Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 165 of 222
Found at i:52848370 original size:27 final size:27
Alignment explanation
Indices: 52848266--52848463 Score: 166
Period size: 27 Copynumber: 7.3 Consensus size: 27
52848256 GGGTATAATA
* *
52848266 GTCATTTTACCCTAT-AGGGGTATTTCG
1 GTCATTTTACCCT-TCAAGGGTATTTTG
** * *
52848293 GTCCGTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCAAGGGTATTTTG
* *
52848320 GTCATTTTACCCTTTAGGGGTATTTTG
1 GTCATTTTACCCTTCAAGGGTATTTTG
* * *
52848347 GTCATTTTACCTTTCAAGGATATTTTA
1 GTCATTTTACCCTTCAAGGGTATTTTG
* * * *
52848374 GTCATTTTAACCATCGATGGTATTTTG
1 GTCATTTTACCCTTCAAGGGTATTTTG
* * * *
52848401 ATAATTTTACCCATT-GAGGGTATTTTA
1 GTCATTTTACCC-TTCAAGGGTATTTTG
* * *
52848428 GTCATTTTACCCATCGAGGTTATTTTG
1 GTCATTTTACCCTTCAAGGGTATTTTG
52848455 GTCATTTTA
1 GTCATTTTA
52848464 AAGGCCTATT
Statistics
Matches: 135, Mismatches: 33, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
26 2 0.01
27 132 0.98
28 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTTCAAGGGTATTTTG
Found at i:52848396 original size:81 final size:81
Alignment explanation
Indices: 52848306--52848464 Score: 203
Period size: 81 Copynumber: 2.0 Consensus size: 81
52848296 CGTTTACCCT
* * * * **
52848306 TCGAGGGTATTTCGGTCATTTTACCC-TTTAGGGGTATTTTGGTCATTTTACCTTTCAAGGATAT
1 TCGAGGGTATTTCGATAATTTTACCCATTGA-GGGTATTTTAGTCATTTTACCCATCAAGGATAT
52848370 TTTAGTCATTTTAACCA
65 TTTAGTCATTTTAACCA
* * * *
52848387 TCGATGGTATTTTGATAATTTTACCCATTGAGGGTATTTTAGTCATTTTACCCATCGAGGTTATT
1 TCGAGGGTATTTCGATAATTTTACCCATTGAGGGTATTTTAGTCATTTTACCCATCAAGGATATT
*
52848452 TTGGTCATTTTAA
66 TTAGTCATTTTAA
52848465 AGGCCTATTT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
81 63 0.95
82 3 0.05
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.45
Consensus pattern (81 bp):
TCGAGGGTATTTCGATAATTTTACCCATTGAGGGTATTTTAGTCATTTTACCCATCAAGGATATT
TTAGTCATTTTAACCA
Found at i:52851003 original size:12 final size:12
Alignment explanation
Indices: 52850963--52851004 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
52850953 GAAAAAGTTT
52850963 GTGAAAAAGAAA
1 GTGAAAAAGAAA
**
52850975 ACGAAAAAGAAA
1 GTGAAAAAGAAA
*
52850987 TTGAAAAAGAAA
1 GTGAAAAAGAAA
52850999 GTGAAA
1 GTGAAA
52851005 GTGAGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.67, C:0.02, G:0.21, T:0.10
Consensus pattern (12 bp):
GTGAAAAAGAAA
Found at i:52851025 original size:21 final size:20
Alignment explanation
Indices: 52850989--52851031 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
52850979 AAAAGAAATT
*
52850989 GAAAAAGAAAGTGAAAGTGA
1 GAAAAAGAAAGCGAAAGTGA
*
52851009 GAAAAAGAAAGACGAAATTGA
1 GAAAAAGAAAG-CGAAAGTGA
52851030 GA
1 GA
52851032 TTAAACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.60, C:0.02, G:0.28, T:0.09
Consensus pattern (20 bp):
GAAAAAGAAAGCGAAAGTGA
Found at i:52852226 original size:14 final size:14
Alignment explanation
Indices: 52852202--52852238 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
52852192 AGAAAAATGT
*
52852202 GAGAGGTGAGAGAA
1 GAGATGTGAGAGAA
*
52852216 GAGTTGTGAGAGAA
1 GAGATGTGAGAGAA
52852230 GAGATGTGA
1 GAGATGTGA
52852239 ATGAGGGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.46, T:0.16
Consensus pattern (14 bp):
GAGATGTGAGAGAA
Found at i:52856742 original size:5 final size:5
Alignment explanation
Indices: 52856713--52856751 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
52856703 TAAATTTAAA
* *
52856713 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
52856752 CATCTTAGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:52857047 original size:19 final size:19
Alignment explanation
Indices: 52857023--52857061 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
52857013 TCTACCATAA
52857023 AACTTCATAATTCATGCAT
1 AACTTCATAATTCATGCAT
52857042 AACTTCATAATTCATGCAT
1 AACTTCATAATTCATGCAT
52857061 A
1 A
52857062 CTCATCCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (19 bp):
AACTTCATAATTCATGCAT
Found at i:52857547 original size:13 final size:14
Alignment explanation
Indices: 52857518--52857550 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
52857508 GTAATCAGTA
*
52857518 AAATTTTCTTAACG
1 AAATTTTCATAACG
52857532 AAATTTTCAT-ACG
1 AAATTTTCATAACG
52857545 AAATTT
1 AAATTT
52857551 CTATCATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (14 bp):
AAATTTTCATAACG
Found at i:52859060 original size:15 final size:15
Alignment explanation
Indices: 52859040--52859071 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
52859030 TAGCAATAGG
52859040 AAAAAATATTATGCA
1 AAAAAATATTATGCA
52859055 AAAAAATATTATGCA
1 AAAAAATATTATGCA
52859070 AA
1 AA
52859072 GAAGAAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.25
Consensus pattern (15 bp):
AAAAAATATTATGCA
Found at i:52861310 original size:31 final size:31
Alignment explanation
Indices: 52861272--52861333 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
52861262 TGATCGTATC
* * *
52861272 GCAAAGATGGTTACAGAAATGAGTACTTATT
1 GCAAAGATGGCTACAGAAAGGAGTACATATT
52861303 GCAAAGATGGCTACAGAAAGGAGTACATATT
1 GCAAAGATGGCTACAGAAAGGAGTACATATT
52861334 TGCAGATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.24
Consensus pattern (31 bp):
GCAAAGATGGCTACAGAAAGGAGTACATATT
Found at i:52861481 original size:7 final size:7
Alignment explanation
Indices: 52861448--52861477 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
52861438 CACCAAAAAA
52861448 AATATTT
1 AATATTT
52861455 AATATTT
1 AATATTT
52861462 AATATTT
1 AATATTT
52861469 AAT-TTT
1 AATATTT
52861475 AAT
1 AAT
52861478 TTTTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATATTT
Found at i:52862017 original size:22 final size:21
Alignment explanation
Indices: 52861992--52862034 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
52861982 TTCTTTATTT
*
52861992 TTCTATTCTCCTCTGCTTCTCC
1 TTCTATTCTCCTC-CCTTCTCC
*
52862014 TTCTATTTTCCTCCCTTCTCC
1 TTCTATTCTCCTCCCTTCTCC
52862035 ATCTCTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.05, C:0.42, G:0.02, T:0.51
Consensus pattern (21 bp):
TTCTATTCTCCTCCCTTCTCC
Found at i:52862033 original size:21 final size:22
Alignment explanation
Indices: 52861992--52862043 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
52861982 TTCTTTATTT
* *
52861992 TTCTATTCTCCTCTGCTTCTCC
1 TTCTATTTTCCTCTCCTTCTCC
52862014 TTCTATTTTCCTC-CCTTCTCC
1 TTCTATTTTCCTCTCCTTCTCC
* *
52862035 ATCTCTTTT
1 TTCTATTTT
52862044 AACGTAGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.06, C:0.38, G:0.02, T:0.54
Consensus pattern (22 bp):
TTCTATTTTCCTCTCCTTCTCC
Found at i:52862916 original size:20 final size:19
Alignment explanation
Indices: 52862878--52862916 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
52862868 GGGGAAGAAG
* *
52862878 AAAAGGAAAATAAAAAAAT
1 AAAAAGAAAAAAAAAAAAT
52862897 AAAAAGAAAAAAAAATAAAT
1 AAAAAGAAAAAAAAA-AAAT
52862917 TATTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (19 bp):
AAAAAGAAAAAAAAAAAAT
Found at i:52867630 original size:27 final size:27
Alignment explanation
Indices: 52867589--52867642 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
52867579 GTCAAGGTGA
*
52867589 TTAACCATTTGCTCACTAAACTATGAT
1 TTAACCATTTGCTCACTAAACCATGAT
* * *
52867616 TTAACCTTTTTCTCATTAAACCATGAT
1 TTAACCATTTGCTCACTAAACCATGAT
52867643 CATTTTGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (27 bp):
TTAACCATTTGCTCACTAAACCATGAT
Found at i:52880009 original size:11 final size:11
Alignment explanation
Indices: 52879995--52880023 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
52879985 AAAATTAAAA
52879995 AAAATTATTTT
1 AAAATTATTTT
52880006 AAAATTATTTT
1 AAAATTATTTT
52880017 AAAATTA
1 AAAATTA
52880024 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:52880080 original size:11 final size:11
Alignment explanation
Indices: 52880066--52880091 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
52880056 AAAATTTAAA
52880066 AAAAGTATTTT
1 AAAAGTATTTT
52880077 AAAAGTATTTT
1 AAAAGTATTTT
52880088 AAAA
1 AAAA
52880092 TTAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:52882909 original size:21 final size:22
Alignment explanation
Indices: 52882876--52882927 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
52882866 AAACTACGTT
* * *
52882876 AAAAGAGATGGAGAAG-GGAGG
1 AAAATAGAAGGAGAAGCAGAGG
52882897 AAAATAGAAGGAGAAGCAGAGG
1 AAAATAGAAGGAGAAGCAGAGG
*
52882919 AGAATAGAA
1 AAAATAGAA
52882928 AATAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.54, C:0.02, G:0.38, T:0.06
Consensus pattern (22 bp):
AAAATAGAAGGAGAAGCAGAGG
Found at i:52890846 original size:44 final size:43
Alignment explanation
Indices: 52890791--52890898 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 43
52890781 CTACTCTGCT
* * * *
52890791 ACTGCAGCTTCAAAAGTATAGGATTTGTCATTTTAATCTGCTTC
1 ACTGCAACTTCAAAAG-ATAGGATTGGTCACTTCAATCTGCTTC
** **
52890835 ACTGCAACTTCATGGAGATAGGATTGGTGGCTTCAATCTGCTTC
1 ACTGCAACTTCA-AAAGATAGGATTGGTCACTTCAATCTGCTTC
52890879 ACTGCAACTTCAAGAAGATA
1 ACTGCAACTTCAA-AAGATA
52890899 AGATCCGCCA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
44 50 0.96
45 2 0.04
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (43 bp):
ACTGCAACTTCAAAAGATAGGATTGGTCACTTCAATCTGCTTC
Found at i:52891019 original size:51 final size:51
Alignment explanation
Indices: 52890917--52891712 Score: 831
Period size: 51 Copynumber: 15.9 Consensus size: 51
52890907 CATAATTTGT
* * * * *
52890917 AGCTTTAATCTATTCCACTGCAACACTAGGGAAAAAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTC
* * * * *
52890968 AGCTTTAATCTGTTCCACTACAACGCTAGAGAAATAAGATCCGTTGTCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTC
*** * *
52891019 AG------TCTGCTT-CACTGCAATTTCAGAGAGATAAG----GCTG--GT-
1 AGCTTTAATCTG-TTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTC
* * * ** ** *
52891057 GGCTTCAATCTGCTCCACTGCAACTTCAG-GAAGATAAG-TTCCGCTATGATTTGT
1 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAA-ATAAGATT-CGC--TGCCTT-C
* * * *
52891111 AGCTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAGATTCGTTGCATTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTC
* ** * * *
52891162 AGCTTTAATCTGTTCCACTTCAATACCAGGGAATTAAGATTCGCTACCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTC
* *
52891213 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTAGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTC
* * * *
52891264 AGCTTTAGTCTGTTCTACTGTAACGCCAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTC
* *
52891315 AGCTTTAATCTGTTCCACTACAACGCCAGAGAAATAAGATTTGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTC
*
52891366 AGCTTTAATCTGTTCCACTGCAACGCCACAGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTC
* * **
52891417 AGCTTTAATCTGTTCCACTGCAACGCTA-AGAAAAAAGATTTTCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTC
* * **
52891467 AACTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTTACTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTC
*
52891518 AGCTTTAATCTGTTCCACTGTAACGCCATG-GAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCA-GAGAAATAAGATTCGCTGCCTTC
* * * * * *
52891569 AACTTTAATTTGTTCCATTGCAACGCCAGAGAAATAAAATTCGTTGCCTTA
1 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTC
* *
52891620 AGCTTTAGTCTGTTCAACTGCAACGCCAG-GAAA-AAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTC
* * *
52891669 AGCTTTAATCTGTTCCACTGCAACACTAGAGAAAAAAGATTCGC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGC
52891713 CATAATGACT
Statistics
Matches: 631, Mismatches: 88, Indels: 52
0.82 0.11 0.07
Matches are distributed among these distances:
38 1 0.00
39 1 0.00
41 3 0.00
43 3 0.00
44 22 0.03
45 21 0.03
46 2 0.00
48 2 0.00
49 38 0.06
50 56 0.09
51 441 0.70
52 6 0.01
54 30 0.05
55 5 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (51 bp):
AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTC
Found at i:52891165 original size:194 final size:194
Alignment explanation
Indices: 52890827--52891180 Score: 550
Period size: 194 Copynumber: 1.8 Consensus size: 194
52890817 GTCATTTTAA
* *
52890827 TCTGCTTCACTGCAACTTCATGGAGATAGGATTGGTGGCTTCAATCTGCTTCACTGCAACTTCAA
1 TCTGCTTCACTGCAACTTCATGGAGATAGGACTGGTGGCTTCAATCTGCTCCACTGCAACTTCAA
*
52890892 GAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTATTCCACTGCAACACTAGGGAAAAAAGAT
66 GAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTATTCCACTGCAACACCAGGGAAAAAAGAT
*
52890957 TCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCTAGAGAAATAAGATCCGTTGTCTTCAG
131 TCGCTGCATTCAGCTTTAATCTGTTCCACTACAACGCTAGAGAAATAAGATCCGTTGTCTTCAG
*
52891021 TCTGCTTCACTGCAATTTCA-GAGAGATAAGG-CTGGTGGCTTCAATCTGCTCCACTGCAACTTC
1 TCTGCTTCACTGCAACTTCATG-GAGAT-AGGACTGGTGGCTTCAATCTGCTCCACTGCAACTTC
* * * * * ** *
52891084 AGGAAGATAAGTTCCGCTATGATTTGTAGCTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAG
64 AAGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTATTCCACTGCAACACCAGGGAAAAAAG
*
52891149 ATTCGTTGCATTCAGCTTTAATCTGTTCCACT
129 ATTCGCTGCATTCAGCTTTAATCTGTTCCACT
52891181 TCAATACCAG
Statistics
Matches: 144, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
193 1 0.01
194 140 0.97
195 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (194 bp):
TCTGCTTCACTGCAACTTCATGGAGATAGGACTGGTGGCTTCAATCTGCTCCACTGCAACTTCAA
GAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTATTCCACTGCAACACCAGGGAAAAAAGAT
TCGCTGCATTCAGCTTTAATCTGTTCCACTACAACGCTAGAGAAATAAGATCCGTTGTCTTCAG
Found at i:52895599 original size:19 final size:20
Alignment explanation
Indices: 52895575--52895621 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
52895565 TGGTGGACTT
* *
52895575 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGAAATG
52895594 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
52895614 -AATGCAAA
1 TAATGCAAA
52895622 AAGAGACGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:52897494 original size:17 final size:18
Alignment explanation
Indices: 52897468--52897501 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52897458 ATGAACTACA
52897468 AATAACCAATA-AATACC
1 AATAACCAATACAATACC
*
52897485 AATAAGCAATACAATAC
1 AATAACCAATACAATAC
52897502 ACACAAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.59, C:0.21, G:0.03, T:0.18
Consensus pattern (18 bp):
AATAACCAATACAATACC
Found at i:52899703 original size:29 final size:29
Alignment explanation
Indices: 52899667--52899731 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
52899657 TGTCGCCAGA
* * *
52899667 CCGTGTGCCTTACACGCCTGTGTCTCAGG
1 CCGTGTGCCTCACACGCCCGTGTCTCAAG
*
52899696 CTGTGTGCCTCACACGCCCGTGTCTCAAG
1 CCGTGTGCCTCACACGCCCGTGTCTCAAG
52899725 CCGTGTG
1 CCGTGTG
52899732 AACCCAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.11, C:0.35, G:0.28, T:0.26
Consensus pattern (29 bp):
CCGTGTGCCTCACACGCCCGTGTCTCAAG
Found at i:52903614 original size:59 final size:59
Alignment explanation
Indices: 52903542--52903663 Score: 244
Period size: 59 Copynumber: 2.1 Consensus size: 59
52903532 TTCTCGTCGA
52903542 TTTTCCCCCGTAGATCCAACTTGTGTAATACTTCCATGTCTCGCGGTGGCGGCGAAATT
1 TTTTCCCCCGTAGATCCAACTTGTGTAATACTTCCATGTCTCGCGGTGGCGGCGAAATT
52903601 TTTTCCCCCGTAGATCCAACTTGTGTAATACTTCCATGTCTCGCGGTGGCGGCGAAATT
1 TTTTCCCCCGTAGATCCAACTTGTGTAATACTTCCATGTCTCGCGGTGGCGGCGAAATT
52903660 TTTT
1 TTTT
52903664 TCCTCTACCC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.34
Consensus pattern (59 bp):
TTTTCCCCCGTAGATCCAACTTGTGTAATACTTCCATGTCTCGCGGTGGCGGCGAAATT
Found at i:52905265 original size:21 final size:22
Alignment explanation
Indices: 52905235--52905275 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
52905225 ATATCTAAAT
*
52905235 TACCACACACTCATA-TATATA
1 TACCACACACACATACTATATA
*
52905256 TACCATACACACATACTATA
1 TACCACACACACATACTATA
52905276 AAACTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (22 bp):
TACCACACACACATACTATATA
Found at i:52907799 original size:21 final size:20
Alignment explanation
Indices: 52907768--52907810 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
52907758 CTATAATATT
52907768 TTTAAACAAACTAG-GAAAA
1 TTTAAACAAACTAGAGAAAA
*
52907787 TTTAGAACAAAACTTGAGAAAA
1 TTTA-AAC-AAACTAGAGAAAA
52907809 TT
1 TT
52907811 GAGAGTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 3 0.15
21 6 0.30
22 7 0.35
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (20 bp):
TTTAAACAAACTAGAGAAAA
Found at i:52908884 original size:40 final size:41
Alignment explanation
Indices: 52908749--52908987 Score: 187
Period size: 41 Copynumber: 5.9 Consensus size: 41
52908739 GATTTTTTGA
* ** *
52908749 GCCTTTAGCGGCGTTTTTGTAAAAGCGACGCTAATGCTC-G
1 GCCTTTAGAGGCGTTTTTGTCTAAGCGCCGCTAATGCTCTG
* * * * ** *
52908789 GATCTTTAGCGGCGTTTCTATCTGGGCGCCGCTAATTCTCTG
1 G-CCTTTAGAGGCGTTTTTGTCTAAGCGCCGCTAATGCTCTG
* ** *
52908831 GCCTTTAGCGGCGTTTTTAACTAAGCGCCGCTAATGGT-TG
1 GCCTTTAGAGGCGTTTTTGTCTAAGCGCCGCTAATGCTCTG
* * ** *
52908871 GCCTTTAGTGGCGTTTTTGTTTGTGCGCCGCTAATGCTGTG
1 GCCTTTAGAGGCGTTTTTGTCTAAGCGCCGCTAATGCTCTG
* * *
52908912 GCCTTTAGAGGCGCTTTTGTGTAAGCGCCGCTAATGCAT-TT
1 GCCTTTAGAGGCGTTTTTGTCTAAGCGCCGCTAATGC-TCTG
* * * * *
52908953 ACCTTTAGCGGCGTTTTGGCCAAAGCGCCGCTAAT
1 GCCTTTAGAGGCGTTTTTGTCTAAGCGCCGCTAAT
52908988 AGTAAAAAAA
Statistics
Matches: 159, Mismatches: 36, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
40 34 0.21
41 122 0.77
42 3 0.02
ACGTcount: A:0.15, C:0.23, G:0.28, T:0.33
Consensus pattern (41 bp):
GCCTTTAGAGGCGTTTTTGTCTAAGCGCCGCTAATGCTCTG
Found at i:52908916 original size:81 final size:81
Alignment explanation
Indices: 52908749--52908968 Score: 223
Period size: 81 Copynumber: 2.7 Consensus size: 81
52908739 GATTTTTTGA
* *
52908749 GCCTTTAGCGGCGTTTTTGTAA-AAGCGACGCTAATGCTCGGATCTTTAGCGGCGTTTCTATCTG
1 GCCTTTAGCGGCG-TTTT-TAATAAGCGCCGCTAATGCTCGGACCTTTAGCGGCGTTTCTATCTG
*
52908813 GGCGCCGCTAATTCTCTG
64 GGCGCCGCTAATGCTCTG
* * * * * * *
52908831 GCCTTTAGCGGCGTTTTTAACTAAGCGCCGCTAATGGTTGG-CCTTTAGTGGCGTTTTTGTTTGT
1 GCCTTTAGCGGCGTTTTTAA-TAAGCGCCGCTAATGCTCGGACCTTTAGCGGCGTTTCTATCTGG
*
52908895 GCGCCGCTAATGCTGTG
65 GCGCCGCTAATGCTCTG
* * **
52908912 GCCTTTAGAGGCGCTTTTGT-GTAAGCGCCGCTAATGCAT-TTACCTTTAGCGGCGTTT
1 GCCTTTAGCGGCG-TTTT-TAATAAGCGCCGCTAATGC-TCGGACCTTTAGCGGCGTTT
52908969 TGGCCAAAGC
Statistics
Matches: 115, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
80 3 0.03
81 63 0.55
82 48 0.42
83 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.28, T:0.35
Consensus pattern (81 bp):
GCCTTTAGCGGCGTTTTTAATAAGCGCCGCTAATGCTCGGACCTTTAGCGGCGTTTCTATCTGGG
CGCCGCTAATGCTCTG
Found at i:52917333 original size:39 final size:40
Alignment explanation
Indices: 52917223--52917445 Score: 275
Period size: 39 Copynumber: 5.7 Consensus size: 40
52917213 GCTCCTCGTT
* *
52917223 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* *
52917263 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
52917303 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
52917342 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
52917381 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
52917422 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52917446 CATCATTCAA
Statistics
Matches: 168, Mismatches: 7, Indels: 17
0.88 0.04 0.09
Matches are distributed among these distances:
38 2 0.01
39 91 0.54
40 64 0.38
41 11 0.07
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:52917341 original size:79 final size:80
Alignment explanation
Indices: 52917217--52917445 Score: 276
Period size: 79 Copynumber: 2.9 Consensus size: 80
52917207 GATATAGCTC
* * *
52917217 CTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACT
1 CTCGTACAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAATCTCGCACAAATGCCTTCGGGACT
*
52917280 TAGCCCGGATTTAGTAT
64 TAGCCCGGAATTAGTAT
52917297 CTCGTACAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTA
1 CTCGTACAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATCTCGCACAAATGCCTTCGGGACTTA
52917360 GCCCGGAATTAGTAT
66 GCCCGGAATTAGTAT
* * * * *
52917375 CTCGCACAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCAC-AA-GCCTTCGGGAC
1 CTCGTACAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGTAATC-TCGCACAAATGCCTTCGGGAC
52917436 TTAGCCCGGA
63 TTAGCCCGGA
52917446 CATCATTCAA
Statistics
Matches: 134, Mismatches: 8, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
78 47 0.35
79 58 0.43
80 29 0.22
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (80 bp):
CTCGTACAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATCTCGCACAAATGCCTTCGGGACTTA
GCCCGGAATTAGTAT
Found at i:52925230 original size:40 final size:40
Alignment explanation
Indices: 52925186--52925447 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
52925176 GCTCCTCGTT
* *
52925186 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
52925226 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
52925266 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
52925305 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
52925344 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
52925383 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
52925424 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52925448 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:52926543 original size:13 final size:13
Alignment explanation
Indices: 52926525--52926549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52926515 AGGATGAGCA
52926525 TTTTTTTTCTTTG
1 TTTTTTTTCTTTG
52926538 TTTTTTTTCTTT
1 TTTTTTTTCTTT
52926550 CTAGTTTCGG
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:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTG
Found at i:52928795 original size:12 final size:12
Alignment explanation
Indices: 52928774--52928849 Score: 104
Period size: 12 Copynumber: 6.4 Consensus size: 12
52928764 AAACAAAGAC
52928774 AACTTAGAAATA
1 AACTTAGAAATA
52928786 AAC-TAGGAAATA
1 AACTTA-GAAATA
52928798 AACTTAGAAATA
1 AACTTAGAAATA
52928810 AACTTAGAAAT-
1 AACTTAGAAATA
*
52928821 AA-TAATGAAATA
1 AACTTA-GAAATA
52928833 AACTTAGAAATA
1 AACTTAGAAATA
52928845 AACTT
1 AACTT
52928850 CTATCGACAA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
10 2 0.04
11 9 0.16
12 42 0.74
13 4 0.07
ACGTcount: A:0.58, C:0.08, G:0.09, T:0.25
Consensus pattern (12 bp):
AACTTAGAAATA
Found at i:52930205 original size:13 final size:13
Alignment explanation
Indices: 52930187--52930219 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
52930177 GGTTCTTCTG
*
52930187 GAAGGCCTGTAAA
1 GAAGGCCTATAAA
52930200 GAAGGCCTATAAA
1 GAAGGCCTATAAA
52930213 GAAGGCC
1 GAAGGCC
52930220 AGATTTGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.18, G:0.30, T:0.12
Consensus pattern (13 bp):
GAAGGCCTATAAA
Found at i:52937419 original size:46 final size:46
Alignment explanation
Indices: 52937361--52937533 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
52937351 TTGTTGAGCA
* *
52937361 TCCGAACCCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
52937407 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
52937454 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
52937500 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
52937534 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 59 0.56
47 29 0.28
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:52937517 original size:93 final size:93
Alignment explanation
Indices: 52937358--52937528 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
52937348 GGATTGTTGA
* *
52937358 GCATCCGAACCCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACCCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
52937423 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
52937451 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACCCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
*
52937516 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
52937529 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACCCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:52937795 original size:19 final size:20
Alignment explanation
Indices: 52937758--52937795 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
52937748 ATATGGTGGT
52937758 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
52937778 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
52937796 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:52938928 original size:39 final size:39
Alignment explanation
Indices: 52938865--52938957 Score: 141
Period size: 39 Copynumber: 2.4 Consensus size: 39
52938855 GACTTTAAGC
* * *
52938865 CCGGATATATTCCCAGCACATAGCCTGCGGACGTCAAGT
1 CCGGATATGTTTCCAGCACATAGCCTGCGGACCTCAAGT
* *
52938904 CCGGATATGTTTCCAGTACGTAGCCTGCGGACCTCAAGT
1 CCGGATATGTTTCCAGCACATAGCCTGCGGACCTCAAGT
52938943 CCGGATATGTTTCCA
1 CCGGATATGTTTCCA
52938958 AGTATCATGC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATGTTTCCAGCACATAGCCTGCGGACCTCAAGT
Found at i:52946685 original size:39 final size:38
Alignment explanation
Indices: 52946604--52946714 Score: 141
Period size: 39 Copynumber: 2.9 Consensus size: 38
52946594 TCTAGCACAA
* * * *
52946604 AGCCTGCGAGACTTTAAGCCCGAATATATTTCCAGCACT
1 AGCCTGCG-GACCTCAAGCCCGGATATGTTTCCAGCACT
** *
52946643 AGCCTGCGGACCTCAAGTTCGGATATGTTTCCAGTACGT
1 AGCCTGCGGACCTCAAGCCCGGATATGTTTCCAGCAC-T
52946682 AGCCTGCGGACCTCAAGCCCGGATATGTTTCCA
1 AGCCTGCGGACCTCAAGCCCGGATATGTTTCCA
52946715 AGTATCATGC
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 22 0.35
39 40 0.65
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (38 bp):
AGCCTGCGGACCTCAAGCCCGGATATGTTTCCAGCACT
Found at i:52954429 original size:39 final size:39
Alignment explanation
Indices: 52954376--52954465 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 39
52954366 GACTTTAAGC
* * *
52954376 CCGGATATATTTCCAGCACATAGCCTGCGGACCTCATGT
1 CCGGATATGTTTCCAGCACATAGCCGGCGGACCTCAAGT
* *
52954415 CCGGATATGTTTCCAGTACGTAGCCGGCGGACCTCAAGT
1 CCGGATATGTTTCCAGCACATAGCCGGCGGACCTCAAGT
52954454 CCGGATATGTTT
1 CCGGATATGTTT
52954466 TCAAGTATCA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (39 bp):
CCGGATATGTTTCCAGCACATAGCCGGCGGACCTCAAGT
Found at i:52957643 original size:33 final size:33
Alignment explanation
Indices: 52957591--52957661 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
52957581 TTGGGCCCAT
* * *
52957591 TCTGCTACTGTATAGGGCTAA-AGCCCAGACTGC
1 TCTGCTACTGAATAAGGCTAAGA-CCCAGACTGA
* *
52957624 TCTGTTACTGAATAAGGCTACGACCCAGACTGA
1 TCTGCTACTGAATAAGGCTAAGACCCAGACTGA
52957657 TCTGC
1 TCTGC
52957662 ATATTCTGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (33 bp):
TCTGCTACTGAATAAGGCTAAGACCCAGACTGA
Found at i:52963312 original size:45 final size:44
Alignment explanation
Indices: 52963144--52963299 Score: 173
Period size: 45 Copynumber: 3.6 Consensus size: 44
52963134 ATATTGTACA
* * *
52963144 ATGCCAACGTCCCAGACGTGGTCTTATATGTAATCAC-ATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCACAATATCG
*
52963187 ATGCC-ACTGTCCCAGACA-GGGCTTACACG-AATCA-AATA-CG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAATCACAATATCG
* * *
52963227 ATG-CAGATGTCCCAAACATGGTCTTACACGTAACCACATATATCG
1 ATGCCA-ACGTCCCAGACATGGTCTTACACGTAATCACA-ATATCG
52963272 ATGCCAACGTCCCAGACATGGTCTTACA
1 ATGCCAACGTCCCAGACATGGTCTTACA
52963300 TGAGCACACA
Statistics
Matches: 93, Mismatches: 10, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
39 1 0.01
40 14 0.15
41 19 0.20
42 14 0.15
43 15 0.16
44 3 0.03
45 25 0.27
46 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (44 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCACAATATCG
Found at i:52971108 original size:12 final size:10
Alignment explanation
Indices: 52971070--52971119 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
52971060 TGTAATTCTG
*
52971070 TCAAAAATAA
1 TCAAAATTAA
*
52971080 CCAAAATTAA
1 TCAAAATTAA
52971090 TCAAAATTAA
1 TCAAAATTAA
52971100 CTACAAAATTAA
1 -T-CAAAATTAA
*
52971112 TTAAAATT
1 TCAAAATT
52971120 CATAATTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
10 23 0.68
11 2 0.06
12 9 0.26
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (10 bp):
TCAAAATTAA
Found at i:52971935 original size:26 final size:26
Alignment explanation
Indices: 52971906--52971958 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
52971896 TCTATGGATG
* * * *
52971906 AATATTTCTATATTAGGGATAGATAT
1 AATATATCTATATCAAGGATAAATAT
52971932 AATATATCTATATCAAGGATAAATAT
1 AATATATCTATATCAAGGATAAATAT
52971958 A
1 A
52971959 CTAAGTCGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (26 bp):
AATATATCTATATCAAGGATAAATAT
Found at i:52984142 original size:32 final size:32
Alignment explanation
Indices: 52984106--52984167 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
52984096 TAGGGTTCAG
*
52984106 TCTTCATTGTCCATTAATTGTCCCTTTCTTGA
1 TCTTCATTGTCCATCAATTGTCCCTTTCTTGA
*
52984138 TCTTCGTTGTCCATCAATTGTCCCTTTCTT
1 TCTTCATTGTCCATCAATTGTCCCTTTCTT
52984168 TCCATCTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.13, C:0.27, G:0.10, T:0.50
Consensus pattern (32 bp):
TCTTCATTGTCCATCAATTGTCCCTTTCTTGA
Found at i:52993005 original size:17 final size:18
Alignment explanation
Indices: 52992985--52993027 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
52992975 TCATAAAATG
*
52992985 AATTATTTTATTGTAT-A
1 AATTATTATATTGTATGA
*
52993002 AATTAATATATTGTATGA
1 AATTATTATATTGTATGA
52993020 AATTATTA
1 AATTATTA
52993028 ATGTAGATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (18 bp):
AATTATTATATTGTATGA
Found at i:52993432 original size:25 final size:25
Alignment explanation
Indices: 52993366--52993472 Score: 103
Period size: 25 Copynumber: 4.3 Consensus size: 25
52993356 CCACAACCCT
*
52993366 TATGAG-TTCACCGATTCTCAGCTCA
1 TATGAGCTT-ACCGATTCTCAGCTCG
*
52993391 TATGAGCTTATCGATTCTCAGCTCG
1 TATGAGCTTACCGATTCTCAGCTCG
* * *
52993416 TATGAGCTTACCAATTCACAGCTTG
1 TATGAGCTTACCGATTCTCAGCTCG
* *
52993441 TGA-GAGCATATCGATTCAT-AGCTCG
1 T-ATGAGCTTACCGATTC-TCAGCTCG
52993466 TATGAGC
1 TATGAGC
52993473 ATACATGTAC
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
24 1 0.01
25 63 0.94
26 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (25 bp):
TATGAGCTTACCGATTCTCAGCTCG
Found at i:52995678 original size:47 final size:47
Alignment explanation
Indices: 52995609--52995871 Score: 391
Period size: 47 Copynumber: 5.6 Consensus size: 47
52995599 CCCTTCGGGA
* * * * * *
52995609 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52995656 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52995703 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTGGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
52995750 CTTATCACATATATATACACTTTCACATTCATCCCATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52995799 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
52995846 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
52995872 CACAATTATC
Statistics
Matches: 197, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
47 153 0.78
49 44 0.22
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52995821 original size:96 final size:96
Alignment explanation
Indices: 52995609--52995871 Score: 399
Period size: 96 Copynumber: 2.8 Consensus size: 96
52995599 CCCTTCGGGA
* * * * * *
52995609 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCTTATCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
52995672 ACTTTCACATTCATCACATCGGCTATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
52995703 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTGGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* * *
52995768 ACTTTCACATTCATCCCATTGGCCATTCGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
52995799 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
52995864 A--TTCACAT
66 ACTTTCACAT
52995872 CACAATTATC
Statistics
Matches: 156, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
94 56 0.36
96 100 0.64
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52995907 original size:143 final size:141
Alignment explanation
Indices: 52995611--52995871 Score: 405
Period size: 143 Copynumber: 1.8 Consensus size: 141
52995601 CTTCGGGACT
* *
52995611 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCTTATCACATATATACACTT
1 TATCACATATATACACTTTCACATCCATCACATTGGCCACTCGGCCTTATCACATATATACACTT
* * *
52995676 TCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
66 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACATTCACATTCATCACATCAG
* *
52995741 CCATTGGGCCT
131 CCATTCGGCCA
* * *
52995752 TATCACATATATATACACTTTCACATTCATCCCATTGGCCATTCGGCCTTATCACATATATACAC
1 TATCAC--ATATATACACTTTCACATCCATCACATTGGCCACTCGGCCTTATCACATATATACAC
*
52995817 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACATTCACAT
64 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACATTCACAT
52995872 CACAATTATC
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
141 6 0.05
143 104 0.95
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (141 bp):
TATCACATATATACACTTTCACATCCATCACATTGGCCACTCGGCCTTATCACATATATACACTT
TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACATTCACATTCATCACATCAG
CCATTCGGCCA
Found at i:53001972 original size:57 final size:56
Alignment explanation
Indices: 53001900--53002028 Score: 168
Period size: 57 Copynumber: 2.3 Consensus size: 56
53001890 GGGTTTAGCC
53001900 TGGACTGGTAATCCTAATCAAGCTTTTTAAGCATACACTATATAAAAGAATTAAACA
1 TGGACTGGTAATCCTAATCAAGCTTTTTAAGCATACACTATAT-AAAGAATTAAACA
* * * * * * * * *
53001957 TGTACTGGTAATCCTAATTAAGCTTTTTGAGCATCCGCTATATAAAGGATTTAGCC
1 TGGACTGGTAATCCTAATCAAGCTTTTTAAGCATACACTATATAAAGAATTAAACA
53002013 TGGACTGGTAATCCTA
1 TGGACTGGTAATCCTA
53002029 TCATATGACA
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
56 24 0.39
57 38 0.61
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (56 bp):
TGGACTGGTAATCCTAATCAAGCTTTTTAAGCATACACTATATAAAGAATTAAACA
Found at i:53006017 original size:46 final size:46
Alignment explanation
Indices: 53005967--53006142 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 46
53005957 TGATTGAGCA
53005967 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
53006013 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATG-TAACTAG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T-G
* *
53006057 CCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGAATGCGAACG
1 ---TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53006106 -CCTGAGCCCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53006143 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 1 0.01
45 4 0.04
46 58 0.55
47 28 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:53006124 original size:93 final size:93
Alignment explanation
Indices: 53005965--53006135 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
53005955 GATGATTGAG
* * *
53005965 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGAATGCGAACGTCCGAACCCGTTGAGTT
*
53006030 GAGTCTGAGTTCGTGAGATGTAACTAGC
66 GAGTCCGAGTTCGTGAGATGTAACTAGC
*
53006058 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGAATGCGAACG-CCTGAGCCCGTTGAGT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGAATGCGAACGTCC-GAACCCGTTGAGT
53006122 TGAGTCCGAGTTCG
65 TGAGTCCGAGTTCG
53006136 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (93 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGAATGCGAACGTCCGAACCCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAGC
Found at i:53010593 original size:23 final size:24
Alignment explanation
Indices: 53010548--53010593 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
53010538 TATATACTGA
*
53010548 TCACAAAAGTCTTAAATACTTGATG
1 TCACAAAAGACTTAAATA-TTGATG
*
53010573 TCACAAAAGACTTGAAT-TTGA
1 TCACAAAAGACTTAAATATTGA
53010594 GACAACGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
25 15 0.79
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
TCACAAAAGACTTAAATATTGATG
Found at i:53021044 original size:39 final size:40
Alignment explanation
Indices: 53020934--53021156 Score: 275
Period size: 39 Copynumber: 5.7 Consensus size: 40
53020924 GCTCCTCGTT
* *
53020934 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* *
53020974 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
53021014 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
53021053 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
53021092 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
53021133 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53021157 CATCATTCAA
Statistics
Matches: 168, Mismatches: 7, Indels: 17
0.88 0.04 0.09
Matches are distributed among these distances:
38 2 0.01
39 91 0.54
40 64 0.38
41 11 0.07
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:53021052 original size:79 final size:80
Alignment explanation
Indices: 53020928--53021156 Score: 276
Period size: 79 Copynumber: 2.9 Consensus size: 80
53020918 GATATAGCTC
* * *
53020928 CTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACT
1 CTCGTACAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAATCTCGCACAAATGCCTTCGGGACT
*
53020991 TAGCCCGGATTTAGTAT
64 TAGCCCGGAATTAGTAT
53021008 CTCGTACAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTA
1 CTCGTACAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATCTCGCACAAATGCCTTCGGGACTTA
53021071 GCCCGGAATTAGTAT
66 GCCCGGAATTAGTAT
* * * * *
53021086 CTCGCACAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCAC-AA-GCCTTCGGGAC
1 CTCGTACAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGTAATC-TCGCACAAATGCCTTCGGGAC
53021147 TTAGCCCGGA
63 TTAGCCCGGA
53021157 CATCATTCAA
Statistics
Matches: 134, Mismatches: 8, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
78 47 0.35
79 58 0.43
80 29 0.22
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (80 bp):
CTCGTACAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATCTCGCACAAATGCCTTCGGGACTTA
GCCCGGAATTAGTAT
Found at i:53028950 original size:40 final size:40
Alignment explanation
Indices: 53028906--53029167 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
53028896 GCTCCTCGTT
* * *
53028906 CAAATGCCTTCGGGACATAGTCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
*
53028946 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
53028986 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
53029025 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
53029064 CGAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
53029103 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
53029144 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53029168 CATCATTCAA
Statistics
Matches: 206, Mismatches: 8, Indels: 17
0.89 0.03 0.07
Matches are distributed among these distances:
38 2 0.01
39 129 0.63
40 64 0.31
41 11 0.05
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:53033463 original size:13 final size:14
Alignment explanation
Indices: 53033427--53033465 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
53033417 TTAAATTTTT
53033427 TTGTTATATTTTAG
1 TTGTTATATTTTAG
53033441 TTGTTATATTTTAG
1 TTGTTATATTTTAG
53033455 TTG-TATATTTT
1 TTGTTATATTTT
53033466 TGTTTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.67
Consensus pattern (14 bp):
TTGTTATATTTTAG
Found at i:53033975 original size:21 final size:21
Alignment explanation
Indices: 53033946--53033998 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
53033936 ACATCTTTGA
* *
53033946 TATATATATTTATATACAGTTT
1 TATATATATTTAT-TAAAATTT
53033968 TA-ATATATTTATTAAAATTT
1 TATATATATTTATTAAAATTT
53033988 TATATATATTT
1 TATATATATTT
53033999 GAAAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.29
21 18 0.64
22 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TATATATATTTATTAAAATTT
Found at i:53034088 original size:12 final size:11
Alignment explanation
Indices: 53034071--53034170 Score: 82
Period size: 12 Copynumber: 9.1 Consensus size: 11
53034061 TACACAACAC
53034071 ATAACTTACAT
1 ATAACTTACAT
53034082 AATAACTTAC--
1 -ATAACTTACAT
* *
53034092 ATAAGTTATAT
1 ATAACTTACAT
*
53034103 ATAAACTTATAT
1 AT-AACTTACAT
53034115 ATAACTTACAT
1 ATAACTTACAT
53034126 AATAACTTAC--
1 -ATAACTTACAT
* *
53034136 ATAAGTTATAT
1 ATAACTTACAT
*
53034147 ATAAACTTATAT
1 AT-AACTTACAT
53034159 ATAACTTACAT
1 ATAACTTACAT
53034170 A
1 A
53034171 CATAATACAT
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
9 14 0.19
11 21 0.29
12 38 0.52
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (11 bp):
ATAACTTACAT
Found at i:53034095 original size:21 final size:21
Alignment explanation
Indices: 53034069--53034223 Score: 95
Period size: 21 Copynumber: 7.2 Consensus size: 21
53034059 CTTACACAAC
53034069 ACATAACTTACATAATAACTT
1 ACATAACTTACATAATAACTT
* *
53034090 ACATAAGTTATAT-ATAAACTTAT
1 ACATAACTTACATAAT-AAC-T-T
*
53034113 ATATAACTTACATAATAACTT
1 ACATAACTTACATAATAACTT
* *
53034134 ACATAAGTTATAT-ATAAACTTAT
1 ACATAACTTACATAAT-AAC-T-T
*
53034157 ATATAACTTACATACATAA--T
1 ACATAACTTACATA-ATAACTT
* *
53034177 ACATAACTTAAATCA-AACTT
1 ACATAACTTACATAATAACTT
* * *
53034197 ATAATAACATACATACATGACTT
1 A-CATAACTTACATA-ATAACTT
53034220 ACAT
1 ACAT
53034224 GCATAATACA
Statistics
Matches: 100, Mismatches: 20, Indels: 27
0.68 0.14 0.18
Matches are distributed among these distances:
18 2 0.02
19 1 0.01
20 18 0.18
21 37 0.37
22 6 0.06
23 30 0.30
24 4 0.04
25 2 0.02
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (21 bp):
ACATAACTTACATAATAACTT
Found at i:53034118 original size:23 final size:23
Alignment explanation
Indices: 53034092--53034162 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
53034082 AATAACTTAC
53034092 ATAAGTTATATATAAACTTATAT
1 ATAAGTTATATATAAACTTATAT
* * *
53034115 ATAACTTACATA-ATAAC-T-TAC
1 ATAAGTTATATATA-AACTTATAT
53034136 ATAAGTTATATATAAACTTATAT
1 ATAAGTTATATATAAACTTATAT
53034159 ATAA
1 ATAA
53034163 CTTACATACA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
21 15 0.39
22 4 0.11
23 19 0.50
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.39
Consensus pattern (23 bp):
ATAAGTTATATATAAACTTATAT
Found at i:53034128 original size:44 final size:45
Alignment explanation
Indices: 53034071--53034223 Score: 221
Period size: 44 Copynumber: 3.5 Consensus size: 45
53034061 TACACAACAC
53034071 ATAACTTACATA-ATAACTTACATAAGTTATATATAAACTTATAT
1 ATAACTTACATACATAACTTACATAAGTTATATATAAACTTATAT
53034115 ATAACTTACATA-ATAACTTACATAAGTTATATATAAACTTATAT
1 ATAACTTACATACATAACTTACATAAGTTATATATAAACTTATAT
*
53034159 ATAACTTACATACATAA--TACATAACTTA-A-ATCAAACTTATA-
1 ATAACTTACATACATAACTTACATAAGTTATATAT-AAACTTATAT
* *
53034200 ATAACATACATACATGACTTACAT
1 ATAACTTACATACATAACTTACAT
53034224 GCATAATACA
Statistics
Matches: 102, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
41 17 0.17
42 10 0.10
43 15 0.15
44 56 0.55
45 4 0.04
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.35
Consensus pattern (45 bp):
ATAACTTACATACATAACTTACATAAGTTATATATAAACTTATAT
Found at i:53034145 original size:32 final size:32
Alignment explanation
Indices: 53034109--53034170 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
53034099 ATATATAAAC
53034109 TTATATAT-AACTTACATAATAACTTACATAAG
1 TTATATATAAACTTACAT-ATAACTTACATAAG
*
53034141 TTATATATAAACTTATATATAACTTACATA
1 TTATATATAAACTTACATATAACTTACATA
53034171 CATAATACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (32 bp):
TTATATATAAACTTACATATAACTTACATAAG
Found at i:53034184 original size:20 final size:19
Alignment explanation
Indices: 53034159--53034240 Score: 57
Period size: 20 Copynumber: 4.4 Consensus size: 19
53034149 AAACTTATAT
53034159 ATAACTTACATACATAATAC
1 ATAACTTACATACA-AATAC
* *
53034179 ATAACTTAAAT-CAAACT-T
1 ATAACTTACATACAAA-TAC
*
53034197 ATAA-TAACATAC--ATAC
1 ATAACTTACATACAAATAC
* *
53034213 ATGACTTACATGCATAATAC
1 ATAACTTACATACA-AATAC
53034233 ATAACTTA
1 ATAACTTA
53034241 TATAAAATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 10 0.22
18 7 0.15
19 3 0.07
20 21 0.46
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.30
Consensus pattern (19 bp):
ATAACTTACATACAAATAC
Found at i:53037490 original size:21 final size:21
Alignment explanation
Indices: 53037466--53037514 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
53037456 GGCAGTAAGG
*
53037466 GAAGCAGAGGCTACAACAAGA
1 GAAGCAGAGGCCACAACAAGA
* *
53037487 GAAGCAGAGGCCGCAGCAAGA
1 GAAGCAGAGGCCACAACAAGA
53037508 GAAGCAG
1 GAAGCAG
53037515 CGATAGAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.35, T:0.02
Consensus pattern (21 bp):
GAAGCAGAGGCCACAACAAGA
Found at i:53037994 original size:43 final size:42
Alignment explanation
Indices: 53037947--53038038 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
53037937 ATCAAATAGT
*
53037947 GGCGTTTGTGAAATAAGCGCCGCTA-AAGAACACTACTTTTAGC
1 GGCGTTTGTG-AACAAGCGCCGCTACAA-AACACTACTTTTAGC
* * *
53037990 GGCGTTTTTGACCAAGCGCCGCTACAAAACATTACTTTTAGC
1 GGCGTTTGTGAACAAGCGCCGCTACAAAACACTACTTTTAGC
53038032 GGCGTTT
1 GGCGTTT
53038039 TATTTCTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 33 0.75
43 11 0.25
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (42 bp):
GGCGTTTGTGAACAAGCGCCGCTACAAAACACTACTTTTAGC
Found at i:53038154 original size:42 final size:42
Alignment explanation
Indices: 53037960--53038187 Score: 225
Period size: 43 Copynumber: 5.4 Consensus size: 42
53037950 GTTTGTGAAA
*
53037960 TAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTT-TTGAC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTATT-TC
* *
53038002 CAAGCGCCGCTACAA-AACATTA-CTTTTAGCGGCGTTTTATTTC
1 TAAGCGCCGCTA-AAGAACATGATC-TTTAGCGGCG-TTTATTTC
* *
53038045 TAAACGCCGCTAAATAACATGATCTTTAGCGGCGTTTATTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTATTT-C
* *
53038088 TTAGCGCTGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTATTTC
* * *
53038129 ATAAGCGCCACTAAAGAATAGGATCTTTAGCGGCGTTTATTTCC
1 -TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTATTT-C
* *
53038173 TTAGTGCCGCTAAAG
1 TAAGCGCCGCTAAAG
53038188 GCCTAAAAAA
Statistics
Matches: 159, Mismatches: 17, Indels: 19
0.82 0.09 0.10
Matches are distributed among these distances:
41 2 0.01
42 72 0.45
43 81 0.51
44 4 0.03
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTATTTC
Found at i:53038155 original size:85 final size:86
Alignment explanation
Indices: 53038004--53038187 Score: 241
Period size: 85 Copynumber: 2.2 Consensus size: 86
53037994 TTTTTGACCA
* * * *
53038004 AGCGCCGCTACAA-AACATTA-CTTTTAGCGGCGTTTTATTTCTAAACGCCGCTAAATAACATGA
1 AGCGCCGCTA-AAGAACATGATC-TTTAGCGGCGTTTTATTTCTAAACGCCACTAAAGAACAGGA
53038067 TCTTTAGCGGCGTTTATTTCCTT
64 TCTTTAGCGGCGTTTATTTCCTT
* * *
53038090 AGCGCTGCTAAAGAACATGATCTTTAGCGGCG-TTT-TTTCATAAGCGCCACTAAAGAATAGGAT
1 AGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTATTTC-TAAACGCCACTAAAGAACAGGAT
53038153 CTTTAGCGGCGTTTATTTCCTT
65 CTTTAGCGGCGTTTATTTCCTT
*
53038175 AGTGCCGCTAAAG
1 AGCGCCGCTAAAG
53038188 GCCTAAAAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
84 4 0.05
85 56 0.65
86 25 0.29
87 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (86 bp):
AGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTATTTCTAAACGCCACTAAAGAACAGGATC
TTTAGCGGCGTTTATTTCCTT
Found at i:53038604 original size:30 final size:30
Alignment explanation
Indices: 53038570--53038632 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
53038560 ACTTATTTTA
53038570 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
**
53038600 TTGTTAATTTTGTTATTATTTTGGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
53038630 TTG
1 TTG
53038633 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:53040770 original size:41 final size:41
Alignment explanation
Indices: 53040725--53040939 Score: 324
Period size: 41 Copynumber: 5.2 Consensus size: 41
53040715 ACTGGCACTT
*
53040725 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
* *
53040766 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCAGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
* * *
53040807 AGCCTGCTAGACTTAAAGTCTAAAATGTTTCATCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
53040848 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGA-CA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGC-ATCA
** * *
53040889 AGCCTGCTAGACTTAAAGTCTGAAACATATCACTGGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
53040930 AGCCTGCTAG
1 AGCCTGCTAG
53040940 GCACCGAGCC
Statistics
Matches: 159, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
40 1 0.01
41 158 0.99
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
Found at i:53041849 original size:2 final size:2
Alignment explanation
Indices: 53041842--53041871 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53041832 TCCAAATACA
*
53041842 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53041872 TAATTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53042613 original size:20 final size:22
Alignment explanation
Indices: 53042588--53042639 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
53042578 TATTATAACA
53042588 TAATAATATAT-TATACCTTAT
1 TAATAATATATATATACCTTAT
* **
53042609 T-ATAACATATATATATTTTAT
1 TAATAATATATATATACCTTAT
53042630 TAATAATATA
1 TAATAATATA
53042640 AGAAAACCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 8 0.32
21 10 0.40
22 7 0.28
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATATATATATACCTTAT
Found at i:53045093 original size:33 final size:33
Alignment explanation
Indices: 53045056--53045189 Score: 172
Period size: 33 Copynumber: 4.2 Consensus size: 33
53045046 CTGCTTTATT
*
53045056 TTTCTCTATTTTCTATTTCTGTACCATGTTTTG
1 TTTCTCTATTTTCTGTTTCTGTACCATGTTTTG
53045089 TTTCTCTATTTTCTGTTTCTGTACCATGTTTTG
1 TTTCTCTATTTTCTGTTTCTGTACCATGTTTTG
* * *
53045122 TTCCTCTATTTTCTGTAGT-GGT----T-TTTTG
1 TTTCTCTATTTTCTGT-TTCTGTACCATGTTTTG
53045150 TTTCTCTATTTTCTGTTTCTGTACCATGTTTTG
1 TTTCTCTATTTTCTGTTTCTGTACCATGTTTTG
*
53045183 TTCCTCT
1 TTTCTCT
53045190 TGCCATTTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
27 1 0.01
28 22 0.26
29 1 0.01
32 1 0.01
33 60 0.70
34 1 0.01
ACGTcount: A:0.09, C:0.19, G:0.12, T:0.60
Consensus pattern (33 bp):
TTTCTCTATTTTCTGTTTCTGTACCATGTTTTG
Found at i:53046287 original size:21 final size:22
Alignment explanation
Indices: 53046261--53046316 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
53046251 AGTTTCCCCC
53046261 GTTTGCAGTGGCTATACAA-TT
1 GTTTGCAGTGGCTATACAATTT
*
53046282 GTTTGCAGTGGCTATATAATTT
1 GTTTGCAGTGGCTATACAATTT
*
53046304 ATTTGCAGTGGCT
1 GTTTGCAGTGGCT
53046317 CCATCTGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.41
Consensus pattern (22 bp):
GTTTGCAGTGGCTATACAATTT
Found at i:53051385 original size:18 final size:17
Alignment explanation
Indices: 53051357--53051391 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53051347 ATTATTAAGA
*
53051357 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
53051374 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
53051392 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:53051463 original size:120 final size:120
Alignment explanation
Indices: 53051266--53051648 Score: 748
Period size: 120 Copynumber: 3.2 Consensus size: 120
53051256 TTTTCAAGTT
* *
53051266 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCGGCAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
53051331 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
53051386 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
53051451 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
53051506 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
53051571 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
53051626 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
53051649 TAAATATGAT
Statistics
Matches: 261, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 261 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
Found at i:53051505 original size:18 final size:17
Alignment explanation
Indices: 53051477--53051511 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53051467 ATTATTAAGA
*
53051477 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
53051494 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
53051512 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:53051625 original size:18 final size:17
Alignment explanation
Indices: 53051597--53051631 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53051587 ATTATTAAGA
*
53051597 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
53051614 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
53051632 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:53054947 original size:33 final size:33
Alignment explanation
Indices: 53054910--53054975 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
53054900 TTTACAGGGA
53054910 GATTGTTGAAGTATATGAAAATATTTGGAATCC
1 GATTGTTGAAGTATATGAAAATATTTGGAATCC
53054943 GATTGTTGAAGTATATGAAAATATTTGGAATCC
1 GATTGTTGAAGTATATGAAAATATTTGGAATCC
53054976 CCTTTGCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (33 bp):
GATTGTTGAAGTATATGAAAATATTTGGAATCC
Found at i:53057061 original size:21 final size:21
Alignment explanation
Indices: 53057036--53057079 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
53057026 CAAATATAAG
53057036 TATTGTAG-TAACCAAATCATT
1 TATTG-AGATAACCAAATCATT
53057057 TATTGAGTATAACCAAATCATT
1 TATTGAG-ATAACCAAATCATT
53057079 T
1 T
53057080 TCATATGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 2 0.10
21 5 0.24
22 14 0.67
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
TATTGAGATAACCAAATCATT
Found at i:53057484 original size:24 final size:23
Alignment explanation
Indices: 53057423--53057484 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
53057413 TATATATTCT
53057423 AATTAA-ATTTTATAAATAATTAA
1 AATTAATA-TTTATAAATAATTAA
* * *
53057446 TATTAATTACTTATAAATATTTAA
1 AATTAA-TATTTATAAATAATTAA
53057470 AATTAATATTATATA
1 AATTAATATT-TATA
53057485 TTAAAATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 8 0.26
24 22 0.71
25 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTAATATTTATAAATAATTAA
Found at i:53057685 original size:13 final size:13
Alignment explanation
Indices: 53057663--53057700 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
53057653 GCACTCAAAT
*
53057663 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
*
53057676 TTCTCTAAAGCAC
1 TTCTCAAAAGCAC
53057689 TTCTCAAAAGCA
1 TTCTCAAAAGCA
53057701 ATAAAGAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:53058715 original size:126 final size:125
Alignment explanation
Indices: 53058495--53059061 Score: 752
Period size: 126 Copynumber: 4.5 Consensus size: 125
53058485 GATAAAATCA
* * * * * * * * *
53058495 AAGCAGGATGATTTATCAAAAGGATTT-TTACAATCACGCCCACGTGTACGGGCTTTT-CTACAG
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGA-AATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* *
53058558 TAGGTCCTAGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
65 TAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* *
53058619 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGTCCTCGTGGATGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * * *
53058684 TGGTCTTGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
66 AGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * * * *
53058745 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATTGCGCCCACGTGGACGCGATTTTTCTATAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
*
53058810 AGGT-CTTGAACAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAACAACGCTGT-
66 AGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAA-AACGCT-TC
*
53058871 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCATGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * * *
53058935 TAGGTCCTGGAAAAATACTTTCGACTTGACGTTTCTGAACAAATAGTAT-AAAATCGCTTC
65 TAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* *
53058995 TAGCAGGATGCTTTATGAGAAGAATTTGTGAAATTGCGCCCAT-GTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCC-TCGTGGACGCGCTTTTGCTACAG
53059059 TAG
65 TAG
53059062 CATGTTTGGG
Statistics
Matches: 391, Mismatches: 42, Indels: 20
0.86 0.09 0.04
Matches are distributed among these distances:
123 3 0.01
124 107 0.27
125 64 0.16
126 209 0.53
127 8 0.02
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (125 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
Found at i:53058967 original size:251 final size:250
Alignment explanation
Indices: 53058531--53059061 Score: 793
Period size: 250 Copynumber: 2.1 Consensus size: 250
53058521 TTTACAATCA
* **
53058531 CGCCCACGTGTACG-GGCTTTTCTACAGTAGGTCCTAGAAAAATAATTTCGAGTTGACGTTTCTG
1 CGCCCACGTGGACGCGATTTTTCTACAGTAGGTCCTAGAAAAATAATTTCGAGTTGACGTTTCTG
* *
53058595 AGCAAATAGTTTAAAAAACGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGTCC
66 AGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCC
* * * * * * *
53058660 TCGTGGATGCGCTTTTGCTACAGTTGGTCTTGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCA
131 TCATGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAACA
*
53058725 AATAGTTTAAAAAACGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATTG
196 AATAGTAT-AAAAACGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATTG
* *
53058781 CGCCCACGTGGACGCGATTTTTCTATAGTAGGT-CTTGAACAAATAATTTCGAGTTGACGTTTCT
1 CGCCCACGTGGACGCGATTTTTCTACAGTAGGTCCTAGAA-AAATAATTTCGAGTTGACGTTTCT
53058845 GAGCAAATAGTATAAAACAACGCTGT-AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGC
65 GAGCAAATAGTATAAAA-AACGCT-TCAAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGC
*
53058908 GCCCTCATGGACGCGCTTTTGCTACAGTAGGTCCTGGAA-AAATACTTTCGACTTGACGTTTCTG
127 GCCCTCATGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTG
* *
53058972 AACAAATAGTATAAAATCGCTTCTAGCAGGATGCTTTATGAGAAGAATTTGTGAAATTG
192 AACAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATTG
* * *
53059031 CGCCCATGTGGACGCGCTTTTGCTACAGTAG
1 CGCCCACGTGGACGCGATTTTTCTACAGTAG
53059062 CATGTTTGGG
Statistics
Matches: 254, Mismatches: 22, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
250 90 0.35
251 87 0.34
252 74 0.29
253 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (250 bp):
CGCCCACGTGGACGCGATTTTTCTACAGTAGGTCCTAGAAAAATAATTTCGAGTTGACGTTTCTG
AGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCC
TCATGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAACA
AATAGTATAAAAACGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATTG
Found at i:53062248 original size:22 final size:22
Alignment explanation
Indices: 53062189--53062304 Score: 73
Period size: 21 Copynumber: 5.5 Consensus size: 22
53062179 TATATTTAAG
* * *
53062189 TTAAGGGTTAGGGTTTTTAAG-
1 TTAAGGGTTATGATTTTTTAGT
* * *
53062210 TTAAGTGTTAGGGTTTTTT-GT
1 TTAAGGGTTATGATTTTTTAGT
*
53062231 TTAAGGGTTATGATTTTTAAG-
1 TTAAGGGTTATGATTTTTTAGT
*
53062252 TTAAGGGTT-T-AGTGTTTTTAAT
1 TTAAGGGTTATGA-T-TTTTTAGT
* **
53062274 TTAAGGGTTACGATTTTAAAG-
1 TTAAGGGTTATGATTTTTTAGT
53062295 TTAAGGGTTA
1 TTAAGGGTTA
53062305 AGGTTTTTAA
Statistics
Matches: 76, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
19 1 0.01
20 3 0.04
21 56 0.74
22 14 0.18
23 1 0.01
24 1 0.01
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.47
Consensus pattern (22 bp):
TTAAGGGTTATGATTTTTTAGT
Found at i:53062283 original size:43 final size:43
Alignment explanation
Indices: 53062183--53062821 Score: 626
Period size: 43 Copynumber: 15.0 Consensus size: 43
53062173 TCAAATTATA
* *
53062183 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGTG-TTAGGGTT
1 TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
** * * *
53062225 TTTTGTTTAAGGGTTATGATTTTTAAGTTAAGGGTTTAGTGTT
1 TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
53062268 TTTAATTTAAGGGTTACGATTTTAAAGTTAAGGG-TTAAGGTT
1 TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
53062310 TTTAAGTTAAGTGTTTAGGGTTTTTAATTTAAAGGTTTAGGG--
1 TTTAATTTAAG-GGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
53062352 -----TTTAAGGGTTTAAGGTTTTGAAGTTAAGGGTTTA-GTTT
1 TTTAATTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
53062390 TTTTAGTTAAGTGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
53062433 TTTAATTTAAAGGTTTAGGGTTTTTAAGTTAAGGGGTTAGGGGT
1 TTTAATTT-AAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
53062477 TTTAAGTTAAGGGTTTAGGG-TTTTAATTTTAAGGG-TTACGGTT
1 TTTAATTTAAGGG-TTAGGGTTTTTAA-GTTAAGGGTTTAGGGTT
* * * **
53062520 TTTAAGTTAAGGGTTTAAGGTTTTAAAGTTAAATG-TTAGGGTT
1 TTTAATTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
** * * *
53062563 TTTAAGCTAAGGGTTTAGTGTTTTTAATTTAAGGGTTTAGAGTT
1 TTTAATTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
53062607 TTTAATTTAAGAGTTTAGAGTTTTTAAGTTAAGGGTTTATGGTT
1 TTTAATTTAAG-GGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
*
53062651 TTTAATTTAAGGGTTTAAGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAATTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
53062695 TTT-ATGTTAAGGGTTTAGGGTTTTTAAGTTAAAGG-TTAGGATT
1 TTTAAT-TTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
** * *
53062738 TTTAGGTTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTATGGTT
1 TTTAATTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
*
53062782 TTTAATTTAAGGGTTAAGGTTTTTAAGTTAAGGG-TTAGGG
1 TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG
53062822 CTAGGGTTTT
Statistics
Matches: 493, Mismatches: 82, Indels: 44
0.80 0.13 0.07
Matches are distributed among these distances:
36 2 0.00
37 26 0.05
42 72 0.15
43 204 0.41
44 188 0.38
45 1 0.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (43 bp):
TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
Found at i:53062331 original size:22 final size:22
Alignment explanation
Indices: 53062183--53062852 Score: 626
Period size: 22 Copynumber: 30.0 Consensus size: 22
53062173 TCAAATTATA
53062183 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
53062204 TTTAAGTTAAGTG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
53062225 TTT-TGTTTAAGGG-TTATGATT
1 TTTAAG-TTAAGGGTTTAGGGTT
*
53062246 TTTAAGTTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
53062268 TTTAATTTAAGGG-TTACGATT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
53062289 TTAAAGTTAAGGG-TTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
53062310 TTTAAGTTAAGTGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
53062332 TTTAATTTAAAGGTTTAGGGTTT
1 TTTAAGTTAAGGGTTTAGGG-TT
** * *
53062355 AAGGGTTTAAGGTTTTGAAGTTAAGGGTT
1 -----TTTAA-GTTAAG-GGTTTAGGGTT
* *
53062384 TAGTTTTTTTAGTTAAGTG-TTAGGGTT
1 T------TTAAGTTAAGGGTTTAGGGTT
53062411 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
53062433 TTTAATTTAAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
53062455 TTTAAGTTAAGGGGTTAGGGGT
1 TTTAAGTTAAGGGTTTAGGGTT
53062477 TTTAAGTTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
* *
53062498 TTTAATTTTAAGGG-TTACGGTT
1 TTTAA-GTTAAGGGTTTAGGGTT
*
53062520 TTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* **
53062542 TTAAAGTTAAATG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
53062563 TTTAAGCTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
53062585 TTTAATTTAAGGGTTTAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
53062607 TTTAATTTAAGAGTTTAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
53062629 TTTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
53062651 TTTAATTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
53062673 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
53062695 TTTATGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
53062717 TTTAAGTTAAAGG-TTAGGATT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
53062738 TTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
53062760 TTTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
53062782 TTTAATTTAAGGG-TTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
53062803 TTTAAGTTAAGGGTTAGGGCTAGGGTT
1 TTTAAGTTAAGGGTT-----TAGGGTT
* *
53062830 TTTAGGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
53062852 T
1 T
53062853 GTCAATTAAA
Statistics
Matches: 536, Mismatches: 83, Indels: 59
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.00
21 159 0.30
22 321 0.60
23 2 0.00
24 1 0.00
27 28 0.05
28 6 0.01
29 8 0.01
30 10 0.02
ACGTcount: A:0.25, C:0.01, G:0.28, T:0.47
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:53062520 original size:65 final size:64
Alignment explanation
Indices: 53062183--53062821 Score: 594
Period size: 65 Copynumber: 10.0 Consensus size: 64
53062173 TCAAATTATA
* * *
53062183 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAA-GTGTTAGGGTTTTT-TGTTTAAGGG-TTATGA
1 TTTAAGTTAAGGGTTTA-GGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAG-TTAAGGGTTTA-GG
*
53062244 TT
63 GT
* * * * * *
53062246 TTTAAGTTAAGGGTTTAGTGTTTTTAATTTAA-GGGTTACGATTTTAAAGTTAAGGGTTAAGGTT
1 TTTAAGTTAAGGGTTTAG-GTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGT
* * * * *
53062310 TTTAAGTTAAGTGTTTAGGGTTTTTAATTTAAAGGTTTAGGG----T---TTAAGGGTTTAAGGT
1 TTTAAGTTAAGGGTTTA-GGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGT
* * *
53062368 TTTGAAGTTAAGGGTTTAGTTTTTTTAGTTAA-GTGTTAGGGTTTTTAAGTTAAGGGTTTAGGGT
1 TTT-AAGTTAAGGGTTTAGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG-
53062432 T
64 T
* * *
53062433 TTTAATTTAAAGGTTTAGGGTTTTTAAGTTAAGGGGTTAGGGGTTTTAAGTTAAGGGTTTAGGGT
1 TTTAAGTTAAGGGTTTA-GGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGT
* * * * **
53062498 TTTAATTTTAAGGG-TTACGGTTTTTAAGTTAAGGGTTTAAGGTTTTAAAGTTAAATG-TTAGGG
1 TTTAA-GTTAAGGGTTTA-GGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG
53062561 TT
64 -T
* * * * * * *
53062563 TTTAAGCTAAGGGTTTAGTGTTTTTAATTTAAGGGTTTAGAGTTTTTAATTTAAGAGTTTAGAGT
1 TTTAAGTTAAGGGTTTAG-GTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAG-GG
53062628 T
64 T
* * *
53062629 TTTAAGTTAAGGGTTTATGGTTTTTAATTTAAGGGTTTAAGGTTTTTAAGTTAAGGGTTTAGGGT
1 TTTAAGTTAAGGGTTTA-GGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG-
53062694 T
64 T
* * * * *
53062695 TTTATGTTAAGGGTTTAGGGTTTTTAAGTTAA-AGGTTAGGATTTTTAGGTTAAGGGTTTATGGT
1 TTTAAGTTAAGGGTTTA-GGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTA-GGG
53062759 T
64 T
* *
53062760 TTTAAGTTAAGGGTTTATGGTTTTTAATTTAA-GGGTTAAGGTTTTTAAGTTAAGGG-TTAGGG
1 TTTAAGTTAAGGGTTTA-GGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG
53062822 CTAGGGTTTT
Statistics
Matches: 480, Mismatches: 70, Indels: 52
0.80 0.12 0.09
Matches are distributed among these distances:
57 7 0.01
58 26 0.05
59 13 0.03
61 1 0.00
63 16 0.03
64 105 0.22
65 182 0.38
66 128 0.27
67 2 0.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (64 bp):
TTTAAGTTAAGGGTTTAGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGT
Found at i:53064298 original size:20 final size:20
Alignment explanation
Indices: 53064261--53064298 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53064251 TTTATTTTTA
*
53064261 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
53064281 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
53064299 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:53065338 original size:20 final size:20
Alignment explanation
Indices: 53065300--53065338 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
53065290 CTTTTATTTT
*
53065300 TAAAATCTACATAATAATTG
1 TAAAATCTACATAAAAATTG
53065320 TAAAATCTA-ATATAAAATT
1 TAAAATCTACATA-AAAATT
53065339 TACCTCGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAAATCTACATAAAAATTG
Found at i:53066330 original size:11 final size:11
Alignment explanation
Indices: 53066294--53066353 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
53066284 GAGAAATTTA
*
53066294 AGAGGAACTTG
1 AGAGGAAATTG
* * *
53066305 GGAGCAAATTC
1 AGAGGAAATTG
53066316 AGAGGAAATTG
1 AGAGGAAATTG
*
53066327 AGAGGAAATTA
1 AGAGGAAATTG
53066338 AGAGGAAATTTG
1 AGAGGAAA-TTG
53066350 AGAG
1 AGAG
53066354 AGGATTAGTT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
11 33 0.85
12 6 0.15
ACGTcount: A:0.43, C:0.05, G:0.33, T:0.18
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:53066360 original size:23 final size:22
Alignment explanation
Indices: 53066286--53066353 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
53066276 TGATTTAAGA
* *
53066286 GAAATTTAAGAGGAACTTGGGAG
1 GAAA-TTAAGAGGAAATTGAGAG
* *
53066309 CAAATTCAGAGGAAATTGAGAG
1 GAAATTAAGAGGAAATTGAGAG
53066331 GAAATTAAGAGGAAATTTGAGAG
1 GAAATTAAGAGGAAA-TTGAGAG
53066354 AGGATTAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 28 0.74
23 10 0.26
ACGTcount: A:0.44, C:0.04, G:0.31, T:0.21
Consensus pattern (22 bp):
GAAATTAAGAGGAAATTGAGAG
Found at i:53066592 original size:40 final size:40
Alignment explanation
Indices: 53066531--53066607 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
53066521 GACGTGGACA
* * * *
53066531 CAAACCGCGCTTACGTGGACACGATTTGCTGCCACGTTAG
1 CAAACCGCGCTGACATAGACACGATTTGCTGACACGTTAG
53066571 CAAACCGCGCTGACATAGACACGATTTGCTGACACGT
1 CAAACCGCGCTGACATAGACACGATTTGCTGACACGT
53066608 CCCCTGACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (40 bp):
CAAACCGCGCTGACATAGACACGATTTGCTGACACGTTAG
Found at i:53067608 original size:93 final size:94
Alignment explanation
Indices: 53067481--53068594 Score: 934
Period size: 93 Copynumber: 12.0 Consensus size: 94
53067471 TCTACCCAGT
* * * *
53067481 TTGGACAGC-TCTTATACATCAGAAATT-GAGCAGCATGTATATACCAATTTGGACAGCACTTAT
1 TTGGACAGCAT-TTATTCA-CA-AAATTGGA-CAGCATGTATATACAAAATTGGACAGCATTTAT
* * * *
53067544 ACA-CAAAATTTGACAACATTTATATA-CAAAA
62 ACACCAAAATTGGACAGCATATATGTAGCAAAA
* * * * * *
53067575 GTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTAGC-AATTTGGACAGCAGTTATAC
1 TTGGACAGCATTTATTCA-CAAAATTGGACAGCATGTATATA-CAAAATTGGACAGCATTTATAC
* *
53067639 A-CAAAATTGGACAGCATGTATATA-CAAAA
64 ACCAAAATTGGACAGCATATATGTAGCAAAA
* * * * * *
53067668 TTGGACAACATTTATTCCCCAAAATTGGGCAGCATATA-AGTAGC-AATTTGGACAGCACTTATA
1 TTGGACAGCATTTATT-CACAAAATTGGACAGCATGTATA-TA-CAAAATTGGACAGCATTTATA
* *
53067731 CA-CAAAATTGGACAGCATTTAT-TCACCAAAA
63 CACCAAAATTGGACAGCATATATGT-AGCAAAA
* * * * *
53067762 TTGGGCAGCATATATGT-AGC-AATTTGGACAGCACT-TATACACAAAATTGG--A-CATGTATA
1 TTGGACAGCATTTAT-TCA-CAAAATTGGACAGCA-TGTATATACAAAATTGGACAGCATTTATA
* * *
53067821 TA-CAAAATTGGACAGCATTTAT-TCACCAAAA
63 CACCAAAATTGGACAGCATATATGT-AGCAAAA
* ** * * *
53067852 TTGCG-CAGCATATATGTGGC-AATTTGGACAGCACT-TATACACAAAATTGGACAGCATGTATA
1 TTG-GACAGCATTTAT-TCACAAAATTGGACAGCA-TGTATATACAAAATTGGACAGCATTTATA
* * *
53067914 TA-CAAAATTGGACAGCATTTAT-TCACCAAAA
63 CACCAAAATTGGACAGCATATATGT-AGCAAAA
* * * * *
53067945 TTGGGCAGCATATATGT-AGC-AATTTGGACAGCACT-TATACACAAAATTGGACAGCATGTATA
1 TTGGACAGCATTTAT-TCA-CAAAATTGGACAGCA-TGTATATACAAAATTGGACAGCATTTATA
* * * *
53068007 TA-CAAAATTGGACAACATTTAT-TCACCAAAA
63 CACCAAAATTGGACAGCATATATGT-AGCAAAA
* * * * *
53068038 TTGGGCAGCATATATGT-AGC-AATTTGGACAGCACT-TATACACAAAATTGGACAGCATTTATT
1 TTGGACAGCATTTAT-TCA-CAAAATTGGACAGCA-TGTATATACAAAATTGGACAGCATTTATA
* *
53068100 CACCAAAATTGGGCAGCATATATGTAGC-AAT
63 CACCAAAATTGGACAGCATATATGTAGCAAAA
* * * * * *
53068131 TTGGACAGCACTTATTGACAAAATTTGACAGCATGTATATACAAAATTGGACAACATTCATTCAC
1 TTGGACAGCATTTATTCACAAAATTGGACAGCATGTATATACAAAATTGGACAGCATTTATACAC
* *
53068196 CAAAATTGGGCAGCATATATGTAGC-AAT
66 CAAAATTGGACAGCATATATGTAGCAAAA
* * *
53068224 TTGGACAGCACTTATACACAAAATTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCAC
1 TTGGACAGCATTTATTCACAAAATTGGACAGCATGTATATACAAAATTGGACAGCATTTATACAC
* *
53068289 CAAAATTGGGCAGCATATATGTAGC-AAT
66 CAAAATTGGACAGCATATATGTAGCAAAA
* * * * *
53068317 TTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGACAACATTTATTCAC
1 TTGGACAGCATTTATTCACAAAATTGGACAGCATGTATATACAAAATTGGACAGCATTTATACAC
* *
53068382 CAAAATTGGGCAGCATATATGTAGC-AAT
66 CAAAATTGGACAGCATATATGTAGCAAAA
* * * * *
53068410 TTGGACAGCACTTATACACAAAATTTGACAGCATGTATAAACAAAATTGGACAGCATTTATTCAC
1 TTGGACAGCATTTATTCACAAAATTGGACAGCATGTATATACAAAATTGGACAGCATTTATACAC
* *
53068475 CAAAATTGGGCAGCATATATGTAGC-AAT
66 CAAAATTGGACAGCATATATGTAGCAAAA
* * * * *
53068503 TTGGACAGCACTTATACAAAAAATTGGACAGCATGTATATACAAAATTGGATAGCATTTATTCAC
1 TTGGACAGCATTTATTCACAAAATTGGACAGCATGTATATACAAAATTGGACAGCATTTATACAC
*
53068568 CAAAATTGGGCAGCATATATGTAGCAA
66 CAAAATTGGACAGCATATATGTAGCAA
53068595 TTTTTGACCA
Statistics
Matches: 936, Mismatches: 59, Indels: 50
0.90 0.06 0.05
Matches are distributed among these distances:
90 82 0.09
91 2 0.00
92 7 0.01
93 783 0.84
94 59 0.06
95 3 0.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (94 bp):
TTGGACAGCATTTATTCACAAAATTGGACAGCATGTATATACAAAATTGGACAGCATTTATACAC
CAAAATTGGACAGCATATATGTAGCAAAA
Found at i:53067650 original size:70 final size:69
Alignment explanation
Indices: 53067529--53068583 Score: 735
Period size: 70 Copynumber: 15.2 Consensus size: 69
53067519 ATATACCAAT
* * * *
53067529 TTGGACAGCACTTA-TACACAAAATTTGACAACATTTATATA-CAAAAGTGGACAGCATTTATTC
1 TTGGACAGCATTTATTAC-CAAAATTGGACAGCA-TTATATAGCAAAATTGGACAGCATTTATTC
53067592 ACCAAAA
64 A-CAAAA
* * * * * *
53067599 TTGGGCAGCATATATGTAGC-AATTTGGACAGCAGTTATACA-CAAAATTGGACAGCATGTATAT
1 TTGGACAGCATTTAT-TACCAAAATTGGACAGCA-TTATATAGCAAAATTGGACAGCATTTAT-T
53067662 -ACAAAA
63 CACAAAA
* * * * * *
53067668 TTGGACAACATTTATTCCCCAAAATTGGGCAGCA-TATAAGTAGC-AATTTGGACAGCACTTATA
1 TTGGACAGCATTTATT-ACCAAAATTGGACAGCATTAT-A-TAGCAAAATTGGACAGCATTTATT
53067731 CACAAAA
63 CACAAAA
* * * * *
53067738 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTAGC-AATTTGGACAGCACTTATAC
1 TTGGACAGCATTTATT-ACCAAAATTGGACAGCAT-TATATAGCAAAATTGGACAGCATTTATTC
53067802 ACAAAA
64 ACAAAA
* * *
53067808 TTGG--A-CATGTATATA-CAAAATTGGACAGCATT-TATTCACCAAAATTGCG-CAGCATATAT
1 TTGGACAGCATTTAT-TACCAAAATTGGACAGCATTATA-T-AGCAAAATTG-GACAGCATTTAT
** *
53067867 GTGGC-AAT
62 -TCACAAAA
*
53067875 TTGGACAGCACTTA-TACACAAAATTGGACAGCATGTATATA-CAAAATTGGACAGCATTTATTC
1 TTGGACAGCATTTATTAC-CAAAATTGGACAGCAT-TATATAGCAAAATTGGACAGCATTTATTC
53067938 ACCAAAA
64 A-CAAAA
* * * * * *
53067945 TTGGGCAGCATATATGTAGC-AATTTGGACAGCACTTATACA-CAAAATTGGACAGCATGTATAT
1 TTGGACAGCATTTAT-TACCAAAATTGGACAGCA-TTATATAGCAAAATTGGACAGCATTTAT-T
53068008 -ACAAAA
63 CACAAAA
* * * * * *
53068014 TTGGACAACATTTATTCACCAAAATTGGGCAGCATATATGTAGC-AATTTGGACAGCACTTATAC
1 TTGGACAGCATTTATT-ACCAAAATTGGACAGCAT-TATATAGCAAAATTGGACAGCATTTATTC
53068078 ACAAAA
64 ACAAAA
* * * * *
53068084 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTAGC-AATTTGGACAGCACTTATTG
1 TTGGACAGCATTTATT-ACCAAAATTGGACAGCAT-TATATAGCAAAATTGGACAGCATTTATTC
53068148 ACAAAA
64 ACAAAA
* * * * * *
53068154 TTTGACAGCATGTATATA-CAAAATTGGACAACATTCAT-TCACCAAAATTGGGCAGCATATATG
1 TTGGACAGCATTTAT-TACCAAAATTGGACAGCATT-ATAT-AGCAAAATTGGACAGCATTTAT-
*
53068217 T-AGC-AAT
62 TCA-CAAAA
*
53068224 TTGGACAGCACTTA-TACACAAAATTGGACAGCATGTATATA-CAAAATTGGACAGCATTTATTC
1 TTGGACAGCATTTATTAC-CAAAATTGGACAGCAT-TATATAGCAAAATTGGACAGCATTTATTC
53068287 ACCAAAA
64 A-CAAAA
* * * * * * *
53068294 TTGGGCAGCATATATGTAGC-AATTTGGACAGCACTTATACA-CAAAATTTGACAGCATGTATAT
1 TTGGACAGCATTTAT-TACCAAAATTGGACAGCA-TTATATAGCAAAATTGGACAGCATTTAT-T
53068357 -ACAAAA
63 CACAAAA
* * * * * *
53068363 TTGGACAACATTTATTCACCAAAATTGGGCAGCATATATGTAGC-AATTTGGACAGCACTTATAC
1 TTGGACAGCATTTATT-ACCAAAATTGGACAGCAT-TATATAGCAAAATTGGACAGCATTTATTC
53068427 ACAAAA
64 ACAAAA
* * * * * * *
53068433 TTTGACAGCATGTATAAACAAAATTGGACAGCATT-TATTCACCAAAATTGGGCAGCATATATGT
1 TTGGACAGCATTTATTACCAAAATTGGACAGCATTATA-T-AGCAAAATTGGACAGCATTTAT-T
*
53068497 -AGC-AAT
63 CA-CAAAA
* * *
53068503 TTGGACAGCACTTA-TACAAAAAATTGGACAGCATGTATATA-CAAAATTGGATAGCATTTATTC
1 TTGGACAGCATTTATTAC-CAAAATTGGACAGCAT-TATATAGCAAAATTGGACAGCATTTATTC
53068566 ACCAAAA
64 A-CAAAA
*
53068573 TTGGGCAGCAT
1 TTGGACAGCAT
53068584 ATATGTAGCA
Statistics
Matches: 787, Mismatches: 131, Indels: 134
0.75 0.12 0.13
Matches are distributed among these distances:
64 1 0.00
65 2 0.00
66 17 0.02
67 27 0.03
68 22 0.03
69 154 0.20
70 530 0.67
71 21 0.03
72 13 0.02
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.27
Consensus pattern (69 bp):
TTGGACAGCATTTATTACCAAAATTGGACAGCATTATATAGCAAAATTGGACAGCATTTATTCAC
AAAA
Found at i:53067825 original size:20 final size:20
Alignment explanation
Indices: 53067797--53067834 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53067787 GGACAGCACT
53067797 TATACACAAAATTGGACATG
1 TATACACAAAATTGGACATG
*
53067817 TATATACAAAATTGGACA
1 TATACACAAAATTGGACA
53067835 GCATTTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (20 bp):
TATACACAAAATTGGACATG
Found at i:53068068 original size:163 final size:163
Alignment explanation
Indices: 53067898--53068280 Score: 664
Period size: 163 Copynumber: 2.4 Consensus size: 163
53067888 ATACACAAAA
*
53067898 TTGGACAGCA-TGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGT
1 TTGGACAGCACT-TATACACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGT
*
53067962 AGCAATTTGGACAGCACTTATACACAAAATTGGACAGCATGTATATACAAAATTGGACAACATTT
65 AGCAATTTGGACAGCACTTATACACAAAATTGGACAGCATGTATATACAAAATTGGACAACATTC
53068027 ATTCACCAAAATTGGGCAGCATATATGTAGCAAT
130 ATTCACCAAAATTGGGCAGCATATATGTAGCAAT
53068061 TTGGACAGCACTTATACACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
1 TTGGACAGCACTTATACACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
** *
53068126 GCAATTTGGACAGCACTTATTGACAAAATTTGACAGCATGTATATACAAAATTGGACAACATTCA
66 GCAATTTGGACAGCACTTATACACAAAATTGGACAGCATGTATATACAAAATTGGACAACATTCA
53068191 TTCACCAAAATTGGGCAGCATATATGTAGCAAT
131 TTCACCAAAATTGGGCAGCATATATGTAGCAAT
* *
53068224 TTGGACAGCACTTATACACAAAATTGGACAGCATGTATAT-A-CAAAATTGGACAGCAT
1 TTGGACAGCACTTATACACAAAATTGGACAGCATTTAT-TCACCAAAATTGGGCAGCAT
53068281 TTATTCACCA
Statistics
Matches: 211, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
162 15 0.07
163 194 0.92
164 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (163 bp):
TTGGACAGCACTTATACACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
GCAATTTGGACAGCACTTATACACAAAATTGGACAGCATGTATATACAAAATTGGACAACATTCA
TTCACCAAAATTGGGCAGCATATATGTAGCAAT
Found at i:53068326 original size:163 final size:163
Alignment explanation
Indices: 53067898--53068346 Score: 630
Period size: 163 Copynumber: 2.8 Consensus size: 163
53067888 ATACACAAAA
*
53067898 TTGGACAGCA-TGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGT
1 TTGGACAGCACT-TATACACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGT
* *
53067962 AGCAATTTGGACAGCACTTA-TACACAAAATTGGACAGCATGTATATACAAAATTGGACAACATT
65 AGCAATTTGGACAGCACTTATTA-GCAAATTTGGACAGCATGTATATACAAAATTGGACAACATT
*
53068026 TATTCACCAAAATTGGGCAGCATATATGTAGCAAT
129 CATTCACCAAAATTGGGCAGCATATATGTAGCAAT
53068061 TTGGACAGCACTTATACACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
1 TTGGACAGCACTTATACACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
53068126 GCAATTTGGACAGCACTTATT-GACAAAATTT-GACAGCATGTATATACAAAATTGGACAACATT
66 GCAATTTGGACAGCACTTATTAG-C-AAATTTGGACAGCATGTATATACAAAATTGGACAACATT
53068189 CATTCACCAAAATTGGGCAGCATATATGTAGCAAT
129 CATTCACCAAAATTGGGCAGCATATATGTAGCAAT
* * *
53068224 TTGGACAGCACTTATACACAAAATTGGACAGCATGTATAT-A-CAAAATTGGACAGCATTTAT-T
1 TTGGACAGCACTTATACACAAAATTGGACAGCATTTAT-TCACCAAAATTGGGCAGCATATATGT
* * * * *
53068286 CACCAAAATTGGGCAGCA-TATATGTAGC-AATTTGGACAGCACT-TATACACAAAATTTGACA
65 -AGC-AATTTGGACAGCACT-TAT-TAGCAAATTTGGACAGCA-TGTATATACAAAATTGGACA
53068347 GCATGTATAT
Statistics
Matches: 262, Mismatches: 12, Indels: 24
0.88 0.04 0.08
Matches are distributed among these distances:
161 1 0.00
162 26 0.10
163 223 0.85
164 11 0.04
165 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (163 bp):
TTGGACAGCACTTATACACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
GCAATTTGGACAGCACTTATTAGCAAATTTGGACAGCATGTATATACAAAATTGGACAACATTCA
TTCACCAAAATTGGGCAGCATATATGTAGCAAT
Found at i:53068595 original size:93 final size:93
Alignment explanation
Indices: 53068061--53068597 Score: 950
Period size: 93 Copynumber: 5.8 Consensus size: 93
53068051 ATGTAGCAAT
*
53068061 TTGGACAGCACT-TATACACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGT
1 TTGGACAGCA-TGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGT
**
53068125 AGCAATTTGGACAGCACTTATTGACAAAA
65 AGCAATTTGGACAGCACTTATACACAAAA
* * *
53068154 TTTGACAGCATGTATATACAAAATTGGACAACATTCATTCACCAAAATTGGGCAGCATATATGTA
1 TTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
53068219 GCAATTTGGACAGCACTTATACACAAAA
66 GCAATTTGGACAGCACTTATACACAAAA
53068247 TTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
1 TTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
53068312 GCAATTTGGACAGCACTTATACACAAAA
66 GCAATTTGGACAGCACTTATACACAAAA
* *
53068340 TTTGACAGCATGTATATACAAAATTGGACAACATTTATTCACCAAAATTGGGCAGCATATATGTA
1 TTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
53068405 GCAATTTGGACAGCACTTATACACAAAA
66 GCAATTTGGACAGCACTTATACACAAAA
* *
53068433 TTTGACAGCATGTATAAACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
1 TTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
*
53068498 GCAATTTGGACAGCACTTATACAAAAAA
66 GCAATTTGGACAGCACTTATACACAAAA
*
53068526 TTGGACAGCATGTATATACAAAATTGGATAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
1 TTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
53068591 GCAATTT
66 GCAATTT
53068598 TTGACCATTA
Statistics
Matches: 426, Mismatches: 17, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
92 1 0.00
93 425 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (93 bp):
TTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTA
GCAATTTGGACAGCACTTATACACAAAA
Found at i:53069347 original size:28 final size:28
Alignment explanation
Indices: 53069288--53069385 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
53069278 TTTAATAAGT
* * * *
53069288 TCGCACACTTAGTG-TTCAATAATCAAAT
1 TCGCACACTTAGTGCTT-TACAATTAAAC
* *
53069316 TCGCACACTTAGTGCTTTGCCATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
53069344 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
53069372 TCGCACACTTAGTG
1 TCGCACACTTAGTG
53069386 TCGAAAGTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
28 59 0.97
29 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTTACAATTAAAC
Found at i:53075755 original size:20 final size:20
Alignment explanation
Indices: 53075727--53075764 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53075717 GGACAGCACT
53075727 TATACACAAAATTGGACATG
1 TATACACAAAATTGGACATG
*
53075747 TATATACAAAATTGGACA
1 TATACACAAAATTGGACA
53075765 GCATTTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (20 bp):
TATACACAAAATTGGACATG
Found at i:53075876 original size:93 final size:93
Alignment explanation
Indices: 53075667--53076024 Score: 589
Period size: 93 Copynumber: 3.9 Consensus size: 93
53075657 TCTACCCAGT
* * * * * *
53075667 TTGGACAGC-TCTTATACATCAGAAATTGAGCAGCATGTATATACCAATTTGGACAGCACTTATA
1 TTGGACAGCAT-TTATTCACCA-AAATTGGGCAGCATATATGTAGCAATTTGGACAGCACTTATA
53075731 CACAAAATTGG--A-CATGTATATACAAAA
64 CACAAAATTGGACAGCATGTATATACAAAA
* *
53075758 TTGGACAGCATTTATTCACCAAAATTGCGCAGCATATATGTGGCAATTTGGACAGCACTTATACA
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTAGCAATTTGGACAGCACTTATACA
53075823 CAAAATTGGACAGCATGTATATACAAAA
66 CAAAATTGGACAGCATGTATATACAAAA
53075851 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTAGCAATTTGGACAGCACTTATACA
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTAGCAATTTGGACAGCACTTATACA
53075916 CAAAATTGGACAGCATGTATATACAAAA
66 CAAAATTGGACAGCATGTATATACAAAA
*
53075944 TTGGACAACATTTATTCACCAAAATTGGGCAGCATATATGTAGCAATTTGGACAGCACTTATACA
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTAGCAATTTGGACAGCACTTATACA
53076009 CAAAATTGGACAGCAT
66 CAAAATTGGACAGCAT
53076025 TTATTCACCA
Statistics
Matches: 253, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
90 48 0.19
91 17 0.07
92 2 0.01
93 186 0.74
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (93 bp):
TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTAGCAATTTGGACAGCACTTATACA
CAAAATTGGACAGCATGTATATACAAAA
Found at i:53075931 original size:163 final size:163
Alignment explanation
Indices: 53075805--53076187 Score: 592
Period size: 163 Copynumber: 2.3 Consensus size: 163
53075795 ATGTGGCAAT
*
53075805 TTGGACAGCACT-TATACA-CAAAATTGGACAGCA-TGTATATACAAAATTGGACAGCATTTATT
1 TTGGACAGCA-TATATACAGC-AAATTGGACAGCACT-TATACACAAAATTGGACAGCATTTATT
*
53075867 CACCAAAATTGGGCAGCATATATGTAGCAATTTGGACAGCACTTATACACAAAATTGGACAGCAT
63 CACCAAAATAGGGCAGCATATATGTAGCAATTTGGACAGCACTTATACACAAAATTGGACAGCAT
*
53075932 GTATATACAAAATTGGACAACATTTATTCACCAAAA
128 GTATATACAAAATTGGACAACATATATTCACCAAAA
* ** *
53075968 TTGGGCAGCATATATGTAGCAATTTGGACAGCACTTATACACAAAATTGGACAGCATTTATTCAC
1 TTGGACAGCATATATACAGCAAATTGGACAGCACTTATACACAAAATTGGACAGCATTTATTCAC
53076033 CAAAATAGGGCAGCATATATGTAGCAATTTGGACAGCACTTATACACAAAATTGGACAGCATGTA
66 CAAAATAGGGCAGCATATATGTAGCAATTTGGACAGCACTTATACACAAAATTGGACAGCATGTA
* * *
53076098 TATACAAAATTGAACAGCATTTATTCACCAAAA
131 TATACAAAATTGGACAACATATATTCACCAAAA
* ** *
53076131 TTGGGCAGCATATATGTAGCAATTTGGACAGCACTTATACACAAAATTGGACAGCAT
1 TTGGACAGCATATATACAGCAAATTGGACAGCACTTATACACAAAATTGGACAGCAT
53076188 GTATATACAA
Statistics
Matches: 209, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
162 1 0.00
163 206 0.99
164 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (163 bp):
TTGGACAGCATATATACAGCAAATTGGACAGCACTTATACACAAAATTGGACAGCATTTATTCAC
CAAAATAGGGCAGCATATATGTAGCAATTTGGACAGCACTTATACACAAAATTGGACAGCATGTA
TATACAAAATTGGACAACATATATTCACCAAAA
Found at i:53076070 original size:93 final size:92
Alignment explanation
Indices: 53075801--53076527 Score: 886
Period size: 93 Copynumber: 7.8 Consensus size: 92
53075791 ATATATGTGG
* * * *
53075801 CAATTTGGACAGCACT-TATACACAAAATTGGACAGCATGTATAT-A-CAAAATTGGACAGCATT
1 CAATTTGGACAGCA-TGTATATACAAAATTGGACAGCATTTAT-TCACCAAAATTGGGCAGCATA
* * * **
53075863 TAT-TCACCAAAATTGGGCAGCA-TATATGTA
64 TATGT-AGC-AATTTGGACAGCACT-TATACA
* * * *
53075893 GCAATTTGGACAGCACT-TATACACAAAATTGGACAGCATGTATAT-A-CAAAATTGGACAACAT
1 -CAATTTGGACAGCA-TGTATATACAAAATTGGACAGCATTTAT-TCACCAAAATTGGGCAGCAT
* * * * **
53075955 TTAT-TCACCAAAATTGGGCAGCA-TATATGTA
63 ATATGT-AGC-AATTTGGACAGCACT-TATACA
* *
53075986 GCAATTTGGACAGCACT-TATACACAAAATTGGACAGCATTTATTCACCAAAATAGGGCAGCATA
1 -CAATTTGGACAGCA-TGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATA
53076050 TATGTAGCAATTTGGACAGCACTTATACA
64 TATGTAGCAATTTGGACAGCACTTATACA
* *
53076079 CAAAATTGGACAGCATGTATATACAAAATTGAACAGCATTTATTCACCAAAATTGGGCAGCATAT
1 C-AATTTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATAT
53076144 ATGTAGCAATTTGGACAGCACTTATACA
65 ATGTAGCAATTTGGACAGCACTTATACA
* * *
53076172 CAAAATTGGACAGCATGTATATACAAAATTTGACAGCATTTATTTACCAAAATTGGGCAGCATAT
1 C-AATTTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATAT
53076237 ATGTAGCAATTTGGACAGCACTTATACA
65 ATGTAGCAATTTGGACAGCACTTATACA
* *
53076265 CAAAATTT-GACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAATTTGGGCAACATA
1 C--AATTTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATA
53076329 TATGTAGCAATTTGGACAGCACTTATACA
64 TATGTAGCAATTTGGACAGCACTTATACA
53076358 CAAAATTT-GACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATA
1 C--AATTTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATA
*
53076422 TATTTAGCAATTTGGACAGCACTTATACAA
64 TATGTAGCAATTTGGACAGCACTTATAC-A
* * * *
53076452 AAAATTGGACAGCATGTATATACAAAATTGGATAGCATTTATTCACCAAAATTGGGTAGCATATA
1 CAATTTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATA
53076517 TGTAGCAATTT
66 TGTAGCAATTT
53076528 TTGACCATTA
Statistics
Matches: 594, Mismatches: 31, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
92 7 0.01
93 561 0.94
94 25 0.04
95 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (92 bp):
CAATTTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATA
TGTAGCAATTTGGACAGCACTTATACA
Found at i:53076214 original size:256 final size:256
Alignment explanation
Indices: 53075747--53076280 Score: 987
Period size: 256 Copynumber: 2.1 Consensus size: 256
53075737 ATTGGACATG
* * *
53075747 TATATACAAAATTGGACAGCATTTATTCACCAAAATTGCGCAGCATATATGTGGCAATTTGGACA
1 TATACACAAAATTGGACAGCATTTATTCACCAAAATAGCGCAGCATATATGTAGCAATTTGGACA
*
53075812 GCACTTATACACAAAATTGGACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATT
66 GCACTTATACACAAAATTGGACAGCATGTATATACAAAATTGAACAGCATTTATTCACCAAAATT
53075877 GGGCAGCATATATGTAGCAATTTGGACAGCACTTATACACAAAATTGGACAGCATGTATATACAA
131 GGGCAGCATATATGTAGCAATTTGGACAGCACTTATACACAAAATTGGACAGCATGTATATACAA
53075942 AATTGGACAACATTTATTCACCAAAATTGGGCAGCATATATGTAGCAATTTGGACAGCACT
196 AATTGGACAACATTTATTCACCAAAATTGGGCAGCATATATGTAGCAATTTGGACAGCACT
*
53076003 TATACACAAAATTGGACAGCATTTATTCACCAAAATAGGGCAGCATATATGTAGCAATTTGGACA
1 TATACACAAAATTGGACAGCATTTATTCACCAAAATAGCGCAGCATATATGTAGCAATTTGGACA
53076068 GCACTTATACACAAAATTGGACAGCATGTATATACAAAATTGAACAGCATTTATTCACCAAAATT
66 GCACTTATACACAAAATTGGACAGCATGTATATACAAAATTGAACAGCATTTATTCACCAAAATT
53076133 GGGCAGCATATATGTAGCAATTTGGACAGCACTTATACACAAAATTGGACAGCATGTATATACAA
131 GGGCAGCATATATGTAGCAATTTGGACAGCACTTATACACAAAATTGGACAGCATGTATATACAA
* * *
53076198 AATTTGACAGCATTTATTTACCAAAATTGGGCAGCATATATGTAGCAATTTGGACAGCACT
196 AATTGGACAACATTTATTCACCAAAATTGGGCAGCATATATGTAGCAATTTGGACAGCACT
*
53076259 TATACACAAAATTTGACAGCAT
1 TATACACAAAATTGGACAGCAT
53076281 GTATATACAA
Statistics
Matches: 269, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
256 269 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.27
Consensus pattern (256 bp):
TATACACAAAATTGGACAGCATTTATTCACCAAAATAGCGCAGCATATATGTAGCAATTTGGACA
GCACTTATACACAAAATTGGACAGCATGTATATACAAAATTGAACAGCATTTATTCACCAAAATT
GGGCAGCATATATGTAGCAATTTGGACAGCACTTATACACAAAATTGGACAGCATGTATATACAA
AATTGGACAACATTTATTCACCAAAATTGGGCAGCATATATGTAGCAATTTGGACAGCACT
Found at i:53077279 original size:28 final size:28
Alignment explanation
Indices: 53077220--53077345 Score: 164
Period size: 28 Copynumber: 4.5 Consensus size: 28
53077210 TTTAATAAGT
* * * *
53077220 TCGCACACTTAGTG-TTCAATAATCAAAG
1 TCGCACACTTAGTGCTT-TACAATTAAAC
* *
53077248 TCGCACACTTAGTGCTTTGCCATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
53077276 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
53077304 TCGCACACTTAGTGCTTTACAATTAAAT
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
53077332 TCGCACACGTAGTG
1 TCGCACACTTAGTG
53077346 TCGAAAGTCA
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
28 85 0.98
29 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTTACAATTAAAC
Found at i:53078749 original size:27 final size:27
Alignment explanation
Indices: 53078687--53078749 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
53078677 AAAAAAAAAA
* ** *
53078687 GCGGCACCAAAGGTGCCTTTCCCATAG
1 GCGGCACCGAAGGTGCCCCTCCCACAG
* *
53078714 GCAGCACCGATGGTGCCCCTCCCACAG
1 GCGGCACCGAAGGTGCCCCTCCCACAG
53078741 GCGGCACCG
1 GCGGCACCG
53078750 CCCATATAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.19, C:0.40, G:0.29, T:0.13
Consensus pattern (27 bp):
GCGGCACCGAAGGTGCCCCTCCCACAG
Found at i:53078831 original size:28 final size:28
Alignment explanation
Indices: 53078800--53079007 Score: 105
Period size: 30 Copynumber: 7.2 Consensus size: 28
53078790 GAAGGAGAGG
53078800 GAAAGAAGAAGAAAGAAAGAAAGAAAAA
1 GAAAGAAGAAGAAAGAAAGAAAGAAAAA
*
53078828 GAAAGAA-AAGGAAAGGAGAGAAAAGAAAGAA
1 GAAAGAAGAA-GAAA-GAAAG-AAAGAAA-AA
*
53078859 -AAAGAAGGAAAGGAGAGGAAAGAAAGAAAAA
1 GAAAGAA-G-AA-GA-AAGAAAGAAAGAAAAA
* *
53078890 GAAGGAAAGAA-AAGGAAAGGAGAAGAAGAAA
1 GAAAG-AAGAAGAAAGAAA-GA-AAGAA-AAA
* * *
53078921 -AAAGAAAGAA-AAAGCAGGAAAG-ATAA
1 GAAAG-AAGAAGAAAGAAAGAAAGAAAAA
*
53078947 GAAAGGAGAAG--AG-AA-AAA-AAAAA
1 GAAAGAAGAAGAAAGAAAGAAAGAAAAA
* *
53078970 GAAAGAAGAAGAAGAGGGAAGGAAGGAAAAA
1 GAAAGAAGAAGAA-A--GAAAGAAAGAAAAA
53079001 GAAAGAA
1 GAAAGAA
53079008 AGAAAAGGTA
Statistics
Matches: 141, Mismatches: 15, Indels: 45
0.70 0.07 0.22
Matches are distributed among these distances:
23 16 0.11
24 1 0.01
25 2 0.01
26 7 0.05
27 7 0.05
28 21 0.15
29 10 0.07
30 33 0.23
31 21 0.15
32 11 0.08
33 11 0.08
34 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.00
Consensus pattern (28 bp):
GAAAGAAGAAGAAAGAAAGAAAGAAAAA
Found at i:53078932 original size:10 final size:10
Alignment explanation
Indices: 53078800--53079008 Score: 79
Period size: 10 Copynumber: 19.8 Consensus size: 10
53078790 GAAGGAGAGG
*
53078800 GAAAGAAGAA
1 GAAAGAAAAA
53078810 GAAAG--AAA
1 GAAAGAAAAA
53078818 GAAAGAAAAA
1 GAAAGAAAAA
*
53078828 GAAAGAAAAG
1 GAAAGAAAAA
53078838 GAAAGGAGAGAAAA
1 G-AA--AGA-AAAA
53078852 GAAAGAAAAA
1 GAAAGAAAAA
*
53078862 GAAGGAAAGGAGA
1 GAAAGAAA--A-A
53078875 GGAAAG--AAA
1 -GAAAGAAAAA
*
53078884 GAAA-AAGAAG
1 GAAAGAA-AAA
*
53078894 GAAAGAAAAG
1 GAAAGAAAAA
* *
53078904 GAAAGGAGAA
1 GAAAGAAAAA
53078914 G-AAGAAAAAA
1 GAAAG-AAAAA
53078924 GAAAGAAAAA
1 GAAAGAAAAA
* *
53078934 GCAGGAAAGATAA
1 GAAAG-AA-A-AA
*
53078947 GAAAGGAGAAGA
1 GAAA-GA-AAAA
*
53078959 GAAAAAAAAAA
1 G-AAAGAAAAA
*
53078970 GAAAGAAGAA
1 GAAAGAAAAA
** *
53078980 GAAGAGGGAAG
1 GAA-AGAAAAA
*
53078991 GAAGGAAAAA
1 GAAAGAAAAA
53079001 GAAAGAAA
1 GAAAGAAA
53079009 GAAAAGGTAA
Statistics
Matches: 147, Mismatches: 29, Indels: 46
0.66 0.13 0.21
Matches are distributed among these distances:
8 11 0.07
9 4 0.03
10 79 0.54
11 22 0.15
12 6 0.04
13 15 0.10
14 10 0.07
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
GAAAGAAAAA
Found at i:53078974 original size:32 final size:33
Alignment explanation
Indices: 53078926--53079010 Score: 86
Period size: 33 Copynumber: 2.5 Consensus size: 33
53078916 AGAAAAAAGA
* * *
53078926 AAGAAAAAGCAGGAAAGATAAGAA-AGGAGAAGAG
1 AAGAAAAAGAAAGAAAGAGAAGAAGAGG-GAAG-G
53078960 AA-AAAAA-AAAGAAAGAAGAAGAAGAGGGAAGG
1 AAGAAAAAGAAAGAAAG-AGAAGAAGAGGGAAGG
53078992 AAGGAAAAAGAAAGAAAGA
1 AA-GAAAAAGAAAGAAAGA
53079011 AAAGGTAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
32 9 0.21
33 15 0.35
34 11 0.26
35 8 0.19
ACGTcount: A:0.67, C:0.01, G:0.31, T:0.01
Consensus pattern (33 bp):
AAGAAAAAGAAAGAAAGAGAAGAAGAGGGAAGG
Found at i:53078996 original size:43 final size:42
Alignment explanation
Indices: 53078850--53079014 Score: 122
Period size: 42 Copynumber: 3.8 Consensus size: 42
53078840 AAGGAGAGAA
* * ** *
53078850 AAGAAAGAAAAAGAAGGA-AAGGAGAGGAAAGAAAGAAAAAG-
1 AAGAAAGAGAAGGAAGGAGAA-GAGAAAAAAAAAAGAAAAAGC
* *
53078891 AAGGAAAGAAAAGGAAAGGAGAAGAAGAAAAAAGAAAGAAAAAGC
1 AA-GAAAGAGAAGG-AAGGAGAAG-AGAAAAAAAAAAGAAAAAGC
* * *
53078936 AGGAAAGATAAGAAAGGAGAAGAGAAAAAAAAAAGAAAGAAG-
1 AAGAAAGAGAAGGAAGGAGAAGAGAAAAAAAAAAGAAA-AAGC
* *
53078978 AAGAAGAGGGAAGGAAGGA-AAAAGAAAGAAAGAAAAG
1 AAGAA-AGAGAAGGAAGGAGAAGAGAAA-AAA-AAAAG
53079015 GTAATTTTTT
Statistics
Matches: 103, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
41 2 0.02
42 36 0.35
43 31 0.30
44 33 0.32
45 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.31, T:0.01
Consensus pattern (42 bp):
AAGAAAGAGAAGGAAGGAGAAGAGAAAAAAAAAAGAAAAAGC
Found at i:53079534 original size:158 final size:151
Alignment explanation
Indices: 53079352--53080106 Score: 662
Period size: 158 Copynumber: 4.9 Consensus size: 151
53079342 TATTTAATAA
53079352 ATTTCAAACATAATGCACTGAAATAATGTAAAACTATAAAATTAGAAATTATGATATTTTTTAAA
1 ATTTCAAACATAATGCACTGAAATAATGTAAAA-TATAAAA-TAGAAATTATGATATTTTTTAAA
* * *
53079417 ATAATAAAATGCGGAGAAAAAAATACGAATAAATGGCCGAAGTAAGAGTGTTTTACTAAATTTTT
64 GTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACTAAATTTTT
*
53079482 TAAAAATTCAGAAATAATTAAGACAAAT
129 TAAAAA-ACA-AAATAATT-A-A-AAAT
* * * * *
53079510 ATTTCAAACAAAATGTACTAAAATAATATAAAATATGAAAATATGAAAATAAT-ATATTTTTATT
1 ATTTCAAACATAATGCACTGAAATAATGTAAAATAT-AAAATA-G-AAATTATGATA-TTTT-TT
* * * * * *
53079574 GAAAGTAATAAAATTCGG-GAAAATAATACGAGCAAAGGGCAGGAA-TAAGGGCTTTTTTACACT
61 -AAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGC-CGAAGTAAGAG-TTTTTT--ACT
* * * *
53079637 AAATTAATTTAAAAAACACATTAAATTAATAA-
121 AAATT-TTTTAAAAAACAAAAT-AATTAAAAAT
* *
53079669 ATTTCAAACATAATGCACTGAAATAAAGTAAAAT-T---AT--AAATTATGATATTTTTTAAAAT
1 ATTTCAAACATAATGCACTGAAATAATGTAAAATATAAAATAGAAATTATGATATTTTTTAAAGT
* **
53079728 AATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGGAGTAAGAGCGTTTTACTAAA-TTTTTA
66 AATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACTAAATTTTTTA
53079792 AAAAATTCAGAAATAATTAATACAAAT
131 AAAAA--CA-AAATAATT-A-A-AAAT
* * * * * *
53079819 ATTTCAAATAAAATGTACTGGAATAATATAAAATAATAAAATACGAAAATAAT-ATATTTTTAGT
1 ATTTCAAACATAATGCACTGAAATAATGTAAAAT-ATAAAATA-G-AAATTATGATATTTTT--T
* * * * * *
53079883 GAAAGTAATAAAATTC-GAGAAAATAATACGAGCAAAGGGCAGGAA-TAAGGGTTTTTTTTACAC
61 -AAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGC-CGAAGTAAGAG--TTTTTT--AC
* ** *
53079946 TAAATTAATTTAAAAAACACTA-AATTAATAAT
120 TAAATT-TTTTAAAAAACAAAATAATTAAAAAT
53079978 -TTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATTTTTTAAA
1 ATTTCAAACATAATGCACTGAAATAATGTAAAA-TATAAAA-TAGAAATTATGATATTTTTTAAA
* *
53080042 GTAATAAAATGCGGAG-AAAAAATACGAACAAATAGCCGAAGTAAGAGTTTTTTACTAACTTTTT
64 GTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACTAAATTTTT
53080106 T
129 T
53080107 TCAACTTGCA
Statistics
Matches: 476, Mismatches: 75, Indels: 100
0.73 0.12 0.15
Matches are distributed among these distances:
144 9 0.02
145 1 0.00
146 12 0.03
147 3 0.01
148 22 0.05
149 28 0.06
150 41 0.09
151 10 0.02
152 1 0.00
153 6 0.01
154 5 0.01
155 37 0.08
156 4 0.01
157 11 0.02
158 88 0.18
159 51 0.11
160 55 0.12
161 40 0.08
162 11 0.02
163 15 0.03
164 16 0.03
165 1 0.00
166 9 0.02
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (151 bp):
ATTTCAAACATAATGCACTGAAATAATGTAAAATATAAAATAGAAATTATGATATTTTTTAAAGT
AATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACTAAATTTTTTA
AAAAACAAAATAATTAAAAAT
Found at i:53079851 original size:150 final size:150
Alignment explanation
Indices: 53079386--53080105 Score: 499
Period size: 160 Copynumber: 4.6 Consensus size: 150
53079376 AATGTAAAAC
* *
53079386 TATAAAATTAGAAATTATGATATTTTTTAAAATAATAAAATGCGGAGAAAAAAATACGAATAAAT
1 TATAAAATTATAAATTATGATATTTTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAAT
* * * *
53079451 GGCCGAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAAGACAAATATTTCA
66 GGCCGGAGTAAGAGCGTTTTACTAAATTTTTAAAAAATTCAGAAATAATTAATACAAATATTTCA
*
53079516 AACAAAATGTACTAAAATAA
131 AACAAAATGTACTGAAATAA
* * *
53079536 TATAAAA-TATGAAAATATGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGG-GAAAATA
1 TATAAAATTAT--AAAT-T----ATGATAT-TTTTTA---AAA-TAATAAAATGCGGAGAAAAAA
* * * * * * * *
53079599 ATACGAGCAAAGGGCAGGAATAAGGGCTTTTTTACACTAAATTAATTTAAAAAA--CA-CATTAA
54 ATACGAACAAATGGCCGGAGTAAGAGC-GTTTT--ACTAAATT--TTTAAAAAATTCAGAAAT-A
* *
53079661 ATTAAT---AA-ATTTCAAACATAATGCACTGAAATAA
113 ATTAATACAAATATTTCAAACAAAATGTACTGAAATAA
53079695 -AGTAAAATTATAAATTATGATATTTTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAA
1 TA-TAAAATTATAAATTATGATATTTTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAA
53079759 TGGCCGGAGTAAGAGCGTTTTACTAAATTTTTAAAAAATTCAGAAATAATTAATACAAATATTTC
65 TGGCCGGAGTAAGAGCGTTTTACTAAATTTTTAAAAAATTCAGAAATAATTAATACAAATATTTC
* *
53079824 AAATAAAATGTACTGGAATAA
130 AAACAAAATGTACTGAAATAA
* * * * *
53079845 TATAAAATAATAAAATACGAAAATAATATATTTTTAGTGAAAGTAATAAAATTC-GAGAAAATAA
1 TATAAAATTAT-AAAT-----TATGATAT-TTTTTA---AAA-TAATAAAATGCGGAGAAAAAAA
* * * * * ** **
53079909 TACGAGCAAAGGGCAGGAATAAGGGTTTTTTTTACACTAAATTAATTTAAAAAA--CA-CTA-AA
55 TACGAACAAATGGCCGGAGTAAGAG--CGTTTT--ACTAAATT--TTTAAAAAATTCAGAAATAA
* *
53079970 TTAAT---AAT-TTTCAAACATAATGCACTGAAATAATGTAAAA
114 TTAATACAAATATTTCAAACAAAATGTACTG--A-AA--T--AA
* *
53080010 TTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAG-AAAAAATACGAACAAA
1 -TATAAAATTATAAATTATGATATTTTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAA
* * ** *
53080074 TAGCCGAAGTAAGAGTTTTTTACTAACTTTTT
65 TGGCCGGAGTAAGAGCGTTTTACTAAATTTTT
53080106 TTCAACTTGC
Statistics
Matches: 447, Mismatches: 68, Indels: 111
0.71 0.11 0.18
Matches are distributed among these distances:
144 9 0.02
146 17 0.04
147 2 0.00
148 16 0.04
149 38 0.09
150 37 0.08
151 16 0.04
152 7 0.02
153 12 0.03
155 33 0.07
156 17 0.04
157 13 0.03
158 21 0.05
159 37 0.08
160 71 0.16
161 28 0.06
162 13 0.03
163 18 0.04
164 10 0.02
165 14 0.03
166 18 0.04
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (150 bp):
TATAAAATTATAAATTATGATATTTTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAAT
GGCCGGAGTAAGAGCGTTTTACTAAATTTTTAAAAAATTCAGAAATAATTAATACAAATATTTCA
AACAAAATGTACTGAAATAA
Found at i:53079912 original size:309 final size:313
Alignment explanation
Indices: 53079345--53080105 Score: 1214
Period size: 309 Copynumber: 2.4 Consensus size: 313
53079335 AATGGTATAT
53079345 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAACTATAAAATTAGAAATTATGATATT
1 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAACTAT--AATTA-AAATTATGATATT
*
53079410 TTTTAAAATAATAAAATGCGGAGAAAAAAATACGAATAAATGGCCGAAGTAAGAGTGTTTTACTA
63 TTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTTTTACTA
*
53079475 AATTTTTTAAAAATTCAGAAATAATTAAGACAAATATTTCAAACAAAATGTACTAAAATAATATA
128 AATTTTTAAAAAATTCAGAAATAATTAAGACAAATATTTCAAACAAAATGTACTAAAATAATATA
* * *
53079540 AAATATGAAAATATGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGAAAATAATACGA
193 AAATATGAAAATACGAAAATAATATATTTTTAGTGAAAGTAATAAAATTCGAGAAAATAATACGA
53079605 GCAAAGGGCAGGAATAAGGG-CTTTTTTACACTAAATTAATTTAAAAAACACATTAAA
258 GCAAAGGGCAGGAATAAGGGTCTTTTTTACACTAAATTAATTTAAAAAACAC--TAAA
*
53079662 TTAATAAATTTCAAACATAATGCACTGAAATAAAGTAAAA-T-T-A-T-AAATTATGATATTTTT
1 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAACTATAATTAAAATTATGATATTTTT
* *
53079722 TAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGGAGTAAGAGCGTTTTACTAAAT
66 TAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTTTTACTAAAT
* * **
53079787 TTTTAAAAAATTCAGAAATAATTAATACAAATATTTCAAATAAAATGTACTGGAATAATATAAAA
131 TTTTAAAAAATTCAGAAATAATTAAGACAAATATTTCAAACAAAATGTACTAAAATAATATAAAA
53079852 TAAT-AAAATACGAAAATAATATATTTTTAGTGAAAGTAATAAAATTCGAGAAAATAATACGAGC
196 T-ATGAAAATACGAAAATAATATATTTTTAGTGAAAGTAATAAAATTCGAGAAAATAATACGAGC
*
53079916 AAAGGGCAGGAATAAGGGTTTTTTTTACACTAAATTAATTTAAAAAACACTAAA
260 AAAGGGCAGGAATAAGGGTCTTTTTTACACTAAATTAATTTAAAAAACACTAAA
* *
53079970 TTAATAATTTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATT
1 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAACTAT--AATTA-AAATTATGATATT
* * *
53080035 TTTTAAAGTAATAAAATGCGGAG-AAAAAATACGAACAAATAGCCGAAGTAAGAGTTTTTTACTA
63 TTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTTTTACTA
*
53080099 ACTTTTT
128 AATTTTT
53080106 TTCAACTTGC
Statistics
Matches: 413, Mismatches: 21, Indels: 22
0.91 0.05 0.05
Matches are distributed among these distances:
308 42 0.10
309 215 0.52
310 33 0.08
311 1 0.00
312 1 0.00
313 1 0.00
314 1 0.00
315 44 0.11
316 36 0.09
317 39 0.09
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (313 bp):
TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAACTATAATTAAAATTATGATATTTTT
TAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTTTTACTAAAT
TTTTAAAAAATTCAGAAATAATTAAGACAAATATTTCAAACAAAATGTACTAAAATAATATAAAA
TATGAAAATACGAAAATAATATATTTTTAGTGAAAGTAATAAAATTCGAGAAAATAATACGAGCA
AAGGGCAGGAATAAGGGTCTTTTTTACACTAAATTAATTTAAAAAACACTAAA
Found at i:53090518 original size:29 final size:29
Alignment explanation
Indices: 53090485--53090547 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
53090475 AATTTGTGAG
* *
53090485 AATTAAATC-AAATCAAAATTGATGTATAA
1 AATTAAA-CAAAATCAAAACTCATGTATAA
* *
53090514 AATTACACAAAATCAAAGCTCATGTATAA
1 AATTAAACAAAATCAAAACTCATGTATAA
53090543 AATTA
1 AATTA
53090548 CACATTAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (29 bp):
AATTAAACAAAATCAAAACTCATGTATAA
Found at i:53094507 original size:3 final size:3
Alignment explanation
Indices: 53094499--53094531 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
53094489 TGTGCGTATG
53094499 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53094532 AAAATTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:53100645 original size:46 final size:46
Alignment explanation
Indices: 53100575--53100751 Score: 230
Period size: 46 Copynumber: 3.8 Consensus size: 46
53100565 ACAATGCTAT
* * *
53100575 AACTCAGTATAGTTTTCTTCACTGAAATATCATACCTACTTTTCAG
1 AACTCAGTATAGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
* * * ** * *
53100621 AATTCAGTATGGTTTTCGTTACTGAAATGTCATATCTACTTCTCAC
1 AACTCAGTATAGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
53100667 AACTCAGTATAGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATAGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
* *
53100713 AACTCAGTATGGTTCTT-TTTACTAAAATACCATACCTAC
1 AACTCAGTATAGTT-TTCTTTACTGAAATACCATACCTAC
53100752 ATTCCACACT
Statistics
Matches: 113, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
46 111 0.98
47 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (46 bp):
AACTCAGTATAGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
Found at i:53110630 original size:21 final size:21
Alignment explanation
Indices: 53110598--53110638 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
53110588 AGGCTCGAGG
53110598 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
53110619 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
53110639 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Done.