Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 91 of 344
Found at i:30361795 original size:44 final size:46
Alignment explanation
Indices: 30361602--30361816 Score: 168
Period size: 46 Copynumber: 4.6 Consensus size: 46
30361592 TTTGTGCACT
* * * **
30361602 AGTGTAAGACATGTCAGGGACCTGCATCGACCACATTAT-TAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCTCAAGATATA-AGCC
* * * ** * * *
30361648 AGTGTAAGACCATGTCTGGGACATGGCATTGGCATTGAGACGA-GAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACCTCAAGA-TATAAGCC
*
30361696 AGTGTAAGACATGTCTGGGATATGCATCGACCTCAAGATATAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCTCAAGATATAAGCC
* * * ** *
30361742 AGTGTAAGACATGTCTGGGACATGCAT-TAGCT-ACGATATGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCTCAAGATATAAGCC
30361786 AGTGTAAGACTATGTCTGGGACATGGCATCG
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATCG
30361817 GCACGGATAT
Statistics
Matches: 131, Mismatches: 30, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
44 18 0.14
45 17 0.13
46 52 0.40
47 25 0.19
48 19 0.15
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACCTCAAGATATAAGCC
Found at i:30369456 original size:46 final size:48
Alignment explanation
Indices: 30369358--30369620 Score: 228
Period size: 46 Copynumber: 5.6 Consensus size: 48
30369348 TTAGAACCAA
* * * * *
30369358 TGTAACACCATGTCTGGGACATGACATCGGCATTGAGACG-AGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAGATGTA-AGCCAG
*
30369406 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCTTGAGATGTAAGCCAT
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAGATGTAAGCCAG
** *
30369452 TGTAAGA-CATGTCTGGGACAT-GCATCGG-CTACAAGATGT--GTCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCT-TGAGATGTAAGCCAG
* * * *
30369496 TGTAAGACCATATCTGGGACATGGCATCGGCAC-GGATATGTGAGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGC-CTTGAGATGT-A-AGCCAG
* * *
30369546 TGTAAGACCATGTTTGGGACATAGCATC-GACTTGATGGATG--AGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTTGA--GATGTAAGCCAG
30369593 T-TAAGACCATGTCTGGGACATGGCATCG
1 TGTAAGACCATGTCTGGGACATGGCATCG
30369621 ACATTATACC
Statistics
Matches: 176, Mismatches: 25, Indels: 29
0.77 0.11 0.13
Matches are distributed among these distances:
44 10 0.06
45 15 0.09
46 88 0.50
47 21 0.12
48 8 0.05
49 3 0.02
50 28 0.16
51 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAGATGTAAGCCAG
Found at i:30369612 original size:141 final size:138
Alignment explanation
Indices: 30369358--30369620 Score: 336
Period size: 141 Copynumber: 1.9 Consensus size: 138
30369348 TTAGAACCAA
* **
30369358 TGTAACACCATGTCTGGGACATGACATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTCTGGG
1 TGTAACACCATATCTGGGACATGACATCGGCACGGAGACGAGAGCTAGTGTAAGACATGTCTGGG
* *
30369423 ACATGCATCGGCCTTGAGATGTAAGCCATTGTAAGACATGTCTGGGACAT-GCATCGGCTACAAG
66 ACATGCATCGGACTTGAGATG-AAGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCTACAAG
30369487 ATGTGTCAG
130 ATGTGTCAG
* * * * *
30369496 TGTAAGACCATATCTGGGACATGGCATCGGCACGGATATGTGAGAGCTAGTGTAAGACCATGTTT
1 TGTAACACCATATCTGGGACATGACATCGGCACGGAGA--CGAGAGCTAGTGTAAGA-CATGTCT
30369561 GGGACATAGCATC-GACTTGATGGATG-AGCCAGT-TAAGACCATGTCTGGGACATGGCATCG
63 GGGACAT-GCATCGGACTTGA--GATGAAGCCAGTGTAAGA-CATGTCTGGGACATGGCATCG
30369621 ACATTATACC
Statistics
Matches: 107, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
138 32 0.30
140 21 0.20
141 39 0.36
142 11 0.10
143 4 0.04
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (138 bp):
TGTAACACCATATCTGGGACATGACATCGGCACGGAGACGAGAGCTAGTGTAAGACATGTCTGGG
ACATGCATCGGACTTGAGATGAAGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCTACAAGA
TGTGTCAG
Found at i:30374095 original size:34 final size:34
Alignment explanation
Indices: 30374028--30374100 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
30374018 AACAGTGCAT
* **
30374028 GCAGTAACAGTCTGGGCCTGAGCCCTATTCAGTA
1 GCAGTAACAGTCTGAGCCTGAGCCCTAAACAGTA
* *
30374062 TCAGT-ACAGTCTGAGCCTTAGCCCCTAAACAGTA
1 GCAGTAACAGTCTGAGCCTGAG-CCCTAAACAGTA
30374096 GCAGT
1 GCAGT
30374101 GTGGGCCTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
33 14 0.44
34 18 0.56
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.23
Consensus pattern (34 bp):
GCAGTAACAGTCTGAGCCTGAGCCCTAAACAGTA
Found at i:30378974 original size:27 final size:26
Alignment explanation
Indices: 30378943--30379120 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 26
30378933 TAAATTGTAC
*
30378943 AGCACTAAGGGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
30378970 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
30378996 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
30379024 GGCACTAAGTGTGCGAGGTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
30379052 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
30379079 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
30379106 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
30379121 GGCTCAAAAT
Statistics
Matches: 127, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.01
27 101 0.80
28 25 0.20
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:30379058 original size:82 final size:81
Alignment explanation
Indices: 30378944--30379099 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 81
30378934 AAATTGTACA
* *
30378944 GCACTAAGGGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGGGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
30379008 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
30379025 GCACTAAGTGTGCGAGGTT-GACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGT
1 GCACTAAGGGTGCGA--TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGT
*
30379089 GTGCGAGTTGA
64 GTGCGAATTGA
30379100 TTATATAGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
81 14 0.22
82 48 0.74
83 3 0.05
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGGGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:30379111 original size:82 final size:81
Alignment explanation
Indices: 30378940--30379120 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
30378930 GATTAAATTG
* * *
30378940 TACAGCACTAAGGGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
30379005 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
30379021 TGCGGCACTAAGTGTGCGAGGTT-GACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCAC
1 TACAGCACTAAGTGTGCGA--TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCAC
* **
30379084 TAAGTGTGCGAGTTGATTA
63 TAAGTGTGCGAATTGACCA
* *
30379103 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
30379121 GGCTCAAAAT
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
81 17 0.21
82 63 0.77
83 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:30384009 original size:21 final size:20
Alignment explanation
Indices: 30383985--30384056 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
30383975 TCTGATGAGC
30383985 TTCAGTTTAACCTTTCTGGGT
1 TTCAGTTTAACCTTT-TGGGT
* * * *
30384006 TTCATTTTAGCTCTTTTGAGC
1 TTCAGTTTAAC-CTTTTGGGT
30384027 TTCAGTTTAACCTTTTTGGGT
1 TTCAGTTTAACC-TTTTGGGT
*
30384048 TTCCGTTTA
1 TTCAGTTTA
30384057 GCTCCTATGA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.03
21 35 0.88
22 4 0.10
ACGTcount: A:0.14, C:0.18, G:0.17, T:0.51
Consensus pattern (20 bp):
TTCAGTTTAACCTTTTGGGT
Found at i:30384028 original size:42 final size:42
Alignment explanation
Indices: 30383963--30384112 Score: 167
Period size: 42 Copynumber: 3.6 Consensus size: 42
30383953 TTGCTTTTAC
* *
30383963 TTTCCGTTTAGCTCTGATGAGCTTCAGTTTAACCTTTCTGGG
1 TTTCAGTTTAGCTCTTATGAGCTTCAGTTTAACCTTTCTGGG
* * *
30384005 TTTCATTTTAGCTCTTTTGAGCTTCAGTTTAACCTTTTTGGG
1 TTTCAGTTTAGCTCTTATGAGCTTCAGTTTAACCTTTCTGGG
* * * * *
30384047 TTTCCGTTTAGCTCCTATGAGCTTCCGTTCAACCCTTAC-GGG
1 TTTCAGTTTAGCTCTTATGAGCTTCAGTTTAA-CCTTTCTGGG
* * *
30384089 TTTCCGTTTAGCACTTATGTGCTT
1 TTTCAGTTTAGCTCTTATGAGCTT
30384113 TTGTGCAGCC
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 87 0.96
43 4 0.04
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.45
Consensus pattern (42 bp):
TTTCAGTTTAGCTCTTATGAGCTTCAGTTTAACCTTTCTGGG
Found at i:30384105 original size:21 final size:21
Alignment explanation
Indices: 30384044--30384105 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 21
30384034 TAACCTTTTT
* * *
30384044 GGGTTTCCGTTTAGCTCCTAT
1 GGGTTTCCGTTTAGCACTTAC
* * * * *
30384065 GAGCTTCCGTTCAACCCTTAC
1 GGGTTTCCGTTTAGCACTTAC
30384086 GGGTTTCCGTTTAGCACTTA
1 GGGTTTCCGTTTAGCACTTA
30384106 TGTGCTTTTG
Statistics
Matches: 29, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.37
Consensus pattern (21 bp):
GGGTTTCCGTTTAGCACTTAC
Found at i:30386247 original size:47 final size:47
Alignment explanation
Indices: 30386169--30386622 Score: 755
Period size: 47 Copynumber: 9.6 Consensus size: 47
30386159 CCCTTCGGGA
* * * * * *
30386169 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
30386216 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
30386263 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
30386310 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
30386357 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
30386406 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
30386455 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
30386502 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
30386549 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
30386596 CTTATCACATATATATATTTTCACATT
1 CTTATCACATATATACACTTTCACATT
30386623 ACAATTATCC
Statistics
Matches: 387, Mismatches: 18, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
47 291 0.75
49 96 0.25
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:30386599 original size:239 final size:237
Alignment explanation
Indices: 30386169--30386612 Score: 780
Period size: 239 Copynumber: 1.9 Consensus size: 237
30386159 CCCTTCGGGA
* * * *
30386169 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
30386234 TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACATC
*
30386299 GGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
30386364 CATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
196 CATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
30386406 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACAT-T-TATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATAC
* *
30386471 ACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACA
30386536 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
129 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
30386601 CACATATATATA
194 CACATATATATA
30386613 TTTTCACATT
Statistics
Matches: 195, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
237 10 0.05
238 1 0.01
239 184 0.94
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (237 bp):
CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
CATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:30392278 original size:40 final size:40
Alignment explanation
Indices: 30392184--30392328 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
30392174 TACTCGAATG
*
30392184 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
30392225 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
30392265 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
30392305 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
30392329 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:30396158 original size:19 final size:20
Alignment explanation
Indices: 30396134--30396173 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
30396124 TAGCATGTGT
30396134 TTTGAA-GTTTCTTGATAGA
1 TTTGAATGTTTCTTGATAGA
*
30396153 TTTGAATGTTTGTTGATAGA
1 TTTGAATGTTTCTTGATAGA
30396173 T
1 T
30396174 ATACAAGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.25, C:0.03, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTGAATGTTTCTTGATAGA
Found at i:30398326 original size:27 final size:27
Alignment explanation
Indices: 30398296--30398585 Score: 420
Period size: 27 Copynumber: 10.7 Consensus size: 27
30398286 TACTGAAATG
*
30398296 CCCTCGATTTGTAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
30398323 CCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* *
30398350 TCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
30398377 CCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
*
30398404 CCCTCGATTT-TCAAAATTACCGTTTTA
1 CCCTCGATTTAT-AGAATTACCGTTTTA
*
30398431 CCCTCGATTTACAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
30398458 CCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* *
30398485 CCCTCAATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* *
30398512 CCCTCGATTTACAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* ** **
30398539 CCCTTGATTTGCAGAATTACTATTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* *
30398566 CCCTCGATTTACAAAATTAC
1 CCCTCGATTTATAGAATTAC
30398586 TAAAATACCT
Statistics
Matches: 242, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
26 1 0.00
27 241 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCGTTTTA
Found at i:30398594 original size:27 final size:27
Alignment explanation
Indices: 30398351--30398783 Score: 138
Period size: 27 Copynumber: 16.1 Consensus size: 27
30398341 ACCGTTTTAT
* * ***
30398351 CCTCGATTTATAGAATTACCATTTTAC
1 CCTCGATTTACAAAATTACCAAAATAC
* * ****
30398378 CCTCGATTTATAGAATTACCGTTTTAC
1 CCTCGATTTACAAAATTACCAAAATAC
* ****
30398405 CCTCGATTTTCAAAATTACCGTTTTAC
1 CCTCGATTTACAAAATTACCAAAATAC
* ****
30398432 CCTCGATTTACAGAATTACCGTTTTAC
1 CCTCGATTTACAAAATTACCAAAATAC
* * ****
30398459 CCTCGATTTATAGAATTACCGTTTTAC
1 CCTCGATTTACAAAATTACCAAAATAC
* * * ***
30398486 CCTCAATTTATAGAATTACCATTTTAC
1 CCTCGATTTACAAAATTACCAAAATAC
* ***
30398513 CCTCGATTTACAGAATTACCATTTTAC
1 CCTCGATTTACAAAATTACCAAAATAC
* * * * ***
30398540 CCTTGATTTGCAGAATTACTATTTTAC
1 CCTCGATTTACAAAATTACCAAAATAC
*
30398567 CCTCGATTTACAAAATTACTAAAATAC
1 CCTCGATTTACAAAATTACCAAAATAC
* * *
30398594 CTTTGGTTTACAAAATTACCAAAATAC
1 CCTCGATTTACAAAATTACCAAAATAC
* *
30398621 CCTCGA-TCAGTAAAATTACCAAAATAC
1 CCTCGATTTA-CAAAATTACCAAAATAC
* * ** * *
30398648 CCTAG-TCTGTAAAATTGCTAAAATAC
1 CCTCGATTTACAAAATTACCAAAATAC
* ** *
30398674 CC-CTGGTTTGTAAAATTACCAAACTAC
1 CCTC-GATTTACAAAATTACCAAAATAC
* ** *
30398701 CC-CTAGTTTGTAAAGTTACCAAAATAC
1 CCTCGA-TTTACAAAATTACCAAAATAC
* *** * *
30398728 CACT-GGTTTGTGAAATTACCGAAATGC
1 C-CTCGATTTACAAAATTACCAAAATAC
* **
30398755 CCTCAATTTGTAAAATTACCAAAATAC
1 CCTCGATTTACAAAATTACCAAAATAC
30398782 CC
1 CC
30398784 CTAATTTACA
Statistics
Matches: 343, Mismatches: 55, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
26 22 0.06
27 320 0.93
28 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (27 bp):
CCTCGATTTACAAAATTACCAAAATAC
Found at i:30398611 original size:54 final size:54
Alignment explanation
Indices: 30398321--30398650 Score: 221
Period size: 54 Copynumber: 6.1 Consensus size: 54
30398311 ATTACCGTTT
* * * * * * * ***
30398321 TACCCTCGATTTATAGAATTACCGTTTTATCCTCGATTTATAGAATTACCATTT
1 TACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAA
* * * * * ****
30398375 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTTCAAAATTACCGTTT
1 TACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAA
* * * * * ****
30398429 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACCGTTT
1 TACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAA
** * * * ***
30398483 TACCCTCAATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCATTT
1 TACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAA
* * * *
30398537 TACCCTTGATTTGCAGAATTACTATTTTACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAA
* * *** * *
30398591 TACCTTTGGTTTACAAAATTACCAAAATACCCTCGA-TCAGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTA-CAAAATTACCAAAA
30398645 TACCCT
1 TACCCT
30398651 AGTCTGTAAA
Statistics
Matches: 239, Mismatches: 36, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
53 2 0.01
54 237 0.99
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (54 bp):
TACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAA
Found at i:30398689 original size:80 final size:81
Alignment explanation
Indices: 30398578--30398784 Score: 213
Period size: 80 Copynumber: 2.6 Consensus size: 81
30398568 CTCGATTTAC
** **
30398578 AAAATTACTAAAATACCTTTGGTTTACAAAATTACCAAAATACCCTCGA-TCAGTAAAATTACCA
1 AAAATTACTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCC-CGAGTCAGTAAAATTACCA
30398642 AAATACC-CTAGTCTGT
65 AAATACCACTAGTCTGT
* * * ** *
30398658 AAAATTGCTAAAATACCCCTGGTTTGTAAAATTACCAAACTACCCCTAGTTTGTAAAGTTACCAA
1 AAAATTACTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCGAGTCAGTAAAATTACCAA
* *
30398723 AATACCACTGGTTTGT
66 AATACCACTAGTCTGT
* ** * **
30398739 GAAATTACCGAAAT-GCCCTCAATTTGTAAAATTACCAAAATACCCC
1 AAAATTACTAAAATACCCCT-GGTTTGTAAAATTACCAAAATACCCC
30398785 TAATTTACAA
Statistics
Matches: 104, Mismatches: 20, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
79 2 0.02
80 62 0.60
81 40 0.38
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.29
Consensus pattern (81 bp):
AAAATTACTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCGAGTCAGTAAAATTACCAA
AATACCACTAGTCTGT
Found at i:30398790 original size:27 final size:27
Alignment explanation
Indices: 30398578--30398786 Score: 190
Period size: 27 Copynumber: 7.8 Consensus size: 27
30398568 CTCGATTTAC
* ** * **
30398578 AAAATTACTAAAATACCTTTGGTTTAC
1 AAAATTACCAAAATACCCCTAGTTTGT
* **
30398605 AAAATTACCAAAATA-CCCTCGATCAGT
1 AAAATTACCAAAATACCCCTAG-TTTGT
*
30398632 AAAATTACCAAAATA-CCCTAGTCTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* * *
30398658 AAAATTGCTAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
*
30398685 AAAATTACCAAACTACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* * *
30398712 AAAGTTACCAAAATACCACTGGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* * * *
30398739 GAAATTACCGAAAT-GCCCTCAATTTGT
1 AAAATTACCAAAATACCCCT-AGTTTGT
30398766 AAAATTACCAAAATACCCCTA
1 AAAATTACCAAAATACCCCTA
30398787 ATTTACAAAT
Statistics
Matches: 146, Mismatches: 32, Indels: 8
0.78 0.17 0.04
Matches are distributed among these distances:
26 23 0.16
27 119 0.82
28 4 0.03
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.29
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTAGTTTGT
Found at i:30398873 original size:27 final size:27
Alignment explanation
Indices: 30398788--30398873 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
30398778 ATACCCCTAA
* *
30398788 TTTACAAATTTATAGAAATACCCTTGAC
1 TTTACAAAATTATAGAAATACCCTTG-G
* *
30398816 TTT-CTAAAAATTATAGAAATACCATTAG
1 TTTAC--AAAATTATAGAAATACCCTTGG
30398844 TTTACAAAATTACT-GAAATACCCTTGG
1 TTTACAAAATTA-TAGAAATACCCTTGG
30398871 TTT
1 TTT
30398874 GTAGATTTAC
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
27 22 0.46
28 7 0.15
29 19 0.40
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (27 bp):
TTTACAAAATTATAGAAATACCCTTGG
Found at i:30399707 original size:20 final size:20
Alignment explanation
Indices: 30399693--30399748 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
30399683 CATGATTGAT
30399693 ATGATATGCACATGATATGC
1 ATGATATGCACATGATATGC
30399713 ATGATATGCACATGATAT-C
1 ATGATATGCACATGATATGC
30399732 TATGCA-ATGCACATGAT
1 -ATG-ATATGCACATGAT
30399749 GAATTCATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (20 bp):
ATGATATGCACATGATATGC
Found at i:30399709 original size:11 final size:11
Alignment explanation
Indices: 30399693--30399730 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
30399683 CATGATTGAT
30399693 ATGATATGCAC
1 ATGATATGCAC
30399704 ATGATATG--C
1 ATGATATGCAC
30399713 ATGATATGCAC
1 ATGATATGCAC
30399724 ATGATAT
1 ATGATAT
30399731 CTATGCAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.36
11 16 0.64
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:30399827 original size:26 final size:26
Alignment explanation
Indices: 30399798--30399920 Score: 169
Period size: 26 Copynumber: 4.8 Consensus size: 26
30399788 GAGGAAGTGC
*
30399798 AAAAGGGCTTATGCCCCAGTTTATTA
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
30399824 AAAAGGGCTTATGCCTCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
30399850 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
30399876 AAAAGGGCTT-TGCCCAAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
30399901 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
30399921 ATTAAAGAGG
Statistics
Matches: 86, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
25 31 0.36
26 55 0.64
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:30399880 original size:52 final size:51
Alignment explanation
Indices: 30399798--30399926 Score: 210
Period size: 52 Copynumber: 2.5 Consensus size: 51
30399788 GAGGAAGTGC
30399798 AAAAGGGCTTATGCCCCAGTTTATTAAAAAGGGCTTATGCCTC-AGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTAAAAAGGGCTT-TGCC-CAAGTTTACCG
*
30399850 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCAAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTAAAAAGGGCTTTGCCCAAGTTTACCG
30399901 AAAAGGGCTT-TGCCCCAG-TTATTAAA
1 AAAAGGGCTTATGCCCCAGTTTATTAAA
30399927 GAGGCTAGGC
Statistics
Matches: 74, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
49 7 0.09
50 9 0.12
51 23 0.31
52 35 0.47
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTATTAAAAAGGGCTTTGCCCAAGTTTACCG
Found at i:30400173 original size:31 final size:31
Alignment explanation
Indices: 30400138--30400216 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
30400128 CGTTTACAAT
*
30400138 AAAGGCTTCGGCCCAGTGATATGCTTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
30400169 AAAGGCTTCGGCCCAGTGATTTGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
30400200 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
30400217 AACCGTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:30408684 original size:21 final size:20
Alignment explanation
Indices: 30408645--30408688 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
30408635 TGTGATTTGG
*
30408645 ACTAAATTGAGTTTCAATTGT
1 ACTAAATTGAGTTTAAATT-T
30408666 ACTAAATTGA-TGTTAAATTT
1 ACTAAATTGAGT-TTAAATTT
30408686 ACT
1 ACT
30408689 CATATAGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (20 bp):
ACTAAATTGAGTTTAAATTT
Found at i:30414136 original size:40 final size:40
Alignment explanation
Indices: 30414006--30414223 Score: 271
Period size: 40 Copynumber: 5.4 Consensus size: 40
30413996 ATGATATCTC
* * *
30414006 GGCTAAGTCCCCAAAGGCATTTGTGCAAGTTACTATATCCG
1 GGCTAAGT-CCCGAAGGCATTTGTGCTAGTGACTATATCCG
*
30414047 GGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTG-CTATACCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC---TAG-TGACTATATCCG
30414090 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCG
**
30414130 GGCTAAGTCCCGAAGGCATTCATGCTAGTGACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCG
* *
30414170 GGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-
1 GGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTATATCCG
* *
30414209 AGCTAAATCCCGAAG
1 GGCTAAGTCCCGAAG
30414224 ATACTTGGGT
Statistics
Matches: 157, Mismatches: 14, Indels: 14
0.85 0.08 0.08
Matches are distributed among these distances:
39 14 0.09
40 97 0.62
41 10 0.06
43 35 0.22
44 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCG
Found at i:30414146 original size:83 final size:80
Alignment explanation
Indices: 30414006--30414223 Score: 271
Period size: 83 Copynumber: 2.7 Consensus size: 80
30413996 ATGATATCTC
* * **
30414006 GGCTAAGTCCCCAAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTG
1 GGCTAAGT-CCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCATG
30414071 CGAGTAGTTG-CTATACCCG
65 C---TAG-TGACTATACCCG
*
30414090 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCATGC
1 GGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCATGC
*
30414155 TAGTGACTATATCCG
66 TAGTGACTATACCCG
* * * *
30414170 GGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-AGCTAAATCCCGAAG
1 GGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG
30414224 ATACTTGGGT
Statistics
Matches: 122, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
79 15 0.12
80 45 0.37
81 2 0.02
83 52 0.43
84 8 0.07
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (80 bp):
GGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCATGC
TAGTGACTATACCCG
Found at i:30422266 original size:40 final size:40
Alignment explanation
Indices: 30422206--30422429 Score: 297
Period size: 40 Copynumber: 5.5 Consensus size: 40
30422196 TATTCGGATG
30422206 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
30422246 ATATTCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
30422289 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
30422329 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
30422369 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
30422409 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
30422430 ATATTTGGGT
Statistics
Matches: 163, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
39 13 0.08
40 113 0.69
41 1 0.01
43 36 0.22
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:30422349 original size:83 final size:80
Alignment explanation
Indices: 30422210--30422429 Score: 293
Period size: 83 Copynumber: 2.7 Consensus size: 80
30422200 CGGATGATAT
* * **
30422210 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATTCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
30422275 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
*
30422293 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
*
30422358 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* * *
30422373 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG
30422430 ATATTTGGGT
Statistics
Matches: 126, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
79 16 0.13
80 45 0.36
81 2 0.02
83 63 0.50
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
TGCTAGTGACTATAC
Found at i:30424300 original size:43 final size:43
Alignment explanation
Indices: 30424253--30424355 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 43
30424243 CCGGACAGGA
* * * * *
30424253 TCTTACACGAAATCA-TATAACGATGCCAATTTCCTAGACATGG
1 TCTTACACGAAATCACAAT-ACAATGCCAATGTCCCAGACATAG
* *
30424296 TCTTACACGTAATCACAATACAATGCCAATGTCCCAGACGTAG
1 TCTTACACGAAATCACAATACAATGCCAATGTCCCAGACATAG
* *
30424339 TCTTACATGTAATCACA
1 TCTTACACGAAATCACA
30424356 TCTCAATAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 49 0.96
44 2 0.04
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (43 bp):
TCTTACACGAAATCACAATACAATGCCAATGTCCCAGACATAG
Found at i:30445220 original size:28 final size:28
Alignment explanation
Indices: 30445171--30445259 Score: 108
Period size: 28 Copynumber: 3.1 Consensus size: 28
30445161 TGACAGAGTT
*
30445171 ACCAGATACAGATATTTTGTGGCAATGCC
1 ACCAGA-ACAGATAATTTGTGGCAATGCC
* **
30445200 ACCAGAATAGATAATTTGTGGCAGGGCC
1 ACCAGAACAGATAATTTGTGGCAATGCC
*
30445228 ACCAGAACAGGTAATTTGTGGC-ATAGCC
1 ACCAGAACAGATAATTTGTGGCAAT-GCC
30445256 ACCA
1 ACCA
30445260 AGACGCTTCC
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 45 0.88
29 6 0.12
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (28 bp):
ACCAGAACAGATAATTTGTGGCAATGCC
Found at i:30445413 original size:28 final size:28
Alignment explanation
Indices: 30445366--30445430 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
30445356 AAATTAACCC
*
30445366 TAGGGGTATAAAGGTCATTTTGCACACA
1 TAGGGGTATAAAGGTAATTTTGCACACA
* *
30445394 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCACACA
30445422 TAGGGGTAT
1 TAGGGGTAT
30445431 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCACACA
Found at i:30446281 original size:12 final size:13
Alignment explanation
Indices: 30446262--30446294 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
30446252 GGGTTCGGCT
30446262 ATGGAGAAGGAAG
1 ATGGAGAAGGAAG
*
30446275 A-GGAGAAGGTAG
1 ATGGAGAAGGAAG
30446287 ATGGAGAA
1 ATGGAGAA
30446295 AAAGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.45, T:0.09
Consensus pattern (13 bp):
ATGGAGAAGGAAG
Found at i:30452276 original size:40 final size:39
Alignment explanation
Indices: 30452099--30452276 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 39
30452089 AAGCCAAGTA
* * *
30452099 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAG-TAACTCGCACAAATG
*
30452138 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACAAATG
30452178 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACAAATG
* * *
30452218 CCTTCGGGACTTAGCCCGGAACTAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATG
30452258 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
30452277 TTATCATCCA
Statistics
Matches: 128, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
39 14 0.11
40 114 0.89
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATG
Found at i:30460173 original size:40 final size:40
Alignment explanation
Indices: 30460111--30460288 Score: 245
Period size: 40 Copynumber: 4.5 Consensus size: 40
30460101 AAGCCAAGTA
* * *
30460111 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
30460150 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
30460190 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * **
30460230 CCTTCGGGACTTAGCCC-GAAACTAGTCACTAGCGTAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
30460270 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
30460289 TTATCATCCA
Statistics
Matches: 127, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
39 16 0.13
40 110 0.87
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:30475169 original size:24 final size:23
Alignment explanation
Indices: 30475142--30475188 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
30475132 AGGCAACTCT
*
30475142 TTATGAGCGTCCTGATATAGGCTC
1 TTATGAGCGTCCTGAGAT-GGCTC
*
30475166 TTATGAGCTTCCTGAGATGGCTC
1 TTATGAGCGTCCTGAGATGGCTC
30475189 GCTTGAACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (23 bp):
TTATGAGCGTCCTGAGATGGCTC
Found at i:30479171 original size:43 final size:43
Alignment explanation
Indices: 30479038--30479191 Score: 143
Period size: 43 Copynumber: 3.6 Consensus size: 43
30479028 AAGCTCGTAT
* * * * *
30479038 AATGCC-ATATCCCAGATATGGTCTTATATGTTATCAC-ATATC
1 AATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATA-C
* * * * * *
30479080 GATGCCACTGTCCTAGACAGGGTCTTACACGTAATC-GATTAAC
1 AATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAAT-AC
*
30479123 GATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATAC
1 AATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATAC
* *
30479166 AATGCCAATGTCACAGAAATGGTCTT
1 AATGCCAATGTCCCAGACATGGTCTT
30479192 GTGACAGCCC
Statistics
Matches: 89, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
42 5 0.06
43 81 0.91
44 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (43 bp):
AATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATAC
Found at i:30480932 original size:27 final size:28
Alignment explanation
Indices: 30480848--30480945 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
30480838 CATGAGATTG
* * * *
30480848 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
30480877 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
30480905 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
30480932 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
30480946 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:30480956 original size:27 final size:27
Alignment explanation
Indices: 30480876--30480958 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
30480866 TAAATTGTAC
* *
30480876 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
30480904 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
30480931 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
30480958 A
1 A
30480959 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:30480959 original size:29 final size:27
Alignment explanation
Indices: 30480848--30480959 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
30480838 CATGAGATTG
** * *
30480848 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
30480877 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
30480905 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
30480932 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
30480960 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:30486611 original size:9 final size:9
Alignment explanation
Indices: 30486590--30486623 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
30486580 AGAAGAAACC
*
30486590 AAAATTAAT
1 AAAAATAAT
30486599 -AAAATAAT
1 AAAAATAAT
30486607 AAAAATAAT
1 AAAAATAAT
30486616 AAAAATAA
1 AAAAATAA
30486624 ACTTTCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAAATAAT
Found at i:30492833 original size:13 final size:13
Alignment explanation
Indices: 30492815--30492840 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30492805 GCTCGGCAGG
30492815 GACACGCCCGTGT
1 GACACGCCCGTGT
30492828 GACACGCCCGTGT
1 GACACGCCCGTGT
30492841 TTGATTACTT
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:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:30494337 original size:43 final size:42
Alignment explanation
Indices: 30494273--30494354 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
30494263 GTCTTTCACA
* *
30494273 AATCAAATACGATGTCGATGTCCCAGACATGGTCTTACACGT
1 AATCAAATACGATGACAATGTCCCAGACATGGTCTTACACGT
* **
30494315 AATCATATATCGATGACAATGTCCCAGATGTGGTCTTACA
1 AATCAAATA-CGATGACAATGTCCCAGACATGGTCTTACA
30494355 TGAGAATAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 8 0.24
43 26 0.76
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (42 bp):
AATCAAATACGATGACAATGTCCCAGACATGGTCTTACACGT
Found at i:30496293 original size:40 final size:40
Alignment explanation
Indices: 30496238--30496415 Score: 254
Period size: 40 Copynumber: 4.5 Consensus size: 40
30496228 TGGATGATAA
** * *
30496238 CCGGGCTAAGTCCCGAAGGCATTTACGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
30496278 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
30496318 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
30496358 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
30496398 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
30496416 TACTTAGCTT
Statistics
Matches: 129, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
39 17 0.13
40 112 0.87
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:30508008 original size:40 final size:40
Alignment explanation
Indices: 30507971--30508196 Score: 307
Period size: 40 Copynumber: 5.7 Consensus size: 40
30507961 GCTACTCGTT
*
30507971 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
30508011 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
30508051 CAAATGCCTTCGGGACTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
30508091 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
30508131 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
30508172 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
30508197 CATCATTCAA
Statistics
Matches: 173, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
39 3 0.02
40 157 0.91
41 13 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:30525596 original size:40 final size:40
Alignment explanation
Indices: 30525522--30525743 Score: 322
Period size: 40 Copynumber: 5.6 Consensus size: 40
30525512 AACCCAAGTA
* * * *
30525522 CCTTCGGAATTTAG-CCGGATATAG-CAACTCGCACAAGTG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
30525561 CCTTTGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
30525601 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
30525641 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* ** *
30525681 CCTTCAGGACTTAGCCCGGATATAGGAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
30525721 CCTTCGGGACTTAGCCCAGATAT
1 CCTTCGGGACTTAGCCCGGATAT
30525744 CATCCGAATA
Statistics
Matches: 167, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
39 10 0.06
40 156 0.93
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:30535445 original size:21 final size:21
Alignment explanation
Indices: 30535419--30535474 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
30535409 CACTAGACAT
*
30535419 AGGGGCACATGCCCATGTGAA
1 AGGGGCACACGCCCATGTGAA
*
30535440 AGGGGCATACGCCCATGTGAA
1 AGGGGCACACGCCCATGTGAA
30535461 AGGGGCACACGCCC
1 AGGGGCACACGCCC
30535475 GTGTAGCCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.27, C:0.29, G:0.34, T:0.11
Consensus pattern (21 bp):
AGGGGCACACGCCCATGTGAA
Found at i:30545258 original size:47 final size:47
Alignment explanation
Indices: 30545151--30545489 Score: 498
Period size: 47 Copynumber: 7.1 Consensus size: 47
30545141 GAAATGATAG
30545151 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
* *
30545200 TAAGGCCTAATGGCCGATGTGATGAATTTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * *
30545247 TAAGGCCTAATGGCCGTTGTGATGAATGTGAAAGCGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
30545294 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG----TATATATGTGA
*
30545345 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
30545392 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
30545439 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
30545486 TAAG
1 TAAG
30545490 TCCCGAAGGG
Statistics
Matches: 264, Mismatches: 22, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
47 184 0.70
49 35 0.13
51 45 0.17
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:30545413 original size:145 final size:144
Alignment explanation
Indices: 30545151--30545489 Score: 524
Period size: 145 Copynumber: 2.4 Consensus size: 144
30545141 GAAATGATAG
30545151 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT-ATATATATGTGATAAGGCCTAATGGCC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAATATATATGTGATAAGGCCTAATGGCC
* *
30545215 GATGTGATGAATTTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGTTGTGATGAATGTGAAA
66 GATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
30545280 GCGTATATATGAGA
131 GCGTATATATGAGA
*
30545294 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTACATATATATGTGATAGGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA-ATATATATGTGATAAGGCCTAATGGC
*
30545359 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
65 CGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
30545424 AGTGTATATATGTGA
130 AGCGTATATATGAGA
* * * * * * *
30545439 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGT-ATA-A-ATGTGATAAG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAATATATATGTGATAAG
30545490 TCCCGAAGGG
Statistics
Matches: 180, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
141 9 0.05
142 1 0.01
143 40 0.22
145 130 0.72
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.28
Consensus pattern (144 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAATATATATGTGATAAGGCCTAATGGCC
GATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
GCGTATATATGAGA
Found at i:30545664 original size:37 final size:37
Alignment explanation
Indices: 30545608--30545686 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
30545598 CCGAGCTCTA
* * *
30545608 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
30545645 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
30545682 AAGAC
1 AAGAC
30545687 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:30555797 original size:13 final size:13
Alignment explanation
Indices: 30555779--30555803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30555769 TTTGTCAATT
30555779 CATCCACAACATC
1 CATCCACAACATC
30555792 CATCCACAACAT
1 CATCCACAACAT
30555804 TATTCCCTTC
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:0.40, C:0.44, G:0.00, T:0.16
Consensus pattern (13 bp):
CATCCACAACATC
Found at i:30560136 original size:43 final size:43
Alignment explanation
Indices: 30560084--30560165 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
30560074 AGGCCATGAT
* * * *
30560084 CTTTAGCGGCGCTTTTACCACAAATGCCGCTAAAGGTCAAAAC
1 CTTTAGCGGCACTTTTACCAAAAACGCCACTAAAGGTCAAAAC
* *
30560127 CTTTGGCGGCACTTTTCCCAAAAACGCCACTAAAGGTCA
1 CTTTAGCGGCACTTTTACCAAAAACGCCACTAAAGGTCA
30560166 TGAAATTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.23
Consensus pattern (43 bp):
CTTTAGCGGCACTTTTACCAAAAACGCCACTAAAGGTCAAAAC
Found at i:30560475 original size:19 final size:19
Alignment explanation
Indices: 30560430--30560476 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
30560420 TAAATATTAA
*
30560430 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
30560449 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
30560468 AATAAAAAT
1 AATAAAAAT
30560477 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:30560969 original size:23 final size:24
Alignment explanation
Indices: 30560880--30560976 Score: 117
Period size: 23 Copynumber: 4.1 Consensus size: 24
30560870 TTCCAGCAAC
* **
30560880 TAAACACTTCAATTTGCATTACTT
1 TAAACACTTCAATTTACAGCACTT
* *
30560904 AAAACACTTCAATTTACAACA-TT
1 TAAACACTTCAATTTACAGCACTT
*
30560927 TAAGCACTTCAATTTACAGCA-TT
1 TAAACACTTCAATTTACAGCACTT
*
30560950 TAAACACTTCAATTTGCAGCACTT
1 TAAACACTTCAATTTACAGCACTT
30560974 TAA
1 TAA
30560977 TTTAGTAGGG
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 41 0.65
24 22 0.35
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (24 bp):
TAAACACTTCAATTTACAGCACTT
Found at i:30564903 original size:8 final size:8
Alignment explanation
Indices: 30564892--30564966 Score: 62
Period size: 8 Copynumber: 8.9 Consensus size: 8
30564882 ATATTAAATA
30564892 TTAAATTT
1 TTAAATTT
*
30564900 TTAAGTTT
1 TTAAATTT
**
30564908 TTTTATTT
1 TTAAATTT
*
30564916 TTTAATTT
1 TTAAATTT
30564924 TT-AATTT
1 TTAAATTT
30564931 TTAAATTTTT
1 TTAAA--TTT
30564941 TTGAAGATTT
1 TT-AA-ATTT
30564951 TTATAATTT
1 TTA-AATTT
30564960 TTAAATT
1 TTAAATT
30564967 ATCATATAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
7 7 0.12
8 27 0.48
9 8 0.14
10 11 0.20
11 2 0.04
12 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (8 bp):
TTAAATTT
Found at i:30564924 original size:6 final size:7
Alignment explanation
Indices: 30564907--30564940 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
30564897 TTTTTAAGTT
*
30564907 TTTTTAT
1 TTTTTAA
30564914 TTTTTAA
1 TTTTTAA
30564921 TTTTTAA
1 TTTTTAA
30564928 TTTTTAAA
1 TTTTT-AA
30564936 TTTTT
1 TTTTT
30564941 TTGAAGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAA
Found at i:30564924 original size:15 final size:15
Alignment explanation
Indices: 30564896--30564941 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
30564886 TAAATATTAA
*
30564896 ATTTTTAAGTTTTTTT
1 ATTTTTAA-ATTTTTT
* *
30564912 ATTTTTTAATTTTTA
1 ATTTTTAAATTTTTT
30564927 ATTTTTAAATTTTTT
1 ATTTTTAAATTTTTT
30564942 TGAAGATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (15 bp):
ATTTTTAAATTTTTT
Found at i:30565558 original size:15 final size:15
Alignment explanation
Indices: 30565526--30565568 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
30565516 TTATCTCTTA
30565526 CATAA-CCATAAA-C
1 CATAATCCATAAACC
*
30565539 CATAATCCCTAAACC
1 CATAATCCATAAACC
30565554 CATAATCCATAAACC
1 CATAATCCATAAACC
30565569 TTAAAATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 5 0.19
14 6 0.23
15 15 0.58
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.19
Consensus pattern (15 bp):
CATAATCCATAAACC
Found at i:30565573 original size:22 final size:22
Alignment explanation
Indices: 30565531--30565631 Score: 59
Period size: 22 Copynumber: 4.7 Consensus size: 22
30565521 TCTTACATAA
*
30565531 CCATAAACCATAATCCCTAAAC
1 CCATAAACCATAAACCCTAAAC
* *
30565553 CCATAATCCATAAACCTTAAA-
1 CCATAAACCATAAACCCTAAAC
* **
30565574 --ATAGTAACTCATACACTTTAAAC
1 CCATA--AAC-CATAAACCCTAAAC
*
30565597 CC-TAAACCATATACCCTAAA-
1 CCATAAACCATAAACCCTAAAC
* *
30565617 CTATAAACCCTAAAC
1 CCATAAACCATAAAC
30565632 TATAATGATA
Statistics
Matches: 60, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.05
20 1 0.02
21 22 0.37
22 32 0.53
24 2 0.03
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.23
Consensus pattern (22 bp):
CCATAAACCATAAACCCTAAAC
Found at i:30565614 original size:14 final size:14
Alignment explanation
Indices: 30565592--30565636 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
30565582 TCATACACTT
30565592 TAAACCCTAAACCA
1 TAAACCCTAAACCA
* *
30565606 TATACCCTAAACTA
1 TAAACCCTAAACCA
*
30565620 TAAACCCTAAACTA
1 TAAACCCTAAACCA
30565634 TAA
1 TAA
30565637 TGATAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:30566495 original size:17 final size:18
Alignment explanation
Indices: 30566469--30566502 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30566459 AAGGTTATAG
*
30566469 TTTAGTGTTT-AGGGTTC
1 TTTAGGGTTTAAGGGTTC
30566486 TTTAGGGTTTAAGGGTT
1 TTTAGGGTTTAAGGGTT
30566503 TAGTGTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.03, G:0.32, T:0.50
Consensus pattern (18 bp):
TTTAGGGTTTAAGGGTTC
Found at i:30566528 original size:54 final size:55
Alignment explanation
Indices: 30566444--30566565 Score: 165
Period size: 54 Copynumber: 2.2 Consensus size: 55
30566434 GATTTTTTGG
* *
30566444 GGGTTTAGGGTTTTAAAGGTTATAGTTTAGTGTTTA-GGGTTCTTTAGGGTTTAA
1 GGGTTTAGGGTTTTAAAGGTTATAGATTAGTGTTTATGAGTTCTTTAGGGTTTAA
* * * *
30566498 GGGTTTAGTGTTTTAAGGGTTATAGATTAGTGTTTATGATTTTTTTAGGGTTTAA
1 GGGTTTAGGGTTTTAAAGGTTATAGATTAGTGTTTATGAGTTCTTTAGGGTTTAA
*
30566553 GGTTTTAAGGGTT
1 GGGTTT-AGGGTT
30566566 ATATGAATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 33 0.57
55 20 0.34
56 5 0.09
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.48
Consensus pattern (55 bp):
GGGTTTAGGGTTTTAAAGGTTATAGATTAGTGTTTATGAGTTCTTTAGGGTTTAA
Found at i:30566688 original size:41 final size:41
Alignment explanation
Indices: 30566607--30566738 Score: 194
Period size: 41 Copynumber: 3.2 Consensus size: 41
30566597 GCCGCTAATA
* * * *
30566607 CTTTGGTTTTAGCGGC-TTTTTACCAAAAACACCACTATTG
1 CTTTGTTTTTAGCGGCGTTTTAACAAAAAACGCCACTATTG
30566647 CTTTGTTTTTAGCGGCGTTTTAACAAAAAACGCCACTATTG
1 CTTTGTTTTTAGCGGCGTTTTAACAAAAAACGCCACTATTG
* * *
30566688 CTTTGTTTTTAGCGGTGTTTTAACAAAAAAAGCCGCTATTG
1 CTTTGTTTTTAGCGGCGTTTTAACAAAAAACGCCACTATTG
30566729 CTTTGTTTTT
1 CTTTGTTTTT
30566739 CGCGTTTTAC
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 15 0.18
41 69 0.82
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (41 bp):
CTTTGTTTTTAGCGGCGTTTTAACAAAAAACGCCACTATTG
Found at i:30568105 original size:20 final size:21
Alignment explanation
Indices: 30568080--30568126 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
30568070 TTAAGTAAGG
*
30568080 TTAAAATTGTAAT-TTAATAA
1 TTAAAATTATAATCTTAATAA
30568100 TTAAAA-TATAATCTTAATAA
1 TTAAAATTATAATCTTAATAA
*
30568120 TAAAAAT
1 TTAAAAT
30568127 AACATGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAAAATTATAATCTTAATAA
Found at i:30568622 original size:13 final size:13
Alignment explanation
Indices: 30568604--30568628 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30568594 CTTATGATAT
30568604 GTGTGAAAATTTC
1 GTGTGAAAATTTC
30568617 GTGTGAAAATTT
1 GTGTGAAAATTT
30568629 GATCATTTGT
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:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:30569876 original size:43 final size:43
Alignment explanation
Indices: 30569718--30569872 Score: 140
Period size: 43 Copynumber: 3.6 Consensus size: 43
30569708 TATATGTTAT
* *
30569718 CGTGTAAGACCACATCTGGGACATTGACATC-A-ACTTATGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGACATCGATA-TT-TGA-TTA
* * *
30569762 CGTGTAAGGCCATGTCTGGGACGTTGACATCG-TATTTGATTT
1 CGTGTAAGACCACGTCTGGGACGTTGACATCGATATTTGATTA
* * * *
30569804 TGTATAAGACC-CTGTCTGGGATAG-TGGCATCGATATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGA-CGTTGACATCGATATTTGATTA
*
30569847 CATGTAAGACCACGTCTGGGACGTTG
1 CGTGTAAGACCACGTCTGGGACGTTG
30569873 GCATTGTACG
Statistics
Matches: 88, Mismatches: 16, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
42 26 0.30
43 31 0.35
44 30 0.34
45 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGACATCGATATTTGATTA
Found at i:30574239 original size:39 final size:40
Alignment explanation
Indices: 30574035--30574257 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
30574025 TTGAATGCTG
* * * * * *
30574035 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
30574075 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
30574115 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
30574155 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
30574195 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
30574234 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
30574258 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 118 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:30574277 original size:79 final size:80
Alignment explanation
Indices: 30574110--30574292 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
30574100 GTGCGAGATA
* * *
30574110 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
30574175 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
30574190 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
30574254 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
30574269 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
30574293 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:30582029 original size:38 final size:40
Alignment explanation
Indices: 30581938--30582103 Score: 207
Period size: 38 Copynumber: 4.3 Consensus size: 40
30581928 GGACTAAGAT
* * *
30581938 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
30581978 CCGAAGGCATTCGTGCGAGTTA-TAAATCCGGGTTAAGT-
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
30582016 CCGAAGGCATTCGTGCGAGTT-GTTAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * * *
30582055 CCGAAGGCATT-GTGTGAGTTACTAAA-ACGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
30582093 CCGAAGGCATT
1 CCGAAGGCATT
30582104 TGAACGAGGA
Statistics
Matches: 113, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
38 64 0.57
39 30 0.27
40 19 0.17
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:30588385 original size:33 final size:32
Alignment explanation
Indices: 30588350--30588422 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 32
30588340 CTATTCAGTA
30588350 ACAGTACAATGTGGGCCTTAGCCCAATACAAT
1 ACAGTACAATGTGGGCCTTAGCCCAATACAAT
30588382 --A--ACAATGTGGGCCTTAGCCCAATACAAT
1 ACAGTACAATGTGGGCCTTAGCCCAATACAAT
30588410 ATCAGTACAATGT
1 A-CAGTACAATGT
30588423 AGTAATGCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
28 27 0.75
30 1 0.03
31 1 0.03
33 7 0.19
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (32 bp):
ACAGTACAATGTGGGCCTTAGCCCAATACAAT
Found at i:30588395 original size:28 final size:28
Alignment explanation
Indices: 30588355--30588410 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
30588345 CAGTAACAGT
30588355 ACAATGTGGGCCTTAGCCCAATACAATA
1 ACAATGTGGGCCTTAGCCCAATACAATA
30588383 ACAATGTGGGCCTTAGCCCAATACAATA
1 ACAATGTGGGCCTTAGCCCAATACAATA
30588411 TCAGTACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (28 bp):
ACAATGTGGGCCTTAGCCCAATACAATA
Found at i:30588546 original size:26 final size:26
Alignment explanation
Indices: 30588517--30588567 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
30588507 AACACACCAA
*
30588517 TATCGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGCAACAG
*
30588543 TATCGTAGCAAAGCTGCCAGCAACA
1 TATCGCAGCAAAGCTGCCAGCAACA
30588568 TTATACTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGCAACAG
Found at i:30589997 original size:17 final size:17
Alignment explanation
Indices: 30589975--30590011 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
30589965 TTTACACAAA
30589975 ACCAAAATGAAG-AGTAT
1 ACCAAAATG-AGCAGTAT
30589992 ACCAAAATGAGCAGTAT
1 ACCAAAATGAGCAGTAT
30590009 ACC
1 ACC
30590012 CCTCTGGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.49, C:0.19, G:0.16, T:0.16
Consensus pattern (17 bp):
ACCAAAATGAGCAGTAT
Found at i:30602471 original size:20 final size:20
Alignment explanation
Indices: 30602446--30602496 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
30602436 AAGGACTATT
30602446 TTGTAAA-GTGGTAAAATAAG
1 TTGTAAATGT-GTAAAATAAG
30602466 TTGTAAATGTGTAAAATAA-
1 TTGTAAATGTGTAAAATAAG
30602485 TTG-AAAT-TGTAA
1 TTGTAAATGTGTAA
30602497 GTTGCTATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.13
19 3 0.10
20 16 0.53
21 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (20 bp):
TTGTAAATGTGTAAAATAAG
Found at i:30603236 original size:46 final size:46
Alignment explanation
Indices: 30603186--30603276 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
30603176 GCCACATTGT
* *
30603186 GAGAGCCAGTGTAAGACATGTCTAGGAAATGCATCGACATTGAGAC
1 GAGAGCCACTGTAAGACATGTCCAGGAAATGCATCGACATTGAGAC
* * * * *
30603232 GAGAGCTACTGTAAGACATGTCCGGGACATGCATCGGCCTTGAGA
1 GAGAGCCACTGTAAGACATGTCCAGGAAATGCATCGACATTGAGA
30603277 TATACAAGCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.20
Consensus pattern (46 bp):
GAGAGCCACTGTAAGACATGTCCAGGAAATGCATCGACATTGAGAC
Found at i:30603389 original size:49 final size:49
Alignment explanation
Indices: 30603330--30603450 Score: 145
Period size: 49 Copynumber: 2.5 Consensus size: 49
30603320 TGTTGTGTGT
* * *
30603330 CAGTGTAAGACCTGTTTGGGACATGGCATCGACAC-CAATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACACGGCATCGAC-CTCAATAGATGAAAGC
* * * *
30603379 CAGTGTAAGACCTGTCTGGGACACGGCATCGGCCTCGATATATGAAAGT
1 CAGTGTAAGACCTGTCTGGGACACGGCATCGACCTCAATAGATGAAAGC
* *
30603428 CAGTGTAAGACCTATCTAGGACA
1 CAGTGTAAGACCTGTCTGGGACA
30603451 TGCCATTGAC
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 1 0.02
49 61 0.98
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.21
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACACGGCATCGACCTCAATAGATGAAAGC
Found at i:30609417 original size:48 final size:48
Alignment explanation
Indices: 30609350--30609568 Score: 288
Period size: 48 Copynumber: 4.6 Consensus size: 48
30609340 TATTCCTGCT
* * * * * *
30609350 GATGCCATGTCCTAGACATGGTCTTACACTAACACCTTTATACGTGTC
1 GATGCCATGTCCCAAACATGGTCTTACACTGACACCTCTATACGCGCC
*
30609398 GATGCTATGTCCCAAACATGGTCTTACACTGACACCTCTATACGCGCC
1 GATGCCATGTCCCAAACATGGTCTTACACTGACACCTCTATACGCGCC
*
30609446 GATGCCATGTCCTAAACATGGTCTTACACTGACACCTCTATACGCGCC
1 GATGCCATGTCCCAAACATGGTCTTACACTGACACCTCTATACGCGCC
*
30609494 GATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCT-TA---GCC
1 GATGCCATGTCCCAAACATGGTCTTACACTGACAC--CTCTATACGCGCC
*
30609540 GATG-CATGTCCCAGACAT-GTCTTACACTG
1 GATGCCATGTCCCAAACATGGTCTTACACTG
30609569 GCTTACATCT
Statistics
Matches: 158, Mismatches: 11, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
44 11 0.07
45 14 0.09
46 7 0.04
48 120 0.76
49 2 0.01
50 4 0.03
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (48 bp):
GATGCCATGTCCCAAACATGGTCTTACACTGACACCTCTATACGCGCC
Found at i:30609577 original size:46 final size:46
Alignment explanation
Indices: 30609397--30609659 Score: 188
Period size: 48 Copynumber: 5.6 Consensus size: 46
30609387 TTATACGTGT
* *
30609397 CGATGCTATGTCCCAAACATGGTCTTACACT-G--ACACCTCTATACGCGC
1 CGATGC-ATGTCCCAGACAT-GTCTTACACTGGCTACATCTCT-TA-G-GC
* * *
30609445 CGATGCCATGTCCTAAACATGGTCTTACACT-G--ACACCTCTATACGCGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTACATCTCT-TA-G-GC
*
30609493 CGATGCCATGTCCCAGACATGGTCTTACACTGAC-ACATCTCTTA-GC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTACATCTCTTAGGC
*
30609539 CGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTC-GAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGC-TACATCTCTTAGGC
** * * * * *
30609585 AAATGCATGTCCTAGACATGTTTTACACTAGCT-C-TCGTCTTAATGT
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTACATC-TCTT-AGGC
30609631 CGATGCATGTCCCAGACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
30609660 AGCATACAAA
Statistics
Matches: 187, Mismatches: 19, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
43 2 0.01
44 15 0.08
45 16 0.09
46 70 0.37
48 74 0.40
49 3 0.02
50 7 0.04
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTACATCTCTTAGGC
Found at i:30609660 original size:46 final size:43
Alignment explanation
Indices: 30609491--30609662 Score: 159
Period size: 46 Copynumber: 3.8 Consensus size: 43
30609481 CTCTATACGC
*
30609491 GCCGATGCCATGTCCCAGACATGGTCTTACACT-GACACATCTCTTA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAG-CTC-TCTCTTA
* *
30609537 GCCGATGCATGTCCCAGACATGTCTTACACTGGCT-TACATCTCGA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-C-TCT-TA
** * *
30609582 GGCAAATGCATGTCCTAGACATGTTTTACACTAGCTCTCGTCTTAA
1 -GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTC-TCTT-A
*
30609628 TGTCGATGCATGTCCCAGACATGTCTTACACTAGC
1 -GCCGATGCATGTCCCAGACATGTCTTACACTAGC
30609663 ATACAAATAA
Statistics
Matches: 104, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 14 0.13
45 16 0.15
46 71 0.68
47 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (43 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCTCTTA
Found at i:30611028 original size:17 final size:17
Alignment explanation
Indices: 30611008--30611046 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
30610998 CTTTAACAAG
30611008 TGCAATACTCTTATTCC
1 TGCAATACTCTTATTCC
30611025 TGCAATACTCTTATTCC
1 TGCAATACTCTTATTCC
30611042 T-CAAT
1 TGCAAT
30611047 TATTTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.26, C:0.28, G:0.05, T:0.41
Consensus pattern (17 bp):
TGCAATACTCTTATTCC
Found at i:30617024 original size:48 final size:48
Alignment explanation
Indices: 30616821--30617183 Score: 271
Period size: 48 Copynumber: 7.6 Consensus size: 48
30616811 ATAATGCCAA
* * * * * *
30616821 ATGCCATGTCCCAGACATGTTCTTACACTGGCTCATCCATCAAGT--CG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACCTCTAT-ACGTGCCG
* * * * *
30616868 ATGCCATGTCCCAAACATGGTCTTACATTGACTA--TCAAAATCGAGACCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGAC-ACCTCTATA-CGTG-CCG
* * * * * * * **
30616917 ACGCCATGTCCCAGGCATGATCTTAGACT-AGCTCTCACATATCCGTGCTA
1 ATGCCATGTCCCAGACATGGTCTTACACTGA-CAC-CTC-TATACGTGCCG
* * * * *
30616967 ATGTCATGTCTCAGACATGGTCTTACGCTAACACCTATATACGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACCTCTATACGTGCCG
* * *
30617015 ATGCCATGTCCAAGACATGGTCTTACACTGACACCTCTATACGTGTCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACCTCTATACGTGCCG
* *
30617063 ATGCCATATCCCAGAC-TCGGTCTTACTCTGACACCTCTATACGTGCCG
1 ATGCCATGTCCCAGACAT-GGTCTTACACTGACACCTCTATACGTGCCG
*
30617111 ATGCCATGTCCCAGACATGGTCTTACACTGACACATCT-T--GTAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACCTCTATACGT-GCCG
* *
30617157 ATG-CATATCCCAGACAT-GTTTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
30617184 AGCTCTCGTC
Statistics
Matches: 248, Mismatches: 54, Indels: 31
0.74 0.16 0.09
Matches are distributed among these distances:
44 9 0.04
45 16 0.06
46 11 0.04
47 30 0.12
48 123 0.50
49 28 0.11
50 25 0.10
51 5 0.02
52 1 0.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACACCTCTATACGTGCCG
Found at i:30623118 original size:63 final size:63
Alignment explanation
Indices: 30623019--30623143 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 63
30623009 TCTAATACAC
* *
30623019 GATTTCAAAAGCTTATTTTAATCAAGATGACATAATTGTGATAGATTAATTACATTTCTTAAT
1 GATTTCAAAAGCTGACTTTAATCAAGATGACATAATTGTGATAGATTAATTACATTTCTTAAT
30623082 GATTTCAAAAGCTGACTTTAATCAAGATGACATAATTGTGATAGATTAATTACATTTCTTAA
1 GATTTCAAAAGCTGACTTTAATCAAGATGACATAATTGTGATAGATTAATTACATTTCTTAA
30623144 CTTATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.39
Consensus pattern (63 bp):
GATTTCAAAAGCTGACTTTAATCAAGATGACATAATTGTGATAGATTAATTACATTTCTTAAT
Found at i:30624620 original size:22 final size:22
Alignment explanation
Indices: 30624594--30624637 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
30624584 GAAAATAATC
*
30624594 AAAATTAATCAAAATTTATTAT
1 AAAATCAATCAAAATTTATTAT
*
30624616 AAAATCAATTAAAATTTATTAT
1 AAAATCAATCAAAATTTATTAT
30624638 GTTAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATCAATCAAAATTTATTAT
Found at i:30627999 original size:28 final size:28
Alignment explanation
Indices: 30627966--30628024 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
30627956 TTCCTCTTTT
*
30627966 CCTTGAGCTACAATATGCTTATCTTCAA
1 CCTTGAGCTACAAAATGCTTATCTTCAA
30627994 CCTTGAGCTACAAAATGCTTATCTTCAA
1 CCTTGAGCTACAAAATGCTTATCTTCAA
30628022 CCT
1 CCT
30628025 CGACAGCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (28 bp):
CCTTGAGCTACAAAATGCTTATCTTCAA
Found at i:30630289 original size:13 final size:13
Alignment explanation
Indices: 30630271--30630295 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30630261 CACGCCGGTG
30630271 TGGCTAGACCGTA
1 TGGCTAGACCGTA
30630284 TGGCTAGACCGT
1 TGGCTAGACCGT
30630296 GTGGTCAATT
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:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (13 bp):
TGGCTAGACCGTA
Found at i:30633491 original size:40 final size:40
Alignment explanation
Indices: 30633431--30633641 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
30633421 ATTTGAATGA
* *
30633431 TATCCGGGCTAAGTCTCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
*
30633471 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * *
30633511 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * *
30633551 TATCCGGGCTAAGACCCGAAGGCATTTATGCAAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * * * * *
30633591 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
30633631 TATCC-GGCTAA
1 TATCCGGGCTAA
30633642 ATTCTGAAGA
Statistics
Matches: 152, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 7 0.05
40 142 0.93
41 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:30638261 original size:22 final size:22
Alignment explanation
Indices: 30638233--30638274 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
30638223 GGACTTATTT
30638233 GTAAAGTGTTGAA-AAATGTATG
1 GTAAAGTG-TGAATAAATGTATG
30638255 GTAAAGTGTGAATAAATGTA
1 GTAAAGTGTGAATAAATGTA
30638275 AAATGTAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (22 bp):
GTAAAGTGTGAATAAATGTATG
Found at i:30643069 original size:37 final size:37
Alignment explanation
Indices: 30642993--30643071 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 37
30642983 TTATTACGAA
* *
30642993 GTCTTACCCGGACATAATCTCCACACGAAGTTATTGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTTATCGG
*
30643030 GTCTTACCCGGACAAAAT-TCCCACACGTAGTCT-TCGG
1 GTCTTACCCGGACAAAATCT-CCACACGAAGT-TATCGG
30643067 GTCTT
1 GTCTT
30643072 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 1 0.03
37 35 0.95
38 1 0.03
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCTCCACACGAAGTTATCGG
Found at i:30643268 original size:47 final size:47
Alignment explanation
Indices: 30643190--30643635 Score: 705
Period size: 47 Copynumber: 9.5 Consensus size: 47
30643180 CCCTTCGGGA
* * * * * * *
30643190 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
30643237 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
30643284 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
30643331 CTTATTA-ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
30643377 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
30643424 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
30643471 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
30643518 CTTATCACATATATATACACTTCCACATTCATCACATCGTCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
30643567 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
30643614 CTTATCACATATATACACTTTC
1 CTTATCACATATATACACTTTC
30643636 TTGGCTGAAT
Statistics
Matches: 375, Mismatches: 21, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
46 44 0.12
47 287 0.77
49 44 0.12
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:30643505 original size:187 final size:189
Alignment explanation
Indices: 30643190--30643635 Score: 707
Period size: 187 Copynumber: 2.4 Consensus size: 189
30643180 CCCTTCGGGA
* * * * * * * * *
30643190 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
30643255 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATC
* * *
30643320 GGCCATTAGGCCTTAT-TA-ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 GGCCATTAGGCCTTATACATATATATACACTTCCACATTCATCACATCGGCCATTAGGC
* * *
30643377 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
30643442 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATC
*
30643507 GGCCATTAGGCCTTATCACATATATATACACTTCCACATTCATCACATCGTCCATTAGGC
131 GGCCATTAGGCCTTAT-ACATATATATACACTTCCACATTCATCACATCGGCCATTAGGC
30643567 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
30643632 TTTC
66 TTTC
30643636 TTGGCTGAAT
Statistics
Matches: 235, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
187 132 0.56
189 1 0.00
190 102 0.43
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (189 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATACATATATATACACTTCCACATTCATCACATCGGCCATTAGGC
Found at i:30646198 original size:17 final size:19
Alignment explanation
Indices: 30646172--30646208 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
30646162 TGTAAAACCC
30646172 ATGAGTATGAACT-TTGGT
1 ATGAGTATGAACTCTTGGT
30646190 ATGAG-ATGAACTCTTGGT
1 ATGAGTATGAACTCTTGGT
30646208 A
1 A
30646209 AGAATGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (19 bp):
ATGAGTATGAACTCTTGGT
Found at i:30650281 original size:14 final size:14
Alignment explanation
Indices: 30650264--30650293 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
30650254 TGATGATTTC
30650264 TACAAAAAGATTGT
1 TACAAAAAGATTGT
30650278 TACAAAAAGATTGT
1 TACAAAAAGATTGT
30650292 TA
1 TA
30650294 AACCTATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (14 bp):
TACAAAAAGATTGT
Found at i:30654137 original size:28 final size:28
Alignment explanation
Indices: 30654072--30654225 Score: 274
Period size: 28 Copynumber: 5.5 Consensus size: 28
30654062 ATATTAAGTC
* *
30654072 CGCACACTCAGTGCTATATAATCAA-CT
1 CGCACACTTAGTGCTACATAATCAAGCT
*
30654099 CGCACACTTAGTGCTATATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
30654127 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
30654155 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
30654183 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAGCT
30654211 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30654226 GTACAATTTA
Statistics
Matches: 124, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
27 24 0.19
28 100 0.81
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAGCT
Found at i:30659488 original size:40 final size:41
Alignment explanation
Indices: 30659435--30659531 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 41
30659425 TAAGTCAGTA
*
30659435 TCGCACACTTAGTGCC-TTATATAGCCAAAGCTAT-GCCAAC
1 TCGCACACTTAGTGCCATT-TATAGCCAAAGCTATAGCAAAC
* * **
30659475 TCGCACACTTAGTGCCATTTATATCCGAAGCTATATTAAAC
1 TCGCACACTTAGTGCCATTTATAGCCAAAGCTATAGCAAAC
30659516 -CGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
30659532 ATCATAGTCG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 45 0.90
41 5 0.10
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (41 bp):
TCGCACACTTAGTGCCATTTATAGCCAAAGCTATAGCAAAC
Found at i:30664188 original size:39 final size:39
Alignment explanation
Indices: 30664145--30664270 Score: 189
Period size: 39 Copynumber: 3.2 Consensus size: 39
30664135 GGACTTTCGC
* * * * *
30664145 CCGGACATATTTCTAGCACGTAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
*
30664184 CCGGATATAATTCCAGCACATAGCCTGCGAACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
*
30664223 CCGAATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
30664262 CCGGATATA
1 CCGGATATA
30664271 CATCACTGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:30665915 original size:20 final size:20
Alignment explanation
Indices: 30665890--30665927 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30665880 TATACATGAC
30665890 AAAAATCTT-CTAAGTTCTGT
1 AAAAAT-TTCCTAAGTTCTGT
30665910 AAAAATTTCCTAAGTTCT
1 AAAAATTTCCTAAGTTCT
30665928 CTGTTTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (20 bp):
AAAAATTTCCTAAGTTCTGT
Found at i:30666406 original size:22 final size:22
Alignment explanation
Indices: 30666380--30666423 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
30666370 GAAAATAATC
*
30666380 AAAATTAATCAAAATTTATTAT
1 AAAATTAATCAAAATTCATTAT
*
30666402 AAAATTAATTAAAATTCATTAT
1 AAAATTAATCAAAATTCATTAT
30666424 GCTAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTAATCAAAATTCATTAT
Found at i:30668475 original size:20 final size:18
Alignment explanation
Indices: 30668430--30668468 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
30668420 AAATTATAGT
**
30668430 ATATGTACTTCAAAGAGC
1 ATATGTACTTCAAAGAAA
30668448 ATATGTACTTCAAAGAAA
1 ATATGTACTTCAAAGAAA
30668466 ATA
1 ATA
30668469 GATGTACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (18 bp):
ATATGTACTTCAAAGAAA
Found at i:30669119 original size:19 final size:19
Alignment explanation
Indices: 30669078--30669119 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
30669068 ATTCTTGTTG
*
30669078 AAAA-AATTTAATTATTAT
1 AAAATAATTTAATTATAAT
*
30669096 AAAATAATTTAATTGTAAT
1 AAAATAATTTAATTATAAT
*
30669115 TAAAT
1 AAAAT
30669120 TATTAACATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAATAATTTAATTATAAT
Found at i:30669333 original size:6 final size:6
Alignment explanation
Indices: 30669322--30669356 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
30669312 CATAATATAA
30669322 TTAATT TTAATT TTAATT TTAATT TTAATT TTAAT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAAT
30669357 CCAATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTAATT
Found at i:30669795 original size:25 final size:25
Alignment explanation
Indices: 30669745--30669795 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
30669735 ACTCTTCTCA
*
30669745 TCTCTTCACTTCTCTCTCATTTTTC
1 TCTCTTCACTTCTCTCTCATTATTC
* * *
30669770 TCTCTTCATTTCTCTTTTATTATTC
1 TCTCTTCACTTCTCTCTCATTATTC
30669795 T
1 T
30669796 TCATTCCCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.10, C:0.29, G:0.00, T:0.61
Consensus pattern (25 bp):
TCTCTTCACTTCTCTCTCATTATTC
Found at i:30672685 original size:29 final size:28
Alignment explanation
Indices: 30672653--30672712 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
30672643 ATAGTCATTT
*
30672653 TTATTTATCTCAAATTATAT-TTTAGTCAC
1 TTATTT-T-TCAAATTATATGTTTACTCAC
* *
30672682 TTATTTTTGAAATTTTATGTTTACTCAC
1 TTATTTTTCAAATTATATGTTTACTCAC
30672710 TTA
1 TTA
30672713 CGTTATCGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.33
28 12 0.44
29 6 0.22
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (28 bp):
TTATTTTTCAAATTATATGTTTACTCAC
Found at i:30674281 original size:25 final size:24
Alignment explanation
Indices: 30674235--30674281 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
30674225 AACTATTCAC
* *
30674235 AAAAATAATAGTATATAAAATTTT
1 AAAAATAATAATAAATAAAATTTT
*
30674259 AAAAATATATAATAAATATAATT
1 AAAAATA-ATAATAAATAAAATT
30674282 ATATTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAAATAATAATAAATAAAATTTT
Found at i:30674717 original size:6 final size:6
Alignment explanation
Indices: 30674708--30674735 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
30674698 TTTTTATTTT
30674708 ATATTA ATATTA ATATTA ATATTA ATAT
1 ATATTA ATATTA ATATTA ATATTA ATAT
30674736 AAAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:30675754 original size:21 final size:22
Alignment explanation
Indices: 30675698--30675754 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 22
30675688 TTACACCACG
30675698 TTGTGGATAAAACCACT-CATCA
1 TTGTGGAT-AAACCACTACATCA
*
30675720 TTGTGGAT-GA--ACTAC-TCA
1 TTGTGGATAAACCACTACATCA
30675738 TTGTGGATAAACCACTA
1 TTGTGGATAAACCACTA
30675755 GTAATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 14 0.48
19 2 0.07
20 1 0.03
21 4 0.14
22 8 0.28
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (22 bp):
TTGTGGATAAACCACTACATCA
Found at i:30675956 original size:35 final size:35
Alignment explanation
Indices: 30675924--30675995 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
30675914 TCAAACAGGT
*
30675924 CAATACGGTAGCATTTAATTATGATTTTAACAGAA
1 CAATACGATAGCATTTAATTATGATTTTAACAGAA
*
30675959 CAATACGATAGCATTTAATTATGCTTTTAACAGAA
1 CAATACGATAGCATTTAATTATGATTTTAACAGAA
30675994 CA
1 CA
30675996 GTACAGTAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (35 bp):
CAATACGATAGCATTTAATTATGATTTTAACAGAA
Found at i:30676006 original size:35 final size:34
Alignment explanation
Indices: 30675924--30676006 Score: 121
Period size: 35 Copynumber: 2.4 Consensus size: 34
30675914 TCAAACAGGT
30675924 CAATACGGTAGCATTTAATTATGATTTTAACAGAA
1 CAATAC-GTAGCATTTAATTATGATTTTAACAGAA
*
30675959 CAATACGATAGCATTTAATTATGCTTTTAACAGAA
1 CAATACG-TAGCATTTAATTATGATTTTAACAGAA
*
30675994 CAGTACAGTAGCA
1 CAATAC-GTAGCA
30676007 ATCAATATGC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 1 0.02
35 42 0.95
36 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (34 bp):
CAATACGTAGCATTTAATTATGATTTTAACAGAA
Found at i:30676073 original size:34 final size:34
Alignment explanation
Indices: 30675978--30676059 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
30675968 AGCATTTAAT
* ** *
30675978 TATGCTTTTAACAGAACAGTACAGTAGCAATCAA
1 TATGCTTATAACAGTTCAATACAGTAGCAATCAA
*
30676012 TATGCTTATAATAGTTCAATACAGTAGCAAAT-AA
1 TATGCTTATAACAGTTCAATACAGTAGC-AATCAA
*
30676046 TATGTTTATAACAG
1 TATGCTTATAACAG
30676060 ATTAACTCAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 37 0.93
35 3 0.08
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (34 bp):
TATGCTTATAACAGTTCAATACAGTAGCAATCAA
Found at i:30676387 original size:28 final size:28
Alignment explanation
Indices: 30676322--30676426 Score: 119
Period size: 28 Copynumber: 3.8 Consensus size: 28
30676312 AATTTTAAGT
*
30676322 AAAACTATAAAATCTAAAAACA-A-GGG-
1 AAAATTATAAAATCTAAAAA-ATAGGGGC
* *
30676348 AAATTTGTAAAATCTAAAAAATAGGGGC
1 AAAATTATAAAATCTAAAAAATAGGGGC
*
30676376 AAAATTATAAAATATAAAAAATAGGGGC
1 AAAATTATAAAATCTAAAAAATAGGGGC
*
30676404 AAAA-CAGTAAAATCTAAAAAATA
1 AAAATTA-TAAAATCTAAAAAATA
30676427 AGGAACACAC
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.01
26 18 0.27
27 4 0.06
28 44 0.66
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.20
Consensus pattern (28 bp):
AAAATTATAAAATCTAAAAAATAGGGGC
Found at i:30687782 original size:44 final size:44
Alignment explanation
Indices: 30687724--30687810 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
30687714 TGAAATAAAA
* *
30687724 TAGAAGTTGTGATAATTA-TACATTTAAAAA-AAATTATAATTTAG
1 TAGAAGTTATGATAATTACGA-ATTTAAAAATAAA-TATAATTTAG
30687768 TAGAAGTTATGATAATTACGAATTTAAAAATAAATATAATTTA
1 TAGAAGTTATGATAATTACGAATTTAAAAATAAATATAATTTA
30687811 AATTACAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 35 0.90
45 4 0.10
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.38
Consensus pattern (44 bp):
TAGAAGTTATGATAATTACGAATTTAAAAATAAATATAATTTAG
Found at i:30692934 original size:18 final size:18
Alignment explanation
Indices: 30692911--30692969 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 18
30692901 ATTTATTTAG
30692911 ATATGTTATTGTGTCTGA
1 ATATGTTATTGTGTCTGA
* *
30692929 ATATGTTATACTCCATTATCTGA
1 ATATGTTAT--T---GTGTCTGA
30692952 ATATGTTATTGTGTCTGA
1 ATATGTTATTGTGTCTGA
30692970 TATTGAATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
18 15 0.47
20 1 0.03
21 1 0.03
23 15 0.47
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.47
Consensus pattern (18 bp):
ATATGTTATTGTGTCTGA
Found at i:30703272 original size:19 final size:19
Alignment explanation
Indices: 30703248--30703305 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
30703238 TATACGGGTT
30703248 TATGCACTTTGTGTGCTAG
1 TATGCACTTTGTGTGCTAG
*
30703267 TATGCA--TTGTGTGTTAG
1 TATGCACTTTGTGTGCTAG
* * *
30703284 TATGTACTATATGTGCTAG
1 TATGCACTTTGTGTGCTAG
30703303 TAT
1 TAT
30703306 ATTTGCTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 15 0.47
19 17 0.53
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.45
Consensus pattern (19 bp):
TATGCACTTTGTGTGCTAG
Found at i:30704201 original size:27 final size:26
Alignment explanation
Indices: 30704141--30704202 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
30704131 ATAAGACTCC
30704141 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * * *
30704167 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
30704195 ATTTTATT
1 ATTTTATT
30704203 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 14 0.48
28 13 0.45
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:30704225 original size:20 final size:20
Alignment explanation
Indices: 30704197--30704244 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
30704187 ATTTTAGGAT
*
30704197 TTTAT-TTTAATT-ATCTTTA
1 TTTATCTTTAATTAAT-TGTA
30704216 TTTATCTTTAATTAATTGTA
1 TTTATCTTTAATTAATTGTA
30704236 TTTATCTTT
1 TTTATCTTT
30704245 TTAGAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 19 0.73
21 2 0.08
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTATCTTTAATTAATTGTA
Found at i:30707912 original size:5 final size:5
Alignment explanation
Indices: 30707902--30707951 Score: 61
Period size: 5 Copynumber: 10.4 Consensus size: 5
30707892 GCAACCCAAT
*
30707902 TTTTA TTTTA TTTTA TTTTA TTTT- TATTTA TTTTA TCTTA --TTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA
30707950 TT
1 TT
30707952 ATTTATTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
3 3 0.08
4 1 0.03
5 35 0.88
6 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:30707956 original size:20 final size:20
Alignment explanation
Indices: 30707904--30707957 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
30707894 AACCCAATTT
*
30707904 TTATTTTA-T-TTTATTTTA
1 TTATTTTATTATTTATCTTA
30707922 -T-TTTTATTTATTTTATCTTA
1 TTATTTTA-TTA-TTTATCTTA
30707942 TTATTTTATTATTTAT
1 TTATTTTATTATTTAT
30707958 TATTTTCAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
16 5 0.17
17 1 0.03
18 1 0.03
20 13 0.45
21 4 0.14
22 5 0.17
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (20 bp):
TTATTTTATTATTTATCTTA
Found at i:30707959 original size:15 final size:14
Alignment explanation
Indices: 30707902--30707963 Score: 72
Period size: 15 Copynumber: 4.3 Consensus size: 14
30707892 GCAACCCAAT
*
30707902 TTTTATTTTATTTTA
1 TTTTATTTT-TATTA
30707917 TTTTATTTTTATTTA
1 TTTTATTTTTA-TTA
*
30707932 TTTTA-TCTTATTA
1 TTTTATTTTTATTA
30707945 TTTTATTATTTATTA
1 TTTTATT-TTTATTA
30707960 TTTT
1 TTTT
30707964 CAGATATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
13 8 0.20
14 6 0.15
15 27 0.66
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTTTTATTA
Found at i:30707972 original size:28 final size:28
Alignment explanation
Indices: 30707903--30707963 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
30707893 CAACCCAATT
30707903 TTTATTTTAT--T-TTATTTTATTTTTA
1 TTTATTTTATCATATTATTTTATTTTTA
*
30707928 TTTATTTTATCTTATTATTTTATTATTTA
1 TTTATTTTATCATATTATTTTATT-TTTA
30707957 -TTATTTT
1 TTTATTTT
30707964 CAGATATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 10 0.31
27 1 0.03
28 17 0.53
29 4 0.12
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTATTTTATCATATTATTTTATTTTTA
Found at i:30708965 original size:11 final size:11
Alignment explanation
Indices: 30708951--30708976 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
30708941 AAAATTCTAT
30708951 AAAAAAAGAAA
1 AAAAAAAGAAA
30708962 AAAAAAAGAAA
1 AAAAAAAGAAA
30708973 AAAA
1 AAAA
30708977 GTCATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Done.