Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 156 of 199
Found at i:45923638 original size:22 final size:22
Alignment explanation
Indices: 45923613--45923656 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
45923603 TTTATATCAT
45923613 ATAT-TGATTAAATAAAATAAAA
1 ATATGTGATTAAAT-AAATAAAA
*
45923635 ATATGTTATTAAATAAATAAAA
1 ATATGTGATTAAATAAATAAAA
45923657 TAATTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (22 bp):
ATATGTGATTAAATAAATAAAA
Found at i:45926208 original size:38 final size:38
Alignment explanation
Indices: 45926175--45926253 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
45926165 CATGTTCAAT
45926175 ATGCCTACTATTACTATTGAACTGAATACATGTTAAGC
1 ATGCCTACTATTACTATTGAACTGAATACATGTTAAGC
* * * *
45926213 ATGCCTACTGTTACTGTTGAACTTAATACATGTTACGC
1 ATGCCTACTATTACTATTGAACTGAATACATGTTAAGC
45926251 ATG
1 ATG
45926254 TTTAATGCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (38 bp):
ATGCCTACTATTACTATTGAACTGAATACATGTTAAGC
Found at i:45926269 original size:38 final size:38
Alignment explanation
Indices: 45926186--45926282 Score: 113
Period size: 38 Copynumber: 2.6 Consensus size: 38
45926176 TGCCTACTAT
* * * *
45926186 TACTATTGAACTGAATACATGTTAAGCATGCCTACTGT
1 TACTGTTGAACTAAATACATGTTAAGCATGCCTAATGC
* * **
45926224 TACTGTTGAACTTAATACATGTTACGCATGTTTAATGC
1 TACTGTTGAACTAAATACATGTTAAGCATGCCTAATGC
*
45926262 TATTGTTGAACTAAATACATG
1 TACTGTTGAACTAAATACATG
45926283 ATAAAACATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (38 bp):
TACTGTTGAACTAAATACATGTTAAGCATGCCTAATGC
Found at i:45934852 original size:139 final size:139
Alignment explanation
Indices: 45934602--45934875 Score: 503
Period size: 139 Copynumber: 2.0 Consensus size: 139
45934592 TCTGACACCA
*
45934602 CTGTTGGATCGCCGGCACCCCTATGGCGCAGCGAAAAATAAAAATCCGGCGATCCTAACCAAGGA
1 CTGTTGGATCGCCGGCACCCCTATGGCGCAGCGAAAAATAAAAATCCGGAGATCCTAACCAAGGA
45934667 TCCATGTGTGAGGAACGAATCGGGGTGAAAGAGGTTGCGAAATTACCTAATGTTTATTCAGAGTA
66 TCCATGTGTGAGGAACGAATCGGGGTGAAAGAGGTTGCGAAATTACCTAATGTTTATTCAGAGTA
45934732 GACAGAGAG
131 GACAGAGAG
* * *
45934741 CTGTTGGATCGCCGGCACCCCTATGGCGCAGTGAAAAATAAAAATTCGGAGATCCTAACCAGGGA
1 CTGTTGGATCGCCGGCACCCCTATGGCGCAGCGAAAAATAAAAATCCGGAGATCCTAACCAAGGA
*
45934806 TCCATGTGTGAGGAACGAATCGTGGTGAAAGAGGTTGCGAAATTACCTAATGTTTATTCAGAGTA
66 TCCATGTGTGAGGAACGAATCGGGGTGAAAGAGGTTGCGAAATTACCTAATGTTTATTCAGAGTA
45934871 GACAG
131 GACAG
45934876 CAACACCTCA
Statistics
Matches: 130, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
139 130 1.00
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (139 bp):
CTGTTGGATCGCCGGCACCCCTATGGCGCAGCGAAAAATAAAAATCCGGAGATCCTAACCAAGGA
TCCATGTGTGAGGAACGAATCGGGGTGAAAGAGGTTGCGAAATTACCTAATGTTTATTCAGAGTA
GACAGAGAG
Found at i:45940887 original size:52 final size:52
Alignment explanation
Indices: 45940819--45940922 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
45940809 GCAGATATGC
* * *
45940819 AAAGTCCTGCCTCTATCCTCTACACACCAACTCCGATCATCCCAACGCACCA
1 AAAGTCCTACCCCTATCCTCTACACACCAACTCCGACCATCCCAACGCACCA
45940871 AAAGTCCTACCCCTATCCTCTACACACCAACTCCGACCATCCCAACGCACCA
1 AAAGTCCTACCCCTATCCTCTACACACCAACTCCGACCATCCCAACGCACCA
45940923 CATGGGGTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.30, C:0.46, G:0.07, T:0.17
Consensus pattern (52 bp):
AAAGTCCTACCCCTATCCTCTACACACCAACTCCGACCATCCCAACGCACCA
Found at i:45940921 original size:23 final size:23
Alignment explanation
Indices: 45940843--45940922 Score: 61
Period size: 23 Copynumber: 3.2 Consensus size: 23
45940833 ATCCTCTACA
*
45940843 CACCAACTCCGATCATCCCAACG
1 CACCAACTCCGACCATCCCAACG
* * * *
45940866 CACCAAAAGTCCTACCCCTATCCTCTACA
1 CACC--AACTCCGA--CC-ATCC-CAACG
45940895 CACCAACTCCGACCATCCCAACG
1 CACCAACTCCGACCATCCCAACG
45940918 CACCA
1 CACCA
45940923 CATGGGGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
23 12 0.29
24 4 0.10
25 8 0.19
27 7 0.17
28 4 0.10
29 7 0.17
ACGTcount: A:0.31, C:0.49, G:0.06, T:0.14
Consensus pattern (23 bp):
CACCAACTCCGACCATCCCAACG
Found at i:45943416 original size:15 final size:16
Alignment explanation
Indices: 45943398--45943432 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
45943388 AAAATAACGG
45943398 TTGAAAAAT-TAAGTA
1 TTGAAAAATGTAAGTA
45943413 TTG-AAAATGTAAGTA
1 TTGAAAAATGTAAGTA
45943428 TTGAA
1 TTGAA
45943433 TTTAAGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.28
15 12 0.67
16 1 0.06
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (16 bp):
TTGAAAAATGTAAGTA
Found at i:45947864 original size:17 final size:18
Alignment explanation
Indices: 45947842--45947875 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
45947832 CAATAAGCAT
45947842 TTATATAAA-TCAAACAC
1 TTATATAAACTCAAACAC
45947859 TTATATAAACTCAAACA
1 TTATATAAACTCAAACA
45947876 TTTCCATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (18 bp):
TTATATAAACTCAAACAC
Found at i:45948139 original size:42 final size:41
Alignment explanation
Indices: 45948093--45948215 Score: 151
Period size: 42 Copynumber: 3.0 Consensus size: 41
45948083 ATGCTATCAT
*
45948093 ATATCGATGCCAATAG-CCCAACTATGGTCTTACACAAATCTC
1 ATATCGATGCCAAT-GTCCCAAC-ATGGTCTTACACGAATCTC
* * *
45948135 ATATCAATGCAAATGTCCAAAACATGGTCTTACACGAATCTC
1 ATATCGATGCCAATGTCC-CAACATGGTCTTACACGAATCTC
*
45948177 ATATCGATGTCAATGTCCCAGA-ATGGTCTTACACGAATC
1 ATATCGATGCCAATGTCCCA-ACATGGTCTTACACGAATC
45948216 ACATCTCAGT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
41 19 0.27
42 48 0.69
43 3 0.04
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (41 bp):
ATATCGATGCCAATGTCCCAACATGGTCTTACACGAATCTC
Found at i:45949712 original size:17 final size:17
Alignment explanation
Indices: 45949690--45949737 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
45949680 AAGTTAGGCG
*
45949690 TGTGGGCCACACGTGCA
1 TGTGGGCCACACGGGCA
*
45949707 TGTGGGCTACACGGGCA
1 TGTGGGCCACACGGGCA
*
45949724 TGTAGGCCCACACG
1 TGT-GGGCCACACG
45949738 AATATGTGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.19, C:0.29, G:0.35, T:0.17
Consensus pattern (17 bp):
TGTGGGCCACACGGGCA
Found at i:45954764 original size:20 final size:20
Alignment explanation
Indices: 45954735--45954773 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
45954725 CTTTTACTGT
45954735 TCTTGCC-AAATCTTTGATAA
1 TCTTGCCAAAATC-TTGATAA
*
45954755 TCTTGTCAAAATCTTGATA
1 TCTTGCCAAAATCTTGATA
45954774 TCAATCGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (20 bp):
TCTTGCCAAAATCTTGATAA
Found at i:45969777 original size:17 final size:16
Alignment explanation
Indices: 45969757--45969789 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
45969747 AATACTTCAG
45969757 TTTAAAAATTTAAAATT
1 TTTAAAAA-TTAAAATT
45969774 TTTAAAAATTAAAATT
1 TTTAAAAATTAAAATT
45969790 GCTTTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAAAATTAAAATT
Found at i:45972696 original size:5 final size:5
Alignment explanation
Indices: 45972686--45972720 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
45972676 ATTTACCTCT
45972686 TACCA TACCA TACCA TACCA TACCA TACCA TACCA
1 TACCA TACCA TACCA TACCA TACCA TACCA TACCA
45972721 CCACCATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
TACCA
Found at i:45976552 original size:16 final size:17
Alignment explanation
Indices: 45976524--45976555 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
45976514 AGAGTTAAAA
45976524 TTAAAATTCTAAAATTT
1 TTAAAATTCTAAAATTT
45976541 TTAAAA-TCTAAAATT
1 TTAAAATTCTAAAATT
45976556 GATTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAAATTCTAAAATTT
Found at i:45976561 original size:17 final size:16
Alignment explanation
Indices: 45976523--45976564 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
45976513 AAGAGTTAAA
45976523 ATTAAAATTCTAAAATT
1 ATTAAAA-TCTAAAATT
*
45976540 TTTAAAATCTAAAATT
1 ATTAAAATCTAAAATT
45976556 GATTAAAAT
1 -ATTAAAAT
45976565 AAATATGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (16 bp):
ATTAAAATCTAAAATT
Found at i:45976755 original size:18 final size:18
Alignment explanation
Indices: 45976732--45976767 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
45976722 TTGAATAAAT
45976732 TATTAAAAA-AAATAAAAA
1 TATTAAAAATAAA-AAAAA
45976750 TATTAAAAATAAAAAAAA
1 TATTAAAAATAAAAAAAA
45976768 CTAGTTCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
TATTAAAAATAAAAAAAA
Found at i:45976991 original size:26 final size:27
Alignment explanation
Indices: 45976962--45977012 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
45976952 ATACAATATA
* *
45976962 AATATTCA-AAATTTCATTTATACCAT
1 AATATCCACAAATTTAATTTATACCAT
*
45976988 AATATCCACAATTTTAATTTATACC
1 AATATCCACAAATTTAATTTATACC
45977013 TAAGTAAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (27 bp):
AATATCCACAAATTTAATTTATACCAT
Found at i:45977072 original size:18 final size:18
Alignment explanation
Indices: 45977043--45977107 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
45977033 AGCACAAATC
45977043 AAATTATCTGAATAAAAGA
1 AAATT-TCTGAATAAAAGA
*
45977062 AAATTTCTGAATAAAATA
1 AAATTTCTGAATAAAAGA
**
45977080 TTACAACATCTGAATAAAAGA
1 --A-AATTTCTGAATAAAAGA
45977101 AAATTTC
1 AAATTTC
45977108 AAGTAATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
18 16 0.43
19 6 0.16
20 1 0.03
21 14 0.38
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.29
Consensus pattern (18 bp):
AAATTTCTGAATAAAAGA
Found at i:45978513 original size:16 final size:16
Alignment explanation
Indices: 45978492--45978524 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
45978482 CGTGCTTGTG
45978492 TGATAAGTGAACTATC
1 TGATAAGTGAACTATC
45978508 TGATAAGTGAACTATC
1 TGATAAGTGAACTATC
45978524 T
1 T
45978525 TAGGGCTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (16 bp):
TGATAAGTGAACTATC
Found at i:45981033 original size:33 final size:33
Alignment explanation
Indices: 45980969--45981033 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
45980959 AACTAAAATT
*
45980969 TGAAACAACTATTGTTTAGAATAATTGTGTTTC
1 TGAAACAACTATTGTTTAGAATAATCGTGTTTC
* *
45981002 TGAAATAACTA-TGTTTGGAATAATCGTTGTTT
1 TGAAACAACTATTGTTTAGAATAATCG-TGTTT
45981034 GGAACAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (33 bp):
TGAAACAACTATTGTTTAGAATAATCGTGTTTC
Found at i:45981850 original size:15 final size:16
Alignment explanation
Indices: 45981832--45981862 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
45981822 TTTAACTAAT
45981832 TAAAAT-AAAATAAAA
1 TAAAATAAAAATAAAA
45981847 TAAAATAAAAATAAAA
1 TAAAATAAAAATAAAA
45981863 GTTCCAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAATAAAAATAAAA
Found at i:45981859 original size:6 final size:5
Alignment explanation
Indices: 45981832--45981862 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
45981822 TTTAACTAAT
45981832 TAAAA TAAAA TAAAA TAAAA TAAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA
45981863 GTTCCAATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:45986480 original size:21 final size:23
Alignment explanation
Indices: 45986447--45986490 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
45986437 TGGTGGGCAA
*
45986447 GCATGGCGCGAGCA-AGGGCTGT
1 GCATGGCGAGAGCACAGGGCTGT
45986469 GCAT-GCGAGAGCAGCAGGGCTG
1 GCATGGCGAGAGCA-CAGGGCTG
45986491 GGACGCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 7 0.37
ACGTcount: A:0.20, C:0.23, G:0.45, T:0.11
Consensus pattern (23 bp):
GCATGGCGAGAGCACAGGGCTGT
Found at i:45986755 original size:9 final size:9
Alignment explanation
Indices: 45986741--45986789 Score: 73
Period size: 9 Copynumber: 5.4 Consensus size: 9
45986731 TTTGGTTAAA
45986741 AATTAACCG
1 AATTAACCG
45986750 AATTAACCG
1 AATTAACCG
45986759 AATTAACCG
1 AATTAACCG
45986768 AATT-ACTCG
1 AATTAAC-CG
*
45986777 AATTACCCG
1 AATTAACCG
45986786 AATT
1 AATT
45986790 GAATCACTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
8 2 0.05
9 34 0.92
10 1 0.03
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:45987077 original size:39 final size:39
Alignment explanation
Indices: 45986990--45987106 Score: 182
Period size: 39 Copynumber: 3.0 Consensus size: 39
45986980 ACTTAAGAGT
*
45986990 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAATTTTATTGGGTTGGGTAATTGGG
* * *
45987028 TAGACTTTAGTTTTAGTTCTATTGGGTTGGGTAATTTGG
1 TAGACTTTAGTTTTAATTTTATTGGGTTGGGTAATTGGG
*
45987067 TAGACGTTAGTTTTAATTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAATTTTATTGGGTTGGGTAATTGGG
45987106 T
1 T
45987107 TGGGTTGGGT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
38 26 0.37
39 45 0.63
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.50
Consensus pattern (39 bp):
TAGACTTTAGTTTTAATTTTATTGGGTTGGGTAATTGGG
Found at i:45987105 original size:13 final size:13
Alignment explanation
Indices: 45987087--45987111 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45987077 TTTTAATTTT
45987087 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
45987100 ATTGGGTTGGGT
1 ATTGGGTTGGGT
45987112 TGGGTAATTT
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:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:45987720 original size:16 final size:15
Alignment explanation
Indices: 45987695--45987728 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
45987685 AAAATTTATA
*
45987695 ATAATTAATATACATT
1 ATAATAAATATA-ATT
45987711 ATAATAAATATAATT
1 ATAATAAATATAATT
45987726 ATA
1 ATA
45987729 TATTAGTTAT
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:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:45987849 original size:29 final size:29
Alignment explanation
Indices: 45987795--45987850 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
45987785 GCTTTTAAAG
* *
45987795 ATATTTACAAAAAGAGACAGCTAATTTCA
1 ATATTTACAAAAAGAGACACCAAATTTCA
45987824 ATATTTACAAAAAGA-ACAACCAAATTT
1 ATATTTACAAAAAGAGAC-ACCAAATTT
45987851 TGCAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.27
Consensus pattern (29 bp):
ATATTTACAAAAAGAGACACCAAATTTCA
Found at i:45997552 original size:4 final size:4
Alignment explanation
Indices: 45997543--45997568 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
45997533 CAAATTATTG
45997543 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
45997569 CGAAGTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:45998555 original size:30 final size:30
Alignment explanation
Indices: 45998514--45998593 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
45998504 GAGTAAGTTG
* *
45998514 CTCACACAAGCTGACATTATATCAGGGTTC
1 CTCAAACAAGCTGACATTATATCAAGGTTC
*** *
45998544 CTCAAACAAGCTGA-AACGTATCAAGGTTG
1 CTCAAACAAGCTGACATTATATCAAGGTTC
45998573 CTCAAACAAGCTGAC-TTATAT
1 CTCAAACAAGCTGACATTATAT
45998594 TAGGTTACCT
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 27 0.68
30 13 0.32
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (30 bp):
CTCAAACAAGCTGACATTATATCAAGGTTC
Found at i:46009849 original size:36 final size:36
Alignment explanation
Indices: 46009756--46009849 Score: 152
Period size: 36 Copynumber: 2.6 Consensus size: 36
46009746 GCTGCAGGTT
* *
46009756 CTGGAGGAGGCTGCAATGGGTCTGGAACTAGTGGAG
1 CTGGTGGAGGCTGCAATGGGTTTGGAACTAGTGGAG
46009792 CTGGTGGAGGCTGCAATGGGTTTGGAACTAGTGGAG
1 CTGGTGGAGGCTGCAATGGGTTTGGAACTAGTGGAG
* *
46009828 CTGGTGGCGGCTGAAATGGGTT
1 CTGGTGGAGGCTGCAATGGGTT
46009850 AGGAGGGAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.19, C:0.13, G:0.45, T:0.23
Consensus pattern (36 bp):
CTGGTGGAGGCTGCAATGGGTTTGGAACTAGTGGAG
Found at i:46009888 original size:33 final size:33
Alignment explanation
Indices: 46009833--46009942 Score: 141
Period size: 33 Copynumber: 3.3 Consensus size: 33
46009823 TGGAGCTGGT
* * * * *
46009833 GGCGGCTGAAATGGGTTAGGAGGGAGCACTGGG-
1 GGCGGCAGAAGTGGGTTTGGAGGAAG-AATGGGC
*
46009866 GGTGGCAGAAGTGGGTTTGGAGGAAGAATGGGC
1 GGCGGCAGAAGTGGGTTTGGAGGAAGAATGGGC
46009899 GGCGGCAGAAGTGGGTTTGGAGGAAGAATGGGC
1 GGCGGCAGAAGTGGGTTTGGAGGAAGAATGGGC
*
46009932 GGCGGAAGAAG
1 GGCGGCAGAAG
46009943 CTGGTTGGGA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 5 0.07
33 63 0.93
ACGTcount: A:0.25, C:0.09, G:0.52, T:0.15
Consensus pattern (33 bp):
GGCGGCAGAAGTGGGTTTGGAGGAAGAATGGGC
Found at i:46009908 original size:15 final size:15
Alignment explanation
Indices: 46009887--46009941 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
46009877 TGGGTTTGGA
46009887 GGAAGAATGGGCGGC
1 GGAAGAATGGGCGGC
* * *
46009902 GGCAGAAGTGGGTTTGGA
1 GGAAGAA-TGGG--CGGC
46009920 GGAAGAATGGGCGGC
1 GGAAGAATGGGCGGC
46009935 GGAAGAA
1 GGAAGAA
46009942 GCTGGTTGGG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 15 0.48
16 4 0.13
17 4 0.13
18 8 0.26
ACGTcount: A:0.29, C:0.09, G:0.51, T:0.11
Consensus pattern (15 bp):
GGAAGAATGGGCGGC
Found at i:46009926 original size:18 final size:17
Alignment explanation
Indices: 46009872--46009930 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
46009862 TGGGGGTGGC
46009872 AGAAGTGGGTTTGGAGGA
1 AGAA-TGGGTTTGGAGGA
* * *
46009890 AGAATGGG--CGGCGGC
1 AGAATGGGTTTGGAGGA
46009905 AGAAGTGGGTTTGGAGGA
1 AGAA-TGGGTTTGGAGGA
46009923 AGAATGGG
1 AGAATGGG
46009931 CGGCGGAAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
15 8 0.25
16 4 0.12
17 8 0.25
18 12 0.38
ACGTcount: A:0.27, C:0.05, G:0.51, T:0.17
Consensus pattern (17 bp):
AGAATGGGTTTGGAGGA
Found at i:46014382 original size:22 final size:22
Alignment explanation
Indices: 46014354--46014397 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
46014344 TTTTGACAAA
46014354 GGCTTGTTTAAATGTCTGAATT
1 GGCTTGTTTAAATGTCTGAATT
46014376 GGCTTGTTTAAATGTCTGAATT
1 GGCTTGTTTAAATGTCTGAATT
46014398 AAATAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (22 bp):
GGCTTGTTTAAATGTCTGAATT
Found at i:46022326 original size:20 final size:19
Alignment explanation
Indices: 46022293--46022331 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
46022283 CATAATTGCC
46022293 CACAATATACATATATATA
1 CACAATATACATATATATA
*
46022312 CACACATATATATATATATA
1 CACA-ATATACATATATATA
46022332 TCATAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.33
Consensus pattern (19 bp):
CACAATATACATATATATA
Found at i:46025268 original size:34 final size:35
Alignment explanation
Indices: 46025204--46025274 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 35
46025194 AACAAGACTT
*
46025204 TTGCTACTGCATTGATCTATCATAAACATGTC-TA
1 TTGCTACTGCATTGATATATCATAAACATGTCATA
* * * *
46025238 TTGCTACTGTATTGATATGTTATAATCATGTCATA
1 TTGCTACTGCATTGATATATCATAAACATGTCATA
46025273 TT
1 TT
46025275 ACATTGCATG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
34 27 0.87
35 4 0.13
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (35 bp):
TTGCTACTGCATTGATATATCATAAACATGTCATA
Found at i:46027909 original size:16 final size:16
Alignment explanation
Indices: 46027885--46027915 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46027875 ATACTATATT
*
46027885 TAATCAAATTATTTTA
1 TAATAAAATTATTTTA
46027901 TAATAAAATTATTTT
1 TAATAAAATTATTTT
46027916 TTATGATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATAAAATTATTTTA
Found at i:46028180 original size:15 final size:15
Alignment explanation
Indices: 46028157--46028186 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46028147 AACTAATTTT
*
46028157 TTAATTAAAATAATA
1 TTAAATAAAATAATA
46028172 TTAAATAAAATAATA
1 TTAAATAAAATAATA
46028187 ATAATTACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAATAAAATAATA
Found at i:46028249 original size:17 final size:18
Alignment explanation
Indices: 46028217--46028250 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46028207 TTTATATTTT
46028217 ATATTGTTCTTAAATAAA
1 ATATTGTTCTTAAATAAA
*
46028235 ATATTTTTC-TAAATAA
1 ATATTGTTCTTAAATAA
46028251 TAATTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (18 bp):
ATATTGTTCTTAAATAAA
Found at i:46034803 original size:10 final size:9
Alignment explanation
Indices: 46034779--46034813 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
46034769 GAGTTTAAAA
46034779 ATAAAAATT
1 ATAAAAATT
46034788 ATAAAAATT
1 ATAAAAATT
*
46034797 ATAAAAAAT
1 ATAAAAATT
*
46034806 ATACAAAT
1 ATAAAAAT
46034814 CATGTTAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (9 bp):
ATAAAAATT
Found at i:46036175 original size:23 final size:23
Alignment explanation
Indices: 46036147--46036194 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
46036137 ATTGGGCTAG
*
46036147 GGTTTAATGGGTAATTCGGGTTA
1 GGTTTAATGAGTAATTCGGGTTA
* * *
46036170 GGTTTAGTTAGTATTTCGGGTTA
1 GGTTTAATGAGTAATTCGGGTTA
46036193 GG
1 GG
46036195 GTATTTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.19, C:0.04, G:0.35, T:0.42
Consensus pattern (23 bp):
GGTTTAATGAGTAATTCGGGTTA
Found at i:46036414 original size:42 final size:40
Alignment explanation
Indices: 46036340--46036447 Score: 153
Period size: 42 Copynumber: 2.6 Consensus size: 40
46036330 TTACACTGGT
* *
46036340 TAACATCCTTTTCAATCTTTTCATTTGTTATCCTTTTCAGA
1 TAACTTCCTTTTCAA-CTTTTCATTTATTATCCTTTTCAGA
*
46036381 TAACTTCCTTTTCAACCTTTTTCATTTATTATCCTTTTCGGA
1 TAACTTCCTTTTCAA-C-TTTTCATTTATTATCCTTTTCAGA
46036423 TAACTTCCTTTTCAACATTTTCATT
1 TAACTTCCTTTTCAAC-TTTTCATT
46036448 GATTCAGAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 24 0.39
42 37 0.61
ACGTcount: A:0.21, C:0.23, G:0.04, T:0.52
Consensus pattern (40 bp):
TAACTTCCTTTTCAACTTTTCATTTATTATCCTTTTCAGA
Found at i:46042770 original size:17 final size:18
Alignment explanation
Indices: 46042745--46042778 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
46042735 TAAATTGAGT
*
46042745 TCATTTTAG-TTAATAAC
1 TCATCTTAGATTAATAAC
46042762 TCATCTTAGATTAATAA
1 TCATCTTAGATTAATAA
46042779 ATGAGTTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (18 bp):
TCATCTTAGATTAATAAC
Found at i:46045696 original size:31 final size:32
Alignment explanation
Indices: 46045660--46045724 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
46045650 CTTAGATAAT
46045660 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
*
46045691 TTTAAAGAGTTTTTATTAGGATTCAGTTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
46045723 TT
1 TT
46045725 GTAATTTGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 9 0.28
32 23 0.72
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:46046286 original size:9 final size:10
Alignment explanation
Indices: 46046268--46046319 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
46046258 TTCTTTAAAT
46046268 AAAAGCAAAA
1 AAAAGCAAAA
46046278 AAAAG-AAAA
1 AAAAGCAAAA
*
46046287 AAAAACAGCAAA
1 AAAAGCA--AAA
*
46046299 AACAGCAAAA
1 AAAAGCAAAA
46046309 AAAAGCAAAA
1 AAAAGCAAAA
46046319 A
1 A
46046320 GCGCAAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 8 0.23
10 19 0.54
12 8 0.23
ACGTcount: A:0.79, C:0.12, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAGCAAAA
Found at i:46046299 original size:19 final size:18
Alignment explanation
Indices: 46046277--46046368 Score: 71
Period size: 19 Copynumber: 4.9 Consensus size: 18
46046267 TAAAAGCAAA
46046277 AAAAAGAAAAAAAAACAGC
1 AAAAAGAAAAAAAAA-AGC
* *
46046296 AAAAACAGCAAAAAAAAGC
1 AAAAAGA-AAAAAAAAAGC
*** *
46046315 AAAAAGCGCAAAAGAA--
1 AAAAAGAAAAAAAAAAGC
46046331 AAAAAGAAAAAAAAAAGC
1 AAAAAGAAAAAAAAAAGC
46046349 AAAAAGCGCAAAAAAAAAAG
1 AAAAA--G-AAAAAAAAAAG
46046369 TTGCCTACCT
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
16 12 0.21
18 11 0.20
19 14 0.25
20 8 0.14
21 11 0.20
ACGTcount: A:0.76, C:0.11, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAAGC
Found at i:46049542 original size:31 final size:32
Alignment explanation
Indices: 46049506--46049570 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
46049496 CTTAGATAAT
46049506 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
46049537 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
46049569 TT
1 TT
46049571 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:46049882 original size:4 final size:4
Alignment explanation
Indices: 46049873--46049903 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
46049863 ATCTATCCTT
46049873 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
46049904 ACTAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:46065230 original size:18 final size:19
Alignment explanation
Indices: 46065204--46065240 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
46065194 CCCACCTTCT
*
46065204 CTTTCCTCCTCCCC-CCTC
1 CTTTACTCCTCCCCTCCTC
46065222 CTTTACTCCTCCCCTCCTC
1 CTTTACTCCTCCCCTCCTC
46065241 TTTCCCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.03, C:0.62, G:0.00, T:0.35
Consensus pattern (19 bp):
CTTTACTCCTCCCCTCCTC
Found at i:46065243 original size:18 final size:17
Alignment explanation
Indices: 46065202--46065243 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
46065192 CACCCACCTT
*
46065202 CTCTTTCCTCCTCCCCC
1 CTCTTTACTCCTCCCCC
46065219 CTCCTTTACTCCTCCCCTC
1 CT-CTTTACTCCTCCCC-C
46065238 CTCTTT
1 CTCTTT
46065244 CCCCAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 17 0.77
19 3 0.14
ACGTcount: A:0.02, C:0.57, G:0.00, T:0.40
Consensus pattern (17 bp):
CTCTTTACTCCTCCCCC
Found at i:46065740 original size:12 final size:11
Alignment explanation
Indices: 46065725--46065757 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
46065715 CTTTTAACTC
46065725 TTCTTTTTCTTT
1 TTCTTTTT-TTT
46065737 TTCTTTTTTTT
1 TTCTTTTTTTT
46065748 TT-TTTTTTTT
1 TTCTTTTTTTT
46065758 GAGATGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
11 5 0.24
12 8 0.38
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:46069674 original size:43 final size:42
Alignment explanation
Indices: 46069588--46069691 Score: 154
Period size: 43 Copynumber: 2.5 Consensus size: 42
46069578 CCGAGATTAT
* *
46069588 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGAATTC
1 GTGTAAGACCATGTCTGGGACATGGCATCGATATGAGAATTC
* *
46069630 GTGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTC
1 GTGTAAGACCATGTCTGGGACA-TGGCATCGATATGAGAATTC
*
46069673 GTGTAAGACCATGACTGGG
1 GTGTAAGACCATGTCTGGG
46069692 CTATTAACAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 20 0.36
43 36 0.64
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (42 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGATATGAGAATTC
Found at i:46069734 original size:43 final size:42
Alignment explanation
Indices: 46069579--46069743 Score: 149
Period size: 43 Copynumber: 3.9 Consensus size: 42
46069569 TTAGGGTTAC
*
46069579 CGAGATTATGTGTAAGACCATATCTGGGATA-TGGCATCGATA
1 CGAGATT-TGTGTAAGACCATATCTGGGCTATTGGCATCGATA
* * *
46069621 TGAGAATTCGTGTAAGACCATGTCTGGGAC-ATTGGCATCGATA
1 CGAG-ATTTGTGTAAGACCATATCTGGG-CTATTGGCATCGATA
* * **
46069664 TGTGATTTCGTGTAAGACCATGA-CTGGGCTATTAACATCGATA
1 CGAGATTT-GTGTAAGACCAT-ATCTGGGCTATTGGCATCGATA
* * *
46069707 CGAGATTATATGTAAGATCATATCTGGGATA-TGGCAT
1 CGAGATT-TGTGTAAGACCATATCTGGGCTATTGGCAT
46069744 TGTTACGGTA
Statistics
Matches: 99, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
42 31 0.31
43 67 0.68
44 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (42 bp):
CGAGATTTGTGTAAGACCATATCTGGGCTATTGGCATCGATA
Found at i:46072366 original size:68 final size:69
Alignment explanation
Indices: 46072239--46072367 Score: 215
Period size: 69 Copynumber: 1.9 Consensus size: 69
46072229 ATTTAACAAA
* *
46072239 TTTTTTTCTCTCATTTTCTCTCTTTCCAAACACCACTTTTTTTTATTCAAAACACATGGTTGCTG
1 TTTTTTTCTCTCATTTTCTCTCTTGCCAAACACCACTTTTTCTTATTCAAAACACATGGTTGCTG
46072304 CTAT
66 CTAT
* *
46072308 TTTTTTTCTCTCATTTTCTCTCTTGCCAAACACCA-TTTTTCTTCTTCAAAACATATGGTT
1 TTTTTTTCTCTCATTTTCTCTCTTGCCAAACACCACTTTTTCTTATTCAAAACACATGGTT
46072368 AGCTCATTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
68 22 0.39
69 34 0.61
ACGTcount: A:0.20, C:0.25, G:0.05, T:0.50
Consensus pattern (69 bp):
TTTTTTTCTCTCATTTTCTCTCTTGCCAAACACCACTTTTTCTTATTCAAAACACATGGTTGCTG
CTAT
Found at i:46072544 original size:21 final size:21
Alignment explanation
Indices: 46072504--46072559 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
46072494 TTTTCTCTCA
*
46072504 TTTTCTCTCTTGCCAAACACCAT
1 TTTTCT-TCTT-CAAAACACCAT
46072527 TTTTCTTCTTCAAAACACCAT
1 TTTTCTTCTTCAAAACACCAT
46072548 TTTTCTTCTTCA
1 TTTTCTTCTTCA
46072560 CTACCTAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 22 0.69
22 4 0.12
23 6 0.19
ACGTcount: A:0.21, C:0.30, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTTCTTCTTCAAAACACCAT
Found at i:46089829 original size:90 final size:90
Alignment explanation
Indices: 46089664--46089830 Score: 205
Period size: 90 Copynumber: 1.9 Consensus size: 90
46089654 TAATATGTTG
* * * * * *
46089664 CCAGATGGTTGTGAATACACAACATAAATGCATATGAGAGTTGTTAGATAATGAGTGGGTGAACT
1 CCAGATGGTTCTGAATACACAACATAAATGCAAATAAAAGTTGTTAGATAATGAGTGGATGAACC
*
46089729 GCCAGTATTGCAGGTTAATACACTA
66 ACCAGTATTGCAGGTTAATACACTA
* *
46089754 CCAGATGGTTCTGAATACACAACTTAATTGCAAATAAAAGTTGTT-GTATAAT-ATGTGGATGAA
1 CCAGATGGTTCTGAATACACAACATAAATGCAAATAAAAGTTGTTAG-ATAATGA-GTGGATGAA
46089817 CCACCA-TAATTGCA
64 CCACCAGT-ATTGCA
46089831 AATTAATATT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
89 3 0.05
90 62 0.95
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (90 bp):
CCAGATGGTTCTGAATACACAACATAAATGCAAATAAAAGTTGTTAGATAATGAGTGGATGAACC
ACCAGTATTGCAGGTTAATACACTA
Found at i:46089848 original size:90 final size:91
Alignment explanation
Indices: 46089628--46089848 Score: 204
Period size: 90 Copynumber: 2.5 Consensus size: 91
46089618 CACACCAGGT
* * *
46089628 TGTGGATAAACCA-CA-AAGTTG-AAAGTTAATATGTTGCCAGATGGTTGTGAATACACAACATA
1 TGTGGATGAACCACCATAA-TTGCAAA-TTAATATATTGCCAGATGGTTCTGAATACACAACATA
* * *
46089690 AATGCATATGAGAGTTGTTAGATAATGA
64 AATGCAAATAAAAGTTGTTAGATAATGA
* ** ** * * * *
46089718 -GTGGGTGAACTGCCAGT-ATTGCAGGTTAATACACTACCAGATGGTTCTGAATACACAACTTAA
1 TGTGGATGAACCACCA-TAATTGCAAATTAATATATTGCCAGATGGTTCTGAATACACAACATAA
*
46089781 TTGCAAATAAAAGTTGTT-GTATAAT-A
65 ATGCAAATAAAAGTTGTTAG-ATAATGA
*
46089807 TGTGGATGAACCACCATAATTGCAAATTAATATTTTGCCAGA
1 TGTGGATGAACCACCATAATTGCAAATTAATATATTGCCAGA
46089849 GCTTCCTCCT
Statistics
Matches: 99, Mismatches: 25, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
89 11 0.11
90 86 0.87
91 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (91 bp):
TGTGGATGAACCACCATAATTGCAAATTAATATATTGCCAGATGGTTCTGAATACACAACATAAA
TGCAAATAAAAGTTGTTAGATAATGA
Found at i:46100055 original size:238 final size:239
Alignment explanation
Indices: 46099637--46100118 Score: 842
Period size: 238 Copynumber: 2.0 Consensus size: 239
46099627 GCAGAAGAAA
**
46099637 GAGAGCATAAGAGTAAGGATCCATATGCATTGGCGATTAGAAGCCTTATGTATGCTATGCTATGC
1 GAGAGCATAAGAGTAAGGATCCATATGCATTGGCGATTAGAAGCCTTATGTATGCTATAATATGC
* *
46099702 TTTGCACACTTCCAGATATATGTTTAGTTGAAGTACTAGTAGATGCGGGGAAAGTAACTTCTCAA
66 TTTGCACACTTCCAGATATATGTTTAGTTGAAGGACTAGTAGACGCGGGGAAAGTAACTTCTCAA
46099767 TATAACCTTTCGGATTCGTTTGTTGAGACTATTATAATTAGGAGTTTTAACAAACATGTCAAGGA
131 TATAACCTTTCGGATTCGTTTGTTGAGACTATTATAATTAGGAGTTTTAACAAACATGTCAAGGA
*
46099832 TATGAGAATGTGAAACATGACACATTTACTTCACTA-GGTAAGT
196 TATGAGAATGTGAAACATGACACATTTACTTCACTAGGGCAAGT
46099875 GAGAGCATAAGAGTAAGGATCCATATGCATTGGCGATTAGAAGCCTTATGTATGCTATAATATGC
1 GAGAGCATAAGAGTAAGGATCCATATGCATTGGCGATTAGAAGCCTTATGTATGCTATAATATGC
* * *
46099940 TTTGCACA-TGTCCAGATGTATGTTTAGTTGAAGGACTAGTAGACGTGGTGAAAGTAACTTCTCA
66 TTTGCACACT-TCCAGATATATGTTTAGTTGAAGGACTAGTAGACGCGGGGAAAGTAACTTCTCA
* * *
46100004 ATATAACCTTTCGGATTCGTTTGTTGGGACTCTTATAATTAGGAGTTTTAACAAATATGTCAAGG
130 ATATAACCTTTCGGATTCGTTTGTTGAGACTATTATAATTAGGAGTTTTAACAAACATGTCAAGG
46100069 ATATGAGAATGTGAAACATGACACATTTACTTCACTAGGGCAAGT
195 ATATGAGAATGTGAAACATGACACATTTACTTCACTAGGGCAAGT
46100114 GAGAG
1 GAGAG
46100119 ATTGTTGGGA
Statistics
Matches: 231, Mismatches: 11, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
237 1 0.00
238 219 0.95
239 11 0.05
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (239 bp):
GAGAGCATAAGAGTAAGGATCCATATGCATTGGCGATTAGAAGCCTTATGTATGCTATAATATGC
TTTGCACACTTCCAGATATATGTTTAGTTGAAGGACTAGTAGACGCGGGGAAAGTAACTTCTCAA
TATAACCTTTCGGATTCGTTTGTTGAGACTATTATAATTAGGAGTTTTAACAAACATGTCAAGGA
TATGAGAATGTGAAACATGACACATTTACTTCACTAGGGCAAGT
Found at i:46101698 original size:56 final size:54
Alignment explanation
Indices: 46101569--46101698 Score: 127
Period size: 56 Copynumber: 2.3 Consensus size: 54
46101559 TTCAAAAATA
*
46101569 ATATTATTTTAATAGTTTTAATATTAAATTTAATATTTATCTTTTAAAGAAGTATT
1 ATATTATTTTAATA--TTTAATATTAAATTTAATATATATCTTTTAAAGAAGTATT
* * * ** *
46101625 TTATTAATTTAATATATTTAATATTAAATTTAATCTAATAT-TTATCTTGATAAGTATT
1 ATATT-ATTTTA-ATATTTAATATTAAATTTAATAT-ATATCTT-T-TAAAGAAGTATT
46101683 ATATTATTTTAATATT
1 ATATTATTTTAATATT
46101699 AAAGTGACTA
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
56 30 0.50
57 14 0.23
58 16 0.27
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (54 bp):
ATATTATTTTAATATTTAATATTAAATTTAATATATATCTTTTAAAGAAGTATT
Found at i:46103657 original size:50 final size:50
Alignment explanation
Indices: 46103544--46103724 Score: 159
Period size: 49 Copynumber: 3.5 Consensus size: 50
46103534 ATTTGGGTAA
* * * *
46103544 AGAGATCCCATGTAAGACCATGTCTGGGACAT-GACATTGACATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATAG-CATGGGCA-C--CGAG---ATG
* *
46103600 AGAGGTCCCATGTAAGACCATGTCTGGGACATAGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATAGCATGGGCACCGAGATG
* * * * *
46103650 ATAGGTCCC-CGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATAGCATGGGCACCGAGATG
** *
46103699 AGAACTCCCATGTAAGACCATATCTG
1 AGAGGTCCCATGTAAGACCATGTCTG
46103725 AGATATGGCA
Statistics
Matches: 106, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
49 40 0.38
50 24 0.23
53 3 0.03
55 1 0.01
56 37 0.35
57 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATAGCATGGGCACCGAGATG
Found at i:46103733 original size:50 final size:50
Alignment explanation
Indices: 46103596--46103735 Score: 165
Period size: 49 Copynumber: 2.8 Consensus size: 50
46103586 TCATTGAGAT
* * *
46103596 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATAGCGTTGGCACCGA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
* * * *
46103646 GATGATAGGTCCC-CGTAAGACCATGTTTGGGACATGGCATGGGCACCGA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
** * * *
46103695 TATGAGAACTCCCATGTAAGACCATATCTGAGATATGGCAT
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCAT
46103736 TGACAGTACA
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
49 40 0.55
50 33 0.45
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
Found at i:46103782 original size:49 final size:50
Alignment explanation
Indices: 46103549--46103782 Score: 143
Period size: 49 Copynumber: 4.6 Consensus size: 50
46103539 GGTAAAGAGA
* * * * **
46103549 TCCCATGTAAGACCATGTCTGGGACATGACATTGACATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CA--GACA--A-GAGAAC
* * * * * * * **
46103605 TCCCATGTAAGACCATGTCTGGGACATAGCGTTGGCACCGAGATGATAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACAGACAAGAGAAC
* * * * *
46103655 TCCC-CGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACAGACAAGAGAAC
* * * *
46103704 TCCCATGTAAGACCATATCTGAGATATGGCAT-TG-ACAGTACAAGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACAG-ACAAGAGAAC
*
46103752 ATCCCGTGTAAGACCATGTCTGGGACATGGC
1 -TCCCATGTAAGACCATGTCTGGGACATGGC
46103783 TTTGGCATGT
Statistics
Matches: 146, Mismatches: 29, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
48 6 0.04
49 71 0.49
50 31 0.21
53 4 0.03
55 1 0.01
56 33 0.23
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACAGACAAGAGAAC
Found at i:46105619 original size:16 final size:16
Alignment explanation
Indices: 46105598--46105630 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
46105588 TTGTACGTTT
46105598 TGTTTGTTTGTTTGTA
1 TGTTTGTTTGTTTGTA
*
46105614 TGTTTGTTTTTTTGTA
1 TGTTTGTTTGTTTGTA
46105630 T
1 T
46105631 TTTTATCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.00, G:0.21, T:0.73
Consensus pattern (16 bp):
TGTTTGTTTGTTTGTA
Found at i:46110894 original size:31 final size:31
Alignment explanation
Indices: 46110859--46110927 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
46110849 CATAACAACT
46110859 CAATGACTTAAATGAAAACTTCTGAATAGTC
1 CAATGACTTAAATGAAAACTTCTGAATAGTC
* * *
46110890 CAATGACTTAAATGAGAACTTTTGAATAGTT
1 CAATGACTTAAATGAAAACTTCTGAATAGTC
46110921 CAATGAC
1 CAATGAC
46110928 CATTTTGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (31 bp):
CAATGACTTAAATGAAAACTTCTGAATAGTC
Found at i:46111410 original size:11 final size:11
Alignment explanation
Indices: 46111394--46111428 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
46111384 AACTAATCAT
46111394 CTCTCAATTTC
1 CTCTCAATTTC
*
46111405 CTCTCAATTTG
1 CTCTCAATTTC
46111416 CTCTCAATTTC
1 CTCTCAATTTC
46111427 CT
1 CT
46111429 TCCAAATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.17, C:0.34, G:0.03, T:0.46
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:46111441 original size:22 final size:22
Alignment explanation
Indices: 46111394--46111444 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
46111384 AACTAATCAT
* *
46111394 CTCTCAATTTCCTCTCAATTTG
1 CTCTCAATTTCCTCTCAAATTA
46111416 CTCTCAATTTCCT-TCCAAATTA
1 CTCTCAATTTCCTCT-CAAATTA
46111438 CTCTCAA
1 CTCTCAA
46111445 ATCCATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.24, C:0.33, G:0.02, T:0.41
Consensus pattern (22 bp):
CTCTCAATTTCCTCTCAAATTA
Found at i:46111487 original size:51 final size:51
Alignment explanation
Indices: 46111408--46111505 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
46111398 CAATTTCCTC
46111408 TCAATTTGCTCTCAATTTCCTTCCAAATTACTCTCAAATCCATATTTAATT
1 TCAATTTGCTCTCAATTTCCTTCCAAATTACTCTCAAATCCATATTTAATT
* * * *
46111459 TCAATTTGCTCTCAATTTCC-TCTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTGCTCTCAATTTCCTTC-CAAATTACTCTCAAATCCATATTT
46111506 TTTTAATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 2 0.05
51 40 0.95
ACGTcount: A:0.27, C:0.26, G:0.02, T:0.46
Consensus pattern (51 bp):
TCAATTTGCTCTCAATTTCCTTCCAAATTACTCTCAAATCCATATTTAATT
Found at i:46113866 original size:7 final size:7
Alignment explanation
Indices: 46113846--46113885 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
46113836 ATTTATTAAA
46113846 AATTTAT
1 AATTTAT
46113853 AAATTTAT
1 -AATTTAT
46113861 AATTTAT
1 AATTTAT
46113868 AA-TTA-
1 AATTTAT
46113873 AATTTAT
1 AATTTAT
46113880 AATTTA
1 AATTTA
46113886 ATTGACAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.07
6 6 0.20
7 15 0.50
8 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AATTTAT
Found at i:46114060 original size:15 final size:15
Alignment explanation
Indices: 46114040--46114093 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
46114030 TAAAAACTCT
46114040 AAACCCTTAACTTAA
1 AAACCCTTAACTTAA
*
46114055 AAACCC-TAAC--CA
1 AAACCCTTAACTTAA
* *
46114067 TAACCCTTAAATTAA
1 AAACCCTTAACTTAA
46114082 AAACCCTTAACT
1 AAACCCTTAACT
46114094 ATCCAAGCCC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
12 6 0.20
13 3 0.10
14 4 0.13
15 17 0.57
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (15 bp):
AAACCCTTAACTTAA
Found at i:46114065 original size:21 final size:22
Alignment explanation
Indices: 46113902--46114063 Score: 231
Period size: 22 Copynumber: 7.5 Consensus size: 22
46113892 AAACCCTAAC
* *
46113902 AAAAACCAT-AACCTTTAACTT
1 AAAAACCCTAAACCCTTAACTT
46113923 AAAAACCCTAAACCCTTAACTT
1 AAAAACCCTAAACCCTTAACTT
*
46113945 GAAAACCCTAAACCCTTAACTT
1 AAAAACCCTAAACCCTTAACTT
46113967 AAAAACCCTAAACCCTTAACTT
1 AAAAACCCTAAACCCTTAACTT
* **
46113989 AAATACCCT-AACGTTTAACTT
1 AAAAACCCTAAACCCTTAACTT
*
46114010 AAATACCCT-AACCCTTAACTT
1 AAAAACCCTAAACCCTTAACTT
*
46114031 AAAAACTCTAAACCCTTAACTT
1 AAAAACCCTAAACCCTTAACTT
46114053 AAAAACCCTAA
1 AAAAACCCTAA
46114064 CCATAACCCT
Statistics
Matches: 127, Mismatches: 12, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
21 44 0.35
22 83 0.65
ACGTcount: A:0.44, C:0.29, G:0.01, T:0.25
Consensus pattern (22 bp):
AAAAACCCTAAACCCTTAACTT
Found at i:46114078 original size:86 final size:87
Alignment explanation
Indices: 46113910--46114070 Score: 256
Period size: 86 Copynumber: 1.9 Consensus size: 87
46113900 ACAAAAACCA
*
46113910 TAACCTTTAACTTAAAAACCCTAAACCCTTAACTTGAAAACCCTAAACCCTTAACTTAAAAACCC
1 TAACCTTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
*
46113975 TAAACCCTTAACTTAAATACCC
66 TAAACCCATAACTTAAATACCC
* * *
46113997 TAACGTTTAACTTAAATACCCT-AACCCTTAACTTAAAAACTCTAAACCCTTAACTTAAAAACCC
1 TAACCTTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
46114061 T-AA-CCATAAC
66 TAAACCCATAAC
46114071 CCTTAAATTA
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
84 6 0.09
85 2 0.03
86 41 0.59
87 20 0.29
ACGTcount: A:0.43, C:0.30, G:0.01, T:0.26
Consensus pattern (87 bp):
TAACCTTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
TAAACCCATAACTTAAATACCC
Found at i:46114087 original size:64 final size:63
Alignment explanation
Indices: 46113902--46114093 Score: 185
Period size: 64 Copynumber: 3.0 Consensus size: 63
46113892 AAACCCTAAC
* * * * *
46113902 AAAAACCAT-AACCTTTAACTTAAAAACCCTAAACCCTTAACTTGAAA-ACCCTAAACCCTTAAC
1 AAAAACCCTAAACCCTTAACTTAAAAACCCT-AACGCATAACTT-AAATA--CAAAACCCTTAAC
46113965 TT
62 TT
* ** **
46113967 AAAAACCCTAAACCCTTAACTTAAATACCCTAACGTTTAACTTAAATACCCTAACCCTTAACTT
1 AAAAACCCTAAACCCTTAACTTAAAAACCCTAACGCATAACTTAAATA-CAAAACCCTTAACTT
*
46114031 AAAAACTCTAAACCCTTAACTTAAAAACCCTAAC-CATAACCCTTAAATTA-AAAACCCTTAACT
1 AAAAACCCTAAACCCTTAACTTAAAAACCCTAACGCATAA--CTTAAA-TACAAAACCCTTAACT
46114094 ATCCAAGCCC
Statistics
Matches: 109, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
63 3 0.03
64 60 0.55
65 25 0.23
66 21 0.19
ACGTcount: A:0.44, C:0.29, G:0.01, T:0.26
Consensus pattern (63 bp):
AAAAACCCTAAACCCTTAACTTAAAAACCCTAACGCATAACTTAAATACAAAACCCTTAACTT
Found at i:46114092 original size:22 final size:22
Alignment explanation
Indices: 46113902--46114092 Score: 199
Period size: 22 Copynumber: 8.6 Consensus size: 22
46113892 AAACCCTAAC
* *
46113902 AAAAA-CCATAACCTTTAACTT
1 AAAAACCCTTAACCCTTAACTT
*
46113923 AAAAACCCTAAACCCTTAACTT
1 AAAAACCCTTAACCCTTAACTT
* *
46113945 GAAAACCCTAAACCCTTAACTT
1 AAAAACCCTTAACCCTTAACTT
*
46113967 AAAAACCCTAAACCCTTAACTT
1 AAAAACCCTTAACCCTTAACTT
* **
46113989 AAATACCC-TAACGTTTAACTT
1 AAAAACCCTTAACCCTTAACTT
*
46114010 AAATACCC-TAACCCTTAACTT
1 AAAAACCCTTAACCCTTAACTT
* *
46114031 AAAAACTCTAAACCCTTAACTT
1 AAAAACCCTTAACCCTTAACTT
*
46114053 AAAAACCCTAACCATAACCCTTAAATT
1 AAAAACCCT-----TAACCCTTAACTT
46114080 AAAAACCCTTAAC
1 AAAAACCCTTAAC
46114093 TATCCAAGCC
Statistics
Matches: 146, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
21 40 0.27
22 86 0.59
27 20 0.14
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (22 bp):
AAAAACCCTTAACCCTTAACTT
Found at i:46114106 original size:86 final size:84
Alignment explanation
Indices: 46113902--46114093 Score: 213
Period size: 86 Copynumber: 2.2 Consensus size: 84
46113892 AAACCCTAAC
* * * *
46113902 AAAAACCATAACCTTTAACTTAAAAACCCTAAACCCTTAACTTGAAAACCCTAAACCCTTAACTT
1 AAAAACCCTAA-C-TTAACTCAAATACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTT
*
46113967 AAAAACCCTAAACCCTTAACTT
63 AAAAACCCTAAACCCTTAAATT
* * *
46113989 AAATACCCTAACGTTTAACTTAAATACCCTAACCCTTAACTTAAAAACTCTAAACCCTTAACTTA
1 AAAAACCCTAAC--TTAACTCAAATACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTA
46114054 AAAACCCTAACCATAACCCTTAAATT
64 AAAACCCT----A-AACCCTTAAATT
46114080 AAAAACCCTTAACT
1 AAAAACCC-TAACT
46114094 ATCCAAGCCC
Statistics
Matches: 91, Mismatches: 7, Indels: 11
0.83 0.06 0.10
Matches are distributed among these distances:
86 42 0.46
87 25 0.27
90 2 0.02
91 18 0.20
92 4 0.04
ACGTcount: A:0.44, C:0.29, G:0.01, T:0.26
Consensus pattern (84 bp):
AAAAACCCTAACTTAACTCAAATACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
AACCCTAAACCCTTAAATT
Found at i:46114139 original size:18 final size:18
Alignment explanation
Indices: 46114105--46114139 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46114095 TCCAAGCCCT
* *
46114105 AAAACCCTAATCTTAACA
1 AAAACCCTAACCCTAACA
46114123 AAAACCCTAACCCTAAC
1 AAAACCCTAACCCTAAC
46114140 CCTAATATGA
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:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAACCCTAACCCTAACA
Found at i:46114305 original size:53 final size:53
Alignment explanation
Indices: 46114142--46114367 Score: 249
Period size: 53 Copynumber: 4.2 Consensus size: 53
46114132 ACCCTAACCC
* *
46114142 TAATATGATATAATTTGATAAATTTACTAACAATTAATACAATTAATAATTAA
1 TAATTTGATATAATTTGATAAATTTACTAACAATTAATACAATTAACAATTAA
* ** * * ** * *
46114195 TAATTTGACTAACAAAATGTTAGATTTTAC-AA-AATGTTTTGACTGGTACTAACAATTAA
1 TAATTTGA-T-ATAATTTGATA-AATTTACTAACAAT-TAAT-AC---AATTAACAATTAA
*
46114254 TAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAA
1 TAATTTGATATAATTTGATAAATTTACTAACAATTAATACAATTAACAATTAA
*
46114307 TAATTTGATATAATTTGATAAATTTACTAACAATTAATACAATTAATAATTAA
1 TAATTTGATATAATTTGATAAATTTACTAACAATTAATACAATTAACAATTAA
46114360 TAATTTGA
1 TAATTTGA
46114368 CTAACAAAAT
Statistics
Matches: 142, Mismatches: 21, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
53 77 0.54
54 4 0.03
55 11 0.08
56 17 0.12
57 11 0.08
58 4 0.03
59 18 0.13
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.40
Consensus pattern (53 bp):
TAATTTGATATAATTTGATAAATTTACTAACAATTAATACAATTAACAATTAA
Found at i:46114313 original size:43 final size:46
Alignment explanation
Indices: 46114244--46114374 Score: 132
Period size: 43 Copynumber: 2.9 Consensus size: 46
46114234 TGACTGGTAC
* *
46114244 TAACAATTAATA-ATTTGATATAATTTGATAATTTTACTAACAATTAA
1 TAACAATTAATACAATT-A-ATAATTTGATAATTTGACTAACAATTAA
* *
46114291 T-ACAATT-A-ACAATTAATAATTTGATATAATTTGA-TAA-ATTTAC
1 TAACAATTAATACAATTAATAATTTG--ATAATTTGACTAACAATTAA
*
46114334 TAACAATTAATACAATTAATAA-TTAATAATTTGACTAACAA
1 TAACAATTAATACAATTAATAATTTGATAATTTGACTAACAA
46114375 AATGTTAGAT
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
43 22 0.31
44 14 0.20
45 16 0.23
46 17 0.24
47 1 0.01
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.40
Consensus pattern (46 bp):
TAACAATTAATACAATTAATAATTTGATAATTTGACTAACAATTAA
Found at i:46117637 original size:124 final size:125
Alignment explanation
Indices: 46117373--46117677 Score: 479
Period size: 124 Copynumber: 2.4 Consensus size: 125
46117363 CCCAAACATG
* * *
46117373 CTACTGTAGCAAAAGTGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGAGTCCACGAGGGCGCGATTTCAGAAATTCTTCTGATAAAACATCCTGC
*
46117438 TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAGGAC
66 TTGAAGCAGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAGGAC
* *
46117498 CTACTGTAGCAAAAGCGAGTCCATGAGGGCGCAATTTCAGAAATTCTTCTGATAAAACATCCTGC
1 CTACTGTAGCAAAAGCGAGTCCACGAGGGCGCGATTTCAGAAATTCTTCTGATAAAACATCCTGC
* * *
46117563 TTGAAGC-GTTTTTATACTATTTGCTTAGAAATGTCAACTCGAAATTATTTTTCCAGGAC
66 TTGAAGCAGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAGGAC
* * *
46117622 CTACTGTAGCAAAAGC-ATGTCCACGTGAGCGCGACTTCAGAAATTCTTCTGATAAA
1 CTACTGTAGCAAAAGCGA-GTCCACGAGGGCGCGATTTCAGAAATTCTTCTGATAAA
46117678 GCATATTGCT
Statistics
Matches: 165, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
123 1 0.01
124 97 0.59
125 67 0.41
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGAGTCCACGAGGGCGCGATTTCAGAAATTCTTCTGATAAAACATCCTGC
TTGAAGCAGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAGGAC
Found at i:46117845 original size:22 final size:21
Alignment explanation
Indices: 46117805--46117850 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
46117795 TTTTTTCCAA
* *
46117805 AACCTTAAAAACCTTAAACCCT
1 AACCTTAAAAACC-CAAAACCT
46117827 AACCTTAAAAACCCAAAACCT
1 AACCTTAAAAACCCAAAACCT
46117848 AAC
1 AAC
46117851 GTTGAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (21 bp):
AACCTTAAAAACCCAAAACCT
Found at i:46119720 original size:27 final size:27
Alignment explanation
Indices: 46119690--46119743 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
46119680 CATCTCTATC
*
46119690 GTTAATGCAGGCAAAGTCCTTTGTTAA
1 GTTAATGCAGGAAAAGTCCTTTGTTAA
46119717 GTTAATGCAGGAAAAGTCCTTTGTTAA
1 GTTAATGCAGGAAAAGTCCTTTGTTAA
46119744 CTTTTTTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (27 bp):
GTTAATGCAGGAAAAGTCCTTTGTTAA
Found at i:46122441 original size:32 final size:32
Alignment explanation
Indices: 46122405--46122469 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
46122395 ATCATATGCA
46122405 TATGATTGTTGGAAATCAAAGTGTGGATTTTT
1 TATGATTGTTGGAAATCAAAGTGTGGATTTTT
46122437 TATGATTGTTGGAAATCAAAGTGTGGATTTTT
1 TATGATTGTTGGAAATCAAAGTGTGGATTTTT
46122469 T
1 T
46122470 TTTCTTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.45
Consensus pattern (32 bp):
TATGATTGTTGGAAATCAAAGTGTGGATTTTT
Found at i:46126506 original size:16 final size:16
Alignment explanation
Indices: 46126487--46126524 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
46126477 ATTAAATTTT
46126487 AATATGATTATTATTA
1 AATATGATTATTATTA
* *
46126503 AATATAATTATTATTC
1 AATATGATTATTATTA
46126519 AATATG
1 AATATG
46126525 TAACATGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (16 bp):
AATATGATTATTATTA
Found at i:46127609 original size:27 final size:24
Alignment explanation
Indices: 46127553--46127609 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
46127543 ATAATAAGGT
*
46127553 AATATTTTTACTAGTTATTATAAA
1 AATATTTTTACTAATTATTATAAA
46127577 ATATATTTTTACTAATTAAATTATGAAA
1 A-ATATTTTTACTAATT--ATTAT-AAA
46127605 AATAT
1 AATAT
46127610 AATATTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 1 0.04
25 14 0.50
27 9 0.32
28 4 0.14
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (24 bp):
AATATTTTTACTAATTATTATAAA
Found at i:46129118 original size:3 final size:3
Alignment explanation
Indices: 46129110--46129155 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
46129100 ATGTTATGTC
* * *
46129110 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAG CAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
46129156 GTAAATATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:46129280 original size:23 final size:23
Alignment explanation
Indices: 46129252--46129305 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
46129242 AAAGTAAAAA
*
46129252 AATAATAGTAATACATTAATAAG
1 AATAATAGTAATACATTAATAAC
* * *
46129275 AATAATAATAGTATATTAATAAC
1 AATAATAGTAATACATTAATAAC
46129298 AATAATAG
1 AATAATAG
46129306 AAAATAATGA
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:0.57, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
AATAATAGTAATACATTAATAAC
Found at i:46129451 original size:3 final size:3
Alignment explanation
Indices: 46129222--46129438 Score: 51
Period size: 3 Copynumber: 73.3 Consensus size: 3
46129212 TGATGATAGC
* * * * *
46129222 AAT AGT AAT AAT -GT AAT AAT AA- AGT AA- AAA AAT AAT AGT AAT ACATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T
* * * * *
46129269 AAT AAG AAT AAT AAT AGT -AT ATT AAT AAC AAT AAT AGAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* * * * * * *
46129314 GAC GA- AAT AAT AAT AAT AAT AA- ACT AA- AGAGT ACT AAT AGT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT
* * * * *
46129358 AAC AAT AAT -AT AAAT AAT AAT GAA- AAC AAC AAG AGA- AAT AAT AAC
1 AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT
* * * *
46129403 AAT AA- CAG AAT AAG AAT AAT GAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
46129439 GCAAAAATAA
Statistics
Matches: 154, Mismatches: 41, Indels: 38
0.66 0.18 0.16
Matches are distributed among these distances:
2 14 0.09
3 128 0.83
4 9 0.06
5 3 0.02
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:46130636 original size:35 final size:35
Alignment explanation
Indices: 46130591--46130659 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
46130581 GGGTGTGTGA
46130591 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
*
46130626 TGGTGTTGGTGGCAGACAGCATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
46130660 AGAGGCAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.20, C:0.10, G:0.51, T:0.19
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
Found at i:46131624 original size:20 final size:21
Alignment explanation
Indices: 46131578--46131624 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
46131568 AAACAGACCT
*
46131578 AACCCAAAACAATAAAATTAC
1 AACCCAAAACAATAAAATTAA
*
46131599 AGCCCAAAA-AGA-AAAATTAA
1 AACCCAAAACA-ATAAAATTAA
46131619 AACCCA
1 AACCCA
46131625 GTCCAAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.62, C:0.23, G:0.04, T:0.11
Consensus pattern (21 bp):
AACCCAAAACAATAAAATTAA
Found at i:46132030 original size:2 final size:2
Alignment explanation
Indices: 46132023--46132049 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46132013 CTTTTCGATT
46132023 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
46132050 TATATAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:46132632 original size:3 final size:3
Alignment explanation
Indices: 46132626--46132706 Score: 71
Period size: 3 Copynumber: 27.7 Consensus size: 3
46132616 TTTAGCATTT
* * * *
46132626 TTA TTA TT- TTC TTCA TTA TTT TTA ATA TT- TTA TCA -TA TT- TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
46132668 TTA TTA TTG TTA TTA TTA GTTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT
46132707 TCTTCATCCA
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
2 7 0.11
3 51 0.81
4 5 0.08
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:46132642 original size:18 final size:18
Alignment explanation
Indices: 46132614--46132672 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 18
46132604 TTAACCCCTT
*
46132614 TTTTTAGCATTTTTATTA
1 TTTTTATCATTTTTATTA
46132632 TTTTCT-TCATTATTT-TTAA
1 TTTT-TATCATT-TTTATT-A
46132651 TATTTTATCATATTTTATTA
1 T-TTTTATCAT-TTTTATTA
46132671 TT
1 TT
46132673 ATTGTTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 13
0.70 0.02 0.28
Matches are distributed among these distances:
18 10 0.30
19 8 0.24
20 12 0.36
21 3 0.09
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTTATCATTTTTATTA
Found at i:46132648 original size:22 final size:20
Alignment explanation
Indices: 46132622--46132707 Score: 63
Period size: 22 Copynumber: 4.2 Consensus size: 20
46132612 TTTTTTTAGC
46132622 ATTTTTATTATTTTCTTCATT
1 ATTTTTATTATTTT-TTCATT
* *
46132643 ATTTTTAATATTTTATCA-T
1 ATTTTTATTATTTTTTCATT
46132662 A-TTTTATTATTATTGTT-ATT
1 ATTTTTATTATT-TT-TTCATT
*
46132682 ATTAGTTATTATTATTATT-ATT
1 ATT-TTTATTATT-TT-TTCATT
46132704 ATTT
1 ATTT
46132708 CTTCATCCAT
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
18 9 0.17
19 5 0.09
20 6 0.11
21 14 0.26
22 19 0.36
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTTTTATTATTTTTTCATT
Found at i:46132692 original size:19 final size:19
Alignment explanation
Indices: 46132668--46132704 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
46132658 TCATATTTTA
*
46132668 TTATTATTGTTATTATTAG
1 TTATTATTATTATTATTAG
46132687 TTATTATTATTATTATTA
1 TTATTATTATTATTATTA
46132705 TTTCTTCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
TTATTATTATTATTATTAG
Found at i:46133085 original size:26 final size:26
Alignment explanation
Indices: 46133033--46133085 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
46133023 TTTATGTTCA
*
46133033 TTTATGTATTTATTTATATGTTCATT
1 TTTATGTATTTATTTATATATTCATT
* *
46133059 TTTATGT-TTTAGTTTATTTATTTATT
1 TTTATGTATTTA-TTTATATATTCATT
46133085 T
1 T
46133086 ATTTGCCGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.70
Consensus pattern (26 bp):
TTTATGTATTTATTTATATATTCATT
Found at i:46133408 original size:110 final size:110
Alignment explanation
Indices: 46133210--46133524 Score: 427
Period size: 110 Copynumber: 2.9 Consensus size: 110
46133200 AACAAAATTT
*
46133210 TTTTCAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
1 TTTTAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
* * *
46133275 CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAAA
66 CGATTTTTCTCGTTTAACCAAATGGCTAAATACCCTTTTAAAAAA
* *
46133320 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCTTAAGGTGCTGGGTGT
1 TTTTAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
* *
46133385 CGATTTTTCTCATTTAACCAAATGGCTAAATACCCTTTTTAAAAA
66 CGATTTTTCTCGTTTAACCAAATGGCTAAATACCCTTTTAAAAAA
** * * * ** * * * *
46133430 TTTCGAAGTAAGATAATATTTTGCGTTTGGAAATTTAAGGAAACGTACCCTAAGGTGCTGGGTTT
1 TTTTAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
* *
46133495 CGA--TTTCTCGTTTAACCAAATAGCCAAATA
66 CGATTTTTCTCGTTTAACCAAATGGCTAAATA
46133525 TCCTCTCGAA
Statistics
Matches: 181, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
108 24 0.13
110 157 0.87
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (110 bp):
TTTTAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
CGATTTTTCTCGTTTAACCAAATGGCTAAATACCCTTTTAAAAAA
Found at i:46134824 original size:25 final size:25
Alignment explanation
Indices: 46134783--46134834 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
46134773 TTGAGTTAGA
* * *
46134783 AATTATTATTATTTATTTTTTAATT
1 AATTATTATTATATATTATTAAATT
46134808 AATTATTAATTA-ATATTATTAAATT
1 AATTATT-ATTATATATTATTAAATT
46134833 AA
1 AA
46134835 AAAGTCTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
AATTATTATTATATATTATTAAATT
Found at i:46148904 original size:21 final size:25
Alignment explanation
Indices: 46148852--46148898 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
46148842 AAAAAATACT
46148852 AACAATATT-AAAATAAATATTTTTG
1 AACAA-ATTGAAAATAAATATTTTTG
46148877 AACAAATTGAAAATAAAT-TTTT
1 AACAAATTGAAAATAAATATTTT
46148899 AAAAATATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (25 bp):
AACAAATTGAAAATAAATATTTTTG
Found at i:46149691 original size:26 final size:27
Alignment explanation
Indices: 46149662--46149717 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
46149652 TTAAAATTCA
46149662 TTGAGTATTAATATTTCA-ATTAATAT
1 TTGAGTATTAATATTTCAGATTAATAT
*
46149688 TTGAGTGTTAATATTTCAGTATTAATAT
1 TTGAGTATTAATATTTCAG-ATTAATAT
46149716 TT
1 TT
46149718 ATCACAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 17 0.63
28 10 0.37
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.52
Consensus pattern (27 bp):
TTGAGTATTAATATTTCAGATTAATAT
Found at i:46149700 original size:14 final size:14
Alignment explanation
Indices: 46149639--46149717 Score: 72
Period size: 14 Copynumber: 5.6 Consensus size: 14
46149629 ATATTTTAAC
*
46149639 TAATATTTGAGTGT
1 TAATATTTGAGTAT
*
46149653 TAAAATTCATTGAGTAT
1 TAATA-T--TTGAGTAT
*
46149670 TAATATTTCA--AT
1 TAATATTTGAGTAT
*
46149682 TAATATTTGAGTGT
1 TAATATTTGAGTAT
*
46149696 TAATATTTCAGTAT
1 TAATATTTGAGTAT
46149710 TAATATTT
1 TAATATTT
46149718 ATCACAAGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
12 11 0.21
14 28 0.54
15 1 0.02
16 1 0.02
17 11 0.21
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.49
Consensus pattern (14 bp):
TAATATTTGAGTAT
Found at i:46150336 original size:23 final size:26
Alignment explanation
Indices: 46150309--46150367 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 26
46150299 ATTATTAACA
46150309 AATATTTGAATTAAATA-ATTA-AT-
1 AATATTTGAATTAAATATATTACATG
*
46150332 AATATTTTG-GTTAAATATATTACATG
1 AATA-TTTGAATTAAATATATTACATG
46150358 AATATTTGAA
1 AATATTTGAA
46150368 AAATAACTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
23 11 0.38
24 8 0.28
25 6 0.21
26 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
AATATTTGAATTAAATATATTACATG
Found at i:46150779 original size:10 final size:9
Alignment explanation
Indices: 46150698--46150871 Score: 67
Period size: 9 Copynumber: 18.9 Consensus size: 9
46150688 TATATAAAGC
*
46150698 TATAAAAAT
1 TATAAAAAA
46150707 TATAAAAAA
1 TATAAAAAA
*
46150716 TAAAATAAACA
1 TATAA-AAA-A
46150727 TATAAAAAA
1 TATAAAAAA
*
46150736 TTTAGAAAAA
1 TATA-AAAAA
46150746 -ATTAAAAAA
1 TA-TAAAAAA
46150755 T-T-AAAAA
1 TATAAAAAA
46150762 TATAAAAATA
1 TATAAAAA-A
*
46150772 TATGAAAAA
1 TATAAAAAA
**
46150781 TGGAAATAAA
1 TATAAA-AAA
* *
46150791 -ATTAGAAA
1 TATAAAAAA
46150799 TAT---AAA
1 TATAAAAAA
46150805 TATAAATAAA
1 TATAAA-AAA
46150815 T-TCAAAAAA
1 TAT-AAAAAA
46150824 TATAGATAAAA
1 TATA-A-AAAA
*
46150835 TCTAAAAATA
1 TATAAAAA-A
**
46150845 TATATGAAA
1 TATAAAAAA
* *
46150854 TAGATAAATA
1 TATA-AAAAA
46150864 TATAAAAA
1 TATAAAAA
46150872 TTAAGACTAG
Statistics
Matches: 122, Mismatches: 23, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
6 6 0.05
7 6 0.05
8 5 0.04
9 48 0.39
10 45 0.37
11 12 0.10
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (9 bp):
TATAAAAAA
Found at i:46150848 original size:21 final size:19
Alignment explanation
Indices: 46150802--46150846 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
46150792 TTAGAAATAT
*
46150802 AAATATAAATAAATTCAAA
1 AAATATAAATAAAATCAAA
* *
46150821 AAATATAGATAAAATCTAA
1 AAATATAAATAAAATCAAA
46150840 AAATATA
1 AAATATA
46150847 TATGAAATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATATAAATAAAATCAAA
Found at i:46154864 original size:22 final size:21
Alignment explanation
Indices: 46154838--46154878 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
46154828 TTAAAATAGT
46154838 AAAAATGTAATAATATTTTACA
1 AAAAATGTAAT-ATATTTTACA
* *
46154860 AAAAATTTTATATATTTTA
1 AAAAATGTAATATATTTTA
46154879 TGATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
AAAAATGTAATATATTTTACA
Found at i:46160093 original size:3 final size:3
Alignment explanation
Indices: 46160085--46160126 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
46160075 ATGAAGCTTA
46160085 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
46160127 TTCAAAAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:46161969 original size:20 final size:24
Alignment explanation
Indices: 46161923--46161969 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 24
46161913 CTTTATAAAA
*
46161923 TAAATTTATATTATAATATTTATT
1 TAAATTTATATTATAATATTTAGT
46161947 TAAA-TTATA-TA-AATA-TTAGT
1 TAAATTTATATTATAATATTTAGT
46161967 TAA
1 TAA
46161970 TTTTTTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 2 0.09
23 5 0.23
24 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TAAATTTATATTATAATATTTAGT
Found at i:46163897 original size:16 final size:16
Alignment explanation
Indices: 46163857--46163898 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
46163847 GCAATTAGAG
*
46163857 TTAGGGTTTTTGGATT
1 TTAGGGTTTTTAGATT
* *
46163873 TTTGAGTTTTTAGATT
1 TTAGGGTTTTTAGATT
46163889 TTAGGGTTTT
1 TTAGGGTTTT
46163899 AAGGAAAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.26, T:0.60
Consensus pattern (16 bp):
TTAGGGTTTTTAGATT
Found at i:46164631 original size:96 final size:96
Alignment explanation
Indices: 46164523--46164844 Score: 394
Period size: 96 Copynumber: 3.4 Consensus size: 96
46164513 AACAACTAGC
* *
46164523 TTTATTTGA-TTTTTCCTTAAAAACCCTAAATACTAAACCCCAATCTAATTTTTTAAAAATTTAT
1 TTTATTTAATTTTTTCCTTAAAAACCCTAAA-ACTAAACCCTAATCTAATTTTTTAAAAATTTAT
*
46164587 AATTAATTTACTCAAGTATCCCTAAACCCTAT
65 AATTAATTTACTCAAGTAACCCTAAACCCTAT
* *
46164619 TTTATTTAATTTTTTTCCTTAAAAA-CC-----CTAAACCCTAATCTATTTTTTTTAAAAAATTA
1 TTTATTTAA-TTTTTTCCTTAAAAACCCTAAAACTAAACCCTAATCTA-ATTTTTTAAAAATTTA
*
46164678 TAATTAATTTACTCAAGTAACCCTAAACCCTAA
64 TAATTAATTTACTCAAGTAACCCTAAACCCTAT
* * *
46164711 TTTATTTGATTTTTTCCTTAAAAACCATAAACATTAAACCCTAATCTAATTTTTT-AAAATTTAT
1 TTTATTTAATTTTTTCCTTAAAAACCCTAAA-ACTAAACCCTAATCTAATTTTTTAAAAATTTAT
* * *
46164775 AATTAATTTAATTAAGAAACCCTAAACCCT-T
65 AATTAATTTACTCAAGTAACCCTAAACCCTAT
*
46164806 ATTTATTTAATTTTTTTCCTT-AAAATCCTAAAATCTAAA
1 -TTTATTTAA-TTTTTTCCTTAAAAACCCTAAAA-CTAAA
46164845 ACCTCAAAAA
Statistics
Matches: 194, Mismatches: 19, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
91 29 0.15
92 54 0.28
95 1 0.01
96 64 0.33
97 18 0.09
98 28 0.14
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.43
Consensus pattern (96 bp):
TTTATTTAATTTTTTCCTTAAAAACCCTAAAACTAAACCCTAATCTAATTTTTTAAAAATTTATA
ATTAATTTACTCAAGTAACCCTAAACCCTAT
Found at i:46164688 original size:92 final size:92
Alignment explanation
Indices: 46164554--46164830 Score: 373
Period size: 92 Copynumber: 3.0 Consensus size: 92
46164544 AACCCTAAAT
* *
46164554 ACTAAACCCCAATCTAATTTTTTAAAAATTTATAATTAATTTACTCAAGTATCCCTAAACCCTAT
1 ACTAAACCCTAATCTAATTTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAT
46164619 TTTATTTAATTTTTTTCCTTAAAAACC
66 TTTATTTAATTTTTTTCCTTAAAAACC
* *
46164646 -CTAAACCCTAATCTATTTTTTTTAAAAAATTATAATTAATTTACTCAAGTAACCCTAAACCCTA
1 ACTAAACCCTAATCTA-ATTTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTA
* *
46164710 ATTTATTTGA-TTTTTTCCTTAAAAACC
65 TTTTATTTAATTTTTTTCCTTAAAAACC
* * *
46164737 ATAAACATTAAACCCTAATCTAATTTTTT-AAAATTTATAATTAATTTAATTAAGAAACCCTAAA
1 ----AC--TAAACCCTAATCTAATTTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCTAAA
46164801 CCCT-TATTTATTTAATTTTTTTCCTTAAAA
60 CCCTAT-TTTATTTAATTTTTTTCCTTAAAA
46164831 TCCTAAAATC
Statistics
Matches: 162, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
91 31 0.19
92 53 0.33
96 44 0.27
97 20 0.12
98 14 0.09
ACGTcount: A:0.39, C:0.17, G:0.01, T:0.43
Consensus pattern (92 bp):
ACTAAACCCTAATCTAATTTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAT
TTTATTTAATTTTTTTCCTTAAAAACC
Found at i:46164890 original size:188 final size:188
Alignment explanation
Indices: 46164523--46164892 Score: 401
Period size: 188 Copynumber: 2.0 Consensus size: 188
46164513 AACAACTAGC
* *
46164523 TTTATTTGATTTTTCCTTAAAAACCCTAAATACTAAACCCCAATCTAATTTTTTAAAAATTTATA
1 TTTATTTGATTTTTCCTTAAAAACCATAAACACTAAACCCCAATCTAATTTTTTAAAAATTTATA
* * * *
46164588 ATTAATTTACTCAAGTATCCCTAAACCCTATTTTATTTAATTTTTTTCCTTAAAAACCCTAAACC
66 ATTAATTTAATCAAGAAACCCTAAACCCTATTTTATTTAATTTTTTTCCTTAAAAACCCTAAAAC
* ******** * * **
46164653 CTAATCTATTTTTTTTAAAAAATTATAATTAATTTACTCAAGTAACCCTAAACCCTAA
131 CTAACCTAAAAACCCCAAAAAACTATAATTAATTTACTAAAAAAACCCTAAACCCTAA
* *
46164711 TTTATTTGATTTTTTCCTTAAAAACCATAAACATTAAACCCTAATCTAATTTTTT-AAAATTTAT
1 TTTATTTGA-TTTTTCCTTAAAAACCATAAACACTAAACCCCAATCTAATTTTTTAAAAATTTAT
* *
46164775 AATTAATTTAATTAAGAAACCCTAAACCCT-TATTTATTTAATTTTTTTCCTT-AAAATCCTAAA
65 AATTAATTTAATCAAGAAACCCTAAACCCTAT-TTTATTTAATTTTTTTCCTTAAAAACCCTAAA
* ** *
46164838 ATCTAAAACCTCAAAAACCCCAAAACCCTA-ACTCTAA-TTAC-AAAAAAACCCTAAA
129 ACCT--AACCT-AAAAACCCCAAAAAACTATAAT-TAATTTACTAAAAAAACCCTAAA
46164893 TCCAAAAAAA
Statistics
Matches: 149, Mismatches: 27, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
187 13 0.09
188 75 0.50
189 51 0.34
190 10 0.07
ACGTcount: A:0.40, C:0.19, G:0.01, T:0.39
Consensus pattern (188 bp):
TTTATTTGATTTTTCCTTAAAAACCATAAACACTAAACCCCAATCTAATTTTTTAAAAATTTATA
ATTAATTTAATCAAGAAACCCTAAACCCTATTTTATTTAATTTTTTTCCTTAAAAACCCTAAAAC
CTAACCTAAAAACCCCAAAAAACTATAATTAATTTACTAAAAAAACCCTAAACCCTAA
Found at i:46175875 original size:26 final size:26
Alignment explanation
Indices: 46175837--46175894 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
46175827 CCCGATATAT
*
46175837 GGCTCTTCATGAGCTTTCC-GATTAAA
1 GGCTCTTCATGAG-GTTCCTGATTAAA
** *
46175863 GGCTCTTTGTGAGGTTCCTGATTAAT
1 GGCTCTTCATGAGGTTCCTGATTAAA
46175889 GGCTCT
1 GGCTCT
46175895 CCGGAGCTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (26 bp):
GGCTCTTCATGAGGTTCCTGATTAAA
Found at i:46176085 original size:24 final size:25
Alignment explanation
Indices: 46175947--46176087 Score: 103
Period size: 24 Copynumber: 5.8 Consensus size: 25
46175937 GGCTATTCGG
* **
46175947 AGCTTCCTGGTTA-ATGGCTCTTCGA
1 AGCTTCCT-GTTATATGGCTCATATA
* * *
46175972 AGCTACCCGTTAT-TGGCTCGTATA
1 AGCTTCCTGTTATATGGCTCATATA
* * *
46175996 AGCTTCCTG-AATATGGCTCTTATG
1 AGCTTCCTGTTATATGGCTCATATA
*** *
46176020 AGCTTCCTGTTATACATCCCGA-ATA
1 AGCTTCCTGTTATATGGCTC-ATATA
*
46176045 AGCTTCCTGTTACATGGCTCATATA
1 AGCTTCCTGTTATATGGCTCATATA
46176070 AGCTT-CTGTTATATGGCT
1 AGCTTCCTGTTATATGGCT
46176088 TGAGAGAGTG
Statistics
Matches: 88, Mismatches: 23, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
23 2 0.02
24 50 0.57
25 36 0.41
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (25 bp):
AGCTTCCTGTTATATGGCTCATATA
Found at i:46177439 original size:24 final size:24
Alignment explanation
Indices: 46177412--46177467 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
46177402 TGATTTGTAA
**
46177412 ATTTTGGTAATGCTTTGTAACCCT
1 ATTTTGGTAATGCTCCGTAACCCT
* *
46177436 ATTTCGGTAATGCTCCGTAATCCT
1 ATTTTGGTAATGCTCCGTAACCCT
*
46177460 ATTCTGGT
1 ATTTTGGT
46177468 GACGAATATG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.43
Consensus pattern (24 bp):
ATTTTGGTAATGCTCCGTAACCCT
Found at i:46188807 original size:21 final size:21
Alignment explanation
Indices: 46188766--46188807 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
46188756 CTTTTGTCTA
* *
46188766 AAATATGAATTTGATTGAATT
1 AAATATGAATTTGACTAAATT
46188787 AAATATGAA-TTGTACTAAATT
1 AAATATGAATTTG-ACTAAATT
46188808 GAGTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.40
Consensus pattern (21 bp):
AAATATGAATTTGACTAAATT
Found at i:46189362 original size:25 final size:23
Alignment explanation
Indices: 46189308--46189362 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
46189298 GGCTCTTTGT
*
46189308 GAGCTTCCTAATATGGCTCACTT
1 GAGCTTCCTAATATGGCTCACTG
*
46189331 GAACTTCCTGATATATGGCT-ATCTG
1 GAGCTTCCT-A-ATATGGCTCA-CTG
46189356 GAGCTTC
1 GAGCTTC
46189363 ACGTTAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 8 0.31
24 2 0.08
25 16 0.62
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (23 bp):
GAGCTTCCTAATATGGCTCACTG
Found at i:46191886 original size:27 final size:25
Alignment explanation
Indices: 46191856--46191907 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
46191846 TTACTCTAGT
*
46191856 TGACACTTCCCATTCAAGGTACTATTA
1 TGACACTTACCATTCAA-GT-CTATTA
*
46191883 TGACACTTACGATTCAAGTCTATTA
1 TGACACTTACCATTCAAGTCTATTA
46191908 CAACTTTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 2 0.09
27 15 0.65
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (25 bp):
TGACACTTACCATTCAAGTCTATTA
Found at i:46196184 original size:138 final size:138
Alignment explanation
Indices: 46195936--46196249 Score: 531
Period size: 138 Copynumber: 2.3 Consensus size: 138
46195926 GGTTAGGTGC
* * ** * *
46195936 TTGGGTTGTCA-TCTGTCTTCGCGTCTAAAGATTAAGTGGCATTCTAAGCTATTCATTTTCTCCA
1 TTGGGTTTTCATTCT-TCTTTGCGTAAAAAGATTGAGTGGCATTCTAAGCTATTCACTTTCTCCA
46196000 CTAGTCTTAACAATTATGAGTAAAGCTAGTAGCCATCTAGAGATGTGACTGATCGAGTAACCGGG
65 CTAGTCTTAACAATTATGAGTAAAGCTAGTAGCCATCTAGAGATGTGACTGATCGAGTAACCGGG
46196065 GTGGGGTAT
130 GTGGGGTAT
*
46196074 TTGGGTTTTCATTCTTCTTTGCGTAAAAATATTGAGTGGCATTCTAAGCTATTCACTTTCTCCAC
1 TTGGGTTTTCATTCTTCTTTGCGTAAAAAGATTGAGTGGCATTCTAAGCTATTCACTTTCTCCAC
46196139 TAGTCTTAACAATTATGAGTAAAGCTAGTAGCCATCTAGAGATGTGACTGATCGAGTAACCGGGG
66 TAGTCTTAACAATTATGAGTAAAGCTAGTAGCCATCTAGAGATGTGACTGATCGAGTAACCGGGG
*
46196204 TGGGGTGT
131 TGGGGTAT
*
46196212 TTGGGTTTTCATTCTTCTTTGCGTAAAAAGATTTAGTG
1 TTGGGTTTTCATTCTTCTTTGCGTAAAAAGATTGAGTG
46196250 ACACTCTAGA
Statistics
Matches: 165, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
138 162 0.98
139 3 0.02
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (138 bp):
TTGGGTTTTCATTCTTCTTTGCGTAAAAAGATTGAGTGGCATTCTAAGCTATTCACTTTCTCCAC
TAGTCTTAACAATTATGAGTAAAGCTAGTAGCCATCTAGAGATGTGACTGATCGAGTAACCGGGG
TGGGGTAT
Found at i:46198471 original size:21 final size:19
Alignment explanation
Indices: 46198445--46198483 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
46198435 AGGGAAGGAA
46198445 AAGAAGGAAGAAGAAAAAAAT
1 AAGAA-GAA-AAGAAAAAAAT
46198466 AAGAAGAAAAGAAAAAAA
1 AAGAAGAAAAGAAAAAAA
46198484 AACTTAACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (19 bp):
AAGAAGAAAAGAAAAAAAT
Found at i:46202600 original size:15 final size:16
Alignment explanation
Indices: 46202570--46202604 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
46202560 TGTAATTTTT
46202570 TATAAAATTGTAAAAA
1 TATAAAATTGTAAAAA
*
46202586 TATAAATTTGTAAAAA
1 TATAAAATTGTAAAAA
46202602 TAT
1 TAT
46202605 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (16 bp):
TATAAAATTGTAAAAA
Found at i:46203096 original size:19 final size:19
Alignment explanation
Indices: 46203072--46203143 Score: 58
Period size: 21 Copynumber: 3.6 Consensus size: 19
46203062 ATACGATAAT
46203072 TTTTATAATTTTTTACGAA
1 TTTTATAATTTTTTACGAA
*
46203091 TTTTAT-ATTTCTTTAC-ATT
1 TTTTATAATTT-TTTACGA-A
*
46203110 TTTTAATAATTTTCTTACGAC
1 TTTT-ATAATTTT-TTACGAA
*
46203131 TTTATAAAATTTT
1 TTT-TATAATTTT
46203144 ATTATTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.12
19 15 0.35
20 3 0.07
21 18 0.42
22 2 0.05
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (19 bp):
TTTTATAATTTTTTACGAA
Done.