Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 77 of 214
Found at i:21657690 original size:21 final size:21
Alignment explanation
Indices: 21657633--21657690 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
21657623 AAGGCAAAGG
21657633 AACAAAAAG-AAAAGATG-GAA
1 AACAAAAAGAAAAAG-TGAGAA
* *
21657653 AA-GAAAA-AAAGAGTGAGAA
1 AACAAAAAGAAAAAGTGAGAA
21657672 AACAAAAAGAAAAAGTGAG
1 AACAAAAAGAAAAAGTGAG
21657691 TTGAAATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
18 2 0.07
19 13 0.43
20 6 0.20
21 9 0.30
ACGTcount: A:0.69, C:0.03, G:0.22, T:0.05
Consensus pattern (21 bp):
AACAAAAAGAAAAAGTGAGAA
Found at i:21663250 original size:23 final size:22
Alignment explanation
Indices: 21663199--21663250 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
21663189 CCTCGTCTTT
*
21663199 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
21663221 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
21663244 TTCTTTT
1 TTCTTTT
21663251 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:21664760 original size:20 final size:19
Alignment explanation
Indices: 21664737--21664801 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
21664727 AAGCTCAAAC
21664737 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
21664757 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
21664777 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
21664797 GAGCT
1 GAGCT
21664802 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:21665396 original size:22 final size:22
Alignment explanation
Indices: 21665345--21665410 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
21665335 GGTATTTGGG
* *
21665345 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
21665366 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
21665388 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
21665411 TCAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:21671698 original size:12 final size:11
Alignment explanation
Indices: 21671678--21671710 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
21671668 AAACCGTATG
21671678 CAATTTTTTTT
1 CAATTTTTTTT
21671689 CAATTTTTTTT
1 CAATTTTTTTT
21671700 CAAATTTTTTT
1 C-AATTTTTTT
21671711 ACGTACCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (11 bp):
CAATTTTTTTT
Found at i:21672062 original size:22 final size:22
Alignment explanation
Indices: 21672011--21672076 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
21672001 GGTATTTGGG
* *
21672011 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
21672032 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
21672054 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
21672077 TCAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:21682725 original size:11 final size:12
Alignment explanation
Indices: 21682700--21682742 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
21682690 TAGTTTCTCG
*
21682700 AAAAAAACTCGA
1 AAAAAAATTCGA
21682712 AAAAAAATTC-A
1 AAAAAAATTCGA
*
21682723 AAAAAAATTTTGA
1 AAAAAAA-TTCGA
21682736 AAAAAAA
1 AAAAAAA
21682743 ACTAGTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 8 0.30
12 11 0.41
13 8 0.30
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16
Consensus pattern (12 bp):
AAAAAAATTCGA
Found at i:21682799 original size:13 final size:14
Alignment explanation
Indices: 21682781--21682820 Score: 73
Period size: 13 Copynumber: 2.9 Consensus size: 14
21682771 GGATATCAAG
21682781 TTGTGAAAAAAAA-
1 TTGTGAAAAAAAAT
21682794 TTGTGAAAAAAAAT
1 TTGTGAAAAAAAAT
21682808 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
21682821 AGAGAGCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (14 bp):
TTGTGAAAAAAAAT
Found at i:21682805 original size:14 final size:14
Alignment explanation
Indices: 21682781--21682821 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
21682771 GGATATCAAG
21682781 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
*
21682794 TTGTGAAAAAAAAT
1 TTGTGAAAAAAAAA
21682808 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
21682822 GAGAGCTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:21684321 original size:30 final size:30
Alignment explanation
Indices: 21684287--21684383 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
21684277 AGCTCACTCC
21684287 TAGCTCATA-TTTAGCTCACGAGCTAGACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAGACCT
* * * *
21684317 TAGCTCAACTTCAGCTTAGGAGTTTAG-CCT
1 TAGCTCAACTTTAGCTCACGAG-CTAGACCT
* * *
21684347 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAGACCT
21684377 TAGCTCA
1 TAGCTCA
21684384 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 3 0.06
30 46 0.88
31 3 0.06
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAGACCT
Found at i:21685884 original size:1 final size:1
Alignment explanation
Indices: 21685873--21685990 Score: 209
Period size: 1 Copynumber: 118.0 Consensus size: 1
21685863 ATCGGGCAAT
* * *
21685873 AAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21685938 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21685991 TCATCGAACG
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 111 1.00
ACGTcount: A:0.97, C:0.02, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:21688051 original size:17 final size:18
Alignment explanation
Indices: 21688029--21688064 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21688019 TTTCTTTCTC
21688029 CAATTTTT-TCTCTTTTT
1 CAATTTTTGTCTCTTTTT
*
21688046 CAATTTTTGTTTCTTTTT
1 CAATTTTTGTCTCTTTTT
21688064 C
1 C
21688065 GGTTTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.11, C:0.17, G:0.03, T:0.69
Consensus pattern (18 bp):
CAATTTTTGTCTCTTTTT
Found at i:21689003 original size:13 final size:13
Alignment explanation
Indices: 21688985--21689017 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
21688975 CTAGCTCTCT
*
21688985 TTTTTTTCATGAA
1 TTTTTTTCACGAA
21688998 TTTTTTTCACGAA
1 TTTTTTTCACGAA
21689011 TTTTTTT
1 TTTTTTT
21689018 TTCAACTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.67
Consensus pattern (13 bp):
TTTTTTTCACGAA
Found at i:21689089 original size:11 final size:11
Alignment explanation
Indices: 21689060--21689103 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
21689050 TGGAAACTAG
*
21689060 TTTTTTTCGAA
1 TTTTTTTTGAA
21689071 TTTTTTTTGAA
1 TTTTTTTTGAA
*
21689082 TTTTTTTTTGAG
1 -TTTTTTTTGAA
21689094 TTTTTTTTGA
1 TTTTTTTTGA
21689104 GAAACTACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.14, C:0.02, G:0.11, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:21689097 original size:23 final size:23
Alignment explanation
Indices: 21689060--21689103 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
21689050 TGGAAACTAG
21689060 TTTTTTTCGAATTTTTTTTGAAT
1 TTTTTTTCGAATTTTTTTTGAAT
* *
21689083 TTTTTTTTGAGTTTTTTTTGA
1 TTTTTTTCGAATTTTTTTTGA
21689104 GAAACTACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.02, G:0.11, T:0.73
Consensus pattern (23 bp):
TTTTTTTCGAATTTTTTTTGAAT
Found at i:21714072 original size:17 final size:18
Alignment explanation
Indices: 21714038--21714080 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
21714028 TGCCCCATAG
21714038 CTAGATACAAACAGAATA
1 CTAGATACAAACAGAATA
*
21714056 CTAGATATAAA-AGAATA
1 CTAGATACAAACAGAATA
*
21714073 ATAGATAC
1 CTAGATAC
21714081 CAGAATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.21
Consensus pattern (18 bp):
CTAGATACAAACAGAATA
Found at i:21716951 original size:21 final size:21
Alignment explanation
Indices: 21716912--21716965 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
21716902 TATGCCAACT
*
21716912 GAAGCTCG-AA-AGCTGAACA
1 GAAGCTCGTAAGAGCTAAACA
21716931 GAAGCTCGTAAGAGCTAAACA
1 GAAGCTCGTAAGAGCTAAACA
21716952 GAAGCTCGTAAGAG
1 GAAGCTCGTAAGAG
21716966 TGATCCATCC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 8 0.25
20 2 0.06
21 22 0.69
ACGTcount: A:0.41, C:0.19, G:0.28, T:0.13
Consensus pattern (21 bp):
GAAGCTCGTAAGAGCTAAACA
Found at i:21718350 original size:24 final size:25
Alignment explanation
Indices: 21718304--21718366 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
21718294 CCAGTTGGAT
* *
21718304 ATCGAGGCAGAGG-AGGTTTATTTC
1 ATCGAGGTAGAGGCAGGTTCATTTC
*
21718328 ATCGAGGTAGAGGCA-GTTCATTTT
1 ATCGAGGTAGAGGCAGGTTCATTTC
* *
21718352 ATCAAGGTAGCGGCA
1 ATCGAGGTAGAGGCA
21718367 AAGGTCATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 32 0.97
25 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (25 bp):
ATCGAGGTAGAGGCAGGTTCATTTC
Found at i:21718837 original size:30 final size:30
Alignment explanation
Indices: 21718801--21718907 Score: 196
Period size: 30 Copynumber: 3.6 Consensus size: 30
21718791 TCTTCATATG
21718801 AAAACTTGATGTATGTGCCTGGCATAACAA
1 AAAACTTGATGTATGTGCCTGGCATAACAA
*
21718831 AAAACTTGATGTATGTGCCTGGCATAAAAA
1 AAAACTTGATGTATGTGCCTGGCATAACAA
21718861 AAAACTTGATGTATGTGCCTGGCATAACAA
1 AAAACTTGATGTATGTGCCTGGCATAACAA
*
21718891 AAAACTTGATGTCTGTG
1 AAAACTTGATGTATGTG
21718908 TCACAATTCT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 74 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (30 bp):
AAAACTTGATGTATGTGCCTGGCATAACAA
Found at i:21722417 original size:3 final size:3
Alignment explanation
Indices: 21722409--21722453 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
21722399 ACATAGTAAA
* *
21722409 AAC AAC AAC AAA AAC AAC AAC AAC AAC AAC AAA AAC AAC AA- AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
21722454 CCCATGCCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:21727771 original size:13 final size:14
Alignment explanation
Indices: 21727750--21727780 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
21727740 CCCTGAACGG
21727750 TTTATTTTTAGAGT
1 TTTATTTTTAGAGT
21727764 TTTA-TTTTAGAGT
1 TTTATTTTTAGAGT
21727777 TTTA
1 TTTA
21727781 CAATTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.65
Consensus pattern (14 bp):
TTTATTTTTAGAGT
Found at i:21727834 original size:30 final size:30
Alignment explanation
Indices: 21727753--21727834 Score: 121
Period size: 30 Copynumber: 2.7 Consensus size: 30
21727743 TGAACGGTTT
*
21727753 ATTTTTAG-AGTTTTATTTTAGAGTTTTACA
1 ATTTTTAGTA-TTTTATTTTAGTGTTTTACA
* *
21727783 ATTTTTAGTGTTTTATGTTAGTGTTTTACA
1 ATTTTTAGTATTTTATTTTAGTGTTTTACA
21727813 ATTTTTAGTATTTTATTTTAGT
1 ATTTTTAGTATTTTATTTTAGT
21727835 CCCTGGATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.23, C:0.02, G:0.13, T:0.61
Consensus pattern (30 bp):
ATTTTTAGTATTTTATTTTAGTGTTTTACA
Found at i:21728486 original size:16 final size:17
Alignment explanation
Indices: 21728465--21728503 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
21728455 GAATTGTGAT
21728465 TTATTCTA-TGGATTGA
1 TTATTCTACTGGATTGA
*
21728481 TTATTCTACTTGATTGA
1 TTATTCTACTGGATTGA
21728498 TCTATT
1 T-TATT
21728504 GTTTGCTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 8 0.40
18 4 0.20
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54
Consensus pattern (17 bp):
TTATTCTACTGGATTGA
Found at i:21729869 original size:45 final size:45
Alignment explanation
Indices: 21729796--21729966 Score: 202
Period size: 45 Copynumber: 3.8 Consensus size: 45
21729786 TACTACGTGT
* *
21729796 ACTGAGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
1 ACTGAATATCATTGATTATAAAGGTGGTTGCTATGTGATGATTCC
** * * *
21729841 ACTGGGTACCATTGATTATAAAGGTGGTTGCTATGTGAGGACTCC
1 ACTGAATATCATTGATTATAAAGGTGGTTGCTATGTGATGATTCC
** *
21729886 ACTGGAA-ATCATTGAAAATAAATGTGGTTGCTATGTGATGATTCC
1 ACT-GAATATCATTGATTATAAAGGTGGTTGCTATGTGATGATTCC
* * *
21729931 ACCGAATATAATTGATTATAAGGGTGG-TGCTATGTG
1 ACTGAATATCATTGATTATAAAGGTGGTTGCTATGTG
21729967 CTGACCCACC
Statistics
Matches: 105, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
44 12 0.11
45 92 0.88
46 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (45 bp):
ACTGAATATCATTGATTATAAAGGTGGTTGCTATGTGATGATTCC
Found at i:21729957 original size:90 final size:89
Alignment explanation
Indices: 21729803--21729966 Score: 229
Period size: 90 Copynumber: 1.8 Consensus size: 89
21729793 TGTACTGAGT
** * * ** *
21729803 ATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACTGGGTACCATTGATTATAAAGGTGG
1 ATCATTGAAAATAAAGGTGGTTGCTATGTGATGATTCCACCGAATACAATTGATTATAAAGGTGG
21729868 TTGCTATGTGAGGACTCCACTGGAA
66 -TGCTATGTGAGGACTCCACTGGAA
* * *
21729893 ATCATTGAAAATAAATGTGGTTGCTATGTGATGATTCCACCGAATATAATTGATTATAAGGGTGG
1 ATCATTGAAAATAAAGGTGGTTGCTATGTGATGATTCCACCGAATACAATTGATTATAAAGGTGG
21729958 TGCTATGTG
66 TGCTATGTG
21729967 CTGACCCACC
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
89 9 0.14
90 55 0.86
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (89 bp):
ATCATTGAAAATAAAGGTGGTTGCTATGTGATGATTCCACCGAATACAATTGATTATAAAGGTGG
TGCTATGTGAGGACTCCACTGGAA
Found at i:21732988 original size:17 final size:17
Alignment explanation
Indices: 21732966--21733007 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
21732956 TTATATAGCT
21732966 TATTAAGTAAA-AAAATA
1 TATTAA-TAAATAAAATA
21732983 TATTAATAAATAAAAT-
1 TATTAATAAATAAAATA
21732999 TATCTAATA
1 TAT-TAATA
21733008 TCTAATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
TATTAATAAATAAAATA
Found at i:21733477 original size:3 final size:3
Alignment explanation
Indices: 21733469--21733511 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
21733459 GGATGAAGGC
21733469 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
21733512 AGTCCAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21734028 original size:18 final size:18
Alignment explanation
Indices: 21733993--21734032 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
21733983 ATAAATGGTA
*
21733993 CTTTTCATATTATCTCCT
1 CTTTTCATATCATCTCCT
21734011 CTTTTCATATCA-CTTCCT
1 CTTTTCATATCATC-TCCT
21734029 CTTT
1 CTTT
21734033 GGTCCTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.55
Consensus pattern (18 bp):
CTTTTCATATCATCTCCT
Found at i:21736209 original size:19 final size:19
Alignment explanation
Indices: 21736185--21736233 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
21736175 TGAGAGTTTC
* *
21736185 TTTTATATTTCTTCTTTTG
1 TTTTATATTTCCTCTTCTG
*
21736204 TTTTATTAGTTCCTCTTCTG
1 TTTTA-TATTTCCTCTTCTG
*
21736224 TTTAATATTT
1 TTTTATATTT
21736234 TGAAGCTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.14, C:0.12, G:0.06, T:0.67
Consensus pattern (19 bp):
TTTTATATTTCCTCTTCTG
Found at i:21736254 original size:11 final size:11
Alignment explanation
Indices: 21736238--21736263 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21736228 ATATTTTGAA
21736238 GCTGTTGATTT
1 GCTGTTGATTT
21736249 GCTGTTGATTT
1 GCTGTTGATTT
21736260 GCTG
1 GCTG
21736264 GTATTTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.12, G:0.31, T:0.50
Consensus pattern (11 bp):
GCTGTTGATTT
Found at i:21737857 original size:13 final size:13
Alignment explanation
Indices: 21737839--21737863 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21737829 ACACTCAAAT
21737839 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
21737852 TTCTCAAAAGCA
1 TTCTCAAAAGCA
21737864 ATAAAGAATT
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:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:21740805 original size:21 final size:21
Alignment explanation
Indices: 21740771--21740810 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21740761 ACGGTGGTGA
* *
21740771 TGAGATTAGTTACTGTAACAG
1 TGAGATTAGATACTATAACAG
*
21740792 TGAGATTGGATACTATAAC
1 TGAGATTAGATACTATAAC
21740811 GATGAAATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (21 bp):
TGAGATTAGATACTATAACAG
Found at i:21745413 original size:52 final size:50
Alignment explanation
Indices: 21745352--21745462 Score: 129
Period size: 49 Copynumber: 2.2 Consensus size: 50
21745342 ACAGTGTTTC
*
21745352 AGGTGTGTTTC-AAGGGCGGATGTAAAGCCTACCGGCTTGGCACTTGGTG-CCG
1 AGGTGTGTTTCGAA--G-GGATGT-AAGCCTACCAGCTTGGCACTTGGTGCCCG
* * *
21745404 AGGTGTGTTTCGAAGGGATGTTAGGCTACTAGCTTGGCACTTGGTGCCCG
1 AGGTGTGTTTCGAAGGGATGTAAGCCTACCAGCTTGGCACTTGGTGCCCG
21745454 -GGTGTGTTT
1 AGGTGTGTTT
21745463 TTGGATGGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
49 30 0.57
50 9 0.17
51 1 0.02
52 11 0.21
53 2 0.04
ACGTcount: A:0.15, C:0.18, G:0.37, T:0.30
Consensus pattern (50 bp):
AGGTGTGTTTCGAAGGGATGTAAGCCTACCAGCTTGGCACTTGGTGCCCG
Found at i:21747562 original size:3 final size:3
Alignment explanation
Indices: 21747554--21747588 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
21747544 AACAAATAGG
21747554 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
21747589 GGACTAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:21749324 original size:44 final size:44
Alignment explanation
Indices: 21749252--21749651 Score: 209
Period size: 44 Copynumber: 8.8 Consensus size: 44
21749242 ATCTGATGTG
* *
21749252 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTA
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGAT-CTGTTATTTTA
* * ** * *
21749296 ATCCGCTCCACTGTAACTTCAGAGAGATAGGAT-TACTAGCTTCA
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGATCTGTTA-TTTTA
* * * * *** *
21749340 ATCTACTCCGCTGTAATTTCAGAGAGATAAGATCTCTGGCTTCA
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGATCTGTTATTTTA
* * ** *
21749384 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTTTTCG
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGATCTGTTA-TTTT-A
* * * *
21749430 GTCTGTTCCACTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTG
1 ATCTGCTCCACTGTAACT-TCAGAGAGATAAGA--TCT-G-TT--AT-T--T-TA
* *
21749484 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTA
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGAT-CTGTTATTTTA
* * ** * *
21749528 ATCCGCTCCACTGTAACTTCAGAGAGATAGGAT-TACTAGCTTCA
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGATCTGTTA-TTTTA
* * * * *** *
21749572 ATCTACTCCGCTGTAA-TCTCAAAGAGATAAGATCTCTGGCTTCA
1 ATCTGCTCCACTGTAACT-TCAGAGAGATAAGATCTGTTATTTTA
* *
21749616 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTG
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGATCTG
21749652 AAATTCTTCG
Statistics
Matches: 272, Mismatches: 61, Indels: 46
0.72 0.16 0.12
Matches are distributed among these distances:
42 2 0.01
43 5 0.02
44 188 0.69
45 5 0.02
46 28 0.10
47 1 0.00
48 5 0.02
49 1 0.00
50 2 0.01
51 1 0.00
52 3 0.01
53 2 0.01
54 27 0.10
55 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (44 bp):
ATCTGCTCCACTGTAACTTCAGAGAGATAAGATCTGTTATTTTA
Found at i:21749604 original size:232 final size:232
Alignment explanation
Indices: 21749192--21749693 Score: 925
Period size: 232 Copynumber: 2.2 Consensus size: 232
21749182 GAAATTTATG
* *
21749192 TTTTCAGTCTGTTCCACTGCAA-CATCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCT
1 TTTTCGGTCTGTTCCACTGTAATC-TCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCT
21749256 ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGAGA
65 ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGAGA
* *
21749321 GATAGGATTACTAGCTTCAATCTACTCCGCTGTAATTTCAGAGAGATAAGATCTCTGGCTTCAAT
130 GATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAAAGAGATAAGATCTCTGGCTTCAAT
21749386 CTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
195 CTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
21749424 TTTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTA
1 TTTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTA
21749489 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGAGAG
66 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGAGAG
21749554 ATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAAAGAGATAAGATCTCTGGCTTCAATC
131 ATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAAAGAGATAAGATCTCTGGCTTCAATC
21749619 TGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
196 TGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
* **
21749656 TCTTCGGTCTACTCCACTGTAATCTCAGGGAGATAAGA
1 TTTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
21749694 CCTGTATGAT
Statistics
Matches: 262, Mismatches: 7, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
232 261 1.00
233 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (232 bp):
TTTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTA
CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGAGAG
ATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAAAGAGATAAGATCTCTGGCTTCAATC
TGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
Found at i:21774268 original size:23 final size:23
Alignment explanation
Indices: 21774215--21774268 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
21774205 ACCATCTACT
* *
21774215 GGCAAATCTAAGAACTGTGCTAA
1 GGCAAATCTAAAAACAGTGCTAA
*
21774238 GTCAAATCTAAAAACAGTGCTAA
1 GGCAAATCTAAAAACAGTGCTAA
*
21774261 GGCTAATC
1 GGCAAATC
21774269 CATTCACAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (23 bp):
GGCAAATCTAAAAACAGTGCTAA
Found at i:21777134 original size:28 final size:28
Alignment explanation
Indices: 21777090--21777143 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
21777080 GGTGTTTTTG
*
21777090 AACCAATAACTCAGATATCACTTGTTCA
1 AACCAATAACTCAGATACCACTTGTTCA
* *
21777118 AACCAATAGCTCGGATACCACTTGTT
1 AACCAATAACTCAGATACCACTTGTT
21777144 ATGGGACTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.28
Consensus pattern (28 bp):
AACCAATAACTCAGATACCACTTGTTCA
Found at i:21779056 original size:5 final size:5
Alignment explanation
Indices: 21779046--21779070 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
21779036 TGTCATCTCC
21779046 AATCT AATCT AATCT AATCT AATCT
1 AATCT AATCT AATCT AATCT AATCT
21779071 TTACAAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
AATCT
Found at i:21784114 original size:256 final size:256
Alignment explanation
Indices: 21783659--21784174 Score: 1014
Period size: 256 Copynumber: 2.0 Consensus size: 256
21783649 GTCAGCCAAC
* *
21783659 ATATGAACAATCCAACTGAATATCATTTAGAGGTAGTAAATAGAATCTTGAGGTATTTAAAAATG
1 ATATGAACAATCCAACTGAATATCATTTAGAGGTAGTAAATAAAATCTTAAGGTATTTAAAAATG
21783724 ACTCCGGGACTTGGTCTACTATTCAGGAAGTGTGCAAACCGAGAAGTGGAAATTTACACCGATAC
66 ACTCCGGGACTTGGTCTACTATTCAGGAAGTGTGCAAACCGAGAAGTGGAAATTTACACCGATAC
21783789 TAGTTGGGCAAGAGAGCAAACTGATCGAAGATCAATCACTGGTTATTGGTCCTATGTTTGGGGTA
131 TAGTTGGGCAAGAGAGCAAACTGATCGAAGATCAATCACTGGTTATTGGTCCTATGTTTGGGGTA
21783854 ATCTTATTACTTGGAGGAGCAAAAAGCAAGCTGTAGTCTCACGGAGTAGTGCAGAATCAAA
196 ATCTTATTACTTGGAGGAGCAAAAAGCAAGCTGTAGTCTCACGGAGTAGTGCAGAATCAAA
21783915 ATATGAACAATCCAACTGAATATCATTTAGAGGTAGTAAATAAAATCTTAAGGTATTTAAAAATG
1 ATATGAACAATCCAACTGAATATCATTTAGAGGTAGTAAATAAAATCTTAAGGTATTTAAAAATG
21783980 ACTCCGGGACTTGGTCTACTATTCAGGAAGTGTGCAAACCGAGAAGTGGAAATTTACACCGATAC
66 ACTCCGGGACTTGGTCTACTATTCAGGAAGTGTGCAAACCGAGAAGTGGAAATTTACACCGATAC
21784045 TAGTTGGGCAAGAGAGCAAACTGATCGAAGATCAATCACTGGTTATTGGTCCTATGTTTGGGGTA
131 TAGTTGGGCAAGAGAGCAAACTGATCGAAGATCAATCACTGGTTATTGGTCCTATGTTTGGGGTA
21784110 ATCTTATTACTTGGAGGAGCAAAAAGCAAGCTGTAGTCTCACGGAGTAGTGCAGAATCAAA
196 ATCTTATTACTTGGAGGAGCAAAAAGCAAGCTGTAGTCTCACGGAGTAGTGCAGAATCAAA
21784171 ATAT
1 ATAT
21784175 CGTGCTCTTA
Statistics
Matches: 258, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
256 258 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (256 bp):
ATATGAACAATCCAACTGAATATCATTTAGAGGTAGTAAATAAAATCTTAAGGTATTTAAAAATG
ACTCCGGGACTTGGTCTACTATTCAGGAAGTGTGCAAACCGAGAAGTGGAAATTTACACCGATAC
TAGTTGGGCAAGAGAGCAAACTGATCGAAGATCAATCACTGGTTATTGGTCCTATGTTTGGGGTA
ATCTTATTACTTGGAGGAGCAAAAAGCAAGCTGTAGTCTCACGGAGTAGTGCAGAATCAAA
Found at i:21787291 original size:6 final size:6
Alignment explanation
Indices: 21787282--21787311 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
21787272 AGAAGAAAAT
21787282 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
21787312 AGATAAGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:21787292 original size:18 final size:18
Alignment explanation
Indices: 21787257--21787310 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
21787247 TTGAAGGAGG
**
21787257 AGAAAAAGAAGAACAAGA
1 AGAAAAAGAAGAGGAAGA
*
21787275 AGAAAATGAAGAGGAAGA
1 AGAAAAAGAAGAGGAAGA
* * *
21787293 GGAAGAGGAAGAGGAAGA
1 AGAAAAAGAAGAGGAAGA
21787311 GAGATAAGGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.61, C:0.02, G:0.35, T:0.02
Consensus pattern (18 bp):
AGAAAAAGAAGAGGAAGA
Found at i:21789844 original size:23 final size:23
Alignment explanation
Indices: 21789810--21789856 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
21789800 ATATATAATC
21789810 ACTCAACCCTTCATTAATTTTTA
1 ACTCAACCCTTCATTAATTTTTA
*
21789833 ACTCAACTCTTCATTAATTTTTA
1 ACTCAACCCTTCATTAATTTTTA
21789856 A
1 A
21789857 TTGGCCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (23 bp):
ACTCAACCCTTCATTAATTTTTA
Found at i:21790120 original size:18 final size:17
Alignment explanation
Indices: 21790094--21790127 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21790084 TTGTAAAATT
*
21790094 TTTATAAATTTATATAAC
1 TTTAAAAATTT-TATAAC
21790112 TTTAAAAATTTTATAA
1 TTTAAAAATTTTATAA
21790128 TTTGGTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAAAAATTTTATAAC
Found at i:21792352 original size:25 final size:25
Alignment explanation
Indices: 21792318--21792372 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
21792308 CACAAGTCCA
* *
21792318 CCTTCAACTGGGCTATATGTAAAGG
1 CCTTCAACTGGACTATATGAAAAGG
*
21792343 CCTTCAACTGGACTATATGAAAAGT
1 CCTTCAACTGGACTATATGAAAAGG
21792368 CCTTC
1 CCTTC
21792373 TCTTTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (25 bp):
CCTTCAACTGGACTATATGAAAAGG
Found at i:21793012 original size:12 final size:12
Alignment explanation
Indices: 21792995--21793025 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21792985 TAATAATTTT
*
21792995 GTTAAAAGTTAA
1 GTTAAAAATTAA
21793007 GTTAAAAATTAA
1 GTTAAAAATTAA
21793019 GTTAAAA
1 GTTAAAA
21793026 TATATTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (12 bp):
GTTAAAAATTAA
Found at i:21794092 original size:20 final size:20
Alignment explanation
Indices: 21794063--21794101 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21794053 ATGGGATTGC
21794063 ACTTTAGTGCCTCTGTTTGA
1 ACTTTAGTGCCTCTGTTTGA
*
21794083 ACTTTGGTGCCTCTGTTTG
1 ACTTTAGTGCCTCTGTTTG
21794102 CACTACGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (20 bp):
ACTTTAGTGCCTCTGTTTGA
Found at i:21794113 original size:20 final size:20
Alignment explanation
Indices: 21794070--21794156 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
21794060 TGCACTTTAG
* ** *
21794070 TGCCTCTGTTTGAACTTTGG
1 TGCCTCTGTTTGCACTACGA
21794090 TGCCTCTGTTTGCACTACGA
1 TGCCTCTGTTTGCACTACGA
* * *
21794110 TGCCTTTGATTGCACAATCG-
1 TGCCTCTGTTTGCACTA-CGA
* *
21794130 TGTCTTTGTTTGCACTACGA
1 TGCCTCTGTTTGCACTACGA
21794150 TGCCTCT
1 TGCCTCT
21794157 ATATAGCATT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 2 0.04
20 49 0.92
21 2 0.04
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.40
Consensus pattern (20 bp):
TGCCTCTGTTTGCACTACGA
Found at i:21794114 original size:40 final size:40
Alignment explanation
Indices: 21794070--21794156 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 40
21794060 TGCACTTTAG
* ** *
21794070 TGCCTCTGTTTGAACTTTGGTGCCTCTGTTTGCACTACGA
1 TGCCTCTGATTGAACAATCGTGCCTCTGTTTGCACTACGA
* * * *
21794110 TGCCTTTGATTGCACAATCGTGTCTTTGTTTGCACTACGA
1 TGCCTCTGATTGAACAATCGTGCCTCTGTTTGCACTACGA
21794150 TGCCTCT
1 TGCCTCT
21794157 ATATAGCATT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.40
Consensus pattern (40 bp):
TGCCTCTGATTGAACAATCGTGCCTCTGTTTGCACTACGA
Found at i:21794343 original size:24 final size:24
Alignment explanation
Indices: 21794311--21794364 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
21794301 GACTTAAATA
* *
21794311 AATATACATGAATGTTTTCGATCG
1 AATATACATGAATGATTTCAATCG
*
21794335 AATATACATGAATGATTTCAATGG
1 AATATACATGAATGATTTCAATCG
21794359 AATATA
1 AATATA
21794365 TATATGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (24 bp):
AATATACATGAATGATTTCAATCG
Found at i:21805864 original size:14 final size:14
Alignment explanation
Indices: 21805845--21805872 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21805835 TGATAAAAGC
21805845 TGATAATATGAAAT
1 TGATAATATGAAAT
21805859 TGATAATATGAAAT
1 TGATAATATGAAAT
21805873 GGATTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (14 bp):
TGATAATATGAAAT
Found at i:21809344 original size:21 final size:23
Alignment explanation
Indices: 21809305--21809346 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
21809295 TACAGCTTCG
*
21809305 TGTTTGTGTTAAATGTGTCCTAA
1 TGTTTGTGTTAAATATGTCCTAA
21809328 TGTTTGT-TT-AATATGTCCT
1 TGTTTGTGTTAAATATGTCCT
21809347 GGGAGAAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 2 0.11
23 7 0.39
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (23 bp):
TGTTTGTGTTAAATATGTCCTAA
Found at i:21815224 original size:12 final size:12
Alignment explanation
Indices: 21815207--21815239 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
21815197 AATATAATCC
21815207 ATAATTATTTTT-
1 ATAATT-TTTTTA
21815219 ATAATTTTTTTA
1 ATAATTTTTTTA
21815231 ATAATTTTT
1 ATAATTTTT
21815240 GGAAATCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATAATTTTTTTA
Found at i:21833509 original size:9 final size:9
Alignment explanation
Indices: 21833477--21833525 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 9
21833467 AATAATTAAC
21833477 AAAAAATTT
1 AAAAAATTT
*
21833486 -CAAAATTT
1 AAAAAATTT
*
21833494 ATGAAAATTT
1 A-AAAAATTT
21833504 AAAAAA-TT
1 AAAAAATTT
21833512 AAAAAA-TT
1 AAAAAATTT
21833520 AAAAAA
1 AAAAAA
21833526 CTGATGCAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 23 0.66
9 4 0.11
10 8 0.23
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAAAATTT
Found at i:21834131 original size:13 final size:13
Alignment explanation
Indices: 21834115--21834139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21834105 TCTCCCTTCC
21834115 TCTCTGTCCATCA
1 TCTCTGTCCATCA
21834128 TCTCTGTCCATC
1 TCTCTGTCCATC
21834140 GTCCCTTCTC
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:0.12, C:0.40, G:0.08, T:0.40
Consensus pattern (13 bp):
TCTCTGTCCATCA
Found at i:21835732 original size:22 final size:20
Alignment explanation
Indices: 21835689--21835727 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21835679 CAATTTAAAA
21835689 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
21835709 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
21835728 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:21835789 original size:32 final size:32
Alignment explanation
Indices: 21835748--21835831 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 32
21835738 AACTTTTTTG
*
21835748 GAAAATATTTTCAGGAAATT-TGCCAAACAACA
1 GAAAATATTTTCAGCAAATTAT-CCAAACAACA
* *
21835780 GAAAATATTTTACA-CAGATTCATCCAAACATCA
1 GAAAATATTTT-CAGCAAATT-ATCCAAACAACA
*
21835813 GAAAATATTTTCAGTAAAT
1 GAAAATATTTTCAGCAAAT
21835832 CATTTTCCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
32 17 0.40
33 25 0.58
34 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (32 bp):
GAAAATATTTTCAGCAAATTATCCAAACAACA
Found at i:21835850 original size:20 final size:19
Alignment explanation
Indices: 21835825--21835864 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
21835815 AAATATTTTC
21835825 AGTAAATCATTTTCCAAGAA
1 AGTAAATCATTTTCC-AGAA
21835845 AGTAAATCATTTTCCAGAA
1 AGTAAATCATTTTCCAGAA
21835864 A
1 A
21835865 TCATTTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (19 bp):
AGTAAATCATTTTCCAGAA
Found at i:21836153 original size:14 final size:13
Alignment explanation
Indices: 21836132--21836161 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
21836122 GTAAAATATT
21836132 TTTCGGAAAATGA
1 TTTCGGAAAATGA
21836145 TTTCTGGAAAATGA
1 TTTC-GGAAAATGA
21836159 TTT
1 TTT
21836162 ACTTTTCTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (13 bp):
TTTCGGAAAATGA
Found at i:21836170 original size:20 final size:20
Alignment explanation
Indices: 21836145--21836184 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
21836135 CGGAAAATGA
21836145 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
21836165 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
21836185 GAAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:21836174 original size:34 final size:32
Alignment explanation
Indices: 21836131--21836194 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 32
21836121 AGTAAAATAT
21836131 TTTTCGGAAAATGATTT-CTGGAAAATGATTTAC
1 TTTTCGGAAAATGATTTACT-GAAAAT-ATTTAC
21836164 TTTTCTGGAAAATGATTTACTGAAAATATTT
1 TTTTC-GGAAAATGATTTACTGAAAATATTT
21836195 TCTGGTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 9 0.31
34 18 0.62
35 2 0.07
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (32 bp):
TTTTCGGAAAATGATTTACTGAAAATATTTAC
Found at i:21836260 original size:32 final size:32
Alignment explanation
Indices: 21836175--21836262 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 32
21836165 TTTCTGGAAA
*
21836175 ATGATTTACTGAAAATATTTTCTGGTGTTTGG
1 ATGATTTCCTGAAAATATTTTCTGGTGTTTGG
* * *
21836207 ATGA-ATCTGTGTAAAATATTTTCTGTTGTTTGG
1 ATGATTTC-CTG-AAAATATTTTCTGGTGTTTGG
21836240 CA-GATTTCCTGAAAATATTTTCT
1 -ATGATTTCCTGAAAATATTTTCT
21836263 AGAAAAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
31 1 0.02
32 18 0.39
33 24 0.52
34 3 0.07
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (32 bp):
ATGATTTCCTGAAAATATTTTCTGGTGTTTGG
Found at i:21836303 original size:22 final size:22
Alignment explanation
Indices: 21836277--21836322 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
21836267 AAATTATTTT
21836277 TACATATATTAATAAATTTATA
1 TACATATATTAATAAATTTATA
*
21836299 TACATATATTAATAAATTTTTA
1 TACATATATTAATAAATTTATA
21836321 TA
1 TA
21836323 TTTTAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
TACATATATTAATAAATTTATA
Found at i:21837621 original size:32 final size:32
Alignment explanation
Indices: 21837575--21837654 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
21837565 TGTCAATCAT
*
21837575 TTCAATATCCAACAAGCTT-AAAACATAATAAA
1 TTCAATATCCAACAA-ATTCAAAACATAATAAA
* * *
21837607 TTCAATATCTAACAAATTCAATACATAATAAT
1 TTCAATATCCAACAAATTCAAAACATAATAAA
*
21837639 TTCAAAATCCAACAAA
1 TTCAATATCCAACAAA
21837655 CTAAAATTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 2 0.05
32 39 0.95
ACGTcount: A:0.53, C:0.19, G:0.01, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAATTCAAAACATAATAAA
Found at i:21837642 original size:16 final size:16
Alignment explanation
Indices: 21837597--21837643 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
21837587 CAAGCTTAAA
21837597 ACATAATAAATTCAAT
1 ACATAATAAATTCAAT
*
21837613 ATC-TAACAAATTCAAT
1 A-CATAATAAATTCAAT
*
21837629 ACATAATAATTTCAA
1 ACATAATAAATTCAA
21837644 AATCCAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (16 bp):
ACATAATAAATTCAAT
Found at i:21839886 original size:91 final size:91
Alignment explanation
Indices: 21839749--21839930 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
21839739 AAGAAGTTGA
21839749 AAGTTGCTATGAATACATGCTGGAATTATATGATGATTTAGCATGGAATTAGAGCTTTAAATTGT
1 AAGTTGCTATGAATACATGCTGGAATTATATGATGATTTAGCATGGAATTAGAGCTTTAAATTGT
21839814 TCATATGCTGATTTTATTGAAAGAAT
66 TCATATGCTGATTTTATTGAAAGAAT
21839840 AAGTTGCTATGAATACATGCTGGAATTATATGATGATTTAGCATGGAATTAGAGCTTTAAATTGT
1 AAGTTGCTATGAATACATGCTGGAATTATATGATGATTTAGCATGGAATTAGAGCTTTAAATTGT
21839905 TCATATGCTGATTTTATTGAAAGAAT
66 TCATATGCTGATTTTATTGAAAGAAT
21839931 TGAATAGAAA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (91 bp):
AAGTTGCTATGAATACATGCTGGAATTATATGATGATTTAGCATGGAATTAGAGCTTTAAATTGT
TCATATGCTGATTTTATTGAAAGAAT
Found at i:21841622 original size:51 final size:51
Alignment explanation
Indices: 21841541--21841708 Score: 264
Period size: 51 Copynumber: 3.3 Consensus size: 51
21841531 ACTTTTGATT
* *
21841541 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
21841592 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGTCA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* * * *
21841643 AGTAACAAGTGATAAGTGATAGCTTTAGCTACACTTATTTGATCAGGGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
21841694 AGGGACAAGTGATAA
1 AGTGACAAGTGATAA
21841709 ATGTGATCTG
Statistics
Matches: 107, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 107 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:21842624 original size:13 final size:13
Alignment explanation
Indices: 21842606--21842631 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21842596 AGATAAATAA
21842606 AAATTGAGATATG
1 AAATTGAGATATG
21842619 AAATTGAGATATG
1 AAATTGAGATATG
21842632 TTTTATAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (13 bp):
AAATTGAGATATG
Found at i:21843856 original size:59 final size:59
Alignment explanation
Indices: 21843786--21843903 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
21843776 GAAGTGAAAG
21843786 TTATTAAAAAATGTGATCACATGCATAATTATTAGTCATTGGATGACATAATAATGTAA
1 TTATTAAAAAATGTGATCACATGCATAATTATTAGTCATTGGATGACATAATAATGTAA
* * *
21843845 TTATTATAAAATGTGATCACATGCATGATTATTAGTCATTGGATGGCATAATAATGTAA
1 TTATTAAAAAATGTGATCACATGCATAATTATTAGTCATTGGATGACATAATAATGTAA
21843904 CAATATTTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.36
Consensus pattern (59 bp):
TTATTAAAAAATGTGATCACATGCATAATTATTAGTCATTGGATGACATAATAATGTAA
Found at i:21845900 original size:17 final size:17
Alignment explanation
Indices: 21845878--21845914 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
21845868 ATAGTAGTAG
21845878 TAAACTATTCATAATAA
1 TAAACTATTCATAATAA
*
21845895 TAAACTTTTCATAATAA
1 TAAACTATTCATAATAA
21845912 TAA
1 TAA
21845915 TAATAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAACTATTCATAATAA
Found at i:21846664 original size:30 final size:30
Alignment explanation
Indices: 21846628--21846691 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
21846618 AACAAATATG
*
21846628 TATGTTGAAAACTTTAACTAGGAAGTTACA
1 TATGTTGAAAACTCTAACTAGGAAGTTACA
21846658 TATGTTGAAAACTCTAACTAGGAAGTTACA
1 TATGTTGAAAACTCTAACTAGGAAGTTACA
21846688 TATG
1 TATG
21846692 AAGCAACACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (30 bp):
TATGTTGAAAACTCTAACTAGGAAGTTACA
Found at i:21850438 original size:10 final size:10
Alignment explanation
Indices: 21850423--21850455 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
21850413 AAATACAGTG
21850423 ATAAAATAAA
1 ATAAAATAAA
21850433 ATAAAATAAA
1 ATAAAATAAA
21850443 ATAAAAGTAAA
1 ATAAAA-TAAA
21850454 AT
1 AT
21850456 CCATATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (10 bp):
ATAAAATAAA
Found at i:21850443 original size:15 final size:16
Alignment explanation
Indices: 21850423--21850455 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
21850413 AAATACAGTG
21850423 ATAAAATAAAA-TAAA
1 ATAAAATAAAAGTAAA
21850438 ATAAAATAAAAGTAAA
1 ATAAAATAAAAGTAAA
21850454 AT
1 AT
21850456 CCATATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
ATAAAATAAAAGTAAA
Found at i:21855913 original size:33 final size:33
Alignment explanation
Indices: 21855871--21855940 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
21855861 ATTTAATAAA
21855871 ATTATTCATGAATTACGTTAATACCATTTGTAC
1 ATTATTCATGAATTACGTTAATACCATTTGTAC
21855904 ATTATTCATGAATTACGTTAATACCATTTGTAC
1 ATTATTCATGAATTACGTTAATACCATTTGTAC
21855937 ATTA
1 ATTA
21855941 CCCTCAATGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (33 bp):
ATTATTCATGAATTACGTTAATACCATTTGTAC
Found at i:21859311 original size:20 final size:20
Alignment explanation
Indices: 21859270--21859353 Score: 53
Period size: 20 Copynumber: 4.2 Consensus size: 20
21859260 TACGTCCAGT
**
21859270 CAGGGGCACCAAAGTGTGAA
1 CAGGGGCACCAAAGTGCAAA
21859290 CAGGGGCA-CAAACGTGCAAA
1 CAGGGGCACCAAA-GTGCAAA
* * * * *
21859310 CATGGACACCGAAGTGTATA
1 CAGGGGCACCAAAGTGCAAA
* * * *
21859330 CAAGGGCATCGAAGTGCGAA
1 CAGGGGCACCAAAGTGCAAA
21859350 CAGG
1 CAGG
21859354 ATCACATAGG
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
19 4 0.08
20 41 0.85
21 3 0.06
ACGTcount: A:0.36, C:0.21, G:0.32, T:0.11
Consensus pattern (20 bp):
CAGGGGCACCAAAGTGCAAA
Found at i:21859406 original size:61 final size:60
Alignment explanation
Indices: 21859270--21859413 Score: 164
Period size: 61 Copynumber: 2.4 Consensus size: 60
21859260 TACGTCCAGT
* * *
21859270 CAGGGGCACCAAAGTGTGAACAGGGGCACAAACGTGCAAACATGGACACCGAAGTGTATA
1 CAGGGGCACCAAAGTGCGAACAGGAGCACAAACGTGCAAACATGGACAACGAAGTGTATA
* * * * * * * *
21859330 CAAGGGCATCGAAGTGCGAACAGGATCACATAGGTGCAAA-TTAGAGACAATGAAGTGTATA
1 CAGGGGCACCAAAGTGCGAACAGGAGCACAAACGTGCAAACAT-G-GACAACGAAGTGTATA
21859391 CAGGGGCACCAAAGTGCGAACAG
1 CAGGGGCACCAAAGTGCGAACAG
21859414 AGGCACAGTT
Statistics
Matches: 68, Mismatches: 14, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
59 1 0.01
60 33 0.49
61 34 0.50
ACGTcount: A:0.38, C:0.19, G:0.30, T:0.13
Consensus pattern (60 bp):
CAGGGGCACCAAAGTGCGAACAGGAGCACAAACGTGCAAACATGGACAACGAAGTGTATA
Found at i:21859428 original size:61 final size:58
Alignment explanation
Indices: 21859270--21859431 Score: 146
Period size: 61 Copynumber: 2.7 Consensus size: 58
21859260 TACGTCCAGT
* * *
21859270 CAGGGGCACCAAAGTGTGAACAGGGGCACAAACGTGCAAACATGGACACCGAAGTGTATA
1 CAGGGGCACCAAAGTGCGAACA-GGGCAC-ATCGTGCAAACATGGACAACGAAGTGTATA
* * * * * * *
21859330 CAAGGGCATCGAAGTGCGAACAGGATCACATAGGTGCAAA-TTAGAGACAATGAAGTGTATA
1 CAGGGGCACCAAAGTGCGAACAGG-GCACAT-CGTGCAAACAT-G-GACAACGAAGTGTATA
*
21859391 CAGGGGCACCAAAGTGCGAACAGAGGCACAGTTGTGCAAAC
1 CAGGGGCACCAAAGTGCGAACAG-GGCACA-TCGTGCAAAC
21859432 GGGGGCACTT
Statistics
Matches: 80, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
59 4 0.05
60 29 0.36
61 45 0.56
62 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.14
Consensus pattern (58 bp):
CAGGGGCACCAAAGTGCGAACAGGGCACATCGTGCAAACATGGACAACGAAGTGTATA
Found at i:21866403 original size:62 final size:59
Alignment explanation
Indices: 21866334--21866450 Score: 153
Period size: 59 Copynumber: 1.9 Consensus size: 59
21866324 AGTGATTATC
* * *
21866334 TTAATATTAAATTAAATTTAATGTTTATTTTGTAGATAAATATTCTATTAATTAAATAATAT
1 TTAATATTAAATTAAATATAATATTTA---TGTAGATAAATATTATATTAATTAAATAATAT
* * *
21866396 TTAATATTAAATTTAATATAATATTTATGTTGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTAAATATAATATTTATGTAGATAAATATTATATTAATTAAATA
21866451 TTAAAGTGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 25 0.51
62 24 0.49
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTAAATATAATATTTATGTAGATAAATATTATATTAATTAAATAATAT
Found at i:21866421 original size:12 final size:12
Alignment explanation
Indices: 21866385--21866422 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
21866375 ATTCTATTAA
21866385 TTAA-ATAATAT
1 TTAATATAATAT
21866396 TTAATATTAA-AT
1 TTAATA-TAATAT
21866408 TTAATATAATAT
1 TTAATATAATAT
21866420 TTA
1 TTA
21866423 TGTTGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.29
12 14 0.58
13 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAATATAATAT
Found at i:21868342 original size:21 final size:22
Alignment explanation
Indices: 21868318--21868360 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
21868308 GTGTTATAAG
*
21868318 TTAAAATTAAATA-AATAAAAC
1 TTAAAATAAAATACAATAAAAC
21868339 TTAAAATAAAATACAATAAAAC
1 TTAAAATAAAATACAATAAAAC
21868361 ATAATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (22 bp):
TTAAAATAAAATACAATAAAAC
Found at i:21881060 original size:8 final size:8
Alignment explanation
Indices: 21881047--21881081 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
21881037 TCTAGATGTT
21881047 TAATTTCA
1 TAATTTCA
21881055 TAATTTCA
1 TAATTTCA
21881063 TAATTTCA
1 TAATTTCA
21881071 TAATTTCA
1 TAATTTCA
21881079 TAA
1 TAA
21881082 ATGATTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (8 bp):
TAATTTCA
Found at i:21902420 original size:21 final size:20
Alignment explanation
Indices: 21902364--21902411 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
21902354 CTGAGAAAGA
21902364 CAAAACAAAAGAAGAATTGC
1 CAAAACAAAAGAAGAATTGC
*
21902384 CAAAACAAAAGAAGAATTGT
1 CAAAACAAAAGAAGAATTGC
21902404 CAAAACAA
1 CAAAACAA
21902412 TTAGAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.62, C:0.15, G:0.12, T:0.10
Consensus pattern (20 bp):
CAAAACAAAAGAAGAATTGC
Found at i:21905121 original size:56 final size:57
Alignment explanation
Indices: 21905034--21905201 Score: 259
Period size: 56 Copynumber: 2.9 Consensus size: 57
21905024 GCTTTGAAAA
* *
21905034 GAAAAAGAAAAAAAAGAAAATTGAGAGGCCAAGGTGAAAACCCGCAAAGGGCT-CTTT
1 GAAAAA-AATAAAAAGAAAATGGAGAGGCCAAGGTGAAAACCCGCAAAGGGCTGCTTT
21905091 GAAAAAAATAAAAAGAAAATGGAGAGGCCAAGGTGAAAACCCGCAAA-GGCTGCTTT
1 GAAAAAAATAAAAAGAAAATGGAGAGGCCAAGGTGAAAACCCGCAAAGGGCTGCTTT
21905147 GAAAAAAAATAAAAAAAGAAAATGGAGAGGGCCAAGGTGAAAACCCGCAAAGGGC
1 G-AAAAAAAT--AAAAAGAAAATGGAGA-GGCCAAGGTGAAAACCCGCAAAGGGC
21905202 ACCTTGAGAC
Statistics
Matches: 103, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
55 4 0.04
56 44 0.43
57 14 0.14
59 16 0.16
60 22 0.21
61 3 0.03
ACGTcount: A:0.51, C:0.14, G:0.26, T:0.10
Consensus pattern (57 bp):
GAAAAAAATAAAAAGAAAATGGAGAGGCCAAGGTGAAAACCCGCAAAGGGCTGCTTT
Found at i:21906242 original size:43 final size:43
Alignment explanation
Indices: 21906181--21906399 Score: 225
Period size: 43 Copynumber: 5.1 Consensus size: 43
21906171 ATTCCCCGAT
21906181 GGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAG
1 GGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAG
* * * * *
21906224 GGGTTGCTATGTGCTGATTCC-CCGTATCA-CTGAATATAAAAG
1 GGGTTGCTAAGTGCTGATTCCACCGTAT-ATTTGATTGTGAAAG
*
21906266 TGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAG
1 GGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAG
* * * * *
21906309 GGGTTGCTATA-TGTTGATTCC-CTGTATCA-CTGAATAT-AAAG
1 GGGTTGCTA-AGTGCTGATTCCACCGTAT-ATTTGATTGTGAAAG
* * * *
21906350 GTGGTTGCTAAGTGCTGATTCCACCATGTGTTTCATTGTGAAAG
1 G-GGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAG
21906394 GGGTTG
1 GGGTTG
21906400 TTGTGTGTTG
Statistics
Matches: 140, Mismatches: 26, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
41 6 0.04
42 62 0.44
43 66 0.47
44 6 0.04
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.35
Consensus pattern (43 bp):
GGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAG
Found at i:21906271 original size:42 final size:43
Alignment explanation
Indices: 21906181--21906374 Score: 202
Period size: 42 Copynumber: 4.6 Consensus size: 43
21906171 ATTCCCCGAT
* * * *
21906181 GGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAG
1 GGGTTGCTAAGTGCTGATTCCACCGTATATCTGAATATAAAAG
*
21906224 GGGTTGCTATGTGCTGATTCC-CCGTATCA-CTGAATATAAAAG
1 GGGTTGCTAAGTGCTGATTCCACCGTAT-ATCTGAATATAAAAG
* * * * *
21906266 TGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAG
1 GGGTTGCTAAGTGCTGATTCCACCGTATATCTGAATATAAAAG
* *
21906309 GGGTTGCTATA-TGTTGATTCC-CTGTATCA-CTGAATAT-AAAG
1 GGGTTGCTA-AGTGCTGATTCCACCGTAT-ATCTGAATATAAAAG
21906350 GTGGTTGCTAAGTGCTGATTCCACC
1 G-GGTTGCTAAGTGCTGATTCCACC
21906375 ATGTGTTTCA
Statistics
Matches: 124, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
41 6 0.05
42 62 0.50
43 55 0.44
44 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (43 bp):
GGGTTGCTAAGTGCTGATTCCACCGTATATCTGAATATAAAAG
Found at i:21906327 original size:85 final size:85
Alignment explanation
Indices: 21906182--21906417 Score: 382
Period size: 85 Copynumber: 2.8 Consensus size: 85
21906172 TTCCCCGATG
*
21906182 GGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCC
1 GGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATGTGTTGATTCCCC
21906247 GTATCACTGAATATAAAAGT
66 GTATCACTGAATATAAAAGT
* *
21906267 GGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATATGTTGATTCCCT
1 GGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATGTGTTGATTCCCC
*
21906332 GTATCACTGAATATAAAGGT
66 GTATCACTGAATATAAAAGT
* * * * * *
21906352 GGTTGCTAAGTGCTGATTCCACCATGTGTTTCATTGTGAAAGGGGTTGTTGTGTGTTGATTCCCC
1 GGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATGTGTTGATTCCCC
21906417 G
66 G
21906418 CCGACCAATT
Statistics
Matches: 139, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 139 1.00
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (85 bp):
GGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTTGCTATGTGTTGATTCCCC
GTATCACTGAATATAAAAGT
Found at i:21908377 original size:14 final size:14
Alignment explanation
Indices: 21908350--21908384 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
21908340 CTAGTTTTAC
*
21908350 CTTTTCTTCCTTTT
1 CTTTTTTTCCTTTT
*
21908364 CTTTTTTTCTTTTT
1 CTTTTTTTCCTTTT
21908378 CTTTTTT
1 CTTTTTT
21908385 CCATAGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
CTTTTTTTCCTTTT
Found at i:21924594 original size:99 final size:98
Alignment explanation
Indices: 21924419--21924962 Score: 526
Period size: 99 Copynumber: 5.5 Consensus size: 98
21924409 CCCGGTCTCG
* * * * * * * **
21924419 CTGAGGAAATAAGATTCACCGTTGCGGCTTTAATC-TTTAGTTGTAATATC-GGGAAAGCAAGAT
1 CTGA-GAAGTAAGATTCACCGTTGTGGCCTCAATCTTTTAATTGCAATGTCAGGG-AAGTGAGAT
* * *
21924482 TCGCCATCGTAGCTTCAATCTGTTCTACTGCATCGC
64 TC-CCTTTGTAGCTTCAATCTGTTCCACTGCATCGC
* *
21924518 CTGAGAAGTAAGATTCACCGTTGTGGCCTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTC
1 CTGAGAAGTAAGATTCACCGTTGTGGCCTCAATCTTTTAATTGCAATGTCAGGGAAGTGAGATTC
*
21924583 ACCTTTGTAGCTTCAATCTGTTCCACTGTAAT-G-
66 -CCTTTGTAGCTTCAATCTGTTCCACTG-CATCGC
* ** *
21924616 CT-AGGAAATTAAGATTTGCCATTGTGGCCTCAATCTTTTGAATTGCAATGTCAGGGAAGTGAGA
1 CTGA-G-AAGTAAGATTCACCGTTGTGGCCTCAATCTTTT-AATTGCAATGTCAGGGAAGTGAGA
* * **
21924680 TTCGCTGTTGTAGCTTCAATCTGTTTCGTTGCATCGC
63 TTCCCT-TTGTAGCTTCAATCTGTTCCACTGCATCGC
* * * * *
21924717 CTGA-AAGTAAGATTCACCGTTGTGGCTTCGATCCTTTAAACTGCAATGTCAGGGAAGTAAGA-T
1 CTGAGAAGTAAGATTCACCGTTGTGGCCTCAAT-CTTTTAATTGCAATGTCAGGGAAGTGAGATT
* *
21924780 CCGCTGTTGTAGCTTCAATTTGTTCCACTGCAACGC
65 CC-CT-TTGTAGCTTCAATCTGTTCCACTGCATCGC
* * ** * * *
21924816 CTGGGAAGTAAGGTTTGCCGTTGTGGCTTCAATCTTTTGATTGCAATGTCAGGGAAGTGAGATCC
1 CTGAGAAGTAAGATTCACCGTTGTGGCCTCAATCTTTTAATTGCAATGTCAGGGAAGTGAGATTC
* * *
21924881 ACCGTTGTAGCTTCAATCTGTTCCGCTGCACCGC
66 -CCTTTGTAGCTTCAATCTGTTCCACTGCATCGC
* *
21924915 TTGAGAAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTAAATTGCAA
1 CTGAG-AAGTAAGATTCACCGTTGTGGCCTCAATCTTTT-AATTGCAA
21924963 ACTATGGTTA
Statistics
Matches: 369, Mismatches: 59, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
97 1 0.00
98 31 0.08
99 214 0.58
100 112 0.30
101 10 0.03
102 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.32
Consensus pattern (98 bp):
CTGAGAAGTAAGATTCACCGTTGTGGCCTCAATCTTTTAATTGCAATGTCAGGGAAGTGAGATTC
CCTTTGTAGCTTCAATCTGTTCCACTGCATCGC
Found at i:21924699 original size:50 final size:50
Alignment explanation
Indices: 21924522--21924899 Score: 259
Period size: 50 Copynumber: 7.6 Consensus size: 50
21924512 CATCGCCTGA
* * * *
21924522 GAAGTAAGATTCACCGTTGTGGCCTCAATCTTTT-AATTGCAATGTCGGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTGAATTGCAATGTCAGG
** * * * ** * *
21924571 GAAGCGAGATTCACCTTTGTAGCTTCAATCTGTTCCACTGTAATG-CTAGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTGAATTGCAATGTC-AGG
* * * * * *
21924621 AAATTAAGATTTGCCATTGTGGCCTCAATCTTTTGAATTGCAATGTCAGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTGAATTGCAATGTCAGG
* * **
21924671 GAAGTGAGATTCGCTGTTGTAGCTTCAATCTGTTTCG--TTGC-ATCG-CCTG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTT-GAATTGCAAT-GTCAGG
* * * * * * *
21924720 AAAGTAAGATTCACCGTTGTGGCTTCGATCCTTTAAACTGCAATGTCAGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTGAATTGCAATGTCAGG
* * ** * * * *
21924770 GAAGTAAGATCCGCTGTTGTAGCTTCAAT-TTGTTCCACTGCAACGCCTGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTT-TTGAATTGCAATGTCAGG
* * *
21924820 GAAGTAAGGTTTGCCGTTGTGGCTTCAATCTTTTG-ATTGCAATGTCAGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTGAATTGCAATGTCAGG
* * *
21924869 GAAGTGAGATCCACCGTTGTAGCTTCAATCT
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCT
21924900 GTTCCGCTGC
Statistics
Matches: 244, Mismatches: 73, Indels: 24
0.72 0.21 0.07
Matches are distributed among these distances:
48 3 0.01
49 97 0.40
50 137 0.56
51 6 0.02
52 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (50 bp):
GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTGAATTGCAATGTCAGG
Found at i:21943485 original size:18 final size:20
Alignment explanation
Indices: 21943457--21943498 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
21943447 GTTTTCCTAC
*
21943457 AAAAATAAAATAA-AATAGT
1 AAAAATAAAATAATAATAGG
21943476 AAAAAT-AAATAATAATAGG
1 AAAAATAAAATAATAATAGG
21943495 AAAA
1 AAAA
21943499 TTAATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (20 bp):
AAAAATAAAATAATAATAGG
Found at i:21954831 original size:22 final size:22
Alignment explanation
Indices: 21954805--21954853 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
21954795 TTGCAATGGG
*
21954805 TTCTTACACCATTC-TTTTCCTC
1 TTCTTACACCA-TCATTTTCCTA
**
21954827 TTCTTGTACCATCATTTTCCTA
1 TTCTTACACCATCATTTTCCTA
21954849 TTCTT
1 TTCTT
21954854 GCTTTCATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.14, C:0.31, G:0.02, T:0.53
Consensus pattern (22 bp):
TTCTTACACCATCATTTTCCTA
Found at i:21956934 original size:51 final size:50
Alignment explanation
Indices: 21956811--21956998 Score: 207
Period size: 51 Copynumber: 3.7 Consensus size: 50
21956801 TATCATTCAA
* * * * *
21956811 TACACGTAGTAGCCTTCACATAGTACTACACATGTGATCAAACTTTCTGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACCTTCCGG
* *
21956861 TTCACGTAGTAGGCTGCACATAGTACTACACACGTGACCAAAGCCTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAA-CCTTCCGG
* * * * * * *
21956912 TGCACATAGTAGCCTGCACATAGTACTACACATGTAACCATTATCTAT-CGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-AACCT-TCCGG
*
21956963 TACACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTG
21956999 TTTATAGTCA
Statistics
Matches: 115, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
50 37 0.32
51 76 0.66
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACCTTCCGG
Found at i:21959929 original size:12 final size:12
Alignment explanation
Indices: 21959914--21959944 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
21959904 AATTCGAATT
21959914 TTATTATTAGGA
1 TTATTATTAGGA
21959926 TTATTATTAGGA
1 TTATTATTAGGA
21959938 TTATTAT
1 TTATTAT
21959945 GATATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (12 bp):
TTATTATTAGGA
Found at i:21961340 original size:11 final size:13
Alignment explanation
Indices: 21961324--21961355 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
21961314 AATTTCACGA
21961324 AAAAATTTCG-T-
1 AAAAATTTCGTTC
21961335 AAAAATTTCGTTC
1 AAAAATTTCGTTC
21961348 AAAAATTT
1 AAAAATTT
21961356 TGACGTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:21962452 original size:26 final size:26
Alignment explanation
Indices: 21962415--21962464 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
21962405 GAATATAAAG
*
21962415 GGGGTTGTTAAGTGCTGATTCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCAA
21962441 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
21962465 GAATCATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.16, C:0.22, G:0.32, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCAA
Found at i:21962597 original size:102 final size:102
Alignment explanation
Indices: 21962412--21962845 Score: 753
Period size: 102 Copynumber: 4.3 Consensus size: 102
21962402 ATTGAATATA
*
21962412 AAGGGGGTTGTTAAGTGCTGATT-CCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
21962476 GGTTGCTAAGTGTTTATTCCATCGTATTTTAAATGTG
66 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
*
21962513 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTCAGTGCTGATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
21962578 GGTTGCTAAATGCTGATTCCACCGTATTTTAAATGTG
66 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
21962615 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
21962680 GGTTGCTAAGTGCTGATTCCATCGTATTTTAAATGTG
66 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
* *
21962717 AAGGGGGCTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
21962782 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
66 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
*
21962819 AAAGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
21962846 AAATCACTGG
Statistics
Matches: 316, Mismatches: 16, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
101 22 0.07
102 294 0.93
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.32
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
Found at i:21968290 original size:21 final size:21
Alignment explanation
Indices: 21968264--21968311 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
21968254 TTAGAAATGT
21968264 CTATGTAATTCTTACGGTAGA
1 CTATGTAATTCTTACGGTAGA
21968285 CTATGTAATTCTTACGGTAGA
1 CTATGTAATTCTTACGGTAGA
21968306 CTATGT
1 CTATGT
21968312 TTTTAAGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (21 bp):
CTATGTAATTCTTACGGTAGA
Found at i:21969186 original size:5 final size:5
Alignment explanation
Indices: 21969160--21969197 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
21969150 TAAAAAATTA
21969160 TTTATT TTTAT TATTA- TTTAT TTTAT TTTAT TTTAT TT
1 TTTA-T TTTAT T-TTAT TTTAT TTTAT TTTAT TTTAT TT
21969198 GCATCTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 3 0.10
5 20 0.67
6 7 0.23
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:21972730 original size:20 final size:20
Alignment explanation
Indices: 21972702--21972776 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
21972692 AGGGGTACTG
* *
21972702 AAGTACAAATAGGGGCACGT
1 AAGTGCAAACAGGGGCACGT
* *
21972722 ATGTGCAAACAGGGGTACCG-
1 AAGTGCAAACAGGGGCA-CGT
* * *
21972742 AAGTACAAAGAGGGGCATGT
1 AAGTGCAAACAGGGGCACGT
*
21972762 AGGTGCAAACAGGGG
1 AAGTGCAAACAGGGG
21972777 TACCAAGTAC
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 1 0.02
20 38 0.93
21 2 0.05
ACGTcount: A:0.36, C:0.15, G:0.36, T:0.13
Consensus pattern (20 bp):
AAGTGCAAACAGGGGCACGT
Found at i:21972735 original size:40 final size:40
Alignment explanation
Indices: 21972691--21972853 Score: 159
Period size: 40 Copynumber: 4.1 Consensus size: 40
21972681 TAAATGCGTT
21972691 CAGGGGTACTGAAGTACAAATAGGGGCACGTATGTGCAAA
1 CAGGGGTACTGAAGTACAAATAGGGGCACGTATGTGCAAA
* * * *
21972731 CAGGGGTACCGAAGTACAAAGAGGGGCATGTAGGTGCAAA
1 CAGGGGTACTGAAGTACAAATAGGGGCACGTATGTGCAAA
* * * * **
21972771 CAGGGGTAC-CAAGTACAATTAAGGGCATGTACATGCAAA
1 CAGGGGTACTGAAGTACAAATAGGGGCACGTATGTGCAAA
* * * ** *
21972810 CAGGGGTATTGAGGTA-GAATCAGGCACACGTATGTACAAA
1 CAGGGGTACTGAAGTACAAAT-AGGGGCACGTATGTGCAAA
21972850 CAGG
1 CAGG
21972854 AGCACATATG
Statistics
Matches: 99, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
39 34 0.34
40 65 0.66
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.17
Consensus pattern (40 bp):
CAGGGGTACTGAAGTACAAATAGGGGCACGTATGTGCAAA
Found at i:21972797 original size:39 final size:39
Alignment explanation
Indices: 21972691--21972817 Score: 164
Period size: 40 Copynumber: 3.2 Consensus size: 39
21972681 TAAATGCGTT
* * *
21972691 CAGGGGTACTGAAGTACAAATAGGGGCACGTATGTGCAAA
1 CAGGGGTAC-CAAGTACAAATAGGGGCATGTACGTGCAAA
* *
21972731 CAGGGGTACCGAAGTACAAAGAGGGGCATGTAGGTGCAAA
1 CAGGGGTACC-AAGTACAAATAGGGGCATGTACGTGCAAA
* * *
21972771 CAGGGGTACCAAGTACAATTAAGGGCATGTACATGCAAA
1 CAGGGGTACCAAGTACAAATAGGGGCATGTACGTGCAAA
21972810 CAGGGGTA
1 CAGGGGTA
21972818 TTGAGGTAGA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
39 32 0.42
40 45 0.58
ACGTcount: A:0.35, C:0.16, G:0.33, T:0.16
Consensus pattern (39 bp):
CAGGGGTACCAAGTACAAATAGGGGCATGTACGTGCAAA
Found at i:21972863 original size:20 final size:19
Alignment explanation
Indices: 21972840--21972914 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 19
21972830 CAGGCACACG
21972840 TATGTACAAACAGGAGCACA
1 TATGTACAAACAGG-GCACA
* *
21972860 TATGTACAAATAGGG-ATA
1 TATGTACAAACAGGGCACA
* *
21972878 TCGAAGTACAATCAGGGGCACA
1 T--ATGTACAAACA-GGGCACA
*
21972900 TATGTGCAAACAGGG
1 TATGTACAAACAGGG
21972915 GTACCGAAGT
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
18 3 0.07
19 4 0.10
20 29 0.69
21 3 0.07
22 3 0.07
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.19
Consensus pattern (19 bp):
TATGTACAAACAGGGCACA
Found at i:21972887 original size:40 final size:40
Alignment explanation
Indices: 21972843--21972928 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
21972833 GCACACGTAT
* *
21972843 GTACAAACAGGAGCACATATGTACAAATAGGGATATCGAA
1 GTACAAACAGGAGCACATATGTACAAACAGGGATACCGAA
* * * *
21972883 GTACAATCAGGGGCACATATGTGCAAACAGGGGTACCGAA
1 GTACAAACAGGAGCACATATGTACAAACAGGGATACCGAA
21972923 GTACAA
1 GTACAA
21972929 CCAATGGCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.41, C:0.17, G:0.26, T:0.16
Consensus pattern (40 bp):
GTACAAACAGGAGCACATATGTACAAACAGGGATACCGAA
Found at i:21976599 original size:16 final size:17
Alignment explanation
Indices: 21976578--21976610 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21976568 CACATTAAAG
21976578 TGTTTT-TTGAAAACCA
1 TGTTTTATTGAAAACCA
21976594 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
21976611 CTTCTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (17 bp):
TGTTTTATTGAAAACCA
Found at i:21977742 original size:54 final size:54
Alignment explanation
Indices: 21977659--21977907 Score: 179
Period size: 54 Copynumber: 4.6 Consensus size: 54
21977649 TAAAATAATC
* * *
21977659 ATTTTACCCTATAG-GGGTATTTTGTTCATTTTACCCTTCGGGGGTATTTCGATA
1 ATTTTACCCT-TAGAGGGTATTTAGATCATTTTACCCTTCGAGGGTATTTCGATA
* * * *
21977713 ATTTTACCCTTCGAGGGTATTTCAG-TCATTTTACCCTTCGAAGGTAATTT-GGTT
1 ATTTTACCCTTAGAGGGTATTT-AGATCATTTTACCCTTCGAGGGT-ATTTCGATA
* * * * **
21977767 ATTTTACCCTTAGATGGTAATTTAG-TCATTTTA-CATGTCGAGGATAATTCGAGC
1 ATTTTACCCTTAGAGGGT-ATTTAGATCATTTTACCCT-TCGAGGGTATTTCGATA
* ** * * * * *
21977821 ATTTTAACCTCCGAGGGTATTTCGATAATTTTACCCTTCGAAGGTAATTT-GGTC
1 ATTTTACCCTTAGAGGGTATTTAGATCATTTTACCCTTCGAGGGT-ATTTCGATA
* *
21977875 ATTTTACCCTTTAG-GGGTAATTCGATCATTTTA
1 ATTTTACCC-TTAGAGGGTATTTAGATCATTTTA
21977908 ACAACATTTC
Statistics
Matches: 153, Mismatches: 32, Indels: 20
0.75 0.16 0.10
Matches are distributed among these distances:
53 12 0.08
54 125 0.82
55 16 0.10
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (54 bp):
ATTTTACCCTTAGAGGGTATTTAGATCATTTTACCCTTCGAGGGTATTTCGATA
Found at i:21977866 original size:27 final size:27
Alignment explanation
Indices: 21977656--21977907 Score: 160
Period size: 27 Copynumber: 9.3 Consensus size: 27
21977646 CGGTAAAATA
* * *
21977656 ATCATTTTACCCTATAG-GGGTATTTTG
1 ATCATTTTACCCT-TCGAAGGTATTTCG
* **
21977683 TTCATTTTACCCTTCGGGGGTATTTCG
1 ATCATTTTACCCTTCGAAGGTATTTCG
* *
21977710 ATAATTTTACCCTTCGAGGGTATTTC-
1 ATCATTTTACCCTTCGAAGGTATTTCG
21977736 AGTCATTTTACCCTTCGAAGGTAATTT-G
1 A-TCATTTTACCCTTCGAAGGT-ATTTCG
* * * * *
21977764 GTTATTTTACCCTTAGATGGTAATTTAG
1 ATCATTTTACCCTTCGAAGGT-ATTTCG
* *
21977792 -TCATTTTA-CATGTCG-AGGATAATTCG
1 ATCATTTTACCCT-TCGAAGG-TATTTCG
* * * *
21977818 AGCATTTTAACCTCCGAGGGTATTTCG
1 ATCATTTTACCCTTCGAAGGTATTTCG
*
21977845 ATAATTTTACCCTTCGAAGGTAATTT-G
1 ATCATTTTACCCTTCGAAGGT-ATTTCG
* * * *
21977872 GTCATTTTACCCTT-TAGGGGTAATTCG
1 ATCATTTTACCCTTCGA-AGGTATTTCG
21977899 ATCATTTTA
1 ATCATTTTA
21977908 ACAACATTTC
Statistics
Matches: 178, Mismatches: 34, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
26 15 0.08
27 150 0.84
28 13 0.07
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (27 bp):
ATCATTTTACCCTTCGAAGGTATTTCG
Found at i:21977894 original size:108 final size:109
Alignment explanation
Indices: 21977657--21977896 Score: 301
Period size: 108 Copynumber: 2.2 Consensus size: 109
21977647 GGTAAAATAA
* * * * * * * *
21977657 TCATTTTACCCTATAGGGGT-ATTTTGTTCATTTTACCCTTCGGGGGTATTTCGATAATTTTACC
1 TCATTTTACCCTTTAGGGGTAATTTAGTTCATTTTACCATTCGAGGATAATTCGAGAATTTTAAC
* *
21977721 CTTCGAGGGTATTTCAGTCATTTTACCCTTCGAAGGTAATTTGG
66 CTCCGAGGGTATTTCAGTAATTTTACCCTTCGAAGGTAATTTGG
* * *
21977765 TTATTTTACCC-TTAGATGGTAATTTAG-TCATTTTA-CATGTCGAGGATAATTCGAGCATTTTA
1 TCATTTTACCCTTTAG-GGGTAATTTAGTTCATTTTACCAT-TCGAGGATAATTCGAGAATTTTA
21977827 ACCTCCGAGGGTATTTC-GATAATTTTACCCTTCGAAGGTAATTTGG
64 ACCTCCGAGGGTATTTCAG-TAATTTTACCCTTCGAAGGTAATTTGG
21977873 TCATTTTACCCTTTAGGGGTAATT
1 TCATTTTACCCTTTAGGGGTAATT
21977897 CGATCATTTT
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
107 6 0.05
108 97 0.87
109 9 0.08
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (109 bp):
TCATTTTACCCTTTAGGGGTAATTTAGTTCATTTTACCATTCGAGGATAATTCGAGAATTTTAAC
CTCCGAGGGTATTTCAGTAATTTTACCCTTCGAAGGTAATTTGG
Found at i:21984166 original size:14 final size:13
Alignment explanation
Indices: 21984147--21984176 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
21984137 TGGACTGTTA
21984147 TTTTATTTATTTAT
1 TTTTATTTATTT-T
21984161 TTTTATTTATTTT
1 TTTTATTTATTTT
21984174 TTT
1 TTT
21984177 CTAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTATTTATTTT
Found at i:21984615 original size:45 final size:44
Alignment explanation
Indices: 21984570--21984966 Score: 118
Period size: 42 Copynumber: 9.1 Consensus size: 44
21984560 GACGCAGGAG
21984570 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
1 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
* * * * * * *
21984614 GGCAAG----GCTTTGTTT-TCGATTGCTTCGCTGTTAA-CGCA-GGAA
1 GGCAAGATCTGCTATCTTTAACCA--GCTCCACTG-CAACCG-ATGG-A
21984656 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
1 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
* * ** * * *** * *
21984700 GGCAAGGCTTTG-T-T-TTCGATCTGCTTTGCTGTTAA-TGCA-GGAA
1 GGCAA-GATCTGCTATCTTTAACCAGCTCCACTG-CAACCG-ATGG-A
* *
21984743 GGCAAGATCTACTATCTTTAACCAGCTCCACTACAACCGATGGA
1 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
* * ** * * * * *
21984787 GGCAAGGCTTTG-T-T-TTCGATCTGCTTCGCTGTTAACAC-A-GGAA
1 GGCAA-GATCTGCTATCTTTAACCAGCTCCACTG-CAAC-CGATGG-A
*
21984830 GGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGA
1 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
* * ** * * * * *
21984874 GGCAAGGCTTTG-T-T-TTCGATCTGCTTCGCTGTTAA-CGCA-GGAA
1 GGCAA-GATCTGCTATCTTTAACCAGCTCCACTG-CAACCG-ATGG-A
* *
21984917 GGCAAGATCTGCTATCTTTAACCAACTCCACTACAACCGATGGA
1 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
21984961 GGCAAG
1 GGCAAG
21984967 GCTTTGTTTT
Statistics
Matches: 234, Mismatches: 80, Indels: 78
0.60 0.20 0.20
Matches are distributed among these distances:
39 2 0.01
40 7 0.03
41 11 0.05
42 60 0.26
43 35 0.15
44 51 0.22
45 59 0.25
46 7 0.03
47 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (44 bp):
GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
Found at i:21984780 original size:87 final size:87
Alignment explanation
Indices: 21984541--21985156 Score: 1018
Period size: 87 Copynumber: 7.1 Consensus size: 87
21984531 ACTTGTAATC
* ** * *
21984541 TTCGATCTGCTTCACTGTCGACGCAGGAGGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAA
21984606 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
*
21984628 TTCGAT-TGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAA
21984692 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * *
21984714 TTCGATCTGCTTTGCTGTTAATGCAGGAAGGCAAGATCTACTATCTTTAACCAGCTCCACTACAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAA
21984779 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
*
21984801 TTCGATCTGCTTCGCTGTTAACACAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAA
21984866 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
*
21984888 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAACTCCACTACAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAA
21984953 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * * * * * *
21984975 TTCGATCTGCTTCGCTGTCAATGCAGGAATGTAAGATCTACTATCTTTAACCAACTCTACTACAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAA
21985040 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * * *
21985062 TTCGATCTGCTTCGTTGTCAATGCAGGAAGACAAGATCTGCTATCTTTAACCAGCTCCACTACAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAA
*
21985127 CCGATAGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
21985149 TTCGATCT
1 TTCGATCT
21985157 TCACTGATCT
Statistics
Matches: 500, Mismatches: 28, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
86 82 0.16
87 418 0.84
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (87 bp):
TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAA
CCGATGGAGGCAAGGCTTTGTT
Found at i:21993102 original size:26 final size:26
Alignment explanation
Indices: 21993048--21993102 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
21993038 TATTAATGAA
* * *
21993048 GAAGCAAAAAAGAGAAAGAAAATAGT
1 GAAGCAAAAAACAAAAAGAAAAAAGT
21993074 GAAG-AAAAAACAAAAAGAAAAAAGAT
1 GAAGCAAAAAACAAAAAGAAAAAAG-T
21993100 GAA
1 GAA
21993103 TATACCTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.71, C:0.04, G:0.20, T:0.05
Consensus pattern (26 bp):
GAAGCAAAAAACAAAAAGAAAAAAGT
Found at i:21994147 original size:13 final size:13
Alignment explanation
Indices: 21994129--21994161 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
21994119 TTGAGTATGA
21994129 TCACACGGTCGTG
1 TCACACGGTCGTG
21994142 TCACACGGTCGTG
1 TCACACGGTCGTG
21994155 TCACACG
1 TCACACG
21994162 CCCGTGTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.21
Consensus pattern (13 bp):
TCACACGGTCGTG
Found at i:21994185 original size:25 final size:25
Alignment explanation
Indices: 21994151--21994204 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
21994141 GTCACACGGT
*
21994151 CGTGTCACACGCCCGTGTGCCAGGC
1 CGTGTCACACACCCGTGTGCCAGGC
* * *
21994176 CGTGTTACACACTCGTGTGCCTGGC
1 CGTGTCACACACCCGTGTGCCAGGC
21994201 CGTG
1 CGTG
21994205 AAACTCTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.11, C:0.35, G:0.31, T:0.22
Consensus pattern (25 bp):
CGTGTCACACACCCGTGTGCCAGGC
Found at i:21995053 original size:40 final size:40
Alignment explanation
Indices: 21994999--21995270 Score: 318
Period size: 40 Copynumber: 6.8 Consensus size: 40
21994989 CAAAGGTATC
* *
21994999 GAAGTACAAATAGGGGCACATATGTGCAAACAAGGATA-T
1 GAAGTACAAATAGGGGCACGTATGTGCAAACAAGGGTACT
* * * * * *
21995038 CGAAGTACAATTAGGGGTACGTAGGTGCAAATAGGGGTTCT
1 -GAAGTACAAATAGGGGCACGTATGTGCAAACAAGGGTACT
21995079 GAAGTAC-AATCAGGGGCACGTATGTGCAAACAAGGGTACT
1 GAAGTACAAAT-AGGGGCACGTATGTGCAAACAAGGGTACT
* *
21995119 GAAGTACAAATAGGGGCACATATGTGCAAA-ATGGGGTACT
1 GAAGTACAAATAGGGGCACGTATGTGCAAACA-AGGGTACT
*
21995159 GAAGTACAAATAGGGGCACGTATGTGCAAACATGGGTACT
1 GAAGTACAAATAGGGGCACGTATGTGCAAACAAGGGTACT
* * * * *
21995199 AAAGTAC-AATCAAGGGCACGTATGTGCAACCATGGGTACC
1 GAAGTACAAAT-AGGGGCACGTATGTGCAAACAAGGGTACT
* *
21995239 GAAGTACAAATAGGGGCATGCATGTGCAAACA
1 GAAGTACAAATAGGGGCACGTATGTGCAAACA
21995271 TTCAATAATT
Statistics
Matches: 198, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
39 6 0.03
40 184 0.93
41 8 0.04
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.19
Consensus pattern (40 bp):
GAAGTACAAATAGGGGCACGTATGTGCAAACAAGGGTACT
Found at i:21995074 original size:20 final size:19
Alignment explanation
Indices: 21995049--21995200 Score: 74
Period size: 20 Copynumber: 7.6 Consensus size: 19
21995039 GAAGTACAAT
*
21995049 TAGGGGTACGTAGGTGCAAA
1 TAGGGGTAC-TAAGTGCAAA
* *
21995069 TAGGGGTTCTGAAGTAC-AA
1 TAGGGGTACT-AAGTGCAAA
* *
21995088 TCAGGGGCACGTATGTGCAAA
1 T-AGGGGTAC-TAAGTGCAAA
* * *
21995109 CAAGGGTACTGAAGTACAAA
1 TAGGGGTACT-AAGTGCAAA
* *
21995129 TAGGGGCACATATGTGCAAA
1 TAGGGGTAC-TAAGTGCAAA
*
21995149 -ATGGGGTACTGAAGTACAAA
1 TA-GGGGTACT-AAGTGCAAA
* *
21995169 TAGGGGCACGTATGTGCAAA
1 TAGGGGTAC-TAAGTGCAAA
* *
21995189 CATGGGTACTAA
1 TAGGGGTACTAA
21995201 AGTACAATCA
Statistics
Matches: 95, Mismatches: 27, Indels: 21
0.66 0.19 0.15
Matches are distributed among these distances:
19 9 0.09
20 80 0.84
21 6 0.06
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (19 bp):
TAGGGGTACTAAGTGCAAA
Found at i:21995165 original size:120 final size:120
Alignment explanation
Indices: 21994993--21995270 Score: 371
Period size: 120 Copynumber: 2.3 Consensus size: 120
21994983 TGCATTCAAA
* * *
21994993 GGTATCGAAGTACAAATAGGGGCACATATGTGCAAACAAGGATATCGAAGTACAATTAGGGGTAC
1 GGTACCGAAGTACAAATAGGGGCACATATGTGCAAACAAGGATATCGAAGTACAAATAGGGGCAC
* * * *
21995058 GTAGGTGCAAATAGGGGTTCTGAAGTACAATCAGGGGCACGTATGTGCAAACAAG
66 GTAGGTGCAAACAGGGGTACTAAAGTACAATCAAGGGCACGTATGTGCAAACAAG
* * *
21995113 GGTACTGAAGTACAAATAGGGGCACATATGTGCAAA-ATGGGGTA-CTGAAGTACAAATAGGGGC
1 GGTACCGAAGTACAAATAGGGGCACATATGTGCAAACA-AGGATATC-GAAGTACAAATAGGGGC
* * * *
21995176 ACGTATGTGCAAACATGGGTACTAAAGTACAATCAAGGGCACGTATGTGCAACCATG
64 ACGTAGGTGCAAACAGGGGTACTAAAGTACAATCAAGGGCACGTATGTGCAAACAAG
***
21995233 GGTACCGAAGTACAAATAGGGGCATGCATGTGCAAACA
1 GGTACCGAAGTACAAATAGGGGCACATATGTGCAAACA
21995271 TTCAATAATT
Statistics
Matches: 137, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
119 2 0.01
120 134 0.98
121 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.19
Consensus pattern (120 bp):
GGTACCGAAGTACAAATAGGGGCACATATGTGCAAACAAGGATATCGAAGTACAAATAGGGGCAC
GTAGGTGCAAACAGGGGTACTAAAGTACAATCAAGGGCACGTATGTGCAAACAAG
Found at i:21999021 original size:18 final size:19
Alignment explanation
Indices: 21998991--21999027 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
21998981 TTTTCACAAA
*
21998991 CATCACAATCACATAATAT
1 CATCACAATCACACAATAT
21999010 CATCAC-ATCACACAATAT
1 CATCACAATCACACAATAT
21999028 ACTTTTCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (19 bp):
CATCACAATCACACAATAT
Found at i:22002304 original size:18 final size:18
Alignment explanation
Indices: 22002281--22002315 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22002271 TAAGTTTAGA
22002281 AAGCATCAAAATAGTTTC
1 AAGCATCAAAATAGTTTC
* *
22002299 AAGCATGAAAGTAGTTT
1 AAGCATCAAAATAGTTT
22002316 GGCACATCGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (18 bp):
AAGCATCAAAATAGTTTC
Found at i:22010354 original size:24 final size:24
Alignment explanation
Indices: 22010327--22010407 Score: 78
Period size: 23 Copynumber: 3.4 Consensus size: 24
22010317 TTTGATTTCA
** *
22010327 ATTTATTTTTGCAATTATT-TATTT
1 ATTTATTTTTAAAATTTTTATA-TT
22010351 ATTTA-TTTTAAAATTTTTATATT
1 ATTTATTTTTAAAATTTTTATATT
*
22010374 ATTTA-TTTTAAATTGTTTTATTATT
1 ATTTATTTTTAAAAT-TTTTA-TATT
22010399 ATTTATTTT
1 ATTTATTTT
22010408 AAGTTTTTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
23 25 0.51
24 12 0.24
25 9 0.18
26 3 0.06
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.68
Consensus pattern (24 bp):
ATTTATTTTTAAAATTTTTATATT
Found at i:22010398 original size:25 final size:23
Alignment explanation
Indices: 22010339--22010409 Score: 99
Period size: 23 Copynumber: 3.0 Consensus size: 23
22010329 TTATTTTTGC
22010339 AATTATTTAT-TTATTTATTTTAA
1 AATT-TTTATATTATTTATTTTAA
22010362 AATTTTTATATTATTTATTTTAA
1 AATTTTTATATTATTTATTTTAA
*
22010385 ATTGTTTTATTATTATTTATTTTAA
1 AAT-TTTTA-TATTATTTATTTTAA
22010410 GTTTTTCACA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
22 5 0.11
23 19 0.43
24 5 0.11
25 15 0.34
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (23 bp):
AATTTTTATATTATTTATTTTAA
Done.