Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 55 of 97
Found at i:22090846 original size:25 final size:25
Alignment explanation
Indices: 22090812--22090866 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
22090802 TCATGATTTC
22090812 AATTTGTTCCACAAAATGCAAGCAT
1 AATTTGTTCCACAAAATGCAAGCAT
**
22090837 AATTTGTTCCATGAAATGCAAGCAT
1 AATTTGTTCCACAAAATGCAAGCAT
*
22090862 GATTT
1 AATTT
22090867 CACTCTTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (25 bp):
AATTTGTTCCACAAAATGCAAGCAT
Found at i:22114206 original size:2 final size:2
Alignment explanation
Indices: 22114199--22114236 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
22114189 TGGTCAAGAA
*
22114199 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22114237 TATCATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:22117385 original size:14 final size:15
Alignment explanation
Indices: 22117366--22117398 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
22117356 TCTATCTTAA
22117366 ATTAGTTATTAT-TT
1 ATTAGTTATTATGTT
*
22117380 ATTAGTTTTTATGTT
1 ATTAGTTATTATGTT
22117395 ATTA
1 ATTA
22117399 TAGGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (15 bp):
ATTAGTTATTATGTT
Found at i:22121704 original size:35 final size:35
Alignment explanation
Indices: 22121635--22121846 Score: 199
Period size: 35 Copynumber: 6.1 Consensus size: 35
22121625 CACTTGATTA
* *
22121635 AAATTGTTTAATTAAG---TTGTGCGTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* *
22121667 AAATTGTTTATTTAAGTCAATGGGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
*
22121702 AAATTGTTTAATTAAGTTAAGTCATTGGGCCTAATTGATT
1 AAATTG--T--TTAA-TTAAGTCATTGGGCCTAATTAATT
* * *
22121742 AAAATTGTTTACTTAAGTTATTAGGCC---TT-A--
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* * *
22121772 AAATTCTTTAATTAAGTCATTGAGCCTAATTAACT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
*
22121807 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
22121842 AAATT
1 AAATT
22121847 AGACAATTAA
Statistics
Matches: 146, Mismatches: 19, Indels: 27
0.76 0.10 0.14
Matches are distributed among these distances:
29 21 0.14
32 18 0.12
33 3 0.02
35 55 0.38
36 13 0.09
37 4 0.03
39 4 0.03
40 22 0.15
41 6 0.04
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:22121759 original size:41 final size:40
Alignment explanation
Indices: 22121658--22121761 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 40
22121648 AAGTTGTGCG
22121658 TAATTAATTAAATTGTTT-A-T---TTAAGTCAATGGGCC
1 TAATTAATTAAATTGTTTAATTAAGTTAAGTCAATGGGCC
*
22121693 TAATTAATTAAATTGTTTAATTAAGTTAAGTCATTGGGCC
1 TAATTAATTAAATTGTTTAATTAAGTTAAGTCAATGGGCC
* *
22121733 TAATTGATTAAAATTGTTTACTTAAGTTA
1 TAATTAATT-AAATTGTTTAATTAAGTTA
22121762 TTAGGCCTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
35 18 0.30
36 1 0.02
37 1 0.02
40 22 0.37
41 18 0.30
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (40 bp):
TAATTAATTAAATTGTTTAATTAAGTTAAGTCAATGGGCC
Found at i:22121855 original size:35 final size:35
Alignment explanation
Indices: 22121781--22121860 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
22121771 AAAATTCTTT
* **
22121781 AATTAAGTCATTGAGCCTAATTAACTAAATTGTTT
1 AATTAAGTTATTGAGCCTAATTAACTAAATTGTAC
* *
22121816 AATTAAGTTATTGGGCCTAATTAATTAAATTAG-AC
1 AATTAAGTTATTGAGCCTAATTAACTAAATT-GTAC
22121851 AATTAAGTTA
1 AATTAAGTTA
22121861 ATTACGCTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 38 0.97
36 1 0.03
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (35 bp):
AATTAAGTTATTGAGCCTAATTAACTAAATTGTAC
Found at i:22126930 original size:37 final size:37
Alignment explanation
Indices: 22126876--22126948 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
22126866 TTGATCAAGG
* *
22126876 TTCAATACAAATGCTTTTTGTGGATCAAGCATAACCT
1 TTCAATACAAATGCTTTTTATGGATAAAGCATAACCT
*
22126913 TTCAATAC-AATGCCTTTTTATGGTTAAAGCATAACC
1 TTCAATACAAATG-CTTTTTATGGATAAAGCATAACC
22126949 ACTATACCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 4 0.12
37 28 0.88
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (37 bp):
TTCAATACAAATGCTTTTTATGGATAAAGCATAACCT
Found at i:22126970 original size:32 final size:30
Alignment explanation
Indices: 22126925--22126983 Score: 100
Period size: 32 Copynumber: 1.9 Consensus size: 30
22126915 CAATACAATG
22126925 CCTTTTTATGGTTAAAGCATAACCACTATA
1 CCTTTTTATGGTTAAAGCATAACCACTATA
22126955 CCTTTTCTATTGGTTAAAGCATAACCACT
1 CCTTTT-TA-TGGTTAAAGCATAACCACT
22126984 TAAGCAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 6 0.22
31 2 0.07
32 19 0.70
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (30 bp):
CCTTTTTATGGTTAAAGCATAACCACTATA
Found at i:22141679 original size:2 final size:2
Alignment explanation
Indices: 22141623--22141660 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
22141613 TCGTGTTTAA
* *
22141623 AT AT AT AT AT AT AT AT AT AT AT AT GT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22141661 GAGAAGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22145859 original size:2 final size:2
Alignment explanation
Indices: 22145852--22145880 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22145842 ACGGGAACAG
22145852 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
22145881 TCTTTTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:22154260 original size:39 final size:39
Alignment explanation
Indices: 22154209--22154291 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
22154199 TATTTTGGAC
*
22154209 TTATTCAAATGATGAACATTGATTTACAAATAATTTGGT
1 TTATTCAAATGATGAACATTGATTCACAAATAATTTGGT
* * * * **
22154248 TTATTCATATGATGAGCATTGCTTCACGAATGTTTTGGT
1 TTATTCAAATGATGAACATTGATTCACAAATAATTTGGT
22154287 TTATT
1 TTATT
22154292 GACAATTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.45
Consensus pattern (39 bp):
TTATTCAAATGATGAACATTGATTCACAAATAATTTGGT
Found at i:22159833 original size:73 final size:74
Alignment explanation
Indices: 22159725--22159919 Score: 204
Period size: 73 Copynumber: 2.7 Consensus size: 74
22159715 AACAGAATGA
* * *
22159725 TCTTAGTTGACTAACTGTGC-TCTTAGTCGACTAAGTTGTCTCTATCTTCTGA-TCCCAG-TTTC
1 TCTTAGTCGACTAACT-TACTTCTTAGTCGACTAAGTTGTCTCTATCTTCTAAGT-CCAGATTTC
22159787 TAGCAGT-GAGC
64 TAGCAGTAG-GC
* * * * * *
22159798 TCTTAGTCGACTAACTTCCTTGTTAGTCGATTAAGTTGTTTCTGTCTT-TAAGTCTAGATTTCTA
1 TCTTAGTCGACTAACTTACTTCTTAGTCGACTAAGTTGTCTCTATCTTCTAAGTCCAGATTTCTA
22159862 GCAGTAGGC
66 GCAGTAGGC
* * * *
22159871 TCTTAGTCTACTGACTTACTTCTTGGTCGACTAAGTTTTCTCTAT-TTCT
1 TCTTAGTCGACTAACTTACTTCTTAGTCGACTAAGTTGTCTCTATCTTCT
22159920 CAAACTTCTT
Statistics
Matches: 100, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
72 9 0.09
73 90 0.90
74 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (74 bp):
TCTTAGTCGACTAACTTACTTCTTAGTCGACTAAGTTGTCTCTATCTTCTAAGTCCAGATTTCTA
GCAGTAGGC
Found at i:22160699 original size:18 final size:19
Alignment explanation
Indices: 22160674--22160716 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
22160664 GGCTGAGAAG
22160674 AATATTTTA-AAATAAAAT
1 AATATTTTATAAATAAAAT
*
22160692 ATTATTTTATAAATAAAAT
1 AATATTTTATAAATAAAAT
22160711 AATATT
1 AATATT
22160717 AAAATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATTTTATAAATAAAAT
Found at i:22161085 original size:2 final size:2
Alignment explanation
Indices: 22161078--22161109 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
22161068 AAAGTTAATA
22161078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22161110 GTACAAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22162296 original size:119 final size:118
Alignment explanation
Indices: 22162151--22162382 Score: 358
Period size: 119 Copynumber: 2.0 Consensus size: 118
22162141 TTTAAAAAAA
* * * *
22162151 GGGACTTGAAGCCCCGATTTATATATGGTGGCGTGGGTAGTTCCCACGAGTAGGT-AAGGGGGAC
1 GGGACCTGAAGCCCCGATTTATATATGGTGACCTGGGTAGTTCCCACGAGTAGGTAAAGAGGGAC
* * *
22162215 CTGAAGCCCTGATTTATATGTGGTGGCATGGGTAGTTCCCACGAGTAGGTAAAGG
66 CTGAAGCCCCGATTCATA--TGGTGGCATGGGCAGTTCCCACGAGTAGGTAAAGG
*
22162270 GGGACCTGAAGCCTCGATTTATATATGGTGACCTGGGTAGTTCCCACGAGTAGGTAAAGAGGGAC
1 GGGACCTGAAGCCCCGATTTATATATGGTGACCTGGGTAGTTCCCACGAGTAGGTAAAGAGGGAC
*
22162335 CTGAAGCCCCGATTCATATGGTGGCGTGGGCAGTTCCCACGAGTAGGT
66 CTGAAGCCCCGATTCATATGGTGGCATGGGCAGTTCCCACGAGTAGGT
22162383 GATGATGTCT
Statistics
Matches: 103, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
118 28 0.27
119 51 0.50
120 24 0.23
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (118 bp):
GGGACCTGAAGCCCCGATTTATATATGGTGACCTGGGTAGTTCCCACGAGTAGGTAAAGAGGGAC
CTGAAGCCCCGATTCATATGGTGGCATGGGCAGTTCCCACGAGTAGGTAAAGG
Found at i:22162299 original size:60 final size:60
Alignment explanation
Indices: 22162151--22162382 Score: 353
Period size: 60 Copynumber: 3.9 Consensus size: 60
22162141 TTTAAAAAAA
*
22162151 GGGACTTGAAGCCCCGATTTATATATGGTGGCGTGGGTAGTTCCCACGAGTAGGT-AAGG
1 GGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGG
* * *
22162210 GGGACCTGAAGCCCTGATTTATATGTGGTGGCATGGGTAGTTCCCACGAGTAGGTAAAGG
1 GGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGG
* * * *
22162270 GGGACCTGAAGCCTCGATTTATATATGGTGACCTGGGTAGTTCCCACGAGTAGGTAAAGA
1 GGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGG
* *
22162330 GGGACCTGAAGCCCCGA-TT-CATATGGTGGCGTGGGCAGTTCCCACGAGTAGGT
1 GGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGGTAGTTCCCACGAGTAGGT
22162383 GATGATGTCT
Statistics
Matches: 157, Mismatches: 15, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
58 30 0.19
59 53 0.34
60 74 0.47
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (60 bp):
GGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGG
Found at i:22164900 original size:63 final size:62
Alignment explanation
Indices: 22164799--22164959 Score: 241
Period size: 62 Copynumber: 2.6 Consensus size: 62
22164789 ACATCATAGT
* *
22164799 CGGCATATGCACTTCCCACTCTGCACATGCACGATTGTAATTGTCACAACATTGTCATTCAAC
1 CGGCATGTGCACTGCCCACTCTGCACATGCACGATTGTAATTG-CACAACATTGTCATTCAAC
* * * *
22164862 CGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAATTGCACAACATTGTCGTTCAGC
1 CGGCATGTGCACTGCCCACTCTGCACATGCACGATTGTAATTGCACAACATTGTCATTCAAC
* *
22164924 CGGCATGCGCACTGCCTACTCTGCACATGCACGATT
1 CGGCATGTGCACTGCCCACTCTGCACATGCACGATT
22164960 ACATCAATTA
Statistics
Matches: 88, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
62 49 0.56
63 39 0.44
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (62 bp):
CGGCATGTGCACTGCCCACTCTGCACATGCACGATTGTAATTGCACAACATTGTCATTCAAC
Found at i:22167341 original size:22 final size:22
Alignment explanation
Indices: 22167313--22167419 Score: 115
Period size: 22 Copynumber: 4.9 Consensus size: 22
22167303 GCAATGCCTA
22167313 AGTCACGCAATGCCTAAAAGCC
1 AGTCACGCAATGCCTAAAAGCC
* *
22167335 AGTCACGCAATGTCTAAAAGCT
1 AGTCACGCAATGCCTAAAAGCC
* * *
22167357 AGTCACGTAATGCCTAATATCC
1 AGTCACGCAATGCCTAAAAGCC
*** * *
22167379 AGTCATATAATGCCTAATATCC
1 AGTCACGCAATGCCTAAAAGCC
*
22167401 AGTCACACAATGCCTAAAA
1 AGTCACGCAATGCCTAAAA
22167420 AATTATCACG
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 73 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.22
Consensus pattern (22 bp):
AGTCACGCAATGCCTAAAAGCC
Found at i:22167532 original size:10 final size:10
Alignment explanation
Indices: 22167517--22167543 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
22167507 GGGGCCACAC
22167517 AATGCCTAAT
1 AATGCCTAAT
22167527 AATGCCTAAT
1 AATGCCTAAT
22167537 AATGCCT
1 AATGCCT
22167544 CAAAACCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (10 bp):
AATGCCTAAT
Found at i:22168882 original size:36 final size:36
Alignment explanation
Indices: 22168824--22168894 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 36
22168814 AGAAAAGGTG
* * * *
22168824 TGCTTTGAGCATGTTGTAGGGCCTTAAGTGGAGTTA
1 TGCTATGAGCAAGATGTAGGGCCTCAAGTGGAGTTA
* *
22168860 TGCTATGAGCAAGATGTGGGGCCTCAATTGGAGTT
1 TGCTATGAGCAAGATGTAGGGCCTCAAGTGGAGTT
22168895 GAGCTATAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.21, C:0.13, G:0.34, T:0.32
Consensus pattern (36 bp):
TGCTATGAGCAAGATGTAGGGCCTCAAGTGGAGTTA
Found at i:22170990 original size:45 final size:44
Alignment explanation
Indices: 22170926--22171048 Score: 113
Period size: 45 Copynumber: 2.8 Consensus size: 44
22170916 ATCGTCATGT
* * * *
22170926 AATGCCCAATCAAGTAGTCATGTAATGCCTAAAAACCAATTACGC
1 AATGCCCAATCAA-CAGTCACGTAATGCCTAAAAACCAATAACAC
* ** * *
22170971 AATGCCCCATCAACCAGTCACACAATGCCCTATAAACCAGTAACAC
1 AATGCCCAATCAA-CAGTCACGTAATG-CCTAAAAACCAATAACAC
* *
22171017 AATG-GCTATCAACAGTCACGTAATGCCTAAAA
1 AATGCCCAATCAACAGTCACGTAATGCCTAAAA
22171049 GCTAGTCATG
Statistics
Matches: 62, Mismatches: 15, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
43 6 0.10
44 11 0.18
45 27 0.44
46 18 0.29
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.20
Consensus pattern (44 bp):
AATGCCCAATCAACAGTCACGTAATGCCTAAAAACCAATAACAC
Found at i:22170996 original size:23 final size:23
Alignment explanation
Indices: 22170970--22171020 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
22170960 ACCAATTACG
* *
22170970 CAATGCCCCATCAACCAGTCACA
1 CAATGCCCCATAAACCAGTAACA
*
22170993 CAATGCCCTATAAACCAGTAACA
1 CAATGCCCCATAAACCAGTAACA
22171016 CAATG
1 CAATG
22171021 GCTATCAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.39, C:0.35, G:0.10, T:0.16
Consensus pattern (23 bp):
CAATGCCCCATAAACCAGTAACA
Found at i:22171063 original size:22 final size:21
Alignment explanation
Indices: 22171038--22171124 Score: 77
Period size: 22 Copynumber: 4.0 Consensus size: 21
22171028 ACAGTCACGT
*
22171038 AATGCCTAAAAGCTAGTCATGC
1 AATGACTAAAA-CTAGTCATGC
*
22171060 AATGACTAACAACCAAG-CATGC
1 AATGACTAA-AA-CTAGTCATGC
* *
22171082 AATGCCTAAAAATCAGTCATGC
1 AATGACTAAAACT-AGTCATGC
*
22171104 AATGACTAACAATTAGTCATG
1 AATGACTAA-AACTAGTCATG
22171125 TAATATTCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
21 4 0.08
22 41 0.77
23 8 0.15
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (21 bp):
AATGACTAAAACTAGTCATGC
Found at i:22171181 original size:45 final size:45
Alignment explanation
Indices: 22171132--22171240 Score: 148
Period size: 45 Copynumber: 2.4 Consensus size: 45
22171122 ATGTAATATT
* * *
22171132 CTATCAACGAGTCACGCAATGAC-TAAATATCAATCACGCAATGCC
1 CTATCAACTAGTCACGCAAT-ACTTAAAAATCAATCACGCAATCCC
* *
22171177 CTATCAACTATTCACGCAATACTTAAAAATCGATCACGCAATCCC
1 CTATCAACTAGTCACGCAATACTTAAAAATCAATCACGCAATCCC
*
22171222 CTATCAACTAGTCAGGCAA
1 CTATCAACTAGTCACGCAA
22171241 ACCCTAAGTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 2 0.04
45 54 0.96
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.22
Consensus pattern (45 bp):
CTATCAACTAGTCACGCAATACTTAAAAATCAATCACGCAATCCC
Found at i:22171312 original size:81 final size:81
Alignment explanation
Indices: 22171210--22171397 Score: 259
Period size: 81 Copynumber: 2.3 Consensus size: 81
22171200 TAAAAATCGA
* *
22171210 TCACGCAATCCCCTATCAACTAGTCAGGCAAACCCTAAGTCACGCAATGCCTAAAACCCATAAAC
1 TCACGC-ATGCCCTATCAACTAGTCAGGCAAACCCCAAGTCACGCAATGCCTAAAACCCATAAAC
* * *
22171275 CCAATGCCCAAAACCAT
65 CCAACGCACAAAACCAG
* * *
22171292 TCACGCATGCCCTATCAACTAGTCATGCAAACCCCAAGTCATGCAATGCCTAAAACCCCTAAACC
1 TCACGCATGCCCTATCAACTAGTCAGGCAAACCCCAAGTCACGCAATGCCTAAAACCCATAAACC
* *
22171357 CAACGCATAAAACTAG
66 CAACGCACAAAACCAG
* *
22171373 TCACGTATGCCCTCTCAACTAGTCA
1 TCACGCATGCCCTATCAACTAGTCA
22171398 CACATGCCCT
Statistics
Matches: 94, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
81 88 0.94
82 6 0.06
ACGTcount: A:0.36, C:0.36, G:0.11, T:0.18
Consensus pattern (81 bp):
TCACGCATGCCCTATCAACTAGTCAGGCAAACCCCAAGTCACGCAATGCCTAAAACCCATAAACC
CAACGCACAAAACCAG
Found at i:22171395 original size:22 final size:22
Alignment explanation
Indices: 22171367--22171412 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
22171357 CAACGCATAA
**
22171367 AACTAGTCACGTATGCCCTCTC
1 AACTAGTCACACATGCCCTCTC
22171389 AACTAGTCACACATGCCCTCTC
1 AACTAGTCACACATGCCCTCTC
22171411 AA
1 AA
22171413 TGTTCAACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.37, G:0.11, T:0.24
Consensus pattern (22 bp):
AACTAGTCACACATGCCCTCTC
Found at i:22171646 original size:19 final size:19
Alignment explanation
Indices: 22171601--22171637 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
22171591 TTTGACTGGC
* *
22171601 AAGGAATGCTTGGTCTGTA
1 AAGGAAAGCTTGGTCTATA
22171620 AAGGAAAGCTTGGTCTAT
1 AAGGAAAGCTTGGTCTAT
22171638 CGAGGAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (19 bp):
AAGGAAAGCTTGGTCTATA
Found at i:22172910 original size:2 final size:2
Alignment explanation
Indices: 22172903--22172927 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22172893 AAACGGCATT
22172903 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
22172928 ATTAGAGTAC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22179169 original size:99 final size:99
Alignment explanation
Indices: 22178998--22179295 Score: 571
Period size: 99 Copynumber: 3.0 Consensus size: 99
22178988 TGTGAGCACG
22178998 GCTGGTACTTTCTTTTACACCCATCTTTGCGGCTTTCAACCTCTTTTCACTACTTCTCCCTTCTG
1 GCTGGTACTTTCTTTTACACCCATCTTTGCGGCTTTCAACCTCTTTTCACTACTTCTCCCTTCTG
22179063 TTGCCTTGTTGTCTTCTACCCTTAACACTTTAAT
66 TTGCCTTGTTGTCTTCTACCCTTAACACTTTAAT
22179097 GCTGGTACTTTCTTTTACACCCATCTTTGCGGCTTTCAACCTCTTTTCACTACTTCTCCCTTCTG
1 GCTGGTACTTTCTTTTACACCCATCTTTGCGGCTTTCAACCTCTTTTCACTACTTCTCCCTTCTG
22179162 TTGCCTTGTTGTCTTCTACCCTTAACACGTTT-AT
66 TTGCCTTGTTGTCTTCTACCCTTAACAC-TTTAAT
22179196 GCTGGTACTTTCTTTTACACCCATCTTTGCGGCTTTCAACCTCTTTTCACTACTTCTCCCTTCTG
1 GCTGGTACTTTCTTTTACACCCATCTTTGCGGCTTTCAACCTCTTTTCACTACTTCTCCCTTCTG
*
22179261 TTGCTTTGTTGTCTTCTACCCTTAACACTTTAAT
66 TTGCCTTGTTGTCTTCTACCCTTAACACTTTAAT
22179295 G
1 G
22179296 AGTCTTTTCT
Statistics
Matches: 196, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
98 3 0.02
99 190 0.97
100 3 0.02
ACGTcount: A:0.14, C:0.31, G:0.11, T:0.45
Consensus pattern (99 bp):
GCTGGTACTTTCTTTTACACCCATCTTTGCGGCTTTCAACCTCTTTTCACTACTTCTCCCTTCTG
TTGCCTTGTTGTCTTCTACCCTTAACACTTTAAT
Found at i:22182867 original size:56 final size:56
Alignment explanation
Indices: 22182796--22182936 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 56
22182786 AATTTTTTTT
* * *
22182796 GGTAATTTAGTCATTACCTATAGATTTTCGTTGGAAATTGCAAACAAATTTCCATC
1 GGTAATTTAGTCATTACCTATAGATTTTCGTTGAAAATTACAAACAAAGTTCCATC
* * * * *
22182852 GGTAATTTAGTCATTACTTTTAGATTTTTTCGTTGAAAATTACCAACGAAGTTCCTTC
1 GGTAATTTAGTCATTACCTATAGA--TTTTCGTTGAAAATTACAAACAAAGTTCCATC
* *
22182910 GATAATTTAGTCATTACCTACAGATTT
1 GGTAATTTAGTCATTACCTATAGATTT
22182937 CTATTGGAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
56 25 0.35
58 46 0.65
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (56 bp):
GGTAATTTAGTCATTACCTATAGATTTTCGTTGAAAATTACAAACAAAGTTCCATC
Found at i:22186385 original size:17 final size:17
Alignment explanation
Indices: 22186354--22186386 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22186344 TTCTTAATAA
22186354 AATAAAACTCGTTATTG
1 AATAAAACTCGTTATTG
22186371 AATAATAACTC-TTATT
1 AATAA-AACTCGTTATT
22186387 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (17 bp):
AATAAAACTCGTTATTG
Found at i:22186589 original size:28 final size:28
Alignment explanation
Indices: 22186528--22186699 Score: 184
Period size: 28 Copynumber: 6.0 Consensus size: 28
22186518 TTAAGACAAC
* *
22186528 TCTTGTCTATAATTAAGATAAA-ATATTTT
1 TCTTGTCTA-AATTAAGACAAACAT-GTTT
* *
22186557 ATCTTGTCTAAATTGAGACAAATATGTTT
1 -TCTTGTCTAAATTAAGACAAACATGTTT
* * *
22186586 TCTTGTCTAGATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAACAT-GTTT
22186616 TCTTGTCTTAAATTAAGACAAACATGTTT
1 TCTTGTC-TAAATTAAGACAAACATGTTT
*
22186645 TCTTGTTTAAATTAAGACAAACATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* * *
22186673 TATTATTTAAATTAAGACAAACATGTT
1 TCTTGTCTAAATTAAGACAAACATGTT
22186700 AAATTTGTCA
Statistics
Matches: 125, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
28 62 0.50
29 27 0.22
30 26 0.21
31 10 0.08
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:22186635 original size:59 final size:58
Alignment explanation
Indices: 22186528--22186699 Score: 208
Period size: 59 Copynumber: 3.0 Consensus size: 58
22186518 TTAAGACAAC
* * *
22186528 TCTTGTCTATAATTAAGA-TAAAATATTTTATCTTGTC-TAAATTGAGACAAATATGTTT
1 TCTTGTCTA-AATTAAGACAAAAATATTTT-TCTTGTCTTAAATTAAGACAAACATGTTT
*
22186586 TCTTGTCTAGATTAAGACAAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATGTTT
1 TCTTGTCTAAATTAAGAC-AAAAATATTTTTCTTGTCTTAAATTAAGACAAACATGTTT
* * * * *
22186645 TCTTGTTTAAATTAAGACAAACAT-GTTTTATTAT-TTAAATTAAGACAAACATGTT
1 TCTTGTCTAAATTAAGACAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATGTT
22186700 AAATTTGTCA
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
56 21 0.21
57 14 0.14
58 21 0.21
59 45 0.45
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (58 bp):
TCTTGTCTAAATTAAGACAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATGTTT
Found at i:22186687 original size:87 final size:88
Alignment explanation
Indices: 22186528--22186693 Score: 212
Period size: 87 Copynumber: 1.9 Consensus size: 88
22186518 TTAAGACAAC
* * * * * *
22186528 TCTTGTCTATAATTAAGATAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCTTGTC
1 TCTTGTCTATAATTAAGACAAAATAGTTTATCTTGTCTAAATTAAGACAAACATGTTTTATTATC
*
22186593 TAGATTAAGACAAAAAATATTTT
66 TAAATTAAGACAAAAAATATTTT
*
22186616 TCTTGTCT-TAAATTAAGACAAACAT-GTTT-TCTTGTTTAAATTAAGACAAACATGTTTTATTA
1 TCTTGTCTAT-AATTAAGACAAA-ATAGTTTATCTTGTCTAAATTAAGACAAACATGTTTTATTA
*
22186678 TTTAAATTAAGACAAA
64 TCTAAATTAAGACAAA
22186694 CATGTTAAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
87 43 0.64
88 22 0.33
89 2 0.03
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42
Consensus pattern (88 bp):
TCTTGTCTATAATTAAGACAAAATAGTTTATCTTGTCTAAATTAAGACAAACATGTTTTATTATC
TAAATTAAGACAAAAAATATTTT
Found at i:22193218 original size:21 final size:22
Alignment explanation
Indices: 22193188--22193229 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
22193178 GTAGAAAAGG
*
22193188 CTTAATCGATT-AAAGCTCACC
1 CTTAACCGATTAAAAGCTCACC
22193209 CTTAACCGATTAAAAGCTCAC
1 CTTAACCGATTAAAAGCTCAC
22193230 TGTTAGCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.36, C:0.29, G:0.10, T:0.26
Consensus pattern (22 bp):
CTTAACCGATTAAAAGCTCACC
Found at i:22194161 original size:18 final size:19
Alignment explanation
Indices: 22194114--22194168 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
22194104 CATGAGCTAG
*
22194114 AAATGAAAAAAGAAGAAG-C
1 AAATGAAAAAA-AAGAAGTT
*
22194133 AAATGAGAAAAAAGAAGTT
1 AAATGAAAAAAAAGAAGTT
22194152 AAA-GAAAAAAAA-AAGTT
1 AAATGAAAAAAAAGAAGTT
22194169 TAGCATTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 5 0.16
18 14 0.44
19 13 0.41
ACGTcount: A:0.69, C:0.02, G:0.18, T:0.11
Consensus pattern (19 bp):
AAATGAAAAAAAAGAAGTT
Found at i:22210254 original size:19 final size:19
Alignment explanation
Indices: 22210216--22210258 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
22210206 AAGATTACAC
* *
22210216 TGAATCACATTATAGCCAA
1 TGAATCACATTACAACCAA
*
22210235 TGAATCACATTACAATCAA
1 TGAATCACATTACAACCAA
22210254 TGAAT
1 TGAAT
22210259 GTAATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (19 bp):
TGAATCACATTACAACCAA
Found at i:22210542 original size:40 final size:40
Alignment explanation
Indices: 22210469--22210553 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
22210459 CTTTTAAAAG
* * *
22210469 AAAAAAATTAAAATAAAATATATAATATAAAAAATTTATT
1 AAAAAAATAAAAATAAAATATATAACATAAAAAATATATT
* * *
22210509 AAAAAAATAAAAATAACATATATGACATTAAAAATATATT
1 AAAAAAATAAAAATAAAATATATAACATAAAAAATATATT
*
22210549 TAAAA
1 AAAAA
22210554 GATGATAGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.29
Consensus pattern (40 bp):
AAAAAAATAAAAATAAAATATATAACATAAAAAATATATT
Found at i:22216030 original size:40 final size:40
Alignment explanation
Indices: 22215978--22216058 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
22215968 TCTACATCCA
* *
22215978 CCAAAACATCTCATCTAGCATACATGCATCTTATACTCAT
1 CCAAAACATCTCATCTAGCATACATGCATCTCAAACTCAT
22216018 CCAAAACATCTCATCTAGCATACATGCATCTCAAACTCAT
1 CCAAAACATCTCATCTAGCATACATGCATCTCAAACTCAT
22216058 C
1 C
22216059 ATATCAACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.32, G:0.05, T:0.27
Consensus pattern (40 bp):
CCAAAACATCTCATCTAGCATACATGCATCTCAAACTCAT
Found at i:22216047 original size:20 final size:20
Alignment explanation
Indices: 22215984--22216050 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
22215974 TCCACCAAAA
22215984 CATCTCATCTAGCATACATG
1 CATCTCATCTAGCATACATG
* * **
22216004 CATCTTATACT--CATCCAAAA
1 CATCTCAT-CTAGCATAC-ATG
22216024 CATCTCATCTAGCATACATG
1 CATCTCATCTAGCATACATG
22216044 CATCTCA
1 CATCTCA
22216051 AACTCATCAT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
19 6 0.17
20 23 0.66
21 6 0.17
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.30
Consensus pattern (20 bp):
CATCTCATCTAGCATACATG
Found at i:22222150 original size:39 final size:38
Alignment explanation
Indices: 22222096--22222202 Score: 107
Period size: 37 Copynumber: 2.9 Consensus size: 38
22222086 ACCCAGCTCA
* *
22222096 TGTGCAACCCCCACATCGCGCACATAGCTGAAGT-CATCG
1 TGTGCATCCCCCACATCGCGCACATAGCT-AA-TACACCG
* *
22222135 TGTGCATCCCCCACATCGTG--CATAGCTAATACCGCCG
1 TGTGCATCCCCCACATCGCGCACATAGCTAATA-CACCG
*
22222172 TGTGCATCCCCCACATTGCGCACA-AGC-AATA
1 TGTGCATCCCCCACATCGCGCACATAGCTAATA
22222203 TCATCATCCA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
35 1 0.02
36 2 0.03
37 32 0.55
38 3 0.05
39 20 0.34
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.20
Consensus pattern (38 bp):
TGTGCATCCCCCACATCGCGCACATAGCTAATACACCG
Found at i:22224190 original size:11 final size:11
Alignment explanation
Indices: 22224174--22224198 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
22224164 TGGTAAACTA
22224174 GTATTGATATG
1 GTATTGATATG
22224185 GTATTGATATG
1 GTATTGATATG
22224196 GTA
1 GTA
22224199 AACTAGTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (11 bp):
GTATTGATATG
Found at i:22234232 original size:42 final size:43
Alignment explanation
Indices: 22234168--22234276 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 43
22234158 TCACCAACTC
* ** * **
22234168 ATGCGCATTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGACTT
*
22234211 ATGCGC-CTCCCTACTAGCACATAACCGGGTCATCCTCGACTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGACTT
22234253 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
22234277 GCCGAGTCCA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.02
42 33 0.59
43 22 0.39
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGACTT
Found at i:22241125 original size:43 final size:43
Alignment explanation
Indices: 22241077--22241159 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
22241067 GAGAGTGGAA
* **
22241077 AGTGGAGAC-GAGACGGTAGTTGGAAGAAACCAAAAAGGGCAAG
1 AGTGGAGACAG-GACGATAGTCAGAAGAAACCAAAAAGGGCAAG
* *
22241120 AGTGGAGACAGGACGATAGTCAGCAGAAACCAGAAAGGGC
1 AGTGGAGACAGGACGATAGTCAGAAGAAACCAAAAAGGGC
22241160 GATTGTGGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 33 0.97
44 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.36, T:0.08
Consensus pattern (43 bp):
AGTGGAGACAGGACGATAGTCAGAAGAAACCAAAAAGGGCAAG
Found at i:22241168 original size:43 final size:43
Alignment explanation
Indices: 22241101--22241202 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 43
22241091 GGTAGTTGGA
* * *
22241101 AGAAACCAAAAAGGGCAAGAGTGGAGACAGGAC-GATAGTCAGC
1 AGAAACCAGAAAGGGCAAGAGTGGAGACAAGACAG-CAGTCAGC
* ** *
22241144 AGAAACCAGAAAGGGCGATTGTGGAGACAAGACAGCAGTCGGC
1 AGAAACCAGAAAGGGCAAGAGTGGAGACAAGACAGCAGTCAGC
*
22241187 AGAAATCAGAAAGGGC
1 AGAAACCAGAAAGGGC
22241203 CAAAGGGGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
43 49 0.98
44 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.33, T:0.08
Consensus pattern (43 bp):
AGAAACCAGAAAGGGCAAGAGTGGAGACAAGACAGCAGTCAGC
Found at i:22242835 original size:25 final size:25
Alignment explanation
Indices: 22242803--22242856 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
22242793 CATAACCATG
*
22242803 TATA-CAACTTGTGG-CTTGGCCACA
1 TATATCAACCTGTGGCCTT-GCCACA
*
22242827 TATATCAACCTGTGGCCTTGCCACG
1 TATATCAACCTGTGGCCTTGCCACA
22242852 TATAT
1 TATAT
22242857 ATCACAGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 4 0.15
25 19 0.73
26 3 0.12
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (25 bp):
TATATCAACCTGTGGCCTTGCCACA
Found at i:22243261 original size:2 final size:2
Alignment explanation
Indices: 22243256--22243310 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
22243246 CATATATGTG
22243256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22243298 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
22243311 TCTNNNNNNN
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22253670 original size:18 final size:18
Alignment explanation
Indices: 22253649--22253683 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
22253639 AACTCTCTCC
22253649 TTTC-TTCTCTTTCTCTTT
1 TTTCTTTCTCTTT-TCTTT
22253667 TTTCTTTCTCTTTTCTT
1 TTTCTTTCTCTTTTCTT
22253684 CTTCTCGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTCTTTCTCTTTTCTTT
Found at i:22253674 original size:13 final size:14
Alignment explanation
Indices: 22253656--22253686 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
22253646 TCCTTTCTTC
22253656 TCTTTCTCTTTT-T
1 TCTTTCTCTTTTCT
22253669 TCTTTCTCTTTTCT
1 TCTTTCTCTTTTCT
22253683 TCTT
1 TCTT
22253687 CTCGGGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TCTTTCTCTTTTCT
Found at i:22256437 original size:2 final size:2
Alignment explanation
Indices: 22256430--22256462 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
22256420 TACCTCCAAC
22256430 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22256463 CCTTACTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:22258115 original size:19 final size:20
Alignment explanation
Indices: 22258088--22258133 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
22258078 AGGAGACAAG
*
22258088 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
22258107 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
22258126 ATAATATT
1 ATAATATT
22258134 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:22258561 original size:20 final size:20
Alignment explanation
Indices: 22258536--22258581 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
22258526 TTTTGGCCCC
22258536 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
22258556 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
22258576 ATTTGA
1 ATTTGA
22258582 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:22259530 original size:13 final size:13
Alignment explanation
Indices: 22259512--22259536 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22259502 AGAGAAATTG
22259512 TGATTTTATAAAA
1 TGATTTTATAAAA
22259525 TGATTTTATAAA
1 TGATTTTATAAA
22259537 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:22260961 original size:15 final size:15
Alignment explanation
Indices: 22260936--22260976 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
22260926 GATCACAGAT
22260936 TTTGG-TTTTAAAGC
1 TTTGGATTTTAAAGC
*
22260950 TTTGGATTTTAAAGT
1 TTTGGATTTTAAAGC
*
22260965 TTTTGATTTTAA
1 TTTGGATTTTAA
22260977 GGTTGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.56
Consensus pattern (15 bp):
TTTGGATTTTAAAGC
Found at i:22262613 original size:54 final size:54
Alignment explanation
Indices: 22262527--22262635 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
22262517 AATAGCTACA
* *
22262527 GTACTTTAGCATTGACTGTTCAACGCTGTAATGCTTCGAATACCTCACGCCTAT
1 GTACTTTAGCATTGACTGTTCAACGCTATAATGCTCCGAATACCTCACGCCTAT
22262581 GTACTTTAGCATTGACTGTTCAACGCTATAATGCTCCGAATACCTCACGCCTAT
1 GTACTTTAGCATTGACTGTTCAACGCTATAATGCTCCGAATACCTCACGCCTAT
22262635 G
1 G
22262636 ATGCACAAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.32
Consensus pattern (54 bp):
GTACTTTAGCATTGACTGTTCAACGCTATAATGCTCCGAATACCTCACGCCTAT
Found at i:22266526 original size:13 final size:13
Alignment explanation
Indices: 22266508--22266532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22266498 AGAGAAATTG
22266508 TGATTTTATAAAA
1 TGATTTTATAAAA
22266521 TGATTTTATAAA
1 TGATTTTATAAA
22266533 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:22267780 original size:220 final size:214
Alignment explanation
Indices: 22267398--22267828 Score: 772
Period size: 220 Copynumber: 2.0 Consensus size: 214
22267388 CTGTAAAAGA
* *
22267398 AATTTTATGCTTTGGTTATTTGCTTTATAGTATATATAAATATAATTAACTTTTAGGCTATAAGA
1 AATTTTATGCTTTGGTTATTTGCTTTATAGTATATATAAATATAATTAACTTTTACGCCATAAGA
22267463 ATTATGTACCGATAGTTTTATGAAAATTATTTTACAAGAAAATAGTTTATTTTATTGAATATTTT
66 ATTATGTACCGATAGTTTTATGAAAATTATTTTACAAGAAAATAGTTTATTTTATTGAATATTTT
22267528 TATTATATTCAAATGGTCAAATTTTCACTTCAAATGAACGTTTTAGATACTTAATTTGTTTTTAA
131 TATTATATTCAAATGGTCAAATTTTCACTTCAAATGAACGTTTTAGATACTTAATTTGTTTTTAA
22267593 ATCATTAAATATATATTTT
196 ATCATTAAATATATATTTT
*
22267612 NNNNNNAATTTTATGCTTTGGTTATTTGCTTTATAGTATATATGAATATAATTAACTTTTACGCC
1 ------AATTTTATGCTTTGGTTATTTGCTTTATAGTATATATAAATATAATTAACTTTTACGCC
22267677 ATAAGAATTATGTACCGATAGTTTTATGAAAATTATTTTACAAGAAAATAGTTTATTTTATTGAA
60 ATAAGAATTATGTACCGATAGTTTTATGAAAATTATTTTACAAGAAAATAGTTTATTTTATTGAA
*
22267742 TATTTTTATTATATTCAATTGGTCAAATTTTCACTTCAAATGAACGTTTTAGATACTTAATTTGT
125 TATTTTTATTATATTCAAATGGTCAAATTTTCACTTCAAATGAACGTTTTAGATACTTAATTTGT
22267807 TTTTAAATCATTAAATATATAT
190 TTTTAAATCATTAAATATATAT
22267829 ATATTTTGCT
Statistics
Matches: 207, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
220 207 1.00
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.47
Consensus pattern (214 bp):
AATTTTATGCTTTGGTTATTTGCTTTATAGTATATATAAATATAATTAACTTTTACGCCATAAGA
ATTATGTACCGATAGTTTTATGAAAATTATTTTACAAGAAAATAGTTTATTTTATTGAATATTTT
TATTATATTCAAATGGTCAAATTTTCACTTCAAATGAACGTTTTAGATACTTAATTTGTTTTTAA
ATCATTAAATATATATTTT
Found at i:22270529 original size:63 final size:63
Alignment explanation
Indices: 22270455--22270613 Score: 248
Period size: 63 Copynumber: 2.5 Consensus size: 63
22270445 TTAATGTAAC
*
22270455 CGTGCATGTGTGGAGTGGGCAGTGCACACGCCGGTTGAATGACAATGTTAG-GACAATTACAAT
1 CGTGCATGTGTGGAGTGGGCAGTGCACATGCCGGTTGAATGACAATGTT-GTGACAATTACAAT
* * *
22270518 TGTGCATGTGTGGAGTGGGCAGTGCACATACTGGTTGAATGACAATGTTGTGACAATTACAAT
1 CGTGCATGTGTGGAGTGGGCAGTGCACATGCCGGTTGAATGACAATGTTGTGACAATTACAAT
* *
22270581 CGTGCATGTGCGGAGTGGGAAGTGCACATGCCG
1 CGTGCATGTGTGGAGTGGGCAGTGCACATGCCG
22270614 ACTATGATGT
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
62 1 0.01
63 85 0.99
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.25
Consensus pattern (63 bp):
CGTGCATGTGTGGAGTGGGCAGTGCACATGCCGGTTGAATGACAATGTTGTGACAATTACAAT
Found at i:22270679 original size:2 final size:2
Alignment explanation
Indices: 22270672--22270699 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22270662 TAGCCGTGTT
22270672 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22270700 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22271006 original size:2 final size:2
Alignment explanation
Indices: 22270999--22271030 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
22270989 NNNNNCGTGT
22270999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22271031 CATGCGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22297939 original size:28 final size:27
Alignment explanation
Indices: 22297900--22297953 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
22297890 ATGTCCTGGT
22297900 GGTGGAAAATTACAATTTTACCCCTAA
1 GGTGGAAAATTACAATTTTACCCCTAA
*
22297927 GGTGGCAAAATTACCATTTTACCCCTA
1 GGTGG-AAAATTACAATTTTACCCCTA
22297954 TACTCCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTAA
Found at i:22301136 original size:22 final size:21
Alignment explanation
Indices: 22301111--22301152 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
22301101 AAAATGTTGC
22301111 AAACAACAAT-AAGCAAGCTAGA
1 AAACAA-AATGAAGCAA-CTAGA
*
22301133 AAACGAAATGAAGCAACTAG
1 AAACAAAATGAAGCAACTAG
22301153 TGCAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.57, C:0.17, G:0.17, T:0.10
Consensus pattern (21 bp):
AAACAAAATGAAGCAACTAGA
Found at i:22310087 original size:21 final size:21
Alignment explanation
Indices: 22310054--22310129 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 21
22310044 CATTTACTTA
* *
22310054 AATGAATCGATACATGTTCAT
1 AATGTATCCATACATGTTCAT
* * **
22310075 GATGTATCCATACAT-ATGGT
1 AATGTATCCATACATGTTCAT
* *
22310095 CATGTATCGATACATGTTCAT
1 AATGTATCCATACATGTTCAT
22310116 AATGTA-CCGATACA
1 AATGTATCC-ATACA
22310130 ATTTTTTCAA
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (21 bp):
AATGTATCCATACATGTTCAT
Found at i:22317521 original size:29 final size:27
Alignment explanation
Indices: 22317451--22317642 Score: 150
Period size: 28 Copynumber: 6.7 Consensus size: 27
22317441 AACCATTGCA
* * *
22317451 TGTCTTAATTTAGACAAAAAAAATGTG
1 TGTCTTAATTTAGACAAGAAATATGTT
22317478 TGTCTTAATTTAGACAAGAAATCATGTT
1 TGTCTTAATTTAGACAAGAAAT-ATGTT
*
22317506 TGGTCTTAATTTAGACAAGAAAATATGTC
1 T-GTCTTAATTTAGACAAG-AAATATGTT
* *
22317535 TGTCTTAATTTAAGATAAGAAAAATATTTTT
1 TGTCTTAATTT-AGACAAG--AAATA-TGTT
* * * * *
22317566 TGTCTTAATCTAGATAACAAAACATATT
1 TGTCTTAATTTAGACAA-GAAATATGTT
* *
22317594 TGTCTCAATTTAGACAAGATAAAATATTTT
1 TGTCTTAATTTAGACAAG---AAATATGTT
*
22317624 TGCCTTAATTTAAGACAAG
1 TGTCTTAATTT-AGACAAG
22317643 TCTTAATTAA
Statistics
Matches: 135, Mismatches: 19, Indels: 18
0.78 0.11 0.10
Matches are distributed among these distances:
27 20 0.15
28 32 0.24
29 32 0.24
30 32 0.24
31 19 0.14
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (27 bp):
TGTCTTAATTTAGACAAGAAATATGTT
Found at i:22317598 original size:59 final size:57
Alignment explanation
Indices: 22317451--22317641 Score: 199
Period size: 59 Copynumber: 3.3 Consensus size: 57
22317441 AACCATTGCA
* *
22317451 TGTCTTAATTTAGACAAAAAAAATGTGTGTCTTAATTTAGACAAG--AAATCATGTTT
1 TGTCTTAATTTAGACAAAAAAAATGTCTGTCTTAATTTAGACAAGAAAAAT-ATTTTT
* * *
22317507 GGTCTTAATTTAGACAAGAAAATATGTCTGTCTTAATTTAAGATAAGAAAAATATTTTT
1 TGTCTTAATTTAGACAA-AAAAAATGTCTGTCTTAATTT-AGACAAGAAAAATATTTTT
* * * * * *
22317566 TGTCTTAATCTAGATAACAAAACATATTTGTCTCAATTTAGACAAGATAAAATA-TTTT
1 TGTCTTAATTTAGACAA-AAAAAATGTCTGTCTTAATTTAGACAAGA-AAAATATTTTT
*
22317624 TGCCTTAATTTAAGACAA
1 TGTCTTAATTT-AGACAA
22317642 GTCTTAATTA
Statistics
Matches: 112, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
56 16 0.14
57 19 0.17
58 26 0.23
59 47 0.42
60 4 0.04
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (57 bp):
TGTCTTAATTTAGACAAAAAAAATGTCTGTCTTAATTTAGACAAGAAAAATATTTTT
Found at i:22317607 original size:28 final size:28
Alignment explanation
Indices: 22317414--22317642 Score: 183
Period size: 29 Copynumber: 7.9 Consensus size: 28
22317404 ATGACAATTT
*
22317414 AACATGTTTGTCTTAATTTATACATA-AA
1 AACATGTTTGTCTTAATTTAGACA-AGAA
* **
22317442 ACCATTGCATGTCTTAATTTAGACAA-AA
1 AACA-TGTTTGTCTTAATTTAGACAAGAA
* *
22317470 AAAATGTGTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
*
22317498 ATCATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
* * *
22317527 AATATGTCTGTCTTAATTTAAGATAAGAAA
1 AACATGTTTGTCTTAATTT-AGACAAG-AA
* * * * *
22317557 AATATTTTTTGTCTTAATCTAGATAACAA
1 AACA-TGTTTGTCTTAATTTAGACAAGAA
* *
22317586 AACATATTTGTCTCAATTTAGACAAGATAA
1 AACATGTTTGTCTTAATTTAGACAAG--AA
* * *
22317616 AATATTTTTGCCTTAATTTAAGACAAG
1 AACATGTTTGTCTTAATTT-AGACAAG
22317643 TCTTAATTAA
Statistics
Matches: 163, Mismatches: 29, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
27 19 0.12
28 43 0.26
29 53 0.33
30 29 0.18
31 19 0.12
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.38
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:22326198 original size:14 final size:14
Alignment explanation
Indices: 22326176--22326217 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
22326166 CAAAAATAAG
*
22326176 GAAGGAAAGAGAAA
1 GAAGAAAAGAGAAA
22326190 GAAGAAAAGAGAAA
1 GAAGAAAAGAGAAA
*
22326204 -AGAGAAAAAAGAAA
1 GA-AGAAAAGAGAAA
22326218 AAGGCTTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 1 0.04
14 24 0.96
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
GAAGAAAAGAGAAA
Found at i:22326202 original size:7 final size:7
Alignment explanation
Indices: 22326181--22326218 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
22326171 ATAAGGAAGG
22326181 AAAGAG-
1 AAAGAGA
22326187 AAAGAAGA
1 AAAG-AGA
22326195 AAAGAGA
1 AAAGAGA
22326202 AAAGAGA
1 AAAGAGA
*
22326209 AAAAAGA
1 AAAGAGA
22326216 AAA
1 AAA
22326219 AGGCTTGGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 4 0.14
7 21 0.72
8 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAGAGA
Found at i:22327854 original size:12 final size:12
Alignment explanation
Indices: 22327837--22327869 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
22327827 CGAGTTGATT
22327837 TATGAGCTTATG
1 TATGAGCTTATG
22327849 TATGAGCTTATG
1 TATGAGCTTATG
*
22327861 TATAAGCTT
1 TATGAGCTT
22327870 TGATAATGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.42
Consensus pattern (12 bp):
TATGAGCTTATG
Found at i:22329478 original size:2 final size:2
Alignment explanation
Indices: 22329473--22329497 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22329463 TATATATATA
22329473 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
22329498 ATGATGATTG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:22329650 original size:38 final size:40
Alignment explanation
Indices: 22329608--22329710 Score: 151
Period size: 38 Copynumber: 2.6 Consensus size: 40
22329598 ATAGTGCCCG
22329608 TGTGCACGATGTGGGGGGATGTACACGAT-G-G-CA-CTGA
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGCCAGCT-A
*
22329645 TTGTGCACGATGTGGGGGGATGCACACGATGGTGCCAGCTA
1 -TGTGCACGATGTGGGGGGATGTACACGATGGTGCCAGCTA
22329686 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
22329711 TGAGCCGGGT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
38 28 0.47
39 1 0.02
40 25 0.42
41 3 0.05
42 2 0.03
ACGTcount: A:0.20, C:0.17, G:0.41, T:0.22
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGTGCCAGCTA
Found at i:22338369 original size:18 final size:18
Alignment explanation
Indices: 22338346--22338381 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
22338336 AATTCAATTC
*
22338346 GGTTTTGTTTCAATCTTT
1 GGTTTTGTTGCAATCTTT
22338364 GGTTTTGTTGCAATCTTT
1 GGTTTTGTTGCAATCTTT
22338382 AATTTGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.58
Consensus pattern (18 bp):
GGTTTTGTTGCAATCTTT
Found at i:22344272 original size:23 final size:23
Alignment explanation
Indices: 22344246--22344295 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
22344236 TTCAACCCTC
22344246 TCTTTCTCTCTTT-TTCCTTCCTT
1 TCTTTCTC-CTTTCTTCCTTCCTT
* *
22344269 TCTTTCTCCTTTCTTCTTTCTTT
1 TCTTTCTCCTTTCTTCCTTCCTT
22344292 TCTT
1 TCTT
22344296 CTTAGCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (23 bp):
TCTTTCTCCTTTCTTCCTTCCTT
Found at i:22345513 original size:52 final size:51
Alignment explanation
Indices: 22345469--22345639 Score: 216
Period size: 51 Copynumber: 3.3 Consensus size: 51
22345459 TTTGGACTAT
* * * * * *
22345469 GATATTTGTTTGGCTTTGATGTTCTAAATTTGTTATATTTGATTTGGACTTTC
1 GATATTTGTTTGG-TTTGATGTT-TGAACTTGATACATTTGATTCGGACTTTG
* * * *
22345522 AACAATTGTTTGGTTTGATGTTTGAACTTGATACATTTGATTCGAACTTTG
1 GATATTTGTTTGGTTTGATGTTTGAACTTGATACATTTGATTCGGACTTTG
* *
22345573 GATATTTCTTTGGTATGATGTTTGAACTTGATACATTTGATTCGGACTTTG
1 GATATTTGTTTGGTTTGATGTTTGAACTTGATACATTTGATTCGGACTTTG
22345624 GATATTTGTTTGGTTT
1 GATATTTGTTTGGTTT
22345640 AAAGTTTGGA
Statistics
Matches: 100, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
51 81 0.81
52 9 0.09
53 10 0.10
ACGTcount: A:0.21, C:0.08, G:0.20, T:0.50
Consensus pattern (51 bp):
GATATTTGTTTGGTTTGATGTTTGAACTTGATACATTTGATTCGGACTTTG
Found at i:22346773 original size:15 final size:15
Alignment explanation
Indices: 22346753--22346785 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
22346743 GTTAACATTG
*
22346753 TAAAATTATTACTTA
1 TAAAATTATTAATTA
22346768 TAAAATTATTAATTA
1 TAAAATTATTAATTA
22346783 TAA
1 TAA
22346786 TATTTATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAATTATTAATTA
Found at i:22347027 original size:345 final size:344
Alignment explanation
Indices: 22346352--22347027 Score: 884
Period size: 345 Copynumber: 2.0 Consensus size: 344
22346342 ATTATATATA
* ***
22346352 TATATATATACTTTTAACATAAATGTATTTACTTTCTATTTTGTGTTTTAACATTACAAAAATTA
1 TATATATATACTTTAAACATAAACACATTTACTTTCTATTTTGTG-TTTAACATTACAAAAATTA
* *
22346417 TGACTTATAAAATTATTAATTATAATATATATACCATTATTTATATAAACTTATAACATATATAC
65 TGACTTATAAAATTATTAATTATAATATATATAACATTATTTATATAAACTTATAACATATAAAC
* * * * *
22346482 TTAAAGAGAGCTTTTGACATTAGAATAGTTTTGGAACCTAACTATTTTTTTTTAATTTCATGAAA
130 CTAAAGAGAGCTTGTGACATTAGAATAGTTCTGGAAACGAACTATTTTTTTTTAATTTCATGAAA
* *
22346547 TTAAAGACAAATGCATATAGTTAGTTAAATTAATTCATAAAACTATTATTATTAATTAACTTGTA
195 TTAAAGACAAATGCATATAGTTAATTAAATTAATTCATAAAACTATAATTATTAATTAACTTGTA
* **
22346612 ATATCTTTCAATATATATAGTTTATATATTGTGTTAGTTTATAAGAAATATAATTACTATTATAT
260 ATATCTTTAAATATATATAGTTTATATATTAAGTTAGTTTATAAGAAATATAATTAC--TTATAT
22346677 ATATATACTAAAATATTTTTAG
323 ATATATACTAAAATATTTTTAG
* * **
22346699 TATATATATACTTTAAATATAAACACATTTACTTTTTATTTTGTG-TTAACATT-GTAAAATTAT
1 TATATATATACTTTAAACATAAACACATTTACTTTCTATTTTGTGTTTAACATTACAAAAATTAT
* * * * *
22346762 TACTTATAAAATTATTAATTATAATATTTATAACTTTGTTTATATAAACTTATAATATATAAACC
66 GACTTATAAAATTATTAATTATAATATATATAACATTATTTATATAAACTTATAACATATAAACC
* * *
22346827 TAAAGAGAAG-TTGTGAGATTAGAATAGTTCT-GAAACGAAGTTATTTTTTTTTTAATTTCATGT
131 TAAAGAG-AGCTTGTGACATTAGAATAGTTCTGGAAACGAA-CTA-TTTTTTTTTAATTTCATGA
* *
22346890 AATT-AAGAACAAACT-CGTATAGTTAATTAAATTAATTCATGAAACTATAATTATTAATTAACT
193 AATTAAAG-ACAAA-TGCATATAGTTAATTAAATTAATTCATAAAACTATAATTATTAATTAACT
* *
22346953 TGTAATGTCTTTTAATATATATATACGTTATATATATTAAGTTCA-TTTATAAGGAATATAATTA
256 TGTAATATC-TTTAA-ATATATATA-GTT-TATATATTAAGTT-AGTTTATAAGAAATATAATTA
22347017 C-TAT-TATATAT
316 CTTATATATATAT
22347028 GTATATGTAT
Statistics
Matches: 287, Mismatches: 32, Indels: 22
0.84 0.09 0.06
Matches are distributed among these distances:
343 6 0.02
344 95 0.33
345 96 0.33
346 8 0.03
347 48 0.17
348 3 0.01
349 30 0.10
350 1 0.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (344 bp):
TATATATATACTTTAAACATAAACACATTTACTTTCTATTTTGTGTTTAACATTACAAAAATTAT
GACTTATAAAATTATTAATTATAATATATATAACATTATTTATATAAACTTATAACATATAAACC
TAAAGAGAGCTTGTGACATTAGAATAGTTCTGGAAACGAACTATTTTTTTTTAATTTCATGAAAT
TAAAGACAAATGCATATAGTTAATTAAATTAATTCATAAAACTATAATTATTAATTAACTTGTAA
TATCTTTAAATATATATAGTTTATATATTAAGTTAGTTTATAAGAAATATAATTACTTATATATA
TATACTAAAATATTTTTAG
Found at i:22351155 original size:43 final size:44
Alignment explanation
Indices: 22351102--22351206 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
22351092 CATGCAATTT
* * * * * *
22351102 TTTGAAATATTTGATACGC-TTGCAA-AAGTGGACTTTGAGAATT
1 TTTGATATATTTGATACGCATT-CAACAAATGAACTCTGAAAATC
22351145 TTTG-TGATATTTGATACGCATTCAACAAATGAACTCTGAAAATC
1 TTTGAT-ATATTTGATACGCATTCAACAAATGAACTCTGAAAATC
22351189 TTTGATATATTTGATACG
1 TTTGATATATTTGATACG
22351207 TTTGAAAGGA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
43 20 0.38
44 31 0.60
45 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (44 bp):
TTTGATATATTTGATACGCATTCAACAAATGAACTCTGAAAATC
Found at i:22353852 original size:20 final size:20
Alignment explanation
Indices: 22353820--22353875 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
22353810 CCCTTTTATT
22353820 CTTTTCT-TCCCTTTCTTCTC
1 CTTTTCTCT-CCTTTCTTCTC
*
22353840 CTTTTCTCTCCTTT-TTTTC
1 CTTTTCTCTCCTTTCTTCTC
* *
22353859 ATTTT-TCTTCTTTCTTC
1 CTTTTCTCTCCTTTCTTC
22353876 CCAACCTCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.23
19 10 0.33
20 12 0.40
21 1 0.03
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (20 bp):
CTTTTCTCTCCTTTCTTCTC
Found at i:22353853 original size:38 final size:36
Alignment explanation
Indices: 22353801--22353875 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 36
22353791 TTTGTTATTT
*
22353801 TCCTTTTTTCCCTTTTATTC-TTTTCTTCCCTTTCTTC
1 TCCTTTTCTCCCTTTTATTCATTTTCTT--CTTTCTTC
*
22353838 TCCTTTTCTCTCCTTTTTTTCATTTTTCTTCTTTCTTC
1 TCCTTTTCTC-CCTTTTATTCA-TTTTCTTCTTTCTTC
22353876 CCAACCTCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 9 0.27
38 17 0.52
40 7 0.21
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (36 bp):
TCCTTTTCTCCCTTTTATTCATTTTCTTCTTTCTTC
Found at i:22355770 original size:295 final size:297
Alignment explanation
Indices: 22355411--22355969 Score: 917
Period size: 295 Copynumber: 1.9 Consensus size: 297
22355401 ACATGAGATG
*
22355411 CATTTTTCTCAAGTTTCTACAAAATCAAACTAAAACCTACAAAGTAAACTTGGAGAACAAGCTTC
1 CATTTTTCTCAAGTTTCTACAAAATCAAACTAAAACCTACAAAGTAAACCTGGAGAACAAGCTTC
* *
22355476 AAATCTAGACAAACCACTTGGAGCATCAAAATCAAGCAAATACCATCCAAGTCACTTCCCAATTT
66 AAATCTAGACAAACCACTTGAAGCATCAAAATCAAGCAAATACCATCCAACTCACTTCCCAATTT
* *
22355541 CCATAAGACA-CA-AGCACAAATTAAATCAGTACAGACCTATTTGACTAAAAACGAATGAATATC
131 CCATAAGACACCACA-CACAAATTAAATCAGTACAAACCCATTTGACTAAAAACGAATGAATATC
*
22355604 TTTAGAAGTAA-TTAAATTTTAAATCCAACCAAAAAATGCTTCAATTCCAAACTAAACAACTAGA
195 TTTAGAAGTAATTTAAATTTTAAATCCAACCAAAAAAAGCTTCAATTCCAAACTAAACAACTAGA
22355668 ACATTTAAATAACCATAGAGTACATAGTACACAAGAAA
260 ACATTTAAATAACCATAGAGTACATAGTACACAAGAAA
22355706 CATTTTTCTCAAGTTTCTACAAAATCAAACTAAAACCTACAAAGTAAACCTGGAGAACAAGCTTC
1 CATTTTTCTCAAGTTTCTACAAAATCAAACTAAAACCTACAAAGTAAACCTGGAGAACAAGCTTC
* * * *
22355771 AAGTCTAGACAAATCATTTGAAGCATCAAAATCAAGCAAATACCATCCAACTCACTTTCCAATTT
66 AAATCTAGACAAACCACTTGAAGCATCAAAATCAAGCAAATACCATCCAACTCACTTCCCAATTT
* * *
22355836 CTATAAGACACGCACACACAAATTAAATCAGTACAAACCCATTTGACTAAACATGAATGAATATC
131 CCATAAGACAC-CACACACAAATTAAATCAGTACAAACCCATTTGACTAAAAACGAATGAATATC
* * * * *
22355901 TTTAGGAGTAATTTAAATTTTAAATCTAATCAAAAAAAGCTTCAATTCCAATCTAAACACCTAGA
195 TTTAGAAGTAATTTAAATTTTAAATCCAACCAAAAAAAGCTTCAATTCCAAACTAAACAACTAGA
22355966 ACAT
260 ACAT
22355970 CAAAATCATT
Statistics
Matches: 242, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
295 132 0.55
297 57 0.24
298 53 0.22
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.25
Consensus pattern (297 bp):
CATTTTTCTCAAGTTTCTACAAAATCAAACTAAAACCTACAAAGTAAACCTGGAGAACAAGCTTC
AAATCTAGACAAACCACTTGAAGCATCAAAATCAAGCAAATACCATCCAACTCACTTCCCAATTT
CCATAAGACACCACACACAAATTAAATCAGTACAAACCCATTTGACTAAAAACGAATGAATATCT
TTAGAAGTAATTTAAATTTTAAATCCAACCAAAAAAAGCTTCAATTCCAAACTAAACAACTAGAA
CATTTAAATAACCATAGAGTACATAGTACACAAGAAA
Found at i:22365285 original size:71 final size:71
Alignment explanation
Indices: 22365169--22365323 Score: 310
Period size: 71 Copynumber: 2.2 Consensus size: 71
22365159 TAATGAAGAG
22365169 TTAATCAGTTAAGAGGGAAAGAGCAAATAATGAACAAAAATAGAACCTTAGTAACTAATTATCGC
1 TTAATCAGTTAAGAGGGAAAGAGCAAATAATGAACAAAAATAGAACCTTAGTAACTAATTATCGC
22365234 GTGACC
66 GTGACC
22365240 TTAATCAGTTAAGAGGGAAAGAGCAAATAATGAACAAAAATAGAACCTTAGTAACTAATTATCGC
1 TTAATCAGTTAAGAGGGAAAGAGCAAATAATGAACAAAAATAGAACCTTAGTAACTAATTATCGC
22365305 GTGACC
66 GTGACC
22365311 TTAATCAGTTAAG
1 TTAATCAGTTAAG
22365324 GCATGGTTGT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 84 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (71 bp):
TTAATCAGTTAAGAGGGAAAGAGCAAATAATGAACAAAAATAGAACCTTAGTAACTAATTATCGC
GTGACC
Found at i:22371952 original size:23 final size:23
Alignment explanation
Indices: 22371903--22371953 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
22371893 GTCTGCTATG
* * *
22371903 TTTCCGATTTCTCTCTCTCGCGT
1 TTTCAGATTTCTCTCTCTCACGC
* *
22371926 TTTCAGATTTCTCTTTCTTACGC
1 TTTCAGATTTCTCTCTCTCACGC
22371949 TTTCA
1 TTTCA
22371954 AGACACCAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.10, C:0.29, G:0.10, T:0.51
Consensus pattern (23 bp):
TTTCAGATTTCTCTCTCTCACGC
Found at i:22372392 original size:31 final size:30
Alignment explanation
Indices: 22372339--22372490 Score: 139
Period size: 31 Copynumber: 5.4 Consensus size: 30
22372329 TTGAATATGT
22372339 CGTGTAACAACAATA-TTTTTTCAACATGG
1 CGTGTAACAACAATACTTTTTTCAACATGG
*
22372368 CGTGTAACAACAATATTTTTTTTCAACATGG
1 CGTGTAACAACAATA-CTTTTTTCAACATGG
*
22372399 CGTGTAATAAC----CTTTTTT-AATCATGG
1 CGTGTAACAACAATACTTTTTTCAA-CATGG
* *
22372425 CTTGT---AAC-ATGCTTTTTT--ACATGG
1 CGTGTAACAACAATACTTTTTTCAACATGG
* *
22372449 CGTGTAACAATAATATTTTTTTCCAACATGG
1 CGTGTAACAACAATACTTTTTT-CAACATGG
22372480 CGTGTAACAAC
1 CGTGTAACAAC
22372491 CTAACCATGG
Statistics
Matches: 102, Mismatches: 8, Indels: 24
0.76 0.06 0.18
Matches are distributed among these distances:
23 3 0.03
24 9 0.09
25 3 0.03
26 22 0.22
27 2 0.02
28 8 0.08
29 15 0.15
31 40 0.39
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (30 bp):
CGTGTAACAACAATACTTTTTTCAACATGG
Found at i:22372423 original size:26 final size:25
Alignment explanation
Indices: 22372385--22372458 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
22372375 CAACAATATT
*
22372385 TTTTTTCAACATGGCGTGTAATAACC
1 TTTTTT-AACATGGCGTGTAACAACC
* **
22372411 TTTTTTAATCATGGCTTGTAACATGC
1 TTTTTTAA-CATGGCGTGTAACAACC
22372437 TTTTTT-ACATGGCGTGTAACAA
1 TTTTTTAACATGGCGTGTAACAA
22372459 TAATATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 13 0.32
25 3 0.07
26 25 0.61
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (25 bp):
TTTTTTAACATGGCGTGTAACAACC
Found at i:22372528 original size:45 final size:45
Alignment explanation
Indices: 22372476--22372592 Score: 137
Period size: 45 Copynumber: 2.6 Consensus size: 45
22372466 TTTTTCCAAC
*
22372476 ATGGCGTGTAACAACCTAACCATGGCTCATCACATATTTTTGTAT
1 ATGGCGTGTAACAACCTAACCATGGCTCATCACATATTTTTGTAA
* * * **
22372521 ATGGCGTGTAACAAGCTAACTATAGCTTGTCACATATTTTTGTAA
1 ATGGCGTGTAACAACCTAACCATGGCTCATCACATATTTTTGTAA
* * *
22372566 ATAGCGTAT-ACCACCATAACCATGGCT
1 ATGGCGTGTAACAACC-TAACCATGGCT
22372593 TGTCACAGGT
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 4 0.07
45 55 0.93
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (45 bp):
ATGGCGTGTAACAACCTAACCATGGCTCATCACATATTTTTGTAA
Found at i:22372689 original size:45 final size:45
Alignment explanation
Indices: 22372640--22372729 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
22372630 TACACATAGT
* *
22372640 GTGTAACACGCTAACCATGGCTTGTCAC-AGATTTTTGTACATGAC
1 GTGTAACAAGCTAACCATAGCTTGTCACAAG-TTTTTGTACATGAC
*
22372685 GTGTAACAAGTTAACCATAGCTTGTCACAAGTTTTTGTACATGAC
1 GTGTAACAAGCTAACCATAGCTTGTCACAAGTTTTTGTACATGAC
22372730 TTGTCACATA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 39 0.95
46 2 0.05
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (45 bp):
GTGTAACAAGCTAACCATAGCTTGTCACAAGTTTTTGTACATGAC
Found at i:22372708 original size:114 final size:113
Alignment explanation
Indices: 22372526--22372859 Score: 371
Period size: 114 Copynumber: 2.9 Consensus size: 113
22372516 TGTATATGGC
* * * * * **
22372526 GTGTAACAAGCTAACTATAGCTTGTCACATATTTTTGTAAATAGCGTATACCACCATAACCATGG
1 GTGTAACAAGCTAACAATGGCTTGTCACATATTTTTGTACATA-CGTGTAACAAGATAACCATGG
* * *
22372591 CTTGTCACAGGTTTTTATACATAACGTGTCACATATTTTTACACATAGT
65 CTTGTCACAAGTTTTTGTACATGACGTGTCACATATTTTTACACATAGT
* * * * *
22372640 GTGTAACACGCTAACCATGGCTTGTCACAGATTTTTGTACATGACGTGTAACAAGTTAACCATAG
1 GTGTAACAAGCTAACAATGGCTTGTCACATATTTTTGTACAT-ACGTGTAACAAGATAACCATGG
* ** *
22372705 CTTGTCACAAGTTTTTGTACATGACTTGTCACATATTTTTGTACATGGT
65 CTTGTCACAAGTTTTTGTACATGACGTGTCACATATTTTTACACATAGT
* * * * * * * *
22372754 ATGTAATAAGTTAACAATGACTTGTCACATATTTTTGTACATAATGTGTAACATGCTAATCATGG
1 GTGTAACAAGCTAACAATGGCTTGTCACATATTTTTGTACAT-ACGTGTAACAAGATAACCATGG
* *
22372819 CTTGTCACAAGTTTTTGTACATGATGTGTCATATATATTTT
65 CTTGTCACAAGTTTTTGTACATGACGTGTCACATAT-TTTT
22372860 TGTATATAAC
Statistics
Matches: 184, Mismatches: 34, Indels: 3
0.83 0.15 0.01
Matches are distributed among these distances:
114 179 0.97
115 5 0.03
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (113 bp):
GTGTAACAAGCTAACAATGGCTTGTCACATATTTTTGTACATACGTGTAACAAGATAACCATGGC
TTGTCACAAGTTTTTGTACATGACGTGTCACATATTTTTACACATAGT
Found at i:22372733 original size:69 final size:69
Alignment explanation
Indices: 22372655--22372795 Score: 187
Period size: 69 Copynumber: 2.0 Consensus size: 69
22372645 ACACGCTAAC
* * *
22372655 CATGGCTTGTCACAGATTTTTGTACATGACGTGTAACAAGTTAACCAT-AGCTTGTCACA-AGTT
1 CATGACTTGTCACAGATTTTTGTACATGACATGTAACAAGTTAACAATGA-CTTGTCACATA-TT
22372718 TTTGTA
64 TTTGTA
* ** *
22372724 CATGACTTGTCACATATTTTTGTACATGGTATGTAATAAGTTAACAATGACTTGTCACATATTTT
1 CATGACTTGTCACAGATTTTTGTACATGACATGTAACAAGTTAACAATGACTTGTCACATATTTT
22372789 TGTA
66 TGTA
22372793 CAT
1 CAT
22372796 AATGTGTAAC
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
69 61 0.97
70 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (69 bp):
CATGACTTGTCACAGATTTTTGTACATGACATGTAACAAGTTAACAATGACTTGTCACATATTTT
TGTA
Found at i:22372735 original size:24 final size:24
Alignment explanation
Indices: 22372705--22372751 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
22372695 TTAACCATAG
22372705 CTTGTCACA-AGTTTTTGTACATGA
1 CTTGTCACATA-TTTTTGTACATGA
22372729 CTTGTCACATATTTTTGTACATG
1 CTTGTCACATATTTTTGTACATG
22372752 GTATGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (24 bp):
CTTGTCACATATTTTTGTACATGA
Found at i:22372804 original size:45 final size:45
Alignment explanation
Indices: 22372724--22372847 Score: 153
Period size: 45 Copynumber: 2.8 Consensus size: 45
22372714 AGTTTTTGTA
* * * *
22372724 CATGACTTGTCACATATTTTTGTACATGGTATGTAATAAGTTAA-
1 CATGACTTGTCACATATTTTTGTACATGATGTGTAACAAGCTAAT
* *
22372768 CAATGACTTGTCACATATTTTTGTACATAATGTGTAACATGCTAAT
1 C-ATGACTTGTCACATATTTTTGTACATGATGTGTAACAAGCTAAT
*
22372814 CATGGCTTGTCACA-AGTTTTTGTACATGATGTGT
1 CATGACTTGTCACATA-TTTTTGTACATGATGTGT
22372848 CATATATATT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
44 2 0.03
45 66 0.96
46 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (45 bp):
CATGACTTGTCACATATTTTTGTACATGATGTGTAACAAGCTAAT
Found at i:22372849 original size:69 final size:69
Alignment explanation
Indices: 22372776--22372987 Score: 250
Period size: 69 Copynumber: 3.0 Consensus size: 69
22372766 AACAATGACT
* *
22372776 TGTCACATATTTTTGTACATAATGTGTAACATGCTAATCATGGCTTGTCACAAGTTTTTGTACAT
1 TGTCACATATTTTTGTACATAACGTGTAACATGCTAATCATGACTTGTCACAAGTTTTTGTACAT
*
22372841 GATG
66 GATA
* * * * *
22372845 TGTCATATATATTTTTGTATATAACGTATAAC-TCACTAA-CTATGACTTATCACAAGTTTTTGT
1 TGTC--ACATATTTTTGTACATAACGTGTAACAT-GCTAATC-ATGACTTGTCACAAGTTTTTGT
22372908 ACATGATA
62 ACATGATA
* * *
22372916 TGTCACATATTTTTGTACATAGCGTGTAACACGCTAATAATGACTTGTCAC-AGATTTTTGTACA
1 TGTCACATATTTTTGTACATAACGTGTAACATGCTAATCATGACTTGTCACAAG-TTTTTGTACA
*
22372980 TGACA
65 TGATA
22372985 TGT
1 TGT
22372988 AATATCATAG
Statistics
Matches: 119, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
68 2 0.02
69 58 0.49
70 2 0.02
71 57 0.48
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (69 bp):
TGTCACATATTTTTGTACATAACGTGTAACATGCTAATCATGACTTGTCACAAGTTTTTGTACAT
GATA
Found at i:22373991 original size:21 final size:22
Alignment explanation
Indices: 22373948--22373992 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
22373938 GATATAGAGA
*
22373948 TTGTTTTGTGGTTCTAAATTCT
1 TTGTTTAGTGGTTCTAAATTCT
*
22373970 TTGTTTAGTGGTTCT-CATTCT
1 TTGTTTAGTGGTTCTAAATTCT
22373991 TT
1 TT
22373993 TTTTGAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.60
Consensus pattern (22 bp):
TTGTTTAGTGGTTCTAAATTCT
Found at i:22378905 original size:15 final size:15
Alignment explanation
Indices: 22378887--22378938 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
22378877 CAAATCCACC
22378887 ACCACCAGAAGCCAG
1 ACCACCAGAAGCCAG
* *
22378902 ACCACCA-AATCCAAC
1 ACCACCAGAAGCC-AG
22378917 ACCACCAGAAGCCAG
1 ACCACCAGAAGCCAG
22378932 ACCACCA
1 ACCACCA
22378939 AATCCCCCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 4 0.13
15 23 0.74
16 4 0.13
ACGTcount: A:0.42, C:0.44, G:0.12, T:0.02
Consensus pattern (15 bp):
ACCACCAGAAGCCAG
Found at i:22378911 original size:30 final size:30
Alignment explanation
Indices: 22378875--22378978 Score: 145
Period size: 30 Copynumber: 3.5 Consensus size: 30
22378865 CTGAACCCAG
22378875 ACCAAATCCACCACCACCAGAAGCCAGACC
1 ACCAAATCCACCACCACCAGAAGCCAGACC
*
22378905 ACCAAATCCAACACCACCAGAAGCCAGACC
1 ACCAAATCCACCACCACCAGAAGCCAGACC
* * * *
22378935 ACCAAATCCCCCACCACCTGAAGCCAAAGC
1 ACCAAATCCACCACCACCAGAAGCCAGACC
* *
22378965 AGCAAAGCCACCAC
1 ACCAAATCCACCAC
22378979 TACTAGAGGC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.40, C:0.45, G:0.11, T:0.04
Consensus pattern (30 bp):
ACCAAATCCACCACCACCAGAAGCCAGACC
Found at i:22378950 original size:15 final size:15
Alignment explanation
Indices: 22378875--22378952 Score: 54
Period size: 15 Copynumber: 5.2 Consensus size: 15
22378865 CTGAACCCAG
22378875 ACCAAAT-CCACCACC
1 ACCAAATCCCA-CACC
* *
22378890 ACCAGAA-GCCAGACC
1 ACCA-AATCCCACACC
*
22378905 ACCAAATCCAACACC
1 ACCAAATCCCACACC
* *
22378920 ACCAGAA-GCCAGACC
1 ACCA-AATCCCACACC
*
22378935 ACCAAATCCCCCACC
1 ACCAAATCCCACACC
22378950 ACC
1 ACC
22378953 TGAAGCCAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
14 4 0.08
15 37 0.77
16 7 0.15
ACGTcount: A:0.40, C:0.49, G:0.08, T:0.04
Consensus pattern (15 bp):
ACCAAATCCCACACC
Found at i:22383599 original size:151 final size:151
Alignment explanation
Indices: 22383325--22383626 Score: 480
Period size: 151 Copynumber: 2.0 Consensus size: 151
22383315 CAGCTTACAA
* *
22383325 AGCCATTGTGGTAAAGTACAGAAAAATAGTTCGTCACCACACTACAAATGTCAGTAAACTCAATC
1 AGCCATTGTGGTAAAGCACAGAAAAATAGTTCGTCACAACACTACAAATGTCAGTAAACTCAATC
* * *
22383390 CAATCACCTCTGCTGGCCAGTAGGATAACTCTAATTAAACATTGTCTAATGCATATTGATTACTT
66 CAATCACCTATGCTGGCCAGTAAGATAACTCTAATTAAACATTATCTAATGCATATTGATTACTT
22383455 TTATTATTTTGAGCCTTATTG
131 TTATTATTTTGAGCCTTATTG
* * * *
22383476 AGCCATTGTGGTAAAGCACAGCAACATAGTTCGTCACAACAGTACAAATGTCAGTAACCTCAATC
1 AGCCATTGTGGTAAAGCACAGAAAAATAGTTCGTCACAACACTACAAATGTCAGTAAACTCAATC
* * *
22383541 CAATCACCTATGGTGG-CTGTTAAGATATCTCTAATTAAACATTATCTAATGCATATTGATTACT
66 CAATCACCTATGCTGGCCAG-TAAGATAACTCTAATTAAACATTATCTAATGCATATTGATTACT
22383605 TTTATTATTTTGAGCCTTATTG
130 TTTATTATTTTGAGCCTTATTG
22383627 TGGGTGGGGG
Statistics
Matches: 138, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
150 2 0.01
151 136 0.99
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (151 bp):
AGCCATTGTGGTAAAGCACAGAAAAATAGTTCGTCACAACACTACAAATGTCAGTAAACTCAATC
CAATCACCTATGCTGGCCAGTAAGATAACTCTAATTAAACATTATCTAATGCATATTGATTACTT
TTATTATTTTGAGCCTTATTG
Found at i:22387879 original size:21 final size:20
Alignment explanation
Indices: 22387835--22387891 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
22387825 CTCACCAGCT
*
22387835 GGAAAGAGAAAAG-AAGAAAA
1 GGAAAGA-AAAAGAAAAAAAA
22387855 GGAAAGAAAAAGAAAAAAGAA
1 GGAAAGAAAAAGAAAAAA-AA
*
22387876 GGAAGGAAAAAGAAAA
1 GGAAAGAAAAAGAAAA
22387892 TCAGGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 11 0.33
21 17 0.52
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (20 bp):
GGAAAGAAAAAGAAAAAAAA
Found at i:22387891 original size:26 final size:26
Alignment explanation
Indices: 22387837--22387891 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
22387827 CACCAGCTGG
* *
22387837 AAAGAGAAAAGAAGAAAAGGAAAGAA
1 AAAGAAAAAAGAAGAAAAGGAAAAAA
*
22387863 AAAGAAAAAAGAAG-GAAGGAAAAAGA
1 AAAGAAAAAAGAAGAAAAGGAAAAA-A
22387889 AAA
1 AAA
22387892 TCAGGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (26 bp):
AAAGAAAAAAGAAGAAAAGGAAAAAA
Found at i:22393947 original size:204 final size:200
Alignment explanation
Indices: 22393586--22393964 Score: 485
Period size: 204 Copynumber: 1.9 Consensus size: 200
22393576 CTGAATTAAG
* *
22393586 ATAAGAGCATTCATGCACAAGCTCAGCAAATGTGGGACAAATTCATTAAATTAGCCCATGAGACC
1 ATAAGAGCATCCATGCACAAGCTCAGCAAATGTAGGACAAATTCATTAAATTAGCCCATGAGACC
* *
22393651 TTTTGGTGAGTTGGTTTAAAGAAAGAAAGCATTTACGGTTTATATTAGAAGAAGAACAGGTTTAA
66 TTTTGCTGAGTTGGTTTAAAGAAAGAAAGCATTTACGGTTTATATTAGAAGAAGAACAGATTTAA
* * * *
22393716 ATATTAAACAAGATGAGGAACTGATCCAGGTTCTGGCATGTTCAAGAGGTTGTCAGCAGTTAATA
131 ATATCAAACAAGAAGAGCAAATGATCCA-G---TGGCATGTTCAAGAGGTTGTCAGCAGTTAATA
22393781 TGGTGCATA
192 TGGTGCATA
* *
22393790 ATAAGAGCATCCATGCACAAGCTCAGCAAATGTAGGACAAATTCATTAAATTAGCTCATTAGACC
1 ATAAGAGCATCCATGCACAAGCTCAGCAAATGTAGGACAAATTCATTAAATTAGCCCATGAGACC
* ** ** * * * * *
22393855 TTTTGCTGTGTTGGTTTAGGGAAATG-GGGGATTTATGGTTTGA-ATTAGATGGAGAATAGATTT
66 TTTTGCTGAGTTGGTTTAAAGAAA-GAAAGCATTTACGGTTT-ATATTAGAAGAAGAACAGATTT
*
22393918 AAATATCAAACATGAAGA-CAATATGATCCAGTGGCATGTTCAAGAGG
129 AAATATCAAACAAGAAGAGCAA-ATGATCCAGTGGCATGTTCAAGAGG
22393965 CCGGCAGCTG
Statistics
Matches: 151, Mismatches: 21, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
200 16 0.11
203 3 0.02
204 130 0.86
205 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.28
Consensus pattern (200 bp):
ATAAGAGCATCCATGCACAAGCTCAGCAAATGTAGGACAAATTCATTAAATTAGCCCATGAGACC
TTTTGCTGAGTTGGTTTAAAGAAAGAAAGCATTTACGGTTTATATTAGAAGAAGAACAGATTTAA
ATATCAAACAAGAAGAGCAAATGATCCAGTGGCATGTTCAAGAGGTTGTCAGCAGTTAATATGGT
GCATA
Found at i:22396908 original size:30 final size:29
Alignment explanation
Indices: 22396839--22396932 Score: 118
Period size: 30 Copynumber: 3.2 Consensus size: 29
22396829 AAAAAATTTT
**
22396839 AAATAAATTTTTATATTTTTA-TTACGTC
1 AAATAAATTTTTATATTTTTATTTAAATC
*
22396867 TAATCAAATTTTTATATTTTTATTTTAAATC
1 AAAT-AAATTTTTATATTTTTA-TTTAAATC
*
22396898 AAATAAATTTTTATATTTTTAATTTAATTC
1 AAATAAATTTTTATATTTTT-ATTTAAATC
22396928 AAATA
1 AAATA
22396933 TACTCTTATA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
28 3 0.05
29 17 0.30
30 28 0.49
31 9 0.16
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.54
Consensus pattern (29 bp):
AAATAAATTTTTATATTTTTATTTAAATC
Found at i:22396942 original size:30 final size:30
Alignment explanation
Indices: 22396878--22396942 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
22396868 AATCAAATTT
* * *
22396878 TTATATTTTTATTTTAAATCAAATAAATTT
1 TTATATTTTTAATTTAAATCAAATAAACTC
* *
22396908 TTATATTTTTAATTTAATTCAAATATACTC
1 TTATATTTTTAATTTAAATCAAATAAACTC
22396938 TTATA
1 TTATA
22396943 ACTAATTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (30 bp):
TTATATTTTTAATTTAAATCAAATAAACTC
Found at i:22397078 original size:33 final size:33
Alignment explanation
Indices: 22397000--22397078 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
22396990 AAACACTAAC
22397000 ATAACATATTAATATATCATAATTAATAATAAT
1 ATAACATATTAATATATCATAATTAATAATAAT
* * * * * *
22397033 GTGATATGTTAATATATTATAATTAATGATAAT
1 ATAACATATTAATATATCATAATTAATAATAAT
22397066 ATAACATATTAAT
1 ATAACATATTAAT
22397079 GTGGTACAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (33 bp):
ATAACATATTAATATATCATAATTAATAATAAT
Found at i:22397240 original size:21 final size:21
Alignment explanation
Indices: 22397199--22397240 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
22397189 ATCATCAATT
*
22397199 ATAAAAACTTATTTGATCCAAA
1 ATAAAAAC-TATTTGACCCAAA
22397221 ATAAAAA-TATTATGACCCAA
1 ATAAAAACTATT-TGACCCAA
22397241 TTAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (21 bp):
ATAAAAACTATTTGACCCAAA
Found at i:22397747 original size:33 final size:33
Alignment explanation
Indices: 22397710--22397774 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
22397700 ACCGTATTAG
* * *
22397710 CATGTTACATTATCATCAATTATAATATGTTAA
1 CATGTCACATCATCATCAATTATAACATGTTAA
* *
22397743 CATGTCATATCATTATCAATTATAACATGTTA
1 CATGTCACATCATCATCAATTATAACATGTTA
22397775 GTATGCACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (33 bp):
CATGTCACATCATCATCAATTATAACATGTTAA
Found at i:22400703 original size:13 final size:13
Alignment explanation
Indices: 22400685--22400709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22400675 TTCCAGAAAA
22400685 TTTATAAAATCAT
1 TTTATAAAATCAT
22400698 TTTATAAAATCA
1 TTTATAAAATCA
22400710 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:22404063 original size:19 final size:20
Alignment explanation
Indices: 22404041--22404081 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
22404031 ACAAAAGGAA
22404041 ATTTTTA-GAATAAAATAAT
1 ATTTTTATGAATAAAATAAT
*
22404060 A-TTTTATTAATAAAATAAT
1 ATTTTTATGAATAAAATAAT
22404079 ATT
1 ATT
22404082 AAAATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 5 0.26
19 13 0.68
20 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
ATTTTTATGAATAAAATAAT
Found at i:22407199 original size:42 final size:42
Alignment explanation
Indices: 22407140--22407264 Score: 178
Period size: 42 Copynumber: 3.0 Consensus size: 42
22407130 TGTTGATGTG
* * *
22407140 GACCCGGTTATGTGCGAGTAGGAGTGCACATAAGCCGTTGTT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
*
22407182 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCTGTTGCT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
** * *
22407224 GACCTAGCTATGTGCGAGTGGGAGTGCGCATAAGTCGTTGC
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
22407265 ATATGAGATG
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.20, C:0.20, G:0.35, T:0.25
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
Found at i:22411341 original size:28 final size:29
Alignment explanation
Indices: 22411300--22411359 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
22411290 GTCTATGGGC
*
22411300 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
22411328 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
22411358 AA
1 AA
22411360 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:22414257 original size:26 final size:26
Alignment explanation
Indices: 22414221--22414274 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
22414211 AGTACAGCAG
22414221 TTCTTTGCATCAAACACAACAATTCT
1 TTCTTTGCATCAAACACAACAATTCT
* *
22414247 TTCTTTTCATCAAACACAATAATTCT
1 TTCTTTGCATCAAACACAACAATTCT
22414273 TT
1 TT
22414275 ATTCTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (26 bp):
TTCTTTGCATCAAACACAACAATTCT
Found at i:22416506 original size:49 final size:49
Alignment explanation
Indices: 22416447--22416544 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
22416437 TACATCATCA
*
22416447 AAAATATATTCAATTTAGCTTAATTCAAGC-TCATGCACATCAAGCATTC
1 AAAACATATTCAATTTAGCTTAATTCAAGCTTC-TGCACATCAAGCATTC
*
22416496 AAAACATATTCAATTTAGCTTAATTCAAGCTTCTGCACATTAAGCATTC
1 AAAACATATTCAATTTAGCTTAATTCAAGCTTCTGCACATCAAGCATTC
22416545 CTAGTTCTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 44 0.96
50 2 0.04
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (49 bp):
AAAACATATTCAATTTAGCTTAATTCAAGCTTCTGCACATCAAGCATTC
Found at i:22418078 original size:29 final size:28
Alignment explanation
Indices: 22418031--22418184 Score: 134
Period size: 29 Copynumber: 5.3 Consensus size: 28
22418021 TGACAGCTTT
*
22418031 AACATGTTTGTCTTAATTTAGATAAGAA
1 AACATATTTGTCTTAATTTAGATAAGAA
22418059 AACATATTTGATCTTAATTTAGATAAGAA
1 AACATATTTG-TCTTAATTTAGATAAGAA
* * *
22418088 AATATGTTTATCTTAATTTAAGATGACA-AA
1 AACATATTTGTCTTAATTT-AGAT-A-AGAA
* * *
22418118 AAAATATTTTTTGTCTTAATCTAGACAAG-A
1 AACATA---TTTGTCTTAATTTAGATAAGAA
* *
22418148 AACATATTTGTCTCAATTTAGACAAGATA
1 AACATATTTGTCTTAATTTAGATAAGA-A
22418177 AA-ATATTT
1 AACATATTT
22418185 TTATCTTAAT
Statistics
Matches: 104, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
27 18 0.17
28 24 0.23
29 32 0.31
30 14 0.13
31 2 0.02
32 3 0.03
33 11 0.11
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.39
Consensus pattern (28 bp):
AACATATTTGTCTTAATTTAGATAAGAA
Found at i:22418180 original size:90 final size:90
Alignment explanation
Indices: 22418037--22418201 Score: 244
Period size: 90 Copynumber: 1.8 Consensus size: 90
22418027 CTTTAACATG
* * * *
22418037 TTTGTCTTAATTTAGATAAGAAAACATATTTGATCTTAATTTAGATAAGAAAATATGTTTATCTT
1 TTTGTCTTAATCTAGACAAGAAAACATATTTGATCTCAATTTAGACAAGAAAATATGTTTATCTT
*
22418102 AATTTAAGATGACAAAAAAATATTT
66 AATTAAAGATGACAAAAAAATATTT
*
22418127 TTTGTCTTAATCTAGACAAG-AAACATATTTG-TCTCAATTTAGACAAGATAAAATATTTTTATC
1 TTTGTCTTAATCTAGACAAGAAAACATATTTGATCTCAATTTAGACAAG--AAAATATGTTTATC
22418190 TTAATTAAAGAT
64 TTAATTAAAGAT
22418202 AAGAGTTGTT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
88 14 0.21
89 11 0.16
90 42 0.63
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.41
Consensus pattern (90 bp):
TTTGTCTTAATCTAGACAAGAAAACATATTTGATCTCAATTTAGACAAGAAAATATGTTTATCTT
AATTAAAGATGACAAAAAAATATTT
Found at i:22418368 original size:17 final size:17
Alignment explanation
Indices: 22418346--22418378 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22418336 ATAATAATAA
22418346 AATAAG-AGCTATTATTC
1 AATAAGAAG-TATTATTC
22418363 AATAAGAAGTATTATT
1 AATAAGAAGTATTATT
22418379 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (17 bp):
AATAAGAAGTATTATTC
Found at i:22429402 original size:27 final size:27
Alignment explanation
Indices: 22429351--22429402 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
22429341 ATGTCCTGAT
*
22429351 GGTGGAAAATTACAATTTTGCCCCTAG
1 GGTGGAAAATTACAATTTTGACCCTAG
*
22429378 GGTGGCAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
22429403 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTAG
Found at i:22429473 original size:20 final size:20
Alignment explanation
Indices: 22429448--22429493 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
22429438 CTTCTAAACC
*
22429448 TCAAATCCTACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
22429468 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
22429488 TCAAAT
1 TCAAAT
22429494 GGGGTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:22432382 original size:74 final size:74
Alignment explanation
Indices: 22432271--22432430 Score: 196
Period size: 74 Copynumber: 2.2 Consensus size: 74
22432261 TACAAGCAAA
* *
22432271 TCTAACTGATTACAACTTTTCTGCCTTGCACTGTCTTGTTATTGTATTCTCTACTCTAACCAATT
1 TCTAACTGATTACAACTTTTCTGCCTTGCACTATCTTGCTATTGTATTCTCTACTCTAACCAATT
*
22432336 ACATGAAGC
66 ACAAGAAGC
* * * * * * ***
22432345 TCTAATTGATTAC-AGTTTCTCTGTCTTTCACTATCTTGCTATTGTGTTCTCTACTTTAATTGAT
1 TCTAACTGATTACAACTTT-TCTGCCTTGCACTATCTTGCTATTGTATTCTCTACTCTAACCAAT
22432409 TACAAGAAGC
65 TACAAGAAGC
22432419 TCTAACTGATTA
1 TCTAACTGATTA
22432431 AGAGATCTCT
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
73 4 0.06
74 68 0.94
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.43
Consensus pattern (74 bp):
TCTAACTGATTACAACTTTTCTGCCTTGCACTATCTTGCTATTGTATTCTCTACTCTAACCAATT
ACAAGAAGC
Found at i:22433911 original size:20 final size:20
Alignment explanation
Indices: 22433886--22433931 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
22433876 TTTTGACCCC
22433886 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
22433906 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
22433926 ATTTGA
1 ATTTGA
22433932 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:22434007 original size:28 final size:27
Alignment explanation
Indices: 22433976--22434028 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
22433966 TTTGGAGTAT
*
22433976 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
22434004 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
22434029 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:22434034 original size:28 final size:28
Alignment explanation
Indices: 22433976--22434034 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
22433966 TTTGGAGTAT
* *
22433976 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
22434004 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
22434032 AGG
1 AGG
22434035 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:22439037 original size:21 final size:22
Alignment explanation
Indices: 22438988--22439039 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
22438978 ATTTTAAAAA
* *
22438988 ATTATTAAAAATATTAATAAATT
1 ATTATTTAAAATATTAAT-AATG
*
22439011 ATTATTTAAAATTTTAAT-ATG
1 ATTATTTAAAATATTAATAATG
22439032 ATTATTTA
1 ATTATTTA
22439040 TTTTTATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 10 0.38
23 16 0.62
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTATTTAAAATATTAATAATG
Done.