Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 85 of 167
Found at i:28021810 original size:40 final size:40
Alignment explanation
Indices: 28021755--28021972 Score: 350
Period size: 40 Copynumber: 5.5 Consensus size: 40
28021745 CGGATGATAA
*
28021755 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
28021795 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
28021835 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
28021875 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
28021915 CCGGGCTAGGTCCCAAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
28021955 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
28021973 TACTTGGTTT
Statistics
Matches: 168, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 15 0.09
40 153 0.91
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28030067 original size:40 final size:40
Alignment explanation
Indices: 28030012--28030233 Score: 385
Period size: 40 Copynumber: 5.6 Consensus size: 40
28030002 TATCCGGATG
28030012 ATAACCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACT
28030052 ATAACCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACT
28030092 ATAACCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACT
*
28030132 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACT
*
28030172 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTA-CT
* *
28030212 ATATCC-GGCTAAATCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
28030234 TACTTGTTTT
Statistics
Matches: 177, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
39 17 0.10
40 160 0.90
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTTACT
Found at i:28033554 original size:39 final size:40
Alignment explanation
Indices: 28033476--28033665 Score: 168
Period size: 39 Copynumber: 5.0 Consensus size: 40
28033466 CAAATCCAAT
* * *
28033476 CACCACCA-CAAAGCATGCGTGACTTTAAGCCCGGATATAA
1 CACCAGCACCAAAGCCTGCGGGACTTT-AGCCCGGATATAA
* *
28033516 TACCAGC-CCAAAGCCTGCAGGACTTTAGCCCGGATATAA
1 CACCAGCACCAAAGCCTGCGGGACTTTAGCCCGGATATAA
* * *
28033555 CACCAGCACGAATGCCT------C-TTAGCCCGGATATAG
1 CACCAGCACCAAAGCCTGCGGGACTTTAGCCCGGATATAA
* * *
28033588 CACCAGCACGAATGCCTTCGGGAC-TTAGCCCGGATATAA
1 CACCAGCACCAAAGCCTGCGGGACTTTAGCCCGGATATAA
* * *
28033627 CACCAGCACGAATGCCTTCGGGAC-TTAGCCCGGATATAA
1 CACCAGCACCAAAGCCTGCGGGACTTTAGCCCGGATATAA
28033666 TTATCCATTA
Statistics
Matches: 132, Mismatches: 10, Indels: 17
0.83 0.06 0.11
Matches are distributed among these distances:
33 31 0.23
34 1 0.01
39 73 0.55
40 27 0.20
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (40 bp):
CACCAGCACCAAAGCCTGCGGGACTTTAGCCCGGATATAA
Found at i:28033620 original size:72 final size:72
Alignment explanation
Indices: 28033503--28033643 Score: 212
Period size: 72 Copynumber: 2.0 Consensus size: 72
28033493 CGTGACTTTA
*
28033503 AGCCCGGATATAATACCAGCCCAAAGCCTGCAGGACTTTAGCCCGGATATAACACCAGCACGAAT
1 AGCCCGGATATAACACCAGCCCAAAGCCTGCAGGACTTTAGCCCGGATATAACACCAGCACGAAT
28033568 GCCTCTT
66 GCCTCTT
* * * * *
28033575 AGCCCGGATATAGCACCAGCACGAATGCCTTCGGGAC-TTAGCCCGGATATAACACCAGCACGAA
1 AGCCCGGATATAACACCAGC-CCAAAGCCTGCAGGACTTTAGCCCGGATATAACACCAGCACGAA
28033639 TGCCT
65 TGCCT
28033644 TCGGGACTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
72 50 0.81
73 12 0.19
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (72 bp):
AGCCCGGATATAACACCAGCCCAAAGCCTGCAGGACTTTAGCCCGGATATAACACCAGCACGAAT
GCCTCTT
Found at i:28040038 original size:39 final size:39
Alignment explanation
Indices: 28039948--28040165 Score: 321
Period size: 39 Copynumber: 5.5 Consensus size: 39
28039938 ACAAAGCATG
* * * *
28039948 CGGGACTTTAAGCCCGAATATAATACCAGCA-GAAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
28039988 CGGGACTTTAGCCCGGATATAACACCAACACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
28040028 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
28040067 CGGGACTTAGCCCGAATATAATACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
28040106 CAGGACCTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
28040145 CGGGACTTAGCCCGGATATAA
1 CGGGACTTAGCCCGGATATAA
28040166 TTCTCCATTA
Statistics
Matches: 163, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
39 141 0.87
40 22 0.13
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:28040164 original size:117 final size:119
Alignment explanation
Indices: 28039948--28040165 Score: 361
Period size: 117 Copynumber: 1.8 Consensus size: 119
28039938 ACAAAGCATG
* *
28039948 CGGGACTTTAAGCCCGAATATAATACCAGCAGAAAGCCTGCGGGACTTTAGCCCGGATATAACAC
1 CGGGACTTTAAGCCCGAATATAATACCAGCAGAAAGCCTGCAGGACTCTAGCCCGGATATAACAC
28040013 CAACACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
66 CAACACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
28040067 CGGGAC-TT-AGCCCGAATATAATACCAGCACGAATGCCTTCAGGAC-CTAGCCCGGATATAACA
1 CGGGACTTTAAGCCCGAATATAATACCAGCA-GAAAGCCTGCAGGACTCTAGCCCGGATATAACA
*
28040129 CCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAA
65 CCAACACGAATGCCTTCGGGACTTAGCCCGGATATAA
28040166 TTCTCCATTA
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
117 73 0.78
118 14 0.15
119 6 0.06
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (119 bp):
CGGGACTTTAAGCCCGAATATAATACCAGCAGAAAGCCTGCAGGACTCTAGCCCGGATATAACAC
CAACACGAATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:28045498 original size:9 final size:9
Alignment explanation
Indices: 28045484--28045510 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
28045474 ATATGGTGAG
28045484 ATTTTGTGT
1 ATTTTGTGT
28045493 ATTTTGTGT
1 ATTTTGTGT
28045502 ATTTTGTGT
1 ATTTTGTGT
28045511 TTTATGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.22, T:0.67
Consensus pattern (9 bp):
ATTTTGTGT
Found at i:28046237 original size:35 final size:35
Alignment explanation
Indices: 28046194--28046317 Score: 153
Period size: 35 Copynumber: 3.5 Consensus size: 35
28046184 CATAGGTAAG
28046194 TACATGTGAGCTTATATTGAACTTGTATATTCGGC
1 TACATGTGAGCTTATATTGAACTTGTATATTCGGC
* * * **
28046229 TGCATGTGAGGTTATATTGAACTTG-AGTATTTGAT
1 TACATGTGAGCTTATATTGAACTTGTA-TATTCGGC
*
28046264 TACATGTGAGCTTATATTGAACTTGTATATTCGGT
1 TACATGTGAGCTTATATTGAACTTGTATATTCGGC
*
28046299 TATATGTGAAG-TTATATTG
1 TACATGTG-AGCTTATATTG
28046318 CATGTACATA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
34 1 0.01
35 72 0.95
36 3 0.04
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.43
Consensus pattern (35 bp):
TACATGTGAGCTTATATTGAACTTGTATATTCGGC
Found at i:28046555 original size:37 final size:37
Alignment explanation
Indices: 28046514--28046587 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
28046504 ACTCTGTGTG
28046514 TGTTTTTGTTACTCTATTTTATATATTTTGGTGGTAA
1 TGTTTTTGTTACTCTATTTTATATATTTTGGTGGTAA
*
28046551 TGTTTTTGTTACTCTGTTTTATATATTTTGGTGGTAA
1 TGTTTTTGTTACTCTATTTTATATATTTTGGTGGTAA
28046588 GTTACGAGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.18, C:0.05, G:0.18, T:0.59
Consensus pattern (37 bp):
TGTTTTTGTTACTCTATTTTATATATTTTGGTGGTAA
Found at i:28066040 original size:13 final size:13
Alignment explanation
Indices: 28066022--28066046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28066012 AACAATGCCA
28066022 GACACGGCCGTGC
1 GACACGGCCGTGC
28066035 GACACGGCCGTG
1 GACACGGCCGTG
28066047 TGCACCCACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.36, G:0.40, T:0.08
Consensus pattern (13 bp):
GACACGGCCGTGC
Found at i:28068807 original size:40 final size:40
Alignment explanation
Indices: 28068610--28068800 Score: 233
Period size: 40 Copynumber: 4.8 Consensus size: 40
28068600 TGGATGATAA
* * * * * * **
28068610 CCGGGCTAAGTCGCGAAGCCATCTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
28068650 CCGGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
28068689 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* * * *
28068729 TCGGGCTAAGTCTCGAAGGCAATTGTGCGAGTTACTCTAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
* *
28068769 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
28068801 AGCTCTATCC
Statistics
Matches: 132, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 31 0.23
40 99 0.75
41 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:28079206 original size:21 final size:21
Alignment explanation
Indices: 28079180--28079222 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28079170 GCATGATAAG
28079180 TTGATTTTTAAGAATTTAAAA
1 TTGATTTTTAAGAATTTAAAA
28079201 TTGATTTTTAAGAATTTAAAA
1 TTGATTTTTAAGAATTTAAAA
28079222 T
1 T
28079223 CTTAGGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (21 bp):
TTGATTTTTAAGAATTTAAAA
Found at i:28086878 original size:44 final size:43
Alignment explanation
Indices: 28086802--28086888 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 43
28086792 TAAGAGAGAA
* *
28086802 GCTCAAGTTTCGAGTGAGAGGTCTAGCAGCAGAGCACACTCTT
1 GCTCAAGTTTCGAGTAAGAGGTATAGCAGCAGAGCACACTCTT
* * *
28086845 NGCTCGAGTTTCGAGTAAGAGGTATCGCGGCAGAGCACACTCTT
1 -GCTCAAGTTTCGAGTAAGAGGTATAGCAGCAGAGCACACTCTT
28086889 TCCTCACAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.23
Consensus pattern (43 bp):
GCTCAAGTTTCGAGTAAGAGGTATAGCAGCAGAGCACACTCTT
Found at i:28089519 original size:35 final size:35
Alignment explanation
Indices: 28089469--28089538 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
28089459 TGATTTAAAG
*
28089469 AAAATGTACTTGTGGAAGGGCATGAAAAGAGACAT
1 AAAATGTACTGGTGGAAGGGCATGAAAAGAGACAT
28089504 AAAATGTACTGGTGGAAGGGCATGAAAAGAGACAT
1 AAAATGTACTGGTGGAAGGGCATGAAAAGAGACAT
28089539 CTTCGAATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.19
Consensus pattern (35 bp):
AAAATGTACTGGTGGAAGGGCATGAAAAGAGACAT
Found at i:28094198 original size:39 final size:40
Alignment explanation
Indices: 28094103--28094325 Score: 248
Period size: 39 Copynumber: 5.7 Consensus size: 40
28094093 TTGAATGATG
*
28094103 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
28094141 ATCCGGACTAAGAT-CCGAAGGCATTTGTCCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
28094182 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28094221 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28094260 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
28094299 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
28094326 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 14, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
39 92 0.57
40 58 0.36
41 10 0.06
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28094287 original size:79 final size:81
Alignment explanation
Indices: 28094103--28094325 Score: 264
Period size: 79 Copynumber: 2.8 Consensus size: 81
28094093 TTGAATGATG
* * *
28094103 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
28094165 TTGTCCGAGATACTAAT
65 TTGTCCGAGATACTAAA
28094182 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
* *
28094243 TTGTGCGAGTTACTAAA
65 TTGTCCGAGATACTAAA
* * * * * *
28094260 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
28094324 TG
66 TG
28094326 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 45 0.36
79 55 0.44
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTCCGAGATACTAAA
Found at i:28094347 original size:79 final size:79
Alignment explanation
Indices: 28094103--28094358 Score: 208
Period size: 79 Copynumber: 3.3 Consensus size: 79
28094093 TTGAATGATG
* * * *
28094103 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
28094164 TTTGTCCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
28094182 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
28094246 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
* *
28094260 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
28094323 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
28094340 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28094359 TACGTGATTT
Statistics
Matches: 151, Mismatches: 16, Indels: 20
0.81 0.09 0.11
Matches are distributed among these distances:
77 1 0.01
78 45 0.30
79 68 0.45
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:28102163 original size:39 final size:40
Alignment explanation
Indices: 28102068--28102329 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
28102058 TTGAATGATG
*
28102068 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
28102106 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
28102147 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
28102186 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28102225 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
28102264 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
28102303 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
28102330 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28109659 original size:53 final size:53
Alignment explanation
Indices: 28109579--28109684 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 53
28109569 TTCGTCGCAC
* * * * *
28109579 GTAATTAGTCCATCAGAGGTTGAAATTCAATCTGACATGAGTTATGAAGAAGA
1 GTAATTAGCCCATCAAAGGTTGAAATTCAAGCCGACATGAGTTATGAAAAAGA
*
28109632 GTAATTAGCCCATCAAAGGTTGAAATTCAAGCCGATATGAGTTATGAAAAAGA
1 GTAATTAGCCCATCAAAGGTTGAAATTCAAGCCGACATGAGTTATGAAAAAGA
28109685 ACCGATGCGT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (53 bp):
GTAATTAGCCCATCAAAGGTTGAAATTCAAGCCGACATGAGTTATGAAAAAGA
Found at i:28109984 original size:54 final size:54
Alignment explanation
Indices: 28109921--28110028 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
28109911 GTTTCGGGAC
*
28109921 CACAAAACCGAGTCATAAAACTAATTGATTTCCATATTCTATGCTTATTATGTG
1 CACAAAACCGAGTCATAAAAATAATTGATTTCCATATTCTATGCTTATTATGTG
28109975 CACAAAACCGAGTCATAAAAATAATTGATTTCCATATTCTATGCTTATTATGTG
1 CACAAAACCGAGTCATAAAAATAATTGATTTCCATATTCTATGCTTATTATGTG
28110029 TGTACATGAG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (54 bp):
CACAAAACCGAGTCATAAAAATAATTGATTTCCATATTCTATGCTTATTATGTG
Found at i:28111627 original size:39 final size:39
Alignment explanation
Indices: 28111532--28111988 Score: 719
Period size: 39 Copynumber: 11.6 Consensus size: 39
28111522 TTGAATGATG
*
28111532 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
28111570 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
28111611 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
28111650 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
28111689 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
28111728 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
28111767 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
28111806 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
28111845 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28111884 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
*
28111923 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
28111962 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAG-CCCGAAGGCATTTG
28111989 AACGAGGAGC
Statistics
Matches: 397, Mismatches: 14, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
39 327 0.82
40 58 0.15
41 11 0.03
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28115833 original size:115 final size:115
Alignment explanation
Indices: 28115708--28115936 Score: 442
Period size: 115 Copynumber: 2.0 Consensus size: 115
28115698 CAATAAATAA
28115708 TTTAAAAATATTATTCA-CATAAATAATTTTAAAAGAGGATATATATACATAGAAAAATATTTAC
1 TTTAAAAATATTATT-AGCATAAATAATTTTAAAAGAGGATATATATACATAGAAAAATATTTAC
28115772 ATAAAGTTATATGAAAATAATAACATGTACCATAGCAAAAATAATTTAATT
65 ATAAAGTTATATGAAAATAATAACATGTACCATAGCAAAAATAATTTAATT
28115823 TTTAAAAATATTATTAGCATAAATAATTTTAAAAGAGGATATATATACATAGAAAAATATTTACA
1 TTTAAAAATATTATTAGCATAAATAATTTTAAAAGAGGATATATATACATAGAAAAATATTTACA
28115888 TAAAGTTATATGAAAATAATAACATGTACCATAGCAAAAATAATTTAAT
66 TAAAGTTATATGAAAATAATAACATGTACCATAGCAAAAATAATTTAAT
28115937 ATGTGCCCTA
Statistics
Matches: 113, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
114 1 0.01
115 112 0.99
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (115 bp):
TTTAAAAATATTATTAGCATAAATAATTTTAAAAGAGGATATATATACATAGAAAAATATTTACA
TAAAGTTATATGAAAATAATAACATGTACCATAGCAAAAATAATTTAATT
Found at i:28117204 original size:23 final size:22
Alignment explanation
Indices: 28117162--28117205 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28117152 TAGATAAATA
*
28117162 AAAGAAAACAGAAATGAAATCG
1 AAAGAAAACAGAAATCAAATCG
28117184 AAAGAAAA-ATGAGAATCAAATC
1 AAAGAAAACA-GA-AATCAAATC
28117206 ACCTTGTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.05
22 10 0.53
23 8 0.42
ACGTcount: A:0.64, C:0.09, G:0.16, T:0.11
Consensus pattern (22 bp):
AAAGAAAACAGAAATCAAATCG
Found at i:28126206 original size:18 final size:18
Alignment explanation
Indices: 28126183--28126221 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
28126173 TTAAATAACT
28126183 TAAAATGAACTTTAAAAA
1 TAAAATGAACTTTAAAAA
* *
28126201 TAAAATTAAGTTTAAAAA
1 TAAAATGAACTTTAAAAA
28126219 TAA
1 TAA
28126222 CTAAGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (18 bp):
TAAAATGAACTTTAAAAA
Found at i:28131195 original size:48 final size:48
Alignment explanation
Indices: 28131106--28131509 Score: 209
Period size: 46 Copynumber: 8.5 Consensus size: 48
28131096 TTCGTGTACT
* * *
28131106 AGTGTAAGA-CATGTCTGAGACAT-GCATCGGCCA-C-ATTATGAGAGAC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GACATCGA-GATGAGAGAC
* * * * *
28131152 TGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGATGAGCG-C
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGATGAGAGAC
* * ** * *
28131199 AAGTGTAAG-GCATGTTTGGGACAT-GCATCGACCCCAAGATGTA-AGCC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGATG-AGAGAC
* *
28131246 AGTGTAAGA-CATGTCT-GGAGCAT-GCATC-AGCAAT-GAGAT--GTGTC
1 AGTGTAAGACCATGTCTGGGA-CATGGCATCGA-C-ATCGAGATGAGAGAC
* * * *
28131290 AGTGTAAGACCATGCCTAGGACATGGCATCAACA-CGA-ATAGAGGTGAC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGAT-GA-GAGAC
* * * *
28131338 AGTGTAAGACCATTTCTGGGACATGGCATCGACATGGATATGTGAGAGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGATGAGAGA-C
* * * * * ** * *
28131387 TAGTGTAAGACCACGTCTGGGACATGGCGTTGTCCTCGATTTCGATAGTC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGAT-GAGAGAC
** * *
28131437 AGTGTAAGACCATGTCTAAGACATGGCATCGAC-T--TGATGGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGAT-GA-GAGAC
28131484 AGTGTAAGACCATGTCTGGGACATGG
1 AGTGTAAGACCATGTCTGGGACATGG
28131510 AATCAGCTCT
Statistics
Matches: 276, Mismatches: 55, Indels: 53
0.72 0.14 0.14
Matches are distributed among these distances:
44 13 0.05
45 16 0.06
46 60 0.22
47 60 0.22
48 56 0.20
49 32 0.12
50 36 0.13
51 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGATGAGAGAC
Found at i:28134642 original size:85 final size:85
Alignment explanation
Indices: 28134499--28134666 Score: 318
Period size: 85 Copynumber: 2.0 Consensus size: 85
28134489 TTTCTTATAA
* *
28134499 TGATTAGAGGTCATTGTTTTCCAACTAACCTCATGCTACTACCGTTTGATGAATTTGATCTAATT
1 TGATTAGACGTCATCGTTTTCCAACTAACCTCATGCTACTACCGTTTGATGAATTTGATCTAATT
28134564 CTTGGCATGGATTTGTTGTC
66 CTTGGCATGGATTTGTTGTC
28134584 TGATTAGACGTCATCGTTTTCCAACTAACCTCATGCTACTACCGTTTGATGAATTTGATCTAATT
1 TGATTAGACGTCATCGTTTTCCAACTAACCTCATGCTACTACCGTTTGATGAATTTGATCTAATT
28134649 CTTGGCATGGATTTGTTG
66 CTTGGCATGGATTTGTTG
28134667 ACTGCTCATA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (85 bp):
TGATTAGACGTCATCGTTTTCCAACTAACCTCATGCTACTACCGTTTGATGAATTTGATCTAATT
CTTGGCATGGATTTGTTGTC
Found at i:28143810 original size:49 final size:49
Alignment explanation
Indices: 28143753--28143940 Score: 209
Period size: 49 Copynumber: 3.8 Consensus size: 49
28143743 TAGCCAAAGC
*
28143753 TATCTGGTACGCATAGTAGCCCGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCCGCACTTAGTACTACACATGCGACCAAT
** * * * * *
28143802 TATCTGGTACATGTAGTAGCCTGCACTTAATACTACACACGTGATCGAAGT
1 TATCTGGTACACATAGTAGCCCGCACTTAGTACTACACATGCGA-CCAA-T
* ** *
28143853 TATCGGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCCGCACTTAGTACTACACATGCGACCAAT
*
28143902 TATAC-GGTACACGTAGTAG-CCGACACTTAGTACTACACA
1 TAT-CTGGTACACATAGTAGCCCG-CACTTAGTACTACACA
28143941 CGTGACCTCA
Statistics
Matches: 114, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
48 2 0.02
49 68 0.60
50 7 0.06
51 37 0.32
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCCGCACTTAGTACTACACATGCGACCAAT
Found at i:28143893 original size:100 final size:100
Alignment explanation
Indices: 28143753--28143945 Score: 309
Period size: 100 Copynumber: 1.9 Consensus size: 100
28143743 TAGCCAAAGC
* *
28143753 TATCTGGTACGCATAGTAGCCCGCACTTAGTACTACACATGCGACCAATTAT-CTGGTACATGTA
1 TATCGGGTACGCATAGTAGCCCGCACTTAGTACTACACATGCGACCAATTATAC-GGTACACGTA
28143817 GTAGCCTG-CACTTAATACTACACACGTGATCGAAGT
65 GTAGCC-GACACTTAATACTACACACGTGATCGAAGT
* *
28143853 TATCGGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATACGGTACACGTAG
1 TATCGGGTACGCATAGTAGCCCGCACTTAGTACTACACATGCGACCAATTATACGGTACACGTAG
*
28143918 TAGCCGACACTTAGTACTACACACGTGA
66 TAGCCGACACTTAATACTACACACGTGA
28143946 CCTCACAATA
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
99 1 0.01
100 84 0.98
101 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (100 bp):
TATCGGGTACGCATAGTAGCCCGCACTTAGTACTACACATGCGACCAATTATACGGTACACGTAG
TAGCCGACACTTAATACTACACACGTGATCGAAGT
Found at i:28145234 original size:48 final size:47
Alignment explanation
Indices: 28145156--28145293 Score: 140
Period size: 46 Copynumber: 2.9 Consensus size: 47
28145146 GGATGTTATA
* * *
28145156 GTCTGGGACATGCATCGACCA-C-ATTATGAGAGCCAGTGTAAGACCAT
1 GTCTGGGACATGAATCGA-CATCGA-GATGAGAGCCAGTGTAAGACAAT
*
28145203 GTCTGGGACATGGAATCGACATTGAGATGAGAGCCAGTGTAAGA-AAT
1 GTCTGGGACAT-GAATCGACATCGAGATGAGAGCCAGTGTAAGACAAT
* * * *
28145250 GTTTGGGACATGCATCGGCCTCGAGATGTA-AGCCAGTGTAAGAC
1 GTCTGGGACATGAATCGACATCGAGATG-AGAGCCAGTGTAAGAC
28145294 GTGTCTAAGA
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
46 26 0.34
47 26 0.34
48 24 0.31
49 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.22
Consensus pattern (47 bp):
GTCTGGGACATGAATCGACATCGAGATGAGAGCCAGTGTAAGACAAT
Found at i:28145291 original size:46 final size:48
Alignment explanation
Indices: 28145181--28145293 Score: 142
Period size: 46 Copynumber: 2.4 Consensus size: 48
28145171 CGACCACATT
* *
28145181 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGAATCGACATTGAG
1 ATGAGAGCCAGTGTAAGACAATGTCTGGGACATGGAATCGACATCGAG
* * * *
28145229 ATGAGAGCCAGTGTAAGA-AATGTTTGGGACAT-GCATCGGCCTCGAG
1 ATGAGAGCCAGTGTAAGACAATGTCTGGGACATGGAATCGACATCGAG
28145275 ATGTA-AGCCAGTGTAAGAC
1 ATG-AGAGCCAGTGTAAGAC
28145294 GTGTCTAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
46 26 0.46
47 13 0.23
48 18 0.32
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (48 bp):
ATGAGAGCCAGTGTAAGACAATGTCTGGGACATGGAATCGACATCGAG
Found at i:28147818 original size:16 final size:17
Alignment explanation
Indices: 28147779--28147820 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
28147769 ATATGTAAAA
*
28147779 AAATATATAGAAAATGC
1 AAATATATAGAAAATCC
* *
28147796 AAGTATAT-GTAAATCC
1 AAATATATAGAAAATCC
28147812 AAATATATA
1 AAATATATA
28147821 TGGGAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.29
Consensus pattern (17 bp):
AAATATATAGAAAATCC
Found at i:28154605 original size:17 final size:17
Alignment explanation
Indices: 28154562--28154631 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 17
28154552 TATGCAGTAT
* *
28154562 AATATAAAAGAAAATAA
1 AATAAAAAATAAAATAA
* *
28154579 ATTAATAAATAAAATAA
1 AATAAAAAATAAAATAA
*
28154596 AATAAAAAATTAAAGT--
1 AATAAAAAA-TAAAATAA
* *
28154612 AATAAAAAATGAAACAA
1 AATAAAAAATAAAATAA
28154629 AAT
1 AAT
28154632 TTAGAACAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
15 3 0.08
16 9 0.22
17 23 0.57
18 5 0.12
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (17 bp):
AATAAAAAATAAAATAA
Found at i:28154609 original size:22 final size:22
Alignment explanation
Indices: 28154560--28154605 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28154550 AATATGCAGT
*
28154560 ATAATATAAAAGAAAATAAATTA
1 ATAA-ATAAAAGAAAATAAATAA
*
28154583 ATAAATAAAATAAAATAAA-AA
1 ATAAATAAAAGAAAATAAATAA
28154604 AT
1 AT
28154606 TAAAGTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 14 0.67
23 4 0.19
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
ATAAATAAAAGAAAATAAATAA
Found at i:28178563 original size:23 final size:24
Alignment explanation
Indices: 28178513--28178567 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
28178503 AGAAAAATTC
*
28178513 TAAATTTTATAGAATGTATATGCTA
1 TAAATTTTATAG-ATGTACATGCTA
28178538 TAAATTTTATAG-TGTACATTGC-A
1 TAAATTTTATAGATGTACA-TGCTA
28178561 TAAATTT
1 TAAATTT
28178568 CATTTTCCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 13 0.46
24 3 0.11
25 12 0.43
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.45
Consensus pattern (24 bp):
TAAATTTTATAGATGTACATGCTA
Found at i:28179109 original size:57 final size:57
Alignment explanation
Indices: 28178988--28179183 Score: 250
Period size: 57 Copynumber: 3.4 Consensus size: 57
28178978 TTACTGATGG
* * * * * * * **
28178988 GATTTAGCCTGAACTGGTAATCCTGATATAATC-CCTCTCGAGCATATGTTACAATTAA
1 GATTTAGCCTGGACTGGTAATCCTAAT-TGAGCTCTTCT-AAGCATATATTACAAAAAA
*
28179046 GATTTAGCCTAGACTGGTAATCCTAATTGAGCTCTTCTAAGCATATATTACAAAAAA
1 GATTTAGCCTGGACTGGTAATCCTAATTGAGCTCTTCTAAGCATATATTACAAAAAA
* * *
28179103 GATTTAGCCTGGACTGGTAATCCTAATTGAGCTCTTCTGAGCATATATTCCAAAAAG
1 GATTTAGCCTGGACTGGTAATCCTAATTGAGCTCTTCTAAGCATATATTACAAAAAA
28179160 GATTTAGCCTGGACTGGTAATCCT
1 GATTTAGCCTGGACTGGTAATCCT
28179184 GTTATATGTT
Statistics
Matches: 123, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
57 95 0.77
58 28 0.23
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (57 bp):
GATTTAGCCTGGACTGGTAATCCTAATTGAGCTCTTCTAAGCATATATTACAAAAAA
Found at i:28180562 original size:46 final size:45
Alignment explanation
Indices: 28180508--28180771 Score: 173
Period size: 46 Copynumber: 5.6 Consensus size: 45
28180498 ATTTGTGTGA
* *
28180508 TAGTGTAAGATATGTCTGGGACATGCATCGGCCACATTATGAGAGC
1 TAGTGTAAGACATGTCTGGGACATGCATCGGCC-CATTACGAGAGC
* * * *
28180554 CAGTGTAAGACCATGCCTGAGACATGGCATCAG--CATTGGGACGAGAGC
1 TAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCCATT---ACGAGAGC
* * *
28180602 TAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGTGACGTA-AGC
1 TAGTGTAAGACATGTCTGGGACATGCATCGGCC-CATTACG-AGAGC
*
28180648 TAGTGTAAGACATGTCTGGGACATGCATCGG--C--TACGAGATGTG
1 TAGTGTAAGACATGTCTGGGACATGCATCGGCCCATTACGAGA-G-C
* * *** * *
28180691 TCAATGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATTTTAATAGT
1 T-AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCC-C-ATTACGAGAGC
28180741 TAGTGTAAGACCATGTCTGGGACATGGCATC
1 TAGTGTAAGA-CATGTCTGGGACAT-GCATC
28180772 TACTGGATGG
Statistics
Matches: 172, Mismatches: 25, Indels: 39
0.73 0.11 0.17
Matches are distributed among these distances:
40 1 0.01
41 4 0.02
42 1 0.01
43 2 0.01
44 8 0.05
45 18 0.10
46 57 0.33
47 23 0.13
48 22 0.13
49 31 0.18
50 1 0.01
51 1 0.01
52 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.25
Consensus pattern (45 bp):
TAGTGTAAGACATGTCTGGGACATGCATCGGCCCATTACGAGAGC
Found at i:28190691 original size:39 final size:39
Alignment explanation
Indices: 28190596--28190818 Score: 215
Period size: 39 Copynumber: 5.6 Consensus size: 39
28190586 TTGAATGATG
*
28190596 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACAAAT
* *
28190634 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACAAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACAAAT
* *
28190675 TTCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACAAAT
* *
28190714 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTATTAAA-
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATA-CAAAT
* * *
28190753 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-ATAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACAAAT
* *
28190792 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAG-CCCGAAGGCATTTG
28190819 AACGAGGAGC
Statistics
Matches: 159, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 86 0.54
40 59 0.37
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACAAAT
Found at i:28190773 original size:79 final size:81
Alignment explanation
Indices: 28190596--28190818 Score: 248
Period size: 79 Copynumber: 2.8 Consensus size: 81
28190586 TTGAATGATG
* * *
28190596 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATATCCGGGCTAAGACCCGAAGGCA
28190657 TTTGTGCGAGATACAAAT
64 TTTGTGCGAGATACAAAT
*
28190675 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT-TCCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
* *
28190737 TGTGCGAGTTATTAAA-
66 TGTGCGAGATA-CAAAT
* * * * * *
28190753 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTAAT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
28190817 TG
66 TG
28190819 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
78 41 0.33
79 57 0.46
80 25 0.20
81 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACAAAT
Found at i:28190840 original size:79 final size:79
Alignment explanation
Indices: 28190596--28190851 Score: 188
Period size: 79 Copynumber: 3.3 Consensus size: 79
28190586 TTGAATGATG
* * * * * *
28190596 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGACAATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TAATAATA-CCGGGCTAAG-CCCGAAGGCAT
**
28190658 TTGTGCGAGAT-AC-AAA
63 TTGAACGAG-TGACTAAA
* * * *
28190674 TTTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTT
1 -TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATAATAATACCGGGCTAAGCCCGAAGGCATTT
** * *
28190738 GTGCGAGTTATTAAA
65 GAACGAGTGACTAAA
* *
28190753 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTAAT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATAATAAT-ACCGGGCTAAG-CCCGAAGGCATT
*
28190817 TGAACGAG-GAGCTATA
64 TGAACGAGTGA-CTAAA
* *
28190833 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28190852 TACGTGATTT
Statistics
Matches: 146, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
77 1 0.01
78 40 0.27
79 69 0.47
80 35 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATAATAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:28192546 original size:18 final size:18
Alignment explanation
Indices: 28192523--28192566 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
28192513 CATGAGGGTC
28192523 AATCACCACTTGGGAACA
1 AATCACCACTTGGGAACA
28192541 AATCACCACTTGGGAACA
1 AATCACCACTTGGGAACA
*
28192559 AATGACCA
1 AATCACCA
28192567 AAAAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (18 bp):
AATCACCACTTGGGAACA
Found at i:28195371 original size:19 final size:20
Alignment explanation
Indices: 28195346--28195411 Score: 68
Period size: 19 Copynumber: 3.4 Consensus size: 20
28195336 TCGCTCTCCC
28195346 CTTCTTTTCTCTTCTTTCCT
1 CTTCTTTTCTCTTCTTTCCT
*
28195366 -TTCTTTT-TCTTTCATTCCCT
1 CTTCTTTTCTC-TTC-TTTCCT
28195386 CTTC-TTTC-CTTCTTTCCT
1 CTTCTTTTCTCTTCTTTCCT
28195404 CCTTCTTT
1 -CTTCTTT
28195412 CCCTTTCCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
18 7 0.18
19 17 0.45
20 11 0.29
21 3 0.08
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTCTTTTCTCTTCTTTCCT
Found at i:28195412 original size:19 final size:19
Alignment explanation
Indices: 28195345--28195425 Score: 62
Period size: 19 Copynumber: 4.3 Consensus size: 19
28195335 ATCGCTCTCC
28195345 CCTTCTTTTCTCTTCTTTCCTT
1 CCTTC-TTTC-CTTCTTTCC-T
* * *
28195367 TCTT-TTTCTTTCATTCC-
1 CCTTCTTTCCTTCTTTCCT
28195384 CTCTTCTTTCCTTCTTTCCT
1 C-CTTCTTTCCTTCTTTCCT
28195404 CCTTCTTTCC--CTTTCCT
1 CCTTCTTTCCTTCTTTCCT
*
28195421 TCTTC
1 CCTTC
28195426 CCTCATATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
17 11 0.22
18 3 0.06
19 27 0.55
20 5 0.10
22 3 0.06
ACGTcount: A:0.01, C:0.38, G:0.00, T:0.60
Consensus pattern (19 bp):
CCTTCTTTCCTTCTTTCCT
Found at i:28195414 original size:30 final size:30
Alignment explanation
Indices: 28195345--28195415 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
28195335 ATCGCTCTCC
* *
28195345 CCTTCTTT-TCTCTTCTTTCCTTTCTTTTT
1 CCTTCTTTCCCTCTTCTTTCCTTTCTTTCT
* *
28195374 CTTTCATTCCCTCTTCTTTCC-TTCTTTCCT
1 CCTTCTTTCCCTCTTCTTTCCTTTCTTT-CT
28195404 CCTTCTTTCCCT
1 CCTTCTTTCCCT
28195416 TTCCTTCTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 12 0.35
30 22 0.65
ACGTcount: A:0.01, C:0.38, G:0.00, T:0.61
Consensus pattern (30 bp):
CCTTCTTTCCCTCTTCTTTCCTTTCTTTCT
Found at i:28197203 original size:6 final size:6
Alignment explanation
Indices: 28197192--28197225 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
28197182 CCTTTTATTC
28197192 TATTTT TATTTT TATTTT TATTTT TATTTT TATT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATT
28197226 ACAATTCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TATTTT
Found at i:28200365 original size:48 final size:48
Alignment explanation
Indices: 28200294--28200574 Score: 262
Period size: 48 Copynumber: 5.9 Consensus size: 48
28200284 TAAGATGCCA
28200294 ATGCCATGTCCCAGACATGGTCTTACACTAGCCCACATATCGAGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCCCACATATCGAGGCTG
* * * * ** *
28200342 ATGCCATGTCCCAGACATTGTCTTACACTAGCTCTCGTATAAATG-TCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCCCACATATCGAGGCT-G
* * * * * *
28200390 ATGTCACG-CTCCAAACATGGTCTTACACTGGCTCACATATCGAAGCTG
1 ATGCCATGTC-CCAGACATGGTCTTACACTAGCCCACATATCGAGGCTG
* * * * *
28200438 ATGTCATGTCCCAAATATGGTCTTACACTAACCCACATATCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCCCACATATCGAGGCTG
* * * ** *
28200486 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATAAATGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCCCACATATCGAGGCTG
* * * *
28200534 ATGCCATGCTCCAAG-CATGGTCTTTCACTGGCTCACATATC
1 ATGCCATG-TCCCAGACATGGTCTTACACTAGCCCACATATC
28200575 CCTAGTATCA
Statistics
Matches: 187, Mismatches: 41, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
47 2 0.01
48 178 0.95
49 7 0.04
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCCCACATATCGAGGCTG
Found at i:28200563 original size:144 final size:144
Alignment explanation
Indices: 28200298--28200574 Score: 457
Period size: 144 Copynumber: 1.9 Consensus size: 144
28200288 ATGCCAATGC
* * * *
28200298 CATGTCCCAGACATGGTCTTACACTAGCCCACATATCGAGGCTGATGCCATGTCCCAGACATTGT
1 CATGTCCCAAACATGGTCTTACACTAACCCACATATCGAGGCCGATGCCATGTCCCAGACATGGT
*
28200363 CTTACACTAGCTCTCGTATAAATGTCGATGTCACGCTCCAAACATGGTCTTACACTGGCTCACAT
66 CTTACACTAGCTCTCGTATAAATGTCGATGCCACGCTCCAAACATGGTCTTACACTGGCTCACAT
28200428 ATCGAAGCTGATGT
131 ATCGAAGCTGATGT
*
28200442 CATGTCCCAAATATGGTCTTACACTAACCCACATATCGAGGCCGATGCCATGTCCCAGACATGGT
1 CATGTCCCAAACATGGTCTTACACTAACCCACATATCGAGGCCGATGCCATGTCCCAGACATGGT
* * *
28200507 CTTACACTAGCTCTCGTATAAATG-CTGATGCCATGCTCCAAGCATGGTCTTTCACTGGCTCACA
66 CTTACACTAGCTCTCGTATAAATGTC-GATGCCACGCTCCAAACATGGTCTTACACTGGCTCACA
28200571 TATC
130 TATC
28200575 CCTAGTATCA
Statistics
Matches: 123, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
143 1 0.01
144 122 0.99
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (144 bp):
CATGTCCCAAACATGGTCTTACACTAACCCACATATCGAGGCCGATGCCATGTCCCAGACATGGT
CTTACACTAGCTCTCGTATAAATGTCGATGCCACGCTCCAAACATGGTCTTACACTGGCTCACAT
ATCGAAGCTGATGT
Found at i:28205495 original size:40 final size:40
Alignment explanation
Indices: 28205440--28205534 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 40
28205430 ACTGCATTTG
** *
28205440 GCACTAAGTGTGCGATTCAAAATAGCTTTGGTTATAAATA
1 GCACTAAGTGTGCGATTCAAAATAGCTTCAGCTATAAATA
*
28205480 GCACTAAGTGTGCGATTCAAAATATCTTCAGCTATAAATA
1 GCACTAAGTGTGCGATTCAAAATAGCTTCAGCTATAAATA
28205520 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
28205535 AATGGTATAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (40 bp):
GCACTAAGTGTGCGATTCAAAATAGCTTCAGCTATAAATA
Found at i:28207642 original size:25 final size:27
Alignment explanation
Indices: 28207614--28207663 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
28207604 AGTTTAGCCA
28207614 ATTTAAACCCT-AGGGGT-ATTTCGGT
1 ATTTAAACCCTGAGGGGTAATTTCGGT
**
28207639 ATTTATGCCCTGAGGGGTAATTTCG
1 ATTTAAACCCTGAGGGGTAATTTCG
28207664 TACTTACGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 6 0.29
27 6 0.29
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (27 bp):
ATTTAAACCCTGAGGGGTAATTTCGGT
Found at i:28208345 original size:27 final size:27
Alignment explanation
Indices: 28208299--28208373 Score: 116
Period size: 27 Copynumber: 2.8 Consensus size: 27
28208289 TTCTACCCTA
*
28208299 CAGGGGTA-TTTAGTAATTTTGCAAAC
1 CAGGGGTATTTTGGTAATTTTGCAAAC
* *
28208325 CATGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTGCAAAC
28208352 CAGGGGTATTTTGGTAATTTTG
1 CAGGGGTATTTTGGTAATTTTG
28208374 TAAATCAAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 7 0.16
27 36 0.84
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTTGCAAAC
Found at i:28208385 original size:27 final size:27
Alignment explanation
Indices: 28208302--28208386 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 27
28208292 TACCCTACAG
* *
28208302 GGGTA-TTTAGTAATTTTGCAAACCAT
1 GGGTATTTTGGTAATTTTGCAAACCAA
* *
28208328 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTGCAAACCAA
* *
28208355 GGGTATTTTGGTAATTTTGTAAATCAA
1 GGGTATTTTGGTAATTTTGCAAACCAA
28208382 GGGTA
1 GGGTA
28208387 AAACGGTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 5 0.10
27 46 0.90
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTGCAAACCAA
Found at i:28208394 original size:27 final size:27
Alignment explanation
Indices: 28208364--28208517 Score: 188
Period size: 27 Copynumber: 5.7 Consensus size: 27
28208354 GGGGTATTTT
* *
28208364 GGTAATTTTGTAAATCAAGGGTAAAAC
1 GGTAATTCTGTAAATCGAGGGTAAAAC
*
28208391 GGTAATTCTATAAATCGAGGGT-AAAC
1 GGTAATTCTGTAAATCGAGGGTAAAAC
* * *
28208417 TAGTAATTCTATAAA-CTGAGGGTAAAAT
1 -GGTAATTCTGTAAATC-GAGGGTAAAAC
*
28208445 GGTAATTCTGTAAATCGAGGGTAAAAT
1 GGTAATTCTGTAAATCGAGGGTAAAAC
28208472 GGTAATTCTGTAAA-CTGAGGGTAAAAC
1 GGTAATTCTGTAAATC-GAGGGTAAAAC
*
28208499 GGTAATTTTGTAAATCGAG
1 GGTAATTCTGTAAATCGAG
28208518 AGTACTTTGG
Statistics
Matches: 112, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
26 6 0.05
27 101 0.90
28 5 0.04
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.30
Consensus pattern (27 bp):
GGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:28208413 original size:54 final size:54
Alignment explanation
Indices: 28208362--28208532 Score: 218
Period size: 54 Copynumber: 3.2 Consensus size: 54
28208352 CAGGGGTATT
* * *
28208362 TTGGTAATTTTGTAAA-TCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAA
1 TTGGTAATTCTGTAAACT-GAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAA
* * * *
28208416 CTAGTAATTCTATAAACTGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAA
1 TTGGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAA
* * * **
28208470 ATGGTAATTCTGTAAACTGAGGGTAAAACGGTAATTTTGTAAATCGAGAGTACT
1 TTGGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAA
28208524 TTGGTAATT
1 TTGGTAATT
28208533 TTACAAGTCG
Statistics
Matches: 100, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
54 99 0.99
55 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (54 bp):
TTGGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAA
Found at i:28208529 original size:81 final size:81
Alignment explanation
Indices: 28208361--28208532 Score: 197
Period size: 81 Copynumber: 2.1 Consensus size: 81
28208351 CCAGGGGTAT
*
28208361 TTTGGTAATTTTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAACTAGTAATTC
1 TTTGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAACTAGTAATTC
*
28208426 TATAAACTGAGGGTAA
66 TATAAACTGAGAGTAA
** * * * *
28208442 AATGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAA-CTGAGGGTAAAAC-GGTAAT
1 TTTGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAATC-GAGGGT-AAACTAGTAAT
* * *
28208505 TTTGTAAA-TCGAGAGTAC
64 TCTATAAACT-GAGAGTAA
28208523 TTTGGTAATT
1 TTTGGTAATT
28208533 TTACAAGTCG
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
80 2 0.03
81 69 0.92
82 4 0.05
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.33
Consensus pattern (81 bp):
TTTGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAACTAGTAATTC
TATAAACTGAGAGTAA
Found at i:28211215 original size:43 final size:44
Alignment explanation
Indices: 28211146--28211263 Score: 168
Period size: 43 Copynumber: 2.7 Consensus size: 44
28211136 CGTCACGTAC
* *
28211146 ATCATGAACTCAGACCAACTCGATGAGCTCAAG-TGGCACATGT
1 ATCATGAACTCAGACCAACTCAATGAGCTCAAGATGGCACATAT
* * *
28211189 ATCATGAACTCAAACCAATTCAATGAGCTC-GGATGGCACATAT
1 ATCATGAACTCAGACCAACTCAATGAGCTCAAGATGGCACATAT
*
28211232 ATCATGAACTCAGACCAACTCAATGAGTTCAA
1 ATCATGAACTCAGACCAACTCAATGAGCTCAA
28211264 ATCATATAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.02
43 63 0.98
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (44 bp):
ATCATGAACTCAGACCAACTCAATGAGCTCAAGATGGCACATAT
Found at i:28218293 original size:43 final size:43
Alignment explanation
Indices: 28218231--28218350 Score: 170
Period size: 43 Copynumber: 2.8 Consensus size: 43
28218221 TGTCACGTAC
* *
28218231 ATCATGAACTCAGATCAACTCAATGAGCTCA-AGTGGCACATGT
1 ATCATGAACTCAGACCAACTCAATGAGCTCAGA-TGGCACATAT
* * *
28218274 ATCATGAACTTAGACCAACTCAATGAGTTCGGATGGCACATAT
1 ATCATGAACTCAGACCAACTCAATGAGCTCAGATGGCACATAT
*
28218317 ATCATGAACTCAGACCAACTCAATGAGTTCAGAT
1 ATCATGAACTCAGACCAACTCAATGAGCTCAGAT
28218351 CATATAATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 68 0.99
44 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (43 bp):
ATCATGAACTCAGACCAACTCAATGAGCTCAGATGGCACATAT
Found at i:28223892 original size:16 final size:16
Alignment explanation
Indices: 28223873--28223907 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
28223863 GCAAAAGCCG
*
28223873 AAATGTCGAAAAGTCA
1 AAATGCCGAAAAGTCA
28223889 AAATGCCGAAAAGTCA
1 AAATGCCGAAAAGTCA
28223905 AAA
1 AAA
28223908 GTTTGGCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.14, G:0.17, T:0.14
Consensus pattern (16 bp):
AAATGCCGAAAAGTCA
Found at i:28223897 original size:24 final size:22
Alignment explanation
Indices: 28223864--28223909 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
28223854 AGTAGATCAG
*
28223864 CAAAAGCCGAAATGTCGAAAAGT
1 CAAAAGCCGAAAAGTC-AAAAGT
28223887 CAAAATGCCGAAAAGTCAAAAGT
1 CAAAA-GCCGAAAAGTCAAAAGT
28223910 TTGGCTACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (22 bp):
CAAAAGCCGAAAAGTCAAAAGT
Found at i:28224186 original size:57 final size:57
Alignment explanation
Indices: 28224119--28224279 Score: 200
Period size: 58 Copynumber: 2.8 Consensus size: 57
28224109 GTCAGCATGA
* *
28224119 ATAT-AATGTGATTTGGGCCGGATTGGCCATATAAATGAGATTGGGCCCAATGGGCC
1 ATATGAATGTGAATTGGGCCGGATGGGCCATATAAATGAGATTGGGCCCAATGGGCC
* * * * **
28224175 ATATGAATGTGAATTGGGGCTGATGGGCCATATGAATGTGAATTGGGCCTGATGGGCC
1 ATATGAATGTGAATTGGGCCGGATGGGCCATATAAATGAG-ATTGGGCCCAATGGGCC
* * *
28224233 ATAAGAACGTGAATTGGGCTGGATGGGCCATATAAATGAGA-TGGGCC
1 ATATGAATGTGAATTGGGCCGGATGGGCCATATAAATGAGATTGGGCC
28224280 TAGTGAACCA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
56 10 0.11
57 30 0.34
58 48 0.55
ACGTcount: A:0.27, C:0.14, G:0.34, T:0.25
Consensus pattern (57 bp):
ATATGAATGTGAATTGGGCCGGATGGGCCATATAAATGAGATTGGGCCCAATGGGCC
Found at i:28224246 original size:35 final size:29
Alignment explanation
Indices: 28224119--28224270 Score: 175
Period size: 29 Copynumber: 5.3 Consensus size: 29
28224109 GTCAGCATGA
* * *
28224119 ATAT-AATGTGATTTGGGCCGGATTGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* * **
28224147 ATATAAATGAG-ATTGGGCCCAATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
*
28224175 ATATGAATGTGAATTGGGGCTGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
28224204 ATATGAATGTGAATTGGGCCTGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* *
28224233 ATAAGAACGTGAATTGGG-CTGGATGGGCC
1 ATATGAATGTGAATTGGGCCT-GATGGGCC
*
28224262 ATATAAATG
1 ATATGAATG
28224271 AGATGGGCCT
Statistics
Matches: 105, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
28 28 0.27
29 77 0.73
ACGTcount: A:0.28, C:0.13, G:0.33, T:0.26
Consensus pattern (29 bp):
ATATGAATGTGAATTGGGCCTGATGGGCC
Found at i:28229601 original size:16 final size:16
Alignment explanation
Indices: 28229559--28229601 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
28229549 GTAGATCAGC
*
28229559 AAAAGCTAAAATGCCG
1 AAAAGCTGAAATGCCG
* *
28229575 AAAAGCCGAAATGTCG
1 AAAAGCTGAAATGCCG
28229591 AAAAGCTGAAA
1 AAAAGCTGAAA
28229602 GTTTGGCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.51, C:0.16, G:0.21, T:0.12
Consensus pattern (16 bp):
AAAAGCTGAAATGCCG
Found at i:28229922 original size:58 final size:57
Alignment explanation
Indices: 28229821--28229966 Score: 184
Period size: 58 Copynumber: 2.5 Consensus size: 57
28229811 TGACTTGGGT
* * *
28229821 CGGATGGGCCATATAAATGAGATTGGGCCCAATGGGTCATATGAATGTGAATTGCGC
1 CGGATGGGCCATATAAATGAGATTGGGCCTAATGGGCCATATGAACGTGAATTGCGC
* * * * * * * *
28229878 CTGATGGGCTATATGAATGTGAATTGGGCCTGATGGGCCTTATGAACGTGAATTGGGT
1 CGGATGGGCCATATAAATGAG-ATTGGGCCTAATGGGCCATATGAACGTGAATTGCGC
28229936 CGGATGGGCCATATAAATGAGATTGGGCCTA
1 CGGATGGGCCATATAAATGAGATTGGGCCTA
28229967 GTAAGCCATA
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
57 26 0.36
58 46 0.64
ACGTcount: A:0.26, C:0.14, G:0.33, T:0.27
Consensus pattern (57 bp):
CGGATGGGCCATATAAATGAGATTGGGCCTAATGGGCCATATGAACGTGAATTGCGC
Found at i:28229933 original size:29 final size:29
Alignment explanation
Indices: 28229807--28229965 Score: 135
Period size: 29 Copynumber: 5.6 Consensus size: 29
28229797 GCATGAATAT
* * * * *
28229807 AATGTGACTTGGGTCGGATGGGCCATATA
1 AATGTGAATTGGGCCTGATGGGCCTTATG
* ** * *
28229836 AATGAG-ATTGGGCCCAATGGGTCATATG
1 AATGTGAATTGGGCCTGATGGGCCTTATG
*
28229864 AATGTGAATTGCGCCTGATGGG-CTATATG
1 AATGTGAATTGGGCCTGATGGGCCT-TATG
28229893 AATGTGAATTGGGCCTGATGGGCCTTATG
1 AATGTGAATTGGGCCTGATGGGCCTTATG
* * * * *
28229922 AACGTGAATTGGGTCGGATGGGCCATATA
1 AATGTGAATTGGGCCTGATGGGCCTTATG
*
28229951 AATGAG-ATTGGGCCT
1 AATGTGAATTGGGCCT
28229966 AGTAAGCCAT
Statistics
Matches: 105, Mismatches: 22, Indels: 7
0.78 0.16 0.05
Matches are distributed among these distances:
28 29 0.28
29 74 0.70
30 2 0.02
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.28
Consensus pattern (29 bp):
AATGTGAATTGGGCCTGATGGGCCTTATG
Found at i:28232485 original size:27 final size:27
Alignment explanation
Indices: 28232455--28232632 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
28232445 ATATTGAGCC
* *
28232455 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
28232482 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
28232509 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
28232537 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
28232564 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
28232591 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
28232618 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28232633 GTACAATTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 104 0.81
28 25 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:28232594 original size:82 final size:81
Alignment explanation
Indices: 28232476--28232631 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
28232466 TGCTATATAA
* * *
28232476 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTC-GAATCGCA
28232541 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28232558 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCA
28232622 CACTTAGTGC
65 CACTTAGTGC
28232632 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28243674 original size:42 final size:42
Alignment explanation
Indices: 28243628--28243778 Score: 182
Period size: 42 Copynumber: 3.7 Consensus size: 42
28243618 ATGAGTTTAT
*
28243628 GTGTAAGACCATATCTGGGATATGGCATCGTTATGAGATTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTC
* * * * *
28243670 GTGTAAAACCATGTCTAGGACATGGCATCGATATGAGA-ATC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTC
* * **
28243711 GTGTAAGACCATAGCTGGGCTAT--CATCGATATGAGATCCC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTC
*
28243751 ATGTAAGACCATATCTGGGATATGGCAT
1 GTGTAAGACCATATCTGGGATATGGCAT
28243779 TGGTATGATT
Statistics
Matches: 89, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
39 13 0.15
40 21 0.24
41 19 0.21
42 36 0.40
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTC
Found at i:28243786 original size:81 final size:82
Alignment explanation
Indices: 28243628--28243778 Score: 196
Period size: 81 Copynumber: 1.8 Consensus size: 82
28243618 ATGAGTTTAT
* * ** * *
28243628 GTGTAAGACCATATCTGGGATATGGCATCGTTATGAGATTTCGTGTAAAACCATGTCTAGGACAT
1 GTGTAAGACCATAGCTGGGATAT-GCATCGATATGAGATCCCATGTAAAACCATATCTAGGACAT
28243693 GGCATCGATATGAGAATC
65 GGCATCGATATGAGAATC
* * * *
28243711 GTGTAAGACCATAGCTGGGCTAT-CATCGATATGAGATCCCATGTAAGACCATATCTGGGATATG
1 GTGTAAGACCATAGCTGGGATATGCATCGATATGAGATCCCATGTAAAACCATATCTAGGACATG
28243775 GCAT
66 GCAT
28243779 TGGTATGATT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
81 37 0.64
83 21 0.36
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (82 bp):
GTGTAAGACCATAGCTGGGATATGCATCGATATGAGATCCCATGTAAAACCATATCTAGGACATG
GCATCGATATGAGAATC
Found at i:28245246 original size:30 final size:30
Alignment explanation
Indices: 28245206--28245282 Score: 120
Period size: 29 Copynumber: 2.6 Consensus size: 30
28245196 CTTTGGCTAC
*
28245206 CAAATTATGAAAAGGGATGGTGACGACCAT
1 CAAATAATGAAAAGGGATGGTGACGACCAT
*
28245236 CGAATAATGAAAA-GGATGGTGACGACCAT
1 CAAATAATGAAAAGGGATGGTGACGACCAT
*
28245265 CAAATTATGAAAAGGGAT
1 CAAATAATGAAAAGGGAT
28245283 AGCTTCGGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 27 0.64
30 15 0.36
ACGTcount: A:0.43, C:0.12, G:0.26, T:0.19
Consensus pattern (30 bp):
CAAATAATGAAAAGGGATGGTGACGACCAT
Found at i:28245306 original size:30 final size:30
Alignment explanation
Indices: 28245270--28245342 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
28245260 ACCATCAAAT
* *
28245270 TATGAAAAGGGATAGCTTCGGCTGTCGAAC
1 TATGAAAAGGGATAACTTCGGCTATCGAAC
* * *
28245300 TATGAAAAGGGATAACTTTGGTTATCGAAT
1 TATGAAAAGGGATAACTTCGGCTATCGAAC
*
28245330 TACGAAAAGGGAT
1 TATGAAAAGGGAT
28245343 GGGTCAACCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (30 bp):
TATGAAAAGGGATAACTTCGGCTATCGAAC
Found at i:28247780 original size:27 final size:27
Alignment explanation
Indices: 28247750--28247927 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
28247740 ATATTGAGCC
* *
28247750 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
28247777 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
28247804 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
28247832 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
28247859 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
28247886 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
28247913 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28247928 GTACAATTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 104 0.81
28 25 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:28247889 original size:82 final size:81
Alignment explanation
Indices: 28247771--28247926 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
28247761 TGCTATATAA
* * *
28247771 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTC-GAATCGCA
28247836 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28247853 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCA
28247917 CACTTAGTGC
65 CACTTAGTGC
28247927 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28260418 original size:30 final size:30
Alignment explanation
Indices: 28260378--28260454 Score: 120
Period size: 29 Copynumber: 2.6 Consensus size: 30
28260368 CTTTGGCTAC
*
28260378 CAAATTATGAAAAGGGATGGTGACGACCAT
1 CAAATAATGAAAAGGGATGGTGACGACCAT
*
28260408 CGAATAATGAAAA-GGATGGTGACGACCAT
1 CAAATAATGAAAAGGGATGGTGACGACCAT
*
28260437 CAAATTATGAAAAGGGAT
1 CAAATAATGAAAAGGGAT
28260455 AGCTTCGGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 27 0.64
30 15 0.36
ACGTcount: A:0.43, C:0.12, G:0.26, T:0.19
Consensus pattern (30 bp):
CAAATAATGAAAAGGGATGGTGACGACCAT
Found at i:28260478 original size:30 final size:30
Alignment explanation
Indices: 28260442--28260514 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
28260432 ACCATCAAAT
* *
28260442 TATGAAAAGGGATAGCTTCGGCTGTCGAAC
1 TATGAAAAGGGATAACTTCGGCTATCGAAC
* * *
28260472 TATGAAAAGGGATAACTTTGGTTATCGAAT
1 TATGAAAAGGGATAACTTCGGCTATCGAAC
*
28260502 TACGAAAAGGGAT
1 TATGAAAAGGGAT
28260515 GGGTCAACCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (30 bp):
TATGAAAAGGGATAACTTCGGCTATCGAAC
Found at i:28271555 original size:37 final size:37
Alignment explanation
Indices: 28271514--28271587 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
28271504 AAATTCCAAC
28271514 ATAAATGCTCACAATTTTTACCCTATTACAAATCAGT
1 ATAAATGCTCACAATTTTTACCCTATTACAAATCAGT
28271551 ATAAATGCTCACAATTTTTACCCTATTACAAATCAGT
1 ATAAATGCTCACAATTTTTACCCTATTACAAATCAGT
28271588 CATTTTCCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (37 bp):
ATAAATGCTCACAATTTTTACCCTATTACAAATCAGT
Found at i:28272517 original size:17 final size:17
Alignment explanation
Indices: 28272487--28272520 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28272477 TTAATGATTG
*
28272487 GACGATTAAATTCAAAT
1 GACGACTAAATTCAAAT
*
28272504 GACGACTAAGTTCAAAT
1 GACGACTAAATTCAAAT
28272521 CTCTTCATAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (17 bp):
GACGACTAAATTCAAAT
Found at i:28273141 original size:15 final size:15
Alignment explanation
Indices: 28273121--28273167 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
28273111 AAAACTATGT
28273121 TTAAAAAATTAAGTG
1 TTAAAAAATTAAGTG
*
28273136 TTAAAAAAATAAGT-
1 TTAAAAAATTAAGTG
*
28273150 ATAAAAACATTAAGTG
1 TTAAAAA-ATTAAGTG
28273166 TT
1 TT
28273168 GAATTTAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 6 0.23
15 19 0.73
16 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.11, T:0.32
Consensus pattern (15 bp):
TTAAAAAATTAAGTG
Found at i:28273142 original size:16 final size:16
Alignment explanation
Indices: 28273118--28273167 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
28273108 AATAAAACTA
*
28273118 TGTTTAAAAAATTAAG
1 TGTTAAAAAAATTAAG
28273134 TGTTAAAAAAA-TAAG
1 TGTTAAAAAAATTAAG
* *
28273149 T-ATAAAAACATTAAG
1 TGTTAAAAAAATTAAG
28273164 TGTT
1 TGTT
28273168 GAATTTAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 7 0.25
15 10 0.36
16 11 0.39
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.34
Consensus pattern (16 bp):
TGTTAAAAAAATTAAG
Found at i:28275302 original size:39 final size:36
Alignment explanation
Indices: 28275222--28275302 Score: 90
Period size: 39 Copynumber: 2.2 Consensus size: 36
28275212 CTTGTTGAAG
*
28275222 AAATTAGCGAGCTTTAAAAACGACAGTCGTGATCGT
1 AAATCAGCGAGCTTTAAAAACGACAGTCGTGATCGT
* ** *
28275258 GAATCAGCGAGCTGTTAGAAAATCGAGGGTCGTGATCTT
1 AAATCAGCGAGCT-TTA-AAAA-CGACAGTCGTGATCGT
28275297 AAATCA
1 AAATCA
28275303 ATAGCCCATA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
36 11 0.31
37 3 0.08
38 4 0.11
39 18 0.50
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.25
Consensus pattern (36 bp):
AAATCAGCGAGCTTTAAAAACGACAGTCGTGATCGT
Found at i:28275675 original size:228 final size:227
Alignment explanation
Indices: 28275368--28275909 Score: 674
Period size: 228 Copynumber: 2.4 Consensus size: 227
28275358 GGATCGTGAC
* * * * *
28275368 CTTAAATCAGCGAACCGTAAAAATAACAGTTGTGAACATAGGTCAACAAGCTATTAGAAAATCGA
1 CTTAAATCAGCGAACCGAAAAAATATCAATTGTGAACATAGGTCAACAAGTTGTTAGAAAATCGA
* * * * *
28275433 GGGTCGCGATCTTAAAGCAGCGGA-TAGTAAAAAATATCAGA-TGTGAACGTAGGTCAACAAGCT
66 GGGTCACAATCTTAAATCAGCGGACCA-TAAAAAATATCA-ACTATGAACGTAGGTCAACAAGCT
** *
28275496 ATTAGAAAACCGAGGGTCGCAATATTAAATCAGTGGACCGTAAAAAATAACAACTGTGAACGTAG
129 ATTAGAAAACCGAGGGTCGCAATATTAAATCAGCAGACCATAAAAAATAACAACTGTGAACGTAG
* * *
28275561 GTAAGAAAGCTGTTAAAAAACCAAGGGTCGCGAT
194 GTAAGAAAGCTGTTAAAAAACAAAAGGTCACGAT
* *
28275595 CTTAAATCAGCGGACCGCAAAAAATATCAATTGTGAACGTAGGTCAACAAGTTGTTAGAAAATCG
1 CTTAAATCAGCGAACCG-AAAAAATATCAATTGTGAACATAGGTCAACAAGTTGTTAGAAAATCG
* ***
28275660 AGGGTCACAATCTTAAATAAGCGGACCATAAAAAATATCAACTATGAACGTAGGTCAGTGAGCTA
65 AGGGTCACAATCTTAAATCAGCGGACCATAAAAAATATCAACTATGAACGTAGGTCAACAAGCTA
* * ** * * *
28275725 TTAGAAAATCGAGGGTTGTGATCTTAAATCAGCAGACCATAAAAAATATCAGCTGTGAACGTAGG
130 TTAGAAAACCGAGGGTCGCAATATTAAATCAGCAGACCATAAAAAATAACAACTGTGAACGTAGG
* ** *
28275790 TTAGCGAGCTGTTAGAAAACAAAAGGTCACGAT
195 TAAGAAAGCTGTTAAAAAACAAAAGGTCACGAT
* * * * * * *
28275823 CTTAAATCAGCAAACCGTAAAAAATATCAACTGTGAACATAGGTTAGCGAGTTGTTAGAAAACCA
1 CTTAAATCAGCGAACCG-AAAAAATATCAATTGTGAACATAGGTCAACAAGTTGTTAGAAAATCG
28275888 AGGGTCACAATCTTAAATCAGC
65 AGGGTCACAATCTTAAATCAGC
28275910 AAGCCTTAGT
Statistics
Matches: 268, Mismatches: 44, Indels: 5
0.85 0.14 0.02
Matches are distributed among these distances:
227 17 0.06
228 250 0.93
229 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (227 bp):
CTTAAATCAGCGAACCGAAAAAATATCAATTGTGAACATAGGTCAACAAGTTGTTAGAAAATCGA
GGGTCACAATCTTAAATCAGCGGACCATAAAAAATATCAACTATGAACGTAGGTCAACAAGCTAT
TAGAAAACCGAGGGTCGCAATATTAAATCAGCAGACCATAAAAAATAACAACTGTGAACGTAGGT
AAGAAAGCTGTTAAAAAACAAAAGGTCACGAT
Found at i:28275911 original size:76 final size:76
Alignment explanation
Indices: 28275261--28275909 Score: 604
Period size: 76 Copynumber: 8.6 Consensus size: 76
28275251 TGATCGTGAA
* * * *** * * *
28275261 TCAGCGAGCTGTTAGAAAATCGAGGGTCGTGATCTTAAATCAATAGCCCAT-AAAAATATCAATT
1 TCAGCAAGCTGTTAGAAAACCGAGGGTCGCGATCTTAAATCAGCGGACCGTAAAAAATATCAACT
*
28275325 GTGAACATAGG
66 GTGAACGTAGG
* * * * * * * * * * **
28275336 TCAACGAGCTATCAGAAAA-CTAGGATCGTGACCTTAAATCAGCGAACCGT-AAAAATAACAGTT
1 TCAGCAAGCTGTTAGAAAACCGAGGGTCGCGATCTTAAATCAGCGGACCGTAAAAAATATCAACT
*
28275399 GTGAACATAGG
66 GTGAACGTAGG
* * * * **
28275410 TCAACAAGCTATTAGAAAATCGAGGGTCGCGATCTTAAAGCAGCGGATAGTAAAAAATATCAGA-
1 TCAGCAAGCTGTTAGAAAACCGAGGGTCGCGATCTTAAATCAGCGGACCGTAAAAAATATCA-AC
28275474 TGTGAACGTAGG
65 TGTGAACGTAGG
* * * * * *
28275486 TCAACAAGCTATTAGAAAACCGAGGGTCGCAATATTAAATCAGTGGACCGTAAAAAATAACAACT
1 TCAGCAAGCTGTTAGAAAACCGAGGGTCGCGATCTTAAATCAGCGGACCGTAAAAAATATCAACT
28275551 GTGAACGTAGG
66 GTGAACGTAGG
* * * * * *
28275562 TAAGAAAGCTGTTAAAAAACCAAGGGTCGCGATCTTAAATCAGCGGACCGCAAAAAATATCAATT
1 TCAGCAAGCTGTTAGAAAACCGAGGGTCGCGATCTTAAATCAGCGGACCGTAAAAAATATCAACT
28275627 GTGAACGTAGG
66 GTGAACGTAGG
* * * * * * *
28275638 TCAACAAGTTGTTAGAAAATCGAGGGTCACAATCTTAAATAAGCGGACCATAAAAAATATCAACT
1 TCAGCAAGCTGTTAGAAAACCGAGGGTCGCGATCTTAAATCAGCGGACCGTAAAAAATATCAACT
*
28275703 ATGAACGTAGG
66 GTGAACGTAGG
** * * * * * * *
28275714 TCAGTGAGCTATTAGAAAATCGAGGGTTGTGATCTTAAATCAGCAGACCATAAAAAATATCAGCT
1 TCAGCAAGCTGTTAGAAAACCGAGGGTCGCGATCTTAAATCAGCGGACCGTAAAAAATATCAACT
28275779 GTGAACGTAGG
66 GTGAACGTAGG
* * ** * * **
28275790 TTAGCGAGCTGTTAGAAAACAAAAGGTCACGATCTTAAATCAGCAAACCGTAAAAAATATCAACT
1 TCAGCAAGCTGTTAGAAAACCGAGGGTCGCGATCTTAAATCAGCGGACCGTAAAAAATATCAACT
*
28275855 GTGAACATAGG
66 GTGAACGTAGG
* * * * * *
28275866 TTAGCGAGTTGTTAGAAAACCAAGGGTCACAATCTTAAATCAGC
1 TCAGCAAGCTGTTAGAAAACCGAGGGTCGCGATCTTAAATCAGC
28275910 AAGCCTTAGT
Statistics
Matches: 478, Mismatches: 92, Indels: 7
0.83 0.16 0.01
Matches are distributed among these distances:
74 61 0.13
75 40 0.08
76 377 0.79
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.22
Consensus pattern (76 bp):
TCAGCAAGCTGTTAGAAAACCGAGGGTCGCGATCTTAAATCAGCGGACCGTAAAAAATATCAACT
GTGAACGTAGG
Found at i:28276310 original size:26 final size:24
Alignment explanation
Indices: 28276266--28276315 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
28276256 ATTTGTTTTA
*
28276266 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
28276290 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
28276316 TTAATGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:28280123 original size:15 final size:16
Alignment explanation
Indices: 28280105--28280137 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
28280095 TTGAATATGA
28280105 AAATATAT-TATATAT
1 AAATATATGTATATAT
*
28280120 AAATATATGTGTATAT
1 AAATATATGTATATAT
28280136 AA
1 AA
28280138 TTAAAATTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
AAATATATGTATATAT
Found at i:28280503 original size:54 final size:52
Alignment explanation
Indices: 28280443--28280553 Score: 143
Period size: 53 Copynumber: 2.1 Consensus size: 52
28280433 AATGAAAAAT
**
28280443 AATGAAAACTT-GATGTGATTAAATTGTGTTATTATAAAAGTTAAAGATATTAAA
1 AATGAAAACTTAG-TGTGATT-AATTGTACTATTATAAAAGTTAAA-ATATTAAA
* * *
28280497 AATGAAAAGTTAGTGTGATTAATTTTACTATTATAAAAGTTAGAATATTAAA
1 AATGAAAACTTAGTGTGATTAATTGTACTATTATAAAAGTTAAAATATTAAA
28280549 AATGA
1 AATGA
28280554 CTGTTAATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
52 13 0.25
53 20 0.39
54 17 0.33
55 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (52 bp):
AATGAAAACTTAGTGTGATTAATTGTACTATTATAAAAGTTAAAATATTAAA
Found at i:28287511 original size:23 final size:23
Alignment explanation
Indices: 28287481--28287527 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
28287471 TTAACATAGT
*
28287481 ACATGGCATCATAAAGAAATATG
1 ACATGGCATCATAAAGAAAAATG
28287504 ACATGGCATCATAAAGAAAAATG
1 ACATGGCATCATAAAGAAAAATG
28287527 A
1 A
28287528 ACAACCATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.51, C:0.13, G:0.17, T:0.19
Consensus pattern (23 bp):
ACATGGCATCATAAAGAAAAATG
Found at i:28289444 original size:15 final size:15
Alignment explanation
Indices: 28289426--28289473 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
28289416 TTTTCTCGAG
28289426 TTATATTTTAATTAT
1 TTATATTTTAATTAT
* *
28289441 TTATATTTAAAATA-
1 TTATATTTTAATTAT
* *
28289455 TTATGTTTTAGTTAT
1 TTATATTTTAATTAT
28289470 TTAT
1 TTAT
28289474 GTTATTATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:28289621 original size:14 final size:15
Alignment explanation
Indices: 28289602--28289635 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
28289592 GAAAATAATT
28289602 TTTTAATTAA-AAAA
1 TTTTAATTAATAAAA
28289616 TTTTAATTAATTAAAA
1 TTTTAATTAA-TAAAA
28289632 TTTT
1 TTTT
28289636 CAAACCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
16 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTAATTAATAAAA
Found at i:28291088 original size:36 final size:34
Alignment explanation
Indices: 28291056--28291121 Score: 98
Period size: 36 Copynumber: 1.9 Consensus size: 34
28291046 TGAAAATATA
*
28291056 TAAAATTTTAT-AATATATAAATTAATAAAAAAT
1 TAAAATTTTATAAATATATAAATAAATAAAAAAT
28291089 TAAAATTTTATAAAAATATATAAATAAATAAAA
1 TAAAATTTTAT--AAATATATAAATAAATAAAA
28291122 GAACTGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 11 0.38
36 18 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (34 bp):
TAAAATTTTATAAATATATAAATAAATAAAAAAT
Found at i:28293459 original size:40 final size:38
Alignment explanation
Indices: 28293379--28293477 Score: 92
Period size: 40 Copynumber: 2.5 Consensus size: 38
28293369 CACACTATCT
* * *
28293379 CCAACCAACCCAACACACC-ATGTGGGGATAAAATCGAC
1 CCAACC-ACCCTACACACCAATGTGGGGACAAAATCAAC
* *
28293417 CCAACCTACCCTACACACCAAGTTTGGGGACATAATCAAC
1 CCAACC-ACCCTACACACCAA-TGTGGGGACAAAATCAAC
**
28293457 CCATGCAGCCCTACACACCAA
1 CCAACCA-CCCTACACACCAA
28293478 AAGGTACCGT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 17 0.34
39 2 0.04
40 31 0.62
ACGTcount: A:0.36, C:0.37, G:0.13, T:0.13
Consensus pattern (38 bp):
CCAACCACCCTACACACCAATGTGGGGACAAAATCAAC
Found at i:28296321 original size:51 final size:54
Alignment explanation
Indices: 28296261--28296379 Score: 147
Period size: 51 Copynumber: 2.3 Consensus size: 54
28296251 AAGTGTCGCC
*
28296261 TTACTGTTACTGTTCTGGATTCGTTCCGAAGAGGT-A-CT-TCGTACC-TTACTG
1 TTACTGTTACTGTTCTGGATTCGTTCCGAAGAGGTAATCTGT-GTACCGCTACTG
** ** *
28296312 TTACTGTTACTAATCTGGATTTTTTCCGATGAGGTAATCTGTGTACCGCTACTG
1 TTACTGTTACTGTTCTGGATTCGTTCCGAAGAGGTAATCTGTGTACCGCTACTG
28296366 TTACTGTTACTGTT
1 TTACTGTTACTGTT
28296380 ACCGTTACAG
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
51 30 0.54
52 1 0.02
53 7 0.12
54 18 0.32
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.42
Consensus pattern (54 bp):
TTACTGTTACTGTTCTGGATTCGTTCCGAAGAGGTAATCTGTGTACCGCTACTG
Found at i:28296524 original size:18 final size:18
Alignment explanation
Indices: 28296500--28296586 Score: 104
Period size: 18 Copynumber: 4.8 Consensus size: 18
28296490 AAAGGTATTA
28296500 AATAACTGACTGTTACTG
1 AATAACTGACTGTTACTG
* * *
28296518 GATAACTGATTGCTACTG
1 AATAACTGACTGTTACTG
*
28296536 AATAATTGACTGTTACTG
1 AATAACTGACTGTTACTG
* *
28296554 AATAATTTA-TCGTTACTG
1 AATAACTGACT-GTTACTG
28296572 AATAACTGACTGTTA
1 AATAACTGACTGTTA
28296587 AAGAGTGACT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
17 1 0.02
18 55 0.96
19 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (18 bp):
AATAACTGACTGTTACTG
Found at i:28296540 original size:36 final size:36
Alignment explanation
Indices: 28296500--28296586 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
28296490 AAAGGTATTA
* *
28296500 AATAACTGACTGTTACTGGATAACTGATTGCTACTG
1 AATAACTGACTGTTACTGAATAACTGATCGCTACTG
* * * *
28296536 AATAATTGACTGTTACTGAATAATTTATCGTTACTG
1 AATAACTGACTGTTACTGAATAACTGATCGCTACTG
28296572 AATAACTGACTGTTA
1 AATAACTGACTGTTA
28296587 AAGAGTGACT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (36 bp):
AATAACTGACTGTTACTGAATAACTGATCGCTACTG
Found at i:28296646 original size:18 final size:18
Alignment explanation
Indices: 28296504--28296648 Score: 62
Period size: 18 Copynumber: 8.1 Consensus size: 18
28296494 GTATTAAATA
* * *
28296504 ACTGACTGTTACTGGATA
1 ACTGAATGTTACTGAATG
* * *
28296522 ACTGATTGCTACTGAATA
1 ACTGAATGTTACTGAATG
* *
28296540 ATTGACTGTTACTGAAT-
1 ACTGAATGTTACTGAATG
* ** *
28296557 AATTTATCGTTACTGAATA
1 ACTGAAT-GTTACTGAATG
* ** *
28296576 ACTGACTGTTAAAGAGTG
1 ACTGAATGTTACTGAATG
* * *
28296594 ACTGAATATTATTGAACG
1 ACTGAATGTTACTGAATG
28296612 ACT-AATTGTTA-TCGAATG
1 ACTGAA-TGTTACT-GAATG
*
28296630 ATTGAATGTTACTGAATG
1 ACTGAATGTTACTGAATG
28296648 A
1 A
28296649 AACTGATAAA
Statistics
Matches: 94, Mismatches: 27, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
17 6 0.06
18 82 0.87
19 6 0.06
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.36
Consensus pattern (18 bp):
ACTGAATGTTACTGAATG
Found at i:28297829 original size:45 final size:43
Alignment explanation
Indices: 28297746--28297830 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 43
28297736 ATTTCACTTG
*
28297746 CTAGGCTCGAAGCCCGATATCATTTCACCGGTATTATAGCCTT
1 CTAGGCTCGAAGCCCGATATCATTTCACCGGCATTATAGCCTT
28297789 CTAGGCTCGAAGGCCCGAATAGT-ATCTT-ACCGGCATTATAGC
1 CTAGGCTCGAA-GCCCG-ATA-TCAT-TTCACCGGCATTATAGC
28297831 TCACCGGCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
43 11 0.30
44 5 0.14
45 18 0.49
46 3 0.08
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (43 bp):
CTAGGCTCGAAGCCCGATATCATTTCACCGGCATTATAGCCTT
Found at i:28297908 original size:103 final size:103
Alignment explanation
Indices: 28297729--28297933 Score: 410
Period size: 103 Copynumber: 2.0 Consensus size: 103
28297719 CGAATTCATC
28297729 CACCGGCATTTCACTTGCTAGGCTCGAAGCCCGATATCATTTCACCGGTATTATAGCCTTCTAGG
1 CACCGGCATTTCACTTGCTAGGCTCGAAGCCCGATATCATTTCACCGGTATTATAGCCTTCTAGG
28297794 CTCGAAGGCCCGAATAGTATCTTACCGGCATTATAGCT
66 CTCGAAGGCCCGAATAGTATCTTACCGGCATTATAGCT
28297832 CACCGGCATTTCACTTGCTAGGCTCGAAGCCCGATATCATTTCACCGGTATTATAGCCTTCTAGG
1 CACCGGCATTTCACTTGCTAGGCTCGAAGCCCGATATCATTTCACCGGTATTATAGCCTTCTAGG
28297897 CTCGAAGGCCCGAATAGTATCTTACCGGCATTATAGC
66 CTCGAAGGCCCGAATAGTATCTTACCGGCATTATAGC
28297934 CTGCTAGGCT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (103 bp):
CACCGGCATTTCACTTGCTAGGCTCGAAGCCCGATATCATTTCACCGGTATTATAGCCTTCTAGG
CTCGAAGGCCCGAATAGTATCTTACCGGCATTATAGCT
Found at i:28297932 original size:45 final size:45
Alignment explanation
Indices: 28297831--28297960 Score: 155
Period size: 45 Copynumber: 3.0 Consensus size: 45
28297821 GCATTATAGC
*
28297831 TCACCGGCATT-TCA-CTTGCTAGGCTCGAA-GCCCG-ATA-TCATT
1 TCACCGGCATTAT-AGCCTGCTAGGCTCGAAGGCCCGAATAGT-ATT
* *
28297873 TCACCGGTATTATAGCCTTCTAGGCTCGAAGGCCCGAATAGTATCT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTAT-T
*
28297919 T-ACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTA
28297961 CCGTATGATA
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
42 11 0.14
43 14 0.18
44 5 0.07
45 43 0.57
46 3 0.04
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATT
Found at i:28297971 original size:103 final size:100
Alignment explanation
Indices: 28297754--28297958 Score: 270
Period size: 103 Copynumber: 2.0 Consensus size: 100
28297744 TGCTAGGCTC
28297754 GAAGCCCGATATCATTTCACCGGTATTATAGCCTTCTAGGCTCGAAGGCCCGAATAGTATCTTAC
1 GAAGCCCGATATCATTTCACCGGTATTATAGCCTTCTAGGCTCGAAGGCCCGAATAGTATCTTAC
*** * ** *
28297819 CGGCATTATAGCTCACCGGCATTTCACTTGCTAGGCTC
66 CGGCATTATAGCTCA-CGGC--TTCAAAGGCCAGAATA
28297857 GAAGCCCGATATCATTTCACCGGTATTATAGCCTTCTAGGCTCGAAGGCCCGAATAGTATCTTAC
1 GAAGCCCGATATCATTTCACCGGTATTATAGCCTTCTAGGCTCGAAGGCCCGAATAGTATCTTAC
*
28297922 CGGCATTATAGCCTGCTA-GGC-TCAAAGGCCCGAATA
66 CGGCATTATAG-CT-C-ACGGCTTCAAAGGCCAGAATA
28297958 G
1 G
28297959 TACCGTATGA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
101 8 0.09
103 76 0.84
104 5 0.05
105 1 0.01
106 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (100 bp):
GAAGCCCGATATCATTTCACCGGTATTATAGCCTTCTAGGCTCGAAGGCCCGAATAGTATCTTAC
CGGCATTATAGCTCACGGCTTCAAAGGCCAGAATA
Found at i:28300607 original size:17 final size:17
Alignment explanation
Indices: 28300568--28300609 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
28300558 TATTTAATTG
* *
28300568 TATATTTTTTAAATATT
1 TATATTTTTTAAAAATA
*
28300585 TTTATTTTTTAAAAATA
1 TATATTTTTTAAAAATA
28300602 TATATTTT
1 TATATTTT
28300610 CCACATGACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATATTTTTTAAAAATA
Found at i:28300645 original size:23 final size:23
Alignment explanation
Indices: 28300610--28300662 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
28300600 TATATATTTT
28300610 CCACATGACATACTGAGAGGTTG
1 CCACATGACATACTGAGAGGTTG
**
28300633 CCACATGGTATACTGAGAGGTTG
1 CCACATGACATACTGAGAGGTTG
*
28300656 TCACATG
1 CCACATG
28300663 TCACCGCTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (23 bp):
CCACATGACATACTGAGAGGTTG
Found at i:28309247 original size:43 final size:43
Alignment explanation
Indices: 28309198--28309354 Score: 165
Period size: 43 Copynumber: 3.7 Consensus size: 43
28309188 TATCCTAGAT
* * *
28309198 ATGGTCTTACATGTTATCACATATCGATGCCACTGTCCTAGAC
1 ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
* *** * *
28309241 AGGGTCTTACACAAAATCGA-TTAACGATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATC-ACATATCGATGCCAATGTCCCAGAC
* * *
28309284 ATGGTCCTACATGTAATCTCA-ATACAATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCACATAT-CGATGCCAATGTCCCAGAC
*
28309327 ATGGTCTTACATGTAATCACATCTCGAT
1 ATGGTCTTACATGTAATCACATATCGAT
28309355 AACCTAATGT
Statistics
Matches: 88, Mismatches: 22, Indels: 8
0.75 0.19 0.07
Matches are distributed among these distances:
42 1 0.01
43 85 0.97
44 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
Found at i:28314399 original size:28 final size:28
Alignment explanation
Indices: 28314368--28314423 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
28314358 AAATCAAGTT
*
28314368 GACATACTCATAGCCAAAAATAAAATGA
1 GACATACTCATAACCAAAAATAAAATGA
28314396 GACATACTCATAACCAAAAATAAAATGA
1 GACATACTCATAACCAAAAATAAAATGA
28314424 ACACGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.55, C:0.18, G:0.09, T:0.18
Consensus pattern (28 bp):
GACATACTCATAACCAAAAATAAAATGA
Found at i:28322415 original size:48 final size:48
Alignment explanation
Indices: 28322344--28323429 Score: 1816
Period size: 48 Copynumber: 22.6 Consensus size: 48
28322334 TATATGTACT
* * * ** * *
28322344 AGTGTAAGACCATGTCTAGGACATGGCGTTAGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
* * * * * *
28322392 AGTGTAAGGCCATGTTTGGGACATGGCATTGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
** * * * *
28322440 AGTGTAAGATTATGTCTGGGACATGGTATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28322488 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
* *
28322536 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28322584 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28322632 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28322680 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28322728 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28322776 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28322824 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28322872 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28322920 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28322968 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28323016 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28323064 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28323112 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28323160 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28323208 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
28323256 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
* * * ** * *
28323304 AGTGTAAGACCATGTCTGGGACATGGCATCGACCTCGA-CGTGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGC-ATTATGAGAGGC
* * * * * * *
28323352 AATGTAAGTCCATGTCTGGGACATGGCATCGGCCTCGA-CATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGC-ATTATGAGAGGC
*
28323400 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATAGCATC
28323430 AGCAATTTAC
Statistics
Matches: 1003, Mismatches: 34, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
48 1002 1.00
49 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.22
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATAGCATCGGCCGCATTATGAGAGGC
Found at i:28330962 original size:48 final size:48
Alignment explanation
Indices: 28330891--28331080 Score: 222
Period size: 48 Copynumber: 4.0 Consensus size: 48
28330881 TATGTGTGCT
28330891 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGTGACGAGAACC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGTGACGAGAACC
* * * *
28330939 AGTGTAAGACCATGTCTGGGACATTGCATCGG-CTT-CGACGTGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGTGAC--GAGAACC
* **** * * *
28330987 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCAACATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGTGACGAGAACC
* *
28331035 AATGTAAGACCATGTCTGGGACATGGCATCGGCATTGTGACGAGAA
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGTGACGAGAA
28331081 GCATGGCATC
Statistics
Matches: 118, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
46 3 0.03
47 3 0.03
48 109 0.92
49 2 0.02
50 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGTGACGAGAACC
Found at i:28331055 original size:96 final size:96
Alignment explanation
Indices: 28330891--28331067 Score: 264
Period size: 96 Copynumber: 1.8 Consensus size: 96
28330881 TATGTGTGCT
* **** *
28330891 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGTGACGAGAACCAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCAACACGAGAACCAATGTAAGACCATGTCT
*
28330956 GGGACATTGCATCGGCTTCGACGTGTGAGCC
66 GGGACATGGCATCGGCTTCGACGTGTGAGCC
* * *
28330987 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCAACATGTGAGCCAATGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCAACACGAGAACCAATGTAAGACCATGTCT
28331052 GGGACATGGCATCGGC
66 GGGACATGGCATCGGC
28331068 ATTGTGACGA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 71 1.00
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.22
Consensus pattern (96 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCAACACGAGAACCAATGTAAGACCATGTCT
GGGACATGGCATCGGCTTCGACGTGTGAGCC
Found at i:28331164 original size:48 final size:46
Alignment explanation
Indices: 28331102--28331282 Score: 211
Period size: 48 Copynumber: 3.8 Consensus size: 46
28331092 ACAATGTTAT
* *
28331102 GTGAGCCAGAGTAAGACCATGTCTGGGACATGGCATCGGCATTGTGAC
1 GTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TT-AGAC
* * * *
28331150 GAGAACCAGTGTAAGACCATGTCTGGGACATTGCATCGGCTTCGAC
1 GTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTAGAC
* *
28331196 GTGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCA-AC
1 --GTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CTTAGAC
*
28331244 ATGTGAGCCAATGTAAGACCATGTCTGGGACATGGCATC
1 --GTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
28331283 AGTAATTTAC
Statistics
Matches: 116, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
46 3 0.03
47 2 0.02
48 109 0.94
49 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.22
Consensus pattern (46 bp):
GTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTAGAC
Found at i:28331259 original size:96 final size:96
Alignment explanation
Indices: 28331101--28331282 Score: 256
Period size: 96 Copynumber: 1.9 Consensus size: 96
28331091 GACAATGTTA
* **** *
28331101 TGTGAGCCAGAGTAAGACCATGTCTGGGACATGGCATCGGCATTGTGACGAGAACCAGTGTAAGA
1 TGTGAGCCAGAGTAAGACCATGTCTAGGACATGGCATCGGCATCAACACGAGAACCAATGTAAGA
*
28331166 CCATGTCTGGGACATTGCATCGGCTTCGACG
66 CCATGTCTGGGACATGGCATCGGCTTCGACG
* * * * *
28331197 TGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCAACATGTGAGCCAATGTAAGA
1 TGTGAGCCAGAGTAAGACCATGTCTAGGACATGGCATCGGCATCAACACGAGAACCAATGTAAGA
28331262 CCATGTCTGGGACATGGCATC
66 CCATGTCTGGGACATGGCATC
28331283 AGTAATTTAC
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 74 1.00
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.22
Consensus pattern (96 bp):
TGTGAGCCAGAGTAAGACCATGTCTAGGACATGGCATCGGCATCAACACGAGAACCAATGTAAGA
CCATGTCTGGGACATGGCATCGGCTTCGACG
Found at i:28337620 original size:10 final size:10
Alignment explanation
Indices: 28337605--28337633 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
28337595 GCGCGATAGA
28337605 AGAGAGAAAG
1 AGAGAGAAAG
28337615 AGAGAGAAAG
1 AGAGAGAAAG
28337625 AGAGAGAAA
1 AGAGAGAAA
28337634 TAGTTAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
AGAGAGAAAG
Found at i:28338164 original size:12 final size:12
Alignment explanation
Indices: 28338147--28338176 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28338137 ACCTCTCCTC
28338147 CACTCCTTAATT
1 CACTCCTTAATT
28338159 CACTCCTTAATT
1 CACTCCTTAATT
*
28338171 CTCTCC
1 CACTCC
28338177 CCAAATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (12 bp):
CACTCCTTAATT
Found at i:28341409 original size:90 final size:90
Alignment explanation
Indices: 28341314--28341675 Score: 715
Period size: 90 Copynumber: 4.0 Consensus size: 90
28341304 AAAATTATGG
28341314 TTTTGATATCAAACTTGTAAATTTTAAAATGTCAAGATAATACTTCAGTTTAAGGAGACAACCTA
1 TTTTGATATCAAACTTGTAAATTTTAAAATGTCAAGATAATACTTCAGTTTAAGGAGACAACCTA
28341379 AAATAATAATTTCTAAAAAAACTTA
66 AAATAATAATTTCTAAAAAAACTTA
28341404 TTTTGATATCAAACTTGTAAATTTTAAAATGTCAAGATAATACTTCAGTTTAAGGAGACAACCTA
1 TTTTGATATCAAACTTGTAAATTTTAAAATGTCAAGATAATACTTCAGTTTAAGGAGACAACCTA
28341469 AAATAATAATTTCTAAAAAAACTTA
66 AAATAATAATTTCTAAAAAAACTTA
28341494 TTTTGATATCAAACTTGTAAATTTTAAAATGTCAAGATAATACTTCAGTTTAAGGAGACAACCTA
1 TTTTGATATCAAACTTGTAAATTTTAAAATGTCAAGATAATACTTCAGTTTAAGGAGACAACCTA
28341559 AAATAATAATTTCTAAAAAAACTTA
66 AAATAATAATTTCTAAAAAAACTTA
28341584 TTTTGATATCAAACTTGTAAATTTTAAAATGTCAAGATAATACTTCAGTTTAAGGAGACAACCTA
1 TTTTGATATCAAACTTGTAAATTTTAAAATGTCAAGATAATACTTCAGTTTAAGGAGACAACCTA
28341649 AAATAATAATTTCTAAAAAAAACTTA
66 AAATAATAATTTCT-AAAAAAACTTA
28341675 T
1 T
28341676 CATGCTGGAC
Statistics
Matches: 271, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
90 259 0.96
91 12 0.04
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.35
Consensus pattern (90 bp):
TTTTGATATCAAACTTGTAAATTTTAAAATGTCAAGATAATACTTCAGTTTAAGGAGACAACCTA
AAATAATAATTTCTAAAAAAACTTA
Found at i:28347098 original size:21 final size:21
Alignment explanation
Indices: 28347073--28347112 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28347063 ATATAATGAG
*
28347073 TATATCATGCGCATCTCATAA
1 TATATCATGCGCATATCATAA
*
28347094 TATATCATGTGCATATCAT
1 TATATCATGCGCATATCAT
28347113 GTCATATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (21 bp):
TATATCATGCGCATATCATAA
Found at i:28347118 original size:10 final size:10
Alignment explanation
Indices: 28347095--28347130 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
28347085 ATCTCATAAT
28347095 ATATCATGTGC
1 ATATCATGT-C
28347106 ATATCATGTC
1 ATATCATGTC
28347116 ATATCATGT-
1 ATATCATGTC
28347125 ATATCA
1 ATATCA
28347131 AAATCTCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.24
10 10 0.40
11 9 0.36
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (10 bp):
ATATCATGTC
Found at i:28354375 original size:41 final size:41
Alignment explanation
Indices: 28354330--28354411 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
28354320 GTGGTGGCCA
*
28354330 GAGAGGGACTTCTGATACGGCTGTTCGGTTTGAGACTCGTG
1 GAGAGGGACTTCTGATACGGCTGTTCGATTTGAGACTCGTG
28354371 GAGAGGGACTTCTGATACGGCTGTTCGATTTGAGACTCGTG
1 GAGAGGGACTTCTGATACGGCTGTTCGATTTGAGACTCGTG
28354412 CTCCCGCTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.18, C:0.17, G:0.35, T:0.29
Consensus pattern (41 bp):
GAGAGGGACTTCTGATACGGCTGTTCGATTTGAGACTCGTG
Found at i:28372538 original size:23 final size:23
Alignment explanation
Indices: 28372508--28372553 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
28372498 GTGAAAAAAT
28372508 CAGGTAGAAGCCCAATTCATTGA
1 CAGGTAGAAGCCCAATTCATTGA
*
28372531 CAGGTAGAAGCTCAATTCATTGA
1 CAGGTAGAAGCCCAATTCATTGA
28372554 AGGAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (23 bp):
CAGGTAGAAGCCCAATTCATTGA
Found at i:28378767 original size:210 final size:211
Alignment explanation
Indices: 28378404--28378827 Score: 661
Period size: 210 Copynumber: 2.0 Consensus size: 211
28378394 CAAGAAGTTT
* * * *
28378404 ATAGTCTTGATTGCTGGTTCAGTTTCCCAATAATAGTTGGGGTCAAGAAATAACATTTTGAGAGA
1 ATAGTCTTGATTGCTAGTTCAGTTTCCCAATAATAGTAGGGCTCAAGAAATAACATTGTGAGAGA
** * *
28378469 TGAGAGTGGTGCATATGATTCTTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAATT
66 CAAGAGTGGTGCACATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAATT
* * * *
28378534 CGATATTGTAATTAACGAATTTTCATATGATGTCCTAGTTTACTAAATACAGAAGAGTAGGTTTA
131 CGATATTGTAACTAAAGAATTTTCATATGATGCCCTAGTTTACTAAAGACAGAAGAGTAGGTTTA
28378599 ATATGGTTCAACTTCC
196 ATATGGTTCAACTTCC
* * * *
28378615 ATAGTCTTGATTGCTAGTTCAGTTTTCCGATATTGGTAGGGCTCAAGAAATAACATTGT-AGAGA
1 ATAGTCTTGATTGCTAGTTCAGTTTCCCAATAATAGTAGGGCTCAAGAAATAACATTGTGAGAGA
* *
28378679 CAAGGGTGGTGCACATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGGTGAAAATT
66 CAAGAGTGGTGCACATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAATT
* *
28378744 TGATATTGTGACTAAAGAATTTTCATATGATGCCCTAGTTTACTAAAGACAGAAGAGTAGGTTTA
131 CGATATTGTAACTAAAGAATTTTCATATGATGCCCTAGTTTACTAAAGACAGAAGAGTAGGTTTA
28378809 ATATGGTTCAACTTCC
196 ATATGGTTCAACTTCC
28378825 ATA
1 ATA
28378828 AAGAAGTGGC
Statistics
Matches: 193, Mismatches: 20, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
210 142 0.74
211 51 0.26
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (211 bp):
ATAGTCTTGATTGCTAGTTCAGTTTCCCAATAATAGTAGGGCTCAAGAAATAACATTGTGAGAGA
CAAGAGTGGTGCACATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAATT
CGATATTGTAACTAAAGAATTTTCATATGATGCCCTAGTTTACTAAAGACAGAAGAGTAGGTTTA
ATATGGTTCAACTTCC
Found at i:28380822 original size:6 final size:6
Alignment explanation
Indices: 28380813--28380845 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
28380803 ATAGTAGTAT
*
28380813 AGTACA AGTAGA AGTAGA AGTAGA AGTAGA AGT
1 AGTAGA AGTAGA AGTAGA AGTAGA AGTAGA AGT
28380846 TTATATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.30, T:0.18
Consensus pattern (6 bp):
AGTAGA
Found at i:28382268 original size:53 final size:53
Alignment explanation
Indices: 28382166--28382321 Score: 143
Period size: 53 Copynumber: 2.9 Consensus size: 53
28382156 CTTTTTCTTA
* * * ** *
28382166 TTTTGAATCGATTGTTTATATGTTCAAAAT-AATTGTTATGTCGGGATACTAAT
1 TTTTTAATAGATTGTTTATATGTT-TAAATCAATTGTTATGTAAGAATACTAAT
* * *
28382219 TTTTTAATTGATTGTTTACATGTTTAAATCAATTGTTATGTAAGAATACTACT
1 TTTTTAATAGATTGTTTATATGTTTAAATCAATTGTTATGTAAGAATACTAAT
* * * * * *
28382272 TCTTTTGAATAAATTATTTATACGGTTCAATCGATTGTTATGTAAGAATA
1 T-TTTT-AATAGATTGTTTATATGTTTAAATCAATTGTTATGTAAGAATA
28382322 TTATTTCTTC
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
52 4 0.05
53 41 0.49
54 4 0.05
55 35 0.42
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (53 bp):
TTTTTAATAGATTGTTTATATGTTTAAATCAATTGTTATGTAAGAATACTAAT
Found at i:28390418 original size:58 final size:58
Alignment explanation
Indices: 28390353--28390469 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
28390343 ACTGGGTAGG
*
28390353 TAAACCTTGCCCGTTTTTTGAGCTCGTATTAACTTAATATAGCTAACCCGGGGACTAT
1 TAAACCTTGCCCGTTTTTCGAGCTCGTATTAACTTAATATAGCTAACCCGGGGACTAT
28390411 TAAACCTTGCCCGTTTTTCGAGCTCGTATTAACTTAATATAGCTAACCCGGGGACTAT
1 TAAACCTTGCCCGTTTTTCGAGCTCGTATTAACTTAATATAGCTAACCCGGGGACTAT
28390469 T
1 T
28390470 TGCAAAACTG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (58 bp):
TAAACCTTGCCCGTTTTTCGAGCTCGTATTAACTTAATATAGCTAACCCGGGGACTAT
Found at i:28397759 original size:3 final size:3
Alignment explanation
Indices: 28397751--28397779 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28397741 TTATCAAAGA
28397751 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28397780 AGACATTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28401310 original size:15 final size:14
Alignment explanation
Indices: 28401277--28401313 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28401267 ATTTTTCATA
28401277 TTTTTTATAGAAAT
1 TTTTTTATAGAAAT
*
28401291 TTTTTTATCGAAAT
1 TTTTTTATAGAAAT
28401305 TGTTTTTAT
1 T-TTTTTAT
28401314 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (14 bp):
TTTTTTATAGAAAT
Found at i:28405674 original size:16 final size:17
Alignment explanation
Indices: 28405644--28405676 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28405634 TATGCAAAAG
*
28405644 AAAATTATTACTTCAAA
1 AAAATTAATACTTCAAA
28405661 AAAATTAATA-TTCAAA
1 AAAATTAATACTTCAAA
28405677 TATCATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTAATACTTCAAA
Found at i:28409194 original size:26 final size:27
Alignment explanation
Indices: 28409165--28409225 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
28409155 TCAAAAAAAA
28409165 AAGAAAATAAAAAAG-AACA-A-ATGAGG
1 AAGAAAA-AAAAAAGAAACAGAGA-GAGG
*
28409191 AAGAGAAAAGAAAAGAAACAGAGAGAGG
1 AAGA-AAAAAAAAAGAAACAGAGAGAGG
28409219 AAGAAAA
1 AAGAAAA
28409226 CAGAACGTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 10 0.33
27 10 0.33
28 9 0.30
29 1 0.03
ACGTcount: A:0.69, C:0.03, G:0.25, T:0.03
Consensus pattern (27 bp):
AAGAAAAAAAAAAGAAACAGAGAGAGG
Found at i:28410757 original size:22 final size:21
Alignment explanation
Indices: 28410732--28410801 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
28410722 GATTTTATGA
*
28410732 GATTTGGACTATGATGCCTACT
1 GATTTGCACTATG-TGCCTACT
* *
28410754 GATTTACACTATTGTGCCTATT
1 GATTTGCACTA-TGTGCCTACT
* *
28410776 GATTTGCACTACGGTGCCTAGT
1 GATTTGCACTA-TGTGCCTACT
28410798 GATT
1 GATT
28410802 CGCATTTTGA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 38 0.95
23 2 0.05
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (21 bp):
GATTTGCACTATGTGCCTACT
Done.