Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 175 of 222
Found at i:56221880 original size:44 final size:43
Alignment explanation
Indices: 56221804--56222401 Score: 396
Period size: 44 Copynumber: 13.8 Consensus size: 43
56221794 AGATTCATCC
* * * *
56221804 TTTTAATCCGCCCCACTGCAACTTCAGGGAGATAGGATTAGTAG
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATT-GTAG
* *
56221848 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGATA-
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTG-TAG
* * * *
56221891 TCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTATG
1 T-TTTAATCTGCTCCACTGCAACTTCAGAGAGATAA-GATTG-TA-G
* * * * *
56221938 GTGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGT-G
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGTAG
* * *
56221981 ATTTTAAT-TCGCTCCACTGCAACTTCCGAGAGATAGGATTGGT-T
1 -TTTTAATCT-GCTCCACTGCAACTTCAGAGAGATAAGATT-GTAG
** * *
56222025 TCTTTTGTCTGATCTACTGCAACTTCAGAGAGATAAGATTG--G
1 T-TTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGTAG
* *** * * *
56222067 ATGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGTAG
** * * *
56222111 TTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTG-ATT
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGTA-G
** * *
56222154 TTTTTTTCTGCTCCACTGCAACTTCAGGGAGATAAGACTG--G
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGTAG
* *** * * *
56222195 ATGCGATCTGCTCTATTGCAACTTCAGAGAGATAAGATATGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGTAG
* * * *
56222239 TTTTAATCTGCTCCACTGCAACTTCCGGGAGATAGGATTGGT-T
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATT-GTAG
** *
56222282 TCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-A-
1 T-TTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TTGTAG
*** * * *
56222325 -TACGATCTTCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGTAG
*
56222368 TTTTAATCCGCTCCACTGCAACTTCA-AGGAGATA
1 TTTTAATCTGCTCCACTGCAACTTCAGA-GAGATA
56222402 GGAGTGGATG
Statistics
Matches: 429, Mismatches: 98, Indels: 54
0.74 0.17 0.09
Matches are distributed among these distances:
40 1 0.00
41 91 0.21
42 4 0.01
43 45 0.10
44 247 0.58
45 12 0.03
46 29 0.07
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (43 bp):
TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGTAG
Found at i:56222132 original size:129 final size:129
Alignment explanation
Indices: 56221818--56222404 Score: 748
Period size: 129 Copynumber: 4.5 Consensus size: 129
56221808 AATCCGCCCC
* * * * * * * *
56221818 ACTGCAACTTCAGGGAGATAGGAT-TAGTAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATA
1 ACTGCAACTTCAGAGAGATAAGATCT-GTGGTTTTAATCCGCTCCACTGCAACTTCCGGGAGATA
* * * **** * * *
56221882 AGATTGATATCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTATGGTGTGATCT
65 GGATTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAA-GATTG----GATGCGATCT
*
56221947 ACTCT
125 GCTCT
* * *
56221952 ACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATTCGCTCCACTGCAACTTCCGAGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCCGGGAGATAG
* * *
56222017 GATTGGTTTCTTTTGTCTGATCTACTGCAACTTCAGAGAGATAAGATTGGATGCGATCTGCTCT
66 GATTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCT
* * *
56222081 ACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCCGGGAGATAG
* * *
56222146 GATTGATTT-TTTTTTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCT
66 GATTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCT
* * *
56222209 ATTGCAACTTCAGAGAGATAAGATATGTGGTTTTAATCTGCTCCACTGCAACTTCCGGGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCCGGGAGATAG
* *
56222274 GATTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GATACGATCTTCTCT
66 GATTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGATGCGATCTGCTCT
**
56222338 ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAAGGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCCGGGAGATAG
56222403 GA
66 GA
56222405 GTGGATGCGG
Statistics
Matches: 399, Mismatches: 51, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
128 116 0.29
129 189 0.47
130 1 0.00
133 4 0.01
134 88 0.22
135 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (129 bp):
ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCCGGGAGATAG
GATTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCT
Found at i:56222143 original size:85 final size:85
Alignment explanation
Indices: 56222040--56222453 Score: 356
Period size: 85 Copynumber: 4.8 Consensus size: 85
56222030 TGTCTGATCT
* *
56222040 ACTGCAACTTCAGAGAGATAAGATTGGATGCGATCTGCTCTACTACAACTTCAGAGAGATAAGAT
1 ACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGAT
*
56222105 CTGTGGTTTTAATCCACTCC
66 CTGTGGTTTTAATCCGCTCC
* **** * *
56222125 ACTGCAACTTCAGGGAGATAGGATT-GATTTTTTTTTCTGCTCCACTGCAACTTCAGGGAGATAA
1 ACTGCAACTTCAGGGAGATAAGATTGGA---TGCGATCTGCTCTACTGCAACTTCAGAGAGATAA
* *** * *
56222189 GA-C--TGGATGCGATCTGCTCT
63 GATCTGTGGTTTTAATCCGCTCC
* * * *** * * * *
56222209 ATTGCAACTTCAGAGAGATAAGATATGTGGTTTTAATCTGCTCCACTGCAACTTCCGGGAGATAG
1 ACTGCAACTTCAGGGAGATAAG--AT-TGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAA
* ** *
56222274 GAT-TG-GTTTCTTTTGTCTGCTCC
63 GATCTGTG-GT-TTTAATCCGCTCC
* *
56222297 ACTGCAACTTCAGGGAGATAAGACTT-GATACGATCTTCTCTACTGCAACTTCAGAGAGATAAGA
1 ACTGCAACTTCAGGGAGATAAGA-TTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGA
56222361 TCTGTGGTTTTAATCCGCTCC
65 TCTGTGGTTTTAATCCGCTCC
* * * * * *
56222382 ACTGCAACTTCAAGGAGATAGGAGTGGATGCGGTCTGCTCTACTGCAACCTCAGAGAGACAAGAT
1 ACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGAT
56222447 CTGTGGT
66 CTGTGGT
56222454 GTATGGCTTC
Statistics
Matches: 259, Mismatches: 54, Indels: 32
0.75 0.16 0.09
Matches are distributed among these distances:
84 32 0.12
85 157 0.61
86 9 0.03
87 32 0.12
88 29 0.11
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (85 bp):
ACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGAT
CTGTGGTTTTAATCCGCTCC
Found at i:56222254 original size:257 final size:260
Alignment explanation
Indices: 56221858--56222404 Score: 798
Period size: 257 Copynumber: 2.1 Consensus size: 260
56221848 CTTCAATCTG
* *
56221858 CTCCACTGCAACTTCAGAGAGATAAGATTGATATCTTCAACCTGCTCCACTGCAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGATATCTTCAACCTGCTCCACTGCAACTTCAGGGAG
** * * *
56221923 ATAAGGTTTGTTATGGTGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAA
66 ATAAGGACTG---TGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATATGTGATTTTAA
*
56221988 TTCGCTCCACTGCAACTTCCGAGAGATAGGATTGGTTTCTTTTGTCTGATCTACTGCAACTTCAG
128 TTCGCTCCACTGCAACTTCCGAGAGATAGGATTGGTTTCTTTTGTCTGATCCACTGCAACTTCAG
*
56222053 AGAGATAAGA-TTGGATGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAA
193 AGAGATAAGACTT-GATACGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAA
56222117 TCCA
257 TCCA
* ****
56222121 CTCCACTGCAACTTCAGGGAGATAGGATTGAT-TTTTTTTTCTGCTCCACTGCAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGATATCTTCAACCTGCTCCACTGCAACTTCAGGGAG
* * *
56222185 ATAA-GACTG-GATGCGATCTGCTCTATTGCAACTTCAGAGAGATAAGATATGTGGTTTTAA-TC
66 ATAAGGACTGTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATATGTGATTTTAATTC
* * *
56222247 TGCTCCACTGCAACTTCCGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGGG
131 -GCTCCACTGCAACTTCCGAGAGATAGGATTGGTTTCTTTTGTCTGATCCACTGCAACTTCAGAG
* *
56222312 AGATAAGACTTGATACGATCTTCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
195 AGATAAGACTTGATACGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
*
56222377 G
260 A
*
56222378 CTCCACTGCAACTTCAAGGAGATAGGA
1 CTCCACTGCAACTTCAGGGAGATAGGA
56222405 GTGGATGCGG
Statistics
Matches: 258, Mismatches: 24, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
256 2 0.01
257 190 0.74
258 2 0.01
261 3 0.01
262 31 0.12
263 30 0.12
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (260 bp):
CTCCACTGCAACTTCAGGGAGATAGGATTGATATCTTCAACCTGCTCCACTGCAACTTCAGGGAG
ATAAGGACTGTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATATGTGATTTTAATTC
GCTCCACTGCAACTTCCGAGAGATAGGATTGGTTTCTTTTGTCTGATCCACTGCAACTTCAGAGA
GATAAGACTTGATACGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCA
Found at i:56222619 original size:100 final size:101
Alignment explanation
Indices: 56222457--56222871 Score: 563
Period size: 100 Copynumber: 4.1 Consensus size: 101
56222447 CTGTGGTGTA
* *
56222457 TGGCTTCAATCTTTTAAAATGCAATGTCAGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGC
1 TGGCTTCAATCTTTTAAATTGCAATGTCAGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
* * *
56222522 TCCACTGCGAAC-TCAGGGAGGTAAGATTCACCGTCG
66 TCCACTGC-AACGCCAGGGAAGTAAGATTCACCGTTG
* * * *
56222558 TGGCTTCAATCTTTTAAATTGCAATATC-GGAGAAGCAAGATTCACCGACGTAGCTTTAATCTGC
1 TGGCTTCAATCTTTTAAATTGCAATGTCAGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
* *
56222622 TCCACTGCACCGCCAGGAAAGTAAGATTCACCGTTG
66 TCCACTGCAACGCCAGGGAAGTAAGATTCACCGTTG
*
56222658 TGGCTTCAATCTTTTAGAA-TGCAATGTCGGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTG
1 TGGCTTCAATCTTTTA-AATTGCAATGTCAGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTG
* *
56222722 CTCCACTGC-ACGCCAAGGAAGTAAGATTCGCCGTTG
65 CTCCACTGCAACGCCAGGGAAGTAAGATTCACCGTTG
* * * * * *
56222758 CGGCTTCAATCTTTTCAATTGCAATGT-TGGGGAA-CAAGATTCGCCGTTGTAGCTTCAATCTGT
1 TGGCTTCAATCTTTTAAATTGCAATGTCAGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
* *
56222821 TCCACTGCACCACCAGGGAAGTAAGATTCACCGTTG
66 TCCACTGCAACGCCAGGGAAGTAAGATTCACCGTTG
*
56222857 CGGCTTCAATCTTTT
1 TGGCTTCAATCTTTT
56222872 TAACCGTAAT
Statistics
Matches: 280, Mismatches: 29, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
98 34 0.12
99 48 0.17
100 129 0.46
101 69 0.25
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (101 bp):
TGGCTTCAATCTTTTAAATTGCAATGTCAGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
TCCACTGCAACGCCAGGGAAGTAAGATTCACCGTTG
Found at i:56222764 original size:49 final size:49
Alignment explanation
Indices: 56222487--56222868 Score: 248
Period size: 50 Copynumber: 7.7 Consensus size: 49
56222477 GCAATGTCAG
* * * *
56222487 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCGAAC-TCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGC--ACGCCA
* * * ** * ***
56222537 GGGAGGTAAGATTCACCGTCGTGGCTTCAATCTTTTAAATTGCAATATC-
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGC-ACGCCA
* ** * * *
56222586 GGAGAAGCAAGATTCACCGACGTAGCTTTAATCTGCTCCACTGCACCGCCA
1 GG-GAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGCA-CGCCA
* * ** * * **
56222637 GGAAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAGAATGCAATGTCGG
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGC-ACG-CCA
* * * *
56222688 GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGCACGCCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGCACGCCA
* * * * * * * ***
56222737 AGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTCAATTGCAATGTTG
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGC-ACGCCA
* * * *
56222787 GGGAA-CAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCACCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGCA-CGCCA
*
56222836 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCT
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
56222869 TTTTAACCGT
Statistics
Matches: 244, Mismatches: 79, Indels: 18
0.72 0.23 0.05
Matches are distributed among these distances:
48 1 0.00
49 75 0.31
50 130 0.53
51 38 0.16
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.27
Consensus pattern (49 bp):
GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGCACGCCA
Found at i:56225184 original size:33 final size:33
Alignment explanation
Indices: 56225142--56225263 Score: 118
Period size: 33 Copynumber: 3.4 Consensus size: 33
56225132 CGGTGGATTT
56225142 AGCACTTAGCAACCACCAATGAGTCAGGGAATC
1 AGCACTTAGCAACCACCAATGAGTCAGGGAATC
* * *
56225175 AGCACTTAGCAACCCCTTTCACATTGAAGATACGGTGGGATC
1 AGCACTTAGCAACCAC---CA-A-TG-AG-T-CAG-GGAATC
* *
56225217 AGCACTTAGCAACCACCAGTGATTCAGGGAATC
1 AGCACTTAGCAACCACCAATGAGTCAGGGAATC
56225250 AGCACTTAGCAACC
1 AGCACTTAGCAACC
56225264 CCTCGGGGGA
Statistics
Matches: 72, Mismatches: 8, Indels: 18
0.73 0.08 0.18
Matches are distributed among these distances:
33 34 0.47
34 2 0.03
35 1 0.01
36 3 0.04
37 3 0.04
38 2 0.03
39 4 0.06
40 1 0.01
41 2 0.03
42 20 0.28
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (33 bp):
AGCACTTAGCAACCACCAATGAGTCAGGGAATC
Found at i:56225330 original size:42 final size:42
Alignment explanation
Indices: 56225271--56225374 Score: 199
Period size: 42 Copynumber: 2.5 Consensus size: 42
56225261 ACCCCTCGGG
56225271 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
*
56225313 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
56225355 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
56225375 ACCAATGAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
Found at i:56225435 original size:144 final size:144
Alignment explanation
Indices: 56225169--56225438 Score: 452
Period size: 144 Copynumber: 1.9 Consensus size: 144
56225159 AATGAGTCAG
*
56225169 GGAATCAGCACTTAGCAACCCCTTTCACATTGAAGATACGGTGGGATCAGCACTTAGCAACCACC
1 GGAATCAGCACTTAGCAACCCCTTTCACATTGAAGATACGGTGGAATCAGCACTTAGCAACCACC
* * *
56225234 AGTGATTCAGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACTTAGCAACCCCCTTCAC
66 AATGAATCAGGGAATCAACACTTAGCAACCCCTCGGGGGAATCAGCACTTAGCAACCCCCTTCAC
56225299 ATTTAAGATACGGT
131 ATTTAAGATACGGT
*
56225313 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACC
1 GGAATCAGCACTTAGCAACCCCTTTCACATTGAAGATACGGTGGAATCAGCACTTAGCAACCACC
* * * *
56225378 AATGAATCGGGGAATCAACACTTAGCAGCCCCT-TGGGGAATCAGCACTTAGCAAACCCCTT
66 AATGAATCAGGGAATCAACACTTAGCAACCCCTCGGGGGAATCAGCACTTAGCAACCCCCTT
56225439 TATATTCAAA
Statistics
Matches: 117, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
143 26 0.22
144 91 0.78
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.21
Consensus pattern (144 bp):
GGAATCAGCACTTAGCAACCCCTTTCACATTGAAGATACGGTGGAATCAGCACTTAGCAACCACC
AATGAATCAGGGAATCAACACTTAGCAACCCCTCGGGGGAATCAGCACTTAGCAACCCCCTTCAC
ATTTAAGATACGGT
Found at i:56226944 original size:11 final size:11
Alignment explanation
Indices: 56226920--56226981 Score: 54
Period size: 12 Copynumber: 5.4 Consensus size: 11
56226910 CCGGTAGAGG
56226920 TTTTTTTTCTT
1 TTTTTTTTCTT
56226931 TTTTATTTTCTT
1 TTTT-TTTTCTT
56226943 TTTTGTTTT-TT
1 TTTT-TTTTCTT
* *
56226954 TTTTACTTTTATG
1 TTTT--TTTTCTT
*
56226967 TTTTTTTGCTT
1 TTTTTTTTCTT
56226978 TTTT
1 TTTT
56226982 GCTCTCTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
11 18 0.43
12 19 0.45
13 5 0.12
ACGTcount: A:0.05, C:0.06, G:0.05, T:0.84
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:56226946 original size:19 final size:19
Alignment explanation
Indices: 56226922--56226973 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
56226912 GGTAGAGGTT
56226922 TTTTTTCTTTTTTATTTT-C
1 TTTTTTCTTTTTT-TTTTAC
*
56226941 TTTTTTGTTTTTTTTTTAC
1 TTTTTTCTTTTTTTTTTAC
* *
56226960 TTTTATGTTTTTTT
1 TTTTTTCTTTTTTT
56226974 GCTTTTTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 4 0.13
19 26 0.87
ACGTcount: A:0.06, C:0.06, G:0.04, T:0.85
Consensus pattern (19 bp):
TTTTTTCTTTTTTTTTTAC
Found at i:56226972 original size:18 final size:19
Alignment explanation
Indices: 56226929--56226973 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
56226919 GTTTTTTTTC
*
56226929 TTTTTTATTTT-CTTTTTTG
1 TTTTTT-TTTTACTTTTATG
56226948 TTTTTTTTTTACTTTTATG
1 TTTTTTTTTTACTTTTATG
56226967 TTTTTTT
1 TTTTTTT
56226974 GCTTTTTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.07, C:0.04, G:0.04, T:0.84
Consensus pattern (19 bp):
TTTTTTTTTTACTTTTATG
Found at i:56236572 original size:50 final size:50
Alignment explanation
Indices: 56236508--56236606 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
56236498 AACGAGCAAT
* * **
56236508 GAATCGGTATGCTCTCACGAGCTGTGAATCGGTAAGCTCATACGAGCTGA
1 GAATCGATAAGCTCTCACGAGCTGCAAATCGGTAAGCTCATACGAGCTGA
56236558 GAATCGATAAGCTCTCACGAGCTGCAAATCGGTAAGCTCATACGAGCTG
1 GAATCGATAAGCTCTCACGAGCTGCAAATCGGTAAGCTCATACGAGCTG
56236607 TGGTGTGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.22
Consensus pattern (50 bp):
GAATCGATAAGCTCTCACGAGCTGCAAATCGGTAAGCTCATACGAGCTGA
Found at i:56236605 original size:25 final size:24
Alignment explanation
Indices: 56236509--56236606 Score: 110
Period size: 25 Copynumber: 4.0 Consensus size: 24
56236499 ACGAGCAATG
* *
56236509 AATCGGTATGCTCTCACGAGCTGTG
1 AATCGGTAAGCTCTCACGAGCTG-A
56236534 AATCGGTAAGCTCAT-ACGAGCTGA
1 AATCGGTAAGCTC-TCACGAGCTGA
*
56236558 GAATCGATAAGCTCTCACGAGCTGCA
1 -AATCGGTAAGCTCTCACGAGCTG-A
56236584 AATCGGTAAGCTCAT-ACGAGCTG
1 AATCGGTAAGCTC-TCACGAGCTG
56236607 TGGTGTGTCA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
24 1 0.02
25 60 0.94
26 3 0.05
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (24 bp):
AATCGGTAAGCTCTCACGAGCTGA
Found at i:56239590 original size:7 final size:7
Alignment explanation
Indices: 56239578--56239608 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
56239568 CAATAACAAT
56239578 AATAATA
1 AATAATA
56239585 AATAATA
1 AATAATA
56239592 AATAATA
1 AATAATA
56239599 AATAAATA
1 AAT-AATA
56239607 AA
1 AA
56239609 ATAAGAAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.74
8 6 0.26
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AATAATA
Found at i:56239953 original size:7 final size:7
Alignment explanation
Indices: 56239943--56239970 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
56239933 AATGGAGCAA
56239943 CGAGGGG
1 CGAGGGG
56239950 CGAGGGG
1 CGAGGGG
56239957 CGAGGGG
1 CGAGGGG
56239964 CGAGGGG
1 CGAGGGG
56239971 AAAGGATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.71, T:0.00
Consensus pattern (7 bp):
CGAGGGG
Found at i:56249081 original size:20 final size:20
Alignment explanation
Indices: 56249041--56249081 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
56249031 AAACAAAAAT
*
56249041 ATTAAAAATATAAAAATTAA
1 ATTAAAAATATAAAAAATAA
56249061 ATTAAAAATA-AATAAAATAA
1 ATTAAAAATATAA-AAAATAA
56249081 A
1 A
56249082 AAATGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
ATTAAAAATATAAAAAATAA
Found at i:56259504 original size:19 final size:20
Alignment explanation
Indices: 56259480--56259519 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
56259470 TTTAAGTTTT
56259480 TTTA-TTTTTAATTAATAAA
1 TTTATTTTTTAATTAATAAA
56259499 TTTATTGTTTTTAATTAATAA
1 TTTA-T-TTTTTAATTAATAA
56259520 TTATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
22 14 0.78
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TTTATTTTTTAATTAATAAA
Found at i:56260929 original size:3 final size:3
Alignment explanation
Indices: 56260916--56260949 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
56260906 AAAGAAATTT
56260916 GAA GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
56260950 GAGCGGGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:56262212 original size:48 final size:48
Alignment explanation
Indices: 56262130--56262223 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
56262120 TTTCTTGGCT
* *
56262130 TAAAAACGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
56262178 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
56262224 AGAATTCCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 4 0.10
48 38 0.90
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:56262936 original size:17 final size:17
Alignment explanation
Indices: 56262922--56262965 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 17
56262912 ATAATCTTCA
56262922 AAGATATGCAATCTTAG
1 AAGATATGCAATCTTAG
56262939 ATATGATATGCAATCTTAG
1 A-A-GATATGCAATCTTAG
56262958 AAGATATG
1 AAGATATG
56262966 ATTTTGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.28
18 2 0.08
19 16 0.64
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (17 bp):
AAGATATGCAATCTTAG
Found at i:56262984 original size:22 final size:22
Alignment explanation
Indices: 56262924--56262981 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
56262914 AATCTTCAAA
56262924 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
56262943 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
56262965 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
56262982 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:56269613 original size:29 final size:29
Alignment explanation
Indices: 56269568--56269629 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
56269558 TATTTTTTAG
* * *
56269568 AATATTAAAAAATTTTATTATATAATTCA
1 AATAATAAAAAATTTTAATATATAATTAA
*
56269597 AATAATAATAAAA-TTTAATATTTAATTAA
1 AATAATAA-AAAATTTTAATATATAATTAA
56269626 AATA
1 AATA
56269630 TTTTATCCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
AATAATAAAAAATTTTAATATATAATTAA
Found at i:56279473 original size:27 final size:27
Alignment explanation
Indices: 56279435--56279490 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
56279425 ATCACTAACT
56279435 AATACTAATCTAATACTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
56279462 AATACTAATCTAATACTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
56279489 AA
1 AA
56279491 AAAATATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.29
Consensus pattern (27 bp):
AATACTAATCTAATACTAATAGAATAG
Found at i:56279475 original size:5 final size:6
Alignment explanation
Indices: 56279432--56279482 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
56279422 AGGATCACTA
* *
56279432 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT A-GAAT ACTAAT -CTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
56279476 ACTAAT A
1 ACTAAT A
56279483 GAATAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 19 0.47
6 21 0.52
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (6 bp):
ACTAAT
Found at i:56283167 original size:16 final size:16
Alignment explanation
Indices: 56283146--56283178 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56283136 TCTTATTGTT
*
56283146 TTGCTACTATAGAATA
1 TTGCTACTATAAAATA
56283162 TTGCTACTATAAAATA
1 TTGCTACTATAAAATA
56283178 T
1 T
56283179 AGAATACCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (16 bp):
TTGCTACTATAAAATA
Found at i:56285256 original size:33 final size:33
Alignment explanation
Indices: 56285219--56285287 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
56285209 CATACATGTG
56285219 AATACGAATCCATTTTCCTTTTTCTCCGTAATC
1 AATACGAATCCATTTTCCTTTTTCTCCGTAATC
56285252 AATACGAATCCATTTTCCTTTTTCTCCGTAATC
1 AATACGAATCCATTTTCCTTTTTCTCCGTAATC
56285285 AAT
1 AAT
56285288 CTTCTCATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.42
Consensus pattern (33 bp):
AATACGAATCCATTTTCCTTTTTCTCCGTAATC
Found at i:56286508 original size:29 final size:29
Alignment explanation
Indices: 56286466--56286523 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
56286456 GCAACCCATT
*
56286466 TTTATTATCATATCGAAA-TGCTATTCCTA
1 TTTATTATCATATCAAAACT-CTATTCCTA
56286495 TTTATTATCATATCAAAACTCTATTCCTA
1 TTTATTATCATATCAAAACTCTATTCCTA
56286524 ATAAAAGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.45
Consensus pattern (29 bp):
TTTATTATCATATCAAAACTCTATTCCTA
Found at i:56288966 original size:18 final size:18
Alignment explanation
Indices: 56288943--56289048 Score: 79
Period size: 18 Copynumber: 5.4 Consensus size: 18
56288933 CTTCTTTTTT
56288943 TTTTCTCTTCTCCTTTCC
1 TTTTCTCTTCTCCTTTCC
* *
56288961 TTTTCT-TTCCTTCTTTTTCTT
1 TTTTCTCTT-C-TC-CTTTC-C
56288982 TCTTTCTTCTTCTCCTTTCC
1 T-TTTC-TCTTCTCCTTTCC
* **
56289002 TCTTTTTCTTCTTTCCTTTTT
1 T-TTTCTCTTC--TCCTTTCC
56289023 TTTTCTCTTCTCCTTTCC
1 TTTTCTCTTCTCCTTTCC
56289041 TTTTCTCT
1 TTTTCTCT
56289049 CCTTCTTTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
17 2 0.03
18 21 0.30
19 7 0.10
20 17 0.25
21 12 0.17
22 6 0.09
23 2 0.03
24 2 0.03
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTCTCTTCTCCTTTCC
Found at i:56289028 original size:44 final size:42
Alignment explanation
Indices: 56288930--56289091 Score: 161
Period size: 39 Copynumber: 4.0 Consensus size: 42
56288920 CTTCCCTCTT
56288930 CTTCTTCTTTTTTT-TTTC-TCTTCTCCTTTCCT-TTTCTTTC
1 CTTCTT-TTTTTTTCTTTCTTCTTCTCCTTTCCTCTTTCTTTC
*
56288970 CTTCTTTTTCTTTCTTTCTTCTTCTCCTTTCCTC-TT-TTT-
1 CTTCTTTTTTTTTCTTTCTTCTTCTCCTTTCCTCTTTCTTTC
*
56289009 CTTCTTTCCTTTTTT-TTTC-TCTTCTCCTTTCCT-TTTCTCTC
1 CTTCTTT--TTTTTTCTTTCTTCTTCTCCTTTCCTCTTTCTTTC
*
56289050 CTTCTTTTTCTTTCTTTC--C-TCTCC-TTCCTTTCTTTCTTTC
1 CTTCTTTTTTTTTCTTTCTTCTTCTCCTTTCC--TCTTTCTTTC
56289090 CT
1 CT
56289092 CTCATTCCTT
Statistics
Matches: 105, Mismatches: 5, Indels: 24
0.78 0.04 0.18
Matches are distributed among these distances:
37 4 0.04
38 5 0.05
39 36 0.34
40 32 0.30
41 28 0.27
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (42 bp):
CTTCTTTTTTTTTCTTTCTTCTTCTCCTTTCCTCTTTCTTTC
Found at i:56289037 original size:80 final size:80
Alignment explanation
Indices: 56288928--56289081 Score: 256
Period size: 80 Copynumber: 1.9 Consensus size: 80
56288918 TCCTTCCCTC
* * * *
56288928 TTCTTCTTCTTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCTTCTT
1 TTCTTCTTCCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTCTCCTTCTTTTTCTTTCTTTCCTCTC
56288993 C-TCCTTTCCTCTTT
66 CTTCCTTTCCTCTTT
56289007 TTCTTCTTTCCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTCTCCTTCTTTTTCTTTCTTTCCTCT
1 TTCTTC-TTCCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTCTCCTTCTTTTTCTTTCTTTCCTCT
56289072 CCTTCCTTTC
65 CCTTCCTTTC
56289082 TTTCTTTCCT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
79 6 0.09
80 56 0.81
81 7 0.10
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (80 bp):
TTCTTCTTCCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTCTCCTTCTTTTTCTTTCTTTCCTCTC
CTTCCTTTCCTCTTT
Found at i:56289063 original size:18 final size:18
Alignment explanation
Indices: 56288962--56289091 Score: 88
Period size: 16 Copynumber: 7.6 Consensus size: 18
56288952 CTCCTTTCCT
56288962 TTTCTTTCCTTCTTTTTC
1 TTTCTTTCCTTCTTTTTC
56288980 TTTCTTT-CTTC---TTC
1 TTTCTTTCCTTCTTTTTC
*
56288994 -TCCTTTCC-TCTTTTTC
1 TTTCTTTCCTTCTTTTTC
56289010 -TTCTTTCCTT-TTTTT-
1 TTTCTTTCCTTCTTTTTC
*
56289025 TTCTCTTCTCCTTTCCTTTTC
1 TT-TCTT-TCC-TTCTTTTTC
56289046 --TC--TCCTTCTTTTTC
1 TTTCTTTCCTTCTTTTTC
56289060 TTTCTTTCCTCTCCTTCCTTTC
1 TTTCTTTCCT-T-CTT--TTTC
56289082 TTTCTTTCCT
1 TTTCTTTCCT
56289092 CTCATTCCTT
Statistics
Matches: 89, Mismatches: 4, Indels: 34
0.70 0.03 0.27
Matches are distributed among these distances:
13 7 0.08
14 12 0.13
15 3 0.03
16 18 0.20
17 9 0.10
18 16 0.18
19 3 0.03
20 7 0.08
22 14 0.16
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTCTTTCCTTCTTTTTC
Found at i:56289100 original size:26 final size:22
Alignment explanation
Indices: 56289035--56289121 Score: 111
Period size: 22 Copynumber: 3.8 Consensus size: 22
56289025 TTCTCTTCTC
* *
56289035 CTTTCCTTTTCTCTCCTTCTTTTT
1 CTTT-CTTTCCTCTCCTTC-CTTT
56289059 CTTTCTTTCCTCTCCTTCCTTT
1 CTTTCTTTCCTCTCCTTCCTTT
* *
56289081 CTTTCTTTCCTCTCATTCCTTC
1 CTTTCTTTCCTCTCCTTCCTTT
56289103 CTTTCTTTCCCTCTCCTTC
1 CTTTCTTT-CCTCTCCTTC
56289122 TCCCCCCACC
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
22 31 0.54
23 22 0.39
24 4 0.07
ACGTcount: A:0.01, C:0.40, G:0.00, T:0.59
Consensus pattern (22 bp):
CTTTCTTTCCTCTCCTTCCTTT
Found at i:56289108 original size:80 final size:79
Alignment explanation
Indices: 56288944--56289120 Score: 211
Period size: 80 Copynumber: 2.2 Consensus size: 79
56288934 TTCTTTTTTT
* * *
56288944 TTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCTTCTTCTCCTTTCCTCTTTTT
1 TTTCTCTTCTCCTTTCCTTTTCTCTCCTTCTTTTTCTTTCTTTCCTCTCCTCCTTTCCTCTTTTT
* **
56289009 CTTCTTTCCTTTTTT
66 CTTCATTCC-TTTCC
56289024 TTTCTCTTCTCCTTTCCTTTTCTCTCCTTCTTTTTCTTTCTTTCCTCTCCTTCCTTT-CT-TTCT
1 TTTCTCTTCTCCTTTCCTTTTCTCTCCTTCTTTTTCTTTCTTTCCTCTCC-TCCTTTCCTCTT-T
56289087 TTCCTCTCATTCC-TTCC
64 TT-CT-TCATTCCTTTCC
*
56289104 TTTCT-TTC-CCTCTCCTT
1 TTTCTCTTCTCCTTTCCTT
56289121 CTCCCCCCAC
Statistics
Matches: 86, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
78 8 0.09
79 5 0.06
80 59 0.69
81 8 0.09
82 6 0.07
ACGTcount: A:0.01, C:0.36, G:0.00, T:0.64
Consensus pattern (79 bp):
TTTCTCTTCTCCTTTCCTTTTCTCTCCTTCTTTTTCTTTCTTTCCTCTCCTCCTTTCCTCTTTTT
CTTCATTCCTTTCC
Found at i:56289229 original size:27 final size:27
Alignment explanation
Indices: 56289151--56289221 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
56289141 CCTATTATGG
*
56289151 CATTGGTGCCGCCAATGGTTTTGGCAC
1 CATTGGTGCCGCCAATGGCTTTGGCAC
*
56289178 CATTGGTGCCACCAATGGCTTTGGCAC
1 CATTGGTGCCGCCAATGGCTTTGGCAC
*
56289205 CTTTGGTGCCGCCAATG
1 CATTGGTGCCGCCAATG
56289222 CCATTGGCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.28
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCTTTGGCAC
Found at i:56289344 original size:28 final size:30
Alignment explanation
Indices: 56289275--56289346 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
56289265 TGCATTTTTT
56289275 TTAT-ATATTTTGGTAAATAATAAAAATAA
1 TTATAATATTTTGGTAAATAATAAAAATAA
*
56289304 TTATAATATTTTGGTAAATAAT-AAAA-AG
1 TTATAATATTTTGGTAAATAATAAAAATAA
56289332 TTATAATATTTTGGT
1 TTATAATATTTTGGT
56289347 TATTTTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 16 0.39
29 8 0.20
30 17 0.41
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (30 bp):
TTATAATATTTTGGTAAATAATAAAAATAA
Found at i:56290150 original size:6 final size:6
Alignment explanation
Indices: 56290107--56290148 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
56290097 TCCAGATTTG
* *
56290107 AGCACA AGCAAA AGCAAA AGCAAA AGCAAA A-CAAA ATCAAA A
1 AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA A
56290149 TCGATTTAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.67, C:0.19, G:0.12, T:0.02
Consensus pattern (6 bp):
AGCAAA
Found at i:56290233 original size:14 final size:14
Alignment explanation
Indices: 56290214--56290241 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56290204 AGCAGAAATC
56290214 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
56290228 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
56290242 GAAATGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:56290239 original size:19 final size:18
Alignment explanation
Indices: 56290217--56290261 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
56290207 AGAAATCTGG
56290217 AGAAAAGAAAATG-GAGAAA
1 AGAAAAGAAAATGTGAG--A
56290236 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGTGAGA
56290253 AGAAAAGAA
1 AGAAAAGAA
56290262 GCGTACCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGTGAGA
Found at i:56292050 original size:19 final size:20
Alignment explanation
Indices: 56292017--56292056 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
56292007 AAATTGGGAT
56292017 GAAGGAAAATAGGGAA-AAA
1 GAAGGAAAATAGGGAAGAAA
56292036 GAAGAGAAAAT-GGGAAGAAA
1 GAAG-GAAAATAGGGAAGAAA
56292056 G
1 G
56292057 TAGAAATAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.35, T:0.05
Consensus pattern (20 bp):
GAAGGAAAATAGGGAAGAAA
Found at i:56294001 original size:31 final size:29
Alignment explanation
Indices: 56293966--56294042 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
56293956 ATTAACGATC
*
56293966 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* ***
56293997 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
56294026 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
56294043 CTAAGGTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 1 0.03
31 17 0.43
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:56294254 original size:31 final size:29
Alignment explanation
Indices: 56294185--56294258 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
56294175 AATAAATGAT
**
56294185 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATGACA
*
56294214 AACATAAGTGACTAAAATGTAACCTGAGACA
1 AACATAAGTGACTAAAATGTAACAT--GACA
*
56294245 AACAAAAGTGACTA
1 AACATAAGTGACTA
56294259 TTTTGGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATGACA
Found at i:56315977 original size:34 final size:34
Alignment explanation
Indices: 56315939--56316045 Score: 78
Period size: 34 Copynumber: 3.1 Consensus size: 34
56315929 ATGAAAATAC
56315939 AAAAGTATCACTATAATAATATTGATTATCATTT
1 AAAAGTATCACTATAATAATATTGATTATCATTT
* * * ** **
56315973 AAAAG-A--AATATGAA-AATAAGTCGCATGAAAATAC
1 AAAAGTATCACTAT-AATAAT-A-TTG-ATTATCATTT
*
56316007 AAAAGTATCACCATAATAATATTGATTATCATTT
1 AAAAGTATCACTATAATAATATTGATTATCATTT
56316041 AAAAG
1 AAAAG
56316046 AAATATGTAA
Statistics
Matches: 50, Mismatches: 15, Indels: 16
0.62 0.19 0.20
Matches are distributed among these distances:
31 7 0.14
32 3 0.06
33 3 0.06
34 25 0.50
35 3 0.06
36 3 0.06
37 6 0.12
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.31
Consensus pattern (34 bp):
AAAAGTATCACTATAATAATATTGATTATCATTT
Found at i:56316009 original size:68 final size:68
Alignment explanation
Indices: 56315929--56316059 Score: 244
Period size: 68 Copynumber: 1.9 Consensus size: 68
56315919 ATATAAAAGT
*
56315929 ATGAAAATACAAAAGTATCACTATAATAATATTGATTATCATTTAAAAGAAATATGAAAATAAGT
1 ATGAAAATACAAAAGTATCACCATAATAATATTGATTATCATTTAAAAGAAATATGAAAATAAGT
56315994 CGC
66 CGC
*
56315997 ATGAAAATACAAAAGTATCACCATAATAATATTGATTATCATTTAAAAGAAATATGTAAATAA
1 ATGAAAATACAAAAGTATCACCATAATAATATTGATTATCATTTAAAAGAAATATGAAAATAA
56316060 ATCGTTTTCA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.30
Consensus pattern (68 bp):
ATGAAAATACAAAAGTATCACCATAATAATATTGATTATCATTTAAAAGAAATATGAAAATAAGT
CGC
Found at i:56316208 original size:25 final size:26
Alignment explanation
Indices: 56316174--56316222 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
56316164 ATTATGATTT
* *
56316174 AAAATAAAAAATAATT-ATAAAATTA
1 AAAACAAAAAAAAATTAATAAAATTA
56316199 AAAACAAAAAAAAATTAATAAAAT
1 AAAACAAAAAAAAATTAATAAAAT
56316223 ATCTCAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (26 bp):
AAAACAAAAAAAAATTAATAAAATTA
Found at i:56318105 original size:25 final size:26
Alignment explanation
Indices: 56318077--56318125 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
56318067 AATTAGGCAA
*
56318077 AAAATA-ATAATGATTAAAAAAAGAG
1 AAAATAGATAATGACTAAAAAAAGAG
* *
56318102 AAAATAGGTTATGACTAAAAAAAG
1 AAAATAGATAATGACTAAAAAAAG
56318126 GGTATTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.63, C:0.02, G:0.14, T:0.20
Consensus pattern (26 bp):
AAAATAGATAATGACTAAAAAAAGAG
Found at i:56319005 original size:2 final size:2
Alignment explanation
Indices: 56318998--56319022 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56318988 TTGAAATCTA
56318998 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
56319023 AAATAAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56319811 original size:16 final size:16
Alignment explanation
Indices: 56319790--56319822 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56319780 ATATGAAGAT
56319790 AAAAAAA-TCTTATGGG
1 AAAAAAATTCTTA-GGG
56319806 AAAAAAATTCTTAGGG
1 AAAAAAATTCTTAGGG
56319822 A
1 A
56319823 CGGAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (16 bp):
AAAAAAATTCTTAGGG
Found at i:56321949 original size:24 final size:23
Alignment explanation
Indices: 56321922--56321999 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 23
56321912 GTCCCATTGT
*
56321922 TAGCTCTCATGAGCATCCCGTTAA
1 TAGCTCTC-TGAGCTTCCCGTTAA
* *
56321946 TAGCCCTCTCGAGCTTCCCATTATA
1 TAGCTCTCT-GAGCTTCCCGTTA-A
*
56321971 TAGTTCT-TGCGAGCTTCCCGTTAA
1 TAGCTCTCT--GAGCTTCCCGTTAA
56321995 TAGCT
1 TAGCT
56322000 TTTCGGAGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
23 1 0.02
24 24 0.55
25 19 0.43
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (23 bp):
TAGCTCTCTGAGCTTCCCGTTAA
Found at i:56322008 original size:24 final size:24
Alignment explanation
Indices: 56321932--56322014 Score: 64
Period size: 24 Copynumber: 3.4 Consensus size: 24
56321922 TAGCTCTCAT
* *
56321932 GAGCATCCCGTTAATAGCCCTCTC-
1 GAGCATCCCGTTAATAG-CTTTTCG
* *
56321956 GAGCTTCCCATTATATAG-TTCTT-G
1 GAGCATCCCGTTA-ATAGCTT-TTCG
*
56321980 CGAGCTTCCCGTTAATAGCTTTTCG
1 -GAGCATCCCGTTAATAGCTTTTCG
56322005 GAGCATCCCG
1 GAGCATCCCG
56322015 ATTGGTTGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
23 1 0.02
24 27 0.57
25 19 0.40
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.31
Consensus pattern (24 bp):
GAGCATCCCGTTAATAGCTTTTCG
Found at i:56322126 original size:25 final size:26
Alignment explanation
Indices: 56322077--56322148 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
56322067 CCTATTATAT
*
56322077 GGCTCTTCGTGAGCTTTCCGATTAAA
1 GGCTCTTCGTGAGCTTCCCGATTAAA
* *
56322103 GGCTCTTTGTGAGCTTCCCG-TTAAT
1 GGCTCTTCGTGAGCTTCCCGATTAAA
*
56322128 GACT-TTCCG-GAGCTTCCCGAT
1 GGCTCTT-CGTGAGCTTCCCGAT
56322149 ATGGCTCGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 12 0.31
25 9 0.23
26 18 0.46
ACGTcount: A:0.15, C:0.26, G:0.24, T:0.35
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCCGATTAAA
Found at i:56324688 original size:33 final size:34
Alignment explanation
Indices: 56324616--56324739 Score: 86
Period size: 33 Copynumber: 3.9 Consensus size: 34
56324606 TCCACATAAC
* * ** *
56324616 AGAGATAG-TCAGTTGGGACAGTAAGCACAGAAC
1 AGAGATAGTTCAGTTGGGACAATAAACATGGAAT
*
56324649 ATAGATAGTTC-GTTGGGACAATAAACATGGAAT
1 AGAGATAGTTCAGTTGGGACAATAAACATGGAAT
* * * *
56324682 AGAGATA-ATCTGTTAGGACAATTAACATGG-AT
1 AGAGATAGTTCAGTTGGGACAATAAACATGGAAT
*
56324714 --A-A-AG-TCCGTTGGGACAATAAACATGG
1 AGAGATAGTTCAGTTGGGACAATAAACATGG
56324740 GATAAGTTCG
Statistics
Matches: 75, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
28 20 0.27
29 1 0.01
30 1 0.01
32 4 0.05
33 47 0.63
34 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.23
Consensus pattern (34 bp):
AGAGATAGTTCAGTTGGGACAATAAACATGGAAT
Found at i:56324746 original size:28 final size:28
Alignment explanation
Indices: 56324659--56324746 Score: 79
Period size: 28 Copynumber: 3.0 Consensus size: 28
56324649 ATAGATAGTT
*
56324659 CGTTGGGACAATAAACATGGAATAGAGATAATC
1 CGTTGGGACAATAAACATGGGATA-AG----TC
* * *
56324692 TGTTAGGACAATTAACAT-GGATAAAGTC
1 CGTTGGGACAATAAACATGGGAT-AAGTC
56324720 CGTTGGGACAATAAACATGGGATAAGT
1 CGTTGGGACAATAAACATGGGATAAGT
56324747 TCGACGAGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
28 21 0.46
29 4 0.09
32 5 0.11
33 16 0.35
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (28 bp):
CGTTGGGACAATAAACATGGGATAAGTC
Found at i:56325457 original size:18 final size:18
Alignment explanation
Indices: 56325431--56325466 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
56325421 ATTTGATTTG
*
56325431 ACTCGAATAACTCAATTA
1 ACTCAAATAACTCAATTA
*
56325449 ACTCAAATAACTCGATTA
1 ACTCAAATAACTCAATTA
56325467 GTTTAACTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (18 bp):
ACTCAAATAACTCAATTA
Found at i:56328192 original size:42 final size:41
Alignment explanation
Indices: 56328118--56328206 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 41
56328108 TTTATTATTC
* * *
56328118 TAAAAATTTTAGATTAAATAACGTTAATAACAATAAAACTA
1 TAAAAAGTTTAGATTAAATAACGTTAATAACAAAAAAAATA
* ** *
56328159 TTAAAAGTTTAGATTAAATAAATTTTATTAACAAAAAAAATA
1 TAAAAAGTTTAGATTAAAT-AACGTTAATAACAAAAAAAATA
56328201 TAAAAA
1 TAAAAA
56328207 TTGAAAATTG
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 17 0.44
42 22 0.56
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (41 bp):
TAAAAAGTTTAGATTAAATAACGTTAATAACAAAAAAAATA
Found at i:56336413 original size:5 final size:5
Alignment explanation
Indices: 56336403--56336428 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
56336393 ATTAGCTAAG
56336403 GAAAA GAAAA GAAAA GAAAA GAAAA G
1 GAAAA GAAAA GAAAA GAAAA GAAAA G
56336429 CTACATTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:56337290 original size:43 final size:43
Alignment explanation
Indices: 56337210--56337291 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
56337200 TTCTGATAAA
* *** *
56337210 TGTTTTCGTGTAAGACCACTTCTGGGACGTTGGCATCGACTTG
1 TGTTTTCGTGTAAGACCACTTCCGGGACAACGACATCGACTTG
56337253 TGTTTTCGTGTAAGACC-CTGTCCGGGACAACGACATCGA
1 TGTTTTCGTGTAAGACCACT-TCCGGGACAACGACATCGA
56337292 TCAGTGATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 2 0.06
43 31 0.94
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (43 bp):
TGTTTTCGTGTAAGACCACTTCCGGGACAACGACATCGACTTG
Found at i:56341021 original size:21 final size:21
Alignment explanation
Indices: 56340995--56341209 Score: 148
Period size: 21 Copynumber: 10.3 Consensus size: 21
56340985 ATGTTTTACT
*
56340995 TTCTGTTTAGCTCTTAAGAGC
1 TTCTGTTTAGCTCTTATGAGC
* * * *
56341016 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTTAGCTCTTATGAGC
* *
56341037 TTCTATTTAGCTCTTTTGAGC
1 TTCTGTTTAGCTCTTATGAGC
* * * *
56341058 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTTAGCTCTTATGAGC
* *
56341079 TTCTATTTAGCTCTTTTGAGC
1 TTCTGTTTAGCTCTTATGAGC
* * * *
56341100 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTTAGCTCTTATGAGC
** * *
56341121 TTCCATTCAGCTCTTACGAGC
1 TTCTGTTTAGCTCTTATGAGC
* * * * *
56341142 TTCTGTTCAACCCTTATGGGT
1 TTCTGTTTAGCTCTTATGAGC
*
56341163 TTCTG-TTATGCTCTCATGAGC
1 TTCTGTTTA-GCTCTTATGAGC
*
56341184 TTCTGTTTAGCT-TT-CGAGC
1 TTCTGTTTAGCTCTTATGAGC
56341203 TTCTGTT
1 TTCTGTT
56341210 AACGATGTAC
Statistics
Matches: 140, Mismatches: 52, Indels: 6
0.71 0.26 0.03
Matches are distributed among these distances:
19 11 0.08
20 3 0.02
21 123 0.88
22 3 0.02
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (21 bp):
TTCTGTTTAGCTCTTATGAGC
Found at i:56341058 original size:42 final size:42
Alignment explanation
Indices: 56340994--56341192 Score: 292
Period size: 42 Copynumber: 4.7 Consensus size: 42
56340984 CATGTTTTAC
* *
56340994 TTTCTGTTTAGCTCTTAAGAGCTTCTGTTTAACCCTTATGGG
1 TTTCTATTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
*
56341036 TTTCTATTTAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGG
1 TTTCTATTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
*
56341078 TTTCTATTTAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGG
1 TTTCTATTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
* * * *
56341120 TTTCCATTCAGCTCTTACGAGCTTCTGTTCAACCCTTATGGG
1 TTTCTATTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
* *
56341162 TTTCT-GTTATGCTCTCATGAGCTTCTGTTTA
1 TTTCTATTTA-GCTCTTATGAGCTTCTGTTTA
56341193 GCTTTCGAGC
Statistics
Matches: 142, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
41 2 0.01
42 140 0.99
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (42 bp):
TTTCTATTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
Found at i:56343289 original size:12 final size:13
Alignment explanation
Indices: 56343265--56343293 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
56343255 TTTTAAAAGA
56343265 AAAATTATCTTTT
1 AAAATTATCTTTT
56343278 AAAATT-TCTTTT
1 AAAATTATCTTTT
56343290 AAAA
1 AAAA
56343294 AAGTCGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAATTATCTTTT
Found at i:56343926 original size:10 final size:10
Alignment explanation
Indices: 56343911--56343940 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
56343901 TTGGGATCCC
56343911 TTTTCTTTTT
1 TTTTCTTTTT
*
56343921 TTTTCTCTTT
1 TTTTCTTTTT
56343931 TTTTCTTTTT
1 TTTTCTTTTT
56343941 CTGCTTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:56343941 original size:16 final size:17
Alignment explanation
Indices: 56343910--56343942 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
56343900 CTTGGGATCC
*
56343910 CTTTTCTTTTTTTTTCT
1 CTTTTCTTTCTTTTTCT
56343927 CTTTT-TTTCTTTTTCT
1 CTTTTCTTTCTTTTTCT
56343943 GCTTATTGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
CTTTTCTTTCTTTTTCT
Found at i:56344091 original size:14 final size:14
Alignment explanation
Indices: 56344072--56344136 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 14
56344062 GTAGGGACTG
56344072 GGCCTGCTGCTGAT
1 GGCCTGCTGCTGAT
* *
56344086 GGCCTGATGCCGAT
1 GGCCTGCTGCTGAT
** *
56344100 GGCCTATTGCTGGT
1 GGCCTGCTGCTGAT
* *
56344114 GGCCTGTTGCTGGT
1 GGCCTGCTGCTGAT
*
56344128 GGCTTGCTG
1 GGCCTGCTG
56344137 TGGGATTTGG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.06, C:0.25, G:0.38, T:0.31
Consensus pattern (14 bp):
GGCCTGCTGCTGAT
Found at i:56344254 original size:8 final size:8
Alignment explanation
Indices: 56344243--56344279 Score: 56
Period size: 8 Copynumber: 4.4 Consensus size: 8
56344233 TATTTTTTCC
56344243 TTTCTTTT
1 TTTCTTTT
56344251 TTTCTTTT
1 TTTCTTTT
56344259 TTTCTTTT
1 TTTCTTTT
56344267 TCTTCTTTCT
1 T-TTCTTT-T
56344277 TTT
1 TTT
56344280 TCAAACCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 17 0.63
9 8 0.30
10 2 0.07
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTCTTTT
Found at i:56344281 original size:13 final size:14
Alignment explanation
Indices: 56344236--56344281 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
56344226 ATATTTTTAT
56344236 TTTTTCCTTTC-TT-
1 TTTTT-CTTTCTTTC
*
56344249 TTTTTCTTTTTTTC
1 TTTTTCTTTCTTTC
56344263 TTTTTC-TTCTTTC
1 TTTTTCTTTCTTTC
56344276 TTTTTC
1 TTTTTC
56344282 AAACCCTAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 4 0.14
13 19 0.66
14 6 0.21
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTTTCTTTC
Found at i:56344375 original size:19 final size:20
Alignment explanation
Indices: 56344351--56344391 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
56344341 GTCTCCCTCT
56344351 TTTTCTC-CCTCTATTTTTC
1 TTTTCTCTCCTCTATTTTTC
* *
56344370 TTTTCTCTTCTCTTTTTTTC
1 TTTTCTCTCCTCTATTTTTC
56344390 TT
1 TT
56344392 CCTTTCTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTCTCTCCTCTATTTTTC
Found at i:56346888 original size:21 final size:21
Alignment explanation
Indices: 56346851--56347026 Score: 106
Period size: 21 Copynumber: 8.4 Consensus size: 21
56346841 CGTGTTTTAC
* * *
56346851 TTTCTGTTTAGCTCTTACGAG
1 TTTCTGTTTAACCCTTATGAG
*
56346872 TTTCTGTTTAACCCTTATGGG
1 TTTCTGTTTAACCCTTATGAG
* * *
56346893 TTT-TCGTTCAACTCTTTTGAG
1 TTTCT-GTTTAACCCTTATGAG
* *
56346914 CTTCTGTTTAACCCTTATGGG
1 TTTCTGTTTAACCCTTATGAG
** * *
56346935 TTTC-CATTAAGCTCTTTTGAG
1 TTTCTGTTTAA-CCCTTATGAG
*
56346956 CTTT-TGTTTAACCCTTATGGG
1 -TTTCTGTTTAACCCTTATGAG
* * * * *
56346977 TTTCTATTCAGCTCTTACGAG
1 TTTCTGTTTAACCCTTATGAG
* * *
56346998 CTTCTGTTCAACCCTTATGGG
1 TTTCTGTTTAACCCTTATGAG
56347019 TTTCTGTT
1 TTTCTGTT
56347027 AAGGTCTCAT
Statistics
Matches: 112, Mismatches: 37, Indels: 12
0.70 0.23 0.07
Matches are distributed among these distances:
20 8 0.07
21 96 0.86
22 8 0.07
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (21 bp):
TTTCTGTTTAACCCTTATGAG
Found at i:56347022 original size:42 final size:42
Alignment explanation
Indices: 56346851--56347049 Score: 240
Period size: 42 Copynumber: 4.7 Consensus size: 42
56346841 CGTGTTTTAC
* * *
56346851 TTTCTGTTTAGCTCTTACGAGTTTCTGTTTAACCCTTATGGG
1 TTTCTGTTAAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
*
56346893 TTT-TCGTTCAA-CTCTTTTGAGCTTCTGTTTAACCCTTATGGG
1 TTTCT-GTT-AAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
** * *
56346935 TTTCCATTAAGCTCTTTTGAGCTTTTGTTTAACCCTTATGGG
1 TTTCTGTTAAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
* * * *
56346977 TTTCTATTCAGCTCTTACGAGCTTCTGTTCAACCCTTATGGG
1 TTTCTGTTAAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
* *
56347019 TTTCTGTTAAGGTCTCATGAGCTTCTGTTTA
1 TTTCTGTTAAGCTCTTATGAGCTTCTGTTTA
56347050 GCTTTCGAAC
Statistics
Matches: 134, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
41 3 0.02
42 130 0.97
43 1 0.01
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTCTGTTAAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
Found at i:56351612 original size:26 final size:26
Alignment explanation
Indices: 56351583--56351642 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
56351573 TTCCCCCAGC
56351583 AAAATTTTGATGATTTTA-CTCCTAGT
1 AAAATTTTGATGATTTTACCT-CTAGT
* *
56351609 AAAATTTTGATGATTTTGCCTCTGGT
1 AAAATTTTGATGATTTTACCTCTAGT
56351635 AAAATTTT
1 AAAATTTT
56351643 TAGAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 29 0.94
27 2 0.06
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (26 bp):
AAAATTTTGATGATTTTACCTCTAGT
Found at i:56358298 original size:13 final size:14
Alignment explanation
Indices: 56358273--56358301 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56358263 CTTTGTTGTT
56358273 TGTTTTTCTTTATG
1 TGTTTTTCTTTATG
56358287 TGTTTTTC-TTATG
1 TGTTTTTCTTTATG
56358300 TG
1 TG
56358302 CAACAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.69
Consensus pattern (14 bp):
TGTTTTTCTTTATG
Found at i:56360568 original size:10 final size:10
Alignment explanation
Indices: 56360538--56360587 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 10
56360528 TAGTTTTAGG
56360538 TTTAGTTTTC
1 TTTAGTTTTC
**
56360548 TCGAGGTTTTC
1 TTTA-GTTTTC
56360559 TTTAGTTTTC
1 TTTAGTTTTC
*
56360569 TCTAGGTTTTC
1 TTTA-GTTTTC
56360580 TTTAGTTT
1 TTTAGTTT
56360588 CCTCTGTACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
10 15 0.47
11 17 0.53
ACGTcount: A:0.10, C:0.12, G:0.16, T:0.62
Consensus pattern (10 bp):
TTTAGTTTTC
Found at i:56360592 original size:21 final size:21
Alignment explanation
Indices: 56360538--56360592 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
56360528 TAGTTTTAGG
*
56360538 TTTAGTTTTCTCGAGGTTTTC
1 TTTAGTTTTCTCTAGGTTTTC
56360559 TTTAGTTTTCTCTAGGTTTTC
1 TTTAGTTTTCTCTAGGTTTTC
*
56360580 TTTAGTTTCCTCT
1 TTTAGTTTTCTCT
56360593 GTACTTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.09, C:0.16, G:0.15, T:0.60
Consensus pattern (21 bp):
TTTAGTTTTCTCTAGGTTTTC
Found at i:56370498 original size:24 final size:24
Alignment explanation
Indices: 56370470--56370533 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
56370460 TTTCTAGAAG
* *
56370470 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
56370494 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
56370518 ATTT-GACATTTATTAG
1 ATTTAG-CATTTATTAG
56370534 AAATAGATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 36 0.97
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:56374953 original size:23 final size:23
Alignment explanation
Indices: 56374927--56374972 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
56374917 TTCTAGAAGA
* * *
56374927 TTTAGTATTTATTGGTATAATAT
1 TTTAGCATTTATTAGCATAATAT
56374950 TTTAGCATTTATTAGCATAATAT
1 TTTAGCATTTATTAGCATAATAT
56374973 ATTTGACATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (23 bp):
TTTAGCATTTATTAGCATAATAT
Found at i:56374987 original size:24 final size:23
Alignment explanation
Indices: 56374943--56374987 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
56374933 ATTTATTGGT
*
56374943 ATAATATTTTAGCATTTATTAGC
1 ATAATATTTTAGCATTGATTAGC
56374966 ATAATATATTT-GACATTGATTA
1 ATAATAT-TTTAG-CATTGATTA
56374988 AAATTAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (23 bp):
ATAATATTTTAGCATTGATTAGC
Found at i:56382200 original size:21 final size:21
Alignment explanation
Indices: 56382159--56382200 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
56382149 TTTTCTCAAA
* *
56382159 TCGAGTCGAATGAGATGGAAT
1 TCGAATCGAATGAGATCGAAT
56382180 TCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAAT-GAGATCGAAT
56382201 ATATTTGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (21 bp):
TCGAATCGAATGAGATCGAAT
Found at i:56383073 original size:21 final size:21
Alignment explanation
Indices: 56383039--56383079 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
56383029 GGGGGAAAGT
*
56383039 GGGAAAGAGTAAAAGTTTTGA
1 GGGAAAGAGTAAAAGGTTTGA
56383060 GGGAAA-AGTAAAAAGGTTTG
1 GGGAAAGAGT-AAAAGGTTTG
56383080 GGAATTTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (21 bp):
GGGAAAGAGTAAAAGGTTTGA
Found at i:56383074 original size:29 final size:29
Alignment explanation
Indices: 56383016--56383074 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
56383006 GAGGGGAGGG
* **
56383016 GAGTAAAAGTTTTGGGGGAAAGTGGGAAA
1 GAGTAAAAGTTTTGGGGAAAAGTGAAAAA
56383045 GAGTAAAAGTTTTGAGGGAAAAGT-AAAAA
1 GAGTAAAAGTTTTG-GGGAAAAGTGAAAAA
56383074 G
1 G
56383075 GTTTGGGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (29 bp):
GAGTAAAAGTTTTGGGGAAAAGTGAAAAA
Found at i:56383131 original size:9 final size:9
Alignment explanation
Indices: 56383117--56383153 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
56383107 TATAGTTTGA
56383117 TATTCGAAT
1 TATTCGAAT
56383126 TATTCGAAT
1 TATTCGAAT
56383135 TATTC-AAGT
1 TATTCGAA-T
56383144 TATTCGAAT
1 TATTCGAAT
56383153 T
1 T
56383154 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:56384848 original size:16 final size:16
Alignment explanation
Indices: 56384829--56384861 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56384819 AAGGAACATC
56384829 AGAAAAAATAGAAATA
1 AGAAAAAATAGAAATA
*
56384845 AGAAAAAATATAAATA
1 AGAAAAAATAGAAATA
56384861 A
1 A
56384862 TTTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AGAAAAAATAGAAATA
Found at i:56384901 original size:22 final size:22
Alignment explanation
Indices: 56384859--56384899 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
56384849 AAAATATAAA
56384859 TAATTTTTAAAAATATTTTTAT
1 TAATTTTTAAAAATATTTTTAT
*
56384881 TAATTTTT-AATATATTTTT
1 TAATTTTTAAAAATATTTTT
56384900 TAGATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TAATTTTTAAAAATATTTTTAT
Found at i:56387396 original size:9 final size:9
Alignment explanation
Indices: 56387382--56387411 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
56387372 CATTACCCAA
56387382 TCTCCTTCT
1 TCTCCTTCT
56387391 TCTCCTTCT
1 TCTCCTTCT
*
56387400 TCTTCTTCT
1 TCTCCTTCT
56387409 TCT
1 TCT
56387412 TATTCTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (9 bp):
TCTCCTTCT
Found at i:56387401 original size:3 final size:3
Alignment explanation
Indices: 56387386--56387424 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
56387376 ACCCAATCTC
* * *
56387386 CTT CTT CTC CTT CTT CTT CTT CTT CTT ATT CTT CAT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
56387425 TATCTACATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.05, C:0.33, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:56390811 original size:19 final size:19
Alignment explanation
Indices: 56390787--56390855 Score: 93
Period size: 19 Copynumber: 3.5 Consensus size: 19
56390777 CTTCAAGGAC
*
56390787 ATGCAATCTTATATATGAT
1 ATGCAATCTTAGATATGAT
56390806 ATGCAATCTTAGATATGATAT
1 ATGCAATCTTAGATATG--AT
*
56390827 ATGCAATCTTGGATATGAT
1 ATGCAATCTTAGATATGAT
*
56390846 ATGTAATCTT
1 ATGCAATCTT
56390856 GGAAGATATG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 27 0.60
21 18 0.40
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (19 bp):
ATGCAATCTTAGATATGAT
Found at i:56390828 original size:21 final size:21
Alignment explanation
Indices: 56390787--56390847 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
56390777 CTTCAAGGAC
*
56390787 ATGCAATCTTATATATG--AT
1 ATGCAATCTTAGATATGATAT
56390806 ATGCAATCTTAGATATGATAT
1 ATGCAATCTTAGATATGATAT
*
56390827 ATGCAATCTTGGATATGATAT
1 ATGCAATCTTAGATATGATAT
56390848 GTAATCTTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 16 0.42
21 22 0.58
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (21 bp):
ATGCAATCTTAGATATGATAT
Found at i:56390891 original size:22 final size:23
Alignment explanation
Indices: 56390847--56390891 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
56390837 GGATATGATA
* *
56390847 TGTAATCTTGGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
56390870 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
56390892 GTAGATACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:56394688 original size:20 final size:19
Alignment explanation
Indices: 56394658--56394744 Score: 74
Period size: 20 Copynumber: 4.6 Consensus size: 19
56394648 ATCAACTATG
56394658 ATTAAACTTAATCATTTTAAT
1 ATTAAA-TTAATCA-TTTAAT
* *
56394679 ATTAAATTAATGA-TAAAT
1 ATTAAATTAATCATTTAAT
* *
56394697 ATTAGACTAA--ATTTAAT
1 ATTAAATTAATCATTTAAT
56394714 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAATCA-TTTAAT
56394734 ATTAAATTAAT
1 ATTAAATTAAT
56394745 AAAATACTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
16 1 0.02
17 11 0.20
18 13 0.24
19 2 0.04
20 21 0.39
21 6 0.11
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (19 bp):
ATTAAATTAATCATTTAAT
Found at i:56411440 original size:7 final size:7
Alignment explanation
Indices: 56411430--56411459 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
56411420 TGAGAGATGG
*
56411430 GAGGGTT
1 GAGGGAT
56411437 GAGGGAT
1 GAGGGAT
56411444 GAGGGAT
1 GAGGGAT
56411451 GAGGGAT
1 GAGGGAT
56411458 GA
1 GA
56411460 TTGAAAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.57, T:0.17
Consensus pattern (7 bp):
GAGGGAT
Found at i:56413085 original size:12 final size:12
Alignment explanation
Indices: 56413060--56413092 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
56413050 TTTATCAACA
56413060 TAAATATTAAAT
1 TAAATATTAAAT
56413072 TAAAT-TTAATAT
1 TAAATATTAA-AT
56413084 TAAATATTA
1 TAAATATTA
56413093 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 12 0.63
13 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:56413173 original size:20 final size:18
Alignment explanation
Indices: 56413123--56413174 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
56413113 CTACAAGATA
56413123 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
56413140 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
56413160 AATATTAAATTAATA
1 AATATTAAATTAATA
56413175 AAATATTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:56418536 original size:51 final size:52
Alignment explanation
Indices: 56418466--56418569 Score: 183
Period size: 51 Copynumber: 2.0 Consensus size: 52
56418456 TCTAAATTTG
*
56418466 ATTTGATTTGATTTCGTTAATGGTAAACTATAAAAGAAAGA-TTGAGTTAAA
1 ATTTGATTTGATTTCGTTAATGGTAAACGATAAAAGAAAGATTTGAGTTAAA
*
56418517 ATTTGATTTGATTTGGTTAATGGTAAACGATAAAAGAAAGATTTGAGTTAAA
1 ATTTGATTTGATTTCGTTAATGGTAAACGATAAAAGAAAGATTTGAGTTAAA
56418569 A
1 A
56418570 GAAAATTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 39 0.78
52 11 0.22
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.37
Consensus pattern (52 bp):
ATTTGATTTGATTTCGTTAATGGTAAACGATAAAAGAAAGATTTGAGTTAAA
Found at i:56427031 original size:25 final size:26
Alignment explanation
Indices: 56426988--56427058 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 26
56426978 ATTTTCTCGA
56426988 AATTTTACCAGGGGTAAAATCATCAT
1 AATTTTACCAGGGGTAAAATCATCAT
* *
56427014 AATTTTACC-GGGGTAAAATCGTTAT
1 AATTTTACCAGGGGTAAAATCATCAT
* *
56427039 AATTTTATCAAGGGTAAAAT
1 AATTTTACCAGGGGTAAAAT
56427059 TGGGATTAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 22 0.55
26 18 0.45
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (26 bp):
AATTTTACCAGGGGTAAAATCATCAT
Found at i:56452968 original size:20 final size:20
Alignment explanation
Indices: 56452943--56452984 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
56452933 TATCAGTTAA
56452943 ATCCATCACATGTGTTATCT
1 ATCCATCACATGTGTTATCT
56452963 ATCCATCACATGTGTTATCT
1 ATCCATCACATGTGTTATCT
56452983 AT
1 AT
56452985 GGATGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (20 bp):
ATCCATCACATGTGTTATCT
Found at i:56456134 original size:29 final size:31
Alignment explanation
Indices: 56456102--56456161 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
56456092 ATGTGAAAAG
*
56456102 AAAGTGCAAGAAAACCA-TAAAG-ATGGAAA
1 AAAGAGCAAGAAAACCATTAAAGTATGGAAA
* *
56456131 AAAGAGCAAGAAAGCTATTAAAGTATGGAAA
1 AAAGAGCAAGAAAACCATTAAAGTATGGAAA
56456162 CCCAATTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 14 0.54
30 5 0.19
31 7 0.27
ACGTcount: A:0.57, C:0.08, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAGAGCAAGAAAACCATTAAAGTATGGAAA
Found at i:56457327 original size:10 final size:10
Alignment explanation
Indices: 56457312--56457336 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56457302 TTAGTAACTA
56457312 TATTTTATAT
1 TATTTTATAT
56457322 TATTTTATAT
1 TATTTTATAT
56457332 TATTT
1 TATTT
56457337 ATTTGTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTATAT
Found at i:56457643 original size:19 final size:19
Alignment explanation
Indices: 56457619--56457666 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
56457609 ATTTTCAGGA
56457619 TCCACACGGGCTGGGCATT
1 TCCACACGGGCTGGGCATT
56457638 TCCACACGGGCTGGGCATT
1 TCCACACGGGCTGGGCATT
56457657 TCCACACGGG
1 TCCACACGGG
56457667 TTGGCCACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.17, C:0.33, G:0.31, T:0.19
Consensus pattern (19 bp):
TCCACACGGGCTGGGCATT
Found at i:56457709 original size:30 final size:30
Alignment explanation
Indices: 56457672--56457774 Score: 127
Period size: 30 Copynumber: 3.5 Consensus size: 30
56457662 ACGGGTTGGC
* * *
56457672 CACACGCCCGTGTGAGCCACATGGGCTGGA
1 CACACGCCCGTGTGAGCCACACGGACTAGA
* *
56457702 CATACGCCCGTGTGAGCCATACGGACTAGA
1 CACACGCCCGTGTGAGCCACACGGACTAGA
* *
56457732 CACACACCCGTGTGAGCCACACGG-CTAGC
1 CACACGCCCGTGTGAGCCACACGGACTAGA
*
56457761 CACACGCCCATGTG
1 CACACGCCCGTGTG
56457775 CTAGCCTGTG
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
29 16 0.26
30 46 0.74
ACGTcount: A:0.23, C:0.36, G:0.27, T:0.14
Consensus pattern (30 bp):
CACACGCCCGTGTGAGCCACACGGACTAGA
Found at i:56469204 original size:22 final size:22
Alignment explanation
Indices: 56469164--56469206 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
56469154 TAATAATAAA
* *
56469164 TTTTAATTGATATTTTTAATTT
1 TTTTAATTGATAATGTTAATTT
*
56469186 TTTTAATTTATAATGTTAATT
1 TTTTAATTGATAATGTTAATT
56469207 AAAAGTATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (22 bp):
TTTTAATTGATAATGTTAATTT
Found at i:56470300 original size:13 final size:13
Alignment explanation
Indices: 56470282--56470306 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56470272 TTAAAAATAA
56470282 AATTAACTAAATT
1 AATTAACTAAATT
56470295 AATTAACTAAAT
1 AATTAACTAAAT
56470307 AACACGACAA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAACTAAATT
Found at i:56471149 original size:17 final size:17
Alignment explanation
Indices: 56471127--56471160 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
56471117 ACACGGTCTG
*
56471127 GCATATGGCCATGTGGC
1 GCATATGGCCATATGGC
56471144 GCATATGGCCATATGGC
1 GCATATGGCCATATGGC
56471161 AGACGTGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.24
Consensus pattern (17 bp):
GCATATGGCCATATGGC
Found at i:56475362 original size:104 final size:104
Alignment explanation
Indices: 56475182--56475387 Score: 358
Period size: 104 Copynumber: 2.0 Consensus size: 104
56475172 CTATCCAACA
* *
56475182 GCTCCCGAATATTGGTTTCAGAACTTTGCCCTCTTTCCCATGTAAACTAGGGTCATTTGAAGCCC
1 GCTCCCGAATATTGGTTTCAGAACTCTGCCCTCTTTCCCATATAAACTAGGGTCATTTGAAGCCC
* *
56475247 AGATTAGCTAACGAGCAGTCATCTAAATCCTGACGAATT
66 AGATTAGCTAACGAGCAGTCATCCAAAGCCTGACGAATT
* *
56475286 GCTCCCGAATATTGGTTTCAGAGCTCTGCCCTCTTTCCCATATATACTAGGGTCATTTGAAGCCC
1 GCTCCCGAATATTGGTTTCAGAACTCTGCCCTCTTTCCCATATAAACTAGGGTCATTTGAAGCCC
56475351 AGATTAGCTAACGAGCAGTCATCCAAAGCCTGACGAA
66 AGATTAGCTAACGAGCAGTCATCCAAAGCCTGACGAA
56475388 ATTCTTCTAT
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 96 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (104 bp):
GCTCCCGAATATTGGTTTCAGAACTCTGCCCTCTTTCCCATATAAACTAGGGTCATTTGAAGCCC
AGATTAGCTAACGAGCAGTCATCCAAAGCCTGACGAATT
Found at i:56482091 original size:15 final size:15
Alignment explanation
Indices: 56482071--56482100 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
56482061 CATGCAAATT
56482071 AGAAAAGAAAGAAAA
1 AGAAAAGAAAGAAAA
56482086 AGAAAAGAAAGAAAA
1 AGAAAAGAAAGAAAA
56482101 GAGAGAAAGG
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAGAAAA
Found at i:56488661 original size:16 final size:16
Alignment explanation
Indices: 56488640--56488672 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56488630 TAGCATAAAT
56488640 AACAGT-CTTCTGAGAC
1 AACAGTCCTT-TGAGAC
56488656 AACAGTCCTTTGAGAC
1 AACAGTCCTTTGAGAC
56488672 A
1 A
56488673 TTTCTGCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (16 bp):
AACAGTCCTTTGAGAC
Found at i:56516971 original size:27 final size:26
Alignment explanation
Indices: 56516904--56516971 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 26
56516894 AATAAACACC
*
56516904 AAAAATTTATTTTAAAAATAAAAAAAT
1 AAAAATATATTTT-AAAATAAAAAAAT
*
56516931 AAAAA-AGTATTTTAAAATTAAAAAAT
1 AAAAATA-TATTTTAAAATAAAAAAAT
56516957 AAAAATATATATTTA
1 AAAAATATAT-TTTA
56516972 TTATATATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 20 0.56
27 16 0.44
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (26 bp):
AAAAATATATTTTAAAATAAAAAAAT
Found at i:56537076 original size:22 final size:22
Alignment explanation
Indices: 56537045--56537088 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
56537035 ATTGTTCACT
*
56537045 TTTTTTTTCTT-TTTCTTTTCCC
1 TTTTTCTTCTTCTTT-TTTTCCC
56537067 TTTTTCTTCTTCTTTTTTTCCC
1 TTTTTCTTCTTCTTTTTTTCCC
56537089 ACTATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTCTTCTTCTTTTTTTCCC
Found at i:56539923 original size:36 final size:35
Alignment explanation
Indices: 56539826--56539932 Score: 87
Period size: 36 Copynumber: 3.0 Consensus size: 35
56539816 ATAAACATTA
*
56539826 AATTTAATTTAAT-TT-AA-TATTAAGATAACCACTTT
1 AATTTAA-TTAATATTAAACTATTAAGATAA-TA-TTT
* *
56539861 AATATTAAATTAATA-AAATACCATTAAGATAAGTATTT
1 AAT-TT-AATTAATATTAA-ACTATTAAGATAA-TATTT
*
56539899 AATTTAATTAATATTAAACTATTAAAATAATATT
1 AATTTAATTAATATTAAACTATTAAGATAATATT
56539933 ATTTTTGGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
35 7 0.12
36 26 0.45
37 7 0.12
38 7 0.12
39 11 0.19
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (35 bp):
AATTTAATTAATATTAAACTATTAAGATAATATTT
Found at i:56541659 original size:24 final size:24
Alignment explanation
Indices: 56541631--56541681 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
56541621 TTCTAGAAGT
* * *
56541631 TTTAGTATTTATGAGTATAATATA
1 TTTAGCATTTATAAGCATAATATA
56541655 TTTAGCATTTATAAGCATAATATA
1 TTTAGCATTTATAAGCATAATATA
56541679 TTT
1 TTT
56541682 GACTTTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTAGCATTTATAAGCATAATATA
Found at i:56546100 original size:41 final size:41
Alignment explanation
Indices: 56546033--56546141 Score: 164
Period size: 41 Copynumber: 2.7 Consensus size: 41
56546023 TTTCGGGACA
* * * *
56546033 TTAGCGGTGTTTTTAGAAAAGTGCCGCTAATGCTCTGGTTT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCT
*
56546074 TTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCT
*
56546115 TTAGCAGCGTTTTTGGAAAAGCGCCGC
1 TTAGCGGCGTTTTTGGAAAAGCGCCGC
56546142 AAAAACATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.33
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCT
Found at i:56546532 original size:22 final size:21
Alignment explanation
Indices: 56546483--56546560 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 21
56546473 TATGATTTAG
*
56546483 AGTTTAAGGTTTA-AGAGTTACT
1 AGTTTAAGGTTTATGGA-TTA-T
*
56546505 ATTTTAAGGTTTATGGATTAT
1 AGTTTAAGGTTTATGGATTAT
* *
56546526 GAGTTTAAGGGTTATGGTTTAT
1 -AGTTTAAGGTTTATGGATTAT
*
56546548 AGTTTATGGTTTA
1 AGTTTAAGGTTTA
56546561 AGATTTAGGG
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 12 0.26
22 33 0.70
23 2 0.04
ACGTcount: A:0.27, C:0.01, G:0.24, T:0.47
Consensus pattern (21 bp):
AGTTTAAGGTTTATGGATTAT
Found at i:56546552 original size:7 final size:7
Alignment explanation
Indices: 56546507--56546595 Score: 61
Period size: 7 Copynumber: 12.6 Consensus size: 7
56546497 GAGTTACTAT
*
56546507 TTTAAGG
1 TTTATGG
56546514 TTTATGG
1 TTTATGG
*
56546521 ATTATGAG
1 TTTATG-G
*
56546529 TTTAAGG
1 TTTATGG
*
56546536 GTTATGG
1 TTTATGG
*
56546543 TTTATAG
1 TTTATGG
56546550 TTTATGG
1 TTTATGG
* *
56546557 TTTAAGA
1 TTTATGG
*
56546564 TTTAGGG
1 TTTATGG
*
56546571 TTTAAGG
1 TTTATGG
* * *
56546578 GTTGTGA
1 TTTATGG
56546585 TTTATGG
1 TTTATGG
56546592 TTTA
1 TTTA
56546596 ATGTTATAGG
Statistics
Matches: 60, Mismatches: 21, Indels: 2
0.72 0.25 0.02
Matches are distributed among these distances:
7 55 0.92
8 5 0.08
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (7 bp):
TTTATGG
Found at i:56546553 original size:21 final size:21
Alignment explanation
Indices: 56546463--56546596 Score: 92
Period size: 21 Copynumber: 6.3 Consensus size: 21
56546453 AAGGTTTTTG
*
56546463 GTTT-AGGGTATATGATTTAGA
1 GTTTAAGGGT-TATGATTTATA
* * *
56546484 GTTTAAGGTTTAAGAGTTACTA
1 GTTTAAGGGTTATGATTTA-TA
* *
56546506 TTTTAAGGTTTATGGA-TTATGA
1 GTTTAAGGGTTAT-GATTTAT-A
*
56546528 GTTTAAGGGTTATGGTTTATA
1 GTTTAAGGGTTATGATTTATA
* * * **
56546549 GTTTATGGTTTAAGATTTAGG
1 GTTTAAGGGTTATGATTTATA
* *
56546570 GTTTAAGGGTTGTGATTTATG
1 GTTTAAGGGTTATGATTTATA
56546591 GTTTAA
1 GTTTAA
56546597 TGTTATAGGT
Statistics
Matches: 88, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
21 51 0.58
22 35 0.40
23 2 0.02
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.46
Consensus pattern (21 bp):
GTTTAAGGGTTATGATTTATA
Found at i:56546634 original size:21 final size:21
Alignment explanation
Indices: 56546610--56546673 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
56546600 TATAGGTTAA
56546610 GGGTTGAGGTTTAAGGTTTAG
1 GGGTTGAGGTTTAAGGTTTAG
56546631 GGGTTGAGAG-TTAAGAG-TTAG
1 GGGTTGAG-GTTTAAG-GTTTAG
* *
56546652 GGGTTTAGGATTTAGGGTTTAG
1 GGGTTGAGG-TTTAAGGTTTAG
56546674 ATTAATTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 1 0.03
21 25 0.69
22 10 0.28
ACGTcount: A:0.22, C:0.00, G:0.42, T:0.36
Consensus pattern (21 bp):
GGGTTGAGGTTTAAGGTTTAG
Found at i:56546800 original size:16 final size:17
Alignment explanation
Indices: 56546781--56546819 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
56546771 AAATTCTTTA
56546781 TAAATAATTT-ATATAT
1 TAAATAATTTAATATAT
56546797 TAAATAATTTAATATAT
1 TAAATAATTTAATATAT
56546814 TAAATA
1 TAAATA
56546820 TAGTGTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATAATTTAATATAT
Found at i:56547030 original size:21 final size:22
Alignment explanation
Indices: 56547006--56547046 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
56546996 ATGGTTTATT
56547006 GTTTAAGGGTT-GGGATTTAAA
1 GTTTAAGGGTTAGGGATTTAAA
* *
56547027 GTTTAGGGGTTAGGGGTTTA
1 GTTTAAGGGTTAGGGATTTA
56547047 GGGGTTTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (22 bp):
GTTTAAGGGTTAGGGATTTAAA
Found at i:56547049 original size:8 final size:8
Alignment explanation
Indices: 56547027--56547055 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
56547017 GGGATTTAAA
56547027 GTTTAGGG
1 GTTTAGGG
56547035 G-TTAGGG
1 GTTTAGGG
56547042 GTTTAGGG
1 GTTTAGGG
56547050 GTTTAG
1 GTTTAG
56547056 AGTTATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.14, C:0.00, G:0.48, T:0.38
Consensus pattern (8 bp):
GTTTAGGG
Found at i:56547498 original size:39 final size:39
Alignment explanation
Indices: 56547455--56547539 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
56547445 AATAAAATCA
*
56547455 CTAAAAATAAGCATTAGCGGCGCTTTTCGAAAAACGCCG
1 CTAAAAATAAGCATTAGCGGCGCTTTTAGAAAAACGCCG
* * * *
56547494 CTAAAAATGAGCATTAGTGGCGTTTTTAGAAAAGCGCCG
1 CTAAAAATAAGCATTAGCGGCGCTTTTAGAAAAACGCCG
*
56547533 CAAAAAA
1 CTAAAAA
56547540 ACTAGGCCCA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (39 bp):
CTAAAAATAAGCATTAGCGGCGCTTTTAGAAAAACGCCG
Found at i:56548356 original size:38 final size:38
Alignment explanation
Indices: 56548276--56548357 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
56548266 GGTTACAAAC
* * * *
56548276 TTTATCTGTTTTTTATATGTTTATCTCACAAATTTTCT
1 TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTCG
56548314 TTTATCTGCTTTTTACATGTTTATCTCACAAA-GTTCGG
1 TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTC-G
56548352 TTTATC
1 TTTATC
56548358 AATTGTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 3 0.08
38 36 0.92
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.55
Consensus pattern (38 bp):
TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTCG
Found at i:56552561 original size:43 final size:43
Alignment explanation
Indices: 56552514--56552827 Score: 441
Period size: 43 Copynumber: 7.3 Consensus size: 43
56552504 TTTGTTGTTT
* ** *
56552514 AAGCGTCGCTAAAGGTTGTGGTCTTTAGCGGCGTTTTTGGGAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
* * * *
56552557 AAGCGTCGCTAAAGGTCAGGGTCTTTAGTGGCGTTTGTCGGAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
* * * *
56552600 AAGCGTCGCTAAAAGTCATCGTCTTTAGCGGCGTTTGTCGGAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
* *
56552643 AAGCGCCGCTAAAGATCATGGTCTATAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
* *
56552686 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTCGGAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
* * *
56552729 AAGCGTCGCTAAAGATCATGGTCTTTAGCGTCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
*
56552772 AAGCGCCGCTAAAGGTCATGGTCTTTAGTGGCGTTTGTGGG-A
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
56552814 AAGCGCCGCTAAAG
1 AAGCGCCGCTAAAG
56552828 TTAGCGACGC
Statistics
Matches: 243, Mismatches: 28, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
42 15 0.06
43 228 0.94
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
Found at i:56552699 original size:129 final size:129
Alignment explanation
Indices: 56552470--56552827 Score: 479
Period size: 129 Copynumber: 2.8 Consensus size: 129
56552460 GTGTTTGTTA
* * * * * * *** * **
56552470 AAAAGCGCCGCTAAAACTCATCTTCATT-GTGGCGTTTGTTGTTTAAGCGTCGCTAAAGGTTGTG
1 AAAAGCGTCGCTAAAAGTCATCGTCTTTAGCGGCGTTTGTCGGAAAAGCGCCGCTAAAGGTCATG
* * * *
56552534 GTCTTTAGCGGCGTTTTTGGGAAAAGCGTCGCTAAAGGTCAGGGTCTTTAGTGGCGTTTGTCGG
66 GTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGACGTTTGTCGG
*
56552598 AAAAGCGTCGCTAAAAGTCATCGTCTTTAGCGGCGTTTGTCGGAAAAGCGCCGCTAAAGATCATG
1 AAAAGCGTCGCTAAAAGTCATCGTCTTTAGCGGCGTTTGTCGGAAAAGCGCCGCTAAAGGTCATG
* *
56552663 GTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTCGG
66 GTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGACGTTTGTCGG
* * *
56552727 AAAAGCGTCGCT-AAAGATCATGGTCTTTAGCGTCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAT
1 AAAAGCGTCGCTAAAAG-TCATCGTCTTTAGCGGCGTTTGTCGGAAAAGCGCCGCTAAAGGTCAT
*
56552791 GGTCTTTAGTGGCGTTTGTGGG-AAAGCGCCGCTAAAG
65 GGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
56552828 TTAGCGACGC
Statistics
Matches: 203, Mismatches: 25, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
128 43 0.21
129 160 0.79
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (129 bp):
AAAAGCGTCGCTAAAAGTCATCGTCTTTAGCGGCGTTTGTCGGAAAAGCGCCGCTAAAGGTCATG
GTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGACGTTTGTCGG
Found at i:56552934 original size:22 final size:21
Alignment explanation
Indices: 56552897--56552941 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
56552887 TTTAGCGGCG
* *
56552897 CTAAAAAACGCTGCTAAAGGC
1 CTAAAAAACGCCGCTAAAAGC
56552918 CTAAAAAAGCGCCGCTAAAAGC
1 CTAAAAAA-CGCCGCTAAAAGC
56552940 CT
1 CT
56552942 GTTTTGGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.42, C:0.27, G:0.18, T:0.13
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Done.