Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 162 of 295
Found at i:55304554 original size:8 final size:8
Alignment explanation
Indices: 55304538--55304568 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
55304528 TATAATTTAA
55304538 TTTACAAAT
1 TTTA-AAAT
55304547 TTTAAAAT
1 TTTAAAAT
55304555 TTTAAAAT
1 TTTAAAAT
55304563 TTTAAA
1 TTTAAA
55304569 TAATATAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (8 bp):
TTTAAAAT
Found at i:55304793 original size:19 final size:18
Alignment explanation
Indices: 55304771--55304830 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
55304761 TAAAAACAAT
55304771 ATATATAAATAATTAATAA
1 ATATATAAATAATTAA-AA
* *
55304790 ATATATAATAAAAGTAAAA
1 ATATATAA-ATAATTAAAA
*
55304809 ATATAAAAATAATATAAAA
1 ATATATAAATAAT-TAAAA
55304828 ATA
1 ATA
55304831 ATGACATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 3 0.09
19 25 0.74
20 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
ATATATAAATAATTAAAA
Found at i:55306967 original size:18 final size:18
Alignment explanation
Indices: 55306940--55306974 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55306930 ATAAATATGA
*
55306940 AAATTAAATAAATAATAT
1 AAATTAAATAAAAAATAT
*
55306958 AAATTGAATAAAAAATA
1 AAATTAAATAAAAAATA
55306975 AAAACGTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
AAATTAAATAAAAAATAT
Found at i:55307564 original size:94 final size:94
Alignment explanation
Indices: 55307389--55307565 Score: 257
Period size: 94 Copynumber: 1.9 Consensus size: 94
55307379 AACTAAAAAT
* * *
55307389 AAATAAGAATGGTTTTGGTGGCCGTAGAGCCTCCCCTATTCACATCTATCTATATGTATATTAAA
1 AAATAAGAATGGTTTTGATGGCCGTAGAGCCTCCCCTATTCACATCTATCTACATATATATTAAA
** *
55307454 AATAGAAGGTAGAAGAAAGCGTATGTTAA
66 AATAGAACCTAAAAGAAAGCGTATGTTAA
** *
55307483 AAATAAGAATGGTTTTGATGGTTGTAGTGCCTCCCCTATTCACATCTATCTACATA-ATTATTAA
1 AAATAAGAATGGTTTTGATGGCCGTAGAGCCTCCCCTATTCACATCTATCTACATATA-TATTAA
55307547 AAATAGAACCTAAAAGAAA
65 AAATAGAACCTAAAAGAAA
55307566 TCAGCCCCGC
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
93 1 0.01
94 72 0.99
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (94 bp):
AAATAAGAATGGTTTTGATGGCCGTAGAGCCTCCCCTATTCACATCTATCTACATATATATTAAA
AATAGAACCTAAAAGAAAGCGTATGTTAA
Found at i:55315059 original size:15 final size:15
Alignment explanation
Indices: 55315041--55315070 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55315031 GTTCAGTTCA
55315041 GTTCAGTTCTACTCT
1 GTTCAGTTCTACTCT
*
55315056 GTTCCGTTCTACTCT
1 GTTCAGTTCTACTCT
55315071 ATTATGTTCT
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:0.10, C:0.30, G:0.13, T:0.47
Consensus pattern (15 bp):
GTTCAGTTCTACTCT
Found at i:55315071 original size:20 final size:20
Alignment explanation
Indices: 55315048--55315098 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
55315038 TCAGTTCAGT
55315048 TCTACTCTGTTCCGTTCTAC
1 TCTACTCTGTTCCGTTCTAC
* * * *
55315068 TCTATTATGTTCTGTTCTGC
1 TCTACTCTGTTCCGTTCTAC
*
55315088 TTTACTCTGTT
1 TCTACTCTGTT
55315099 TTGTTCTGTC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.10, C:0.25, G:0.12, T:0.53
Consensus pattern (20 bp):
TCTACTCTGTTCCGTTCTAC
Found at i:55315081 original size:25 final size:25
Alignment explanation
Indices: 55315053--55315107 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
55315043 TCAGTTCTAC
55315053 TCTGTTCCG-TTCTACTCTATTATGT
1 TCTGTTCCGCTT-TACTCTATTATGT
* * *
55315078 TCTGTTCTGCTTTACTCTGTTTTGT
1 TCTGTTCCGCTTTACTCTATTATGT
55315103 TCTGT
1 TCTGT
55315108 CATATTCTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.07, C:0.22, G:0.15, T:0.56
Consensus pattern (25 bp):
TCTGTTCCGCTTTACTCTATTATGT
Found at i:55321120 original size:21 final size:21
Alignment explanation
Indices: 55321094--55321137 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
55321084 TCATACACTT
55321094 TTCTTTTC-TTTCGTTCATTAA
1 TTCTTTTCGTTT-GTTCATTAA
*
55321115 TTCTTTTCGTTTGTTCTTTAA
1 TTCTTTTCGTTTGTTCATTAA
55321136 TT
1 TT
55321138 TATTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.11, C:0.16, G:0.07, T:0.66
Consensus pattern (21 bp):
TTCTTTTCGTTTGTTCATTAA
Found at i:55324547 original size:18 final size:19
Alignment explanation
Indices: 55324524--55324566 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
55324514 CAAACTTTTG
55324524 TTTTTATATTT-TTAT-ACA
1 TTTTTAT-TTTATTATCACA
55324542 TTTTTATTTTATTATGCACA
1 TTTTTATTTTATTAT-CACA
55324562 TTTTT
1 TTTTT
55324567 TTATCAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.14
18 11 0.50
20 8 0.36
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTATTTTATTATCACA
Found at i:55326679 original size:40 final size:40
Alignment explanation
Indices: 55326633--55326716 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
55326623 TAAGTTTCGT
*
55326633 GTAAGTATGGTGTTTTTCTTTTTGAGAAGGATGTTTTTAG
1 GTAAGTATGGTGTTTGTCTTTTTGAGAAGGATGTTTTTAG
*
55326673 GTAAGTATGGTGTTTGTCTTTTTGATAAGGATGTTTTTAG
1 GTAAGTATGGTGTTTGTCTTTTTGAGAAGGATGTTTTTAG
55326713 GTAA
1 GTAA
55326717 TCTTATTTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.21, C:0.02, G:0.27, T:0.49
Consensus pattern (40 bp):
GTAAGTATGGTGTTTGTCTTTTTGAGAAGGATGTTTTTAG
Found at i:55328244 original size:26 final size:24
Alignment explanation
Indices: 55328206--55328274 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
55328196 CTCACCACAG
*
55328206 TTCGTATGTGCTTACTGATATATCAA
1 TTCGTATGAGCTTACT-AT-TATCAA
* *
55328232 TTCGTAAGAGCTTACTATTCTCAA
1 TTCGTATGAGCTTACTATTATCAA
*
55328256 CTCGTATGAGCTTACTATT
1 TTCGTATGAGCTTACTATT
55328275 CACCTCTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
24 22 0.58
25 2 0.05
26 14 0.37
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (24 bp):
TTCGTATGAGCTTACTATTATCAA
Found at i:55328260 original size:24 final size:24
Alignment explanation
Indices: 55328228--55328344 Score: 82
Period size: 24 Copynumber: 5.0 Consensus size: 24
55328218 TACTGATATA
*
55328228 TCAATTCGTAAGAGCTTACTATTC
1 TCAACTCGTAAGAGCTTACTATTC
*
55328252 TCAACTCGTATGAGCTTACTA-T-
1 TCAACTCGTAAGAGCTTACTATTC
* * * **
55328274 TCACCTCTTCAGAGCTTACCGTT-
1 TCAACTCGTAAGAGCTTACTATTC
* *
55328297 TCAGCT--TAATAGAGCTTACTGTTC
1 TCAACTCGT-A-AGAGCTTACTATTC
* *
55328321 TCAACTCATATGAGCTTACTATTC
1 TCAACTCGTAAGAGCTTACTATTC
55328345 ACCTCTTCAG
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
21 1 0.01
22 15 0.21
23 19 0.26
24 36 0.49
25 1 0.01
26 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.37
Consensus pattern (24 bp):
TCAACTCGTAAGAGCTTACTATTC
Found at i:55328291 original size:22 final size:21
Alignment explanation
Indices: 55328238--55328361 Score: 72
Period size: 22 Copynumber: 5.4 Consensus size: 21
55328228 TCAATTCGTA
* *
55328238 AGAGCTTACTATTCTCAACTCGT
1 AGAGCTTACTA-T-TCACCTCTT
55328261 ATGAGCTTACTATTCACCTCTT
1 A-GAGCTTACTATTCACCTCTT
*
55328283 CAGAGCTTACCGT-TTCAGCT-TAAT
1 -AGAGCTTA-C-TATTCACCTCT--T
* * *
55328307 AGAGCTTACTGTTCTCAACTCAT
1 AGAGCTTACT-AT-TCACCTCTT
55328330 ATGAGCTTACTATTCACCTCTT
1 A-GAGCTTACTATTCACCTCTT
55328352 CAGAGCTTAC
1 -AGAGCTTAC
55328362 CGTTTCAGCT
Statistics
Matches: 81, Mismatches: 8, Indels: 25
0.71 0.07 0.22
Matches are distributed among these distances:
21 1 0.01
22 31 0.38
23 23 0.28
24 26 0.32
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (21 bp):
AGAGCTTACTATTCACCTCTT
Found at i:55328310 original size:23 final size:23
Alignment explanation
Indices: 55328284--55328384 Score: 77
Period size: 23 Copynumber: 4.4 Consensus size: 23
55328274 TCACCTCTTC
55328284 AGAGCTTACCGTTTCAGCTTAAT
1 AGAGCTTACCGTTTCAGCTTAAT
* * *
55328307 AGAGCTTACTGTTCTCAAC-TCAT
1 AGAGCTTACCGTT-TCAGCTTAAT
*
55328330 ATGAGCTTA-C-TATTCACCTCT--T
1 A-GAGCTTACCGT-TTCAGCT-TAAT
*
55328352 CAGAGCTTACCGTTTCAGCTCAAT
1 -AGAGCTTACCGTTTCAGCTTAAT
55328376 AGAGCTTAC
1 AGAGCTTAC
55328385 TGTTCATCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
22 13 0.21
23 34 0.56
24 14 0.23
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (23 bp):
AGAGCTTACCGTTTCAGCTTAAT
Found at i:55328349 original size:69 final size:69
Alignment explanation
Indices: 55328238--55328395 Score: 280
Period size: 69 Copynumber: 2.3 Consensus size: 69
55328228 TCAATTCGTA
* *
55328238 AGAGCTTACTATTCTCAACTCGTATGAGCTTACTATTCACCTCTTCAGAGCTTACCGTTTCAGCT
1 AGAGCTTACTGTTCTCAACTCATATGAGCTTACTATTCACCTCTTCAGAGCTTACCGTTTCAGCT
*
55328303 TAAT
66 CAAT
55328307 AGAGCTTACTGTTCTCAACTCATATGAGCTTACTATTCACCTCTTCAGAGCTTACCGTTTCAGCT
1 AGAGCTTACTGTTCTCAACTCATATGAGCTTACTATTCACCTCTTCAGAGCTTACCGTTTCAGCT
55328372 CAAT
66 CAAT
55328376 AGAGCTTACTGTTCATCAAC
1 AGAGCTTACTGTTC-TCAAC
55328396 ATAGGAGGAG
Statistics
Matches: 85, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
69 80 0.94
70 5 0.06
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (69 bp):
AGAGCTTACTGTTCTCAACTCATATGAGCTTACTATTCACCTCTTCAGAGCTTACCGTTTCAGCT
CAAT
Found at i:55329473 original size:65 final size:65
Alignment explanation
Indices: 55329404--55329546 Score: 164
Period size: 65 Copynumber: 2.2 Consensus size: 65
55329394 CACGGTCTCA
*
55329404 CACATGGGCGTGTGAC-CGACCGTGTGGTACAAGTCAGTATATCCC-CTAATTGGCACACGGCAT
1 CACATGGGCGTGTGACTCGACCGTGTGG-ACAAGTCAGTATA-CCCTCCAATTGGCACACGGCAT
55329467 AG
64 AG
* * * * * ** * *
55329469 CACATGGGCGTGTGACTTGGCCGTGTTGATAAGTCAGTATACCCTCCAGTTTTCATACGGCCTAG
1 CACATGGGCGTGTGACTCGACCGTGTGGACAAGTCAGTATACCCTCCAATTGGCACACGGCATAG
55329534 CACATGGGCGTGT
1 CACATGGGCGTGT
55329547 CTTCGGCCGT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
64 3 0.05
65 55 0.83
66 8 0.12
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.25
Consensus pattern (65 bp):
CACATGGGCGTGTGACTCGACCGTGTGGACAAGTCAGTATACCCTCCAATTGGCACACGGCATAG
Found at i:55332015 original size:68 final size:64
Alignment explanation
Indices: 55331950--55332157 Score: 215
Period size: 67 Copynumber: 3.2 Consensus size: 64
55331940 CATCATGTGT
*
55331950 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATG
1 ACAAGAGAGCTAC--GAGA-TAT-ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATG
55332015 TAG
62 TAG
* * * * * *
55332018 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGG-TACTA-TG-TGTACACCATGT
55332083 AG
63 AG
* * * *
55332085 ACAAGAGAGCTACGAGATAAACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-G
1 ACAAGAGAGCTACGAGATATA-TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG
55332147 TACAAGAGAGC
1 -ACAAGAGAGC
55332158 CGAACTATAT
Statistics
Matches: 118, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.16
64 23 0.19
65 9 0.08
66 20 0.17
67 31 0.26
68 15 0.13
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.22
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG
Found at i:55340684 original size:17 final size:18
Alignment explanation
Indices: 55340662--55340697 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
55340652 TAATTTTTAA
55340662 TAAAAATTTTATAA-TTT
1 TAAAAATTTTATAACTTT
55340679 TAAAAATTTTATAACTTT
1 TAAAAATTTTATAACTTT
55340697 T
1 T
55340698 TTTTATAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAAAATTTTATAACTTT
Found at i:55346260 original size:16 final size:16
Alignment explanation
Indices: 55346229--55346265 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
55346219 ATGTGAATAA
55346229 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
55346245 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
55346261 TATTA
1 TATTA
55346266 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:55358483 original size:17 final size:17
Alignment explanation
Indices: 55358440--55358500 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
55358430 ATATGTCATA
*
55358440 ATATTTTTATAT-A-TT
1 ATATTATTATATAATTT
55358455 ATATTA-TATATACATTT
1 ATATTATTATATA-ATTT
*
55358472 TTA-TATTATATAATTT
1 ATATTATTATATAATTT
55358488 ATATTATTATATA
1 ATATTATTATATA
55358501 TTTTTATTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 5 0.13
15 5 0.13
16 9 0.24
17 19 0.50
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATTATTATATAATTT
Found at i:55358483 original size:26 final size:26
Alignment explanation
Indices: 55358442--55358491 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
55358432 ATGTCATAAT
55358442 ATTTTTATATATTAT-ATTATATATAC
1 ATTTTTATATATTATAATT-TATATAC
55358468 ATTTTTATAT-TATATAATTTATAT
1 ATTTTTATATAT-TATAATTTATAT
55358492 TATTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 1 0.05
26 18 0.82
27 3 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTTATATATTATAATTTATATAC
Found at i:55358490 original size:24 final size:25
Alignment explanation
Indices: 55358444--55358502 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
55358434 GTCATAATAT
*
55358444 TTTTATATATTATATTATATATACA
1 TTTTATATATTATATAATATATACA
*
55358469 TTTT-TATATTATATAAT-T-TATA
1 TTTTATATATTATATAATATATACA
55358491 TTATTATATATT
1 TT-TTATATATT
55358503 TTTATTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 5 0.17
23 3 0.10
24 18 0.60
25 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTTATATATTATATAATATATACA
Found at i:55358500 original size:19 final size:19
Alignment explanation
Indices: 55358454--55358501 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
55358444 TTTTATATAT
*
55358454 TATATTATATATACATTTT
1 TATATTATATATACATTTA
55358473 TATA-T-TATATA-ATTTA
1 TATATTATATATACATTTA
55358489 TATTATTATATAT
1 TA-TATTATATAT
55358502 TTTTATTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 6 0.24
17 8 0.32
18 2 0.08
19 9 0.36
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATATACATTTA
Found at i:55370929 original size:176 final size:175
Alignment explanation
Indices: 55370686--55371072 Score: 544
Period size: 176 Copynumber: 2.2 Consensus size: 175
55370676 ATCTTCAACG
* * * * *
55370686 AGAAGCAAATTGAAGACATAGCAGATCTAACTTTCAGATGTTTTCACATCAAAACAGATCCAAGA
1 AGAAGCAAATCGAAGACATAGCAGATTTGACTTTCAGATGTTCTCACACCAAAACAGATCCAAGA
* * *
55370751 TAACAGATCTGGCATCTCCATTTCGACGGAGAGCATG-TACATAGCAGGTCTAACCTTCAGGTG-
66 TAACAGATCTAGCATCTCCATTTCGACGGAGAGCA-GATACATAGCAGATCTAACCTTCAGATGA
* * * *
55370814 TTTATACTGAAGCAGATCTAAGATGATTTGGGCATTCTTGTGTTTACA
130 TTT-TACTGAAGCAGATCCAAGATGATTT-GGCATCCTTATGTTCACA
* * *
55370862 AGAAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAAGA
1 AGAAGCAAATCGAAGACATAGCAGATTTGACTTTCAGATGTTCTCACACCAAAACAGATCCAAGA
* * *
55370927 TAACAGATCTAGTATCTCCATTTCGATGGAGAGCAGATACATAGTAGATCTAACCTTCAGATGAT
66 TAACAGATCTAGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGAT
*
55370992 TTTATTGAAGCAGATCCAAGATGATTTGGCATCCTTATGTTCACA
131 TTTACTGAAGCAGATCCAAGATGATTTGGCATCCTTATGTTCACA
* *
55371037 AGAAGCAAATCGAAGACACAGCAGATTTGGCTTTCA
1 AGAAGCAAATCGAAGACATAGCAGATTTGACTTTCA
55371073 CGTGTTTACG
Statistics
Matches: 186, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
175 48 0.26
176 135 0.73
177 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (175 bp):
AGAAGCAAATCGAAGACATAGCAGATTTGACTTTCAGATGTTCTCACACCAAAACAGATCCAAGA
TAACAGATCTAGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGAT
TTTACTGAAGCAGATCCAAGATGATTTGGCATCCTTATGTTCACA
Found at i:55371184 original size:84 final size:86
Alignment explanation
Indices: 55370998--55371156 Score: 193
Period size: 87 Copynumber: 1.8 Consensus size: 86
55370988 TGATTTTATT
55370998 GAAGCAGATCCAAGATGATTTGGCATCCTTATGTTCACAAGAAGCAAATCGAAGACACAGCAGAT
1 GAAGCAGATCCAAGATGATTTGGCATCCTTATGTTCACAAGAAGCAAATCGAAGA-ACAGCAGAT
* *
55371063 TTGGCTTTCACGTGTTTACGCT
65 TTGGCTCTCACGTGTTTACGCA
* * *
55371085 GAAGTAGATCTAAGATGATTTGGCATCTCTGTAT-TGTCAGAA-AA-CAAATCGAAG-A-AGCAG
1 GAAGCAGATCCAAGATGATTTGGCATC-CT-TATGT-TCACAAGAAGCAAATCGAAGAACAGCAG
55371145 ATTTGGCGTCTC
63 ATTTGGC-TCTC
55371157 TGTGTTCGAC
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
84 12 0.19
85 4 0.06
87 35 0.55
88 5 0.08
89 8 0.12
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (86 bp):
GAAGCAGATCCAAGATGATTTGGCATCCTTATGTTCACAAGAAGCAAATCGAAGAACAGCAGATT
TGGCTCTCACGTGTTTACGCA
Found at i:55372786 original size:32 final size:32
Alignment explanation
Indices: 55372746--55372806 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
55372736 TTATTTGTAA
*
55372746 TTAACCCTAAATTCC-TTAATTAAATTTAATT
1 TTAACCCTAAATACCTTTAATTAAATTTAATT
* *
55372777 TTAATCCCTATATACCTTTAATTCAATTTA
1 TTAA-CCCTAAATACCTTTAATTAAATTTA
55372807 TTTAAAATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 4 0.16
32 9 0.36
33 12 0.48
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46
Consensus pattern (32 bp):
TTAACCCTAAATACCTTTAATTAAATTTAATT
Found at i:55373099 original size:24 final size:22
Alignment explanation
Indices: 55373062--55373117 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 22
55373052 TCATAATATT
55373062 TTTTATATATTATATTATATATACA
1 TTTT-TATATTATA-TA-ATATACA
* *
55373087 TTTTTATATTATATAATTTATA
1 TTTTTATATTATATAATATACA
55373109 TTTTTATAT
1 TTTTTATAT
55373118 ATTTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 14 0.48
23 2 0.07
24 9 0.31
25 4 0.14
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTTATATTATATAATATACA
Found at i:55373101 original size:17 final size:15
Alignment explanation
Indices: 55373054--55373127 Score: 55
Period size: 16 Copynumber: 4.9 Consensus size: 15
55373044 ACCATCTGTC
*
55373054 ATAATATTT-TTTAT
1 ATAATTTTTATTTAT
*
55373068 AT-A-TTATATTATAT
1 ATAATTTTTATT-TAT
55373082 ATACATTTTTATATTAT
1 ATA-ATTTTTAT-TTAT
* *
55373099 ATAATTTATATTTTT
1 ATAATTTTTATTTAT
55373114 ATATATTTTTATTT
1 ATA-ATTTTTATTT
55373128 GTAAATTATG
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
12 2 0.04
13 3 0.06
14 7 0.15
15 6 0.13
16 17 0.36
17 11 0.23
18 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (15 bp):
ATAATTTTTATTTAT
Found at i:55373118 original size:24 final size:25
Alignment explanation
Indices: 55373061--55373120 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
55373051 GTCATAATAT
*
55373061 TTTTTATATATTATATTATATATAC
1 TTTTTATATATTATATAATATATAC
* *
55373086 ATTTT-TATATTATATAATTTATA-
1 TTTTTATATATTATATAATATATAC
55373109 TTTTTATATATT
1 TTTTTATATATT
55373121 TTTATTTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 4 0.13
24 22 0.73
25 4 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTTATATATTATATAATATATAC
Found at i:55375831 original size:5 final size:6
Alignment explanation
Indices: 55375812--55375858 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
55375802 ATAATTTACT
* *
55375812 AAATAA AAATAA AAATAA AAATCTAA AACTAA AAATGA AAATAA AAA
1 AAATAA AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA
55375859 ATATATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
6 30 0.86
8 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:55375844 original size:20 final size:20
Alignment explanation
Indices: 55375815--55375853 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55375805 ATTTACTAAA
55375815 TAAAAATAAAAATAAAAATC
1 TAAAAATAAAAATAAAAATC
* *
55375835 TAAAACTAAAAATGAAAAT
1 TAAAAATAAAAATAAAAAT
55375854 AAAAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.21
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAATC
Found at i:55375894 original size:9 final size:9
Alignment explanation
Indices: 55375880--55375956 Score: 77
Period size: 9 Copynumber: 8.6 Consensus size: 9
55375870 TTTATACAAA
55375880 TAATTCGGT
1 TAATTCGGT
*
55375889 TAATTCGGG
1 TAATTCGGT
*
55375898 TAATTCAGT
1 TAATTCGGT
55375907 TAATAT-GAG-
1 TAAT-TCG-GT
*
55375916 TAATTCGGG
1 TAATTCGGT
55375925 TAATTCGGT
1 TAATTCGGT
*
55375934 TAATTCGAT
1 TAATTCGGT
*
55375943 TAATTCGAT
1 TAATTCGGT
55375952 TAATT
1 TAATT
55375957 TTATACTTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
8 2 0.03
9 54 0.93
10 2 0.03
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (9 bp):
TAATTCGGT
Found at i:55375956 original size:27 final size:27
Alignment explanation
Indices: 55375880--55375949 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
55375870 TTTATACAAA
*
55375880 TAATTCGGTTAATTCGGGTAATTCAGT
1 TAATTCGATTAATTCGGGTAATTCAGT
* *
55375907 TAATAT-GAGTAATTCGGGTAATTCGGT
1 TAAT-TCGATTAATTCGGGTAATTCAGT
55375934 TAATTCGATTAATTCG
1 TAATTCGATTAATTCG
55375950 ATTAATTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 35 0.95
28 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (27 bp):
TAATTCGATTAATTCGGGTAATTCAGT
Found at i:55385787 original size:53 final size:54
Alignment explanation
Indices: 55385608--55385798 Score: 170
Period size: 53 Copynumber: 3.4 Consensus size: 54
55385598 TCACATCATG
* * *
55385608 TTAAAAATGTTGTTATATAACTATATATTGTTATATATCATAGATTTTGGTAGTTATTA
1 TTAAAAATGTTGTTATATAA--ATAAATTGTTATATATTATAGATTTTGGTA--TA-CA
* * * * *
55385667 TAAAAAATGTTCTTATATAAACAAATATGTTGTTATATATTATAAATTTTGGCAT-CGA
1 TTAAAAATGTTGTTATATAAA-TAA-A--TTGTTATATATTATAGATTTTGGTATAC-A
* * *
55385725 TTAGAAATGTTGTTATATAAATAAATT-TCATATATTATAGATCTTGGTATACA
1 TTAAAAATGTTGTTATATAAATAAATTGTTATATATTATAGATTTTGGTATACA
*
55385778 TTAAAAATGTTGTTATGTAAA
1 TTAAAAATGTTGTTATATAAA
55385799 CAGTTATTGT
Statistics
Matches: 108, Mismatches: 18, Indels: 18
0.75 0.12 0.12
Matches are distributed among these distances:
53 39 0.36
54 3 0.03
56 1 0.01
57 3 0.03
58 20 0.19
59 20 0.19
61 22 0.20
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.45
Consensus pattern (54 bp):
TTAAAAATGTTGTTATATAAATAAATTGTTATATATTATAGATTTTGGTATACA
Found at i:55387019 original size:30 final size:31
Alignment explanation
Indices: 55386950--55387024 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
55386940 AATCATCGAC
*
55386950 TAATGAAAAGGGATAGCTTCAGCTATCAAAA
1 TAATGAAAAGGGATAGCCTCAGCTATCAAAA
55386981 TAATGAAAAGGGATAGCCTCAGCTATC-AAA
1 TAATGAAAAGGGATAGCCTCAGCTATCAAAA
* *
55387011 TTATGAAAAAGGAT
1 TAATGAAAAGGGAT
55387025 GGTGATGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 15 0.37
31 26 0.63
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (31 bp):
TAATGAAAAGGGATAGCCTCAGCTATCAAAA
Found at i:55387105 original size:87 final size:89
Alignment explanation
Indices: 55386982--55387170 Score: 235
Period size: 87 Copynumber: 2.1 Consensus size: 89
55386972 CTATCAAAAT
* * *
55386982 AATGAAAAGGGATAGCCTCAGCTATCAAATTATGAAAAAGGAT-GGTGATG-AA-TCAATAATGA
1 AATGAAAAGGGATAGCCTCAGCTATCAAATTATGAAAAAGGATAGCTGAGGCAATTAAATAATGA
55387044 AAAGGGATGGTGACGACC-ATCGAAC
66 AAAGGGATGGTGACGACCAAT--AAC
* * * ** *
55387069 AATGAAAAGGGATAGCTTC-GACTATCGAATTGTGAAAAAGGATAGCTTCGGCAATTAAATTATG
1 AATGAAAAGGGATAGCCTCAG-CTATCAAATTATGAAAAAGGATAGCTGAGGCAATTAAATAATG
55387133 AAAAGGGATGGTGACGACCAATAAC
65 AAAAGGGATGGTGACGACCAATAAC
55387158 AATGAAAAGGGAT
1 AATGAAAAGGGAT
55387171 GGTGACAACC
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
86 1 0.01
87 38 0.43
88 3 0.03
89 18 0.20
90 26 0.30
91 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (89 bp):
AATGAAAAGGGATAGCCTCAGCTATCAAATTATGAAAAAGGATAGCTGAGGCAATTAAATAATGA
AAAGGGATGGTGACGACCAATAAC
Found at i:55387162 original size:29 final size:29
Alignment explanation
Indices: 55387130--55387200 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
55387120 CAATTAAATT
*
55387130 ATGAAAAGGGATGGTGACGACCA-ATAACA
1 ATGAAAAGGGATGGTGACAACCATA-AACA
*
55387159 ATGAAAAGGGATGGTGACAACCATCAAATA
1 ATGAAAAGGGATGGTGACAACCAT-AAACA
55387189 ATGAAAAGGGAT
1 ATGAAAAGGGAT
55387201 AGCTTCGGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 22 0.58
30 15 0.39
31 1 0.03
ACGTcount: A:0.46, C:0.11, G:0.27, T:0.15
Consensus pattern (29 bp):
ATGAAAAGGGATGGTGACAACCATAAACA
Found at i:55387201 original size:89 final size:89
Alignment explanation
Indices: 55387040--55387209 Score: 227
Period size: 89 Copynumber: 1.9 Consensus size: 89
55387030 TGAATCAATA
* * * * **
55387040 ATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATAGCTTCGACTATCGAATTGTGAA
1 ATGAAAAGGGATGGTGACGACCATC-AACAATGAAAAGGGATAGCTACAACCATCAAATAATGAA
55387105 AAAGGATAGCTTCGGCAATTAAATT
65 AAAGGATAGCTTCGGCAATTAAATT
*
55387130 ATGAAAAGGGATGGTGACGACCAAT-AACAATGAAAAGGGAT-GGTGACAACCATCAAATAATGA
1 ATGAAAAGGGATGGTGACGACC-ATCAACAATGAAAAGGGATAGCT-ACAACCATCAAATAATGA
*
55387193 AAAGGGATAGCTTCGGC
64 AAAAGGATAGCTTCGGC
55387210 TATCAAGCTG
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
88 2 0.03
89 44 0.63
90 22 0.31
91 2 0.03
ACGTcount: A:0.41, C:0.14, G:0.26, T:0.19
Consensus pattern (89 bp):
ATGAAAAGGGATGGTGACGACCATCAACAATGAAAAGGGATAGCTACAACCATCAAATAATGAAA
AAGGATAGCTTCGGCAATTAAATT
Found at i:55387215 original size:30 final size:30
Alignment explanation
Indices: 55386950--55387215 Score: 125
Period size: 30 Copynumber: 9.0 Consensus size: 30
55386940 AATCATCGAC
*
55386950 TAATGAAAAGGGATAGCTTCAGCTATCAAAA
1 TAATGAAAAGGGATAGCTTCGGCTATC-AAA
* *
55386981 TAATGAAAAGGGATAGCCTCAGCTATCAAA
1 TAATGAAAAGGGATAGCTTCGGCTATCAAA
* * * *** *
55387011 TTATGAAAAAGGAT-GGTGATG-AATC-AA
1 TAATGAAAAGGGATAGCTTCGGCTATCAAA
* * * * *
55387038 TAATGAAAAGGGAT-GGTGACGACCATCGAA
1 TAATGAAAAGGGATAGCT-TCGGCTATCAAA
* * *
55387068 CAATGAAAAGGGATAGCTTCGACTATCGAA
1 TAATGAAAAGGGATAGCTTCGGCTATCAAA
** * * *
55387098 TTGTGAAAAAGGATAGCTTCGGCAATTAAA
1 TAATGAAAAGGGATAGCTTCGGCTATCAAA
* * * * *
55387128 TTATGAAAAGGGAT-G-GT-GACGACCAATAA
1 TAATGAAAAGGGATAGCTTCGGCTATC-A-AA
* * * ** *
55387157 CAATGAAAAGGGAT-GGTGACAACCATCAAA
1 TAATGAAAAGGGATAGCT-TCGGCTATCAAA
55387187 TAATGAAAAGGGATAGCTTCGGCTATCAA
1 TAATGAAAAGGGATAGCTTCGGCTATCAA
55387216 GCTGTGAGAA
Statistics
Matches: 177, Mismatches: 48, Indels: 21
0.72 0.20 0.09
Matches are distributed among these distances:
27 20 0.11
28 5 0.03
29 21 0.12
30 96 0.54
31 31 0.18
32 4 0.02
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (30 bp):
TAATGAAAAGGGATAGCTTCGGCTATCAAA
Found at i:55387228 original size:89 final size:89
Alignment explanation
Indices: 55386982--55387230 Score: 215
Period size: 89 Copynumber: 2.8 Consensus size: 89
55386972 CTATCAAAAT
* * * * ***
55386982 AATGAAAAGGGATAGCCT-CAGCTATCAAATTATGAAAAAGGAT-GGTGATG-AATC-AA-TAAT
1 AATGAAAAGGGATAG-CTACAACCATCAAATAATGAAAAAGGATAGCTTCGGCAATCAAACT-AT
55387042 GAAAAGGGATGGTGACGACCATCGAAC
64 GAAAAGGGATGGTGACGACCATC-AAC
* * * * ** * *
55387069 AATGAAAAGGGATAGCTTCGACTATCGAATTGTGAAAAAGGATAGCTTCGGCAATTAAATTATGA
1 AATGAAAAGGGATAGCTACAACCATCAAATAATGAAAAAGGATAGCTTCGGCAATCAAACTATGA
55387134 AAAGGGATGGTGACGACCAAT-AAC
66 AAAGGGATGGTGACGACC-ATCAAC
* * * * *
55387158 AATGAAAAGGGAT-GGTGACAACCATCAAATAATGAAAAGGGATAGCTTCGGCTATCAAGCTGTG
1 AATGAAAAGGGATAGCT-ACAACCATCAAATAATGAAAAAGGATAGCTTCGGCAATCAAACTATG
*
55387222 AGAAGGGAT
65 AAAAGGGAT
55387231 AACTTTATCT
Statistics
Matches: 132, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
86 2 0.02
87 36 0.27
88 5 0.04
89 62 0.47
90 24 0.18
91 3 0.02
ACGTcount: A:0.41, C:0.12, G:0.26, T:0.20
Consensus pattern (89 bp):
AATGAAAAGGGATAGCTACAACCATCAAATAATGAAAAAGGATAGCTTCGGCAATCAAACTATGA
AAAGGGATGGTGACGACCATCAAC
Found at i:55387252 original size:119 final size:116
Alignment explanation
Indices: 55386950--55387258 Score: 341
Period size: 119 Copynumber: 2.6 Consensus size: 116
55386940 AATCATCGAC
* * *
55386950 TAATGAAAAGGGATAGCTTCAGCTATCAAAATAATGAAAAGGGATAGCCTCAGCTATCAAATTAT
1 TAATGAAAAGGGATAGCTTCGGCTATC-AAAT-GTGAAAAGGGATAGCTTCAGCTATCAAATTAT
* * * *
55387015 GAAAAAGGATGGTGATGAATCAATAATGAAAAGGGATGGTGACGACCATCGAA
64 GAAAAAGGATGGTGACGAATCAACAATGAAAAGGGATGGTGACAACCATCAAA
* * * * * * *
55387068 CAATGAAAAGGGATAGCTTCGACTATCGAATTGTGAAAAAGGATAGCTTCGGCAATTAAATTATG
1 TAATGAAAAGGGATAGCTTCGGCTATC-AAATGTGAAAAGGGATAGCTTCAGCTATCAAATTATG
*
55387133 AAAAGGGATGGTGACGACCAAT-AACAATGAAAAGGGATGGTGACAACCATCAAA
65 AAAAAGGATGGTGACG---AATCAACAATGAAAAGGGATGGTGACAACCATCAAA
* * * * * * **
55387187 TAATGAAAAGGGATAGCTTCGGCTATCAAGCTGTGAGAAGGGATAACTTTATCTATCGAGCTATG
1 TAATGAAAAGGGATAGCTTCGGCTATCAA-ATGTGAAAAGGGATAGCTTCAGCTATCAAATTATG
55387252 AAAAAGG
65 AAAAAGG
55387259 TTGGGACAGC
Statistics
Matches: 156, Mismatches: 31, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
117 41 0.26
118 29 0.19
119 83 0.53
120 3 0.02
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.22
Consensus pattern (116 bp):
TAATGAAAAGGGATAGCTTCGGCTATCAAATGTGAAAAGGGATAGCTTCAGCTATCAAATTATGA
AAAAGGATGGTGACGAATCAACAATGAAAAGGGATGGTGACAACCATCAAA
Found at i:55389286 original size:15 final size:15
Alignment explanation
Indices: 55389261--55389297 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
55389251 ACTAAACTTT
55389261 AAATGATTTGTCTTGG
1 AAAT-ATTTGTCTTGG
55389277 AAATATTTGTCTTGG
1 AAATATTTGTCTTGG
55389292 AAATAT
1 AAATAT
55389298 ACATGTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.43
Consensus pattern (15 bp):
AAATATTTGTCTTGG
Found at i:55394837 original size:13 final size:13
Alignment explanation
Indices: 55394819--55394844 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55394809 TTTAGTCCTG
55394819 ACCCCTTTCTAAA
1 ACCCCTTTCTAAA
55394832 ACCCCTTTCTAAA
1 ACCCCTTTCTAAA
55394845 GCATGTTTAA
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:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (13 bp):
ACCCCTTTCTAAA
Found at i:55401800 original size:18 final size:18
Alignment explanation
Indices: 55401750--55401791 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
55401740 ATCTTAAAAG
55401750 ATAAAATAAATTAAT-AACT
1 ATAAAATAAA--AATAAACT
55401769 ATAAAATAAAAATAAACT
1 ATAAAATAAAAATAAACT
55401787 ATAAA
1 ATAAA
55401792 CTTAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 9 0.41
19 10 0.45
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAAAATAAAAATAAACT
Found at i:55401810 original size:25 final size:25
Alignment explanation
Indices: 55401731--55401803 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 25
55401721 TCGACTTCAT
*
55401731 AACTATAAAATCTTAAAAGATAAAATA
1 AACTAT-AAA-CTTAAAATATAAAATA
*
55401758 AATTA-ATAACTATAAAATA-AAAATA
1 AACTATA-AACT-TAAAATATAAAATA
55401783 AACTATAAACTTAAAATATAA
1 AACTATAAACTTAAAATATAA
55401804 TAAAAACGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
24 7 0.18
25 19 0.49
26 9 0.23
27 4 0.10
ACGTcount: A:0.64, C:0.07, G:0.01, T:0.27
Consensus pattern (25 bp):
AACTATAAACTTAAAATATAAAATA
Found at i:55419312 original size:18 final size:18
Alignment explanation
Indices: 55419289--55419330 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
55419279 ACCTGTATAA
55419289 AGCCAACATTGGCTTCTT
1 AGCCAACATTGGCTTCTT
55419307 AGCCAACATTGGCTTCTT
1 AGCCAACATTGGCTTCTT
*
55419325 GGCCAA
1 AGCCAA
55419331 GTTTTGTGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (18 bp):
AGCCAACATTGGCTTCTT
Found at i:55422523 original size:48 final size:47
Alignment explanation
Indices: 55422297--55422570 Score: 286
Period size: 48 Copynumber: 5.7 Consensus size: 47
55422287 TGATATGTGT
*
55422297 GCTAGTGTAAGACCATGTCTGGGACATGGCATCCGCCACATTATGAGA
1 GCTAGTGTAAGACCATGTCTGGAACATGGCAT-CGCCACATTATGAGA
* * *
55422345 GCCAGTGTAAGACCATGTTTGGAACATGGCATTAGCCACATTATGAGA
1 GCTAGTGTAAGACCATGTCTGGAACATGGCA-TCGCCACATTATGAGA
* *
55422393 GCTAGTGTAAGACCATGTTTGGAACATGACATCGACCACATTATGAGA
1 GCTAGTGTAAGACCATGTCTGGAACATGGCATCG-CCACATTATGAGA
* * * * * *
55422441 GCCAGTGTAAAACCATGTCTAGAACATGGCATCGGCATCGA-GACGAGA
1 GCTAGTGTAAGACCATGTCTGGAACATGGCATCGCCA-C-ATTATGAGA
* * * *
55422489 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGC-C-TTGACATGTGA
1 GCTAGTGTAAGACCATGTCTGGAACATGGCATCGCCACATT---ATGAGA
*
55422537 GCTAGTGTAAGACAATGTCTAGG-ACATGGCATCG
1 GCTAGTGTAAGACCATGTCT-GGAACATGGCATCG
55422571 GCAGTTTACC
Statistics
Matches: 192, Mismatches: 25, Indels: 18
0.82 0.11 0.08
Matches are distributed among these distances:
46 1 0.01
47 4 0.02
48 183 0.95
49 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (47 bp):
GCTAGTGTAAGACCATGTCTGGAACATGGCATCGCCACATTATGAGA
Found at i:55422544 original size:96 final size:95
Alignment explanation
Indices: 55422297--55422573 Score: 333
Period size: 96 Copynumber: 2.9 Consensus size: 95
55422287 TGATATGTGT
* *
55422297 GCTAGTGTAAGACCATGTCTGGGACATGGCATCCGCCACATTATGAGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATG
* * * * * *
55422362 TTTGGAACATGGCATTAGCCACATTATGAGA
66 TCTAGAACATGGCA-TCGGCACATGACGAGA
* * * *
55422393 GCTAGTGTAAGACCATGTTTGGAACATGACATCGACCACATTATGAGAGCCAGTGTAAAACCATG
1 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATG
55422458 TCTAGAACATGGCATCGGCATCGA-GACGAGA
66 TCTAGAACATGGCATCGGCA-C-ATGACGAGA
** * * * *
55422489 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTTGA-CATGTGAGCTAGTGTAAGACAAT
1 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCC-ACATTATGAGAGCCAGTGTAAGACCAT
*
55422553 GTCTAGGACATGGCATCGGCA
65 GTCTAGAACATGGCATCGGCA
55422574 GTTTACCCTC
Statistics
Matches: 155, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
95 4 0.03
96 149 0.96
97 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (95 bp):
GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATG
TCTAGAACATGGCATCGGCACATGACGAGA
Found at i:55430496 original size:45 final size:45
Alignment explanation
Indices: 55430432--55430605 Score: 219
Period size: 45 Copynumber: 3.8 Consensus size: 45
55430422 TGTAACCCGC
* *
55430432 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCAT
*
55430477 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A--T
* * *
55430523 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCAT
55430570 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
55430606 ATGCTCAACC
Statistics
Matches: 110, Mismatches: 10, Indels: 17
0.80 0.07 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 37 0.34
46 31 0.28
47 31 0.28
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCAT
Found at i:55430598 original size:93 final size:92
Alignment explanation
Indices: 55430440--55430609 Score: 313
Period size: 93 Copynumber: 1.8 Consensus size: 92
55430430 GCCCATAAGT
*
55430440 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
55430505 GAGTTCGGATGCCTAGTTACATTTCAC
66 GAGTTCGGATGCCTAGTTACATTTCAC
*
55430532 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
55430597 CGAGTTCGGATGC
65 CGAGTTCGGATGC
55430610 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 27 0.36
93 48 0.64
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATTTCAC
Found at i:55436797 original size:20 final size:20
Alignment explanation
Indices: 55436757--55436810 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
55436747 AGATTTGCAT
* * *
55436757 TTCGGTGCCCTTGTTTGCAC
1 TTCGGTGCCCCTGTATACAC
55436777 TTCGGTGCCCCTGTATACAC
1 TTCGGTGCCCCTGTATACAC
*
55436797 TTCGGTGTCCCTGT
1 TTCGGTGCCCCTGT
55436811 TCTCACTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.07, C:0.31, G:0.24, T:0.37
Consensus pattern (20 bp):
TTCGGTGCCCCTGTATACAC
Found at i:55436817 original size:20 final size:18
Alignment explanation
Indices: 55436757--55436817 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 18
55436747 AGATTTGCAT
55436757 TTCGGTGCCCTTGTTTGCAC
1 TTCGGTGCCC-TGTTT-CAC
*
55436777 TTCGGTGCCCCTGTATACAC
1 TTCGGTG-CCCTGT-TTCAC
55436797 TTCGGTGTCCCTGTTCTCAC
1 TTCGGTG-CCCTGTT-TCAC
55436817 T
1 T
55436818 ATAATGCCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 1 0.03
20 30 0.86
21 4 0.11
ACGTcount: A:0.08, C:0.33, G:0.21, T:0.38
Consensus pattern (18 bp):
TTCGGTGCCCTGTTTCAC
Found at i:55437021 original size:7 final size:7
Alignment explanation
Indices: 55437009--55437040 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
55436999 AACGTTAGTA
55437009 AATGTTC
1 AATGTTC
55437016 AATGTTC
1 AATGTTC
55437023 AATGTTC
1 AATGTTC
55437030 AATGTTC
1 AATGTTC
55437037 AATG
1 AATG
55437041 AATTACTTGA
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:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (7 bp):
AATGTTC
Found at i:55442225 original size:13 final size:13
Alignment explanation
Indices: 55442207--55442241 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
55442197 CCGGACACAC
55442207 GCCCGTGTCAATG
1 GCCCGTGTCAATG
55442220 GCCCGTGTCAATG
1 GCCCGTGTCAATG
55442233 GCCCGTGTC
1 GCCCGTGTC
55442242 CTTCACACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.11, C:0.34, G:0.31, T:0.23
Consensus pattern (13 bp):
GCCCGTGTCAATG
Found at i:55443307 original size:45 final size:46
Alignment explanation
Indices: 55443256--55443373 Score: 143
Period size: 46 Copynumber: 2.6 Consensus size: 46
55443246 CGTGCCAACG
*
55443256 GCATGTCCCAGACATGGTCTTACACTGACACAT-T-TCGTA-GCCGAT
1 GCATGTCCCAGACAT-GTCTTACACTGACACATGTCCCG-AGGCCGAT
* **
55443301 GCATGTCCCAGACATGTCTTACACTGGCTTATGTCCCGAGGCCGAT
1 GCATGTCCCAGACATGTCTTACACTGACACATGTCCCGAGGCCGAT
*
55443347 GCATGTCCCAAACATAGTCTTACACTG
1 GCATGTCCCAGACAT-GTCTTACACTG
55443374 GCTCTCATAA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
44 14 0.22
45 17 0.27
46 22 0.34
47 11 0.17
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (46 bp):
GCATGTCCCAGACATGTCTTACACTGACACATGTCCCGAGGCCGAT
Found at i:55443393 original size:47 final size:44
Alignment explanation
Indices: 55443256--55443418 Score: 159
Period size: 47 Copynumber: 3.6 Consensus size: 44
55443246 CGTGCCAACG
* ** *
55443256 GCATGTCCCAGACATGGTCTTACACTGACACATTTCGTA-GCCGAT
1 GCATGTCCCAGACAT-GTCTTACACTGGCTTATATCG-AGGCCGAT
*
55443301 GCATGTCCCAGACATGTCTTACACTGGCTTATGTCCCGAGGCCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTTATAT--CGAGGCCGAT
* * *
55443347 GCATGTCCCAAACATAGTCTTACACTGGCTCTCATAAT-GCGTCCGAT
1 GCATGTCCCAGACAT-GTCTTACACTGGCT-T-AT-ATCGAGGCCGAT
*
55443394 GTATGTCCCAGACATGTCTTACACT
1 GCATGTCCCAGACATGTCTTACACT
55443419 AGCCCACAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 13
0.81 0.08 0.10
Matches are distributed among these distances:
44 15 0.15
45 16 0.16
46 32 0.32
47 34 0.34
48 1 0.01
49 2 0.02
50 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (44 bp):
GCATGTCCCAGACATGTCTTACACTGGCTTATATCGAGGCCGAT
Found at i:55446630 original size:18 final size:19
Alignment explanation
Indices: 55446599--55446635 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
55446589 CCTTATTTTG
55446599 GAACTTACTAAGTT-CTTT
1 GAACTTACTAAGTTACTTT
55446617 GAACTTACCT-AGTTACTTT
1 GAACTTA-CTAAGTTACTTT
55446636 CCATTCTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (19 bp):
GAACTTACTAAGTTACTTT
Found at i:55448358 original size:32 final size:32
Alignment explanation
Indices: 55448321--55448385 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
55448311 CTAAGCACTT
55448321 TGAAAATAATTTTAAGAGCTTATATCAATTTA
1 TGAAAATAATTTTAAGAGCTTATATCAATTTA
55448353 TGAAAATAATTTTAAGAGCTTATATCAATTTA
1 TGAAAATAATTTTAAGAGCTTATATCAATTTA
55448385 T
1 T
55448386 TGCAAATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (32 bp):
TGAAAATAATTTTAAGAGCTTATATCAATTTA
Found at i:55449519 original size:19 final size:19
Alignment explanation
Indices: 55449495--55449532 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
55449485 TTCAAATTCA
55449495 AAAAGTTAAGGG-ACTAAAT
1 AAAAG-TAAGGGAACTAAAT
*
55449514 AAAAGTATGGGAACTAAAT
1 AAAAGTAAGGGAACTAAAT
55449533 TCTATAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AAAAGTAAGGGAACTAAAT
Found at i:55460724 original size:30 final size:30
Alignment explanation
Indices: 55460690--55460748 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
55460680 AAGGAATGAG
55460690 ATGAAGAGAGAGATCAACATTGAGGTTGAT
1 ATGAAGAGAGAGATCAACATTGAGGTTGAT
55460720 ATGAAGAGAGAGATCAACATTGAGGTTGA
1 ATGAAGAGAGAGATCAACATTGAGGTTGA
55460749 GGTGAATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.31, T:0.22
Consensus pattern (30 bp):
ATGAAGAGAGAGATCAACATTGAGGTTGAT
Found at i:55469342 original size:24 final size:24
Alignment explanation
Indices: 55469315--55469362 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
55469305 TTGTTCTGTA
55469315 TAAATTATATGCGAAATTTGAGTT
1 TAAATTATATGCGAAATTTGAGTT
* ***
55469339 TAAATTTTATTTTAAATTTGAGTT
1 TAAATTATATGCGAAATTTGAGTT
55469363 CATATTTGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (24 bp):
TAAATTATATGCGAAATTTGAGTT
Found at i:55469343 original size:12 final size:12
Alignment explanation
Indices: 55469328--55469362 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
55469318 ATTATATGCG
55469328 AAATTTGAGTTT
1 AAATTTGAGTTT
* *
55469340 AAATTTTATTTT
1 AAATTTGAGTTT
55469352 AAATTTGAGTT
1 AAATTTGAGTT
55469363 CATATTTGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (12 bp):
AAATTTGAGTTT
Found at i:55469369 original size:24 final size:25
Alignment explanation
Indices: 55469328--55469378 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
55469318 ATTATATGCG
*
55469328 AAATTTGAGTTTAAATTT-TATTTT
1 AAATTTGAGTTCAAATTTATATTTT
*
55469352 AAATTTGAGTTCATATTTGATATTTT
1 AAATTTGAGTTCAAATTT-ATATTTT
55469378 A
1 A
55469379 TGTGTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
26 7 0.30
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (25 bp):
AAATTTGAGTTCAAATTTATATTTT
Found at i:55472258 original size:34 final size:34
Alignment explanation
Indices: 55472213--55472288 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
55472203 AGGCTGTATA
*
55472213 ACACACTGACTTGATATACCAAAATTAACAAGTG
1 ACACACGGACTTGATATACCAAAATTAACAAGTG
55472247 ACACACGGACTTGATATACCAAAATTAACAAGTG
1 ACACACGGACTTGATATACCAAAATTAACAAGTG
55472281 ACACACGG
1 ACACACGG
55472289 CCGTGCGACA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.20
Consensus pattern (34 bp):
ACACACGGACTTGATATACCAAAATTAACAAGTG
Found at i:55474399 original size:21 final size:21
Alignment explanation
Indices: 55474344--55474393 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
55474334 ATGGTCCAAG
55474344 GGACACGCCAGTGTGACCCTA
1 GGACACGCCAGTGTGACCCTA
55474365 GGACACGCCAGTGTGACCCTA
1 GGACACGCCAGTGTGACCCTA
55474386 GGACACGC
1 GGACACGC
55474394 TCGTGTTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.34, G:0.30, T:0.12
Consensus pattern (21 bp):
GGACACGCCAGTGTGACCCTA
Found at i:55487196 original size:35 final size:35
Alignment explanation
Indices: 55487150--55487220 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
55487140 ATTGGCTTGG
55487150 AAAATAGCATTAAATTTTTCAACACGGGTAGACAC
1 AAAATAGCATTAAATTTTTCAACACGGGTAGACAC
55487185 AAAATAGCATTAAATTTTTCAACACGGGTAGACAC
1 AAAATAGCATTAAATTTTTCAACACGGGTAGACAC
55487220 A
1 A
55487221 CAAGCGTGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (35 bp):
AAAATAGCATTAAATTTTTCAACACGGGTAGACAC
Found at i:55488585 original size:46 final size:44
Alignment explanation
Indices: 55488518--55488635 Score: 148
Period size: 46 Copynumber: 2.6 Consensus size: 44
55488508 TGTGTGCTAG
55488518 TGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCGG-CTACGAGATGT--GCCAA
* * * *
55488564 TGTAAGACATGTATGGGACATGCATCGGTTACGAGATGTGTCAG
1 TGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGCCAA
55488608 TGTAAGACCATGTCTGGGACATGGCATC
1 TGTAAGA-CATGTCTGGGACAT-GCATC
55488636 AGGACGTATA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
44 10 0.16
45 14 0.22
46 40 0.62
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.25
Consensus pattern (44 bp):
TGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGCCAA
Found at i:55488662 original size:48 final size:47
Alignment explanation
Indices: 55488606--55488779 Score: 165
Period size: 47 Copynumber: 3.6 Consensus size: 47
55488596 GAGATGTGTC
* *
55488606 AGTGTAAGACCATGTCTGGGACATGGCATCAGGACGTATAGAGGTG-T
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GGACATATAGAGGAGCT
* * * *
55488653 CAGTGTAAGACCATTTTTGTGG-CATGGCATCGGCACAAATATGTGAGAGCT
1 -AGTGTAAGACCATGTCTG-GGACATGGCATCGG-ACATATA-GAG-GAGCT
* * * * *
55488704 AGTGTAAGACTATGTCTAGGACATGGCATC-GACTTGATGGATGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGACAT-ATAGAGGAGCT
55488751 AGTGTAAGACCATGTCTGGGACATGGCAT
1 AGTGTAAGACCATGTCTGGGACATGGCAT
55488780 AGGCATTGTA
Statistics
Matches: 102, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
47 34 0.33
48 33 0.32
49 9 0.09
50 25 0.25
51 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGACATATAGAGGAGCT
Found at i:55490501 original size:20 final size:20
Alignment explanation
Indices: 55490476--55490514 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
55490466 CGGACTTAGG
55490476 ACACGGGCGTGTCCCAAGCT
1 ACACGGGCGTGTCCCAAGCT
55490496 ACACGGGCGTGTCCCAAGC
1 ACACGGGCGTGTCCCAAGC
55490515 CCCACGGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.36, G:0.31, T:0.13
Consensus pattern (20 bp):
ACACGGGCGTGTCCCAAGCT
Found at i:55490520 original size:20 final size:20
Alignment explanation
Indices: 55490476--55490521 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
55490466 CGGACTTAGG
*
55490476 ACACGGGCGTGTCCCAAGCT
1 ACACGGGCGTGTCCCAAGCC
55490496 ACACGGGCGTGTCCCAAGCC
1 ACACGGGCGTGTCCCAAGCC
*
55490516 CCACGG
1 ACACGG
55490522 CCTACCCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.39, G:0.30, T:0.11
Consensus pattern (20 bp):
ACACGGGCGTGTCCCAAGCC
Found at i:55491545 original size:28 final size:26
Alignment explanation
Indices: 55491514--55491565 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
55491504 TAGAATTGGG
55491514 TTGAGAAGATTATTTAATTGGAAATATA
1 TTGAGAAGATTATTT--TTGGAAATATA
* *
55491542 TTGAGATGTTTATTTTTGGAAATA
1 TTGAGAAGATTATTTTTGGAAATA
55491566 CAAAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
28 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (26 bp):
TTGAGAAGATTATTTTTGGAAATATA
Found at i:55492126 original size:125 final size:125
Alignment explanation
Indices: 55491904--55492150 Score: 388
Period size: 125 Copynumber: 2.0 Consensus size: 125
55491894 TCGAAGTATC
* *
55491904 GTGTTTAGAGCAAGTTCTGAGTGGGTAAGGTATTAACTATGACTAAGAATGTAAGTCCGCAAGTG
1 GTGTTTAGAGCAAGTTCTGAATGGGTAACGTATTAACTATGACTAAGAATGTAAGTCCGCAAGTG
* *
55491969 TGCCTTTTAGCGGAGTCTACATTAGGCGAGCTTGATGGTTTGGTGGACTCCCTTGTAATA
66 CGCCTTTTAGCGAAGTCTACATTAGGCGAGCTTGATGGTTTGGTGGACTCCCTTGTAATA
* * *
55492029 GTGTTTAGAGCAAGTTCTGAATGGGTAACGTATTAACTGTGACTAAGATTGTAAGTCTGCAAGTG
1 GTGTTTAGAGCAAGTTCTGAATGGGTAACGTATTAACTATGACTAAGAATGTAAGTCCGCAAGTG
* * *
55492094 CG-CTTTTCGATGAAGTCTACATTAGGCGAGCTTGGTGGTTTGGTGGACTCCCTTGTA
66 CGCCTTTTAG-CGAAGTCTACATTAGGCGAGCTTGATGGTTTGGTGGACTCCCTTGTA
55492151 GAGTATACGC
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
124 6 0.05
125 105 0.95
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.33
Consensus pattern (125 bp):
GTGTTTAGAGCAAGTTCTGAATGGGTAACGTATTAACTATGACTAAGAATGTAAGTCCGCAAGTG
CGCCTTTTAGCGAAGTCTACATTAGGCGAGCTTGATGGTTTGGTGGACTCCCTTGTAATA
Found at i:55503032 original size:15 final size:16
Alignment explanation
Indices: 55503012--55503041 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55503002 GGTTTAAGCC
55503012 AGATAA-GATTTTAAA
1 AGATAATGATTTTAAA
55503027 AGATAATGATTTTAA
1 AGATAATGATTTTAA
55503042 GGTAGTGTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (16 bp):
AGATAATGATTTTAAA
Found at i:55509694 original size:58 final size:57
Alignment explanation
Indices: 55509557--55509695 Score: 158
Period size: 57 Copynumber: 2.4 Consensus size: 57
55509547 TGTACTACAA
* * * *
55509557 GATTACCAGTCCAGGCTAAATCCTCTATGTAACGTATGCTCAGAAGAGCTCAATTAG
1 GATTACCAGTCCAGGCTAAATCCTATATGTAACATATGCTCAGAAGAGATCAATCAG
* * *
55509614 GATTACCAGTCTAGGCTAAATCCTA-ATTGTAACATATGCTC-GAGAGGGATTACATCAG
1 GATTACCAGTCCAGGCTAAATCCTATA-TGTAACATATGCTCAGA-AGAGATCA-ATCAG
55509672 GATTACCCA-TCCAGGCTAAATCCT
1 GATTA-CCAGTCCAGGCTAAATCCT
55509696 TTCTATAACA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
56 3 0.04
57 41 0.59
58 23 0.33
59 3 0.04
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (57 bp):
GATTACCAGTCCAGGCTAAATCCTATATGTAACATATGCTCAGAAGAGATCAATCAG
Found at i:55530435 original size:75 final size:75
Alignment explanation
Indices: 55530243--55530445 Score: 246
Period size: 75 Copynumber: 2.7 Consensus size: 75
55530233 AGCCAAATCG
* * * * *
55530243 AGCCTTTG-AGACGAGTAATCTGTAAAGCCTTTTTGGTGAATTATCTTAAAGGCCTTTATGGCGT
1 AGCCTTTGTAG-CGAGTAATTTGTAAAGCCTTTATGGTGAATTATCTGAATGGCCTTTATGGCAT
55530307 ATTATTCGGAA
65 ATTATTCGGAA
* * ** * **
55530318 AGCCTTTGTAGTGGGTAATTTGTAAAATCTTTACGGCAAATTATCTGAATGGCCTTTATGGCATA
1 AGCCTTTGTAGCGAGTAATTTGTAAAGCCTTTATGGTGAATTATCTGAATGGCCTTTATGGCATA
* *
55530383 TTATTTGGGA
66 TTATTCGGAA
* *
55530393 AGCCTTTGTAGCGAGTAATTTGTAAAGCCTTTGTGGTGAATTATTTGAATGGC
1 AGCCTTTGTAGCGAGTAATTTGTAAAGCCTTTATGGTGAATTATCTGAATGGC
55530446 ATTTGTAGTG
Statistics
Matches: 104, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
75 102 0.98
76 2 0.02
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (75 bp):
AGCCTTTGTAGCGAGTAATTTGTAAAGCCTTTATGGTGAATTATCTGAATGGCCTTTATGGCATA
TTATTCGGAA
Found at i:55530438 original size:25 final size:25
Alignment explanation
Indices: 55530263--55530439 Score: 72
Period size: 25 Copynumber: 7.1 Consensus size: 25
55530253 ACGAGTAATC
* * *
55530263 TGTAAAGCCTTTTTGGTGAATTATC
1 TGTAAAGCCTTTATGGCGAATTATT
*
55530288 T-TAAAGGCCTTTATGGCGTATTATT
1 TGTAAA-GCCTTTATGGCGAATTATT
* * * * * ** *
55530313 CGGAAAGCCTTTGTAGTGGGTAATT
1 TGTAAAGCCTTTATGGCGAATTATT
** * * *
55530338 TGTAAAATCTTTACGGCAAATTATC
1 TGTAAAGCCTTTATGGCGAATTATT
*
55530363 TG-AATGGCCTTTATGGC-ATATTATT
1 TGTAA-AGCCTTTATGGCGA-ATTATT
** * * * *
55530388 TGGGAAGCCTTTGTAGCGAGTAATT
1 TGTAAAGCCTTTATGGCGAATTATT
* *
55530413 TGTAAAGCCTTTGTGGTGAATTATT
1 TGTAAAGCCTTTATGGCGAATTATT
55530438 TG
1 TG
55530440 AATGGCATTT
Statistics
Matches: 104, Mismatches: 42, Indels: 12
0.66 0.27 0.08
Matches are distributed among these distances:
24 7 0.07
25 92 0.88
26 5 0.05
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (25 bp):
TGTAAAGCCTTTATGGCGAATTATT
Found at i:55530460 original size:75 final size:75
Alignment explanation
Indices: 55530243--55530625 Score: 245
Period size: 75 Copynumber: 5.1 Consensus size: 75
55530233 AGCCAAATCG
* * *
55530243 AGCCTTTG-AGACGAGTAATCTGTAAAGCCTTTTTGGTGAATTATCTT-AAAGGCCTTTATGGCG
1 AGCCTTTGTAG-CGAGTAATTTGTAAAGCCTTTATGGTGAATTAT-TTGAATGGCCTTTATGGCG
55530306 TATTATTCGGAA
64 TATTATTCGGAA
* * ** * ** * *
55530318 AGCCTTTGTAGTGGGTAATTTGTAAAATCTTTACGGCAAATTATCTGAATGGCCTTTATGGCATA
1 AGCCTTTGTAGCGAGTAATTTGTAAAGCCTTTATGGTGAATTATTTGAATGGCCTTTATGGCGTA
* *
55530383 TTATTTGGGA
66 TTATTCGGAA
* * * * *
55530393 AGCCTTTGTAGCGAGTAATTTGTAAAGCCTTTGTGGTGAATTATTTGAATGGCATTTGTAGTGTA
1 AGCCTTTGTAGCGAGTAATTTGTAAAGCCTTTATGGTGAATTATTTGAATGGCCTTTATGGCGTA
*
55530458 TTATTCAGAA
66 TTATTCGGAA
* * * * ** * ** * ** * **
55530468 AGCATTAGTAGTGAAGTTACCTATAAAG-CTTTAGTGGCAAATTATCTGAAAAGCC-TAAGTGAT
1 AGCCTTTGTAGCG-AGTAATTTGTAAAGCCTTTA-TGGTGAATTATTTGAATGGCCTTTA-TGGC
**
55530531 GTATTATTCAAAA
63 GTATTATTCGGAA
* * * * * * * * *
55530544 AGCCTTAGT-GACAAAGTTATATGTAAAGCCTTTGTGGCGAATTATCTGAAAGGCCTATATGGCG
1 AGCCTTTGTAG-C-GAGTAATTTGTAAAGCCTTTATGGTGAATTATTTGAATGGCCTTTATGGCG
*
55530608 TATTATTCGAAA
64 TATTATTCGGAA
55530620 AGCCTT
1 AGCCTT
55530626 AGTGGTGAAG
Statistics
Matches: 235, Mismatches: 64, Indels: 17
0.74 0.20 0.05
Matches are distributed among these distances:
74 1 0.00
75 130 0.55
76 99 0.42
77 5 0.02
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.36
Consensus pattern (75 bp):
AGCCTTTGTAGCGAGTAATTTGTAAAGCCTTTATGGTGAATTATTTGAATGGCCTTTATGGCGTA
TTATTCGGAA
Found at i:55530528 original size:25 final size:24
Alignment explanation
Indices: 55530492--55530630 Score: 91
Period size: 25 Copynumber: 5.5 Consensus size: 24
55530482 AGTTACCTAT
* *
55530492 AAAGCTTTAGTGGCAAATTATCTGA
1 AAAGCCTTAGTGGCGAATTAT-TGA
* ** * *
55530517 AAAGCCTAAGTGATGTATTATTCAA
1 AAAGCCTTAGTGGCGAATTATT-GA
* * *
55530542 AAAGCCTTAGTGACAAAGTTATATGT
1 AAAGCCTTAGTGGCGAA-TTAT-TGA
*
55530568 AAAGCCTTTGTGGCGAATTATCTGA
1 AAAGCCTTAGTGGCGAATTAT-TGA
* *
55530593 AAGGCCTATA-TGGCGTATTATTCGA
1 AAAGCCT-TAGTGGCGAATTATT-GA
55530618 AAAGCCTTAGTGG
1 AAAGCCTTAGTGG
55530631 TGAAGTCATT
Statistics
Matches: 86, Mismatches: 22, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
24 4 0.05
25 62 0.72
26 19 0.22
27 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.31
Consensus pattern (24 bp):
AAAGCCTTAGTGGCGAATTATTGA
Found at i:55530546 original size:76 final size:75
Alignment explanation
Indices: 55530454--55530636 Score: 199
Period size: 76 Copynumber: 2.4 Consensus size: 75
55530444 GCATTTGTAG
* * *
55530454 TGTATTATTCAGAAAGCATTAGTAGTGAAGTTACCTATAAAG-CTTTAGTGGCAAATTATCTGAA
1 TGTATTATTCAAAAAGCCTTAGT-GTGAAGTTACATATAAAGCCTTT-GTGGCAAATTATCTGAA
55530518 AAGCCTA-AGTGA
64 AAGCCTATA-TGA
** * * *
55530530 TGTATTATTCAAAAAGCCTTAGTGACAAAGTTATATGTAAAGCCTTTGTGGCGAATTATCTGAAA
1 TGTATTATTCAAAAAGCCTTAGTG-TGAAGTTACATATAAAGCCTTTGTGGCAAATTATCTGAAA
* *
55530595 GGCCTATATGG
65 AGCCTATATGA
* *
55530606 CGTATTATTCGAAAAGCCTTAGTGGTGAAGT
1 TGTATTATTCAAAAAGCCTTAGT-GTGAAGT
55530637 CATTTGGGAA
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
75 1 0.01
76 82 0.92
77 6 0.07
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (75 bp):
TGTATTATTCAAAAAGCCTTAGTGTGAAGTTACATATAAAGCCTTTGTGGCAAATTATCTGAAAA
GCCTATATGA
Found at i:55530655 original size:76 final size:75
Alignment explanation
Indices: 55530492--55530659 Score: 185
Period size: 76 Copynumber: 2.2 Consensus size: 75
55530482 AGTTACCTAT
* *
55530492 AAAGCTTTAGTGGCAAATTATCTGAAAAGCCTAAGTGATGTATTATTCAAAAAGCCTTAGTGACA
1 AAAGCTTT-GTGGCGAATTATCTGAAAAGCCTAAGTGACGTATTATTCAAAAAGCCTTAGTGACA
* *
55530557 AAGTTATATGT
65 AAGTCATATGG
* * * **
55530568 AAAGCCTTTGTGGCGAATTATCTGAAAGGCCTATA-TGGCGTATTATTCGAAAAGCCTTAGTGGT
1 AAAG-CTTTGTGGCGAATTATCTGAAAAGCCTA-AGTGACGTATTATTCAAAAAGCCTTAGTGAC
* *
55530632 GAAGTCATTTGG
64 AAAGTCATATGG
*
55530644 GAAGCTATTGTGGCGA
1 AAAGCT-TTGTGGCGA
55530660 GTCATCTGGA
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
75 2 0.03
76 70 0.91
77 5 0.06
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (75 bp):
AAAGCTTTGTGGCGAATTATCTGAAAAGCCTAAGTGACGTATTATTCAAAAAGCCTTAGTGACAA
AGTCATATGG
Found at i:55539854 original size:22 final size:23
Alignment explanation
Indices: 55539829--55539877 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
55539819 TCATATTTGG
55539829 AATTTAATA-ATTTCATTTA-TAT
1 AATTTAATAGA-TTCATTTATTAT
* *
55539851 AATTTTATAGATTCCTTTATTAT
1 AATTTAATAGATTCATTTATTAT
55539874 AATT
1 AATT
55539878 ATATTTAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (23 bp):
AATTTAATAGATTCATTTATTAT
Found at i:55541140 original size:23 final size:19
Alignment explanation
Indices: 55541091--55541127 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
55541081 CCCTGTTTTA
*
55541091 CCCTCTGCCTCTTCTGTTC
1 CCCTTTGCCTCTTCTGTTC
55541110 CCCTTTGCCTCTTCTGTT
1 CCCTTTGCCTCTTCTGTT
55541128 TCGCCCGATT
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:0.43, G:0.11, T:0.46
Consensus pattern (19 bp):
CCCTTTGCCTCTTCTGTTC
Found at i:55541169 original size:15 final size:15
Alignment explanation
Indices: 55541149--55541210 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
55541139 GCTCCCTCCG
* *
55541149 TTTCTTTTCTTTTCT
1 TTTCTTTGCTTTGCT
55541164 TTTCTTTGCTTTGCT
1 TTTCTTTGCTTTGCT
55541179 TTCTCCTTTGCTTT-C-
1 TT-T-CTTTGCTTTGCT
*
55541194 TTCCTTTGCTTTGCT
1 TTTCTTTGCTTTGCT
55541209 TT
1 TT
55541211 CTCCAGTCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
15 19 0.47
16 2 0.05
17 9 0.22
ACGTcount: A:0.00, C:0.24, G:0.08, T:0.68
Consensus pattern (15 bp):
TTTCTTTGCTTTGCT
Found at i:55541189 original size:12 final size:13
Alignment explanation
Indices: 55541172--55541205 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
55541162 CTTTTCTTTG
55541172 CTTTGCTTTC-TC
1 CTTTGCTTTCTTC
55541184 CTTTGCTTTCTTC
1 CTTTGCTTTCTTC
55541197 CTTTGCTTT
1 CTTTGCTTT
55541206 GCTTTCTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.00, C:0.29, G:0.09, T:0.62
Consensus pattern (13 bp):
CTTTGCTTTCTTC
Found at i:55541230 original size:31 final size:30
Alignment explanation
Indices: 55541167--55541236 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
55541157 CTTTTCTTTT
* * *
55541167 CTTTGCTTTGCTTTCTCCTTTGCTTTCTTC
1 CTTTGCTTTGCTTTCTCCGTCGCTATCTTC
55541197 CTTTGCTTTGCTTTCTCCAGTCGAC-ATCTTC
1 CTTTGCTTTGCTTTCTCC-GTCG-CTATCTTC
55541228 CTTTGCTTT
1 CTTTGCTTT
55541237 CTCCAGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 18 0.51
31 16 0.46
32 1 0.03
ACGTcount: A:0.04, C:0.30, G:0.11, T:0.54
Consensus pattern (30 bp):
CTTTGCTTTGCTTTCTCCGTCGCTATCTTC
Found at i:55543544 original size:18 final size:18
Alignment explanation
Indices: 55543498--55543545 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
55543488 TATAAGAATA
*
55543498 TTAATTATTA-ATA-ATT
1 TTAATTATAATATATATT
55543514 TT-ATTA-AATTATATATT
1 TTAATTATAA-TATATATT
55543531 TTAATTATAATATAT
1 TTAATTATAATATAT
55543546 TTAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 5 0.19
17 5 0.19
18 9 0.35
19 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATAATATATATT
Found at i:55543550 original size:15 final size:15
Alignment explanation
Indices: 55543515--55543566 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
55543505 TTAATAATTT
*
55543515 TATTAAATTAT-ATA
1 TATTTAATTATAATA
55543529 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
55543543 TATTTAATAATAAT-
1 TATTTAATTATAATA
55543557 TATGTTAATT
1 TAT-TTAATT
55543567 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:55543633 original size:66 final size:65
Alignment explanation
Indices: 55543563--55543757 Score: 182
Period size: 56 Copynumber: 3.1 Consensus size: 65
55543553 TAATTATGTT
55543563 AATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTAA
1 AATTT-TATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTAA
55543628 G
65 G
* * * * * *
55543629 AATTTTA--TTA-A--ATTATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATT-ATGTTA
1 AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTAATTTTA
*
55543683 AT
64 AG
* *
55543685 T--TATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAA
1 AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATT-TTAA
55543748 G
65 G
55543749 AATTTTATT
1 AATTTTATT
55543758 AAATTATATA
Statistics
Matches: 95, Mismatches: 18, Indels: 32
0.66 0.12 0.22
Matches are distributed among these distances:
54 3 0.03
56 20 0.21
57 6 0.06
58 1 0.01
59 13 0.14
60 13 0.14
61 1 0.01
62 6 0.06
63 16 0.17
64 4 0.04
65 2 0.02
66 10 0.11
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (65 bp):
AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTAAG
Found at i:55543663 original size:119 final size:120
Alignment explanation
Indices: 55543481--55543801 Score: 619
Period size: 119 Copynumber: 2.7 Consensus size: 120
55543471 ATTGTTTTAT
*
55543481 TAAATT-ATATAAGAATATTAATTATTAATAATTTTATTAAATTATATATTTTAATTATAATATA
1 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
55543545 TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
66 TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
55543600 TAAATTCATATAAGAATATTAATT-TTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
1 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
55543664 TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
66 TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
55543719 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
1 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
55543784 TTTAATAATAATTATGTT
66 TTTAATAATAATTATGTT
55543802 TAAATATGAT
Statistics
Matches: 199, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
119 124 0.62
120 75 0.38
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.50
Consensus pattern (120 bp):
TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
Found at i:55543669 original size:15 final size:15
Alignment explanation
Indices: 55543634--55543685 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
55543624 TTAAGAATTT
*
55543634 TATTAAATTAT-ATA
1 TATTTAATTATAATA
55543648 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
55543662 TATTTAATAATAAT-
1 TATTTAATTATAATA
55543676 TATGTTAATT
1 TAT-TTAATT
55543686 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:55543784 original size:16 final size:16
Alignment explanation
Indices: 55543763--55543804 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
55543753 TTATTAAATT
*
55543763 ATATATTTTAATTATA
1 ATATATTTTAATAATA
55543779 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
55543794 AT-TATGTTTAA
1 ATATAT-TTTAA
55543805 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:55543789 original size:15 final size:15
Alignment explanation
Indices: 55543754--55543795 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
55543744 TTAAGAATTT
*
55543754 TATTAAATTAT-ATA
1 TATTTAATTATAATA
55543768 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
55543782 TATTTAATAATAAT
1 TATTTAATTATAAT
55543796 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:55544391 original size:19 final size:19
Alignment explanation
Indices: 55544360--55544407 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
55544350 AAATAATTCA
*
55544360 AAATAATTT-TAAAAAATTT
1 AAAT-ATTTATAAAAAATCT
55544379 AAATATTTATAAAAAATCT
1 AAATATTTATAAAAAATCT
55544398 AAA-ATTTATA
1 AAATATTTATA
55544408 TATTTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATTTATAAAAAATCT
Found at i:55544402 original size:26 final size:26
Alignment explanation
Indices: 55544372--55544421 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
55544362 ATAATTTTAA
55544372 AAAATTTAAATATTTATAAAAAATCT
1 AAAATTTAAATATTTATAAAAAATCT
* *
55544398 AAAATTTATATATTTTTAAAAAAT
1 AAAATTTAAATATTTATAAAAAAT
55544422 ATAACGTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
AAAATTTAAATATTTATAAAAAATCT
Found at i:55548704 original size:20 final size:20
Alignment explanation
Indices: 55548679--55548730 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
55548669 TAAATTGTAT
55548679 TATCACATTATATAATACTA
1 TATCACATTATATAATACTA
55548699 TATCACA-TACTATAATACTA
1 TATCACATTA-TATAATACTA
*
55548719 -AT-ACATAATATA
1 TATCACATTATATA
55548731 TTAATTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 7 0.24
19 5 0.17
20 17 0.59
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (20 bp):
TATCACATTATATAATACTA
Found at i:55549507 original size:32 final size:31
Alignment explanation
Indices: 55549438--55549507 Score: 72
Period size: 32 Copynumber: 2.2 Consensus size: 31
55549428 TCTTACTATG
*
55549438 TTATATAATGCTATATAATATATTAGTATCA
1 TTATATAATGCTATATAATATATTAGTATAA
*
55549469 TATATATATATG-TAT-TAATAGTTTTAGTAATAA
1 T-TATATA-ATGCTATATAATA-TATTAGT-ATAA
55549502 TTATAT
1 TTATAT
55549508 GCTATATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
31 6 0.18
32 20 0.61
33 7 0.21
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (31 bp):
TTATATAATGCTATATAATATATTAGTATAA
Found at i:55549906 original size:19 final size:16
Alignment explanation
Indices: 55549844--55549899 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 16
55549834 AACCCAATCC
*
55549844 AAAATAAAAATTAATA
1 AAAATAAATATTAATA
55549860 TAAAGATAATAATATTAATA
1 -AAA-AT-A-AATATTAATA
55549880 AAAATAAATATTAATA
1 AAAATAAATATTAATA
55549896 AAAA
1 AAAA
55549900 CATTAAACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
16 14 0.40
17 4 0.11
18 4 0.11
19 4 0.11
20 9 0.26
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (16 bp):
AAAATAAATATTAATA
Found at i:55549911 original size:19 final size:16
Alignment explanation
Indices: 55549844--55549913 Score: 50
Period size: 19 Copynumber: 3.9 Consensus size: 16
55549834 AACCCAATCC
*
55549844 AAAATAAAAATTAATA
1 AAAATAAACATTAATA
*
55549860 TAAAGATAATAATATTAATA
1 -AAA-AT-A-AACATTAATA
*
55549880 AAAATAAATATTAATAA
1 AAAATAAACATTAAT-A
55549897 AAACATTAAACATTAAT
1 AAA-A-TAAACATTAAT
55549914 CAAATGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
16 9 0.20
17 8 0.18
18 5 0.11
19 14 0.31
20 9 0.20
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (16 bp):
AAAATAAACATTAATA
Found at i:55552551 original size:54 final size:55
Alignment explanation
Indices: 55552411--55552554 Score: 161
Period size: 56 Copynumber: 2.6 Consensus size: 55
55552401 CCACATAACA
* * * * *
55552411 CCATAGTCCTAAACTAGGTCTTACACTATGTGG-TTCTCTTATCCTCATATGATG
1 CCATAGTCCCAGACTAGGTCTTACACTATATGGTTTCACTTACCCTCATATGATG
55552465 CCATAG-CAACCATGACTAGGTCTTACACTATATGGTTTTCACTT-CCCT-ATATGATG
1 CCATAGTC--CCA-GACTAGGTCTTACACTATATGG-TTTCACTTACCCTCATATGATG
* *
55552521 CTATAGTCCCAGACTAGGTCTTATACTATATGGT
1 CCATAGTCCCAGACTAGGTCTTACACTATATGGT
55552555 CTTCTTGCCA
Statistics
Matches: 77, Mismatches: 7, Indels: 13
0.79 0.07 0.13
Matches are distributed among these distances:
53 2 0.03
54 27 0.35
55 5 0.06
56 33 0.43
57 4 0.05
58 6 0.08
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (55 bp):
CCATAGTCCCAGACTAGGTCTTACACTATATGGTTTCACTTACCCTCATATGATG
Found at i:55552657 original size:9 final size:9
Alignment explanation
Indices: 55552633--55552667 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
55552623 AGCAAACTCT
55552633 TTATGCAAAC
1 TTATGC-AAC
55552643 TTATGCAAC
1 TTATGCAAC
*
55552652 TCATGCAAC
1 TTATGCAAC
55552661 TTATGCA
1 TTATGCA
55552668 CATACTCCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (9 bp):
TTATGCAAC
Found at i:55556834 original size:20 final size:20
Alignment explanation
Indices: 55556809--55556848 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
55556799 CTTAATTCAT
55556809 CAACAAACCAAATCTATCCA
1 CAACAAACCAAATCTATCCA
55556829 CAACAAACCAAATCTATCCA
1 CAACAAACCAAATCTATCCA
55556849 TAAGTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (20 bp):
CAACAAACCAAATCTATCCA
Found at i:55559827 original size:13 final size:13
Alignment explanation
Indices: 55559806--55559848 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
55559796 AGGATTCATT
*
55559806 TATTTTTTTAACC
1 TATTATTTTAACC
*
55559819 TATTATTTTAACA
1 TATTATTTTAACC
* *
55559832 TACTATTTTAAAC
1 TATTATTTTAACC
55559845 TATT
1 TATT
55559849 TTATTAATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATTTTAACC
Found at i:55570085 original size:15 final size:15
Alignment explanation
Indices: 55570053--55570081 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55570043 ATTTTCTATG
55570053 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
55570068 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
55570082 ATTTTCGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:55571343 original size:41 final size:41
Alignment explanation
Indices: 55571232--55571343 Score: 120
Period size: 41 Copynumber: 2.7 Consensus size: 41
55571222 GATATTCGGG
* * * * *
55571232 CTTTGAGCCTAGCAAGCCTTGTGCTGGTGAATTAAATCGGG
1 CTTTGAGCCTAGCAGGCCTTGTGCTGGTGTATAAAATCAGA
*
55571273 CTTT-ATGCCTAGCAGG-CTTATTGCTGGTGTATAAAATCAGA
1 CTTTGA-GCCTAGCAGGCCTT-GTGCTGGTGTATAAAATCAGA
* *
55571314 CTTTGAGTCTAGCAGGCCTTGTGCCGGTGT
1 CTTTGAGCCTAGCAGGCCTTGTGCTGGTGT
55571344 GTGATACAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
40 4 0.07
41 50 0.86
42 4 0.07
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.32
Consensus pattern (41 bp):
CTTTGAGCCTAGCAGGCCTTGTGCTGGTGTATAAAATCAGA
Found at i:55573700 original size:37 final size:37
Alignment explanation
Indices: 55573648--55573742 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 37
55573638 GGCGGATGTA
* *
55573648 TAGCTATTATGAGCATTTGGCGTGGTATCGGTTAG-AT
1 TAGCTCTTATAAGCATTTGGCGTGGTATCGGTT-GCAT
* *
55573685 TAGCTCTTATAAGCATTTGTCGTGTTATCGGTTGCAT
1 TAGCTCTTATAAGCATTTGGCGTGGTATCGGTTGCAT
* *
55573722 TAACTCTTATTAGCATTTGGC
1 TAGCTCTTATAAGCATTTGGC
55573743 ATGTTTTGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 1 0.02
37 49 0.98
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (37 bp):
TAGCTCTTATAAGCATTTGGCGTGGTATCGGTTGCAT
Found at i:55577437 original size:21 final size:22
Alignment explanation
Indices: 55577411--55577451 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
55577401 AACTTGACAC
55577411 AGGGGC-ACACGCCCGTGTGGA
1 AGGGGCAACACGCCCGTGTGGA
55577432 AGGGGCAACACGCCCGTGTG
1 AGGGGCAACACGCCCGTGTG
55577452 ATCAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.20, C:0.29, G:0.41, T:0.10
Consensus pattern (22 bp):
AGGGGCAACACGCCCGTGTGGA
Found at i:55578631 original size:46 final size:47
Alignment explanation
Indices: 55578500--55578755 Score: 194
Period size: 46 Copynumber: 5.5 Consensus size: 47
55578490 ATGCCGGTGC
* * * * *
55578500 CATGTCCCAGACATAGTCTTATACAGGCTCTAGCATATC-TATGCCGATG
1 CATGTCCCAGACATGGTCTTACACTGACT-TA-CATCTCGTA-GCCGATG
* *
55578549 CCATGTCCCAGACATGGTCTTATACTGAC--ACATCTCGTAGCTGATG
1 -CATGTCCCAGACATGGTCTTACACTGACTTACATCTCGTAGCCGATG
55578595 CATGTCCCAGACAT-GTCTTACACTGACTTACATCTCG-AGGCCGATG
1 CATGTCCCAGACATGGTCTTACACTGACTTACATCTCGTA-GCCGATG
* * * *
55578641 CATGTCCTAGACAT-GTCTTACACTAGCAC-T-CGTCTCAATA-CCGATTC
1 CATGTCCCAGACATGGTCTTACACT-G-ACTTACATCTC-GTAGCCGA-TG
* * * *
55578688 CATGTCCCAGACATGGTCTTACACTGGCCCTCACA-AT-GTGGCCGATG
1 CATGTCCCAGACATGGTCTTACACT-G-ACTTACATCTCGTAGCCGATG
55578735 CATGTCCCAGACAT-GTCTTAC
1 CATGTCCCAGACATGGTCTTAC
55578756 GCTAACTCAT
Statistics
Matches: 173, Mismatches: 20, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
44 12 0.07
45 15 0.09
46 64 0.37
47 35 0.20
48 20 0.12
49 1 0.01
50 26 0.15
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (47 bp):
CATGTCCCAGACATGGTCTTACACTGACTTACATCTCGTAGCCGATG
Found at i:55586323 original size:46 final size:44
Alignment explanation
Indices: 55586228--55586436 Score: 156
Period size: 46 Copynumber: 4.5 Consensus size: 44
55586218 GTGTCGATGC
*
55586228 CATGTCCCAGACATGGTCTTACACTGACACATCTAGTAGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTGACACATCTAGTAGCCAATG
* * *
55586273 CATGTCCCAGACATTTCTTACACTGACATACATCTCG-AGGCTAATG
1 CATGTCCCAGACATGTCTTACACTGAC--ACATCTAGTA-GCCAATG
* * * *
55586319 CATGTCCCAAACATGTCTTACACT-AGCATTCGTCTCAAT-GCCGATG
1 CATGTCCCAGACATGTCTTACACTGA-CA--CATCT-AGTAGCCAATG
* * * * *
55586365 CGATGTCCCAGACATGGTCTTACACAGGCTC-TCACAATATGGCCAATG
1 C-ATGTCCCAGACAT-GTCTTACACTGACACATC-TAGTA--GCCAATG
55586413 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
55586437 AGCTCACAAT
Statistics
Matches: 131, Mismatches: 18, Indels: 29
0.74 0.10 0.16
Matches are distributed among these distances:
44 13 0.10
45 21 0.16
46 55 0.42
47 25 0.19
48 17 0.13
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (44 bp):
CATGTCCCAGACATGTCTTACACTGACACATCTAGTAGCCAATG
Found at i:55586414 original size:94 final size:88
Alignment explanation
Indices: 55586168--55586439 Score: 262
Period size: 94 Copynumber: 2.9 Consensus size: 88
55586158 ATGGGGTAAG
* *
55586168 ATGCCGATGCCATGTCCCAGACATGGTCTTACACAGGCTTTAGCATATCTGTGTCGATGCCATGT
1 ATGCCGATG-CATGTCCCAGACATGGTCTTACACAGGC-TTA-CA-ATCTG-GCCAATG-CATGT
55586233 CCCAGACATGGTCTTACACT-GACACATCTA
60 CCCAGACAT-GTCTTACACTAG-CACATCTA
* * * * * *
55586263 GTAGCCGATGCATGTCCCAGACAT-TTCTTACACTGACATAC-ATCTCGAGGCTAATGCATGTCC
1 AT-GCCGATGCATGTCCCAGACATGGTCTTACACAGGCTTACAATCT---GGCCAATGCATGTCC
* *
55586326 CAAACATGTCTTACACTAGCATTCGTCTCA
62 CAGACATGTCTTACACTAGCA--CATCT-A
*
55586356 ATGCCGATGCGATGTCCCAGACATGGTCTTACACAGGCTCTCACAATATGGCCAATGCATGTCCC
1 ATGCCGATGC-ATGTCCCAGACATGGTCTTACACAGGCT-T-ACAATCTGGCCAATGCATGTCCC
55586421 AGACATGTCTTACACTAGC
63 AGACATGTCTTACACTAGC
55586440 TCACAATAGC
Statistics
Matches: 146, Mismatches: 18, Indels: 27
0.76 0.09 0.14
Matches are distributed among these distances:
90 16 0.11
91 14 0.10
92 17 0.12
93 18 0.12
94 53 0.36
95 16 0.11
96 9 0.06
97 3 0.02
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (88 bp):
ATGCCGATGCATGTCCCAGACATGGTCTTACACAGGCTTACAATCTGGCCAATGCATGTCCCAGA
CATGTCTTACACTAGCACATCTA
Found at i:55586810 original size:30 final size:30
Alignment explanation
Indices: 55586776--55586833 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
55586766 ATAACCTATA
*
55586776 TTTTGGAAAAATGACCA-TTTCCCCCTAGAC
1 TTTT-GAAAAATGACCATTTTACCCCTAGAC
*
55586806 TTTTGCAAAATGACCATTTTACCCCTAG
1 TTTTGAAAAATGACCATTTTACCCCTAG
55586834 GTCCGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (30 bp):
TTTTGAAAAATGACCATTTTACCCCTAGAC
Found at i:55587707 original size:13 final size:13
Alignment explanation
Indices: 55587689--55587715 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55587679 GAAAGAATCG
55587689 CACACGGGCGTGT
1 CACACGGGCGTGT
55587702 CACACGGGCGTGT
1 CACACGGGCGTGT
55587715 C
1 C
55587716 CTTGTCGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:55610762 original size:29 final size:30
Alignment explanation
Indices: 55610729--55610802 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
55610719 GTTGTGAGAT
* *
55610729 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAACTTGAAAGTACA
* *
55610758 TGGCACTAAGTGTGC-AAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAACTTGAAAGTACA
55610787 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
55610803 CGGTTGATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 7 0.18
29 32 0.82
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (30 bp):
TGGCACTAAGTGTGCGAACTTGAAAGTACA
Found at i:55625246 original size:79 final size:81
Alignment explanation
Indices: 55625137--55625319 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
55625127 TACTCGTTCA
* *
55625137 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
55625200 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
55625217 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
55625280 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
55625296 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
55625320 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:55625319 original size:40 final size:40
Alignment explanation
Indices: 55625116--55625319 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
55625106 CAGAATTTAA
** *
55625116 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55625156 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55625196 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
55625235 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
55625275 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
55625315 CCGGA
1 CCGGA
55625320 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:55626513 original size:56 final size:56
Alignment explanation
Indices: 55626446--55626565 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
55626436 TATTAGTTTA
55626446 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
55626502 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
55626558 TTGCCCAT
1 TTGCCCAT
55626566 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:55633135 original size:79 final size:81
Alignment explanation
Indices: 55633026--55633208 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
55633016 TACTCGTTCA
* *
55633026 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
55633089 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
55633106 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
55633169 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
55633185 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
55633209 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:55633208 original size:40 final size:40
Alignment explanation
Indices: 55633005--55633208 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
55632995 CGGAATTTAA
** *
55633005 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55633045 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55633085 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
55633124 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
55633164 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
55633204 CCGGA
1 CCGGA
55633209 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:55636954 original size:43 final size:43
Alignment explanation
Indices: 55636822--55636978 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 43
55636812 AAGCTCATAC
* * * * * *
55636822 AATGCC-ATATCCCAGATATGGTATTACATGTTATCAC-ATAT
1 AATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCAATAT
* * * * * * * *
55636863 AGATGCCACTGTCCCAAATAGGGTCTTACACGAAAT-TGATTAAC
1 A-ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCAAT-AT
55636907 AATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCAATAT
1 AATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCAATAT
*
55636950 AATGCCAACGTCCCAGACATGGTCTTACA
1 AATGCCAATGTCCCAGACATGGTCTTACA
55636979 TATAATCACA
Statistics
Matches: 90, Mismatches: 21, Indels: 8
0.76 0.18 0.07
Matches are distributed among these distances:
41 1 0.01
42 5 0.06
43 79 0.88
44 5 0.06
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (43 bp):
AATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCAATAT
Found at i:55636976 original size:86 final size:85
Alignment explanation
Indices: 55636820--55636978 Score: 196
Period size: 86 Copynumber: 1.9 Consensus size: 85
55636810 AGAAGCTCAT
* * * *
55636820 ACAATGCCATATCCCAGATATGGTATTACATGTTATCACATATAGATGCCACTGTCCCAAATAGG
1 ACAATGCCATATCCCAGACATGGTATTACACGTAATCACATATAGATGCCACTGTCCCAAACAGG
55636885 GTCTTACACGAAATTGATTA
66 GTCTTACACGAAATTGATTA
* * * *
55636905 ACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCAATATA-ATGCCAAC-GTCCCAGAC
1 ACAATGCC-ATATCCCAGACATGGTATTACACGTAATCAC-ATATAGATGCC-ACTGTCCCAAAC
*
55636968 ATGGTCTTACA
63 AGGGTCTTACA
55636979 TATAATCACA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
85 8 0.13
86 47 0.76
87 7 0.11
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (85 bp):
ACAATGCCATATCCCAGACATGGTATTACACGTAATCACATATAGATGCCACTGTCCCAAACAGG
GTCTTACACGAAATTGATTA
Found at i:55644494 original size:26 final size:26
Alignment explanation
Indices: 55644464--55644519 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
55644454 TGAAATTCCC
55644464 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
55644490 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
55644516 ATCA
1 ATCA
55644520 ATTTGTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Done.