Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 127 of 255
Found at i:40551469 original size:64 final size:64
Alignment explanation
Indices: 40551389--40551572 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
40551379 AGACATTATG
* *
40551389 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
40551453 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
40551518 AA
63 AA
* * * *
40551520 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
40551573 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:40554248 original size:15 final size:17
Alignment explanation
Indices: 40554218--40554249 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
40554208 ATAATACTTG
40554218 TGAATGTGAGTTTGGTA
1 TGAATGTGAGTTTGGTA
40554235 TGAAT-TGA-TTTGGTA
1 TGAATGTGAGTTTGGTA
40554250 AATTATGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (17 bp):
TGAATGTGAGTTTGGTA
Found at i:40557365 original size:29 final size:29
Alignment explanation
Indices: 40557332--40557389 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
40557322 TGAGGTGAGC
*
40557332 TTTATGTTTAAACCATATGAACTTACTAA
1 TTTATGTTTAAAACATATGAACTTACTAA
40557361 TTTATGTTTAAAACATATGAACTTACTAA
1 TTTATGTTTAAAACATATGAACTTACTAA
40557390 GCATATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (29 bp):
TTTATGTTTAAAACATATGAACTTACTAA
Found at i:40560916 original size:14 final size:14
Alignment explanation
Indices: 40560892--40560924 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
40560882 ATAATTACTC
40560892 TATTT-CTAATTTA
1 TATTTACTAATTTA
40560905 TATTTACTAATTTA
1 TATTTACTAATTTA
40560919 TATTTA
1 TATTTA
40560925 TTTTTTCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTTACTAATTTA
Found at i:40564052 original size:19 final size:18
Alignment explanation
Indices: 40563990--40564050 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
40563980 GCCCTCTTAC
40563990 TATATTATATAATGT-TATA
1 TATATTATAT-A-GTATATA
40564009 TCATATTATATAGTATATA
1 T-ATATTATATAGTATATA
*
40564028 CTATATTA-ATAGTTTATA
1 -TATATTATATAGTATATA
40564046 TATAT
1 TATAT
40564051 ATGGATCAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 5 0.13
18 11 0.29
19 12 0.32
20 10 0.26
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TATATTATATAGTATATA
Found at i:40564396 original size:241 final size:238
Alignment explanation
Indices: 40563889--40564355 Score: 635
Period size: 241 Copynumber: 2.0 Consensus size: 238
40563879 GTAGTATGTA
* * * * *
40563889 ATATATTAATTAGTACCATATATTATTGTTTATTATTATATTGGTTGAAATATGCTCTAAATCCC
1 ATATATTACTTATTATCATATATTA-T-TTTATTATTATATTAGTTGAAATATGATCTAAATCCC
* *
40563954 TATACTTTTAGCATATTTGAAAGTTAGCCCTCTTACTATATTATATAATGTTATATCATATTATA
64 TATACTTTTAGCACATTTGAAAGTTAGCCCTCCTACTATATTATATAATGTTATATCA-ATTATA
* * * *
40564019 TAGTATATACTATATTAATAGTTTATATATATATGGATCAATGACTAAGCATTATAATATCATGT
128 CAGTATATACTATATTAATAGTTTATACATATATGCATCAATGACTAAACATTATAATATCATGT
*
40564084 AATACTATATCATTTATTATAATCCATATTATAATAATAGTACATT
193 AATACTATATCATTTATTATAATACATATTATAATAATAGTACATT
* *
40564130 ATATATTACTTATTATCATATATTATCATTTATTATTATATTAGTTGAAATATGATCTAATTCTC
1 ATATATTACTTATTATCATATATTAT--TTTATTATTATATTAGTTGAAATATGATCTAAATCCC
* * * * *
40564195 TATACTTTTCGTACATTTGAAAGTTAGCTCTCCTATTATATTATATAATGTTGTATC-A-TAT-C
64 TATACTTTTAGCACATTTGAAAGTTAGCCCTCCTACTATATTATATAATGTTATATCAATTATAC
*
40564257 A-TATA-A-TATATTAATAG-TT-TACATATATGCATCAATGACTAAATATTATAATATCATGTA
129 AGTATATACTATATTAATAGTTTATACATATATGCATCAATGACTAAACATTATAATATCATGTA
* *
40564317 ATACTATATCTTTTATTATAATATATATTATAATAATAG
194 ATACTATATCATTTATTATAATACATATTATAATAATAG
40564356 GTATATATGT
Statistics
Matches: 202, Mismatches: 23, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
232 73 0.36
233 2 0.01
234 11 0.05
235 1 0.00
236 4 0.02
237 1 0.00
238 3 0.01
239 1 0.00
240 1 0.00
241 105 0.52
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.45
Consensus pattern (238 bp):
ATATATTACTTATTATCATATATTATTTTATTATTATATTAGTTGAAATATGATCTAAATCCCTA
TACTTTTAGCACATTTGAAAGTTAGCCCTCCTACTATATTATATAATGTTATATCAATTATACAG
TATATACTATATTAATAGTTTATACATATATGCATCAATGACTAAACATTATAATATCATGTAAT
ACTATATCATTTATTATAATACATATTATAATAATAGTACATT
Found at i:40568906 original size:16 final size:16
Alignment explanation
Indices: 40568885--40568953 Score: 61
Period size: 16 Copynumber: 4.3 Consensus size: 16
40568875 GTTATTTGAT
40568885 AACAACTAAAGTTTAG
1 AACAACTAAAGTTTAG
***
40568901 AACAACTCTTGTTTAG
1 AACAACTAAAGTTTAG
*
40568917 AATAAC-AAAGTTTTAGG
1 AACAACTAAAG-TTTA-G
*
40568934 AACAACT-ATGTTTAG
1 AACAACTAAAGTTTAG
40568949 AACAA
1 AACAA
40568954 TCATTGTTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
15 7 0.17
16 26 0.63
17 8 0.20
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (16 bp):
AACAACTAAAGTTTAG
Found at i:40568961 original size:16 final size:15
Alignment explanation
Indices: 40568928--40568974 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
40568918 ATAACAAAGT
40568928 TTTAGGAACAA-CTATG
1 TTTA-GAACAATCT-TG
40568944 TTTAGAACAATCATTG
1 TTTAGAACAATC-TTG
40568960 TTTAGAACAAT-TTG
1 TTTAGAACAATCTTG
40568974 T
1 T
40568975 ATTTTGAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
16 18 0.62
17 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (15 bp):
TTTAGAACAATCTTG
Found at i:40569133 original size:17 final size:17
Alignment explanation
Indices: 40569108--40569144 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
40569098 AAGTTAAAAT
*
40569108 AACTATTATTCAAGAAC
1 AACTATTATCCAAGAAC
*
40569125 AACTCTTATCCAAGAAC
1 AACTATTATCCAAGAAC
40569142 AAC
1 AAC
40569145 CATTGTCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.24
Consensus pattern (17 bp):
AACTATTATCCAAGAAC
Found at i:40589189 original size:11 final size:11
Alignment explanation
Indices: 40589162--40589191 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
40589152 CAATCATATC
*
40589162 ATAATCATAAA
1 ATAATTATAAA
40589173 ATAATTATAAA
1 ATAATTATAAA
40589184 ATAATTAT
1 ATAATTAT
40589192 TTCTATCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (11 bp):
ATAATTATAAA
Found at i:40595481 original size:93 final size:93
Alignment explanation
Indices: 40595368--40595539 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
40595358 CGCCCATAAG
* * *
40595368 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCT
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
**
40595433 TTGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
40595461 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40595526 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
40595540 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:40595536 original size:46 final size:46
Alignment explanation
Indices: 40595361--40595536 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
40595351 TGTAACCCGC
* * *
40595361 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *** *
40595407 CCATAAGTGAACTCGGACTCAACTCTTTGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
40595457 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
40595500 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
40595537 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 16, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 60 0.57
47 26 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:40598306 original size:27 final size:27
Alignment explanation
Indices: 40598276--40598343 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
40598266 TTGAGAAAGT
*
40598276 AAACACAGGGTAGTCTG-CCGAGACATC
1 AAACACAGGGTAGTCTGCCCGA-ACAAC
*
40598303 AAACACTGGGTAGTCTGCCCGAACAAC
1 AAACACAGGGTAGTCTGCCCGAACAAC
* *
40598330 AAATACAGCGTAGT
1 AAACACAGGGTAGT
40598344 GATCACCTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 31 0.89
28 4 0.11
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (27 bp):
AAACACAGGGTAGTCTGCCCGAACAAC
Found at i:40604476 original size:16 final size:16
Alignment explanation
Indices: 40604451--40604488 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
40604441 AATTTACAGG
*
40604451 GAAAAATTGAGAATAT
1 GAAAAGTTGAGAATAT
40604467 GAAAAGTTGAGAATAT
1 GAAAAGTTGAGAATAT
40604483 GAAAAG
1 GAAAAG
40604489 CTGTCCCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (16 bp):
GAAAAGTTGAGAATAT
Found at i:40615591 original size:29 final size:28
Alignment explanation
Indices: 40615512--40615646 Score: 137
Period size: 29 Copynumber: 4.8 Consensus size: 28
40615502 TACATACATG
* *
40615512 CATATGGCCCATTATGCCCAATCTCATT
1 CATATGGCCCATCAGGCCCAATCTCATT
* * * *
40615540 TATATGGCCCATCCGACCTAAT-TCACGTT
1 CATATGGCCCATCAGGCCCAATCTCA--TT
*
40615569 CATATGGCCCATCAGGCCCAATTCACATT
1 CATATGGCCCATCAGGCCCAA-TCTCATT
*
40615598 CATATGGCCCATTAGGCCCAATCTCATT
1 CATATGGCCCATCAGGCCCAATCTCATT
* * *
40615626 TATATGGTCCATCTGGCCCAA
1 CATATGGCCCATCAGGCCCAA
40615647 ATCATATTAT
Statistics
Matches: 86, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
27 3 0.03
28 39 0.45
29 41 0.48
30 1 0.01
31 2 0.02
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (28 bp):
CATATGGCCCATCAGGCCCAATCTCATT
Found at i:40615631 original size:57 final size:56
Alignment explanation
Indices: 40615512--40615646 Score: 137
Period size: 57 Copynumber: 2.4 Consensus size: 56
40615502 TACATACATG
* * * * * *
40615512 CATATGGCCCATTATGCCCAATCTCATTTATATGGCCCATCCGACCTAATTCACGTT
1 CATATGGCCCATCAGGCCCAATCACATTCATATGGCCCATCAGACCCAATTCAC-TT
* *
40615569 CATATGGCCCATCAGGCCCAATTCACATTCATATGGCCCATTAGGCCCAATCTCA-TT
1 CATATGGCCCATCAGGCCCAA-TCACATTCATATGGCCCATCAGACCCAAT-TCACTT
* * *
40615626 TATATGGTCCATCTGGCCCAA
1 CATATGGCCCATCAGGCCCAA
40615647 ATCATATTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 39 0.60
58 23 0.35
59 3 0.05
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (56 bp):
CATATGGCCCATCAGGCCCAATCACATTCATATGGCCCATCAGACCCAATTCACTT
Found at i:40636183 original size:16 final size:16
Alignment explanation
Indices: 40636164--40636197 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
40636154 TAGAGATTTT
40636164 ATGGCTCAAACACGGG
1 ATGGCTCAAACACGGG
40636180 ATGGCTCAAACACGGG
1 ATGGCTCAAACACGGG
40636196 AT
1 AT
40636198 AGAAGAAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.29, T:0.15
Consensus pattern (16 bp):
ATGGCTCAAACACGGG
Found at i:40638081 original size:40 final size:40
Alignment explanation
Indices: 40637973--40638173 Score: 318
Period size: 40 Copynumber: 5.0 Consensus size: 40
40637963 GATGATAACG
40637973 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
40638013 GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
40638052 GGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* **
40638092 GGGCTAAGTCTCGAAGGCATTTGTGCGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
40638132 GGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
40638172 GG
1 GG
40638174 TTAAATTCCG
Statistics
Matches: 150, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
39 39 0.26
40 111 0.74
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:40653234 original size:40 final size:40
Alignment explanation
Indices: 40653178--40653419 Score: 346
Period size: 40 Copynumber: 6.0 Consensus size: 40
40653168 GATGATAACG
* * *
40653178 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
* *
40653218 GGGCTAAGTCCTGAAGGCATTTGTACGAGTTACTA-ACTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
*
40653258 GGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
40653298 GAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
**
40653338 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
40653378 GGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
40653418 GG
1 GG
40653420 TTAAATTCTG
Statistics
Matches: 184, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 2 0.01
40 181 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:40656589 original size:47 final size:47
Alignment explanation
Indices: 40656520--40656742 Score: 242
Period size: 47 Copynumber: 4.8 Consensus size: 47
40656510 GGTATGGTGC
40656520 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAGT
* * * *
40656567 CGATGCCATGTCCTAGACATGGTCTTACACTGACT-ATCATCTCGTAGG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCA-CATCTC-AAGT
* * * * * *
40656615 CAATG-CATGTTCCAGACAT-GTCTTACACTAGCTTACATCACAAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAA-GT
* *
40656661 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTCAA-T
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAGT
*
40656705 GCTGATGCCATGTCCCAGGCATGGTCTTACACTGGCTC
1 -C-GATGCCATGTCCCAGACATGGTCTTACACTGGCTC
40656743 TCATAATGTG
Statistics
Matches: 148, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
45 2 0.01
46 61 0.41
47 65 0.44
48 20 0.14
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAGT
Found at i:40656715 original size:140 final size:141
Alignment explanation
Indices: 40656518--40656786 Score: 386
Period size: 140 Copynumber: 1.9 Consensus size: 141
40656508 TGGGTATGGT
* *
40656518 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAGTCGATGCCATGTCCTAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATCTCAAGTCGATGCCATGTCCCAG
* * *
40656583 ACATGGTCTTACACTGACTATCAT-CTCGTAGG-CAATGCATGTTCCAGACATGTCTTACACTAG
66 ACATGGTCTTACACTGACTATCATAAT-GT-GGCCAATGCATGTCCCAAACATGTCTTACACTAG
40656646 CTTACATCACAAG
129 CTTACATCACAAG
*
40656659 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTCAA-TGCTGATGCCATGTCCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATCTCAAGT-C-GATGCCATGTCCC
* * *
40656721 AGGCATGGTCTTACACTGGCTCTCATAATGTGGCCAATGCATGTCCCAAACATGTCTTACACTAG
64 AGACATGGTCTTACACTGACTATCATAATGTGGCCAATGCATGTCCCAAACATGTCTTACACTAG
40656786 C
129 C
40656787 CAACAATAAC
Statistics
Matches: 115, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
138 1 0.01
139 25 0.22
140 81 0.70
141 8 0.07
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (141 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATCTCAAGTCGATGCCATGTCCCAG
ACATGGTCTTACACTGACTATCATAATGTGGCCAATGCATGTCCCAAACATGTCTTACACTAGCT
TACATCACAAG
Found at i:40656765 original size:94 final size:93
Alignment explanation
Indices: 40656520--40656786 Score: 276
Period size: 94 Copynumber: 2.8 Consensus size: 93
40656510 GGTATGGTGC
* * * *
40656520 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAA-GTCGATGCCATGTCCTAGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAT-AAGGCCGATG-CATGTCCCAGA
*
40656584 CATGGTCTTACACT-GACTATCATCTCGTAGG
64 CAT-GTCTTACACTAG-CTATCATCTCGAAGG
* * * *
40656615 CAATG-CATGTTCCAGACAT-GTCTTACACTAGCT-TACATCACAAGGCCGATGCATGTCCCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CAT-ATAAGGCCGATGCATGTCCCAGA
* *
40656677 CATGTCTTACACTAGCTCTCATCTC-AATG
64 CATGTCTTACACTAGCTATCATCTCGAAGG
* ** * *
40656706 CTGATGCCATGTCCCAGGCATGGTCTTACACTGGCTCTCATAATGTGGCCAATGCATGTCCCAAA
1 C-GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATAAGGCCGATGCATGTCCCAGA
40656771 CATGTCTTACACTAGC
64 CATGTCTTACACTAGC
40656787 CAACAATAAC
Statistics
Matches: 143, Mismatches: 21, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
91 3 0.02
92 22 0.15
93 44 0.31
94 69 0.48
95 5 0.03
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (93 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATAAGGCCGATGCATGTCCCAGACA
TGTCTTACACTAGCTATCATCTCGAAGG
Found at i:40657158 original size:30 final size:30
Alignment explanation
Indices: 40657123--40657179 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
40657113 AAATTCACAT
* * *
40657123 CTTTGGTAAAATGATCATTTTGCCCCTGAA
1 CTTTGGCAAAATGACCATTTTACCCCTGAA
40657153 CTTTGGCAAAATGACCATTTTACCCCT
1 CTTTGGCAAAATGACCATTTTACCCCT
40657180 ATGCTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (30 bp):
CTTTGGCAAAATGACCATTTTACCCCTGAA
Found at i:40665240 original size:24 final size:24
Alignment explanation
Indices: 40665206--40665386 Score: 247
Period size: 24 Copynumber: 7.5 Consensus size: 24
40665196 AAGGAAATTT
* * *
40665206 GCACACATAGTGCCATGCTAACCC
1 GCACACATAGTGCCATTCAAATCC
* *
40665230 GTACACATAGTGCC-TTGCTAATCC
1 GCACACATAGTGCCATT-CAAATCC
* * *
40665254 ACACACGTAGTGCCATTCAAATTC
1 GCACACATAGTGCCATTCAAATCC
*
40665278 GCACACATAGTGCCATACAAATCC
1 GCACACATAGTGCCATTCAAATCC
40665302 GCACACATAGTGCCATTCAAATCC
1 GCACACATAGTGCCATTCAAATCC
40665326 GCACACATAGTGCCATTCAAATCC
1 GCACACATAGTGCCATTCAAATCC
*
40665350 ACACACATAGTGCCATTCAAATCC
1 GCACACATAGTGCCATTCAAATCC
*
40665374 GCACATATAGTGC
1 GCACACATAGTGC
40665387 GAATGTCATT
Statistics
Matches: 139, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
23 1 0.01
24 136 0.98
25 2 0.01
ACGTcount: A:0.33, C:0.32, G:0.14, T:0.22
Consensus pattern (24 bp):
GCACACATAGTGCCATTCAAATCC
Found at i:40667179 original size:51 final size:49
Alignment explanation
Indices: 40667113--40667287 Score: 152
Period size: 49 Copynumber: 3.5 Consensus size: 49
40667103 TGAGGTCGCA
* * **
40667113 TGTGTAATACTAAGTGTAGGCTACTATGCGTACCCAAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACACGTACCCAAAAA-T-TGATCACG
* * ** * *
40667164 TGTGTAGTACTAAGTGCAGGCTGCTACATGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACACGTACCCAAAAATTGATCACG
** *** * * * *
40667213 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACATGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACACGTACCCAAAAATTGATCACG
*
40667262 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
40667288 TGCATACCAG
Statistics
Matches: 107, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 75 0.70
50 1 0.01
51 31 0.29
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACACGTACCCAAAAATTGATCACG
Found at i:40667226 original size:49 final size:49
Alignment explanation
Indices: 40667159--40667287 Score: 195
Period size: 49 Copynumber: 2.6 Consensus size: 49
40667149 AAAACTGTGA
* *
40667159 TCACGTGTGTAGTACTAAGTGCAGGCTGCTACATGTACCGGATAATTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACAGGATAATTGG
* *
40667208 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACATGATAATTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACAGGATAATTGG
* * *
40667257 TCGCATGTGTAGTACTATGTGCAGGCTACTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTA
40667288 TGCATACCAG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 73 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACAGGATAATTGG
Found at i:40669767 original size:17 final size:17
Alignment explanation
Indices: 40669745--40669778 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40669735 CCCCACTTAA
*
40669745 TATATTATAACTTATTT
1 TATATTATAACATATTT
40669762 TATATTATAACATATTT
1 TATATTATAACATATTT
40669779 CAAATATATA
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:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATAACATATTT
Found at i:40676084 original size:24 final size:24
Alignment explanation
Indices: 40676057--40676191 Score: 173
Period size: 24 Copynumber: 5.6 Consensus size: 24
40676047 AAGGAAATTT
* * * *
40676057 GCACACATAGTACCATGCTAACCC
1 GCACACATAGTGCCATTCAAATCC
* *
40676081 GCACAGATAGTGCC-TTGCTAATCC
1 GCACACATAGTGCCATT-CAAATCC
* *
40676105 ACACACGTAGTGCCATTCAAATCC
1 GCACACATAGTGCCATTCAAATCC
40676129 GCACACATAGTGCCATTCAAATCC
1 GCACACATAGTGCCATTCAAATCC
40676153 GCACACATAGTGCCATTCAAATCC
1 GCACACATAGTGCCATTCAAATCC
*
40676177 ACACACATAGTGCCA
1 GCACACATAGTGCCA
40676192 ATGTCATTTC
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 95 0.97
25 2 0.02
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.20
Consensus pattern (24 bp):
GCACACATAGTGCCATTCAAATCC
Found at i:40676155 original size:72 final size:72
Alignment explanation
Indices: 40676057--40676191 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 72
40676047 AAGGAAATTT
* * * *
40676057 GCACACATAGTACCATGCTAACCCGCACAGATAGTGCC-TTGCTAATCCACACACGTAGTGCCAT
1 GCACACATAGTACCATGCAAACCCGCACACATAGTGCCATT-CAAATCCACACACATAGTGCCAT
40676121 TCAAATCC
65 TCAAATCC
* * *
40676129 GCACACATAGTGCCATTCAAATCCGCACACATAGTGCCATTCAAATCCACACACATAGTGCCA
1 GCACACATAGTACCATGCAAACCCGCACACATAGTGCCATTCAAATCCACACACATAGTGCCA
40676192 ATGTCATTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 53 0.96
73 2 0.04
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.20
Consensus pattern (72 bp):
GCACACATAGTACCATGCAAACCCGCACACATAGTGCCATTCAAATCCACACACATAGTGCCATT
CAAATCC
Found at i:40677536 original size:17 final size:17
Alignment explanation
Indices: 40677514--40677547 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40677504 CCTCACTTAA
*
40677514 TATATTATAACTTATTT
1 TATATTATAACATATTT
40677531 TATATTATAACATATTT
1 TATATTATAACATATTT
40677548 CAAATATATA
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:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATAACATATTT
Found at i:40678081 original size:46 final size:45
Alignment explanation
Indices: 40677897--40678105 Score: 168
Period size: 46 Copynumber: 4.5 Consensus size: 45
40677887 ACACTAATGC
* * * * *
40677897 CATGTCCTAGACATGGTCTTACACTGGCTCACATCTCAAGTCGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTCTCATTTGAAGCCGATG
* * * * *
40677943 CCATGTCCTAGACATGGTCTTACACTGACTATCATTTGTAGCCAATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCTCATTTGAAGCCGATG
* * * * *
40677990 CATGTTCCAGACAAGTCTTACACTAGCT-TACTTCTTGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCT-CAT-TTGAAGCCGATG
* ** *
40678036 CATGTCCCAGACATGTCTTACACTGGCTCTCATAATGTGGTCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCTCAT-TTGAAGCCGATG
* *
40678082 CATGTCCCCGACATATCTTACACT
1 CATGTCCCAGACATGTCTTACACT
40678106 AGCCAACAAT
Statistics
Matches: 132, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
44 1 0.01
45 14 0.11
46 78 0.59
47 39 0.30
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTGGCTCTCATTTGAAGCCGATG
Found at i:40678083 original size:92 final size:93
Alignment explanation
Indices: 40677938--40678108 Score: 222
Period size: 92 Copynumber: 1.8 Consensus size: 93
40677928 CATCTCAAGT
* * *
40677938 CGATGCCATGTCCTAGACATGGTCTTACACTGACTATCATTTGTAGCCAATGCATGTTCCAGACA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATATGTAGCCAATGCATGTCCCAGACA
40678003 -AGTCTTACACTAGCTTACTTCTTGAGGC
66 TA-TCTTACACTAGCTTACTTCTTGAGGC
* * * * * *
40678031 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGTGGTCGATGCATGTCCCCGAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCAT-ATGTAGCCAATGCATGTCCCAGAC
40678094 ATATCTTACACTAGC
65 ATATCTTACACTAGC
40678109 CAACAATAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
91 17 0.25
92 44 0.66
93 6 0.09
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (93 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATATGTAGCCAATGCATGTCCCAGACA
TATCTTACACTAGCTTACTTCTTGAGGC
Found at i:40686844 original size:15 final size:15
Alignment explanation
Indices: 40686824--40686853 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40686814 ATGTTTAGAC
40686824 TTAAATGATATTTAT
1 TTAAATGATATTTAT
*
40686839 TTAAATGATGTTTAT
1 TTAAATGATATTTAT
40686854 GAAAATGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (15 bp):
TTAAATGATATTTAT
Found at i:40690365 original size:46 final size:46
Alignment explanation
Indices: 40690312--40690580 Score: 239
Period size: 46 Copynumber: 5.8 Consensus size: 46
40690302 TATTTGGGCA
40690312 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *** * *
40690358 TCCGAACTCATTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
* *
40690405 TCCGAGCTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
** * * *
40690451 TCTAAACTCGTTGAGTTGAGTCTGAGTT---TGA-GAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G
* *
40690496 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
40690544 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40690581 GCGGGTTACA
Statistics
Matches: 176, Mismatches: 29, Indels: 36
0.73 0.12 0.15
Matches are distributed among these distances:
42 3 0.02
43 8 0.05
44 3 0.02
45 2 0.01
46 91 0.52
47 54 0.31
48 2 0.01
49 3 0.02
50 7 0.04
51 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:40690427 original size:47 final size:47
Alignment explanation
Indices: 40690358--40690526 Score: 166
Period size: 47 Copynumber: 3.6 Consensus size: 47
40690348 GATGCGAATG
* *
40690358 TCCGAACTCATTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA
* *** * *
40690405 TCCGAGCTCGTCGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAA
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA
** * * *
40690449 TGTCTAAACTCGTTGAGTTGAGTCTGAGTTTGAGAGATGTAACTAGGCA
1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA
40690498 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC
40690527 ACTTATGGAT
Statistics
Matches: 91, Mismatches: 24, Indels: 14
0.71 0.19 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 27 0.30
47 54 0.59
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (47 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA
Found at i:40690467 original size:93 final size:93
Alignment explanation
Indices: 40690308--40690572 Score: 440
Period size: 93 Copynumber: 2.8 Consensus size: 93
40690298 AGGATATTTG
* *
40690308 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCATTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
40690373 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* **
40690401 GGCATCCGAGCTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTAAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
* *
40690466 TTGAGTCTGAGTTTGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
40690494 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
40690559 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
40690573 ACTTATGGGC
Statistics
Matches: 157, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 157 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:40694812 original size:49 final size:48
Alignment explanation
Indices: 40694752--40694886 Score: 155
Period size: 48 Copynumber: 2.8 Consensus size: 48
40694742 CGGCAGATGA
* *
40694752 GAGCCAGTGTAAGACCATGTTTGGGA-ATGGCATCGGCTTCGATATAT
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCTTCGATATAT
* * * * * *
40694799 AAGAGTCAATGTAAGACCATGTCTGGGACATGGCATTGACTTTGATGTGT
1 --GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCTTCGATATAT
* *
40694849 GAGCCAGTGTAAGACCATGTCCGGGACATGGCATCGGC
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGC
40694887 ATCTTACCCT
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
48 33 0.46
49 23 0.32
50 16 0.22
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (48 bp):
GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCTTCGATATAT
Found at i:40694869 original size:48 final size:48
Alignment explanation
Indices: 40694711--40694882 Score: 168
Period size: 49 Copynumber: 3.5 Consensus size: 48
40694701 AAAGTTAGTA
* ** *
40694711 TAAGACCATGTCTTGGACATGGCATTGACACCGGCA-GATGAGAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATTGACTTC-G-ATG-TGTGAGCCAGTG
* * * * * * *
40694761 TAAGACCATGTTTGGGA-ATGGCATCGGCTTCGATATATAAGAGTCAATG
1 TAAGACCATGTCTGGGACATGGCATTGACTTCGATGTGT--GAGCCAGTG
*
40694810 TAAGACCATGTCTGGGACATGGCATTGACTTTGATGTGTGAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATTGACTTCGATGTGTGAGCCAGTG
*
40694858 TAAGACCATGTCCGGGACATGGCAT
1 TAAGACCATGTCTGGGACATGGCAT
40694883 CGGCATCTTA
Statistics
Matches: 98, Mismatches: 20, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
47 2 0.02
48 32 0.33
49 33 0.34
50 31 0.32
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCATTGACTTCGATGTGTGAGCCAGTG
Found at i:40698600 original size:32 final size:33
Alignment explanation
Indices: 40698522--40698601 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 33
40698512 TGCATCTTGC
* *
40698522 ACTGTACTGCTACTGTATAAGGGCTTGGCCCAA
1 ACTGTACTGATACTGAATAAGGGCTTGGCCCAA
* * * *
40698555 ATTGCAC-GAATACTGAAT-AGGGCTTGGGCCAG
1 ACTGTACTG-ATACTGAATAAGGGCTTGGCCCAA
40698587 ACTGTACTGATACTG
1 ACTGTACTGATACTG
40698602 TGTTGTTCAC
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
32 24 0.65
33 13 0.35
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (33 bp):
ACTGTACTGATACTGAATAAGGGCTTGGCCCAA
Found at i:40717798 original size:49 final size:49
Alignment explanation
Indices: 40717737--40717968 Score: 268
Period size: 49 Copynumber: 4.7 Consensus size: 49
40717727 CTGGTACGCA
* * *
40717737 TAGTAGCATGCACTTAGTACTACACATGTGACCAATAATCCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACG
* ** *
40717786 TAGTAGCCTGCACTTAGCACTACACACGTGACCTAACCAT-CTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCAG-TACACG
* ** * * *
40717836 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATTGAGAACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCAGTACACG
* * *
40717887 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACG
*
40717936 TAGTAGCCTGCACTTAGTACTACACACATGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
40717969 TTACAATAGA
Statistics
Matches: 151, Mismatches: 27, Indels: 10
0.80 0.14 0.05
Matches are distributed among these distances:
49 70 0.46
50 45 0.30
51 35 0.23
52 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACG
Found at i:40720440 original size:27 final size:27
Alignment explanation
Indices: 40720399--40720452 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
40720389 TGTCATGTGA
*
40720399 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTATTATTACATG
**
40720426 AATTGAATGTTAAATTATTATTACATG
1 AATTGAATGGCAAATTATTATTACATG
40720453 GGTTGTACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.41
Consensus pattern (27 bp):
AATTGAATGGCAAATTATTATTACATG
Found at i:40720756 original size:49 final size:50
Alignment explanation
Indices: 40720678--40720910 Score: 263
Period size: 49 Copynumber: 4.7 Consensus size: 50
40720668 ATCTATTGTG
*
40720678 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* * * **
40720728 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACCATGTGTACCCAATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT
* * * * *** **
40720778 CGATCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTATTAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* *
40720828 AGGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
** *
40720878 -GGTTGCATGTGTAGTACTAAGTACAGGCTACTA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
40720911 TACGTACCAG
Statistics
Matches: 149, Mismatches: 32, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
49 69 0.46
50 45 0.30
51 35 0.23
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
Found at i:40720915 original size:101 final size:98
Alignment explanation
Indices: 40720684--40720910 Score: 276
Period size: 101 Copynumber: 2.3 Consensus size: 98
40720674 TGTGAGGTCA
* *
40720684 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTACTAAG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAATTGGTCACATGTGTAGTACTAAG
*
40720749 TGCAGGCTACCATGTGTACCCAATAACTTCGAT
66 TGCAGGCTACCACGTGTACCCAATAACTTCGAT
* * ** *
40720782 CACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTATTAGATGGTTAGGTCACGTGTGTAGTACT
1 CA--TGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAATT-GGTCACATGTGTAGTACT
* * ** * *
40720847 AAGTGTAGGCTACTACGTGTACCGGATAA-TTGGTT
63 AAGTGCAGGCTACCACGTGTACCCAATAACTTCGAT
*
40720882 GCATGTGTAGTACTAAGTACAGGCTACTA
1 -CATGTGTAGTACTAAGTGCAGGCTACTA
40720911 TACGTACCAG
Statistics
Matches: 109, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
98 2 0.02
99 24 0.22
100 41 0.38
101 42 0.39
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (98 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAATTGGTCACATGTGTAGTACTAAG
TGCAGGCTACCACGTGTACCCAATAACTTCGAT
Found at i:40722902 original size:23 final size:23
Alignment explanation
Indices: 40722876--40722928 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
40722866 AAAGTGCCAT
*
40722876 ACTGTAATATAGCCGAAGCTATC
1 ACTGTAATATAGCCGAAGCTACC
*
40722899 ACTGTAATGTAGCCGAAGCTACC
1 ACTGTAATATAGCCGAAGCTACC
40722922 ACTGTAA
1 ACTGTAA
40722929 CACTTATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (23 bp):
ACTGTAATATAGCCGAAGCTACC
Found at i:40722949 original size:15 final size:15
Alignment explanation
Indices: 40722929--40722968 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
40722919 ACCACTGTAA
*
40722929 CACTTATTCAACATT
1 CACTTAATCAACATT
40722944 CACTTAATCAACATT
1 CACTTAATCAACATT
40722959 CACTTAATCA
1 CACTTAATCA
40722969 CTTATCTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.35
Consensus pattern (15 bp):
CACTTAATCAACATT
Found at i:40728355 original size:28 final size:27
Alignment explanation
Indices: 40728295--40728446 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
40728285 TAAATTGTGC
*
40728295 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
40728322 AGCACTAAGTGTGCGAGTTTAACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
40728350 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
40728377 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
40728405 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
40728432 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40728447 GACTTAATAT
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
27 65 0.56
28 52 0.44
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:40728362 original size:55 final size:55
Alignment explanation
Indices: 40728295--40728446 Score: 250
Period size: 55 Copynumber: 2.8 Consensus size: 55
40728285 TAAATTGTGC
*
40728295 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTAACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTAACTATGT
* *
40728350 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTAACTATGT
* * *
40728405 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
40728447 GACTTAATAT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 91 1.00
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTAACTATGT
Found at i:40736378 original size:28 final size:27
Alignment explanation
Indices: 40736321--40736472 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
40736311 TAAATTGTGC
*
40736321 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
40736348 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
40736376 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
40736403 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
40736431 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
40736458 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40736473 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:40736385 original size:55 final size:55
Alignment explanation
Indices: 40736321--40736472 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
40736311 TAAATTGTGC
*
40736321 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
40736376 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
40736431 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
40736473 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:40744417 original size:72 final size:72
Alignment explanation
Indices: 40744295--40744449 Score: 229
Period size: 72 Copynumber: 2.2 Consensus size: 72
40744285 ACAGTCTAAA
* * * **
40744295 GGAAAGCCCTAGCGGCTATCATCTGAAGGGAACACCTTTGTGGCGGACCCTGAAGAAAGAAATGG
1 GGAAAGCCCTAGCAGCTATCATATGAAGAGAACACCTTTGTGGCAAACCCTGAAGAAAGAAATGG
40744360 TGAGTAT
66 TGAGTAT
* * *
40744367 GGAAAGCCCTTGTAGCTATCATATGAAGAGAACACCTTTGTGGCAAACCCTGAAGAAAGAAGTGG
1 GGAAAGCCCTAGCAGCTATCATATGAAGAGAACACCTTTGTGGCAAACCCTGAAGAAAGAAATGG
40744432 TGAGTAT
66 TGAGTAT
*
40744439 GGAAAACCCTA
1 GGAAAGCCCTA
40744450 AGAAGTAGTA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.20
Consensus pattern (72 bp):
GGAAAGCCCTAGCAGCTATCATATGAAGAGAACACCTTTGTGGCAAACCCTGAAGAAAGAAATGG
TGAGTAT
Found at i:40748026 original size:40 final size:35
Alignment explanation
Indices: 40747947--40748016 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
40747937 AAAGTTGGTG
40747947 AAAGTTTCTTAAATTATCAGTTTAGTCCCAAACCA
1 AAAGTTTCTTAAATTATCAGTTTAGTCCCAAACCA
* * *
40747982 AAAGTTTCTTAAGTTATCGGTTTATTCCCAAACCA
1 AAAGTTTCTTAAATTATCAGTTTAGTCCCAAACCA
40748017 CTCCAAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (35 bp):
AAAGTTTCTTAAATTATCAGTTTAGTCCCAAACCA
Found at i:40772993 original size:38 final size:39
Alignment explanation
Indices: 40772943--40773037 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 39
40772933 CCATCTCCAT
* * *
40772943 CCAACCCAACACACCATGTA-GGGATAAAATCGACCCAC
1 CCAACCCTACACACCAAGTAGGGGATAAAATCAACCCAC
* *
40772981 CCAGCCCTACACACCAAGTATGGGGATAAAATCAACCCAT
1 CCAACCCTACACACCAAGTA-GGGGATAAAATCAACCCAC
40773021 CCAACCCTACACACCAA
1 CCAACCCTACACACCAA
40773038 ATGGTACCGT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
38 17 0.35
40 32 0.65
ACGTcount: A:0.39, C:0.38, G:0.12, T:0.12
Consensus pattern (39 bp):
CCAACCCTACACACCAAGTAGGGGATAAAATCAACCCAC
Found at i:40782174 original size:6 final size:6
Alignment explanation
Indices: 40782163--40782253 Score: 107
Period size: 6 Copynumber: 15.3 Consensus size: 6
40782153 AATCCTCCTA
*
40782163 TTTTAT TTTTAT TTTTAT TTTTA- -TTTAT TCTTAT TTTTA- TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* * *
40782208 TTTATTT ATTTTAT TCTTAT TTTTAT TTTTAT TTTTAT TTTCAT TT
1 TTT-TAT -TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
40782254 CAATTTTCTT
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
4 4 0.05
5 5 0.07
6 57 0.78
7 4 0.05
8 3 0.04
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:40782486 original size:45 final size:45
Alignment explanation
Indices: 40782422--40782513 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
40782412 TTTACGCAAT
*
40782422 GAGGAAACAAATAGGGAACAATACCTAACGAGTGCCATGTTCAAC
1 GAGGAAACAAATAGGGAACAATACCTAACAAGTGCCATGTTCAAC
*
40782467 GAGGAAACAAATAGGGAACAATACCTAACAAGTGTCATGTTCAAC
1 GAGGAAACAAATAGGGAACAATACCTAACAAGTGCCATGTTCAAC
40782512 GA
1 GA
40782514 CCCAATTTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.16
Consensus pattern (45 bp):
GAGGAAACAAATAGGGAACAATACCTAACAAGTGCCATGTTCAAC
Found at i:40785204 original size:13 final size:13
Alignment explanation
Indices: 40785188--40785220 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
40785178 TTTAATTAAA
*
40785188 TTAGTTAATTAGT
1 TTAGATAATTAGT
40785201 TTAGATAATTAGT
1 TTAGATAATTAGT
40785214 TTA-ATAA
1 TTAGATAA
40785221 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:40789920 original size:47 final size:47
Alignment explanation
Indices: 40789841--40790022 Score: 184
Period size: 47 Copynumber: 3.8 Consensus size: 47
40789831 TATAGAATAA
* * * *
40789841 GAAGCCGACGCCATGTCTCAGACATGGTCTTACACTGGCTAGCACATC
1 GAAGTCGATGCCATGTCCCAGACA-GGTCTTACACTGGCTATCACATC
* * * * * *
40789889 AAAGTCGATGCCATGTCCCAGATAGGTCTTACACTGACTTTTATATC
1 GAAGTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTATCACATC
* * * *
40789936 GAGGTCGATGCCATGTCCCTGACAGGTCTTACACTAGCTCTCATCTATC
1 GAAGTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTATCA-C-ATC
** *
40789985 GGTGTCGATGCCATGTCCCAGACAAGTCTTACACTGGC
1 GAAGTCGATGCCATGTCCCAGACAGGTCTTACACTGGC
40790023 ACACAACAAG
Statistics
Matches: 108, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
47 53 0.49
48 19 0.18
49 36 0.33
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (47 bp):
GAAGTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTATCACATC
Found at i:40790660 original size:30 final size:31
Alignment explanation
Indices: 40790624--40790686 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
40790614 TTCTATAATT
*
40790624 TATACTTTGGC-AAAATGACCATTTTACCCC
1 TATACTTTGACAAAAATGACCATTTTACCCC
* * *
40790654 TATACTTTTACAAAAATTACGATTTTACCCC
1 TATACTTTGACAAAAATGACCATTTTACCCC
40790685 TA
1 TA
40790687 AGCTTGTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (31 bp):
TATACTTTGACAAAAATGACCATTTTACCCC
Found at i:40798357 original size:24 final size:27
Alignment explanation
Indices: 40798310--40798363 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
40798300 TTCTCCTAAA
* *
40798310 TTTCAAATTTATTTAATTATTTAAT-T
1 TTTCAAATTCATTGAATTATTTAATAT
40798336 TTTC-AATTCATTGAATTA-TTAATAT
1 TTTCAAATTCATTGAATTATTTAATAT
40798361 TTT
1 TTT
40798364 ATACAAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 16 0.64
26 4 0.16
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTCAAATTCATTGAATTATTTAATAT
Found at i:40800670 original size:38 final size:38
Alignment explanation
Indices: 40800628--40800704 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
40800618 ATGATTTTTC
40800628 AGTCATTATCTAACTAAATTGTGTTTGATTGACTTGTA
1 AGTCATTATCTAACTAAATTGTGTTTGATTGACTTGTA
*
40800666 AGTCATTATTTAACTAAATTGTGTTTGATTGACTTGTA
1 AGTCATTATCTAACTAAATTGTGTTTGATTGACTTGTA
40800704 A
1 A
40800705 CACTAACTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (38 bp):
AGTCATTATCTAACTAAATTGTGTTTGATTGACTTGTA
Found at i:40810346 original size:25 final size:25
Alignment explanation
Indices: 40810299--40810346 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
40810289 ATGTGACTCT
*
40810299 GTATGTTGCCTTTGGGGCATATTTC
1 GTATGTTGCCTTTAGGGCATATTTC
* * *
40810324 GTATGTTTCCTTTATGGCGTATT
1 GTATGTTGCCTTTAGGGCATATT
40810347 CTATTTAGCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.48
Consensus pattern (25 bp):
GTATGTTGCCTTTAGGGCATATTTC
Found at i:40824044 original size:39 final size:39
Alignment explanation
Indices: 40823990--40824069 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
40823980 GTATGCCAGG
40823990 AATGCCTCATAACCCTTGCGAACCAGTTTCTCGGCCCTT
1 AATGCCTCATAACCCTTGCGAACCAGTTTCTCGGCCCTT
40824029 AATGCCTCATAACCCTTGCGAACCAGTTTCTCGGCCCTT
1 AATGCCTCATAACCCTTGCGAACCAGTTTCTCGGCCCTT
40824068 AA
1 AA
40824070 CGTTGAAATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.23, C:0.35, G:0.15, T:0.28
Consensus pattern (39 bp):
AATGCCTCATAACCCTTGCGAACCAGTTTCTCGGCCCTT
Found at i:40830221 original size:29 final size:29
Alignment explanation
Indices: 40830187--40830260 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
40830177 TCATCAACCA
*
40830187 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
40830216 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
40830245 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
40830261 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:40836192 original size:28 final size:28
Alignment explanation
Indices: 40836132--40836198 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
40836122 TGATATTTTG
*
40836132 CACACTAAGTGTCATTCTCAATATCTCG
1 CACACTAAGTGTCATTCTCAATATCTCA
*
40836160 CACACTAAGTGTCATTCTCAATATTTCA
1 CACACTAAGTGTCATTCTCAATATCTCA
* *
40836188 TACACTGAGTG
1 CACACTAAGTG
40836199 CCATATTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (28 bp):
CACACTAAGTGTCATTCTCAATATCTCA
Found at i:40853632 original size:45 final size:42
Alignment explanation
Indices: 40853567--40853689 Score: 133
Period size: 45 Copynumber: 2.9 Consensus size: 42
40853557 ATTTGTGTTC
** * *
40853567 TCGTGTAAGACCACATCTGGGACGTTGGCATCGATATATGTGGT
1 TCGTGTAAGACCATGTCTGGGACATTGGCATCGATAT-T-TGAT
* *
40853611 TACGTGTAAGACCATGTCTGGGACATCGACATC-ATATTTGAT
1 T-CGTGTAAGACCATGTCTGGGACATTGGCATCGATATTTGAT
*
40853653 TCGTGTAAGA-CACTGTCTGGGACAATGGCATCGATAT
1 TCGTGTAAGACCA-TGTCTGGGACATTGGCATCGATAT
40853690 GAGATAGCAT
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
40 2 0.03
41 25 0.37
42 8 0.12
43 1 0.01
44 5 0.07
45 26 0.39
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (42 bp):
TCGTGTAAGACCATGTCTGGGACATTGGCATCGATATTTGAT
Found at i:40860850 original size:93 final size:93
Alignment explanation
Indices: 40860743--40860914 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
40860733 CGCCCTAAGT
* * *
40860743 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
40860808 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
40860836 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
40860901 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
40860915 AAACATCCTA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40860910 original size:46 final size:46
Alignment explanation
Indices: 40860738--40860910 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
40860728 TAACCCGCCC
* * * *
40860738 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
40860784 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
40860832 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
*
40860877 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40860911 TGCCAAACAT
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
44 1 0.01
45 2 0.02
46 60 0.57
47 29 0.28
48 2 0.02
49 1 0.01
50 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:40861369 original size:30 final size:29
Alignment explanation
Indices: 40861335--40861393 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
40861325 ATTTAATACG
40861335 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGG-AAAATTACACTTTTGCCCCTA
* *
40861365 AACTTTTGATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAATTACACTTTTGCCCCTA
40861394 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (29 bp):
AACTTTGGAAAATTACACTTTTGCCCCTA
Found at i:40868805 original size:30 final size:30
Alignment explanation
Indices: 40868771--40868830 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40868761 ATTTAATACG
40868771 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
40868801 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
40868831 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:40869778 original size:12 final size:12
Alignment explanation
Indices: 40869755--40869789 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
40869745 CAAATCATGA
40869755 GAAATG-GAAAT
1 GAAATGTGAAAT
40869766 GAAATGTGAAAT
1 GAAATGTGAAAT
*
40869778 GAAATATGAAAT
1 GAAATGTGAAAT
40869790 ATGAAATGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (12 bp):
GAAATGTGAAAT
Found at i:40869788 original size:19 final size:18
Alignment explanation
Indices: 40869755--40869797 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
40869745 CAAATCATGA
* *
40869755 GAAATGGAAATGAAATGT
1 GAAATGAAAATGAAATAT
40869773 GAAATGAAATATGAAATAT
1 GAAATGAAA-ATGAAATAT
40869792 GAAATG
1 GAAATG
40869798 GTGGATTGAG
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:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (18 bp):
GAAATGAAAATGAAATAT
Found at i:40874256 original size:13 final size:13
Alignment explanation
Indices: 40874238--40874263 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40874228 ATTTTGACTA
40874238 TATATGAATATGC
1 TATATGAATATGC
40874251 TATATGAATATGC
1 TATATGAATATGC
40874264 ATGTGACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
TATATGAATATGC
Found at i:40878269 original size:28 final size:28
Alignment explanation
Indices: 40878233--40878307 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
40878223 TCAAATATGG
* *
40878233 CACTCAGTGTATGAAATATTGAGAATGA
1 CACTTAGTGTACGAAATATTGAGAATGA
* *
40878261 CACTTAGTGTGCGAGATATTGAGAATGA
1 CACTTAGTGTACGAAATATTGAGAATGA
* *
40878289 CACTTAGTGTGCAAAATAT
1 CACTTAGTGTACGAAATAT
40878308 CAAATGATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (28 bp):
CACTTAGTGTACGAAATATTGAGAATGA
Found at i:40884210 original size:29 final size:29
Alignment explanation
Indices: 40884177--40884250 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
40884167 GTTGTGAGAT
* *
40884177 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA
* *
40884206 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGACTTGAAAGTACA
40884235 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
40884251 TGGTTGATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGACTTGAAAGTACA
Found at i:40904349 original size:46 final size:46
Alignment explanation
Indices: 40904299--40904473 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
40904289 GGTTGAGCAA
40904299 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
* * * *
40904345 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGCAT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--T
* *
40904392 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
* * *
40904438 CCGAGCTCATTGAGTTGAGTCTGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40904474 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
Found at i:40913112 original size:26 final size:26
Alignment explanation
Indices: 40913083--40913191 Score: 209
Period size: 26 Copynumber: 4.2 Consensus size: 26
40913073 TGGTACAAAT
40913083 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
40913109 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40913135 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40913161 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40913187 TGATA
1 TGATA
40913192 GGAATTTCAT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:40916942 original size:27 final size:29
Alignment explanation
Indices: 40916881--40916942 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 29
40916871 AAAATAATAA
*
40916881 AAATATATTATATGATATAATAGCTTAAT
1 AAATATATTATATGAAATAATAGCTTAAT
* *
40916910 ATATAT-TTATAT-AAATAATA-CTATATT
1 AAATATATTATATGAAATAATAGCT-TAAT
40916937 AAATAT
1 AAATAT
40916943 GTATGAAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.07
27 15 0.54
28 6 0.21
29 5 0.18
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (29 bp):
AAATATATTATATGAAATAATAGCTTAAT
Found at i:40917092 original size:9 final size:10
Alignment explanation
Indices: 40917071--40917143 Score: 51
Period size: 10 Copynumber: 7.1 Consensus size: 10
40917061 TTGAAGTAAT
40917071 ATAAAATATA
1 ATAAAATATA
40917081 ATAAAA-ATA
1 ATAAAATATA
*
40917090 ATATAATGAATA
1 ATAAAAT--ATA
*
40917102 ATATATATATA
1 ATA-AAATATA
*
40917113 GTAAAATGAT-
1 ATAAAAT-ATA
* *
40917123 ATAATATATT
1 ATAAAATATA
40917133 ATAAAATATA
1 ATAAAATATA
40917143 A
1 A
40917144 ATAATAAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
9 10 0.21
10 23 0.48
11 7 0.15
12 6 0.12
13 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (10 bp):
ATAAAATATA
Found at i:40917111 original size:18 final size:18
Alignment explanation
Indices: 40917048--40917112 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 18
40917038 AAAATTATAC
* *
40917048 ATAATA-ATAAATATTGA
1 ATAATATATATATAATGA
*
40917065 AGTAATATAAAATATAAT-A
1 A-TAATAT-ATATATAATGA
40917084 A-AA-ATA-ATATAATGA
1 ATAATATATATATAATGA
40917099 ATAATATATATATA
1 ATAATATATATATA
40917113 GTAAAATGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
14 7 0.18
15 3 0.08
16 4 0.11
17 6 0.16
18 10 0.26
19 2 0.05
20 6 0.16
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
ATAATATATATATAATGA
Found at i:40927292 original size:16 final size:17
Alignment explanation
Indices: 40927261--40927296 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40927251 TTGAGGGTCA
40927261 AATTTATTTAAAATTTT
1 AATTTATTTAAAATTTT
* *
40927278 AATTTTTTTAAATTTTT
1 AATTTATTTAAAATTTT
40927295 AA
1 AA
40927297 AATTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTATTTAAAATTTT
Found at i:40927699 original size:19 final size:20
Alignment explanation
Indices: 40927675--40927713 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40927665 ACCATTTTCT
40927675 GTTAAAAA-GAAAAAAAATA
1 GTTAAAAACGAAAAAAAATA
*
40927694 GTTAAAAACGGAAAAAAATA
1 GTTAAAAACGAAAAAAAATA
40927714 AAAAGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.69, C:0.03, G:0.13, T:0.15
Consensus pattern (20 bp):
GTTAAAAACGAAAAAAAATA
Found at i:40928415 original size:151 final size:152
Alignment explanation
Indices: 40928239--40928560 Score: 540
Period size: 152 Copynumber: 2.1 Consensus size: 152
40928229 ATTTTTAAAG
* * * *
40928239 TTTTAAAATTTTCGAATTTTATTTTTTAAAATATATTATTTTCGTATTTTATT-TTTTTATATTA
1 TTTTAAAATTTTCGAATCTTATTTTTTAAAATATACTATTTTCCTATTCTATTCTTTTTATATTA
* *
40928303 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAATAACCTT
66 TTTTAATACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAATAACCCT
*
40928368 AATTTTGTTCC-TTTGTTTGTAT
131 AATTTTG-TCCGTTTATTTGTAT
*
40928390 TTTTAAAATTTTCGGATCTTATTTTTTAAAATATACTATTTTCCTATTCTATTCTTTTTATATTA
1 TTTTAAAATTTTCGAATCTTATTTTTTAAAATATACTATTTTCCTATTCTATTCTTTTTATATTA
40928455 TTTTAATACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAATAACCCT
66 TTTTAATACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAATAACCCT
40928520 AATTTTGTCCGTTTATTTGTAT
131 AATTTTGTCCGTTTATTTGTAT
*
40928542 TTTCAAAATTTTCGAATCT
1 TTTTAAAATTTTCGAATCT
40928561 AAATTTTATA
Statistics
Matches: 159, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
151 51 0.32
152 108 0.68
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (152 bp):
TTTTAAAATTTTCGAATCTTATTTTTTAAAATATACTATTTTCCTATTCTATTCTTTTTATATTA
TTTTAATACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAATAACCCT
AATTTTGTCCGTTTATTTGTAT
Found at i:40928682 original size:20 final size:19
Alignment explanation
Indices: 40928657--40928695 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
40928647 TTTTGTTTTT
40928657 TATTTTTTTCCGTTTTTAAC
1 TATTTTTTTCC-TTTTTAAC
40928677 TATTTTTTTCCTTTTTAAC
1 TATTTTTTTCCTTTTTAAC
40928696 AAAAAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.15, C:0.15, G:0.03, T:0.67
Consensus pattern (19 bp):
TATTTTTTTCCTTTTTAAC
Found at i:40932804 original size:2 final size:2
Alignment explanation
Indices: 40932797--40932833 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
40932787 TAGGGTTTGT
40932797 TC TC TC TC 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 TC TC TC TC T
40932834 GCTGCCAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:40934882 original size:12 final size:12
Alignment explanation
Indices: 40934854--40934892 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
40934844 TCGGAAATAG
40934854 TTGTGTTTGTTTGT
1 TTGT-TTTGTTT-T
40934868 TTGTTTTGTTTT
1 TTGTTTTGTTTT
40934880 TTGTTTT-TTTT
1 TTGTTTTGTTTT
40934891 TT
1 TT
40934893 TAATGTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 6 0.24
12 8 0.32
13 7 0.28
14 4 0.16
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (12 bp):
TTGTTTTGTTTT
Found at i:40937285 original size:88 final size:86
Alignment explanation
Indices: 40936982--40937500 Score: 426
Period size: 88 Copynumber: 6.0 Consensus size: 86
40936972 AAAATAAAAA
* ** *
40936982 AATTAAAATTAAATAAAATCTGTTTCAGGAATTTATTCATGCCGTTCAACAGATTTTATT-TCAT
1 AATTAAAATTAAATAAAATCTGTTTC-GGGATTTATTCCCGCCGTTCAACAAATTTTATTCT-AT
40937046 TTTTTATTTTGTTTCCAAACGAG
64 TTTTTATTTTGTTTCCAAACGAG
* * * * * *
40937069 TATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCTGCTGTTCAACAGATTTTATTCAATTT
1 AATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAAATTTTATTC--TAT
40937134 TTTTTATTTTGTTTCCAAACGAG
64 TTTTTATTTTGTTTCCAAACGAG
* * * * *
40937157 TATTAAAATTAAAAAATATATATATTTCGGGATTTATTCCCGCTGTTCAACAAATTTTATTCTAT
1 AATTAAAATTAAATAA-A-ATCTGTTTCGGGATTTATTCCCGCCGTTCAACAAATTTTATTCTAT
*
40937222 TTTTTATTTTGTTGCCAAACGAG
64 TTTTTATTTTGTTTCCAAACGAG
* * * *
40937245 AAATTAAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCACCGTTTAACTAATTTTATTCCA-
1 -AATT-AAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAAATTTTATTCTAT
* * * **
40937309 TTTTAATTTAGTTTCTAAAATAG
64 TTTTTATTTTGTTTCCAAACGAG
* * * * * * * * *
40937332 -ATTTAAATTGAAT-AATTTTGTTTTGGGGGTTTATTCCCACCG-TCTAACAGATTTTATTC-AA
1 AATTAAAATTAAATAAAATCTG-TTTCGGGATTTATTCCCGCCGTTC-AACAAATTTTATTCTAT
* * **
40937393 TTTTAATTTTGTTTCTAAAATAG
64 TTTTTATTTTGTTTCCAAACGAG
* * * * * * * * * *
40937416 AATT-AAATTGAAT-AATTTTGTTTCAGGATTTATTCTCGCCATTTAACAGATTTTCTTCGA-TT
1 AATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAAATTTTATTCTATTT
** *
40937478 TCGATTTTGCTTCCAAACGAG
66 TTTATTTTGTTTCCAAACGAG
40937499 AA
1 AA
40937501 GACTTAATCA
Statistics
Matches: 366, Mismatches: 53, Indels: 30
0.82 0.12 0.07
Matches are distributed among these distances:
83 54 0.15
84 79 0.22
85 6 0.02
86 29 0.08
87 42 0.11
88 101 0.28
89 6 0.02
90 49 0.13
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (86 bp):
AATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAAATTTTATTCTATTT
TTTATTTTGTTTCCAAACGAG
Found at i:40937373 original size:84 final size:84
Alignment explanation
Indices: 40937277--40937438 Score: 272
Period size: 84 Copynumber: 1.9 Consensus size: 84
40937267 TGTTTCGGGA
* * *
40937277 TTTATTCCCACCGTTTAACTA-ATTTTATTCCATTTTAATTTAGTTTCTAAAATAGATTTAAATT
1 TTTATTCCCACCGTCTAAC-AGATTTTATTCAATTTTAATTTAGTTTCTAAAATAGAATTAAATT
40937341 GAATAATTTTGTTTTGGGGG
65 GAATAATTTTGTTTTGGGGG
*
40937361 TTTATTCCCACCGTCTAACAGATTTTATTCAATTTTAATTTTGTTTCTAAAATAGAATTAAATTG
1 TTTATTCCCACCGTCTAACAGATTTTATTCAATTTTAATTTAGTTTCTAAAATAGAATTAAATTG
40937426 AATAATTTTGTTT
66 AATAATTTTGTTT
40937439 CAGGATTTAT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
83 1 0.01
84 72 0.99
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (84 bp):
TTTATTCCCACCGTCTAACAGATTTTATTCAATTTTAATTTAGTTTCTAAAATAGAATTAAATTG
AATAATTTTGTTTTGGGGG
Found at i:40937609 original size:77 final size:78
Alignment explanation
Indices: 40937474--40937647 Score: 183
Period size: 77 Copynumber: 2.2 Consensus size: 78
40937464 GATTTTCTTC
* * * *
40937474 GATTTCGATTTTGCTTCCAAACGAGAAGACTTAATCAAATAATTCTGTTTTGAAATTTAATCCTG
1 GATTTTGATTTTGTTTCCAAAC--GAAGACTTAATCAAATAATTCTATTTCGAAATTTAATCCTG
*
40937539 -CTGCTT-AACAGATTT
64 TC-G-TTCAACAGACTT
* * * * * *
40937554 TATTTTGATTTTGTTTCCAAAC-AAGATTTAATTAAATAATTTTATTTCGAGATTTAATCTTGTC
1 GATTTTGATTTTGTTTCCAAACGAAGACTTAATCAAATAATTCTATTTCGAAATTTAATCCTGTC
40937618 GTTCAACAGACTT
66 GTTCAACAGACTT
*
40937631 GATCTTGATTTTGTTTC
1 GATTTTGATTTTGTTTC
40937648 AGAAATTTAA
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
76 2 0.03
77 57 0.72
78 1 0.01
80 19 0.24
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (78 bp):
GATTTTGATTTTGTTTCCAAACGAAGACTTAATCAAATAATTCTATTTCGAAATTTAATCCTGTC
GTTCAACAGACTT
Found at i:40938141 original size:40 final size:40
Alignment explanation
Indices: 40938083--40938172 Score: 137
Period size: 40 Copynumber: 2.2 Consensus size: 40
40938073 CGAAAAACTC
* *
40938083 CAAGCATTAGCGGTGC-TTTCCTGAAAACGCCGCTAAATAT
1 CAAGCATTAGCGGCGCTTTTCC-GAAAACGCCGCTAAAGAT
*
40938123 CAAGCATTAGCTGCGCTTTTCCGAAAACGCCGCTAAAGAT
1 CAAGCATTAGCGGCGCTTTTCCGAAAACGCCGCTAAAGAT
40938163 CAAGCATTAG
1 CAAGCATTAG
40938173 TGGAAATCGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 41 0.89
41 5 0.11
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (40 bp):
CAAGCATTAGCGGCGCTTTTCCGAAAACGCCGCTAAAGAT
Found at i:40938286 original size:40 final size:40
Alignment explanation
Indices: 40938186--40938286 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 40
40938176 AAATCGGGAT
* * * *
40938186 TTAGCGGCGCTTTTCGAAAAATGCTGCTAAATATCAAGCA
1 TTAGCGGCGCTTTTAGAAAAACGCCGCTAAAGATCAAGCA
* * **
40938226 TTAGCGGCGCTTTCAAAAAAACGCCGCTAAAGATTGAGCA
1 TTAGCGGCGCTTTTAGAAAAACGCCGCTAAAGATCAAGCA
* *
40938266 TTAGCGGCGTTTTTTGAAAAA
1 TTAGCGGCGCTTTTAGAAAAA
40938287 TGCCACAAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (40 bp):
TTAGCGGCGCTTTTAGAAAAACGCCGCTAAAGATCAAGCA
Found at i:40938559 original size:14 final size:14
Alignment explanation
Indices: 40938542--40938592 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
40938532 TATTTTGTGA
40938542 TTAGAGTTTTGAGT
1 TTAGAGTTTTGAGT
* *
40938556 TTAGGGTTTAGAGT
1 TTAGAGTTTTGAGT
*
40938570 TTAAAGTTTGTG-GT
1 TTAGAGTTT-TGAGT
*
40938584 TTAGGGTTT
1 TTAGAGTTT
40938593 ATTTTTTATA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
14 28 0.97
15 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (14 bp):
TTAGAGTTTTGAGT
Found at i:40938577 original size:21 final size:21
Alignment explanation
Indices: 40938542--40938593 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
40938532 TATTTTGTGA
**
40938542 TTAGAGTTTTGAGTTTAG-GGT
1 TTAGAGTTTAAAGTTT-GTGGT
40938563 TTAGAGTTTAAAGTTTGTGGT
1 TTAGAGTTTAAAGTTTGTGGT
*
40938584 TTAGGGTTTA
1 TTAGAGTTTA
40938594 TTTTTTATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (21 bp):
TTAGAGTTTAAAGTTTGTGGT
Found at i:40938834 original size:13 final size:14
Alignment explanation
Indices: 40938805--40938831 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40938795 TGGTTTATGA
40938805 TTTAGGGGTTGGGG
1 TTTAGGGGTTGGGG
40938819 TTTAGGGGTTGGG
1 TTTAGGGGTTGGG
40938832 TTTGGGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.00, G:0.56, T:0.37
Consensus pattern (14 bp):
TTTAGGGGTTGGGG
Found at i:40941077 original size:23 final size:22
Alignment explanation
Indices: 40941051--40941104 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
40941041 TGTATACGCG
40941051 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATA-ATACTAA
* *
40941074 TACATAATAATAATAATAGTAA
1 TACATAATAAAAATAATACTAA
40941096 TAC-TAATAA
1 TACATAATAA
40941105 TACTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (22 bp):
TACATAATAAAAATAATACTAA
Found at i:40941085 original size:3 final size:3
Alignment explanation
Indices: 40941054--40941122 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
40941044 ATACGCGTAC
* * * *
40941054 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
40941101 ATA ATA CTA ATA ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
40941123 CAAGGATATT
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:40941604 original size:13 final size:12
Alignment explanation
Indices: 40941586--40941623 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
40941576 AAGAAAAAAA
40941586 GAAGAGAGAGAGG
1 GAAGAGAGA-AGG
40941599 GAAGAGAGAAGG
1 GAAGAGAGAAGG
40941611 G-AGAGAGAAGG
1 GAAGAGAGAAGG
40941622 GA
1 GA
40941624 GGGGGAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.46
12 4 0.17
13 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:40942502 original size:7 final size:7
Alignment explanation
Indices: 40942490--40942514 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40942480 AATCTTCAAA
40942490 AAAATTT
1 AAAATTT
40942497 AAAATTT
1 AAAATTT
40942504 AAAATTT
1 AAAATTT
40942511 AAAA
1 AAAA
40942515 CTAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTT
Found at i:40942514 original size:22 final size:22
Alignment explanation
Indices: 40942497--40942554 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
40942487 AAAAAAATTT
40942497 AAAATTTAAAATTTAAAACTAA
1 AAAATTTAAAATTTAAAACTAA
** * *
40942519 AAAATAAAAAACTTAAAACTTA
1 AAAATTTAAAATTTAAAACTAA
*
40942541 AAAATTTAATATTT
1 AAAATTTAAAATTT
40942555 TAGTCCATAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAATTTAAAATTTAAAACTAA
Found at i:40942520 original size:29 final size:29
Alignment explanation
Indices: 40942488--40942543 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
40942478 AAAATCTTCA
** * *
40942488 AAAAAATTTAAAATTTAAAATTTAAAACT
1 AAAAAATAAAAAACTTAAAACTTAAAACT
40942517 AAAAAATAAAAAACTTAAAACTTAAAA
1 AAAAAATAAAAAACTTAAAACTTAAAA
40942544 ATTTAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (29 bp):
AAAAAATAAAAAACTTAAAACTTAAAACT
Found at i:40942543 original size:14 final size:14
Alignment explanation
Indices: 40942490--40942543 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
40942480 AATCTTCAAA
*
40942490 AAAATTTAAAATTT
1 AAAATTTAAAACTT
*
40942504 AAAATTTAAAACTAA
1 AAAATTTAAAACT-T
**
40942519 AAAATAAAAAACTT
1 AAAATTTAAAACTT
*
40942533 AAAACTTAAAA
1 AAAATTTAAAA
40942544 ATTTAATATT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATTTAAAACTT
Found at i:40945167 original size:8 final size:8
Alignment explanation
Indices: 40945154--40945190 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
40945144 TTACTACGTT
40945154 TTTTAAAA
1 TTTTAAAA
40945162 TTTTAAAA
1 TTTTAAAA
*
40945170 TTTTAACA
1 TTTTAAAA
40945178 TTTTGAAAA
1 TTTT-AAAA
40945187 TTTT
1 TTTT
40945191 TATTAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (8 bp):
TTTTAAAA
Found at i:40947165 original size:15 final size:16
Alignment explanation
Indices: 40947147--40947176 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40947137 TTTTTGTCTC
40947147 ATATATGAT-TAAAAT
1 ATATATGATCTAAAAT
40947162 ATATATGATCTAAAA
1 ATATATGATCTAAAA
40947177 GCAAGAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (16 bp):
ATATATGATCTAAAAT
Found at i:40952746 original size:30 final size:30
Alignment explanation
Indices: 40952712--40952772 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40952702 TCCTTAACTC
40952712 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
40952742 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
40952772 A
1 A
40952773 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:40957192 original size:30 final size:30
Alignment explanation
Indices: 40957158--40957218 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40957148 TCCTTAACTC
40957158 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
40957188 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
40957218 A
1 A
40957219 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:40958942 original size:28 final size:29
Alignment explanation
Indices: 40958910--40958967 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
40958900 TTTTATATAT
*
40958910 ATATTTTTATATTATTTA-TTTATTTTAA
1 ATATTTTTATATTATTTATTTTACTTTAA
40958938 ATATTTTTATATTATTTATTTTACTTTAA
1 ATATTTTTATATTATTTATTTTACTTTAA
40958967 A
1 A
40958968 CCTTATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (29 bp):
ATATTTTTATATTATTTATTTTACTTTAA
Found at i:40958957 original size:15 final size:15
Alignment explanation
Indices: 40958900--40958959 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
40958890 ATTTTAATCC
40958900 TTTTATA-TATATAT
1 TTTTATATTATATAT
40958914 TTTTATATTAT-T-T
1 TTTTATATTATATAT
* * *
40958927 ATTTATTTTAAATAT
1 TTTTATATTATATAT
*
40958942 TTTTATATTATTTAT
1 TTTTATATTATATAT
40958957 TTT
1 TTT
40958960 ACTTTAAACC
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
13 9 0.25
14 9 0.25
15 18 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTATATTATATAT
Found at i:40959020 original size:12 final size:12
Alignment explanation
Indices: 40959003--40959053 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
40958993 ATTTTATTTG
40959003 TATTATTTATTA
1 TATTATTTATTA
40959015 TATTATTTATT-
1 TATTATTTATTA
*
40959026 TTTTATTGTA-TA
1 TATTATT-TATTA
40959038 -A-TATTTATTA
1 TATTATTTATTA
40959048 TATTAT
1 TATTAT
40959054 GTATAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
9 2 0.06
10 6 0.19
11 8 0.25
12 16 0.50
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TATTATTTATTA
Found at i:40959048 original size:33 final size:30
Alignment explanation
Indices: 40958911--40959053 Score: 96
Period size: 28 Copynumber: 4.5 Consensus size: 30
40958901 TTTATATATA
*
40958911 TATTT-TTATATTATTTA-TTTATTT-TAAA
1 TATTTATTATATTATTTATTTTATTTGT-AT
**
40958939 TATTT-TTATATTATTTATTTTACTTTAAACCT
1 TATTTATTATATTATTTATTTTA-TTTGTA--T
* *
40958971 TATTTATATGCAAAAAATATTTATTTTATTTGTAT
1 TATTTAT-T----ATATTATTTATTTTATTTGTAT
*
40959006 TATTTATTATATTATTTATTTTTTATTGTAT
1 TATTTATTATATTATTTATTTTAT-TTGTAT
40959037 AATATTTATTATATTAT
1 --TATTTATTATATTAT
40959054 GTATAATTTT
Statistics
Matches: 92, Mismatches: 9, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
28 17 0.18
29 4 0.04
30 17 0.18
31 6 0.07
32 5 0.05
33 16 0.17
34 2 0.02
35 8 0.09
37 4 0.04
38 13 0.14
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (30 bp):
TATTTATTATATTATTTATTTTATTTGTAT
Found at i:40959119 original size:15 final size:15
Alignment explanation
Indices: 40959080--40959120 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
40959070 TTTGTAAATT
40959080 ATTATTAAATATTAC
1 ATTATTAAATATTAC
* *
40959095 ATTTTTATATA-T-C
1 ATTATTAAATATTAC
40959108 ATTATTAAATATT
1 ATTATTAAATATT
40959121 TAGTATATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
13 10 0.48
14 2 0.10
15 9 0.43
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTATTAAATATTAC
Found at i:40959134 original size:21 final size:21
Alignment explanation
Indices: 40959087--40959134 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
40959077 ATTATTATTA
* *
40959087 AATATTACATTTTTATATATC
1 AATATTAAATATTTATATATC
*
40959108 ATTATTAAATATTTAGTATAT-
1 AATATTAAATATTTA-TATATC
40959129 AATATT
1 AATATT
40959135 CTAAAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (21 bp):
AATATTAAATATTTATATATC
Found at i:40959746 original size:31 final size:31
Alignment explanation
Indices: 40959670--40959743 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
40959660 TCAAGTTATC
*
40959670 TTAAATATTAAAATAAAAATAAAAATTTTGAA
1 TTAAATA-TAAAATAAAAATAAAAATTTAGAA
*
40959702 TCAAA-ACTAAAATAAATAATAAAAA-TTAG-A
1 TTAAATA-TAAAATAAA-AATAAAAATTTAGAA
40959732 TTAAATATAAAA
1 TTAAATATAAAA
40959744 ATATCAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 10 0.28
31 14 0.39
32 12 0.33
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (31 bp):
TTAAATATAAAATAAAAATAAAAATTTAGAA
Found at i:40964426 original size:34 final size:34
Alignment explanation
Indices: 40964386--40964453 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
40964376 AGTAAACCTT
40964386 AAATCCTAAACCATTTAATATATAAAAAGCCTAA
1 AAATCCTAAACCATTTAATATATAAAAAGCCTAA
*
40964420 AAATCCTAAACCATTTAATATATATAAAGCCTAA
1 AAATCCTAAACCATTTAATATATAAAAAGCCTAA
40964454 TCCTTAAGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (34 bp):
AAATCCTAAACCATTTAATATATAAAAAGCCTAA
Found at i:40964507 original size:21 final size:21
Alignment explanation
Indices: 40964483--40964541 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
40964473 CTTAACCCTT
* *
40964483 AACCCCTAAGCCTTAAACCCC
1 AACCCCTAAACCATAAACCCC
* **
40964504 AACCCTTAAACCATAAACCAT
1 AACCCCTAAACCATAAACCCC
*
40964525 AATCCCTAAACCCATAA
1 AACCCCTAAA-CCATAA
40964542 TCCATAAACC
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 24 0.80
22 6 0.20
ACGTcount: A:0.42, C:0.39, G:0.02, T:0.17
Consensus pattern (21 bp):
AACCCCTAAACCATAAACCCC
Found at i:40964513 original size:14 final size:15
Alignment explanation
Indices: 40964475--40964515 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
40964465 ACCTAACACT
40964475 TAACCCTT-AACCCC
1 TAACCCTTAAACCCC
*
40964489 TAAGCCTTAAACCCC
1 TAACCCTTAAACCCC
40964504 -AACCCTTAAACC
1 TAACCCTTAAACC
40964516 ATAAACCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.34, C:0.44, G:0.02, T:0.20
Consensus pattern (15 bp):
TAACCCTTAAACCCC
Found at i:40964556 original size:22 final size:21
Alignment explanation
Indices: 40964507--40964614 Score: 69
Period size: 22 Copynumber: 5.0 Consensus size: 21
40964497 AAACCCCAAC
*
40964507 CCTTAAACCATAAACCATAAT
1 CCTTAAACCATAAACCATAAA
* *
40964528 CCCTAAACCCATAATCCATAAA
1 CCTTAAA-CCATAAACCATAAA
*
40964550 CCTTAAA--ATAGTAACTCATACA
1 CCTTAAACCATA--AAC-CATAAA
* *
40964572 CTTTAAACTC-TAAACCATATA
1 CCTTAAAC-CATAAACCATAAA
* * *
40964593 CCCTAAATCATAAACCCTAAA
1 CCTTAAACCATAAACCATAAA
40964614 C
1 C
40964615 TATAATGATA
Statistics
Matches: 66, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.05
20 1 0.02
21 28 0.42
22 32 0.48
24 2 0.03
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (21 bp):
CCTTAAACCATAAACCATAAA
Found at i:40964604 original size:14 final size:14
Alignment explanation
Indices: 40964575--40964619 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
40964565 TCATACACTT
*
40964575 TAAACTCTAAACCA
1 TAAACCCTAAACCA
* *
40964589 TATACCCTAAATCA
1 TAAACCCTAAACCA
*
40964603 TAAACCCTAAACTA
1 TAAACCCTAAACCA
40964617 TAA
1 TAA
40964620 TGATAATTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:40964725 original size:7 final size:7
Alignment explanation
Indices: 40964713--40964760 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
40964703 ACTAATTAAT
40964713 CTAAACC
1 CTAAACC
40964720 CTAAACTC
1 CTAAAC-C
*
40964728 CTAATCC
1 CTAAACC
*
40964735 CTAATCC
1 CTAAACC
40964742 CTAAACC
1 CTAAACC
* *
40964749 GTAAATC
1 CTAAACC
40964756 CTAAA
1 CTAAA
40964761 ACATGAACCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
7 29 0.83
8 6 0.17
ACGTcount: A:0.40, C:0.35, G:0.02, T:0.23
Consensus pattern (7 bp):
CTAAACC
Found at i:40964792 original size:23 final size:21
Alignment explanation
Indices: 40964766--40964813 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
40964756 CTAAAACATG
40964766 AACCTTAAACCCACTAACACTTA
1 AACCTTAAA-CCAC-AACACTTA
*
40964789 AACCTTAAACCACAACCCTTA
1 AACCTTAAACCACAACACTTA
40964810 AACC
1 AACC
40964814 ACCCTTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.46
22 4 0.17
23 9 0.38
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.19
Consensus pattern (21 bp):
AACCTTAAACCACAACACTTA
Found at i:40964822 original size:25 final size:25
Alignment explanation
Indices: 40964791--40964838 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
40964781 AACACTTAAA
40964791 CCTTAAACCACAA-CCCTTAAACCAC
1 CCTTAAACCACAATCCC-TAAACCAC
*
40964816 CCTTAAACCATAATCCCTAAACC
1 CCTTAAACCACAATCCCTAAACC
40964839 CATAATCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.40, C:0.42, G:0.00, T:0.19
Consensus pattern (25 bp):
CCTTAAACCACAATCCCTAAACCAC
Found at i:40964841 original size:15 final size:15
Alignment explanation
Indices: 40964819--40964853 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
40964809 AAACCACCCT
*
40964819 TAAA-CCATAATCCC
1 TAAACCCATAATCCA
40964833 TAAACCCATAATCCA
1 TAAACCCATAATCCA
40964848 TAAACC
1 TAAACC
40964854 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAACCCATAATCCA
Found at i:40964858 original size:22 final size:21
Alignment explanation
Indices: 40964821--40964904 Score: 69
Period size: 22 Copynumber: 3.9 Consensus size: 21
40964811 ACCACCCTTA
* *
40964821 AACCATAATCCCTAAACCCAT
1 AACCATAAACCTTAAACCCAT
***
40964842 AATCCATAAACCTTAAAATAAT
1 AA-CCATAAACCTTAAACCCAT
* *
40964864 AACTCATAAACATTAAACCCTT
1 AAC-CATAAACCTTAAACCCAT
* *
40964886 AACCATATACCGTAAACCC
1 AACCATAAACCTTAAACCC
40964905 TAAACTATAA
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
21 16 0.33
22 32 0.67
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.23
Consensus pattern (21 bp):
AACCATAAACCTTAAACCCAT
Done.