Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 210 of 228
Found at i:61387386 original size:18 final size:17
Alignment explanation
Indices: 61387358--61387392 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
61387348 ATTATTAAGA
*
61387358 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
61387375 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
61387393 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:61387511 original size:16 final size:16
Alignment explanation
Indices: 61387490--61387536 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
61387480 TTATTAAATT
61387490 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
61387506 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
61387521 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
61387537 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:61387625 original size:18 final size:17
Alignment explanation
Indices: 61387597--61387631 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
61387587 ATTATTAAGA
*
61387597 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
61387614 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
61387632 TTCATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:61387751 original size:16 final size:16
Alignment explanation
Indices: 61387730--61387776 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
61387720 TTATTAAATT
61387730 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
61387746 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
61387761 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
61387777 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:61388085 original size:44 final size:45
Alignment explanation
Indices: 61388036--61388126 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 45
61388026 ACCTCTATTC
*
61388036 CATTCAACCAAACACA-GGA-ATACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACA-ATGGATATACTATTACGCCTCTATTCCACTA
* *
61388080 CATTCAACCAAACAATTGATTTACTATTACGCCTCTATTCCACTA
1 CATTCAACCAAACAATGGATATACTATTACGCCTCTATTCCACTA
61388125 CA
1 CA
61388127 GCGAACCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.38
45 25 0.60
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (45 bp):
CATTCAACCAAACAATGGATATACTATTACGCCTCTATTCCACTA
Found at i:61391862 original size:87 final size:87
Alignment explanation
Indices: 61391716--61391889 Score: 339
Period size: 87 Copynumber: 2.0 Consensus size: 87
61391706 TCATTCTTCC
61391716 ATTTTCAATATGCAAAATGAAAATTCAGCTGCTATAACTCTGGCTTCAATGTGTAAGCTGTGACA
1 ATTTTCAATATGCAAAATGAAAATTCAGCTGCTATAACTCTGGCTTCAATGTGTAAGCTGTGACA
*
61391781 TGTATTACGGCCAAATCGCTTT
66 TGTATCACGGCCAAATCGCTTT
61391803 ATTTTCAATATGCAAAATGAAAATTCAGCTGCTATAACTCTGGCTTCAATGTGTAAGCTGTGACA
1 ATTTTCAATATGCAAAATGAAAATTCAGCTGCTATAACTCTGGCTTCAATGTGTAAGCTGTGACA
61391868 TGTATCACGGCCAAATCGCTTT
66 TGTATCACGGCCAAATCGCTTT
61391890 GGATTTAGGT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (87 bp):
ATTTTCAATATGCAAAATGAAAATTCAGCTGCTATAACTCTGGCTTCAATGTGTAAGCTGTGACA
TGTATCACGGCCAAATCGCTTT
Found at i:61392527 original size:28 final size:28
Alignment explanation
Indices: 61392495--61392556 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
61392485 CTATAAAATA
61392495 ATAAATCCTAAAC-CACAAACTCTAA-CCC
1 ATAAATCC-AAACTCA-AAACTCTAATCCC
61392523 ATAAACTCCAAACTCAAAACTCTAATCCC
1 ATAAA-TCCAAACTCAAAACTCTAATCCC
61392552 A-AAAT
1 ATAAAT
61392557 AATAAACATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
27 1 0.03
28 21 0.68
29 9 0.29
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.19
Consensus pattern (28 bp):
ATAAATCCAAACTCAAAACTCTAATCCC
Found at i:61392783 original size:40 final size:40
Alignment explanation
Indices: 61392725--61392802 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
61392715 AACTTTTTTA
61392725 TGGCGTTTTACGAAAAGCGCCGCTAATGCTCGATCTATAG
1 TGGCGTTTTACGAAAAGCGCCGCTAATGCTCGATCTATAG
* * *
61392765 TGGCGTTTTTC-AACAAGCGCCGCTAATTCTTGATCTAT
1 TGGCGTTTTACGAA-AAGCGCCGCTAATGCTCGATCTAT
61392803 TACGACATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 2 0.06
40 32 0.94
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (40 bp):
TGGCGTTTTACGAAAAGCGCCGCTAATGCTCGATCTATAG
Found at i:61392814 original size:40 final size:40
Alignment explanation
Indices: 61392737--61392833 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 40
61392727 GCGTTTTACG
* * *
61392737 AAAAGCGCCGCTAATGCTCGATCTATAGTGGCGTTTTTCA
1 AAAAGCGCCGCTAATGCTCGATCTATAGCGACATTTTTCA
* * * *
61392777 ACAAGCGCCGCTAATTCTTGATCTATTA-CGACATTTTTTA
1 AAAAGCGCCGCTAATGCTCGATCTA-TAGCGACATTTTTCA
*
61392817 AAAAGCGCCACTAATGC
1 AAAAGCGCCGCTAATGC
61392834 CACTAAACCT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
40 44 0.96
41 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (40 bp):
AAAAGCGCCGCTAATGCTCGATCTATAGCGACATTTTTCA
Found at i:61392921 original size:40 final size:40
Alignment explanation
Indices: 61392877--61392984 Score: 144
Period size: 40 Copynumber: 2.7 Consensus size: 40
61392867 ACTTTTTTGT
*
61392877 GGCGTTTTCCAAAAAGCGCCGCTAATGCTCGATCTATAGC
1 GGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGC
* * * *
61392917 GGCGTTTTTCAAATATCGCCACTAATGCTCGATCTATTGC
1 GGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGC
* * *
61392957 GGCATTTTTTAAAAAGCGCTGCTAATGC
1 GGCGTTTTTCAAAAAGCGCCGCTAATGC
61392985 CACTAAAGCT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (40 bp):
GGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGC
Found at i:61393074 original size:40 final size:40
Alignment explanation
Indices: 61393030--61393159 Score: 120
Period size: 40 Copynumber: 3.2 Consensus size: 40
61393020 AACTTTTTAT
* * *
61393030 GGCGTTTTCTGAAAAA-TACCGCTAATGCTCAATCTATAGC
1 GGCGTTTT-TCAAAAAGCACCGCTAATGCTCAACCTATAGC
*
61393070 GGCGTTTTTCAAAAAGCACCGCTAATGCTCGACCTATAGC
1 GGCGTTTTTCAAAAAGCACCGCTAATGCTCAACCTATAGC
** * ** * *
61393110 GATGTTTGTTTCAAAAA-CGCCGCTAATGCTTGACCTCTTGC
1 GGCG-TT-TTTCAAAAAGCACCGCTAATGCTCAACCTATAGC
61393151 GGCGTTTTT
1 GGCGTTTTT
61393160 GTCATAAACG
Statistics
Matches: 75, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
39 9 0.12
40 33 0.44
41 24 0.32
42 9 0.12
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.32
Consensus pattern (40 bp):
GGCGTTTTTCAAAAAGCACCGCTAATGCTCAACCTATAGC
Found at i:61393095 original size:153 final size:153
Alignment explanation
Indices: 61392673--61393106 Score: 585
Period size: 151 Copynumber: 2.8 Consensus size: 153
61392663 AAAAATGCCT
61392673 CTAATGCCACTAAAGCTCAACAACAAACAAC-TCCGTTTT-CTCAACTTTTTTATGGCGTTTTAC
1 CTAATGCCACTAAAGCTCAACAACAAACAACGT--GTTTTGCTCAACTTTTTTATGGCGTTTT-C
* * * * *
61392736 GAAAAGCGCCGCTAATGCTCGATCTATAGTGGCGTTTTTCAACAAGCGCCGCTAATTCTTGATCT
63 GAAAAACGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCT
61392801 ATTACGACATTTTTTAAAAAGCGCCA
128 ATTACGACATTTTTTAAAAAGCGCCA
* * *
61392827 CTAATGCCACTAAA-C-C-TCAAC-AACAACGTTGTTTTGCTCAACTTTTTTGTGGCGTTTTCCA
1 CTAATGCCACTAAAGCTCAACAACAAACAACG-TGTTTTGCTCAACTTTTTTATGGCGTTTTCGA
* * *
61392888 AAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAATATCGCCACTAATGCTCGATCTA
65 AAAA-CGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTA
* * **
61392953 TTGCGGCATTTTTTAAAAAGCGCTG
129 TTACGACATTTTTTAAAAAGCGCCA
61392978 CTAATGCCACTAAAGCTCAACAACAAACAACGTGTTTTGCTCAAC-TTTTTATGGCGTTTTCTGA
1 CTAATGCCACTAAAGCTCAACAACAAACAACGTGTTTTGCTCAACTTTTTTATGGCGTTTTC-GA
** * * *
61393042 AAAATACCGCTAATGCTCAATCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGCTCGACCTAT
65 AAAACGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTAT
61393107 AGCGATGTTT
Statistics
Matches: 245, Mismatches: 26, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
150 16 0.07
151 113 0.46
152 3 0.01
153 70 0.29
154 36 0.15
155 7 0.03
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (153 bp):
CTAATGCCACTAAAGCTCAACAACAAACAACGTGTTTTGCTCAACTTTTTTATGGCGTTTTCGAA
AAACGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATT
ACGACATTTTTTAAAAAGCGCCA
Found at i:61393169 original size:41 final size:41
Alignment explanation
Indices: 61393048--61393175 Score: 127
Period size: 41 Copynumber: 3.1 Consensus size: 41
61393038 CTGAAAAATA
* * * *
61393048 CCGCTAATGCTCAATCTATAGCGGCG-TT-TTTCAAAAAGCA
1 CCGCTAATGCTCGACCTATAGCGACGTTTGTTTCAAAAA-CG
*
61393088 CCGCTAATGCTCGACCTATAGCGATGTTTGTTTCAAAAACG
1 CCGCTAATGCTCGACCTATAGCGACGTTTGTTTCAAAAACG
* * * * *
61393129 CCGCTAATGCTTGACCTCTTGCGGCGTTT-TTGTCATAAACG
1 CCGCTAATGCTCGACCTATAGCGACGTTTGTT-TCAAAAACG
61393170 CCGCTA
1 CCGCTA
61393176 TAGCTCTAAC
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
40 24 0.32
41 41 0.55
42 9 0.12
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.30
Consensus pattern (41 bp):
CCGCTAATGCTCGACCTATAGCGACGTTTGTTTCAAAAACG
Found at i:61396832 original size:25 final size:24
Alignment explanation
Indices: 61396804--61396865 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
61396794 CACTTTCACA
61396804 TATTTTAATAATTTTT-ATTATTTAT
1 TATTTTAATAATTTTTAATT-TTT-T
**
61396829 TATTTTCTTATATTTTTAATTTTTT
1 TATTTTAATA-ATTTTTAATTTTTT
61396854 TATTTTCAATAA
1 TATTTT-AATAA
61396866 AAGTATCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
25 16 0.53
26 11 0.37
27 3 0.10
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (24 bp):
TATTTTAATAATTTTTAATTTTTT
Found at i:61399430 original size:3 final size:3
Alignment explanation
Indices: 61399422--61399464 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
61399412 GAAAACAATT
* *
61399422 ATA ATA ATA ATA ATA ACA ATA ATA ATA GTA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
61399465 AATTGCTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:61401310 original size:82 final size:84
Alignment explanation
Indices: 61401205--61401361 Score: 210
Period size: 82 Copynumber: 1.9 Consensus size: 84
61401195 AGACTTGATG
* * *
61401205 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-C-TTTAATCCGCTCCACTGTAACTTCGG
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTTTTAATCCGCTCCACTGTAACCTCAG
61401268 GGAGATAGGATAGTGTCTT
66 GGAGATAGGATAGTGTCTT
* * * *
61401287 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTATTTTAATCTGCTCCACTGTAACCT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTC---TTTTAATCCGCTCCACTGTAACCT
61401352 CAGGGAGATA
63 CAGGGAGATA
61401362 AGATCTGAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
82 32 0.51
83 1 0.02
87 30 0.48
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (84 bp):
CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTTTTAATCCGCTCCACTGTAACCTCAG
GGAGATAGGATAGTGTCTT
Found at i:61401403 original size:46 final size:44
Alignment explanation
Indices: 61401241--61401580 Score: 242
Period size: 44 Copynumber: 7.8 Consensus size: 44
61401231 AGATAAGATC
* * * * *
61401241 CTTTAATCCGCTCCACTGTAA-CTTCGGGGAGATAGGATAGTG--T
1 CTTTGATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-CTGAAT
* * **
61401284 CTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTAT
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT-GAAT
* *
61401329 -TTTAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATT
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AA-T
* * *
61401374 CTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG-A-
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* * * *
61401416 -TGTGATCTTCTCTACTGTAA-CTTCAGAGAGATAAGATC-----
1 CTTTGATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGAAT
* * * * *
61401454 CTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGAT-T-ACTAT
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGA--AT
* *
61401498 CCTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AA-T
* *
61401544 CTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGA
61401581 CCTGTATAAT
Statistics
Matches: 231, Mismatches: 46, Indels: 37
0.74 0.15 0.12
Matches are distributed among these distances:
39 26 0.11
40 2 0.01
41 29 0.13
42 1 0.00
43 30 0.13
44 69 0.30
45 4 0.02
46 69 0.30
47 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (44 bp):
CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
Found at i:61401468 original size:213 final size:216
Alignment explanation
Indices: 61401166--61401580 Score: 590
Period size: 213 Copynumber: 1.9 Consensus size: 216
61401156 ATTGTTTTCA
* * *
61401166 GTCTGTTCCACTGCATCTTCAGGGAAATAAGACTTGATGCGATCTACTCTGCTGTAACCTCAGAG
1 GTCTGTTCCACTGAATCTTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
** * *
61401231 AGATAAGATCCTTTAATCCGCTCCACTGTAA-CTTCGGGGAGATAGGA-TAGTGT-CTTCGATCT
66 AGATAAGATCCTTTAATCCGCTCCACTGTAATC-TCAAGGAGATAGGATTACTATCCTT-GATCT
**
61401293 GCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTA-T-TTTAATCTGCTCCACTGTAACCTCAGG
129 GCTCCGCTGTAATCTCAGGGAGATAAGATCTCAAATTCTTTAATCTGCTCCACTGTAACCTCAGG
61401356 GAGATAAGATCTGAAATTCTTTG
194 GAGATAAGATCTGAAATTCTTTG
* * * *
61401379 GTCTGTTCCACTGTAATC-TCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
1 GTCTGTTCCACTG-AATCTTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGA
*
61401443 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCCTTGATCTG
65 GAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTATCCTTGATCTG
* ** * *
61401508 CTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTGTAATCTCAGGG
130 CTCCGCTGTAATCTCAGGGAGATAAGATCTCAAATTCTTTAATCTGCTCCACTGTAACCTCAGGG
61401573 AGATAAGA
195 AGATAAGA
61401581 CCTGTATAAT
Statistics
Matches: 177, Mismatches: 19, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
213 96 0.54
214 45 0.25
215 4 0.02
216 32 0.18
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (216 bp):
GTCTGTTCCACTGAATCTTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
AGATAAGATCCTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTATCCTTGATCTGC
TCCGCTGTAATCTCAGGGAGATAAGATCTCAAATTCTTTAATCTGCTCCACTGTAACCTCAGGGA
GATAAGATCTGAAATTCTTTG
Found at i:61423310 original size:87 final size:87
Alignment explanation
Indices: 61423152--61423311 Score: 216
Period size: 87 Copynumber: 1.8 Consensus size: 87
61423142 ACGAGCCACC
** * *
61423152 AGAAATACAGATAAACTGCCAATACAATTGAGGTAAACTGCCAATAATAGATTGTAAACAAGCTG
1 AGAAATACAGATAAACTGCCAATACAATTGAGGTAAACAACCAATAAGAGATTGCAAACAAGCTG
61423217 TTGATAATGTGGACGAGGCCTT
66 TTGATAATGTGGACGAGGCCTT
* * * *
61423239 AGAAATACAGATAAACTGTCAATATAATT-ACGGTAAACAACCAATAAGAGATTGCAGACGAGCT
1 AGAAATACAGATAAACTGCCAATACAATTGA-GGTAAACAACCAATAAGAGATTGCAAACAAGCT
61423303 -TTCGATAAT
65 GTT-GATAAT
61423312 TTTGTGGGCA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
86 3 0.05
87 60 0.95
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (87 bp):
AGAAATACAGATAAACTGCCAATACAATTGAGGTAAACAACCAATAAGAGATTGCAAACAAGCTG
TTGATAATGTGGACGAGGCCTT
Found at i:61432640 original size:45 final size:45
Alignment explanation
Indices: 61432586--61432767 Score: 242
Period size: 45 Copynumber: 4.0 Consensus size: 45
61432576 AAGTAGCAGC
*
61432586 AAATGTGCACACATATGTGGCATTTTACTCAATAAAAA-AATAGCA
1 AAATGTGCACACATATGTGGCA-TTTACTCAACAAAAATAATAGCA
* * * *
61432631 AAATGTGCACACATATGTGACATTTACGCAACAAAAATAGTACCA
1 AAATGTGCACACATATGTGGCATTTACTCAACAAAAATAATAGCA
61432676 AAATGTGCACACATATGTGGCATTTACTCAACAAAAATAGA-AGCA
1 AAATGTGCACACATATGTGGCATTTACTCAACAAAAATA-ATAGCA
* * * * *
61432721 AAATGTGCACACATATGCGACATTCACTCAACAAAAACAACAGCA
1 AAATGTGCACACATATGTGGCATTTACTCAACAAAAATAATAGCA
61432766 AA
1 AA
61432768 TGTTCATTAC
Statistics
Matches: 121, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
44 14 0.12
45 107 0.88
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (45 bp):
AAATGTGCACACATATGTGGCATTTACTCAACAAAAATAATAGCA
Found at i:61432689 original size:90 final size:90
Alignment explanation
Indices: 61432586--61432757 Score: 276
Period size: 90 Copynumber: 1.9 Consensus size: 90
61432576 AAGTAGCAGC
* *
61432586 AAATGTGCACACATATGTGGCATTTTACTCAATAAAAA-A-ATAGCAAAATGTGCACACATATGT
1 AAATGTGCACACATATGTGGCA-TTTACTCAACAAAAATAGA-AGCAAAATGTGCACACATATGC
*
61432649 GACATTTACGCAACAAAAATAGTACCA
64 GACATTCACGCAACAAAAATAGTACCA
61432676 AAATGTGCACACATATGTGGCATTTACTCAACAAAAATAGAAGCAAAATGTGCACACATATGCGA
1 AAATGTGCACACATATGTGGCATTTACTCAACAAAAATAGAAGCAAAATGTGCACACATATGCGA
*
61432741 CATTCACTCAACAAAAA
66 CATTCACGCAACAAAAA
61432758 CAACAGCAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
89 14 0.18
90 61 0.80
91 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (90 bp):
AAATGTGCACACATATGTGGCATTTACTCAACAAAAATAGAAGCAAAATGTGCACACATATGCGA
CATTCACGCAACAAAAATAGTACCA
Found at i:61434411 original size:20 final size:20
Alignment explanation
Indices: 61434383--61434426 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
61434373 CATATTTTCT
*
61434383 CTCATGTTTCTCCATTCTTG
1 CTCACGTTTCTCCATTCTTG
*
61434403 CTCACGTTTCTCTATTCTTG
1 CTCACGTTTCTCCATTCTTG
61434423 CTCA
1 CTCA
61434427 TGCTTTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.32, G:0.09, T:0.48
Consensus pattern (20 bp):
CTCACGTTTCTCCATTCTTG
Found at i:61434825 original size:16 final size:16
Alignment explanation
Indices: 61434804--61434835 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
61434794 GTGTGTGTGT
61434804 GTGCGTGAGTACGTGC
1 GTGCGTGAGTACGTGC
*
61434820 GTGCGTGCGTACGTGC
1 GTGCGTGAGTACGTGC
61434836 ATGTGTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.22, G:0.44, T:0.25
Consensus pattern (16 bp):
GTGCGTGAGTACGTGC
Found at i:61438436 original size:20 final size:20
Alignment explanation
Indices: 61438411--61438455 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
61438401 CACGACACGG
61438411 GAAAA-TCACTATTTCTAATT
1 GAAAATTCA-TATTTCTAATT
*
61438431 GAAAATTGATATTTCTAATT
1 GAAAATTCATATTTCTAATT
*
61438451 CAAAA
1 GAAAA
61438456 GAAAAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (20 bp):
GAAAATTCATATTTCTAATT
Found at i:61441140 original size:12 final size:12
Alignment explanation
Indices: 61441123--61441150 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
61441113 TTACATAAGT
61441123 AAATCTAAATGG
1 AAATCTAAATGG
61441135 AAATCTAAATGG
1 AAATCTAAATGG
61441147 AAAT
1 AAAT
61441151 GTAATGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (12 bp):
AAATCTAAATGG
Found at i:61441191 original size:21 final size:21
Alignment explanation
Indices: 61441152--61441197 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
61441142 AATGGAAATG
* *
61441152 TAATGATAATAACAGTAATAT
1 TAATGATAATAACAATAATAA
61441173 TAATGATAAT-ACTAATAATAA
1 TAATGATAATAAC-AATAATAA
61441194 TAAT
1 TAAT
61441198 AACCTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (21 bp):
TAATGATAATAACAATAATAA
Found at i:61443514 original size:20 final size:20
Alignment explanation
Indices: 61443478--61443518 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
61443468 TTAACTTTCT
61443478 TTATATATTCTTTAAAAATA
1 TTATATATTCTTTAAAAATA
*
61443498 TTATA-ATTTTTTGAAAAATA
1 TTATATATTCTTT-AAAAATA
61443518 T
1 T
61443519 AAAATTTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TTATATATTCTTTAAAAATA
Found at i:61443553 original size:20 final size:19
Alignment explanation
Indices: 61443517--61443552 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
61443507 TTTGAAAAAT
*
61443517 ATAAA-ATTTGGAATTTTC
1 ATAAATATTTTGAATTTTC
61443535 ATAAATATTTTGAATTTT
1 ATAAATATTTTGAATTTT
61443553 TGAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (19 bp):
ATAAATATTTTGAATTTTC
Found at i:61443735 original size:16 final size:15
Alignment explanation
Indices: 61443699--61443738 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
61443689 TTGACTCAAA
61443699 AAATTCGAATAACTT
1 AAATTCGAATAACTT
*
61443714 -AATTCGATTAACTT
1 AAATTCGAATAACTT
61443728 GAAATTCGAAT
1 -AAATTCGAAT
61443739 TATTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 13 0.62
16 8 0.38
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (15 bp):
AAATTCGAATAACTT
Found at i:61447302 original size:16 final size:17
Alignment explanation
Indices: 61447267--61447303 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
61447257 GAATCAGATT
*
61447267 TTTTTTATTTTTAATAA
1 TTTTTTATTTTAAATAA
61447284 TTTTTTATTTTAAAT-A
1 TTTTTTATTTTAAATAA
61447300 TTTT
1 TTTT
61447304 AATGATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTATTTTAAATAA
Found at i:61450056 original size:31 final size:31
Alignment explanation
Indices: 61449968--61450056 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 31
61449958 ATAAAATCTC
* * * *
61449968 TAAAAATTTTAATTAGACTTACCAAAATTTT
1 TAAAAATTTTAATTAAACCTCCCAAAACTTT
* * * * *
61449999 TAGAAATTCTCACTAAAACC-CTCAAAACTTT
1 TAAAAATT-TTAATTAAACCTCCCAAAACTTT
61450030 TAAAAATTTTAATTAAACCTCCCAAAA
1 TAAAAATTTTAATTAAACCTCCCAAAA
61450057 ATTAATGCTA
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
30 8 0.19
31 28 0.67
32 6 0.14
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (31 bp):
TAAAAATTTTAATTAAACCTCCCAAAACTTT
Found at i:61452540 original size:29 final size:29
Alignment explanation
Indices: 61452507--61452562 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
61452497 TTTGATCTTT
**
61452507 ATATTCTTATAATGTTTTTAATTAGTTTA
1 ATATTCTTATAATGTAATTAATTAGTTTA
*
61452536 ATATTTTTATAATGTAATTAATTAGTT
1 ATATTCTTATAATGTAATTAATTAGTT
61452563 CATATAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (29 bp):
ATATTCTTATAATGTAATTAATTAGTTTA
Found at i:61454494 original size:12 final size:12
Alignment explanation
Indices: 61454468--61454501 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
61454458 TAATGATACA
61454468 AATAGTAAC-AT
1 AATAGTAACAAT
61454479 AATAGTAACAAT
1 AATAGTAACAAT
*
61454491 AATAATAACAA
1 AATAGTAACAA
61454502 CAAAAGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.24
Consensus pattern (12 bp):
AATAGTAACAAT
Found at i:61457939 original size:15 final size:15
Alignment explanation
Indices: 61457919--61457951 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
61457909 GATTACATTT
61457919 TTACTATCGTAAAAA
1 TTACTATCGTAAAAA
61457934 TTACTATCGTAAAAA
1 TTACTATCGTAAAAA
61457949 TTA
1 TTA
61457952 TAATTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (15 bp):
TTACTATCGTAAAAA
Found at i:61458911 original size:22 final size:21
Alignment explanation
Indices: 61458885--61458975 Score: 63
Period size: 19 Copynumber: 4.5 Consensus size: 21
61458875 TTATTTTTTA
61458885 TTTTTAAAATACTTTTAAAATAC
1 TTTTTAAAAT--TTTTAAAATAC
61458908 TTTTTTAAAATTTTT-AAA-A-
1 -TTTTTAAAATTTTTAAAATAC
*
61458927 -TTTT-AATTTTTTAAAAAATAC
1 TTTTTAAAATTTTT--AAAATAC
*
61458948 TTTTT-TAA-TTTTAAAATA-
1 TTTTTAAAATTTTTAAAATAC
61458966 TTTTTAAAAT
1 TTTTTAAAAT
61458976 ACTTTTTTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
16 7 0.13
17 4 0.07
18 5 0.09
19 11 0.20
20 2 0.04
21 7 0.13
22 9 0.16
24 10 0.18
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTTAAAATTTTTAAAATAC
Found at i:61458912 original size:30 final size:31
Alignment explanation
Indices: 61458878--61458990 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
61458868 AAATTTTTTA
*
61458878 TTTTTT-ATTTTTAAAATACTTTTAAAATAC
1 TTTTTTAATTTTTAAAATATTTTTAAAATAC
61458908 TTTTTTAAAATTTTTAAAATTTTAATTTTTTAAAAAATAC
1 TTTTTT--AATTTTTAAAA---T-A-TTTTT--AAAATAC
61458948 TTTTTTAA-TTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTTTTAAAATATTTTTAAAATAC
61458978 TTTTTTAATTTTT
1 TTTTTTAATTTTT
61458991 GTTTTAATTT
Statistics
Matches: 71, Mismatches: 1, Indels: 21
0.76 0.01 0.23
Matches are distributed among these distances:
30 21 0.30
31 4 0.06
32 5 0.07
33 11 0.15
34 1 0.01
36 1 0.01
37 9 0.13
38 6 0.08
40 13 0.18
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTTTAATTTTTAAAATATTTTTAAAATAC
Found at i:61458915 original size:13 final size:12
Alignment explanation
Indices: 61458885--61458927 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
61458875 TTATTTTTTA
61458885 TTTTTAAAATAC
1 TTTTTAAAATAC
61458897 -TTTTAAAATAC
1 TTTTTAAAATAC
*
61458908 TTTTTTAAA-A-
1 TTTTTAAAATAC
61458918 TTTTTAAAAT
1 TTTTTAAAAT
61458928 TTTAATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 8 0.30
11 12 0.44
12 7 0.26
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTTTAAAATAC
Found at i:61459947 original size:16 final size:16
Alignment explanation
Indices: 61459926--61459977 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
61459916 TTTGGTTCGC
*
61459926 TGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
61459942 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
61459958 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
61459974 TGTA
1 TGTA
61459978 ATAGCAAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:61460234 original size:18 final size:17
Alignment explanation
Indices: 61460213--61460247 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
61460203 TTATTATTAA
*
61460213 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
61460231 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
61460248 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:61461011 original size:13 final size:13
Alignment explanation
Indices: 61460993--61461022 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
61460983 TTAAAAGCTA
61460993 AATTCAGAAAAAC
1 AATTCAGAAAAAC
61461006 AATTCAGAAAAAC
1 AATTCAGAAAAAC
61461019 AATT
1 AATT
61461023 ACATGACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (13 bp):
AATTCAGAAAAAC
Found at i:61466627 original size:6 final size:6
Alignment explanation
Indices: 61466618--61466669 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
61466608 ATTCGGATTC
61466618 GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT
1 GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT
61466666 GGGT
1 GGGT
61466670 TTTTATGATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (6 bp):
GGGTGT
Found at i:61469216 original size:7 final size:7
Alignment explanation
Indices: 61469206--61469231 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
61469196 TTTTATATTT
61469206 TTTAAAA
1 TTTAAAA
61469213 TTTAAAA
1 TTTAAAA
61469220 TTTAAAA
1 TTTAAAA
61469227 TTTAA
1 TTTAA
61469232 GTTTAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:61470663 original size:31 final size:31
Alignment explanation
Indices: 61470628--61470693 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
61470618 ATTTAGTTTG
* *
61470628 GTCACTCAATTTTTAGGGT-GCTTTCATTTTA
1 GTCACCCAACTTTTA-GGTCGCTTTCATTTTA
61470659 GTCACCCAACTTTTAGGTCGCTTTCATTTTA
1 GTCACCCAACTTTTAGGTCGCTTTCATTTTA
61470690 GTCA
1 GTCA
61470694 ATTAAGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.44
Consensus pattern (31 bp):
GTCACCCAACTTTTAGGTCGCTTTCATTTTA
Found at i:61477838 original size:16 final size:16
Alignment explanation
Indices: 61477814--61477848 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
61477804 AAAACTTTCT
61477814 TCACAACAACTACACA
1 TCACAACAACTACACA
*
61477830 TCACCACAACTACACA
1 TCACAACAACTACACA
61477846 TCA
1 TCA
61477849 AGATTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.14
Consensus pattern (16 bp):
TCACAACAACTACACA
Found at i:61480765 original size:2 final size:2
Alignment explanation
Indices: 61480758--61480790 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
61480748 TGTAGGCCCA
*
61480758 AT AT AT AT AT AT A- AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61480791 CAAGTCAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:61480777 original size:15 final size:15
Alignment explanation
Indices: 61480757--61480785 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
61480747 TTGTAGGCCC
61480757 AATATATATATATAA
1 AATATATATATATAA
61480772 AATATATATATATA
1 AATATATATATATA
61480786 TATATCAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATATATATATATAA
Found at i:61484851 original size:34 final size:33
Alignment explanation
Indices: 61484788--61484852 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
61484778 AGGTTAATTT
* **
61484788 TTTTTTATTTTGATTTTTTATTATAAATAAACC
1 TTTTTTATTTTCATTTTTTAACATAAATAAACC
61484821 TTTTTTATTTTCACTTTTATTAACAT-AATAAA
1 TTTTTTATTTTCA-TTTT-TTAACATAAATAAA
61484853 ATAAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 12 0.44
34 10 0.37
35 5 0.19
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (33 bp):
TTTTTTATTTTCATTTTTTAACATAAATAAACC
Found at i:61496925 original size:30 final size:29
Alignment explanation
Indices: 61496891--61496952 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
61496881 TTAAATTAGT
*
61496891 AATAAT-AAAATTATAATTTGATCTCCTAAA
1 AATAATAAAAATT-TAATTTAATCT-CTAAA
*
61496921 AATAATAAAAATTTAATTTAATCTTTAAA
1 AATAATAAAAATTTAATTTAATCTCTAAA
61496950 AAT
1 AAT
61496953 TATTAAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 7 0.24
30 16 0.55
31 6 0.21
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (29 bp):
AATAATAAAAATTTAATTTAATCTCTAAA
Found at i:61499031 original size:16 final size:16
Alignment explanation
Indices: 61499010--61499040 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
61499000 TTTTCTACTA
61499010 ATAAAAGAAATAAAAT
1 ATAAAAGAAATAAAAT
61499026 ATAAAAGAAATAAAA
1 ATAAAAGAAATAAAA
61499041 AAACTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (16 bp):
ATAAAAGAAATAAAAT
Found at i:61513188 original size:4 final size:4
Alignment explanation
Indices: 61513179--61513209 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
61513169 AGAAATAAGC
*
61513179 AAAT AAAT AAAT ACAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
61513210 ATTCATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:61514071 original size:24 final size:24
Alignment explanation
Indices: 61514044--61514089 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
61514034 GAAACACGAA
*
61514044 GCTTCTGGTAAGTTTTTTGACTTT
1 GCTTCTGGTAAGTTTTTCGACTTT
61514068 GCTTCTGGTAAGTTTTTCGACT
1 GCTTCTGGTAAGTTTTTCGACT
61514090 GTTTCCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.15, G:0.22, T:0.50
Consensus pattern (24 bp):
GCTTCTGGTAAGTTTTTCGACTTT
Found at i:61514357 original size:37 final size:37
Alignment explanation
Indices: 61514315--61514392 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
61514305 TCAACGATGA
61514315 CGACGAGAAGTGCACATTTTCCATTTTGGTGCAATGG
1 CGACGAGAAGTGCACATTTTCCATTTTGGTGCAATGG
61514352 CGACGAGAAGTGCACATTTTCCATTTTGGTGCAATGG
1 CGACGAGAAGTGCACATTTTCCATTTTGGTGCAATGG
61514389 CGAC
1 CGAC
61514393 AGGGGCGCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (37 bp):
CGACGAGAAGTGCACATTTTCCATTTTGGTGCAATGG
Found at i:61517076 original size:11 final size:11
Alignment explanation
Indices: 61517062--61517118 Score: 69
Period size: 11 Copynumber: 5.2 Consensus size: 11
61517052 ATACCCAAAC
61517062 AATAATAACAA
1 AATAATAACAA
* *
61517073 AATAGTAGCAA
1 AATAATAACAA
*
61517084 TATAATAACAA
1 AATAATAACAA
*
61517095 AATAACAACAA
1 AATAATAACAA
*
61517106 AATAATGACAA
1 AATAATAACAA
61517117 AA
1 AA
61517119 CAGTAGCAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 37 1.00
ACGTcount: A:0.67, C:0.11, G:0.05, T:0.18
Consensus pattern (11 bp):
AATAATAACAA
Found at i:61517088 original size:22 final size:22
Alignment explanation
Indices: 61517062--61517129 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 22
61517052 ATACCCAAAC
61517062 AATAATAACAAAATAGTAGCAA
1 AATAATAACAAAATAGTAGCAA
* ** *
61517084 TATAATAACAAAATAACAACAA
1 AATAATAACAAAATAGTAGCAA
* *
61517106 AATAATGACAAAACAGTAGCAA
1 AATAATAACAAAATAGTAGCAA
61517128 AA
1 AA
61517130 CAATGATAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.16
Consensus pattern (22 bp):
AATAATAACAAAATAGTAGCAA
Found at i:61518280 original size:15 final size:15
Alignment explanation
Indices: 61518256--61518285 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61518246 AAGTCGATTA
*
61518256 CATATTTTTAAATTT
1 CATATATTTAAATTT
61518271 CATATATTTAAATTT
1 CATATATTTAAATTT
61518286 TGTATCATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
CATATATTTAAATTT
Found at i:61519020 original size:53 final size:53
Alignment explanation
Indices: 61518962--61519069 Score: 171
Period size: 53 Copynumber: 2.0 Consensus size: 53
61518952 ATATTATAAA
* * *
61518962 TGTGTAATTATAAGCAATTACAAACACACGTGGTATCATATATTTTATCATAT
1 TGTGTAATTATAAACAATTACAAACACACATGGTATCATATATTTTATCACAT
* *
61519015 TGTGTAATTATAAACAATTACAAACACACATTGTTTCATATATTTTATCACAT
1 TGTGTAATTATAAACAATTACAAACACACATGGTATCATATATTTTATCACAT
61519068 TG
1 TG
61519070 ATGTTAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (53 bp):
TGTGTAATTATAAACAATTACAAACACACATGGTATCATATATTTTATCACAT
Found at i:61524130 original size:48 final size:48
Alignment explanation
Indices: 61524059--61524162 Score: 190
Period size: 48 Copynumber: 2.2 Consensus size: 48
61524049 TGGAGAAACT
61524059 ATTTCTAAGAATATTACAGGTGCAGCAAAGAGACACTAACAGTGTTTA
1 ATTTCTAAGAATATTACAGGTGCAGCAAAGAGACACTAACAGTGTTTA
*
61524107 ATTTCTAAGAATATTACAGGTGCAGCAAAGATACACTAACAGTGTTTA
1 ATTTCTAAGAATATTACAGGTGCAGCAAAGAGACACTAACAGTGTTTA
*
61524155 ATCTCTAA
1 ATTTCTAA
61524163 CAAACATACA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.29
Consensus pattern (48 bp):
ATTTCTAAGAATATTACAGGTGCAGCAAAGAGACACTAACAGTGTTTA
Found at i:61534235 original size:3 final size:3
Alignment explanation
Indices: 61534227--61534267 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
61534217 ACAAATACAA
*
61534227 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
61534268 AGTTGATAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:61538199 original size:14 final size:14
Alignment explanation
Indices: 61538182--61538226 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
61538172 CCTAAATCCC
61538182 AAACTCCAAACTCT
1 AAACTCCAAACTCT
* *
61538196 AAACTCTAAACTTT
1 AAACTCCAAACTCT
* *
61538210 AAACCCCAAACCCT
1 AAACTCCAAACTCT
61538224 AAA
1 AAA
61538227 TATTGAATCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACTCCAAACTCT
Found at i:61539164 original size:20 final size:20
Alignment explanation
Indices: 61539135--61539195 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
61539125 TTAAAAGTCC
61539135 AAAAAATATATATATTTAAT
1 AAAAAATATATATATTTAAT
* *
61539155 AAAAAGTATATTTGA-TTAA-
1 AAAAAATATATAT-ATTTAAT
61539174 AAATAAATATATATATTTAAT
1 AAA-AAATATATATATTTAAT
61539195 A
1 A
61539196 TATAATTCGG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.12
20 27 0.82
21 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
AAAAAATATATATATTTAAT
Found at i:61541528 original size:23 final size:23
Alignment explanation
Indices: 61541502--61541547 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
61541492 TAATATTTAC
61541502 GAGTCAAATGTGATTTTTTTAAA
1 GAGTCAAATGTGATTTTTTTAAA
61541525 GAGTCAAATGTGATTTTTTTAAA
1 GAGTCAAATGTGATTTTTTTAAA
61541548 AAAAAATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.43
Consensus pattern (23 bp):
GAGTCAAATGTGATTTTTTTAAA
Found at i:61541986 original size:26 final size:27
Alignment explanation
Indices: 61541946--61542002 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
61541936 ACAGAGAAGC
* *
61541946 AAAACGAAAACAGGGGA-GAAAGAAAAG
1 AAAAAGAAAACAGGGAAGGAAAG-AAAG
61541973 AAAAAGAAAA-AGGGAAGGAAAGAAAG
1 AAAAAGAAAACAGGGAAGGAAAGAAAG
61541999 AAAA
1 AAAA
61542003 TTTGGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.68, C:0.04, G:0.28, T:0.00
Consensus pattern (27 bp):
AAAAAGAAAACAGGGAAGGAAAGAAAG
Found at i:61542953 original size:22 final size:22
Alignment explanation
Indices: 61542901--61542953 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
61542891 ATTATTAGCA
61542901 CTCTCTGTTTAGCACATTTGTG
1 CTCTCTGTTTAGCACATTTGTG
* *
61542923 TTCTTTGTTTAGCAC-TTTAGTG
1 CTCTCTGTTTAGCACATTT-GTG
61542945 CTCTCTGTT
1 CTCTCTGTT
61542954 CATTAGTGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.11, C:0.21, G:0.17, T:0.51
Consensus pattern (22 bp):
CTCTCTGTTTAGCACATTTGTG
Found at i:61546655 original size:97 final size:97
Alignment explanation
Indices: 61546467--61546657 Score: 258
Period size: 97 Copynumber: 2.0 Consensus size: 97
61546457 TTCATTATGG
*
61546467 ACATGTCAAGTTGAGTAACCGGGGTGAGGTGCTTGGGTTATCATCTCACTTCGCGTCAAAAGATT
1 ACATGTCAAGTTAAGTAACCGGGGTGAGGTGCTTGGGTTATCATCTCACTTCGCGTCAAAAGATT
* ** **
61546532 TAGCTATGTCTTGAATTCGTAAAAAAAAAAGA
66 GAGCTATGTCACGAATAAGTAAAAAAAAAAGA
* * * *
61546564 ACATGTCGAGTTAAGTAACCGGGGTGAGGTGCTTGGGTTGTCATCTCATTTCGTGTCAAAAGACT
1 ACATGTCAAGTTAAGTAACCGGGGTGAGGTGCTTGGGTTATCATCTCACTTCGCGTCAAAAGA-T
**
61546629 TGA-CTATGTCACGAATAAGTTTAAAAAAA
65 TGAGCTATGTCACGAATAAGTAAAAAAAAA
61546658 TAATAAAATG
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
97 78 0.96
98 3 0.04
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.29
Consensus pattern (97 bp):
ACATGTCAAGTTAAGTAACCGGGGTGAGGTGCTTGGGTTATCATCTCACTTCGCGTCAAAAGATT
GAGCTATGTCACGAATAAGTAAAAAAAAAAGA
Found at i:61547214 original size:18 final size:19
Alignment explanation
Indices: 61547193--61547238 Score: 76
Period size: 18 Copynumber: 2.5 Consensus size: 19
61547183 CTGTAATTAG
61547193 TTTAAATTTGATTTTT-AA
1 TTTAAATTTGATTTTTAAA
61547211 TTTAAATTTGATTTTTAAA
1 TTTAAATTTGATTTTTAAA
*
61547230 TTTTAATTT
1 TTTAAATTT
61547239 ATCCAGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTAAATTTGATTTTTAAA
Found at i:61548557 original size:105 final size:106
Alignment explanation
Indices: 61548416--61548611 Score: 256
Period size: 107 Copynumber: 1.8 Consensus size: 106
61548406 CATTATAATT
* * * *
61548416 AATGTCAAGGCACGAAGTAATATTTCCCATAAAAATA-TTTTT-TAATTAATAAATCATAATATA
1 AATGTCAAGGCACGAAGTAATATTTCACAGAAAAATATTTTTTATAAATAATAAATAATAATATA
**
61548479 AATCAAATCAATCATCAAGATTATAAATTACCCTGGTTTGTC
66 AAT-AAAAAAATCATCAAGATTATAAATTACCCTGGTTTGTC
61548521 AATGTCAATGGGCACGAA-TAATA-TTCACAGAAAAATATTTTTTCATAAATAATAAATAATAAT
1 AATGTCAA--GGCACGAAGTAATATTTCACAGAAAAATATTTTTT-ATAAATAATAAATAATAAT
* *
61548584 TTAAATAAAAAAATCCTCAAGATTATAA
63 ATAAATAAAAAAATCATCAAGATTATAA
61548612 CATATTATTT
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
105 20 0.26
106 10 0.13
107 27 0.35
108 21 0.27
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (106 bp):
AATGTCAAGGCACGAAGTAATATTTCACAGAAAAATATTTTTTATAAATAATAAATAATAATATA
AATAAAAAAATCATCAAGATTATAAATTACCCTGGTTTGTC
Found at i:61548730 original size:5 final size:5
Alignment explanation
Indices: 61548716--61548749 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
61548706 CCTAAACATG
*
61548716 TTAA- TTAAT TTAAT TTAAT TTAAT TTAAA TTAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT
61548750 AATCATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TTAAT
Found at i:61551878 original size:45 final size:45
Alignment explanation
Indices: 61551817--61551982 Score: 167
Period size: 45 Copynumber: 3.7 Consensus size: 45
61551807 TTGTAGCTTT
* *
61551817 AATCTGTTTCACTGCAACTTTAGGAAGATAAGGTTTTCTATCTTC
1 AATCTGCTCCACTGCAACTTTAGGAAGATAAGGTTTTCTATCTTC
* * * * *
61551862 AATCTGCTCCATTGCAACTTCAGGGAGATAA-GATTTGTAGT-TTC
1 AATCTGCTCCACTGCAACTTTAGGAAGATAAGGTTTTCTA-TCTTC
* * **
61551906 AATCTGCTCTACTGTAACTTTA-GAGAGATAAGGTTCACTATCTTC
1 AATCTGCTCCACTGCAACTTTAGGA-AGATAAGGTTTTCTATCTTC
* * *
61551951 AATTTGTTCCACTGCAAGTTTAGGAAGATAAG
1 AATCTGCTCCACTGCAACTTTAGGAAGATAAG
61551983 ATTTGTAGCT
Statistics
Matches: 95, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
43 1 0.01
44 34 0.36
45 58 0.61
46 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTTAGGAAGATAAGGTTTTCTATCTTC
Found at i:61551925 original size:44 final size:44
Alignment explanation
Indices: 61551785--61552029 Score: 169
Period size: 44 Copynumber: 5.5 Consensus size: 44
61551775 TCTAACCCAT
* * *
61551785 TGCAACTTCAGAG-GTATAGGATTTGTAGCTTT-AATCTGTTTCAC
1 TGCAACTTCAGAGAG-ATAAGATTTGTAG-TTTCAATCTGCTCCAC
* * * *
61551829 TGCAACTTTAG-GAAGATAAGGTTTTCTA-TCTTCAATCTGCTCCAT
1 TGCAACTTCAGAG-AGATAA-GATTTGTAGT-TTCAATCTGCTCCAC
* *
61551874 TGCAACTTCAGGGAGATAAGATTTGTAGTTTCAATCTGCTCTAC
1 TGCAACTTCAGAGAGATAAGATTTGTAGTTTCAATCTGCTCCAC
* * * ** * *
61551918 TGTAACTTTAGAGAGATAAGGTTCACTA-TCTTCAATTTGTTCCAC
1 TGCAACTTCAGAGAGATAAGATT-TGTAGT-TTCAATCTGCTCCAC
* * * * **
61551963 TGCAAGTTTAG-GAAGATAAGATTTGTAGCTTCAATATGCTTTAC
1 TGCAACTTCAGAG-AGATAAGATTTGTAGTTTCAATCTGCTCCAC
*
61552007 TACAACTTCAGAGAGATAAGATT
1 TGCAACTTCAGAGAGATAAGATT
61552030 CGTAATTTGT
Statistics
Matches: 155, Mismatches: 34, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
43 2 0.01
44 86 0.55
45 66 0.43
46 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (44 bp):
TGCAACTTCAGAGAGATAAGATTTGTAGTTTCAATCTGCTCCAC
Found at i:61551925 original size:89 final size:89
Alignment explanation
Indices: 61551781--61552026 Score: 284
Period size: 89 Copynumber: 2.8 Consensus size: 89
61551771 TCATTCTAAC
* *
61551781 CCATTGCAACTTCAGAGG-TATAGGATTTGTAGCTTT-AATCTG-TTTCACTGCAACTTTAG-GA
1 CCATTGCAACTTCAG-GGAGATAAGATTTGTAG-TTTCAATCTGCTTT-ACTGCAACTTTAGAG-
**
61551842 AGATAAGGTTTTCTATCTTCAATCTGCT
62 AGATAAGGTTCACTATCTTCAATCTGCT
* *
61551870 CCATTGCAACTTCAGGGAGATAAGATTTGTAGTTTCAATCTGCTCTACTGTAACTTTAGAGAGAT
1 CCATTGCAACTTCAGGGAGATAAGATTTGTAGTTTCAATCTGCTTTACTGCAACTTTAGAGAGAT
* *
61551935 AAGGTTCACTATCTTCAATTTGTT
66 AAGGTTCACTATCTTCAATCTGCT
* * * * * * * *
61551959 CCACTGCAAGTTTAGGAAGATAAGATTTGTAGCTTCAATATGCTTTACTACAACTTCAGAGAGAT
1 CCATTGCAACTTCAGGGAGATAAGATTTGTAGTTTCAATCTGCTTTACTGCAACTTTAGAGAGAT
61552024 AAG
66 AAG
61552027 ATTCGTAATT
Statistics
Matches: 135, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
88 5 0.04
89 127 0.94
90 3 0.02
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (89 bp):
CCATTGCAACTTCAGGGAGATAAGATTTGTAGTTTCAATCTGCTTTACTGCAACTTTAGAGAGAT
AAGGTTCACTATCTTCAATCTGCT
Found at i:61552119 original size:50 final size:51
Alignment explanation
Indices: 61552009--61552120 Score: 138
Period size: 50 Copynumber: 2.2 Consensus size: 51
61551999 TGCTTTACTA
* * * * * *
61552009 CAACTTCAGAGAGATAAGATTCGTAATTTGTAGCTTTAATCCATTCCACTT
1 CAACTTCAGGGAGATAAGATTCGCAATATGTAGCTTCAATCCATCCCACTG
*
61552060 CAACTTCAGGGAGATAAGATTCGCCATAATG-A-CTTCAATCCATCCCACTG
1 CAACTTCAGGGAGATAAGATTCGCAAT-ATGTAGCTTCAATCCATCCCACTG
61552110 CAACTTCAGGG
1 CAACTTCAGGG
61552121 GTATAGGTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
50 26 0.49
51 25 0.47
52 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (51 bp):
CAACTTCAGGGAGATAAGATTCGCAATATGTAGCTTCAATCCATCCCACTG
Found at i:61556446 original size:31 final size:31
Alignment explanation
Indices: 61556408--61556469 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
61556398 AAATCAGGAG
61556408 ATAGGTTACAATCTCTGTCATCTCTAAAGTC
1 ATAGGTTACAATCTCTGTCATCTCTAAAGTC
*
61556439 ATAGGTTACAATCTCTGTTATCTCTAAAGTC
1 ATAGGTTACAATCTCTGTCATCTCTAAAGTC
61556470 CTGAGGTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (31 bp):
ATAGGTTACAATCTCTGTCATCTCTAAAGTC
Found at i:61563203 original size:52 final size:48
Alignment explanation
Indices: 61563184--61563484 Score: 357
Period size: 46 Copynumber: 6.3 Consensus size: 48
61563174 TGACAAGTGG
* *
61563184 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
* **
61563230 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
* *
61563278 GTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 ----AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
61563328 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* * *
61563380 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATGAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
61563426 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
61563472 AAAGTGATAAGTG
1 AAAGTGATAAGTG
61563485 GCTACACTTA
Statistics
Matches: 224, Mismatches: 19, Indels: 24
0.84 0.07 0.09
Matches are distributed among these distances:
46 140 0.62
52 84 0.38
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:61563238 original size:98 final size:98
Alignment explanation
Indices: 61563118--61563473 Score: 631
Period size: 98 Copynumber: 3.6 Consensus size: 98
61563108 TTTGAGTACT
*
61563118 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
61563183 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
61563216 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
61563281 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
61563314 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
* *
61563379 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* * *
61563412 TCTGATGAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAA
61563474 AGTGATAAGT
Statistics
Matches: 248, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 248 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:61563492 original size:37 final size:37
Alignment explanation
Indices: 61563448--61563556 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
61563438 GATAGCTTTA
61563448 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
61563485 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
61563522 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
61563557 ATCATACGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:61568167 original size:33 final size:32
Alignment explanation
Indices: 61568123--61568186 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
61568113 AGATTCAAAA
61568123 AAAAAAGAAAAAATAGTCACCTTTTGAAGTTT
1 AAAAAAGAAAAAATAGTCACCTTTTGAAGTTT
*
61568155 AAAAAAGAAAAAATGGTCACCTTTTGAAGTTT
1 AAAAAAGAAAAAATAGTCACCTTTTGAAGTTT
61568187 TCTTTATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.28
Consensus pattern (32 bp):
AAAAAAGAAAAAATAGTCACCTTTTGAAGTTT
Found at i:61578104 original size:9 final size:9
Alignment explanation
Indices: 61578090--61578118 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
61578080 GTTAGCAATA
61578090 AATTATAAT
1 AATTATAAT
61578099 AATTATAAT
1 AATTATAAT
61578108 AATTATAAT
1 AATTATAAT
61578117 AA
1 AA
61578119 AAATTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AATTATAAT
Found at i:61586475 original size:18 final size:19
Alignment explanation
Indices: 61586448--61586487 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
61586438 AGACATATAG
61586448 TATTTATAACTAT-AATTA
1 TATTTATAACTATAAATTA
* *
61586466 TATTTGTAACTTTAAATTA
1 TATTTATAACTATAAATTA
61586485 TAT
1 TAT
61586488 AAATACGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (19 bp):
TATTTATAACTATAAATTA
Found at i:61586550 original size:21 final size:20
Alignment explanation
Indices: 61586524--61586568 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
61586514 ATTCACAATT
61586524 TTAAACATCAAATA-AATAATA
1 TTAAACAT-AAATATAATAA-A
*
61586545 TTAAACATATATATAATAAA
1 TTAAACATAAATATAATAAA
61586565 TTAA
1 TTAA
61586569 TAATTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAACATAAATATAATAAA
Found at i:61587926 original size:4 final size:4
Alignment explanation
Indices: 61587917--61587942 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
61587907 ACATGATTAT
61587917 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
61587943 GTAACTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:61589671 original size:19 final size:18
Alignment explanation
Indices: 61589644--61589683 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
61589634 CTTTTTGTAA
61589644 TTGGACTTGTAATTTTTAT
1 TTGGACTTGTAA-TTTTAT
* *
61589663 TTGGGCTTGTGATTTTAT
1 TTGGACTTGTAATTTTAT
61589681 TTG
1 TTG
61589684 TTTATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.15, C:0.05, G:0.23, T:0.57
Consensus pattern (18 bp):
TTGGACTTGTAATTTTAT
Found at i:61591438 original size:55 final size:55
Alignment explanation
Indices: 61591375--61591479 Score: 201
Period size: 55 Copynumber: 1.9 Consensus size: 55
61591365 TTAACAGATA
*
61591375 ATATCCCATAATAATATCCTATAATATCCCATTAGGAATCAAATTGCTAAGAAGT
1 ATATCCCATAATAATATCCTATAATATCCCAATAGGAATCAAATTGCTAAGAAGT
61591430 ATATCCCATAATAATATCCTATAATATCCCAATAGGAATCAAATTGCTAA
1 ATATCCCATAATAATATCCTATAATATCCCAATAGGAATCAAATTGCTAA
61591480 AAGATAATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (55 bp):
ATATCCCATAATAATATCCTATAATATCCCAATAGGAATCAAATTGCTAAGAAGT
Found at i:61593074 original size:156 final size:156
Alignment explanation
Indices: 61592779--61593102 Score: 441
Period size: 156 Copynumber: 2.1 Consensus size: 156
61592769 ACAAGTGCGA
* *
61592779 AAGTTTCATTATAGTCAATTCCTTCTACCTAATGATTACCAAAAACAACAAGACGAGTTTTAAGT
1 AAGTGTCATTATAGTCAATTCCTTCTACCTAATGATTACCAAAAACAACAAGACGAGCTTTAAGT
* * *** * ** *
61592844 CTCTTCATACTTCCATCGGAGTTATATTTAATCTTGTACTGTCACTTATTACTTATTGTTTTATT
66 CTCTTAATACTTCCATCAGAGTTATATTTAATCTTGTACACCCACTTACTACCCAGTGTTTTATT
* * * *
61592909 TATAGGAGGAAGTATTTCTATAGACC
131 TACAAGAGGAAGTATTTCCACAGACC
* * * *
61592935 AAGTGTTATTATAGTCAATTCCTTCTACCTAGTGATTACCAAAAACAACAAGATGTGCTTTAAGT
1 AAGTGTCATTATAGTCAATTCCTTCTACCTAATGATTACCAAAAACAACAAGACGAGCTTTAAGT
* *
61593000 CTCTTAATACTTCCATTAGAGTTATATTTAATCTTGTACACCCACTTACTACCCAGTGTTTTCTT
66 CTCTTAATACTTCCATCAGAGTTATATTTAATCTTGTACACCCACTTACTACCCAGTGTTTTATT
* *
61593065 TCCAAGAGGAAGTGTTTCCACAGACC
131 TACAAGAGGAAGTATTTCCACAGACC
61593091 AAGTGTCATTAT
1 AAGTGTCATTAT
61593103 CCTCTAAAGC
Statistics
Matches: 144, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
156 144 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (156 bp):
AAGTGTCATTATAGTCAATTCCTTCTACCTAATGATTACCAAAAACAACAAGACGAGCTTTAAGT
CTCTTAATACTTCCATCAGAGTTATATTTAATCTTGTACACCCACTTACTACCCAGTGTTTTATT
TACAAGAGGAAGTATTTCCACAGACC
Found at i:61595229 original size:59 final size:56
Alignment explanation
Indices: 61595123--61595279 Score: 251
Period size: 59 Copynumber: 2.8 Consensus size: 56
61595113 AGTAGTCACG
* *
61595123 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTATAATATCTCAT
1 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCATATAATATCCCAT
*
61595179 TAGGAATCAAATTGCTAAGAAGAAATAATATCTCATAATAATATCATATAATATCCCAT
1 TAGGAATCAAATTGCTAA-AAG--ATAATATCCCATAATAATATCATATAATATCCCAT
*
61595238 TAGGAATCAAATTGATAAAAGATAATATCCCATAATAATATC
1 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATC
61595280 CTGACAGATC
Statistics
Matches: 93, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
56 38 0.41
57 3 0.03
58 3 0.03
59 49 0.53
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (56 bp):
TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCATATAATATCCCAT
Found at i:61597294 original size:243 final size:228
Alignment explanation
Indices: 61596884--61597338 Score: 523
Period size: 243 Copynumber: 1.9 Consensus size: 228
61596874 ATATTAATAC
*
61596884 ATATATAACTATTATAATAGAGATTATAATAAAATATATAGTATTAAATGATATTATAATGGTTA
1 ATATATAACTATTATAATAGAGATTATAATAAAATATATAGTATTAAATGATACTATAATGGTTA
* * * *
61596949 ATTATCGATGCATATATATAAATTATTAATTTATTATATGATGTCATATAACACTATATAATATA
66 ATTATCGATACATATATATAAACTATTAATTTATTATATGATATCATATAACAATATATAATATA
* ** * * * * *
61597014 GTAGGAGGGATAATTTTTAAATATACGAAAAGTATAGGGGCTTAGAGCATATTTCAACTAGTATA
131 ATAAAAGGGATAACTTTCAAATATACGAAAAGTATAGGGACTTAGAGCATATTTCAACCAATATA
61597079 ACAATAAACAATAATATTTAATGTACTATTGTT
196 ACAATAAACAATAATATTTAATGTACTATTGTT
* ** *
61597112 ATATATAACTATTATTATATTATAGATTATAATAAAATATATAGTATTACGTGATACTATAATGT
1 ATATATAACTATTA-TA-A-TAGAGATTATAATAAAATATATAGTATTAAATGATACTATAATGG
** *
61597177 TTAATAAATATTTATACATATATATAAACTATTAATATATATTATATACTATATCGTATGATATA
63 TTAAT---TATCGATACATATATATAAACTATTAAT-T-TATTATAT--GATATC--AT-ATA-A
* * * * *
61597242 GAATAATATAATATAATAAAAGGGTTAACTTTCAAATGTATGAAACGTATAGGGACTTAGAGCAT
117 CAAT-ATATAATATAATAAAAGGGATAACTTTCAAATATACGAAAAGTATAGGGACTTAGAGCAT
* **
61597307 ATTTCAACCAATATAATAATAAGTAATAATAT
181 ATTTCAACCAATATAACAATAAACAATAATAT
61597339 ATGATAAAAA
Statistics
Matches: 184, Mismatches: 28, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
228 14 0.08
229 2 0.01
230 1 0.01
231 45 0.24
234 24 0.13
235 1 0.01
236 8 0.04
238 4 0.02
240 2 0.01
241 3 0.02
242 3 0.02
243 77 0.42
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.38
Consensus pattern (228 bp):
ATATATAACTATTATAATAGAGATTATAATAAAATATATAGTATTAAATGATACTATAATGGTTA
ATTATCGATACATATATATAAACTATTAATTTATTATATGATATCATATAACAATATATAATATA
ATAAAAGGGATAACTTTCAAATATACGAAAAGTATAGGGACTTAGAGCATATTTCAACCAATATA
ACAATAAACAATAATATTTAATGTACTATTGTT
Found at i:61602406 original size:34 final size:35
Alignment explanation
Indices: 61602362--61602428 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
61602352 CAGTAAAATG
61602362 TTTTCCGTAAAATGATTT-CTGAAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
61602396 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
61602429 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:61607361 original size:10 final size:9
Alignment explanation
Indices: 61607339--61607369 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
61607329 GTAATTGTTT
61607339 AAAAATGGC
1 AAAAATGGC
61607348 AAAAATGGC
1 AAAAATGGC
*
61607357 AAAAATGAC
1 AAAAATGGC
61607366 AAAA
1 AAAA
61607370 TTTCAAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.65, C:0.10, G:0.16, T:0.10
Consensus pattern (9 bp):
AAAAATGGC
Found at i:61609795 original size:41 final size:41
Alignment explanation
Indices: 61609722--61609877 Score: 177
Period size: 41 Copynumber: 3.8 Consensus size: 41
61609712 TTCTATGGGC
* * * *
61609722 TTTAGCGGTGTTTATGAAAAAGCGCCGGTAATGTTCGGGGT
1 TTTAACGGCGTTTATGAAAAAGCGCCGCTAATGCTCGGGGT
* * * *
61609763 TTTAATGGCGTTTATGAAAAAGCACCGCTAATGCTCTGAGT
1 TTTAACGGCGTTTATGAAAAAGCGCCGCTAATGCTCGGGGT
* * *
61609804 TTTAACGGCGTTTATGAAAAAACGCCACTAATGCTCGGGGA
1 TTTAACGGCGTTTATGAAAAAGCGCCGCTAATGCTCGGGGT
* * * *
61609845 TTTAGCGGCGTTTTTAAAAAAGCGCTGCTAATG
1 TTTAACGGCGTTTATGAAAAAGCGCCGCTAATG
61609878 TTCCAGGATT
Statistics
Matches: 94, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (41 bp):
TTTAACGGCGTTTATGAAAAAGCGCCGCTAATGCTCGGGGT
Found at i:61609875 original size:82 final size:82
Alignment explanation
Indices: 61609722--61609877 Score: 195
Period size: 82 Copynumber: 1.9 Consensus size: 82
61609712 TTCTATGGGC
* * * ** * * * *
61609722 TTTAGCGGTGTTTATGAAAAAGCGCCGGTAATGTTCGGGGTTTTAATGGCGTTTATGAAAAAGCA
1 TTTAACGGCGTTTATGAAAAAACGCCACTAATGCTCGGGGATTTAACGGCGTTTATAAAAAAGCA
61609787 CCGCTAATGCTCTGAGT
66 CCGCTAATGCTCTGAGT
* * *
61609804 TTTAACGGCGTTTATGAAAAAACGCCACTAATGCTCGGGGATTTAGCGGCGTTTTTAAAAAAGCG
1 TTTAACGGCGTTTATGAAAAAACGCCACTAATGCTCGGGGATTTAACGGCGTTTATAAAAAAGCA
*
61609869 CTGCTAATG
66 CCGCTAATG
61609878 TTCCAGGATT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
82 61 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (82 bp):
TTTAACGGCGTTTATGAAAAAACGCCACTAATGCTCGGGGATTTAACGGCGTTTATAAAAAAGCA
CCGCTAATGCTCTGAGT
Found at i:61609900 original size:82 final size:82
Alignment explanation
Indices: 61609722--61609906 Score: 192
Period size: 82 Copynumber: 2.2 Consensus size: 82
61609712 TTCTATGGGC
* * ** * * * *
61609722 TTTAGCGGTGTTTATGAAAAAGCGCCGGTAATGTTCGGGGTTTTAATGGCGTTTATGAAAAAGCA
1 TTTAGCGGCGTTTATGAAAAAACGCCACTAATGCTCGGGGATTTAACGGCGTTTATAAAAAAGCA
* *
61609787 CCGCTAATGCTCTGAGT
66 CCGCTAATGCTCAGAGA
* * * *
61609804 TTTAACGGCGTTTATGAAAAAACGCCACTAATGCTCGGGGATTTAGCGGCGTTTTTAAAAAAGCG
1 TTTAGCGGCGTTTATGAAAAAACGCCACTAATGCTCGGGGATTTAACGGCGTTTATAAAAAAGCA
* *
61609869 CTGCTAATGTTCCAG-GA
66 CCGCTAATGCT-CAGAGA
*
61609886 TTTAGCGGCATTTATAGAAAA
1 TTTAGCGGCGTTTAT-GAAAA
61609907 GCACCGCTCG
Statistics
Matches: 83, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
82 76 0.92
83 7 0.08
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (82 bp):
TTTAGCGGCGTTTATGAAAAAACGCCACTAATGCTCGGGGATTTAACGGCGTTTATAAAAAAGCA
CCGCTAATGCTCAGAGA
Found at i:61610424 original size:14 final size:14
Alignment explanation
Indices: 61610407--61610441 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
61610397 ATTTTTAGGG
61610407 GTTAGGGGTT-AGA
1 GTTAGGGGTTAAGA
61610420 TGTTAGGGGTTAAGA
1 -GTTAGGGGTTAAGA
61610435 GTTAGGG
1 GTTAGGG
61610442 ATTTAAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.23, C:0.00, G:0.46, T:0.31
Consensus pattern (14 bp):
GTTAGGGGTTAAGA
Found at i:61610702 original size:14 final size:14
Alignment explanation
Indices: 61610685--61610719 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
61610675 TTGAAATTTA
61610685 AAGGTTTAGGGGTT
1 AAGGTTTAGGGGTT
*
61610699 AAGGGTTAGGGGTT
1 AAGGTTTAGGGGTT
61610713 AGAGGTT
1 A-AGGTT
61610720 AAGAAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.23, C:0.00, G:0.46, T:0.31
Consensus pattern (14 bp):
AAGGTTTAGGGGTT
Found at i:61610935 original size:18 final size:18
Alignment explanation
Indices: 61610912--61610946 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
61610902 TGTATTGAAT
61610912 GGTTAACTT-AGGGTTTAA
1 GGTTAA-TTAAGGGTTTAA
61610930 GGTTAATTAAGGGTTTA
1 GGTTAATTAAGGGTTTA
61610947 GTACTTGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.40
Consensus pattern (18 bp):
GGTTAATTAAGGGTTTAA
Found at i:61619208 original size:8 final size:8
Alignment explanation
Indices: 61619195--61619221 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
61619185 GAGAATCAAT
61619195 ATTTCATA
1 ATTTCATA
61619203 ATTTCATA
1 ATTTCATA
61619211 ATTTCATA
1 ATTTCATA
61619219 ATT
1 ATT
61619222 ATGAAATACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (8 bp):
ATTTCATA
Found at i:61633304 original size:19 final size:19
Alignment explanation
Indices: 61633282--61633325 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
61633272 TTTTTGGAAT
*
61633282 TTTTATGAAATTTT-TATAA
1 TTTTATG-AATTTTAAATAA
*
61633301 TTTTTTGAATTTTAAATAA
1 TTTTATGAATTTTAAATAA
61633320 TTTTAT
1 TTTTAT
61633326 TTTTTATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTATGAATTTTAAATAA
Found at i:61634176 original size:26 final size:26
Alignment explanation
Indices: 61634147--61634203 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
61634137 TTCTAGATTT
61634147 TTTTTTA-ATTTTTTTAACTTTATATA
1 TTTTTTAGATTTTTTTAA-TTTATATA
*
61634173 TTTTTTAGATTTTTTTAATTTCTATA
1 TTTTTTAGATTTTTTTAATTTATATA
*
61634199 ATTTT
1 TTTTT
61634204 AAAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTTTAGATTTTTTTAATTTATATA
Found at i:61634296 original size:21 final size:20
Alignment explanation
Indices: 61634217--61634290 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
61634207 AAATATAAAT
*
61634217 TTTTGGATTTTTTATAAA-TA
1 TTTTGAATTTTTTA-AAATTA
** *
61634237 TTTTGAATTTTAAAAAATCA
1 TTTTGAATTTTTTAAAATTA
61634257 TTTTGAATTTTTTAAAATTA
1 TTTTGAATTTTTTAAAATTA
61634277 TTTTGAATTATTTT
1 TTTTGAATT-TTTT
61634291 GTAATTTTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
19 3 0.07
20 38 0.84
21 4 0.09
ACGTcount: A:0.34, C:0.01, G:0.07, T:0.58
Consensus pattern (20 bp):
TTTTGAATTTTTTAAAATTA
Found at i:61634383 original size:9 final size:9
Alignment explanation
Indices: 61634369--61634399 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
61634359 CACCAATATG
61634369 TTATTTGAA
1 TTATTTGAA
61634378 TTATTTGAA
1 TTATTTGAA
*
61634387 TTATTCGAA
1 TTATTTGAA
61634396 TTAT
1 TTAT
61634400 AAAGTTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (9 bp):
TTATTTGAA
Found at i:61641364 original size:37 final size:37
Alignment explanation
Indices: 61641316--61641393 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
61641306 TACTTTAGGG
61641316 TGCATGCCACCATATAATCACATCTTACACTAGATCA
1 TGCATGCCACCATATAATCACATCTTACACTAGATCA
61641353 TGCATGCCACCATATAATCACATCTTACACTAGATCA
1 TGCATGCCACCATATAATCACATCTTACACTAGATCA
61641390 TGCA
1 TGCA
61641394 AAGAGAACTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.27
Consensus pattern (37 bp):
TGCATGCCACCATATAATCACATCTTACACTAGATCA
Found at i:61641727 original size:34 final size:34
Alignment explanation
Indices: 61641649--61641736 Score: 97
Period size: 33 Copynumber: 2.6 Consensus size: 34
61641639 CGAGTGAGAT
* **
61641649 AGGGTTTGGGGAAAAGCAAAAGGAAAAAAGTTTTTA
1 AGGGTTTGGGG-AAAGTAAAAGGAAAAAAG-TTAAA
*
61641685 GGGGTTTGGGGAAAGTAAAAGGAAAAAA-TTAAA
1 AGGGTTTGGGGAAAGTAAAAGGAAAAAAGTTAAA
* *
61641718 AGGGTTTTGGAAAAGTAAA
1 AGGGTTTGGGGAAAGTAAA
61641737 TGTTTTAGGG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
33 19 0.42
35 16 0.36
36 10 0.22
ACGTcount: A:0.45, C:0.01, G:0.32, T:0.22
Consensus pattern (34 bp):
AGGGTTTGGGGAAAGTAAAAGGAAAAAAGTTAAA
Found at i:61641750 original size:53 final size:54
Alignment explanation
Indices: 61641692--61641812 Score: 158
Period size: 54 Copynumber: 2.3 Consensus size: 54
61641682 TTAGGGGTTT
*
61641692 GGGGAAAGTAAAAGGAAAAAA-TTAAA-AGGGTTTTGGAAAAGTA-AATGTTTTAG
1 GGGGAAAGTAAAAGGAAAAAAGTTAAAGA-GGTTTGGGAAAAGTACAAT-TTTTAG
*** *
61641745 GGGGAAAGTAAAAGGAAAAAAGTTTTGGAGGTTTGGGGAAAGTACAATTTTTAG
1 GGGGAAAGTAAAAGGAAAAAAGTTAAAGAGGTTTGGGAAAAGTACAATTTTTAG
61641799 GGGGAAAGTAAAAG
1 GGGGAAAGTAAAAG
61641813 TGTTTGAAGA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
53 21 0.35
54 35 0.58
55 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.32, T:0.23
Consensus pattern (54 bp):
GGGGAAAGTAAAAGGAAAAAAGTTAAAGAGGTTTGGGAAAAGTACAATTTTTAG
Found at i:61642894 original size:23 final size:21
Alignment explanation
Indices: 61642868--61642909 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
61642858 TTTTGTCCTA
*
61642868 CTTTTATTTTCAAGAATTTAATC
1 CTTTTAATTTC-AG-ATTTAATC
61642891 CTTTTAATTTCAGATTTAA
1 CTTTTAATTTCAGATTTAA
61642910 AATTGTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 2 0.11
23 10 0.56
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.52
Consensus pattern (21 bp):
CTTTTAATTTCAGATTTAATC
Found at i:61649616 original size:28 final size:27
Alignment explanation
Indices: 61649559--61649619 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 27
61649549 AAAAGGGTAC
* *
61649559 AAAATATATACATGTACATATATAAAA
1 AAAATATATACATATACATAGATAAAA
*
61649586 AAAATTATATACATATATATAGATTATAAA
1 AAAA-TATATACATATACATAGA-TA-AAA
61649616 AAAA
1 AAAA
61649620 AGATAATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.14
28 15 0.54
29 2 0.07
30 7 0.25
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (27 bp):
AAAATATATACATATACATAGATAAAA
Found at i:61649631 original size:32 final size:33
Alignment explanation
Indices: 61649577--61649638 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
61649567 TACATGTACA
*
61649577 TATATAAAAAAAATTATATACATATATATAGAT
1 TATATAAAAAAAATAATATACATATATATAGAT
61649610 TATA-AAAAAAAGATAAT-TACATATATATA
1 TATATAAAAAAA-ATAATATACATATATATA
61649639 TAAACAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 19 0.70
33 8 0.30
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (33 bp):
TATATAAAAAAAATAATATACATATATATAGAT
Found at i:61649831 original size:17 final size:17
Alignment explanation
Indices: 61649809--61649852 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
61649799 TAGGAAATAA
61649809 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
61649826 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
61649843 -ATATGTATAT
1 AAAATGTATAT
61649853 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:61649891 original size:66 final size:60
Alignment explanation
Indices: 61649760--61649892 Score: 142
Period size: 60 Copynumber: 2.1 Consensus size: 60
61649750 CAAAGTAAAA
* * *
61649760 AATATATAAAAGTATATATATATATATGCATATAAAAGTTAGGAAATAAAAAATGTATAT
1 AATATATAAAAGTAAATATATATATATGCATATAAAAGTTAGCAAATAAAAAATATATAT
* * * *
61649820 -GTATATAAAATGTAAATGTATATATATGTATATAAAAGTTATGCAAATAGAATAATAATAATAA
1 AATATATAAAA-GTAAATATATATATATGCATATAAAAGTTA-GCAAATA-AAAAAT-AT-AT-A
61649884 T
60 T
61649885 AATATATA
1 AATATATA
61649893 TAATATGTGC
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
59 9 0.16
60 27 0.47
61 6 0.10
62 5 0.09
63 1 0.02
64 2 0.03
65 2 0.03
66 6 0.10
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.35
Consensus pattern (60 bp):
AATATATAAAAGTAAATATATATATATGCATATAAAAGTTAGCAAATAAAAAATATATAT
Found at i:61649989 original size:3 final size:3
Alignment explanation
Indices: 61649981--61650031 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
61649971 GTATATATAG
* *
61649981 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
61650029 TAA
1 TAA
61650032 CTTAATAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:61651372 original size:29 final size:30
Alignment explanation
Indices: 61651340--61651401 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
61651330 AATTTTTTAG
**
61651340 ATTT-TATTTTTCTAGAATTTTTATATAGA
1 ATTTCTATTTTTAAAGAATTTTTATATAGA
*
61651369 ATTTTCTATTTTTAAATAATTTTTATATAGA
1 A-TTTCTATTTTTAAAGAATTTTTATATAGA
61651400 AT
1 AT
61651402 CAATGTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 1 0.04
30 4 0.14
31 23 0.82
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (30 bp):
ATTTCTATTTTTAAAGAATTTTTATATAGA
Found at i:61653019 original size:16 final size:16
Alignment explanation
Indices: 61652988--61653024 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
61652978 ATGTGAAGAA
61652988 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
61653004 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
61653020 TATTA
1 TATTA
61653025 AAATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:61653084 original size:16 final size:16
Alignment explanation
Indices: 61653038--61653087 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
61653028 TAAAATAAAA
61653038 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
**
61653055 A-A--AATAATAAATT
1 ATATTAATAATTTATT
61653068 ATATTAATAATTTATT
1 ATATTAATAATTTATT
61653084 ATAT
1 ATAT
61653088 GATTAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
16 14 0.54
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:61653095 original size:29 final size:30
Alignment explanation
Indices: 61653019--61653084 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 30
61653009 TTAAAATTTA
*
61653019 TTATTAAAATAAAATAAA-AATATTAAATAAT
1 TTATTAAAAT--AATAAATTATATTAAATAAT
61653050 TTATTAAAATAATAAATTATATT-AATAAT
1 TTATTAAAATAATAAATTATATTAAATAAT
61653079 TTATTA
1 TTATTA
61653085 TATGATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 18 0.55
30 5 0.15
31 10 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TTATTAAAATAATAAATTATATTAAATAAT
Found at i:61653104 original size:26 final size:26
Alignment explanation
Indices: 61653028--61653105 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 26
61653018 ATTATTAAAA
61653028 TAAAATAA-AAATATTAAATAATTTAT
1 TAAAATAATAAATA-TAAATAATTTAT
61653054 TAAAATAATAAATTATATTAATAATTTAT
1 TAAAATAATAAA-TATA--AATAATTTAT
* *
61653083 T-ATATGATTAAATATAAATAATT
1 TAAAAT-AATAAATATAAATAATT
61653106 AAATATGTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
26 15 0.33
27 5 0.11
28 9 0.20
29 16 0.36
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (26 bp):
TAAAATAATAAATATAAATAATTTAT
Found at i:61653151 original size:13 final size:14
Alignment explanation
Indices: 61653131--61653162 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
61653121 ATAATATGAA
61653131 AATA-TAATATTTT
1 AATATTAATATTTT
61653144 -ATATTAATATTTT
1 AATATTAATATTTT
61653157 AATATT
1 AATATT
61653163 TTTAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 9 0.53
14 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATATTAATATTTT
Found at i:61654933 original size:29 final size:27
Alignment explanation
Indices: 61654900--61654954 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
61654890 TAGAATCCAA
61654900 TCTTTATT-TTTTTTATTTTAAAAATTTAT
1 TCTTT-TTATTTTTTA-TTT-AAAATTTAT
61654929 TCTTTTTATTTTTTATTTAAAATTTA
1 TCTTTTTATTTTTTATTTAAAATTTA
61654955 ATTTTAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 8 0.32
28 5 0.20
29 12 0.48
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (27 bp):
TCTTTTTATTTTTTATTTAAAATTTAT
Found at i:61664045 original size:9 final size:9
Alignment explanation
Indices: 61664031--61664096 Score: 89
Period size: 9 Copynumber: 7.2 Consensus size: 9
61664021 TTTGGTTAAA
61664031 AATTACCCG
1 AATTACCCG
61664040 AATTACCCG
1 AATTACCCG
*
61664049 -ATTAACCG
1 AATTACCCG
*
61664057 AATTAACCG
1 AATTACCCG
61664066 AATTACCCG
1 AATTACCCG
61664075 AAAATTACCCG
1 --AATTACCCG
61664086 AATTACCCG
1 AATTACCCG
61664095 AA
1 AA
61664097 AATTACCCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
8 7 0.13
9 36 0.69
11 9 0.17
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (9 bp):
AATTACCCG
Found at i:61664104 original size:20 final size:18
Alignment explanation
Indices: 61664031--61664096 Score: 89
Period size: 20 Copynumber: 3.6 Consensus size: 18
61664021 TTTGGTTAAA
61664031 AATTACCCGAATTACCCG
1 AATTACCCGAATTACCCG
* *
61664049 -ATTAACCGAATTAACCG
1 AATTACCCGAATTACCCG
61664066 AATTACCCGAAAATTACCCG
1 AATTACCCG--AATTACCCG
61664086 AATTACCCGAA
1 AATTACCCGAA
61664097 AATTACCCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 15 0.37
18 9 0.22
20 17 0.41
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (18 bp):
AATTACCCGAATTACCCG
Found at i:61664109 original size:11 final size:11
Alignment explanation
Indices: 61664066--61664108 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
61664056 GAATTAACCG
61664066 AATTACCCGAA
1 AATTACCCGAA
61664077 AATTACCCG--
1 AATTACCCGAA
61664086 AATTACCCGAA
1 AATTACCCGAA
61664097 AATTACCC-AA
1 AATTACCCGAA
61664107 AA
1 AA
61664109 AGTTTGGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.30
10 4 0.13
11 17 0.57
ACGTcount: A:0.47, C:0.28, G:0.07, T:0.19
Consensus pattern (11 bp):
AATTACCCGAA
Found at i:61666456 original size:16 final size:16
Alignment explanation
Indices: 61666435--61666468 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
61666425 AGTTATTACT
61666435 TTAATTTTT-TTATAAA
1 TTAATTTTTCTT-TAAA
61666451 TTAATTTTTCTTTAAA
1 TTAATTTTTCTTTAAA
61666467 TT
1 TT
61666469 TTTTAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTAATTTTTCTTTAAA
Found at i:61668944 original size:31 final size:31
Alignment explanation
Indices: 61668906--61668966 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
61668896 GGGATGAACA
*
61668906 TGTTGGGTCCGTCTCCTGTACTGGGTACAAC
1 TGTTGGGTCCGTCTCCTGTACTGAGTACAAC
61668937 TGTTGGGTCCGTCTCCTGTACTGAGTACAA
1 TGTTGGGTCCGTCTCCTGTACTGAGTACAA
61668967 TTATATGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.25, G:0.28, T:0.33
Consensus pattern (31 bp):
TGTTGGGTCCGTCTCCTGTACTGAGTACAAC
Found at i:61688582 original size:21 final size:21
Alignment explanation
Indices: 61688556--61688596 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
61688546 ATCTGCTCAA
* *
61688556 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
61688577 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
61688597 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Done.