Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 30 of 199
Found at i:12511770 original size:7 final size:7
Alignment explanation
Indices: 12511760--12511818 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
12511750 TAAAAAATAA
12511760 AAATATT
1 AAATATT
12511767 AAAT-TT
1 AAATATT
*
12511773 AAATTTTT
1 AAA-TATT
*
12511781 AAA-AAT
1 AAATATT
12511787 AAA-ATT
1 AAATATT
12511793 ATAATATT
1 A-AATATT
12511801 AAATATTT
1 AAATA-TT
12511809 AAATATT
1 AAATATT
12511816 AAA
1 AAA
12511819 AAATATTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
6 12 0.27
7 16 0.36
8 16 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATATT
Found at i:12511786 original size:29 final size:30
Alignment explanation
Indices: 12511746--12511826 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 30
12511736 AATTATATAT
12511746 TTTTTAAAAAATAAAAATATTAAAT-TTAAA
1 TTTTT-AAAAATAAAAATATTAAATATTAAA
*
12511776 TTTTTAAAAATAAAATTA-T-AATATTAAA
1 TTTTTAAAAATAAAAATATTAAATATTAAA
* *
12511804 TATTTAAATATTAAAAAATATTA
1 TTTTTAAA-AAT-AAAAATATTA
12511827 TTTACTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
27 3 0.07
28 13 0.31
29 14 0.33
30 11 0.26
31 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TTTTTAAAAATAAAAATATTAAATATTAAA
Found at i:12511867 original size:21 final size:21
Alignment explanation
Indices: 12511843--12511884 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12511833 TTGATCGGCC
*
12511843 ATTAATCGACGTTGACCAACT
1 ATTAATCGACATTGACCAACT
*
12511864 ATTAATTGACATTGACCAACT
1 ATTAATCGACATTGACCAACT
12511885 GTTGACCAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (21 bp):
ATTAATCGACATTGACCAACT
Found at i:12523911 original size:16 final size:15
Alignment explanation
Indices: 12523890--12523923 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
12523880 ATCACTCTTT
*
12523890 TTTTATTTTTTTAATC
1 TTTTATCTTTTT-ATC
12523906 TTTTATCTTTTTATC
1 TTTTATCTTTTTATC
12523921 TTT
1 TTT
12523924 CCAAGCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATCTTTTTATC
Found at i:12535730 original size:18 final size:18
Alignment explanation
Indices: 12535704--12535740 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
12535694 ATTTTTCAAG
12535704 TTTTTAAAT-TTTGAATT
1 TTTTTAAATATTTGAATT
12535721 TTTTTGAAATATTTGAATT
1 TTTTT-AAATATTTGAATT
12535740 T
1 T
12535741 GGACTAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 4 0.22
19 9 0.50
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (18 bp):
TTTTTAAATATTTGAATT
Found at i:12536350 original size:31 final size:29
Alignment explanation
Indices: 12536315--12536387 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
12536305 ATGTATAAGC
* *
12536315 GACAAAAATATAACATTTTGATAATTTTAAT
1 GACAAAAATATAAC-TTTTGA-AAGTTGAAT
**
12536346 GACAATTATATAACTTTTGAAAGTTGAAT
1 GACAAAAATATAACTTTTGAAAGTTGAAT
* *
12536375 AACTAAAATATAA
1 GACAAAAATATAA
12536388 TTTAAATCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 16 0.47
30 6 0.18
31 12 0.35
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (29 bp):
GACAAAAATATAACTTTTGAAAGTTGAAT
Found at i:12539099 original size:33 final size:33
Alignment explanation
Indices: 12539046--12539123 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
12539036 TGGCCCTGCC
*
12539046 ATGGTCTTACACTCGTAATGCCATAACCCAGTT
1 ATGGTCTTACACTCGTAATGCCATAACCCAGCT
*
12539079 ATGGTCTTATCA-TCAG-AATGCCATAGCCCAGCT
1 ATGGTCTTA-CACTC-GTAATGCCATAACCCAGCT
12539112 ATGGTCTTACAC
1 ATGGTCTTACAC
12539124 GTATACATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
32 2 0.05
33 35 0.88
34 3 0.08
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (33 bp):
ATGGTCTTACACTCGTAATGCCATAACCCAGCT
Found at i:12541278 original size:12 final size:13
Alignment explanation
Indices: 12541261--12541293 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
12541251 TCGATTGATA
12541261 GTGAAATAT-TGT
1 GTGAAATATATGT
12541273 GTGAAA-ATATGT
1 GTGAAATATATGT
12541285 GTGAAATAT
1 GTGAAATAT
12541294 GATAGGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 15 0.79
13 2 0.11
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.36
Consensus pattern (13 bp):
GTGAAATATATGT
Found at i:12542261 original size:18 final size:17
Alignment explanation
Indices: 12542228--12542266 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
12542218 TTGTATAAAT
12542228 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
12542246 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
12542263 TGTG
1 TGTG
12542267 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:12542398 original size:8 final size:8
Alignment explanation
Indices: 12542385--12542413 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
12542375 CACTAGAGAC
12542385 CAGTGTTA
1 CAGTGTTA
12542393 CAGTGTTA
1 CAGTGTTA
12542401 CAGTGTTA
1 CAGTGTTA
12542409 CAGTG
1 CAGTG
12542414 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:12542527 original size:23 final size:23
Alignment explanation
Indices: 12542500--12542575 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
12542490 AGTGTTATTG
12542500 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
12542523 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
12542546 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
12542569 ATCAGTG
1 ATCAGTG
12542576 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:12549746 original size:8 final size:8
Alignment explanation
Indices: 12549733--12549761 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
12549723 CACTAGAGAC
12549733 CAGTGTTA
1 CAGTGTTA
12549741 CAGTGTTA
1 CAGTGTTA
12549749 CAGTGTTA
1 CAGTGTTA
12549757 CAGTG
1 CAGTG
12549762 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:12549875 original size:23 final size:23
Alignment explanation
Indices: 12549848--12549920 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
12549838 AGTGTTATTG
12549848 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
12549871 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
12549894 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
12549917 ATCA
1 ATCA
12549921 ATGTGGCACT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:12551327 original size:41 final size:41
Alignment explanation
Indices: 12551282--12551380 Score: 137
Period size: 41 Copynumber: 2.4 Consensus size: 41
12551272 TAGCGCTTAG
*
12551282 CAGGCTTATTGCCGGTGAAACACTTCAGACTAAATGTCTAA
1 CAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTCTAA
* * * *
12551323 CAGGCTTAATGCCGGTGAAATATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTCTAA
12551364 CAGGC-TAAGTGCCGGTG
1 CAGGCTTAA-TGCCGGTG
12551381 TACTGAATCA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
40 3 0.06
41 49 0.94
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (41 bp):
CAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTCTAA
Found at i:12556288 original size:3 final size:3
Alignment explanation
Indices: 12556280--12556314 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
12556270 TATATATGAT
12556280 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
12556315 TTTTATATAT
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:12561814 original size:22 final size:21
Alignment explanation
Indices: 12561756--12561814 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
12561746 AAATGACAGT
*
12561756 AAAACAATGAGAAAATAGCAAG
1 AAAACAA-CAGAAAATAGCAAG
**
12561778 AAAACAACAGCAAAATAGTGAG
1 AAAACAACAG-AAAATAGCAAG
*
12561800 GAAACAACAAGAAAA
1 AAAACAAC-AGAAAA
12561815 CAACTGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.64, C:0.12, G:0.17, T:0.07
Consensus pattern (21 bp):
AAAACAACAGAAAATAGCAAG
Found at i:12569542 original size:7 final size:7
Alignment explanation
Indices: 12569530--12569555 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12569520 TAATTATCAA
12569530 CATGAAC
1 CATGAAC
12569537 CATGAAC
1 CATGAAC
12569544 CATGAAC
1 CATGAAC
12569551 CATGA
1 CATGA
12569556 CATACTGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.15
Consensus pattern (7 bp):
CATGAAC
Found at i:12571712 original size:20 final size:22
Alignment explanation
Indices: 12571687--12571726 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
12571677 TCACGAGTCG
*
12571687 CAAAA-GATCTAGTC-CCGTGA
1 CAAAAGGACCTAGTCTCCGTGA
12571707 CAAAAGGACCTAGTCTCCGT
1 CAAAAGGACCTAGTCTCCGT
12571727 CAACAGGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (22 bp):
CAAAAGGACCTAGTCTCCGTGA
Found at i:12578050 original size:56 final size:54
Alignment explanation
Indices: 12577978--12578088 Score: 168
Period size: 56 Copynumber: 2.0 Consensus size: 54
12577968 CCACATTAGA
*
12577978 AGATTTAACAAAGTATAAAGGCCAATTATGTCATAATCTTTTTTTTTATCAAATTC
1 AGATTTAACAAAGTATAAAGGCCAATTATGTCATAA-C-TTTTTATTATCAAATTC
* * *
12578034 AGATTTAATAATGTATAAAGGCCATTTATGTCATAACTTTTTATTATCAAATTC
1 AGATTTAACAAAGTATAAAGGCCAATTATGTCATAACTTTTTATTATCAAATTC
12578088 A
1 A
12578089 ACCTTAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 17 0.33
55 1 0.02
56 33 0.65
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (54 bp):
AGATTTAACAAAGTATAAAGGCCAATTATGTCATAACTTTTTATTATCAAATTC
Found at i:12578097 original size:54 final size:56
Alignment explanation
Indices: 12577990--12578097 Score: 159
Period size: 54 Copynumber: 2.0 Consensus size: 56
12577980 ATTTAACAAA
* *
12577990 GTATAAAGGCCAATTATGTCATAATCTTTTTTTTTATCAAATTCAGATTTAATAAT
1 GTATAAAGGCCAATTATGTCATAATCTTTTTTATTATCAAATTCAGACTTAATAAT
*
12578046 GTATAAAGGCCATTTATGTCATAA-C-TTTTTATTATCAAATTCA-ACCTTAATA
1 GTATAAAGGCCAATTATGTCATAATCTTTTTTATTATCAAATTCAGA-CTTAATA
12578098 TATTTTATCA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
53 1 0.02
54 23 0.48
55 1 0.02
56 23 0.48
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (56 bp):
GTATAAAGGCCAATTATGTCATAATCTTTTTTATTATCAAATTCAGACTTAATAAT
Found at i:12578843 original size:13 final size:12
Alignment explanation
Indices: 12578798--12578853 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 12
12578788 TAGATAAATA
12578798 TTATTTTATTA-
1 TTATTTTATTAT
* *
12578809 ATATTTTAATGAT
1 TTATTTT-ATTAT
*
12578822 ATATTTTATTAT
1 TTATTTTATTAT
12578834 TTATTATTATTATT
1 TTATT-TTATTA-T
12578848 TTATTT
1 TTATTT
12578854 AGTATATAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
11 6 0.16
12 11 0.30
13 14 0.38
14 6 0.16
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (12 bp):
TTATTTTATTAT
Found at i:12582154 original size:46 final size:45
Alignment explanation
Indices: 12582101--12582240 Score: 208
Period size: 46 Copynumber: 3.0 Consensus size: 45
12582091 ACATTACTAT
* *
12582101 AACTCAGTATGGTTTCCTTCACTGAAATATCATACCTACTTTTCAC
1 AACTCAGTATGGTTT-CTTCACTGAAACACCATACCTACTTTTCAC
*
12582147 AACTCAGTATGGCTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGG-TTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
12582193 AACTCAATATGCTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATG-GTTTCTTCACTGAAACACCATACCTACTTTTCAC
12582239 AA
1 AA
12582241 TTTGTCATGG
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
46 83 0.97
47 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (45 bp):
AACTCAGTATGGTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:12583513 original size:16 final size:17
Alignment explanation
Indices: 12583467--12583514 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
12583457 AAATTCTTTT
12583467 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
12583484 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
12583501 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
12583515 TTCTAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:12583701 original size:21 final size:21
Alignment explanation
Indices: 12583677--12583757 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 21
12583667 CGAGCTTCTG
*
12583677 TTAACTCATATGAGTTTCAGT
1 TTAACTCTTATGAGTTTCAGT
* *
12583698 TTAACACTTATGGGTTTCCA-T
1 TTAACTCTTATGAGTTT-CAGT
* * *
12583719 TCAACTCTTTTGAGCTTCAGT
1 TTAACTCTTATGAGTTTCAGT
*
12583740 TTAACCCTTATGAGTTTC
1 TTAACTCTTATGAGTTTC
12583758 TGTTCAGCTC
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (21 bp):
TTAACTCTTATGAGTTTCAGT
Found at i:12583776 original size:42 final size:42
Alignment explanation
Indices: 12583692--12583803 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 42
12583682 TCATATGAGT
* * * **
12583692 TTCAGTTTAACACTTATGGGTTTCCATTCAACTCTTTTGAGC
1 TTCAGTTTAACCCTTATGGGTTTCTATTCAACTCCTACGAGC
* * *
12583734 TTCAGTTTAACCCTTATGAGTTTCTGTTCAGCTCCTACGAGC
1 TTCAGTTTAACCCTTATGGGTTTCTATTCAACTCCTACGAGC
* * *
12583776 TCCCGTTCAACCCTTATGGGTTTCTATT
1 TTCAGTTTAACCCTTATGGGTTTCTATT
12583804 TAGCACTTAT
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.41
Consensus pattern (42 bp):
TTCAGTTTAACCCTTATGGGTTTCTATTCAACTCCTACGAGC
Found at i:12589348 original size:24 final size:24
Alignment explanation
Indices: 12589310--12589364 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
12589300 TTTAGAATCC
* * *
12589310 AATAAAAAAACATTA-TTTTTAGA
1 AATAAAAAAAAATTACCTTTAAGA
12589333 AATAAAAACAAAATTACCTTTAAGA
1 AATAAAAA-AAAATTACCTTTAAGA
12589358 AATAAAA
1 AATAAAA
12589365 TATCATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 8 0.30
24 6 0.22
25 13 0.48
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (24 bp):
AATAAAAAAAAATTACCTTTAAGA
Found at i:12618716 original size:128 final size:126
Alignment explanation
Indices: 12618496--12618757 Score: 330
Period size: 128 Copynumber: 2.1 Consensus size: 126
12618486 GACTACCAGA
* * * *
12618496 AAAGAGCATAATCCATTGAAACAAGACCTGATTTCCAACATGTATTGCAGCAAATTGATAAAAAC
1 AAAGAGCATAATCCATTGAAACAAGACCAGATTTCCAACATGTATGGAAGCAAATTAATAAAAAC
* **
12618561 AACTCAAAATTGCATCCTAAACTTCACAAAAATATGTGCACAGATGAGCAAGCTTACTTGT
66 AACTCAAAATTGCATCCTAAACGTCACAAAAATATGTAAACAGATGAGCAAGCTTACTTGT
* * * *
12618622 AAAGAGCATAATTCATTGAACAACCAAGATCCAG-TTTCCAATATTTATGGAAGCAAATTAAT-G
1 AAAGAGCATAATCCATTG-A-AA-CAAGA-CCAGATTTCCAACATGTATGGAAGCAAATTAATAA
* * * * *
12618685 AAACAATTCAAAATTGCATCCTAGACGTCACAAAAGTATGTAAATAGATGAGCAGGCTTACTTGT
62 AAACAACTCAAAATTGCATCCTAAACGTCACAAAAATATGTAAACAGATGAGCAAGCTTACTTGT
12618750 AAAGAGCA
1 AAAGAGCA
12618758 GCAAGTCGAA
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
126 17 0.15
127 1 0.01
128 67 0.58
129 28 0.24
130 3 0.03
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (126 bp):
AAAGAGCATAATCCATTGAAACAAGACCAGATTTCCAACATGTATGGAAGCAAATTAATAAAAAC
AACTCAAAATTGCATCCTAAACGTCACAAAAATATGTAAACAGATGAGCAAGCTTACTTGT
Found at i:12629636 original size:28 final size:28
Alignment explanation
Indices: 12629470--12629618 Score: 253
Period size: 28 Copynumber: 5.3 Consensus size: 28
12629460 ATATTATTTG
**
12629470 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
*
12629498 ATTAAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACCTA
*
12629527 ATCTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
12629555 ATTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
12629583 ATTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
12629611 ATTTAATT
1 ATTTAATT
12629619 TAATTAAAAA
Statistics
Matches: 114, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 90 0.79
29 24 0.21
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.30
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAACCTA
Found at i:12635083 original size:42 final size:42
Alignment explanation
Indices: 12634986--12635196 Score: 247
Period size: 41 Copynumber: 5.1 Consensus size: 42
12634976 TTTATTGTCA
12634986 GTGAAACAATATCAGACTTTACGTCTAGCA-G-TTAATGCCG
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCG
* * *
12635026 GTGAAATAATTTCAGACTTTACATCTAGCAGGCTTAATGCCG
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCG
12635068 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCG
* * *
12635110 GTGAAAC-ATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCG
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAA-TGCCG
* * * * *
12635151 GTG-TACTGA-ATCAGGCTTTAAGTCTAGCAGGC-TAAGTGCCA
1 GTGAAAC-AATATCAGACTTTACGTCTAGCAGGCTTAA-TGCCG
12635192 GTGAA
1 GTGAA
12635197 TCTGTTTAAA
Statistics
Matches: 149, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
40 32 0.21
41 61 0.41
42 56 0.38
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (42 bp):
GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCG
Found at i:12641936 original size:42 final size:42
Alignment explanation
Indices: 12641903--12642115 Score: 238
Period size: 42 Copynumber: 5.1 Consensus size: 42
12641893 TTTATTGTCA
* *
12641903 GTGAAACAATATCAGACTTTATGTCTAGCAGGTTTAATGCCG
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCG
* * *
12641945 GTGAAATAATTTCAGACTTTACATCTAGCAGGCTTAATGCCG
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCG
*
12641987 GTGAAACAATACCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCG
* * *
12642029 GTGAAAC-ATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCG
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAA-TGCCG
* * * * *
12642070 GTG-TACTGA-ATCAGGCTTTAAGTCTAGCAGGC-TAAGTGCCA
1 GTGAAAC-AATATCAGACTTTACGTCTAGCAGGCTTAA-TGCCG
12642111 GTGAA
1 GTGAA
12642116 TCTGTTTAAA
Statistics
Matches: 147, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
40 5 0.03
41 59 0.40
42 83 0.56
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (42 bp):
GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCG
Found at i:12658529 original size:11 final size:11
Alignment explanation
Indices: 12658515--12658553 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
12658505 TAAAAGAACC
12658515 ATAATTAATAT
1 ATAATTAATAT
* *
12658526 ATAATTTATAA
1 ATAATTAATAT
*
12658537 AAAATTAATAT
1 ATAATTAATAT
12658548 ATAATT
1 ATAATT
12658554 TATAAAAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATAATTAATAT
Found at i:12658542 original size:22 final size:22
Alignment explanation
Indices: 12658517--12658566 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
12658507 AAAGAACCAT
12658517 AATTAATATATAATTTATAAAA
1 AATTAATATATAATTTATAAAA
12658539 AATTAATATATAATTTATAAAA
1 AATTAATATATAATTTATAAAA
12658561 AATTAA
1 AATTAA
12658567 ACTTCAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTAATATATAATTTATAAAA
Found at i:12660509 original size:21 final size:21
Alignment explanation
Indices: 12660485--12660527 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12660475 GAAATGAACT
12660485 TAAATGGTAATTAAACTATGG
1 TAAATGGTAATTAAACTATGG
12660506 TAAATGGTAATTAAACTATGG
1 TAAATGGTAATTAAACTATGG
12660527 T
1 T
12660528 CAAAGTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.35
Consensus pattern (21 bp):
TAAATGGTAATTAAACTATGG
Found at i:12665582 original size:42 final size:43
Alignment explanation
Indices: 12665480--12665589 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 43
12665470 CAATGCCAAC
* * * *
12665480 ATCCCAGACGTGGTCTTACATGTAATCAAATAACGATGCCACA
1 ATCCCAGACATGGTCTTACACGTAATCAAATAACAATGACACA
* *
12665523 ATCCCAGACAGGGTCTTACACGTAATCATAT-ACAAT-ACA-A
1 ATCCCAGACATGGTCTTACACGTAATCAAATAACAATGACACA
12665563 ATGTCCCAGACATGGTCTTACACGTAA
1 A--TCCCAGACATGGTCTTACACGTAA
12665590 ATCTCAAATC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
40 2 0.03
41 2 0.03
42 27 0.47
43 27 0.47
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (43 bp):
ATCCCAGACATGGTCTTACACGTAATCAAATAACAATGACACA
Found at i:12668983 original size:48 final size:50
Alignment explanation
Indices: 12668912--12669039 Score: 156
Period size: 50 Copynumber: 2.6 Consensus size: 50
12668902 TAGGACGCCA
* *
12668912 ATGCCATATCCCAGATATGGTCTTACA-TGGGA-TC-AC-ATATCAGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACT--GACTCTACTATATCAGTGCCG
* * * *
12668960 ATGCCATGTCCCAGACATGGTCTTACACTGACTCTCCTCTGTCCGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTCTACTATATCAGTGCCG
12669010 ATGCCATGTCCCAGACATGGTCTTACACTG
1 ATGCCATGTCCCAGACATGGTCTTACACTG
12669040 GCACACTCAC
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
47 2 0.03
48 27 0.39
49 2 0.03
50 39 0.56
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (50 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACTCTACTATATCAGTGCCG
Found at i:12669067 original size:50 final size:50
Alignment explanation
Indices: 12668955--12669056 Score: 127
Period size: 50 Copynumber: 2.0 Consensus size: 50
12668945 CACATATCAG
* * * *
12668955 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCCTCTGTCCG
1 TGCCGATACCATGTCCCAGACATGGTCTTACACTGACACTCCACTGTCCA
*
12669005 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACT-CACTG-CCA
1 TGCCGATACCATGTCCCAGACATGGTCTTACACT-G-ACACTCCACTGTCCA
12669055 TG
1 TG
12669057 GTCCAACCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
50 38 0.81
51 5 0.11
52 4 0.09
ACGTcount: A:0.19, C:0.35, G:0.21, T:0.25
Consensus pattern (50 bp):
TGCCGATACCATGTCCCAGACATGGTCTTACACTGACACTCCACTGTCCA
Found at i:12669362 original size:41 final size:40
Alignment explanation
Indices: 12669311--12669447 Score: 147
Period size: 41 Copynumber: 3.4 Consensus size: 40
12669301 TTGCCATCGT
* *
12669311 ATAGCTGAAGCTATCATAATCTCGCACACTAAGTGCCTTAC
1 ATAGCCGAAGCTATCATAATCTCGCACACTAAGTG-CTTAA
** *
12669352 ATAGCCGAAGCTATC-TCGGTCTCGCACACTAAGTGTCATAA
1 ATAGCCGAAGCTATCAT-AATCTCGCACACTAAGTG-CTTAA
12669393 ATAGCCGAAGCTATTCCA-AA--TCGCACACTAAGTGCTATAA
1 ATAGCCGAAGCTA-T-CATAATCTCGCACACTAAGTGCT-TAA
12669433 ATAGCCGAAGCTATC
1 ATAGCCGAAGCTATC
12669448 TCGAATTTCA
Statistics
Matches: 82, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
38 1 0.01
39 2 0.02
40 31 0.38
41 46 0.56
42 1 0.01
43 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
ATAGCCGAAGCTATCATAATCTCGCACACTAAGTGCTTAA
Found at i:12669433 original size:40 final size:41
Alignment explanation
Indices: 12669332--12669449 Score: 152
Period size: 40 Copynumber: 2.9 Consensus size: 41
12669322 TATCATAATC
* ****
12669332 TCGCACACTAAGTGCCT-TACATAGCCGAAGCTATCTCGGTC
1 TCGCACACTAAGTG-CTATAAATAGCCGAAGCTATCTCCAAA
12669373 TCGCACACTAAGTG-TCATAAATAGCCGAAGCTAT-TCCAAA
1 TCGCACACTAAGTGCT-ATAAATAGCCGAAGCTATCTCCAAA
12669413 TCGCACACTAAGTGCTATAAATAGCCGAAGCTATCTC
1 TCGCACACTAAGTGCTATAAATAGCCGAAGCTATCTC
12669450 GAATTTCATA
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
39 1 0.01
40 34 0.50
41 33 0.49
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (41 bp):
TCGCACACTAAGTGCTATAAATAGCCGAAGCTATCTCCAAA
Found at i:12670975 original size:30 final size:31
Alignment explanation
Indices: 12670941--12670998 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
12670931 TTTTACGAGC
*
12670941 TTAGGGGCAAAATCATAATTTTG-TAAAACT
1 TTAGGGGCAAAAACATAATTTTGCTAAAACT
12670971 TTAGGGGCAAAAACATAATTTTGCTAAA
1 TTAGGGGCAAAAACATAATTTTGCTAAA
12670999 GTATGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (31 bp):
TTAGGGGCAAAAACATAATTTTGCTAAAACT
Found at i:12671373 original size:45 final size:45
Alignment explanation
Indices: 12671322--12671410 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
12671312 TGTGAACCAA
* *
12671322 ACATCATTGATTAGTAAGGTGGTTGCTATGAGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGAGCTGAATCCACCGG
**
12671367 ACATCATTGATTAATAAGGTGGTTGCTATGTTCTGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGAGCTGAATCCACCG
12671411 AGTATCTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGAGCTGAATCCACCGG
Found at i:12673520 original size:21 final size:21
Alignment explanation
Indices: 12673496--12673539 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12673486 AGTAAATTTA
*
12673496 ATTCATTTTAATACAATTCAC
1 ATTCAATTTAATACAATTCAC
* *
12673517 ATTCAATTTCATCCAATTCAC
1 ATTCAATTTAATACAATTCAC
12673538 AT
1 AT
12673540 CGTAGGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTCAATTTAATACAATTCAC
Found at i:12676962 original size:15 final size:15
Alignment explanation
Indices: 12676942--12676973 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12676932 TAAGCCGTGA
*
12676942 TTCTTTTTCTTTTTC
1 TTCTTTCTCTTTTTC
12676957 TTCTTTCTCTTTTTC
1 TTCTTTCTCTTTTTC
12676972 TT
1 TT
12676974 TCTCAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTCTTTCTCTTTTTC
Found at i:12677013 original size:16 final size:16
Alignment explanation
Indices: 12676992--12677024 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12676982 TTCGTTTTGC
12676992 TTCTCAGTTTCT-TTCT
1 TTCTCA-TTTCTATTCT
12677008 TTCTCATTTCTATTCT
1 TTCTCATTTCTATTCT
12677024 T
1 T
12677025 CCTTTTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.09, C:0.24, G:0.03, T:0.64
Consensus pattern (16 bp):
TTCTCATTTCTATTCT
Found at i:12677057 original size:5 final size:5
Alignment explanation
Indices: 12677033--12677081 Score: 53
Period size: 5 Copynumber: 9.0 Consensus size: 5
12677023 TTCCTTTTGT
*
12677033 TATATA TATATA TAATAA TATAA TATAA TATAT TAATAA TATAA TATAA
1 TATA-A TATA-A T-ATAA TATAA TATAA TATAA T-ATAA TATAA TATAA
12677082 AAACATACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 23 0.59
6 13 0.33
7 3 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:12677058 original size:21 final size:21
Alignment explanation
Indices: 12677033--12677081 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 21
12677023 TTCCTTTTGT
12677033 TATATATATATATAATAATATAA
1 TATA-ATATAT-TAATAATATAA
12677056 TATAATATATTAATAATATAA
1 TATAATATATTAATAATATAA
12677077 TATAA
1 TATAA
12677082 AAACATACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 16 0.62
22 6 0.23
23 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAATATATTAATAATATAA
Found at i:12680646 original size:24 final size:24
Alignment explanation
Indices: 12680619--12680673 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
12680609 TCCGATGCTT
12680619 CCCGTTAATTGCTCTTCGAAGCTA
1 CCCGTTAATTGCTCTTCGAAGCTA
* *
12680643 CCCGTTAATTGCTCTTTGGAGCTA
1 CCCGTTAATTGCTCTTCGAAGCTA
*
12680667 CCAGTTA
1 CCCGTTA
12680674 TAGGCTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (24 bp):
CCCGTTAATTGCTCTTCGAAGCTA
Found at i:12681386 original size:14 final size:15
Alignment explanation
Indices: 12681362--12681390 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12681352 TTTTTCTGTG
12681362 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
12681377 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
12681391 AGTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:12682612 original size:44 final size:42
Alignment explanation
Indices: 12682538--12682688 Score: 110
Period size: 42 Copynumber: 3.5 Consensus size: 42
12682528 ATATATGTTA
* * * * *
12682538 TCGTGTAAGACCACGTCTAGGACGTTGGCATCGAT-TTGAGATT
1 TCGTATAAGACCATGTCTGGGACATCGGCATC-ATATT-AGATT
* *
12682581 TATGTATAAGACCATGTCTGGGACATCGGCATCATATTTGATT
1 T-CGTATAAGACCATGTCTGGGACATCGGCATCATATTAGATT
* * *
12682624 TCGTGTAAGACCCTGTCTGGGACAGT-GCCATCGATATT-GATT
1 TCGTATAAGACCATGTCTGGGACA-TCGGCATC-ATATTAGATT
* * * *
12682666 ACATGTAAGACCACGTCTGGGAC
1 TCGTATAAGACCATGTCTGGGAC
12682689 GTTGGCATTG
Statistics
Matches: 89, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
42 48 0.54
43 14 0.16
44 27 0.30
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (42 bp):
TCGTATAAGACCATGTCTGGGACATCGGCATCATATTAGATT
Found at i:12682641 original size:42 final size:42
Alignment explanation
Indices: 12682587--12682688 Score: 120
Period size: 42 Copynumber: 2.4 Consensus size: 42
12682577 GATTTATGTA
* * * *
12682587 TAAGACCATGTCTGGGACA-TCGGCATC-ATATTTGATTTCGTG
1 TAAGACCCTGTCTGGGACAGT-GCCATCGATA-TTGATTACATG
12682629 TAAGACCCTGTCTGGGACAGTGCCATCGATATTGATTACATG
1 TAAGACCCTGTCTGGGACAGTGCCATCGATATTGATTACATG
12682671 TAAGACCAC-GTCTGGGAC
1 TAAGACC-CTGTCTGGGAC
12682689 GTTGGCATTG
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
42 48 0.91
43 5 0.09
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (42 bp):
TAAGACCCTGTCTGGGACAGTGCCATCGATATTGATTACATG
Found at i:12684963 original size:30 final size:29
Alignment explanation
Indices: 12684924--12684990 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
12684914 TTTTTTATTT
* *
12684924 AAATAACCCAAATAATTTAATTAAGTACCA
1 AAATGACCCAAAT-ATTTAATTAAATACCA
** *
12684954 AAATGACCCACCTTTTTAATTAAATACCA
1 AAATGACCCAAATATTTAATTAAATACCA
12684983 AAATGACC
1 AAATGACC
12684991 TAAAATCTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.48, C:0.21, G:0.04, T:0.27
Consensus pattern (29 bp):
AAATGACCCAAATATTTAATTAAATACCA
Found at i:12685600 original size:38 final size:39
Alignment explanation
Indices: 12685530--12685603 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 39
12685520 TTTATTTTTT
* *
12685530 ATTTTTTACCTTTTTATTAACTTTTGTCTTTTTCTTTAA
1 ATTTTTTACCTTTTTATTAACTTTTATATTTTTCTTTAA
** *
12685569 ATTTTTTTTCTTTTT-TTAAGTTTTATATTTTTCTT
1 ATTTTTTACCTTTTTATTAACTTTTATATTTTTCTT
12685604 ATTTTATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 17 0.57
39 13 0.43
ACGTcount: A:0.16, C:0.09, G:0.03, T:0.72
Consensus pattern (39 bp):
ATTTTTTACCTTTTTATTAACTTTTATATTTTTCTTTAA
Found at i:12685606 original size:9 final size:9
Alignment explanation
Indices: 12685602--12685655 Score: 65
Period size: 9 Copynumber: 5.9 Consensus size: 9
12685592 TATATTTTTC
12685602 TTATTTTATT
1 TTATTTTA-T
*
12685612 TTATTTTGT
1 TTATTTTAT
12685621 TTA-TTTAT
1 TTATTTTAT
12685629 TTATTTTAT
1 TTATTTTAT
12685638 TTATTGTTAT
1 TTATT-TTAT
*
12685648 TAATTTTA
1 TTATTTTA
12685656 AAAATTTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
8 7 0.18
9 17 0.44
10 15 0.38
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (9 bp):
TTATTTTAT
Found at i:12685627 original size:13 final size:13
Alignment explanation
Indices: 12685602--12685642 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
12685592 TATATTTTTC
12685602 TTATTTTATTTTAT
1 TTATTTTA-TTTAT
12685616 TT-TGTTTATTTAT
1 TTAT-TTTATTTAT
12685629 TTATTTTATTTAT
1 TTATTTTATTTAT
12685642 T
1 T
12685643 GTTATTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:12685900 original size:19 final size:19
Alignment explanation
Indices: 12685873--12685920 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
12685863 TAATATTGGT
*
12685873 TATACTTAACATTTTTTAA
1 TATATTTAACATTTTTTAA
**
12685892 TATATTTAATTTTTTTTAA
1 TATATTTAACATTTTTTAA
*
12685911 AATATATTAA
1 TATAT-TTAA
12685921 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTTAACATTTTTTAA
Found at i:12685913 original size:72 final size:72
Alignment explanation
Indices: 12685837--12685975 Score: 206
Period size: 72 Copynumber: 1.9 Consensus size: 72
12685827 ATATTTTTAA
* * * * * *
12685837 AAAATATATTGAATATATTATAATTTTAATATTGGTTATACTTAACATTTTTTAATATATTTAAT
1 AAAATATATTAAAAATATTAAAATTTTAAAATTGGCTATACATAACATTTTTTAATATATTTAAT
12685902 TTTTTTT
66 TTTTTTT
* *
12685909 AAAATATATTAAAAATTTTAAAATTTTAAAATTGGCTATACATAACATTTTTTAATATGTTTAAT
1 AAAATATATTAAAAATATTAAAATTTTAAAATTGGCTATACATAACATTTTTTAATATATTTAAT
12685974 TT
66 TT
12685976 CTTTAAGTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (72 bp):
AAAATATATTAAAAATATTAAAATTTTAAAATTGGCTATACATAACATTTTTTAATATATTTAAT
TTTTTTT
Found at i:12686078 original size:20 final size:20
Alignment explanation
Indices: 12686055--12686119 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
12686045 TTAAGTACAT
*
12686055 AAATTTATGAATGTGTACTA
1 AAATTTATAAATGTGTACTA
* * *
12686075 AAATTAAAAAAT-TAATA-TA
1 AAATTTATAAATGT-GTACTA
12686094 TAAATTTATAAATGTGTACTA
1 -AAATTTATAAATGTGTACTA
12686115 AAATT
1 AAATT
12686120 AAAAAATTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
19 3 0.09
20 28 0.82
21 3 0.09
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (20 bp):
AAATTTATAAATGTGTACTA
Found at i:12686097 original size:40 final size:41
Alignment explanation
Indices: 12686044--12686128 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 41
12686034 AAAAATATAT
*
12686044 ATTAAGTACATAAATTTATGAATGTGTACTAAAATTAAAAA
1 ATTAAGTACATAAATTTATAAATGTGTACTAAAATTAAAAA
*
12686085 ATTAA-TATATAAATTTATAAATGTGTACTAAAATTAAAAA
1 ATTAAGTACATAAATTTATAAATGTGTACTAAAATTAAAAA
12686125 ATTA
1 ATTA
12686129 TAACCAACAC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
40 37 0.88
41 5 0.12
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (41 bp):
ATTAAGTACATAAATTTATAAATGTGTACTAAAATTAAAAA
Found at i:12686126 original size:20 final size:20
Alignment explanation
Indices: 12686064--12686126 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
12686054 TAAATTTATG
12686064 AATGTGTACTAAAATTAAAA
1 AATGTGTACTAAAATTAAAA
* * *
12686084 AAT-TAATA-TATAAATTTATA
1 AATGT-GTACTA-AAATTAAAA
12686104 AATGTGTACTAAAATTAAAA
1 AATGTGTACTAAAATTAAAA
12686124 AAT
1 AAT
12686127 TATAACCAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.09
20 27 0.82
21 3 0.09
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (20 bp):
AATGTGTACTAAAATTAAAA
Found at i:12687389 original size:22 final size:24
Alignment explanation
Indices: 12687337--12687395 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 24
12687327 ATATCTTTAA
12687337 AAATAAT-TTA-AAAATCATAATT
1 AAATAATATTATAAAATCATAATT
*
12687359 TAA-AATATTATAAAA-CA-AATT
1 AAATAATATTATAAAATCATAATT
12687380 AAATAATATT-TAAAAT
1 AAATAATATTATAAAAT
12687396 ATTAAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
21 14 0.45
22 13 0.42
23 4 0.13
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATAATATTATAAAATCATAATT
Found at i:12687494 original size:22 final size:22
Alignment explanation
Indices: 12687445--12687513 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 22
12687435 AAAATATTTA
* *
12687445 AATATTTTATATTATT-AAAACT
1 AATATTTAATATT-TTAAAAAAT
12687467 ATATATTTAATATTTTAAAAAAT
1 A-ATATTTAATATTTTAAAAAAT
* *
12687490 AATATTCAA-AATTTAAAAAAT
1 AATATTTAATATTTTAAAAAAT
12687511 AAT
1 AAT
12687514 TTAAAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 14 0.34
22 10 0.24
23 17 0.41
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (22 bp):
AATATTTAATATTTTAAAAAAT
Found at i:12687506 original size:21 final size:20
Alignment explanation
Indices: 12687480--12687521 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
12687470 TATTTAATAT
*
12687480 TTTAAAAAATAATATTCAAAA
1 TTTAAAAAATAAT-TTAAAAA
12687501 TTTAAAAAATAATTTAAAAA
1 TTTAAAAAATAATTTAAAAA
12687521 T
1 T
12687522 AATATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TTTAAAAAATAATTTAAAAA
Found at i:12687525 original size:32 final size:34
Alignment explanation
Indices: 12687475--12687544 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
12687465 CTATATATTT
*
12687475 AATATTTTAAAAAATAATATTCAAAA-TTTAAAA
1 AATAATTTAAAAAATAATATTCAAAATTTTAAAA
*
12687508 AATAATTT-AAAAATAATATTTAAAATTTTAAAA
1 AATAATTTAAAAAATAATATTCAAAATTTTAAAA
12687541 AATA
1 AATA
12687545 TATATTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 16 0.47
33 18 0.53
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (34 bp):
AATAATTTAAAAAATAATATTCAAAATTTTAAAA
Found at i:12687604 original size:10 final size:9
Alignment explanation
Indices: 12687584--12687639 Score: 67
Period size: 10 Copynumber: 5.9 Consensus size: 9
12687574 TGAAATTTTT
*
12687584 TAAAATTAA
1 TAAAATAAA
12687593 TAACAATAAA
1 TAA-AATAAA
12687603 TAAAATAAAA
1 TAAAAT-AAA
12687613 TAAAATAAA
1 TAAAATAAA
*
12687622 CAAAATAAAA
1 TAAAAT-AAA
12687632 TAAAATAA
1 TAAAATAA
12687640 GAAAAAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 16 0.39
10 25 0.61
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (9 bp):
TAAAATAAA
Found at i:12687610 original size:5 final size:5
Alignment explanation
Indices: 12687591--12687648 Score: 68
Period size: 5 Copynumber: 11.8 Consensus size: 5
12687581 TTTTAAAATT
*
12687591 AATAA CAAT-A AATAA AATAA AATAA AAT-A AACAA AATAA AATAA AATAA
1 AATAA -AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
12687640 GAA-AA AATA
1 -AATAA AATA
12687649 TAAAACTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
4 8 0.17
5 33 0.72
6 5 0.11
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:12687645 original size:19 final size:19
Alignment explanation
Indices: 12687591--12687639 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 19
12687581 TTTTAAAATT
*
12687591 AATAACAATAAATAAAATAA
1 AATAA-AATAAACAAAATAA
12687611 AATAAAATAAACAAAATAA
1 AATAAAATAAACAAAATAA
12687630 AATAAAATAA
1 AATAAAATAA
12687640 GAAAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (19 bp):
AATAAAATAAACAAAATAA
Found at i:12687702 original size:20 final size:21
Alignment explanation
Indices: 12687656--12687702 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
12687646 ATATAAAACT
*
12687656 TAAAAAAAGAAAAAAATTTAA
1 TAAAAAAAGAAAAAAAGTTAA
* *
12687677 -AGAAAAAG-ACAAAAGTTAA
1 TAAAAAAAGAAAAAAAGTTAA
12687696 TAAAAAA
1 TAAAAAA
12687703 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (21 bp):
TAAAAAAAGAAAAAAAGTTAA
Found at i:12701834 original size:30 final size:30
Alignment explanation
Indices: 12701777--12701836 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
12701767 AATTAGTAAA
*
12701777 GATAAAATTATATTTTAGCCTTCTAAAAAT
1 GATAAAATTATATTTAAGCCTTCTAAAAAT
* *
12701807 GATAAAATTTTAATTTAATCCTT-TAAAAAT
1 GATAAAATTAT-ATTTAAGCCTTCTAAAAAT
12701837 TACATTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (30 bp):
GATAAAATTATATTTAAGCCTTCTAAAAAT
Found at i:12706777 original size:6 final size:6
Alignment explanation
Indices: 12706766--12706794 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12706756 GTTCTCCCCA
12706766 CCCTCT CCCTCT CCCTCT CCCTCT CCCTC
1 CCCTCT CCCTCT CCCTCT CCCTCT CCCTC
12706795 CCAACATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (6 bp):
CCCTCT
Found at i:12710468 original size:120 final size:120
Alignment explanation
Indices: 12710330--12710622 Score: 500
Period size: 120 Copynumber: 2.4 Consensus size: 120
12710320 AATTATTTTA
* * * *
12710330 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTATATT
*
12710393 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
12710450 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTACTTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
12710515 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
12710570 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
12710623 TAAATATGAT
Statistics
Matches: 165, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
119 4 0.02
120 159 0.96
121 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:12710490 original size:15 final size:15
Alignment explanation
Indices: 12710455--12710496 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12710445 TTAAGAATTT
*
12710455 TATTAAATTAT-ATA
1 TATTTAATTATAATA
12710469 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
12710483 TATTTAATAATAAT
1 TATTTAATTATAAT
12710497 TATGTTACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:12710605 original size:16 final size:16
Alignment explanation
Indices: 12710584--12710625 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12710574 TTATTAAATT
*
12710584 ATATATTTTAATTATA
1 ATATATTTTAATAATA
12710600 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
12710615 AT-TATGTTTAA
1 ATATAT-TTTAA
12710626 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:12710610 original size:15 final size:15
Alignment explanation
Indices: 12710575--12710616 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12710565 TTAAGAATTT
*
12710575 TATTAAATTAT-ATA
1 TATTTAATTATAATA
12710589 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
12710603 TATTTAATAATAAT
1 TATTTAATTATAAT
12710617 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:12710766 original size:157 final size:157
Alignment explanation
Indices: 12710559--12710875 Score: 555
Period size: 157 Copynumber: 2.0 Consensus size: 157
12710549 ATAAGAATAT
*
12710559 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* * *
12710624 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
12710689 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
12710716 TAATTA-TAAGAATTTTATTAAATTATATATTATTAATTAAAATATATTTAATAATAATTATGTT
1 TAATTATTAAGAATTTTATTAAATTATATATT-TTAATTAAAATATATTTAATAATAATTATGTT
12710780 TAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
65 TAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
* *
12710845 ATAATCATTTACCAAAACAATTTTATGC
130 ATAATAATTTACCAAAACAAATTTATGC
12710873 TAA
1 TAA
12710876 GGGTATTCTA
Statistics
Matches: 152, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
156 25 0.16
157 127 0.84
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:12710992 original size:44 final size:45
Alignment explanation
Indices: 12710927--12711017 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
12710917 ACCTCTATTC
* * *
12710927 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
12710971 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
12711016 CA
1 CA
12711018 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:12711019 original size:16 final size:16
Alignment explanation
Indices: 12710998--12711066 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
12710988 GATTAGCTAT
12710998 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12711014 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
12711031 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12711047 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12711063 TACA
1 TACA
12711067 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:12711040 original size:33 final size:32
Alignment explanation
Indices: 12710998--12711066 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
12710988 GATTAGCTAT
12710998 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
12711031 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
12711063 TACA
1 TACA
12711067 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:12729134 original size:23 final size:22
Alignment explanation
Indices: 12729082--12729134 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
12729072 TCCACGTCTT
*
12729082 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
12729104 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
12729127 TTTCTTTT
1 TTTCTTTT
12729135 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:12738589 original size:21 final size:21
Alignment explanation
Indices: 12738550--12738635 Score: 111
Period size: 21 Copynumber: 4.0 Consensus size: 21
12738540 CCTGATCAAT
*
12738550 AAACGACACA-TAAGTGCCTG
1 AAACGACACACAAAGTGCCTG
*
12738570 AAACGACACACAAGGTGCCTG
1 AAACGACACACAAAGTGCCTG
* *
12738591 ATACGACACATAAAGTGCCTG
1 AAACGACACACAAAGTGCCTG
12738612 AGATACGACACACAAAGTGCCTG
1 A-A-ACGACACACAAAGTGCCTG
12738635 A
1 A
12738636 TCGGCAAAGC
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
20 10 0.18
21 27 0.48
23 19 0.34
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.14
Consensus pattern (21 bp):
AAACGACACACAAAGTGCCTG
Found at i:12738632 original size:44 final size:41
Alignment explanation
Indices: 12738552--12738636 Score: 134
Period size: 44 Copynumber: 2.0 Consensus size: 41
12738542 TGATCAATAA
*
12738552 ACGACACATAAGTGCCTGAAACGACACACAAGGTGCCTGAT
1 ACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTGAT
12738593 ACGACACATAAAGTGCCTGAGATACGACACACAAAGTGCCTGAT
1 ACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTGAT
12738637 CGGCAAAGCC
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
41 9 0.22
42 10 0.25
43 1 0.03
44 20 0.50
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (41 bp):
ACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTGAT
Found at i:12738992 original size:16 final size:16
Alignment explanation
Indices: 12738963--12738995 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12738953 AATAATAATA
12738963 CTTATATTTCACTTAC
1 CTTATATTTCACTTAC
12738979 CTTATTATTT-ACTTAC
1 CTTA-TATTTCACTTAC
12738995 C
1 C
12738996 ATACACATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (16 bp):
CTTATATTTCACTTAC
Found at i:12739236 original size:17 final size:16
Alignment explanation
Indices: 12739205--12739252 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
12739195 CTTCCTTCCT
*
12739205 TCTCTGTTTCGTTTTGC
1 TCTCTGTTTC-TTTTTC
12739222 TCTCTGTTTCTTTTTC
1 TCTCTGTTTCTTTTTC
* *
12739238 TTTTTGTTTCTTTTT
1 TCTCTGTTTCTTTTT
12739253 TTTTCATTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.00, C:0.19, G:0.10, T:0.71
Consensus pattern (16 bp):
TCTCTGTTTCTTTTTC
Found at i:12739245 original size:16 final size:16
Alignment explanation
Indices: 12739226--12739270 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
12739216 TTTTGCTCTC
12739226 TGTTTCTTTTTCTTTT
1 TGTTTCTTTTTCTTTT
12739242 TGTTTCTTTTT-TTTT
1 TGTTTCTTTTTCTTTT
**
12739257 CATTTGCTTTTTCT
1 TGTTT-CTTTTTCT
12739271 AATAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 17 0.68
17 1 0.04
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (16 bp):
TGTTTCTTTTTCTTTT
Found at i:12739923 original size:9 final size:9
Alignment explanation
Indices: 12739906--12739954 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
12739896 TTTGACCATG
*
12739906 ATTCTAAAA
1 ATTCAAAAA
12739915 ATTCAAAAA
1 ATTCAAAAA
*
12739924 ATATAAATTAAA
1 AT-TCAA--AAA
12739936 ATTCAAAAA
1 ATTCAAAAA
12739945 ATTCAAAAA
1 ATTCAAAAA
12739954 A
1 A
12739955 ACTTAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 23 0.68
10 3 0.09
11 3 0.09
12 5 0.15
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (9 bp):
ATTCAAAAA
Found at i:12740597 original size:31 final size:30
Alignment explanation
Indices: 12740561--12740637 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
12740551 ATTTTAACGG
* *
12740561 TAGAGTGACTAAAATTAAGAACTTATTTAA
1 TAGAGTGACTAAAATTAACAACTTATCTAA
* *
12740591 TGAGAGTGACTAAAATTGACAATTTATCTAA
1 T-AGAGTGACTAAAATTAACAACTTATCTAA
12740622 TATGAGTGACTAAAAT
1 TA-GAGTGACTAAAAT
12740638 AAATTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
30 2 0.05
31 39 0.95
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (30 bp):
TAGAGTGACTAAAATTAACAACTTATCTAA
Found at i:12745948 original size:33 final size:33
Alignment explanation
Indices: 12745810--12745952 Score: 96
Period size: 33 Copynumber: 4.3 Consensus size: 33
12745800 TGTTTATATG
*
12745810 TAAGACCATAGTTGGGCTATTG-CATTCTGATGA
1 TAAGACCATAGCTGGGCTA-TGACATTCTGATGA
* * * * *
12745843 TAAGACCATAACTGGGTTATGACACTATGAACG-
1 TAAGACCATAGCTGGGCTATGACATTCTG-ATGA
* * * * * * *
12745876 TAAGACGATGGTTGGACCATGGCAATGT-TTAT-A
1 TAAGACCATAGCTGGGCTATGAC-AT-TCTGATGA
12745909 TTAAGACCATAGCTGGGCTATGACATTCTGATGA
1 -TAAGACCATAGCTGGGCTATGACATTCTGATGA
12745943 TAAGACCATA
1 TAAGACCATA
12745953 ACTAGGTTAT
Statistics
Matches: 78, Mismatches: 24, Indels: 16
0.66 0.20 0.14
Matches are distributed among these distances:
32 3 0.04
33 52 0.67
34 22 0.28
35 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (33 bp):
TAAGACCATAGCTGGGCTATGACATTCTGATGA
Found at i:12745961 original size:100 final size:101
Alignment explanation
Indices: 12745740--12745978 Score: 383
Period size: 101 Copynumber: 2.4 Consensus size: 101
12745730 TAAATTGTCG
* *
12745740 GATAAGACCATAACTAGGTTATGGCATTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTAGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTT
*
12745805 ATATGTAAGACCATAGTTGGGCTATTGCATTCTGAT
66 ATATGTAAGACCATAGCTGGGCTATTGCATTCTGAT
* * *
12745841 GATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACGATGGTTGGACCATGGCAATGTTT
1 GATAAGACCATAACTAGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTT
12745906 ATAT-TAAGACCATAGCTGGGCTA-TGACATTCTGAT
66 ATATGTAAGACCATAGCTGGGCTATTG-CATTCTGAT
* *
12745941 GATAAGACCATAACTAGGTTATGGCACTACGAATGTAA
1 GATAAGACCATAACTAGGTTATGGCACTATGAACGTAA
12745979 ATGATGAATT
Statistics
Matches: 127, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
99 2 0.02
100 61 0.48
101 64 0.50
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (101 bp):
GATAAGACCATAACTAGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTT
ATATGTAAGACCATAGCTGGGCTATTGCATTCTGAT
Found at i:12746279 original size:21 final size:21
Alignment explanation
Indices: 12746255--12746297 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12746245 TATTTTAAGG
*
12746255 GTAGAATAATCTAGAAACTAA
1 GTAGAAAAATCTAGAAACTAA
*
12746276 GTAGAAAAATTTAGAAACTAA
1 GTAGAAAAATCTAGAAACTAA
12746297 G
1 G
12746298 GAAAATGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.23
Consensus pattern (21 bp):
GTAGAAAAATCTAGAAACTAA
Found at i:12746818 original size:20 final size:20
Alignment explanation
Indices: 12746793--12746832 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12746783 CGTAAAATGA
*
12746793 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
12746813 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
12746833 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:12746822 original size:34 final size:35
Alignment explanation
Indices: 12746778--12746844 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
12746768 CAGTAAAATA
*
12746778 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
12746812 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
12746845 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:12750261 original size:36 final size:36
Alignment explanation
Indices: 12750220--12750410 Score: 238
Period size: 36 Copynumber: 5.0 Consensus size: 36
12750210 GGTAGCTTTA
12750220 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
12750256 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
12750301 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
12750338 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
12750374 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
12750410 G
1 G
12750411 GTAGTTTAGC
Statistics
Matches: 137, Mismatches: 8, Indels: 20
0.83 0.05 0.12
Matches are distributed among these distances:
36 99 0.72
37 2 0.01
40 2 0.01
42 2 0.01
45 2 0.01
46 30 0.22
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:12750321 original size:82 final size:82
Alignment explanation
Indices: 12750184--12750374 Score: 337
Period size: 82 Copynumber: 2.3 Consensus size: 82
12750174 TTTGAGTACT
*
12750184 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
12750249 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
*
12750266 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
* *
12750331 GATAAGTGTTATACTTA
66 GATAAGTGCTACACTTA
*
12750348 TCTGATCAAGTGAAAAAGTGATAAGTG
1 TCTGATCAAGAGAAAAAGTGATAAGTG
12750375 CTATACTTAT
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 104 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:12755394 original size:41 final size:41
Alignment explanation
Indices: 12755344--12755600 Score: 399
Period size: 41 Copynumber: 6.3 Consensus size: 41
12755334 AATTCATCAT
* *
12755344 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
12755385 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
12755426 ATTCATATCACCGGCACTTAGCCT-CTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
12755466 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
12755507 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
12755548 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
12755589 ATTCATATCACC
1 ATTCAGATCACC
12755601 AATTCCAAAC
Statistics
Matches: 195, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 36 0.18
41 159 0.82
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
Found at i:12755566 original size:122 final size:123
Alignment explanation
Indices: 12755344--12755600 Score: 399
Period size: 122 Copynumber: 2.1 Consensus size: 123
12755334 AATTCATCAT
* * *
12755344 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCT
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGGCACTTAGCCT
* * *
12755409 GCTAGGTTTATAACCTGATTCATATCACCGGCACTTAGCCT-CTAGGCTTATAGCCTG
66 GCTAGGCTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* * *
12755466 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTGATTCATATCACCGGCACTTAGCCT
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGGCACTTAGCCT
* *
12755531 GCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
66 GCTAGGCTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
12755589 ATTCATATCACC
1 ATTCAGATCACC
12755601 AATTCCAAAC
Statistics
Matches: 122, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
122 97 0.80
123 25 0.20
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (123 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGGCACTTAGCCT
GCTAGGCTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
Found at i:12755840 original size:18 final size:17
Alignment explanation
Indices: 12755813--12755869 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
12755803 TGTTCGATCC
*
12755813 ACACATATATATATATAT
1 ACACACATATA-ATATAT
12755831 ACACACATATACATATAT
1 ACACACATATA-ATATAT
* * *
12755849 TCGCACAT-TAATATAA
1 ACACACATATAATATAT
12755865 ACACA
1 ACACA
12755870 ACCATAACAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
16 8 0.25
17 2 0.06
18 22 0.69
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (17 bp):
ACACACATATAATATAT
Found at i:12768302 original size:78 final size:79
Alignment explanation
Indices: 12768175--12768331 Score: 210
Period size: 78 Copynumber: 2.0 Consensus size: 79
12768165 AATCGAACTG
** *
12768175 GATAGAGTAAATGAAGGGCTTGTTCTGCAAAAAACACTGACACGGATGTGAATGAATTATTTATA
1 GATAGAGTAAATGAAGGGCTTGTTCTGCAAAAAACACTGACACAAATGTGAATGAATGA-TTATA
12768240 AGACAAGTTCAATCT
65 AGACAAGTTCAATCT
* * * * *
12768255 GATAGAGTAACTG-AGGG-TTGTTCTGCAAAAAGCATTGTCACAAATGTGAATGAATGATTGTAA
1 GATAGAGTAAATGAAGGGCTTGTTCTGCAAAAAACACTGACACAAATGTGAATGAATGATTATAA
*
12768318 GCCAAGTTCAATCT
66 GACAAGTTCAATCT
12768332 TCAGTACAGT
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
77 18 0.26
78 34 0.50
79 4 0.06
80 12 0.18
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (79 bp):
GATAGAGTAAATGAAGGGCTTGTTCTGCAAAAAACACTGACACAAATGTGAATGAATGATTATAA
GACAAGTTCAATCT
Found at i:12786260 original size:15 final size:15
Alignment explanation
Indices: 12786240--12786272 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12786230 ATATAATAAT
12786240 TTAATTAT-TAAAATA
1 TTAATTATGTAAAA-A
12786255 TTAATTATGTAAAAA
1 TTAATTATGTAAAAA
12786270 TTA
1 TTA
12786273 CAACTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
TTAATTATGTAAAAA
Found at i:12786308 original size:27 final size:28
Alignment explanation
Indices: 12786257--12786312 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
12786247 TTAAAATATT
*
12786257 AATTATGTAAAAATTACAACTAATATAA
1 AATTATGTAAAAATTACAACAAATATAA
* *
12786285 AATTATTTAAAATTTAC-ACAAATATAA
1 AATTATGTAAAAATTACAACAAATATAA
12786312 A
1 A
12786313 TAAATGCATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (28 bp):
AATTATGTAAAAATTACAACAAATATAA
Found at i:12791673 original size:13 final size:13
Alignment explanation
Indices: 12791655--12791681 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12791645 TTTCTATAGT
12791655 TTTAGTCTCACTA
1 TTTAGTCTCACTA
12791668 TTTAGTCTCACTA
1 TTTAGTCTCACTA
12791681 T
1 T
12791682 ATTGTTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTAGTCTCACTA
Found at i:12793647 original size:21 final size:21
Alignment explanation
Indices: 12793598--12793659 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
12793588 TAGCTCTCAC
12793598 GAGCTTCTGTTTAACTCTTAA
1 GAGCTTCTGTTTAACTCTTAA
* * * **
12793619 GGGTTTCTGTTTAGCTCTTTT
1 GAGCTTCTGTTTAACTCTTAA
* *
12793640 GAGCTTCTATTTAACCCTTA
1 GAGCTTCTGTTTAACTCTTA
12793660 TGGGTTTCCG
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.47
Consensus pattern (21 bp):
GAGCTTCTGTTTAACTCTTAA
Found at i:12793691 original size:21 final size:21
Alignment explanation
Indices: 12793665--12793715 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
12793655 CCTTATGGGT
*
12793665 TTCCGTTCAGCTTGTACAAGC
1 TTCCGTTCAGCTCGTACAAGC
*
12793686 TTCCGTTCAGCTCGTACGAGC
1 TTCCGTTCAGCTCGTACAAGC
*
12793707 TTTCGTTCA
1 TTCCGTTCA
12793716 ACCCTTATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.29, G:0.20, T:0.35
Consensus pattern (21 bp):
TTCCGTTCAGCTCGTACAAGC
Found at i:12796797 original size:22 final size:22
Alignment explanation
Indices: 12796769--12796880 Score: 118
Period size: 22 Copynumber: 5.0 Consensus size: 22
12796759 GCACTAATGA
12796769 ACAGAGAGCACTAAAGTGCTAT
1 ACAGAGAGCACTAAAGTGCTAT
12796791 ACAGAGAGCACTAAAGTGCTAT
1 ACAGAGAGCACTAAAGTGCTAT
* *
12796813 ACAGAGAGCAC-ATATGTGCTAA
1 ACAGAGAGCACTA-AAGTGCTAT
* * *
12796835 ACGGAGAGCACTGACGTGCTAGT
1 ACAGAGAGCACTAAAGTGCTA-T
* *
12796858 AATCAGAGAGCACCAACGTGCTA
1 -A-CAGAGAGCACTAAAGTGCTA
12796881 ATAATCAAAG
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
21 1 0.01
22 57 0.75
24 1 0.01
25 17 0.22
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.17
Consensus pattern (22 bp):
ACAGAGAGCACTAAAGTGCTAT
Found at i:12796892 original size:25 final size:25
Alignment explanation
Indices: 12796839--12796893 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
12796829 TGCTAAACGG
** * *
12796839 AGAGCACTGACGTGCTAGTAATCAG
1 AGAGCACCAACGTGCTAATAATCAA
12796864 AGAGCACCAACGTGCTAATAATCAA
1 AGAGCACCAACGTGCTAATAATCAA
12796889 AGAGC
1 AGAGC
12796894 GCGCTAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (25 bp):
AGAGCACCAACGTGCTAATAATCAA
Found at i:12797860 original size:5 final size:5
Alignment explanation
Indices: 12797850--12797907 Score: 116
Period size: 5 Copynumber: 11.6 Consensus size: 5
12797840 TTATTTCTTT
12797850 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
12797900 TATAA TAT
1 TATAA TAT
12797908 TTATACTTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 53 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:12799629 original size:39 final size:37
Alignment explanation
Indices: 12799562--12799654 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
12799552 ACCAGAATGG
* *
12799562 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
12799601 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
12799638 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
12799655 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:12800031 original size:12 final size:12
Alignment explanation
Indices: 12799989--12800029 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
12799979 TTCTCACTCA
*
12799989 TAATAATAATAC
1 TAATAATAATAT
*
12800001 TAATAATTATAT
1 TAATAATAATAT
*
12800013 TAATACTAATAT
1 TAATAATAATAT
12800025 TAATA
1 TAATA
12800030 CTTACTTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:12800589 original size:19 final size:19
Alignment explanation
Indices: 12800544--12800583 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
12800534 TTTGTTTTGT
*
12800544 TTTTATTT-CTTTACTTTC
1 TTTTATTTACTTTACTTTA
12800562 TTTTATTTACTTTACTTTA
1 TTTTATTTACTTTACTTTA
12800581 TTT
1 TTT
12800584 CTTTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTTACTTTACTTTA
Found at i:12800603 original size:3 final size:3
Alignment explanation
Indices: 12800592--12800621 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
12800582 TTCTTTTATT
12800592 ATA ACTA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA AT
12800622 CTTTTACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12800743 original size:5 final size:5
Alignment explanation
Indices: 12800735--12800789 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
12800725 TATTTAATTT
* *
12800735 ATATA ATATA ATATA ATACA ATATA TTATATT ATATA ATA-A A-ATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA --ATATA ATATA ATATA ATATA ATATA
12800784 ATATA A
1 ATATA A
12800790 AACATAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.20
5 28 0.68
7 4 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:12800760 original size:22 final size:22
Alignment explanation
Indices: 12800734--12800789 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
12800724 CTATTTAATT
*
12800734 TATATAATATAATATAATACAA
1 TATATAATATAATATAATAAAA
* *
12800756 TATATTATATTATATAATAAAA
1 TATATAATATAATATAATAAAA
12800778 TA-ATATATATAA
1 TATATA-ATATAA
12800790 AACATAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TATATAATATAATATAATAAAA
Found at i:12800771 original size:27 final size:27
Alignment explanation
Indices: 12800733--12800787 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
12800723 TCTATTTAAT
*
12800733 TTATATAATATAATATAATACA-ATATA
1 TTATATAATATAATAAAATA-ATATATA
*
12800760 TTATATTATATAATAAAATAATATATA
1 TTATATAATATAATAAAATAATATATA
12800787 T
1 T
12800788 AAAACATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
TTATATAATATAATAAAATAATATATA
Found at i:12803375 original size:25 final size:25
Alignment explanation
Indices: 12803327--12803375 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
12803317 AGCTCTCTCT
* **
12803327 TGAGCCATATAATAGGAATTTCATG
1 TGAGCCATATAACAGGAAGCTCATG
*
12803352 TGAGCCATGTAACAGGAAGCTCAT
1 TGAGCCATATAACAGGAAGCTCAT
12803376 AAGAGCTGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (25 bp):
TGAGCCATATAACAGGAAGCTCATG
Found at i:12804227 original size:11 final size:11
Alignment explanation
Indices: 12804211--12804241 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12804201 TAGTCCCTAT
12804211 ATCATAATTTC
1 ATCATAATTTC
12804222 ATCATAATTTC
1 ATCATAATTTC
*
12804233 ATCAAAATT
1 ATCATAATT
12804242 CCATTTACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (11 bp):
ATCATAATTTC
Found at i:12828142 original size:2 final size:2
Alignment explanation
Indices: 12828135--12828159 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12828125 AGGCTTAAAC
12828135 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
12828160 GGGGGGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12829111 original size:20 final size:22
Alignment explanation
Indices: 12829074--12829114 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
12829064 GGGAACGGGC
12829074 AAGGGGAAGAGTAGCAAAAGAA
1 AAGGGGAAGAGTAGCAAAAGAA
12829096 AAGGGGAA-AG-AGCAAAAGA
1 AAGGGGAAGAGTAGCAAAAGA
12829115 CTGACATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.56, C:0.05, G:0.37, T:0.02
Consensus pattern (22 bp):
AAGGGGAAGAGTAGCAAAAGAA
Found at i:12837785 original size:2 final size:2
Alignment explanation
Indices: 12837780--12837804 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12837770 CACACTCAAC
12837780 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12837805 AACGATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12846973 original size:19 final size:16
Alignment explanation
Indices: 12846932--12846974 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 16
12846922 TAGGCCTTTC
12846932 AATTTTTTTTTTTGAA
1 AATTTTTTTTTTTGAA
*
12846948 TATTTTTGTTTCTTTAGAA
1 AATTTTT-TTT-TTT-GAA
12846967 AATTTTTT
1 AATTTTTT
12846975 ATTAAACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 6 0.27
17 3 0.14
18 4 0.18
19 9 0.41
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.67
Consensus pattern (16 bp):
AATTTTTTTTTTTGAA
Found at i:12855804 original size:21 final size:20
Alignment explanation
Indices: 12855770--12855809 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12855760 CAAATTACAT
*
12855770 CGAAAGAGAAATTACATTAAC
1 CGAAAGACAAATTA-ATTAAC
*
12855791 CGAAAGACACATTAATTAA
1 CGAAAGACAAATTAATTAA
12855810 GATTCAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.20
Consensus pattern (20 bp):
CGAAAGACAAATTAATTAAC
Found at i:12862064 original size:42 final size:42
Alignment explanation
Indices: 12862002--12862115 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 42
12861992 GCTTGAAGGC
* *
12862002 TGAACAGAAGCTCATGAGAGCTAAATAGAAACCCATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * * * *
12862044 TGAACGGAAGCTCGTAAGAGCTTAACGGAAACCCATTAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * *
12862086 TGAACAGAAACTCATATGAGTTAAACAGAA
1 TGAACAGAAGCTCATAAGAGCTAAACAGAA
12862116 GCTTGTGAGA
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
Found at i:12862340 original size:45 final size:45
Alignment explanation
Indices: 12862280--12862372 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
12862270 CTTCAAATTC
* *
12862280 ATAATTTAACAATATTTTATTTTTCAACT-ACATGCTAAATACATA
1 ATAATTTAACAATATTCTATTTTTCAA-TAACATACTAAATACATA
*
12862325 ATAATTTAACAATATTCTATTTTTCAATAATATACTAAATACATA
1 ATAATTTAACAATATTCTATTTTTCAATAACATACTAAATACATA
12862370 ATA
1 ATA
12862373 TCATTAATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 1 0.02
45 43 0.98
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (45 bp):
ATAATTTAACAATATTCTATTTTTCAATAACATACTAAATACATA
Found at i:12863257 original size:18 final size:18
Alignment explanation
Indices: 12863230--12863269 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12863220 TTTGGTTAAG
12863230 AATTAACTGAATTACCCA
1 AATTAACTGAATTACCCA
* *
12863248 AATTACCTGAATTACCCG
1 AATTAACTGAATTACCCA
12863266 AATT
1 AATT
12863270 GAATCACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (18 bp):
AATTAACTGAATTACCCA
Done.