Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 30 of 182
Found at i:11869715 original size:18 final size:18
Alignment explanation
Indices: 11869694--11869728 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11869684 ACTTAGCTTT
11869694 ATTTTAATATTATTATAA
1 ATTTTAATATTATTATAA
*
11869712 ATTTTAATTTTATTATA
1 ATTTTAATATTATTATA
11869729 CATATTTTAT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTAATATTATTATAA
Found at i:11874093 original size:12 final size:11
Alignment explanation
Indices: 11874053--11874095 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
11874043 CGATTTTTAT
11874053 TTTTTTAAATG-
1 TTTTTT-AATGA
*
11874064 TTTTTTTATGA
1 TTTTTTAATGA
11874075 TTTTTTAATGA
1 TTTTTTAATGA
11874086 TTTATTTAAT
1 TTT-TTTAAT
11874096 TCAACCAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 3 0.11
11 19 0.68
12 6 0.21
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (11 bp):
TTTTTTAATGA
Found at i:11874450 original size:36 final size:37
Alignment explanation
Indices: 11874396--11874467 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 37
11874386 GATAGTGGTT
* *
11874396 AAATTTCAATTCTGATTTTT-TTTTTATATTATATAA
1 AAATATCAATTCTGATTTTTATTTTTATAATATATAA
* *
11874432 AAATATCAATTTTTATTTTTGATTTTTATAATATAT
1 AAATATCAATTCTGATTTTT-ATTTTTATAATATAT
11874468 TTTAATTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 17 0.57
38 13 0.43
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (37 bp):
AAATATCAATTCTGATTTTTATTTTTATAATATATAA
Found at i:11877755 original size:23 final size:23
Alignment explanation
Indices: 11877688--11877793 Score: 88
Period size: 23 Copynumber: 4.6 Consensus size: 23
11877678 TAATGCATAG
*
11877688 ATGCGAACCCTATATGTTTTATAC
1 ATGCGAACCCTATATGTTTTA-AT
* * * * *
11877712 ATGTGAACTCTACAAGCTTTAAT
1 ATGCGAACCCTATATGTTTTAAT
* *
11877735 ATGTGAACCCTATATGTTTTATT
1 ATGCGAACCCTATATGTTTTAAT
* ** *
11877758 ATGCAAACCCTA-CGGATTTAAT
1 ATGCGAACCCTATATGTTTTAAT
11877780 ATGCGAACCCTATA
1 ATGCGAACCCTATA
11877794 ATATTATATA
Statistics
Matches: 62, Mismatches: 19, Indels: 3
0.74 0.23 0.04
Matches are distributed among these distances:
22 17 0.27
23 29 0.47
24 16 0.26
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (23 bp):
ATGCGAACCCTATATGTTTTAAT
Found at i:11877792 original size:45 final size:47
Alignment explanation
Indices: 11877688--11877793 Score: 135
Period size: 47 Copynumber: 2.3 Consensus size: 47
11877678 TAATGCATAG
** * *
11877688 ATGCGAACCCTATATGTTTTATACATGTGAACTCTACAAGCTTTAAT
1 ATGCGAACCCTATATGTTTTATACATGCAAACCCTACAAGATTTAAT
* * *
11877735 ATGTGAACCCTATATGTTTTAT-TATGCAAACCCTAC-GGATTTAAT
1 ATGCGAACCCTATATGTTTTATACATGCAAACCCTACAAGATTTAAT
11877780 ATGCGAACCCTATA
1 ATGCGAACCCTATA
11877794 ATATTATATA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 20 0.39
46 10 0.20
47 21 0.41
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (47 bp):
ATGCGAACCCTATATGTTTTATACATGCAAACCCTACAAGATTTAAT
Found at i:11877883 original size:23 final size:22
Alignment explanation
Indices: 11877840--11877901 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
11877830 ACATGCTTTA
* *
11877840 ATATGTAAACCCTATATGTTTT-
1 ATATGTGAACCCT-TAAGTTTTC
11877862 ATTATGTGAACCTCTTAAGTTTTGC
1 A-TATGTGAACC-CTTAAGTTTT-C
11877887 ATATGTGAACCCTTA
1 ATATGTGAACCCTTA
11877902 GAGTACGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 1 0.03
23 20 0.59
24 12 0.35
25 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (22 bp):
ATATGTGAACCCTTAAGTTTTC
Found at i:11900297 original size:34 final size:34
Alignment explanation
Indices: 11900254--11900321 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 34
11900244 CATTTTGTAC
11900254 TATTTATATT-ATTGAATTATTTAATCATATTAAA
1 TATTTATATTAATTGAATTA-TTAATCATATTAAA
*
11900288 TATTTATATTAAAATTGAATTATTAATGATATTA
1 TATTTATATT--AATTGAATTATTAATCATATTA
11900322 TAAAATATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 10 0.33
36 11 0.37
37 9 0.30
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (34 bp):
TATTTATATTAATTGAATTATTAATCATATTAAA
Found at i:11905176 original size:26 final size:26
Alignment explanation
Indices: 11905147--11905201 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
11905137 AAATATAAAG
*
11905147 TCTGAATCAAAAGTTTCAGCAATCTC
1 TCTGAATCAAAAGTTTCAACAATCTC
11905173 TCTGAATCAAAAGTTTCAACAATCTC
1 TCTGAATCAAAAGTTTCAACAATCTC
11905199 TCT
1 TCT
11905202 CTCAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.33
Consensus pattern (26 bp):
TCTGAATCAAAAGTTTCAACAATCTC
Found at i:11908508 original size:59 final size:57
Alignment explanation
Indices: 11908435--11908628 Score: 176
Period size: 59 Copynumber: 3.3 Consensus size: 57
11908425 TGGGTTTTTA
*
11908435 GGGGTAAAATGGTAATTTTTATGAAATCGGGGGCTAAAAATGGAATTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTATGAAATC-GGGACTAAAAATGGAATTTGGAAAGTTTG
* * * * * * *
11908493 GGGAGTAAAATGGTAAATTTT-GGTAAAACAAGGTC-AAAAATGAAATTTTGGAAAGTTCG
1 GGG-GTAAAATGGTAATTTTTATG-AAATC-GGGACTAAAAATGGAA-TTTGGAAAGTTTG
* * * * * * *
11908552 GAGGCAAAACGGTAAGTTTTAGTGAAATCGGGATTAAAAATGGGATTTAGGGAAGTTTG
1 GGGGTAAAATGGTAATTTTTA-TGAAATCGGGACTAAAAATGGAATTT-GGAAAGTTTG
11908611 GGGGTAAAATGGTAATTT
1 GGGGTAAAATGGTAATTT
11908629 CTGAAAGTTT
Statistics
Matches: 104, Mismatches: 25, Indels: 13
0.73 0.18 0.09
Matches are distributed among these distances:
58 32 0.31
59 71 0.68
60 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.30, T:0.29
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTATGAAATCGGGACTAAAAATGGAATTTGGAAAGTTTG
Found at i:11908636 original size:29 final size:30
Alignment explanation
Indices: 11908604--11908897 Score: 360
Period size: 30 Copynumber: 9.8 Consensus size: 30
11908594 GGATTTAGGG
*
11908604 AAGTTTGGGGGT-AAAATGGTAATTTCT-G-A
1 AAGTTTTGGGGTCAAAAT-GTAATTT-TAGAA
* * *
11908633 AAGTTTCGAGGTCAAAATATAATTTTAGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* *
11908663 AAGTTTTTGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
*
11908693 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* * * *
11908723 AAGTTTTAGGGTCAAACTATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* * *
11908753 AAGTTTTAGGGTTAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* * *
11908783 AAGTTTTGGGGTCAAACTATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
*
11908813 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* * *
11908843 AAGTTTTAGGGTCAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
11908873 AAGTTTTGGGGTCAAAATGTAATTT
1 AAGTTTTGGGGTCAAAATGTAATTT
11908898 CTGGATAATT
Statistics
Matches: 237, Mismatches: 25, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
28 1 0.00
29 17 0.07
30 219 0.92
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.37
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATGTAATTTTAGAA
Found at i:11908706 original size:60 final size:60
Alignment explanation
Indices: 11908632--11908902 Score: 434
Period size: 60 Copynumber: 4.5 Consensus size: 60
11908622 GTAATTTCTG
* * * * * *
11908632 AAAGTTTCGAGGTCAAAATATAATTTTAGAAAAGTTTTTGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTGGA
*
11908692 AAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAACTATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTGGA
* * * *
11908752 AAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAACTATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTGGA
11908812 AAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTGGA
11908872 AAAGTTTTGGGGTCAAAATGTAATTTCTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTT-TGGA
11908903 TAATTTAGGG
Statistics
Matches: 196, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
60 192 0.98
61 4 0.02
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (60 bp):
AAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTGGA
Found at i:11908736 original size:90 final size:91
Alignment explanation
Indices: 11908604--11908902 Score: 439
Period size: 90 Copynumber: 3.3 Consensus size: 91
11908594 GGATTTAGGG
* * *
11908604 AAGTTTGGGGGT-AAAATGGTAATTTCT-G-AAAG-TTTCGAGGTCAAAATATAATTTTAGAAAA
1 AAGTTTTGGGGTCAAAAT-GTAATTTCTGGAAAAGTTTTAG-GGTCAAAATATAATTTTGGAAAA
*
11908665 GTTTTTGGGTCAAAATGTAATTTTGGAA
64 GTTTTAGGGTCAAAATGTAATTTTGGAA
*
11908693 AAGTTTTGGGGTCAAAATGTAATTT-TGGAAAAGTTTTAGGGTCAAACTATAATTTTGGAAAAGT
1 AAGTTTTGGGGTCAAAATGTAATTTCTGGAAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGT
*
11908757 TTTAGGGTTAAAATGTAATTTTGGAA
66 TTTAGGGTCAAAATGTAATTTTGGAA
* * * *
11908783 AAGTTTTGGGGTCAAACTATAATTT-TGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGT
1 AAGTTTTGGGGTCAAAATGTAATTTCTGGAAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGT
*
11908847 TTTAGGGTCAAAATATAATTTTGGAA
66 TTTAGGGTCAAAATGTAATTTTGGAA
11908873 AAGTTTTGGGGTCAAAATGTAATTTCTGGA
1 AAGTTTTGGGGTCAAAATGTAATTTCTGGA
11908903 TAATTTAGGG
Statistics
Matches: 190, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
88 1 0.01
89 19 0.10
90 162 0.85
91 8 0.04
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (91 bp):
AAGTTTTGGGGTCAAAATGTAATTTCTGGAAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGT
TTTAGGGTCAAAATGTAATTTTGGAA
Found at i:11910792 original size:6 final size:6
Alignment explanation
Indices: 11910740--11910829 Score: 67
Period size: 6 Copynumber: 14.8 Consensus size: 6
11910730 TTTTTTAATG
* * ** * * *
11910740 TTAAAT TTAGTAT TTTAAT TTTTAT TTAAAT TCAAAT TCAAA- GTAAAT
1 TTAAAT TTA-AAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
11910788 TTAAAT AATTAAAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAA
1 TTAAAT --TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
11910830 ATCAATTTAA
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
5 7 0.10
6 50 0.75
7 4 0.06
8 6 0.09
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:11910800 original size:31 final size:31
Alignment explanation
Indices: 11910765--11910824 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
11910755 TAATTTTTAT
*
11910765 TTAAATTCAAATTCAAAGTAAATTTAAATAA
1 TTAAATTCAAATTCAAAATAAATTTAAATAA
* *
11910796 TTAAATTTAAATTTAAAATAAATTTAAAT
1 TTAAATTCAAATTCAAAATAAATTTAAAT
11910825 TTAAAATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (31 bp):
TTAAATTCAAATTCAAAATAAATTTAAATAA
Found at i:11910846 original size:17 final size:17
Alignment explanation
Indices: 11910766--11910839 Score: 82
Period size: 17 Copynumber: 4.5 Consensus size: 17
11910756 AATTTTTATT
* * *
11910766 TAAATTCAAATTCAAAG
1 TAAATTTAAATTTAAAA
*
11910783 TAAATTTAAA--T-AAT
1 TAAATTTAAATTTAAAA
11910797 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
11910814 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
11910831 TCAATTTAA
1 TAAATTTAA
11910840 CTCTAAATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
14 12 0.24
16 1 0.02
17 36 0.73
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:11911583 original size:14 final size:13
Alignment explanation
Indices: 11911564--11911686 Score: 61
Period size: 14 Copynumber: 8.9 Consensus size: 13
11911554 TGAATTCGAC
11911564 GAGTTTAGGGTTAT
1 GAGTTTAGGGTT-T
11911578 GAGTTTAGGGTTT
1 GAGTTTAGGGTTT
* *
11911591 -AGGATTATGAGTTT
1 GA-GTTTA-GGGTTT
* *
11911605 AGAGTTTACGATTT
1 -GAGTTTAGGGTTT
* * *
11911619 AAGATTTAGGATTGC
1 GAG-TTTAGGGTT-T
11911634 GAGTTTAGGGTTT
1 GAGTTTAGGGTTT
*
11911647 AAGTTTTAGGGTTAT
1 GAG-TTTAGGGTT-T
*
11911662 GAGTTT-GGATTAT
1 GAGTTTAGGGTT-T
*
11911675 GAGTTTAAGGTT
1 GAGTTTAGGGTT
11911687 ACAGGTTTGA
Statistics
Matches: 83, Mismatches: 17, Indels: 18
0.70 0.14 0.15
Matches are distributed among these distances:
12 1 0.01
13 21 0.25
14 51 0.61
15 9 0.11
16 1 0.01
ACGTcount: A:0.24, C:0.02, G:0.31, T:0.43
Consensus pattern (13 bp):
GAGTTTAGGGTTT
Found at i:11911592 original size:21 final size:21
Alignment explanation
Indices: 11911564--11911617 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
11911554 TGAATTCGAC
*
11911564 GAGTTTAGGGTTATGAGTTTA
1 GAGTTTAGGATTATGAGTTTA
*
11911585 GGGTTTAGGATTATGAGTTTA
1 GAGTTTAGGATTATGAGTTTA
*
11911606 GAGTTTACGATT
1 GAGTTTAGGATT
11911618 TAAGATTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.02, G:0.31, T:0.43
Consensus pattern (21 bp):
GAGTTTAGGATTATGAGTTTA
Found at i:11911665 original size:28 final size:28
Alignment explanation
Indices: 11911567--11911667 Score: 98
Period size: 28 Copynumber: 3.6 Consensus size: 28
11911557 ATTCGACGAG
*
11911567 TTTAGGGTTATGAGTTTAGGGTTTAGGA
1 TTTAGGGTTATGAGTTTAGGGTTTAAGA
* * *
11911595 -TTATGAGTT-TAGAGTTTACGATTTAAGA
1 TTTA-GGGTTAT-GAGTTTAGGGTTTAAGA
* ** *
11911623 TTTAGGATTGCGAGTTTAGGGTTTAAGT
1 TTTAGGGTTATGAGTTTAGGGTTTAAGA
11911651 TTTAGGGTTATGAGTTT
1 TTTAGGGTTATGAGTTT
11911668 GGATTATGAG
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
27 4 0.07
28 49 0.88
29 3 0.05
ACGTcount: A:0.24, C:0.02, G:0.30, T:0.45
Consensus pattern (28 bp):
TTTAGGGTTATGAGTTTAGGGTTTAAGA
Found at i:11911725 original size:14 final size:14
Alignment explanation
Indices: 11911689--11911733 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
11911679 TTAAGGTTAC
11911689 AGGTT-TGAGTTTA
1 AGGTTATGAGTTTA
11911702 AGGTTA-GAGTTATA
1 AGGTTATGAGTT-TA
11911716 A-GTTATGAGTTTA
1 AGGTTATGAGTTTA
*
11911729 GGGTT
1 AGGTT
11911734 TTTAGTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (14 bp):
AGGTTATGAGTTTA
Found at i:11911773 original size:31 final size:31
Alignment explanation
Indices: 11911737--11911808 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
11911727 TAGGGTTTTT
* * *
11911737 AGTTTATAATAATGTTGGGTTCATGGTTTAG
1 AGTTTAGAATAATGTTAGGTGCATGGTTTAG
*
11911768 GGTTTAGAATAATGTTAGGTGCATGGTTTAG
1 AGTTTAGAATAATGTTAGGTGCATGGTTTAG
*
11911799 AGTTTCGAAT
1 AGTTTAGAAT
11911809 TTAGAATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.26, C:0.04, G:0.28, T:0.42
Consensus pattern (31 bp):
AGTTTAGAATAATGTTAGGTGCATGGTTTAG
Found at i:11920076 original size:18 final size:18
Alignment explanation
Indices: 11920053--11920087 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11920043 CGTCAGCTTC
*
11920053 GTTCTTCCCTCTCTTTCT
1 GTTCTTCCCTCCCTTTCT
*
11920071 GTTCTTGCCTCCCTTTC
1 GTTCTTCCCTCCCTTTC
11920088 CCTTGTTCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.40, G:0.09, T:0.51
Consensus pattern (18 bp):
GTTCTTCCCTCCCTTTCT
Found at i:11921258 original size:23 final size:22
Alignment explanation
Indices: 11921218--11921265 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
11921208 TTTAATTTAT
* *
11921218 ATAATTAAATTAAATTTTACAA
1 ATAAATAAATTAAATTTTAAAA
*
11921240 ATAAATAATATTAATTTTTAAAA
1 ATAAATAA-ATTAAATTTTAAAA
11921263 ATA
1 ATA
11921266 TTTATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAAATAAATTAAATTTTAAAA
Found at i:11926904 original size:2 final size:2
Alignment explanation
Indices: 11926897--11926922 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11926887 GACCGAAATA
11926897 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
11926923 TAGTTGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11928146 original size:16 final size:16
Alignment explanation
Indices: 11928102--11928149 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
11928092 ATAACTTAAA
11928102 TTCAACACTTAATTTT
1 TTCAACACTTAATTTT
11928118 TT-AGTA-AC-T-ATTTT
1 TTCA--ACACTTAATTTT
11928132 TTCAACACTTAATTTT
1 TTCAACACTTAATTTT
11928148 TT
1 TT
11928150 AATTTATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
13 1 0.04
14 9 0.35
15 4 0.15
16 11 0.42
17 1 0.04
ACGTcount: A:0.29, C:0.15, G:0.02, T:0.54
Consensus pattern (16 bp):
TTCAACACTTAATTTT
Found at i:11938260 original size:2 final size:2
Alignment explanation
Indices: 11938253--11938277 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11938243 TTTGAGGTGA
11938253 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11938278 CTTATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11938807 original size:21 final size:22
Alignment explanation
Indices: 11938777--11938821 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
11938767 ATATTGAGAT
11938777 AATATTATTATATT-AAATATAA
1 AATATTATTAT-TTGAAATATAA
*
11938799 AATA-TATTATTTGTAATATAA
1 AATATTATTATTTGAAATATAA
11938820 AA
1 AA
11938822 GATTTCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 15 0.71
22 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AATATTATTATTTGAAATATAA
Found at i:11947751 original size:3 final size:3
Alignment explanation
Indices: 11947728--11947786 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
11947718 CCCATCATAC
* *
11947728 ATT AAT ATT -TT ATT TTT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11947774 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
11947787 AAGTTATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 4 0.08
3 46 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:11947793 original size:23 final size:23
Alignment explanation
Indices: 11947747--11947795 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
11947737 TTATTTTTAT
*
11947747 TATTATTATTATTATTATTATTA
1 TATTATTATTATTATTATAATTA
11947770 TATTATTATTATTATTA-AAGTTA
1 TATTATTATTATTATTATAA-TTA
11947793 TAT
1 TAT
11947796 AATAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TATTATTATTATTATTATAATTA
Found at i:11948721 original size:31 final size:29
Alignment explanation
Indices: 11948649--11948722 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
11948639 ACAAAATAAT
* **
11948649 AACATAAGTAACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATGGCA
*
11948678 AGCATAAGTGACTAAAATGTAACATGAGGCA
1 AACATAAGTGACTAAAATGTAACAT--GGCA
*
11948709 AACAAAAGTGACTA
1 AACATAAGTGACTA
11948723 TTTTTATAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 23 0.62
31 14 0.38
ACGTcount: A:0.50, C:0.14, G:0.15, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATGGCA
Found at i:11949269 original size:43 final size:43
Alignment explanation
Indices: 11949161--11949343 Score: 249
Period size: 43 Copynumber: 4.2 Consensus size: 43
11949151 TTATGCGAAA
* * * * * *
11949161 AAGCGCCGCTAAATGTCATGTTCTTTAGCGACGCTTTTTCGCAT
1 AAGCGCCGCTGAAGGCCATGTTCTTTAGCGGCGCTTTCTC-CAC
*
11949205 AAACGCCGCTGAAGGCCATGTTCTTTAGCGGCGCTTTCTCCAC
1 AAGCGCCGCTGAAGGCCATGTTCTTTAGCGGCGCTTTCTCCAC
*
11949248 AAGCGCCGCTGAAGGCCATGTTCGTTAGCGGCGCTTTCTCCAC
1 AAGCGCCGCTGAAGGCCATGTTCTTTAGCGGCGCTTTCTCCAC
* * * *
11949291 AAACGCCGCTGAAGGCCATGTTCTTTAGTGGCGCTTTATCCAA
1 AAGCGCCGCTGAAGGCCATGTTCTTTAGCGGCGCTTTCTCCAC
11949334 AAGCGCCGCT
1 AAGCGCCGCT
11949344 AATATAACAG
Statistics
Matches: 124, Mismatches: 15, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
43 90 0.73
44 34 0.27
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.27
Consensus pattern (43 bp):
AAGCGCCGCTGAAGGCCATGTTCTTTAGCGGCGCTTTCTCCAC
Found at i:11949324 original size:86 final size:87
Alignment explanation
Indices: 11949142--11949345 Score: 277
Period size: 86 Copynumber: 2.3 Consensus size: 87
11949132 CCGCAAAAAA
* * * * * *
11949142 TAGCGGCG-TTTATGCGAAAAAGCGCCGCTAAATGTCATGTTCTTTAGCGACGCTTTTTCGCATA
1 TAGCGGCGCTTTAT-C-CAAAAGCGCCGCTAAAGGCCATGTTCGTTAGCGACGCTTTCTCGCACA
11949206 AACGCCGCTGAAGGCCATGTTCTT
64 AACGCCGCTGAAGGCCATGTTCTT
* * * *
11949230 TAGCGGCGCTTTCTCCACAAGCGCCGCTGAAGGCCATGTTCGTTAGCGGCGCTTTCTC-CACAAA
1 TAGCGGCGCTTTATCCAAAAGCGCCGCTAAAGGCCATGTTCGTTAGCGACGCTTTCTCGCACAAA
11949294 CGCCGCTGAAGGCCATGTTCTT
66 CGCCGCTGAAGGCCATGTTCTT
*
11949316 TAGTGGCGCTTTATCCAAAAGCGCCGCTAA
1 TAGCGGCGCTTTATCCAAAAGCGCCGCTAA
11949346 TATAACAGAT
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
86 53 0.52
87 35 0.35
88 9 0.09
89 4 0.04
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (87 bp):
TAGCGGCGCTTTATCCAAAAGCGCCGCTAAAGGCCATGTTCGTTAGCGACGCTTTCTCGCACAAA
CGCCGCTGAAGGCCATGTTCTT
Found at i:11950574 original size:15 final size:15
Alignment explanation
Indices: 11950554--11950584 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11950544 TTTGATAGTT
*
11950554 CAAATTTAGTATTTA
1 CAAATTCAGTATTTA
11950569 CAAATTCAGTATTTA
1 CAAATTCAGTATTTA
11950584 C
1 C
11950585 TCCTATGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (15 bp):
CAAATTCAGTATTTA
Found at i:11950961 original size:22 final size:22
Alignment explanation
Indices: 11950933--11950990 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
11950923 AAGACAACTC
11950933 TGCTTACAGTTTTCCTTCTTGT
1 TGCTTACAGTTTTCCTTCTTGT
11950955 TGCTTACAGTTTTCCTTCTTGT
1 TGCTTACAGTTTTCCTTCTTGT
11950977 TGCTTACAGTTTTC
1 TGCTTACAGTTTTC
11950991 AAACCCGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.10, C:0.22, G:0.14, T:0.53
Consensus pattern (22 bp):
TGCTTACAGTTTTCCTTCTTGT
Found at i:11951279 original size:26 final size:27
Alignment explanation
Indices: 11951249--11951322 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 27
11951239 TATAATAAAG
11951249 TTTAATTAAATATTATGTTTAATTTT-
1 TTTAATTAAATATTATGTTTAATTTTA
* * *
11951275 TTTAAATAATTATTAATG-AT-ATTTTA
1 TTTAATTAAATATT-ATGTTTAATTTTA
* *
11951301 TTAAATTAAA-ATAATGTTTAAT
1 TTTAATTAAATATTATGTTTAAT
11951323 AAACAGAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
24 3 0.08
25 8 0.22
26 22 0.61
27 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
TTTAATTAAATATTATGTTTAATTTTA
Found at i:11952139 original size:41 final size:41
Alignment explanation
Indices: 11952070--11952533 Score: 405
Period size: 41 Copynumber: 11.3 Consensus size: 41
11952060 TTTAAATAAA
*
11952070 TTAGCGGCGC-TTATGGGAAAGCGCCGCTAATGACCTGACCT
1 TTAGCGGCGCTTTA-GTGAAAGCGCCGCTAATGACCTGACCT
* * *
11952111 TTAGCGGCGCTTTAGTAAAAGTGTCGCTAAATGATCCT-ACCT
1 TTAGCGGCGCTTTAGTGAAAGCGCCGCT-AATGA-CCTGACCT
** *
11952153 TTAGCGGCGCTTGGGGGAAAGCGCCGCTAATGA-CTCGACCTT
1 TTAGCGGCGCTTTAGTGAAAGCGCCGCTAATGACCT-GACC-T
* * *
11952195 TTAGTGGCGCTTTAGGGAAAGCGCCGCTAATGATCAT-ACCT
1 TTAGCGGCGCTTTAGTGAAAGCGCCGCTAATGA-CCTGACCT
* * *
11952236 TTAGCGGCGCTTAAGGGAAAGCGCCGCTAATTACCTGACCT
1 TTAGCGGCGCTTTAGTGAAAGCGCCGCTAATGACCTGACCT
* *
11952277 TTAGCGGCGCTTGAGTGAAAGCGCCGCTAATTACCCT-ACCT
1 TTAGCGGCGCTTTAGTGAAAGCGCCGCTAATGA-CCTGACCT
* * * * * *
11952318 TTAGCGGTGCATTAGAGAAAGCACCGCTAATGACTTGAACT
1 TTAGCGGCGCTTTAGTGAAAGCGCCGCTAATGACCTGACCT
* *
11952359 TTAGCGGCGCTTTA-TCACAAGCACCGCTAATGACCTGACCT
1 TTAGCGGCGCTTTAGTGA-AAGCGCCGCTAATGACCTGACCT
* * *
11952400 TTACCGGCACTTGT-GGGTAAAGCGCCGCTAATGACCCT-ACCT
1 TTAGCGGCGCTT-TAGTG-AAAGCGCCGCTAATGA-CCTGACCT
* * *
11952442 TTAGCGGCGC-TT-GTGTTAAGCGCCGCTAATG-CTTTACCT
1 TTAGCGGCGCTTTAGTG-AAAGCGCCGCTAATGACCTGACCT
* * * * *
11952481 TTTGCGGCGCATTAAG-AAAAGCGCCGCTAATG-CTTTACCT
1 TTAGCGGCGC-TTTAGTGAAAGCGCCGCTAATGACCTGACCT
*
11952521 TTTGCGGCGCTTT
1 TTAGCGGCGCTTT
11952534 GTTTCCAAAC
Statistics
Matches: 354, Mismatches: 49, Indels: 42
0.80 0.11 0.09
Matches are distributed among these distances:
38 2 0.01
39 17 0.05
40 55 0.16
41 173 0.49
42 99 0.28
43 7 0.02
44 1 0.00
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (41 bp):
TTAGCGGCGCTTTAGTGAAAGCGCCGCTAATGACCTGACCT
Found at i:11952227 original size:83 final size:81
Alignment explanation
Indices: 11952070--11952533 Score: 458
Period size: 82 Copynumber: 5.7 Consensus size: 81
11952060 TTTAAATAAA
* *
11952070 TTAGCGGCGCTTATGGGAAAGCGCCGCTAATGAC-CTGACCTTTAGCGGCGCTTTAGTAAAAGTG
1 TTAGCGGCGCTTA-GGGAAAGCGCCGCTAATGACTC-GACCTTTAGCGGCGCTTTAGTGAAAGCG
*
11952134 TCGCTAAATGATCCTACCT
64 CCGCT-AATGATCCTACCT
* * *
11952153 TTAGCGGCGCTTGGGGGAAAGCGCCGCTAATGACTCGACCTTTTAGTGGCGCTTTAGGGAAAGCG
1 TTAGCGGCGCTT-AGGGAAAGCGCCGCTAATGACTCGACC-TTTAGCGGCGCTTTAGTGAAAGCG
*
11952218 CCGCTAATGATCATACCT
64 CCGCTAATGATCCTACCT
* *
11952236 TTAGCGGCGCTTAAGGGAAAGCGCCGCTAATTAC-CTGACCTTTAGCGGCGCTTGAGTGAAAGCG
1 TTAGCGGCGCTT-AGGGAAAGCGCCGCTAATGACTC-GACCTTTAGCGGCGCTTTAGTGAAAGCG
* *
11952300 CCGCTAATTACCCTACCT
64 CCGCTAATGATCCTACCT
* * * * * * *
11952318 TTAGCGGTGCATTAGAGAAAGCACCGCTAATGACTTGAACTTTAGCGGCGCTTTA-TCACAAGCA
1 TTAGCGGCGC-TTAGGGAAAGCGCCGCTAATGACTCGACCTTTAGCGGCGCTTTAGTGA-AAGCG
11952382 CCGCTAATGA-CCTGACCT
64 CCGCTAATGATCCT-ACCT
* * * * * *
11952400 TTACCGGCACTTGTGGGTAAAGCGCCGCTAATGACCCTACCTTTAGCGGCGC-TT-GTGTTAAGC
1 TTAGCGGCGCTT-AGGG-AAAGCGCCGCTAATGACTCGACCTTTAGCGGCGCTTTAGTG-AAAGC
* *
11952463 GCCGCTAATGCT-TTACCT
63 GCCGCTAATGATCCTACCT
* * * ** *
11952481 TTTGCGGCGCATTAAGAAAAGCGCCGCTAATG-CTTTACCTTTTGCGGCGCTTT
1 TTAGCGGCGC-TTAGGGAAAGCGCCGCTAATGACTCGACCTTTAGCGGCGCTTT
11952534 GTTTCCAAAC
Statistics
Matches: 316, Mismatches: 50, Indels: 33
0.79 0.13 0.08
Matches are distributed among these distances:
79 15 0.05
80 17 0.05
81 19 0.06
82 126 0.40
83 114 0.36
84 25 0.08
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (81 bp):
TTAGCGGCGCTTAGGGAAAGCGCCGCTAATGACTCGACCTTTAGCGGCGCTTTAGTGAAAGCGCC
GCTAATGATCCTACCT
Found at i:11957650 original size:30 final size:30
Alignment explanation
Indices: 11957599--11957656 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
11957589 TTTAATAATA
**
11957599 TGTAATTTTATACATGTAATTTTGATTTTT
1 TGTAATTTTATACATAAAATTTTGATTTTT
* *
11957629 TGTATTTTTATACATAAAATTTTTATTT
1 TGTAATTTTATACATAAAATTTTGATTT
11957657 GATCCAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.60
Consensus pattern (30 bp):
TGTAATTTTATACATAAAATTTTGATTTTT
Found at i:11958790 original size:3 final size:3
Alignment explanation
Indices: 11958777--11958810 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
11958767 AGTTCCCGCA
*
11958777 CTT CAT CTT CTT CTT CTT CTT CTT CTT CTT -TT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
11958811 AATAAAACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:11963392 original size:16 final size:16
Alignment explanation
Indices: 11963361--11963407 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
11963351 AACATTTACT
11963361 TAATTATAAAATTTTAAA
1 TAATTA-AAAA-TTTAAA
11963379 TAATTAAAAATTTAAA
1 TAATTAAAAATTTAAA
*
11963395 -AAATAACAAATTT
1 TAATTAA-AAATTT
11963408 TTTTATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 5 0.19
16 12 0.44
17 4 0.15
18 6 0.22
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATTAAAAATTTAAA
Found at i:11965153 original size:14 final size:15
Alignment explanation
Indices: 11965117--11965153 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
11965107 GGCATCTCCA
11965117 TTTTTTC-TCTTCTC
1 TTTTTTCTTCTTCTC
11965131 TTTTTTCTTCTTCT-
1 TTTTTTCTTCTTCTC
11965145 TTTTTTCTT
1 TTTTTTCTT
11965154 TTTTTTCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTCTTCTTCTC
Found at i:11965459 original size:12 final size:11
Alignment explanation
Indices: 11965433--11965466 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
11965423 ACTCAATTAT
11965433 AAAATATTTAA
1 AAAATATTTAA
11965444 AAAATATTTAA
1 AAAATATTTAA
11965455 AAAA-A-TTAA
1 AAAATATTTAA
11965464 AAA
1 AAA
11965467 TGATTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 7 0.30
10 1 0.04
11 15 0.65
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAATATTTAA
Found at i:11965680 original size:15 final size:15
Alignment explanation
Indices: 11965642--11965680 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
11965632 TTAAAAACTT
*
11965642 AAATTTTTAAAATAA
1 AAATTTTTATAATAA
*
11965657 AAA-TTTTATTATAA
1 AAATTTTTATAATAA
11965671 AAATTTTTAT
1 AAATTTTTAT
11965681 GAATTTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATTTTTATAATAA
Found at i:11967443 original size:359 final size:359
Alignment explanation
Indices: 11966784--11967502 Score: 1429
Period size: 359 Copynumber: 2.0 Consensus size: 359
11966774 ACACAAACTC
11966784 AATAAAACACTTAAATAATACTAAAAATACTATCACACACATATGCTTTGTGAAAACCACGGATT
1 AATAAAACACTTAAATAATACTAAAAATACTATCACACACATATGCTTTGTGAAAACCACGGATT
11966849 TAGAACACAGATGTGTGTTAAAAATAACATACAATAAACAATAAAACGTATAGTTTAAAACTAAT
66 TAGAACACAGATGTGTGTTAAAAATAACATACAATAAACAATAAAACGTATAGTTTAAAACTAAT
11966914 TAATCGTAATAACAAATGAGATATGTGTTGCATAAAATAAAAAAATTAGATTAAATTATTAGTAA
131 TAATCGTAATAACAAATGAGATATGTGTTGCATAAAATAAAAAAATTAGATTAAATTATTAGTAA
11966979 AACGAAATTTAAACACATAAATACATAAGATGAACAATACTAAATGCACTACAATTATTTTTCAT
196 AACGAAATTTAAACACATAAATACATAAGATGAACAATACTAAATGCACTACAATTATTTTTCAT
11967044 GGTTTCATTATCAATTGTGATTTTGTGTTAAGTTGACACGTGACACTAACTTAATTAACAATGCT
261 GGTTTCATTATCAATTGTGATTTTGTGTTAAGTTGACACGTGACACTAACTTAATTAACAATGCT
11967109 AATCCAATTGATGTGGGTTCAAATCTCACCATAT
326 AATCCAATTGATGTGGGTTCAAATCTCACCATAT
11967143 AATAAAACACTTAAATAATACTAAAAATACTATCACACACATATGCTTTGTGAAAACCACGGATT
1 AATAAAACACTTAAATAATACTAAAAATACTATCACACACATATGCTTTGTGAAAACCACGGATT
*
11967208 TAGAACACAGATGTGTGTTAAAAATAACATACAATAAACAATAAAACGTATGGTTTAAAACTAAT
66 TAGAACACAGATGTGTGTTAAAAATAACATACAATAAACAATAAAACGTATAGTTTAAAACTAAT
11967273 TAATCGTAATAACAAATGAGATATGTGTTGCATAAAATAAAAAAATTAGATTAAATTATTAGTAA
131 TAATCGTAATAACAAATGAGATATGTGTTGCATAAAATAAAAAAATTAGATTAAATTATTAGTAA
11967338 AACGAAATTTAAACACATAAATACATAAGATGAACAATACTAAATGCACTACAATTATTTTTCAT
196 AACGAAATTTAAACACATAAATACATAAGATGAACAATACTAAATGCACTACAATTATTTTTCAT
11967403 GGTTTCATTATCAATTGTGATTTTGTGTTAAGTTGACACGTGACACTAACTTAATTAACAATGCT
261 GGTTTCATTATCAATTGTGATTTTGTGTTAAGTTGACACGTGACACTAACTTAATTAACAATGCT
11967468 AATCCAATTGATGTGGGTTCAAATCTCACCATAT
326 AATCCAATTGATGTGGGTTCAAATCTCACCATAT
11967502 A
1 A
11967503 CATATTTTAT
Statistics
Matches: 359, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
359 359 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (359 bp):
AATAAAACACTTAAATAATACTAAAAATACTATCACACACATATGCTTTGTGAAAACCACGGATT
TAGAACACAGATGTGTGTTAAAAATAACATACAATAAACAATAAAACGTATAGTTTAAAACTAAT
TAATCGTAATAACAAATGAGATATGTGTTGCATAAAATAAAAAAATTAGATTAAATTATTAGTAA
AACGAAATTTAAACACATAAATACATAAGATGAACAATACTAAATGCACTACAATTATTTTTCAT
GGTTTCATTATCAATTGTGATTTTGTGTTAAGTTGACACGTGACACTAACTTAATTAACAATGCT
AATCCAATTGATGTGGGTTCAAATCTCACCATAT
Found at i:11969686 original size:15 final size:16
Alignment explanation
Indices: 11969613--11969686 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
11969603 TACTCAATTA
* *
11969613 TAAAATCTTTAAAAAA
1 TAAAATTTTTAAAAAC
* *
11969629 T-AATTTTTTAAAAAAT
1 TAAAATTTTT-AAAAAC
*
11969645 TAAAAATTATTAAAAAC
1 T-AAAATTTTTAAAAAC
* *
11969662 TAAAAGTTTTAAAGA-
1 TAAAATTTTTAAAAAC
11969677 TAAAATTTTT
1 TAAAATTTTT
11969687 TATTATAACA
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
15 15 0.33
16 18 0.40
17 6 0.13
18 6 0.13
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
TAAAATTTTTAAAAAC
Found at i:11973268 original size:18 final size:18
Alignment explanation
Indices: 11973247--11973291 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
11973237 TAATTTTATA
*
11973247 ATATATTATATTATTTTT
1 ATATATTATAGTATTTTT
*
11973265 ATATATTATGGTATTTTT
1 ATATATTATAGTATTTTT
*
11973283 -TATAATATA
1 ATATATTATA
11973292 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
ATATATTATAGTATTTTT
Found at i:11973403 original size:23 final size:23
Alignment explanation
Indices: 11973364--11973412 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
11973354 TATAATTTAT
* *
11973364 TAAATTTTAAATTAAAAATAATA
1 TAAATTTTAAATAAAAAATAAAA
*
11973387 TAAATATTTAAA-AAAAATTAAAA
1 TAAAT-TTTAAATAAAAAATAAAA
11973410 TAA
1 TAA
11973413 TGTGGACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAATTTTAAATAAAAAATAAAA
Found at i:11974404 original size:2 final size:2
Alignment explanation
Indices: 11974397--11974422 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11974387 TAATATGTCA
11974397 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
11974423 GATTAAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11974998 original size:6 final size:6
Alignment explanation
Indices: 11974985--11975015 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
11974975 GAATCATTTC
11974985 AATT-T AATTAT AATTAT AATTAT AATTAT AA
1 AATTAT AATTAT AATTAT AATTAT AATTAT AA
11975016 ACTTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:11978242 original size:3 final size:3
Alignment explanation
Indices: 11978234--11978272 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
11978224 AATCATGTCA
11978234 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11978273 TACAATTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11983958 original size:13 final size:13
Alignment explanation
Indices: 11983910--11983961 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
11983900 TTTGGGATCT
*
11983910 AAATTTTAAATTC
1 AAATTTTGAATTC
* *
11983923 AAATATTGAACATTA
1 AAATTTTG-A-ATTC
11983938 AAATTTTGAATTC
1 AAATTTTGAATTC
11983951 AAATTTTGAAT
1 AAATTTTGAAT
11983962 CTTGAGATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 20 0.62
14 2 0.06
15 10 0.31
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (13 bp):
AAATTTTGAATTC
Found at i:11983997 original size:21 final size:20
Alignment explanation
Indices: 11983968--11984013 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
11983958 GAATCTTGAG
*
11983968 ATTTGGAGTTCAAAATTTAAA
1 ATTTAGAGTTC-AAATTTAAA
* *
11983989 ATTTAGAGTTCGAGTTTAAA
1 ATTTAGAGTTCAAATTTAAA
11984009 ATTTA
1 ATTTA
11984014 AAATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.41
Consensus pattern (20 bp):
ATTTAGAGTTCAAATTTAAA
Found at i:11984604 original size:19 final size:19
Alignment explanation
Indices: 11984582--11984626 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
11984572 TTATATTAGG
11984582 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
11984601 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
11984620 ATTTAAT
1 ATTTAAT
11984627 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:11991362 original size:16 final size:16
Alignment explanation
Indices: 11991338--11991368 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11991328 CAAATGTCTA
11991338 TTTTAGTAATTAATTT
1 TTTTAGTAATTAATTT
*
11991354 TTTTTGTAATTAATT
1 TTTTAGTAATTAATT
11991369 ATTATTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTTAGTAATTAATTT
Found at i:11994776 original size:44 final size:44
Alignment explanation
Indices: 11994713--11994796 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
11994703 CTGAAAAAAA
11994713 ATAAAGGTGGCCAAAAACCTATTAATGATTAACATTAACAGAAG
1 ATAAAGGTGGCCAAAAACCTATTAATGATTAACATTAACAGAAG
11994757 ATAAAGGTGGCCAAAAACCTATTAATGATTAACATTAACA
1 ATAAAGGTGGCCAAAAACCTATTAATGATTAACATTAACA
11994797 CTTCTGTGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (44 bp):
ATAAAGGTGGCCAAAAACCTATTAATGATTAACATTAACAGAAG
Found at i:12003863 original size:39 final size:37
Alignment explanation
Indices: 12003789--12003864 Score: 109
Period size: 37 Copynumber: 2.0 Consensus size: 37
12003779 CAACTTAATG
*
12003789 ACACTAATTCAATTAAAAAATTACACAAACTAATTTA
1 ACACTAATTCAATTAAAAAATTACAAAAACTAATTTA
12003826 ACACTAATTCAATTAAAAAAATTACATAAAAAC-AATTTA
1 ACACTAATTCAATT-AAAAAATTAC--AAAAACTAATTTA
12003865 TGTATTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
37 14 0.40
38 10 0.29
39 6 0.17
40 5 0.14
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (37 bp):
ACACTAATTCAATTAAAAAATTACAAAAACTAATTTA
Found at i:12005123 original size:27 final size:30
Alignment explanation
Indices: 12005063--12005123 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
12005053 TTAAAATTAC
* *
12005063 ACATGAATTTTGATTTAATGTGTAATTTGAT
1 ACATGAACTTTGATTT-AGGTGTAATTTGAT
12005094 ACATGAACTTTGATTT-GGTGT-ATTT-AT
1 ACATGAACTTTGATTTAGGTGTAATTTGAT
12005121 ACA
1 ACA
12005124 CATAAAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.18
28 4 0.14
29 4 0.14
31 15 0.54
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (30 bp):
ACATGAACTTTGATTTAGGTGTAATTTGAT
Found at i:12005358 original size:29 final size:30
Alignment explanation
Indices: 12005316--12005382 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
12005306 GATTAAATAA
* *
12005316 AAAATTCATATATAAAATTACACA-AAATC
1 AAAATTTATATATAAAATTACAAATAAATC
* **
12005345 AAAATTTATTTATATGATTACAAATTAAATC
1 AAAATTTATATATAAAATTACAAA-TAAATC
12005376 AAAATTT
1 AAAATTT
12005383 GTGTATAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 19 0.61
31 12 0.39
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAATTTATATATAAAATTACAAATAAATC
Found at i:12009044 original size:17 final size:18
Alignment explanation
Indices: 12009004--12009048 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
12008994 TATTTGAATA
* *
12009004 TGTATTTACAATTTATTT
1 TGTATTTATAATTTATAT
*
12009022 TCTATTTATAA-TTATAT
1 TGTATTTATAATTTATAT
12009039 TGTATTTATA
1 TGTATTTATA
12009049 TATATAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (18 bp):
TGTATTTATAATTTATAT
Found at i:12014490 original size:30 final size:30
Alignment explanation
Indices: 12014466--12014523 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
12014456 GATTTACGTG
12014466 TAATTGTATACAT-AAATTTTGATTTGATA
1 TAATTGTATACATAAAATTTTGATTTGATA
* *
12014495 TATTTTTATACATAAAATTTTGATTTGAT
1 TAATTGTATACATAAAATTTTGATTTGAT
12014524 CCAATTATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (30 bp):
TAATTGTATACATAAAATTTTGATTTGATA
Found at i:12015068 original size:2 final size:2
Alignment explanation
Indices: 12015061--12015123 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
12015051 TTTCAATGAT
12015061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12015103 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
12015124 TTGTTAATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12019639 original size:6 final size:6
Alignment explanation
Indices: 12019628--12019666 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
12019618 TGAGCAAAAT
* * *
12019628 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
12019667 TATGAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:12020716 original size:23 final size:23
Alignment explanation
Indices: 12020664--12020718 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
12020654 TTTATTTTTT
*
12020664 ATATAAT-TTAAAATGAAATATA
1 ATATAATATTAAAATGAAAAATA
*
12020686 ATAAAATATTAAAAT-AACAAATA
1 ATATAATATTAAAATGAA-AAATA
*
12020709 TTATAATATT
1 ATATAATATT
12020719 TAATTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
ATATAATATTAAAATGAAAAATA
Found at i:12023709 original size:2 final size:2
Alignment explanation
Indices: 12023702--12023728 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12023692 ATTATTGGAA
12023702 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
12023729 CATTTCCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:12025896 original size:3 final size:3
Alignment explanation
Indices: 12025888--12025919 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12025878 TTTGGACCGT
12025888 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12025920 CATAATGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12028555 original size:75 final size:75
Alignment explanation
Indices: 12028426--12028666 Score: 319
Period size: 75 Copynumber: 3.3 Consensus size: 75
12028416 TGAACCATGA
* * *
12028426 CTCCATTTTGAGAAGCTTGCTG---ATTTCTAAGATCTTCTTGGAGCCAACTGTTGGTAAAAGAG
1 CTCCATTTTGAGAAGCTTGCTGATCATTTCTATGATCTTCTTGAAACCAACTGTTGGTAAAAGAG
12028488 ACACCATTGG
66 ACACCATTGG
* * * * *
12028498 CTCCATTTTGAGAAGCTTGGTGATCATTTCGATGATTTTCTTGAAACCAACTATTGGTAAAATA-
1 CTCCATTTTGAGAAGCTTGCTGATCATTTCTATGATCTTCTTGAAACCAACTGTTGGTAAAAGAG
12028562 AGCACCATTGG
66 A-CACCATTGG
* * * * *
12028573 CTCCATTTCGAGAAGTTTTCTGATCATTTCTATGATCTTCTTGAAACCAATTGTTGGGAAAAGAG
1 CTCCATTTTGAGAAGCTTGCTGATCATTTCTATGATCTTCTTGAAACCAACTGTTGGTAAAAGAG
*
12028638 ACACCATTAG
66 ACACCATTGG
12028648 CTCCATTTTGAGAAGCTTG
1 CTCCATTTTGAGAAGCTTG
12028667 GTCTTGCGGA
Statistics
Matches: 142, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
72 21 0.15
74 1 0.01
75 119 0.84
76 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (75 bp):
CTCCATTTTGAGAAGCTTGCTGATCATTTCTATGATCTTCTTGAAACCAACTGTTGGTAAAAGAG
ACACCATTGG
Found at i:12031045 original size:22 final size:22
Alignment explanation
Indices: 12031019--12031061 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12031009 AATTTACCAG
12031019 ACTAAAGTTATAATCCCGTGAT
1 ACTAAAGTTATAATCCCGTGAT
* *
12031041 ACTAAAGTTCTAATCTCGTGA
1 ACTAAAGTTATAATCCCGTGA
12031062 CATAAGCAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (22 bp):
ACTAAAGTTATAATCCCGTGAT
Found at i:12031301 original size:24 final size:24
Alignment explanation
Indices: 12031272--12031319 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12031262 GGTATGTACA
* *
12031272 TTTTTATAATAGTATCTATTATTT
1 TTTTTAAAAAAGTATCTATTATTT
*
12031296 TTTTTAAAAAATTATCTATTATTT
1 TTTTTAAAAAAGTATCTATTATTT
12031320 CAATCGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTTAAAAAAGTATCTATTATTT
Found at i:12046252 original size:28 final size:28
Alignment explanation
Indices: 12046212--12046267 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
12046202 GAGAGATAGT
12046212 TATTTTGTCAGTGCAGTCATATTGAAGA
1 TATTTTGTCAGTGCAGTCATATTGAAGA
12046240 TATTTTGTCAGTGCAGTCATATTGAAGA
1 TATTTTGTCAGTGCAGTCATATTGAAGA
12046268 GCTAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (28 bp):
TATTTTGTCAGTGCAGTCATATTGAAGA
Found at i:12048254 original size:22 final size:21
Alignment explanation
Indices: 12048220--12048260 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
12048210 GTGTTTTTTT
* *
12048220 TTTGTTTATTTATTTGTATGGA
1 TTTGCTTAATTATTT-TATGGA
12048242 TTTGCTTAATTATTTTATG
1 TTTGCTTAATTATTTTATG
12048261 TTACTACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.20, C:0.02, G:0.15, T:0.63
Consensus pattern (21 bp):
TTTGCTTAATTATTTTATGGA
Found at i:12048839 original size:22 final size:22
Alignment explanation
Indices: 12048812--12048870 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
12048802 AGCATGGGTG
* * *
12048812 TTACAAGGAAAATTTTGGATTT
1 TTACAAGAAAAAATCTGGATTT
12048834 TTACAAGAAAAAATCTGGATTT
1 TTACAAGAAAAAATCTGGATTT
**
12048856 TTACGTGAAAAAATC
1 TTACAAGAAAAAATC
12048871 ATTTTATCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.34
Consensus pattern (22 bp):
TTACAAGAAAAAATCTGGATTT
Found at i:12049820 original size:3 final size:3
Alignment explanation
Indices: 12049812--12049848 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
12049802 TTTTTAACAC
12049812 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12049849 AGGAAACACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12051082 original size:17 final size:17
Alignment explanation
Indices: 12051060--12051092 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12051050 ACTTTGTTTT
*
12051060 TTATTTTTATTTATTTA
1 TTATTTCTATTTATTTA
12051077 TTATTTCTATTTATTT
1 TTATTTCTATTTATTT
12051093 TTTGTTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTTCTATTTATTTA
Found at i:12053476 original size:12 final size:12
Alignment explanation
Indices: 12053454--12053487 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12053444 GTGATCAAAG
12053454 TTGAAAGTGAAA
1 TTGAAAGTGAAA
* *
12053466 GTGAAATTGAAA
1 TTGAAAGTGAAA
12053478 TTGAAAGTGA
1 TTGAAAGTGA
12053488 TATGAATTGC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (12 bp):
TTGAAAGTGAAA
Found at i:12056388 original size:23 final size:22
Alignment explanation
Indices: 12056358--12056509 Score: 133
Period size: 23 Copynumber: 6.5 Consensus size: 22
12056348 ACACTAGCGC
*
12056358 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGTTTAGCACGTGT-GT
12056381 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCAC-GTGTGT
* *
12056406 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCAC-GTGTGT
* * *
12056429 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCAC-GTGTGT
*
12056452 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCAC-GTGTGT
* *
12056475 GCTCTCTGTTTCCCAGCACTTATGT
1 GCTCTCTGTTT---AGCACGTGTGT
12056500 GCTCTCTGTT
1 GCTCTCTGTT
12056510 AGTACTTTGG
Statistics
Matches: 112, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
23 72 0.64
24 1 0.01
25 31 0.28
26 8 0.07
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.43
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACGTGTGT
Found at i:12056458 original size:46 final size:47
Alignment explanation
Indices: 12056359--12056483 Score: 155
Period size: 46 Copynumber: 2.7 Consensus size: 47
12056349 CACTAGCGCG
* * *
12056359 CTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGTTATTAGCACTGTGTGTG
1 CTCTCTGATTAGCACTGTGT-GTGCTCTCTG-TATTAGCACTGTGTGTA
* * *
12056407 CTCTCTGATTAGCACTTTGTGTGCTCTCTG-ATTAGTACTTTGTGTA
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGTATTAGCACTGTGTGTA
*
12056453 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGT
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGT
12056484 TTCCCAGCAC
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
46 41 0.61
48 24 0.36
49 2 0.03
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (47 bp):
CTCTCTGATTAGCACTGTGTGTGCTCTCTGTATTAGCACTGTGTGTA
Found at i:12056523 original size:69 final size:71
Alignment explanation
Indices: 12056382--12056528 Score: 214
Period size: 69 Copynumber: 2.1 Consensus size: 71
12056372 ACGTCTCGTG
*
12056382 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTT
12056447 TGTGTA
66 TGTGTA
*
12056453 CTCTCTG-T-TTAGCACTGTGTGTGCTCTCTGTTTCCCAGCAC-TTATGTGCTCTCTG-TTAGTA
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATT---AGCACTTTATGTGCTCTCTGATTAGTA
12056514 CTTTG-GTA
63 CTTTGTGTA
12056522 CTCTCTG
1 CTCTCTG
12056529 CTTGTTCCGT
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
69 34 0.48
70 12 0.17
71 20 0.28
72 5 0.07
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.44
Consensus pattern (71 bp):
CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTT
TGTGTA
Found at i:12056526 original size:46 final size:44
Alignment explanation
Indices: 12056379--12056528 Score: 142
Period size: 46 Copynumber: 3.2 Consensus size: 44
12056369 AGCACGTCTC
12056379 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTG--ATTAGCACT-T-TGTGCTCTCTGATTAGCACTTTGT
* * *
12056427 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGTG--CTCTCTGATTAGCACTTTGT
* *
12056473 GTGCTCTCTGTTTCCCAGCACTTATGTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATT---AGCACTT-TGTGCTCTCTGATTAGCACTTTGT
*
12056519 GTACTCTCTG
1 GTGCTCTCTG
12056529 CTTGTTCCGT
Statistics
Matches: 88, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
44 4 0.05
45 1 0.01
46 47 0.53
47 9 0.10
48 17 0.19
49 6 0.07
50 4 0.05
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (44 bp):
GTGCTCTCTGATTAGCACTTTGTGCTCTCTGATTAGCACTTTGT
Found at i:12063746 original size:23 final size:23
Alignment explanation
Indices: 12063720--12063911 Score: 239
Period size: 23 Copynumber: 8.3 Consensus size: 23
12063710 ACACTAGCGC
* *
12063720 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
12063743 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
12063766 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
12063789 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
*
12063812 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* * *
12063835 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
*
12063858 GCTCTCTG-TTGCACAGCAC-TTATGT
1 GCTCTCTGATT----AGCACTTTGTGT
*
12063883 GCTCTCTG-TTAGTACTTTG-GT
1 GCTCTCTGATTAGCACTTTGTGT
*
12063904 ACTCTCTG
1 GCTCTCTG
12063912 CTTGTTCCGT
Statistics
Matches: 151, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.09
22 4 0.03
23 115 0.76
25 14 0.09
26 5 0.03
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTTGTGT
Found at i:12066115 original size:104 final size:103
Alignment explanation
Indices: 12065960--12066165 Score: 247
Period size: 104 Copynumber: 2.0 Consensus size: 103
12065950 AATTGGTTCC
* **
12065960 GAATAAGATATTCAATTATTTAGGTTCAAAGAAAAATCATACCCAACACGTTAGGGCACAA-TTC
1 GAATAAGATATTCAATTACTTAGGTTCAAAGAAAAATCATACCCAACACGTTACAGCACAATTTC
12066024 TTCGACTTCCCTAAAATAAA-AGAACATTGCCTCGATTTTT
66 -TCGACTT-CCTAAAATAAAGA-AACATTGCCTCGATTTTT
* ** * * *
12066064 GAATAGGATATTCAATTACTTAGGTTTGAAGAAAAATCGTA-CCAAGTACGTTTCAGCACAATTT
1 GAATAAGATATTCAATTACTTAGGTTCAAAGAAAAATCATACCCAA-CACGTTACAGCACAATTT
* * *
12066128 CTCGAGTTTCTTAAATAAAGAAACATTGCCTCGATTTT
65 CTCGACTTCCTAAAATAAAGAAACATTGCCTCGATTTT
12066166 GAAAATATTT
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
103 30 0.34
104 54 0.62
105 3 0.03
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (103 bp):
GAATAAGATATTCAATTACTTAGGTTCAAAGAAAAATCATACCCAACACGTTACAGCACAATTTC
TCGACTTCCTAAAATAAAGAAACATTGCCTCGATTTTT
Found at i:12066433 original size:26 final size:26
Alignment explanation
Indices: 12066404--12066471 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
12066394 GAAATATCGA
**
12066404 AAAAATAAAAAAGACTAGATTAATTT
1 AAAAATAAAAAAGAAAAGATTAATTT
*
12066430 AAAAA-AAAGAAATAAAAGATTAATTT
1 AAAAATAAA-AAAGAAAAGATTAATTT
*
12066456 -AAAATAAAAATGAAAA
1 AAAAATAAAAAAGAAAA
12066472 TTTTGGGGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
25 13 0.37
26 22 0.63
ACGTcount: A:0.69, C:0.01, G:0.07, T:0.22
Consensus pattern (26 bp):
AAAAATAAAAAAGAAAAGATTAATTT
Found at i:12066540 original size:30 final size:30
Alignment explanation
Indices: 12066506--12066603 Score: 117
Period size: 30 Copynumber: 3.3 Consensus size: 30
12066496 AGGAAAAATA
**
12066506 GGGTCAAAAACAAAATTTTGGAAAGTTTAG
1 GGGTCAAAAATGAAATTTTGGAAAGTTTAG
*
12066536 GGGTCAAAAATGAAATTTTGGAAAG-TTAA
1 GGGTCAAAAATGAAATTTTGGAAAGTTTAG
* ** * *
12066565 GGGTTAAATTTGAATTTTTAGAAAGTTTAG
1 GGGTCAAAAATGAAATTTTGGAAAGTTTAG
12066595 GGGTCAAAA
1 GGGTCAAAA
12066604 TATCATTTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 23 0.41
30 33 0.59
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGTCAAAAATGAAATTTTGGAAAGTTTAG
Found at i:12066614 original size:30 final size:31
Alignment explanation
Indices: 12066521--12066614 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 31
12066511 AAAAACAAAA
* *
12066521 TTTTGGAAAGTTTAGGGGTCAAAA-ATGAAA
1 TTTTAGAAAGTTTAGGGGTCAAAATATGAAT
* * * *
12066551 TTTTGGAAAG-TTAAGGGT-TAAATTTGAAT
1 TTTTAGAAAGTTTAGGGGTCAAAATATGAAT
*
12066580 TTTTAGAAAGTTTAGGGGTCAAAATAT-CAT
1 TTTTAGAAAGTTTAGGGGTCAAAATATGAAT
12066610 TTTTA
1 TTTTA
12066615 AATAAAACAA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
28 3 0.06
29 20 0.38
30 24 0.46
31 5 0.10
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.38
Consensus pattern (31 bp):
TTTTAGAAAGTTTAGGGGTCAAAATATGAAT
Found at i:12071993 original size:21 final size:21
Alignment explanation
Indices: 12071969--12072021 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
12071959 TTGTGCTAAC
*
12071969 TCTACCGATACAAGT-ATGGA
1 TCTACCGATACAAGTCATGCA
* *
12071989 TTCTATCAATACAAGTCATGCA
1 -TCTACCGATACAAGTCATGCA
*
12072011 ACTACCGATAC
1 TCTACCGATAC
12072022 CAAAAACTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (21 bp):
TCTACCGATACAAGTCATGCA
Found at i:12072099 original size:21 final size:22
Alignment explanation
Indices: 12072075--12072137 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 22
12072065 CGATATAAGC
12072075 ATACAAACTACCGATACAT-TA
1 ATACAAACTACCGATACATGTA
* *
12072096 ATACTAAAAACTACCAATACTTGTA
1 ATAC---AAACTACCGATACATGTA
*
12072121 ATTC-AACTACCGATACA
1 ATACAAACTACCGATACA
12072138 ACTCAAGTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
21 15 0.45
24 13 0.39
25 5 0.15
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.25
Consensus pattern (22 bp):
ATACAAACTACCGATACATGTA
Found at i:12076023 original size:22 final size:23
Alignment explanation
Indices: 12075987--12076029 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
12075977 ATTTTTTTAT
12075987 AAAAATATTAAAAATT-TAAAAG
1 AAAAATATTAAAAATTATAAAAG
12076009 AAAAATA-TATAAAATTATAAA
1 AAAAATATTA-AAAATTATAAA
12076030 TTATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 2 0.11
22 13 0.68
23 4 0.21
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAAATATTAAAAATTATAAAAG
Found at i:12077026 original size:2 final size:2
Alignment explanation
Indices: 12077019--12077069 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
12077009 CCTTGTACCT
12077019 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12077061 TC TC TC TC T
1 TC TC TC TC T
12077070 TCAAGCACAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:12085999 original size:16 final size:16
Alignment explanation
Indices: 12085990--12086093 Score: 83
Period size: 16 Copynumber: 6.4 Consensus size: 16
12085980 TATTCAATTT
12085990 TTTATATATTATATTA
1 TTTATATATTATATTA
12086006 TTTATATATTATATCTA
1 TTTATATATTATAT-TA
*
12086023 TTT-TATTTTATATATA
1 TTTATATATTATAT-TA
*
12086039 TTCTAAATATT-TGATATA
1 TT-TATATATTAT-AT-TA
*
12086057 TTTTTATA-T-TATT-
1 TTTATATATTATATTA
12086070 TTTATATATTATTATTA
1 TTTATATATTA-TATTA
*
12086087 TATATAT
1 TTTATAT
12086094 TTTTATTTCT
Statistics
Matches: 72, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
13 7 0.10
14 2 0.03
15 2 0.03
16 33 0.46
17 17 0.24
18 11 0.15
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (16 bp):
TTTATATATTATATTA
Found at i:12086002 original size:29 final size:30
Alignment explanation
Indices: 12085956--12086012 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
12085946 CTTTTGGTTT
12085956 AATTTATTAATATGTATAATA-TTATATTC
1 AATTTATTAATATGTATAATATTTATATTC
* *
12085985 AATTTTTTATATAT-TATATTATTTATAT
1 AATTTATTA-ATATGTATAATATTTATAT
12086013 ATTATATCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (30 bp):
AATTTATTAATATGTATAATATTTATATTC
Found at i:12086015 original size:11 final size:11
Alignment explanation
Indices: 12085999--12086095 Score: 64
Period size: 11 Copynumber: 8.9 Consensus size: 11
12085989 TTTTATATAT
12085999 TATATTATTTA
1 TATATTATTTA
* *
12086010 TATATTATATC
1 TATATTATTTA
*
12086021 TATTTTATTT-
1 TATATTATTTA
12086031 TATATATATTCTA
1 TATAT-TATT-TA
12086044 -A-A-TATTTGA
1 TATATTATTT-A
12086053 TATATT-TTTA
1 TATATTATTTA
12086063 TATTATT-TTTA
1 TA-TATTATTTA
12086074 TATATTA-TTA
1 TATATTATTTA
12086084 TTATATATATTT
1 -TATAT-TATTT
12086096 TTATTTCTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
8 1 0.01
9 5 0.07
10 15 0.22
11 41 0.59
12 5 0.07
13 2 0.03
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (11 bp):
TATATTATTTA
Found at i:12090308 original size:17 final size:18
Alignment explanation
Indices: 12090266--12090308 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
12090256 AAAAGTTATG
12090266 ATAATTATATATTTAAAA
1 ATAATTATATATTTAAAA
*
12090284 ATATTTATA-ATTTAATAA
1 ATAATTATATATTTAA-AA
12090302 A-AATTAT
1 ATAATTAT
12090309 GTTGACTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAATTATATATTTAAAA
Found at i:12091677 original size:35 final size:36
Alignment explanation
Indices: 12091641--12091711 Score: 83
Period size: 37 Copynumber: 2.0 Consensus size: 36
12091631 TCTTACCAAA
* *
12091641 TTGAA-AT-AAAAATAATATTTTTTTTAATATTAAAAT
1 TTGAATATCAAAAA-AATATTTTATTAAAT-TTAAAAT
*
12091677 TTGAATATCAAGAAAATATTTTATTAAATTTAAAA
1 TTGAATATCAAAAAAATATTTTATTAAATTTAAAA
12091712 CTACGCGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 11 0.37
37 15 0.50
38 4 0.13
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (36 bp):
TTGAATATCAAAAAAATATTTTATTAAATTTAAAAT
Found at i:12091825 original size:3 final size:3
Alignment explanation
Indices: 12091809--12091859 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
12091799 TTGTTTCAAA
*
12091809 TAT TAT TGT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12091856 TAT T
1 TAT T
12091860 TTAATTATGG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:12096496 original size:23 final size:21
Alignment explanation
Indices: 12096458--12096527 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 21
12096448 TATTTTATAG
12096458 AAAATAAATTATTTTAATATTCT
1 AAAATAAA-TATTTTAATATT-T
12096481 AATAATAAATATTTT-ATAATTT
1 AA-AATAAATATTTTAAT-ATTT
* *
12096503 AAAATATAACATTTTAATAATT
1 AAAATA-AATATTTTAATATTT
12096525 AAA
1 AAA
12096528 GTATGAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 4 0.10
22 18 0.44
23 13 0.32
24 6 0.15
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATAAATATTTTAATATTT
Found at i:12096539 original size:23 final size:22
Alignment explanation
Indices: 12096458--12096539 Score: 64
Period size: 23 Copynumber: 3.6 Consensus size: 22
12096448 TATTTTATAG
12096458 AAAATA-AATTATTTTA-ATATTCT
1 AAAATATAA-TATTTTATA-ATT-T
12096481 AATAATA-AATATTTTATAATTT
1 AA-AATATAATATTTTATAATTT
*
12096503 AAAATATAACATTTTAATAA-TT
1 AAAATATAATATTTT-ATAATTT
*
12096525 AAAGTATGAATATTT
1 AAAATAT-AATATTT
12096540 ATTTAAATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
21 4 0.08
22 18 0.35
23 22 0.43
24 7 0.14
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
AAAATATAATATTTTATAATTT
Found at i:12096540 original size:22 final size:22
Alignment explanation
Indices: 12096470--12096540 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
12096460 AATAAATTAT
12096470 TTTAAT-ATTCTAATAATA-AATA
1 TTTAATAATT-TAA-AATATAATA
* *
12096492 TTTTATAATTTAAAATATAACA
1 TTTAATAATTTAAAATATAATA
*
12096514 TTTTAATAA-TTAAAGTATGAATA
1 -TTTAATAATTTAAAATAT-AATA
12096537 TTTA
1 TTTA
12096541 TTTAAATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
21 4 0.10
22 23 0.57
23 13 0.32
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (22 bp):
TTTAATAATTTAAAATATAATA
Found at i:12096796 original size:25 final size:25
Alignment explanation
Indices: 12096742--12096796 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
12096732 TAATATCATG
* *
12096742 ATTAAATTATTATTTTATAAAATAA
1 ATTATATTATTATTTTATAAAAGAA
12096767 ATTATATTATT-TTTTA-AAAGAGAA
1 ATTATATTATTATTTTATAAA-AGAA
12096791 AGTTAT
1 A-TTAT
12096797 TAATTTATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 3 0.12
24 9 0.35
25 14 0.54
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (25 bp):
ATTATATTATTATTTTATAAAAGAA
Found at i:12112269 original size:31 final size:31
Alignment explanation
Indices: 12112234--12112297 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
12112224 TTTGAGGCTG
*
12112234 ATTCAATCTAAATCATCAAATGACCCGTTTT
1 ATTCAATCTAAATCATCAAACGACCCGTTTT
*
12112265 ATTCAATCTAAATCATCAAACGACTCGTTTT
1 ATTCAATCTAAATCATCAAACGACCCGTTTT
12112296 AT
1 AT
12112298 CATTTAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (31 bp):
ATTCAATCTAAATCATCAAACGACCCGTTTT
Found at i:12112368 original size:73 final size:73
Alignment explanation
Indices: 12112291--12112436 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
12112281 CAAACGACTC
*
12112291 GTTTTATCATTTAAAAGATAATAGCATATTAAAAATTATATAACTTTATATTAATACTTGAATCA
1 GTTTTATCATTTAAAAGATAATAGCATATTAAAAATTATATAACCTTATATTAATACTTGAATCA
12112356 AAATTGTT
66 AAATTGTT
*
12112364 GTTTTATCATTTAAAAGATAGTAGCATATTAAAAATTATATAACCTTATATTAATACTTGAATCA
1 GTTTTATCATTTAAAAGATAATAGCATATTAAAAATTATATAACCTTATATTAATACTTGAATCA
12112429 AAATTGTT
66 AAATTGTT
12112437 ACACCCCATC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (73 bp):
GTTTTATCATTTAAAAGATAATAGCATATTAAAAATTATATAACCTTATATTAATACTTGAATCA
AAATTGTT
Found at i:12117122 original size:28 final size:28
Alignment explanation
Indices: 12117099--12117152 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
12117089 ACTTTTGGAT
12117099 ACCC-GGGGGCAAAATGGT-AATTTTGG
1 ACCCTGGGGGCAAAATGGTAAATTTTGG
*
12117125 ACCCTGGGGGGAAAATGGTAAATTTTGG
1 ACCCTGGGGGCAAAATGGTAAATTTTGG
12117153 TGAAATCAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.16
27 13 0.52
28 8 0.32
ACGTcount: A:0.28, C:0.13, G:0.35, T:0.24
Consensus pattern (28 bp):
ACCCTGGGGGCAAAATGGTAAATTTTGG
Found at i:12117237 original size:30 final size:30
Alignment explanation
Indices: 12117136--12117349 Score: 164
Period size: 30 Copynumber: 7.2 Consensus size: 30
12117126 CCCTGGGGGG
* *
12117136 AAAATGGTAAATTTTGGTGAAATCAGGGTT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTT
* * *
12117166 AAAAATGG-AA-TTTT--AGAAAGTTTGGGGCT
1 -AAAATGGTAATTTTTGGTGAAA--TCGGGGTT
*
12117195 AAAATGGTAATTTTTGGTGGAATCGGGGTT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTT
*
12117225 AAAAATGG-AA-TTTT-G-GAAAGTTCGGGGGT
1 -AAAATGGTAATTTTTGGTGAAA--TCGGGGTT
* *
12117254 AAAATGGTTATTTTTGGTGAAATCGGGGTGA
1 AAAATGGTAATTTTTGGTGAAATCGGGGT-T
*
12117285 AAAATGG-AA-TTTT-G-GAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAA--TCGGGGTT
*
12117313 AAAATGGTAAATTTTGGTGAAATCGGGGTT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTT
12117343 AAAATGG
1 AAAATGG
12117350 GATTTTGGAA
Statistics
Matches: 146, Mismatches: 17, Indels: 41
0.72 0.08 0.20
Matches are distributed among these distances:
27 11 0.08
28 23 0.16
29 35 0.24
30 43 0.29
31 23 0.16
32 11 0.08
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTT
Found at i:12117375 original size:58 final size:59
Alignment explanation
Indices: 12117130--12117387 Score: 392
Period size: 59 Copynumber: 4.4 Consensus size: 59
12117120 TTTGGACCCT
* * * * *
12117130 GGGGGGAAAATGGTAAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
* *
12117189 GGGGCTAAAATGGTAATTTTTGGTGGAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
* *
12117248 GGGGGTAAAATGGTTATTTTTGGTGAAATCGGGGTGAAAAATGGAATTTTGGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
* * *
12117307 GGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTT-AAAATGGGATTTTGGAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
*
12117365 AGGGGTAAAATGGTAATTTTTGG
1 GGGGGTAAAATGGTAATTTTTGG
12117388 AAGTTTCAGG
Statistics
Matches: 181, Mismatches: 18, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
58 41 0.23
59 140 0.77
ACGTcount: A:0.32, C:0.03, G:0.33, T:0.32
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
Found at i:12117388 original size:30 final size:28
Alignment explanation
Indices: 12117167--12117417 Score: 128
Period size: 30 Copynumber: 8.6 Consensus size: 28
12117157 ATCAGGGTTA
*
12117167 AAAATGGAATTTTAGAAAGTTT-GGGGCT
1 AAAATGGAATTTTGGAAAGTTTCGGGG-T
** **
12117195 AAAATGGTAATTTTTGG-TGGAATCGGGGTT
1 AAAATGG-AA-TTTTGGAAAGTTTCGGGG-T
12117225 AAAAATGGAATTTTGGAAAG-TTCGGGGGT
1 -AAAATGGAATTTTGGAAAGTTTC-GGGGT
*
12117254 AAAATGGTTATTTTTGGTGAAA---TCGGGGT
1 AAAATGG--AATTTT-G-GAAAGTTTCGGGGT
12117283 GAAAAATGGAATTTTGGAAAG-TTCGGGGGT
1 --AAAATGGAATTTTGGAAAGTTTC-GGGGT
12117313 AAAATGGTAAATTTTGGTGAAA---TCGGGGTT
1 AAAATGG--AATTTT-G-GAAAGTTTCGGGG-T
* *
12117343 AAAATGGGATTTTGGAAAGTTTAGGGGT
1 AAAATGGAATTTTGGAAAGTTTCGGGGT
* *
12117371 AAAATGGTAATTTTTGG-AAGTTTCAGGAT
1 AAAATGG-AA-TTTTGGAAAGTTTCGGGGT
*
12117400 CAAAATGTAATTTCTGGA
1 -AAAATGGAATTT-TGGA
12117418 CTGTTTTGGG
Statistics
Matches: 177, Mismatches: 18, Indels: 54
0.71 0.07 0.22
Matches are distributed among these distances:
26 4 0.02
27 5 0.03
28 38 0.21
29 49 0.28
30 57 0.32
31 16 0.09
32 8 0.05
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTCGGGGT
Found at i:12118220 original size:20 final size:20
Alignment explanation
Indices: 12118183--12118220 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12118173 CTTTTTTATT
*
12118183 AAACCATTTCATTTATTTAA
1 AAACCATTTCATTCATTTAA
*
12118203 AAACCATTTGATTCATTT
1 AAACCATTTCATTCATTT
12118221 GGTTTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.45
Consensus pattern (20 bp):
AAACCATTTCATTCATTTAA
Found at i:12118497 original size:17 final size:16
Alignment explanation
Indices: 12118451--12118489 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
12118441 TTTTATTTGT
*
12118451 TTTATTATTATTAATA
1 TTTATTAATATTAATA
*
12118467 TTTATTAATAATTATTA
1 TTTATTAAT-ATTAATA
12118484 TTTATT
1 TTTATT
12118490 TACTATTACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTATTAATATTAATA
Found at i:12119302 original size:6 final size:6
Alignment explanation
Indices: 12119291--12119387 Score: 94
Period size: 6 Copynumber: 16.2 Consensus size: 6
12119281 TCATAATTTG
* *
12119291 ATTTAA ATTTAA ATTTAA A-ATAA ATTTAA ATAGTTGA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA ATTTAA ATTTAA
* *
12119340 A-ATAA ATTTAA ATTTAA A--TAA ATTTAAA ATTTAA ATTCAAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA ATT-TAA ATTTAA
12119387 A
1 A
12119388 ACATAAAAGT
Statistics
Matches: 75, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.05
5 8 0.11
6 47 0.63
7 11 0.15
8 5 0.07
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:12119314 original size:17 final size:17
Alignment explanation
Indices: 12119294--12119374 Score: 98
Period size: 17 Copynumber: 4.9 Consensus size: 17
12119284 TAATTTGATT
12119294 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
**
12119311 TAAATTTAAA--T-AGT
1 TAAATTTAAATTTAAAA
*
12119325 TGAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
12119342 TAAATTTAAATTT-AAA
1 TAAATTTAAATTTAAAA
12119358 TAAATTTAAAATTTAAA
1 TAAATTT-AAATTTAAA
12119375 TTCAAAATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 11 0.21
17 29 0.55
18 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:12119317 original size:23 final size:23
Alignment explanation
Indices: 12119291--12119382 Score: 98
Period size: 23 Copynumber: 3.9 Consensus size: 23
12119281 TCATAATTTG
12119291 ATTTAAATTTAAATTTAAAATAA
1 ATTTAAATTTAAATTTAAAATAA
* *
12119314 ATTTAAATAGTTGAATTTAAATTTAA
1 ATTTAAAT--TTAAATTTAAA-ATAA
*
12119340 A-ATAAATTTAAATTT-AAATAA
1 ATTTAAATTTAAATTTAAAATAA
*
12119361 ATTTAAAATTTAAATTCAAAAT
1 ATTT-AAATTTAAATTTAAAAT
12119383 TTAAAACATA
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
21 4 0.07
22 3 0.05
23 26 0.46
24 4 0.07
25 15 0.27
26 4 0.07
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTTAAATTTAAATTTAAAATAA
Found at i:12119369 original size:11 final size:11
Alignment explanation
Indices: 12119300--12119351 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
12119290 GATTTAAATT
12119300 TAAATTTAAAA
1 TAAATTTAAAA
12119311 TAAATTT-AAA
1 TAAATTTAAAA
* * **
12119321 T-AGTTGAATT
1 TAAATTTAAAA
12119331 TAAATTTAAAA
1 TAAATTTAAAA
12119342 TAAATTTAAA
1 TAAATTTAAA
12119352 TTTAAATAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
9 3 0.10
10 6 0.19
11 22 0.71
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:12120130 original size:9 final size:10
Alignment explanation
Indices: 12120108--12120132 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12120098 GGATCACCAC
12120108 AAAACGTTTA
1 AAAACGTTTA
12120118 AAAACGTTTA
1 AAAACGTTTA
12120128 AAAAC
1 AAAAC
12120133 AGTTAGTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAACGTTTA
Found at i:12121483 original size:60 final size:57
Alignment explanation
Indices: 12121272--12121566 Score: 299
Period size: 59 Copynumber: 5.0 Consensus size: 57
12121262 AATTTTGGGG
* * * *
12121272 AAATTCGGGGTTAAAAATAGGATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGT
1 AAATTTGGGGTCAAAAAT-GGATTTTGGAAGGTTTGGGGGTAAAATGGTAATTTTT-GT
* * * * *
12121331 AAAATTAGGGTTAAAAACAT-GATTTTGAAAGGTTTGGGGGTAAAATGGTAATTTTGGAT
1 -AAATTTGGGGTCAAAA-ATGGATTTTGGAAGGTTTGGGGGTAAAATGGTAATTTTTG-T
* * *
12121390 GAAA-TCGGGGTTAAAAATGGGATTTTGGAAGGTTTGGGGGTGAAATGGTAATTTTT-T
1 -AAATTTGGGGTCAAAAAT-GGATTTTGGAAGGTTTGGGGGTAAAATGGTAATTTTTGT
*
12121447 AGAAGTTTTGGGGTCAAAAATGGAATTTTGGAAGGTTCGGGGGGTAAAATGGTAATTTTTGGT
1 A-AA--TTTGGGGTCAAAAATGG-ATTTTGGAAGGTT-TGGGGGTAAAATGGTAATTTTT-GT
* * *
12121510 AAATTTGGGGTCAAAAATGGAATTTTGGAAAGTTTAGAGGTAAAATGGTAATTTTTG
1 AAATTTGGGGTCAAAAATGG-ATTTTGGAAGGTTTGGGGGTAAAATGGTAATTTTTG
12121567 GTGAAATCGA
Statistics
Matches: 201, Mismatches: 22, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
56 1 0.00
57 5 0.02
58 11 0.05
59 90 0.45
60 68 0.34
61 22 0.11
62 2 0.01
63 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.34
Consensus pattern (57 bp):
AAATTTGGGGTCAAAAATGGATTTTGGAAGGTTTGGGGGTAAAATGGTAATTTTTGT
Found at i:12121554 original size:29 final size:29
Alignment explanation
Indices: 12121293--12121564 Score: 173
Period size: 29 Copynumber: 9.2 Consensus size: 29
12121283 TAAAAATAGG
*
12121293 ATTTTGGAAAGTTCGGGGGTAAAATGGTA
1 ATTTTGGAAAGTTTGGGGGTAAAATGGTA
* * * *** *
12121322 ATTTTTGGTAAA-ATTAGGGTTAAAAACATG
1 A-TTTTGG-AAAGTTTGGGGGTAAAATGGTA
12121352 ATTTT-GAAAGGTTTGGGGGTAAAATGGTA
1 ATTTTGGAAA-GTTTGGGGGTAAAATGGTA
* * * *
12121381 ATTTTGGATGAA-ATCGGGGTTAAAAATGG-G
1 ATTTTGGA--AAGTTTGGGGGT-AAAATGGTA
* *
12121411 ATTTTGGAAGGTTTGGGGGTGAAATGGTA
1 ATTTTGGAAAGTTTGGGGGTAAAATGGTA
** *
12121440 ATTTTTTAGAAGTTTTGGGGTCAAAAATGG-A
1 ATTTTGGA-AAGTTTGGGGGT--AAAATGGTA
* *
12121471 ATTTTGGAAGGTTCGGGGGGTAAAATGGTA
1 ATTTTGGAAAGTT-TGGGGGTAAAATGGTA
12121501 ATTTTTGGTAAA-TTT-GGGGTCAAAAATGG-A
1 A-TTTTGG-AAAGTTTGGGGGT--AAAATGGTA
* *
12121531 ATTTTGGAAAGTTTAGAGGTAAAATGGTA
1 ATTTTGGAAAGTTTGGGGGTAAAATGGTA
12121560 ATTTT
1 ATTTT
12121565 TGGTGAAATC
Statistics
Matches: 183, Mismatches: 38, Indels: 44
0.69 0.14 0.17
Matches are distributed among these distances:
27 3 0.02
28 18 0.10
29 60 0.33
30 55 0.30
31 37 0.20
32 10 0.05
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.35
Consensus pattern (29 bp):
ATTTTGGAAAGTTTGGGGGTAAAATGGTA
Found at i:12121585 original size:30 final size:30
Alignment explanation
Indices: 12121492--12121594 Score: 92
Period size: 29 Copynumber: 3.5 Consensus size: 30
12121482 TTCGGGGGGT
* *
12121492 AAAATGGTAATTTTTGGT-AAATTTGGGGTC
1 AAAATGG-AATTTTTGGTGAAATTAGAGGTC
12121522 AAAAATGGAA-TTTT-G-GAAAGTTTAGAGGT-
1 -AAAATGGAATTTTTGGTGAAA--TTAGAGGTC
*
12121551 AAAATGGTAATTTTTGGTGAAA-TCGAGGTC
1 AAAATGG-AATTTTTGGTGAAATTAGAGGTC
12121581 AAAATGGAATTTTT
1 AAAATGGAATTTTT
12121595 TGAAAGTGAC
Statistics
Matches: 61, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
28 11 0.18
29 19 0.31
30 19 0.31
31 8 0.13
32 4 0.07
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAATGGAATTTTTGGTGAAATTAGAGGTC
Found at i:12121601 original size:59 final size:59
Alignment explanation
Indices: 12121264--12121593 Score: 327
Period size: 60 Copynumber: 5.6 Consensus size: 59
12121254 AAAAATGAAA
* * *
12121264 TTTTGGGGAAATTCGGGGTTAAAAATAGG-ATTTTGGAAAGTTCGGGGGTAAAATGGTAAT
1 TTTTGGTGAAA-TCGGGGTCAAAAAT-GGAATTTTGGAAAGTTTGGGGGTAAAATGGTAAT
* * * *
12121324 TTTTGGTAAAATTAGGGTTAAAAACAT-G-ATTTT-GAAAGGTTTGGGGGTAAAATGGTAA-
1 TTTTGGTGAAA-TCGGGGTCAAAA-ATGGAATTTTGGAAA-GTTTGGGGGTAAAATGGTAAT
* * * *
12121382 TTTTGGATGAAATCGGGGTTAAAAATGGGATTTTGGAAGGTTTGGGGGTGAAATGGTAAT
1 TTTTGG-TGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAAT
* * * *
12121442 TTTT--TAGAAGTTTTGGGGTCAAAAATGGAATTTTGGAAGGTTCGGGGGGTAAAATGGTAAT
1 TTTTGGT-GAA--ATCGGGGTCAAAAATGGAATTTTGGAAAGTT-TGGGGGTAAAATGGTAAT
* * *
12121503 TTTTGGT-AAATTTGGGGTCAAAAATGGAATTTTGGAAAGTTTAGAGGTAAAATGGTAAT
1 TTTTGGTGAAA-TCGGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAAT
*
12121562 TTTTGGTGAAATCGAGGTC-AAAATGGAATTTT
1 TTTTGGTGAAATCGGGGTCAAAAATGGAATTTT
12121594 TTGAAAGTGA
Statistics
Matches: 230, Mismatches: 25, Indels: 32
0.80 0.09 0.11
Matches are distributed among these distances:
57 3 0.01
58 36 0.16
59 81 0.35
60 85 0.37
61 24 0.10
63 1 0.00
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (59 bp):
TTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAAT
Found at i:12123766 original size:23 final size:23
Alignment explanation
Indices: 12123739--12123856 Score: 150
Period size: 23 Copynumber: 5.0 Consensus size: 23
12123729 CTAGCGCGCG
12123739 CTCTGATTAGCACTGTGTGTGCT
1 CTCTGATTAGCACTGTGTGTGCT
* *
12123762 CTCTGTTTAGCAC-GTCTCGTGCT
1 CTCTGATTAGCACTGTGT-GTGCT
12123785 CTCTGTTATTAGCACTGTGTGTGCT
1 CTCTG--ATTAGCACTGTGTGTGCT
*
12123810 CTCCGATTAGCACT-TCGTGTGCT
1 CTCTGATTAGCACTGT-GTGTGCT
*
12123833 CTCTGATTAGCACTTTGTGTGCT
1 CTCTGATTAGCACTGTGTGTGCT
12123856 C
1 C
12123857 AGTACTTTGT
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.05
23 59 0.71
24 1 0.01
25 16 0.19
26 3 0.04
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
CTCTGATTAGCACTGTGTGTGCT
Found at i:12123805 original size:48 final size:46
Alignment explanation
Indices: 12123739--12123856 Score: 166
Period size: 48 Copynumber: 2.5 Consensus size: 46
12123729 CTAGCGCGCG
* *
12123739 CTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGTGCT
1 CTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGT-GTGCT
*
12123785 CTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCT
1 CTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGTGCT
*
12123833 CTCTGATTAGCACTTTGTGTGCTC
1 CTCTGATTAGCACTGTGTGTGCTC
12123857 AGTACTTTGT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 23 0.35
48 41 0.63
49 1 0.02
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (46 bp):
CTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGTGCT
Found at i:12123885 original size:39 final size:39
Alignment explanation
Indices: 12123821--12123895 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
12123811 TCCGATTAGC
*
12123821 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
12123860 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
12123896 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:12123890 original size:23 final size:23
Alignment explanation
Indices: 12123855--12123948 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
12123845 CTTTGTGTGC
*
12123855 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
12123878 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
12123901 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
12123926 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
12123948 T
1 T
12123949 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:12130208 original size:23 final size:23
Alignment explanation
Indices: 12130181--12130298 Score: 150
Period size: 23 Copynumber: 5.0 Consensus size: 23
12130171 CTAGCGCGCG
12130181 CTCTGATTAGCACTGTGTGTGCT
1 CTCTGATTAGCACTGTGTGTGCT
* *
12130204 CTCTGTTTAGCAC-GTCTCGTGCT
1 CTCTGATTAGCACTGTGT-GTGCT
12130227 CTCTGTTATTAGCACTGTGTGTGCT
1 CTCTG--ATTAGCACTGTGTGTGCT
*
12130252 CTCCGATTAGCACT-TCGTGTGCT
1 CTCTGATTAGCACTGT-GTGTGCT
*
12130275 CTCTGATTAGCACTTTGTGTGCT
1 CTCTGATTAGCACTGTGTGTGCT
12130298 C
1 C
12130299 AGTACTTTGT
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.05
23 59 0.71
24 1 0.01
25 16 0.19
26 3 0.04
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
CTCTGATTAGCACTGTGTGTGCT
Found at i:12130247 original size:48 final size:46
Alignment explanation
Indices: 12130181--12130298 Score: 166
Period size: 48 Copynumber: 2.5 Consensus size: 46
12130171 CTAGCGCGCG
* *
12130181 CTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGTGCT
1 CTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGT-GTGCT
*
12130227 CTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCT
1 CTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGTGCT
*
12130275 CTCTGATTAGCACTTTGTGTGCTC
1 CTCTGATTAGCACTGTGTGTGCTC
12130299 AGTACTTTGT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 23 0.35
48 41 0.63
49 1 0.02
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (46 bp):
CTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGTGCT
Found at i:12130327 original size:39 final size:39
Alignment explanation
Indices: 12130263--12130337 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
12130253 TCCGATTAGC
*
12130263 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
12130302 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
12130338 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Done.