Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 86 of 259
Found at i:27981811 original size:27 final size:27
Alignment explanation
Indices: 27981760--27981849 Score: 110
Period size: 27 Copynumber: 3.2 Consensus size: 27
27981750 GTGACGGAGT
27981760 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
* * *
27981789 CACCAGAACAGGTATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
27981816 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
27981844 CACCAG
1 CACCAG
27981850 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 23 0.43
28 23 0.43
29 7 0.13
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:27987626 original size:34 final size:33
Alignment explanation
Indices: 27987584--27987678 Score: 100
Period size: 34 Copynumber: 2.8 Consensus size: 33
27987574 TTATTTGCAT
27987584 ACTGTACTGAAATGGGCTAAGGCCCAGACTGCC
1 ACTGTACTGAAATGGGCTAAGGCCCAGACTGCC
* * * *
27987617 ACTGTTACTGAAATGGGCTCAGGCCTAGATTGCT
1 ACTG-TACTGAAATGGGCTAAGGCCCAGACTGCC
* *
27987651 ACGGCTACTGAAAGAGGGGCTAAGGCCC
1 ACTG-TACTG-AA-ATGGGCTAAGGCCC
27987679 TTAACTGAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
33 4 0.08
34 33 0.66
35 2 0.04
36 11 0.22
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (33 bp):
ACTGTACTGAAATGGGCTAAGGCCCAGACTGCC
Found at i:27990328 original size:13 final size:13
Alignment explanation
Indices: 27990310--27990336 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27990300 TGAATTGATA
27990310 TGTGTGAAAATTT
1 TGTGTGAAAATTT
27990323 TGTGTGAAAATTT
1 TGTGTGAAAATTT
27990336 T
1 T
27990337 ATCGTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:27991515 original size:44 final size:43
Alignment explanation
Indices: 27991451--27991575 Score: 135
Period size: 44 Copynumber: 2.9 Consensus size: 43
27991441 TAGGATTCCG
*
27991451 ATATGTGATT-CGTGTAAGACCATGTCTGGGACGTTGGCATCA
1 ATATGTGATTACGTGTAAGACCATATCTGGGACGTTGGCATCA
* * * * ** *
27991493 ATTTGTGATTTACGTGTAAGACCCTCTTTGGGACGACGGCATTA
1 ATATGTGA-TTACGTGTAAGACCATATCTGGGACGTTGGCATCA
* * *
27991537 ATATGTGATTACATGTAAGACCACATCTGAGACGTTGGC
1 ATATGTGATTACGTGTAAGACCATATCTGGGACGTTGGC
27991576 GTTGTACGAG
Statistics
Matches: 65, Mismatches: 16, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
42 7 0.11
43 25 0.38
44 33 0.51
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (43 bp):
ATATGTGATTACGTGTAAGACCATATCTGGGACGTTGGCATCA
Found at i:27997888 original size:40 final size:40
Alignment explanation
Indices: 27997782--27997991 Score: 264
Period size: 40 Copynumber: 5.3 Consensus size: 40
27997772 ATCAGCATCT
* * *
27997782 ACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGG
1 ACTTAGCCCGGATATAATAACTCGCACAAATGCCTTCGGG
27997822 ACTTAGCCCGG-TATAATAACTCGCACAAATGCCTTCGGG
1 ACTTAGCCCGGATATAATAACTCGCACAAATGCCTTCGGG
* *
27997861 ACTTAGCCCGGATATAATAGCTCGCACAAACGCCTTCGGG
1 ACTTAGCCCGGATATAATAACTCGCACAAATGCCTTCGGG
* * *
27997901 ACTTAGCCCGGATATAGTAGCTCGCACGAATGCCTTCGGG
1 ACTTAGCCCGGATATAATAACTCGCACAAATGCCTTCGGG
*** * *
27997941 ACTTAGCCCGGA-ATTAGCCACTAGCTCAAATG-CTCTCGGG
1 ACTTAGCCCGGATA-TAATAACTCGCACAAATGCCT-TCGGG
27997981 ACTTAGCCCGG
1 ACTTAGCCCGG
27997992 TTATCATCCG
Statistics
Matches: 154, Mismatches: 13, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
39 40 0.26
40 114 0.74
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
ACTTAGCCCGGATATAATAACTCGCACAAATGCCTTCGGG
Found at i:28015796 original size:13 final size:14
Alignment explanation
Indices: 28015780--28015808 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28015770 TTAAAGCATA
28015780 TAATTACAC-AATT
1 TAATTACACGAATT
28015793 TAATTACACGAATT
1 TAATTACACGAATT
28015807 TA
1 TA
28015809 CCTCGACTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (14 bp):
TAATTACACGAATT
Found at i:28021183 original size:24 final size:25
Alignment explanation
Indices: 28021155--28021201 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
28021145 TCCGACCCAA
*
28021155 TTTTACTGAAATATG-AATGGAAGC
1 TTTTACTGAAATAAGTAATGGAAGC
* *
28021179 TTTTAGTGGAATAAGTAATGGAA
1 TTTTACTGAAATAAGTAATGGAA
28021202 CTTGGAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.34
Consensus pattern (25 bp):
TTTTACTGAAATAAGTAATGGAAGC
Found at i:28023330 original size:33 final size:33
Alignment explanation
Indices: 28023288--28023353 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
28023278 ATGAAGAAAC
28023288 CATGGCTAGGGTTTTCCAAGCTTCCAAGCTTGA
1 CATGGCTAGGGTTTTCCAAGCTTCCAAGCTTGA
28023321 CATGGCTAGGGTTTTCCAAGCTTCCAAGCTTGA
1 CATGGCTAGGGTTTTCCAAGCTTCCAAGCTTGA
28023354 TTGTAAGTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.30
Consensus pattern (33 bp):
CATGGCTAGGGTTTTCCAAGCTTCCAAGCTTGA
Found at i:28030168 original size:23 final size:23
Alignment explanation
Indices: 28030142--28030186 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28030132 TGGGTATGTG
*
28030142 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
28030165 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
28030187 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:28035350 original size:29 final size:29
Alignment explanation
Indices: 28035289--28035377 Score: 117
Period size: 29 Copynumber: 3.1 Consensus size: 29
28035279 ACATACATGT
* *
28035289 ATATGGCCCACTAGGCCC-AATCTCATTC
1 ATATGGCCCATTAGGCCCAAATCACATTC
* *
28035317 ATATGGCCCATTGGGCCCAAATCACATTT
1 ATATGGCCCATTAGGCCCAAATCACATTC
* *
28035346 GTATGGCCCATTAGGCCCAAATCACATAC
1 ATATGGCCCATTAGGCCCAAATCACATTC
28035375 ATA
1 ATA
28035378 GTCATGCTTC
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
28 16 0.31
29 35 0.69
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACATTC
Found at i:28045353 original size:36 final size:36
Alignment explanation
Indices: 28045313--28045388 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
28045303 TTGAAATTAC
28045313 ATGTTTTGGTTATGGAATTGAGTAATTGAGATGGTT
1 ATGTTTTGGTTATGGAATTGAGTAATTGAGATGGTT
28045349 ATGTTTTGGTTATGGAATTGAGTAATTGAGATGGTT
1 ATGTTTTGGTTATGGAATTGAGTAATTGAGATGGTT
28045385 ATGT
1 ATGT
28045389 ATAGATGACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (36 bp):
ATGTTTTGGTTATGGAATTGAGTAATTGAGATGGTT
Found at i:28048049 original size:43 final size:43
Alignment explanation
Indices: 28048012--28048117 Score: 160
Period size: 43 Copynumber: 2.5 Consensus size: 43
28048002 GGTCTTGCAT
28048012 GTAATCACATATCGATGCCACTGTCCCAGACAGGGTCTTACTC
1 GTAATCACATATCGATGCCACTGTCCCAGACAGGGTCTTACTC
* * * *
28048055 GTAATCACATATCAATGCCTCTGTCCTAGATAGGGTCTTACTC
1 GTAATCACATATCGATGCCACTGTCCCAGACAGGGTCTTACTC
28048098 GTAATCACATA-CTGATGCCA
1 GTAATCACATATC-GATGCCA
28048118 ACGTATTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.02
43 55 0.98
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (43 bp):
GTAATCACATATCGATGCCACTGTCCCAGACAGGGTCTTACTC
Found at i:28054745 original size:30 final size:30
Alignment explanation
Indices: 28054700--28054759 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
28054690 ATTTAATACG
28054700 AACTTTGGCAAAATTACA-TTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTT-CCCCTA
* *
28054730 AACTTTTGCATAATTACACTTTTTCCCCTA
1 AACTTTGGCAAAATTACACTTTTTCCCCTA
28054760 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTTCCCCTA
Found at i:28057258 original size:23 final size:24
Alignment explanation
Indices: 28057226--28057272 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
28057216 AGACCGTATC
*
28057226 TAGATCGATTTGTTG-TTGTATTCA
1 TAGATCGATTTCTTGATT-TATTCA
28057250 TAGAT-GATTTCTTGATTTATTCA
1 TAGATCGATTTCTTGATTTATTCA
28057273 AAAAATGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.51
Consensus pattern (24 bp):
TAGATCGATTTCTTGATTTATTCA
Found at i:28059233 original size:42 final size:42
Alignment explanation
Indices: 28059187--28059282 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 42
28059177 TCCCAGACAG
*
28059187 GGTCTTACACAAAAT-CAAATACGATGCCAACGTCCCAGATCT
1 GGTCTTACACAAAATACAAAT-CGATGCCAACATCCCAGATCT
* * * *
28059229 GGTCTTACATGTAAATTACAAGTCGATGCCAACATCCCAGATGT
1 GGTCTTACA--CAAAATACAAATCGATGCCAACATCCCAGATCT
28059273 GGTCTTACAC
1 GGTCTTACAC
28059283 GATAACACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
42 9 0.20
44 32 0.71
45 4 0.09
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (42 bp):
GGTCTTACACAAAATACAAATCGATGCCAACATCCCAGATCT
Found at i:28067155 original size:29 final size:29
Alignment explanation
Indices: 28067083--28067199 Score: 98
Period size: 29 Copynumber: 4.1 Consensus size: 29
28067073 CATACATGCT
* * *
28067083 TATGGCCCACTAGGCCGAA-TCTTATTCA
1 TATGGCCCAGTAGGCCCAATTCATATTCA
* * * *
28067111 AATGGCCCA-TCTGGCCCAGTTCATATTCT
1 TATGGCCCAGT-AGGCCCAATTCATATTCA
*
28067140 TATGGCCCGGTAGGCCCAATTC-TCATTCA
1 TATGGCCCAGTAGGCCCAATTCAT-ATTCA
* *
28067169 TATGGCCCATTAGGCCCAAATCATATT-A
1 TATGGCCCAGTAGGCCCAATTCATATTCA
28067197 TAT
1 TAT
28067200 TCATGCTCAC
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
27 1 0.01
28 18 0.26
29 49 0.70
30 2 0.03
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (29 bp):
TATGGCCCAGTAGGCCCAATTCATATTCA
Found at i:28067185 original size:58 final size:57
Alignment explanation
Indices: 28067081--28067195 Score: 142
Period size: 58 Copynumber: 2.0 Consensus size: 57
28067071 TACATACATG
* * **
28067081 CTTATGGCCCACTAGGCCGAATCTTATTCAAATGGCCCATCTGGCCCAGTTCATATT
1 CTTATGGCCCACTAGGCCCAATCTCATTCAAATGGCCCATCTGGCCCAAATCATATT
** *
28067138 CTTATGGCCCGGTAGGCCCAATTCTCATTCATATGGCCCAT-TAGGCCCAAATCATATT
1 CTTATGGCCCACTAGGCCCAA-TCTCATTCAAATGGCCCATCT-GGCCCAAATCATATT
28067196 ATATTCATGC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
57 19 0.39
58 30 0.61
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (57 bp):
CTTATGGCCCACTAGGCCCAATCTCATTCAAATGGCCCATCTGGCCCAAATCATATT
Found at i:28067432 original size:16 final size:15
Alignment explanation
Indices: 28067410--28067445 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
28067400 CGTAGCCCAA
*
28067410 CTTTTAGCTTTTCGG
1 CTTTTAGCTCTTCGG
28067425 CATTTTAGCTCTTCGG
1 C-TTTTAGCTCTTCGG
28067441 CTTTT
1 CTTTT
28067446 CGACATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.08, C:0.22, G:0.17, T:0.53
Consensus pattern (15 bp):
CTTTTAGCTCTTCGG
Found at i:28069797 original size:46 final size:46
Alignment explanation
Indices: 28069747--28069922 Score: 167
Period size: 46 Copynumber: 3.8 Consensus size: 46
28069737 TGTTTGGGCA
*
28069747 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*** * * ** *
28069793 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACG
** * *
28069840 TCCGTGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* **
28069886 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTTGCTTATGG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28069923 GCCGGTTACA
Statistics
Matches: 100, Mismatches: 26, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
45 2 0.02
46 64 0.64
47 34 0.34
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:28069902 original size:93 final size:93
Alignment explanation
Indices: 28069743--28069913 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
28069733 AGGATGTTTG
* * *
28069743 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCCAACTCGTTGAG
28069808 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
** *
28069836 GGCATCCGTGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG-CCCAAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCCAA-CTCGTTGA
28069900 GTTGAGTCCGAGTT
65 GTTGAGTCCGAGTT
28069914 TGCTTATGGG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 4 0.06
93 67 0.94
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCCAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:28077460 original size:29 final size:30
Alignment explanation
Indices: 28077396--28077497 Score: 99
Period size: 29 Copynumber: 3.6 Consensus size: 30
28077386 CATACATGCA
* *
28077396 TATGGCCCA-CTAGGCCCAA-TCTTATTCA
1 TATGGCCCATCTAGGCCCAATTCTCATTCG
* * *
28077424 AATGGCCCATCT-GGCCCAGTTCAT-ATTCT
1 TATGGCCCATCTAGGCCCAATTC-TCATTCG
*
28077453 TATGGCCC-GCTAGGCCCAATTCTCATTCG
1 TATGGCCCATCTAGGCCCAATTCTCATTCG
28077482 TATGGCCCAT-TAGGCC
1 TATGGCCCATCTAGGCC
28077498 TAAATCGTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
28 17 0.28
29 42 0.70
30 1 0.02
ACGTcount: A:0.21, C:0.32, G:0.19, T:0.28
Consensus pattern (30 bp):
TATGGCCCATCTAGGCCCAATTCTCATTCG
Found at i:28077618 original size:19 final size:19
Alignment explanation
Indices: 28077579--28077618 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
28077569 TATAGGCCTA
*
28077579 TCAGGCCCATTTAGCCCAT
1 TCAGGCCCATTTAGCCAAT
*
28077598 TCAGGCCCATTTGGCCAAT
1 TCAGGCCCATTTAGCCAAT
28077617 TC
1 TC
28077619 TCTACCCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.35, G:0.17, T:0.28
Consensus pattern (19 bp):
TCAGGCCCATTTAGCCAAT
Found at i:28078984 original size:7 final size:8
Alignment explanation
Indices: 28078972--28079003 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
28078962 AAAATTCAAA
28078972 ATTTTTGG
1 ATTTTTGG
28078980 ATTTTTGG
1 ATTTTTGG
28078988 ATTTTTGG
1 ATTTTTGG
28078996 ATTTTTGG
1 ATTTTTGG
28079004 GGCGTTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.25, T:0.62
Consensus pattern (8 bp):
ATTTTTGG
Found at i:28079873 original size:43 final size:42
Alignment explanation
Indices: 28079807--28079963 Score: 167
Period size: 43 Copynumber: 3.7 Consensus size: 42
28079797 ATCTTGTACA
28079807 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAATTATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAA-TATCG
* * * *
28079850 ATGCCACTGTCCCAGACAG-GGTCTTACACGAAACCAA-ATACG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACATGTAATCAATAT-CG
* *
28079892 ATGCCAACGTCCCAGACGTGGTCTTACGTGTAAATCACA-AGTCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGT-AATCA-ATA-TCG
* *
28079936 ATGCCAATGTCCCAGGCATGGTCTTACA
1 ATGCCAATGTCCCAGACGTGGTCTTACA
28079964 CGATAACACA
Statistics
Matches: 94, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
41 3 0.03
42 26 0.28
43 35 0.37
44 29 0.31
45 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAATATCG
Found at i:28079963 original size:86 final size:84
Alignment explanation
Indices: 28079807--28079966 Score: 232
Period size: 86 Copynumber: 1.9 Consensus size: 84
28079797 ATCTTGTACA
* *
28079807 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAATTATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAA-TATCGATGCCAATGTCCCAGACAGGGT
28079872 CTTACACGAAACCAAATACG
65 CTTACACGAAACCAAATACG
* * *
28079892 ATGCCAACGTCCCAGACGTGGTCTTACGTGTAAATCACA-AGTCGATGCCAATGTCCCAGGCATG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGT-AATCA-ATA-TCGATGCCAATGTCCCAGACAGG
28079956 GTCTTACACGA
63 GTCTTACACGA
28079967 TAACACATAT
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
85 30 0.45
86 36 0.54
87 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAATATCGATGCCAATGTCCCAGACAGGGTC
TTACACGAAACCAAATACG
Found at i:28087508 original size:44 final size:44
Alignment explanation
Indices: 28087445--28087528 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
28087435 TGTTACATTT
28087445 AGTGGTATCAGAGCTATGATTTAGTCAATTCTCAAACTAACATA
1 AGTGGTATCAGAGCTATGATTTAGTCAATTCTCAAACTAACATA
28087489 AGTGGTATCAGAGCTATGATTTAGTCAATTCTCAAACTAA
1 AGTGGTATCAGAGCTATGATTTAGTCAATTCTCAAACTAA
28087529 TATAGCGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (44 bp):
AGTGGTATCAGAGCTATGATTTAGTCAATTCTCAAACTAACATA
Found at i:28095594 original size:24 final size:24
Alignment explanation
Indices: 28095562--28095611 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
28095552 AATGATGTAT
28095562 AATGTCTCCCTTGTATGTAACCGA
1 AATGTCTCCCTTGTATGTAACCGA
* *
28095586 AATGTCTCCCTTGTATTTAATCGA
1 AATGTCTCCCTTGTATGTAACCGA
28095610 AA
1 AA
28095612 ATCACTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (24 bp):
AATGTCTCCCTTGTATGTAACCGA
Found at i:28095702 original size:9 final size:9
Alignment explanation
Indices: 28095688--28095760 Score: 52
Period size: 9 Copynumber: 8.6 Consensus size: 9
28095678 GACACTTGCA
28095688 ATTAAACAC
1 ATTAAACAC
28095697 ATTAAA-AC
1 ATTAAACAC
*
28095705 ---AAACAT
1 ATTAAACAC
28095711 ATTAAACAC
1 ATTAAACAC
*
28095720 ATTTAAGCAC
1 A-TTAAACAC
28095730 TTATTAAACAC
1 --ATTAAACAC
28095741 A--AAACAC
1 ATTAAACAC
28095748 ATTAAACAC
1 ATTAAACAC
28095757 -TTAA
1 ATTAA
28095761 CTTAAATAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
5 3 0.06
6 1 0.02
7 7 0.14
8 6 0.12
9 19 0.37
10 7 0.14
11 7 0.14
12 1 0.02
ACGTcount: A:0.55, C:0.19, G:0.01, T:0.25
Consensus pattern (9 bp):
ATTAAACAC
Found at i:28096011 original size:50 final size:52
Alignment explanation
Indices: 28095902--28096017 Score: 148
Period size: 50 Copynumber: 2.3 Consensus size: 52
28095892 TAAATAGATG
* **
28095902 AGTTACTTAATGCAAGACTTAATTTAATAATGCAGACTTAAACTAACATGGG
1 AGTTACATAATGCAAGACTTAATTTAATAATGCAGACTTAAACTAACATGAA
* * *
28095954 AGTTACATAATGCAAGTCATT-ATTT-ATGATGCATACTT-AACTAACATGAA
1 AGTTACATAATGCAAGAC-TTAATTTAATAATGCAGACTTAAACTAACATGAA
28096004 AGTTACATAATGCA
1 AGTTACATAATGCA
28096018 TTACTTTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
50 24 0.42
51 11 0.19
52 20 0.35
53 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (52 bp):
AGTTACATAATGCAAGACTTAATTTAATAATGCAGACTTAAACTAACATGAA
Found at i:28096110 original size:19 final size:19
Alignment explanation
Indices: 28096070--28096110 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
28096060 TAAAATATGC
* *
28096070 AAACTTATTAATTTAAATA
1 AAACTTATTAAATTAAAAA
28096089 AAACTTATTAAATTAAAAA
1 AAACTTATTAAATTAAAAA
28096108 AAA
1 AAA
28096111 TCCTTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (19 bp):
AAACTTATTAAATTAAAAA
Found at i:28098078 original size:36 final size:36
Alignment explanation
Indices: 28098031--28098112 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 36
28098021 AAGACTTGTA
28098031 TACTGTTACTACA-CTGATTACTGTTACTGCACTGAT
1 TACTGTTACTACATC-GATTACTGTTACTGCACTGAT
*
28098067 TACTGTTACTACATCGGTTACTGTTACTGCACTGAT
1 TACTGTTACTACATCGATTACTGTTACTGCACTGAT
*
28098103 TATTGTTACT
1 TACTGTTACT
28098113 GTAATGGGCC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 42 0.98
37 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (36 bp):
TACTGTTACTACATCGATTACTGTTACTGCACTGAT
Found at i:28098113 original size:18 final size:18
Alignment explanation
Indices: 28098031--28098113 Score: 114
Period size: 18 Copynumber: 4.6 Consensus size: 18
28098021 AAGACTTGTA
*
28098031 TACTGTTACTACACTGAT
1 TACTGTTACTGCACTGAT
28098049 TACTGTTACTGCACTGAT
1 TACTGTTACTGCACTGAT
* *
28098067 TACTGTTACTACA-TCGGT
1 TACTGTTACTGCACT-GAT
28098085 TACTGTTACTGCACTGAT
1 TACTGTTACTGCACTGAT
*
28098103 TATTGTTACTG
1 TACTGTTACTG
28098114 TAATGGGCCA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
17 1 0.02
18 55 0.96
19 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (18 bp):
TACTGTTACTGCACTGAT
Found at i:28101034 original size:10 final size:10
Alignment explanation
Indices: 28101019--28101050 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
28101009 GGGCCGAGGT
28101019 CATTTTGGGC
1 CATTTTGGGC
28101029 CATTTTGGGC
1 CATTTTGGGC
28101039 CATTTTGGGC
1 CATTTTGGGC
28101049 CA
1 CA
28101051 AACTGAGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.28, T:0.38
Consensus pattern (10 bp):
CATTTTGGGC
Found at i:28101918 original size:33 final size:34
Alignment explanation
Indices: 28101841--28101938 Score: 110
Period size: 34 Copynumber: 2.9 Consensus size: 34
28101831 GTTTCAGTTA
* * *
28101841 GGGCCTTAGCCCATATCAGTAACAGTAGCAGTCT
1 GGGCCTAAGCCCATTTCAGTAACAGTAGCAGTCG
* **
28101875 TGGCCTAAGCCCATTTCAGTAACAGTATTAGT-G
1 GGGCCTAAGCCCATTTCAGTAACAGTAGCAGTCG
* *
28101908 GGGCCTAAGCCCATTACAGTATCAGTA-CAGT
1 GGGCCTAAGCCCATTTCAGTAACAGTAGCAGT
28101939 ATGCAATCAG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 3 0.06
33 24 0.44
34 27 0.50
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (34 bp):
GGGCCTAAGCCCATTTCAGTAACAGTAGCAGTCG
Found at i:28102633 original size:8 final size:8
Alignment explanation
Indices: 28102615--28102650 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
28102605 GACAGCCTAT
*
28102615 TTTTCGGC
1 TTTTCAGC
*
28102623 TTTTCAAC
1 TTTTCAGC
28102631 TTTTCAGC
1 TTTTCAGC
28102639 TTTTCAGC
1 TTTTCAGC
28102647 TTTT
1 TTTT
28102651 ACCGTTTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.11, C:0.22, G:0.11, T:0.56
Consensus pattern (8 bp):
TTTTCAGC
Found at i:28104867 original size:53 final size:53
Alignment explanation
Indices: 28104685--28104891 Score: 198
Period size: 53 Copynumber: 3.8 Consensus size: 53
28104675 ATTAGAGTTT
* * * * * *
28104685 AAGGATACCAAGTAGGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * ** * *
28104739 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTTATAAACTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * *
28104794 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* * *
28104847 AAGGATACCACGTAAGACCATGTCAAGACATGACAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
28104892 TAAAAAGGAA
Statistics
Matches: 120, Mismatches: 31, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
53 45 0.38
54 36 0.30
55 39 0.32
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:28109325 original size:40 final size:40
Alignment explanation
Indices: 28109281--28109385 Score: 192
Period size: 40 Copynumber: 2.6 Consensus size: 40
28109271 GGATATAGCT
* *
28109281 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
1 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTA
28109321 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTA
1 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTA
28109361 ACTCGCACAATTGCCTTCGGGACTT
1 ACTCGCACAATTGCCTTCGGGACTT
28109386 GACTCGCACA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.28
Consensus pattern (40 bp):
ACTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:28109401 original size:26 final size:26
Alignment explanation
Indices: 28109361--28109412 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
28109351 GGTTATAGTA
*
28109361 ACTCGCACAATTGCCTTCGGGACTTG
1 ACTCGCACAAATGCCTTCGGGACTTG
28109387 ACTCGCACAAATGCCTTCGGGACTTG
1 ACTCGCACAAATGCCTTCGGGACTTG
28109413 GCCCGGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (26 bp):
ACTCGCACAAATGCCTTCGGGACTTG
Found at i:28109427 original size:66 final size:66
Alignment explanation
Indices: 28109321--28109451 Score: 217
Period size: 66 Copynumber: 2.0 Consensus size: 66
28109311 GGTTATAGTA
* *
28109321 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT
28109386 G
66 G
* * *
28109387 ACTCGCACAAATGCCTTCGGGACTTGGCCCGGTTATAGTAACTTGCACAAATGTCTTCGGGACTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT
28109452 AGCCCGGATA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.27
Consensus pattern (66 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT
G
Found at i:28109446 original size:40 final size:40
Alignment explanation
Indices: 28109387--28109501 Score: 187
Period size: 40 Copynumber: 2.9 Consensus size: 40
28109377 TCGGGACTTG
*
28109387 ACTCGCACAAATGCCTTCGGGACTTGGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* * *
28109427 ACTTGCACAAATGTCTTCGGGACTTAGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
28109467 ACTCGCACAAATGCCTTCGGG-CTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
28109502 TAATCCGAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
39 13 0.19
40 55 0.81
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:28109466 original size:106 final size:106
Alignment explanation
Indices: 28109281--28109487 Score: 351
Period size: 106 Copynumber: 2.0 Consensus size: 106
28109271 GGATATAGCT
* *
28109281 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT
* *
28109346 AGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTG
66 AGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTG
* * *
28109387 ACTCGCACAAATGCCTTCGGGACTTGGCCCGGTTATAGTAACTTGCACAAATGTCTTCGGGACTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT
28109452 AGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG
66 AGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG
28109488 CTTAGCCCGG
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 94 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (106 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT
AGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTG
Found at i:28117429 original size:40 final size:40
Alignment explanation
Indices: 28117369--28117619 Score: 366
Period size: 40 Copynumber: 6.3 Consensus size: 40
28117359 CCTTTGGGGT
* *
28117369 TTAG-CCGGATATAGCT-ACTCGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGTTATAG-TAACTCGCACAAATGCCTTCGGGAC
*
28117408 TTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGAC
1 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
* *
28117448 TTAGCCTGGTTATAGTAACTCGCACAATTGCCTTCGGGAC
1 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
*
28117488 TT-GACCCGGTTATAGTAACTCACACAAATGCCTTCGGGAC
1 TTAG-CCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
* *
28117528 TTGGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGAC
1 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
* *
28117568 TTAGCCCGGATATAGTAACTCGCACAAATGCCTACGGG-C
1 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
28117607 TTAGCCCGGTTAT
1 TTAGCCCGGTTAT
28117620 CAATCCGAAT
Statistics
Matches: 194, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
39 19 0.10
40 174 0.90
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:28126081 original size:99 final size:92
Alignment explanation
Indices: 28125954--28126174 Score: 245
Period size: 99 Copynumber: 2.3 Consensus size: 92
28125944 TCCATCAAGT
*
28125954 CGATGCCATGTCCCAGACATGGTTTTACACTGACAATCAAA-ATCG-AGGCTGATGCCATGCCCC
1 CGATGCCATGTCCCAGACATGGTCTTACACT---AA-CAAATATCGTAGGC-GATG-CATGCCCC
* *
28126017 AGACATGGTCTTAGACTAGCTCTCACATATCCG-TGC
60 AGACAT-GTCTTACACTAGCT-T-ACATAT-CGAGGC
* * *
28126053 CGATGCCATGTCCCAGACATGGTCTTACACTAACAAATCTCGTAGTCGATGCATGTCCCAGACAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAACAAATATCGTAGGCGATGCATGCCCCAGACAT
* *
28126118 GTCTTACACTGGCTTACATCTCGAGGC
66 GTCTTACACTAGCTTACATATCGAGGC
28126145 CGATG-CATGTCCCAGACAT-GTCTTACACTA
1 CGATGCCATGTCCCAGACATGGTCTTACACTA
28126175 GCTCTCGTCT
Statistics
Matches: 111, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
90 11 0.10
91 16 0.14
92 12 0.11
93 1 0.01
94 12 0.11
95 17 0.15
96 9 0.08
97 3 0.03
99 30 0.27
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (92 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAACAAATATCGTAGGCGATGCATGCCCCAGACAT
GTCTTACACTAGCTTACATATCGAGGC
Found at i:28126149 original size:46 final size:49
Alignment explanation
Indices: 28125912--28126270 Score: 256
Period size: 46 Copynumber: 7.6 Consensus size: 49
28125902 AATGTCGAGT
* * * * * *
28125912 CCATGTCCCAGATATGGTCTTACGCTGGCTCATCCA--TC-AAGTCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTC-TACATCTCGAGGCCGATG
* ** *
28125959 CCATGTCCCAGACATGGTTTTACACT-GACAATC-A-AAATCGAGGCTGATG
1 CCATGTCCCAGACATGGTCTTACACTAG-C--TCTACATCTCGAGGCCGATG
* * * *
28126008 CCATGCCCCAGACATGGTCTTAGACTAGCTCTCACATATCCG-TGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCT-ACATCT-CGAGGCCGATG
* * *
28126058 CCATGTCCCAGACATGGTCTTACACTA--AC-AAATCTCGTA-GTCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCG-AGGCCGATG
*
28126104 -CATGTCCCAGACAT-GTCTTACACTGGCT-TACATCTCGAGGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCGAGGCCGATG
* * *
28126150 -CATGTCCCAGACAT-GTCTTACACTAGCTCT-CGTCTCAATGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCGAGGCCGATG
* * * * *
28126196 CCATGTCCCAAACATGGTCTTACATTGGCTCT-CATAAT-GTGGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTACAT-CTCGAGGCCGATG
*
28126244 -CATGTCCCAAACAT-GTCTTACACTAGC
1 CCATGTCCCAGACATGGTCTTACACTAGC
28126271 ACACACACAT
Statistics
Matches: 254, Mismatches: 37, Indels: 43
0.76 0.11 0.13
Matches are distributed among these distances:
44 10 0.04
45 17 0.07
46 76 0.30
47 54 0.21
48 26 0.10
49 34 0.13
50 35 0.14
51 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (49 bp):
CCATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCGAGGCCGATG
Found at i:28126211 original size:138 final size:144
Alignment explanation
Indices: 28125951--28126219 Score: 354
Period size: 138 Copynumber: 1.9 Consensus size: 144
28125941 TCATCCATCA
* *
28125951 AGTCGATGCCATGTCCCAGACATGGTTTTACACTGACAATCAAAATCGAGGCTGATGCCATGCCC
1 AGTCGATGCCATGTCCCAGACATGGTCTTACACTGACAATCAAAATCGAGGCCGATGCCATGCCC
* ** *
28126016 CAGACATGGTCTTAGACTAGCTCTCACATATCCGTGCCGATGCCATGTCCCAGACATGGTCTTAC
66 CAGACATGGTCTTACACTAGCTCT-ACATATCAATGCCGATGCCATGTCCCAAACATGGTCTTAC
28126081 ACTAACAAATCTCGT
130 ACTAACAAATCTCGT
* * ** *
28126096 AGTCGATG-CATGTCCCAGACAT-GTCTTACACTGGC--TTACATCTCGAGGCCGATG-CATGTC
1 AGTCGATGCCATGTCCCAGACATGGTCTTACACTGACAATCA-AAATCGAGGCCGATGCCATGCC
* *
28126156 CCAGACAT-GTCTTACACTAGCTCT-CGTCTCAATGCCGATGCCATGTCCCAAACATGGTCTTAC
65 CCAGACATGGTCTTACACTAGCTCTACATATCAATGCCGATGCCATGTCCCAAACATGGTCTTAC
28126219 A
130 A
28126220 TTGGCTCTCA
Statistics
Matches: 110, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
138 35 0.32
140 15 0.14
141 15 0.14
142 12 0.11
143 11 0.10
144 14 0.13
145 8 0.07
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (144 bp):
AGTCGATGCCATGTCCCAGACATGGTCTTACACTGACAATCAAAATCGAGGCCGATGCCATGCCC
CAGACATGGTCTTACACTAGCTCTACATATCAATGCCGATGCCATGTCCCAAACATGGTCTTACA
CTAACAAATCTCGT
Found at i:28126240 original size:94 final size:91
Alignment explanation
Indices: 28126004--28126271 Score: 280
Period size: 94 Copynumber: 2.9 Consensus size: 91
28125994 AATCGAGGCT
* * * *
28126004 GATGCCATGCCCCAGACATGGTCTTAGACTAGCTCTCACATATCCGT-GCCGATGCCATGTCCCA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-AT-CGTGGCCGATG-CATGTCCCA
* *
28126068 GACATGGTCTTACACTAACAAATCTCGTAGTC
63 GACAT-GTCTTACACTAGC--ATCTCGTAGCC
* *
28126100 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-CTCGAGGCCGATGCATGTCCCAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAATCGTGGCCGATGCATGTCCCAGA
28126161 CATGTCTTACACTAGC-TCTCGTCTCAATGCC
65 CATGTCTTACACTAGCATCTCG--T--A-GCC
* * *
28126192 GATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCATAAT-GTGGCCGATGCATGTCCCAAAC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATCGTGGCCGATGCATGTCCCAGAC
28126256 ATGTCTTACACTAGCA
66 ATGTCTTACACTAGCA
28126272 CACACACATC
Statistics
Matches: 147, Mismatches: 13, Indels: 25
0.79 0.07 0.14
Matches are distributed among these distances:
87 5 0.03
89 1 0.01
90 12 0.08
91 17 0.12
92 14 0.10
93 14 0.10
94 65 0.44
95 15 0.10
96 4 0.03
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (91 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATCGTGGCCGATGCATGTCCCAGAC
ATGTCTTACACTAGCATCTCGTAGCC
Found at i:28126258 original size:140 final size:140
Alignment explanation
Indices: 28125996--28126267 Score: 329
Period size: 140 Copynumber: 1.9 Consensus size: 140
28125986 ACAATCAAAA
* * **
28125996 TCGAGGCTGATGCCATGCCCCAGACATGGTCTTAGACTAGCTCTCACATATCCGTGCCGATGCCA
1 TCGAGGCCGATGCCATGCCCCAGACATGGTCTTACACTAGCTCT-ACATATCAATGCCGATGCCA
* * *
28126061 TGTCCCAGACATGGTCTTACACTAACAAATCTCGTAGTCGATGCATGTCCCAGACATGTCTTACA
65 TGTCCCAAACATGGTCTTACACTAACAAA-CTCGTAGCCGATGCATGTCCCAAACATGTCTTACA
28126126 CTGGCTTACATC
129 CTGGCTTACATC
* * *
28126138 TCGAGGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT-CGTCTCAATGCCGATGCCAT
1 TCGAGGCCGATGCCATGCCCCAGACATGGTCTTACACTAGCTCTACATATCAATGCCGATGCCAT
** *
28126200 GTCCCAAACATGGTCTTACATTGGCTCTCATAA-T-GTGGCCGATGCATGTCCCAAACATGTCTT
66 GTCCCAAACATGGTCTTACA----CTAACA-AACTCGTAGCCGATGCATGTCCCAAACATGTCTT
28126263 ACACT
126 ACACT
28126268 AGCACACACA
Statistics
Matches: 112, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
138 35 0.31
140 46 0.41
141 14 0.12
142 15 0.13
143 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (140 bp):
TCGAGGCCGATGCCATGCCCCAGACATGGTCTTACACTAGCTCTACATATCAATGCCGATGCCAT
GTCCCAAACATGGTCTTACACTAACAAACTCGTAGCCGATGCATGTCCCAAACATGTCTTACACT
GGCTTACATC
Found at i:28127297 original size:14 final size:13
Alignment explanation
Indices: 28127274--28127305 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
28127264 GGAATATCAA
28127274 AACAATAATTAAG
1 AACAATAATTAAG
28127287 AACACATAATTAAG
1 AACA-ATAATTAAG
28127301 AACAA
1 AACAA
28127306 GTCAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:28142085 original size:21 final size:22
Alignment explanation
Indices: 28142038--28142091 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
28142028 AAAGGAAGTG
*
28142038 AGAAAAAGAAATCGAGAGAAGA
1 AGAAAAAGAAATCGAGAGAAAA
* *
28142060 A-AAAAAGACATGGA-AGAAAA
1 AGAAAAAGAAATCGAGAGAAAA
*
28142080 AGAAAAGGAAAT
1 AGAAAAAGAAAT
28142092 AAAAAGAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 6 0.23
21 19 0.73
22 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.24, T:0.06
Consensus pattern (22 bp):
AGAAAAAGAAATCGAGAGAAAA
Found at i:28144159 original size:18 final size:18
Alignment explanation
Indices: 28144136--28144200 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
28144126 TGGCCCATTA
*
28144136 CAGTAACAATAATCAGTG
1 CAGTAACAGTAATCAGTG
* *
28144154 CAGTAACAGTAATCGGTA
1 CAGTAACAGTAATCAGTG
*
28144172 CAGTAACAGTAATTAGTG
1 CAGTAACAGTAATCAGTG
28144190 CAGTAACAGTA
1 CAGTAACAGTA
28144201 TACAAGTCCT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (18 bp):
CAGTAACAGTAATCAGTG
Found at i:28152440 original size:40 final size:40
Alignment explanation
Indices: 28152393--28152492 Score: 164
Period size: 40 Copynumber: 2.5 Consensus size: 40
28152383 CCGGGCTATG
* *
28152393 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCCAAGTC
*
28152433 CCGAAGGCATTTGTGCAAGTTACTATAACCGGGCCAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCCAAGTC
28152473 CCGAAAGGCATTTGTGCGAG
1 CCG-AAGGCATTTGTGCGAG
28152493 CCAAGTCCCG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
40 40 0.73
41 15 0.27
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCCAAGTC
Found at i:28152513 original size:26 final size:27
Alignment explanation
Indices: 28152465--28152518 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
28152455 CTATAACCGG
*
28152465 GCCAAGTCCCGAAAGGCATTTGTGCGA
1 GCCAAGTCCCGAAAGGCAATTGTGCGA
28152492 GCCAAGTCCCG-AAGGCAATTGTGCGA
1 GCCAAGTCCCGAAAGGCAATTGTGCGA
28152518 G
1 G
28152519 TTACTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.26, C:0.26, G:0.31, T:0.17
Consensus pattern (27 bp):
GCCAAGTCCCGAAAGGCAATTGTGCGA
Found at i:28152539 original size:67 final size:66
Alignment explanation
Indices: 28152428--28152558 Score: 199
Period size: 67 Copynumber: 2.0 Consensus size: 66
28152418 TATCCGGGCT
* *
28152428 AAGTCCCGAAGGCATTTGTGCAAGTTACTATAACCGGGCCAAGTCCCGAAAGGCATTTGTGCGAG
1 AAGTCCCGAAGGCAATTGTGCAAGTTACTATAACCGGGCCAAGTCCC-AAAGGCAATTGTGCGAG
28152493 CC
65 CC
* ** *
28152495 AAGTCCCGAAGGCAATTGTGCGAGTTACTATAATTGGGCTAAGTCCCAAAGGCAATTGTGCGAG
1 AAGTCCCGAAGGCAATTGTGCAAGTTACTATAACCGGGCCAAGTCCCAAAGGCAATTGTGCGAG
28152559 TTACTATAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
66 16 0.28
67 42 0.72
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.22
Consensus pattern (66 bp):
AAGTCCCGAAGGCAATTGTGCAAGTTACTATAACCGGGCCAAGTCCCAAAGGCAATTGTGCGAGC
C
Found at i:28152550 original size:40 final size:40
Alignment explanation
Indices: 28152495--28152625 Score: 167
Period size: 40 Copynumber: 3.3 Consensus size: 40
28152485 TGTGCGAGCC
**
28152495 AAGTCCCGAAGGCAATTGTGCGAGTTACTATAATTGGGCT
1 AAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCT
*
28152535 AAGTCCCAAAGGCAATTGTGCGAGTTACTATAACCGGGCT
1 AAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCT
* * *
28152575 AAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC-GGCT
1 AAGTCCCGAAGGCAATTGTGCGAGTTA-CTATAACCGGGCT
**
28152614 AAACCCCGAAGG
1 AAGTCCCGAAGG
28152626 TACTTGGTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
39 16 0.20
40 65 0.80
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (40 bp):
AAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCT
Found at i:28152579 original size:107 final size:106
Alignment explanation
Indices: 28152393--28152598 Score: 324
Period size: 107 Copynumber: 1.9 Consensus size: 106
28152383 CCGGGCTATG
* * *
28152393 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTA
1 CCGAAGGCAATTGTGCGAGTTACTATATCCGGGCTAAGTCCCAAAGGCAATTGTGCAAGTTACTA
*
28152458 TAACCGGGCCAAGTCCCGAAAGGCATTTGTGCGAGCCAAGTC
66 TAACCGGGCCAAGTCCCG-AAGGCATTTGAGCGAGCCAAGTC
* *
28152500 CCGAAGGCAATTGTGCGAGTTACTATAAT-TGGGCTAAGTCCCAAAGGCAATTGTGCGAGTTACT
1 CCGAAGGCAATTGTGCGAGTTACTAT-ATCCGGGCTAAGTCCCAAAGGCAATTGTGCAAGTTACT
*
28152564 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG
65 ATAACCGGGCCAAGTCCCGAAGGCATTTGAGCGAG
28152599 TAGCTATATC
Statistics
Matches: 91, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
106 15 0.16
107 74 0.81
108 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (106 bp):
CCGAAGGCAATTGTGCGAGTTACTATATCCGGGCTAAGTCCCAAAGGCAATTGTGCAAGTTACTA
TAACCGGGCCAAGTCCCGAAGGCATTTGAGCGAGCCAAGTC
Found at i:28160613 original size:42 final size:40
Alignment explanation
Indices: 28160506--28160613 Score: 143
Period size: 38 Copynumber: 2.8 Consensus size: 40
28160496 CGGATTAATA
*
28160506 AACCGGGCTAAG-CCCGAA-GCATTTGTGCGAGTTACTAT
1 AACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAT
* *
28160544 ATCCGGGCTAA-T-CCGAAGACATTTGTGCAAGTTACTAT
1 AACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAT
28160582 AACCGGGACCTAAGTCCCGAAGGCATTTGTGC
1 AACCGGG--CTAAGTCCCGAAGGCATTTGTGC
28160614 NNNNNNNNNN
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
37 5 0.08
38 34 0.58
40 4 0.07
41 1 0.02
42 15 0.25
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (40 bp):
AACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAT
Found at i:28178037 original size:43 final size:43
Alignment explanation
Indices: 28177971--28178056 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
28177961 AAATCATACA
* *
28177971 ATGCCAATGTCCTAGACGTGGTCTTACAT-GTAACCACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTAC-TCGTAAACACATATCG
*
28178014 ATGCCATTGTCCCAGACAG-GGTCTTACTCGTAAACACATATCG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACTCGTAAACACATATCG
28178057 GAATCACAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 1 0.03
43 36 0.95
44 1 0.03
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACTCGTAAACACATATCG
Found at i:28196527 original size:18 final size:20
Alignment explanation
Indices: 28196486--28196528 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
28196476 TTACAAAAAG
*
28196486 AAATTCAAAAATAGTTTTTA
1 AAATTCAAAAATAGTTTATA
28196506 AAATTC-AAAATA-TTTATA
1 AAATTCAAAAATAGTTTATA
28196524 AAATT
1 AAATT
28196529 TCCAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 6 0.27
20 6 0.27
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATTCAAAAATAGTTTATA
Found at i:28198933 original size:30 final size:30
Alignment explanation
Indices: 28198892--28198948 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
28198882 ATTTCTAGCA
* *
28198892 TAGGGGTAAAATGGTCATTTTGCCAAAGTC
1 TAGGGGCAAAATGGTCATTTTACCAAAGTC
28198922 TAGGGGCAAAATGGTCATTTTACCAAA
1 TAGGGGCAAAATGGTCATTTTACCAAA
28198949 TATGTGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTACCAAAGTC
Found at i:28199544 original size:49 final size:48
Alignment explanation
Indices: 28199290--28199543 Score: 188
Period size: 46 Copynumber: 5.4 Consensus size: 48
28199280 TTACTTGTGT
* * * * *
28199290 GCCAGTGAAAGA-CATGTCTGAGACATGCATCGGCCACAAT-ATG-TA
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCAGCCTCGATGATGATA
*
28199335 GCCAGTGTAAGACCATGTCTGGGACATGTATCAGCCTCGATGATGATA
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCAGCCTCGATGATGATA
* * * * * *
28199383 GCCAGTGTAAGA-CGTGTTTGGGACACGCATC-GGCTAAGA-GTTG-T-
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCAGCCT-CGATGATGATA
* * * **
28199427 GCTAGTGTAAGA-CATGTTTGGGACATGCATCAGCACAT--ATAGAAGAGG
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCAGC-C-TCGAT-GATGATA
* * * *
28199475 GCTAGTATAAGACCCTGTCTAGGACATGGCATCAGCCTCGATGATGATA
1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCAGCCTCGATGATGATA
*
28199524 GCCAGTGTAAGACCAAGTCT
1 GCCAGTGTAAGACCATGTCT
28199544 AAAACATGGC
Statistics
Matches: 163, Mismatches: 31, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
44 29 0.18
45 13 0.08
46 32 0.20
47 21 0.13
48 26 0.16
49 32 0.20
50 10 0.06
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (48 bp):
GCCAGTGTAAGACCATGTCTGGGACATGCATCAGCCTCGATGATGATA
Found at i:28200410 original size:55 final size:55
Alignment explanation
Indices: 28200321--28200510 Score: 272
Period size: 55 Copynumber: 3.5 Consensus size: 55
28200311 GTACTTAAAA
* * * * * *
28200321 TTTAAAGTTAGTGTTGAACACGAGCAAGCCACACGGGCGTGTATCAAGGCCGTGT
1 TTTAAAGTCAGTGTCGTACACGGGCAGGCCACACGGGCGTGTGTCAAGGCCGTGT
*
28200376 TTTAAAGTCAGTGTCGTACACGGGCAGGCTACACGGGCGTGTGTCAAGGCCGTGT
1 TTTAAAGTCAGTGTCGTACACGGGCAGGCCACACGGGCGTGTGTCAAGGCCGTGT
* * *
28200431 TTTAAAGTCAGTGTCGTACACGGGTAGGCCACACGGGCATGTGTCATGGCCGTGT
1 TTTAAAGTCAGTGTCGTACACGGGCAGGCCACACGGGCGTGTGTCAAGGCCGTGT
* *
28200486 TTTAAAGTCAGTGTTGCACACGGGC
1 TTTAAAGTCAGTGTCGTACACGGGC
28200511 TAAGGGCACA
Statistics
Matches: 121, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 121 1.00
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.25
Consensus pattern (55 bp):
TTTAAAGTCAGTGTCGTACACGGGCAGGCCACACGGGCGTGTGTCAAGGCCGTGT
Found at i:28203972 original size:21 final size:19
Alignment explanation
Indices: 28203925--28203973 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
28203915 AAAAAGGAAG
*
28203925 AGAAAGGAAAAGGGAGAAA
1 AGAAAAGAAAAGGGAGAAA
* *
28203944 ATAAAAGAAAAGGTGAAGAGA
1 AGAAAAGAAAAGG-G-AGAAA
28203965 AGAAAAGAA
1 AGAAAAGAA
28203974 GAAAAGGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 11 0.46
20 1 0.04
21 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (19 bp):
AGAAAAGAAAAGGGAGAAA
Found at i:28209849 original size:47 final size:47
Alignment explanation
Indices: 28209774--28209900 Score: 141
Period size: 47 Copynumber: 2.7 Consensus size: 47
28209764 ACAATTGATA
* * *
28209774 AGTACCTATACCATGTCCCGTA-ACCAAATCAAGATAACTTATCCCAT-
1 AGTACCTATACCATGGCCTGTAGA-CAAATCAAGATAACTCAT-CCATG
* * *
28209821 AGTACCTATACCATGGCCTGTAGACAAATCAAGGTAACTCCTCTATG
1 AGTACCTATACCATGGCCTGTAGACAAATCAAGATAACTCATCCATG
* * *
28209868 AATACCTATACCATGGCCTGTAGCCACATCAAG
1 AGTACCTATACCATGGCCTGTAGACAAATCAAG
28209901 GTATTATTCA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 3 0.04
47 65 0.94
48 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.24
Consensus pattern (47 bp):
AGTACCTATACCATGGCCTGTAGACAAATCAAGATAACTCATCCATG
Found at i:28211559 original size:5 final size:5
Alignment explanation
Indices: 28211549--28211602 Score: 65
Period size: 5 Copynumber: 10.6 Consensus size: 5
28211539 AATATTAAAC
* *
28211549 TATAT TATAT TTTGAAT TATAT TA-AT TATAT TATGT TATAT TATAT TATAT
1 TATAT TATAT TAT--AT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
28211600 TAT
1 TAT
28211603 TATGAAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
4 4 0.10
5 34 0.81
7 4 0.10
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:28212494 original size:12 final size:11
Alignment explanation
Indices: 28212474--28212525 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
28212464 GTTAAGATTA
*
28212474 AAATTGAAATT
1 AAATAGAAATT
28212485 AAAGTAGAAATT
1 AAA-TAGAAATT
*
28212497 GAATAGAAATT
1 AAATAGAAATT
*
28212508 GAATAAGAAATTT
1 AAAT-AGAAA-TT
28212521 AAATA
1 AAATA
28212526 TTAAATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 15 0.43
12 15 0.43
13 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (11 bp):
AAATAGAAATT
Found at i:28212505 original size:11 final size:11
Alignment explanation
Indices: 28212479--28212519 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
28212469 GATTAAAATT
*
28212479 GAAATTAAAGTA
1 GAAATTGAA-TA
28212491 GAAATTGAATA
1 GAAATTGAATA
28212502 GAAATTGAATAA
1 GAAATTGAAT-A
28212514 GAAATT
1 GAAATT
28212520 TAAATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 12 0.44
12 15 0.56
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.27
Consensus pattern (11 bp):
GAAATTGAATA
Found at i:28212778 original size:24 final size:24
Alignment explanation
Indices: 28212750--28212803 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
28212740 TTAGAATTGG
28212750 AGTGAACCTTGGTTGAAATTGAAT
1 AGTGAACCTTGGTTGAAATTGAAT
28212774 AGTGAACCTTGGTTGAAATTGAAT
1 AGTGAACCTTGGTTGAAATTGAAT
28212798 AGTGAA
1 AGTGAA
28212804 TTTCCGGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.31
Consensus pattern (24 bp):
AGTGAACCTTGGTTGAAATTGAAT
Found at i:28215190 original size:5 final size:5
Alignment explanation
Indices: 28215180--28215233 Score: 65
Period size: 5 Copynumber: 10.6 Consensus size: 5
28215170 AATATTAAAC
* *
28215180 TATAT TATATTT TAAAT TATAT TA-AT TATAT TATGT TATAT TATAT TATAT
1 TATAT TATA--T TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
28215231 TAT
1 TAT
28215234 TATGAAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
4 4 0.10
5 34 0.81
7 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:28215204 original size:10 final size:10
Alignment explanation
Indices: 28215171--28215232 Score: 51
Period size: 10 Copynumber: 6.6 Consensus size: 10
28215161 ATGTTGATTA
*
28215171 ATATTAAACT
1 ATATTAAATT
28215181 ATATT--A-T
1 ATATTAAATT
*
28215188 ATTTTAAATT
1 ATATTAAATT
28215198 ATATT-AATT
1 ATATTAAATT
**
28215207 ATATTATGTT
1 ATATTAAATT
*
28215217 ATATTATATT
1 ATATTAAATT
28215227 ATATTA
1 ATATTA
28215233 TTATGAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
7 5 0.12
8 1 0.02
9 10 0.23
10 27 0.63
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (10 bp):
ATATTAAATT
Found at i:28216121 original size:12 final size:11
Alignment explanation
Indices: 28216101--28216152 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
28216091 GTTAAGATTA
*
28216101 AAATTGAAATT
1 AAATAGAAATT
28216112 AAAGTAGAAATT
1 AAA-TAGAAATT
*
28216124 GAATAGAAATT
1 AAATAGAAATT
*
28216135 GAATAAGAAATTT
1 AAAT-AGAAA-TT
28216148 AAATA
1 AAATA
28216153 TTAAATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 15 0.43
12 15 0.43
13 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (11 bp):
AAATAGAAATT
Found at i:28216132 original size:11 final size:11
Alignment explanation
Indices: 28216106--28216146 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
28216096 GATTAAAATT
*
28216106 GAAATTAAAGTA
1 GAAATTGAA-TA
28216118 GAAATTGAATA
1 GAAATTGAATA
28216129 GAAATTGAATAA
1 GAAATTGAAT-A
28216141 GAAATT
1 GAAATT
28216147 TAAATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 12 0.44
12 15 0.56
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.27
Consensus pattern (11 bp):
GAAATTGAATA
Found at i:28216845 original size:44 final size:44
Alignment explanation
Indices: 28216796--28216887 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
28216786 TGTTCAGGGA
*
28216796 TACTTCGACATTGAGTCGATGAGGCA-CTATAAGTGTCGTACTGT
1 TACTTCGACATTAAGTCGATGAGGCACCT-TAAGTGTCGTACTGT
* * **
28216840 TACTTCGACTTTAAGTTGATGAGGCACCTTGTGTGTCGTACTGT
1 TACTTCGACATTAAGTCGATGAGGCACCTTAAGTGTCGTACTGT
28216884 TACT
1 TACT
28216888 GTTAATTCGG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 40 0.95
45 2 0.05
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (44 bp):
TACTTCGACATTAAGTCGATGAGGCACCTTAAGTGTCGTACTGT
Found at i:28218326 original size:27 final size:27
Alignment explanation
Indices: 28218291--28218496 Score: 186
Period size: 27 Copynumber: 7.6 Consensus size: 27
28218281 TTAGTTTACC
* * *
28218291 AAATTACCAAAATACCCTCGATTAGCA
1 AAATTACCAAAATACCCTCGGTTTGTA
28218318 AAATTACCAAAATATCCCT-GGTTTGTA
1 AAATTACCAAAATA-CCCTCGGTTTGTA
*
28218345 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCGGTTTGTA
28218372 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
** *
28218399 AAATTACCAAAATACCC-CTGACTTGTG
1 AAATTACCAAAATACCCTC-GGTTTGTA
** ***
28218426 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTCGGTTTGTA
** ***
28218453 AAATTATTGAAAA-ACCCTCAACTTGTA
1 AAATTA-CCAAAATACCCTCGGTTTGTA
*
28218480 AAATTACCAAAGTACCC
1 AAATTACCAAAATACCC
28218497 CCAATTTACA
Statistics
Matches: 154, Mismatches: 19, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
26 7 0.05
27 139 0.90
28 8 0.05
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.28
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGGTTTGTA
Found at i:28218375 original size:54 final size:54
Alignment explanation
Indices: 28218291--28218415 Score: 205
Period size: 54 Copynumber: 2.3 Consensus size: 54
28218281 TTAGTTTACC
*
28218291 AAATTACCAAAATACCCTCGATTAGCAAAATTACCAAAATATCCCTGGTTTGTA
1 AAATTACCAAAATACCCTCGATTAGCAAAATTACCAAAATACCCCTGGTTTGTA
* * * *
28218345 AAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTCGATTAGCAAAATTACCAAAATACCCCTGGTTTGTA
28218399 AAATTACCAAAATACCC
1 AAATTACCAAAATACCC
28218416 CTGACTTGTG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (54 bp):
AAATTACCAAAATACCCTCGATTAGCAAAATTACCAAAATACCCCTGGTTTGTA
Found at i:28218430 original size:81 final size:81
Alignment explanation
Indices: 28218291--28218443 Score: 209
Period size: 81 Copynumber: 1.9 Consensus size: 81
28218281 TTAGTTTACC
* **
28218291 AAATTACCAAAATACCCTCGATTAGCAAAATTACCAAAATATCCCTGGTTTGTAAAATTACCAAA
1 AAATTACCAAAATACCCTCGATTAGCAAAATTACCAAAATACCCCTGACTTGTAAAATTACCAAA
28218356 ATACCCTTGGTTTGTA
66 ATACCCTTGGTTTGTA
* * * * **
28218372 AAATTACCAAAATACCC-CTGGTTTGTAAAATTACCAAAATACCCCTGACTTGTGAAATTACTGA
1 AAATTACCAAAATACCCTC-GATTAGCAAAATTACCAAAATACCCCTGACTTGTAAAATTACCAA
28218436 AATACCCT
65 AATACCCT
28218444 CGACCTGTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
80 1 0.02
81 61 0.98
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (81 bp):
AAATTACCAAAATACCCTCGATTAGCAAAATTACCAAAATACCCCTGACTTGTAAAATTACCAAA
ATACCCTTGGTTTGTA
Found at i:28218564 original size:27 final size:27
Alignment explanation
Indices: 28218543--28218727 Score: 235
Period size: 27 Copynumber: 6.9 Consensus size: 27
28218533 GAAATTATTA
*
28218543 AAATACCCCTGTAGGGTAAAATTACTG
1 AAATACCCCTGTAGGGTAAAATTACCG
* * *
28218570 AAATACCCCTGTATGGTAGAATTATCG
1 AAATACCCCTGTAGGGTAAAATTACCG
* *
28218597 AAATACCCTTGTAGGGTAAAAATACCG
1 AAATACCCCTGTAGGGTAAAATTACCG
* *
28218624 AAATACCCCTGTAGGGTAGAATTATCG
1 AAATACCCCTGTAGGGTAAAATTACCG
* *
28218651 AAATACCCTTGTAGGGTAAAAATACCG
1 AAATACCCCTGTAGGGTAAAATTACCG
* *
28218678 AAATACCCCTGTAGGATAGAATTACCG
1 AAATACCCCTGTAGGGTAAAATTACCG
* * *
28218705 AGATACCCTTGTGGGGTAAAATT
1 AAATACCCCTGTAGGGTAAAATT
28218728 TCCATTTTTC
Statistics
Matches: 132, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 132 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAAAATTACCG
Found at i:28218741 original size:54 final size:53
Alignment explanation
Indices: 28218543--28218725 Score: 285
Period size: 54 Copynumber: 3.4 Consensus size: 53
28218533 GAAATTATTA
* * *
28218543 AAATACCCCTGTAGGGTAAAATTACTGAAATACCCCTGTATGGTAGAATTATCG
1 AAATACCCTTGTAGGGTAAAAATACCGAAATACCCCTGTA-GGTAGAATTATCG
28218597 AAATACCCTTGTAGGGTAAAAATACCGAAATACCCCTGTAGGGTAGAATTATCG
1 AAATACCCTTGTAGGGTAAAAATACCGAAATACCCCTGTA-GGTAGAATTATCG
*
28218651 AAATACCCTTGTAGGGTAAAAATACCGAAATACCCCTGTAGGATAGAATTACCG
1 AAATACCCTTGTAGGGTAAAAATACCGAAATACCCCTGTAGG-TAGAATTATCG
* *
28218705 AGATACCCTTGTGGGGTAAAA
1 AAATACCCTTGTAGGGTAAAA
28218726 TTTCCATTTT
Statistics
Matches: 121, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 2 0.02
54 119 0.98
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (53 bp):
AAATACCCTTGTAGGGTAAAAATACCGAAATACCCCTGTAGGTAGAATTATCG
Found at i:28219403 original size:27 final size:27
Alignment explanation
Indices: 28219373--28219453 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 27
28219363 ATTCTATTAA
*
28219373 GTGGCTTTGCCACATTATCTGATTCTG
1 GTGGCTTTGCCACAATATCTGATTCTG
*
28219400 GTGGCTCTGCCACAATATCTG-TATCTG
1 GTGGCTTTGCCACAATATCTGAT-TCTG
** *
28219427 GTGATTTTGTCACAATATCT-ATTCTG
1 GTGGCTTTGCCACAATATCTGATTCTG
28219453 G
1 G
28219454 AAGCCATGCT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
26 6 0.13
27 40 0.87
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (27 bp):
GTGGCTTTGCCACAATATCTGATTCTG
Found at i:28219579 original size:6 final size:6
Alignment explanation
Indices: 28219570--28219731 Score: 100
Period size: 6 Copynumber: 26.3 Consensus size: 6
28219560 TTGCATTCAC
* * *
28219570 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG -TCACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG
* * * *
28219620 ATACTG ATTCTG ATTCTG ATTCTA ATTTTG ATTCTA ATTCTG -TTACCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG
* * * * *
28219669 ATACTG ATTCTG ATTCTG -TCACCTG ATTCTG ATTCTA ATTCTC ATTTTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
28219718 ATTCT- AGTTCTG AT
1 ATTCTG A-TTCTG AT
28219732 AATGTTTCTT
Statistics
Matches: 120, Mismatches: 22, Indels: 28
0.71 0.13 0.16
Matches are distributed among these distances:
5 7 0.06
6 97 0.81
7 12 0.10
8 4 0.03
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (6 bp):
ATTCTG
Found at i:28219601 original size:25 final size:25
Alignment explanation
Indices: 28219573--28219710 Score: 172
Period size: 25 Copynumber: 5.6 Consensus size: 25
28219563 CATTCACATT
28219573 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTTACCTGATA
* *
28219598 CTGATTCTGATTCTGTCACCTAATA
1 CTGATTCTGATTCTGTTACCTGATA
* *
28219623 CTGATTCTGATTCTGATT--CTAATT
1 CTGATTCTGATTCTG-TTACCTGATA
* *
28219647 TTGATTCTAATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTTACCTGATA
* *
28219672 CTGATTCTGATTCTGTCACCTGATT
1 CTGATTCTGATTCTGTTACCTGATA
*
28219697 CTGATTCTAATTCT
1 CTGATTCTGATTCT
28219711 CATTTTGATT
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
23 2 0.02
24 18 0.19
25 76 0.78
26 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (25 bp):
CTGATTCTGATTCTGTTACCTGATA
Found at i:28219679 original size:68 final size:68
Alignment explanation
Indices: 28219574--28219729 Score: 186
Period size: 74 Copynumber: 2.2 Consensus size: 68
28219564 ATTCACATTC
* * * *
28219574 TGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAATACTGATTCTGATTCTGA
1 TGATTCTAATTCTGTTACCTGATACTGATTCTGATCCTATCA-C-----CTGATTCTGATTCTAA
28219639 TTCTAATTT
60 TTCTAATTT
* * *
28219648 TGATTCTAATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTGATTCTGATTCTAATTCTCA
1 TGATTCTAATTCTGTTACCTGATACTGATTCTGATCCTATCACCTGATTCTGATTCTAATTCTAA
28219713 TTT
66 TTT
*
28219716 TGATTCTAGTTCTG
1 TGATTCTAATTCTG
28219730 ATAATGTTTC
Statistics
Matches: 78, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
68 36 0.46
73 1 0.01
74 41 0.53
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (68 bp):
TGATTCTAATTCTGTTACCTGATACTGATTCTGATCCTATCACCTGATTCTGATTCTAATTCTAA
TTT
Found at i:28232546 original size:50 final size:50
Alignment explanation
Indices: 28232422--28232656 Score: 224
Period size: 50 Copynumber: 4.7 Consensus size: 50
28232412 CGAAGCTATC
* * * * * *
28232422 TGATACGCATAGTAGCCTGCACTTAGTACTACTCATGCGACC-AACAATC
1 TGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATT
* * * *
28232471 CGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCATT
1 TGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATT
* * * ** *
28232521 TGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTAAT
1 TGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATT
* * * * * *
28232571 TGAGTACGCATAGTAGCCTGCACTTAGTACTAAACATGCGACTTAA-CAGTA
1 TGA-TACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCA-TT
*
28232622 TGGTACACGTAGTAGCCTGCACTTAGTAC-ACACAC
1 TGATACACGTAGTAGCCTGCACTTAGTACTACACAC
28232657 ATGTATTCAC
Statistics
Matches: 149, Mismatches: 34, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
49 39 0.26
50 74 0.50
51 36 0.24
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (50 bp):
TGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATT
Found at i:28238912 original size:40 final size:40
Alignment explanation
Indices: 28238868--28238972 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
28238858 CGACAACAAA
* * * *
28238868 TCGGCTATTTGTGGCACCTAGTGTGCGATTCGACATAGCT
1 TCGGCTATATATGGCACTTAGTGTGCAATTCGACATAGCT
* * *
28238908 TCGGCTATATATGGCAATTAGTGTGCAATTTGAGATAGCT
1 TCGGCTATATATGGCACTTAGTGTGCAATTCGACATAGCT
* *
28238948 TCGACTATGTATGGCACTTAGTGTG
1 TCGGCTATATATGGCACTTAGTGTG
28238973 TGAGATATCG
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (40 bp):
TCGGCTATATATGGCACTTAGTGTGCAATTCGACATAGCT
Found at i:28238999 original size:28 final size:28
Alignment explanation
Indices: 28238956--28239043 Score: 131
Period size: 28 Copynumber: 3.1 Consensus size: 28
28238946 CTTCGACTAT
*
28238956 GTATGGCACTTAGTGTGTGAGATATCGA
1 GTATGGCACTTAGTGTGCGAGATATCGA
*
28238984 GTGTGGCACTTAGTGTGCGAGATATCGA
1 GTATGGCACTTAGTGTGCGAGATATCGA
* * *
28239012 GTATGGCACTTAGTATGCGAGACATTGA
1 GTATGGCACTTAGTGTGCGAGATATCGA
28239040 GTAT
1 GTAT
28239044 TCAATGGTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.25, C:0.12, G:0.32, T:0.31
Consensus pattern (28 bp):
GTATGGCACTTAGTGTGCGAGATATCGA
Found at i:28254780 original size:23 final size:23
Alignment explanation
Indices: 28254750--28254795 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
28254740 TATCTTTAGT
*
28254750 ATTTACAATAATTACCCTGATAA
1 ATTTACAATAATTACCATGATAA
28254773 ATTTACAATAATTACCATGATAA
1 ATTTACAATAATTACCATGATAA
28254796 CTCTAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (23 bp):
ATTTACAATAATTACCATGATAA
Found at i:28255776 original size:20 final size:21
Alignment explanation
Indices: 28255743--28255781 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
28255733 GGCAAAAAGA
28255743 ATCAAAAGAGAATT-AATCTG
1 ATCAAAAGAGAATTCAATCTG
28255763 ATCAAGAAGA-AATTCAATC
1 ATCAA-AAGAGAATTCAATC
28255782 CAAACACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (21 bp):
ATCAAAAGAGAATTCAATCTG
Found at i:28257920 original size:45 final size:45
Alignment explanation
Indices: 28257879--28257966 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 45
28257869 TGTCTTTGAG
* * *
28257879 CTATGGTCTTACTCAATTTTATCCTGATGCCATAGCATCTTTCAA
1 CTATGGTATTACTCAATTTTATCCTAATGACATAGCATCTTTCAA
* ** *
28257924 TTATGGTATTACTCTTTTTTATCCTAATTACATAGCATCTTTC
1 CTATGGTATTACTCAATTTTATCCTAATGACATAGCATCTTTC
28257967 GGCATTGTCT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (45 bp):
CTATGGTATTACTCAATTTTATCCTAATGACATAGCATCTTTCAA
Found at i:28259304 original size:25 final size:24
Alignment explanation
Indices: 28259253--28259305 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
28259243 GCCATTAGGG
* * * *
28259253 TTACCGATTCCAGCTCTTATTAGC
1 TTACCGATACCAGCTCGTATGAAC
28259277 TTACCGATACTCAGCTCGTATGAAC
1 TTACCGATAC-CAGCTCGTATGAAC
28259302 TTAC
1 TTAC
28259306 TGTTTTTCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (24 bp):
TTACCGATACCAGCTCGTATGAAC
Found at i:28265993 original size:18 final size:19
Alignment explanation
Indices: 28265971--28266016 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
28265961 TATTTTTATT
*
28265971 TTTTTATTTTTTTCTTTTC
1 TTTTTATTTTTCTCTTTTC
*
28265990 -TTTTA-TCTTCTCTTTTC
1 TTTTTATTTTTCTCTTTTC
28266007 TTTTTATTTT
1 TTTTTATTTT
28266017 ATGTTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
17 10 0.45
18 10 0.45
19 2 0.09
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTATTTTTCTCTTTTC
Found at i:28274158 original size:24 final size:22
Alignment explanation
Indices: 28274131--28274184 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
28274121 AGAGGTGTTA
28274131 CATCCATGATCTTTCCTATCCACT
1 CATCCAT-ATCTTT-CTATCCACT
* *
28274155 CATCCCATTTCTTTCTATCCATT
1 CAT-CCATATCTTTCTATCCACT
*
28274178 CCTCCAT
1 CATCCAT
28274185 TTCACCATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 10 0.38
24 8 0.31
25 4 0.15
ACGTcount: A:0.19, C:0.39, G:0.02, T:0.41
Consensus pattern (22 bp):
CATCCATATCTTTCTATCCACT
Found at i:28281026 original size:13 final size:12
Alignment explanation
Indices: 28281008--28281045 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
28280998 ATAAAAACAC
28281008 AAATTTAAAGATG
1 AAATTTAAA-ATG
28281021 AAATTT-AAATG
1 AAATTTAAAATG
28281032 AAATGTTAAAATG
1 AAAT-TTAAAATG
28281045 A
1 A
28281046 TTTTTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 7 0.30
12 4 0.17
13 12 0.52
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (12 bp):
AAATTTAAAATG
Found at i:28285468 original size:49 final size:48
Alignment explanation
Indices: 28285396--28285520 Score: 160
Period size: 48 Copynumber: 2.6 Consensus size: 48
28285386 AGATCCCGTC
*
28285396 TAAGACCATGTATGAGACATGGCATCGGCATTCGAGATGAGAGCCAGTG
1 TAAGACCATGTATGGGACATGGCATCGGCATT-GAGATGAGAGCCAGTG
* * * * *
28285445 TAAGACCATGTTTGGGACATGGCATCGGCGTTGATATGTGTGCCAGTG
1 TAAGACCATGTATGGGACATGGCATCGGCATTGAGATGAGAGCCAGTG
* * *
28285493 TAAGACCATGTCTGGAAAATGGCATCGG
1 TAAGACCATGTATGGGACATGGCATCGG
28285521 TACCGATATG
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
48 38 0.57
49 29 0.43
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (48 bp):
TAAGACCATGTATGGGACATGGCATCGGCATTGAGATGAGAGCCAGTG
Found at i:28290900 original size:235 final size:235
Alignment explanation
Indices: 28290386--28291075 Score: 1127
Period size: 235 Copynumber: 2.9 Consensus size: 235
28290376 AAATCATTTG
*
28290386 ATAAAACGTTTCCAAGTTTTGCAAGAAATCCTAAGAATGTGAGGCTTGGGCTTGCATCTGATGGC
1 ATAAAA-GTTTCTAAGTTTTGCAAGAAATCCTAAGAATGTGAGGCTTGGGCTTGCATCTGATGGC
*
28290451 CTTAATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCTTGTTGTGTTTGTTCCTTACAA
65 CTTAATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCTTGTTGTGCTTGTTCCTTACAA
* * *
28290516 TTTGCCTCCATGAATTT-CATGAAACAAAT-TTCTTTTATCTTATCTATGATAATCTTTGGGGTG
130 TTTGCCTCCATGGATTTGCATGAAAC-AATCTTCTTTTATCTTATCTATGATAATCCTTGGGGAG
*
28290579 AAAGGTCTAAAGAACGATATTGGCATTTATATGCAGTCACTT
194 AAAGGTCTAAAGAATGATATTGGCATTTATATGCAGTCACTT
* *
28290621 ATAAAAGTTTCTAAGTTTTGCAAGAAATCCTAAGAATGTGAGGCTTAGGCTTGCATCTGATAGCC
1 ATAAAAGTTTCTAAGTTTTGCAAGAAATCCTAAGAATGTGAGGCTTGGGCTTGCATCTGATGGCC
28290686 TTAATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCTTGTTGTGCTTGTTCCTTACAAT
66 TTAATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCTTGTTGTGCTTGTTCCTTACAAT
* * * *
28290751 TTGCCTCTATGGATTTGCATGAAACAATCTTATTTTATCTTATCTATGATAATCCCTAGGGAGAA
131 TTGCCTCCATGGATTTGCATGAAACAATCTTCTTTTATCTTATCTATGATAATCCTTGGGGAGAA
*
28290816 AGGTCTAAAGAATGATATTGGCATTTATATGCAGTCGCTT
196 AGGTCTAAAGAATGATATTGGCATTTATATGCAGTCACTT
*
28290856 ATAAAAGTTTCTAAGTTTTGCAA-ACAATCTTAAGAATGTGAGGCTTGGGCTTGCATCTGATGGC
1 ATAAAAGTTTCTAAGTTTTGCAAGA-AATCCTAAGAATGTGAGGCTTGGGCTTGCATCTGATGGC
* * * *
28290920 CTTAATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTCGCCTGTTATGCTTGATCCTTACAA
65 CTTAATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCTTGTTGTGCTTGTTCCTTACAA
* * *
28290985 TATGCCTCCATAGATTTGCATGAAACAATCTTCTTTTATTTTATCTATGATAATCCTTGGGGAGA
130 TTTGCCTCCATGGATTTGCATGAAACAATCTTCTTTTATCTTATCTATGATAATCCTTGGGGAGA
28291050 AAGGTCTAAAGAACT-ATATTGGCATT
195 AAGGTCTAAAGAA-TGATATTGGCATT
28291076 ACTATACATA
Statistics
Matches: 424, Mismatches: 27, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
234 138 0.33
235 285 0.67
236 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (235 bp):
ATAAAAGTTTCTAAGTTTTGCAAGAAATCCTAAGAATGTGAGGCTTGGGCTTGCATCTGATGGCC
TTAATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCTTGTTGTGCTTGTTCCTTACAAT
TTGCCTCCATGGATTTGCATGAAACAATCTTCTTTTATCTTATCTATGATAATCCTTGGGGAGAA
AGGTCTAAAGAATGATATTGGCATTTATATGCAGTCACTT
Found at i:28298984 original size:31 final size:31
Alignment explanation
Indices: 28298949--28299008 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
28298939 ACAACACAGT
*
28298949 AACTTACATAAAAACTTTTCAATAATTCAGC
1 AACTTAAATAAAAACTTTTCAATAATTCAGC
* ** *
28298980 AACTTAAATGAAATTTTTTGAATAATTCA
1 AACTTAAATAAAAACTTTTCAATAATTCA
28299009 ACGACTAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (31 bp):
AACTTAAATAAAAACTTTTCAATAATTCAGC
Found at i:28299100 original size:26 final size:26
Alignment explanation
Indices: 28299064--28299113 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
28299054 TTACTCATAA
28299064 TTTAATAACTAATGATATAGTTTATG
1 TTTAATAACTAATGATATAGTTTATG
*
28299090 TTTAATGACTAATGATATAGTTTA
1 TTTAATAACTAATGATATAGTTTA
28299114 CTTTAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (26 bp):
TTTAATAACTAATGATATAGTTTATG
Found at i:28299218 original size:33 final size:30
Alignment explanation
Indices: 28299160--28299245 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 30
28299150 ATTCATAATT
* *
28299160 TTTTATATGTTAATTATTCATTTATACAAAA
1 TTTTATAT-TTAATTCTTTATTTATACAAAA
* *
28299191 TTTAATATATTTAATTCTTTATATTATATAATA
1 TTT--TATATTTAATTCTTTAT-TTATACAAAA
* *
28299224 TTTCATATTTATTTCTTTATTT
1 TTTTATATTTAATTCTTTATTT
28299246 GAAAGGTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
30 2 0.04
31 18 0.39
32 10 0.22
33 16 0.35
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (30 bp):
TTTTATATTTAATTCTTTATTTATACAAAA
Found at i:28301173 original size:35 final size:35
Alignment explanation
Indices: 28301127--28301196 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
28301117 AATTTGACTA
28301127 GTTTTTGAGTAGAGAGAGCAAAATGCAATCTGAGT
1 GTTTTTGAGTAGAGAGAGCAAAATGCAATCTGAGT
28301162 GTTTTTGAGTAGAGAGAGCAAAATGCAATCTGAGT
1 GTTTTTGAGTAGAGAGAGCAAAATGCAATCTGAGT
28301197 CCTAGTATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.29
Consensus pattern (35 bp):
GTTTTTGAGTAGAGAGAGCAAAATGCAATCTGAGT
Found at i:28307687 original size:9 final size:9
Alignment explanation
Indices: 28307673--28307698 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28307663 TTCATATCAC
28307673 TGTGAATTT
1 TGTGAATTT
28307682 TGTGAATTT
1 TGTGAATTT
28307691 TGTGAATT
1 TGTGAATT
28307699 AGCAAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (9 bp):
TGTGAATTT
Found at i:28310528 original size:19 final size:19
Alignment explanation
Indices: 28310504--28310547 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
28310494 ATATTTTAAA
*
28310504 TTTATTTAGGTAGACAAAT
1 TTTATTTAGGAAGACAAAT
* *
28310523 TTTATTTAGGAAGATAAGT
1 TTTATTTAGGAAGACAAAT
28310542 TTTATT
1 TTTATT
28310548 CTTATTCTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (19 bp):
TTTATTTAGGAAGACAAAT
Found at i:28311963 original size:13 final size:13
Alignment explanation
Indices: 28311947--28311976 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28311937 AGACTGAAAA
*
28311947 GCAAAACTGCAAT
1 GCAAAACCGCAAT
28311960 GCAAAACCGCAAT
1 GCAAAACCGCAAT
28311973 GCAA
1 GCAA
28311977 TTTTCATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.10
Consensus pattern (13 bp):
GCAAAACCGCAAT
Found at i:28321910 original size:45 final size:42
Alignment explanation
Indices: 28321836--28321959 Score: 133
Period size: 41 Copynumber: 2.9 Consensus size: 42
28321826 GATATGTGTT
* * * * *
28321836 TTCGTGTAAGACCACGTTTGGAACGTTGGCATCGATATATGTGG
1 TTCGTGTAAGACCATGTCTGGGACATTGGCATCGATAT-T-TGA
* *
28321880 TTACTTGTAAGACCATGTCTGGGACATTGGCTTCG-TATTTGA
1 TT-CGTGTAAGACCATGTCTGGGACATTGGCATCGATATTTGA
* *
28321922 TTCGTGTAAGACCTTGTCTGGGACAGTGGCATCGATAT
1 TTCGTGTAAGACCATGTCTGGGACATTGGCATCGATAT
28321960 GAGATAGCAT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 28 0.42
42 7 0.10
43 1 0.01
44 5 0.07
45 26 0.39
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (42 bp):
TTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATTTGA
Found at i:28333131 original size:24 final size:24
Alignment explanation
Indices: 28333104--28333155 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
28333094 CTATCCGGAG
* *
28333104 CTTCCTGATATGGTTTTTTGTGAA
1 CTTCCTGATAAGGTTCTTTGTGAA
28333128 CTTCCTGATAAGGTTCTTTGTGAA
1 CTTCCTGATAAGGTTCTTTGTGAA
28333152 CTTC
1 CTTC
28333156 TCTATTATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.46
Consensus pattern (24 bp):
CTTCCTGATAAGGTTCTTTGTGAA
Found at i:28336810 original size:19 final size:19
Alignment explanation
Indices: 28336763--28336810 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
28336753 ATGGTAAAGT
*
28336763 ATGTGATTTAGAAATGAAA
1 ATGTGAATTAGAAATGAAA
* *
28336782 AAGTGGATTAGAAAATG-AA
1 ATGTGAATTAG-AAATGAAA
28336801 ATGTGAATTA
1 ATGTGAATTA
28336811 TGTTGTGAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (19 bp):
ATGTGAATTAGAAATGAAA
Found at i:28339336 original size:38 final size:38
Alignment explanation
Indices: 28339285--28339359 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
28339275 CTATTAGGAA
28339285 TTGGTTTTGGAACCATTTCTACAAGGTTTTGTATATTG
1 TTGGTTTTGGAACCATTTCTACAAGGTTTTGTATATTG
28339323 TTGGTTTTGGAACCATTTCTACAAGGTTTTGTATATT
1 TTGGTTTTGGAACCATTTCTACAAGGTTTTGTATATT
28339360 CTCAAAAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.21, C:0.11, G:0.20, T:0.48
Consensus pattern (38 bp):
TTGGTTTTGGAACCATTTCTACAAGGTTTTGTATATTG
Found at i:28339353 original size:22 final size:22
Alignment explanation
Indices: 28339287--28339353 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
28339277 ATTAGGAATT
28339287 GGTTTTGGAACCATTTCTACAA
1 GGTTTTGGAACCATTTCTACAA
* *
28339309 GGTTTT-GTA-TATTGT-T----
1 GGTTTTGGAACCATT-TCTACAA
28339325 GGTTTTGGAACCATTTCTACAA
1 GGTTTTGGAACCATTTCTACAA
28339347 GGTTTTG
1 GGTTTTG
28339354 TATATTCTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 16
0.62 0.08 0.30
Matches are distributed among these distances:
16 6 0.18
17 3 0.09
18 4 0.12
20 4 0.12
21 3 0.09
22 13 0.39
ACGTcount: A:0.21, C:0.12, G:0.22, T:0.45
Consensus pattern (22 bp):
GGTTTTGGAACCATTTCTACAA
Found at i:28351091 original size:6 final size:6
Alignment explanation
Indices: 28351082--28351184 Score: 111
Period size: 6 Copynumber: 16.8 Consensus size: 6
28351072 AATAAAAATG
*
28351082 AGAATC AGAATC AGAATC AGAATT AGAATC AGAATC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC
* * * *
28351130 AG-GTGAC AGAATT AGAATC AGAATC AGTATC AGGTAA-C AGAATC AAAATC
1 AGAAT--C AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC
28351180 AGAAT
1 AGAAT
28351185 GTGAATGCAA
Statistics
Matches: 81, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
5 3 0.04
6 70 0.86
7 6 0.07
8 2 0.02
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:28351147 original size:31 final size:31
Alignment explanation
Indices: 28351082--28351184 Score: 138
Period size: 31 Copynumber: 3.4 Consensus size: 31
28351072 AATAAAAATG
*
28351082 AGAATCAGAATCAGAATCA-G-AATTAGAATC
1 AGAATCAGAATCAGAATCAGGTAA-CAGAATC
* *
28351112 AGAATCAGAATCAGAATCAGGTGACAGAATT
1 AGAATCAGAATCAGAATCAGGTAACAGAATC
*
28351143 AGAATCAGAATCAGTATCAGGTAACAGAATC
1 AGAATCAGAATCAGAATCAGGTAACAGAATC
*
28351174 AAAATCAGAAT
1 AGAATCAGAAT
28351185 GTGAATGCAA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
30 19 0.30
31 44 0.69
32 1 0.02
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTAACAGAATC
Found at i:28351381 original size:31 final size:32
Alignment explanation
Indices: 28351324--28351385 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
28351314 ATGAAGTCAC
* *
28351324 CAGATATAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATAGATATTGTGGCGAAGCCACCAGAA
*
28351356 CAGATATATATA-TGTGGCGAAGCCACCAGA
1 CAGATATAGATATTGTGGCGAAGCCACCAGA
28351386 TTGCAGCGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.21
Consensus pattern (32 bp):
CAGATATAGATATTGTGGCGAAGCCACCAGAA
Found at i:28351716 original size:27 final size:26
Alignment explanation
Indices: 28351688--28351907 Score: 217
Period size: 27 Copynumber: 8.2 Consensus size: 26
28351678 AACACCCTAG
* *
28351688 GGGTAAAATAGTAATTTCTAAATCGA
1 GGGTAAAATGGTAATTTATAAATCGA
*
28351714 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTAAAATGGTAATT-TATAAATCGA
* * *
28351741 TGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAATGGTAA-TTTATAAATCGA
*
28351768 GGGTAAAATGGTAATTCTATAAATCAA
1 GGGTAAAATGGTAATT-TATAAATCGA
*** *
28351795 GGGTAAAACAATAATTTTGTAAATCGA
1 GGGTAAAATGGTAA-TTTATAAATCGA
*
28351822 GGGTAAAATGGTAATTTTGTAAATCGA
1 GGGTAAAATGGTAA-TTTATAAATCGA
*
28351849 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTAAAATGGTAATT-TATAAATCGA
***
28351876 GGGTACTTTGGTAATTT-TACAAGTCGA
1 GGGTAAAATGGTAATTTATA-AA-TCGA
28351903 GGGTA
1 GGGTA
28351908 TTTCAGTAAT
Statistics
Matches: 162, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
25 2 0.01
26 21 0.13
27 135 0.83
28 4 0.02
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (26 bp):
GGGTAAAATGGTAATTTATAAATCGA
Found at i:28351775 original size:54 final size:54
Alignment explanation
Indices: 28351688--28351925 Score: 271
Period size: 54 Copynumber: 4.4 Consensus size: 54
28351678 AACACCCTAG
* * *
28351688 GGGTAAAATAGTAA-TTTCTAAATCGAGGGTAAAACGGTAATTCTATAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGA
* * *
28351741 TGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCAA
1 GGGTAAAACAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGA
* * *
28351795 GGGTAAAACAATAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGA
* * * *** * * *
28351849 GGGTAAAACGGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTAAAACAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGA
*** *
28351903 GGGTATTTCAGTAATTTGGTAAA
1 GGGTAAAACAGTAATTTTGTAAA
28351926 CTAAAGTATT
Statistics
Matches: 157, Mismatches: 27, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
53 13 0.08
54 144 0.92
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.32
Consensus pattern (54 bp):
GGGTAAAACAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGA
Found at i:28351891 original size:81 final size:81
Alignment explanation
Indices: 28351688--28351907 Score: 289
Period size: 81 Copynumber: 2.7 Consensus size: 81
28351678 AACACCCTAG
* * * *
28351688 GGGTAAAATAGTAATT-TCTAAATCGAGGGTAAAACGGTAATTCTATAAATCGATGGTAAAATAG
1 GGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAATAG
28351752 TAATTTTGTAAATCGA
66 TAATTTTGTAAATCGA
* ** * *
28351768 GGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACAATAATTTTGTAAATCGAGGGTAAAATGG
1 GGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAATAG
28351833 TAATTTTGTAAATCGA
66 TAATTTTGTAAATCGA
* **** * *
28351849 GGGTAAAACGGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTACAAGTCGAGGGTA
1 GGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTATAAATCGAGGGTA
28351908 TTTCAGTAAT
Statistics
Matches: 119, Mismatches: 20, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
80 15 0.13
81 104 0.87
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (81 bp):
GGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAATAG
TAATTTTGTAAATCGA
Found at i:28352236 original size:27 final size:27
Alignment explanation
Indices: 28352206--28352426 Score: 271
Period size: 27 Copynumber: 8.2 Consensus size: 27
28352196 AACACCCTAG
*
28352206 GGGTAAAATGGTAATTTTCTAAATCGA
1 GGGTAAAATGGTAATTTTATAAATCGA
* *
28352233 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTAAAATGGTAATTTTATAAATCGA
* * *
28352260 TGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAATGGTAATTTTATAAATCGA
* *
28352287 GGGTAAAATGGTAATTCTATAAATCAA
1 GGGTAAAATGGTAATTTTATAAATCGA
*** *
28352314 GGGTAAAACAATAATTTTGTAAATCGA
1 GGGTAAAATGGTAATTTTATAAATCGA
28352341 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAATGGTAATTTTATAAATCGA
* *
28352368 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTAAAATGGTAATTTTATAAATCGA
*** * *
28352395 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTAAAATGGTAATTTTATAAATCGA
28352422 GGGTA
1 GGGTA
28352427 TTTCAGTAAT
Statistics
Matches: 162, Mismatches: 32, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 162 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (27 bp):
GGGTAAAATGGTAATTTTATAAATCGA
Found at i:28352460 original size:519 final size:518
Alignment explanation
Indices: 28351464--28352501 Score: 2031
Period size: 519 Copynumber: 2.0 Consensus size: 518
28351454 TGCAGCGAGG
28351464 CTGCCAGAACGCTTCCTCTATCAATATAACCCATATCCCATGCAACAGATATACATGTCATGGCA
1 CTGCCAGAACGCTTCCTCTATCAATATAACCCATATCCCATGCAACAGATATACATGTCATGGCA
28351529 TACAACATACAGAATCAGAATATCATGCCCATATTTGAATCAAACAGTCACAGTCAAGTCATTCA
66 TACAACATACAGAATCAGAATATCATGCCCATATTTGAATCAAACAGTCACAGTCAAGTCATTCA
*
28351594 TATCACCAACATATATTTACAATCAAATCTGTCAACCACACAGTCCAAGTCAGTCACTTGCCCAC
131 TATCACCAACATATATTTACAATCAAATCCGTCAACCACACAGTCCAAGTCAGTCACTTGCCCAC
28351659 AAGGGCAAAACAATCATTTAACACCCTAGGGGTAAAATAGTAATTTCTAAATCGAGGGTAAAACG
196 AAGGGCAAAACAATCATTTAACACCCTAGGGGTAAAATAGTAATTTCTAAATCGAGGGTAAAACG
28351724 GTAATTCTATAAATCGATGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
261 GTAATTCTATAAATCGATGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
*
28351789 AATCAAGGGTAAAACAATAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
326 AATCAAGGGTAAAACAATAATTTTGTAAATCGAGGGTAAAATGGTAATTTTATAAATCGAGGGTA
28351854 AAACGGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTCAGTAATT
391 AAACGGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTCAGTAATT
28351919 TGGTAAACTAAAGTATTCTAAATAGGGATAACAATACGAATGGACCTAAAGCCCATTCTCGGC
456 TGGTAAACTAAAGTATTCTAAATAGGGATAACAATACGAATGGACCTAAAGCCCATTCTCGGC
28351982 CTGCCAGAACGCTTCCTCTATCAATATAACCCATATCCCATGCAACAGATATACATGTCATGGCA
1 CTGCCAGAACGCTTCCTCTATCAATATAACCCATATCCCATGCAACAGATATACATGTCATGGCA
28352047 TACAACATACAGAATCAGAATATCATGCCCATATTTGAATCAAACAGTCACAGTCAAGTCATTCA
66 TACAACATACAGAATCAGAATATCATGCCCATATTTGAATCAAACAGTCACAGTCAAGTCATTCA
28352112 TATCACCAACATATATTTACAATCAAATCCGTCAACCACACAGTCCAAGTCAGTCACTTGCCCAC
131 TATCACCAACATATATTTACAATCAAATCCGTCAACCACACAGTCCAAGTCAGTCACTTGCCCAC
*
28352177 AAGGGCAAAACAATCATTTAACACCCTAGGGGTAAAATGGTAATTTTCTAAATCGAGGGTAAAAC
196 AAGGGCAAAACAATCATTTAACACCCTAGGGGTAAAATAGTAA-TTTCTAAATCGAGGGTAAAAC
28352242 GGTAATTCTATAAATCGATGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTAT
260 GGTAATTCTATAAATCGATGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTAT
28352307 AAATCAAGGGTAAAACAATAATTTTGTAAATCGAGGGTAAAATGGTAATTTTATAAATCGAGGGT
325 AAATCAAGGGTAAAACAATAATTTTGTAAATCGAGGGTAAAATGGTAATTTTATAAATCGAGGGT
28352372 AAAACGGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTCAGTAAT
390 AAAACGGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTCAGTAAT
*
28352437 TTGGTAAACTAAAGTATTCTAAATAGGGATAATAATACGAATGGACCTAAAGCCCATTCTCGGC
455 TTGGTAAACTAAAGTATTCTAAATAGGGATAACAATACGAATGGACCTAAAGCCCATTCTCGGC
28352501 C
1 C
28352502 CAATGGGCCC
Statistics
Matches: 515, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
518 236 0.46
519 279 0.54
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (518 bp):
CTGCCAGAACGCTTCCTCTATCAATATAACCCATATCCCATGCAACAGATATACATGTCATGGCA
TACAACATACAGAATCAGAATATCATGCCCATATTTGAATCAAACAGTCACAGTCAAGTCATTCA
TATCACCAACATATATTTACAATCAAATCCGTCAACCACACAGTCCAAGTCAGTCACTTGCCCAC
AAGGGCAAAACAATCATTTAACACCCTAGGGGTAAAATAGTAATTTCTAAATCGAGGGTAAAACG
GTAATTCTATAAATCGATGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
AATCAAGGGTAAAACAATAATTTTGTAAATCGAGGGTAAAATGGTAATTTTATAAATCGAGGGTA
AAACGGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTCAGTAATT
TGGTAAACTAAAGTATTCTAAATAGGGATAACAATACGAATGGACCTAAAGCCCATTCTCGGC
Found at i:28356808 original size:6 final size:7
Alignment explanation
Indices: 28356777--28356820 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
28356767 TGAAATCAAC
28356777 CATTTCT
1 CATTTCT
28356784 CATTTCT
1 CATTTCT
28356791 CATTTCT
1 CATTTCT
28356798 CATTT-T
1 CATTTCT
28356804 CATTTC-
1 CATTTCT
28356810 CATTTC-
1 CATTTCT
28356816 CATTT
1 CATTT
28356821 AATTTTTGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.47
7 19 0.53
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (7 bp):
CATTTCT
Found at i:28362129 original size:14 final size:15
Alignment explanation
Indices: 28362112--28362140 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28362102 GACTATGGTA
28362112 AAATA-TTAAAAAAT
1 AAATATTTAAAAAAT
28362126 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
28362141 TATTAATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:28368783 original size:48 final size:48
Alignment explanation
Indices: 28368712--28368850 Score: 199
Period size: 48 Copynumber: 2.9 Consensus size: 48
28368702 CACCACGATT
28368712 TATGAGAGCCAGTGTAAGACCATGTCTGAGACATGGCATCAGCATTGA
1 TATGAGAGCCAGTGTAAGACCATGTCTGAGACATGGCATCAGCATTGA
* *
28368760 TATGAGAGCCAGTGTAAAACCATGTCT-AGGACATGGCATCGGCATTGA
1 TATGAGAGCCAGTGTAAGACCATGTCTGA-GACATGGCATCAGCATTGA
* * * * *
28368808 TATGTGTGCCAGTGTAAGACCATATCTGGGATATGGCATCAGC
1 TATGAGAGCCAGTGTAAGACCATGTCTGAGACATGGCATCAGC
28368851 CTCCGTATCT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
47 1 0.01
48 79 0.99
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (48 bp):
TATGAGAGCCAGTGTAAGACCATGTCTGAGACATGGCATCAGCATTGA
Found at i:28368920 original size:42 final size:42
Alignment explanation
Indices: 28368861--28368978 Score: 137
Period size: 42 Copynumber: 2.8 Consensus size: 42
28368851 CTCCGTATCT
* * *
28368861 GATTTCATGTAAGACCATATCTGGGATATGTCGTTGATATGA
1 GATTTCATGTAAGACCATATCTGGGACATGGCATTGATATGA
* *
28368903 GATTTCATGTAAGACCATGTCTTGGACATGGCATTGATATGA
1 GATTTCATGTAAGACCATATCTGGGACATGGCATTGATATGA
* ** * * *
28368945 GGTCCCATATAAGACTATGTCTGGGACATGGCAT
1 GATTTCATGTAAGACCATATCTGGGACATGGCAT
28368979 CGGCACCGAA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (42 bp):
GATTTCATGTAAGACCATATCTGGGACATGGCATTGATATGA
Found at i:28368993 original size:90 final size:90
Alignment explanation
Indices: 28368899--28369065 Score: 210
Period size: 90 Copynumber: 1.9 Consensus size: 90
28368889 TGTCGTTGAT
* * * * * *
28368899 ATGAGATTTCATGTAAGACCATGTCTTGGACATGGCATTGATATG-AGGTCCCATATAAGACTAT
1 ATGAGACTTCATGTAAGACCATATCTGGGACATGGCATCGATATGTA-GACCCATATAAGACCAT
*
28368963 GTCTGGGACATGGCATCGGCACCGAA
65 GTCAGGGACATGGCATCGGCACCGAA
* * * * *
28368989 ATGAGACTTCGTTTAAGACCATATCTGGGATATGGCATCGGTATGTAGACCCATGTAAGACCATG
1 ATGAGACTTCATGTAAGACCATATCTGGGACATGGCATCGATATGTAGACCCATATAAGACCATG
28369054 TCAGGGACATGG
66 TCAGGGACATGG
28369066 AATTGGCATT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
90 63 0.98
91 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (90 bp):
ATGAGACTTCATGTAAGACCATATCTGGGACATGGCATCGATATGTAGACCCATATAAGACCATG
TCAGGGACATGGCATCGGCACCGAA
Found at i:28376643 original size:48 final size:49
Alignment explanation
Indices: 28376565--28376701 Score: 161
Period size: 48 Copynumber: 2.8 Consensus size: 49
28376555 CACTATGATT
* *
28376565 TATGAGAGCCAGTGTAAGACAATGTCTGGGACATGGCATCAG-CGTTGA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCATTGA
* * *
28376613 TGTGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATC-GCCATTGA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCATTGA
* * * * * *
28376661 TATGTGTGCCAGTGTGAGACCATATGTGGGATATGGCATCA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCA
28376702 ACCTCGGTTT
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
47 1 0.01
48 73 0.99
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.26
Consensus pattern (49 bp):
TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCATTGA
Found at i:28378791 original size:27 final size:27
Alignment explanation
Indices: 28378761--28378938 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
28378751 ATATTGAGCC
* *
28378761 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
28378788 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
28378815 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
28378843 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
28378870 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
28378897 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
28378924 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28378939 GTACAATTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 104 0.81
28 25 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Done.