Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 40 of 202
Found at i:11791818 original size:12 final size:10
Alignment explanation
Indices: 11791772--11791830 Score: 73
Period size: 11 Copynumber: 5.5 Consensus size: 10
11791762 TTTTTTAAGA
*
11791772 AGAATTTGAG
1 AGAAATTGAG
11791782 AGGAAATTGAG
1 A-GAAATTGAG
11791793 AGAAATTTGAG
1 AGAAA-TTGAG
11791804 AGAATATTGGAG
1 AGAA-ATT-GAG
11791816 AGAAATTGAG
1 AGAAATTGAG
11791826 AGAAA
1 AGAAA
11791831 GGATTTAGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 13 0.30
11 23 0.52
12 8 0.18
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (10 bp):
AGAAATTGAG
Found at i:11796315 original size:15 final size:14
Alignment explanation
Indices: 11796291--11796321 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
11796281 CCATGATTAA
11796291 TTTTATCATTTTAT
1 TTTTATCATTTTAT
11796305 TTTTCATCATTTTAT
1 TTTT-ATCATTTTAT
11796320 TT
1 TT
11796322 GTTTATTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATCATTTTAT
Found at i:11801081 original size:25 final size:26
Alignment explanation
Indices: 11801031--11801081 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
11801021 TATTATATAC
*
11801031 AAAAACAATTTTAAAATACTACGTAT
1 AAAAACAATTTTAAAATAATACGTAT
*
11801057 AAAAA-AA-TTTAAAAGTAATATGTAT
1 AAAAACAATTTTAAAA-TAATACGTAT
11801082 GTACATATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 7 0.32
25 10 0.45
26 5 0.23
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (26 bp):
AAAAACAATTTTAAAATAATACGTAT
Found at i:11803363 original size:49 final size:49
Alignment explanation
Indices: 11803307--11803507 Score: 330
Period size: 49 Copynumber: 4.1 Consensus size: 49
11803297 TATTTAATAA
* *
11803307 TAATTTTATACAGTGTTGAGCTTTTGATTTATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
* *
11803356 TAATTTTATAAAGTGTTGAGCTTTTGATTTATGATATTTAACTTAATTT
1 TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
11803405 TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
* * * *
11803454 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAACTT
1 TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
11803503 TAATT
1 TAATT
11803508 GTTTTTTTTC
Statistics
Matches: 144, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 144 1.00
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
Found at i:11804994 original size:15 final size:16
Alignment explanation
Indices: 11804966--11804995 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11804956 TAAATTCATA
11804966 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
11804982 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
11804996 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:11805015 original size:18 final size:17
Alignment explanation
Indices: 11804987--11805021 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11804977 ATTATTAAGA
*
11804987 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
11805004 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
11805022 TTAAGAATAA
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:11805435 original size:46 final size:44
Alignment explanation
Indices: 11805353--11805440 Score: 115
Period size: 46 Copynumber: 2.0 Consensus size: 44
11805343 ACACAGTTCC
* *
11805353 ATTCAACCAAACACAAGAATACTATTACAGTTCTATTCCATTTT
1 ATTCAACCAAACAAAAGAATACTATTACAGCTCTATTCCATTTT
*
11805397 ATTCAACCAAACAAAAGGATTACCTATTAC-GCCTCTATTCCATT
1 ATTCAACCAAACAAAA-GAATA-CTATTACAG-CTCTATTCCATT
11805441 ACAGCGAACC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 15 0.39
45 5 0.13
46 18 0.47
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.32
Consensus pattern (44 bp):
ATTCAACCAAACAAAAGAATACTATTACAGCTCTATTCCATTTT
Found at i:11818487 original size:16 final size:16
Alignment explanation
Indices: 11818456--11818491 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
11818446 ATGCGAAGAA
11818456 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
11818472 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
11818488 TATT
1 TATT
11818492 GAAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:11826086 original size:20 final size:20
Alignment explanation
Indices: 11826049--11826089 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
11826039 TTAAAAGGCA
* *
11826049 TATATTTATTCATCTAATAT
1 TATAATTATTCAACTAATAT
*
11826069 TATAATTATTCAAGTAATAT
1 TATAATTATTCAACTAATAT
11826089 T
1 T
11826090 GTTTGAATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (20 bp):
TATAATTATTCAACTAATAT
Found at i:11829248 original size:2 final size:2
Alignment explanation
Indices: 11829243--11829281 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
11829233 TTTTTTTTAA
11829243 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11829282 CATAACAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11851377 original size:20 final size:18
Alignment explanation
Indices: 11851330--11851378 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
11851320 TAAGATAAAC
11851330 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
11851347 ATTAAGA-TAATTACTTTAAT
1 ATTAA-ATTAA-TA-TTTAAT
11851367 ATTAAATTAATA
1 ATTAAATTAATA
11851379 AAATACTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 4 0.15
20 14 0.52
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:11874675 original size:17 final size:18
Alignment explanation
Indices: 11874661--11874703 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
11874651 TAAAAAAATT
11874661 ATAAAAAAT-TTAAAACA
1 ATAAAAAATATTAAAACA
11874678 ATAAAAAATATTAAAA-A
1 ATAAAAAATATTAAAACA
11874695 ATAATAAAA
1 ATAA-AAAA
11874704 CTCAGTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAAAAATATTAAAACA
Found at i:11881290 original size:33 final size:33
Alignment explanation
Indices: 11881253--11881323 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
11881243 ATATCATGCA
* *
11881253 TACCCTCCTAGGCTTAACACGTATTCTTAGAGT
1 TACCCTCCTAGGCTTAACACGAATCCTTAGAGT
* *
11881286 TACCCTCTTAGGCTTAACATGAATCCTTAGAGT
1 TACCCTCCTAGGCTTAACACGAATCCTTAGAGT
11881319 TACCC
1 TACCC
11881324 CTGCTAAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.32
Consensus pattern (33 bp):
TACCCTCCTAGGCTTAACACGAATCCTTAGAGT
Found at i:11881366 original size:16 final size:16
Alignment explanation
Indices: 11881345--11881417 Score: 55
Period size: 16 Copynumber: 4.6 Consensus size: 16
11881335 CCATGAGCTA
11881345 GTGAGCTAGCGAGGAG
1 GTGAGCTAGCGAGGAG
*
11881361 GTGAGCTAG-TA-GAG
1 GTGAGCTAGCGAGGAG
*
11881375 TGATGAGCTAGCAGAGTAG
1 -G-TGAGCTAGC-GAGGAG
*
11881394 G-GAGCTAGC-AGAGTG
1 GTGAGCTAGCGAG-GAG
11881409 GTGAGCTAG
1 GTGAGCTAG
11881418 TCAGGAGATA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
14 5 0.11
15 4 0.09
16 32 0.71
18 2 0.04
19 2 0.04
ACGTcount: A:0.27, C:0.11, G:0.44, T:0.18
Consensus pattern (16 bp):
GTGAGCTAGCGAGGAG
Found at i:11881382 original size:32 final size:32
Alignment explanation
Indices: 11881346--11881417 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 32
11881336 CATGAGCTAG
*
11881346 TGAGCTAGC-GAGGAGGTGAGCTAGTAGAGTGA
1 TGAGCTAGCAGAGGAGG-GAGCTAGCAGAGTGA
* *
11881378 TGAGCTAGCAGAGTAGGGAGCTAGCAGAGTGG
1 TGAGCTAGCAGAGGAGGGAGCTAGCAGAGTGA
11881410 TGAGCTAG
1 TGAGCTAG
11881418 TCAGGAGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 30 0.83
33 6 0.17
ACGTcount: A:0.28, C:0.11, G:0.43, T:0.18
Consensus pattern (32 bp):
TGAGCTAGCAGAGGAGGGAGCTAGCAGAGTGA
Found at i:11882557 original size:30 final size:30
Alignment explanation
Indices: 11882500--11882557 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
11882490 CACAGGCTGG
* * *
11882500 CACATGGGCGTGTGTCCAGCTCTTGTGGTA
1 CACATGGGCGTGTATCCAGCCCGTGTGGTA
* *
11882530 CACATGGGTGTGTATCCATCCCGTGTGG
1 CACATGGGCGTGTATCCAGCCCGTGTGG
11882558 AAATGCCCAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.14, C:0.24, G:0.33, T:0.29
Consensus pattern (30 bp):
CACATGGGCGTGTATCCAGCCCGTGTGGTA
Found at i:11884377 original size:23 final size:25
Alignment explanation
Indices: 11884336--11884426 Score: 87
Period size: 26 Copynumber: 3.4 Consensus size: 25
11884326 GAAGTCAAAG
11884336 AAAATAAAAATTAAAAAACT-AAAAAAA
1 AAAATAAAAA-T--AAAACTAAAAAAAA
11884363 AAAATAAAAAT-AAACATAAACATAAAATA
1 AAAATAAAAATAAAAC-T-AA-A-AAAA-A
11884392 AAAATAAAAATAAAACTAAAAAGAAA
1 AAAATAAAAATAAAACTAAAAA-AAA
11884418 AAAATAAAA
1 AAAATAAAA
11884427 TCAATGATCC
Statistics
Matches: 56, Mismatches: 0, Indels: 17
0.77 0.00 0.23
Matches are distributed among these distances:
23 4 0.07
24 1 0.02
26 14 0.25
27 14 0.25
28 6 0.11
29 13 0.23
30 4 0.07
ACGTcount: A:0.80, C:0.04, G:0.01, T:0.14
Consensus pattern (25 bp):
AAAATAAAAATAAAACTAAAAAAAA
Found at i:11884426 original size:6 final size:6
Alignment explanation
Indices: 11884336--11884419 Score: 89
Period size: 6 Copynumber: 13.7 Consensus size: 6
11884326 GAAGTCAAAG
* * *
11884336 AAAATA AAAATTAA AAAACTA AAAAAA AAAATA AAAATA AACATA AACAT-
1 AAAATA AAAA-T-A AAAA-TA AAAATA AAAATA AAAATA AAAATA AAAATA
* *
11884386 AAAATA AAAATA AAAATA AAACTA AAAAGA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
11884420 AATAAAATCA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
5 4 0.06
6 51 0.76
7 6 0.09
8 6 0.09
ACGTcount: A:0.80, C:0.05, G:0.01, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:11884648 original size:4 final size:4
Alignment explanation
Indices: 11884639--11884751 Score: 51
Period size: 4 Copynumber: 27.8 Consensus size: 4
11884629 TACTAAGTGG
* *
11884639 AATA AATAA AATA AAT- AA-A AATA AGTA GAATA AGA-A AATA AATA TATA
1 AATA AAT-A AATA AATA AATA AATA AATA -AATA A-ATA AATA AATA AATA
*
11884687 AATA AATTA AAGA AA-A TAATA AA-A TAATA AA-A TAATA AA-A TAATAA
1 AATA AA-TA AATA AATA -AATA AATA -AATA AATA -AATA AATA -AAT-A
* *
11884733 AATA ATTA AATA ATTA AAT
1 AATA AATA AATA AATA AAT
11884752 GATAAAATAA
Statistics
Matches: 84, Mismatches: 9, Indels: 32
0.67 0.07 0.26
Matches are distributed among these distances:
3 9 0.11
4 56 0.67
5 18 0.21
6 1 0.01
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:11884657 original size:31 final size:27
Alignment explanation
Indices: 11884632--11884734 Score: 76
Period size: 25 Copynumber: 4.0 Consensus size: 27
11884622 ATAAAATTAC
* *
11884632 TAAGTGGAATAAATAAAATAAATAAAAA
1 TAAGTAGAAT-AAGAAAATAAATAAAAA
*
11884660 TAAGTAGAATAAGAAAATAAAT--ATA
1 TAAGTAGAATAAGAAAATAAATAAAAA
*
11884685 TAAATA-AATTAAAGAAAAT-AAT-AAAA
1 TAAGTAGAA-T-AAGAAAATAAATAAAAA
* *
11884711 TAA-TAAAATAATAAAAT-AATAAAA
1 TAAGTAGAATAAGAAAATAAATAAAA
11884735 TAATTAAATA
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
24 12 0.19
25 17 0.27
26 15 0.23
27 11 0.17
28 9 0.14
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (27 bp):
TAAGTAGAATAAGAAAATAAATAAAAA
Found at i:11884663 original size:28 final size:29
Alignment explanation
Indices: 11884632--11884691 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
11884622 ATAAAATTAC
* *
11884632 TAAGTGGAATAAATAAAATAAATA-A-AAA
1 TAAGTAGAAT-AAGAAAATAAATATATAAA
11884660 TAAGTAGAATAAGAAAATAAATATATAAA
1 TAAGTAGAATAAGAAAATAAATATATAAA
11884689 TAA
1 TAA
11884692 ATTAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 12 0.43
28 10 0.36
29 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (29 bp):
TAAGTAGAATAAGAAAATAAATATATAAA
Found at i:11884712 original size:8 final size:8
Alignment explanation
Indices: 11884643--11884765 Score: 113
Period size: 8 Copynumber: 14.8 Consensus size: 8
11884633 AAGTGGAATA
11884643 AATAAAAT
1 AATAAAAT
11884651 AAATAAAAAT
1 -AAT-AAAAT
*
11884661 AAGTAGAAT
1 AA-TAAAAT
*
11884670 AAGAAAAT
1 AATAAAAT
*
11884678 AA-ATATAT
1 AATA-AAAT
*
11884686 AAATAAATT
1 -AATAAAAT
*
11884695 AAAGAAAAT
1 -AATAAAAT
11884704 AATAAAAT
1 AATAAAAT
11884712 AATAAAAT
1 AATAAAAT
11884720 AATAAAAT
1 AATAAAAT
11884728 AATAAAAT
1 AATAAAAT
*
11884736 AATTAAAT
1 AATAAAAT
*
11884744 AATTAAAT
1 AATAAAAT
*
11884752 GATAAAAT
1 AATAAAAT
11884760 AATAAA
1 AATAAA
11884766 GAATTAAAAA
Statistics
Matches: 96, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
7 1 0.01
8 66 0.69
9 22 0.23
10 7 0.07
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (8 bp):
AATAAAAT
Found at i:11884773 original size:16 final size:16
Alignment explanation
Indices: 11884706--11884774 Score: 56
Period size: 16 Copynumber: 4.3 Consensus size: 16
11884696 AAGAAAATAA
*
11884706 TAAAATAATAAA-ATAA
1 TAAAATAATAAAGA-AT
*
11884722 TAAAATAATAAAATAAT
1 TAAAATAAT-AAAGAAT
11884739 T-AAATAATTAAATG-A-
1 TAAAATAA-TAAA-GAAT
11884754 TAAAATAATAAAGAAT
1 TAAAATAATAAAGAAT
11884770 TAAAA
1 TAAAA
11884775 ATAGGGGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
14 1 0.02
15 6 0.14
16 30 0.68
17 6 0.14
18 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (16 bp):
TAAAATAATAAAGAAT
Found at i:11890227 original size:21 final size:20
Alignment explanation
Indices: 11890189--11890251 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
11890179 ATTCAATTTC
11890189 TCAATCC-AAT-ATA-CATT
1 TCAATCCAAATCATATCATT
11890206 TCAATACCACAATCAT-TCATT
1 TCAAT-CCA-AATCATATCATT
*
11890227 T-AATTCAAATCATATCATT
1 TCAATCCAAATCATATCATT
11890246 TGCAAT
1 T-CAAT
11890252 TTTCATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.14
18 8 0.22
19 8 0.22
20 6 0.16
21 10 0.27
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.37
Consensus pattern (20 bp):
TCAATCCAAATCATATCATT
Found at i:11891971 original size:50 final size:50
Alignment explanation
Indices: 11891847--11891998 Score: 200
Period size: 50 Copynumber: 3.0 Consensus size: 50
11891837 CAATGATGTC
* * * *
11891847 CGGTTCACATAGTAGCCTGCACATAGTACTACACACGTGATCGA-AACTATT
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGA-CTATCACT-TT
* *
11891898 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-TTT
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGA-CTATCACTTT
*
11891948 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACTATCACTTT
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACTATCACTTT
11891998 C
1 C
11891999 ACTTTTACAT
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
49 6 0.07
50 43 0.48
51 39 0.44
52 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (50 bp):
CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACTATCACTTT
Found at i:11893944 original size:14 final size:14
Alignment explanation
Indices: 11893927--11893953 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11893917 TTGCTCAATT
11893927 TGGTTCAACTGGTG
1 TGGTTCAACTGGTG
11893941 TGGTTCAACTGGT
1 TGGTTCAACTGGT
11893954 CCTTTTTTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.33, T:0.37
Consensus pattern (14 bp):
TGGTTCAACTGGTG
Found at i:11896155 original size:23 final size:23
Alignment explanation
Indices: 11896129--11896207 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
11896119 AGGGAAAGAT
* *
11896129 AATGTATCCCTTGAGGGAGTGAG
1 AATGTATCCCTTAAAGGAGTGAG
* * *
11896152 AATGTGTACCATAAAGGAGTGAG
1 AATGTATCCCTTAAAGGAGTGAG
* * *
11896175 AATGGATCCCTTAAATGAATGAG
1 AATGTATCCCTTAAAGGAGTGAG
11896198 AATGTATCCC
1 AATGTATCCC
11896208 CCAAGGGAAT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (23 bp):
AATGTATCCCTTAAAGGAGTGAG
Found at i:11896320 original size:23 final size:22
Alignment explanation
Indices: 11896270--11896323 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
11896260 GAATGATAAA
*
11896270 ATGTATCCCTTAAGGAAATGAG
1 ATGTATCCCATAAGGAAATGAG
* *
11896292 ATTGTATCCCATAAGGGAATGTTG
1 A-TGTATCCCATAAGGAAATG-AG
11896316 ATGTATCC
1 ATGTATCC
11896324 TCTAAGAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 24 0.89
24 2 0.07
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (22 bp):
ATGTATCCCATAAGGAAATGAG
Found at i:11899364 original size:27 final size:27
Alignment explanation
Indices: 11899334--11899519 Score: 169
Period size: 27 Copynumber: 6.9 Consensus size: 27
11899324 TTTAACCTCT
*
11899334 AGGGGCCTTACGATCATTTTACCCTAC
1 AGGGGCATTACGATCATTTTACCCTAC
11899361 AGGGGCATTACGATCATTTTACCCTA-
1 AGGGGCATTACGATCATTTTACCCTAC
* * * * *
11899387 TGAGAGCATTATGGTCATTTTACCCTAT
1 AG-GGGCATTACGATCATTTTACCCTAC
* *
11899415 ATGGGGTATTACGGTCATTTTACCCTAC
1 A-GGGGCATTACGATCATTTTACCCTAC
* *
11899443 AAGGGCATTAC-AGTTATTTTACCCTAC
1 AGGGGCATTACGA-TCATTTTACCCTAC
* * * * *
11899470 AAGGGTATTACGGTCATTTTACCCGAT
1 AGGGGCATTACGATCATTTTACCCTAC
* * *
11899497 AGGGGTATTACGATTATTATACC
1 AGGGGCATTACGATCATTTTACC
11899520 TATTTTAGGG
Statistics
Matches: 131, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
26 1 0.01
27 107 0.82
28 22 0.17
29 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (27 bp):
AGGGGCATTACGATCATTTTACCCTAC
Found at i:11899435 original size:55 final size:54
Alignment explanation
Indices: 11899347--11899493 Score: 195
Period size: 55 Copynumber: 2.7 Consensus size: 54
11899337 GGCCTTACGA
* * ** **
11899347 TCATTTTACCCTACAGGGGCATTACGATCATTTTACCCTATGAGAGCATTATGG
1 TCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAAGAGCATTACAG
* *
11899401 TCATTTTACCCTATATGGGGTATTACGGTCATTTTACCCTACAAGGGCATTACAG
1 TCATTTTACCCTACA-GGGGTATTACGGTCATTTTACCCTACAAGAGCATTACAG
* *
11899456 TTATTTTACCCTACAAGGGTATTACGGTCATTTTACCC
1 TCATTTTACCCTACAGGGGTATTACGGTCATTTTACCC
11899494 GATAGGGGTA
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
54 36 0.44
55 45 0.56
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.35
Consensus pattern (54 bp):
TCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAAGAGCATTACAG
Found at i:11899435 original size:82 final size:81
Alignment explanation
Indices: 11899341--11899519 Score: 234
Period size: 82 Copynumber: 2.2 Consensus size: 81
11899331 TCTAGGGGCC
* ** *
11899341 TTACGATCATTTTACCCTACAGGGGCATTAC-GATCATTTTACCCTATGAGAGCATTATGGTCAT
1 TTACGATCATTTTACCCTACAAGGGCATTACAG-TCATTTTACCCTACAAGAGCATTACGGTCAT
*
11899405 TTTACCCTATATGGGGTA
65 TTTACCCGATA-GGGGTA
* * * *
11899423 TTACGGTCATTTTACCCTACAAGGGCATTACAGTTATTTTACCCTACAAGGGTATTACGGTCATT
1 TTACGATCATTTTACCCTACAAGGGCATTACAGTCATTTTACCCTACAAGAGCATTACGGTCATT
11899488 TTACCCGATAGGGGTA
66 TTACCCGATAGGGGTA
* *
11899504 TTACGATTATTATACC
1 TTACGATCATTTTACC
11899520 TATTTTAGGG
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
81 19 0.23
82 64 0.76
83 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (81 bp):
TTACGATCATTTTACCCTACAAGGGCATTACAGTCATTTTACCCTACAAGAGCATTACGGTCATT
TTACCCGATAGGGGTA
Found at i:11899514 original size:54 final size:54
Alignment explanation
Indices: 11899324--11899519 Score: 198
Period size: 54 Copynumber: 3.6 Consensus size: 54
11899314 AAAATAATCA
* * * * *
11899324 TTTAACCTCTAGGGGCCTTACGATCATTTTACCCTACAGGGGCATTACGATCAT
1 TTTACCCTATAGGGGCATTACGATCATTTTACCCTACAGGGGTATTACGGTCAT
* * * *
11899378 TTTACCCTAT-GAGAGCATTATGGTCATTTTACCCTATATGGGGTATTACGGTCAT
1 TTTACCCTATAG-GGGCATTACGATCATTTTACCCTACA-GGGGTATTACGGTCAT
* * * *
11899433 TTTACCCTACAAGGGCATTAC-AGTTATTTTACCCTACAAGGGTATTACGGTCAT
1 TTTACCCTATAGGGGCATTACGA-TCATTTTACCCTACAGGGGTATTACGGTCAT
* * * *
11899487 TTTACCCGATAGGGGTATTACGATTATTATACC
1 TTTACCCTATAGGGGCATTACGATCATTTTACC
11899520 TATTTTAGGG
Statistics
Matches: 115, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 70 0.61
55 44 0.38
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (54 bp):
TTTACCCTATAGGGGCATTACGATCATTTTACCCTACAGGGGTATTACGGTCAT
Found at i:11907906 original size:21 final size:19
Alignment explanation
Indices: 11907841--11907974 Score: 205
Period size: 19 Copynumber: 6.8 Consensus size: 19
11907831 AATTTTTGAG
11907841 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
11907860 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
11907879 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11907898 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
11907919 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
**
11907940 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11907959 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
11907975 ATATATGATT
Statistics
Matches: 107, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
19 67 0.63
21 40 0.37
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:11907993 original size:61 final size:58
Alignment explanation
Indices: 11907841--11907997 Score: 208
Period size: 61 Copynumber: 2.6 Consensus size: 58
11907831 AATTTTTGAG
* *
11907841 GATATGCAATCTTAGATATGA-TATGCAATCCTAGATATGATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATTATGCAATCTTAGATATGATATACAATCTTAGATAT
*
11907898 GATATATGCAATCTTAGATATGATATATGCAATCTTAGATATGATATATAATCTTAGATAT
1 G--ATATGCAATCTTAGATATGAT-TATGCAATCTTAGATATGATATACAATCTTAGATAT
* *
11907959 GATATGCAATCTTAGAATATATGATTTTGTAATCTTAGA
1 GATATGCAATCTTAG---ATATGATTATGCAATCTTAGA
11907998 GATTTAATTT
Statistics
Matches: 88, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
57 1 0.01
59 34 0.39
61 46 0.52
62 7 0.08
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (58 bp):
GATATGCAATCTTAGATATGATTATGCAATCTTAGATATGATATACAATCTTAGATAT
Found at i:11909157 original size:19 final size:20
Alignment explanation
Indices: 11909116--11909157 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
11909106 ATTTCTTGGC
* *
11909116 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
11909136 CATTGT-ATATTTAATATAG
1 CATTGTAATATTTAATATAG
11909155 CAT
1 CAT
11909158 CACATCATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:11909531 original size:98 final size:98
Alignment explanation
Indices: 11909398--11909592 Score: 327
Period size: 98 Copynumber: 2.0 Consensus size: 98
11909388 CTAAAAACAA
* * * *
11909398 TAAAGGAAATATTCTGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
11909463 TTAAATCTTGGATAAGTAGATGTTTTTTTAAAG
66 TTAAATCTTGGATAAGTAGATGTTCTTTTAAAG
*
11909496 TAAAGGAAATATTCCGAGTTTGAGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
11909561 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 TTAAATCTTGGATAAGTAGATGTTCTTTTAAA
11909593 ATTTTATTGT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTAGATGTTCTTTTAAAG
Found at i:11915661 original size:43 final size:44
Alignment explanation
Indices: 11915602--11915707 Score: 110
Period size: 43 Copynumber: 2.4 Consensus size: 44
11915592 CCTGTGGTTA
* *
11915602 CAGTGGAGTACATTGAAG-TCAGTAA-TCCTATCTCCCTG-GTCAG
1 CAGTGGAATAGATTGAAGAT-AGTAAGTCCTATCTCCCTGAGT-AG
* * * *
11915645 CAGTGGAATAGGTTGAAGATTGTAAGTCTTATCTCCCTGCAGTTG
1 CAGTGGAATAGATTGAAGATAGTAAGTCCTATCTCCCTG-AGTAG
11915690 CAGTGGAATAGATTGAAG
1 CAGTGGAATAGATTGAAG
11915708 CACTAGCTCC
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
43 19 0.37
44 13 0.25
45 18 0.35
46 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (44 bp):
CAGTGGAATAGATTGAAGATAGTAAGTCCTATCTCCCTGAGTAG
Found at i:11915937 original size:19 final size:19
Alignment explanation
Indices: 11915913--11916044 Score: 219
Period size: 19 Copynumber: 6.8 Consensus size: 19
11915903 AATTTTTGAG
11915913 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
11915932 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
11915951 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11915970 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
11915991 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
11916010 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11916029 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
11916045 ATATATGATT
Statistics
Matches: 105, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
19 86 0.82
21 19 0.18
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:11915980 original size:59 final size:57
Alignment explanation
Indices: 11915913--11916051 Score: 219
Period size: 59 Copynumber: 2.4 Consensus size: 57
11915903 AATTTTTGAG
*
11915913 GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
* *
11915970 GATATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATATAATCTTAGATAT
1 G--ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
11916029 GATATGCAATCTTAGA-AT-ATATG
1 GATATGCAATCTTAGATATGATATG
11916052 ATTTTGTAAT
Statistics
Matches: 77, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
55 5 0.06
56 2 0.03
57 16 0.21
59 54 0.70
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (57 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
Found at i:11917323 original size:98 final size:98
Alignment explanation
Indices: 11917190--11917384 Score: 327
Period size: 98 Copynumber: 2.0 Consensus size: 98
11917180 CTAAAAACAA
* *
11917190 TAAAGGAAATATTCCGAGTTTGAGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
11917255 TTAAATCTTGGATAAGTGGATATTCTTTTAAAG
66 TTAAATCTTGGATAAGCGGATATTCTTTTAAAG
* * *
11917288 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGTGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
11917353 TTAAATCTTGGATAAGCGGATGTTCTTTTAAA
66 TTAAATCTTGGATAAGCGGATATTCTTTTAAA
11917385 ATTTTATTGT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGCGGATATTCTTTTAAAG
Found at i:11921353 original size:43 final size:43
Alignment explanation
Indices: 11921209--11921356 Score: 128
Period size: 42 Copynumber: 3.4 Consensus size: 43
11921199 TGAGTTATCG
11921209 TGTAAGACCACGTCTGGGAC-GTTGGCATCGAT-TTGAGATTTACA
1 TGTAAGACCACGTCTGGGACAG-TGGCATCGATATT-AGA-TTACA
* * * ***
11921253 CGTAAGACCATGTCTGGGACA-TCGGCATCG-TA-TACAATTTTG
1 TGTAAGACCACGTCTGGGACAGT-GGCATCGATATTA-GATTACA
* *
11921295 TGTAAGACC-CTGTCTGGGACAGTGGAATCGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGACAGTGGCATCGATATTAGATTACA
11921338 TGTAAGACCACGTCTGGGA
1 TGTAAGACCACGTCTGGGA
11921357 TGTTGGCATT
Statistics
Matches: 81, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
42 27 0.33
43 27 0.33
44 27 0.33
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACAGTGGCATCGATATTAGATTACA
Found at i:11921574 original size:18 final size:19
Alignment explanation
Indices: 11921539--11921575 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
11921529 CATGACATTG
11921539 AATGAAATGTATGTATACA
1 AATGAAATGTATGTATACA
11921558 AATG-AATGT-TGTGATACA
1 AATGAAATGTATGT-ATACA
11921576 TATGCTCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 10 0.59
19 4 0.24
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.32
Consensus pattern (19 bp):
AATGAAATGTATGTATACA
Found at i:11926525 original size:13 final size:14
Alignment explanation
Indices: 11926509--11926541 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
11926499 TATATTTTTC
11926509 TTTATATAT-AATA
1 TTTATATATAAATA
11926522 TTTATATATCAAATA
1 TTTATATAT-AAATA
11926537 TTTAT
1 TTTAT
11926542 TTCTCCACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
15 9 0.50
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTATATATAAATA
Found at i:11927078 original size:3 final size:3
Alignment explanation
Indices: 11927070--11927098 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11927060 CATTCATTAA
11927070 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
11927099 ACTTAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:11927587 original size:29 final size:30
Alignment explanation
Indices: 11927554--11927610 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
11927544 TAGTTTAATG
*
11927554 TATAATTCTATATATG-AATTTAAATTTTA
1 TATAATTCTATACATGAAATTTAAATTTTA
* *
11927583 TATAATTTTATACATGAAATTTTAATTT
1 TATAATTCTATACATGAAATTTAAATTT
11927611 GATTCAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (30 bp):
TATAATTCTATACATGAAATTTAAATTTTA
Found at i:11928337 original size:24 final size:24
Alignment explanation
Indices: 11928309--11928360 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
11928299 TTCGTAGGTC
* * * *
11928309 AAATAAATTGTGCTAATCAATGCT
1 AAATAAATTATACTAATAAATACT
*
11928333 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
11928357 AAAT
1 AAAT
11928361 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:11929545 original size:6 final size:6
Alignment explanation
Indices: 11929534--11929568 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
11929524 TGCTTGTCTT
11929534 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCT
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCT
11929569 TCTTTGTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CCTCTC
Found at i:11936569 original size:27 final size:27
Alignment explanation
Indices: 11936498--11936557 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
11936488 TAACCGATTA
11936498 ATATAACCATTTCATATATCATTTTTC
1 ATATAACCATTTCATATATCATTTTTC
*
11936525 ATATAACCATTTCATATATTATTTTTC
1 ATATAACCATTTCATATATCATTTTTC
11936552 ATATAA
1 ATATAA
11936558 TTGATTCGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATAACCATTTCATATATCATTTTTC
Found at i:11939282 original size:21 final size:21
Alignment explanation
Indices: 11939247--11939301 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
11939237 GGAAAAGGTT
* *
11939247 ACACACCCGTCTGCAAGAAGC
1 ACACGCCCGTGTGCAAGAAGC
*
11939268 ACACGCCTGTGTGCAAGAAGC
1 ACACGCCCGTGTGCAAGAAGC
11939289 ACACGCCCGTGTG
1 ACACGCCCGTGTG
11939302 GAGGAGACAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.35, G:0.25, T:0.13
Consensus pattern (21 bp):
ACACGCCCGTGTGCAAGAAGC
Found at i:11944465 original size:57 final size:57
Alignment explanation
Indices: 11944404--11944536 Score: 194
Period size: 57 Copynumber: 2.3 Consensus size: 57
11944394 GCCATTATTC
* *
11944404 ACATTTTGACAACATAAATATACGCATTAAGAGACATTATGACAACAACTATAAATT
1 ACATTTAGACAACATAAATATACACATTAAGAGACATTATGACAACAACTATAAATT
* * * * *
11944461 ACATTTGGACAACATAAATATGCATATTAAGAGACATTTTGACAGCAACTATAAATT
1 ACATTTAGACAACATAAATATACACATTAAGAGACATTATGACAACAACTATAAATT
*
11944518 ACATTAAGACAACATAAAT
1 ACATTTAGACAACATAAAT
11944537 GTAGAAATAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 68 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (57 bp):
ACATTTAGACAACATAAATATACACATTAAGAGACATTATGACAACAACTATAAATT
Found at i:11954810 original size:31 final size:30
Alignment explanation
Indices: 11954775--11954834 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
11954765 AGAGGTGGGA
*
11954775 TGGGAAAGGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AAGGAATAAAAATTTTAGGGGAAAAG
* * *
11954806 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGAATAAAAATTTTAGGGGAAAA
11954835 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAAGGAATAAAAATTTTAGGGGAAAAG
Found at i:11956115 original size:25 final size:24
Alignment explanation
Indices: 11956087--11956150 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 24
11956077 CGGACACATA
*
11956087 AACGGGAAGCTCATATGAGCCATGT
1 AACGGGAAGCTCATAAGAGCCAT-T
* **
11956112 AACGAGAAGCTCCGAAGAGCCATT
1 AACGGGAAGCTCATAAGAGCCATT
11956136 AACGGGAAGCTCATA
1 AACGGGAAGCTCATA
11956151 CTAGCCAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 13 0.41
25 19 0.59
ACGTcount: A:0.36, C:0.22, G:0.27, T:0.16
Consensus pattern (24 bp):
AACGGGAAGCTCATAAGAGCCATT
Found at i:11956156 original size:24 final size:24
Alignment explanation
Indices: 11956087--11956157 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 24
11956077 CGGACACATA
11956087 AACGGGAAGCTCATATGAGCCATGT
1 AACGGGAAGCTCATAT-AGCCATGT
* *
11956112 AACGAGAAGCTCCGA-AGAGCCAT-T
1 AACGGGAAGCT-C-ATATAGCCATGT
11956136 AACGGGAAGCTCATACTAGCCA
1 AACGGGAAGCTCATA-TAGCCA
11956158 ATATTGGGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
22 1 0.03
23 2 0.05
24 16 0.42
25 16 0.42
26 2 0.05
27 1 0.03
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.15
Consensus pattern (24 bp):
AACGGGAAGCTCATATAGCCATGT
Found at i:11969731 original size:13 final size:13
Alignment explanation
Indices: 11969713--11969738 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11969703 AGTTATGGAC
11969713 AATTTTTAATTAA
1 AATTTTTAATTAA
11969726 AATTTTTAATTAA
1 AATTTTTAATTAA
11969739 TAATAAGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTTTAATTAA
Found at i:11970500 original size:34 final size:34
Alignment explanation
Indices: 11970459--11970526 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
11970449 AATGATAGTT
11970459 TGATTGGTTATAGGTTATATTGTGTTAGTTATAA
1 TGATTGGTTATAGGTTATATTGTGTTAGTTATAA
11970493 TGATTGGTTATAGGTTATATTGTGTTAGTTATAA
1 TGATTGGTTATAGGTTATATTGTGTTAGTTATAA
11970527 ACTGACTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (34 bp):
TGATTGGTTATAGGTTATATTGTGTTAGTTATAA
Found at i:11970519 original size:17 final size:17
Alignment explanation
Indices: 11970461--11970519 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 17
11970451 TGATAGTTTG
11970461 ATTG-GTTATAGGTTAT
1 ATTGTGTTATAGGTTAT
11970477 ATTGTG-T-TA-GTTAT
1 ATTGTGTTATAGGTTAT
*
11970491 AATGATTGGTTATAGGTTAT
1 ATTG--T-GTTATAGGTTAT
11970511 ATTGTGTTA
1 ATTGTGTTA
11970520 GTTATAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
14 8 0.24
15 2 0.06
16 6 0.18
17 6 0.18
18 2 0.06
19 2 0.06
20 8 0.24
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (17 bp):
ATTGTGTTATAGGTTAT
Found at i:11972746 original size:15 final size:17
Alignment explanation
Indices: 11972726--11972758 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
11972716 GAAAGTTTAT
11972726 AATAAAT-AAT-ATAAA
1 AATAAATCAATAATAAA
11972741 AATAAATCAATAATAAA
1 AATAAATCAATAATAAA
11972758 A
1 A
11972759 TATGAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AATAAATCAATAATAAA
Found at i:11974606 original size:156 final size:156
Alignment explanation
Indices: 11974321--11974607 Score: 333
Period size: 156 Copynumber: 1.8 Consensus size: 156
11974311 TAAAAAAATG
* * * * * * ** * *
11974321 AAAATGGGTTTTGTGATCAGGGATTAATACGATGGCTTGAAATCCAACATAAGTTGTTGATTCTT
1 AAAATGGGTGTTGCGATCAAGAATTAATACGATGACTGGAAATCCAACATAAGTTGCAGATCCTC
* * * * * ** *
11974386 TAAAGCTAGTGTTAATAGCATCGTACTAAGCTAGTGTTAGCAACCTTGGTCTGAAGCTAGTGTTA
66 TAAAGCTAGTGCTAACAGCATCGAACTAAGCTAGTGTCAGCAACCTAGACCTGAAACTAGTGTTA
11974451 GCAGTCTGAATATGCCAACTTGTATA
131 GCAGTCTGAATATGCCAACTTGTATA
* * *
11974477 AAAATGGGTGTTGCGATCAAGAATTAATTCGATGACTGGAGATCCAACATATGTTGCAGATCCTC
1 AAAATGGGTGTTGCGATCAAGAATTAATACGATGACTGGAAATCCAACATAAGTTGCAGATCCTC
* * * *
11974542 TGAAGCTAGTGCTAACA-TATTCGAACTAAGCTAGTGTCAGCATCCTAGACCTGAAACTATTGTT
66 TAAAGCTAGTGCTAACAGCA-TCGAACTAAGCTAGTGTCAGCAACCTAGACCTGAAACTAGTGTT
11974606 AG
130 AG
11974608 TAGCTCAATA
Statistics
Matches: 105, Mismatches: 25, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
155 1 0.01
156 104 0.99
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (156 bp):
AAAATGGGTGTTGCGATCAAGAATTAATACGATGACTGGAAATCCAACATAAGTTGCAGATCCTC
TAAAGCTAGTGCTAACAGCATCGAACTAAGCTAGTGTCAGCAACCTAGACCTGAAACTAGTGTTA
GCAGTCTGAATATGCCAACTTGTATA
Found at i:11975581 original size:14 final size:17
Alignment explanation
Indices: 11975541--11975575 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11975531 GTGAATGGTA
11975541 AATGAAGATGTGAGCTTG
1 AATGAA-ATGTGAGCTTG
11975559 AATGAAATGTGA-CTTG
1 AATGAAATGTGAGCTTG
11975575 A
1 A
11975576 GAAATGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 6 0.35
18 6 0.35
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (17 bp):
AATGAAATGTGAGCTTG
Found at i:11980176 original size:39 final size:39
Alignment explanation
Indices: 11980133--11980270 Score: 168
Period size: 39 Copynumber: 3.5 Consensus size: 39
11980123 CATATTCACT
* *
11980133 TTTAAGCATATGTCACATTACACATATAATTACATAACA
1 TTTAAGCATATATCACAATACACATATAATTACATAACA
*
11980172 TTTAAGCATATATCACAATACTCATATAATTACATAACA
1 TTTAAGCATATATCACAATACACATATAATTACATAACA
* * *** ***
11980211 TTCAAGCATATATCACAACACTTGTATAATCGTATAACA
1 TTTAAGCATATATCACAATACACATATAATTACATAACA
*
11980250 TTCAAGCATATATCACAATAC
1 TTTAAGCATATATCACAATAC
11980271 TCAAAGACAT
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 88 1.00
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACACATATAATTACATAACA
Found at i:11991945 original size:33 final size:33
Alignment explanation
Indices: 11991892--11991978 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 33
11991882 TGAAGAAGGA
* * *
11991892 GTAACA-GTATAGAAGATGAAGGTGAAATAGGG
1 GTAACAGGTATAGAAGGTGAAGGAGAAATAGAG
* * *
11991924 GTAACCGGTATAGAGGGTGAAGGAGATATAGAG
1 GTAACAGGTATAGAAGGTGAAGGAGAAATAGAG
11991957 GTAACAGGTATAGAAGGTGAAG
1 GTAACAGGTATAGAAGGTGAAG
11991979 CTAAAGGCTC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
32 5 0.11
33 41 0.89
ACGTcount: A:0.40, C:0.05, G:0.37, T:0.18
Consensus pattern (33 bp):
GTAACAGGTATAGAAGGTGAAGGAGAAATAGAG
Found at i:11998106 original size:21 final size:22
Alignment explanation
Indices: 11998082--11998122 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
11998072 TTGAATTAAT
*
11998082 TTAATTCATTTAA-TCGGTCGG
1 TTAATTCATCTAATTCGGTCGG
*
11998103 TTAATTGATCTAATTCGGTC
1 TTAATTCATCTAATTCGGTC
11998123 AGAAGTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (22 bp):
TTAATTCATCTAATTCGGTCGG
Found at i:12000601 original size:50 final size:50
Alignment explanation
Indices: 12000480--12000608 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 50
12000470 TTGTGAGAGG
* * * **
12000480 TCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
** * *
12000530 TCCCCCGTAAAACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
* *
12000580 TCCCATGTAAGACCATATCTGGGATATGG
1 TCCCATGTAAGACCATGTCTGGGACATGG
12000609 AATTGGCAAT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
Found at i:12014984 original size:69 final size:69
Alignment explanation
Indices: 12014813--12015069 Score: 225
Period size: 69 Copynumber: 3.7 Consensus size: 69
12014803 AGTTTACCGG
* * * * * ** * *
12014813 TTTATGATCGCAACCTCCAAAATAGTTAGCGGCCCTACACTCCCAACTGATACT-CGAAGAGCTT
1 TTTATGATCTCAAACTCCAAAACAGCTAGCGGACCTACACTCCCAACTGATGTTACAAAG-GTTT
*
12014877 GCAAA
65 GCCAA
* * * * * *
12014882 GTTAAGCT-TGC-AACTCCAACACGGCTAGCGGACCTACACTCCCAAATGATGTTACAAAGGTTT
1 TTTATGATCT-CAAACTCCAAAACAGCTAGCGGACCTACACTCCCAACTGATGTTACAAAGGTTT
* *
12014945 GTCAG
65 GCCAA
* * *
12014950 TTTATGAT-TACAAACTCCAAAACAGCTAGTGGACCTACACTCCCAGCTAATGTTACAAAGGTTT
1 TTTATGATCT-CAAACTCCAAAACAGCTAGCGGACCTACACTCCCAACTGATGTTACAAAGGTTT
12015014 GCCAA
65 GCCAA
* * * * *
12015019 TTTATTATCTCAACCTCCAAAACAACTAGCAGACCTACACCCCCAACTGAT
1 TTTATGATCTCAAACTCCAAAACAGCTAGCGGACCTACACTCCCAACTGAT
12015070 ACTCTAAGAG
Statistics
Matches: 146, Mismatches: 38, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
68 45 0.31
69 100 0.68
70 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (69 bp):
TTTATGATCTCAAACTCCAAAACAGCTAGCGGACCTACACTCCCAACTGATGTTACAAAGGTTTG
CCAA
Found at i:12015125 original size:67 final size:66
Alignment explanation
Indices: 12015033--12015242 Score: 242
Period size: 67 Copynumber: 3.1 Consensus size: 66
12015023 TTATCTCAAC
* *
12015033 CTCCAAAACAACTAGCAGACCTACACCCCCAACTGATACTCTAAGAGCTCGTAGAGTTAAGCTCA
1 CTCCAACA-AACTAGCAGACCTACACTCCCAACTGATACTCTAAGAGCTCG-AGAGTTAAGCTCA
12015098 CAA
64 CAA
** * * * *
12015101 CTCCAACACAA-TAGTGGACCTACACTCCTAGCTGATACTCTAAGAGCTCACAGAGTTAAGCTCG
1 CTCCAACA-AACTAGCAGACCTACACTCCCAACTGATACTCTAAGAGCTC-GAGAGTTAAGCTCA
* *
12015165 TAG
64 CAA
* * *
12015168 CTCCAACAAACTAGCAGACCTACGCTCTCAACTGATACTCTAAGAGCTCGATGAGCTAAGCTCAC
1 CTCCAACAAACTAGCAGACCTACACTCCCAACTGATACTCTAAGAGCTCGA-GAGTTAAGCTCAC
12015233 AA
65 AA
*
12015235 ATCCAACA
1 CTCCAACA
12015243 TATCTAGGTA
Statistics
Matches: 117, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
66 3 0.03
67 104 0.89
68 10 0.09
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.20
Consensus pattern (66 bp):
CTCCAACAAACTAGCAGACCTACACTCCCAACTGATACTCTAAGAGCTCGAGAGTTAAGCTCACA
A
Found at i:12045125 original size:43 final size:43
Alignment explanation
Indices: 12045063--12045147 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
12045053 TCATGTCTCA
12045063 TTTCTCACCTCATAATCATTTCTCATATTTGT-CATTTCAATAT
1 TTTCTCACCTCATAATCATTTCTCATATTT-TCCATTTCAATAT
* * *
12045106 TTTCTCATCTCATATTCATTTCTCATCTTTTCCATTTCAATA
1 TTTCTCACCTCATAATCATTTCTCATATTTTCCATTTCAATA
12045148 CCAATCATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 37 0.97
ACGTcount: A:0.24, C:0.25, G:0.01, T:0.51
Consensus pattern (43 bp):
TTTCTCACCTCATAATCATTTCTCATATTTTCCATTTCAATAT
Found at i:12046392 original size:15 final size:15
Alignment explanation
Indices: 12046372--12046404 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12046362 CTTTAATTTT
12046372 TATTATTATAACATA
1 TATTATTATAACATA
*
12046387 TATTATTATAACTTA
1 TATTATTATAACATA
12046402 TAT
1 TAT
12046405 ATATATTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTATTATAACATA
Found at i:12053351 original size:17 final size:17
Alignment explanation
Indices: 12053326--12053382 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
12053316 CTTTCACCAC
*
12053326 TAAATTCACCTAGCAAT
1 TAAAATCACCTAGCAAT
* *
12053343 TAAAATCA-C-AAC-AC
1 TAAAATCACCTAGCAAT
*
12053357 TAAATTCACCTAGCAAT
1 TAAAATCACCTAGCAAT
12053374 TAAAATCAC
1 TAAAATCAC
12053383 AACACAAAGG
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
14 8 0.27
15 3 0.10
16 3 0.10
17 16 0.53
ACGTcount: A:0.47, C:0.25, G:0.04, T:0.25
Consensus pattern (17 bp):
TAAAATCACCTAGCAAT
Found at i:12053358 original size:31 final size:31
Alignment explanation
Indices: 12053323--12053387 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
12053313 ATACTTTCAC
12053323 CACTAAATTCACCTAGCAATTAAAATCACAA
1 CACTAAATTCACCTAGCAATTAAAATCACAA
12053354 CACTAAATTCACCTAGCAATTAAAATCACAA
1 CACTAAATTCACCTAGCAATTAAAATCACAA
12053385 CAC
1 CAC
12053388 AAAGGTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.48, C:0.28, G:0.03, T:0.22
Consensus pattern (31 bp):
CACTAAATTCACCTAGCAATTAAAATCACAA
Found at i:12059717 original size:22 final size:22
Alignment explanation
Indices: 12059691--12059735 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
12059681 TAAGAATGAG
12059691 AAAGAATGCTGCAAAGCTACGA
1 AAAGAATGCTGCAAAGCTACGA
12059713 AAAGAATGCTGCAAAGCTACGA
1 AAAGAATGCTGCAAAGCTACGA
12059735 A
1 A
12059736 TTTCTACTTG
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:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (22 bp):
AAAGAATGCTGCAAAGCTACGA
Found at i:12068600 original size:32 final size:32
Alignment explanation
Indices: 12068563--12068631 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
12068553 ACTAAAAAAA
* * *
12068563 AAAAAGATTTCGTTAGGGATTTGGGGTTTGAAG
1 AAAAGGATTTCGTTAGAG-TTTAGGGTTTGAAG
* * *
12068596 AAAAGGGTTTTGTTAGAGTTTAGGGTTTGAAT
1 AAAAGGATTTCGTTAGAGTTTAGGGTTTGAAG
12068628 AAAA
1 AAAA
12068632 AAAGATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.33, C:0.01, G:0.30, T:0.35
Consensus pattern (32 bp):
AAAAGGATTTCGTTAGAGTTTAGGGTTTGAAG
Found at i:12068709 original size:32 final size:32
Alignment explanation
Indices: 12068671--12068734 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
12068661 AAAAAAAGAG
12068671 GGATTAGAGGGCTTTGTTTAGGGTTTAAAAAA
1 GGATTAGAGGGCTTTGTTTAGGGTTTAAAAAA
*
12068703 GGATTAGAGGGTTTTGTTTAGGGTTTAAAAAA
1 GGATTAGAGGGCTTTGTTTAGGGTTTAAAAAA
12068735 AGATCAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.36
Consensus pattern (32 bp):
GGATTAGAGGGCTTTGTTTAGGGTTTAAAAAA
Found at i:12069194 original size:14 final size:13
Alignment explanation
Indices: 12069172--12069221 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
12069162 AACTGTTTAG
*
12069172 TATTTTTGTAATGA
1 TATTATTGTAAT-A
*
12069186 TATTATTGTACTA
1 TATTATTGTAATA
12069199 TATTTATTGTAATA
1 TA-TTATTGTAATA
12069213 T-TTATTGTA
1 TATTATTGTA
12069222 TTACATTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 8 0.25
13 3 0.09
14 21 0.66
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (13 bp):
TATTATTGTAATA
Found at i:12069215 original size:12 final size:12
Alignment explanation
Indices: 12069172--12069221 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
12069162 AACTGTTTAG
12069172 TATTT-TTGTAA
1 TATTTATTGTAA
12069183 TGATATTATTGTACTA
1 T-AT-TTATTGTA--A
12069199 TATTTATTGTAA
1 TATTTATTGTAA
12069211 TATTTATTGTA
1 TATTTATTGTA
12069222 TTACATTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.03
12 14 0.41
13 2 0.06
14 13 0.38
15 2 0.06
16 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (12 bp):
TATTTATTGTAA
Found at i:12069220 original size:26 final size:28
Alignment explanation
Indices: 12069172--12069230 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
12069162 AACTGTTTAG
12069172 TATTT-TTGTAATGATATTATTGTACTA
1 TATTTATTGTAATGATATTATTGTACTA
*
12069199 TATTTATTGTAAT-AT-TTATTGTATTA
1 TATTTATTGTAATGATATTATTGTACTA
*
12069225 CATTTA
1 TATTTA
12069231 GGTGTTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 15 0.52
27 7 0.24
28 7 0.24
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (28 bp):
TATTTATTGTAATGATATTATTGTACTA
Found at i:12071704 original size:33 final size:34
Alignment explanation
Indices: 12071662--12071737 Score: 127
Period size: 34 Copynumber: 2.3 Consensus size: 34
12071652 ATGCAAAAAT
12071662 AACAAACTTTG-AAATTTAAATGAGATGTATTGG
1 AACAAACTTTGTAAATTTAAATGAGATGTATTGG
* *
12071695 AACAAACTTTGTAATTTTAAATGAGATGTGTTGG
1 AACAAACTTTGTAAATTTAAATGAGATGTATTGG
12071729 AACAAACTT
1 AACAAACTT
12071738 GGAACAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 11 0.28
34 29 0.73
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (34 bp):
AACAAACTTTGTAAATTTAAATGAGATGTATTGG
Found at i:12071756 original size:45 final size:45
Alignment explanation
Indices: 12071691--12071792 Score: 186
Period size: 45 Copynumber: 2.3 Consensus size: 45
12071681 ATGAGATGTA
**
12071691 TTGGAACAAACTTTGTAATTTTAAATGAGATGTGTTGGAACAAAC
1 TTGGAACAAACTTTCCAATTTTAAATGAGATGTGTTGGAACAAAC
12071736 TTGGAACAAACTTTCCAATTTTAAATGAGATGTGTTGGAACAAAC
1 TTGGAACAAACTTTCCAATTTTAAATGAGATGTGTTGGAACAAAC
12071781 TTGGAACAAACT
1 TTGGAACAAACT
12071793 ATGTAATATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (45 bp):
TTGGAACAAACTTTCCAATTTTAAATGAGATGTGTTGGAACAAAC
Found at i:12086150 original size:44 final size:42
Alignment explanation
Indices: 12086066--12086172 Score: 117
Period size: 44 Copynumber: 2.5 Consensus size: 42
12086056 GGAAATCTAA
* * * *
12086066 TATATGATATCGTGTAAGACCTTGTTTGGGACGCTGGCATCG
1 TATAAGATTTCGTGTAAGACCATGTTTGAGACGCTGGCATCG
* * *
12086108 ATTTGAGATTTACGTGTAAGACCATGTTTGAGACATCT-GCATCG
1 -TATAAGATTT-CGTGTAAGACCATGTTTGAGAC-GCTGGCATCG
12086152 TATAAGATTTCGTGTAAGACC
1 TATAAGATTTCGTGTAAGACC
12086173 CTATCTGGGA
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
42 11 0.21
43 14 0.26
44 26 0.49
45 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (42 bp):
TATAAGATTTCGTGTAAGACCATGTTTGAGACGCTGGCATCG
Found at i:12087263 original size:81 final size:80
Alignment explanation
Indices: 12087099--12087377 Score: 323
Period size: 81 Copynumber: 3.5 Consensus size: 80
12087089 GTAATGGGCC
* * * * *
12087099 TAAAATGA-CAGAAATGCCCTCGAAAGG-TAAAGTGACCAAAATACCCTTGAAGGTAAAATGA-T
1 TAAAATGATC-GAAATACCCCCG-AAGGATAAAATGACTAAAATACCCTCGAAGGTAAAATGACT
*
12087161 CGAAATACCCCCGAAGGG
64 -GAAATACCCTCGAAGGG
* * *
12087179 TAAAATG-GCTGAAATACCCCCGAAGGATAAAATGGCTGAAATACCCTCGAAGGGTAAAATGACT
1 TAAAATGATC-GAAATACCCCCGAAGGATAAAATGACTAAAATACCCTCGAA-GGTAAAATGACT
* *
12087243 GAGATACCCTTGAAGGG
64 GAAATACCCTCGAAGGG
** * * *
12087260 TAAAATGATCGAAATACCCTTGAAGGGTAAAATGATTAAAATACCCCCGAAAGGTAAAATGACTG
1 TAAAATGATCGAAATACCCCCGAAGGATAAAATGACTAAAATACCCTCG-AAGGTAAAATGACTG
12087325 AAATACCCTCGAAGGG
65 AAATACCCTCGAAGGG
*
12087341 TAAAATGATCGAAATACCCCCGTAGGATAAAATGACT
1 TAAAATGATCGAAATACCCCCGAAGGATAAAATGACT
12087378 GTTATACCCT
Statistics
Matches: 167, Mismatches: 26, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
79 4 0.02
80 37 0.22
81 122 0.73
82 4 0.02
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (80 bp):
TAAAATGATCGAAATACCCCCGAAGGATAAAATGACTAAAATACCCTCGAAGGTAAAATGACTGA
AATACCCTCGAAGGG
Found at i:12087386 original size:27 final size:27
Alignment explanation
Indices: 12087099--12087378 Score: 289
Period size: 27 Copynumber: 10.4 Consensus size: 27
12087089 GTAATGGGCC
* * * *
12087099 TAAAATGACAGAAATGCCCTCGAAAGG
1 TAAAATGACTGAAATACCCCCGAAGGG
* ** **
12087126 TAAAGTGACCAAAATACCCTTGAA-GG
1 TAAAATGACTGAAATACCCCCGAAGGG
12087152 TAAAATGA-TCGAAATACCCCCGAAGGG
1 TAAAATGACT-GAAATACCCCCGAAGGG
* *
12087179 TAAAATGGCTGAAATACCCCCGAAGGA
1 TAAAATGACTGAAATACCCCCGAAGGG
* *
12087206 TAAAATGGCTGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
* **
12087233 TAAAATGACTGAGATACCCTTGAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
**
12087260 TAAAATGA-TCGAAATACCCTTGAAGGG
1 TAAAATGACT-GAAATACCCCCGAAGGG
* * *
12087287 TAAAATGATTAAAATACCCCCGAAAGG
1 TAAAATGACTGAAATACCCCCGAAGGG
*
12087314 TAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
* *
12087341 TAAAATGA-TCGAAATACCCCCGTAGGA
1 TAAAATGACT-GAAATACCCCCGAAGGG
12087368 TAAAATGACTG
1 TAAAATGACTG
12087379 TTATACCCTT
Statistics
Matches: 217, Mismatches: 29, Indels: 14
0.83 0.11 0.05
Matches are distributed among these distances:
26 22 0.10
27 192 0.88
28 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCCCGAAGGG
Found at i:12087580 original size:26 final size:26
Alignment explanation
Indices: 12087551--12087625 Score: 123
Period size: 26 Copynumber: 2.9 Consensus size: 26
12087541 TTGCCACATA
*
12087551 TACTGTTACTAGCAGCTTTGCTGCAT
1 TACTGTTACTGGCAGCTTTGCTGCAT
12087577 TACTGTTACTGGCAGCTTTGCTGCAT
1 TACTGTTACTGGCAGCTTTGCTGCAT
* *
12087603 CACTATTACTGGCAGCTTTGCTG
1 TACTGTTACTGGCAGCTTTGCTG
12087626 AGATATTGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.37
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCTGCAT
Found at i:12090869 original size:21 final size:21
Alignment explanation
Indices: 12090845--12090892 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
12090835 TTTGTGAAAA
*
12090845 TTTTTAAG-AATTTTATGGTAT
1 TTTTTAAGAAATTTTA-GGGAT
**
12090866 TTTTTTGGAAATTTTAGGGAT
1 TTTTTAAGAAATTTTAGGGAT
12090887 TTTTTA
1 TTTTTA
12090893 TTTTTATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (21 bp):
TTTTTAAGAAATTTTAGGGAT
Found at i:12092163 original size:35 final size:35
Alignment explanation
Indices: 12092120--12092186 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
12092110 ACTGTGATAA
* *
12092120 TTTATAACAGTATATTAAAATAGTATATTACAAAT
1 TTTATAACAATATATTAAAACAGTATATTACAAAT
*
12092155 TTTATAACAATATATTAAACCAGTATATTACA
1 TTTATAACAATATATTAAAACAGTATATTACA
12092187 TTAATAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (35 bp):
TTTATAACAATATATTAAAACAGTATATTACAAAT
Found at i:12092230 original size:13 final size:13
Alignment explanation
Indices: 12092203--12092235 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12092193 ATTAAGGTGT
*
12092203 AGTAT-TTATAAC
1 AGTATATTAAAAC
12092215 AGTATATTAAAAC
1 AGTATATTAAAAC
12092228 AGTATATT
1 AGTATATT
12092236 TATAACTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (13 bp):
AGTATATTAAAAC
Found at i:12094796 original size:84 final size:84
Alignment explanation
Indices: 12094655--12094810 Score: 212
Period size: 84 Copynumber: 1.9 Consensus size: 84
12094645 GGCTCGTACA
* * *
12094655 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACTGTCCCAGACAG-GG
1 ATGCCAACGTCCCAGACATAGTCTTACACGTAATCACATATCGATGCCACTGTCCCAGAC-GTGG
12094719 TCTTACACAAATCAAATACG
65 TCTTACACAAATCAAATACG
*
12094739 ATGCCAATGTCCCAGACATAGTCTTACACGT-ATACACA-ATTCGATGCCAAC-GTCCCAGACGT
1 ATGCCAACGTCCCAGACATAGTCTTACACGTAAT-CACATA-TCGATGCC-ACTGTCCCAGACGT
12094801 GGTCTTACAC
63 GGTCTTACAC
12094811 GAAAATACAT
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
83 4 0.06
84 58 0.91
85 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATAGTCTTACACGTAATCACATATCGATGCCACTGTCCCAGACGTGGT
CTTACACAAATCAAATACG
Found at i:12094810 original size:43 final size:43
Alignment explanation
Indices: 12094655--12094811 Score: 173
Period size: 43 Copynumber: 3.7 Consensus size: 43
12094645 GGCTCGTACA
*
12094655 ATGCCAACGTCCCAGACGTGGTCTTACATGTA-ATCAC-ATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTATA-CACAAT-TCG
** *
12094698 ATGCC-ACTGTCCCAGACAG-GGTCTTACACAAAT-CA-AATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTATACACAATTCG
* * *
12094739 ATGCCAATGTCCCAGACATAGTCTTACACGTATACACAATTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTATACACAATTCG
12094782 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
12094812 AAAATACATA
Statistics
Matches: 93, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
41 27 0.29
42 9 0.10
43 56 0.60
44 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTATACACAATTCG
Found at i:12102364 original size:43 final size:42
Alignment explanation
Indices: 12102298--12102452 Score: 156
Period size: 43 Copynumber: 3.7 Consensus size: 42
12102288 GGCTTGTACA
*
12102298 ATGCCAATGTCCCAAACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACA-GTAATCACATATCG
* * ** *
12102341 ATGCCACTGTCCCAGACAG-GGTCTTGCACAAATCAAATA-CG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACAGTAATCACATATCG
* *
12102382 ATGCCAATGTCCCAGACATGGTCTTACACGT-ATACACA-ATTTG
1 ATGCCAATGTCCCAGACGTGGTCTTACA-GTAAT-CACATA-TCG
*
12102425 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAATGTCCCAGACGTGGTCTTACA
12102453 CGAAAATACA
Statistics
Matches: 91, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
41 29 0.32
42 11 0.12
43 50 0.55
44 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACAGTAATCACATATCG
Found at i:12103755 original size:13 final size:13
Alignment explanation
Indices: 12103723--12103838 Score: 126
Period size: 13 Copynumber: 8.8 Consensus size: 13
12103713 TCACAATTAT
*
12103723 AGTATATTTATAAC
1 AGTATA-TTAAAAC
12103737 AGTATATTAAAAC
1 AGTATATTAAAAC
*
12103750 ATTATATTAAAAC
1 AGTATATTAAAAC
* *
12103763 ATTATATTAAAAT
1 AGTATATTAAAAC
*
12103776 AGTATATTTATAAC
1 AGTATA-TTAAAAC
* *
12103790 AGCATACTAAAAC
1 AGTATATTAAAAC
12103803 AGTATATTAAAA-
1 AGTATATTAAAAC
*
12103815 AATATATTAAAAC
1 AGTATATTAAAAC
*
12103828 AGTATAATAAA
1 AGTATATTAAA
12103839 CTAGTTATTT
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
12 11 0.13
13 59 0.69
14 16 0.19
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.34
Consensus pattern (13 bp):
AGTATATTAAAAC
Found at i:12103755 original size:27 final size:26
Alignment explanation
Indices: 12103723--12103833 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
12103713 TCACAATTAT
12103723 AGTATATTTATAACAGTATATTAAAAC
1 AGTATA-TTATAACAGTATATTAAAAC
* * * *
12103750 ATTATATTAAAACATTATATTAAAAT
1 AGTATATTATAACAGTATATTAAAAC
* *
12103776 AGTATATTTATAACAGCATACTAAAAC
1 AGTATA-TTATAACAGTATATTAAAAC
* *
12103803 AGTATATTA-AAAAATATATTAAAAC
1 AGTATATTATAACAGTATATTAAAAC
12103828 AGTATA
1 AGTATA
12103834 ATAAACTAGT
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
25 18 0.26
26 25 0.36
27 26 0.38
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.35
Consensus pattern (26 bp):
AGTATATTATAACAGTATATTAAAAC
Found at i:12103801 original size:53 final size:52
Alignment explanation
Indices: 12103721--12103833 Score: 172
Period size: 53 Copynumber: 2.2 Consensus size: 52
12103711 TGTCACAATT
* * * *
12103721 ATAGTATATTTATAACAGTATATTAAAACATTATATTAAAACATTATATTAAA
1 ATAGTATATTTATAACAGCATACTAAAACAGTATATTAAAA-AATATATTAAA
12103774 ATAGTATATTTATAACAGCATACTAAAACAGTATATTAAAAAATATATTAAA
1 ATAGTATATTTATAACAGCATACTAAAACAGTATATTAAAAAATATATTAAA
*
12103826 ACAGTATA
1 ATAGTATA
12103834 ATAAACTAGT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 17 0.31
53 38 0.69
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.35
Consensus pattern (52 bp):
ATAGTATATTTATAACAGCATACTAAAACAGTATATTAAAAAATATATTAAA
Found at i:12103847 original size:25 final size:25
Alignment explanation
Indices: 12103739--12103838 Score: 83
Period size: 25 Copynumber: 3.9 Consensus size: 25
12103729 TTTATAACAG
* * *
12103739 TATATTAAAACATTATATTAAAACAT
1 TATATTAAAACAGTATAATAAAA-AA
* * * *
12103765 TATATTAAAATAGTATATTTATAACAG
1 TATATTAAAACAGTATA-ATA-AAAAA
* * *
12103792 CATACTAAAACAGTATATTAAAAAA
1 TATATTAAAACAGTATAATAAAAAA
12103817 TATATTAAAACAGTATAATAAA
1 TATATTAAAACAGTATAATAAA
12103839 CTAGTTATTT
Statistics
Matches: 60, Mismatches: 12, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
25 22 0.37
26 18 0.30
27 18 0.30
28 2 0.03
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (25 bp):
TATATTAAAACAGTATAATAAAAAA
Found at i:12106464 original size:139 final size:139
Alignment explanation
Indices: 12106200--12106543 Score: 435
Period size: 139 Copynumber: 2.5 Consensus size: 139
12106190 CTGGAATCAG
* * * *
12106200 GAAGTGAAAGGTTTACACGAGTATTTGTTCCATATAACGCC-AAATTGGGAGTGAAGTCAAGAAA
1 GAAGCGAAAGATTTACACGAGTATTTGTTCCATATAACGCCGAAATCGGGAGTGAAGTCGAGAAA
* * * * * *
12106264 ATAGTTAACGTAAAATAATAACCCTTCTTCTTCATTCACCACTGTTGAACCTAGTGCGGTTGTTT
66 GTAGTTAACGTAAAACAATAACCCTTCTTCTTCATCCACCACTGTTGAACCCAGCGAGGTTGTTT
12106329 TCAAACAAA
131 TCAAACAAA
* * *
12106338 GAAGCGAAAGATTTATACGAGTATTTGTTCCA-ATTAACGCCGGAATCGGGAATGAAGTCGAGAA
1 GAAGCGAAAGATTTACACGAGTATTTGTTCCATA-TAACGCCGAAATCGGGAGTGAAGTCGAGAA
12106402 AGTAGTT-A-GTAGAAAACAATAACCCTTCTTCTTCATCCACCACTGTTGAACCCAGCGAGGTTG
65 AGTAGTTAACGT--AAAACAATAACCCTTCTTCTTCATCCACCACTGTTGAACCCAGCGAGGTTG
* *
12106465 TTTTGAGACAAA
128 TTTTCAAACAAA
* * * * * *
12106477 CAAACAAAATATTTACACGAGTATTTGTTCCATATAATGTCGAAATCGGGGAGTGAAGTCGAGAA
1 GAAGCGAAAGATTTACACGAGTATTTGTTCCATATAACGCCGAAATC-GGGAGTGAAGTCGAGAA
12106542 AG
65 AG
12106544 GAGTATTTGT
Statistics
Matches: 176, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
137 3 0.02
138 37 0.21
139 117 0.66
140 19 0.11
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (139 bp):
GAAGCGAAAGATTTACACGAGTATTTGTTCCATATAACGCCGAAATCGGGAGTGAAGTCGAGAAA
GTAGTTAACGTAAAACAATAACCCTTCTTCTTCATCCACCACTGTTGAACCCAGCGAGGTTGTTT
TCAAACAAA
Found at i:12109444 original size:20 final size:20
Alignment explanation
Indices: 12109421--12109459 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12109411 AATGTGTAAT
* *
12109421 CAGAGGAACTGAAGTGCAAA
1 CAGAGGAACCGAAATGCAAA
12109441 CAGAGGAACCGAAATGCAA
1 CAGAGGAACCGAAATGCAA
12109460 TCTCGTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.18, G:0.28, T:0.08
Consensus pattern (20 bp):
CAGAGGAACCGAAATGCAAA
Found at i:12117958 original size:15 final size:14
Alignment explanation
Indices: 12117930--12117972 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
12117920 AATTAAAGTT
12117930 AAAATAAAGTACATAA
1 AAAATAAA--ACATAA
*
12117946 AAACTTAAAACATAA
1 AAA-ATAAAACATAA
12117961 AAAATAAAACAT
1 AAAATAAAACAT
12117973 CATCTTCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 8 0.33
15 9 0.38
16 3 0.12
17 4 0.17
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.19
Consensus pattern (14 bp):
AAAATAAAACATAA
Found at i:12123396 original size:12 final size:12
Alignment explanation
Indices: 12123379--12123408 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12123369 AGCCACATGC
12123379 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
12123391 CCGTGTGCGAGG
1 CCGTGTGCCAGG
12123403 CCGTGT
1 CCGTGT
12123409 AGCAGCCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.43, T:0.20
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:12130211 original size:40 final size:40
Alignment explanation
Indices: 12130167--12130403 Score: 332
Period size: 40 Copynumber: 5.9 Consensus size: 40
12130157 AATTAATGTC
12130167 TGAATGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCT
1 TGAATGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCT
* * *
12130207 TGAATGCACATTTGTGCCTCTGTTTGTACTTTGGTACCCT
1 TGAATGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCT
*
12130247 TGAATGCACATTCGTGCCCCTGTTTGTACTTCAGTACCCT
1 TGAATGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCT
* * * *
12130287 TGAATGCACATTTGTGCCCCTATTTGTACTACGATATCCC-
1 TGAATGCACATTCGTGCCCCTGTTTGTACTTCGGTA-CCCT
* * *
12130327 TGAATGCACATTCGTGCCCCCGTTTGTACTTCAGTACCCC
1 TGAATGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCT
* * *
12130367 TGAATGCACATTCATGCCCCTATTAGTACTTCGGTAC
1 TGAATGCACATTCGTGCCCCTGTTTGTACTTCGGTAC
12130404 TCCTGAAGGC
Statistics
Matches: 172, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
39 3 0.02
40 166 0.97
41 3 0.02
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.35
Consensus pattern (40 bp):
TGAATGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCT
Found at i:12137989 original size:6 final size:6
Alignment explanation
Indices: 12137978--12138046 Score: 138
Period size: 6 Copynumber: 11.5 Consensus size: 6
12137968 GAACTTGATA
12137978 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
12138026 TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TAT
12138047 GTATCCTAGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:12141010 original size:3 final size:3
Alignment explanation
Indices: 12141002--12141034 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
12140992 TTGATACTTT
12141002 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
12141035 ATGGAGGCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:12143037 original size:18 final size:18
Alignment explanation
Indices: 12143014--12143053 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12143004 TAAAACCATT
*
12143014 TATAAATATTTT-TAATAA
1 TATAAA-ATTTTAAAATAA
12143032 TATAAAATTTTAAAATAA
1 TATAAAATTTTAAAATAA
12143050 TATA
1 TATA
12143054 TTAAAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATAAAATTTTAAAATAA
Found at i:12151009 original size:22 final size:22
Alignment explanation
Indices: 12150984--12151044 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
12150974 TCAACACTTC
*
12150984 TGTGCTCTTTGATTAGCTCTTA
1 TGTGCTATTTGATTAGCTCTTA
*
12151006 TGTGCTATCTGATTAGCTCTTA
1 TGTGCTATTTGATTAGCTCTTA
*
12151028 TGTGCTATTTGTTTAGC
1 TGTGCTATTTGATTAGC
12151045 ACTTTGATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.15, C:0.16, G:0.20, T:0.49
Consensus pattern (22 bp):
TGTGCTATTTGATTAGCTCTTA
Found at i:12151108 original size:20 final size:20
Alignment explanation
Indices: 12151043--12151099 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
12151033 TATTTGTTTA
*
12151043 GCACTTTGATGCCTTTGATT
1 GCACTTTGATGCCTCTGATT
* *
12151063 GCACTTTGGTGCCTCTGTTT
1 GCACTTTGATGCCTCTGATT
*
12151083 GCACTTTGTTGCCTCTG
1 GCACTTTGATGCCTCTG
12151100 GTTACACTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (20 bp):
GCACTTTGATGCCTCTGATT
Found at i:12157888 original size:27 final size:26
Alignment explanation
Indices: 12157820--12157891 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 26
12157810 CTAATAGATG
12157820 AAAATGAATGAAATACCCCATAGGGT
1 AAAATGAATGAAATACCCCATAGGGT
*
12157846 AAAATG-ATCAAAATACCCTCATAGGGT
1 AAAATGAAT-GAAATACCC-CATAGGGT
**
12157873 AAAATGAATGTTATACCCC
1 AAAATGAATGAAATACCCC
12157892 TAAGAGATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 2 0.05
26 15 0.38
27 20 0.51
28 2 0.05
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.22
Consensus pattern (26 bp):
AAAATGAATGAAATACCCCATAGGGT
Found at i:12158143 original size:26 final size:26
Alignment explanation
Indices: 12158114--12158194 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
12158104 TTTGCCACAT
* *
12158114 ATACTGTTACTGGCAACTTTACTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
* * *
12158140 ATACTGATATTGGCAGCTCTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
* *
12158166 ATGCTATTACTTGG-AGCTTTGCTGCG
1 ATACTGTTAC-TGGCAGCTTTGCTGCG
12158192 ATA
1 ATA
12158195 TTGGTGTGTT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
26 40 0.93
27 3 0.07
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTGCG
Found at i:12158286 original size:58 final size:58
Alignment explanation
Indices: 12158196--12158326 Score: 226
Period size: 58 Copynumber: 2.3 Consensus size: 58
12158186 GCTGCGATAT
* *
12158196 TGGTGTGTTGGCTAGGTGGGTCAATTTTATCCCTACATGGTGTGTTGGTGGTACAGAG
1 TGGTGTGTTGGCTGGGTGGGTCAATTTTATCCCCACATGGTGTGTTGGTGGTACAGAG
* *
12158254 TGGTGTGTTGGCTGGGTGGGTCGATTTTATCCCCACATGGTGTGTTGGTGGTACGGAG
1 TGGTGTGTTGGCTGGGTGGGTCAATTTTATCCCCACATGGTGTGTTGGTGGTACAGAG
12158312 TGGTGTGTTGGCTGG
1 TGGTGTGTTGGCTGG
12158327 ATTGTTATGG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 69 1.00
ACGTcount: A:0.11, C:0.12, G:0.40, T:0.36
Consensus pattern (58 bp):
TGGTGTGTTGGCTGGGTGGGTCAATTTTATCCCCACATGGTGTGTTGGTGGTACAGAG
Found at i:12158385 original size:28 final size:28
Alignment explanation
Indices: 12158354--12158555 Score: 318
Period size: 28 Copynumber: 7.2 Consensus size: 28
12158344 TATTGCACTG
12158354 CACTGTTACTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
*
12158382 CACTGTTACTGTATTGAGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
12158410 CACTGATT-CTGTATTGGGCTAAGGCCCA
1 CACTG-TTACTGTATTGGGCTAAGGCCCA
12158438 CACTGATT-CTGTATTGGGCTAAGGCCCA
1 CACTG-TTACTGTATTGGGCTAAGGCCCA
* *
12158466 CATTGTTACTGTATTGGGCTAAGGGCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
* **
12158494 CACTGTGACTGTATTGGGCTAAGGATCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
12158522 CACTGTTACTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
12158550 CACTGT
1 CACTGT
12158556 ATTGTCTTTG
Statistics
Matches: 161, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
27 2 0.01
28 157 0.98
29 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.29
Consensus pattern (28 bp):
CACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:12159323 original size:22 final size:22
Alignment explanation
Indices: 12159298--12159344 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
12159288 AATAAATAGG
12159298 AATAAATA-AAATAAAATATTAA
1 AATAAATAGAAATAAAA-ATTAA
* *
12159320 AATAATTAGAATTAAAAATTAA
1 AATAAATAGAAATAAAAATTAA
12159342 AAT
1 AAT
12159345 TAGGTGTCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
AATAAATAGAAATAAAAATTAA
Found at i:12173435 original size:6 final size:6
Alignment explanation
Indices: 12173435--12173465 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
12173425 TTTATTTTTA
12173435 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT T
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT T
12173466 CACGCTTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTGT
Found at i:12175686 original size:17 final size:16
Alignment explanation
Indices: 12175664--12175698 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
12175654 GTTAGTGAAC
*
12175664 ATTGTCATTGCATTGTT
1 ATTGTCATCGCATT-TT
12175681 ATTGTCATCGCATTTT
1 ATTGTCATCGCATTTT
12175697 AT
1 AT
12175699 GCATGATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.51
Consensus pattern (16 bp):
ATTGTCATCGCATTTT
Found at i:12179000 original size:49 final size:48
Alignment explanation
Indices: 12178902--12179030 Score: 132
Period size: 49 Copynumber: 2.6 Consensus size: 48
12178892 ATGTGCTAGA
*
12178902 CCACTGGTAGAGCATGCTAGTTGCTAACTAGATAGGAGAATATGATGGG
1 CCACTGGTAGA-CATGCTAGTTGCTAACCAGATAGGAGAATATGATGGG
* ** * ** *
12178951 CCACTGGTAGCATATGCTAGTTGCTAACCAGATTTGCGTGTATGTTGGG
1 CCACTGGTAG-ACATGCTAGTTGCTAACCAGATAGGAGAATATGATGGG
* * *
12179000 CCACTGATAGGACATGTTAGTTGTTAACCAG
1 CCACTGGTA-GACATGCTAGTTGCTAACCAG
12179031 GTTGGTGACC
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
49 64 0.97
50 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (48 bp):
CCACTGGTAGACATGCTAGTTGCTAACCAGATAGGAGAATATGATGGG
Found at i:12179354 original size:48 final size:48
Alignment explanation
Indices: 12179276--12179372 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 48
12179266 AATGAGAGAT
* * *
12179276 TTGAAAAGAGTAAGTTAATATGACTCTGTATCTGATATATGTTATGTA
1 TTGAAAAGAGTAAATTAACATGACTCTGTATCTGATAAATGTTATGTA
* * * *
12179324 TTGAAAAGATTAAATTAACATGA-TAGTGTATGTGTTAAATGTTATGTA
1 TTGAAAAGAGTAAATTAACATGACT-CTGTATCTGATAAATGTTATGTA
12179372 T
1 T
12179373 AATTGCTGAC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
47 1 0.02
48 40 0.98
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40
Consensus pattern (48 bp):
TTGAAAAGAGTAAATTAACATGACTCTGTATCTGATAAATGTTATGTA
Found at i:12179638 original size:26 final size:26
Alignment explanation
Indices: 12179608--12179664 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
12179598 CTCTTTGGTG
* * *
12179608 TAAAGATGAAAGTATTCGCCCAATGT
1 TAAAGAAGAAAGTATACGCCCAATAT
*
12179634 TAAAGAAGAAAGTATACGCCCGATAT
1 TAAAGAAGAAAGTATACGCCCAATAT
12179660 TAAAG
1 TAAAG
12179665 TTCACCCGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (26 bp):
TAAAGAAGAAAGTATACGCCCAATAT
Found at i:12188298 original size:19 final size:19
Alignment explanation
Indices: 12188274--12188346 Score: 137
Period size: 19 Copynumber: 3.8 Consensus size: 19
12188264 AATCTTCAAG
*
12188274 GATATGCAATCTTAGATGT
1 GATATGCAATCTTAGATAT
12188293 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12188312 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12188331 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
12188347 AGATATGATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:12188372 original size:22 final size:22
Alignment explanation
Indices: 12188274--12188369 Score: 93
Period size: 19 Copynumber: 4.7 Consensus size: 22
12188264 AATCTTCAAG
*
12188274 GATATGCAATCTT---AGATGT
1 GATATGCAATCTTAGAAGATAT
12188293 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
12188312 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
12188331 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
12188353 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
12188370 GATTTAATTT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
19 50 0.71
22 8 0.11
23 12 0.17
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:12188953 original size:36 final size:38
Alignment explanation
Indices: 12188890--12188967 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
12188880 CATACATGCA
*
12188890 TTTTATAATATATACATATACGTACATA-TTTTTTA-AT
1 TTTTATAATATATACATATACG-ACATACTTTTATATAT
*
12188927 TTTTATAAATATATATATATAC-ACATACTTTTATATAT
1 TTTTAT-AATATATACATATACGACATACTTTTATATAT
12188965 TTT
1 TTT
12188968 CTATGTTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
36 5 0.14
37 12 0.33
38 19 0.53
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (38 bp):
TTTTATAATATATACATATACGACATACTTTTATATAT
Found at i:12189291 original size:3 final size:3
Alignment explanation
Indices: 12189285--12189332 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
12189275 CATCATCATC
12189285 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12189333 TTCTTGATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12190329 original size:3 final size:3
Alignment explanation
Indices: 12190321--12190398 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
12190311 TATGTTACCT
12190321 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12190369 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12190399 AGCTATTTTA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12191836 original size:31 final size:31
Alignment explanation
Indices: 12191737--12191839 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 31
12191727 TACTCACGTT
* * * * *
12191737 AATATTAAATTAATAAAATACTATCAAGATC
1 AATATTAAATTCATAAATTAATATCAACATA
* * * * *
12191768 AATATTTAA-CCA-AATTTAATATCTCACATT
1 AATATTAAATTCATAAATTAATATC-AACATA
*
12191798 AATATTAAATTCATAAATTAATATCAATATA
1 AATATTAAATTCATAAATTAATATCAACATA
12191829 AATATTAAATT
1 AATATTAAATT
12191840 AAATTAAATA
Statistics
Matches: 54, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
29 8 0.15
30 12 0.22
31 24 0.44
32 10 0.19
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.38
Consensus pattern (31 bp):
AATATTAAATTCATAAATTAATATCAACATA
Found at i:12191844 original size:61 final size:61
Alignment explanation
Indices: 12191729--12191850 Score: 154
Period size: 61 Copynumber: 2.0 Consensus size: 61
12191719 ATTGAAATTA
* * * * *
12191729 CTCACGTTAATATTAAATTAATAAAATACTATCAAGATCAATATTTAACCAAATTTAATAT
1 CTCACATTAATATTAAATTAATAAAATAATATCAAGATAAATATTAAACCAAATTAAATAT
* * * **
12191790 CTCACATTAATATTAAATTCATAAATTAATATCAATATAAATATTAAATTAAATTAAATAT
1 CTCACATTAATATTAAATTAATAAAATAATATCAAGATAAATATTAAACCAAATTAAATAT
12191851 TAAATTTATT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.38
Consensus pattern (61 bp):
CTCACATTAATATTAAATTAATAAAATAATATCAAGATAAATATTAAACCAAATTAAATAT
Found at i:12195362 original size:43 final size:43
Alignment explanation
Indices: 12195286--12195418 Score: 137
Period size: 43 Copynumber: 3.1 Consensus size: 43
12195276 AAACACATAT
* * * * *
12195286 ATCACATA-CAATGCC-ATATCCCAGATATGGTCTTACATGTT
1 ATCACATATCGATGCCAATGTCCCAGACATGGTCTTACACGTA
* *
12195327 ATCACATATCGATGTCACTGTCCCAGACA-GAGTCTTACACGTA
1 ATCACATATCGATGCCAATGTCCCAGACATG-GTCTTACACGTA
* * **
12195370 ATCTCATATTGATGCCAATGTCCCAGACATGGTCTTACACAAA
1 ATCACATATCGATGCCAATGTCCCAGACATGGTCTTACACGTA
12195413 ATCACA
1 ATCACA
12195419 CCTCAGGAGT
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
41 8 0.11
42 6 0.08
43 59 0.80
44 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (43 bp):
ATCACATATCGATGCCAATGTCCCAGACATGGTCTTACACGTA
Found at i:12202968 original size:43 final size:42
Alignment explanation
Indices: 12202872--12202978 Score: 106
Period size: 43 Copynumber: 2.5 Consensus size: 42
12202862 TATCTCAAAT
* * * *
12202872 ATGGTCTTACATGTTATCACATATCGATGCCACTGTCTCAGA
1 ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGA
* * * * *
12202914 AAGAATTTTACACGTAATCTCATATTGATGCCAATGTCCCAGA
1 ATG-GTCTTACACGTAATCACATATCGATGCCAATGTCCCAGA
*
12202957 CATGGTCTTACACGAAATCACA
1 -ATGGTCTTACACGTAATCACA
12202979 CCTCGGGAGT
Statistics
Matches: 49, Mismatches: 14, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
42 2 0.04
43 45 0.92
44 2 0.04
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGA
Done.