Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 205 of 230
Found at i:61247215 original size:19 final size:21
Alignment explanation
Indices: 61247178--61247218 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
61247168 AAAATATATT
*
61247178 AAATATATATATTTATTTTTA
1 AAATATATATAGTTATTTTTA
61247199 AAATATA-ATAGTT-TTTTTA
1 AAATATATATAGTTATTTTTA
61247218 A
1 A
61247219 TACTTTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 5 0.26
21 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
AAATATATATAGTTATTTTTA
Found at i:61247959 original size:57 final size:58
Alignment explanation
Indices: 61247898--61248015 Score: 168
Period size: 57 Copynumber: 2.1 Consensus size: 58
61247888 ATCAAGTTTG
* * * *
61247898 TTTTACTAATCAAATGTTAGATTTTGTTATAATAATT-A-ACAATTAATAATTTGATAA
1 TTTTACTAATCAAATGTTAGATTTTATTACAATAATTAATACAATTAACAA-TTAATAA
*
61247955 TTTTATTAATCAAATGTTAGATTTTATTACAATAATTAATACAATTAACAATTAATAA
1 TTTTACTAATCAAATGTTAGATTTTATTACAATAATTAATACAATTAACAATTAATAA
61248013 TTT
1 TTT
61248016 GATAATTTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
57 34 0.63
58 10 0.19
59 10 0.19
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (58 bp):
TTTTACTAATCAAATGTTAGATTTTATTACAATAATTAATACAATTAACAATTAATAA
Found at i:61248068 original size:16 final size:17
Alignment explanation
Indices: 61248047--61248078 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
61248037 CAACTAATTT
61248047 TAATTTT-ATTAAAAAA
1 TAATTTTAATTAAAAAA
61248063 TAATTTTAATTAAAAA
1 TAATTTTAATTAAAAA
61248079 TGGGCCGGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTTTAATTAAAAAA
Found at i:61248261 original size:21 final size:22
Alignment explanation
Indices: 61248237--61248278 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
61248227 AACCAAAGGC
*
61248237 GAATCTA-GGTGGTTGGCAGGT
1 GAATCTAGGGGGGTTGGCAGGT
61248258 GAATCTAGGGGGGTTGGCAGG
1 GAATCTAGGGGGGTTGGCAGG
61248279 CGCCCCAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.10, G:0.48, T:0.24
Consensus pattern (22 bp):
GAATCTAGGGGGGTTGGCAGGT
Found at i:61249607 original size:16 final size:16
Alignment explanation
Indices: 61249588--61249621 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61249578 AGTTGATTTG
* *
61249588 ATTTTAAATTTTAATA
1 ATTTTAAACTTAAATA
61249604 ATTTTAAACTTAAATA
1 ATTTTAAACTTAAATA
61249620 AT
1 AT
61249622 CTAAATTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAAACTTAAATA
Found at i:61252594 original size:25 final size:25
Alignment explanation
Indices: 61252566--61252616 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
61252556 TTCTTAATTT
61252566 TATTTAT-TTAA-ATATAATTATAAAA
1 TATTTATATTAATAT-TAA-TATAAAA
61252591 TATTTATATTAATATTAATATAAAA
1 TATTTATATTAATATTAATATAAAA
61252616 T
1 T
61252617 TATAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 15 0.62
26 7 0.29
27 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TATTTATATTAATATTAATATAAAA
Found at i:61267889 original size:20 final size:20
Alignment explanation
Indices: 61267836--61267889 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
61267826 AAAATGGGGT
*
61267836 TTAATTAAATTTTTATCAGA
1 TTAATTAAATTTTTAACAGA
* * *
61267856 TTAA-TAAGAATTTTAAGAGC
1 TTAATTAA-ATTTTTAACAGA
61267876 TTAATTAAATTTTT
1 TTAATTAAATTTTT
61267890 TTAAAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.11
20 21 0.78
21 3 0.11
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (20 bp):
TTAATTAAATTTTTAACAGA
Found at i:61268186 original size:18 final size:18
Alignment explanation
Indices: 61268145--61268187 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
61268135 TCTATACTTG
* *
61268145 AATCTGACTCTATGCTGA
1 AATCTAACTCTAAGCTGA
**
61268163 CGTCTAACTCTAAGCTGA
1 AATCTAACTCTAAGCTGA
61268181 AATCTAA
1 AATCTAA
61268188 TTATAAGATT
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (18 bp):
AATCTAACTCTAAGCTGA
Found at i:61269681 original size:18 final size:18
Alignment explanation
Indices: 61269637--61269688 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
61269627 ATTTAGGTCC
*
61269637 AAAAATTAT-TATTCTATA
1 AAAAATTATATATT-TTTA
* *
61269655 GAAATTTATATATTTTTA
1 AAAAATTATATATTTTTA
*
61269673 AAAAATTATAAATTTT
1 AAAAATTATATATTTT
61269689 GAAATTTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
AAAAATTATATATTTTTA
Found at i:61269715 original size:18 final size:19
Alignment explanation
Indices: 61269684--61269733 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
61269674 AAAATTATAA
*
61269684 ATTTTGAAATTTTTACAAA-T
1 ATTTTG-AA-TTTTAAAAATT
61269704 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAATT
61269723 ATTTTG-ATTTT
1 ATTTTGAATTTT
61269734 TTTGTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 13 0.46
19 9 0.32
20 6 0.21
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:61269715 original size:19 final size:20
Alignment explanation
Indices: 61269684--61269734 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
61269674 AAAATTATAA
*
61269684 ATTTTGAAATTTTTACAAA-T
1 ATTTTG-AATTTTTAAAAATT
61269704 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
61269723 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
61269735 TTGTAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.32
19 13 0.46
20 6 0.21
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATT
Found at i:61271283 original size:14 final size:14
Alignment explanation
Indices: 61271264--61271300 Score: 60
Period size: 12 Copynumber: 2.8 Consensus size: 14
61271254 TAAATTTACA
61271264 AATTTTATCAATCT
1 AATTTTATCAATCT
61271278 AATTTTA--AATCT
1 AATTTTATCAATCT
61271290 AATTTTATCAA
1 AATTTTATCAA
61271301 ATGTATTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.57
14 9 0.43
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTTTATCAATCT
Found at i:61272361 original size:32 final size:32
Alignment explanation
Indices: 61272324--61272400 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
61272314 ATGCATGTGT
* * **
61272324 GTAACTTTTCATCTTCAAGTCTCTTTGCATTA
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
* * *
61272356 TTAACTCTTCATATTCAAGCCTCTTCACATTC
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
61272388 GTAACTTTTCATA
1 GTAACTTTTCATA
61272401 ATTTATTTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (32 bp):
GTAACTTTTCATATTCAAGCCTCTTCACATTA
Found at i:61276871 original size:32 final size:32
Alignment explanation
Indices: 61276834--61276910 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
61276824 ATGCATGTGT
* * **
61276834 GTAACTTTTCATCTTCAAGTCTCTTTGCATTA
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
* * *
61276866 TTAACTCTTCATATTCAAGCCTCTTCACATTC
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
61276898 GTAACTTTTCATA
1 GTAACTTTTCATA
61276911 ATTTATTTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (32 bp):
GTAACTTTTCATATTCAAGCCTCTTCACATTA
Found at i:61280469 original size:214 final size:214
Alignment explanation
Indices: 61280093--61280502 Score: 775
Period size: 214 Copynumber: 1.9 Consensus size: 214
61280083 AAGTATCCAC
* * *
61280093 AAAGATTAAGAACTATTTCATGAAATGAAAGAACCCCATCAAAACAATAGCTTAAGTTAATGGAA
1 AAAGATAAAGAACTATTGCATGAAATGAAAGAACCCAATCAAAACAATAGCTTAAGTTAATGGAA
61280158 AACCTTTCAAGATAACAAGTGAAAAGAAAGATGGCATGAAATGGAAAGAACCCCATCAAAACAAC
66 AACCTTTCAAGATAACAAGTGAAAAGAAAGATGGCATGAAATGGAAAGAACCCCATCAAAACAAC
*
61280223 ACCTAAAGTTAACGGAAACCTTTCAAGATAACAAGAAAAAGAGAAGGCAATGGCATGGAATGAGA
131 ACCTAAAGTTAACGGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATGGAATGAGA
61280288 ACCCCCCCCCAAAAAAAAA
196 ACCCCCCCCCAAAAAAAAA
61280307 AAAGATAAAGAACTATTGCATGAAATGAAAGAACCCAATCAAAACAATAGCTTAAGTTAATGGAA
1 AAAGATAAAGAACTATTGCATGAAATGAAAGAACCCAATCAAAACAATAGCTTAAGTTAATGGAA
*
61280372 AACCTTTCAAGATAACAAGTGAAAAGAAAGATGGCATGAAATGGAAAGAACCCCATCAAAACAAT
66 AACCTTTCAAGATAACAAGTGAAAAGAAAGATGGCATGAAATGGAAAGAACCCCATCAAAACAAC
61280437 ACCTAAAGTTAACGGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATGGAATGAGA
131 ACCTAAAGTTAACGGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATGGAATGAGA
61280502 A
196 A
61280503 AACCCCCCAT
Statistics
Matches: 191, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
214 191 1.00
ACGTcount: A:0.50, C:0.16, G:0.17, T:0.16
Consensus pattern (214 bp):
AAAGATAAAGAACTATTGCATGAAATGAAAGAACCCAATCAAAACAATAGCTTAAGTTAATGGAA
AACCTTTCAAGATAACAAGTGAAAAGAAAGATGGCATGAAATGGAAAGAACCCCATCAAAACAAC
ACCTAAAGTTAACGGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATGGAATGAGA
ACCCCCCCCCAAAAAAAAA
Found at i:61280628 original size:89 final size:88
Alignment explanation
Indices: 61280514--61280832 Score: 380
Period size: 89 Copynumber: 3.6 Consensus size: 88
61280504 ACCCCCCATT
* *
61280514 AAAACATTACCTGAAGCAAAAGAAACCTTTCAAGGAAACAAGAAAGGAACAAAAAGAAACCATTG
1 AAAACATTACCTGAAGTAAAAGAAACCTTCCAA-GAAACAAGAAAGGAACAAAAAGAAACCATTG
* *
61280579 CATGAAATAAAAAATATCCAACTG
65 CATGAAATGAAAAATATCCAACTA
* * * * * * *
61280603 AAAACAGTACCTGAAGTAAATGAAACCTTTCAAGATAACAAGAAA--AA-GAGAAGAGA--ATGG
1 AAAACATTACCTGAAGTAAAAGAAACCTTCCAAGA-AACAAGAAAGGAACAAAAAGAAACCATTG
* * *** * *
61280663 CATGGAATGAGAAACCCCCCA-TT
65 CATGAAATGAAAAATATCCAACTA
61280686 AAAACATTACCTGAAGTAAAAGAAACCTTCCAAAGAAACAAGAAAGGAACAAAAAGAAACCATTG
1 AAAACATTACCTGAAGTAAAAGAAACCTTCC-AAGAAACAAGAAAGGAACAAAAAGAAACCATTG
61280751 CATGAAATGAAAAATATCCAACTA
65 CATGAAATGAAAAATATCCAACTA
* *
61280775 AAAACATTACCTAAAGTAAATGAAACCTTCCAAGAAAGCAAGAAAGGAACAAAAAGAA
1 AAAACATTACCTGAAGTAAAAGAAACCTTCCAAGAAA-CAAGAAAGGAACAAAAAGAA
61280833 CGATTGAATG
Statistics
Matches: 190, Mismatches: 31, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
83 38 0.20
84 21 0.11
85 2 0.01
86 12 0.06
87 2 0.01
88 26 0.14
89 89 0.47
ACGTcount: A:0.54, C:0.17, G:0.15, T:0.14
Consensus pattern (88 bp):
AAAACATTACCTGAAGTAAAAGAAACCTTCCAAGAAACAAGAAAGGAACAAAAAGAAACCATTGC
ATGAAATGAAAAATATCCAACTA
Found at i:61280713 original size:172 final size:173
Alignment explanation
Indices: 61280429--61280819 Score: 642
Period size: 172 Copynumber: 2.3 Consensus size: 173
61280419 GAACCCCATC
* **
61280429 AAAACAATACCTAAAGTTAACGGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATG
1 AAAACAGTACCTAAAG-TAAATGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATG
* *
61280494 GAATGAGAAAACCCCCCATTAAAACATTACCTGAAGCAAAAGAAACCTTTCAAGGAAACAAGAAA
65 GAATGAGAAAACCCCCCATTAAAACATTACCTGAAGCAAAAGAAACCTTCCAAAGAAACAAGAAA
*
61280559 GGAACAAAAAGAAACCATTGCATGAAATAAAAAATATCCAACTG
130 GGAACAAAAAGAAACCATTGCATGAAATAAAAAATATCCAACTA
* *
61280603 AAAACAGTACCTGAAGTAAATGAAACCTTTCAAGATAACAAGAAAAAGAGAAGAGAATGGCATGG
1 AAAACAGTACCTAAAGTAAATGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATGG
*
61280668 AATGAG-AAACCCCCCATTAAAACATTACCTGAAGTAAAAGAAACCTTCCAAAGAAACAAGAAAG
66 AATGAGAAAACCCCCCATTAAAACATTACCTGAAGCAAAAGAAACCTTCCAAAGAAACAAGAAAG
*
61280732 GAACAAAAAGAAACCATTGCATGAAATGAAAAATATCCAACTA
131 GAACAAAAAGAAACCATTGCATGAAATAAAAAATATCCAACTA
* *
61280775 AAAACATTACCTAAAGTAAATGAAACCTTCCAAGA-AAGCAAGAAA
1 AAAACAGTACCTAAAGTAAATGAAACCTTTCAAGATAA-CAAGAAA
61280820 GGAACAAAAA
Statistics
Matches: 203, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
171 2 0.01
172 135 0.67
173 52 0.26
174 14 0.07
ACGTcount: A:0.53, C:0.17, G:0.15, T:0.15
Consensus pattern (173 bp):
AAAACAGTACCTAAAGTAAATGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATGG
AATGAGAAAACCCCCCATTAAAACATTACCTGAAGCAAAAGAAACCTTCCAAAGAAACAAGAAAG
GAACAAAAAGAAACCATTGCATGAAATAAAAAATATCCAACTA
Found at i:61286347 original size:19 final size:19
Alignment explanation
Indices: 61286323--61286385 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
61286313 TCTAATTAAG
61286323 TAATAACTCTATTTTACTT
1 TAATAACTCTATTTTACTT
* * ** ***
61286342 TAATAAGTTTATTAAAAAG
1 TAATAACTCTATTTTACTT
61286361 TAATAACTCTATTTTACTT
1 TAATAACTCTATTTTACTT
61286380 TAATAA
1 TAATAA
61286386 ATTATTGCTT
Statistics
Matches: 30, Mismatches: 14, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (19 bp):
TAATAACTCTATTTTACTT
Found at i:61287891 original size:26 final size:27
Alignment explanation
Indices: 61287838--61287891 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
61287828 TTTTTTTTGT
**
61287838 ATATTTTGGTAAATAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAATGGATA
61287865 ATATTTTGGTAAATAAAAAAA-GGATA
1 ATATTTTGGTAAATAAAAAAATGGATA
61287891 A
1 A
61287892 CATTATAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAATGGATA
Found at i:61288753 original size:23 final size:25
Alignment explanation
Indices: 61288725--61288789 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
61288715 ATTTAATACA
**
61288725 ACAAGTTAC-T-TATTTTAATTGTG
1 ACAAGTTACATGTATTAAAATTGTG
**
61288748 ACAAGTGGCATGTATTAAAATTGTG
1 ACAAGTTACATGTATTAAAATTGTG
*
61288773 ACAAGTTACATATATTA
1 ACAAGTTACATGTATTA
61288790 CATATTTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 7 0.21
24 1 0.03
25 25 0.76
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (25 bp):
ACAAGTTACATGTATTAAAATTGTG
Found at i:61294439 original size:12 final size:13
Alignment explanation
Indices: 61294415--61294443 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
61294405 GGGCTATAAC
61294415 TATTGCATTTATT
1 TATTGCATTTATT
61294428 TATTGC-TTTATT
1 TATTGCATTTATT
61294440 TATT
1 TATT
61294444 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:61296034 original size:22 final size:22
Alignment explanation
Indices: 61296006--61296050 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
61295996 GATCTATAGA
61296006 GATAGATCAAAACGACTACTAG
1 GATAGATCAAAACGACTACTAG
61296028 GATAGATCAAAACGACTACTAG
1 GATAGATCAAAACGACTACTAG
61296050 G
1 G
61296051 TCTAAGCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (22 bp):
GATAGATCAAAACGACTACTAG
Found at i:61306400 original size:39 final size:39
Alignment explanation
Indices: 61306346--61306423 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
61306336 GTCAAGACAA
61306346 AGATTGAAAATCTAATGGCCTATGAAAAAGCAGAAAACT
1 AGATTGAAAATCTAATGGCCTATGAAAAAGCAGAAAACT
61306385 AGATTGAAAATCTAATGGCCTATGAAAAAGCAGAAAACT
1 AGATTGAAAATCTAATGGCCTATGAAAAAGCAGAAAACT
61306424 TGAAACGGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.21
Consensus pattern (39 bp):
AGATTGAAAATCTAATGGCCTATGAAAAAGCAGAAAACT
Found at i:61307432 original size:18 final size:18
Alignment explanation
Indices: 61307409--61307451 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
61307399 GAATGAGTTT
61307409 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
61307427 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
61307445 TTAATTA
1 TTAATTA
61307452 CACCCTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:61317248 original size:109 final size:105
Alignment explanation
Indices: 61317043--61317249 Score: 276
Period size: 109 Copynumber: 1.9 Consensus size: 105
61317033 ATAATATTGA
* **
61317043 TTGAAAGTTAAGAAGATATTTAGCTATTTGGTCGAACGAGCAATCGAAACCCAGCACGTTAGGGC
1 TTGAAAGTTAAAAAGATATTTAGCTATTTGGTCGAACGAAAAATCGAAACCCAGCACGTTAGGGC
* *
61317108 ACGTTCTCTCGAATTTTTAAATGCGAAACATTGCCTCGTT
66 ACGTTCTCTCGAATTTTCAAACGCGAAACATTGCCTCGTT
61317148 TTGAAAGTTTAAAAAGGATATTT-GACTATTTGGTCGAACGAAAAAAATCGAAACCCAGCACGTT
1 TTGAAAG-TTAAAAA-GATATTTAG-CTATTTGGTCGAACG--AAAAATCGAAACCCAGCACGTT
*
61317212 AGGGCACGTTTTCTCG-ATTTTCCAAACGC-AAGACATTG
61 AGGGCACGTTCTCTCGAATTTT-CAAACGCGAA-ACATTG
61317250 TCTTATTTAG
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
105 7 0.08
106 7 0.08
107 22 0.25
108 7 0.08
109 46 0.52
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (105 bp):
TTGAAAGTTAAAAAGATATTTAGCTATTTGGTCGAACGAAAAATCGAAACCCAGCACGTTAGGGC
ACGTTCTCTCGAATTTTCAAACGCGAAACATTGCCTCGTT
Found at i:61319008 original size:28 final size:29
Alignment explanation
Indices: 61318976--61319030 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
61318966 TTTAGGGAGG
*
61318976 TTAAAGTGCAATTTTAT-TATATATTAAT
1 TTAAAGTGCAAGTTTATATATATATTAAT
*
61319004 TTAAAGTGCAAGTTTATATATTTATTA
1 TTAAAGTGCAAGTTTATATATATATTA
61319031 GTAATTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (29 bp):
TTAAAGTGCAAGTTTATATATATATTAAT
Found at i:61319535 original size:22 final size:22
Alignment explanation
Indices: 61319486--61319537 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
61319476 TCATTAACAA
* *
61319486 TAAAATAGTAGCAACATAATAG
1 TAAAATAGTAGCAAAACAATAG
*
61319508 TGAAATAGTAGCAAAACAATGAG
1 TAAAATAGTAGCAAAACAAT-AG
61319531 -AAAATAG
1 TAAAATAG
61319538 CAATAAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.56, C:0.08, G:0.17, T:0.19
Consensus pattern (22 bp):
TAAAATAGTAGCAAAACAATAG
Found at i:61320391 original size:7 final size:7
Alignment explanation
Indices: 61320379--61320406 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
61320369 ATTGTAATAA
61320379 TTAAATT
1 TTAAATT
61320386 TTAAATT
1 TTAAATT
61320393 TTAAATT
1 TTAAATT
61320400 TTAAATT
1 TTAAATT
61320407 AAGAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTAAATT
Found at i:61323735 original size:26 final size:26
Alignment explanation
Indices: 61323706--61323767 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
61323696 TACCCTCAAC
*
61323706 AAAATTTTGACGAGTTTAC-CGTTGGT
1 AAAATTTTGACGAGTTTACTC-CTGGT
* * *
61323732 AAAACTTTGACGATTTTGCTCCTGGT
1 AAAATTTTGACGAGTTTACTCCTGGT
61323758 AAAATTTTGA
1 AAAATTTTGA
61323768 AAAAATATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (26 bp):
AAAATTTTGACGAGTTTACTCCTGGT
Found at i:61323918 original size:6 final size:6
Alignment explanation
Indices: 61323907--61323939 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
61323897 ATGATTGCAA
*
61323907 ATTTCC ATTTCC ATTT-C ATTTTC ATTTCC ATTT
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTT
61323940 TTGAAAACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (6 bp):
ATTTCC
Found at i:61323929 original size:12 final size:12
Alignment explanation
Indices: 61323907--61323940 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
61323897 ATGATTGCAA
*
61323907 ATTTCCATTTCC
1 ATTTCCATTTTC
61323919 ATTT-CATTTTC
1 ATTTCCATTTTC
61323930 ATTTCCATTTT
1 ATTTCCATTTT
61323941 TGAAAACCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTCCATTTTC
Found at i:61323932 original size:17 final size:17
Alignment explanation
Indices: 61323907--61323939 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
61323897 ATGATTGCAA
61323907 ATTTCCATTTCCATTTC
1 ATTTCCATTTCCATTTC
*
61323924 ATTTTCATTTCCATTT
1 ATTTCCATTTCCATTT
61323940 TTGAAAACCT
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:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTCCATTTCCATTTC
Found at i:61326722 original size:25 final size:25
Alignment explanation
Indices: 61326684--61326734 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
61326674 ATAAATACGA
61326684 AAAAAATCGCAATAAAAAATTAATT
1 AAAAAATCGCAATAAAAAATTAATT
* * *
61326709 AAAAAATTGTAATACAAAATTAATT
1 AAAAAATCGCAATAAAAAATTAATT
61326734 A
1 A
61326735 GGCTAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (25 bp):
AAAAAATCGCAATAAAAAATTAATT
Found at i:61328609 original size:8 final size:8
Alignment explanation
Indices: 61328596--61328668 Score: 58
Period size: 8 Copynumber: 8.9 Consensus size: 8
61328586 TTTTGAAAAT
61328596 TAAATTTA
1 TAAATTTA
*
61328604 TAAATTTT
1 TAAATTTA
**
61328612 TAGTTTTTA
1 TA-AATTTA
*
61328621 TATATTTA
1 TAAATTTA
*
61328629 TACATTTA
1 TAAATTTA
*
61328637 TACATTTATA
1 TA-AATT-TA
61328647 TAAATTTA
1 TAAATTTA
61328655 TAAA-TTA
1 TAAATTTA
61328662 TAAATTT
1 TAAATTT
61328669 TATATTTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
7 7 0.13
8 31 0.60
9 10 0.19
10 4 0.08
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (8 bp):
TAAATTTA
Found at i:61328655 original size:26 final size:24
Alignment explanation
Indices: 61328596--61328743 Score: 70
Period size: 25 Copynumber: 5.9 Consensus size: 24
61328586 TTTTGAAAAT
* * *
61328596 TAAATTTATAAATTTTTAGTTTTTA
1 TAAATTTAT-AATTTATAATTTATA
*
61328621 TATATTTATACATTTATACATTTATA
1 TAAATTTATA-ATTTATA-ATTTATA
*
61328647 TAAATTTATAAATTATAAATTT-TA
1 TAAATTTATAATTTAT-AATTTATA
** * *
61328671 TATTTTTAAAATATTGTAGGATTT-TA
1 TAAATTTATAAT-TTATA--ATTTATA
* *
61328697 TATAATTT-TAATTGTATACGTTTTTA
1 TA-AATTTATAATT-TATA-ATTTATA
61328723 TAAATTTAT-ATTTATATATTT
1 TAAATTTATAATTTATA-ATTT
61328744 CAAACTAATT
Statistics
Matches: 94, Mismatches: 19, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
24 19 0.20
25 38 0.40
26 34 0.36
27 3 0.03
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
TAAATTTATAATTTATAATTTATA
Found at i:61328724 original size:24 final size:25
Alignment explanation
Indices: 61328692--61328738 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
61328682 TATTGTAGGA
*
61328692 TTTTATATAATTTTA-ATTGTATACG
1 TTTTATATAAATTTATATT-TATACG
61328717 TTTT-TATAAATTTATATTTATA
1 TTTTATATAAATTTATATTTATA
61328739 TATTTCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTTATATAAATTTATATTTATACG
Found at i:61331374 original size:25 final size:25
Alignment explanation
Indices: 61331326--61331374 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
61331316 CTAGGTTAAT
* **
61331326 TAAAGTTTAAATGGGAAACTAAAAA
1 TAAAGTTTAAATAGGAAAAGAAAAA
*
61331351 TAAAGTTTAACTAGGAAAAGAAAA
1 TAAAGTTTAAATAGGAAAAGAAAA
61331375 GACAAAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.57, C:0.04, G:0.16, T:0.22
Consensus pattern (25 bp):
TAAAGTTTAAATAGGAAAAGAAAAA
Found at i:61335785 original size:28 final size:31
Alignment explanation
Indices: 61335753--61335811 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
61335743 TGTTTTGTTT
61335753 TTATTATAATAA-CATTAT-AAT-ATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
* *
61335781 TTATTATTATAACCTTTATAAATAATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
61335812 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.42
29 5 0.19
30 3 0.12
31 7 0.27
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
TTATTATAATAACCATTATAAATAATATAAA
Found at i:61338737 original size:17 final size:17
Alignment explanation
Indices: 61338715--61338787 Score: 51
Period size: 17 Copynumber: 4.4 Consensus size: 17
61338705 TTTTCTATTA
61338715 ATTAAATAAAATTTAAT
1 ATTAAATAAAATTTAAT
** *
61338732 ATTAAATTTAATCTAAT
1 ATTAAATAAAATTTAAT
* *
61338749 ATT-TATCAAAA-TAAAT
1 ATTAAAT-AAAATTTAAT
* * *
61338765 ATTAGATTAAATTTAGT
1 ATTAAATAAAATTTAAT
61338782 ATTAAA
1 ATTAAA
61338788 ATGATTAAGT
Statistics
Matches: 40, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
16 11 0.28
17 29 0.73
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTAAATAAAATTTAAT
Found at i:61342614 original size:6 final size:6
Alignment explanation
Indices: 61342599--61342638 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
61342589 GCATTACAAA
*
61342599 AAAAAGG AAAAAG AAAAAG AAAAAG AAAAAG AAAAGG AAA
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
61342639 TAAATAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:61347844 original size:27 final size:27
Alignment explanation
Indices: 61347814--61347869 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
61347804 AGTTCGAGAG
* *
61347814 CAATGAAGCGTCAACGAAGTGGACCAT
1 CAATGAAGCGTCAACGAAGCGGAACAT
**
61347841 CAATGATTCGTCAACGAAGCGGAACAT
1 CAATGAAGCGTCAACGAAGCGGAACAT
61347868 CA
1 CA
61347870 TCGAAACACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (27 bp):
CAATGAAGCGTCAACGAAGCGGAACAT
Found at i:61367442 original size:93 final size:91
Alignment explanation
Indices: 61367265--61367474 Score: 271
Period size: 93 Copynumber: 2.3 Consensus size: 91
61367255 TTGATTTTAG
* * * *
61367265 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATAACAATATTAAATTAT
* *
61367330 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATATTAATTATTTTAAATTATA
61367357 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTTAATATTAACAAT-TTAAATT
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAA-TT-ATA-TAACAATATTAAATT
61367421 ATATGTAATAATT-ATTATTTTAAATTATA
63 ATATGTAAT-ATTAATTATTTTAAATTATA
* * * *
61367450 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
61367475 GTTAGAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
91 24 0.23
92 18 0.17
93 54 0.52
94 8 0.08
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATAACAATATTAAATTATA
TGTAATATTAATTATTTTAAATTATA
Found at i:61367604 original size:66 final size:63
Alignment explanation
Indices: 61367520--61367738 Score: 190
Period size: 66 Copynumber: 3.5 Consensus size: 63
61367510 TTTACATAAA
*
61367520 ATATATGATATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAAT
1 ATATAAGA-ATATTAATTATTT-AAATTTT-ATTTA-AGTATCATATATTATGATTTGAGTAAAT
61367585 TC
62 TC
* * * *
61367587 ATATAAGAATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT-TTAATT-A-T-AA-T-
1 ATATAAGAATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTC
** *
61367642 ATAT-TTAATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATAAGAATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTTGAGTAAAT
61367705 TC
62 TC
*
61367707 ATATAAGAATATTAATTATTAAGAATTTTATT
1 ATATAAGAATATTAATTATTTA-AATTTTATT
61367739 AAATTATATA
Statistics
Matches: 119, Mismatches: 16, Indels: 36
0.70 0.09 0.21
Matches are distributed among these distances:
53 5 0.04
54 13 0.11
55 5 0.04
56 4 0.03
57 3 0.03
58 1 0.01
59 10 0.08
60 8 0.07
61 10 0.08
62 1 0.01
63 3 0.03
64 4 0.03
65 9 0.08
66 31 0.26
67 12 0.10
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (63 bp):
ATATAAGAATATTAATTATTTAAATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTC
Found at i:61367616 original size:120 final size:120
Alignment explanation
Indices: 61367490--61367782 Score: 443
Period size: 120 Copynumber: 2.4 Consensus size: 120
61367480 AATTATTTTA
* *
61367490 AATTTTATTAAATCATATATTTTACA-TAAAATATATGAT-ATATTAATTAT-TTCAAATTT-TC
1 AATTTTATTAAATTATATATTTTA-ATTAAAATATAT-ATAATAATAATTATGTT--AATTTAT-
*
61367551 A-TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
61 ATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
61367610 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATATAATAATAATTATGTTAATTTATATTTT
61367675 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
61367730 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATATAATAATAATTATGTT
61367783 TAAATATGAT
Statistics
Matches: 163, Mismatches: 5, Indels: 10
0.92 0.03 0.06
Matches are distributed among these distances:
119 8 0.05
120 153 0.94
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATATAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:61367650 original size:15 final size:15
Alignment explanation
Indices: 61367615--61367666 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
61367605 TTAAGAATTT
*
61367615 TATTAAATTAT-ATA
1 TATTTAATTATAATA
61367629 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
61367643 TATTTAATAATAAT-
1 TATTTAATTATAATA
61367657 TATGTTAATT
1 TAT-TTAATT
61367667 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:61367765 original size:16 final size:16
Alignment explanation
Indices: 61367744--61367785 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
61367734 TTATTAAATT
*
61367744 ATATATTTTAATTATA
1 ATATATTTTAATAATA
61367760 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
61367775 AT-TATGTTTAA
1 ATATAT-TTTAA
61367786 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:61367770 original size:15 final size:15
Alignment explanation
Indices: 61367735--61367776 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
61367725 TTAAGAATTT
*
61367735 TATTAAATTAT-ATA
1 TATTTAATTATAATA
61367749 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
61367763 TATTTAATAATAAT
1 TATTTAATTATAAT
61367777 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:61367874 original size:151 final size:151
Alignment explanation
Indices: 61367719--61367996 Score: 538
Period size: 151 Copynumber: 1.8 Consensus size: 151
61367709 ATAAGAATAT
*
61367719 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
61367784 AAATATGATTAAAATATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAATAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAATAA
61367849 TTTACCAAAACAAATTTCTGC
131 TTTACCAAAACAAATTTCTGC
61367870 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
61367935 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAA
61367997 CAATAATCAT
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
151 125 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (151 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAATAA
TTTACCAAAACAAATTTCTGC
Found at i:61367910 original size:18 final size:17
Alignment explanation
Indices: 61367882--61367916 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
61367872 ATTATTAAGA
*
61367882 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
61367899 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
61367917 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:61368173 original size:16 final size:16
Alignment explanation
Indices: 61368152--61368203 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
61368142 GATTTGCTAT
61368152 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
61368168 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
61368184 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
61368200 TACA
1 TACA
61368204 GCGAACCAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:61369375 original size:3 final size:3
Alignment explanation
Indices: 61369367--61369416 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
61369357 AAATGCAATG
* *
61369367 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ACTA ATTA ATT TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA A-TA ATA ATA ATA
61369413 ATA A
1 ATA A
61369417 AGTAACCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:61370118 original size:17 final size:17
Alignment explanation
Indices: 61370092--61370130 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
61370082 AGAGATCGAA
*
61370092 AAAAATGAAATAAGAAC
1 AAAAACGAAATAAGAAC
61370109 AAAAACGAAATAAGAAC
1 AAAAACGAAATAAGAAC
61370126 AAAAA
1 AAAAA
61370131 GGTTACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.74, C:0.08, G:0.10, T:0.08
Consensus pattern (17 bp):
AAAAACGAAATAAGAAC
Found at i:61374700 original size:25 final size:25
Alignment explanation
Indices: 61374672--61374726 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
61374662 TGGATATGCT
61374672 ATTCTGATTCTGAAAATGAAATGTC
1 ATTCTGATTCTGAAAATGAAATGTC
* *
61374697 ATTCTGATTCTGAAAGTGACATGTC
1 ATTCTGATTCTGAAAATGAAATGTC
61374722 ATTCT
1 ATTCT
61374727 AATTTGATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (25 bp):
ATTCTGATTCTGAAAATGAAATGTC
Found at i:61379844 original size:18 final size:20
Alignment explanation
Indices: 61379802--61379848 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
61379792 ACTTTTAAAA
*
61379802 TTTTAACTTTCTTTATATAT
1 TTTTAAATTTCTTTATATAT
*
61379822 TTTTAAATTT-TTT-TATTT
1 TTTTAAATTTCTTTATATAT
61379840 TTTTAAATT
1 TTTTAAATT
61379849 ATAAAATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.52
19 3 0.12
20 9 0.36
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTAAATTTCTTTATATAT
Found at i:61379884 original size:19 final size:19
Alignment explanation
Indices: 61379847--61379905 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
61379837 TTTTTTTAAA
* *
61379847 TTATAAA-ATTTGGAGTTT
1 TTATAAATATTTTGAATTT
61379865 TTATAAATATTTTGAATTT
1 TTATAAATATTTTGAATTT
*
61379884 TTGA-AAATTATTTTAAATTT
1 TT-ATAAA-TATTTTGAATTT
61379904 TT
1 TT
61379906 TTTATAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.20
19 14 0.40
20 14 0.40
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (19 bp):
TTATAAATATTTTGAATTT
Found at i:61379885 original size:20 final size:20
Alignment explanation
Indices: 61379862--61379906 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
61379852 AAATTTGGAG
*
61379862 TTTTTATAAA-TATTTTGAAT
1 TTTTTA-AAATTATTTTAAAT
*
61379882 TTTTGAAAATTATTTTAAAT
1 TTTTTAAAATTATTTTAAAT
61379902 TTTTT
1 TTTTT
61379907 TTATAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTTTAAAATTATTTTAAAT
Found at i:61382911 original size:115 final size:115
Alignment explanation
Indices: 61382772--61383004 Score: 448
Period size: 115 Copynumber: 2.0 Consensus size: 115
61382762 AGTCTGAACA
* *
61382772 TTTACTCACAATTATATTTTATTTTTTATAAATATATTTTTATATTTTCAATTAGACTTAAATAA
1 TTTACTCACAAATATATTTTATTTTTTATAAATATATTTGTATATTTTCAATTAGACTTAAATAA
61382837 AATTTTTAATTAATAAATATGAATATGTGCTGGGTTCCAGCTTATGAATT
66 AATTTTTAATTAATAAATATGAATATGTGCTGGGTTCCAGCTTATGAATT
61382887 TTTACTCACAAATATATTTTATTTTTTATAAATATATTTGTATATTTTCAATTAGACTTAAATAA
1 TTTACTCACAAATATATTTTATTTTTTATAAATATATTTGTATATTTTCAATTAGACTTAAATAA
61382952 AATTTTTAATTAATAAATATGAATATGTGCTGGGTTCCAGCTTATGAATT
66 AATTTTTAATTAATAAATATGAATATGTGCTGGGTTCCAGCTTATGAATT
61383002 TTT
1 TTT
61383005 TTGACTAAGG
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 116 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (115 bp):
TTTACTCACAAATATATTTTATTTTTTATAAATATATTTGTATATTTTCAATTAGACTTAAATAA
AATTTTTAATTAATAAATATGAATATGTGCTGGGTTCCAGCTTATGAATT
Found at i:61386119 original size:44 final size:44
Alignment explanation
Indices: 61385992--61386130 Score: 122
Period size: 47 Copynumber: 3.0 Consensus size: 44
61385982 TTGATTTTAG
*
61385992 TAAATTCATATAAGAACATTATATTATTAAGAATTTTATGAAATTA
1 TAAATTCATATAAGAAAATT-TATTATTAAGAATTTTA-GAAATTA
* * * ** *
61386038 TATA-TCATTATTAA-ATTATATTTAATATTAATTATTTTA-AATTGTA
1 TAAATTCA-TA-TAAGA--AAATTTATTATTAAGAATTTTAGAAAT-TA
61386084 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTA-GAAATTA
61386129 TA
1 TA
61386131 TATTATTATT
Statistics
Matches: 72, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
44 18 0.25
45 13 0.18
46 17 0.24
47 20 0.28
48 4 0.06
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (44 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAATTTTAGAAATTA
Found at i:61386139 original size:91 final size:92
Alignment explanation
Indices: 61385992--61386161 Score: 297
Period size: 91 Copynumber: 1.9 Consensus size: 92
61385982 TTGATTTTAG
*
61385992 TAAATTCATATAAGAACATTATATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAAAATTATATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* *
61386057 ATTTAATATTAATTATTTTAAATTGTA
66 ATGTAATAATAATTATTTTAAATTGTA
*
61386084 TAAATTCATATAAGAAAATT-TATTATTAAGAATTTTATGAAATTATATATTATTATTAAATTAT
1 TAAATTCATATAAGAAAATTATATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
61386148 ATGTAATAATAATT
66 ATGTAATAATAATT
61386162 TTAAATTTTA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
91 55 0.74
92 19 0.26
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTATATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
ATGTAATAATAATTATTTTAAATTGTA
Found at i:61386162 original size:44 final size:43
Alignment explanation
Indices: 61386009--61386164 Score: 136
Period size: 44 Copynumber: 3.5 Consensus size: 43
61385999 ATATAAGAAC
* *
61386009 ATTATATTATTAAGAATTTTATGAAATTATATATCATTATTAA
1 ATTATATTAATAAGAATTTTATGAAATTATATATTATTATTAA
** * * **
61386052 ATTATATTTAATATTAATTATT-TTAAATTGTATAAATTCATATAAGAAA
1 ATTATA-TTAATAAGAATT-TTATGAAA-T-TATATATT-AT-T-ATTAA
*
61386101 ATT-TATTATTAAGAATTTTATGAAATTATATATTATTATTAA
1 ATTATATTAATAAGAATTTTATGAAATTATATATTATTATTAA
*
61386143 ATTATATGTAATAATAATTTTA
1 ATTATAT-TAATAAGAATTTTA
61386165 AATTTTATTA
Statistics
Matches: 86, Mismatches: 17, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
42 6 0.07
43 10 0.12
44 27 0.31
45 10 0.12
46 9 0.10
47 15 0.17
48 3 0.03
49 6 0.07
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (43 bp):
ATTATATTAATAAGAATTTTATGAAATTATATATTATTATTAA
Found at i:61386183 original size:51 final size:51
Alignment explanation
Indices: 61386114--61386212 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
61386104 TATTATTAAG
* *
61386114 AATTTTATGAAATTATATATTATT-ATTAAATTATATGTAATAATAATTTTA
1 AATTTTATGAAATCATATATT-TTAATTAAAATATATGTAATAATAATTTTA
* * * *
61386165 AATTTTATTAAGTCATATATTTTAATTAAAATATATTTAATATTAATT
1 AATTTTATGAAATCATATATTTTAATTAAAATATATGTAATAATAATT
61386213 ATTCCAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.05
51 39 0.95
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (51 bp):
AATTTTATGAAATCATATATTTTAATTAAAATATATGTAATAATAATTTTA
Found at i:61386243 original size:59 final size:57
Alignment explanation
Indices: 61386128--61386364 Score: 154
Period size: 51 Copynumber: 4.1 Consensus size: 57
61386118 TTATGAAATT
* * * *
61386128 ATATATTATT-ATTAAATTATATGTAATAATAATT-TTAAATT-T-TATTA-AG--TC
1 ATATATT-TTAATTAAAATATATTTAATATTAATTATTAAATTATATTTTATAGTATC
*
61386179 ATATATTTTAATTAAAATATATTTAATATTAATTATTCCAAATTATCTTTTATAGTATC
1 ATATATTTTAATTAAAATATATTTAATATTAATTATT--AAATTATATTTTATAGTATC
* * ** * *
61386238 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATT-AA-TA-ATTTTATTA-AATT
1 ATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTAAATTATATTTTA-TAGTATC
* * *
61386299 ATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATC
1 ATATATTTTAATTAAAATATATTTAATATTAATTA--TTAAATTATATTTTATAGTATC
61386358 ATATATT
1 ATATATT
61386365 ATGATTTGAG
Statistics
Matches: 143, Mismatches: 20, Indels: 38
0.71 0.10 0.19
Matches are distributed among these distances:
50 2 0.01
51 28 0.20
52 2 0.01
54 15 0.10
55 5 0.03
56 7 0.05
57 5 0.03
58 4 0.03
59 25 0.17
60 8 0.06
61 15 0.10
62 4 0.03
63 5 0.03
64 1 0.01
65 4 0.03
66 13 0.09
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATATATTTTAATTAAAATATATTTAATATTAATTATTAAATTATATTTTATAGTATC
Found at i:61386274 original size:66 final size:64
Alignment explanation
Indices: 61386203--61386403 Score: 199
Period size: 59 Copynumber: 3.2 Consensus size: 64
61386193 AAATATATTT
*
61386203 AATATTAATTATTCCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATT--AAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
61386268 G
64 G
* * * * *
61386269 AATATTAATTATT-AA-TA-ATTTTATTA-AATTATATATT-TTAATT-A-T-AATAT-ATTTAA
1 AATATTAATTATTAAATTATATTTTA-TAGTATCATATATTATGATTTGAGTAAAT-TCATATAA
*
61386325 T
64 G
* *
61386326 AATAATT-A-TGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
1 AAT-ATTAATTATTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
61386389 AATATTAATTATTAA
1 AATATTAATTATTAA
61386404 GAATTTTATT
Statistics
Matches: 105, Mismatches: 16, Indels: 30
0.70 0.11 0.20
Matches are distributed among these distances:
56 3 0.03
57 13 0.12
58 9 0.09
59 16 0.15
60 8 0.08
61 15 0.14
62 9 0.09
63 14 0.13
64 5 0.05
66 13 0.12
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:61386305 original size:61 final size:61
Alignment explanation
Indices: 61386238--61386425 Score: 201
Period size: 61 Copynumber: 3.1 Consensus size: 61
61386228 TTATAGTATC
61386238 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAATAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAATAATTTTATTAAATT
* * * * * * *
61386299 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTAT-ATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAATAATTTTATTA-AAT
*
61386357 C
61 T
*
61386358 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAATAATTTTATTAAATT
61386419 ATATATT
1 ATATATT
61386426 TTAATTATAA
Statistics
Matches: 98, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.18
60 17 0.17
61 25 0.26
62 8 0.08
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAATAATTTTATTAAATT
Found at i:61386319 original size:18 final size:18
Alignment explanation
Indices: 61386273--61386320 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
61386263 TATAAGAATA
*
61386273 TTAATTATTA-ATA-ATT
1 TTAATTATAATATATATT
61386289 TT-ATTA-AATTATATATT
1 TTAATTATAA-TATATATT
61386306 TTAATTATAATATAT
1 TTAATTATAATATAT
61386321 TTAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 5 0.19
17 5 0.19
18 9 0.35
19 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATAATATATATT
Found at i:61386325 original size:15 final size:15
Alignment explanation
Indices: 61386290--61386341 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
61386280 TTAATAATTT
*
61386290 TATTAAATTAT-ATA
1 TATTTAATTATAATA
61386304 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
61386318 TATTTAATAATAAT-
1 TATTTAATTATAATA
61386332 TATGTTAATT
1 TAT-TTAATT
61386342 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:61386440 original size:16 final size:16
Alignment explanation
Indices: 61386419--61386460 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
61386409 TTATTAAATT
*
61386419 ATATATTTTAATTATA
1 ATATATTTTAATAATA
61386435 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
61386450 AT-TATGTTTAA
1 ATATAT-TTTAA
61386461 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:61386445 original size:15 final size:15
Alignment explanation
Indices: 61386410--61386451 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
61386400 TTAAGAATTT
*
61386410 TATTAAATTAT-ATA
1 TATTTAATTATAATA
61386424 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
61386438 TATTTAATAATAAT
1 TATTTAATTATAAT
61386452 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:61386457 original size:120 final size:120
Alignment explanation
Indices: 61386165--61386462 Score: 499
Period size: 120 Copynumber: 2.5 Consensus size: 120
61386155 AATAATTTTA
* * * * * *
61386165 AATTTTATTAAGTCATATATTTTAATTAAAATATATTTAATATTAATTAT-TCCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGT-TAAATTATATTT
*
61386229 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAT
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
61386285 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
61386350 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
61386405 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
61386463 ATGATTAAAT
Statistics
Matches: 167, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
120 161 0.96
121 6 0.04
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:61386686 original size:45 final size:44
Alignment explanation
Indices: 61386606--61386696 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 44
61386596 ACCTCTATTC
61386606 CATTCAACCAAACACAAGATGACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATGACTATTACGCCTCTATTCCATTA
* * *
61386650 CATTCAACCAAACA-ATTGATTTACTATTACGTCTCTATTCCATTA
1 CATTCAACCAAACACA-AGA-TGACTATTACGCCTCTATTCCATTA
61386695 CA
1 CA
61386697 CCTCTATTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.38
45 25 0.60
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATGACTATTACGCCTCTATTCCATTA
Found at i:61386701 original size:16 final size:16
Alignment explanation
Indices: 61386682--61386712 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61386672 ACTATTACGT
*
61386682 CTCTATTCCATTACAC
1 CTCTATTCCAATACAC
61386698 CTCTATTCCAATACA
1 CTCTATTCCAATACA
61386713 GCGAACCAAA
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:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (16 bp):
CTCTATTCCAATACAC
Found at i:61386840 original size:48 final size:48
Alignment explanation
Indices: 61386755--61386850 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
61386745 TATAAGTGCT
* * *
61386755 CATATAACTATAAATAAATTGTTATACAACCATACTTACTTTTATCGA
1 CATATAACTACAAATAAATTGTCATACAACCACACTTACTTTTATCGA
*
61386803 CATATAACTACAAATAAATTGTCATA-TACCAACACTTACTTTTATCGA
1 CATATAACTACAAATAAATTGTCATACAACC-ACACTTACTTTTATCGA
61386851 TAATCAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 3 0.07
48 40 0.93
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.35
Consensus pattern (48 bp):
CATATAACTACAAATAAATTGTCATACAACCACACTTACTTTTATCGA
Found at i:61400943 original size:5 final size:5
Alignment explanation
Indices: 61400933--61400966 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
61400923 AGATGTCTTG
61400933 TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGT
1 TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGT
61400967 GCAGCACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.18, C:0.00, G:0.21, T:0.62
Consensus pattern (5 bp):
TTGTA
Found at i:61402219 original size:23 final size:23
Alignment explanation
Indices: 61402184--61402228 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
61402174 CACTTAGCAT
*
61402184 TTTTAGCTCAATATGTAT-TAATA
1 TTTTACCTCAATAT-TATATAATA
*
61402207 TTTTACCTTAATATTATATAAT
1 TTTTACCTCAATATTATATAAT
61402229 GCAATATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (23 bp):
TTTTACCTCAATATTATATAATA
Found at i:61404519 original size:25 final size:25
Alignment explanation
Indices: 61404460--61404507 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
61404450 GGTAGGATAT
* *
61404460 GATATGTTATGCTATGATTTGATTC
1 GATATGATATGCTATGATCTGATTC
*
61404485 GATATGATATGCTATGGTCTGAT
1 GATATGATATGCTATGATCTGAT
61404508 CTGATCTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (25 bp):
GATATGATATGCTATGATCTGATTC
Found at i:61404519 original size:30 final size:30
Alignment explanation
Indices: 61404455--61404512 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
61404445 ATGGGGGTAG
* *
61404455 GATATGATATGTTATGCTATGATTTGATTC
1 GATATGATATGCTATGCTATGATCTGATTC
* *
61404485 GATATGATATGCTATGGTCTGATCTGAT
1 GATATGATATGCTATGCTATGATCTGAT
61404513 CTGATATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (30 bp):
GATATGATATGCTATGCTATGATCTGATTC
Found at i:61407859 original size:44 final size:42
Alignment explanation
Indices: 61407714--61407872 Score: 159
Period size: 42 Copynumber: 3.8 Consensus size: 42
61407704 CAAAAAGCTC
* * *
61407714 ATACAATGCCAACGTCCCAGACGTGGTCTT--A--T-ATCAA
1 ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAATCAA
* * *
61407751 ATAACGATGCCACTGTCCCAGACAGGGTCTTACACGTAATCAT
1 AT-ACGATGCCAATGTCCCAGACATGGTCTTACACGTAATCAA
*
61407794 ATACGATGCCAATGTCTCAGACATGGTCTTACACGTAAATCCCAA
1 ATACGATGCCAATGTCCCAGACATGGTCTTACACGT-AAT--CAA
* *
61407839 AT-TGATGCCAATGTCCCAGACGTGGTCTTACACG
1 ATACGATGCCAATGTCCCAGACATGGTCTTACACG
61407873 ATATCACATA
Statistics
Matches: 100, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
37 2 0.02
38 23 0.23
40 1 0.01
42 32 0.32
43 9 0.09
44 29 0.29
45 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (42 bp):
ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAATCAA
Found at i:61408978 original size:13 final size:13
Alignment explanation
Indices: 61408960--61408984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61408950 ACAAACGATA
61408960 AAATTTTCACACG
1 AAATTTTCACACG
61408973 AAATTTTCACAC
1 AAATTTTCACAC
61408985 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:61412989 original size:41 final size:41
Alignment explanation
Indices: 61412944--61413119 Score: 298
Period size: 41 Copynumber: 4.3 Consensus size: 41
61412934 AATTTAACAT
* *
61412944 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* *
61412985 ATTCATATCACCGGCACTTAGCCTACTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
61413026 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* *
61413067 ATTCAGATCATCGACACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
61413108 ATTCAGATCACC
1 ATTCAGATCACC
61413120 AATTTCAAAC
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 126 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:61417459 original size:16 final size:16
Alignment explanation
Indices: 61417440--61417485 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
61417430 ACCCAAATCT
61417440 AAAATGACTTGAACCC
1 AAAATGACTTGAACCC
* *
61417456 AAAATGACTTTAACCT
1 AAAATGACTTGAACCC
* *
61417472 GAAATGACCTGAAC
1 AAAATGACTTGAAC
61417486 AAGTAATTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.22
Consensus pattern (16 bp):
AAAATGACTTGAACCC
Found at i:61417506 original size:23 final size:23
Alignment explanation
Indices: 61417473--61417531 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
61417463 CTTTAACCTG
*
61417473 AAATGACCTGAACAAGTAATTCA
1 AAATGATCTGAACAAGTAATTCA
61417496 AAATGATCTGAACAAGTAATTCA
1 AAATGATCTGAACAAGTAATTCA
61417519 AAATGATCTGAAC
1 AAATGATCTGAAC
61417532 TTAAATGAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (23 bp):
AAATGATCTGAACAAGTAATTCA
Found at i:61420940 original size:16 final size:16
Alignment explanation
Indices: 61420919--61420949 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61420909 TTATATTCGA
*
61420919 TAAAAATTTTGCATAT
1 TAAAAATTTTACATAT
61420935 TAAAAATTTTACATA
1 TAAAAATTTTACATA
61420950 AATTTTAACA
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:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAAAATTTTACATAT
Found at i:61428039 original size:27 final size:28
Alignment explanation
Indices: 61428009--61428075 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 28
61427999 GTATAGGATG
* *
61428009 ATTTTAAAATAATTATTATATAAAA-CA
1 ATTTTAAAATAATAACTATATAAAAGCA
** *
61428036 A-TTTGGAATAA-AACTATATAAAAGTA
1 ATTTTAAAATAATAACTATATAAAAGCA
61428062 ATTTTAAAATAATA
1 ATTTTAAAATAATA
61428076 TGTAGTAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
25 10 0.33
26 10 0.33
27 9 0.30
28 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.37
Consensus pattern (28 bp):
ATTTTAAAATAATAACTATATAAAAGCA
Found at i:61429225 original size:22 final size:22
Alignment explanation
Indices: 61429200--61429245 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
61429190 CTTGGCTTAA
*
61429200 TGGATTTGATTTATTTTGTGTT
1 TGGATTTGATTTATTTTGGGTT
*
61429222 TGGATTTGATTTGTTTTGGGTT
1 TGGATTTGATTTATTTTGGGTT
61429244 TG
1 TG
61429246 TTTCTGTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.00, G:0.28, T:0.61
Consensus pattern (22 bp):
TGGATTTGATTTATTTTGGGTT
Found at i:61429234 original size:17 final size:16
Alignment explanation
Indices: 61429214--61429255 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
61429204 TTTGATTTAT
61429214 TTTGTGTTTGGATTTG
1 TTTGTGTTTGGATTTG
*
61429230 ATTTGT-TTTGGGTTTG
1 -TTTGTGTTTGGATTTG
*
61429246 TTTCTGTTTG
1 TTTGTGTTTG
61429256 CCTGGGCCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 4 0.18
16 13 0.59
17 5 0.23
ACGTcount: A:0.05, C:0.02, G:0.29, T:0.64
Consensus pattern (16 bp):
TTTGTGTTTGGATTTG
Found at i:61430334 original size:23 final size:24
Alignment explanation
Indices: 61430308--61430355 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
61430298 GTCTCAACAG
61430308 AATTAAA-ATGATAAATTTTGTAA
1 AATTAAAGATGATAAATTTTGTAA
* * *
61430331 AATTAAAGTTGTTAAATTTTTTAA
1 AATTAAAGATGATAAATTTTGTAA
61430355 A
1 A
61430356 TCTAGGATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (24 bp):
AATTAAAGATGATAAATTTTGTAA
Found at i:61432361 original size:15 final size:16
Alignment explanation
Indices: 61432329--61432364 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
61432319 AATCTCTTCA
61432329 AAATTAATGAAATCAT
1 AAATTAATGAAATCAT
*
61432345 AAATTAAT-AAATGAT
1 AAATTAATGAAATCAT
61432360 AAATT
1 AAATT
61432365 TATATTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (16 bp):
AAATTAATGAAATCAT
Found at i:61433636 original size:24 final size:24
Alignment explanation
Indices: 61433595--61433661 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
61433585 TATTTTAAAA
*
61433595 ATTTT-AAAAAATTAAAAAAAAGT
1 ATTTTAAAAAAATTTAAAAAAAGT
61433618 ATTTTAAAAAAATTTAAAAAAAGT
1 ATTTTAAAAAAATTTAAAAAAAGT
* *
61433642 ATTTTAAAAATATTTTAAAA
1 ATTTTAAAAAAATTTAAAAA
61433662 TTAAAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 5 0.12
24 35 0.88
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (24 bp):
ATTTTAAAAAAATTTAAAAAAAGT
Found at i:61433650 original size:11 final size:11
Alignment explanation
Indices: 61433585--61433702 Score: 72
Period size: 11 Copynumber: 10.9 Consensus size: 11
61433575 GGCCCATTTT
61433585 TATTTT-AAAA
1 TATTTTAAAAA
61433595 -ATTTTAAAAA
1 TATTTTAAAAA
**
61433605 -ATTAAAAAAAA
1 TATT-TTAAAAA
61433616 GTATTTTAAAAA
1 -TATTTTAAAAA
* *
61433628 AATTTAAAAAAA
1 TATTT-TAAAAA
61433640 GTATTTTAAAAA
1 -TATTTTAAAAA
61433652 TATTTT--AAA
1 TATTTTAAAAA
61433661 -A--TTAAAAA
1 TATTTTAAAAA
* *
61433669 AATTTAAAAAAA
1 TATTT-TAAAAA
61433681 GTATTTTAAAAA
1 -TATTTTAAAAA
61433693 TATTTTAAAA
1 TATTTTAAAA
61433703 TTAAAAAAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
6 2 0.02
8 4 0.05
9 9 0.11
10 7 0.08
11 26 0.31
12 25 0.30
13 11 0.13
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:61433678 original size:17 final size:17
Alignment explanation
Indices: 61433645--61433678 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
61433635 AAAAAGTATT
* *
61433645 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTAAAAA
61433662 TTAAAAAAATTTAAAAA
1 TTAAAAAAATTTAAAAA
61433679 AAGTATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAA
Found at i:61433679 original size:40 final size:41
Alignment explanation
Indices: 61433621--61433751 Score: 230
Period size: 41 Copynumber: 3.2 Consensus size: 41
61433611 AAAAAGTATT
61433621 TTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAA
61433662 TTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAA
* *
61433703 TTAAAAAAA-TTAAAAAAAGTA-TGTAAAAATATTTTACAA
1 TTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAA
61433742 TTAAAAAAAT
1 TTAAAAAAAT
61433752 AAATATATTT
Statistics
Matches: 87, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
39 25 0.29
40 12 0.14
41 50 0.57
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (41 bp):
TTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:61434028 original size:17 final size:17
Alignment explanation
Indices: 61433989--61434028 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
61433979 ATATTACTTT
*
61433989 AATATATATATAAATAC
1 AATATTTATATAAATAC
61434006 AATATTTATATTAAATA-
1 AATATTTATA-TAAATAC
61434023 AATATT
1 AATATT
61434029 GTTCGAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATTTATATAAATAC
Found at i:61437111 original size:14 final size:14
Alignment explanation
Indices: 61437092--61437120 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
61437082 TCCTTTCAGG
61437092 TACTTTCCGTGTTT
1 TACTTTCCGTGTTT
61437106 TACTTTCCGTGTTT
1 TACTTTCCGTGTTT
61437120 T
1 T
61437121 GGAGCTGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.14, T:0.59
Consensus pattern (14 bp):
TACTTTCCGTGTTT
Found at i:61437291 original size:16 final size:17
Alignment explanation
Indices: 61437269--61437306 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
61437259 AAAAAGTACA
*
61437269 AATTTTTAAAAATAATT
1 AATTTTAAAAAATAATT
61437286 AATTTTAAAAAATAATT
1 AATTTTAAAAAATAATT
61437303 AATT
1 AATT
61437307 GCTAACATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTTAAAAAATAATT
Found at i:61444290 original size:28 final size:28
Alignment explanation
Indices: 61444228--61444282 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
61444218 AAAATATTAA
*
61444228 ATATAAAAAATAAAAATTATGAAAATTG
1 ATATAAAAAATAAAAAATATGAAAATTG
61444256 ATATAAAAAATATAAAAATAT-AAAATT
1 ATATAAAAAATA-AAAAATATGAAAATT
61444283 CTAATAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (28 bp):
ATATAAAAAATAAAAAATATGAAAATTG
Found at i:61444767 original size:4 final size:4
Alignment explanation
Indices: 61444760--61444802 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
61444750 ATAATATATA
*
61444760 TATG TATG TATG TATG TATG TATG TATG TATG TATG TCTG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
61444803 CTGCTGGCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.23, C:0.02, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:61448671 original size:13 final size:13
Alignment explanation
Indices: 61448653--61448694 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
61448643 GAATATTGAT
61448653 AAATATTTTATAA
1 AAATATTTTATAA
*
61448666 AAATA-TTTAAAA
1 AAATATTTTATAA
*
61448678 TAAATATTTTTTAA
1 -AAATATTTTATAA
61448692 AAA
1 AAA
61448695 ATTAGCATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 6 0.25
13 13 0.54
14 5 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATATTTTATAA
Found at i:61449323 original size:12 final size:12
Alignment explanation
Indices: 61449306--61449330 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61449296 TTTACATGTG
61449306 TTTAAATTTTCA
1 TTTAAATTTTCA
61449318 TTTAAATTTTCA
1 TTTAAATTTTCA
61449330 T
1 T
61449331 CGTTTATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTAAATTTTCA
Found at i:61465568 original size:7 final size:7
Alignment explanation
Indices: 61465556--61465591 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
61465546 ATCATCAAAC
61465556 ACATATT
1 ACATATT
61465563 ACATATT
1 ACATATT
*
61465570 ATATATT
1 ACATATT
61465577 ACATATT
1 ACATATT
61465584 ACATATT
1 ACATATT
61465591 A
1 A
61465592 TAAGATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
ACATATT
Found at i:61468820 original size:27 final size:30
Alignment explanation
Indices: 61468790--61468850 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 30
61468780 CATTTTAAGG
61468790 CATAATTAAATT-TGAGTC-TATATG-TTT
1 CATAATTAAATTCTGAGTCATATATGATTT
* *
61468817 CAT-ATTTATTTCTGAGTCATATATGATTT
1 CATAATTAAATTCTGAGTCATATATGATTT
61468846 -ATAAT
1 CATAAT
61468851 AGCTTTCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
26 6 0.21
27 9 0.32
28 8 0.29
29 5 0.18
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (30 bp):
CATAATTAAATTCTGAGTCATATATGATTT
Found at i:61473639 original size:31 final size:31
Alignment explanation
Indices: 61473596--61473667 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
61473586 ATTTAGTCCA
61473596 TGTA-TTTT-AATTTGATT-AATTTCAATCCT
1 TGTACTTTTCAATTTG-TTCAATTTCAATCCT
* * *
61473625 TTTACTTTTCAATTTGTTCAATTTTAGTCCT
1 TGTACTTTTCAATTTGTTCAATTTCAATCCT
61473656 TGTAC-TTTCAAT
1 TGTACTTTTCAAT
61473668 CTTTTGAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 3 0.08
30 13 0.36
31 20 0.56
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.56
Consensus pattern (31 bp):
TGTACTTTTCAATTTGTTCAATTTCAATCCT
Found at i:61474404 original size:34 final size:31
Alignment explanation
Indices: 61474342--61474418 Score: 77
Period size: 34 Copynumber: 2.4 Consensus size: 31
61474332 TAGGCTCACC
**
61474342 TATATGATTTTTTTAATTTTTTTAAAAATATT
1 TATATGATTTTTTTAATTTTAATAAAAAT-TT
61474374 TATATGATTTTATTTTAATATTTAAT-AAAATTT
1 TATATGA-TTT-TTTTAAT-TTTAATAAAAATTT
*
61474407 TATA-CATTTTTT
1 TATATGATTTTTT
61474419 ATTTATTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 3 0.08
31 3 0.08
32 8 0.21
33 9 0.23
34 12 0.31
35 4 0.10
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (31 bp):
TATATGATTTTTTTAATTTTAATAAAAATTT
Found at i:61480645 original size:61 final size:61
Alignment explanation
Indices: 61480580--61480768 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
61480570 TATATAATTT
*
61480580 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATAA
1 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTTAAATCATAATATATGATAA
* * * * * * * **
61480641 AATAAAA-T-ATAATTTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAAAATATATAATTT
1 AATAAAATTCTTAA--TAATCAAT-ATTCTTATATGAATTTACTTA-AATCATAATATATGATAA
* *
61480700 AATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTTAAATCATAATATATGATAC
1 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTTAAATCATAATATATGATAA
*
61480761 TATAAAAT
1 AATAAAAT
61480769 ATAATTTAAC
Statistics
Matches: 97, Mismatches: 21, Indels: 20
0.70 0.15 0.14
Matches are distributed among these distances:
58 2 0.02
59 34 0.35
60 17 0.18
61 41 0.42
62 3 0.03
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (61 bp):
AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTTAAATCATAATATATGATAA
Found at i:61480692 original size:16 final size:16
Alignment explanation
Indices: 61480638--61480694 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
61480628 TAATATATGA
* *
61480638 TAAAATAAAATATAATT
1 TAAAATATATTATAA-T
* *
61480655 TAACATA-ATTATTAT
1 TAAAATATATTATAAT
61480670 T-AAATATATTATAAT
1 TAAAATATATTATAAT
61480685 TAAAATATAT
1 TAAAATATAT
61480695 AATTTAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 4 0.12
15 10 0.30
16 13 0.39
17 6 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATATATTATAAT
Found at i:61480814 original size:18 final size:17
Alignment explanation
Indices: 61480791--61480827 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
61480781 AATTATTATT
61480791 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
61480807 AAATATATGATTTAATA
1 AAATATATGATTTAATA
61480824 AAAT
1 AAAT
61480828 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:61480839 original size:120 final size:120
Alignment explanation
Indices: 61480530--61480828 Score: 517
Period size: 120 Copynumber: 2.5 Consensus size: 120
61480520 ATTTAATCAT
*
61480530 ATTTAAACATAAATTATTATTAAATATATTCTAATTAAAATATATAATTTAATAAAATTCTTAAT
1 ATTT-AACAT-AATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
*
61480595 AATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATAAAATAAAATATA
64 AATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATAAAATAAAATATA
61480652 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
* **
61480717 TTAATATTCTTATATGAATTTACTTAAATCATAATATATGATACTATAAAATATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATAAAATAAAATATA
* *
61480772 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
61480829 TAAAATAATT
Statistics
Matches: 170, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
120 161 0.95
121 5 0.03
122 4 0.02
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATAAAATAAAATATA
Found at i:61480884 original size:101 final size:95
Alignment explanation
Indices: 61480767--61481098 Score: 352
Period size: 91 Copynumber: 3.5 Consensus size: 95
61480757 ATACTATAAA
* * *
61480767 ATATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTTAA
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAA-TAAAATATAT-ATTT-ATAAAATTT-A
*
61480832 AATAATTATAACTAATAAATTTTCTTATATGAATTT
62 AATAATT-TGA-TAATAAATTTTCTTATATGAATTT
* *
61480868 GTATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAA--T--
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAATAA-AATATAT-ATTT-ATAAAATTTAA
* *
61480929 -T--CTTGATAATAAATTTTTTTATATGAATTT
63 ATAATTTGATAATAAATTTTCTTATATGAATTT
61480959 ATATAATTTAAAATAATTAATATTAAATATAATTTAAT--AAT-TATA--TAT--AATTTCATAA
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAATAAAATATATATTTATAAAATTT-A-AA
61481017 -AATTCTTGATAATAAATTTTCTTATATGAATTT
64 TAA-T-TTGATAATAAATTTTCTTATATGAATTT
*
61481050 ATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATA
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAATAA-AATATATA
61481099 ATTTCATATA
Statistics
Matches: 202, Mismatches: 13, Indels: 38
0.80 0.05 0.15
Matches are distributed among these distances:
81 2 0.01
83 3 0.01
84 1 0.00
86 1 0.00
87 3 0.01
88 3 0.01
91 124 0.61
92 2 0.01
93 1 0.00
94 2 0.01
95 5 0.02
99 1 0.00
100 3 0.01
101 51 0.25
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (95 bp):
ATATAATTTAAAATAATTAATATTAAATATAATTTAATAAAATATATATTTATAAAATTTAAATA
ATTTGATAATAAATTTTCTTATATGAATTT
Found at i:61480940 original size:91 final size:91
Alignment explanation
Indices: 61480844--61481141 Score: 524
Period size: 91 Copynumber: 3.3 Consensus size: 91
61480834 TAATTATAAC
* *
61480844 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
61480909 AATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTGA
*
61480935 TAATAAATTTTTTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
61481000 TATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTGA
61481026 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
* * *
61481091 GATATATAATTTCATATAATTCTTAA
66 AATATATAATTTCATAAAATTCTTGA
*
61481117 TAATAAATGTTCTTATATGAATTTA
1 TAATAAATTTTCTTATATGAATTTA
61481142 CTAAAATCAT
Statistics
Matches: 198, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 198 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTGA
Found at i:61480961 original size:10 final size:9
Alignment explanation
Indices: 61480946--61481111 Score: 57
Period size: 10 Copynumber: 18.2 Consensus size: 9
61480936 AATAAATTTT
61480946 TTTATATGAA
1 TTTATAT-AA
61480956 TTTATATAA
1 TTTATATAA
*
61480965 TTTAAAATAA
1 TTT-ATATAA
61480975 -TTA-AT-A
1 TTTATATAA
*
61480981 TTAAATATAA
1 TT-TATATAA
61480991 TTTA-ATAA
1 TTTATATAA
61480999 TTATATATAA
1 TT-TATATAA
*
61481009 TTTCATAAAA
1 TTT-ATATAA
61481019 TTCT-TGATAA
1 TT-TAT-ATAA
* **
61481029 --TAAATTT
1 TTTATATAA
61481036 TCTTATATGAA
1 T-TTATAT-AA
61481047 TTTATATAA
1 TTTATATAA
*
61481056 TTTAAAATAA
1 TTT-ATATAA
61481066 -TTA-AT-A
1 TTTATATAA
*
61481072 TTAAATATAA
1 TT-TATATAA
61481082 TTTA-ATAA
1 TTTATATAA
*
61481090 TGATATATAA
1 T-TTATATAA
61481100 TTTCATATAA
1 TTT-ATATAA
61481110 TT
1 TT
61481112 CTTAATAATA
Statistics
Matches: 117, Mismatches: 16, Indels: 46
0.65 0.09 0.26
Matches are distributed among these distances:
6 2 0.02
7 9 0.08
8 15 0.13
9 27 0.23
10 62 0.53
11 2 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (9 bp):
TTTATATAA
Found at i:61482409 original size:39 final size:39
Alignment explanation
Indices: 61482355--61482436 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
61482345 TTATCTTAAG
61482355 AAAAAAAAATTATATTAATTACTATTAATATCATGAATC
1 AAAAAAAAATTATATTAATTACTATTAATATCATGAATC
*
61482394 AAAAACAAATTATATTAATTACTATTAATATCATGAATC
1 AAAAAAAAATTATATTAATTACTATTAATATCATGAATC
61482433 AAAA
1 AAAA
61482437 GGTGAACACT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (39 bp):
AAAAAAAAATTATATTAATTACTATTAATATCATGAATC
Found at i:61492211 original size:29 final size:29
Alignment explanation
Indices: 61492179--61492327 Score: 124
Period size: 30 Copynumber: 5.0 Consensus size: 29
61492169 TAACCCTGTT
* *
61492179 ACTTTTTGAAATTTATATTTTGACCCCAA
1 ACTTTTTGAAAATTACATTTTGACCCCAA
**
61492208 ACTTTTCT-AAAATTACATTTCAACCCCTAA
1 ACTTTT-TGAAAATTACATTTTGACCCC-AA
* * * *
61492238 ACTTTCTCAAAATTACACTTTGACCCTTAA
1 ACTTTTTGAAAATTACATTTTGACCC-CAA
* *
61492268 ACTTTTTGAAAATTACATTTTGGCCCCCAT
1 ACTTTTTGAAAATTACATTTT-GACCCCAA
*
61492298 A-TTTTCCT-AAAATTACATTTTTACCCCAA
1 ACTTTT--TGAAAATTACATTTTGACCCCAA
61492327 A
1 A
61492328 TATTTTGCGT
Statistics
Matches: 95, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
29 32 0.34
30 58 0.61
31 5 0.05
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (29 bp):
ACTTTTTGAAAATTACATTTTGACCCCAA
Found at i:61492221 original size:30 final size:29
Alignment explanation
Indices: 61492195--61492327 Score: 128
Period size: 30 Copynumber: 4.5 Consensus size: 29
61492185 TGAAATTTAT
61492195 ATTTTGACCCCAAACTTTTCTAAAATTAC
1 ATTTTGACCCCAAACTTTTCTAAAATTAC
**
61492224 ATTTCAACCCCTAAAC-TTTCTCAAAATTAC
1 ATTTTGACCCC-AAACTTTTCT-AAAATTAC
* *
61492254 ACTTTGACCCTTAAACTTTT-TGAAAATTAC
1 ATTTTGACCC-CAAACTTTTCT-AAAATTAC
* *
61492284 ATTTTGGCCCCCATA-TTTTCCTAAAATTAC
1 ATTTT-GACCCCAAACTTTT-CTAAAATTAC
*
61492314 ATTTTTACCCCAAA
1 ATTTTGACCCCAAA
61492328 TATTTTGCGT
Statistics
Matches: 83, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
29 24 0.29
30 51 0.61
31 8 0.10
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.38
Consensus pattern (29 bp):
ATTTTGACCCCAAACTTTTCTAAAATTAC
Found at i:61492242 original size:59 final size:60
Alignment explanation
Indices: 61492157--61492287 Score: 142
Period size: 59 Copynumber: 2.2 Consensus size: 60
61492147 CAAAAAAATA
* ** * * * * *
61492157 AAAATTACATTTTAACCCTGTTACTTTTTGAAATTTATATTTTGACCC-CAAACTTTTCT-
1 AAAATTACATTTCAACCCTGAAACTTTCTCAAAATTACACTTTGACCCTCAAACTTTT-TG
*
61492216 AAAATTACATTTCAACCCCT-AAACTTTCTCAAAATTACACTTTGACCCTTAAACTTTTTG
1 AAAATTACATTTCAA-CCCTGAAACTTTCTCAAAATTACACTTTGACCCTCAAACTTTTTG
61492276 AAAATTACATTT
1 AAAATTACATTT
61492288 TGGCCCCCAT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 36 0.60
60 24 0.40
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (60 bp):
AAAATTACATTTCAACCCTGAAACTTTCTCAAAATTACACTTTGACCCTCAAACTTTTTG
Found at i:61492844 original size:4 final size:4
Alignment explanation
Indices: 61492835--61492893 Score: 56
Period size: 4 Copynumber: 15.5 Consensus size: 4
61492825 TGACCCGAAG
*
61492835 AAGA AAGA AA-A AAGG AAGA AA-A AAGA AAG- AA-A AAGA AAGA AAGGGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA--GA
61492881 AAGA AA-A AAGA AA
1 AAGA AAGA AAGA AA
61492894 AAAATAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
3 13 0.28
4 29 0.63
6 4 0.09
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:61492867 original size:10 final size:11
Alignment explanation
Indices: 61492835--61492897 Score: 78
Period size: 11 Copynumber: 6.0 Consensus size: 11
61492825 TGACCCGAAG
61492835 AAGAAAGAAAA
1 AAGAAAGAAAA
*
61492846 AAGGAAGAAAA
1 AAGAAAGAAAA
61492857 AAGAAAG-AAA
1 AAGAAAGAAAA
61492867 AAGAAAG-AAA
1 AAGAAAGAAAA
**
61492877 GGGAAAGAAAA
1 AAGAAAGAAAA
61492888 AAGAAA-AAAA
1 AAGAAAGAAAA
61492898 TAAAAATTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
10 22 0.49
11 23 0.51
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAAA
Found at i:61493917 original size:18 final size:18
Alignment explanation
Indices: 61493894--61494040 Score: 109
Period size: 18 Copynumber: 7.7 Consensus size: 18
61493884 TGTTTCTTTC
61493894 TTTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
* *
61493912 TTTTCAAAAATTCTCATG
1 TTTTCAAAAATTTTCGTG
* *
61493930 -TTTCAAAAATTTTTGAG
1 TTTTCAAAAATTTTCGTG
61493947 TTTTCAAAATTTTCATGTTTTCGTG
1 TTTTCAAAA-----A--TTTTCGTG
*
61493972 TTTTCAAAAAAAATTCTCGTG
1 TTTTC---AAAAATTTTCGTG
*
61493993 TTTTCAAAAAAATTTCGTG
1 TTTTC-AAAAATTTTCGTG
* *
61494012 -TTTCAAAAATCTTCATG
1 TTTTCAAAAATTTTCGTG
61494029 TTTTCAAAAATT
1 TTTTCAAAAATT
61494041 ATTATTGTGT
Statistics
Matches: 102, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
17 23 0.23
18 38 0.37
19 12 0.12
21 12 0.12
23 2 0.02
25 11 0.11
28 4 0.04
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.46
Consensus pattern (18 bp):
TTTTCAAAAATTTTCGTG
Found at i:61493941 original size:35 final size:34
Alignment explanation
Indices: 61493895--61493966 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 34
61493885 GTTTCTTTCT
*
61493895 TTTCAAAAATTTTCGTGTTTTCAAAAATTCTCATG
1 TTTCAAAAATTTTCGAGTTTTC-AAAATTCTCATG
* *
61493930 TTTCAAAAATTTTTGAGTTTTCAAAATTTTCATG
1 TTTCAAAAATTTTCGAGTTTTCAAAATTCTCATG
61493964 TTT
1 TTT
61493967 TCGTGTTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 14 0.41
35 20 0.59
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (34 bp):
TTTCAAAAATTTTCGAGTTTTCAAAATTCTCATG
Found at i:61493993 original size:21 final size:20
Alignment explanation
Indices: 61493965--61494020 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
61493955 ATTTTCATGT
61493965 TTTCGTGTTTTCAAAAAAAA
1 TTTCGTGTTTTCAAAAAAAA
61493985 TTCTCGTGTTTTC-AAAAAAA
1 TT-TCGTGTTTTCAAAAAAAA
61494005 TTTCGTG-TTTCAAAAA
1 TTTCGTGTTTTCAAAAA
61494021 TCTTCATGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.12
19 9 0.26
20 11 0.32
21 10 0.29
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (20 bp):
TTTCGTGTTTTCAAAAAAAA
Found at i:61501032 original size:19 final size:18
Alignment explanation
Indices: 61501005--61501043 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
61500995 GCGTATATAT
*
61501005 ATTTAAAACAGAATAATAA
1 ATTTAAAACAAAATAA-AA
*
61501024 ATTTTAAACAAAATAAAA
1 ATTTAAAACAAAATAAAA
61501042 AT
1 AT
61501044 CAAGTGCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (18 bp):
ATTTAAAACAAAATAAAA
Found at i:61509179 original size:21 final size:22
Alignment explanation
Indices: 61509150--61509196 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
61509140 CAGAAGGAGT
*
61509150 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
61509172 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
61509193 GAGT
1 GAGT
61509197 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Done.