Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 199 of 349
Found at i:64244150 original size:13 final size:13
Alignment explanation
Indices: 64244116--64244152 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
64244106 AAAAAGTTCG
64244116 AAAAAAAAATTGA
1 AAAAAAAAATTGA
64244129 AAAAAAAAATTGA
1 AAAAAAAAATTGA
64244142 AAAAAAAAATT
1 AAAAAAAAATT
64244153 TGCATACGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:64246389 original size:20 final size:17
Alignment explanation
Indices: 64246345--64246397 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 17
64246335 CAAATGAGAG
64246345 AAAAAGAAAAGACGAAAAT
1 AAAAAGAAAAGA--AAAAT
64246364 ACAAAAGAAAAGAAAAAT
1 A-AAAAGAAAAGAAAAAT
64246382 GATAAAA-AAAAGAAAA
1 -A-AAAAGAAAAGAAAA
64246398 TTCAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 14 0.45
19 6 0.19
20 11 0.35
ACGTcount: A:0.77, C:0.04, G:0.13, T:0.06
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAAT
Found at i:64246398 original size:17 final size:17
Alignment explanation
Indices: 64246366--64246415 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 17
64246356 ACGAAAATAC
64246366 AAAAGAAAAGAAAAATGAT
1 AAAA-AAAAG-AAAATGAT
64246385 AAAAAAAAGAAAAT--T
1 AAAAAAAAGAAAATGAT
* *
64246400 CAAAAAAAGAGAATGA
1 AAAAAAAAGAAAATGA
64246416 AAAGAGAGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 13 0.48
17 5 0.19
18 5 0.19
19 4 0.15
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.10
Consensus pattern (17 bp):
AAAAAAAAGAAAATGAT
Found at i:64250702 original size:21 final size:21
Alignment explanation
Indices: 64250653--64250719 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
64250643 CCTCTTTGAA
* * *
64250653 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
64250676 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
64250697 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
64250718 CC
1 CC
64250720 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:64252712 original size:11 final size:11
Alignment explanation
Indices: 64252696--64252734 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
64252686 TTGTCACTTC
64252696 TTTTTTTTAAT
1 TTTTTTTTAAT
**
64252707 TTTTTTCGAAT
1 TTTTTTTTAAT
64252718 TTTTTTTT-AT
1 TTTTTTTTAAT
64252728 TTTTTTT
1 TTTTTTT
64252735 GTTACTCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTTTTTAAT
Found at i:64252847 original size:48 final size:47
Alignment explanation
Indices: 64252770--64252874 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 47
64252760 AATACAAGGG
*
64252770 AAAAGAAAGTGAGACTGAAAAAGGATGTGA-AAAAGAGAAAGAAATCGA
1 AAAAGAAAGTGAGACTGAAAAAAGATGTGAGAAAA-AGAAA-AAATCGA
* * * *
64252818 AAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATTGA
1 AAAAGAAAGTGAGACTGAA-AAAAGATGTGA-GAAAAAGAAAAAATCGA
64252866 AAAAGAAAG
1 AAAAGAAAG
64252875 AAAAGACAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
48 36 0.75
49 8 0.17
50 4 0.08
ACGTcount: A:0.59, C:0.03, G:0.26, T:0.12
Consensus pattern (47 bp):
AAAAGAAAGTGAGACTGAAAAAAGATGTGAGAAAAAGAAAAAATCGA
Found at i:64255706 original size:13 final size:13
Alignment explanation
Indices: 64255688--64255713 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64255678 CGTAGCTTCG
64255688 AAAAAAAAAAGTT
1 AAAAAAAAAAGTT
64255701 AAAAAAAAAAGTT
1 AAAAAAAAAAGTT
64255714 TCGAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAAAAAAAAGTT
Found at i:64255734 original size:29 final size:29
Alignment explanation
Indices: 64255684--64255740 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
64255674 AAATCGTAGC
*
64255684 TTCGAAAAAAAAAAGTTAAAAAAAAAAGT
1 TTCGAAAAAAAAAAGTCAAAAAAAAAAGT
*
64255713 TTCGAAAAAAAAAA-TCCGAAAAAAAAAG
1 TTCGAAAAAAAAAAGT-CAAAAAAAAAAG
64255741 AAGGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.68, C:0.07, G:0.11, T:0.14
Consensus pattern (29 bp):
TTCGAAAAAAAAAAGTCAAAAAAAAAAGT
Found at i:64255739 original size:14 final size:15
Alignment explanation
Indices: 64255686--64255739 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 15
64255676 ATCGTAGCTT
64255686 CGAAAAAAAAAAGT-
1 CGAAAAAAAAAAGTC
* *
64255700 -TAAAAAAAAAAGTTT
1 CGAAAAAAAAAAG-TC
64255715 CGAAAAAAAAAA-TC
1 CGAAAAAAAAAAGTC
64255729 CGAAAAAAAAA
1 CGAAAAAAAAA
64255740 GAAGGAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 11 0.32
14 13 0.38
16 10 0.29
ACGTcount: A:0.72, C:0.07, G:0.09, T:0.11
Consensus pattern (15 bp):
CGAAAAAAAAAAGTC
Found at i:64255763 original size:15 final size:15
Alignment explanation
Indices: 64255745--64255773 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
64255735 AAAAAGAAGG
64255745 AAAAAAAAATTGCAA
1 AAAAAAAAATTGCAA
64255760 AAAAAAAAATTGCA
1 AAAAAAAAATTGCA
64255774 TACGGTCTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAAAAAAATTGCAA
Found at i:64256517 original size:15 final size:15
Alignment explanation
Indices: 64256485--64256518 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
64256475 GTTCAACGAA
*
64256485 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
64256500 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
64256515 GAGG
1 GAGG
64256519 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:64260853 original size:20 final size:20
Alignment explanation
Indices: 64260807--64260853 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
64260797 AGCTCGTTTC
*
64260807 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
64260827 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
64260847 CAGCTCA
1 CAGCTCA
64260854 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:64267786 original size:45 final size:45
Alignment explanation
Indices: 64267710--64267804 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 45
64267700 TCGAAAGCCC
* * * **
64267710 GAATAGTATCTCACCGGCATTATAGCATGCTAGGCTTAAAGGCCT
1 GAATAGTATCTCACCAGCATCACAGCATGCTAGGCACAAAGGCCT
* *
64267755 GAATAGTAT-TCCACCAGCATCACAGCCTGCTAGGCACGAAGGCCT
1 GAATAGTATCT-CACCAGCATCACAGCATGCTAGGCACAAAGGCCT
64267800 GAATA
1 GAATA
64267805 CACAACACCA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 1 0.02
45 41 0.98
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (45 bp):
GAATAGTATCTCACCAGCATCACAGCATGCTAGGCACAAAGGCCT
Found at i:64267834 original size:43 final size:43
Alignment explanation
Indices: 64267778--64268062 Score: 435
Period size: 43 Copynumber: 6.6 Consensus size: 43
64267768 CCAGCATCAC
* * *
64267778 AGCCTGCTAGGCACGAAGGCCTGAATACACAACACCAGCACGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGA
*
64267821 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGA
* *
64267864 AGCCTGCTAGGTACGAAGGCCCAAATACACATCACCGGCACGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGA
* *
64267907 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACTGGCACAA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGA
* * *
64267950 ATCTTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGA
* **
64267993 AGCCTGCTAGGCACGAAGGCCCGAATACGCATCACCGGCATAA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGA
*
64268036 AGCCTGCTAGGCACGAAGGCCCAAATA
1 AGCCTGCTAGGCACGAAGGCCCGAATA
64268063 TAATACCAGC
Statistics
Matches: 221, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 221 1.00
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (43 bp):
AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGA
Found at i:64271596 original size:13 final size:13
Alignment explanation
Indices: 64271578--64271602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64271568 GACATGAACA
64271578 CATTTAATTATAT
1 CATTTAATTATAT
64271591 CATTTAATTATA
1 CATTTAATTATA
64271603 ATTAAACAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
CATTTAATTATAT
Found at i:64273408 original size:10 final size:10
Alignment explanation
Indices: 64273393--64273430 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
64273383 GCTCGTTTCC
*
64273393 AGCTCACTCG
1 AGCTCAATCG
64273403 AGCTCAAGTC-
1 AGCTCAA-TCG
64273413 AGCTCAATCG
1 AGCTCAATCG
64273423 AGCTCAAT
1 AGCTCAAT
64273431 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:64273417 original size:20 final size:20
Alignment explanation
Indices: 64273392--64273429 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
64273382 AGCTCGTTTC
*
64273392 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
64273412 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
64273430 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:64273436 original size:20 final size:20
Alignment explanation
Indices: 64273393--64273453 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
64273383 GCTCGTTTCC
* * *
64273393 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
64273413 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
64273433 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
64273453 A
1 A
64273454 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:64273447 original size:11 final size:10
Alignment explanation
Indices: 64273403--64273449 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
64273393 AGCTCACTCG
*
64273403 AGCTCAAGTC
1 AGCTCAATTC
64273413 AGCTCAA-TC
1 AGCTCAATTC
*
64273422 GAGCTCAATTT
1 -AGCTCAATTC
64273433 AGCTACAATTC
1 AGCT-CAATTC
64273444 AGCTCA
1 AGCTCA
64273450 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:64274848 original size:13 final size:13
Alignment explanation
Indices: 64274830--64274892 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
64274820 TTGGAGTAAC
64274830 AAAAAAAATCAAA
1 AAAAAAAATCAAA
*
64274843 AAAAAAATTCGAAA
1 AAAAAAAATC-AAA
*
64274857 AAAAAAATTGATTGAAA
1 AAAAAAA---A-TCAAA
*
64274874 AAAAAAATTCAAA
1 AAAAAAAATCAAA
64274887 AAAAAA
1 AAAAAA
64274893 GTGAAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
13 19 0.47
14 10 0.25
17 10 0.25
18 1 0.03
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (13 bp):
AAAAAAAATCAAA
Found at i:64274900 original size:13 final size:13
Alignment explanation
Indices: 64274830--64274957 Score: 55
Period size: 12 Copynumber: 9.2 Consensus size: 13
64274820 TTGGAGTAAC
*
64274830 AAAAAAAA-TCAA
1 AAAAAAAAGTGAA
*
64274842 AAAAAAAATTCGAA
1 AAAAAAAAGT-GAA
64274856 AAAAAAAATTGATTGAA
1 AAAAAAAA--G--TGAA
**
64274873 AAAAAAAA-TTCA
1 AAAAAAAAGTGAA
64274885 AAAAAAAAGTGAA
1 AAAAAAAAGTGAA
* **
64274898 AAAAAATCGAGCAAA
1 AAAAAA--AAGTGAA
64274913 AAAAAAAAGGTGACCA
1 AAAAAAAA-GTGA--A
*
64274929 AAAAAATCAAGT-TA
1 AAAAAA--AAGTGAA
64274943 AAAAAAAAGTGAA
1 AAAAAAAAGTGAA
64274956 AA
1 AA
64274958 GTTTTGCGAG
Statistics
Matches: 87, Mismatches: 14, Indels: 29
0.67 0.11 0.22
Matches are distributed among these distances:
12 22 0.25
13 13 0.15
14 19 0.22
15 10 0.11
16 7 0.08
17 13 0.15
18 3 0.03
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.12
Consensus pattern (13 bp):
AAAAAAAAGTGAA
Found at i:64274932 original size:31 final size:28
Alignment explanation
Indices: 64274884--64274957 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 28
64274874 AAAAAAATTC
*
64274884 AAAAAAAAAGTGAAAAAAAATCGAGCAA
1 AAAAAAAAAGTGAAAAAAAATCAAGCAA
**
64274912 AAAAAAAAAGGTGACCAAAAAAATCAAG-TT
1 AAAAAAAAA-GTGA--AAAAAAATCAAGCAA
64274942 AAAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
64274958 GTTTTGCGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 3 0.08
28 9 0.22
29 8 0.20
30 9 0.22
31 11 0.28
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (28 bp):
AAAAAAAAAGTGAAAAAAAATCAAGCAA
Found at i:64277619 original size:10 final size:10
Alignment explanation
Indices: 64277604--64277641 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
64277594 ACTCGTTTCC
*
64277604 AGCTCACTCG
1 AGCTCAATCG
64277614 AGCTCAAGTC-
1 AGCTCAA-TCG
64277624 AGCTCAATCG
1 AGCTCAATCG
64277634 AGCTCAAT
1 AGCTCAAT
64277642 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:64277628 original size:20 final size:20
Alignment explanation
Indices: 64277603--64277640 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
64277593 AACTCGTTTC
*
64277603 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
64277623 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
64277641 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:64277647 original size:20 final size:20
Alignment explanation
Indices: 64277604--64277664 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
64277594 ACTCGTTTCC
* * *
64277604 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
64277624 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
64277644 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
64277664 A
1 A
64277665 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:64277658 original size:11 final size:10
Alignment explanation
Indices: 64277614--64277660 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
64277604 AGCTCACTCG
*
64277614 AGCTCAAGTC
1 AGCTCAATTC
64277624 AGCTCAA-TC
1 AGCTCAATTC
*
64277633 GAGCTCAATTT
1 -AGCTCAATTC
64277644 AGCTACAATTC
1 AGCT-CAATTC
64277655 AGCTCA
1 AGCTCA
64277661 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:64286895 original size:318 final size:318
Alignment explanation
Indices: 64286318--64286954 Score: 1238
Period size: 318 Copynumber: 2.0 Consensus size: 318
64286308 CTGATACGAG
* *
64286318 CTCGATTTGGATGATGTGACGAGTCGTATTATATTCCTGATCGAATTTAGGTAGTGTCGATTTAG
1 CTCGATTCGGATGATGTGACGAGTCGTATTATATTCCCGATCGAATTTAGGTAGTGTCGATTTAG
64286383 TTCAAAATTCAATAAGATGAGTTATATTGGTTTTAAATGAATTAGAAAGCAAAACGGGGATAAAT
66 TTCAAAATTCAATAAGATGAGTTATATTGGTTTTAAATGAATTAGAAAGCAAAACGGGGATAAAT
64286448 GGTTTCCAATGAAACAAGTACGAACCCTTATTAACAAATAAGGACCCGGGCTTAAAGGTTTCAAA
131 GGTTTCCAATGAAACAAGTACGAACCCTTATTAACAAATAAGGACCCGGGCTTAAAGGTTTCAAA
64286513 GAAAAGGAAAGAAATGGTAGATAAAACCGAGACCCTCTATTTAGCAAAATAGGAACCTTCGGTAT
196 GAAAAGGAAAGAAATGGTAGATAAAACCGAGACCCTCTATTTAGCAAAATAGGAACCTTCGGTAT
64286578 AGTTGGAACGCCACACCTTATGGTGATAAGTTCAAAACAAAGTCAGATTGACGCCACT
261 AGTTGGAACGCCACACCTTATGGTGATAAGTTCAAAACAAAGTCAGATTGACGCCACT
64286636 CTCGATTCGGATGATGTGACGAGTCGTATTATATTCCCGATCGAATTTAGGTAGTGTCGATTTAG
1 CTCGATTCGGATGATGTGACGAGTCGTATTATATTCCCGATCGAATTTAGGTAGTGTCGATTTAG
*
64286701 TTCAAAATTCAATAAGATGAGTTATATTGGTTTTAAATGAATTAGGAAGCAAAACGGGGATAAAT
66 TTCAAAATTCAATAAGATGAGTTATATTGGTTTTAAATGAATTAGAAAGCAAAACGGGGATAAAT
64286766 GGTTTCCAATGAAACAAGTACGAACCCTTATTAACAAATAAGGACCCGGGCTTAAAGGTTTCAAA
131 GGTTTCCAATGAAACAAGTACGAACCCTTATTAACAAATAAGGACCCGGGCTTAAAGGTTTCAAA
64286831 GAAAAGGAAAGAAATGGTAGATAAAACCGAGACCCTCTATTTAGCAAAATAGGAACCTTCGGTAT
196 GAAAAGGAAAGAAATGGTAGATAAAACCGAGACCCTCTATTTAGCAAAATAGGAACCTTCGGTAT
*
64286896 AGTTGGAACGCCACACCTTATGGTGATAAGTTCAAAACAGAGTCAGATTGACGCCACT
261 AGTTGGAACGCCACACCTTATGGTGATAAGTTCAAAACAAAGTCAGATTGACGCCACT
64286954 C
1 C
64286955 GTAAAGATAA
Statistics
Matches: 315, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
318 315 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (318 bp):
CTCGATTCGGATGATGTGACGAGTCGTATTATATTCCCGATCGAATTTAGGTAGTGTCGATTTAG
TTCAAAATTCAATAAGATGAGTTATATTGGTTTTAAATGAATTAGAAAGCAAAACGGGGATAAAT
GGTTTCCAATGAAACAAGTACGAACCCTTATTAACAAATAAGGACCCGGGCTTAAAGGTTTCAAA
GAAAAGGAAAGAAATGGTAGATAAAACCGAGACCCTCTATTTAGCAAAATAGGAACCTTCGGTAT
AGTTGGAACGCCACACCTTATGGTGATAAGTTCAAAACAAAGTCAGATTGACGCCACT
Found at i:64288857 original size:12 final size:12
Alignment explanation
Indices: 64288842--64288872 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
64288832 TTCTTTTTGC
64288842 TTTTCAAAGGCT
1 TTTTCAAAGGCT
64288854 TTTTCAAAGGCT
1 TTTTCAAAGGCT
64288866 TTTTCAA
1 TTTTCAA
64288873 GTTTTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:64288949 original size:6 final size:6
Alignment explanation
Indices: 64288933--64288982 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
64288923 TTTATTTTTA
*
64288933 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
64288982 T
1 T
64288983 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:64288993 original size:16 final size:16
Alignment explanation
Indices: 64288918--64288978 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
64288908 GCCTCTTGCC
* *
64288918 TCTCTTTTATTTTTAT
1 TCTCTTTTCTTTTTCT
64288934 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
64288950 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
64288966 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
64288979 CTTTGTTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
15 11 0.31
16 16 0.44
17 9 0.25
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:64289961 original size:22 final size:22
Alignment explanation
Indices: 64289912--64289965 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
64289902 TTTTAACTCG
* **
64289912 ATTTTTTTGTCACTTTTTTTTTC
1 ATTTTTTT-TCAATTTTTTTTGA
*
64289935 CTTTTTTTTCAATTTTTTTTGA
1 ATTTTTTTTCAATTTTTTTTGA
64289957 ATTTTTTTT
1 ATTTTTTTT
64289966 TCTGAATTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.76
Consensus pattern (22 bp):
ATTTTTTTTCAATTTTTTTTGA
Found at i:64289966 original size:12 final size:11
Alignment explanation
Indices: 64289912--64289965 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
64289902 TTTTAACTCG
64289912 ATTTTTTTGTCA
1 ATTTTTTT-TCA
*
64289924 CTTTTTTTTTC-
1 -ATTTTTTTTCA
*
64289935 CTTTTTTTTCA
1 ATTTTTTTTCA
*
64289946 ATTTTTTTTGA
1 ATTTTTTTTCA
64289957 ATTTTTTTT
1 ATTTTTTTT
64289966 TCTGAATTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
10 9 0.25
11 18 0.50
12 2 0.06
13 7 0.19
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.76
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:64291730 original size:30 final size:30
Alignment explanation
Indices: 64291696--64291792 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
64291686 TAAACTAAAA
*
64291696 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * *
64291726 TGAGCTGAGGCTAAACTCCTAAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
64291756 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
64291785 ATGAGCTA
1 -TGAGCTA
64291793 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:64292493 original size:10 final size:10
Alignment explanation
Indices: 64292478--64292504 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
64292468 TACTCCTTCA
64292478 AGCTCAAATC
1 AGCTCAAATC
64292488 AGCTCAAATC
1 AGCTCAAATC
64292498 AGCTCAA
1 AGCTCAA
64292505 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:64295939 original size:30 final size:30
Alignment explanation
Indices: 64295905--64295965 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
64295895 TCCTTAACTC
64295905 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
64295935 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
64295965 A
1 A
64295966 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:64297535 original size:30 final size:31
Alignment explanation
Indices: 64297501--64297597 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
64297491 AGCTCACTCC
*
64297501 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
64297531 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
64297561 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
64297591 TAGCTCA
1 TAGCTCA
64297598 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:64300177 original size:21 final size:20
Alignment explanation
Indices: 64300143--64300208 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
64300133 ACATTTTTGT
64300143 AAAGAGAAAACAAAGAAAAG-A
1 AAAGA-AAAACAAA-AAAAGAA
*
64300164 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAA-CAAAAAAAGAA
*
64300185 AAAGAAAACAAAATAAAAAGAA
1 AAAGAAAA-ACAA-AAAAAGAA
64300207 AA
1 AA
64300209 GAGAGGCAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 8 0.21
21 20 0.53
22 10 0.26
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.02
Consensus pattern (20 bp):
AAAGAAAAACAAAAAAAGAA
Found at i:64300178 original size:6 final size:5
Alignment explanation
Indices: 64300154--64300210 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
64300144 AAGAGAAAAC
* * *
64300154 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACA AAATAA
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAAGA AAA-GA
64300201 AAAGA AAAGA
1 AAAGA AAAGA
64300211 GAGGCAAGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
4 3 0.07
5 26 0.60
6 14 0.33
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:64300203 original size:25 final size:25
Alignment explanation
Indices: 64300158--64300206 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
64300148 GAAAACAAAG
*
64300158 AAAAGAAAAGAAAAAGCAAAAGAAGA
1 AAAAGAAAACAAAAA-CAAAAGAAGA
64300184 AAAAGAAAACAAAATA-AAAAGAA
1 AAAAGAAAACAAAA-ACAAAAGAA
64300207 AAGAGAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (25 bp):
AAAAGAAAACAAAAACAAAAGAAGA
Found at i:64300333 original size:24 final size:24
Alignment explanation
Indices: 64300284--64300330 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
64300274 AAAGCAAAAA
*
64300284 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAAATT
* *
64300308 GAAAAAGAGAACGAAAA-GAAATT
1 GAAAAAGAAAAAGAAAATGAAATT
64300331 TGAGAGTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.66, C:0.02, G:0.21, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAAATT
Found at i:64300354 original size:30 final size:31
Alignment explanation
Indices: 64300279--64300361 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
64300269 TTTGAAAAGC
* * * *
64300279 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAGAACGAAAAAGAAATTTGAGAGTG
64300309 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAGAACGAAAAAGAAATTTGAGAGTG
*
64300339 AAAAAGA-AGCTGAAAAAGAAATT
1 AAAAAGAGAAC-GAAAAAGAAATT
64300362 GAAACAAAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.22
30 25 0.56
31 10 0.22
ACGTcount: A:0.64, C:0.02, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAGAACGAAAAAGAAATTTGAGAGTG
Found at i:64306624 original size:15 final size:15
Alignment explanation
Indices: 64306604--64306658 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
64306594 ACTCTCCTCA
*
64306604 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
64306619 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
64306634 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
64306648 TTCTTTT-TCTC
1 TTCTTTTCTCTC
64306659 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:64308694 original size:11 final size:11
Alignment explanation
Indices: 64308675--64308707 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
64308665 TTTTAATCAC
*
64308675 TTCTCTTTTTT
1 TTCTTTTTTTT
64308686 TTC-TTTTTTT
1 TTCTTTTTTTT
64308696 TTCTTTTTTTT
1 TTCTTTTTTTT
64308707 T
1 T
64308708 AATTCCGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:64308695 original size:10 final size:10
Alignment explanation
Indices: 64308675--64308707 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
64308665 TTTTAATCAC
64308675 TTCTCTTTTTT
1 TTCT-TTTTTT
64308686 TTCTTTTTTT
1 TTCTTTTTTT
64308696 TTCTTTTTTT
1 TTCTTTTTTT
64308706 TT
1 TT
64308708 AATTCCGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:64311772 original size:20 final size:20
Alignment explanation
Indices: 64311719--64311772 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
64311709 GCTGAAAGTA
*
64311719 AGCTCAGTTGAGCTCAAACG
1 AGCTGAGTTGAGCTCAAACG
**** *
64311739 AGCTGAAACAAGCTCAAATG
1 AGCTGAGTTGAGCTCAAACG
64311759 AGCTGAGTTGAGCT
1 AGCTGAGTTGAGCT
64311773 GGACGGTGCT
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.20
Consensus pattern (20 bp):
AGCTGAGTTGAGCTCAAACG
Found at i:64313441 original size:11 final size:12
Alignment explanation
Indices: 64313411--64313442 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
64313401 TTTCACTCTT
64313411 CTCTTTTTCAAA
1 CTCTTTTTCAAA
64313423 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
64313435 TTCTTTTT
1 CTCTTTTT
64313443 TCGCTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:64313454 original size:27 final size:27
Alignment explanation
Indices: 64313424--64313485 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
64313414 TTTTTCAAAC
*
64313424 TCTTTTTCAAATTCTT-TTTTC-GCTTTT
1 TCTTTTTC-AATT-TTCTTTTCTGCATTT
*
64313451 TCTTTTTCAATTTTCTTTTCTTCATTT
1 TCTTTTTCAATTTTCTTTTCTGCATTT
64313478 TCTTTTTC
1 TCTTTTTC
64313486 TCTCACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 9 0.29
27 20 0.65
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (27 bp):
TCTTTTTCAATTTTCTTTTCTGCATTT
Found at i:64313464 original size:13 final size:12
Alignment explanation
Indices: 64313448--64313567 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
64313438 TTTTTTCGCT
64313448 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
64313461 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
64313475 TTTTCTTTTTC-
1 TTTTCTTTTTCA
** *
64313486 TCTCACTTTTTTGA
1 T-TTTC-TTTTTCA
64313500 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
64313510 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
*
64313523 TTTTCTTTTTCG
1 TTTTCTTTTTCA
*
64313535 TTTTCTTTTT-G
1 TTTTCTTTTTCA
64313546 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
64313556 ATTTCTTTTTCA
1 TTTTCTTTTTCA
64313568 ATCTCTTTCT
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 15 0.18
12 32 0.39
13 17 0.20
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:64313477 original size:14 final size:14
Alignment explanation
Indices: 64313426--64313484 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
64313416 TTTCAAACTC
*
64313426 TTTTTCAA-ATTCT
1 TTTTTCAATTTTCT
**
64313439 TTTTTCGCTTTT-T
1 TTTTTCAATTTTCT
64313452 CTTTTTCAATTTTCT
1 -TTTTTCAATTTTCT
64313467 TTTCTTC-ATTTTCT
1 TTT-TTCAATTTTCT
64313481 TTTT
1 TTTT
64313485 CTCTCACTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 8 0.22
14 25 0.68
15 4 0.11
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTCAATTTTCT
Found at i:64313566 original size:6 final size:6
Alignment explanation
Indices: 64313446--64313553 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
64313436 TCTTTTTTCG
* * * **
64313446 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
64313497 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
64313545 -GTTTT CTTT
1 CTTTTT CTTT
64313554 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 23, Indels: 10
0.69 0.21 0.09
Matches are distributed among these distances:
5 5 0.07
6 56 0.76
7 10 0.14
8 3 0.04
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:64314652 original size:12 final size:12
Alignment explanation
Indices: 64314637--64314661 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
64314627 TTTTTTTCGA
64314637 TTTTTTTGAATT
1 TTTTTTTGAATT
64314649 TTTTTTTGAATT
1 TTTTTTTGAATT
64314661 T
1 T
64314662 CTATTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:64314754 original size:11 final size:12
Alignment explanation
Indices: 64314738--64314768 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
64314728 CCAACTCAAA
64314738 TTTTTTTTGA-T
1 TTTTTTTTGACT
64314749 TTTTTTTTGACT
1 TTTTTTTTGACT
64314761 TTTTTTTT
1 TTTTTTTT
64314769 ACATTACGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTTTTTGACT
Found at i:64318177 original size:10 final size:10
Alignment explanation
Indices: 64318136--64318187 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
64318126 GTATTACGGT
64318136 ATTGTAAAAAA
1 ATTG-AAAAAA
64318147 A-TGAAAAAAA
1 ATTG-AAAAAA
64318157 ATT-AAAAAA
1 ATTGAAAAAA
64318166 ATTGAAAAAA
1 ATTGAAAAAA
*
64318176 ATCCGAAAAAA
1 AT-TGAAAAAA
64318187 A
1 A
64318188 AAGTTTGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
9 9 0.25
10 17 0.47
11 10 0.28
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.17
Consensus pattern (10 bp):
ATTGAAAAAA
Found at i:64319226 original size:21 final size:21
Alignment explanation
Indices: 64319202--64319244 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
64319192 GAGAGAAGCA
* *
64319202 AAAAAGAAATGAGAGAAAAAG
1 AAAAAGAAATAAAAGAAAAAG
64319223 AAAAAGAAATAAAAGAAAAAG
1 AAAAAGAAATAAAAGAAAAAG
64319244 A
1 A
64319245 TGAAAATGAG
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:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (21 bp):
AAAAAGAAATAAAAGAAAAAG
Found at i:64323190 original size:23 final size:22
Alignment explanation
Indices: 64323138--64323190 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
64323128 TCCACGCCTT
*
64323138 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
64323160 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
64323183 TTTCTTTT
1 TTTCTTTT
64323191 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:64325142 original size:24 final size:23
Alignment explanation
Indices: 64325088--64325165 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
64325078 GGATAATTAA
**
64325088 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
64325111 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
64325135 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
64325156 GAAATAGTAT
1 GAAATGGTAT
64325166 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:64325150 original size:21 final size:21
Alignment explanation
Indices: 64325124--64325190 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
64325114 TTGGTATTTG
64325124 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
64325145 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
64325166 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
64325189 GG
1 GG
64325191 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:64343657 original size:17 final size:17
Alignment explanation
Indices: 64343637--64343671 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
64343627 TTAAACTAAG
* *
64343637 TAAATAAATAAATAAAC
1 TAAATAAAAAAAAAAAC
64343654 TAAATAAAAAAAAAAAC
1 TAAATAAAAAAAAAAAC
64343671 T
1 T
64343672 TTACAACTTG
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:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (17 bp):
TAAATAAAAAAAAAAAC
Found at i:64347970 original size:20 final size:20
Alignment explanation
Indices: 64347938--64348012 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 20
64347928 AACTTAAGCC
64347938 AAGCTCAAA-TGAGCTAAAGT
1 AAGCT-AAATTGAGCTAAAGT
64347958 AAGCTAAATTGAGCTCAAACG-
1 AAGCTAAATTGAGCT-AAA-GT
* * *
64347979 -AGCTAAATTAAGCTCATGT
1 AAGCTAAATTGAGCTAAAGT
* *
64347998 GAGCTAAATCGAGCT
1 AAGCTAAATTGAGCT
64348013 GGGAAAAACT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 1 0.02
19 4 0.09
20 36 0.80
21 3 0.07
22 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (20 bp):
AAGCTAAATTGAGCTAAAGT
Found at i:64348011 original size:30 final size:31
Alignment explanation
Indices: 64347939--64348012 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
64347929 ACTTAAGCCA
64347939 AGCTCAAAT-GAGCTAAAGTAAGCTAAATTG
1 AGCTCAAATCGAGCTAAAGTAAGCTAAATTG
* *
64347969 AGCTCAAA-CGAGCTAAATTAAGCT-CATGTG
1 AGCTCAAATCGAGCTAAAGTAAGCTAAAT-TG
64347999 AGCT-AAATCGAGCT
1 AGCTCAAATCGAGCT
64348013 GGGAAAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 5 0.13
30 34 0.87
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (31 bp):
AGCTCAAATCGAGCTAAAGTAAGCTAAATTG
Found at i:64352146 original size:12 final size:11
Alignment explanation
Indices: 64352129--64352192 Score: 85
Period size: 11 Copynumber: 5.5 Consensus size: 11
64352119 TACAAGTTTG
64352129 AAAAAAATTCGAA
1 AAAAAAATTC--A
64352142 AAAAAAATTTC-
1 AAAAAAA-TTCA
64352153 AAAAAAATTCGA
1 AAAAAAATTC-A
64352165 AAAAAAATTCA
1 AAAAAAATTCA
64352176 AAAAAAATTCA
1 AAAAAAATTCA
64352187 AAAAAA
1 AAAAAA
64352193 GTGATTTATG
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.06
11 25 0.52
12 10 0.21
13 7 0.15
14 3 0.06
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:64352181 original size:23 final size:23
Alignment explanation
Indices: 64352129--64352192 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 23
64352119 TACAAGTTTG
64352129 AAAAAAATTCGAAAAAAAAATTTC
1 AAAAAAATTCG-AAAAAAAATTTC
64352153 AAAAAAATTCGAAAAAAAA-TTC
1 AAAAAAATTCGAAAAAAAATTTC
64352175 AAAAAAAATTC-AAAAAAA
1 -AAAAAAATTCGAAAAAAA
64352193 GTGATTTATG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.26
23 18 0.46
24 11 0.28
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.17
Consensus pattern (23 bp):
AAAAAAATTCGAAAAAAAATTTC
Found at i:64353100 original size:9 final size:10
Alignment explanation
Indices: 64353093--64353149 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
64353083 AAGAGAAAAT
64353093 AAAGAAAAGA
1 AAAGAAAAGA
64353103 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
64353115 AAAGAAGA-A
1 AAAGAAAAGA
64353124 AAAGAAAATGA
1 AAAGAAAA-GA
64353135 AATA-AAAAGA
1 AA-AGAAAAGA
64353145 AAAGA
1 AAAGA
64353150 GAGGTAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:64353117 original size:6 final size:5
Alignment explanation
Indices: 64353093--64353149 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
64353083 AAGAGAAAAT
*
64353093 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
64353140 AAAGA AAAGA
1 AAAGA AAAGA
64353150 GAGGTAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:64353124 original size:15 final size:14
Alignment explanation
Indices: 64353093--64353149 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
64353083 AAGAGAAAAT
64353093 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
64353109 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
64353124 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
64353140 AAAGAAAAGA
1 AAAGAAAAGA
64353150 GAGGTAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:64354308 original size:20 final size:20
Alignment explanation
Indices: 64354285--64354338 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
64354275 AGCTCCGTCC
64354285 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
64354305 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
*
64354325 AGCTCAACTGAGCT
1 AGCTCAACTCAGCT
64354339 TACTTTCAGC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:64363377 original size:17 final size:17
Alignment explanation
Indices: 64363355--64363390 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
64363345 ACGAGTTACT
64363355 TGGGATTTCTTCCAAGC
1 TGGGATTTCTTCCAAGC
64363372 TGGGATTTCTTCCAAGC
1 TGGGATTTCTTCCAAGC
64363389 TG
1 TG
64363391 AATTCCAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (17 bp):
TGGGATTTCTTCCAAGC
Found at i:64364130 original size:12 final size:12
Alignment explanation
Indices: 64364113--64364142 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
64364103 AATCTGAGGA
64364113 CAGAGCACCTGC
1 CAGAGCACCTGC
64364125 CAGAGCACCTGC
1 CAGAGCACCTGC
64364137 CAGAGC
1 CAGAGC
64364143 CTATGCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.40, G:0.27, T:0.07
Consensus pattern (12 bp):
CAGAGCACCTGC
Found at i:64369686 original size:13 final size:13
Alignment explanation
Indices: 64369668--64369696 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
64369658 TGGCTAACCT
64369668 ACATAATTAAATA
1 ACATAATTAAATA
64369681 ACATAATTAAATA
1 ACATAATTAAATA
64369694 ACA
1 ACA
64369697 CATAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:64369953 original size:10 final size:10
Alignment explanation
Indices: 64369920--64369968 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
64369910 AAAAAGGAAT
*
64369920 GAGCTGAAAC
1 GAGCTCAAAC
64369930 GAGCT-AAATTC
1 GAGCTCAAA--C
64369941 GAGCTCAAAC
1 GAGCTCAAAC
*
64369951 GAGCTAAAAC
1 GAGCTCAAAC
64369961 GAGCTCAA
1 GAGCTCAA
64369969 GTGAGCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.65
11 6 0.18
12 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:64369975 original size:20 final size:21
Alignment explanation
Indices: 64369920--64369968 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
64369910 AAAAAGGAAT
* *
64369920 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAATAC
64369941 GAGCTCAAACGAGCTAAA-AC
1 GAGCTCAAACGAGCTAAATAC
64369961 GAGCTCAA
1 GAGCTCAA
64369969 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAATAC
Found at i:64371795 original size:10 final size:10
Alignment explanation
Indices: 64371780--64371817 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
64371770 GCTCGTTTCC
*
64371780 AGCTCACTCG
1 AGCTCAATCG
64371790 AGCTCAAGTC-
1 AGCTCAA-TCG
64371800 AGCTCAATCG
1 AGCTCAATCG
64371810 AGCTCAAT
1 AGCTCAAT
64371818 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:64371804 original size:20 final size:20
Alignment explanation
Indices: 64371779--64371816 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
64371769 AGCTCGTTTC
*
64371779 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
64371799 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
64371817 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:64371823 original size:20 final size:20
Alignment explanation
Indices: 64371780--64371840 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
64371770 GCTCGTTTCC
* * *
64371780 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
64371800 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
64371820 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
64371840 A
1 A
64371841 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:64371834 original size:11 final size:10
Alignment explanation
Indices: 64371790--64371836 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
64371780 AGCTCACTCG
*
64371790 AGCTCAAGTC
1 AGCTCAATTC
64371800 AGCTCAA-TC
1 AGCTCAATTC
*
64371809 GAGCTCAATTT
1 -AGCTCAATTC
64371820 AGCTACAATTC
1 AGCT-CAATTC
64371831 AGCTCA
1 AGCTCA
64371837 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:64373223 original size:13 final size:13
Alignment explanation
Indices: 64373198--64373284 Score: 65
Period size: 14 Copynumber: 6.5 Consensus size: 13
64373188 GTATTGAAGT
64373198 AAAAAAA-TC-AA
1 AAAAAAATTCGAA
64373209 AAAAAAATTCGAA
1 AAAAAAATTCGAA
*
64373222 AAAAAAATTGATTGAA
1 AAAAAAA-T--TCGAA
*
64373238 AAAAAAATTTCAAA
1 AAAAAAA-TTCGAA
*
64373252 AAAAAAAGT-GAA
1 AAAAAAATTCGAA
64373264 AAAAAAA-TCGAGCA
1 AAAAAAATTCGA--A
64373278 AAAAAAA
1 AAAAAAA
64373285 AGAAGAAAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
11 8 0.13
12 13 0.21
13 10 0.16
14 19 0.30
16 13 0.21
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (13 bp):
AAAAAAATTCGAA
Found at i:64373270 original size:30 final size:29
Alignment explanation
Indices: 64373207--64373270 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
64373197 TAAAAAAATC
* * **
64373207 AAAAAAAAATTCGAAAAAAAAATTGATTGA
1 AAAAAAAAATTCAAAAAAAAAAGTGA-AAA
*
64373237 AAAAAAAATTTCAAAAAAAAAAGTGAAAA
1 AAAAAAAAATTCAAAAAAAAAAGTGAAAA
64373266 AAAAA
1 AAAAA
64373271 TCGAGCAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 6 0.21
30 23 0.79
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (29 bp):
AAAAAAAAATTCAAAAAAAAAAGTGAAAA
Found at i:64374252 original size:18 final size:18
Alignment explanation
Indices: 64374214--64374255 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
64374204 ACATCGAAAG
* **
64374214 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
64374232 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
64374250 AAAAGA
1 AAAAGA
64374256 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:64374320 original size:33 final size:34
Alignment explanation
Indices: 64374283--64374347 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 34
64374273 AAAGTGAAAA
*
64374283 TGAGA-GAGGAAATGAAA-AGAGAAAAAGAGAAGT
1 TGAGATGA-GAAAAGAAACAGAGAAAAAGAGAAGT
*
64374316 TGAGATTAGAAAAGAAACGAGAGAAAAAGAGA
1 TGAGATGAGAAAAGAAAC-AGAGAAAAAGAGA
64374348 TAAACGAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 13 0.48
34 1 0.04
35 13 0.48
ACGTcount: A:0.58, C:0.02, G:0.31, T:0.09
Consensus pattern (34 bp):
TGAGATGAGAAAAGAAACAGAGAAAAAGAGAAGT
Found at i:64375405 original size:10 final size:10
Alignment explanation
Indices: 64375390--64375427 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
64375380 GCTCGTTTCC
*
64375390 AGCTCACTCG
1 AGCTCAATCG
64375400 AGCTCAAGTC-
1 AGCTCAA-TCG
64375410 AGCTCAATCG
1 AGCTCAATCG
64375420 AGCTCAAT
1 AGCTCAAT
64375428 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:64375414 original size:20 final size:20
Alignment explanation
Indices: 64375389--64375426 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
64375379 AGCTCGTTTC
*
64375389 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
64375409 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
64375427 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:64375433 original size:20 final size:20
Alignment explanation
Indices: 64375390--64375450 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
64375380 GCTCGTTTCC
* * *
64375390 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
64375410 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
64375430 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
64375450 A
1 A
64375451 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:64375444 original size:11 final size:10
Alignment explanation
Indices: 64375400--64375446 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
64375390 AGCTCACTCG
*
64375400 AGCTCAAGTC
1 AGCTCAATTC
64375410 AGCTCAA-TC
1 AGCTCAATTC
*
64375419 GAGCTCAATTT
1 -AGCTCAATTC
64375430 AGCTACAATTC
1 AGCT-CAATTC
64375441 AGCTCA
1 AGCTCA
64375447 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:64378602 original size:23 final size:22
Alignment explanation
Indices: 64378550--64378602 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
64378540 TCCACGTCTT
*
64378550 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
64378572 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
64378595 TTTCTTTT
1 TTTCTTTT
64378603 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:64384997 original size:42 final size:42
Alignment explanation
Indices: 64384919--64385065 Score: 152
Period size: 42 Copynumber: 3.4 Consensus size: 42
64384909 ATTCCAAACC
* * * * *
64384919 TGGTCTTACATGTAATCAAACATCGATGCCACTGTCCCAGACA
1 TGGTCTTACACGAAATCAGA-AGCGATGCCAATGTCCCAGACA
* * * *
64384962 GGGTCTTACACGAAATTAGATA-CGATGTCGATGTCCCAGACA
1 TGGTCTTACACGAAATCAGA-AGCGATGCCAATGTCCCAGACA
* *
64385004 TGGTCTTACACGTAAAACAGAAGTTGATGCCAATGTCCCAGACA
1 TGGTCTTACACG-AAATCAGAAG-CGATGCCAATGTCCCAGACA
64385048 TGGTCTTACACGAAATCA
1 TGGTCTTACACGAAATCA
64385066 CAAAACGCAA
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
42 29 0.34
43 27 0.32
44 29 0.34
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (42 bp):
TGGTCTTACACGAAATCAGAAGCGATGCCAATGTCCCAGACA
Found at i:64387903 original size:10 final size:10
Alignment explanation
Indices: 64387890--64387927 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
64387880 TTGTAGCTAA
64387890 ATTGAGCTCG
1 ATTGAGCTCG
64387900 ATTGAGCT-G
1 ATTGAGCTCG
64387909 ACTTGAGCTCG
1 A-TTGAGCTCG
*
64387920 AGTGAGCT
1 ATTGAGCT
64387928 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:64387907 original size:20 final size:20
Alignment explanation
Indices: 64387867--64387927 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
64387857 ACCAATAAAA
64387867 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
64387887 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
64387907 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
64387927 T
1 T
64387928 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:64387928 original size:20 final size:20
Alignment explanation
Indices: 64387891--64387928 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
64387881 TGTAGCTAAA
*
64387891 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
64387911 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
64387929 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:64390994 original size:38 final size:38
Alignment explanation
Indices: 64390943--64391020 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
64390933 ATGTTCATGC
64390943 ATACATACGAATGTGTTGATCCAGGATCTATCAAAGCA
1 ATACATACGAATGTGTTGATCCAGGATCTATCAAAGCA
64390981 ATACATACGAATGTGTTGATCCAGGATCTATCAAAGCA
1 ATACATACGAATGTGTTGATCCAGGATCTATCAAAGCA
64391019 AT
1 AT
64391021 CACAGAAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (38 bp):
ATACATACGAATGTGTTGATCCAGGATCTATCAAAGCA
Found at i:64394695 original size:30 final size:30
Alignment explanation
Indices: 64394661--64394757 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
64394651 TAAACTAAAA
*
64394661 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
64394691 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
64394721 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
64394750 ATGAGCTA
1 -TGAGCTA
64394758 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:64395152 original size:20 final size:20
Alignment explanation
Indices: 64395127--64395166 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
64395117 CTATACATGC
64395127 CATACTTTAATATATACATT
1 CATACTTTAATATATACATT
64395147 CATACTTTAATATATACATT
1 CATACTTTAATATATACATT
64395167 TTCAAAGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (20 bp):
CATACTTTAATATATACATT
Found at i:64403465 original size:16 final size:16
Alignment explanation
Indices: 64403434--64403468 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
64403424 TTGTAACGCC
*
64403434 CCAAAAATCCCGAAAT
1 CCAAAAATCCCAAAAT
*
64403450 CCAAAAATCCTAAAAT
1 CCAAAAATCCCAAAAT
64403466 CCA
1 CCA
64403469 GAATTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.31, G:0.03, T:0.14
Consensus pattern (16 bp):
CCAAAAATCCCAAAAT
Found at i:64404883 original size:29 final size:28
Alignment explanation
Indices: 64404840--64404894 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
64404830 CATGAATATG
64404840 AATGTGACTGGGCCTAACGGGCCATAAA
1 AATGTGACTGGGCCTAACGGGCCATAAA
* *
64404868 AATGTGATTTGGGCCTAATGGGCCATA
1 AATGTGA-CTGGGCCTAACGGGCCATA
64404895 TGAATATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (28 bp):
AATGTGACTGGGCCTAACGGGCCATAAA
Found at i:64404917 original size:28 final size:28
Alignment explanation
Indices: 64404835--64404920 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
64404825 ATGAGCATGA
* *
64404835 ATATGAATGTGACTGGGCCTAACGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
**
64404863 ATAAAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGA-TTGGGCCTAATGGGCC
* * *
64404892 ATATGAATATGATTGGGCTTAGTGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
64404920 A
1 A
64404921 AATACAGGTA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
28 25 0.52
29 23 0.48
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATGGGCC
Found at i:64407159 original size:24 final size:23
Alignment explanation
Indices: 64407105--64407182 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
64407095 GGATAATTAA
**
64407105 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
64407128 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
64407152 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
64407173 GAAATAGTAT
1 GAAATGGTAT
64407183 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:64407167 original size:21 final size:21
Alignment explanation
Indices: 64407141--64407207 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
64407131 TTGGTATTTG
64407141 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
64407162 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
64407183 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
64407206 GG
1 GG
64407208 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:64411811 original size:22 final size:22
Alignment explanation
Indices: 64411760--64411825 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
64411750 GGTATTTGGG
* *
64411760 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
64411781 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
64411803 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
64411826 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:64416685 original size:10 final size:10
Alignment explanation
Indices: 64416672--64416717 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
64416662 AGCTCACTTG
64416672 AGCTCGTTTT
1 AGCTCGTTTT
*
64416682 AGCTCGTTTG
1 AGCTCGTTTT
*
64416692 AGCTCGAATTT
1 AGCTCG-TTTT
*
64416703 AGCTCGTTTC
1 AGCTCGTTTT
64416713 AGCTC
1 AGCTC
64416718 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:64416685 original size:20 final size:21
Alignment explanation
Indices: 64416662--64416707 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
64416652 AGTTCCCATC
*
64416662 AGCTCACTTGAGCTCG-TTTT
1 AGCTCACTTGAGCTCGAATTT
**
64416682 AGCTCGTTTGAGCTCGAATTT
1 AGCTCACTTGAGCTCGAATTT
64416703 AGCTC
1 AGCTC
64416708 GTTTCAGCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (21 bp):
AGCTCACTTGAGCTCGAATTT
Found at i:64416705 original size:21 final size:20
Alignment explanation
Indices: 64416669--64416717 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
64416659 ATCAGCTCAC
*
64416669 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
64416689 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
64416710 TTCAGCTC
1 TTGAGCTC
64416718 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:64416960 original size:13 final size:13
Alignment explanation
Indices: 64416942--64416970 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
64416932 AATAGTTGTG
64416942 TGTTATTTAATTA
1 TGTTATTTAATTA
64416955 TGTTATTTAATTA
1 TGTTATTTAATTA
64416968 TGT
1 TGT
64416971 AGGTTAGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:64425864 original size:14 final size:14
Alignment explanation
Indices: 64425817--64425864 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
64425807 GTACGAATGG
*
64425817 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
64425831 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
64425845 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
64425859 ATTGGT
1 AATGGT
64425865 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:64428411 original size:20 final size:20
Alignment explanation
Indices: 64428386--64428431 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
64428376 CCCAGCTCGA
*
64428386 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
64428406 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
64428426 TTAGCT
1 TTAGCT
64428432 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:64428422 original size:30 final size:30
Alignment explanation
Indices: 64428379--64428451 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
64428369 AGTTTTTCCC
*
64428379 AGCTCGATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCGTTTGAGCTCA-ATTGAGCTTAATTT
* *
64428408 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
64428438 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
64428452 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.23
30 30 0.77
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:64430057 original size:12 final size:12
Alignment explanation
Indices: 64430042--64430100 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 12
64430032 ACAAAAAAAT
64430042 AAAAAAAATTCG
1 AAAAAAAATTCG
*
64430054 AAAAAAAATTTGATTG
1 AAAAAAAA--T--TCG
64430070 AAAAAAAATTC-
1 AAAAAAAATTCG
*
64430081 AAAAAAAAGT-G
1 AAAAAAAATTCG
64430092 AAAAAAAAT
1 AAAAAAAAT
64430101 CGAGCAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
11 17 0.45
12 9 0.24
14 2 0.05
16 10 0.26
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.19
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:64430112 original size:28 final size:26
Alignment explanation
Indices: 64430081--64430141 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
64430071 AAAAAAATTC
**
64430081 AAAAAAAAGTGAAAAAAAA-TCGAGCA
1 AAAAAAAAAAGAAAAAAAAGT-GAGCA
64430107 AAAAAAGAAAAGAAAAAAAAGGTGAGCA
1 AAAAAA-AAAAGAAAAAAAA-GTGAGCA
64430135 AAAAAAA
1 AAAAAAA
64430142 TCAAGTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 6 0.20
27 12 0.40
28 11 0.37
29 1 0.03
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (26 bp):
AAAAAAAAAAGAAAAAAAAGTGAGCA
Found at i:64431189 original size:11 final size:11
Alignment explanation
Indices: 64431173--64431202 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
64431163 AAAGAAATTG
64431173 AAAGAAAACAA
1 AAAGAAAACAA
*
64431184 AAAGAAAACGA
1 AAAGAAAACAA
64431195 AAAGAAAA
1 AAAGAAAA
64431203 AGAAATTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAGAAAACAA
Found at i:64431196 original size:6 final size:6
Alignment explanation
Indices: 64431173--64431279 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
64431163 AAAGAAATTG
* * ** *
64431173 AAAG-A AAACAA AAAGAA AACG-A AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
64431219 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
64431270 AAAGAA AAAG
1 AAAGAA AAAG
64431280 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 24, Indels: 9
0.69 0.23 0.08
Matches are distributed among these distances:
5 7 0.10
6 55 0.75
7 7 0.10
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:64431234 original size:18 final size:17
Alignment explanation
Indices: 64431176--64431232 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
64431166 GAAATTGAAA
* *
64431176 GAAAACAAAAAGAAAAC
1 GAAAAGAAAAAGAAATC
*
64431193 GAAAAGAAAAAGAAATT
1 GAAAAGAAAAAGAAATC
64431210 GCAAAAGAAAAAGAAATC
1 G-AAAAGAAAAAGAAATC
64431228 GAAAA
1 GAAAA
64431233 AGTGAGAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 19 0.54
18 16 0.46
ACGTcount: A:0.72, C:0.07, G:0.16, T:0.05
Consensus pattern (17 bp):
GAAAAGAAAAAGAAATC
Found at i:64431261 original size:14 final size:13
Alignment explanation
Indices: 64431240--64431277 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
64431230 AAAAGTGAGA
64431240 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
64431252 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
64431267 GAAAAAGAAAA
1 GAAAAAGAAAA
64431278 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:64431291 original size:21 final size:21
Alignment explanation
Indices: 64431241--64431291 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
64431231 AAAGTGAGAG
*
64431241 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
64431262 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
64431283 AAAAAGAAA
1 AAAAAGAAA
64431292 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:64431331 original size:33 final size:33
Alignment explanation
Indices: 64431294--64431356 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
64431284 AAAAGAAATT
64431294 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
64431327 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
64431357 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:64433165 original size:20 final size:20
Alignment explanation
Indices: 64433140--64433185 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
64433130 CCCAGCTCGA
*
64433140 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
64433160 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
64433180 TTAGCT
1 TTAGCT
64433186 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:64433176 original size:30 final size:30
Alignment explanation
Indices: 64433133--64433205 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
64433123 AGTTTTTCCC
*
64433133 AGCTCGATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCGTTTGAGCTCA-ATTGAGCTTAATTT
* *
64433162 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
64433192 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
64433206 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.23
30 30 0.77
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:64437181 original size:46 final size:46
Alignment explanation
Indices: 64437114--64437289 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
64437104 TATTTGGGCA
64437114 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
64437160 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
64437205 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
64437253 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
64437290 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 63 0.58
47 29 0.27
48 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:64437269 original size:93 final size:93
Alignment explanation
Indices: 64437110--64437281 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
64437100 GGGATATTTG
* * *
64437110 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAG
64437175 TTGAGTCCGAGTTCGTGAAATGTAACTA
66 TTGAGTCCGAGTTCGTGAAATGTAACTA
*
64437203 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAG
64437268 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
64437282 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAAATGTAACTA
Found at i:64438617 original size:45 final size:45
Alignment explanation
Indices: 64438347--64438609 Score: 438
Period size: 45 Copynumber: 5.9 Consensus size: 45
64438337 AAGAGGTGGA
64438347 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
*
64438392 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* *
64438437 CAACGTCATGCATAATTCATAGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
64438482 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* *
64438527 CAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* * * *
64438572 CAACATCAT-CATAATTTAAGGAACAAATTGAGGAAGCA
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCA
64438610 CCATGGCCGA
Statistics
Matches: 205, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
44 24 0.12
45 181 0.88
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
Found at i:64439408 original size:21 final size:19
Alignment explanation
Indices: 64439363--64439410 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 19
64439353 TAAAAAAAGA
64439363 GAAATTCAAAAAAAAATTT
1 GAAATTCAAAAAAAAATTT
*
64439382 GGAATT-AAAAAAAAAGTGATT
1 GAAATTCAAAAAAAAA-T--TT
64439403 GAAATTCA
1 GAAATTCA
64439411 TTTTAAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 9 0.39
19 6 0.26
21 7 0.30
22 1 0.04
ACGTcount: A:0.58, C:0.04, G:0.12, T:0.25
Consensus pattern (19 bp):
GAAATTCAAAAAAAAATTT
Found at i:64444657 original size:45 final size:45
Alignment explanation
Indices: 64444607--64444870 Score: 474
Period size: 45 Copynumber: 5.9 Consensus size: 45
64444597 AAGAGGTGGA
64444607 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
64444652 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
64444697 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
64444742 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* *
64444787 CAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* * * *
64444832 CAACATCATGCATAATTTAAGGAACAAATTGAGGAAGCA
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCA
64444871 CCATGGCCGA
Statistics
Matches: 212, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 212 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
Found at i:64449075 original size:15 final size:15
Alignment explanation
Indices: 64449040--64449118 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
64449030 GTATCTTGGG
*
64449040 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
64449055 -TTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
64449069 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
64449084 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
64449099 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
64449113 TTTCTT
1 TTTCTT
64449119 GTTATCTTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
14 23 0.42
15 30 0.55
16 2 0.04
ACGTcount: A:0.10, C:0.16, G:0.14, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Done.