Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 89 of 141
Found at i:25162741 original size:44 final size:44
Alignment explanation
Indices: 25162679--25162972 Score: 184
Period size: 44 Copynumber: 6.8 Consensus size: 44
25162669 GACTGGATGC
* *
25162679 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTT
1 GATCCGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTT
* * * *
25162723 AATCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TGAT-TTCTTT
1 GATCCGCTCCACTGCAACTTCAGAGAGATAAGATCTG-TGGT-TTT
* **
25162767 CG-TCCGCTCCACTGCAACTTCAG-GAAGATAAGA-C--TGGATAC
1 -GATCCGCTCCACTGCAACTTCAGAG-AGATAAGATCTGTGGTTTT
* * * * *
25162808 GATCTGCTCTACTACAACTTTAGAGAGATAAGATCTATGGTTTT
1 GATCCGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTT
* * * *
25162852 GATCCGCTCCACCGTAACTTCA-AGGAGATAGGAT-TGAT-TTCTTT
1 GATCCGCTCCACTGCAACTTCAGA-GAGATAAGATCTG-TGGT-TTT
* * * * **
25162896 CG-TCTGCTACACTGCAACTTCAGGGAGATAAGA-C--TGGATGC
1 -GATCCGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTT
* *
25162937 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCT
1 GATCCGCTCCACTGCAACTTCAGAGAGATAAGATCT
25162973 ACTACTTCAA
Statistics
Matches: 188, Mismatches: 41, Indels: 43
0.69 0.15 0.16
Matches are distributed among these distances:
40 2 0.01
41 57 0.30
42 3 0.02
43 7 0.04
44 118 0.63
45 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (44 bp):
GATCCGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTT
Found at i:25162796 original size:129 final size:129
Alignment explanation
Indices: 25162558--25163015 Score: 611
Period size: 129 Copynumber: 3.6 Consensus size: 129
25162548 TTAATCCGAC
* ** * *
25162558 CTACTGCAACTTCAGAG-GTATAGGAT-TCATCATTTTAATCCGTTCCACTGCAACTTCAGGGAG
1 CTACTGCAACTTCAGAGAG-ATAAGATCT-ATGGTTTTAATCCGCTCCACTGCAACTTCAAGGAG
* * * * *
25162621 ATAGGATT-AGCTTC-TTCTATCTACTTCACTGCAACTTTAGGGAGATAAGACTGGATGCGATCT
64 ATAGGATTGA-TTTCTTTC-GTCTGCTACACTGCAACTTCAGGGAGATAAGACTGGATGCGATCT
25162684 GCT
127 GCT
* *
25162687 CTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
1 CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCAAGGAGAT
* * * *
25162752 AGGATTGATTTCTTTCGTCCGCTCCACTGCAACTTCAGGAAGATAAGACTGGATACGATCTGCT
66 AGGATTGATTTCTTTCGTCTGCTACACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCT
* * * * *
25162816 CTACTACAACTTTAGAGAGATAAGATCTATGGTTTTGATCCGCTCCACCGTAACTTCAAGGAGAT
1 CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCAAGGAGAT
25162881 AGGATTGATTTCTTTCGTCTGCTACACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCT
66 AGGATTGATTTCTTTCGTCTGCTACACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCT
** * *
25162945 CTACTGCAACTTCAGAGAGATAAGATCTACT-ACTTCAATCCGCTCCTCTGCAACTTCAAGGAGA
1 CTACTGCAACTTCAGAGAGATAAGATCTA-TGGTTTTAATCCGCTCCACTGCAACTTCAAGGAGA
25163009 TAGGATT
65 TAGGATT
25163016 AAAGCCCAAT
Statistics
Matches: 291, Mismatches: 33, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
129 284 0.98
130 7 0.02
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (129 bp):
CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCAAGGAGAT
AGGATTGATTTCTTTCGTCTGCTACACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCT
Found at i:25162996 original size:85 final size:85
Alignment explanation
Indices: 25162601--25163010 Score: 264
Period size: 85 Copynumber: 4.8 Consensus size: 85
25162591 TTTAATCCGT
* * * * * * *
25162601 TCCACTGCAACTTCAGGGAGATAGGAT-TAGCTTCTTCTATCTACTTCACTGCAACTTTAGGGAG
1 TCCACTGCAACTTCAGAGAGATAAGATCTA-CTACTTCAATCTGCTCCACTGCAACTTCAGGGAG
25162665 ATAAGACTGGATGCGATCTGC
65 ATAAGACTGGATGCGATCTGC
* * ** * *
25162686 TCTACTGCAACTTCAGAGAGATAAGATCT-GTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAG
1 TCCACTGCAACTTCAGAGAGATAAGATCTACT-ACTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * * **
25162750 ATAGGA-TTGATTTCTTTCGTCCGC
65 ATAAGACTGGA-TGCGATC-T--GC
** * * * * * *
25162774 TCCACTGCAACTTCAG-GAAGATAAGA-CT-GGA-TACGATCTGCTCTACTACAACTTTAGAGAG
1 TCCACTGCAACTTCAGAG-AGATAAGATCTACTACTTCAATCTGCTCCACTGCAACTTCAGGGAG
* ** *
25162835 ATAAGATCTATGGTTTTGATCCGC
65 ATAAGA-C--TGGATGCGATCTGC
* * * * * * *
25162859 TCCACCGTAACTTCA-AGGAGATAGGAT-TGATTTCTTTC-GTCTGCTACACTGCAACTTCAGGG
1 TCCACTGCAACTTCAGA-GAGATAAGATCT-ACTAC-TTCAATCTGCTCCACTGCAACTTCAGGG
25162921 AGATAAGACTGGATGCGATCTGC
63 AGATAAGACTGGATGCGATCTGC
* * * *
25162944 TCTACTGCAACTTCAGAGAGATAAGATCTACTACTTCAATCCGCTCCTCTGCAACTTCAAGGAGA
1 TCCACTGCAACTTCAGAGAGATAAGATCTACTACTTCAATCTGCTCCACTGCAACTTCAGGGAGA
25163009 TA
66 TA
25163011 GGATTAAAGC
Statistics
Matches: 241, Mismatches: 63, Indels: 42
0.70 0.18 0.12
Matches are distributed among these distances:
84 7 0.03
85 165 0.68
86 5 0.02
87 5 0.02
88 55 0.23
89 4 0.02
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (85 bp):
TCCACTGCAACTTCAGAGAGATAAGATCTACTACTTCAATCTGCTCCACTGCAACTTCAGGGAGA
TAAGACTGGATGCGATCTGC
Found at i:25163794 original size:24 final size:21
Alignment explanation
Indices: 25163745--25163799 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
25163735 TGACACCGTG
* *
25163745 TTTTATTTCATGTTAGATTAA
1 TTTTATTTGATGTTAAATTAA
25163766 TTTTATTTGATGTATAAATTATGA
1 TTTTATTTGATGT-TAAATTA--A
25163790 TTTTATTTGA
1 TTTTATTTGA
25163800 ATAAGCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.41
22 6 0.21
24 11 0.38
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.58
Consensus pattern (21 bp):
TTTTATTTGATGTTAAATTAA
Found at i:25167539 original size:45 final size:44
Alignment explanation
Indices: 25167489--25167581 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
25167479 GGTTCGTTGT
*
25167489 AATGGAATAGAGCCGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACCGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
* *
25167534 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACCGTAATAGTATTCATGTGTTTGGTTGAATGG
25167578 AATG
1 AATG
25167582 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.52
45 20 0.45
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAACCGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:25167979 original size:121 final size:121
Alignment explanation
Indices: 25167720--25167959 Score: 387
Period size: 121 Copynumber: 2.0 Consensus size: 121
25167710 TTAATCATAT
* * *
25167720 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAATATATAATACTAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATATAATAATAT
*
25167785 AAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATAATATAAAATATAA
**
25167841 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT-TCTTAATAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATATAATAATAT
* *
25167905 -AATTATTCTTATATGAATTTACTAAAATCATAATATATAATAATATAAAA-ATAA
66 AAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATAATATAAAATATAA
25167959 T
1 T
25167960 ATATAATCTA
Statistics
Matches: 111, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
118 5 0.05
119 47 0.42
120 6 0.05
121 53 0.48
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (121 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATATAATAATAT
AAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATAATATAAAATATAA
Found at i:25172409 original size:27 final size:27
Alignment explanation
Indices: 25172373--25172432 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
25172363 GTATACGTAT
* *
25172373 ATATATAAAAAATATTTAA-ATTATAAA
1 ATATAGAAAAAATA-TAAATATTATAAA
*
25172400 ATATAGAAAACATATAAATATTATAAA
1 ATATAGAAAAAATATAAATATTATAAA
25172427 AGTATA
1 A-TATA
25172433 TACGCATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 3 0.11
27 21 0.75
28 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (27 bp):
ATATAGAAAAAATATAAATATTATAAA
Found at i:25173244 original size:17 final size:18
Alignment explanation
Indices: 25173211--25173244 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
25173201 ACAAGATGGA
*
25173211 AAATGAAAAAGGAAAAAC
1 AAATGAAAAAGAAAAAAC
25173229 AAAT-AAAAAGAAAAAA
1 AAATGAAAAAGAAAAAA
25173245 AGGAACAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.79, C:0.03, G:0.12, T:0.06
Consensus pattern (18 bp):
AAATGAAAAAGAAAAAAC
Found at i:25175012 original size:39 final size:40
Alignment explanation
Indices: 25174969--25175086 Score: 104
Period size: 39 Copynumber: 3.1 Consensus size: 40
25174959 TAGAATAGTG
* * *
25174969 GTTTTTGACTTAGTGCTA-TTAGGTTGATTTGTGATTTTT
1 GTTTTTGACTCAATGCTACTGAGGTTGATTTGTGATTTTT
* *
25175008 G-TTTTGACTCAATGTTACTGGGGTTGATTTGTGATTTTT
1 GTTTTTGACTCAATGCTACTGAGGTTGATTTGTGATTTTT
* * * *
25175047 G-TTCTGACACAATG-TCACTG-GGTT-AATTGTGGTTTTT
1 GTTTTTGACTCAATGCT-ACTGAGGTTGATTTGTGATTTTT
25175084 GTT
1 GTT
25175087 CCGACCAATT
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
37 12 0.18
38 19 0.28
39 36 0.54
ACGTcount: A:0.16, C:0.08, G:0.25, T:0.51
Consensus pattern (40 bp):
GTTTTTGACTCAATGCTACTGAGGTTGATTTGTGATTTTT
Found at i:25175086 original size:37 final size:37
Alignment explanation
Indices: 25174997--25175122 Score: 137
Period size: 39 Copynumber: 3.3 Consensus size: 37
25174987 TTAGGTTGAT
* * *
25174997 TTGTGATTTTTGTTTTGACTCAATGTTACTGGGGTTGAT
1 TTGTGATTTTTGTTCTGAC-CAATGTCACTGGGGTT-AA
25175036 TTGTGATTTTTGTTCTGACACAATGTCACT-GGGTTAA
1 TTGTGATTTTTGTTCTGAC-CAATGTCACTGGGGTTAA
* * * * *
25175073 TTGTGGTTTTTGTTCCGACCAATTGCCATTGGGGCTAA
1 TTGTGATTTTTGTTCTGACCAA-TGTCACTGGGGTTAA
25175111 TTGTGATTTTTG
1 TTGTGATTTTTG
25175123 ATCTTTGTCA
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
36 3 0.04
37 23 0.31
38 22 0.29
39 27 0.36
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.47
Consensus pattern (37 bp):
TTGTGATTTTTGTTCTGACCAATGTCACTGGGGTTAA
Found at i:25175121 original size:38 final size:37
Alignment explanation
Indices: 25175036--25175122 Score: 104
Period size: 37 Copynumber: 2.3 Consensus size: 37
25175026 TGGGGTTGAT
* * *
25175036 TTGTGATTTTTGTTCTGACACAATGTCACTGGGTTAA
1 TTGTGATTTTTGTTCCGACACAATGCCACTGGGCTAA
* *
25175073 TTGTGGTTTTTGTTCCGAC-CAATTGCCATTGGGGCTAA
1 TTGTGATTTTTGTTCCGACACAA-TGCCACT-GGGCTAA
25175111 TTGTGATTTTTG
1 TTGTGATTTTTG
25175123 ATCTTTGTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 3 0.07
37 22 0.52
38 17 0.40
ACGTcount: A:0.17, C:0.14, G:0.24, T:0.45
Consensus pattern (37 bp):
TTGTGATTTTTGTTCCGACACAATGCCACTGGGCTAA
Found at i:25177730 original size:20 final size:20
Alignment explanation
Indices: 25177694--25177731 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25177684 ATTTTTACCA
*
25177694 CTAAATTAAAAGGTTATTGG
1 CTAAATTAAAAGATTATTGG
*
25177714 CTAAATTAAAATATTATT
1 CTAAATTAAAAGATTATT
25177732 ATTCATTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (20 bp):
CTAAATTAAAAGATTATTGG
Found at i:25185975 original size:3 final size:3
Alignment explanation
Indices: 25185967--25186006 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
25185957 TACCACCCTT
25185967 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
25186007 CTTTTCTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:25189463 original size:13 final size:14
Alignment explanation
Indices: 25189431--25189461 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
25189421 TCTAAACAAG
25189431 TTTTAAAATATTTT
1 TTTTAAAATATTTT
25189445 TTTTAAAATATTTT
1 TTTTAAAATATTTT
25189459 TTT
1 TTT
25189462 AACTTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTAAAATATTTT
Found at i:25189871 original size:11 final size:11
Alignment explanation
Indices: 25189858--25189900 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
25189848 TGCCTACTTT
*
25189858 TTTTA-TATTT
1 TTTTATTATTA
*
25189868 TTTTATCATTA
1 TTTTATTATTA
25189879 TTTTATTATTTA
1 TTTTATTA-TTA
25189891 TTTTATTATT
1 TTTTATTATT
25189901 TCTGATACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 5 0.18
11 12 0.43
12 11 0.39
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:25189891 original size:12 final size:12
Alignment explanation
Indices: 25189858--25189901 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
25189848 TGCCTACTTT
25189858 TTTTA-TATTT-
1 TTTTATTATTTA
*
25189868 TTTTATCA-TTA
1 TTTTATTATTTA
25189879 TTTTATTATTTA
1 TTTTATTATTTA
25189891 TTTTATTATTT
1 TTTTATTATTT
25189902 CTGATACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 7 0.24
11 8 0.28
12 14 0.48
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTATTATTTA
Found at i:25201384 original size:24 final size:24
Alignment explanation
Indices: 25201352--25201401 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
25201342 GGGGGGATGC
25201352 TGCGCATGATAAATCTTCATAAGT
1 TGCGCATGATAAATCTTCATAAGT
25201376 TGCGCATGATAAATCTTCATAAGT
1 TGCGCATGATAAATCTTCATAAGT
25201400 TG
1 TG
25201402 GGAGCCTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (24 bp):
TGCGCATGATAAATCTTCATAAGT
Found at i:25218812 original size:23 final size:25
Alignment explanation
Indices: 25218764--25218812 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
25218754 GTTATGTGCA
*
25218764 TATTAAGTGCTTTTGTTGAGTGTTT
1 TATTAAGTGCTTTTGTTGAGTATTT
*
25218789 TATTAA-T-CTTTTGTTGGGTATTT
1 TATTAAGTGCTTTTGTTGAGTATTT
25218812 T
1 T
25218813 GGAGAGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
24 1 0.05
25 6 0.27
ACGTcount: A:0.16, C:0.04, G:0.20, T:0.59
Consensus pattern (25 bp):
TATTAAGTGCTTTTGTTGAGTATTT
Found at i:25223885 original size:42 final size:41
Alignment explanation
Indices: 25223822--25223949 Score: 157
Period size: 42 Copynumber: 3.0 Consensus size: 41
25223812 ATTCGACGTT
* * *
25223822 TTGGTTGATACATCCAATGATTTAACGAGCTTGGTTTGGTTC
1 TTGGTCGATACATTC-ATGATTTAACAAGCTTGGTTTGGTTC
*
25223864 TTGGTCGATACATTCACTGATTTAACCAGCTTGGTTTGGTTC
1 TTGGTCGATACATTCA-TGATTTAACAAGCTTGGTTTGGTTC
* * * *
25223906 TTGGTGGATACATTTGATGGTTTAACAAGCTTGGTTTGATTC
1 TTGGTCGATACA-TTCATGATTTAACAAGCTTGGTTTGGTTC
25223948 TT
1 TT
25223950 CTTGTTGGAA
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.01
42 72 0.95
43 3 0.04
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.42
Consensus pattern (41 bp):
TTGGTCGATACATTCATGATTTAACAAGCTTGGTTTGGTTC
Found at i:25228120 original size:19 final size:20
Alignment explanation
Indices: 25228083--25228123 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
25228073 TACAACACAA
*
25228083 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
25228103 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
25228122 TT
1 TT
25228124 GCCTAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:25231836 original size:24 final size:24
Alignment explanation
Indices: 25231807--25231852 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
25231797 ACCCTAAAAC
25231807 TTGAATTAAATCAAATTAATCAGG
1 TTGAATTAAATCAAATTAATCAGG
25231831 TTGAATTAAATCAAATTAATCA
1 TTGAATTAAATCAAATTAATCA
25231853 AGCTGCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.35
Consensus pattern (24 bp):
TTGAATTAAATCAAATTAATCAGG
Found at i:25239934 original size:26 final size:26
Alignment explanation
Indices: 25239851--25239919 Score: 120
Period size: 26 Copynumber: 2.7 Consensus size: 26
25239841 CCCGATATAT
**
25239851 GGCTCTTCATGAGCTTCTCGATTAAA
1 GGCTCTTTGTGAGCTTCTCGATTAAA
25239877 GGCTCTTTGTGAGCTTCTCGATTAAA
1 GGCTCTTTGTGAGCTTCTCGATTAAA
25239903 GGCTCTTTGTGAGCTTC
1 GGCTCTTTGTGAGCTTC
25239920 CTGATTGATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (26 bp):
GGCTCTTTGTGAGCTTCTCGATTAAA
Found at i:25240112 original size:25 final size:27
Alignment explanation
Indices: 25240084--25240146 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 27
25240074 AGCCTGGATA
25240084 AGCTTCCCGATATATGGCTC-ACA-AG
1 AGCTTCCCGATATATGGCTCGACAGAG
* * * *
25240109 AGCTTCTCGTTCTATGGCTCGAGAGAG
1 AGCTTCCCGATATATGGCTCGACAGAG
*
25240136 GGCTTCCCGAT
1 AGCTTCCCGAT
25240147 CATGTGCTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
25 17 0.59
26 2 0.07
27 10 0.34
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (27 bp):
AGCTTCCCGATATATGGCTCGACAGAG
Found at i:25248754 original size:27 final size:27
Alignment explanation
Indices: 25248724--25248797 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 27
25248714 ACTAACTCGT
25248724 CAGACCTACTGGCGTATACCATCTAAC
1 CAGACCTACTGGCGTATACCATCTAAC
* ** * **
25248751 CAGACTTGTTGACGTA-ACCATCTTGC
1 CAGACCTACTGGCGTATACCATCTAAC
*
25248777 CAGACCTACTGGTGTTATACC
1 CAGACCTACTGGCG-TATACC
25248798 GCCACCACAA
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
26 17 0.50
27 14 0.41
28 3 0.09
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (27 bp):
CAGACCTACTGGCGTATACCATCTAAC
Found at i:25250305 original size:20 final size:18
Alignment explanation
Indices: 25250258--25250364 Score: 62
Period size: 20 Copynumber: 5.8 Consensus size: 18
25250248 CTAGATAAAC
25250258 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
25250275 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
25250295 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
25250314 ATTAAGA-TAAGTA-TTAA-
1 ATTAA-ATTAA-TATTTAAT
*
25250331 ATTAAATTAAATATTAAACT
1 ATTAAATT-AATATTTAA-T
*
25250351 ATTAAAATAATATT
1 ATTAAATTAATATT
25250365 AATTTTAGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
16 1 0.01
17 16 0.23
18 8 0.11
19 20 0.29
20 25 0.36
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:25251845 original size:21 final size:21
Alignment explanation
Indices: 25251821--25251888 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
25251811 CCATAGAGAG
25251821 AAAATAGTAGGAGATAATAAC
1 AAAATAGTAGGAGATAATAAC
* * *
25251842 AAAA-A--AGGAGTCCTATAGAGAG
1 AAAATAGTAGGAG--ATA-ATA-AC
25251864 AAAATAGTAGGAGATAATAAC
1 AAAATAGTAGGAGATAATAAC
25251885 AAAA
1 AAAA
25251889 AAATAGGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
18 5 0.15
20 3 0.09
21 11 0.32
22 7 0.21
23 3 0.09
25 5 0.15
ACGTcount: A:0.57, C:0.06, G:0.21, T:0.16
Consensus pattern (21 bp):
AAAATAGTAGGAGATAATAAC
Found at i:25251846 original size:22 final size:22
Alignment explanation
Indices: 25251821--25251889 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
25251811 CCATAGAGAG
25251821 AAAATAGTAGGAGATAATAACA
1 AAAATAGTAGGAGATAATAACA
* *** *
25251843 AAAA-AGGA-GTCCT-ATAGAGA
1 AAAATAGTAGGAGATAATA-ACA
25251863 GAAAATAGTAGGAGATAATAACA
1 -AAAATAGTAGGAGATAATAACA
25251886 AAAA
1 AAAA
25251890 AATAGGATAA
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.22
22 11 0.34
23 4 0.12
24 3 0.09
ACGTcount: A:0.58, C:0.06, G:0.20, T:0.16
Consensus pattern (22 bp):
AAAATAGTAGGAGATAATAACA
Found at i:25251852 original size:43 final size:43
Alignment explanation
Indices: 25251794--25251890 Score: 176
Period size: 43 Copynumber: 2.3 Consensus size: 43
25251784 CATAGCCCGG
*
25251794 ATAACAAAAAGGGAGTCCCATAGAGAGAAAATAGTAGGAGATA
1 ATAACAAAAAAGGAGTCCCATAGAGAGAAAATAGTAGGAGATA
*
25251837 ATAACAAAAAAGGAGTCCTATAGAGAGAAAATAGTAGGAGATA
1 ATAACAAAAAAGGAGTCCCATAGAGAGAAAATAGTAGGAGATA
25251880 ATAACAAAAAA
1 ATAACAAAAAA
25251891 ATAGGATAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.56, C:0.08, G:0.22, T:0.14
Consensus pattern (43 bp):
ATAACAAAAAAGGAGTCCCATAGAGAGAAAATAGTAGGAGATA
Found at i:25252055 original size:12 final size:13
Alignment explanation
Indices: 25252029--25252061 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
25252019 AGTTTATTTA
25252029 TTTACTTTTTGTT
1 TTTACTTTTTGTT
25252042 TTTACTTTTT-TT
1 TTTACTTTTTGTT
25252054 TTTA-TTTT
1 TTTACTTTT
25252062 CGAAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 6 0.30
13 10 0.50
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (13 bp):
TTTACTTTTTGTT
Found at i:25252749 original size:21 final size:21
Alignment explanation
Indices: 25252725--25252764 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25252715 ATATTCGCTG
*
25252725 TTATTATTATCATTCTTATCT
1 TTATTATTACCATTCTTATCT
*
25252746 TTATTATTACCATTGTTAT
1 TTATTATTACCATTCTTAT
25252765 TATATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.60
Consensus pattern (21 bp):
TTATTATTACCATTCTTATCT
Found at i:25255149 original size:13 final size:14
Alignment explanation
Indices: 25255131--25255163 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
25255121 ACTCTAATCT
*
25255131 CTTTTTCT-TTTTC
1 CTTTTTCTCTCTTC
25255144 CTTTTTCTCTCTTC
1 CTTTTTCTCTCTTC
25255158 CTTTTT
1 CTTTTT
25255164 GATGTTAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
CTTTTTCTCTCTTC
Found at i:25263422 original size:27 final size:27
Alignment explanation
Indices: 25263392--25263482 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 27
25263382 TTTTTTTTTT
25263392 CAATTTGATACTTGAGTTTTTTTGTCC
1 CAATTTGATACTTGAGTTTTTTTGTCC
* * *
25263419 CAATTTAAGTACTTGAGTTTAGCTTTAATAT-T
1 CAATTTGA-TACTTGAGTTT---TTT--TGTCC
*
25263451 CAATTTGATACTTTAGTTTTTTTGTCC
1 CAATTTGATACTTGAGTTTTTTTGTCC
*
25263478 TAATT
1 CAATT
25263483 ACATACTTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
26 2 0.04
27 11 0.22
28 14 0.29
31 13 0.27
32 7 0.14
33 2 0.04
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (27 bp):
CAATTTGATACTTGAGTTTTTTTGTCC
Found at i:25264128 original size:31 final size:31
Alignment explanation
Indices: 25264078--25264139 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
25264068 ATTTGATCTG
* * * **
25264078 AATATCAAATTGAATATTAAAATTAAATTCA
1 AATACCAAATTAAACATTAAAACCAAATTCA
25264109 AATACCAAATTAAACATTAAAACCAAATTCA
1 AATACCAAATTAAACATTAAAACCAAATTCA
25264140 TGTAGCAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.29
Consensus pattern (31 bp):
AATACCAAATTAAACATTAAAACCAAATTCA
Found at i:25265020 original size:7 final size:7
Alignment explanation
Indices: 25265008--25265052 Score: 76
Period size: 7 Copynumber: 6.7 Consensus size: 7
25264998 CGATTTTAAG
25265008 TAAAAAA
1 TAAAAAA
25265015 TAAAAAA
1 TAAAAAA
25265022 TAAAAAA
1 TAAAAAA
25265029 TAAAAAA
1 TAAAAAA
25265036 T-AAAAA
1 TAAAAAA
25265042 T-AAAAA
1 TAAAAAA
25265048 TAAAA
1 TAAAA
25265053 TAAAAACAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 12 0.32
7 25 0.68
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:25265026 original size:6 final size:6
Alignment explanation
Indices: 25265010--25265058 Score: 64
Period size: 7 Copynumber: 7.8 Consensus size: 6
25265000 ATTTTAAGTA
25265010 AAAAAT AAAAAAT AAAAAAT AAAAAAT AAAAAT AAAAAT -AAAAT AAAAA
1 AAAAAT -AAAAAT -AAAAAT -AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
25265059 CAGTTATCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.12
6 16 0.39
7 20 0.49
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:25265404 original size:16 final size:17
Alignment explanation
Indices: 25265380--25265412 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
25265370 AAATATTTAA
25265380 AAAATAAAAACAAAAAC
1 AAAATAAAAACAAAAAC
*
25265397 AAAA-AAAAATAAAAAC
1 AAAATAAAAACAAAAAC
25265413 GTAGATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAATAAAAACAAAAAC
Found at i:25279023 original size:3 final size:3
Alignment explanation
Indices: 25279005--25279055 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
25278995 TCAAATATCC
* * * * *
25279005 TTA TTA TTT TTA -TA TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25279052 TTA T
1 TTA T
25279056 GTACTAGTGT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:25279185 original size:3 final size:3
Alignment explanation
Indices: 25279177--25279323 Score: 294
Period size: 3 Copynumber: 49.0 Consensus size: 3
25279167 TATTCCAATG
25279177 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25279225 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25279273 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25279321 TTA
1 TTA
25279324 GTTTATGCTT
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 144 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:25300223 original size:73 final size:73
Alignment explanation
Indices: 25300104--25300242 Score: 278
Period size: 73 Copynumber: 1.9 Consensus size: 73
25300094 CCAAACCACG
25300104 TAATAAATTAAAGGAACCACATAATCCTTGTGTCATTTTATTTACTCCTTTTTTGCACATTATTT
1 TAATAAATTAAAGGAACCACATAATCCTTGTGTCATTTTATTTACTCCTTTTTTGCACATTATTT
25300169 AAATACCA
66 AAATACCA
25300177 TAATAAATTAAAGGAACCACATAATCCTTGTGTCATTTTATTTACTCCTTTTTTGCACATTATTT
1 TAATAAATTAAAGGAACCACATAATCCTTGTGTCATTTTATTTACTCCTTTTTTGCACATTATTT
25300242 A
66 A
25300243 TTGTTAAGTG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.42
Consensus pattern (73 bp):
TAATAAATTAAAGGAACCACATAATCCTTGTGTCATTTTATTTACTCCTTTTTTGCACATTATTT
AAATACCA
Found at i:25300475 original size:27 final size:27
Alignment explanation
Indices: 25300437--25300518 Score: 164
Period size: 27 Copynumber: 3.0 Consensus size: 27
25300427 ACTTTCCAAT
25300437 ATTATAAACTACTAACATAATATATAA
1 ATTATAAACTACTAACATAATATATAA
25300464 ATTATAAACTACTAACATAATATATAA
1 ATTATAAACTACTAACATAATATATAA
25300491 ATTATAAACTACTAACATAATATATAA
1 ATTATAAACTACTAACATAATATATAA
25300518 A
1 A
25300519 CATAGTATTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (27 bp):
ATTATAAACTACTAACATAATATATAA
Found at i:25304386 original size:125 final size:126
Alignment explanation
Indices: 25304092--25304656 Score: 702
Period size: 125 Copynumber: 4.5 Consensus size: 126
25304082 GATAAAATCA
* * * * * * *
25304092 AAGCAGGATGATTTATCAGAAGGATTTTTGCAGTCGCGCCCACGTGTACGCGCTTTTGCT----T
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
25304153 AGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
66 AGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
** *
25304213 AAGCAGGATGCTACATGCGAAGAATTTGTGAAATCGCGCCCTAC-TGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCC-ACGTGGACGCGCTTTTGCTACAG
* ** *
25304277 TTGGTCCAAGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTC
65 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* *
25304338 TA-CTAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCTACAG
1 AAGC-AGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * *
25304402 TAGGTCCT-GAAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAAACACTTC
65 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT--AAAAAACGCTTC
* * ** *
25304465 AAGCAGGATGCTATT-TGAGAAGAATTTTTGAAATTGCGCCCTTGTGGACGCGCTTTTCCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * * * *
25304529 TTGGTCCTGGAAGAAATAATTTCGAGTAGATGTTTCTAAGCAAATAGTAT-AAAATCGCTTC
65 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * * * *
25304590 TACCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGTGCTTTTGTTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
25304655 AG
66 AG
25304657 CATGTTTGGG
Statistics
Matches: 378, Mismatches: 51, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
121 47 0.12
122 2 0.01
124 44 0.12
125 141 0.37
126 37 0.10
127 68 0.18
128 39 0.10
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (126 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
Found at i:25304607 original size:252 final size:250
Alignment explanation
Indices: 25304095--25304656 Score: 826
Period size: 252 Copynumber: 2.3 Consensus size: 250
25304085 AAAATCAAAG
* * * * * *
25304095 CAGGATGATTTATCAGAAGGATTTTTGCAGTCGCGCCCACGTGTACGCGCTTTTGCT----TAGG
1 CAGGATGATTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGG
* *
25304156 TCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGA
66 TCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACACTTCAAGCAGGA
* *
25304221 TGCTACATGCGAAGAATTTGTGAAATCGCGCCCTACTGGACGCGCTTTTGCTACAGTTGGTCCAA
131 TGCTACATGAGAAGAATTTGTGAAATCGCGCCCTACTGGACGCGCTTTTCCTACAGTTGGTCCAA
* *
25304286 GAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAC
196 GAAGAAATAATTTCGAGTAGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAC
* * *
25304341 TAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCTACAGTAGG
1 CAGGATGATTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGG
*
25304406 TCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAAACACTTCAAGCAG
66 TCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT--AAAAAACACTTCAAGCAG
** * * **
25304471 GATGCTATTTGAGAAGAATTTTTGAAATTGCGCCCTTGTGGACGCGCTTTTCCTACAGTTGGTCC
129 GATGCTACATGAGAAGAATTTGTGAAATCGCGCCCTACTGGACGCGCTTTTCCTACAGTTGGTCC
** *
25304536 TGGAAGAAATAATTTCGAGTAGATGTTTCTAAGCAAATAGTATAAAATCGCTTCTAC
194 AAGAAGAAATAATTTCGAGTAGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAC
* * *
25304593 CAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGTGCTTTTGTTACAGTAG
1 CAGGATGATTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
25304657 CATGTTTGGG
Statistics
Matches: 280, Mismatches: 30, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
246 48 0.17
250 47 0.17
252 185 0.66
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (250 bp):
CAGGATGATTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGG
TCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACACTTCAAGCAGGA
TGCTACATGAGAAGAATTTGTGAAATCGCGCCCTACTGGACGCGCTTTTCCTACAGTTGGTCCAA
GAAGAAATAATTTCGAGTAGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAC
Found at i:25307887 original size:15 final size:16
Alignment explanation
Indices: 25307862--25307894 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
25307852 GAAGTTAAGG
*
25307862 TTTTAAGGTTTAGTGT
1 TTTTAAGGTTTAGGGT
25307878 TTTTAA-GTTTAGGGT
1 TTTTAAGGTTTAGGGT
25307893 TT
1 TT
25307895 AGGATTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.58
Consensus pattern (16 bp):
TTTTAAGGTTTAGGGT
Found at i:25307888 original size:22 final size:22
Alignment explanation
Indices: 25307863--25307916 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
25307853 AAGTTAAGGT
*
25307863 TTTAAGGTTTAGTG-TTTTTAAG
1 TTTAGGGTTTAG-GATTTTTAAG
*
25307885 TTTAGGGTTTAGGATTTTTGAG
1 TTTAGGGTTTAGGATTTTTAAG
25307907 TTTAGGGTTT
1 TTTAGGGTTT
25307917 GTGGTTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.54
Consensus pattern (22 bp):
TTTAGGGTTTAGGATTTTTAAG
Found at i:25307916 original size:29 final size:29
Alignment explanation
Indices: 25307884--25307952 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
25307874 GTGTTTTTAA
* *
25307884 GTTTAGGGTTTAG-GATTTTTGAGTTTAGG
1 GTTTAGGGTTT-GTGATTTTTAAGTTAAGG
*
25307913 GTTT-GTGGTTTGTGGTTTTTAAGTTAAGG
1 GTTTAG-GGTTTGTGATTTTTAAGTTAAGG
*
25307942 GTTTAAGGTTT
1 GTTTAGGGTTT
25307953 TTAGGTTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
28 2 0.06
29 31 0.94
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (29 bp):
GTTTAGGGTTTGTGATTTTTAAGTTAAGG
Found at i:25307932 original size:51 final size:51
Alignment explanation
Indices: 25307868--25308104 Score: 157
Period size: 43 Copynumber: 5.1 Consensus size: 51
25307858 AAGGTTTTAA
*
25307868 GGTTTAGTGTTTTTAAGTTTAGGGTTT-AGGATTTTT-GAGTTTAGGGTTTGT
1 GGTTTAGTGTTTTTAAGTTAAGGGTTTAAGG-TTTTTAG-GTTTAGGGTTTGT
25307919 GGTTT-GTGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAGGG-TT-T
1 GGTTTAGT-GTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAGGGTTTGT
* * * *
25307968 -G--TA--ATTTTTAAGTTTAGGGTTT-AGGGTTTTAGGTTTAGAG-TT-T
1 GGTTTAGTGTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAGGGTTTGT
* * * *
25308011 -G--T-G-GTTTTTAATTTAAGGTTTTAAGGTTTTTAGGTTTAGAG-AT-T
1 GGTTTAGTGTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAGGGTTTGT
* * *
25308055 -G--T-G-GTTTTTAAGTTAAGGG-TTAGGGTTTTTAGGTTTAGGTTTTAT
1 GGTTTAGTGTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAGGGTTTGT
25308100 GGTTT
1 GGTTT
25308105 TTAAGTTTAG
Statistics
Matches: 158, Mismatches: 17, Indels: 25
0.79 0.09 0.12
Matches are distributed among these distances:
43 54 0.34
44 54 0.34
45 1 0.01
46 2 0.01
48 2 0.01
49 1 0.01
50 4 0.03
51 36 0.23
52 4 0.03
ACGTcount: A:0.18, C:0.00, G:0.30, T:0.52
Consensus pattern (51 bp):
GGTTTAGTGTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAGGGTTTGT
Found at i:25307944 original size:22 final size:22
Alignment explanation
Indices: 25307919--25308119 Score: 187
Period size: 22 Copynumber: 9.2 Consensus size: 22
25307909 TAGGGTTTGT
*
25307919 GGTTTGTGGTTTTTAAGTTAAG
1 GGTTTGTGGTTTTTAAGTTTAG
** *
25307941 GGTTTAAGGTTTTTAGGTTTAG
1 GGTTTGTGGTTTTTAAGTTTAG
**
25307963 GGTTTGTAATTTTTAAGTTTAG
1 GGTTTGTGGTTTTTAAGTTTAG
*
25307985 GGTTTAG-GG-TTTTAGGTTTAG
1 GGTTT-GTGGTTTTTAAGTTTAG
* *
25308006 AGTTTGTGGTTTTTAA-TTTAA
1 GGTTTGTGGTTTTTAAGTTTAG
*
25308027 GGTTT-TAAGGTTTTTAGGTTTAG
1 GGTTTGT--GGTTTTTAAGTTTAG
* * *
25308050 AGATTGTGGTTTTTAAGTTAAG
1 GGTTTGTGGTTTTTAAGTTTAG
* *
25308072 GGTTAG-GGTTTTTAGGTTTAG
1 GGTTTGTGGTTTTTAAGTTTAG
* *
25308093 GTTTTATGGTTTTTAAGTTTAG
1 GGTTTGTGGTTTTTAAGTTTAG
25308115 GGTTT
1 GGTTT
25308120 AGGGTTAGGG
Statistics
Matches: 139, Mismatches: 32, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
20 2 0.01
21 41 0.29
22 87 0.63
23 8 0.06
24 1 0.01
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (22 bp):
GGTTTGTGGTTTTTAAGTTTAG
Found at i:25307976 original size:44 final size:44
Alignment explanation
Indices: 25307919--25308125 Score: 274
Period size: 43 Copynumber: 4.8 Consensus size: 44
25307909 TAGGGTTTGT
25307919 GGTTTGTGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAG
1 GGTTTGTGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAG
** * *
25307963 GGTTTGTAATTTTTAAGTTTAGGGTTT-AGGGTTTTAGGTTTAG
1 GGTTTGTGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAG
* * *
25308006 AGTTTGTGGTTTTTAATTTAAGGTTTTAAGGTTTTTAGGTTTAG
1 GGTTTGTGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAG
* * *
25308050 AGATTGTGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAGGTTTAG
1 GGTTTGTGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAG
* * * *
25308093 GTTTTATGGTTTTTAAGTTTAGGGTTTAGGGTT
1 GGTTTGTGGTTTTTAAGTTAAGGGTTTAAGGTT
25308126 AGGGTTTTTT
Statistics
Matches: 141, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
43 73 0.52
44 68 0.48
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (44 bp):
GGTTTGTGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAG
Found at i:25308034 original size:87 final size:86
Alignment explanation
Indices: 25307919--25308119 Score: 278
Period size: 87 Copynumber: 2.3 Consensus size: 86
25307909 TAGGGTTTGT
* * * * *
25307919 GGTTTGTGGTTTTTAAGTTAAGGGTTTAAGGTTTTTAGGTTTAGGGTTTGTAATTTTTAAGTTTA
1 GGTTTGTGGTTTTTAATTTAAGGTTTTAAGGTTTTTAGGTTTAGAGATTGTAATTTTTAAGTTAA
25307984 GGGTTTAGGG-TTTTAGGTTTA
66 GGG-TTAGGGTTTTTAGGTTTA
**
25308005 GAGTTTGTGGTTTTTAATTTAAGGTTTTAAGGTTTTTAGGTTTAGAGATTGTGGTTTTTAAGTTA
1 G-GTTTGTGGTTTTTAATTTAAGGTTTTAAGGTTTTTAGGTTTAGAGATTGTAATTTTTAAGTTA
25308070 AGGGTTAGGGTTTTTAGGTTTA
65 AGGGTTAGGGTTTTTAGGTTTA
* *
25308092 GGTTTTATGGTTTTTAAGTTTAGGGTTT
1 GG-TTTGTGGTTTTTAA-TTTAAGGTTT
25308120 AGGGTTAGGG
Statistics
Matches: 102, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
86 8 0.08
87 85 0.83
88 9 0.09
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (86 bp):
GGTTTGTGGTTTTTAATTTAAGGTTTTAAGGTTTTTAGGTTTAGAGATTGTAATTTTTAAGTTAA
GGGTTAGGGTTTTTAGGTTTA
Found at i:25308118 original size:29 final size:30
Alignment explanation
Indices: 25308082--25308156 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 30
25308072 GGTTAGGGTT
*
25308082 TTTA-GGTTTAGGTTTTATGG-TTTTTAAG
1 TTTAGGGTTTAGGTTTTAGGGTTTTTTAAG
*
25308110 TTTAGGGTTTAGG-GTTAGGGTTTTTTAAG
1 TTTAGGGTTTAGGTTTTAGGGTTTTTTAAG
*
25308139 TTTAGAGTTTAGAGTTTT
1 TTTAGGGTTTAG-GTTTT
25308157 TATGTTAAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 9 0.23
29 27 0.69
30 1 0.03
31 2 0.05
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (30 bp):
TTTAGGGTTTAGGTTTTAGGGTTTTTTAAG
Found at i:25308141 original size:22 final size:21
Alignment explanation
Indices: 25308116--25308170 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
25308106 TAAGTTTAGG
*
25308116 GTTTAGGGTTAGGGTTTTTTAA
1 GTTTAGGGTTAGAG-TTTTTAA
* *
25308138 GTTTAGAGTTTAGAGTTTTTAT
1 GTTTAG-GGTTAGAGTTTTTAA
*
25308160 GTTAAGGGTTA
1 GTTTAGGGTTA
25308171 TGATTAGGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 4 0.15
22 17 0.63
23 6 0.22
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (21 bp):
GTTTAGGGTTAGAGTTTTTAA
Found at i:25311440 original size:26 final size:26
Alignment explanation
Indices: 25311407--25311464 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
25311397 ATATCAAAAT
*
25311407 TTATAGAGACCAATTTAAAATCTTGA
1 TTATAGAGACCAATTTAAAATCTAGA
*
25311433 TTATAGAGACCAATTTAATATCTAGA
1 TTATAGAGACCAATTTAAAATCTAGA
25311459 TTATAG
1 TTATAG
25311465 TTTGAGGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.36
Consensus pattern (26 bp):
TTATAGAGACCAATTTAAAATCTAGA
Found at i:25314265 original size:11 final size:12
Alignment explanation
Indices: 25314249--25314292 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
25314239 ATTAAATATG
25314249 AATTTGAGA-GA
1 AATTTGAGAGGA
25314260 AATTTG-GAAGGA
1 AATTTGAG-AGGA
25314272 AA-TTGAGAGGA
1 AATTTGAGAGGA
25314283 AATTTGAGAG
1 AATTTGAGAG
25314293 CGGATTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 16 0.55
12 12 0.41
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (12 bp):
AATTTGAGAGGA
Found at i:25315341 original size:102 final size:101
Alignment explanation
Indices: 25315126--25315352 Score: 285
Period size: 102 Copynumber: 2.2 Consensus size: 101
25315116 ATACAGTCAT
* * *
25315126 ATGATGTCATAGAGTCTTTCATTTATGGTCTTACTCACTATACCTGGCTGCCATAGCATCTTTCA
1 ATGATGTCAT-GAGTCTTTCATCTATGGCCTTACTCACTATACCTGGCTGCCATAACATCTTTCA
* *
25315191 TCTATGGTCTTATACCTTATATCTTATACATTGTACT
65 TCTATGGTCTTATACCTTATATCTTATACATTATACC
* * * * * ** *
25315228 AAGCTGCCATGACGTCTTTCATCTATGGCCTTATTCACTATACTTGGCTGTTATAACATCTTTTA
1 ATGATGTCATGA-GTCTTTCATCTATGGCCTTACTCACTATACCTGGCTGCCATAACATCTTTCA
*
25315293 TCTATGGTCTTATA-CTGTATATCTTATACCTTATACC
65 TCTATGGTCTTATACCT-TATATCTTATACATTATACC
25315330 ATGATGTCATGATGTCTTTCATC
1 ATGATGTCATGA-GTCTTTCATC
25315353 CATAGTCTTA
Statistics
Matches: 105, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
101 4 0.04
102 101 0.96
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (101 bp):
ATGATGTCATGAGTCTTTCATCTATGGCCTTACTCACTATACCTGGCTGCCATAACATCTTTCAT
CTATGGTCTTATACCTTATATCTTATACATTATACC
Found at i:25315578 original size:57 final size:56
Alignment explanation
Indices: 25315507--25315652 Score: 150
Period size: 57 Copynumber: 2.6 Consensus size: 56
25315497 AGTTAGGCAA
** * *
25315507 AAAAAAATTTAGGCCCAAATGTGGTAACAATTGCCAAGTGCAAGTG-CTAACTTGGAC
1 AAAAAAATCCAGGCCC-AATGTGGAAACAATTGCCAAGTGCAAG-GACTAACTTAGAC
* * * *
25315564 AAAAAAGTCCAGGCCCTAATTTGCAAACAATTGCCAAGTTCAAGGACTAACTTAGAC
1 AAAAAAATCCAGGCCC-AATGTGGAAACAATTGCCAAGTGCAAGGACTAACTTAGAC
* * *
25315621 AAAAAAATTCAAGCACCAATGTGGGAACAATT
1 AAAAAAATCCAGGC-CCAATGTGGAAACAATT
25315653 ATTAAGTTCA
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
56 1 0.01
57 69 0.96
58 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (56 bp):
AAAAAAATCCAGGCCCAATGTGGAAACAATTGCCAAGTGCAAGGACTAACTTAGAC
Found at i:25331234 original size:24 final size:24
Alignment explanation
Indices: 25331180--25331284 Score: 77
Period size: 25 Copynumber: 4.3 Consensus size: 24
25331170 TTGCTCTCCG
*
25331180 GAGCTTCCCGATATTGGCTCGCTT
1 GAGCTTCCCGATATTGGCTCGCAT
* * *
25331204 GAACTTCCCGAT-TATGGCTTGGAT
1 GAGCTTCCCGATAT-TGGCTCGCAT
* * *
25331228 GAGCTTCCCGTTACATGGCTCACAT
1 GAGCTTCCCGATA-TTGGCTCGCAT
* * * *
25331253 GAGCTTCTCGTTATATGGCTCGAAA
1 GAGCTTCCCGATAT-TGGCTCGCAT
25331278 GAGCTTC
1 GAGCTTC
25331285 TCGTTTACAT
Statistics
Matches: 62, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
23 1 0.02
24 28 0.45
25 33 0.53
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (24 bp):
GAGCTTCCCGATATTGGCTCGCAT
Found at i:25331254 original size:25 final size:25
Alignment explanation
Indices: 25331217--25331295 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 25
25331207 CTTCCCGATT
* * *
25331217 ATGGCTTGGATGAGCTTCCCGTTAC
1 ATGGCTCGAATGAGCTTCTCGTTAC
*
25331242 ATGGCTC-ACATGAGCTTCTCGTTAT
1 ATGGCTCGA-ATGAGCTTCTCGTTAC
*
25331267 ATGGCTCGAAAGAGCTTCTCGTTTAC
1 ATGGCTCGAATGAGCTTCTCG-TTAC
25331293 ATG
1 ATG
25331296 TTTGCATGAG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
25 38 0.84
26 7 0.16
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (25 bp):
ATGGCTCGAATGAGCTTCTCGTTAC
Found at i:25348002 original size:22 final size:22
Alignment explanation
Indices: 25347974--25348029 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
25347964 CCAAAAGGAA
25347974 AAAAGGAAGAAGA-AAATAAAAT
1 AAAAGGAAGAAGATAAAT-AAAT
*
25347996 AAAAGGAAGAAAATAAATAAAT
1 AAAAGGAAGAAGATAAATAAAT
25348018 AAAAGGAAGAAG
1 AAAAGGAAGAAG
25348030 GAAAGAAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (22 bp):
AAAAGGAAGAAGATAAATAAAT
Found at i:25348140 original size:41 final size:41
Alignment explanation
Indices: 25348093--25348176 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
25348083 GGAGAAATGA
25348093 AAAAATAATATTCCTCAATGCACACGTAGAGATTCGAACAT
1 AAAAATAATATTCCTCAATGCACACGTAGAGATTCGAACAT
*
25348134 AAAAATAATATTCCTCAATGCACATGTAGAGATTCGAACAT
1 AAAAATAATATTCCTCAATGCACACGTAGAGATTCGAACAT
25348175 AA
1 AA
25348177 GACCACTGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (41 bp):
AAAAATAATATTCCTCAATGCACACGTAGAGATTCGAACAT
Found at i:25349030 original size:21 final size:21
Alignment explanation
Indices: 25348999--25349048 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
25348989 ATAGGCCGTG
*
25348999 TGGAATGGGTTACACGACCATA
1 TGGAA-GGGTTACAAGACCATA
*
25349021 TGGAAGGGTTACAAGACCATG
1 TGGAAGGGTTACAAGACCATA
25349042 TGGAAGG
1 TGGAAGG
25349049 TTTTTGGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.32, C:0.14, G:0.34, T:0.20
Consensus pattern (21 bp):
TGGAAGGGTTACAAGACCATA
Found at i:25354643 original size:140 final size:140
Alignment explanation
Indices: 25354398--25354656 Score: 330
Period size: 140 Copynumber: 1.9 Consensus size: 140
25354388 TTTTGATTTT
** *
25354398 TGAACTTGAAAATTGTTATTTATTTAACTACATTTCGTCAATGACAGTGGAAAAAATGGGAATAA
1 TGAACTTGAAAATTGTTATCCATTTAACTACATTTCGTCAATGACAGTGAAAAAAATGGGAATAA
* *
25354463 TGTAACTTTTAGCCCCTGAACTTGACAATTTAATCTACATT-GCCTCTTGAACTTTTTTTTATCC
66 TGTAACTTTTAGCCCCTGAACTTGACAATGTAATCCACATTGGCCTC-TGAACTTTTTTTTATCC
25354527 ACTTTTACCCC
130 ACTTTTACCCC
* *
25354538 TGAACTTGAAAATTGTTATCCATTTAAGCT-CA-TTCTGTTAATGACCGTGAAAAAAATAGGG-A
1 TGAACTTGAAAATTGTTATCCATTTAA-CTACATTTC-GTCAATGACAGTGAAAAAAAT-GGGAA
* ** **
25354600 TAATGTAACTTTTGGCCTTTGAACTTGGTAA-GTAGATCCACATTGGCCTCTGAACTT
63 TAATGTAACTTTTAGCCCCTGAACTTGACAATGTA-ATCCACATTGGCCTCTGAACTT
25354657 GACAACTAGG
Statistics
Matches: 102, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
139 5 0.05
140 87 0.85
141 10 0.10
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (140 bp):
TGAACTTGAAAATTGTTATCCATTTAACTACATTTCGTCAATGACAGTGAAAAAAATGGGAATAA
TGTAACTTTTAGCCCCTGAACTTGACAATGTAATCCACATTGGCCTCTGAACTTTTTTTTATCCA
CTTTTACCCC
Found at i:25355549 original size:18 final size:17
Alignment explanation
Indices: 25355526--25355562 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
25355516 CATTATTATA
25355526 ATAGTTAATACATAACAT
1 ATAGTTAATACA-AACAT
*
25355544 ATAGTTAATATAAACAT
1 ATAGTTAATACAAACAT
25355561 AT
1 AT
25355563 TATATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (17 bp):
ATAGTTAATACAAACAT
Found at i:25378778 original size:24 final size:24
Alignment explanation
Indices: 25378715--25378766 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
25378705 TTTCTAGAAG
* * *
25378715 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
25378739 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
25378763 ATTT
1 ATTT
25378767 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:25379527 original size:24 final size:24
Alignment explanation
Indices: 25379464--25379515 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
25379454 TTTCCAGAAG
* * *
25379464 ATTTAGTATTTATAAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
25379488 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
25379512 ATTT
1 ATTT
25379516 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:25379994 original size:29 final size:27
Alignment explanation
Indices: 25379941--25379994 Score: 63
Period size: 29 Copynumber: 1.9 Consensus size: 27
25379931 TTTAACATTT
*
25379941 ATATTTTTTGTCAATTTGGTCATTATG
1 ATATTTTTTGTCAATTTGATCATTATG
* *
25379968 ATATTTTTTAGTTTAATTTGATTATTA
1 ATATTTTTT-G-TCAATTTGATCATTA
25379995 GTCTTTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 9 0.41
28 1 0.05
29 12 0.55
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.59
Consensus pattern (27 bp):
ATATTTTTTGTCAATTTGATCATTATG
Found at i:25380200 original size:24 final size:23
Alignment explanation
Indices: 25380173--25380217 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
25380163 AAGATGTTCC
25380173 GAAAAATAAAAATAAACTCAAACT
1 GAAAAATAAAAA-AAACTCAAACT
* *
25380197 GAAAAATATAAAAAATTCAAA
1 GAAAAATAAAAAAAACTCAAA
25380218 AAATTGGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.69, C:0.09, G:0.04, T:0.18
Consensus pattern (23 bp):
GAAAAATAAAAAAAACTCAAACT
Found at i:25381401 original size:31 final size:31
Alignment explanation
Indices: 25381366--25381446 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
25381356 GATTGTTTTG
*
25381366 AAAGTTTTCATTTAAGTCATTAAATTATTCA
1 AAAGTTTTCATTTAAGTCATTAAACTATTCA
* * *
25381397 AAAGTTTTCATTTGAGTCATTGAACTATTCG
1 AAAGTTTTCATTTAAGTCATTAAACTATTCA
*
25381428 AAAGTTTTTATTTAAGTCA
1 AAAGTTTTCATTTAAGTCA
25381447 CTCGGTTGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (31 bp):
AAAGTTTTCATTTAAGTCATTAAACTATTCA
Found at i:25384064 original size:30 final size:32
Alignment explanation
Indices: 25384030--25384088 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
25384020 TTTTGAATTC
25384030 GATTTT-ATTTAAAATAT-ATTT-TTCGATCTT
1 GATTTTAATTTAAAAT-TGATTTCTTCGATCTT
*
25384060 GATTTTAATTTTAAATTGATTTCTTCGAT
1 GATTTTAATTTAAAATTGATTTCTTCGAT
25384089 TTTACCTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 7 0.28
31 12 0.48
32 6 0.24
ACGTcount: A:0.29, C:0.07, G:0.08, T:0.56
Consensus pattern (32 bp):
GATTTTAATTTAAAATTGATTTCTTCGATCTT
Found at i:25384971 original size:18 final size:18
Alignment explanation
Indices: 25384933--25384968 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
25384923 AAAATTTGTT
25384933 ATAATTATAAATTTAACA
1 ATAATTATAAATTTAACA
25384951 ATAATTAT-AATTTAACA
1 ATAATTATAAATTTAACA
25384968 A
1 A
25384969 ATATTGTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATTATAAATTTAACA
Found at i:25385006 original size:47 final size:43
Alignment explanation
Indices: 25384924--25385012 Score: 115
Period size: 47 Copynumber: 2.0 Consensus size: 43
25384914 ACATAAAATA
* *
25384924 AAATTTGTTATAATTATAAATTTAACAATAATTATAATTTAAC
1 AAATTTGTGATAATTATAAATTTAAAAATAATTATAATTTAAC
*
25384967 AAATATTGTGATAATTATTACATATTTAAAAATACTTATAATTTAA
1 AAAT-TTGTGATAATTA-TA-A-ATTTAAAAATAATTATAATTTAA
25385013 TTACATTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
43 4 0.10
44 11 0.28
45 2 0.05
46 1 0.03
47 21 0.54
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.44
Consensus pattern (43 bp):
AAATTTGTGATAATTATAAATTTAAAAATAATTATAATTTAAC
Found at i:25385238 original size:1 final size:1
Alignment explanation
Indices: 25385234--25385276 Score: 77
Period size: 1 Copynumber: 43.0 Consensus size: 1
25385224 CCCCCCCCCC
*
25385234 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25385277 CAGATATCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.98, C:0.00, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:25387459 original size:2 final size:2
Alignment explanation
Indices: 25387454--25387490 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
25387444 TATATATATA
*
25387454 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
25387491 ATATATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:25393776 original size:88 final size:88
Alignment explanation
Indices: 25393627--25393972 Score: 683
Period size: 88 Copynumber: 3.9 Consensus size: 88
25393617 AGGTATCTTT
*
25393627 CCTTGTTTTTGGGGGTTTATTTCTGGAGCATTCTAATAATTTCCAAATTAGCTGGAAAATCTCAC
1 CCTTGTTTTTGGGGGTTTATTTCAGGAGCATTCTAATAATTTCCAAATTAGCTGGAAAATCTCAC
25393692 AATTTGAGTCTAATGGGGTTTTC
66 AATTTGAGTCTAATGGGGTTTTC
25393715 CCTTGTTTTTGGGGGTTTATTTCAGGAGCATTCTAATAATTTCCAAATTAGCTGGAAAATCTCAC
1 CCTTGTTTTTGGGGGTTTATTTCAGGAGCATTCTAATAATTTCCAAATTAGCTGGAAAATCTCAC
25393780 AATTTGAGTCTAATGGGGTTTTC
66 AATTTGAGTCTAATGGGGTTTTC
25393803 CCTTGTTTTTGGGGGTTTATTTCAGGAGCATTCTAATAATTTCCAAATTAGCTGGAAAATCTCAC
1 CCTTGTTTTTGGGGGTTTATTTCAGGAGCATTCTAATAATTTCCAAATTAGCTGGAAAATCTCAC
25393868 AATTTGAGTCTAATGGGGTTTTC
66 AATTTGAGTCTAATGGGGTTTTC
25393891 CCTTGTTTTTGGGGGTTTATTTCAGGAGCATTCTAATAATTTCCAAATTAGCTGGAAAATCTCAC
1 CCTTGTTTTTGGGGGTTTATTTCAGGAGCATTCTAATAATTTCCAAATTAGCTGGAAAATCTCAC
25393956 AATTTGAGTCTAATGGG
66 AATTTGAGTCTAATGGG
25393973 TTTCTTCTAG
Statistics
Matches: 257, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 257 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (88 bp):
CCTTGTTTTTGGGGGTTTATTTCAGGAGCATTCTAATAATTTCCAAATTAGCTGGAAAATCTCAC
AATTTGAGTCTAATGGGGTTTTC
Found at i:25397228 original size:29 final size:29
Alignment explanation
Indices: 25397174--25397231 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
25397164 TGAAATGTAA
25397174 TCTCTCTACTTTTATTTCCAAGAATTTAG
1 TCTCTCTACTTTTATTTCCAAGAATTTAG
25397203 TCTCTCTACTTTCATATTT-CAA-AATTTAG
1 TCTCTCTACTTT--TATTTCCAAGAATTTAG
25397232 GTCCAATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 19 0.70
30 3 0.11
31 5 0.19
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (29 bp):
TCTCTCTACTTTTATTTCCAAGAATTTAG
Found at i:25401099 original size:12 final size:12
Alignment explanation
Indices: 25401079--25401109 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
25401069 CCATTTATGA
*
25401079 CAACTGAATAAG
1 CAACAGAATAAG
25401091 CAACAGAATAAG
1 CAACAGAATAAG
25401103 CAACAGA
1 CAACAGA
25401110 TGACACATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.55, C:0.19, G:0.16, T:0.10
Consensus pattern (12 bp):
CAACAGAATAAG
Found at i:25410862 original size:26 final size:24
Alignment explanation
Indices: 25410807--25410862 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
25410797 TTCAGTTGGT
* *
25410807 TTATTAATGATATGTATTAATATG
1 TTATTAATGATATATATTAAAATG
*
25410831 AT-TTAATGATTATATATTTAAAATG
1 TTATTAATGA-TATATA-TTAAAATG
25410856 TTATTAA
1 TTATTAA
25410863 CAGGGCTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 7 0.28
24 6 0.24
25 8 0.32
26 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (24 bp):
TTATTAATGATATATATTAAAATG
Found at i:25414425 original size:22 final size:21
Alignment explanation
Indices: 25414380--25414425 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
25414370 TTTAATTTTC
* *
25414380 ATATAATATAAATTACATGAT
1 ATATAAAATAAATAACATGAT
*
25414401 ATATAAAATAAATAAACATGTT
1 ATATAAAATAAAT-AACATGAT
25414423 ATA
1 ATA
25414426 AACTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (21 bp):
ATATAAAATAAATAACATGAT
Found at i:25418675 original size:30 final size:30
Alignment explanation
Indices: 25418619--25418677 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
25418609 GACTCATCCA
*
25418619 TAGAAAATAAAATAAAGAAAAGGATGATAT
1 TAGAAAATAAAAAAAAGAAAAGGATGATAT
* *
25418649 TAGAAAGTGAAAAAAAATAAAA-GATGATA
1 TAGAAAAT-AAAAAAAAGAAAAGGATGATA
25418678 ATTAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (30 bp):
TAGAAAATAAAAAAAAGAAAAGGATGATAT
Found at i:25420125 original size:27 final size:25
Alignment explanation
Indices: 25420090--25420160 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 25
25420080 AAACTTAAAA
25420090 TATATATTATAATATTATAATATTATAT
1 TATA-ATTATAATA-TAT-ATATTATAT
25420118 CT-TAATTATTAAGTATATATATTATAT
1 -TATAATTA-TAA-TATATATATTATAT
25420145 TATAATTATAAT-TATA
1 TATAATTATAATATATA
25420161 AAATAAAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
24 4 0.10
25 1 0.03
26 4 0.10
27 19 0.49
28 8 0.21
29 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (25 bp):
TATAATTATAATATATATATTATAT
Found at i:25420183 original size:4 final size:4
Alignment explanation
Indices: 25420176--25420258 Score: 50
Period size: 4 Copynumber: 20.5 Consensus size: 4
25420166 AAGAATAAAT
* *
25420176 AGAA AGAA AGAA AGAT AGAA ACGAAA CAGAA AG-A A-AA AGAA AGAA ATAA
1 AGAA AGAA AGAA AGAA AGAA A-G-AA -AGAA AGAA AGAA AGAA AGAA AGAA
*
25420225 ATGAAA CAGAA AG-A A-AA AGAA A-AA GGAA AGAA AG
1 A-G-AA -AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
25420259 GAAGGAGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
3 10 0.16
4 39 0.63
5 5 0.08
6 6 0.10
7 2 0.03
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.04
Consensus pattern (4 bp):
AGAA
Found at i:25420219 original size:29 final size:29
Alignment explanation
Indices: 25420182--25420246 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
25420172 AAATAGAAAG
*
25420182 AAAGAAAGATAGAAACGAAACAGAAAGAA
1 AAAGAAAGAAAGAAACGAAACAGAAAGAA
* *
25420211 AAAGAAAGAAATAAATGAAACAGAAAGAA
1 AAAGAAAGAAAGAAACGAAACAGAAAGAA
25420240 AAAGAAA
1 AAAGAAA
25420247 AAGGAAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.72, C:0.05, G:0.18, T:0.05
Consensus pattern (29 bp):
AAAGAAAGAAAGAAACGAAACAGAAAGAA
Found at i:25421264 original size:40 final size:40
Alignment explanation
Indices: 25421135--25421273 Score: 151
Period size: 40 Copynumber: 3.5 Consensus size: 40
25421125 GACTTCGAGT
* * *
25421135 CGATGAGACACTGGGTGTCAAATTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATT-ATA
* * *
25421176 CGATGAGGCACTGAGTGTC-AA-T-TTACTTCGATTTA-A
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATA
* *
25421212 CAATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATA
* *
25421252 CGATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
25421274 CTGGTGTGTT
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
36 16 0.20
37 3 0.04
38 10 0.12
39 13 0.16
40 21 0.26
41 17 0.21
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATA
Found at i:25422478 original size:26 final size:26
Alignment explanation
Indices: 25422449--25422603 Score: 96
Period size: 26 Copynumber: 6.2 Consensus size: 26
25422439 TATCCGGAAC
*
25422449 TCCTGATTAAAGGCTCTTCGTGAGCT
1 TCCTGATTAAAGGCTCTTTGTGAGCT
* * *
25422475 TCCT-AGTTAAAAGTTCTTTGTGAACT
1 TCCTGA-TTAAAGGCTCTTTGTGAGCT
* *
25422501 TCCTGATT-ATGGCTC-TTATGAGCT
1 TCCTGATTAAAGGCTCTTTGTGAGCT
** *
25422525 TCCT-ATTATATA-GC-C-CAGATAAGCT
1 TCCTGATTA-A-AGGCTCTTTG-TGAGCT
25422550 TCCTGA-T-AA-GCTCTTTGTGAGCT
1 TCCTGATTAAAGGCTCTTTGTGAGCT
* * *
25422573 TCCCGATTAATGGTTCTTTGTGAGCT
1 TCCTGATTAAAGGCTCTTTGTGAGCT
25422599 TCCTG
1 TCCTG
25422604 TTATATGGCT
Statistics
Matches: 96, Mismatches: 21, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
22 3 0.03
23 15 0.16
24 14 0.15
25 19 0.20
26 44 0.46
27 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (26 bp):
TCCTGATTAAAGGCTCTTTGTGAGCT
Found at i:25425758 original size:23 final size:22
Alignment explanation
Indices: 25425713--25425759 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
25425703 CAAAAATATA
*
25425713 TTAAATATATATATTTTTATTT
1 TTAAATATATATAGTTTTATTT
*
25425735 TTAAA-ATATACTAGTTTTAGTT
1 TTAAATATATA-TAGTTTTATTT
25425757 TTA
1 TTA
25425760 TTTTAAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (22 bp):
TTAAATATATATAGTTTTATTT
Found at i:25425922 original size:83 final size:86
Alignment explanation
Indices: 25425806--25425974 Score: 290
Period size: 83 Copynumber: 2.0 Consensus size: 86
25425796 TTAATACAAT
25425806 TAACAATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATA
1 TAACAATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATA
25425871 ATTTTACTAACAAAATGTTAG
66 ATTTTACTAACAAAATGTTAG
* * *
25425892 TAACAATTAATAA-TT-A-ATAATTTGATAATTTTAGTAACAATTAATATAATTAATAATTAATA
1 TAACAATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATA
25425954 ATTTTACTAACAAAATGTTAG
66 ATTTTACTAACAAAATGTTAG
25425975 ATTTTATAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
83 64 0.80
84 1 0.01
85 2 0.03
86 13 0.16
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (86 bp):
TAACAATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATA
ATTTTACTAACAAAATGTTAG
Found at i:25425931 original size:34 final size:35
Alignment explanation
Indices: 25425888--25425966 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
25425878 TAACAAAATG
*
25425888 TTAGTAACAATT-A-ATAATTAATAATTTGATAATT
1 TTAGTAACAATTAATATAATTAATAA-TTAATAATT
25425922 TTAGTAACAATTAATATAATTAATAATTAATAATT
1 TTAGTAACAATTAATATAATTAATAATTAATAATT
*
25425957 TTACTAACAA
1 TTAGTAACAA
25425967 AATGTTAGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
34 12 0.29
35 18 0.44
36 11 0.27
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (35 bp):
TTAGTAACAATTAATATAATTAATAATTAATAATT
Found at i:25425983 original size:43 final size:42
Alignment explanation
Indices: 25425856--25425983 Score: 108
Period size: 35 Copynumber: 3.0 Consensus size: 42
25425846 CAATTAATAC
* *
25425856 AATTAACAATTAATAATTTTACTAACAAAATGTTAGTAACAATTAAT
1 AATTAATAATTAATAATTTTACTAACAAAATGTTAG-----ATTTAT
* *
25425903 AATTAATAATTTGATAATTTTAGTAAC--AA--TTA-A--TAT
1 AATTAATAA-TTAATAATTTTACTAACAAAATGTTAGATTTAT
25425939 AATTAATAATTAATAATTTTACTAACAAAATGTTAGATTTTAT
1 AATTAATAATTAATAATTTTACTAACAAAATGTTAGA-TTTAT
25425982 AA
1 AA
25425984 AATGTTGACT
Statistics
Matches: 66, Mismatches: 6, Indels: 22
0.70 0.06 0.23
Matches are distributed among these distances:
35 15 0.23
36 11 0.17
37 2 0.03
38 1 0.02
39 3 0.05
40 1 0.02
43 5 0.08
44 3 0.05
46 2 0.03
47 8 0.12
48 15 0.23
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (42 bp):
AATTAATAATTAATAATTTTACTAACAAAATGTTAGATTTAT
Found at i:25426038 original size:16 final size:16
Alignment explanation
Indices: 25426019--25426059 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
25426009 AATTTGATAC
25426019 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
25426035 AATTTTGATAACAATT
1 AATTTTAATAACAATT
*
25426051 AGTTTTAAT
1 AATTTTAAT
25426060 TTTAATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:25431265 original size:22 final size:22
Alignment explanation
Indices: 25431237--25431300 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
25431227 AATTCAAAAT
25431237 TTATATTTATCAAATAATTTAA
1 TTATATTTATCAAATAATTTAA
** * *
25431259 TTATATTCCTTAATTAATTTTAA
1 TTATATTTATCAAATAA-TTTAA
* *
25431282 ATA-ATATATCAAATAATTT
1 TTATATTTATCAAATAATTT
25431301 TATAATTTAA
Statistics
Matches: 31, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
21 3 0.10
22 21 0.68
23 7 0.23
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (22 bp):
TTATATTTATCAAATAATTTAA
Found at i:25431643 original size:19 final size:19
Alignment explanation
Indices: 25431603--25431720 Score: 80
Period size: 19 Copynumber: 6.1 Consensus size: 19
25431593 TCTCTCAACA
*
25431603 AAAAATTTAAAATAAATT-T
1 AAAAATTTAAAAT-ATTTAT
*
25431622 AAAATTTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
* * * *
25431641 AAAAATTT-CAATCTCTCAACA
1 AAAAATTTAAAATAT-T-TA-T
*
25431662 AAAAATTTAAAATAAATT-T
1 AAAAATTTAAAAT-ATTTAT
*
25431681 AAAATTTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
*
25431700 AAAAATTTCAAAATTTTTAT
1 AAAAATTT-AAAATATTTAT
25431720 A
1 A
25431721 TTTTTAAAAA
Statistics
Matches: 75, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
18 10 0.13
19 41 0.55
20 12 0.16
21 8 0.11
22 4 0.05
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:25431647 original size:20 final size:20
Alignment explanation
Indices: 25431622--25431720 Score: 76
Period size: 20 Copynumber: 5.0 Consensus size: 20
25431612 AAATAAATTT
25431622 AAAATTTTAAAATATTTATA
1 AAAATTTTAAAATATTTATA
* ** * ** *
25431642 AAAATTTCAATCTCTCAACA
1 AAAATTTTAAAATATTTATA
* *
25431662 AAAAATTTAAAATAAATT-T-
1 AAAATTTTAAAAT-ATTTATA
25431681 AAAATTTTAAAATATTTATA
1 AAAATTTTAAAATATTTATA
* *
25431701 AAAATTTCAAAATTTTTATA
1 AAAATTTTAAAATATTTATA
25431721 TTTTTAAAAA
Statistics
Matches: 56, Mismatches: 20, Indels: 6
0.68 0.24 0.07
Matches are distributed among these distances:
18 3 0.05
19 13 0.23
20 40 0.71
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATTTTAAAATATTTATA
Found at i:25431657 original size:59 final size:59
Alignment explanation
Indices: 25431593--25431710 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
25431583 CAAATTGATC
25431593 TCTCTCAACAAAAAATTTAAAATAAATTTAAAATTTTAAAATATTTATAAAAATTTCAA
1 TCTCTCAACAAAAAATTTAAAATAAATTTAAAATTTTAAAATATTTATAAAAATTTCAA
25431652 TCTCTCAACAAAAAATTTAAAATAAATTTAAAATTTTAAAATATTTATAAAAATTTCAA
1 TCTCTCAACAAAAAATTTAAAATAAATTTAAAATTTTAAAATATTTATAAAAATTTCAA
25431711 AATTTTTATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.37
Consensus pattern (59 bp):
TCTCTCAACAAAAAATTTAAAATAAATTTAAAATTTTAAAATATTTATAAAAATTTCAA
Found at i:25431726 original size:28 final size:26
Alignment explanation
Indices: 25431602--25431730 Score: 80
Period size: 28 Copynumber: 4.5 Consensus size: 26
25431592 CTCTCTCAAC
*
25431602 AAAAAATTTAAAATAAATTTAAAATTTT
1 AAAATATTT-AAA-AAATTTAAAATTTT
* *
25431630 AAAATATTTATAAAAATTT-CAATCTCTCAAC
1 AAAATATTTA-AAAAATTTAAAAT-T-T---T
*
25431661 AAAAAATTTAAAATAAATTTAAAATTTT
1 AAAATATTT-AAA-AAATTTAAAATTTT
25431689 AAAATATTTATAAAAATTTCAAAATTTT
1 AAAATATTTA-AAAAATTT-AAAATTTT
* * *
25431717 TATATTTTTAAAAA
1 AAAATATTTAAAAA
25431731 TTATAATAAC
Statistics
Matches: 80, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
26 3 0.04
27 19 0.24
28 36 0.45
31 11 0.14
32 8 0.10
33 3 0.04
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (26 bp):
AAAATATTTAAAAAATTTAAAATTTT
Found at i:25436666 original size:16 final size:16
Alignment explanation
Indices: 25436644--25436712 Score: 111
Period size: 16 Copynumber: 4.2 Consensus size: 16
25436634 TTTGGTTCGC
25436644 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
25436660 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
25436676 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
*
25436693 TATATTGGATTAGAGG
1 TGTATTGGATTAGAGG
25436709 TGTA
1 TGTA
25436713 ATAGCTAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
16 33 0.69
17 15 0.31
ACGTcount: A:0.26, C:0.01, G:0.36, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:25436690 original size:33 final size:32
Alignment explanation
Indices: 25436644--25436712 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
25436634 TTTGGTTCGC
*
25436644 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCATATTGGATTAGAGG
*
25436676 TGTATTGGGATTAGAGGTATATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCATATTGGATTAGAGG
25436709 TGTA
1 TGTA
25436713 ATAGCTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.26, C:0.01, G:0.36, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCATATTGGATTAGAGG
Found at i:25436777 original size:44 final size:45
Alignment explanation
Indices: 25436698--25436783 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 45
25436688 AGAGGTATAT
* *
25436698 TGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAATGTAA
1 TGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAATGTAA
***
25436743 TGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAATG
1 TGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAATG
25436784 GAATAGAGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 19 0.53
45 17 0.47
ACGTcount: A:0.28, C:0.07, G:0.29, T:0.36
Consensus pattern (45 bp):
TGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAATGTAA
Found at i:25436969 original size:18 final size:17
Alignment explanation
Indices: 25436948--25436982 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
25436938 TTATTATTAA
*
25436948 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
25436966 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
25436983 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:25437144 original size:120 final size:120
Alignment explanation
Indices: 25436931--25437193 Score: 508
Period size: 120 Copynumber: 2.2 Consensus size: 120
25436921 ATCATATTTA
*
25436931 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAAAAAATTCTTAATAATTAA
25436996 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
25437051 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAAAAAATTCTTAATAATTAA
25437116 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
25437171 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
25437194 AACTTGAAAA
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 141 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAAAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:25440636 original size:13 final size:13
Alignment explanation
Indices: 25440620--25440650 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
25440610 AAAAGGTGCA
25440620 AGAAATCGGGAAG
1 AGAAATCGGGAAG
25440633 AGAAATCGGGAAG
1 AGAAATCGGGAAG
25440646 AGAAA
1 AGAAA
25440651 CAGTGCTCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.35, T:0.06
Consensus pattern (13 bp):
AGAAATCGGGAAG
Found at i:25442387 original size:18 final size:18
Alignment explanation
Indices: 25442357--25442391 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25442347 CATCATTTTT
25442357 AAAATCTTTTTTTTTATC
1 AAAATCTTTTTTTTTATC
25442375 AAAAT-TTTATTTTTTAT
1 AAAATCTTT-TTTTTTAT
25442392 GACACTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (18 bp):
AAAATCTTTTTTTTTATC
Found at i:25446199 original size:21 final size:20
Alignment explanation
Indices: 25446169--25446208 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
25446159 ACTTAATACA
25446169 TTTTAAGTATTTGTAATTTT
1 TTTTAAGTATTTGTAATTTT
25446189 TTTTAAAGTATTTGTAATTT
1 TTTT-AAGTATTTGTAATTT
25446209 CTTTCATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (20 bp):
TTTTAAGTATTTGTAATTTT
Found at i:25446779 original size:9 final size:9
Alignment explanation
Indices: 25446762--25446828 Score: 107
Period size: 9 Copynumber: 7.4 Consensus size: 9
25446752 TGTATGATTC
*
25446762 AATTAGGTT
1 AATTCGGTT
25446771 AATTCGGTT
1 AATTCGGTT
*
25446780 AATTCGGGT
1 AATTCGGTT
25446789 AATTCGGTT
1 AATTCGGTT
25446798 AATTCGGTT
1 AATTCGGTT
*
25446807 AATTTGGTT
1 AATTCGGTT
25446816 AATTCGGTT
1 AATTCGGTT
25446825 AATT
1 AATT
25446829 TTTAACCAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:25448710 original size:41 final size:41
Alignment explanation
Indices: 25448649--25448758 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 41
25448639 CTTTCGGGGC
*
25448649 TTTAGCGGCGTTTTTGGAAAAGCGCTGCTAATGCTCAAGGA
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAAGGA
* * *
25448690 TTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAAGGA
*
25448731 TTTAGCGGCGTTTTTGGATAAGCGCCGC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGC
25448759 AAAAACATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAAGGA
Found at i:25449389 original size:20 final size:21
Alignment explanation
Indices: 25449343--25449391 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
25449333 ATTAAATAAG
* *
25449343 GTTTAGGGGTTAGTGGTTAGG
1 GTTTAGGGGCTAGTGGTTAGA
* *
25449364 GGTTAGGGGCTCG-GGTTAGA
1 GTTTAGGGGCTAGTGGTTAGA
25449384 GTTTAGGG
1 GTTTAGGG
25449392 TTTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.14, C:0.04, G:0.49, T:0.33
Consensus pattern (21 bp):
GTTTAGGGGCTAGTGGTTAGA
Found at i:25449431 original size:21 final size:21
Alignment explanation
Indices: 25449345--25449447 Score: 57
Period size: 21 Copynumber: 4.9 Consensus size: 21
25449335 TAAATAAGGT
*
25449345 TTAGGGGTT-AGTGGTTAGGGG
1 TTAGGGGTTAAG-GGTTAGAGG
* * *
25449366 TTAGGGGCT-CGGGTTAGAGT
1 TTAGGGGTTAAGGGTTAGAGG
* *** *
25449386 TTAGGGTTTAGATTATTTAGTGG
1 TTAGGGGTTA-A-GGGTTAGAGG
25449409 TTAGGGGTTAAGGGTTAGAGG
1 TTAGGGGTTAAGGGTTAGAGG
** *
25449430 TTATAGGTTAAGAGTTAG
1 TTAGGGGTTAAGGGTTAG
25449448 TGATTTAGGG
Statistics
Matches: 59, Mismatches: 20, Indels: 6
0.69 0.24 0.07
Matches are distributed among these distances:
20 14 0.24
21 30 0.51
22 1 0.02
23 14 0.24
ACGTcount: A:0.21, C:0.02, G:0.41, T:0.36
Consensus pattern (21 bp):
TTAGGGGTTAAGGGTTAGAGG
Found at i:25449454 original size:50 final size:50
Alignment explanation
Indices: 25449352--25449459 Score: 114
Period size: 50 Copynumber: 2.2 Consensus size: 50
25449342 GGTTTAGGGG
* * * * *
25449352 TTAGTGGTTAGGGGTTAGGGGCTCGGGTTAGAGTTTAGGGTTTAGATTAT
1 TTAGTGGTTAGGGGTTAAGGGCTAGGGTTAGAGTTAAGAGTTTAGATGAT
* *
25449402 TTAGTGGTTAGGGGTTAAGGGTTAGAGGTTATAGGTTAAGAG-TTAG-TGAT
1 TTAGTGGTTAGGGGTTAAGGGCTAG-GGTTAGA-GTTAAGAGTTTAGATGAT
25449452 TTAG-GGTT
1 TTAGTGGTT
25449460 TAGAGATTCG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
49 4 0.08
50 29 0.59
51 10 0.20
52 6 0.12
ACGTcount: A:0.21, C:0.02, G:0.39, T:0.38
Consensus pattern (50 bp):
TTAGTGGTTAGGGGTTAAGGGCTAGGGTTAGAGTTAAGAGTTTAGATGAT
Found at i:25449459 original size:21 final size:22
Alignment explanation
Indices: 25449413--25449464 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
25449403 TAGTGGTTAG
* *
25449413 GGGTTAAGGGTTAGAGGTTATA
1 GGGTTAAGAGTTAGAGATTATA
*
25449435 -GGTTAAGAGTTAGTGATT-TA
1 GGGTTAAGAGTTAGAGATTATA
*
25449455 GGGTTTAGAG
1 GGGTTAAGAG
25449465 ATTCGAGGCC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.27, C:0.00, G:0.38, T:0.35
Consensus pattern (22 bp):
GGGTTAAGAGTTAGAGATTATA
Found at i:25450101 original size:13 final size:13
Alignment explanation
Indices: 25450083--25450107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25450073 ATGAAATATT
25450083 CTTCTTTTTCCCC
1 CTTCTTTTTCCCC
25450096 CTTCTTTTTCCC
1 CTTCTTTTTCCC
25450108 AAAATCGATT
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:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (13 bp):
CTTCTTTTTCCCC
Found at i:25450318 original size:23 final size:21
Alignment explanation
Indices: 25450276--25450318 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
25450266 CCCTTCCCTC
*
25450276 CAAAACCCAAATTCCTTCAAG
1 CAAAACCCAAACTCCTTCAAG
25450297 CAAAACCCAAACCCTCCTTCAA
1 CAAAACCCAAA--CTCCTTCAA
25450319 ATTATCCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.42, C:0.40, G:0.02, T:0.16
Consensus pattern (21 bp):
CAAAACCCAAACTCCTTCAAG
Found at i:25454660 original size:43 final size:43
Alignment explanation
Indices: 25454543--25454833 Score: 349
Period size: 43 Copynumber: 6.8 Consensus size: 43
25454533 AAGATATATT
* *
25454543 TTTAGCGGCGTTTGT-GTCAAAAGCGTCGCTAAAGGTCTAT--TC
1 TTTAGCGGCGTTTGTAG-GAAAAGCGCCGCTAAAGGTC-ATGGTC
* *
25454585 TATAGCGGCGTTTG-AGGGAAAAGTGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTA-GGAAAAGCGCCGCTAAAGGTCATGGTC
* *
25454628 TTTAGCGGCGTTTGTAGGAGAAGCGCCACTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
25454671 TTTAGCGGCGATTGTAGGAGAAGCGCAGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
25454714 TTTAGCGGCGTTCGTAGGAGAAGCGCCGCTAAAGATCTTGGTC
1 TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
25454757 TTTAGCGGCGTTTGTAGGAAAAACGCTGCTAAAGATCTTGGTC
1 TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGGTC
*
25454800 TTTAGCGGCATTTGT-GGTAAAAGCGCCGCTAAAG
1 TTTAGCGGCGTTTGTAGG-AAAAGCGCCGCTAAAG
25454834 TTAGCGGCGT
Statistics
Matches: 220, Mismatches: 23, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
41 2 0.01
42 32 0.15
43 185 0.84
44 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:25457002 original size:30 final size:30
Alignment explanation
Indices: 25456963--25457026 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
25456953 TTAGTAATAT
*
25456963 TCTTTCCACATTAATTTAATTGAGAACTTA
1 TCTTCCCACATTAATTTAATTGAGAACTTA
25456993 TCTTCCCACATTAATTTAATTGAGAACTTA
1 TCTTCCCACATTAATTTAATTGAGAACTTA
25457023 TCTT
1 TCTT
25457027 AATTGTTACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (30 bp):
TCTTCCCACATTAATTTAATTGAGAACTTA
Found at i:25459530 original size:22 final size:23
Alignment explanation
Indices: 25459505--25459571 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 23
25459495 CCACATTGAT
25459505 ATGTAGCCGAAGCTACCACTGA-
1 ATGTAGCCGAAGCTACCACTGAG
25459527 ATGTAGCCGAAGCTACCACTGAG
1 ATGTAGCCGAAGCTACCACTGAG
25459550 ATGTAGCCGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
25459572 TCAATAACAC
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 22 0.50
23 22 0.50
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAG
Found at i:25459672 original size:8 final size:8
Alignment explanation
Indices: 25459659--25459687 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
25459649 ACCCGGGACT
25459659 CACTGTAA
1 CACTGTAA
25459667 CACTGTAA
1 CACTGTAA
25459675 CACTGTAA
1 CACTGTAA
25459683 CACTG
1 CACTG
25459688 GTCTCTAGTG
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:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:25459841 original size:18 final size:18
Alignment explanation
Indices: 25459813--25459849 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25459803 TTCCACATTC
25459813 AATATTAATTCACATATTT
1 AATATTAATTCACA-ATTT
25459832 AATA-TAATTCACAATTT
1 AATATTAATTCACAATTT
25459849 A
1 A
25459850 TACAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 9 0.50
19 4 0.22
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATTAATTCACAATTT
Found at i:25461062 original size:23 final size:24
Alignment explanation
Indices: 25461023--25461070 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
25461013 TTATTTGTAC
*
25461023 TTAGTGCATTTTTTTTTGTATATT
1 TTAGGGCATTTTTTTTTGTATATT
25461047 TTAGGGCA-TTTTTTTTGTATATT
1 TTAGGGCATTTTTTTTTGTATATT
25461070 T
1 T
25461071 ATTTTCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.17, C:0.04, G:0.15, T:0.65
Consensus pattern (24 bp):
TTAGGGCATTTTTTTTTGTATATT
Found at i:25461319 original size:22 final size:22
Alignment explanation
Indices: 25461291--25461334 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
25461281 ATTGTACTAT
25461291 TCAAAAAATTGTATCTAAGTCA
1 TCAAAAAATTGTATCTAAGTCA
25461313 TCAAAAAATTGTATCTAAGTCA
1 TCAAAAAATTGTATCTAAGTCA
25461335 CTAGACTGTT
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:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
TCAAAAAATTGTATCTAAGTCA
Found at i:25464326 original size:31 final size:31
Alignment explanation
Indices: 25464290--25464352 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
25464280 ATTTGGTTGG
25464290 GAAGTTTGGTTTTTTCTTAATTTGGGTTATT
1 GAAGTTTGGTTTTTTCTTAATTTGGGTTATT
25464321 GAAGTTTGGTTTTTTCTTAATTTGGGTTATT
1 GAAGTTTGGTTTTTTCTTAATTTGGGTTATT
25464352 G
1 G
25464353 TAGGTATGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.16, C:0.03, G:0.24, T:0.57
Consensus pattern (31 bp):
GAAGTTTGGTTTTTTCTTAATTTGGGTTATT
Found at i:25469036 original size:8 final size:8
Alignment explanation
Indices: 25469025--25469113 Score: 58
Period size: 8 Copynumber: 11.0 Consensus size: 8
25469015 TAATTTACGT
25469025 TTTTAAAA
1 TTTTAAAA
25469033 TTTTAAAAA
1 TTTT-AAAA
25469042 TTTTAAAA
1 TTTTAAAA
* *
25469050 ATATAAAA
1 TTTTAAAA
*
25469058 -TTT--AT
1 TTTTAAAA
25469063 TTTTAAAA
1 TTTTAAAA
* *
25469071 ATTAAAAA
1 TTTTAAAA
25469079 TTATTAAAA
1 TT-TTAAAA
25469088 TTATTAAAAA
1 TT-TT-AAAA
*
25469098 TTATAAAA
1 TTTTAAAA
*
25469106 TTATAAAA
1 TTTTAAAA
25469114 AAAAATATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
5 1 0.02
6 3 0.05
7 2 0.03
8 34 0.52
9 19 0.29
10 6 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TTTTAAAA
Found at i:25469064 original size:29 final size:28
Alignment explanation
Indices: 25469032--25469113 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 28
25469022 CGTTTTTAAA
25469032 ATTTTAAAAATTTTAAAAATATAAAATTT
1 ATTTTAAAAATTTTAAAAATATAAAA-TT
25469061 ATTTTTAAAAA--TTAAAAATTATTAAAATT
1 A-TTTTAAAAATTTTAAAAA-TA-TAAAATT
* *
25469090 A--TTAAAAATTATAAAATTATAAAA
1 ATTTTAAAAATTTTAAAAATATAAAA
25469114 AAAAATATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
26 12 0.26
27 2 0.04
28 12 0.26
29 6 0.13
30 14 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATTTTAAAAATTTTAAAAATATAAAATT
Found at i:25469068 original size:21 final size:20
Alignment explanation
Indices: 25469042--25469083 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
25469032 ATTTTAAAAA
*
25469042 TTTTAAAAATATAAAATTTAT
1 TTTTAAAAAT-TAAAAATTAT
25469063 TTTTAAAAATTAAAAATTAT
1 TTTTAAAAATTAAAAATTAT
25469083 T
1 T
25469084 AAAATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTTAAAAATTAAAAATTAT
Done.