Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 78
Found at i:1023473 original size:31 final size:31
Alignment explanation
Indices: 1023438--1023501 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1023428 AAATTGTGCT
*
1023438 ATTCATTTATAATCTTGCTAATAAACGGGTG
1 ATTCATTTATAATCTTACTAATAAACGGGTG
* * * *
1023469 ATTCATTTGTACTTTTACTAATAAATGGGTG
1 ATTCATTTATAATCTTACTAATAAACGGGTG
1023500 AT
1 AT
1023502 CTGTAGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (31 bp):
ATTCATTTATAATCTTACTAATAAACGGGTG
Found at i:1024043 original size:16 final size:16
Alignment explanation
Indices: 1024024--1024057 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1024014 CAATATACGA
1024024 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
1024040 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
1024056 AT
1 AT
1024058 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:1025250 original size:34 final size:35
Alignment explanation
Indices: 1025212--1025283 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
1025202 TTGAATTTAA
*
1025212 TGAATTA-TTTGGAATTTAGGGTTTAGAATGAAAT
1 TGAATTACTTTGGAAATTAGGGTTTAGAATGAAAT
*
1025246 TGAATTACTTTGGAAATTGGGGTTTAGAATGAAAT
1 TGAATTACTTTGGAAATTAGGGTTTAGAATGAAAT
1025281 TGA
1 TGA
1025284 GTACTGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 7 0.20
35 28 0.80
ACGTcount: A:0.35, C:0.01, G:0.25, T:0.39
Consensus pattern (35 bp):
TGAATTACTTTGGAAATTAGGGTTTAGAATGAAAT
Found at i:1025770 original size:24 final size:27
Alignment explanation
Indices: 1025725--1025773 Score: 68
Period size: 24 Copynumber: 1.9 Consensus size: 27
1025715 TAAATTGACA
*
1025725 ATTATTATATTTTCGTAGTATTATGGT
1 ATTATTATATTTTCATAGTATTATGGT
1025752 ATTATT-TATTTT-ATA-TATTATG
1 ATTATTATATTTTCATAGTATTATG
1025774 CCAATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 2 0.10
26 6 0.29
27 6 0.29
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (27 bp):
ATTATTATATTTTCATAGTATTATGGT
Found at i:1026689 original size:28 final size:28
Alignment explanation
Indices: 1026656--1026730 Score: 116
Period size: 28 Copynumber: 2.7 Consensus size: 28
1026646 CATTTATATT
1026656 GTTGAACTAGTGCTTGAAATATTATGCC
1 GTTGAACTAGTGCTTGAAATATTATGCC
1026684 GTTGAACTAGTGCTTGAAATATTATGCC
1 GTTGAACTAGTGCTTGAAATATTATGCC
* *
1026712 ATTGAA-TCAGTGTTTGAAA
1 GTTGAACT-AGTGCTTGAAA
1026731 GCAACGGTGG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.98
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (28 bp):
GTTGAACTAGTGCTTGAAATATTATGCC
Found at i:1031747 original size:53 final size:53
Alignment explanation
Indices: 1031580--1032157 Score: 746
Period size: 53 Copynumber: 10.7 Consensus size: 53
1031570 TGGGTTCGCT
* ** * ** *
1031580 CCCTATTTCTTCAGAGGGTATAAGACTTGA-ATCATCTTCAACAAACTTGTTTGCC
1 CCCTATTTCTTCAGAGAGTATAAGAC-CCACA--ATCTTCAACAATCGCGTCTGCC
* * *
1031635 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATCGCGTCTGCC
* * *
1031690 CCCTATTTCTTCAGAGAGTATAAGACCCATAATCTTCATCAATCGCATCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCTGCC
* * *
1031743 CCCTA-TTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTC-TTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATCGCGTCTGCC
* * *
1031798 CCCTATTTCTTCAGAGAGTATAAGACCCATAATCTTCATCAATCGCATCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCTGCC
* * * *
1031851 CCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATCGCGTCTGCC
* *
1031906 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCTGCC
* * *
1031959 CCCTATTTCTTCAAAGAGTATAAGACCCGAACAATCTTCAACTATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACCC--ACAATCTTCAACAATCGCGTCTGCC
*
1032014 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCTGCC
* *
1032067 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCTGCC
*
1032120 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCA
1 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCA
1032158 TCAAATGGGT
Statistics
Matches: 460, Mismatches: 53, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
52 3 0.01
53 244 0.53
54 5 0.01
55 203 0.44
56 4 0.01
57 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (53 bp):
CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCTGCC
Found at i:1031758 original size:108 final size:108
Alignment explanation
Indices: 1031631--1032161 Score: 915
Period size: 108 Copynumber: 4.9 Consensus size: 108
1031621 CAAACTTGTT
1031631 TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
1 TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
*
1031696 TTCTTCAGAGAGTATAAGACCCATAATCTTCATCAATCGCATC
66 TTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATC
1031739 TGCCCCCTA-TTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTA
1 TGCCCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTA
*
1031803 TTTCTTCAGAGAGTATAAGACCCATAATCTTCATCAATCGCATC
65 TTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATC
*
1031847 TGCCCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
1 TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
1031912 TTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATC
66 TTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATC
* * *
1031955 TGCCCCCTATTTCTTCAAAGAGTATAAGACCCGAACAATCTTCAACTATTGCGTCTGCCCCCTAT
1 TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
*
1032020 TTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTC
66 TTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATC
* * * * *
1032063 TGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATCGTGTCTGCTCCCTAT
1 TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
*
1032126 TTCTTCAGAGAGTATAAGACTCACAATCTTCATCAA
66 TTCTTCAGAGAGTATAAGACCCACAATCTTCATCAA
1032162 ATGGGTTCGC
Statistics
Matches: 407, Mismatches: 14, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
106 62 0.15
107 4 0.01
108 339 0.83
109 2 0.00
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (108 bp):
TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
TTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATC
Found at i:1032215 original size:53 final size:53
Alignment explanation
Indices: 1032158--1032513 Score: 433
Period size: 51 Copynumber: 6.8 Consensus size: 53
1032148 ACAATCTTCA
* * * * *
1032158 TCAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTCGAACATCTCT
1 TCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCT
*
1032211 TCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAATTCGAACATCTTCT
1 TCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATC-TCT
** * *
1032265 TCTTACGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAACA--TCT
1 TCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCT
* * * *
1032316 TCAAAACGGGTTCGC-CCTTCTTTCATTAAGGAGTATGGAACTCG--GATATCT
1 TC-AAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCT
* * * * *
1032367 TCACACGGGTTCGCTCC-TCTTTCTCTAGGGAGTATGGAACT-TAGACATCTCT
1 TCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGA-ACATCTCT
*
1032419 TCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACA--TCT
1 TCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCT
*
1032470 TCAAACGGGTTCGTTCCTTCTTTCTTTAAGGAGTATAGAACTCG
1 TCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCG
1032514 CATATCTTCA
Statistics
Matches: 262, Mismatches: 31, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
49 1 0.00
50 32 0.12
51 82 0.31
52 31 0.12
53 69 0.26
54 47 0.18
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (53 bp):
TCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCT
Found at i:1032437 original size:154 final size:156
Alignment explanation
Indices: 1032187--1032523 Score: 475
Period size: 154 Copynumber: 2.2 Consensus size: 156
1032177 ATTTCTCTAG
* *
1032187 GGAGTATAGAACTCGAACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAAT
1 GGAGTATAGAACTCG--CATATCTTCAAACGGGTTCGCTCCTTCTTTCTCTAAGGAGTATAGAAT
* **
1032252 TCGAACATCTTCTTCTTACGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAACATCTT
64 TAGAACATCTTCTTCAAACGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAACATCTT
1032317 CAAAACGGGTTCG-CCCTTCTTTCATTAA
129 C-AAACGGGTTCGTCCCTTCTTTCATTAA
* * * * *
1032345 GGAGTATGGAACTCGGATATCTTCACACGGGTTCGCTCC-TCTTTCTCTAGGGAGTATGGAACTT
1 GGAGTATAGAACTCGCATATCTTCAAACGGGTTCGCTCCTTCTTTCTCTAAGGAGTATAGAA-TT
* * *
1032409 AG-ACATC-TCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTC
65 AGAACATCTTCTTCAAACGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTC
* *
1032472 AAACGGGTTCGTTCCTTCTTTCTTTAA
130 AAACGGGTTCGTCCCTTCTTTCATTAA
1032499 GGAGTATAGAACTCGCATATCTTCA
1 GGAGTATAGAACTCGCATATCTTCA
1032524 TTTGCTTCAC
Statistics
Matches: 160, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
153 11 0.07
154 87 0.54
155 24 0.15
156 24 0.15
158 14 0.09
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (156 bp):
GGAGTATAGAACTCGCATATCTTCAAACGGGTTCGCTCCTTCTTTCTCTAAGGAGTATAGAATTA
GAACATCTTCTTCAAACGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTCA
AACGGGTTCGTCCCTTCTTTCATTAA
Found at i:1032949 original size:36 final size:36
Alignment explanation
Indices: 1032891--1033080 Score: 182
Period size: 36 Copynumber: 5.2 Consensus size: 36
1032881 ACACTCTTGA
* * * * * *
1032891 GAAGGCTTAAAATGGATATGCTTAACTACTTTTTGGT
1 GAAGACTTAAGATGG-TTTGCTTCACTACTCTCTGGT
*
1032928 GAGGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
1 GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
* * *
1032964 GAAGACTTATGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
* * * * * *
1033000 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
* * * *
1033036 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
*
1033072 GAAGGCTTA
1 GAAGACTTA
1033081 GGATTGACTT
Statistics
Matches: 134, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 122 0.91
37 12 0.09
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (36 bp):
GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
Found at i:1033001 original size:72 final size:71
Alignment explanation
Indices: 1032925--1033080 Score: 215
Period size: 72 Copynumber: 2.2 Consensus size: 71
1032915 ACTACTTTTT
* *
1032925 GGTGAGGACTTAAGATGGTTTGCTTCACTACTCTCTGGTGAAGACTT-ATGATGGTTTGCTTCAC
1 GGTGAGG-CTTAAGATGGATTGCTTCACTACTCTCCGGTGAAGACTTCA-GATGGTTTGCTTCAC
1032989 TATTCTCC
64 TATTCTCC
* * * *
1032997 GGTGAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGTGAAGGCTTCAGATGGTTTGCTTCACT
1 GGTG-AGGCTTAAGATGGATTGCTTCACTACTCTCCGGTGAAGACTTCAGATGGTTTGCTTCACT
1033062 ATTCTCC
65 ATTCTCC
1033069 GGTGAAGGCTTA
1 GGTG-AGGCTTA
1033081 GGATTGACTT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
72 71 0.95
73 4 0.05
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (71 bp):
GGTGAGGCTTAAGATGGATTGCTTCACTACTCTCCGGTGAAGACTTCAGATGGTTTGCTTCACTA
TTCTCC
Found at i:1033086 original size:72 final size:72
Alignment explanation
Indices: 1032944--1033087 Score: 229
Period size: 72 Copynumber: 2.0 Consensus size: 72
1032934 TTAAGATGGT
*
1032944 TTGCTTCACTACTCTCTGGTGAAGACTTATGATGGTTTGCTTCACTATTCTCCGGTGAAGGCTTC
1 TTGCTTCACTACTCTCCGGTGAAGACTTATGATGGTTTGCTTCACTATTCTCCGGTGAAGGCTTC
1033009 AGATTGA
66 AGATTGA
* *
1033016 TTGCTTCACTATTCTCCGGTGAAGGCTTCA-GATGGTTTGCTTCACTATTCTCCGGTGAAGGCTT
1 TTGCTTCACTACTCTCCGGTGAAGACTT-ATGATGGTTTGCTTCACTATTCTCCGGTGAAGGCTT
1033080 -AGGATTGA
65 CA-GATTGA
1033088 CTTTGCTCCA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
71 1 0.01
72 65 0.97
73 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.37
Consensus pattern (72 bp):
TTGCTTCACTACTCTCCGGTGAAGACTTATGATGGTTTGCTTCACTATTCTCCGGTGAAGGCTTC
AGATTGA
Found at i:1034066 original size:124 final size:125
Alignment explanation
Indices: 1033806--1034109 Score: 448
Period size: 124 Copynumber: 2.4 Consensus size: 125
1033796 TCAATAATTT
* * * ** *
1033806 CTTGGTCTGAATCTTTTCATCTCCATATGACGTGGGTTGGGTCGCGCCCCAACATTATCTTACAC
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTATCTTACAC
** * *
1033871 TGGTACGGGCCTTCAAAATACCCCATCACCTCAAATTGTAAGGCTCATTCTTCATGCCTC
66 TGGTACGGGCAATCAAAATACCCCAACACCTCAAATTGTAAGGCTCATTCTTAATGCCTC
* * *
1033931 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCATGCCCCTACATTATCTTATAC
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTATCTTACAC
*
1033996 TGGTACGGG-AATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATGCCTC
66 TGGTACGGGCAATCAAAATACCCCAACACCTCAAATTGTAAGGCTCATTCTTAATGCCTC
* * *
1034055 CTTGGTCTGAATCTTGTCTTCTCAACATGATGTGGGTTCATTCGTGCCCCAACAT
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACAT
1034110 ATCACAACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
124 95 0.59
125 65 0.41
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (125 bp):
CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTATCTTACAC
TGGTACGGGCAATCAAAATACCCCAACACCTCAAATTGTAAGGCTCATTCTTAATGCCTC
Found at i:1035380 original size:24 final size:23
Alignment explanation
Indices: 1035352--1035452 Score: 82
Period size: 25 Copynumber: 4.3 Consensus size: 23
1035342 GTTTGATCGA
1035352 TTTTCTTTCATTCTTTT-TTTTCAT
1 TTTTCTTTCATT-TTTTATTTTC-T
**
1035376 TTTTC--TCATTTTCAATTTTTCT
1 TTTTCTTTCATTTTTTA-TTTTCT
* *
1035398 CTTTCTTTTCCTTTTTTATTTTCT
1 TTTTC-TTTCATTTTTTATTTTCT
*
1035422 TTTTCATTTCATTTTTTTCTTTTCT
1 TTTTC-TTTCA-TTTTTTATTTTCT
1035447 TTTTCT
1 TTTTCT
1035453 CTTTCTATAT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
21 2 0.03
22 10 0.16
23 5 0.08
24 20 0.33
25 24 0.39
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTCTTTCATTTTTTATTTTCT
Found at i:1035418 original size:25 final size:25
Alignment explanation
Indices: 1035352--1035457 Score: 82
Period size: 24 Copynumber: 4.4 Consensus size: 25
1035342 GTTTGATCGA
*
1035352 TTTTC-TTTCATTCTTT-TTTTTCAT
1 TTTTCTTTTCATTTTTTATTTTTC-T
**
1035376 TTTTC---TCATTTTCAATTTTTCT
1 TTTTCTTTTCATTTTTTATTTTTCT
* *
1035398 CTTTCTTTTCCTTTTTTA-TTTTCT
1 TTTTCTTTTCATTTTTTATTTTTCT
*
1035422 TTTTCATTTCATTTTTT-TCTTTTCT
1 TTTTCTTTTCATTTTTTAT-TTTTCT
1035447 TTTTCTCTTTC
1 TTTTCT-TTTC
1035458 TATATTTCTC
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
22 11 0.17
23 6 0.09
24 25 0.39
25 18 0.28
26 4 0.06
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTCTTTTCATTTTTTATTTTTCT
Found at i:1035425 original size:6 final size:6
Alignment explanation
Indices: 1035368--1035458 Score: 53
Period size: 6 Copynumber: 14.2 Consensus size: 6
1035358 TTCATTCTTT
* *
1035368 TTTTTC ATTTTTC TCATTTTC AATTTTTC TCTTTC TTTTCC TTTTT- TATTTTC
1 TTTTTC -TTTTTC T--TTTTC --TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC
*
1035421 TTTTTC ATTTCATT- TTTTTC -TTTTC TTTTTC TCTTTC T
1 TTTTTC -TTT--TTC TTTTTC TTTTTC TTTTTC TTTTTC T
1035459 ATATTTCTCT
Statistics
Matches: 68, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
5 8 0.12
6 34 0.50
7 13 0.19
8 10 0.15
9 2 0.03
10 1 0.01
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTTC
Found at i:1038066 original size:20 final size:21
Alignment explanation
Indices: 1038041--1038092 Score: 88
Period size: 20 Copynumber: 2.5 Consensus size: 21
1038031 TGAATGTGGC
1038041 CTTCTCGTCTTTACGAA-GGT
1 CTTCTCGTCTTTACGAAGGGT
*
1038061 CTTCTCGTCTTTATGAAGGGT
1 CTTCTCGTCTTTACGAAGGGT
1038082 CTTCTCGTCTT
1 CTTCTCGTCTT
1038093 GATGAATGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (21 bp):
CTTCTCGTCTTTACGAAGGGT
Found at i:1038084 original size:21 final size:20
Alignment explanation
Indices: 1038041--1038153 Score: 111
Period size: 21 Copynumber: 5.5 Consensus size: 20
1038031 TGAATGTGGC
* *
1038041 CTTCTCGTCTTTACGAAGGT
1 CTTCTCGTCTTGATGAAGGT
*
1038061 CTTCTCGTCTTTATGAAGGGT
1 CTTCTCGTCTTGATGAA-GGT
1038082 CTTCTCGTCTTGATGAATGG-
1 CTTCTCGTCTTGATGAA-GGT
* * *
1038102 CATTCTTGTCTTGATGAATGA
1 C-TTCTCGTCTTGATGAAGGT
*
1038123 CATTCTCGTCTTGATGAATGCT
1 C-TTCTCGTCTTGATGAA-GGT
1038145 CTTCTCGTC
1 CTTCTCGTC
1038154 CTTGGTATGA
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
20 18 0.22
21 61 0.76
22 1 0.01
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (20 bp):
CTTCTCGTCTTGATGAAGGT
Found at i:1042713 original size:28 final size:30
Alignment explanation
Indices: 1042649--1042714 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
1042639 TTGACCAAAA
*
1042649 AATTTAAGGACTTTAAGCAAAAAAAGGACAT
1 AATTTAAGGACTTAAAG-AAAAAAAGGACAT
* *
1042680 AGTTTAAGGACTTAAAG-AAAAAAGG-TAT
1 AATTTAAGGACTTAAAGAAAAAAAGGACAT
1042708 AATTTAA
1 AATTTAA
1042715 AGATTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 8 0.26
29 8 0.26
31 15 0.48
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.26
Consensus pattern (30 bp):
AATTTAAGGACTTAAAGAAAAAAAGGACAT
Found at i:1052837 original size:18 final size:18
Alignment explanation
Indices: 1052814--1052848 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1052804 AGGGATTATC
1052814 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1052832 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTCGGGACA
1052849 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1054191 original size:34 final size:33
Alignment explanation
Indices: 1054125--1054191 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
1054115 GACCATTAAA
* *
1054125 ATGGAAAAGAGTTTTCATAATAGGGTAGAAAAAC
1 ATGGAAAAGAGTTTTCATAAAAGGG-ACAAAAAC
1054159 ATGGAAAAGAGTTTTCATAACAAAGGG-CAAAAA
1 ATGGAAAAGAGTTTTCAT-A-AAAGGGACAAAAA
1054192 GGAGATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 23 0.79
35 1 0.03
36 5 0.17
ACGTcount: A:0.49, C:0.07, G:0.22, T:0.21
Consensus pattern (33 bp):
ATGGAAAAGAGTTTTCATAAAAGGGACAAAAAC
Found at i:1057979 original size:36 final size:37
Alignment explanation
Indices: 1057934--1058009 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
1057924 CTCGCTAGAT
* *
1057934 ACAAATTTCT-TTAAAACAAATTTTGTCTCTCTTGAG
1 ACAAATTTCTCTAAAAACAAATTTTGTCTCACTTGAG
*
1057970 ACAACTTTCTCTAAAAACAAATTTTGTCTCACTTGAG
1 ACAAATTTCTCTAAAAACAAATTTTGTCTCACTTGAG
1058007 ACA
1 ACA
1058010 TTTTTTTCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
36 9 0.25
37 27 0.75
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.37
Consensus pattern (37 bp):
ACAAATTTCTCTAAAAACAAATTTTGTCTCACTTGAG
Found at i:1058427 original size:132 final size:132
Alignment explanation
Indices: 1058228--1058521 Score: 394
Period size: 132 Copynumber: 2.2 Consensus size: 132
1058218 AACAGCAAAC
* *
1058228 CATCTTTGATATCGTTTCCCTTGAAACAAAATTTTGACTCTCATAAGACAATTTCTCTTAAAACA
1 CATCTTTGA-GTCATTTCCCTTGAAACAAAATTTTGA-TCTCATAAGACAATTTCTCTTAAAACA
* * *
1058293 AAATCATCTTTGAGTCGTTTCTCTTGAAATGAATTTTGTCTCTTTTGAGACAGATTCTCTTAAAA
64 AAATCATCTTTGAGTCGTTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACAGATTCTATTAAAA
1058358 CAAAAT
129 C--AAT
** * *
1058364 CATCTTTGAGTCATTTCCCTTGAAA-TGAATTTTG-TCTCTTAAGACAGTTTCTCTTAAAACAAA
1 CATCTTTGAGTCATTTCCCTTGAAACAAAATTTTGATCTCATAAGACAATTTCTCTTAAAACAAA
* * *
1058427 ATCATCTTTGAGTCGTTTCCCTTGAAATGATTTTTGTCTCTCTTGAGACAGTTTCTATTGAAACA
66 ATCATCTTTGAGTCGTTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACAGATTCTATTAAAACA
1058492 AT
131 AT
* **
1058494 CATATTTGAGTTTTTTTCCCTTGAAACA
1 CATCTTTGAG-TCATTTCCCTTGAAACA
1058522 GTTCCCTAAA
Statistics
Matches: 140, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
130 12 0.09
131 13 0.09
132 85 0.61
134 7 0.05
135 14 0.10
136 9 0.06
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (132 bp):
CATCTTTGAGTCATTTCCCTTGAAACAAAATTTTGATCTCATAAGACAATTTCTCTTAAAACAAA
ATCATCTTTGAGTCGTTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACAGATTCTATTAAAACA
AT
Found at i:1058446 original size:65 final size:66
Alignment explanation
Indices: 1058228--1058519 Score: 356
Period size: 67 Copynumber: 4.4 Consensus size: 66
1058218 AACAGCAAAC
* ** * *
1058228 CATCTTTGATATCGTTTCCCTTGAAACAAAATTTTGACTCTCATAAGACAATTTCTCTTAAAACA
1 CATCTTTGA-GTCGTTTCCCTTGAAA-TGAATTTTG-CTCTCTTAAGACAGTTTCTCTTAAAACA
1058293 AAAT
63 AAAT
* * * *
1058297 CATCTTTGAGTCGTTTCTCTTGAAATGAATTTTGTCTCTTTTGAGACAGATTCTCTTAAAACAAA
1 CATCTTTGAGTCGTTTCCCTTGAAATGAATTTTG-CTCTCTTAAGACAGTTTCTCTTAAAACAAA
1058362 AT
65 AT
*
1058364 CATCTTTGAGTCATTTCCCTTGAAATGAATTTTG-TCTCTTAAGACAGTTTCTCTTAAAACAAAA
1 CATCTTTGAGTCGTTTCCCTTGAAATGAATTTTGCTCTCTTAAGACAGTTTCTCTTAAAACAAAA
1058428 T
66 T
* * * *
1058429 CATCTTTGAGTCGTTTCCCTTGAAATGATTTTTGTCTCTCTTGAGACAGTTTCTATTGAAAC--A
1 CATCTTTGAGTCGTTTCCCTTGAAATGAATTTTG-CTCTCTTAAGACAGTTTCTCTTAAAACAAA
1058492 AT
65 AT
* **
1058494 CATATTTGAGTTTTTTTCCCTTGAAA
1 CATCTTTGAG-TCGTTTCCCTTGAAA
1058520 CAGTTCCCTA
Statistics
Matches: 197, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
65 72 0.37
66 13 0.07
67 89 0.45
68 14 0.07
69 9 0.05
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (66 bp):
CATCTTTGAGTCGTTTCCCTTGAAATGAATTTTGCTCTCTTAAGACAGTTTCTCTTAAAACAAAA
T
Found at i:1060449 original size:76 final size:75
Alignment explanation
Indices: 1060297--1060449 Score: 171
Period size: 76 Copynumber: 2.0 Consensus size: 75
1060287 TCAGCACTTA
* * * **
1060297 TAATTTAGTCCTTTTATTGTTTGTTAGGTTATTTTTGTTAACATTTGACTTTGGCCACAATGTTT
1 TAATTTAATCCTTTTATTGTTTATTAGGTTATTTTTGTTAACATTTGAATTTGGCCACAACATTT
* *
1060362 GTGATTATTT
66 GTAAATATTT
* * * * **
1060372 TAATTTAATCCTTTTATTGTTTATTTGTTTATTTTTTGTTAATATTTGAATTTGGCTATGACATT
1 TAATTTAATCCTTTTATTGTTTATTAGGTTA-TTTTTGTTAACATTTGAATTTGGCCACAACATT
*
1060437 TGTAAATCTTT
65 TGTAAATATTT
1060448 TA
1 TA
1060450 TTATAGTCAT
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
75 27 0.43
76 36 0.57
ACGTcount: A:0.22, C:0.08, G:0.13, T:0.57
Consensus pattern (75 bp):
TAATTTAATCCTTTTATTGTTTATTAGGTTATTTTTGTTAACATTTGAATTTGGCCACAACATTT
GTAAATATTT
Found at i:1064824 original size:12 final size:12
Alignment explanation
Indices: 1064807--1064838 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1064797 GTTTATTTAT
1064807 TGTTCGTGAGCA
1 TGTTCGTGAGCA
1064819 TGTTCGTGAGCA
1 TGTTCGTGAGCA
1064831 TGTTCGTG
1 TGTTCGTG
1064839 TAATGTTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.16, G:0.34, T:0.38
Consensus pattern (12 bp):
TGTTCGTGAGCA
Found at i:1064857 original size:23 final size:23
Alignment explanation
Indices: 1064831--1064875 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1064821 TTCGTGAGCA
*
1064831 TGTTCGTGTAATGTTCACGAACT
1 TGTTCATGTAATGTTCACGAACT
*
1064854 TGTTCATTTAATGTTCACGAAC
1 TGTTCATGTAATGTTCACGAAC
1064876 ATATTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (23 bp):
TGTTCATGTAATGTTCACGAACT
Found at i:1064882 original size:23 final size:23
Alignment explanation
Indices: 1064839--1064892 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
1064829 CATGTTCGTG
* *
1064839 TAATGTTCACGAACTTGTTCATT
1 TAATGTTCACGAACATATTCATT
1064862 TAATGTTCACGAACATATTCATT
1 TAATGTTCACGAACATATTCATT
*
1064885 TAGTGTTC
1 TAATGTTC
1064893 TTTTAGCGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (23 bp):
TAATGTTCACGAACATATTCATT
Found at i:1066045 original size:22 final size:22
Alignment explanation
Indices: 1066011--1066070 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
1066001 CGGTTGTAAG
1066011 AATGAAGAAAGAAAGATGAAGGA
1 AATGAA-AAAGAAAGATGAAGGA
*
1066034 AATGAAAAAGAAAGGTGAAGGA
1 AATGAAAAAGAAAGATGAAGGA
1066056 AAT-AAAGAAGAAAGA
1 AATGAAA-AAGAAAGA
1066071 AAGAAGAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 3 0.09
22 25 0.74
23 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.28, T:0.08
Consensus pattern (22 bp):
AATGAAAAAGAAAGATGAAGGA
Found at i:1066068 original size:11 final size:11
Alignment explanation
Indices: 1066054--1066086 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1066044 AAAGGTGAAG
*
1066054 GAAATAAAGAA
1 GAAAGAAAGAA
1066065 GAAAGAAAGAA
1 GAAAGAAAGAA
1066076 GAAAGAAAGAA
1 GAAAGAAAGAA
1066087 AGGTAACCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (11 bp):
GAAAGAAAGAA
Found at i:1066079 original size:22 final size:22
Alignment explanation
Indices: 1066008--1066086 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 22
1065998 TGTCGGTTGT
* *
1066008 AAGAATGAAGAAAGAAAGATGA
1 AAGAAAGAAGAAAGAAAGAAGA
*
1066030 AGGAAATGAA-AAAGAAAGGTGAAGGA
1 AAGAAA-GAAGAAAGAAA---GAA-GA
*
1066056 AATAAAGAAGAAAGAAAGAAGA
1 AAGAAAGAAGAAAGAAAGAAGA
1066078 AAGAAAGAA
1 AAGAAAGAA
1066087 AGGTAACCGA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
22 21 0.47
23 6 0.13
25 5 0.11
26 13 0.29
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.06
Consensus pattern (22 bp):
AAGAAAGAAGAAAGAAAGAAGA
Found at i:1068826 original size:21 final size:21
Alignment explanation
Indices: 1068811--1068861 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1068801 CATTAGTATC
1068811 AAATCATTAAATATTAATAAT
1 AAATCATTAAATATTAATAAT
1068832 AAATCATTAAATATTAATAAT
1 AAATCATTAAATATTAATAAT
1068853 AAATCATTA
1 AAATCATTA
1068862 TTATCAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATCATTAAATATTAATAAT
Found at i:1068881 original size:46 final size:47
Alignment explanation
Indices: 1068831--1068979 Score: 196
Period size: 46 Copynumber: 3.2 Consensus size: 47
1068821 ATATTAATAA
1068831 TAAATCATTAAAT-ATTAATAATAAATCATTATTATCAAATCATTAC
1 TAAATCATTAAATCATTAATAATAAATCATTATTATCAAATCATTAC
* * *
1068877 TAAATCATTATTATCATT-ATTAT-AATGATTATTATCAAATCATTAC
1 TAAATCATTA-AATCATTAATAATAAATCATTATTATCAAATCATTAC
* * *
1068923 TAAATCATCAAATCATTAAATATTAAAATCATTATTAACAAATCATTAC
1 TAAATCATTAAATCATT-AATAAT-AAATCATTATTATCAAATCATTAC
1068972 TAAATCAT
1 TAAATCAT
1068980 ATAATTATTA
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
45 6 0.07
46 41 0.47
47 9 0.10
48 3 0.03
49 29 0.33
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.40
Consensus pattern (47 bp):
TAAATCATTAAATCATTAATAATAAATCATTATTATCAAATCATTAC
Found at i:1068990 original size:49 final size:48
Alignment explanation
Indices: 1068831--1068991 Score: 195
Period size: 49 Copynumber: 3.4 Consensus size: 48
1068821 ATATTAATAA
* *
1068831 TAAATCATTAAATATT-AATAAT-AAATCATTATTATCAAATCATTAC
1 TAAATCATTAATTATTAAATATTAAAATCATTATTATCAAATCATTAC
* * * *
1068877 TAAATCATT-ATTA-TCATTATTATAATGATTATTATCAAATCATTAC
1 TAAATCATTAATTATTAAATATTAAAATCATTATTATCAAATCATTAC
* * *
1068923 TAAATCATCAAATCATTAAATATTAAAATCATTATTAACAAATCATTAC
1 TAAATCAT-TAATTATTAAATATTAAAATCATTATTATCAAATCATTAC
1068972 TAAATCATATAATTATTAAA
1 TAAATCAT-TAATTATTAAA
1068992 AATCGTATGT
Statistics
Matches: 95, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
44 1 0.01
45 7 0.07
46 39 0.41
48 3 0.03
49 45 0.47
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (48 bp):
TAAATCATTAATTATTAAATATTAAAATCATTATTATCAAATCATTAC
Found at i:1069250 original size:24 final size:25
Alignment explanation
Indices: 1069223--1069302 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
1069213 ATATCAAATC
*
1069223 ATTAAATATTAA-TAATAAATCATT
1 ATTAAATAATAATTAATAAATCATT
*
1069247 ATT-AATAATAATTACTAAATCATT
1 ATTAAATAATAATTAATAAATCATT
* * *
1069271 ATTATCA-AATCATTACTAAATCATT
1 ATTA-AATAATAATTAATAAATCATT
*
1069296 GTTAAAT
1 ATTAAAT
1069303 TATTATTATC
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
23 7 0.15
24 18 0.39
25 20 0.43
26 1 0.02
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (25 bp):
ATTAAATAATAATTAATAAATCATT
Found at i:1069252 original size:14 final size:14
Alignment explanation
Indices: 1069225--1069285 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
1069215 ATCAAATCAT
*
1069225 TAAAT-ATTAATAA
1 TAAATCATTATTAA
1069238 TAAATCATTATTAA
1 TAAATCATTATTAA
*
1069252 T-AAT-A--ATTAC
1 TAAATCATTATTAA
1069262 TAAATCATTATT-A
1 TAAATCATTATTAA
1069275 TCAAATCATTA
1 T-AAATCATTA
1069286 CTAAATCATT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
10 5 0.13
11 3 0.08
12 2 0.05
13 9 0.23
14 20 0.51
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATCATTATTAA
Found at i:1069641 original size:21 final size:21
Alignment explanation
Indices: 1069617--1069709 Score: 61
Period size: 21 Copynumber: 4.6 Consensus size: 21
1069607 TAATTTCATT
*
1069617 ATTACTAATCATTACTAAATA
1 ATTACTAATAATTACTAAATA
* * *
1069638 ATTACTATTAAATCATTAAAT-
1 ATTACTAAT-AATTACTAAATA
* * *
1069659 ATTAATAATAATT--T-CATT
1 ATTACTAATAATTACTAAATA
*
1069677 ATTACTAATCATTACTAAATA
1 ATTACTAATAATTACTAAATA
*
1069698 ATTA-TTATAATT
1 ATTACTAATAATT
1069710 TTAAATATAA
Statistics
Matches: 53, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
17 2 0.04
18 12 0.23
20 10 0.19
21 21 0.40
22 8 0.15
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTACTAATAATTACTAAATA
Found at i:1072524 original size:21 final size:20
Alignment explanation
Indices: 1072503--1072560 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 20
1072493 TTATTTTTTA
1072503 AAATATCAAATAAATTTGTT
1 AAATATCAAATAAATTTGTT
*
1072523 AATTAATC-AATCAAATTTGTT
1 AAAT-ATCAAAT-AAATTTGTT
1072544 AAATATCAAATAAATTT
1 AAATATCAAATAAATTT
1072561 AAATATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (20 bp):
AAATATCAAATAAATTTGTT
Found at i:1072665 original size:19 final size:20
Alignment explanation
Indices: 1072627--1072679 Score: 74
Period size: 18 Copynumber: 2.7 Consensus size: 20
1072617 TAAATTAAAA
1072627 AAATATTTTTTAAACAACAAT
1 AAATA-TTTTTAAACAACAAT
1072648 AAATATTTTTAAAC-ACAAT
1 AAATATTTTTAAACAACAAT
*
1072667 ATAT-TTTTTAAAC
1 AAATATTTTTAAAC
1072680 GGGAATAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 9 0.29
19 8 0.26
20 9 0.29
21 5 0.16
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATATTTTTAAACAACAAT
Found at i:1072772 original size:17 final size:17
Alignment explanation
Indices: 1072750--1072782 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1072740 TTACACATAC
1072750 ACAACAACAAAA-AATAG
1 ACAACAA-AAAACAATAG
1072767 ACAACAAAAAACAATA
1 ACAACAAAAAACAATA
1072783 AATTACCCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.18, G:0.03, T:0.06
Consensus pattern (17 bp):
ACAACAAAAAACAATAG
Found at i:1073155 original size:28 final size:30
Alignment explanation
Indices: 1073115--1073171 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 30
1073105 ATTTTTTATA
1073115 TAATATAATATATAACTTAAACTAACAAAT
1 TAATATAATATATAACTTAAACTAACAAAT
1073145 TAATAT-A-ATATAACTTAAACTAACAAA
1 TAATATAATATATAACTTAAACTAACAAA
1073172 CCAATAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 20 0.74
29 1 0.04
30 6 0.22
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAT
Found at i:1073177 original size:28 final size:28
Alignment explanation
Indices: 1073124--1073177 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
1073114 ATAATATAAT
**
1073124 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACCAATATA
1073152 ATATAACTTAAACTAACAAACCAATA
1 ATATAACTTAAACTAACAAACCAATA
1073178 ATTTATTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACCAATATA
Found at i:1073178 original size:21 final size:21
Alignment explanation
Indices: 1073154--1073202 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1073144 TTAATATAAT
1073154 ATAACTTAAACTAACAAACCA
1 ATAACTTAAACTAACAAACCA
* ** *
1073175 ATAATTTATTCTAACAAACTA
1 ATAACTTAAACTAACAAACCA
1073196 ATTAACT
1 A-TAACT
1073203 AAATTTTAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACCA
Found at i:1074597 original size:20 final size:21
Alignment explanation
Indices: 1074572--1074623 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1074562 TTTTCCCAAT
*
1074572 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1074592 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1074613 TCGCAATGCGA
1 TCGCAATGCGA
1074624 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1074637 original size:20 final size:20
Alignment explanation
Indices: 1074612--1074726 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 20
1074602 AATTGGGAAA
1074612 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
1074632 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
*
1074653 ATCGCAATGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1074673 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
1074693 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1074713 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1074727 TTTCAAAGCG
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 4 0.05
20 46 0.60
21 25 0.32
22 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1074922 original size:22 final size:22
Alignment explanation
Indices: 1074894--1074937 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1074884 CACTCTCTCA
1074894 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1074916 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1074938 TATCTCCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1075239 original size:20 final size:20
Alignment explanation
Indices: 1075200--1075258 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1075190 GCGATTCTCT
**
1075200 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
1075220 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1075240 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1075259 AGAAACTATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1075449 original size:25 final size:24
Alignment explanation
Indices: 1075395--1075449 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1075385 TGTTTATTAT
* *
1075395 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1075419 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1075445 TGTTT
1 TGTTT
1075450 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1076605 original size:18 final size:18
Alignment explanation
Indices: 1076579--1076623 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1076569 TCCACTTCGG
*
1076579 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1076597 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1076615 GAGCCATCA
1 GAGCCATCA
1076624 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1077156 original size:19 final size:20
Alignment explanation
Indices: 1077102--1077168 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1077092 TAGTTTACTT
* *
1077102 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1077122 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1077142 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1077161 TCGCAACG
1 TCGCAACG
1077169 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1077176 original size:14 final size:14
Alignment explanation
Indices: 1077157--1077214 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1077147 ATGCGAAATG
1077157 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1077171 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1077187 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1077203 AAAATCGCAACG
1 AAAATCGCAACG
1077215 TGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1077199 original size:32 final size:33
Alignment explanation
Indices: 1077141--1077231 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1077131 GGAAATGGCT
1077141 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1077174 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
1077206 ATCGCAACGTGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1077232 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1077267 original size:14 final size:14
Alignment explanation
Indices: 1077248--1077338 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
1077238 TTGTGTTTCG
1077248 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1077262 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1077278 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1077294 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
1077311 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1077327 CGTTGCGATTTT
1 CGTTGCGATTTT
1077339 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 27 0.42
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.09
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1077312 original size:33 final size:33
Alignment explanation
Indices: 1077243--1077354 Score: 208
Period size: 33 Copynumber: 3.4 Consensus size: 33
1077233 GCGATTTGTG
*
1077243 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1077275 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1077308 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1077341 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1077355 AGCCATTTCC
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 26 0.33
33 52 0.67
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1077826 original size:19 final size:19
Alignment explanation
Indices: 1077764--1077829 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
1077754 CTGTCATCCC
*
1077764 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCC-CC-ACCGT
* * * *
1077785 TCAAGAGGCCCTACCTCC-C
1 TCAAGAGTCCC-CCCACCGT
1077804 TCAAGAGTCCCCCCACCGT
1 TCAAGAGTCCCCCCACCGT
1077823 TCAAGAG
1 TCAAGAG
1077830 GCCACTGTCA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
18 4 0.12
19 17 0.50
20 1 0.03
21 12 0.35
ACGTcount: A:0.24, C:0.41, G:0.17, T:0.18
Consensus pattern (19 bp):
TCAAGAGTCCCCCCACCGT
Found at i:1079770 original size:19 final size:19
Alignment explanation
Indices: 1079748--1079806 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1079738 GGAAATTACT
1079748 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1079767 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1079781 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1079800 ATCGCAA
1 ATCGCAA
1079807 CGCTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1079790 original size:33 final size:33
Alignment explanation
Indices: 1079748--1079874 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
1079738 GGAAATTACT
1079748 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1079781 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * *
1079813 TTTCGCAATGTGAAATGAAAATTGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1079847 ATCACAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1079875 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 78 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1079855 original size:66 final size:66
Alignment explanation
Indices: 1079749--1079881 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
1079739 GAAATTACTA
* *
1079749 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1079814 T
66 T
* * *
1079815 TCGCAATGTGAAATGAAAATTGCAACGAGGGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1079880 T
66 T
1079881 T
1 T
1079882 AATTTCGTGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1079927 original size:33 final size:33
Alignment explanation
Indices: 1079874--1079963 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
1079864 AAATCGCAAC
* * *
1079874 GCGAATTTAATTTCGTGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
1079907 GTGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
1079940 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
1079964 AGTACTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:1079931 original size:19 final size:19
Alignment explanation
Indices: 1079903--1079963 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
1079893 GCGATTCTCT
*
1079903 CGTTGTGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1079922 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
1079936 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1079955 CATTGCGAT
1 CGTTGCGAT
1079964 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 10 0.30
16 3 0.09
17 3 0.09
19 17 0.52
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1080091 original size:14 final size:14
Alignment explanation
Indices: 1080070--1080106 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1080060 CATCAATTAA
1080070 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
1080084 ATAAATCACCTTTT
1 ACAAATCAACTTTT
1080098 ACAAATCAA
1 ACAAATCAA
1080107 TTAAACAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1081509 original size:21 final size:21
Alignment explanation
Indices: 1081483--1081592 Score: 55
Period size: 21 Copynumber: 5.3 Consensus size: 21
1081473 GTGAGAGGGA
1081483 CCTCTTCAACGATGACAGTGG
1 CCTCTTCAACGATGACAGTGG
* * ** *
1081504 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTCAACGATGACAGTGG
* * * *
1081525 ACTC-TCGAGGAATGATAG-GG
1 CCTCTTCAACG-ATGACAGTGG
*
1081545 CCTCTTCAACGAT-ATGAGTGG
1 CCTCTTCAACGATGA-CAGTGG
* * **
1081566 ACTCTTGAGGGATGACAGTGG
1 CCTCTTCAACGATGACAGTGG
1081587 CCTCTT
1 CCTCTT
1081593 GAATGGTGGG
Statistics
Matches: 62, Mismatches: 22, Indels: 10
0.66 0.23 0.11
Matches are distributed among these distances:
19 1 0.02
20 12 0.19
21 48 0.77
22 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.32, T:0.25
Consensus pattern (21 bp):
CCTCTTCAACGATGACAGTGG
Found at i:1081591 original size:42 final size:42
Alignment explanation
Indices: 1081493--1081667 Score: 190
Period size: 42 Copynumber: 4.2 Consensus size: 42
1081483 CCTCTTCAAC
* * *
1081493 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGG
1 GATGACAGTGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
* * * * *
1081535 AATGATAG-GGCCTCTTCAACGATATGAGTGGACTCTTGAGG
1 GATGACAGTGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
* * * *
1081576 GATGACAGTGGCCTCTTGAATGGTGGGAGGGGACTCTCGAGG
1 GATGACAGTGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
* * * * *
1081618 AATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGG
1 GATGACAGTGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
1081660 GATGACAG
1 GATGACAG
1081668 GCGAGTCGGG
Statistics
Matches: 104, Mismatches: 28, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
41 33 0.32
42 71 0.68
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.22
Consensus pattern (42 bp):
GATGACAGTGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
Found at i:1081623 original size:83 final size:84
Alignment explanation
Indices: 1081493--1081667 Score: 325
Period size: 83 Copynumber: 2.1 Consensus size: 84
1081483 CCTCTTCAAC
1081493 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATA-GGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
*
1081557 TATGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
*
1081576 GATGACAGTGGCCTCTTGAATGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1081641 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1081660 GATGACAG
1 GATGACAG
1081668 GCGAGTCGGG
Statistics
Matches: 89, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
83 48 0.54
84 41 0.46
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:1082053 original size:91 final size:90
Alignment explanation
Indices: 1081885--1082066 Score: 296
Period size: 91 Copynumber: 2.0 Consensus size: 90
1081875 TATTCAAACT
1081885 TTCAACCAAAAGAAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACAATTTAGCAGA
1 TTCAACCAAAAGAAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACAATTTAGCAGA
1081950 ATTGGCAGCAACCGAATAAATTTAC
66 ATTGGCAGCAACCGAATAAATTTAC
* *
1081975 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAA-ACAGTTTAGC
1 TTCAACCAAAAGA-AAAAC--AAAGACAAATACTAACTTCACAGTGTTAAAGAATACAATTTAGC
*
1082038 AGTATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
1082066 T
1 T
1082067 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
90 13 0.15
91 42 0.49
92 4 0.05
93 27 0.31
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGAAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACAATTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:1083753 original size:20 final size:19
Alignment explanation
Indices: 1083722--1083843 Score: 75
Period size: 20 Copynumber: 6.8 Consensus size: 19
1083712 TCTTTTGGTT
1083722 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1083741 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1083762 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1083781 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
1083795 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
1083814 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1083828 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1083844 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
14 19 0.24
16 4 0.05
17 4 0.05
19 20 0.26
20 29 0.37
21 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1083804 original size:33 final size:33
Alignment explanation
Indices: 1083747--1083843 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 33
1083737 ACGAGATAAT
1083747 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
1083781 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
1083814 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
1083844 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:1083877 original size:19 final size:19
Alignment explanation
Indices: 1083844--1083928 Score: 65
Period size: 19 Copynumber: 4.7 Consensus size: 19
1083834 AAAATCGCAA
**
1083844 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
1083863 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
* *
1083882 TGTGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
1083896 TGCGATAGTT-ATTTCCGCGT
1 TGCGAT-TTTCATTT-CGCGT
1083916 TGCGATTTTCATT
1 TGCGATTTTCATT
1083929 CGAAACTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
14 9 0.18
17 5 0.10
19 24 0.47
20 13 0.25
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:1084459 original size:20 final size:20
Alignment explanation
Indices: 1084434--1084486 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1084424 GCGCTATGTA
1084434 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
1084454 AATCGCGTTGTGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1084474 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1084487 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1084520 original size:20 final size:20
Alignment explanation
Indices: 1084495--1084548 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1084485 GATTTTGTAT
1084495 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1084515 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1084535 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1084549 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1084533 original size:61 final size:61
Alignment explanation
Indices: 1084435--1084551 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
1084425 CGCTATGTAA
* * * * * *
1084435 ATCGCGTTGCGAAAGTCAGAATCGCGTTGTGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1084496 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1084552 CCCAATTTCT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1087799 original size:39 final size:39
Alignment explanation
Indices: 1087743--1087893 Score: 135
Period size: 39 Copynumber: 3.9 Consensus size: 39
1087733 TTGTACACCT
*
1087743 AGTAAGGGCTTACCCTGTGCACAAAGCAGAGGAGTCAG-
1 AGTAAGGACTTACCCTGTGCACAAAGCAGAGGAGTCAGC
* * * * *
1087781 ATGTAAGGTCTTATCCTGTGCACAAAGTATAGGAGTCTGC
1 A-GTAAGGACTTACCCTGTGCACAAAGCAGAGGAGTCAGC
* * * *
1087821 A-TAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGC
1 AGTAAGGACTTACCCTGTGCACAAAGCAGAGGAGTCAGC
* * ** * *
1087859 GGGAAGGACTTACCCTGAACACAAAACCGAGGAGT
1 AGTAAGGACTTACCCTGTGCACAAAGCAGAGGAGT
1087894 ATGCGGTAAA
Statistics
Matches: 93, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
38 31 0.33
39 61 0.66
40 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.18
Consensus pattern (39 bp):
AGTAAGGACTTACCCTGTGCACAAAGCAGAGGAGTCAGC
Found at i:1088531 original size:21 final size:22
Alignment explanation
Indices: 1088507--1088548 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1088497 ATCCATAATC
*
1088507 AAATCCTAAAAA-ATTAAGCAA
1 AAATCCTAAAAACACTAAGCAA
*
1088528 AAATGCTAAAAACACTAAGCA
1 AAATCCTAAAAACACTAAGCA
1088549 TTTTGGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.60, C:0.17, G:0.07, T:0.17
Consensus pattern (22 bp):
AAATCCTAAAAACACTAAGCAA
Found at i:1093638 original size:2 final size:2
Alignment explanation
Indices: 1093594--1093618 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1093584 TAGCCAATTG
1093594 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1093619 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1094748 original size:23 final size:22
Alignment explanation
Indices: 1094722--1094788 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 22
1094712 CACCACAGCT
*
1094722 CGTATAAATGCATCGAAGTGCCA
1 CGTAGAAATGCA-CGAAGTGCCA
* *
1094745 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCA-CGAAGTGCCA
1094768 CGTAGAAATGCACTGAAGTGC
1 CGTAGAAATGCAC-GAAGTGC
1094789 ATATAATATG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
22 1 0.03
23 37 0.97
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.19
Consensus pattern (22 bp):
CGTAGAAATGCACGAAGTGCCA
Found at i:1101609 original size:23 final size:23
Alignment explanation
Indices: 1101559--1101625 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
1101549 CACCACAGCT
* * * *
1101559 CGTATAAATGCACCG-AGTACCA
1 CGTAGAAATACACCGAAGTGCCG
*
1101581 CGTAGAATTACACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCG
*
1101604 CGTAGAAATGCACCGAAGTGCC
1 CGTAGAAATACACCGAAGTGCC
1101626 ATATAATATG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 12 0.32
23 25 0.68
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCG
Found at i:1104809 original size:23 final size:23
Alignment explanation
Indices: 1104776--1104853 Score: 124
Period size: 23 Copynumber: 3.5 Consensus size: 23
1104766 CCCGTGAGGG
1104776 GTATCGATACACATTCAAGGAAT
1 GTATCGATACACATTCAAGGAAT
*
1104799 GTATCGGTACACATTCAAGGAAT
1 GTATCGATACACATTCAAGGAAT
*
1104822 GTATCGGTACACATTCAAGG--T
1 GTATCGATACACATTCAAGGAAT
1104843 GTATCGATACA
1 GTATCGATACA
1104854 TAGCAAGGGG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
21 11 0.21
23 42 0.79
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (23 bp):
GTATCGATACACATTCAAGGAAT
Found at i:1119624 original size:20 final size:20
Alignment explanation
Indices: 1119595--1119642 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1119585 TATGTTCTCA
* *
1119595 AATGACTAGTTTCTTGTGTT
1 AATGATTAGTTTCTTATGTT
1119615 AATGATTAGTTTCTTATGTT
1 AATGATTAGTTTCTTATGTT
1119635 AATGATTA
1 AATGATTA
1119643 TAATGATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (20 bp):
AATGATTAGTTTCTTATGTT
Found at i:1120029 original size:24 final size:24
Alignment explanation
Indices: 1119995--1120040 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1119985 ATTCTATTAA
*
1119995 AAAATTTTAATTTATAAAAATATC
1 AAAATTATAATTTATAAAAATATC
*
1120019 AAAATTATAATTTCTAAAAATA
1 AAAATTATAATTTATAAAAATA
1120041 AACTATAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAATTATAATTTATAAAAATATC
Found at i:1124604 original size:33 final size:33
Alignment explanation
Indices: 1124567--1124629 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
1124557 CGCAGAGGAT
*
1124567 GCATCCACCGCATCTGATGCAGCAGACCTTGGA
1 GCATCCACCACATCTGATGCAGCAGACCTTGGA
* *
1124600 GCATCCACCACGTCTGTTGCAGCAGACCTT
1 GCATCCACCACATCTGATGCAGCAGACCTT
1124630 CGATGTCGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.21
Consensus pattern (33 bp):
GCATCCACCACATCTGATGCAGCAGACCTTGGA
Found at i:1133372 original size:24 final size:24
Alignment explanation
Indices: 1133345--1133391 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1133335 GAAATAGGGT
1133345 TAGGGATTTTAATTAAAGGGAGGA
1 TAGGGATTTTAATTAAAGGGAGGA
*
1133369 TAGGGATTTTAATTAAGGGGAGG
1 TAGGGATTTTAATTAAAGGGAGG
1133392 GGTACTGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.30
Consensus pattern (24 bp):
TAGGGATTTTAATTAAAGGGAGGA
Found at i:1136879 original size:25 final size:25
Alignment explanation
Indices: 1136850--1136905 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1136840 GAATTAGGGA
*
1136850 AATTAAAAATAG-GGTTAGGGATTTT
1 AATTAAAAAGAGAGGTTAGGGA-TTT
* *
1136875 AATTAAAGAGGGAGGTTAGGGATTT
1 AATTAAAAAGAGAGGTTAGGGATTT
1136900 AATTAA
1 AATTAA
1136906 GGGAGGGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (25 bp):
AATTAAAAAGAGAGGTTAGGGATTT
Found at i:1142446 original size:23 final size:23
Alignment explanation
Indices: 1142396--1142446 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
1142386 ACACTAAAGA
* *
1142396 GAGGAACGTAGCCTAGGCGCAGT
1 GAGGCACGTAGCCTAGGCGCAGC
1142419 GAGGCACGTAGCCTAGGCGCAGC
1 GAGGCACGTAGCCTAGGCGCAGC
1142442 GAGGC
1 GAGGC
1142447 GCAACGAGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.25, G:0.41, T:0.10
Consensus pattern (23 bp):
GAGGCACGTAGCCTAGGCGCAGC
Found at i:1142929 original size:21 final size:21
Alignment explanation
Indices: 1142905--1142944 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1142895 AAAATAATTA
* *
1142905 AATTTATTTATTTTGAAATCT
1 AATTTAATTATTCTGAAATCT
1142926 AATTTAATTATTCTGAAAT
1 AATTTAATTATTCTGAAAT
1142945 TTACATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (21 bp):
AATTTAATTATTCTGAAATCT
Found at i:1146056 original size:9 final size:9
Alignment explanation
Indices: 1146042--1146066 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1146032 ACACCTTGTA
1146042 GATGAAGAT
1 GATGAAGAT
1146051 GATGAAGAT
1 GATGAAGAT
1146060 GATGAAG
1 GATGAAG
1146067 TTGTTATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (9 bp):
GATGAAGAT
Found at i:1146436 original size:18 final size:18
Alignment explanation
Indices: 1146413--1146455 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1146403 TCGTGAATTC
*
1146413 CGCGCCTTTCATGTACCT
1 CGCGCCTTTCATGCACCT
*
1146431 CGCGCCTTTCATGCGCCT
1 CGCGCCTTTCATGCACCT
1146449 CGCGCCT
1 CGCGCCT
1146456 CAAGGCTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.07, C:0.44, G:0.21, T:0.28
Consensus pattern (18 bp):
CGCGCCTTTCATGCACCT
Found at i:1153274 original size:20 final size:20
Alignment explanation
Indices: 1153249--1153290 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1153239 CTCAAATGAC
*
1153249 TAGTTTCTTGTGTTAAAGAT
1 TAGTTTCTTATGTTAAAGAT
*
1153269 TAGTTTCTTATGTTAATGAT
1 TAGTTTCTTATGTTAAAGAT
1153289 TA
1 TA
1153291 TAATGATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.17, T:0.52
Consensus pattern (20 bp):
TAGTTTCTTATGTTAAAGAT
Found at i:1153454 original size:17 final size:17
Alignment explanation
Indices: 1153432--1153475 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1153422 GTATAAAAAT
1153432 TTATAACTTATTTTT-AA
1 TTATAA-TTATTTTTAAA
*
1153449 TTATAATTTTTTTTAAA
1 TTATAATTATTTTTAAA
1153466 TTATAATTAT
1 TTATAATTAT
1153476 GAGAAAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATAATTATTTTTAAA
Found at i:1156448 original size:41 final size:40
Alignment explanation
Indices: 1156402--1156504 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 40
1156392 GTTTGTATCG
* *
1156402 AAAAACGCCGCTATAGGTTCGTCTATAGTGGCGTTTTTATA
1 AAAAACGCCGCTATAGGTTCATCTATAGTGGCGTTTTT-CA
* *
1156443 AAAAACGCCG-TAAAAGGGTTAATCTATAGTGGCGTTTTTCA
1 AAAAACGCCGCT-ATA-GGTTCATCTATAGTGGCGTTTTTCA
* *
1156484 ACAAACGCCGCAATAGGTTCA
1 AAAAACGCCGCTATAGGTTCA
1156505 ACCATACATT
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
40 6 0.12
41 24 0.47
42 21 0.41
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (40 bp):
AAAAACGCCGCTATAGGTTCATCTATAGTGGCGTTTTTCA
Found at i:1157000 original size:84 final size:84
Alignment explanation
Indices: 1156905--1157060 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 84
1156895 AATTGTATAA
* *
1156905 TTAGCGGCGTTTAT-ACACAAACGCCGTAAAAGGGT-TAATCTATAGTGGCGTTT-TTTTTAACA
1 TTAGCGGCGTTT-TGACAAAAACGCAGTAAAA-GGTATAATCTATAGTGGCGTTTGTTTTT-ACA
1156967 AACGCCGCAATAGAGTAGTACT
63 AACGCCGCAATAGAGTAGTACT
* * * *
1156989 TTAGCGGCGTTTTGAGAAAAACGTAGTGATAGGTATAATCTATAGTGGCGTTTGTTTTTACAAAC
1 TTAGCGGCGTTTTGACAAAAACGCAGTAAAAGGTATAATCTATAGTGGCGTTTGTTTTTACAAAC
1157054 GCCGCAA
66 GCCGCAA
1157061 CATAATTGTA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
83 4 0.06
84 54 0.86
85 5 0.08
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (84 bp):
TTAGCGGCGTTTTGACAAAAACGCAGTAAAAGGTATAATCTATAGTGGCGTTTGTTTTTACAAAC
GCCGCAATAGAGTAGTACT
Found at i:1166071 original size:43 final size:44
Alignment explanation
Indices: 1166005--1166105 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 44
1165995 ATTTTGTGTT
* * * * * * *
1166005 ATTTAGCGGCGTTTGTTACAAAAAATGCTGCAATATA-TCATAC
1 ATTTAGCGGTGTTTGTAAAAAAAAATGCCGCAAAATAGTAACAC
1166048 ATTTAGCGGTGTTTGTAAAAAAAAATGCCGCAAAATAGTAACAC
1 ATTTAGCGGTGTTTGTAAAAAAAAATGCCGCAAAATAGTAACAC
*
1166092 ATATAGCGGTGTTT
1 ATTTAGCGGTGTTT
1166106 TTTCTGTTGC
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 32 0.65
44 17 0.35
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (44 bp):
ATTTAGCGGTGTTTGTAAAAAAAAATGCCGCAAAATAGTAACAC
Found at i:1166287 original size:43 final size:43
Alignment explanation
Indices: 1166210--1166291 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
1166200 AAGCGCCGCT
* * * *
1166210 AAATGTCAAAACCTATTGCTGTGTTTGTAAAAAAAACGCTGCG
1 AAATGTCAAAACCTATTACGGCGGTTGTAAAAAAAACGCTGCG
**
1166253 AAATGTCAAAACCTATTACGGCGGTTGTTGAAAAAACGC
1 AAATGTCAAAACCTATTACGGCGGTTGTAAAAAAAACGC
1166292 CGCTATATAT
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:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (43 bp):
AAATGTCAAAACCTATTACGGCGGTTGTAAAAAAAACGCTGCG
Found at i:1172239 original size:20 final size:20
Alignment explanation
Indices: 1172198--1172240 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1172188 TCAACACACA
*
1172198 AAATTCTCTCAAATCTTCTC
1 AAATTCTCTCAAATCATCTC
*
1172218 AAATTCTCTCAAATCATGTC
1 AAATTCTCTCAAATCATCTC
1172238 AAA
1 AAA
1172241 AACCAAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (20 bp):
AAATTCTCTCAAATCATCTC
Found at i:1180538 original size:21 final size:23
Alignment explanation
Indices: 1180499--1180549 Score: 88
Period size: 21 Copynumber: 2.3 Consensus size: 23
1180489 CTCGTATAAA
1180499 TGCACCGAAGTGCCCTGTAGAAT
1 TGCACCGAAGTGCCCTGTAGAAT
1180522 TGCACCG-AGTG-CCTGTAGAAT
1 TGCACCGAAGTGCCCTGTAGAAT
1180543 TGCACCG
1 TGCACCG
1180550 TAGCCATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 17 0.61
22 4 0.14
23 7 0.25
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
TGCACCGAAGTGCCCTGTAGAAT
Found at i:1180800 original size:30 final size:30
Alignment explanation
Indices: 1180765--1180841 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
1180755 CCGTAGTTCA
* * *
1180765 TATCACGTAGTCATATTATTTCCATACCTT
1 TATCACATAGTCATATCATTTACATACCTT
1180795 TATCACATAGTCATATCATTTACATACCTT
1 TATCACATAGTCATATCATTTACATACCTT
1180825 TATCACATAGCTCATAT
1 TATCACATAG-TCATAT
1180842 AACTTTTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.40
Consensus pattern (30 bp):
TATCACATAGTCATATCATTTACATACCTT
Found at i:1180922 original size:27 final size:28
Alignment explanation
Indices: 1180856--1180930 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 28
1180846 TTTTCTGCAT
* *
1180856 ATTCATGTCATGCAATACATATCATATGA
1 ATTCATGTCATG-TATACATATAATATGA
*
1180885 ATTCATGTCATGTATACATTTAATAT-A
1 ATTCATGTCATGTATACATATAATATGA
1180912 ATTCATGTCATGTAT-CATA
1 ATTCATGTCATGTATACATA
1180931 ATATGGAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 3 0.07
27 16 0.38
28 11 0.26
29 12 0.29
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (28 bp):
ATTCATGTCATGTATACATATAATATGA
Found at i:1181392 original size:67 final size:67
Alignment explanation
Indices: 1181219--1181370 Score: 225
Period size: 67 Copynumber: 2.3 Consensus size: 67
1181209 TTTTTTTCAT
* *
1181219 GGGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTT--CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACG
1181284 ATGA
64 ATGA
* * * *
1181288 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
1181352 GA
66 GA
1181354 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
1181371 TCGAATGGGT
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
66 23 0.30
67 42 0.55
69 12 0.16
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:1181867 original size:14 final size:16
Alignment explanation
Indices: 1181848--1181879 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1181838 ACGTTGAGAG
1181848 AAGGAAG-A-GAAGAA
1 AAGGAAGAAGGAAGAA
1181862 AAGGAAGAAGGAAGAA
1 AAGGAAGAAGGAAGAA
1181878 AA
1 AA
1181880 TGGGAGGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 1 0.06
16 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (16 bp):
AAGGAAGAAGGAAGAA
Found at i:1187397 original size:21 final size:23
Alignment explanation
Indices: 1187358--1187408 Score: 88
Period size: 21 Copynumber: 2.3 Consensus size: 23
1187348 GCTCGTATAA
1187358 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
1187381 TGCACCGAA-TG-CCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
1187402 TGCACCG
1 TGCACCG
1187409 TAGGCCATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 17 0.61
22 2 0.07
23 9 0.32
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:1187658 original size:30 final size:29
Alignment explanation
Indices: 1187623--1187698 Score: 107
Period size: 30 Copynumber: 2.6 Consensus size: 29
1187613 CCGTAGTTCA
* * *
1187623 TATCACGTAGTCATATTATTTCCATACCTT
1 TATCACATAGTCATATCATTTACATACC-T
1187653 TATCACATAGTCATATCATTTACATACCT
1 TATCACATAGTCATATCATTTACATACCT
1187682 TATCACATAGCTCATAT
1 TATCACATAG-TCATAT
1187699 AACTTTTCTG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
29 11 0.26
30 31 0.74
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (29 bp):
TATCACATAGTCATATCATTTACATACCT
Found at i:1187741 original size:26 final size:28
Alignment explanation
Indices: 1187712--1187776 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 28
1187702 TTTTCTGCAT
* *
1187712 ATTCATGTCATGCAAT-CA-TCATATGA
1 ATTCATGTCATGCAATACATTAATATAA
*
1187738 ATTCATGTCATGTAATACATTTAATATAA
1 ATTCATGTCATGCAATACA-TTAATATAA
1187767 ATTCATGTCA
1 ATTCATGTCA
1187777 GTATCATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.45
27 2 0.06
29 16 0.48
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (28 bp):
ATTCATGTCATGCAATACATTAATATAA
Found at i:1188180 original size:66 final size:63
Alignment explanation
Indices: 1188066--1188211 Score: 195
Period size: 66 Copynumber: 2.3 Consensus size: 63
1188056 TTTTTTTCAT
*
1188066 GGGGGAATCGGTTCCCCCCCTGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATG
1 GGGGGTATCGGTT-CCCCCCTGGGTATCGATTCCCCTCAAGCAATCTGGAA-TTCAT-TACGATG
1188131 A
63 A
* * * *
1188132 GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAATTCATTTCGTTGA
1 GGGGGTATCGGTTCCCCCCT-GGGTATCGATTCCCCTCAAGCAATCTGGAATTCATTACGATGA
*
1188196 -GGGGTATCAGTTCCCC
1 GGGGGTATCGGTTCCCC
1188212 TTGATGGGTA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
63 15 0.21
64 6 0.08
65 12 0.16
66 40 0.55
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (63 bp):
GGGGGTATCGGTTCCCCCCTGGGTATCGATTCCCCTCAAGCAATCTGGAATTCATTACGATGA
Found at i:1188231 original size:64 final size:67
Alignment explanation
Indices: 1188066--1188232 Score: 193
Period size: 66 Copynumber: 2.6 Consensus size: 67
1188056 TTTTTTTCAT
* * *
1188066 GGGGGAATCGGTTCCCCCC-CTGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGGTATCAGTTCCCCCCTGTGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1188130 GA
66 GA
* * * * *
1188132 GGGGGTATCGGTTCCCCCCTG-GGGTATCGATTCCCCTCTAGCATTCTGGAA-TTCAT-TTCGTT
1 GGGGGTATCAGTTCCCCCCTGTGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1188194 GA
66 GA
* *
1188196 -GGGGTATCAGTT-CCCCTTGATGGGTACCGATTCCCCT
1 GGGGGTATCAGTTCCCCCCTG-TGGGTATCGATTCCCCT
1188233 AACCCAAAAT
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
62 6 0.07
63 11 0.12
64 21 0.24
65 5 0.06
66 46 0.52
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (67 bp):
GGGGGTATCAGTTCCCCCCTGTGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
GA
Found at i:1194498 original size:16 final size:19
Alignment explanation
Indices: 1194462--1194499 Score: 55
Period size: 16 Copynumber: 2.2 Consensus size: 19
1194452 CAAATAATCA
1194462 TATATAATTATAAAAATAT
1 TATATAATTATAAAAATAT
1194481 TATAT-ATTA-AAAAA-AT
1 TATATAATTATAAAAATAT
1194497 TAT
1 TAT
1194500 CTTACAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 4 0.21
19 5 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATATAATTATAAAAATAT
Found at i:1194801 original size:40 final size:40
Alignment explanation
Indices: 1194740--1194817 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
1194730 CAGACGATAG
*
1194740 TAAGGCGCGACCCATGCACCGCGCCTTACCCTACGTGGTA
1 TAAGGCGCGACCCATGCACCGCACCTTACCCTACGTGGTA
* * *
1194780 TAAGGCGCGACCTATGTACCGCACCTTACCCTGCGTGG
1 TAAGGCGCGACCCATGCACCGCACCTTACCCTACGTGG
1194818 CACCACATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.19, C:0.36, G:0.26, T:0.19
Consensus pattern (40 bp):
TAAGGCGCGACCCATGCACCGCACCTTACCCTACGTGGTA
Found at i:1194908 original size:51 final size:51
Alignment explanation
Indices: 1194798--1194908 Score: 125
Period size: 51 Copynumber: 2.2 Consensus size: 51
1194788 GACCTATGTA
* ** *
1194798 CCGCACCTTACCCTGCGTGGCACCACATCAACGTAAGGCGCGGTGCATGGG
1 CCGCGCCTTACCCCACGTGGCACCACATCAACGTAAGGCGCAGTGCATGGG
* * * * *
1194849 TCGTGCCTTACCCCACGTGGCGCCACATCAGCGTAAGGTGCAGTGTC-TGGG
1 CCGCGCCTTACCCCACGTGGCACCACATCAACGTAAGGCGCAGTG-CATGGG
1194900 CCGCGCCTT
1 CCGCGCCTT
1194909 TCTGCTAAGG
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
51 47 0.98
52 1 0.02
ACGTcount: A:0.16, C:0.35, G:0.30, T:0.19
Consensus pattern (51 bp):
CCGCGCCTTACCCCACGTGGCACCACATCAACGTAAGGCGCAGTGCATGGG
Found at i:1195233 original size:37 final size:37
Alignment explanation
Indices: 1195183--1195260 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
1195173 CATAGAATAC
*
1195183 AGTGCGACTCTAATATAAAATTGAGG-AAGACACATGG
1 AGTGCAACTCTAATAT-AAATTGAGGTAAGACACATGG
*
1195220 AGTGCAACTCTAATATAAATTTAGGTAAGACACATGG
1 AGTGCAACTCTAATATAAATTGAGGTAAGACACATGG
1195257 AGTG
1 AGTG
1195261 TAATGATTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 8 0.21
37 30 0.79
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (37 bp):
AGTGCAACTCTAATATAAATTGAGGTAAGACACATGG
Found at i:1195736 original size:19 final size:19
Alignment explanation
Indices: 1195712--1195748 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1195702 ATGACCAACA
*
1195712 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1195731 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1195749 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1195840 original size:21 final size:20
Alignment explanation
Indices: 1195793--1195840 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
1195783 GATTTTGACC
*
1195793 ATCGCATTGCGATTTTTGAA
1 ATCGCATTGCGATTTTAGAA
1195813 ATCCGCATTGCGATTTTAGATA
1 AT-CGCATTGCGATTTTAGA-A
1195835 ATCGCA
1 ATCGCA
1195841 ATGAGAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.80
22 3 0.12
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATTTTAGAA
Found at i:1195886 original size:20 final size:20
Alignment explanation
Indices: 1195834--1195886 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1195824 GATTTTAGAT
*
1195834 AATCGCAATGAGAATATGTA
1 AATCGCAATGCGAATATGTA
*
1195854 AATCGTAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
*
1195874 AATCGCAACGCGA
1 AATCGCAATGCGA
1195887 TAACACTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.23
Consensus pattern (20 bp):
AATCGCAATGCGAATATGTA
Found at i:1195921 original size:20 final size:20
Alignment explanation
Indices: 1195896--1196002 Score: 119
Period size: 20 Copynumber: 5.3 Consensus size: 20
1195886 ATAACACTTG
1195896 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1195916 ATCGCAACGCAATT-TGGACT
1 ATCGCAACGCGATTCT-GACT
* **
1195936 ATCGCAACACGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
*
1195956 GATCGCAACACGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
1195977 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1195997 AACGCA
1 ATCGCA
1196003 TCACTGAATT
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
19 3 0.04
20 53 0.72
21 16 0.22
22 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1196855 original size:24 final size:24
Alignment explanation
Indices: 1196823--1196876 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1196813 GTATTCGAAA
1196823 TTTGATCTTCGTCAATACCCGGAC
1 TTTGATCTTCGTCAATACCCGGAC
* * *
1196847 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTCGTCAATACCCGGAC
1196871 TTTGAT
1 TTTGAT
1196877 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTCGTCAATACCCGGAC
Found at i:1197095 original size:14 final size:14
Alignment explanation
Indices: 1197066--1197102 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1197056 AGAAAAAGAA
1197066 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
1197081 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
1197095 GAAGAAAA
1 GAAGAAAA
1197103 TACCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:1199115 original size:18 final size:18
Alignment explanation
Indices: 1199092--1199126 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1199082 AGCAAAAGGC
*
1199092 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
1199110 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1199127 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1199331 original size:20 final size:20
Alignment explanation
Indices: 1199306--1199564 Score: 222
Period size: 20 Copynumber: 13.6 Consensus size: 20
1199296 CATTCATTTA
1199306 ACTATCGCAACGCGAATATG
1 ACTATCGCAACGCGAATATG
** *
1199326 ACTATCGCAACATGAATTTG
1 ACTATCGCAACGCGAATATG
* *
1199346 AATATCGCAACG-G--GAT-
1 ACTATCGCAACGCGAATATG
* *
1199362 A--ATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAATATG
* *
1199380 ACTATCGTAACGCGAATTTG
1 ACTATCGCAACGCGAATATG
*
1199400 ACTATCGCAACG-G--GAT-
1 ACTATCGCAACGCGAATATG
* *
1199416 A--ATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAATATG
* *
1199434 AAC-ATTGCAACGCGAAAATG
1 -ACTATCGCAACGCGAATATG
*
1199454 ACTATCGCAACGCGAATTTG
1 ACTATCGCAACGCGAATATG
* *
1199474 ACTATCGCAATGCGAATTTG
1 ACTATCGCAACGCGAATATG
1199494 ACTATCGCAACGCGAA-ATG
1 ACTATCGCAACGCGAATATG
*
1199513 ACTATCGCAACGCGAATTTG
1 ACTATCGCAACGCGAATATG
* * *
1199533 ATTATCGCAACGGGAATTTG
1 ACTATCGCAACGCGAATATG
1199553 ACTATCGCAACG
1 ACTATCGCAACG
1199565 AGAAAATCGC
Statistics
Matches: 195, Mismatches: 30, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
14 16 0.08
15 2 0.01
16 2 0.01
17 6 0.03
18 1 0.01
19 23 0.12
20 145 0.74
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (20 bp):
ACTATCGCAACGCGAATATG
Found at i:1199375 original size:54 final size:54
Alignment explanation
Indices: 1199309--1199524 Score: 202
Period size: 54 Copynumber: 3.9 Consensus size: 54
1199299 TCATTTAACT
* * *
1199309 ATCGCAACGCGAATATGACTATCGCAACATGAATTTGAATATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACACGAATTTGAATATCGCAACGGGATA
* * *
1199363 ATCGCAATGCGAAAATGACTATCGTAACGCGAATTTGACTATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACACGAATTTGAATATCGCAACGGGATA
* * ** * *
1199417 ATCGCAATGCGAAAATGAAC-ATTGCAACGCGAAAATGACTATCGCAACGCGAATTTGA
1 ATCGCAATGCGAAAATG-ACTATCGCAACACGAATTTGAATATCGCAACG-GGA--T-A
** * * *
1199475 CTATCGCAATGCGAATTTGACTATCGCAACGCGAA-ATGACTATCGCAACG
1 --ATCGCAATGCGAAAATGACTATCGCAACACGAATTTGAATATCGCAACG
1199525 CGAATTTGAT
Statistics
Matches: 140, Mismatches: 14, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
54 90 0.64
55 4 0.03
57 1 0.01
58 1 0.01
59 17 0.12
60 27 0.19
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGACTATCGCAACACGAATTTGAATATCGCAACGGGATA
Found at i:1199750 original size:30 final size:30
Alignment explanation
Indices: 1199714--1199779 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
1199704 TTAAACAAGC
1199714 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
*
1199744 ATAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
1199774 ACAAAT
1 ACAAAT
1199780 CAACTCTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:1201198 original size:21 final size:21
Alignment explanation
Indices: 1201138--1201255 Score: 92
Period size: 21 Copynumber: 5.6 Consensus size: 21
1201128 GTGAATCGGG
* * *
1201138 CTCTAGAATGTTGGGAGGGAC
1 CTCTTGAATGATGGGAGGGGC
* * **
1201159 CTCTTCAACGATGATAGGGGC
1 CTCTTGAATGATGGGAGGGGC
* *
1201180 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGATGGGAGGGGC
** **
1201201 CTCTTGAGGGATGATAGGGGC
1 CTCTTGAATGATGGGAGGGGC
* *
1201222 CTCTTGAATGATAGGAGAGGC
1 CTCTTGAATGATGGGAGGGGC
*
1201243 CTCTTGAACGATG
1 CTCTTGAATGATG
1201256 ACAGGTGAGT
Statistics
Matches: 70, Mismatches: 27, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.23, C:0.16, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGATGGGAGGGGC
Found at i:1201205 original size:42 final size:42
Alignment explanation
Indices: 1201138--1201256 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
1201128 GTGAATCGGG
* * *
1201138 CTCTAGAATGTTGGGA-GGGACCTCTTCAACGATGATAGGGGC
1 CTCTTGAATGATGGGAGGGGA-CTCTTGAACGATGATAGGGGC
* **
1201180 CTCTTGAATGGTGGGAGGGGACTCTTGAGGGATGATAGGGGC
1 CTCTTGAATGATGGGAGGGGACTCTTGAACGATGATAGGGGC
* * *
1201222 CTCTTGAATGATAGGAGAGGCCTCTTGAACGATGA
1 CTCTTGAATGATGGGAGGGGACTCTTGAACGATGA
1201257 CAGGTGAGTC
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 61 0.94
43 4 0.06
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (42 bp):
CTCTTGAATGATGGGAGGGGACTCTTGAACGATGATAGGGGC
Found at i:1201761 original size:20 final size:20
Alignment explanation
Indices: 1201736--1201780 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1201726 GAATAGTTTC
1201736 TGAAACTTAAAATCGCAACA
1 TGAAACTTAAAATCGCAACA
1201756 TGAAACTTAAAATCGCAACA
1 TGAAACTTAAAATCGCAACA
*
1201776 CGAAA
1 TGAAA
1201781 ATGATTATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.51, C:0.20, G:0.11, T:0.18
Consensus pattern (20 bp):
TGAAACTTAAAATCGCAACA
Done.