Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 44 of 318
Found at i:12296508 original size:49 final size:49
Alignment explanation
Indices: 12296434--12296642 Score: 341
Period size: 49 Copynumber: 4.3 Consensus size: 49
12296424 CCCTTCGGGA
* * * * * *
12296434 CTTATCACAT-T-TACACACTTCCACATCCATCACGTTGACCACTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
12296481 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
12296530 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
*
12296579 CTTATCACATATATACACACTTTCTCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
12296628 CTTATCACATATATA
1 CTTATCACATATATA
12296643 TATCTCATAC
Statistics
Matches: 153, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
47 10 0.07
48 1 0.01
49 142 0.93
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.31
Consensus pattern (49 bp):
CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12302865 original size:20 final size:20
Alignment explanation
Indices: 12302840--12302877 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12302830 ATCACATATA
12302840 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
* *
12302860 TCATGAGCTCAGATCACA
1 TCATGAACTCAGACCACA
12302878 TAGTTCCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (20 bp):
TCATGAACTCAGACCACAAC
Found at i:12306298 original size:29 final size:29
Alignment explanation
Indices: 12306265--12306367 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
12306255 GTGACGAGAT
12306265 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
12306294 TGGCACTAAGTGTGCGTGCTGGAAATATT
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
** *
12306323 TGGCACTAAGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* **
12306352 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
12306368 AGTTCGGAGG
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:12314242 original size:29 final size:29
Alignment explanation
Indices: 12314209--12314311 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
12314199 GTGACGAGAT
12314209 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
12314238 TGGCACTAAGTGTGCGTGCTGGAAATATT
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
** *
12314267 TGGCACTAAGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* **
12314296 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
12314312 AGTTCGGAGG
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:12321463 original size:41 final size:42
Alignment explanation
Indices: 12321406--12321507 Score: 134
Period size: 41 Copynumber: 2.4 Consensus size: 42
12321396 CTCGATTTGA
* *
12321406 GATTTACGTGTAAGACCATGTCTGGGACATAGGCATCTAT-CT
1 GATTT-CGTGTAAGACCATGTCTGGGACAGAGGCATCGATACT
*
12321448 GATTTCGTGTAAGACCCTGTCTGGGACAGAGGCATCGATACT
1 GATTTCGTGTAAGACCATGTCTGGGACAGAGGCATCGATACT
* *
12321490 GAATTACATGTAAGACCA
1 G-ATTTCGTGTAAGACCA
12321508 CGTTCGGGAC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 31 0.60
42 8 0.15
43 13 0.25
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (42 bp):
GATTTCGTGTAAGACCATGTCTGGGACAGAGGCATCGATACT
Found at i:12326388 original size:43 final size:42
Alignment explanation
Indices: 12326294--12326458 Score: 113
Period size: 43 Copynumber: 3.9 Consensus size: 42
12326284 CCTATGGTGT
****
12326294 CCGAAGCTCCCGCACATCCAA-GCACCAAGGTACCAAT-GCTGC
1 CCGAAGCTCCCGCACAT-CAAGGCACCAAGGTGTTGATAG-TGC
* * *
12326336 TCGAGGCTCCCGCACATCTGAGGCACCAAGGTGTTGATAGTGC
1 CCGAAGCTCCCGCACATC-AAGGCACCAAGGTGTTGATAGTGC
* * * * ** *
12326379 CCGAAGCTCCAGCACGACCAAGG-GCCTAGGTTGCCGATGGTGC
1 CCGAAGCTCCCGCAC-ATCAAGGCACCAAGG-TGTTGATAGTGC
*
12326422 CCGAGGCTCCCGCACATCCAA-GCACCAAGGTGTTGAT
1 CCGAAGCTCCCGCACAT-CAAGGCACCAAGGTGTTGAT
12326459 GCTGCTCGAG
Statistics
Matches: 92, Mismatches: 24, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
41 1 0.01
42 28 0.30
43 60 0.65
44 3 0.03
ACGTcount: A:0.24, C:0.34, G:0.27, T:0.16
Consensus pattern (42 bp):
CCGAAGCTCCCGCACATCAAGGCACCAAGGTGTTGATAGTGC
Found at i:12326447 original size:85 final size:85
Alignment explanation
Indices: 12326337--12326530 Score: 225
Period size: 85 Copynumber: 2.3 Consensus size: 85
12326327 CAATGCTGCT
* * *
12326337 CGAGGCTCCCGCACATCTGAGGCACCAAGGTGTTGATAG-TGCCCGA-AGC-TCCAGCACGA-CC
1 CGAGGCTCCCGCACATC-AAAGCACCAAGGTGTTGAT-GCTGCCCGAGA-CACCCA-CAC-ATCC
*
12326398 AAGGGCCTAGGTTGCCGATGGTGCC
61 AACGGCCTAGGTTGCCGATGGTGCC
* * *
12326423 CGAGGCTCCCGCACATCCAAGCACCAAGGTGTTGATGCTGCTCGAGACACCCACACATCCAACGT
1 CGAGGCTCCCGCACATCAAAGCACCAAGGTGTTGATGCTGCCCGAGACACCCACACATCCAACGG
* *
12326488 CCTAGGTTGCCTATGGTGTC
66 CCTAGGTTGCCGATGGTGCC
*
12326508 TGAGGCTCCCGCACATCAAAGCA
1 CGAGGCTCCCGCACATCAAAGCA
12326531 TGTAACATCC
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
84 2 0.02
85 71 0.76
86 21 0.22
ACGTcount: A:0.23, C:0.33, G:0.27, T:0.18
Consensus pattern (85 bp):
CGAGGCTCCCGCACATCAAAGCACCAAGGTGTTGATGCTGCCCGAGACACCCACACATCCAACGG
CCTAGGTTGCCGATGGTGCC
Found at i:12326987 original size:9 final size:9
Alignment explanation
Indices: 12326973--12327000 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12326963 ATGGTTAGGG
12326973 TTTCCAAGC
1 TTTCCAAGC
12326982 TTTCCAAGC
1 TTTCCAAGC
12326991 TTTCCAAGC
1 TTTCCAAGC
12327000 T
1 T
12327001 CAATAGTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.36
Consensus pattern (9 bp):
TTTCCAAGC
Found at i:12327397 original size:30 final size:31
Alignment explanation
Indices: 12327356--12327413 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
12327346 TTTTCGAGCC
*
12327356 TAGGGGAAAAATCATAATTTTG-CAAAGGTT
1 TAGGGGAAAAATCATAACTTTGCCAAAGGTT
* *
12327386 TAGGGGCAAAATTATAACTTTGCCAAAG
1 TAGGGGAAAAATCATAACTTTGCCAAAG
12327414 TTTGAGCTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (31 bp):
TAGGGGAAAAATCATAACTTTGCCAAAGGTT
Found at i:12328232 original size:47 final size:47
Alignment explanation
Indices: 12328174--12328295 Score: 181
Period size: 47 Copynumber: 2.6 Consensus size: 47
12328164 GCATTGGCAC
*
12328174 TAAGACAAGGATACGATATAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATATAAGACCATGTTTGGAACATGGCATTTGG
* *
12328221 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGTATTTGG
1 TAAGACAAGGATACCATATAAGACCATGTTTGGAACATGGCATTTGG
* ** *
12328268 TAAGATAAGGATGTCATGTAAGACCATG
1 TAAGACAAGGATACCATATAAGACCATG
12328296 CCAAGGCATG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.26
Consensus pattern (47 bp):
TAAGACAAGGATACCATATAAGACCATGTTTGGAACATGGCATTTGG
Found at i:12328339 original size:54 final size:54
Alignment explanation
Indices: 12328281--12328535 Score: 300
Period size: 54 Copynumber: 4.7 Consensus size: 54
12328271 GATAAGGATG
12328281 TCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAA
1 TCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAA
* *
12328335 TCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCCATAAAGCAAGGAAA
1 TCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAA
* * * * **
12328389 TCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGAAAAGG-TC
1 TCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTT-CTATAAGG-CAAGGAAA
* * *
12328444 CCATGTAAGACCATGCCAAGGCATGGCATTGGTGAA-TTC-ATAAGGCAAGGATA
1 TCATGTAAGACCATGCCAAGGCATGGCATTGAT-AAGTTCTATAAGGCAAGGAAA
* * * * * * *
12328497 CCACGTAAGATCATGTCAAGACATGGCAATGGTAAGTTC
1 TCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTC
12328536 AAAAAGAAAA
Statistics
Matches: 174, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
52 6 0.03
53 38 0.22
54 88 0.51
55 37 0.21
56 5 0.03
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
TCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAA
Found at i:12328658 original size:16 final size:16
Alignment explanation
Indices: 12328636--12328674 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
12328626 GCTTATTTAA
*
12328636 TATTGAGATTGT-AAG
1 TATTGAGATTATCAAG
12328651 TAATTGAGATTATCAAG
1 T-ATTGAGATTATCAAG
12328668 TATTGAG
1 TATTGAG
12328675 TAAGTGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.76
17 4 0.19
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (16 bp):
TATTGAGATTATCAAG
Found at i:12330488 original size:71 final size:71
Alignment explanation
Indices: 12330405--12330568 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
12330395 GAGATGTATC
12330405 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
12330470 AGGACA
66 AGGACA
*
12330476 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTGGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
12330541 CGGACA
66 AGGACA
12330547 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
12330569 AGACAAATCG
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:12333073 original size:77 final size:77
Alignment explanation
Indices: 12332981--12333178 Score: 227
Period size: 86 Copynumber: 2.5 Consensus size: 77
12332971 CAAAGTGCCA
* * ***
12332981 ATGGTGCCTGAGGCTCCCGCACGACCAAGGGCCTATGGTGTTTGAGGCACCTGCACATCCAATGT
1 ATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTATGGTGTTTGAGGCACCCGCACATCCAACAC
*
12333046 TCTAGGTTG-CTT
66 CCTAGGTTGTC-T
12333058 ATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGTCGATGGTGTTTGAGGCACCCGCAC
1 ATGGTGCCCGAGGCTCCCGCACGACCAAGGGCC-------T--ATGGTGTTTGAGGCACCCGCAC
*
12333123 ATGCAACACCCTAGGTTGTCT
57 ATCCAACACCCTAGGTTGTCT
*
12333144 ATGGTGCCCGAGGCTCCCACACGACCAAGGGCCTA
1 ATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTA
12333179 GCGTCACGGG
Statistics
Matches: 103, Mismatches: 8, Indels: 20
0.79 0.06 0.15
Matches are distributed among these distances:
77 33 0.32
79 1 0.01
84 1 0.01
86 67 0.65
87 1 0.01
ACGTcount: A:0.19, C:0.30, G:0.29, T:0.21
Consensus pattern (77 bp):
ATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTATGGTGTTTGAGGCACCCGCACATCCAACAC
CCTAGGTTGTCT
Found at i:12333094 original size:43 final size:43
Alignment explanation
Indices: 12333047--12333179 Score: 144
Period size: 43 Copynumber: 3.1 Consensus size: 43
12333037 ATCCAATGTT
12333047 CTAGGTTG-CTTATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
1 CTAGGTTGTC-TATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
* *** * * ***
12333090 CTAGGTTGTCGATGGTGTTTGAGGCACCCGCAC-ATGCAACACC
1 CTAGGTTGTCTATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGC
*
12333133 CTAGGTTGTCTATGGTGCCCGAGGCTCCCACACGACCAAGGGC
1 CTAGGTTGTCTATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
12333176 CTAG
1 CTAG
12333180 CGTCACGGGC
Statistics
Matches: 68, Mismatches: 19, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
42 1 0.01
43 65 0.96
44 2 0.03
ACGTcount: A:0.19, C:0.31, G:0.30, T:0.20
Consensus pattern (43 bp):
CTAGGTTGTCTATGGTGCCCGAGGCTCCCGCACGACCAAGGGC
Found at i:12333137 original size:86 final size:86
Alignment explanation
Indices: 12333015--12333179 Score: 251
Period size: 86 Copynumber: 1.9 Consensus size: 86
12333005 CCAAGGGCCT
* **** *
12333015 ATGGTGTTTGAGGCACCTGCACATCCAATGTTCTAGGTTG-CTTATGGTGCCCGAGGCTCCCGCA
1 ATGGTGTTTGAGGCACCCGCACATCCAACACCCTAGGTTGTC-TATGGTGCCCGAGGCTCCCACA
12333079 CGACCAAGGGCCTAGGTTGTCG
65 CGACCAAGGGCCTAGGTTGTCG
*
12333101 ATGGTGTTTGAGGCACCCGCACATGCAACACCCTAGGTTGTCTATGGTGCCCGAGGCTCCCACAC
1 ATGGTGTTTGAGGCACCCGCACATCCAACACCCTAGGTTGTCTATGGTGCCCGAGGCTCCCACAC
12333166 GACCAAGGGCCTAG
66 GACCAAGGGCCTAG
12333180 CGTCACGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
86 70 0.99
87 1 0.01
ACGTcount: A:0.19, C:0.29, G:0.29, T:0.22
Consensus pattern (86 bp):
ATGGTGTTTGAGGCACCCGCACATCCAACACCCTAGGTTGTCTATGGTGCCCGAGGCTCCCACAC
GACCAAGGGCCTAGGTTGTCG
Found at i:12335255 original size:95 final size:96
Alignment explanation
Indices: 12335108--12335286 Score: 261
Period size: 95 Copynumber: 1.9 Consensus size: 96
12335098 TGTCTGAGGA
* * * * * * * *
12335108 AGTCTGTCATTGATGGGAACGATGGAGTAGATACGGAGTCCAAGAAGCTTGGTTCGAGCAAGGGA
1 AGTCTGTCATCGATAGGAACGATGAAGCAGACAAGGAGCCCAAGAAGATTGGTTCGAGCAAGGGA
*
12335173 AAAGTCGAAGCCAAGAGGGCAAAGAGGAGCG
66 AAAGCCGAAGCCAAGAGGGCAAAGAGGAGCG
*
12335204 AGTCTGTCATCGA-AGGAACGATGAAGCAGACAAGGAGCCCAAGAAGATTGGTTCGAGCAAGGGT
1 AGTCTGTCATCGATAGGAACGATGAAGCAGACAAGGAGCCCAAGAAGATTGGTTCGAGCAAGGGA
12335268 AAAGCCGAAGCCAAGAGGG
66 AAAGCCGAAGCCAAGAGGG
12335287 TTAAGACGAG
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
95 61 0.84
96 12 0.16
ACGTcount: A:0.35, C:0.16, G:0.35, T:0.14
Consensus pattern (96 bp):
AGTCTGTCATCGATAGGAACGATGAAGCAGACAAGGAGCCCAAGAAGATTGGTTCGAGCAAGGGA
AAAGCCGAAGCCAAGAGGGCAAAGAGGAGCG
Found at i:12336773 original size:42 final size:42
Alignment explanation
Indices: 12336724--12337068 Score: 238
Period size: 43 Copynumber: 8.1 Consensus size: 42
12336714 CAATGGTGTC
*
12336724 CGAGGCTCCTGCACATCCAAGCACCAAGGTGCCGATGCTGCT
1 CGAGGCTCCTGCACATCCAAGCACCAAGGTACCGATGCTGCT
* * * *
12336766 CAAGGCTCCTGCACATCTAAGGCACCAAGGTTCCGATAG-TGCC
1 CGAGGCTCCTGCACATCCAA-GCACCAAGGTACCGAT-GCTGCT
* * * ** * *
12336809 CAAAGCT-CTAGCACGA-CCAAAG-GCCTTGGTTACCGATGGTGCC
1 CGAGGCTCCT-GCAC-ATCC-AAGCACCAAGG-TACCGATGCTGCT
** *
12336852 CGAGGCTCCCACACATCCAAGCACCAATGTACCGATGCTGCT
1 CGAGGCTCCTGCACATCCAAGCACCAAGGTACCGATGCTGCT
* * *
12336894 CGAGGCTGCTGTACATCCAAGCACCAAGGTGCCGATGCTGCT
1 CGAGGCTCCTGCACATCCAAGCACCAAGGTACCGATGCTGCT
* * * * *
12336936 CGAGGCT-CTAGCACATCCGAGGCACCAAGGTGCTGATGGTACT
1 CGAGGCTCCT-GCACATCC-AAGCACCAAGGTACCGATGCTGCT
** * *
12336979 CGAGGCT-CTAGCACGA-CCAAGGGCCTAGGTTACCGATGGTG-T
1 CGAGGCTCCT-GCAC-ATCCAAGCACCAAGG-TACCGATGCTGCT
* * * * *
12337021 CCAAGGCTCCCGCACATCCAAGCACTAAGGTATCGATGGTGCT
1 -CGAGGCTCCTGCACATCCAAGCACCAAGGTACCGATGCTGCT
12337064 CGAGG
1 CGAGG
12337069 TTCTCACACC
Statistics
Matches: 239, Mismatches: 46, Indels: 36
0.74 0.14 0.11
Matches are distributed among these distances:
41 2 0.01
42 113 0.47
43 117 0.49
44 7 0.03
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.18
Consensus pattern (42 bp):
CGAGGCTCCTGCACATCCAAGCACCAAGGTACCGATGCTGCT
Found at i:12336981 original size:43 final size:42
Alignment explanation
Indices: 12336724--12336992 Score: 183
Period size: 42 Copynumber: 6.3 Consensus size: 42
12336714 CAATGGTGTC
*
12336724 CGAGGCTCCT-GCACATCCAAGCACCAAGGTGCCGATGCTGCT
1 CGAGGCT-CTAGCACATCCAAGCACCAAGGTGCCGATGCTACT
* * * * *
12336766 CAAGGCTCCT-GCACATCTAAGGCACCAAGGTTCCGATAG-TGCC
1 CGAGGCT-CTAGCACATCCAA-GCACCAAGGTGCCGAT-GCTACT
* * * ** * * * *
12336809 CAAAGCTCTAGCACGA-CCAAAG-GCCTTGGTTACCGATGGTGCC
1 CGAGGCTCTAGCAC-ATCC-AAGCACCAAGG-TGCCGATGCTACT
* * * *
12336852 CGAGGCTCCCA-CACATCCAAGCACCAATGTACCGATGCTGCT
1 CGAGGCT-CTAGCACATCCAAGCACCAAGGTGCCGATGCTACT
* *
12336894 CGAGGCTGCT-GTACATCCAAGCACCAAGGTGCCGATGCTGCT
1 CGAGGCT-CTAGCACATCCAAGCACCAAGGTGCCGATGCTACT
* * *
12336936 CGAGGCTCTAGCACATCCGAGGCACCAAGGTGCTGATGGTACT
1 CGAGGCTCTAGCACATCC-AAGCACCAAGGTGCCGATGCTACT
12336979 CGAGGCTCTAGCAC
1 CGAGGCTCTAGCAC
12336993 GACCAAGGGC
Statistics
Matches: 185, Mismatches: 29, Indels: 25
0.77 0.12 0.10
Matches are distributed among these distances:
41 2 0.01
42 90 0.49
43 87 0.47
44 6 0.03
ACGTcount: A:0.24, C:0.33, G:0.26, T:0.18
Consensus pattern (42 bp):
CGAGGCTCTAGCACATCCAAGCACCAAGGTGCCGATGCTACT
Found at i:12337012 original size:170 final size:170
Alignment explanation
Indices: 12336724--12337068 Score: 485
Period size: 170 Copynumber: 2.0 Consensus size: 170
12336714 CAATGGTGTC
*
12336724 CGAGGCTCCTGCACATCCAAGCACCAAGGTGCCGATGCTGCTCAAGGCTCCTGCACATCTAAGGC
1 CGAGGCTCCTGCACATCCAAGCACCAAGGTGCCGATGCTGCTCAAGGCTCCTGCACATCCAAGGC
* * * *
12336789 ACCAAGGTTCCGATAGTGCCCAAAGCTCTAGCACGACCAAAGGCCTTGGTTACCGATGGTGCCCG
66 ACCAAGGTGCCGATAGTACCCAAAGCTCTAGCACGACCAAAGGCCTAGGTTACCGATGGTGCCCA
*
12336854 AGGCTCCCACACATCCAAGCACCAATGTACCGATGCTGCT
131 AGGCTCCCACACATCCAAGCACCAAGGTACCGATGCTGCT
* * * *
12336894 CGAGGCTGCTGTACATCCAAGCACCAAGGTGCCGATGCTGCTCGAGGCT-CTAGCACATCCGAGG
1 CGAGGCTCCTGCACATCCAAGCACCAAGGTGCCGATGCTGCTCAAGGCTCCT-GCACATCCAAGG
* * * * * * *
12336958 CACCAAGGTGCTGATGGTACTCGAGGCTCTAGCACGACCAAGGGCCTAGGTTACCGATGGTGTCC
65 CACCAAGGTGCCGATAGTACCCAAAGCTCTAGCACGACCAAAGGCCTAGGTTACCGATGGTGCCC
* * * *
12337023 AAGGCTCCCGCACATCCAAGCACTAAGGTATCGATGGTGCT
130 AAGGCTCCCACACATCCAAGCACCAAGGTACCGATGCTGCT
12337064 CGAGG
1 CGAGG
12337069 TTCTCACACC
Statistics
Matches: 153, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
169 2 0.01
170 151 0.99
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.18
Consensus pattern (170 bp):
CGAGGCTCCTGCACATCCAAGCACCAAGGTGCCGATGCTGCTCAAGGCTCCTGCACATCCAAGGC
ACCAAGGTGCCGATAGTACCCAAAGCTCTAGCACGACCAAAGGCCTAGGTTACCGATGGTGCCCA
AGGCTCCCACACATCCAAGCACCAAGGTACCGATGCTGCT
Found at i:12337083 original size:85 final size:82
Alignment explanation
Indices: 12336768--12337079 Score: 232
Period size: 85 Copynumber: 3.7 Consensus size: 82
12336758 ATGCTGCTCA
* * * * * * * * *
12336768 AGGCTCCTGCACATCTAAGGCACCAAGGTTCCGATAGTGCCCAAAGCTCTAGCACGACCAAAGGC
1 AGGCTCCCGCACATCCAA-GCACCAAGGTACCGATGGTGCTCGAGGTTCTA-CAC-ACCAAGGGC
*
12336833 CTTGGTTACCGATGGTGCCCG
63 CTAGGTTACCGATGGTG-CCG
* * * * ** **
12336854 AGGCTCCCACACATCCAAGCACCAATGTACCGATGCTGCTCGAGGCTGCTGTACATCCAAGCACC
1 AGGCTCCCGCACATCCAAGCACCAAGGTACCGATGGTGCTCGAGG-TTCTACACA-CCAAGGGCC
* * *
12336919 AAGG-TGCCGATGCTGCTCG
64 TAGGTTACCGATGGTGC-CG
** * * * * *
12336938 AGGCTCTAGCACATCCGAGGCACCAAGGTGCTGATGGTACTCGAGGCTCTAGCACGACCAAGGGC
1 AGGCTCCCGCACATCC-AAGCACCAAGGTACCGATGGTGCTCGAGGTTCTA-CAC-ACCAAGGGC
*
12337003 CTAGGTTACCGATGGTGTCCA
63 CTAGGTTACCGATGGTG-CCG
* *
12337024 AGGCTCCCGCACATCCAAGCACTAAGGTATCGATGGTGCTCGAGGTTCT-CACACCA
1 AGGCTCCCGCACATCCAAGCACCAAGGTACCGATGGTGCTCGAGGTTCTACACACCA
12337080 CCAACTTAGA
Statistics
Matches: 169, Mismatches: 49, Indels: 20
0.71 0.21 0.08
Matches are distributed among these distances:
82 4 0.02
83 4 0.02
84 27 0.16
85 91 0.54
86 42 0.25
87 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.19
Consensus pattern (82 bp):
AGGCTCCCGCACATCCAAGCACCAAGGTACCGATGGTGCTCGAGGTTCTACACACCAAGGGCCTA
GGTTACCGATGGTGCCG
Found at i:12340291 original size:28 final size:28
Alignment explanation
Indices: 12340260--12340348 Score: 76
Period size: 30 Copynumber: 3.1 Consensus size: 28
12340250 TAATAAGAGC
12340260 AAAAAA-TAAAAATAAAAATAAGATAAAT
1 AAAAAAGTAAAAA-AAAAATAAGATAAAT
* *
12340288 AAAAAAATTAAAAAAAAACAAACCAGATAAA-
1 -AAAAAAGTAAAAAAAAA-ATA--AGATAAAT
*
12340319 AAAATAAGTAAATAAAAAATAAGA-AAAT
1 AAAA-AAGTAAAAAAAAAATAAGATAAAT
12340347 AA
1 AA
12340349 TGAAAAAGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
27 3 0.06
28 5 0.10
29 10 0.20
30 14 0.28
31 11 0.22
32 7 0.14
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.15
Consensus pattern (28 bp):
AAAAAAGTAAAAAAAAAATAAGATAAAT
Found at i:12340335 original size:15 final size:15
Alignment explanation
Indices: 12340317--12340348 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12340307 AAACCAGATA
*
12340317 AAAAAATAAGTAAAT
1 AAAAAATAAGAAAAT
12340332 AAAAAATAAGAAAAT
1 AAAAAATAAGAAAAT
12340347 AA
1 AA
12340349 TGAAAAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (15 bp):
AAAAAATAAGAAAAT
Found at i:12340387 original size:12 final size:12
Alignment explanation
Indices: 12340314--12340464 Score: 54
Period size: 12 Copynumber: 12.8 Consensus size: 12
12340304 AACAAACCAG
12340314 ATAAA-AAAATA
1 ATAAATAAAATA
12340325 AGTAAATAAAA-A
1 A-TAAATAAAATA
*
12340337 AT-AAGAAAATA
1 ATAAATAAAATA
** *
12340348 ATGAAA-AAGTTG
1 AT-AAATAAAATA
12340360 A-AAATAAGAA-A
1 ATAAATAA-AATA
*
12340371 TTAAATAAAATA
1 ATAAATAAAATA
*
12340383 ATAAA-GAAATA
1 ATAAATAAAATA
*
12340394 TTAAATAAAATA
1 ATAAATAAAATA
* *
12340406 AT-TA-AAAATG
1 ATAAATAAAATA
12340416 AT-AATAATAATA
1 ATAAATAA-AATA
*
12340428 ATAGTAATAGTAATA
1 ATA--AATA-AAATA
*
12340443 ATAAAT-AAGTA
1 ATAAATAAAATA
12340454 GATAAATAAAA
1 -ATAAATAAAA
12340465 CACATATACA
Statistics
Matches: 101, Mismatches: 21, Indels: 34
0.65 0.13 0.22
Matches are distributed among these distances:
10 17 0.17
11 24 0.24
12 38 0.38
13 11 0.11
15 11 0.11
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.25
Consensus pattern (12 bp):
ATAAATAAAATA
Found at i:12348633 original size:14 final size:14
Alignment explanation
Indices: 12348614--12348643 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12348604 TATCCATGTC
*
12348614 TTCAGGATGTATCT
1 TTCAGGATGTAACT
12348628 TTCAGGATGTAACT
1 TTCAGGATGTAACT
12348642 TT
1 TT
12348644 ATCTGGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.43
Consensus pattern (14 bp):
TTCAGGATGTAACT
Found at i:12349685 original size:11 final size:10
Alignment explanation
Indices: 12349660--12349686 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
12349650 TTATGTTCAG
12349660 ATTTTTTATC
1 ATTTTTTATC
12349670 ATTTTTTATC
1 ATTTTTTATC
12349680 ATTTTTT
1 ATTTTTT
12349687 CAGCAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTTTTATC
Found at i:12349839 original size:15 final size:15
Alignment explanation
Indices: 12349821--12349854 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
12349811 TCTCCTCTTA
12349821 CTTCTTCTCCAACTC
1 CTTCTTCTCCAACTC
*
12349836 CTTCTTCTCTAACTC
1 CTTCTTCTCCAACTC
12349851 CTTC
1 CTTC
12349855 ATTTGTTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.44
Consensus pattern (15 bp):
CTTCTTCTCCAACTC
Found at i:12352822 original size:22 final size:23
Alignment explanation
Indices: 12352795--12352839 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
12352785 GGATATCTAC
12352795 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
*
12352817 AAATCATATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
12352840 TATCATATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:12352843 original size:17 final size:17
Alignment explanation
Indices: 12352821--12352873 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
12352811 ATTACAAAAT
*
12352821 CATATCTTCTAAGATTA
1 CATATCTTCAAAGATTA
* *
12352838 CATATCATATCCAAGATTG
1 CATATC-T-TCAAAGATTA
*
12352857 CATATCCTCAAAGATTA
1 CATATCTTCAAAGATTA
12352874 TGTTTCCATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 14 0.48
18 1 0.03
19 14 0.48
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.34
Consensus pattern (17 bp):
CATATCTTCAAAGATTA
Found at i:12352844 original size:22 final size:21
Alignment explanation
Indices: 12352792--12352855 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
12352782 AAAGGATATC
*
12352792 TACAAATCAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
12352813 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
*
12352836 TACATATCATATC-C-AAGAT
1 TACAAATCATATCTCTAAGAT
12352855 T
1 T
12352856 GCATATCCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 6 0.15
20 1 0.03
21 3 0.08
22 18 0.46
23 11 0.28
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.33
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:12353206 original size:24 final size:24
Alignment explanation
Indices: 12353186--12353239 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
12353176 TGCCTCGTCG
*
12353186 GAGCACCACCGGAATGGCTCGCTA
1 GAGCACCACCAGAATGGCTCGCTA
* *
12353210 GAGCACCACCAGAATGGCTTGCCA
1 GAGCACCACCAGAATGGCTCGCTA
12353234 GAGCAC
1 GAGCAC
12353240 TTCCGAGAAC
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:0.28, C:0.33, G:0.28, T:0.11
Consensus pattern (24 bp):
GAGCACCACCAGAATGGCTCGCTA
Found at i:12355313 original size:40 final size:40
Alignment explanation
Indices: 12355258--12355427 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
12355248 AACATTGGAA
12355258 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
12355298 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
12355338 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
12355377 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
12355418 CTATATCCGG
1 ATATATCCGG
12355428 TTAAATCCCG
Statistics
Matches: 111, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.02
40 109 0.98
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:12363409 original size:40 final size:40
Alignment explanation
Indices: 12363354--12363523 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
12363344 AACATTGGAA
12363354 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
12363394 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
12363434 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
12363473 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
12363514 CTATATCCGG
1 ATATATCCGG
12363524 TTAAATCCCG
Statistics
Matches: 111, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.02
40 109 0.98
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:12367895 original size:30 final size:30
Alignment explanation
Indices: 12367852--12367910 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
12367842 AACTTTTTAT
*
12367852 TTTCCCCCAAAATTTTTAC-TCTTTCCCAC
1 TTTCCCCCAAAATTTTTACTTCCTTCCCAC
*
12367881 TTTCCCTCTAAAATTTTTACTTCCTTCCCA
1 TTTCCC-CCAAAATTTTTACTTCCTTCCCA
12367911 TCTCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 12 0.46
31 8 0.31
ACGTcount: A:0.20, C:0.36, G:0.00, T:0.44
Consensus pattern (30 bp):
TTTCCCCCAAAATTTTTACTTCCTTCCCAC
Found at i:12370348 original size:53 final size:53
Alignment explanation
Indices: 12370267--12370377 Score: 186
Period size: 53 Copynumber: 2.1 Consensus size: 53
12370257 GCCCAATACT
12370267 TTTCCTATTGATTCATCAAATTCCTAAGTTTACTATTCAAAGCTTTAAGTCTA
1 TTTCCTATTGATTCATCAAATTCCTAAGTTTACTATTCAAAGCTTTAAGTCTA
* * * *
12370320 TTTCCTCTTGATTCATCAAATTCTTAAGTTTACTCTTCAAAGCTTTAAGTCTG
1 TTTCCTATTGATTCATCAAATTCCTAAGTTTACTATTCAAAGCTTTAAGTCTA
12370373 TTTCC
1 TTTCC
12370378 CTCATACGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (53 bp):
TTTCCTATTGATTCATCAAATTCCTAAGTTTACTATTCAAAGCTTTAAGTCTA
Found at i:12373750 original size:94 final size:94
Alignment explanation
Indices: 12373589--12373762 Score: 339
Period size: 94 Copynumber: 1.9 Consensus size: 94
12373579 ATCCCATCTA
12373589 AATGCGAGCACCGTCCTTACAATGCCAAAAGGGTTTAAGGGTCTCGATTGACGAACATGCACGAC
1 AATGCGAGCACCGTCCTTACAATGCCAAAAGGGTTTAAGGGTCTCGATTGACGAACATGCACGAC
*
12373654 TCCGAATGAGGTTACAAACCTGGGGTCAC
66 TCCGAACGAGGTTACAAACCTGGGGTCAC
12373683 AATGCGAGCACCGTCCTTACAATGCCAAAAGGGTTTAAGGGTCTCGATTGACGAACATGCACGAC
1 AATGCGAGCACCGTCCTTACAATGCCAAAAGGGTTTAAGGGTCTCGATTGACGAACATGCACGAC
12373748 TCCGAACGAGGTTAC
66 TCCGAACGAGGTTAC
12373763 TTATAACATT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 79 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (94 bp):
AATGCGAGCACCGTCCTTACAATGCCAAAAGGGTTTAAGGGTCTCGATTGACGAACATGCACGAC
TCCGAACGAGGTTACAAACCTGGGGTCAC
Found at i:12374914 original size:20 final size:20
Alignment explanation
Indices: 12374886--12374926 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12374876 TTTTTGAATC
*
12374886 ATTGTCCTATTCTAAGGGAT
1 ATTGCCCTATTCTAAGGGAT
*
12374906 ATTGCCCTATTCTAATGGAT
1 ATTGCCCTATTCTAAGGGAT
12374926 A
1 A
12374927 CTGTAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (20 bp):
ATTGCCCTATTCTAAGGGAT
Found at i:12377105 original size:20 final size:21
Alignment explanation
Indices: 12377076--12377149 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
12377066 AAATAAGGGC
12377076 ATACCAAAAAAATGAGAGGAA
1 ATACCAAAAAAATGAGAGGAA
12377097 ATACCAAAAAAATGAGAGGAA
1 ATACCAAAAAAATGAGAGGAA
*
12377118 ATACC-AAAAAATTAGA-G-A
1 ATACCAAAAAAATGAGAGGAA
*
12377136 ATACTAAAAAAATG
1 ATACCAAAAAAATG
12377150 TGAGAGTATA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 5 0.10
19 8 0.16
20 10 0.20
21 26 0.53
ACGTcount: A:0.62, C:0.09, G:0.15, T:0.14
Consensus pattern (21 bp):
ATACCAAAAAAATGAGAGGAA
Found at i:12377155 original size:21 final size:20
Alignment explanation
Indices: 12377080--12377171 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 20
12377070 AAGGGCATAC
12377080 CAAAAAAATGAGAGGAAATA
1 CAAAAAAATGAGAGGAAATA
12377100 CCAAAAAAATGAGAGGAAATA
1 -CAAAAAAATGAGAGGAAATA
* *
12377121 CCAAAAAATTAGA-G-AATA
1 CAAAAAAATGAGAGGAAATA
* *
12377139 CTAAAAAAATGTGA-GAGTATA
1 C-AAAAAAATGAGAGGA-AATA
12377160 CAAAAAATATGA
1 CAAAAAA-ATGA
12377172 TGGTGTGCCA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
18 5 0.08
19 11 0.18
20 17 0.28
21 27 0.45
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.15
Consensus pattern (20 bp):
CAAAAAAATGAGAGGAAATA
Found at i:12377166 original size:39 final size:41
Alignment explanation
Indices: 12377080--12377171 Score: 100
Period size: 39 Copynumber: 2.3 Consensus size: 41
12377070 AAGGGCATAC
12377080 CAAAAAAATGAGAGGAAATACCAAAAAAATGAGAGGAAATA
1 CAAAAAAATGAGAGGAAATACCAAAAAAATGAGAGGAAATA
* * * * *
12377121 CCAAAAAATTAGA-G-AATACTAAAAAAATGTGA-GAGTATA
1 CAAAAAAATGAGAGGAAATACCAAAAAAATGAGAGGA-AATA
12377160 CAAAAAATATGA
1 CAAAAAA-ATGA
12377172 TGGTGTGCCA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
38 2 0.05
39 25 0.60
40 4 0.10
41 11 0.26
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.15
Consensus pattern (41 bp):
CAAAAAAATGAGAGGAAATACCAAAAAAATGAGAGGAAATA
Found at i:12377166 original size:60 final size:60
Alignment explanation
Indices: 12377057--12377171 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
12377047 GTTACAAGAG
* * * *
12377057 AATACTAAAAAATAAGGGCATACCAAAAAAATGAGAGGAAATACCAAAAAAATGAGAGGA
1 AATACCAAAAAATAAGAGAATACCAAAAAAATGAGAGGAAATACAAAAAAAATGAGAGGA
* * * * *
12377117 AATACCAAAAAATTAGAGAATACTAAAAAAATGTGA-GAGTATACAAAAAATATGA
1 AATACCAAAAAATAAGAGAATACCAAAAAAATGAGAGGA-AATACAAAAAAAATGA
12377172 TGGTGTGCCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
59 2 0.04
60 43 0.96
ACGTcount: A:0.60, C:0.09, G:0.16, T:0.16
Consensus pattern (60 bp):
AATACCAAAAAATAAGAGAATACCAAAAAAATGAGAGGAAATACAAAAAAAATGAGAGGA
Found at i:12377529 original size:21 final size:20
Alignment explanation
Indices: 12377496--12377538 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
12377486 TAAAAAAAAC
12377496 AAAAAACTATGAGGAAGTACT
1 AAAAAACTATGAGGAA-TACT
*
12377517 AAAAAAC-ACTGAGGGATACT
1 AAAAAACTA-TGAGGAATACT
12377537 AA
1 AA
12377539 TTTTCTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.53, C:0.12, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAAAACTATGAGGAATACT
Found at i:12379722 original size:40 final size:40
Alignment explanation
Indices: 12379601--12379745 Score: 134
Period size: 40 Copynumber: 3.6 Consensus size: 40
12379591 CGTGCACAAA
* *
12379601 TGCCTTCGGGTCTTAGCCCGGATAGAATGTTTC-GCATGAA-
1 TGCCTTCGGGTCTTAGCCCGGATATAAT-TTCCAGCAT-AAT
* **** * **
12379641 TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCGCAAT
1 TGCCTTCGGGTCTTAGCCCGGATATAATTTCCAGCATAAT
*
12379681 TGCCTTCGGGTCTTAACCCGGATATAATTTCCAGCATAAT
1 TGCCTTCGGGTCTTAGCCCGGATATAATTTCCAGCATAAT
*
12379721 TGTCTTCGGGAT-TTAGCCCGGATAT
1 TGCCTTCGGG-TCTTAGCCCGGATAT
12379746 CATTCAATTT
Statistics
Matches: 81, Mismatches: 21, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
39 2 0.02
40 78 0.96
41 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATAATTTCCAGCATAAT
Found at i:12383720 original size:46 final size:47
Alignment explanation
Indices: 12383598--12383755 Score: 175
Period size: 46 Copynumber: 3.4 Consensus size: 47
12383588 ATGCCGAGCC
* * *
12383598 CCAGACATGGTCTTACACTGGCTTATATCTC-AGGTCAAAGCCATGTC
1 CCAGACATGGTCTTACACTGGCTTACATCTCGAGGCCAAAG-CATGTT
* *
12383645 CCAGACATGGTCTTACACTGGC-TATCATCTCGTA-GCCGACGCATGTT
1 CCAGACATGGTCTTACACTGGCTTA-CATCTCG-AGGCCAAAGCATGTT
*
12383692 CCAGACAT-GTCTTACACTGGCTTACATCTCGAGGCCAATGCATG-T
1 CCAGACATGGTCTTACACTGGCTTACATCTCGAGGCCAAAGCATGTT
*
12383737 CTCAAACAT-GTCTTACACT
1 C-CAGACATGGTCTTACACT
12383756 AACACTCGTC
Statistics
Matches: 97, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
45 3 0.03
46 47 0.48
47 42 0.43
48 4 0.04
49 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (47 bp):
CCAGACATGGTCTTACACTGGCTTACATCTCGAGGCCAAAGCATGTT
Found at i:12383783 original size:93 final size:94
Alignment explanation
Indices: 12383597--12383803 Score: 235
Period size: 93 Copynumber: 2.2 Consensus size: 94
12383587 GATGCCGAGC
* * *
12383597 CCCAGACATGGTCTTACACTGGCTTATATCTCAGGTCAAAGCCATGTCCCAGACATGGTCTTACA
1 CCCAGACATGGTCTTACACTGGCTTACATCTCAGGCCAAAGCCATGTCCCAAACATGGTCTTACA
** *
12383662 CTGGCTATCATCTCGTAGCCGACGCATGT
66 CTAACTATCATCTCATAGCCGACGCATGT
* * *
12383691 TCCAGACAT-GTCTTACACTGGCTTACATCTCGAGGCCAATG-CATGTCTCAAACAT-GTCTTAC
1 CCCAGACATGGTCTTACACTGGCTTACATCTC-AGGCCAAAGCCATGTCCCAAACATGGTCTTAC
* *
12383753 ACTAAC-ACTCGTCTCAATA-CCGATGCCATGT
65 ACTAACTA-TCATCTC-ATAGCCGACG-CATGT
*
12383784 CCCAGGCATGGTCTTACACT
1 CCCAGACATGGTCTTACACT
12383804 AGCTCTCACA
Statistics
Matches: 95, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
91 1 0.01
92 22 0.23
93 47 0.49
94 25 0.26
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (94 bp):
CCCAGACATGGTCTTACACTGGCTTACATCTCAGGCCAAAGCCATGTCCCAAACATGGTCTTACA
CTAACTATCATCTCATAGCCGACGCATGT
Found at i:12391937 original size:20 final size:20
Alignment explanation
Indices: 12391912--12391959 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
12391902 ATTCTGTATG
*
12391912 CACACCTCCTTCACTTGAGT
1 CACACCTCCTCCACTTGAGT
12391932 CACACCTCCTCCACTTGAGT
1 CACACCTCCTCCACTTGAGT
12391952 CACACCTC
1 CACACCTC
12391960 ATTACTAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.21, C:0.46, G:0.08, T:0.25
Consensus pattern (20 bp):
CACACCTCCTCCACTTGAGT
Found at i:12400044 original size:30 final size:30
Alignment explanation
Indices: 12400010--12400070 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
12400000 TCCTTAACTC
12400010 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
12400040 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
12400070 A
1 A
12400071 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:12402455 original size:32 final size:33
Alignment explanation
Indices: 12402383--12402455 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
12402373 TGGAAAAGTT
*
12402383 AATATTTTCTGCTGTTTGGATGAATCTGTGTAA
1 AATATTTTCTGCTGTTTGGATGAATCTCTGTAA
*
12402416 AATATTTTCTGTTGTTTGGCA-G-ATCTCCTG-AA
1 AATATTTTCTGCTGTTTGG-ATGAATCT-CTGTAA
12402448 AATATTTT
1 AATATTTT
12402456 AGGAAAACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
32 14 0.39
33 21 0.58
34 1 0.03
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.47
Consensus pattern (33 bp):
AATATTTTCTGCTGTTTGGATGAATCTCTGTAA
Found at i:12402977 original size:19 final size:19
Alignment explanation
Indices: 12402953--12402991 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
12402943 CGACCAACAC
12402953 GATAATCAAATACACTAAA
1 GATAATCAAATACACTAAA
12402972 GATAATCAAATACACTAAA
1 GATAATCAAATACACTAAA
12402991 G
1 G
12402992 GAATATCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.21
Consensus pattern (19 bp):
GATAATCAAATACACTAAA
Found at i:12403435 original size:18 final size:18
Alignment explanation
Indices: 12403402--12403436 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12403392 GAAGATGAAA
*
12403402 CATAAAAATAACAAAAAC
1 CATAAAAAAAACAAAAAC
*
12403420 CATAAAAAAAATAAAAA
1 CATAAAAAAAACAAAAA
12403437 AGAGGGATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.11, G:0.00, T:0.11
Consensus pattern (18 bp):
CATAAAAAAAACAAAAAC
Found at i:12413393 original size:28 final size:27
Alignment explanation
Indices: 12413330--12413399 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
12413320 ATAGTGAGTC
12413330 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
12413357 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
12413385 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
12413400 GTACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:12417424 original size:27 final size:26
Alignment explanation
Indices: 12417383--12417488 Score: 124
Period size: 27 Copynumber: 3.9 Consensus size: 26
12417373 AGGAAGCGTC
*
12417383 CTGGTGGCTAC-GCCACAATTATTTGAT
1 CTGGTGGCT-CTGCCAC-ATTATCTGAT
*
12417410 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
12417437 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* *
12417465 CTGGTGACTCTGTCACATTATCTG
1 CTGGTGGCTCTGCCACATTATCTG
12417489 TTCTAGCAGC
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
26 3 0.04
27 50 0.71
28 17 0.24
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:12417487 original size:54 final size:54
Alignment explanation
Indices: 12417383--12417492 Score: 152
Period size: 54 Copynumber: 2.0 Consensus size: 54
12417373 AGGAAGCGTC
* *
12417383 CTGGTGGCTACGCCACAATTATTTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTACGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* *
12417437 CTGGTGGCT-CTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTAC-GCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
12417491 CT
1 CT
12417493 AGCAGCCATG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
53 1 0.02
54 31 0.62
55 18 0.36
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTACGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:12421045 original size:46 final size:46
Alignment explanation
Indices: 12420995--12421170 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
12420985 TATTTGGGCA
12420995 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
12421041 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
12421088 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
12421134 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12421171 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:12421150 original size:93 final size:93
Alignment explanation
Indices: 12420991--12421162 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
12420981 TGGATATTTG
* *
12420991 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
12421056 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
12421084 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
12421149 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
12421163 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:12424158 original size:15 final size:15
Alignment explanation
Indices: 12424119--12424198 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
12424109 GTATCTTGGG
*
12424119 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
12424134 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
12424149 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
12424164 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
12424179 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
12424193 TTTCTT
1 TTTCTT
12424199 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:12424188 original size:30 final size:30
Alignment explanation
Indices: 12424110--12424197 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
12424100 CATAGTATCG
* * *
12424110 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
12424140 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
12424170 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
12424198 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:12426632 original size:46 final size:45
Alignment explanation
Indices: 12426579--12426749 Score: 194
Period size: 41 Copynumber: 3.8 Consensus size: 45
12426569 TATTTGGGCA
12426579 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AGCG
* * *
12426625 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C-A-GCG
12426672 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA---A-CG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAGCG
* *
12426713 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12426750 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
41 36 0.33
43 5 0.05
45 2 0.02
46 31 0.28
47 31 0.28
48 2 0.02
50 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAGCG
Found at i:12426694 original size:47 final size:46
Alignment explanation
Indices: 12426575--12426744 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 46
12426565 GGGATATTTG
*
12426575 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGA
* * *
12426622 -GCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATG---CGA
*
12426668 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT---TATG-GAA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCG-A
* *
12426711 CGC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
12426745 TATGGGCGGG
Statistics
Matches: 107, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
41 30 0.28
43 7 0.07
45 2 0.02
46 36 0.34
47 31 0.29
48 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (46 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCGA
Found at i:12428128 original size:17 final size:18
Alignment explanation
Indices: 12428106--12428141 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12428096 AGATAACTAT
12428106 ATAAAAAT-TTAAAATAA
1 ATAAAAATATTAAAATAA
*
12428123 ATAAAAATATTAAATTAA
1 ATAAAAATATTAAAATAA
12428141 A
1 A
12428142 ATGACATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAAATATTAAAATAA
Found at i:12428521 original size:113 final size:114
Alignment explanation
Indices: 12428316--12428609 Score: 385
Period size: 113 Copynumber: 2.6 Consensus size: 114
12428306 TAGCAATTGC
* * *
12428316 GGCGTTTTTTCAAAAACGCCGCTAAAGTTTGATCTTTTGCGGCGTTTTTGGGAAAACGCCGCTAC
1 GGCGTTTTTTCAAAAACGCCGCTAAAGTTTGATCTATTGCGGCGTTTTTGCGAAAACGCCACTAC
* *
12428381 TGCCAAAGGAGCACATATAAAACGACGTCGTTTTCCTTAACATTTTAGT
66 TGCCAAAGAAGCACATAGAAAACGACGTCGTTTTCCTTAACATTTTAGT
12428430 GGCGTTTTTTCAAAAACGCCGCTAAAG-TTGATCTATTGCGGCGTTTTAT-CGAAAACGCCACTA
1 GGCGTTTTTTCAAAAACGCCGCTAAAGTTTGATCTATTGCGGCGTTTT-TGCGAAAACGCCACTA
* * * *
12428493 CTGCCAATGAAGCTCATAGAAAATGACGTCGTTTTTCTTAACATTTTAGT
65 CTGCCAAAGAAGCACATAGAAAACGACGTCGTTTTCCTTAACATTTTAGT
* * * * * * **
12428543 GGCGTTTTTATAAAAAACGCCGCGAAAGGTGGACCTTATAGCGGCGTTTTTAGAAAAAACGCCAC
1 GGCGTTTTT-TCAAAAACGCCGCTAAAGTTTGATC-TATTGCGGCGTTTTT-GCGAAAACGCCAC
12428608 TA
63 TA
12428610 AAGTTTGATC
Statistics
Matches: 158, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
113 84 0.53
114 44 0.28
115 5 0.03
116 13 0.08
117 12 0.08
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (114 bp):
GGCGTTTTTTCAAAAACGCCGCTAAAGTTTGATCTATTGCGGCGTTTTTGCGAAAACGCCACTAC
TGCCAAAGAAGCACATAGAAAACGACGTCGTTTTCCTTAACATTTTAGT
Found at i:12428624 original size:41 final size:42
Alignment explanation
Indices: 12428543--12428651 Score: 150
Period size: 42 Copynumber: 2.6 Consensus size: 42
12428533 ACATTTTAGT
* * *
12428543 GGCGTTTTTATAAAAAACGCCGCGAAAGGTGGACCTTATAGC
1 GGCGTTTTTAGAAAAAACGCCACTAAAGGTGGACCTTATAGC
* * *
12428585 GGCGTTTTTAGAAAAAACGCCACTAAAGTTTGATC-TATAGC
1 GGCGTTTTTAGAAAAAACGCCACTAAAGGTGGACCTTATAGC
12428626 GGCGTTTTTAG-AAAAACGCCACTAAA
1 GGCGTTTTTAGAAAAAACGCCACTAAA
12428652 ATGTTAAGCT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 15 0.25
41 17 0.28
42 29 0.48
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (42 bp):
GGCGTTTTTAGAAAAAACGCCACTAAAGGTGGACCTTATAGC
Found at i:12428679 original size:155 final size:150
Alignment explanation
Indices: 12428430--12428763 Score: 377
Period size: 155 Copynumber: 2.2 Consensus size: 150
12428420 ACATTTTAGT
** * *
12428430 GGCGTTTTTTCAAAAACGCCGCTAAAGTTGATCTATTGCGGCGTTTTATCGAAAACGCCACTACT
1 GGCGTTTTTGAAAAAACGCCGCTAAAGTTGATCTATAGCGGCGTTTTATAGAAAACGCCACTA--
* * *** * *
12428495 GCCAATGAAGCTCATAGAAAATGACGTCGTTTTTCTTAACATTTTAGTGGCGTTTTTATAAAAAA
64 -CAAATGAAGCTCATAGAAAACGACGTCGTTTTGAGTAACATCTTAGCGGCGTTTTTAT-AAAAA
*
12428560 CGCCGCGAAAGGTGGACCTTATAGC
127 CGCCGCGAAAGGTCGACC-TATAGC
*
12428585 GGCGTTTTTAGAAAAAACGCCACTAAAGTTTGATCTATAGCGGCGTTTT-TAGAAAAACGCCACT
1 GGCGTTTTT-GAAAAAACGCCGCTAAAG-TTGATCTATAGCGGCGTTTTATAG-AAAACGCCACT
*
12428649 A-AAATGTTAAGCTCAT-GTAAAACGACGTCGTTTTGAGTAACCTCTTAGCGGCGTTTTTATAAA
63 ACAAATG--AAGCTCATAG-AAAACGACGTCGTTTTGAGTAACATCTTAGCGGCGTTTTTATAAA
* * *
12428712 AACGCCGCTAAAGGTCGACCTATTGT
125 AACGCCGCGAAAGGTCGACCTATAGC
**
12428738 GGCGTTTTTTTAAAAACGCCGCTAAA
1 GGCGTTTTTGAAAAAACGCCGCTAAA
12428764 ACTCCATCTA
Statistics
Matches: 153, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
152 14 0.09
153 17 0.11
154 22 0.14
155 52 0.34
156 17 0.11
157 31 0.20
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (150 bp):
GGCGTTTTTGAAAAAACGCCGCTAAAGTTGATCTATAGCGGCGTTTTATAGAAAACGCCACTACA
AATGAAGCTCATAGAAAACGACGTCGTTTTGAGTAACATCTTAGCGGCGTTTTTATAAAAACGCC
GCGAAAGGTCGACCTATAGC
Found at i:12428775 original size:40 final size:40
Alignment explanation
Indices: 12428698--12428775 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
12428688 ACCTCTTAGC
** *
12428698 GGCGTTTTTATAAAAACGCCGCTAAAGGTCGACCTATTGT
1 GGCGTTTTTATAAAAACGCCGCTAAAACTCCACCTATTGT
* *
12428738 GGCGTTTTTTTAAAAACGCCGCTAAAACTCCATCTATT
1 GGCGTTTTTATAAAAACGCCGCTAAAACTCCACCTATT
12428776 CGATTTTTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (40 bp):
GGCGTTTTTATAAAAACGCCGCTAAAACTCCACCTATTGT
Found at i:12433197 original size:40 final size:40
Alignment explanation
Indices: 12433151--12433279 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
12433141 GACTAGCTCA
*
12433151 AATGCCTTCGGGAC-AAACCCCGGTTATAGTAACTCGCACG
1 AATGCCTTCGGGACTTAACCCCGGTT-TAGTAACTCGCACG
* *
12433191 AATGCCTTCGGGACTTAACCCGGGTTTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAACCCCGGTTTAGTAACTCGCACG
*
12433231 AATGCCTTCGGG-CTTAA-CCCGGATTTATTAACTCGCACG
1 AATGCCTTCGGGACTTAACCCCGG-TTTAGTAACTCGCACG
*
12433270 AACGCCTTCG
1 AATGCCTTCG
12433280 ATCTTAGTCC
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
38 4 0.05
39 28 0.35
40 39 0.49
41 9 0.11
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCCGGTTTAGTAACTCGCACG
Found at i:12433293 original size:39 final size:38
Alignment explanation
Indices: 12433169--12433285 Score: 137
Period size: 39 Copynumber: 3.0 Consensus size: 38
12433159 CGGGACAAAC
12433169 CCCGG-TTATAGTAACTCGCACGAATGCCTTCGGGACTTAA
1 CCCGGATT-TAGTAACTCGCACGAATGCCTTC--GACTTAA
* * *
12433209 CCCGGGTTTAGTAACTCGCACAAATGCCTTCGGGCTTAA
1 CCCGGATTTAGTAACTCGCACGAATGCCTTC-GACTTAA
* *
12433248 CCCGGATTTATTAACTCGCACGAACGCCTTCGATCTTA
1 CCCGGATTTAGTAACTCGCACGAATGCCTTCGA-CTTA
12433286 GTCCGGATAT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
38 1 0.01
39 38 0.56
40 27 0.40
41 2 0.03
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (38 bp):
CCCGGATTTAGTAACTCGCACGAATGCCTTCGACTTAA
Found at i:12436195 original size:26 final size:26
Alignment explanation
Indices: 12436165--12436242 Score: 147
Period size: 26 Copynumber: 3.0 Consensus size: 26
12436155 TGAAATGCCC
12436165 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12436191 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
12436217 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12436243 GTCAATTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.35, C:0.26, G:0.08, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12436887 original size:45 final size:45
Alignment explanation
Indices: 12436758--12436888 Score: 151
Period size: 45 Copynumber: 2.9 Consensus size: 45
12436748 TTGGCTTGAA
* *
12436758 GAAAACGAGTAAGACCATAGTTGAAAGA-TCTATGGCA-CTATGCC
1 GAAAACGAGTAAGACCATAGTTGAAAGACACTATGGCATC-ATACC
* *
12436802 G-AAACTGAATAAGACCATAGTTGAAAGACACTACGGCATCATACC
1 GAAAAC-GAGTAAGACCATAGTTGAAAGACACTATGGCATCATACC
* * * *
12436847 GAAAACGAGTAAGACCATAGCTAAAAGACGCTATGACATCAT
1 GAAAACGAGTAAGACCATAGTTGAAAGACACTATGGCATCAT
12436889 GAATTAGACA
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
43 4 0.05
44 22 0.30
45 42 0.58
46 5 0.07
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (45 bp):
GAAAACGAGTAAGACCATAGTTGAAAGACACTATGGCATCATACC
Found at i:12439672 original size:26 final size:26
Alignment explanation
Indices: 12439636--12439719 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
12439626 TGATACAAAT
12439636 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
12439662 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
12439688 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
12439714 TGATAA
1 TGATAA
12439720 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:12441379 original size:27 final size:27
Alignment explanation
Indices: 12441338--12441450 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
12441328 GAGGAAGCGT
*
12441338 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
12441365 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
12441392 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
12441420 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
12441446 TCTGG
1 TCTGG
12441451 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:12441443 original size:54 final size:54
Alignment explanation
Indices: 12441336--12441450 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
12441326 TGGAGGAAGC
*
12441336 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
12441390 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
12441444 GTTCTGG
1 GTTCTGG
12441451 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:12441536 original size:19 final size:22
Alignment explanation
Indices: 12441512--12441551 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
12441502 CTCCCCACAC
12441512 GGTGTA-A-GGTTGG-TATGGG
1 GGTGTATACGGTTGGATATGGG
12441531 GGTGTATACGGTTGGATATGG
1 GGTGTATACGGTTGGATATGG
12441552 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTGTATACGGTTGGATATGGG
Found at i:12444627 original size:20 final size:20
Alignment explanation
Indices: 12444589--12444629 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12444579 TAAATTTTAA
* **
12444589 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGGTAATT
12444609 AAAGATAAATAAAGGTAATT
1 AAAGATAAATAAAGGTAATT
12444629 A
1 A
12444630 GAATAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (20 bp):
AAAGATAAATAAAGGTAATT
Found at i:12445239 original size:28 final size:28
Alignment explanation
Indices: 12445182--12445243 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
12445172 AATTATAATA
**
12445182 ATTATCTCTTAAATTTAAAATAATTGTT
1 ATTATCTCTTAAATTTAAAATAATCATT
*
12445210 ATTATCTCTTAAAATTTTAAA-AATCATT
1 ATTATCTCTT-AAATTTAAAATAATCATT
12445238 ATTATC
1 ATTATC
12445244 ATAAATTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (28 bp):
ATTATCTCTTAAATTTAAAATAATCATT
Found at i:12448760 original size:21 final size:20
Alignment explanation
Indices: 12448735--12448773 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
12448725 ATGTAAAACT
*
12448735 ATCATCAACTATTCAAATTCC
1 ATCATCAACCA-TCAAATTCC
12448756 ATCATCAACCATCAAATT
1 ATCATCAACCATCAAATT
12448774 ACTCAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (20 bp):
ATCATCAACCATCAAATTCC
Found at i:12457621 original size:26 final size:26
Alignment explanation
Indices: 12457590--12457695 Score: 176
Period size: 26 Copynumber: 4.1 Consensus size: 26
12457580 TGAAATGCCC
*
12457590 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
12457616 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
12457642 ATCGTGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
12457668 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12457694 AT
1 AT
12457696 TAATTTGTAC
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12464650 original size:26 final size:26
Alignment explanation
Indices: 12464618--12464721 Score: 163
Period size: 26 Copynumber: 4.0 Consensus size: 26
12464608 TGAAATGCCC
*
12464618 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
12464644 ATAATGGAACATTTACCTAACCCGTT
1 ATCATGGAACATTTACCTAACCCATT
* *
12464670 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
12464696 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12464722 CTCAATTTGT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 69 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12467351 original size:40 final size:40
Alignment explanation
Indices: 12467119--12467366 Score: 266
Period size: 40 Copynumber: 6.2 Consensus size: 40
12467109 CAATTGAATG
* * ** ** **
12467119 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
* * *
12467159 ATATCTGGGTTAAGACCCGAAGGCAATT-GTGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTG-TT
* *
12467199 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
* *
12467239 AAATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
* * * *
12467279 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
* * *
12467319 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
12467359 ATATCCGG
1 ATATCCGG
12467367 TCGTATTCCG
Statistics
Matches: 180, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
39 3 0.02
40 172 0.96
41 5 0.03
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
Found at i:12467365 original size:120 final size:120
Alignment explanation
Indices: 12467119--12467366 Score: 306
Period size: 120 Copynumber: 2.1 Consensus size: 120
12467109 CAATTGAATG
* * * * *
12467119 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATTATATCTGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGACATTCATGCTGGTAATTAAATCCGGGCTAAGACCCGAAGGCA
* *
12467184 ATTGTGCTAGTGATTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTT
66 ATTGTGCAAGTGATTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGGTT
* * * ** *
12467239 AAATCCGGGCTAAGACCCGAAGGCATTCGTGC-GAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGACATTCATGCTG-GTAATTAAATCCGGGCTAAGACCCGAAGGC
*
12467303 ATTTGTGCAAGTCG-TT-CTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ATGTGGTT
65 AATTGTGCAAGT-GATTAC-ATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGGTT
12467359 ATATCCGG
1 ATATCCGG
12467367 TCGTATTCCG
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
119 3 0.03
120 105 0.96
121 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (120 bp):
ATATCCGGGCTAAGACCCGAAGACATTCATGCTGGTAATTAAATCCGGGCTAAGACCCGAAGGCA
ATTGTGCAAGTGATTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGGTT
Found at i:12473837 original size:49 final size:49
Alignment explanation
Indices: 12473765--12474549 Score: 1191
Period size: 49 Copynumber: 16.1 Consensus size: 49
12473755 ACATAATAAT
12473765 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
12473814 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* * * * * * * *
12473863 ATATGTGATAA-ACGTGAT-G--AATGTGA-AAATGT----A--TACAT
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* *
12473901 ATGTG--ATAAGGCCTAATGGCCGACGTCATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* * *
12473948 ATATGTGATAAGGCCTAATGGCCGACGTCATGAATGTGAAACTGTATAG
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
12473997 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
12474046 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* *
12474095 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAACTGTATAT
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
12474144 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
12474193 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* *
12474242 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAACTGTATAT
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
12474291 ATATGTGATAAGGCCTAATGGCCGAATTAGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCC---T-----AA-T-GGCCGACGTGATGAATGTGAAAATGTATAC
12474350 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
12474399 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* * *
12474448 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAACTGTATAT
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* *
12474497 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTATAT
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
12474546 ATAT
1 ATAT
12474550 ATGTGGTAAA
Statistics
Matches: 676, Mismatches: 37, Indels: 46
0.89 0.05 0.06
Matches are distributed among these distances:
36 4 0.01
37 4 0.01
38 8 0.01
40 5 0.01
41 5 0.01
44 5 0.01
45 6 0.01
47 8 0.01
48 4 0.01
49 576 0.85
50 1 0.00
51 2 0.00
52 1 0.00
56 1 0.00
57 2 0.00
58 1 0.00
59 43 0.06
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.27
Consensus pattern (49 bp):
ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
Found at i:12473870 original size:18 final size:18
Alignment explanation
Indices: 12473847--12473906 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
12473837 GACGTGATGA
12473847 ATGTGAAAATGTATACAT
1 ATGTGAAAATGTATACAT
* *
12473865 ATGTGATAAACGTGAT-GA-
1 ATGTGA-AAATGT-ATACAT
12473883 ATGTGAAAATGTATACAT
1 ATGTGAAAATGTATACAT
12473901 ATGTGA
1 ATGTGA
12473907 TAAGGCCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 2 0.06
17 6 0.18
18 18 0.53
19 6 0.18
20 2 0.06
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.32
Consensus pattern (18 bp):
ATGTGAAAATGTATACAT
Found at i:12473885 original size:36 final size:36
Alignment explanation
Indices: 12473838--12473909 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
12473828 CTAATGGCCG
12473838 ACGTGATGAATGTGAAAATGTATACATATGTGATAA
1 ACGTGATGAATGTGAAAATGTATACATATGTGATAA
12473874 ACGTGATGAATGTGAAAATGTATACATATGTGATAA
1 ACGTGATGAATGTGAAAATGTATACATATGTGATAA
12473910 GGCCTAATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (36 bp):
ACGTGATGAATGTGAAAATGTATACATATGTGATAA
Found at i:12474673 original size:37 final size:36
Alignment explanation
Indices: 12474618--12474704 Score: 129
Period size: 37 Copynumber: 2.3 Consensus size: 36
12474608 AACTTAGAAA
*
12474618 TATGTTCCGGGTGAGACCCGATGACTATGTGTGGAGAT
1 TATG-TCCGGGT-AGACCCGATGACTACGTGTGGAGAT
12474656 TATGTCCGGGTACGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTA-GACCCGATGACTACGTGTGGAGAT
*
12474693 TATGTTCGGGTA
1 TATGTCCGGGTA
12474705 AGACTTCGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 1 0.02
37 41 0.89
38 4 0.09
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (36 bp):
TATGTCCGGGTAGACCCGATGACTACGTGTGGAGAT
Found at i:12477748 original size:48 final size:48
Alignment explanation
Indices: 12477691--12478052 Score: 276
Period size: 48 Copynumber: 7.7 Consensus size: 48
12477681 CATTATGAGA
*
12477691 GCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATCCAGACGA-AG
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCAGA-GATAG
* *
12477739 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCAGACGA-GG
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCAGA-GATAG
* * * * * *
12477787 GCTAGTGTAAGA-CATGTGTGGGATAT-GAATCAGCCATACTA-AGATA-
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATC-GGCAT-CCAGAGATAG
12477833 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA--CAGAGATGAG
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCAGAGAT-AG
* *
12477880 TGCCAGTGTAAGA-CATTTCTGGGACAT-GCATCGGCCTCGACAGAGATA-
1 -GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATC--CAGAGATAG
* * * * * *
12477928 GCCAGTGTAAGA-CGTGTTTGGGACA-CGCATCGAC-T-AAGAG-TTG
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCAGAGATAG
* * * *
12477971 TGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCA-CGCATATATGAG
1 -GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATC-CAGAGAT-AG
* *
12478019 AGCCAGAGTAAGACCATGTCTGGAACATGGCATC
1 -GCCAGTGTAAGACCATGTCTGGGACATGGCATC
12478053 AGCAATATAT
Statistics
Matches: 254, Mismatches: 36, Indels: 46
0.76 0.11 0.14
Matches are distributed among these distances:
42 1 0.00
43 4 0.02
44 29 0.11
45 4 0.02
46 29 0.11
47 75 0.30
48 86 0.34
49 14 0.06
50 12 0.05
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.21
Consensus pattern (48 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCAGAGATAG
Found at i:12477844 original size:94 final size:93
Alignment explanation
Indices: 12477742--12478052 Score: 323
Period size: 94 Copynumber: 3.3 Consensus size: 93
12477732 GACGAAGGCT
* * *
12477742 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCAGACGAGGGCTAGTGTAAGACATGTGTG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATCAAGA-GAGTGCTAGTGTAAGACATGTCTG
* *
12477807 GGATATGAATCAGCCATACTAAGATAGCC
65 GGACATGCATCAGCCATACTAAGATAGCC
* *
12477836 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CAGAGATGAGTGCCAGTGTAAGACATTTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATCA-AGA-GAGTGCTAGTGTAAGACATGTCT
*
12477900 GGGACATGCATCGGCC-TCGAC-AGAGATAGCC
64 GGGACATGCATCAGCCAT--ACTA-AGATAGCC
* * * * *
12477931 AGTGTAAGA-CGTGTTTGGGACA-CGCATCGAC-T-AAGAGTTGTGCTAGTGTAAGACATGTCTG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATCAAGAG-AGTGCTAGTGTAAGACATGTCTG
* *
12477992 GGACATGCATCAGCACGCATA-TATGAGAGCC
65 GGACATGCATCAG--C-CATACTAAGATAGCC
* *
12478023 AGAGTAAGACCATGTCTGGAACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
12478053 AGCAATATAT
Statistics
Matches: 180, Mismatches: 24, Indels: 26
0.78 0.10 0.11
Matches are distributed among these distances:
90 1 0.01
91 35 0.19
92 15 0.08
93 22 0.12
94 87 0.48
95 20 0.11
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.22
Consensus pattern (93 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCATCAAGAGAGTGCTAGTGTAAGACATGTCTGG
GACATGCATCAGCCATACTAAGATAGCC
Found at i:12477994 original size:44 final size:45
Alignment explanation
Indices: 12477647--12478002 Score: 170
Period size: 47 Copynumber: 7.6 Consensus size: 45
12477637 ATTTGTGCGT
* * * * * * *
12477647 CAGTGTAAGACATGTATGGGACATGCTTCGGCCACATTA-TGAGAGC
1 CAGTGTAAGACATGTCTGGGACATGCATCGACTACA-GAGT-TGTGC
* * * **
12477693 CAGTGTAAGACCATGTCTAGGACATGGCATCGGCATCCAGACGAAG-GC
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCGAC-TACAGA-GTTGTGC
* * * * *
12477741 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCAGACG-AGGGC
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCGAC-TACAGA-GTTGTGC
* * * * * * *
12477789 TAGTGTAAGACATGTGTGGGATATGAATCAGCCATACTA-AGAT-AGC
1 CAGTGTAAGACATGTCTGGGACATGCATC-GAC-TAC-AGAGTTGTGC
* *
12477835 CAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACAGAGATGAGTGC
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCGACTACAGAG-T-TGTGC
* * * *
12477883 CAGTGTAAGACATTTCTGGGACATGCATCGGCCTCGACAGAGAT-AGC
1 CAGTGTAAGACATGTCTGGGACATGCATC-GACT--ACAGAGTTGTGC
* * *
12477930 CAGTGTAAGACGTGTTTGGGACACGCATCGACTA-AGAGTTGTGC
1 CAGTGTAAGACATGTCTGGGACATGCATCGACTACAGAGTTGTGC
*
12477974 TAGTGTAAGACATGTCTGGGACATGCATC
1 CAGTGTAAGACATGTCTGGGACATGCATC
12478003 AGCACGCATA
Statistics
Matches: 250, Mismatches: 40, Indels: 42
0.75 0.12 0.13
Matches are distributed among these distances:
43 5 0.02
44 29 0.12
45 4 0.02
46 34 0.14
47 88 0.35
48 80 0.32
49 4 0.02
50 6 0.02
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (45 bp):
CAGTGTAAGACATGTCTGGGACATGCATCGACTACAGAGTTGTGC
Found at i:12490388 original size:40 final size:40
Alignment explanation
Indices: 12490343--12490510 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
12490333 CGGAATATAA
12490343 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
12490383 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
12490423 CCGGATGTAGCCACTAGCGCAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
12490463 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
12490503 CCGGATAT
1 CCGGATAT
12490511 CATTCAATTT
Statistics
Matches: 101, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
39 1 0.01
40 99 0.98
41 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:12498395 original size:40 final size:40
Alignment explanation
Indices: 12498350--12498517 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
12498340 CGGAATATAA
12498350 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
12498390 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
12498430 CCGGATGTAGCCACTAGCGCAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
12498470 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
12498510 CCGGATAT
1 CCGGATAT
12498518 CATTCAATTT
Statistics
Matches: 101, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
39 1 0.01
40 99 0.98
41 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:12502996 original size:19 final size:19
Alignment explanation
Indices: 12502962--12503014 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
12502952 GATGCACCTT
12502962 GTGTGCCAGATATGCGCTTC
1 GTGTGCCAG-TATGCGCTTC
* *
12502982 GTGTGCTAGTATGCGGTTC
1 GTGTGCCAGTATGCGCTTC
*
12503001 ATGTGCCAGTATGC
1 GTGTGCCAGTATGC
12503015 TACATTCGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (19 bp):
GTGTGCCAGTATGCGCTTC
Found at i:12504425 original size:21 final size:21
Alignment explanation
Indices: 12504400--12504439 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12504390 CAAAAAGGGC
*
12504400 TTAATCGTGTAAAG-TGAAAAG
1 TTAATAGT-TAAAGATGAAAAG
12504421 TTAATAGTTAAAGATGAAA
1 TTAATAGTTAAAGATGAAA
12504440 GTGCTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (21 bp):
TTAATAGTTAAAGATGAAAAG
Found at i:12504554 original size:21 final size:22
Alignment explanation
Indices: 12504528--12504573 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12504518 GGACAACCAA
* *
12504528 TATAAAGATT-TTATATTAATT
1 TATAAAGATTATTATAGTAAAT
*
12504549 TATAAAGGTTATTATAGTAAAT
1 TATAAAGATTATTATAGTAAAT
12504571 TAT
1 TAT
12504574 GAATTATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (22 bp):
TATAAAGATTATTATAGTAAAT
Found at i:12508766 original size:35 final size:35
Alignment explanation
Indices: 12508717--12508795 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
12508707 AATCCCTCCA
* * *
12508717 AAACATACCAAATGCTCACAAGAGCTAGTCTAACTG
1 AAACATGCC-AATGCTCACAAGAGCTAGTCCAACCG
* *
12508753 AGACATGCCAATGCTCATAAGAGCTAGTCCAACCG
1 AAACATGCCAATGCTCACAAGAGCTAGTCCAACCG
12508788 AAACATGC
1 AAACATGC
12508796 TAAGCAGAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 30 0.81
36 7 0.19
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (35 bp):
AAACATGCCAATGCTCACAAGAGCTAGTCCAACCG
Found at i:12515475 original size:48 final size:48
Alignment explanation
Indices: 12515341--12515568 Score: 186
Period size: 48 Copynumber: 4.9 Consensus size: 48
12515331 GGTTATGTGC
*
12515341 GATCCCATGTAAGACCATGTCT-AGGACATGGCTTTGGCATCGATATGT
1 GATCCCATGTAAGACCATGTCTGA-GACATGGCATTGGCATCGATATGT
* **** * *
12515389 AATTTTGTGTAAGTCCATAGT-TG-GGCTAT--CA---GCATCGATATGT
1 GATCCCATGTAAGACCAT-GTCTGAGAC-ATGGCATTGGCATCGATATGT
* **
12515432 GATCCCATGTAAGACCATGTCTGAGACATGGCATTGGCATCGATCTAC
1 GATCCCATGTAAGACCATGTCTGAGACATGGCATTGGCATCGATATGT
* * * *
12515480 GATCCCATGTAAGGCCATGTCTGGGACATGGCATTAGCATTGATATGT
1 GATCCCATGTAAGACCATGTCTGAGACATGGCATTGGCATCGATATGT
* * * *
12515528 GATCCCATGT-AGTACCATATCTGGGATATGGCATTGACATC
1 GATCCCATGTAAG-ACCATGTCTGAGACATGGCATTGGCATC
12515569 CTACCATGTG
Statistics
Matches: 138, Mismatches: 31, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
42 2 0.01
43 28 0.20
44 2 0.01
45 2 0.01
46 1 0.01
47 4 0.03
48 97 0.70
49 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (48 bp):
GATCCCATGTAAGACCATGTCTGAGACATGGCATTGGCATCGATATGT
Found at i:12517995 original size:49 final size:48
Alignment explanation
Indices: 12517881--12518240 Score: 241
Period size: 47 Copynumber: 7.6 Consensus size: 48
12517871 ATGATCCTGT
* *
12517881 TGCCATGTCCCAGACATGGTCTTACACTGGCTCATC--TATCAAGTCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCT-ATCAATATCAAGCCGA
* * * *
12517928 TGCCATGGCCCAGACATGGTCTTACACTAACTATCAAAATCGAGGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTATCAATATC-AAGCCGA
* * *
12517977 TGCCATATCCCAGACATGGTCTTACACTAGCTCTCACATATCCATGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTATCA-ATAT-CAAGCCGA
* * *
12518027 TGCCATGTCCCAGACATTGTCTTAC-CT-G--A-CACATCTCGTAGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTATCA-ATATC-AAGCCGA
* * * * * *
12518072 -GGCATGTCCCAGACAT-GTCTTACACTGGCT-T-ACATCTTGAGGTCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTATCA-AT-ATCAAGCCGA
* * * * *
12518118 TG-CATGTCCTAGACAT-GTCTTACACTAGCTCT-AGTCTCAATGCTGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTATCAATATCAA-GCCGA
* * ***
12518164 TGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-ATAATGTGGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTATCAAT-ATCAAGCCGA
* *
12518212 TG-CACGTCCCATACAT-GTCTTACACTAGC
1 TGCCATGTCCCAGACATGGTCTTACACTAGC
12518241 ACACAAATAA
Statistics
Matches: 251, Mismatches: 43, Indels: 39
0.75 0.13 0.12
Matches are distributed among these distances:
43 7 0.03
44 18 0.07
45 14 0.06
46 55 0.22
47 58 0.23
48 26 0.10
49 40 0.16
50 32 0.13
51 1 0.00
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
TGCCATGTCCCAGACATGGTCTTACACTAGCTATCAATATCAAGCCGA
Found at i:12518213 original size:94 final size:92
Alignment explanation
Indices: 12517881--12518240 Score: 292
Period size: 94 Copynumber: 3.8 Consensus size: 92
12517871 ATGATCCTGT
*
12517881 TGCCATGTCCCAGACATGGTCTTACACTGGCTCATCTATCAA-GT--CGATGCCATGGCCCAGAC
1 TGCCATGTCCCAGACATGGTCTTACACTGGCTC-TC-AT-AATGTGCCGATGCCATGTCCCAGAC
* * ** *
12517943 ATGGTCTTACACTAACTATCAAAATCGAGGCCGA
63 AT-GTCTTACACTAGC--TCTATCTC-ATGCCGA
* * * *
12517977 TGCCATATCCCAGACATGGTCTTACACTAGCTCTCACATATCCATGCCGATGCCATGTCCCAGAC
1 TGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-AT--GTGCCGATGCCATGTCCCAGAC
* *
12518042 ATTGTCTTAC-CT-GACAC-ATCTCGTAGCCGA
63 A-TGTCTTACACTAG-CTCTATCTCAT-GCCGA
* ** * * *
12518072 -GGCATGTCCCAGACAT-GTCTTACACTGGCT-TACATCTTGAGGTCGATG-CATGTCCTAGACA
1 TGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAATG-TGCCGATGCCATGTCCCAGACA
*
12518133 TGTCTTACACTAGCTCTAGTCTCAATGCTGA
64 TGTCTTACACTAGCTCTA-TCTC-ATGCCGA
* *
12518164 TGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATG-CACGTCCCATACAT
1 TGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT-GCCGATGCCATGTCCCAGACAT
12518228 GTCTTACACTAGC
65 GTCTTACACTAGC
12518241 ACACAAATAA
Statistics
Matches: 212, Mismatches: 32, Indels: 42
0.74 0.11 0.15
Matches are distributed among these distances:
89 8 0.04
90 16 0.08
91 8 0.04
92 10 0.05
93 32 0.15
94 65 0.31
95 11 0.05
96 32 0.15
97 1 0.00
98 3 0.01
99 25 0.12
100 1 0.00
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (92 bp):
TGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGCCGATGCCATGTCCCAGACATG
TCTTACACTAGCTCTATCTCATGCCGA
Found at i:12519590 original size:83 final size:83
Alignment explanation
Indices: 12519483--12519656 Score: 330
Period size: 83 Copynumber: 2.1 Consensus size: 83
12519473 ATGTGATTCG
*
12519483 GCCATGTGTCCCCTGCACCCTAATTAGGTAAAATAGAATGCCCAGTAGTAAACACATGGGTAGAG
1 GCCATGTGCCCCCTGCACCCTAATTAGGTAAAATAGAATGCCCAGTAGTAAACACATGGGTAGAG
12519548 ACACGGTCGTGTGTCTCA
66 ACACGGTCGTGTGTCTCA
*
12519566 GCCATGTGCCCCCTGCACCCTAATTAGGTAAAATAGAATGCCTAGTAGTAAACACATGGGTAGAG
1 GCCATGTGCCCCCTGCACCCTAATTAGGTAAAATAGAATGCCCAGTAGTAAACACATGGGTAGAG
12519631 ACACGGTCGTGTGTCTCA
66 ACACGGTCGTGTGTCTCA
12519649 GCCATGTG
1 GCCATGTG
12519657 AAGGACATAG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 89 1.00
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (83 bp):
GCCATGTGCCCCCTGCACCCTAATTAGGTAAAATAGAATGCCCAGTAGTAAACACATGGGTAGAG
ACACGGTCGTGTGTCTCA
Found at i:12522225 original size:40 final size:41
Alignment explanation
Indices: 12522180--12522346 Score: 164
Period size: 40 Copynumber: 4.2 Consensus size: 41
12522170 CGGAATATAA
*
12522180 CCGGATATAATCAAGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
12522220 CCGGATAGAAT-AACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
12522260 CCGGATGT-AGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
12522300 CCGGATATAAT-TTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
12522339 CCGGATAT
1 CCGGATAT
12522347 CATTCAATTT
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
39 17 0.16
40 87 0.83
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (41 bp):
CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:12523195 original size:17 final size:19
Alignment explanation
Indices: 12523172--12523217 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
12523162 AAGAAGCATG
12523172 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
12523190 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
12523208 AATCATGCTC
1 AATCATGCTC
12523218 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:12530247 original size:40 final size:41
Alignment explanation
Indices: 12530202--12530368 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 41
12530192 CGGAATATAA
*
12530202 CCGGATATAATCAAGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
12530242 CCGGATAGAAT-AACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
12530282 CCGGATAT-AGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
12530322 CCGGATATAAT-TTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
12530361 CCGGATAT
1 CCGGATAT
12530369 CATTCAATTT
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
39 17 0.16
40 89 0.83
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (41 bp):
CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:12530352 original size:80 final size:79
Alignment explanation
Indices: 12530218--12530368 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
12530208 ATAATCAAGT
*
12530218 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
12530283 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
12530298 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
12530361 CCGGATAT
64 CCGGATAT
12530369 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:12531218 original size:17 final size:19
Alignment explanation
Indices: 12531195--12531240 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
12531185 AAGAAGCATG
12531195 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
12531213 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
12531231 AATCATGCTC
1 AATCATGCTC
12531241 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:12541008 original size:22 final size:21
Alignment explanation
Indices: 12540983--12541039 Score: 53
Period size: 23 Copynumber: 2.6 Consensus size: 21
12540973 CTCGTATGAA
*
12540983 CTTACTGTTCAA-CTTGATAGAG
1 CTTACTGTTCAATCAT--TAGAG
*
12541005 CTTACCGTTTCAGATCATTAGAG
1 CTTACTG-TTCA-ATCATTAGAG
12541028 CTTACTGTTCAA
1 CTTACTGTTCAA
12541040 AAACTCAGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 1 0.03
22 10 0.34
23 15 0.52
24 1 0.03
25 2 0.07
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (21 bp):
CTTACTGTTCAATCATTAGAG
Found at i:12548088 original size:68 final size:68
Alignment explanation
Indices: 12547986--12548116 Score: 262
Period size: 68 Copynumber: 1.9 Consensus size: 68
12547976 AGAAATTCTG
12547986 CACAGCTGGGTTGGGCTTATTTATCTATAAGCAAATTTTTAACAACATTAGTAAGCTTATCAATT
1 CACAGCTGGGTTGGGCTTATTTATCTATAAGCAAATTTTTAACAACATTAGTAAGCTTATCAATT
12548051 CAA
66 CAA
12548054 CACAGCTGGGTTGGGCTTATTTATCTATAAGCAAATTTTTAACAACATTAGTAAGCTTATCAA
1 CACAGCTGGGTTGGGCTTATTTATCTATAAGCAAATTTTTAACAACATTAGTAAGCTTATCAA
12548117 CTTTATCTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (68 bp):
CACAGCTGGGTTGGGCTTATTTATCTATAAGCAAATTTTTAACAACATTAGTAAGCTTATCAATT
CAA
Found at i:12551874 original size:37 final size:37
Alignment explanation
Indices: 12551824--12551914 Score: 164
Period size: 37 Copynumber: 2.4 Consensus size: 37
12551814 TTATTACGAA
12551824 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
12551861 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
12551898 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
12551915 TTTCCAAGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 47 0.90
38 5 0.10
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:12552009 original size:48 final size:48
Alignment explanation
Indices: 12551954--12552153 Score: 355
Period size: 48 Copynumber: 4.2 Consensus size: 48
12551944 TGTTACAACA
*
12551954 TTCACATTAGCCATTCGGCTTTACCACACATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
*
12552002 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
*
12552050 TTCACATTAGCCCTTCGGCTTTACCACATATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
* *
12552098 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATGT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
12552146 TTCACATT
1 TTCACATT
12552154 CATCACATCG
Statistics
Matches: 145, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 145 1.00
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.33
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
Found at i:12552199 original size:49 final size:49
Alignment explanation
Indices: 12552146--12552431 Score: 456
Period size: 47 Copynumber: 5.9 Consensus size: 49
12552136 ACACATATGT
12552146 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACC
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACC
* *
12552195 TTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACTCT
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACC
12552242 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACA-C
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACC
*
12552290 TTGCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATATACACC
1 TT-CACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATATACACC
* *
12552342 TTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACTCT
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACC
*
12552389 TTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
12552432 CATCTCCTAC
Statistics
Matches: 220, Mismatches: 9, Indels: 16
0.90 0.04 0.07
Matches are distributed among these distances:
47 89 0.40
48 2 0.01
49 82 0.37
51 44 0.20
52 3 0.01
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (49 bp):
TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACC
Found at i:12552369 original size:147 final size:145
Alignment explanation
Indices: 12552148--12552431 Score: 532
Period size: 147 Copynumber: 1.9 Consensus size: 145
12552138 ACATATGTTT
12552148 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACATCG
1 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACATCG
12552213 GCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
66 GCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
12552278 ATATATATACACTTG
131 ATATATATACACTTG
*
12552293 CACATTCATCACATTGGCCATTAGGCCTTATCACATATATATATACACCTTCACATTCATCACAT
1 CACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATATACACCTTCACATTCATCACAT
*
12552358 CGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTATC
64 CGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATCGGCCATTAGGCCTTATC
12552423 ACATATATA
129 ACATATATA
12552432 CATCTCCTAC
Statistics
Matches: 135, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
145 33 0.24
147 102 0.76
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (145 bp):
CACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACATCG
GCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
ATATATATACACTTG
Found at i:12555649 original size:14 final size:15
Alignment explanation
Indices: 12555627--12555668 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
12555617 TATACTTTTG
12555627 ATTAAAC-TTAATTA
1 ATTAAACTTTAATTA
*
12555641 ATTACACTTTAATTA
1 ATTAAACTTTAATTA
**
12555656 ACCAAACTTTAAT
1 ATTAAACTTTAAT
12555669 CTTAATTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTAAACTTTAATTA
Found at i:12555682 original size:21 final size:20
Alignment explanation
Indices: 12555649--12555688 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12555639 TAATTACACT
12555649 TTAATTAACCAAACTTTAATC
1 TTAATTAACCAAA-TTTAATC
**
12555670 TTAATTAGTCAAATTTAAT
1 TTAATTAACCAAATTTAAT
12555689 GGTTTTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (20 bp):
TTAATTAACCAAATTTAATC
Found at i:12560571 original size:40 final size:40
Alignment explanation
Indices: 12560513--12560760 Score: 259
Period size: 40 Copynumber: 6.2 Consensus size: 40
12560503 TGAATGATAC
* * *
12560513 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATTATAT
* * *
12560553 CCAGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAG-TGATTATAT
* ** *
12560593 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATTATAT
* *
12560633 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAG-TGATTATAT
* * ** *
12560673 CCAGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATTATAT
* * ** *
12560713 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATTATAT
12560753 CC-GGCTAA
1 CCGGGCTAA
12560761 ATTCCGAAGA
Statistics
Matches: 168, Mismatches: 36, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
39 7 0.04
40 158 0.94
41 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATTATAT
Found at i:12560646 original size:80 final size:80
Alignment explanation
Indices: 12560513--12560760 Score: 356
Period size: 80 Copynumber: 3.1 Consensus size: 80
12560503 TGAATGATAC
* * * * ** * *
12560513 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCAGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGCTAAGACCCGAAGGCATTCG
12560578 TGCGAGTTGTTATAT
66 TGCGAGTTGTTATAT
12560593 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGCTAAGACCCGAAGGCATTCG
12560658 TGCGAGTTGTTATAT
66 TGCGAGTTGTTATAT
* *
12560673 CCAGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATT-
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGCTAAGACCCGAAGGC-ATTC
** *
12560737 GTGCTTGTGGTTATAT
65 GTGCGAGTTGTTATAT
12560753 CC-GGCTAA
1 CCGGGCTAA
12560761 ATTCCGAAGA
Statistics
Matches: 154, Mismatches: 13, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
79 6 0.04
80 145 0.94
81 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGCTAAGACCCGAAGGCATTCG
TGCGAGTTGTTATAT
Found at i:12560726 original size:120 final size:120
Alignment explanation
Indices: 12560513--12560740 Score: 332
Period size: 120 Copynumber: 1.9 Consensus size: 120
12560503 TGAATGATAC
* * *
12560513 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCAGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCATTCATGCGAGTGATTATATCCAGGCTAAGACCCGAAGGCATTCG
* *** * *
12560578 TGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
66 TGCAAGTTACCAAATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAAT
* *
12560633 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATATCCAGGCTAAGACCCGAAGGCATTT
1 CCGGGCTAAGACCCGAAGGCATTCATGCGAG-TGATTATATCCAGGCTAAGACCCGAAGGCATTC
*
12560697 GTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATTGTGC
65 GTGCAAGTTACCAAATCCGGGCTAAGACCCGAAGGCAATTGTGC
12560741 TTGTGGTTAT
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
120 93 0.98
121 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (120 bp):
CCGGGCTAAGACCCGAAGGCATTCATGCGAGTGATTATATCCAGGCTAAGACCCGAAGGCATTCG
TGCAAGTTACCAAATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAAT
Found at i:12562558 original size:38 final size:38
Alignment explanation
Indices: 12562507--12562661 Score: 247
Period size: 38 Copynumber: 4.0 Consensus size: 38
12562497 GATGTGTATG
12562507 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
12562545 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
** *
12562583 AATGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGC
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
* *
12562621 AATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGC
1 AA-TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGC
12562661 A
1 A
12562662 TTTGTGCGGG
Statistics
Matches: 109, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
38 75 0.69
39 24 0.22
40 10 0.09
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.22
Consensus pattern (38 bp):
AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
Found at i:12562685 original size:40 final size:40
Alignment explanation
Indices: 12562526--12562705 Score: 145
Period size: 38 Copynumber: 4.6 Consensus size: 40
12562516 ATTGTGATAT
* * *** *
12562526 CCGGGCTAAG-CCCGAAGGCA-ATGTGCGAATTGTGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* * ** *
12562564 CCGGGCTAAG-CCCGAAGGCA-ATGTGCGAGCTATGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* *** *
12562602 CCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTGTGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* *
12562641 CCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* *
12562681 CCGGGCTATGTCCCGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
12562706 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
38 55 0.44
39 24 0.19
40 45 0.36
ACGTcount: A:0.23, C:0.23, G:0.32, T:0.22
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
Found at i:12570502 original size:38 final size:38
Alignment explanation
Indices: 12570451--12570605 Score: 249
Period size: 38 Copynumber: 4.0 Consensus size: 38
12570441 GATGTGTATG
12570451 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
12570489 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
*
12570527 AATGTGCGAGA-TATGATATCCGGGCTAAGCCCGAAGGC
1 AATGTGCGA-ATTGTGATATCCGGGCTAAGCCCGAAGGC
* *
12570565 AATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGC
1 AA-TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGC
12570605 A
1 A
12570606 TTTGTGCGGG
Statistics
Matches: 109, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
38 75 0.69
39 24 0.22
40 10 0.09
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (38 bp):
AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
Found at i:12570629 original size:40 final size:40
Alignment explanation
Indices: 12570470--12570649 Score: 145
Period size: 38 Copynumber: 4.6 Consensus size: 40
12570460 ATTGTGATAT
* * *** *
12570470 CCGGGCTAAG-CCCGAAGGCA-ATGTGCGAATTGTGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* * ** *
12570508 CCGGGCTAAG-CCCGAAGGCA-ATGTGCGAGATATGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* *** *
12570546 CCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTGTGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* *
12570585 CCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* *
12570625 CCGGGCTATGTCCCGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
12570650 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
38 55 0.44
39 24 0.19
40 45 0.36
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.22
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
Found at i:12573488 original size:41 final size:43
Alignment explanation
Indices: 12573385--12573497 Score: 133
Period size: 41 Copynumber: 2.7 Consensus size: 43
12573375 ATCCCAAATA
* * *
12573385 CCCAAATATGGTCTTACATGAGATCTCATATCGATGCCAATAGT
1 CCCAGATATGGTCTTACACGAAATCTCA-ATCGATGCCAATAGT
* *
12573429 -CTAGGTATGGTCTTACACGAAATCTCAATCGATGCC-ATA-T
1 CCCAGATATGGTCTTACACGAAATCTCAATCGATGCCAATAGT
* *
12573469 CCCAGATATGGTCTAACACGTAATCTCAA
1 CCCAGATATGGTCTTACACGAAATCTCAA
12573498 CTAATCCTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
40 1 0.02
41 27 0.46
42 9 0.15
43 22 0.37
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (43 bp):
CCCAGATATGGTCTTACACGAAATCTCAATCGATGCCAATAGT
Found at i:12578554 original size:40 final size:40
Alignment explanation
Indices: 12578480--12578701 Score: 331
Period size: 40 Copynumber: 5.6 Consensus size: 40
12578470 AACCCAAGTA
* * *
12578480 CCTTCGGGATTTAG-CTGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* * *
12578519 CCTTTGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
12578559 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATA
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
12578599 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
12578639 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
12578679 CCTTCGGGACTTATCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
12578702 CATTCGAATA
Statistics
Matches: 165, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
39 11 0.07
40 151 0.92
41 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:12584425 original size:42 final size:43
Alignment explanation
Indices: 12584344--12584434 Score: 114
Period size: 42 Copynumber: 2.1 Consensus size: 43
12584334 CTTACATGGG
**
12584344 ATCTCATATCGATGCCAATAGCCCAGCTATGGTCTTACACGAA
1 ATCTCATATCGATGCCAATAGCCCAAATATGGTCTTACACGAA
* * *
12584387 ATCTTATATCGATGTC-ATATCCCAAATATGGTCTTACAC-ATA
1 ATCTCATATCGATGCCAATAGCCCAAATATGGTCTTACACGA-A
12584429 ATCTCA
1 ATCTCA
12584435 ACTAACCCTA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.02
42 26 0.63
43 14 0.34
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (43 bp):
ATCTCATATCGATGCCAATAGCCCAAATATGGTCTTACACGAA
Found at i:12586341 original size:4 final size:4
Alignment explanation
Indices: 12586332--12586357 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12586322 ATTGAAAAGC
12586332 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
12586358 ATTGTAGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Done.