Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 74 of 82
Found at i:27338654 original size:18 final size:18
Alignment explanation
Indices: 27338594--27338655 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
27338584 CCATATGAAC
27338594 AAATAGAATAGAAATG-AAA
1 AAATA-AATAGAAA-GAAAA
* *
27338613 AAATAAATA-ATAATAATA
1 AAATAAATAGA-AAGAAAA
*
27338631 ATATAAATAGAAAGAAAA
1 AAATAAATAGAAAGAAAA
27338649 AAATAAA
1 AAATAAA
27338656 AACAAAACTT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
17 1 0.03
18 27 0.79
19 6 0.18
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (18 bp):
AAATAAATAGAAAGAAAA
Found at i:27341632 original size:27 final size:27
Alignment explanation
Indices: 27341594--27341665 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
27341584 GGGCGTTTCT
*
27341594 ACGCTTGAAACACCCCTAGGCACTTTC
1 ACGCTTGAAACACCCCTAGGCACTTCC
* *
27341621 ATGCTTGGAACACCCCTAGGCACTTCC
1 ACGCTTGAAACACCCCTAGGCACTTCC
*
27341648 ACGCTTAAAACACCCCTA
1 ACGCTTGAAACACCCCTA
27341666 AGTGCTTCTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.28, C:0.38, G:0.14, T:0.21
Consensus pattern (27 bp):
ACGCTTGAAACACCCCTAGGCACTTCC
Found at i:27347548 original size:23 final size:23
Alignment explanation
Indices: 27347509--27347557 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
27347499 GTATATAATC
*
27347509 TTTTTTAATATAAA-TTTAAATAT
1 TTTTTTAATAAAAATTTTAAA-AT
27347532 TTTTTTAA-AAAATATTTTAAAAT
1 TTTTTTAATAAAA-ATTTTAAAAT
27347555 TTT
1 TTT
27347558 AATATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 3 0.13
23 14 0.61
24 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTTTAATAAAAATTTTAAAAT
Found at i:27353448 original size:2 final size:2
Alignment explanation
Indices: 27353441--27353471 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27353431 GGGAGTTTCA
27353441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27353472 ATTTAATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27364772 original size:2 final size:2
Alignment explanation
Indices: 27364765--27364795 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
27364755 ATTTTGCCTT
*
27364765 TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
27364796 TGATCTCACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.03, T:0.48
Consensus pattern (2 bp):
TC
Found at i:27370089 original size:36 final size:36
Alignment explanation
Indices: 27370012--27370094 Score: 116
Period size: 36 Copynumber: 2.3 Consensus size: 36
27370002 TACTCCCCTC
*
27370012 CTTCCATCTCCTCATCCTCCCGCCAATCTTTCCATG
1 CTTCCATCTCCTCATCCTCCCACCAATCTTTCCATG
*
27370048 CTTCCACCTCCTCATCCTCCCACCAAT-TTTCCTATAG
1 CTTCCATCTCCTCATCCTCCCACCAATCTTTCC-AT-G
27370085 -TTCCATCTCC
1 CTTCCATCTCC
27370095 CAATTCTTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 5 0.12
36 36 0.86
37 1 0.02
ACGTcount: A:0.16, C:0.47, G:0.04, T:0.34
Consensus pattern (36 bp):
CTTCCATCTCCTCATCCTCCCACCAATCTTTCCATG
Found at i:27375020 original size:21 final size:21
Alignment explanation
Indices: 27374996--27375036 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
27374986 GGTCAAATTT
*
27374996 TGGTGCTGGCTCAGGAGGAGG
1 TGGTGCTGGATCAGGAGGAGG
*
27375017 TGGTGCTGGATCTGGAGGAG
1 TGGTGCTGGATCAGGAGGAG
27375037 AAAATAATGA
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:0.15, C:0.12, G:0.51, T:0.22
Consensus pattern (21 bp):
TGGTGCTGGATCAGGAGGAGG
Found at i:27376455 original size:35 final size:35
Alignment explanation
Indices: 27376400--27376476 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
27376390 TATTATATAA
*
27376400 AGAACAACCAGAACAAGTGAAGTGTTACTTCACGC
1 AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
* *
27376435 AGAATAACTAGAACAAGTGAAGCGTTACTTCACGC
1 AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
*
27376470 CGAACAA
1 AGAACAA
27376477 GTGAAGCGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (35 bp):
AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
Found at i:27376481 original size:26 final size:26
Alignment explanation
Indices: 27376444--27376518 Score: 132
Period size: 26 Copynumber: 2.9 Consensus size: 26
27376434 CAGAATAACT
*
27376444 AGAACAAGTGAAGCGTTACTTCACGC
1 AGAACAAGTGAAGCGCTACTTCACGC
*
27376470 CGAACAAGTGAAGCGCTACTTCACGC
1 AGAACAAGTGAAGCGCTACTTCACGC
27376496 AGAACAAGTGAAGCGCTACTTCA
1 AGAACAAGTGAAGCGCTACTTCA
27376519 AGTATTACTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (26 bp):
AGAACAAGTGAAGCGCTACTTCACGC
Found at i:27383436 original size:15 final size:15
Alignment explanation
Indices: 27383418--27383461 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
27383408 GTGTTACTAC
27383418 CTAAAGTATTACTGG
1 CTAAAGTATTACTGG
* * *
27383433 CTAAGGTGTTACTGT
1 CTAAAGTATTACTGG
*
27383448 CTAAAGTAGTACTG
1 CTAAAGTATTACTG
27383462 CCCAAGGCAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (15 bp):
CTAAAGTATTACTGG
Found at i:27383475 original size:30 final size:30
Alignment explanation
Indices: 27383418--27383485 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
27383408 GTGTTACTAC
* * * **
27383418 CTAAAGTATTACTGGCTAAGGTGTTACTGT
1 CTAAAGTAGTACTGCCCAAGGCATTACTGT
27383448 CTAAAGTAGTACTGCCCAAGGCATTACTGT
1 CTAAAGTAGTACTGCCCAAGGCATTACTGT
27383478 -TCAAAGTA
1 CT-AAAGTA
27383486 ATACAATACA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (30 bp):
CTAAAGTAGTACTGCCCAAGGCATTACTGT
Found at i:27383703 original size:35 final size:35
Alignment explanation
Indices: 27383648--27383724 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
27383638 TATTATATAG
*
27383648 AGAACAACCAGAACAAGTGAAGTGTTACTTCACGC
1 AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
* *
27383683 AGAATAACTAGAACAAGTGAAGCGTTACTTCACGC
1 AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
27383718 AGAACAA
1 AGAACAA
27383725 GTGAAGCGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (35 bp):
AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
Found at i:27383728 original size:26 final size:26
Alignment explanation
Indices: 27383692--27383766 Score: 141
Period size: 26 Copynumber: 2.9 Consensus size: 26
27383682 CAGAATAACT
*
27383692 AGAACAAGTGAAGCGTTACTTCACGC
1 AGAACAAGTGAAGCGCTACTTCACGC
27383718 AGAACAAGTGAAGCGCTACTTCACGC
1 AGAACAAGTGAAGCGCTACTTCACGC
27383744 AGAACAAGTGAAGCGCTACTTCA
1 AGAACAAGTGAAGCGCTACTTCA
27383767 AGTATTACTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (26 bp):
AGAACAAGTGAAGCGCTACTTCACGC
Found at i:27384078 original size:29 final size:28
Alignment explanation
Indices: 27384046--27384115 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
27384036 CTCGTATACT
*
27384046 TATTCATGTACAGCTTATTCTCTTGTACC
1 TATTC-TGTACAGCTTATTCTCTCGTACC
* *
27384075 TATTCTCATACAGCTTCTTCTCTCGTACC
1 TATTCT-GTACAGCTTATTCTCTCGTACC
27384104 TATTCTTGTACA
1 TATTC-TGTACA
27384116 CCTCTTTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 33 0.94
30 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.09, T:0.44
Consensus pattern (28 bp):
TATTCTGTACAGCTTATTCTCTCGTACC
Found at i:27384353 original size:13 final size:13
Alignment explanation
Indices: 27384335--27384359 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27384325 ACTTGAGAGC
27384335 TTCTCTCTCTAAA
1 TTCTCTCTCTAAA
27384348 TTCTCTCTCTAA
1 TTCTCTCTCTAA
27384360 TTATCTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCTCTCTCTAAA
Found at i:27392010 original size:2 final size:2
Alignment explanation
Indices: 27392003--27392032 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27391993 AAGAAAATAA
27392003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27392033 TTAAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27392081 original size:2 final size:2
Alignment explanation
Indices: 27392074--27392103 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27392064 GTCNAAATAA
27392074 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27392104 TTAAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27392082 original size:71 final size:70
Alignment explanation
Indices: 27391997--27392138 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 70
27391987 TTGATTAAGA
27391997 AAATAAATATATATATATATATATATATATATATATTTAAAATAAAATGGCCTTGAACTTGATCA
1 AAATAAATATATATATATATATATATATATATATATTTAAAATAAAATGGCCTTGAACTTGATCA
27392062 TTGTC
66 TTGTC
27392067 NAAATAAATATATATATATATATATATATATATATATTTAAAATAAAATGGCCTTGAACTTGATC
1 -AAATAAATATATATATATATATATATATATATATATTTAAAATAAAATGGCCTTGAACTTGATC
27392132 ATTGTC
65 ATTGTC
27392138 A
1 A
27392139 TTCCACCACT
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 1 0.01
71 70 0.99
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (70 bp):
AAATAAATATATATATATATATATATATATATATATTTAAAATAAAATGGCCTTGAACTTGATCA
TTGTC
Found at i:27397994 original size:18 final size:18
Alignment explanation
Indices: 27397970--27398012 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
27397960 ACTTCATTGA
27397970 TGATGATTACGATGA-CT
1 TGATGATTACGATGATCT
*
27397987 TGGATGATTATGATGATCT
1 T-GATGATTACGATGATCT
27398006 TGATGAT
1 TGATGAT
27398013 GATGAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 19 0.83
19 3 0.13
ACGTcount: A:0.28, C:0.07, G:0.26, T:0.40
Consensus pattern (18 bp):
TGATGATTACGATGATCT
Found at i:27398017 original size:18 final size:17
Alignment explanation
Indices: 27397970--27398017 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
27397960 ACTTCATTGA
*
27397970 TGATGATTACGATGACT
1 TGATGATTATGATGACT
27397987 TGGATGATTATGATGATCT
1 T-GATGATTATGATGA-CT
*
27398006 TGATGATGATGA
1 TGATGATTATGA
27398018 ATATGATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 1 0.04
18 23 0.85
19 3 0.11
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (17 bp):
TGATGATTATGATGACT
Found at i:27398303 original size:3 final size:3
Alignment explanation
Indices: 27398295--27398332 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
27398285 AGGTAAAAAA
* *
27398295 GGT GGT GGT GGT GGT GGT GGT GGC GGT GGC GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
27398333 AGGAAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.05, G:0.68, T:0.26
Consensus pattern (3 bp):
GGT
Found at i:27398687 original size:6 final size:6
Alignment explanation
Indices: 27398675--27398713 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
27398665 CTGCCCTGAA
*
27398675 CGGTGG TGGTGG TC-GTGG CGGTGG CGGTGG CGGTGG CGG
1 CGGTGG CGGTGG -CGGTGG CGGTGG CGGTGG CGGTGG CGG
27398714 GTACTTCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 1 0.03
6 28 0.97
ACGTcount: A:0.00, C:0.15, G:0.64, T:0.21
Consensus pattern (6 bp):
CGGTGG
Found at i:27403640 original size:65 final size:65
Alignment explanation
Indices: 27403516--27403640 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 65
27403506 TGCTTTGTCG
* * * *
27403516 TTGAAAGTGAACCATACAATTGATTGAACGTGTTTATTTTTAGACTAAATCGGCAATAAACAAGC
1 TTGAAAGTGAACCATACAATTGAATAAACGTGTTTACTTTTAGACTAAATCGACAATAAACAAGC
* * *
27403581 TTGATAGTGAACCATATAATTGAATAAACGTGTTTACTTTTAGACTAAATCGACTATAAA
1 TTGAAAGTGAACCATACAATTGAATAAACGTGTTTACTTTTAGACTAAATCGACAATAAA
27403641 TCTCAATTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (65 bp):
TTGAAAGTGAACCATACAATTGAATAAACGTGTTTACTTTTAGACTAAATCGACAATAAACAAGC
Found at i:27411071 original size:2 final size:2
Alignment explanation
Indices: 27411066--27411095 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27411056 TTTTATTTTA
27411066 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27411096 TCAAACAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27426357 original size:18 final size:18
Alignment explanation
Indices: 27426334--27426369 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
27426324 CTTCAGTAAT
*
27426334 TGAGTTTTCAGAATCAAA
1 TGAGTTTTCAGAACCAAA
27426352 TGAGTTTTCAGAACCAAA
1 TGAGTTTTCAGAACCAAA
27426370 ATCACTCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAGTTTTCAGAACCAAA
Found at i:27461616 original size:18 final size:18
Alignment explanation
Indices: 27461593--27461633 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
27461583 AACACGTTTA
27461593 TTTAATCATGTTATCGTG
1 TTTAATCATGTTATCGTG
* *
27461611 TTTAATCGTGTTATCTTG
1 TTTAATCATGTTATCGTG
27461629 TTTAA
1 TTTAA
27461634 ACGTATATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.10, G:0.15, T:0.54
Consensus pattern (18 bp):
TTTAATCATGTTATCGTG
Found at i:27461831 original size:17 final size:16
Alignment explanation
Indices: 27461809--27461857 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 16
27461799 TTATTTGATG
27461809 TTATTATTATTTTTGTT
1 TTATTATTATTTTT-TT
*
27461826 TTATTATAATTTTTTT
1 TTATTATTATTTTTTT
27461842 TATAATTATATATTTT
1 T-T-ATTAT-TATTTT
27461858 AAATTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 3 0.11
17 14 0.52
18 5 0.19
19 5 0.19
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTATTATTTTTTT
Found at i:27461903 original size:20 final size:19
Alignment explanation
Indices: 27461816--27461905 Score: 62
Period size: 20 Copynumber: 4.7 Consensus size: 19
27461806 ATGTTATTAT
* *
27461816 TATTTTTGTTTTATTATAA
1 TATTTTTATTTAATTATAA
27461835 T-TTTTT-TTATAATTAT-A
1 TATTTTTATT-TAATTATAA
* *
27461852 TATTTTAAATTTAAATAATAA
1 TATTTT-TATTT-AATTATAA
* *
27461873 -AATTATATTTAATTATAAA
1 TATTTTTATTTAATTAT-AA
27461892 TATTTTTATTTAAT
1 TATTTTTATTTAAT
27461906 CGTGTTAAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
17 4 0.07
18 20 0.37
19 8 0.15
20 21 0.39
21 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (19 bp):
TATTTTTATTTAATTATAA
Found at i:27462629 original size:4 final size:4
Alignment explanation
Indices: 27462620--27462645 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
27462610 AATATTTAAA
27462620 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
27462646 TTCATCATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:27472708 original size:4 final size:4
Alignment explanation
Indices: 27472701--27472726 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
27472691 AACTGCTTGC
27472701 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
27472727 AAGTTGCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:27476096 original size:18 final size:17
Alignment explanation
Indices: 27476062--27476104 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
27476052 TTCTTTTGGC
27476062 AAAAAAAAAGAAAAAAG
1 AAAAAAAAAGAAAAAAG
* *
27476079 AAAAAAGAAGATAGAAAG
1 AAAAAAAAAGA-AAAAAG
27476097 AAAAAAAA
1 AAAAAAAA
27476105 TGCAAGTGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAAG
Found at i:27481399 original size:69 final size:69
Alignment explanation
Indices: 27481288--27481495 Score: 326
Period size: 69 Copynumber: 3.0 Consensus size: 69
27481278 TTTTTGTGGC
* *
27481288 TAACCAAGTATGAAAGACTTTCAGGATGAGATCTCACCGTGATTATACGTCCATTTACATTCCGT
1 TAACCAAGTAGGCAAGACTTTCAGGATGAGATCTCACCGTGATTATACGTCCATTTACATTCCGT
27481353 TCTT
66 TCTT
27481357 TAACCAAGTAGGCAAGACTTTCAGGATGAGATCTCACCGTGATTATACGTCCATTTACATTCCGT
1 TAACCAAGTAGGCAAGACTTTCAGGATGAGATCTCACCGTGATTATACGTCCATTTACATTCCGT
27481422 TCTT
66 TCTT
* **** * * *
27481426 TAACCAAGTAGGCAAGACTTTCAGGATAAGATCTCACCCCCTTTATACATCCATTCACATTCCAT
1 TAACCAAGTAGGCAAGACTTTCAGGATGAGATCTCACCGTGATTATACGTCCATTTACATTCCGT
27481491 TCTT
66 TCTT
27481495 T
1 T
27481496 TTGTGGCTAA
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 129 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (69 bp):
TAACCAAGTAGGCAAGACTTTCAGGATGAGATCTCACCGTGATTATACGTCCATTTACATTCCGT
TCTT
Found at i:27498706 original size:16 final size:16
Alignment explanation
Indices: 27498687--27498724 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
27498677 TTTATATTAC
*
27498687 ATAAATTTTATTTTTT
1 ATAAATTTTAATTTTT
27498703 AT-AATTTTAATTTTT
1 ATAAATTTTAATTTTT
*
27498718 AAAAATT
1 ATAAATT
27498725 AATAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATAAATTTTAATTTTT
Found at i:27506763 original size:25 final size:24
Alignment explanation
Indices: 27506729--27506779 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
27506719 GTAGATTTTG
27506729 TTAAAAATTTATATATTAATAATAT
1 TTAAAAATTTATATATT-ATAATAT
* * *
27506754 TTAAATATTTATTTATTATATTAT
1 TTAAAAATTTATATATTATAATAT
27506778 TT
1 TT
27506780 TTTAGAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTAAAAATTTATATATTATAATAT
Found at i:27506912 original size:25 final size:24
Alignment explanation
Indices: 27506884--27506945 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 24
27506874 AATATATATT
27506884 AATAATATTT-AAATATTATTTCAAA
1 AATAATATTTAAAATATTA--TCAAA
27506909 AATAATAATATTAAAATATTATCAAA
1 AATAAT-AT-TTAAAATATTATCAAA
27506935 AAGTAA-ATTTA
1 AA-TAATATTTA
27506946 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
24 3 0.09
25 8 0.24
26 9 0.27
27 5 0.15
28 8 0.24
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (24 bp):
AATAATATTTAAAATATTATCAAA
Found at i:27507978 original size:12 final size:12
Alignment explanation
Indices: 27507953--27507987 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
27507943 TAAAATATTG
27507953 TTTTTCTTTCTCA
1 TTTTT-TTTCTCA
*
27507966 TTTTTTTTTTCA
1 TTTTTTTTCTCA
27507978 TTTTTTTTCT
1 TTTTTTTTCT
27507988 TTCTTTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTTCTCA
Found at i:27516181 original size:22 final size:20
Alignment explanation
Indices: 27516149--27516189 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
27516139 TACTTTACCT
*
27516149 TTTTCTCTCTCTTTCTTTTC
1 TTTTCTCTCTCTATCTTTTC
27516169 TTTTCTCCTTCTCTATCTTTT
1 TTTTCT-C-TCTCTATCTTTT
27516190 TTCCCTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTCTCTCTCTATCTTTTC
Found at i:27517515 original size:38 final size:38
Alignment explanation
Indices: 27517464--27517545 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
27517454 ACAAAGCAGG
27517464 AAATGGAAGACGATTTGGAACTTACCAAATCCTCATTA
1 AAATGGAAGACGATTTGGAACTTACCAAATCCTCATTA
*
27517502 AAATGGAAGACGATTTGGAACTTACCAAATCCTCATTG
1 AAATGGAAGACGATTTGGAACTTACCAAATCCTCATTA
27517540 AAATGG
1 AAATGG
27517546 TACAAAGCAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (38 bp):
AAATGGAAGACGATTTGGAACTTACCAAATCCTCATTA
Found at i:27520144 original size:2 final size:2
Alignment explanation
Indices: 27520137--27520163 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27520127 TGTTACTATC
27520137 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
27520164 CTAAAATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27525378 original size:2 final size:2
Alignment explanation
Indices: 27525371--27525420 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
27525361 GGTAAGGATC
27525371 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
27525413 CT CT CT CT
1 CT CT CT CT
27525421 TTGTTTGCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:27529983 original size:2 final size:2
Alignment explanation
Indices: 27529976--27530004 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27529966 GCTATATGTT
27529976 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
27530005 ATATACGGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:27533093 original size:31 final size:29
Alignment explanation
Indices: 27533040--27533103 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
27533030 ATCTGTAAAC
*
27533040 TTAATTTTTAATTCTAAAAATTAAAAAATAT
1 TTAATTTTTAATTATAAAAATT--AAAATAT
* *
27533071 TTAATTTTTAATTATTACAATTAAAATAT
1 TTAATTTTTAATTATAAAAATTAAAATAT
27533100 TTAA
1 TTAA
27533104 CTCATAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 11 0.37
31 19 0.63
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (29 bp):
TTAATTTTTAATTATAAAAATTAAAATAT
Found at i:27561755 original size:2 final size:2
Alignment explanation
Indices: 27561750--27561779 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27561740 TCTCTCTTTC
27561750 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27561780 GATTAGTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27563503 original size:2 final size:2
Alignment explanation
Indices: 27563496--27563526 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27563486 TTCTTTGGAC
27563496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27563527 GATGGATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27564078 original size:2 final size:2
Alignment explanation
Indices: 27564066--27564098 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
27564056 AATGACCTAA
*
27564066 AT AT AT GT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27564099 TTGTTGGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:27564088 original size:17 final size:17
Alignment explanation
Indices: 27564066--27564099 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27564056 AATGACCTAA
*
27564066 ATATATGTATATATATT
1 ATATATATATATATATT
27564083 ATATATATATATATATT
1 ATATATATATATATATT
27564100 TGTTGGAGAG
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:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATATATATATATATATT
Found at i:27564091 original size:15 final size:15
Alignment explanation
Indices: 27564067--27564096 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27564057 ATGACCTAAA
*
27564067 TATATGTATATATAT
1 TATATATATATATAT
27564082 TATATATATATATAT
1 TATATATATATATAT
27564097 ATTTGTTGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:27567671 original size:6 final size:6
Alignment explanation
Indices: 27567660--27567704 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
27567650 ATCCACTGTA
* * * *
27567660 TTCCTC TTCCTC TGCCTC TTCCTC TTCTTC TTCTTC TTCTTC TTC
1 TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTC
27567705 TTCGGCTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.00, C:0.42, G:0.02, T:0.56
Consensus pattern (6 bp):
TTCCTC
Found at i:27567690 original size:3 final size:3
Alignment explanation
Indices: 27567676--27567707 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
27567666 TTCCTCTGCC
*
27567676 TCT TCC TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
27567708 GGCTTCACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:27571147 original size:16 final size:16
Alignment explanation
Indices: 27571126--27571156 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
27571116 TTTATTTAAT
27571126 ACATATATATTTATTA
1 ACATATATATTTATTA
27571142 ACATATATATTTATT
1 ACATATATATTTATT
27571157 CATGTACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
ACATATATATTTATTA
Found at i:27571167 original size:20 final size:17
Alignment explanation
Indices: 27571110--27571156 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
27571100 ACAATAGATT
*
27571110 TATATTTTTATTTAATACA
1 TATATATTTA-TT-ATACA
27571129 TATATATTTATTA-ACA
1 TATATATTTATTATACA
27571145 TATATATTTATT
1 TATATATTTATT
27571157 CATGTACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 15 0.56
17 1 0.04
18 2 0.07
19 9 0.33
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATATTTATTATACA
Found at i:27571557 original size:13 final size:15
Alignment explanation
Indices: 27571529--27571575 Score: 62
Period size: 14 Copynumber: 3.2 Consensus size: 15
27571519 AAAAAATAAA
27571529 AAAATATTTAATTTT
1 AAAATATTTAATTTT
*
27571544 AAAAT-TTTAATTTA
1 AAAATATTTAATTTT
27571558 AAAATA-TTAATATTT
1 AAAATATTTAAT-TTT
27571573 AAA
1 AAA
27571576 TTATATAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATATTTAATTTT
Found at i:27589358 original size:68 final size:68
Alignment explanation
Indices: 27589272--27589405 Score: 250
Period size: 68 Copynumber: 2.0 Consensus size: 68
27589262 GAAATATATA
* *
27589272 ATAAAACTGTAGTTCAACCTCATGGAATGAGGTGACACTGAGAAATTTATGGTTGCTATTTAGTA
1 ATAAAAATGTAGTTCAACCTCATGGAATGAGGTGACACTGAGAAATTTATGGTTGCCATTTAGTA
27589337 TCT
66 TCT
27589340 ATAAAAATGTAGTTCAACCTCATGGAATGAGGTGACACTGAGAAATTTATGGTTGCCATTTAGTA
1 ATAAAAATGTAGTTCAACCTCATGGAATGAGGTGACACTGAGAAATTTATGGTTGCCATTTAGTA
27589405 T
66 T
27589406 TTACCTATCA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.33
Consensus pattern (68 bp):
ATAAAAATGTAGTTCAACCTCATGGAATGAGGTGACACTGAGAAATTTATGGTTGCCATTTAGTA
TCT
Found at i:27592225 original size:2 final size:2
Alignment explanation
Indices: 27592218--27592249 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
27592208 TCCTCCTTCC
27592218 CT CT CT CT CT CT CT CT -T 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 C
27592250 ACGCATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:27592239 original size:13 final size:13
Alignment explanation
Indices: 27592221--27592246 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27592211 TCCTTCCCTC
27592221 TCTCTCTCTCTCT
1 TCTCTCTCTCTCT
27592234 TCTCTCTCTCTCT
1 TCTCTCTCTCTCT
27592247 CTCACGCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (13 bp):
TCTCTCTCTCTCT
Found at i:27592239 original size:15 final size:15
Alignment explanation
Indices: 27592219--27592248 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27592209 CCTCCTTCCC
27592219 TCTCTCTCTCTCTCT
1 TCTCTCTCTCTCTCT
27592234 TCTCTCTCTCTCTCT
1 TCTCTCTCTCTCTCT
27592249 CACGCATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (15 bp):
TCTCTCTCTCTCTCT
Found at i:27592240 original size:19 final size:19
Alignment explanation
Indices: 27592213--27592249 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
27592203 CATCTTCCTC
27592213 CTTCCCTCTCTCTCTCTCT
1 CTTCCCTCTCTCTCTCTCT
*
27592232 CTTCTCTCTCTCTCTCTC
1 CTTCCCTCTCTCTCTCTC
27592250 ACGCATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (19 bp):
CTTCCCTCTCTCTCTCTCT
Found at i:27599034 original size:40 final size:40
Alignment explanation
Indices: 27598928--27599048 Score: 143
Period size: 44 Copynumber: 2.9 Consensus size: 40
27598918 TGCAAGTCAA
* *
27598928 ATACATACATGTGTATGTATGTATCTTTTTACATACATAC
1 ATACATACATGTGTATGCATGTATCTTTTCACATACATAC
* * ** *
27598968 ATTCATCCGCGTGTATGTACGTATGTATCTTTTCACATACATGC
1 ATACATACATGTGTATG--C--ATGTATCTTTTCACATACATAC
27599012 ATACATACATGTGTATGCATGTATCTTTTCACATACA
1 ATACATACATGTGTATGCATGTATCTTTTCACATACA
27599049 AACGCACGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
40 32 0.48
42 1 0.02
44 33 0.50
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (40 bp):
ATACATACATGTGTATGCATGTATCTTTTCACATACATAC
Found at i:27599968 original size:14 final size:14
Alignment explanation
Indices: 27599949--27599975 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27599939 GAAACGAGAG
27599949 AGAGAGTGAGAGTA
1 AGAGAGTGAGAGTA
27599963 AGAGAGTGAGAGT
1 AGAGAGTGAGAGT
27599976 GTGAGTGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.15
Consensus pattern (14 bp):
AGAGAGTGAGAGTA
Found at i:27606284 original size:67 final size:67
Alignment explanation
Indices: 27606176--27606306 Score: 262
Period size: 67 Copynumber: 2.0 Consensus size: 67
27606166 AGAAGAAAGT
27606176 TAATGAGCTGATAAACTGATAACGTTCAATTAAAAGCCAATAGAATTTTCCAAGAACTAAAGGTG
1 TAATGAGCTGATAAACTGATAACGTTCAATTAAAAGCCAATAGAATTTTCCAAGAACTAAAGGTG
27606241 GA
66 GA
27606243 TAATGAGCTGATAAACTGATAACGTTCAATTAAAAGCCAATAGAATTTTCCAAGAACTAAAGGT
1 TAATGAGCTGATAAACTGATAACGTTCAATTAAAAGCCAATAGAATTTTCCAAGAACTAAAGGT
27606307 CGATTTTGGC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.26
Consensus pattern (67 bp):
TAATGAGCTGATAAACTGATAACGTTCAATTAAAAGCCAATAGAATTTTCCAAGAACTAAAGGTG
GA
Found at i:27606806 original size:10 final size:10
Alignment explanation
Indices: 27606793--27606822 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
27606783 TCTGTCTGCT
27606793 GCTGTTATGG
1 GCTGTTATGG
27606803 GCTGTTATGG
1 GCTGTTATGG
*
27606813 GCTGTCATGG
1 GCTGTTATGG
27606823 CGACCCACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.13, G:0.40, T:0.37
Consensus pattern (10 bp):
GCTGTTATGG
Found at i:27607649 original size:26 final size:24
Alignment explanation
Indices: 27607612--27607659 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
27607602 TTAAACCAAA
27607612 TTCTCTCTTTTG-TTTATTTTATCT
1 TTCTCTCTTTTGATTT-TTTTATCT
27607636 TTCTCCTCATTTTGATTTTTTTAT
1 TTCT-CTC-TTTTGATTTTTTTAT
27607660 TTAATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.19
25 3 0.14
26 11 0.52
27 3 0.14
ACGTcount: A:0.10, C:0.17, G:0.04, T:0.69
Consensus pattern (24 bp):
TTCTCTCTTTTGATTTTTTTATCT
Found at i:27612794 original size:45 final size:45
Alignment explanation
Indices: 27612730--27612820 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
27612720 TAATATTAGT
*
27612730 GAAGACGAAAGCAAGCTACATCATGAAAATGCCGCAGACAAGCAG
1 GAAGACGAAAGCAAGCTACATCATGAAAATACCGCAGACAAGCAG
* *
27612775 GAAGATGAAAGCATGCTACATCATGAAAATACCGCAGACAAGCAG
1 GAAGACGAAAGCAAGCTACATCATGAAAATACCGCAGACAAGCAG
27612820 G
1 G
27612821 TACACAACTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (45 bp):
GAAGACGAAAGCAAGCTACATCATGAAAATACCGCAGACAAGCAG
Found at i:27616724 original size:227 final size:227
Alignment explanation
Indices: 27616316--27616767 Score: 728
Period size: 227 Copynumber: 2.0 Consensus size: 227
27616306 CAGGAAACTT
27616316 AGTTGACAGTATCAAGTTTCACAGCAACATAAGAAAACAATCACTGGAGATTTTATAACTACACA
1 AGTTGACAGTATCAAGTTTCACAGCAACATAAGAAAACAATCACTGGAGATTTTATAACTACACA
*
27616381 TGTTGAAAATGTGAGTAGCAAAGCCCTTGCAATGTGTAACAGAAACAAAAAGATTGAGCTCAAGA
66 TGTTGAAAATGTGAATAGCAAAGCCCTTGCAATGTGTAACAGAAACAAAAAGATTGAGCTCAAGA
*
27616446 GAAACTCGTATCCATTCAATGCTGTGGAGCAAAGACTCTTAAAATATCAGGCAGAAAATATGATA
131 GAAACTCGTATCCATTCAATGCTGTGGAGCAAAGACTCTTAAAACATCAGGCAGAAAATATGATA
27616511 TGCCAACAGACATGC-CAAAATGTTGAGAGATG
196 TGCCAACAGACATGCTCAAAA-GTTGAGAGATG
* * ** * * *
27616543 AGTTGAGAGTCTCAAGTTTTGCAGTAACATAAGACAACAATTACTGGAGATTTTATAACTACACA
1 AGTTGACAGTATCAAGTTTCACAGCAACATAAGAAAACAATCACTGGAGATTTTATAACTACACA
* *
27616608 TGTTGAAAATGTGAATAGCAAAGCCCTTGTAATGTGTAAC-GAAAACAAAAAGATTGAGCTCCAG
66 TGTTGAAAATGTGAATAGCAAAGCCCTTGCAATGTGTAACAG-AAACAAAAAGATTGAGCTCAAG
* * * *
27616672 AGAAACTTGTATCCATTCAGTGCTGTGGAGCAAAGACTCTTAAGACATCAGGCAGAAAATTTGAT
130 AGAAACTCGTATCCATTCAATGCTGTGGAGCAAAGACTCTTAAAACATCAGGCAGAAAATATGAT
*
27616737 ATGCCAACAGACATGCTGAAAAGTTGAGAGA
195 ATGCCAACAGACATGCTCAAAAGTTGAGAGA
27616768 CGAGAAACAT
Statistics
Matches: 207, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
226 1 0.00
227 202 0.98
228 4 0.02
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (227 bp):
AGTTGACAGTATCAAGTTTCACAGCAACATAAGAAAACAATCACTGGAGATTTTATAACTACACA
TGTTGAAAATGTGAATAGCAAAGCCCTTGCAATGTGTAACAGAAACAAAAAGATTGAGCTCAAGA
GAAACTCGTATCCATTCAATGCTGTGGAGCAAAGACTCTTAAAACATCAGGCAGAAAATATGATA
TGCCAACAGACATGCTCAAAAGTTGAGAGATG
Found at i:27619718 original size:6 final size:6
Alignment explanation
Indices: 27619694--27619736 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
27619684 AAAGAGGTAA
27619694 CTTTTT CTTTCTT -TCTTTT CTTTTT CTTTTT CTTTTT CTTTTT
1 CTTTTT CTTT-TT CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT
27619737 TTCTCTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:27622328 original size:23 final size:23
Alignment explanation
Indices: 27622297--27622345 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
27622287 TTGAATTTAC
*
27622297 AATAAAAT-ATAAATACTTAATTT
1 AATAAAATAAAAAATA-TTAATTT
* *
27622320 AATATAATAAAAAATATTTATTT
1 AATAAAATAAAAAATATTAATTT
27622343 AAT
1 AAT
27622346 TTTTTAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AATAAAATAAAAAATATTAATTT
Found at i:27623730 original size:21 final size:20
Alignment explanation
Indices: 27623676--27623738 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 20
27623666 TTCCACCATG
27623676 TCCTCTCCTTTCCGCCTCTTCCTT
1 TCCTC-CCTTT-C-CCTC-TCCTT
* *
27623700 TCCTCTCTTTTCCTCTCCTT
1 TCCTCCCTTTCCCTCTCCTT
27623720 TCTCTCCCTTTCCCTCTCC
1 TC-CTCCCTTTCCCTCTCC
27623739 CAACAGCCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
23 4 0.12
24 5 0.15
ACGTcount: A:0.00, C:0.51, G:0.02, T:0.48
Consensus pattern (20 bp):
TCCTCCCTTTCCCTCTCCTT
Found at i:27634594 original size:2 final size:2
Alignment explanation
Indices: 27634589--27634627 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
27634579 AATGTGTGTG
27634589 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27634628 TTTAACTAAC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27635791 original size:43 final size:43
Alignment explanation
Indices: 27635743--27635830 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
27635733 TTTCCGTTTC
27635743 CTGTGTAACAAGCTTGTTGAGTTCTTACCAGGAGTAACTAGTT
1 CTGTGTAACAAGCTTGTTGAGTTCTTACCAGGAGTAACTAGTT
*
27635786 CTGTGTAACAAGCTTGTTGAGTTCTTACCAGGAGTATCTAGTT
1 CTGTGTAACAAGCTTGTTGAGTTCTTACCAGGAGTAACTAGTT
27635829 CT
1 CT
27635831 TTTGCTTTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (43 bp):
CTGTGTAACAAGCTTGTTGAGTTCTTACCAGGAGTAACTAGTT
Found at i:27640863 original size:33 final size:33
Alignment explanation
Indices: 27640801--27640863 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
27640791 GCATGCTAAC
*
27640801 ATATCATAATTGATGATAATGTGACATGTTGAT
1 ATATCATAATTGATGATAATGTAACATGTTGAT
* * *
27640834 ATATTATAATTGATGATGATGTAATATGTT
1 ATATCATAATTGATGATAATGTAACATGTT
27640864 AATTTCATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.43
Consensus pattern (33 bp):
ATATCATAATTGATGATAATGTAACATGTTGAT
Found at i:27644729 original size:17 final size:17
Alignment explanation
Indices: 27644689--27644722 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27644679 TTTTTTTGTA
*
27644689 AAAATAAATAAAAAGCAC
1 AAAA-AAATAAAAACCAC
27644707 AAAAAAATAAAAACCA
1 AAAAAAATAAAAACCA
27644723 AATAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.76, C:0.12, G:0.03, T:0.09
Consensus pattern (17 bp):
AAAAAAATAAAAACCAC
Found at i:27645376 original size:3 final size:3
Alignment explanation
Indices: 27645368--27645406 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
27645358 TGGAACTAAA
27645368 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
27645407 CTGAATCCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:27646354 original size:18 final size:18
Alignment explanation
Indices: 27646331--27646368 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
27646321 AGGCGGTGGC
27646331 GGAGGAGGTG-TCGGAGGA
1 GGAGGAGGTGCT-GGAGGA
27646349 GGAGGAGGTGCTGGAGGA
1 GGAGGAGGTGCTGGAGGA
27646367 GG
1 GG
27646369 CTAAGAGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.21, C:0.05, G:0.63, T:0.11
Consensus pattern (18 bp):
GGAGGAGGTGCTGGAGGA
Found at i:27646774 original size:2 final size:2
Alignment explanation
Indices: 27646767--27646795 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27646757 TGATATAGGA
27646767 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
27646796 AAAGCATGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27669738 original size:26 final size:27
Alignment explanation
Indices: 27669687--27669750 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
27669677 AAGATAAAAA
27669687 TTATATTTTATTATAATATATTATTAT
1 TTATATTTTATTATAATATATTATTAT
* *
27669714 TTAT-TTTTATT-TTATTTATTAATTAT
1 TTATATTTTATTATAATATATT-ATTAT
* *
27669740 TAATAATTTAT
1 TTATATTTTAT
27669751 AATTTATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 7 0.23
26 15 0.48
27 9 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TTATATTTTATTATAATATATTATTAT
Found at i:27669794 original size:28 final size:28
Alignment explanation
Indices: 27669730--27669796 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
27669720 TTATTTTATT
**
27669730 TATTAATTATTAATAATTTATAATTTATT
1 TATTAA-TATTAATAATTTATAATTTAAA
** *
27669759 TAAAAATATTAATAATTTATAGTTTAAA
1 TATTAATATTAATAATTTATAATTTAAA
27669787 TATTAATATT
1 TATTAATATT
27669797 TTTAAAAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (28 bp):
TATTAATATTAATAATTTATAATTTAAA
Found at i:27669833 original size:24 final size:24
Alignment explanation
Indices: 27669781--27669827 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
27669771 TAATTTATAG
**
27669781 TTTAAATATTAATATTTTTAAAAA
1 TTTAAATATTAATATGATTAAAAA
*
27669805 TTTAAATATTATTATGATTAAAA
1 TTTAAATATTAATATGATTAAAA
27669828 TATTAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTAAATATTAATATGATTAAAAA
Found at i:27679055 original size:31 final size:31
Alignment explanation
Indices: 27678992--27679068 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
27678982 TTTTATTTAA
*
27678992 TTTAGTTTTTCTAATTATAGTTGGTTTAGGAT
1 TTTA-TTTTTCTAATTATAGTTAGTTTAGGAT
* * * *
27679024 TTTATTTTTCTTATTCTATTTAGTTTGGGAT
1 TTTATTTTTCTAATTATAGTTAGTTTAGGAT
27679055 TTT-TTTTT-TAATTA
1 TTTATTTTTCTAATTA
27679069 GGATTTTAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 4 0.11
30 5 0.13
31 25 0.66
32 4 0.11
ACGTcount: A:0.19, C:0.04, G:0.13, T:0.64
Consensus pattern (31 bp):
TTTATTTTTCTAATTATAGTTAGTTTAGGAT
Found at i:27682668 original size:2 final size:2
Alignment explanation
Indices: 27682661--27682703 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
27682651 TCATTGAGTC
* *
27682661 TA TA TA TA TA CA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27682703 T
1 T
27682704 GTATGAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:27700571 original size:18 final size:18
Alignment explanation
Indices: 27700548--27700583 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
27700538 TTATTAAAAT
*
27700548 GGTGATTAATTAAGATTA
1 GGTGATTAACTAAGATTA
27700566 GGTGATTAACTAAGATTA
1 GGTGATTAACTAAGATTA
27700584 ACATATGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
GGTGATTAACTAAGATTA
Found at i:27703565 original size:214 final size:216
Alignment explanation
Indices: 27703159--27703619 Score: 603
Period size: 214 Copynumber: 2.1 Consensus size: 216
27703149 AATATACAAA
* *
27703159 TTATGTATAAATTAAATATATAAATATATATAATATATTATTTTATTATATATGTAAAATTAATG
1 TTATGTATAAATTAAATATAT-AATATATATAATATATTACTTTATTATATATATAAAATTAATG
* * *
27703224 ACACAACTTATATGTTATAATATTTTAATTTTTAAATCAAAGTTTGTGTAAATAATAATTAATTA
65 ACACAACTTATATGTTATAATATTTTAA---TT-AATCAAAATTTGTATAAATAACAATTAATTA
* * * *
27703289 TAAATAATATGTTATAAAAATTAAGGTAATAACTAATAAAATTATTAAGTGTAATGATATAAATA
126 TAAATAATATATTATAAAAACTAAAGTAATAACTAATAAAATTATTAAGTGTAATCATATAAATA
*
27703354 A-AGTCTATTATAGGTTACAATAATAC
191 AGA-TCTATTATAAGTTACAATAATAC
* * *
27703380 TTATGTATAAATTAAATATAT-GTATCTATAATATATTACTTTATTATGTATATATGAAATTAAT
1 TTATGTATAAATTAAATATATAATATATATAATATATTACTTTATTA--TATATATAAAATTAAT
* *
27703444 GACACAACTTGTATGTTATAATGTTTT-A-T-ATCAAAATTTGTATAAATAACAATTAATTATAA
64 GACACAACTTATATGTTATAATATTTTAATTAATCAAAATTTGTATAAATAACAATTAATTATAA
* *
27703506 ATAATATATTATAAAAACTAAAGTGATAATTAATAAAATTATTTAA-TGTAATCATATAAATAAG
129 ATAATATATTATAAAAACTAAAGTAATAACTAATAAAATTA-TTAAGTGTAATCATATAAATAAG
* * *
27703570 ATTTATTATAAGTTATACTAATAC
193 ATCTATTATAAGTTACAATAATAC
*
27703594 TTATGTATAAATTATATATAT-ATATA
1 TTATGTATAAATTAAATATATAATATA
27703620 AAATGTTTAT
Statistics
Matches: 213, Mismatches: 23, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
214 124 0.58
215 5 0.02
216 1 0.00
219 22 0.10
220 1 0.00
221 60 0.28
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (216 bp):
TTATGTATAAATTAAATATATAATATATATAATATATTACTTTATTATATATATAAAATTAATGA
CACAACTTATATGTTATAATATTTTAATTAATCAAAATTTGTATAAATAACAATTAATTATAAAT
AATATATTATAAAAACTAAAGTAATAACTAATAAAATTATTAAGTGTAATCATATAAATAAGATC
TATTATAAGTTACAATAATAC
Found at i:27703635 original size:29 final size:28
Alignment explanation
Indices: 27703603--27703657 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
27703593 CTTATGTATA
27703603 AATTATATATATATATAAAATGTTTATGC
1 AATTATATATATATATAAAAT-TTTATGC
* *
27703632 AATTATATATATTTATAACATTTTAT
1 AATTATATATATATATAAAATTTTAT
27703658 ATTACGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (28 bp):
AATTATATATATATATAAAATTTTATGC
Found at i:27706545 original size:31 final size:29
Alignment explanation
Indices: 27706471--27706558 Score: 76
Period size: 30 Copynumber: 3.0 Consensus size: 29
27706461 CTATTCAAAA
*
27706471 AAATT-AAAT-ATATTTTTATTTTT-TATT
1 AAATTCAAATAAT-TTTTTATTTTTATTTT
*
27706498 AAATTCAATTAATTTTTTGTATTTTTATTTT
1 AAATTCAAATAA-TTTTT-TATTTTTATTTT
*
27706529 AAA-TCAAATAAGTTTTTATATCTTTATTTT
1 AAATTCAAATAA-TTTTT-TATTTTTATTTT
27706559 GAGCAAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
27 5 0.10
28 3 0.06
29 5 0.10
30 31 0.62
31 6 0.12
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (29 bp):
AAATTCAAATAATTTTTTATTTTTATTTT
Found at i:27706556 original size:30 final size:31
Alignment explanation
Indices: 27706496--27706558 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
27706486 TTATTTTTTA
* * * *
27706496 TTAAATTCAATTAATTTTTTGTATTTTTATT
1 TTAAATTCAAATAAGTTTTTATATCTTTATT
27706527 TTAAA-TCAAATAAGTTTTTATATCTTTATT
1 TTAAATTCAAATAAGTTTTTATATCTTTATT
27706557 TT
1 TT
27706559 GAGCAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (31 bp):
TTAAATTCAAATAAGTTTTTATATCTTTATT
Found at i:27708638 original size:21 final size:24
Alignment explanation
Indices: 27708591--27708642 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
27708581 TAAAATATTT
*
27708591 AAAAATATTATTATATTTGAGACA
1 AAAAATATTATTATATATGAGACA
* *
27708615 AAAAATATTATTATA-ATAAGAAA
1 AAAAATATTATTATATATGAGACA
27708638 AAAAA
1 AAAAA
27708643 AATAAGAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (24 bp):
AAAAATATTATTATATATGAGACA
Found at i:27709849 original size:27 final size:27
Alignment explanation
Indices: 27709821--27709971 Score: 122
Period size: 27 Copynumber: 5.6 Consensus size: 27
27709811 ATATGACGTG
* * * * *
27709821 TAATAATTAAATTTTTAACATAATATG
1 TAATAACTAAATTTTCAATATAACATA
* ***
27709848 TAATAAATAAATTTTCAATACGGCATA
1 TAATAACTAAATTTTCAATATAACATA
* * *
27709875 TAACAACTAAATTTTTTAATATAACATG
1 TAATAACTAAA-TTTTCAATATAACATA
*
27709903 TAATAACTAAATTTTCAATATAATATA
1 TAATAACTAAATTTTCAATATAACATA
* * * *
27709930 TAATAGCTACATTTTCAACAAAACATA
1 TAATAACTAAATTTTCAATATAACATA
* *
27709957 TAATGATTAAATTTT
1 TAATAACTAAATTTT
27709972 AAAATATGAT
Statistics
Matches: 95, Mismatches: 28, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
27 74 0.78
28 21 0.22
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (27 bp):
TAATAACTAAATTTTCAATATAACATA
Found at i:27709931 original size:55 final size:54
Alignment explanation
Indices: 27709828--27709971 Score: 144
Period size: 55 Copynumber: 2.6 Consensus size: 54
27709818 GTGTAATAAT
* **
27709828 TAAATTTTTAACATAATATGTAATAAATAAATTTTCAATACGGCATATAACAAC
1 TAAATTTTTAACATAACATGTAATAAATAAATTTTCAATACAACATATAACAAC
* * * * * *
27709882 TAAATTTTTTAATATAACATGTAATAACTAAATTTTCAATATAATATATAATAGC
1 TAAA-TTTTTAACATAACATGTAATAAATAAATTTTCAATACAACATATAACAAC
* * * * * *
27709937 TACATTTTCAACAAAACATATAATGATTAAATTTT
1 TAAATTTTTAACATAACATGTAATAAATAAATTTT
27709972 AAAATATGAT
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
54 29 0.40
55 44 0.60
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (54 bp):
TAAATTTTTAACATAACATGTAATAAATAAATTTTCAATACAACATATAACAAC
Found at i:27709987 original size:82 final size:81
Alignment explanation
Indices: 27709800--27709987 Score: 187
Period size: 82 Copynumber: 2.3 Consensus size: 81
27709790 AATGTGGACG
* * * *
27709800 TTAAATCTTAAATATGACGTGTAATAATTAAATTTTTAACATAATATGTAATAAATAAATTTTCA
1 TTAAATTTTAAATATGACGTGTAATAACTAAATTTTCAACATAATATATAATAAATAAATTTTCA
* ***
27709865 ATACGGCATATAACAA
66 ACAAAACATATAACAA
* * * * * ** *
27709881 CTAAATTTTTTAATATAACATGTAATAACTAAATTTTCAATATAATATATAATAGCTACATTTTC
1 TTAAA-TTTTAAATATGACGTGTAATAACTAAATTTTCAACATAATATATAATAAATAAATTTTC
**
27709946 AACAAAACATATAATGA
65 AACAAAACATATAACAA
*
27709963 TTAAATTTTAAAATATGATGTGTAA
1 TTAAATTTT-AAATATGACGTGTAA
27709988 CATTATATTT
Statistics
Matches: 82, Mismatches: 23, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
81 8 0.10
82 74 0.90
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (81 bp):
TTAAATTTTAAATATGACGTGTAATAACTAAATTTTCAACATAATATATAATAAATAAATTTTCA
ACAAAACATATAACAA
Found at i:27712899 original size:18 final size:18
Alignment explanation
Indices: 27712872--27712907 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27712862 AACACAAAAA
27712872 GAGGAAAGAGAGAAAGAG
1 GAGGAAAGAGAGAAAGAG
* *
27712890 GAGGAGAGAGAGAGAGAG
1 GAGGAAAGAGAGAAAGAG
27712908 AGAAATAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (18 bp):
GAGGAAAGAGAGAAAGAG
Found at i:27713399 original size:12 final size:12
Alignment explanation
Indices: 27713390--27713465 Score: 55
Period size: 12 Copynumber: 6.3 Consensus size: 12
27713380 GATCGAGATC
*
27713390 GAGAAAGAGAAA
1 GAGAACGAGAAA
* *
27713402 GGGAACGAGAAC
1 GAGAACGAGAAA
* * *
27713414 GGGATCGAGATA
1 GAGAACGAGAAA
*
27713426 GAGAACGAGATA
1 GAGAACGAGAAA
* *
27713438 GGGAACGAGATA
1 GAGAACGAGAAA
27713450 GAGAGA-GAGAAA
1 GAGA-ACGAGAAA
27713462 GAGA
1 GAGA
27713466 TCGCTTGAGT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
12 51 0.98
13 1 0.02
ACGTcount: A:0.49, C:0.07, G:0.39, T:0.05
Consensus pattern (12 bp):
GAGAACGAGAAA
Found at i:27713419 original size:36 final size:36
Alignment explanation
Indices: 27713379--27713447 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
27713369 ATCGAAAGAA
*
27713379 GGATCGAGATCGAGAAAGAGAAAGGGAACGAGAACG
1 GGATCGAGATAGAGAAAGAGAAAGGGAACGAGAACG
* *
27713415 GGATCGAGATAGAGAACGAGATAGGGAACGAGA
1 GGATCGAGATAGAGAAAGAGAAAGGGAACGAGA
27713448 TAGAGAGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.39, T:0.07
Consensus pattern (36 bp):
GGATCGAGATAGAGAAAGAGAAAGGGAACGAGAACG
Found at i:27713459 original size:24 final size:24
Alignment explanation
Indices: 27713404--27713453 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
27713394 AAGAGAAAGG
*
27713404 GAACGAGA-ACGGGATCGAGATAGA
1 GAACGAGATA-GGGAACGAGATAGA
27713428 GAACGAGATAGGGAACGAGATAGA
1 GAACGAGATAGGGAACGAGATAGA
27713452 GA
1 GA
27713454 GAGAGAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.44, C:0.10, G:0.38, T:0.08
Consensus pattern (24 bp):
GAACGAGATAGGGAACGAGATAGA
Found at i:27713701 original size:18 final size:18
Alignment explanation
Indices: 27713665--27713711 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
27713655 GTCAAATCAT
* *
27713665 CATCATCAGCAACATCAG
1 CATCATCAACAACAGCAG
*
27713683 CATCATCAACAGCAGCAG
1 CATCATCAACAACAGCAG
*
27713701 CAGCATCAACA
1 CATCATCAACA
27713712 TCGGAAGAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.40, C:0.34, G:0.13, T:0.13
Consensus pattern (18 bp):
CATCATCAACAACAGCAG
Found at i:27714640 original size:7 final size:7
Alignment explanation
Indices: 27714628--27714659 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
27714618 ATTTGGATTG
27714628 TTTTTAT
1 TTTTTAT
27714635 TTTTTAT
1 TTTTTAT
27714642 TTTTTAT
1 TTTTTAT
27714649 TTTTTAT
1 TTTTTAT
27714656 TTTT
1 TTTT
27714660 CTGCAGCTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:27721348 original size:4 final size:4
Alignment explanation
Indices: 27721339--27721374 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
27721329 AAGAAGTAGC
27721339 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
27721375 GCGGAATTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:27723940 original size:2 final size:2
Alignment explanation
Indices: 27723933--27723971 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
27723923 AGATTCCGTG
27723933 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27723972 ACTTGCATGG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27725346 original size:220 final size:213
Alignment explanation
Indices: 27725032--27725470 Score: 637
Period size: 220 Copynumber: 2.0 Consensus size: 213
27725022 TGTAATCAAA
* *
27725032 TTTATAAAGATGTTGGAAAATATATAAAAATATTTTTAATAATATAATTTGAAAAACGAACACTT
1 TTTATAAAGATATTGGAAAATATATAAAAACATTTTTAATAATATAATTTGAAAAACGAACACTT
* * *
27725097 TTAAATCAAATTTATTGTAATGGATAATTATCCTATTTTATCAAAAAAATCATTGCTTATGGTCC
66 GTAAATCAAATTTATTGTAATGAATAATTATCCTATTTTATC--AAAAATCATTACTTATGGTCC
*
27725162 TCGATTAACAAGCGAATCTTACACGCTTGATAAATCAAGATATAATACACATATATATATACAAT
129 TCGATTAACAAGCGAATCTTACAAGCTTGATAAATCAAG--ATAAT----ATATATATATACAAT
27725227 CCATCATCTTTGAATTATATATTGAG
188 CCATCATCTTTGAATTATATATTGAG
* ** *
27725253 TTTATAAAGATATTGTAAAATATATAAAAACATTTTTAATGTTAT-ATTTGAAAAATGAACACTT
1 TTTATAAAGATATTGGAAAATATATAAAAACATTTTTAATAATATAATTTGAAAAACGAACACTT
* * * *
27725317 GTACATCAAATTTATTGTAGTGAATAATTATCCTATTTTATCGAAAATCATTACTTATGGTGCTC
66 GTAAATCAAATTTATTGTAATGAATAATTATCCTATTTTATCAAAAATCATTACTTATGGTCCTC
** * *
27725382 GATTAACTTGCGAATTTTACAAGCTTGATAAATCAAGATAATATATATATATATAATCCATCATC
131 GATTAACAAGCGAATCTTACAAGCTTGATAAATCAAGATAATATATATATATACAATCCATCATC
27725447 TTTGAATTATATATTGAG
196 TTTGAATTATATATTGAG
27725465 TTTATA
1 TTTATA
27725471 GCTAAGATGA
Statistics
Matches: 200, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
212 46 0.23
216 5 0.03
218 53 0.26
220 56 0.28
221 40 0.20
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.39
Consensus pattern (213 bp):
TTTATAAAGATATTGGAAAATATATAAAAACATTTTTAATAATATAATTTGAAAAACGAACACTT
GTAAATCAAATTTATTGTAATGAATAATTATCCTATTTTATCAAAAATCATTACTTATGGTCCTC
GATTAACAAGCGAATCTTACAAGCTTGATAAATCAAGATAATATATATATATACAATCCATCATC
TTTGAATTATATATTGAG
Found at i:27725994 original size:5 final size:5
Alignment explanation
Indices: 27725984--27726010 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
27725974 TTCTTACCAT
27725984 GGTGG GGTGG GGTGG GGTGG GGTGG GG
1 GGTGG GGTGG GGTGG GGTGG GGTGG GG
27726011 CAGGGAGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.81, T:0.19
Consensus pattern (5 bp):
GGTGG
Found at i:27728709 original size:2 final size:2
Alignment explanation
Indices: 27728704--27728745 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
27728694 GTAGCCACAC
27728704 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
27728746 TATCCAATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27743813 original size:22 final size:22
Alignment explanation
Indices: 27743786--27743838 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
27743776 ACTATGTAAC
*
27743786 TAGTTTTTAGGCATTACGTAAT
1 TAGTTTTTAGGCATTACATAAT
* *
27743808 T-GGTTTTAGGCATTACATGAT
1 TAGTTTTTAGGCATTACATAAT
27743829 TAGTTTTTAG
1 TAGTTTTTAG
27743839 ATATTGCGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.47
Consensus pattern (22 bp):
TAGTTTTTAGGCATTACATAAT
Found at i:27743922 original size:26 final size:27
Alignment explanation
Indices: 27743890--27743958 Score: 106
Period size: 26 Copynumber: 2.6 Consensus size: 27
27743880 ATGCCTTACT
*
27743890 AACTAGTCACGCAATACT-TTATCAGA
1 AACTAGTCACGCAATACTCTTATCAAA
*
27743916 AACTAGTCATGCAATA-TCTTATCAAA
1 AACTAGTCACGCAATACTCTTATCAAA
27743942 AACTAGTCACGCAATAC
1 AACTAGTCACGCAATAC
27743959 CCAAAGTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (27 bp):
AACTAGTCACGCAATACTCTTATCAAA
Found at i:27744594 original size:22 final size:20
Alignment explanation
Indices: 27744551--27744592 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
27744541 AAGCCAATTC
27744551 TTCATATATTATGAATCATT
1 TTCATATATTATGAATCATT
27744571 TTCATATATTATGAATCATT
1 TTCATATATTATGAATCATT
27744591 TT
1 TT
27744593 TTTCTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (20 bp):
TTCATATATTATGAATCATT
Found at i:27748363 original size:14 final size:14
Alignment explanation
Indices: 27748344--27748370 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27748334 TATAATTATG
27748344 TTGAAAAATATTAA
1 TTGAAAAATATTAA
27748358 TTGAAAAATATTA
1 TTGAAAAATATTA
27748371 TAATTATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
TTGAAAAATATTAA
Found at i:27749799 original size:37 final size:33
Alignment explanation
Indices: 27749758--27749850 Score: 114
Period size: 37 Copynumber: 2.7 Consensus size: 33
27749748 AAGATGACCA
27749758 GCTGAGAGAGGAGATGAAGACGGGGGAAGGACGGTTG
1 GCTGAGAGAGGAGATGAAGACGGGGGAA-G--GG-TG
* *
27749795 GCTGAGAGAGGAGATGAACATGGGGGAAGGGTG
1 GCTGAGAGAGGAGATGAAGACGGGGGAAGGGTG
* *
27749828 GCTGATAGAGGAGAGGAAGACGG
1 GCTGAGAGAGGAGATGAAGACGG
27749851 TCGGCTGAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
33 21 0.42
34 2 0.04
36 1 0.02
37 26 0.52
ACGTcount: A:0.31, C:0.08, G:0.51, T:0.11
Consensus pattern (33 bp):
GCTGAGAGAGGAGATGAAGACGGGGGAAGGGTG
Found at i:27750230 original size:26 final size:26
Alignment explanation
Indices: 27750201--27750276 Score: 134
Period size: 26 Copynumber: 2.9 Consensus size: 26
27750191 ACATGCAGAT
*
27750201 AATGCCTTATTAAAAACTAGTCACGC
1 AATGCCTTATTAAAAATTAGTCACGC
*
27750227 AATGCTTTATTAAAAATTAGTCACGC
1 AATGCCTTATTAAAAATTAGTCACGC
27750253 AATGCCTTATTAAAAATTAGTCAC
1 AATGCCTTATTAAAAATTAGTCAC
27750277 ATAATTTCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (26 bp):
AATGCCTTATTAAAAATTAGTCACGC
Found at i:27750353 original size:21 final size:21
Alignment explanation
Indices: 27750291--27750353 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
27750281 TTTCCAAAGT
*
27750291 CAGTCACGCAATATCTAAAAT
1 CAGTCACGCAATATCTAAAAA
**
27750312 CAGTCACGCAATGCCTAAAAA
1 CAGTCACGCAATATCTAAAAA
*
27750333 CTAGTCACGTAAT-TCTAAAAA
1 C-AGTCACGCAATATCTAAAAA
27750354 ATCATCAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 26 0.72
22 10 0.28
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.22
Consensus pattern (21 bp):
CAGTCACGCAATATCTAAAAA
Found at i:27750529 original size:19 final size:19
Alignment explanation
Indices: 27750481--27750530 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
27750471 TTATATATCA
*
27750481 AAAAACACTCTAAAATGCTT
1 AAAAACGCTC-AAAATGCTT
*
27750501 AAAAATGCTCAAAACTGCTT
1 AAAAACGCTCAAAA-TGCTT
27750521 -AAAACGCTCA
1 AAAAACGCTCA
27750531 TAGATTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.48, C:0.22, G:0.08, T:0.22
Consensus pattern (19 bp):
AAAAACGCTCAAAATGCTT
Found at i:27759692 original size:32 final size:32
Alignment explanation
Indices: 27759653--27759714 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
27759643 TTACATTTAA
* * *
27759653 TTTTTAATTTTTTATTTAAATTATAAAATAAT
1 TTTTTAATTTCTAAATTAAATTATAAAATAAT
27759685 TTTTTAATTTCTAAATTAAATTATAAAATA
1 TTTTTAATTTCTAAATTAAATTATAAAATA
27759715 CAATTATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (32 bp):
TTTTTAATTTCTAAATTAAATTATAAAATAAT
Found at i:27759713 original size:13 final size:14
Alignment explanation
Indices: 27759697--27759730 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
27759687 TTTAATTTCT
27759697 AAATTA-AATTATA
1 AAATTACAATTATA
27759710 AAA-TACAATTATA
1 AAATTACAATTATA
27759723 AAATTACA
1 AAATTACA
27759731 TCTATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 13 0.68
14 4 0.21
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATTACAATTATA
Found at i:27759915 original size:33 final size:33
Alignment explanation
Indices: 27759877--27759940 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
27759867 TATTATTAAT
27759877 TTTTGACAATTT-TTATTCAAATTACAAAGTAAA
1 TTTTGACAATTTGTTA-TCAAATTACAAAGTAAA
* *
27759910 TTTTGACATTTTGTTATCAAATTATAAAGTA
1 TTTTGACAATTTGTTATCAAATTACAAAGTA
27759941 CAACTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.89
34 3 0.11
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (33 bp):
TTTTGACAATTTGTTATCAAATTACAAAGTAAA
Found at i:27764046 original size:19 final size:17
Alignment explanation
Indices: 27764004--27764048 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
27763994 TTCACACCTC
*
27764004 TTTCTATCTCTTTCTTT
1 TTTCTTTCTCTTTCTTT
27764021 TTGTCTTTCTCTTCTCTTT
1 TT-TCTTTCTCTT-TCTTT
27764040 TATTCTTTC
1 T-TTCTTTC
27764049 ATTGTGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.08
18 9 0.38
19 12 0.50
20 1 0.04
ACGTcount: A:0.04, C:0.24, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTCTTTCTCTTTCTTT
Found at i:27767387 original size:20 final size:20
Alignment explanation
Indices: 27767362--27767399 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27767352 TTAAATTTGA
*
27767362 TGTTATTATTATTCTTATTT
1 TGTTATAATTATTCTTATTT
*
27767382 TGTTATAATTATTTTTAT
1 TGTTATAATTATTCTTAT
27767400 AATTATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (20 bp):
TGTTATAATTATTCTTATTT
Found at i:27770154 original size:2 final size:2
Alignment explanation
Indices: 27770147--27770173 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27770137 ATGAGGAGTT
27770147 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
27770174 GATTTGGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27771550 original size:8 final size:7
Alignment explanation
Indices: 27771535--27771574 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
27771525 ACCCATGAAG
27771535 AAGAAAA
1 AAGAAAA
27771542 AAGGAAAA
1 AA-GAAAA
27771550 AAGAAAA
1 AAGAAAA
27771557 AA-AAAA
1 AAGAAAA
27771563 AA-AAAA
1 AAGAAAA
27771569 AA-AAAA
1 AAGAAAA
27771575 TTATGTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 16 0.50
7 9 0.28
8 7 0.22
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:27772158 original size:15 final size:15
Alignment explanation
Indices: 27772135--27772182 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
27772125 NNNNNNTAAA
*
27772135 TAAAATATTAATAAT
1 TAAATTATTAATAAT
*
27772150 TAAATTATTAATTAT
1 TAAATTATTAATAAT
* *
27772165 TAATATTTTTATTAAT
1 TAA-ATTATTAATAAT
27772181 TA
1 TA
27772183 TAAAATATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAATTATTAATAAT
Found at i:27772162 original size:7 final size:7
Alignment explanation
Indices: 27772140--27772199 Score: 54
Period size: 7 Copynumber: 8.9 Consensus size: 7
27772130 NTAAATAAAA
27772140 TATTAAT
1 TATTAAT
*
27772147 AATTAAAT
1 TATT-AAT
27772155 TATTAAT
1 TATTAAT
27772162 TATTAA-
1 TATTAAT
*
27772168 TATT-TT
1 TATTAAT
27772174 TATTAAT
1 TATTAAT
* *
27772181 TATAAAA
1 TATTAAT
27772188 TATTAAT
1 TATTAAT
27772195 T-TTAA
1 TATTAA
27772200 AATAAAAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
6 12 0.29
7 24 0.57
8 6 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TATTAAT
Found at i:27772193 original size:14 final size:14
Alignment explanation
Indices: 27772174--27772203 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27772164 TTAATATTTT
27772174 TATTAATTATAAAA
1 TATTAATTATAAAA
*
27772188 TATTAATTTTAAAA
1 TATTAATTATAAAA
27772202 TA
1 TA
27772204 AAAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTAATTATAAAA
Found at i:27778385 original size:2 final size:2
Alignment explanation
Indices: 27778373--27778414 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
27778363 ATGTCCGGGC
*
27778373 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27778415 CTGTATAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27794805 original size:7 final size:7
Alignment explanation
Indices: 27794783--27794841 Score: 57
Period size: 7 Copynumber: 8.0 Consensus size: 7
27794773 AAGGAGAAGG
27794783 AGAAGTAA
1 AGAAG-AA
27794791 AGGAAGAA
1 A-GAAGAA
27794799 AGAAGAA
1 AGAAGAA
27794806 A-AAGAA
1 AGAAGAA
*
27794812 AAAAGAGA
1 AGAAGA-A
*
27794820 AGGAGAA
1 AGAAGAA
27794827 AGAAAGAA
1 AG-AAGAA
27794835 AGAAGAA
1 AGAAGAA
27794842 GCCAACGGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
6 6 0.14
7 19 0.43
8 15 0.34
9 4 0.09
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (7 bp):
AGAAGAA
Found at i:27794821 original size:40 final size:40
Alignment explanation
Indices: 27794767--27794906 Score: 149
Period size: 40 Copynumber: 3.4 Consensus size: 40
27794757 TACGCCGGGG
*
27794767 AGAAAGAAGGAGAAGGAG-AAGTAAAGGAAGAAAGAAGAAAA
1 AGAAA-AAAGAGAAGGAGAAAG-AAAGGAAGAAAGAAGAAAA
* **
27794808 AGAAAAAAGAGAAGGAGAAAGAAAGAAAG-AAGAAGCCAACGGGG
1 AGAAAAAAGAGAAGGAGAAAGAAAGGAAGAAAGAAG--AA---AA
* *
27794852 AGAAGAAGGAGAAGGAGAAAGAAAGGAAGAAAGAAGAAAA
1 AGAAAAAAGAGAAGGAGAAAGAAAGGAAGAAAGAAGAAAA
27794892 AGAAAAAAGAGAAGG
1 AGAAAAAAGAGAAGG
27794907 GGGACCCGCG
Statistics
Matches: 81, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
39 6 0.07
40 31 0.38
41 10 0.12
43 2 0.02
44 26 0.32
45 6 0.07
ACGTcount: A:0.63, C:0.02, G:0.34, T:0.01
Consensus pattern (40 bp):
AGAAAAAAGAGAAGGAGAAAGAAAGGAAGAAAGAAGAAAA
Done.