Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 64 of 135
Found at i:18891135 original size:74 final size:72
Alignment explanation
Indices: 18890927--18891147 Score: 318
Period size: 72 Copynumber: 3.0 Consensus size: 72
18890917 TATAGTCTGA
* * * * * *
18890927 CCCAATTTAACCTTAGAATGCCAAAAATGTCCCTAAATGATAAATGACTTAAGGTT-GCTTGACA
1 CCCAAATTAACCTAAGAATGACAAAAATATCCCTAAATGATAGATG-CTTAAGCTTGGCTTGACA
*
18890991 TTAAATTT
65 TTAAATTG
* *
18890999 CTCAAATTAACCTAAGAATGACAAAAATATCCCTAAATGATAGATGGTTAAGCTTGGCTTGACAT
1 CCCAAATTAACCTAAGAATGACAAAAATATCCCTAAATGATAGATGCTTAAGCTTGGCTTGACAT
18891064 TAAATTG
66 TAAATTG
*
18891071 CCCAAATTAACCTAAGAATGACAAAAAAATATCCCTAAATGATAGATGTTTAAGCTTGGCTTGAC
1 CCCAAATTAACCTAAGAATGAC--AAAAATATCCCTAAATGATAGATGCTTAAGCTTGGCTTGAC
18891136 ATTAAATTG
64 ATTAAATTG
18891145 CCC
1 CCC
18891148 CTACGAAATT
Statistics
Matches: 135, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
71 7 0.05
72 76 0.56
74 52 0.39
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (72 bp):
CCCAAATTAACCTAAGAATGACAAAAATATCCCTAAATGATAGATGCTTAAGCTTGGCTTGACAT
TAAATTG
Found at i:18892836 original size:81 final size:83
Alignment explanation
Indices: 18892701--18892864 Score: 314
Period size: 81 Copynumber: 2.0 Consensus size: 83
18892691 AATAAAAAAG
18892701 CAAGTATAGCTCAAGTGCTAAATTGTGAATAAAACCTAAATTTTATTCCAGTCAAA-AAAAAAAA
1 CAAGTATAGCTCAAGTGCTAAATTGTGAATAAAACCTAAATTTTATTCCAGTCAAACAAAAAAAA
18892765 A-CAATCAATATTATCAT
66 ATCAATCAATATTATCAT
18892782 CAAGTATAGCTCAAGTGCTAAATTGTGAATAAAACCTAAATTTTATTCCAGTCAAACAAAAAAAA
1 CAAGTATAGCTCAAGTGCTAAATTGTGAATAAAACCTAAATTTTATTCCAGTCAAACAAAAAAAA
18892847 ATCAATCAATATTATCAT
66 ATCAATCAATATTATCAT
18892865 TTACTTATAT
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
81 56 0.69
82 9 0.11
83 16 0.20
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.29
Consensus pattern (83 bp):
CAAGTATAGCTCAAGTGCTAAATTGTGAATAAAACCTAAATTTTATTCCAGTCAAACAAAAAAAA
ATCAATCAATATTATCAT
Found at i:18893080 original size:17 final size:17
Alignment explanation
Indices: 18893034--18893081 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
18893024 CTACTTAATT
18893034 GAGTGGAAAAGT-GAAA
1 GAGTGGAAAAGTGGAAA
*
18893050 G-G-AGAAAA--GGAAA
1 GAGTGGAAAAGTGGAAA
18893063 GAGTGGAAAAGTGGAAA
1 GAGTGGAAAAGTGGAAA
18893080 GA
1 GA
18893082 AAATAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 9
0.69 0.06 0.25
Matches are distributed among these distances:
13 5 0.20
14 6 0.24
15 6 0.24
16 1 0.04
17 7 0.28
ACGTcount: A:0.52, C:0.00, G:0.40, T:0.08
Consensus pattern (17 bp):
GAGTGGAAAAGTGGAAA
Found at i:18897822 original size:21 final size:21
Alignment explanation
Indices: 18897798--18897840 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
18897788 ATCTTTACAA
*
18897798 GAAAAGAAGATGAATCTCTTG
1 GAAAAGAACATGAATCTCTTG
18897819 GAAAAGAACATGAATCTCTTG
1 GAAAAGAACATGAATCTCTTG
18897840 G
1 G
18897841 TAAACTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (21 bp):
GAAAAGAACATGAATCTCTTG
Found at i:18899005 original size:12 final size:11
Alignment explanation
Indices: 18898989--18899038 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 11
18898979 AGGGGGGAGA
18898989 GGGATGGGGAT
1 GGGATGGGGAT
18899000 GAGGATGGGGATT
1 G-GGATGGGGA-T
18899013 GGG-TAGGGGAT
1 GGGAT-GGGGAT
18899024 GGGAT-GGGAT
1 GGGATGGGGAT
18899034 GGGAT
1 GGGAT
18899039 TTTTTTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
10 10 0.29
11 6 0.17
12 17 0.49
13 2 0.06
ACGTcount: A:0.20, C:0.00, G:0.60, T:0.20
Consensus pattern (11 bp):
GGGATGGGGAT
Found at i:18899639 original size:29 final size:32
Alignment explanation
Indices: 18899607--18899669 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 32
18899597 TTCATTTTCC
**
18899607 CTTTTTTA-ATAAATGGTTCAATAT-TTT-TA
1 CTTTTTTACATAAATGGCCCAATATGTTTATA
18899636 C-TTTTTACATAAATGGCCCAATATGTTTATA
1 CTTTTTTACATAAATGGCCCAATATGTTTATA
18899667 CTT
1 CTT
18899670 CTTCTCCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
28 6 0.21
29 15 0.54
30 3 0.11
31 3 0.11
32 1 0.04
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (32 bp):
CTTTTTTACATAAATGGCCCAATATGTTTATA
Found at i:18902482 original size:29 final size:29
Alignment explanation
Indices: 18902441--18902629 Score: 190
Period size: 29 Copynumber: 6.7 Consensus size: 29
18902431 GATGGCCATG
18902441 AAGGC-TC-CTTTAATAGATTCAACCACA
1 AAGGCTTCACTTTAATAGATTCAACCACA
* *
18902468 AAGGCTTCACTTTAACAGAATT-AGCCACA
1 AAGGCTTCACTTTAATAG-ATTCAACCACA
* * *
18902497 AAAGC-TCACTTTAATAGAATCAGCCACA
1 AAGGCTTCACTTTAATAGATTCAACCACA
* *
18902525 AAGGCTTCACTTTTATAGAATCAACCACA
1 AAGGCTTCACTTTAATAGATTCAACCACA
* * * **
18902554 AAGGCTT-ACTTTAACATATCCAGTCACA
1 AAGGCTTCACTTTAATAGATTCAACCACA
* *
18902582 AAGACTTCACTTTAATAGATTCAATCACA
1 AAGGCTTCACTTTAATAGATTCAACCACA
* *
18902611 AAGGCCTCACTTTTATAGA
1 AAGGCTTCACTTTAATAGA
18902630 AGCTGGTGTT
Statistics
Matches: 133, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
27 7 0.05
28 44 0.33
29 79 0.59
30 3 0.02
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (29 bp):
AAGGCTTCACTTTAATAGATTCAACCACA
Found at i:18902514 original size:57 final size:57
Alignment explanation
Indices: 18902444--18902629 Score: 194
Period size: 57 Copynumber: 3.3 Consensus size: 57
18902434 GGCCATGAAG
* * *
18902444 GCTC-CTTTAATAGATTCAACCACAAAGGCTTCACTTTAACAGAATTAGCCACAAAA
1 GCTCACTTTAATAGATTCAGCCACAAAGGCTTCACTTTAACAGAATCAACCACAAAA
* * * *
18902500 GCTCACTTTAATAGAATCAGCCACAAAGGCTTCACTTTTATAGAATCAACCACAAAG
1 GCTCACTTTAATAGATTCAGCCACAAAGGCTTCACTTTAACAGAATCAACCACAAAA
* * * * * * * * * *
18902557 GCTTACTTTAACATATCCAGTCACAAAGACTTCACTTTAATAGATTCAATCACAAAG
1 GCTCACTTTAATAGATTCAGCCACAAAGGCTTCACTTTAACAGAATCAACCACAAAA
*
18902614 GCCTCACTTTTATAGA
1 G-CTCACTTTAATAGA
18902630 AGCTGGTGTT
Statistics
Matches: 107, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
56 4 0.04
57 93 0.87
58 10 0.09
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (57 bp):
GCTCACTTTAATAGATTCAGCCACAAAGGCTTCACTTTAACAGAATCAACCACAAAA
Found at i:18902553 original size:86 final size:85
Alignment explanation
Indices: 18902441--18902630 Score: 235
Period size: 86 Copynumber: 2.2 Consensus size: 85
18902431 GATGGCCATG
* * *
18902441 AAGGCTC-CTTTAATAGATTCAACCACAAAGGCTTCACTTTAACAGAAT-TAGCCACAAA-AGC-
1 AAGGCTCACTTTTATAGAATCAACCACAAAGGCTT-ACTTTAACA-AATCCAGCCACAAAGA-CT
*
18902502 TCACTTTAATAGAATCAGCCACA
63 TCACTTTAATAGAATCAACCACA
* *
18902525 AAGGCTTCACTTTTATAGAATCAACCACAAAGGCTTACTTTAACATATCCAGTCACAAAGACTTC
1 AAGGC-TCACTTTTATAGAATCAACCACAAAGGCTTACTTTAACAAATCCAGCCACAAAGACTTC
* *
18902590 ACTTTAATAGATTCAATCACA
65 ACTTTAATAGAATCAACCACA
18902611 AAGGCCTCACTTTTATAGAA
1 AAGG-CTCACTTTTATAGAA
18902631 GCTGGTGTTT
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
84 7 0.08
85 20 0.22
86 64 0.70
87 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (85 bp):
AAGGCTCACTTTTATAGAATCAACCACAAAGGCTTACTTTAACAAATCCAGCCACAAAGACTTCA
CTTTAATAGAATCAACCACA
Found at i:18902813 original size:55 final size:55
Alignment explanation
Indices: 18902729--18902832 Score: 172
Period size: 55 Copynumber: 1.9 Consensus size: 55
18902719 CACCTTTTTT
18902729 CATATGATGTCATAACCACCATGACTAGGTCTTACACTATATGATCTTCATTCCC
1 CATATGATGTCATAACCACCATGACTAGGTCTTACACTATATGATCTTCATTCCC
** * *
18902784 CATATGATGTCATAGTCACCTTGACTAGGTCTTACACTATATGGTCTTC
1 CATATGATGTCATAACCACCATGACTAGGTCTTACACTATATGATCTTC
18902833 GATTTCCATG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (55 bp):
CATATGATGTCATAACCACCATGACTAGGTCTTACACTATATGATCTTCATTCCC
Found at i:18907399 original size:18 final size:18
Alignment explanation
Indices: 18907376--18907427 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
18907366 TCAATCTCCA
18907376 CAGGATCTTCTTCTTCCT
1 CAGGATCTTCTTCTTCCT
* *
18907394 CGGGATTTTCTTCTTCCT
1 CAGGATCTTCTTCTTCCT
* *
18907412 TAGGATCTTTTTCTTC
1 CAGGATCTTCTTCTTC
18907428 TTTAACAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.10, C:0.27, G:0.13, T:0.50
Consensus pattern (18 bp):
CAGGATCTTCTTCTTCCT
Found at i:18908282 original size:16 final size:15
Alignment explanation
Indices: 18908263--18908304 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
18908253 AACAATTTAA
18908263 AATAAATTAAAAAGTT
1 AATAAATTAAAAA-TT
18908279 AATAAATT-AAAATT
1 AATAAATTAAAAATT
18908293 AA-AAATTAAAAA
1 AATAAATTAAAAA
18908305 ATGAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 4 0.16
16 8 0.32
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
AATAAATTAAAAATT
Found at i:18908294 original size:22 final size:21
Alignment explanation
Indices: 18908266--18908306 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
18908256 AATTTAAAAT
*
18908266 AAATTAAAAAGTTAATAAATTA
1 AAATTAAAAA-TTAAAAAATTA
18908288 AAATTAAAAATTAAAAAAT
1 AAATTAAAAATTAAAAAAT
18908307 GAATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
AAATTAAAAATTAAAAAATTA
Found at i:18908299 original size:7 final size:7
Alignment explanation
Indices: 18908266--18908304 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
18908256 AATTTAAAAT
18908266 AAATTAA
1 AAATTAA
18908273 AAAGTTAA
1 AAA-TTAA
18908281 TAAATT-A
1 -AAATTAA
18908288 AAATTAA
1 AAATTAA
18908295 AAATTAA
1 AAATTAA
18908302 AAA
1 AAA
18908305 ATGAATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 5 0.17
7 15 0.52
8 6 0.21
9 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (7 bp):
AAATTAA
Found at i:18908968 original size:105 final size:105
Alignment explanation
Indices: 18908853--18909053 Score: 325
Period size: 106 Copynumber: 1.9 Consensus size: 105
18908843 TATTAAAAAC
18908853 AAATCCTAATTCAAACT-TTGATAA-ATATTAATATAAATTATAAAATTTAATTTATAATTAATA
1 AAATCCTAATTCAAACTCTTGATAATA-ATTAATATAAATTATAAAATTTAATTTATAATTAATA
*
18908916 TTAAGAGTTATCAAAATTTTGAAAAAATAAAAAATTAATGAA
65 TTAAGAATTATCAAAATTTTG-AAAAATAAAAAATTAATGAA
*
18908958 AAATCTTAATTCAAACTCTTGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATAT
1 AAATCCTAATTCAAACTCTTGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATAT
* * *
18909023 TAATAATTATCCAAATTTTGAAAGATAAAAA
66 TAAGAATTATCAAAATTTTGAAAAATAAAAA
18909054 TAAAATAAAA
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
105 26 0.29
106 62 0.70
107 1 0.01
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.38
Consensus pattern (105 bp):
AAATCCTAATTCAAACTCTTGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATAT
TAAGAATTATCAAAATTTTGAAAAATAAAAAATTAATGAA
Found at i:18909151 original size:19 final size:20
Alignment explanation
Indices: 18909129--18909176 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
18909119 CAAACTCTTG
18909129 ATAATAATTAATATA-AATT
1 ATAATAATTAATATATAATT
*
18909148 ATAA-AATTTAATTTATAATT
1 ATAATAA-TTAATATATAATT
18909168 -TAAT-ATTAA
1 ATAATAATTAA
18909177 GAATTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 15 0.60
20 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATAATTAATATATAATT
Found at i:18915897 original size:21 final size:21
Alignment explanation
Indices: 18915873--18915917 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
18915863 CTAGTGAAAC
* **
18915873 TGGTTCAGGTTCTGGTAAAGT
1 TGGTTCAGATTCTGACAAAGT
*
18915894 TGGTTCTGATTCTGACAAAGT
1 TGGTTCAGATTCTGACAAAGT
18915915 TGG
1 TGG
18915918 AGTTTCAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.11, G:0.31, T:0.38
Consensus pattern (21 bp):
TGGTTCAGATTCTGACAAAGT
Found at i:18919751 original size:15 final size:12
Alignment explanation
Indices: 18919717--18919741 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18919707 TGGTAGGCTC
18919717 TTCTTCTTCCTT
1 TTCTTCTTCCTT
18919729 TTCTTCTTCCTT
1 TTCTTCTTCCTT
18919741 T
1 T
18919742 CCCTCTTCTT
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TTCTTCTTCCTT
Found at i:18924617 original size:19 final size:19
Alignment explanation
Indices: 18924581--18924618 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18924571 GTACTGCCAC
**
18924581 TTTCAATTGCATTGAAGTG
1 TTTCAATTGCATCAAAGTG
18924600 TTTCAATTGCATCAAAGTG
1 TTTCAATTGCATCAAAGTG
18924619 ATACTTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39
Consensus pattern (19 bp):
TTTCAATTGCATCAAAGTG
Found at i:18924647 original size:23 final size:23
Alignment explanation
Indices: 18924549--18924653 Score: 83
Period size: 23 Copynumber: 4.7 Consensus size: 23
18924539 ATTTTCACCC
* * *
18924549 AAGTGCCACTGTCAAGTGCACCG
1 AAGTGCCACTTTCAATTGCATCG
* * *
18924572 TACTGCCACTTTCAATTGCATTG
1 AAGTGCCACTTTCAATTGCATCG
*
18924595 AAGTG----TTTCAATTGCATCA
1 AAGTGCCACTTTCAATTGCATCG
** *
18924614 AAGTGATACTTTCAATTACATCG
1 AAGTGCCACTTTCAATTGCATCG
*
18924637 AAGTGCCACTTTTAATT
1 AAGTGCCACTTTCAATT
18924654 TGCGTGCTAA
Statistics
Matches: 63, Mismatches: 15, Indels: 8
0.73 0.17 0.09
Matches are distributed among these distances:
19 17 0.27
23 46 0.73
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (23 bp):
AAGTGCCACTTTCAATTGCATCG
Found at i:18926052 original size:109 final size:110
Alignment explanation
Indices: 18925855--18926066 Score: 347
Period size: 109 Copynumber: 1.9 Consensus size: 110
18925845 AAAAAGAACA
*
18925855 TTATTGATTTAAAATAGGATACTCGATTATTTAGGTTCAGAGAAAAAAATCATACCCAGTACGTT
1 TTATTGATTTAAAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAAATCATACCCAGTACGTT
* *
18925920 TGAGTACAATTTCTCAAATTCCCTAAATAAAAGAACATCGAACCT
66 TGAGCACAATTTCTCAAATTCCCTAAATAAAAAAACATCGAACCT
* *
18925965 TTATTGATTTTAAAA-AGGATACTCGATTATTTAGGTTCAAAG-AAAAAATTATACCTAGTACGT
1 TTATTGA-TTTAAAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAAATCATACCCAGTACGT
*
18926028 TTGAGCACAATTTCTTAAATTCCCTAAATAAAAAAACAT
65 TTGAGCACAATTTCTCAAATTCCCTAAATAAAAAAACAT
18926067 TTTTTTAAAC
Statistics
Matches: 95, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
109 55 0.58
110 33 0.35
111 7 0.07
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.33
Consensus pattern (110 bp):
TTATTGATTTAAAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAAATCATACCCAGTACGTT
TGAGCACAATTTCTCAAATTCCCTAAATAAAAAAACATCGAACCT
Found at i:18927687 original size:6 final size:6
Alignment explanation
Indices: 18927678--18927736 Score: 57
Period size: 6 Copynumber: 9.7 Consensus size: 6
18927668 TGGGTCAAGT
* * * *
18927678 GTTTGG GTTTGG TAGTTTGG TTTTGG GTAT-A ATTTGG GTTTGG GTTTGG
1 GTTTGG GTTTGG --GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
18927727 GTTTGG GTTT
1 GTTTGG GTTT
18927737 TGTGATTGGG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
5 2 0.05
6 34 0.81
8 6 0.14
ACGTcount: A:0.07, C:0.00, G:0.41, T:0.53
Consensus pattern (6 bp):
GTTTGG
Found at i:18927754 original size:21 final size:22
Alignment explanation
Indices: 18927728--18927771 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
18927718 TGGGTTTGGG
*
18927728 TTTGGGT-TTTGTGATTGGGTT
1 TTTGGGTATTTGTAATTGGGTT
*
18927749 TTTGGGTATTTTTAATTGGGTT
1 TTTGGGTATTTGTAATTGGGTT
18927771 T
1 T
18927772 GTAAACAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.09, C:0.00, G:0.32, T:0.59
Consensus pattern (22 bp):
TTTGGGTATTTGTAATTGGGTT
Found at i:18928368 original size:85 final size:85
Alignment explanation
Indices: 18928124--18928878 Score: 699
Period size: 85 Copynumber: 8.9 Consensus size: 85
18928114 GTGTGTGTGT
* * * * * * * *
18928124 CTTCAACCTG-CCTCTCTAGATTAGGGGTAAAAGATTGGATGACTTTAATTTACCCC-ACTAAAT
1 CTTCAATCTGCCCT-TCTAGATTAAGGGTAAAAGACTGGATGGCTTCAATCTGCCCCTACTAGAT
*
18928187 TAGAGGTAAAAGATTGGATGG
65 TAGGGGTAAAAGATTGGATGG
* * * * * * * * *
18928208 CTTTAATTTGCCC-TCTATATTAGGGGTAAAAGATTGGATAGCTTTAATCTG-CTCTACTGGATT
1 CTTCAATCTGCCCTTCTAGATTAAGGGTAAAAGACTGGATGGCTTCAATCTGCCCCTACTAGATT
*
18928271 AGGGGTAAAAGATTCGATGG
66 AGGGGTAAAAGATTGGATGG
* * * * * *
18928291 CTTCAATCTTCCCTTTTGGATTAATGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTTGATT
1 CTTCAATCTGCCCTTCTAGATTAAGGGTAAAAGACTGGATGGCTTCAATCTGCCCCTACTAGATT
*
18928356 AGGGGTAAAAGATTAGATGG
66 AGGGGTAAAAGATTGGATGG
* * * * * * * * *
18928376 TTTCAATCTGCCCCTC-CGAATAGGGGTAAAAGAATGGATGGTTTCAATCTGCCCCTATTGGATT
1 CTTCAATCTGCCCTTCTAGATTAAGGGTAAAAGACTGGATGGCTTCAATCTGCCCCTACTAGATT
* *
18928440 AAGGGTAAAAGATTGGATGA
66 AGGGGTAAAAGATTGGATGG
* * *
18928460 CTTCAATCTGCCCTTACTAGATTAAGGTTAAAAGACTAGATGGCTTCAATCTG-CCCTACTAGTT
1 CTTCAATCTGCCCTT-CTAGATTAAGGGTAAAAGACTGGATGGCTTCAATCTGCCCCTACTAGAT
* *
18928524 TAAGGGTAAAAGATTGGATGA
65 TAGGGGTAAAAGATTGGATGG
* * * * * * *
18928545 TTTTAATCTGCCCCTACTAGATTAGGGGTAAAAGACTAGATGGCTTCAATCTGCCCCT-CTGGGT
1 CTTCAATCTG-CCCTTCTAGATTAAGGGTAAAAGACTGGATGGCTTCAATCTGCCCCTACTAGAT
18928609 TAGGGGTAAAAGATTGGATGG
65 TAGGGGTAAAAGATTGGATGG
* * * * *
18928630 CTTCAATCTGCCCTTACTAGATTAGGGGTAAAAGATTGGATGGCTTCAATTTG--CCTATTTGGA
1 CTTCAATCTGCCCTT-CTAGATTAAGGGTAAAAGACTGGATGGCTTCAATCTGCCCCTA-CTAGA
* * *
18928693 TTACGAGTAAAAGACTGGATGG
64 TTAGGGGTAAAAGATTGGATGG
* * * * * * * *
18928715 TTTCAATCTGCTCATACT-GTATTAAGGATAAAAGACTAGATGACTT-AAGTCTGCCCTTACTGG
1 CTTCAATCTGC-CCTTCTAG-ATTAAGGGTAAAAGACTGGATGGCTTCAA-TCTGCCCCTACTAG
* * *
18928778 ATTAGAGGTAAAAGACTGGATAG
63 ATTAGGGGTAAAAGATTGGATGG
*
18928801 CTTCAATCTGCCCCTAT-TGGATT-AGAGGTAAAAGACTGGATGGCTTCAATCTGCCCCTACTAG
1 CTTCAATCTG-CCCT-TCTAGATTAAG-GGTAAAAGACTGGATGGCTTCAATCTGCCCCTACTAG
18928864 ATTAGGGGTAAAAGA
63 ATTAGGGGTAAAAGA
18928879 CGGGATGGTG
Statistics
Matches: 553, Mismatches: 97, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
82 2 0.00
83 70 0.13
84 115 0.21
85 241 0.44
86 118 0.21
87 7 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (85 bp):
CTTCAATCTGCCCTTCTAGATTAAGGGTAAAAGACTGGATGGCTTCAATCTGCCCCTACTAGATT
AGGGGTAAAAGATTGGATGG
Found at i:18928886 original size:43 final size:43
Alignment explanation
Indices: 18928124--18928878 Score: 746
Period size: 43 Copynumber: 17.8 Consensus size: 43
18928114 GTGTGTGTGT
* * *
18928124 CTTCAACCTGCCTCT-CTAGATTAGGGGTAAAAGATTGGATGA
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
* * * * *
18928166 CTTTAATTTACCCC-ACTAAATTAGAGGTAAAAGATTGGATGG
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
* * * *
18928208 CTTTAATTTG-CCCT-CTATATTAGGGGTAAAAGATTGGATAG
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
* * * *
18928249 CTTTAATCTG-CTCTACTGGATTAGGGGTAAAAGATTCGATGG
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
* ** * **
18928291 CTTCAATCT-TCCCTTTTGGATTAATGGTAAAAGATTGGATGG
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
* *
18928333 CTTCAATCTGCCCCTACTTGATTAGGGGTAAAAGATTAGATGG
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
* * * *
18928376 TTTCAATCTGCCCCT-C-CGAATAGGGGTAAAAGAATGGATGG
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
* * * * *
18928417 TTTCAATCTGCCCCTATTGGATTAAGGGTAAAAGATTGGATGA
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
* * * * *
18928460 CTTCAATCTGCCCTTACTAGATTAAGGTTAAAAGACTAGATGG
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
* * *
18928503 CTTCAATCTG-CCCTACTAGTTTAAGGGTAAAAGATTGGATGA
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
* * * *
18928545 TTTTAATCTGCCCCTACTAGATTAGGGGTAAAAGACTAGATGG
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
* *
18928588 CTTCAATCTGCCCCT-CTGGGTTAGGGGTAAAAGATTGGATGG
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
*
18928630 CTTCAATCTGCCCTTACTAGATTAGGGGTAAAAGATTGGATGG
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
* * * * * *
18928673 CTTCAATTTG--CCTATTTGGATTACGAGTAAAAGACTGGATGG
1 CTTCAATCTGCCCCTA-CTAGATTAGGGGTAAAAGATTGGATGG
* * * * * * * *
18928715 TTTCAATCTGCTCATACT-GTATTAAGGATAAAAGACTAGATGA
1 CTTCAATCTGCCCCTACTAG-ATTAGGGGTAAAAGATTGGATGG
* * * * *
18928758 CTT-AAGTCTGCCCTTACTGGATTAGAGGTAAAAGACTGGATAG
1 CTTCAA-TCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
* * * *
18928801 CTTCAATCTGCCCCTATTGGATTAGAGGTAAAAGACTGGATGG
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
18928844 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGA
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGA
18928879 CGGGATGGTG
Statistics
Matches: 593, Mismatches: 104, Indels: 31
0.81 0.14 0.04
Matches are distributed among these distances:
41 78 0.13
42 213 0.36
43 296 0.50
44 6 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (43 bp):
CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGG
Found at i:18929895 original size:1 final size:1
Alignment explanation
Indices: 18929889--18929988 Score: 56
Period size: 1 Copynumber: 100.0 Consensus size: 1
18929879 CCTCTCCTTC
* * * * * * * * * *
18929889 TTTTTTTTCTTTTTTCTTTTTCTTTTCTTCTTTTTTTCTTTTTCTTTTTTCTTTTTTCTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** * * *
18929954 TTTCTTTTTCCTTTTTCTTTTCTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
18929989 AGTGAAATAC
Statistics
Matches: 69, Mismatches: 30, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (1 bp):
T
Found at i:18929903 original size:7 final size:7
Alignment explanation
Indices: 18929891--18929986 Score: 103
Period size: 7 Copynumber: 13.9 Consensus size: 7
18929881 TCTCCTTCTT
18929891 TTTTTTC
1 TTTTTTC
18929898 TTTTTTC
1 TTTTTTC
18929905 -TTTTTC
1 TTTTTTC
18929911 TTTTCTTC
1 TTTT-TTC
18929919 TTTTTT-
1 TTTTTTC
18929925 TCTTTTTC
1 T-TTTTTC
18929933 TTTTTTC
1 TTTTTTC
18929940 TTTTTTC
1 TTTTTTC
18929947 TTTTTTC
1 TTTTTTC
18929954 ---TTTC
1 TTTTTTC
*
18929958 TTTTTCC
1 TTTTTTC
*
18929965 TTTTTCTT
1 TTTTT-TC
18929973 TTCTTTTC
1 TT-TTTTC
18929981 TTTTTT
1 TTTTTT
18929987 TTAGTGAAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
4 4 0.05
6 7 0.09
7 49 0.64
8 13 0.17
9 3 0.04
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTTC
Found at i:18929946 original size:42 final size:42
Alignment explanation
Indices: 18929891--18929988 Score: 130
Period size: 42 Copynumber: 2.3 Consensus size: 42
18929881 TCTCCTTCTT
18929891 TTTTTTCTTTTTTC-TTTTTCTTTTCTTCTT-TTTTTCTTTTTC
1 TTTTTTCTTTTTTCTTTTTTC-TTTCTTCTTCTTTTTC-TTTTC
*
18929933 TTTTTTCTTTTTTCTTTTTTCTTTCTTTTTCCTTTTTCTTTTC
1 TTTTTTCTTTTTTCTTTTTTCTTTCTTCTT-CTTTTTCTTTTC
18929976 TTTTCTT-TTTTTT
1 TTTT-TTCTTTTTT
18929989 AGTGAAATAC
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
42 22 0.43
43 21 0.41
44 8 0.16
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (42 bp):
TTTTTTCTTTTTTCTTTTTTCTTTCTTCTTCTTTTTCTTTTC
Found at i:18929987 original size:49 final size:49
Alignment explanation
Indices: 18929891--18929986 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
18929881 TCTCCTTCTT
*
18929891 TTTTTTCTTTTTTCTTTTTCTTTTCTTCTTTTTTTCTTTTTCTTTTTTC
1 TTTTTTCTTTTTTCTTTTTCTTTCCTTCTTTTTTTCTTTTTCTTTTTTC
18929940 TTTTTTCTTTTTTCTTTCTT-TTTCCTT-TTTCTTTTC-TTTTCTTTTTT
1 TTTTTTCTTTTTTCTTT-TTCTTTCCTTCTTT-TTTTCTTTTTCTTTTTT
18929987 TTAGTGAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
48 14 0.32
49 28 0.64
50 2 0.05
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (49 bp):
TTTTTTCTTTTTTCTTTTTCTTTCCTTCTTTTTTTCTTTTTCTTTTTTC
Found at i:18936332 original size:111 final size:109
Alignment explanation
Indices: 18936200--18936417 Score: 323
Period size: 109 Copynumber: 2.0 Consensus size: 109
18936190 GAAAATATAG
*
18936200 AACATTTATTGATTTAAAATAGGATACTTGATTATTTAGGTTCAAAGAAAAAAAATCATAC-CTA
1 AACATTTATTGATTTAAAATAGGATACTCGATTATTTAGGTTCAAAG--AAAAAATCATACTC-A
** *
18936264 GTACATTTGAGTACAA-TTCCTCGAATTCCCTAAATAAAAGAACATCA
63 GTACATTTGAACACAAGTT-CTCGAATTCCCTAAATAAAACAACATCA
*
18936311 AACATTTATTGATTTTAAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAATCATACTCAGTA
1 AACATTTATTGATTTAAAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAATCATACTCAGTA
* *
18936376 CGTTTGAACACAAGTTCTCGAATTCCCTAAATGAAACAACAT
66 CATTTGAACACAAGTTCTCGAATTCCCTAAATAAAACAACAT
18936418 TGCAATTTTT
Statistics
Matches: 98, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
109 50 0.51
110 3 0.03
111 45 0.46
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (109 bp):
AACATTTATTGATTTAAAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAATCATACTCAGTA
CATTTGAACACAAGTTCTCGAATTCCCTAAATAAAACAACATCA
Found at i:18936604 original size:21 final size:20
Alignment explanation
Indices: 18936573--18936612 Score: 55
Period size: 19 Copynumber: 1.9 Consensus size: 20
18936563 TGGATATAAT
18936573 TAAATTTAAATTGCAAAAAATA
1 TAAATTTAAATT--AAAAAATA
18936595 TAAA-TTAAATTAAAAAAT
1 TAAATTTAAATTAAAAAAT
18936613 GGTAATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (20 bp):
TAAATTTAAATTAAAAAATA
Found at i:18936730 original size:26 final size:26
Alignment explanation
Indices: 18936685--18936739 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
18936675 GGAAATACAT
*
18936685 AAAATAAAAGGGGAATATTTTAGAAAA
1 AAAATAAAAGGGCAATATTTT-GAAAA
* *
18936712 AAAATAGAAGGGCAA-ATTTTTAAAA
1 AAAATAAAAGGGCAATATTTTGAAAA
18936737 AAA
1 AAA
18936740 GAAAAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 5 0.20
27 13 0.52
ACGTcount: A:0.60, C:0.02, G:0.16, T:0.22
Consensus pattern (26 bp):
AAAATAAAAGGGCAATATTTTGAAAA
Found at i:18938713 original size:19 final size:19
Alignment explanation
Indices: 18938686--18938734 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
18938676 AATTTTAATT
18938686 AAAAA-TATAAAAAT-AGA
1 AAAAATTATAAAAATCAGA
*
18938703 AAAGAATTATAAAAATCATA
1 AAA-AATTATAAAAATCAGA
18938723 AAAAATTATAAA
1 AAAAATTATAAA
18938735 TTTTGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 3 0.11
18 2 0.07
19 18 0.64
20 5 0.18
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (19 bp):
AAAAATTATAAAAATCAGA
Found at i:18939108 original size:19 final size:18
Alignment explanation
Indices: 18939020--18939116 Score: 65
Period size: 17 Copynumber: 5.4 Consensus size: 18
18939010 TTATAATTTC
* *
18939020 TTTTTTATACTTCTATAT
1 TTTTTTATAATTTTATAT
* * *
18939038 TTTTTTTTTATTTT-GAT
1 TTTTTTATAATTTTATAT
* * *
18939055 TTTTATAAAATTTTACA-
1 TTTTTTATAATTTTATAT
*
18939072 ATTTTTATAATTTTATAT
1 TTTTTTATAATTTTATAT
18939090 TTTTTTA-AATTTTTAATAT
1 TTTTTTATAA-TTTT-ATAT
*
18939109 TTATTTAT
1 TTTTTTAT
18939117 TAAAATTTAA
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
17 27 0.47
18 21 0.36
19 10 0.17
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTTTTATAATTTTATAT
Found at i:18939474 original size:90 final size:92
Alignment explanation
Indices: 18939253--18939481 Score: 306
Period size: 89 Copynumber: 2.5 Consensus size: 92
18939243 GGTCAAAGGG
* * * *
18939253 TCTTTTTGATGCATTTTGACAGTTCAAGTACCCAATTGAGTGAAAAAAAAAAGCATGTGCTTAAT
1 TCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAAT
* *
18939318 TGCGTCTTTTGAAAATGTTTGAGGGCA
66 TGCGTATTTTGAAAAGGTTTGAGGGCA
* ** *
18939345 T-TTTTT--TGCATTTTGAATGTTTTAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGTTTAAT
1 TCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAAT
*
18939407 TGCTTATTTTGAAAAGGTTTGA-GG-A
66 TGCGTATTTTGAAAAGGTTTGAGGGCA
* *
18939432 TCTTTTTGATGAATTTTGAAAGCTCAAGTACCCAATTGAGTGCAAAAAAA
1 TCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAA
18939482 GGCAAGGAAT
Statistics
Matches: 118, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
87 2 0.02
88 7 0.06
89 67 0.57
90 36 0.31
91 5 0.04
92 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (92 bp):
TCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAAT
TGCGTATTTTGAAAAGGTTTGAGGGCA
Found at i:18941306 original size:30 final size:30
Alignment explanation
Indices: 18941265--18941337 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
18941255 TTTTAATCTA
* *
18941265 AGGACTTAATTGTAATTTTAGTGGAATTT-
1 AGGACTAAATTGTAATTTTAGTGAAATTTG
* *
18941294 AGGGACTAAATTGGAGTTTTAGTGAAATTTG
1 A-GGACTAAATTGTAATTTTAGTGAAATTTG
*
18941325 AGGACTGAATTGT
1 AGGACTAAATTGT
18941338 GCTTTAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 1 0.03
30 34 0.94
31 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (30 bp):
AGGACTAAATTGTAATTTTAGTGAAATTTG
Found at i:18942152 original size:19 final size:18
Alignment explanation
Indices: 18942130--18942180 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
18942120 CCCATGACCT
18942130 TGACCCGAACCCGTAACCC
1 TGACCCGAACCCGTAA-CC
* *
18942149 TGACCCAAACCCGTGACC
1 TGACCCGAACCCGTAACC
18942167 TCGACCCG-ACCCGT
1 T-GACCCGAACCCGT
18942181 TGACCCAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.24, C:0.47, G:0.18, T:0.12
Consensus pattern (18 bp):
TGACCCGAACCCGTAACC
Found at i:18942194 original size:17 final size:17
Alignment explanation
Indices: 18942172--18942219 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
18942162 TGACCTCGAC
18942172 CCGACCCGTTGACCCAA
1 CCGACCCGTTGACCCAA
* * * *
18942189 CCGACCTGTTGGCCGAC
1 CCGACCCGTTGACCCAA
*
18942206 CCGACTCGTTGACC
1 CCGACCCGTTGACC
18942220 ATTGACCCTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.17, C:0.44, G:0.23, T:0.17
Consensus pattern (17 bp):
CCGACCCGTTGACCCAA
Found at i:18942708 original size:29 final size:29
Alignment explanation
Indices: 18942650--18942714 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
18942640 CCTGCTTGAG
* * *
18942650 GTGTGTCTCTGTCTATGCTACATACTGTT
1 GTGTGTTTCTATCTATGCTACATACGGTT
* *
18942679 GTGTGTTTCTATCTGTGCTACATTCGGTT
1 GTGTGTTTCTATCTATGCTACATACGGTT
*
18942708 GCGTGTT
1 GTGTGTT
18942715 AATGTTTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.46
Consensus pattern (29 bp):
GTGTGTTTCTATCTATGCTACATACGGTT
Found at i:18947807 original size:2 final size:2
Alignment explanation
Indices: 18947800--18947834 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
18947790 GGAGTCATCA
18947800 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
18947835 TGTGTGTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18948070 original size:2 final size:2
Alignment explanation
Indices: 18948065--18948102 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
18948055 AATATAACAC
18948065 AT AT AT AT AT AT 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 AT AT AT AT AT AT
18948103 GACATTTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18955161 original size:13 final size:13
Alignment explanation
Indices: 18955139--18955172 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
18955129 TAAAGAAATA
18955139 GTTTTT-TCCTTC
1 GTTTTTGTCCTTC
18955151 GTTTTTGTCCTTC
1 GTTTTTGTCCTTC
*
18955164 ATTTTTGTC
1 GTTTTTGTC
18955173 TTGTTTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.03, C:0.21, G:0.12, T:0.65
Consensus pattern (13 bp):
GTTTTTGTCCTTC
Found at i:18956044 original size:45 final size:45
Alignment explanation
Indices: 18955955--18956228 Score: 309
Period size: 45 Copynumber: 6.1 Consensus size: 45
18955945 ACTTCTGTGA
* *
18955955 GATGGTAGCTTCAATCTGCCCCTCTTGATTTAGAGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTG
* * * * * *
18956001 GACGATTGCTTCAATCTGGCCCTTTTGGTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
* * *
18956046 GATGGTGGCTTCAGTCAGCCCCTCTTGATTAGGGGTAAAAGATTA
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
* * *
18956091 GATGGTGGCTTCAATCTGCTCTTCTCGATTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
* * * * * *
18956136 AATGGT--CTTTAATCTACCCCTTTTGATTTAAGAGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTG
** *
18956180 GATGGTTACTTCAATCTGCCCCTCTTAATTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
18956225 GATG
1 GATG
18956229 CTTTAATCTA
Statistics
Matches: 187, Mismatches: 38, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
43 14 0.07
44 20 0.11
45 115 0.61
46 38 0.20
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (45 bp):
GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
Found at i:18956198 original size:89 final size:89
Alignment explanation
Indices: 18955967--18956242 Score: 312
Period size: 89 Copynumber: 3.1 Consensus size: 89
18955957 TGGTAGCTTC
* * * *
18955967 AATCTGCCCCTCTTGATTT-AGAGGTAAAAGATTGGACGATTGCTTCAATCTGGCCCTT-TTGGT
1 AATCTACCCCTCTTGATTTAAGA-GTAAAAGATTGGATGGTTGCTTCAATCT-GCCCTTCTTGAT
*
18956030 TAGGGGTAAAAGATTGGATGGTGGCTTC
64 TAGGGGTAAAAGATTGGATGGT--CTTT
* * * * * * *
18956058 AGTC-AGCCCCTCTTGA-TTAGGGGTAAAAGATTAGATGGTGGCTTCAATCTGCTCTTCTCGATT
1 AATCTA-CCCCTCTTGATTTAAGAGTAAAAGATTGGATGGTTGCTTCAATCTGCCCTTCTTGATT
*
18956121 AGGGGTAAAAGATTGAATGGTCTTT
65 AGGGGTAAAAGATTGGATGGTCTTT
* * * *
18956146 AATCTACCCCTTTTGATTTAAGAGTAAAAGATTGGATGGTTACTTCAATCTGCCCCTCTTAATTA
1 AATCTACCCCTCTTGATTTAAGAGTAAAAGATTGGATGGTTGCTTCAATCTGCCCTTCTTGATTA
18956211 GGGGTAAAAGATTGGAT-G-CTTT
66 GGGGTAAAAGATTGGATGGTCTTT
18956233 AATCTACCCC
1 AATCTACCCC
18956243 ATGGTCGGGG
Statistics
Matches: 155, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
87 14 0.09
88 16 0.10
89 61 0.39
90 50 0.32
91 14 0.09
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (89 bp):
AATCTACCCCTCTTGATTTAAGAGTAAAAGATTGGATGGTTGCTTCAATCTGCCCTTCTTGATTA
GGGGTAAAAGATTGGATGGTCTTT
Found at i:18956253 original size:38 final size:38
Alignment explanation
Indices: 18956211--18956348 Score: 132
Period size: 38 Copynumber: 3.5 Consensus size: 38
18956201 CTCTTAATTA
18956211 GGGGTAAAAGATTGGATGCTTTAATCTACCCCATGGTC
1 GGGGTAAAAGATTGGATGCTTTAATCTACCCCATGGTC
* * * * * *
18956249 GGGGTAAGAGATTGGAGTGTCTTCAATCAATCTGCCATCTGATT
1 GGGGTAAAAGATTGGA-TG-CTTTAATCTA-C-CCCA--TGGTC
* * *
18956293 AGGGTAAAAGATTGGATGCTTTAATTTGCCCCATGGTC
1 GGGGTAAAAGATTGGATGCTTTAATCTACCCCATGGTC
*
18956331 GGGGTAAGAGATTGGATG
1 GGGGTAAAAGATTGGATG
18956349 GTAGCTTCGC
Statistics
Matches: 77, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
38 34 0.44
39 2 0.03
40 11 0.14
41 2 0.03
42 9 0.12
43 2 0.03
44 17 0.22
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (38 bp):
GGGGTAAAAGATTGGATGCTTTAATCTACCCCATGGTC
Found at i:18956257 original size:89 final size:89
Alignment explanation
Indices: 18956080--18956340 Score: 231
Period size: 89 Copynumber: 3.0 Consensus size: 89
18956070 TTGATTAGGG
* ** * * * *
18956080 GTAAAAGATTAGATGGTGGCTTCAATCTGCTCTTCTCGATTAGGGGTAAAAGATTGAATGGTCTT
1 GTAAAAGATTGGATGGTTACTTCAATCTGCCCATCTTGATTAGGGGTAAAAGATTGGAT-G-CTT
* * ***
18956145 TAATCTACCCC-T-TTTGATTTAAGA
64 TAATCTACCCCATGGTCGGGGTAAGA
* *
18956169 GTAAAAGATTGGATGGTTACTTCAATCTGCCCCTCTTAATTAGGGGTAAAAGATTGGATGCTTTA
1 GTAAAAGATTGGATGGTTACTTCAATCTGCCCATCTTGATTAGGGGTAAAAGATTGGATGCTTTA
18956234 ATCTACCCCATGGTCGGGGT-A-A
66 ATCTACCCCATGGTCGGGGTAAGA
* *
18956256 G----AGATTGGA-GTGTCTTCAATCAATCTG-CCATC-TGATTA-GGGTAAAAGATTGGATGCT
1 GTAAAAGATTGGATG-GT-TAC-TTCAATCTGCCCATCTTGATTAGGGGTAAAAGATTGGATGCT
* *
18956313 TTAATTTGCCCCATGGTCGGGGTAAGA
63 TTAATCTACCCCATGGTCGGGGTAAGA
18956340 G
1 G
18956341 ATTGGATGGT
Statistics
Matches: 146, Mismatches: 19, Indels: 19
0.79 0.10 0.10
Matches are distributed among these distances:
82 41 0.28
83 16 0.11
84 8 0.05
85 8 0.05
87 16 0.11
88 3 0.02
89 54 0.37
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.33
Consensus pattern (89 bp):
GTAAAAGATTGGATGGTTACTTCAATCTGCCCATCTTGATTAGGGGTAAAAGATTGGATGCTTTA
ATCTACCCCATGGTCGGGGTAAGA
Found at i:18956574 original size:24 final size:24
Alignment explanation
Indices: 18956542--18956588 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
18956532 TAAGTCAAAT
* *
18956542 GCTCCTAACTAGATGGGTATGAAC
1 GCTCCTAACAAGATAGGTATGAAC
18956566 GCTCCTAACAAGATAGGTATGAA
1 GCTCCTAACAAGATAGGTATGAA
18956589 TGATGAATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (24 bp):
GCTCCTAACAAGATAGGTATGAAC
Found at i:18957313 original size:13 final size:13
Alignment explanation
Indices: 18957290--18957323 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
18957280 ACCTCTCCTT
18957290 TTTCTTTTTCTTTC
1 TTTC-TTTTCTTTC
18957304 TTTCTTTTCTTTC
1 TTTCTTTTCTTTC
18957317 TTT-TTTT
1 TTTCTTTT
18957324 GGGTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 12 0.60
14 4 0.20
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTCTTTTCTTTC
Found at i:18958233 original size:9 final size:8
Alignment explanation
Indices: 18958219--18958255 Score: 51
Period size: 7 Copynumber: 4.8 Consensus size: 8
18958209 TTCATCTTGA
18958219 CTTTTTCTT
1 CTTTTTC-T
18958228 CTTTTTCT
1 CTTTTTCT
18958236 -TTTTTCT
1 CTTTTTCT
18958243 CTTTTT-T
1 CTTTTTCT
18958250 CTTTTT
1 CTTTTT
18958256 TTTTGTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 14 0.52
8 6 0.22
9 7 0.26
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
CTTTTTCT
Found at i:18958241 original size:16 final size:16
Alignment explanation
Indices: 18958220--18958256 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
18958210 TCATCTTGAC
18958220 TTTTTCT-TCTTTTTCT
1 TTTTTCTCT-TTTTTCT
18958236 TTTTTCTCTTTTTTCT
1 TTTTTCTCTTTTTTCT
18958252 TTTTT
1 TTTTT
18958257 TTTGTTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTCTCTTTTTTCT
Found at i:18966375 original size:24 final size:24
Alignment explanation
Indices: 18966343--18966388 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
18966333 CATCGTCAAA
18966343 ACATGGGAAAGACCTGAGCTATGT
1 ACATGGGAAAGACCTGAGCTATGT
*
18966367 ACATGGGAAAGACTTGAGCTAT
1 ACATGGGAAAGACCTGAGCTAT
18966389 ATAAAGGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (24 bp):
ACATGGGAAAGACCTGAGCTATGT
Found at i:18970840 original size:23 final size:23
Alignment explanation
Indices: 18970814--18970940 Score: 139
Period size: 23 Copynumber: 5.4 Consensus size: 23
18970804 AGTGTTGGGC
*
18970814 AACAGAGAGCACACACAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* * *
18970837 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* *
18970860 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* *
18970883 ATCAGAGAGCACACACAATGCTGA
1 AACAGAGAGCACACACAGTGCT-A
*
18970907 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
18970931 AACAGAGAGC
1 AACAGAGAGC
18970941 GCGCTAGTGT
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
23 71 0.78
24 2 0.02
25 15 0.16
26 3 0.03
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:18972879 original size:65 final size:65
Alignment explanation
Indices: 18972798--18972924 Score: 254
Period size: 65 Copynumber: 2.0 Consensus size: 65
18972788 AAAATACTAG
18972798 CTTTATTTAATCTTACACATTCATTTACAACCTTTGAATCAATCAAGAATCAAATTCAATCACAA
1 CTTTATTTAATCTTACACATTCATTTACAACCTTTGAATCAATCAAGAATCAAATTCAATCACAA
18972863 CTTTATTTAATCTTACACATTCATTTACAACCTTTGAATCAATCAAGAATCAAATTCAATCA
1 CTTTATTTAATCTTACACATTCATTTACAACCTTTGAATCAATCAAGAATCAAATTCAATCA
18972925 AGCAAGAATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.36
Consensus pattern (65 bp):
CTTTATTTAATCTTACACATTCATTTACAACCTTTGAATCAATCAAGAATCAAATTCAATCACAA
Found at i:18973470 original size:21 final size:22
Alignment explanation
Indices: 18973424--18973473 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
18973414 ATAGTGTAGA
*
18973424 CTTCTACCGATACCTATGACAG
1 CTTCTACCGATACCAATGACAG
18973446 -TTCTACCGATA-CAAGTGA-AG
1 CTTCTACCGATACCAA-TGACAG
18973466 CTTCTACC
1 CTTCTACC
18973474 AAAACAAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (22 bp):
CTTCTACCGATACCAATGACAG
Found at i:18974522 original size:34 final size:33
Alignment explanation
Indices: 18974459--18974524 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
18974449 GTTGGATTAT
* * **
18974459 CCAACGGTTTGCGCCCAGTGCTACTCGGATAAA
1 CCAACGGTTTGCACCCAGTGCCAAGCGGATAAA
18974492 CCAACGGTTTGGCACCCAGTGCCAAGCGGATAA
1 CCAACGGTTT-GCACCCAGTGCCAAGCGGATAA
18974525 TCCGCGATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.18
Consensus pattern (33 bp):
CCAACGGTTTGCACCCAGTGCCAAGCGGATAAA
Found at i:18974576 original size:101 final size:102
Alignment explanation
Indices: 18974399--18974652 Score: 305
Period size: 101 Copynumber: 2.5 Consensus size: 102
18974389 CCATCAATTC
* * *
18974399 ATGGCACCCGGTGCCTAGCGGATATAT-CGCGGTATGTGAGCCCAGCTCTAGTTGGATTATCCAA
1 ATGGCACCCAGTGCCTAGCGGATA-ATCCGCGATATGTGAGCCCAGCTCTAGTTGGATTAACCAA
* * *
18974463 CGGTTTGCGCCCAGTGCTACTCGGATAAACCAACGGTT
65 CGGTTTGCGCCCAGCGCTACTCAGATAAACCAACAGTT
* * * **
18974501 -TGGCACCCAGTGCCAAGCGGATAATCCGCGATATGTAAGCCTATTTCTAGTTGGATTAACCAAC
1 ATGGCACCCAGTGCCTAGCGGATAATCCGCGATATGTGAGCCCAGCTCTAGTTGGATTAACCAAC
* * * *
18974565 GGTTTGTGCCCAGCGCTAGTTAGATAAACTAACAGTT
66 GGTTTGCGCCCAGCGCTACTCAGATAAACCAACAGTT
* * * * *
18974602 ATGGCACTCAATGCCTAGCAGATAAACCGCGATATGTGAGCCCCGCTCTAG
1 ATGGCACCCAGTGCCTAGCGGATAATCCGCGATATGTGAGCCCAGCTCTAG
18974653 CCAGTTAAAC
Statistics
Matches: 125, Mismatches: 25, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
100 2 0.02
101 83 0.66
102 40 0.32
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.24
Consensus pattern (102 bp):
ATGGCACCCAGTGCCTAGCGGATAATCCGCGATATGTGAGCCCAGCTCTAGTTGGATTAACCAAC
GGTTTGCGCCCAGCGCTACTCAGATAAACCAACAGTT
Found at i:18975205 original size:135 final size:135
Alignment explanation
Indices: 18974964--18975228 Score: 458
Period size: 135 Copynumber: 2.0 Consensus size: 135
18974954 TTTCTTGCTC
* *
18974964 TATATATATAACAATTCAAATCTTTAATTAATCCTTTGTATTCAACACATATCCAACAATTCAAA
1 TATATATATAACAATTCAAACCTTTAATTAATCCTTTGTATTCAACACATATCCAACAATCCAAA
* *
18975029 ATGTTCAATATAATTCACATGGCAAGAAGCATTTATTTATTTATTTCCAGCCACCATATATGCAT
66 ATGTTCAATATAATTCACATGGCAAAAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCAT
18975094 ATCAA
131 ATCAA
* **
18975099 TATATATATAACAATTCAAACCTTTAATTAATCCTTTGTATTCAACTCATATTTAACAATCCAAA
1 TATATATATAACAATTCAAACCTTTAATTAATCCTTTGTATTCAACACATATCCAACAATCCAAA
*
18975164 ATGTTCAATATAATTCACATGGCAAAAAGCATTTATTTATTTATTTCTAGCCACCAAATATGCAT
66 ATGTTCAATATAATTCACATGGCAAAAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCAT
18975229 TCCATCTAAC
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
135 122 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (135 bp):
TATATATATAACAATTCAAACCTTTAATTAATCCTTTGTATTCAACACATATCCAACAATCCAAA
ATGTTCAATATAATTCACATGGCAAAAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCAT
ATCAA
Found at i:18979104 original size:36 final size:36
Alignment explanation
Indices: 18979057--18979135 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
18979047 TAATAAGACT
18979057 CTGTAAATATTTAATAAAAATATTTACAGCTCTTAA
1 CTGTAAATATTTAATAAAAATATTTACAGCTCTTAA
18979093 CTGTAAATATTTAATAAAAATATTTACAGCTCTTAA
1 CTGTAAATATTTAATAAAAATATTTACAGCTCTTAA
*
18979129 CTTTAAA
1 CTGTAAA
18979136 AATGAGGTCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.39
Consensus pattern (36 bp):
CTGTAAATATTTAATAAAAATATTTACAGCTCTTAA
Found at i:18981274 original size:21 final size:21
Alignment explanation
Indices: 18981248--18981301 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
18981238 CTATGGGCAG
**
18981248 AACTACCGATACTTATTATGT
1 AACTACCGATACTTATTATCC
18981269 AACTACCGATACTTATTATCC
1 AACTACCGATACTTATTATCC
18981290 AACTACCGATAC
1 AACTACCGATAC
18981302 AACTCAAGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.31
Consensus pattern (21 bp):
AACTACCGATACTTATTATCC
Found at i:18983081 original size:20 final size:19
Alignment explanation
Indices: 18983041--18983082 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
18983031 TCTTTTATAA
*
18983041 TTAACTTAATTAACCTTAC
1 TTAACTTAATTAACATTAC
18983060 TTAAGCTTAATTAA-ATTCAC
1 TTAA-CTTAATTAACATT-AC
18983080 TTA
1 TTA
18983083 TTACATCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAACTTAATTAACATTAC
Found at i:18985151 original size:34 final size:34
Alignment explanation
Indices: 18985113--18985262 Score: 135
Period size: 34 Copynumber: 4.5 Consensus size: 34
18985103 ACACAGTTAA
* *
18985113 CCATCCAACACACCAGATGCTTGTATGAGCCAAT
1 CCATCCAACACACCAAATGCTCGTATGAGCCAAT
* *
18985147 CCATCCAGCACACCAAATGCTCGTATGAGCTAAT
1 CCATCCAACACACCAAATGCTCGTATGAGCCAAT
* * * * * * *
18985181 CCATCTAGCACTCCAAATGCTCGTCTAAGCTAGT
1 CCATCCAACACACCAAATGCTCGTATGAGCCAAT
* * * *
18985215 CCAACCAACACACCACACGCTCGTAAGAG-C--T
1 CCATCCAACACACCAAATGCTCGTATGAGCCAAT
*
18985246 CCATCCAGCACACCAAA
1 CCATCCAACACACCAAA
18985263 ACACTACAAC
Statistics
Matches: 94, Mismatches: 22, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
31 15 0.16
34 79 0.84
ACGTcount: A:0.33, C:0.36, G:0.13, T:0.18
Consensus pattern (34 bp):
CCATCCAACACACCAAATGCTCGTATGAGCCAAT
Found at i:18993893 original size:21 final size:21
Alignment explanation
Indices: 18993863--18993903 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
18993853 AGTCTAAAAA
*
18993863 CCCTATTATACTATATGCGAG
1 CCCTAATATACTATATGCGAG
*
18993884 CCCTAATATACTATGTGCGA
1 CCCTAATATACTATATGCGA
18993904 ACCCATGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (21 bp):
CCCTAATATACTATATGCGAG
Found at i:18993945 original size:17 final size:17
Alignment explanation
Indices: 18993890--18993980 Score: 76
Period size: 17 Copynumber: 5.4 Consensus size: 17
18993880 CGAGCCCTAA
18993890 TATACTATGTGCGAACC
1 TATACTATGTGCGAACC
* * * * *
18993907 CATGCTATTATGTGAACG
1 TATACTA-TGTGCGAACC
*
18993925 TATACCATGTGCGAACC
1 TATACTATGTGCGAACC
* **
18993942 TATACTATGCGTAAACC
1 TATACTATGTGCGAACC
*
18993959 TATATTATGTGCGAA-C
1 TATACTATGTGCGAACC
18993975 TATACT
1 TATACT
18993981 GTTATGCGAG
Statistics
Matches: 53, Mismatches: 20, Indels: 3
0.70 0.26 0.04
Matches are distributed among these distances:
16 6 0.11
17 36 0.68
18 11 0.21
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (17 bp):
TATACTATGTGCGAACC
Found at i:18995275 original size:18 final size:18
Alignment explanation
Indices: 18995250--18995297 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
18995240 TTTGCGAAAA
18995250 TAAG-GGGTTCACCAAGG
1 TAAGTGGGTTCACCAAGG
*
18995267 TAAGTGGGTACACCAAGG
1 TAAGTGGGTTCACCAAGG
18995285 TAA-TGGAGTTCAC
1 TAAGTGG-GTTCAC
18995298 GGGTGTACCG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (18 bp):
TAAGTGGGTTCACCAAGG
Found at i:19012300 original size:19 final size:18
Alignment explanation
Indices: 19012265--19012301 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
19012255 GCTCATCGAA
*
19012265 AAAGGGAGAAAATGAGAG
1 AAAGGGAGAAAAGGAGAG
19012283 AAAGGGAGAAAAAGGAGAG
1 AAAGGGAG-AAAAGGAGAG
19012302 TTCGATTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.41, T:0.03
Consensus pattern (18 bp):
AAAGGGAGAAAAGGAGAG
Found at i:19016030 original size:21 final size:20
Alignment explanation
Indices: 19016006--19016058 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
19015996 GACCGACCCG
19016006 TTGACTGTTGACCATTGACAA
1 TTGACTGTTGACCATTGAC-A
* *
19016027 TTGACCT-TTGACCGTTGACT
1 TTGA-CTGTTGACCATTGACA
*
19016047 TTGATTGTTGAC
1 TTGACTGTTGAC
19016059 TTTTTTTGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.04
20 9 0.33
21 15 0.56
22 2 0.07
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGACTGTTGACCATTGACA
Found at i:19022962 original size:23 final size:24
Alignment explanation
Indices: 19022936--19022981 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
19022926 AACACTTACC
19022936 CAAGCCCAAACCTCAAAC-CAAAG
1 CAAGCCCAAACCTCAAACTCAAAG
*
19022959 CAAGCCCAAATCTCAAACTCAAA
1 CAAGCCCAAACCTCAAACTCAAA
19022982 CCAAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.48, C:0.37, G:0.07, T:0.09
Consensus pattern (24 bp):
CAAGCCCAAACCTCAAACTCAAAG
Found at i:19025749 original size:29 final size:30
Alignment explanation
Indices: 19025673--19025737 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
19025663 TAATTAGAGT
*
19025673 TCAATTAAGTCCCC-AAACTTCTCCAAAATTA
1 TCAATT-AGACCCCTAAA-TTCTCCAAAATTA
*
19025704 TGAATTAGACCCCTAAATTCT-CAAAATTA
1 TCAATTAGACCCCTAAATTCTCCAAAATTA
19025733 TCAAT
1 TCAAT
19025738 CTAATCCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 12 0.40
30 10 0.33
31 8 0.27
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.31
Consensus pattern (30 bp):
TCAATTAGACCCCTAAATTCTCCAAAATTA
Found at i:19027231 original size:18 final size:18
Alignment explanation
Indices: 19027208--19027251 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
19027198 AAAACTAGAT
19027208 AAGAAAAACTAAGAA-CTA
1 AAGAAAAACTAA-AATCTA
*
19027226 AAGAAAATCTAAAATCTA
1 AAGAAAAACTAAAATCTA
*
19027244 AACAAAAA
1 AAGAAAAA
19027252 ACTCTGTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.68, C:0.11, G:0.07, T:0.14
Consensus pattern (18 bp):
AAGAAAAACTAAAATCTA
Found at i:19028963 original size:3 final size:3
Alignment explanation
Indices: 19028955--19028997 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
19028945 AAAGGCCCAA
* ** *
19028955 ATT ATT ATT ATC ATT ACC ATT ATC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
19028998 GGGTTTCATG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:19028988 original size:12 final size:12
Alignment explanation
Indices: 19028955--19028997 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
19028945 AAAGGCCCAA
19028955 ATTATTATTATC
1 ATTATTATTATC
**
19028967 ATTACCATTATC
1 ATTATTATTATC
*
19028979 ATTATTATTATT
1 ATTATTATTATC
19028991 ATTATTA
1 ATTATTA
19028998 GGGTTTCATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTATTATTATC
Found at i:19029653 original size:149 final size:150
Alignment explanation
Indices: 19029411--19029777 Score: 569
Period size: 150 Copynumber: 2.4 Consensus size: 150
19029401 TGATTTTGGA
* *
19029411 AAAGTTTTGGTTTTTTTTAAGCAATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATT
1 AAAGTTTTGATTTTTTTTAA-CTATTTCGAAATAAAAGTTT-GATTTTTAAGTAAAGTAGTGATT
* * *
19029476 TTCATTTAAAAAGAAAAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTTAAA-
64 TTCATTAAAAAAGAAAAAAGTTTATATTTTAAAAAATAAAAATCTATTTTTTAGTGATTTTAAAG
*
19029540 GAAAAAATTTAAATTTTTAAAT
129 GAAAAAATTTAAATTTTTAAAC
19029562 AAAGTTTTGATATTTTTTT-ACTATTTCGAAATAAAAGTTTAGATTTTTAAG-AAAGTAGTGATT
1 AAAGTTTTGAT-TTTTTTTAACTATTTCGAAATAAAAGTTT-GATTTTTAAGTAAAGTAGTGATT
* * *
19029625 TTCATTAAAAAAGGAGAAAGTTTATATTTTAAAAAATAAAAATCTGTTTTTTAGTGATTTTAAAG
64 TTCATTAAAAAAGAAAAAAGTTTATATTTTAAAAAATAAAAATCTATTTTTTAGTGATTTTAAAG
*
19029690 GAAAAAGTTTAAATTTTTAAAC
129 GAAAAAATTTAAATTTTTAAAC
*
19029712 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTCTGATTTTGAAGTAAAGTAGTGATTT
1 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTT-TGATTTTTAAGTAAAGTAGTGATTT
19029777 T
65 T
19029778 GTTTTAATCA
Statistics
Matches: 199, Mismatches: 12, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
149 77 0.39
150 89 0.45
151 26 0.13
152 7 0.04
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (150 bp):
AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGATTTTTAAGTAAAGTAGTGATTTT
CATTAAAAAAGAAAAAAGTTTATATTTTAAAAAATAAAAATCTATTTTTTAGTGATTTTAAAGGA
AAAAATTTAAATTTTTAAAC
Found at i:19031247 original size:240 final size:237
Alignment explanation
Indices: 19030826--19031291 Score: 713
Period size: 240 Copynumber: 2.0 Consensus size: 237
19030816 CATAATAATC
* * *
19030826 ATAAAAGATCGAATAAGTTGTAGATGGATTTTAATATTTCTCTTAATACGTTAGTAACTTTTAGT
1 ATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATACATTAGCAACTTTTAGT
*
19030891 TTTTTTTAGGATTTTAAAATAGAATAAATTTTAAGAATTGAAGATATTTTACTAGAATTATTCAA
66 TTTTTTTAGGATTCTAAAATAGAATAAATTTTAAGAATTGAAGATATTTTACTAGAATTATTCAA
* * *
19030956 GTATCTTTTAGGATTCTCGTTAGAAATAAAAATCTCTAATTTAAATTTTAAATTAGATAAGTTTG
131 GTATCCTTTAGGATTCTCATTAGAAATAAAAATCTCTAATTCAAATTTTAAATTAGATAAGTTTG
19031021 GTGAACACGTCTTAGTCAAGTTACAAGTAAACCGGAGCAATG
196 GTGAACACGTCTTAGTCAAGTTACAAGTAAACCGGAGCAATG
* *
19031063 ATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGCAA-TTTTTGT
1 ATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATACATTAGCAACTTTTAG-
*
19031127 TTAGGTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAA-AGTATTTTACTAGAATTA
65 TT---TTTTTTAGGATTCTAAAATAGAATAAATTTTAAGAATTGAAGA-TATTTTACTAGAATTA
* * * * * *
19031191 TTTAGGTATCCTTTAGCG-TTCTTATTAGGAGTAAAAATCTCTAATTCAAGTTTTAAATTAGATA
126 TTCAAGTATCCTTTAG-GATTCTCATTAGAAATAAAAATCTCTAATTCAAATTTTAAATTAGATA
19031255 AGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAA
190 AGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAA
19031292 ATCGAGGCAT
Statistics
Matches: 207, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
236 5 0.02
237 55 0.27
239 1 0.00
240 145 0.70
241 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (237 bp):
ATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATACATTAGCAACTTTTAGT
TTTTTTTAGGATTCTAAAATAGAATAAATTTTAAGAATTGAAGATATTTTACTAGAATTATTCAA
GTATCCTTTAGGATTCTCATTAGAAATAAAAATCTCTAATTCAAATTTTAAATTAGATAAGTTTG
GTGAACACGTCTTAGTCAAGTTACAAGTAAACCGGAGCAATG
Found at i:19032184 original size:22 final size:23
Alignment explanation
Indices: 19032159--19032216 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
19032149 AAGCTAGGTT
*
19032159 TGTTTGTATGTTGTGTATGTT-A
1 TGTTTGTATGTTGTGTATATTCA
**
19032181 TGTTTGTAACTTGTGTATATTCA
1 TGTTTGTATGTTGTGTATATTCA
*
19032204 TGTGTGTATGTTG
1 TGTTTGTATGTTG
19032217 CAAACCATCC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.16, C:0.03, G:0.26, T:0.55
Consensus pattern (23 bp):
TGTTTGTATGTTGTGTATATTCA
Found at i:19035057 original size:30 final size:30
Alignment explanation
Indices: 19035023--19035099 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
19035013 CCCCTTTTTA
*
19035023 TTCCAAAACTATATTTTAACCC-CTAAACTT
1 TTCCAAAACTACATTTTAACCCTC-AAACTT
* * *
19035053 TTCCAAAATTACATTTTGACCCTCGAACTT
1 TTCCAAAACTACATTTTAACCCTCAAACTT
*
19035083 TTCCAAAACTTCATTTT
1 TTCCAAAACTACATTTT
19035100 TGACCCCTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
30 39 0.98
31 1 0.03
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (30 bp):
TTCCAAAACTACATTTTAACCCTCAAACTT
Found at i:19035104 original size:31 final size:30
Alignment explanation
Indices: 19035048--19035105 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
19035038 TTAACCCCTA
19035048 AACTTTTCCAAAATTACATTTTGACCCTCG
1 AACTTTTCCAAAATTACATTTTGACCCTCG
19035078 AACTTTTCCAAAACTT-CATTTTTGACCC
1 AACTTTTCCAAAA-TTACA-TTTTGACCC
19035106 CTTTTTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.29, C:0.28, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTTCCAAAATTACATTTTGACCCTCG
Found at i:19037889 original size:25 final size:23
Alignment explanation
Indices: 19037852--19037979 Score: 132
Period size: 23 Copynumber: 5.5 Consensus size: 23
19037842 ACACTAGCGC
*
19037852 GCTCTCTGTTTAGCAC-GTCTTGT
1 GCTCTCTGTTTAGCACTGT-GTGT
19037875 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
** *
19037900 GCTCTCTAATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * * * *
19037923 GCTATCTGATCAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
19037946 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
19037969 GCTCTCTGTTT
1 GCTCTCTGTTT
19037980 CCTAGCACTT
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
23 67 0.77
24 1 0.01
25 17 0.20
26 2 0.02
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:19038017 original size:69 final size:71
Alignment explanation
Indices: 19037876--19038022 Score: 178
Period size: 69 Copynumber: 2.1 Consensus size: 71
19037866 ACGTCTTGTG
* *
19037876 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTAATTAGCACTTTGTGTGCTATCTGATCAGTACTT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTAATTAGCACTTTATGTGATATCTGATCAGTACTT
19037941 TGTGTA
66 TGTGTA
** * *
19037947 CTCTCTG-T-TTAGCACTGTGTGTGCTCTCTGTTTCCTAGCAC-TTATGTGATCTCT-ATTAGTA
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCT-AAT--TAGCACTTTATGTGATATCTGATCAGTA
19038008 CTTTG-GTA
63 CTTTGTGTA
19038016 CTCTCTG
1 CTCTCTG
19038023 CTCGTTCCGT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
69 31 0.46
70 13 0.19
71 17 0.25
72 6 0.09
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (71 bp):
CTCTCTGTTATTAGCACTGTGTGTGCTCTCTAATTAGCACTTTATGTGATATCTGATCAGTACTT
TGTGTA
Found at i:19045249 original size:25 final size:23
Alignment explanation
Indices: 19045212--19045338 Score: 139
Period size: 23 Copynumber: 5.4 Consensus size: 23
19045202 ACATTAGCGC
*
19045212 GCTCTCTGTTTAGCA-TGTCTTGT
1 GCTCTCTGTTTAGCACTGT-GTGT
19045235 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
** *
19045260 GCTCTCTAATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * * *
19045283 GCTCTCTGATCAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
19045306 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
19045329 GCTCTCTGTT
1 GCTCTCTGTT
19045339 GCCCAGTACT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
23 68 0.77
24 1 0.01
25 16 0.18
26 3 0.03
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:19045304 original size:21 final size:22
Alignment explanation
Indices: 19045232--19045370 Score: 93
Period size: 23 Copynumber: 6.0 Consensus size: 22
19045222 TAGCATGTCT
*
19045232 TGTGCTCTCTGTTATTAGCACTGTG
1 TGTGCTCTCTG--ATTAGTACT-TG
* *
19045257 TGTGCTCTCTAATTAGCACTTTG
1 TGTGCTCTCTGATTAGTAC-TTG
*
19045280 TGTGCTCTCTGATCAGTACTTTG
1 TGTGCTCTCTGATTAGTAC-TTG
* * *
19045303 TGTACTCTCTGTTTAGCACTGTG
1 TGTGCTCTCTGATTAGTACT-TG
*
19045326 TGTGCTCTCTG-TTGCCCAGTACTTA
1 TGTGCTCTCTGATT----AGTACTTG
*
19045351 TGTGGTCTCT-ATTAGTACTT
1 TGTGCTCTCTGATTAGTACTT
19045371 TGGTACTCTT
Statistics
Matches: 95, Mismatches: 12, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
21 7 0.07
22 3 0.03
23 57 0.60
24 1 0.01
25 22 0.23
26 5 0.05
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (22 bp):
TGTGCTCTCTGATTAGTACTTG
Found at i:19052031 original size:25 final size:25
Alignment explanation
Indices: 19052003--19052051 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
19051993 GTGCCTTGGT
19052003 TTATCCCTAATGAGAGTCTCTATCA
1 TTATCCCTAATGAGAGTCTCTATCA
*
19052028 TTATCCCTAATGAGATTCTCTATC
1 TTATCCCTAATGAGAGTCTCTATC
19052052 GATGTCATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (25 bp):
TTATCCCTAATGAGAGTCTCTATCA
Found at i:19061626 original size:110 final size:110
Alignment explanation
Indices: 19061425--19061767 Score: 380
Period size: 110 Copynumber: 3.0 Consensus size: 110
19061415 ACAGTCATAT
19061425 TCCTGATGAGATACAGAGAAGTGAACCAAGACAATGAAGCAAAGCTCAATGTGAGTGAAACTTCA
1 TCCTGATGAGATACAGAGAAGTGAACCAAGACAATGAAGCAAAGCTCAATGTGAGTGAAACTTCA
* * * *
19061490 AACCCCCATCTTCCTGATAAGGTACAGAGAAGTGGGTCAGAATAA
66 AACCCCCATCGTCCTGATAAGATACAGAGAAGTGGATCAAAATAA
* *
19061535 TCCTGATGAGATATAGAGAAGTGAACCAAGACATTGAAGCAAAGCTCAATGTGAGTGAAACTTCA
1 TCCTGATGAGATACAGAGAAGTGAACCAAGACAATGAAGCAAAGCTCAATGTGAGTGAAACTTCA
* *
19061600 AATCCCCATCGTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGTGGTCA
66 AACCCCCATCGTCCTGATAAGATACAGAGAAGTGGATC--AA-AAT--A------A
* * * * * *
19061656 TCTTCCTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAAATATGAGTAAAAC
1 ---TCCTGATGAGATACAGAGAAGTGAACCAAGACAATGAAGCAAAGCTC-AATGTGAGTGAAAC
* * * * *
19061721 ATCAAACCCCCATCTTCCTAATGAGATACAAAGAAGTGGATCAAAAT
62 TTCAAACCCCCATCGTCCTGATAAGATACAGAGAAGTGGATCAAAAT
19061768 GATAAAGCAG
Statistics
Matches: 197, Mismatches: 21, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
110 96 0.49
112 1 0.01
113 3 0.02
115 1 0.01
121 1 0.01
122 3 0.02
123 2 0.01
124 41 0.21
125 49 0.25
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (110 bp):
TCCTGATGAGATACAGAGAAGTGAACCAAGACAATGAAGCAAAGCTCAATGTGAGTGAAACTTCA
AACCCCCATCGTCCTGATAAGATACAGAGAAGTGGATCAAAATAA
Found at i:19061689 original size:48 final size:48
Alignment explanation
Indices: 19061606--19061697 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
19061596 TTCAAATCCC
* * *
19061606 CATCGTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGTGGT
1 CATCGTCCTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGTGGT
*
19061654 CATCTTCCTAATGAGATACAGAGAAGTGGACCAAAACAATGAAG
1 CATCGTCCTAATGAGATACAGAGAAGTGGACCAAAACAATGAAG
19061698 CGAAGCTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (48 bp):
CATCGTCCTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGTGGT
Found at i:19061761 original size:125 final size:124
Alignment explanation
Indices: 19061535--19061767 Score: 340
Period size: 125 Copynumber: 1.9 Consensus size: 124
19061525 GTCAGAATAA
* * * * * * *
19061535 TCCTGATGAGATATAGAGAAGTGAACCAAGACATTGAAGCAAAGCTCAATGTGAGTGAAACTTCA
1 TCCTAATGAGATACAGAGAAGTGAACCAAAACAATGAAGCAAAGCTCAATATGAGTAAAACATCA
* * *
19061600 AATCCCCATCGTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGTGGTCATCT
66 AACCCCCATCGTCCTAATGAGATACAAAGAAGTGGATCAAAATAATGAAGTGGTCATCT
* *
19061659 TCCTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAAATATGAGTAAAACATC
1 TCCTAATGAGATACAGAGAAGTGAACCAAAACAATGAAGCAAAGCTC-AATATGAGTAAAACATC
*
19061724 AAACCCCCATCTTCCTAATGAGATACAAAGAAGTGGATCAAAAT
65 AAACCCCCATCGTCCTAATGAGATACAAAGAAGTGGATCAAAAT
19061768 GATAAAGCAG
Statistics
Matches: 95, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
124 41 0.43
125 54 0.57
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (124 bp):
TCCTAATGAGATACAGAGAAGTGAACCAAAACAATGAAGCAAAGCTCAATATGAGTAAAACATCA
AACCCCCATCGTCCTAATGAGATACAAAGAAGTGGATCAAAATAATGAAGTGGTCATCT
Found at i:19074501 original size:30 final size:29
Alignment explanation
Indices: 19074465--19074546 Score: 110
Period size: 30 Copynumber: 2.8 Consensus size: 29
19074455 TTGAAACCCT
*
19074465 AAACTTTTCTAAAATTATATTTTAACACTC
1 AAACTTTCCTAAAATTATATTTTAACAC-C
* * *
19074495 AAACTTTCCTAAAATTACATTTTGACTCC
1 AAACTTTCCTAAAATTATATTTTAACACC
*
19074524 AAACTTTCCCAAAATTATATTTT
1 AAACTTTCCTAAAATTATATTTT
19074547 GCCTAAACTT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 22 0.48
30 24 0.52
ACGTcount: A:0.38, C:0.20, G:0.01, T:0.41
Consensus pattern (29 bp):
AAACTTTCCTAAAATTATATTTTAACACC
Found at i:19074527 original size:29 final size:28
Alignment explanation
Indices: 19074460--19074578 Score: 107
Period size: 29 Copynumber: 4.1 Consensus size: 28
19074450 AACTTTTGAA
* * *
19074460 ACCCTAAACTTTTCTAAAATTATATTTTA
1 ACCC-AAACTTTCCTAAAATTACATTTTG
19074489 ACACTCAAACTTTCCTAAAATTACATTTTG
1 AC-C-CAAACTTTCCTAAAATTACATTTTG
* *
19074519 ACTCCAAACTTTCCCAAAATTATATTTTG
1 AC-CCAAACTTTCCTAAAATTACATTTTG
* * *
19074548 -CCTAAACTTTTCC-AACATTACGTTTTG
1 ACCCAAAC-TTTCCTAAAATTACATTTTG
19074575 ACCC
1 ACCC
19074579 CTAAAATTCT
Statistics
Matches: 75, Mismatches: 11, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
27 16 0.21
28 8 0.11
29 25 0.33
30 25 0.33
31 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (28 bp):
ACCCAAACTTTCCTAAAATTACATTTTG
Found at i:19078020 original size:12 final size:13
Alignment explanation
Indices: 19077997--19078025 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
19077987 GCAAACAGTT
19077997 TTTTCTTCTTTTC
1 TTTTCTTCTTTTC
19078010 TTTTC-TCTTTTC
1 TTTTCTTCTTTTC
19078022 TTTT
1 TTTT
19078026 TTCCTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTCTTTTC
Found at i:19082088 original size:23 final size:24
Alignment explanation
Indices: 19082058--19082108 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
19082048 TAGCCCAAAG
*
19082058 GACAAC-TTCCATTGCCTCACATT
1 GACAACTTTCCATTGCCTCACATC
*
19082081 GACAACTTTTCATTGCCTCACATC
1 GACAACTTTCCATTGCCTCACATC
19082105 GACA
1 GACA
19082109 CCTTAGTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.27, C:0.33, G:0.10, T:0.29
Consensus pattern (24 bp):
GACAACTTTCCATTGCCTCACATC
Found at i:19086139 original size:125 final size:124
Alignment explanation
Indices: 19085780--19086449 Score: 833
Period size: 124 Copynumber: 5.4 Consensus size: 124
19085770 AAACTTCAAA
* * * * * *
19085780 CGGTCATATTCCTGATAAGATACAGAGAAGTGAACTAAGATAATGAAGTAAAGCTCAATGTGAGT
1 CGGTCATCTTCCTGATGAGATATAGAGAAGTGGACCAAAATAATGAAGTAAAGCTCAATGTGAGT
* * * * *
19085845 GAAACTTCAAACCCCCATCTTCCTGATGAGATATAGAAAAGTGGATCAGAATAATGAAG
66 AAAACTTCAAACCCCCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAG
* * * * * * *
19085904 CGATCATCTTCCTGATGAGATATAGTGAAGTGAACCAAGACATTGAAGTAAAGATCAATGTGAGT
1 CGGTCATCTTCCTGATGAGATATAGAGAAGTGGACCAAAATAATGAAGTAAAGCTCAATGTGAGT
* * * *
19085969 GAAACTTCAAACCCCTATCTTCTTGATGAGATATAGAGAAGTGGATCGAAATAATGAAG
66 AAAACTTCAAACCCCCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAG
* * * * **
19086028 CGGTCATATTCTTGATGAGACACAGAGAAGTGGACCAAAATAATGAAGCGAAGCTCAAATGTGAG
1 CGGTCATCTTCCTGATGAGATATAGAGAAGTGGACCAAAATAATGAAGTAAAGCTC-AATGTGAG
* * * *
19086093 TAAAATTTCAAACCTCCATCTTCATGATGAGATACAGAGAAGTGGATCGAAATAATGAAG
65 TAAAACTTCAAACCCCCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAG
* *
19086153 CGGTCATCTTCCTGATGAGATATAGAGAAGTGGACCAAAACAATGAAGCAAAGCTCAAATGTGAG
1 CGGTCATCTTCCTGATGAGATATAGAGAAGTGGACCAAAATAATGAAGTAAAGCTC-AATGTGAG
* * *
19086218 TAAAACTTCAAACCCCCATGTT-TCTGATGAGATACAAAGAAGTGGATCAAAATGATGAAG
65 TAAAACTTCAAACCCCCATCTTCT-TGATGAGATACAGAGAAGTGGATCAAAATAATGAAG
* * * * * * *
19086278 CGGTAATTTTCCTCATGAGATATAGAGAAGTAGATC-AAATCAATGAAGTGAAGCTCAGTGTGAG
1 CGGTCATCTTCCTGATGAGATATAGAGAAGTGGACCAAAAT-AATGAAGTAAAGCTCAATGTGAG
* * * *
19086342 TAAAACTTCAAACCCCCATCTTCTTGATGAGATACAAAGAAGTGGCTCAAAATGATGAGG
65 TAAAACTTCAAACCCCCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAG
* *
19086402 CGATCATCTTCCTGATGAGATATAGAGAAGTGGACCAAAA-GATGAAGT
1 CGGTCATCTTCCTGATGAGATATAGAGAAGTGGACCAAAATAATGAAGT
19086450 TACAAACACC
Statistics
Matches: 476, Mismatches: 65, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
123 7 0.01
124 248 0.52
125 221 0.46
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (124 bp):
CGGTCATCTTCCTGATGAGATATAGAGAAGTGGACCAAAATAATGAAGTAAAGCTCAATGTGAGT
AAAACTTCAAACCCCCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAG
Found at i:19086180 original size:48 final size:48
Alignment explanation
Indices: 19086109--19086201 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
19086099 TTCAAACCTC
* * *
19086109 CATCTTCATGATGAGATACAGAGAAGTGGATCGAAATAATGAAGCGGT
1 CATCTTCATGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGGT
* *
19086157 CATCTTCCTGATGAGATATAGAGAAGTGGACCAAAACAATGAAGC
1 CATCTTCATGATGAGATACAGAGAAGTGGACCAAAACAATGAAGC
19086202 AAAGCTCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.22
Consensus pattern (48 bp):
CATCTTCATGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGGT
Found at i:19086342 original size:249 final size:247
Alignment explanation
Indices: 19085780--19086441 Score: 853
Period size: 249 Copynumber: 2.7 Consensus size: 247
19085770 AAACTTCAAA
* * * * * * *
19085780 CGGTCATATTCCTGATAAGATACAGAGAAGT-GAACTAAGATAATGAAGTAAAGCTCAATGTGAG
1 CGGTAATATTCCTCATGAGACACAGAGAAGTAG-ACCAAAATAATGAAGTGAAGCTCAATGTGAG
* * * *
19085844 TGAAACTTCAAACCCCCATCTTCCTGATGAGATATAGAAAAGTGGATCAGAATAATGAAGCGATC
65 TAAAACTTCAAACCCCCATCTTCATGATGAGATACAGAGAAGTGGATCA-AATAATGAAGCGATC
* * * * * *
19085909 ATCTTCCTGATGAGATATAGTGAAGTGAACCAAGACATTGAAGTAAAGATCAATGTGAGTGAAAC
129 ATCTTCCTGATGAGATATAGAGAAGTGGACCAAAACAATGAAGCAAAGATCAATGTGAGTAAAAC
* * * *
19085974 TTCAAACCCCTATCTTCTTGATGAGATATAGAGAAGTGGATCGAAATAATGAAG
194 TTCAAACCCCCATCTTCTTGATGAGATACAAAGAAGTGGATCAAAATAATGAAG
* * * * *
19086028 CGGTCATATTCTTGATGAGACACAGAGAAGTGGACCAAAATAATGAAGCGAAGCTCAAATGTGAG
1 CGGTAATATTCCTCATGAGACACAGAGAAGTAGACCAAAATAATGAAGTGAAGCTC-AATGTGAG
* * *
19086093 TAAAATTTCAAACCTCCATCTTCATGATGAGATACAGAGAAGTGGATCGAAATAATGAAGCGGTC
65 TAAAACTTCAAACCCCCATCTTCATGATGAGATACAGAGAAGTGGATC-AAATAATGAAGCGATC
*
19086158 ATCTTCCTGATGAGATATAGAGAAGTGGACCAAAACAATGAAGCAAAGCTCAAATGTGAGTAAAA
129 ATCTTCCTGATGAGATATAGAGAAGTGGACCAAAACAATGAAGCAAAGATC-AATGTGAGTAAAA
* *
19086223 CTTCAAACCCCCATGTT-TCTGATGAGATACAAAGAAGTGGATCAAAATGATGAAG
193 CTTCAAACCCCCATCTTCT-TGATGAGATACAAAGAAGTGGATCAAAATAATGAAG
* * * * *
19086278 CGGTAATTTTCCTCATGAGATATAGAGAAGTAGATC-AAATCAATGAAGTGAAGCTCAGTGTGAG
1 CGGTAATATTCCTCATGAGACACAGAGAAGTAGACCAAAAT-AATGAAGTGAAGCTCAATGTGAG
* * * * *
19086342 TAAAACTTCAAACCCCCATCTTCTTGATGAGATACAAAGAAGTGGCTCAAAATGATGAGGCGATC
65 TAAAACTTCAAACCCCCATCTTCATGATGAGATACAGAGAAGTGGATC-AAATAATGAAGCGATC
19086407 ATCTTCCTGATGAGATATAGAGAAGTGGACCAAAA
129 ATCTTCCTGATGAGATATAGAGAAGTGGACCAAAA
19086442 GATGAAGTTA
Statistics
Matches: 362, Mismatches: 46, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
248 47 0.13
249 213 0.59
250 102 0.28
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (247 bp):
CGGTAATATTCCTCATGAGACACAGAGAAGTAGACCAAAATAATGAAGTGAAGCTCAATGTGAGT
AAAACTTCAAACCCCCATCTTCATGATGAGATACAGAGAAGTGGATCAAATAATGAAGCGATCAT
CTTCCTGATGAGATATAGAGAAGTGGACCAAAACAATGAAGCAAAGATCAATGTGAGTAAAACTT
CAAACCCCCATCTTCTTGATGAGATACAAAGAAGTGGATCAAAATAATGAAG
Found at i:19088206 original size:30 final size:30
Alignment explanation
Indices: 19088167--19088277 Score: 138
Period size: 30 Copynumber: 3.7 Consensus size: 30
19088157 CCTTATTATA
* *
19088167 TTCCAAAATTATATTTTAACCCCAAAACTT
1 TTCCAAAATTACATTTTGACCCCAAAACTT
*
19088197 TTTCAAAATTACATTTTGACCCTC-AAACTT
1 TTCCAAAATTACATTTTGACCC-CAAAACTT
19088227 TTCCAAAATTACATTTTGACCCCTAAAA-TT
1 TTCCAAAATTACATTTTGACCCC-AAAACTT
*
19088257 CTCCAAAACTT-CATTTTGACC
1 TTCCAAAA-TTACATTTTGACC
19088278 TCGTTTTTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
29 1 0.01
30 65 0.90
31 6 0.08
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (30 bp):
TTCCAAAATTACATTTTGACCCCAAAACTT
Found at i:19092171 original size:7 final size:6
Alignment explanation
Indices: 19092149--19092197 Score: 55
Period size: 7 Copynumber: 7.8 Consensus size: 6
19092139 TATAGTAATA
*
19092149 TTTCTT TTTTTCT TTTCTAT TTTCTT TTCTCTT TTTC-T TTTCTT TTTCT
1 TTTCTT TTTCT-T TTTCT-T TTTCTT TT-TCTT TTTCTT TTTCTT TTTCT
19092198 CATTCAACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
5 5 0.14
6 15 0.41
7 17 0.46
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:19092171 original size:13 final size:12
Alignment explanation
Indices: 19092149--19092195 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
19092139 TATAGTAATA
19092149 TTTCTTTTTTTCT
1 TTTC-TTTTTTCT
*
19092162 TTTCTATTTTCT
1 TTTCTTTTTTCT
19092174 TTTCTCTTTTTCT
1 TTTCT-TTTTTCT
19092187 TTTCTTTTT
1 TTTCTTTTT
19092196 CTCATTCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
12 16 0.52
13 15 0.48
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTCTTTTTTCT
Found at i:19092173 original size:12 final size:11
Alignment explanation
Indices: 19092155--19092197 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 11
19092145 AATATTTCTT
19092155 TTTTTCTTTTC
1 TTTTTCTTTTC
19092166 TATTTTCTTTTCTC
1 T-TTTTC-TTT-TC
19092180 TTTTTCTTTTC
1 TTTTTCTTTTC
19092191 TTTTTCT
1 TTTTTCT
19092198 CATTCAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 10 0.34
12 8 0.28
13 8 0.28
14 3 0.10
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:19092183 original size:25 final size:24
Alignment explanation
Indices: 19092149--19092197 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
19092139 TATAGTAATA
*
19092149 TTTCTTTTTTTCTTTTCTATTTTCT
1 TTTCTCTTTTTCTTTTCT-TTTTCT
19092174 TTTCTCTTTTTCTTTTCTTTTTCT
1 TTTCTCTTTTTCTTTTCTTTTTCT
19092198 CATTCAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTCTCTTTTTCTTTTCTTTTTCT
Found at i:19092196 original size:19 final size:20
Alignment explanation
Indices: 19092149--19092198 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
19092139 TATAGTAATA
*
19092149 TTTCTTTTTTTCTTTTCTAT
1 TTTCTTTTTCTCTTTTCTAT
*
19092169 TTTC-TTTTCTCTTTT-TCT
1 TTTCTTTTTCTCTTTTCTAT
19092187 TTTCTTTTTCTC
1 TTTCTTTTTCTC
19092199 ATTCAACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 6 0.22
19 17 0.63
20 4 0.15
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTCTTTTTCTCTTTTCTAT
Found at i:19092977 original size:21 final size:21
Alignment explanation
Indices: 19092947--19092986 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19092937 TCTTCTTTGT
* * *
19092947 GCTTCTTCTTTTTGTCCTTGC
1 GCTTCCTCTTCTTATCCTTGC
19092968 GCTTCCTCTTCTTATCCTT
1 GCTTCCTCTTCTTATCCTT
19092987 CGAACCAACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.33, G:0.10, T:0.55
Consensus pattern (21 bp):
GCTTCCTCTTCTTATCCTTGC
Found at i:19109540 original size:20 final size:20
Alignment explanation
Indices: 19109517--19109601 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 20
19109507 CCCCTATTTA
**
19109517 CACTTTAATGTCTGTGTTTG
1 CACTTTAATGTCCATGTTTG
* * * *
19109537 CACTTTAGTGTCCCTATTTA
1 CACTTTAATGTCCATGTTTG
*
19109557 CACTTTCATGTCCATGTTTG
1 CACTTTAATGTCCATGTTTG
* * *
19109577 CACTTTAGTGCCCCTGTTTG
1 CACTTTAATGTCCATGTTTG
19109597 CACTT
1 CACTT
19109602 CGGTGCCCTA
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.15, C:0.25, G:0.15, T:0.45
Consensus pattern (20 bp):
CACTTTAATGTCCATGTTTG
Found at i:19109552 original size:40 final size:40
Alignment explanation
Indices: 19109497--19109601 Score: 147
Period size: 40 Copynumber: 2.6 Consensus size: 40
19109487 CCACTATTTT
* **
19109497 CACTTCAGTGCCCCTATTTACACTTTAATGTCTGTGTTTG
1 CACTTTAGTGCCCCTATTTACACTTTAATGTCCATGTTTG
* *
19109537 CACTTTAGTGTCCCTATTTACACTTTCATGTCCATGTTTG
1 CACTTTAGTGCCCCTATTTACACTTTAATGTCCATGTTTG
* *
19109577 CACTTTAGTGCCCCTGTTTGCACTT
1 CACTTTAGTGCCCCTATTTACACTT
19109602 CGGTGCCCTA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.16, C:0.27, G:0.14, T:0.43
Consensus pattern (40 bp):
CACTTTAGTGCCCCTATTTACACTTTAATGTCCATGTTTG
Found at i:19109607 original size:20 final size:20
Alignment explanation
Indices: 19109497--19109609 Score: 75
Period size: 20 Copynumber: 5.7 Consensus size: 20
19109487 CCACTATTTT
* *
19109497 CACTTCAGTGCCCCTATTTA
1 CACTTCAGTGCCCCTGTTTG
* * * **
19109517 CACTTTAATGTCTGTGTTTG
1 CACTTCAGTGCCCCTGTTTG
* * * *
19109537 CACTTTAGTGTCCCTATTTA
1 CACTTCAGTGCCCCTGTTTG
* *
19109557 CACTTTCA-TGTCCATGTTTG
1 CAC-TTCAGTGCCCCTGTTTG
*
19109577 CACTTTAGTGCCCCTGTTTG
1 CACTTCAGTGCCCCTGTTTG
*
19109597 CACTTCGGTGCCC
1 CACTTCAGTGCCC
19109610 TAGATAGTAC
Statistics
Matches: 70, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
19 3 0.04
20 64 0.91
21 3 0.04
ACGTcount: A:0.15, C:0.28, G:0.16, T:0.41
Consensus pattern (20 bp):
CACTTCAGTGCCCCTGTTTG
Found at i:19113679 original size:22 final size:24
Alignment explanation
Indices: 19113653--19113698 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
19113643 TTTGTCCCTA
19113653 TTTAG-TTTT-CTTCAGTAAATAT
1 TTTAGATTTTACTTCAGTAAATAT
19113675 TTTAGCATTTTCACTTCAGTAAAT
1 TTTAG-ATTTT-ACTTCAGTAAAT
19113699 TGCATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
24 4 0.20
26 11 0.55
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (24 bp):
TTTAGATTTTACTTCAGTAAATAT
Found at i:19116196 original size:21 final size:21
Alignment explanation
Indices: 19116170--19116225 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
19116160 GCACACTCAA
19116170 ATGCATCCACAACA-AAGCCAG
1 ATGCATCCACAACAGAA-CCAG
* *
19116191 ATGCATCCACACCAGAATCAG
1 ATGCATCCACAACAGAACCAG
*
19116212 ATGCAACCACAACA
1 ATGCATCCACAACA
19116226 CTCTTCAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.43, C:0.34, G:0.12, T:0.11
Consensus pattern (21 bp):
ATGCATCCACAACAGAACCAG
Found at i:19123615 original size:22 final size:22
Alignment explanation
Indices: 19123577--19123626 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
19123567 AACGGTCAAT
* **
19123577 GGTCAACGGTCGATCAATGGTC
1 GGTCAACGGTAGATCAACAGTC
19123599 GGTCAACGGCTAG-TCAACAGTC
1 GGTCAACGG-TAGATCAACAGTC
19123621 GGTCAA
1 GGTCAA
19123627 TGGTTTGACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (22 bp):
GGTCAACGGTAGATCAACAGTC
Found at i:19143174 original size:17 final size:18
Alignment explanation
Indices: 19143144--19143185 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
19143134 ACTACAATGC
19143144 AAATGTACTAACAACT-A
1 AAATGTACTAACAACTAA
* * *
19143161 AAATGTAGTGACAATTAA
1 AAATGTACTAACAACTAA
19143179 AAATGTA
1 AAATGTA
19143186 ATCAGAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATGTACTAACAACTAA
Found at i:19143333 original size:21 final size:21
Alignment explanation
Indices: 19143309--19143352 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19143299 GCCTTCCTCT
*
19143309 TTGCGC-TTCTTTTTCTTATCC
1 TTGCGCTTTCTCTTT-TTATCC
19143330 TTGCGCTTTCTCTTTTTATCC
1 TTGCGCTTTCTCTTTTTATCC
19143351 TT
1 TT
19143353 TGAATCAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.05, C:0.27, G:0.09, T:0.59
Consensus pattern (21 bp):
TTGCGCTTTCTCTTTTTATCC
Found at i:19161205 original size:21 final size:21
Alignment explanation
Indices: 19161179--19161222 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19161169 GGTTGATTCA
*
19161179 AAGGATAA-AAAGAGAAAGCAC
1 AAGGATAAGAAAAAG-AAGCAC
19161200 AAGGATAAGAAAAAGAAGCAC
1 AAGGATAAGAAAAAGAAGCAC
19161221 AA
1 AA
19161223 AGAGGAAGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.64, C:0.09, G:0.23, T:0.05
Consensus pattern (21 bp):
AAGGATAAGAAAAAGAAGCAC
Found at i:19167515 original size:11 final size:11
Alignment explanation
Indices: 19167499--19167528 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
19167489 TCTTATCTAA
19167499 TTATTAATTAT
1 TTATTAATTAT
19167510 TTATTAATTAT
1 TTATTAATTAT
19167521 TTATTAAT
1 TTATTAAT
19167529 GTGGAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTATTAATTAT
Found at i:19168009 original size:21 final size:21
Alignment explanation
Indices: 19167981--19168021 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19167971 GTGTTAAAAA
*
19167981 TTAAATTTTAA-ACCCAATTT
1 TTAAATTTTAATAACCAATTT
19168001 TTAATATTTTAATAACCAATT
1 TTAA-ATTTTAATAACCAATT
19168022 AAACCTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAAATTTTAATAACCAATTT
Found at i:19184698 original size:15 final size:15
Alignment explanation
Indices: 19184675--19184705 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19184665 TGCAACGCAG
19184675 GAAGATAAGCTCATT
1 GAAGATAAGCTCATT
*
19184690 GAAGGTAAGCTCATT
1 GAAGATAAGCTCATT
19184705 G
1 G
19184706 CTAATTTTTG
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:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (15 bp):
GAAGATAAGCTCATT
Found at i:19192254 original size:19 final size:21
Alignment explanation
Indices: 19192219--19192257 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
19192209 GAGACAAAGA
19192219 AAATGTAATGACAACTAAATG
1 AAATGTAATGACAACTAAATG
19192240 AAATG-AATG-CAACTAAAT
1 AAATGTAATGACAACTAAAT
19192258 TAAGTATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 4 0.22
21 5 0.28
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (21 bp):
AAATGTAATGACAACTAAATG
Found at i:19221769 original size:84 final size:83
Alignment explanation
Indices: 19221626--19221787 Score: 279
Period size: 84 Copynumber: 1.9 Consensus size: 83
19221616 AATGTTGCTT
19221626 TTCCTCATGCTAATTTTGTGCCCAGAGAACCATAAAACTAATCTAAGATTTCTACTAGAAATTGA
1 TTCCTCATGCTAATTTTGTGCCCAGAGAACCATAAAACTAATCTAAGATTTCTACTAGAAATTGA
19221691 GCTTGATCCAAATTACTC
66 GCTTGATCCAAATTACTC
* * * *
19221709 TTCCTCGTGCTAATTTTGTGCCTAGAGAACTCATAAAACTGATCTAAGATTTCTGCTAGAAATTG
1 TTCCTCATGCTAATTTTGTGCCCAGAGAAC-CATAAAACTAATCTAAGATTTCTACTAGAAATTG
19221774 AGCTTGATCCAAAT
65 AGCTTGATCCAAAT
19221788 CCACTTTGCT
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
83 28 0.38
84 46 0.62
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.33
Consensus pattern (83 bp):
TTCCTCATGCTAATTTTGTGCCCAGAGAACCATAAAACTAATCTAAGATTTCTACTAGAAATTGA
GCTTGATCCAAATTACTC
Found at i:19242282 original size:34 final size:35
Alignment explanation
Indices: 19242230--19242300 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 35
19242220 GTAATTGTAA
* * *
19242230 TTTAATTGTCACCACATTCTC-TTTTTCATTGCAT
1 TTTAATTGTCACCACATTCACATTTGTCATCGCAT
**
19242264 TTTAATTGTCACTGCATTCACATTTGTCATCGCAT
1 TTTAATTGTCACCACATTCACATTTGTCATCGCAT
19242299 TT
1 TT
19242301 CCATTTGTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.21, C:0.23, G:0.08, T:0.48
Consensus pattern (35 bp):
TTTAATTGTCACCACATTCACATTTGTCATCGCAT
Found at i:19244834 original size:24 final size:24
Alignment explanation
Indices: 19244807--19244889 Score: 62
Period size: 24 Copynumber: 3.3 Consensus size: 24
19244797 ACTTCAGATG
19244807 AGTAGGAAATGGCTTCAATTCCAA
1 AGTAGGAAATGGCTTCAATTCCAA
** *
19244831 AGTAGGAGCT-TCTTCCATACTT-CAGA
1 AGTAGGAAATGGCTT-CA-A-TTCCA-A
*
19244857 TGAGTAGGCAATGGCTTCAATTCCAA
1 --AGTAGGAAATGGCTTCAATTCCAA
19244883 AGTAGGA
1 AGTAGGA
19244890 GCTTCTTCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
23 3 0.07
24 16 0.37
25 3 0.07
26 6 0.14
27 3 0.07
28 9 0.21
29 3 0.07
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.27
Consensus pattern (24 bp):
AGTAGGAAATGGCTTCAATTCCAA
Found at i:19244872 original size:52 final size:52
Alignment explanation
Indices: 19244794--19244897 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
19244784 CCAAGAAAAA
19244794 CATACTTCAGATGAGTAGGAAATGGCTTCAATTCCAAAGTAGGAGCTTCTTC
1 CATACTTCAGATGAGTAGGAAATGGCTTCAATTCCAAAGTAGGAGCTTCTTC
*
19244846 CATACTTCAGATGAGTAGGCAATGGCTTCAATTCCAAAGTAGGAGCTTCTTC
1 CATACTTCAGATGAGTAGGAAATGGCTTCAATTCCAAAGTAGGAGCTTCTTC
19244898 AATAGATGGC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (52 bp):
CATACTTCAGATGAGTAGGAAATGGCTTCAATTCCAAAGTAGGAGCTTCTTC
Found at i:19244898 original size:23 final size:23
Alignment explanation
Indices: 19244819--19244900 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
19244809 TAGGAAATGG
19244819 CTTCAATTCCAAAGTAGGAGCTT
1 CTTCAATTCCAAAGTAGGAGCTT
* *
19244842 CTTCCATACTT-CAGATGAGTAGGCA-ATGG
1 CTT-CA-A-TTCCA-A--AGTAGG-AGCT-T
19244871 CTTCAATTCCAAAGTAGGAGCTT
1 CTTCAATTCCAAAGTAGGAGCTT
19244894 CTTCAAT
1 CTTCAAT
19244901 AGATGGCTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 20
0.65 0.06 0.29
Matches are distributed among these distances:
23 11 0.24
24 9 0.20
25 3 0.07
26 6 0.13
27 3 0.07
28 9 0.20
29 4 0.09
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (23 bp):
CTTCAATTCCAAAGTAGGAGCTT
Found at i:19249729 original size:34 final size:34
Alignment explanation
Indices: 19249686--19249754 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
19249676 TACTAATGTA
19249686 AAGATTTTTATGATGTATTTGTTATATAAAAATT
1 AAGATTTTTATGATGTATTTGTTATATAAAAATT
19249720 AAGATTTTTATGATGTATTTGTTATATAAAAATT
1 AAGATTTTTATGATGTATTTGTTATATAAAAATT
19249754 A
1 A
19249755 CCCCTTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (34 bp):
AAGATTTTTATGATGTATTTGTTATATAAAAATT
Found at i:19249967 original size:21 final size:20
Alignment explanation
Indices: 19249943--19250039 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 20
19249933 TATAACTGTA
19249943 TTAATATCTAATTATAAATAT
1 TTAATAT-TAATTATAAATAT
19249964 TTAATGATTATATT-TAAATAT
1 TTAAT-ATTA-ATTATAAATAT
* *
19249985 TTAAAATGTAATT-TATATAT
1 TTAATAT-TAATTATAAATAT
* *
19250005 TCTAAT-TAAATTTTATAAATAA
1 T-TAATATTAA--TTATAAATAT
19250027 TTAATATTAATTA
1 TTAATATTAATTA
19250040 CTTAGAAATA
Statistics
Matches: 61, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
19 2 0.03
20 16 0.26
21 29 0.48
22 14 0.23
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TTAATATTAATTATAAATAT
Found at i:19249999 original size:33 final size:33
Alignment explanation
Indices: 19249962--19250024 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
19249952 AATTATAAAT
*
19249962 ATTTA-ATGATTATATTTAAATATTTA-AAATGTA
1 ATTTATAT-ATTATAATTAAAT-TTTATAAATGTA
*
19249995 ATTTATATATTCTAATTAAATTTTATAAAT
1 ATTTATATATTATAATTAAATTTTATAAAT
19250025 AATTAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
32 4 0.15
33 20 0.77
34 2 0.08
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (33 bp):
ATTTATATATTATAATTAAATTTTATAAATGTA
Found at i:19250480 original size:96 final size:96
Alignment explanation
Indices: 19250367--19250555 Score: 263
Period size: 96 Copynumber: 2.0 Consensus size: 96
19250357 AAAGGAGGAC
** * * **
19250367 TACGATTGATTTATCACCTTTAATG-AAGTGTTATTGGTGTAGTTCAAACGATCATGAGAGTTTT
1 TACGATTGAACTATCACCTTTAATGCAA-TGTTATTGGTGTAGTTCAAAAGATCATAAGAGTTAC
*
19250431 CAATGTCCAATTAAATATCCAAATAGAGAGAA
65 CAATGTCCAACTAAATATCCAAATAGAGAGAA
** *
19250463 TACGATTGAACTATCACCTTTTGTGCAATGTTATTGGTGTAGTTTAAAAGATCATAAGAGTTACC
1 TACGATTGAACTATCACCTTTAATGCAATGTTATTGGTGTAGTTCAAAAGATCATAAGAGTTACC
*
19250528 AATGTCCAACTAAATATCCAACTAGAGA
66 AATGTCCAACTAAATATCCAAATAGAGA
19250556 AGAAAGTAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
96 79 0.98
97 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (96 bp):
TACGATTGAACTATCACCTTTAATGCAATGTTATTGGTGTAGTTCAAAAGATCATAAGAGTTACC
AATGTCCAACTAAATATCCAAATAGAGAGAA
Done.