Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 103 of 171
Found at i:33247532 original size:469 final size:469
Alignment explanation
Indices: 33246654--33248061 Score: 2474
Period size: 469 Copynumber: 3.0 Consensus size: 469
33246644 ATACAGTTAC
33246654 AGATGCAGACATGATACCCCCATCAGCTATACACCATCTCCGTCCAACCCAACACACCAATATCC
1 AGATGCAGACATGATACCCCCATCAGCTATACACCATCTCCGTCCAACCCAACACACCAATATCC
** ** *
33246719 AACCCTACACACAATATAGTGTCGGTATGACATATCACAGTGTTTACAGTTTCACAGCCAGATTA
66 AACCCTACACACAATATAGTGTCGGTATGACACGTCGTAGTGTTCACAGTTTCACAGCCAGATTA
33246784 GATAATCTCAAGTGGATTAACCACTGAAACAATTAAGATAACTTCCTTCAAATCACAATTTCCAA
131 GATAATCTCAAGTGGATTAACCACTGAAACAATTAAGATAACTTCCTTCAAATCACAATTTCCAA
*
33246849 CCAATGTAGATGTACAGAACGTATGACAGATATGTATAATTACCAATAGACGTGATCATACAATC
196 CCCATGTAGATGTACAGAACGTATGACAGATATGTATAATTACCAATAGACGTGATCATACAATC
33246914 TTAGTATAATAGTATGCTGAGAATATTCCTAATCATTTCGTACAGTTATCCAGATATCGCATATC
261 TTAGTATAATAGTATGCTGAGAATATTCCTAATCATTTCGTACAGTTATCCAGATATCGCATATC
*
33246979 CTTAATCAAAATAGTAACATAGAATCGTACCTGTATGCTTAACAAAATACGAATTGTACCTGAAC
326 CTTAATCAAAATAGTAACATAGAAGCGTACCTGTATGCTTAACAAAATACGAATTGTACCTGAAC
*
33247044 AGAATACATACTTTAATGCATCCAAACAAATTAACATTACACATTATCGAGTCAATATTAATTTT
391 AGAATACATACTTTAATGCATCCAAACAAATTCACATTACACATTATCGAGTCAATATTAATTTT
33247109 CTTATATTCGTATA
456 CTTATATTCGTATA
33247123 AGATGCAGACATGATACCCCCATCAGCTATACACCATCTCCGTCCAACCCAACACACCAATATCC
1 AGATGCAGACATGATACCCCCATCAGCTATACACCATCTCCGTCCAACCCAACACACCAATATCC
*
33247188 AACCCTACACACAATATAGTGTCGGTATGACACGTCGTAGTGTTCACAGTTTCACAGCTAGATTA
66 AACCCTACACACAATATAGTGTCGGTATGACACGTCGTAGTGTTCACAGTTTCACAGCCAGATTA
33247253 GATAATCTCAAGTGGATTAACCACTGAAACAATTAAGATAACTTCCTTCAAATCACAATTTCCAA
131 GATAATCTCAAGTGGATTAACCACTGAAACAATTAAGATAACTTCCTTCAAATCACAATTTCCAA
33247318 CCCATGTAGATGTACAGAACGTATGACAGATATGTATAATTACCAATAGACGTGATCATACAATC
196 CCCATGTAGATGTACAGAACGTATGACAGATATGTATAATTACCAATAGACGTGATCATACAATC
*
33247383 TTAGTATAATAGTATGCTGAGAATATTCCTAATCATTTCGTATAGTTATCCAGATATCGCATATC
261 TTAGTATAATAGTATGCTGAGAATATTCCTAATCATTTCGTACAGTTATCCAGATATCGCATATC
33247448 CTTAATCAAAATAGTAACATAGAAGCGTACCTGTATGCTTAACAAAATACGAATTGTACCTGAAC
326 CTTAATCAAAATAGTAACATAGAAGCGTACCTGTATGCTTAACAAAATACGAATTGTACCTGAAC
*
33247513 AGAATACATACTTTAATGCATCCAAACAAATTCATATTACACATTATCGAGTCAATATTAATTTT
391 AGAATACATACTTTAATGCATCCAAACAAATTCACATTACACATTATCGAGTCAATATTAATTTT
33247578 CTTATATTCGTATA
456 CTTATATTCGTATA
* * *
33247592 AGATGCAGACATGATACCCTCATCAGCTATACACCATCTCCATCCAACCCAACACACAAATATCC
1 AGATGCAGACATGATACCCCCATCAGCTATACACCATCTCCGTCCAACCCAACACACCAATATCC
* *
33247657 AACCCTACACACAATATAGTGTCGGTATGACACGTCGTAGTGTTCACAGTTTCACGGCCAGATCA
66 AACCCTACACACAATATAGTGTCGGTATGACACGTCGTAGTGTTCACAGTTTCACAGCCAGATTA
* * *
33247722 GATAATCTCAAGTGGGTTAACCACTGAAACAGTTTAGATAACTTCCTTCAAATCACAATTTCCAA
131 GATAATCTCAAGTGGATTAACCACTGAAACAATTAAGATAACTTCCTTCAAATCACAATTTCCAA
* * *
33247787 CCCATGTAGATGTACAGAATGTATGATAGATATGTATAATTACCAATAGATGTGATCATACAATC
196 CCCATGTAGATGTACAGAACGTATGACAGATATGTATAATTACCAATAGACGTGATCATACAATC
* * * * * * * * **
33247852 CTACTGTAACAATGTGCTGAGAATATTCCTAATCTTTTCGTACAGTTATCCAGATACCATATATC
261 TTAGTATAATAGTATGCTGAGAATATTCCTAATCATTTCGTACAGTTATCCAGATATCGCATATC
* * * * * *
33247917 CTTAATCAAAATTGTAACACAGAAGCATACTTGTATGCTTAACAAAATACGAATAGTACATGAAC
326 CTTAATCAAAATAGTAACATAGAAGCGTACCTGTATGCTTAACAAAATACGAATTGTACCTGAAC
33247982 AGAATACATACTTTAATGCATCCAAACAAATTCACATTACACATTATCGAGTCAATATTAATTTT
391 AGAATACATACTTTAATGCATCCAAACAAATTCACATTACACATTATCGAGTCAATATTAATTTT
33248047 CTTATATTCGTATA
456 CTTATATTCGTATA
33248061 A
1 A
33248062 CATACGTATA
Statistics
Matches: 898, Mismatches: 41, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
469 898 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (469 bp):
AGATGCAGACATGATACCCCCATCAGCTATACACCATCTCCGTCCAACCCAACACACCAATATCC
AACCCTACACACAATATAGTGTCGGTATGACACGTCGTAGTGTTCACAGTTTCACAGCCAGATTA
GATAATCTCAAGTGGATTAACCACTGAAACAATTAAGATAACTTCCTTCAAATCACAATTTCCAA
CCCATGTAGATGTACAGAACGTATGACAGATATGTATAATTACCAATAGACGTGATCATACAATC
TTAGTATAATAGTATGCTGAGAATATTCCTAATCATTTCGTACAGTTATCCAGATATCGCATATC
CTTAATCAAAATAGTAACATAGAAGCGTACCTGTATGCTTAACAAAATACGAATTGTACCTGAAC
AGAATACATACTTTAATGCATCCAAACAAATTCACATTACACATTATCGAGTCAATATTAATTTT
CTTATATTCGTATA
Found at i:33247658 original size:20 final size:20
Alignment explanation
Indices: 33247633--33247670 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
33247623 CACCATCTCC
33247633 ATCCAACCCAACACACAAAT
1 ATCCAACCCAACACACAAAT
*
33247653 ATCCAACCCTACACACAA
1 ATCCAACCCAACACACAA
33247671 TATAGTGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.42, G:0.00, T:0.11
Consensus pattern (20 bp):
ATCCAACCCAACACACAAAT
Found at i:33248419 original size:55 final size:54
Alignment explanation
Indices: 33248330--33248469 Score: 156
Period size: 55 Copynumber: 2.6 Consensus size: 54
33248320 AACAAAATAG
** * *
33248330 TATACACACACACCCTGACACACACCCGTTTGTCAGCCCGTGCACCTCAAAACAA
1 TATACACACAC-CCCTGACACATGCCTGTGTGTCAGCCCGTGCACCTCAAAACAA
* ** ** *
33248385 TATACACACACCCCCTGACACATGTCTGTGTGTCAGGTCGTGTGCCTCAAAACAG
1 TATACACACA-CCCCTGACACATGCCTGTGTGTCAGCCCGTGCACCTCAAAACAA
*
33248440 TATACACACA-CCTTGACACATGCCTGTGTG
1 TATACACACACCCCTGACACATGCCTGTGTG
33248470 CTTCAAAACA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
53 18 0.25
55 53 0.74
56 1 0.01
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.21
Consensus pattern (54 bp):
TATACACACACCCCTGACACATGCCTGTGTGTCAGCCCGTGCACCTCAAAACAA
Found at i:33248508 original size:39 final size:41
Alignment explanation
Indices: 33248423--33248512 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
33248413 TGTGTCAGGT
*
33248423 CGTGTGCCTCAAAACAGTATACACACACCTTGACACATGCC
1 CGTGTGCCTCAAAACAGTATACACACACCTTGACACACGCC
* * * *
33248464 TGTGTGCTTCAAAACAGTATACACA-GCC-TGGCACACGCC
1 CGTGTGCCTCAAAACAGTATACACACACCTTGACACACGCC
33248503 CGTGTGCCTC
1 CGTGTGCCTC
33248513 CTGCAACTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 17 0.40
40 2 0.05
41 23 0.55
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.21
Consensus pattern (41 bp):
CGTGTGCCTCAAAACAGTATACACACACCTTGACACACGCC
Found at i:33250903 original size:53 final size:53
Alignment explanation
Indices: 33250823--33251007 Score: 235
Period size: 53 Copynumber: 3.5 Consensus size: 53
33250813 TAGTATACAA
* * * *
33250823 ACACACACCCTAACACACACCCATGTGTCAGACCGTGTGCCTCAAACCAGTAT
1 ACACACACCCTAACACACGCCCGTGTGTCAGCCCGTGTGCCTCAAAACAGTAT
* *
33250876 ACACACATCCTAACACACGCCCGTGTGTCAGCCCGTGTGCCTTAAAACAGTAT
1 ACACACACCCTAACACACGCCCGTGTGTCAGCCCGTGTGCCTCAAAACAGTAT
* * * * * *
33250929 ACACGCACACCCTAACAGATGCCCGTATGTCAGCCCATGTACTTCAAAACAGTAT
1 ACA--CACACCCTAACACACGCCCGTGTGTCAGCCCGTGTGCCTCAAAACAGTAT
*
33250984 ACACACACCCTGACACACGCCCGT
1 ACACACACCCTAACACACGCCCGT
33251008 ATATCTTGGC
Statistics
Matches: 113, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
53 68 0.60
55 45 0.40
ACGTcount: A:0.31, C:0.37, G:0.15, T:0.18
Consensus pattern (53 bp):
ACACACACCCTAACACACGCCCGTGTGTCAGCCCGTGTGCCTCAAAACAGTAT
Found at i:33253107 original size:53 final size:52
Alignment explanation
Indices: 33252990--33253115 Score: 135
Period size: 53 Copynumber: 2.4 Consensus size: 52
33252980 CCCGTGTGCA
* ** * *
33252990 TCAAACCAGTATACACACACCCTGACACACATTCGTGTGTCAGCCCATGTGCC
1 TCAAAACAGTATACACACA-CCTGACACACACCCGTATGTCAGCCCATGCGCC
* * * * * *
33253043 TTAAAATAGTATACACACACCTAGATACATACCCGTATGTTAGCTCATGCGCC
1 TCAAAACAGTATACACACACCT-GACACACACCCGTATGTCAGCCCATGCGCC
33253096 TCAAAACAGTATACACACAC
1 TCAAAACAGTATACACACAC
33253116 ACCCTAACAC
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
52 3 0.05
53 56 0.95
ACGTcount: A:0.34, C:0.31, G:0.13, T:0.22
Consensus pattern (52 bp):
TCAAAACAGTATACACACACCTGACACACACCCGTATGTCAGCCCATGCGCC
Found at i:33255957 original size:36 final size:36
Alignment explanation
Indices: 33255868--33256020 Score: 148
Period size: 36 Copynumber: 4.2 Consensus size: 36
33255858 TTTATTCAAT
* * * *
33255868 GGAAGAGCTTACGTCTCGGTTAGAGCGTAATGCTGTA
1 GGAAGTGCTTACATCTCGGTTAGAGCGTATTGCT-AA
* * * * * *
33255905 TG-ATTACATACGTCTCGGTTAGAGCGTATTGCTAC
1 GGAAGTGCTTACATCTCGGTTAGAGCGTATTGCTAA
*
33255940 GGAAGTGCTTACATCTCGGTTAGAGCGTAATGCTAA
1 GGAAGTGCTTACATCTCGGTTAGAGCGTATTGCTAA
* * *
33255976 GGAAGTACTTACATCTCAGTTAGAGTGT-TATGCTAA
1 GGAAGTGCTTACATCTCGGTTAGAGCGTAT-TGCTAA
33256012 GGAAGTGCT
1 GGAAGTGCT
33256021 AATGTCTCAG
Statistics
Matches: 94, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
35 1 0.01
36 92 0.98
37 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (36 bp):
GGAAGTGCTTACATCTCGGTTAGAGCGTATTGCTAA
Found at i:33255998 original size:72 final size:72
Alignment explanation
Indices: 33255868--33256020 Score: 184
Period size: 72 Copynumber: 2.1 Consensus size: 72
33255858 TTTATTCAAT
* * * * * * *
33255868 GGAAGAGCTTACGTCTCGGTTAGAGCGTAATGCTGTATGATTACATACGTCTCGGTTAGAGCG-T
1 GGAAGTGCTTACATCTCGGTTAGAGCGTAATGCTGAAGGAGTACATACATCTCAGTTAGAGCGTT
*
33255932 ATTGCTAC
66 A-TGCTAA
* *
33255940 GGAAGTGCTTACATCTCGGTTAGAGCGTAATGCT-AAGGAAGTACTTACATCTCAGTTAGAGTGT
1 GGAAGTGCTTACATCTCGGTTAGAGCGTAATGCTGAAGG-AGTACATACATCTCAGTTAGAGCGT
33256004 TATGCTAA
65 TATGCTAA
33256012 GGAAGTGCT
1 GGAAGTGCT
33256021 AATGTCTCAG
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
71 2 0.03
72 65 0.94
73 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (72 bp):
GGAAGTGCTTACATCTCGGTTAGAGCGTAATGCTGAAGGAGTACATACATCTCAGTTAGAGCGTT
ATGCTAA
Found at i:33256029 original size:36 final size:36
Alignment explanation
Indices: 33255917--33256037 Score: 145
Period size: 36 Copynumber: 3.4 Consensus size: 36
33255907 ATTACATACG
* *
33255917 TCTCGGTTAGAGCG-TATTGCTACGGAAGTGCTTACA
1 TCTCAGTTAGAGCGTTA-TGCTAAGGAAGTGCTTACA
* * *
33255953 TCTCGGTTAGAGCGTAATGCTAAGGAAGTACTTACA
1 TCTCAGTTAGAGCGTTATGCTAAGGAAGTGCTTACA
* * **
33255989 TCTCAGTTAGAGTGTTATGCTAAGGAAGTGCTAATG
1 TCTCAGTTAGAGCGTTATGCTAAGGAAGTGCTTACA
33256025 TCTCAGTTAGAGC
1 TCTCAGTTAGAGC
33256038 ATAAGGTCGT
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
36 72 0.99
37 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (36 bp):
TCTCAGTTAGAGCGTTATGCTAAGGAAGTGCTTACA
Found at i:33259818 original size:27 final size:27
Alignment explanation
Indices: 33259786--33259839 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
33259776 ATATTATTTT
33259786 GCAAAACTTAGAGTTTGCATTTTATTG
1 GCAAAACTTAGAGTTTGCATTTTATTG
33259813 GCAAAACTTAGAGTTTGCATTTTATTG
1 GCAAAACTTAGAGTTTGCATTTTATTG
33259840 CTATTGCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (27 bp):
GCAAAACTTAGAGTTTGCATTTTATTG
Found at i:33262533 original size:19 final size:19
Alignment explanation
Indices: 33262488--33262534 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
33262478 ATATAAATAT
33262488 AAATTAAATACAAATTTAA
1 AAATTAAATACAAATTTAA
*
33262507 ATAA-TAAATA-ATATCTTAA
1 A-AATTAAATACAAAT-TTAA
33262526 AAATTAAAT
1 AAATTAAAT
33262535 CCTAATGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 5 0.21
19 17 0.71
20 2 0.08
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATTAAATACAAATTTAA
Found at i:33270911 original size:17 final size:17
Alignment explanation
Indices: 33270891--33270932 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
33270881 CTTCCTTGAC
*
33270891 CTTTAACCTTCCATCTT
1 CTTTAACCTTCCATATT
*
33270908 CTTTAACCTTTCATATT
1 CTTTAACCTTCCATATT
33270925 CTTGTAAC
1 CTT-TAAC
33270933 TATTTTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:33277596 original size:18 final size:18
Alignment explanation
Indices: 33277554--33277623 Score: 79
Period size: 18 Copynumber: 3.8 Consensus size: 18
33277544 TATTACTCAT
* *
33277554 ACGAGCCAGTATTGCTCTT
1 ACGAGCCAATA-TGCTCTA
*
33277573 ATGAGCCAATATGCT-TGA
1 ACGAGCCAATATGCTCT-A
33277591 ACGAGCCAATATGCTCTA
1 ACGAGCCAATATGCTCTA
*
33277609 ACGAGCCAGTATGCT
1 ACGAGCCAATATGCT
33277624 ATTCCTTCCG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.02
18 33 0.75
19 10 0.23
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (18 bp):
ACGAGCCAATATGCTCTA
Found at i:33277615 original size:36 final size:37
Alignment explanation
Indices: 33277554--33277623 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 37
33277544 TATTACTCAT
* * *
33277554 ACGAGCCAGTATTGCTCTTATGAGCCAATATGCTTGA
1 ACGAGCCAATATTGCTCTAACGAGCCAATATGCTTGA
*
33277591 ACGAGCCAATA-TGCTCTAACGAGCCAGTATGCT
1 ACGAGCCAATATTGCTCTAACGAGCCAATATGCT
33277624 ATTCCTTCCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 19 0.66
37 10 0.34
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (37 bp):
ACGAGCCAATATTGCTCTAACGAGCCAATATGCTTGA
Found at i:33284403 original size:18 final size:18
Alignment explanation
Indices: 33284382--33284416 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
33284372 ACGGGCCAGT
33284382 ATGCTCGAACGAGCCAAC
1 ATGCTCGAACGAGCCAAC
*
33284400 ATGCTCTAACGAGCCAA
1 ATGCTCGAACGAGCCAA
33284417 TATGATATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.31, G:0.20, T:0.14
Consensus pattern (18 bp):
ATGCTCGAACGAGCCAAC
Found at i:33290013 original size:28 final size:28
Alignment explanation
Indices: 33289981--33290039 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
33289971 CACAATGCAA
*
33289981 ATCTGGTATTGCGATCCAACAGTAGAAT
1 ATCTGGTATTGCGATCCAACAGCAGAAT
33290009 ATCTGGTATTGCGATCCAACAGCAGAAT
1 ATCTGGTATTGCGATCCAACAGCAGAAT
33290037 ATC
1 ATC
33290040 ATACTTCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (28 bp):
ATCTGGTATTGCGATCCAACAGCAGAAT
Found at i:33294318 original size:51 final size:51
Alignment explanation
Indices: 33294242--33294341 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
33294232 ATGCAGCGAC
* *
33294242 AACCTGTAGATATCTGAAGAAAACATCAAATATGCGTGAGTGA-ACAGCCGT
1 AACCTGAAGATATCTGAAGAAAACATAAAATATGCGTGAGT-ACACAGCCGT
33294293 AACCTGAAGATATCTGAAGAAAACATAAAATATGCGTGAGTACACAGCC
1 AACCTGAAGATATCTGAAGAAAACATAAAATATGCGTGAGTACACAGCC
33294342 ATATTATAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 1 0.02
51 45 0.98
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (51 bp):
AACCTGAAGATATCTGAAGAAAACATAAAATATGCGTGAGTACACAGCCGT
Found at i:33315125 original size:18 final size:18
Alignment explanation
Indices: 33315102--33315136 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
33315092 ACTTTACTTT
*
33315102 TATTTTATTTTATCATTG
1 TATTTTATTTTAACATTG
33315120 TATTTTATTTTAACATT
1 TATTTTATTTTAACATT
33315137 AATTCTAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.66
Consensus pattern (18 bp):
TATTTTATTTTAACATTG
Found at i:33321066 original size:12 final size:12
Alignment explanation
Indices: 33321035--33321077 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
33321025 CAATACTTTC
33321035 TTCTTCTTCCTT
1 TTCTTCTTCCTT
* *
33321047 CTCCTCTTCCTT
1 TTCTTCTTCCTT
* *
33321059 TTCTTCTTTCTC
1 TTCTTCTTCCTT
33321071 TTCTTCT
1 TTCTTCT
33321078 CTTGCTCCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (12 bp):
TTCTTCTTCCTT
Found at i:33330134 original size:13 final size:13
Alignment explanation
Indices: 33330116--33330140 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33330106 TAAGTATGAA
33330116 ATGCTAAAAATGC
1 ATGCTAAAAATGC
33330129 ATGCTAAAAATG
1 ATGCTAAAAATG
33330141 ATACAAAAGG
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:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Found at i:33332788 original size:14 final size:15
Alignment explanation
Indices: 33332768--33332801 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
33332758 GTAATGATTA
33332768 AATTAATTAA-TTAT
1 AATTAATTAACTTAT
*
33332782 GATTAATTAACTTAT
1 AATTAATTAACTTAT
33332797 AATTA
1 AATTA
33332802 TAGTATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (15 bp):
AATTAATTAACTTAT
Found at i:33333315 original size:2 final size:2
Alignment explanation
Indices: 33333308--33333343 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
33333298 TGTAATTGTA
33333308 AT 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
33333344 GTTTGAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33333558 original size:22 final size:22
Alignment explanation
Indices: 33333532--33333599 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
33333522 ACAGGTTAAA
*
33333532 CACTTCAGTGCTCTTTGGTTAG
1 CACTTCAGTGCTCTTTGCTTAG
*
33333554 CACTTC-GATGCCCTTTGCTTAG
1 CACTTCAG-TGCTCTTTGCTTAG
* * *
33333576 TACTTCAATGCTCTTTGTTTAG
1 CACTTCAGTGCTCTTTGCTTAG
33333598 CA
1 CA
33333600 GTACGGTGCT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 1 0.03
22 36 0.97
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (22 bp):
CACTTCAGTGCTCTTTGCTTAG
Found at i:33338620 original size:18 final size:18
Alignment explanation
Indices: 33338597--33338636 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
33338587 ATTGCCTGGA
*
33338597 GCATTTTAGATATCAGAG
1 GCATTTCAGATATCAGAG
33338615 GCATTTCAGATATCAGAG
1 GCATTTCAGATATCAGAG
33338633 GCAT
1 GCAT
33338637 AAACTCAGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (18 bp):
GCATTTCAGATATCAGAG
Found at i:33353242 original size:106 final size:108
Alignment explanation
Indices: 33353122--33353328 Score: 292
Period size: 107 Copynumber: 1.9 Consensus size: 108
33353112 TCGAATCTTC
* * * *
33353122 AAGAATAAAGAACATTTATTGA-TTTAAAATAGGATATTCAATTATTTAAGCTCGAAGAAAAATC
1 AAGAATAAAGAACATTTATTCATTTTAAAAAAGGATATTCAATTATTTAAGCTCAAAGAAAAACC
* * *
33353186 ATACCTAGTACTTTTGAGCACAATTTTT-GAATTCCCTGAGTA
66 ATACCCAATACGTTTGAGCACAATTTTTCGAATTCCCTGAGTA
** * * *
33353228 AAGAATATCGAACATTTGTTCATTTTAAAAAAGGATATTCGATTATTTAAGTTCAAAGAAAAACC
1 AAGAATAAAGAACATTTATTCATTTTAAAAAAGGATATTCAATTATTTAAGCTCAAAGAAAAACC
33353293 ATACCCAATACGTTTGAGCACAATTTTTCGAATTCC
66 ATACCCAATACGTTTGAGCACAATTTTTCGAATTCC
33353329 TTAAAAAGAA
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
106 18 0.21
107 62 0.71
108 7 0.08
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (108 bp):
AAGAATAAAGAACATTTATTCATTTTAAAAAAGGATATTCAATTATTTAAGCTCAAAGAAAAACC
ATACCCAATACGTTTGAGCACAATTTTTCGAATTCCCTGAGTA
Found at i:33353481 original size:22 final size:22
Alignment explanation
Indices: 33353453--33353497 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
33353443 TAGTTTAAAA
33353453 ATATACATGGATGAAGTAATGG
1 ATATACATGGATGAAGTAATGG
33353475 ATATACATGGATGAAGTAATGG
1 ATATACATGGATGAAGTAATGG
33353497 A
1 A
33353498 GTGAGCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.27, T:0.27
Consensus pattern (22 bp):
ATATACATGGATGAAGTAATGG
Found at i:33353840 original size:31 final size:32
Alignment explanation
Indices: 33353746--33353859 Score: 89
Period size: 31 Copynumber: 3.7 Consensus size: 32
33353736 AGATTTAATT
* * *
33353746 AATAAAAACAAAAGGA-TTAAAATATAAAAGA
1 AATAAAAATAAAAGGAGTTAAATTTTAAAAGA
* * *
33353777 AA-CAGAATAAAA-CAG--AAATTTTTAAAAGA
1 AATAAAAATAAAAGGAGTTAAA-TTTTAAAAGA
33353806 AATAAAAATAAAA-GAGTTAAATTTTAACAA-A
1 AATAAAAATAAAAGGAGTTAAATTTTAA-AAGA
* *
33353837 AATACAAATAAAAGGATTTAAAT
1 AATAAAAATAAAAGGAGTTAAAT
33353860 AAAAAAAGAG
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
28 3 0.05
29 11 0.17
30 17 0.26
31 21 0.32
32 13 0.20
ACGTcount: A:0.65, C:0.04, G:0.09, T:0.22
Consensus pattern (32 bp):
AATAAAAATAAAAGGAGTTAAATTTTAAAAGA
Found at i:33353962 original size:30 final size:30
Alignment explanation
Indices: 33353906--33353962 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
33353896 AGGGAAAAAT
* *
33353906 AATTTAAGGGTTAAATTAGAATAAAAATAA
1 AATTTAAGGGTAAAATTAGAAAAAAAATAA
*
33353936 AATTTAA-GGTAAAATATATAAAAAAAA
1 AATTTAAGGGTAAAAT-TAGAAAAAAAA
33353963 CCAGAAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (30 bp):
AATTTAAGGGTAAAATTAGAAAAAAAATAA
Found at i:33355317 original size:14 final size:15
Alignment explanation
Indices: 33355298--33355326 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33355288 GGACTTTAAA
33355298 TTTTG-TTTTGTTTT
1 TTTTGTTTTTGTTTT
33355312 TTTTGTTTTTGTTTT
1 TTTTGTTTTTGTTTT
33355327 GGTTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (15 bp):
TTTTGTTTTTGTTTT
Found at i:33355975 original size:79 final size:78
Alignment explanation
Indices: 33355776--33356328 Score: 669
Period size: 79 Copynumber: 6.9 Consensus size: 78
33355766 GAGATGATAG
*
33355776 CTTCAATCTACCCCTCCTGATTTAGGGGTAAAAGATTGGATGATGGCTTCAATCTGCCCCATGAT
1 CTTCAATCT-GCCCT-CTGA-TTA-GGGTAAAAGATT-G--GAT-GCTTCAATCTGCCCCATGAT
*
33355841 AGGGGTAAGAGATTGGGTGATGT
58 CGGGGTAAGAGATT-GGTG-TGT
* * * * *
33355864 CTTCAATCTGCCCTGTAATTAGGGTAAGAGATTAGATGGCTTCAACCTGCCCCATGATCGGGGTA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGAT-GCTTCAATCTGCCCCATGATCGGGGTA
* ** *
33355929 AAAGATCAGTTTGT
65 AGAGATTGGTGTGT
* **
33355943 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGGTCAAGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
33356008 GAGATTGGTGTGT
66 GAGATTGGTGTGT
* * * * * *
33356021 CTTCATTCTGCCTTCTGATTAGGGTAAAAGATCGGGTGCTTCAAT-TGCCTCATGATCAGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
* *
33356085 AAGATTGGTGTAT
66 GAGATTGGTGTGT
* * *
33356098 CCTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTG-CCCGTGGTCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
33356162 GAGATTGGATGATGT
66 GAGATTGG-TG-TGT
* * * *
33356177 CTTCAATCTTCCCTCTGATTAGGGTAAAATATTAGATGCTTCAATCTGCCCCATGATCAGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
33356242 GAGATTGGTGTGT
66 GAGATTGGTGTGT
* * *
33356255 CTTCAATATGCCCTCTGATCAGGGTAAAATATTGGGATGCTTCAATCTGCCCCATGATCGGGGTA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATT-GGATGCTTCAATCTGCCCCATGATCGGGGTA
*
33356320 TGAGATTGG
65 AGAGATTGG
33356329 ATGGTAGCTT
Statistics
Matches: 404, Mismatches: 56, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
77 86 0.21
78 111 0.27
79 121 0.30
80 23 0.06
81 34 0.08
84 11 0.03
85 3 0.01
86 2 0.00
87 4 0.01
88 9 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (78 bp):
CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
GAGATTGGTGTGT
Found at i:33356281 original size:234 final size:237
Alignment explanation
Indices: 33355801--33356328 Score: 690
Period size: 234 Copynumber: 2.2 Consensus size: 237
33355791 CCTGATTTAG
* *
33355801 GGGTAAAAGATTGGATGATGGCTTCAATCTGCCCCATGAT-AGGGGTAAGAGATTGGGTGATGTC
1 GGGTAAAAGATCGG--GAT-GCTTCAATCTGCCCCATGATCA-GGGTAAGAGATT-GGTGATATC
* * *
33355865 TTCAATCTGCCCTGTAATTAGGGTAAGAGATTAGATGGCTTCAACCTGCCCCATGATCGGGGTAA
61 CTCAATCTGCCCTCTAATTAGGGTAAAAGATTAGATGGCTTCAACCTGCCCCATGATCGGGGTAA
* *
33355930 AAGATCAGTTTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCC
126 AAGATCAGTATGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTAGATGCTTCAATCTGCCCC
* * * * *
33355995 ATGGTCAAGGTAAGAGATTGGTGTGTCTTCATTCTGCCTTCTGATTA
191 ATGATCAAGGTAAGAGATTGGTGTGTCTTCAATATGCCCTCTGATCA
* *
33356042 GGGTAAAAGATCGGG-TGCTTCAAT-TGCCTCATGATCAGGGTAAAAGATTGGTG-TATCCTCAA
1 GGGTAAAAGATCGGGATGCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGTGATATCCTCAA
* * * * * *
33356104 TCTGCCCTCTGATTAGGGTAAAAGATTGGAT-GCTTCAATCTG-CCCGTGGTCGGGGTAAGAGAT
66 TCTGCCCTCTAATTAGGGTAAAAGATTAGATGGCTTCAACCTGCCCCATGATCGGGGTAAAAGAT
** * *
33356167 TGGATGATGTCTTCAATCTTCCCTCTGATTAGGGTAAAATATTAGATGCTTCAATCTGCCCCATG
131 CAG-T-ATGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTAGATGCTTCAATCTGCCCCATG
*
33356232 ATCAGGGTAAGAGATTGGTGTGTCTTCAATATGCCCTCTGATCA
194 ATCAAGGTAAGAGATTGGTGTGTCTTCAATATGCCCTCTGATCA
* * * *
33356276 GGGTAAAATATTGGGATGCTTCAATCTGCCCCATGATCGGGGTATGAGATTGG
1 GGGTAAAAGATCGGGATGCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGG
33356329 ATGGTAGCTT
Statistics
Matches: 251, Mismatches: 31, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
232 19 0.08
233 11 0.04
234 140 0.56
235 13 0.05
236 44 0.18
237 9 0.04
238 1 0.00
239 1 0.00
241 13 0.05
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (237 bp):
GGGTAAAAGATCGGGATGCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGTGATATCCTCAA
TCTGCCCTCTAATTAGGGTAAAAGATTAGATGGCTTCAACCTGCCCCATGATCGGGGTAAAAGAT
CAGTATGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTAGATGCTTCAATCTGCCCCATGAT
CAAGGTAAGAGATTGGTGTGTCTTCAATATGCCCTCTGATCA
Found at i:33356741 original size:98 final size:97
Alignment explanation
Indices: 33356597--33356929 Score: 348
Period size: 98 Copynumber: 3.4 Consensus size: 97
33356587 TCATCTTCTG
* ** * *
33356597 GGTATAAGATTCATCGTTATGGCCTCAATCTTTCCCTTCACATCTCTAAGGTATAAGGTTCGTCG
1 GGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCTAAGGTACAAGGTTC-TCG
* * *
33356662 TTGCGGCTTCAACCTTTCCCTTCATATCTCCAT
65 TTGCGACTTCAACCTTTCCCTTCATATCTCTAA
* * * *
33356695 GGTATAAGATTCGTTGTTGCGGCTTCAATCTTTCCCATCACGTCTCTAAGGTACAAGTGTAC-CG
1 GGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCTAAGGTACAAG-GTTCTCG
* * *
33356759 TTACGACTTCAACCTTCCCCTCCATATCTCTAA
65 TTGCGACTTCAACCTTTCCCTTCATATCTCTAA
* * * * * * * *
33356792 GATATTAGATT-TTCCATTGTGGCTTCAATATTTCCCTTCACATCTCTAAGGTACAAGGTTTTTT
1 GGTATAAGATTCGT-CGTTGCGGCTTCAATCTTTCCCTTCACATCTCTAAGGTACAAGG-TTCTC
** *
33356856 GTTGATACTTCAACCTTTCCC-TCTATATCTCTAG
64 GTTGCGACTTCAACCTTTCCCTTC-ATATCTCTAA
* *
33356890 GGTATTAGATTTGTCGTTGCGGCTTCAATCTTTCCCTTCA
1 GGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCA
33356930 AACCTGTAGA
Statistics
Matches: 191, Mismatches: 38, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
96 2 0.01
97 77 0.40
98 108 0.57
99 4 0.02
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (97 bp):
GGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCTAAGGTACAAGGTTCTCGT
TGCGACTTCAACCTTTCCCTTCATATCTCTAA
Found at i:33356916 original size:49 final size:49
Alignment explanation
Indices: 33356597--33356929 Score: 258
Period size: 49 Copynumber: 6.8 Consensus size: 49
33356587 TCATCTTCTG
** ** *
33356597 GGTATAAGATTCATCGTTATGGCCTCAATCTTTCCCTTCACATCTCTAA
1 GGTATAAGATTTGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCTAA
* * * * * *
33356646 GGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTTCATATCTCCAT
1 GGTATAAGATTTGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCTAA
* * * *
33356695 GGTATAAGATTCGTTGTTGCGGCTTCAATCTTTCCCATCACGTCTCTAA
1 GGTATAAGATTTGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCTAA
* * ** * * * * * *
33356744 GGTACAAG-TGTACCGTTACGACTTCAACCTTCCCCTCCATATCTCTAA
1 GGTATAAGATTTGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCTAA
* * * * *
33356792 GATATTAGATTT-TCCATTGTGGCTTCAATATTTCCCTTCACATCTCTAA
1 GGTATAAGATTTGT-CGTTGCGGCTTCAATCTTTCCCTTCACATCTCTAA
* * * * *** * * *
33356841 GGTACAAGGTTTTTTGTTGATACTTCAACCTTTCCC-TCTATATCTCTAG
1 GGTATAAGATTTGTCGTTGCGGCTTCAATCTTTCCCTTC-ACATCTCTAA
*
33356890 GGTATTAGATTTGTCGTTGCGGCTTCAATCTTTCCCTTCA
1 GGTATAAGATTTGTCGTTGCGGCTTCAATCTTTCCCTTCA
33356930 AACCTGTAGA
Statistics
Matches: 212, Mismatches: 67, Indels: 10
0.73 0.23 0.03
Matches are distributed among these distances:
48 34 0.16
49 175 0.83
50 3 0.01
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (49 bp):
GGTATAAGATTTGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCTAA
Found at i:33358411 original size:43 final size:42
Alignment explanation
Indices: 33358257--33358477 Score: 257
Period size: 41 Copynumber: 5.3 Consensus size: 42
33358247 CCGAGTCGTA
*
33358257 AGTCTTTCTTTAAACATAATCTCATGCTCATTTCGAGTCACG
1 AGTCTTTCTTTAAACATAATCTCATGCTCATTCCGAGTCACG
* *
33358299 AGTC-TTCCTTAAATATAATCTCATGCTCATTCCGAGTCACG
1 AGTCTTTCTTTAAACATAATCTCATGCTCATTCCGAGTCACG
* * *
33358340 AGTC-TTCCTAAAACATAATCTCATGCTCATTTCGAGTCACG
1 AGTCTTTCTTTAAACATAATCTCATGCTCATTCCGAGTCACG
* * * * *
33358381 AGTCTTTCATTTATACATAATCCCATGCTCATCCCGAGACATG
1 AGTCTTTC-TTTAAACATAATCTCATGCTCATTCCGAGTCACG
* * * * * *
33358424 AGTCTTCCATTTATACATAATCTCATTCTCATCCCGAGACAAG
1 AGTCTTTC-TTTAAACATAATCTCATGCTCATTCCGAGTCACG
33358467 AGTCTTTCTTT
1 AGTCTTTCTTT
33358478 TTCTTTTGAG
Statistics
Matches: 158, Mismatches: 19, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
41 76 0.48
42 10 0.06
43 72 0.46
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.35
Consensus pattern (42 bp):
AGTCTTTCTTTAAACATAATCTCATGCTCATTCCGAGTCACG
Found at i:33361268 original size:10 final size:10
Alignment explanation
Indices: 33361261--33361307 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
33361251 TCCTTTTTCC
*
33361261 TTCTTTTTTT
1 TTCTTTTTAT
33361271 TTCTTTTTAT
1 TTCTTTTTAT
33361281 TTCTTTTT-T
1 TTCTTTTTAT
**
33361290 CCCTTTTTAT
1 TTCTTTTTAT
*
33361300 TTATTTTT
1 TTCTTTTT
33361308 TTAGGTGAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (10 bp):
TTCTTTTTAT
Found at i:33361276 original size:20 final size:20
Alignment explanation
Indices: 33361248--33361309 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
33361238 CGACCTCTCC
*
33361248 TTTTCCTTTTTCCTTCTTTT
1 TTTTCCTTTTTACTTCTTTT
* *
33361268 TTTTTCTTTTTATTTC-TTT
1 TTTTCCTTTTTACTTCTTTT
* * *
33361287 TTTCCCTTTTTATTTATTTT
1 TTTTCCTTTTTACTTCTTTT
33361307 TTT
1 TTT
33361310 AGGTGAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTCCTTTTTACTTCTTTT
Found at i:33368513 original size:108 final size:108
Alignment explanation
Indices: 33368370--33368581 Score: 286
Period size: 108 Copynumber: 2.0 Consensus size: 108
33368360 CAAAAATAAA
* * *
33368370 GAACATTTATTGATTTAAAATAGGATATTCGATTATTTAAGTT-AGAAGAAAAATCATACAAAAT
1 GAACATTTATTGATTTAAAATAGGATACTCAATTATTTAAGTTCA-AAAAAAAATCATACAAAAT
* *
33368434 ACGTTTGAGCACAAATTTT-GAATT-CTCTATATAAAAGAATACC
65 ACATTTGAGCACAAATTTTCGAATTCCT-TAAATAAAAGAATACC
* ** *
33368477 GAACATTTGTTGATTTTAAAATAGGATACTCAATTATTTAAGTTCAAAAAAAAATCATACCCAGT
1 GAACATTTATTGA-TTTAAAATAGGATACTCAATTATTTAAGTTCAAAAAAAAATCATACAAAAT
*
33368542 ACATTTGAGCACAATTTTTCGAATTCCTTAAATAAAAGAA
65 ACATTTGAGCACAAATTTTCGAATTCCTTAAATAAAAGAA
33368582 CATTGCCCTC
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
107 12 0.13
108 60 0.66
109 17 0.19
110 2 0.02
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.33
Consensus pattern (108 bp):
GAACATTTATTGATTTAAAATAGGATACTCAATTATTTAAGTTCAAAAAAAAATCATACAAAATA
CATTTGAGCACAAATTTTCGAATTCCTTAAATAAAAGAATACC
Found at i:33368995 original size:19 final size:19
Alignment explanation
Indices: 33368951--33368994 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
33368941 TTTAATTTTT
* *
33368951 TAAAAAAGGATTTAATTAA
1 TAAAAAAGGATTAAAATAA
33368970 TAAAAAAGGATTAAAAT-A
1 TAAAAAAGGATTAAAATAA
33368988 TAAAAAA
1 TAAAAAA
33368995 ACAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (19 bp):
TAAAAAAGGATTAAAATAA
Found at i:33369057 original size:31 final size:28
Alignment explanation
Indices: 33368973--33369068 Score: 93
Period size: 31 Copynumber: 3.2 Consensus size: 28
33368963 TAATTAATAA
* * *
33368973 AAAAGGATTAAAATATAAAAAAACAAAAT
1 AAAAGG-TTAAATTTTAAAAAAATAAAAT
* *
33369002 AAAAGGGTAATTTTTAAAAGAAATAATAAT
1 AAAAGGTTAAATTTTAAAA-AAATAA-AAT
33369032 AAAAGAGTTAAATTTTAACAAAAATACAAAT
1 AAAAG-GTTAAATTTTAA-AAAAATA-AAAT
33369063 AAAAGG
1 AAAAGG
33369069 ATTTAAATAA
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
28 9 0.16
29 11 0.20
30 9 0.16
31 23 0.42
32 3 0.05
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.23
Consensus pattern (28 bp):
AAAAGGTTAAATTTTAAAAAAATAAAAT
Found at i:33369228 original size:27 final size:27
Alignment explanation
Indices: 33369174--33369234 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
33369164 AATATATAAG
*
33369174 AACTAGAA-AGTATAAGGTTAAATCTAA
1 AACTA-AATAGTAAAAGGTTAAATCTAA
*
33369201 AATTAAATAGTAAAAGGATTAAAT-TAA
1 AACTAAATAGTAAAAGG-TTAAATCTAA
33369228 AACTAAA
1 AACTAAA
33369235 AATAAAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 2 0.07
27 21 0.72
28 6 0.21
ACGTcount: A:0.57, C:0.05, G:0.11, T:0.26
Consensus pattern (27 bp):
AACTAAATAGTAAAAGGTTAAATCTAA
Found at i:33370421 original size:11 final size:11
Alignment explanation
Indices: 33370390--33370428 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
33370380 GGGCTAATTG
33370390 GGATTGGGCTTA
1 GGATTGGG-TTA
* *
33370402 GGTTTGGGTTT
1 GGATTGGGTTA
33370413 GGATTGGGTTA
1 GGATTGGGTTA
33370424 GGATT
1 GGATT
33370429 TAGTGGATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.13, C:0.03, G:0.44, T:0.41
Consensus pattern (11 bp):
GGATTGGGTTA
Found at i:33371981 original size:53 final size:53
Alignment explanation
Indices: 33371869--33372146 Score: 312
Period size: 53 Copynumber: 5.1 Consensus size: 53
33371859 CGATATTTTA
* *
33371869 AAAAAAAAATTGGTGTTGGTCAATGCTTGGCCGACACCACCTTTTTTATCTGAT
1 AAAAAAAATTTGGTGTTGG-CAATGCTTGGCCGACACCACCTTTTTTATCAGAT
* * *
33371923 AAAAAAAATTTGGTGTTGGCCATGCATTAGCCAACACCACCTTTTTTATCAGAT
1 AAAAAAAATTTGGTGTTGGCAATGC-TTGGCCGACACCACCTTTTTTATCAGAT
* * *
33371977 -AAAAAAATTTGGTGTTAGCTAATGTTTGGCCGACACCACC-TTTTTATCATAT
1 AAAAAAAATTTGGTGTTGGC-AATGCTTGGCCGACACCACCTTTTTTATCAGAT
* * * *
33372029 AAAAAAAAATTGGAGTTGGTC-ATGCATTGGTCGACACCACCTTTTTTATCATAT
1 AAAAAAAATTTGGTGTTGG-CAATGC-TTGGCCGACACCACCTTTTTTATCAGAT
* *
33372083 AAGAAAAAAATTTTGGTGTTGTACAATGCTTGGCCGACACCACTTTTTTTAT-ATGAT
1 -A-AAAAAAA-TTTGGTGTTG-GCAATGCTTGGCCGACACCACCTTTTTTATCA-GAT
33372140 AAAAAAA
1 AAAAAAA
33372147 TAATTTTTTT
Statistics
Matches: 190, Mismatches: 22, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
52 14 0.07
53 65 0.34
54 59 0.31
55 7 0.04
56 9 0.05
57 32 0.17
58 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (53 bp):
AAAAAAAATTTGGTGTTGGCAATGCTTGGCCGACACCACCTTTTTTATCAGAT
Found at i:33372066 original size:106 final size:107
Alignment explanation
Indices: 33371869--33372151 Score: 351
Period size: 106 Copynumber: 2.6 Consensus size: 107
33371859 CGATATTTTA
* *
33371869 AAAAAAAAATTGGTGTTGGTCAATGCTTGGCCGACACCACCTTTTTTATC-TGATAAAAAAAATT
1 AAAAAAAATTTGGTGTT-GTCAATGCTTGGCCGACACCACC-TTTTTATCATGATAAAAAAAAAT
*
33371933 TGGTGTTGGCCATGCATTAGCCAACACCACCTTTTTTATCAGAT
64 TGGAGTTGGCCATGCATTAGCCAACACCACCTTTTTTATCAGAT
*
33371977 -AAAAAAATTTGGTGTTAG-CTAATGTTTGGCCGACACCACCTTTTTATCAT-ATAAAAAAAAAT
1 AAAAAAAATTTGGTGTT-GTC-AATGCTTGGCCGACACCACCTTTTTATCATGATAAAAAAAAAT
* * * * *
33372039 TGGAGTTGGTCATGCATTGGTCGACACCACCTTTTTTATCATAT
64 TGGAGTTGGCCATGCATTAGCCAACACCACCTTTTTTATCAGAT
*
33372083 AAGAAAAAAATTTTGGTGTTGTACAATGCTTGGCCGACACCACTTTTTTTAT-ATGATAAAAAAA
1 -A-AAAAAAA-TTTGGTGTTGT-CAATGCTTGGCCGACACCAC-CTTTTTATCATGATAAAAAAA
33372147 TAATT
61 -AATT
33372152 TTTTTTGGTA
Statistics
Matches: 152, Mismatches: 12, Indels: 18
0.84 0.07 0.10
Matches are distributed among these distances:
106 58 0.38
107 36 0.24
109 8 0.05
110 29 0.19
111 17 0.11
112 4 0.03
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (107 bp):
AAAAAAAATTTGGTGTTGTCAATGCTTGGCCGACACCACCTTTTTATCATGATAAAAAAAAATTG
GAGTTGGCCATGCATTAGCCAACACCACCTTTTTTATCAGAT
Found at i:33372182 original size:61 final size:57
Alignment explanation
Indices: 33371891--33372190 Score: 215
Period size: 53 Copynumber: 5.4 Consensus size: 57
33371881 GTGTTGGTCA
* * *
33371891 ATGC-TTGGCCGACACCACCTTTTTTATC-TGAT-A-AAAAAAA-TTTGGTGTTGGCC
1 ATGCATTGGCCGACACCACTTTTTTTATCAT-ATAAGAAAAAAATTTTGGTATTGGAC
* * * * * *
33371944 ATGCATTAGCCAACACCACCTTTTTTATCAGAT---AAAAAAA-TTTGGTGTTAG-C
1 ATGCATTGGCCGACACCACTTTTTTTATCATATAAGAAAAAAATTTTGGTATTGGAC
* * *
33371996 TAATG-TTTGGCCGACACCAC-CTTTTTATCATATAA-AAAAAAA--TTGG-AGTTGGTC
1 --ATGCATTGGCCGACACCACTTTTTTTATCATATAAGAAAAAAATTTTGGTA-TTGGAC
* * * *
33372050 ATGCATTGGTCGACACCACCTTTTTTATCATATAAGAAAAAAATTTTGGTGTTGTAC
1 ATGCATTGGCCGACACCACTTTTTTTATCATATAAGAAAAAAATTTTGGTATTGGAC
33372107 AATGC-TTGGCCGACACCACTTTTTTTAT-ATGATAA-AAAAATAATTTTTTTTGGTATTGGAC
1 -ATGCATTGGCCGACACCACTTTTTTTATCAT-ATAAGAAAAA-AA----TTTTGGTATTGGAC
33372168 ATGCATTGGCCGACACCAACTTT
1 ATGCATTGGCCGACACC-ACTTT
33372191 CCCTCTTTTT
Statistics
Matches: 203, Mismatches: 21, Indels: 37
0.78 0.08 0.14
Matches are distributed among these distances:
52 15 0.07
53 53 0.26
54 49 0.24
55 7 0.03
56 7 0.03
57 35 0.17
58 4 0.02
60 4 0.02
61 24 0.12
62 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (57 bp):
ATGCATTGGCCGACACCACTTTTTTTATCATATAAGAAAAAAATTTTGGTATTGGAC
Found at i:33373062 original size:30 final size:30
Alignment explanation
Indices: 33373026--33373117 Score: 139
Period size: 30 Copynumber: 3.1 Consensus size: 30
33373016 AAAAAATAAT
*
33373026 AATTAGAAATGAAATTTAAAATATAAACGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
*
33373056 AATTAGAAATTAAATTTAAAATATAAACAA
1 AATTAGAAATTAAATTTAAAATATAAACGA
* * *
33373086 AATTACAAATTAAATTTAAAAAATAAATGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
33373116 AA
1 AA
33373118 AAAATCAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.28
Consensus pattern (30 bp):
AATTAGAAATTAAATTTAAAATATAAACGA
Found at i:33374310 original size:36 final size:36
Alignment explanation
Indices: 33374260--33374331 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
33374250 ATTTTTTAAT
33374260 ATTTCGAAAATATAAAAAAT-ATATGTAAAAAAATTC
1 ATTTCGAAAATATAAAAAATAAT-TGTAAAAAAATTC
* * *
33374296 ATTTTGAAGATATAAAAAATAATTTTAAAAAAATTC
1 ATTTCGAAAATATAAAAAATAATTGTAAAAAAATTC
33374332 GAAAGCTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 30 0.94
37 2 0.06
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (36 bp):
ATTTCGAAAATATAAAAAATAATTGTAAAAAAATTC
Found at i:33374488 original size:157 final size:156
Alignment explanation
Indices: 33374184--33374505 Score: 531
Period size: 155 Copynumber: 2.1 Consensus size: 156
33374174 TCATTTGTAA
*
33374184 AAAAAATATTTTGAAAATATAAAAAATATAAGATTTTTAATTTGTCAAAAAATATTTCAAAAATT
1 AAAAAATATTTTGAAAATATAAAAAATATAAGATTTTTAATTTGTAAAAAAATATTTCAAAAATT
* *
33374249 TATTTTTTAATATTTCGAAAATATAAAAAATATATGTAAAAAAATTCATTTTGAAGATATAAAAA
66 AATTTTTTAATATTTCGAAAATATAAAAAATATATGTAAAAAAATTCATTTCGAAGATATAAAAA
*
33374314 ATAATTTTAAAAAAATTC-GAAAGCT
131 ATAATTTTAAAAAAATTCAAAAAGCT
**
33374339 AAAAAATATTTTGAAAATATAAAAAATATAAGATTTTTAATTTGTAAAAAAATATTTTGAAAATG
1 AAAAAATATTTTGAAAATATAAAAAATATAAGATTTTTAATTTGTAAAAAAATATTTCAAAAAT-
*
33374404 TAATTTTTTAATATTTC-AAAATTATAAAAAAATATATGTAAAAAATTTCATTTCGAAGATATAA
65 TAATTTTTTAATATTTCGAAAA-TAT-AAAAAATATATGTAAAAAAATTCATTTCGAAGATATAA
*
33374468 AAAATAATTTTAGAAAAATTCAAAAAGCT
128 AAAATAATTTTAAAAAAATTCAAAAAGCT
33374497 AAAAAATAT
1 AAAAAATAT
33374506 ATGTAAAAAA
Statistics
Matches: 155, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
155 65 0.42
156 19 0.12
157 56 0.36
158 15 0.10
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.36
Consensus pattern (156 bp):
AAAAAATATTTTGAAAATATAAAAAATATAAGATTTTTAATTTGTAAAAAAATATTTCAAAAATT
AATTTTTTAATATTTCGAAAATATAAAAAATATATGTAAAAAAATTCATTTCGAAGATATAAAAA
ATAATTTTAAAAAAATTCAAAAAGCT
Found at i:33375515 original size:93 final size:93
Alignment explanation
Indices: 33375353--33375991 Score: 987
Period size: 93 Copynumber: 6.8 Consensus size: 93
33375343 GACTAAGGAT
* * * *
33375353 AATATTATAATAATCATTTTTAATTTAAATAATTTTTAATTTTTAATTTGATAAATAATATATTA
1 AATATTATAATAATC---TTTAATTTAAATAATTTTAAAATTTGAATTTGATAAATAATATATTG
33375418 TCAAATCAACACATTATTTGATATAAATTGA
63 TCAAATCAACACATTATTTGATATAAATTGA
*
33375449 AATATTATAATAATCTTTAATTTAAATAATTTTAAAATTTAAATTTGATAAATAATATATTGTCA
1 AATATTATAATAATCTTTAATTTAAATAATTTTAAAATTTGAATTTGATAAATAATATATTGTCA
33375514 AATCAACACATTATTTGATATAAATTGA
66 AATCAACACATTATTTGATATAAATTGA
33375542 AATATTATAATAATCTTTAATTTAAATAATTTTAAAATTTGAATTTGATAAATAATATATTGTCA
1 AATATTATAATAATCTTTAATTTAAATAATTTTAAAATTTGAATTTGATAAATAATATATTGTCA
* *
33375607 AATAAACACATTATTTTATATAAATTGA
66 AATCAACACATTATTTGATATAAATTGA
*
33375635 AATATTATAATAATCATTTTTAATTTAAATAATTTTAAATTTTTGAATTTGATAAATAATATATT
1 AATATTATAATAATC---TTTAATTTAAATAATTTTAAA-ATTTGAATTTGATAAATAATATATT
* *
33375700 ATCAAATCAACACATTATTTTATATAAATTGA
62 GTCAAATCAACACATTATTTGATATAAATTGA
* *
33375732 AATATTATAATAATCATTTTAATTTAAATAATTTT-AAATTTGAATTTAATAAATAATGTATTGT
1 AATATTATAATAATC--TTTAATTTAAATAATTTTAAAATTTGAATTTGATAAATAATATATTGT
33375796 CAAATCAACACATTATTTGATATAAATTGA
64 CAAATCAACACATTATTTGATATAAATTGA
*
33375826 AATATTATAATAATCTTTAATTTAAATAATTTTAAAATTTAAATTTGATAAATAATATATTGTCA
1 AATATTATAATAATCTTTAATTTAAATAATTTTAAAATTTGAATTTGATAAATAATATATTGTCA
* *
33375891 AATCAACATATTGTTTGATATAAATTGA
66 AATCAACACATTATTTGATATAAATTGA
* *
33375919 AATATTATACTAATCAACTTTAATTTAAATAATTTT-AAATTTGAATTT-AGTAAATAATGTATT
1 AATATTATAATAAT---CTTTAATTTAAATAATTTTAAAATTTGAATTTGA-TAAATAATATATT
33375982 GTCAAATCAA
62 GTCAAATCAA
33375992 ATTAATTTTT
Statistics
Matches: 510, Mismatches: 24, Indels: 19
0.92 0.04 0.03
Matches are distributed among these distances:
92 18 0.04
93 246 0.48
94 68 0.13
95 35 0.07
96 74 0.15
97 69 0.14
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (93 bp):
AATATTATAATAATCTTTAATTTAAATAATTTTAAAATTTGAATTTGATAAATAATATATTGTCA
AATCAACACATTATTTGATATAAATTGA
Found at i:33375861 original size:284 final size:283
Alignment explanation
Indices: 33375353--33375991 Score: 1081
Period size: 284 Copynumber: 2.3 Consensus size: 283
33375343 GACTAAGGAT
*
33375353 AATATTATAATAATCATTTTTAATTTAAATAATTTTTAATTTTT-AATTTGATAAATAATATATT
1 AATATTATAATAATCATTTTTAATTTAAATAATTTTAAATTTTTGAATTTGATAAATAATATATT
33375417 ATCAAATCAACACATTATTTGATATAAATTGAAATATTATAATAATCTTTAATTTAAATAATTTT
66 ATCAAATCAACACATTATTTGATATAAATTGAAATATTATAATAATCTTTAATTTAAATAATTTT
*
33375482 AAAATTTAAATTTGATAAATAATATATTGTCAAATCAACACATTATTTGATATAAATTGAAATAT
131 AAAATTTAAATTTAATAAATAATATATTGTCAAATCAACACATTATTTGATATAAATTGAAATAT
*
33375547 TATAATAATCTTTAATTTAAATAATTTTAAAATTTGAATTTGATAAATAATATATTGTCAAATAA
196 TATAATAATCTTTAATTTAAATAATTTTAAAATTTAAATTTGATAAATAATATATTGTCAAATAA
*
33375612 ACACATTATTTTATATAAATTGA
261 ACACATTATTTGATATAAATTGA
33375635 AATATTATAATAATCATTTTTAATTTAAATAATTTTAAATTTTTGAATTTGATAAATAATATATT
1 AATATTATAATAATCATTTTTAATTTAAATAATTTTAAATTTTTGAATTTGATAAATAATATATT
*
33375700 ATCAAATCAACACATTATTTTATATAAATTGAAATATTATAATAATCATTTTAATTTAAATAATT
66 ATCAAATCAACACATTATTTGATATAAATTGAAATATTATAATAATC--TTTAATTTAAATAATT
* *
33375765 TT-AAATTTGAATTTAATAAATAATGTATTGTCAAATCAACACATTATTTGATATAAATTGAAAT
129 TTAAAATTTAAATTTAATAAATAATATATTGTCAAATCAACACATTATTTGATATAAATTGAAAT
33375829 ATTATAATAATCTTTAATTTAAATAATTTTAAAATTTAAATTTGATAAATAATATATTGTCAAAT
194 ATTATAATAATCTTTAATTTAAATAATTTTAAAATTTAAATTTGATAAATAATATATTGTCAAAT
* * *
33375894 CAACATATTGTTTGATATAAATTGA
259 AAACACATTATTTGATATAAATTGA
* ** *
33375919 AATATTATACTAATCAACTTTAATTTAAATAATTTTAAA--TTTGAATTT-AGTAAATAATGTAT
1 AATATTATAATAATCATTTTTAATTTAAATAATTTTAAATTTTTGAATTTGA-TAAATAATATAT
*
33375981 TGTCAAATCAA
65 TATCAAATCAA
33375992 ATTAATTTTT
Statistics
Matches: 338, Mismatches: 15, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
281 1 0.00
282 73 0.22
283 66 0.20
284 180 0.53
285 18 0.05
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (283 bp):
AATATTATAATAATCATTTTTAATTTAAATAATTTTAAATTTTTGAATTTGATAAATAATATATT
ATCAAATCAACACATTATTTGATATAAATTGAAATATTATAATAATCTTTAATTTAAATAATTTT
AAAATTTAAATTTAATAAATAATATATTGTCAAATCAACACATTATTTGATATAAATTGAAATAT
TATAATAATCTTTAATTTAAATAATTTTAAAATTTAAATTTGATAAATAATATATTGTCAAATAA
ACACATTATTTGATATAAATTGA
Found at i:33376312 original size:25 final size:25
Alignment explanation
Indices: 33376254--33376343 Score: 146
Period size: 25 Copynumber: 3.6 Consensus size: 25
33376244 CAATTTCATT
* * *
33376254 TAATTTTAATTTCAAATGT-AATTT
1 TAATTTTAATTTCAAATTTAAACTA
33376278 TAATTTTAATTTCAAATTTAAACTA
1 TAATTTTAATTTCAAATTTAAACTA
33376303 TAATTTTAATTTCAAATTTAAACTA
1 TAATTTTAATTTCAAATTTAAACTA
33376328 TAATTTTAATTTCAAA
1 TAATTTTAATTTCAAA
33376344 CTAGTATTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
24 18 0.29
25 44 0.71
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (25 bp):
TAATTTTAATTTCAAATTTAAACTA
Found at i:33376333 original size:19 final size:19
Alignment explanation
Indices: 33376309--33376380 Score: 53
Period size: 19 Copynumber: 3.9 Consensus size: 19
33376299 ACTATAATTT
33376309 TAATTTCAAATTT-AAACTA
1 TAATTT-AAATTTCAAACTA
*
33376328 TAATTTTAATTTCAAACTA
1 TAATTTAAATTTCAAACTA
* * **
33376347 GT-ATTTTAATTTGAAGTTA
1 -TAATTTAAATTTCAAACTA
33376366 -AATTTAAATTT-AAAC
1 TAATTTAAATTTCAAAC
33376381 ATGTATTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
17 2 0.05
18 14 0.33
19 26 0.60
20 1 0.02
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (19 bp):
TAATTTAAATTTCAAACTA
Found at i:33376358 original size:6 final size:6
Alignment explanation
Indices: 33376252--33376339 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
33376242 TCCAATTTCA
* * * * * *
33376252 TTTAAT TTTAAT TTCAAA TGTAAT TTTAAT TTTAAT TTCAAAT TTAAAC
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TT-TAAT TTTAAT
* * * * *
33376301 TATAAT TTTAAT TTCAAAT TTAAAC TATAAT TTTAAT TT
1 TTTAAT TTTAAT TT-TAAT TTTAAT TTTAAT TTTAAT TT
33376340 CAAACTAGTA
Statistics
Matches: 62, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
6 52 0.84
7 10 0.16
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (6 bp):
TTTAAT
Found at i:33376387 original size:36 final size:38
Alignment explanation
Indices: 33376329--33376403 Score: 102
Period size: 37 Copynumber: 2.0 Consensus size: 38
33376319 TTTAAACTAT
* *
33376329 AATTTTAATTTCAAACTAGTATTTTAA-TTTGAAGTTA
1 AATTTAAATTTCAAACTAGTATTTTAATTTTGAAATTA
33376366 AATTTAAATTT-AAAC-ATGTATTTTAATTTTGAAATTA
1 AATTTAAATTTCAAACTA-GTATTTTAATTTTGAAATTA
33376403 A
1 A
33376404 TTTCAACTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 1 0.03
36 13 0.38
37 20 0.59
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (38 bp):
AATTTAAATTTCAAACTAGTATTTTAATTTTGAAATTA
Found at i:33376406 original size:18 final size:17
Alignment explanation
Indices: 33376253--33376406 Score: 53
Period size: 18 Copynumber: 8.4 Consensus size: 17
33376243 CCAATTTCAT
*
33376253 TTAATTTTAATTTCAAA
1 TTAATTTTAATTTGAAA
* *
33376270 TGTAATTTTAATTTTAAT
1 T-TAATTTTAATTTGAAA
* * *
33376288 TTCAAATTTAAACTAT-AATT
1 TT--AATTTTAA-TTTGAA-A
*
33376308 TTAATTTCAAATTT-AAA
1 TTAATTT-TAATTTGAAA
*
33376325 CTATAATTTTAATTTCAAA
1 -T-TAATTTTAATTTGAAA
* *
33376344 CTAGTATTTTAATTTGAAG
1 TTA--ATTTTAATTTGAAA
* *
33376363 TTAAATTTAAATTTAAACA
1 TT-AATTTTAATTTGAA-A
33376382 TGT-ATTTTAATTTTGAAA
1 T-TAATTTTAA-TTTGAAA
33376400 TTAATTT
1 TTAATTT
33376407 CAACTTAATT
Statistics
Matches: 105, Mismatches: 16, Indels: 31
0.69 0.11 0.20
Matches are distributed among these distances:
17 5 0.05
18 53 0.50
19 40 0.38
20 7 0.07
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (17 bp):
TTAATTTTAATTTGAAA
Found at i:33376406 original size:36 final size:36
Alignment explanation
Indices: 33376328--33376406 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
33376318 ATTTAAACTA
* *
33376328 TAATTTTAATTTCAAACTAGTATTTTAATTTGAAGT
1 TAATTTAAATTTCAAACTAGTATTTTAATTTGAAAT
33376364 TAAATTTAAATTT-AAAC-ATGTATTTTAATTTTGAAAT
1 T-AATTTAAATTTCAAACTA-GTATTTTAA-TTTGAAAT
33376401 TAATTT
1 TAATTT
33376407 CAACTTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
35 1 0.03
36 19 0.50
37 18 0.47
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (36 bp):
TAATTTAAATTTCAAACTAGTATTTTAATTTGAAAT
Found at i:33376426 original size:17 final size:16
Alignment explanation
Indices: 33376400--33376434 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
33376390 AATTTTGAAA
*
33376400 TTAATTTCAACTTAAT
1 TTAATTTCAAATTAAT
33376416 TTAATTTTCAAATTAAT
1 TTAA-TTTCAAATTAAT
33376433 TT
1 TT
33376435 CAACATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAATTTCAAATTAAT
Found at i:33380509 original size:61 final size:59
Alignment explanation
Indices: 33380385--33380877 Score: 479
Period size: 55 Copynumber: 8.5 Consensus size: 59
33380375 GAAAACTTGA
* *
33380385 TGTCGGCCAATGCATGGCCAACACAAAAAAATTTTATTTTTTTTCTCTGATAAAAAAGATGG
1 TGTCGGCCAATGCATGGCCAACACCAAAAAA--TT-TTTTTTTTATCTGATAAAAAAGATGG
*
33380447 TGTCGGCCAATGCATGGCCAACACCAAAAAATTTTATTTTTTTATCAGATAAAAAA-AGTGG
1 TGTCGGCCAATGCATGGCCAACACCAAAAAA-TTT-TTTTTTTATCTGATAAAAAAGA-TGG
*
33380508 TGTCGGCCAA-GCATTGGCCAACACC--AAAA--TTTTTTTTATCTGATAAAAAAGGTGG
1 TGTCGGCCAATGCA-TGGCCAACACCAAAAAATTTTTTTTTTATCTGATAAAAAAGATGG
* * * * ***
33380563 TGTCGACAAATGCATGGCCAATACCAAAAAAATTTGTTTATTTATCACTTAAAAAAGATGG
1 TGTCGGCCAATGCATGGCCAACACC-AAAAAATTT-TTTTTTTATCTGATAAAAAAGATGG
* * *
33380624 TGCCGACCAA-GCATTGTCCAACACC--AAAATTTTTTTTATTATCTGATAAAAAAGATGG
1 TGTCGGCCAATGCA-TGGCCAACACCAAAAAATTTTTTTT-TTATCTGATAAAAAAGATGG
* ** * * *
33380682 TGTCGACCAATGCATATCCAACACAAAAAAAATTATTTTTTATCTGATAAAAAAGATGG
1 TGTCGGCCAATGCATGGCCAACACCAAAAAATTTTTTTTTTATCTGATAAAAAAGATGG
* **
33380741 TGTCGGCCAATGCATGACC-A-A-CATTAAA-TTTTTTTTT-TCTGATAAAAAACG-TGG
1 TGTCGGCCAATGCATGGCCAACACCAAAAAATTTTTTTTTTATCTGATAAAAAA-GATGG
* * *
33380795 TGTCGGCTAA-GCATTGGCCAACACC---AAA-TTTTTTTTTATCTGATCAAAAAGGTGG
1 TGTCGGCCAATGCA-TGGCCAACACCAAAAAATTTTTTTTTTATCTGATAAAAAAGATGG
33380850 TGTCGGCCAA-GCATTGGCCAACACCAAA
1 TGTCGGCCAATGCA-TGGCCAACACCAAA
33380878 TTTTTTTTCA
Statistics
Matches: 368, Mismatches: 37, Indels: 56
0.80 0.08 0.12
Matches are distributed among these distances:
53 3 0.01
54 41 0.11
55 88 0.24
56 9 0.02
57 6 0.02
58 47 0.13
59 43 0.12
60 19 0.05
61 82 0.22
62 30 0.08
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (59 bp):
TGTCGGCCAATGCATGGCCAACACCAAAAAATTTTTTTTTTATCTGATAAAAAAGATGG
Found at i:33380607 original size:116 final size:115
Alignment explanation
Indices: 33380420--33380885 Score: 542
Period size: 116 Copynumber: 4.1 Consensus size: 115
33380410 AAAAAATTTT
* * *
33380420 ATTTTTTTTCTCTGATAAAAAAGATGGTGTCGGCCAATGCATGGCCAACACCAAAAAATTTTATT
1 ATTTTTTTTATCTGATAAAAAAGATGGTGTCGACCAATGCATGGCCAACACCAAAAAAATTTA-T
33380485 TTTTTATCAGATAAAAAA-AGTGGTGTCGGCCAAGCATTGGCCAACACCAAA
65 TTTTTATCAGATAAAAAAGA-TGGTGTCGGCCAAGCATTGGCCAACACCAAA
* * * *
33380536 ATTTTTTTTATCTGATAAAAAAGGTGGTGTCGACAAATGCATGGCCAATACCAAAAAAATTTGTT
1 ATTTTTTTTATCTGATAAAAAAGATGGTGTCGACCAATGCATGGCCAACACCAAAAAAATTTATT
** * * *
33380601 TATTTATCACTTAAAAAAGATGGTGCCGACCAAGCATTGTCCAACACCAAA
66 T-TTTATCAGATAAAAAAGATGGTGTCGGCCAAGCATTGGCCAACACCAAA
** *
33380652 ATTTTTTTTATTATCTGATAAAAAAGATGGTGTCGACCAATGCATATCCAACA-CAAAAAAAATT
1 A--TTTTTT-TTATCTGATAAAAAAGATGGTGTCGACCAATGCATGGCCAACACCAAAAAAATTT
* * **
33380716 ATTTTTTATCTGATAAAAAAGATGGTGTCGGCCAATGCA-TGACCAACA-TTAA
63 ATTTTTTATCAGATAAAAAAGATGGTGTCGGCCAA-GCATTGGCCAACACCAAA
* * *
33380768 ATTTTTTTTTTCTGATAAAAAACG-TGGTGTCGGCTAA-GCATTGGCCAACACC----AAATTT-
1 ATTTTTTTTATCTGATAAAAAA-GATGGTGTCGACCAATGCA-TGGCCAACACCAAAAAAATTTA
* * *
33380826 TTTTTTATCTGATCAAAAAGGTGGTGTCGGCCAAGCATTGGCCAACACC-AA
64 TTTTTTATCAGATAAAAAAGATGGTGTCGGCCAAGCATTGGCCAACACCAAA
33380877 ATTTTTTTT
1 ATTTTTTTT
33380886 CAAAATCTCG
Statistics
Matches: 302, Mismatches: 37, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
108 3 0.01
109 51 0.17
110 5 0.02
112 3 0.01
113 32 0.11
114 8 0.03
115 3 0.01
116 102 0.34
117 35 0.12
118 22 0.07
119 38 0.13
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (115 bp):
ATTTTTTTTATCTGATAAAAAAGATGGTGTCGACCAATGCATGGCCAACACCAAAAAAATTTATT
TTTTATCAGATAAAAAAGATGGTGTCGGCCAAGCATTGGCCAACACCAAA
Found at i:33381511 original size:25 final size:26
Alignment explanation
Indices: 33381447--33381511 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 26
33381437 TTAAACTCAT
*
33381447 TTATATA-ATAATTTGAATTTATATA
1 TTATATATATCATTTGAATTTATATA
*
33381472 TGATATTATATCATTT-AGATTTA-ATA
1 TTATA-TATATCATTTGA-ATTTATATA
33381498 TTATATATATCATT
1 TTATATATATCATT
33381512 AAATAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 13 0.38
26 10 0.29
27 11 0.32
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (26 bp):
TTATATATATCATTTGAATTTATATA
Found at i:33385459 original size:38 final size:38
Alignment explanation
Indices: 33385408--33385483 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
33385398 AGATAAAAGA
33385408 AAGGGAAAATTGTAATGCTGATCCCAGTGGTTCTCTAT
1 AAGGGAAAATTGTAATGCTGATCCCAGTGGTTCTCTAT
*
33385446 AAGGGAAAATTGTAATGCTGATCCTAGTGGTTCTCTAT
1 AAGGGAAAATTGTAATGCTGATCCCAGTGGTTCTCTAT
33385484 GGCACTGCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (38 bp):
AAGGGAAAATTGTAATGCTGATCCCAGTGGTTCTCTAT
Found at i:33386454 original size:23 final size:23
Alignment explanation
Indices: 33386428--33386472 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
33386418 GGAACGAATT
* *
33386428 TGAACACTACTGAAGTGGATAAC
1 TGAACACCACTGAAGCGGATAAC
33386451 TGAACACCACTGAAGCGGATAA
1 TGAACACCACTGAAGCGGATAA
33386473 ACAATAAGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (23 bp):
TGAACACCACTGAAGCGGATAAC
Found at i:33393433 original size:18 final size:18
Alignment explanation
Indices: 33393412--33393446 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33393402 TTTCAAATAT
33393412 TTCATTATT-AAATAAAAA
1 TTCATT-TTCAAATAAAAA
33393430 TTCATTTTCAAATAAAA
1 TTCATTTTCAAATAAAA
33393447 TATTTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (18 bp):
TTCATTTTCAAATAAAAA
Found at i:33394793 original size:20 final size:19
Alignment explanation
Indices: 33394768--33394824 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 19
33394758 AACTTTTGAA
*
33394768 TAAAAAATTGTAAAAATTAT
1 TAAAAAATTATAAAAATT-T
* *
33394788 TAAAAATTTATAAAACTTT
1 TAAAAAATTATAAAAATTT
* *
33394807 AAAATAAATTTTAAAAAT
1 TAAA-AAATTATAAAAAT
33394825 ACGAAATATA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAAAAATTATAAAAATTT
Found at i:33397349 original size:21 final size:19
Alignment explanation
Indices: 33397325--33397387 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
33397315 ACTAAAGGAC
*
33397325 TTAATTGTATAAAATTGTTAT
1 TTAATTG-ATGAAATT-TTAT
* *
33397346 TTAAGTGCTGAAATTTTA-
1 TTAATTGATGAAATTTTAT
33397364 TTAATTGAATGAAATTATTAT
1 TTAATTG-ATGAAATT-TTAT
33397385 TTA
1 TTA
33397388 GATCAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 6 0.18
19 10 0.29
20 9 0.26
21 9 0.26
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (19 bp):
TTAATTGATGAAATTTTAT
Found at i:33399480 original size:29 final size:29
Alignment explanation
Indices: 33399448--33399735 Score: 245
Period size: 30 Copynumber: 9.8 Consensus size: 29
33399438 TTTCAGAGAA
**
33399448 TTTAGGGTTAAAACATAATTTTAGAAAAG
1 TTTAGGGTTAAAATGTAATTTTAGAAAAG
* * **
33399477 TTTAAGGGTAAAAAATGTAATTTTGGGGAAG
1 TTT-AGGGT-TAAAATGTAATTTTAGAAAAG
* * *
33399508 TTTGGGGGTTAAAATGTGATTTTAGGAAAG
1 TTT-AGGGTTAAAATGTAATTTTAGAAAAG
* * *
33399538 TTTAAGATTAAAATGTAATTTTTGAAAAG
1 TTTAGGGTTAAAATGTAATTTTAGAAAAG
* *
33399567 TTTAAGGGTTAAAATATAATTTTTGAAAAG
1 TTT-AGGGTTAAAATGTAATTTTAGAAAAG
** * *
33399597 TTTAGGGGCCAAAATGTGATTTTAGAAAAA
1 TTTA-GGGTTAAAATGTAATTTTAGAAAAG
* * * *
33399627 TTTAGGGTTAAATTGTGATTTTGGGAAAG
1 TTTAGGGTTAAAATGTAATTTTAGAAAAG
33399656 TTTAGGGTTAAAATGTAATTTTAGAAAAG
1 TTTAGGGTTAAAATGTAATTTTAGAAAAG
** * * * *
33399685 TTCGGGGGTCAGAATGTGATTTTAGAAATG
1 TT-TAGGGTTAAAATGTAATTTTAGAAAAG
* *
33399715 TTT-GGGGTAAAATGTGATTTT
1 TTTAGGGTTAAAATGTAATTTT
33399736 TAAATAAAAT
Statistics
Matches: 207, Mismatches: 47, Indels: 11
0.78 0.18 0.04
Matches are distributed among these distances:
28 15 0.07
29 73 0.35
30 97 0.47
31 22 0.11
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
TTTAGGGTTAAAATGTAATTTTAGAAAAG
Found at i:33399580 original size:59 final size:59
Alignment explanation
Indices: 33399451--33399735 Score: 234
Period size: 59 Copynumber: 4.8 Consensus size: 59
33399441 CAGAGAATTT
** * * * * **
33399451 AGGGTTAAAACATAATTTTAGAAAAGTTTAAGGGTAAAAAATGTAATTTTGGGGAAGTTTG
1 AGGGTTAAAATGTGATTTTAGGAAAGTTTAA-GGT-TAAAATGTAATTTTAGAAAAGTTTG
* * * *
33399512 GGGGTTAAAATGTGATTTTAGGAAAGTTTAAGATTAAAATGTAATTTTTGAAAAGTTTA
1 AGGGTTAAAATGTGATTTTAGGAAAGTTTAAGGTTAAAATGTAATTTTAGAAAAGTTTG
* * * * * ** * *
33399571 AGGGTTAAAATATAATTTTTGAAAAGTTTAGGGGCCAAAATGTGATTTTAGAAAAATTT-
1 AGGGTTAAAATGTGATTTTAGGAAAGTTTA-AGGTTAAAATGTAATTTTAGAAAAGTTTG
* * * *
33399630 AGGGTTAAATTGTGATTTTGGGAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAGTTCG
1 AGGGTTAAAATGTGATTTTAGGAAAGTTTAAGGTTAAAATGTAATTTTAGAAAAGTTTG
* * * * * *
33399689 GGGGTCAGAATGTGATTTTA-GAAATGTTT-GGGGTAAAATGTGATTTT
1 AGGGTTAAAATGTGATTTTAGGAAA-GTTTAAGGTTAAAATGTAATTTT
33399736 TAAATAAAAT
Statistics
Matches: 181, Mismatches: 40, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
58 43 0.24
59 89 0.49
60 23 0.13
61 26 0.14
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (59 bp):
AGGGTTAAAATGTGATTTTAGGAAAGTTTAAGGTTAAAATGTAATTTTAGAAAAGTTTG
Found at i:33400554 original size:24 final size:26
Alignment explanation
Indices: 33400503--33400563 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
33400493 AGCTATCCCC
*
33400503 TTTTTTAGAATCTGTTTCTTATGTTT
1 TTTTTTAGAATCTGTTTCTAATGTTT
*
33400529 TTTTTTA-AATTTGTTTCTAATGTTT
1 TTTTTTAGAATCTGTTTCTAATGTTT
*
33400554 TCTTTGTAGA
1 T-TTTTTAGA
33400564 TTTGCCATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.57
26 12 0.40
27 1 0.03
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.64
Consensus pattern (26 bp):
TTTTTTAGAATCTGTTTCTAATGTTT
Found at i:33401891 original size:125 final size:123
Alignment explanation
Indices: 33401669--33401998 Score: 371
Period size: 125 Copynumber: 2.6 Consensus size: 123
33401659 GCTTCATCTC
* * * * *
33401669 TTGGTCTACTTCTCTGTATCACATCAGAAAGATAACCAG-TTTATTGTTTCGACCCACTTCTCTA
1 TTGGTCTACTTCTCTGTATCTCATCAGAAAGATGACC-GCTTCATTGTTT-GATCCACTTCTCTG
*** * * *
33401733 TATCTCATCAGGAAGATAGGGATTTGGAGTTTCATTCGCATTGAACG-TT-GCTTCATTTGAT
64 TATCTCATCAGGAAGATAGGGATTCAAAGTTTCACTCACATTG-A-GTTTCGCTTCA-TCGAT
* * * *
33401794 TTGGTCTAGTTCTCTGTATCTCATTAGAAAGATGACCGCTTCATTATTGTGATCCACTTCTTTGT
1 TTGGTCTACTTCTCTGTATCTCATCAGAAAGATGACCGCTTCATTGTT-TGATCCACTTCTCTGT
*
33401859 ATCTCATCAGGAAGATGGGGATTCAAAGTTTCACTCACATTGAGTTTCGCTTCATCGAT
65 ATCTCATCAGGAAGATAGGGATTCAAAGTTTCACTCACATTGAGTTTCGCTTCATCGAT
* * * *
33401918 TTGGTCTACTTCTCTATATCTCATCA-AGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCT
1 TTGGTCTACTTCTCTGTATCTCATCAGA-AAGATGACCGCTTCA-TTG-TTTGATCCACTTCTCT
33401982 GTATCTCATCAGGAAGA
63 GTATCTCATCAGGAAGA
33401999 CAGATTTGGT
Statistics
Matches: 174, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
123 2 0.01
124 45 0.26
125 124 0.71
126 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.37
Consensus pattern (123 bp):
TTGGTCTACTTCTCTGTATCTCATCAGAAAGATGACCGCTTCATTGTTTGATCCACTTCTCTGTA
TCTCATCAGGAAGATAGGGATTCAAAGTTTCACTCACATTGAGTTTCGCTTCATCGAT
Found at i:33402077 original size:210 final size:210
Alignment explanation
Indices: 33401791--33402597 Score: 1143
Period size: 210 Copynumber: 3.8 Consensus size: 210
33401781 TGCTTCATTT
* * * * * * * *
33401791 GATTTGGTCTAGTTCTCTGTATCTCATTAGAAAGATGACCGCTTCATT-ATTGTGATCCACTTCT
1 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCGCTTTATTGCTT-TGACCCACTTCT
* *
33401855 TTGTATCTCATCAGGAAGATGGGGATTCAAAGTTTCACTCACATTGAGTTTCGCTTCATCGATTT
65 TTGTATCTCATCAGGAAGATGGGGGTTCAAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTT
*
33401920 GGTCTACTTCTCTATATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTA
130 GGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTA
*
33401985 TCTCATCAGGAAGACA
195 TCTCATCAGGAAGACG
** * * *
33402001 GATTTGGTCTTCTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGCTTTGACCCA-TTTTT
1 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCGCTTTATTGCTTTGACCCACTTCTT
* * * * *
33402065 CTGTATCTCATCAAGAAGATGGGGGTTCGAAGTTTCACTCATATTGAGCTCCGTTTCATCGATTT
66 -TGTATCTCATCAGGAAGATGGGGGTTCAAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTT
*
33402130 GGTCTACTTCTCTGTATCTCATCAAGAATATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTA
130 GGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTA
33402195 TCTCATCAGGAAGACG
195 TCTCATCAGGAAGACG
* * *
33402211 GATTTGGTCCACTTCTCTGTATCTTATAAGGAAGACGACCACTTTATTGCTTTGACCCACTTCTT
1 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCGCTTTATTGCTTTGACCCACTTCTT
* * * *
33402276 TGTATCTCATCAGGAAGATGGGGGTTCGAAGTTTCACTCACATTGAGTTTTGCTTCATTGATTTG
66 TGTATCTCATCAGGAAGATGGGGGTTCAAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTG
* * ** * **
33402341 GTCTACTTCTTTGTATCTCATCAGGAAGATGACCATATCATTTGTTTTAATCCATTTCTCTGTAT
131 GTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTAT
*
33402406 CTTATCAGGAAGACG
196 CTCATCAGGAAGACG
* * * * * *
33402421 GATTTAGTCCACTTCTCTGTATCTTATCAAGACGACGACTGCTTTATTGCTTTGACCCACTTCTC
1 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCGCTTTATTGCTTTGACCCACTTCTT
* * *
33402486 TGTATCTCATCAGGAAGATGGGGGTTCAAAGTTTCACTCATATTGAGCTTCGCTTTATCAATTTG
66 TGTATCTCATCAGGAAGATGGGGGTTCAAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTG
*
33402551 GTCTACTTCTCTGTATTTCATCAAGAAGATGACCGCATCAC-TGTTTT
131 GTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCATCACTTGTTTT
33402598 GACATTTCAC
Statistics
Matches: 531, Mismatches: 63, Indels: 7
0.88 0.10 0.01
Matches are distributed among these distances:
209 10 0.02
210 515 0.97
211 6 0.01
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.38
Consensus pattern (210 bp):
GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCGCTTTATTGCTTTGACCCACTTCTT
TGTATCTCATCAGGAAGATGGGGGTTCAAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTG
GTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTAT
CTCATCAGGAAGACG
Found at i:33414543 original size:29 final size:29
Alignment explanation
Indices: 33414502--33414785 Score: 265
Period size: 30 Copynumber: 9.8 Consensus size: 29
33414492 TTTTAGAGAA
*
33414502 TTTAGGGTCAAAATGTAATTTTGGAAAAG
1 TTTAGGGTTAAAATGTAATTTTGGAAAAG
* **
33414531 TTTAGGGTTAAAATGTATTTTTTTAAAAAG
1 TTTAGGGTTAAAATGTA-ATTTTGGAAAAG
* *
33414561 TTTAAGGGTTAAAATATAATTTTTGAAAAG
1 TTT-AGGGTTAAAATGTAATTTTGGAAAAG
* *
33414591 TTTAGGGTTAAAATGTGATTTTGGAAAAA
1 TTTAGGGTTAAAATGTAATTTTGGAAAAG
* *
33414620 TTTA--GTCAAAATGTTATTTTAGG-AAAG
1 TTTAGGGTTAAAATGTAATTTT-GGAAAAG
*
33414647 TTTAGGGGTCAAAATGTAATTTTGGAAAAG
1 TTTA-GGGTTAAAATGTAATTTTGGAAAAG
* * * * *
33414677 -CTAGGGGTCAAATGTGATTTTGGAAAAA
1 TTTAGGGTTAAAATGTAATTTTGGAAAAG
* *
33414705 TTGA-GGTCAAAATGTAATTTTAGG-AAAG
1 TTTAGGGTTAAAATGTAATTTT-GGAAAAG
*
33414733 TTTGGGGGTTAAAATGTAATTTTGGAAAAG
1 TTT-AGGGTTAAAATGTAATTTTGGAAAAG
* * *
33414763 TTTAAGGATAAAAATGTGATTTT
1 TTT-AGGGTTAAAATGTAATTTT
33414786 TAAATAAAAT
Statistics
Matches: 207, Mismatches: 36, Indels: 23
0.78 0.14 0.09
Matches are distributed among these distances:
27 21 0.10
28 40 0.19
29 51 0.25
30 82 0.40
31 13 0.06
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (29 bp):
TTTAGGGTTAAAATGTAATTTTGGAAAAG
Found at i:33414715 original size:86 final size:87
Alignment explanation
Indices: 33414506--33414763 Score: 324
Period size: 86 Copynumber: 3.0 Consensus size: 87
33414496 AGAGAATTTA
* * * * * *
33414506 GGGTCAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTATTTTTTTA-AAAAGTTTAAGGGT
1 GGGTC-AAATGTGATTTTGGAAAAATTTA-GGTCAAAATG--TTATTTTAGGAAAGTTTAGGGGT
* * *
33414570 TAAAATATAATTTTTGAAAAGTTTAG
62 TAAAATGTAATTTTGGAAAAGTCTAG
* * *
33414596 GGTTAAAATGTGATTTTGGAAAAATTTA-GTCAAAATGTTATTTTAGGAAAGTTTAGGGGTCAAA
1 GGGTCAAATGTGATTTTGGAAAAATTTAGGTCAAAATGTTATTTTAGGAAAGTTTAGGGGTTAAA
33414660 ATGTAATTTTGGAAAAG-CTAG
66 ATGTAATTTTGGAAAAGTCTAG
* * *
33414681 GGGTCAAATGTGATTTTGGAAAAATTGAGGTCAAAATGTAATTTTAGGAAAGTTTGGGGGTTAAA
1 GGGTCAAATGTGATTTTGGAAAAATTTAGGTCAAAATGTTATTTTAGGAAAGTTTAGGGGTTAAA
33414746 ATGTAATTTTGGAAAAGT
66 ATGTAATTTTGGAAAAGT
33414764 TTAAGGATAA
Statistics
Matches: 147, Mismatches: 18, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
85 35 0.24
86 80 0.54
87 8 0.05
89 21 0.14
90 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (87 bp):
GGGTCAAATGTGATTTTGGAAAAATTTAGGTCAAAATGTTATTTTAGGAAAGTTTAGGGGTTAAA
ATGTAATTTTGGAAAAGTCTAG
Found at i:33415587 original size:27 final size:27
Alignment explanation
Indices: 33415549--33415601 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
33415539 AGCTATCCCC
33415549 TTTTTTAAAATTTATTTCTTATGTTTG
1 TTTTTTAAAATTTATTTCTTATGTTTG
* *
33415576 TTTTTTTAAATTTGTTTCTTATGTTT
1 TTTTTTAAAATTTATTTCTTATGTTT
33415602 CACGGCTCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.04, G:0.08, T:0.70
Consensus pattern (27 bp):
TTTTTTAAAATTTATTTCTTATGTTTG
Found at i:33420644 original size:15 final size:15
Alignment explanation
Indices: 33420626--33420659 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
33420616 TCATCCTAAG
33420626 TTAGTATAGAACTTA
1 TTAGTATAGAACTTA
*
33420641 TTAGTGTAGAACTTA
1 TTAGTATAGAACTTA
33420656 TTAG
1 TTAG
33420660 AACTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (15 bp):
TTAGTATAGAACTTA
Found at i:33420743 original size:20 final size:19
Alignment explanation
Indices: 33420718--33420767 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
33420708 CAGCATTTGG
*
33420718 TATCGATACCAATTAAAAAA
1 TATCGATACCAA-GAAAAAA
*
33420738 TATCGATACTCGAGAAAAAA
1 TATCGATAC-CAAGAAAAAA
33420758 TATCGATACC
1 TATCGATACC
33420768 TCTAGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 1 0.04
20 24 0.89
21 2 0.07
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.24
Consensus pattern (19 bp):
TATCGATACCAAGAAAAAA
Found at i:33425365 original size:54 final size:55
Alignment explanation
Indices: 33425306--33425418 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 55
33425296 GATAGCTTTA
* * * *
33425306 AGGTTGAATTGAAAATGAGAGAGTCGATTAACTTGAAATTT-TTACCCTTTAAAG
1 AGGTTGAATTGAAAATAAAAGAGTCAATTAAATTGAAATTTATTACCCTTTAAAG
* * *
33425360 AGGTTGCATTGAAACTAAAAGAGTCAATTAAATTGAAATTTAGTTATCCTTTAAAG
1 AGGTTGAATTGAAAATAAAAGAGTCAATTAAATTGAAATTTA-TTACCCTTTAAAG
33425416 AGG
1 AGG
33425419 AACTCAAGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 35 0.70
56 15 0.30
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (55 bp):
AGGTTGAATTGAAAATAAAAGAGTCAATTAAATTGAAATTTATTACCCTTTAAAG
Found at i:33427651 original size:26 final size:26
Alignment explanation
Indices: 33427615--33427677 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
33427605 ATTATAATGA
* **
33427615 AAAATATTAATAAAATAATTAA-ATAT
1 AAAATTTTAAT-AAATAAAAAATATAT
33427641 AAAATTTTAATAAATAAAAAATATAT
1 AAAATTTTAATAAATAAAAAATATAT
33427667 AAAATTATTAA
1 AAAATT-TTAA
33427678 ATATTAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.25
26 20 0.62
27 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAATTTTAATAAATAAAAAATATAT
Found at i:33427692 original size:31 final size:30
Alignment explanation
Indices: 33427637--33427740 Score: 83
Period size: 31 Copynumber: 3.5 Consensus size: 30
33427627 AAATAATTAA
*
33427637 ATATAAAATT-TT-AA--TAAATAAAAAAT
1 ATATAAAATTATTAAATTTAAATTAAAAAT
33427663 ATATAAAATTATTAAATATTAAATTAAAAAT
1 ATATAAAATTATTAAAT-TTAAATTAAAAAT
** * * *
33427694 ATATTTATTTATTTTAATTTAAACTTAATAA-
1 ATATAAAATTA-TTAAATTTAAA-TTAAAAAT
33427725 ATATAAAATATATTAA
1 ATATAAAAT-TATTAA
33427741 TATCATATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
26 10 0.17
27 2 0.03
28 2 0.03
31 33 0.55
32 13 0.22
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (30 bp):
ATATAAAATTATTAAATTTAAATTAAAAAT
Found at i:33431431 original size:39 final size:38
Alignment explanation
Indices: 33431360--33431440 Score: 94
Period size: 38 Copynumber: 2.1 Consensus size: 38
33431350 AAGCTCGTTC
*
33431360 ATATTATTTTTAATTTTTTAAAAATATTTATATTATATT
1 ATATTATTTTTAATTGTTTAAAAATATTTATATT-TATT
* *
33431399 ATATTA-TTTTAA-TGTTTAATAAATTTTATATATTTTTT
1 ATATTATTTTTAATTGTTTAA-AAATATT-TATATTTATT
33431437 ATAT
1 ATAT
33431441 AGTTATCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
37 6 0.16
38 19 0.51
39 12 0.32
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (38 bp):
ATATTATTTTTAATTGTTTAAAAATATTTATATTTATT
Found at i:33438591 original size:21 final size:21
Alignment explanation
Indices: 33438542--33438594 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
33438532 AATACTAGTG
*
33438542 ATAGTTCTACCGATAAAAGTG
1 ATAGTTCTACCGATAAAAGTC
33438563 ATAGTTCTACCGA-AACAAGTC
1 ATAGTTCTACCGATAA-AAGTC
33438584 AT-GCTTCTACC
1 ATAG-TTCTACC
33438595 AATACTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 3 0.10
21 26 0.90
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (21 bp):
ATAGTTCTACCGATAAAAGTC
Found at i:33453885 original size:22 final size:21
Alignment explanation
Indices: 33453843--33453889 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
33453833 TTTTACGTAA
*
33453843 TTTTATTTTATTTTATTTTTG
1 TTTTATTTTATTTTATATTTG
*
33453864 CTTTTGTTTTATTTCT-TATTTG
1 -TTTTATTTTATTT-TATATTTG
33453886 TTTT
1 TTTT
33453890 CTACAGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 4 0.18
22 17 0.77
23 1 0.05
ACGTcount: A:0.11, C:0.04, G:0.06, T:0.79
Consensus pattern (21 bp):
TTTTATTTTATTTTATATTTG
Found at i:33455972 original size:18 final size:19
Alignment explanation
Indices: 33455922--33455973 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
33455912 CGAAACCCAA
33455922 AGAAAGGAAGAGAAAGTGCT
1 AGAAAGGAAGA-AAAGTGCT
*
33455942 A-CAAGGACA-AAAAGTGC-
1 AGAAAGGA-AGAAAAGTGCT
33455959 AGAAAGGAAGAAAAG
1 AGAAAGGAAGAAAAG
33455974 AATAGAAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
17 2 0.07
18 17 0.63
19 6 0.22
20 2 0.07
ACGTcount: A:0.56, C:0.08, G:0.31, T:0.06
Consensus pattern (19 bp):
AGAAAGGAAGAAAAGTGCT
Found at i:33456123 original size:17 final size:17
Alignment explanation
Indices: 33456101--33456133 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
33456091 TGTTAGTGCA
33456101 CATTGTCATTGCATTTC
1 CATTGTCATTGCATTTC
*
33456118 CATTGTCATTGTATTT
1 CATTGTCATTGCATTT
33456134 TAGTGTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (17 bp):
CATTGTCATTGCATTTC
Found at i:33456474 original size:2 final size:2
Alignment explanation
Indices: 33456467--33456496 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
33456457 TACAACTGCT
*
33456467 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33456497 GTTATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:33456531 original size:35 final size:35
Alignment explanation
Indices: 33456486--33456555 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
33456476 ATATATATAC
33456486 ATATATATATAGTTATAAAAAAGAGACACTTGAAT
1 ATATATATATAGTTATAAAAAAGAGACACTTGAAT
33456521 ATATATATATAGTTATAAAAAAGAGACACTTGAAT
1 ATATATATATAGTTATAAAAAAGAGACACTTGAAT
33456556 GTGGGTGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.31
Consensus pattern (35 bp):
ATATATATATAGTTATAAAAAAGAGACACTTGAAT
Found at i:33459114 original size:36 final size:36
Alignment explanation
Indices: 33459067--33459137 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
33459057 ACGCAAGAGA
33459067 GAAGTAAGAGAGCAAGTCGAGTAGCCTAGGAATAGG
1 GAAGTAAGAGAGCAAGTCGAGTAGCCTAGGAATAGG
33459103 GAAGTAAGAGAGCAAGTCGAGTAGCCTAGGAATAG
1 GAAGTAAGAGAGCAAGTCGAGTAGCCTAGGAATAG
33459138 TATTATCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.35, T:0.14
Consensus pattern (36 bp):
GAAGTAAGAGAGCAAGTCGAGTAGCCTAGGAATAGG
Found at i:33465652 original size:28 final size:28
Alignment explanation
Indices: 33465620--33465679 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
33465610 AAAACGGGAC
*
33465620 TTTTGGA-TACCCGAGGGTAAAATGGTAA
1 TTTTGGACT-CCCGAGGGCAAAATGGTAA
*
33465648 TTTTGGACTCGCGAGGGCAAAATGGTAA
1 TTTTGGACTCCCGAGGGCAAAATGGTAA
33465676 TTTT
1 TTTT
33465680 CAGTGAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (28 bp):
TTTTGGACTCCCGAGGGCAAAATGGTAA
Found at i:33465723 original size:29 final size:28
Alignment explanation
Indices: 33465685--33465772 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 28
33465675 ATTTTCAGTG
*
33465685 AAATCG-GGGTCAAAAGGGAATTTTGGA
1 AAATCGAGGGTCAAAAAGGAATTTTGGA
* *
33465712 AAATTCGAGGGT-AAAATAGTAATTTTTGGTG
1 AAA-TCGAGGGTCAAAA-AGGAA-TTTTGG-A
33465743 AAATCGA-GGTCAAAAATGGAATTTTGGA
1 AAATCGAGGGTCAAAAA-GGAATTTTGGA
33465771 AA
1 AA
33465773 GTTTAGGGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
27 3 0.06
28 9 0.18
29 17 0.35
30 17 0.35
31 3 0.06
ACGTcount: A:0.40, C:0.06, G:0.27, T:0.27
Consensus pattern (28 bp):
AAATCGAGGGTCAAAAAGGAATTTTGGA
Found at i:33465793 original size:59 final size:59
Alignment explanation
Indices: 33465666--33466034 Score: 494
Period size: 59 Copynumber: 6.3 Consensus size: 59
33465656 TCGCGAGGGC
** * * * *
33465666 AAAATGGTAATTTTCAGTGAAATCGGGGTC-AAAAGGGAATTTTGGAAA-ATTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAAGTTTAG-GGGT
* * *
33465724 AAAATAGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAAGTTTAGGGGT
* * *
33465783 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGAAATTTTAGAAAGTTTTGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAAGTTTAGGGGT
* *
33465842 AAAATGGTAATTTTTGGCGAAATCGGGGT-TAAAATGGAATTTTAGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAAGTTTAGGGGT
* * *
33465900 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAAGTTTAGGGGT
* * * * *
33465959 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATATG-ATTTCAAAAAGTTCAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAAT-GGAATTTTAGAAAGTTTAGGGGT
33466018 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
33466035 ACAGTCTAAG
Statistics
Matches: 281, Mismatches: 26, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
58 80 0.28
59 197 0.70
60 4 0.01
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAAGTTTAGGGGT
Found at i:33465876 original size:117 final size:117
Alignment explanation
Indices: 33465666--33466034 Score: 510
Period size: 117 Copynumber: 3.1 Consensus size: 117
33465656 TCGCGAGGGC
** * *
33465666 AAAATGGTAATTTTCAGTGAAATCGGGGTC-AAAAGGGAATTTTGGAAA-ATTCGAGGGTAAAAT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTCG-GGGTAAAAT
* * * *
33465729 AGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGT
65 GGTAATTTTTGGTGAAATCGGGGT-TAAAATGGAATTTTAGAAAGTTTAGGGGT
* * * *
33465783 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGAAATTTTAGAAAGTTTTGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTCGGGGTAAAATG
*
33465848 GTAATTTTTGGCGAAATCGGGGTTAAAATGGAATTTTAGAAAGTTTAGGGGT
66 GTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTAGAAAGTTTAGGGGT
* *
33465900 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTCGGGGTAAAATG
* * * *
33465965 GTAATTTTTGGTGAAATCGGGGTTAAAAATATG-ATTTCAAAAAGTTCAGGGGT
66 GTAATTTTTGGTGAAATCGGGGTT-AAAAT-GGAATTTTAGAAAGTTTAGGGGT
33466018 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
33466035 ACAGTCTAAG
Statistics
Matches: 225, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
117 137 0.61
118 84 0.37
119 4 0.02
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.33
Consensus pattern (117 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTCGGGGTAAAATG
GTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTAGAAAGTTTAGGGGT
Found at i:33465960 original size:176 final size:176
Alignment explanation
Indices: 33465666--33466034 Score: 535
Period size: 176 Copynumber: 2.1 Consensus size: 176
33465656 TCGCGAGGGC
** * * *
33465666 AAAATGGTAATTTTCAGTGAAATCGGGGTCAAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAG
1 AAAATGGTAATTTTTGGCGAAATCGGGGTCAAAAGGGAATTTTAGAAAATTAGAGGGTAAAATAG
33465731 TAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTT
66 TAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTT
* * **
33465796 TTGGTGAAATCGAGGTCAAAAATGA-AATTTTAGAAAGTTTTGGGGT
131 TTGGTGAAATCGAGGTCAAAAAT-ATAATTTCAAAAAGTTCAGGGGT
* * * *
33465842 AAAATGGTAATTTTTGGCGAAATCGGGGTTAAAATGGAATTTTAGAAAGTTTAG-GGGTAAAATG
1 AAAATGGTAATTTTTGGCGAAATCGGGGTCAAAAGGGAATTTTAGAAA-ATTAGAGGGTAAAATA
* * *
33465906 GTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATT
65 GTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATT
* * *
33465971 TTTGGTGAAATCGGGGTTAAAAATATGATTTCAAAAAGTTCAGGGGT
130 TTTGGTGAAATCGAGGTCAAAAATATAATTTCAAAAAGTTCAGGGGT
33466018 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
33466035 ACAGTCTAAG
Statistics
Matches: 172, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
175 1 0.01
176 168 0.98
177 3 0.02
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.33
Consensus pattern (176 bp):
AAAATGGTAATTTTTGGCGAAATCGGGGTCAAAAGGGAATTTTAGAAAATTAGAGGGTAAAATAG
TAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTT
TTGGTGAAATCGAGGTCAAAAATATAATTTCAAAAAGTTCAGGGGT
Found at i:33467924 original size:6 final size:6
Alignment explanation
Indices: 33467909--33467967 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
33467899 TTAAATTTGA
* * *
33467909 TTAAAC TTAAAT TTAAA- GTAAAT TTAAAT AAATAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
33467957 ATAAAT TTAAA
1 TTAAAT TTAAA
33467968 ACCCATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:33467968 original size:11 final size:11
Alignment explanation
Indices: 33467916--33467968 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
33467906 TGATTAAACT
*
33467916 TAAATTTAAAG
1 TAAATTTAAAA
33467927 TAAATTT-AAA
1 TAAATTTAAAA
*
33467937 TAAA--TAAATT
1 TAAATTTAAA-A
33467947 TAAATTTAAAA
1 TAAATTTAAAA
33467958 TAAATTTAAAA
1 TAAATTTAAAA
33467969 CCCATTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
8 1 0.03
9 2 0.06
10 10 0.29
11 18 0.51
12 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:33469824 original size:22 final size:21
Alignment explanation
Indices: 33469796--33469846 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 21
33469786 TTTAATTAGT
33469796 AAAAATATATTTTTAA-AATTTA
1 AAAAATAT-TTTTTAAGAA-TTA
33469818 AAAAATATTTTTTAATGAATTA
1 AAAAATATTTTTTAA-GAATTA
33469840 AAAAATA
1 AAAAATA
33469847 AATATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.26
22 18 0.67
23 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAAATATTTTTTAAGAATTA
Found at i:33475126 original size:24 final size:25
Alignment explanation
Indices: 33475079--33475128 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
33475069 GGGTACTTGA
*
33475079 ACTTTCAAAATACATAAAAAAAAAG
1 ACTTTCAAAATACAAAAAAAAAAAG
* *
33475104 ACTTTCAAACTAAAAAAAAAAAAAG
1 ACTTTCAAAATACAAAAAAAAAAAG
33475129 CAATTAAGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.66, C:0.12, G:0.04, T:0.18
Consensus pattern (25 bp):
ACTTTCAAAATACAAAAAAAAAAAG
Found at i:33482405 original size:32 final size:32
Alignment explanation
Indices: 33482364--33482428 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
33482354 CTGAGAATAC
33482364 ATCGAATAGGACCCAAGTAGAATAGATCTTAT
1 ATCGAATAGGACCCAAGTAGAATAGATCTTAT
33482396 ATCGAATAGGACCCAAGTAGAATAGATCTTAT
1 ATCGAATAGGACCCAAGTAGAATAGATCTTAT
33482428 A
1 A
33482429 CTCGTTTATA
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:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (32 bp):
ATCGAATAGGACCCAAGTAGAATAGATCTTAT
Found at i:33483137 original size:29 final size:30
Alignment explanation
Indices: 33483074--33483138 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
33483064 GGCGCACAGT
*
33483074 CATGTGAGCCACACGGGCTAGGCACACAAC
1 CATGTGAGCCACACGGGCTAGCCACACAAC
* *
33483104 CATGTGAGCCACATGGG-TTGCCACACAAC
1 CATGTGAGCCACACGGGCTAGCCACACAAC
33483133 CATGTG
1 CATGTG
33483139 CCAAATTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.28, C:0.31, G:0.26, T:0.15
Consensus pattern (30 bp):
CATGTGAGCCACACGGGCTAGCCACACAAC
Found at i:33485662 original size:13 final size:12
Alignment explanation
Indices: 33485644--33485678 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
33485634 CTTTTGAAAA
33485644 TATGTTTATGAAG
1 TATGTTTATG-AG
33485657 TATGTTTATGAG
1 TATGTTTATGAG
*
33485669 TATATTTATG
1 TATGTTTATG
33485679 TCGGATTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (12 bp):
TATGTTTATGAG
Found at i:33487999 original size:3 final size:3
Alignment explanation
Indices: 33487991--33488024 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
33487981 GAAGTAAAAT
*
33487991 TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
33488025 ATCATTACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:33495968 original size:20 final size:19
Alignment explanation
Indices: 33495939--33495980 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
33495929 TTATTATTTT
*
33495939 TTAATATAAAATTATTAAAA
1 TTAATATAAAA-TAATAAAA
*
33495959 TTAATTTAAAATAATAAAA
1 TTAATATAAAATAATAAAA
33495978 TTA
1 TTA
33495981 TTAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAATATAAAATAATAAAA
Found at i:33496936 original size:11 final size:10
Alignment explanation
Indices: 33496917--33496991 Score: 64
Period size: 9 Copynumber: 7.3 Consensus size: 10
33496907 TTTTTTAAAA
33496917 AAATAATTTT
1 AAATAATTTT
33496927 AAATTAATTTT
1 AAA-TAATTTT
33496938 AAAATAATTTT
1 -AAATAATTTT
33496949 -AATAATTTT
1 AAATAATTTT
* **
33496958 ATATTTTTTT
1 AAATAATTTT
33496968 AAAAATAATTTT
1 --AAATAATTTT
*
33496980 -TATAATTTT
1 AAATAATTTT
33496989 AAA
1 AAA
33496992 ATCATTTGCT
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
9 17 0.33
10 10 0.20
11 14 0.27
12 10 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AAATAATTTT
Found at i:33496953 original size:31 final size:31
Alignment explanation
Indices: 33496918--33496991 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
33496908 TTTTTAAAAA
33496918 AATAATTTTAAATTAATTTT-AAAATAATTTT
1 AATAATTTTAAATT-ATTTTAAAAATAATTTT
* *
33496949 AATAATTTTATATTTTTTTAAAAATAATTTT
1 AATAATTTTAAATTATTTTAAAAATAATTTT
*
33496980 TATAATTTTAAA
1 AATAATTTTAAA
33496992 ATCATTTGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
AATAATTTTAAATTATTTTAAAAATAATTTT
Found at i:33496977 original size:22 final size:21
Alignment explanation
Indices: 33496949--33496992 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
33496939 AAATAATTTT
**
33496949 AATAATTTTATATTTTTTTAAA
1 AATAATTTT-TATAATTTTAAA
33496971 AATAATTTTTATAATTTTAAA
1 AATAATTTTTATAATTTTAAA
33496992 A
1 A
33496993 TCATTTGCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AATAATTTTTATAATTTTAAA
Found at i:33496990 original size:21 final size:22
Alignment explanation
Indices: 33496919--33496992 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
33496909 TTTTAAAAAA
* *
33496919 ATAATTTT-AAATTAATTTTAAA
1 ATAATTTTAAAAATAATTTT-AT
33496941 ATAATTTT---AATAATTTTAT
1 ATAATTTTAAAAATAATTTTAT
**
33496960 ATTTTTTTAAAAATAATTTT-T
1 ATAATTTTAAAAATAATTTTAT
33496981 ATAATTTTAAAA
1 ATAATTTTAAAA
33496993 TCATTTGCTG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
19 7 0.16
20 8 0.19
21 11 0.26
22 17 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAATTTTAAAAATAATTTTAT
Found at i:33499752 original size:49 final size:49
Alignment explanation
Indices: 33499675--33499768 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
33499665 GCAACCCAGG
* *
33499675 CTCCTAGTTCACGATGGTTATACAATCACAAG-TTGAAGTATAACTAGGA
1 CTCCTAGTTAACAATGGTTATACAATCAC-AGCTTGAAGTATAACTAGGA
* * *
33499724 CTCCTAGTTAACAATGGTTATGCGATCACGGCTTGAAGTATAACT
1 CTCCTAGTTAACAATGGTTATACAATCACAGCTTGAAGTATAACT
33499769 CAAGTCCTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 1 0.03
49 38 0.97
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (49 bp):
CTCCTAGTTAACAATGGTTATACAATCACAGCTTGAAGTATAACTAGGA
Found at i:33501078 original size:72 final size:75
Alignment explanation
Indices: 33500905--33501081 Score: 234
Period size: 76 Copynumber: 2.4 Consensus size: 75
33500895 GTAAATATTG
** *
33500905 ATATATTATTAATGTAAAATACGGTAGAATACAATATAAACAATTTTTTTTATTTTTTCTTAGAT
1 ATATATTATTAATGTAAAATACAATAGAATACAATACAAACAA-TTTTTTTATTTTTTCTTAGAT
33500970 TCTAAACAAGA
65 TCTAAACAAGA
* * * *
33500981 ATATATTATTTATATGAAATACAATAGAATACAATACAAGCAA-TTTTTTATTTTTTCTTAGATT
1 ATATATTATTAATGTAAAATACAATAGAATACAATACAAACAATTTTTTTATTTTTTCTTAGATT
* *
33501045 GTAAA-TA-A
66 CTAAACAAGA
*
33501053 ATATATTATTGATGTAAAATACAATAGAA
1 ATATATTATTAATGTAAAATACAATAGAA
33501082 CAACTTTTTG
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
72 27 0.30
73 1 0.01
74 25 0.28
76 36 0.40
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (75 bp):
ATATATTATTAATGTAAAATACAATAGAATACAATACAAACAATTTTTTTATTTTTTCTTAGATT
CTAAACAAGA
Found at i:33505356 original size:15 final size:16
Alignment explanation
Indices: 33505336--33505365 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33505326 CAACCTGCAA
33505336 ACAG-AAAGAAAAAGG
1 ACAGAAAAGAAAAAGG
33505351 ACAGAAAAGAAAAAG
1 ACAGAAAAGAAAAAG
33505366 AAAATTGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.07, G:0.23, T:0.00
Consensus pattern (16 bp):
ACAGAAAAGAAAAAGG
Found at i:33506642 original size:4 final size:4
Alignment explanation
Indices: 33506633--33506661 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
33506623 CCTTTGCTAT
33506633 TTTA TTTA TTTA TTTA TTTA TTT- TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
33506662 ATTCCCATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:33512780 original size:128 final size:126
Alignment explanation
Indices: 33512563--33512798 Score: 312
Period size: 128 Copynumber: 1.9 Consensus size: 126
33512553 AAGGAGGGGA
* * ** *
33512563 AGAGGTCGAGATGAAAACCCGAAAAGGGAGTTTTGAAACCTAAAGAGTTTGAGTCAAAACCCGAA
1 AGAGGTCGAGATGAAAACCCGAAAAGGCAGTCTCAAAACCTAAAGAGTTTGAGTCAAAACCCAAA
* *
33512628 AGGGCCGCTCAAATTTGGACCAAAGAATTGACATGCAATGGTCGCTTCACCCTAAAAAAAG
66 AGGGCCGCTCAAATTTGGACCAAAGAATAGACATGAAATGGTCGCTTCACCCTAAAAAAAG
* * * *
33512689 AGAGGTCGAGATGAAAACTCGCAAAAGGCA-TCTCAAAACCTAAGGAGATTTGAGTTGAAAACTC
1 AGAGGTCGAGATGAAAACCCG-AAAAGGCAGTCTCAAAACCTAAAGAG-TTTGAG-TCAAAACCC
* * *
33512753 AAAAGGGCGGCTCAAATTTGGATCAAAGAATAGGCATGAAATGGTC
63 AAAAGGGCCGCTCAAATTTGGACCAAAGAATAGACATGAAATGGTC
33512799 TTTTCTCTCA
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
126 33 0.35
127 13 0.14
128 47 0.51
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (126 bp):
AGAGGTCGAGATGAAAACCCGAAAAGGCAGTCTCAAAACCTAAAGAGTTTGAGTCAAAACCCAAA
AGGGCCGCTCAAATTTGGACCAAAGAATAGACATGAAATGGTCGCTTCACCCTAAAAAAAG
Found at i:33513903 original size:50 final size:50
Alignment explanation
Indices: 33513849--33514105 Score: 123
Period size: 50 Copynumber: 5.1 Consensus size: 50
33513839 CTAAAGATAC
* *
33513849 AGTGGAGTAAGATAAAGTTACGAAATCAAATCCTATATCCCTGAAATTGT
1 AGTGGAGTAAGATAAAGCTACGAAAGCAAATCCTATATCCCTGAAATTGT
** * * * ** *
33513899 AGTGGA-TTGGATTAAAGCTAC-AGTAGCAAAT-CTTTATCTCTTTGAAGGTGC
1 AGTGGAGTAAGA-TAAAGCTACGA-AAGCAAATCCTATATC-C-CTGAAATTGT
* * * * * * *
33513950 AGTAGAGCAAGATAAAGCTACCATATCAAATCCTATACCCCTGAAGTTGT
1 AGTGGAGTAAGATAAAGCTACGAAAGCAAATCCTATATCCCTGAAATTGT
** * * * * * * **
33514000 AGTGG-GTCGGATTGAAGCTACAAAAGCAAATCTTATCTCTCT-AAAGATAC
1 AGTGGAGTAAGA-TAAAGCTACGAAAGCAAATCCTATATCCCTGAAA-TTGT
* * *
33514050 AATGGAGTAAGATGAAGTTACGACAA-CAAATCCTATATCCCT-AAAGTTGT
1 AGTGGAGTAAGATAAAGCTACGA-AAGCAAATCCTATATCCCTGAAA-TTGT
33514100 AGTGGA
1 AGTGGA
33514106 TCAAATTAAA
Statistics
Matches: 148, Mismatches: 48, Indels: 22
0.68 0.22 0.10
Matches are distributed among these distances:
49 15 0.10
50 91 0.61
51 34 0.23
52 8 0.05
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (50 bp):
AGTGGAGTAAGATAAAGCTACGAAAGCAAATCCTATATCCCTGAAATTGT
Found at i:33513956 original size:201 final size:201
Alignment explanation
Indices: 33513706--33514106 Score: 626
Period size: 201 Copynumber: 2.0 Consensus size: 201
33513696 TACAGGGACC
* *
33513706 GGATTAAAGCTACAATAGCAAATCTTTATCTCTCTAAAGTTGAAGTAGAGCAAGATTAAGCTACC
1 GGATTAAAGCTACAATAGCAAATCTTTATCTCTCTAAAGGTGAAGTAGAGCAAGATAAAGCTACC
* * * *
33513771 ATATCAAATCATATACCCCTGAAGTTGCAGTGGGTTAGATTGAAGTTATAAAAGCAAATTTTATC
66 ATATCAAATCATATACCCCTGAAGTTGCAGTGGGTCAGATTGAAGCTACAAAAGCAAATCTTATC
*
33513836 TCCCTAAAGATACAGTGGAGTAAGATAAAGTTACGA-AATCAAATCCTATATCCCTGAAA-TTGT
131 TCCCTAAAGATACAATGGAGTAAGATAAAGTTACGACAA-CAAATCCTATATCCCT-AAAGTTGT
33513899 AGTGGATT
194 AGTGGATT
* * * *
33513907 GGATTAAAGCTACAGTAGCAAATCTTTATCTCTTTGAAGGTGCAGTAGAGCAAGATAAAGCTACC
1 GGATTAAAGCTACAATAGCAAATCTTTATCTCTCTAAAGGTGAAGTAGAGCAAGATAAAGCTACC
* * *
33513972 ATATCAAATCCTATACCCCTGAAGTTGTAGTGGGTCGGATTGAAGCTACAAAAGCAAATCTTATC
66 ATATCAAATCATATACCCCTGAAGTTGCAGTGGGTCAGATTGAAGCTACAAAAGCAAATCTTATC
* *
33514037 TCTCTAAAGATACAATGGAGTAAGATGAAGTTACGACAACAAATCCTATATCCCTAAAGTTGTAG
131 TCCCTAAAGATACAATGGAGTAAGATAAAGTTACGACAACAAATCCTATATCCCTAAAGTTGTAG
33514102 TGGAT
196 TGGAT
33514107 CAAATTAAAG
Statistics
Matches: 182, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
200 3 0.02
201 177 0.97
202 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (201 bp):
GGATTAAAGCTACAATAGCAAATCTTTATCTCTCTAAAGGTGAAGTAGAGCAAGATAAAGCTACC
ATATCAAATCATATACCCCTGAAGTTGCAGTGGGTCAGATTGAAGCTACAAAAGCAAATCTTATC
TCCCTAAAGATACAATGGAGTAAGATAAAGTTACGACAACAAATCCTATATCCCTAAAGTTGTAG
TGGATT
Found at i:33514100 original size:100 final size:101
Alignment explanation
Indices: 33513705--33514104 Score: 405
Period size: 100 Copynumber: 4.0 Consensus size: 101
33513695 TTACAGGGAC
* * *
33513705 CGGATTAAAGCTACAATAGCAAATCTTTATCTCTCTAAAGTTGA-AGTAGAGCAAGATTAAGCTA
1 CGGATTAAAGCTACAAAAGCAAATCTTTATCTCTCTAAAGAT-ACAGTAGAGCAAGATAAAGCTA
* * * *
33513769 CCATATCAAATCATATACCCCTGAAGTTGCAGTGGGT
65 CCATAACAAATCCTATACCCCTAAAGTTGTAGTGGGT
** * * * * * * *
33513806 TAGATTGAAGTTATAAAAGCAAAT-TTTATCTCCCTAAAGATACAGTGGAGTAAGATAAAGTTAC
1 CGGATTAAAGCTACAAAAGCAAATCTTTATCTCTCTAAAGATACAGTAGAGCAAGATAAAGCTAC
* * *
33513870 GA-AATCAAATCCTATATCCCTGAAA-TTGTAGTGGAT
66 CATAA-CAAATCCTATACCCCT-AAAGTTGTAGTGGGT
* ** * * * *
33513906 TGGATTAAAGCTACAGTAGCAAATCTTTATCTCTTTGAAGGTGCAGTAGAGCAAGATAAAGCTAC
1 CGGATTAAAGCTACAAAAGCAAATCTTTATCTCTCTAAAGATACAGTAGAGCAAGATAAAGCTAC
* *
33513971 CATATCAAATCCTATACCCCTGAAGTTGTAGTGGGT
66 CATAACAAATCCTATACCCCTAAAGTTGTAGTGGGT
* * * * * *
33514007 CGGATTGAAGCTACAAAAGCAAATC-TTATCTCTCTAAAGATACAATGGAGTAAGATGAAGTTAC
1 CGGATTAAAGCTACAAAAGCAAATCTTTATCTCTCTAAAGATACAGTAGAGCAAGATAAAGCTAC
* * *
33514071 GACAACAAATCCTATATCCCTAAAGTTGTAGTGG
66 CATAACAAATCCTATACCCCTAAAGTTGTAGTGG
33514105 ATCAAATTAA
Statistics
Matches: 237, Mismatches: 56, Indels: 13
0.77 0.18 0.04
Matches are distributed among these distances:
99 2 0.01
100 135 0.57
101 99 0.42
102 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (101 bp):
CGGATTAAAGCTACAAAAGCAAATCTTTATCTCTCTAAAGATACAGTAGAGCAAGATAAAGCTAC
CATAACAAATCCTATACCCCTAAAGTTGTAGTGGGT
Found at i:33514180 original size:100 final size:100
Alignment explanation
Indices: 33513663--33514181 Score: 366
Period size: 100 Copynumber: 5.2 Consensus size: 100
33513653 GAATGGAGTG
* * * ** ** *
33513663 AAGCTACAACACCAAATCATATATCTTTAAAGTTACAG-GGACCGGATTAAAGCTACAATAGCAA
1 AAGCTACAATATCAAATCCTATATCCCTAAAGTTGTAGTGGATCGGATTAAAGCTACAATAGCAA
* * * * *
33513727 ATCTTTATCTCTCTAAAGTTGA-AGTAGAGC-AAGATT
66 A-CCTTATCTCCCTAAAGAT-ACAGTGGA-CTAAGATA
* * * * * * ** * * * *
33513763 AAGCTACCATATCAAATCATATACCCCTGAAGTTGCAGTGGGTTAGATTGAAGTTATAAAAGCAA
1 AAGCTACAATATCAAATCCTATATCCCTAAAGTTGTAGTGGATCGGATTAAAGCTACAATAGCAA
** *
33513828 ATTTTATCTCCCTAAAGATACAGTGGAGTAAGATA
66 ACCTTATCTCCCTAAAGATACAGTGGACTAAGATA
* * *
33513863 AAGTTACGAA-ATCAAATCCTATATCCCTGAAA-TTGTAGTGGATTGGATTAAAGCTACAGTAGC
1 AAGCTAC-AATATCAAATCCTATATCCCT-AAAGTTGTAGTGGATCGGATTAAAGCTACAATAGC
* ** * * * *
33513926 AAATCTTTATCTCTTTGAAGGTGCAGTAGAGC-AAGATA
64 AAA-CCTTATCTCCCTAAAGATACAGTGGA-CTAAGATA
* * * * * *
33513964 AAGCTACCATATCAAATCCTATACCCCTGAAGTTGTAGTGGGTCGGATTGAAGCTACAAAAGCAA
1 AAGCTACAATATCAAATCCTATATCCCTAAAGTTGTAGTGGATCGGATTAAAGCTACAATAGCAA
* * * * *
33514029 ATCTTATCTCTCTAAAGATACAATGGAGTAAGATG
66 ACCTTATCTCCCTAAAGATACAGTGGACTAAGATA
* * * * ** * * *
33514064 AAGTTACGACAACAAATCCTATATCCCTAAAGTTGTAGTGGATCAAATTAAAGTTACATTAGCAG
1 AAGCTACAATATCAAATCCTATATCCCTAAAGTTGTAGTGGATCGGATTAAAGCTACAATAGCAA
* * * * *
33514129 GCCCTATCTCCCCAAAGATGCATTGGACTAAGATA
66 ACCTTATCTCCCTAAAGATACAGTGGACTAAGATA
33514164 AAGCTACAATATCAAATC
1 AAGCTACAATATCAAATC
33514182 TTATCTTCTT
Statistics
Matches: 320, Mismatches: 89, Indels: 20
0.75 0.21 0.05
Matches are distributed among these distances:
99 1 0.00
100 220 0.69
101 99 0.31
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (100 bp):
AAGCTACAATATCAAATCCTATATCCCTAAAGTTGTAGTGGATCGGATTAAAGCTACAATAGCAA
ACCTTATCTCCCTAAAGATACAGTGGACTAAGATA
Found at i:33514828 original size:15 final size:16
Alignment explanation
Indices: 33514808--33514837 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33514798 CAAGCAATAA
33514808 ACAG-AAAGAAAAAGG
1 ACAGAAAAGAAAAAGG
33514823 ACAGAAAAGAAAAAG
1 ACAGAAAAGAAAAAG
33514838 AAAATTGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.07, G:0.23, T:0.00
Consensus pattern (16 bp):
ACAGAAAAGAAAAAGG
Found at i:33515593 original size:14 final size:14
Alignment explanation
Indices: 33515574--33515603 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
33515564 GGGTCAATTT
*
33515574 TCAATATCGGTCCC
1 TCAATATCGGGCCC
33515588 TCAATATCGGGCCC
1 TCAATATCGGGCCC
33515602 TC
1 TC
33515604 CACTTCTTGA
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:0.20, C:0.37, G:0.17, T:0.27
Consensus pattern (14 bp):
TCAATATCGGGCCC
Found at i:33516338 original size:25 final size:25
Alignment explanation
Indices: 33516302--33516350 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
33516292 TTTTACATCT
33516302 TTTATTTATGTTATTAATTGTATTA
1 TTTATTTATGTTATTAATTGTATTA
* *
33516327 TTTA-TTATTGTTATTTATTTTATT
1 TTTATTTA-TGTTATTAATTGTATT
33516351 CTATTATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.69
Consensus pattern (25 bp):
TTTATTTATGTTATTAATTGTATTA
Found at i:33518107 original size:25 final size:25
Alignment explanation
Indices: 33518057--33518114 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
33518047 TTATGTTTAA
** *
33518057 AATTTTAAATATTTTATATATCATT
1 AATTTTAAATAAATTATATATAATT
33518082 AATTTTCAAATAAATTATA-ATAATT
1 AATTTT-AAATAAATTATATATAATT
33518107 -A-TTTAAAT
1 AATTTTAAAT
33518115 GATATTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 4 0.14
23 3 0.10
24 1 0.03
25 11 0.38
26 10 0.34
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (25 bp):
AATTTTAAATAAATTATATATAATT
Found at i:33519253 original size:3 final size:3
Alignment explanation
Indices: 33519245--33519281 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
33519235 TGGTGTCTTA
33519245 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
33519282 TTAAAAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:33521254 original size:37 final size:38
Alignment explanation
Indices: 33521195--33521273 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 38
33521185 TTCGAAGCAA
** *
33521195 TAAAGTGAAACCCAGTGTCTCATC-AGCCTAGCCGAAG
1 TAAAGTGAAACCCAGTACCTCATCGAACCTAGCCGAAG
** * *
33521232 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAGTGAAACCCAGTACCTCATCGAACCTAGCCGAAG
33521270 TAAA
1 TAAA
33521274 ATAATGACAC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 20 0.59
38 14 0.41
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAGTGAAACCCAGTACCTCATCGAACCTAGCCGAAG
Found at i:33521426 original size:6 final size:6
Alignment explanation
Indices: 33521401--33521463 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
33521391 ACAATTCATA
* * *
33521401 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCACTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
33521449 TCACTT TCACTT TCA
1 TCACTT TCACTT TCA
33521464 ATTTTGATCA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.21, C:0.32, G:0.00, T:0.48
Consensus pattern (6 bp):
TCACTT
Found at i:33522802 original size:14 final size:14
Alignment explanation
Indices: 33522785--33522815 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
33522775 AAAGTTGAAA
33522785 TGGTGGAAAAATGG
1 TGGTGGAAAAATGG
33522799 TGGTGGAAAAATGG
1 TGGTGGAAAAATGG
33522813 TGG
1 TGG
33522816 CTAACGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.45, T:0.23
Consensus pattern (14 bp):
TGGTGGAAAAATGG
Done.