Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold150
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: 1465027
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 98465 characters in sequence are not A, C, G, or T
File 4 of 9
Found at i:445006 original size:40 final size:38
Alignment explanation
Indices: 444947--445023 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 38
444937 GGGTAAAAGA
444947 CATAATGTATCGATACATTGA-AGAATGTATCGATACATT
1 CATAATGTATCGATACATTGAGA-AATGTAT-GATACATT
444986 CATACATGTATCGATACATTGAGAAATGTATGATACAT
1 CATA-ATGTATCGATACATTGAGAAATGTATGATACAT
445024 ATGGGTACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
39 11 0.31
40 24 0.67
41 1 0.03
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (38 bp):
CATAATGTATCGATACATTGAGAAATGTATGATACATT
Found at i:446091 original size:115 final size:117
Alignment explanation
Indices: 445896--446543 Score: 801
Period size: 115 Copynumber: 5.6 Consensus size: 117
445886 CACTAACTTG
* * *
445896 TGTGGGCTTTGAAAAGAGTTACCACTGACTCGTGTGGGCTTTGAAAA-GAGTGCTACTGACTTGT
1 TGTGGGCTTTGAAAAG-GGTGCCACTGACT--TGTGGGCTTTGAAAAGGA-TGCCACTGACTTGT
* * * * *
445960 GAGCTTTGAAAGGGTGCCACTGACTTGTGGTCTTTG-AAAG-GGTGCCACTGACT-
62 GGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTC
* * * *
446013 TGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGGGCTGT-AAAAGGAATGCCACTGACTTGTGG
1 TGTGGGCTTTGAAAAG-GGTGCCACTGACTTGTGGGCTTTGAAAAGG-ATGCCACTGACTTGTGG
* * **
446077 GCTTTGAAAGGGTGCCACTGACTTATGGGCTTT-AAAAG-GATT-CCATTGACT-
64 GCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAG-TTGCCACCGACTC
* * *
446128 TGTGGGCTTTG-AAAGGATGCCACTGACTTGTGAGCTTTGAAAA-GATGCCACTGACTTATGGGC
1 TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGC
446191 TTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCA-CGACTC
66 TTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTC
* * * * *
446242 GTGCGGGATTTG-AAAGGGTGCCATTGACTTGTGGTCTTTGAAAAGG-TGCCACTAACTTGTGGG
1 -TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGG
446305 CTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTC
65 CTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTC
* *
446358 ATGCGGGCTTT-AAAAGGGTGCCACTGACTTATGGGCTTTGAAAAGG-TGCCACTGACTTGTGGG
1 -TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGG
*
446421 CTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAAGAGTTGCCACCGACTC
65 CTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTC
* * * *
446474 ATGTGGGCTTTG-AAATGGTGCCTCTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTATAGG
1 -TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGG
446537 CTTTGAA
65 CTTTGAA
446544 GAGATGAACG
Statistics
Matches: 476, Mismatches: 40, Indels: 31
0.87 0.07 0.06
Matches are distributed among these distances:
112 47 0.10
113 30 0.06
114 16 0.03
115 181 0.38
116 174 0.37
117 28 0.06
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (117 bp):
TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGC
TTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTC
Found at i:446549 original size:28 final size:28
Alignment explanation
Indices: 445896--446543 Score: 701
Period size: 28 Copynumber: 22.5 Consensus size: 28
445886 CACTAACTTG
* *
445896 TGTGGGCTTTGAAAAGAGTTACCACTGACT
1 TGTGGGCTTTG-AAAG-GATGCCACTGACT
* *
445926 CGTGTGGGCTTTGAAAAGAGTGCTACTGACT
1 --TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
445957 TGTGAGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
445985 TGTGGTCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
446013 TGTGGGCTTTGAAAAGAGTTGCCACCGACT
1 TGTGGGCTTTG-AAAG-GATGCCACTGACT
* * *
446043 CGTGGGCTGTAAAAGGAATGCCACTGACT
1 TGTGGGCTTTGAAAGG-ATGCCACTGACT
*
446072 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
446100 TATGGGCTTTAAAAGGATTCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
446128 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
446156 TGTGAGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
446184 TATGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
446212 TGTGGGCTTTGAAAAGAGTTGCCAC-GACT
1 TGTGGGCTTTG-AAAG-GATGCCACTGACT
* * * *
446241 CGTGCGGGATTTGAAAGGGTGCCATTGACT
1 --TGTGGGCTTTGAAAGGATGCCACTGACT
* *
446271 TGTGGTCTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
446299 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
446327 TGTGGGCTTTGAAAAGAGTTGCCACCGACT
1 TGTGGGCTTTG-AAAG-GATGCCACTGACT
* * *
446357 CATGCGGGCTTTAAAAGGGTGCCACTGACT
1 --TGTGGGCTTTGAAAGGATGCCACTGACT
*
446387 TATGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
446415 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
446443 TATGGGCTTTGAAAAGAGTTGCCACCGACT
1 TGTGGGCTTTG-AAAG-GATGCCACTGACT
*
446473 CATGTGGGCTTTGAAATGG-TGCCTCTGACT
1 --TGTGGGCTTTGAAA-GGATGCCACTGACT
446503 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
446531 TATAGGCTTTGAA
1 TGTGGGCTTTGAA
446544 GAGATGAACG
Statistics
Matches: 525, Mismatches: 68, Indels: 50
0.82 0.11 0.08
Matches are distributed among these distances:
27 12 0.02
28 299 0.57
29 77 0.15
30 77 0.15
31 29 0.06
32 31 0.06
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:447756 original size:1 final size:1
Alignment explanation
Indices: 447750--447826 Score: 55
Period size: 1 Copynumber: 77.0 Consensus size: 1
447740 TGTTTGTTTG
* * ** * * ** * *
447750 TTTTTTTTTTTTGTTTTTTGTTTTGGTTTTTTTTGTTTTTTTGTTTTTTTGGTTTTTTTCTATTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
447815 TTTTATTTTTTT
1 TTTTTTTTTTTT
447827 GGGTATGAAG
Statistics
Matches: 58, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.03, C:0.01, G:0.10, T:0.86
Consensus pattern (1 bp):
T
Found at i:447764 original size:17 final size:17
Alignment explanation
Indices: 447746--447827 Score: 87
Period size: 17 Copynumber: 4.7 Consensus size: 17
447736 TTTCTGTTTG
447746 TTTGTTTTTTT-TTTTT
1 TTTGTTTTTTTGTTTTT
447762 GTTT-TTTGTTTTGGTTTTT
1 -TTTGTTT-TTTT-GTTTTT
447781 TTTGTTTTTTTGTTTTT
1 TTTGTTTTTTTGTTTTT
* *
447798 TTGGTTTTTTTCTATTTT
1 TTTGTTTTTTTGT-TTTT
*
447816 TTTATTTTTTTG
1 TTTGTTTTTTTG
447828 GGTATGAAGG
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
16 3 0.05
17 24 0.44
18 20 0.36
19 8 0.15
ACGTcount: A:0.02, C:0.01, G:0.12, T:0.84
Consensus pattern (17 bp):
TTTGTTTTTTTGTTTTT
Found at i:447783 original size:23 final size:23
Alignment explanation
Indices: 447740--447823 Score: 84
Period size: 26 Copynumber: 3.6 Consensus size: 23
447730 GACCCCTTTC
*
447740 TGTTTGTTTGTTTT--TTTTTTT
1 TGTTTTTTTGTTTTGGTTTTTTT
447761 TG-TTTTTTGTTTTGGTTTTTTT
1 TGTTTTTTTGTTTTGGTTTTTTT
447783 TGTTTTTTTGTTTTTTTGGTTTTTTT
1 TGTTTTTTTG---TTTTGGTTTTTTT
* *
447809 CTATTTTTTTATTTT
1 -TGTTTTTTTGTTTT
447824 TTTGGGTATG
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
20 10 0.19
21 2 0.04
22 9 0.17
23 7 0.13
24 4 0.08
26 13 0.25
27 8 0.15
ACGTcount: A:0.02, C:0.01, G:0.13, T:0.83
Consensus pattern (23 bp):
TGTTTTTTTGTTTTGGTTTTTTT
Found at i:461787 original size:20 final size:20
Alignment explanation
Indices: 461758--461814 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
461748 GGTAAAAGAC
461758 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
461778 AGAATCTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
461798 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
461815 CTGGATACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:462145 original size:20 final size:19
Alignment explanation
Indices: 462116--462154 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
462106 AGGTCAAAAC
*
462116 CCTTAAATGTATTGATACA
1 CCTTAAATGTATCGATACA
462135 CCTTCAAATGTATCGATACA
1 CCTT-AAATGTATCGATACA
462155 TAATGCACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (19 bp):
CCTTAAATGTATCGATACA
Found at i:462182 original size:13 final size:13
Alignment explanation
Indices: 462164--462188 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
462154 ATAATGCACA
462164 GTATCGATACATT
1 GTATCGATACATT
462177 GTATCGATACAT
1 GTATCGATACAT
462189 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:462201 original size:20 final size:21
Alignment explanation
Indices: 462176--462228 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
462166 ATCGATACAT
*
462176 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
462196 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
462217 TGTATCGATACA
1 TGTATCGATACA
462229 GTTGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:462325 original size:33 final size:32
Alignment explanation
Indices: 462270--462333 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
462260 CTTAATTGTT
*
462270 TGTATCAATACACACAAGATGTATCAATACAA
1 TGTATCAATACACACAAAATGTATCAATACAA
* *
462302 TGTATCGATACATCACAAAATGTATCGATACA
1 TGTATCAATACA-CACAAAATGTATCAATACA
462334 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.27
Consensus pattern (32 bp):
TGTATCAATACACACAAAATGTATCAATACAA
Found at i:468500 original size:13 final size:13
Alignment explanation
Indices: 468482--468507 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
468472 ATAGCATTCT
468482 TTGTATCGATACA
1 TTGTATCGATACA
468495 TTGTATCGATACA
1 TTGTATCGATACA
468508 AAGGGTTTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:468974 original size:20 final size:22
Alignment explanation
Indices: 468949--468993 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
468939 GCAGCACTCA
*
468949 CCAGGTCGCGACC-GGCA-CCC
1 CCAGGTCGCAACCGGGCAGCCC
468969 CCAGGTCGCAACCGGGCAGCCC
1 CCAGGTCGCAACCGGGCAGCCC
468991 CCA
1 CCA
468994 CACTAACAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.55
21 4 0.18
22 6 0.27
ACGTcount: A:0.18, C:0.49, G:0.29, T:0.04
Consensus pattern (22 bp):
CCAGGTCGCAACCGGGCAGCCC
Found at i:470973 original size:20 final size:19
Alignment explanation
Indices: 470944--470982 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
470934 AGGTCAAAAC
470944 CCTTAAATGTATTGATACA
1 CCTTAAATGTATTGATACA
470963 CCTTCAAATGTATTGATACA
1 CCTT-AAATGTATTGATACA
470983 TAATGCACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (19 bp):
CCTTAAATGTATTGATACA
Found at i:471010 original size:13 final size:13
Alignment explanation
Indices: 470992--471016 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
470982 ATAATGCACA
470992 GTATCGATACATT
1 GTATCGATACATT
471005 GTATCGATACAT
1 GTATCGATACAT
471017 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:471029 original size:20 final size:21
Alignment explanation
Indices: 471004--471056 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
470994 ATCGATACAT
*
471004 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
471024 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
471045 TGTATCGATACA
1 TGTATCGATACA
471057 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:471160 original size:33 final size:32
Alignment explanation
Indices: 471098--471161 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
471088 CTTAACTATT
* *
471098 TGTATCGATACACACAAGATGTATTGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
471130 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
471162 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:473061 original size:44 final size:43
Alignment explanation
Indices: 472963--473087 Score: 139
Period size: 43 Copynumber: 2.9 Consensus size: 43
472953 TTTATCTTAT
* * *
472963 AAAATATTTTATCTTAAATCTCAAAGTATTATTTAAAATAATAAA
1 AAAATATTTTATATTAAATCTCAAATTACTATTT-AAA-AATAAA
* *
473008 AAAA-A--TTATATTCAATCTCGAATTTACTATTTAAAAATAAA
1 AAAATATTTTATATTAAATCTC-AAATTACTATTTAAAAATAAA
* *
473049 AAAATATTTTATATTAAATCTTAAATTACTAATTAAAAA
1 AAAATATTTTATATTAAATCTCAAATTACTATTTAAAAA
473088 ATGATAAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
41 10 0.15
42 16 0.24
43 24 0.36
44 13 0.19
45 4 0.06
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (43 bp):
AAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAAA
Found at i:473088 original size:44 final size:44
Alignment explanation
Indices: 472963--473099 Score: 138
Period size: 44 Copynumber: 3.1 Consensus size: 44
472953 TTTATCTTAT
* * * *
472963 AAAATATTTTATCTTAAATCTCAAAGTATTATTTAAAATAATAAA
1 AAAATATTTTATATTAAATCTCAAATTACTAATTAAAA-AATAAA
* * *
473008 AAAA-A--TTATATTCAATCTCGAATTTACT-ATTTAAAAATAAA
1 AAAATATTTTATATTAAATCTC-AAATTACTAATTAAAAAATAAA
*
473049 AAAATATTTTATATTAAATCTTAAATTACTAATTAAAAAATGATAA
1 AAAATATTTTATATTAAATCTCAAATTACTAATTAAAAAAT-A-AA
473095 AAAAT
1 AAAAT
473100 TAAAAAAATA
Statistics
Matches: 74, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
41 10 0.14
42 18 0.24
43 12 0.16
44 22 0.30
45 5 0.07
46 7 0.09
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (44 bp):
AAAATATTTTATATTAAATCTCAAATTACTAATTAAAAAATAAA
Found at i:473139 original size:27 final size:27
Alignment explanation
Indices: 473107--473162 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
473097 AATTAAAAAA
473107 ATATTTTATA-TAAAATCTTGAATTACT
1 ATATTTTATATTAAAAT-TTGAATTACT
473134 ATATTTTATATTAAAATTTGAATTACT
1 ATATTTTATATTAAAATTTGAATTACT
473161 AT
1 AT
473163 TTACAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (27 bp):
ATATTTTATATTAAAATTTGAATTACT
Found at i:473158 original size:82 final size:81
Alignment explanation
Indices: 473052--473201 Score: 221
Period size: 82 Copynumber: 1.8 Consensus size: 81
473042 AAATAAAAAA
*
473052 ATATTTTATATTAAATCTTAAATTACTAATTAAAAAATGATAAAAAATTAAAAAAATATTTTATA
1 ATATTTTATATTAAATCTTAAATTACTAATTAAAAAATAAT-AAAAATTAAAAAAATATTTTATA
473117 TAAAATCTTGAATTACT
65 TAAAATCTTGAATTACT
* * * * *
473134 ATATTTTATATTAAAAT-TTGAATTACTATTTACAAAATAATAAAAATTAAATATATATTTTATA
1 ATATTTTATATT-AAATCTTAAATTACTAATTAAAAAATAATAAAAATTAAAAAAATATTTTATA
473198 TAAA
65 TAAA
473202 TCTCAAATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 25 0.41
82 32 0.52
83 4 0.07
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (81 bp):
ATATTTTATATTAAATCTTAAATTACTAATTAAAAAATAATAAAAATTAAAAAAATATTTTATAT
AAAATCTTGAATTACT
Found at i:473225 original size:52 final size:51
Alignment explanation
Indices: 473154--473736 Score: 340
Period size: 53 Copynumber: 11.7 Consensus size: 51
473144 TTAAAATTTG
473154 AATTACTATTTACAAAATAATAAAAATTAAATATATATTTTATATAAATCTCA
1 AATTACTATTTA-AAAATAATAAAAATTAAA-ATATATTTTATATAAATCTCA
* * * *
473207 AATTAATTTTTAAAAATAATAAAAATTAAAA-ATATTTTATTTTAGATGC-CA
1 AATTACTATTTAAAAATAATAAAAATTAAAATATATTTTA-TATAAAT-CTCA
* * * **
473258 AATTACTA-TTAACAATAAT-AAAATTAAAATAAGATTTTATATTAAATTTTG
1 AATTACTATTTAAAAATAATAAAAATTAAAAT-ATATTTTATA-TAAATCTCA
*
473309 AATTGCTATTTAAAAATAA-AAAAA-T----T-TA---TAT-TAAATCT-A
1 AATTACTATTTAAAAATAATAAAAATTAAAATATATTTTATATAAATCTCA
*
473348 GAATTACTAATTAAAAATAATAAAAAATTAAAATAATATTTTATATAAATCTCA
1 -AATTACTATTTAAAAATAAT-AAAAATTAAAAT-ATATTTTATATAAATCTCA
* * **
473402 AATTACTATTT---AA-AA-AAAATTTAAAA-ATAGTTTATATTAAATCTTG
1 AATTACTATTTAAAAATAATAAAAATTAAAATATATTTTATA-TAAATCTCA
* ** * * * **
473448 AATTAATATTTAAAAATTTTTAAAAAATAAAAAAATATTTTATATTACATCTTG
1 AATTACTATTTAAAAA-TAAT-AAAAATTAAAATATATTTTATA-TAAATCTCA
* * **
473502 AATTACTTTTTAAAAATAATAAAAATTTAAAA-ATATTTTATATTAATCTTG
1 AATTACTATTTAAAAATAATAAAAA-TTAAAATATATTTTATATAAATCTCA
* * * * * **
473553 TATTA-TTTTTTAAAATAATAAAAAATTAAAAATGTATTTTATATTCAATCTTT
1 AATTACTATTTAAAAATAAT-AAAAATT-AAAATATATTTTATA-TAAATCTCA
* * *
473606 AATTACCATTTAAAAA-AAT----A--AAAA-AT-TTATAT-TAAATCTCG
1 AATTACTATTTAAAAATAATAAAAATTAAAATATATTTTATATAAATCTCA
*
473647 AATTGCTATTTAAAATATAATAAAAATTAAACA-ATATTTTA-AGGTAAATCTCA
1 AATTACTATTTAAAA-ATAATAAAAATTAAA-ATATATTTTATA--TAAATCTCA
* *
473700 AATTACT-TTTAAAAATATAATAAAAATGAAAAAATAT
1 AATTACTATTT-AAAA-ATAATAAAAATTAAAATATAT
473737 CTGATATATG
Statistics
Matches: 418, Mismatches: 59, Indels: 106
0.72 0.10 0.18
Matches are distributed among these distances:
40 23 0.06
41 19 0.05
42 9 0.02
43 9 0.02
44 1 0.00
45 14 0.03
46 17 0.04
47 13 0.03
48 1 0.00
49 19 0.05
50 39 0.09
51 57 0.14
52 63 0.15
53 94 0.22
54 40 0.10
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (51 bp):
AATTACTATTTAAAAATAATAAAAATTAAAATATATTTTATATAAATCTCA
Found at i:473230 original size:81 final size:81
Alignment explanation
Indices: 473052--473218 Score: 191
Period size: 82 Copynumber: 2.1 Consensus size: 81
473042 AAATAAAAAA
* * *
473052 ATATTTTAT-ATTAAATCTTAAATTACTAATTAAAAAATGATAAAAAATTAAAAAAATATTTTAT
1 ATATTTTATAATAAAAT-TTGAATTACTAATTAAAAAATAATAAAAAATTAAAAAAATATTTTAT
**
473116 ATAAAATCTTGAATTAC
65 ATAAAATCTCAAATTAC
* * * * *
473133 TATATTTTATATTAAAATTTGAATTACTATTTACAAAATAAT-AAAAATTAAATATATATTTTAT
1 -ATATTTTATAATAAAATTTGAATTACTAATTAAAAAATAATAAAAAATTAAAAAAATATTTTAT
473197 AT-AAATCTCAAATTA-
65 ATAAAATCTCAAATTAC
473212 AT-TTTTA
1 ATATTTTA
473219 AAAATAATAA
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
77 5 0.07
78 2 0.03
80 11 0.15
81 22 0.30
82 29 0.39
83 5 0.07
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (81 bp):
ATATTTTATAATAAAATTTGAATTACTAATTAAAAAATAATAAAAAATTAAAAAAATATTTTATA
TAAAATCTCAAATTAC
Found at i:473342 original size:40 final size:41
Alignment explanation
Indices: 473293--473373 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 41
473283 AAAATAAGAT
* * * *
473293 TTTATATTAAATTTTGAATTGCTATTTAAAAATAA-AAAAA
1 TTTATATTAAATCTAGAATTACTAATTAAAAATAATAAAAA
473333 TTTATATTAAATCTAGAATTACTAATTAAAAATAATAAAAA
1 TTTATATTAAATCTAGAATTACTAATTAAAAATAATAAAAA
473374 ATTAAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 31 0.86
41 5 0.14
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (41 bp):
TTTATATTAAATCTAGAATTACTAATTAAAAATAATAAAAA
Found at i:473419 original size:46 final size:47
Alignment explanation
Indices: 473175--473463 Score: 172
Period size: 51 Copynumber: 6.0 Consensus size: 47
473165 ACAAAATAAT
* *
473175 AAAAATT-AAATATATATTTTATA-TAAATCTCAAATTAATTTTTAAA
1 AAAAATTAAAATA-ATATTTTATATTAAATCTCAAATTACTATTTAAA
* * * * *
473221 AATAATAAAAATTAAAAATATTTTATTTTAGATGC-CAAATTACTATTAACAATA
1 AAAAATTAAAA-T---AATATTTTATATTAAAT-CTCAAATTACTATT--TAA-A
* * ** *
473275 ATAAAATTAAAATAAGATTTTATATTAAATTTTGAATTGCTATTT---
1 A-AAAATTAAAATAATATTTTATATTAAATCTCAAATTACTATTTAAA
473320 AAAAA-TAAAA-AA-A-TTTATATTAAATCT-AGAATTACTAATTAAAAATAATA
1 AAAAATTAAAATAATATTTTATATTAAATCTCA-AATTACT-ATT-----TAA-A
473370 AAAAATTAAAATAATATTTTATA-TAAATCTCAAATTACTATTTAAA
1 AAAAATTAAAATAATATTTTATATTAAATCTCAAATTACTATTTAAA
* * ** *
473416 AAAAATTTAAA-AATAGTTTATATTAAATCTTGAATTAATATTTAAA
1 AAAAATTAAAATAATATTTTATATTAAATCTCAAATTACTATTTAAA
473462 AA
1 AA
473464 TTTTTAAAAA
Statistics
Matches: 189, Mismatches: 25, Indels: 58
0.69 0.09 0.21
Matches are distributed among these distances:
40 19 0.10
41 4 0.02
42 2 0.01
43 5 0.03
44 4 0.02
45 11 0.06
46 39 0.21
47 6 0.03
48 1 0.01
50 14 0.07
51 43 0.23
52 6 0.03
53 17 0.09
54 10 0.05
55 8 0.04
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.39
Consensus pattern (47 bp):
AAAAATTAAAATAATATTTTATATTAAATCTCAAATTACTATTTAAA
Found at i:473437 original size:45 final size:47
Alignment explanation
Indices: 473369--473463 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 47
473359 TAAAAATAAT
* *
473369 AAAAAATTAAAATAATATTTTATA-TAAATCTCAAATTACTATTTAA
1 AAAAAATTAAAATAATAGTTTATATTAAATCTCAAATTAATATTTAA
* **
473415 AAAAAATTTAAA-AATAGTTTATATTAAATCTTGAATTAATATTTAA
1 AAAAAATTAAAATAATAGTTTATATTAAATCTCAAATTAATATTTAA
473461 AAA
1 AAA
473464 TTTTTAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 10 0.23
46 33 0.77
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (47 bp):
AAAAAATTAAAATAATAGTTTATATTAAATCTCAAATTAATATTTAA
Found at i:473474 original size:46 final size:46
Alignment explanation
Indices: 473369--473476 Score: 123
Period size: 46 Copynumber: 2.4 Consensus size: 46
473359 TAAAAATAAT
* *
473369 AAAAAA-TTAAAATAATATTTTATATAAATCTCAAATTACTATTTAA
1 AAAAAATTTAAAA-AATAGTTTATATAAATCTCAAATTAATATTTAA
**
473415 AAAAAATTT-AAAAATAGTTTATATTAAATCTTGAATTAATATTT-A
1 AAAAAATTTAAAAAATAGTTTATA-TAAATCTCAAATTAATATTTAA
**
473460 AAAATTTTTAAAAAATA
1 AAAAAATTTAAAAAATA
473477 AAAAAATATT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
45 18 0.34
46 33 0.62
47 2 0.04
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (46 bp):
AAAAAATTTAAAAAATAGTTTATATAAATCTCAAATTAATATTTAA
Found at i:473633 original size:104 final size:107
Alignment explanation
Indices: 473415--473634 Score: 281
Period size: 104 Copynumber: 2.1 Consensus size: 107
473405 TACTATTTAA
**
473415 AAAAAATTTAAAAATAGTTTATATTAAATCTTGAATTAATATTTAAAAATTTTTAAAAAATAAAA
1 AAAAAATTTAAAAATAGTTTATATTAAATCTTGAATTAATATTTAAAAATTAATAAAAAATAAAA
**
473480 AAATATTTTATATTACATCTTGAATTACTTTTTAAAAATAAT
66 AAATATTTTATATTACATCTTGAATTACCATTTAAAAATAAT
* * * *
473522 -AAAAATTTAAAAATATTTTATATT-AATCTTGTATT-ATTTTTTAAAA-TAATAAAAAATTAAA
1 AAAAAATTTAAAAATAGTTTATATTAAATCTTGAATTAATATTTAAAAATTAATAAAAAA-TAAA
** *
473583 AATGTATTTTATATT-CAATCTTTAATTACCATTTAAAAA-AAT
65 AAAATATTTTATATTAC-ATCTTGAATTACCATTTAAAAATAAT
473625 AAAAAATTTA
1 AAAAAATTTA
473635 TATTAAATCT
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
103 12 0.12
104 54 0.55
105 10 0.10
106 23 0.23
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (107 bp):
AAAAAATTTAAAAATAGTTTATATTAAATCTTGAATTAATATTTAAAAATTAATAAAAAATAAAA
AAATATTTTATATTACATCTTGAATTACCATTTAAAAATAAT
Found at i:473644 original size:41 final size:43
Alignment explanation
Indices: 473590--473672 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 43
473580 AAAAATGTAT
* **
473590 TTTATATTCAATCTTTAATTACCATTTAAAA-A-AATAAAAAA
1 TTTATATTAAATCTCGAATTACCATTTAAAATATAATAAAAAA
* *
473631 TTTATATTAAATCTCGAATTGCTATTTAAAATATAATAAAAA
1 TTTATATTAAATCTCGAATTACCATTTAAAATATAATAAAAA
473673 TTAAACAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 26 0.74
42 1 0.03
43 8 0.23
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.40
Consensus pattern (43 bp):
TTTATATTAAATCTCGAATTACCATTTAAAATATAATAAAAAA
Found at i:473698 original size:298 final size:293
Alignment explanation
Indices: 473138--473714 Score: 724
Period size: 298 Copynumber: 2.0 Consensus size: 293
473128 ATTACTATAT
* * * *
473138 TTTATATTAAAATTTGAATTACTATTTACAAAATAATAAAAATTAAATATATATTTTATATAAAT
1 TTTATATTAAAATTTGAATTAATATTTACAAAATAATAAAAAATAAAAAAATATTTTATATAAAT
*
473203 CTCAAATTAATTTTTAAAAATAATAAAAATTAAAAATATTTTATTTTAGATGCCAAATTACTATT
66 CTCAAATTAATTTTTAAAAATAATAAAAATTAAAAATATTTTATATTAGATGCCAAATTACTATT
* * *
473268 AACAATAATAAAATTAAAATAAGATTTTATATTAAATTTTGAATTGCTATTTAAAAATAAAAAAA
131 AACAATAATAAAATTAAAATAAGATTTTATATTAAATTTTGAATTACCATTTAAAAAAAAAAAAA
*
473333 TTTATATTAAATCTAGAATTACTAATTAAAAATAATAAAAAATTAAAATAATATTTTATATAAAT
196 TTTATATTAAATCTAGAATTACTAATTAAAAATAATAAAAAATTAAAACAATATTTTATATAAAT
473398 CTCAAATTACTATTTAAAAAAAATTTAAAAATAG
261 CTCAAATTACT-TTTAAAAAAAATTTAAAAATAG
**
473432 TTTATATT-AAATCTTGAATTAATATTTA-AAAATTTTTAAAAAATAAAAAAATATTTTATATTA
1 TTTATATTAAAAT-TTGAATTAATATTTACAAAA-TAATAAAAAATAAAAAAATATTTTATA-TA
* ** * ***
473495 CATCTTGAATTACTTTTTAAAAATAATAAAAATTTAAAAATATTTTATATTA-AT-CTTGTATTA
63 AATCTCAAATTAATTTTTAAAAATAATAAAAA-TTAAAAATATTTTATATTAGATGC-CAAATTA
* * * *
473558 TTTTTTAA-AATAATAAAAAATTAAAA-ATGTATTTTATATTCAATCTTT-AATTACCATTTAAA
126 -CTATTAACAATAAT--AAAATTAAAATAAG-ATTTTATATTAAAT-TTTGAATTACCATTTAAA
* * *
473620 AAAATAAAAAATTTATATTAAATCTCGAATTGCTATTTAAAATATAAT-AAAAATT-AAACAATA
186 AAAA-AAAAAATTTATATTAAATCTAGAATTACTAATTAAAA-ATAATAAAAAATTAAAACAATA
473683 TTTTA-AGGTAAATCTCAAATTACTTTTAAAAA
249 TTTTATA--TAAATCTCAAATTACTTTTAAAAA
473715 TATAATAAAA
Statistics
Matches: 244, Mismatches: 25, Indels: 25
0.83 0.09 0.09
Matches are distributed among these distances:
293 8 0.03
294 45 0.18
295 42 0.17
296 26 0.11
297 58 0.24
298 60 0.25
299 5 0.02
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (293 bp):
TTTATATTAAAATTTGAATTAATATTTACAAAATAATAAAAAATAAAAAAATATTTTATATAAAT
CTCAAATTAATTTTTAAAAATAATAAAAATTAAAAATATTTTATATTAGATGCCAAATTACTATT
AACAATAATAAAATTAAAATAAGATTTTATATTAAATTTTGAATTACCATTTAAAAAAAAAAAAA
TTTATATTAAATCTAGAATTACTAATTAAAAATAATAAAAAATTAAAACAATATTTTATATAAAT
CTCAAATTACTTTTAAAAAAAATTTAAAAATAG
Found at i:474135 original size:22 final size:22
Alignment explanation
Indices: 474104--474158 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
474094 TCACTTCTAC
*
474104 CATATGTACAT-TTAGTTAAAGT
1 CATATGTACATGCT-GTTAAAGT
* *
474126 CATATATACATGCTGTTATAGT
1 CATATGTACATGCTGTTAAAGT
474148 CATATGTACAT
1 CATATGTACAT
474159 ATTCTTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
CATATGTACATGCTGTTAAAGT
Found at i:474305 original size:22 final size:22
Alignment explanation
Indices: 474280--474328 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
474270 AAGTTATTTG
*
474280 TACATGCTATTATAATCATATA
1 TACATGCAATTATAATCATATA
* * *
474302 TACATTCAATTATAATTATATG
1 TACATGCAATTATAATCATATA
474324 TACAT
1 TACAT
474329 ATTCTTGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (22 bp):
TACATGCAATTATAATCATATA
Found at i:474634 original size:22 final size:23
Alignment explanation
Indices: 474609--474654 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
474599 TAAATATCAC
*
474609 TTTTACT-ATATGTATATATTAT
1 TTTTACTAATATATATATATTAT
*
474631 TTTTATTAGATATATATATATTAT
1 TTTTACTA-ATATATATATATTAT
474655 CTTATTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
24 14 0.70
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (23 bp):
TTTTACTAATATATATATATTAT
Found at i:475200 original size:22 final size:22
Alignment explanation
Indices: 475154--475215 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
475144 TATAACTAAG
*
475154 TGTATATATGATCTTAATAATA
1 TGTATATATGATTTTAATAATA
*
475176 TGTATATATGATTTTAATCGA-A
1 TGTATATATGATTTTAAT-AATA
* *
475198 TGTATGTATAATTTTAAT
1 TGTATATATGATTTTAAT
475216 TAAATCTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.48
Consensus pattern (22 bp):
TGTATATATGATTTTAATAATA
Found at i:475376 original size:31 final size:31
Alignment explanation
Indices: 475341--475404 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
475331 CGATAAAAAA
*
475341 TCAATACTTTCAAGTTAAACCTAATACTAAT
1 TCAATACTTTCAAATTAAACCTAATACTAAT
* * *
475372 TCAATATTTTCAAATTAAATCTAATACTGAT
1 TCAATACTTTCAAATTAAACCTAATACTAAT
475403 TC
1 TC
475405 CATAGAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (31 bp):
TCAATACTTTCAAATTAAACCTAATACTAAT
Found at i:479968 original size:17 final size:17
Alignment explanation
Indices: 479943--479986 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
479933 TTAAACATAT
*
479943 TATAAATTATA-ACTAAA
1 TATAGATTATAGA-TAAA
*
479960 TATAGATTATAGATAGA
1 TATAGATTATAGATAAA
479977 TATAGATTAT
1 TATAGATTAT
479987 CAATAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 23 0.96
18 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (17 bp):
TATAGATTATAGATAAA
Found at i:487830 original size:5 final size:5
Alignment explanation
Indices: 487783--487818 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
487773 AAATTAATTA
487783 AAATC AAAT- AAA-- AAATC AAATC AAATC AAATC AAAT
1 AAATC AAATC AAATC AAATC AAATC AAATC AAATC AAAT
487819 AATTTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
4 3 0.10
5 23 0.79
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATC
Found at i:488639 original size:30 final size:30
Alignment explanation
Indices: 488605--488720 Score: 169
Period size: 30 Copynumber: 3.9 Consensus size: 30
488595 CCTTGCAACA
488605 AAAGTAAAGTGCATAAATTAAAATTGCATT
1 AAAGTAAAGTGCATAAATTAAAATTGCATT
* **
488635 AAAGTAAATTGCATAAATTAAAATTGCAAG
1 AAAGTAAAGTGCATAAATTAAAATTGCATT
* *
488665 AAAATAAAGTGCATAAATTAAAATTTCATT
1 AAAGTAAAGTGCATAAATTAAAATTGCATT
* *
488695 AAAGTAAATTGCATAAATTTAAATTG
1 AAAGTAAAGTGCATAAATTAAAATTG
488721 TAAGAAAACA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 74 1.00
ACGTcount: A:0.52, C:0.06, G:0.11, T:0.31
Consensus pattern (30 bp):
AAAGTAAAGTGCATAAATTAAAATTGCATT
Found at i:488643 original size:15 final size:14
Alignment explanation
Indices: 488605--488711 Score: 88
Period size: 15 Copynumber: 7.2 Consensus size: 14
488595 CCTTGCAACA
*
488605 AAAGTAAAGTGCAT
1 AAAGTAAATTGCAT
*
488619 AAATTAAAATTGCATT
1 AAAGT-AAATTGCA-T
488635 AAAGTAAATTGCAT
1 AAAGTAAATTGCAT
* *
488649 AAATTAAAATTGCAAG
1 AAAGT-AAATTGC-AT
* *
488665 AAAATAAAGTGCAT
1 AAAGTAAATTGCAT
* *
488679 AAATTAAAATTTCATT
1 AAAGT-AAATTGCA-T
488695 AAAGTAAATTGCAT
1 AAAGTAAATTGCAT
488709 AAA
1 AAA
488712 TTTAAATTGT
Statistics
Matches: 74, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
14 18 0.24
15 41 0.55
16 15 0.20
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.29
Consensus pattern (14 bp):
AAAGTAAATTGCAT
Found at i:488677 original size:60 final size:61
Alignment explanation
Indices: 488597--488728 Score: 221
Period size: 60 Copynumber: 2.2 Consensus size: 61
488587 CATAATTACC
*
488597 TTGCAACAAAAGTAAAGTGCATAAATTAAAATTGCATTAAAGTAAATTGCATAAATTAAAA
1 TTGCAAGAAAAGTAAAGTGCATAAATTAAAATTGCATTAAAGTAAATTGCATAAATTAAAA
* *
488658 TTGCAAGAAAA-TAAAGTGCATAAATTAAAATTTCATTAAAGTAAATTGCATAAATTTAAA
1 TTGCAAGAAAAGTAAAGTGCATAAATTAAAATTGCATTAAAGTAAATTGCATAAATTAAAA
*
488718 TTGTAAGAAAA
1 TTGCAAGAAAA
488729 CAGATTACAA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
60 57 0.85
61 10 0.15
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (61 bp):
TTGCAAGAAAAGTAAAGTGCATAAATTAAAATTGCATTAAAGTAAATTGCATAAATTAAAA
Found at i:489878 original size:103 final size:100
Alignment explanation
Indices: 489697--489932 Score: 253
Period size: 103 Copynumber: 2.3 Consensus size: 100
489687 ACCATGTAAT
* * * *
489697 TAAGTAGATTTTTTTCAATATTTAATAACAATGGATTGATGTTACGATAAAAGTCATGTATGCTT
1 TAAGTAAATTTTTTT-AATATTTAATAA-AATGGATTGACGTTACGATAAAAGCCATGTATGCTA
* *
489762 GTTATATGCTACACTTAATTTACCATATA-A-TT-GA
64 GTGATATGCTACACTTAATTCACCATATATATTTGGA
* * *
489796 GTAAGTAAATTTTTTTAATATCTAATAAAATGGATTTACGTTACAGTAACATAAATGCCATGTAT
1 -TAAGTAAATTTTTTTAATATTTAATAAAATGGATTGACGTTAC-G----ATAAAAGCCATGTAT
* *
489861 GCTAGTGATGTGTTACACTTAATTCACCATATATTATTTGGA
60 GCTAGTGATATGCTACACTTAATTCACCATATA-TATTTGGA
* *
489903 TAGGTAAAGTTTTTTAATATTTAATAAAAT
1 TAAGTAAATTTTTTTAATATTTAATAAAAT
489933 TAAAAGATGT
Statistics
Matches: 113, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
98 14 0.12
99 12 0.11
100 14 0.12
103 41 0.36
105 1 0.01
106 29 0.26
107 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.41
Consensus pattern (100 bp):
TAAGTAAATTTTTTTAATATTTAATAAAATGGATTGACGTTACGATAAAAGCCATGTATGCTAGT
GATATGCTACACTTAATTCACCATATATATTTGGA
Found at i:491999 original size:23 final size:22
Alignment explanation
Indices: 491950--492021 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
491940 GTTGCTTTTT
* *
491950 TTTAATTAGGCTTTTAATTTAA
1 TTTAAATAGGCTTTTAGTTTAA
*
491972 GTTTAGATAGGCTTTTAGTTTAGA
1 -TTTAAATAGGCTTTTAGTTTA-A
* *
491996 TTTAAAT-GGGTTTAAGTTTAAA
1 TTTAAATAGGCTTTTAGTTT-AA
492018 TTTA
1 TTTA
492022 TATTTTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
22 15 0.37
23 25 0.61
24 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.50
Consensus pattern (22 bp):
TTTAAATAGGCTTTTAGTTTAA
Found at i:492020 original size:22 final size:23
Alignment explanation
Indices: 491950--492021 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 23
491940 GTTGCTTTTT
* *
491950 TTTAATTAGGCTTTTAA-TTTAAG
1 TTTAAATAGGC-TTTAAGTTTAAA
* * *
491973 TTTAGATAGGCTTTTAGTTTAGA
1 TTTAAATAGGCTTTAAGTTTAAA
*
491996 TTTAAAT-GGGTTTAAGTTTAAA
1 TTTAAATAGGCTTTAAGTTTAAA
492018 TTTA
1 TTTA
492022 TATTTTATTA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
22 20 0.51
23 19 0.49
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.50
Consensus pattern (23 bp):
TTTAAATAGGCTTTAAGTTTAAA
Found at i:494717 original size:104 final size:104
Alignment explanation
Indices: 494532--495510 Score: 472
Period size: 108 Copynumber: 9.3 Consensus size: 104
494522 GTGAATATGC
* * * * * ** *
494532 AATATTTAATGAAATTAAAAGACATCACAATTACATAAA-GTTATGTAGGTTGGTGAAGCGTTAC
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATGTATGCTGGCAAAGTGTTAC
494596 ACTTAATTTACCATATAAAGAAATAGGTAGATTTTTTTT
66 ACTTAATTTACCATATAAAGAAATAGGTAGATTTTTTTT
* ** *
494635 AATAGTTAATGAAATTGAAAGACGTTGTAGTTACATAAATGTTATGTATGCTGGCAAAGTGTTAC
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATGTATGCTGGCAAAGTGTTAC
* * * * *
494700 ACTGAATTTACCGTAT-AATAATTGGGTAAGTAGGTTTTTTTT
66 ACTTAATTTACCATATAAAGAAATAGGT-AG-A--TTTTTTTT
* * * * *
494742 AATATTTAATGAAATTGAAAAACGTTACAATTACATAAATGTCATATTTGCTGGCCAAACT-TTA
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATGTATGCTGG-CAAAGTGTTA
*
494806 CACTTAATTTACCATATAATAATTAGAAA-A-ATAGATTTTTTTT
65 CACTTAATTTACC--AT-ATAA--AGAAATAGGTAGATTTTTTTT
* * * * * *
494849 AATATTTAATGAAATTGAAAGACGTTACAAATACATAAATATTTTATAAGTTGGC-AAGATGTTA
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATGTATGCTGGCAAAG-TGTTA
* * * * *
494913 CACTTAATTTACCATA-GAATAATTAGGCATGTAAATTTCTTTTC
65 CACTTAATTTACCATATAAAGAAATA-G---GTAGATTT-TTTTT
* * * * * ** *
494957 AATATTCAATGAAATTGAAAGATGTTACAATTATATAAATGTCATGCATATTGGCAACA-TATTA
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATGTATGCTGGCAA-AGTGTTA
* * *
495021 CACTTAATTTACCATAT-AATAATTGGAGATGTAGATTCTTTTTC
65 CACTTAATTTACCATATAAAGAAAT--AG--GTAGATT-TTTTTT
* * * * * * * * * *
495065 AATATTTAATGAAATTGATATATGTTACAATTATAT-ATTCATTATATATGATGGCAATGTATTA
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAAT-GTTATGTATGCTGGCAAAGTGTTA
* * * * * * *
495129 CACTTAATTTATCATAT-AATAATTGGGTTGGTGAATTTTTT
65 CACTTAATTTACCATATAAAGAAATAGGTAGAT--TTTTTTT
* * * ** * * * * * **
495170 AAAATTTAATAAAATTAAAAGATATTACTATTACAGAAATGTAATGT-TGGT-G--ACGCATTA-
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATGTATGCTGGCAAAGTGTTAC
* ** * * *
495230 ACATAATTTACCATATAATAG-GGTTGGT-GAATTTTTCTC
66 ACTTAATTTACCATATAA-AGAAATAGGTAG-ATTTTTTTT
* * * * * *
495269 CATATTTAATAAAATTGAAAGATGTTACAATTAAATAAATGTAATGTGTGCTGGCAACA-TGTTA
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATGTATGCTGGCAA-AGTGTTA
* * * * * * * *
495333 TACTTTATCTACAAAAT-AA-TAATTGGATAGCTATTTTTTTC
65 CACTTAATTTACCATATAAAGAAATAGG-TAG--ATTTTTTTT
* * * ** * * * * * * *
495374 AATACTTAATTAACTCAAAAGATGTTACGATCACATAAATGTTATGTATGTTGGCAATGTGCTAT
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATGTATGCTGGCAAAGTGTTAC
* * *
495439 ACTTAATTTACTAAATAATA-ATTGGATAGGTAGAATTGTTTTTT
66 ACTTAATTTACCATATAA-AGA---AATAGGTAG-ATT-TTTTTT
*
495483 CAATATTTAATGAAATTGAAAGATGTTA
1 -AATATTTAATGAAATTGAAAGACGTTA
495511 TGATCACATA
Statistics
Matches: 673, Mismatches: 150, Indels: 99
0.73 0.16 0.11
Matches are distributed among these distances:
99 44 0.07
100 18 0.03
101 16 0.02
102 7 0.01
103 48 0.07
104 56 0.08
105 112 0.17
106 6 0.01
107 148 0.22
108 168 0.25
109 13 0.02
110 32 0.05
111 2 0.00
113 3 0.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (104 bp):
AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATGTATGCTGGCAAAGTGTTAC
ACTTAATTTACCATATAAAGAAATAGGTAGATTTTTTTT
Found at i:494776 original size:107 final size:107
Alignment explanation
Indices: 494532--495510 Score: 639
Period size: 107 Copynumber: 9.3 Consensus size: 107
494522 GTGAATATGC
* * * * * ** *
494532 AATATTTAATGAAATTAAAAGACATCACAATTACATAAA-GTTATGTAGGTTGGTGAAGCGTTAC
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATATATGTTGGCAAAGTGTTAC
* *
494596 ACTTAATTTACCATATAA-AGA--A-ATAGGTAGATTTTTTTT
66 ACTTAATTTACCATATAATA-ATTAGGTAAGTAGATTTTTTTT
* ** * * *
494635 AATAGTTAATGAAATTGAAAGACGTTGTAGTTACATAAATGTTATGTATGCTGGCAAAGTGTTAC
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATATATGTTGGCAAAGTGTTAC
* * * *
494700 ACTGAATTTACCGTATAATAATTGGGTAAGTAGGTTTTTTTT
66 ACTTAATTTACCATATAATAATTAGGTAAGTAGATTTTTTTT
* * * * *
494742 AATATTTAATGAAATTGAAAAACGTTACAATTACATAAATGTCATATTTGCTGGCCAAACT-TTA
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATATATGTTGG-CAAAGTGTTA
** *
494806 CACTTAATTTACCATATAATAATTAGAAAAATAGATTTTTTTT
65 CACTTAATTTACCATATAATAATTAGGTAAGTAGATTTTTTTT
* * * *
494849 AATATTTAATGAAATTGAAAGACGTTACAAATACATAAATATTTTATAAGTTGGC-AAGATGTTA
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATATATGTTGGCAAAG-TGTTA
* * * * *
494913 CACTTAATTTACCATAGAATAATTAGGCATGTAAATTTCTTTTC
65 CACTTAATTTACCATATAATAATTAGGTAAGTAGATTT-TTTTT
* * * * ** * *
494957 AATATTCAATGAAATTGAAAGATGTTACAATTATATAAATGTCATGCATATTGGCAACA-TATTA
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATATATGTTGGCAA-AGTGTTA
*
495021 CACTTAATTTACCATATAATAATT-GG-AGATGTAGATTCTTTTTC
65 CACTTAATTTACCATATAATAATTAGGTA-A-GTAGATT-TTTTTT
* * * * * * * * *
495065 AATATTTAATGAAATTGATATATGTTACAATTATAT-ATTCATTATATATGATGGCAATGTATTA
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAAT-GTTATATATGTTGGCAAAGTGTTA
* * ** *
495129 CACTTAATTTATCATATAATAATTGGGTTGGT-GA-ATTTTTT
65 CACTTAATTTACCATATAATAATTAGGTAAGTAGATTTTTTTT
* * * ** * * ** * **
495170 AAAATTTAATAAAATTAAAAGATATTACTATTACAGAAATG---TA-ATGTTGGTGACGCATTA-
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATATATGTTGGCAAAGTGTTAC
* * * *
495230 ACATAATTTACCATATAATAGGGTT-GGT--G-A-ATTTTTCTC
66 ACTTAATTTACCATATAATA--ATTAGGTAAGTAGATTTTTTTT
* * * * * * * *
495269 CATATTTAATAAAATTGAAAGATGTTACAATTAAATAAATGTAATGTGTGCTGGCAACA-TGTTA
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATATATGTTGGCAA-AGTGTTA
* * * * * *
495333 TACTTTATCTACAAAATAATAATT-GG--A-TAGCTATTTTTTTC
65 CACTTAATTTACCATATAATAATTAGGTAAGTAG--ATTTTTTTT
* * * ** * * * * * * *
495374 AATACTTAATTAACTCAAAAGATGTTACGATCACATAAATGTTATGTATGTTGGCAATGTGCTAT
1 AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATATATGTTGGCAAAGTGTTAC
* * *
495439 ACTTAATTTACTAAATAATAATT-GGATAGGTAGAATTGTTTTTT
66 ACTTAATTTACCATATAATAATTAGG-TAAGTAG-ATT-TTTTTT
*
495483 CAATATTTAATGAAATTGAAAGATGTTA
1 -AATATTTAATGAAATTGAAAGACGTTA
495511 TGATCACATA
Statistics
Matches: 685, Mismatches: 150, Indels: 75
0.75 0.16 0.08
Matches are distributed among these distances:
98 1 0.00
99 39 0.06
100 18 0.03
101 15 0.02
102 10 0.01
103 41 0.06
104 52 0.08
105 115 0.17
106 5 0.01
107 186 0.27
108 168 0.25
109 12 0.02
110 23 0.03
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (107 bp):
AATATTTAATGAAATTGAAAGACGTTACAATTACATAAATGTTATATATGTTGGCAAAGTGTTAC
ACTTAATTTACCATATAATAATTAGGTAAGTAGATTTTTTTT
Found at i:495309 original size:99 final size:99
Alignment explanation
Indices: 495133--495315 Score: 253
Period size: 99 Copynumber: 1.8 Consensus size: 99
495123 GTATTACACT
*
495133 TAATTTATCATATAATAATTGGGTTGGTGAATTTTTTAAAATTTAATAAAATTAAAAGATATTAC
1 TAATTTACCATATAATAA-TGGGTTGGTGAATTTTTTAAAATTTAATAAAATTAAAAGATATTAC
* *
495198 TATTACAGAAATGTAATGTTGGTGACGCATTAACA
65 AATTAAAGAAATGTAATGTTGGTGACGCATTAACA
* * * *
495233 TAATTTACCATATAAT-A-GGGTTGGTGAATTTTTCTCCATATTTAATAAAATTGAAAGATGTTA
1 TAATTTACCATATAATAATGGGTTGGTGAATTTTT-T-AAAATTTAATAAAATTAAAAGATATTA
*
495296 CAATTAAATAAATGTAATGT
64 CAATTAAAGAAATGTAATGT
495316 GTGCTGGCAA
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
97 16 0.22
98 1 0.01
99 41 0.56
100 15 0.21
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (99 bp):
TAATTTACCATATAATAATGGGTTGGTGAATTTTTTAAAATTTAATAAAATTAAAAGATATTACA
ATTAAAGAAATGTAATGTTGGTGACGCATTAACA
Found at i:495531 original size:110 final size:105
Alignment explanation
Indices: 495286--495533 Score: 237
Period size: 105 Copynumber: 2.3 Consensus size: 105
495276 AATAAAATTG
* * * * * * * ** * *
495286 AAAGATGTTACAATTAAATAAATGTAATGTGTGCTGGCAACATGTTATACTTTATCTACAAAATA
1 AAAGATGTTACGATCACATAAATATCATGTATGTTGGCAATGTGCTATACTTAATCTACAAAATA
* *
495351 ATAATTGGATAGCTATTTTTTTCAATACTTAATTAACTCA
66 ATAATTGGATAGCTATTTTTTTCAATACTTAATGAAATCA
* * * *
495391 AAAGATGTTACGATCACATAAATGTTATGTATGTTGGCAATGTGCTATACTTAATTTACTAAATA
1 AAAGATGTTACGATCACATAAATATCATGTATGTTGGCAATGTGCTATACTTAATCTACAAAATA
* * **
495456 ATAATTGGATAGGTAGAATTGTTTTTTCAATATTTAATGAAATTG
66 ATAATTGGATAGCT---A-T-TTTTTTCAATACTTAATGAAATCA
*
495501 AAAGATGTTATGATCACATACAA-ATCATGTATG
1 AAAGATGTTACGATCACATA-AATATCATGTATG
495534 ATGGTGACAT
Statistics
Matches: 116, Mismatches: 21, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
105 66 0.57
108 1 0.01
109 1 0.01
110 46 0.40
111 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (105 bp):
AAAGATGTTACGATCACATAAATATCATGTATGTTGGCAATGTGCTATACTTAATCTACAAAATA
ATAATTGGATAGCTATTTTTTTCAATACTTAATGAAATCA
Found at i:497226 original size:33 final size:33
Alignment explanation
Indices: 497181--497260 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
497171 ACACACCAAG
**
497181 ATGTATCGATACATTATGCTTTGTATTGATACA
1 ATGTATCGATACATTATGCTTTGTATCCATACA
*
497214 ATGTATCAATACATTATGCTTTGTATCCATACA
1 ATGTATCGATACATTATGCTTTGTATCCATACA
497247 ATGTATCGATACAT
1 ATGTATCGATACAT
497261 GAAACTGGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (33 bp):
ATGTATCGATACATTATGCTTTGTATCCATACA
Found at i:502869 original size:13 final size:13
Alignment explanation
Indices: 502851--502875 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
502841 TAATATTCTT
502851 TGTATCGATACAC
1 TGTATCGATACAC
502864 TGTATCGATACA
1 TGTATCGATACA
502876 AGGGTTACTA
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:503008 original size:21 final size:22
Alignment explanation
Indices: 502994--503033 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
502984 CTTCAAATTT
502994 CTTATTTTTCACTTCAAAATAC
1 CTTATTTTTCACTTCAAAATAC
503016 CTTATTTTTCA--TCAAAAT
1 CTTATTTTTCACTTCAAAAT
503034 CATCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (22 bp):
CTTATTTTTCACTTCAAAATAC
Found at i:504988 original size:13 final size:14
Alignment explanation
Indices: 504970--504998 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
504960 GTAAGTTCAT
504970 AAATGC-TATTTGA
1 AAATGCATATTTGA
504983 AAATGCATATTTGA
1 AAATGCATATTTGA
504997 AA
1 AA
504999 TTTATATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (14 bp):
AAATGCATATTTGA
Found at i:505420 original size:19 final size:19
Alignment explanation
Indices: 505392--505445 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
505382 ATCGATACAA
* *
505392 TGTATCGATACATGTTCAT
1 TGTATCGATACATGATAAT
*
505411 TGTATTGATACATGGATAAT
1 TGTATCGATACAT-GATAAT
505431 TGTATCGATACATGA
1 TGTATCGATACATGA
505446 AACTGGCAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATGATAAT
Found at i:505492 original size:13 final size:13
Alignment explanation
Indices: 505474--505498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
505464 TACCACTGTT
505474 TGTATCGATACAA
1 TGTATCGATACAA
505487 TGTATCGATACA
1 TGTATCGATACA
505499 TGATGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:507598 original size:20 final size:19
Alignment explanation
Indices: 507573--507622 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
507563 CCCTTATTTG
507573 TATCGATATACATGCAGATA
1 TATCGATATACATGCA-ATA
* * *
507593 TATCGATACAACTTGCAATG
1 TATCGATA-TACATGCAATA
507613 TATCGATATA
1 TATCGATATA
507623 GTATGTGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 18 0.72
21 6 0.24
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (19 bp):
TATCGATATACATGCAATA
Found at i:514165 original size:20 final size:20
Alignment explanation
Indices: 514140--514191 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
514130 AACCCTTATT
*
514140 TGTATCGATACACA-TGCAGA
1 TGTATCGATACAAATTGCA-A
514160 TGTATCGATACAAATTGCAA
1 TGTATCGATACAAATTGCAA
514180 TGTATCGATACA
1 TGTATCGATACA
514192 TTATGTGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (20 bp):
TGTATCGATACAAATTGCAA
Found at i:520470 original size:113 final size:113
Alignment explanation
Indices: 520124--520650 Score: 599
Period size: 113 Copynumber: 4.6 Consensus size: 113
520114 AAAAAAAGTA
* * * * * *
520124 CCACTAACTTGCGTGGGCTTTGAAAAGAGTTACCACCGACTCGTGTGGGCTTTTAAAAGAGTCAC
1 CCACTAACTT--GTGGGCTTTG-AAAG-GGTGCCACTGACT--TGTGGGC-TTTGAAAGGGT-GC
* * ** *
520189 CACTATCTTGTGGGATTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATG
58 CACTAACTTGTGGGCTTTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAGGGTG
* * * * ** * * * **
520244 CCATTGACTTCTGGGCTCTGAAAAAAGTGCCACTAACTTCTGGGCTCTGAAAAAAGTGCCACTAA
1 CCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAA
*
520309 CTTGTGGGCTCTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAGGGTG
64 CTTGTGGGCTTTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAGGGTG
* * * *
520359 CCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGAGCTTTGAAAGGGTGTCACTGACT
1 CCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* *
520424 TCTAGGCTTTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAGGGTG
66 TGTGGGCTTTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAGGGTG
* * *
520472 CCACTGACTTGTGGGCTTTGAAAGGATGTCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
1 CCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
** * **
520537 TGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGACTTTGAAAAAAGTG
66 TGTGGGCTTTGAAAAAAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTG
*
520585 CCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
1 CCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
520650 T
66 T
520651 ATGAGGTTTG
Statistics
Matches: 348, Mismatches: 56, Indels: 13
0.83 0.13 0.03
Matches are distributed among these distances:
112 21 0.06
113 197 0.57
114 41 0.12
115 61 0.18
117 8 0.02
118 12 0.03
120 8 0.02
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (113 bp):
CCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
TGTGGGCTTTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAGGGTG
Found at i:520662 original size:28 final size:28
Alignment explanation
Indices: 520195--520650 Score: 579
Period size: 28 Copynumber: 16.1 Consensus size: 28
520185 TCACCACTAT
*
520195 CTTGTGGGATTTGAAAGGGTGCCACTGA
1 CTTGTGGGCTTTGAAAGGGTGCCACTGA
* *
520223 CTTGTGGGCTTTGAAAGGATGCCATTGA
1 CTTGTGGGCTTTGAAAGGGTGCCACTGA
* * ** *
520251 CTTCTGGGCTCTGAAAAAAGTGCCACTAA
1 CTTGTGGGCTTTG-AAAGGGTGCCACTGA
* * ** *
520280 CTTCTGGGCTCTGAAAAAAGTGCCACTAA
1 CTTGTGGGCTTTG-AAAGGGTGCCACTGA
* **
520309 CTTGTGGGCTCTGAAAAAAGTGCCACTGA
1 CTTGTGGGCTTTG-AAAGGGTGCCACTGA
*
520338 CTTGTGGGCTTTGAAAGGGTGCCACTAA
1 CTTGTGGGCTTTGAAAGGGTGCCACTGA
520366 CTTGTGGGCTTTGAAAGGGTGCCACTGA
1 CTTGTGGGCTTTGAAAGGGTGCCACTGA
* * *
520394 CTTATGAGCTTTGAAAGGGTGTCACTGA
1 CTTGTGGGCTTTGAAAGGGTGCCACTGA
* * **
520422 CTTCTAGGCTTTGAAAAAAGTGCCACTGA
1 CTTGTGGGCTTTG-AAAGGGTGCCACTGA
520451 CTTGTGGGCTTTGAAAGGGTGCCACTGA
1 CTTGTGGGCTTTGAAAGGGTGCCACTGA
* *
520479 CTTGTGGGCTTTGAAAGGATGTCACTGA
1 CTTGTGGGCTTTGAAAGGGTGCCACTGA
*
520507 CTTGTGGGCTTTGAAAGGGTGCCACTAA
1 CTTGTGGGCTTTGAAAGGGTGCCACTGA
*
520535 CTTGTGGGCTTTGAAAGGATGCCACTGA
1 CTTGTGGGCTTTGAAAGGGTGCCACTGA
* ** *
520563 CTTGTGGACTTTGAAAAAAGTGCCACTAA
1 CTTGTGGGCTTTG-AAAGGGTGCCACTGA
520592 CTTGTGGGCTTTGAAAGGGTGCCACTGA
1 CTTGTGGGCTTTGAAAGGGTGCCACTGA
520620 CTTGTGGGCTTTGAAAGGGTGCCACTGA
1 CTTGTGGGCTTTGAAAGGGTGCCACTGA
520648 CTT
1 CTT
520651 ATGAGGTTTG
Statistics
Matches: 379, Mismatches: 46, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
28 255 0.67
29 124 0.33
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
CTTGTGGGCTTTGAAAGGGTGCCACTGA
Found at i:520662 original size:85 final size:85
Alignment explanation
Indices: 520136--520650 Score: 613
Period size: 85 Copynumber: 6.0 Consensus size: 85
520126 ACTAACTTGC
* * * * * *
520136 GTGGGCTTTGAAAAGAGTTACCACCGACTCGTGTGGGCTTTTAAAAGAGTCACCACTATCTTGTG
1 GTGGGCTTTGAAAAGAG-TGCCACTGACT--TGTGGGC-TTTGAAAGGGT-GCCACTAACTTGTG
*
520201 GGATTTGAAAGGGTGCCACTGACTT
61 GGCTTTGAAAGGGTGCCACTGACTT
* * * * ** *
520226 GTGGGCTTTGAAAGGA-TGCCATTGACTTCTGGGCTCTGAAAAAAGTGCCACTAACTTCTGGGCT
1 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCT
* ** *
520290 CTGAAAAAAGTGCCACTAACTT
65 TTG-AAAGGGTGCCACTGACTT
* *
520312 GTGGGCTCTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
1 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
520377 TGAAAGGGTGCCACTGACTT
66 TGAAAGGGTGCCACTGACTT
* * * * * * ** *
520397 ATGAGCTTTG-AAAGGGTGTCACTGACTTCTAGGCTTTGAAAAAAGTGCCACTGACTTGTGGGCT
1 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCT
520461 TTGAAAGGGTGCCACTGACTT
65 TTGAAAGGGTGCCACTGACTT
* *
520482 GTGGGCTTTGAAAGGA-TGTCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
1 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
*
520546 TGAAAGGATGCCACTGACTT
66 TGAAAGGGTGCCACTGACTT
* * * *
520566 GTGGACTTTGAAAAAAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
1 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
520631 TGAAAGGGTGCCACTGACTT
66 TGAAAGGGTGCCACTGACTT
520651 ATGAGGTTTG
Statistics
Matches: 362, Mismatches: 57, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
84 78 0.22
85 175 0.48
86 67 0.19
87 19 0.05
88 8 0.02
90 15 0.04
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (85 bp):
GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
TGAAAGGGTGCCACTGACTT
Found at i:521871 original size:12 final size:12
Alignment explanation
Indices: 521856--521899 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
521846 CCCCTTTCTA
521856 TTTTTTTGTTAT
1 TTTTTTTGTTAT
*
521868 TTTTTTCT-TTGT
1 TTTTTT-TGTTAT
*
521880 TTTTTTTGTTTT
1 TTTTTTTGTTAT
521892 TTTTTTTG
1 TTTTTTTG
521900 GTATGAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 26 0.93
13 1 0.04
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.86
Consensus pattern (12 bp):
TTTTTTTGTTAT
Found at i:521880 original size:15 final size:13
Alignment explanation
Indices: 521856--521898 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
521846 CCCCTTTCTA
521856 TTTTTTTGTTATTT
1 TTTTTTTGTT-TTT
521870 TTTTCTTTGTTTTT
1 TTTT-TTTGTTTTT
521884 TTTGTTTT-TTTTT
1 TTT-TTTTGTTTTT
521897 TT
1 TT
521899 GGTATGAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.26
14 13 0.48
15 7 0.26
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.88
Consensus pattern (13 bp):
TTTTTTTGTTTTT
Found at i:521882 original size:21 final size:21
Alignment explanation
Indices: 521850--521899 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
521840 TCTAGACCCC
521850 TTTCTATT-TTTTTGTTATTTT
1 TTTCT-TTGTTTTTGTTATTTT
* *
521871 TTTCTTTGTTTTTTTTGTTTT
1 TTTCTTTGTTTTTGTTATTTT
*
521892 TTTTTTTG
1 TTTCTTTG
521900 GTATGAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.04, C:0.04, G:0.08, T:0.84
Consensus pattern (21 bp):
TTTCTTTGTTTTTGTTATTTT
Found at i:531407 original size:19 final size:19
Alignment explanation
Indices: 531383--531422 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
531373 AAATAATAGG
*
531383 AATGAATAGCAAGAAAAAA
1 AATGAACAGCAAGAAAAAA
*
531402 AATGAACATCAAGAAAAAA
1 AATGAACAGCAAGAAAAAA
531421 AA
1 AA
531423 AGTGGCCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.10
Consensus pattern (19 bp):
AATGAACAGCAAGAAAAAA
Found at i:535650 original size:20 final size:20
Alignment explanation
Indices: 535624--535678 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
535614 AAAAAGACAG
*
535624 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
535644 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
535664 AATGTATCGATACAT
1 AATGTATCGATACAT
535679 CTGAGTACCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:538783 original size:35 final size:33
Alignment explanation
Indices: 538721--538787 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 33
538711 AATTATTTTT
538721 ATATATATTTTAATAATATTTAATATTTTAACC
1 ATATATATTTTAATAATATTTAATATTTTAACC
*
538754 ATAT-TATTTTATATATTTATTTAAATATTTTAAC
1 ATATATATTTTA-ATA-ATATTT-AATATTTTAAC
538788 TAGTTACCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 7 0.23
33 7 0.23
34 5 0.17
35 11 0.37
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (33 bp):
ATATATATTTTAATAATATTTAATATTTTAACC
Found at i:547007 original size:3 final size:3
Alignment explanation
Indices: 546999--547030 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
546989 CGAGTCAACT
*
546999 TCA TCA TCA TCA TCA TCA TCT TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
547031 TTTGATAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:547510 original size:20 final size:20
Alignment explanation
Indices: 547456--547511 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
547446 TTTTCATAAT
* *
547456 TTGTACCGATACATCCTTCA
1 TTGTATCGATACATTCTTCA
*
547476 TTATATCGATACATTCTTCA
1 TTGTATCGATACATTCTTCA
547496 TTGTATCGATACATTC
1 TTGTATCGATACATTC
547512 GGCATTTTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.41
Consensus pattern (20 bp):
TTGTATCGATACATTCTTCA
Found at i:547517 original size:20 final size:20
Alignment explanation
Indices: 547474--547517 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
547464 ATACATCCTT
**
547474 CATTATATCGATACATTCTT
1 CATTATATCGATACATTCGG
*
547494 CATTGTATCGATACATTCGG
1 CATTATATCGATACATTCGG
547514 CATT
1 CATT
547518 TTCGACCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
CATTATATCGATACATTCGG
Found at i:549967 original size:79 final size:78
Alignment explanation
Indices: 549862--550143 Score: 221
Period size: 79 Copynumber: 3.6 Consensus size: 78
549852 ACTTTCCACC
* * * *
549862 ATCGGGGATACTCCAACCCTATTATTTCCGAGGGGATACTCTAACCCCGCTTTTATTTCCAAAAT
1 ATCGAGGATACTCCAACCATA-TATTTCCGAGGGGATACTCTAACCCCGATTTTATTTCCAAAAC
549927 ATCAATTTTTCACA
65 ATCAATTTTTCACA
* * * * *
549941 ATCGAGGATACTCCAACCATGATATTTTCGAGGGGATACTC-CACCTCGGTTTTATTTTCAAAAC
1 ATCGAGGATACTCCAACCAT-ATATTTCCGAGGGGATACTCTAACCCCGATTTTATTTCCAAAAC
** *
550005 ATTGATTTTTCACC
65 ATCAATTTTTCACA
** * * ** ** *
550019 ATCGAAAATGCTCCAACC-TCGTTATTTTTGAGAAGATACT-TCAACCCCGATTTTATTTCTAAA
1 ATCGAGGATACTCCAACCAT--ATATTTCCGAGGGGATACTCT-AACCCCGATTTTATTTCCAAA
* *
550082 ACACCAATTTTTCACG
63 ACATCAATTTTTCACA
* * * * *
550098 ACCGGGGATACTCAAATCCCAT-TATTTCTGAGGGGATACTCCAACC
1 ATCGAGGATACTCCAA--CCATATATTTCCGAGGGGATACTCTAACC
550144 TCTTTATTTT
Statistics
Matches: 158, Mismatches: 37, Indels: 16
0.75 0.18 0.08
Matches are distributed among these distances:
77 1 0.01
78 60 0.38
79 93 0.59
80 1 0.01
81 2 0.01
82 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (78 bp):
ATCGAGGATACTCCAACCATATATTTCCGAGGGGATACTCTAACCCCGATTTTATTTCCAAAACA
TCAATTTTTCACA
Found at i:550033 original size:78 final size:79
Alignment explanation
Indices: 549869--550096 Score: 212
Period size: 78 Copynumber: 2.9 Consensus size: 79
549859 ACCATCGGGG
* *
549869 ATACTCCAACCCT-ATTATTTCCGAGGGGATACTCTAACCCCGCTTTTATTTCCAAAATATCAAT
1 ATACTCCAACCATGA-TATTTCCGAGGGGATACTCTAACCCCGCTTTTATTTCCAAAACATCAAT
**
549933 TTTTCACAATCGAGG
65 TTTTCACAATCGAAA
* * * * * **
549948 ATACTCCAACCATGATATTTTCGAGGGGATACTC-CACCTCGGTTTTATTTTCAAAACATTGATT
1 ATACTCCAACCATGATATTTCCGAGGGGATACTCTAACCCCGCTTTTATTTCCAAAACATCAATT
*
550012 TTTCACCATCGAAA
66 TTTCACAATCGAAA
* * ** ** * * *
550026 ATGCTCCAACC-TCGTTATTTTTGAGAAGATACT-TCAACCCCGATTTTATTTCTAAAACACCAA
1 ATACTCCAACCAT-GATATTTCCGAGGGGATACTCT-AACCCCGCTTTTATTTCCAAAACATCAA
550089 TTTTTCAC
64 TTTTTCAC
550097 GACCGGGGAT
Statistics
Matches: 120, Mismatches: 25, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
77 1 0.01
78 60 0.50
79 58 0.48
80 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (79 bp):
ATACTCCAACCATGATATTTCCGAGGGGATACTCTAACCCCGCTTTTATTTCCAAAACATCAATT
TTTCACAATCGAAA
Found at i:550150 original size:28 final size:28
Alignment explanation
Indices: 550101--550169 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
550091 TTTCACGACC
*
550101 GGGGATACTCAAATCCCATTA-TTTCTGA
1 GGGGATACTCCAATCCCATTATTTTC-GA
*
550129 GGGGATACTCCAA-CCTCTTTATTTTCGA
1 GGGGATACTCCAATCC-CATTATTTTCGA
550157 GGGGATACTCCAA
1 GGGGATACTCCAA
550170 ACCCGATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 2 0.05
28 31 0.84
29 4 0.11
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (28 bp):
GGGGATACTCCAATCCCATTATTTTCGA
Found at i:550151 original size:107 final size:107
Alignment explanation
Indices: 550029--550250 Score: 302
Period size: 107 Copynumber: 2.1 Consensus size: 107
550019 ATCGAAAATG
* * *
550029 CTCCAACCTCGTTATTTTTGAGAAGATACTTCAACCCCGATTTTATTTCTAAAACACCAATTTTT
1 CTCCAACCTCGTTATTTTCGAGAAGATACTCCAAACCCGATTTTATTTCTAAAACACCAATTTTT
* * * *
550094 CACGACCGGGGATACTC-AAATCCCATTATTTCTGAGGGGATA
66 CACAACC-GGGACACTCTAAATCCCATTATTTCTGAGAGAATA
* ** *
550136 CTCCAACCTCTTTATTTTCGAGGGGATACTCCAAACCCGATTTTATTTCTAAAACACCGATTTTT
1 CTCCAACCTCGTTATTTTCGAGAAGATACTCCAAACCCGATTTTATTTCTAAAACACCAATTTTT
* * *
550201 CACAATCGGGACACTCTAAATCTCATTATTTTTGAGAGAATA
66 CACAACCGGGACACTCTAAATCCCATTATTTCTGAGAGAATA
550243 CTCCAACC
1 CTCCAACC
550251 CCGATTTTAT
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
106 8 0.08
107 92 0.92
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (107 bp):
CTCCAACCTCGTTATTTTCGAGAAGATACTCCAAACCCGATTTTATTTCTAAAACACCAATTTTT
CACAACCGGGACACTCTAAATCCCATTATTTCTGAGAGAATA
Found at i:550259 original size:186 final size:185
Alignment explanation
Indices: 549946--550334 Score: 445
Period size: 186 Copynumber: 2.1 Consensus size: 185
549936 TCACAATCGA
* **
549946 GGATACTCCAACCATGATATTTTCGAGGGGATACTCCACCTCGGTTTTATTTTCAAAACATTGAT
1 GGATACTCCAACCATGATATTTTCGAGGGGATACTCCACCTCGATTTTATTTTCAAAACACCGAT
* * * *
550011 TTTTCACCATCGAAAATGCTCCAACCTCGTTATTTTTGAGAAGATACTTCAACCCCGATTTTATT
66 TTTTCACAATCGAAAATGCTCAAACCTCATTATTTTTGAGAAGATACTCCAACCCCGATTTTATT
* *
550076 TCTAAAACACCAATTTTTCACGACCGGGGATA-CTCAAATCCC-ATTA-TTTCTGAGG
131 TCTAAAACACCAATTTTTCACCACCAGGGATACCT-AAA-CCCTATTATTTTC-GAGG
**
550131 GGATACTCCAACC-TCTTTATTTTCGAGGGGATACTCCAAACC-CGATTTTA-TTTCTAAAACAC
1 GGATACTCCAACCAT-GATATTTTCGAGGGGATACTCC--ACCTCGATTTTATTTTC-AAAACAC
* * *
550193 CGATTTTTCACAATCGGGACA--CTCTAAATCTCATTATTTTTGAG-AGAATACTCCAACCCCGA
62 CGATTTTTCACAATC-GAAAATGCTC-AAACCTCATTATTTTTGAGAAG-ATACTCCAACCCCGA
* * * * *
550255 TTTTATTTCTAAAATATCAATTTTTCACCATCAGGGATACCTTAACCCTGTTATTTTCGAGG
124 TTTTATTTCTAAAACACCAATTTTTCACCACCAGGGATACCTAAACCCTATTATTTTCGAGG
*
550317 GGATACTCCAACCCTGAT
1 GGATACTCCAACCATGAT
550335 TTTATTTTCA
Statistics
Matches: 172, Mismatches: 21, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
184 1 0.01
185 45 0.26
186 113 0.66
187 13 0.08
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (185 bp):
GGATACTCCAACCATGATATTTTCGAGGGGATACTCCACCTCGATTTTATTTTCAAAACACCGAT
TTTTCACAATCGAAAATGCTCAAACCTCATTATTTTTGAGAAGATACTCCAACCCCGATTTTATT
TCTAAAACACCAATTTTTCACCACCAGGGATACCTAAACCCTATTATTTTCGAGG
Found at i:550278 original size:79 final size:80
Alignment explanation
Indices: 550130--550563 Score: 397
Period size: 79 Copynumber: 5.5 Consensus size: 80
550120 TATTTCTGAG
* * * *
550130 GGGATACTC-CAACCTCTTTATTTTCGAGGGGATACTCCAAACCC-GATTTTATTTCTAAAACAC
1 GGGATACTCTAAACCTCGTTATTTTTGAGGGGATACTCC-AACCCTGATTTTATTTCTAAAACAT
550193 CGATTTTTCACAATC-
65 CGATTTTTCACAATCA
* * * * * * *
550208 GGGACACTCTAAATCTCATTATTTTTGAGAGAATACTCCAACCCCGATTTTATTTCTAAAATATC
1 GGGATACTCTAAACCTCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTTCTAAAACATC
* *
550273 AATTTTTCACCATCA
66 GATTTTTCACAATCA
* *
550288 GGGATAC-CTTAACC-CTGTTATTTTCGAGGGGATACTCCAACCCTGATTTTATTT-TCAAAACA
1 GGGATACTCTAAACCTC-GTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTTCT-AAAAC-
*
550350 AT-AATTTTTCACAATCA
63 ATCGATTTTTCACAATCA
* * * * *
550367 AGTATACTCTAACCCT-ATTATTTCTGAGGGGATACTCCAACCCTGATTTTATTTAC-AAAACAT
1 GGGATACTCTAAACCTCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTT-CTAAAACAT
*
550430 TGATTTTTCACAATCA
65 CGATTTTTCACAATCA
* * * * * * * * *
550446 AGGATGCTC-CAACCCCGTTATTTTTTAGAGGATACTTCAACCTTGGTTTTATTTCTAAAACATC
1 GGGATACTCTAAACCTCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTTCTAAAACATC
*
550510 GATTTTCCACAATC-
66 GATTTTTCACAATCA
* * * ** *
550524 GAGATACTC-CAATCTCGTTATTTCCGAAGGGATACTCCAA
1 GGGATACTCTAAACCTCGTTATTTTTGAGGGGATACTCCAA
550564 TCTTGTTTTT
Statistics
Matches: 289, Mismatches: 54, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
78 50 0.17
79 226 0.78
80 13 0.04
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (80 bp):
GGGATACTCTAAACCTCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTTCTAAAACATC
GATTTTTCACAATCA
Found at i:550392 original size:265 final size:263
Alignment explanation
Indices: 549865--550410 Score: 606
Period size: 265 Copynumber: 2.1 Consensus size: 263
549855 TTCCACCATC
* * * * *
549865 GGGGATACTCCAACCCTATTATTTCCGAGGGGATACTCTAACCCCGCTTTTATTTCCAAAATATC
1 GGGGATACTCCAACCCTATTATTTCCGAGGGGATACTCCAAACCCGATTTTATTTCCAAAACACC
* * * * * *
549930 AATTTTTCACAATCGAGGATACTCCAACCATGATATTTTCGAGGGGATACTCCACCTCGGTTTTA
66 AATTTTTCACAATCGAGGACACTCAAACCAT-ATATTTTCGAGAGAATACTCCACCCCGATTTTA
** * * *
549995 TTTTCAAAACATTGATTTTTCACCATCGAAAATGCTCCAACCTCGTTATTTTTGAGAAGATACTT
130 TTTTCAAAACATCAATTTTTCACCATCGAAAATCCTCCAACCTCGTTATTTTCGAGAAGATACTC
* * **
550060 CAACCCCGATTTTATTTCTAAAACACCAATTTTTCACGACCGGGGATACTCAAATCCCATTATTT
195 CAACCCCGATTTTATTTCTAAAACAACAATTTTTCACAACCAAGGATACTCAAATCCCATTATTT
550125 CTGA
260 CTGA
* *
550129 GGGGATACTCCAACCTCT-TTATTTTCGAGGGGATACTCCAAACCCGATTTTATTTCTAAAACAC
1 GGGGATACTCCAACC-CTATTATTTCCGAGGGGATACTCCAAACCCGATTTTATTTCCAAAACAC
* *
550193 CGATTTTTCACAATCG-GGACACTCTAAATCTCAT-TATTTTTGAGAGAATACTCCAACCCCGAT
65 CAATTTTTCACAATCGAGGACACTC-AAA-C-CATATATTTTCGAGAGAATACTCC-ACCCCGAT
* ** * *
550256 TTTA-TTTCTAAAATATCAATTTTTCACCATC-AGGGATACCT-TAACC-CTGTTATTTTCGAGG
126 TTTATTTTC-AAAACATCAATTTTTCACCATCGA-AAAT-CCTCCAACCTC-GTTATTTTCGAGA
* * * * * *
550317 GGATACTCCAACCCTGATTTTATTT-TCAAAACAATAATTTTTCACAATCAAGTATACTCTAA-C
187 AGATACTCCAACCCCGATTTTATTTCT-AAAACAACAATTTTTCACAACCAAGGATACTCAAATC
550380 CCTATTATTTCTGA
251 CC-ATTATTTCTGA
550394 GGGGATACTCCAACCCT
1 GGGGATACTCCAACCCT
550411 GATTTTATTT
Statistics
Matches: 236, Mismatches: 35, Indels: 22
0.81 0.12 0.08
Matches are distributed among these distances:
263 7 0.03
264 100 0.42
265 124 0.53
266 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (263 bp):
GGGGATACTCCAACCCTATTATTTCCGAGGGGATACTCCAAACCCGATTTTATTTCCAAAACACC
AATTTTTCACAATCGAGGACACTCAAACCATATATTTTCGAGAGAATACTCCACCCCGATTTTAT
TTTCAAAACATCAATTTTTCACCATCGAAAATCCTCCAACCTCGTTATTTTCGAGAAGATACTCC
AACCCCGATTTTATTTCTAAAACAACAATTTTTCACAACCAAGGATACTCAAATCCCATTATTTC
TGA
Found at i:550418 original size:158 final size:155
Alignment explanation
Indices: 550131--550585 Score: 443
Period size: 158 Copynumber: 2.9 Consensus size: 155
550121 ATTTCTGAGG
* * * **
550131 GGATACTCCAACCTCTTTATTTTCGAGGGGATACTCCAAACCC-GATTTTATTTCTAAAACACCG
1 GGATCCTCCAACCCCGTTATTTTCGAGGGGATACTCC-AACCCTGATTTTATTTCTAAAACAATG
* * * * * *
550195 ATTTTTCACAATCGGGACACTCTAAATCTCATTATTTTTGAGAGAATACTCCAACCCCGATTTTA
65 ATTTTTCACAATC-AGATACTCT-AATCTCATTATTTCTGAGGGGATACTCCAACCCTGATTTTA
* *
550260 TTTCTAAAATATCAATTTTTCACCATCAG
128 TTTC-AAAATATCAATTTTTCACAATCAA
* *
550289 GGATACCT-TAACCCTGTTATTTTCGAGGGGATACTCCAACCCTGATTTTATTT-TCAAAACAAT
1 GGAT-CCTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGATTTTATTTCT-AAAACAAT
* *
550352 AATTTTTCACAATCAAGTATACTCTAA-CCCTATTATTTCTGAGGGGATACTCCAACCCTGATTT
64 GATTTTTCACAATC-AG-ATACTCTAATCTC-ATTATTTCTGAGGGGATACTCCAACCCTGATTT
* **
550416 TATTTACAAAACATTGATTTTTCACAATCAA
126 TATTT-CAAAATATCAATTTTTCACAATCAA
* ** * * * *
550447 GGATGCTCCAACCCCGTTATTTTTTAGAGGATACTTCAACCTTGGTTTTATTTCTAAAAC-ATCG
1 GGATCCTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGATTTTATTTCTAAAACAAT-G
* * * * * * * *
550511 ATTTTCCACAATCGAGATACTCCAATCTCGTTATTTCCGAAGGGATACTCCAATCTTGTTTTTAT
65 ATTTTTCACAATC-AGATACTCTAATCTCATTATTTCTGAGGGGATACTCCAACCCTGATTTTAT
*
550576 CTCAAAATAT
129 TTCAAAATAT
550586 TAAACTTTTC
Statistics
Matches: 244, Mismatches: 43, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
156 7 0.03
157 51 0.21
158 176 0.72
159 10 0.04
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (155 bp):
GGATCCTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGATTTTATTTCTAAAACAATGA
TTTTTCACAATCAGATACTCTAATCTCATTATTTCTGAGGGGATACTCCAACCCTGATTTTATTT
CAAAATATCAATTTTTCACAATCAA
Found at i:553213 original size:3 final size:3
Alignment explanation
Indices: 553198--553231 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
553188 AACCATCAAA
*
553198 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
553232 GAGACTCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:560344 original size:20 final size:19
Alignment explanation
Indices: 560319--560372 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
560309 TTACCACTAT
560319 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAG-A-A
*
560339 TTGTATCGACACATGATGAA
1 TTGTATCGATACATGA-GAA
560359 TTGTATCGATACAT
1 TTGTATCGATACAT
560373 TGCTTCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 28 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:564814 original size:79 final size:78
Alignment explanation
Indices: 564725--565342 Score: 405
Period size: 79 Copynumber: 7.8 Consensus size: 78
564715 TCAAAATATA
* ** **
564725 ATTTTCCACCATCGGGGACGCTCCAACCTTGTTATTTTCGAGGGGATACTCCAACCTCGGCTTTA
1 ATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTTCGAGGGGATACTCCAACC-CGATTTTA
564790 TTTCTAAAACACTG
65 TTTCTAAAACACTG
* * * * * * * *
564804 ATTTTTCACCATCGAGGAAACTCCAAGCTCGTTA-TTTCTGAAGGGACACTCTAACCCTAGTTTT
1 ATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTTC-GAGGGGATACTCCAACCCGA-TTTT
*
564868 ATTCCTAAAACACCT-
64 ATTTCTAAAACA-CTG
* * * ** * ** * * *
564883 ATTTTTC-CGTTATCGGGGATATTCTAACCCCGTTATTTCCGAGGAAAAACTCTAACCCTAGTTT
1 ATTTTTCAC--CATCGGGGATACTCCAACCTTGTTATTTTCGAGGGGATACTCCAACCCGA-TTT
* *
564947 TATTCCTAAAACA-TCA
63 TATTTCTAAAACACT-G
* * * * *
564963 ATTTTTCCACTATC-AGGATACTCCAACCCTGTTATTTTCGAGGGCATACTCCAACCCCAATTTT
1 ATTTTT-CACCATCGGGGATACTCCAACCTTGTTATTTTCGAGGGGATACTCCAA-CCCGATTTT
* *
565027 ATTTTTAAAACCCTG
64 ATTTCTAAAACACTG
* * * * *
565042 ATTTTCCACCATCGAGGATACTCAAACCCTGTTA-TTTCTGAAGGGATACTCCAACCCCGATTTT
1 ATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTTC-GAGGGGATACTCCAA-CCCGATTTT
*
565106 ATTTCTAAAGCACTG
64 ATTTCTAAAACACTG
* * * **
565121 A-TTTTC-CCTAATCAGGGATATTCCAAGCC-TGTTATTTTTGAAAGGATACTCCAACCCTGATT
1 ATTTTTCACC--ATCGGGGATACTCCAA-CCTTGTTATTTTCGAGGGGATACTCCAACCC-GATT
*
565183 TTATTTCTAAAACACCG
62 TTATTTCTAAAACACTG
* * * * * * * *
565200 ATCTTCCACCATCGGGGATACTCCAACCTCGTTATTTTTGAGGGAATACTCTAACCTTGTTTTTA
1 ATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTTCGAGGGGATACTCCAACC-CGATTTTA
* * * *
565265 TCTCTAAAATATTAA
65 TTTCTAAAACACT-G
* * * *
565280 ATTTTT---CATCGAGGGATGTACTCCAATCTTGTTATTTTTGAGGGAATACTCCAACCCCATTT
1 ATTTTTCACCATCG-GGGA--TACTCCAACCTTGTTATTTTCGAGGGGATACTCCAACCCGATTT
565342 T
63 T
565343 TATCTCCAAA
Statistics
Matches: 431, Mismatches: 81, Indels: 54
0.76 0.14 0.10
Matches are distributed among these distances:
77 7 0.02
78 30 0.07
79 272 0.63
80 115 0.27
81 6 0.01
82 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (78 bp):
ATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTTCGAGGGGATACTCCAACCCGATTTTAT
TTCTAAAACACTG
Found at i:565125 original size:158 final size:157
Alignment explanation
Indices: 564725--565273 Score: 483
Period size: 158 Copynumber: 3.5 Consensus size: 157
564715 TCAAAATATA
** * * **
564725 ATTTTCCACCATCGGGGACGCTCCAACCTTGTTATTT-TCGAGGGGATACTCCAACCTCGGCTTT
1 ATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTCT-GA-GGGATACTCCAACCCCGATTTT
* * * *
564789 ATTTCTAAAACACTGATTTTT-CACCATCGAGGAAACTCCAAGCTCGTTA-TTTCTGAAGGGACA
64 ATTTCTAAAACACTGATTTTTCCACTATC-AGGATACTCCAACCT-GTTATTTTC-GAAGGGATA
* * *
564852 CTCTAACCCTAGTTTTATTCCTAAAACACCT-
126 CTCCAACCCTAATTTTATTTCTAAAACACCTG
*** * * * * * * * *
564883 ATTTTTCCGTTATCGGGGATATTCTAACCCCGTTATTTCCGAGGAAAAACTCTAA-CCCTAGTTT
1 A-TTTTCCACCATCGGGGATACTCCAACCCTGTTATTTCTGAGG-GATACTCCAACCCCGA-TTT
* *
564947 TATTCCTAAAACA-TCAATTTTTCCACTATCAGGATACTCCAACCCTGTTATTTTCG-AGGGCAT
63 TATTTCTAAAACACT-GATTTTTCCACTATCAGGATACTCCAA-CCTGTTATTTTCGAAGGG-AT
* *
565010 ACTCCAACCCCAATTTTATTTTTAAAAC-CCTG
125 ACTCCAACCCTAATTTTATTTCTAAAACACCTG
* *
565042 ATTTTCCACCATCGAGGATACTCAAACCCTGTTATTTCTGAAGGGATACTCCAACCCCGATTTTA
1 ATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTCTG-AGGGATACTCCAACCCCGATTTTA
* * * *
565107 TTTCTAAAGCACTGA-TTTTCC-CTAATCAGGGATATTCCAAGCCTGTTATTTTTGAAAGGATAC
65 TTTCTAAAACACTGATTTTTCCACT-ATCA-GGATACTCCAA-CCTGTTATTTTCGAAGGGATAC
*
565170 TCCAACCCTGATTTTATTTCTAAAACACC-G
127 TCCAACCCTAATTTTATTTCTAAAACACCTG
* * * ** *
565200 ATCTTCCACCATCGGGGATACTCCAA-CCTCGTTATTTTTGAGGGAATACTCTAACCTTGTTTTT
1 ATTTTCCACCATCGGGGATACTCCAACCCT-GTTATTTCTGAGGG-ATACTCCAACCCCGATTTT
*
565264 ATCTCTAAAA
64 ATTTCTAAAA
565274 TATTAAATTT
Statistics
Matches: 312, Mismatches: 60, Indels: 38
0.76 0.15 0.09
Matches are distributed among these distances:
156 2 0.01
157 17 0.05
158 171 0.55
159 110 0.35
160 12 0.04
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (157 bp):
ATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTCTGAGGGATACTCCAACCCCGATTTTAT
TTCTAAAACACTGATTTTTCCACTATCAGGATACTCCAACCTGTTATTTTCGAAGGGATACTCCA
ACCCTAATTTTATTTCTAAAACACCTG
Found at i:565285 original size:317 final size:316
Alignment explanation
Indices: 564725--565345 Score: 699
Period size: 317 Copynumber: 2.0 Consensus size: 316
564715 TCAAAATATA
* * * * * * *
564725 ATTTTCCACCATCGGGGACGCTCCAACCTTGTTATTTTCGAGGGGATACTCCAACCTCGGCTTTA
1 ATTTTCCACCATCGAGGACACTCAAACCCTGTTATTTTCGAAGGGATACTCCAACCCCGACTTTA
*
564790 TTTCTAAAACACTGATTTTTCACCATCGAGGAAACTCCAAGCTCGTTATTTCTGAAGGGACACTC
66 TTTCTAAAACACTGATTTTTCACCATCGAGGAAACTCCAAGCTCGTTATTTCTGAAAGGACACTC
* * * *** * *
564855 TAACCCTAGTTTTATTCCTAAAACACCTATTTTTCCGTTATCGGGGATATTCTAACCCCGTTATT
131 CAACCCTAGTTTTATTCCTAAAACACCGATTCTTCCACCATCGGGGATACTCCAACCCCGTTATT
*
564920 TCCGAGGAAAAACTCTAACCCTAGTTTTATTCCTAAAACATCAATTTTTCCACTATC-A-GGA-T
196 TCCGAGGAAAAACTCTAACCCTAGTTTTATTCCTAAAACATAAATTTTT---C-ATCGAGGGAGT
*
564982 ACTCCAACCCTGTTATTTTCGAGGGCATACTCCAACCCCAATTTTATTTTTAAAACCCTG
257 ACTCCAACCCTGTTATTTTCGAGGGAATACTCCAACCCCAATTTTATTTTTAAAACCCTG
* *
565042 ATTTTCCACCATCGAGGATACTCAAACCCTGTTA-TTTCTGAAGGGATACTCCAACCCCGATTTT
1 ATTTTCCACCATCGAGGACACTCAAACCCTGTTATTTTC-GAAGGGATACTCCAACCCCGACTTT
* * * *
565106 ATTTCTAAAGCACTGA-TTTTC-CCTAATC-AGGGATATTCCAAGC-CTGTTATTTTTGAAAGGA
65 ATTTCTAAAACACTGATTTTTCACC--ATCGA-GGAAACTCCAAGCTC-GTTATTTCTGAAAGGA
* * *
565167 TACTCCAACCCT-GATTTTATTTCTAAAACACCGA-TCTTCCACCATCGGGGATACTCCAACCTC
126 CACTCCAACCCTAG-TTTTATTCCTAAAACACCGATTCTTCCACCATCGGGGATACTCCAACCCC
** * * * *
565230 GTTATTTTTGAGGGAATACTCTAA-CCTTGTTTT-TATCTCTAAAATATTAAATTTTTCATCGAG
190 GTTATTTCCGAGGAAAAACTCTAACCCTAGTTTTAT-TC-CTAAAACA-TAAATTTTTCATCGAG
* * * *
565293 GGATGTACTCCAATCTTGTTATTTTTGAGGGAATACTCCAACCCCATTTTTAT
252 GGA-GTACTCCAACCCTGTTATTTTCGAGGGAATACTCCAACCCCAATTTTAT
565346 CTCCAAAATA
Statistics
Matches: 254, Mismatches: 37, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
313 3 0.01
314 3 0.01
315 15 0.06
316 61 0.24
317 172 0.68
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (316 bp):
ATTTTCCACCATCGAGGACACTCAAACCCTGTTATTTTCGAAGGGATACTCCAACCCCGACTTTA
TTTCTAAAACACTGATTTTTCACCATCGAGGAAACTCCAAGCTCGTTATTTCTGAAAGGACACTC
CAACCCTAGTTTTATTCCTAAAACACCGATTCTTCCACCATCGGGGATACTCCAACCCCGTTATT
TCCGAGGAAAAACTCTAACCCTAGTTTTATTCCTAAAACATAAATTTTTCATCGAGGGAGTACTC
CAACCCTGTTATTTTCGAGGGAATACTCCAACCCCAATTTTATTTTTAAAACCCTG
Found at i:565320 original size:80 final size:80
Alignment explanation
Indices: 565218--565386 Score: 266
Period size: 80 Copynumber: 2.1 Consensus size: 80
565208 CCATCGGGGA
* *** *
565218 TACTCCAACCTCGTTATTTTTGAGGGAATACTCTAACCTTGTTTTTATCTCTAAAATATTAAATT
1 TACTCCAACCTCGTTATTTTTGAGGGAATACTCCAACCCCATTTTTATCTCCAAAATATTAAATT
565283 TTTCATCGAGGGATG
66 TTTCATCGAGGGATG
* *
565298 TACTCCAATCTTGTTATTTTTGAGGGAATACTCCAACCCCATTTTTATCTCCAAAATATTAAATT
1 TACTCCAACCTCGTTATTTTTGAGGGAATACTCCAACCCCATTTTTATCTCCAAAATATTAAATT
*
565363 TTTCATCGGGGGATG
66 TTTCATCGAGGGATG
565378 TACTCCAAC
1 TACTCCAAC
565387 TACGTACCCC
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (80 bp):
TACTCCAACCTCGTTATTTTTGAGGGAATACTCCAACCCCATTTTTATCTCCAAAATATTAAATT
TTTCATCGAGGGATG
Found at i:573750 original size:39 final size:39
Alignment explanation
Indices: 573707--573908 Score: 268
Period size: 39 Copynumber: 5.3 Consensus size: 39
573697 TTGTTTGCTG
* *
573707 CATCATTTCAAACTTGCATCCACATTACATGCTTTGCAT
1 CATCATTTCATACTTGCATCCACCTTACATGCTTTGCAT
* * * *
573746 CATCATTTCATGCTTTCA-CAACCTT-TATGCTTTGCAT
1 CATCATTTCATACTTGCATCCACCTTACATGCTTTGCAT
*
573783 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCAT
1 CATCATTTCATACTTGCATCCACCTTACATGCTTTGCAT
* * * *
573822 CATCATTTCATGCTTTCA-CAACCTT-TATGCTTTGCAT
1 CATCATTTCATACTTGCATCCACCTTACATGCTTTGCAT
*
573859 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCAT
1 CATCATTTCATACTTGCATCCACCTTACATGCTTTGCAT
573898 CATCATTTCAT
1 CATCATTTCAT
573909 GCTTTCACAA
Statistics
Matches: 138, Mismatches: 21, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
37 54 0.39
38 20 0.14
39 64 0.46
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (39 bp):
CATCATTTCATACTTGCATCCACCTTACATGCTTTGCAT
Found at i:573782 original size:37 final size:38
Alignment explanation
Indices: 573731--573919 Score: 256
Period size: 37 Copynumber: 5.0 Consensus size: 38
573721 TGCATCCACA
573731 TTACATGCTTTGCATCATCATTTCATGCTTTCACAACC
1 TTACATGCTTTGCATCATCATTTCATGCTTTCACAACC
* * * * *
573769 TT-TATGCTTTGCATCATCATTTCATACTTGCATCCACG
1 TTACATGCTTTGCATCATCATTTCATGCTTTCA-CAACC
573807 TTACATGCTTTGCATCATCATTTCATGCTTTCACAACC
1 TTACATGCTTTGCATCATCATTTCATGCTTTCACAACC
* * * * *
573845 TT-TATGCTTTGCATCATCATTTCATACTTGCATCCACG
1 TTACATGCTTTGCATCATCATTTCATGCTTTCA-CAACC
573883 TTACATGCTTTGCATCATCATTTCATGCTTTCACAAC
1 TTACATGCTTTGCATCATCATTTCATGCTTTCACAAC
573920 TTTCATTCAT
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
37 54 0.42
38 20 0.16
39 54 0.42
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.41
Consensus pattern (38 bp):
TTACATGCTTTGCATCATCATTTCATGCTTTCACAACC
Found at i:573826 original size:76 final size:76
Alignment explanation
Indices: 573707--573919 Score: 408
Period size: 76 Copynumber: 2.8 Consensus size: 76
573697 TTGTTTGCTG
* *
573707 CATCATTTCAAACTTGCATCCACATTACATGCTTTGCATCATCATTTCATGCTTTCACAACCTTT
1 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCATCATCATTTCATGCTTTCACAACCTTT
573772 ATGCTTTGCAT
66 ATGCTTTGCAT
573783 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCATCATCATTTCATGCTTTCACAACCTTT
1 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCATCATCATTTCATGCTTTCACAACCTTT
573848 ATGCTTTGCAT
66 ATGCTTTGCAT
573859 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCATCATCATTTCATGCTTTCACAAC
1 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCATCATCATTTCATGCTTTCACAAC
573920 TTTCATTCAT
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 135 1.00
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.39
Consensus pattern (76 bp):
CATCATTTCATACTTGCATCCACGTTACATGCTTTGCATCATCATTTCATGCTTTCACAACCTTT
ATGCTTTGCAT
Found at i:575437 original size:61 final size:61
Alignment explanation
Indices: 575257--576203 Score: 908
Period size: 61 Copynumber: 15.4 Consensus size: 61
575247 CCCCTTTTAT
* ** * * * * *
575257 CCTTTTAGTCCTCAAAGAACAGGACGTTTTTTTTCTTTCAAAGCCCATACAAGTTAGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACG-CCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
* * * * * * *
575319 CCTTTCAGTCCTCAAAAAGCAAGAC-AC-TTTCCCTTTAAAGCCCACACAAGCTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
** * * * * *
575378 CCTTCCAGTCCTCAAAGAGTAGGACACATTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
* * * * **
575439 --TTATACAGTCCTCAAAGAGCAGGGCG-CTCTTCCTTTTTAAAGCCCACACAAGTTGGTATCA
1 CCTT-T-TAGTCCTCAAAGAGCAGGACGCCTTTTCC-TTTTAAAGCCCACACGAGTTGGTGGCA
* * * * * * *
575500 TCTTTTAGTCCTCAAAGAGCAGGATGCTTTTTTCTTTTAAAGCCTACATGAGTTTGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
** ** * * *
575561 TATTTTAGTCCTCAAAGAGCAGGATACCTTTTTCTTTTCAAAGCCAACACGAGTTGGTGGCC
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACGAGTTGGTGGCA
* * * * * *
575623 CCTTTCTCA-TCTTCAGAGAGCAAGACACCATTTT-CTTTTAAAGCCCCCATGAGTTGGTGGCA
1 CCTTT-T-AGTCCTCAAAGAGCAGGACGCC-TTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
*
575685 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
* * *
575746 CTTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCTACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACGAGTTGGTGGCA
* * * * *
575808 CCCTTTAGTCCTCAAAGAACAGGACGCCTTCTT-CTTTTCAAAGCCTACATGTGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTT-TTCCTTTT-AAAGCCCACACGAGTTGGTGGCA
* * * *
575870 CAC-TTTAGTCCTCAAAGAACAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTAGCA
1 C-CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACGAGTTGGTGGCA
* * * * * * * *
575932 CCCTTTAGTCCTCAAAGAGTAGGATGCCTTTTTCTTTTGAAGCCCACACGAGCTAGTAGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
* * * * * *
575993 CATTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTGAAGCCCATAGGAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
* ** *
576054 CCTTTTAGTCCTCAAAGAGTAGGAC-ATTTTTTCTTTTAAAG-CCACACGAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
** *
576113 CCTTTTAGTCCTCAAAGATTAGGACGCTTTCTTTTTTCCTTTTAAAGCCCACACGAGTTAGTGGC
1 CCTTTTAGTCCTCAAAGAGCAGGACGC---C--TTTTCCTTTTAAAGCCCACACGAGTTGGTGGC
576178 A
61 A
*
576179 CTTTTTAGTCCTCAAAGAGCAGGAC
1 CCTTTTAGTCCTCAAAGAGCAGGAC
576204 TCATTTCTTT
Statistics
Matches: 750, Mismatches: 109, Indels: 48
0.83 0.12 0.05
Matches are distributed among these distances:
59 89 0.12
60 23 0.03
61 322 0.43
62 232 0.31
63 27 0.04
64 5 0.01
65 13 0.02
66 39 0.05
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (61 bp):
CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCA
Found at i:575692 original size:185 final size:183
Alignment explanation
Indices: 575257--576203 Score: 891
Period size: 185 Copynumber: 5.1 Consensus size: 183
575247 CCCCTTTTAT
* ** * * ** *
575257 CCTTTTAGTCCTCAAAGAACAGGACGTTTTTTTTCTTTCAAAGCCCATACAAGTTAGTGGCACCT
1 CCTTTTAGTCCTCAAAGAGCAGGACG--CCTTTTCTTTTAAAGCCCACATGAGTTGGTGGCACCT
* * * * * * * **
575322 TTCAGTCCTCAAAAAGCAAGA--CAC-TTTCCCTTTAAAGCCCACACAAGCTGGTGGCACCTTCC
64 TTTAGTCCTCAAAGAGCAGGATGC-CTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTT
* * * * *
575384 AGTCCTCAAAGAGTAGGA--CACATTTTCCTTTCAAAGCCCACACAAGTTGGTGG--
128 AGTCCTCAAAGAGCAGGATGC-CTTTTTCTTTTCAAAGCCAACACGAGTTGGTGGCC
* * * * ** ** *
575437 CATTATACAGTCCTCAAAGAGCAGGGCG-CTCTTCCTTTTTAAAGCCCACACAAGTTGGTATCAT
1 CCTT-T-TAGTCCTCAAAGAGCAGGACGCCT-TTTC-TTTTAAAGCCCACATGAGTTGGTGGCAC
* * * * **
575501 CTTTTAGTCCTCAAAGAGCAGGATGCTTTTTTCTTTTAAAGCCTACATGAGTTTGTGGCATATTT
62 CTTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCTTT
*
575566 TAGTCCTCAAAGAGCAGGATACCTTTTTCTTTTCAAAGCCAACACGAGTTGGTGGCC
127 TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCAACACGAGTTGGTGGCC
* * * * *
575623 CCTTTCTCA-TCTTCAGAGAGCAAGACACCATTTTCTTTTAAAGCCCCCATGAGTTGGTGGCACC
1 CCTTT-T-AGTCCTCAAAGAGCAGGACGCC-TTTTCTTTTAAAGCCCACATGAGTTGGTGGCACC
* *
575687 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACTTTTT
63 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTT
* * * *
575752 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCTACACAAGTTGGTGGCAC
128 AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCAACACGAGTTGGTGGC-C
* * *
575809 CC-TTTAGTCCTCAAAGAACAGGACGCCTTCTTCTTTTCAAAGCCTACATGTGTTGGTGGCACAC
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTT-TTCTTTT-AAAGCCCACATGAGTTGGTGGCAC-C
* * *
575873 -TTTAGTCCTCAAAGAACAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTAGCACCCTT
63 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTT-AAAGCCCACACGAGTTGGTGGCACCTTT
* * * * * * *
575937 TAGTCCTCAAAGAGTAGGATGCCTTTTTCTTTT-GAAGCCCACACGAGCTAGTAGCA
127 TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCAACACGAGTTGGTGGCC
* * * * *
575993 CATTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTGAAGCCCATAGGAGTTGGTGGCACCTT
1 CCTTTTAGTCCTCAAAGAGCAGGACGCC-TTTTCTTTTAAAGCCCACATGAGTTGGTGGCACCTT
* *
576058 TTAGTCCTCAAAGAGTAGGA--CATTTTTTCTTTTAAAG-CCACACGAGTTGGTGGCACCTTTTA
65 TTAGTCCTCAAAGAGCAGGATGC-CTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTA
** * * * *
576120 GTCCTCAAAGATTAGGACGCTTTCTTTTTTCCTTTT-AAAGCCCACACGAGTTAGTGGCA
129 GTCCTCAAAGAGCAGGATGC---C-TTTTT-CTTTTCAAAGCCAACACGAGTTGGTGGCC
*
576179 CTTTTTAGTCCTCAAAGAGCAGGAC
1 CCTTTTAGTCCTCAAAGAGCAGGAC
576204 TCATTTCTTT
Statistics
Matches: 636, Mismatches: 102, Indels: 52
0.81 0.13 0.07
Matches are distributed among these distances:
179 1 0.00
180 6 0.01
181 84 0.13
182 23 0.04
183 59 0.09
184 92 0.14
185 253 0.40
186 117 0.18
187 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (183 bp):
CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACATGAGTTGGTGGCACCTTT
TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGT
CCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCAACACGAGTTGGTGGCC
Found at i:576271 original size:44 final size:43
Alignment explanation
Indices: 576186--576701 Score: 321
Period size: 44 Copynumber: 12.4 Consensus size: 43
576176 GCACTTTTTA
* * *
576186 GTCCTCAAAGAGCAGGACTCATTTC-TTT-C-T-TTTCCCATT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCTTT
* *
576225 GTCCTCAAAGAGCATGACATATTTCATTTCCTTCTTTTCCCTTT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTT-CCTTT
* * * *
576269 GTCCTCAAAGAGTAAGACACATCTCATTTCC-TCATTTTCTTTT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTC-TTTTCCTTT
* * * *
576312 ATCCTCAAAAAGTAGGACATATTTCATTTCCTTCTTTTCCCTTT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTT-CCTTT
* * * *
576356 ATCCTCAAAAAGCAGGACACACTTT-ATTTCCTT-TTCTACTTT
1 GTCCTCAAAGAGCAGGACACA-TTTCATTTCCTTCTTTTCCTTT
* * **
576398 GTCCTCAAAGAGTAAGATGC-TTTC----CCTT-TTTTCCTTT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCTTT
* *
576435 GTTCTCAAAAAGCAGGACACATTTCATTTCCTTCTTTTCCTTTT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCC-TTT
* * ** ** * *
576479 ATCCTTAAAGAATAGGATGCATTTTATTTCCTT-TTCTCCTTT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCTTT
* * *
576521 GTCCTCAAAGAGCA-AAGCGCACTTCATTTCC-TCTTTTCCTTT
1 GTCCTCAAAGAGCAGGA-CACATTTCATTTCCTTCTTTTCCTTT
* * * * *
576563 ATCTTCGAAGAGCAGG--ACA--T-A-CT-CTT-TTTCCCTTT
1 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCTTT
* * * *
576598 GTCCTCAAGGAGCAAGACAC-TTTCCTTTTCCTTTTTCTTTCCTTT
1 GTCCTCAAAGAGCAGGACACATTT-CATTTCC-TTCT-TTTCCTTT
* * *
576643 GTCCTCAAAGAGCAGGACCCATTTTATTCTCCTTC--TTCCATT
1 GTCCTCAAAGAGCAGGACACATTTCATT-TCCTTCTTTTCCTTT
* *
576685 GTCCTTAAAGAGTAGGA
1 GTCCTCAAAGAGCAGGA
576702 TGTACTTCTT
Statistics
Matches: 366, Mismatches: 77, Indels: 65
0.72 0.15 0.13
Matches are distributed among these distances:
35 20 0.05
36 2 0.01
37 28 0.08
38 6 0.02
39 22 0.06
40 8 0.02
41 4 0.01
42 88 0.24
43 55 0.15
44 96 0.26
45 31 0.08
46 6 0.02
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCTTT
Found at i:576375 original size:87 final size:84
Alignment explanation
Indices: 576226--576583 Score: 260
Period size: 87 Copynumber: 4.2 Consensus size: 84
576216 TTTCCCATTG
* * * * * *
576226 TCCTCAAAGAGCATGACATATTTCATTTCCTTCTTTTCCCTTTGTCCTCAAAGAGTAAGACACAT
1 TCCTCAAAAAGTAGGACATATTTCATTTCCTT-TTTT-CCTTTGTCCTCAAAAAGCAGGACACAT
576291 CTCATTTCCTCATTTTCTTTTA
64 CTCATTTCCTC-TTTTCTTTTA
*
576313 TCCTCAAAAAGTAGGACATATTTCATTTCCTTCTTTTCCCTTTATCCTCAAAAAGCAGGACACA-
1 TCCTCAAAAAGTAGGACATATTTCATTTCCTT-TTTT-CCTTTGTCCTCAAAAAGCAGGACACAT
* *
576377 CTTTATTT-C-CTTTTCTACTTTG
64 C-TCATTTCCTCTTTTCT--TTTA
* * * * *
576399 TCCTC--AAAG-AGTA-AGA-TGC-TTTCCCTTTTTTCCTTTGTTCTCAAAAAGCAGGACACATT
1 TCCTCAAAAAGTAGGACATATTTCATTT-CCTTTTTTCCTTTGTCCTCAAAAAGCAGGACACATC
576458 TCATTTCCTTCTTTTCCTTTTA
65 TCATTTCC-TCTTTT-CTTTTA
* * *
576480 TCCTTAAAGAA-TAGGATGCAT-TTT-ATTTCCTTTTCTCCTTTGTCCTCAAAGAGCAAAGCG-C
1 TCCTCAAA-AAGTAGGA--CATATTTCATTTCCTTTTTTCCTTTGTCCTCAAAAAGC--AG-GAC
*
576541 AC-T-TCATTTCCTCTTTTCCTTTA
60 ACATCTCATTTCCTCTTTTCTTTTA
* * * *
576564 TCTTCGAAGAGCAGGACATA
1 TCCTCAAAAAGTAGGACATA
576584 CTCTTTTTCC
Statistics
Matches: 218, Mismatches: 30, Indels: 50
0.73 0.10 0.17
Matches are distributed among these distances:
79 29 0.13
80 8 0.04
81 13 0.06
82 10 0.05
83 7 0.03
84 29 0.13
85 7 0.03
86 41 0.19
87 68 0.31
88 5 0.02
89 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.10, T:0.41
Consensus pattern (84 bp):
TCCTCAAAAAGTAGGACATATTTCATTTCCTTTTTTCCTTTGTCCTCAAAAAGCAGGACACATCT
CATTTCCTCTTTTCTTTTA
Found at i:576462 original size:123 final size:124
Alignment explanation
Indices: 576204--576532 Score: 351
Period size: 123 Copynumber: 2.6 Consensus size: 124
576194 AGAGCAGGAC
* * * * * * *
576204 TCATTTCTTTCTTTTCCCATTGTCCTCAAAGAGCATGACATATTTCATTTCCTTCTTTTCCCTTT
1 TCATTTCCTTCTTTTCCCTTTATCCTCAAAAAGCAGGACACATTT-ATTTCCTT-TTCT-CCTTT
* * * *
576269 GTCCTCAAAGAGTAAGACACATCTCATTTCCTCATTTTCTTTTATCCTCAAAAAGTAGGACATAT
63 GTCCTCAAAGAGTAAG--A-ATCT-ATTCCCTCATTTTCCTTTATCCTCAAAAAGCAGGACACAT
576334 T
124 T
*
576335 TCATTTCCTTCTTTTCCCTTTATCCTCAAAAAGCAGGACACACTTTATTTCCTTTTCTACTTTGT
1 TCATTTCCTTCTTTTCCCTTTATCCTCAAAAAGCAGGACACA-TTTATTTCCTTTTCTCCTTTGT
* * *
576400 CCTCAAAGAGTAAG-ATGCT-TTCCCT-TTTTTCCTTTGTTCTCAAAAAGCAGGACACATT
65 CCTCAAAGAGTAAGAAT-CTATTCCCTCATTTTCCTTTATCCTCAAAAAGCAGGACACATT
* * * **
576458 TCATTTCCTTCTTTTCCTTTTATCCTTAAAGAA-TAGGATGCATTTTATTTCCTTTTCTCCTTTG
1 TCATTTCCTTCTTTTCCCTTTATCCTCAAA-AAGCAGGACACA-TTTATTTCCTTTTCTCCTTTG
576522 TCCTCAAAGAG
64 TCCTCAAAGAG
576533 CAAAGCGCAC
Statistics
Matches: 173, Mismatches: 22, Indels: 14
0.83 0.11 0.07
Matches are distributed among these distances:
123 92 0.53
124 7 0.04
125 2 0.01
126 2 0.01
129 20 0.12
130 3 0.02
131 44 0.25
132 3 0.02
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.43
Consensus pattern (124 bp):
TCATTTCCTTCTTTTCCCTTTATCCTCAAAAAGCAGGACACATTTATTTCCTTTTCTCCTTTGTC
CTCAAAGAGTAAGAATCTATTCCCTCATTTTCCTTTATCCTCAAAAAGCAGGACACATT
Found at i:576519 original size:86 final size:85
Alignment explanation
Indices: 576258--576562 Score: 260
Period size: 86 Copynumber: 3.6 Consensus size: 85
576248 TCATTTCCTT
* * * *
576258 CTTTTC-CCTTTGTCCTCAAAGAGTAAGACACATCTCATTTCCTCATTTT-CTTTTATCCTCAAA
1 CTTTTCTCCTTTGTCCTCAAAAAGCAGGACACATTTCATTTCCTC-TTTTCCTTTTATCCTCAAA
576321 -AAGTAGGA--CATATTTCATTTC
65 GAA-TAGGATGCAT-TTT-ATTTC
* * * *
576342 CTTCTTTTCCCTTTATCCTCAAAAAGCAGGACACACTTT-ATTTCCT-TTTCTAC-TTTGTCCTC
1 CTT-TTCT-CCTTTGTCCTCAAAAAGCAGGACACA-TTTCATTTCCTCTTT-TCCTTTTATCCTC
* * *
576404 AAAGAGTAAGATGC----T-TTCC
62 AAAGAATAGGATGCATTTTATTTC
* * *
576423 CTTTTTTCCTTTGTTCTCAAAAAGCAGGACACATTTCATTTCCTTCTTTTCCTTTTATCCTTAAA
1 CTTTTCTCCTTTGTCCTCAAAAAGCAGGACACATTTCATTTCC-TCTTTTCCTTTTATCCTCAAA
576488 GAATAGGATGCATTTTATTTC
65 GAATAGGATGCATTTTATTTC
* * * *
576509 CTTTTCTCCTTTGTCCTCAAAGAGCA-AAGCGCACTTCATTTCCTCTTTTCCTTT
1 CTTTTCTCCTTTGTCCTCAAAAAGCAGGA-CACATTTCATTTCCTCTTTTCCTTT
576563 ATCTTCGAAG
Statistics
Matches: 178, Mismatches: 24, Indels: 37
0.74 0.10 0.15
Matches are distributed among these distances:
78 3 0.02
79 30 0.17
80 7 0.04
81 28 0.16
83 1 0.01
84 3 0.02
85 18 0.10
86 54 0.30
87 31 0.17
88 3 0.02
ACGTcount: A:0.23, C:0.26, G:0.09, T:0.42
Consensus pattern (85 bp):
CTTTTCTCCTTTGTCCTCAAAAAGCAGGACACATTTCATTTCCTCTTTTCCTTTTATCCTCAAAG
AATAGGATGCATTTTATTTC
Found at i:579782 original size:79 final size:79
Alignment explanation
Indices: 579696--580148 Score: 362
Period size: 80 Copynumber: 5.7 Consensus size: 79
579686 TCCAAAATAT
* * * ** * * *
579696 AATTTTCCGCCATCGGGGACACTCCATCCCCATTATTTTCGAGGGGATACTCCAACCCCAGCTTT
1 AATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCTAACCCCAGTTTT
*
579761 ATTTCTAAAACACC
66 ATTCCTAAAACACC
* * * *
579775 AATTTTCCACCATTGGGGAAACTCTAACCCTGTTATTTTCGAGGAGATACTCTAACCTC-GATTT
1 AATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCTAACCCCAG-TTT
* *
579839 TATTCCTAAAATACTG
65 TATTCCTAAAACAC-C
* * * * * * * * * *
579855 ATTTTTCCACTATCGGGAATACTCTAATCATGTTATTTTTGAGGAAATACTCTAACCTCGGTTTT
1 AATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCTAACCCCAGTTTT
*
579920 ATTCCTAAAACATC
66 ATTCCTAAAACACC
* ** * * * * * *
579934 ATTTTTTTTACTATCTGAGATACTCTAACCCCGTTATTTTCGAGGGGATACTCTAACCCCTA-TT
1 A-ATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCTAACCCC-AGTT
*
579998 TTATTTCTAAAACACC
64 TTATTCCTAAAACACC
* * * *
580014 AATTTTTCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGAGATACT-TTACCTCGGTTTT
1 AATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCTAACCCCAGTTTT
* * *
580078 ATT-TTTAAA-ACT
66 ATTCCTAAAACACC
* *** * *
580090 AATTTTTCGTAATCAGGGATACTCCAA-CCTCATTATTTTCGAAGGA-ATACTCTAACCCC
1 AATTTTCCACCATCGGGGATACTCCAACCCT-GTTATTTTCG-AGGAGATACTCTAACCCC
580149 GTTATTTTTG
Statistics
Matches: 303, Mismatches: 62, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
75 3 0.01
76 39 0.13
77 13 0.04
78 13 0.04
79 106 0.35
80 128 0.42
81 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (79 bp):
AATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCTAACCCCAGTTTT
ATTCCTAAAACACC
Found at i:580001 original size:160 final size:155
Alignment explanation
Indices: 579795--580149 Score: 413
Period size: 160 Copynumber: 2.3 Consensus size: 155
579785 CATTGGGGAA
* * * * **
579795 ACTCTAACCCTGTTATTTTCGAGGAGATACTCTAACCTCGATTTTATTCCTAAAATACTGATTTT
1 ACTCTAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTATTCCTAAAACACCAATTTT
* * * *
579860 TCCACTATCGGGAATACTCTAATCATGTTATTTTTGAGGAAATACTCTAACCTCGGTTTTATTCC
66 T-CACCATCGGGAATACTCCAACCATGTTATTTTCGAGGAAATACT-TAACCTCGGTTTTATTCC
* ** *
579925 TAAAACATCATTTTTTTTACTATCTGAGAT
129 TAAAAC-TAATTTTTCGTA--ATCAGAGAT
* *
579955 ACTCTAACCCCGTTATTTTCGAGGGGATACTCTAACCCCTATTTTATTTCTAAAACACCAATTTT
1 ACTCTAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTATTCCTAAAACACCAATTTT
* * * * **
580020 TCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTTTACCTCGGTTTTATTTTTA
66 TCACCATCGGGAATACTCCAACCATGTTATTTTCGAGGAAATACTTAACCTCGGTTTTATTCCTA
*
580085 AAACTAATTTTTCGTAATCAGGGAT
131 AAACTAATTTTTCGTAATCAGAGAT
* * * * *
580110 ACTCCAACCTCATTATTTTCGAAGGAATACTCTAACCCCG
1 ACTCTAACCCCGTTATTTTCGAGGGGATACTCTAACCCCG
580150 TTATTTTTGA
Statistics
Matches: 166, Mismatches: 29, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
155 41 0.25
157 9 0.05
158 21 0.13
159 37 0.22
160 58 0.35
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (155 bp):
ACTCTAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTATTCCTAAAACACCAATTTT
TCACCATCGGGAATACTCCAACCATGTTATTTTCGAGGAAATACTTAACCTCGGTTTTATTCCTA
AAACTAATTTTTCGTAATCAGAGAT
Found at i:580153 original size:28 final size:28
Alignment explanation
Indices: 580106--580177 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
580096 TCGTAATCAG
*
580106 GGATACTCCAACCTCATTATTTTCG-AA
1 GGATACTCCAACCCCATTATTTTCGAAA
* * *
580133 GGAATACTCTAACCCCGTTATTTTTGAAA
1 GG-ATACTCCAACCCCATTATTTTCGAAA
580162 GGATACTCCAACCCCA
1 GGATACTCCAACCCCA
580178 GTTTTATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
27 2 0.05
28 31 0.84
29 4 0.11
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (28 bp):
GGATACTCCAACCCCATTATTTTCGAAA
Found at i:580244 original size:107 final size:107
Alignment explanation
Indices: 580105--580342 Score: 440
Period size: 107 Copynumber: 2.2 Consensus size: 107
580095 TTCGTAATCA
* * *
580105 GGGATACTCCAACCTCATTATTTTCGAAGGAATACTCTAACCCCGTTATTTTTGAAAGGATACTC
1 GGGATACTCTAACCTCGTTATTTTCGAAGGAATACTCTAACCCCATTATTTTTGAAAGGATACTC
580170 CAACCCCAGTTTTATTTTTAAACTACTGATCTTCCACCATCG
66 CAACCCCAGTTTTATTTTTAAACTACTGATCTTCCACCATCG
580212 GGGATACTCTAACCTCGTTATTTTCGAAGGAATACTCTAACCCCATTATTTTTGAAAGGATACTC
1 GGGATACTCTAACCTCGTTATTTTCGAAGGAATACTCTAACCCCATTATTTTTGAAAGGATACTC
580277 CAACCCCAGTTTTATTTTTAAACTACTGATCTTCCACCATCG
66 CAACCCCAGTTTTATTTTTAAACTACTGATCTTCCACCATCG
*
580319 GGGATACTCTAACCCCGTTATTTT
1 GGGATACTCTAACCTCGTTATTTT
580343 TGAGGGGATA
Statistics
Matches: 127, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 127 1.00
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (107 bp):
GGGATACTCTAACCTCGTTATTTTCGAAGGAATACTCTAACCCCATTATTTTTGAAAGGATACTC
CAACCCCAGTTTTATTTTTAAACTACTGATCTTCCACCATCG
Found at i:580260 original size:28 final size:28
Alignment explanation
Indices: 580213--580284 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
580203 CCACCATCGG
* *
580213 GGATACTCTAACCTCGTTATTTTCG-AA
1 GGATACTCTAACCCCATTATTTTCGAAA
*
580240 GGAATACTCTAACCCCATTATTTTTGAAA
1 GG-ATACTCTAACCCCATTATTTTCGAAA
*
580269 GGATACTCCAACCCCA
1 GGATACTCTAACCCCA
580285 GTTTTATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
27 2 0.05
28 33 0.85
29 4 0.10
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (28 bp):
GGATACTCTAACCCCATTATTTTCGAAA
Found at i:581477 original size:32 final size:33
Alignment explanation
Indices: 581441--581502 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
581431 TAATTCAATG
*
581441 TGTATCGATACCAAG-AATATGTATCGATATAA
1 TGTATCAATACCAAGCAATATGTATCGATATAA
*
581473 TGTATCAATACTAAGCAATATGTATCGATA
1 TGTATCAATACCAAGCAATATGTATCGATA
581503 CGTCTAGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (33 bp):
TGTATCAATACCAAGCAATATGTATCGATATAA
Found at i:592181 original size:30 final size:29
Alignment explanation
Indices: 592145--592240 Score: 93
Period size: 30 Copynumber: 3.6 Consensus size: 29
592135 ACATCTTCAT
592145 TGTATCGATACATTTTAAGTTTTACCCAGA
1 TGTATCGATACATTTT-AGTTTTACCCAGA
*
592175 TGTATCGATACA--TTA---TT---CA-T
1 TGTATCGATACATTTTAGTTTTACCCAGA
*
592195 TGTATCGATACATTTTGGGTTTTACCCAGA
1 TGTATCGATACATTTT-AGTTTTACCCAGA
592225 TGTATCGATACATTTT
1 TGTATCGATACATTTT
592241 TCATTGTATC
Statistics
Matches: 53, Mismatches: 3, Indels: 20
0.70 0.04 0.26
Matches are distributed among these distances:
20 12 0.23
21 2 0.04
22 2 0.04
24 2 0.04
26 2 0.04
27 1 0.02
28 2 0.04
29 2 0.04
30 28 0.53
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.43
Consensus pattern (29 bp):
TGTATCGATACATTTTAGTTTTACCCAGA
Found at i:592202 original size:50 final size:50
Alignment explanation
Indices: 592128--592258 Score: 219
Period size: 50 Copynumber: 2.6 Consensus size: 50
592118 TCACAATTTA
*
592128 TATCGATACA-TCTTCATTGTATCGATACATTTTAAGTTTTACCCAGATG
1 TATCGATACATTATTCATTGTATCGATACATTTTAAGTTTTACCCAGATG
**
592177 TATCGATACATTATTCATTGTATCGATACATTTTGGGTTTTACCCAGATG
1 TATCGATACATTATTCATTGTATCGATACATTTTAAGTTTTACCCAGATG
*
592227 TATCGATACATTTTTCATTGTATCGATACATT
1 TATCGATACATTATTCATTGTATCGATACATT
592259 CTGGATCTTA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
49 10 0.13
50 67 0.87
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (50 bp):
TATCGATACATTATTCATTGTATCGATACATTTTAAGTTTTACCCAGATG
Found at i:592278 original size:50 final size:50
Alignment explanation
Indices: 592128--592318 Score: 208
Period size: 50 Copynumber: 3.8 Consensus size: 50
592118 TCACAATTTA
* **
592128 TATCGATACA-TCTTCATTGTATCGATACATT-TTAAGTTTTACCCAGATG
1 TATCGATACATTTTTCATTGTATCGATACATTCTGGA-TTTTACCCAGATG
* * *
592177 TATCGATACATTATTCATTGTATCGATACATTTTGGGTTTTACCCAGATG
1 TATCGATACATTTTTCATTGTATCGATACATTCTGGATTTTACCCAGATG
* * *
592227 TATCGATACATTTTTCATTGTATCGATACATTCTGGATCTTATCCAAATG
1 TATCGATACATTTTTCATTGTATCGATACATTCTGGATTTTACCCAGATG
* * * * *
592277 TATTGATATATTTCTT-AATGTATTGATACATTCAGGCATTTT
1 TATCGATACATTT-TTCATTGTATCGATACATTCTGG-ATTTT
592319 TGACCATTTT
Statistics
Matches: 122, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
49 10 0.08
50 105 0.86
51 7 0.06
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (50 bp):
TATCGATACATTTTTCATTGTATCGATACATTCTGGATTTTACCCAGATG
Found at i:594756 original size:79 final size:79
Alignment explanation
Indices: 594668--595169 Score: 500
Period size: 79 Copynumber: 6.4 Consensus size: 79
594658 TTTCCGAGGG
* * * *
594668 GATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATATTCAAATCCT
1 GATACTCCAACCCTGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCAAACCCC
594733 GTTATTTCTAAGGA
66 GTTATTTCTAAGGA
*
594747 GATACTCCAACCCTGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCTAACCCC
1 GATACTCCAACCCTGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCAAACCCC
*
594812 GTTATTTCTAA-AA
66 GTTATTTCTAAGGA
* ** * * * *
594825 TGATACTCTAACCCCAGTTTTATTTCCAAAATACCAATTTTTCATAATCGGGGATACTCAGACCC
1 -GATACTCCAACCCTGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCAAACCC
* *
594890 CATTATATT-TGA-GA
65 CGTTAT-TTCTAAGGA
* * * * * *
594904 GGATACTCCAACCCTAGTTTTATTTCCAAAGCA-TCGA-TTTTCACAATCAGGGATACTCTAACT
1 -GATACTCCAACCCTGGTTTTATTTCCAAAACACT-AATTTTTCACAATCGGGGATACTCAAACC
* *
594967 CCGTTATTTTTGAGGA
64 CCGTTATTTCTAAGGA
* * * * * *
594983 GATACTCCAA-CCTAGTTTTATTTTCAAAACACTGATTTTTCACAATCGAGGATACTCTAACCAC
1 GATACTCCAACCCTGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCAAACCCC
* *
595047 GTTATTTTCGAAAG-
66 GTTA-TTTCTAAGGA
* * * * * * *
595061 GATACTCCAACTCTGGTTTTATTTTCAAAACACCAATTTTTCACAATTGAGGATACTCCAACCCT
1 GATACTCCAACCCTGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCAAACCCC
*
595126 GTTATTTTCGAAGG-
66 GTTA-TTTCTAAGGA
* * *
595140 GATACTCTAACCCCGATTTTATCTT-CAAAA
1 GATACTCCAACCCTGGTTTTAT-TTCCAAAA
595170 TATTAAACTT
Statistics
Matches: 360, Mismatches: 53, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
77 23 0.06
78 80 0.22
79 253 0.70
80 4 0.01
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.34
Consensus pattern (79 bp):
GATACTCCAACCCTGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCAAACCCC
GTTATTTCTAAGGA
Found at i:594856 original size:31 final size:28
Alignment explanation
Indices: 594798--594856 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
594788 CACAATCGGG
*
594798 GATACTCTAACCCCGTTATTTCTAAAAT
1 GATACTCTAACCCCGTTATTTCCAAAAT
594826 GATACTCTAACCCCAGTTTTATTTCCAAAAT
1 GATACTCTAACCCC-G--TTATTTCCAAAAT
594857 ACCAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 14 0.52
29 1 0.04
31 12 0.44
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (28 bp):
GATACTCTAACCCCGTTATTTCCAAAAT
Found at i:595038 original size:235 final size:237
Alignment explanation
Indices: 594667--595118 Score: 617
Period size: 235 Copynumber: 1.9 Consensus size: 237
594657 ATTTCCGAGG
* * *
594667 GGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATATTCAAATCC
1 GGATACTCCAACCCCAGTTTTATTTCCAAAACACTAATTTTTCACAATCAGGGATACTCAAATCC
* *
594732 TGTTATTTCTAAGGAGATACTCCAACCCTGGTTTTATTTCCAAAACACTAATTTTTCACAATCGG
66 TGTTATTTCTAAGGAGATACTCCAACCCTAGTTTTATTTCCAAAACACTAATTTTTCACAATCGA
* * * *
594797 GGATACTCTAACCCCGTTA-TTTCTAAAATGATACTCTAACCCCAGTTTTATTTCCAAAATACCA
131 GGATACTCTAACCACGTTATTTTC-AAAAGGATACTCCAACCCCAGTTTTATTTCCAAAACACCA
* *
594861 ATTTTTCATAATCGGGGATACTCAGACCCCATTATATTTGAGA
195 ATTTTTCACAATCGAGGATACTCAGACCCCATTATATTTGAGA
* * * *
594904 GGATACTCCAACCCTAGTTTTATTTCCAAAGCA-TCGA-TTTTCACAATCAGGGATACTCTAACT
1 GGATACTCCAACCCCAGTTTTATTTCCAAAACACT-AATTTTTCACAATCAGGGATACTC-AAAT
* * * *
594967 CC-GTTATTTTTGAGGAGATACTCCAA-CCTAGTTTTATTTTCAAAACACTGATTTTTCACAATC
64 CCTGTTATTTCTAAGGAGATACTCCAACCCTAGTTTTATTTCCAAAACACTAATTTTTCACAATC
* * ** *
595030 GAGGATACTCTAACCACGTTATTTTCGAAAGGATACTCCAACTCTGGTTTTATTTTCAAAACACC
129 GAGGATACTCTAACCACGTTATTTTCAAAAGGATACTCCAACCCCAGTTTTATTTCCAAAACACC
*
595095 AATTTTTCACAATTGAGGATACTC
194 AATTTTTCACAATCGAGGATACTC
595119 CAACCCTGTT
Statistics
Matches: 187, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
235 105 0.56
236 46 0.25
237 36 0.19
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (237 bp):
GGATACTCCAACCCCAGTTTTATTTCCAAAACACTAATTTTTCACAATCAGGGATACTCAAATCC
TGTTATTTCTAAGGAGATACTCCAACCCTAGTTTTATTTCCAAAACACTAATTTTTCACAATCGA
GGATACTCTAACCACGTTATTTTCAAAAGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAA
TTTTTCACAATCGAGGATACTCAGACCCCATTATATTTGAGA
Found at i:601421 original size:6 final size:6
Alignment explanation
Indices: 601412--601443 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
601402 TTTTTTTATT
601412 TTTTAA TTTTAA -TTT-A TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
601444 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 1 0.04
5 6 0.25
6 17 0.71
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTAA
Found at i:601431 original size:16 final size:16
Alignment explanation
Indices: 601412--601442 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
601402 TTTTTTTATT
601412 TTTTAATTTTAATTTA
1 TTTTAATTTTAATTTA
601428 TTTTAATTTTAATTT
1 TTTTAATTTTAATTT
601443 TTTAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTAATTTTAATTTA
Found at i:602032 original size:22 final size:22
Alignment explanation
Indices: 601989--602032 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
601979 ATCTTGTAAT
**
601989 ATTAATAAATTATTTATTAAAA
1 ATTAATAAATTATTTAAAAAAA
* *
602011 ATTAATTATTTATTTAAAAAAA
1 ATTAATAAATTATTTAAAAAAA
602033 TATTTTTATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTAATAAATTATTTAAAAAAA
Found at i:602746 original size:152 final size:150
Alignment explanation
Indices: 602315--602770 Score: 801
Period size: 149 Copynumber: 3.0 Consensus size: 150
602305 TTTATTTGCG
* *
602315 AAACCAAATCGATTTGCTC-TTTTTTTTATAGATCTTTGTTTTACGATTTTGGGATTTATTGAAG
1 AAACCAAATCGATTTGCGCTTTTTTTTTATAGATCTTTGTTTTACGATTTTGGGATTTTTTGAAG
*
602379 CAATTTTTTTTTGAGTTGTCTGTCTTTGTCTTGTAAAGCTCTTGATCTGATTCCCGATCATTTCT
66 CAATTTTTTTTTGAGTTGTCTGTCTTTGGCTTGTAAAGCTCTTGATCTGATTCCCGATCATTTCT
602444 AAATACATCAATTAAATAGA
131 AAATACATCAATTAAATAGA
602464 AAACCAAATCGATTTGCGC--TTTTTTTATAGATCTTTGTTTTACGATTTTGGGATTTTTTTGAA
1 AAACCAAATCGATTTGCGCTTTTTTTTTATAGATCTTTGTTTTACGATTTTGGGA-TTTTTTGAA
602527 GCAATTTTTTTTTGAGTTGTCTGTCTTTGGCTTGTAAAGCTCTTGATCTGATTCCCGATCATTTC
65 GCAATTTTTTTTTGAGTTGTCTGTCTTTGGCTTGTAAAGCTCTTGATCTGATTCCCGATCATTTC
*
602592 TAAATATATCAATTAAATAGA
130 TAAATACATCAATTAAATAGA
*
602613 AAACCAAATCGATTTGCGCTTTTTTTTTTTGTAGATCTTTGTTTTACGATTTTGGGATTTTTTGA
1 AAACCAAATCGATTTGCGC--TTTTTTTTTATAGATCTTTGTTTTACGATTTTGGGATTTTTTGA
* *
602678 AGCAATTTTTTTTTGAGTTGTCTGTCTTTGGCTTGTAAAGCTGTTGATCTGATGCCCGATCATTT
64 AGCAATTTTTTTTTGAGTTGTCTGTCTTTGGCTTGTAAAGCTCTTGATCTGATTCCCGATCATTT
602743 CTAAATACATCAATTAAATAGA
129 CTAAATACATCAATTAAATAGA
602765 AAACCA
1 AAACCA
602771 TAGCATAATA
Statistics
Matches: 294, Mismatches: 8, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
148 34 0.12
149 129 0.44
152 98 0.33
153 33 0.11
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (150 bp):
AAACCAAATCGATTTGCGCTTTTTTTTTATAGATCTTTGTTTTACGATTTTGGGATTTTTTGAAG
CAATTTTTTTTTGAGTTGTCTGTCTTTGGCTTGTAAAGCTCTTGATCTGATTCCCGATCATTTCT
AAATACATCAATTAAATAGA
Found at i:613277 original size:85 final size:83
Alignment explanation
Indices: 613135--613299 Score: 251
Period size: 85 Copynumber: 2.0 Consensus size: 83
613125 GTCTTTTAAG
*
613135 AAAAATAATGATATTGTGATATTGTAATTAGTCATTTAATTGTTAGATTTAAGAAAAAAAAAAGT
1 AAAAATAATGATATTGTGATATTGTAATTAATCATTTAATTGTTAGATTTAAG-AAAAAAAAAGT
613200 AGGTTGCATTAATTTTACTT
65 A-GTTGCATTAATTTTACTT
** * *
613220 AAAAATAATGAGT-TTGTGATATTGTAATTAATTTTTTAATTGTTCGATTTAAGAAAAAGAAAGT
1 AAAAATAATGA-TATTGTGATATTGTAATTAATCATTTAATTGTTAGATTTAAGAAAAAAAAAGT
613284 AGTTGCATTAATTTTA
65 AGTTGCATTAATTTTA
613300 TATTAGATAA
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
83 15 0.20
84 11 0.15
85 47 0.64
86 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (83 bp):
AAAAATAATGATATTGTGATATTGTAATTAATCATTTAATTGTTAGATTTAAGAAAAAAAAAGTA
GTTGCATTAATTTTACTT
Found at i:613534 original size:32 final size:31
Alignment explanation
Indices: 613490--613591 Score: 115
Period size: 32 Copynumber: 3.4 Consensus size: 31
613480 TTAATAATTT
*
613490 TTTAATAT-AATATAATTTAATAAGTTTATTA
1 TTTAACATAAATATAATTTAATAA-TTTATTA
613521 TTTAACATAAATATAATTTAATATATATT-TTA
1 TTTAACATAAATATAATTTAATA-AT-TTATTA
* *
613553 TTAAATATAAATATAATTT--TAA-TTATTA
1 TTTAACATAAATATAATTTAATAATTTATTA
613581 TTTAACATAAA
1 TTTAACATAAA
613592 CAAATTTTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
27 2 0.03
28 12 0.19
29 1 0.02
30 2 0.03
31 7 0.11
32 35 0.56
33 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (31 bp):
TTTAACATAAATATAATTTAATAATTTATTA
Found at i:613539 original size:16 final size:16
Alignment explanation
Indices: 613490--613571 Score: 69
Period size: 16 Copynumber: 5.2 Consensus size: 16
613480 TTAATAATTT
613490 TTTAATAT-AATATAA
1 TTTAATATAAATATAA
** *
613505 TTTAATA-AGTTTATTA
1 TTTAATATA-AATATAA
*
613521 TTTAACATAAATATAA
1 TTTAATATAAATATAA
* * *
613537 TTTAATATATATTTTA
1 TTTAATATAAATATAA
*
613553 TTAAATATAAATATAA
1 TTTAATATAAATATAA
613569 TTT
1 TTT
613572 TAATTATTAT
Statistics
Matches: 48, Mismatches: 16, Indels: 5
0.70 0.23 0.07
Matches are distributed among these distances:
15 7 0.15
16 40 0.83
17 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (16 bp):
TTTAATATAAATATAA
Found at i:614053 original size:24 final size:21
Alignment explanation
Indices: 614027--614072 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
614017 AAAAGTAAAA
* *
614027 ATAATAGTAAAATTAATTATT
1 ATAATAATAAAATTAAATATT
614048 ATAATAATAAAATTAAATATT
1 ATAATAATAAAATTAAATATT
614069 ATAA
1 ATAA
614073 CGATGAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATAAAATTAAATATT
Found at i:614244 original size:18 final size:18
Alignment explanation
Indices: 614217--614261 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
614207 TAACAAAATA
614217 AATA-TTTAATTA-ATTAT
1 AATATTTTAATTATATT-T
*
614234 TATATTTTAATTATATTT
1 AATATTTTAATTATATTT
614252 AATATTTTAA
1 AATATTTTAA
614262 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AATATTTTAATTATATTT
Found at i:614773 original size:18 final size:17
Alignment explanation
Indices: 614741--614783 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 17
614731 AATATCATAT
614741 TATATTTAAAATTTTAA
1 TATATTTAAAATTTTAA
*
614758 TATATTTAATAATTTTAT
1 TATATTTAA-AATTTTAA
614776 TATATTTA
1 TATATTTA
614784 TATACATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTAAAATTTTAA
Found at i:616749 original size:21 final size:21
Alignment explanation
Indices: 616673--616751 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
616663 TGAAACATGC
* *
616673 ATTGTATCAATACAAGGCTAT
1 ATTGTATCAATACAATGCCAT
* * *
616694 ATTGTATCGATACAGT-TC-T
1 ATTGTATCAATACAATGCCAT
* **
616713 CATTATATTGATACAATGCCAT
1 -ATTGTATCAATACAATGCCAT
616735 ATTGTATCAATACAATG
1 ATTGTATCAATACAATG
616752 TCATGTTTTG
Statistics
Matches: 43, Mismatches: 12, Indels: 6
0.70 0.20 0.10
Matches are distributed among these distances:
19 1 0.02
20 13 0.30
21 28 0.65
22 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (21 bp):
ATTGTATCAATACAATGCCAT
Found at i:617434 original size:12 final size:12
Alignment explanation
Indices: 617413--617446 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
617403 TCAACTGAGA
617413 AAAAATAAAAGGT
1 AAAAA-AAAAGGT
*
617426 AAAAAAAAAGTT
1 AAAAAAAAAGGT
617438 AAAAAAAAA
1 AAAAAAAAA
617447 AAGAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (12 bp):
AAAAAAAAAGGT
Found at i:617982 original size:2 final size:2
Alignment explanation
Indices: 617975--618000 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
617965 TGTTTAGATA
617975 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
618001 TCAGGAGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:618978 original size:36 final size:38
Alignment explanation
Indices: 618937--619020 Score: 111
Period size: 36 Copynumber: 2.3 Consensus size: 38
618927 ACTTAAAAAA
618937 ATAATATAAATTATAAACAATTT-AAAAAA-GAAAATT
1 ATAATATAAATTATAAACAATTTAAAAAAAGGAAAATT
* * *
618973 ATAATATTAATTATAAATAGTTTAAAAAAAGGAAAATT
1 ATAATATAAATTATAAACAATTTAAAAAAAGGAAAATT
*
619011 ACAAT-TAAAT
1 ATAATATAAAT
619021 ACCAAAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 20 0.49
37 10 0.24
38 11 0.27
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (38 bp):
ATAATATAAATTATAAACAATTTAAAAAAAGGAAAATT
Found at i:621726 original size:62 final size:62
Alignment explanation
Indices: 621603--621727 Score: 144
Period size: 62 Copynumber: 2.0 Consensus size: 62
621593 TAAAATTAAG
* * * ** ** *
621603 TAAAAACTATATTATTAAAAAAAGTATTTGGATAAAATTAAATTTAAATGATCCCTCAAATTT
1 TAAAAACTAAATTACTAAAAAAAG-ATTTAGATAAAATTAAATTTAAAAAATAACTAAAATTT
*
621666 TAAAAACTAAATTACTAAAAAATA-ATTTAGATAAAATTAAATTTAAAAAATAATTAAAATTT
1 TAAAAACTAAATTACTAAAAAA-AGATTTAGATAAAATTAAATTTAAAAAATAACTAAAATTT
621728 AAATGTCATA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
62 31 0.60
63 20 0.38
64 1 0.02
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (62 bp):
TAAAAACTAAATTACTAAAAAAAGATTTAGATAAAATTAAATTTAAAAAATAACTAAAATTT
Found at i:623335 original size:20 final size:20
Alignment explanation
Indices: 623310--623347 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
623300 CTAGAAAAAA
*
623310 ATTGTATCGATATATTTTTT
1 ATTGTATCGATACATTTTTT
623330 ATTGTATCGATACATTTT
1 ATTGTATCGATACATTTT
623348 GGATTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (20 bp):
ATTGTATCGATACATTTTTT
Found at i:627915 original size:22 final size:22
Alignment explanation
Indices: 627873--627916 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
627863 ACTTAAAAAT
* *
627873 TTTTAAAGTAAAAAATTTTGTA
1 TTTTAAAATAAAAAATATTGTA
627895 TTTTAATAATAAAAAA-ATTGTA
1 TTTTAA-AATAAAAAATATTGTA
627917 AAACTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAAAAATATTGTA
Found at i:633453 original size:24 final size:24
Alignment explanation
Indices: 633421--633484 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
633411 TTATTTTTAA
**
633421 ATATATTATATTATATAATTATATT
1 ATAT-TTATATTATATAAACATATT
*
633446 ATTTTTATATTGAT-TAAACATATT
1 ATATTTATATT-ATATAAACATATT
*
633470 ATATTTATTTTATAT
1 ATATTTATATTATAT
633485 TTAAAATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.06
24 25 0.78
25 5 0.16
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
ATATTTATATTATATAAACATATT
Done.