTACACC
*
55171802 TCCATTCCATTCAACCAAACACA-AGA-ATACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGATATACTATTACGCCTCTAT
* * *
55171846 TCCATTACATTCAACCAAACAATTGATTTGCTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGATATACTATTACGCCTCTAT
55171891 TCCATTAC
1 TCCATTAC
55171899 GCCTTTATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.47
45 24 0.51
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGATATACTATTACGCCTCTAT
Found at i:55171927 original size:16 final size:16
Alignment explanation
Indices: 55171880--55171930 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
55171870 GATTTGCTAT
* *
55171880 TACGCCTCTATTCCAT
1 TACGCCTTTATTCCAA
55171896 TACGCCTTTATTCCAA
1 TACGCCTTTATTCCAA
*
55171912 TACGTCTTTATTCCAA
1 TACGCCTTTATTCCAA
55171928 TAC
1 TAC
55171931 AGCGAACCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.24, C:0.31, G:0.06, T:0.39
Consensus pattern (16 bp):
TACGCCTTTATTCCAA
Found at i:55176896 original size:51 final size:51
Alignment explanation
Indices: 55176767--55176962 Score: 200
Period size: 51 Copynumber: 3.9 Consensus size: 51
55176757 AGTGAAAATG
* * * *
55176767 ATGGTCACGTGTGTAGTACTATGTGTAAGCTACTACGTGTACCGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * * *
55176816 ATAGGTCGCATGTGTAGTACTATGCGCAGGCTACTATGCGTACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * * * * *
55176867 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * *
55176919 ATGGTCACATGTGTAGTACTATGTGCAGGGTACTATGTGAACCG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCG
55176963 AACATCATTG
Statistics
Matches: 117, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
49 2 0.02
50 37 0.32
51 76 0.65
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
Found at i:55176957 original size:26 final size:26
Alignment explanation
Indices: 55176877--55176957 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
55176867 TTCGATCACG
*
55176877 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGGTACTA
* * * *
55176903 CGTGTA-T-CAGATG-GTAATGGTCAC-A
1 TGTGTAGTAC-TATGTG-CAGGGT-ACTA
55176928 TGTGTAGTACTATGTGCAGGGTACTA
1 TGTGTAGTACTATGTGCAGGGTACTA
55176954 TGTG
1 TGTG
55176958 AACCGAACAT
Statistics
Matches: 39, Mismatches: 9, Indels: 14
0.63 0.15 0.23
Matches are distributed among these distances:
24 2 0.05
25 15 0.38
26 20 0.51
27 2 0.05
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGGTACTA
Found at i:55177015 original size:45 final size:46
Alignment explanation
Indices: 55176959--55177054 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 46
55176949 TACTATGTGA
* *
55176959 ACCGAACATCATTGATTAGTAAGGTGG-CTGCTATGTAG-TGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTCTGCTATGT-GCTGAATCC
* *
55177004 ACCGGACATCATTGATTAATAAGGTGGTTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTCTGCTATGTGCTGAATCC
55177050 ACCGA
1 ACCGA
55177055 GTATATGTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
45 26 0.59
46 18 0.41
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (46 bp):
ACCGAACATCATTGATTAATAAGGTGGTCTGCTATGTGCTGAATCC
Found at i:55179695 original size:47 final size:48
Alignment explanation
Indices: 55179624--55179716 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 48
55179614 CCTGGCAACA
* *
55179624 TGTGATATGTGATTTTCGTATAAGACCATATCCGGGATATGGCATCGG
1 TGTGATATGTGATATTCGTATAAGACCATAGCCGGGATATGGCATCGG
* * *
55179672 TGTGATATGTGCTATT-GTGTAAGACCATAGCTGGGATATGGCATC
1 TGTGATATGTGATATTCGTATAAGACCATAGCCGGGATATGGCATC
55179717 AATATGTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 26 0.65
48 14 0.35
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (48 bp):
TGTGATATGTGATATTCGTATAAGACCATAGCCGGGATATGGCATCGG
Found at i:55192088 original size:22 final size:22
Alignment explanation
Indices: 55192073--55192118 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
55192063 GATAAGGATT
55192073 AAATTGAAAAGGGATAAAAATG
1 AAATTGAAAAGGGATAAAAATG
55192095 AAATTGAAAAGGGATAAAAATG
1 AAATTGAAAAGGGATAAAAATG
55192117 AA
1 AA
55192119 CTTACATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (22 bp):
AAATTGAAAAGGGATAAAAATG
Found at i:55196087 original size:28 final size:28
Alignment explanation
Indices: 55196028--55196117 Score: 101
Period size: 28 Copynumber: 3.2 Consensus size: 28
55196018 AGGCTAAATG
*
55196028 GAGAGTTCGCACAAAGCAAA-CCAAACA
1 GAGAGCTCGCACAAAGCAAAGCCAAACA
* * * * *
55196055 AAGAGCTCGTACAAATCAGAGCCAAATA
1 GAGAGCTCGCACAAAGCAAAGCCAAACA
* *
55196083 GAGAGCGCGCACAAAGCAAAGCCAAACC
1 GAGAGCTCGCACAAAGCAAAGCCAAACA
55196111 GAGAGCT
1 GAGAGCT
55196118 AAAACATTAG
Statistics
Matches: 48, Mismatches: 14, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
27 15 0.31
28 33 0.69
ACGTcount: A:0.44, C:0.26, G:0.22, T:0.08
Consensus pattern (28 bp):
GAGAGCTCGCACAAAGCAAAGCCAAACA
Found at i:55196927 original size:27 final size:28
Alignment explanation
Indices: 55196895--55196956 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
55196885 GGAACTGTGT
*
55196895 TCGCCATACAGACTGACGAACCCC-AGC
1 TCGCCAAACAGACTGACGAACCCCTAGC
* **
55196922 TTGCCAAACAGACTGGTGAACCCCTAGC
1 TCGCCAAACAGACTGACGAACCCCTAGC
55196950 TCGCCAA
1 TCGCCAA
55196957 CACATTAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 20 0.69
28 9 0.31
ACGTcount: A:0.29, C:0.37, G:0.19, T:0.15
Consensus pattern (28 bp):
TCGCCAAACAGACTGACGAACCCCTAGC
Found at i:55203961 original size:139 final size:139
Alignment explanation
Indices: 55203711--55203989 Score: 558
Period size: 139 Copynumber: 2.0 Consensus size: 139
55203701 AACTCCCTAC
55203711 CTAACCTCCAACATACCACTTGCACATAGCATGCGAACATAGTGTTAACCATCAACAAAGTAGCA
1 CTAACCTCCAACATACCACTTGCACATAGCATGCGAACATAGTGTTAACCATCAACAAAGTAGCA
55203776 AAAAATGCACACATAAAACATAGGGGTTCGCATGCAAAACACATTAGAGTTCACTACTATGCAAA
66 AAAAATGCACACATAAAACATAGGGGTTCGCATGCAAAACACATTAGAGTTCACTACTATGCAAA
55203841 ACAATAATT
131 ACAATAATT
55203850 CTAACCTCCAACATACCACTTGCACATAGCATGCGAACATAGTGTTAACCATCAACAAAGTAGCA
1 CTAACCTCCAACATACCACTTGCACATAGCATGCGAACATAGTGTTAACCATCAACAAAGTAGCA
55203915 AAAAATGCACACATAAAACATAGGGGTTCGCATGCAAAACACATTAGAGTTCACTACTATGCAAA
66 AAAAATGCACACATAAAACATAGGGGTTCGCATGCAAAACACATTAGAGTTCACTACTATGCAAA
55203980 ACAATAATT
131 ACAATAATT
55203989 C
1 C
55203990 CAAACACTTA
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 140 1.00
ACGTcount: A:0.42, C:0.24, G:0.13, T:0.21
Consensus pattern (139 bp):
CTAACCTCCAACATACCACTTGCACATAGCATGCGAACATAGTGTTAACCATCAACAAAGTAGCA
AAAAATGCACACATAAAACATAGGGGTTCGCATGCAAAACACATTAGAGTTCACTACTATGCAAA
ACAATAATT
Found at i:55205384 original size:27 final size:27
Alignment explanation
Indices: 55205272--55205428 Score: 97
Period size: 27 Copynumber: 5.7 Consensus size: 27
55205262 AGGCAAGGCT
* *
55205272 AAATAGAGAGCTCACATAAAGTAGAGCC
1 AAATAGAGAGCTCACACAAAATAGA-CC
* * ** *
55205300 AGA-CGAAGAGCTTGCACAAAAT-GAACA
1 AAATAG-AGAGCTCACACAAAATAG-ACC
*
55205327 AAATAGAGAGCTTACACAAAATAGACC
1 AAATAGAGAGCTCACACAAAATAGACC
*
55205354 AAATAGAGAGCTCACACAAGCAA-A-ACT
1 AAATAGAGAGCTCACACAA--AATAGACC
* ** *
55205381 AAATAGAAAGCTCGTACAAAGTAGAGCC
1 AAATAGAGAGCTCACACAAAATAGA-CC
* *
55205409 AAACAGAGAGCTCGCACAAA
1 AAATAGAGAGCTCACACAAA
55205429 GCAGAGCTAA
Statistics
Matches: 99, Mismatches: 21, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
25 1 0.01
26 1 0.01
27 59 0.60
28 36 0.36
29 2 0.02
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.12
Consensus pattern (27 bp):
AAATAGAGAGCTCACACAAAATAGACC
Found at i:55205421 original size:28 final size:28
Alignment explanation
Indices: 55205352--55205448 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 28
55205342 ACAAAATAGA
* * * *
55205352 CCAAATAGAGAGCTCACAC-AAGCAAAA
1 CCAAACAGAGAGCTCGCACAAAGCAGAG
* * * * *
55205379 CTAAATAGAAAGCTCGTACAAAGTAGAG
1 CCAAACAGAGAGCTCGCACAAAGCAGAG
55205407 CCAAACAGAGAGCTCGCACAAAGCAGAG
1 CCAAACAGAGAGCTCGCACAAAGCAGAG
*
55205435 CTAAACAGAGAGCT
1 CCAAACAGAGAGCT
55205449 AAACATTTTC
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
27 15 0.27
28 41 0.73
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (28 bp):
CCAAACAGAGAGCTCGCACAAAGCAGAG
Found at i:55206180 original size:27 final size:28
Alignment explanation
Indices: 55206150--55206211 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 28
55206140 CTTGTTTGAA
55206150 TTTTGGCGAA-CACCCAATTCGCACC-AC
1 TTTTGGCGAAGC-CCCAATTCGCACCAAC
* *
55206177 TTTTGG-TAAGCCCCAGTTCGCACCAAC
1 TTTTGGCGAAGCCCCAATTCGCACCAAC
55206204 -TTTGGCGA
1 TTTTGGCGA
55206212 TCACAGTTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (28 bp):
TTTTGGCGAAGCCCCAATTCGCACCAAC
Found at i:55208057 original size:57 final size:57
Alignment explanation
Indices: 55207989--55208143 Score: 195
Period size: 57 Copynumber: 2.7 Consensus size: 57
55207979 GGAAAAATAG
* *
55207989 GAAAT-ATTTGGAAATCATTATGGTTTTTTCCAAAATGAAAACGAAAATAGAGAAAT
1 GAAATCATTTGGAAATCATTATGGTTTTCTCCAAAATAAAAACGAAAATAGAGAAAT
** * * *
55208045 GAAATCATTTGGAAATGGTTATGGTTTTCTCCAAAATAAAAATGAAACTGGAGAAAT
1 GAAATCATTTGGAAATCATTATGGTTTTCTCCAAAATAAAAACGAAAATAGAGAAAT
* * * * *
55208102 GGAATCATTTGGAAATGAATGTGGTTTACTCCAAAATAAAAA
1 GAAATCATTTGGAAATCATTATGGTTTTCTCCAAAATAAAAA
55208144 AATGAAATGA
Statistics
Matches: 86, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
56 5 0.06
57 81 0.94
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (57 bp):
GAAATCATTTGGAAATCATTATGGTTTTCTCCAAAATAAAAACGAAAATAGAGAAAT
Found at i:55209667 original size:18 final size:18
Alignment explanation
Indices: 55209644--55209683 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
55209634 TTGTGAATTT
55209644 TTGTAGTACCTATGCCTA
1 TTGTAGTACCTATGCCTA
55209662 TTGTAGTACCTATGCCTA
1 TTGTAGTACCTATGCCTA
55209680 TTGT
1 TTGT
55209684 CCGACGGGCA
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:0.20, C:0.20, G:0.17, T:0.42
Consensus pattern (18 bp):
TTGTAGTACCTATGCCTA
Found at i:55216813 original size:24 final size:24
Alignment explanation
Indices: 55216785--55216832 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
55216775 TTTCTAAAAG
* *
55216785 ATTTAATATTTATGAGTATAATAT
1 ATTTAACATTTATGAGCATAATAT
* *
55216809 ATTTAGCATTTATTAGCATAATAT
1 ATTTAACATTTATGAGCATAATAT
55216833 GTTTGATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (24 bp):
ATTTAACATTTATGAGCATAATAT
Found at i:55220191 original size:6 final size:6
Alignment explanation
Indices: 55220177--55220207 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
55220167 AGATGAAAGA
*
55220177 TTTGGC TTTGTC TTTGTC TTTGTC TTTGTC T
1 TTTGTC TTTGTC TTTGTC TTTGTC TTTGTC T
55220208 CCATAATCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.16, G:0.19, T:0.65
Consensus pattern (6 bp):
TTTGTC
Found at i:55221112 original size:24 final size:24
Alignment explanation
Indices: 55221049--55221100 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
55221039 CTTCTAGAAG
* * *
55221049 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
55221073 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
55221097 ATTT
1 ATTT
55221101 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:55225746 original size:20 final size:20
Alignment explanation
Indices: 55225721--55225761 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
55225711 TAATTTAAAG
55225721 ATGAAATTGATGCTTAGTAT
1 ATGAAATTGATGCTTAGTAT
55225741 ATGAAATTGATGCTTAGTAT
1 ATGAAATTGATGCTTAGTAT
55225761 A
1 A
55225762 AGTGTATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (20 bp):
ATGAAATTGATGCTTAGTAT
Found at i:55229551 original size:43 final size:42
Alignment explanation
Indices: 55229499--55229579 Score: 135
Period size: 43 Copynumber: 1.9 Consensus size: 42
55229489 TTATATCTTA
*
55229499 CTATTTTATATATCTATACGTACATATTTATATACATTAATC
1 CTATTTTATATATCTATACGTACATATATATATACATTAATC
*
55229541 CTATCTTTATATATCTATACGTACATATATATTTACATT
1 CTAT-TTTATATATCTATACGTACATATATATATACATT
55229580 TTTTGTCTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
42 4 0.11
43 32 0.89
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (42 bp):
CTATTTTATATATCTATACGTACATATATATATACATTAATC
Found at i:55229609 original size:17 final size:17
Alignment explanation
Indices: 55229587--55229668 Score: 75
Period size: 17 Copynumber: 5.1 Consensus size: 17
55229577 ATTTTTTGTC
55229587 TATATATATTATGTTTA
1 TATATATATTATGTTTA
*
55229604 TATATATGTTATGTTTA
1 TATATATATTATGTTTA
55229621 TAT-T-TA-TA--TTTA
1 TATATATATTATGTTTA
* * *
55229633 TATACATATTCTATTTA
1 TATATATATTATGTTTA
* *
55229650 TATATTTTTTATGTTTA
1 TATATATATTATGTTTA
55229667 TA
1 TA
55229669 AAAAATACTT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
12 7 0.14
14 4 0.08
15 2 0.04
16 1 0.02
17 37 0.73
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (17 bp):
TATATATATTATGTTTA
Found at i:55230251 original size:18 final size:18
Alignment explanation
Indices: 55230228--55230264 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
55230218 TTGCAAAAAA
*
55230228 TATTCTAGTTTTAAGAAT
1 TATTCTAGTTTCAAGAAT
55230246 TATTCTAGTTTCAAGAAT
1 TATTCTAGTTTCAAGAAT
55230264 T
1 T
55230265 CATATTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (18 bp):
TATTCTAGTTTCAAGAAT
Found at i:55231797 original size:28 final size:28
Alignment explanation
Indices: 55231730--55231947 Score: 140
Period size: 28 Copynumber: 7.6 Consensus size: 28
55231720 CTTTCACAAT
* * *
55231730 AGATAGATAGCCAAAAAGGCATCCAAAC
1 AGATAGATAGCCATAAAGGCTTCCATAC
*
55231758 A-TTAGATAGCCATAAAGGCTTCCATAC
1 AGATAGATAGCCATAAAGGCTTCCATAC
*
55231785 AGATAGATAGCCATATAGG-TGTCCATAC
1 AGATAGATAGCCATAAAGGCT-TCCATAC
* * *
55231813 AGATAGATAGCCACAAAAGCATCCACATAAC
1 AGATAGATAGCCATAAAGGC-TTC-CAT-AC
* * *
55231844 A-TTAGATAGCCATAAATGCGTCCACATA-
1 AGATAGATAGCCATAAAGGC-TTC-CATAC
* * * * *
55231872 ACATCAAAAAGCCACAAAGGCGTCCATAC
1 AGAT-AGATAGCCATAAAGGCTTCCATAC
* *
55231901 AGATAGATAGCCACAAAGGCATCCACATAAC
1 AGATAGATAGCCATAAAGGC-TTC-CAT-AC
*
55231932 A-TTAGATAGCCATAAA
1 AGATAGATAGCCATAAA
55231948 TGCGTCCACA
Statistics
Matches: 150, Mismatches: 28, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
27 24 0.16
28 58 0.39
29 8 0.05
30 54 0.36
31 6 0.04
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.18
Consensus pattern (28 bp):
AGATAGATAGCCATAAAGGCTTCCATAC
Found at i:55231852 original size:30 final size:30
Alignment explanation
Indices: 55231733--55231985 Score: 179
Period size: 30 Copynumber: 8.7 Consensus size: 30
55231723 TCACAATAGA
* *
55231733 TAGATAGCCAAAAAGGCAT-C-CA-AACAT
1 TAGATAGCCACAAAGGCGTCCACATAACAT
* * *
55231760 TAGATAGCCATAAAGGC-TTC-CAT-ACAGA
1 TAGATAGCCACAAAGGCGTCCACATAACA-T
* * * *
55231788 TAGATAGCCATATAGGTGT-C-CAT-ACAGA
1 TAGATAGCCACAAAGGCGTCCACATAACA-T
* *
55231816 TAGATAGCCACAAAAGCATCCACATAACAT
1 TAGATAGCCACAAAGGCGTCCACATAACAT
* *
55231846 TAGATAGCCATAAATGCGTCCACATAACAT
1 TAGATAGCCACAAAGGCGTCCACATAACAT
* * * *
55231876 CAAAAAGCCACAAAGGCGT-C-CAT-ACAGA
1 TAGATAGCCACAAAGGCGTCCACATAACA-T
*
55231904 TAGATAGCCACAAAGGCATCCACATAACAT
1 TAGATAGCCACAAAGGCGTCCACATAACAT
* * *
55231934 TAGATAGCCATAAATGCGTCCACATAAAAT
1 TAGATAGCCACAAAGGCGTCCACATAACAT
* * *
55231964 CAAAAAGCCACAAAGGCGTCCA
1 TAGATAGCCACAAAGGCGTCCA
55231986 AACACATATA
Statistics
Matches: 182, Mismatches: 33, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
26 1 0.01
27 25 0.14
28 56 0.31
29 4 0.02
30 90 0.49
31 6 0.03
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.17
Consensus pattern (30 bp):
TAGATAGCCACAAAGGCGTCCACATAACAT
Found at i:55231907 original size:88 final size:88
Alignment explanation
Indices: 55231730--55231985 Score: 355
Period size: 88 Copynumber: 3.0 Consensus size: 88
55231720 CTTTCACAAT
* * *
55231730 AGATAGATAGCCA-AAAAGGCAT-C-CA-AACATTAGATAGCCATAAAGGC-TTC-CATACAGAT
1 AGATAGATAGCCACAAAA-GCATCCACATAACATTAGATAGCCATAAATGCGTCCACATA-AAAT
* * * * *
55231789 -AGATAGCCATATAGGTGTCCATAC
64 CAAAAAGCCACAAAGGCGTCCATAC
*
55231813 AGATAGATAGCCACAAAAGCATCCACATAACATTAGATAGCCATAAATGCGTCCACATAACATCA
1 AGATAGATAGCCACAAAAGCATCCACATAACATTAGATAGCCATAAATGCGTCCACATAAAATCA
55231878 AAAAGCCACAAAGGCGTCCATAC
66 AAAAGCCACAAAGGCGTCCATAC
*
55231901 AGATAGATAGCCACAAAGGCATCCACATAACATTAGATAGCCATAAATGCGTCCACATAAAATCA
1 AGATAGATAGCCACAAAAGCATCCACATAACATTAGATAGCCATAAATGCGTCCACATAAAATCA
55231966 AAAAGCCACAAAGGCGTCCA
66 AAAAGCCACAAAGGCGTCCA
55231986 AACACATATA
Statistics
Matches: 156, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
83 17 0.11
84 5 0.03
85 2 0.01
86 21 0.13
87 5 0.03
88 106 0.68
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.17
Consensus pattern (88 bp):
AGATAGATAGCCACAAAAGCATCCACATAACATTAGATAGCCATAAATGCGTCCACATAAAATCA
AAAAGCCACAAAGGCGTCCATAC
Found at i:55231943 original size:58 final size:56
Alignment explanation
Indices: 55231730--55231955 Score: 197
Period size: 58 Copynumber: 3.9 Consensus size: 56
55231720 CTTTCACAAT
* * *
55231730 AGATAGATAGCCAAAAAGGCATCCA-AACATTAGATAGCCATAAAGGCTTCCATAC
1 AGATAGATAGCCATAAAGGCATCCATAACATTAGATAGCCACAAAGGCGTCCATAC
* ** * * *
55231785 AGATAGATAGCCATATAGGTGTCCAT-ACAGATAGATAGCCACAAAAGCATCCACATAAC
1 AGATAGATAGCCATAAAGGCATCCATAACA-TTAGATAGCCACAAAGGCGT-C-CAT-AC
* * * * * *
55231844 A-TTAGATAGCCATAAATGCGTCCACATAACATCAAAAAGCCACAAAGGCGTCCATAC
1 AGATAGATAGCCATAAAGGCAT-C-CATAACATTAGATAGCCACAAAGGCGTCCATAC
* * *
55231901 AGATAGATAGCCACAAAGGCATCCACATAACATTAGATAGCCATAAATGCGTCCA
1 AGATAGATAGCCATAAAGGCAT-C-CATAACATTAGATAGCCACAAAGGCGTCCA
55231956 CATAAAATCA
Statistics
Matches: 135, Mismatches: 27, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
55 24 0.18
56 16 0.12
57 4 0.03
58 66 0.49
59 5 0.04
60 17 0.13
61 3 0.02
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.18
Consensus pattern (56 bp):
AGATAGATAGCCATAAAGGCATCCATAACATTAGATAGCCACAAAGGCGTCCATAC
Found at i:55232451 original size:54 final size:54
Alignment explanation
Indices: 55232308--55232458 Score: 212
Period size: 56 Copynumber: 2.8 Consensus size: 54
55232298 TCCCTACATA
* * ** *
55232308 ATGCCATAGTCCCGGACTAGGTCTTACACTATGTGGTCTTCTTTTCCCCATATT
1 ATGCCATAGTCCCAGACTAGGTCTTACACTATATGGTCTTCACTTCCCCATATG
* *
55232362 ATGCCATAGCCACCATGACTAGGTCTTACACTATATGGCCTTCACTTCCCCATATG
1 ATGCCATAGTC-CCA-GACTAGGTCTTACACTATATGGTCTTCACTTCCCCATATG
*
55232418 ATGCCATAGTCCCAGACTAGGTCTTACATTATATGGTCTTC
1 ATGCCATAGTCCCAGACTAGGTCTTACACTATATGGTCTTC
55232459 TTGCCATGGC
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
54 35 0.41
55 5 0.06
56 45 0.53
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (54 bp):
ATGCCATAGTCCCAGACTAGGTCTTACACTATATGGTCTTCACTTCCCCATATG
Found at i:55236048 original size:22 final size:22
Alignment explanation
Indices: 55236023--55236102 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
55236013 TAAAATCTAT
55236023 AGCTTAGTACGTTAGCCATGAG
1 AGCTTAGTACGTTAGCCATGAG
55236045 AGCTTAGTACGTTAGCCATGAG
1 AGCTTAGTACGTTAGCCATGAG
* * * **
55236067 GGTTTAGTTCGTTAAACATGAG
1 AGCTTAGTACGTTAGCCATGAG
55236089 AGCTTAGTACGTTA
1 AGCTTAGTACGTTA
55236103 ATTATCAACT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (22 bp):
AGCTTAGTACGTTAGCCATGAG
Found at i:55240628 original size:103 final size:104
Alignment explanation
Indices: 55240288--55240658 Score: 611
Period size: 105 Copynumber: 3.6 Consensus size: 104
55240278 TGTATATAAA
** * * *
55240288 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
**
55240352 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
55240392 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
*
55240457 TTGAAATGAAAAGGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
55240497 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
55240562 TGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
55240600 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
55240659 ATAACGGCTA
Statistics
Matches: 253, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
103 87 0.34
104 69 0.27
105 96 0.38
106 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:55246440 original size:22 final size:22
Alignment explanation
Indices: 55246412--55246564 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
55246402 TGTTGATAGT
*
55246412 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
55246434 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
55246456 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
55246478 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
55246500 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
55246522 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
55246544 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
55246565 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:55253381 original size:105 final size:104
Alignment explanation
Indices: 55253195--55253565 Score: 597
Period size: 105 Copynumber: 3.6 Consensus size: 104
55253185 TGTATATAAA
** * *
55253195 AGGGGTTGCTGTGTGCTGATTCCCCGATTT-ATGGGTGGTGCTATGTGCG-TGATCCACCATATC
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATC
*
55253258 TTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
55253299 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
55253364 TTGAAATGAAAAGGGGGGTTGCTATGTGCTGATTCCCCCG
66 TTGAAATGAAAA-GGGGGTTGCTATGTGCTGATTCCCCCG
55253404 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
*
55253468 TTGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* * **
55253507 AGGGGTTGCTAAGTGCTGATTCCCC-AATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCA
55253566 ATAACGGCTA
Statistics
Matches: 254, Mismatches: 9, Indels: 9
0.93 0.03 0.03
Matches are distributed among these distances:
102 1 0.00
103 81 0.32
104 79 0.31
105 92 0.36
106 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:55254881 original size:27 final size:24
Alignment explanation
Indices: 55254859--55254916 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
55254849 AGAAATAACC
55254859 ATAAAAATATATTTCAAAAAAATAATA
1 ATAAAAATA-ATTTCAAAAAAAT-A-A
* * *
55254886 ATTAAAATAATTTTAAGAAAATAA
1 ATAAAAATAATTTCAAAAAAATAA
55254910 ATAAAAA
1 ATAAAAA
55254917 ATAAAGCAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 7 0.26
25 1 0.04
26 11 0.41
27 8 0.30
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
ATAAAAATAATTTCAAAAAAATAA
Found at i:55259784 original size:18 final size:18
Alignment explanation
Indices: 55259761--55259796 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
55259751 CTATTTAAAG
55259761 AAAGAATTAACCAGAAGT
1 AAAGAATTAACCAGAAGT
55259779 AAAGAATTAACCAGAAGT
1 AAAGAATTAACCAGAAGT
55259797 TTTTCTGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.17, T:0.17
Consensus pattern (18 bp):
AAAGAATTAACCAGAAGT
Found at i:55261648 original size:45 final size:44
Alignment explanation
Indices: 55261584--55261671 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 44
55261574 TGTGAACTGA
* *
55261584 ACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGTT-AATCCACCGG
55261629 ACATCATTGATTAATAAGGTGGTTGCTATGTGTTAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGTTAATCCACCG
55261672 AGTATCTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 8 0.20
45 33 0.80
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (44 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGTTAATCCACCGG
Found at i:55269516 original size:5 final size:5
Alignment explanation
Indices: 55269506--55269535 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
55269496 GTCACATGAA
55269506 TTAAT TTAAT TTAAT TTAAT TTAA- TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
55269536 ATCGAATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTAAT
Found at i:55270735 original size:17 final size:17
Alignment explanation
Indices: 55270713--55270746 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
55270703 GACTAAATAC
55270713 ATATTATATGTTGTATG
1 ATATTATATGTTGTATG
55270730 ATATTATATGTTGTATG
1 ATATTATATGTTGTATG
55270747 TTCTAATTGA
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:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (17 bp):
ATATTATATGTTGTATG
Found at i:55275650 original size:46 final size:46
Alignment explanation
Indices: 55275597--55275685 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
55275587 TAGATATATG
55275597 ATTGTTTGGTCTTAGTGCTAGTGGGAGATTGTTAGAGTATGCCTAA
1 ATTGTTTGGTCTTAGTGCTAGTGGGAGATTGTTAGAGTATGCCTAA
55275643 ATTGTTTGGTCTTAGTGCTAGTGGGAGATTGTTAGAGTATGCC
1 ATTGTTTGGTCTTAGTGCTAGTGGGAGATTGTTAGAGTATGCC
55275686 CAGAGACCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.20, C:0.09, G:0.31, T:0.39
Consensus pattern (46 bp):
ATTGTTTGGTCTTAGTGCTAGTGGGAGATTGTTAGAGTATGCCTAA
Found at i:55277183 original size:17 final size:17
Alignment explanation
Indices: 55277158--55277192 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
55277148 AAGTTTTTTA
*
55277158 CCGTGACTATACTATTG
1 CCGTCACTATACTATTG
55277175 CCGTCACTATACTATTG
1 CCGTCACTATACTATTG
55277192 C
1 C
55277193 ATCGAGAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (17 bp):
CCGTCACTATACTATTG
Found at i:55277345 original size:18 final size:19
Alignment explanation
Indices: 55277322--55277370 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
55277312 TAAAAATATG
55277322 AAAAATAAAAAAT-TAT-AA
1 AAAAATAAAAAATCT-TCAA
*
55277340 AAAAATAAAAACTCTTCAA
1 AAAAATAAAAAATCTTCAA
55277359 AAAAATAAAAAA
1 AAAAATAAAAAA
55277371 GATTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAATAAAAAATCTTCAA
Found at i:55278199 original size:6 final size:6
Alignment explanation
Indices: 55278188--55278213 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
55278178 TACCAATTGC
55278188 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
55278214 GCAAAAGCAA
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:55279662 original size:40 final size:40
Alignment explanation
Indices: 55279630--55279707 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 40
55279620 GATTTGTGTC
*
55279630 CACGTAAGC-AAATCGCACTGACGTGGACGCGATGTTCTGA
1 CACGTAACCGAAATCGCACTGACGTGGACGCGAT-TTCTGA
* * *
55279670 CACGTACCCTGACATCGCGCTGACGTGGACGCGATTTC
1 CACGTAACC-GAAATCGCACTGACGTGGACGCGATTTC
55279708 GCGGAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 7 0.22
41 3 0.09
42 22 0.69
ACGTcount: A:0.23, C:0.29, G:0.27, T:0.21
Consensus pattern (40 bp):
CACGTAACCGAAATCGCACTGACGTGGACGCGATTTCTGA
Found at i:55289373 original size:26 final size:27
Alignment explanation
Indices: 55289333--55289384 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
55289323 TTTTATGAAC
55289333 TTTTTATATATTTTTTA-AAATTTTAT
1 TTTTTATATATTTTTTACAAATTTTAT
55289359 TTTTTA-ATATCTTTTTACAAATTTTA
1 TTTTTATATAT-TTTTTACAAATTTTA
55289385 AATTATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 4 0.17
26 12 0.50
27 8 0.33
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTTATATATTTTTTACAAATTTTAT
Found at i:55292956 original size:25 final size:25
Alignment explanation
Indices: 55292917--55292994 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 25
55292907 TCATTAGGGT
*
55292917 TACCGATTC-TCAGCTCGTATGAGCT
1 TACCGATTCAT-AGCTCGTATGAGCA
*
55292942 TACCGATTTATAGCTCGTGA-GAGCA
1 TACCGATTCATAGCTCGT-ATGAGCA
* *
55292967 TACCTATTCATAGCTCGTATAAGCA
1 TACCGATTCATAGCTCGTATGAGCA
55292992 TAC
1 TAC
55292995 ATGTACAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.02
25 42 0.93
26 2 0.04
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (25 bp):
TACCGATTCATAGCTCGTATGAGCA
Done.