Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 91 of 356
Found at i:28648823 original size:3 final size:3
Alignment explanation
Indices: 28648815--28648866 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
28648805 ACTAGTAGAA
28648815 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
28648863 TCT T
1 TCT T
28648867 AATTAAGTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:28649135 original size:2 final size:2
Alignment explanation
Indices: 28649128--28649166 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
28649118 GAAAGACACC
28649128 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
28649167 ATGGGCATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:28649900 original size:2 final size:2
Alignment explanation
Indices: 28649893--28649964 Score: 78
Period size: 2 Copynumber: 37.0 Consensus size: 2
28649883 CAGCTTTAAT
*
28649893 TC TC TC TC TC TC TC TC TC TC TC TC TC TC GT- TC TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC
* * *
28649935 TC TC TC TT TC TT TC -C T- TT TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28649965 ATATCAAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
1 3 0.05
2 55 0.93
3 1 0.02
ACGTcount: A:0.00, C:0.43, G:0.01, T:0.56
Consensus pattern (2 bp):
TC
Found at i:28649937 original size:26 final size:25
Alignment explanation
Indices: 28649903--28649964 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 25
28649893 TCTCTCTCTC
*
28649903 TCTCTCTCTCTCTCTCTCGTT-CTT
1 TCTCTCTCTCTCTCTTTCGTTCCTT
*
28649927 TCTCTCTCTCTCTCTTTCTTTCCTT
1 TCTCTCTCTCTCTCTTTCGTTCCTT
28649952 T-TCTCTCTCTCTC
1 TCTCTCTCTCTCTC
28649965 ATATCAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 31 0.89
25 4 0.11
ACGTcount: A:0.00, C:0.42, G:0.02, T:0.56
Consensus pattern (25 bp):
TCTCTCTCTCTCTCTTTCGTTCCTT
Found at i:28654012 original size:61 final size:61
Alignment explanation
Indices: 28653937--28654058 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
28653927 GTAAGCCCCT
28653937 TAATCTTCCAGGCTTCAACCCATATGGGGTGCTAACCTACTAATACTATATATAATTACAG
1 TAATCTTCCAGGCTTCAACCCATATGGGGTGCTAACCTACTAATACTATATATAATTACAG
28653998 TAATCTTCCAGGCTTCAACCCATATGGGGTGCTAACCTACTAATACTATATATAATTACAG
1 TAATCTTCCAGGCTTCAACCCATATGGGGTGCTAACCTACTAATACTATATATAATTACAG
28654059 AGGAGTTCGT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (61 bp):
TAATCTTCCAGGCTTCAACCCATATGGGGTGCTAACCTACTAATACTATATATAATTACAG
Found at i:28654987 original size:22 final size:22
Alignment explanation
Indices: 28654956--28655000 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
28654946 TGAGCAACAG
28654956 TAAGTCTAAGCTTCAATAACTT
1 TAAGTCTAAGCTTCAATAACTT
*
28654978 TAAGTTTAAGCTTCAATAACTT
1 TAAGTCTAAGCTTCAATAACTT
28655000 T
1 T
28655001 CTCTAGTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TAAGTCTAAGCTTCAATAACTT
Found at i:28657073 original size:919 final size:920
Alignment explanation
Indices: 28655414--28657244 Score: 3477
Period size: 919 Copynumber: 2.0 Consensus size: 920
28655404 GAGGGCTATG
28655414 AACTGATCGGTTTTCTCGATGGCACTTTGGCTAGTCCACTGCGGTTTGTGCAGTCTCTAGACGGC
1 AACTGATCGGTTTTCTCGATGGCACTTTGGCTAGTCCACTGCGGTTTGTGCAGTCTCTAGACGGC
28655479 TCGCTCATTCCGAATCCTGATGCTTCAACCTTTGTGCAACAAGATCGGTTATTAACCTCATGGCT
66 TCGCTCATTCCGAATCCTGATGCTTCAACCTTTGTGCAACAAGATCGGTTATTAACCTCATGGCT
*
28655544 TCTTTCCACAATTAATCATTCTATTTTGTCTTCTTTTGCAGAGGCTCGATCTGCTTGTGATGTAT
131 TCTTTCCACAATTAATCATTCTATTTTGTCTTCTTTTACAGAGGCTCGATCTGCTTGTGATGTAT
28655609 GGACTACCGCAACCCGTCTTTTTGCCCCTTTCACTGGAGCGAAGCTTGCTCGTCTTCGACACGAT
196 GGACTACCGCAACCCGTCTTTTTGCCCCTTTCACTGGAGCGAAGCTTGCTCGTCTTCGACACGAT
28655674 TTGCTTTCTCTCAAGAAAGGCAGTCTTTCAATCAAAGAATTTGTGGCCAAAATCCAGAATATGAG
261 TTGCTTTCTCTCAAGAAAGGCAGTCTTTCAATCAAAGAATTTGTGGCCAAAATCCAGAATATGAG
28655739 TGCTTTGATAACTGTCTCTGGTTCGTGCATCTCAGAAGAAGAGAAGGTCCAAACTCTGCTTGTGG
326 TGCTTTGATAACTGTCTCTGGTTCGTGCATCTCAGAAGAAGAGAAGGTCCAAACTCTGCTTGTGG
*
28655804 GCTTACCCTCTGATTTTGATTCTGTCATTACGCTCGCCTCGTTCTCATCGGAACCTTTGCGATTT
391 GCTTACCCTCTGATTTTGATTCTGTCATTACGCTCGCCTCGTTCTCATCAGAACCTTTGCGATTT
* *
28655869 CAACAACTTGTTGAAGTGCTTCTTGAGTTCGAGAATCGTCAGGCGCGTGTAGCTTCAGAGATACC
456 CAACAACTTGTTGAAGAGCTTCTTGAGTTCGAGAATCGTCAAGCGCGTGTAGCTTCAGAGATACC
* *
28655934 TCTTCATTCTAATCTCTTGGAGACTGTTCCTTTACCGATCATAGGGGGTTATGTTCGTGGTGTTC
521 TCTTCATGCTAATCTCTTGGAGACTGTTCCTTTACCGATCATAGGGGGTTATGTTCGTGGTATTC
* *
28655999 GTCCCCCATCTAGAGGTCGTGGGCGTGGGTTTTGATCCCGAGTTCAATGCCAAATCTGCGGATGG
586 ATCCCCCATCTAGAGGTCGTGGGCGTGGGTTCTGATCCCGAGTTCAATGCCAAATCTGCGGATGG
28656064 TTTGGGCATCTTACTCAATGGTGTTTCTACCGTTACGACCGTGACCATGAGGGATCGTCGTCGGA
651 TTTGGGCATCTTACTCAATGGTGTTTCTACCGTTACGACCGTGACCATGAGGGATCGTCGTCGGA
* *
28656129 TGCTTGAGCATCGTCTTCGGTAGGTCGTCGATGGACATCCATCTGATTCTGTTGTCAAATCTGTT
716 TGCTTGAGCATCGTCTTCAGTAGGTCGTCGATGGACATCCATCTGACTCTGTTGTCAAATCTGTT
28656194 TTGAATAAATGTAGTATTTCTTCAAATAAA-TTTCTATGGACACTGCATGCTCTGCATGTCAAAA
781 TTGAATAAATGTAGTATTTCTTCAAATAAATTTTCTATGGACACTGCATGCTCTGCATGTCAAAA
28656258 AAGGAAATCACATAAATTGCCCTTTACCGATTCGACCACTAAATACACTAATCCGTTTACTTTGG
846 AAGGAAATCACATAAATTGCCCTTTACCGATTCGACCACTAAATACACTAATCCGTTTACTTTGG
28656323 TTATGTTAAC
911 TTATGTTAAC
28656333 AACTGATCGGTTTTCTCGATGGCACTTTGGCTAGTCCACTGCGGTTTGTGCAGTCTCTAGACGGC
1 AACTGATCGGTTTTCTCGATGGCACTTTGGCTAGTCCACTGCGGTTTGTGCAGTCTCTAGACGGC
28656398 TCGCTCATTCCGAATCCTGATGCTTCAACCTTTGTGCAACAAGATCGGTTATTAACCTCATGGCT
66 TCGCTCATTCCGAATCCTGATGCTTCAACCTTTGTGCAACAAGATCGGTTATTAACCTCATGGCT
28656463 TCTTTCCACAATTAATCATTCTATTTTGTCTTCTTTTACAGAGGCTCGATCTGCTTGTGATGTAT
131 TCTTTCCACAATTAATCATTCTATTTTGTCTTCTTTTACAGAGGCTCGATCTGCTTGTGATGTAT
*
28656528 GGACTACCGTAACCCGTCTTTTTGCCCCTTTCACTAGG-GCGAAGCTTGCTCGTCTTCGACACGA
196 GGACTACCGCAACCCGTCTTTTTGCCCCTTTCACT-GGAGCGAAGCTTGCTCGTCTTCGACACGA
28656592 TTTGCTTTCTCTCAAGAAAGGCAGTCTTTCAATCAAAGAATTTGTGGCCAAAATCCAGAATATGA
260 TTTGCTTTCTCTCAAGAAAGGCAGTCTTTCAATCAAAGAATTTGTGGCCAAAATCCAGAATATGA
28656657 GTGCTTTGATAACTGTCTCTGGTTCGTGCATCTCAGAAGAAGAGAAGGTCCAAACTCTGCTTGTG
325 GTGCTTTGATAACTGTCTCTGGTTCGTGCATCTCAGAAGAAGAGAAGGTCCAAACTCTGCTTGTG
28656722 GGCTTACCCTCTGATTTTGATTCTGTCATTACGCTCGCCTCGTTCTCATCAGAACCTTTGCGATT
390 GGCTTACCCTCTGATTTTGATTCTGTCATTACGCTCGCCTCGTTCTCATCAGAACCTTTGCGATT
* *
28656787 TCAACAACTTGTTGAAGAGCTTCTTGAGTTCGAGAATCTTCAAGCGCGTGTGGCTTCAGAGATAC
455 TCAACAACTTGTTGAAGAGCTTCTTGAGTTCGAGAATCGTCAAGCGCGTGTAGCTTCAGAGATAC
* *
28656852 CTCTTCATGCTAATCTCTTGGAGACTGTTCCTTTACCGATCATAGGGGGTTCTGTTCGTGTTATT
520 CTCTTCATGCTAATCTCTTGGAGACTGTTCCTTTACCGATCATAGGGGGTTATGTTCGTGGTATT
28656917 CATCCCCCATCTAGAGGTCGTGGGCGTGGGTTCTGATCCCGAGTTCAATGCCAAATCTGCGGATG
585 CATCCCCCATCTAGAGGTCGTGGGCGTGGGTTCTGATCCCGAGTTCAATGCCAAATCTGCGGATG
*
28656982 GTTTGGGCATCTTGCTCAATGGTGTTTCTACCGTTACGACCGTGACCATGAGGGATCGTCGTCGG
650 GTTTGGGCATCTTACTCAATGGTGTTTCTACCGTTACGACCGTGACCATGAGGGATCGTCGTCGG
28657047 ATGCTTGAGCATCGTCTTCAGTAGGTCGTCGATGGACATCCATCTGACTCTGTTGTCAAATCTGT
715 ATGCTTGAGCATCGTCTTCAGTAGGTCGTCGATGGACATCCATCTGACTCTGTTGTCAAATCTGT
*
28657112 TTTGAATAAATGTAGTATTTCTTCAAATAAATTTTGTATGGACACTGCATGCTCTGCATGTCAAA
780 TTTGAATAAATGTAGTATTTCTTCAAATAAATTTTCTATGGACACTGCATGCTCTGCATGTCAAA
*
28657177 AAAGGAAATCACATAAATTGCCCTTTACCGATTCGACCACTAAATACACTGATCCGTTTACTTTG
845 AAAGGAAATCACATAAATTGCCCTTTACCGATTCGACCACTAAATACACTAATCCGTTTACTTTG
28657242 GTT
910 GTT
28657245 GTTTCTGATC
Statistics
Matches: 892, Mismatches: 18, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
919 791 0.89
920 101 0.11
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.33
Consensus pattern (920 bp):
AACTGATCGGTTTTCTCGATGGCACTTTGGCTAGTCCACTGCGGTTTGTGCAGTCTCTAGACGGC
TCGCTCATTCCGAATCCTGATGCTTCAACCTTTGTGCAACAAGATCGGTTATTAACCTCATGGCT
TCTTTCCACAATTAATCATTCTATTTTGTCTTCTTTTACAGAGGCTCGATCTGCTTGTGATGTAT
GGACTACCGCAACCCGTCTTTTTGCCCCTTTCACTGGAGCGAAGCTTGCTCGTCTTCGACACGAT
TTGCTTTCTCTCAAGAAAGGCAGTCTTTCAATCAAAGAATTTGTGGCCAAAATCCAGAATATGAG
TGCTTTGATAACTGTCTCTGGTTCGTGCATCTCAGAAGAAGAGAAGGTCCAAACTCTGCTTGTGG
GCTTACCCTCTGATTTTGATTCTGTCATTACGCTCGCCTCGTTCTCATCAGAACCTTTGCGATTT
CAACAACTTGTTGAAGAGCTTCTTGAGTTCGAGAATCGTCAAGCGCGTGTAGCTTCAGAGATACC
TCTTCATGCTAATCTCTTGGAGACTGTTCCTTTACCGATCATAGGGGGTTATGTTCGTGGTATTC
ATCCCCCATCTAGAGGTCGTGGGCGTGGGTTCTGATCCCGAGTTCAATGCCAAATCTGCGGATGG
TTTGGGCATCTTACTCAATGGTGTTTCTACCGTTACGACCGTGACCATGAGGGATCGTCGTCGGA
TGCTTGAGCATCGTCTTCAGTAGGTCGTCGATGGACATCCATCTGACTCTGTTGTCAAATCTGTT
TTGAATAAATGTAGTATTTCTTCAAATAAATTTTCTATGGACACTGCATGCTCTGCATGTCAAAA
AAGGAAATCACATAAATTGCCCTTTACCGATTCGACCACTAAATACACTAATCCGTTTACTTTGG
TTATGTTAAC
Found at i:28660005 original size:51 final size:50
Alignment explanation
Indices: 28659929--28660114 Score: 216
Period size: 50 Copynumber: 3.7 Consensus size: 50
28659919 ATTGTGAATA
* *
28659929 CACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACTC-AATGACTTCGAT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACTCAAATGA-TT-GGT
* * *
28659980 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TCAAATGGTGAGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACTCAAATGAT-TGGT
* ** *
28660030 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CGGATTATTGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACTCAAATGATTGGT
* * *
28660079 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTA
28660115 TCAGATAGCT
Statistics
Matches: 118, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
49 35 0.30
50 45 0.38
51 38 0.32
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (50 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACTCAAATGATTGGT
Found at i:28662190 original size:42 final size:46
Alignment explanation
Indices: 28662126--28662291 Score: 148
Period size: 47 Copynumber: 3.6 Consensus size: 46
28662116 CTTCGTTTTC
**
28662126 TCGATGCCATAGTTCA-ATTATGGTCTTACAC-AT-C-T-TCACATAA
1 TCGATGCCATAGCCCAGA-TATGGTCTTACACAATACATATCACAT-A
*
28662169 T-GATGCCATAGCCCAGCTATGGTCTTACACATAATCACATATCACATA
1 TCGATGCCATAGCCCAGATATGGTCTTACAC--AAT-ACATATCACATA
* * *
28662217 TCGATGCCATAGCCCAGATATGGTCTTATACAGTAGCATAT-ATCACA
1 TCGATGCCATAGCCCAGATATGGTCTTACACAATA-CATATCA-CATA
* *
28662264 CCGATGCCATATCCCAGATATGGTCTTA
1 TCGATGCCATAGCCCAGATATGGTCTTA
28662292 TACGGAAATC
Statistics
Matches: 103, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
42 25 0.24
43 1 0.01
45 2 0.02
46 2 0.02
47 37 0.36
48 3 0.03
49 33 0.32
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (46 bp):
TCGATGCCATAGCCCAGATATGGTCTTACACAATACATATCACATA
Found at i:28662280 original size:47 final size:48
Alignment explanation
Indices: 28662170--28662294 Score: 164
Period size: 49 Copynumber: 2.6 Consensus size: 48
28662160 TTCACATAAT
* * * *
28662170 GATGCCATAGCCCAGCTATGGTCTTACACATAATCACATATCACATATC
1 GATGCCATAGCCCAGATATGGTCTTATACATAAGCACATATCACA-ACC
*
28662219 GATGCCATAGCCCAGATATGGTCTTATACAGT-AGCATATATCAC-ACC
1 GATGCCATAGCCCAGATATGGTCTTATACA-TAAGCACATATCACAACC
*
28662266 GATGCCATATCCCAGATATGGTCTTATAC
1 GATGCCATAGCCCAGATATGGTCTTATAC
28662295 GGAAATCACT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
47 30 0.43
49 38 0.55
50 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.27
Consensus pattern (48 bp):
GATGCCATAGCCCAGATATGGTCTTATACATAAGCACATATCACAACC
Found at i:28662356 original size:31 final size:31
Alignment explanation
Indices: 28662313--28662430 Score: 173
Period size: 31 Copynumber: 3.8 Consensus size: 31
28662303 CTTGTTACTT
* *
28662313 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
* *
28662344 GTAGTCTGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
28662375 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
***
28662406 GTAGCAAAAGCTACCACTTTTCACT
1 GTAGCCGGAGCTACCACTTTTCACT
28662431 TGTCATTTGT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGGAGCTACCACTTTTCACTGATCAG
Found at i:28662505 original size:50 final size:51
Alignment explanation
Indices: 28662413--28662534 Score: 210
Period size: 50 Copynumber: 2.4 Consensus size: 51
28662403 CAGGTAGCAA
* *
28662413 AAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCCG
1 AAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCCG
*
28662464 AAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGTGTAGCCG
1 AAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCCG
28662514 AAGCTATCACTTATCACTTGT
1 AAGCTATCACTTATCACTTGT
28662535 TGCCATGGTC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
50 49 0.73
51 18 0.27
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
AAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCCG
Found at i:28663621 original size:16 final size:18
Alignment explanation
Indices: 28663590--28663624 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
28663580 CAATTAACCC
28663590 CTCAATTAAGATAATTTT
1 CTCAATTAAGATAATTTT
28663608 CTCAATT-A-ATAATTTT
1 CTCAATTAAGATAATTTT
28663624 C
1 C
28663625 CTAGACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (18 bp):
CTCAATTAAGATAATTTT
Found at i:28676670 original size:21 final size:21
Alignment explanation
Indices: 28676644--28676684 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28676634 ATCTGCTCAA
* *
28676644 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
28676665 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
28676685 TTGCTCATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:28702206 original size:29 final size:31
Alignment explanation
Indices: 28702137--28702214 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 31
28702127 AAATCAAAAG
*
28702137 TAAAGCTTCAAGTATATATTTGAACCGCAAC
1 TAAAGCTTCAAGTATATATTTGAACCGAAAC
* * * * *
28702168 TAGAGTTTCACGTATATATTTGCACC-AAAT
1 TAAAGCTTCAAGTATATATTTGAACCGAAAC
*
28702198 TAAAG-TTCATGTATATA
1 TAAAGCTTCAAGTATATA
28702215 ATTGTACATT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 11 0.28
30 6 0.15
31 22 0.56
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (31 bp):
TAAAGCTTCAAGTATATATTTGAACCGAAAC
Found at i:28704446 original size:22 final size:22
Alignment explanation
Indices: 28704421--28704467 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
28704411 GTAGGTACTG
*
28704421 AAGTGCGGAAC-GATAAGCACCA
1 AAGTGCGAAACAG-TAAGCACCA
*
28704443 AAGTGCGAAACAGTAAGCACTA
1 AAGTGCGAAACAGTAAGCACCA
28704465 AAG
1 AAG
28704468 CGTAAGATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.45, C:0.19, G:0.26, T:0.11
Consensus pattern (22 bp):
AAGTGCGAAACAGTAAGCACCA
Found at i:28705799 original size:18 final size:17
Alignment explanation
Indices: 28705761--28705799 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
28705751 AGGCCAATAT
*
28705761 GGGCGTGTAGGCCACAT
1 GGGCGTGTAGGCCACAC
28705778 GGGCGTGTAGGCCCACAC
1 GGGCGTGTAGG-CCACAC
28705796 GGGC
1 GGGC
28705800 AAACCAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.15, C:0.28, G:0.44, T:0.13
Consensus pattern (17 bp):
GGGCGTGTAGGCCACAC
Found at i:28706941 original size:15 final size:16
Alignment explanation
Indices: 28706921--28706953 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28706911 GACAATGTGA
*
28706921 TTATGT-TTGATGGAT
1 TTATGTGTTAATGGAT
28706936 TTATGTGTTAATGGAT
1 TTATGTGTTAATGGAT
28706952 TT
1 TT
28706954 TCATGTGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (16 bp):
TTATGTGTTAATGGAT
Found at i:28713399 original size:9 final size:10
Alignment explanation
Indices: 28713376--28713401 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28713366 TTTTTTCTAG
28713376 AAAAAATAAT
1 AAAAAATAAT
28713386 AAAAAATAAT
1 AAAAAATAAT
28713396 AAAAAA
1 AAAAAA
28713402 GAGAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:28714010 original size:22 final size:24
Alignment explanation
Indices: 28713985--28714032 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
28713975 TTAATTTTAA
28713985 TATTAC-TTA-TACTATTATATTT
1 TATTACGTTATTACTATTATATTT
*
28714007 TATTACTGTTATTATTATTATATTT
1 TATTAC-GTTATTACTATTATATTT
28714032 T
1 T
28714033 TATTTATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
24 3 0.14
25 13 0.59
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.62
Consensus pattern (24 bp):
TATTACGTTATTACTATTATATTT
Found at i:28714228 original size:14 final size:15
Alignment explanation
Indices: 28714210--28714247 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
28714200 TTATATTACG
28714210 TATATTATTTTTTTA
1 TATATTATTTTTTTA
*
28714225 -ATATTAGATTTTTTA
1 TATATTA-TTTTTTTA
28714240 TATATTAT
1 TATATTAT
28714248 GTATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
14 6 0.32
15 7 0.37
16 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
TATATTATTTTTTTA
Found at i:28714279 original size:26 final size:24
Alignment explanation
Indices: 28714232--28714344 Score: 90
Period size: 24 Copynumber: 4.5 Consensus size: 24
28714222 TTAATATTAG
28714232 ATTTTTTATATATTATGTATATAT
1 ATTTTTTATATATTATGTATATAT
*
28714256 ATTTTTATATCATATTAT-T-CATAT
1 ATTTTT-TAT-ATATTATGTATATAT
* * *
28714280 ATCTTAT-TATCTTATGTATATAT
1 ATTTTTTATATATTATGTATATAT
28714303 ATTTTTTAATAACTATATTATGTATATAT
1 A-TTTTT--T-A-TATATTATGTATATAT
28714332 ATTCTTTTA-ATAT
1 ATT-TTTTATATAT
28714345 CTTATTATCT
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
21 6 0.09
22 2 0.03
23 6 0.09
24 21 0.30
25 4 0.06
26 9 0.13
27 1 0.01
28 2 0.03
29 19 0.27
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (24 bp):
ATTTTTTATATATTATGTATATAT
Found at i:28714333 original size:29 final size:29
Alignment explanation
Indices: 28714291--28714352 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
28714281 TCTTATTATC
28714291 TTATGTATATATATT-TTTTAATAACTATA
1 TTATGTATATATATTCTTTTAATAACT-TA
*
28714320 TTATGTATATATATTCTTTTAATATCTTA
1 TTATGTATATATATTCTTTTAATAACTTA
28714349 TTAT
1 TTAT
28714353 CTTATTATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (29 bp):
TTATGTATATATATTCTTTTAATAACTTA
Found at i:28714403 original size:25 final size:25
Alignment explanation
Indices: 28714375--28714435 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
28714365 ATACTCAAAA
* *
28714375 ATATTATGTATGTATTTTTAACACT
1 ATATTACGTACGTATTTTTAACACT
28714400 ATATTACGTACGTATTTTTAACACT
1 ATATTACGTACGTATTTTTAACACT
28714425 ATATTACGTAC
1 ATATTACGTAC
28714436 ATGCTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (25 bp):
ATATTACGTACGTATTTTTAACACT
Found at i:28714443 original size:25 final size:25
Alignment explanation
Indices: 28714390--28714445 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
28714380 ATGTATGTAT
* *
28714390 TTTTAACACTATATTACGTACGTAT
1 TTTTAACACTATATTACGTACATAC
*
28714415 TTTTAACACTATATTACGTACATGC
1 TTTTAACACTATATTACGTACATAC
28714440 TTTTAA
1 TTTTAA
28714446 TATCATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.45
Consensus pattern (25 bp):
TTTTAACACTATATTACGTACATAC
Found at i:28714487 original size:23 final size:26
Alignment explanation
Indices: 28714242--28714490 Score: 80
Period size: 25 Copynumber: 9.6 Consensus size: 26
28714232 ATTTTTTATA
*
28714242 TATTATGTATATATATTTTTATATCA-
1 TATTATGTATATAT-TTTTAATATCAT
* *
28714268 TATTAT-TCATATA-TCTTATTATC-T
1 TATTATGT-ATATATTTTTAATATCAT
* *
28714292 TATGTATATATAT-TTTTTAATAAC-T
1 TAT-TATGTATATATTTTTAATATCAT
28714317 ATATTATGTATATATATTCTTTTAATATC-T
1 -TATTATG--TATATA-T-TTTTAATATCAT
* * *
28714347 TATTATCT-TAT-TATCTTAATACTCAAAAA
1 TATTATGTATATAT-TTTTAATA-TC---AT
* *
28714376 TATTATGTATGTATTTTTAACA-C-T
1 TATTATGTATATATTTTTAATATCAT
* ** *
28714400 ATATTACGTACGTATTTTTAACA-C-T
1 -TATTATGTATATATTTTTAATATCAT
* * **
28714425 ATATTACGTACATGCTTTTAATATCAT
1 -TATTATGTATATATTTTTAATATCAT
28714452 TATTATGTATATATTTTTAATAT-A-
1 TATTATGTATATATTTTTAATATCAT
*
28714476 TA-TATGTGTATATTT
1 TATTATGTATATATTT
28714491 ATGTAGTATT
Statistics
Matches: 174, Mismatches: 28, Indels: 45
0.70 0.11 0.18
Matches are distributed among these distances:
23 12 0.07
24 20 0.11
25 63 0.36
26 38 0.22
27 7 0.04
28 1 0.01
29 14 0.08
30 18 0.10
31 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (26 bp):
TATTATGTATATATTTTTAATATCAT
Found at i:28714573 original size:20 final size:19
Alignment explanation
Indices: 28714548--28714597 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
28714538 ATGTATATAA
28714548 TATATATTTTTAATACTAT
1 TATATATTTTTAATACTAT
*
28714567 GTATATACTTTTTAATATTAT
1 -TATATA-TTTTTAATACTAT
28714588 TATTATATTT
1 TA-TATATTT
28714598 ATATTTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (19 bp):
TATATATTTTTAATACTAT
Found at i:28714718 original size:21 final size:21
Alignment explanation
Indices: 28714692--28714735 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
28714682 TATATGTATA
*
28714692 TATATTTATTATTATTATCAT
1 TATATTTATTATTAATATCAT
*
28714713 TATATTTATTATTAATATTAT
1 TATATTTATTATTAATATCAT
28714734 TA
1 TA
28714736 GTACTAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATTTATTATTAATATCAT
Found at i:28714884 original size:24 final size:24
Alignment explanation
Indices: 28714856--28715006 Score: 108
Period size: 25 Copynumber: 6.0 Consensus size: 24
28714846 ATCATTTCTA
*
28714856 ATATATATATATTGTATATGTTTTTT
1 ATATATAT-TA-TGTATATATTTTTT
*
28714882 ATATATATTATGTATATATTTTTA
1 ATATATATTATGTATATATTTTTT
* * *
28714906 ATACCATACTAT-TCATATACTTTTT
1 ATA-TATATTATGT-ATATATTTTTT
*
28714931 ATGT-TATCTCATGTATATATTTTTT
1 ATATATAT-T-ATGTATATATTTTTT
* *
28714956 AATAACTATATTATGTATGTATTTTTA
1 -AT-A-TATATTATGTATATATTTTTT
* *
28714983 ACACTATATTATGTACATATTTTT
1 ATA-TATATTATGTATATATTTTT
28715007 AATACTATGT
Statistics
Matches: 100, Mismatches: 16, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
23 2 0.02
24 17 0.17
25 51 0.51
26 12 0.12
27 13 0.13
28 2 0.02
29 3 0.03
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.55
Consensus pattern (24 bp):
ATATATATTATGTATATATTTTTT
Found at i:28717578 original size:50 final size:50
Alignment explanation
Indices: 28717503--28717679 Score: 309
Period size: 50 Copynumber: 3.5 Consensus size: 50
28717493 CTATGGCAAT
*
28717503 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
*
28717553 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
*
28717603 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
*
28717653 CAAGTGAAAAGTGATAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
28717680 CTGATCAGTG
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
50 96 0.79
51 25 0.21
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
Found at i:28717690 original size:31 final size:31
Alignment explanation
Indices: 28717655--28717771 Score: 189
Period size: 31 Copynumber: 3.8 Consensus size: 31
28717645 ACAAATGACA
28717655 AGTGAAAAGTGATAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGATAGCTTCGGCTACCTGATC
*
28717686 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGATAGCTTCGGCTACCTGATC
* *
28717717 AGTGAAAAATGATAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGATAGCTTCGGCTACCTGATC
* *
28717748 AGTGAATAGTGGTAGCTTCGGCTA
1 AGTGAAAAGTGATAGCTTCGGCTA
28717772 AAAGTGACAA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGATAGCTTCGGCTACCTGATC
Found at i:28717913 original size:10 final size:10
Alignment explanation
Indices: 28717898--28717925 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
28717888 ATGCTATGGC
28717898 ATCAGTGATT
1 ATCAGTGATT
28717908 ATCAGTGATT
1 ATCAGTGATT
28717918 ATCAGTGA
1 ATCAGTGA
28717926 AATTCAGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (10 bp):
ATCAGTGATT
Found at i:28720136 original size:21 final size:21
Alignment explanation
Indices: 28720093--28720259 Score: 113
Period size: 21 Copynumber: 8.0 Consensus size: 21
28720083 ACATCATTTT
* *
28720093 CAGAAGCCCA-AAG-GCTGAA
1 CAGAAGCTCATAAGAGCTAAA
*
28720112 CAGAAGCTCATGAGAGCTAAA
1 CAGAAGCTCATAAGAGCTAAA
* * * * *
28720133 CAGAAACCCATAAGGGTTGAA
1 CAGAAGCTCATAAGAGCTAAA
* *
28720154 CGGAAGCTCATAAGAGCTGAA
1 CAGAAGCTCATAAGAGCTAAA
* * * * *
28720175 CGGAAACTTATAAGGGTTAAA
1 CAGAAGCTCATAAGAGCTAAA
* *
28720196 CAGAAGCTCAAAAGAGCTGAA
1 CAGAAGCTCATAAGAGCTAAA
* * *
28720217 CAGAAACTCATATGAGTTAAA
1 CAGAAGCTCATAAGAGCTAAA
* * *
28720238 TAGAAGCTTATGAGAGCTAAA
1 CAGAAGCTCATAAGAGCTAAA
28720259 C
1 C
28720260 GAAAAGTAAA
Statistics
Matches: 108, Mismatches: 38, Indels: 2
0.73 0.26 0.01
Matches are distributed among these distances:
19 9 0.08
20 2 0.02
21 97 0.90
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.16
Consensus pattern (21 bp):
CAGAAGCTCATAAGAGCTAAA
Found at i:28720160 original size:42 final size:42
Alignment explanation
Indices: 28720110--28720263 Score: 175
Period size: 42 Copynumber: 3.7 Consensus size: 42
28720100 CCAAAGGCTG
* * *
28720110 AACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGGGTTA
* * * *
28720152 AACGGAAGCTCATAAGAGCTGAACGGAAACTTATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGGGTTA
* * * *
28720194 AACAGAAGCTCAAAAGAGCTGAACAGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGGGTTA
* * *
28720236 AATAGAAGCTTATGAGAGCTAAAC-GAAA
1 AACAGAAGCTCATAAGAGCTAAACAGAAA
28720264 AGTAAACAAG
Statistics
Matches: 94, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 4 0.04
42 90 0.96
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGGGTTA
Found at i:28723208 original size:23 final size:23
Alignment explanation
Indices: 28723182--28723227 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
28723172 ATCTGTATTC
28723182 ATCTATATATTAAT-TTTATAAAT
1 ATCTATAT-TTAATATTTATAAAT
*
28723205 ATCTTTATTTAATATTTATAAAT
1 ATCTATATTTAATATTTATAAAT
28723228 TCAGTTTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
ATCTATATTTAATATTTATAAAT
Found at i:28726989 original size:6 final size:6
Alignment explanation
Indices: 28726978--28727002 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28726968 CCTTGAACTG
28726978 CCCTCT CCCTCT CCCTCT CCCTCT C
1 CCCTCT CCCTCT CCCTCT CCCTCT C
28727003 TTCTCCCCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCCTCT
Found at i:28728896 original size:20 final size:21
Alignment explanation
Indices: 28728851--28728896 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
28728841 GCTCATCTGG
* *
28728851 TTTTGCTGCTGCTCCCTCCCT
1 TTTTCCTGCTGCTCCCGCCCT
*
28728872 GTTTCCTGCTGC-CCCGCCCT
1 TTTTCCTGCTGCTCCCGCCCT
28728892 TTTTC
1 TTTTC
28728897 TAATATTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.00, C:0.43, G:0.15, T:0.41
Consensus pattern (21 bp):
TTTTCCTGCTGCTCCCGCCCT
Found at i:28730646 original size:10 final size:8
Alignment explanation
Indices: 28730618--28730642 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28730608 TTATAAGGGT
28730618 ATATTAAA
1 ATATTAAA
28730626 ATATTAAA
1 ATATTAAA
28730634 ATATTAAA
1 ATATTAAA
28730642 A
1 A
28730643 AATAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATTAAA
Found at i:28731815 original size:12 final size:12
Alignment explanation
Indices: 28731798--28731825 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28731788 AAAGTCATTG
28731798 TTAATATAGACA
1 TTAATATAGACA
28731810 TTAATATAGACA
1 TTAATATAGACA
28731822 TTAA
1 TTAA
28731826 GGGTGTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (12 bp):
TTAATATAGACA
Found at i:28734435 original size:25 final size:23
Alignment explanation
Indices: 28734383--28734437 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
28734373 TATAAATAGT
28734383 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
28734406 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
28734431 AATAGTG
1 AATAGTG
28734438 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:28734525 original size:24 final size:23
Alignment explanation
Indices: 28734498--28734687 Score: 86
Period size: 22 Copynumber: 8.0 Consensus size: 23
28734488 AATAGATATA
* *
28734498 AAAAATATGTACATAATATAGTGT
1 AAAAATATATACATAATATAAT-T
*
28734522 AAAAATACATACATAATATAATT
1 AAAAATATATACATAATATAATT
*
28734545 -AAAATATATACATAAGATAACATGT
1 AAAAATATATACATAATAT-A-AT-T
* *
28734570 AGAAAAAAAATATAAATAATATAGTATT
1 ---AAAAATATATACATAATATA--ATT
* * *
28734598 AAAGATATATACATAAAAT-AGT
1 AAAAATATATACATAATATAATT
* *
28734620 ATAATATATATACGTAATATAGAATT
1 A-AAAATATATACATAATAT--AATT
* * *
28734646 -TAGA-ATATACCTAATAT-ATT
1 AAAAATATATACATAATATAATT
*
28734666 AAAAGA-ATATATATAATATAAT
1 AAAA-ATATATACATAATATAAT
28734688 ATTAAGAAAT
Statistics
Matches: 126, Mismatches: 25, Indels: 31
0.69 0.14 0.17
Matches are distributed among these distances:
20 3 0.02
21 1 0.01
22 31 0.25
23 31 0.25
24 23 0.18
25 16 0.13
26 2 0.02
28 2 0.02
29 17 0.13
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (23 bp):
AAAAATATATACATAATATAATT
Found at i:28734607 original size:25 final size:23
Alignment explanation
Indices: 28734578--28734706 Score: 102
Period size: 23 Copynumber: 5.6 Consensus size: 23
28734568 GTAGAAAAAA
*
28734578 AATATAAATAATATAGTATTAAAG
1 AATATACATAATATAGTATT-AAG
* *
28734602 ATATATACATAAAATAGTA-TAAT
1 A-ATATACATAATATAGTATTAAG
* * *
28734625 ATATATACGTAATATAGAATTTAG
1 A-ATATACATAATATAGTATTAAG
* * *
28734649 AATATACCTAATATATTA-AAAG
1 AATATACATAATATAGTATTAAG
* *
28734671 AATATATATAATATAATATTAAG
1 AATATACATAATATAGTATTAAG
28734694 AAATATA-ATAATA
1 -AATATACATAATA
28734707 ACAAAAAAAG
Statistics
Matches: 84, Mismatches: 17, Indels: 9
0.76 0.15 0.08
Matches are distributed among these distances:
22 17 0.20
23 41 0.49
24 11 0.13
25 15 0.18
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (23 bp):
AATATACATAATATAGTATTAAG
Found at i:28734613 original size:29 final size:28
Alignment explanation
Indices: 28734526--28734614 Score: 73
Period size: 26 Copynumber: 3.3 Consensus size: 28
28734516 TAGTGTAAAA
*
28734526 ATACATACATAATATA--ATTAAAATAT
1 ATACATAAATAATATAGTATTAAAATAT
* *
28734552 ATACATAAGATAACAT-GTA-GAAAA-A-
1 ATACATAA-ATAATATAGTATTAAAATAT
* *
28734577 AAATATAAATAATATAGTATTAAAGATAT
1 ATACATAAATAATATAGTATTAAA-ATAT
28734606 ATACATAAA
1 ATACATAAA
28734615 ATAGTATAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 13
0.68 0.13 0.19
Matches are distributed among these distances:
24 6 0.13
25 9 0.20
26 11 0.24
27 11 0.24
28 2 0.04
29 7 0.15
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (28 bp):
ATACATAAATAATATAGTATTAAAATAT
Found at i:28735016 original size:16 final size:16
Alignment explanation
Indices: 28734978--28735016 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28734968 TCTCCAAAAA
*
28734978 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
28734994 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
28735010 AATAACT
1 AAAAACT
28735017 CTTCTCCTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:28736895 original size:52 final size:48
Alignment explanation
Indices: 28736801--28737007 Score: 188
Period size: 47 Copynumber: 4.2 Consensus size: 48
28736791 CCATGGCAGC
* * *
28736801 ATGTGAAATGTGATTTCCGTATAAGACCATAGT-TGGGCTATGGCTTCGGAG
1 ATGTGATATGTG-TTTCCGTATAAGACCATA-TCTGGGATATGGCATC-G-G
*
28736852 AAATGTGATATGTGTTTCCGTATAAGACCATATCCGGGATATGGCATCGG
1 --ATGTGATATGTGTTTCCGTATAAGACCATATCTGGGATATGGCATCGG
* * * *
28736902 -TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCAG
1 ATGTGATATGTGTTTCCGTATAAGACCATATCTGGGATATGGCATCGG
* * ** * * *
28736949 -TGTGATATGTG-ATCCGTGTAAGACCATGGCTAGGCTATGGCCTCGG
1 ATGTGATATGTGTTTCCGTATAAGACCATATCTGGGATATGGCATCGG
28736995 TATGTGATATGTG
1 -ATGTGATATGTG
28737008 ACTATGTGCA
Statistics
Matches: 132, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
46 25 0.19
47 53 0.40
48 11 0.08
50 1 0.01
51 2 0.02
52 29 0.22
53 11 0.08
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (48 bp):
ATGTGATATGTGTTTCCGTATAAGACCATATCTGGGATATGGCATCGG
Found at i:28745202 original size:111 final size:111
Alignment explanation
Indices: 28745008--28745230 Score: 437
Period size: 111 Copynumber: 2.0 Consensus size: 111
28744998 AATTTTTTTG
28745008 AAGTACAGAATAAAGTGGTTATATTCATTGTCTTAAGATTGATCCAGATGGTTTGTGCTGATCTA
1 AAGTACAGAATAAAGTGGTTATATTCATTGTCTTAAGATTGATCCAGATGGTTTGTGCTGATCTA
28745073 TAGAAGTTAGATAGCAGATACAGACAGTGCCTCATTATCTAGTTTC
66 TAGAAGTTAGATAGCAGATACAGACAGTGCCTCATTATCTAGTTTC
28745119 AAGTACAGAATAAAGTGGTTATATTCATTGTCTTAAGATTGATCCAGATGGTTTGTGCTGATCTA
1 AAGTACAGAATAAAGTGGTTATATTCATTGTCTTAAGATTGATCCAGATGGTTTGTGCTGATCTA
*
28745184 TAGAAGTTAGATAGCAGATACAGACAGTGCCTCATTATCTGGTTTC
66 TAGAAGTTAGATAGCAGATACAGACAGTGCCTCATTATCTAGTTTC
28745230 A
1 A
28745231 TCTTTCCAGA
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (111 bp):
AAGTACAGAATAAAGTGGTTATATTCATTGTCTTAAGATTGATCCAGATGGTTTGTGCTGATCTA
TAGAAGTTAGATAGCAGATACAGACAGTGCCTCATTATCTAGTTTC
Found at i:28747132 original size:6 final size:6
Alignment explanation
Indices: 28747121--28747145 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28747111 TACTTGTCAA
28747121 TCTGCT TCTGCT TCTGCT TCTGCT T
1 TCTGCT TCTGCT TCTGCT TCTGCT T
28747146 TTTCAACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.16, T:0.52
Consensus pattern (6 bp):
TCTGCT
Found at i:28748953 original size:16 final size:16
Alignment explanation
Indices: 28748924--28748966 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
28748914 AAATATTTTA
28748924 TAATATTTTATAATTT
1 TAATATTTTATAATTT
28748940 TAATGATTTT-TAATTTT
1 TAAT-ATTTTATAA-TTT
*
28748957 TAAAATTTTA
1 TAATATTTTA
28748967 AAAATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TAATATTTTATAATTT
Found at i:28749994 original size:17 final size:17
Alignment explanation
Indices: 28749972--28750005 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28749962 AGGTTTAGAT
28749972 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
*
28749989 TTAAAATTTTTAATTAA
1 TTAAAAATTTTAATTAA
28750006 AAATCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:28755472 original size:22 final size:22
Alignment explanation
Indices: 28755444--28755488 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
28755434 CCAACAAGAT
28755444 TGTCAATTTCTGCTTCTTTATC
1 TGTCAATTTCTGCTTCTTTATC
28755466 TGTCAATTTCTGCTTCTTTATC
1 TGTCAATTTCTGCTTCTTTATC
28755488 T
1 T
28755489 TTGACAGATA
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:0.13, C:0.22, G:0.09, T:0.56
Consensus pattern (22 bp):
TGTCAATTTCTGCTTCTTTATC
Found at i:28756890 original size:40 final size:40
Alignment explanation
Indices: 28756837--28756931 Score: 181
Period size: 40 Copynumber: 2.4 Consensus size: 40
28756827 CAAGTTAATG
*
28756837 AAAAAAGTTAAAATTTTTATTTTTCTTAAAAAGAAAGGGA
1 AAAAAAATTAAAATTTTTATTTTTCTTAAAAAGAAAGGGA
28756877 AAAAAAATTAAAATTTTTATTTTTCTTAAAAAGAAAGGGA
1 AAAAAAATTAAAATTTTTATTTTTCTTAAAAAGAAAGGGA
28756917 AAAAAAATTAAAATT
1 AAAAAAATTAAAATT
28756932 AAAAAGGGGG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (40 bp):
AAAAAAATTAAAATTTTTATTTTTCTTAAAAAGAAAGGGA
Found at i:28767448 original size:5 final size:5
Alignment explanation
Indices: 28767440--28767464 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28767430 GGGAGGTGTT
28767440 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
28767465 ATATAATTAT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:28767474 original size:24 final size:24
Alignment explanation
Indices: 28767447--28767508 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
28767437 GTTTTTTATT
* **
28767447 TTATTTTATTTTATTTTAATATAA
1 TTATTTTATTTAACATTAATATAA
28767471 TTATTTTTATTTAACATTAATATAA
1 TTA-TTTTATTTAACATTAATATAA
**
28767496 AAATTTTATTTAA
1 TTATTTTATTTAA
28767509 TTATTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 13 0.41
25 19 0.59
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTATTTTATTTAACATTAATATAA
Found at i:28768338 original size:8 final size:8
Alignment explanation
Indices: 28768325--28768394 Score: 50
Period size: 8 Copynumber: 7.9 Consensus size: 8
28768315 TAATTTTTTT
28768325 AAAATTTA
1 AAAATTTA
*
28768333 AAAATTCA
1 AAAATTTA
28768341 AAAATTATA
1 AAAATT-TA
*
28768350 AAAGTTATTTTT
1 AAA---A-TTTA
28768362 AAAATTTA
1 AAAATTTA
28768370 AAAATTATTA
1 AAAA-T-TTA
28768380 AAAATTTA
1 AAAATTTA
*
28768388 TAAATTT
1 AAAATTT
28768395 TTTAATTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
8 29 0.58
9 7 0.14
10 7 0.14
12 5 0.10
13 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (8 bp):
AAAATTTA
Found at i:28779693 original size:6 final size:6
Alignment explanation
Indices: 28779657--28779692 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
28779647 TTTATGTGTC
*
28779657 TATGTG TATGTG TATGTG TATGTG TATGTG CATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
28779693 CCTGTGCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.03, G:0.33, T:0.47
Consensus pattern (6 bp):
TATGTG
Found at i:28779698 original size:18 final size:18
Alignment explanation
Indices: 28779658--28779698 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
28779648 TTATGTGTCT
* *
28779658 ATGTGTATGTGTATGTGT
1 ATGTGTATGTGCATGTGC
28779676 ATGTGTATGTGCATGTGC
1 ATGTGTATGTGCATGTGC
*
28779694 CTGTG
1 ATGTG
28779699 CATTTATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.07, G:0.34, T:0.44
Consensus pattern (18 bp):
ATGTGTATGTGCATGTGC
Found at i:28795250 original size:25 final size:25
Alignment explanation
Indices: 28795216--28795264 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
28795206 CATGAATGTT
28795216 CTTGAATGGTTATTGATATTAAATC
1 CTTGAATGGTTATTGATATTAAATC
28795241 CTTGAATGGTTATTGATATTAAAT
1 CTTGAATGGTTATTGATATTAAAT
28795265 TCTAGATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (25 bp):
CTTGAATGGTTATTGATATTAAATC
Found at i:28801589 original size:23 final size:22
Alignment explanation
Indices: 28801557--28801612 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
28801547 TAATTTTGGT
28801557 ATATGATGAAGT-TATCTT-ATAA
1 ATATGATGAA-TCTATCTTGA-AA
28801579 ATATGCATGAATCTATCTTGAAA
1 ATATG-ATGAATCTATCTTGAAA
*
28801602 ATATGTTGAAT
1 ATATGATGAAT
28801613 TGGATTGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 11 0.37
23 18 0.60
24 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (22 bp):
ATATGATGAATCTATCTTGAAA
Found at i:28803633 original size:12 final size:12
Alignment explanation
Indices: 28803616--28803645 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28803606 CTTATGATTG
28803616 TATATATGTATA
1 TATATATGTATA
*
28803628 TGTATATGTATA
1 TATATATGTATA
28803640 TATATA
1 TATATA
28803646 GTTTAATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (12 bp):
TATATATGTATA
Found at i:28809975 original size:20 final size:20
Alignment explanation
Indices: 28809950--28809988 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
28809940 TCTAAGGGGG
28809950 ATGCTG-CAGCAAAGTTGGTA
1 ATGCTGCCA-CAAAGTTGGTA
28809970 ATGCTGCCACAAAGTTGGT
1 ATGCTGCCACAAAGTTGGT
28809989 TTTAATAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (20 bp):
ATGCTGCCACAAAGTTGGTA
Found at i:28814325 original size:9 final size:9
Alignment explanation
Indices: 28814311--28814369 Score: 73
Period size: 9 Copynumber: 6.6 Consensus size: 9
28814301 ATAAGAATAA
28814311 AATTAACCG
1 AATTAACCG
*
28814320 AATTAACCA
1 AATTAACCG
*
28814329 AATTAATCG
1 AATTAACCG
* *
28814338 AATTACCCC
1 AATTAACCG
*
28814347 AATTAACCA
1 AATTAACCG
28814356 AATTAACCG
1 AATTAACCG
28814365 AATTA
1 AATTA
28814370 TTCAAATTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.47, C:0.22, G:0.05, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:28814341 original size:27 final size:27
Alignment explanation
Indices: 28814311--28814369 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
28814301 ATAAGAATAA
* *
28814311 AATTAACCGAATTAACCAAATTAATCG
1 AATTAACCCAATTAACCAAATTAACCG
*
28814338 AATTACCCCAATTAACCAAATTAACCG
1 AATTAACCCAATTAACCAAATTAACCG
28814365 AATTA
1 AATTA
28814370 TTCAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.47, C:0.22, G:0.05, T:0.25
Consensus pattern (27 bp):
AATTAACCCAATTAACCAAATTAACCG
Found at i:28814375 original size:18 final size:18
Alignment explanation
Indices: 28814310--28814378 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
28814300 AATAAGAATA
* *
28814310 AAATTAACCGAATTAACC
1 AAATTAATCAAATTAACC
* *
28814328 AAATTAATCGAATTACCC
1 AAATTAATCAAATTAACC
* *
28814346 CAATTAACCAAATTAACC
1 AAATTAATCAAATTAACC
* *
28814364 GAATTATTCAAATTA
1 AAATTAATCAAATTA
28814379 TTTGTATAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.48, C:0.20, G:0.04, T:0.28
Consensus pattern (18 bp):
AAATTAATCAAATTAACC
Found at i:28814377 original size:27 final size:27
Alignment explanation
Indices: 28814311--28814378 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
28814301 ATAAGAATAA
* * *
28814311 AATTAACCGAATTAACCAAATTAATCG
1 AATTACCCAAATTAACCAAATTAACCG
*
28814338 AATTACCCCAATTAACCAAATTAACCG
1 AATTACCCAAATTAACCAAATTAACCG
**
28814365 AATTATTCAAATTA
1 AATTACCCAAATTA
28814379 TTTGTATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.28
Consensus pattern (27 bp):
AATTACCCAAATTAACCAAATTAACCG
Found at i:28816427 original size:21 final size:20
Alignment explanation
Indices: 28816394--28816433 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28816384 ATGTTCAAGT
28816394 TCCACACAAGCGTGTCGCCCA
1 TCCACACAAGCGTGT-GCCCA
**
28816415 TCCACACGGGCGTGTGCCC
1 TCCACACAAGCGTGTGCCC
28816434 TGTTTCAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.17, C:0.42, G:0.25, T:0.15
Consensus pattern (20 bp):
TCCACACAAGCGTGTGCCCA
Found at i:28818526 original size:7 final size:7
Alignment explanation
Indices: 28818514--28818543 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
28818504 TTCATATGAA
28818514 TTTTATT
1 TTTTATT
28818521 TTTTATT
1 TTTTATT
28818528 TTTTATT
1 TTTTATT
28818535 TTTTATT
1 TTTTATT
28818542 TT
1 TT
28818544 AGCTATCGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTATT
Found at i:28822720 original size:16 final size:17
Alignment explanation
Indices: 28822699--28822731 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
28822689 GTCATTTTCT
28822699 GTTAAAAA-GAAAAAAA
1 GTTAAAAACGAAAAAAA
28822715 GTTAAAAACGAAAAAAA
1 GTTAAAAACGAAAAAAA
28822732 TAAAAAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (17 bp):
GTTAAAAACGAAAAAAA
Found at i:28822851 original size:15 final size:15
Alignment explanation
Indices: 28822831--28822867 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
28822821 GAAGCAAGTA
28822831 GAAGCAGCAACTCGG
1 GAAGCAGCAACTCGG
28822846 GAAGCAGCAACTCGG
1 GAAGCAGCAACTCGG
28822861 GAAGCAG
1 GAAGCAG
28822868 GAAGCAGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.35, C:0.24, G:0.35, T:0.05
Consensus pattern (15 bp):
GAAGCAGCAACTCGG
Found at i:28822903 original size:19 final size:19
Alignment explanation
Indices: 28822879--28822941 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 19
28822869 AAGCAGTAGC
28822879 AAGGAGAAGAAAAGAAAGA
1 AAGGAGAAGAAAAGAAAGA
*
28822898 AAGGAGAAGAGAAG-AAGAA
1 AAGGAGAAGAAAAGAAAG-A
28822917 GAAGGAGAAAGAAAAAGAAAAGA
1 -AAGGAG-AAG-AAAAG-AAAGA
28822940 AA
1 AA
28822942 AGAGTAGGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 3 0.08
19 14 0.39
20 6 0.17
21 3 0.08
22 6 0.17
23 1 0.03
24 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (19 bp):
AAGGAGAAGAAAAGAAAGA
Found at i:28822925 original size:27 final size:24
Alignment explanation
Indices: 28822882--28822944 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 24
28822872 CAGTAGCAAG
* *
28822882 GAGAAGAAAAGAAAGAAAGGAGAA
1 GAGAAGAAAAGAAAGAAAGAAAAA
28822906 GAGAAGAAGAAGAAGGAGAAAGAAAAA
1 GAGAAGAA-AAGAA--AGAAAGAAAAA
*
28822933 GAAAAGAAAAGA
1 GAGAAGAAAAGA
28822945 GTAGGTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 8 0.24
25 5 0.15
26 4 0.12
27 16 0.48
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (24 bp):
GAGAAGAAAAGAAAGAAAGAAAAA
Found at i:28823044 original size:16 final size:16
Alignment explanation
Indices: 28823000--28823046 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
28822990 TGTTTTTGCT
28823000 GTTATTATTATTGTT-
1 GTTATTATTATTGTTA
28823015 GATT-TT-TT-TTGTTA
1 G-TTATTATTATTGTTA
28823029 GTTATTATTATTGTTA
1 GTTATTATTATTGTTA
28823045 GT
1 GT
28823047 AAAAAACCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
13 7 0.26
14 5 0.19
15 5 0.19
16 10 0.37
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.66
Consensus pattern (16 bp):
GTTATTATTATTGTTA
Found at i:28823059 original size:26 final size:26
Alignment explanation
Indices: 28823030--28823079 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
28823020 TTTTTGTTAG
28823030 TTATTATTATTGTTAGTAAAAAACCC
1 TTATTATTATTGTTAGTAAAAAACCC
28823056 TTATTATTATTGTTAGTAAAAAAC
1 TTATTATTATTGTTAGTAAAAAAC
28823080 TATTATTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (26 bp):
TTATTATTATTGTTAGTAAAAAACCC
Found at i:28823085 original size:26 final size:26
Alignment explanation
Indices: 28823030--28823087 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
28823020 TTTTTGTTAG
*
28823030 TTATTATTATTGTTAGTAAAAAACCC
1 TTATTATTATTGTTAGTAAAAAACCA
*
28823056 TTATTATTATTGTTAGTAAAAAACTA
1 TTATTATTATTGTTAGTAAAAAACCA
28823082 TTATTA
1 TTATTA
28823088 GGATTGTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (26 bp):
TTATTATTATTGTTAGTAAAAAACCA
Found at i:28823093 original size:26 final size:26
Alignment explanation
Indices: 28823038--28823095 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
28823028 AGTTATTATT
* **
28823038 ATTGTTAGTAAAAAACCCTTATTATT
1 ATTGTTAGTAAAAAACCATTATTAGG
*
28823064 ATTGTTAGTAAAAAACTATTATTAGG
1 ATTGTTAGTAAAAAACCATTATTAGG
28823090 ATTGTT
1 ATTGTT
28823096 GGTTATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (26 bp):
ATTGTTAGTAAAAAACCATTATTAGG
Found at i:28823141 original size:39 final size:38
Alignment explanation
Indices: 28823056--28823148 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 38
28823046 TAAAAAACCC
*
28823056 TTATTATTATTGTTAGTAAAAAACTATTATTAGGATTG
1 TTATTATTATTGTTAGTAAAAAACTATAATTAGGATTG
* * *
28823094 TTGGTTATTATTGTTAGTAAAAAACTCTAATTATTG-TTAG
1 TT-ATTATTATTGTTAGTAAAAAACTATAATTA-GGATT-G
28823134 TTATTATTATTGTTA
1 TTATTATTATTGTTA
28823149 ATTTATATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
38 2 0.04
39 41 0.87
40 4 0.09
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (38 bp):
TTATTATTATTGTTAGTAAAAAACTATAATTAGGATTG
Found at i:28829055 original size:39 final size:40
Alignment explanation
Indices: 28829008--28829088 Score: 155
Period size: 39 Copynumber: 2.0 Consensus size: 40
28828998 ATAATAACAT
28829008 AATTTATTTCCTTAAATTACGTAGATC-TTTTTTTAATGA
1 AATTTATTTCCTTAAATTACGTAGATCTTTTTTTTAATGA
28829047 AATTTATTTCCTTAAATTACGTAGATCTTTTTTTTAATGA
1 AATTTATTTCCTTAAATTACGTAGATCTTTTTTTTAATGA
28829087 AA
1 AA
28829089 CCCGTGATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 27 0.66
40 14 0.34
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.51
Consensus pattern (40 bp):
AATTTATTTCCTTAAATTACGTAGATCTTTTTTTTAATGA
Found at i:28830083 original size:151 final size:151
Alignment explanation
Indices: 28829610--28830883 Score: 1922
Period size: 152 Copynumber: 8.5 Consensus size: 151
28829600 TATTTTTAAA
* *
28829610 ATTTTTAAAATTTTTGGATCTTATTTTTTAAAATATACTA-TTTT-TA---TA--TTTTATATTA
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTTTTATATTA
*
28829668 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTTAATATTAATTTAGT-AATGAC
66 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTG-TTTTTT-ATATTAATTTAGTAAATAAC
*
28829732 CCTAATTTTGTCCCTTTGTTTGT
129 CCTAATTTTGGCCCTTTGTTTGT
* * ** *
28829755 ATTTTTAAAATTTTTGGATTTTATTTTTAAAAATATACTATTTTCATATTTTATTTTTTATGTTA
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTTTTATATTA
*
28829820 TTTTAGTATATAATGTTTCAAATGTATTATTTTAGTGTTTTTTTATATTAATTTAGTAAATAACC
66 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTG-TTTTTTATATTAATTTAGTAAATAACC
* * *
28829885 CTGATTTTGGCCATTTCTTTGT
130 CTAATTTTGGCCCTTTGTTTGT
*
28829907 ATTTTTAAAATTTTCGAATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTTTTATATTA
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTTTTATATTA
* *
28829972 TTTTAGTACATAATGTTTTAAATGTATTATTTTAGTGTTTTTTATATTAATTAAGTAAATAACCC
66 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCC
*
28830037 TAATTTTGTCCCTTTGTTTGT
131 TAATTTTGGCCCTTTGTTTGT
* *
28830058 ATTTTTAAAATTTTTGGATTTTA-TTTTTAAAATTATACTATTTTCGTATTTTATTTTTTATATT
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAA-TATACTATTTTTGTATTTTATTTTTTATATT
* *
28830122 ATTTTAGTATATAATGTTTCAAATATATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACC
65 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACC
* *
28830187 TTGATTTTGGCCCTTTGTTTGT
130 CTAATTTTGGCCCTTTGTTTGT
** * *
28830209 ATTTTTAAAATTTTTAGATTTTATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTTATATT
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTA-TTTTTTATATT
* * *
28830274 ATTTTAGTACATAATATTTCAAATGTATTATTTTATTATTATTTTATATTAATTTAGTAAATAAC
65 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTT-TTTTATATTAATTTAGTAAATAAC
* * *
28830339 CCTGATTTCGGTCCTTTGTTTGT
129 CCTAATTTTGGCCCTTTGTTTGT
* * *
28830362 GTTTTTAAAATTTTCGGATTTTATTTTTAAAAATATACTATTTTTTTATTTTATTTTTTTATATT
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTA-TTTTTTATATT
* *
28830427 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAATATTTTTTATATTAATTTAGTAAATAACC
65 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACC
* * *
28830492 CTGATTTTGGCCATTTCTTTGT
130 CTAATTTTGGCCCTTTGTTTGT
* **
28830514 ATTTTTAAAATTTTCGAATTTTATTTTTTAAAATATACTATTTTCATATTTTATTTTTTATATTA
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTTTTATATTA
* *
28830579 TTTTTGTACATAATGTTTCAAATGTATTATTTTAGTG-TTTTTATATTAATTTAATAAATAACCC
66 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCC
28830643 TAATTTTGGCCCTTTGTTTGT
131 TAATTTTGGCCCTTTGTTTGT
28830664 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTAATTTTTTATATT
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTT-ATTTTTTATATT
*
28830729 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAATC
65 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACC
* *
28830794 CTAATTTTGTCCCTTTATTTGT
130 CTAATTTTGGCCCTTTGTTTGT
* * *
28830816 ATTATTT-AAATTTTCAGATTTTATTTTTTGAAATATATTATTTTTGTATTTTATTTTTTATATT
1 ATT-TTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTTTTATATT
28830880 ATTT
65 ATTT
28830884 AAAAAAACCG
Statistics
Matches: 1037, Mismatches: 77, Indels: 24
0.91 0.07 0.02
Matches are distributed among these distances:
145 38 0.04
146 3 0.00
147 2 0.00
150 104 0.10
151 341 0.33
152 404 0.39
153 145 0.14
ACGTcount: A:0.29, C:0.06, G:0.07, T:0.58
Consensus pattern (151 bp):
ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTTTTATATTA
TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCC
TAATTTTGGCCCTTTGTTTGT
Found at i:28830100 original size:22 final size:22
Alignment explanation
Indices: 28830057--28830101 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28830047 CCTTTGTTTG
* **
28830057 TATTTTTAAAATTTTTGGATTT
1 TATTTTTAAAATTATACGATTT
*
28830079 TATTTTTAAAATTATACTATTT
1 TATTTTTAAAATTATACGATTT
28830101 T
1 T
28830102 CGTATTTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (22 bp):
TATTTTTAAAATTATACGATTT
Found at i:28830414 original size:607 final size:605
Alignment explanation
Indices: 28829610--28830883 Score: 2054
Period size: 607 Copynumber: 2.1 Consensus size: 605
28829600 TATTTTTAAA
* *
28829610 ATTTTTAAAATTTTTGGATCTTATTTTTTAAAATATACTATTTT-TA---TA--TTTTATATTAT
1 ATTTTTAAAATTTTTAGATTTTATTTTTTAAAATATACTATTTTGTATTTTATTTTTTATATTAT
* * * *
28829669 TTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTTAATATTAATTTAGTAATGACCC
66 TTTAGTACATAATATTTCAAATGTATTATTTTAGTATTATTTTAATATTAATTTAGTAATAACCC
* *
28829734 TAATTTTGTCCCTTTGTTTGTATTTTTAAAATTTTTGGATTTTATTTTTAAAAATATACTATTTT
131 TAATTTGGTCCCTTTGTTTGTATTTTTAAAATTTTCGGATTTTATTTTTAAAAATATACTATTTT
* * * *
28829799 CATATTTTA-TTTTTTATGTTATTTTAGTATATAATGTTTCAAATGTATTATTTTAGTGTTTTTT
196 CATATTTTATTTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAAT-ATTTTT
28829863 TATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTCTTTGTATTTTTAAAATTTTCGAATTT
260 TATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTCTTTGTATTTTTAAAATTTTCGAATTT
** *
28829928 TATTTTTTAAAATATACTATTTTTGTATTTTATTTTTTATATTATTTTAGTACATAATGTTTTAA
325 TATTTTTTAAAATATACTATTTTCATATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAA
*
28829993 ATGTATTATTTTAGTGTTTTTTATATTAA-TTAAGTAAATAACCCTAATTTTGTCCCTTTGTTTG
390 ATGTATTATTTTAGTG-TTTTTATATTAATTTAA-TAAATAACCCTAATTTTGGCCCTTTGTTTG
*
28830057 TATTTTTAAAATTTTTGGATTTTA-TTTTTAAAATTATACTATTTTCGTATTTT-ATTTTTTATA
453 TATTTTTAAAATTTTCGGATTTTATTTTTTAAAA-TATACTATTTTCGTATTTTAATTTTTTATA
*
28830120 TTATTTTAGTATATAATGTTTCAAATATATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAA
517 TTATTTTAGTACATAATGTTTCAAATATATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAA
* *
28830185 -CCTTGATTTTGGCCCTTTGTTTGT
582 TCC-TAATTTTGGCCCTTTATTTGT
*
28830209 ATTTTTAAAATTTTTAGATTTTATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTTATATT
1 ATTTTTAAAATTTTTAGATTTTATTTTTTAAAATATACTATTTT-GTATTTTA-TTTTTTATATT
*
28830274 ATTTTAGTACATAATATTTCAAATGTATTATTTTATTATTATTTT-ATATTAATTTAGTAAATAA
64 ATTTTAGTACATAATATTTCAAATGTATTATTTTAGTATTATTTTAATATTAATTTAGT-AATAA
* *
28830338 CCCTGATTTCGGT-CCTTTGTTTGTGTTTTTAAAATTTTCGGATTTTATTTTTAAAAATATACTA
128 CCCTAATTT-GGTCCCTTTGTTTGTATTTTTAAAATTTTCGGATTTTATTTTTAAAAATATACTA
**
28830402 TTTTTTTATTTTATTTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAATATT
192 TTTTCATATTTTATTTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAATATT
28830467 TTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTCTTTGTATTTTTAAAATTTTCGAA
257 TTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTCTTTGTATTTTTAAAATTTTCGAA
*
28830532 TTTTATTTTTTAAAATATACTATTTTCATATTTTATTTTTTATATTATTTTTGTACATAATGTTT
322 TTTTATTTTTTAAAATATACTATTTTCATATTTTATTTTTTATATTATTTTAGTACATAATGTTT
28830597 CAAATGTATTATTTTAGTGTTTTTATATTAATTTAATAAATAACCCTAATTTTGGCCCTTTGTTT
387 CAAATGTATTATTTTAGTGTTTTTATATTAATTTAATAAATAACCCTAATTTTGGCCCTTTGTTT
*
28830662 GTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTTGTATTTTAATTTTTTATA
452 GTATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTAATTTTTTATA
*
28830727 TTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAA
517 TTATTTTAGTACATAATGTTTCAAATATATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAA
*
28830792 TCCTAATTTTGTCCCTTTATTTGT
582 TCCTAATTTTGGCCCTTTATTTGT
* * *
28830816 ATTATTT-AAATTTTCAGATTTTATTTTTTGAAATATATTATTTTTGTATTTTATTTTTTATATT
1 ATT-TTTAAAATTTTTAGATTTTATTTTTTAAAATATACTA-TTTTGTATTTTATTTTTTATATT
28830880 ATTT
64 ATTT
28830884 AAAAAAACCG
Statistics
Matches: 624, Mismatches: 34, Indels: 27
0.91 0.05 0.04
Matches are distributed among these distances:
599 41 0.07
601 2 0.00
604 2 0.00
606 110 0.18
607 413 0.66
608 56 0.09
ACGTcount: A:0.29, C:0.06, G:0.07, T:0.58
Consensus pattern (605 bp):
ATTTTTAAAATTTTTAGATTTTATTTTTTAAAATATACTATTTTGTATTTTATTTTTTATATTAT
TTTAGTACATAATATTTCAAATGTATTATTTTAGTATTATTTTAATATTAATTTAGTAATAACCC
TAATTTGGTCCCTTTGTTTGTATTTTTAAAATTTTCGGATTTTATTTTTAAAAATATACTATTTT
CATATTTTATTTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAATATTTTTT
ATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTCTTTGTATTTTTAAAATTTTCGAATTTT
ATTTTTTAAAATATACTATTTTCATATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAA
TGTATTATTTTAGTGTTTTTATATTAATTTAATAAATAACCCTAATTTTGGCCCTTTGTTTGTAT
TTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTAATTTTTTATATTAT
TTTAGTACATAATGTTTCAAATATATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAATCCT
AATTTTGGCCCTTTATTTGT
Found at i:28830418 original size:13 final size:13
Alignment explanation
Indices: 28830395--28830431 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
28830385 TTTTTAAAAA
*
28830395 TATACTATTTTTT
1 TATATTATTTTTT
*
28830408 TATTTTATTTTTT
1 TATATTATTTTTT
28830421 TATATTATTTT
1 TATATTATTTT
28830432 AGTACATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
TATATTATTTTTT
Found at i:28830881 original size:12 final size:13
Alignment explanation
Indices: 28830849--28830883 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
28830839 TTTTTTGAAA
28830849 TATATTATTTTTG
1 TATATTATTTTTG
*
28830862 TATTTTATTTTT-
1 TATATTATTTTTG
28830874 TATATTATTT
1 TATATTATTT
28830884 AAAAAAACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TATATTATTTTTG
Found at i:28830940 original size:16 final size:15
Alignment explanation
Indices: 28830919--28831002 Score: 60
Period size: 16 Copynumber: 5.1 Consensus size: 15
28830909 TCAAAAAAAA
28830919 TTATTTTTTTCATATT
1 TTATTTTTTT-ATATT
*
28830935 TTATTTCTTTTTGTATT
1 TTA-TT-TTTTTATATT
**
28830952 TTATTTTTTTATTAAG
1 TTATTTTTTTA-TATT
* *
28830968 ATATTTTTTAAATATT
1 TTATTTTTT-TATATT
28830984 TTATTTTTTATACTATT
1 TTATTTTTT-TA-TATT
28831001 TT
1 TT
28831003 TGTAAAATAG
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
15 5 0.09
16 27 0.51
17 16 0.30
18 5 0.09
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (15 bp):
TTATTTTTTTATATT
Found at i:28831328 original size:10 final size:10
Alignment explanation
Indices: 28831313--28831346 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
28831303 AAAAAAATTA
28831313 CCTTTTTTTT
1 CCTTTTTTTT
28831323 CCTTTTTTTT
1 CCTTTTTTTT
28831333 -CTTTCTTTTT
1 CCTTT-TTTTT
28831343 CCTT
1 CCTT
28831347 CCCTCCTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.18
10 15 0.68
11 3 0.14
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (10 bp):
CCTTTTTTTT
Found at i:28837443 original size:23 final size:24
Alignment explanation
Indices: 28837390--28837479 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 24
28837380 GCCATGATCG
*
28837390 GTAAGCTCCTCTTGAGCTGATGAACA
1 GTAAGCT-CTATTGAGCTGA-GAACA
28837416 GTAAGCTCTATTGAGCTGA-AACTA
1 GTAAGCTCTATTGAGCTGAGAAC-A
* * * *
28837440 -TAAGCTCCAATGAGTTGAAAACA
1 GTAAGCTCTATTGAGCTGAGAACA
28837463 GTAAGCTCT-TATGAGCT
1 GTAAGCTCTAT-TGAGCT
28837480 AACATATCGG
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
23 19 0.36
24 16 0.30
25 11 0.21
26 7 0.13
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (24 bp):
GTAAGCTCTATTGAGCTGAGAACA
Found at i:28840426 original size:20 final size:20
Alignment explanation
Indices: 28840401--28840439 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
28840391 ATTGATTGTT
28840401 TTGTTTGAA-TTGATTCAAAG
1 TTGTTT-AATTTGATTCAAAG
28840421 TTGTTTAATTTGATTCAAA
1 TTGTTTAATTTGATTCAAA
28840440 ACCCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (20 bp):
TTGTTTAATTTGATTCAAAG
Found at i:28842423 original size:183 final size:185
Alignment explanation
Indices: 28842091--28842463 Score: 457
Period size: 183 Copynumber: 2.0 Consensus size: 185
28842081 AGACAAGGAA
* * *
28842091 GATGGAGAAGACTGTGAAGATATTATAGACTTGGAGAAACCCCATATACAGAAAAGGAAGATCAA
1 GATGGAGAAGACTATGAAGACATTATAGACTTGGAGAAAACCCATATACAGAAAA-GAAGATCAA
* * * * * * *
28842156 GAAGGGAAGAGGAAGACCAAGTTCAAAAGCTGTTGACGCTGATAATCGTCATCAATCGAAGGGAA
65 GAAGAGAAGAGGAAGACCAAGCTCAAAAGCTGTTGACACTAATAACCATCATCAATCGAAGGCAA
** * * * * * *
28842221 GGGAGGACAAGCAGCCTCGAGTTGGCAAATCTGCTGTCG-AGAGGGAAGTATTGATT
130 CAGAGAAAAAGCAGCCTCGAGTTAGAAAATCTGCTGTCGAAG-GGGAAGTATCGATC
* * *
28842277 GATGGAGATGACTATGAAGACATTATAGATTTGGAGAAAATCCATA-AGCA-AAAA-AAGATCAA
1 GATGGAGAAGACTATGAAGACATTATAGACTTGGAGAAAACCCATATA-CAGAAAAGAAGATCAA
* *
28842339 GAAGAGAAGAGGAAGACCGAGCTCAAAAGCTGTTGACACTAATAACCATCATCAATCTAAGGCAA
65 GAAGAGAAGAGGAAGACCAAGCTCAAAAGCTGTTGACACTAATAACCATCATCAATCGAAGGCAA
* * *
28842404 CAGAGAAAAAGCGGCCTCGAGTTATAAAATCTGCTGTTGAAGGGGAAGTATCGATC
130 CAGAGAAAAAGCAGCCTCGAGTTAGAAAATCTGCTGTCGAAGGGGAAGTATCGATC
28842460 GATG
1 GATG
28842464 AATCGGATGG
Statistics
Matches: 159, Mismatches: 26, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
183 110 0.69
184 2 0.01
185 5 0.03
186 42 0.26
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.19
Consensus pattern (185 bp):
GATGGAGAAGACTATGAAGACATTATAGACTTGGAGAAAACCCATATACAGAAAAGAAGATCAAG
AAGAGAAGAGGAAGACCAAGCTCAAAAGCTGTTGACACTAATAACCATCATCAATCGAAGGCAAC
AGAGAAAAAGCAGCCTCGAGTTAGAAAATCTGCTGTCGAAGGGGAAGTATCGATC
Found at i:28846678 original size:14 final size:13
Alignment explanation
Indices: 28846661--28846717 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 13
28846651 TAAGAAATAA
28846661 AAAATATGAAAAAT
1 AAAATAT-AAAAAT
*
28846675 -AAA-A-AAAATT
1 AAAATATAAAAAT
28846685 AAAATA-AAAAAT
1 AAAATATAAAAAT
*
28846697 AAAAAATAAAAAAT
1 AAAATAT-AAAAAT
28846711 AAAATAT
1 AAAATAT
28846718 TTTAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 5 0.14
11 3 0.09
12 12 0.34
13 3 0.09
14 12 0.34
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (13 bp):
AAAATATAAAAAT
Found at i:28846679 original size:7 final size:7
Alignment explanation
Indices: 28846655--28846714 Score: 77
Period size: 7 Copynumber: 8.1 Consensus size: 7
28846645 AATTTTTAAG
28846655 AAATAAA
1 AAATAAA
28846662 AAATATGAA
1 AAATA--AA
28846671 AAATAAA
1 AAATAAA
28846678 AAA-AATTA
1 AAATAA--A
28846686 AAATAAA
1 AAATAAA
28846693 AAATAAA
1 AAATAAA
28846700 AAATAAA
1 AAATAAA
28846707 AAATAAA
1 AAATAAA
28846714 A
1 A
28846715 TATTTTAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
6 2 0.04
7 33 0.69
8 4 0.08
9 9 0.19
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.17
Consensus pattern (7 bp):
AAATAAA
Found at i:28846728 original size:14 final size:14
Alignment explanation
Indices: 28846706--28846739 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28846696 TAAAAAATAA
*
28846706 AAAATAAAATATTTT
1 AAAA-AAAATATTGT
28846721 AAAAAAAATATTGT
1 AAAAAAAATATTGT
28846735 AAAAA
1 AAAAA
28846740 TATAAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
AAAAAAAATATTGT
Found at i:28848040 original size:90 final size:91
Alignment explanation
Indices: 28847854--28848061 Score: 231
Period size: 91 Copynumber: 2.3 Consensus size: 91
28847844 GGAAACTCTG
* * * * * * * *
28847854 ATTTGTGGATAAACCACCAGTA-TTGCAGGTTAATACATTGCCATTAGTAGTGAGTATACAACGG
1 ATTTGTGGACAAACCACCAGTATTTGCAAGTTAATACACTACCAGTAGTAGTAAATACACAACGG
* *
28847918 GTTTACAAATAAAAGCTGGCAATAAA
66 GTTTACAAATAAAAGATGCCAATAAA
* * * *
28847944 AATTGTGGACAAACCACCAGTATTTGCAAGTTAATACGCTACCAGTAGTTGTAAATACACAATGG
1 ATTTGTGGACAAACCACCAGTATTTGCAAGTTAATACACTACCAGTAGTAGTAAATACACAACGG
* * *
28848009 GTTTGCAGATAAAAGATGCCAGT-AA
66 GTTTACAAATAAAAGATGCCAATAAA
* *
28848034 GTTTGTGGACAAACCACCAGTGTTTGCA
1 ATTTGTGGACAAACCACCAGTATTTGCA
28848062 GATAAACTAC
Statistics
Matches: 97, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
90 47 0.48
91 50 0.52
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (91 bp):
ATTTGTGGACAAACCACCAGTATTTGCAAGTTAATACACTACCAGTAGTAGTAAATACACAACGG
GTTTACAAATAAAAGATGCCAATAAA
Found at i:28854930 original size:16 final size:17
Alignment explanation
Indices: 28854907--28854949 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
28854897 TATTTAATTT
28854907 TAATTATTATATTATA-
1 TAATTATTATATTATAG
* *
28854923 TTATTATTATATTTTAG
1 TAATTATTATATTATAG
28854940 TAATTATTAT
1 TAATTATTAT
28854950 TATTTACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TAATTATTATATTATAG
Found at i:28856320 original size:31 final size:31
Alignment explanation
Indices: 28856285--28856347 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
28856275 CTTTTCACAC
*
28856285 TTCATATTTCATAACACTGGGCCGAAGACTT
1 TTCATACTTCATAACACTGGGCCGAAGACTT
** *
28856316 TTCATACTTCATATTACTGGGCCGAAGCCTT
1 TTCATACTTCATAACACTGGGCCGAAGACTT
28856347 T
1 T
28856348 ACTGTAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (31 bp):
TTCATACTTCATAACACTGGGCCGAAGACTT
Found at i:28856618 original size:48 final size:49
Alignment explanation
Indices: 28856541--28856637 Score: 137
Period size: 48 Copynumber: 2.0 Consensus size: 49
28856531 GCTTTATCAT
*
28856541 ATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCATAAGCCCTTTTA
*
28856589 ATAACTGG-GGCATAAGCC-CTTTATCATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGAGGCAT-AGCCTCTTT-TAATAACTGGGGCATAAGCCCTTTTA
28856638 CACTTCCTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
47 8 0.18
48 25 0.57
49 11 0.25
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (49 bp):
ATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCATAAGCCCTTTTA
Found at i:28856623 original size:25 final size:24
Alignment explanation
Indices: 28856541--28856637 Score: 135
Period size: 25 Copynumber: 4.0 Consensus size: 24
28856531 GCTTTATCAT
*
28856541 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
28856566 ATAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
28856589 ATAACTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TA
28856614 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28856638 CACTTCCTCC
Statistics
Matches: 66, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.27
24 17 0.26
25 31 0.47
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:28856711 original size:20 final size:20
Alignment explanation
Indices: 28856686--28856732 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
28856676 TTATGAATAC
28856686 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
28856706 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
28856726 ACCATGT
1 ATCATGT
28856733 TTATCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:28859640 original size:20 final size:19
Alignment explanation
Indices: 28859604--28859653 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
28859594 AATAGCTATT
28859604 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTAAAATAA
*
28859623 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTAAAATAA
*
28859643 TTGAAAATGTG
1 TTGTAAATGTG
28859654 AGTTGCTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 10 0.37
20 16 0.59
21 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (19 bp):
TTGTAAATGTGTAAAATAA
Found at i:28860324 original size:47 final size:48
Alignment explanation
Indices: 28860263--28860385 Score: 194
Period size: 47 Copynumber: 2.6 Consensus size: 48
28860253 ATATTACGCG
28860263 AGCCAGTGTAAGACATGTCTGGGACATGCATCAACCTCGAGATATACA
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCAACCTCGAGATATACA
* **
28860311 A-CCAGTGTAAGACATGTCTGGGACATTCATCGGCCTCGAGATATACA
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCAACCTCGAGATATACA
* *
28860358 AGCTAGTGTAAGACCTGTCTGGGACATG
1 AGCCAGTGTAAGACATGTCTGGGACATG
28860386 GCGTCAGCTT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
47 44 0.65
48 24 0.35
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (48 bp):
AGCCAGTGTAAGACATGTCTGGGACATGCATCAACCTCGAGATATACA
Found at i:28860480 original size:49 final size:49
Alignment explanation
Indices: 28860263--28860577 Score: 179
Period size: 49 Copynumber: 6.6 Consensus size: 49
28860253 ATATTACGCG
* * * * *
28860263 AGCCAGTGTAAGACATGTCTGGGACAT-GCATCAACCTCGAGATAT-ACA
1 AGCCAATGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGA-A
* * * * * *
28860311 A-CCAGTGTAAGACATGTCTGGGACAT-TCATCGGCCTCGAGATAT-ACA
1 AGCCAATGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGA-A
* * * * * **
28860358 AGCTAGTGTAAGACCTGTCTGGGACATGGCGTC-AGCT---T-GTTGTT
1 AGCCAATGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAA
* * * *
28860402 TGTCAGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGATGAG
1 AGCCAATGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAGATGAA
* * *
28860451 AGCCAATGTAATACCTGTCTGGGACATGGCATCGGCCTCGATATATGAA
1 AGCCAATGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAA
* * * * * * * **
28860500 AGTCAGTGTAAGACCTATCTAGGATATGGCATCGACTTTGAT--ATGCT
1 AGCCAATGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAA
* *
28860547 AGCCAGTGTAAGACCATGTTTGGGACATGGC
1 AGCCAATGTAAGACC-TGTCTGGGACATGGC
28860578 GTCGGCATCT
Statistics
Matches: 211, Mismatches: 45, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
44 30 0.14
45 1 0.00
46 1 0.00
47 61 0.29
48 39 0.18
49 79 0.37
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (49 bp):
AGCCAATGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAA
Found at i:28860529 original size:142 final size:139
Alignment explanation
Indices: 28860266--28860529 Score: 327
Period size: 142 Copynumber: 1.9 Consensus size: 139
28860256 TTACGCGAGC
* *
28860266 CAGTGTAAGACATGTCTGGGACATGCATCAACCTCGAGATATACAACCAGTGTAAGACATGTCTG
1 CAGTGTAAGACATGTCTGGGACATGCATCAACCTCGAGAGATACAACCAATGTAAGACATGTCTG
* * *
28860331 GGACATTCATCGGCCTCGAGATATACAAGCTAGTGTAAGACCTGTCTGGGACATGGCGTCAGCTT
66 GGACATGCATCGGCCTCGAGATATACAAGCTAGTGTAAGACCTATCTAGGACATGGCGTCAGCTT
28860396 GTTGTTTGT
131 GTTGTTTGT
* * * * * * *
28860405 CAGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGATGAGAGCCAATGTAATACCTGT
1 CAGTGTAAGACATGTCTGGGACAT-GCATCAAC-CTCGAGAGAT-ACAACCAATGTAAGACATGT
* *
28860469 CTGGGACATGGCATCGGCCTCGATATATGA-AAG-TCAGTGTAAGACCTATCTAGGATATGGC
63 CTGGGACAT-GCATCGGCCTCGAGATAT-ACAAGCT-AGTGTAAGACCTATCTAGGACATGGC
28860530 ATCGACTTTG
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
139 23 0.22
140 13 0.12
141 26 0.25
142 42 0.40
143 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.25
Consensus pattern (139 bp):
CAGTGTAAGACATGTCTGGGACATGCATCAACCTCGAGAGATACAACCAATGTAAGACATGTCTG
GGACATGCATCGGCCTCGAGATATACAAGCTAGTGTAAGACCTATCTAGGACATGGCGTCAGCTT
GTTGTTTGT
Found at i:28864336 original size:40 final size:40
Alignment explanation
Indices: 28864231--28864447 Score: 262
Period size: 40 Copynumber: 5.5 Consensus size: 40
28864221 CGGATGATAG
* * **
28864231 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
28864271 CCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
28864310 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
28864350 CCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTATTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
28864390 CCGGGCTAAGTCCCGAAGGCATTTGAGTGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
28864430 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
28864448 TACTTGGTTG
Statistics
Matches: 155, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 49 0.32
40 106 0.68
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28872410 original size:40 final size:40
Alignment explanation
Indices: 28872305--28872521 Score: 280
Period size: 40 Copynumber: 5.5 Consensus size: 40
28872295 CGGATGATAA
* *
28872305 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
28872345 CCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
28872384 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
28872424 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTATTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
28872464 CCGGGCTAAGTCCCGAAGGCATTTGAGTGAG-TAGTTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
28872504 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
28872522 TACTTGGTTG
Statistics
Matches: 161, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
39 51 0.32
40 110 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28872517 original size:119 final size:119
Alignment explanation
Indices: 28872301--28872521 Score: 297
Period size: 119 Copynumber: 1.9 Consensus size: 119
28872291 TATTCGGATG
* *
28872301 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAA
* *
28872366 TTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
66 TTGAGCGAGTTACTATATCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT
* *
28872420 ATAACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCT-A-TTATAACCGGGCTAAGTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACTAAT-ACCGGGCTAAG-CCCGAAGG
* * *
28872483 CATTTGAGTGAG-TAGTTATATCC-GGCTAAATCCCGAAGG
63 CAATTGAGCGAGTTA-CTATATCCGGGCTAAATCCCGAAGG
28872522 TACTTGGTTG
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
118 3 0.03
119 61 0.69
120 25 0.28
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAA
TTGAGCGAGTTACTATATCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT
Found at i:28888608 original size:40 final size:40
Alignment explanation
Indices: 28888564--28888644 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
28888554 GTACCTAGGA
28888564 TAGTAAATTTAAATTGTTTTTCTTTCAATTTAGGTAAGTT
1 TAGTAAATTTAAATTGTTTTTCTTTCAATTTAGGTAAGTT
*
28888604 TAGTAAATTTAAATTGTTTTTCTTTCAATTTTGGTAAGTT
1 TAGTAAATTTAAATTGTTTTTCTTTCAATTTAGGTAAGTT
28888644 T
1 T
28888645 TTTCTGAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.54
Consensus pattern (40 bp):
TAGTAAATTTAAATTGTTTTTCTTTCAATTTAGGTAAGTT
Found at i:28892935 original size:40 final size:40
Alignment explanation
Indices: 28892848--28893033 Score: 272
Period size: 40 Copynumber: 4.7 Consensus size: 40
28892838 ACTACTCACT
*
28892848 CAAATGCCTTC-GGACTTAGCCCGGTTATA-TAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
28892886 CAAATGCCTTCGGGACTTAACCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
28892926 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * *
28892966 CAATTGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
28893005 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
28893034 CATCCGAATA
Statistics
Matches: 133, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
38 12 0.09
39 50 0.38
40 70 0.53
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:28892950 original size:79 final size:79
Alignment explanation
Indices: 28892848--28893033 Score: 270
Period size: 79 Copynumber: 2.4 Consensus size: 79
28892838 ACTACTCACT
*
28892848 CAAATGCCTTC-GGACTTAGCCCGGTTATA-TAGCTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAACCCGG
* *
28892911 -TTATAGTAACTCGCA
65 AAT-TAGTAACTAGCA
* * *
28892926 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAATTGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGA
*
28892991 ATTAGTCACTAGCA
66 ATTAGTAACTAGCA
28893005 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
28893034 CATCCGAATA
Statistics
Matches: 97, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
78 11 0.11
79 64 0.66
80 22 0.23
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGA
ATTAGTAACTAGCA
Found at i:28900888 original size:40 final size:41
Alignment explanation
Indices: 28900821--28900985 Score: 186
Period size: 40 Copynumber: 4.2 Consensus size: 41
28900811 CCTTCGAGGT
* *
28900821 TTAG-CCGGATATAGCT-ACTCGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGATAACTCGCACAAATGCCTTCGGGAC
*
28900860 TTAGCCCGGTTATAG-TAACTCGCACAAATGCCTTC-GGAC
1 TTAGCCCGGATATAGATAACTCGCACAAATGCCTTCGGGAC
* *
28900899 TTAGCCCGGA-ATATGATAACTCGCACAATTGGCTTCGGG-C
1 TTAGCCCGGATATA-GATAACTCGCACAAATGCCTTCGGGAC
* * *
28900939 TTAGCCCGAAT-TAG-TCACTAGCACAAAT-CCTTCGGGAC
1 TTAGCCCGGATATAGATAACTCGCACAAATGCCTTCGGGAC
28900977 TTAGCCCGG
1 TTAGCCCGG
28900986 TTATCATCCG
Statistics
Matches: 108, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
37 7 0.06
38 23 0.21
39 20 0.19
40 56 0.52
41 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (41 bp):
TTAGCCCGGATATAGATAACTCGCACAAATGCCTTCGGGAC
Found at i:28900977 original size:78 final size:80
Alignment explanation
Indices: 28900837--28900985 Score: 205
Period size: 78 Copynumber: 1.9 Consensus size: 80
28900827 GGATATAGCT
* ** *
28900837 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGACTTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGGACTTA
28900902 GCCCGGAATATGATA
66 GCCCGGAATATGATA
* * *
28900917 ACTCGCACAATTGGCTTCGGG-CTTAGCCCGAAT-TAGTCACTAGCACAAAT-CCTTCGGGACTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTC-GGACTT
28900979 AGCCCGG
65 AGCCCGG
28900986 TTATCATCCG
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
77 5 0.08
78 28 0.46
79 10 0.16
80 18 0.30
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (80 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGGACTTA
GCCCGGAATATGATA
Found at i:28908896 original size:40 final size:40
Alignment explanation
Indices: 28908819--28909035 Score: 275
Period size: 40 Copynumber: 5.5 Consensus size: 40
28908809 AAACCAAGTA
** *
28908819 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
28908858 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
28908898 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
28908938 CCTTCGGGACTTAGCCCGGATAT-GATAACTCACAC-AATCG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAAT-G
* * *
28908978 CCTTCGGGA-TTAGCCC-GAAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
28909017 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
28909036 TTATCATCCG
Statistics
Matches: 159, Mismatches: 10, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
38 3 0.02
39 42 0.26
40 113 0.71
41 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:28915473 original size:39 final size:40
Alignment explanation
Indices: 28915316--28915540 Score: 246
Period size: 40 Copynumber: 5.7 Consensus size: 40
28915306 GCTCCTCGTT
* * *
28915316 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAAT-TAGTAACTCGCA
28915356 CAAATGCCTTCGGGACTTAACCC-GAATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAA-TTAGTAACTCGCA
*
28915396 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
* * *
28915436 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
** * * *
28915475 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAAT-TAGTAAC-TCGCA
*
28915516 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
28915541 CATCATTCAA
Statistics
Matches: 161, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
38 2 0.01
39 35 0.22
40 110 0.68
41 14 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
Found at i:28915524 original size:119 final size:120
Alignment explanation
Indices: 28915318--28915540 Score: 292
Period size: 119 Copynumber: 1.9 Consensus size: 120
28915308 TCCTCGTTCA
*
28915318 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAAT
* *
28915383 TTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * ** *
28915438 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGA
* * *
28915500 ATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
64 ATATAGTAAC-TAGCACAAATGCCTTCGGGACTTAACCCGGA
28915541 CATCATTCAA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.04
119 65 0.73
120 20 0.22
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAAT
ATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:28923410 original size:119 final size:120
Alignment explanation
Indices: 28923228--28923450 Score: 292
Period size: 119 Copynumber: 1.9 Consensus size: 120
28923218 TCCTCGTTCA
*
28923228 AATGCCTTCGGGACATAGCCCGGTTATAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
28923293 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * * **
28923348 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
28923410 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
28923451 CATCATTCAA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.04
119 65 0.73
120 20 0.22
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:28923450 original size:40 final size:40
Alignment explanation
Indices: 28923226--28923450 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
28923216 GCTCCTCGTT
* * *
28923226 CAAATGCCTTCGGGACATAGCCCGGTTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
28923266 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
28923306 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
28923346 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
28923385 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
28923426 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28923451 CATCATTCAA
Statistics
Matches: 163, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 31 0.19
40 118 0.72
41 12 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:28926158 original size:46 final size:46
Alignment explanation
Indices: 28926092--28926257 Score: 165
Period size: 46 Copynumber: 3.6 Consensus size: 46
28926082 CTCGTAGCTG
28926092 ATGCATGT-CCAGACATGTCTTACACTGGCT-TACATATTGAGGCCA
1 ATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATATTGAGGCCA
* * * * ** *
28926137 ATGCATGTCTCAGACATGTCTTACACTAGCTCTCGTCTCAATGCCA
1 ATGCATGTCCCAGACATGTCTTACACTGGCTCTCATATTGAGGCCA
* * * * * **
28926183 TTGCCATGTCCCAGACATGGTCTTCCACTGGCTCTTATAATGTGGCTG
1 ATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATATTGAGGCCA
28926231 ATGCATGTCCCAGACATGTCTTACACT
1 ATGCATGTCCCAGACATGTCTTACACT
28926258 AGCACACAAA
Statistics
Matches: 94, Mismatches: 23, Indels: 7
0.76 0.19 0.06
Matches are distributed among these distances:
45 8 0.09
46 39 0.41
47 28 0.30
48 19 0.20
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.31
Consensus pattern (46 bp):
ATGCATGTCCCAGACATGTCTTACACTGGCTCTCATATTGAGGCCA
Found at i:28932639 original size:22 final size:22
Alignment explanation
Indices: 28932611--28932655 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
28932601 TCTTTTAAAC
28932611 TTTTCTTTATACATTTTGGCAT
1 TTTTCTTTATACATTTTGGCAT
28932633 TTTTCTTTATACATTTTGGCAT
1 TTTTCTTTATACATTTTGGCAT
28932655 T
1 T
28932656 CTCGTATGAA
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:0.18, C:0.13, G:0.09, T:0.60
Consensus pattern (22 bp):
TTTTCTTTATACATTTTGGCAT
Found at i:28940062 original size:27 final size:27
Alignment explanation
Indices: 28940054--28940455 Score: 554
Period size: 27 Copynumber: 14.9 Consensus size: 27
28940044 AAAATTACTG
* *
28940054 TTTTACCCTCAATTTACAGAATTACCG
1 TTTTACCCTCGATTTACAGAATTACCA
* * *
28940081 TTTTACCCTCGATTTATAAAATTACCG
1 TTTTACCCTCGATTTACAGAATTACCA
** * *
28940108 TTTTACCCTCGATTTGTAAAATTACCG
1 TTTTACCCTCGATTTACAGAATTACCA
** *
28940135 TTTTACCCTCGATTTGTAAAATTACCA
1 TTTTACCCTCGATTTACAGAATTACCA
28940162 TTTTACCCTCGA-TTACAGAATTACCA
1 TTTTACCCTCGATTTACAGAATTACCA
*
28940188 TTTTACCCTCAATTTACAGAATTACCA
1 TTTTACCCTCGATTTACAGAATTACCA
*
28940215 TTTTACCCTCGATTTACAGAATTACAA
1 TTTTACCCTCGATTTACAGAATTACCA
* *
28940242 TTTTACCCTCGATTTATAGAATTACAA
1 TTTTACCCTCGATTTACAGAATTACCA
28940269 TTTTACCCTCGATTTACAGAATTACCA
1 TTTTACCCTCGATTTACAGAATTACCA
*
28940296 TTTTACCCTCGATTTATAGAATTACCA
1 TTTTACCCTCGATTTACAGAATTACCA
*
28940323 TTTTACCCTCGATTTATAGAATTACCA
1 TTTTACCCTCGATTTACAGAATTACCA
* * * *
28940350 TTTTACCCTCAATTTATAGAACTATCA
1 TTTTACCCTCGATTTACAGAATTACCA
*
28940377 TTTTACCCTCGATTTACAAAATTACCA
1 TTTTACCCTCGATTTACAGAATTACCA
* * *
28940404 TTTTACCCTCGATTTACAAAATTATCG
1 TTTTACCCTCGATTTACAGAATTACCA
*
28940431 TTTTACCCTCGATTTACAAAATTAC
1 TTTTACCCTCGATTTACAGAATTAC
28940456 TAAAATACCC
Statistics
Matches: 348, Mismatches: 26, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
26 22 0.06
27 326 0.94
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (27 bp):
TTTTACCCTCGATTTACAGAATTACCA
Found at i:28940464 original size:27 final size:27
Alignment explanation
Indices: 28940084--28940668 Score: 281
Period size: 27 Copynumber: 21.7 Consensus size: 27
28940074 ATTACCGTTT
****
28940084 TACCCTCGATTTATAAAATTACCGTTT
1 TACCCTCGATTTATAAAATTACCAAAA
* ****
28940111 TACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTATAAAATTACCAAAA
* ***
28940138 TACCCTCGATTTGTAAAATTACCATTT
1 TACCCTCGATTTATAAAATTACCAAAA
* * ***
28940165 TACCCTCGA-TTACAGAATTACCATTT
1 TACCCTCGATTTATAAAATTACCAAAA
* * * ***
28940191 TACCCTCAATTTACAGAATTACCATTT
1 TACCCTCGATTTATAAAATTACCAAAA
* * **
28940218 TACCCTCGATTTACAGAATTA-CAATTT
1 TACCCTCGATTTATAAAATTACCAA-AA
* **
28940245 TACCCTCGATTTATAGAATTA-CAATTT
1 TACCCTCGATTTATAAAATTACCAA-AA
* * ***
28940272 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTATAAAATTACCAAAA
* ***
28940299 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAAAATTACCAAAA
* ***
28940326 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAAAATTACCAAAA
* * * * ***
28940353 TACCCTCAATTTATAGAACTATCATTT
1 TACCCTCGATTTATAAAATTACCAAAA
* ***
28940380 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTATAAAATTACCAAAA
* * ****
28940407 TACCCTCGATTTACAAAATTATCGTTT
1 TACCCTCGATTTATAAAATTACCAAAA
* *
28940434 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
*
28940461 TACCCT-TAGTTTCA-AAAATTACCAAAA
1 TACCCTCGA-TTT-ATAAAATTACCAAAA
*
28940488 TACCCTCGA-TCAGTAAAATTACCAAAA
1 TACCCTCGATTTA-TAAAATTACCAAAA
* * *
28940515 TACCCATTG-TTTGTAAAATTACTAAAA
1 TACCC-TCGATTTATAAAATTACCAAAA
* * *
28940542 TACCC-CTAGTTTGTAAAATTACTAAAA
1 TACCCTCGA-TTTATAAAATTACCAAAA
* *
28940569 TACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTATAAAATTACCAAAA
** *
28940596 TACCC-CTGGCTTGTAAAATTACCAAAA
1 TACCCTC-GATTTATAAAATTACCAAAA
* * * *
28940623 TACCCTTGATTTGTGAAATTATCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* *
28940650 TACTCTCGATTTGTAAAAT
1 TACCCTCGATTTATAAAAT
28940669 ATCGAAATAC
Statistics
Matches: 494, Mismatches: 50, Indels: 28
0.86 0.09 0.05
Matches are distributed among these distances:
25 1 0.00
26 26 0.05
27 460 0.93
28 7 0.01
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.36
Consensus pattern (27 bp):
TACCCTCGATTTATAAAATTACCAAAA
Found at i:28940703 original size:27 final size:27
Alignment explanation
Indices: 28940671--28940888 Score: 292
Period size: 27 Copynumber: 8.0 Consensus size: 27
28940661 TGTAAAATAT
28940671 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
28940698 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
28940725 CGAAATACCCCTATAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
28940752 CGAAATACCCATGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* *
28940779 TGAAATACCCCTGTAGGGTAGAATTAT
1 CGAAATACCCCTGTAGGGTAGAATTAC
* * * *
28940806 TGAAATACGCTTGTAGGGTAGAAATAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* *
28940833 CGAAATACCCTTATAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* * * * *
28940860 TGAGATACCCTTGTGGGGTAAAAATTAC
1 CGAAATACCCCTGTAGGGT-AGAATTAC
28940888 C
1 C
28940889 ATTTTGCCCC
Statistics
Matches: 170, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 163 0.96
28 7 0.04
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (27 bp):
CGAAATACCCCTGTAGGGTAGAATTAC
Found at i:28941136 original size:25 final size:25
Alignment explanation
Indices: 28941092--28941186 Score: 145
Period size: 25 Copynumber: 3.8 Consensus size: 25
28941082 AGGAAGTGCT
*
28941092 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* *
28941117 AAAAGGGCTTTGTCCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* *
28941142 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCG
28941167 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
28941187 ATTAAAAGAG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:28941199 original size:24 final size:25
Alignment explanation
Indices: 28941092--28941199 Score: 100
Period size: 25 Copynumber: 4.4 Consensus size: 25
28941082 AGGAAGTGCT
* *
28941092 AAAAG-GGCTATGCCCCAGTTTACC
1 AAAAGAGGCTTTGCCCCAGTTTATC
* * *
28941116 GAAAAG-GGCTTTGTCCTAGTTTACC
1 -AAAAGAGGCTTTGCCCCAGTTTATC
28941141 GAAAAG-GGCTTTGCCCCAGTTTATC
1 -AAAAGAGGCTTTGCCCCAGTTTATC
*
28941166 AAAA-AGGGCTTTGCCCCAG-TTATT
1 AAAAGA-GGCTTTGCCCCAGTTTATC
28941190 AAAAGAGGCT
1 AAAAGAGGCT
28941200 AGGCCACCAA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.22
25 57 0.78
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGAGGCTTTGCCCCAGTTTATC
Found at i:28946227 original size:6 final size:6
Alignment explanation
Indices: 28946209--28946302 Score: 59
Period size: 6 Copynumber: 15.3 Consensus size: 6
28946199 AAGAAACATT
* * *
28946209 ATCAGA A-CTAGA ATCAGA ATCAGA ATTAGA ATCAG- GTGACAGA TTCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * * *
28946258 ATCAGA ATCAGT ATCAGGTA A-CAGA ACCAAA ATCAGA ATGAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA AT
28946303 GCAATCCCAG
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
5 4 0.06
6 56 0.81
7 7 0.10
8 2 0.03
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
ATCAGA
Done.