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 27 of 182
Found at i:10931591 original size:17 final size:17
Alignment explanation
Indices: 10931569--10931618 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
10931559 TGTGTAAATT
10931569 TAATATTTTAATTTTTA
1 TAATATTTTAATTTTTA
10931586 TAATATCTTTAATTAGTTTA
1 TAATAT-TTTAATT--TTTA
10931606 -AATA-TTTAATTTT
1 TAATATTTTAATTTT
10931619 AATTAAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
17 13 0.43
18 7 0.23
19 4 0.13
20 4 0.13
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TAATATTTTAATTTTTA
Found at i:10933794 original size:2 final size:2
Alignment explanation
Indices: 10933787--10933820 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10933777 AAATTATTTC
10933787 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
10933821 TAAAAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10937659 original size:41 final size:41
Alignment explanation
Indices: 10937614--10938027 Score: 223
Period size: 41 Copynumber: 10.1 Consensus size: 41
10937604 AGTAAATAAA
*
10937614 TTAGCGGCGCTTTATAATAAACGCCACTAATGCTCTAACTT
1 TTAGCGGCGCTTTATAATAAACGCCGCTAATGCTCTAACTT
*** * * * * *
10937655 TTAGCGGTATTTTTTTATAAACGTCGCTAATGCTTTAATTT
1 TTAGCGGCGCTTTATAATAAACGCCGCTAATGCTCTAACTT
* * * *
10937696 TTAGCGGCGCTTTTTTATAAACGCCTCTAATACTCTAACTT
1 TTAGCGGCGCTTTATAATAAACGCCGCTAATGCTCTAACTT
*** * * * * * *
10937737 TTAGC-GATATTTTTCATATAAACGTCGTTATTGCTTTACCTT
1 TTAGCGGCGCTTTAT-A-ATAAACGCCGCTAATGCTCTAACTT
* * * * *
10937779 TT-GCGGTG-TTTATCGAA-AAACGCCGTTATTG-TTTTACTT
1 TTAGCGGCGCTTTAT--AATAAACGCCGCTAATGCTCTAACTT
* * * * * * *
10937818 TTTGCGGCG-TTTATAAAAAACGCCGTTATTGAT-TTAGTT
1 TTAGCGGCGCTTTATAATAAACGCCGCTAATGCTCTAACTT
* * * ** * * *
10937857 TTTGCAGCG-TTTTTTGTCCAAACTCCGCTAATACTCTAACCT
1 TTAGCGGCGCTTTATAAT--AAACGCCGCTAATGCTCTAACTT
* * *
10937899 TTAGCGACGCTTTATAATAAACGCCACTAATGCTCTAACAT
1 TTAGCGGCGCTTTATAATAAACGCCGCTAATGCTCTAACTT
** * * * *
10937940 TTAGCGGCATTTTCTTATAAACGTCGCTAATGCTCTAACCT
1 TTAGCGGCGCTTTATAATAAACGCCGCTAATGCTCTAACTT
* * * *
10937981 TTAGCGGCGCTTTCTTATAAACGCCGCTAATACTCTAACCT
1 TTAGCGGCGCTTTATAATAAACGCCGCTAATGCTCTAACTT
10938022 TTAGCG
1 TTAGCG
10938028 ATATTTTTCC
Statistics
Matches: 290, Mismatches: 72, Indels: 22
0.76 0.19 0.06
Matches are distributed among these distances:
38 2 0.01
39 39 0.13
40 30 0.10
41 183 0.63
42 31 0.11
43 5 0.02
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (41 bp):
TTAGCGGCGCTTTATAATAAACGCCGCTAATGCTCTAACTT
Found at i:10937837 original size:39 final size:40
Alignment explanation
Indices: 10937756--10937868 Score: 147
Period size: 39 Copynumber: 2.9 Consensus size: 40
10937746 TTTTTCATAT
* * * * *
10937756 AAACGTCGTTATTGCTTTACCTTTTGCGGTGTTTATCGAA
1 AAACGCCGTTATTGATTTACTTTTTGCGGCGTTTATCAAA
*
10937796 AAACGCCGTTATTGTTTTACTTTTTGCGGCGTTTAT-AAA
1 AAACGCCGTTATTGATTTACTTTTTGCGGCGTTTATCAAA
* *
10937835 AAACGCCGTTATTGATTTAGTTTTTGCAGCGTTT
1 AAACGCCGTTATTGATTTACTTTTTGCGGCGTTT
10937869 TTTGTCCAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 33 0.51
40 32 0.49
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.43
Consensus pattern (40 bp):
AAACGCCGTTATTGATTTACTTTTTGCGGCGTTTATCAAA
Found at i:10938063 original size:41 final size:41
Alignment explanation
Indices: 10937882--10938074 Score: 176
Period size: 41 Copynumber: 4.7 Consensus size: 41
10937872 GTCCAAACTC
* * * * *
10937882 CGCTAATACTCTAACCTTTAGC-GACGCTTTATAATAAACGC
1 CGCTAATGCTCTAACCTTTAGCGGA-GTTTTCTTATAAACGT
* *
10937923 CACTAATGCTCTAACATTTAGCGGCA-TTTTCTTATAAACGT
1 CGCTAATGCTCTAACCTTTAGCGG-AGTTTTCTTATAAACGT
* * *
10937964 CGCTAATGCTCTAACCTTTAGCGGCGCTTTCTTATAAACGC
1 CGCTAATGCTCTAACCTTTAGCGGAGTTTTCTTATAAACGT
* * * *
10938005 CGCTAATACTCTAACCTTTAGCGATATTTTTCCTATAAACGT
1 CGCTAATGCTCTAACCTTTAGCG-GAGTTTTCTTATAAACGT
* * * *
10938047 CGCTATTGCT-TTACCTTTTGCGGCGTTT
1 CGCTAATGCTCTAACCTTTAGCGGAGTTT
10938075 ATGAAAAAAT
Statistics
Matches: 122, Mismatches: 26, Indels: 9
0.78 0.17 0.06
Matches are distributed among these distances:
40 3 0.02
41 97 0.80
42 21 0.17
43 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (41 bp):
CGCTAATGCTCTAACCTTTAGCGGAGTTTTCTTATAAACGT
Found at i:10938070 original size:82 final size:82
Alignment explanation
Indices: 10937882--10938076 Score: 250
Period size: 82 Copynumber: 2.4 Consensus size: 82
10937872 GTCCAAACTC
* * * *
10937882 CGCTAATACTCTAACCTTTAGCGACGCTTTATAATAAACGCCACTAATGCTCTAACATTTAGCGG
1 CGCTAATGCTCTAACCTTTAGCGGCGCTTTATAATAAACGCCACTAATACTCTAACATTTAGCGA
*
10937947 CATTTTCTTATAAACGT
66 CATTTTCCTATAAACGT
* * * *
10937964 CGCTAATGCTCTAACCTTTAGCGGCGCTTTCTTATAAACGCCGCTAATACTCTAACCTTTAGCGA
1 CGCTAATGCTCTAACCTTTAGCGGCGCTTTATAATAAACGCCACTAATACTCTAACATTTAGCGA
*
10938029 TATTTTTCCTATAAACGT
66 CA-TTTTCCTATAAACGT
* * *
10938047 CGCTATTGCT-TTACCTTTTGCGGCG-TTTAT
1 CGCTAATGCTCTAACCTTTAGCGGCGCTTTAT
10938077 GAAAAAATGC
Statistics
Matches: 98, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
81 4 0.04
82 71 0.72
83 23 0.23
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (82 bp):
CGCTAATGCTCTAACCTTTAGCGGCGCTTTATAATAAACGCCACTAATACTCTAACATTTAGCGA
CATTTTCCTATAAACGT
Found at i:10938132 original size:123 final size:121
Alignment explanation
Indices: 10937796--10938135 Score: 308
Period size: 123 Copynumber: 2.8 Consensus size: 121
10937786 GTTTATCGAA
* * *
10937796 AAACGCCGTTATTGTTTTACTTTTTGCGGCGTTTATAAAAAACGCCGTTATTGATTTAGTTTTTG
1 AAACGCCGCTATTGCTTTACATTTTGCGGCGTTTATAAAAAACGCCGTTATTGATTTAGTTTTTG
* *
10937861 CAGCGTTTTTTGTCCAAACTCCGCTAATACTCTAACCTTTAGCGACGCTTTATAAT
66 CAGCGTTTTTTGTCCAAACGCCGCTAATACTCTAACCTTTAGCGACGATTTATAAT
* * * * * * * * * * * * * **
10937917 AAACGCCACTAATGCTCTAACATTTAGCGGCATTTTCTTATAAACGTCGCTAATGCTCTAACCTT
1 AAACGCCGCTATTGCT-TTACATTTTGCGGC-GTTTATAAAAAACGCCGTTATTGAT-TTAGTTT
* * * * * * *
10937982 TAGCGGCGCTTTCTTAT--AAACGCCGCTAATACTCTAACCTTTAGCGA-TATTTTTCCTAT
63 TTGCAGCG-TTTTTTGTCCAAACGCCGCTAATACTCTAACCTTTAGCGACGATTTAT--AAT
* * * *
10938041 AAACGTCGCTATTGCTTTACCTTTTGCGGCGTTTATGAAAAAATGCCGTTATTTATTTAGTTTTT
1 AAACGCCGCTATTGCTTTACATTTTGCGGCGTTTAT-AAAAAACGCCGTTATTGATTTAGTTTTT
*
10938106 GCAGCGTTTTTTGTCCAATCGCCGCTAATA
65 GCAGCGTTTTTTGTCCAAACGCCGCTAATA
10938136 ACCTGTTTTG
Statistics
Matches: 159, Mismatches: 51, Indels: 16
0.70 0.23 0.07
Matches are distributed among these distances:
121 18 0.11
122 29 0.18
123 81 0.51
124 25 0.16
125 6 0.04
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (121 bp):
AAACGCCGCTATTGCTTTACATTTTGCGGCGTTTATAAAAAACGCCGTTATTGATTTAGTTTTTG
CAGCGTTTTTTGTCCAAACGCCGCTAATACTCTAACCTTTAGCGACGATTTATAAT
Found at i:10943670 original size:40 final size:40
Alignment explanation
Indices: 10943620--10943707 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
10943610 TAACCTTTAA
* * *
10943620 CGGCGCTTATGGAAAAACGCCGCTATTGTTTTACTTTTTG
1 CGGCGTTTATGAAAAAACGCCGCTATTGATTTACTTTTTG
* *
10943660 CGGCGTTTATGAAAAAACGCCGTTATTGATTTAGTTTTTG
1 CGGCGTTTATGAAAAAACGCCGCTATTGATTTACTTTTTG
*
10943700 CAGCGTTT
1 CGGCGTTT
10943708 TTTATCCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (40 bp):
CGGCGTTTATGAAAAAACGCCGCTATTGATTTACTTTTTG
Found at i:10949261 original size:40 final size:40
Alignment explanation
Indices: 10949211--10949298 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
10949201 TAACCTTTAA
* * *
10949211 CGGCGCTTATGGAAAAACGCCGCTATTGTTTTACTTTTTG
1 CGGCGTTTATGAAAAAACGCCGCTATTGATTTACTTTTTG
* *
10949251 CGGCGTTTATGAAAAAACGCCGTTATTGATTTAGTTTTTG
1 CGGCGTTTATGAAAAAACGCCGCTATTGATTTACTTTTTG
*
10949291 CAGCGTTT
1 CGGCGTTT
10949299 TTTATCCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (40 bp):
CGGCGTTTATGAAAAAACGCCGCTATTGATTTACTTTTTG
Found at i:10952325 original size:21 final size:21
Alignment explanation
Indices: 10952291--10952335 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
10952281 ACATGTGCCT
* *
10952291 TTTTAAAATAAATTCTATTTC
1 TTTTAAAATAAATTATATTGC
* *
10952312 TTTTAAATTTAATTATATTGC
1 TTTTAAAATAAATTATATTGC
10952333 TTT
1 TTT
10952336 CAATTGATTA
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:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTAAAATAAATTATATTGC
Found at i:10952621 original size:61 final size:60
Alignment explanation
Indices: 10952465--10952660 Score: 218
Period size: 60 Copynumber: 3.3 Consensus size: 60
10952455 TTAATATAAT
* * * * * ** *
10952465 ATTTGATATTTGAATTTGATATTTTTTT-TAATTTGGTACTTAAACTTTTTTTTTACCCA
1 ATTTGGTATCTGAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTTTTTTAGATCCA
* * * *
10952524 ATTTGGTATCTAAATTTGACA-CTTTTTCTTAATTTGGTACCTAAACTTTTTTTGGATCCA
1 ATTTGGTATCTGAACTTGACATTTTTTTC-TAATTTGGTACCTAAACTTTTTTTAGATCCA
* *
10952584 ATTTGGTATCTGAACTTGACATTTTTTTCCTAATTTGGTACCTAAGCTTTTTTTAGATTCA
1 ATTTGGTATCTGAACTTGACATTTTTTT-CTAATTTGGTACCTAAACTTTTTTTAGATCCA
*
10952645 ATTTGGTACCT-AACTT
1 ATTTGGTATCTGAACTT
10952661 TATTAAATAT
Statistics
Matches: 117, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
58 5 0.04
59 17 0.15
60 51 0.44
61 43 0.37
62 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.51
Consensus pattern (60 bp):
ATTTGGTATCTGAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTTTTTTAGATCCA
Found at i:10952913 original size:31 final size:30
Alignment explanation
Indices: 10952877--10952994 Score: 145
Period size: 31 Copynumber: 3.9 Consensus size: 30
10952867 TACTAACTTA
10952877 AAAAAAGTGTCAAGTTTAAATACCAAATTAAG
1 AAAAAA-TGTCAAGTTTAAATACCAAATT-AG
10952909 AAAAAATGTCAAGTTTAAATACCAAATTAG
1 AAAAAATGTCAAGTTTAAATACCAAATTAG
*
10952939 ACTAAAAA----AAGTTTAAGTACCAAATTAG
1 A--AAAAATGTCAAGTTTAAATACCAAATTAG
*
10952967 AAAAAAATGTCAAATTTAAATACCAAAT
1 -AAAAAATGTCAAGTTTAAATACCAAAT
10952995 ATTATATTAA
Statistics
Matches: 76, Mismatches: 3, Indels: 15
0.81 0.03 0.16
Matches are distributed among these distances:
27 5 0.07
28 19 0.25
29 1 0.01
30 3 0.04
31 37 0.49
32 11 0.14
ACGTcount: A:0.55, C:0.10, G:0.09, T:0.25
Consensus pattern (30 bp):
AAAAAATGTCAAGTTTAAATACCAAATTAG
Found at i:10952971 original size:89 final size:90
Alignment explanation
Indices: 10952808--10952994 Score: 227
Period size: 89 Copynumber: 2.1 Consensus size: 90
10952798 ACAAATTAGG
* ** * * *
10952808 TACCACATTAGAAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCTCAAAAAATTTAAGTACTAA
1 TACCAAATTAGAAAAAAGAGTCAAGTTCAAATACCAAATTAGACCTAAAAAAATTTAAGTACCAA
* * *
10952873 CTT-AAAAAAAGTGTCAAGTTTAAA
66 ATTAAAAAAAAATGTCAAATTTAAA
* *
10952897 TACCAAATTAAGAAAAAA-TGTCAAGTTTAAATACCAAATTAGA-CTAAAAAAAGTTTAAGTACC
1 TACCAAATT-AGAAAAAAGAGTCAAGTTCAAATACCAAATTAGACCTAAAAAAA-TTTAAGTACC
*
10952960 AAATTAGAAAAAAATGTCAAATTTAAA
64 AAATTAAAAAAAAATGTCAAATTTAAA
10952987 TACCAAAT
1 TACCAAAT
10952995 ATTATATTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
88 8 0.10
89 41 0.49
90 34 0.41
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (90 bp):
TACCAAATTAGAAAAAAGAGTCAAGTTCAAATACCAAATTAGACCTAAAAAAATTTAAGTACCAA
ATTAAAAAAAAATGTCAAATTTAAA
Found at i:10952973 original size:28 final size:28
Alignment explanation
Indices: 10952888--10952973 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
10952878 AAAAAGTGTC
**
10952888 AAGTTTAAATACCAAATTAAGAAAAAATGTC
1 AAGTTTAAATACCAAATT-AGAAAAAA--AA
**
10952919 AAGTTTAAATACCAAATTAGACTAAAAA
1 AAGTTTAAATACCAAATTAGAAAAAAAA
*
10952947 AAGTTTAAGTACCAAATTAGAAAAAAA
1 AAGTTTAAATACCAAATTAGAAAAAAA
10952974 TGTCAAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
28 24 0.50
30 6 0.12
31 18 0.38
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.24
Consensus pattern (28 bp):
AAGTTTAAATACCAAATTAGAAAAAAAA
Found at i:10953844 original size:16 final size:17
Alignment explanation
Indices: 10953810--10953844 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
10953800 TTTTCTTGTC
10953810 TTTTCTTATTTGATTTG
1 TTTTCTTATTTGATTTG
*
10953827 TTTTCTTTTTTG-TTTG
1 TTTTCTTATTTGATTTG
10953843 TT
1 TT
10953845 CAGTAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.06, C:0.06, G:0.11, T:0.77
Consensus pattern (17 bp):
TTTTCTTATTTGATTTG
Found at i:10955299 original size:24 final size:24
Alignment explanation
Indices: 10955269--10955334 Score: 132
Period size: 24 Copynumber: 2.8 Consensus size: 24
10955259 ACATTATTTA
10955269 TTGTGAGACAATTGTTTCTTTCAT
1 TTGTGAGACAATTGTTTCTTTCAT
10955293 TTGTGAGACAATTGTTTCTTTCAT
1 TTGTGAGACAATTGTTTCTTTCAT
10955317 TTGTGAGACAATTGTTTC
1 TTGTGAGACAATTGTTTC
10955335 CTGGAAAAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.48
Consensus pattern (24 bp):
TTGTGAGACAATTGTTTCTTTCAT
Found at i:10959785 original size:23 final size:24
Alignment explanation
Indices: 10959745--10959790 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
10959735 TATGGGTTTT
10959745 AATTAATTTTTCATAATTTTTATA
1 AATTAATTTTTCATAATTTTTATA
10959769 AATT-ATTTTTC-TAAATTTTTAT
1 AATTAATTTTTCAT-AATTTTTAT
10959791 GGTTTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 1 0.05
23 16 0.76
24 4 0.19
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
AATTAATTTTTCATAATTTTTATA
Found at i:10959862 original size:20 final size:19
Alignment explanation
Indices: 10959817--10959864 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
10959807 TGGTCTTTAA
10959817 TTGATTTTTAATAATTATT
1 TTGATTTTTAATAATTATT
*
10959836 TTAATTTTTAATCAATT-TT
1 TTGATTTTTAAT-AATTATT
10959855 TATGATTTTT
1 T-TGATTTTT
10959865 TTTATCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (19 bp):
TTGATTTTTAATAATTATT
Found at i:10959886 original size:21 final size:22
Alignment explanation
Indices: 10959838--10959886 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
10959828 TAATTATTTT
*
10959838 AATTTTTAATCAATTTTTATGA
1 AATTTTTAATCAATTTTTATAA
** *
10959860 TTTTTTTTATC-ATTTTTATAA
1 AATTTTTAATCAATTTTTATAA
10959881 AATTTT
1 AATTTT
10959887 CAATGTTTTT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (22 bp):
AATTTTTAATCAATTTTTATAA
Found at i:10964879 original size:17 final size:16
Alignment explanation
Indices: 10964857--10964913 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
10964847 ATGCAACTTC
10964857 AATATATTATATTATTT
1 AATATATTATATT-TTT
**
10964874 AATATAAAATATTTTT
1 AATATATTATATTTTT
*
10964890 -TTATTATTATATTTTT
1 AATA-TATTATATTTTT
10964906 ACATATAT
1 A-ATATAT
10964914 AAAAACTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 2 0.06
16 13 0.42
17 14 0.45
18 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
AATATATTATATTTTT
Found at i:10965732 original size:22 final size:23
Alignment explanation
Indices: 10965694--10965738 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
10965684 GTAAAATTAT
10965694 TAAATATTAAAATAAAA-TAAAA
1 TAAATATTAAAATAAAATTAAAA
*
10965716 TAAATATTTTAAA-AAAATTAAAA
1 TAAATA-TTAAAATAAAATTAAAA
10965739 ATAATATAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAATATTAAAATAAAATTAAAA
Found at i:10966563 original size:29 final size:31
Alignment explanation
Indices: 10966521--10966585 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
10966511 TAGTAAAAAT
* *
10966521 AAAATTGTACTTTACATT-CTTGAAAA-TATA
1 AAAATTGTAATTTA-ATTACTTAAAAATTATA
*
10966551 AAAATT-TAATTTAATTATTTAAAAATTATA
1 AAAATTGTAATTTAATTACTTAAAAATTATA
10966581 AAAAT
1 AAAAT
10966586 ATAAATTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 3 0.10
29 12 0.40
30 15 0.50
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (31 bp):
AAAATTGTAATTTAATTACTTAAAAATTATA
Found at i:10966593 original size:15 final size:16
Alignment explanation
Indices: 10966573--10966606 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
10966563 AATTATTTAA
10966573 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
10966588 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
10966604 AAA
1 AAA
10966607 ACAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:10969195 original size:22 final size:21
Alignment explanation
Indices: 10969147--10969196 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
10969137 AGTGCAAATT
* **
10969147 CAAATATAAATTATTTATAAA
1 CAAATTTAAATTATCAATAAA
10969168 CTAAATTTAAATTATCAATTAAA
1 C-AAATTTAAATTATCAA-TAAA
10969191 CAAATT
1 CAAATT
10969197 AATATAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.75
23 5 0.21
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (21 bp):
CAAATTTAAATTATCAATAAA
Found at i:10969790 original size:27 final size:27
Alignment explanation
Indices: 10969760--10969817 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
10969750 AATAAAAAAG
* * * * *
10969760 AAAACAACAAAAATAAAATCTATTCTA
1 AAAAAAACGAAAAAAAAACCTAATCTA
*
10969787 AAAAAAACGAAGAAAAAACCTAATCTA
1 AAAAAAACGAAAAAAAAACCTAATCTA
10969814 AAAA
1 AAAA
10969818 TGAAAAGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.67, C:0.14, G:0.03, T:0.16
Consensus pattern (27 bp):
AAAAAAACGAAAAAAAAACCTAATCTA
Found at i:10970394 original size:23 final size:23
Alignment explanation
Indices: 10970368--10970416 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
10970358 TGAAAAGCAT
*
10970368 AAAAAAAACTCA-TAAATCACTTG
1 AAAAAAAACTCATTAAAT-ACTCG
*
10970391 AAAACAAACTCATTAAATACTCG
1 AAAAAAAACTCATTAAATACTCG
10970414 AAA
1 AAA
10970417 GAGCTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.57, C:0.18, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAAAAAACTCATTAAATACTCG
Found at i:10972040 original size:14 final size:15
Alignment explanation
Indices: 10972015--10972044 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
10972005 TTCATTTAGT
10972015 TTTATATTTTATTTA
1 TTTATATTTTATTTA
10972030 TTTAT-TTTTATTTA
1 TTTATATTTTATTTA
10972044 T
1 T
10972045 ATTCTGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATATTTTATTTA
Found at i:10980492 original size:2 final size:2
Alignment explanation
Indices: 10980485--10980515 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10980475 CAATAAGTAT
10980485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10980516 GAATTTAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10984199 original size:51 final size:51
Alignment explanation
Indices: 10984080--10984318 Score: 309
Period size: 51 Copynumber: 4.6 Consensus size: 51
10984070 TTTCATTTAA
** * *
10984080 TACTCACGATGACA-TATAGTCATCGGACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATT
* * *
10984133 TACTCACGATGACACTGAGTCATCGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* * * *
10984184 TATTCACGATGACACTTAGTCATCGGACTTTTAATCCGTAAAGGATTCGTT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* *
10984235 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
10984286 TACTCACGATGACACTTAGTCATTTGGACCTTT
1 TACTCACGATGACACTTAGTCA-TCGGACCTTT
10984319 TCGTTTATAG
Statistics
Matches: 164, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
51 119 0.73
52 17 0.10
53 27 0.16
54 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:10986833 original size:4 final size:4
Alignment explanation
Indices: 10986813--10986861 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
10986803 AACGAAGAGA
* *
10986813 AAAG AAGAG AGAAG AAAG AAAG AAAG AAAG AAAG -AAG AAGG AGAG AAAG
1 AAAG AA-AG A-AAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
10986862 GTAAATTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
3 3 0.08
4 28 0.74
5 6 0.16
6 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:10986861 original size:23 final size:24
Alignment explanation
Indices: 10986808--10986861 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
10986798 GACCAAACGA
*
10986808 AGAGAAA-AGAAGAGAGAAGAAAG
1 AGAGAAAGAGAAGAAAGAAGAAAG
* *
10986831 AAAGAAAGA-AAGAAAGAAGAAGG
1 AGAGAAAGAGAAGAAAGAAGAAAG
10986854 AGAGAAAG
1 AGAGAAAG
10986862 GTAAATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (24 bp):
AGAGAAAGAGAAGAAAGAAGAAAG
Found at i:10989887 original size:35 final size:35
Alignment explanation
Indices: 10989848--10989927 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
10989838 ATTAATTTAT
* * *
10989848 ATTACTTACTTACTTACTACTATTAACAAAATAAA
1 ATTACTAACTTACTAACTACTACTAACAAAATAAA
10989883 ATTACTAACTTACTAACTACTACTAACAAAATAAA
1 ATTACTAACTTACTAACTACTACTAACAAAATAAA
10989918 ATTACTAACT
1 ATTACTAACT
10989928 AACAAAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (35 bp):
ATTACTAACTTACTAACTACTACTAACAAAATAAA
Found at i:10989929 original size:21 final size:20
Alignment explanation
Indices: 10989900--10989940 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
10989890 ACTTACTAAC
10989900 TACTACTAACAAAATAAAAT
1 TACTACTAACAAAATAAAAT
10989920 TACTAACTAACAAAATAAAAT
1 TACT-ACTAACAAAATAAAAT
10989941 AAAATAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (20 bp):
TACTACTAACAAAATAAAAT
Found at i:10990322 original size:12 final size:14
Alignment explanation
Indices: 10990299--10990341 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 14
10990289 AAAATTACTT
10990299 TTCTCTCCTTCTTTC
1 TTCTCT-CTTCTTTC
10990314 TT-TCT-TTCTTTC
1 TTCTCTCTTCTTTC
10990326 TTCTCTCTTCTCTTC
1 TTCTCTCTTCT-TTC
10990341 T
1 T
10990342 CCCCCGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 9 0.36
13 3 0.12
14 7 0.28
15 6 0.24
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (14 bp):
TTCTCTCTTCTTTC
Found at i:10993476 original size:58 final size:58
Alignment explanation
Indices: 10993414--10993528 Score: 162
Period size: 58 Copynumber: 2.0 Consensus size: 58
10993404 ATCAACAAAC
* *
10993414 TAAACCAAAATATTTTTAAA-TCCAAATATAATTTCATTCTTCAAA-AACACTTATAAAT
1 TAAACCAAAATATTTTTAAACT-CAAATATAATTTCATTCCT-AAATAACACTCATAAAT
* *
10993472 TAAACCCAAATATTTTTAAACTCAAATATAATTTTATTCCTAAATAACACTCATAAA
1 TAAACCAAAATATTTTTAAACTCAAATATAATTTCATTCCTAAATAACACTCATAAA
10993529 CAACTCATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
57 3 0.06
58 47 0.92
59 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.36
Consensus pattern (58 bp):
TAAACCAAAATATTTTTAAACTCAAATATAATTTCATTCCTAAATAACACTCATAAAT
Found at i:10994364 original size:65 final size:65
Alignment explanation
Indices: 10994260--10994391 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 65
10994250 TTTCAACGGT
*
10994260 GGCAATAGGCAATTTGATAAATGCAAGATCATGTGATAGAAAGGGAAAAGGACAAATTTTAGGTG
1 GGCAATAGGCAATTTGATAAATGCAAGACCATGTGATAGAAAGGGAAAAGGACAAATTTTAGGTG
*
10994325 GGCAATAGGCAATTTGATAAATGCAAGACCATGTGATAGAAAGGGAAAAGGACAAGTTTTAGGTG
1 GGCAATAGGCAATTTGATAAATGCAAGACCATGTGATAGAAAGGGAAAAGGACAAATTTTAGGTG
10994390 GG
1 GG
10994392 TTATTTATAG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.40, C:0.08, G:0.30, T:0.22
Consensus pattern (65 bp):
GGCAATAGGCAATTTGATAAATGCAAGACCATGTGATAGAAAGGGAAAAGGACAAATTTTAGGTG
Found at i:11013297 original size:31 final size:32
Alignment explanation
Indices: 11013259--11013341 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 32
11013249 TACTTTAATA
**
11013259 AATTTAATATTTATCTAGATAATATTTTA-TT
1 AATTTAATATTTATCTAGATAATATTAAATTT
* ** *
11013290 AATTTAATATTAATAAAAAT-ATATTAAATTT
1 AATTTAATATTTATCTAGATAATATTAAATTT
11013321 AATTTAATATTTATCTAGATA
1 AATTTAATATTTATCTAGATA
11013342 TTTTATTAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
30 6 0.15
31 34 0.85
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (32 bp):
AATTTAATATTTATCTAGATAATATTAAATTT
Found at i:11014343 original size:21 final size:23
Alignment explanation
Indices: 11014303--11014349 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
11014293 AATAATTTTT
* *
11014303 AAATTTTTATGTATTTTTTA-TA
1 AAATTTGTATGCATTTTTTATTA
11014325 AAATTTGTATGCA-TTTTTATTA
1 AAATTTGTATGCATTTTTTATTA
11014347 AAA
1 AAA
11014350 ATTATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (23 bp):
AAATTTGTATGCATTTTTTATTA
Found at i:11014957 original size:14 final size:15
Alignment explanation
Indices: 11014938--11014971 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11014928 ACATGTAGAT
11014938 ATTTTTT-ATAATAA
1 ATTTTTTGATAATAA
11014952 ATTTTTTGATAATAA
1 ATTTTTTGATAATAA
*
11014967 CTTTT
1 ATTTT
11014972 AAAAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (15 bp):
ATTTTTTGATAATAA
Found at i:11015807 original size:14 final size:14
Alignment explanation
Indices: 11015788--11015816 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11015778 GAATATCCGA
11015788 TTACATTTACTGCG
1 TTACATTTACTGCG
11015802 TTACATTTACTGCG
1 TTACATTTACTGCG
11015816 T
1 T
11015817 GACTGTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (14 bp):
TTACATTTACTGCG
Found at i:11020886 original size:16 final size:16
Alignment explanation
Indices: 11020862--11020897 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11020852 AATTTAATAC
11020862 AAAAATCCAAAACCAT
1 AAAAATCCAAAACCAT
* *
11020878 AAAATTCCAAAATCAT
1 AAAAATCCAAAACCAT
11020894 AAAA
1 AAAA
11020898 GAAAAAGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.19, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAATCCAAAACCAT
Found at i:11034106 original size:15 final size:16
Alignment explanation
Indices: 11034086--11034118 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
11034076 TTAAAATTGT
*
11034086 TATGTTATATATA-TA
1 TATGTTAAATATACTA
11034101 TATGTTAAATATACTA
1 TATGTTAAATATACTA
11034117 TA
1 TA
11034119 CGTACGGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (16 bp):
TATGTTAAATATACTA
Found at i:11035614 original size:37 final size:37
Alignment explanation
Indices: 11035564--11035654 Score: 182
Period size: 37 Copynumber: 2.5 Consensus size: 37
11035554 AGAAGAAAAT
11035564 GGTGGAGATAGTATATCCGGTTGGTTCAACTACGATA
1 GGTGGAGATAGTATATCCGGTTGGTTCAACTACGATA
11035601 GGTGGAGATAGTATATCCGGTTGGTTCAACTACGATA
1 GGTGGAGATAGTATATCCGGTTGGTTCAACTACGATA
11035638 GGTGGAGATAGTATATC
1 GGTGGAGATAGTATATC
11035655 ATAAAAAATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.30
Consensus pattern (37 bp):
GGTGGAGATAGTATATCCGGTTGGTTCAACTACGATA
Found at i:11036032 original size:19 final size:19
Alignment explanation
Indices: 11035990--11036033 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
11035980 CTCGTTTAGA
* *
11035990 AATTTTTTATCATATTGAT
1 AATTTTTTATAATATTAAT
11036009 AATTTTTTATAATAATTAAT
1 AATTTTTTATAAT-ATTAAT
11036029 -ATTTT
1 AATTTT
11036034 AAAAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
AATTTTTTATAATATTAAT
Found at i:11046953 original size:24 final size:24
Alignment explanation
Indices: 11046932--11046985 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
11046922 TTTATCTGTT
11046932 TTTGTGGCACACTTTTCCTCTGCC
1 TTTGTGGCACACTTTTCCTCTGCC
*
11046956 TTTGTGGCACGCTTTTCCTCTGCC
1 TTTGTGGCACACTTTTCCTCTGCC
11046980 -TTGTGG
1 TTTGTGG
11046986 TAGATTTGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.06, C:0.30, G:0.22, T:0.43
Consensus pattern (24 bp):
TTTGTGGCACACTTTTCCTCTGCC
Found at i:11051578 original size:2 final size:2
Alignment explanation
Indices: 11051571--11051597 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11051561 TGAATGATAA
11051571 AT 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 AT A
11051598 CACTAATAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11052639 original size:22 final size:22
Alignment explanation
Indices: 11052585--11052655 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
11052575 ATTTATTTTA
* *
11052585 ATATTTTAAAAATTATAAAAAT
1 ATATTTTTAAAATAATAAAAAT
* * *
11052607 ATAAATATTAAAATAATAAAATT
1 AT-ATTTTTAAAATAATAAAAAT
* *
11052630 ATATTTTTAATATCATAAAAAT
1 ATATTTTTAAAATAATAAAAAT
11052652 ATAT
1 ATAT
11052656 AATTTAATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 21 0.55
23 17 0.45
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATTTTTAAAATAATAAAAAT
Found at i:11058735 original size:15 final size:15
Alignment explanation
Indices: 11058717--11058773 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
11058707 GAAAATATCT
11058717 AATATTTTAATAATA
1 AATATTTTAATAATA
*
11058732 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
11058751 AATATATTAATAATA
1 AATATTTTAATAATA
*
11058766 AATGTTTT
1 AATATTTT
11058774 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:11059069 original size:15 final size:14
Alignment explanation
Indices: 11059024--11059070 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
11059014 AAGTATTTTT
*
11059024 AATATATGAAA-AA
1 AATATATAAAATAA
11059037 AATATATAAAATATA
1 AATATATAAAATA-A
*
11059052 AATTTATAAATATAA
1 AATATATAAA-ATAA
11059067 AATA
1 AATA
11059071 AACTTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 10 0.36
14 1 0.04
15 14 0.50
16 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (14 bp):
AATATATAAAATAA
Found at i:11059082 original size:21 final size:21
Alignment explanation
Indices: 11059040--11059084 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
11059030 TGAAAAAAAT
*
11059040 ATATAAAATATAAATTTATAA
1 ATATAAAATATAAATTAATAA
*
11059061 ATATAAAATA-AACTTAATTAA
1 ATATAAAATATAAATTAA-TAA
11059082 ATA
1 ATA
11059085 ATGAAAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATAAAATATAAATTAATAA
Found at i:11061055 original size:2 final size:2
Alignment explanation
Indices: 11061043--11061075 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
11061033 TGACCTTGTA
11061043 AT AT AT GAT 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
11061076 TAGTTTAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11062166 original size:21 final size:20
Alignment explanation
Indices: 11062142--11062180 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
11062132 ATTGTAAGTG
*
11062142 CATCACTATTATCTCTTTTAT
1 CATCACTAATAT-TCTTTTAT
*
11062163 CATCAGTAATATTCTTTT
1 CATCACTAATATTCTTTT
11062181 TTTTGTAGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.51
Consensus pattern (20 bp):
CATCACTAATATTCTTTTAT
Found at i:11075010 original size:9 final size:9
Alignment explanation
Indices: 11074996--11075023 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
11074986 TGTAAACAGT
11074996 GCCTTGCCC
1 GCCTTGCCC
11075005 GCCTTGCCC
1 GCCTTGCCC
11075014 GCCTTGCCC
1 GCCTTGCCC
11075023 G
1 G
11075024 AGCACTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.54, G:0.25, T:0.21
Consensus pattern (9 bp):
GCCTTGCCC
Found at i:11079632 original size:22 final size:22
Alignment explanation
Indices: 11079583--11079633 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
11079573 AGGGTGTGAA
* *
11079583 ATTAAATTGTAATTTTTACAAT
1 ATTAAAATGTAATTTTTACAAG
11079605 AGTTAAAATGTAATTTTTA-AAGG
1 A-TTAAAATGTAATTTTTACAA-G
11079628 ATTAAA
1 ATTAAA
11079634 TCAAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (22 bp):
ATTAAAATGTAATTTTTACAAG
Found at i:11082382 original size:14 final size:14
Alignment explanation
Indices: 11082360--11082395 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
11082350 CTTCACCCTA
11082360 AGTTGTAATCATTC
1 AGTTGTAATCATTC
*
11082374 AGTTTTAATCATTC
1 AGTTGTAATCATTC
11082388 A-TTGTAAT
1 AGTTGTAAT
11082396 TGAAAGCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (14 bp):
AGTTGTAATCATTC
Found at i:11086918 original size:12 final size:12
Alignment explanation
Indices: 11086901--11086925 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11086891 TATCCGCATC
11086901 CCCAGCCAGCCA
1 CCCAGCCAGCCA
11086913 CCCAGCCAGCCA
1 CCCAGCCAGCCA
11086925 C
1 C
11086926 GTGAGATTAT
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:0.24, C:0.60, G:0.16, T:0.00
Consensus pattern (12 bp):
CCCAGCCAGCCA
Found at i:11092391 original size:21 final size:18
Alignment explanation
Indices: 11092358--11092401 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
11092348 TTTCTACAAT
11092358 GAAAAATACGAGAAGAGATA
1 GAAAAATACGAGAA-AGA-A
*
11092378 GAAAAATAAGGAGAAAGAA
1 GAAAAAT-ACGAGAAAGAA
11092397 GAAAA
1 GAAAA
11092402 GGAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.66, C:0.02, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAATACGAGAAAGAA
Found at i:11092538 original size:20 final size:20
Alignment explanation
Indices: 11092499--11092540 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
11092489 AAATTACGTT
*
11092499 AAAAAAAATAGAGAAGGGAG
1 AAAAAAAAAAGAGAAGGGAG
11092519 AAAAACAAAAAGAGAA-GGAG
1 AAAAA-AAAAAGAGAAGGGAG
11092539 AA
1 AA
11092541 GAGAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.69, C:0.02, G:0.26, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAGAGAAGGGAG
Found at i:11092539 original size:27 final size:25
Alignment explanation
Indices: 11092500--11092558 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
11092490 AATTACGTTA
11092500 AAAAAAATAGAGAAGG-G-AGA-AA-
1 AAAAAAA-AGAGAAGGAGAAGAGAAT
*
11092522 AACAAAAAGAGAAGGAGAAGAGAAT
1 AAAAAAAAGAGAAGGAGAAGAGAAT
11092547 AAAAAAAAGAGA
1 AAAAAAAAGAGA
11092559 GGAAAGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 8 0.26
22 7 0.23
23 3 0.10
24 2 0.06
25 11 0.35
ACGTcount: A:0.69, C:0.02, G:0.25, T:0.03
Consensus pattern (25 bp):
AAAAAAAAGAGAAGGAGAAGAGAAT
Found at i:11096747 original size:2 final size:2
Alignment explanation
Indices: 11096740--11096766 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11096730 CTATTCTAGA
11096740 AT 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 AT A
11096767 GTTTTAATTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11098053 original size:24 final size:24
Alignment explanation
Indices: 11098026--11098072 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
11098016 ACACTTATTT
11098026 TTTAA-AATTTAAAAAAAAAACCTA
1 TTTAACAA-TTAAAAAAAAAACCTA
*
11098050 TTTAATCAATTAATAAAAAAACC
1 TTTAA-CAATTAAAAAAAAAACC
11098073 GACATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 13 0.65
26 2 0.10
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (24 bp):
TTTAACAATTAAAAAAAAAACCTA
Found at i:11099093 original size:2 final size:2
Alignment explanation
Indices: 11099086--11099121 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11099076 TTTATTTGCA
11099086 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
11099122 TTATTTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11113875 original size:28 final size:28
Alignment explanation
Indices: 11113819--11113882 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
11113809 TCGAATACAT
11113819 TATGTTATAACAAATATTATATTAATTA
1 TATGTTATAACAAATATTATATTAATTA
* * *
11113847 TATGTTA-AATAATTATTATATATATTTA
1 TATGTTATAACAAATATTATAT-TAATTA
11113875 TAT-TTATA
1 TATGTTATA
11113883 TTTATATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (28 bp):
TATGTTATAACAAATATTATATTAATTA
Found at i:11116826 original size:14 final size:15
Alignment explanation
Indices: 11116797--11116835 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
11116787 TTTTAAAATG
11116797 TATAATATATAATAA
1 TATAATATATAATAA
11116812 TATAATATA-AATAA
1 TATAATATATAATAA
*
11116826 TTTAATATAT
1 TATAATATAT
11116836 TTTTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATAATATATAATAA
Found at i:11117025 original size:23 final size:24
Alignment explanation
Indices: 11116981--11117026 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
11116971 TAATAATTTT
* *
11116981 TTTATTAATTTATAAAATAAAAAA
1 TTTATTAATCTATAAAACAAAAAA
*
11117005 TTTATT-ATCTATATAACAAAAA
1 TTTATTAATCTATAAAACAAAAA
11117027 GAAAATCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTATTAATCTATAAAACAAAAAA
Found at i:11118843 original size:20 final size:19
Alignment explanation
Indices: 11118818--11118861 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
11118808 TAACTTAGCC
*
11118818 ATTTTTATTTTTATTTTAA
1 ATTTTTATTTTTAATTTAA
*
11118837 TATTTTTGTTTTTAATTTAA
1 -ATTTTTATTTTTAATTTAA
11118857 ATTTT
1 ATTTT
11118862 ACATTCTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
ATTTTTATTTTTAATTTAA
Found at i:11123349 original size:6 final size:6
Alignment explanation
Indices: 11123338--11123363 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11123328 CTTCAGCCTT
11123338 GGTGCC GGTGCC GGTGCC GGTGCC GG
1 GGTGCC GGTGCC GGTGCC GGTGCC GG
11123364 GGGGGGGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.54, T:0.15
Consensus pattern (6 bp):
GGTGCC
Found at i:11123865 original size:20 final size:21
Alignment explanation
Indices: 11123833--11123871 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
11123823 TATCAGTCTA
11123833 TCTTTTGCTTCTTTTTCTTAG
1 TCTTTTGCTTCTTTTTCTTAG
11123854 TCTTTT-CTTCTTTTTCTT
1 TCTTTTGCTTCTTTTTCTT
11123872 TTTCCGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.03, C:0.21, G:0.05, T:0.72
Consensus pattern (21 bp):
TCTTTTGCTTCTTTTTCTTAG
Found at i:11126422 original size:48 final size:48
Alignment explanation
Indices: 11126312--11126423 Score: 127
Period size: 48 Copynumber: 2.3 Consensus size: 48
11126302 GTGGTTATAC
* * *
11126312 AATCACATGTTAAAATATAACTAGGGCTCCCAATTGACAGTGGTTATG
1 AATCACATGTTCAAGTATAACTAGGGCTCCCAATTGACAGTGATTATG
** ** * *
11126360 CGTCACGGGTTCAAGTATAACTCGGGC-CCCAATTGACGGTGATTATG
1 AATCACATGTTCAAGTATAACTAGGGCTCCCAATTGACAGTGATTATG
11126407 TAATCACATGTTCAAGT
1 -AATCACATGTTCAAGT
11126424 TTTATGCTAC
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
47 18 0.36
48 32 0.64
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (48 bp):
AATCACATGTTCAAGTATAACTAGGGCTCCCAATTGACAGTGATTATG
Found at i:11131518 original size:43 final size:43
Alignment explanation
Indices: 11131470--11131602 Score: 248
Period size: 43 Copynumber: 3.1 Consensus size: 43
11131460 TGAACATATC
11131470 CTTAACATCATAATCAAACAGGACACTGATTCATTCATCAACG
1 CTTAACATCATAATCAAACAGGACACTGATTCATTCATCAACG
*
11131513 CTTAACATCATAATCCAACAGGACACTGATTCATTCATCAACG
1 CTTAACATCATAATCAAACAGGACACTGATTCATTCATCAACG
*
11131556 CTTAACATCATAATCAAACAGGACACTGATTCATTCATCAATG
1 CTTAACATCATAATCAAACAGGACACTGATTCATTCATCAACG
11131599 CTTA
1 CTTA
11131603 CACACACATG
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 87 1.00
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.27
Consensus pattern (43 bp):
CTTAACATCATAATCAAACAGGACACTGATTCATTCATCAACG
Found at i:11132745 original size:15 final size:15
Alignment explanation
Indices: 11132721--11132751 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11132711 ATGTCTTACC
*
11132721 GAAAACAAAAGAAAA
1 GAAAAAAAAAGAAAA
11132736 GAAAAAAAAAGAAAA
1 GAAAAAAAAAGAAAA
11132751 G
1 G
11132752 GTTTTACATT
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:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAAGAAAA
Found at i:11133183 original size:18 final size:16
Alignment explanation
Indices: 11133123--11133172 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
11133113 TTTTTATAAA
*
11133123 TTAAAATATATAATATAT
1 TTAAAATA-ATTA-ATAT
**
11133141 TTAATGTAATTAATAT
1 TTAAAATAATTAATAT
11133157 TTAAAATAATTAATAT
1 TTAAAATAATTAATAT
11133173 CTTTTAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 18 0.67
17 3 0.11
18 6 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
TTAAAATAATTAATAT
Found at i:11133218 original size:17 final size:18
Alignment explanation
Indices: 11133196--11133229 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11133186 AATTTAGAAC
11133196 TATATTA-TAAAATAAAT
1 TATATTATTAAAATAAAT
11133213 TATATTATTAAAATAAA
1 TATATTATTAAAATAAA
11133230 AGTAAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATATTATTAAAATAAAT
Found at i:11145945 original size:5 final size:5
Alignment explanation
Indices: 11145935--11145967 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
11145925 GTTTCTTAGT
11145935 TGGAG TGGAG TGGAG TGGAG TGGAG TGGAG TGG
1 TGGAG TGGAG TGGAG TGGAG TGGAG TGGAG TGG
11145968 GAATTCTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.61, T:0.21
Consensus pattern (5 bp):
TGGAG
Found at i:11149976 original size:3 final size:3
Alignment explanation
Indices: 11149968--11149998 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
11149958 ATCTGACACA
11149968 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
11149999 ACTAAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:11154198 original size:25 final size:24
Alignment explanation
Indices: 11154156--11154207 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
11154146 TGCTAATATC
*
11154156 ATATAAATCATTACATAAATAATAA
1 ATATAAATAATTACATAAA-AATAA
*
11154181 ATATAAATTAATTA-ATAAAAGTAA
1 ATATAAA-TAATTACATAAAAATAA
11154205 ATA
1 ATA
11154208 AATAACAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 12 0.50
26 5 0.21
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (24 bp):
ATATAAATAATTACATAAAAATAA
Found at i:11155710 original size:18 final size:18
Alignment explanation
Indices: 11155659--11155716 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
11155649 CTTTTATTTT
11155659 ATATTATTATATAA-TAAA
1 ATATTATTAT-TAATTAAA
* *
11155677 ATATTATTATTTATTATA
1 ATATTATTATTAATTAAA
*
11155695 ATATTATTATTAATTAAT
1 ATATTATTATTAATTAAA
11155713 ATAT
1 ATAT
11155717 CTTTTGATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 2 0.06
18 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTATTATTAATTAAA
Found at i:11160510 original size:27 final size:27
Alignment explanation
Indices: 11160479--11160530 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
11160469 GAATAGCAAT
11160479 TAATAAG-AGATTAAATACGAA-GCAAGA
1 TAATAAGCAGA-TAAATA-GAATGCAAGA
11160506 TAATAAGCAGATAAATAGAATGCAA
1 TAATAAGCAGATAAATAGAATGCAA
11160531 AAATATAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 3 0.13
27 17 0.74
28 3 0.13
ACGTcount: A:0.56, C:0.08, G:0.17, T:0.19
Consensus pattern (27 bp):
TAATAAGCAGATAAATAGAATGCAAGA
Found at i:11160725 original size:59 final size:59
Alignment explanation
Indices: 11160659--11161264 Score: 609
Period size: 59 Copynumber: 10.3 Consensus size: 59
11160649 TTTGACTTTC
* ** *
11160659 GGGGGTAAAAAT-GTAATTTTTGATGAAACCAAGGTTAAAAATGGAATTTTGGAGAGTTT
1 GGGGGT-AAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
* *** * * *
11160718 GGAGGTAAAACAATAATTTTTGGT-AGAATTGGGGTTAAAAATAGG-GTTTTGGAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGATGA-AATCGGGGTTAAAAAT-GGAATTTTGGAAAGTTT
* * * * * *
11160777 AGGGATAAAATGGTAATTTTT-AGTGAAATTGGGATTAAAAATAGAATTTTGGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGA-TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
* *
11160836 GGGGGTAAAATGGTAATTTTT-AGTGAAATCGGGGTTGAAAATGGTATTTTGGAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGA-TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
* * * * **
11160895 GGGGGTAAAATGGTAATTTTTGGTGAAATTGAGGTTAAAAATGGGATTTTTAAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
* * * *
11160954 GAGGGTAAAATGGTAATTTTTGATGAAATTGAGGTTAAAAATGG-ATTTTGGAGAGTTT
1 GGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
* * * * * * * *
11161012 GGGAGTAAAACGGTAATTTTT-AGTGGAATCGAGGAT-AAAATGGGATTTTGAAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGA-TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
* ** * *
11161070 AGGGGTAAAATAATATTTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
* * *
11161129 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAT-GAGATTTTGAAAAGTTCA
1 GGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGA-ATTTTGGAAAGTT-T
* * * * * *
11161189 GGGGATAAAATGGTAATTTTTGGTTAAACCGGGGTTAAAAATGGAATTTCGAAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
11161248 GGGGGTCAAAATGGTAA
1 GGGGGT-AAAATGGTAA
11161265 GTTATGAACA
Statistics
Matches: 457, Mismatches: 75, Indels: 29
0.81 0.13 0.05
Matches are distributed among these distances:
57 8 0.02
58 83 0.18
59 300 0.66
60 64 0.14
61 2 0.00
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.33
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
Found at i:11160885 original size:30 final size:30
Alignment explanation
Indices: 11160782--11161168 Score: 162
Period size: 30 Copynumber: 13.2 Consensus size: 30
11160772 AGTTTAGGGA
*
11160782 TAAAATGGTAATTTTTAGTGAAATTGGGAT
1 TAAAATGGTAATTTTTAGTGAAATTGGGGT
* *
11160812 TAAAAATAG-AA-TTTT-G-GAAAGTTCGGGGG
1 T-AAAATGGTAATTTTTAGTGAAA-TT-GGGGT
*
11160841 TAAAATGGTAATTTTTAGTGAAATCGGGGT
1 TAAAATGGTAATTTTTAGTGAAATTGGGGT
*
11160871 TGAAAATGGT-A-TTTT-G-GAAAGTTTGGGGG
1 T-AAAATGGTAATTTTTAGTGAAA--TTGGGGT
* *
11160900 TAAAATGGTAATTTTTGGTGAAATTGAGGT
1 TAAAATGGTAATTTTTAGTGAAATTGGGGT
*
11160930 TAAAAATGG-GATTTTTA---AAAGTTTGAGGG-
1 T-AAAATGGTAATTTTTAGTGAAA--TTG-GGGT
*
11160959 TAAAATGGTAATTTTT-GATGAAATTGAGGT
1 TAAAATGGTAATTTTTAG-TGAAATTGGGGT
* * **
11160989 TAAAAATGG--A-TTTTGGAGAGTTTGGGAG-
1 T-AAAATGGTAATTTTTAGTGAAATTGGG-GT
* * * * *
11161017 TAAAACGGTAATTTTTAGTGGAATCGAGGA
1 TAAAATGGTAATTTTTAGTGAAATTGGGGT
* *
11161047 TAAAATGG-GA-TTTT-G-AAAAGTTCAGGGG-
1 TAAAATGGTAATTTTTAGTGAAA-TT--GGGGT
** * * *
11161075 TAAAATAATATTTTTTGGTGAAATCGGGGT
1 TAAAATGGTAATTTTTAGTGAAATTGGGGT
*
11161105 TAAAAATGG-AA-TTTT-G-GAAAGTTTGGGGG
1 T-AAAATGGTAATTTTTAGTGAAA--TTGGGGT
* *
11161134 TAAAATGGTAATTTTTGGTGAAATCGGGGT
1 TAAAATGGTAATTTTTAGTGAAATTGGGGT
11161164 TAAAA
1 TAAAA
11161169 ATGAGATTTT
Statistics
Matches: 265, Mismatches: 46, Indels: 92
0.66 0.11 0.23
Matches are distributed among these distances:
26 2 0.01
27 23 0.09
28 54 0.20
29 58 0.22
30 71 0.27
31 39 0.15
32 18 0.07
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.35
Consensus pattern (30 bp):
TAAAATGGTAATTTTTAGTGAAATTGGGGT
Found at i:11160953 original size:177 final size:173
Alignment explanation
Indices: 11160656--11161259 Score: 687
Period size: 177 Copynumber: 3.4 Consensus size: 173
11160646 ATTTTTGACT
* * *
11160656 TTCGGGGGTAAAAAT-GTAATTTTT-GATGAAACCAAGGTTAAAAATGGAATTTTGGAGAGTTTG
1 TTCGGGGGT-AAAATGGTAATTTTTAG-TGAAACCGAGGTTAAAAATGGAATTTTGAAAAGTTTG
* *
11160719 GAGGTAAAACAATAATTTTTGGT-AGAATTGGGGTTAAAAATAGGG-TTTTGGAAAGTTTAGGGA
64 GGGGTAAAATAATAATTTTTGGTGA-AATTGGGGTTAAAAAT-GGGATTTTGGAAAGTTTAGGG-
11160782 TAAAATGGTAATTTTTAGTGAAATTGGGATTAAAAATAGAATTTTGGAAAG
126 TAAAATGGTAATTTTT-GTGAAATTGGG-TTAAAAAT-GAATTTTGGAAAG
* * * * *
11160833 TTCGGGGGTAAAATGGTAATTTTTAGTGAAATCGGGGTTGAAAATGGTATTTTGGAAAGTTTGGG
1 TTCGGGGGTAAAATGGTAATTTTTAGTGAAACCGAGGTTAAAAATGGAATTTTGAAAAGTTTGGG
** * **
11160898 GGTAAAATGGTAATTTTTGGTGAAATTGAGGTTAAAAATGGGATTTTTAAAAGTTTGAGGGTAAA
66 GGTAAAATAATAATTTTTGGTGAAATTGGGGTTAAAAATGGGATTTTGGAAAGTTT-AGGGTAAA
* *
11160963 ATGGTAATTTTTGATGAAATTGAGGTTAAAAATGGATTTTGGAGAG
130 ATGGTAATTTTTG-TGAAATTG-GGTTAAAAATGAATTTTGGAAAG
* * * * * * * **
11161009 TTTGGGAGTAAAACGGTAATTTTTAGTGGAATCGAGGAT-AAAATGGGATTTTGAAAAGTTCAGG
1 TTCGGGGGTAAAATGGTAATTTTTAGTGAAACCGAGGTTAAAAATGGAATTTTGAAAAGTTTGGG
* * * *
11161073 GGTAAAATAATATTTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAA
66 GGTAAAATAATAATTTTTGGTGAAATTGGGGTTAAAAATGGGATTTTGGAAAGTTT-AGGGTAAA
* *
11161138 ATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAGATTTTGAAAAG
130 ATGGTAATTTTT-GTGAAAT-TGGGTTAAAAATGA-ATTTTGGAAAG
* * * * *
11161185 TTCAGGGGATAAAATGGTAATTTTTGGTTAAACCGGGGTTAAAAATGGAATTTCGAAAAGTTTGG
1 TTC-GGGGGTAAAATGGTAATTTTTAGTGAAACCGAGGTTAAAAATGGAATTTTGAAAAGTTTGG
11161250 GGGTCAAAAT
65 GGGT-AAAAT
11161260 GGTAAGTTAT
Statistics
Matches: 362, Mismatches: 52, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
175 106 0.29
176 66 0.18
177 153 0.42
178 32 0.09
179 5 0.01
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (173 bp):
TTCGGGGGTAAAATGGTAATTTTTAGTGAAACCGAGGTTAAAAATGGAATTTTGAAAAGTTTGGG
GGTAAAATAATAATTTTTGGTGAAATTGGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGTAAAA
TGGTAATTTTTGTGAAATTGGGTTAAAAATGAATTTTGGAAAG
Found at i:11161727 original size:12 final size:12
Alignment explanation
Indices: 11161718--11161742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11161708 TAGGTTTTAT
11161718 TTTTATTTTTTC
1 TTTTATTTTTTC
11161730 TTTTATTTTTTC
1 TTTTATTTTTTC
11161742 T
1 T
11161743 GGAATTTTAT
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:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTATTTTTTC
Found at i:11162384 original size:14 final size:14
Alignment explanation
Indices: 11162362--11162391 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11162352 TTTAATAATA
11162362 ATATCATTATTATT
1 ATATCATTATTATT
*
11162376 ATATTATTATTATT
1 ATATCATTATTATT
11162390 AT
1 AT
11162392 TATAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (14 bp):
ATATCATTATTATT
Found at i:11163057 original size:14 final size:15
Alignment explanation
Indices: 11163032--11163063 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
11163022 CAATTAGGCC
11163032 TTTGTAATTTGGACA
1 TTTGTAATTTGGACA
11163047 TTTGTAA-TTGGACA
1 TTTGTAATTTGGACA
11163061 TTT
1 TTT
11163064 AATTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (15 bp):
TTTGTAATTTGGACA
Found at i:11163507 original size:60 final size:58
Alignment explanation
Indices: 11163425--11163688 Score: 223
Period size: 60 Copynumber: 4.4 Consensus size: 58
11163415 AAAATTGGGG
* * *
11163425 TGTTGGCCATGC-AATGGCCGACACTCCTTTTTTGTCAAAAAAAAATTCAAAATTTTTTGA
1 TGTTGGCCAT-CAAAT-GTCGACAC-CCCTTTTTCTCAAAAAAAAATTCAAAATTTTTTGA
* * * * *
11163485 TGTTGGCCATCAAATAGTCGACACCCCATTTTCTC-GAAAAAAATT--ACATTTTTGGG
1 TGTTGGCCATCAAAT-GTCGACACCCCTTTTTCTCAAAAAAAAATTCAAAATTTTTTGA
** * *
11163541 TGTTGGCCATCAAATGATCGACA-CCCTCTTTTCTCGAGAAAAAAGTTTCAAATTTTTTTGG
1 TGTTGGCCATCAAATG-TCGACACCCCT-TTTTCTC-A-AAAAAAAATTCAAAATTTTTTGA
* * ** *
11163602 TGTTAGCCATCAAATGATCGACACCCCTTTTTCTCAAGAAAAAAATTTAATTTTTTTTTA
1 TGTTGGCCATCAAATG-TCGACACCCCTTTTTCTCAA-AAAAAAATTCAAAATTTTTTGA
**
11163662 TGTTGGATATCAAATTGTCGACACCCC
1 TGTTGGCCATCAAA-TGTCGACACCCC
11163689 AAATTTTAAA
Statistics
Matches: 167, Mismatches: 26, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
55 4 0.02
56 36 0.22
58 9 0.05
59 17 0.10
60 58 0.35
61 39 0.23
62 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (58 bp):
TGTTGGCCATCAAATGTCGACACCCCTTTTTCTCAAAAAAAAATTCAAAATTTTTTGA
Found at i:11163598 original size:117 final size:117
Alignment explanation
Indices: 11163422--11163656 Score: 291
Period size: 117 Copynumber: 2.0 Consensus size: 117
11163412 AAAAAAATTG
* * *
11163422 GGGTGTTGGCCATGCAATGGCCGACACTCCTTTTTTGTCAAAAAAAAATTCAAAATTTTTTGATG
1 GGGTGTTGGCCATGCAATGACCGACACTCCTCTTTTCTCAAAAAAAAATTCAAAATTTTTTGATG
*
11163487 TTGGCCATCAAAT-AGTCGACACCCCATTTTCTC-GAAAAAAA-TTACATTTTT
66 TTAGCCATCAAATGA-TCGACACCCCATTTTCTCAGAAAAAAATTTA-ATTTTT
* ** *
11163538 GGGTGTTGGCCAT-CAAATGATCGACAC-CCTCTTTTCTCGAGAAAAAAGTTTCAAATTTTTTTG
1 GGGTGTTGGCCATGC-AATGACCGACACTCCTCTTTTCTC-A-AAAAAAAATTCAAAATTTTTTG
* *
11163601 GTGTTAGCCATCAAATGATCGACACCCCTTTTTCTCAAGAAAAAAATTTAATTTTT
63 ATGTTAGCCATCAAATGATCGACACCCCATTTTCTC-AGAAAAAAATTTAATTTTT
11163657 TTTTATGTTG
Statistics
Matches: 102, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
115 10 0.10
116 24 0.24
117 50 0.49
118 1 0.01
119 14 0.14
120 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (117 bp):
GGGTGTTGGCCATGCAATGACCGACACTCCTCTTTTCTCAAAAAAAAATTCAAAATTTTTTGATG
TTAGCCATCAAATGATCGACACCCCATTTTCTCAGAAAAAAATTTAATTTTT
Found at i:11163618 original size:61 final size:59
Alignment explanation
Indices: 11163464--11163689 Score: 239
Period size: 61 Copynumber: 3.8 Consensus size: 59
11163454 TTTTGTCAAA
* * *
11163464 AAAAAATTCAAAATTTTTTGATGTTGGCCATCAAAT-AGTCGACACCCCATTTTCTCGA-
1 AAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGA-TCGACACCCCATTTTCTCGAG
* *
11163522 AAAAAA-TTACA-TTTTTGGGTGTTGGCCATCAAATGATCGACACCCTC-TTTTCTCGAG
1 AAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGATCGACACCC-CATTTTCTCGAG
* * *
11163579 AAAAAAGTTTCAAATTTTTTTGGTGTTAGCCATCAAATGATCGACACCCCTTTTTCTCAAG
1 AAAAAA-TTT-AAATTTTTTTGGTGTTGGCCATCAAATGATCGACACCCCATTTTCTCGAG
* ** **
11163640 AAAAAAATTTAATTTTTTTTTATGTTGGATATCAAATTG-TCGACACCCCA
1 -AAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAA-TGATCGACACCCCA
11163690 AATTTTAAAA
Statistics
Matches: 143, Mismatches: 15, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
56 39 0.27
57 11 0.08
58 6 0.04
59 2 0.01
60 33 0.23
61 46 0.32
62 6 0.04
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (59 bp):
AAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGATCGACACCCCATTTTCTCGAG
Found at i:11164705 original size:23 final size:23
Alignment explanation
Indices: 11164653--11164805 Score: 139
Period size: 23 Copynumber: 6.5 Consensus size: 23
11164643 TAAATGGAAC
*
11164653 AAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
11164675 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
11164701 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* * *
11164724 GATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
11164747 AAAAACAGAGAGCACGA-GACGTGCT
1 --AAACAGAGAGCAC-ACAAAGTGCT
*
11164772 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
11164795 AATCAGAGAGC
1 AAACAGAGAGC
11164806 GCGCTAGTGT
Statistics
Matches: 104, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.01
23 66 0.63
25 29 0.28
26 8 0.08
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:11164740 original size:48 final size:46
Alignment explanation
Indices: 11164679--11164805 Score: 150
Period size: 48 Copynumber: 2.7 Consensus size: 46
11164669 AGTGCTGGGC
* *
11164679 AACAGAGAGCACACAAAGTGCTAAACAGAGAGTACAC-A-AAGTACTG
1 AACAGAGAGCACACACAGTGCTAAACAGAGAG--CACGAGAAGTACTA
* * *
11164725 ATCAGAGAGCACACACAGTGCTAAAAACAGAGAGCACGAGACGTGCTA
1 AACAGAGAGCACACACAGTGCT--AAACAGAGAGCACGAGAAGTACTA
*
11164773 AACAGAGAGCACACACAGTGCTAATCAGAGAGC
1 AACAGAGAGCACACACAGTGCTAAACAGAGAGC
11164806 GCGCTAGTGT
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
46 33 0.47
47 1 0.01
48 36 0.51
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (46 bp):
AACAGAGAGCACACACAGTGCTAAACAGAGAGCACGAGAAGTACTA
Found at i:11165432 original size:11 final size:11
Alignment explanation
Indices: 11165404--11165437 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
11165394 TTCAGTCTCT
11165404 AATAATTTTTC
1 AATAATTTTTC
*
11165415 TAT-ATTTTTC
1 AATAATTTTTC
11165425 AATAATTTTTC
1 AATAATTTTTC
11165436 AA
1 AA
11165438 AGTCAGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (11 bp):
AATAATTTTTC
Found at i:11168595 original size:2 final size:2
Alignment explanation
Indices: 11168588--11168634 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
11168578 TACTGACGGT
11168588 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
11168630 TA TA T
1 TA TA T
11168635 CTAGTGTTGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11169527 original size:62 final size:60
Alignment explanation
Indices: 11169454--11169797 Score: 323
Period size: 62 Copynumber: 5.8 Consensus size: 60
11169444 AGGAGAAGTT
** *
11169454 GGTGTCGGCCATTACATGGCAAACACAAAAAAAATTTGAAATTTTTTTATCCGAGAAAAAGG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAAATTTTTTT-T-CGAGAAAAAGG
* * * *
11169516 GGTGTCGGCCATTTGATGGTCAATACAAAAAAAATTTTAAATTTTTTTCTCGAG-AAAAGAA
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAAATTTTTTT-TCGAGAAAAAG-G
* *** ** * *
11169577 GGTGTCGGTCATGCAATGGCCAACA-ACTAAAAA--TGTAA-TTTTTTT--A-AATAAGG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAAATTTTTTTTCGAGAAAAAGG
* * *
11169630 GGTGTCGGCCATTTGATGGCCTACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAAGGAG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAAATTTTTTT-TCGAGAAAAAG-G
* * * *
11169692 GGTGTCGGCTATTTGATGGTCAACACCAAAAAAAA-TTGAAA-TTTTTTTCGAGAAAATGA
1 GGTGTCGGCCATTTGATGGCCAACA-CAAAAAAAATTTGAAATTTTTTTTCGAGAAAAAGG
* * *
11169751 GATGTCGGCCATTTGATGACCAACACAAAAAAATTTTG-AATTTTTTT
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAAATTTTTTT
11169798 CACAAACAAG
Statistics
Matches: 226, Mismatches: 42, Indels: 31
0.76 0.14 0.10
Matches are distributed among these distances:
53 20 0.09
54 10 0.04
56 5 0.02
57 12 0.05
58 14 0.06
59 30 0.13
60 22 0.10
61 33 0.15
62 72 0.32
63 8 0.04
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (60 bp):
GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAAATTTTTTTTCGAGAAAAAGG
Found at i:11169723 original size:114 final size:117
Alignment explanation
Indices: 11169482--11169798 Score: 317
Period size: 114 Copynumber: 2.7 Consensus size: 117
11169472 GCAAACACAA
* * *
11169482 AAAAAATTTGAAATTTTTTTATCCGAGAAAAAGGGGTGTCGGCCATTTGATGGTCAATACAAAAA
1 AAAAAA-TTGAAA-TTTTTT-T-C-AG-AAAAGGGGTGTCGGCCATTTGATGGCCAACACCAAAA
*
11169547 AAATTTTAAATTTTTTTCTCGAGAAAAGAAGGTGTCGGTCATGCAATGGCCAACAA-C
60 AAATTTGAAATTTTTTTCTCGAGAAAAGAAGGTGTCGGTCATGCAATGGCCAACAACC
* * *
11169604 TAAAAA-TGTAATTTTTTT-A-AATAAGGGGTGTCGGCCATTTGATGGCCTACACCAAAAAAATT
1 AAAAAATTGAAATTTTTTTCAGAA-AAGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAAATT
* *** *
11169666 TGAAATTTTTTTCTCGAGAAAAGGAGGGTGTCGG-CTATTTGATGGTCAAC-ACC
65 TGAAATTTTTTTCTCGAGAAAA-GAAGGTGTCGGTC-ATGCAATGGCCAACAACC
* * *
11169719 AAAAAAAATTGAAATTTTTTTCGAGAAAATGAGATGTCGGCCATTTGATGACCAACA-CAAAAAA
1 --AAAAAATTGAAATTTTTTTC-AGAAAA-GGGGTGTCGGCCATTTGATGGCCAACACCAAAAAA
11169783 ATTTTG-AATTTTTTTC
62 A-TTTGAAATTTTTTTC
11169799 ACAAACAAGG
Statistics
Matches: 165, Mismatches: 18, Indels: 26
0.79 0.09 0.12
Matches are distributed among these distances:
113 2 0.01
114 59 0.36
115 22 0.13
117 5 0.03
118 12 0.07
119 6 0.04
120 25 0.15
121 29 0.18
122 5 0.03
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (117 bp):
AAAAAATTGAAATTTTTTTCAGAAAAGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTT
GAAATTTTTTTCTCGAGAAAAGAAGGTGTCGGTCATGCAATGGCCAACAACC
Found at i:11169797 original size:176 final size:176
Alignment explanation
Indices: 11169454--11169782 Score: 436
Period size: 176 Copynumber: 1.9 Consensus size: 176
11169444 AGGAGAAGTT
11169454 GGTGTCGGCCATTACATGGCAAACACAAAAAAAATTTGAAATTTTTTTATCCGAGAAAAAGGGGT
1 GGTGTCGGCCATTACATGGCAAACACAAAAAAAATTTGAAATTTTTTTATCCGAGAAAAAGGGGT
* * *
11169519 GTCGGCCATTTGATGGTCAATACAAAAAAAATTTTAAATTTTTTTCTCGAGAAAAGAAGGTGTCG
66 GTCGGCCATTTGATGGTCAACACAAAAAAAATTTGAAATTTTTTTCTCGAGAAAAGAAGATGTCG
* * *
11169584 GTCATGCAATGGCCAACAACTAAAAATGTAATTTTTTTAAATAAGG
131 GCCATGCAATGACCAACAACAAAAAATGTAATTTTTTTAAATAAGG
** ** * * *
11169630 GGTGTCGGCCATTTGATGGCCTACACCAAAAAAATTTGAAATTTTTTTCT-CGAGAAAAGGAGGG
1 GGTGTCGGCCATTACATGGCAAACACAAAAAAAATTTGAAATTTTTTTATCCGAGAAAAAG-GGG
*
11169694 TGTCGGCTATTTGATGGTCAACACCAAAAAAAA-TTGAAA-TTTTTT-TCGAGAAAATG-AGATG
65 TGTCGGCCATTTGATGGTCAACA-CAAAAAAAATTTGAAATTTTTTTCTCGAGAAAA-GAAGATG
***
11169755 TCGGCCATTTGATGACCAAC-ACAAAAAA
128 TCGGCCATGCAATGACCAACAACAAAAAA
11169783 ATTTTGAATT
Statistics
Matches: 133, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
173 7 0.05
174 28 0.21
175 16 0.12
176 73 0.55
177 9 0.07
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (176 bp):
GGTGTCGGCCATTACATGGCAAACACAAAAAAAATTTGAAATTTTTTTATCCGAGAAAAAGGGGT
GTCGGCCATTTGATGGTCAACACAAAAAAAATTTGAAATTTTTTTCTCGAGAAAAGAAGATGTCG
GCCATGCAATGACCAACAACAAAAAATGTAATTTTTTTAAATAAGG
Found at i:11179060 original size:15 final size:16
Alignment explanation
Indices: 11179034--11179063 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11179024 AGGCTTATAG
11179034 CAATATTAAATATAAT
1 CAATATTAAATATAAT
11179050 CAATATT-AATATAA
1 CAATATTAAATATAA
11179064 AATTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (16 bp):
CAATATTAAATATAAT
Found at i:11182855 original size:95 final size:94
Alignment explanation
Indices: 11182735--11182912 Score: 266
Period size: 95 Copynumber: 1.9 Consensus size: 94
11182725 AATACAAGTT
* * * *
11182735 CTGTCAAAAAACCATTTGAATATTTCACATATGCAAAAGAATACAAATTGATGGCTTATGATGTT
1 CTGTCAAAAAACAATTTCAATATTTCACATACGCAAAAGAATACAAATTGATGACTTATGATGTT
11182800 TTCTTCAATTAGTATAAAAGGAATATGAA
66 TTCTTCAATTAGTATAAAAGGAATATGAA
* * * *
11182829 CTGTCCAAAAAACAATTTCAATATTTCATATACGTAGAGGAATACAAATTGATGACTTATGATGT
1 CTGT-CAAAAAACAATTTCAATATTTCACATACGCAAAAGAATACAAATTGATGACTTATGATGT
*
11182894 TTTCTTCAATTAGTGTAAA
65 TTTCTTCAATTAGTATAAA
11182913 TTGTAATGAG
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
94 4 0.05
95 70 0.95
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (94 bp):
CTGTCAAAAAACAATTTCAATATTTCACATACGCAAAAGAATACAAATTGATGACTTATGATGTT
TTCTTCAATTAGTATAAAAGGAATATGAA
Found at i:11189656 original size:18 final size:18
Alignment explanation
Indices: 11189633--11189669 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11189623 TTTGTGATCA
11189633 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
11189651 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
11189669 A
1 A
11189670 TATTAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:11199073 original size:18 final size:19
Alignment explanation
Indices: 11199052--11199092 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
11199042 CTTTATTTAT
*
11199052 TTATTTCT-ATATTAAGTA
1 TTATTTCTAATAATAAGTA
*
11199070 TTA-TTCTAATAATAATTA
1 TTATTTCTAATAATAAGTA
11199088 TTATT
1 TTATT
11199093 ATTATTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 4 0.21
18 14 0.74
19 1 0.05
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTTCTAATAATAAGTA
Found at i:11200028 original size:30 final size:26
Alignment explanation
Indices: 11199977--11200026 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
11199967 ACTAAACGTT
11199977 AACTAACTAATTAACTAAAATAAAAA
1 AACTAACTAATTAACTAAAATAAAAA
*
11200003 AACTAACTAATTAACTAGAATAAA
1 AACTAACTAATTAACTAAAATAAA
11200027 TATAAAAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (26 bp):
AACTAACTAATTAACTAAAATAAAAA
Found at i:11200325 original size:25 final size:25
Alignment explanation
Indices: 11200297--11200369 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 25
11200287 TAATTAACCT
11200297 TTAACCCATATGTTATAATAATATG
1 TTAACCCATATGTTATAATAATATG
*
11200322 TTAA-CCATA-GTTA-ATTAACT-T-
1 TTAACCCATATGTTATAATAA-TATG
11200343 TTAACCCATATGTTATAATAATATG
1 TTAACCCATATGTTATAATAATATG
11200368 TT
1 TT
11200370 CGCTAATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
21 4 0.10
22 10 0.25
23 10 0.25
24 10 0.25
25 6 0.15
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (25 bp):
TTAACCCATATGTTATAATAATATG
Found at i:11200334 original size:46 final size:46
Alignment explanation
Indices: 11200278--11200369 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
11200268 ATAAAATAAA
11200278 AACCATAGTTAATTAACCTTTAACCCATATGTTATAATAATATGTT
1 AACCATAGTTAATTAACCTTTAACCCATATGTTATAATAATATGTT
*
11200324 AACCATAGTTAATTAACTTTTAACCCATATGTTATAATAATATGTT
1 AACCATAGTTAATTAACCTTTAACCCATATGTTATAATAATATGTT
11200370 CGCTAATATG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (46 bp):
AACCATAGTTAATTAACCTTTAACCCATATGTTATAATAATATGTT
Found at i:11203007 original size:24 final size:24
Alignment explanation
Indices: 11202975--11203038 Score: 128
Period size: 24 Copynumber: 2.7 Consensus size: 24
11202965 AATATTTATT
11202975 TGATTTCCATTTATTTTGGGTAAA
1 TGATTTCCATTTATTTTGGGTAAA
11202999 TGATTTCCATTTATTTTGGGTAAA
1 TGATTTCCATTTATTTTGGGTAAA
11203023 TGATTTCCATTTATTT
1 TGATTTCCATTTATTT
11203039 ATTATTCGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.53
Consensus pattern (24 bp):
TGATTTCCATTTATTTTGGGTAAA
Found at i:11207991 original size:20 final size:20
Alignment explanation
Indices: 11207966--11208008 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
11207956 TTTATAAAAG
11207966 TTTTAGATGCAATGCCTAAA
1 TTTTAGATGCAATGCCTAAA
* *
11207986 TTTTAGATGCGATTCCTAAA
1 TTTTAGATGCAATGCCTAAA
11208006 TTT
1 TTT
11208009 ATCCATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (20 bp):
TTTTAGATGCAATGCCTAAA
Found at i:11208511 original size:29 final size:30
Alignment explanation
Indices: 11208456--11208525 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
11208446 ACATTTAAAG
* * *
11208456 AAATAAATAT-ATCAATTTATTTTTATATT
1 AAATAAATATAATCAATTTATGTATATAAT
*
11208485 AAATAAATATAAT-TATTTATGTATATAAT
1 AAATAAATATAATCAATTTATGTATATAAT
* *
11208514 ATATAAACATAA
1 AAATAAATATAA
11208526 AATGATGTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 32 0.94
30 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (30 bp):
AAATAAATATAATCAATTTATGTATATAAT
Found at i:11211191 original size:29 final size:29
Alignment explanation
Indices: 11211133--11211191 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
11211123 AAATCTAAAT
* * * *
11211133 ATTTTTAAGAAATTTCATTAACTCCTAAA
1 ATTTTTAAAAAATTTCATAAACCCCCAAA
11211162 ATTTTTAAAAAATTTGCA-AAACCCCCAAA
1 ATTTTTAAAAAATTT-CATAAACCCCCAAA
11211191 A
1 A
11211192 ATTAGTGTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (29 bp):
ATTTTTAAAAAATTTCATAAACCCCCAAA
Found at i:11211652 original size:29 final size:29
Alignment explanation
Indices: 11211593--11211652 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
11211583 ATGGCTAAGG
* **
11211593 TTTTATTTTATAATACACATATTTCCTTT
1 TTTTATTTAATAATACACATATTTCAATT
* *
11211622 TTTTATTTAATAATACA-TTATTTCAAAT
1 TTTTATTTAATAATACACATATTTCAATT
11211650 TTT
1 TTT
11211653 AAAAAATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTTATTTAATAATACACATATTTCAATT
Found at i:11213612 original size:17 final size:17
Alignment explanation
Indices: 11213586--11213620 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
11213576 AAGAAGTCAC
11213586 AATAAAGTGATAATTCA
1 AATAAAGTGATAATTCA
*
11213603 AATAATGTGATAATTCA
1 AATAAAGTGATAATTCA
11213620 A
1 A
11213621 TTGGATAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.31
Consensus pattern (17 bp):
AATAAAGTGATAATTCA
Found at i:11213955 original size:21 final size:21
Alignment explanation
Indices: 11213931--11214006 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 21
11213921 TATATTTTCA
11213931 AATTTTAAATTTTGAGTTTAT
1 AATTTTAAATTTTGAGTTTAT
* * **
11213952 AATTTGAAGTTTAAAGTTTATATCT
1 AATTTTAAATTTTGAG-TT-TA--T
*
11213977 AATTTTAAATTTATGA-TTTAA
1 AATTTTAAATTT-TGAGTTTAT
11213998 AATTTTAAA
1 AATTTTAAA
11214007 ATTTAAGACC
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
21 21 0.51
22 2 0.05
23 4 0.10
24 2 0.05
25 11 0.27
26 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.51
Consensus pattern (21 bp):
AATTTTAAATTTTGAGTTTAT
Found at i:11214487 original size:93 final size:93
Alignment explanation
Indices: 11214328--11214514 Score: 356
Period size: 93 Copynumber: 2.0 Consensus size: 93
11214318 ACTCGTGGTC
11214328 AGCATCCACCTCCTTAATAGACCTGCAAAATACTAAAAATTAGTTACTAAACTCATTCCGATAAA
1 AGCATCCACCTCCTTAATAGACCTGCAAAATACTAAAAATTAGTTACTAAACTCATTCCGATAAA
*
11214393 TATACTTTTGAGAAATAAATAAATACTA
66 TATACTTTTAAGAAATAAATAAATACTA
*
11214421 AGCATCCACCTCCTTAATAGACCTGCAAAATACTAAAAATTAGTTACTAAACTCATTTCGATAAA
1 AGCATCCACCTCCTTAATAGACCTGCAAAATACTAAAAATTAGTTACTAAACTCATTCCGATAAA
11214486 TATACTTTTAAGAAATAAATAAATACTA
66 TATACTTTTAAGAAATAAATAAATACTA
11214514 A
1 A
11214515 TAATTCTTTC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.45, C:0.19, G:0.07, T:0.29
Consensus pattern (93 bp):
AGCATCCACCTCCTTAATAGACCTGCAAAATACTAAAAATTAGTTACTAAACTCATTCCGATAAA
TATACTTTTAAGAAATAAATAAATACTA
Found at i:11230452 original size:1 final size:1
Alignment explanation
Indices: 11230446--11230471 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
11230436 CTTTCTCTTG
11230446 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
11230472 AATATGGCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:11244249 original size:128 final size:129
Alignment explanation
Indices: 11244003--11244249 Score: 329
Period size: 128 Copynumber: 1.9 Consensus size: 129
11243993 ATTATGATTG
* * *
11244003 TCTTTGAAACAACTTATTGCATTGATATTTATCACATCCAATATAATAAAACTTCATTTTATCCT
1 TCTTTGAAACAACTTATTGCATTGATATTTATCACATCCAACATAATAAAACCTCATTTTACCCT
* * * ** *
11244068 CTAGAATTTAGAGTTTTGGTTACTGAGAATTTCGAACTGCACCTATTGGTGGTACTAGCTATTA
66 CTAGAACTTAGAGTTTTGGTTACTAAGAATTTCAAACAACACCTATTGATGGTACTAGCTATTA
*
11244132 TCTTTGAAACAA-TTCATTGCATTGATATTTATCACATCCAACATCA-AAAACCTCATTTTACCC
1 TCTTTGAAACAACTT-ATTGCATTGATATTTATCACATCCAACATAATAAAACCTCATTTTACCC
* * * *
11244195 TCTATAACTTCGAGTTCTT-GTTGCTAAGATTTTCAAACAACACCTATTGATGGTA
65 TCTAGAACTTAGAGTT-TTGGTTACTAAGAATTTCAAACAACACCTATTGATGGTA
11244250 TCTGCAAGAT
Statistics
Matches: 102, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
128 59 0.58
129 43 0.42
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (129 bp):
TCTTTGAAACAACTTATTGCATTGATATTTATCACATCCAACATAATAAAACCTCATTTTACCCT
CTAGAACTTAGAGTTTTGGTTACTAAGAATTTCAAACAACACCTATTGATGGTACTAGCTATTA
Found at i:11244967 original size:17 final size:17
Alignment explanation
Indices: 11244926--11244977 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
11244916 CTGAATTTAG
11244926 TTTT-TATA-TTTTAA-
1 TTTTATATATTTTTAAT
*
11244940 TTTGA-ATATTTTTAAT
1 TTTTATATATTTTTAAT
11244956 TTTTATATATTTTTAAT
1 TTTTATATATTTTTAAT
*
11244973 ATTTA
1 TTTTA
11244978 AAATTTTAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 6 0.19
15 6 0.19
16 4 0.13
17 15 0.48
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTATATATTTTTAAT
Found at i:11251283 original size:14 final size:13
Alignment explanation
Indices: 11251266--11251297 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
11251256 AAGTGTTCTG
11251266 AAAAAATAATTTT
1 AAAAAATAATTTT
*
11251279 AAAAAATACTTTT
1 AAAAAATAATTTT
11251292 AAAAAA
1 AAAAAA
11251298 CTTGATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAAATAATTTT
Found at i:11257365 original size:21 final size:21
Alignment explanation
Indices: 11257336--11257393 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
11257326 TTTGAATGGG
11257336 AAAGAAAAAGAGAATATATGAA
1 AAAG-AAAAGAGAATATATGAA
* * * *
11257358 AAATAAAAAATCAA-ATATGAG
1 AAAGAAAAGA-GAATATATGAA
11257379 AAAGAAAAGAGAATA
1 AAAGAAAAGAGAATA
11257394 ACAAATATGA
Statistics
Matches: 27, Mismatches: 7, Indels: 5
0.69 0.18 0.13
Matches are distributed among these distances:
20 2 0.07
21 20 0.74
22 5 0.19
ACGTcount: A:0.69, C:0.02, G:0.16, T:0.14
Consensus pattern (21 bp):
AAAGAAAAGAGAATATATGAA
Found at i:11257626 original size:19 final size:18
Alignment explanation
Indices: 11257583--11257625 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
11257573 GATTTTTTTA
11257583 TTTTTTTCTATTTCAATT
1 TTTTTTTCTATTTCAATT
* * *
11257601 GTTTTTTCTATTTTACTT
1 TTTTTTTCTATTTCAATT
11257619 TTTTTTT
1 TTTTTTT
11257626 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.09, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTTTTCTATTTCAATT
Found at i:11261060 original size:18 final size:19
Alignment explanation
Indices: 11261036--11261077 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
11261026 TAATTTAATT
*
11261036 TTTTTTATAATTTT-TATA
1 TTTTTAATAATTTTATATA
11261054 CTTTTTAATAATTTTATATA
1 -TTTTTAATAATTTTATATA
11261074 TTTT
1 TTTT
11261078 GAATTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTAATAATTTTATATA
Found at i:11263200 original size:20 final size:20
Alignment explanation
Indices: 11263177--11263217 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
11263167 CGCTTTGTTT
11263177 TTTCTGCCTCATGTTTGTGC
1 TTTCTGCCTCATGTTTGTGC
11263197 TTTCTGCCTCATGTTTGTGC
1 TTTCTGCCTCATGTTTGTGC
11263217 T
1 T
11263218 ATGAAAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.05, C:0.24, G:0.20, T:0.51
Consensus pattern (20 bp):
TTTCTGCCTCATGTTTGTGC
Found at i:11285009 original size:23 final size:23
Alignment explanation
Indices: 11284983--11285032 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
11284973 GAATCGAATT
* * *
11284983 ATTCGAGTCAATTCGAATAAGTA
1 ATTCGAGTAAACTCAAATAAGTA
11285006 ATTCGAGTAAACTCAAATAAGTA
1 ATTCGAGTAAACTCAAATAAGTA
11285029 ATTC
1 ATTC
11285033 AAGTTTCAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (23 bp):
ATTCGAGTAAACTCAAATAAGTA
Found at i:11285558 original size:5 final size:5
Alignment explanation
Indices: 11285548--11285578 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
11285538 AGTATGATAG
11285548 AAATA AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA AAATA A
11285579 CTCACTATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:11291575 original size:43 final size:42
Alignment explanation
Indices: 11291496--11291601 Score: 97
Period size: 43 Copynumber: 2.5 Consensus size: 42
11291486 ACTTTCGTGT
* * **
11291496 TGTTTTTACTATTATTTTTGTTGCTATTTTTTTTGTT-TTTAA
1 TGTTTTTACTGTTATTTTTGCTGCTATTTTGGTTGTTATTT-A
* * *
11291538 TGTTGTTTACTGTTATTTTTGCTGTTGTTTTGGTTGTTATTTT
1 TGTT-TTTACTGTTATTTTTGCTGCTATTTTGGTTGTTATTTA
*
11291581 TGTTATTTGAATGTTATTTTT
1 TGTT-TTT-ACTGTTATTTTT
11291602 TATGCGTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
42 4 0.08
43 34 0.65
44 14 0.27
ACGTcount: A:0.12, C:0.04, G:0.15, T:0.69
Consensus pattern (42 bp):
TGTTTTTACTGTTATTTTTGCTGCTATTTTGGTTGTTATTTA
Done.