Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007905.1 Hibiscus syriacus cultivar Beakdansim tig00110299_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2946335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:465864 original size:43 final size:43
Alignment explanation
Indices: 465816--465897 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
465806 ATGAAGGGGC
*
465816 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCATACCCACA
* *
465859 CATCCACGATTTTAACTCCACGATGGAGGATATCATACC
1 CATCCACGATTTCAACTCCACGACGGAGGATATCATACC
465898 ATTCGGGGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.22
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCATACCCACA
Found at i:466136 original size:110 final size:109
Alignment explanation
Indices: 465936--466138 Score: 309
Period size: 110 Copynumber: 1.8 Consensus size: 109
465926 GCTTCCCAAT
* *
465936 TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTAGACTTAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGTGAAAGATATTAGACTCAAGACAACACAAGCTCAACTTCA
*
466001 CGACGAAGGGGCGGCTGATTATCAACAAATAACTTTTCAATTTCA
66 CGAC-AAGGGGCGGCTGACTATCAACAAATAACTTTTCAATTTCA
* * *
466046 TTCAGAGTCAATTTCAACTTCATAGTGAAAGATATTAGACTCAAGACAGCACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGTGAAAGATATTAGACTCAAGACAACACAAGCTCAACTTCA
*
466111 CAGTA-AAGGGGCGGCTGACTGTCAACAA
66 C-G-ACAAGGGGCGGCTGACTATCAACAA
466139 GCATTTTCCC
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
110 82 0.98
111 1 0.01
112 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (109 bp):
TTCAGAGCCAATTTCAACTTCACAGTGAAAGATATTAGACTCAAGACAACACAAGCTCAACTTCA
CGACAAGGGGCGGCTGACTATCAACAAATAACTTTTCAATTTCA
Found at i:466667 original size:36 final size:36
Alignment explanation
Indices: 466627--466698 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
466617 ATTTGAAATG
* *
466627 AATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
1 AATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
* *
466663 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
466699 TAAACTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (36 bp):
AATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
Found at i:466753 original size:29 final size:29
Alignment explanation
Indices: 466681--466759 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 29
466671 CTCCCTTGAG
466681 ACAGTTTCTCTTGAAACATAAACTTTGAAA
1 ACAGTTTCTCTTGAAACA-AAACTTTGAAA
* * *
466711 ACAGATTCCCTTGAAACAAAACCTTTGAAT
1 ACAGTTTCTCTTGAAACAAAA-CTTTGAAA
*
466741 A-TGTTTCTCTTGAAACAAA
1 ACAGTTTCTCTTGAAACAAA
466760 TTTTTTTCTC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 18 0.43
30 24 0.57
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (29 bp):
ACAGTTTCTCTTGAAACAAAACTTTGAAA
Found at i:466770 original size:96 final size:96
Alignment explanation
Indices: 466567--466792 Score: 262
Period size: 96 Copynumber: 2.4 Consensus size: 96
466557 ACTTGTAATG
* * ***
466567 AATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTGAAATGAATTT
1 AATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACAATTCAAATGAAACA
* *
466632 TATCTCTCTTGAGATAGTTTCCCTTGAAACA
66 AAACTCTCTTGAGATAGTTTCCCTTGAAACA
* * ***
466663 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACAGATTCCCTTGAAAC
1 AATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA-ATTCAAATGAAAC
*
466728 AAAAC-CT-TTGA-ATATGTTTCTCTTGAAACA
65 AAAACTCTCTTGAGATA-GTTTCCCTTGAAACA
*
466758 AATTTTTTTCTCCC-TGAAGACAATTTCTCTTGAAA
1 AA-TTTTTTCTCCCTTG-AGACAGTTTCTCTTGAAA
466793 AAGAAAAGCT
Statistics
Matches: 111, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
94 3 0.03
95 22 0.20
96 78 0.70
97 8 0.07
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (96 bp):
AATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACAATTCAAATGAAACA
AAACTCTCTTGAGATAGTTTCCCTTGAAACA
Found at i:466881 original size:40 final size:38
Alignment explanation
Indices: 466790--466902 Score: 140
Period size: 40 Copynumber: 2.9 Consensus size: 38
466780 ATTTCTCTTG
* * * * *
466790 AAAAAGAAAAGCTTTGAAGTCGTTTCTCTTGGAAC-AC
1 AAAAAGAAAACCTTTGAAATTGTTTCTCTTGAAACAAA
466827 AAAAAGAAAACCTTTGAAATTGTTTCTCTTGAAACAAAAA
1 AAAAAGAAAACCTTTGAAATTGTTTCTCTTGAAAC--AAA
466867 AAAAAGAAAACCTTTGAACA-TGTTTCTCTTGAAACA
1 AAAAAGAAAACCTTTGAA-ATTGTTTCTCTTGAAACA
466903 CCAAAGCTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
37 31 0.46
38 1 0.01
40 34 0.51
41 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.27
Consensus pattern (38 bp):
AAAAAGAAAACCTTTGAAATTGTTTCTCTTGAAACAAA
Found at i:468772 original size:15 final size:14
Alignment explanation
Indices: 468754--468783 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
468744 TCATTATTTG
468754 TATATATTTTATTAT
1 TATATATTTT-TTAT
468769 TATATATTTTTTAT
1 TATATATTTTTTAT
468783 T
1 T
468784 TTTATGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATATATTTTTTAT
Found at i:468780 original size:17 final size:17
Alignment explanation
Indices: 468754--468788 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
468744 TCATTATTTG
468754 TATATATTTTATTATTA
1 TATATATTTTATTATTA
* *
468771 TATATTTTTTATTTTTA
1 TATATATTTTATTATTA
468788 T
1 T
468789 GGTTATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATATATTTTATTATTA
Found at i:477837 original size:45 final size:46
Alignment explanation
Indices: 477771--477894 Score: 187
Period size: 46 Copynumber: 2.7 Consensus size: 46
477761 GGTGCACTAA
* * * * *
477771 GAGTGCAACGATGCATAAAATGCATTCGATGTTTTGA-AATAGCCT
1 GAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCT
477816 GAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCT
1 GAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCT
*
477862 GAGTGCATTGATGCATCAAATGCATTCGATGTT
1 GAGTGCATCGATGCATCAAATGCATTCGATGTT
477895 CAATTAATTC
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 34 0.47
46 38 0.53
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (46 bp):
GAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCT
Found at i:480503 original size:22 final size:22
Alignment explanation
Indices: 480473--480531 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
480463 TTTGTACAGA
**
480473 GGAATCGATACCCCCTTGAAGG
1 GGAATCGATACCCCCTACAAGG
* *
480495 GGAACCGATTCCCCC-ACAAGG
1 GGAATCGATACCCCCTACAAGG
480516 GGAATCGATACCCCCT
1 GGAATCGATACCCCCT
480532 GAGGGTTCTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.27, C:0.34, G:0.24, T:0.15
Consensus pattern (22 bp):
GGAATCGATACCCCCTACAAGG
Found at i:484222 original size:16 final size:16
Alignment explanation
Indices: 484201--484251 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
484191 TGCAGCCAGG
484201 GTGTATCGATACACTA
1 GTGTATCGATACACTA
*
484217 GTGTATGGATACACTCAGA
1 GTGTATCGATACACT---A
*
484236 GTGTATCGGTACACTA
1 GTGTATCGATACACTA
484252 TTTGCATTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 15 0.52
19 14 0.48
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (16 bp):
GTGTATCGATACACTA
Found at i:484305 original size:21 final size:20
Alignment explanation
Indices: 484279--484348 Score: 85
Period size: 16 Copynumber: 3.6 Consensus size: 20
484269 AGCAGTCATA
*
484279 GGTGTATGGATACACCTGCAG
1 GGTGTATCGATACA-CTGCAG
484300 GGTGTATCGATACAC--CA-
1 GGTGTATCGATACACTGCAG
*
484317 -GTGTATGGATACACTGCAG
1 GGTGTATCGATACACTGCAG
484336 GGTGTATCGATAC
1 GGTGTATCGATAC
484349 CCTTTGACAC
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
16 13 0.31
18 4 0.10
20 12 0.29
21 13 0.31
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
GGTGTATCGATACACTGCAG
Found at i:486324 original size:20 final size:20
Alignment explanation
Indices: 486299--486391 Score: 132
Period size: 20 Copynumber: 4.6 Consensus size: 20
486289 TAGTTGAAAA
486299 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
486319 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
486339 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
486360 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
486380 TCGCGTTGCGAT
1 TCGCGTTGCGAT
486392 AGTCTACAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
20 47 0.76
21 15 0.24
ACGTcount: A:0.14, C:0.23, G:0.24, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:486341 original size:61 final size:61
Alignment explanation
Indices: 486274--486391 Score: 236
Period size: 61 Copynumber: 1.9 Consensus size: 61
486264 ATTCGCGTTG
486274 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
486335 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
486392 AGTCTACAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (61 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
Found at i:486364 original size:41 final size:41
Alignment explanation
Indices: 486319--486437 Score: 165
Period size: 41 Copynumber: 2.9 Consensus size: 41
486309 ATTTTCCATT
486319 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-AAAA
*
486360 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTAAAA
*
486401 T-GTCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTA
1 TCG-CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTA
486438 CAGTTGTTGT
Statistics
Matches: 73, Mismatches: 2, Indels: 7
0.89 0.02 0.09
Matches are distributed among these distances:
40 16 0.22
41 53 0.73
42 4 0.05
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTAAAA
Found at i:486446 original size:19 final size:20
Alignment explanation
Indices: 486384--486466 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 20
486374 TCCATTTCGC
*
486384 GTTGCGATAGTCTACAATGTC
1 GTTGCGATAGTCTAC-ATGTT
** * * *
486405 GTTGCGATTTTCCAAAT-TC
1 GTTGCGATAGTCTACATGTT
486424 GTTGCGATAGTCTACAGTTGTT
1 GTTGCGATAGTCTACA--TGTT
*
486446 GTTGCGAAAGTCTACA-GTT
1 GTTGCGATAGTCTACATGTT
486465 GT
1 GT
486467 CGTTGCGATT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
19 19 0.39
20 2 0.04
21 12 0.24
22 16 0.33
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCTACATGTT
Found at i:486451 original size:22 final size:22
Alignment explanation
Indices: 486383--486475 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
486373 TTCCATTTCG
*
486383 CGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
486404 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
486423 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
486445 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
486467 CGTTGCGAT
1 CGTTGCGAT
486476 TTTCCAAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
19 14 0.24
20 2 0.03
21 14 0.24
22 28 0.48
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:486569 original size:6 final size:6
Alignment explanation
Indices: 486558--486629 Score: 126
Period size: 6 Copynumber: 12.0 Consensus size: 6
486548 CGAAGACACG
*
486558 TATTAC TATTAC TATTAC TATTAC TATTAC AATTAC TATTAC TATTAC
1 TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC
*
486606 TATTAC TATTAC TATTAC AATTAC
1 TATTAC TATTAC TATTAC TATTAC
486630 CACGACCACG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (6 bp):
TATTAC
Found at i:486637 original size:6 final size:6
Alignment explanation
Indices: 486628--486666 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
486618 TATTACAATT
486628 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
486667 CGAGACGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:487336 original size:19 final size:19
Alignment explanation
Indices: 487312--487380 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
487302 AACGCGATTT
487312 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
487331 TCGCAACCGCAACTGTAGACTA
1 TCGCAA-CG-AA-TTTGGAAAA
*
487353 TCGCAACAAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
*
487372 TTGCAACGA
1 TCGCAACGA
487381 CAACTGTAGA
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
19 18 0.50
20 4 0.11
21 3 0.08
22 11 0.31
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:487358 original size:41 final size:41
Alignment explanation
Indices: 487312--487398 Score: 140
Period size: 41 Copynumber: 2.1 Consensus size: 41
487302 AACGCGATTT
*
487312 TCGCAACGAATTTGGAAAATCGCAACCG-CAACTGTAGACTA
1 TCGCAACAAATTTGGAAAATCGCAA-CGACAACTGTAGACTA
*
487353 TCGCAACAAATTTGGAAAATTGCAACGACAACTGTAGACTA
1 TCGCAACAAATTTGGAAAATCGCAACGACAACTGTAGACTA
487394 TCGCA
1 TCGCA
487399 TCGCGATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 2 0.05
41 41 0.95
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (41 bp):
TCGCAACAAATTTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:487416 original size:21 final size:21
Alignment explanation
Indices: 487390--487446 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
487380 ACAACTGTAG
*
487390 ACTATCGCATCGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
*
487411 ACTATCGCAACGTGATTTTCA
1 ACTATCGCAACGCGATTTTCA
487432 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
487447 ACTGGAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:487460 original size:20 final size:20
Alignment explanation
Indices: 487435--487490 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
487425 ATTTTCAACT
* *
487435 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGAAAA
487455 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
487475 ATCGCAACTCGAAATG
1 ATCGCAACGCGAAATG
487491 CAACGCGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:490797 original size:20 final size:20
Alignment explanation
Indices: 490774--490825 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
490764 TACCACGTGA
*
490774 ACAATATCGGTATTGTTCAT
1 ACAATATCGATATTGTTCAT
*
490794 ACAATATCGATATTGTTTAT
1 ACAATATCGATATTGTTCAT
490814 ACAATATCGATA
1 ACAATATCGATA
490826 CTATACGAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (20 bp):
ACAATATCGATATTGTTCAT
Found at i:508373 original size:28 final size:28
Alignment explanation
Indices: 508342--508395 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
508332 TTTAACTACT
508342 CAAATTTACTAATATT-TATTAAATTAAA
1 CAAATTT-CTAATATTATATTAAATTAAA
* *
508370 CAAATTTCTATTATTATATTATATTA
1 CAAATTTCTAATATTATATTAAATTA
508396 TTATATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (28 bp):
CAAATTTCTAATATTATATTAAATTAAA
Found at i:508396 original size:13 final size:14
Alignment explanation
Indices: 508378--508411 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
508368 AACAAATTTC
508378 TATTATTATATTA-
1 TATTATTATATTAT
508391 TATTATTATATTAT
1 TATTATTATATTAT
508405 TATTATT
1 TATTATT
508412 TTGAGTAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTATTATATTAT
Found at i:508877 original size:20 final size:21
Alignment explanation
Indices: 508791--508879 Score: 60
Period size: 20 Copynumber: 4.1 Consensus size: 21
508781 TAAAAGAGAT
*
508791 TTTTTAATGTGAGTTA-ATAAA
1 TTTTT-ATTTGAGTTACATAAA
*
508812 TTTTTATTTGAGCTACA-AAA
1 TTTTTATTTGAGTTACATAAA
* *
508832 TTTTAATTAAATTT-ATTTAAATAAA
1 -TTT--TT--ATTTGAGTTACATAAA
508857 TTTTTATTTGAGTTACA-AAA
1 TTTTTATTTGAGTTACATAAA
508877 TTT
1 TTT
508880 AATTAATTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 17
0.69 0.09 0.22
Matches are distributed among these distances:
20 21 0.40
21 14 0.26
22 2 0.04
23 2 0.04
24 7 0.13
25 7 0.13
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (21 bp):
TTTTTATTTGAGTTACATAAA
Found at i:509517 original size:27 final size:27
Alignment explanation
Indices: 509487--509575 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 27
509477 AAAACTATTA
509487 ATAAATTACAA-AAGTACATATTTTTTT
1 ATAAATTACAATAAGTACA-ATTTTTTT
* * *
509514 AT-AATCACAATAAGTACAATACTATTT
1 ATAAATTACAATAAGTACAAT-TTTTTT
*
509541 ATAAATTACAATTAAATACAAATTTTTTT
1 ATAAATTACAA-TAAGTAC-AATTTTTTT
*
509570 AAAAAT
1 ATAAAT
509576 AAAAAAATAC
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
26 9 0.18
27 15 0.31
28 7 0.14
29 15 0.31
30 3 0.06
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.39
Consensus pattern (27 bp):
ATAAATTACAATAAGTACAATTTTTTT
Found at i:509545 original size:54 final size:52
Alignment explanation
Indices: 509475--509612 Score: 145
Period size: 54 Copynumber: 2.6 Consensus size: 52
509465 ATCATAAAGA
* * * * *
509475 ACAAAACTATTAATAAATTACAAAAGTACATATTTTTTT-ATAATCACAATAAGT
1 ACAAAACTATTTATAAATTACAAAA-TACAAATTTTTTTAAAAAT-A-AAAAAAT
*
509529 ACAATACTATTTATAAATTACAATTAAATACAAATTTTTTTAAAAATAAAAAAAT
1 ACAAAACTATTTATAAATTAC-A--AAATACAAATTTTTTTAAAAATAAAAAAAT
*
509584 ACAAAAC-ATTTATAAATTATAAAATACAA
1 ACAAAACTATTTATAAATTACAAAATACAA
509613 TAAAAGGAAC
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
51 8 0.11
53 1 0.01
54 31 0.43
55 12 0.17
56 13 0.18
57 7 0.10
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.34
Consensus pattern (52 bp):
ACAAAACTATTTATAAATTACAAAATACAAATTTTTTTAAAAATAAAAAAAT
Found at i:510192 original size:24 final size:24
Alignment explanation
Indices: 510159--510220 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
510149 GTTGATGTCA
510159 AGGTCGCCATGCACGCCGTAGGGT
1 AGGTCGCCATGCACGCCGTAGGGT
* *
510183 AGGTCACCATGCACGCCGTTGGGT
1 AGGTCGCCATGCACGCCGTAGGGT
510207 AGGTCGCCATGCAC
1 AGGTCGCCATGCAC
510221 TCCTAGCGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.18, C:0.31, G:0.34, T:0.18
Consensus pattern (24 bp):
AGGTCGCCATGCACGCCGTAGGGT
Found at i:518517 original size:29 final size:29
Alignment explanation
Indices: 518482--518563 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
518472 AAACTAAATT
* *
518482 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
* *
518511 GTTGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
518540 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
518564 GTTAGGTGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 42 0.89
30 5 0.11
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:519874 original size:15 final size:15
Alignment explanation
Indices: 519851--519880 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
519841 ACGAGGCTGG
519851 AATTACAACAACAAC
1 AATTACAACAACAAC
*
519866 AATTCCAACAACAAC
1 AATTACAACAACAAC
519881 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:523230 original size:29 final size:29
Alignment explanation
Indices: 523195--523281 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
523185 AAACTAAATT
*
523195 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
* * *
523224 GCTGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
*
523253 GATGTCATTGCTTACATCAATTTAGTTAA
1 GATGTCATTGCTTACATC-ATTTAATTAA
523282 GTGAGAGTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 42 0.84
30 8 0.16
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:525337 original size:29 final size:29
Alignment explanation
Indices: 525267--525443 Score: 160
Period size: 29 Copynumber: 6.2 Consensus size: 29
525257 TTTTTGTTTG
** *
525267 TTTGTATTTTATAATAATTTATAAATTGT
1 TTTGTATTTTATTTTAATTTATAAATAGT
*
525296 TTTGTATTTTATTTTAATTTATAAATTGT
1 TTTGTATTTTATTTTAATTTATAAATAGT
**
525325 TTTGTATTTTATTTTAATTT-TAAA-AAA
1 TTTGTATTTTATTTTAATTTATAAATAGT
* * * *
525352 ATTGTATTTAATTGTAATTTATAAATAGC
1 TTTGTATTTTATTTTAATTTATAAATAGT
* * * * * *
525381 ATTGTACTTTATTGTGATTTATAAAAAAT
1 TTTGTATTTTATTTTAATTTATAAATAGT
* * * *
525410 TATGTACTTTATTTTGATTTATTAATAGT
1 TTTGTATTTTATTTTAATTTATAAATAGT
525439 TTTGT
1 TTTGT
525444 TCTTTATGAT
Statistics
Matches: 123, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
27 17 0.14
28 8 0.07
29 98 0.80
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (29 bp):
TTTGTATTTTATTTTAATTTATAAATAGT
Found at i:525386 original size:56 final size:57
Alignment explanation
Indices: 525297--525408 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 57
525287 ATAAATTGTT
* * * ** * *
525297 TTGTATTTTATTTTAATTTATAAATTGTTTTGTATTTTATTTTAATTT-TAAAAAAA
1 TTGTATTTAATTGTAATTTATAAATAGCATTGTACTTTATTGTAATTTATAAAAAAA
*
525353 TTGTATTTAATTGTAATTTATAAATAGCATTGTACTTTATTGTGATTTATAAAAAA
1 TTGTATTTAATTGTAATTTATAAATAGCATTGTACTTTATTGTAATTTATAAAAAA
525409 TTATGTACTT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
56 40 0.85
57 7 0.15
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (57 bp):
TTGTATTTAATTGTAATTTATAAATAGCATTGTACTTTATTGTAATTTATAAAAAAA
Found at i:526152 original size:21 final size:22
Alignment explanation
Indices: 526126--526167 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
526116 CTTTTTACCT
*
526126 AATTTC-AAATCTTAAACCCTA
1 AATTTCAAAATCTCAAACCCTA
526147 AATTTCAAAATCTCAAACCCT
1 AATTTCAAAATCTCAAACCCT
526168 CAAACAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31
Consensus pattern (22 bp):
AATTTCAAAATCTCAAACCCTA
Found at i:528303 original size:43 final size:42
Alignment explanation
Indices: 528256--528437 Score: 134
Period size: 43 Copynumber: 4.2 Consensus size: 42
528246 ATTGTTCAAC
528256 AAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTATCATTA
1 AAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTT-TCATTA
* * * **
528299 AAACGCCGCAATA-GTCGTTGATGTTTAGCGGCGTTTTCTACAA
1 AAACGCCGCAAAAGGT-ATTGATATTTAGCGGCGTTTTC-ATTA
** * * * * *
528342 AAACGCCGCAGTAGTTTTTTATTTTTACCGGCGTTTTC-TTA
1 AAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTTCATTA
* * * * *
528383 CAAACGCCGCAGAATATGTATTGAGATTTTGCGGCGTTTTTATCAA
1 -AAACGCCGCA-AA-AGGTATTGATATTTAGCGGCGTTTTCAT-TA
528429 AAACGCCGC
1 AAACGCCGC
528438 TAACTGTATG
Statistics
Matches: 106, Mismatches: 25, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
41 1 0.01
42 14 0.13
43 62 0.58
44 18 0.17
45 10 0.09
46 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTTCATTA
Found at i:528346 original size:86 final size:86
Alignment explanation
Indices: 528238--528437 Score: 196
Period size: 86 Copynumber: 2.3 Consensus size: 86
528228 TTACAACATA
* * *
528238 TAGCGGCGATTGT-TCAACAAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTATCATTA-AA
1 TAGCGGCGTTTTTATCAA-AAACGCCGCAAAAGGTATTGATATTTACCGGCGTTT-TC-TTACAA
*
528301 ACGCCGC-AATA-GTCGTTGATG-TT
63 ACGCCGCAAATATGT-ATTGA-GATT
** * * * *
528324 TAGCGGCGTTTTCTA-CAAAAACGCCGCAGTAGTTTTTTATTTTTACCGGCGTTTTCTTACAAAC
1 TAGCGGCGTTTT-TATCAAAAACGCCGCAAAAGGTATTGATATTTACCGGCGTTTTCTTACAAAC
528388 GCCGCAGAATATGTATTGAGATT
65 GCCGCA-AATATGTATTGAGATT
*
528411 TTGCGGCGTTTTTATCAAAAACGCCGC
1 TAGCGGCGTTTTTATCAAAAACGCCGC
528438 TAACTGTATG
Statistics
Matches: 95, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
84 3 0.03
85 11 0.12
86 42 0.44
87 37 0.39
88 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (86 bp):
TAGCGGCGTTTTTATCAAAAACGCCGCAAAAGGTATTGATATTTACCGGCGTTTTCTTACAAACG
CCGCAAATATGTATTGAGATT
Found at i:528840 original size:21 final size:21
Alignment explanation
Indices: 528776--528884 Score: 103
Period size: 21 Copynumber: 5.2 Consensus size: 21
528766 TGATATATTA
* * *
528776 CTTCTCTCTGTTCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* * *
528797 CCTCTCTCTGTGCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
528818 CTTCTCTCTCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* **
528839 CTGCTCTAGCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* *
528860 CTGCTCTCTCTGTTTCC-CTTG
1 CTTCTCTCTCTGCTTCCGC-TG
528881 CTTC
1 CTTC
528885 ATTTTCCGCT
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
20 1 0.01
21 74 0.99
ACGTcount: A:0.01, C:0.40, G:0.18, T:0.40
Consensus pattern (21 bp):
CTTCTCTCTCTGCTTCCGCTG
Found at i:539464 original size:15 final size:15
Alignment explanation
Indices: 539444--539474 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
539434 CGTAATAGGA
539444 GCATATGTTTGACAT
1 GCATATGTTTGACAT
539459 GCATATGTTTGACAT
1 GCATATGTTTGACAT
539474 G
1 G
539475 ATGTATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (15 bp):
GCATATGTTTGACAT
Found at i:540008 original size:31 final size:31
Alignment explanation
Indices: 539970--540123 Score: 179
Period size: 31 Copynumber: 4.9 Consensus size: 31
539960 GAGTCGAGGG
*
539970 TTACCTATGTCTTTCGAGG-CATATGGACAGA
1 TTACCTATGTCTTTTG-GGACATATGGACAGA
540001 TTACCTATGTCTTTTGGGACATATGGACAGA
1 TTACCTATGTCTTTTGGGACATATGGACAGA
* * *
540032 TTACCTATGTATTTTGAGACATATGGATAGGA
1 TTACCTATGTCTTTTGGGACATATGGACA-GA
* *
540064 TTACCTATGTCCTTTGGGACATATGGATA-A
1 TTACCTATGTCTTTTGGGACATATGGACAGA
* *
540094 TTTACCTATGT-TCTTAGGAACATATGGACA
1 -TTACCTATGTCT-TTTGGGACATATGGACA
540124 TGTCCTTCGA
Statistics
Matches: 108, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
30 3 0.03
31 77 0.71
32 28 0.26
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (31 bp):
TTACCTATGTCTTTTGGGACATATGGACAGA
Found at i:540080 original size:63 final size:62
Alignment explanation
Indices: 539970--540104 Score: 191
Period size: 63 Copynumber: 2.2 Consensus size: 62
539960 GAGTCGAGGG
* * *
539970 TTACCTATGTCTTTCGAGGCATATGGACAGATTACCTATGTCTTTTGGGACATATGGACAGA-
1 TTACCTATGTATTTCGAGACATATGGACAGATTACCTATGTCCTTTGGGACATATGGACA-AT
* * *
540032 TTACCTATGTATTTTGAGACATATGGATAGGATTACCTATGTCCTTTGGGACATATGGATAAT
1 TTACCTATGTATTTCGAGACATATGGACA-GATTACCTATGTCCTTTGGGACATATGGACAAT
540095 TTACCTATGT
1 TTACCTATGT
540105 TCTTAGGAAC
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
62 26 0.40
63 39 0.60
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (62 bp):
TTACCTATGTATTTCGAGACATATGGACAGATTACCTATGTCCTTTGGGACATATGGACAAT
Found at i:540117 original size:63 final size:62
Alignment explanation
Indices: 539970--540123 Score: 188
Period size: 63 Copynumber: 2.5 Consensus size: 62
539960 GAGTCGAGGG
* * * *
539970 TTACCTATGTCTTTCGAGGCATATGGACAGATTACCTATGTCTTTTGGGACATATGGACAGA
1 TTACCTATGTATTTGGAGACATATGGACAGATTACCTATGTCCTTTGGGACATATGGACAGA
* * *
540032 TTACCTATGTATTTTGAGACATATGGATAGGATTACCTATGTCCTTTGGGACATATGGATA-A
1 TTACCTATGTATTTGGAGACATATGGACA-GATTACCTATGTCCTTTGGGACATATGGACAGA
540094 TTTACCTATGT-TCTTAGGA-ACATATGGACA
1 -TTACCTATGTAT-TT-GGAGACATATGGACA
540124 TGTCCTTCGA
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
62 27 0.34
63 51 0.64
64 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (62 bp):
TTACCTATGTATTTGGAGACATATGGACAGATTACCTATGTCCTTTGGGACATATGGACAGA
Found at i:550439 original size:25 final size:25
Alignment explanation
Indices: 550411--550460 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
550401 GACATTAATC
550411 ATGTTTGTAGTTCAATCTATTAAAA
1 ATGTTTGTAGTTCAATCTATTAAAA
550436 ATGTTTGTAGTTCAATCTATTAAAA
1 ATGTTTGTAGTTCAATCTATTAAAA
550461 TATAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (25 bp):
ATGTTTGTAGTTCAATCTATTAAAA
Found at i:552656 original size:3 final size:3
Alignment explanation
Indices: 552643--552716 Score: 51
Period size: 3 Copynumber: 25.0 Consensus size: 3
552633 TTACCCATTT
* * * * * * * *
552643 TTA TT- TTA TTA TTA TAA TTA TTA TTA TAA TAA TAA TAA TAA TAA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
552690 TAA TAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
552717 AAAAAATAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (3 bp):
TTA
Found at i:552657 original size:6 final size:6
Alignment explanation
Indices: 552648--552716 Score: 57
Period size: 6 Copynumber: 11.5 Consensus size: 6
552638 CATTTTTATT
* * * * * *
552648 TTATTA TTATAA TTATTA TTATAA TAATAA TAATAA TAATAA TAATAA
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA
* * *
552696 TTATTA TTATTA TTATTA TTA
1 TTATAA TTATAA TTATAA TTA
552717 AAAAAATAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTATAA
Found at i:554064 original size:22 final size:21
Alignment explanation
Indices: 554009--554065 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
553999 GTTCTAATTG
* *
554009 TATTTTTATTGT-TTTAATTT
1 TATTTTTATTATATTTAATAT
554029 TACTTATTTA-TATATTTAAATAT
1 TA-TT-TTTATTATATTT-AATAT
554052 TATTTTTATTATAT
1 TATTTTTATTATAT
554066 AGTCATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
20 2 0.07
21 8 0.27
22 14 0.47
23 6 0.20
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTTTTATTATATTTAATAT
Found at i:558225 original size:15 final size:15
Alignment explanation
Indices: 558205--558236 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
558195 ATCAATACCT
558205 TTTTGCATACATACA
1 TTTTGCATACATACA
*
558220 TTTTGCATACATTCA
1 TTTTGCATACATACA
558235 TT
1 TT
558237 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:565583 original size:1 final size:1
Alignment explanation
Indices: 565577--565632 Score: 67
Period size: 1 Copynumber: 56.0 Consensus size: 1
565567 ATGCTTGAAG
* * * * *
565577 AAAAAAAAAAGAAAAAAAAAAGAAACAAAAAAGAAAAAAAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
565633 GGGGTCAAGA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.91, C:0.02, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:565632 original size:11 final size:11
Alignment explanation
Indices: 565574--565630 Score: 89
Period size: 11 Copynumber: 5.2 Consensus size: 11
565564 ATTATGCTTG
565574 AAGAAAAAAAA
1 AAGAAAAAAAA
565585 AAGAAAAAAAA
1 AAGAAAAAAAA
*
565596 AAGAAACAAAA
1 AAGAAAAAAAA
565607 AAGAAAAAAAA
1 AAGAAAAAAAA
565618 AA-AAAAAGAAA
1 AAGAAAAA-AAA
565629 AA
1 AA
565631 AAGGGGTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.12
11 38 0.88
ACGTcount: A:0.89, C:0.02, G:0.09, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:567073 original size:115 final size:114
Alignment explanation
Indices: 566910--567139 Score: 361
Period size: 115 Copynumber: 2.0 Consensus size: 114
566900 AGCAAGTACC
*
566910 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATATTATGGAAGTGTTCTTTGAGTTATCTG
* * * * * * *
566975 ATCTGGTTTGGTATGAACCCCAAAAACCAATTATTGGATTTGAAAGATGA
66 ATCTGGTTCGGTAGGAACCAC-AAAACCAATCATTAGAATTAAAAGATGA
*
567025 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATATTATGGAAGTGTTCTTTGAGTTATCTG
*
567090 ATCTGGTTCGGTAGGAACCACAGAACCAATCATTAGAATTAAAAGATGA
66 ATCTGGTTCGGTAGGAACCACAAAACCAATCATTAGAATTAAAAGATGA
567139 A
1 A
567140 CTGCATGATC
Statistics
Matches: 105, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
114 24 0.23
115 81 0.77
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (114 bp):
ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATATTATGGAAGTGTTCTTTGAGTTATCTG
ATCTGGTTCGGTAGGAACCACAAAACCAATCATTAGAATTAAAAGATGA
Found at i:568100 original size:113 final size:113
Alignment explanation
Indices: 567826--568449 Score: 1126
Period size: 113 Copynumber: 5.5 Consensus size: 113
567816 TAGCAAAGAT
*
567826 TCAAATCCATCATTTGATGGATCAACTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
567891 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
567940 TCAAATCCATCATTTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAATAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
568005 AGAA-GAAGAAGAAATTCATAATGAGAAGAAGTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
568052 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
*
568117 AAGAAGGAAAAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
568166 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAA-TTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGA-AAAAGTTCATAATGAGAAGAACTCATCTG
568230 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
568279 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
568344 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
568392 TCAAATCCATCATTTGATGGATCAACCTTTCCAGAAAAAGTTCATAATGAGAAGAACT
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACT
568450 TGTTCAACTT
Statistics
Matches: 491, Mismatches: 15, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
112 78 0.16
113 302 0.62
114 111 0.23
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:568478 original size:73 final size:73
Alignment explanation
Indices: 568351--568488 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 73
568341 TGAAGAAGGA
* **
568351 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
1 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
568416 ACCTTTCC
66 ACCTTTCC
* ** *
568424 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATC
1 AGAAGAAA-TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATC
568488 A
65 A
568489 GCATTACCAG
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 3 0.05
73 54 0.95
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (73 bp):
AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
ACCTTTCC
Found at i:568478 original size:186 final size:186
Alignment explanation
Indices: 568238--568635 Score: 573
Period size: 186 Copynumber: 2.1 Consensus size: 186
568228 TGAAGAAGGA
* **
568238 AGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATC
1 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATC
* * *
568302 AGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
65 AGCATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
*
568367 GAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACCTTTCC
130 GAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTTCC
* ** *
568424 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCA
1 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
**** *
568489 GCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
66 GCATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * *
568554 AGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTTCC
131 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTTCC
** *
568610 AGGTAGAGTTCATAATGAGAAGAACT
1 AGAAAAAGTTCATAATGAGAAGAACT
568636 CGTCATCTGA
Statistics
Matches: 188, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
185 3 0.02
186 185 0.98
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (186 bp):
AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
GCATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTTCC
Found at i:568507 original size:73 final size:73
Alignment explanation
Indices: 568351--568522 Score: 193
Period size: 73 Copynumber: 2.4 Consensus size: 73
568341 TGAAGAAGGA
* **
568351 AGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATC
1 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATC
* *
568415 AACCTTTCC
65 AACATTACC
* ** *
568424 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCA
1 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
*
568489 GCATTACC
66 ACATTACC
**** *
568497 AGTTCGAGTTCATAATAAGAAGAACT
1 AGAAAAAGTTCATAATGAGAAGAACT
568523 CATCTGAAGA
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
72 3 0.04
73 80 0.96
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (73 bp):
AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
ACATTACC
Found at i:568511 original size:299 final size:298
Alignment explanation
Indices: 568133--568747 Score: 910
Period size: 299 Copynumber: 2.1 Consensus size: 298
568123 GAAAAAGAAA
* ** * *
568133 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACC
*
568198 AGAGAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
66 AGAGAAAATTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
* *
568263 TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAAT
131 TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTTCCAG-GTAAAGTTCATAAT
568327 GAGAAGAACTCATC-TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
195 GAGAAGAACTCATCAT-AAGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
*
568391 CTCAAATCCATCATTTGATGGATCAACCTTTCCAGAAAAAG
258 CTCAAATCCATCACTTGATGGATCAACCTTTCCAGAAAAAG
* ** *
568432 TTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACC
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACC
**** * *
568497 AGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
66 AGAGAAAATTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
* * * * *
568562 TTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTTCCAGGTAGAGTTCATAATG
131 TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTTCCAGGTAAAGTTCATAATG
* ** *
568627 AGAAGAACTCGTCATCTGAAGAAGAATAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
196 AGAAGAACTCATCATAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
568692 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAG
261 AAATCCATCACTTGATGGATCAACCTTTCCAGAAAAAG
568730 TTCATAATGAGAAGAACT
1 TTCATAATGAGAAGAACT
568748 CATCTGAAGA
Statistics
Matches: 283, Mismatches: 31, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
298 97 0.34
299 185 0.65
300 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (298 bp):
TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACC
AGAGAAAATTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTTCCAGGTAAAGTTCATAATG
AGAAGAACTCATCATAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
AAATCCATCACTTGATGGATCAACCTTTCCAGAAAAAG
Found at i:568680 original size:20 final size:20
Alignment explanation
Indices: 568616--568680 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
568606 TTCCAGGTAG
*
568616 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAATT
* * *
568636 CG-TCAT-CTGAAGAAGAATA
1 AGTTCATAATG-AGAAGAATT
*
568655 AATTCATAATGAGAAGAATT
1 AGTTCATAATGAGAAGAATT
*
568675 TGTTCA
1 AGTTCA
568681 ACCTTTTGCT
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
18 2 0.06
19 11 0.34
20 17 0.53
21 2 0.06
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAATT
Found at i:568701 original size:112 final size:109
Alignment explanation
Indices: 568424--568796 Score: 462
Period size: 113 Copynumber: 3.4 Consensus size: 109
568414 CAACCTTTCC
* * **
568424 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCA
1 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCA
* * * *
568489 GCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGA
66 GCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
568533 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGG
1 A-G-A-AA-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGG
* *
568598 ATTAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
62 ATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGA
* * * *
568649 AGAATAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
1 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATC
* *
568713 AGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGA
65 AGCATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
568758 AGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTT
1 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
568797 ACATAATTTT
Statistics
Matches: 230, Mismatches: 24, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
108 2 0.01
109 44 0.19
110 2 0.01
111 1 0.00
112 81 0.35
113 84 0.37
114 2 0.01
115 2 0.01
116 12 0.05
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (109 bp):
AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCA
GCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
Found at i:568937 original size:124 final size:124
Alignment explanation
Indices: 568717--569009 Score: 361
Period size: 124 Copynumber: 2.4 Consensus size: 124
568707 TGGATCAGCT
*
568717 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG---AAG-AAGAAGAAGTTCACAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCACAATGAGA
* * * * * *
568778 AGAGCTTGTTCAACCTTTTACATAATTTTATCACAGAA-GAAGATATATTAGCATCAACC
66 AGAGCTTATTCAACCTTTTACATAACTCTATCACAGAAGGAA-ATAGATCAACATCAACC
*
568837 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCACAATGAGA
* * * *
568902 GGAGCTTATTCAACCTTTTGA-ATGACTCTATCACAGAAGGAAATAGGTCAACATCATCC
66 AGAGCTTATTCAACCTTTT-ACATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
*
568961 ---CCAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAGAAGAA
1 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAA-AAAGA-AAGAA
569010 TTTATTCAAC
Statistics
Matches: 151, Mismatches: 13, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
120 37 0.25
121 4 0.03
122 31 0.21
123 8 0.05
124 67 0.44
125 4 0.03
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (124 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCACAATGAGA
AGAGCTTATTCAACCTTTTACATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
Found at i:569162 original size:3 final size:3
Alignment explanation
Indices: 569154--569211 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
569144 TTTTTATTTA
* * *
569154 ATT ATT ATT ATT ATA ATA ATT ATT ATT A-T AAT ATAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
569199 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
569212 AAAAAAATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:569175 original size:15 final size:15
Alignment explanation
Indices: 569147--569211 Score: 89
Period size: 15 Copynumber: 4.4 Consensus size: 15
569137 TTACCCATTT
569147 TTATT-TAATTATTA
1 TTATTATAATTATTA
*
569161 TTATTATAATAATTA
1 TTATTATAATTATTA
569176 TTATTATAA-TATATA
1 TTATTATAATTAT-TA
*
569191 TTATTATTATTATTA
1 TTATTATAATTATTA
569206 TTATTA
1 TTATTA
569212 AAAAAAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
14 7 0.16
15 35 0.78
16 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTATAATTATTA
Found at i:569175 original size:18 final size:17
Alignment explanation
Indices: 569147--569211 Score: 80
Period size: 18 Copynumber: 3.8 Consensus size: 17
569137 TTACCCATTT
*
569147 TTATTTAATTATTATTA
1 TTATATAATTATTATTA
569164 TTATAATAATTATTATTA
1 TTAT-ATAATTATTATTA
*
569182 TAATATATATTATTATTA
1 TTATATA-ATTATTATTA
569200 TTAT-T-ATTATTA
1 TTATATAATTATTA
569212 AAAAAAATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
15 7 0.16
17 8 0.19
18 28 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATATAATTATTATTA
Found at i:573635 original size:30 final size:31
Alignment explanation
Indices: 573593--573677 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 31
573583 AAATTATATA
*
573593 TTTAATATCTAAATTATTAATTTTGATC-AGT
1 TTTAATACCTAAATTATTAATTTTGATCTA-T
* *
573624 TTTAATA-CTAAACTATTAATTATGATCTAT
1 TTTAATACCTAAATTATTAATTTTGATCTAT
*
573654 TTTAGTACCTAAACTT-TTAATTTT
1 TTTAATACCTAAA-TTATTAATTTT
573678 TTAAAAATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
30 25 0.54
31 20 0.43
32 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (31 bp):
TTTAATACCTAAATTATTAATTTTGATCTAT
Found at i:593562 original size:19 final size:19
Alignment explanation
Indices: 593537--593585 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
593527 GTCTTCACTG
593537 ATTTTACTCCCTCAGATCT
1 ATTTTACTCCCTCAGATCT
*
593556 GTTTTACTCCCTCAGATCT
1 ATTTTACTCCCTCAGATCT
593575 ATTTTACTCCC
1 ATTTTACTCCC
593586 AATCTCCTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.18, C:0.33, G:0.06, T:0.43
Consensus pattern (19 bp):
ATTTTACTCCCTCAGATCT
Found at i:594055 original size:51 final size:51
Alignment explanation
Indices: 593979--594084 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 51
593969 AAACCAAAGG
593979 AGTAAAACCAACCTTTCTTGCCCCCT-TGTCTTTGCCACCTGCAACACATAA
1 AGTAAAACCAACCTTTCTTGCCCCCTCT-TCTTTGCCACCTGCAACACATAA
594030 AGTAAAACCAACCTTTCTTGCCCCCTCTTCTTTGCCACCTGCAACACATAA
1 AGTAAAACCAACCTTTCTTGCCCCCTCTTCTTTGCCACCTGCAACACATAA
594081 AGTA
1 AGTA
594085 TTCAATGAGT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 53 0.98
52 1 0.02
ACGTcount: A:0.28, C:0.35, G:0.09, T:0.27
Consensus pattern (51 bp):
AGTAAAACCAACCTTTCTTGCCCCCTCTTCTTTGCCACCTGCAACACATAA
Found at i:602838 original size:25 final size:25
Alignment explanation
Indices: 602810--602859 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
602800 GACATTAATC
602810 ATGTTTGTAGTTCAATCTATTAAAA
1 ATGTTTGTAGTTCAATCTATTAAAA
602835 ATGTTTGTAGTTCAATCTATTAAAA
1 ATGTTTGTAGTTCAATCTATTAAAA
602860 TGTAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (25 bp):
ATGTTTGTAGTTCAATCTATTAAAA
Found at i:610255 original size:60 final size:60
Alignment explanation
Indices: 610184--610373 Score: 168
Period size: 60 Copynumber: 3.2 Consensus size: 60
610174 TATTTGGTTG
* * * *
610184 AATTTGGGGATGAAATTGGAA-GATCTAAAA-CTTTAGGGACCAATTTAGAATGAGATTCAT
1 AATTTGAGGATGAAATTGGAATGATC-AAAAGC-TTAAGGACCAATATAGAATGAAATTCAT
* * * *
610244 AATTTGAGGATGCAATTGGAATGCTCAAAAGCTTAAGGACTAATATGGAATGAAATTCAT
1 AATTTGAGGATGAAATTGGAATGATCAAAAGCTTAAGGACCAATATAGAATGAAATTCAT
* * ** * * * * * * *
610304 AGTTTGAGGATGAGATTAAAATGTTTAAAAGTTTAAGGACTAATTTAAAATGAAAATCAT
1 AATTTGAGGATGAAATTGGAATGATCAAAAGCTTAAGGACCAATATAGAATGAAATTCAT
*
610364 AGTTTGAGGA
1 AATTTGAGGA
610374 CATATGATAC
Statistics
Matches: 108, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
60 104 0.96
61 4 0.04
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.31
Consensus pattern (60 bp):
AATTTGAGGATGAAATTGGAATGATCAAAAGCTTAAGGACCAATATAGAATGAAATTCAT
Found at i:611574 original size:34 final size:35
Alignment explanation
Indices: 611530--611603 Score: 123
Period size: 34 Copynumber: 2.1 Consensus size: 35
611520 AAAATACTTC
611530 AATTTAGGGTTTAGAATGTAATTGAAGTATTTT-G
1 AATTTAGGGTTTAGAATGTAATTGAAGTATTTTGG
* *
611564 AATTTGGGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAGGGTTTAGAATGTAATTGAAGTATTTTGG
611599 AATTT
1 AATTT
611604 TGAACATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
34 31 0.84
35 6 0.16
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.45
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATGTAATTGAAGTATTTTGG
Found at i:623552 original size:21 final size:21
Alignment explanation
Indices: 623528--623570 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
623518 GTTTTGATAA
623528 AAAATTGAAAGTTTAGGTACT
1 AAAATTGAAAGTTTAGGTACT
* *
623549 AAAATTGATAGTTTGGGTACT
1 AAAATTGAAAGTTTAGGTACT
623570 A
1 A
623571 GATACATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (21 bp):
AAAATTGAAAGTTTAGGTACT
Found at i:626551 original size:84 final size:83
Alignment explanation
Indices: 626463--626625 Score: 215
Period size: 84 Copynumber: 2.0 Consensus size: 83
626453 AAATGCATTT
*
626463 CATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGATT-TTATGAAACCATCGAATGA-A
1 CATGCATCGATGCACCA-ACCATGCACCGATGCACTCAGG-TTATTATGAAA-CATCGAAT-ACA
*
626525 TTTGATGCATCGATGCACCAGC
62 CTTGATGCATCGATGCACCAGC
* * * *
626547 CATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGTTATTTTGAAACATCGAATACACTTG
1 CATGCATCGATGCACCAACCATGCACCGATGCACTCAGGTTATTATGAAACATCGAATACACTTG
626612 ATGCATCGATGCAC
66 ATGCATCGATGCAC
626626 TCTTAGTGCA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
82 1 0.01
83 28 0.40
84 39 0.56
85 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (83 bp):
CATGCATCGATGCACCAACCATGCACCGATGCACTCAGGTTATTATGAAACATCGAATACACTTG
ATGCATCGATGCACCAGC
Found at i:626553 original size:19 final size:19
Alignment explanation
Indices: 626529--626580 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
626519 AATGAATTTG
626529 ATGCATCGATGCACCAGCC
1 ATGCATCGATGCACCAGCC
626548 ATGCATCGATGCACCAGCC
1 ATGCATCGATGCACCAGCC
626567 ATGCATCGATGCAC
1 ATGCATCGATGCAC
626581 TCTGGTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.27, C:0.35, G:0.21, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACCAGCC
Found at i:634043 original size:21 final size:21
Alignment explanation
Indices: 634001--634044 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
633991 ACTCCGGGAG
* *
634001 CTAGTTCCTCGCGAGCTGCTC
1 CTAGCTCCTCGCGAGCTCCTC
* *
634022 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCGCGAGCTCCTC
634043 CT
1 CT
634045 CCTCCAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.43, G:0.18, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCGCGAGCTCCTC
Found at i:635290 original size:64 final size:66
Alignment explanation
Indices: 635132--635291 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 66
635122 AATTAAATTG
* * *
635132 AACATCGAATGCATTTCATGCATCGGTGCA-CATACCATGCACCGATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATTTTATGA
635196 A
66 A
* * * * *
635197 AACATCGAATGCATTTGATGCATCAATGCACCA-GCCATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGAT-TTTATG
635260 -A
65 AA
*
635261 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
635292 TCTTAGTCCA
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 30 0.36
65 48 0.58
66 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (66 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATTTTATGA
A
Found at i:640860 original size:22 final size:20
Alignment explanation
Indices: 640820--640861 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
640810 AAAACTGTTG
*
640820 ACCGTTGACCGGCTTTGACC
1 ACCGTTGACCGACTTTGACC
640840 ACCGTTGACCAGAACTTTGACC
1 ACCGTTGACC-G-ACTTTGACC
640862 GGCGTTGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.24
Consensus pattern (20 bp):
ACCGTTGACCGACTTTGACC
Found at i:666633 original size:22 final size:22
Alignment explanation
Indices: 666580--666633 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
666570 ATTTCCTTAG
666580 AAACATTTCATATAAAACTAAT
1 AAACATTTCATATAAAACTAAT
* *
666602 AAACAATTCATA-AAAACATCAT
1 AAACATTTCATATAAAAC-TAAT
*
666624 ATACATTTCA
1 AAACATTTCA
666634 ATTCTTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.30
Consensus pattern (22 bp):
AAACATTTCATATAAAACTAAT
Found at i:666805 original size:19 final size:19
Alignment explanation
Indices: 666781--666824 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
666771 CTTATACACT
*
666781 TTTAATCCATATCAATTTG
1 TTTAATCCATATCAATTTA
** *
666800 TTTAATTTATATCCATTTA
1 TTTAATCCATATCAATTTA
666819 TTTAAT
1 TTTAAT
666825 TAGCCCAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTAATCCATATCAATTTA
Found at i:666825 original size:19 final size:19
Alignment explanation
Indices: 666789--666825 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
666779 CTTTTAATCC
*
666789 ATATCAATTTGTTTAATTT
1 ATATCAATTTATTTAATTT
*
666808 ATATCCATTTATTTAATT
1 ATATCAATTTATTTAATT
666826 AGCCCAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (19 bp):
ATATCAATTTATTTAATTT
Found at i:666946 original size:24 final size:23
Alignment explanation
Indices: 666914--666959 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
666904 TATAATTTGC
*
666914 ACCGAAGTGCCACGTAGAATATGG
1 ACCGAAGTGCCACATAG-ATATGG
666938 ACCGAAGTGCCACATAGATATG
1 ACCGAAGTGCCACATAGATATG
666960 TCCCAAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.17
Consensus pattern (23 bp):
ACCGAAGTGCCACATAGATATGG
Found at i:667000 original size:24 final size:24
Alignment explanation
Indices: 666973--667026 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
666963 CAAAGGGTCG
* *
666973 CGTAGAATTTGTCCCGAATGACCA
1 CGTAGAAGTTGTCCCGAAGGACCA
*
666997 CGTAG-AGTTGTCCCGAAGGACCG
1 CGTAGAAGTTGTCCCGAAGGACCA
667020 CGTAGAA
1 CGTAGAA
667027 CCCTCGACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (24 bp):
CGTAGAAGTTGTCCCGAAGGACCA
Found at i:667317 original size:27 final size:22
Alignment explanation
Indices: 667260--667302 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
667250 TGAATTTATT
*
667260 ATTTATTCACATAGAACCTATC
1 ATTTCTTCACATAGAACCTATC
667282 ATTTCTTCACATAGAACCTAT
1 ATTTCTTCACATAGAACCTAT
667303 ACTCATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (22 bp):
ATTTCTTCACATAGAACCTATC
Found at i:667920 original size:21 final size:20
Alignment explanation
Indices: 667875--667924 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
667865 CTTACTCTTG
667875 ATATCGATACCTCCACATCA
1 ATATCGATACCTCCACATCA
* *
667895 GTATCGATACTACTTCA-ATCA
1 ATATCGATAC--CTCCACATCA
667916 ATATCGATA
1 ATATCGATA
667925 TTGTTCATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 9 0.36
21 12 0.48
22 4 0.16
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (20 bp):
ATATCGATACCTCCACATCA
Found at i:675438 original size:102 final size:101
Alignment explanation
Indices: 675285--675488 Score: 335
Period size: 102 Copynumber: 2.0 Consensus size: 101
675275 TATGCAATTC
675285 AATTAATCCCAAACTCAATTGATCCTCATATTTCAAGGTTCTCTCAATCAATCCTAATGGGCAAA
1 AATTAATCCCAAACTCAATTGATCCTCATATTTCAAGGTTCTCTCAATCAATCCTAATGGGC-AA
675350 GTTTT-GAAAAACTTTTAAAAAA-ATTGG-TTTGAGAA
65 GTTTTCGAAAAACTTTTAAAAAATA-TGGTTTTGAGAA
675385 AATTAATCCCAAAACTCAATTGAGTCCTCAATATTTCAAGGTTCTCT-AATCAATCCTAATGGGC
1 AATTAATCCC-AAACTCAATTGA-TCCTC-ATATTTCAAGGTTCTCTCAATCAATCCTAATGGGC
675449 AAGTTTTCGAAAAACTTTTAAAAAATATGGTTTTGAGAA
63 AAGTTTTCGAAAAACTTTTAAAAAATATGGTTTTGAGAA
675488 A
1 A
675489 CAATATATGT
Statistics
Matches: 98, Mismatches: 0, Indels: 9
0.92 0.00 0.08
Matches are distributed among these distances:
100 10 0.10
101 19 0.19
102 42 0.43
103 27 0.28
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (101 bp):
AATTAATCCCAAACTCAATTGATCCTCATATTTCAAGGTTCTCTCAATCAATCCTAATGGGCAAG
TTTTCGAAAAACTTTTAAAAAATATGGTTTTGAGAA
Found at i:676010 original size:19 final size:20
Alignment explanation
Indices: 675960--676018 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
675950 TTCCCCTGTG
675960 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGG-ATCGGTT-CCC-TCAAA
* *
675983 GGGGAATCGGTTCCCTC-AT
1 GGGGGATCGGTTCCCTCAAA
*
676002 GGGGGATCGATTCCCTC
1 GGGGGATCGGTTCCCTC
676019 TGCACCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.50
20 2 0.06
21 3 0.09
22 7 0.22
23 4 0.12
ACGTcount: A:0.17, C:0.27, G:0.32, T:0.24
Consensus pattern (20 bp):
GGGGGATCGGTTCCCTCAAA
Found at i:681665 original size:18 final size:18
Alignment explanation
Indices: 681642--681676 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
681632 TGGAGCGTGG
681642 GGGGAATCGGTACCCTAT
1 GGGGAATCGGTACCCTAT
*
681660 GGGGAATCGGTTCCCTA
1 GGGGAATCGGTACCCTA
681677 AGTGTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (18 bp):
GGGGAATCGGTACCCTAT
Found at i:682765 original size:16 final size:15
Alignment explanation
Indices: 682727--682775 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
682717 TAGACTAGCG
*
682727 CATTTTCACATAGAA
1 CATTTTCACGTAGAA
*
682742 CATTTTCACGTAGAT
1 CATTTTCACGTAGAA
*
682757 CATTTTTCACGTATAA
1 CA-TTTTCACGTAGAA
682773 CAT
1 CAT
682776 ATCACTTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (15 bp):
CATTTTCACGTAGAA
Found at i:684309 original size:29 final size:29
Alignment explanation
Indices: 684275--684333 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
684265 CCTAAATTAA
684275 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
684304 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
684333 T
1 T
684334 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:688761 original size:29 final size:29
Alignment explanation
Indices: 688727--688785 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
688717 CCTAAATTAA
688727 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
688756 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
688785 T
1 T
688786 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:691272 original size:31 final size:30
Alignment explanation
Indices: 691203--691283 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
691193 TTGGAAAATT
* *
691203 TTGGGGACC-ATTTTATAATTTTATGTAAG
1 TTGGGGACCTATTTGATAATTTTATGAAAG
691232 TTGGGGACCTATTTGATAATTTTATGAAAG
1 TTGGGGACCTATTTGATAATTTTATGAAAG
691262 TTGGGGGACCTATTTGATAATT
1 TT-GGGGACCTATTTGATAATT
691284 ATGGAAAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 9 0.19
30 20 0.42
31 19 0.40
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.42
Consensus pattern (30 bp):
TTGGGGACCTATTTGATAATTTTATGAAAG
Found at i:691381 original size:19 final size:20
Alignment explanation
Indices: 691338--691383 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
691328 TACTATGCTG
* *
691338 GAAATTAATATTAGAGTGTT
1 GAAATTGATATTAGAATGTT
*
691358 GAAATTGATGTTAGAATG-T
1 GAAATTGATATTAGAATGTT
691377 GAAATTG
1 GAAATTG
691384 GATCATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (20 bp):
GAAATTGATATTAGAATGTT
Found at i:693178 original size:20 final size:20
Alignment explanation
Indices: 693153--693240 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
693143 TATACATTGG
*
693153 GTTATGAATATGAAAGTAAA
1 GTTATGAATCTGAAAGTAAA
693173 GTTATGAATCTGAAAGTAAA
1 GTTATGAATCTGAAAGTAAA
*
693193 GATATGAATCTGAAA-TAAA
1 GTTATGAATCTGAAAGTAAA
*
693212 -TTATGAATTTG---G-AAA
1 GTTATGAATCTGAAAGTAAA
693227 GTTATGAATCTGAA
1 GTTATGAATCTGAA
693241 TATGAAAGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
15 3 0.05
16 10 0.17
18 9 0.15
19 4 0.07
20 33 0.56
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.32
Consensus pattern (20 bp):
GTTATGAATCTGAAAGTAAA
Found at i:693233 original size:34 final size:38
Alignment explanation
Indices: 693153--693240 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 38
693143 TATACATTGG
*
693153 GTTATGAATATGAAAGTAAAGTTATGAATCTGAAAGTAAA
1 GTTATGAATCTGAAAGTAAAGTTATGAATCTG--AGTAAA
* *
693193 GATATGAATCTGAAA-TAAA-TTATGAATTTG-G-AAA
1 GTTATGAATCTGAAAGTAAAGTTATGAATCTGAGTAAA
693227 GTTATGAATCTGAA
1 GTTATGAATCTGAA
693241 TATGAAAGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
34 16 0.36
35 1 0.02
38 10 0.23
39 4 0.09
40 13 0.30
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.32
Consensus pattern (38 bp):
GTTATGAATCTGAAAGTAAAGTTATGAATCTGAGTAAA
Found at i:696082 original size:22 final size:22
Alignment explanation
Indices: 696057--696103 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
696047 ACGTGAGAAT
*
696057 CACGGGTTCTGCAAGGAGAGAG
1 CACGGGTTCTGCAAGGAGAAAG
696079 CACGGGTTCTGCAAGGAGAAAG
1 CACGGGTTCTGCAAGGAGAAAG
696101 CAC
1 CAC
696104 AGAAATCACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.21, G:0.36, T:0.13
Consensus pattern (22 bp):
CACGGGTTCTGCAAGGAGAAAG
Found at i:696159 original size:23 final size:23
Alignment explanation
Indices: 696133--696176 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
696123 TCCTGCAAGG
696133 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
696156 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
696177 GCATGCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:696183 original size:23 final size:23
Alignment explanation
Indices: 696134--696183 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
696124 CCTGCAAGGC
* *
696134 TGCACGTCTGCATGTGGGGGTCC
1 TGCACGTCTGCATGTGGGGGGCA
696157 TGCACGTCTGCATGTGGGGGGCA
1 TGCACGTCTGCATGTGGGGGGCA
696180 TGCA
1 TGCA
696184 ACTGTTGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (23 bp):
TGCACGTCTGCATGTGGGGGGCA
Found at i:696924 original size:171 final size:173
Alignment explanation
Indices: 696638--696995 Score: 560
Period size: 171 Copynumber: 2.1 Consensus size: 173
696628 TTGTAAAGTT
* * * *
696638 TTAGGGACCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGCTAT
1 TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
*
696703 ACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTAGAAAGAATTTA-AAATTTA-T
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
*
696766 GGATTAAATTGCTAACTTTGAAAATGTTGAGAACCAAATA-TAA
131 -GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
* * *
696809 TTAGGGATCGTTTTGCAAAATTTGAGGAATTTAAGAAATTAGAGTAAATTATAAAAAGTTGGTAT
1 TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
* *
696874 ACTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
* *
696939 GATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTAA
131 GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
*
696982 TTAGGGATCATTTT
1 TTAGGGATCGTTTT
696996 ATATTTGATG
Statistics
Matches: 170, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
171 110 0.65
172 43 0.25
173 17 0.10
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (173 bp):
TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
Found at i:698735 original size:6 final size:6
Alignment explanation
Indices: 698724--698760 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
698714 CAAGAAGGAC
698724 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG T
1 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG T
698761 TCTTCTCACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.65, T:0.19
Consensus pattern (6 bp):
TGGGAG
Found at i:699273 original size:8 final size:8
Alignment explanation
Indices: 699260--699723 Score: 297
Period size: 8 Copynumber: 61.8 Consensus size: 8
699250 AGTAATTATT
699260 ATTAAATC
1 ATTAAATC
699268 ATTAAA--
1 ATTAAATC
699274 ATTAAATC
1 ATTAAATC
699282 ATTAAA--
1 ATTAAATC
* *
699288 ATTAAGTA
1 ATTAAATC
*
699296 ATT--ATT
1 ATTAAATC
*
699302 ATTAAATT
1 ATTAAATC
699310 ATTAAA--
1 ATTAAATC
699316 ATTAAATC
1 ATTAAATC
*
699324 ATTAAAGTA
1 ATTAAA-TC
*
699333 ATT--ATT
1 ATTAAATC
699339 ATTAAATC
1 ATTAAATC
699347 ATTAAATC
1 ATTAAATC
699355 ATTAAATC
1 ATTAAATC
*
699363 ATTAAAGTA
1 ATTAAA-TC
*
699372 ATT--ATT
1 ATTAAATC
*
699378 ATTAAAGC
1 ATTAAATC
699386 ATTAAA--
1 ATTAAATC
*
699392 GTTAAATC
1 ATTAAATC
*
699400 ATTAAAGTA
1 ATTAAA-TC
*
699409 ATT--ATT
1 ATTAAATC
699415 ATTAAATC
1 ATTAAATC
699423 ATTAAATC
1 ATTAAATC
699431 ATTAAATC
1 ATTAAATC
699439 ATTAAATC
1 ATTAAATC
*
699447 ATTAAAATA
1 ATT-AAATC
*
699456 ATT--ATT
1 ATTAAATC
699462 ATTAAATC
1 ATTAAATC
699470 ATTAAATC
1 ATTAAATC
699478 ATTAAATC
1 ATTAAATC
*
699486 ATTAAAGTA
1 ATTAAA-TC
*
699495 ATT--ATT
1 ATTAAATC
699501 ATTAAATC
1 ATTAAATC
699509 ATTAAATC
1 ATTAAATC
699517 ATTAAATC
1 ATTAAATC
*
699525 ATTAAAGTA
1 ATTAAA-TC
*
699534 ATT--ATT
1 ATTAAATC
699540 ATTAAATC
1 ATTAAATC
699548 ATTAAA--
1 ATTAAATC
*
699554 GTTAAATC
1 ATTAAATC
*
699562 ATTAAAGTA
1 ATTAAA-TC
*
699571 ATT--ATT
1 ATTAAATC
699577 ATTAAATC
1 ATTAAATC
699585 ATTAAA--
1 ATTAAATC
*
699591 GTTAAATC
1 ATTAAATC
699599 ATTAAATC
1 ATTAAATC
699607 ATTAAA--
1 ATTAAATC
699613 ATTAAATC
1 ATTAAATC
*
699621 ATTAAAGTA
1 ATTAAA-TC
*
699630 ATT--ATT
1 ATTAAATC
699636 ATTAAATC
1 ATTAAATC
699644 ATTAAA--
1 ATTAAATC
699650 ATTAAATC
1 ATTAAATC
*
699658 ATTAAAGTA
1 ATTAAA-TC
*
699667 ATT--ATT
1 ATTAAATC
699673 ATTAAATC
1 ATTAAATC
699681 ATTAAA--
1 ATTAAATC
*
699687 GTTAAATC
1 ATTAAATC
*
699695 ATTAAAGTA
1 ATTAAA-TC
*
699704 ATT--ATT
1 ATTAAATC
699710 ATTAAATC
1 ATTAAATC
699718 ATTAAA
1 ATTAAA
699724 GTTAAATAAA
Statistics
Matches: 364, Mismatches: 42, Indels: 100
0.72 0.08 0.20
Matches are distributed among these distances:
6 94 0.26
7 9 0.02
8 218 0.60
9 43 0.12
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (8 bp):
ATTAAATC
Found at i:699319 original size:9 final size:8
Alignment explanation
Indices: 699257--699786 Score: 154
Period size: 8 Copynumber: 69.2 Consensus size: 8
699247 TCAAGTAATT
699257 ATTATTAA
1 ATTATTAA
*
699265 ATCATTAA
1 ATTATTAA
699273 A--ATTAA
1 ATTATTAA
*
699279 ATCATTAAA
1 ATTATT-AA
*
699288 ATTAAGTAA
1 ATT-ATTAA
699297 TTATTATTAA
1 --ATTATTAA
699307 ATTATTAA
1 ATTATTAA
699315 A--ATTAA
1 ATTATTAA
*
699321 ATCATTAA
1 ATTATTAA
*
699329 AGTAATT--
1 A-TTATTAA
699336 ATTATTAA
1 ATTATTAA
*
699344 ATCATTAA
1 ATTATTAA
*
699352 ATCATTAA
1 ATTATTAA
*
699360 ATCATTAA
1 ATTATTAA
*
699368 AGTAATT--
1 A-TTATTAA
699375 ATTATTAA
1 ATTATTAA
**
699383 AGCATTAA
1 ATTATTAA
*
699391 A--GTTAA
1 ATTATTAA
*
699397 ATCATTAA
1 ATTATTAA
*
699405 AGTAATT--
1 A-TTATTAA
699412 ATTATTAA
1 ATTATTAA
*
699420 ATCATTAA
1 ATTATTAA
*
699428 ATCATTAA
1 ATTATTAA
*
699436 ATCATTAA
1 ATTATTAA
*
699444 ATCATTAAA
1 ATTATT-AA
*
699453 ATAATT--
1 ATTATTAA
699459 ATTATTAA
1 ATTATTAA
*
699467 ATCATTAA
1 ATTATTAA
*
699475 ATCATTAA
1 ATTATTAA
*
699483 ATCATTAA
1 ATTATTAA
*
699491 AGTAATT--
1 A-TTATTAA
699498 ATTATTAA
1 ATTATTAA
*
699506 ATCATTAA
1 ATTATTAA
*
699514 ATCATTAA
1 ATTATTAA
*
699522 ATCATTAA
1 ATTATTAA
*
699530 AGTAATT--
1 A-TTATTAA
699537 ATTATTAA
1 ATTATTAA
*
699545 ATCATTAA
1 ATTATTAA
*
699553 A--GTTAA
1 ATTATTAA
*
699559 ATCATTAA
1 ATTATTAA
*
699567 AGTAATT--
1 A-TTATTAA
699574 ATTATTAA
1 ATTATTAA
*
699582 ATCATTAA
1 ATTATTAA
*
699590 A--GTTAA
1 ATTATTAA
*
699596 ATCATTAA
1 ATTATTAA
*
699604 ATCATTAA
1 ATTATTAA
699612 A--ATTAA
1 ATTATTAA
*
699618 ATCATTAA
1 ATTATTAA
*
699626 AGTAATT--
1 A-TTATTAA
699633 ATTATTAA
1 ATTATTAA
*
699641 ATCATTAA
1 ATTATTAA
699649 A--ATTAA
1 ATTATTAA
*
699655 ATCATTAA
1 ATTATTAA
*
699663 AGTAATT--
1 A-TTATTAA
699670 ATTATTAA
1 ATTATTAA
*
699678 ATCATTAA
1 ATTATTAA
*
699686 A--GTTAA
1 ATTATTAA
*
699692 ATCATTAA
1 ATTATTAA
*
699700 AGTAATT--
1 A-TTATTAA
699707 ATTATTAA
1 ATTATTAA
*
699715 ATCATTAA
1 ATTATTAA
*
699723 AGTTAAATAAA
1 A-TT--ATTAA
699734 TATTATTAA
1 -ATTATTAA
*
699743 ATCATTAA
1 ATTATTAA
*
699751 A--GTTAA
1 ATTATTAA
*
699757 ATAATTAA
1 ATTATTAA
699765 A-T-TTAA
1 ATTATTAA
*
699771 ATAATT--
1 ATTATTAA
699777 ATTATTAA
1 ATTATTAA
699785 AT
1 AT
699787 ATGTACTCGA
Statistics
Matches: 410, Mismatches: 52, Indels: 120
0.70 0.09 0.21
Matches are distributed among these distances:
6 100 0.24
7 9 0.02
8 231 0.56
9 54 0.13
10 6 0.01
11 9 0.02
12 1 0.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (8 bp):
ATTATTAA
Found at i:699341 original size:37 final size:37
Alignment explanation
Indices: 699291--699730 Score: 463
Period size: 37 Copynumber: 11.9 Consensus size: 37
699281 CATTAAAATT
*
699291 AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
699328 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTA
* *
699367 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
699404 AAGTAATTATTATTAAATCATTAAATCATTAAATCATT-
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTA
* * **
699442 -A--AATCATTA--AAATAATTATTATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* * * **
699474 AA-TCATTAAATCATTAAAGTAATTATTATTAAATCATTA
1 AAGTAATT--ATTATTAAA-TCATTAAAATTAAATCATTA
* * * **
699513 AA-TCATTAAATCATTAAAGTAATTATTATTAAATCATTA
1 AAGTAATT--ATTATTAAA-TCATTAAAATTAAATCATTA
* * **
699552 AAGTTAA--ATCATTAAAGTAATTATTATTAAATCATTA
1 AAG-TAATTATTATTAAA-TCATTAAAATTAAATCATTA
*
699589 AAGTTAA--ATCATTAAATCATTAAAATTAAATCATTA
1 AAG-TAATTATTATTAAATCATTAAAATTAAATCATTA
699625 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
*
699662 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
*
699699 AAGTAATTATTATTAAATCATTAAAGTTAAAT
1 AAGTAATTATTATTAAATCATTAAAATTAAAT
699731 AAATATTATT
Statistics
Matches: 369, Mismatches: 18, Indels: 32
0.88 0.04 0.08
Matches are distributed among these distances:
31 11 0.03
33 9 0.02
34 2 0.01
35 10 0.03
36 23 0.06
37 202 0.55
38 3 0.01
39 107 0.29
41 2 0.01
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (37 bp):
AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
Found at i:699370 original size:39 final size:39
Alignment explanation
Indices: 699274--699626 Score: 469
Period size: 39 Copynumber: 9.2 Consensus size: 39
699264 AATCATTAAA
*
699274 ATTAAATCATTAAA--ATT-AAGTAATTATTATTAAATT
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
699310 ATTAAA--ATTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
*
699347 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAAGC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
*
699386 ATTAAA--GTTAAATCATTAAAGTAATTATTATTAAATCATTAAATC
1 ATTAAATCATTAAATCATTAAAGT-A--ATTA-T---T-ATTAAATC
*
699431 ATTAAATCATTAAATCATTAAAATAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
699470 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
699509 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
*
699548 ATTAAA--GTTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
* * **
699585 ATTAAA--GTTAAATCATTAAA-TCATTAAAATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
699621 ATTAAA
1 ATTAAA
699627 GTAATTATTA
Statistics
Matches: 291, Mismatches: 11, Indels: 30
0.88 0.03 0.09
Matches are distributed among these distances:
34 6 0.02
36 28 0.10
37 89 0.31
38 1 0.00
39 127 0.44
40 5 0.02
41 1 0.00
43 1 0.00
44 5 0.02
45 13 0.04
46 1 0.00
47 14 0.05
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (39 bp):
ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
Found at i:699412 original size:23 final size:21
Alignment explanation
Indices: 699347--699656 Score: 174
Period size: 23 Copynumber: 14.1 Consensus size: 21
699337 TTATTAAATC
699347 ATTAAATCATTAAATCATTAA
1 ATTAAATCATTAAATCATTAA
* * *
699368 AGTAATTATTATTAAAGCATTAA
1 ATTAA--ATCATTAAATCATTAA
* *
699391 AGTTAAATCATTAAAGTAATTATT
1 A-TTAAATCATTAAA-TCATTA-A
699415 ATTAAATCATTAAATCATTAAA
1 ATTAAATCATTAAATCATT-AA
* *
699437 TCATTAAATCATTAAAATAATTATT
1 --ATTAAATCATT-AAATCATTA-A
699462 ATTAAATCATTAAATC-----
1 ATTAAATCATTAAATCATTAA
* *
699478 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAA-TCATTA-A
699501 ATTAAATCATTAAATCATTAAA
1 ATTAAATCATTAAATCATT-AA
* *
699523 TCATTAAAGTAATT--ATTATTAA
1 --ATTAAA-TCATTAAATCATTAA
*
699545 ATCATTAA--AGTTAAATCATTAA
1 AT--TAAATCA-TTAAATCATTAA
* *
699567 AGTAATTATTATTAAATCATTAA
1 ATTAA--ATCATTAAATCATTAA
699590 AGTTAAATCATTAAATCATTAAA
1 A-TTAAATCATTAAATCATT-AA
* *
699613 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAA-TCATTA-A
699636 ATTAAATCATTAAA--ATTAA
1 ATTAAATCATTAAATCATTAA
699655 AT
1 AT
699657 CATTAAAGTA
Statistics
Matches: 228, Mismatches: 27, Indels: 70
0.70 0.08 0.22
Matches are distributed among these distances:
16 14 0.06
17 1 0.00
19 3 0.01
20 10 0.04
21 4 0.02
22 61 0.27
23 98 0.43
24 26 0.11
25 11 0.05
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (21 bp):
ATTAAATCATTAAATCATTAA
Found at i:699670 original size:23 final size:22
Alignment explanation
Indices: 699274--699686 Score: 139
Period size: 23 Copynumber: 18.3 Consensus size: 22
699264 AATCATTAAA
* *
699274 ATTAAATCATTAAAATTAAGTA
1 ATTAAATCATTAAAATTAAATC
*
699296 ATT--ATTATTAAATTATTAAA--
1 ATTAAATCATTAAA--ATTAAATC
* *
699316 ATTAAATCATT-AAAGTAATTATT
1 ATTAAATCATTAAAATTAA--ATC
699339 ATTAAATCATTAAATCATTAAATC
1 ATTAAATCATTAAA--ATTAAATC
* ** *
699363 ATTAAAGTAATTATTATTAAAGC
1 ATTAAA-TCATTAAAATTAAATC
* *
699386 ATTAAA--GTTAAATCATTAAAGTA
1 ATTAAATCATTAAA--ATTAAA-TC
*
699409 ATT--ATTATTAAATCATTAAATC
1 ATTAAATCATTAAA--ATTAAATC
*
699431 ATTAAATCATTAAATCATTAAAATA
1 ATTAAATCATTAAA--ATT-AAATC
*
699456 ATT--ATTATTAAATCATTAAATC
1 ATTAAATCATTAAA--ATTAAATC
* *
699478 ATTAAATCATT-AAAGTAATTATT
1 ATTAAATCATTAAAATTAA--ATC
699501 ATTAAATCATTAAATCATTAAATC
1 ATTAAATCATTAAA--ATTAAATC
* **
699525 ATTAAAGTAATTATTATTAAATC
1 ATTAAA-TCATTAAAATTAAATC
* *
699548 ATTAAA--GTTAAATCATTAAAGTA
1 ATTAAATCATTAAA--ATTAAA-TC
*
699571 ATT--ATTATTAAATCATTAAA--
1 ATTAAATCATTAAA--ATTAAATC
*
699591 GTTAAATCATTAAATCATTAAA--
1 ATTAAATCATTAAA--ATTAAATC
* *
699613 ATTAAATCATT-AAAGTAATTATT
1 ATTAAATCATTAAAATTAA--ATC
699636 ATTAAATCATTAAAATTAAATC
1 ATTAAATCATTAAAATTAAATC
* **
699658 ATTAAAGTAATTATTATTAAATC
1 ATTAAA-TCATTAAAATTAAATC
699681 ATTAAA
1 ATTAAA
699687 GTTAAATCAT
Statistics
Matches: 307, Mismatches: 43, Indels: 81
0.71 0.10 0.19
Matches are distributed among these distances:
19 8 0.03
20 19 0.06
21 12 0.04
22 70 0.23
23 129 0.42
24 44 0.14
25 17 0.06
26 8 0.03
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (22 bp):
ATTAAATCATTAAAATTAAATC
Found at i:699699 original size:59 final size:60
Alignment explanation
Indices: 699260--699730 Score: 324
Period size: 59 Copynumber: 8.1 Consensus size: 60
699250 AGTAATTATT
*
699260 ATTAAATCATT-AA--AATTAAATCATTAAA--ATT-AAGTAATTATTATTAAATTATTAAA
1 ATTAAATCATTAAAGTAATTAAA--ATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
** *
699316 ATTAAATCATTAAAGTAATTATTATTAAATCA-T----TAA--ATCATTAAATCATT-AA
1 ATTAAATCATTAAAGTAATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
* * * *
699368 AGTAATTATTATTAAAG-CATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAA
1 ATTAA--ATCATTAAAGTAATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
* * * *
699429 TCATTAAATCATTAAA-TCATTAAAA-TAATTATTATTAAA-TCATTAAATCATTAAATCATT-A
1 --ATTAAATCATTAAAGTAATTAAAATTAA--ATCATTAAAGTAATT--ATTATTAAATCATTAA
699490 A
60 A
* * *
699491 AGTAATTATTATTAAA-TCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
1 ATTAA--ATCATTAAAGTAATTAAA--ATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
* ** *
699554 GTTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAA--ATCATTAAATCATTAAA
1 ATTAAATCATTAAAGTAATTAAAATTAAATCATTAAAG-TAATTATTATTAAATCATTAAA
**
699613 ATTAAATCATTAAAGTAATTATTATTAAATCA-T----TAA--A--ATTAAATCATT-AA
1 ATTAAATCATTAAAGTAATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
* * * *
699663 AGTAATTATTATTAAA-TCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAA
1 ATTAA--ATCATTAAAGTAATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
*
699724 GTTAAAT
1 ATTAAAT
699731 AAATATTATT
Statistics
Matches: 334, Mismatches: 38, Indels: 83
0.73 0.08 0.18
Matches are distributed among these distances:
50 6 0.02
51 24 0.07
52 15 0.04
53 28 0.08
54 10 0.03
55 3 0.01
56 14 0.04
57 8 0.02
58 6 0.02
59 55 0.16
60 46 0.14
61 37 0.11
62 44 0.13
63 30 0.09
64 5 0.01
65 3 0.01
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (60 bp):
ATTAAATCATTAAAGTAATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
Found at i:699701 original size:14 final size:14
Alignment explanation
Indices: 699234--699777 Score: 244
Period size: 14 Copynumber: 41.7 Consensus size: 14
699224 TCAGTAAATA
699234 TAAATCATTAAAGT
1 TAAATCATTAAAGT
* * * *
699248 CAAGTAATTATTA-T
1 TAAATCATTA-AAGT
*
699262 TAAATCATTAAAAT
1 TAAATCATTAAAGT
*
699276 TAAATCATTAAAAT
1 TAAATCATTAAAGT
* * *
699290 TAAGTAATTATTA-T
1 TAAATCATTA-AAGT
* *
699304 TAAATTATTAAAAT
1 TAAATCATTAAAGT
699318 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
699331 T-AATTATT--A-T
1 TAAATCATTAAAGT
*
699341 TAAATCATTAAATCAT
1 TAAATCATTAAA--GT
699357 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
699370 T-AATTATT--A-T
1 TAAATCATTAAAGT
*
699380 TAAAGCATTAAAGT
1 TAAATCATTAAAGT
699394 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
699407 T-AATTATT--A-T
1 TAAATCATTAAAGT
*
699417 TAAATCATTAAATCAT
1 TAAATCATTAAA--GT
*
699433 TAAATCATTAAATCAT
1 TAAATCATTAAA--GT
* *
699449 TAAAATAATTATTA-T
1 T-AAATCATTA-AAGT
*
699464 TAAATCATTAAATCAT
1 TAAATCATTAAA--GT
699480 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
699493 T-AATTATT--A-T
1 TAAATCATTAAAGT
*
699503 TAAATCATTAAATCAT
1 TAAATCATTAAA--GT
699519 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
699532 T-AATTATT--A-T
1 TAAATCATTAAAGT
699542 TAAATCATTAAAGT
1 TAAATCATTAAAGT
699556 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
699569 T-AATTATT--A-T
1 TAAATCATTAAAGT
699579 TAAATCATTAAAGT
1 TAAATCATTAAAGT
699593 TAAATC-----A-T
1 TAAATCATTAAAGT
*
699601 TAAATCATTAAAAT
1 TAAATCATTAAAGT
699615 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
699628 T-AATTATT--A-T
1 TAAATCATTAAAGT
*
699638 TAAATCATTAAAAT
1 TAAATCATTAAAGT
699652 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
699665 T-AATTATT--A-T
1 TAAATCATTAAAGT
699675 TAAATCATTAAAGT
1 TAAATCATTAAAGT
699689 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
699702 T-AATTATT--A-T
1 TAAATCATTAAAGT
699712 TAAATCATTAAAGT
1 TAAATCATTAAAGT
* * *
699726 TAAATAAATATTA-T
1 TAAATCATTA-AAGT
699740 TAAATCATTAAAGT
1 TAAATCATTAAAGT
* *
699754 TAAATAATTAAATT
1 TAAATCATTAAAGT
*
699768 TAAATAATTA
1 TAAATCATTA
699778 TTATTAAATA
Statistics
Matches: 409, Mismatches: 53, Indels: 136
0.68 0.09 0.23
Matches are distributed among these distances:
8 7 0.02
9 1 0.00
10 18 0.04
11 53 0.13
12 54 0.13
13 23 0.06
14 182 0.44
15 5 0.01
16 57 0.14
17 8 0.02
18 1 0.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (14 bp):
TAAATCATTAAAGT
Found at i:699729 original size:74 final size:73
Alignment explanation
Indices: 699423--699786 Score: 298
Period size: 74 Copynumber: 4.9 Consensus size: 73
699413 TTATTAAATC
* * ** * *
699423 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATTATTAAATCATTAAA-TCATTAAATCA
1 ATTAAATCATTAAA--GTTAAATCATT-AAATCATTAAAATTAAATCATTAAAGTAATT--ATTA
* **
699487 TTAAAGTAATTATT
61 TTAAA-TCATTAAA
* * ** *
699501 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAA--ATCAT
1 ATTAAATCATTAAA--GTTAAATCATTAAA-TCATTAAAATTAAATCATTAAAG-TAATTATTAT
* **
699564 TAAAGTAATTATT
62 TAAA-TCATTAAA
699577 ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
1 ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
699642 TCATTAAA
66 TCATTAAA
* *
699650 ATTAAATCATTAAAG-TAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTA
1 ATTAAATCATTAAAGTTAA--ATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTA
699714 AATCATTAAA
64 AATCATTAAA
* * * * *
699724 GTTAAATAAATATTA-TTAAATCATTAAAGT--TAAATAATTAAAT--TTAAA-TAATTATTATT
1 ATTAAATCATTA-AAGTTAAATCATTAAA-TCATTAA-AATTAAATCATTAAAGTAATTATTATT
699783 AAAT
63 AAAT
699787 ATGTACTCGA
Statistics
Matches: 257, Mismatches: 18, Indels: 30
0.84 0.06 0.10
Matches are distributed among these distances:
70 15 0.06
71 5 0.02
72 9 0.04
73 55 0.21
74 83 0.32
75 4 0.02
76 32 0.12
77 3 0.01
78 49 0.19
80 2 0.01
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.41
Consensus pattern (73 bp):
ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
TCATTAAA
Found at i:699770 original size:28 final size:27
Alignment explanation
Indices: 699518--699777 Score: 120
Period size: 23 Copynumber: 10.4 Consensus size: 27
699508 CATTAAATCA
*
699518 TTAAATCATTAAAG-T-AATTATT-A-
1 TTAAATCATTAAAGTTAAATAATTAAT
* *
699541 TTAAATCATTAAAGTTAAATCATTAAA
1 TTAAATCATTAAAGTTAAATAATTAAT
* * * *
699568 GT-AATTATT--A-TTAAATCATTAAAG
1 TTAAATCATTAAAGTTAAATAATT-AAT
* *
699592 TTAAATCATTAAA--TCATTAA--AA-
1 TTAAATCATTAAAGTTAAATAATTAAT
*
699614 TTAAATCATTAAAG-T-AATTATT-A-
1 TTAAATCATTAAAGTTAAATAATTAAT
* * *
699637 TTAAATCATTAAAATTAAATCATTAAA
1 TTAAATCATTAAAGTTAAATAATTAAT
* * * *
699664 GT-AATTATT--A-TTAAATCATTAAAG
1 TTAAATCATTAAAGTTAAATAATT-AAT
*
699688 TTAAATCATTAAAG-T-AATTATT-A-
1 TTAAATCATTAAAGTTAAATAATTAAT
* *
699711 TTAAATCATTAAAGTTAAATAAATATT
1 TTAAATCATTAAAGTTAAATAATTAAT
699738 ATTAAATCATTAAAGTTAAATAATTAAAT
1 -TTAAATCATTAAAGTTAAATAATT-AAT
*
699767 TTAAATAATTA
1 TTAAATCATTA
699778 TTATTAAATA
Statistics
Matches: 186, Mismatches: 25, Indels: 47
0.72 0.10 0.18
Matches are distributed among these distances:
22 16 0.09
23 65 0.35
24 12 0.06
25 29 0.16
26 24 0.13
27 5 0.03
28 33 0.18
29 2 0.01
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (27 bp):
TTAAATCATTAAAGTTAAATAATTAAT
Found at i:703134 original size:18 final size:18
Alignment explanation
Indices: 703111--703157 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
703101 AAATTATTAG
703111 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
703129 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
703147 TCTCACGCTTC
1 TCTCACGCTTC
703158 GGCCACAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (18 bp):
TCTCACGCTTCAGACGAA
Found at i:704567 original size:15 final size:15
Alignment explanation
Indices: 704547--704576 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
704537 GTGAGTTGGA
704547 TAGTGTTCGACTCGT
1 TAGTGTTCGACTCGT
704562 TAGTGTTCGACTCGT
1 TAGTGTTCGACTCGT
704577 GTTCGTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (15 bp):
TAGTGTTCGACTCGT
Found at i:704701 original size:16 final size:16
Alignment explanation
Indices: 704680--704710 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
704670 CTCGATTCAT
*
704680 TGCTCGTTAAGCTCAA
1 TGCTCGTTAAACTCAA
704696 TGCTCGTTAAACTCA
1 TGCTCGTTAAACTCA
704711 CCGAAATTTT
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:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (16 bp):
TGCTCGTTAAACTCAA
Found at i:706416 original size:2 final size:2
Alignment explanation
Indices: 706409--706446 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
706399 TATTCTCTAT
706409 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
706447 AATTAATTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:710961 original size:21 final size:20
Alignment explanation
Indices: 710876--711030 Score: 104
Period size: 20 Copynumber: 7.7 Consensus size: 20
710866 AATGACCAAT
**
710876 AAATTCGCAACGCG-ATCTC
1 AAATTCGCAACGCGAAAGTC
710895 AAATTCGCAATC-C--AAGTTCC
1 AAATTCGCAA-CGCGAAAG-T-C
710915 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
*
710935 AAATTCGCAACGTGAAAGTC
1 AAATTCGCAACGCGAAAGTC
** *
710955 GAAATTCGCAACGCG-ATTTT
1 -AAATTCGCAACGCGAAAGTC
* * *
710975 AAGATTCGTAACGCGATAGTAG
1 AA-ATTCGCAACGCGAAAGT-C
**
710997 AAATTCGCAACGCGATACTTC
1 AAATTCGCAACGCGA-AAGTC
*
711018 AAAATCGCAACGC
1 AAATTCGCAACGC
711031 ATTTGTTTCT
Statistics
Matches: 107, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
18 1 0.01
19 15 0.14
20 46 0.43
21 39 0.36
22 6 0.06
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:710968 original size:41 final size:40
Alignment explanation
Indices: 710876--711029 Score: 141
Period size: 41 Copynumber: 3.8 Consensus size: 40
710866 AATGACCAAT
* ** *
710876 AAATTCGCAACGCGATCTCAAATTCGCAA--TCCAAGTTCC
1 AAATTCGCAACGCGATTTCAAATTCGCAACGTGAAAG-TCG
**
710915 AAATTCGCAACGCGAAAGTCAAATTCGCAACGTGAAAGTCG
1 AAATTCGCAACGCG-ATTTCAAATTCGCAACGTGAAAGTCG
* * * * *
710956 AAATTCGCAACGCGATTTTAAGATTCGTAACGCGATAGTAG
1 AAATTCGCAACGCGATTTCAA-ATTCGCAACGTGAAAGTCG
*
710997 AAATTCGCAACGCGATACTTCAAAATCGCAACG
1 AAATTCGCAACGCGAT--TTCAAATTCGCAACG
711030 CATTTGTTTC
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
39 14 0.15
40 17 0.18
41 47 0.50
42 12 0.13
43 4 0.04
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (40 bp):
AAATTCGCAACGCGATTTCAAATTCGCAACGTGAAAGTCG
Found at i:712012 original size:21 final size:21
Alignment explanation
Indices: 711948--712039 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
711938 AACAAATGCA
* * *
711948 TTGCGATTTTGGAGTATCGCG
1 TTGCGAATTTCGACTATCGCG
*
711969 TTGCGAATCTT--A-AATCGCG
1 TTGCGAAT-TTCGACTATCGCG
*
711988 TTGCGAATTTCGACTATCGCA
1 TTGCGAATTTCGACTATCGCG
*
712009 TTGCGAATTTCGACTTTCGCG
1 TTGCGAATTTCGACTATCGCG
*
712030 CTGCGAATTT
1 TTGCGAATTT
712040 GGAACCTGGA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
18 2 0.03
19 14 0.23
20 2 0.03
21 40 0.67
22 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.36
Consensus pattern (21 bp):
TTGCGAATTTCGACTATCGCG
Found at i:716337 original size:12 final size:12
Alignment explanation
Indices: 716317--716388 Score: 53
Period size: 12 Copynumber: 5.9 Consensus size: 12
716307 CTTTTTTATT
*
716317 TTTTTTATTTTA
1 TTTTATATTTTA
716329 TTTTATATTTTA
1 TTTTATATTTTA
716341 TTTTA-ATTATTA
1 TTTTATATT-TTA
716353 TTATTAGTA--TTA
1 TT-TTA-TATTTTA
*
716365 TTATATATTATTA
1 TTTTATATT-TTA
716378 TTATT-TATTTT
1 TT-TTATATTTT
716389 GTTTACATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
10 2 0.04
11 5 0.10
12 28 0.57
13 12 0.24
14 1 0.02
15 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (12 bp):
TTTTATATTTTA
Found at i:716354 original size:3 final size:3
Alignment explanation
Indices: 716321--716382 Score: 62
Period size: 3 Copynumber: 21.7 Consensus size: 3
716311 TTTATTTTTT
*
716321 TTA TT- TTA TT- TTA -TA TT- TTA TT- TTAA TTA TTA TTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
716362 TTA TTA TATA TTA TTA TTA TT
1 TTA TTA T-TA TTA TTA TTA TT
716383 TATTTTGTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
2 10 0.20
3 35 0.70
4 5 0.10
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:716354 original size:17 final size:17
Alignment explanation
Indices: 716319--716379 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
716309 TTTTTATTTT
*
716319 TTTTATTTTATTTTATA
1 TTTTATTTTATTATATA
716336 TTTTATTTTAATTAT-TA
1 TTTTATTTT-ATTATATA
*
716353 TTATTAGTATTATTATATA
1 TT-TTA-TTTTATTATATA
716372 TTATTATT
1 TT-TTATT
716380 ATTTATTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 13 0.35
18 13 0.35
19 11 0.30
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTATTTTATTATATA
Found at i:720822 original size:15 final size:14
Alignment explanation
Indices: 720802--720903 Score: 66
Period size: 15 Copynumber: 6.9 Consensus size: 14
720792 GATCAAATCA
720802 AAACAAAGAGAAAAG
1 AAACAAAGA-AAAAG
*
720817 AAACAAAGAAAAACA
1 AAACAAAGAAAAA-G
720832 AAGAGCAAAGAGAAAAAG
1 AA-A-C-AA-AGAAAAAG
*
720850 TAAAGAAAGAAAAAG
1 -AAACAAAGAAAAAG
720865 AAA-AAAGAAAAA-
1 AAACAAAGAAAAAG
*
720877 AAGCAAAGAGAAAA-
1 AAACAAAGA-AAAAG
* *
720891 AATCAAATAAAAA
1 AAACAAAGAAAAA
720904 TAACAAAAGA
Statistics
Matches: 73, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
12 2 0.03
13 18 0.25
14 18 0.25
15 19 0.26
16 3 0.04
17 1 0.01
18 3 0.04
19 9 0.12
ACGTcount: A:0.75, C:0.06, G:0.16, T:0.03
Consensus pattern (14 bp):
AAACAAAGAAAAAG
Found at i:720823 original size:25 final size:25
Alignment explanation
Indices: 720801--720903 Score: 90
Period size: 25 Copynumber: 4.2 Consensus size: 25
720791 AGATCAAATC
720801 AAAACAAAGAGAAAAGAAACAAAGA
1 AAAACAAAGAGAAAAGAAACAAAGA
*
720826 AAAACAAAGAGCAAAGAGAA-AAAG-
1 AAAACAAAGAGAAAAGA-AACAAAGA
* *
720850 TAAAGAAAGA-AAAAGAAA-AAAGAAA
1 AAAACAAAGAGAAAAGAAACAAAG--A
* *
720875 AAAAGCAAAGAGAAAA-AATCAAATA
1 AAAA-CAAAGAGAAAAGAAACAAAGA
720900 AAAA
1 AAAA
720904 TAACAAAAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
22 6 0.10
23 5 0.08
24 8 0.13
25 28 0.44
26 9 0.14
27 7 0.11
ACGTcount: A:0.76, C:0.06, G:0.16, T:0.03
Consensus pattern (25 bp):
AAAACAAAGAGAAAAGAAACAAAGA
Found at i:720857 original size:30 final size:29
Alignment explanation
Indices: 720810--720892 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 29
720800 CAAAACAAAG
**
720810 AGAAAAGAAA-CAAAGAAAAACAAAGAGCAA
1 AGAAAA-AAAGCAAAGAAAAA-AAAGAAAAA
* *
720840 AGAGAAAAAGTAAAGAAAGAAAAAGAAAAA
1 AGAAAAAAAGCAAAGAAA-AAAAAGAAAAA
*
720870 AGAAAAAAAGCAAAGAGAAAAAA
1 AGAAAAAAAGCAAAGAAAAAAAA
720893 TCAAATAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 8 0.18
30 34 0.77
31 2 0.05
ACGTcount: A:0.76, C:0.05, G:0.18, T:0.01
Consensus pattern (29 bp):
AGAAAAAAAGCAAAGAAAAAAAAGAAAAA
Found at i:720868 original size:21 final size:21
Alignment explanation
Indices: 720835--720891 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
720825 AAAAACAAAG
* *
720835 AGCAAAGAGAAAAAGTAAAGAA
1 AGCAAAAAGAAAAAG-AAAAAA
720857 AG-AAAAAGAAAAAAGAAAAAA
1 AGCAAAAAG-AAAAAGAAAAAA
*
720878 AGCAAAGAGAAAAA
1 AGCAAAAAGAAAAA
720892 ATCAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (21 bp):
AGCAAAAAGAAAAAGAAAAAA
Done.