Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 15 of 172
Found at i:4730627 original size:13 final size:14
Alignment explanation
Indices: 4730611--4730652 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
4730601 TTTCAATTTT
4730611 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
4730624 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
4730639 ATTTTAAATAATAT
1 ATTTT-AATAATAT
4730653 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:4730637 original size:16 final size:16
Alignment explanation
Indices: 4730615--4730651 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
4730605 AATTTTATTT
4730615 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
4730632 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
4730647 TAATA
1 TAATA
4730652 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:4730704 original size:15 final size:15
Alignment explanation
Indices: 4730684--4730740 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
4730674 ATTCAACATT
4730684 AATATTTTAATAATA
1 AATATTTTAATAATA
*
4730699 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
4730718 AATATATTAATAATA
1 AATATTTTAATAATA
*
4730733 AATGTTTT
1 AATATTTT
4730741 GTAGTATANT
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:4731978 original size:34 final size:34
Alignment explanation
Indices: 4731939--4732050 Score: 102
Period size: 34 Copynumber: 3.2 Consensus size: 34
4731929 TATTTAGTTG
4731939 TTTAAAACATTTGATAAATTATATTTATATTGTA
1 TTTAAAACATTTGATAAATTATATTTATATTGTA
* * * * * * *
4731973 TTTAAAAGCGTTTTATTTAGTTATTTAGTTTAAAATGCA
1 TTTAAAA-CATTTGA-TAAATTA--TA-TTTATATTGTA
4732012 --TAAAACATTTGATAAATTATATTTATATTGTA
1 TTTAAAACATTTGATAAATTATATTTATATTGTA
4732044 TTTAAAA
1 TTTAAAA
4732051 GCGTTTTTAT
Statistics
Matches: 57, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
32 8 0.14
33 2 0.04
34 12 0.21
35 10 0.18
36 10 0.18
37 5 0.09
38 2 0.04
39 8 0.14
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (34 bp):
TTTAAAACATTTGATAAATTATATTTATATTGTA
Found at i:4733390 original size:44 final size:45
Alignment explanation
Indices: 4733327--4733416 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 45
4733317 ACTGAGCTAG
* *
4733327 GCTCCGTAGATGTAGGGAAACTAAACTACGT-GA-AAAACTTTGT
1 GCTCCGTAGATGGAGGGAAACTAAACTACGTAAACAAAACTTTGT
* *
4733370 NGCTCCGTAGATGGAGGGAAACTGAACTGCGTAAACAAAACTTTGT
1 -GCTCCGTAGATGGAGGGAAACTAAACTACGTAAACAAAACTTTGT
4733416 G
1 G
4733417 TTATTTCTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 28 0.70
45 2 0.05
46 10 0.25
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.23
Consensus pattern (45 bp):
GCTCCGTAGATGGAGGGAAACTAAACTACGTAAACAAAACTTTGT
Found at i:4739656 original size:25 final size:23
Alignment explanation
Indices: 4739634--4739679 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
4739624 GATCCATTGA
*
4739634 AACAGGTACACGAAATATACATT
1 AACAGATACACGAAATATACATT
*
4739657 AATAGATACACGAAATATACATT
1 AACAGATACACGAAATATACATT
4739680 TATGCTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (23 bp):
AACAGATACACGAAATATACATT
Found at i:4740406 original size:45 final size:45
Alignment explanation
Indices: 4740355--4740753 Score: 191
Period size: 45 Copynumber: 8.9 Consensus size: 45
4740345 GATCACCGGA
* * *
4740355 AGCAGATTTGACGTCTCTGTATTAGACGAGGAGTAGATCGAAGAT
1 AGCAGATTTGGCATCTCTGTATTAGACGAGGAGCAGATCGAAGAT
* * * *
4740400 AGCAGATCTGGCAT-TCGTGTGTTTACATC-A-AAGCAGATCGAAGAT
1 AGCAGATTTGGCATCTC-TGT-ATTAGA-CGAGGAGCAGATCGAAGAT
* * * * * *
4740445 -GACAAATTTGGCATCTCTATATTTGACGGGGAGTAGATCAAAGAT
1 AG-CAGATTTGGCATCTCTGTATTAGACGAGGAGCAGATCGAAGAT
* * * * *
4740490 AGCAAATCTGACAT-TCATGTGTTTACATCGA--AGCAGATCGAAGAT
1 AGCAGATTTGGCATCTC-TGT-ATTAGA-CGAGGAGCAGATCGAAGAT
* * * *
4740535 -GACAGATTTGGCGTCTCTGTATTAGACGGGGAGTAGATTGAAGAT
1 AG-CAGATTTGGCATCTCTGTATTAGACGAGGAGCAGATCGAAGAT
* * * * *
4740580 AGAAGATCTGACAT-TCGTGTGTTTACATCGA--AGCAGATCGAAGAT
1 AGCAGATTTGGCATCTC-TGT-ATTAGA-CGAGGAGCAGATCGAAGAT
* * * * * *
4740625 -GACAAATTTGGCATCTCTATATTTGACGGGGAGTAGATCAAAGAT
1 AG-CAGATTTGGCATCTCTGTATTAGACGAGGAGCAGATCGAAGAT
* * * * *
4740670 AGCAAATCTGACAT-TCATGTGTTTACATCGA--AGCAGATCGAAGAT
1 AGCAGATTTGGCATCTC-TGT-ATTAGA-CGAGGAGCAGATCGAAGAT
*
4740715 -GACAGATTTGGCATCTCTGTATTAGACGCGGAGCAGATC
1 AG-CAGATTTGGCATCTCTGTATTAGACGAGGAGCAGATC
4740754 TGACATTCGT
Statistics
Matches: 253, Mismatches: 70, Indels: 62
0.66 0.18 0.16
Matches are distributed among these distances:
43 7 0.03
44 26 0.10
45 187 0.74
46 26 0.10
47 7 0.03
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (45 bp):
AGCAGATTTGGCATCTCTGTATTAGACGAGGAGCAGATCGAAGAT
Found at i:4740499 original size:90 final size:90
Alignment explanation
Indices: 4740368--4741251 Score: 762
Period size: 90 Copynumber: 10.3 Consensus size: 90
4740358 AGATTTGACG
* * * * * *
4740368 TCTCTGTATTAGACGAGGAGTAGATCGAAGATAGCAGATCTGGCATTCGTGTGTTTACATCAAAG
1 TCTCTGTATTAGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAG
4740433 CAGATCGAAGATGACAAATTTGGCA
66 CAGATCGAAGATGACAAATTTGGCA
* *
4740458 TCTCTATATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAG
1 TCTCTGTATTAGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAG
* *
4740523 CAGATCGAAGATGACAGATTTGGCG
66 CAGATCGAAGATGACAAATTTGGCA
** *
4740548 TCTCTGTATTAGACGGGGAGTAGATTGAAGATAG-AAGATCTGACATTCGTGTGTTTACATCGAA
1 TCTCTGTATTAGACGGGGAGTAGATCAAAGATAGCAA-ATCTGACATTCATGTGTTTACATCGAA
4740612 GCAGATCGAAGATGACAAATTTGGCA
65 GCAGATCGAAGATGACAAATTTGGCA
* *
4740638 TCTCTATATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAG
1 TCTCTGTATTAGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAG
*
4740703 CAGATCGAAGATGACAGATTTGGCA
66 CAGATCGAAGATGACAAATTTGGCA
* * ** * * *** * * **
4740728 TCTCTGTATTAGACGCGGAGCAGATCTGACAT-TCGTGTGTTTACA-TCA-AAG----CA--G-A
1 TCTCTGTATTAGACGGGGAGTAGATCAAAGATAGCAAAT-CTGACATTCATGTGTTTACATCGAA
* *
4740783 TC-GA-AG-A--TGACAAATTTGGCA
65 GCAGATCGAAGATGACAAATTTGGCA
* *
4740804 TCTCTATATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAG
1 TCTCTGTATTAGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAG
*
4740869 CAGATCGAAGATGACAGATTTGGCA
66 CAGATCGAAGATGACAAATTTGGCA
* * ** * * *** * * **
4740894 TCTCTGTATTAGACGCGGAGCAGATCTGACAT-TCGTGTGTTTACA-TCA-AAG----CA--G-A
1 TCTCTGTATTAGACGGGGAGTAGATCAAAGATAGCAAAT-CTGACATTCATGTGTTTACATCGAA
* *
4740949 TC-GA-AG-A--TGACAAATTTGGCA
65 GCAGATCGAAGATGACAAATTTGGCA
* *
4740970 TCTCTATATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAG
1 TCTCTGTATTAGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAG
*
4741035 CAGATCGAAGATGACAGATTTGGCA
66 CAGATCGAAGATGACAAATTTGGCA
* * ** * * *** * * **
4741060 TCTCTGTATTAGACGCGGAGCAGATCTGACAT-TCGTGTGTTTACA-TCA-AAG----CA--G-A
1 TCTCTGTATTAGACGGGGAGTAGATCAAAGATAGCAAAT-CTGACATTCATGTGTTTACATCGAA
* *
4741115 TC-GA-AG-A--TGACAAATTTGGCA
65 GCAGATCGAAGATGACAAATTTGGCA
* *
4741136 TCTCTATATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAG
1 TCTCTGTATTAGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAG
*
4741201 CAGATCGAAGATGACAGATTTGGCA
66 CAGATCGAAGATGACAAATTTGGCA
* *
4741226 TCTCTGTATTAGACGCGGAGCAGATC
1 TCTCTGTATTAGACGGGGAGTAGATC
4741252 TGACATTCGT
Statistics
Matches: 609, Mismatches: 135, Indels: 100
0.72 0.16 0.12
Matches are distributed among these distances:
76 126 0.21
77 15 0.02
78 6 0.01
79 3 0.00
80 6 0.01
81 6 0.01
82 9 0.01
84 9 0.01
85 6 0.01
86 6 0.01
87 3 0.00
88 6 0.01
89 17 0.03
90 389 0.64
91 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (90 bp):
TCTCTGTATTAGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAG
CAGATCGAAGATGACAAATTTGGCA
Found at i:4740767 original size:76 final size:76
Alignment explanation
Indices: 4740670--4741516 Score: 890
Period size: 76 Copynumber: 10.6 Consensus size: 76
4740660 GATCAAAGAT
* * *
4740670 AGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
4740735 ATTAGACGCGG
66 ATTAGACGCGG
* *
4740746 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
* *
4740811 ATTTGACGGGG
66 ATTAGACGCGG
* * * * * ** **
4740822 AGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTA-CATCGAAGCAGATCGAAGATGACAG
1 AGCAGATC-----T-G-ACAT-T--C-GT-GTGTTTACATCAAAG---CAGATCGAAGATGACAG
4740886 ATTTGGCATCTCTGTATTAGACGCGG
51 ATTTGGCATCTCTGTATTAGACGCGG
* *
4740912 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
* *
4740977 ATTTGACGGGG
66 ATTAGACGCGG
* * * * * ** **
4740988 AGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTA-CATCGAAGCAGATCGAAGATGACAG
1 AGCAGATC-----T-G-ACAT-T--C-GT-GTGTTTACATCAAAG---CAGATCGAAGATGACAG
4741052 ATTTGGCATCTCTGTATTAGACGCGG
51 ATTTGGCATCTCTGTATTAGACGCGG
* *
4741078 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
* *
4741143 ATTTGACGGGG
66 ATTAGACGCGG
* * * * * ** **
4741154 AGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTA-CATCGAAGCAGATCGAAGATGACAG
1 AGCAGATC-----T-G-ACAT-T--C-GT-GTGTTTACATCAAAG---CAGATCGAAGATGACAG
4741218 ATTTGGCATCTCTGTATTAGACGCGG
51 ATTTGGCATCTCTGTATTAGACGCGG
4741244 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
4741309 ATTAGACGCGG
66 ATTAGACGCGG
4741320 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
4741385 ATTAGACGCGG
66 ATTAGACGCGG
4741396 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
4741461 ATTAGACGCGG
66 ATTAGACGCGG
4741472 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGAT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGAT
4741517 AGCAGATCTG
Statistics
Matches: 642, Mismatches: 81, Indels: 96
0.78 0.10 0.12
Matches are distributed among these distances:
76 408 0.64
78 15 0.02
79 12 0.02
80 3 0.00
81 3 0.00
82 6 0.01
83 18 0.03
84 6 0.01
85 3 0.00
86 3 0.00
87 12 0.02
88 15 0.02
90 138 0.21
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (76 bp):
AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
ATTAGACGCGG
Found at i:4740857 original size:166 final size:166
Alignment explanation
Indices: 4740400--4741479 Score: 1792
Period size: 166 Copynumber: 6.5 Consensus size: 166
4740390 GATCGAAGAT
*
4740400 AGCAGATCTGGCATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
4740465 ATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCG
66 ATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCG
* *
4740530 AAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGTAGATTGAAG
131 AAGATGACAGATTTGGCATCTCTGTATTAGAC--------G--CG--G
* *
4740578 ATAGAAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAAATTTGGCATCTCT
1 --AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCT
4740643 ATATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAGCAGAT
64 ATATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAGCAGAT
4740708 CGAAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
129 CGAAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
4740746 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
4740811 ATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCG
66 ATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCG
4740876 AAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
131 AAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
4740912 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
4740977 ATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCG
66 ATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCG
4741042 AAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
131 AAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
4741078 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
4741143 ATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCG
66 ATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCG
4741208 AAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
131 AAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
* *
4741244 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
* * * *
4741309 ATTAGAC-GCG-G-AG--C------AG---ATCTGACATTCGTGTGTTTACATCAAAGCAGATCG
66 ATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCG
4741360 AAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
131 AAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
* *
4741396 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
* * *
4741461 ATTAGACGCGGAGCAGATC
66 ATTTGACGGGGAGTAGATC
4741480 TGACATTCGT
Statistics
Matches: 880, Mismatches: 15, Indels: 33
0.95 0.02 0.04
Matches are distributed among these distances:
152 141 0.16
153 1 0.00
154 1 0.00
155 4 0.00
157 1 0.00
161 1 0.00
163 2 0.00
164 1 0.00
165 2 0.00
166 565 0.64
168 1 0.00
170 1 0.00
172 1 0.00
180 158 0.18
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (166 bp):
AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
ATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCG
AAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
Found at i:4740874 original size:45 final size:45
Alignment explanation
Indices: 4740746--4740880 Score: 114
Period size: 45 Copynumber: 3.0 Consensus size: 45
4740736 TTAGACGCGG
* * *
4740746 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGAT
1 AGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCGAAGAT
* * * * ** * * *
4740791 -GACAAATTTGGCATCTCTATAT-TTGAC-GGGGAGTAGATCAAAGAT
1 AG-CAAATCTGACAT-TC-ATGTGTTTACATCGAAGCAGATCGAAGAT
4740836 AGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCGAAGAT
1 AGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCGAAGAT
4740881 GACAGATTTG
Statistics
Matches: 63, Mismatches: 21, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
43 3 0.05
44 7 0.11
45 44 0.70
46 7 0.11
47 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (45 bp):
AGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCGAAGAT
Found at i:4740916 original size:45 final size:44
Alignment explanation
Indices: 4740777--4740919 Score: 128
Period size: 45 Copynumber: 3.2 Consensus size: 44
4740767 TTTACATCAA
* *
4740777 AGCAGATCGAAGATGACAAATTTGGCATCTCTATATTTGACGGGG
1 AGCAGATCGAAGATGACAAATTTGGCATCTCTGTA-TTGACGCGG
* * * * * * * *
4740822 AGTAGATCAAAGAT-AGCAAATCTGACAT-TCATGTGTTTACATCGA
1 AGCAGATCGAAGATGA-CAAATTTGGCATCTC-TGTATTGAC-GCGG
*
4740867 AGCAGATCGAAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
1 AGCAGATCGAAGATGACAAATTTGGCATCTCTGTATT-GACGCGG
4740912 AGCAGATC
1 AGCAGATC
4740920 TGACATTCGT
Statistics
Matches: 73, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
44 7 0.10
45 61 0.84
46 5 0.07
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (44 bp):
AGCAGATCGAAGATGACAAATTTGGCATCTCTGTATTGACGCGG
Found at i:4741040 original size:45 final size:45
Alignment explanation
Indices: 4740912--4741046 Score: 114
Period size: 45 Copynumber: 3.0 Consensus size: 45
4740902 TTAGACGCGG
* * *
4740912 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGAT
1 AGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCGAAGAT
* * * * ** * * *
4740957 -GACAAATTTGGCATCTCTATAT-TTGAC-GGGGAGTAGATCAAAGAT
1 AG-CAAATCTGACAT-TC-ATGTGTTTACATCGAAGCAGATCGAAGAT
4741002 AGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCGAAGAT
1 AGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCGAAGAT
4741047 GACAGATTTG
Statistics
Matches: 63, Mismatches: 21, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
43 3 0.05
44 7 0.11
45 44 0.70
46 7 0.11
47 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (45 bp):
AGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCGAAGAT
Found at i:4741082 original size:45 final size:44
Alignment explanation
Indices: 4740943--4741085 Score: 128
Period size: 45 Copynumber: 3.2 Consensus size: 44
4740933 TTTACATCAA
* *
4740943 AGCAGATCGAAGATGACAAATTTGGCATCTCTATATTTGACGGGG
1 AGCAGATCGAAGATGACAAATTTGGCATCTCTGTA-TTGACGCGG
* * * * * * * *
4740988 AGTAGATCAAAGAT-AGCAAATCTGACAT-TCATGTGTTTACATCGA
1 AGCAGATCGAAGATGA-CAAATTTGGCATCTC-TGTATTGAC-GCGG
*
4741033 AGCAGATCGAAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
1 AGCAGATCGAAGATGACAAATTTGGCATCTCTGTATT-GACGCGG
4741078 AGCAGATC
1 AGCAGATC
4741086 TGACATTCGT
Statistics
Matches: 73, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
44 7 0.10
45 61 0.84
46 5 0.07
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (44 bp):
AGCAGATCGAAGATGACAAATTTGGCATCTCTGTATTGACGCGG
Found at i:4741101 original size:242 final size:232
Alignment explanation
Indices: 4740836--4741516 Score: 937
Period size: 242 Copynumber: 2.9 Consensus size: 232
4740826 GATCAAAGAT
* * *
4740836 AGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
*
4740901 ATTAGACGCGGAGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTT
66 ATTAGACGCGGAGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTT
* *
4740966 GGCATCTCTATATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATC
131 GGCATCTCTGTATTAGACGGGGAG-AGATC------AG---ATCTGACATTCATGTGTTTACATC
*
4741031 GAAGCAGATCGAAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
186 AAAGCAGATCGAAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
* *
4741078 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAAATTTGGCATCTCTAT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
* * * *
4741143 ATTTGACGGGGAGTAGATCAAAGATAGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCG
66 ATTAGAC-GCG-G-AG--C------AG---ATCTGACATTCGTGTGTTTACATCAAAGCAGATCG
* *
4741208 AAGATGACAGATTTGGCATCTCTGTATTAGAC-GCG-GAG--CAGATCTGACATTCGTGTGTTTA
117 AAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGAGATCAGATCTGACATTCATGTGTTTA
4741269 CATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
182 CATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
4741320 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
1 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
4741385 ATTAGACGCGGAGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTT
66 ATTAGACGCGGAGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTT
* *
4741450 GGCATCTCTGTATTAGAC-GCG-GAG--CAGATCTGACATTCGTGTGTTTACATCAAAGCAGATC
131 GGCATCTCTGTATTAGACGGGGAGAGATCAGATCTGACATTCATGTGTTTACATCAAAGCAGATC
4741511 GAAGAT
196 GAAGAT
4741517 AGCAGATCTG
Statistics
Matches: 404, Mismatches: 21, Indels: 42
0.87 0.04 0.09
Matches are distributed among these distances:
228 114 0.28
231 2 0.00
237 1 0.00
239 2 0.00
240 1 0.00
241 2 0.00
242 204 0.50
243 2 0.00
244 1 0.00
245 4 0.01
247 1 0.00
251 1 0.00
253 4 0.01
254 1 0.00
255 2 0.00
256 62 0.15
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (232 bp):
AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTTGGCATCTCTGT
ATTAGACGCGGAGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGATGACAGATTT
GGCATCTCTGTATTAGACGGGGAGAGATCAGATCTGACATTCATGTGTTTACATCAAAGCAGATC
GAAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
Found at i:4741206 original size:45 final size:45
Alignment explanation
Indices: 4741078--4741212 Score: 114
Period size: 45 Copynumber: 3.0 Consensus size: 45
4741068 TTAGACGCGG
* * *
4741078 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGAT
1 AGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCGAAGAT
* * * * ** * * *
4741123 -GACAAATTTGGCATCTCTATAT-TTGAC-GGGGAGTAGATCAAAGAT
1 AG-CAAATCTGACAT-TC-ATGTGTTTACATCGAAGCAGATCGAAGAT
4741168 AGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCGAAGAT
1 AGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCGAAGAT
4741213 GACAGATTTG
Statistics
Matches: 63, Mismatches: 21, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
43 3 0.05
44 7 0.11
45 44 0.70
46 7 0.11
47 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (45 bp):
AGCAAATCTGACATTCATGTGTTTACATCGAAGCAGATCGAAGAT
Found at i:4741248 original size:45 final size:44
Alignment explanation
Indices: 4741109--4741251 Score: 128
Period size: 45 Copynumber: 3.2 Consensus size: 44
4741099 TTTACATCAA
* *
4741109 AGCAGATCGAAGATGACAAATTTGGCATCTCTATATTTGACGGGG
1 AGCAGATCGAAGATGACAAATTTGGCATCTCTGTA-TTGACGCGG
* * * * * * * *
4741154 AGTAGATCAAAGAT-AGCAAATCTGACAT-TCATGTGTTTACATCGA
1 AGCAGATCGAAGATGA-CAAATTTGGCATCTC-TGTATTGAC-GCGG
*
4741199 AGCAGATCGAAGATGACAGATTTGGCATCTCTGTATTAGACGCGG
1 AGCAGATCGAAGATGACAAATTTGGCATCTCTGTATT-GACGCGG
4741244 AGCAGATC
1 AGCAGATC
4741252 TGACATTCGT
Statistics
Matches: 73, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
44 7 0.10
45 61 0.84
46 5 0.07
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (44 bp):
AGCAGATCGAAGATGACAAATTTGGCATCTCTGTATTGACGCGG
Found at i:4741521 original size:45 final size:45
Alignment explanation
Indices: 4741472--4741748 Score: 212
Period size: 45 Copynumber: 6.2 Consensus size: 45
4741462 TTAGACGCGG
*
4741472 AGCAGATCTGACATTCGTGTGTTTACATCAAAGCAGATCGAAGAT
1 AGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGAT
* * *
4741517 AGCAGATCTGACATTTGTGTGTTTACATCGAAGTAGATCGAAAAT
1 AGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGAT
* * * *
4741562 -GACAGAGT-TGGCATCTC-TGT-ATTA-AACGGGGAGCAGATCGAAGAT
1 AG-CAGA-TCTGACAT-TCGTGTGTTTACATC--GAAGCAGATCGAAGAT
* * *
4741607 AGCAGATCTGACATTTGTGTGTTTACATTGAAGCAGATCTAAGAT
1 AGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGAT
* * * * * * *
4741652 -GACAGATTTGGCGTCTC-TGT-ATTAGA-CGGGGAGCAGATCAAAGAT
1 AG-CAGATCTGACAT-TCGTGTGTTTACATC--GAAGCAGATCGAAGAT
* * *
4741697 AGCAGATCTGACATTTGCGTGTTTACATCGAAGCAAATCGAAGAT
1 AGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGAT
*
4741742 AACAGAT
1 AGCAGAT
4741749 TTGGCGTCTC
Statistics
Matches: 176, Mismatches: 38, Indels: 36
0.70 0.15 0.14
Matches are distributed among these distances:
43 2 0.01
44 12 0.07
45 148 0.84
46 12 0.07
47 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (45 bp):
AGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGAT
Found at i:4741766 original size:90 final size:90
Alignment explanation
Indices: 4741503--4741769 Score: 435
Period size: 90 Copynumber: 3.0 Consensus size: 90
4741493 TTTACATCAA
* *
4741503 AGCAGATCGAAGATAGCAGATCTGACATTTGTGTGTTTACATCGAAGTAGATCGAAAATGACAGA
1 AGCAGATCGAAGATAGCAGATCTGACATTTGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
* * *
4741568 GTTGGCATCTCTGTATTAAACGGGG
66 TTTGGCGTCTCTGTATTAGACGGGG
* *
4741593 AGCAGATCGAAGATAGCAGATCTGACATTTGTGTGTTTACATTGAAGCAGATCTAAGATGACAGA
1 AGCAGATCGAAGATAGCAGATCTGACATTTGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
4741658 TTTGGCGTCTCTGTATTAGACGGGG
66 TTTGGCGTCTCTGTATTAGACGGGG
* * * *
4741683 AGCAGATCAAAGATAGCAGATCTGACATTTGCGTGTTTACATCGAAGCAAATCGAAGATAACAGA
1 AGCAGATCGAAGATAGCAGATCTGACATTTGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
4741748 TTTGGCGTCTCTGTATTAGACG
66 TTTGGCGTCTCTGTATTAGACG
4741770 AAAAACAGGT
Statistics
Matches: 164, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 164 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.27
Consensus pattern (90 bp):
AGCAGATCGAAGATAGCAGATCTGACATTTGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
TTTGGCGTCTCTGTATTAGACGGGG
Found at i:4741972 original size:17 final size:17
Alignment explanation
Indices: 4741950--4741989 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
4741940 TCGCCCGGGC
*
4741950 CCAAAAAAAACAATAAA
1 CCAAAAAAAACAAAAAA
* *
4741967 CCAAAATACACAAAAAA
1 CCAAAAAAAACAAAAAA
4741984 CCAAAA
1 CCAAAA
4741990 TAATTAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.72, C:0.23, G:0.00, T:0.05
Consensus pattern (17 bp):
CCAAAAAAAACAAAAAA
Found at i:4741990 original size:17 final size:17
Alignment explanation
Indices: 4741959--4741991 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4741949 CCCAAAAAAA
*
4741959 ACAATAAACCAAAATAC
1 ACAAAAAACCAAAATAC
4741976 ACAAAAAACCAAAATA
1 ACAAAAAACCAAAATA
4741992 ATTAAATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.21, G:0.00, T:0.09
Consensus pattern (17 bp):
ACAAAAAACCAAAATAC
Found at i:4745627 original size:16 final size:16
Alignment explanation
Indices: 4745594--4745627 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4745584 GCGAGCTGTT
* *
4745594 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
4745610 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
4745626 AA
1 AA
4745628 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:4748455 original size:21 final size:21
Alignment explanation
Indices: 4748429--4748469 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4748419 AGACGAGCAA
* *
4748429 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
4748450 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
4748470 TTGAGCAGAT
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:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:4750408 original size:16 final size:16
Alignment explanation
Indices: 4750375--4750408 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4750365 GGAGATTGTT
* *
4750375 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
4750391 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
4750407 AA
1 AA
4750409 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:4756225 original size:42 final size:42
Alignment explanation
Indices: 4756162--4756268 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
4756152 CATATGAGTC
* * * * * *
4756162 TCAATTTAACCCTTTTAGGTTTTAGTTCAGCTCTTTTGAGCT
1 TCAATTTAACCCTTATGGGTTTCAGTTCAGCTATTATAAGCT
*
4756204 TCAATTTAACCCTTATGGGTTTCCGTTCAGCTATTATAAGCT
1 TCAATTTAACCCTTATGGGTTTCAGTTCAGCTATTATAAGCT
** *
4756246 TCTGTTTAACCCTTACGGGTTTC
1 TCAATTTAACCCTTATGGGTTTC
4756269 CGTTTAGCAC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.44
Consensus pattern (42 bp):
TCAATTTAACCCTTATGGGTTTCAGTTCAGCTATTATAAGCT
Found at i:4756529 original size:11 final size:11
Alignment explanation
Indices: 4756513--4756537 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4756503 TAGGAGAGCG
4756513 AAATGAGCCAA
1 AAATGAGCCAA
4756524 AAATGAGCCAA
1 AAATGAGCCAA
4756535 AAA
1 AAA
4756538 GGGACAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.08
Consensus pattern (11 bp):
AAATGAGCCAA
Found at i:4756733 original size:13 final size:13
Alignment explanation
Indices: 4756715--4756739 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4756705 GCAATCATGT
4756715 CACACGGGCGTGG
1 CACACGGGCGTGG
4756728 CACACGGGCGTG
1 CACACGGGCGTG
4756740 TCCCTGCCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.44, T:0.08
Consensus pattern (13 bp):
CACACGGGCGTGG
Found at i:4760906 original size:36 final size:36
Alignment explanation
Indices: 4760866--4760938 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
4760856 TGCCCCGAAA
4760866 TGCTTTCATATTTTCCAGAATACCTTTCAGCTTATT
1 TGCTTTCATATTTTCCAGAATACCTTTCAGCTTATT
4760902 TGCTTTCATATTTTCCAGAATACCTTTCAGCTTATT
1 TGCTTTCATATTTTCCAGAATACCTTTCAGCTTATT
4760938 T
1 T
4760939 TCCCCTTTCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.48
Consensus pattern (36 bp):
TGCTTTCATATTTTCCAGAATACCTTTCAGCTTATT
Found at i:4763586 original size:12 final size:12
Alignment explanation
Indices: 4763571--4763595 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4763561 GAGATATGAT
4763571 TAAATAAGTTAA
1 TAAATAAGTTAA
4763583 TAAATAAGTTAA
1 TAAATAAGTTAA
4763595 T
1 T
4763596 TTTGAATATA
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TAAATAAGTTAA
Found at i:4767304 original size:83 final size:83
Alignment explanation
Indices: 4767165--4767323 Score: 318
Period size: 83 Copynumber: 1.9 Consensus size: 83
4767155 GTGGGGATAA
4767165 AATCAACCCACCTATTCCTACACTCCAAAATAGCACCGGTTGCAGCTCTAAATAGTATTTGCAGT
1 AATCAACCCACCTATTCCTACACTCCAAAATAGCACCGGTTGCAGCTCTAAATAGTATTTGCAGT
4767230 AGAGCTGCCAGAGCGTGG
66 AGAGCTGCCAGAGCGTGG
4767248 AATCAACCCACCTATTCCTACACTCCAAAATAGCACCGGTTGCAGCTCTAAATAGTATTTGCAGT
1 AATCAACCCACCTATTCCTACACTCCAAAATAGCACCGGTTGCAGCTCTAAATAGTATTTGCAGT
4767313 AGAGCTGCCAG
66 AGAGCTGCCAG
4767324 TACAGTACAC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (83 bp):
AATCAACCCACCTATTCCTACACTCCAAAATAGCACCGGTTGCAGCTCTAAATAGTATTTGCAGT
AGAGCTGCCAGAGCGTGG
Found at i:4781740 original size:12 final size:12
Alignment explanation
Indices: 4781723--4781764 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
4781713 CAGTATGCTC
4781723 CACACGACCTAG
1 CACACGACCTAG
*
4781735 CACACGGCCTAG
1 CACACGACCTAG
4781747 CACAC-AGCCTAG
1 CACACGA-CCTAG
4781759 CACACG
1 CACACG
4781765 GCTTGTGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.31, C:0.43, G:0.19, T:0.07
Consensus pattern (12 bp):
CACACGACCTAG
Found at i:4784509 original size:66 final size:66
Alignment explanation
Indices: 4784433--4784706 Score: 539
Period size: 66 Copynumber: 4.2 Consensus size: 66
4784423 AAGCAGGGAA
*
4784433 AGAAAGAGATGAGAGGTAGAGATACCCTACTAATATTCAACCAAAGTACCAGTTGAAGGAAAGGA
1 AGAAAGAGATGACAGGTAGAGATACCCTACTAATATTCAACCAAAGTACCAGTTGAAGGAAAGGA
4784498 G
66 G
4784499 AGAAAGAGATGACAGGTAGAGATACCCTACTAATATTCAACCAAAGTACCAGTTGAAGGAAAGGA
1 AGAAAGAGATGACAGGTAGAGATACCCTACTAATATTCAACCAAAGTACCAGTTGAAGGAAAGGA
4784564 G
66 G
4784565 AGAAAGAGATGACAGGTAGAGATACCCTACTAATATTCAACCAAAGTACCAGTTGAAGGAAAGGA
1 AGAAAGAGATGACAGGTAGAGATACCCTACTAATATTCAACCAAAGTACCAGTTGAAGGAAAGGA
4784630 G
66 G
4784631 AGAAAGAGATGACAGGTAGAGATACCCTACTAATATTCAACCAAAGTACCAGTTGAAGGAAAGGA
1 AGAAAGAGATGACAGGTAGAGATACCCTACTAATATTCAACCAAAGTACCAGTTGAAGGAAAGGA
4784696 G
66 G
4784697 AGAAAGAGAT
1 AGAAAGAGAT
4784707 CGATAGAATA
Statistics
Matches: 207, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 207 1.00
ACGTcount: A:0.45, C:0.14, G:0.25, T:0.16
Consensus pattern (66 bp):
AGAAAGAGATGACAGGTAGAGATACCCTACTAATATTCAACCAAAGTACCAGTTGAAGGAAAGGA
G
Found at i:4785399 original size:126 final size:126
Alignment explanation
Indices: 4785164--4785410 Score: 323
Period size: 126 Copynumber: 1.9 Consensus size: 126
4785154 GGTCTTCCAG
* * * * *
4785164 CAGGAGTAACACGCCACTCTCCCTTTAACCAACAAGCTTTTTATGACACGACCTAACCATATTTA
1 CAGGAATAACACACCACTCACCCATGAACCAACAAGCTTTTTATGACACGACCTAACCATATTTA
* ** *
4785229 TTTAAGAACCCTACTGTCCAGAGATGGGTTTATTCAAGCAAAAACAAGATTTTGTCCAAGC
66 TTTAAGAACCCTACTGTCCAGAGAAGGGTCAACTCAAGCAAAAACAAGATTTTGTCCAAGC
* * * ***
4785290 CAGGAATAACACACCACTCACCCATGAGCCAGCAAGCTTTTTATGTCACTTTCTAACCATATTTA
1 CAGGAATAACACACCACTCACCCATGAACCAACAAGCTTTTTATGACACGACCTAACCATATTTA
* *
4785355 TTTAAGAACCCTACTGTCTAGAGACAGGGTCAACTCAAGCAAAACACAAAATTTTG
66 TTTAAGAACCCTACTGTCCAGAGA-AGGGTCAACTCAAGCAAAA-ACAAGATTTTG
4785411 CCTAAGCTAC
Statistics
Matches: 102, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
126 77 0.75
127 15 0.15
128 10 0.10
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (126 bp):
CAGGAATAACACACCACTCACCCATGAACCAACAAGCTTTTTATGACACGACCTAACCATATTTA
TTTAAGAACCCTACTGTCCAGAGAAGGGTCAACTCAAGCAAAAACAAGATTTTGTCCAAGC
Found at i:4788625 original size:49 final size:49
Alignment explanation
Indices: 4788560--4788657 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
4788550 ACTCAATTAA
4788560 CTATTTCTTTTTAAAATACTTCAGACACTAATTATAAAAGAATGCATTT
1 CTATTTCTTTTTAAAATACTTCAGACACTAATTATAAAAGAATGCATTT
*
4788609 CTATTTTTTTTTAAAATACTTCAGACACTAATTATAAAAGAATGCATTT
1 CTATTTCTTTTTAAAATACTTCAGACACTAATTATAAAAGAATGCATTT
4788658 GGGGTAAACA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (49 bp):
CTATTTCTTTTTAAAATACTTCAGACACTAATTATAAAAGAATGCATTT
Found at i:4792863 original size:31 final size:30
Alignment explanation
Indices: 4792828--4792902 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 30
4792818 AAAATTAATA
*
4792828 ATTTAAATATTGAATTATTTGAAAATTTTTT
1 ATTTAAATATTAAATTATTT-AAAATTTTTT
*
4792859 ATTTAAGTTATTAAATTATTTAAAATTTTTT
1 ATTTAA-ATATTAAATTATTTAAAATTTTTT
*
4792890 ATATAAAGTATTA
1 ATTTAAA-TATTA
4792903 GTTTGTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 26 0.68
32 12 0.32
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (30 bp):
ATTTAAATATTAAATTATTTAAAATTTTTT
Found at i:4793700 original size:20 final size:20
Alignment explanation
Indices: 4793663--4793702 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4793653 ATAATACAGA
* *
4793663 AGTGATATCATATATTGAAT
1 AGTGATACCAAATATTGAAT
*
4793683 AGTGATACCAAATTTTGAAT
1 AGTGATACCAAATATTGAAT
4793703 GGTGTAATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (20 bp):
AGTGATACCAAATATTGAAT
Found at i:4796217 original size:11 final size:11
Alignment explanation
Indices: 4796196--4796224 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4796186 AATCACTGTG
4796196 AAAAT-AAAAT
1 AAAATAAAAAT
4796206 AAAATAAAAAT
1 AAAATAAAAAT
4796217 AAAATAAA
1 AAAATAAA
4796225 GAACACACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:4800665 original size:11 final size:11
Alignment explanation
Indices: 4800644--4800672 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4800634 CCAATTTGTG
4800644 AAAAT-AAAAT
1 AAAATAAAAAT
4800654 AAAATAAAAAT
1 AAAATAAAAAT
4800665 AAAATAAA
1 AAAATAAA
4800673 GAACACACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:4805305 original size:31 final size:31
Alignment explanation
Indices: 4805267--4805335 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
4805257 ATTTTGGGTT
* *
4805267 CAAAAGTGCTTTTGGAAAA-CACTTCTGACTC
1 CAAAAGTGCTTTT-CAAAAGCACTTCTAACTC
*
4805298 CAAAAGTGCTTTTCAAAAGCACTTCTAACTT
1 CAAAAGTGCTTTTCAAAAGCACTTCTAACTC
4805329 CAAAAGT
1 CAAAAGT
4805336 TGTCTGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (31 bp):
CAAAAGTGCTTTTCAAAAGCACTTCTAACTC
Found at i:4807710 original size:21 final size:21
Alignment explanation
Indices: 4807659--4807710 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
4807649 TACCAAAACC
4807659 AAACAGCAAAAGAAAACCACCT
1 AAAC-GCAAAAGAAAACCACCT
* * *
4807681 TAA-GCCAAAAGAAAAGCTCCT
1 AAACG-CAAAAGAAAACCACCT
4807702 AAACGCAAA
1 AAACGCAAA
4807711 GCCAAATATC
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
20 1 0.04
21 20 0.83
22 3 0.12
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.08
Consensus pattern (21 bp):
AAACGCAAAAGAAAACCACCT
Found at i:4814763 original size:15 final size:15
Alignment explanation
Indices: 4814745--4814782 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
4814735 AGTCTAATTT
*
4814745 AAAATGTCTATTTCA
1 AAAATGTCTATATCA
*
4814760 AAAAT-TCTATATCT
1 AAAATGTCTATATCA
4814774 AAAATGTCT
1 AAAATGTCT
4814783 TATAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (15 bp):
AAAATGTCTATATCA
Found at i:4815650 original size:9 final size:9
Alignment explanation
Indices: 4815636--4815686 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
4815626 TACATTTTTA
4815636 AAAAATTAT
1 AAAAATTAT
*
4815645 AAAAATTCT
1 AAAAATTAT
*
4815654 AAAAAACATAT
1 -AAAAA-TTAT
4815665 AAAAATT-T
1 AAAAATTAT
*
4815673 AAAAATTTT
1 AAAAATTAT
4815682 AAAAA
1 AAAAA
4815687 AATCTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 8 0.23
9 15 0.43
10 10 0.29
11 2 0.06
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:4824087 original size:17 final size:19
Alignment explanation
Indices: 4824058--4824093 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
4824048 AAACAACGTC
4824058 AATTTTTCTAAAA-AAAAG
1 AATTTTTCTAAAATAAAAG
4824076 AATTTTTC-AAAATAAAAG
1 AATTTTTCTAAAATAAAAG
4824094 TCATTATCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (19 bp):
AATTTTTCTAAAATAAAAG
Found at i:4838958 original size:17 final size:17
Alignment explanation
Indices: 4838932--4838977 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
4838922 CCTGCTTTAA
* *
4838932 ATTTTGTTTTAT-TTTT
1 ATTTTATTTTATCGTTT
4838948 ATTTTTATTTT-TCGTTT
1 A-TTTTATTTTATCGTTT
4838965 ATTTTATTTTATC
1 ATTTTATTTTATC
4838978 AATATTAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.76
Consensus pattern (17 bp):
ATTTTATTTTATCGTTT
Found at i:4850346 original size:25 final size:25
Alignment explanation
Indices: 4850307--4850400 Score: 91
Period size: 25 Copynumber: 3.8 Consensus size: 25
4850297 CCTTCTCTCA
*
4850307 AGCCATATAATGGGAAGCTCATATG
1 AGCCATATAACGGGAAGCTCATATG
* * **
4850332 AGCCATGTAACGGGAAGCTTATCCG
1 AGCCATATAACGGGAAGCTCATATG
* ** *
4850357 AACTGTATAATGGGAAGCTCATATG
1 AGCCATATAACGGGAAGCTCATATG
4850382 AGCCA-AGTAACGGGAAGCT
1 AGCCATA-TAACGGGAAGCT
4850401 TTTCCGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
24 1 0.02
25 50 0.98
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATATG
Found at i:4850368 original size:50 final size:50
Alignment explanation
Indices: 4850312--4850416 Score: 183
Period size: 50 Copynumber: 2.1 Consensus size: 50
4850302 TCTCAAGCCA
*
4850312 TATAATGGGAAGCTCATATGAGCCATGTAACGGGAAGCTTATCCGAACTG
1 TATAATGGGAAGCTCATATGAGCCAAGTAACGGGAAGCTTATCCGAACTG
* *
4850362 TATAATGGGAAGCTCATATGAGCCAAGTAACGGGAAGCTTTTCCGAGCTG
1 TATAATGGGAAGCTCATATGAGCCAAGTAACGGGAAGCTTATCCGAACTG
4850412 TATAA
1 TATAA
4850417 CAGGAAACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (50 bp):
TATAATGGGAAGCTCATATGAGCCAAGTAACGGGAAGCTTATCCGAACTG
Found at i:4850417 original size:25 final size:25
Alignment explanation
Indices: 4850339--4850422 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 25
4850329 ATGAGCCATG
*
4850339 TAACGGGAAGCTTATCCGAACTGTA
1 TAACGGGAAGCTTATCCGAGCTGTA
* * ** **
4850364 TAATGGGAAGCTCATATGAGC-CAA
1 TAACGGGAAGCTTATCCGAGCTGTA
*
4850388 GTAACGGGAAGCTTTTCCGAGCTGTA
1 -TAACGGGAAGCTTATCCGAGCTGTA
*
4850414 TAACAGGAA
1 TAACGGGAA
4850423 ACTCGTAGAA
Statistics
Matches: 42, Mismatches: 15, Indels: 4
0.69 0.25 0.07
Matches are distributed among these distances:
24 1 0.02
25 40 0.95
26 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (25 bp):
TAACGGGAAGCTTATCCGAGCTGTA
Found at i:4850499 original size:24 final size:24
Alignment explanation
Indices: 4850455--4850500 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
4850445 AAGCTCATGC
* *
4850455 GAGCCAATAACGGGTAGCTCCGAA
1 GAGCCAATAACGGGAAACTCCGAA
*
4850479 GAGCCATTAACGGGAAACTCCG
1 GAGCCAATAACGGGAAACTCCG
4850501 TATAACCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.28, T:0.13
Consensus pattern (24 bp):
GAGCCAATAACGGGAAACTCCGAA
Found at i:4850997 original size:26 final size:26
Alignment explanation
Indices: 4850961--4851012 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
4850951 ATGTTCGTGA
4850961 ACTCGTATACTACTAATCCATTACTT
1 ACTCGTATACTACTAATCCATTACTT
4850987 ACTCGTATACTACTAATCCATTACTT
1 ACTCGTATACTACTAATCCATTACTT
4851013 TTTCTTTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (26 bp):
ACTCGTATACTACTAATCCATTACTT
Found at i:4851670 original size:16 final size:13
Alignment explanation
Indices: 4851636--4851663 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4851626 CTTTATTTTA
4851636 TTATTTATCATCT
1 TTATTTATCATCT
4851649 TTATTTATCATCT
1 TTATTTATCATCT
4851662 TT
1 TT
4851664 CCAATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTATCATCT
Found at i:4852672 original size:30 final size:31
Alignment explanation
Indices: 4852630--4852694 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 31
4852620 CTCCAAAATG
4852630 ATTTGAAAAAGAATAAAATTCAAAACCAAAC
1 ATTTGAAAAAGAATAAAATTCAAAACCAAAC
4852661 ATTTG-AAAAGAATAAAATTCAAAACCAAAC
1 ATTTGAAAAAGAATAAAATTCAAAACCAAAC
4852691 -TTTG
1 ATTTG
4852695 TTGGAACAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 4 0.12
30 25 0.74
31 5 0.15
ACGTcount: A:0.57, C:0.12, G:0.08, T:0.23
Consensus pattern (31 bp):
ATTTGAAAAAGAATAAAATTCAAAACCAAAC
Found at i:4857988 original size:76 final size:75
Alignment explanation
Indices: 4857858--4858120 Score: 305
Period size: 76 Copynumber: 3.5 Consensus size: 75
4857848 TATCTAAACT
* * * * * *
4857858 TTGCGCCCAGTGCTAGTCGGATGAACTGACAAATATA-AAGGGTGTGCCCAACACTAGTCAAATA
1 TTGCGCCCAGAGCTAGT-TGATGAACCGACAGATATAGAA-AGTGTGCCCAACACTAGTCAGATA
4857922 AACTAACAGAAG
64 AACTAACAGAAG
* * * *
4857934 TTGTGCCCAAAGCTAGTTAGATAAACCGATAGATATAGAAAGTGTGCCCAACACTAGTCAGATAA
1 TTGCGCCCAGAGCTAGTT-GATGAACCGACAGATATAGAAAGTGTGCCCAACACTAGTCAGATAA
*
4857999 ACTAATAGAAG
65 ACTAACAGAAG
* * * * * *
4858010 TTGCGGCCAGCGCCAGTCTGATGAACCAACAGATATAGAAAGTGTACCTAACACTAGTCAGATAA
1 TTGCGCCCAGAGCTAGT-TGATGAACCGACAGATATAGAAAGTGTGCCCAACACTAGTCAGATAA
*
4858075 ACTGACAGAAG
65 ACTAACAGAAG
4858086 TTGCGCCCAGAGCTAGTTGGATGAACCGACA-ATAT
1 TTGCGCCCAGAGCTAGTT-GATGAACCGACAGATAT
4858121 CAATTACTCA
Statistics
Matches: 156, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
75 5 0.03
76 148 0.95
77 3 0.02
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (75 bp):
TTGCGCCCAGAGCTAGTTGATGAACCGACAGATATAGAAAGTGTGCCCAACACTAGTCAGATAAA
CTAACAGAAG
Found at i:4858170 original size:20 final size:20
Alignment explanation
Indices: 4858147--4858194 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
4858137 AGTCCATAAA
*
4858147 ATCATATTTCATAACCCAAT
1 ATCACATTTCATAACCCAAT
*
4858167 ATCACATTTCATAACTCAAT
1 ATCACATTTCATAACCCAAT
4858187 ATCACATT
1 ATCACATT
4858195 CACTTCAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
ATCACATTTCATAACCCAAT
Found at i:4865006 original size:28 final size:28
Alignment explanation
Indices: 4864966--4865022 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
4864956 AGATTGATAG
*
4864966 CAGGCATGAGGAGTATAAACTCTTCGAA
1 CAGGAATGAGGAGTATAAACTCTTCGAA
4864994 CAGGAATGAGGAGTATAAACTCTTCGAA
1 CAGGAATGAGGAGTATAAACTCTTCGAA
4865022 C
1 C
4865023 CACCCTGACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.21
Consensus pattern (28 bp):
CAGGAATGAGGAGTATAAACTCTTCGAA
Found at i:4867436 original size:6 final size:6
Alignment explanation
Indices: 4867425--4867462 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
4867415 TGGAATTATC
4867425 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT
4867463 ATTTTCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:4877600 original size:27 final size:26
Alignment explanation
Indices: 4877562--4877632 Score: 97
Period size: 27 Copynumber: 2.7 Consensus size: 26
4877552 CCAAATTGAC
4877562 AAATGACTGTTTTGCTCCTATGTGGTA
1 AAATGACTGTTTTGC-CCTATGTGGTA
* *
4877589 AAATAACTGTTTTTCCCTTATGTGGTA
1 AAATGACTGTTTTGCCC-TATGTGGTA
*
4877616 AAATGACTGATTTGCCC
1 AAATGACTGTTTTGCCC
4877633 CTACGTGAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 2 0.05
27 36 0.95
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (26 bp):
AAATGACTGTTTTGCCCTATGTGGTA
Found at i:4878416 original size:18 final size:17
Alignment explanation
Indices: 4878389--4878424 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
4878379 GCATATATGT
4878389 ACTGTTACTGTTACTGC
1 ACTGTTACTGTTACTGC
4878406 ACTGATTACTGTTACTGC
1 ACTG-TTACTGTTACTGC
4878424 A
1 A
4878425 ATGGGCCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (17 bp):
ACTGTTACTGTTACTGC
Found at i:4878495 original size:400 final size:393
Alignment explanation
Indices: 4877716--4878511 Score: 1263
Period size: 400 Copynumber: 2.0 Consensus size: 393
4877706 TGTATGATTT
* * *
4877716 CTATGATATGACATGACATGACTGTATGATGCATTGCATTGGGTTTATTATGATTGGAGGAAGTG
1 CTATAATATGACATGACATGACTCTATGATGCATTGCATTGGGTTTATTATGATTGGAGGAAATG
*
4877781 TACTGTACTGGCAGCTCTACTACAAATCACTGATGGCTCTAAGCCTATTATACTGGCATCTCTAC
66 TACTGTACTGACAGCTCTACTACAAATCACTGATGGCTCTAAGCCTATTATACTGGCATCTCTAC
* **
4877846 TGCAAATACTGTTTAGTGCCGTAATTGATGCTATTTTTGGTGTGTAAGGATGGGTGGGTTGATTT
131 TGCAAATACTATTTAGTGCCGTAACCGATGCTATTTTTGGTGTGTAAGGATGGGTGGGTTGATTT
* *
4877911 TATCCCCACATGGTGTGTAGGGCTGGACGGAGTGGTGTGTAGAGGCTGGTTGGGTAGGATTTCTG
196 TATCCCCACATGGTGTGTAAGGCTGGACGGAGTGGTGTATAGAGGCTGGTTGGGTAGGATTTCTG
4877976 ATTACATATCTATTATGTTACTGTTACTGCACTGATTACTGTTACAGCAATGGGCCAAGGCCCAA
261 ATTACATA-CTATTATGTTACTGTTACTGCACTGATTACTGTTACAGCAATGGGCCAAGGCCCAA
* *
4878041 ACACATGACTGTTTCTGTATTGAGATGGGCTAAAGCCCAAACTGATATTGTCACTGTTACTAAAA
325 ACACATGACTGTTTCTGTATTGAAATGGGCTAAAGCCCAAACTCATATTGTCACTGTTACT-AAA
4878106 AAGGG
389 AAGGG
* *
4878111 CTATAATATGACATGATATGACTCTATGATGCATTGCATGGGGATGGGTTTGTTATGATTGGAGG
1 CTATAATATGACATGACATGACTCTATGATGCATTGCAT-----TGGGTTTATTATGATTGGAGG
* * * *
4878176 AAATGTACTGTACTGACAGCTCTGCTGCAAATCACTGTTGGCTTTAAGCCTATTATACTGGCAGT
61 AAATGTACTGTACTGACAGCTCTACTACAAATCACTGATGGCTCTAAGCCTATTATACTGGCA-T
* * * *
4878241 -TTTACTGCAAATACTATTTAGTGCCGTAACCGGTGCTATTTTTGGTGTGTAGGGATTGGTGGGT
125 CTCTACTGCAAATACTATTTAGTGCCGTAACCGATGCTATTTTTGGTGTGTAAGGATGGGTGGGT
*
4878305 TGATTTTATCCCTACATGGTGTGTAAGGCTGGACGGAGTGGTGTATAGAGGCTGGTTGGGTAGGA
190 TGATTTTATCCCCACATGGTGTGTAAGGCTGGACGGAGTGGTGTATAGAGGCTGGTTGGGTAGGA
* * *
4878370 TTTCTTATTGCATA-TATGTACTGTTACTGTTACTGCACTGATTACTGTTACTGCAATGGGCCAA
255 TTTCTGATTACATACTAT-TA-TGTTACTGTTACTGCACTGATTACTGTTACAGCAATGGGCCAA
4878434 GGCCCAAACACATGACTGTTTCTGTATTGAAATGGGCTAAAGCCCAAACTCATATTGTCACTGTT
318 GGCCCAAACACATGACTGTTTCTGTATTGAAATGGGCTAAAGCCCAAACTCATATTGTCACTGTT
4878499 ACTAAAAAGGG
383 ACTAAAAAGGG
4878510 CT
1 CT
4878512 TAGGCCCAGG
Statistics
Matches: 368, Mismatches: 25, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
395 36 0.10
398 3 0.01
399 12 0.03
400 316 0.86
401 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (393 bp):
CTATAATATGACATGACATGACTCTATGATGCATTGCATTGGGTTTATTATGATTGGAGGAAATG
TACTGTACTGACAGCTCTACTACAAATCACTGATGGCTCTAAGCCTATTATACTGGCATCTCTAC
TGCAAATACTATTTAGTGCCGTAACCGATGCTATTTTTGGTGTGTAAGGATGGGTGGGTTGATTT
TATCCCCACATGGTGTGTAAGGCTGGACGGAGTGGTGTATAGAGGCTGGTTGGGTAGGATTTCTG
ATTACATACTATTATGTTACTGTTACTGCACTGATTACTGTTACAGCAATGGGCCAAGGCCCAAA
CACATGACTGTTTCTGTATTGAAATGGGCTAAAGCCCAAACTCATATTGTCACTGTTACTAAAAA
GGG
Found at i:4880194 original size:6 final size:6
Alignment explanation
Indices: 4880179--4880210 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
4880169 TTACCATCTC
4880179 TTTC-T TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
4880211 GCCACAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:4883312 original size:28 final size:26
Alignment explanation
Indices: 4883281--4883343 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
4883271 AATTACTTGA
* *
4883281 ATACCCCTATGTATGGAAAATTACTACT
1 ATACCCCTA-G-ATGCAAAATTACCACT
* *
4883309 ATACCCCTAGGTGCAAAATTACCATT
1 ATACCCCTAGATGCAAAATTACCACT
4883335 ATACCCCTA
1 ATACCCCTA
4883344 AGGTTACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 21 0.68
27 1 0.03
28 9 0.29
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.29
Consensus pattern (26 bp):
ATACCCCTAGATGCAAAATTACCACT
Found at i:4883489 original size:27 final size:26
Alignment explanation
Indices: 4883449--4883589 Score: 174
Period size: 27 Copynumber: 5.2 Consensus size: 26
4883439 AGAAAACGTC
*
4883449 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
4883476 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
4883503 CTGGTGGCTATGCCACGATTATCTGAC
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
4883530 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
4883557 CTGGTGGCTCTGCTACAATATCTGTAT
1 CTGGTGGCTCTGCCACATTATCTG-AT
4883584 CTGGTG
1 CTGGTG
4883590 ACTTCGTCAC
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
26 10 0.10
27 87 0.88
28 2 0.02
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:4883534 original size:54 final size:54
Alignment explanation
Indices: 4883449--4883589 Score: 221
Period size: 54 Copynumber: 2.6 Consensus size: 54
4883439 AGAAAACGTC
*
4883449 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGACCTGGTGGCTCTGCCACATATATCTGTT
*
4883503 CTGGTGGCTATGCCACGATTATCTGACCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGACCTGGTGGCTCTGCCACATATATCTGTT
* * *
4883557 CTGGTGGCTCTGCTACAA-TATCTGTATCTGGTG
1 CTGGTGGCTATGCCACAATTATCTG-ACCTGGTG
4883590 ACTTCGTCAC
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 6 0.08
54 74 0.93
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGACCTGGTGGCTCTGCCACATATATCTGTT
Found at i:4884619 original size:27 final size:27
Alignment explanation
Indices: 4884589--4884642 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
4884579 TATTGAAAGT
4884589 ATGTGAGTATTGAGGACATATTGAGCA
1 ATGTGAGTATTGAGGACATATTGAGCA
4884616 ATGTGAGTATTGAGGACATATTGAGCA
1 ATGTGAGTATTGAGGACATATTGAGCA
4884643 TGCCAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (27 bp):
ATGTGAGTATTGAGGACATATTGAGCA
Found at i:4888070 original size:21 final size:22
Alignment explanation
Indices: 4888032--4888081 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
4888022 AAAACCCTCT
*
4888032 CAAATCTCTCCTAATTTTTTCA-
1 CAAATCTCTCCCAA-TTTTTCAC
*
4888054 CAAATC-CTCCCACTTTTTCAC
1 CAAATCTCTCCCAATTTTTCAC
4888075 CAAATCT
1 CAAATCT
4888082 TTGCTCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 7 0.29
21 11 0.46
22 6 0.25
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (22 bp):
CAAATCTCTCCCAATTTTTCAC
Found at i:4890214 original size:20 final size:19
Alignment explanation
Indices: 4890186--4890238 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
4890176 ATCAACCTTT
4890186 AATCAAGTTAAAATTATTTC
1 AATCAAGTTAAAATT-TTTC
* * *
4890206 AATCGAGTTAGACTTTTTC
1 AATCAAGTTAAAATTTTTC
4890225 AATCAAAGTTAAAA
1 AATC-AAGTTAAAA
4890239 ATGTTTTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (19 bp):
AATCAAGTTAAAATTTTTC
Found at i:4895049 original size:51 final size:50
Alignment explanation
Indices: 4894971--4895071 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 50
4894961 TAATTGGTTA
* *
4894971 GTAGCTTTTGTTTTTTTAAATTATATTTTTATGTTATTAGTTTTATCTGC
1 GTAGCTTTTGTTTTTTTAAACTATATTTCTATGTTATTAGTTTTATCTGC
4895021 GTAGCTTTTGTTTTTTTTAAACTATATTTCTATGTTATTAGTTTTATCTGC
1 GTAGCTTTTG-TTTTTTTAAACTATATTTCTATGTTATTAGTTTTATCTGC
4895072 TTGGTACTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 10 0.21
51 38 0.79
ACGTcount: A:0.20, C:0.08, G:0.12, T:0.60
Consensus pattern (50 bp):
GTAGCTTTTGTTTTTTTAAACTATATTTCTATGTTATTAGTTTTATCTGC
Found at i:4905174 original size:104 final size:104
Alignment explanation
Indices: 4905052--4905275 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
4905042 AATGGATATC
4905052 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
4905117 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
4905156 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
4905221 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
4905260 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
4905276 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:4912209 original size:104 final size:104
Alignment explanation
Indices: 4912029--4912295 Score: 428
Period size: 104 Copynumber: 2.6 Consensus size: 104
4912019 TAACCGTTAT
* * *
4912029 TGGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCATCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
4912094 AATCAGCACATAGCAACCCCCTTTTACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
4912133 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
4912198 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* * * **
4912237 TGGTGGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
4912296 TTTATATACA
Statistics
Matches: 151, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
104 150 0.99
105 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:4912657 original size:29 final size:29
Alignment explanation
Indices: 4912624--4912687 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
4912614 TAATCCACCA
4912624 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
4912653 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
4912683 CCCAA
1 CCCAA
4912688 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:4912661 original size:30 final size:30
Alignment explanation
Indices: 4912631--4912687 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4912621 CCACCCAACT
4912631 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
4912660 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
4912688 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:4917073 original size:18 final size:18
Alignment explanation
Indices: 4917013--4917079 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
4917003 ATATAAATTG
*
4917013 TAATATACATAGCATACA
1 TAATATACATAACATACA
* *
4917031 TCATATGCAT-ACATAAACAA
1 TAATATACATAACAT--AC-A
4917051 TAATATACATAACATACA
1 TAATATACATAACATACA
*
4917069 TAATATCCATA
1 TAATATACATA
4917080 GTAATATACA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
17 3 0.08
18 19 0.49
19 4 0.10
20 9 0.23
21 4 0.10
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (18 bp):
TAATATACATAACATACA
Found at i:4917079 original size:9 final size:9
Alignment explanation
Indices: 4917013--4917079 Score: 53
Period size: 9 Copynumber: 7.2 Consensus size: 9
4917003 ATATAAATTG
4917013 TAATATACA
1 TAATATACA
**
4917022 TAGCATACA
1 TAATATACA
* *
4917031 TCATATGCA
1 TAATATACA
*
4917040 TACATAAACAA
1 TA-ATATAC-A
4917051 TAATATACA
1 TAATATACA
*
4917060 TAACATACA
1 TAATATACA
*
4917069 TAATATCCA
1 TAATATACA
4917078 TA
1 TA
4917080 GTAATATACA
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
9 31 0.72
10 9 0.21
11 3 0.07
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (9 bp):
TAATATACA
Found at i:4917842 original size:23 final size:23
Alignment explanation
Indices: 4917812--4917858 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4917802 AATTATGTAT
4917812 AACTATGTAGTATTTGTGGTTGG
1 AACTATGTAGTATTTGTGGTTGG
4917835 AACTATGTAGTATTTGTGGTTGG
1 AACTATGTAGTATTTGTGGTTGG
4917858 A
1 A
4917859 TTGTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.04, G:0.30, T:0.43
Consensus pattern (23 bp):
AACTATGTAGTATTTGTGGTTGG
Found at i:4920801 original size:17 final size:19
Alignment explanation
Indices: 4920779--4920813 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
4920769 GAAAAATAGT
4920779 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
4920796 AACAAAAGTTATACAATA
1 AACAAAAGTTATACAATA
4920814 TCCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:4920895 original size:10 final size:10
Alignment explanation
Indices: 4920882--4920917 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
4920872 AAAAAAAAAG
4920882 AAAATAATAA
1 AAAATAATAA
**
4920892 AAAATAGCAA
1 AAAATAATAA
4920902 AAAATAATAA
1 AAAATAATAA
4920912 AAAATA
1 AAAATA
4920918 GTAGGTTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (10 bp):
AAAATAATAA
Found at i:4937256 original size:17 final size:19
Alignment explanation
Indices: 4937236--4937278 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
4937226 AAAATAAATA
4937236 AATAAATCAA-A-TAGAAC
1 AATAAATCAAGATTAGAAC
4937253 AATAAATCAAGTATTAGAAC
1 AATAAATCAAG-ATTAGAAC
4937273 AATAAA
1 AATAAA
4937279 AAAGAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.43
19 1 0.04
20 12 0.52
ACGTcount: A:0.63, C:0.09, G:0.07, T:0.21
Consensus pattern (19 bp):
AATAAATCAAGATTAGAAC
Found at i:4937523 original size:19 final size:20
Alignment explanation
Indices: 4937499--4937537 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4937489 TGAAAAGAAA
*
4937499 AACTC-AAAGAGAATTTATT
1 AACTCAAAAGAGAAGTTATT
4937518 AACTCAAAAGAGAAGTTATT
1 AACTCAAAAGAGAAGTTATT
4937538 GAATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (20 bp):
AACTCAAAAGAGAAGTTATT
Found at i:4945841 original size:23 final size:23
Alignment explanation
Indices: 4945813--4945863 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
4945803 GATTATCTTA
4945813 ATATTAAATTAAATTTAATGTTT
1 ATATTAAATTAAATTTAATGTTT
4945836 ATATTAAATTAAATTTAATGTTT
1 ATATTAAATTAAATTTAATGTTT
4945859 ATATT
1 ATATT
4945864 GTAGATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
ATATTAAATTAAATTTAATGTTT
Found at i:4946395 original size:38 final size:39
Alignment explanation
Indices: 4946339--4946414 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 39
4946329 ATCTTATTGC
* *
4946339 ACATATAATCTCCTAACATCCAAG-GTATATCACAATAT
1 ACATATAATCTCCCAACATCCAAGCATATATCACAATAT
**
4946377 ACATATAATC-CCACAACATTTAAGCATATATCACAATA
1 ACATATAATCTCC-CAACATCCAAGCATATATCACAATA
4946415 ATAAAAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 2 0.06
38 18 0.56
39 12 0.38
ACGTcount: A:0.45, C:0.24, G:0.04, T:0.28
Consensus pattern (39 bp):
ACATATAATCTCCCAACATCCAAGCATATATCACAATAT
Found at i:4955589 original size:11 final size:11
Alignment explanation
Indices: 4955549--4955600 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
4955539 ATTTATGATT
*
4955549 TGAATATGAAA
1 TGAAAATGAAA
*
4955560 TGAAATTGAAA
1 TGAAAATGAAA
* *
4955571 TGAGAATGATA
1 TGAAAATGAAA
4955582 TGAAAATGGAAA
1 TGAAAAT-GAAA
4955594 T-AAAATG
1 TGAAAATG
4955601 GATTATAGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 1 0.03
11 28 0.85
12 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.25
Consensus pattern (11 bp):
TGAAAATGAAA
Found at i:4961214 original size:17 final size:17
Alignment explanation
Indices: 4961192--4961225 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4961182 GTATATTTTC
4961192 TTGTTAATAGATTAATT
1 TTGTTAATAGATTAATT
4961209 TTGTTAATAGATTAATT
1 TTGTTAATAGATTAATT
4961226 CATCTTCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (17 bp):
TTGTTAATAGATTAATT
Found at i:4961637 original size:18 final size:19
Alignment explanation
Indices: 4961614--4961692 Score: 60
Period size: 18 Copynumber: 4.3 Consensus size: 19
4961604 CGATTTTTTA
4961614 TATGTTTAAATCGATTG-T
1 TATGTTTAAATCGATTGTT
**
4961632 TATGTTGGAAT-G-TTGCTT
1 TATGTTTAAATCGATTG-TT
*
4961650 TAT-TTTGAATCGATTGTTT
1 TATGTTTAAATCGATTG-TT
*
4961669 ATATGTTTAAATCAATTG-T
1 -TATGTTTAAATCGATTGTT
4961688 TATGT
1 TATGT
4961693 AGCACGTCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
16 3 0.06
17 7 0.14
18 19 0.39
19 6 0.12
20 3 0.06
21 11 0.22
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.52
Consensus pattern (19 bp):
TATGTTTAAATCGATTGTT
Found at i:4961678 original size:56 final size:56
Alignment explanation
Indices: 4961477--4961692 Score: 211
Period size: 56 Copynumber: 3.8 Consensus size: 56
4961467 GGAATACGAC
* * * * **
4961477 TTCTTTTAAATCAATTGTCTATATGTTTAAATCGATTGTCATGTTGGAAT-AAGAC-
1 TTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATGTTG-CT
* * * * * * * *
4961532 TTCTTTTGAATTGACTATTAACATGTTTAAATCGATTCTTATGGTGGAATATTGTTTCTT
1 TTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGG-A-A-TGTTGC-T
*
4961592 CTTCTTTTGAATCGATTTTTTATATGTTTAAATCGATTGTTATGTTGGAATGTTGCT
1 -TTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATGTTGCT
* *
4961649 TTATTTTGAATCGATTGTTTATATGTTTAAATCAATTGTTATGT
1 TTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGT
4961693 AGCACGTCTA
Statistics
Matches: 129, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
55 36 0.28
56 42 0.33
57 2 0.02
58 7 0.05
59 1 0.01
60 1 0.01
61 40 0.31
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (56 bp):
TTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATGTTGCT
Found at i:4971463 original size:15 final size:16
Alignment explanation
Indices: 4971443--4971472 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4971433 TTTGATGATC
4971443 TCATTGT-TTTATTTG
1 TCATTGTATTTATTTG
4971458 TCATTGTATTTATTT
1 TCATTGTATTTATTT
4971473 ATTTTTGTAT
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:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (16 bp):
TCATTGTATTTATTTG
Found at i:4978491 original size:26 final size:26
Alignment explanation
Indices: 4978462--4978569 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
4978452 TGGTACAAAT
4978462 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
4978488 TGATAATGGATTAGGTAAATATTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
4978514 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
4978540 TGATAATGGTTTAAGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
4978566 TGAT
1 TGAT
4978570 GGGCATTTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:4980206 original size:27 final size:27
Alignment explanation
Indices: 4980166--4980306 Score: 173
Period size: 27 Copynumber: 5.2 Consensus size: 27
4980156 AGGAAGCGTC
*
4980166 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
4980193 TTGGTGGCTCTGCCAC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
4980219 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
*
4980247 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
4980274 CTGGTGGCTCTACCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
4980301 CTGGTG
1 CTGGTG
4980307 ACGTTGTCAC
Statistics
Matches: 99, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
26 11 0.11
27 84 0.85
28 4 0.04
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:4980245 original size:54 final size:54
Alignment explanation
Indices: 4980163--4980306 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
4980153 TGGAGGAAGC
*
4980163 GTCCTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
4980217 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
* * *
4980271 GTTCTGGTGGCTCTACCACAA-TATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
4980307 ACGTTGTCAC
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
53 6 0.07
54 79 0.93
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
Found at i:4980318 original size:81 final size:80
Alignment explanation
Indices: 4980166--4980324 Score: 200
Period size: 81 Copynumber: 2.0 Consensus size: 80
4980156 AGGAAGCGTC
* *
4980166 CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTGCCACATATATCTGTCCTGGTGGCTAT
1 CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTACCACATATATCTGTCCTGGTGACTAT
4980231 GCCACAATTATCTGAT
66 GCCACAA-TATCTGAT
* *
4980247 CTGGTGGCTCTGCCAC-ATATATCTG-TTCTGGTGGCTCTACCACA-ATATCTGTATCTGGTGAC
1 CTGGTGGCTATGCCACAAT-TATCTGATT-TGGTGGCTCTACCACATATATCTGT-CCTGGTGAC
*
4980309 GT-TGTCACAATATCTG
63 -TATGCCACAATATCTG
4980325 GCAGCCTCGT
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
80 18 0.26
81 50 0.72
82 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (80 bp):
CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTACCACATATATCTGTCCTGGTGACTAT
GCCACAATATCTGAT
Found at i:4982512 original size:19 final size:19
Alignment explanation
Indices: 4982484--4982526 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
4982474 AGGATGGCAC
4982484 TAAA-GGAGTTAGTGGAGT
1 TAAAGGGAGTTAGTGGAGT
4982502 TAAAGGGAGTTAGTGGAGT
1 TAAAGGGAGTTAGTGGAGT
4982521 TAAAGG
1 TAAAGG
4982527 CTCAAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.35, C:0.00, G:0.40, T:0.26
Consensus pattern (19 bp):
TAAAGGGAGTTAGTGGAGT
Found at i:4985460 original size:26 final size:26
Alignment explanation
Indices: 4985431--4985486 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
4985421 TGGTACAAAT
4985431 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
4985457 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
4985483 TGAT
1 TGAT
4985487 GGGCATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:4987124 original size:27 final size:27
Alignment explanation
Indices: 4987084--4987170 Score: 115
Period size: 27 Copynumber: 3.2 Consensus size: 27
4987074 AGGAAGCGTC
*
4987084 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
4987111 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
4987138 CTGGTGGCTCTACCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
4987165 CTGGTG
1 CTGGTG
4987171 ACGTTGTCAC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
26 8 0.15
27 44 0.83
28 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:4994669 original size:86 final size:86
Alignment explanation
Indices: 4994518--4994679 Score: 195
Period size: 86 Copynumber: 1.9 Consensus size: 86
4994508 CATAAGCTCG
* * * *
4994518 TACAATGTCAACGTCCCAGACGTGGTCTTATAATGTAATCAATTATCGATGCCACTATCCCAGAC
1 TACAATGGCAACGTCCCAGACATGGTCTTATAACGTAATCAATAATCGATGCCACTATCCCAGAC
4994583 AGGGTCTTACATGAAATAATA
66 AGGGTCTTACATGAAATAATA
* * * *
4994604 TACAATGGCAATGTCCCAGACATGGTCTTA-CACGTAAAT-AATAAATCGATGCCAAC-ATTCTA
1 TACAATGGCAACGTCCCAGACATGGTCTTATAACGT-AATCAAT-AATCGATGCC-ACTATCCCA
*
4994666 GACATGGTCTTACA
63 GACAGGGTCTTACA
4994680 AGATAACACA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
85 6 0.09
86 56 0.88
87 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (86 bp):
TACAATGGCAACGTCCCAGACATGGTCTTATAACGTAATCAATAATCGATGCCACTATCCCAGAC
AGGGTCTTACATGAAATAATA
Found at i:5001244 original size:43 final size:43
Alignment explanation
Indices: 5001196--5001308 Score: 122
Period size: 42 Copynumber: 2.6 Consensus size: 43
5001186 TGCCAGACGT
*
5001196 GGTCTTACATGTAATCAAATATCGATGCCACTGTCCCACACAG
1 GGTCTTACATGTAATCAAATATCGATGCCAATGTCCCACACAG
* * * * * * *
5001239 GGTCTTACACGAAATCATATA-AGATACCAATGTCCCAGACAT
1 GGTCTTACATGTAATCAAATATCGATGCCAATGTCCCACACAG
5001281 GGTCTTACATGTAAATCATAA-ATCGATG
1 GGTCTTACATGT-AATCA-AATATCGATG
5001309 AAAACGTCCC
Statistics
Matches: 54, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
42 26 0.48
43 24 0.44
44 4 0.07
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (43 bp):
GGTCTTACATGTAATCAAATATCGATGCCAATGTCCCACACAG
Found at i:5001286 original size:42 final size:42
Alignment explanation
Indices: 5001188--5001336 Score: 122
Period size: 43 Copynumber: 3.5 Consensus size: 42
5001178 TGCCAACGTG
* * * * * * *
5001188 CCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTC
1 CCAGACATGGTCTTACACGAAATCATATA-AGATACCAATGTC
* *
5001231 CCACACAGGGTCTTACACGAAATCATATAAGATACCAATGTC
1 CCAGACATGGTCTTACACGAAATCATATAAGATACCAATGTC
* * *
5001273 CCAGACATGGTCTTACATGTAAATCATA-AATCGATGA-AAACGTC
1 CCAGACATGGTCTTACACG-AAATCATATAA--GAT-ACCAATGTC
*
5001317 CCAGACGTGGTCTTACACGA
1 CCAGACATGGTCTTACACGA
5001337 TAACACATAT
Statistics
Matches: 86, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
42 28 0.33
43 32 0.37
44 25 0.29
45 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (42 bp):
CCAGACATGGTCTTACACGAAATCATATAAGATACCAATGTC
Found at i:5004490 original size:27 final size:27
Alignment explanation
Indices: 5004460--5004511 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
5004450 ACCTACATTC
5004460 ATTTTCAAATGATTCCATTTCTCCAAA
1 ATTTTCAAATGATTCCATTTCTCCAAA
5004487 ATTTTCAAATGATTCCATTTCTCCA
1 ATTTTCAAATGATTCCATTTCTCCA
5004512 TTTTGAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42
Consensus pattern (27 bp):
ATTTTCAAATGATTCCATTTCTCCAAA
Found at i:5006341 original size:26 final size:26
Alignment explanation
Indices: 5006274--5006341 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
5006264 TTGCAACTTG
* * * *
5006274 CCAAGCTCATTGGCAATCTTTGCTCG
1 CCAAGCCCATTGGCGATCTTAGCTCA
*
5006300 CCAAGCCCACTT-GCGATCTTAGCTTA
1 CCAAGCCCA-TTGGCGATCTTAGCTCA
*
5006326 CCAGGCCCATTGGCGA
1 CCAAGCCCATTGGCGA
5006342 ATACCAACTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 2 0.06
26 30 0.88
27 2 0.06
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.25
Consensus pattern (26 bp):
CCAAGCCCATTGGCGATCTTAGCTCA
Found at i:5006397 original size:27 final size:27
Alignment explanation
Indices: 5006365--5006465 Score: 130
Period size: 27 Copynumber: 3.7 Consensus size: 27
5006355 AGACCCTCTG
*
5006365 GCGAACCCCAGCTCACTAGGCTTACTA
1 GCGAACCCCAGCTCACCAGGCTTACTA
*
5006392 GTGAACCCCAGCTCACCAGGCTTACTA
1 GCGAACCCCAGCTCACCAGGCTTACTA
* * * * *
5006419 GCAAACCCCAACTCGCCAGGCCTACTG
1 GCGAACCCCAGCTCACCAGGCTTACTA
*
5006446 GCGAACCTCAGCTCACCAGG
1 GCGAACCCCAGCTCACCAGG
5006466 TCTAAACTTG
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.26, C:0.40, G:0.20, T:0.15
Consensus pattern (27 bp):
GCGAACCCCAGCTCACCAGGCTTACTA
Found at i:5016387 original size:12 final size:12
Alignment explanation
Indices: 5016370--5016394 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5016360 TTGTGTGTTC
5016370 TTTATTTTATTT
1 TTTATTTTATTT
5016382 TTTATTTTATTT
1 TTTATTTTATTT
5016394 T
1 T
5016395 ATTTTTCACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:5017657 original size:16 final size:16
Alignment explanation
Indices: 5017638--5017668 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5017628 AATCACAAAG
5017638 CATGCAAATTCAAGTT
1 CATGCAAATTCAAGTT
*
5017654 CATGCACATTCAAGT
1 CATGCAAATTCAAGT
5017669 ACAAAATACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (16 bp):
CATGCAAATTCAAGTT
Found at i:5023439 original size:23 final size:23
Alignment explanation
Indices: 5023394--5023481 Score: 74
Period size: 24 Copynumber: 3.7 Consensus size: 23
5023384 CCCGTTACAT
5023394 GGCTCTTTGTGAGCTTCCTGATA
1 GGCTCTTTGTGAGCTTCCTGATA
5023417 GGCT-TTTCGTGAGCTT-CTCGATA
1 GGCTCTTT-GTGAGCTTCCT-GATA
* * *
5023440 TGGTTCTTTGTGAACTTTCTGATTA
1 -GGCTCTTTGTGAGCTTCCTGA-TA
*
5023465 TGGCTC-TTATGAGCTTC
1 -GGCTCTTTGTGAGCTTC
5023482 TCGTTAGAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
22 5 0.09
23 16 0.30
24 20 0.38
25 12 0.23
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (23 bp):
GGCTCTTTGTGAGCTTCCTGATA
Found at i:5023462 original size:47 final size:48
Alignment explanation
Indices: 5023352--5023484 Score: 119
Period size: 47 Copynumber: 2.7 Consensus size: 48
5023342 AGTGCTCGCT
* * * *
5023352 TGAACTTCCTGATATATGGCTATCTA-GAGTTTCCCGTTACATGGCTCTTTG
1 TGAACTTCCTGAT-TATGGCTCT-TATGAGCTTCTCG--ATATGGCTCTTTG
* * * *
5023403 TGAGCTTCCTGA-TA-GGCTTTTCGTGAGCTTCTCGATATGGTTCTTTG
1 TGAACTTCCTGATTATGGCTCTT-ATGAGCTTCTCGATATGGCTCTTTG
*
5023450 TGAACTTTCTGATTATGGCTCTTATGAGCTTCTCG
1 TGAACTTCCTGATTATGGCTCTTATGAGCTTCTCG
5023485 TTAGAAAGCT
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
47 22 0.33
48 18 0.27
49 16 0.24
51 11 0.16
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (48 bp):
TGAACTTCCTGATTATGGCTCTTATGAGCTTCTCGATATGGCTCTTTG
Found at i:5035164 original size:5 final size:5
Alignment explanation
Indices: 5035154--5035192 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
5035144 TCCATCACCA
*
5035154 CATAT CATAT CATAT CATAT CGTAT CATAT CATAT CATA
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATA
5035193 CGTATCAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (5 bp):
CATAT
Found at i:5036635 original size:206 final size:204
Alignment explanation
Indices: 5036276--5036683 Score: 559
Period size: 206 Copynumber: 2.0 Consensus size: 204
5036266 ACTACCTGTA
*
5036276 ATGTTGCAACACAGAGCTTCAATATCGCAACACAGTGAACAAAGTACTCAAAAGGAGTAGTCTGC
1 ATGTTGCAACACAGAGCTTCAATATCGCAACACAGTGAACAAAGTACTCAAAAGGAGTAGTATGC
* ** * * *
5036341 CTTTAGTGTCGAGGCACAACCTTGAAGACATGCCTAAGACTAGTAGACTGCTATCAATGTTGCAA
66 CTTCAGTGTCGAAACACAACCTTGAAGACATGCATAAGACTAGTAGACTACCATCAATGTTGCAA
* * * * * *
5036406 CACTGACGTAATGAGGTCAATTAATAAGCCAAGAGTGTTTTCATCTACACAACAACTTTTAAC-A
131 CACTAACATAATGAAGCCAATTAATAAGCCAAGAGTGTTTTCATCCACAAAACAACTTTTAACGA
5036470 GGAAATATTG
196 -GAAATATTG
* * * *
5036480 ATGTTGCAACACGGAGCTTCGATGTCGCAACACAGTGAACAGAGTACTCAAAAAAGGAGTAGTAT
1 ATGTTGCAACACAGAGCTTCAATATCGCAACACAGTGAACAAAGTACTC--AAAAGGAGTAGTAT
5036545 GCCTTCAGTGTC-ACAACACAACCTTGAAGACATGCATAAGACTAGTAGACTACCATCAATGTTG
64 GCCTTCAGTGTCGA-AACACAACCTTGAAGACATGCATAAGACTAGTAGACTACCATCAATGTTG
* * * * **
5036609 CGACACTAATATGATGAAGCCAATTAATGAGCCAAGAGTGTTTTTGTCCACAAAACAACTTTTAA
128 CAACACTAACATAATGAAGCCAATTAATAAGCCAAGAGTGTTTTCATCCACAAAACAACTTTTAA
5036674 CGAGAAATAT
193 CGAGAAATAT
5036684 CCAATCAAAT
Statistics
Matches: 177, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
204 45 0.25
205 1 0.01
206 130 0.73
207 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (204 bp):
ATGTTGCAACACAGAGCTTCAATATCGCAACACAGTGAACAAAGTACTCAAAAGGAGTAGTATGC
CTTCAGTGTCGAAACACAACCTTGAAGACATGCATAAGACTAGTAGACTACCATCAATGTTGCAA
CACTAACATAATGAAGCCAATTAATAAGCCAAGAGTGTTTTCATCCACAAAACAACTTTTAACGA
GAAATATTG
Found at i:5046260 original size:8 final size:9
Alignment explanation
Indices: 5046230--5046258 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
5046220 ATTTTAACCC
5046230 TTTAAAATT
1 TTTAAAATT
5046239 TTTAAAATT
1 TTTAAAATT
5046248 TTTAAAATT
1 TTTAAAATT
5046257 TT
1 TT
5046259 AATTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAAAATT
Found at i:5046276 original size:22 final size:20
Alignment explanation
Indices: 5046244--5046290 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
5046234 AAATTTTTAA
**
5046244 AATTTTTAAAATTTTAATTT
1 AATTTTTAAAATTACAATTT
5046264 AATTATTTAAAAATTACAATTT
1 AATT-TTT-AAAATTACAATTT
5046286 AATTT
1 AATTT
5046291 CGGTCTCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 15 0.65
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTTTTAAAATTACAATTT
Found at i:5048169 original size:50 final size:50
Alignment explanation
Indices: 5048104--5048205 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
5048094 GATATATTAT
*
5048104 ATTATTTATATACACTAAAAAATATATATGATGCGATGTATTATTATTGG
1 ATTATTAATATACACTAAAAAATATATATGATGCGATGTATTATTATTGG
5048154 ATTATTAATATACACTAAAAAATATATATGATGCGATGTATTATTATTGG
1 ATTATTAATATACACTAAAAAATATATATGATGCGATGTATTATTATTGG
5048204 AT
1 AT
5048206 ATGTAAAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (50 bp):
ATTATTAATATACACTAAAAAATATATATGATGCGATGTATTATTATTGG
Found at i:5052349 original size:58 final size:60
Alignment explanation
Indices: 5052235--5052359 Score: 155
Period size: 58 Copynumber: 2.1 Consensus size: 60
5052225 ACTACACTAG
** * * *
5052235 TAGTCACCCAACTATTAGTGAATTTGTTTTTTGGTCACCCAATTATGAGAAGTTACAAAA
1 TAGTCACCTGACTATTAGTGAAATTGTTTTTTGGTCACCCAATTATGAAAAATTACAAAA
* * * *
5052295 TGGTCACCTGACTATTAGT-AAATT-TTTTTTGGTCACCTAGTTATGAAAAATTACAAGA
1 TAGTCACCTGACTATTAGTGAAATTGTTTTTTGGTCACCCAATTATGAAAAATTACAAAA
5052353 TAGTCAC
1 TAGTCAC
5052360 TCAGCTATTC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 35 0.64
59 4 0.07
60 16 0.29
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (60 bp):
TAGTCACCTGACTATTAGTGAAATTGTTTTTTGGTCACCCAATTATGAAAAATTACAAAA
Found at i:5055460 original size:18 final size:18
Alignment explanation
Indices: 5055423--5055460 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5055413 CAAGCCCTAC
*
5055423 AAAAATAAAATTCTATTA
1 AAAAATAAAATTCTAGTA
5055441 AAAAATATAAATT-TAGTA
1 AAAAATA-AAATTCTAGTA
5055459 AA
1 AA
5055461 TAAAACTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
AAAAATAAAATTCTAGTA
Found at i:5057463 original size:22 final size:22
Alignment explanation
Indices: 5057435--5057477 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5057425 TCAAATGCCC
5057435 CTGTAAAGAAAGGCACACGCCT
1 CTGTAAAGAAAGGCACACGCCT
*
5057457 CTGTAAAGAGAGGCACACGCC
1 CTGTAAAGAAAGGCACACGCC
5057478 CGTGTGAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.28, G:0.26, T:0.12
Consensus pattern (22 bp):
CTGTAAAGAAAGGCACACGCCT
Found at i:5057629 original size:21 final size:21
Alignment explanation
Indices: 5057577--5057632 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
5057567 ATGAGGGTCT
**
5057577 CACACGCCCGTGTGCCCACCA
1 CACACGCCCGTGTGCCCAAAA
* * * *
5057598 GACATGGCCGTGTGTCCAAAA
1 CACACGCCCGTGTGCCCAAAA
5057619 CACACGCCCGTGTG
1 CACACGCCCGTGTG
5057633 GGTTAGCCAC
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.39, G:0.25, T:0.14
Consensus pattern (21 bp):
CACACGCCCGTGTGCCCAAAA
Found at i:5058181 original size:23 final size:25
Alignment explanation
Indices: 5058153--5058216 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 25
5058143 AACTGTTTTT
*
5058153 AAAAGAAAAAGAAAAGAA-A-CCCA
1 AAAAGAAAAAGAAAAGAACATCCAA
* *
5058176 AGAAGAAGAAGAAAAGAACATCCAA
1 AAAAGAAAAAGAAAAGAACATCCAA
5058201 AAAAGAAAAAAGAAAA
1 AAAAG-AAAAAGAAAA
5058217 AAAAGAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 16 0.48
24 1 0.03
25 7 0.21
26 9 0.27
ACGTcount: A:0.73, C:0.09, G:0.16, T:0.02
Consensus pattern (25 bp):
AAAAGAAAAAGAAAAGAACATCCAA
Found at i:5058220 original size:16 final size:16
Alignment explanation
Indices: 5058199--5058243 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
5058189 AAGAACATCC
5058199 AAAAAAGAAAAAAGAA
1 AAAAAAGAAAAAAGAA
5058215 AAAAAAGAAAAAAGAA
1 AAAAAAGAAAAAAGAA
*
5058231 ATAAAAATAAAAA
1 A-AAAAAGAAAAA
5058244 CAAAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.87, C:0.00, G:0.09, T:0.04
Consensus pattern (16 bp):
AAAAAAGAAAAAAGAA
Found at i:5058229 original size:23 final size:23
Alignment explanation
Indices: 5058198--5058249 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
5058188 AAAGAACATC
5058198 CAAAAAAGAAA-AAAGAAAAAAAA
1 CAAAAAAGAAATAAA-AAAAAAAA
* *
5058221 GAAAAAAGAAATAAAAATAAAAA
1 CAAAAAAGAAATAAAAAAAAAAA
5058244 CAAAAA
1 CAAAAA
5058250 TAATAGATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.85, C:0.04, G:0.08, T:0.04
Consensus pattern (23 bp):
CAAAAAAGAAATAAAAAAAAAAA
Found at i:5059069 original size:21 final size:21
Alignment explanation
Indices: 5059045--5059100 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 21
5059035 ATTTTTTAAT
* *
5059045 ATTTTAAGAAAATTTAATAAA
1 ATTTTAAAAAAATATAATAAA
5059066 ATTTTCGAAAAAAATATAATAAA
1 ATTTT--AAAAAAATATAATAAA
*
5059089 TTTTTAAAAAAA
1 ATTTTAAAAAAA
5059101 AAATTCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 12 0.40
23 18 0.60
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (21 bp):
ATTTTAAAAAAATATAATAAA
Found at i:5063590 original size:17 final size:17
Alignment explanation
Indices: 5063568--5063600 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5063558 GTTCCATCAC
5063568 AAGAAAATCAGTGCCAT
1 AAGAAAATCAGTGCCAT
5063585 AAGAAAATCAGTGCCA
1 AAGAAAATCAGTGCCA
5063601 AACATTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.15
Consensus pattern (17 bp):
AAGAAAATCAGTGCCAT
Found at i:5065922 original size:25 final size:25
Alignment explanation
Indices: 5065892--5065939 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5065882 TATAGCCAGG
*
5065892 ATAAGCTTCCTGTTACATGGCTCAT
1 ATAAGCATCCTGTTACATGGCTCAT
**
5065917 ATAAGCATCCTGTTTTATGGCTC
1 ATAAGCATCCTGTTACATGGCTC
5065940 GAAAGAGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (25 bp):
ATAAGCATCCTGTTACATGGCTCAT
Found at i:5068628 original size:21 final size:20
Alignment explanation
Indices: 5068604--5068649 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
5068594 AAACTTAGAG
5068604 TTTTATTAAAGTAATAATTCT
1 TTTTATTAAAGTAATAATT-T
* * *
5068625 TTTTTTTAAATTATTAATTT
1 TTTTATTAAAGTAATAATTT
5068645 TTTTA
1 TTTTA
5068650 AATAATAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTATTAAAGTAATAATTT
Found at i:5072782 original size:19 final size:19
Alignment explanation
Indices: 5072758--5072848 Score: 134
Period size: 19 Copynumber: 4.9 Consensus size: 19
5072748 AATCATATCT
*
5072758 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
*
5072777 TCTAAGATTGGA-ATCATA
1 TCTAAGATTGCATATCATA
5072795 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
*
5072812 TCTAAGATTGCATATCACA
1 TCTAAGATTGCATATCATA
5072831 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
5072849 TGAAGATTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 34 0.52
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:5072816 original size:35 final size:37
Alignment explanation
Indices: 5072758--5072848 Score: 132
Period size: 35 Copynumber: 2.5 Consensus size: 37
5072748 AATCATATCT
* *
5072758 TCTAAGATTGTATATCATATCTAAGATTGGA-ATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTGCATATCACA
5072795 TCTAAGATTG-TATCATATCTAAGATTGCATATCACA
1 TCTAAGATTGATATCATATCTAAGATTGCATATCACA
5072831 TCTAAGATTGCATATCAT
1 TCTAAGATTG-ATATCAT
5072849 TGAAGATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
35 18 0.37
36 15 0.31
37 10 0.20
38 6 0.12
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (37 bp):
TCTAAGATTGATATCATATCTAAGATTGCATATCACA
Found at i:5072827 original size:14 final size:15
Alignment explanation
Indices: 5072772--5072827 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
5072762 AGATTGTATA
5072772 TCATATCTAAGATTGG
1 TCATATCTAAGATT-G
5072788 AATCATATCTAAGATTG
1 --TCATATCTAAGATTG
5072805 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
5072822 -CATATC
1 TCATATC
5072828 ACATCTAAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 6 0.16
17 17 0.46
18 14 0.38
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (15 bp):
TCATATCTAAGATTG
Done.