Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002755.1 Hibiscus syriacus cultivar Beakdansim tig00005678_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: 722678
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 3 of 4
Found at i:441885 original size:26 final size:28
Alignment explanation
Indices: 441848--441902 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
441838 TAAAGTAAAG
441848 ATATTAATAAAA-AATAA-TATATATAA
1 ATATTAATAAAATAATAAGTATATATAA
441874 ATATT-ATGAAAATAATAAGTATATATAA
1 ATATTAAT-AAAATAATAAGTATATATAA
441902 A
1 A
441903 AATTTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 2 0.08
26 9 0.35
27 5 0.19
28 10 0.38
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (28 bp):
ATATTAATAAAATAATAAGTATATATAA
Found at i:443829 original size:18 final size:18
Alignment explanation
Indices: 443803--443837 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
443793 TTTTTCTTTT
*
443803 TTTTTTGGTTGCTTTCTG
1 TTTTCTGGTTGCTTTCTG
443821 TTTTCTGGTTGCTTTCT
1 TTTTCTGGTTGCTTTCT
443838 CGTGTTTTTC
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:0.00, C:0.14, G:0.20, T:0.66
Consensus pattern (18 bp):
TTTTCTGGTTGCTTTCTG
Found at i:444306 original size:3 final size:3
Alignment explanation
Indices: 444298--444397 Score: 67
Period size: 3 Copynumber: 33.3 Consensus size: 3
444288 GCATGTTTTG
* * * * * *
444298 TAA TAA TAA TATT TAT TAA TAA TAA AAA AAA T-A TTA TAA TAA TTA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
444343 TTA TAA TTA TAA TAA TTA TAA CAA TTA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
444391 AAA TAA T
1 TAA TAA T
444398 CGGGCAAAAC
Statistics
Matches: 76, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
2 2 0.03
3 72 0.95
4 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:444342 original size:9 final size:9
Alignment explanation
Indices: 444330--444390 Score: 95
Period size: 9 Copynumber: 6.8 Consensus size: 9
444320 TAAAAAAAAT
444330 ATTATAATA
1 ATTATAATA
*
444339 ATTATTATA
1 ATTATAATA
444348 ATTATAATA
1 ATTATAATA
*
444357 ATTATAACA
1 ATTATAATA
444366 ATTATAATA
1 ATTATAATA
444375 ATTATAATA
1 ATTATAATA
*
444384 ATAATAA
1 ATTATAA
444391 AAATAATCGG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (9 bp):
ATTATAATA
Found at i:447721 original size:17 final size:17
Alignment explanation
Indices: 447711--447744 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
447701 ATTAGATCAC
447711 TATTTTTATTAAATAAA
1 TATTTTTATTAAATAAA
*
447728 TATTTTTATTGAATAAA
1 TATTTTTATTAAATAAA
447745 AATTATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTTTTATTAAATAAA
Found at i:447755 original size:22 final size:22
Alignment explanation
Indices: 447727--447848 Score: 99
Period size: 22 Copynumber: 5.5 Consensus size: 22
447717 TATTAAATAA
447727 ATATTTTTATTGAATAAAAATT
1 ATATTTTTATTGAATAAAAATT
*
447749 ATATTTTT-TT-ATATAATTAGATTT
1 ATATTTTTATTGA-ATAA--A-AATT
* *
447773 CTATTTTTATTGAATAAAAATA
1 ATATTTTTATTGAATAAAAATT
* *
447795 ATATTTTTATAT-AAT-TATATCT
1 ATATTTTTAT-TGAATAAAAAT-T
* *
447817 CTATTTTTATTGAATAAAAATA
1 ATATTTTTATTGAATAAAAATT
447839 ATATTTTTAT
1 ATATTTTTAT
447849 AAGTATATTT
Statistics
Matches: 77, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
20 1 0.01
21 10 0.13
22 43 0.56
23 6 0.08
24 10 0.13
25 6 0.08
26 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.54
Consensus pattern (22 bp):
ATATTTTTATTGAATAAAAATT
Found at i:447820 original size:44 final size:44
Alignment explanation
Indices: 447728--447849 Score: 199
Period size: 44 Copynumber: 2.7 Consensus size: 44
447718 ATTAAATAAA
* *
447728 TATTTTTATTGAATAAAAATTATATTTTTTTATATAATTAGATTTC
1 TATTTTTATTGAATAAAAA-TA-ATATTTTTATATAATTAGATCTC
*
447774 TATTTTTATTGAATAAAAATAATATTTTTATATAATTATATCTC
1 TATTTTTATTGAATAAAAATAATATTTTTATATAATTAGATCTC
447818 TATTTTTATTGAATAAAAATAATATTTTTATA
1 TATTTTTATTGAATAAAAATAATATTTTTATA
447850 AGTATATTTA
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
44 52 0.71
45 2 0.03
46 19 0.26
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.54
Consensus pattern (44 bp):
TATTTTTATTGAATAAAAATAATATTTTTATATAATTAGATCTC
Found at i:456459 original size:16 final size:16
Alignment explanation
Indices: 456308--456452 Score: 245
Period size: 16 Copynumber: 9.1 Consensus size: 16
456298 TAAAAAATTA
456308 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
456324 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
456340 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
456356 ACGAACATAAACGAAT
1 ACGAACATAAACGAAC
456372 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
456388 ACGAACATAAACGAAT
1 ACGAACATAAACGAAC
456404 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
**
456420 ACGAACATAAATAAAC
1 ACGAACATAAACGAAC
456436 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
456452 A
1 A
456453 TAAACATTGG
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 119 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:456710 original size:23 final size:24
Alignment explanation
Indices: 456656--456721 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
456646 AAAAATTTAA
*
456656 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTAAAGCTCGAGACTC
* **
456680 GAGCTCGATTGAAGCTCGATTCT-
1 GAGCTCGATTAAAGCTCGAGACTC
*
456703 GAGCTCGATTCAAGCTCGA
1 GAGCTCGATTAAAGCTCGA
456722 CATTGCCCCA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (24 bp):
GAGCTCGATTAAAGCTCGAGACTC
Found at i:457598 original size:24 final size:25
Alignment explanation
Indices: 457571--457632 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
457561 GATTGGGTTA
* *
457571 AACATTAA-TGAATGAACATAAACG
1 AACATTAACCGAACGAACATAAACG
457595 AACA-TAACCGAACGAACATAAACG
1 AACATTAACCGAACGAACATAAACG
*
457619 AACA-TAATCGAACG
1 AACATTAACCGAACG
457633 TTCACGAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 3 0.09
24 31 0.91
ACGTcount: A:0.53, C:0.19, G:0.13, T:0.15
Consensus pattern (25 bp):
AACATTAACCGAACGAACATAAACG
Found at i:457599 original size:10 final size:10
Alignment explanation
Indices: 457584--457631 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
457574 ATTAATGAAT
457584 GAACATAAAC
1 GAACATAAAC
457594 GAACATAACCGAAC
1 GAACAT-A---AAC
457608 GAACATAAAC
1 GAACATAAAC
*
457618 GAACATAATC
1 GAACATAAAC
457628 GAAC
1 GAAC
457632 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:457608 original size:14 final size:14
Alignment explanation
Indices: 457591--457621 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
457581 AATGAACATA
*
457591 AACGAACATAACCG
1 AACGAACATAAACG
457605 AACGAACATAAACG
1 AACGAACATAAACG
457619 AAC
1 AAC
457622 ATAATCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.26, G:0.13, T:0.06
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:458529 original size:112 final size:112
Alignment explanation
Indices: 458332--458565 Score: 450
Period size: 112 Copynumber: 2.1 Consensus size: 112
458322 ACACGAAAGC
458332 TAATAAATTCAAAGAGAGAACTAATAATTTCAAATTGCTGTCTACGCGACCGAGGATGGCATCAT
1 TAATAAATTCAAAGAGAGAACTAATAATTTCAAATTGCTGTCTACGCGACCGAGGATGGCATCAT
458397 ACGGCATTGTCTGTGAGCATTTCCCGTTTCTTAATACTATAAAATAG
66 ACGGCATTGTCTGTGAGCATTTCCCGTTTCTTAATACTATAAAATAG
*
458444 TAATAAATTCAAAGAGAGAACTAATAATTTCAAATTGCTGTCTACGCGGCCGAGGATGGCATCAT
1 TAATAAATTCAAAGAGAGAACTAATAATTTCAAATTGCTGTCTACGCGACCGAGGATGGCATCAT
*
458509 ACGGCATTGTCTGTGAGCATTTCCCGTTTCTTAATACTATAACATAG
66 ACGGCATTGTCTGTGAGCATTTCCCGTTTCTTAATACTATAAAATAG
458556 TAATAAATTC
1 TAATAAATTC
458566 TTATGATCAA
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 120 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (112 bp):
TAATAAATTCAAAGAGAGAACTAATAATTTCAAATTGCTGTCTACGCGACCGAGGATGGCATCAT
ACGGCATTGTCTGTGAGCATTTCCCGTTTCTTAATACTATAAAATAG
Found at i:459294 original size:5 final size:6
Alignment explanation
Indices: 459280--459310 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
459270 TCAAAGAAAT
459280 AAAAGA AAAAGA AAAAGA AAAAG- AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AA
459311 TAAAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:460575 original size:33 final size:34
Alignment explanation
Indices: 460522--460586 Score: 82
Period size: 33 Copynumber: 1.9 Consensus size: 34
460512 GAAGAAAAAA
*
460522 AATTAATAAATAAATAAAATA-AAATAAATAACT
1 AATTAATAAATAAATAAAATAGAAAAAAATAACT
460555 AATTAATAAA-ACAAGT-AAATAGAAAAAAATAA
1 AATTAATAAATA-AA-TAAAATAGAAAAAAATAA
460587 TACTATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 1 0.04
33 17 0.61
34 10 0.36
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (34 bp):
AATTAATAAATAAATAAAATAGAAAAAAATAACT
Found at i:460625 original size:33 final size:34
Alignment explanation
Indices: 460577--460795 Score: 91
Period size: 35 Copynumber: 6.1 Consensus size: 34
460567 AAGTAAATAG
*
460577 AAAAAAA-TAATACTATAAAATATAT-ATTTCAA
1 AAAAAAATTAAAACTATAAAATATATAATTTCAA
* *
460609 AAAAAAATTAAAACTATATATTATATAATTTTACAA
1 AAAAAAATTAAAACTATAAAATATATAA-TTT-CAA
** * *
460645 AAAAATGTTTTTTAAAACTATACATTATATAATTTCAA
1 AAAAA----AATTAAAACTATAAAATATATAATTTCAA
* *** * * *
460683 AACTATTTTTAAAATTATACATTATATAATTTCAA
1 AA-AAAAATTAAAACTATAAAATATATAATTTCAA
**** * *
460718 AAATGTTTTTAAAACTATATATTATATAATTTTCTAA
1 AAA-AAAATTAAAACTATAAAATATATAA-TTTC-AA
*** * *
460755 AAATATTTTTAAAACTATATATTATATAATTTTCAA
1 AAA-AAAATTAAAACTATAAAATATATAA-TTTCAA
460791 AAAAA
1 AAAAA
460796 TGTTTTAAAA
Statistics
Matches: 160, Mismatches: 15, Indels: 21
0.82 0.08 0.11
Matches are distributed among these distances:
32 7 0.04
33 15 0.09
34 1 0.01
35 56 0.35
36 17 0.11
37 35 0.22
38 5 0.03
39 4 0.03
40 20 0.12
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (34 bp):
AAAAAAATTAAAACTATAAAATATATAATTTCAA
Found at i:460766 original size:37 final size:37
Alignment explanation
Indices: 460616--461005 Score: 274
Period size: 35 Copynumber: 10.5 Consensus size: 37
460606 CAAAAAAAAA
* *
460616 TTAAAACTATATATTATATAATTTTACAAAAAAATGTTTT
1 TTAAAACTATATATTATATAATTTT-C-TAAAAAT-ATTT
* *
460656 TTAAAACTATACATTATATAA-TTTC-AAAACTATTT
1 TTAAAACTATATATTATATAATTTTCTAAAAATATTT
* * *
460691 TTAAAATTATACATTATATAA-TTTC-AAAAATGTTT
1 TTAAAACTATATATTATATAATTTTCTAAAAATATTT
460726 TTAAAACTATATATTATATAATTTTCTAAAAATATTT
1 TTAAAACTATATATTATATAATTTTCTAAAAATATTT
*
460763 TTAAAACTATATATTATATAATTTTC-AAAAAAATGTT
1 TTAAAACTATATATTATATAATTTTCTAAAAATAT-TT
* *
460800 TT--AA--A-A-ACTATATAA-TTTCTCAAAAATGTTT
1 TTAAAACTATATATTATATAATTTTCT-AAAAATATTT
* * * * *
460831 TAAAGAACTATATAATATATAAATTTTTTCAAAATGTTT
1 TTAA-AACTATATATTATAT-AATTTTCTAAAAATATTT
* ** * *
460870 TAAAAACTATATAAAATATAAATGTTT-TCAAAATGTTT
1 TTAAAACTATATATTATAT-AAT-TTTCTAAAAATATTT
* *
460908 TCAAAAACTATATAATATATAAATTTTCT-AAAATCATTT
1 T-TAAAACTATATATTATAT-AATTTTCTAAAAAT-ATTT
* *
460947 TCTGAAAATTATATATTATAT--TTCGTC-AAAAATATTT
1 T-T-AAAACTATATATTATATAATT-TTCTAAAAATATTT
* *
460984 TCACAAATTATATTATTATATA
1 TTA-AAACTATA-TATTATATA
461006 CATATATAAT
Statistics
Matches: 301, Mismatches: 25, Indels: 50
0.80 0.07 0.13
Matches are distributed among these distances:
30 4 0.01
31 11 0.04
32 7 0.02
33 1 0.00
34 2 0.01
35 57 0.19
36 25 0.08
37 55 0.18
38 52 0.17
39 48 0.16
40 39 0.13
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (37 bp):
TTAAAACTATATATTATATAATTTTCTAAAAATATTT
Found at i:460812 original size:38 final size:38
Alignment explanation
Indices: 460618--460967 Score: 265
Period size: 38 Copynumber: 9.4 Consensus size: 38
460608 AAAAAAAATT
*
460618 AAAACTATATATTATATAATTTTACAAAAAAATGTTTTTT
1 AAAACTATATATTATATAATTTT-CAAAAAAATG-TTTTA
* **
460658 AAAACTATACATTATATAA-TTTCAAAACTAT-TTTT-
1 AAAACTATATATTATATAATTTTCAAAAAAATGTTTTA
* * *
460693 AAAATTATACATTATATAA-TTTC--AAAAATGTTTTT
1 AAAACTATATATTATATAATTTTCAAAAAAATGTTTTA
*
460728 AAAACTATATATTATATAATTTTCTAAAAATAT-TTTT-
1 AAAACTATATATTATATAATTTTC-AAAAAAATGTTTTA
460765 AAAACTATATATTATATAATTTTCAAAAAAATGTTTTA
1 AAAACTATATATTATATAATTTTCAAAAAAATGTTTTA
*
460803 AAAAC--TATA-TA-AT--TTCTC--AAAAATGTTTTA
1 AAAACTATATATTATATAATTTTCAAAAAAATGTTTTA
* ***
460833 AAGAACTATATAATATATAAATTTT-TTCAAAATGTTTTA
1 AA-AACTATATATTATAT-AATTTTCAAAAAAATGTTTTA
**
460872 AAAACTATATAAAATATAAATGTTTTC---AAAATGTTTTCA
1 AAAACTATATATTATAT-AA--TTTTCAAAAAAATGTTTT-A
* ** *
460911 AAAACTATATAATATATAAATTTTCTAAAATCAT-TTTCTG
1 AAAACTATATATTATAT-AATTTTC-AAAAAAATGTTT-TA
*
460951 AAAATTATATATTATAT
1 AAAACTATATATTATAT
460968 TTCGTCAAAA
Statistics
Matches: 263, Mismatches: 20, Indels: 54
0.78 0.06 0.16
Matches are distributed among these distances:
30 14 0.05
31 3 0.01
32 4 0.02
33 8 0.03
34 8 0.03
35 43 0.16
36 19 0.07
37 33 0.13
38 46 0.17
39 41 0.16
40 40 0.15
41 4 0.02
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (38 bp):
AAAACTATATATTATATAATTTTCAAAAAAATGTTTTA
Found at i:460827 original size:30 final size:31
Alignment explanation
Indices: 460777--460846 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
460767 AACTATATAT
460777 TATATAATTTTCAAAAAAATGTTTTAAA-AAC
1 TATATAATTTTC-AAAAAATGTTTTAAAGAAC
460808 TATATAATTTCTC-AAAAATGTTTTAAAGAAC
1 TATATAATTT-TCAAAAAATGTTTTAAAGAAC
460839 TATATAAT
1 TATATAAT
460847 ATATAAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
30 14 0.38
31 21 0.57
32 2 0.05
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (31 bp):
TATATAATTTTCAAAAAATGTTTTAAAGAAC
Found at i:460856 original size:107 final size:105
Alignment explanation
Indices: 460618--460923 Score: 311
Period size: 107 Copynumber: 2.8 Consensus size: 105
460608 AAAAAAAATT
* * *
460618 AAAACTATATATTATATAATTTTACAAAAAAATGTTTTTTAAAACTATACATTATATAA-TTTCA
1 AAAACTATATATTATATAATTTT-C-TAAAAAT-ATTTTTAAAACTATATATTATATAATTTTCA
** *
460682 AAACTAT-TTTTAAAATTATACATTATATAA-TTTCAAAAATGTTTTT
63 AAAAAATGTTTTAAAA--A-AC--TATATAATTTTCAAAAATGTTTTA
460728 AAAACTATATATTATATAATTTTCTAAAAATATTTTTAAAACTATATATTATATAATTTTCAAAA
1 AAAACTATATATTATATAATTTTCTAAAAATATTTTTAAAACTATATATTATATAATTTTCAAAA
460793 AAATGTTTT-AAAAACTATATAATTTCTCAAAAATGTTTTA
66 AAATGTTTTAAAAAACTATATAATTT-TCAAAAATGTTTTA
* * * * * **
460833 AAGAACTATATAATATATAAATTTTTTCAAAATGTTTTAAAAACTATATAAAATATAAATGTTTT
1 AA-AACTATATATTATAT-AATTTTCTAAAAATATTTTTAAAACTATATATTATAT-AA--TTTT
*
460898 C---AAAATGTTTTCAAAAACTATATAAT
61 CAAAAAAATGTTTTAAAAAACTATATAAT
460924 ATATAAATTT
Statistics
Matches: 173, Mismatches: 13, Indels: 22
0.83 0.06 0.11
Matches are distributed among these distances:
103 7 0.04
104 2 0.01
105 17 0.10
106 15 0.09
107 64 0.37
108 35 0.20
109 5 0.03
110 28 0.16
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.43
Consensus pattern (105 bp):
AAAACTATATATTATATAATTTTCTAAAAATATTTTTAAAACTATATATTATATAATTTTCAAAA
AAATGTTTTAAAAAACTATATAATTTTCAAAAATGTTTTA
Found at i:460865 original size:39 final size:38
Alignment explanation
Indices: 460822--460934 Score: 190
Period size: 39 Copynumber: 2.9 Consensus size: 38
460812 TAATTTCTCA
460822 AAAATGTTTTAAAGAACTATATAATATATAAATTTTTTC
1 AAAATGTTTTAAA-AACTATATAATATATAAATTTTTTC
* *
460861 AAAATGTTTTAAAAACTATATAAAATATAAATGTTTTC
1 AAAATGTTTTAAAAACTATATAATATATAAATTTTTTC
460899 AAAATGTTTTCAAAAACTATATAATATATAAATTTT
1 AAAATGTTTT-AAAAACTATATAATATATAAATTTT
460935 CTAAAATCAT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 33 0.48
39 36 0.52
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (38 bp):
AAAATGTTTTAAAAACTATATAATATATAAATTTTTTC
Found at i:460866 original size:69 final size:68
Alignment explanation
Indices: 460618--460883 Score: 202
Period size: 69 Copynumber: 3.7 Consensus size: 68
460608 AAAAAAAATT
* *
460618 AAAACTATATATTATATAATTTTACAAAAAAATGTTTTTTAAAACTATACATTATATAATTTC-A
1 AAAACTATATAATATATAATTTT-CAAAAAAATG-TTTTAAAAACTAT--A-TA-AT--TTTCTA
* *
460682 AAACTATTTTT
58 AAAATATTTTA
* * * *
460693 AAAATTATACATTATATAA-TTTC--AAAAATGTTTTTAAAACTATATATTATATAATTTTCTAA
1 AAAACTATATAATATATAATTTTCAAAAAAATG-TTTT--AA--A-A-ACTATATAATTTTCTAA
*
460755 AAATATTTTT
59 AAATATTTTA
* *
460765 AAAACTATATATTATATAATTTTCAAAAAAATGTTTTAAAAACTATATAA-TTTCTCAAAAATGT
1 AAAACTATATAATATATAATTTTCAAAAAAATGTTTTAAAAACTATATAATTTTCT-AAAAATAT
460829 TTTA
65 TTTA
***
460833 AAGAACTATATAATATATAAATTTT-TTCAAAATGTTTTAAAAACTATATAA
1 AA-AACTATATAATATAT-AATTTTCAAAAAAATGTTTTAAAAACTATATAA
460884 AATATAAATG
Statistics
Matches: 164, Mismatches: 14, Indels: 32
0.78 0.07 0.15
Matches are distributed among these distances:
67 5 0.03
68 20 0.12
69 38 0.23
70 7 0.04
71 16 0.10
72 30 0.18
73 8 0.05
74 9 0.05
75 26 0.16
76 1 0.01
77 4 0.02
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (68 bp):
AAAACTATATAATATATAATTTTCAAAAAAATGTTTTAAAAACTATATAATTTTCTAAAAATATT
TTA
Found at i:460903 original size:11 final size:11
Alignment explanation
Indices: 460889--460913 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
460879 TATAAAATAT
460889 AAATGTTTTCA
1 AAATGTTTTCA
460900 AAATGTTTTCA
1 AAATGTTTTCA
460911 AAA
1 AAA
460914 ACTATATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:461024 original size:19 final size:19
Alignment explanation
Indices: 461000--461036 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
460990 ATTATATTAT
461000 TATATACATATATAATAAA
1 TATATACATATATAATAAA
*
461019 TATATATATATATAATAA
1 TATATACATATATAATAA
461037 CTCCGACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
TATATACATATATAATAAA
Found at i:462271 original size:2 final size:2
Alignment explanation
Indices: 462264--462322 Score: 70
Period size: 2 Copynumber: 30.0 Consensus size: 2
462254 AATCAATCAT
462264 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
462304 -A GTA TA AA TCA TA TA TA TA
1 TA -TA TA TA T-A TA TA TA TA
462323 ATAAACGTAC
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
1 3 0.06
2 44 0.88
3 3 0.06
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:466618 original size:17 final size:19
Alignment explanation
Indices: 466596--466682 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 19
466586 CGAATTATAA
466596 ATATTA-TATTATAAT-TT
1 ATATTATTATTATAATATT
*
466613 ATATTATTATTATTATTATT
1 ATATTATTATTA-TAATATT
466633 ATATTATTATTATAACTATT
1 ATATTATTATTATAA-TATT
466653 ATATTA-TA--ATAATTATT
1 ATATTATTATTATAA-TATT
466670 AGTATTATTATTA
1 A-TATTATTATTA
466683 CTCATGTTTA
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
17 15 0.25
18 10 0.17
19 9 0.15
20 24 0.41
21 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (19 bp):
ATATTATTATTATAATATT
Found at i:466696 original size:3 final size:3
Alignment explanation
Indices: 466597--466682 Score: 81
Period size: 3 Copynumber: 29.7 Consensus size: 3
466587 GAATTATAAA
*
466597 TAT TA- TAT TAT AAT T-T ATAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
466640 TAT TAT AAC TAT TA- TAT TAT AAT AAT TAT TAG TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
466683 CTCATGTTTA
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
2 7 0.10
3 60 0.88
4 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:475074 original size:7 final size:7
Alignment explanation
Indices: 475055--475171 Score: 111
Period size: 7 Copynumber: 16.4 Consensus size: 7
475045 ATTTTGCTTG
475055 AGAAAAA
1 AGAAAAA
475062 ATGAAAAA
1 A-GAAAAA
475070 AGAAAAAA
1 AG-AAAAA
475078 AGAGAGAAA
1 AGA-A-AAA
475087 A-AAAGGAA
1 AGAAA--AA
475095 A-AAAAA
1 AGAAAAA
475101 A-AAAAA
1 AGAAAAA
475107 AGAAAAA
1 AGAAAAA
475114 AGAAAAA
1 AGAAAAA
475121 AG-AAAA
1 AGAAAAA
475127 AGAAAAA
1 AGAAAAA
475134 A-AAAAA
1 AGAAAAA
*
475140 AAAAGAGAA
1 AGAA-A-AA
475149 AG-AAAA
1 AGAAAAA
475155 AGAAAAA
1 AGAAAAA
475162 AGAAAAA
1 AGAAAAA
475169 AGA
1 AGA
475172 GAGAAAATAA
Statistics
Matches: 97, Mismatches: 1, Indels: 24
0.80 0.01 0.20
Matches are distributed among these distances:
6 26 0.27
7 40 0.41
8 24 0.25
9 7 0.07
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (7 bp):
AGAAAAA
Found at i:475095 original size:28 final size:24
Alignment explanation
Indices: 475055--475171 Score: 141
Period size: 24 Copynumber: 4.7 Consensus size: 24
475045 ATTTTGCTTG
475055 AGAAAAAATGAAAAAAGAAAAAAAGA
1 AGAAAAAA-GAAAAAAGAAAAAAA-A
475081 GAGAAAAAAAGGAAAAAA-AAAAAAAA
1 -AG-AAAAAA-GAAAAAAGAAAAAAAA
475107 AGAAAAAAGAAAAAAGAAAAAGAAA
1 AGAAAAAAGAAAAAAGAAAAA-AAA
*
475132 A-AAAAAA-AAAAAGAGAAAGAAAA
1 AGAAAAAAGAAAAA-AGAAAAAAAA
475155 AGAAAAAAGAAAAAAGA
1 AGAAAAAAGAAAAAAGA
475172 GAGAAAATAA
Statistics
Matches: 82, Mismatches: 2, Indels: 15
0.83 0.02 0.15
Matches are distributed among these distances:
23 16 0.20
24 32 0.39
25 11 0.13
26 1 0.01
27 9 0.11
28 13 0.16
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (24 bp):
AGAAAAAAGAAAAAAGAAAAAAAA
Found at i:475105 original size:36 final size:36
Alignment explanation
Indices: 475056--475169 Score: 121
Period size: 36 Copynumber: 3.2 Consensus size: 36
475046 TTTTGCTTGA
**
475056 GAAAAAATGAAAAAAGA-AAAAAAGAGAGAAAAAAAG
1 GAAAAAAAAAAAAAAGAGAAAAAAGA-AGAAAAAAAG
*
475092 GAAAAAAAAAAAAAA-AGAAAAAAGAAAAAAGAAAAAG
1 GAAAAAAAAAAAAAAGAGAAAAAAG-AAGAA-AAAAAG
*
475129 AAAAAAAAAAAAAAAGAGAAAGAAA-AAG-AAAAAA-
1 GAAAAAAAAAAAAAAGAGAAA-AAAGAAGAAAAAAAG
475163 GAAAAAA
1 GAAAAAA
475170 GAGAGAAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
34 6 0.09
35 6 0.09
36 24 0.36
37 23 0.34
38 5 0.07
39 3 0.04
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (36 bp):
GAAAAAAAAAAAAAAGAGAAAAAAGAAGAAAAAAAG
Found at i:475163 original size:41 final size:38
Alignment explanation
Indices: 475065--475169 Score: 131
Period size: 41 Copynumber: 2.7 Consensus size: 38
475055 AGAAAAAATG
* * **
475065 AAAAAAGAAAAA-AAGAGAGAAAAAAAGGAAAAAAAAA
1 AAAAAAGAAAAAGAAAAAAGAAAAAAAAAAAAAAAAAA
475102 AAAAAAGAAAAAAGAAAAAAGAAAAAGAAAAAAAAAAAAA
1 AAAAAAG-AAAAAGAAAAAAGAAAAA-AAAAAAAAAAAAA
475142 AAGAGAAAGAAAAAGAAAAAAGAAAAAA
1 AA-A-AAAGAAAAAGAAAAAAGAAAAAA
475170 GAGAGAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
37 7 0.12
38 5 0.08
39 10 0.17
40 14 0.24
41 19 0.32
42 4 0.07
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (38 bp):
AAAAAAGAAAAAGAAAAAAGAAAAAAAAAAAAAAAAAA
Found at i:475184 original size:1 final size:1
Alignment explanation
Indices: 475065--475169 Score: 75
Period size: 1 Copynumber: 105.0 Consensus size: 1
475055 AGAAAAAATG
* * * * ** * * * *
475065 AAAAAAGAAAAAAAGAGAGAAAAAAAGGAAAAAAAAAAAAAAAGAAAAAAGAAAAAAGAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
475130 AAAAAAAAAAAAAAGAGAAAGAAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
475170 GAGAGAAAAT
Statistics
Matches: 76, Mismatches: 28, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (1 bp):
A
Found at i:476522 original size:54 final size:54
Alignment explanation
Indices: 476440--477365 Score: 1154
Period size: 54 Copynumber: 17.1 Consensus size: 54
476430 TGAAGCAAAT
* * *
476440 GAAGATTGTTCGAGTTCGTACTCCCTAAATAAAGAGGGAGCAAACCCGTTGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * * * *
476494 GAAGATTGTTTGCGTTCCTACTCCCTAAAGAAATAGGGAGCGAACTCGTGGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* *
476548 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCATGGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * * *
476602 GAAGATTGTTTGAGTTCCTACTCCCTAAAGAAAGAGTGAGCGAACCCGTAGGTA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * * **
476656 GAAGATTATTCGAGTTCCTACTCCCTAAAGAAAAAGGGAGCAAACCCGTAAGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* *
476710 GAAGAATGTTCGAGTTCCTACTCCCTAAAGAAAGAGAGAGCGAACCCGTTGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* ** * *
476764 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAATAAAGAGCAAACCCGTAGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * * * *
476818 GAAGATTGTTTGAGTTCCTACACCCTCAAGAAAGATGGAGCGAACCCGTTAGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * * *
476872 GAAGATTGTTTTGAGTTCCTGCTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGTA
1 GAAGATTG-TTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * * * ** * * *
476927 GAAGATTGTTTGAGTTCCTATTACCTAAAGAAAGAGAGAAAGAACCTGTAGACA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * *
476981 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAAGGAGCAAACCCGTAT-GAA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGT-TGGCA
** *
477035 GAAGATTGTTATAGTTCCAACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * *
477089 GAAGATTGTTCGAGTTCTTACTCCCTAAAGAAAAAGAGAGCGAACCCGTTGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * *
477143 GAAGATTGTTCGAGTTCCTACTCCCTAAAAAAAGAGGAAGCGAACTCGTTGGCA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
* * * * * * *
477197 AAAGATTATTCGAGTTCCTACTTCTTAAAGAAAGAGGCAGCGAACCCATTGACA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
** *
477251 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAAAGAGCGAACCC-TTAGACA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTT-GGCA
* * * * * * *
477305 AAAGATTATTTGAGTTCCTACTCCCTAAAGAAAGAGGAAACGAACCTGTTGACA
1 GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
477359 GAAGATT
1 GAAGATT
477366 TTTCAAGTCT
Statistics
Matches: 750, Mismatches: 117, Indels: 10
0.86 0.13 0.01
Matches are distributed among these distances:
53 3 0.00
54 698 0.93
55 49 0.07
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (54 bp):
GAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCA
Found at i:477554 original size:12 final size:13
Alignment explanation
Indices: 477527--477589 Score: 64
Period size: 14 Copynumber: 5.0 Consensus size: 13
477517 TTTTGTCCAG
477527 ATTATAAATATTAT
1 ATTAT-AATATTAT
477541 ATTATAAT-TTAT
1 ATTATAATATTAT
477553 ATTAT--TA-T-T
1 ATTATAATATTAT
477562 ATTATAACTATTAT
1 ATTATAA-TATTAT
477576 ATTATAATAATTAT
1 ATTATAAT-ATTAT
477590 TAATATTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.14
10 2 0.05
12 11 0.26
13 5 0.12
14 18 0.43
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATAATATTAT
Found at i:477563 original size:23 final size:23
Alignment explanation
Indices: 477535--477598 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
477525 AGATTATAAA
477535 TATTA-TATTATAA-T-TTATAT
1 TATTATTATTATAACTATTATAT
477555 TATTATTATTATAACTATTATAT
1 TATTATTATTATAACTATTATAT
* *
477578 TATAATAATTATTAA-TATTAT
1 TATTATTATTA-TAACTATTAT
477599 TACTACTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 5 0.13
21 8 0.21
22 1 0.03
23 21 0.55
24 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTATTATTATAACTATTATAT
Found at i:477574 original size:35 final size:32
Alignment explanation
Indices: 477527--477603 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 32
477517 TTTTGTCCAG
* *
477527 ATTATAAATATTATATTATAATTTATATTATTATT
1 ATTATAACTATTATATTATAA--TA-ATTATTAAT
477562 ATTATAACTATTATATTATAATAATTATTAAT
1 ATTATAACTATTATATTATAATAATTATTAAT
*
477594 ATTATTACTA
1 ATTATAACTA
477604 CTCATGTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 17 0.44
33 2 0.05
35 20 0.51
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (32 bp):
ATTATAACTATTATATTATAATAATTATTAAT
Found at i:480183 original size:21 final size:21
Alignment explanation
Indices: 480154--480206 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
480144 ATTCTGACTA
480154 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
480175 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
480196 TCGCAATGCGA
1 TCGCATTGCGA
480207 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:480351 original size:20 final size:20
Alignment explanation
Indices: 480196--480348 Score: 222
Period size: 20 Copynumber: 7.7 Consensus size: 20
480186 TTTTCCTAAT
480196 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
480216 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
480236 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
480256 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
480276 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
480296 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
480316 TCGCAATAG-GAAT-CTGTAAA
1 TCGCAAT-GCGAATAC-GTAAA
*
480336 TCGCAACGCGAAT
1 TCGCAATGCGAAT
480349 CTGACTATTG
Statistics
Matches: 127, Mismatches: 3, Indels: 6
0.93 0.02 0.04
Matches are distributed among these distances:
19 2 0.02
20 124 0.98
21 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:481229 original size:24 final size:24
Alignment explanation
Indices: 481202--481255 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
481192 GTATTCGAAA
481202 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
481226 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
481250 TTTGAT
1 TTTGAT
481256 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:483713 original size:20 final size:21
Alignment explanation
Indices: 483688--483756 Score: 108
Period size: 20 Copynumber: 3.4 Consensus size: 21
483678 CAACGCAAAA
*
483688 ATCGCAACGC-GAATATAACT
1 ATCGCAACGCGGAATATGACT
483708 ATCGCAACGCGGAAT-TGACT
1 ATCGCAACGCGGAATATGACT
483728 ATCGCAACGCGGAA-ATGACT
1 ATCGCAACGCGGAATATGACT
483748 ATCGCAACG
1 ATCGCAACG
483757 AGAGAATCGC
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
20 42 0.91
21 4 0.09
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGGAATATGACT
Found at i:483778 original size:33 final size:34
Alignment explanation
Indices: 483669--483825 Score: 122
Period size: 34 Copynumber: 4.5 Consensus size: 34
483659 GACATTCATT
*
483669 TGACTATCGCAACGCA-AAAATCGCAACGCGAATA
1 TGACTATCGCAACGCAGAGAATCGCAACGCGAA-A
* *
483703 TAACTATCGCAACGCGGAATTGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCAG-A--GA--ATCGCAACGC-GAAA
*
483743 TGACTATCGCAACG-AGAGAATCGCAATGCGAAA
1 TGACTATCGCAACGCAGAGAATCGCAACGCGAAA
** * * *
483776 TGAAAATCGCAACG-AGTGAATCACAATGCGAAAA
1 TGACTATCGCAACGCAGAGAATCGCAACGCG-AAA
**
483810 TGAAAATCGCAACGCA
1 TGACTATCGCAACGCA
483826 AAATTAGTTT
Statistics
Matches: 104, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
33 30 0.29
34 40 0.38
35 1 0.01
36 3 0.03
38 2 0.02
39 1 0.01
40 24 0.23
41 3 0.03
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (34 bp):
TGACTATCGCAACGCAGAGAATCGCAACGCGAAA
Found at i:483816 original size:34 final size:33
Alignment explanation
Indices: 483739--483823 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
483729 TCGCAACGCG
** *
483739 GAAATGACTATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGC
*
483772 GAAATGAAAATCGCAACGAGTGAATCACAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGC
483805 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
483824 CAAAATTAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 30 0.64
34 17 0.36
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAATGC
Found at i:483893 original size:33 final size:33
Alignment explanation
Indices: 483844--483921 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 33
483834 TTCGCGTTGT
*
483844 GATTTTCATTTTGCATTGCGATTCACTCATTGC
1 GATTTTCATTTCGCATTGCGATTCACTCATTGC
* * *
483877 GATTTTTATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCACTCATTGC
**
483910 GATAGTCATTTC
1 GATTTTCATTTC
483922 CGTGTTGCGA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.46
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTCACTCATTGC
Found at i:484053 original size:14 final size:14
Alignment explanation
Indices: 484034--484070 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
484024 CATCAATTAA
484034 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
484048 ACAAATCATCTTTT
1 ACAAATCAACATTT
484062 ACAAATCAA
1 ACAAATCAA
484071 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:485517 original size:42 final size:42
Alignment explanation
Indices: 485419--485530 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
485409 TCTAGAATGT
* * ** *
485419 TGGGAG-GGACCTCTTCAACGATGACAATGGCCTCTTGAACGG
1 TGGGAGAGGA-CTCTTGAACGATGATAGGGGCCTCTTGAACGA
* **
485461 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGACTCTTGAACGATGATAGGGGCCTCTTGAACGA
*
485503 TAGGG-GAGGCCTCTTGAACGATGATAGG
1 T-GGGAGAGGACTCTTGAACGATGATAGG
485531 TGAGTCGGGA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 51 0.89
43 6 0.11
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGACTCTTGAACGATGATAGGGGCCTCTTGAACGA
Found at i:486025 original size:20 final size:20
Alignment explanation
Indices: 486000--486066 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
485990 GAAACTTAAA
*
486000 ATCGCAAAGAAAAAATGACT
1 ATCGCAAAGCAAAAATGACT
* *
486020 ATCGCAACGCGAAAATGACT
1 ATCGCAAAGCAAAAATGACT
*
486040 ATCGCAATGCAAAAATGACT
1 ATCGCAAAGCAAAAATGACT
486060 ATCGCAA
1 ATCGCAA
486067 CGAGAGAATC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.46, C:0.21, G:0.16, T:0.16
Consensus pattern (20 bp):
ATCGCAAAGCAAAAATGACT
Found at i:486055 original size:40 final size:36
Alignment explanation
Indices: 485999--486189 Score: 146
Period size: 40 Copynumber: 5.3 Consensus size: 36
485989 TGAAACTTAA
* *
485999 AATCGCAAAGAAAAAATGACTATCGCAACGCGAAAATG
1 AATCGCAATGCAAAAATGACTATCGCAA-GCGAAAA-G
*
486037 ACTATCGCAATGCAAAAATGACTATCGCAA-CG-AGAG
1 A--ATCGCAATGCAAAAATGACTATCGCAAGCGAAAAG
**
486073 AATCGCAATGC-AAAATGAAAATCGCAA-C-AACAA-
1 AATCGCAATGCAAAAATGACTATCGCAAGCGAA-AAG
* *
486106 AATCGCAACGCGAAAATGACTATCGCAATGCGAAAATG
1 AATCGCAATGCAAAAATGACTATCGCAA-GCGAAAA-G
* ** *
486144 ACTATCGCAATGCGAATTTGACTATCGCAA-CG-AGAG
1 A--ATCGCAATGCAAAAATGACTATCGCAAGCGAAAAG
486180 AATCGCAATG
1 AATCGCAATG
486190 AGATTTTCAT
Statistics
Matches: 128, Mismatches: 13, Indels: 28
0.76 0.08 0.17
Matches are distributed among these distances:
33 26 0.20
34 34 0.27
36 7 0.05
37 6 0.05
38 6 0.05
40 49 0.38
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (36 bp):
AATCGCAATGCAAAAATGACTATCGCAAGCGAAAAG
Found at i:486132 original size:20 final size:20
Alignment explanation
Indices: 486107--486175 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
486097 CAACAACAAA
486107 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
486127 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
486147 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
486167 ATCGCAACG
1 ATCGCAACG
486176 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:486205 original size:107 final size:107
Alignment explanation
Indices: 485997--486189 Score: 323
Period size: 107 Copynumber: 1.8 Consensus size: 107
485987 TTTGAAACTT
485997 AAAATCGCAAAGAAAAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCAAAAATGACTAT
1 AAAATCGCAAAGAAAAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCAAAAATGACTAT
486062 CGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACAAC
66 CGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACAAC
* ** * * **
486104 AAAATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTAT
1 AAAATCGCAAAGAAAAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCAAAAATGACTAT
486169 CGCAACGAGAGAATCGCAATG
66 CGCAACGAGAGAATCGCAATG
486190 AGATTTTCAT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 79 1.00
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.16
Consensus pattern (107 bp):
AAAATCGCAAAGAAAAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCAAAAATGACTAT
CGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACAAC
Found at i:486249 original size:20 final size:20
Alignment explanation
Indices: 486223--486376 Score: 102
Period size: 20 Copynumber: 8.3 Consensus size: 20
486213 TCTTTCGTTA
**
486223 CGATAGTCAAATTCGCATTG
1 CGATAGTCATTTTCGCATTG
*
486243 TGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
*
486263 CAATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
486283 CGAT--T--TTGTT-G--TTG
1 CGATAGTCATT-TTCGCATTG
* **
486297 CAATTTTCA-TTTCGCATTG
1 CGATAGTCATTTTCGCATTG
*
486316 CGAT--TC--TCTCG--TTG
1 CGATAGTCATTTTCGCATTG
* *
486330 CGATAGTCATTTTTGCGTTG
1 CGATAGTCATTTTCGCATTG
*
486350 CGATAGTCATTTTCTCATTG
1 CGATAGTCATTTTCGCATTG
486370 CGATAGT
1 CGATAGT
486377 AAACTATTCT
Statistics
Matches: 106, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
14 13 0.12
16 12 0.11
17 6 0.06
18 4 0.04
19 6 0.06
20 65 0.61
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.43
Consensus pattern (20 bp):
CGATAGTCATTTTCGCATTG
Found at i:486279 original size:107 final size:107
Alignment explanation
Indices: 486168--486376 Score: 224
Period size: 107 Copynumber: 2.0 Consensus size: 107
486158 AATTTGACTA
*
486168 TCGCAACGAGAGAATCG-CAATG-AGATTTTCATTTCGCATTGCGATTCTTTCGTTACGATAGTC
1 TCGCAACGAGA-AATCGTCAATGCA-ATTTTCATTTCGCATTGCGATTCTCTCGTTACGATAGTC
*
486231 AAATTCGCATTGTGATAGTCATTTTCGCATTGCAATAGTCATTT
64 AAATTCGCATTGCGATAGTCATTTTCGCATTGCAATAGTCATTT
** * ** * *** * *
486275 TCGCATTGCGATTTTGTTGTTGCAATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
1 TCGCAACGAGAAATCGTCAATGCAATTTTCATTTCGCATTGCGATTCTCTCGTTACGATAGTCAA
* * * * *
486340 TTTTGCGTTGCGATAGTCATTTTCTCATTGCGATAGT
66 ATTCGCATTGCGATAGTCATTTTCGCATTGCAATAGT
486377 AAACTATTCT
Statistics
Matches: 82, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
106 2 0.02
107 79 0.96
108 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (107 bp):
TCGCAACGAGAAATCGTCAATGCAATTTTCATTTCGCATTGCGATTCTCTCGTTACGATAGTCAA
ATTCGCATTGCGATAGTCATTTTCGCATTGCAATAGTCATTT
Found at i:488281 original size:20 final size:20
Alignment explanation
Indices: 488232--488269 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
488222 CTAAAACTTT
488232 AAATCGCAACACGAAAATAA
1 AAATCGCAACACGAAAATAA
488252 AAATCGCAACACGAAAAT
1 AAATCGCAACACGAAAAT
488270 GACTATCGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.58, C:0.21, G:0.11, T:0.11
Consensus pattern (20 bp):
AAATCGCAACACGAAAATAA
Found at i:488311 original size:33 final size:34
Alignment explanation
Indices: 488253--488326 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
488243 CGAAAATAAA
**
488253 AATCGCAACACGAAAATGACTATCGCAACG-CAAG
1 AATCGCAACACGAAAATGAAAATCGCAACGAC-AG
488287 AATCGCAACACG-AAATGAAAATCGCAACGACAG
1 AATCGCAACACGAAAATGAAAATCGCAACGACAG
488320 AATCGCA
1 AATCGCA
488327 TTGCGATAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 24 0.65
34 13 0.35
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.11
Consensus pattern (34 bp):
AATCGCAACACGAAAATGAAAATCGCAACGACAG
Found at i:488713 original size:22 final size:22
Alignment explanation
Indices: 488651--488715 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
488641 TGACCGTGAA
* *
488651 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
488673 TGATATCGTCGGCGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
488695 TGATTTCGTCGGAGATGGGGA
1 TGATTTCGTCGGAGATGGGGA
488716 TAGATGTCGC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:488936 original size:20 final size:20
Alignment explanation
Indices: 488913--489006 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
488903 CGATAGTCAG
*
488913 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
488933 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * * **
488953 AATCGTATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* *
488974 ATTCGCGTTGGGATTTACGT
1 ATTCGCATTGCGATTTACGT
488994 ATTCGCATTGCGA
1 ATTCGCATTGCGA
489007 ATTAGGAAAA
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:489027 original size:21 final size:21
Alignment explanation
Indices: 489003--489048 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
488993 TATTCGCATT
489003 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
489024 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
489045 GCGA
1 GCGA
489049 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:492033 original size:24 final size:24
Alignment explanation
Indices: 491982--492043 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
491972 CATAAATTCT
**
491982 ATTTTAAAATATAATTAATATAAG
1 ATTTTAAAATATAAAAAATATAAG
* *
492006 A-TTTAAAATAATAAAAAATTTAAT
1 ATTTTAAAAT-ATAAAAAATATAAG
492030 ATTTTAAAAT-TAAA
1 ATTTTAAAATATAAA
492044 TTTAATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 12 0.38
24 12 0.38
25 8 0.25
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
ATTTTAAAATATAAAAAATATAAG
Found at i:492046 original size:20 final size:20
Alignment explanation
Indices: 492021--492086 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
492011 AAATAATAAA
492021 AAATTTAATATTTTAAAATT
1 AAATTTAATATTTTAAAATT
* * *
492041 AAATTTAATATATAAAAAAT
1 AAATTTAATATTTTAAAATT
* * *
492061 GAATTTACTATTTTTAAAATA
1 AAATTTAATA-TTTTAAAATT
492082 AAATT
1 AAATT
492087 AAATTTAGAA
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
20 25 0.71
21 10 0.29
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
AAATTTAATATTTTAAAATT
Found at i:494088 original size:17 final size:16
Alignment explanation
Indices: 494034--494088 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 16
494024 ATTCAACTTG
*
494034 TTTAAAAAAATATATA
1 TTTAATAAAATATATA
* *
494050 TATAAT-AAGTATA-A
1 TTTAATAAAATATATA
*
494064 TTTGATAAAATATATA
1 TTTAATAAAATATATA
494080 TTTCAATAA
1 TTT-AATAA
494089 TCTTTTATTC
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
14 5 0.17
15 12 0.41
16 8 0.28
17 4 0.14
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (16 bp):
TTTAATAAAATATATA
Found at i:500744 original size:3 final size:3
Alignment explanation
Indices: 500738--500772 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
500728 GTCATCATCA
* *
500738 TCG TCG TCG TCG TCG TCA TCG TCG TCG TCA TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
500773 CTGAGCAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.06, C:0.34, G:0.26, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:500759 original size:12 final size:12
Alignment explanation
Indices: 500728--500772 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
500718 ACTCCTCGCT
* *
500728 GTCATCATCATC
1 GTCATCGTCGTC
*
500740 GTCGTCGTCGTC
1 GTCATCGTCGTC
500752 GTCATCGTCGTC
1 GTCATCGTCGTC
500764 GTCATCGTC
1 GTCATCGTC
500773 CTGAGCAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.11, C:0.33, G:0.22, T:0.33
Consensus pattern (12 bp):
GTCATCGTCGTC
Found at i:502794 original size:17 final size:18
Alignment explanation
Indices: 502774--502821 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
502764 CAATTATATT
502774 AGTAAAATA-ATAAATAA
1 AGTAAAATACATAAATAA
*
502791 AGTAAAATACTTAAATAA
1 AGTAAAATACATAAATAA
*
502809 A-TTAAATACATAA
1 AGTAAAATACATAA
502822 TATTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (18 bp):
AGTAAAATACATAAATAA
Found at i:502807 original size:18 final size:17
Alignment explanation
Indices: 502774--502814 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
502764 CAATTATATT
502774 AGTAAAATAATAAATAA
1 AGTAAAATAATAAATAA
*
502791 AGTAAAATACTTAAATAA
1 AGTAAAATA-ATAAATAA
*
502809 ATTAAA
1 AGTAAA
502815 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (17 bp):
AGTAAAATAATAAATAA
Found at i:503088 original size:51 final size:50
Alignment explanation
Indices: 502953--503100 Score: 149
Period size: 51 Copynumber: 2.9 Consensus size: 50
502943 CCCTGTACCG
**
502953 CGCTATACCCCACGTGTCAGATAAAT-AGCTATAGCGCGGAACAGGGGGTA
1 CGCTATACCCCACGTGT-AGCCAAATCAGCTATAGCGCGGAACAGGGGGTA
* ** * * *
503003 GGCTATA-CCCACGTGTAAGCCATGTCAGTGTATAGCGTGGTACAGGGGGTA
1 CGCTATACCCCACGTGT-AGCCAAATCAG-CTATAGCGCGGAACAGGGGGTA
*
503054 CGCTATACCCCACGTGGT-GCCAAATCAGCATATAGCGCGGGACAGGG
1 CGCTATACCCCACGT-GTAGCCAAATCAGC-TATAGCGCGGAACAGGG
503101 AGCGCGCTTT
Statistics
Matches: 78, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
49 13 0.17
50 8 0.10
51 48 0.62
52 7 0.09
53 2 0.03
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.19
Consensus pattern (50 bp):
CGCTATACCCCACGTGTAGCCAAATCAGCTATAGCGCGGAACAGGGGGTA
Found at i:504615 original size:21 final size:20
Alignment explanation
Indices: 504591--504661 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
504581 ATATTTTAAT
504591 TATATTTATTTATTTATTTA
1 TATATTTATTTATTTATTTA
** *
504611 CTATATTCCTTTTTTTATTTA
1 -TATATTTATTTATTTATTTA
*
504632 TAT-TATA-TTATTTTATTATA
1 TATATTTATTTA-TTTATT-TA
504652 TATATCTTAT
1 TATAT-TTAT
504662 ATCATTATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
18 2 0.05
19 7 0.19
20 8 0.22
21 18 0.49
22 2 0.05
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (20 bp):
TATATTTATTTATTTATTTA
Found at i:504650 original size:13 final size:14
Alignment explanation
Indices: 504625--504663 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
504615 ATTCCTTTTT
504625 TTATTTATATTATA
1 TTATTTATATTATA
504639 TTATTT-TATTATA
1 TTATTTATATTATA
504652 TATATCTTATAT
1 T-TAT-TTATAT
504664 CATTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.36
14 9 0.41
15 2 0.09
16 3 0.14
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:504661 original size:19 final size:19
Alignment explanation
Indices: 504570--504677 Score: 80
Period size: 19 Copynumber: 5.6 Consensus size: 19
504560 TTTCATCCCC
504570 TATATATATATATATTTTAAT
1 TATATATATAT-TATTTT-AT
*
504591 TATATTTAT-TTA-TTTAT
1 TATATATATATTATTTTAT
* *
504608 T-TACTATATTCCTTTTTTTAT
1 TATA-TATA-T-ATTATTTTAT
504629 T-TATATTATATTATTTTAT
1 TATATA-TATATTATTTTAT
* * *
504648 TATATATATCTTATATCAT
1 TATATATATATTATTTTAT
504667 TATATATATAT
1 TATATATATAT
504678 ATATATATGT
Statistics
Matches: 71, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
16 2 0.03
17 6 0.08
18 4 0.06
19 31 0.44
20 10 0.14
21 18 0.25
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATATATATTATTTTAT
Found at i:504829 original size:27 final size:27
Alignment explanation
Indices: 504779--504830 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
504769 TATTTTCTTA
* *
504779 ATATTCTATTTTTATTTTTATTTATAT
1 ATATTATATTTTTATTTATATTTATAT
504806 ATATTATATTTTTACTTTAT-TTTAT
1 ATATTATATTTTTA-TTTATATTTAT
504831 TTTTTTCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (27 bp):
ATATTATATTTTTATTTATATTTATAT
Found at i:504832 original size:31 final size:32
Alignment explanation
Indices: 504789--504849 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
504779 ATATTCTATT
504789 TTTATTTTTATTTATATATATTATATTTTTAC
1 TTTATTTTTATTTATATATATTATATTTTTAC
* * *
504821 TTTA-TTTTATTTTTTTCTATTATATTTTT
1 TTTATTTTTATTTATATATATTATATTTTT
504850 CTTAATATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (32 bp):
TTTATTTTTATTTATATATATTATATTTTTAC
Found at i:504982 original size:18 final size:17
Alignment explanation
Indices: 504950--504994 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
504940 TGTACACATT
504950 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
*
504967 ATTTCTTTTACCTTTTTT
1 ATTT-TTTTACCTTTTTA
504985 ATTTTTTTAC
1 ATTTTTTTAC
504995 TTCATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:504992 original size:17 final size:17
Alignment explanation
Indices: 504948--504994 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
504938 TATGTACACA
504948 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
*
504965 TAATTTCTTTTACCTTTT
1 TTATTT-TTTTACCTTTT
504983 TTATTTTTTTAC
1 TTATTTTTTTAC
504995 TTCATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:505068 original size:18 final size:19
Alignment explanation
Indices: 505041--505077 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
505031 TTTAAACATT
505041 TTATTCATTTTGTTTATTA
1 TTATTCATTTTGTTTATTA
*
505060 TTATT-ATTTTTTTTATTA
1 TTATTCATTTTGTTTATTA
505078 ATTTTTACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.73
Consensus pattern (19 bp):
TTATTCATTTTGTTTATTA
Found at i:508216 original size:15 final size:14
Alignment explanation
Indices: 508196--508238 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
508186 ACAAAAAGAG
508196 AAAAAAGAGAAAAA
1 AAAAAAGAGAAAAA
508210 AAGAAAAGAG-AAAA
1 AA-AAAAGAGAAAAA
*
508224 TAAAAAGAGAAAAA
1 AAAAAAGAGAAAAA
508238 A
1 A
508239 CAAGGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 7 0.28
14 11 0.44
15 7 0.28
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAAAAGAGAAAAA
Found at i:508229 original size:13 final size:13
Alignment explanation
Indices: 508197--508248 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
508187 CAAAAAGAGA
*
508197 AAAAAGAGAAAAAA
1 AAAAAGAG-AAAAT
508211 AGAAAAGAGAAAAT
1 A-AAAAGAGAAAAT
508225 AAAAAGAGAAAA-
1 AAAAAGAGAAAAT
*
508237 AACAAG-GAAAAT
1 AAAAAGAGAAAAT
508249 TGAAGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 5 0.15
12 5 0.15
13 11 0.32
14 6 0.18
15 7 0.21
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (13 bp):
AAAAAGAGAAAAT
Found at i:508261 original size:30 final size:27
Alignment explanation
Indices: 508194--508261 Score: 73
Period size: 30 Copynumber: 2.4 Consensus size: 27
508184 AAACAAAAAG
508194 AGAAAAAAGAGAAAAAAAGAAAAGAGA
1 AGAAAAAAGAGAAAAAAAGAAAAGAGA
* **
508221 AAATAAAAAGAGAAAAAACAAGGAAAATTGA
1 AGA-AAAAAGAG-AAAAA-AA-GAAAAGAGA
508252 AGAAAAAAGA
1 AGAAAAAAGA
508262 AGACAATATG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
27 2 0.06
28 8 0.24
29 5 0.15
30 9 0.27
31 9 0.27
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.04
Consensus pattern (27 bp):
AGAAAAAAGAGAAAAAAAGAAAAGAGA
Found at i:508263 original size:10 final size:10
Alignment explanation
Indices: 508188--508264 Score: 56
Period size: 9 Copynumber: 8.0 Consensus size: 10
508178 CAATCAAAAC
508188 AAAAAG-AGA
1 AAAAAGAAGA
508197 AAAAAG-AG-
1 AAAAAGAAGA
508205 AAAAA-AAGA
1 AAAAAGAAGA
* *
508214 AAAGAGAAAA
1 AAAAAGAAGA
508224 TAAAAAG-AGA
1 -AAAAAGAAGA
*
508234 AAAAACAAGGA
1 AAAAAGAA-GA
**
508245 AAATTGAAGA
1 AAAAAGAAGA
508255 AAAAAGAAGA
1 AAAAAGAAGA
508265 CAATATGCAT
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
8 7 0.13
9 17 0.33
10 16 0.31
11 12 0.23
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.04
Consensus pattern (10 bp):
AAAAAGAAGA
Found at i:509954 original size:37 final size:37
Alignment explanation
Indices: 509902--510075 Score: 116
Period size: 37 Copynumber: 4.9 Consensus size: 37
509892 TAAAAAGAAG
* * *
509902 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
* *
509939 ATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
* * * ** **
509976 A--------ACATTGAAAACA-TTTCATTTGAAA-TGA
1 ATTTTGTCTCCCTTG-AGACAGTTTCCCTTGAAACAAA
* *
510004 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
* * *
510041 ATTTTGCCTCCATTGAGACAGTTTCTCTTGAAACA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
510076 TAAACATTGA
Statistics
Matches: 100, Mismatches: 26, Indels: 22
0.68 0.18 0.15
Matches are distributed among these distances:
28 2 0.02
29 14 0.14
30 4 0.04
35 3 0.03
36 13 0.13
37 64 0.64
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (37 bp):
ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:510081 original size:102 final size:101
Alignment explanation
Indices: 509908--510280 Score: 480
Period size: 102 Copynumber: 3.7 Consensus size: 101
509898 GAAGATTTTA
* * * *
509908 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
* *
509973 AAAAACATTGAAAACATTTCATTTGAAATGAATTTTG
66 -AAAACATTGAAAACATTTCATTTGAAATAAATTTCG
* *
510010 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGCCTC-CATTGAGACAGTTTCTCTTGAAA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTC-TTGAGACAGTTTCTCTTGAAA
**
510074 CATAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
65 CA-AAACATTGAAAACATTTCATTTGAAATAAATTTCG
*
510112 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
* * ** * *
510176 AAAATATTTGAATATGTTTTATTTGAAACAAATTTCG
66 AAAACA-TTGAAAACATTTCATTTGAAATAAATTTCG
* ** * * * *
510213 TCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
510278 AAA
66 AAA
510281 TTTCGTCTCT
Statistics
Matches: 241, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
100 4 0.02
101 82 0.34
102 155 0.64
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (101 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
AAAACATTGAAAACATTTCATTTGAAATAAATTTCG
Found at i:510138 original size:36 final size:36
Alignment explanation
Indices: 510091--510316 Score: 234
Period size: 36 Copynumber: 6.4 Consensus size: 36
510081 ATTGAAAACA
*
510091 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
510127 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
510163 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
*** *
510192 TTTTATTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * * *
510228 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
**
510265 TTTCTTTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
510301 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
510317 ATCTTTAAAT
Statistics
Matches: 157, Mismatches: 23, Indels: 20
0.79 0.12 0.10
Matches are distributed among these distances:
28 2 0.01
29 18 0.11
30 2 0.01
35 1 0.01
36 100 0.64
37 34 0.22
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:510202 original size:203 final size:204
Alignment explanation
Indices: 509908--510278 Score: 505
Period size: 203 Copynumber: 1.8 Consensus size: 204
509898 GAAGATTTTA
* *
509908 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAAC
1 TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAAC
** * * *
509973 AAAAACATTGAAAACATTTCATTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
66 AAAAACATTGAAAACATTTCATTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAAC
510038 AAAATTTTGCCTC-CATTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAA
131 AAAATTTTGCCTCTC-TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAA
510102 ATAAATTTCG
195 ATAAATTTCG
* * *
510112 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAAC
* * ** * ** *
510176 AAAATA-TTTGAATATGTTTTATTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAA
66 AAAA-ACATTGAAAACATTTCATTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAA
* * * *
510240 CTAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTGAAACA
130 CAAAATTTTGCCTCTCTTGAGACAGTTTCTCTTGAAACA
510279 AATTTCGTCT
Statistics
Matches: 143, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
203 115 0.80
204 28 0.20
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (204 bp):
TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAAC
AAAAACATTGAAAACATTTCATTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAAC
AAAATTTTGCCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
TAAATTTCG
Found at i:510253 original size:138 final size:138
Alignment explanation
Indices: 510111--510370 Score: 403
Period size: 138 Copynumber: 1.9 Consensus size: 138
510101 AATAAATTTC
*
510111 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * ** *
510176 AAAATATTTGAATATGTTTTATTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAC
66 AAAATATTTAAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAC
510241 TAAGTTTT
131 TAAGTTTT
**
510249 GTCTCTCTTGAGACAGTTTCTTTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * *
510314 AAAATCTTTAAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
66 AAAATATTTAAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCT
510371 CTTGAAACAC
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
138 109 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (138 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATATTTAAATATATTTCACCTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAC
TAAGTTTT
Found at i:510378 original size:65 final size:65
Alignment explanation
Indices: 510274--510447 Score: 242
Period size: 65 Copynumber: 2.6 Consensus size: 65
510264 GTTTCTTTTG
* * * *
510274 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTAAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
*
510339 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
510404 TA
64 TA
* * *
510406 AAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACAA
1 AAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
510448 CAGATATCTT
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
65 37 0.38
66 4 0.04
67 33 0.34
68 24 0.24
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:510444 original size:67 final size:67
Alignment explanation
Indices: 510274--510446 Score: 235
Period size: 67 Copynumber: 2.6 Consensus size: 67
510264 GTTTCTTTTG
* * * * *
510274 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTAAATTTATTTCCCC
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
510337 TA
66 TA
* *
510339 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
510404 TA
66 TA
* *
510406 AAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACA
1 AAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACA
510447 ACAGATATCT
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
65 33 0.34
66 2 0.02
67 38 0.39
68 24 0.25
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:511361 original size:110 final size:108
Alignment explanation
Indices: 511155--511421 Score: 366
Period size: 110 Copynumber: 2.5 Consensus size: 108
511145 ACGAAGGGGC
* * * **
511155 TTCCCAG-T-TTCAGAGCCAATTTTAACTTCACAGCGAGGGATATTGGACTTAAGACAACACAAG
1 TTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAG
*
511218 CTCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAACT
66 CTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAA-T
* *
511262 TT-TCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACA
1 TTCCCAG-TTC-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACA
*
511326 AGCTCAACTTCACAACGAAGGGGCGACTGGCTGTCAACAAACAAT
64 AGCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAAT
*
511371 TTCCCAGTTC--CAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGAACTCG
1 TTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGAACTCG
511422 GAACAATACT
Statistics
Matches: 142, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
105 1 0.01
106 40 0.28
107 2 0.01
108 1 0.01
109 6 0.04
110 92 0.65
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (108 bp):
TTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAG
CTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAAT
Found at i:512788 original size:16 final size:17
Alignment explanation
Indices: 512769--512813 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
512759 TATATTTTTT
512769 TTATTTATTTA-CTATA
1 TTATTTATTTATCTATA
*
512785 TTATTT-TTTATTTATA
1 TTATTTATTTATCTATA
512801 TTATATTATTTAT
1 TTAT-TTATTTAT
512814 ATTATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 4 0.16
16 14 0.56
17 2 0.08
18 5 0.20
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTTATTTATCTATA
Found at i:512791 original size:21 final size:20
Alignment explanation
Indices: 512741--512822 Score: 61
Period size: 18 Copynumber: 4.3 Consensus size: 20
512731 TTTCGTCCCC
* *
512741 TATATA-TATATT-TTTAAT
1 TATATATTATTTTATTTATT
*
512759 TATAT-TTTTTTTATTTATT
1 TATATATTATTTTATTTATT
512778 TACTATATTA-TTT-TTTA-T
1 TA-TATATTATTTTATTTATT
*
512796 T-TATATTATATTATTTATAT
1 TATATATTATTTTATTTAT-T
512816 TATATAT
1 TATATAT
512823 ATCTTATATC
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
16 7 0.14
17 2 0.04
18 15 0.30
19 11 0.22
20 8 0.16
21 7 0.14
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (20 bp):
TATATATTATTTTATTTATT
Found at i:512810 original size:37 final size:41
Alignment explanation
Indices: 512740--512824 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 41
512730 ATTTCGTCCC
* *
512740 CTATATATATATTTTTAATTATATTTTTTTTATTTAT-TTA
1 CTATATATATATTTTTAATTATATTTATATTATTTATATTA
*
512780 CTATAT-TAT-TTTTTATTTATA-TTATATTATTTATATTA
1 CTATATATATATTTTTAATTATATTTATATTATTTATATTA
512818 -TATATAT
1 CTATATAT
512825 CTTATATCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
37 16 0.40
38 15 0.38
39 3 0.08
40 6 0.15
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (41 bp):
CTATATATATATTTTTAATTATATTTATATTATTTATATTA
Found at i:512813 original size:25 final size:24
Alignment explanation
Indices: 512753--512831 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 24
512743 TATATATATT
512753 TTTA-ATTATATT-TTTTTTATTTA
1 TTTATATTAT-TTATTTTTTATTTA
512776 TTTACTA-TA-TTATTTTTTATTTA
1 TTTA-TATTATTTATTTTTTATTTA
* * *
512799 TATTATATTATTTATATTATATATA
1 T-TTATATTATTTATTTTTTATTTA
512824 TCTTATAT
1 T-TTATAT
512832 CATTATATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
22 2 0.04
23 18 0.39
24 7 0.15
25 19 0.41
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTATATTATTTATTTTTTATTTA
Found at i:512818 original size:23 final size:21
Alignment explanation
Indices: 512753--512811 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
512743 TATATATATT
512753 TTTA-ATTATATT-TTTTTTA
1 TTTATATTATATTATTTTTTA
*
512772 TTTATTTACTATATTATTTTTTA
1 TTTA--TATTATATTATTTTTTA
512795 TTTATATTATATTATTT
1 TTTATATTATATTATTT
512812 ATATTATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.12
21 12 0.35
22 7 0.21
23 11 0.32
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTATATTATATTATTTTTTA
Found at i:512821 original size:16 final size:16
Alignment explanation
Indices: 512741--512831 Score: 60
Period size: 14 Copynumber: 6.3 Consensus size: 16
512731 TTTCGTCCCC
512741 TATA-TATATATT-TT
1 TATATTATATATTATT
512755 TA-ATTATAT-TT-TT
1 TATATTATATATTATT
* *
512768 TTTATT-TAT-TTA-C
1 TATATTATATATTATT
* *
512781 TATATTATTTTTTATT
1 TATATTATATATTATT
512797 TATA-T-TATATTATT
1 TATATTATATATTATT
512811 TATATTATATA-TATCT
1 TATATTATATATTAT-T
512827 TATAT
1 TATAT
512832 CATTATATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
13 16 0.26
14 23 0.38
15 8 0.13
16 14 0.23
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TATATTATATATTATT
Found at i:512823 original size:23 final size:23
Alignment explanation
Indices: 512743--512850 Score: 55
Period size: 21 Copynumber: 4.7 Consensus size: 23
512733 TCGTCCCCTA
*
512743 TATATATATT-TTTA-ATTATAT
1 TATATATATTATATATATTATAT
* * * * *
512764 TTTTTTTATT-TATTTACTATAT
1 TATATATATTATATATATTATAT
* *
512786 TAT-T-TTTTATTTATATTATAT
1 TATATATATTATATATATTATAT
*
512807 TATTTATATTATATATATCTTATAT
1 TATATATATTATATATA--TTATAT
*
512832 CATTATATATATATATATA
1 TA-TATATAT-TATATATA
512851 GATGTATTAA
Statistics
Matches: 64, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
20 3 0.05
21 22 0.34
22 9 0.14
23 9 0.14
25 7 0.11
26 6 0.09
27 8 0.12
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (23 bp):
TATATATATTATATATATTATAT
Found at i:512844 original size:25 final size:25
Alignment explanation
Indices: 512801--512850 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
512791 TTTATTTATA
*
512801 TTATATTATTTATATTATATATATC
1 TTATATCATTTATATTATATATATC
512826 TTATATCATTATATATATATATATA
1 TTATATCATT-TATAT-TATATATA
512851 GATGTATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
26 5 0.23
27 8 0.36
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATATCATTTATATTATATATATC
Found at i:513134 original size:19 final size:18
Alignment explanation
Indices: 513107--513152 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
513097 TATATGTACA
*
513107 TATTATTTTTAT-TCTTTT
1 TATTTTTTTTATAT-TTTT
513125 TAATTTTTTTTATATTTTT
1 T-ATTTTTTTTATATTTTT
513144 TATTTTTTT
1 TATTTTTTT
513153 ACTCCATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 9 0.36
19 15 0.60
20 1 0.04
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (18 bp):
TATTTTTTTTATATTTTT
Found at i:513261 original size:19 final size:19
Alignment explanation
Indices: 513225--513273 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
513215 TATTTTATTA
**
513225 TTATTTTTTACGTGTTTTG
1 TTATTTTTTATTTGTTTTG
*
513244 TTATTTTTTATTTTTTTTG
1 TTATTTTTTATTTGTTTTG
*
513263 TT-TTATTTATT
1 TTATTTTTTATT
513274 ATTCTCACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.12, C:0.02, G:0.08, T:0.78
Consensus pattern (19 bp):
TTATTTTTTATTTGTTTTG
Found at i:518272 original size:39 final size:40
Alignment explanation
Indices: 518220--518313 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 40
518210 AAATTTCACT
* * *
518220 CTAACCTTCTAAATTCCTAATTTATTAAATTTTGTTAC-CA
1 CTAACATTCTAAATTCCTAATTT-TTAAAATTTATTACACA
** *
518260 -TAACATTCTAAATTTTTAATTTTTAAAATTTATTTCACA
1 CTAACATTCTAAATTCCTAATTTTTAAAATTTATTACACA
518299 CTAACATTCTAAATT
1 CTAACATTCTAAATT
518314 ATTTTTTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 11 0.24
39 21 0.46
40 14 0.30
ACGTcount: A:0.36, C:0.16, G:0.01, T:0.47
Consensus pattern (40 bp):
CTAACATTCTAAATTCCTAATTTTTAAAATTTATTACACA
Found at i:519301 original size:14 final size:16
Alignment explanation
Indices: 519282--519314 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
519272 ATTATATATT
519282 TTTAATAT-TTAA-TA
1 TTTAATATATTAATTA
519296 TTTAATATATTAATTA
1 TTTAATATATTAATTA
519312 TTT
1 TTT
519315 GTAGTTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAATATATTAATTA
Found at i:519466 original size:17 final size:18
Alignment explanation
Indices: 519443--519489 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
519433 TAGATATCAT
519443 AATATTATTTTTTATA-G
1 AATATTATTTTTTATATG
*
519460 TATATTATATTTTTTATATG
1 AATA-T-TATTTTTTATATG
519480 AATATTATTT
1 AATATTATTT
519490 AAAAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 3 0.12
18 6 0.24
19 12 0.48
20 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (18 bp):
AATATTATTTTTTATATG
Found at i:519472 original size:19 final size:20
Alignment explanation
Indices: 519448--519487 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
519438 ATCATAATAT
*
519448 TATTTTTTATA-GTATATTA
1 TATTTTTTATATGAATATTA
519467 TATTTTTTATATGAATATTA
1 TATTTTTTATATGAATATTA
519487 T
1 T
519488 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TATTTTTTATATGAATATTA
Found at i:519530 original size:9 final size:9
Alignment explanation
Indices: 519516--519540 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
519506 TGTATTAATT
519516 ATATATTAA
1 ATATATTAA
519525 ATATATTAA
1 ATATATTAA
519534 ATATATT
1 ATATATT
519541 TTTCTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
ATATATTAA
Found at i:520636 original size:18 final size:19
Alignment explanation
Indices: 520607--520647 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
520597 ATATTTATGA
520607 GTTTTTTAATCTAATGATT
1 GTTTTTTAATCTAATGATT
520626 GTTTTTT-ATCTAATGATT
1 GTTTTTTAATCTAATGATT
520644 GTTT
1 GTTT
520648 AAAAGTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.22, C:0.05, G:0.12, T:0.61
Consensus pattern (19 bp):
GTTTTTTAATCTAATGATT
Found at i:524471 original size:15 final size:14
Alignment explanation
Indices: 524433--524806 Score: 69
Period size: 15 Copynumber: 25.6 Consensus size: 14
524423 AAATAATTAT
524433 AATATATTAGTATATA
1 AATATA-TA-TATATA
*
524449 TATATATATATATA
1 AATATATATATATA
*
524463 AA-CTATATA-AT-
1 AATATATATATATA
524474 AATATAATATATATA
1 AATAT-ATATATATA
*
524489 AATTATATAGTTTATA
1 AA-TATATA-TATATA
* *
524505 CAT-TATAGAATATA
1 AATATATA-TATATA
* *
524519 AGTATAAACTATAT-
1 AATATATA-TATATA
** * *
524533 GGTTTATATATAGTT
1 AATATATATATA-TA
* *
524548 TATATATAAACTATA
1 AATATATATA-TATA
* *
524563 TAGTTTATAT-TAATA
1 -AATATATATAT-ATA
524578 AACTATATAGTTTATATA
1 AA-TATATA---TATATA
*
524596 TATATAGTATATATA
1 AATATA-TATATATA
**
524611 GTTTATATATAGTATA
1 -AATATATATA-TATA
524627 TAATA-ATATAATATA
1 -AATATATAT-ATATA
524642 AACTATATATACTATA
1 AA-TATATATA-TATA
* *
524658 TATATAAACTATAT-
1 AATATATA-TATATA
*
524672 AATCTATATATA-A
1 AATATATATATATA
* *
524685 ACTATATAGTTTATA
1 AATATATA-TATATA
*
524700 CATAGTAGTATATA-A
1 AATA-TA-TATATATA
* *
524715 ACTATATATAAACTA
1 AATATATATATA-TA
*
524730 AATAAAT-TATAT-
1 AATATATATATATA
* *
524742 AGT-T-TACATATGA
1 AATATATATATAT-A
*
524755 ACTATATATATATA
1 AATATATATATATA
*
524769 AACTAATAAACTATATA
1 AA-T-ATATA-TATATA
524786 AAT-TATATATA-A
1 AATATATATATATA
*
524798 ACTATATAT
1 AATATATAT
524807 GAACTATACA
Statistics
Matches: 259, Mismatches: 58, Indels: 85
0.64 0.14 0.21
Matches are distributed among these distances:
10 1 0.00
11 6 0.02
12 8 0.03
13 42 0.16
14 48 0.19
15 78 0.30
16 54 0.21
17 14 0.05
18 7 0.03
19 1 0.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (14 bp):
AATATATATATATA
Found at i:524548 original size:11 final size:11
Alignment explanation
Indices: 524528--524628 Score: 68
Period size: 11 Copynumber: 9.2 Consensus size: 11
524518 AAGTATAAAC
*
524528 TATATGGTTTA
1 TATATAGTTTA
524539 TATATAGTTTA
1 TATATAGTTTA
*
524550 TATATA---AA
1 TATATAGTTTA
524558 CTATATAGTTTA
1 -TATATAGTTTA
* **
524570 TAT-TAATAAA
1 TATATAGTTTA
524580 CTATATAGTTTA
1 -TATATAGTTTA
524592 TATATA-TATAGTA
1 TATATAGT-T--TA
524605 TATATAGTTTA
1 TATATAGTTTA
*
524616 TATATAGTATA
1 TATATAGTTTA
524627 TA
1 TA
524629 ATAATATAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
8 1 0.01
9 6 0.09
10 5 0.07
11 43 0.61
12 5 0.07
13 9 0.13
14 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.49
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:524626 original size:9 final size:9
Alignment explanation
Indices: 524581--524661 Score: 61
Period size: 9 Copynumber: 9.7 Consensus size: 9
524571 ATTAATAAAC
524581 TATATAGT-
1 TATATAGTA
524589 T-TATA-TA
1 TATATAGTA
524596 TATATAGTA
1 TATATAGTA
524605 TATATAGTTTA
1 TATATAG--TA
524616 TATATAGTA
1 TATATAGTA
524625 TATA-A-TA
1 TATATAGTA
524632 -ATATA--A
1 TATATAGTA
* *
524638 TATAAACTA
1 TATATAGTA
*
524647 TATATACTA
1 TATATAGTA
524656 TATATA
1 TATATA
524662 TAAACTATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 17
0.77 0.02 0.21
Matches are distributed among these distances:
6 5 0.08
7 12 0.19
8 6 0.10
9 30 0.48
11 9 0.15
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (9 bp):
TATATAGTA
Found at i:524659 original size:11 final size:11
Alignment explanation
Indices: 524590--524692 Score: 81
Period size: 11 Copynumber: 9.5 Consensus size: 11
524580 CTATATAGTT
524590 TATATATATA-
1 TATATATATAC
*
524600 TAGTATATATAG
1 TA-TATATATAC
* *
524612 TTTATATATAG
1 TATATATATAC
*
524623 TATATA-ATAA
1 TATATATATAC
*
524633 TATAATATAAAC
1 TAT-ATATATAC
524645 TATATATACTA-
1 TATATATA-TAC
*
524656 TATATATAAAC
1 TATATATATAC
524667 TATATA-AT-C
1 TATATATATAC
*
524676 TATATATAAAC
1 TATATATATAC
524687 TATATA
1 TATATA
524693 GTTTATACAT
Statistics
Matches: 76, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
9 7 0.09
10 11 0.14
11 51 0.67
12 7 0.09
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.43
Consensus pattern (11 bp):
TATATATATAC
Found at i:524670 original size:9 final size:9
Alignment explanation
Indices: 524658--524869 Score: 55
Period size: 9 Copynumber: 22.7 Consensus size: 9
524648 ATATACTATA
524658 TATATAAAC
1 TATATAAAC
*
524667 TATATAATC
1 TATATAAAC
524676 TATATATAAAC
1 --TATATAAAC
***
524687 TATATAGTT
1 TATATAAAC
* *
524696 TATACATAGTAG
1 TAT--ATA-AAC
524708 TATATAAAC
1 TATATAAAC
524717 TATATATAAAC
1 --TATATAAAC
* *
524728 TAAATAAAT
1 TATATAAAC
*
524737 TATATAGTTTAC
1 TATATA---AAC
*
524749 -ATATGAAC
1 TATATAAAC
524757 TATAT--A-
1 TATATAAAC
524763 TATATAAAC
1 TATATAAAC
524772 TA-ATAAAC
1 TATATAAAC
*
524780 TATATAAATTA
1 TATATAAA--C
524791 TATATAAAC
1 TATATAAAC
524800 TATATATGAAC
1 TATATA--AAC
524811 TATACATAAA-
1 TAT--ATAAAC
* *
524821 AAT-TATA-
1 TATATAAAC
524828 TATATAAAC
1 TATATAAAC
* *
524837 AATATAAAT
1 TATATAAAC
**
524846 TATAATTTA-
1 TAT-ATAAAC
524855 TATATAAAC
1 TATATAAAC
524864 TATATA
1 TATATA
524870 CTATAGTTTA
Statistics
Matches: 148, Mismatches: 30, Indels: 50
0.65 0.13 0.22
Matches are distributed among these distances:
6 5 0.03
7 6 0.04
8 17 0.11
9 65 0.44
10 8 0.05
11 40 0.27
12 4 0.03
13 3 0.02
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (9 bp):
TATATAAAC
Found at i:524699 original size:20 final size:20
Alignment explanation
Indices: 524539--524699 Score: 148
Period size: 20 Copynumber: 7.7 Consensus size: 20
524529 ATATGGTTTA
524539 TATATAGTTTATATATAAAC
1 TATATAGTTTATATATAAAC
524559 TATATAGTTTATATTAATAAAC
1 TATATAGTTTATA-T-ATAAAC
*
524581 TATATAGTTTATATATATATAGTA
1 TATATAGTTTATATATA-A-A--C
*
524605 TATATAGTTTATATAT--AG
1 TATATAGTTTATATATAAAC
* *
524623 TATATAATAATATAATATAAAC
1 TATATAGT-TTAT-ATATAAAC
524645 TATATA-TACTATATATATAAAC
1 TATATAGT--T-TATATATAAAC
* *
524667 TATATAATCTATATATAAAC
1 TATATAGTTTATATATAAAC
524687 TATATAGTTTATA
1 TATATAGTTTATA
524700 CATAGTAGTA
Statistics
Matches: 118, Mismatches: 10, Indels: 26
0.77 0.06 0.17
Matches are distributed among these distances:
18 7 0.06
19 3 0.03
20 43 0.36
21 4 0.03
22 41 0.35
23 4 0.03
24 16 0.14
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (20 bp):
TATATAGTTTATATATAAAC
Found at i:524722 original size:11 final size:11
Alignment explanation
Indices: 524708--524820 Score: 69
Period size: 11 Copynumber: 10.7 Consensus size: 11
524698 TACATAGTAG
524708 TATATAAACTA
1 TATATAAACTA
524719 TATATAAACTA
1 TATATAAACTA
524730 -A-ATAAA-T-
1 TATATAAACTA
***
524737 TATATAGTTTA
1 TATATAAACTA
* *
524748 CATATGAACTA
1 TATATAAACTA
*
524759 TATATATA-TA
1 TATATAAACTA
*
524769 AACTAATAAAC--
1 TA-T-ATAAACTA
*
524780 TATATAAATTA
1 TATATAAACTA
524791 TATATAAACTA
1 TATATAAACTA
*
524802 TATATGAACTA
1 TATATAAACTA
*
524813 TACATAAA
1 TATATAAA
524821 AATTATATAT
Statistics
Matches: 75, Mismatches: 18, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
8 2 0.03
9 13 0.17
10 6 0.08
11 50 0.67
12 4 0.05
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (11 bp):
TATATAAACTA
Found at i:524740 original size:20 final size:20
Alignment explanation
Indices: 524547--524849 Score: 141
Period size: 20 Copynumber: 14.2 Consensus size: 20
524537 TATATATAGT
**
524547 TTATATATAAACTATATAGT
1 TTATATATAAACTATATAAA
**
524567 TTATATTAATAAACTATATAGT
1 TTATA-T-ATAAACTATATAAA
* *
524589 TTATATATATATAGTATATATAG
1 TTATATATA-A-ACTATATA-AA
* *
524612 TT-TATATATAGTATATAATA
1 TTATATATAAACTATATAA-A
* *
524632 ATATAATATAAACTATATATAC
1 TTAT-ATATAAACTATATA-AA
524654 TATATATATAAACTATAT-AA
1 T-TATATATAAACTATATAAA
**
524674 TCTATATATAAACTATATAGT
1 T-TATATATAAACTATATAAA
* * *
524695 TTATACATAGTAGTATATAAA
1 TTATATATA-AACTATATAAA
* *
524716 CTATATATAAACTAAATAAA
1 TTATATATAAACTATATAAA
**
524736 TTATATAGTTTAC-ATATGAACTA
1 TTATATA-TAAACTATAT-AA--A
524759 TATATATATAAACTA-ATAAA
1 T-TATATATAAACTATATAAA
*
524779 CTATATA-AATTA-TATATAAA
1 TTATATATAA--ACTATATAAA
* *
524799 CTATATATGAACTATACATAAAAA
1 TTATATATAAACTAT--AT--AAA
*
524823 TTATATATATAAACAATATAAA
1 -T-TATATATAAACTATATAAA
524845 TTATA
1 TTATA
524850 ATTTATATAT
Statistics
Matches: 219, Mismatches: 35, Indels: 58
0.70 0.11 0.19
Matches are distributed among these distances:
18 2 0.01
19 10 0.05
20 80 0.37
21 26 0.12
22 64 0.29
23 13 0.06
24 12 0.05
26 12 0.05
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (20 bp):
TTATATATAAACTATATAAA
Found at i:524742 original size:2 final size:2
Alignment explanation
Indices: 524430--524724 Score: 98
Period size: 2 Copynumber: 144.0 Consensus size: 2
524420 TTAAAATAAT
*
524430 TA TA -A TA TA T- TA GTA TA TA TA TA TA TA TA TA TA AA CTA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
524472 -A TA -A TA TA -A TA TA TA TA AA T- TA TA TA GTT TA TA CA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * * *
524510 TA GA -A TA TA -A GTA TA AA CTA TA TGG TT TA TA TA TA GTT TA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA T-A TA TA TA TA TA -TA TA TA
* * * *
524552 TA TA AA CTA TA TA GTT TA TA T- TA -A TA AA CTA TA TA GTT TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
*
524594 TA TA TA TA GTA TA TA TA GTT TA TA TA TA GTA TA TA -A TA -A TA
1 TA TA TA TA -TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
524635 TA -A TA TA AA CTA TA TA TA CTA TA TA TA TA AA CTA TA TA -A TC
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA
* * * *
524676 TA TA TA TA AA CTA TA TA GTT TA TA CA TA GTA GTA TA TA AA CTA TA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA -TA -TA TA TA TA -TA TA
524721 TA TA
1 TA TA
524725 AACTAAATAA
Statistics
Matches: 217, Mismatches: 40, Indels: 72
0.66 0.12 0.22
Matches are distributed among these distances:
1 15 0.07
2 173 0.80
3 29 0.13
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (2 bp):
TA
Found at i:524801 original size:43 final size:44
Alignment explanation
Indices: 524717--524806 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 44
524707 GTATATAAAC
* ** *
524717 TATATATAAACTAAATAAATTATATAGTTTACATATGAACTATA
1 TATATATAAACTAAATAAACTATATAAATTACATATAAACTATA
*
524761 TATATATAAACT-AATAAACTATATAAATTATATATAAACTATA
1 TATATATAAACTAAATAAACTATATAAATTACATATAAACTATA
524804 TAT
1 TAT
524807 GAACTATACA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 29 0.71
44 12 0.29
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (44 bp):
TATATATAAACTAAATAAACTATATAAATTACATATAAACTATA
Found at i:525650 original size:32 final size:32
Alignment explanation
Indices: 525624--525700 Score: 145
Period size: 32 Copynumber: 2.4 Consensus size: 32
525614 GGGCCCGAGA
525624 GCCTACCCAAGAAAGTTACTCAGGGCCACGGG
1 GCCTACCCAAGAAAGTTACTCAGGGCCACGGG
*
525656 GCCTCCCCAAGAAAGTTACTCAGGGCCACGGG
1 GCCTACCCAAGAAAGTTACTCAGGGCCACGGG
525688 GCCTACCCAAGAA
1 GCCTACCCAAGAA
525701 GAATCTCGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.29, C:0.34, G:0.26, T:0.12
Consensus pattern (32 bp):
GCCTACCCAAGAAAGTTACTCAGGGCCACGGG
Found at i:525755 original size:31 final size:32
Alignment explanation
Indices: 525614--525760 Score: 140
Period size: 32 Copynumber: 4.7 Consensus size: 32
525604 GAATGCCTTG
*
525614 GGGCC-CGAGAGCCTACCCAAGAAAGTTACTCA
1 GGGCCACG-GAGCCTACCCAAGAAAGATACTCA
* * *
525646 GGGCCACGGGGCCTCCCCAAGAAAGTTACTCA
1 GGGCCACGGAGCCTACCCAAGAAAGATACTCA
* *
525678 GGGCCACGGGGCCTACCCAAG-AAGA-ATCTCG
1 GGGCCACGGAGCCTACCCAAGAAAGATA-CTCA
** * *
525709 GGGCCACATACCCTACCCAAGAAAGAT-CTCG
1 GGGCCACGGAGCCTACCCAAGAAAGATACTCA
* *
525740 GGGCCTCGGATCCTACCCAAG
1 GGGCCACGGAGCCTACCCAAG
525761 GGTCTCCTTA
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
30 1 0.01
31 44 0.45
32 51 0.52
33 2 0.02
ACGTcount: A:0.27, C:0.34, G:0.27, T:0.12
Consensus pattern (32 bp):
GGGCCACGGAGCCTACCCAAGAAAGATACTCA
Found at i:539427 original size:22 final size:23
Alignment explanation
Indices: 539388--539447 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
539378 GTGAACCAGT
* *
539388 TGAGCCAACTGAGCCGACCGA-C
1 TGAGCCGACCGAGCCGACCGATC
*
539410 TGAGCCGACCGAGTCGACCGATC
1 TGAGCCGACCGAGCCGACCGATC
*
539433 CGA-CCGACCGAGCCG
1 TGAGCCGACCGAGCCG
539448 CTTAGACTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 29 0.91
23 3 0.09
ACGTcount: A:0.23, C:0.38, G:0.30, T:0.08
Consensus pattern (23 bp):
TGAGCCGACCGAGCCGACCGATC
Found at i:539430 original size:13 final size:13
Alignment explanation
Indices: 539395--539421 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
539385 AGTTGAGCCA
539395 ACTGAGCCGACCG
1 ACTGAGCCGACCG
539408 ACTGAGCCGACCG
1 ACTGAGCCGACCG
539421 A
1 A
539422 GTCGACCGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.37, G:0.30, T:0.07
Consensus pattern (13 bp):
ACTGAGCCGACCG
Found at i:544545 original size:9 final size:9
Alignment explanation
Indices: 544531--544642 Score: 79
Period size: 9 Copynumber: 11.8 Consensus size: 9
544521 TGAACCAGTT
544531 GAGCCGACC
1 GAGCCGACC
544540 GAGCCGACC
1 GAGCCGACC
*
544549 GA-CTGAGCC
1 GAGCCGA-CC
544558 GA-CCGAGCC
1 GAGCCGA-CC
*
544567 GA-CCGACT
1 GAGCCGACC
544575 GAGCCGACC
1 GAGCCGACC
544584 GAGCCGATCGATC
1 GAGCCGA-C---C
544597 GAGCCGACC
1 GAGCCGACC
544606 GAGCCGATCGATC
1 GAGCCGA-C---C
*
544619 GAGACGACC
1 GAGCCGACC
544628 GAGCCGACC
1 GAGCCGACC
544637 GA-CCGA
1 GAGCCGA
544643 GCCACTTAGA
Statistics
Matches: 87, Mismatches: 6, Indels: 21
0.76 0.05 0.18
Matches are distributed among these distances:
8 10 0.11
9 58 0.67
10 2 0.02
12 2 0.02
13 15 0.17
ACGTcount: A:0.24, C:0.38, G:0.32, T:0.05
Consensus pattern (9 bp):
GAGCCGACC
Found at i:544558 original size:22 final size:22
Alignment explanation
Indices: 544530--544645 Score: 164
Period size: 22 Copynumber: 5.3 Consensus size: 22
544520 GTGAACCAGT
544530 TGAGCCGACCGAGCCGACCGAC
1 TGAGCCGACCGAGCCGACCGAC
544552 TGAGCCGACCGAGCCGACCGAC
1 TGAGCCGACCGAGCCGACCGAC
*
544574 TGAGCCGACCGAGCCGATCGA-
1 TGAGCCGACCGAGCCGACCGAC
*
544595 TCGAGCCGACCGAGCCGATCGA-
1 T-GAGCCGACCGAGCCGACCGAC
*
544617 TCGAGACGACCGAGCCGACCGAC
1 T-GAGCCGACCGAGCCGACCGAC
*
544640 CGAGCC
1 TGAGCC
544646 ACTTAGACTG
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
21 1 0.01
22 86 0.99
ACGTcount: A:0.23, C:0.39, G:0.32, T:0.06
Consensus pattern (22 bp):
TGAGCCGACCGAGCCGACCGAC
Found at i:544639 original size:13 final size:13
Alignment explanation
Indices: 544534--544645 Score: 85
Period size: 13 Copynumber: 8.8 Consensus size: 13
544524 ACCAGTTGAG
544534 CCGACCGAGCCGA
1 CCGACCGAGCCGA
*
544547 CCGACTGAGCCGA
1 CCGACCGAGCCGA
544560 CCGAGCCGA-CCGA
1 CCGA-CCGAGCCGA
*
544573 CTGAGCCGA-CCGA
1 CCGA-CCGAGCCGA
* *
544586 GCCGATCGA-TCGA
1 -CCGACCGAGCCGA
544599 GCCGACCGAGCCGA
1 -CCGACCGAGCCGA
* *
544613 TCGATCGA---GA
1 CCGACCGAGCCGA
544623 -CGACCGAGCCGA
1 CCGACCGAGCCGA
544635 CCGACCGAGCC
1 CCGACCGAGCC
544646 ACTTAGACTG
Statistics
Matches: 81, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
9 6 0.07
10 2 0.02
12 2 0.02
13 62 0.77
14 9 0.11
ACGTcount: A:0.23, C:0.40, G:0.31, T:0.05
Consensus pattern (13 bp):
CCGACCGAGCCGA
Found at i:555827 original size:27 final size:25
Alignment explanation
Indices: 555797--555848 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
555787 AAAGTACTTC
*
555797 AATACTTATGTTACACGATATGAGATG
1 AATACTTAT-ATACAC-ATATGAGATG
* *
555824 AATATTTATATGCACATATGAGATG
1 AATACTTATATACACATATGAGATG
555849 TGATAGAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 10 0.45
26 4 0.18
27 8 0.36
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (25 bp):
AATACTTATATACACATATGAGATG
Found at i:556011 original size:22 final size:22
Alignment explanation
Indices: 555981--556022 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
555971 AGTCGAGGGT
* *
555981 TTCATAGGTCATTCGGGACATA
1 TTCACAGGTCATTAGGGACATA
*
556003 TTCACAGGTCCTTAGGGACA
1 TTCACAGGTCATTAGGGACA
556023 AATTTCATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (22 bp):
TTCACAGGTCATTAGGGACATA
Found at i:557927 original size:6 final size:6
Alignment explanation
Indices: 557916--557993 Score: 138
Period size: 6 Copynumber: 13.0 Consensus size: 6
557906 AGGGTGACTT
*
557916 TACATA TACATA TACATA TACATA TACATA TACATA TGCATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
557964 TACATA TACATA TACATA TACATA GACATA
1 TACATA TACATA TACATA TACATA TACATA
557994 CTTACTAGGG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.32
Consensus pattern (6 bp):
TACATA
Done.