Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 69 of 207
Found at i:19994447 original size:9 final size:9
Alignment explanation
Indices: 19994411--19994446 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
19994401 AATATATAAT
19994411 ATAATAAAA
1 ATAATAAAA
19994420 ATAATAAAA
1 ATAATAAAA
*
19994429 ATAACAAAA
1 ATAATAAAA
*
19994438 TTAATAAAA
1 ATAATAAAA
19994447 TAGACTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (9 bp):
ATAATAAAA
Found at i:19994447 original size:17 final size:17
Alignment explanation
Indices: 19994401--19994448 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
19994391 TAGGTATAAT
* *
19994401 AATATATAATATAATAAA
1 AATA-ATAAAATAACAAA
19994419 AATAATAAAAATAACAAA
1 AATAAT-AAAATAACAAA
*
19994437 ATTAATAAAATA
1 AATAATAAAATA
19994449 GACTAAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAATAAAATAACAAA
Found at i:19994690 original size:19 final size:21
Alignment explanation
Indices: 19994652--19994692 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
19994642 CCTTTTTTAA
*
19994652 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
19994673 AATCG-AAA-AAGAAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
19994692 A
1 A
19994693 GTAAGCCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 3 0.16
21 5 0.26
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:19994885 original size:23 final size:22
Alignment explanation
Indices: 19994857--19994899 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
19994847 AAATTAAATC
19994857 TCTAAGATTACAAAATCATATAT
1 TCTAAGATTAC-AAATCATATAT
*
19994880 TCTAAGATTACATATCATAT
1 TCTAAGATTACAAATCATAT
19994900 CTAAGATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATAT
Found at i:19994904 original size:19 final size:19
Alignment explanation
Indices: 19994857--19994933 Score: 91
Period size: 19 Copynumber: 3.8 Consensus size: 19
19994847 AAATTAAATC
*
19994857 TCTAAGATTACAAAATCATATA
1 TCTAAGATTAC-ATATC--ATA
19994879 TTCTAAGATTACATATCATA
1 -TCTAAGATTACATATCATA
*
19994899 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
19994918 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
19994934 CTCGAAGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
20 3 0.06
22 4 0.08
23 11 0.21
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:19994943 original size:17 final size:18
Alignment explanation
Indices: 19994883--19994943 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
19994873 CATATATTCT
* *
19994883 AAGATTACATATCATATCT
1 AAGATTGCATATCA-ATCG
*
19994902 AAGATTGCATATCATATCT
1 AAGATTGCATATCA-ATCG
*
19994921 AAGATTGCATATC-CTCG
1 AAGATTGCATATCAATCG
19994938 AAGATT
1 AAGATT
19994944 ATGTTTCCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
17 8 0.21
19 31 0.79
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (18 bp):
AAGATTGCATATCAATCG
Found at i:19995846 original size:44 final size:44
Alignment explanation
Indices: 19995774--19996149 Score: 401
Period size: 44 Copynumber: 8.7 Consensus size: 44
19995764 GTTATTTTCC
* * * * *
19995774 ACCTACTCCACTACT-ACTCAGAGAGATAGGGTTCACGATCTTCA
1 ACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTCA
* * *
19995818 ACCTATTTCACTGTTGACCAGGGAGATAGGA-CCTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATCTTCA
* * * *
19995862 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * *
19995906 ACCTATTCCACTGCTGACCAAGGAGATAGGATTCATAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
*
19995950 ACCTATTCCACTGCTGTCCAGGGAGATAGGATT--C--T-TT-A
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * *
19995988 ATCTATTCCACTGCT-ACCCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGA-CCAGGGAGATAGGATTCACAATCTTCA
* * *
19996032 ACCTATTCCACTACTGACCAGGAAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * * *
19996076 ACCTATTCCACTGTTGTCCAGGGAGATAGGATTCACAATATTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
** *
19996120 ACCTATAACACTGTTGACCAGGGAGATAGG
1 ACCTATTCCACTGCTGACCAGGGAGATAGG
19996150 GCTGGGGTCA
Statistics
Matches: 279, Mismatches: 42, Indels: 22
0.81 0.12 0.06
Matches are distributed among these distances:
38 30 0.11
39 2 0.01
40 2 0.01
42 1 0.00
43 3 0.01
44 237 0.85
45 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (44 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
Found at i:19996038 original size:126 final size:125
Alignment explanation
Indices: 19995774--19996109 Score: 476
Period size: 126 Copynumber: 2.6 Consensus size: 125
19995764 GTTATTTTCC
* * * * * *
19995774 ACCTACTCCACTACT-ACTCAGAGAGATAGGGTTCACGATCTTCAACCTATTTCACTGTTGACCA
1 ACCTATTCCACTACTGAC-CAG-GAGATAGGATTCACAATCTTTAACCTATTCCACTGTTGTCCA
*
19995838 GGGAGATAGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCT
64 GGGAGATAGGA--T----TCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTCTCAATCT
19995903 TCA
123 TCA
* * *
19995906 ACCTATTCCACTGCTGACCAAGGAGATAGGATTCATAATCTTTAACCTATTCCACTGCTGTCCAG
1 ACCTATTCCACTACTGACC-AGGAGATAGGATTCACAATCTTTAACCTATTCCACTGTTGTCCAG
*
19995971 GGAGATAGGATTCTTTAATCTATTCCACTGCTACCCAGGGAGATAGAATTCTCAATCTTCA
65 GGAGATAGGATTCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTCTCAATCTTCA
19996032 ACCTATTCCACTACTGACCAGGAAGATAGGATTCACAATCTTTAACCTATTCCACTGTTGTCCAG
1 ACCTATTCCACTACTGACCAGG-AGATAGGATTCACAATCTTTAACCTATTCCACTGTTGTCCAG
19996097 GGAGATAGGATTC
65 GGAGATAGGATTC
19996110 ACAATATTTA
Statistics
Matches: 187, Mismatches: 14, Indels: 12
0.88 0.07 0.06
Matches are distributed among these distances:
125 3 0.02
126 119 0.64
130 1 0.01
132 60 0.32
133 4 0.02
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (125 bp):
ACCTATTCCACTACTGACCAGGAGATAGGATTCACAATCTTTAACCTATTCCACTGTTGTCCAGG
GAGATAGGATTCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTCTCAATCTTCA
Found at i:19996040 original size:170 final size:170
Alignment explanation
Indices: 19995835--19996149 Score: 452
Period size: 170 Copynumber: 1.9 Consensus size: 170
19995825 TCACTGTTGA
* * * * * *
19995835 CCAGGGAGATAGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAA
1 CCAGGGAGATAGAACCTACAATCTTCAACCTATTCCACTACTGACCAGGAAGATAGAATTCACAA
* * **
19995900 TCTTCAACCTATTCCACTGCTGACCAAGGAGATAGGATTCATAATCTTTAACCTATTCCACTGCT
66 TCTTCAACCTATTCCACTGCTGACCAAGGAGATAGGATTCACAATATTTAACCTATAACACTGCT
*
19995965 GTCCAGGGAGATAGGATTCTTTAATCTATTCCACTGCTAC
131 GACCAGGGAGATAGGATTCTTTAATCTATTCCACTGCTAC
* *
19996005 CCAGGGAGATAGAATTCT-CAATCTTCAACCTATTCCACTACTGACCAGGAAGATAGGATTCACA
1 CCAGGGAGATAGAA-CCTACAATCTTCAACCTATTCCACTACTGACCAGGAAGATAGAATTCACA
* * * * *
19996069 ATCTTTAACCTATTCCACTGTTGTCCAGGGAGATAGGATTCACAATATTTAACCTATAACACTGT
65 ATCTTCAACCTATTCCACTGCTGACCAAGGAGATAGGATTCACAATATTTAACCTATAACACTGC
19996134 TGACCAGGGAGATAGG
130 TGACCAGGGAGATAGG
19996150 GCTGGGGTCA
Statistics
Matches: 126, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
170 124 0.98
171 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (170 bp):
CCAGGGAGATAGAACCTACAATCTTCAACCTATTCCACTACTGACCAGGAAGATAGAATTCACAA
TCTTCAACCTATTCCACTGCTGACCAAGGAGATAGGATTCACAATATTTAACCTATAACACTGCT
GACCAGGGAGATAGGATTCTTTAATCTATTCCACTGCTAC
Found at i:19996231 original size:88 final size:88
Alignment explanation
Indices: 19996149--19996638 Score: 611
Period size: 88 Copynumber: 5.6 Consensus size: 88
19996139 AGGGAGATAG
* * * * * * *
19996149 GGCTGGGGTCATCAATCTACTTCACTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
* *
19996214 TCCGTTGTAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * * *
19996237 AGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTGCTGGAAAGAAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
*
19996302 TCCACTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * *
19996325 GGCTGGTGACTTCGATCTGCTTCGTTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTCAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
*
19996390 TCCGCTGCAACCCAAGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * * *
19996413 GGCTGGTATCTTCGATCTGCTTCGCTGTAGGTGCAGGAAGGCAAGATCTACTATTTTCAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
19996478 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * *
19996501 GACTGGTGTCTTCGACCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAGCCTAC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
* **
19996566 TCCGCTGCCACTAAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* ** ** ** **
19996589 GGCTAGTGTCTTTAATCTGCTTTACTGTTAGTATAGGAAGGCAAGATCTG
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
19996639 TTATCTTCAC
Statistics
Matches: 346, Mismatches: 56, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
88 346 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
TCCGCTGCAACCCAGGGAGGCAA
Found at i:19996411 original size:44 final size:44
Alignment explanation
Indices: 19996363--19996573 Score: 135
Period size: 43 Copynumber: 4.8 Consensus size: 44
19996353 CAGTGCAGGA
19996363 AGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGCAACCCAAGG
1 AGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGCAACCCAAGG
* * * * * * ***
19996407 AGGCAAG-GCTGGTATCTTC-GATCTGCTTCGCTGTAGGTGC-AGG
1 AGGCAAGATCTGCTATTTTCAG-CCTGCTCCGCTGCA-ACCCAAGG
* * *
19996450 AAGGCAAGATCTACTATTTTCAACCTGCTCCGCTGCAACCCAGGG
1 -AGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGCAACCCAAGG
* * * * **** *
19996495 AGGCAAGA-CTGGTGTCTTC-GACCTGCTTCGCTGTCGGTGCAAGA
1 AGGCAAGATCTGCTATTTTCAG-CCTGCTCCGCTG-CAACCCAAGG
* *
19996539 AGGCAAGATCTGCTATTTTTAGCCTACTCCGCTGC
1 AGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGC
19996574 CACTAAGGGA
Statistics
Matches: 118, Mismatches: 39, Indels: 20
0.67 0.22 0.11
Matches are distributed among these distances:
42 1 0.01
43 41 0.35
44 37 0.31
45 38 0.32
46 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.26, T:0.26
Consensus pattern (44 bp):
AGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGCAACCCAAGG
Found at i:19998897 original size:25 final size:25
Alignment explanation
Indices: 19998845--19998897 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
19998835 AAGAAAATCC
*
19998845 AAAAGAATGAAAGAATAATTATTCA
1 AAAAGAATGAAAGAATAATTACTCA
19998870 AAAAGAATGAAA-AAT-ATTAGCTCA
1 AAAAGAATGAAAGAATAATTA-CTCA
19998894 AAAA
1 AAAA
19998898 TAAATGCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 4 0.15
24 10 0.38
25 12 0.46
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:19998903 original size:25 final size:23
Alignment explanation
Indices: 19998845--19998912 Score: 55
Period size: 25 Copynumber: 2.7 Consensus size: 23
19998835 AAGAAAATCC
* *
19998845 AAAAGAATGAAAGAATAATTATTCA
1 AAAAAAATGAAA-AAT-ATTACTCA
*
19998870 AAAAGAATGAAAAATATTAGCTCA
1 AAAAAAATGAAAAATATTA-CTCA
*
19998894 AAAATAAATGCAAAGATAT
1 AAAA-AAATG-AAAAATAT
19998913 ATTTTATTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.11
24 10 0.27
25 16 0.43
26 7 0.19
ACGTcount: A:0.60, C:0.06, G:0.12, T:0.22
Consensus pattern (23 bp):
AAAAAAATGAAAAATATTACTCA
Found at i:20003152 original size:3 final size:3
Alignment explanation
Indices: 20003144--20003177 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
20003134 ATATGTAGGT
20003144 ATA ATA ATA ATA TATA AT- ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A
20003178 CAAAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:20003158 original size:21 final size:18
Alignment explanation
Indices: 20003143--20003177 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20003133 TATATGTAGG
20003143 TATAATAATAATATATAA
1 TATAATAATAATATATAA
20003161 TATAATAATAATA-ATAA
1 TATAATAATAATATATAA
20003178 CAAAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAATAATAATATATAA
Found at i:20003187 original size:21 final size:21
Alignment explanation
Indices: 20003144--20003193 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
20003134 ATATGTAGGT
* *
20003144 ATAATAATAATATATAATATA
1 ATAATAATAATACAAAATATA
20003165 ATAATAATAATAACAAAAT-TA
1 ATAATAATAAT-ACAAAATATA
20003186 ATAA-AATA
1 ATAATAATA
20003194 GACTAAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.15
21 17 0.65
22 5 0.19
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAATAATAATACAAAATATA
Found at i:20003436 original size:19 final size:21
Alignment explanation
Indices: 20003398--20003436 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
20003388 CCTTTTTTAA
*
20003398 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
20003419 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
20003437 ACAGTAAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:20003638 original size:23 final size:22
Alignment explanation
Indices: 20003595--20003652 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
20003585 AAAGGGTATC
* *
20003595 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
20003616 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
20003639 TACATATCATATCT
1 TACAAATCATATCT
20003653 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:20003655 original size:19 final size:19
Alignment explanation
Indices: 20003608--20003705 Score: 115
Period size: 19 Copynumber: 4.8 Consensus size: 19
20003598 AAATTAAATC
*
20003608 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
20003628 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
20003650 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
20003671 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
20003690 TCTAAGATTACATATC
1 TCTAAGATTACATATC
20003706 CTCGAAGATT
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
19 32 0.47
21 18 0.26
22 7 0.10
23 11 0.16
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:20003668 original size:21 final size:21
Alignment explanation
Indices: 20003642--20003704 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
20003632 CTAAGATTAC
20003642 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
20003663 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
*
20003682 ATATCATATCTAAGATTACAT
1 ATATCATATCTAAGATTGCAT
20003703 AT
1 AT
20003705 CCTCGAAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 18 0.46
21 21 0.54
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:20004561 original size:7 final size:7
Alignment explanation
Indices: 20004551--20004605 Score: 101
Period size: 7 Copynumber: 7.9 Consensus size: 7
20004541 TATATTTATT
20004551 TTTTAAA
1 TTTTAAA
20004558 TTTTAAA
1 TTTTAAA
20004565 TTTTAAA
1 TTTTAAA
20004572 TTTTAAA
1 TTTTAAA
20004579 TTTTAAA
1 TTTTAAA
20004586 TTTTAAA
1 TTTTAAA
20004593 TTTTAAA
1 TTTTAAA
*
20004600 ATTTAA
1 TTTTAA
20004606 TATTATTAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTTTAAA
Found at i:20004575 original size:21 final size:21
Alignment explanation
Indices: 20004551--20004614 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
20004541 TATATTTATT
20004551 TTTTAAATTTTAAATTTTAAA
1 TTTTAAATTTTAAATTTTAAA
20004572 TTTTAAATTTTAAATTTTAAA
1 TTTTAAATTTTAAATTTTAAA
*
20004593 TTTTAAAATTTAATATTATTAA
1 TTTTAAATTTTAA-ATT-TTAA
20004615 TTAATAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 33 0.82
22 3 0.08
23 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTAAATTTTAAATTTTAAA
Found at i:20004645 original size:12 final size:12
Alignment explanation
Indices: 20004615--20004655 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
20004605 ATATTATTAA
20004615 TTAATAAAA-TT
1 TTAATAAAATTT
*
20004626 TAAATAAAATTT
1 TTAATAAAATTT
20004638 TTAATAAAATTT
1 TTAATAAAATTT
20004650 GTTAAT
1 -TTAAT
20004656 GTGGTTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 8 0.31
12 13 0.50
13 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (12 bp):
TTAATAAAATTT
Found at i:20008711 original size:31 final size:29
Alignment explanation
Indices: 20008646--20008723 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 29
20008636 ACAAGACAAC
*
20008646 AGCAAAAAAAGAAGGAAGAAAAAGAAAAAAAT
1 AGCAAAAAAA-AAAG-A-AAAAAGAAAAAAAT
* *
20008678 AGCAACAGAAAAAGAAAAAGAGAAAAAAGAT
1 AGCAAAAAAAAAAGAAAAA-AGAAAAAA-AT
20008709 AGCAAAAAAAAAAGA
1 AGCAAAAAAAAAAGA
20008724 GATGTATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 4 0.10
30 9 0.23
31 18 0.46
32 8 0.21
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.03
Consensus pattern (29 bp):
AGCAAAAAAAAAAGAAAAAAGAAAAAAAT
Found at i:20011955 original size:37 final size:37
Alignment explanation
Indices: 20011909--20012013 Score: 160
Period size: 37 Copynumber: 2.8 Consensus size: 37
20011899 TGTTTTCTAT
* *
20011909 TGGACTAGCTCTTATGAGCATCT-GCTATGTTGTCGGG
1 TGGATTAGCTCTTATGAGCATCTGGC-ATGTTATCGGG
20011946 TGGATTAGCTCTTATGAGCATCTGGCATGTTATCGGG
1 TGGATTAGCTCTTATGAGCATCTGGCATGTTATCGGG
20011983 TGGATTAGCTCTTATGAGCGAT-TGGCATGTT
1 TGGATTAGCTCTTATGAGC-ATCTGGCATGTT
20012014 TTGGTTGGAA
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
37 60 0.94
38 4 0.06
ACGTcount: A:0.18, C:0.16, G:0.30, T:0.36
Consensus pattern (37 bp):
TGGATTAGCTCTTATGAGCATCTGGCATGTTATCGGG
Found at i:20012992 original size:25 final size:25
Alignment explanation
Indices: 20012964--20013020 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
20012954 GGCCTAACAT
* * *
20012964 ATGGGCGTGTGACACAGCTTGGCAC
1 ATGGGCGTCTAACACAGCCTGGCAC
20012989 ATGGGCGTCTAACACAGCCTGGCAC
1 ATGGGCGTCTAACACAGCCTGGCAC
20013014 ATGGGCG
1 ATGGGCG
20013021 CATGACACGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.21, C:0.26, G:0.35, T:0.18
Consensus pattern (25 bp):
ATGGGCGTCTAACACAGCCTGGCAC
Found at i:20013028 original size:25 final size:24
Alignment explanation
Indices: 20012964--20013028 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 24
20012954 GGCCTAACAT
* *
20012964 ATGGGCGTGTGACACAGCTTGGCAC
1 ATGGGCG-CTGACACAGCCTGGCAC
*
20012989 ATGGGCGTCTAACACAGCCTGGCAC
1 ATGGGCG-CTGACACAGCCTGGCAC
20013014 ATGGGCGCATGACAC
1 ATGGGCGC-TGACAC
20013029 GGTCTTGTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 1 0.03
25 34 0.97
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (24 bp):
ATGGGCGCTGACACAGCCTGGCAC
Found at i:20013795 original size:25 final size:25
Alignment explanation
Indices: 20013763--20013819 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
20013753 CATTCCATAT
* * *
20013763 CTTGTGTGAGCATTTACAGTTATAG
1 CTTGTGTGAGCAATTACAATTACAG
*
20013788 CTTGTGTGATCAATTACAATTACAG
1 CTTGTGTGAGCAATTACAATTACAG
20013813 CTTGTGT
1 CTTGTGT
20013820 TAGTATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (25 bp):
CTTGTGTGAGCAATTACAATTACAG
Found at i:20013889 original size:13 final size:13
Alignment explanation
Indices: 20013871--20013930 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
20013861 GATCAAGTGG
20013871 AAAATGAATATAT
1 AAAATGAATATAT
*
20013884 AAAATGATTATAT
1 AAAATGAATATAT
* *
20013897 -GAATCGATTATAT
1 AAAAT-GAATATAT
20013910 GGAAAATGAATATAT
1 --AAAATGAATATAT
20013925 AAAATG
1 AAAATG
20013931 GTAATATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 3 0.08
13 26 0.67
15 7 0.18
16 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.13, T:0.32
Consensus pattern (13 bp):
AAAATGAATATAT
Found at i:20013913 original size:41 final size:41
Alignment explanation
Indices: 20013868--20013992 Score: 157
Period size: 41 Copynumber: 3.1 Consensus size: 41
20013858 GTTGATCAAG
20013868 TGGAAAATGAATATATAAAATGATTATATGAATCGATTATA
1 TGGAAAATGAATATATAAAATGATTATATGAATCGATTATA
* * *
20013909 TGGAAAATGAATATATAAAATGGTAATATGAAT-TAGTTATA
1 TGGAAAATGAATATATAAAATGATTATATGAATCGA-TTATA
** * *
20013950 TGG-AAATG-ATATATGGAATGATTATATAAATCGGTTATA
1 TGGAAAATGAATATATAAAATGATTATATGAATCGATTATA
20013989 TGGA
1 TGGA
20013993 TAGATATTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
39 26 0.37
40 6 0.08
41 39 0.55
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.34
Consensus pattern (41 bp):
TGGAAAATGAATATATAAAATGATTATATGAATCGATTATA
Found at i:20014832 original size:22 final size:22
Alignment explanation
Indices: 20014804--20014849 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
20014794 AATTGGGTAT
20014804 TGAATTCATGGAATGGAAAGTG
1 TGAATTCATGGAATGGAAAGTG
*
20014826 TGAATTCATGGAATGGAAGGTG
1 TGAATTCATGGAATGGAAAGTG
20014848 TG
1 TG
20014850 GTTAACTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.35, T:0.28
Consensus pattern (22 bp):
TGAATTCATGGAATGGAAAGTG
Found at i:20015630 original size:27 final size:22
Alignment explanation
Indices: 20015578--20015621 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
20015568 GTTTAAACAT
20015578 ATTTCTTTTCCCGTCCCCCCAC
1 ATTTCTTTTCCCGTCCCCCCAC
20015600 ATTTCTTTTCCCGTCCCCCCAC
1 ATTTCTTTTCCCGTCCCCCCAC
20015622 TCCCAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.50, G:0.05, T:0.36
Consensus pattern (22 bp):
ATTTCTTTTCCCGTCCCCCCAC
Found at i:20015888 original size:20 final size:20
Alignment explanation
Indices: 20015863--20015903 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20015853 AAGTTTGTTT
20015863 TATTTTTTCTTTCTCTGATA
1 TATTTTTTCTTTCTCTGATA
20015883 TATTTTTTCTTTCTCTGATA
1 TATTTTTTCTTTCTCTGATA
20015903 T
1 T
20015904 CCAGTACAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (20 bp):
TATTTTTTCTTTCTCTGATA
Found at i:20019046 original size:9 final size:9
Alignment explanation
Indices: 20019018--20019054 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
20019008 GGTTGCAAAA
20019018 AGGACGATG
1 AGGACGATG
*
20019027 ACGACGATG
1 AGGACGATG
20019036 AGGACGATG
1 AGGACGATG
*
20019045 AGGATGATG
1 AGGACGATG
20019054 A
1 A
20019055 TGTTTCTTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.35, C:0.11, G:0.41, T:0.14
Consensus pattern (9 bp):
AGGACGATG
Found at i:20023277 original size:27 final size:27
Alignment explanation
Indices: 20023203--20023279 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
20023193 CCTCATCCCT
* * *
20023203 ATTTTACCCCTATTAAAA-ATTTAACG
1 ATTTTACCCTTATTAAAATTTTTAACA
** *
20023229 ATTTTACCCTTGA-TAATTTTTTTTACA
1 ATTTTACCCTT-ATTAAAATTTTTAACA
20023256 ATTTTACCCTTATTAAAATTTTTA
1 ATTTTACCCTTATTAAAATTTTTA
20023280 GAAAATATGT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
26 14 0.36
27 25 0.64
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (27 bp):
ATTTTACCCTTATTAAAATTTTTAACA
Found at i:20025328 original size:27 final size:27
Alignment explanation
Indices: 20025294--20025471 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
20025284 TAAATTGTAC
20025294 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
20025321 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
20025347 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* * *
20025375 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
20025403 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
20025430 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
20025457 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
20025472 GGCTCAATAT
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 104 0.83
28 21 0.17
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:20025411 original size:82 final size:81
Alignment explanation
Indices: 20025295--20025450 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
20025285 AAATTGTACA
* * * *
20025295 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
20025359 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
20025376 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
20025441 TGCGAGTTGA
65 TGCGAATTGA
20025451 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 49 0.75
83 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:20025462 original size:82 final size:81
Alignment explanation
Indices: 20025291--20025471 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
20025281 GAGTAAATTG
* * * *
20025291 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
20025356 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
20025372 TGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
20025436 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
20025454 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
20025472 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 18 0.22
82 64 0.78
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:20025482 original size:27 final size:27
Alignment explanation
Indices: 20025376--20025482 Score: 81
Period size: 27 Copynumber: 3.9 Consensus size: 27
20025366 TGACCATGCG
*
20025376 GCACTAAGTGTGCGAG-TCTAACTATGTA
1 GCACTAAGTGTGCGAGCTC-AA-TATATA
** * * **
20025404 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
20025431 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
20025458 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
20025483 CATTCGTGAA
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
27 49 0.74
28 16 0.24
29 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:20033423 original size:27 final size:27
Alignment explanation
Indices: 20033389--20033566 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
20033379 TAAATTGTAC
20033389 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
20033416 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
20033442 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* * *
20033470 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
20033498 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
20033525 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
20033552 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
20033567 GGCTCAATAT
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 104 0.83
28 21 0.17
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:20033506 original size:82 final size:81
Alignment explanation
Indices: 20033390--20033545 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
20033380 AAATTGTACA
* * * *
20033390 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
20033454 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
20033471 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
20033536 TGCGAGTTGA
65 TGCGAATTGA
20033546 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 49 0.75
83 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:20033557 original size:82 final size:81
Alignment explanation
Indices: 20033386--20033566 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
20033376 GAGTAAATTG
* * * *
20033386 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
20033451 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
20033467 TGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
20033531 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
20033549 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
20033567 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 18 0.22
82 64 0.78
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:20033577 original size:27 final size:27
Alignment explanation
Indices: 20033471--20033577 Score: 81
Period size: 27 Copynumber: 3.9 Consensus size: 27
20033461 TGACCATGCG
*
20033471 GCACTAAGTGTGCGAG-TCTAACTATGTA
1 GCACTAAGTGTGCGAGCTC-AA-TATATA
** * * **
20033499 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
20033526 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
20033553 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
20033578 CATTCGTGAA
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
27 49 0.74
28 16 0.24
29 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:20034058 original size:24 final size:24
Alignment explanation
Indices: 20034031--20034081 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
20034021 TGTTTCCTTG
20034031 TCACCCATTATAGGTTGCTTGGAC
1 TCACCCATTATAGGTTGCTTGGAC
20034055 TCACCCATTATAGGTTGCTTGGAC
1 TCACCCATTATAGGTTGCTTGGAC
20034079 TCA
1 TCA
20034082 TCTATTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (24 bp):
TCACCCATTATAGGTTGCTTGGAC
Found at i:20043007 original size:30 final size:30
Alignment explanation
Indices: 20042973--20043036 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
20042963 TTCCCATTTT
20042973 GATACATAAATTCCTCTTTTATATATAAAA
1 GATACATAAATTCCTCTTTTATATATAAAA
20043003 GATACATAAATTCCTCTTTTATATATAAAA
1 GATACATAAATTCCTCTTTTATATATAAAA
20043033 GATA
1 GATA
20043037 TAAATATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (30 bp):
GATACATAAATTCCTCTTTTATATATAAAA
Found at i:20050999 original size:85 final size:85
Alignment explanation
Indices: 20050905--20051075 Score: 281
Period size: 85 Copynumber: 2.0 Consensus size: 85
20050895 TCTCATGCTA
* *
20050905 ATTGATCATTTGCTCTTTACAATCCTTAAAAATTTCATCCTTAAATCA-CTACTTAATTTAATGA
1 ATTGATCATTTGCCCTTTACAATCCTTAAAAATTTCATCCTTAAATCATC-ACTTAATTTAATAA
*
20050969 AATTTTGATTTAGTCCCTCAT
65 AATTATGATTTAGTCCCTCAT
* *
20050990 ATTGATCATTTGCCCTTTATAATCCTTAAAAATTTCATCCTTAAATCATCATTTAATTTAATAAA
1 ATTGATCATTTGCCCTTTACAATCCTTAAAAATTTCATCCTTAAATCATCACTTAATTTAATAAA
20051055 ATTATGATTTAGTCCCTCAT
66 ATTATGATTTAGTCCCTCAT
20051075 A
1 A
20051076 ATTCTTTATT
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
85 79 0.99
86 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.43
Consensus pattern (85 bp):
ATTGATCATTTGCCCTTTACAATCCTTAAAAATTTCATCCTTAAATCATCACTTAATTTAATAAA
ATTATGATTTAGTCCCTCAT
Found at i:20052956 original size:47 final size:47
Alignment explanation
Indices: 20052887--20052979 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
20052877 AACCATATTT
*
20052887 AAAGTTTGGTTCCGGCACACGTCAGGCGCCACCCTTTCACTTTTCTA
1 AAAGTTTGGTTCCGGCACACGTCAAGCGCCACCCTTTCACTTTTCTA
20052934 AAAGTTTGGTTCCGGCACACGTCAAGCGCCACCCTTTCACTTTTCT
1 AAAGTTTGGTTCCGGCACACGTCAAGCGCCACCCTTTCACTTTTCT
20052980 TCTAGTAGCC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.19, C:0.32, G:0.18, T:0.30
Consensus pattern (47 bp):
AAAGTTTGGTTCCGGCACACGTCAAGCGCCACCCTTTCACTTTTCTA
Found at i:20053287 original size:30 final size:30
Alignment explanation
Indices: 20053251--20053310 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
20053241 TTAAATAAAA
20053251 GATAAAATACAAAAATGATCATTAAATTAT
1 GATAAAATACAAAAATGATCATTAAATTAT
20053281 GATAAAATACAAAAATGATCATTAAATTAT
1 GATAAAATACAAAAATGATCATTAAATTAT
20053311 TCTTCATGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (30 bp):
GATAAAATACAAAAATGATCATTAAATTAT
Found at i:20054410 original size:16 final size:16
Alignment explanation
Indices: 20054389--20054419 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20054379 GTTTGGTTCG
20054389 CTGTAACGGAATAGAA
1 CTGTAACGGAATAGAA
*
20054405 CTGTAATGGAATAGA
1 CTGTAACGGAATAGA
20054420 GGCGTAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.23
Consensus pattern (16 bp):
CTGTAACGGAATAGAA
Found at i:20054473 original size:45 final size:44
Alignment explanation
Indices: 20054409--20054501 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
20054399 ATAGAACTGT
*
20054409 AATGGAATAGAGGCGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAGACGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
20054454 AATGGAATAGA-ACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGAC-GTAATAGTATTCATGTGTTTGGTTGAATGG
20054498 AATG
1 AATG
20054502 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 1 0.02
44 24 0.55
45 19 0.43
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGACGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:20056390 original size:20 final size:20
Alignment explanation
Indices: 20056365--20056406 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
20056355 AACAAGGATG
20056365 AAAGCATTTGGAACCTTAAT
1 AAAGCATTTGGAACCTTAAT
20056385 AAAGCATTTGGAACCTTAAT
1 AAAGCATTTGGAACCTTAAT
20056405 AA
1 AA
20056407 TTATATCCCT
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (20 bp):
AAAGCATTTGGAACCTTAAT
Found at i:20058142 original size:52 final size:51
Alignment explanation
Indices: 20058064--20058167 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 51
20058054 AATAGCGCCT
*
20058064 GAATGGATTCAGGCTGTAATACCATTACAGCCAACCAAATTAATGTTTGGTG
1 GAATGGATTCAGGCTGTAATACCATTACAGCCAA-CAAAATAATGTTTGGTG
20058116 GAATGGATTCAGGCTGTAATACCATTACAGCCAACAAAATAATGTTTGGTG
1 GAATGGATTCAGGCTGTAATACCATTACAGCCAACAAAATAATGTTTGGTG
20058167 G
1 G
20058168 TGGGCCCACC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 17 0.33
52 34 0.67
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (51 bp):
GAATGGATTCAGGCTGTAATACCATTACAGCCAACAAAATAATGTTTGGTG
Found at i:20059747 original size:46 final size:47
Alignment explanation
Indices: 20059668--20059759 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 47
20059658 ATCATGTCAA
20059668 ATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGC
1 ATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGC
20059715 ATATGGTTCGGTACTT-CTCGAATTGACCTTCAGTGGGTTTAATCG
1 ATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCG
20059760 TGTCTATTCC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 29 0.64
47 16 0.36
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (47 bp):
ATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGC
Found at i:20062525 original size:27 final size:27
Alignment explanation
Indices: 20062487--20062539 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
20062477 AACTGAGAAG
*
20062487 TGAATAGAAAGCACAGAATATTCTATT
1 TGAATAGAAAGCACAGAATATGCTATT
*
20062514 TGAATAGAAAGCACCGAATATGCTAT
1 TGAATAGAAAGCACAGAATATGCTAT
20062540 AGTTTCAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (27 bp):
TGAATAGAAAGCACAGAATATGCTATT
Found at i:20063556 original size:16 final size:18
Alignment explanation
Indices: 20063517--20063550 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20063507 TAAGTTTATG
20063517 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
20063534 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
20063551 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:20064860 original size:21 final size:20
Alignment explanation
Indices: 20064831--20064871 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
20064821 CTCTCTCACC
*
20064831 AAAATTTTCAAAAATATTTAT
1 AAAAATTTCAAAAAT-TTTAT
20064852 AAAAATTTCAAAAATTTTAT
1 AAAAATTTCAAAAATTTTAT
20064872 TTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATTTCAAAAATTTTAT
Found at i:20064880 original size:14 final size:14
Alignment explanation
Indices: 20064863--20064892 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20064853 AAAATTTCAA
*
20064863 AAATTTTATTTTTT
1 AAATTATATTTTTT
20064877 AAATTATATTTTTT
1 AAATTATATTTTTT
20064891 AA
1 AA
20064893 GAAAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AAATTATATTTTTT
Found at i:20067047 original size:19 final size:19
Alignment explanation
Indices: 20067012--20067049 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
20067002 AAGTTACAAA
*
20067012 AAATAAAAAATATAAATAT
1 AAATAAAAAATAAAAATAT
20067031 AAATAAAATAA-AAAAATAT
1 AAATAAAA-AATAAAAATAT
20067050 TAATTACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAAAAATAAAAATAT
Found at i:20068942 original size:40 final size:41
Alignment explanation
Indices: 20068864--20068944 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 41
20068854 AGGAAGCGCT
**
20068864 TGTCCACGTGGACAAAAAACGCTTCCTTGAGGGCGCACTTTG
1 TGTCCACGTGGAC-AAAAACGCTTCCTTGAGGAAGCACTTTG
*
20068906 TGTCCACGTGGAC-AAAGCGCTTCCTTGAGGAAGCACTTT
1 TGTCCACGTGGACAAAAACGCTTCCTTGAGGAAGCACTTT
20068945 TTCCGTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 23 0.64
42 13 0.36
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (41 bp):
TGTCCACGTGGACAAAAACGCTTCCTTGAGGAAGCACTTTG
Found at i:20069131 original size:96 final size:96
Alignment explanation
Indices: 20069023--20069333 Score: 423
Period size: 97 Copynumber: 3.2 Consensus size: 96
20069013 ATTTTAAGGG
* * * * * * * *
20069023 TTTAAGGAAAAAATTAAATAAATAAGGGTTTAGGGTTTCTTAATTAAATTAATTATAGATTTTAA
1 TTTAAGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTTAA
20069088 AAAATTAGATTAGGGTTTAGTGTTTATGGTT
66 AAAATTAGATTAGGGTTTAGTGTTTATGGTT
20069119 TTTAAGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAATTATTTT
1 TTTAAGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAA--ATTTT
**
20069184 TTAAAA-TAGATTAGGGTTTAGTG-TT-TGGTT
64 AAAAAATTAGATTAGGGTTTAGTGTTTATGGTT
20069214 TTTAAGGGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTT
1 TTTAA--GAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTT
* * *
20069279 AAAAAAATTAGATTGGGGTTTAGTATTTAGGGTT
64 -AAAAAATTAGATTAGGGTTTAGTGTTTATGGTT
*
20069313 TTTAA-AGAAAAATCAAATAAA
1 TTTAAGAAAAAAATCAAATAAA
20069334 GCTAGTTGTT
Statistics
Matches: 191, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
95 15 0.08
96 71 0.37
97 85 0.45
98 11 0.06
99 9 0.05
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.39
Consensus pattern (96 bp):
TTTAAGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTTAA
AAAATTAGATTAGGGTTTAGTGTTTATGGTT
Found at i:20069887 original size:11 final size:11
Alignment explanation
Indices: 20069871--20069896 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20069861 GTTAGACTTA
20069871 ATAAATAATTT
1 ATAAATAATTT
20069882 ATAAATAATTT
1 ATAAATAATTT
20069893 ATAA
1 ATAA
20069897 TTTTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATAAATAATTT
Found at i:20069896 original size:18 final size:16
Alignment explanation
Indices: 20069875--20069914 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
20069865 GACTTAATAA
20069875 ATAATTTATAAATAATTT
1 ATAATTT-TAAA-AATTT
*
20069893 ATAATTTTTAAAATTT
1 ATAATTTTAAAAATTT
20069909 ATAATT
1 ATAATT
20069915 AATTTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
17 3 0.14
18 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAATTTTAAAAATTT
Found at i:20076894 original size:21 final size:21
Alignment explanation
Indices: 20076855--20076895 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20076845 TACTTTATTT
*
20076855 CATTTTTCTTTATTTTTCTTC
1 CATTTTTCTTTATTATTCTTC
* *
20076876 CATTTTTTTTTCTTATTCTT
1 CATTTTTCTTTATTATTCTT
20076896 TCCTTTCTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (21 bp):
CATTTTTCTTTATTATTCTTC
Found at i:20076898 original size:22 final size:21
Alignment explanation
Indices: 20076855--20076911 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
20076845 TACTTTATTT
* * *
20076855 CATTTTTCTTTATTTTTCTTC
1 CATTTTTATTTCTTATTCTTC
*
20076876 CATTTTTTTTTCTTATTCTTTC
1 CATTTTTATTTCTTATTC-TTC
20076898 C-TTTCTTATTTCTT
1 CATTT-TTATTTCTT
20076912 TTCCTTCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (21 bp):
CATTTTTATTTCTTATTCTTC
Found at i:20076902 original size:15 final size:17
Alignment explanation
Indices: 20076884--20076917 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
20076874 TCCATTTTTT
20076884 TTTCTTA-TTC-TTTCC
1 TTTCTTATTTCTTTTCC
20076899 TTTCTTATTTCTTTTCC
1 TTTCTTATTTCTTTTCC
20076916 TT
1 TT
20076918 CATTCTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCTTATTTCTTTTCC
Found at i:20079454 original size:30 final size:30
Alignment explanation
Indices: 20079414--20079515 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
20079404 TAAAAAATAA
* *
20079414 AAATTGCATTTTGACCCCTAAACTTTTCCT
1 AAATTTCATTTTGACCCCTAAACTTTTCTT
*
20079444 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTC-TT
* * *
20079474 AAATTTCACTTAGACCCCTAAACTTTTATT
1 AAATTTCATTTTGACCCCTAAACTTTTCTT
20079504 AAATTTCATTTT
1 AAATTTCATTTT
20079516 AATCCTAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
29 4 0.07
30 54 0.89
31 3 0.05
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTT
Found at i:20079902 original size:3 final size:3
Alignment explanation
Indices: 20079894--20079936 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
20079884 GCTAGACTTT
*
20079894 GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAA
1 GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
20079937 AGAAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 27 0.77
4 6 0.17
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:20079909 original size:10 final size:10
Alignment explanation
Indices: 20079894--20079922 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
20079884 GCTAGACTTT
20079894 GAAGAAGAAG
1 GAAGAAGAAG
20079904 GAAGAAGAAG
1 GAAGAAGAAG
20079914 GAAGAAGAA
1 GAAGAAGAA
20079923 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:20079931 original size:24 final size:24
Alignment explanation
Indices: 20079894--20079950 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
20079884 GCTAGACTTT
* *
20079894 GAAGAAGA-AGGAAGAAGAAGGAA
1 GAAGAAAAGAGGAAGAAGAAAGAA
20079917 GAAGAAAAGAGGAAGAAGAAAGAA
1 GAAGAAAAGAGGAAGAAGAAAGAA
* *
20079941 AAAAAAAAGA
1 GAAGAAAAGA
20079951 AAAATCCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (24 bp):
GAAGAAAAGAGGAAGAAGAAAGAA
Found at i:20080055 original size:15 final size:14
Alignment explanation
Indices: 20080033--20080072 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
20080023 GCAGCCCAAG
20080033 AAAAAAACAACAAAA
1 AAAAAAACAA-AAAA
*
20080048 ACAAAAACAAAAAA
1 AAAAAAACAAAAAA
20080062 AAAAGAAACAA
1 AAAA-AAACAA
20080073 GCCCAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAA
Found at i:20080070 original size:21 final size:21
Alignment explanation
Indices: 20080046--20080089 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
20080036 AAAACAACAA
20080046 AAACAAAAACAAAAAAAAAAG
1 AAACAAAAACAAAAAAAAAAG
***
20080067 AAACAAGCCCAAAAAAAAAAG
1 AAACAAAAACAAAAAAAAAAG
20080088 AA
1 AA
20080090 GAGCAGGCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.80, C:0.14, G:0.07, T:0.00
Consensus pattern (21 bp):
AAACAAAAACAAAAAAAAAAG
Found at i:20080249 original size:15 final size:14
Alignment explanation
Indices: 20080227--20080290 Score: 62
Period size: 15 Copynumber: 4.6 Consensus size: 14
20080217 AGCAGAGAAA
20080227 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
*
20080241 AAGAAAAAG-AGAAG
1 AA-AAAAAGAAAAAG
* *
20080255 GAAAAAAG--AAGG
1 AAAAAAAGAAAAAG
20080267 AAAAAAAGGAAAAAG
1 AAAAAAA-GAAAAAG
20080282 AAAAAAAGA
1 AAAAAAAGA
20080291 GGTTCAATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
12 8 0.20
13 7 0.17
14 9 0.22
15 16 0.40
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:20080262 original size:13 final size:11
Alignment explanation
Indices: 20080235--20080280 Score: 62
Period size: 10 Copynumber: 4.4 Consensus size: 11
20080225 AAAAAAAAAG
20080235 AAAAAGAA-GA
1 AAAAAGAAGGA
20080245 AAAAGAGAAGGA
1 AAAA-AGAAGGA
20080257 AAAAAGAAGG-
1 AAAAAGAAGGA
20080267 AAAAA-AAGGA
1 AAAAAGAAGGA
20080277 AAAA
1 AAAA
20080281 GAAAAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.12
10 13 0.39
11 10 0.30
12 6 0.18
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAAGAAGGA
Found at i:20080436 original size:6 final size:6
Alignment explanation
Indices: 20080425--20080493 Score: 62
Period size: 5 Copynumber: 12.5 Consensus size: 6
20080415 TTTATGCATT
*
20080425 TTTATA TTTATA TTTATA TTTTTAA TTTA-A TTTA-A TTTA-A TTTA-A
1 TTTATA TTTATA TTTATA TTTAT-A TTTATA TTTATA TTTATA TTTATA
*
20080470 TTTTTA TTT-TA TTT-TA TTT-TA TTT
1 TTTATA TTTATA TTTATA TTTATA TTT
20080494 TAAATAATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
5 34 0.59
6 20 0.34
7 4 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTATA
Found at i:20080685 original size:20 final size:22
Alignment explanation
Indices: 20080660--20080702 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
20080650 TCGGGTTTCG
20080660 AAATTT-TCGTG-TCTTCAAAA
1 AAATTTCTCGTGTTCTTCAAAA
*
20080680 AAATTTCTCGTGTTTTTCAAAA
1 AAATTTCTCGTGTTCTTCAAAA
20080702 A
1 A
20080703 TAAGGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
AAATTTCTCGTGTTCTTCAAAA
Found at i:20080836 original size:18 final size:18
Alignment explanation
Indices: 20080814--20081157 Score: 163
Period size: 17 Copynumber: 19.5 Consensus size: 18
20080804 GGAAAATTTT
20080814 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
* * *
20080832 CCGTG-TTGCAAAAATTT
1 TCGTGTTTTCAAAAATTC
*
20080849 TCATGTTTTTCAAAAATTC
1 TCGTG-TTTTCAAAAATTC
20080868 TCGTGTTTTCAAAAAAATTC
1 TCGTGTTTTC--AAAAATTC
** * *
20080888 -C-AATTTTCAAAATTTT
1 TCGTGTTTTCAAAAATTC
20080904 TCGTGTTTTCTAAAAACTTC
1 TCGTGTTTTC-AAAAA-TTC
*
20080924 T-GTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
* * *
20080940 TTGTG-TTTCTAAAATTT
1 TCGTGTTTTCAAAAATTC
* *
20080957 TCGT-ATTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
* * *
20080974 TCTTGTTTTC-AAATTTT
1 TCGTGTTTTCAAAAATTC
* * *
20080991 TCGT-ATTTAAAAAATCC
1 TCGTGTTTTCAAAAATTC
20081008 TCGTGTTTTC-AAAATTC
1 TCGTGTTTTCAAAAATTC
* *
20081025 -CAGTG-TTTCAAAATTTT
1 TC-GTGTTTTCAAAAATTC
20081042 TCGTG-TTTCAAAAAAAATTC
1 TCGTGTTTTC---AAAAATTC
*
20081062 TCGT-TTTCCAAAAACTT-
1 TCGTGTTTTCAAAAA-TTC
*
20081079 TCGCGTTTT-AAGAAATTGAC
1 TCGTGTTTTCAA-AAATT--C
* *
20081099 -CGTG-TTTCATAAATTT
1 TCGTGTTTTCAAAAATTC
*
20081115 TCGTG-TTTCAAAGAAATC
1 TCGTGTTTTCAAA-AATTC
*
20081133 TCGTG-TTTC-AAAATTT
1 TCGTGTTTTCAAAAATTC
20081149 TCGTGTTTT
1 TCGTGTTTT
20081158 TTTAAAAAAT
Statistics
Matches: 249, Mismatches: 47, Indels: 61
0.70 0.13 0.17
Matches are distributed among these distances:
16 25 0.10
17 115 0.46
18 59 0.24
19 26 0.10
20 24 0.10
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTC
Found at i:20080859 original size:36 final size:35
Alignment explanation
Indices: 20080806--20080874 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
20080796 TAAAAATCGG
* *
20080806 AAAATTTTTCGTGTTTTCAAAAATTCCCGTGTTGC
1 AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
*
20080841 AAAAATTTTCATGTTTTTCAAAAATTCTCGTGTT
1 AAAAATTTTCATG-TTTTCAAAAATTCCCGTGTT
20080875 TTCAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (35 bp):
AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
Found at i:20081046 original size:34 final size:34
Alignment explanation
Indices: 20080856--20081157 Score: 188
Period size: 34 Copynumber: 8.6 Consensus size: 34
20080846 TTTTCATGTT
* *
20080856 TTTCAAAAATTCTCGTGTTTTCAAAAAAATTCC-AA
1 TTTCAAAAATTTTCGTGTTTTC--AAAAATTCCGTA
* * *
20080891 TTTTCAAAATTTTTCGTGTTTTCTAAAAACTTCTGTG
1 -TTTCAAAAATTTTCGTGTTTTC-AAAAA-TTCCGTA
* * *
20080928 TTTCAAAAATTTTTGTG-TTTCTAAAATTTTCGTA
1 TTTCAAAAATTTTCGTGTTTTC-AAAAATTCCGTA
* ** *
20080962 TTTCAAAAATTTTCTTGTTTTCAAATTTTTCGTA
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTCCGTA
* ** *
20080996 TTTAAAAAATCCTCGTGTTTTC-AAAATTCCAGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTCC-GTA
*
20081030 TTTCAAAATTTTTCGTG-TTTCAAAAAAAATTCTCGT-
1 TTTCAAAAATTTTCGTGTTTTC---AAAAATTC-CGTA
* * *
20081066 TTTCCAAAAACTTTCGCGTTTT-AAGAAATTGACCGTG
1 TTT-CAAAAATTTTCGTGTTTTCAA-AAATT--CCGTA
* * *
20081103 TTTCATAAATTTTCGTG-TTTCAAAGAAATCTCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAA-AATTC-CGTA
20081138 TTTC-AAAATTTTCGTGTTTT
1 TTTCAAAAATTTTCGTGTTTT
20081158 TTTAAAAAAT
Statistics
Matches: 212, Mismatches: 35, Indels: 39
0.74 0.12 0.14
Matches are distributed among these distances:
33 9 0.04
34 77 0.36
35 38 0.18
36 60 0.28
37 24 0.11
38 4 0.02
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (34 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAATTCCGTA
Found at i:20081173 original size:34 final size:33
Alignment explanation
Indices: 20080856--20081212 Score: 156
Period size: 34 Copynumber: 10.2 Consensus size: 33
20080846 TTTTCATGTT
* * *
20080856 TTTCAAAAATTCTCGTGTTTTCAAAAAAATTCCAAT-
1 TTTC-AAAATTTTCGTGTTTT-TAAAAAATT-C-GTG
*
20080892 TTTCAAAATTTTTCGTGTTTTCTAAAAACTTCTGTG
1 TTTCAAAA-TTTTCGTGTTTT-TAAAAAATTC-GTG
* * ** *
20080928 TTTCAAAAATTTTTGTGTTTCTAAAATTTTCGTA
1 TTTC-AAAATTTTCGTGTTTTTAAAAAATTCGTG
* * *** *
20080962 TTTCAAAAATTTTCTTGTTTTCAAATTTTTCGTA
1 TTTC-AAAATTTTCGTGTTTTTAAAAAATTCGTG
* ** *
20080996 TTTAAAAAATCCTCGTG-TTTT-CAAAATTCCAGTG
1 TTT-CAAAATTTTCGTGTTTTTAAAAAATT-C-GTG
**
20081030 TTTCAAAATTTTTCGTGTTTCAAAAAAAATTC-TCG
1 TTTCAAAA-TTTTCGTGTTT-TTAAAAAATTCGT-G
* * *
20081065 TTTTCCAAAAACTTTCGCG-TTTTAAGAAATTGACCGTG
1 -TTT-C-AAAATTTTCGTGTTTTTAAAAAATT---CGTG
*
20081103 TTTCATAAATTTTCGTG-TTTCAAAGAAATCTCGTG
1 TTTCA-AAATTTTCGTGTTTTTAAA-AAAT-TCGTG
20081138 TTTCAAAATTTTCGTGTTTTTTTAAAAAATT-GTG
1 TTTCAAAATTTTCGTG--TTTTTAAAAAATTCGTG
*
20081172 TTTCTAAAATTCTT-GT-ATTTTAAAAAATTCGTG
1 TTTC-AAAATT-TTCGTGTTTTTAAAAAATTCGTG
*
20081205 TTTAAAAA
1 TTTCAAAA
20081213 AAAAAGGAAA
Statistics
Matches: 251, Mismatches: 43, Indels: 58
0.71 0.12 0.16
Matches are distributed among these distances:
32 19 0.08
33 14 0.06
34 73 0.29
35 43 0.17
36 64 0.25
37 30 0.12
38 7 0.03
39 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (33 bp):
TTTCAAAATTTTCGTGTTTTTAAAAAATTCGTG
Found at i:20081210 original size:15 final size:15
Alignment explanation
Indices: 20081158--20081213 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 15
20081148 TTCGTGTTTT
20081158 TTTAAAAAATT-GTG
1 TTTAAAAAATTCGTG
** *
20081172 TTTCTAAAATTCTTGTAT
1 TTTAAAAAATTC--GT-G
20081190 TTTAAAAAATTCGTG
1 TTTAAAAAATTCGTG
20081205 TTTAAAAAA
1 TTTAAAAAA
20081214 AAAAGGAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
14 9 0.28
15 9 0.28
16 2 0.06
17 2 0.06
18 10 0.31
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (15 bp):
TTTAAAAAATTCGTG
Found at i:20085566 original size:44 final size:45
Alignment explanation
Indices: 20085510--20086090 Score: 199
Period size: 44 Copynumber: 13.2 Consensus size: 45
20085500 TTGGGGAGGT
*
20085510 AAGACCTG-TATCTTCGATCTACTTCA-CACTAGTATGGAAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCATCACTAGTATGGAAAGAC
* * * *
20085553 ACGATCTGCTATC-TCTGATCTATTTCATGTCAATA-CAT-GAAA-AC
1 AAGATCTGCTATCTTC-GATCTACTTCA--TCACTAGTATGGAAAGAC
* *** * * *
20085597 AGGATCCATTATCTTTGATCTACTTCACCACTAGTATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCATCACTAGTATGGAAAGAC
* * *
20085642 AAGATCTGCCATCTTCGATCTACTTCATGTCAATA-CAT-G-AAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAAGAC
** * *
20085686 AAGATCCACTATC-TCTGATCTACTTCATGTCAATA-CAT-G-AAGAC
1 AAGATCTGCTATCTTC-GATCTACTTCA--TCACTAGTATGGAAAGAC
*** * *
20085730 AAGATCCATTATCTTCGATCTACTTCATGTCAATA-CAT-G-AAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAAGAC
* * * * *
20085774 AATATCCGCTATCTTCGATATACTTCATGTCAATA-AAT-G-AAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAAGAC
** * *
20085818 AAGATCCACTATC-TCTGATCTACTTCATGTCAATA-CAT-G-AAGAC
1 AAGATCTGCTATCTTC-GATCTACTTCA--TCACTAGTATGGAAAGAC
*** * *
20085862 AAGATCCATTATCTTCGATCTACTTCATGTCAATA-CAT-G-AAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAAGAC
* * *
20085906 AAGATCCGCTATCTTCGATCTACTTCATGTCAATA-CAT-G-AAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAAGAC
** * * *
20085950 AAGATCCACTATCTTTGATCTACTTCATGTCAATA-CAT-G-AAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAAGAC
* *
20085994 AAGATCTGCTATC-TCTGATCTACTTCATGTCAATA-CAT-G-AAGAC
1 AAGATCTGCTATCTTC-GATCTACTTCA--TCACTAGTATGGAAAGAC
* *** * * *
20086038 AATATCCATTATCTTCGATCTACTTCACCACCAGTATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCATCACTAGTATGGAAAGAC
20086083 AAGATCTG
1 AAGATCTG
20086091 TTGCTTTTTC
Statistics
Matches: 462, Mismatches: 56, Indels: 38
0.83 0.10 0.07
Matches are distributed among these distances:
42 7 0.02
43 17 0.04
44 381 0.82
45 45 0.10
46 4 0.01
47 8 0.02
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (45 bp):
AAGATCTGCTATCTTCGATCTACTTCATCACTAGTATGGAAAGAC
Found at i:20085768 original size:88 final size:88
Alignment explanation
Indices: 20085548--20086064 Score: 713
Period size: 88 Copynumber: 5.9 Consensus size: 88
20085538 CTAGTATGGA
* * * * * *
20085548 AAGACACGATCTGCTATC-TCTGATCTATTTCATGTCAATACATGAAAACAGGATCCATTATCTT
1 AAGACAAGATCCGCTATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTT
* * * *
20085612 TGATCTACTTCA--CCACTAGTATGGG
65 CGATCTACTTCATGTCAATA-CAT--G
* *
20085637 AAGACAAGATCTGCCATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATC-TC
1 AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTC
20085701 TGATCTACTTCATGTCAATACATG
66 -GATCTACTTCATGTCAATACATG
** * *
20085725 AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGACAATATCCGCTATCTTC
1 AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTC
* *
20085790 GATATACTTCATGTCAATAAATG
66 GATCTACTTCATGTCAATACATG
* *
20085813 AAGACAAGATCCACTATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTT
1 AAGACAAGATCCGCTATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTT
20085877 CGATCTACTTCATGTCAATACATG
65 CGATCTACTTCATGTCAATACATG
*
20085901 AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTT
1 AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTC
20085966 GATCTACTTCATGTCAATACATG
66 GATCTACTTCATGTCAATACATG
* * *
20085989 AAGACAAGATCTGCTATC-TCTGATCTACTTCATGTCAATACATGAAGACAATATCCATTATCTT
1 AAGACAAGATCCGCTATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTT
20086053 CGATCTACTTCA
65 CGATCTACTTCA
20086065 CCACCAGTAT
Statistics
Matches: 389, Mismatches: 31, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
87 4 0.01
88 309 0.79
89 68 0.17
90 4 0.01
91 4 0.01
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.31
Consensus pattern (88 bp):
AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTC
GATCTACTTCATGTCAATACATG
Found at i:20085833 original size:132 final size:132
Alignment explanation
Indices: 20085561--20086064 Score: 780
Period size: 132 Copynumber: 3.8 Consensus size: 132
20085551 ACACGATCTG
* * * *
20085561 CTATCTCTGATCTATTTCATGTCAATACATGAAAACAGGATCCATTATCTTTGATCTACTTCA--
1 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
* * * * *
20085624 CCACTAGTATGGGAAGACAAGATCTGCCATCTTCGATCTACTTCATGTCAATACATGAAGACAAG
66 TCAATA-CAT--GAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAG
20085689 ATCCA
128 ATCCA
20085694 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
1 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
* * *
20085759 TCAATACATGAAGACAATATCCGCTATCTTCGATATACTTCATGTCAATAAATGAAGACAAGATC
66 TCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
20085824 CA
131 CA
20085826 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
1 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
20085891 TCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
66 TCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
20085956 CA
131 CA
* ***
20085958 CTATCTTTGATCTACTTCATGTCAATACATGAAGACAAGATCTGCTATC-TCTGATCTACTTCAT
1 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTC-GATCTACTTCAT
* **
20086022 GTCAATACATGAAGACAATATCCATTATCTTCGATCTACTTCA
65 GTCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCA
20086065 CCACCAGTAT
Statistics
Matches: 346, Mismatches: 22, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
131 2 0.01
132 279 0.81
133 59 0.17
134 2 0.01
135 4 0.01
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (132 bp):
CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
TCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
CA
Found at i:20102409 original size:19 final size:20
Alignment explanation
Indices: 20102376--20102415 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
20102366 AAGTAGAAAG
*
20102376 AATTTAAAATAATGTTGATA
1 AATTTAAAATAATGTGGATA
*
20102396 AATTT-AAATCATGTGGATA
1 AATTTAAAATAATGTGGATA
20102415 A
1 A
20102416 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (20 bp):
AATTTAAAATAATGTGGATA
Found at i:20108180 original size:21 final size:21
Alignment explanation
Indices: 20108154--20108213 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
20108144 TATTTACTCT
20108154 AAAACCTTAAATCTAAAATTC
1 AAAACCTTAAATCTAAAATTC
* * *
20108175 AAAACCCTAAATCCAAAATTT
1 AAAACCTTAAATCTAAAATTC
* *
20108196 AAAATCTCAAATCCTAAA
1 AAAACCTTAAAT-CTAAA
20108214 TCTAAACCCG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAACCTTAAATCTAAAATTC
Found at i:20113088 original size:20 final size:20
Alignment explanation
Indices: 20113063--20113131 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
20113053 ACATGATATC
20113063 CTTAGAAATTTTGGTAAAAG
1 CTTAGAAATTTTGGTAAAAG
* * *
20113083 CTTAGAAAATTT-GTTAAAT
1 CTTAGAAATTTTGGTAAAAG
* *
20113102 TTATAGGAATTTTGGTAAATAG
1 CT-TAGAAATTTTGGTAAA-AG
20113124 -TTAGAAAT
1 CTTAGAAAT
20113132 AATTGAAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 6 0.16
20 25 0.68
21 5 0.14
22 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.39
Consensus pattern (20 bp):
CTTAGAAATTTTGGTAAAAG
Found at i:20113244 original size:20 final size:20
Alignment explanation
Indices: 20113221--20113304 Score: 53
Period size: 20 Copynumber: 4.2 Consensus size: 20
20113211 GAAATATTAG
20113221 TAAATTTTTAAAAGTTTTGA
1 TAAATTTTTAAAAGTTTTGA
* ** *
20113241 TAAATTCTTGCAAGTTTTGG
1 TAAATTTTTAAAAGTTTTGA
** * * *
20113261 TAAAAGTGTAGAAGTTCTGA
1 TAAATTTTTAAAAGTTTTGA
* *
20113281 TAAATTATTAGATA-TTTTGA
1 TAAATTTTTA-AAAGTTTTGA
20113301 TAAA
1 TAAA
20113305 CCCTAATGAT
Statistics
Matches: 44, Mismatches: 19, Indels: 2
0.68 0.29 0.03
Matches are distributed among these distances:
20 43 0.98
21 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (20 bp):
TAAATTTTTAAAAGTTTTGA
Found at i:20115501 original size:17 final size:17
Alignment explanation
Indices: 20115479--20115512 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20115469 ATCCACTAAT
*
20115479 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
20115496 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
20115513 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:20120140 original size:17 final size:17
Alignment explanation
Indices: 20120118--20120151 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20120108 ATCCACTAAT
*
20120118 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
20120135 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
20120152 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:20125523 original size:13 final size:13
Alignment explanation
Indices: 20125478--20125528 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
20125468 ACATTCTCTC
*
20125478 AAAAT-AATAATG
1 AAAATGAATAAAG
20125490 AAAATGTAAATAAA-
1 AAAATG--AATAAAG
*
20125504 TAAATGAATAAAG
1 AAAATGAATAAAG
20125517 AAAATGAATAAA
1 AAAATGAATAAA
20125529 ATTATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 11 0.34
13 11 0.34
14 5 0.16
15 5 0.16
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.22
Consensus pattern (13 bp):
AAAATGAATAAAG
Found at i:20125771 original size:33 final size:32
Alignment explanation
Indices: 20125728--20125817 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 32
20125718 AAAAGTATGT
* *
20125728 ATATATATATAAGTTATAAAAGTATGTACGTGC
1 ATATGTATATAA-TTATAAAAGTATGTACGTAC
* *
20125761 ATATGTATAT-ATTATAAAAATGTATGTATGTAT
1 ATATGTATATAATTAT-AAAA-GTATGTACGTAC
20125794 ATATGTATATAAATTAT-AAAGTAT
1 ATATGTATAT-AATTATAAAAGTAT
20125818 AACAAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
31 4 0.08
32 9 0.18
33 31 0.63
35 5 0.10
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.41
Consensus pattern (32 bp):
ATATGTATATAATTATAAAAGTATGTACGTAC
Found at i:20126672 original size:27 final size:26
Alignment explanation
Indices: 20126632--20126682 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 26
20126622 ATGCAATTCT
20126632 TACAAACAATATGATTGAATAACAATA
1 TACAAACAATATGA-TGAATAACAATA
20126659 TACAAAGCAA-ATGATGAATAACAA
1 TACAAA-CAATATGATGAATAACAA
20126683 ACAAATTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 10 0.43
27 10 0.43
28 3 0.13
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.22
Consensus pattern (26 bp):
TACAAACAATATGATGAATAACAATA
Found at i:20126892 original size:25 final size:24
Alignment explanation
Indices: 20126855--20126904 Score: 57
Period size: 23 Copynumber: 2.0 Consensus size: 24
20126845 AGAATAAAAA
*
20126855 TTTATAAGGCACAAATTATAATATAT
1 TTTATAAGACACAAA-TAT-ATATAT
*
20126881 TTTATAA-ACACATATATATATAT
1 TTTATAAGACACAAATATATATAT
20126904 T
1 T
20126905 AAATATAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 7 0.32
24 3 0.14
25 5 0.23
26 7 0.32
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (24 bp):
TTTATAAGACACAAATATATATAT
Found at i:20126994 original size:19 final size:20
Alignment explanation
Indices: 20126961--20127000 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
20126951 AAGTAAAAAG
*
20126961 AATTTAAAATAATGTTGATA
1 AATTTAAAATAATGTGGATA
*
20126981 AATTT-AAATCATGTGGATA
1 AATTTAAAATAATGTGGATA
20127000 A
1 A
20127001 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (20 bp):
AATTTAAAATAATGTGGATA
Found at i:20142966 original size:3 final size:3
Alignment explanation
Indices: 20142958--20143006 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
20142948 TTATCAGCTT
20142958 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20143005 TT
1 TT
20143007 TCGAATTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20143239 original size:26 final size:26
Alignment explanation
Indices: 20143210--20143264 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
20143200 TCAACTTATC
20143210 TTTTAAGTT-AATAAATTCTCATTGAG
1 TTTTAAGTTCAATAAATTCTC-TTGAG
* * *
20143236 TTTTCATTTCAATAATTTCTCTTGAG
1 TTTTAAGTTCAATAAATTCTCTTGAG
20143262 TTT
1 TTT
20143265 ATTTTAGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (26 bp):
TTTTAAGTTCAATAAATTCTCTTGAG
Found at i:20144832 original size:96 final size:96
Alignment explanation
Indices: 20144714--20144902 Score: 263
Period size: 96 Copynumber: 2.0 Consensus size: 96
20144704 AAAGGAGGAA
* * * * *
20144714 TACGATTGAGGTATCATCTTTTGTGCGATGTTATTGGTATAGTTCAAAAGATCATAAGGGTTTCC
1 TACGATTGAGATATCATCTTTTGTGCAATGTTATTGGTATAATTCAAAAGATCACAAGAGTTTCC
20144779 AATGTCCAATTAAATATCCAAATAGAGAGAC
66 AATGTCCAATTAAATATCCAAATAGAGAGAC
* * * *
20144810 TACGATTGAGATATCA-CATTTTGTGCAATGTTATTGGTGTAATTCAAAATATTACAAGAGTTTT
1 TACGATTGAGATATCATC-TTTTGTGCAATGTTATTGGTATAATTCAAAAGATCACAAGAGTTTC
* *
20144874 CAATGTCCAGTTAAATATCCAACTAGAGA
65 CAATGTCCAATTAAATATCCAAATAGAGA
20144903 ATAAAGTAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 1 0.01
96 80 0.99
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (96 bp):
TACGATTGAGATATCATCTTTTGTGCAATGTTATTGGTATAATTCAAAAGATCACAAGAGTTTCC
AATGTCCAATTAAATATCCAAATAGAGAGAC
Found at i:20148196 original size:23 final size:22
Alignment explanation
Indices: 20148153--20148197 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
20148143 ATGAGATAAT
*
20148153 TAAAAATAAAAATATTTTTAAA
1 TAAAAATAAAAATATTATTAAA
20148175 TAAAAATATCAAAA-ATTATTAAA
1 TAAAAATA--AAAATATTATTAAA
20148198 AACGAGAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 8 0.40
24 4 0.20
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAAATAAAAATATTATTAAA
Found at i:20159379 original size:42 final size:42
Alignment explanation
Indices: 20159318--20159428 Score: 120
Period size: 42 Copynumber: 2.6 Consensus size: 42
20159308 GATTTAGGAC
* * *
20159318 CACACGACTACGGATATGGGCATGTG-C-CCAGGTCGTGTGAGT
1 CACACGAC-AAGGACATGGGC-TGTGTCTCCAGGCCGTGTGAGT
*
20159360 CACACGGACAAGGACATGGG-TGTGTCTCTAGGCCGTGTGAGT
1 CACAC-GACAAGGACATGGGCTGTGTCTCCAGGCCGTGTGAGT
*
20159402 CACACGACAAGGACATAGGCGTGTGTC
1 CACACGACAAGGACATGGGC-TGTGTC
20159429 CAAGATGTGT
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
40 4 0.07
41 14 0.24
42 32 0.54
43 9 0.15
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.20
Consensus pattern (42 bp):
CACACGACAAGGACATGGGCTGTGTCTCCAGGCCGTGTGAGT
Found at i:20162877 original size:62 final size:63
Alignment explanation
Indices: 20162768--20162915 Score: 158
Period size: 62 Copynumber: 2.4 Consensus size: 63
20162758 CACGGGCAAC
* * * * * *
20162768 GGACACGGGCGTGTGTCTAGGCCGTGTAACTCATTGTTTGTGATTTAGGACCACACG-GCCATA
1 GGACATGGGCGTGTGTCTAGGCCGTGTAACTCACTATTTCTGATTTAGAACCACACGAG-CAGA
* * * *
20162831 -GACATGGGCGTGTGCCTAGGCCGTGTAACTTACTATTTACT-TTTTAGAACCACATGAGCAGA
1 GGACATGGGCGTGTGTCTAGGCCGTGTAACTCACTATTT-CTGATTTAGAACCACACGAGCAGA
*
20162893 GGACATGGGCGTATGTCTAGGCC
1 GGACATGGGCGTGTGTCTAGGCC
20162916 ATGTGGCATA
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
62 48 0.69
63 22 0.31
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (63 bp):
GGACATGGGCGTGTGTCTAGGCCGTGTAACTCACTATTTCTGATTTAGAACCACACGAGCAGA
Found at i:20164299 original size:26 final size:26
Alignment explanation
Indices: 20164254--20164315 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
20164244 ATGGTAATTA
20164254 AATTAAATT-AAATACTATATAATGT
1 AATTAAATTAAAATACTATATAATGT
* **
20164279 GATTAAATTAAAATGTTATATAATGT
1 AATTAAATTAAAATACTATATAATGT
20164305 AATTAAATTAA
1 AATTAAATTAA
20164316 GTTAATAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 8 0.25
26 24 0.75
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (26 bp):
AATTAAATTAAAATACTATATAATGT
Found at i:20166305 original size:3 final size:3
Alignment explanation
Indices: 20166297--20166327 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
20166287 ACGTGAAAGA
20166297 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
20166328 CAACATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:20168660 original size:172 final size:172
Alignment explanation
Indices: 20168369--20168711 Score: 614
Period size: 172 Copynumber: 2.0 Consensus size: 172
20168359 TGCAAAGTAC
*
20168369 AAATATCCACAATCTCTAATCAATCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAATAT
1 AAATATCCACAATATCTAATCAATCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAATAT
* *
20168434 CAGAATAAGTATCATAGTATGCATACAATTATGTTATTCATACGCCCATCACAGAGTATCAGAGA
66 AAGAATAAGTATCATAGTACGCATACAATTATGTTATTCATACGCCCATCACAGAGTATCAGAGA
20168499 GTTCTCGTATAATCAAATTCAAATCATTCATGTATTGGGGAA
131 GTTCTCGTATAATCAAATTCAAATCATTCATGTATTGGGGAA
* *
20168541 AAATGTCCACAATATCTAATCAGTCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAATAT
1 AAATATCCACAATATCTAATCAATCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAATAT
* *
20168606 AAGAATAAGTATCATAGTACGTATACAATTATGTTATTCATACGTCCATCACAGAGTATCAGAGA
66 AAGAATAAGTATCATAGTACGCATACAATTATGTTATTCATACGCCCATCACAGAGTATCAGAGA
*
20168671 GTTTTCGTATAATCAAATTCAAATCATTCATGTATTGGGGA
131 GTTCTCGTATAATCAAATTCAAATCATTCATGTATTGGGGA
20168712 CATCAATATC
Statistics
Matches: 163, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
172 163 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (172 bp):
AAATATCCACAATATCTAATCAATCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAATAT
AAGAATAAGTATCATAGTACGCATACAATTATGTTATTCATACGCCCATCACAGAGTATCAGAGA
GTTCTCGTATAATCAAATTCAAATCATTCATGTATTGGGGAA
Found at i:20171736 original size:21 final size:22
Alignment explanation
Indices: 20171711--20171751 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20171701 AGATATGAAA
* *
20171711 TTAAAT-TATATTTAGGATTCT
1 TTAAATCTAAATTGAGGATTCT
20171732 TTAAATCTAAATTGAGGATT
1 TTAAATCTAAATTGAGGATT
20171752 AGAAACGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (22 bp):
TTAAATCTAAATTGAGGATTCT
Found at i:20184189 original size:21 final size:22
Alignment explanation
Indices: 20184143--20184198 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
20184133 GTGATAGTCC
*
20184143 TACACGATTGTGTGAATGAGAG
1 TACACGATAGTGTGAATGAGAG
* *
20184165 -ACACGCTAGTGTGACTGA-AG
1 TACACGATAGTGTGAATGAGAG
* *
20184185 TACACAATCGTGTG
1 TACACGATAGTGTG
20184199 GGCAGACCGT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (22 bp):
TACACGATAGTGTGAATGAGAG
Found at i:20184705 original size:23 final size:22
Alignment explanation
Indices: 20184658--20184705 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
20184648 CAAACACACT
**
20184658 AACCTATAAGAAAATCAATCTA
1 AACCTATAAGAAAATCAATAGA
20184680 AACCATATATAGAAAATCAA-AGA
1 AACC-TATA-AGAAAATCAATAGA
20184703 AAC
1 AAC
20184706 TGATGTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 8 0.36
24 10 0.45
ACGTcount: A:0.58, C:0.17, G:0.06, T:0.19
Consensus pattern (22 bp):
AACCTATAAGAAAATCAATAGA
Found at i:20184999 original size:3 final size:3
Alignment explanation
Indices: 20184991--20185020 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
20184981 AAAATTAAAT
20184991 ATA ATA ATA A-A ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
20185021 CAACAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:20185013 original size:17 final size:18
Alignment explanation
Indices: 20184978--20185020 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
20184968 TTTTCTTCTC
20184978 AATAAAATTAAATATAAT
1 AATAAAATTAAATATAAT
*
20184996 AATAAAATAATAATAATAAT
1 AATAAAATTA-AAT-ATAAT
20185016 AATAA
1 AATAA
20185021 CAACAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 3 0.14
20 10 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAAAATTAAATATAAT
Found at i:20189002 original size:30 final size:30
Alignment explanation
Indices: 20188958--20189051 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
20188948 TTTTATTATG
* *
20188958 CCAATATCTCGATACCCAGATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
20188989 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
20189019 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
20189049 CCA
1 CCA
20189052 TAAATATGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 50 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:20189013 original size:15 final size:15
Alignment explanation
Indices: 20188968--20189045 Score: 52
Period size: 15 Copynumber: 5.2 Consensus size: 15
20188958 CCAATATCTC
*
20188968 GATACCCAGATCTTT
1 GATACCCATATCTTT
** *
20188983 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
20188998 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
20189013 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
20189028 GATACCCATATCTTT
1 GATACCCATATCTTT
20189043 GAT
1 GAT
20189046 TTTCCATAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:20190357 original size:17 final size:17
Alignment explanation
Indices: 20190331--20190365 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20190321 TTAGTTTTAA
*
20190331 TTTTCTTTTCCCAAAAT
1 TTTTCCTTTCCCAAAAT
*
20190348 TTTTCCTTTCCCCAAAT
1 TTTTCCTTTCCCAAAAT
20190365 T
1 T
20190366 CACGTTCACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.29, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTCCTTTCCCAAAAT
Found at i:20199674 original size:9 final size:9
Alignment explanation
Indices: 20199647--20199683 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
20199637 TGAGTTTTCG
20199647 AATTCGAAT
1 AATTCGAAT
* *
20199656 AACTCAAAT
1 AATTCGAAT
20199665 AATTCGAAT
1 AATTCGAAT
20199674 AATTCGAAT
1 AATTCGAAT
20199683 A
1 A
20199684 TAAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:20199776 original size:30 final size:31
Alignment explanation
Indices: 20199732--20199792 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
20199722 AAACCTTTTT
* *
20199732 ACTTTTCCCTCAAAACTTTTAC-CCCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCCTTCCC
*
20199762 ACTTTCCCCCCAAAACTTTTACTCTCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCCTTCCC
20199793 CTCCCAACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.36
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTCCCTTCCC
Found at i:20201509 original size:30 final size:30
Alignment explanation
Indices: 20201420--20201509 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
20201410 AATGTAATGT
* * *
20201420 TCACACAAGCTGACAGTAT-TTAGGGTTGC
1 TCACACAAGCTGACATTATATTAAGGTTTC
* * * *
20201449 TCACACAAGTTGACATTGTAAT-CGGATTTC
1 TCACACAAGCTGACATTATATTAAGG-TTTC
20201479 TCACACAAGCTGACATTATATTAAGGTTTC
1 TCACACAAGCTGACATTATATTAAGGTTTC
20201509 T
1 T
20201510 TGCACGGGCT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
29 18 0.38
30 28 0.58
31 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (30 bp):
TCACACAAGCTGACATTATATTAAGGTTTC
Found at i:20205218 original size:12 final size:12
Alignment explanation
Indices: 20205186--20205240 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
20205176 GTCCATATAC
20205186 ATAT-TATAAA-
1 ATATATATAAAT
20205196 AT-TAT-TAAAT
1 ATATATATAAAT
20205206 ATATATATAAAT
1 ATATATATAAAT
*
20205218 ATATATATGTAAGT
1 ATATATA--TAAAT
20205232 ATATATATA
1 ATATATATA
20205241 TATTTACAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
9 5 0.13
10 5 0.13
11 3 0.08
12 14 0.37
14 11 0.29
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (12 bp):
ATATATATAAAT
Found at i:20205223 original size:14 final size:14
Alignment explanation
Indices: 20205204--20205242 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
20205194 AAATTATTAA
20205204 ATATATATATAAAT
1 ATATATATATAAAT
* *
20205218 ATATATATGTAAGT
1 ATATATATATAAAT
20205232 ATATATATATA
1 ATATATATATA
20205243 TTTACAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (14 bp):
ATATATATATAAAT
Found at i:20205387 original size:3 final size:3
Alignment explanation
Indices: 20205373--20205443 Score: 65
Period size: 3 Copynumber: 22.7 Consensus size: 3
20205363 TAAATGGGTA
* *
20205373 AAT AAA AAT AAT AAT AAGGT AAGT AAT AAT AAT AACT -AC AAT AAT AAT
1 AAT AAT AAT AAT AAT AA--T AA-T AAT AAT AAT AA-T AAT AAT AAT AAT
20205421 GAA- AAT AAT AAT AAT AAT AAT AA
1 -AAT AAT AAT AAT AAT AAT AAT AA
20205444 AACTAATTAG
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
2 2 0.03
3 46 0.79
4 7 0.12
5 3 0.05
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:20207139 original size:100 final size:100
Alignment explanation
Indices: 20207015--20207596 Score: 756
Period size: 100 Copynumber: 5.8 Consensus size: 100
20207005 CGCCATTGTG
* * * *
20207015 GCTTTAATCTTCTTAACTGCAATGTCAGGGAAGCAAGATACACCGTCGTGGCTTTAATCTGCTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* * * * *
20207080 ACTGCACCACTAGGAAAGTAACACTCGCCGCTGTG
66 ACTGCACCGCTAGGGAAGTAAGACTCGCTGCTGTA
* * * * * *
20207115 GCTTTAGTCTTTTTAACTGCAATGTCGGGGAAGCAAGATACGCCGTCGTGGCTTTAATCTGCTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
** * * * * *
20207180 ACTGCATTGCCAGGGAAGTAACACTCGCCGCTATG
66 ACTGCACCGCTAGGGAAGTAAGACTCGCTGCTGTA
* *
20207215 GCTTTAGTCTTTTTAACTGCAATGTC-GAGGAAGCAGGATTCACCGTTGTGGCTTTAATCTGTTC
1 GCTTTAATCTTTTTAACTGCAATGTCAG-GGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTC
* * *
20207279 CACTGCACTGCCT-GGGAGGTAAGATTCGCTGCTGTA
65 CACTGCACCG-CTAGGGAAGTAAGACTCGCTGCTGTA
* *
20207315 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAGGATTCACCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* *
20207380 ACTGCACCGCCTA-GGAAGTAAGATTCACTGCTGTA
66 ACTGCACCG-CTAGGGAAGTAAGACTCGCTGCTGTA
* *
20207415 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCATCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* * * *
20207480 ACTGCACCGCTTGGGAGGTAAGACTCGTTGTTGTA
66 ACTGCACCGCTAGGGAAGTAAGACTCGCTGCTGTA
* *
20207515 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGGAAGATTCACCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
*
20207580 ACTGCACCGCCAGGGAA
66 ACTGCACCGCTAGGGAA
20207597 ACTAAGATCT
Statistics
Matches: 436, Mismatches: 41, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
99 3 0.01
100 431 0.99
101 2 0.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (100 bp):
GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
ACTGCACCGCTAGGGAAGTAAGACTCGCTGCTGTA
Found at i:20207484 original size:50 final size:50
Alignment explanation
Indices: 20206966--20207585 Score: 392
Period size: 50 Copynumber: 12.4 Consensus size: 50
20206956 TAACTCGTAA
** * * *
20206966 CTTTAATCTGCTT-AACTGTGATGTC-GGAGAAGTAAGATTCGCCATTGTGG
1 CTTTAATCTG-TTCAACTGCAATGTCAGG-GAAGCAAGATTCACCGTTGTGG
* * *
20207016 CTTTAATCT-TCTTAACTGCAATGTCAGGGAAGCAAGATACACCGTCGTGG
1 CTTTAATCTGT-TCAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* * * * * * * * *
20207066 CTTTAATCTGCTCCACTGCACCA-CT-AGGAAAGTAACACTCGCCGCTGTGG
1 CTTTAATCTGTTCAACTGCA--ATGTCAGGGAAGCAAGATTCACCGTTGTGG
* * * * * * *
20207116 CTTTAGTCTTTTTAACTGCAATGTCGGGGAAGCAAGATACGCCGTCGTGG
1 CTTTAATCTGTTCAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* * * * * * * * * *
20207166 CTTTAATCTGCTCCACTGCATTGCCAGGGAAGTAACACTCGCCGCTATGG
1 CTTTAATCTGTTCAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* * * *
20207216 CTTTAGTCTTTTTAACTGCAATGTC-GAGGAAGCAGGATTCACCGTTGTGG
1 CTTTAATCTGTTCAACTGCAATGTCAG-GGAAGCAAGATTCACCGTTGTGG
* * * * * * * * * *
20207266 CTTTAATCTGTTCCACTGCACTGCCTGGGAGGTAAGATTCGCTGCTGTAG
1 CTTTAATCTGTTCAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* * * *
20207316 CTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAGGATTCACCGTTGTGG
1 CTTTAATCTGTTCAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* ** * * * * *
20207366 CTTTAATCTGTTCCACTGCACCGCCTA-GGAAGTAAGATTCACTGCTGTAG
1 CTTTAATCTGTTCAACTGCAATGTC-AGGGAAGCAAGATTCACCGTTGTGG
* * * *
20207416 CTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCATCGTTGTGG
1 CTTTAATCTGTTCAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* ** * * * * *** *
20207466 CTTTAATCTGTTCCACTGCACCG-CTTGGGAGGTAAGACTCGTTGTTGTAG
1 CTTTAATCTGTTCAACTGCAATGTC-AGGGAAGCAAGATTCACCGTTGTGG
* * * *
20207516 CTTTAATCTTTTTAACTGCAATGTCAGGGAGGGAAGATTCACCGTTGTGG
1 CTTTAATCTGTTCAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
*
20207566 CTTTAATCTGTTCCACTGCA
1 CTTTAATCTGTTCAACTGCA
20207586 CCGCCAGGGA
Statistics
Matches: 419, Mismatches: 137, Indels: 28
0.72 0.23 0.05
Matches are distributed among these distances:
48 2 0.00
49 5 0.01
50 405 0.97
51 6 0.01
52 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.32
Consensus pattern (50 bp):
CTTTAATCTGTTCAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
Found at i:20207754 original size:44 final size:44
Alignment explanation
Indices: 20207700--20208317 Score: 431
Period size: 44 Copynumber: 13.8 Consensus size: 44
20207690 CCTTTATTTT
* *
20207700 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* *
20207744 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-GCTTC
* ** * * * *
20207790 AGTCTATTCCACTGTAATCTTAGGGAGATAAGATCCT-TTA-TTTT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT--TACTAGCTTC
20207834 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * *
20207878 AATCTGCTCCGCTGTAATCTCAGGGAGATAATATCTGA-AATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-GCTTC
** ** * *
20207924 GGTCTATTCCACTGTAATCTCAGGGAGATAAGA--CCT-GATGT-
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCT-TC
* * * * * * * *
20207965 GATCTACTCTACTGTAA-CTTCAGAGAGACAAGATCCT-TTA-TTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTC
* * * * *
20208009 AATCCGCTCCACTTTAATCTCAAGGAGATAGGATTACTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
** * *
20208053 AATCTGCTCTGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
*
20208097 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCT-GACTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAG-CTTC
* * * * *
20208141 AATCTGATGCGATCTACTCTACTGTAA-CTTCAGAGAGATGAGATCCT-TTA-TTTT
1 AATC---T--G--CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTC
* *
20208195 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
20208239 AATCTGCTCCACTGTAATCTCAGAGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
*
20208283 AATCTGCTCCACTATAA-CATCAGGGAGATAAGATT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATT
20208318 CACCATTTCC
Statistics
Matches: 453, Mismatches: 80, Indels: 82
0.74 0.13 0.13
Matches are distributed among these distances:
40 1 0.00
41 27 0.06
42 4 0.01
43 8 0.02
44 297 0.66
45 7 0.02
46 69 0.15
47 5 0.01
49 2 0.00
51 2 0.00
52 1 0.00
53 2 0.00
54 26 0.06
55 1 0.00
56 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Done.