Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 136 of 433
Found at i:41911952 original size:40 final size:40
Alignment explanation
Indices: 41911867--41912017 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
41911857 AATTGAATGA
* * *
41911867 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
41911907 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
41911948 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
41911987 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
41912018 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:41912031 original size:40 final size:40
Alignment explanation
Indices: 41911904--41912033 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
41911894 ATGCTGGAAA
* * * *
41911904 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
41911944 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
41911984 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
41912024 TTATATCCGG
1 TTATATCCGG
41912034 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:41917139 original size:20 final size:20
Alignment explanation
Indices: 41917114--41917158 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
41917104 TTATAACTTG
41917114 AAATCTAAACATTTTAATCA
1 AAATCTAAACATTTTAATCA
*
41917134 AAATCTAACCATTTTAATCA
1 AAATCTAAACATTTTAATCA
41917154 AAATC
1 AAATC
41917159 CATGTTAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATCTAAACATTTTAATCA
Found at i:41919218 original size:39 final size:39
Alignment explanation
Indices: 41919137--41919280 Score: 146
Period size: 40 Copynumber: 3.6 Consensus size: 39
41919127 CATTGGAATG
* * * *
41919137 ATATCCGGGCTAAGTCCCGAAGGCAATTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGC-ATTGTGCAAGTTATT
* *
41919177 ATATCCGGGCTAAGACCC-AAGGCATTCGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATT-GTGCAAGTTATT
**
41919216 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCA-TTGTGCAAGTTATT
* ** *
41919256 AAATCCAAGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
41919281 ATCGTGCGAA
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
38 3 0.03
39 31 0.35
40 52 0.59
41 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTGTGCAAGTTATT
Found at i:41919270 original size:79 final size:80
Alignment explanation
Indices: 41919137--41919289 Score: 191
Period size: 79 Copynumber: 1.9 Consensus size: 80
41919127 CATTGGAATG
* * ** * **
41919137 ATATCCGGGCTAAGTCCCGAAGGCAATTATGCTAGTAATTATATCCGGGCTAAGACCC-AAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTAACCAAATCCAAGCTAAGACCCGAAGGCA
*
41919201 TTCGTGCGAGTTGTT
66 ATCGTGCGAGTTGTT
* * * *
41919216 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCAAGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTAACCAAATCCAAGCTAAGACCCGAAGGCA
41919281 ATCGTGCGA
66 ATCGTGCGA
41919290 ATCACTATAA
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
79 47 0.77
80 14 0.23
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTAACCAAATCCAAGCTAAGACCCGAAGGCA
ATCGTGCGAGTTGTT
Found at i:41922764 original size:24 final size:24
Alignment explanation
Indices: 41922732--41922814 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
41922722 ACTTATTCGT
*
41922732 ACACATAGTGCCACGTTTTCTCGC
1 ACACATAGTGCCACATTTTCTCGC
41922756 ACACATAGTGCCACATTTTCTCGC
1 ACACATAGTGCCACATTTTCTCGC
* *** *
41922780 ACACATAGTGCCGCATAGCCTTGC
1 ACACATAGTGCCACATTTTCTCGC
41922804 ACACATAGTGC
1 ACACATAGTGC
41922815 TGCATAGCCT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (24 bp):
ACACATAGTGCCACATTTTCTCGC
Found at i:41922819 original size:24 final size:24
Alignment explanation
Indices: 41922778--41922840 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
41922768 ACATTTTCTC
*
41922778 GCACACATAGTGCCGCATAGCCTT
1 GCACACATAGTGCTGCATAGCCTT
41922802 GCACACATAGTGCTGCATAGCCTT
1 GCACACATAGTGCTGCATAGCCTT
41922826 GCACACATAGTGCTG
1 GCACACATAGTGCTG
41922841 TATTTTCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.22
Consensus pattern (24 bp):
GCACACATAGTGCTGCATAGCCTT
Found at i:41929609 original size:24 final size:24
Alignment explanation
Indices: 41929577--41929640 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
41929567 TCTTACTTAT
*
41929577 TCGCACACATAGTGCCACGTTTTC
1 TCGCACACATAGTGCCACATTTTC
41929601 TCGCACACATAGTGCCACATTTTC
1 TCGCACACATAGTGCCACATTTTC
41929625 TCGCACACATAGTGCC
1 TCGCACACATAGTGCC
41929641 GCATAGCCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.27
Consensus pattern (24 bp):
TCGCACACATAGTGCCACATTTTC
Found at i:41929654 original size:24 final size:24
Alignment explanation
Indices: 41929577--41929661 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
41929567 TCTTACTTAT
* ***
41929577 TCGCACACATAGTGCCACGTTTTC
1 TCGCACACATAGTGCCACATAGCC
***
41929601 TCGCACACATAGTGCCACATTTTC
1 TCGCACACATAGTGCCACATAGCC
*
41929625 TCGCACACATAGTGCCGCATAGCC
1 TCGCACACATAGTGCCACATAGCC
*
41929649 TTGCACACATAGT
1 TCGCACACATAGT
41929662 ACTGTATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (24 bp):
TCGCACACATAGTGCCACATAGCC
Found at i:41934383 original size:2 final size:2
Alignment explanation
Indices: 41934376--41934401 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41934366 CTTATTCATC
41934376 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
41934402 TCTTACCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41942435 original size:46 final size:46
Alignment explanation
Indices: 41942383--41942741 Score: 483
Period size: 46 Copynumber: 7.8 Consensus size: 46
41942373 AGTGTGCTCT
* *
41942383 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
41942429 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
41942475 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
41942521 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
41942567 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
41942613 ATG--ACGAAGATAAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAA-ATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
41942658 ATGACGA-GAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGA-TATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
41942705 ATGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATAC
41942742 TATGACATCA
Statistics
Matches: 291, Mismatches: 17, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
44 4 0.01
45 37 0.13
46 207 0.71
47 40 0.14
48 3 0.01
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:41945262 original size:19 final size:19
Alignment explanation
Indices: 41945238--41945306 Score: 129
Period size: 19 Copynumber: 3.6 Consensus size: 19
41945228 TGGGTTCGGG
41945238 ACACGGGCGTGTCCCTAGC
1 ACACGGGCGTGTCCCTAGC
41945257 ACACGGGCGTGTCCCTAGC
1 ACACGGGCGTGTCCCTAGC
*
41945276 ACACGGGCGTGTCCTTAGC
1 ACACGGGCGTGTCCCTAGC
41945295 ACACGGGCGTGT
1 ACACGGGCGTGT
41945307 GCTCTATACC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.16, C:0.33, G:0.33, T:0.17
Consensus pattern (19 bp):
ACACGGGCGTGTCCCTAGC
Found at i:41945324 original size:23 final size:20
Alignment explanation
Indices: 41945238--41945330 Score: 93
Period size: 19 Copynumber: 4.7 Consensus size: 20
41945228 TGGGTTCGGG
* *
41945238 ACACGGGCGTGT-CCCTAGC
1 ACACGGGCGTGTGCCTTACC
* *
41945257 ACACGGGCGTGT-CCCTAGC
1 ACACGGGCGTGTGCCTTACC
*
41945276 ACACGGGCGTGT-CCTTAGC
1 ACACGGGCGTGTGCCTTACC
41945295 ACACGGGCGTGTGCTCTATACCC
1 ACACGGGCGTGTGC-CT-TA-CC
41945318 ACACGGGCGTGTG
1 ACACGGGCGTGTG
41945331 AAGCCTTGAT
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
19 49 0.72
20 1 0.01
21 2 0.03
22 2 0.03
23 14 0.21
ACGTcount: A:0.16, C:0.33, G:0.32, T:0.18
Consensus pattern (20 bp):
ACACGGGCGTGTGCCTTACC
Found at i:41948032 original size:46 final size:46
Alignment explanation
Indices: 41947883--41948141 Score: 240
Period size: 46 Copynumber: 5.5 Consensus size: 46
41947873 ATTTGTTTGT
* * * *
41947883 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GACGA
* * *
41947929 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGA
* *
41947977 GAGCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-A
*
41948024 -AGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGA
* * * * * * *
41948069 TAGTCAATGTAAGACTGTGTCTGGGACATGGCATC-GACTTGAGA-TA
1 GAGCCAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCCTCGAGACGA
*
41948115 TGAGCCAGTGTAAGACCGTGTCTGGGA
1 -GAGCCAGTGTAAGA-CATGTCTGGGA
41948142 TATAGAATCA
Statistics
Matches: 179, Mismatches: 23, Indels: 21
0.80 0.10 0.09
Matches are distributed among these distances:
45 3 0.02
46 79 0.44
47 64 0.36
48 32 0.18
49 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGA
Found at i:41948121 original size:93 final size:94
Alignment explanation
Indices: 41947883--41948141 Score: 246
Period size: 94 Copynumber: 2.8 Consensus size: 94
41947873 ATTTGTTTGT
* * * *
41947883 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGG-C-C-ACATTATGAGAGCCAGTGTAAGACC
1 GAGCTAATGTAAGACATGTCTAGGACATGCATCGGACTCGAGA-CAT--GAGCCAGTGTAAGACC
* *
41947945 ATGTTTGGGACATGGCATCGGCATTGAGACGA
63 ATGTCTGGGACATGGCATCGGCATCGAGACGA
* * * *
41947977 GAGCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGACGTAAGCCAGTGTAAGA-CATG
1 GAGCTAATGTAAGACATGTCTAGGACATGCATCGGACTCGAGACATGAGCCAGTGTAAGACCATG
*
41948041 TCTGGGACAT-GCATCGGC-TACGAGATGA
66 TCTGGGACATGGCATCGGCAT-CGAGACGA
* * * * *
41948069 TAG-TCAATGTAAGACTGTGTCTGGGACATGGCATC-GACTTGAGATATGAGCCAGTGTAAGACC
1 GAGCT-AATGTAAGAC-ATGTCTAGGACAT-GCATCGGACTCGAGACATGAGCCAGTGTAAGACC
*
41948132 GTGTCTGGGA
63 ATGTCTGGGA
41948142 TATAGAATCA
Statistics
Matches: 139, Mismatches: 18, Indels: 16
0.80 0.10 0.09
Matches are distributed among these distances:
91 2 0.01
92 25 0.18
93 45 0.32
94 62 0.45
95 1 0.01
96 2 0.01
97 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (94 bp):
GAGCTAATGTAAGACATGTCTAGGACATGCATCGGACTCGAGACATGAGCCAGTGTAAGACCATG
TCTGGGACATGGCATCGGCATCGAGACGA
Found at i:41955396 original size:40 final size:40
Alignment explanation
Indices: 41955351--41955480 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
41955341 CGGAATGCAA
41955351 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
41955391 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * * *
41955431 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
41955471 CCGGATATAA
1 CCGGATATAA
41955481 TTTCCAGCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.96
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:41959142 original size:19 final size:19
Alignment explanation
Indices: 41959120--41959156 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41959110 ATCACTGTCA
*
41959120 CCCACCGTAATCAAATTTT
1 CCCACCATAATCAAATTTT
41959139 CCCACCATAATCAAATTT
1 CCCACCATAATCAAATTT
41959157 GATATTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (19 bp):
CCCACCATAATCAAATTTT
Found at i:41959676 original size:23 final size:24
Alignment explanation
Indices: 41959598--41959678 Score: 84
Period size: 23 Copynumber: 3.6 Consensus size: 24
41959588 GGGGAAAATA
*
41959598 AAAAGTTTTGGGGGTTGATGGAGT
1 AAAAGTTTTGGGGGTTGAAGGAGT
* *
41959622 AAAA-TTTTAGAGG--GAA--AGT
1 AAAAGTTTTGGGGGTTGAAGGAGT
41959641 AAAAAGTTTTGGGGGTTGAAGGAGT
1 -AAAAGTTTTGGGGGTTGAAGGAGT
41959666 AAAA-TTTTGGGGG
1 AAAAGTTTTGGGGG
41959679 AAGGTAAAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
19 3 0.07
20 4 0.09
21 9 0.20
23 19 0.41
24 8 0.17
25 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (24 bp):
AAAAGTTTTGGGGGTTGAAGGAGT
Found at i:41959695 original size:43 final size:44
Alignment explanation
Indices: 41959575--41959696 Score: 183
Period size: 44 Copynumber: 2.8 Consensus size: 44
41959565 AAAGGTGAGA
* *
41959575 AGTAAAATTTTAGGGGGAAAATAAAAAGTTTTGGGGGTTGATGG
1 AGTAAAATTTTAGGGGGAAAGTAAAAAGTTTTGGGGGTTGAAGG
*
41959619 AGTAAAATTTTAGAGGGAAAGTAAAAAGTTTTGGGGGTTGAAGG
1 AGTAAAATTTTAGGGGGAAAGTAAAAAGTTTTGGGGGTTGAAGG
* * *
41959663 AGTAAAATTTT-GGGGGAAGGTAAAGAGGTTTGGG
1 AGTAAAATTTTAGGGGGAAAGTAAAAAGTTTTGGG
41959697 AGTTTGGGGT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
43 19 0.27
44 52 0.73
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (44 bp):
AGTAAAATTTTAGGGGGAAAGTAAAAAGTTTTGGGGGTTGAAGG
Found at i:41963067 original size:18 final size:18
Alignment explanation
Indices: 41963040--41963106 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
41963030 ACAATAAGTG
*
41963040 ACGTTTTGAAAATTAATA
1 ACGTTATGAAAATTAATA
*
41963058 ACGTTATGAAAGAGT-ATA
1 ACGTTATGAAA-ATTAATA
* * *
41963076 ACTTTATGATAATGAATA
1 ACGTTATGAAAATTAATA
* *
41963094 ATGTTTTGAAAAT
1 ACGTTATGAAAAT
41963107 GAATGACACG
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
17 1 0.03
18 34 0.92
19 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.37
Consensus pattern (18 bp):
ACGTTATGAAAATTAATA
Found at i:41975495 original size:41 final size:41
Alignment explanation
Indices: 41975450--41975567 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
41975440 TGAAAGATAA
41975450 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
41975491 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
41975521 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
41975562 ATGTAG
1 ATGTAG
41975568 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:41975506 original size:71 final size:71
Alignment explanation
Indices: 41975418--41975581 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
41975408 GAGATGTATC
41975418 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41975483 AGGACA
66 AGGACA
41975489 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41975554 AGGACA
66 AGGACA
41975560 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
41975582 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:41982602 original size:41 final size:41
Alignment explanation
Indices: 41982557--41982674 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
41982547 TGAAAGATAA
41982557 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
41982598 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
41982628 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
41982669 ATGTAG
1 ATGTAG
41982675 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:41982613 original size:71 final size:71
Alignment explanation
Indices: 41982525--41982688 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
41982515 GAGATGTATC
41982525 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41982590 AGGACA
66 AGGACA
41982596 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41982661 AGGACA
66 AGGACA
41982667 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
41982689 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:41988727 original size:68 final size:70
Alignment explanation
Indices: 41988655--41988852 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
41988645 ACACCCTGTA
* * * *
41988655 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
41988717 ATAAAT
65 ATAAAT
*
41988723 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
41988788 ATAAAT
65 ATAAAT
*
41988794 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
41988853 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:41988766 original size:41 final size:41
Alignment explanation
Indices: 41988721--41988838 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
41988711 TGAAAGATAA
41988721 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
41988762 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
41988792 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
41988833 ATGTAG
1 ATGTAG
41988839 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:41988778 original size:71 final size:71
Alignment explanation
Indices: 41988689--41988852 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
41988679 GAGATGTATC
41988689 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41988754 AGGACA
66 AGGACA
41988760 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41988825 AGGACA
66 AGGACA
41988831 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
41988853 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:41995823 original size:68 final size:70
Alignment explanation
Indices: 41995751--41995948 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
41995741 ACACCCTGTA
* * * *
41995751 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
41995813 ATAAAT
65 ATAAAT
*
41995819 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
41995884 ATAAAT
65 ATAAAT
* * *
41995890 GTAGCTGGGTCGCATGCGTGATTCCAAGTGACGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGA-AGACACCATGTAGACAAGAGAGCTACG
41995949 AGACAAATCG
Statistics
Matches: 118, Mismatches: 7, Indels: 7
0.89 0.05 0.05
Matches are distributed among these distances:
68 24 0.20
69 3 0.03
70 1 0.01
71 90 0.76
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:41995874 original size:71 final size:71
Alignment explanation
Indices: 41995785--41995948 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
41995775 GAGATGTATC
41995785 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41995850 AGGACA
66 AGGACA
*
41995856 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTGGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
41995921 CGGACA
66 AGGACA
41995927 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
41995949 AGACAAATCG
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:42008858 original size:21 final size:21
Alignment explanation
Indices: 42008833--42008872 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
42008823 GGTGGACGAT
**
42008833 TTTGGGGAGTGAATTAAGGGA
1 TTTGGGGAGAAAATTAAGGGA
*
42008854 TTTGGTGAGAAAATTAAGG
1 TTTGGGGAGAAAATTAAGG
42008873 AGTAAGGAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.30
Consensus pattern (21 bp):
TTTGGGGAGAAAATTAAGGGA
Found at i:42009858 original size:18 final size:17
Alignment explanation
Indices: 42009825--42009858 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42009815 TTTTTGGCCA
*
42009825 TGTGGGCCATACGGGCG
1 TGTGGGCCACACGGGCG
42009842 TGTGGGCCTACACGGGC
1 TGTGGGCC-ACACGGGC
42009859 TGACAACATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.12, C:0.26, G:0.44, T:0.18
Consensus pattern (17 bp):
TGTGGGCCACACGGGCG
Found at i:42010858 original size:18 final size:18
Alignment explanation
Indices: 42010807--42010874 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
42010797 ATAAGTGACG
* * *
42010807 TTTTAAAAATTAATAACG
1 TTTTGAAAATGAATAACA
*
42010825 TTTTGAAAGA-GTATAAC-
1 TTTTGAAA-ATGAATAACA
*
42010842 TTTGTGATAATGAATAACA
1 TTT-TGAAAATGAATAACA
42010861 TTTTGAAAATGAAT
1 TTTTGAAAATGAAT
42010875 GACACGTCCT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
17 4 0.10
18 32 0.80
19 4 0.10
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.38
Consensus pattern (18 bp):
TTTTGAAAATGAATAACA
Found at i:42011717 original size:3 final size:3
Alignment explanation
Indices: 42011711--42011762 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
42011701 TGCTGCTAAA
* * *
42011711 TAT TAT TAT GAT TAT TAT TAT CAT TAT TAT TAC TACT T-T TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT
42011757 TAT TAT
1 TAT TAT
42011763 AGTAATTACA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.85
4 4 0.10
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:42018834 original size:22 final size:22
Alignment explanation
Indices: 42018809--42018874 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
42018799 AGAACATCCC
42018809 TTCAATTTATAATTAACTTATT
1 TTCAATTTATAATTAACTTATT
* *
42018831 TTC-ACTTACTAA-T---TTAAT
1 TTCAATTTA-TAATTAACTTATT
42018849 TT-AATATTATAATTAACTTATT
1 TTCAAT-TTATAATTAACTTATT
42018871 TTCA
1 TTCA
42018875 GTTAAAACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 15
0.63 0.08 0.29
Matches are distributed among these distances:
18 10 0.31
19 4 0.12
21 5 0.16
22 12 0.38
23 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (22 bp):
TTCAATTTATAATTAACTTATT
Found at i:42023567 original size:36 final size:35
Alignment explanation
Indices: 42023511--42023594 Score: 141
Period size: 36 Copynumber: 2.3 Consensus size: 35
42023501 AACTCTATTT
*
42023511 AGTTCAGCAATCTTTTGGATCTATTCTAACTGATTC
1 AGTTCAGC-AGCTTTTGGATCTATTCTAACTGATTC
42023547 AGTTCAGCAGCTTTTCGGATCTATTCTAACTGATTC
1 AGTTCAGCAGCTTTT-GGATCTATTCTAACTGATTC
42023583 AGTTCAGCAGCT
1 AGTTCAGCAGCT
42023595 CCTCTGTTCT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
35 6 0.13
36 40 0.87
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (35 bp):
AGTTCAGCAGCTTTTGGATCTATTCTAACTGATTC
Found at i:42023809 original size:8 final size:7
Alignment explanation
Indices: 42023774--42023808 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
42023764 ATGAGTTGTG
*
42023774 AGGGATG
1 AGGGATA
42023781 AGGGATA
1 AGGGATA
42023788 AGGGATA
1 AGGGATA
42023795 AGGGATTA
1 AGGGA-TA
42023803 AGGGAT
1 AGGGAT
42023809 TGATGCATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.37, C:0.00, G:0.46, T:0.17
Consensus pattern (7 bp):
AGGGATA
Found at i:42027578 original size:93 final size:93
Alignment explanation
Indices: 42027449--42027620 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
42027439 CGCCCATAAG
* * *
42027449 CGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
42027514 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
42027542 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
42027607 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
42027621 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:42027617 original size:46 final size:46
Alignment explanation
Indices: 42027442--42027617 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
42027432 TGTAACCCGC
* * * *
42027442 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
42027488 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
42027538 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
42027581 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
42027618 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:42027636 original size:46 final size:46
Alignment explanation
Indices: 42027491--42027629 Score: 144
Period size: 47 Copynumber: 3.0 Consensus size: 46
42027481 TTCGCATCCA
42027491 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * * *
42027539 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATC
42027584 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
42027630 CTAGTGACAT
Statistics
Matches: 75, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 28 0.37
47 30 0.40
48 2 0.03
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:42028071 original size:30 final size:30
Alignment explanation
Indices: 42028037--42028096 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
42028027 ATTTAATACG
42028037 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
42028067 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
42028097 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:42030656 original size:20 final size:18
Alignment explanation
Indices: 42030631--42030681 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
42030621 GTGGGGAGGG
42030631 ATTAATTTATTTTTATATAA
1 ATTAATTT-TTTTTATA-AA
*
42030651 ATTAATTTGTTTTATAAA
1 ATTAATTTTTTTTATAAA
*
42030669 GTTAATTTTTTTT
1 ATTAATTTTTTTT
42030682 TTCAAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 13 0.46
19 7 0.25
20 8 0.29
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (18 bp):
ATTAATTTTTTTTATAAA
Found at i:42030668 original size:17 final size:17
Alignment explanation
Indices: 42030639--42030680 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
42030629 GGATTAATTT
*
42030639 ATTTTTATATAAA-TTA
1 ATTTTTTTATAAAGTTA
42030655 ATTTGTTTTATAAAGTTA
1 ATTT-TTTTATAAAGTTA
42030673 ATTTTTTT
1 ATTTTTTT
42030681 TTTCAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 12 0.52
18 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
ATTTTTTTATAAAGTTA
Found at i:42030675 original size:18 final size:16
Alignment explanation
Indices: 42030634--42030680 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
42030624 GGGAGGGATT
* *
42030634 AATTTATTTTTATATA
1 AATTAATTTTTTTATA
42030650 AATTAATTTGTTTTATA
1 AATTAATTT-TTTTATA
42030667 AAGTTAATTTTTTT
1 AA-TTAATTTTTTT
42030681 TTTCAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 8 0.30
17 12 0.44
18 7 0.26
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (16 bp):
AATTAATTTTTTTATA
Found at i:42035032 original size:45 final size:45
Alignment explanation
Indices: 42034956--42035130 Score: 226
Period size: 45 Copynumber: 3.9 Consensus size: 45
42034946 CTTTCCTTTC
** * * *
42034956 TGGCTGTGCAGCCTTTTTGGAATGACCCTCATCAGGAATAGTCTT
1 TGGCTGTGCAGCCTTTTCAGAATGACTCTCATCAGGTATACTCTT
* ** * *
42035001 TGACTGTGCAGCCTTTTTGGATTGACTCTCATCAGGTATACTTTT
1 TGGCTGTGCAGCCTTTTCAGAATGACTCTCATCAGGTATACTCTT
*
42035046 TGGCTGTGCAGCCTTTTCAG-ATCGACTCCCATCAGGTATACTCTT
1 TGGCTGTGCAGCCTTTTCAGAAT-GACTCTCATCAGGTATACTCTT
*
42035091 TGGCTGAGCAGCCTTTTCAGAATGACTCTCATCAGGTATA
1 TGGCTGTGCAGCCTTTTCAGAATGACTCTCATCAGGTATA
42035131 GACCCACTTG
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.01
45 111 0.97
46 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (45 bp):
TGGCTGTGCAGCCTTTTCAGAATGACTCTCATCAGGTATACTCTT
Found at i:42035910 original size:47 final size:48
Alignment explanation
Indices: 42035858--42035953 Score: 142
Period size: 47 Copynumber: 2.0 Consensus size: 48
42035848 ATTAAGGAGA
42035858 ATAAATCAGTTATAACTTCAATGAAG-A-CATAACAAATTTTATTAAGC
1 ATAAATCAGTTATAACTTCAATGAAGAAGCATAACAAATTTTA-TAAGC
* *
42035905 ATAAATCAGTTGTAACTTCAATGAAGAAGGCATAACAGATTTTATAAGC
1 ATAAATCAGTTATAACTTCAATGAAGAA-GCATAACAAATTTTATAAGC
42035954 CAACGACACA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 25 0.57
48 1 0.02
49 5 0.11
50 13 0.30
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (48 bp):
ATAAATCAGTTATAACTTCAATGAAGAAGCATAACAAATTTTATAAGC
Found at i:42037986 original size:94 final size:94
Alignment explanation
Indices: 42037825--42038017 Score: 350
Period size: 94 Copynumber: 2.1 Consensus size: 94
42037815 AAAAAGCATC
* *
42037825 CACTAACATGCACTAGCGTAAGGTAGAACACAAAGGATATTAAACTATTAGAGTACCTAAAATAT
1 CACTAACATGCACTAGCGTAAGGTAGAACACAAAGGATATTAAACTATTAGAGCACCAAAAATAT
42037890 TAAGACAATCAGTCAGTTGTAGCATGATT
66 TAAGACAATCAGTCAGTTGTAGCATGATT
* *
42037919 CACTAACATGCACTAGTGTAAGGTAGAGCACAAAGGATATTAAACTATTAGAGCACCAAAAATAT
1 CACTAACATGCACTAGCGTAAGGTAGAACACAAAGGATATTAAACTATTAGAGCACCAAAAATAT
42037984 TAAGACAATCAGTCAGTTGTAGCATGATT
66 TAAGACAATCAGTCAGTTGTAGCATGATT
42038013 CACTA
1 CACTA
42038018 GTCACAAAAC
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (94 bp):
CACTAACATGCACTAGCGTAAGGTAGAACACAAAGGATATTAAACTATTAGAGCACCAAAAATAT
TAAGACAATCAGTCAGTTGTAGCATGATT
Found at i:42040180 original size:22 final size:22
Alignment explanation
Indices: 42040150--42040204 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
42040140 ATATATACCT
*
42040150 AATAGAATTAATTCCAAAATTA
1 AATAAAATTAATTCCAAAATTA
*
42040172 AATAAAATTCATTCCAAAATTA
1 AATAAAATTAATTCCAAAATTA
42040194 AACT-AAATTAA
1 AA-TAAAATTAA
42040205 AAATATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (22 bp):
AATAAAATTAATTCCAAAATTA
Found at i:42040686 original size:6 final size:6
Alignment explanation
Indices: 42040675--42040722 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
42040665 AATATTCCAA
42040675 ATTTTT ATTTTT ATTTTT ACTTTTTT ATTTTT -TTATTT ATTTTT -TTTT
1 ATTTTT ATTTTT ATTTTT A--TTTTT ATTTTT ATT-TTT ATTTTT ATTTT
42040723 GAAATGAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
5 6 0.16
6 24 0.63
7 2 0.05
8 6 0.16
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:42040709 original size:16 final size:15
Alignment explanation
Indices: 42040678--42040722 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
42040668 ATTCCAAATT
42040678 TTTATTTTTATTTTTA
1 TTTATTTTT-TTTTTA
42040694 CTTT-TTTATTTTTTTA
1 -TTTATTT-TTTTTTTA
42040710 TTTATTTTTTTTT
1 TTTATTTTTTTTT
42040723 GAAATGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 9 0.35
16 12 0.46
17 5 0.19
ACGTcount: A:0.13, C:0.02, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTATTTTTTTTTTA
Found at i:42040720 original size:20 final size:20
Alignment explanation
Indices: 42040676--42040719 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
42040666 ATATTCCAAA
42040676 TTTTTATTTTTATTTTTACT
1 TTTTTATTTTTATTTTTACT
42040696 TTTTTATTTTT-TTATTTA-T
1 TTTTTATTTTTATT-TTTACT
42040715 TTTTT
1 TTTTT
42040720 TTTGAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTATTTTTATTTTTACT
Found at i:42041080 original size:2 final size:2
Alignment explanation
Indices: 42041073--42041106 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
42041063 ATCATTCAAT
42041073 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42041107 CCATTCTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42041429 original size:45 final size:45
Alignment explanation
Indices: 42041315--42041434 Score: 170
Period size: 45 Copynumber: 2.7 Consensus size: 45
42041305 AGCAGCAGCA
* * *
42041315 GTAACAGTAACAATAACAGTATTCAACACACAAAGTGCTGAATCT
1 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAATCG
*
42041360 GTAACAGTAACGGTAACAGTATTCGACACACAAAGTG-TCGAATCG
1 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCT-GAATCG
* *
42041405 GTAACAGTAACAGTAACAATATTCGGCACA
1 GTAACAGTAACAGTAACAGTATTCGACACA
42041435 TAAGTGCCTG
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 1 0.01
45 66 0.99
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAATCG
Found at i:42042530 original size:3 final size:3
Alignment explanation
Indices: 42042522--42042549 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
42042512 TATTAACTTT
42042522 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
42042550 ATATCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:42042576 original size:2 final size:2
Alignment explanation
Indices: 42042569--42042602 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
42042559 TTAATAACAA
42042569 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42042603 TACAATTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42042845 original size:20 final size:20
Alignment explanation
Indices: 42042822--42042876 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
42042812 TTATTTTTAA
42042822 TAATAATAATAATCATAATT
1 TAATAATAATAATCATAATT
*
42042842 TAATAAT-ATAAATTATAATT
1 TAATAATAAT-AATCATAATT
42042862 TAATAGAATAATAAT
1 TAAT--AATAATAAT
42042877 AAATAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.07
20 20 0.67
22 6 0.20
23 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
TAATAATAATAATCATAATT
Found at i:42044949 original size:41 final size:41
Alignment explanation
Indices: 42044904--42045021 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
42044894 TGAAAGATAA
42044904 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
42044945 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
42044975 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
42045016 ATGTAG
1 ATGTAG
42045022 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:42044960 original size:71 final size:71
Alignment explanation
Indices: 42044872--42045035 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
42044862 GAGATGTATC
42044872 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
42044937 AGGACA
66 AGGACA
42044943 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
42045008 AGGACA
66 AGGACA
42045014 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
42045036 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:42052520 original size:41 final size:41
Alignment explanation
Indices: 42052475--42052592 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
42052465 TGAAAGATAA
42052475 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
42052516 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
42052546 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
42052587 ATGTAG
1 ATGTAG
42052593 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:42052531 original size:71 final size:71
Alignment explanation
Indices: 42052443--42052606 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
42052433 GAGATGTATC
42052443 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
42052508 AGGACA
66 AGGACA
42052514 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
42052579 AGGACA
66 AGGACA
42052585 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
42052607 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:42054507 original size:6 final size:6
Alignment explanation
Indices: 42054496--42054615 Score: 226
Period size: 6 Copynumber: 20.3 Consensus size: 6
42054486 TAATCATATA
42054496 TGCGTG TGC--G TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG
1 TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG
42054542 TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG
1 TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG
42054590 TGCGTG TGCGTG TGCGTG TGCGTG TG
1 TGCGTG TGCGTG TGCGTG TGCGTG TG
42054616 TGATGGGTTC
Statistics
Matches: 112, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.04
6 108 0.96
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
TGCGTG
Found at i:42057825 original size:26 final size:26
Alignment explanation
Indices: 42057796--42057849 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
42057786 ATCCTCTCTC
42057796 GAGCCATATAA-CAGGAAACTCACAAA
1 GAGCCAT-TAATCAGGAAACTCACAAA
* *
42057822 GAGCCATTAATCAGGGAGCTCACAAA
1 GAGCCATTAATCAGGAAACTCACAAA
42057848 GA
1 GA
42057850 TCCTATCGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.13
Consensus pattern (26 bp):
GAGCCATTAATCAGGAAACTCACAAA
Found at i:42057911 original size:25 final size:24
Alignment explanation
Indices: 42057883--42057962 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 24
42057873 CTATATAACG
42057883 GGAAGCTCACACAGAGCCATAATCA
1 GGAAGCTCACA-AGAGCCATAATCA
* * **
42057908 GGAAGTTCACATAGAACTTTTAATCA
1 GGAAGCTCACA-AGAGC-CATAATCA
*
42057934 GGAAGCTCATGAAGAGCCATTAATCA
1 GGAAGCTCA-CAAGAGCCA-TAATCA
42057960 GGA
1 GGA
42057963 GCTTCAGATA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
25 14 0.33
26 27 0.64
27 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (24 bp):
GGAAGCTCACAAGAGCCATAATCA
Found at i:42058721 original size:11 final size:12
Alignment explanation
Indices: 42058691--42058721 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
42058681 ATAAAATTCA
42058691 GAATTTTTCCAT
1 GAATTTTTCCAT
42058703 GAATTTTTCCAT
1 GAATTTTTCCAT
42058715 GAATTTT
1 GAATTTT
42058722 ACATCTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.52
Consensus pattern (12 bp):
GAATTTTTCCAT
Found at i:42059436 original size:19 final size:19
Alignment explanation
Indices: 42059396--42059437 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
42059386 AATACATTAA
* *
42059396 ATTATAAATTTATTTATTT
1 ATTATAAATTAATTTATAT
42059415 ATTATAAATTAAATTT-TAT
1 ATTATAAATT-AATTTATAT
42059434 ATTA
1 ATTA
42059438 CATTATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTATAAATTAATTTATAT
Found at i:42061578 original size:28 final size:28
Alignment explanation
Indices: 42061513--42061611 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
42061503 CATGAGATTG
* * *
42061513 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGTT-AGATTATATA
*
42061542 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTAGATTATATA
* *
42061570 GCACTAAGTGTGCGAGTTCGAATAT-TAA
1 GCACTAAGTGTGCGAGTTAGATTATAT-A
42061598 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42061612 GGCTTATTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.71
29 17 0.27
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTAGATTATATA
Found at i:42064221 original size:9 final size:9
Alignment explanation
Indices: 42064196--42064225 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
42064186 TGAAAAATAT
42064196 AATATTTTA
1 AATATTTTA
42064205 AATAATTTTA
1 AAT-ATTTTA
42064215 AATATTTTA
1 AATATTTTA
42064224 AA
1 AA
42064226 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
AATATTTTA
Found at i:42065788 original size:18 final size:18
Alignment explanation
Indices: 42065754--42065795 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
42065744 TTGACCTTTT
42065754 CAAATACATATACAAATA
1 CAAATACATATACAAATA
*
42065772 TAAATACA-ATACAAAATA
1 CAAATACATATAC-AAATA
42065790 CAAATA
1 CAAATA
42065796 ATACGATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (18 bp):
CAAATACATATACAAATA
Found at i:42065794 original size:6 final size:6
Alignment explanation
Indices: 42065754--42065795 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
42065744 TTGACCTTTT
* *
42065754 CAAATA CATATA CAAATA TAAATA C-AATA CAAAATA CAAATA
1 CAAATA CAAATA CAAATA CAAATA CAAATA C-AAATA CAAATA
42065796 ATACGATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 5 0.17
6 20 0.67
7 5 0.17
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (6 bp):
CAAATA
Found at i:42067856 original size:18 final size:18
Alignment explanation
Indices: 42067835--42067882 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
42067825 TTTAAGGAAG
42067835 AAGATAAGAAAAAAGAA-A
1 AAGA-AAGAAAAAAGAATA
*
42067853 AAGAAAAAAAAAAGAATA
1 AAGAAAGAAAAAAGAATA
*
42067871 AGGAAAGAAAAA
1 AAGAAAGAAAAA
42067883 TATAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (18 bp):
AAGAAAGAAAAAAGAATA
Found at i:42067865 original size:17 final size:19
Alignment explanation
Indices: 42067843--42067882 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
42067833 AGAAGATAAG
42067843 AAAAAAGAA-AAAGAAA-A
1 AAAAAAGAATAAAGAAAGA
*
42067860 AAAAAAGAATAAGGAAAGA
1 AAAAAAGAATAAAGAAAGA
42067879 AAAA
1 AAAA
42067883 TATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 6 0.30
19 5 0.25
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAAAAGAATAAAGAAAGA
Found at i:42068641 original size:19 final size:19
Alignment explanation
Indices: 42068596--42068656 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
42068586 ATCTAATTGC
42068596 AAATATTTAATTATTATATTT
1 AAATATTTAATTA-TA-ATTT
*
42068617 AAATATTTAAATATAATTT
1 AAATATTTAATTATAATTT
*
42068636 ATATATTCTAATTA-AATTT
1 AAATATT-TAATTATAATTT
42068655 AA
1 AA
42068657 TAAATAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.46
20 7 0.20
21 12 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATTTAATTATAATTT
Found at i:42068919 original size:26 final size:26
Alignment explanation
Indices: 42068890--42068961 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 26
42068880 AAATTTTTCC
* *
42068890 AAAGCACTTCTCAAAAGTAATTCTCA
1 AAAGCACTTTTCAAAAGCAATTCTCA
* * *
42068916 AAAGCACTTTTCTACAGCACTTCTCA
1 AAAGCACTTTTCAAAAGCAATTCTCA
42068942 AAAGCACTTTTCAAAAGCAA
1 AAAGCACTTTTCAAAAGCAA
42068962 CGAAGAACTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.26
Consensus pattern (26 bp):
AAAGCACTTTTCAAAAGCAATTCTCA
Found at i:42068927 original size:39 final size:39
Alignment explanation
Indices: 42068884--42068960 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
42068874 ACACTTAAAT
*
42068884 TTTTCCAAAGCACTTCTCAAAAGTAATTCTCAAAAGCAC
1 TTTTCCAAAGCACTTCTCAAAAGCAATTCTCAAAAGCAC
* * * *
42068923 TTTTCTACAGCACTTCTCAAAAGCACTTTTCAAAAGCA
1 TTTTCCAAAGCACTTCTCAAAAGCAATTCTCAAAAGCA
42068961 ACGAAGAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (39 bp):
TTTTCCAAAGCACTTCTCAAAAGCAATTCTCAAAAGCAC
Found at i:42068934 original size:13 final size:13
Alignment explanation
Indices: 42068884--42068960 Score: 82
Period size: 13 Copynumber: 5.9 Consensus size: 13
42068874 ACACTTAAAT
*
42068884 TTTTCCAAAGCAC
1 TTTTCAAAAGCAC
* * *
42068897 TTCTCAAAAGTAA
1 TTTTCAAAAGCAC
*
42068910 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
42068923 TTTTCTACAGCAC
1 TTTTCAAAAGCAC
*
42068936 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
42068949 TTTTCAAAAGCA
1 TTTTCAAAAGCA
42068961 ACGAAGAACT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:42072809 original size:66 final size:66
Alignment explanation
Indices: 42072728--42072862 Score: 243
Period size: 66 Copynumber: 2.0 Consensus size: 66
42072718 GAAATTGTGC
*
42072728 AACCTAAAGAAGGGTGGAGTTTGGTATTTAGGCAACTAACTAAATTTAATGTTATTTTTCTGGAA
1 AACCTAAAGAAGGGTGGAGTTTGGTATTTAGGCAACTAACTAAAGTTAATGTTATTTTTCTGGAA
42072793 A
66 A
* *
42072794 AACCTAAAGAAGGGTGGAGTTTGGTATTTAGGCAACTAACTAAAGTTAATGTTGTTTTTTTGGAA
1 AACCTAAAGAAGGGTGGAGTTTGGTATTTAGGCAACTAACTAAAGTTAATGTTATTTTTCTGGAA
42072859 A
66 A
42072860 AAC
1 AAC
42072863 AGGGTTGGAG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (66 bp):
AACCTAAAGAAGGGTGGAGTTTGGTATTTAGGCAACTAACTAAAGTTAATGTTATTTTTCTGGAA
A
Found at i:42072878 original size:60 final size:61
Alignment explanation
Indices: 42072737--42072880 Score: 184
Period size: 66 Copynumber: 2.3 Consensus size: 61
42072727 CAACCTAAAG
*
42072737 AAGGGTGGAGTTTGGTATTTAGGCAACTAACTAAATTTAATGTTATTTTTCTGGAAAAACC
1 AAGGGTGGAGTTTGGTATTTAGGCAACTAACTAAAGTTAATGTTATTTTTCTGGAAAAACC
* *
42072798 TAAAGAAGGGTGGAGTTTGGTATTTAGGCAACTAACTAAAGTTAATGTTGTTTTTTTGGAAAAA-
1 -----AAGGGTGGAGTTTGGTATTTAGGCAACTAACTAAAGTTAATGTTATTTTTCTGGAAAAAC
42072862 C
61 C
*
42072863 -AGGGTTGGAGGTTGGTAT
1 AAGGG-TGGAGTTTGGTAT
42072881 GCAATCCTAC
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
59 4 0.05
60 12 0.16
65 1 0.01
66 56 0.77
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.35
Consensus pattern (61 bp):
AAGGGTGGAGTTTGGTATTTAGGCAACTAACTAAAGTTAATGTTATTTTTCTGGAAAAACC
Found at i:42078090 original size:15 final size:15
Alignment explanation
Indices: 42078070--42078098 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42078060 TTGATTAAAA
42078070 TGTAAGCATTTATGC
1 TGTAAGCATTTATGC
42078085 TGTAAGCATTTATG
1 TGTAAGCATTTATG
42078099 TTGTCTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (15 bp):
TGTAAGCATTTATGC
Found at i:42080260 original size:16 final size:15
Alignment explanation
Indices: 42080226--42080281 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
42080216 ACAACTGAAT
*
42080226 TATTCATTTCAGGTC
1 TATTCATTTCAGCTC
*
42080241 TATTCTATTACAGCTC
1 TATTC-ATTTCAGCTC
*
42080257 TATTCCATTTCAACTC
1 TATT-CATTTCAGCTC
42080273 TATTACATT
1 TATT-CATT
42080282 AGAGTTCTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 5 0.15
16 28 0.82
17 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.46
Consensus pattern (15 bp):
TATTCATTTCAGCTC
Found at i:42080266 original size:32 final size:32
Alignment explanation
Indices: 42080226--42080297 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
42080216 ACAACTGAAT
**
42080226 TATT-CATTTCAGGTCTATT-CTATTACAGCTC
1 TATTCCATTTCAACTCTATTAC-ATTACAGCTC
* *
42080257 TATTCCATTTCAACTCTATTACATTAGAGTTC
1 TATTCCATTTCAACTCTATTACATTACAGCTC
42080289 TATTCCATT
1 TATTCCATT
42080298 CCTCCCAACC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 4 0.11
32 30 0.86
33 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.07, T:0.46
Consensus pattern (32 bp):
TATTCCATTTCAACTCTATTACATTACAGCTC
Found at i:42086329 original size:2 final size:2
Alignment explanation
Indices: 42086322--42086357 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
42086312 TCAGACATGA
42086322 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
42086358 GGATGCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42088249 original size:98 final size:98
Alignment explanation
Indices: 42088078--42088273 Score: 356
Period size: 98 Copynumber: 2.0 Consensus size: 98
42088068 TTCCACCTAC
* *
42088078 TGGTTTCCAAGACCTCATCCCTACCTATATATCCATAATCCTTCCCACCCTTAAGCACAACCTCA
1 TGGTTTCCAAAACCTCATCCCTACCTATATATCCATAATCCTTCCCACCCTCAAGCACAACCTCA
42088143 AATGCAACAAACTTGTTTTAAGCAACAATCTAA
66 AATGCAACAAACTTGTTTTAAGCAACAATCTAA
42088176 TGGTTTCCAAAACCTCATCCCTACCTATATATCCATAATCCTTCCCACCCTCAAGCACAACCTCA
1 TGGTTTCCAAAACCTCATCCCTACCTATATATCCATAATCCTTCCCACCCTCAAGCACAACCTCA
* *
42088241 AATTCAACAAACTTGTTTTAATCAACAATCTAA
66 AATGCAACAAACTTGTTTTAAGCAACAATCTAA
42088274 AGACATCAAT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.34, C:0.32, G:0.06, T:0.28
Consensus pattern (98 bp):
TGGTTTCCAAAACCTCATCCCTACCTATATATCCATAATCCTTCCCACCCTCAAGCACAACCTCA
AATGCAACAAACTTGTTTTAAGCAACAATCTAA
Found at i:42088709 original size:30 final size:30
Alignment explanation
Indices: 42088648--42088710 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
42088638 ACTTATTTTA
* *
42088648 TTGTTAATTTTGTTATTATTTTAGATGCAT
1 TTGTTAATTTTATTATTATTTTAGAAGCAT
42088678 TTGTTAATTTTATTATTATTTTA-AAGACAT
1 TTGTTAATTTTATTATTATTTTAGAAG-CAT
42088708 TTG
1 TTG
42088711 CTCGTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAGAAGCAT
Found at i:42089714 original size:20 final size:20
Alignment explanation
Indices: 42089691--42089742 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
42089681 AATTAAAAAT
**
42089691 TAAAATACTAAAATTTAAGA
1 TAAAATACTAAAATACAAGA
42089711 TAAAAT-CTTAAAATACAAGA
1 TAAAATAC-TAAAATACAAGA
42089731 TAAGAATACTAA
1 TAA-AATACTAA
42089743 TGTGACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 19 0.70
21 6 0.22
22 1 0.04
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.27
Consensus pattern (20 bp):
TAAAATACTAAAATACAAGA
Found at i:42090867 original size:16 final size:16
Alignment explanation
Indices: 42090846--42090879 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42090836 TGGCTTGATA
* *
42090846 AAACTCATACCGACTC
1 AAACTCAAACCAACTC
42090862 AAACTCAAACCAACTC
1 AAACTCAAACCAACTC
42090878 AA
1 AA
42090880 CTTGATTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.35, G:0.03, T:0.15
Consensus pattern (16 bp):
AAACTCAAACCAACTC
Found at i:42098048 original size:191 final size:191
Alignment explanation
Indices: 42097751--42098130 Score: 717
Period size: 191 Copynumber: 2.0 Consensus size: 191
42097741 ATGAAAATAA
42097751 AATAAAATAAAGAACACACAGATTTTACGTGGAAACCCTTTCGGAAAAAAATCACGAGCAGAGAA
1 AATAAAATAAAGAACACACAGATTTTACGTGGAAACCCTTTCGGAAAAAAATCACGAGCAGAGAA
*
42097816 TAAGAAAATTTACTATGTCGAATTCGAATGAATACAAAAGGAATACACTATGTCTATTTATAGGC
66 TAAGAAAATTCACTATGTCGAATTCGAATGAATACAAAAGGAATACACTATGTCTATTTATAGGC
*
42097881 TTGTAAAGCCATATTCTAGTAAGATTGAAACATCTTATTCTAATCAATATAAAATAGATAG
131 TTGTAAAGCCATATTCTAGTAAGATTGAAACACCTTATTCTAATCAATATAAAATAGATAG
*
42097942 AATAAAATAAAGAATACACAGATTTTACGTGGAAACCCTTTCGGAAAAAAATCACGAGCAGAGAA
1 AATAAAATAAAGAACACACAGATTTTACGTGGAAACCCTTTCGGAAAAAAATCACGAGCAGAGAA
42098007 TAAGAAAATTCACTATGTC-AGATTCGAATGAATACAAAAGGAATACACTATGTCTATTTATAGG
66 TAAGAAAATTCACTATGTCGA-ATTCGAATGAATACAAAAGGAATACACTATGTCTATTTATAGG
42098071 CTTGTAAAGCCATATTCTAGTAAGATTGAAACACCTTATTCTAATCAATATAAAATAGAT
130 CTTGTAAAGCCATATTCTAGTAAGATTGAAACACCTTATTCTAATCAATATAAAATAGAT
42098131 GGAGTTTAAT
Statistics
Matches: 185, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
190 1 0.01
191 184 0.99
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.27
Consensus pattern (191 bp):
AATAAAATAAAGAACACACAGATTTTACGTGGAAACCCTTTCGGAAAAAAATCACGAGCAGAGAA
TAAGAAAATTCACTATGTCGAATTCGAATGAATACAAAAGGAATACACTATGTCTATTTATAGGC
TTGTAAAGCCATATTCTAGTAAGATTGAAACACCTTATTCTAATCAATATAAAATAGATAG
Found at i:42105847 original size:13 final size:13
Alignment explanation
Indices: 42105829--42105860 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
42105819 AAAACTAAGG
*
42105829 TATCTACTAGCTT
1 TATCTACTAACTT
42105842 TATCTACTAACTT
1 TATCTACTAACTT
42105855 TATCTA
1 TATCTA
42105861 ATGTCTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.47
Consensus pattern (13 bp):
TATCTACTAACTT
Found at i:42106977 original size:22 final size:22
Alignment explanation
Indices: 42106949--42106993 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
42106939 TGGTGATAGG
42106949 CACCAATCACCCAATTTCCCGC
1 CACCAATCACCCAATTTCCCGC
42106971 CACCAATCACCCAATTTCCCGC
1 CACCAATCACCCAATTTCCCGC
42106993 C
1 C
42106994 CCCTCTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.51, G:0.04, T:0.18
Consensus pattern (22 bp):
CACCAATCACCCAATTTCCCGC
Found at i:42117624 original size:17 final size:18
Alignment explanation
Indices: 42117592--42117625 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42117582 TCCCTTTCAT
*
42117592 TGAAACGATTGAATGCCA
1 TGAAACGATCGAATGCCA
42117610 TGAAA-GATCGAATGCC
1 TGAAACGATCGAATGCC
42117626 TTCATAATTC
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:0.38, C:0.18, G:0.24, T:0.21
Consensus pattern (18 bp):
TGAAACGATCGAATGCCA
Found at i:42118096 original size:31 final size:31
Alignment explanation
Indices: 42118061--42118123 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
42118051 AACAATATAG
*
42118061 TGACTTAGATAAAAACTTTCAAATAATTTAA
1 TGACTTAAATAAAAACTTTCAAATAATTTAA
* *
42118092 TGACTTAAATTAAAACTTTCGAATAATTTAA
1 TGACTTAAATAAAAACTTTCAAATAATTTAA
42118123 T
1 T
42118124 AATTATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAATTTAA
Found at i:42120739 original size:22 final size:22
Alignment explanation
Indices: 42120704--42120745 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42120694 TATACAAGTA
42120704 ATATTACTTAAATAATTATGAG
1 ATATTACTTAAATAATTATGAG
* *
42120726 ATATTAGTTGAATAATTATG
1 ATATTACTTAAATAATTATG
42120746 TCTCTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (22 bp):
ATATTACTTAAATAATTATGAG
Found at i:42122040 original size:38 final size:36
Alignment explanation
Indices: 42121984--42122420 Score: 173
Period size: 36 Copynumber: 11.9 Consensus size: 36
42121974 TTGTGAAAGG
* *
42121984 CCTAGTCAATGTCGACCTTCAAAAAAGGTTGGGATAGA
1 CCTAGTCAAAG-CAACCTT-AAAAAAGGTTGGGATAGA
*
42122022 CCTAGTCAAAGCCAACCTTTGAAAAAGGTTGGGATAGA
1 CCTAGTCAAAG-CAACC-TTAAAAAAGGTTGGGATAGA
* * *
42122060 CCAATTTAAAGCAACCCTTAAAAAAGGTTGGGATAGA
1 CCTAGTCAAAGCAA-CCTTAAAAAAGGTTGGGATAGA
** * *
42122097 -CTCA-TTTAAGATAACCTT-AAAAAGGTTGAGATAGA
1 CCT-AGTCAAAG-CAACCTTAAAAAAGGTTGGGATAGA
* * * *
42122132 CATTGTCTAAAGTAACCCTTAAAAAAGGTTAGGATAGA
1 CCTAGTC-AAAGCAA-CCTTAAAAAAGGTTGGGATAGA
* * * * *
42122170 -CTTGTTTAAGGTAACCTT-AAAAAGGTTTGAGATAGA
1 CCTAG-TCAAAGCAACCTTAAAAAAGG-TTGGGATAGA
* * * * * **
42122206 CTTTATTTAAGGCAACCCTTAAAAAAAGTTAAGATA-A
1 C-CTAGTCAAAGCAA-CCTTAAAAAAGGTTGGGATAGA
* * * * * *
42122243 ACTCGTCTAAAACAACCCT-AAAAAGGTTAGTATAGA
1 CCTAGTC-AAAGCAACCTTAAAAAAGGTTGGGATAGA
* * * *
42122279 CCTTGTCTAAGGCAACCTTTAAAAAA-GTTGAGATAAA
1 CCTAGTC-AAAGCAACC-TTAAAAAAGGTTGGGATAGA
* * * *
42122316 GCC-ATTTAATA-CAACTTTAAAAAA-GTTGGGATATA
1 -CCTAGTCAA-AGCAACCTTAAAAAAGGTTGGGATAGA
* * * *
42122351 CCTTA-TCTAAGACAACTTTTAAAAAGGTTGGAATAGA
1 CC-TAGTCAAAG-CAACCTTAAAAAAGGTTGGGATAGA
* *
42122388 -CTCGTCTAAAGCAACTTTAAAAAA-GTTGGGATA
1 CCTAGTC-AAAGCAACCTTAAAAAAGGTTGGGATA
42122421 AACATTATCT
Statistics
Matches: 306, Mismatches: 65, Indels: 59
0.71 0.15 0.14
Matches are distributed among these distances:
34 3 0.01
35 63 0.21
36 80 0.26
37 76 0.25
38 76 0.25
39 8 0.03
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (36 bp):
CCTAGTCAAAGCAACCTTAAAAAAGGTTGGGATAGA
Found at i:42122084 original size:37 final size:36
Alignment explanation
Indices: 42121999--42122493 Score: 200
Period size: 37 Copynumber: 13.6 Consensus size: 36
42121989 TCAATGTCGA
* *
42121999 CCTTCAAAAAAGGTTGGGATAGACCTAGTCAAAGCCAAC
1 CCTT-AAAAAAGGTTGGGATAGACC-ATTTAAAG-CAAC
* *
42122038 CTTTGAAAAAGGTTGGGATAGACCAATTTAAAGCAAC
1 CCTTAAAAAAGGTTGGGATAGACC-ATTTAAAGCAAC
*
42122075 CCTTAAAAAAGGTTGGGATAGACTCATTT-AAG-ATAA
1 CCTTAAAAAAGGTTGGGATAGAC-CATTTAAAGCA-AC
* *
42122111 CCTT-AAAAAGGTTGAGATAGA-CATTGTCTAAAGTAAC
1 CCTTAAAAAAGGTTGGGATAGACCA-T-T-TAAAGCAAC
* ** * *
42122148 CCTTAAAAAAGGTTAGGATAGACTTGTTTAAGGTAA-
1 CCTTAAAAAAGGTTGGGATAGAC-CATTTAAAGCAAC
* * *
42122184 CCTT-AAAAAGGTTTGAGATAGACTTTATTTAAGGCAAC
1 CCTTAAAAAAGG-TTGGGATAGAC--CATTTAAAGCAAC
* ** * * * *
42122222 CCTTAAAAAAAGTTAAGATAAACTCGTCTAAAACAAC
1 CCTTAAAAAAGGTTGGGATAGAC-CATTTAAAGCAAC
* * * *
42122259 CC-T-AAAAAGGTTAGTATAGACCTTGTCTAAGGCAAC
1 CCTTAAAAAAGGTTGGGATAGACCAT-T-TAAAGCAAC
* * *
42122295 CTTTAAAAAA-GTTGAGATAAAGCCATTTAATA-CAA-
1 CCTTAAAAAAGGTTGGGATAGA-CCATTTAA-AGCAAC
* * *
42122330 CTTTAAAAAA-GTTGGGATATACC-TTATCTAAGACAA-
1 CCTTAAAAAAGGTTGGGATAGACCATT-T-AAAG-CAAC
* * * * *
42122366 CTTTTAAAAAGGTTGGAATAGACTCGTCTAAAGCAA-
1 CCTTAAAAAAGGTTGGGATAGAC-CATTTAAAGCAAC
* * **
42122402 CTTTAAAAAA-GTTGGGATA-AACATTATCTAAAATAAC
1 CCTTAAAAAAGGTTGGGATAGACCA-T-T-TAAAGCAAC
** * ** *
42122439 TTTTAAAAAAAGTTGAAATAGACCCGTTTAAAGCAA-
1 CCTTAAAAAAGGTTGGGATAGA-CCATTTAAAGCAAC
42122475 CCTT-AAAAAGGTTGGGATA
1 CCTTAAAAAAGGTTGGGATA
42122494 AATCAAAAGG
Statistics
Matches: 353, Mismatches: 69, Indels: 72
0.71 0.14 0.15
Matches are distributed among these distances:
33 5 0.01
34 9 0.03
35 79 0.22
36 69 0.20
37 103 0.29
38 74 0.21
39 13 0.04
40 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (36 bp):
CCTTAAAAAAGGTTGGGATAGACCATTTAAAGCAAC
Found at i:42122156 original size:72 final size:72
Alignment explanation
Indices: 42122034--42122493 Score: 333
Period size: 72 Copynumber: 6.3 Consensus size: 72
42122024 TAGTCAAAGC
* * *
42122034 CAACCTTTGAAAAAGGTTGGGATAGACCA--ATTTAAAGCAACCCTTAAAAAAGGTTGGGATAGA
1 CAACC-TT-AAAAAGGTTGGGATAGA-CATTATCTAAAGCAACCCTTAAAAAAAGTTGAGATAGA
*
42122097 CTCATTTAAGA
63 CTCGTTTAA-A
* * * * *
42122108 TAACCTTAAAAAGGTTGAGATAGACATTGTCTAAAGTAACCCTTAAAAAAGGTT-AGGATAGACT
1 CAACCTTAAAAAGGTTGGGATAGACATTATCTAAAGCAACCCTTAAAAAAAGTTGA-GATAGACT
* *
42122172 TGTTTAAGG
65 CGTTTAA-A
* * * * * * *
42122181 TAACCTTAAAAAGGTTTGAGATAGACTTTATTTAAGGCAACCCTTAAAAAAAGTTAAGATAAACT
1 CAACCTTAAAAAGG-TTGGGATAGACATTATCTAAAGCAACCCTTAAAAAAAGTTGAGATAGACT
*
42122246 CGTCTAAAA
65 CGT-TTAAA
* * * * * * * *
42122255 CAACCCTAAAAAGGTTAGTATAGACCTTGTCTAAGGCAA-CCTTTAAAAAAGTTGAGATAAAGC-
1 CAACCTTAAAAAGGTTGGGATAGACATTATCTAAAGCAACCCTTAAAAAAAGTTGAGATAGA-CT
*
42122318 CATTTAATA
65 CGTTTAA-A
* * * * * * *
42122327 CAACTTTAAAAAAGTTGGGATATACCTTATCT-AAGACAA-CTTTTAAAAAGGTTG-GAATAGAC
1 CAACCTTAAAAAGGTTGGGATAGACATTATCTAAAG-CAACCCTTAAAAAAAGTTGAG-ATAGAC
*
42122389 TCGTCTAAA
64 TCGTTTAAA
* * * ** ** * *
42122398 GCAACTTTAAAAAAGTTGGGATAAACATTATCTAAAATAACTTTTAAAAAAAGTTGAAATAGACC
1 -CAACCTTAAAAAGGTTGGGATAGACATTATCTAAAGCAACCCTTAAAAAAAGTTGAGATAGACT
42122463 CGTTTAAA
65 CGTTTAAA
42122471 GCAACCTTAAAAAGGTTGGGATA
1 -CAACCTTAAAAAGGTTGGGATA
42122494 AATCAAAAGG
Statistics
Matches: 315, Mismatches: 56, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
71 10 0.03
72 121 0.38
73 121 0.38
74 59 0.19
75 4 0.01
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.27
Consensus pattern (72 bp):
CAACCTTAAAAAGGTTGGGATAGACATTATCTAAAGCAACCCTTAAAAAAAGTTGAGATAGACTC
GTTTAAA
Found at i:42122161 original size:73 final size:73
Alignment explanation
Indices: 42121999--42122493 Score: 358
Period size: 73 Copynumber: 6.8 Consensus size: 73
42121989 TCAATGTCGA
* ** *
42121999 CCTTCAAAAAAGGTTGGGATAGACCTAGTCAAAGCCAACCTTTGAAAAAGGTTGGGATAGACCA-
1 CCTT-AAAAAAGGTTGGGATAGA-CTCGTTTAAGACAACC-TT-AAAAAGGTTGGGATAGA-CAT
*
42122063 -ATTTAAAGCAAC
61 TATCTAAAGCAAC
* * * *
42122075 CCTTAAAAAAGGTTGGGATAGACTCATTTAAGATAACCTTAAAAAGGTTGAGATAGACATTGTCT
1 CCTTAAAAAAGGTTGGGATAGACTCGTTTAAGACAACCTTAAAAAGGTTGGGATAGACATTATCT
*
42122140 AAAGTAAC
66 AAAGCAAC
* * ** * * *
42122148 CCTTAAAAAAGGTTAGGATAGACTTGTTTAAGGTAACCTTAAAAAGGTTTGAGATAGACTTTATT
1 CCTTAAAAAAGGTTGGGATAGACTCGTTTAAGACAACCTTAAAAAGG-TTGGGATAGACATTATC
*
42122213 TAAGGCAAC
65 TAAAGCAAC
* ** * * * * * * * *
42122222 CCTTAAAAAAAGTTAAGATAAACTCGTCTAAAACAACCCTAAAAAGGTTAGTATAGACCTTGTCT
1 CCTTAAAAAAGGTTGGGATAGACTCGTTTAAGACAACCTTAAAAAGGTTGGGATAGACATTATCT
*
42122287 AAGGCAAC
66 AAAGCAAC
* * * * * * * * *
42122295 CTTTAAAAAA-GTTGAGATAAAGC-CATTTAATACAACTTTAAAAAAGTTGGGATATACCTTATC
1 CCTTAAAAAAGGTTGGGATAGA-CTCGTTTAAGACAACCTTAAAAAGGTTGGGATAGACATTATC
42122358 T-AAGACAA-
65 TAAAG-CAAC
* * * * * * *
42122366 CTTTTAAAAAGGTTGGAATAGACTCGTCTAA-AGCAACTTTAAAAAAGTTGGGATAAACATTATC
1 CCTTAAAAAAGGTTGGGATAGACTCGTTTAAGA-CAACCTTAAAAAGGTTGGGATAGACATTATC
**
42122430 TAAAATAAC
65 TAAAGCAAC
** * ** *
42122439 TTTTAAAAAAAGTTGAAATAGACCCGTTTAA-AGCAACCTTAAAAAGGTTGGGATA
1 CCTTAAAAAAGGTTGGGATAGACTCGTTTAAGA-CAACCTTAAAAAGGTTGGGATA
42122494 AATCAAAAGG
Statistics
Matches: 344, Mismatches: 65, Indels: 23
0.80 0.15 0.05
Matches are distributed among these distances:
71 15 0.04
72 105 0.31
73 133 0.39
74 69 0.20
75 18 0.05
76 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (73 bp):
CCTTAAAAAAGGTTGGGATAGACTCGTTTAAGACAACCTTAAAAAGGTTGGGATAGACATTATCT
AAAGCAAC
Found at i:42122214 original size:110 final size:108
Alignment explanation
Indices: 42121999--42122493 Score: 319
Period size: 110 Copynumber: 4.5 Consensus size: 108
42121989 TCAATGTCGA
* * * **
42121999 CCTTCAAAAAAGGTTGGGATAGACCTAGTC-AAAGCCAACCTTTGAAAAAGGTTGGGATAGACCA
1 CCTT-AAAAAAGGTTGAGATAGA-CTAGTCTAAAG-CAACCCTT-AAAAAGGTTAGGATAGACTT
* * * *
42122063 ATTTAAAGCAACCCTTAAAAAAGGTTGGGATAGACTCATTTAAGATAA-
62 GTTTAAGGCAA-CCTT-AAAAAGGTTGAGATAGACTCATTTAAGACAAC
* *
42122111 CCTT-AAAAAGGTTGAGATAGACATTGTCTAAAGTAACCCTTAAAAAAGGTTAGGATAGACTTGT
1 CCTTAAAAAAGGTTGAGATAGAC-TAGTCTAAAGCAACCCTT-AAAAAGGTTAGGATAGACTTGT
* * *
42122175 TTAAGGTAACCTTAAAAAGGTTTGAGATAGACTTTATTTAAGGCAAC
64 TTAAGGCAACCTTAAAAAGG-TTGAGATAGAC-TCATTTAAGACAAC
* * * * * * *
42122222 CCTTAAAAAAAGTTAAGATAAACTCGTCTAAAACAACCC-TAAAAAGGTTAGTATAGACCTTGTC
1 CCTTAAAAAAGGTTGAGATAGACTAGTCTAAAGCAACCCTTAAAAAGGTTAGGATAGA-CTTGTT
* * *
42122286 TAAGGCAACCTTTAAAAAAGTTGAGATAAAGC-CATTTAATACAA-
65 TAAGGCAACC-TTAAAAAGGTTGAGATAGA-CTCATTTAAGACAAC
* * * ** *
42122330 CTTTAAAAAA-GTTGGGATATACCTTA-TCT-AAGACAACTTTTAAAAAGGTT-GGAATAGACTC
1 CCTTAAAAAAGGTTGAGATAGA-C-TAGTCTAAAG-CAACCCTTAAAAAGGTTAGG-ATAGACTT
* * * * * * * * * *
42122391 GTCTAAAGCAACTTTAAAAAAGTTGGGATAAACATTATCTAAAATAAC
62 GTTTAAGGCAACCTTAAAAAGGTTGAGATAGAC-TCATTTAAGACAAC
** * * ** * *
42122439 TTTTAAAAAAAGTTGAAATAGACCCGTTTAAAGCAA-CCTTAAAAAGGTTGGGATA
1 CCTTAAAAAAGGTTGAGATAGACTAGTCTAAAGCAACCCTTAAAAAGGTTAGGATA
42122494 AATCAAAAGG
Statistics
Matches: 307, Mismatches: 55, Indels: 46
0.75 0.13 0.11
Matches are distributed among these distances:
106 1 0.00
107 28 0.09
108 60 0.20
109 73 0.24
110 96 0.31
111 30 0.10
112 19 0.06
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (108 bp):
CCTTAAAAAAGGTTGAGATAGACTAGTCTAAAGCAACCCTTAAAAAGGTTAGGATAGACTTGTTT
AAGGCAACCTTAAAAAGGTTGAGATAGACTCATTTAAGACAAC
Found at i:42122481 original size:108 final size:107
Alignment explanation
Indices: 42122224--42122489 Score: 240
Period size: 108 Copynumber: 2.5 Consensus size: 107
42122214 AAGGCAACCC
* * * * * * *
42122224 TTAAAAAAAGTT-AAGATAAACTCGTCTAAAACAACCCTAAAAAGGTTAGTATAGACCTTGTCTA
1 TTAAAAAAAGTTGAA-ATAAACCCGTTTAAAGCAACCTTAAAAAGGTTGGAATAGACCTCGTCTA
* *
42122288 AGGCAACCTTTAAAAAAGTTGAGATAAAGCCATTTAATACAACT
65 AAGCAACCTTTAAAAAAGTTGAGATAAA-CCATTTAAAACAACT
** * * *
42122332 TT-AAAAAAGTTGGGATATA-CC-TTATCTAAGACAACTTTTAAAAAGGTTGGAATAGA-CTCGT
1 TTAAAAAAAGTTGAAATAAACCCGTT-T-AAAG-CAAC-CTTAAAAAGGTTGGAATAGACCTCGT
* *
42122393 CTAAAGCAA-CTTTAAAAAAGTTGGGATAAA-CATTATCTAAAATAACTT
62 CTAAAGCAACCTTTAAAAAAGTTGAGATAAACCA-T-T-TAAAACAAC-T
*
42122441 TTAAAAAAAGTTGAAATAGACCCGTTTAAAGCAACCTTAAAAAGGTTGG
1 TTAAAAAAAGTTGAAATAAACCCGTTTAAAGCAACCTTAAAAAGGTTGG
42122490 GATAAATCAA
Statistics
Matches: 125, Mismatches: 21, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
105 3 0.02
106 3 0.02
107 36 0.29
108 38 0.30
109 23 0.18
110 17 0.14
111 3 0.02
112 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (107 bp):
TTAAAAAAAGTTGAAATAAACCCGTTTAAAGCAACCTTAAAAAGGTTGGAATAGACCTCGTCTAA
AGCAACCTTTAAAAAAGTTGAGATAAACCATTTAAAACAACT
Found at i:42122680 original size:6 final size:7
Alignment explanation
Indices: 42122656--42122687 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
42122646 TACAACTAAA
42122656 AAAATAT
1 AAAATAT
42122663 AAAATAT
1 AAAATAT
42122670 AAAAT-T
1 AAAATAT
42122676 AAAAT-T
1 AAAATAT
42122682 AAAATA
1 AAAATA
42122688 ATGATTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAATAT
Found at i:42125861 original size:23 final size:23
Alignment explanation
Indices: 42125800--42125861 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
42125790 ATATTTATCT
*
42125800 TATTTATGATT-AAAATTTTTAAA
1 TATTTAT-ATTAAAAATTTTGAAA
* *
42125823 TATATATAATATAAAATTTTGAAA
1 TATTTATATTA-AAAATTTTGAAA
42125847 TATTTATATTAAAAA
1 TATTTATATTAAAAA
42125862 AACTCTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 2 0.06
23 10 0.31
24 20 0.62
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (23 bp):
TATTTATATTAAAAATTTTGAAA
Found at i:42125913 original size:28 final size:29
Alignment explanation
Indices: 42125875--42125936 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 29
42125865 TCTAAAATCA
* *
42125875 TAAACCCCAAACCCATAAACACAAAACC-
1 TAAAACCCAAACCCACAAACACAAAACCG
*
42125903 TAAAACCCAAACTCACAAACACAAAACCG
1 TAAAACCCAAACCCACAAACACAAAACCG
42125932 TAAAA
1 TAAAA
42125937 TCTTAAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 25 0.83
29 5 0.17
ACGTcount: A:0.56, C:0.34, G:0.02, T:0.08
Consensus pattern (29 bp):
TAAAACCCAAACCCACAAACACAAAACCG
Found at i:42125964 original size:21 final size:22
Alignment explanation
Indices: 42125940--42125995 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
42125930 CGTAAAATCT
* *
42125940 TAAATCATAAACTA-TAATCCC
1 TAAACCATAAACTACTAAACCC
* *
42125961 TAAACCTTAAAC-ACTAAACCT
1 TAAACCATAAACTACTAAACCC
42125982 TAAACCATAAACTA
1 TAAACCATAAACTA
42125996 AATTGATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (22 bp):
TAAACCATAAACTACTAAACCC
Found at i:42125977 original size:14 final size:14
Alignment explanation
Indices: 42125960--42125986 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42125950 ACTATAATCC
42125960 CTAAACCTTAAACA
1 CTAAACCTTAAACA
42125974 CTAAACCTTAAAC
1 CTAAACCTTAAAC
42125987 CATAAACTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (14 bp):
CTAAACCTTAAACA
Found at i:42125992 original size:14 final size:14
Alignment explanation
Indices: 42125938--42125993 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
42125928 ACCGTAAAAT
*
42125938 CTTAAATCATAAA-
1 CTTAAACCATAAAC
* *
42125951 CTATAATCCCTAAAC
1 CT-TAAACCATAAAC
42125966 CTTAAA-CACTAAAC
1 CTTAAACCA-TAAAC
42125980 CTTAAACCATAAAC
1 CTTAAACCATAAAC
42125994 TAAATTGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 3 0.09
14 27 0.79
15 4 0.12
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (14 bp):
CTTAAACCATAAAC
Found at i:42126451 original size:124 final size:125
Alignment explanation
Indices: 42126283--42126942 Score: 522
Period size: 140 Copynumber: 5.0 Consensus size: 125
42126273 TATAACACAA
* * * * *
42126283 GTCGGCATAGTGTTAGATA-AAA-CTGACTCTTATTTAAGCATTGCCTTAGGTATGCATATCCCG
1 GTCGGCATAGTGTT-GA-ACAAAGCCGAATCTTATTTAAGCGTTGCCTTAGGCATGCATAT-CCA
* * * *
42126346 ACCCTTATACAAAGAGTTGGCCAAAGCATATGTTGGC-AGTTTATCCCAACACTTAGGAAAGT
63 ACCCTTATACAAAGAGTTGGCCAAAGCGTATGTCGACAAGTCTATCCCAACACTTAGGAAAGT
* * * * *
42126408 GTCGGCATAGTGTT-CACAAAGTCGAATCTTATTTAAGTGTTGCCTTAGGCATGTATATACCAAT
1 GTCGGCATAGTGTTGAACAAAGCCGAATCTTATTTAAGCGTTGCCTTAGGCATGCATAT-CCAAC
* * * * *
42126472 TCTTATCCAAAGAGTTGGCCAAAACGTATGCCGACAAGTCTATCCCAACACTTAGCAAAGT
65 CCTTATACAAAGAGTTGGCCAAAGCGTATGTCGACAAGTCTATCCCAACACTTAGGAAAGT
* * * *
42126533 GTCGGCATAGTGTTGAACAAAGCCGACTCTTAATTAAGCGTTGTCTTAGGCATGCATATCCTACC
1 GTCGGCATAGTGTTGAACAAAGCCGAATCTTATTTAAGCGTTGCCTTAGGCATGCATATCCAACC
* * * * *
42126598 TCTTATACAAAGGGTTGGCAAAAGTGTATATCAACAAGTCTATCCCAACACTTAGGAAAGT
66 -CTTATACAAAGAGTTGGCCAAAGCGTATGTCGACAAGTCTATCCCAACACTTAGGAAAGT
* * *
42126659 GTCGGCCCAAAAGTGTCGGCATAGTGTTAGACAAAGCC-AACTTTTATTTAAGCGTTGCCTTAGA
1 GTCGG--C-ATA--GT--G--T--TG--A-ACAAAGCCGAA-TCTTATTTAAGCGTTGCCTTAGG
* * * * *
42126723 CATGCATATCCCAACTCTTATATAAAGAGTTGGCCAAAGTGTATATCGACAAATCTATCCCAACA
51 CATGCATAT-CCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTCGACAAGTCTATCCCAACA
42126788 CTTAGGAAAGTGTTAGCCCAAAAGT
115 CTT-----A--G---G----AAAGT
* * * *
42126813 GTCGGCATAGTGTTAGAA-AAAGTCGACTCTTATTTAAGCGTTCCCTTAGGCTTGCATATCCCAA
1 GTCGGCATAGTGTT-GAACAAAGCCGAATCTTATTTAAGCGTTGCCTTAGGCATGCATAT-CCAA
* * * * * * *
42126877 CTCTTATACAAAGTGTTGGCCAAAGTGTATGTCAACAAGTTTATCCTAACACTTAAGAAAGT
64 CCCTTATACAAAGAGTTGGCCAAAGCGTATGTCGACAAGTCTATCCCAACACTTAGGAAAGT
42126939 GTCG
1 GTCG
42126943 CAATAGGCCT
Statistics
Matches: 431, Mismatches: 67, Indels: 73
0.75 0.12 0.13
Matches are distributed among these distances:
122 1 0.00
123 3 0.01
124 61 0.14
125 54 0.13
126 102 0.24
128 1 0.00
129 2 0.00
130 1 0.00
131 2 0.00
133 1 0.00
135 2 0.00
137 2 0.00
139 2 0.00
140 168 0.39
141 6 0.01
142 1 0.00
143 1 0.00
144 1 0.00
145 2 0.00
147 2 0.00
149 2 0.00
150 1 0.00
151 2 0.00
152 1 0.00
154 10 0.02
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (125 bp):
GTCGGCATAGTGTTGAACAAAGCCGAATCTTATTTAAGCGTTGCCTTAGGCATGCATATCCAACC
CTTATACAAAGAGTTGGCCAAAGCGTATGTCGACAAGTCTATCCCAACACTTAGGAAAGT
Found at i:42126780 original size:140 final size:140
Alignment explanation
Indices: 42126528--42126942 Score: 607
Period size: 140 Copynumber: 3.0 Consensus size: 140
42126518 AACACTTAGC
* *
42126528 AAAGTGTCGGCATAGTGTT-GAACAAAGCCGACTCTTAATTAAGCGTTGTCTTAGGCATGCATAT
1 AAAGTGTCGGCATAGTGTTAG-ACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATAT
* * * *
42126592 CCTACCTCTTATACAAAGGGTTGGCAAAAGTGTATATCAACAAGTCTATCCCAACACTTAGGAAA
65 CCCAACTCTTATACAAAGAGTTGGCCAAAGTGTATATCAACAAGTCTATCCCAACACTTAGGAAA
42126657 GTGTCGGCCCA
130 GTGTCGGCCCA
* * *
42126668 AAAGTGTCGGCATAGTGTTAGACAAAGCCAACTTTTATTTAAGCGTTGCCTTAGACATGCATATC
1 AAAGTGTCGGCATAGTGTTAGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATC
* * *
42126733 CCAACTCTTATATAAAGAGTTGGCCAAAGTGTATATCGACAAATCTATCCCAACACTTAGGAAAG
66 CCAACTCTTATACAAAGAGTTGGCCAAAGTGTATATCAACAAGTCTATCCCAACACTTAGGAAAG
**
42126798 TGTTAGCCCA
131 TGTCGGCCCA
* * * *
42126808 AAAGTGTCGGCATAGTGTTAGAAAAAGTCGACTCTTATTTAAGCGTTCCCTTAGGCTTGCATATC
1 AAAGTGTCGGCATAGTGTTAGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATC
* * * * *
42126873 CCAACTCTTATACAAAGTGTTGGCCAAAGTGTATGTCAACAAGTTTATCCTAACACTTAAGAAAG
66 CCAACTCTTATACAAAGAGTTGGCCAAAGTGTATATCAACAAGTCTATCCCAACACTTAGGAAAG
42126938 TGTCG
131 TGTCG
42126943 CAATAGGCCT
Statistics
Matches: 243, Mismatches: 31, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
140 242 1.00
141 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (140 bp):
AAAGTGTCGGCATAGTGTTAGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATC
CCAACTCTTATACAAAGAGTTGGCCAAAGTGTATATCAACAAGTCTATCCCAACACTTAGGAAAG
TGTCGGCCCA
Found at i:42128276 original size:62 final size:58
Alignment explanation
Indices: 42128172--42128286 Score: 149
Period size: 62 Copynumber: 1.9 Consensus size: 58
42128162 CACATTACTT
**
42128172 AATAATATTTATTATCTTATAAAATAATATTTTTTTGATAATTTTACAATTAAATTAA
1 AATAATATTTATTATCTTATAAAATAATATTTTTTAAATAATTTTACAATTAAATTAA
* **
42128230 AATAATATTTATTATTTTTCATAAAATGTTTATTTTTTAAAATAATTTTACAATTAA
1 AATAATATTTATTA-TCTT-ATAAAAT-AATATTTTTT-AAATAATTTTACAATTAA
42128287 GTACAGAAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 14 0.29
59 3 0.06
60 7 0.15
61 8 0.17
62 16 0.33
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.51
Consensus pattern (58 bp):
AATAATATTTATTATCTTATAAAATAATATTTTTTAAATAATTTTACAATTAAATTAA
Found at i:42131048 original size:30 final size:30
Alignment explanation
Indices: 42131014--42131078 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
42131004 ATTTAGACTT
42131014 AACTAATATTCCAATATCAGACTATGAAAA
1 AACTAATATTCCAATATCAGACTATGAAAA
* *
42131044 AACTAATATTTCAATATTAGACTATGAAAA
1 AACTAATATTCCAATATCAGACTATGAAAA
42131074 AACTA
1 AACTA
42131079 TAGACGATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (30 bp):
AACTAATATTCCAATATCAGACTATGAAAA
Found at i:42133793 original size:31 final size:31
Alignment explanation
Indices: 42133747--42133807 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
42133737 ACCCCTTCCT
* *
42133747 GCATTAAATCGAACCAAAAACAGAAAATATA
1 GCATGAAATCCAACCAAAAACAGAAAATATA
*
42133778 GCATGAAATCCAACCAAAAACAGTAAATAT
1 GCATGAAATCCAACCAAAAACAGAAAATAT
42133808 CGTATCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.56, C:0.18, G:0.10, T:0.16
Consensus pattern (31 bp):
GCATGAAATCCAACCAAAAACAGAAAATATA
Found at i:42134576 original size:13 final size:14
Alignment explanation
Indices: 42134550--42134578 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
42134540 ACTAACGACG
42134550 AATTAAACCATTAT
1 AATTAAACCATTAT
42134564 AATTAAA-CATTAT
1 AATTAAACCATTAT
42134577 AA
1 AA
42134579 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:42139886 original size:29 final size:28
Alignment explanation
Indices: 42139852--42139954 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
42139842 TACTCAATCA
*
42139852 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
42139881 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
42139910 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
42139939 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
42139955 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:42147904 original size:29 final size:28
Alignment explanation
Indices: 42147870--42147972 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
42147860 TACTCAATCA
*
42147870 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
42147899 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
42147928 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
42147957 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
42147973 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:42150939 original size:9 final size:9
Alignment explanation
Indices: 42150892--42150980 Score: 74
Period size: 9 Copynumber: 9.7 Consensus size: 9
42150882 ATTTTTATGT
42150892 ATTATGTAA
1 ATTATGTAA
*
42150901 GTTATGTAA
1 ATTATGTAA
42150910 ATTATGTAA
1 ATTATGTAA
* ***
42150919 GTTATCCGA
1 ATTATGTAA
42150928 ATTATGTAA
1 ATTATGTAA
42150937 ATTATGATATA
1 ATTATG-TA-A
42150948 TATTTATGT--
1 -A-TTATGTAA
42150957 ATTATGTAA
1 ATTATGTAA
42150966 ATTATGTAA
1 ATTATGTAA
*
42150975 AATATG
1 ATTATG
42150981 ATATATATTT
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
7 6 0.10
8 1 0.02
9 46 0.73
10 2 0.03
11 1 0.02
12 2 0.03
13 5 0.08
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.45
Consensus pattern (9 bp):
ATTATGTAA
Found at i:42151316 original size:26 final size:27
Alignment explanation
Indices: 42151264--42151317 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
42151254 CTGATTAAAA
42151264 TAAATAAAATAAAACTTTAAATACAAT
1 TAAATAAAATAAAACTTTAAATACAAT
42151291 TAAATAAAATAAAAC-TTAAATACAAT
1 TAAATAAAATAAAACTTTAAATACAAT
42151317 T
1 T
42151318 TACTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (27 bp):
TAAATAAAATAAAACTTTAAATACAAT
Found at i:42151335 original size:116 final size:113
Alignment explanation
Indices: 42151175--42151403 Score: 372
Period size: 116 Copynumber: 2.0 Consensus size: 113
42151165 TTCGTGATTA
*
42151175 AAATAAAATAAAACTTTAAATACAATTTAATTTATTTAGGTAATTTAAAAATAAAATAAAAGTAG
1 AAATAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAG
42151240 AC-AAAAGTTTTTTCCTGATTAAAATAAATAAAATAAAACTTTAAATACAATT
66 ACTAAAA-TTTTTTCCTGATT---A-AAATAAAATAAAACTTTAAATACAATT
*
42151292 AAATAAAATAAAAC-TTAAATACAATTTACTTTAATTAGGTAATTTAAAAATAAAATAAAAGTAG
1 AAATAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAG
*
42151356 ACTAAAATTTTTTCGTGATTAAAATAAAATAAAACTTTAAATACAATT
66 ACTAAAATTTTTTCCTGATTAAAATAAAATAAAACTTTAAATACAATT
42151404 TAATTTAATT
Statistics
Matches: 108, Mismatches: 3, Indels: 7
0.92 0.03 0.06
Matches are distributed among these distances:
112 27 0.25
113 1 0.01
116 62 0.57
117 18 0.17
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (113 bp):
AAATAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAG
ACTAAAATTTTTTCCTGATTAAAATAAAATAAAACTTTAAATACAATT
Found at i:42151413 original size:86 final size:83
Alignment explanation
Indices: 42151288--42151473 Score: 302
Period size: 86 Copynumber: 2.2 Consensus size: 83
42151278 CTTTAAATAC
*
42151288 AATT-AAATAAAATAAAACTTAAATACAATTTACTTTAATTAGGTAATTTAAAAATAAAATAAAA
1 AATTAAAATAAAATAAAACTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAA
*
42151352 GTAGACTAAAATTTTTTCGT
66 GTAGAC--AAATTTTTTCCT
*
42151372 GATTAAAATAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAA
1 AATTAAAATAAAATAAAAC-TTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAA
*
42151437 AGTAGACAAGTTTTTTCCT
65 AGTAGACAAATTTTTTCCT
42151456 AATTAAAATAAAATAAAA
1 AATTAAAATAAAATAAAA
42151474 TAAAATAAAA
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
84 30 0.32
85 14 0.15
86 51 0.54
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.34
Consensus pattern (83 bp):
AATTAAAATAAAATAAAACTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAA
GTAGACAAATTTTTTCCT
Found at i:42151469 original size:5 final size:5
Alignment explanation
Indices: 42151459--42151483 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42151449 TTTTCCTAAT
42151459 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
42151484 CTTTAAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:42151565 original size:5 final size:5
Alignment explanation
Indices: 42151555--42151579 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42151545 TTTTCATAAT
42151555 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
42151580 CTTTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:42151608 original size:96 final size:96
Alignment explanation
Indices: 42151375--42151637 Score: 476
Period size: 96 Copynumber: 2.8 Consensus size: 96
42151365 TTTTCGTGAT
42151375 TAAAATAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGT
1 TAAAATAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGT
*
42151440 AGAC--AAGTTTTTTCCTAATTAAAATAAAA
66 AGACAAAAGTTTTTTCATAATTAAAATAAAA
*
42151469 TAAAATAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAATT
1 TAAAATAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGT
*
42151534 TGACAAAAGTTTTTTCATAATTAAAATAAAA
66 AGACAAAAGTTTTTTCATAATTAAAATAAAA
*
42151565 TAAAATAAAATAAAACTTTAAATATAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGT
1 TAAAATAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGT
42151630 AGACAAAA
66 AGACAAAA
42151638 TATTTTAAAC
Statistics
Matches: 161, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
94 67 0.42
96 94 0.58
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.34
Consensus pattern (96 bp):
TAAAATAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGT
AGACAAAAGTTTTTTCATAATTAAAATAAAA
Found at i:42151634 original size:190 final size:179
Alignment explanation
Indices: 42151282--42151635 Score: 521
Period size: 190 Copynumber: 1.9 Consensus size: 179
42151272 ATAAAACTTT
* * *
42151282 AAATACAATTAAATAAAATAAAACTTAAATACAATTTACTTTAATTAGGTAATTTAAAAATAAAA
1 AAATAAAATAAAATAAAATAAAACTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAA
*
42151347 TAAAAGTAGACTAAAATTTTTTCGTGATTAAAATAAAATAAAACTTTAAATACAATTTAATTTAA
66 TAAAAGTAGACTAAAATTTTTTCGTAATTAAAATAAAATAAAACTTTAAATACAATTTAATTTAA
42151412 TTAGGTAATTTAAAAATAAAATAAAAGTAGACAAGTTTTTTCCTAATTA
131 TTAGGTAATTTAAAAATAAAATAAAAGTAGACAAGTTTTTTCCTAATTA
42151461 AAATAAAATAAAATAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAA
1 AAATAAAATAAAATAAAATAAAAC-TTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAA
* * * *
42151526 ATAAAATTTGAC-AAAAGTTTTTTCATAATTAAAATAAAATAAAATAAAATAAAACTTTAAATAT
65 ATAAAAGTAGACTAAAA-TTTTTTC----GT--AAT----TAAAATAAAATAAAACTTTAAATAC
42151590 AATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAA
119 AATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAA
42151636 AATATTTTAA
Statistics
Matches: 155, Mismatches: 8, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
179 26 0.17
180 56 0.36
184 1 0.01
186 2 0.01
190 70 0.45
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (179 bp):
AAATAAAATAAAATAAAATAAAACTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAA
TAAAAGTAGACTAAAATTTTTTCGTAATTAAAATAAAATAAAACTTTAAATACAATTTAATTTAA
TTAGGTAATTTAAAAATAAAATAAAAGTAGACAAGTTTTTTCCTAATTA
Found at i:42151770 original size:99 final size:98
Alignment explanation
Indices: 42151600--42151881 Score: 421
Period size: 98 Copynumber: 2.9 Consensus size: 98
42151590 AATTTAATTT
* **
42151600 AATTAGGTAATTTAAAAATAAAATAAAAGTA--GACAA--AATATTTTAAACATTGTTAAGTCTT
1 AATTAGGTAATTTAAAAATAAAATAAAA-TATTTA-AATTAATACATTAAAC-TTGTTAAGTCTT
42151661 TCTTTTAATTTGCATTTATTAATTTGTTAATTGAAA
63 TCTTTTAATTTGCATTTATTAATTTGTTAATTGAAA
42151697 AATTAGGTAATTTAAAAATAAAATAAAATATTTAAATTAATCACATTAAACTTGTTAAGTCTTTC
1 AATTAGGTAATTTAAAAATAAAATAAAATATTTAAATTAAT-ACATTAAACTTGTTAAGTCTTTC
*
42151762 TTTTAATTTGCATTTATTAATTTGTTAATTTAAA
65 TTTTAATTTGCATTTATTAATTTGTTAATTGAAA
* * *
42151796 AATTAGGTAATAT-AAAATAAAATAAAATATTTAAATTAATGACATTAAACTTGTTAACTCTTAC
1 AATTAGGTAATTTAAAAATAAAATAAAATATTTAAATTAAT-ACATTAAACTTGTTAAGTCTTTC
42151860 TTTTAATTTGCATTTATTAATT
65 TTTTAATTTGCATTTATTAATT
42151882 CTTTTGGTAA
Statistics
Matches: 172, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
96 2 0.01
97 30 0.17
98 71 0.41
99 62 0.36
100 7 0.04
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (98 bp):
AATTAGGTAATTTAAAAATAAAATAAAATATTTAAATTAATACATTAAACTTGTTAAGTCTTTCT
TTTAATTTGCATTTATTAATTTGTTAATTGAAA
Found at i:42152543 original size:8 final size:8
Alignment explanation
Indices: 42152530--42152584 Score: 67
Period size: 8 Copynumber: 7.0 Consensus size: 8
42152520 CAAAAAATTC
42152530 CACTATTA
1 CACTATTA
42152538 CACTATTA
1 CACTATTA
42152546 CACTA-TA
1 CACTATTA
* *
42152553 CGCAATTA
1 CACTATTA
*
42152561 CACTATTC
1 CACTATTA
*
42152569 CACTATTC
1 CACTATTA
42152577 CACTATTA
1 CACTATTA
42152585 TCATAATCAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
7 5 0.12
8 35 0.88
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.35
Consensus pattern (8 bp):
CACTATTA
Done.