Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold121
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: 1076282
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 28062 characters in sequence are not A, C, G, or T
File 4 of 8
Found at i:414235 original size:156 final size:156
Alignment explanation
Indices: 413789--414236 Score: 499
Period size: 156 Copynumber: 2.9 Consensus size: 156
413779 ATGATAAGAA
* * * * * ** *
413789 TGCTAATGTGCTGATTCATGGCTAGTGACATTGGACTGGAAGAT-AAAAAGAATGCCACTGTGCT
1 TGCTAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAAG-ATGCCAATGTGCT
* * * * *
413853 GATTCAAGGCCAGCGACATTAGACTTAAA-ATAAGAAGAATGCCAATATGCTGATTCAAGGCCAG
65 GATTCAAGGCAAGCGACATTGGACTTAAAGATAAGAAGAATGCCAATGTGTTGATTCAAGGCTAG
* **
413917 CGACATTAGGCTTAAAAATGGTAAAGG
130 CGACATTGGGCTTAAAAATAATAAAGG
* * * *
413944 TGCTAATATACTGATCCAAGGCCAGCGATATTGGACTTAAAGATGATAAAGGTGCCAATGTGCTG
1 TGCTAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAAGATGCCAATGTGCTG
* * * * ** * *
414009 ATTCAAGGCTAA-CGATAGTGGACTTAAAGATGACAAGGGTTCCAACGTGTTGATTCAAGGCTAG
66 ATTCAAGGC-AAGCGACATTGGACTTAAAGATAAGAAGAATGCCAATGTGTTGATTCAAGGCTAG
* * *
414073 TGACATTGGGTTTAAAGAA-AATAGAGG
130 CGACATTGGGCTTAAA-AATAATAAAGG
* * *
414100 TGCTAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGATGACAAAGATGCCAATGTGCTA
1 TGCTAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAAGATGCCAATGTGCTG
* * *
414165 ATTCAAGACAAGCGACATTGGGCTTAAAGATAAGAAAAATGCCAATGTGTTGATTCAAGGCTAGC
66 ATTCAAGGCAAGCGACATTGGACTTAAAGATAAGAAGAATGCCAATGTGTTGATTCAAGGCTAGC
*
414230 AACATTG
131 GACATTG
414237 TACCTAGAAA
Statistics
Matches: 238, Mismatches: 50, Indels: 9
0.80 0.17 0.03
Matches are distributed among these distances:
155 71 0.30
156 165 0.69
157 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.25
Consensus pattern (156 bp):
TGCTAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAAAAGATGCCAATGTGCTG
ATTCAAGGCAAGCGACATTGGACTTAAAGATAAGAAGAATGCCAATGTGTTGATTCAAGGCTAGC
GACATTGGGCTTAAAAATAATAAAGG
Found at i:414236 original size:52 final size:52
Alignment explanation
Indices: 413788--414236 Score: 350
Period size: 52 Copynumber: 8.7 Consensus size: 52
413778 AATGATAAGA
* * * * **
413788 ATGCTAATGTGCTGATTCATGGCTAGTGACATTGGACTGGAAGATAA-AAAG
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGAAAG
* *
413839 AATGCCACTGTGCTGATTCAAGGCCAGCGACATTAGACTTAAA-ATAAG-AAG
1 -ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGAAAG
* * *
413890 AATGCCAATATGCTGATTCAAGGCCAGCGACATTAGG-CTTAAAAAT-GGTAAAG
1 -ATGCCAATGTGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGATAAG-AAAG
* * * * * * * *
413943 GTGCTAATATACTGATCCAAGGCCAGCGATATTGGACTTAAAGATGATAAAG
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGAAAG
* * * * * * * *
413995 GTGCCAATGTGCTGATTCAAGGCTAACGATAGTGGACTTAAAGATGACAAGG
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGAAAG
* * * * * * ** * * *
414047 GTTCCAACGTGTTGATTCAAGGCTAGTGACATTGGGTTTAAAGAAAATAGAG
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGAAAG
* * * * * * *
414099 GTGCTAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGATGACAAAG
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGAAAG
* * * * *
414151 ATGCCAATGTGCTAATTCAAGACAAGCGACATTGGGCTTAAAGATAAGAAAA
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGAAAG
* * *
414203 ATGCCAATGTGTTGATTCAAGGCTAGCAACATTG
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTG
414237 TACCTAGAAA
Statistics
Matches: 315, Mismatches: 75, Indels: 14
0.78 0.19 0.03
Matches are distributed among these distances:
51 48 0.15
52 264 0.84
53 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (52 bp):
ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGAAAG
Found at i:414407 original size:64 final size:64
Alignment explanation
Indices: 414335--414670 Score: 354
Period size: 64 Copynumber: 5.2 Consensus size: 64
414325 TGAGCTTTGG
*
414335 AAAAGGGTTGCCA-TCGACTTGTGTGGGCTTTTGAGAAGGTTGCCA-CGACTTGTGTGGGCTTTA
1 AAAAGGGTTGCCACT-GACTTGTGTGGGCTTTTGAGAGGGTTGCCACCGACTTGTGTGGGCTTTA
* ** * ** * *
414398 AAAAGGGGTTGCCACTGACTTGTGTGGGATTTAAAAAAGGGTTGCCATTGATTTATGTGGGCTTT
1 AAAA-GGGTTGCCACTGACTTGTGTGGGCTTT-TGAGAGGGTTGCCACCGACTTGTGTGGGCTTT
414463 A
64 A
* * * *
414464 GAAAAGGGGTTGCCACTGACTTATGTGGGCTTTAGAGAGGGCTGCCACCGACTTGTGTGGGATTT
1 -AAAA-GGGTTGCCACTGACTTGTGTGGGCTTTTGAGAGGGTTGCCACCGACTTGTGTGGGCTTT
*
414529 T
64 A
* * * * * *
414530 GAGAGGGTTGCCACTGACTTGTGTAGGCTTTTGAGAGGGTTTCCACCGACTTGTGTGGGATTTT
1 AAAAGGGTTGCCACTGACTTGTGTGGGCTTTTGAGAGGGTTGCCACCGACTTGTGTGGGCTTTA
* * * ** * *
414594 GAGAGGGTTGCCACTGACTTGTGTAGGCTTTTGAGAGGGTTGCCACTAACTTGTTTGGGCTTAA
1 AAAAGGGTTGCCACTGACTTGTGTGGGCTTTTGAGAGGGTTGCCACCGACTTGTGTGGGCTTTA
*
414658 AAAAAGG-TGCCAC
1 AAAAGGGTTGCCAC
414671 AAAGTTGTGG
Statistics
Matches: 232, Mismatches: 36, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
63 10 0.04
64 140 0.60
65 13 0.06
66 39 0.17
67 30 0.13
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (64 bp):
AAAAGGGTTGCCACTGACTTGTGTGGGCTTTTGAGAGGGTTGCCACCGACTTGTGTGGGCTTTA
Found at i:414408 original size:32 final size:32
Alignment explanation
Indices: 414310--414670 Score: 298
Period size: 32 Copynumber: 11.2 Consensus size: 32
414300 TAGAAAGAGA
* * * *
414310 TGCCACTAACTTATGTGAGCTTTGGAAAAGGGT
1 TGCCACTGACTTGTGTGGGCTTT-AAAAAGGGT
* *
414343 TGCCA-TCGACTTGTGTGGGCTTTTGAGAA-GGT
1 TGCCACT-GACTTGTGTGGGC-TTTAAAAAGGGT
414375 TGCCAC-GACTTGTGTGGGCTTTAAAAAGGGGT
1 TGCCACTGACTTGTGTGGGCTTTAAAAA-GGGT
*
414407 TGCCACTGACTTGTGTGGGATTTAAAAAAGGGT
1 TGCCACTGACTTGTGTGGGCTTT-AAAAAGGGT
* * *
414440 TGCCATTGATTTATGTGGGCTTTAGAAAAGGGGT
1 TGCCACTGACTTGTGTGGGCTTTA-AAAA-GGGT
* * * *
414474 TGCCACTGACTTATGTGGGCTTTAGAGAGGGC
1 TGCCACTGACTTGTGTGGGCTTTAAAAAGGGT
* * ** *
414506 TGCCACCGACTTGTGTGGGATTTTGAGAGGGT
1 TGCCACTGACTTGTGTGGGCTTTAAAAAGGGT
* ** *
414538 TGCCACTGACTTGTGTAGGCTTTTGAGAGGGT
1 TGCCACTGACTTGTGTGGGCTTTAAAAAGGGT
* * * ** *
414570 TTCCACCGACTTGTGTGGGATTTTGAGAGGGT
1 TGCCACTGACTTGTGTGGGCTTTAAAAAGGGT
* ** *
414602 TGCCACTGACTTGTGTAGGCTTTTGAGAGGGT
1 TGCCACTGACTTGTGTGGGCTTTAAAAAGGGT
* * * *
414634 TGCCACTAACTTGTTTGGGCTTAAAAAAAGG-
1 TGCCACTGACTTGTGTGGGCTTTAAAAAGGGT
414665 TGCCAC
1 TGCCAC
414671 AAAGTTGTGG
Statistics
Matches: 279, Mismatches: 40, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
30 6 0.02
31 19 0.07
32 157 0.56
33 63 0.23
34 34 0.12
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (32 bp):
TGCCACTGACTTGTGTGGGCTTTAAAAAGGGT
Found at i:414599 original size:96 final size:96
Alignment explanation
Indices: 414338--414655 Score: 370
Period size: 96 Copynumber: 3.3 Consensus size: 96
414328 GCTTTGGAAA
* * *
414338 AGGGTTGCCA-TCGACTTGTGTGGGCTTTTGAGAAGGTTGCCA-CGACTTGTGTGGGCTTTAAAA
1 AGGGTTGCCACT-GACTTGTGTGGGCTTTTGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAG
** *
414401 AGGGGTTGCCACTGACTTGTGTGGGATTTAAAAA
65 A-GGGTTGCCACTGACTTGTGTGGGATTT-TGAG
* * * * * * *
414435 AGGGTTGCCATTGATTTATGTGGGCTTTAGAAAAGGGGTTGCCACTGACTTATGTGGGCTTTAGA
1 AGGGTTGCCACTGACTTGTGTGGGCTTTTG-AGA-GGGTTGCCACCGACTTGTGTGGGCTTTAGA
* *
414500 GAGGGCTGCCACCGACTTGTGTGGGATTTTGAG
64 GAGGGTTGCCACTGACTTGTGTGGGATTTTGAG
* * * *
414533 AGGGTTGCCACTGACTTGTGTAGGCTTTTGAGAGGGTTTCCACCGACTTGTGTGGGATTTTGAGA
1 AGGGTTGCCACTGACTTGTGTGGGCTTTTGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGA
* *
414598 GGGTTGCCACTGACTTGTGTAGGCTTTTGAG
66 GGGTTGCCACTGACTTGTGTGGGATTTTGAG
* *
414629 AGGGTTGCCACTAACTTGTTTGGGCTT
1 AGGGTTGCCACTGACTTGTGTGGGCTT
414656 AAAAAAAGGT
Statistics
Matches: 185, Mismatches: 32, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
96 78 0.42
97 27 0.15
98 29 0.16
99 33 0.18
100 18 0.10
ACGTcount: A:0.19, C:0.15, G:0.34, T:0.33
Consensus pattern (96 bp):
AGGGTTGCCACTGACTTGTGTGGGCTTTTGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGA
GGGTTGCCACTGACTTGTGTGGGATTTTGAG
Found at i:414729 original size:32 final size:31
Alignment explanation
Indices: 414654--414883 Score: 217
Period size: 32 Copynumber: 7.6 Consensus size: 31
414644 TTGTTTGGGC
* *
414654 TTAA-AAAAAGGTGCCACAAAGTTGTGGACT
1 TTAAGAAAAAGGTGCCACGAAGTTATGGACT
* * *
414684 TT-AGAAAAGGGTGCTACGGAGTTATGGACT
1 TTAAGAAAAAGGTGCCACGAAGTTATGGACT
*
414714 TTAAAGAAAAAGGTGCCACGAAGTTGTGGACT
1 TT-AAGAAAAAGGTGCCACGAAGTTATGGACT
*
414746 TT--GAAAAA-GTGCTACGAAGTTATGGA-T
1 TTAAGAAAAAGGTGCCACGAAGTTATGGACT
* * * *
414773 TT---AAAAAGATACCATGGAGTTATGGACT
1 TTAAGAAAAAGGTGCCACGAAGTTATGGACT
* * *
414801 TTGAAGAAAAATGTGCCATGGAGTTATGGACT
1 TT-AAGAAAAAGGTGCCACGAAGTTATGGACT
*
414833 TTGAAGAAAAAGGTGCCACGAAGTTGTGGACT
1 TT-AAGAAAAAGGTGCCACGAAGTTATGGACT
*
414865 TTGAAGAAAAATGTGCCAC
1 TT-AAGAAAAAGGTGCCAC
414884 AAAATTGTGA
Statistics
Matches: 167, Mismatches: 24, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
26 5 0.03
27 16 0.10
28 19 0.11
29 7 0.04
30 25 0.15
32 95 0.57
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (31 bp):
TTAAGAAAAAGGTGCCACGAAGTTATGGACT
Found at i:414932 original size:119 final size:115
Alignment explanation
Indices: 414678--414959 Score: 264
Period size: 119 Copynumber: 2.3 Consensus size: 115
414668 CACAAAGTTG
* *
414678 TGGACTTTAGAAAAGGGTGCTACGGAGTTATGGACTTTAAAGAAAAAGGTGCCACGAAGTTGTGG
1 TGGACTTT--AAAATGGTGCCACGGAGTTATGGACTTTAAAGAAAAAGGTGCCACGAAGTTGTGG
* * * * * * *
414743 ACTTTGAAAAAGTGCTACGAAGTTATGGATTTAAAAAGATACCATGGAGTTA
64 ACTTTGAAAAAGTGCCACAAAATTATGAATTTAAAAAAATACCACGGAATTA
* *
414795 TGGACTTTGAAGAAAAAT-GTGCCATGGAGTTATGGACTTTGAAGAAAAAGGTGCCACGAAGTTG
1 TGGACTTT-----AAAATGGTGCCACGGAGTTATGGACTTTAAAGAAAAAGGTGCCACGAAGTTG
* **
414859 TGGACTTTGAAGAAAAATGTGCCACAAAATTGTGAACTTTAAAAGAAATGTCACGGAATTGA
61 TGGACTTT---GAAAAA-GTGCCACAAAATTATGAA-TTTAAAA-AAATACCACGGAATT-A
* *
414921 -GGACTTT-AAATGGGTGCCACGGAGTTGTGGACTTAAAAG
1 TGGACTTTAAAAT-GGTGCCACGGAGTTATGGACTTTAAAG
414960 GTTGCTATAG
Statistics
Matches: 133, Mismatches: 20, Indels: 20
0.77 0.12 0.12
Matches are distributed among these distances:
117 8 0.06
119 55 0.41
120 4 0.03
121 22 0.17
122 6 0.05
123 13 0.10
124 7 0.05
125 17 0.13
126 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (115 bp):
TGGACTTTAAAATGGTGCCACGGAGTTATGGACTTTAAAGAAAAAGGTGCCACGAAGTTGTGGAC
TTTGAAAAAGTGCCACAAAATTATGAATTTAAAAAAATACCACGGAATTA
Found at i:414952 original size:28 final size:28
Alignment explanation
Indices: 414658--415157 Score: 168
Period size: 32 Copynumber: 17.0 Consensus size: 28
414648 TTGGGCTTAA
* **
414658 AAAAAGGTGCCACAAAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTT
* *
414686 AGAAAAGGGTGCTACGGAGTTATGGACTTT
1 --AAAAGGGTGCCACGGAGTTGTGGACTTT
* *
414716 AAAGAAAAAGGTGCCACGAAGTTGTGGACTTT
1 ----AAAAGGGTGCCACGGAGTTGTGGACTTT
* * * *
414748 GAAAA-AGTGCTACGAAGTTATGGA-TTT
1 -AAAAGGGTGCCACGGAGTTGTGGACTTT
* * * * *
414775 AAAAAGATACCATGGAGTTATGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTT
** * *
414803 GAAGAAAAATGTGCCATGGAGTTATGGACTTT
1 ----AAAAGGGTGCCACGGAGTTGTGGACTTT
* *
414835 GAAGAAAAAGGTGCCACGAAGTTGTGGACTTT
1 ----AAAAGGGTGCCACGGAGTTGTGGACTTT
** ** * *
414867 GAAGAAAAATGTGCCACAAAATTGTGAACTTT
1 ----AAAAGGGTGCCACGGAGTTGTGGACTTT
** * * *
414899 AAAAGAAATGTCACGGAATTGAGGACTTT
1 AAAAG-GGTGCCACGGAGTTGTGGACTTT
*
414928 AAATGGGTGCCACGGAGTTGTGGAC-TT
1 AAAAGGGTGCCACGGAGTTGTGGACTTT
* * **
414955 AAAAGGTTGCTATAGAGTTGTGGAC-TT
1 AAAAGGGTGCCACGGAGTTGTGGACTTT
** *
414982 AAAAGGGTGCCA-TAAGTTATGGAC-TT
1 AAAAGGGTGCCACGGAGTTGTGGACTTT
415008 AAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TT
1 AAAAG-----GGTGCCACGGAGTTGTGGACTTT
* * ** * *
415040 AAAAGAAGTACCATAGAGTGGTGGACTTAGAA
1 AAAAG-GGTGCCACGGAGTTGTGGACTT---T
* * *
415072 AAACAAGGTGCCACGGAGTTGTGAATTTT
1 AAA-AGGGTGCCACGGAGTTGTGGACTTT
* * *
415101 AAAAGAGGTGCGACGAAGTTATGGACTTT
1 AAAAG-GGTGCCACGGAGTTGTGGACTTT
* * *
415130 AAAAAGGTGCCACAGAGTTGTAGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTT
415158 GAGAAGGTAT
Statistics
Matches: 366, Mismatches: 83, Indels: 44
0.74 0.17 0.09
Matches are distributed among these distances:
26 20 0.05
27 50 0.14
28 73 0.20
29 51 0.14
30 23 0.06
31 7 0.02
32 141 0.39
33 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.28, T:0.25
Consensus pattern (28 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTT
Found at i:415006 original size:26 final size:27
Alignment explanation
Indices: 414921--415068 Score: 127
Period size: 27 Copynumber: 5.3 Consensus size: 27
414911 ACGGAATTGA
* **
414921 GGACTTTAAATGGGTGCCACGGAGTTGT
1 GGAC-TTAAAAGGGTGCCATAGAGTTGT
* *
414949 GGACTTAAAAGGTTGCTATAGAGTTGT
1 GGACTTAAAAGGGTGCCATAGAGTTGT
*
414976 GGACTTAAAAGGGTGCCATA-AGTTAT
1 GGACTTAAAAGGGTGCCATAGAGTTGT
**
415002 GGACTTAAAAGAAAAAGGTGCCACGGAGTTGT
1 GGACTTAAAAG-----GGTGCCATAGAGTTGT
* * *
415034 GGACTTAAAAGAAGTACCATAGAGTGGT
1 GGACTTAAAAG-GGTGCCATAGAGTTGT
415062 GGACTTA
1 GGACTTA
415069 GAAAAACAAG
Statistics
Matches: 98, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
26 16 0.16
27 36 0.37
28 23 0.23
31 7 0.07
32 16 0.16
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.26
Consensus pattern (27 bp):
GGACTTAAAAGGGTGCCATAGAGTTGT
Found at i:415085 original size:60 final size:58
Alignment explanation
Indices: 414969--415094 Score: 173
Period size: 60 Copynumber: 2.1 Consensus size: 58
414959 GGTTGCTATA
* * *
414969 GAGTTGTGGACTTAAAAGGGTGCCATAAGTTATGGACTTAAAAGAAAAAGGTGCCACG
1 GAGTTGTGGACTTAAAAGAGTACCATAAGTGATGGACTTAAAAGAAAAAGGTGCCACG
* *
415027 GAGTTGTGGACTTAAAAGAAGTACCATAGAGTGGTGGACTTAGAAA-AACAAGGTGCCACG
1 GAGTTGTGGACTTAAAAG-AGTACCATA-AGTGATGGACTTA-AAAGAAAAAGGTGCCACG
415087 GAGTTGTG
1 GAGTTGTG
415095 AATTTTAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
58 18 0.30
59 7 0.12
60 32 0.53
61 3 0.05
ACGTcount: A:0.35, C:0.12, G:0.31, T:0.22
Consensus pattern (58 bp):
GAGTTGTGGACTTAAAAGAGTACCATAAGTGATGGACTTAAAAGAAAAAGGTGCCACG
Found at i:415134 original size:60 final size:57
Alignment explanation
Indices: 414969--415150 Score: 154
Period size: 60 Copynumber: 3.1 Consensus size: 57
414959 GGTTGCTATA
* * * *
414969 GAGTTGTGGACTTAAAAG-GGTGCCATAAGTTATGGACTTAAAAGAAAAAGGTGCCACG
1 GAGTTGTGAACTTAAAAGAAGTACCAGAAGTTATGGACTT-AAA-AAAAAGGTGCCACG
* * **
415027 GAGTTGTGGACTTAAAAGAAGTACCATAGAGTGGTGGACTTAGAAAAACAAGGTGCCACG
1 GAGTTGTGAACTTAAAAGAAGTACCAGA-AGTTATGGACTTA-AAAAA-AAGGTGCCACG
* * * * * *
415087 GAGTTGTGAATTTTAAAAGAGGTGCGACGAAGTTATGGACTT--TAAAAAGGTGCCACA
1 GAGTTGTGAA-CTTAAAAGAAGTACCA-GAAGTTATGGACTTAAAAAAAAGGTGCCACG
415144 GAGTTGT
1 GAGTTGT
415151 AGACTTTGAG
Statistics
Matches: 104, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
57 17 0.16
58 21 0.20
59 11 0.11
60 32 0.31
61 22 0.21
62 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.24
Consensus pattern (57 bp):
GAGTTGTGAACTTAAAAGAAGTACCAGAAGTTATGGACTTAAAAAAAAGGTGCCACG
Found at i:415186 original size:30 final size:30
Alignment explanation
Indices: 415152--415226 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 30
415142 CAGAGTTGTA
* *
415152 GACTTTGAGAAGGTATGCCACTATGCCGTG
1 GACTTTAAGAAGGTATGCCACTAAGCCGTG
* * **
415182 GACTTTAAAGAAGGAATGCTACTAAGTTGTG
1 GACTTT-AAGAAGGTATGCCACTAAGCCGTG
*
415213 GACTTTTAGAAGGT
1 GACTTTAAGAAGGT
415227 TACTTTACTG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
30 12 0.33
31 24 0.67
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.29
Consensus pattern (30 bp):
GACTTTAAGAAGGTATGCCACTAAGCCGTG
Found at i:415214 original size:31 final size:30
Alignment explanation
Indices: 414634--415218 Score: 92
Period size: 32 Copynumber: 19.7 Consensus size: 30
414624 TTGAGAGGGT
* * * *
414634 TGCCACTAACTTGTTTGGGCTTAAAAAAAGG-
1 TGCCACTAAGTTG--TGGACTTTAAAGAAGGA
* *
414665 TGCCACAAAGTTGTGGACTTTAGAA-AAGGG
1 TGCCACTAAGTTGTGGACTTTA-AAGAAGGA
* ** *
414695 TGCTACGGAGTTATGGACTTTAAAGAAAAAGG-
1 TGCCACTAAGTTGTGGACTTTAAAG---AAGGA
*
414727 TGCCACGAAGTTGTGGACTTTGAAA-AA-G-
1 TGCCACTAAGTTGTGGACTTT-AAAGAAGGA
* * *
414755 TGCTACGAAGTTATGGA-TTTAAA-AA-GA
1 TGCCACTAAGTTGTGGACTTTAAAGAAGGA
* * * * **
414782 TACCA-TGGAGTTATGGACTTTGAAGAAAAA
1 TGCCACT-AAGTTGTGGACTTTAAAGAAGGA
* * *
414812 TGTGCCA-TGGAGTTATGGACTTTGAAGAAAAAGG-
1 --TGCCACT-AAGTTGTGGACTTT--A-AAGAAGGA
* * **
414846 TGCCACGAAGTTGTGGACTTTGAAGAAAAA
1 TGCCACTAAGTTGTGGACTTTAAAGAAGGA
* * *
414876 TGTGCCACAAAATTGTGAACTTTAAAAGAA--A
1 --TGCCACTAAGTTGTGGACTTT-AAAGAAGGA
* * *
414907 TGTCACGGAA-TTGAGGACTTTAAATG--GG-
1 TGCCAC-TAAGTTGTGGACTTTAAA-GAAGGA
** *
414935 TGCCACGGAGTTGTGGAC-TT-AA-AAGGT
1 TGCCACTAAGTTGTGGACTTTAAAGAAGGA
* *
414962 TGCTA-TAGAGTTGTGGAC-TT-AA-AAGGG
1 TGCCACTA-AGTTGTGGACTTTAAAGAAGGA
* *
414989 TGCCA-TAAGTTATGGACTTAAAAGAAAAAGG-
1 TGCCACTAAGTTGTGGACTTTAAAG---AAGGA
** *
415020 TGCCACGGAGTTGTGGACTTAAAAGAA-G-
1 TGCCACTAAGTTGTGGACTTTAAAGAAGGA
* * * *
415048 TACCA-TAGAGTGGTGGACTTAGAAAAACAAGG-
1 TGCCACTA-AGTTGTGGACTT---TAAAGAAGGA
** * *
415080 TGCCACGGAGTTGTGAATTTTAAA-AGAGG-
1 TGCCACTAAGTTGTGGACTTTAAAGA-AGGA
* * *
415109 TGCGACGAAGTTATGGACTTTAAA-AAGG-
1 TGCCACTAAGTTGTGGACTTTAAAGAAGGA
* *
415137 TGCCAC-AGAGTTGTAGACTTT-GAGAAGGTA
1 TGCCACTA-AGTTGTGGACTTTAAAGAAGG-A
* **
415167 TGCCACTATGCCGTGGACTTTAAAGAAGGAA
1 TGCCACTAAGTTGTGGACTTTAAAGAAGG-A
*
415198 TGCTACTAAGTTGTGGACTTT
1 TGCCACTAAGTTGTGGACTTT
415219 TAGAAGGTTA
Statistics
Matches: 420, Mismatches: 83, Indels: 102
0.69 0.14 0.17
Matches are distributed among these distances:
26 19 0.05
27 50 0.12
28 78 0.19
29 64 0.15
30 38 0.09
31 48 0.11
32 107 0.25
33 12 0.03
35 4 0.01
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (30 bp):
TGCCACTAAGTTGTGGACTTTAAAGAAGGA
Found at i:416063 original size:19 final size:21
Alignment explanation
Indices: 416017--416070 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
416007 TTTCAACAAT
416017 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAACAGTAA
* *
416038 ATGTATCGATACATA-AGT-A
1 TTGTATCGATACAAACAGTAA
416057 TTGTATCGATACAA
1 TTGTATCGATACAA
416071 TGTATCGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
TTGTATCGATACAAACAGTAA
Found at i:416118 original size:17 final size:17
Alignment explanation
Indices: 416098--416130 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
416088 ACTGCTAAGA
416098 CAATGTATCGATACATT
1 CAATGTATCGATACATT
416115 CAATGTATCGATACAT
1 CAATGTATCGATACAT
416131 GCAGGCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (17 bp):
CAATGTATCGATACATT
Found at i:420194 original size:17 final size:17
Alignment explanation
Indices: 420174--420206 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
420164 CCTTTGCACT
420174 TTTTTTTTTTGTTTTTG
1 TTTTTTTTTTGTTTTTG
420191 TTTTTTTTTTGTTTTT
1 TTTTTTTTTTGTTTTT
420207 CTTTGTGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (17 bp):
TTTTTTTTTTGTTTTTG
Found at i:420206 original size:11 final size:11
Alignment explanation
Indices: 420173--420206 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
420163 GCCTTTGCAC
420173 TTTTTTT-TTT
1 TTTTTTTGTTT
*
420183 TGTTTTTGTTT
1 TTTTTTTGTTT
420194 TTTTTTTGTTT
1 TTTTTTTGTTT
420205 TT
1 TT
420207 CTTTGTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:425216 original size:45 final size:45
Alignment explanation
Indices: 425166--425282 Score: 189
Period size: 45 Copynumber: 2.6 Consensus size: 45
425156 AATATAAATT
425166 TAAACTTAAACCCAAACCCAATTAAAACCGAACTAAAAATCTATA
1 TAAACTTAAACCCAAACCCAATTAAAACCGAACTAAAAATCTATA
* * **
425211 TAAACTTAAACCTAAAGCCAATTAAAACTTAACTAAAAATCTATA
1 TAAACTTAAACCCAAACCCAATTAAAACCGAACTAAAAATCTATA
*
425256 TAAACTTAAACCCAAACCTAATTAAAA
1 TAAACTTAAACCCAAACCCAATTAAAA
425283 AAAATAACAA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.54, C:0.21, G:0.02, T:0.23
Consensus pattern (45 bp):
TAAACTTAAACCCAAACCCAATTAAAACCGAACTAAAAATCTATA
Found at i:425263 original size:22 final size:22
Alignment explanation
Indices: 425196--425264 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
425186 ATTAAAACCG
425196 AACTAAAAATCTATATAAACTT
1 AACTAAAAATCTATATAAACTT
** *
425218 AAACCT-AAAGCCAAT-TAAAACTT
1 -AA-CTAAAAATCTATAT-AAACTT
425241 AACTAAAAATCTATATAAACTT
1 AACTAAAAATCTATATAAACTT
425263 AA
1 AA
425265 ACCCAAACCT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
21 2 0.06
22 17 0.47
23 15 0.42
24 2 0.06
ACGTcount: A:0.55, C:0.16, G:0.01, T:0.28
Consensus pattern (22 bp):
AACTAAAAATCTATATAAACTT
Found at i:425458 original size:42 final size:42
Alignment explanation
Indices: 425406--425486 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
425396 CAACAATCGG
* *
425406 CAACAACAACAGCAACCAAAAGTAGATCGACAATGGCAACGA
1 CAACAACAACAGCAACCAAAAGCAGATCGACAATAGCAACGA
*
425448 CAACAGCAACAGCAACCAAAAGCAGATCGACAATAGCAA
1 CAACAACAACAGCAACCAAAAGCAGATCGACAATAGCAA
425487 TAGCAATCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.51, C:0.27, G:0.16, T:0.06
Consensus pattern (42 bp):
CAACAACAACAGCAACCAAAAGCAGATCGACAATAGCAACGA
Found at i:425486 original size:30 final size:30
Alignment explanation
Indices: 425445--425511 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
425435 ACAATGGCAA
425445 CGACAACAGCAACAGCAACCAAAAGCAGAT
1 CGACAACAGCAACAGCAACCAAAAGCAGAT
* * * *
425475 CGACAATAGCAATAGCAATCAGAAGCAGAT
1 CGACAACAGCAACAGCAACCAAAAGCAGAT
*
425505 CAACAAC
1 CGACAAC
425512 TAGAAGCAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.07
Consensus pattern (30 bp):
CGACAACAGCAACAGCAACCAAAAGCAGAT
Found at i:425518 original size:18 final size:18
Alignment explanation
Indices: 425495--425529 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
425485 AATAGCAATC
425495 AGAAGCAGATCAACAACT
1 AGAAGCAGATCAACAACT
*
425513 AGAAGCAGATCAGCAAC
1 AGAAGCAGATCAACAAC
425530 AGCAACCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.23, G:0.20, T:0.09
Consensus pattern (18 bp):
AGAAGCAGATCAACAACT
Found at i:425535 original size:24 final size:24
Alignment explanation
Indices: 425451--425547 Score: 76
Period size: 24 Copynumber: 4.0 Consensus size: 24
425441 GCAACGACAA
*
425451 CAGCAACAGCAACCAAAAGCAGAT
1 CAGCAACAGCAACCAGAAGCAGAT
* * *
425475 C-GACAATAGCAA-TAGCAATCAGA-
1 CAG-CAACAGCAACCAG-AAGCAGAT
* *
425498 -AGCAGATCAACAACTAGAAGCAGAT
1 CAGCA-A-CAGCAACCAGAAGCAGAT
425523 CAGCAACAGCAACCAGAAGCAGAT
1 CAGCAACAGCAACCAGAAGCAGAT
425547 C
1 C
425548 GACAATAACA
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
22 2 0.04
23 4 0.07
24 42 0.75
25 4 0.07
26 4 0.07
ACGTcount: A:0.47, C:0.26, G:0.19, T:0.08
Consensus pattern (24 bp):
CAGCAACAGCAACCAGAAGCAGAT
Found at i:427212 original size:19 final size:20
Alignment explanation
Indices: 427178--427216 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
427168 AAACATCAAT
427178 TAATGAAAAAGATAATTTTA
1 TAATGAAAAAGATAATTTTA
*
427198 TAATGAAAAA-TTAATTTTA
1 TAATGAAAAAGATAATTTTA
427217 CATGTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (20 bp):
TAATGAAAAAGATAATTTTA
Found at i:429469 original size:15 final size:16
Alignment explanation
Indices: 429440--429475 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
429430 TTGTTTAAAG
*
429440 TTTTAGTTTTGTTATT
1 TTTTAATTTTGTTATT
429456 TTTTAATTTT-TTATT
1 TTTTAATTTTGTTATT
429471 TTTTA
1 TTTTA
429476 TGTTTTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (16 bp):
TTTTAATTTTGTTATT
Found at i:429471 original size:7 final size:7
Alignment explanation
Indices: 429440--429482 Score: 50
Period size: 8 Copynumber: 5.6 Consensus size: 7
429430 TTGTTTAAAG
429440 TTTTAGTT
1 TTTTA-TT
429448 TTGTTATT
1 TT-TTATT
429456 TTTTAATT
1 TTTT-ATT
429464 TTTTATT
1 TTTTATT
429471 TTTTATGT
1 TTTTAT-T
429479 TTTT
1 TTTT
429483 GTAGATTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 11 0.34
8 18 0.56
9 3 0.09
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (7 bp):
TTTTATT
Found at i:432660 original size:31 final size:32
Alignment explanation
Indices: 432607--432675 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
432597 AGAATACATA
*
432607 GATACATTTAGGTCAAAAACCCAGAATGTATT
1 GATACATTTAGGTCAAAAACCCAGAATGTATC
*
432639 GATACATTT-GGATC-AAAACCCATAATGTATC
1 GATACATTTAGG-TCAAAAACCCAGAATGTATC
432670 GATACA
1 GATACA
432676 ATAAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 23 0.68
32 11 0.32
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (32 bp):
GATACATTTAGGTCAAAAACCCAGAATGTATC
Found at i:436064 original size:2 final size:2
Alignment explanation
Indices: 436057--436086 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
436047 GATTTTATTA
*
436057 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
436087 TTCATACAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:437569 original size:10 final size:10
Alignment explanation
Indices: 437537--437570 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
437527 TTTATTGATG
437537 GAAAAAAGAA
1 GAAAAAAGAA
*
437547 CAAAAAAGAAA
1 GAAAAAAG-AA
437558 GAAAAAAGAA
1 GAAAAAAGAA
437568 GAA
1 GAA
437571 GAAGAGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (10 bp):
GAAAAAAGAA
Found at i:437853 original size:14 final size:15
Alignment explanation
Indices: 437832--437866 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
437822 ATACAACTCT
*
437832 GAAAAAAAAAAAGAA
1 GAAAAAAAAAAGGAA
437847 GAAAAAAAAAAGGAA
1 GAAAAAAAAAAGGAA
437862 GAAAA
1 GAAAA
437867 GTTGGGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAAAGGAA
Found at i:438863 original size:25 final size:25
Alignment explanation
Indices: 438835--438981 Score: 75
Period size: 25 Copynumber: 6.1 Consensus size: 25
438825 AATAATCTGT
438835 ATATTAATAATAATATTTTATTATA
1 ATATTAATAATAATATTTTATTATA
*
438860 ATA-TAATAAAAAATAATTTT-TTAT-
1 ATATTAAT-AATAAT-ATTTTATTATA
*
438884 -TATT--TAATAATATATTATTATA
1 ATATTAATAATAATATTTTATTATA
** * * *
438906 ATATT--TTTTATTATTTAATAATA
1 ATATTAATAATAATATTTTATTATA
*
438929 A-ATTATTATAAT-ATTTTTTATTATA
1 ATATTA--ATAATAATATTTTATTATA
*
438954 ATA-AAATAAATAAT-TTATTATTATA
1 ATATTAAT-AATAATATT-TTATTATA
438979 ATA
1 ATA
438982 ATTTTATATT
Statistics
Matches: 92, Mismatches: 16, Indels: 28
0.68 0.12 0.21
Matches are distributed among these distances:
20 4 0.04
21 9 0.10
22 4 0.04
23 21 0.23
24 10 0.11
25 36 0.39
26 8 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATTAATAATAATATTTTATTATA
Found at i:438928 original size:36 final size:36
Alignment explanation
Indices: 438875--438993 Score: 124
Period size: 33 Copynumber: 3.3 Consensus size: 36
438865 ATAAAAAATA
438875 ATTTTTTATTA-TT--TAATAATATATTATTATAAT
1 ATTTTTTATTATTTAATAATAATATATTATTATAAT
438908 ATTTTTTATTATTTAATAAT-A-A-ATTATTATAAT
1 ATTTTTTATTATTTAATAATAATATATTATTATAAT
* *
438941 ATTTTTTATTATAATAAAATAAATAATTTATTATTATAAT
1 ATTTTTTATTAT--T-TAAT-AATAATATATTATTATAAT
*
438981 AATTTTATATTAT
1 -ATTTTTTATTAT
438994 ATTTAAAATT
Statistics
Matches: 72, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
33 34 0.47
34 3 0.04
35 2 0.03
36 7 0.10
37 3 0.04
38 1 0.01
40 11 0.15
41 11 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (36 bp):
ATTTTTTATTATTTAATAATAATATATTATTATAAT
Found at i:438949 original size:15 final size:15
Alignment explanation
Indices: 438875--438956 Score: 65
Period size: 15 Copynumber: 5.1 Consensus size: 15
438865 ATAAAAAATA
438875 ATTTTTTATTATTTAAT
1 ATTTTTTATTA--TAAT
* *
438892 AATATATTATTATAAT
1 -ATTTTTTATTATAAT
438908 ATTTTTTATTATTTAAT
1 ATTTTTTATTA--TAAT
***
438925 AATAAATTATTATAAT
1 -ATTTTTTATTATAAT
438941 ATTTTTTATTATAAT
1 ATTTTTTATTATAAT
438956 A
1 A
438957 AAATAAATAA
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
15 22 0.43
16 8 0.16
17 4 0.08
18 17 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTTTATTATAAT
Found at i:438964 original size:33 final size:33
Alignment explanation
Indices: 438875--438952 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
438865 ATAAAAAATA
*
438875 ATTTTTTATTATTTAATAATATATTATTATAAT
1 ATTTTTTATTATTTAATAATAAATTATTATAAT
438908 ATTTTTTATTATTTAATAATAAATTATTATAAT
1 ATTTTTTATTATTTAATAATAAATTATTATAAT
438941 ATTTTTTATTAT
1 ATTTTTTATTAT
438953 AATAAAATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (33 bp):
ATTTTTTATTATTTAATAATAAATTATTATAAT
Found at i:439868 original size:16 final size:16
Alignment explanation
Indices: 439842--439889 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 16
439832 TTTAATATTT
439842 ATAAAATTTATAATTAA
1 ATAAAA-TTATAATTAA
*
439859 ATAAAATTATAAGT-A
1 ATAAAATTATAATTAA
439874 ATAAAATT-TAATTAA
1 ATAAAATTATAATTAA
439889 A
1 A
439890 AATCTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 4 0.14
15 11 0.39
16 7 0.25
17 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:439941 original size:13 final size:13
Alignment explanation
Indices: 439925--439950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
439915 TAAAATTTAA
439925 TTATATAAAAAAT
1 TTATATAAAAAAT
439938 TTATATAAAAAAT
1 TTATATAAAAAAT
439951 AAAATAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTATATAAAAAAT
Found at i:440620 original size:14 final size:14
Alignment explanation
Indices: 440601--440627 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
440591 ACATAACATA
440601 AATAAAAAATAATT
1 AATAAAAAATAATT
440615 AATAAAAAATAAT
1 AATAAAAAATAAT
440628 ATAAACATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAAAAAATAATT
Found at i:441380 original size:15 final size:15
Alignment explanation
Indices: 441359--441404 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
441349 ATTTTTAAAT
441359 AAATTTTATTAATAA
1 AAATTTTATTAATAA
*
441374 TAATTTTATTTAATTAA
1 AAATTTTA-TTAA-TAA
*
441391 AAATTTTATAAATA
1 AAATTTTATTAATA
441405 TTAAAATCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 9 0.35
16 7 0.27
17 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATTTTATTAATAA
Found at i:441397 original size:17 final size:16
Alignment explanation
Indices: 441359--441399 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
441349 ATTTTTAAAT
441359 AAATTTTA-TTAATAA
1 AAATTTTATTTAATAA
*
441374 TAATTTTATTTAATTAA
1 AAATTTTATTTAA-TAA
441391 AAATTTTAT
1 AAATTTTAT
441400 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 4 0.18
17 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATTTTATTTAATAA
Found at i:442063 original size:18 final size:18
Alignment explanation
Indices: 442013--442072 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
442003 TATATGAAAT
*
442013 AAAAT-AAATTATTAATAT
1 AAAATAAAATTATT-ATAA
*
442031 ATAA-AAAATTATTATAA
1 AAAATAAAATTATTATAA
442048 AAATATAAAATT-TTATAA
1 AAA-ATAAAATTATTATAA
442066 AAAATAA
1 AAAATAA
442073 CATAAATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 9 0.25
18 21 0.58
19 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATAAAATTATTATAA
Found at i:442063 original size:21 final size:21
Alignment explanation
Indices: 442020--442072 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
442010 AATAAAATAA
* *
442020 ATTATTAATATATAAAAAATT
1 ATTATAAAAATATAAAAAATT
442041 ATTATAAAAATAT--AAAATT
1 ATTATAAAAATATAAAAAATT
442060 -TTATAAAAA-ATAA
1 ATTATAAAAATATAA
442073 CATAAATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 2 0.07
18 9 0.32
19 6 0.21
21 11 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTATAAAAATATAAAAAATT
Found at i:442315 original size:314 final size:312
Alignment explanation
Indices: 441659--442535 Score: 1263
Period size: 314 Copynumber: 2.8 Consensus size: 312
441649 TGCATATAAT
*
441659 ATAAATATACGTACATATAAAAATATACATGAAATAAAATAAATTATTAATATATAAAAAATTAT
1 ATAAATATACGTACATATAAAAATATATATGAAATAAAATAAATTATTAATATATAAAAAATTAT
* * *
441724 TATAAAAATAT-AAATTTTATATAAAAAAAACATAAATATGAGTATATAAATTTTTTTCTTTCTT
66 TATAAAAATATAAAATTTTATATAAAAATAACATAAATA-CAATATATAAA-TTTTTTC-TTC-T
* * * *
441788 TCATTCTTTTTTCTCTTTTTTTTCTTTTTCTTTTCAACCTATCAAAAAAGTGGTTGAAAGCAAAA
127 TCCTT-TTTTTTCTC-TTTTTTTCTTTTTCTTTTCAGCCTACCAAAAAA-TGGTTGAAAGCCAAA
* *
441853 AAAAATAAAAATTGCCAAATGTTAAAAATAAAAATATACATTAAATAAAATAAATTATTAATATG
189 AAAAA-AAAAATTACCAAATGTCAAAAA-AAAAATATACATTAAATAAAATAAATTATTAATATG
*
441918 T-AAAAAAATATAAAAATATAATATTTTAAATATAAAAAATATTTAATATATGTACATGAC
252 TAAAAAAAATATAAAAATATAATATTTTAAATATAAAAAATATTTAATATATGCACATGAC
*
441978 ATAAATATACGTATATATAAAAATATATATGAAATAAAATAAATTATTAATATATAAAAAATTAT
1 ATAAATATACGTACATATAAAAATATATATGAAATAAAATAAATTATTAATATATAAAAAATTAT
442043 TATAAAAATATAAAATTTTATA-AAAAATAACATAAATACAAATATATAAATTTTTTCATTCTTG
66 TATAAAAATATAAAATTTTATATAAAAATAACATAAATAC-AATATATAAATTTTTTC-TTCTT-
* * *
442107 CCTTTTTTTTCTCTTTTTTTCTTTTTCTTTTCTGCTTACCAAATAATGGTTGAAAGCCAAAAAAA
128 CCTTTTTTTTCTCTTTTTTTCTTTTTCTTTTCAGCCTACCAAAAAATGGTTGAAAGCCAAAAAAA
442172 AAAAAATTACCAAATGTCAAAAAGAAAAATATACATTAAAT-AAATAAATTATTAATATGTAAAA
193 AAAAAATTACCAAATGTCAAAAA-AAAAATATACATTAAATAAAATAAATTATTAATATGTAAAA
442236 AAATATATAAAAATATAATATTTTAAATAT-AAAAATATTTAATATATGCACATGAC
257 AAA-ATATAAAAATATAATATTTTAAATATAAAAAATATTTAATATATGCACATGAC
* * *
442292 ATAAATATACGTACATATAAAAATATATGTGAAATAAAATGAATTATTAATATGTAAAAAATTAT
1 ATAAATATACGTACATATAAAAATATATATGAAATAAAATAAATTATTAATATATAAAAAATTAT
*
442357 TATAAAAATATAAAATTTTATATAAAAATAACGTAAATACAATATATAAA---TTT-TT-TT-C-
66 TATAAAAATATAAAATTTTATATAAAAATAACATAAATACAATATATAAATTTTTTCTTCTTCCT
* *
442415 TTTTTTTCTCCTTTTTTC-TTTTCTTTTCAGCCTACCAAAAAAAATGGTTGAAAGCC----GAAA
131 TTTTTTTCTCTTTTTTTCTTTTTCTTTTCAGCCTACC--AAAAAATGGTTGAAAGCCAAAAAAAA
* *
442475 AAAAATTACCAAATGTC-AAAAAAAAATATA-A-TAAATAAAATAAATTATGAATATATAAAAA
194 AAAAATTACCAAATGTCAAAAAAAAAATATACATTAAATAAAATAAATTATTAATATGTAAAAA
442536 TATAATATTT
Statistics
Matches: 520, Mismatches: 29, Indels: 38
0.89 0.05 0.06
Matches are distributed among these distances:
298 5 0.01
299 23 0.04
300 9 0.02
301 4 0.01
302 20 0.04
304 16 0.03
305 17 0.03
306 18 0.03
308 2 0.00
309 2 0.00
311 3 0.01
313 19 0.04
314 161 0.31
315 61 0.12
316 28 0.05
317 11 0.02
318 13 0.03
319 98 0.19
320 10 0.02
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.37
Consensus pattern (312 bp):
ATAAATATACGTACATATAAAAATATATATGAAATAAAATAAATTATTAATATATAAAAAATTAT
TATAAAAATATAAAATTTTATATAAAAATAACATAAATACAATATATAAATTTTTTCTTCTTCCT
TTTTTTTCTCTTTTTTTCTTTTTCTTTTCAGCCTACCAAAAAATGGTTGAAAGCCAAAAAAAAAA
AAATTACCAAATGTCAAAAAAAAAATATACATTAAATAAAATAAATTATTAATATGTAAAAAAAA
TATAAAAATATAATATTTTAAATATAAAAAATATTTAATATATGCACATGAC
Found at i:442370 original size:21 final size:20
Alignment explanation
Indices: 442346--442386 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
442336 TATTAATATG
442346 TAAAAAATTATTATAAAAATA
1 TAAAAAATTA-TATAAAAATA
**
442367 TAAAATTTTATATAAAAATA
1 TAAAAAATTATATAAAAATA
442387 ACGTAAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAAATTATATAAAAATA
Found at i:442377 original size:18 final size:19
Alignment explanation
Indices: 442349--442387 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
442339 TAATATGTAA
442349 AAAATTATTATA-AAAATAT
1 AAAATTATTATATAAAA-AT
442368 AAAATT-TTATATAAAAAT
1 AAAATTATTATATAAAAAT
442386 AA
1 AA
442388 CGTAAATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTATTATATAAAAAT
Found at i:442777 original size:22 final size:22
Alignment explanation
Indices: 442728--442777 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
442718 ATACGATATG
*
442728 AATATAACATAAATAAAAAATA
1 AATAAAACATAAATAAAAAATA
* *
442750 ATTAAAACAT-AATAAAAACTA
1 AATAAAACATAAATAAAAAATA
442771 ACATAAA
1 A-ATAAA
442778 CATGATACGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (22 bp):
AATAAAACATAAATAAAAAATA
Found at i:442956 original size:19 final size:19
Alignment explanation
Indices: 442934--442976 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
442924 GATATGAATA
*
442934 TATAAATATAAAATATATT
1 TATAAATATAAAATAAATT
* *
442953 TATAAATATTACATAAATT
1 TATAAATATAAAATAAATT
442972 TATAA
1 TATAA
442977 TATTTTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TATAAATATAAAATAAATT
Found at i:443068 original size:12 final size:12
Alignment explanation
Indices: 443047--443096 Score: 66
Period size: 12 Copynumber: 4.1 Consensus size: 12
443037 ATAAAATAAT
*
443047 AAATACATAAAA
1 AAATATATAAAA
443059 AAATATATAAAA
1 AAATATATAAAA
443071 TAAA-ATATATAAA
1 -AAATATATA-AAA
443084 AAATATATAAAA
1 AAATATATAAAA
443096 A
1 A
443097 TATAATATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
12 23 0.68
13 11 0.32
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATATATAAAA
Found at i:443086 original size:16 final size:16
Alignment explanation
Indices: 443037--443088 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
443027 TTTCTCATAT
*
443037 ATAAAATA-ATAAATAC
1 ATAAAATATATAAA-AA
* *
443053 ATAAAAAAATATATAAA
1 AT-AAAATATATAAAAA
443070 ATAAAATATATAAAAA
1 ATAAAATATATAAAAA
443086 ATA
1 ATA
443089 TATAAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
16 17 0.59
17 8 0.28
18 4 0.14
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
ATAAAATATATAAAAA
Found at i:443110 original size:27 final size:26
Alignment explanation
Indices: 443033--443137 Score: 90
Period size: 26 Copynumber: 4.0 Consensus size: 26
443023 TTTTTTTCTC
** *
443033 ATATATAAAATAATAAATACATAAAAAA
1 ATATATAAAAT-AT-AATATTTTAAAAA
* *
443061 ATATATAAAATAAAATA-TATAAAAA
1 ATATATAAAATATAATATTTTAAAAA
443086 ATATATAAAAATATAATATTTTAAATAA
1 ATATAT-AAAATATAATATTTTAAA-AA
*
443114 A-AAATAAAATATACAT-TTTTAAAA
1 ATATATAAAATATA-ATATTTTAAAA
443138 TTTTTTCTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
25 12 0.18
26 29 0.44
27 11 0.17
28 14 0.21
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
ATATATAAAATATAATATTTTAAAAA
Found at i:443172 original size:18 final size:19
Alignment explanation
Indices: 443141--443182 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
443131 TTTAAAATTT
443141 TTTCTTATAAATTTATTTTC
1 TTTCTTAT-AATTTATTTTC
*
443161 TTTCTTAT-ATTTATTTTT
1 TTTCTTATAATTTATTTTC
443179 TTTC
1 TTTC
443183 ATTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.62
20 8 0.38
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTCTTATAATTTATTTTC
Found at i:443725 original size:14 final size:15
Alignment explanation
Indices: 443698--443735 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
443688 TTTATGTTTG
*
443698 TATATTTATGTTATAT
1 TATATTT-TTTTATAT
443714 T-TATTTTTTTATAT
1 TATATTTTTTTATAT
443728 TATATTTT
1 TATATTTT
443736 AATTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 8 0.40
15 11 0.55
16 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TATATTTTTTTATAT
Found at i:443726 original size:25 final size:24
Alignment explanation
Indices: 443688--443776 Score: 67
Period size: 25 Copynumber: 3.7 Consensus size: 24
443678 AAAAATATTT
* *
443688 TTTATGTTTGTATATT-TATGTTATA
1 TTTATTTTTTTATATTATAT-TT-TA
443713 TTTATTTTTTTATATTATATTTTA
1 TTTATTTTTTTATATTATATTTTA
* * * *
443737 ATTA-TTTTTAATATTGTATTCGTA
1 TTTATTTTTTTATATTATATT-TTA
443761 -TTATTTTTTATATATT
1 TTTATTTTTT-TATATT
443777 TAAAGTAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
23 17 0.32
24 12 0.23
25 21 0.40
26 3 0.06
ACGTcount: A:0.26, C:0.01, G:0.06, T:0.67
Consensus pattern (24 bp):
TTTATTTTTTTATATTATATTTTA
Found at i:443750 original size:23 final size:21
Alignment explanation
Indices: 443702--443777 Score: 70
Period size: 23 Copynumber: 3.7 Consensus size: 21
443692 TGTTTGTATA
*
443702 TTTATGTTATA-TTTATT-TT
1 TTTATATTATATTTTATTATT
443721 TTTATATTATATTTTAATTATT
1 TTTATATTATATTTT-ATTATT
* *
443743 TTTAATATTGTATTCGTATTATT
1 TTT-ATATTATATT-TTATTATT
443766 TTT-TA-TATATTT
1 TTTATATTATATTT
443778 AAAGTAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
19 10 0.21
20 8 0.17
21 5 0.11
22 5 0.11
23 18 0.38
24 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTATATTATATTTTATTATT
Found at i:444779 original size:23 final size:21
Alignment explanation
Indices: 444752--444796 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
444742 TATTCGTTTA
444752 TTCATACTATGTTTTTATTATTT
1 TTCATACTATG-TTTTATT-TTT
**
444775 TTCATGTTATGTTTTATTTTT
1 TTCATACTATGTTTTATTTTT
444796 T
1 T
444797 ATATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 9 0.45
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.69
Consensus pattern (21 bp):
TTCATACTATGTTTTATTTTT
Found at i:446929 original size:14 final size:14
Alignment explanation
Indices: 446910--447011 Score: 82
Period size: 14 Copynumber: 7.2 Consensus size: 14
446900 TATTAGTATC
446910 TTTAGTATAAATAT
1 TTTAGTATAAATAT
*
446924 TTTAGTACAAATAT
1 TTTAGTATAAATAT
*
446938 TTTATTATAAATAT
1 TTTAGTATAAATAT
* * *
446952 TTTTGACATATATAT
1 TTTAG-TATAAATAT
*
446967 TTT-GATATAAGTAT
1 TTTAG-TATAAATAT
* * *
446981 TTTAGCACAATTAT
1 TTTAGTATAAATAT
446995 TTT-GATATAAATAT
1 TTTAG-TATAAATAT
447009 TTT
1 TTT
447012 TTGACAGTAA
Statistics
Matches: 69, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
13 1 0.01
14 57 0.83
15 11 0.16
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (14 bp):
TTTAGTATAAATAT
Found at i:446946 original size:28 final size:27
Alignment explanation
Indices: 446915--447011 Score: 115
Period size: 28 Copynumber: 3.4 Consensus size: 27
446905 GTATCTTTAG
446915 TATAAATATTTTAGTACAAATATTTT-A
1 TATAAATATTTTAG-ACAAATATTTTGA
*
446942 TTATAAATATTTTTGACATATATATTTTGA
1 -TATAAATATTTTAGACA-A-ATATTTTGA
* *
446972 TATAAGTATTTTAGCACAATTATTTTGA
1 TATAAATATTTTAG-ACAAATATTTTGA
447000 TATAAATATTTT
1 TATAAATATTTT
447012 TTGACAGTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.05
28 33 0.55
29 20 0.33
30 4 0.07
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (27 bp):
TATAAATATTTTAGACAAATATTTTGA
Found at i:446967 original size:29 final size:28
Alignment explanation
Indices: 446851--447017 Score: 101
Period size: 29 Copynumber: 5.8 Consensus size: 28
446841 ATAATTCTTA
* * * *
446851 TTTATTATAGATATTTTTTATATATGTAT
1 TTTA-TATAAATATTTTTGACATATATAT
** * *
446880 TTTACTATAAGCACTTTTGATAT-TAGTAT
1 TTTA-TATAAATATTTTTGACATATA-TAT
*
446909 CTTTAGTATAAATATTTTAGTACA-A-ATAT
1 -TTTA-TATAAATATTTTTG-ACATATATAT
446938 TTTATTATAAATATTTTTGACATATATAT
1 TTTA-TATAAATATTTTTGACATATATAT
* *
446967 TTTGATATAAGTATTTTAGCACA-AT-TAT
1 TTT-ATATAAATATTTTTG-ACATATATAT
446995 TTTGATATAAATATTTTTTGACA
1 TTT-ATATAAATA-TTTTTGACA
447018 GTAACGTTTC
Statistics
Matches: 110, Mismatches: 19, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
27 3 0.03
28 37 0.34
29 49 0.45
30 19 0.17
31 2 0.02
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.51
Consensus pattern (28 bp):
TTTATATAAATATTTTTGACATATATAT
Found at i:448678 original size:2 final size:2
Alignment explanation
Indices: 448671--448697 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
448661 ACTAAAATGT
448671 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
448698 TCTAAAAGAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:450041 original size:15 final size:17
Alignment explanation
Indices: 450018--450055 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
450008 TGATTTTCTA
*
450018 AGTTGGTTGTT-TTTG-
1 AGTTAGTTGTTATTTGT
450033 AGTTAGTTGTTATTTGT
1 AGTTAGTTGTTATTTGT
450050 AGTTAG
1 AGTTAG
450056 CAAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 4 0.20
17 6 0.30
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.55
Consensus pattern (17 bp):
AGTTAGTTGTTATTTGT
Found at i:455013 original size:79 final size:79
Alignment explanation
Indices: 454882--455040 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
454872 TTAGGTTTAG
*
454882 AAGTTGTGTAAGAGAATAATGGGATTTTTATTTGTCAACGAAAGTATGCAGCTGATTTATTAAAA
1 AAGTTGTGCAAGAGAATAATGGGATTTTTATTTGTCAACGAAAGTATGCAGCTGATTTATTAAAA
454947 AAGAATGGTATGAT
66 AAGAATGGTATGAT
454961 AAGTTGTGCAAGAGAATAATGGGATTTTTATTTGTCAACGAAAGTATGCAGCTGATTTATTAAAA
1 AAGTTGTGCAAGAGAATAATGGGATTTTTATTTGTCAACGAAAGTATGCAGCTGATTTATTAAAA
455026 AAGAATGGTATGAT
66 AAGAATGGTATGAT
455040 A
1 A
455041 GGTTATAAGC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (79 bp):
AAGTTGTGCAAGAGAATAATGGGATTTTTATTTGTCAACGAAAGTATGCAGCTGATTTATTAAAA
AAGAATGGTATGAT
Found at i:455845 original size:15 final size:15
Alignment explanation
Indices: 455825--455854 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
455815 TTTTGATTGA
455825 TTTTCTGAGTTAGTT
1 TTTTCTGAGTTAGTT
455840 TTTTCTGAGTTAGTT
1 TTTTCTGAGTTAGTT
455855 GTTATTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.20, T:0.60
Consensus pattern (15 bp):
TTTTCTGAGTTAGTT
Found at i:456925 original size:2 final size:2
Alignment explanation
Indices: 456918--456960 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
456908 GTTTGATTTG
456918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
456959 AT
1 AT
456961 CACTACTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:457681 original size:23 final size:23
Alignment explanation
Indices: 457640--457683 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
457630 TAATTGTATT
457640 TATTTATAAAATATAAAAATATA
1 TATTTATAAAATATAAAAATATA
*
457663 TATTTA-AAAATTTATAAAATA
1 TATTTATAAAATATA-AAAATA
457684 ATAAAAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TATTTATAAAATATAAAAATATA
Found at i:460220 original size:25 final size:25
Alignment explanation
Indices: 460192--460242 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
460182 TTTTCACAAT
* *
460192 TTGTATCGATGCATTGTTCATTGTA
1 TTGTATCGATACATTATTCATTGTA
460217 TTGTATCGATACATTATTCATTGTA
1 TTGTATCGATACATTATTCATTGTA
460242 T
1 T
460243 CAATACATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.49
Consensus pattern (25 bp):
TTGTATCGATACATTATTCATTGTA
Found at i:462741 original size:51 final size:52
Alignment explanation
Indices: 462684--462796 Score: 147
Period size: 52 Copynumber: 2.2 Consensus size: 52
462674 CTGAGGGGAC
* *
462684 ACTCCAACCCCGGTTTTATTTCT-AAAACACCAATTTTCCACAATCGGGGAT
1 ACTCCAACCCCGATTTTATTTCTCAAAACACCAATTTTCCACAATCGAGGAT
* * * * * *
462735 ATTCCAACTCCGATTTTTTTTTTCAAAATACCAATTTTTCACAATCGAGGAT
1 ACTCCAACCCCGATTTTATTTCTCAAAACACCAATTTTCCACAATCGAGGAT
462787 ACTCCAACCC
1 ACTCCAACCC
462797 TGTTTTTTCA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
51 18 0.35
52 33 0.65
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (52 bp):
ACTCCAACCCCGATTTTATTTCTCAAAACACCAATTTTCCACAATCGAGGAT
Found at i:462814 original size:28 final size:29
Alignment explanation
Indices: 462778--462859 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 29
462768 ATTTTTCACA
462778 ATCGAGGATACTCCAACCCTGTTTTTTC-
1 ATCGAGGATACTCCAACCCTGTTTTTTCG
* * **
462806 ATCGGGGATACTCCAGCCCCATTATTTTCG
1 ATCGAGGATACTCCAACCCTGTT-TTTTCG
*
462836 A--GAGGATACTCCAACCCTGATTTT
1 ATCGAGGATACTCCAACCCTGTTTTT
462860 ATTTTCAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
27 3 0.07
28 34 0.79
29 5 0.12
30 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (29 bp):
ATCGAGGATACTCCAACCCTGTTTTTTCG
Found at i:462974 original size:79 final size:79
Alignment explanation
Indices: 462806--462986 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 79
462796 CTGTTTTTTC
* *
462806 ATCGGGGATACTCCAGCCCCATTATTTTCGAGAGGATACTCCAACCCTGATTTTATTTTCAAAAC
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTTCAAAAC
462871 ATCGATTTTCTATA
66 ATCGATTTTCTATA
*** * * * * *
462885 ATCAAAGATACTCCAACCCTATTTTTTTCGAGGGGATACTCTAACCCCGATTTTATTTTCAGAAC
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTTCAAAAC
*
462950 ATTGATTTT-TCATA
66 ATCGATTTTCT-ATA
* *
462964 ATTGGGGATACTCCAGCCCCATT
1 ATCGGGGATACTCCAACCCCATT
462987 GTTATCCCCA
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
78 1 0.01
79 83 0.99
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.35
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTTCAAAAC
ATCGATTTTCTATA
Found at i:467191 original size:79 final size:79
Alignment explanation
Indices: 467077--467244 Score: 218
Period size: 79 Copynumber: 2.1 Consensus size: 79
467067 AACAGGGCTA
* *
467077 GAGTATCCCCGATTATGGAAAATCAGTGTTCTGAAAATAAAACCGGGGTT-GAAATATCCCCTCG
1 GAGTATCCCCGATTATAGAAAATCAATGTTCTGAAAATAAAACCGGGGTTAG-AATATCCCCTCG
467141 AAAATAATAG-GGTTG
65 AAAATAA-AGAGGTTG
* * *
467156 GAGTATCCCTGATTATAGAAAATCGAAAT-TT-TGAAAATAAAATCGGGGTTAGAGTATCCCCTC
1 GAGTATCCCCGATTATAGAAAATC--AATGTTCTGAAAATAAAACCGGGGTTAGAATATCCCCTC
*
467219 GAAAATAACGAGGTTG
64 GAAAATAAAGAGGTTG
467235 GAGTATCCCC
1 GAGTATCCCC
467245 AATTGTGAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
78 1 0.01
79 72 0.92
80 3 0.04
81 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.26
Consensus pattern (79 bp):
GAGTATCCCCGATTATAGAAAATCAATGTTCTGAAAATAAAACCGGGGTTAGAATATCCCCTCGA
AAATAAAGAGGTTG
Found at i:467284 original size:130 final size:129
Alignment explanation
Indices: 467149--467517 Score: 442
Period size: 130 Copynumber: 2.8 Consensus size: 129
467139 CGAAAATAAT
467149 AGGGTTGGAGTATCCCTGATTATAGAAAATCGAAATTTTGAAAATAAAATCGGGGTTAGAGTATC
1 AGGGTTGGAGTATCCCTGATTAT-GAAAATCGAAATTTTGAAAATAAAATCGGGGTTAGAGTATC
* * **
467214 CCCTCGAAAATAACGAGGTTGGAGTATCCCCAATTGTGAAAAATCGATGCTTTAGAAAT-AAGGC
65 CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAATAAAATC
* * * * *
467278 TGGGGTTGGAGTAT-CCTCGATTGTGAGAAATC-AATATTTTGGAAATAAAATTGGGGTTGGAGT
1 -AGGGTTGGAGTATCCCT-GATTATGA-AAATCGAA-ATTTTGAAAATAAAATCGGGGTTAGAGT
* * * * *
467341 ATCCCCTC-AGAAATAACGGGGTTGGAGTATCTCCGATTATGAAAAATTGATGTTTTGGAAATAA
62 ATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAATAA
467405 AATC
126 AATC
* * ** *
467409 AGAGTTGGAGTATCCCTGATTATGGAAAATTGATGTTTT-AGAAATAAAACCGGGGTTAGAGTAT
1 AGGGTTGGAGTATCCCTGATTAT-GAAAATCGAAATTTTGA-AAATAAAATCGGGGTTAGAGTAT
* *
467473 CCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTGTAAAAAAT
64 CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAAT
467518 GGGATAACCC
Statistics
Matches: 201, Mismatches: 28, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
129 8 0.04
130 183 0.91
131 10 0.05
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (129 bp):
AGGGTTGGAGTATCCCTGATTATGAAAATCGAAATTTTGAAAATAAAATCGGGGTTAGAGTATCC
CCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAATAAAATC
Found at i:467301 original size:51 final size:51
Alignment explanation
Indices: 467230--467346 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
467220 AAAATAACGA
* * **
467230 GGTTGGAGTATCCCCAATTGTGAAAAATCGATGCTTTAGAAATAAGGCTGG
1 GGTTGGAGTATCCCCAATTGTGAAAAATCAATACTTTAGAAATAAAACTGG
* * * * * *
467281 GGTTGGAGTATCCTCGATTGTGAGAAATCAATATTTTGGAAATAAAATTGG
1 GGTTGGAGTATCCCCAATTGTGAAAAATCAATACTTTAGAAATAAAACTGG
467332 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
467347 TCAGAAATAA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCAATTGTGAAAAATCAATACTTTAGAAATAAAACTGG
Found at i:467362 original size:79 final size:79
Alignment explanation
Indices: 467279--467424 Score: 204
Period size: 79 Copynumber: 1.8 Consensus size: 79
467269 AAATAAGGCT
* * ** *
467279 GGGGTTGGAGTATC-CTCGATTGTGAGAAATCAATATTTTGGAAATAAAATTGGGGTTGGAGTAT
1 GGGGTTGGAGTATCTC-CGATTATGAAAAATCAATATTTTGGAAATAAAATCAGAGTTGGAGTAT
467343 CCCCTCAGAAATAAC
65 CCCCTCAGAAATAAC
** *
467358 GGGGTTGGAGTATCTCCGATTATGAAAAATTGATGTTTTGGAAATAAAATCAGAGTTGGAGTATC
1 GGGGTTGGAGTATCTCCGATTATGAAAAATCAATATTTTGGAAATAAAATCAGAGTTGGAGTATC
467423 CC
66 CC
467425 TGATTATGGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 57 0.98
80 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.30
Consensus pattern (79 bp):
GGGGTTGGAGTATCTCCGATTATGAAAAATCAATATTTTGGAAATAAAATCAGAGTTGGAGTATC
CCCTCAGAAATAAC
Found at i:467430 original size:51 final size:50
Alignment explanation
Indices: 467361--467475 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 50
467351 AAATAACGGG
* *
467361 GTTGGAGTATCTCCGATTATGAAAAATTGATGTTTTGGAAATAAAATCAGA
1 GTTGGAGTATC-CCGATTATGAAAAATTGATGTTTTAGAAATAAAACCAGA
* * *
467412 GTTGGAGTATCCCTGATTATGGAAAATTGATGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCC-GATTATGAAAAATTGATGTTTTAGAAATAAAACCAGA
*
467463 GTTAGAGTATCCC
1 GTTGGAGTATCCC
467476 CTTGAAAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 2 0.04
51 55 0.96
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.32
Consensus pattern (50 bp):
GTTGGAGTATCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCAGA
Found at i:467953 original size:19 final size:20
Alignment explanation
Indices: 467916--467957 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
467906 TTTTTTCCCT
467916 TTTAAAAACCTATACTTTCC
1 TTTAAAAACCTATACTTTCC
467936 TTTAAAAA-CT-TACATTTCC
1 TTTAAAAACCTATAC-TTTCC
467955 TTT
1 TTT
467958 TTCTTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 10 0.48
20 8 0.38
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAAAACCTATACTTTCC
Found at i:469798 original size:2 final size:2
Alignment explanation
Indices: 469791--469828 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
469781 GCTTAGATGC
469791 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
469829 CTCACAAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:473207 original size:22 final size:22
Alignment explanation
Indices: 473159--473222 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 22
473149 TCTTCTCAAT
* *
473159 AATAATAG-TTTTTTTTATTAT
1 AATAATAGATTTATTTTATTAA
**
473180 TCTAATAGATTTATTTTATTAA
1 AATAATAGATTTATTTTATTAA
473202 AATAATA-ATTTA--TTATTAA
1 AATAATAGATTTATTTTATTAA
473221 AA
1 AA
473223 ATTATAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 9 0.25
21 11 0.31
22 16 0.44
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (22 bp):
AATAATAGATTTATTTTATTAA
Found at i:473494 original size:31 final size:28
Alignment explanation
Indices: 473472--473531 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
473462 ATAGTTACAT
473472 TAAT-AATAATATTTTATTATAATATAA
1 TAATAAATAATATTTTATTATAATATAA
*
473499 TAATAAATAATTTTTTATTAT--T-TAA
1 TAATAAATAATATTTTATTATAATATAA
473524 TAATAAAT
1 TAATAAAT
473532 TATTATAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 11 0.35
26 1 0.03
27 4 0.13
28 15 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TAATAAATAATATTTTATTATAATATAA
Found at i:473516 original size:25 final size:25
Alignment explanation
Indices: 473472--473531 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
473462 ATAGTTACAT
473472 TAATAAT-AATATTTTATTATAATA
1 TAATAATAAATATTTTATTATAATA
* *
473496 TAATAATAAATAATTTT-TTATTATT
1 TAATAATAAAT-ATTTTATTATAATA
473521 TAATAATAAAT
1 TAATAATAAAT
473532 TATTATAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 7 0.22
25 20 0.62
26 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TAATAATAAATATTTTATTATAATA
Found at i:473979 original size:28 final size:29
Alignment explanation
Indices: 473946--474021 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 29
473936 TTTAATTTTT
*
473946 TTATAATTTTTAATTATTAATAAA-AGTAA
1 TTATAATTTTTAATT-TTAATAAATAATAA
** *
473975 -TATAAAATTTAATTTTATTAAATAATAA
1 TTATAATTTTTAATTTTAATAAATAATAA
*
474003 TTATATATTTTTATTTTTA
1 TTATA-ATTTTTAATTTTA
474022 TTTATAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 7 0.19
28 16 0.43
29 4 0.11
30 10 0.27
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (29 bp):
TTATAATTTTTAATTTTAATAAATAATAA
Found at i:474044 original size:29 final size:28
Alignment explanation
Indices: 473954--474045 Score: 80
Period size: 30 Copynumber: 3.2 Consensus size: 28
473944 TTTTATAATT
* *
473954 TTTAATTATTAATAAA-AGTAATATAAAA
1 TTTAATT-TTATTAAATAATAATATAAAA
**
473982 TTTAATTTTATTAAATAATAATTATATATT
1 TTTAATTTTATTAAATAATAA-TATA-AAA
*
474012 TTTATTTTTATTTATAATAA-AATATAAAA
1 TTTAATTTTA-TTA-AATAATAATATAAAA
474041 TTTAA
1 TTTAA
474046 ATTAATTTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
27 7 0.14
28 11 0.22
29 9 0.18
30 14 0.27
31 5 0.10
32 5 0.10
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (28 bp):
TTTAATTTTATTAAATAATAATATAAAA
Found at i:474104 original size:24 final size:23
Alignment explanation
Indices: 474077--474125 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
474067 GACCAATTTT
474077 TTAAATATATTATTTAAAAATAAA
1 TTAAATATATTATTTAAAAA-AAA
* * *
474101 TTAAATATTTTTTTTTAAAAAAA
1 TTAAATATATTATTTAAAAAAAA
474124 TT
1 TT
474126 TATTGAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAAATATATTATTTAAAAAAAA
Found at i:474934 original size:16 final size:16
Alignment explanation
Indices: 474913--474959 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
474903 ATTTAGGAAT
*
474913 AAATTAAAACTAAAAA
1 AAATTAAAAATAAAAA
*
474929 AAATTAAAAAT-ACAA
1 AAATTAAAAATAAAAA
*
474944 AACTTAAAAATAAAAA
1 AAATTAAAAATAAAAA
474960 CTTAAGTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATTAAAAATAAAAA
Found at i:474952 original size:14 final size:14
Alignment explanation
Indices: 474926--474964 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
474916 TTAAAACTAA
*
474926 AAAAAATTAAAAAT
1 AAAAACTTAAAAAT
474940 ACAAAACTTAAAAAT
1 A-AAAACTTAAAAAT
474955 AAAAACTTAA
1 AAAAACTTAA
474965 GTAATTTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAACTTAAAAAT
Found at i:475071 original size:17 final size:15
Alignment explanation
Indices: 475045--475086 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
475035 TTTTTTTATT
*
475045 ATATAAATTATATTAAA
1 ATATATATTAT-TT-AA
475062 ATATATATTATTTAA
1 ATATATATTATTTAA
475077 ATAT-TATTAT
1 ATATATATTAT
475087 CATCAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 6 0.25
16 2 0.08
17 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATATTATTTAA
Found at i:475254 original size:18 final size:18
Alignment explanation
Indices: 475231--475265 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
475221 ATATATTATT
475231 TTAAAA-TAAAATTAAAAG
1 TTAAAATTAAAA-TAAAAG
475249 TTAAAATTAAAATAAAA
1 TTAAAATTAAAATAAAA
475266 AATTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
TTAAAATTAAAATAAAAG
Found at i:475443 original size:57 final size:59
Alignment explanation
Indices: 475324--475444 Score: 147
Period size: 58 Copynumber: 2.1 Consensus size: 59
475314 ATTCGTATCG
* * **
475324 TATCTCCATTTATGATATATTTTACATAATTTATCATAATAATTTAATTTAAAGTATCA
1 TATCTCAATTTATGATATATTTTACATAATTTATCATAATAATTCAATTTAAAAAATCA
* * * * *
475383 TATCTCAATTTATGATAT-TTTTTCATAATTTATTATAGTGATTCAA-TTAAAAAATTA
1 TATCTCAATTTATGATATATTTTACATAATTTATCATAATAATTCAATTTAAAAAATCA
475440 TATCT
1 TATCT
475445 TTTTATGTGT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
57 13 0.25
58 23 0.43
59 17 0.32
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (59 bp):
TATCTCAATTTATGATATATTTTACATAATTTATCATAATAATTCAATTTAAAAAATCA
Found at i:475733 original size:16 final size:17
Alignment explanation
Indices: 475701--475744 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
475691 AATATTTTTA
475701 AAAAATATTTA-TTAATT
1 AAAAAT-TTTATTTAATT
*
475718 -ATAATTTTATTTAATT
1 AAAAATTTTATTTAATT
475734 AAAAATTTTAT
1 AAAAATTTTAT
475745 AAATATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 4 0.17
16 10 0.43
17 9 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAAAATTTTATTTAATT
Found at i:476110 original size:9 final size:9
Alignment explanation
Indices: 476096--476134 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
476086 AAAAAAATTC
476096 TTTCTTTCT
1 TTTCTTTCT
*
476105 TTTCTTTTT
1 TTTCTTTCT
* *
476114 TTTCCTTCC
1 TTTCTTTCT
476123 TTTCTTTCT
1 TTTCTTTCT
476132 TTT
1 TTT
476135 GTTTTAGCTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:479451 original size:14 final size:13
Alignment explanation
Indices: 479428--479485 Score: 73
Period size: 14 Copynumber: 4.3 Consensus size: 13
479418 AAACATATAA
479428 TTTTTT-CTTTCTT
1 TTTTTTCCTTT-TT
479441 TTTTTTCCTTTTT
1 TTTTTTCCTTTTT
479454 TCTTTTTCCTTTTT
1 T-TTTTTCCTTTTT
*
479468 TTCTTTTTCTTTTT
1 TT-TTTTCCTTTTT
479482 TTTT
1 TTTT
479486 CTTTCTTCCT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
13 12 0.29
14 29 0.71
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTCCTTTTT
Found at i:479454 original size:21 final size:20
Alignment explanation
Indices: 479428--479485 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
479418 AAACATATAA
479428 TTTTTTCTTTCTTTTTTTTCC
1 TTTTTTCTTT-TTTTTTTTCC
*
479449 TTTTTTCTTTTTCCTTTTTTTC
1 TTTTTTCTTTTT--TTTTTTCC
479471 -TTTTTCTTTTTTTTT
1 TTTTTTCTTTTTTTTT
479486 CTTTCTTCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 21 0.62
22 7 0.21
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTTCTTTTTTTTTTTCC
Found at i:479468 original size:16 final size:16
Alignment explanation
Indices: 479449--479497 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 16
479439 TTTTTTTTCC
479449 TTTTTTCTTTTTCC-T
1 TTTTTTCTTTTTCCTT
*
479464 TTTTTTCTTTTTCTTT
1 TTTTTTCTTTTTCCTT
479480 TTTTTTCTTTCTTCCTT
1 TTTTTTCTTT-TTCCTT
479497 T
1 T
479498 CCTTTTCAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 13 0.43
16 11 0.37
17 6 0.20
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTCTTTTTCCTT
Found at i:479485 original size:32 final size:33
Alignment explanation
Indices: 479430--479502 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 33
479420 ACATATAATT
479430 TTTTCTTTCTTTTTTTTCCTTTTTTCTTT-TTCC
1 TTTTCTTTC-TTTTTTTCCTTTTTTCTTTCTTCC
*
479463 TTTT-TTTCTTTTTCTT-TTTTTTTCTTTCTTCC
1 TTTTCTTTCTTTTT-TTCCTTTTTTCTTTCTTCC
*
479495 TTTCCTTT
1 TTTTCTTT
479503 TCAGCTGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 15 0.43
32 13 0.37
33 7 0.20
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (33 bp):
TTTTCTTTCTTTTTTTCCTTTTTTCTTTCTTCC
Found at i:479490 original size:14 final size:14
Alignment explanation
Indices: 479428--479492 Score: 68
Period size: 14 Copynumber: 4.9 Consensus size: 14
479418 AAACATATAA
479428 TTTTTTCTTTCTTT
1 TTTTTTCTTTCTTT
*
479442 TTTTTCCTTT-TTT
1 TTTTTTCTTTCTTT
*
479455 CTTTTTC---CTTT
1 TTTTTTCTTTCTTT
479466 TTTTCTT-TTTCTTT
1 TTTT-TTCTTTCTTT
479480 TTTTTTCTTTCTT
1 TTTTTTCTTTCTT
479493 CCTTTCCTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
11 6 0.15
12 2 0.05
13 10 0.24
14 23 0.56
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTCTTTCTTT
Found at i:479498 original size:28 final size:28
Alignment explanation
Indices: 479428--479504 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
479418 AAACATATAA
479428 TTTTTTCTTTCTTT-TTTTTCCTTTTTTC
1 TTTTTTCTTTCTTTCTTTTT-CTTTTTTC
* *
479456 TTTTTCCTTTTTTTCTTTTTCTTTTTT-
1 TTTTTTCTTTCTTTCTTTTTCTTTTTTC
* *
479483 TTTCTTTCTTCCTTTCCTTTTC
1 TTT-TTTCTTTCTTTCTTTTTC
479505 AGCTGGAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 3 0.07
28 33 0.80
29 5 0.12
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (28 bp):
TTTTTTCTTTCTTTCTTTTTCTTTTTTC
Found at i:479770 original size:19 final size:18
Alignment explanation
Indices: 479731--479784 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
479721 TAAGATCTTT
479731 TTTTATATTATTT-T-TTAA
1 TTTTATA-TATTTATATT-A
479749 TTTTATATATTTAATATTA
1 TTTTATATATTT-ATATTA
*
479768 TTTTTTATATTTATATT
1 TTTTATATATTTATATT
479785 TAAAATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 5 0.16
18 12 0.38
19 13 0.41
20 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATATATTTATATTA
Found at i:479791 original size:27 final size:27
Alignment explanation
Indices: 479735--479795 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
479725 ATCTTTTTTT
*
479735 ATATTATTTTTTAATTTTATATATTTA
1 ATATTATTTTTTAATTTTATATATTAA
479762 ATATTATTTTTT-ATATTTATAT-TTAAA
1 ATATTATTTTTTAAT-TTTATATATT-AA
479789 ATATTAT
1 ATATTAT
479796 ATATTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
ATATTATTTTTTAATTTTATATATTAA
Found at i:479810 original size:39 final size:39
Alignment explanation
Indices: 479729--479810 Score: 96
Period size: 41 Copynumber: 2.1 Consensus size: 39
479719 AATAAGATCT
** * *
479729 TTTTTTATATTATTTTTTAATTTTATATATTTAATATTA
1 TTTTTTATATTATTTTAAAATATTATATATTTAATATAA
479768 TTTTTTATATTTATATTTAAAATATTATATATTT-AT-TAA
1 TTTTTTATA-TTAT-TTTAAAATATTATATATTTAATATAA
479807 TTTT
1 TTTT
479811 AAATTTACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
39 15 0.41
40 6 0.16
41 16 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (39 bp):
TTTTTTATATTATTTTAAAATATTATATATTTAATATAA
Found at i:479880 original size:25 final size:25
Alignment explanation
Indices: 479849--479896 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
479839 TATATTTTAA
* * *
479849 TAAATTTATTTATAATAATAAATTT
1 TAAATTTAATAATAATAAAAAATTT
479874 TAAATTTAATAATAATAAAAAAT
1 TAAATTTAATAATAATAAAAAAT
479897 ATATCTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TAAATTTAATAATAATAAAAAATTT
Found at i:482032 original size:21 final size:19
Alignment explanation
Indices: 482008--482062 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
481998 TTCAACAATT
482008 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAA-AGT-AA
* **
482029 TGTATCGATACATAAGTGT
1 TGTATCGATACAAAAGTAA
482048 TGTATCGATACAAAA
1 TGTATCGATACAAAA
482063 CTACCCTGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:486147 original size:18 final size:18
Alignment explanation
Indices: 486120--486177 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
486110 AGGAATCAGG
* *
486120 ATTTTTTAAGTATCTTAA
1 ATTTTCTAAGAATCTTAA
* *
486138 ATTTTCTAAGAATCATAT
1 ATTTTCTAAGAATCTTAA
*
486156 ATTTTCTAGGAATCTTAA
1 ATTTTCTAAGAATCTTAA
486174 ATTT
1 ATTT
486178 CTGTAAAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (18 bp):
ATTTTCTAAGAATCTTAA
Found at i:489014 original size:18 final size:18
Alignment explanation
Indices: 488991--489048 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
488981 GGAATTACAG
488991 ATTTTCTAGAAATCTTAA
1 ATTTTCTAGAAATCTTAA
* *
489009 ATTTTCTA-AGAATCATAG
1 ATTTTCTAGA-AATCTTAA
*
489027 ATTTTCTAGGAATCTTAA
1 ATTTTCTAGAAATCTTAA
489045 ATTT
1 ATTT
489049 CTGTAATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 1 0.03
18 32 0.97
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (18 bp):
ATTTTCTAGAAATCTTAA
Found at i:489509 original size:20 final size:19
Alignment explanation
Indices: 489484--489534 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
489474 CCACTATTTC
489484 TATCGATACATG-GCACATTG
1 TATCGATACATGAG-A-ATTG
489504 TATCGATACATGATGAATTG
1 TATCGATACATGA-GAATTG
489524 TATCGATACAT
1 TATCGATACAT
489535 TGCTTCAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 27 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (19 bp):
TATCGATACATGAGAATTG
Found at i:495845 original size:21 final size:22
Alignment explanation
Indices: 495821--495870 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
495811 ATCAAATCTT
* *
495821 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
495842 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
495864 --TCAAAAT
1 CTTCAAAAT
495871 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:498252 original size:20 final size:20
Alignment explanation
Indices: 498227--498280 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
498217 CTACCACTGT
* *
498227 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGACAAA
*
498247 TTGTATCGATACATGATAAA
1 TTGTATCGATACATGACAAA
498267 TTGTATCGATACAT
1 TTGTATCGATACAT
498281 TGCTTCAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGACAAA
Found at i:499303 original size:2 final size:2
Alignment explanation
Indices: 499287--499331 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
499277 ATGGTTTGAT
499287 TA TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
499327 TA TA T
1 TA TA T
499332 TATCACTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:500009 original size:21 final size:21
Alignment explanation
Indices: 499967--500006 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
499957 GTATTATGAA
*
499967 TTTTGATAAAAATAAATAAAT
1 TTTTGATAAAAATAAAAAAAT
*
499988 TTTTGA-AAAATTAAAAAAA
1 TTTTGATAAAAATAAAAAAA
500007 ATTATATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (21 bp):
TTTTGATAAAAATAAAAAAAT
Found at i:501385 original size:24 final size:24
Alignment explanation
Indices: 501323--501385 Score: 56
Period size: 24 Copynumber: 2.6 Consensus size: 24
501313 TATTAAATAT
* *
501323 CTAAATTTATTAAATCATTAAAAAA
1 CTAAATATA-TAAATCAATAAAAAA
* * *
501348 -TGAATATGTAAAATTAATAAAAAA
1 CTAAATATAT-AAATCAATAAAAAA
501372 CTAAATATATAAAT
1 CTAAATATATAAAT
501386 AGATATTAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
23 1 0.03
24 21 0.72
25 7 0.24
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (24 bp):
CTAAATATATAAATCAATAAAAAA
Found at i:504842 original size:42 final size:42
Alignment explanation
Indices: 504783--504867 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
504773 TATCCTTTAG
504783 TCAAACTACTGCAGACACTTACTCAAATCCAAGGTCCAAACC
1 TCAAACTACTGCAGACACTTACTCAAATCCAAGGTCCAAACC
** *
504825 TCAAACTACTGTTGACACTTACTCAAATCCAAGGTCTAAACC
1 TCAAACTACTGCAGACACTTACTCAAATCCAAGGTCCAAACC
504867 T
1 T
504868 TAACAAACAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.36, C:0.31, G:0.09, T:0.24
Consensus pattern (42 bp):
TCAAACTACTGCAGACACTTACTCAAATCCAAGGTCCAAACC
Found at i:505309 original size:12 final size:12
Alignment explanation
Indices: 505292--505316 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
505282 AAAAAAATTC
505292 AAATGTATCGAT
1 AAATGTATCGAT
505304 AAATGTATCGAT
1 AAATGTATCGAT
505316 A
1 A
505317 CATTCTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (12 bp):
AAATGTATCGAT
Found at i:505395 original size:13 final size:13
Alignment explanation
Indices: 505377--505401 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
505367 TTCAACAATT
505377 TGTATCGATACAA
1 TGTATCGATACAA
505390 TGTATCGATACA
1 TGTATCGATACA
505402 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:505468 original size:20 final size:20
Alignment explanation
Indices: 505443--505497 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
505433 GCCAAGGAAA
*
505443 TGTATCGATACATTTTTCTG
1 TGTATCGATACATTTATCTG
* ** *
505463 TGTATCGTTACATGGATCTT
1 TGTATCGATACATTTATCTG
505483 TGTATCGATACATTT
1 TGTATCGATACATTT
505498 GGAAATTTTA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.47
Consensus pattern (20 bp):
TGTATCGATACATTTATCTG
Found at i:507969 original size:54 final size:50
Alignment explanation
Indices: 507846--508183 Score: 168
Period size: 52 Copynumber: 6.4 Consensus size: 50
507836 CTCAATTCTC
* * * * *
507846 CACAATCGGGGATATTTCAACTCCGATTTTATTTTCAAGACACTAATTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACAAATTTT
* *
507896 CTATAATCGGGGATACTCCAACTTCGATTTTATTTCCAAAAAAACACCAAATTTT
1 C-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC---AAAACA-CAAATTTT
* * * ***
507951 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCC--AACCCCGTTATTT
1 CACAATCGGGGATACTCCAACTCCGATT--T--T-----AT-TTCCAAAACACAAAT-TTT
* * * * * * *
508009 C-CGA--GGAGATACTCCAACCCCGACTTTATTTCCAAAATACTGATTTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC-AAATTTT
* * * *
508057 CCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACATCAATTTTT
1 -CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACA-CAAATTTT
* *
508109 C-CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 CAC---AATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACA-CAAATTTT
*
508163 CACAATCGAGGATACTCCAAC
1 CACAATCGGGGATACTCCAAC
508184 CCCGTTAATC
Statistics
Matches: 222, Mismatches: 36, Indels: 58
0.70 0.11 0.18
Matches are distributed among these distances:
46 3 0.01
47 2 0.01
48 6 0.03
49 3 0.01
50 4 0.02
51 31 0.14
52 54 0.24
53 33 0.15
54 41 0.18
55 27 0.12
56 1 0.00
57 5 0.02
58 7 0.03
62 2 0.01
63 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.31
Consensus pattern (50 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACAAATTTT
Found at i:507985 original size:27 final size:25
Alignment explanation
Indices: 507955--508030 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 25
507945 AATTTTCACA
507955 ATCGGGGATACTCCAACCCCGTTAAT
1 ATCGGGGATACTCCAACCCCGTT-AT
507981 CATCGGGGATACTCCAACCCCGTTAT
1 -ATCGGGGATACTCCAACCCCGTTAT
*
508007 TTCCGAGGAGATACTCCAACCCCG
1 AT-CG-GG-GATACTCCAACCCCG
508031 ACTTTATTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 1 0.02
26 4 0.09
27 25 0.56
28 15 0.33
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.21
Consensus pattern (25 bp):
ATCGGGGATACTCCAACCCCGTTAT
Found at i:508082 original size:52 final size:52
Alignment explanation
Indices: 508016--508187 Score: 213
Period size: 52 Copynumber: 3.3 Consensus size: 52
508006 TTTCCGAGGA
* *
508016 GATACTCCAACCCCGACTTTATTTCCAAAATACTGATTTTTCCACAATCGGG
1 GATACTCCAACCCCGATTTTATTTCCAAAATACTAATTTTTCCACAATCGGG
* * * **
508068 GATACTCCAACCCCGGTTTTATTTTCAAAACA-TCAATTTTTCCTTTAATCGGG
1 GATACTCCAACCCCGATTTTATTTCCAAAATACT-AATTTTTCC-ACAATCGGG
* * *
508121 GATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATCGAG
1 GATACTCCAACCCCGATTTTATTTCC-AAAATACTAATTTTTCCACAATCGGG
508173 GATACTCCAACCCCG
1 GATACTCCAACCCCG
508188 TTAATCATCG
Statistics
Matches: 100, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
51 1 0.01
52 56 0.56
53 31 0.31
54 12 0.12
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (52 bp):
GATACTCCAACCCCGATTTTATTTCCAAAATACTAATTTTTCCACAATCGGG
Found at i:508218 original size:212 final size:211
Alignment explanation
Indices: 507841--508291 Score: 683
Period size: 212 Copynumber: 2.1 Consensus size: 211
507831 AGTTTCTCAA
* * * *
507841 TTCTCCACAATCGGGGATATTTCAACTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCGG
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGG
* *
507906 GGATACTCCAACTTCGATTTTATTTCCAAAAAAACACCAAATTTTCACAATCGGGGATACTCCAA
66 GGATACTCCAACTCCGATTTTATTTCC-AAAAAACACCAAATTTTCACAATCGAGGATACTCCAA
*
507971 CCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGAGATACTCCAACCCCGACTTT
130 CCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGAGACACTCCAACCCCGACTTT
*
508036 ATTTCCAAAATACTGAT
195 ATTCCCAAAATACTGAT
* * *
508053 TTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACA-TCAATTTTTCCTTTAAT
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACT-AA-TTTT-CTATAAT
* *
508117 CGGGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTTTTCACAATCGAGGATACTCC
63 CGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCC
* * *
508181 AACCCCGTTAATCATCGGGGATACTCCAACTCCGTTATTTCCGAGGGGACACTCCAACCCCGGCT
128 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGAGACACTCCAACCCCGACT
508246 TTATTCCCAAAATACTGAT
193 TTATTCCCAAAATACTGAT
* *
508265 TTCT-CATAATTGGGGATACTCCAACCC
1 TTCTCCACAATCGGGGATACTCCAACCC
508292 TGTTATTTTC
Statistics
Matches: 217, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
211 22 0.10
212 156 0.72
213 4 0.02
214 35 0.16
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (211 bp):
TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGG
GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAAC
CCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGAGACACTCCAACCCCGACTTTA
TTCCCAAAATACTGAT
Found at i:508378 original size:78 final size:79
Alignment explanation
Indices: 508196--508399 Score: 225
Period size: 79 Copynumber: 2.6 Consensus size: 79
508186 CGTTAATCAT
* *
508196 CGGGGATACTCCAACTCCGTTATTTCCGAGGGGACACTCCAACCCCGGCTTTATTCCCAAAATAC
1 CGGGGATACTCCAACTCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAAAATAC
* * *
508261 TGATTTCTCATAAT
66 TGATTCCTCACAAC
* * * * * * * *
508275 TGGGGATACTCCAAC-CCTGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTCTAATCAT
1 CGGGGATACTCCAACTCC-GTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAA-AAT
508339 -C-GATTCCTCACAAC
64 ACTGATTCCTCACAAC
* * *
508353 CGGGGATACTCCAGCTCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACTCCGTTATTTTCGAGGGGACACTCCAACCCCG
508400 TTATTATCTC
Statistics
Matches: 103, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
78 50 0.49
79 51 0.50
80 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACTCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAAAATAC
TGATTCCTCACAAC
Found at i:510363 original size:20 final size:20
Alignment explanation
Indices: 510335--510386 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
510325 TCGATACAAC
*
510335 AAGTTAATGTATAAATACAT
1 AAGTGAATGTATAAATACAT
** *
510355 AAGTGAATGTATTGATGCAT
1 AAGTGAATGTATAAATACAT
*
510375 AAATGAATGTAT
1 AAGTGAATGTAT
510387 CGAAACTAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (20 bp):
AAGTGAATGTATAAATACAT
Found at i:510541 original size:32 final size:31
Alignment explanation
Indices: 510499--510575 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
510489 CATTCTTCAT
*
510499 TGTATCGATACATTCTAGATTTTTGATCC-AAA
1 TGTATCGATACATT-TAGAGTTTTGA-CCTAAA
* * *
510531 TGTATTGATACATTTTGGGTTTTGACCTAAA
1 TGTATCGATACATTTAGAGTTTTGACCTAAA
510562 TGTATCGATACATT
1 TGTATCGATACATT
510576 ATTCAATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.05
31 24 0.62
32 13 0.33
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (31 bp):
TGTATCGATACATTTAGAGTTTTGACCTAAA
Found at i:513116 original size:97 final size:97
Alignment explanation
Indices: 512947--513164 Score: 294
Period size: 97 Copynumber: 2.2 Consensus size: 97
512937 ATTTTTATTT
* **
512947 ATCGGGGATACACCAACCCCATTCTTCCAAGAGGATACTCCAACCTTGTTTTTAAACTTGTCAAG
1 ATCGGGGATACTCCAACCCCATTCTTCCAAGAGGATACTCCAACCTCATTTTTAAACTTGTCAAG
* *
513012 ATATAAATCTTATTTTTGCTTAAATTGTCATC
66 ATATAAATCTTATTTTCGCCTAAATTGTCATC
**
513044 ATCGGGGATACTCCAACCCCATTCTTCTGAGAGGATACTCCAATCC-CATTTTTAAACTTGTCAA
1 ATCGGGGATACTCCAACCCCATTCTTCCAAGAGGATACTCCAA-CCTCATTTTTAAACTTGTCAA
* *
513108 GATTTAAATCTTATTTTCGCCTAAATTGTTATC
65 GATATAAATCTTATTTTCGCCTAAATTGTCATC
* *** *
513141 GTCAAAGATACTCTAACCCCATTC
1 ATCGGGGATACTCCAACCCCATTC
513165 CTTCGAGGGA
Statistics
Matches: 106, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
97 104 0.98
98 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (97 bp):
ATCGGGGATACTCCAACCCCATTCTTCCAAGAGGATACTCCAACCTCATTTTTAAACTTGTCAAG
ATATAAATCTTATTTTCGCCTAAATTGTCATC
Found at i:516108 original size:15 final size:14
Alignment explanation
Indices: 516088--516131 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
516078 TTTTTCAACT
516088 GGAAAAGAGAAAGAA
1 GGAAAAGA-AAAGAA
*
516103 GGAAAAGAAAAAAAA
1 GGAAAAG-AAAAGAA
*
516118 GAAAAAGAAAAGAA
1 GGAAAAGAAAAGAA
516132 ATGAGAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 6 0.24
15 18 0.72
16 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (14 bp):
GGAAAAGAAAAGAA
Found at i:519444 original size:23 final size:24
Alignment explanation
Indices: 519404--519463 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
519394 AAAAATTGAC
* *
519404 TATTAAATATATTAATTTAA-AAGAG
1 TATTAGATAAATT-ATTTAATAA-AG
*
519429 TATT-GATAAATTATTTAATAAAT
1 TATTAGATAAATTATTTAATAAAG
519452 TATTAGATAAAT
1 TATTAGATAAAT
519464 AATGTAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 11 0.37
24 15 0.50
25 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (24 bp):
TATTAGATAAATTATTTAATAAAG
Done.