Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 99 of 172
Found at i:28527657 original size:45 final size:45
Alignment explanation
Indices: 28527563--28527992 Score: 341
Period size: 45 Copynumber: 9.6 Consensus size: 45
28527553 GATCGCATCT
* * *
28527563 AGTCTTATCTCC-CTGAAGTTGCAGTGGAACAGACT-GAGTAAGCA
1 AGTCTTATC-CCTCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* *
28527607 GGTCTTATCCCTCTGAGGTTGCAGTGTG-GCAGACTCAAGAAAGCA
1 AGTCTTATCCCTCTGAAGTTGCAGTG-GAGCAGACTCAAGAAAGCA
* * *
28527652 AGTCTTAT-CTTCCTGAGGTTGCAGTGGAGCAGATTCAAGAAAGCA
1 AGTCTTATCCCT-CTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
*
28527697 AGTCTTATCTCC-CTAAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
1 AGTCTTATC-CCTCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * * * *
28527742 AGTCTTATCCCCCTAAAATTGCAGTAGG-GCAGACTGAATAAA-CA
1 AGTCTTATCCCTCTGAAGTTGCAGT-GGAGCAGACTCAAGAAAGCA
* * * * * ** * *
28527786 AATCCTAT-CTTCCTAAAGTTGTAGTGGAGTGGA-T-TAGAATG-A
1 AGTCTTATCCCT-CTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* **
28527828 TGGATCTTATATCTCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
1 -AG-TCTTATCCCTCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* *
28527875 AGTCTTATCTCC-ATGAAGTTGCAGTGGAGCAGACTCGAGAAAGCA
1 AGTCTTATC-CCTCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * * * *
28527920 AGTCTTATCCC-CTTGAAATTGCACTGGGGCAGACTGAATAAA-CA
1 AGTCTTATCCCTC-TGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* *
28527964 AATCTTATCTCCT-TGAAGTTGCAATGGAG
1 AGTCTTATC-CCTCTGAAGTTGCAGTGGAG
28527993 TAGATTGAGA
Statistics
Matches: 311, Mismatches: 53, Indels: 44
0.76 0.13 0.11
Matches are distributed among these distances:
42 4 0.01
43 6 0.02
44 101 0.32
45 189 0.61
46 9 0.03
47 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (45 bp):
AGTCTTATCCCTCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
Found at i:28528027 original size:178 final size:178
Alignment explanation
Indices: 28527664--28528036 Score: 502
Period size: 178 Copynumber: 2.1 Consensus size: 178
28527654 TCTTATCTTC
* * *
28527664 CTGAGGTTGCAGTGGAGCAGATTCAAGAAAGCAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAG
1 CTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCTCCATAAAGTTGCAGTGGAGCAG
*
28527729 ACTCAAGAAAGCAAGTCTTATCCCCCTAAAATTGCAGTAGGGCAGACTGAATAAACAAATCCTAT
66 ACTCAAGAAAGCAAGTCTTATCCCCCTAAAATTGCACTAGGGCAGACTGAATAAACAAATCCTAT
* * * * ** *
28527794 CTTCCTAAAGTTGTAGTGGAGTGGATTAGAATGATGGATCTTATATCT
131 CTTCCTAAAGTTGCAATGGAGTAGATTAGAATAATCAATCTCATATCT
*
28527842 CTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCTCCATGAAGTTGCAGTGGAGCAG
1 CTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCTCCATAAAGTTGCAGTGGAGCAG
* * * * *
28527907 ACTCGAGAAAGCAAGTCTTATCCCCTTGAAATTGCACTGGGGCAGACTGAATAAACAAATCTTAT
66 ACTCAAGAAAGCAAGTCTTATCCCCCTAAAATTGCACTAGGGCAGACTGAATAAACAAATCCTAT
*
28527972 C-TCCTTGAAGTTGCAATGGAGTAGATTGAGAA-AATCAATC-CA-ATCT
131 CTTCC-TAAAGTTGCAATGGAGTAGATT-AGAATAATCAATCTCATATCT
* *
28528018 CCTTGAAGTTACAATGGAG
1 -C-TGAAGTTGCAGTGGAG
28528037 TGGACTGGAG
Statistics
Matches: 171, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
176 4 0.02
177 5 0.03
178 158 0.92
179 4 0.02
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (178 bp):
CTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCTCCATAAAGTTGCAGTGGAGCAG
ACTCAAGAAAGCAAGTCTTATCCCCCTAAAATTGCACTAGGGCAGACTGAATAAACAAATCCTAT
CTTCCTAAAGTTGCAATGGAGTAGATTAGAATAATCAATCTCATATCT
Found at i:28533258 original size:11 final size:11
Alignment explanation
Indices: 28533242--28533266 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28533232 TGTAGGTGCC
28533242 AAAGAATATAT
1 AAAGAATATAT
28533253 AAAGAATATAT
1 AAAGAATATAT
28533264 AAA
1 AAA
28533267 TTTATGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (11 bp):
AAAGAATATAT
Found at i:28536335 original size:72 final size:72
Alignment explanation
Indices: 28536251--28536529 Score: 495
Period size: 72 Copynumber: 3.9 Consensus size: 72
28536241 TATCGGGTTT
*
28536251 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
28536316 CTTGAGA
66 CTTGAGA
* * *
28536323 AAAAAAGGGATCATGCCCAGTAAGTTAGGACATGGTCTCTTCTTAATTCCCGAGATCGTCTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
28536388 CTTGAGA
66 CTTGAGA
28536395 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
28536460 CTTGAGA
66 CTTGAGA
** *
28536467 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTTTCGAGATCATTTAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAA
28536530 CTTGAGTTTG
Statistics
Matches: 197, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 197 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (72 bp):
AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
CTTGAGA
Found at i:28537024 original size:10 final size:10
Alignment explanation
Indices: 28537006--28537035 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
28536996 AAAAATGTAC
*
28537006 GTATGTATAT
1 GTATATATAT
28537016 GTATATATAT
1 GTATATATAT
28537026 GTATATATAT
1 GTATATATAT
28537036 AAAGTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (10 bp):
GTATATATAT
Found at i:28537208 original size:19 final size:18
Alignment explanation
Indices: 28537180--28537216 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
28537170 ACATAGATGA
28537180 GTAAATAATAATAATAAT
1 GTAAATAATAATAATAAT
*
28537198 GTAATATAATAGTAATAAT
1 GTAA-ATAATAATAATAAT
28537217 AATATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (18 bp):
GTAAATAATAATAATAAT
Found at i:28539145 original size:23 final size:23
Alignment explanation
Indices: 28539121--28539193 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
28539111 ATTTTTCAAT
28539121 TTTA-AATTATTTAGTGATAATA
1 TTTAGAATTATTTAGTGATAATA
*
28539143 TTTAGAATTATTTGGTGATAATA
1 TTTAGAATTATTTAGTGATAATA
*
28539166 TTTAGGATTATTTAGTGATAATA
1 TTTAGAATTATTTAGTGATAATA
28539189 TTTAG
1 TTTAG
28539194 TAAAAATTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 4 0.09
23 43 0.91
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (23 bp):
TTTAGAATTATTTAGTGATAATA
Found at i:28539146 original size:13 final size:13
Alignment explanation
Indices: 28539128--28539194 Score: 74
Period size: 13 Copynumber: 5.6 Consensus size: 13
28539118 AATTTTAAAT
28539128 TATTTAGTGATAA
1 TATTTAGTGATAA
*
28539141 TATTTA--GA-AT
1 TATTTAGTGATAA
*
28539151 TATTTGGTGATAA
1 TATTTAGTGATAA
28539164 TATTTAG-GAT--
1 TATTTAGTGATAA
28539174 TATTTAGTGATAA
1 TATTTAGTGATAA
28539187 TATTTAGT
1 TATTTAGT
28539195 AAAAATTTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 13 0.30
11 5 0.11
12 5 0.11
13 21 0.48
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.49
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:28539996 original size:30 final size:31
Alignment explanation
Indices: 28539948--28540011 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
28539938 ACTTAACAAG
*
28539948 CAAATGCCTCTAAAAATAATAATAAAATTAA
1 CAAATGCCTCTAAAAATAATAACAAAATTAA
*
28539979 CAAATGCCT-TTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAAATAATAACAAAATTAA
28540009 CAA
1 CAA
28540012 TAAAATATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (31 bp):
CAAATGCCTCTAAAAATAATAACAAAATTAA
Found at i:28545208 original size:13 final size:13
Alignment explanation
Indices: 28545190--28545244 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
28545180 AATTTTGAAT
28545190 TATTTAGTGATAA
1 TATTTAGTGATAA
*
28545203 TATTTAGTAATAA
1 TATTTAGTGATAA
* *
28545216 CATTTA-AGAT--
1 TATTTAGTGATAA
28545226 TATTTAGTGATAA
1 TATTTAGTGATAA
28545239 TATTTA
1 TATTTA
28545245 AAAAAAATCT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 5 0.15
11 3 0.09
12 2 0.06
13 23 0.70
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:28546190 original size:5 final size:5
Alignment explanation
Indices: 28546143--28546171 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28546133 TCGAATATGT
28546143 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
28546172 TGTATTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:28548931 original size:18 final size:17
Alignment explanation
Indices: 28548904--28548939 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
28548894 TTTAATTATT
*
28548904 TTTAAAAATTTTAAAAA
1 TTTAAAAATTATAAAAA
28548921 TTTAAATAATTATAAAAA
1 TTTAAA-AATTATAAAAA
28548939 T
1 T
28548940 ATATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAAAATTATAAAAA
Found at i:28549001 original size:33 final size:34
Alignment explanation
Indices: 28548912--28549001 Score: 89
Period size: 35 Copynumber: 2.7 Consensus size: 34
28548902 TTTTTAAAAA
28548912 TTTTAAAAA-TTTAAA-TAATTATAAAAATATAT
1 TTTTAAAAATTTTAAATTAATTATAAAAATATAT
* *
28548944 TTTTAAAAATTATAAATATAAATTAT-AAAAT-TTT
1 TTTTAAAAATTTTAAAT-T-AATTATAAAAATATAT
**
28548978 TTTTAATATTTTTTAAATTAATTA
1 TTTTAA-AAATTTTAAATTAATTA
28549002 AATATGAACA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
32 9 0.19
33 10 0.21
34 9 0.19
35 14 0.29
36 6 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
TTTTAAAAATTTTAAATTAATTATAAAAATATAT
Found at i:28549815 original size:30 final size:30
Alignment explanation
Indices: 28549730--28549816 Score: 111
Period size: 30 Copynumber: 2.9 Consensus size: 30
28549720 GGATGTAGAG
* * * *
28549730 CTTCGACAGGCGACGGTGCCGGTGAGGGCA
1 CTTCTACAGGTGACGGTGCCGGTGATGACA
*
28549760 CTTCTACAGGTGACGGTGCTGGTGATGACA
1 CTTCTACAGGTGACGGTGCCGGTGATGACA
* *
28549790 CTTGTACAGGTGATGGTGCCGGTGATG
1 CTTCTACAGGTGACGGTGCCGGTGATG
28549817 GAGATGGTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.17, C:0.21, G:0.39, T:0.23
Consensus pattern (30 bp):
CTTCTACAGGTGACGGTGCCGGTGATGACA
Found at i:28553072 original size:26 final size:27
Alignment explanation
Indices: 28553033--28553087 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
28553023 ATTCTTTTAT
*
28553033 TTGTGCATTTTTA-TTTATTTATTATTA
1 TTGTGCATTATTATTTTATTT-TTATTA
28553060 TTGT-CATTATTATTTTATTTTTATTA
1 TTGTGCATTATTATTTTATTTTTATTA
28553086 TT
1 TT
28553088 TTGTTCTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.22, C:0.04, G:0.05, T:0.69
Consensus pattern (27 bp):
TTGTGCATTATTATTTTATTTTTATTA
Found at i:28553079 original size:31 final size:30
Alignment explanation
Indices: 28553041--28553118 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
28553031 ATTTGTGCAT
28553041 TTTTATTTATTTATTATTATTG-TCATTATTA
1 TTTTA-TTATTTATTATTATTGTTC-TTATTA
*
28553072 TTTTATT-TTTATTATT-TTGTTCTTGTTA
1 TTTTATTATTTATTATTATTGTTCTTATTA
*
28553100 TTTTATTATTTCTT-TTATT
1 TTTTATTATTTATTATTATT
28553119 ATTTTTGGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 17 0.40
29 18 0.43
30 2 0.05
31 5 0.12
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (30 bp):
TTTTATTATTTATTATTATTGTTCTTATTA
Found at i:28553089 original size:14 final size:14
Alignment explanation
Indices: 28553066--28553124 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
28553056 ATTATTGTCA
28553066 TTATTATTTTATTT
1 TTATTATTTTATTT
* *
28553080 TTATTATTTTGTTC
1 TTATTATTTTATTT
*
28553094 TTGTTATTTTATTAT
1 TTATTATTTTATT-T
*
28553109 TTCTT-TTATTATTT
1 TTATTATT-TTATTT
28553123 TT
1 TT
28553125 GGTACTTTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
14 28 0.76
15 9 0.24
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.76
Consensus pattern (14 bp):
TTATTATTTTATTT
Found at i:28563296 original size:35 final size:35
Alignment explanation
Indices: 28563257--28563327 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
28563247 ATGTGCCTCA
28563257 TTCACCTCTTCATGTTATGAATTCTCCATGGTCTT
1 TTCACCTCTTCATGTTATGAATTCTCCATGGTCTT
*
28563292 TTCACCTCTTCATGTTATGACTTCTCCATGGTCTT
1 TTCACCTCTTCATGTTATGAATTCTCCATGGTCTT
28563327 T
1 T
28563328 CTCTATATGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.15, C:0.27, G:0.11, T:0.46
Consensus pattern (35 bp):
TTCACCTCTTCATGTTATGAATTCTCCATGGTCTT
Found at i:28565157 original size:44 final size:44
Alignment explanation
Indices: 28565083--28565648 Score: 397
Period size: 44 Copynumber: 12.6 Consensus size: 44
28565073 TACCATAGTG
* * *
28565083 AATCTTATCTCCCTGAAGTTGCATTGGAGCAGATTGAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
* * * * *
28565127 AACCTAATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
* * * * * * *
28565171 AGTCTTATCTCTCTAAAGTTGTAGTGGAGCAGATT-AAGGCCATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAA-GCTACA
* * *
28565215 AGTCTTATTTCCCTGAAGTTGCAGTGGAATAGATTGAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
* * * * * * *
28565259 AATCTTGTTTCCTTGAAGTTGTAGTAGAATAGATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATT---G----AAGCTACA
* ** *
28565310 AATCTTATCTCCCTGAAGTTGCAGTGGAATAGATACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
* * ** *
28565354 AATCTTATCTTCCTGAAGTTACAGTGGAGTAGATACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
* * * * *
28565398 AATCTTATCTCCCTAAAGTTACAGTGGAGCATATTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
* * * *
28565442 AGTCTTATCTCCCCGAAGTTGCAGTAGAGTAGATTGAAACT--A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
* * * * * *
28565484 AATCCTATAC-CTCTGAAGTTGCAGTAGA-TCGGATTAAATCTACCATA
1 AATCTTAT-CTCCCTGAAGTTGCAGTGGAGT-AGATTGAAGCTA-C--A
* * *
28565531 GCGAATCTTATCTCCTTGAAGTGGCAGTGGAGTAGATTGAAGCTACG
1 ---AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
* * * *
28565578 AGTCTCATCTCCCTGAAGTTGCAGCGGAGTAGATTGAAACTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
** * *
28565622 CTTCTTATAC-CCCTAAAGTTACAGTGG
1 AATCTTAT-CTCCCTGAAGTTGCAGTGG
28565649 GTTAGAATAA
Statistics
Matches: 418, Mismatches: 82, Indels: 44
0.77 0.15 0.08
Matches are distributed among these distances:
41 1 0.00
42 31 0.07
43 3 0.01
44 309 0.74
45 3 0.01
47 2 0.00
49 2 0.00
50 30 0.07
51 37 0.09
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
Found at i:28565478 original size:227 final size:224
Alignment explanation
Indices: 28565034--28565648 Score: 603
Period size: 227 Copynumber: 2.7 Consensus size: 224
28565024 GAAACTACCG
* * * * * * * **
28565034 ATCCTATACATCTGAAATTGCAGTGGGA-CAAATTGAATCTACCATAGTGAATCTTATCTCCCTG
1 ATCCTATACCTCTGAAGTTGCAGT-AGATCAGATTAAAGCTACAATAGCAAATCTTATCTCCCTG
* * * * * *
28565098 AAGTTGCATTGGAGCAGATTGAAGCTATAAACCTAATCTCCCTGAAGTTGCAGTAGAGCAGATTG
65 AAGTTGCAGTGGAGTAGATTGAAGCTACAAATCTAATCTCCCTGAAGTTGCAGTGGAGTAGATTG
* * * ** * *
28565163 AAGCCACAAGTCTTATCTCTCTAAAGTTGTAGTGGAGCAGATTAAGGCCATAAGTCTTATTTCCC
130 AAGCTACAAATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAGGCCACAAGTCTTATCTCCC
* * *
28565228 TGAAGTTGCAGTGGAATAGATTGAAGCTACAA
195 CGAAGTTGCAGTAGAATAGATTGAAACT--AA
* * * *
28565260 ATCTTGTTTCCT-TGAAGTTGTAGTAGAAT-AGATTAAAGCTACAAGTTA-CAAATCTTATCTCC
1 ATCCT-ATACCTCTGAAGTTGCAGTAG-ATCAGATTAAAGCTACAA--TAGCAAATCTTATCTCC
* ** * * * *
28565322 CTGAAGTTGCAGTGGAATAGATACAAGTTACAAATCTTATCTTCCTGAAGTTACAGTGGAGTAGA
62 CTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCTAATCTCCCTGAAGTTGCAGTGGAGTAGA
** * * **
28565387 TACAAGTTACAAATCTTATCTCCCTAAAGTTACAGTGGAGCATATTGAA-GTTACAAGTCTTATC
127 TTGAAGCTACAAATCTTATCTCCCTAAAGTTACAGTGGAGCAGATT-AAGGCCACAAGTCTTATC
*
28565451 TCCCCGAAGTTGCAGTAGAGTAGATTGAAACTAA
191 TCCCCGAAGTTGCAGTAGAATAGATTGAAACTAA
* * * * *
28565485 ATCCTATACCTCTGAAGTTGCAGTAGATCGGATTAAATCTACCATAGCGAATCTTATCTCCTTGA
1 ATCCTATACCTCTGAAGTTGCAGTAGATCAGATTAAAGCTACAATAGCAAATCTTATCTCCCTGA
* * * * *
28565550 AGTGGCAGTGGAGTAGATTGAAGCTACGAGTCTCATCTCCCTGAAGTTGCAGCGGAGTAGATTGA
66 AGTTGCAGTGGAGTAGATTGAAGCTACAAATCTAATCTCCCTGAAGTTGCAGTGGAGTAGATTGA
* **
28565615 AACTACACTTCTTATAC-CCCTAAAGTTACAGTGG
131 AGCTACAAATCTTAT-CTCCCTAAAGTTACAGTGG
28565649 GTTAGAATAA
Statistics
Matches: 310, Mismatches: 69, Indels: 22
0.77 0.17 0.05
Matches are distributed among these distances:
223 2 0.01
224 102 0.33
225 33 0.11
226 26 0.08
227 143 0.46
228 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (224 bp):
ATCCTATACCTCTGAAGTTGCAGTAGATCAGATTAAAGCTACAATAGCAAATCTTATCTCCCTGA
AGTTGCAGTGGAGTAGATTGAAGCTACAAATCTAATCTCCCTGAAGTTGCAGTGGAGTAGATTGA
AGCTACAAATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAGGCCACAAGTCTTATCTCCCC
GAAGTTGCAGTAGAATAGATTGAAACTAA
Found at i:28566510 original size:26 final size:27
Alignment explanation
Indices: 28566471--28566522 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
28566461 ATTCTTTTAT
*
28566471 TTGTGCATTTTTA-TTTATTTATTATTA
1 TTGTGCATTATTATTTTATTT-TTATTA
28566498 TTGT-CATTATTATTTTATTTTTATT
1 TTGTGCATTATTATTTTATTTTTATT
28566523 CTTTTGTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.69
Consensus pattern (27 bp):
TTGTGCATTATTATTTTATTTTTATTA
Found at i:28567853 original size:22 final size:22
Alignment explanation
Indices: 28567823--28567864 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28567813 AGTCACTATA
*
28567823 AATTATAGTGACTAGTTTTTAT
1 AATTATAGTGACTAATTTTTAT
*
28567845 AATTTTAGTGACTAATTTTT
1 AATTATAGTGACTAATTTTT
28567865 TTCTCCACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (22 bp):
AATTATAGTGACTAATTTTTAT
Found at i:28568468 original size:25 final size:25
Alignment explanation
Indices: 28568439--28568486 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
28568429 TATTATGAAT
28568439 TTGATTCCTCAGATATGGAAATTTA
1 TTGATTCCTCAGATATGGAAATTTA
28568464 TTGATTCCTCAGATATGGAAATT
1 TTGATTCCTCAGATATGGAAATT
28568487 CAACAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (25 bp):
TTGATTCCTCAGATATGGAAATTTA
Found at i:28569907 original size:26 final size:27
Alignment explanation
Indices: 28569871--28569921 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
28569861 TAAAGTAACG
*
28569871 TTTTTCTAATTTAATCACTCTAATTTT
1 TTTTTCTAATTTAATCAATCTAATTTT
28569898 TTTTTC-AATTTAATCAATCTAATT
1 TTTTTCTAATTTAATCAATCTAATT
28569922 AAGATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTTCTAATTTAATCAATCTAATTTT
Found at i:28570367 original size:93 final size:93
Alignment explanation
Indices: 28570269--28570695 Score: 391
Period size: 93 Copynumber: 4.5 Consensus size: 93
28570259 GGTTATTTCC
* * * * *
28570269 GTTTAAGTTTATAGCTTTCTGTCACCTTTTAAAGCTCTTCTTTGGGTTTA-TCAGTCTTCTTTTC
1 GTTTAAGTTTATACCTTTTTGTCACCTTTTCAAGCTCTTCTTTGGGTTTACTGA-TCTCCTTTTC
* * *
28570333 GGGTT-TCAATAAAGACGATAGTCGCCTTC
65 GGGTTCT-GATAAAGACGATAGTCGCTTTT
* * * * *
28570362 ATTTAAATTTATACCTTTTTGTTACCTTTTCAATCTCTTCTTCTTCAGGTTTACTGATCTCCTTT
1 GTTTAAGTTTATACCTTTTTGTCACCTTTTCAAGCTCTTC-T-TT-GGGTTTACTGATCTCCTTT
* * **
28570427 TCGGGTTCTGATGAAGACGATAGCCATTTTT
63 TCGGGTTCTGATAAAGACGATAGTCGCTTTT
** * * * * *
28570458 GTTTAAGAATGTACCTTTCTGTCACCTTTTCAAGCTCTTCTTCGGGTTTACCGATCTCCTTTTCA
1 GTTTAAGTTTATACCTTTTTGTCACCTTTTCAAGCTCTTCTTTGGGTTTACTGATCTCCTTTTCG
* * * * *
28570523 AGTTCTGATGAAGACAATGGTCTCTTTT
66 GGTTCTGATAAAGACGATAGTCGCTTTT
*
28570551 GTTTAAGTTTATACCTTTTTG-CTACCTTTTCAAGCTCTTCTTCTTCGGGTTTATTGATCTCCTT
1 GTTTAAGTTTATACCTTTTTGTC-ACCTTTTCAAGCTCTTC-T-TT-GGGTTTACTGATCTCCTT
*
28570615 CTT-GGTTTC-GATAACA-ACGATAGTCGCTTTT
62 -TTCGGGTTCTGATAA-AGACGATAGTCGCTTTT
* *
28570646 GTTTAAGTTTATA-GTTTGTTGCCACCTTTTTCAAGCTCTTCTTTGGGTTT
1 GTTTAAGTTTATACCTTT-TTGTCACC-TTTTCAAGCTCTTCTTTGGGTTT
28570696 CTTCCTTTTG
Statistics
Matches: 270, Mismatches: 50, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
92 1 0.00
93 114 0.42
94 8 0.03
95 40 0.15
96 102 0.38
97 5 0.02
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.46
Consensus pattern (93 bp):
GTTTAAGTTTATACCTTTTTGTCACCTTTTCAAGCTCTTCTTTGGGTTTACTGATCTCCTTTTCG
GGTTCTGATAAAGACGATAGTCGCTTTT
Found at i:28571038 original size:18 final size:18
Alignment explanation
Indices: 28571015--28571050 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28571005 CAATTCGAGC
28571015 AATTATCTTATTTAGAGT
1 AATTATCTTATTTAGAGT
28571033 AATTATCTTATTTAGAGT
1 AATTATCTTATTTAGAGT
28571051 GACCAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (18 bp):
AATTATCTTATTTAGAGT
Found at i:28577244 original size:21 final size:21
Alignment explanation
Indices: 28577195--28577238 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28577185 CATTTTAATA
28577195 ATCCAATGGTTGAATTTGTTG
1 ATCCAATGGTTGAATTTGTTG
28577216 ATCCAATGGTTGAATTTGTTG
1 ATCCAATGGTTGAATTTGTTG
28577237 AT
1 AT
28577239 GTAATGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (21 bp):
ATCCAATGGTTGAATTTGTTG
Found at i:28579667 original size:49 final size:48
Alignment explanation
Indices: 28579608--28579708 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 48
28579598 TAAATTTTTA
*
28579608 ATTTATCAAACACTAGTTCAGTTTTAACCTATGTTACTCTTAACTCATC
1 ATTTATCAAACACTAGTTCAATTTTAACCTATGTTACTC-TAACTCATC
28579657 ATTTATCAAACACTAGTTCAATTTTAACCTATGTTACTCTAACTCATC
1 ATTTATCAAACACTAGTTCAATTTTAACCTATGTTACTCTAACTCATC
28579705 ATTT
1 ATTT
28579709 TTCTTTAAGT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 13 0.25
49 38 0.75
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.42
Consensus pattern (48 bp):
ATTTATCAAACACTAGTTCAATTTTAACCTATGTTACTCTAACTCATC
Found at i:28581446 original size:3 final size:3
Alignment explanation
Indices: 28581438--28581463 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28581428 TCCTCTTTCT
28581438 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
28581464 ATTATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:28589837 original size:23 final size:24
Alignment explanation
Indices: 28589791--28589841 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
28589781 TACATTGATT
28589791 AATTATAAATTCAATAAAGTTTCTA
1 AATTATAAATTCAATAAAG-TTCTA
28589816 AATTA-AAATTCAATATAA-TTCTA
1 AATTATAAATTCAATA-AAGTTCTA
28589839 AAT
1 AAT
28589842 AAACTCGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 8 0.32
24 10 0.40
25 7 0.28
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (24 bp):
AATTATAAATTCAATAAAGTTCTA
Found at i:28590138 original size:26 final size:25
Alignment explanation
Indices: 28590102--28590162 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
28590092 ACCTAACTTT
* *
28590102 TAAAAAATAAATTATATAAAATCTAA
1 TAAAATATAAATTATAAAAAAT-TAA
28590128 TAAAATATAAATTATAAAAAATTAA
1 TAAAATATAAATTATAAAAAATTAA
* *
28590153 TTAATTATAA
1 TAAAATATAA
28590163 TAAATATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 11 0.35
26 20 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
TAAAATATAAATTATAAAAAATTAA
Found at i:28596504 original size:37 final size:37
Alignment explanation
Indices: 28596454--28596531 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
28596444 TACGACAGGG
28596454 TTATATGGTTGCGTGTCACTTTTTATTTCAAGTATAA
1 TTATATGGTTGCGTGTCACTTTTTATTTCAAGTATAA
*
28596491 TTATATGGTTGCGTGTCACTTTTTATTTCAAGTATAG
1 TTATATGGTTGCGTGTCACTTTTTATTTCAAGTATAA
28596528 TTAT
1 TTAT
28596532 CACATGGTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.50
Consensus pattern (37 bp):
TTATATGGTTGCGTGTCACTTTTTATTTCAAGTATAA
Found at i:28598698 original size:6 final size:7
Alignment explanation
Indices: 28598677--28598702 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28598667 AATAAATAGC
28598677 AAATAAA
1 AAATAAA
28598684 AAATAAA
1 AAATAAA
28598691 AAATAAA
1 AAATAAA
28598698 AAATA
1 AAATA
28598703 CATGACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAATAAA
Found at i:28599019 original size:26 final size:28
Alignment explanation
Indices: 28598964--28599017 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
28598954 ATAAATACAT
* * *
28598964 TATAAAAAAATATGAGTATTTACATAAA
1 TATAAAAAAATATCAGTATTAAAATAAA
28598992 TATAAAAAAATATCAGT-TTAAAATAA
1 TATAAAAAAATATCAGTATTAAAATAA
28599018 TAACTATGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (28 bp):
TATAAAAAAATATCAGTATTAAAATAAA
Found at i:28607278 original size:27 final size:27
Alignment explanation
Indices: 28607248--28607307 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
28607238 ACCTACCGTT
*
28607248 CCTTTAGAGTTTGCCGTACATACTATC
1 CCTTCAGAGTTTGCCGTACATACTATC
28607275 CCTTCAGAGTTTGCCGTACATACTATC
1 CCTTCAGAGTTTGCCGTACATACTATC
28607302 CCTTCA
1 CCTTCA
28607308 ATGTTCGTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.35
Consensus pattern (27 bp):
CCTTCAGAGTTTGCCGTACATACTATC
Found at i:28607527 original size:27 final size:27
Alignment explanation
Indices: 28607456--28607528 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
28607446 CCTCAGATCT
** * *
28607456 CCACAAAGGCTTCCACATCATAAATCG
1 CCACAAAGGCTTCCATTTTATAAATCA
** *
28607483 CCACAAAGAATTCCATTTTATAAATTA
1 CCACAAAGGCTTCCATTTTATAAATCA
*
28607510 CCACAAAGGCTTCTATTTT
1 CCACAAAGGCTTCCATTTT
28607529 TTTGGCGTGT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (27 bp):
CCACAAAGGCTTCCATTTTATAAATCA
Found at i:28612371 original size:12 final size:12
Alignment explanation
Indices: 28612354--28612418 Score: 57
Period size: 12 Copynumber: 5.4 Consensus size: 12
28612344 ATATTTTAAT
28612354 AATTTAATATTA
1 AATTTAATATTA
28612366 AATTTAAT-TTA
1 AATTTAATATTA
28612377 ATATTT-ATATTA
1 A-ATTTAATATTA
*
28612389 ATAGTATT-TTATT-
1 A-A-T-TTAATATTA
28612402 AATTTAATATTA
1 AATTTAATATTA
28612414 AATTT
1 AATTT
28612419 TATTTAATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
10 2 0.04
11 11 0.24
12 24 0.53
13 2 0.04
14 6 0.13
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
AATTTAATATTA
Found at i:28612375 original size:17 final size:17
Alignment explanation
Indices: 28612353--28612426 Score: 66
Period size: 17 Copynumber: 4.5 Consensus size: 17
28612343 AATATTTTAA
28612353 TAATTTAATATTAAATT
1 TAATTTAATATTAAATT
*
28612370 TAATTTAATATT-TATAT
1 TAATTTAATATTAAAT-T
* **
28612387 TAA--TAGTATTTTA-T
1 TAATTTAATATTAAATT
28612401 TAATTTAATATTAAATT
1 TAATTTAATATTAAATT
*
28612418 TTATTTAAT
1 TAATTTAAT
28612427 GTTTATCTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 4 0.09
15 6 0.13
16 11 0.24
17 25 0.54
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
TAATTTAATATTAAATT
Found at i:28612391 original size:48 final size:48
Alignment explanation
Indices: 28612339--28612432 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
28612329 TTCAAAAAAA
28612339 TAATAATATTTTAATAATTTAATATTAAATTTAATTTAATATTTATAT
1 TAATAATATTTTAATAATTTAATATTAAATTTAATTTAATATTTATAT
* * * *
28612387 TAATAGTATTTTATTAATTTAATATTAAATTTTATTTAATGTTTAT
1 TAATAATATTTTAATAATTTAATATTAAATTTAATTTAATATTTAT
28612433 CTTGTAGATA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (48 bp):
TAATAATATTTTAATAATTTAATATTAAATTTAATTTAATATTTATAT
Found at i:28612539 original size:21 final size:22
Alignment explanation
Indices: 28612499--28612539 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
28612489 TTTATCTTGA
28612499 TAAAATTATATTAATTTAATAT
1 TAAAATTATATTAATTTAATAT
28612521 TAAAA-TA-ATTAAGTTTAAT
1 TAAAATTATATTAA-TTTAAT
28612540 CATAGTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TAAAATTATATTAATTTAATAT
Found at i:28612676 original size:23 final size:25
Alignment explanation
Indices: 28612629--28612677 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
28612619 AGTTGTAGAG
*
28612629 AGAAAATTCTCTAAAGAGATTATTTT
1 AGAAAATTCTCT-AAGAGATAATTTT
28612655 AGAAAATT-TCT-AGAGATAATTTT
1 AGAAAATTCTCTAAGAGATAATTTT
28612678 CTTATTTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 11 0.50
25 3 0.14
26 8 0.36
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (25 bp):
AGAAAATTCTCTAAGAGATAATTTT
Found at i:28616405 original size:24 final size:24
Alignment explanation
Indices: 28616378--28616425 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28616368 CCAAATGTTT
28616378 GAGTAAATGCTCTCAAAAGTATTC
1 GAGTAAATGCTCTCAAAAGTATTC
28616402 GAGTAAATGCTCTCAAAAGTATTC
1 GAGTAAATGCTCTCAAAAGTATTC
28616426 TCTTAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (24 bp):
GAGTAAATGCTCTCAAAAGTATTC
Found at i:28618543 original size:16 final size:17
Alignment explanation
Indices: 28618514--28618555 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
28618504 TATTTGTATA
28618514 TATTATATGCATATATG
1 TATTATATGCATATATG
*
28618531 TATT-TATGTATATATG
1 TATTATATGCATATATG
28618547 TATGTATAT
1 TAT-TATAT
28618556 AGTAAGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 14 0.64
17 5 0.23
18 3 0.14
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (17 bp):
TATTATATGCATATATG
Found at i:28618663 original size:27 final size:27
Alignment explanation
Indices: 28618611--28618672 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
28618601 GGAATACATA
* * *
28618611 ATGTATGTGTGTATATGTAATATATTT
1 ATGTATTTCTGTATATGTAATATATTC
*
28618638 ATGTATTTCTGTATATGTTAA-GTATTC
1 ATGTATTTCTGTATATG-TAATATATTC
*
28618665 ATGCATTT
1 ATGTATTT
28618673 TCCATGTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (27 bp):
ATGTATTTCTGTATATGTAATATATTC
Found at i:28626996 original size:46 final size:46
Alignment explanation
Indices: 28626925--28627086 Score: 249
Period size: 46 Copynumber: 3.6 Consensus size: 46
28626915 TACGTATGAT
* * *
28626925 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
*
28626969 CACTTATCATTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
*
28627015 CGCTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
*
28627061 CACTTATCACTTTGCCAC-TGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
28627087 AGTACTCAAA
Statistics
Matches: 108, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
44 9 0.08
45 13 0.12
46 86 0.80
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
Found at i:28628489 original size:16 final size:17
Alignment explanation
Indices: 28628457--28628489 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28628447 CAATTAACCC
28628457 CTCAATTAATCTAATTTT
1 CTCAATTAA-CTAATTTT
28628475 CTCAATTAA-TAATTT
1 CTCAATTAACTAATTT
28628490 ACCTAGACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
CTCAATTAACTAATTTT
Found at i:28649355 original size:25 final size:25
Alignment explanation
Indices: 28649294--28649406 Score: 90
Period size: 25 Copynumber: 4.6 Consensus size: 25
28649284 ATTCGAGAAT
28649294 GCTCATATGAGCACATA-AACGGGAA
1 GCTCATATGAGC-CATATAACGGGAA
* *
28649319 TCTC-TTTCGAGCCATATAACGGGAA
1 GCTCATAT-GAGCCATATAACGGGAA
* *
28649344 GCTCATATGAGCCATGTAGCGGGAA
1 GCTCATATGAGCCATATAACGGGAA
** **
28649369 GCTC-TGAAAAGCCAT-TAACAAGAA
1 GCTCAT-ATGAGCCATATAACGGGAA
*
28649393 GCTCATACGAGCCA
1 GCTCATATGAGCCA
28649407 ATATTGGGAA
Statistics
Matches: 70, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
24 23 0.33
25 45 0.64
26 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (25 bp):
GCTCATATGAGCCATATAACGGGAA
Found at i:28651563 original size:10 final size:10
Alignment explanation
Indices: 28651548--28651579 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
28651538 AAATCCTAAT
28651548 CCAAAATAAA
1 CCAAAATAAA
28651558 CCAAAATAAA
1 CCAAAATAAA
28651568 --AAAATAAA
1 CCAAAATAAA
28651576 CCAA
1 CCAA
28651580 CCCAAAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.40
10 12 0.60
ACGTcount: A:0.72, C:0.19, G:0.00, T:0.09
Consensus pattern (10 bp):
CCAAAATAAA
Found at i:28652915 original size:29 final size:30
Alignment explanation
Indices: 28652856--28652913 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28652846 TCCGAGCCTT
*
28652856 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
28652886 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
28652914 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:28656641 original size:15 final size:14
Alignment explanation
Indices: 28656606--28656648 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
28656596 TTCCTGTAGC
*
28656606 GATTTTTAGGTTTA
1 GATTTTTAGTTTTA
*
28656620 GACTTTTAGTTTTA
1 GATTTTTAGTTTTA
*
28656634 GGATTTTTATTTTTA
1 -GATTTTTAGTTTTA
28656649 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.21, C:0.02, G:0.16, T:0.60
Consensus pattern (14 bp):
GATTTTTAGTTTTA
Found at i:28658619 original size:22 final size:24
Alignment explanation
Indices: 28658576--28658619 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
28658566 GAGGTGCCAC
*
28658576 GTTTTTAAAGCACCACGTGTCATT
1 GTTTTTAAAGCACCACGGGTCATT
*
28658600 GTTTTT-AA-CACCATGGGTCA
1 GTTTTTAAAGCACCACGGGTCA
28658620 ATTTGGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 2 0.11
24 6 0.33
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (24 bp):
GTTTTTAAAGCACCACGGGTCATT
Found at i:28661157 original size:24 final size:22
Alignment explanation
Indices: 28661129--28661181 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 22
28661119 AAAAATACTA
28661129 AAAAAATT-AAAATAAATATTTCT
1 AAAAAATTAAAAATAAAT-TTT-T
28661152 GAAAAAATTAAAAATAAATTTTT
1 -AAAAAATTAAAAATAAATTTTT
28661175 AAAAAAT
1 AAAAAAT
28661182 ATGTATACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.25
23 1 0.04
24 11 0.39
25 9 0.32
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAAAATTAAAAATAAATTTTT
Found at i:28662968 original size:23 final size:23
Alignment explanation
Indices: 28662916--28662969 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
28662906 ATCGGAATTT
* *
28662916 AATTATAAATTTTTTATATATTA
1 AATTATAAATTTATTATATATGA
* *
28662939 AAATATAAATTTATTATGTATGA
1 AATTATAAATTTATTATATATGA
*
28662962 ATTTATAA
1 AATTATAA
28662970 TTTCATCATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (23 bp):
AATTATAAATTTATTATATATGA
Found at i:28666541 original size:33 final size:33
Alignment explanation
Indices: 28666497--28666596 Score: 128
Period size: 33 Copynumber: 3.0 Consensus size: 33
28666487 CAAACCTTCC
* *
28666497 ACGGAAGCCGCTGATTCCAAACCACCGGAGACG
1 ACGGAAACCGCTGATTCCAAACCACCGGCGACG
* *
28666530 ACGGAAACCGCTGGTTCCAAACCGCCGGCGACG
1 ACGGAAACCGCTGATTCCAAACCACCGGCGACG
* * * *
28666563 ACAGAAACCGCTGACTCCAAGCAACCGGCGACG
1 ACGGAAACCGCTGATTCCAAACCACCGGCGACG
28666596 A
1 A
28666597 AACCTTCGTC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.30, C:0.35, G:0.27, T:0.08
Consensus pattern (33 bp):
ACGGAAACCGCTGATTCCAAACCACCGGCGACG
Found at i:28666631 original size:42 final size:42
Alignment explanation
Indices: 28666578--28666735 Score: 217
Period size: 42 Copynumber: 3.8 Consensus size: 42
28666568 AACCGCTGAC
* *
28666578 TCCAAGCAACCGGCGACGAAACCTTCGTCGGAAACCCCGGAA
1 TCCAAACAACCGGCGACGAAACCTTCGACGGAAACCCCGGAA
*
28666620 TCCAAAAAACCGGCGACGAAACCTTCGACGGAAACCCCGGAA
1 TCCAAACAACCGGCGACGAAACCTTCGACGGAAACCCCGGAA
* ** *
28666662 TCCAAACCACCGGCGACGAAACCTTCGAAAGAAACCTCGGAA
1 TCCAAACAACCGGCGACGAAACCTTCGACGGAAACCCCGGAA
* * * *
28666704 TCTAAACAATCAGCGACGAAACCGTCGACGGA
1 TCCAAACAACCGGCGACGAAACCTTCGACGGA
28666736 CACAGCAGAA
Statistics
Matches: 101, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 101 1.00
ACGTcount: A:0.36, C:0.33, G:0.22, T:0.09
Consensus pattern (42 bp):
TCCAAACAACCGGCGACGAAACCTTCGACGGAAACCCCGGAA
Found at i:28667752 original size:43 final size:44
Alignment explanation
Indices: 28667673--28667762 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
28667663 TCAGTTTAGC
28667673 ATTAAAAAAAACAAAAAAACACTTTTGGGTCAAAAAAAAAAAGT
1 ATTAAAAAAAACAAAAAAACACTTTTGGGTCAAAAAAAAAAAGT
28667717 ATTAAAAAAAACAAAAAAACACTTTTGGGTC-AAAAAAAAAAGT
1 ATTAAAAAAAACAAAAAAACACTTTTGGGTCAAAAAAAAAAAGT
28667760 ATT
1 ATT
28667763 TTTAAAAGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 15 0.33
44 31 0.67
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.20
Consensus pattern (44 bp):
ATTAAAAAAAACAAAAAAACACTTTTGGGTCAAAAAAAAAAAGT
Found at i:28668007 original size:15 final size:17
Alignment explanation
Indices: 28667970--28668009 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
28667960 GGTTTATGTA
28667970 ATTATTTTTTAAAGAAG
1 ATTATTTTTTAAAGAAG
*
28667987 A-CATTTTTT-AAG-AG
1 ATTATTTTTTAAAGAAG
28668001 ATTATTTTT
1 ATTATTTTT
28668010 CTTTATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
14 3 0.15
15 9 0.45
16 7 0.35
17 1 0.05
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (17 bp):
ATTATTTTTTAAAGAAG
Found at i:28683932 original size:20 final size:18
Alignment explanation
Indices: 28683882--28683933 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
28683872 CTACAAGATA
28683882 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
28683899 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
28683919 AATATTAAATTAATA
1 AATATTAAATTAATA
28683934 AAATACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:28690397 original size:26 final size:26
Alignment explanation
Indices: 28690368--28690437 Score: 61
Period size: 26 Copynumber: 2.7 Consensus size: 26
28690358 ATTGATATAT
28690368 GGCTCTTCATGAGCTTCCCAATTAAA
1 GGCTCTTCATGAGCTTCCCAATTAAA
* ** ** * *
28690394 GGCTGTTTGTGAGCTTCCTGATTTAT
1 GGCTCTTCATGAGCTTCCCAATTAAA
*
28690420 GGCTCTCCA-GAGCTTCCC
1 GGCTCTTCATGAGCTTCCC
28690438 GATATAACTC
Statistics
Matches: 32, Mismatches: 12, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
25 8 0.25
26 24 0.75
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.34
Consensus pattern (26 bp):
GGCTCTTCATGAGCTTCCCAATTAAA
Found at i:28693408 original size:22 final size:24
Alignment explanation
Indices: 28693359--28693414 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 24
28693349 TCATTTTGTT
* *
28693359 TAAAAAAATACATAAATTTTATAA
1 TAAATAAATACATAAATTATATAA
28693383 -AAATAAATACA-AAATTATA-AA
1 TAAATAAATACATAAATTATATAA
*
28693404 TAAATGAATAC
1 TAAATAAATAC
28693415 CCATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 2 0.07
22 16 0.57
23 10 0.36
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (24 bp):
TAAATAAATACATAAATTATATAA
Found at i:28699270 original size:59 final size:56
Alignment explanation
Indices: 28699205--28699390 Score: 144
Period size: 59 Copynumber: 3.1 Consensus size: 56
28699195 ATGATAAATT
*
28699205 ATATATTTTTATTAACTTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATT
1 ATATATTTTTATTAA--TATATTTAATAATAATTAT-TTAAATTATATTTTATAGTATC
* * * * * *
28699264 ATATATTATGATT-TTAAAAAATTCATATAAGAA-TATTTAATATTAAGAATTTTATTA-AATC
1 ATATATT-T--TTATTAATATATTTA-ATAATAATTATTTAA-ATT-A-TATTTTA-TAGTATC
* *
28699325 ATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGTATC
1 ATATATTTTTATT--AATATATTTAATAATAATTATTT-AAATTATATTTTATAGTATC
28699384 ATATATT
1 ATATATT
28699391 ATGATTTGAG
Statistics
Matches: 98, Mismatches: 15, Indels: 28
0.70 0.11 0.20
Matches are distributed among these distances:
58 7 0.07
59 36 0.37
60 15 0.15
61 34 0.35
62 6 0.06
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (56 bp):
ATATATTTTTATTAATATATTTAATAATAATTATTTAAATTATATTTTATAGTATC
Found at i:28699316 original size:61 final size:60
Alignment explanation
Indices: 28699251--28699438 Score: 154
Period size: 61 Copynumber: 3.1 Consensus size: 60
28699241 GTTAAATTAT
*
28699251 ATTTTATAGTATTATATATTATGATTTTAAAAAATTCATATAAGAATATTTAATATTAAGA
1 ATTTTATAGTATCATATATTATGATTTTAAAAAATTCATATAAGAATATTTAATATTAA-A
* * * * * * *
28699312 ATTTTATTA-AATCATATATT-TTA-ATTAAAATATATTTAATATTA-ATTATTTCAA-ATT-AT
1 ATTTTA-TAGTATCATATATTATGATTTTAAAA-A-A-TTCATATAAGAATATTT-AATATTAAA
* ** * *
28699371 ATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAAA
1 ATTTTATAGTATCATATATTATGATTTTAAAAAATTCATATAAGAATATTTAATATT-AAA
28699432 ATTTTAT
1 ATTTTAT
28699439 TATAAATTAT
Statistics
Matches: 95, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
58 10 0.11
59 31 0.33
60 7 0.07
61 36 0.38
62 11 0.12
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (60 bp):
ATTTTATAGTATCATATATTATGATTTTAAAAAATTCATATAAGAATATTTAATATTAAA
Found at i:28699352 original size:120 final size:122
Alignment explanation
Indices: 28699198--28699488 Score: 444
Period size: 120 Copynumber: 2.4 Consensus size: 122
28699188 TAGTATGATG
* **
28699198 ATAAATTATATATTTTTATTAACTTATATTTAATAATAATTATGTTAAATTATATTTTATAGTAT
1 ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTAT
* * * *
28699263 TATATATTATGATTTTAAAAAATTCATATAAGAATATTTAATATTAAGAATTTTA-T
66 CATATATTATGATTTGAAAAAATTCATATAAGAATATTGAATATTAAAAATTTTATT
* *
28699319 -TAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTTTATAGTA
1 ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTTTATAGTA
** *
28699382 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAAAATTTTATT
65 TCATATATTATGATTTGAAAAAATTCATATAAGAATATTGAATATTAAAAATTTTATT
28699440 ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
28699489 ATATGATTAA
Statistics
Matches: 152, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
119 2 0.01
120 104 0.68
121 1 0.01
122 43 0.28
123 2 0.01
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (122 bp):
ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTAT
CATATATTATGATTTGAAAAAATTCATATAAGAATATTGAATATTAAAAATTTTATT
Found at i:28699467 original size:18 final size:19
Alignment explanation
Indices: 28699432--28699468 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
28699422 ATTATTAAAA
28699432 ATTTTATTATAAATTATAT
1 ATTTTATTATAAATTATAT
28699451 ATTTTAATTA-AAA-TATAT
1 ATTTT-ATTATAAATTATAT
28699469 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTATTATAAATTATAT
Found at i:28699698 original size:44 final size:45
Alignment explanation
Indices: 28699633--28699723 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
28699623 ACCTCTATTC
* * *
28699633 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
28699677 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
28699722 CA
1 CA
28699724 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:28699738 original size:17 final size:16
Alignment explanation
Indices: 28699704--28699756 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
28699694 GATTAGCTAT
28699704 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28699720 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
28699737 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28699753 TACA
1 TACA
28699757 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:28701084 original size:24 final size:23
Alignment explanation
Indices: 28701017--28701085 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
28701007 CTAATAGTTG
*
28701017 ATTTTAACT-TTAATGTTTAATTTA
1 ATTTTAAATCTTAAT-TTTAA-TTA
* * * *
28701041 ATTTTAATTTTTTATCTTAATTA
1 ATTTTAAATCTTAATTTTAATTA
28701064 ATTATTAAATCTTAATTTTAAT
1 ATT-TTAAATCTTAATTTTAAT
28701086 ATTCAATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
23 6 0.17
24 26 0.72
25 4 0.11
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (23 bp):
ATTTTAAATCTTAATTTTAATTA
Found at i:28703372 original size:20 final size:20
Alignment explanation
Indices: 28703343--28703383 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
28703333 CTAGACCGAA
*
28703343 TTAACTTTGGGTCAACTAAG
1 TTAACATTGGGTCAACTAAG
28703363 TTAACATTGGGTCAACTAAG
1 TTAACATTGGGTCAACTAAG
28703383 T
1 T
28703384 CTGCTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (20 bp):
TTAACATTGGGTCAACTAAG
Found at i:28717440 original size:30 final size:29
Alignment explanation
Indices: 28717406--28717542 Score: 98
Period size: 30 Copynumber: 4.6 Consensus size: 29
28717396 CAAAAAATAC
28717406 AAATTACATTTTAGCCCCTGAATTTTTCAA
1 AAATTACATTTTAGCCCCT-AATTTTTCAA
* *
28717436 AAATTACATTTT-GACCCCTATTTTTTTCTA
1 AAATTACATTTTAG-CCCCTA-ATTTTTCAA
* * * * **
28717466 AATTTACATCTTAACCCCTAATAATTT-GT
1 AAATTACATTTTAGCCCCTAAT-TTTTCAA
** **
28717495 AAATTACATTTGGGCCCCTAAACTTTCTAA
1 AAATTACATTTTAGCCCCTAATTTTTC-AA
*
28717525 AAATTACATTTTGGCCCC
1 AAATTACATTTTAGCCCC
28717543 ATATTTTCCT
Statistics
Matches: 82, Mismatches: 19, Indels: 12
0.73 0.17 0.11
Matches are distributed among these distances:
28 3 0.04
29 19 0.23
30 60 0.73
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (29 bp):
AAATTACATTTTAGCCCCTAATTTTTCAA
Found at i:28717980 original size:18 final size:19
Alignment explanation
Indices: 28717959--28718000 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
28717949 CCAAAAAAAA
*
28717959 AAGAGAA-AATAAGAGAAG
1 AAGAGAAGAAGAAGAGAAG
28717977 AAGA-AAGAAGAAGAGAAG
1 AAGAGAAGAAGAAGAGAAG
*
28717995 AGGAGA
1 AAGAGA
28718001 TGCCGAAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 17 0.85
19 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.02
Consensus pattern (19 bp):
AAGAGAAGAAGAAGAGAAG
Found at i:28718082 original size:8 final size:7
Alignment explanation
Indices: 28718068--28718118 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
28718058 GAAGGAAAGG
28718068 AAGAAGA
1 AAGAAGA
28718075 AGAGAAGA
1 A-AGAAGA
28718083 AAGAAGGA
1 AAGAA-GA
28718091 AA-AA-A
1 AAGAAGA
28718096 AAGAA-A
1 AAGAAGA
*
28718102 AAAAAGA
1 AAGAAGA
28718109 AAGAAGA
1 AAGAAGA
28718116 AAG
1 AAG
28718119 GGAAAGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 3 0.08
6 7 0.18
7 17 0.45
8 11 0.29
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:28718089 original size:22 final size:22
Alignment explanation
Indices: 28718064--28718148 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 22
28718054 GGTCGAAGGA
* * *
28718064 AAGGAAGAAGAAGAGAAGAAAG
1 AAGGAAGAAAAAGAAAAAAAAG
*
28718086 AAGGAAAAAAAAGAAAAAAAAG
1 AAGGAAGAAAAAGAAAAAAAAG
* **
28718108 AAAGAAGAAAGGGAAAGAAAAA-
1 AAGGAAGAAAAAGAAA-AAAAAG
28718130 AAGGGAA-AAAAAGAAAAAA
1 AA-GGAAGAAAAAGAAAAAA
28718149 GAAAAAATAG
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
21 3 0.06
22 39 0.78
23 8 0.16
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (22 bp):
AAGGAAGAAAAAGAAAAAAAAG
Found at i:28718100 original size:13 final size:14
Alignment explanation
Indices: 28718063--28718152 Score: 62
Period size: 13 Copynumber: 6.5 Consensus size: 14
28718053 AGGTCGAAGG
*
28718063 AAAGGAAGAAGAAGA
1 AAAGAAAGAAGAA-A
* *
28718078 GAAGAAAGAAGGAA
1 AAAGAAAGAAGAAA
28718092 AAA-AAAGAA-AAA
1 AAAGAAAGAAGAAA
28718104 AAAGAAAGAAG-AA
1 AAAGAAAGAAGAAA
**
28718117 AGGGAAAGAA-AAA
1 AAAGAAAGAAGAAA
* *
28718130 AAGGGAAAAAAAGAAA
1 AA-AG-AAAGAAGAAA
28718146 AAAGAAA
1 AAAGAAA
28718153 AAATAGAATA
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
12 5 0.08
13 25 0.42
14 8 0.14
15 16 0.27
16 5 0.08
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAGAAA
Found at i:28718101 original size:9 final size:9
Alignment explanation
Indices: 28718089--28718160 Score: 53
Period size: 9 Copynumber: 8.3 Consensus size: 9
28718079 AAGAAAGAAG
28718089 GAAAAAAAA
1 GAAAAAAAA
28718098 GAAAAAAAA
1 GAAAAAAAA
*
28718107 G--AAAGAA
1 GAAAAAAAA
**
28718114 GAAAGGGAAA
1 GAAA-AAAAA
*
28718124 GAAAAAAAG
1 GAAAAAAAA
*
28718133 GGAAAAAAA
1 GAAAAAAAA
28718142 G--AAAAAA
1 GAAAAAAAA
*
28718149 GAAAAAATA
1 GAAAAAAAA
28718158 GAA
1 GAA
28718161 TAGTCGGGTC
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
7 13 0.27
9 29 0.60
10 6 0.12
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:28718115 original size:44 final size:44
Alignment explanation
Indices: 28718062--28718148 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
28718052 AAGGTCGAAG
28718062 GAAAGGAAG-AA-GAAGAGAAGAAAGAAGGAAAAAAAAGAAAAAAAA
1 GAAAGGAAGAAAGGAA-AGAA-AAA-AAGGAAAAAAAAGAAAAAAAA
*
28718107 GAAA-GAAGAAAGGGAAAGAAAAAAAGGGAAAAAAAGAAAAAA
1 GAAAGGAAGAAA-GGAAAGAAAAAAAGGAAAAAAAAGAAAAAA
28718149 GAAAAAATAG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
44 22 0.58
45 9 0.24
46 4 0.11
47 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (44 bp):
GAAAGGAAGAAAGGAAAGAAAAAAAGGAAAAAAAAGAAAAAAAA
Found at i:28718139 original size:35 final size:33
Alignment explanation
Indices: 28718071--28718152 Score: 101
Period size: 35 Copynumber: 2.4 Consensus size: 33
28718061 GGAAAGGAAG
*
28718071 AAGAAGAGAAGAAAGAAGGAAAAAAAAGAAAAAA
1 AAGAA-AGAAGAAAGAAAGAAAAAAAAGAAAAAA
* *
28718105 AAGAAAGAAGAAAGGGAAAGAAAAAAAGGGAAAAA
1 AAGAAAGAAGAAA--GAAAGAAAAAAAAGAAAAAA
*
28718140 AAGAAAAAAGAAA
1 AAGAAAGAAGAAA
28718153 AAATAGAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
33 8 0.19
34 5 0.12
35 29 0.69
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (33 bp):
AAGAAAGAAGAAAGAAAGAAAAAAAAGAAAAAA
Found at i:28718308 original size:24 final size:25
Alignment explanation
Indices: 28718281--28718328 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
28718271 CAAGCAGTCC
28718281 AAAGCAAAAAAAAA-GAAGAAGGCA
1 AAAGCAAAAAAAAAGGAAGAAGGCA
*
28718305 AAAGCAAAAAAAAAGGAAGCAGGC
1 AAAGCAAAAAAAAAGGAAGAAGGC
28718329 CAACAGCAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.67, C:0.10, G:0.23, T:0.00
Consensus pattern (25 bp):
AAAGCAAAAAAAAAGGAAGAAGGCA
Found at i:28718450 original size:7 final size:7
Alignment explanation
Indices: 28718438--28718492 Score: 67
Period size: 7 Copynumber: 7.7 Consensus size: 7
28718428 CCGCCCAGCC
28718438 AAAAAAG
1 AAAAAAG
28718445 AAAAAAG
1 AAAAAAG
28718452 AGAAAAA-
1 A-AAAAAG
*
28718459 AAGAAAAA
1 AA-AAAAG
28718467 AAAAAAG
1 AAAAAAG
28718474 AAAAAAG
1 AAAAAAG
*
28718481 AAGAAAG
1 AAAAAAG
28718488 AAAAA
1 AAAAA
28718493 GGGCCCAAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
6 1 0.02
7 34 0.81
8 7 0.17
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:28718465 original size:22 final size:22
Alignment explanation
Indices: 28718440--28718492 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
28718430 GCCCAGCCAA
28718440 AAAAGAAAAAAGAGAAAAA-AAG
1 AAAAGAAAAAAGA-AAAAAGAAG
*
28718462 AAAAAAAAAAAGAAAAAAGAAG
1 AAAAGAAAAAAGAAAAAAGAAG
28718484 -AAAGAAAAA
1 AAAAGAAAAA
28718493 GGGCCCAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAAGAAAAAAGAAG
Found at i:28718477 original size:17 final size:17
Alignment explanation
Indices: 28718438--28718492 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
28718428 CCGCCCAGCC
*
28718438 AAAAAAGAAAAAAGAGA
1 AAAAAAGAAAAAAGAAA
*
28718455 AAAAAAGAAAAAAAAAAA
1 AAAAAAG-AAAAAAGAAA
*
28718473 GAAAAAAGAAGAAAGAAA
1 -AAAAAAGAAAAAAGAAA
28718491 AA
1 AA
28718493 GGGCCCAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 9 0.28
18 16 0.50
19 7 0.22
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAGAAA
Found at i:28718484 original size:10 final size:10
Alignment explanation
Indices: 28718438--28718486 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
28718428 CCGCCCAGCC
28718438 AAAA-AAGAA
1 AAAAGAAGAA
28718447 AAAAG-AGAAA
1 AAAAGAAG-AA
28718457 AAAAGAA-AA
1 AAAAGAAGAA
*
28718466 AAAAAAAGAA
1 AAAAGAAGAA
28718476 AAAAGAAGAA
1 AAAAGAAGAA
28718486 A
1 A
28718487 GAAAAAGGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
9 14 0.41
10 19 0.56
11 1 0.03
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAGAAGAA
Found at i:28719083 original size:18 final size:17
Alignment explanation
Indices: 28719050--28719267 Score: 214
Period size: 18 Copynumber: 12.5 Consensus size: 17
28719040 TTTCTTTTAA
*
28719050 AAAAAATTCGTG-TTTC
1 AAAAATTTCGTGTTTTC
28719066 AAAAATCTTCGTGTTTTC
1 AAAAAT-TTCGTGTTTTC
28719084 AAAAATTTC-TGTGTTTC
1 AAAAATTTCGTGT-TTTC
28719101 AAAAATCTTCGTGTTTTC
1 AAAAAT-TTCGTGTTTTC
28719119 -AAAATTTCCGATGTTTT-
1 AAAAATTT-CG-TGTTTTC
28719136 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTGTTTTC
* *
28719154 AAAAAATTCCTGTCTTTC
1 AAAAATTTCGTGT-TTTC
28719172 AAAAATTTCGTTGTTTTC
1 AAAAATTTCG-TGTTTTC
28719190 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTGTTTTC
* * *
28719208 AACAATTCCCATG-TTTC
1 AAAAATT-TCGTGTTTTC
*
28719225 ACAAATTTCCGTGTTTTC
1 AAAAATTT-CGTGTTTTC
*
28719243 AAAAATTTTCGTATTTT-
1 AAAAA-TTTCGTGTTTTC
28719260 AAAAATTT
1 AAAAATTT
28719268 TTGTGTTCTT
Statistics
Matches: 171, Mismatches: 14, Indels: 34
0.78 0.06 0.16
Matches are distributed among these distances:
16 13 0.08
17 57 0.33
18 84 0.49
19 17 0.10
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.45
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:28719098 original size:35 final size:35
Alignment explanation
Indices: 28719050--28719315 Score: 212
Period size: 35 Copynumber: 7.6 Consensus size: 35
28719040 TTTCTTTTAA
*
28719050 AAAAAATTC-GTGTTTCAAAAATCTTCGTGTTTTC
1 AAAAATTTCTGTGTTTCAAAAATCTTCGTGTTTTC
28719084 AAAAATTTCTGTGTTTCAAAAATCTTCGTGTTTTC
1 AAAAATTTCTGTGTTTCAAAAATCTTCGTGTTTTC
* * *
28719119 -AAAATTTCCGATGTTTTAAAAATTTTCGTGTTTTC
1 AAAAATTTCTG-TGTTTCAAAAATCTTCGTGTTTTC
* *
28719154 AAAAAATTCCTGTCTTTCAAAAAT-TTCGTTGTTTTC
1 -AAAAATTTCTGTGTTTCAAAAATCTTCG-TGTTTTC
* * *
28719190 AAAAATTT-TCGTGTTTTCAACAAT-TCCCATG-TTTC
1 AAAAATTTCT-GTG-TTTCAAAAATCT-TCGTGTTTTC
* * * *
28719225 ACAAATTTCCGTGTTTTCAAAAATTTTCGTATTTT-
1 AAAAATTTCTGTG-TTTCAAAAATCTTCGTGTTTTC
* * *
28719260 AAAAATTTTTGTG-TTCTTAAAATGC-TCGTATTTT-
1 AAAAATTTCTGTGTTTC-AAAAAT-CTTCGTGTTTTC
*
28719294 AAAAGTTT-TCGTGTTTCAAAAA
1 AAAAATTTCT-GTGTTTCAAAAA
28719316 AAATTCTCAT
Statistics
Matches: 191, Mismatches: 26, Indels: 30
0.77 0.11 0.12
Matches are distributed among these distances:
33 4 0.02
34 46 0.24
35 99 0.52
36 33 0.17
37 9 0.05
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (35 bp):
AAAAATTTCTGTGTTTCAAAAATCTTCGTGTTTTC
Found at i:28719134 original size:53 final size:51
Alignment explanation
Indices: 28719050--28719315 Score: 233
Period size: 53 Copynumber: 5.1 Consensus size: 51
28719040 TTTCTTTTAA
*
28719050 AAAAAATTCGTGTTTCAAAAATCTTCGTGTTTTCAAAAA-TTTC-TGTGTTTC
1 AAAAATTTCGTGTTTCAAAAAT-TTCGTGTTTTCAAAAATTTTCGTGT-TTTC
28719101 AAAAATCTTCGTGTTTTC-AAAATTTCCGATGTTTT-AAAAATTTTCGTGTTTTC
1 AAAAAT-TTCGTG-TTTCAAAAATTT-CG-TGTTTTCAAAAATTTTCGTGTTTTC
* *
28719154 AAAAAATTCCTGTCTTTCAAAAATTTCGTTGTTTTCAAAAATTTTCGTGTTTTC
1 -AAAAATTTC-GTGTTTCAAAAATTTCG-TGTTTTCAAAAATTTTCGTGTTTTC
* * * * *
28719208 AACAATTCCCATGTTTCACAAATTTCCGTGTTTTCAAAAATTTTCGTATTTT-
1 AAAAATT-TCGTGTTTCAAAAATTT-CGTGTTTTCAAAAATTTTCGTGTTTTC
* * * * *
28719260 AAAAATTT-TTGTGTTCTTAAAATGCTCGTATTTT-AAAAGTTTTCGTG-TTTC
1 AAAAATTTCGTGT-TTC-AAAAAT-TTCGTGTTTTCAAAAATTTTCGTGTTTTC
28719311 AAAAA
1 AAAAA
28719316 AAATTCTCAT
Statistics
Matches: 181, Mismatches: 18, Indels: 32
0.78 0.08 0.14
Matches are distributed among these distances:
50 6 0.03
51 26 0.14
52 35 0.19
53 74 0.41
54 40 0.22
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (51 bp):
AAAAATTTCGTGTTTCAAAAATTTCGTGTTTTCAAAAATTTTCGTGTTTTC
Found at i:28719268 original size:17 final size:17
Alignment explanation
Indices: 28719056--28719315 Score: 195
Period size: 17 Copynumber: 14.9 Consensus size: 17
28719046 TTAAAAAAAA
* *
28719056 TTCGTGTTTCAAAAATC
1 TTCGTGTTTTAAAAATT
28719073 TTCGTGTTTTCAAAAA-T
1 TTCGTGTTTT-AAAAATT
* *
28719090 TTCTGTGTTTCAAAAATC
1 TTC-GTGTTTTAAAAATT
*
28719108 TTCGTGTTTTCAAAATT
1 TTCGTGTTTTAAAAATT
*
28719125 TCCGATGTTTTAAAAATT
1 TTCG-TGTTTTAAAAATT
*
28719143 TTCGTGTTTTCAAAAA-A
1 TTCGTGTTTT-AAAAATT
*
28719160 TTCCTGTCTTTCAAAAA-T
1 TTCGTGT-TTT-AAAAATT
28719178 TTCGTTGTTTTCAAAAATT
1 TTCG-TGTTTT-AAAAATT
*
28719197 TTCGTGTTTTCAACAATT
1 TTCGTGTTTT-AAAAATT
** * * *
28719215 CCCATGTTTCACAAATT
1 TTCGTGTTTTAAAAATT
*
28719232 TCCGTGTTTTCAAAAATT
1 TTCGTGTTTT-AAAAATT
*
28719250 TTCGTATTTTAAAAATT
1 TTCGTGTTTTAAAAATT
* *
28719267 TTTGTGTTCTT-AAAATG
1 TTCGTGTT-TTAAAAATT
* * *
28719284 CTCGTATTTTAAAAGTT
1 TTCGTGTTTTAAAAATT
*
28719301 TTCGTGTTTCAAAAA
1 TTCGTGTTTTAAAAA
28719316 AAATTCTCAT
Statistics
Matches: 193, Mismatches: 39, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
16 2 0.01
17 93 0.48
18 90 0.47
19 8 0.04
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (17 bp):
TTCGTGTTTTAAAAATT
Found at i:28723018 original size:9 final size:9
Alignment explanation
Indices: 28723004--28723028 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28722994 CGAACTCAAT
28723004 GAAAGGATG
1 GAAAGGATG
28723013 GAAAGGATG
1 GAAAGGATG
28723022 GAAAGGA
1 GAAAGGA
28723029 CCCAAAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (9 bp):
GAAAGGATG
Found at i:28731293 original size:75 final size:76
Alignment explanation
Indices: 28731082--28731815 Score: 743
Period size: 75 Copynumber: 9.7 Consensus size: 76
28731072 CAAGAAATAT
*** * *
28731082 TTTTCAATTTCTGTTTTT-TTTAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTTGGG-CAC
1 TTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
28731145 ATGCC-AAGGTA
66 AT-CCTGAGGTA
* * *
28731156 TTTCTCAATTTCTGTTTTTCAAAAAAAAATTAACTCATAATGCGAGAGGTGGGTTGAGCCTCGAG
1 TTT-TCAATTTCTGTTTTTC---AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
28731221 TCACATCCTGAGGTA
62 TCACATCCTGAGGTA
* * *
28731236 TTTTCAATTTCTATTTTTC-AAAAATCAACTCATAATGCGAGAAGTGAGTTAAGCCTCGGG-C-C
1 TTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
28731298 A-CGCTGAGGTA
66 ATC-CTGAGGTA
* ** * *
28731309 TTTTTAATTTCTACTTTTCAAAAATATCAACTCATATTGCGATAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAA-ATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
28731374 C--GCTGAGGTA
65 CATCCTGAGGTA
* ** *
28731384 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGTCA
1 TTTTCAATTTCTGTTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
**
28731449 CATGTTGAGGTA
65 CATCCTGAGGTA
* * * *
28731461 TATTTTAATTTCT-ATTTTCCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTTA
1 T-TTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
28731525 C--GCTGAGGTA
65 CATCCTGAGGTA
* * * *
28731535 TTTTTAATTCCTGTTTTCCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTTA
1 TTTTCAATTTCTGTTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
28731600 C--GCTGAGGTA
65 CATCCTGAGGTA
* *
28731610 TTTTTAATTTCTTGTTTTCCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-C
1 TTTTCAATTTC-TGTTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC
* *
28731674 -TATACGCTGAGGCA
64 ACAT-C-CTGAGGTA
* * * * *
28731688 TTTTTAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTAGGGTCAT
1 TTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
28731752 ATGCC-AAGGTA
66 AT-CCTGAGGTA
* ** *
28731763 TTTTTCAATTTCTATTTTTC-AAAGGTCAACTCATAAT-CTGAGAAGTGAGTTGA
1 -TTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGC-GAGAGGTGAGTTGA
28731816 ACTTCGAATC
Statistics
Matches: 572, Mismatches: 61, Indels: 52
0.84 0.09 0.08
Matches are distributed among these distances:
72 1 0.00
73 37 0.06
74 21 0.04
75 252 0.44
76 143 0.25
77 26 0.05
78 28 0.05
79 51 0.09
80 13 0.02
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (76 bp):
TTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
ATCCTGAGGTA
Found at i:28731511 original size:226 final size:224
Alignment explanation
Indices: 28731103--28731815 Score: 896
Period size: 226 Copynumber: 3.1 Consensus size: 224
28731093 TGTTTTTTTT
* * **
28731103 AAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTTGGG-CACATGCCAAGGTATTTCTCAATTT
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC--GCTGAGGTATTT-TCAATTT
* * *
28731167 CTGTTTTTCAAAAAAAAATTAACTCATAATGCGAGAGGTGGGTTGAGCCTCGAGTCACATCCTGA
63 CTGTTTTTC--AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG-GTCACATGCTGA
* *
28731232 GGTATTTTCAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTAAGCCTCGGGC
125 GGTATTTTTAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGC
*
28731297 CACGCTGAGGTATTTTTAATTTCTACTTTTCAAAA
190 TACGCTGAGGTATTTTTAATTTCTACTTTTCAAAA
* * *
28731332 ATATCAACTCATATTGCGATAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTCTG
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTCTG
* ** *
28731397 TTTTTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGTCACATGTTGAGGTAT
66 TTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GGTCACATGCTGAGGTAT
* * *
28731462 ATTTTAATTTCTATTTTCCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTTACG
130 -TTTTAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGCTACG
* *
28731527 CTGAGGTATTTTTAATTCCT-GTTTTCCAAAA
194 CTGAGGTATTTTTAATTTCTACTTTT-CAAAA
* *
28731558 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTTACGCTGAGGTATTTTTAATTTCTT
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTC-T
* * * * *
28731623 GTTTTCCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCTATACGCTGAGGCA
65 GTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGTC-ACATGCTGAGGTA
* * * *
28731688 TTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTAGGGTCATA
129 TTTTTAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGG-C-TA
* ** *
28731753 TGCCAAGGTATTTTTCAATTTCTATTTTTC--AA
192 CGCTGAGGTATTTTT-AATTTCTACTTTTCAAAA
** *
28731785 AGGTCAACTCATAAT-CTGAGAAGTGAGTTGA
1 AAATCAACTCATAATGC-GAGAGGTGAGTTGA
28731816 ACTTCGAATC
Statistics
Matches: 423, Mismatches: 50, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
225 54 0.13
226 199 0.47
227 98 0.23
228 24 0.06
229 41 0.10
230 7 0.02
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (224 bp):
AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTCTG
TTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGTCACATGCTGAGGTATT
TTTAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGCTACGCT
GAGGTATTTTTAATTTCTACTTTTCAAAA
Found at i:28731528 original size:151 final size:148
Alignment explanation
Indices: 28731082--28731815 Score: 807
Period size: 151 Copynumber: 4.9 Consensus size: 148
28731072 CAAGAAATAT
*** * * * *
28731082 TTTTCAATTTCTGTTTTTTTTAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCT-TGGGCACA
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCAGGTCACA
** * * * * *
28731146 TGCCAAGGTATTTCTCAATTTCTGTTTTTCAAAAAAAAATTAACTCATAATGCGAGAGGTGGGTT
66 TGCTGAGGTATTT-TTAATTTCT-ATTTTC---CAAAAATCAACTCATAATGCGAGAGGTGAGTT
* *
28731211 GAGCCTCGAGTCACATCCTGAGGTA
126 GAGCCTCGGGTCAC--GCTGAGGTA
* * *
28731236 TTTTCAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTAAGCCTC-GGGC-CA
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCAGGTCACA
* * * *
28731299 CGCTGAGGTATTTTTAATTTCTACTTTTCAAAAATATCAACTCATATTGCGATAGGTGAGTTGAG
66 TGCTGAGGTATTTTTAATTTCTA-TTTTCCAAAA-ATCAACTCATAATGCGAGAGGTGAGTTGAG
28731364 CCTCGGGTCACGCTGAGGTA
129 CCTCGGGTCACGCTGAGGTA
* *
28731384 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGTCA
1 TTTTCAATTTCTGTTTTTC--AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCAGGTCA
*
28731449 CATGTTGAGGTATATTTTAATTTCTATTTTCCAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
64 CATGCTGAGGTAT-TTTTAATTTCTATTTTCCAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
*
28731514 GCCTCGGGTTACGCTGAGGTA
128 GCCTCGGGTCACGCTGAGGTA
* * * * * *
28731535 TTTTTAATTCCTGTTTTCCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTTA
1 TTTTCAATTTCTGTTTTTC--AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCAGGTCA
*
28731600 C--GCTGAGGTATTTTTAATTTCTTGTTTTCCAAAAAAATCAACTCATAATGCGAGAGGTGAGTT
64 CATGCTGAGGTATTTTTAATTTC-TATTTTCC--AAAAATCAACTCATAATGCGAGAGGTGAGTT
* *
28731663 GAGCCTCGGGCTATACGCTGAGGCA
126 GAGCCTCGGG-T-CACGCTGAGGTA
* * * *
28731688 TTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCT-AGGGTCAT
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCA-GGTCAC
** * ** *
28731752 ATGCCAAGGTATTTTTCAATTTCTATTTTTCAAAGGTCAACTCATAAT-CTGAGAAGTGAGTTGA
65 ATGCTGAGGTATTTTT-AATTTCTATTTTCCAAAAATCAACTCATAATGC-GAGAGGTGAGTTGA
28731816 ACTTCGAATC
Statistics
Matches: 508, Mismatches: 54, Indels: 39
0.85 0.09 0.06
Matches are distributed among these distances:
148 36 0.07
149 21 0.04
150 72 0.14
151 216 0.43
152 34 0.07
153 70 0.14
154 59 0.12
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (148 bp):
TTTTCAATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCAGGTCACA
TGCTGAGGTATTTTTAATTTCTATTTTCCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCC
TCGGGTCACGCTGAGGTA
Found at i:28732240 original size:29 final size:30
Alignment explanation
Indices: 28732134--28732289 Score: 112
Period size: 30 Copynumber: 5.3 Consensus size: 30
28732124 CAAAAAATAC
*
28732134 AAATTACATTTTAG-CCCCTGAACT--TTTCAA
1 AAATTACA-TTTAGACCCCT-AA-TAATTTCTA
* **
28732164 AAATTACATTTTGACCCCTAATTTTTTCTA
1 AAATTACATTTAGACCCCTAATAATTTCTA
*
28732194 AAATTACATCTTA-ACCCCTAATAATTTGT-
1 AAATTACAT-TTAGACCCCTAATAATTTCTA
* *
28732223 AAATTACATTTAGGCCCCTAA-ACTTTCTAA
1 AAATTACATTTAGACCCCTAATAATTTCT-A
* * *
28732253 AAATTACATTTTG-GCCCT-ATATTTTCCTA
1 AAATTACATTTAGACCCCTAATAATTT-CTA
28732282 AAATTACA
1 AAATTACA
28732290 CTTTTATCCT
Statistics
Matches: 105, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
28 10 0.10
29 39 0.37
30 54 0.51
31 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (30 bp):
AAATTACATTTAGACCCCTAATAATTTCTA
Found at i:28732588 original size:15 final size:15
Alignment explanation
Indices: 28732568--28732601 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
28732558 GTCGATTCCC
*
28732568 CCACCGTCACCGCAA
1 CCACCGCCACCGCAA
28732583 CCACCGCCACCGCAA
1 CCACCGCCACCGCAA
28732598 CCAC
1 CCAC
28732602 AACACCGCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.59, G:0.12, T:0.03
Consensus pattern (15 bp):
CCACCGCCACCGCAA
Found at i:28732692 original size:11 final size:11
Alignment explanation
Indices: 28732671--28732700 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
28732661 AACCAAAAAA
28732671 AAGAGAA-AAG
1 AAGAGAAGAAG
28732681 AAGAGAAGAAG
1 AAGAGAAGAAG
28732692 AAGAGAAGA
1 AAGAGAAGA
28732701 GGAGATGCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (11 bp):
AAGAGAAGAAG
Found at i:28732796 original size:7 final size:7
Alignment explanation
Indices: 28732786--28732871 Score: 59
Period size: 7 Copynumber: 12.0 Consensus size: 7
28732776 AGGTCGAAGG
*
28732786 GAAGGAA
1 GAAGAAA
28732793 GAAGAAGA
1 GAAGAA-A
28732801 GAAGAAA
1 GAAGAAA
*
28732808 GAAGGAA
1 GAAGAAA
28732815 GAA-AAA
1 GAAGAAA
*
28732821 AAAGAAA
1 GAAGAAA
28732828 GAAGAAA
1 GAAGAAA
*
28732835 G-GGAAA
1 GAAGAAA
*
28732841 GAAAAAAA
1 G-AAGAAA
*
28732849 GGGAAAAAA
1 --GAAGAAA
28732858 GAAGAAA
1 GAAGAAA
*
28732865 AAAGAAA
1 GAAGAAA
28732872 AAAATAGAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
6 9 0.14
7 37 0.59
8 10 0.16
9 6 0.10
10 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
GAAGAAA
Found at i:28732804 original size:15 final size:16
Alignment explanation
Indices: 28732781--28732832 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
28732771 GAGCAAGGTC
* *
28732781 GAAGGGAAGGAAGAA-
1 GAAGAGAAGAAAGAAG
28732796 GAAGAGAAGAAAGAAG
1 GAAGAGAAGAAAGAAG
* * *
28732812 GAAGAAAAAAAAGAAA
1 GAAGAGAAGAAAGAAG
28732828 GAAGA
1 GAAGA
28732833 AAGGGAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
15 13 0.42
16 18 0.58
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (16 bp):
GAAGAGAAGAAAGAAG
Found at i:28732830 original size:27 final size:28
Alignment explanation
Indices: 28732795--28732880 Score: 81
Period size: 27 Copynumber: 3.1 Consensus size: 28
28732785 GGAAGGAAGA
28732795 AGAAGAGAAGAAAGAAGGAAGAAAAAAA-
1 AGAA-AGAAGAAAGAAGGAAGAAAAAAAG
28732823 AGAAAGAAGAAAG--GGAAAGAAAAAAAG
1 AGAAAGAAGAAAGAAGG-AAGAAAAAAAG
* * ** *
28732850 GGAAAAAAG-AAGAAAAAAGAAAAAAAT
1 AGAAAGAAGAAAGAAGGAAGAAAAAAAG
28732877 AGAA
1 AGAA
28732881 TAGTCGGGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
25 2 0.04
26 13 0.27
27 29 0.60
28 4 0.08
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (28 bp):
AGAAAGAAGAAAGAAGGAAGAAAAAAAG
Found at i:28733033 original size:25 final size:25
Alignment explanation
Indices: 28733001--28733049 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
28732991 CAAGCAGTCC
28733001 AAAGCAAAAAAAAAAAAAGAAGGCA
1 AAAGCAAAAAAAAAAAAAGAAGGCA
* *
28733026 AAAGCAAAAAAAAAAGAAGCAGGC
1 AAAGCAAAAAAAAAAAAAGAAGGC
28733050 CAACAACAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.71, C:0.10, G:0.18, T:0.00
Consensus pattern (25 bp):
AAAGCAAAAAAAAAAAAAGAAGGCA
Found at i:28733698 original size:16 final size:17
Alignment explanation
Indices: 28733679--28733712 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
28733669 TAAAAAAATC
28733679 AAAAAATTCGTGTTTCAA
1 AAAAAATTCGTGTTTC-A
28733697 AAAAAATTCGTGTTTC
1 AAAAAATTCGTGTTTC
28733713 CACAAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
AAAAAATTCGTGTTTCA
Found at i:28733747 original size:29 final size:29
Alignment explanation
Indices: 28733705--28733761 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
28733695 AAAAAAAATT
28733705 CGTGTTTCCACAAATCTTCGTGTTTTTTC
1 CGTGTTTCCACAAATCTTCGTGTTTTTTC
* * *
28733734 CGTGTTTTCACAAATTTTCTTGTTTTTT
1 CGTGTTTCCACAAATCTTCGTGTTTTTT
28733762 TTTAAAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.19, G:0.12, T:0.54
Consensus pattern (29 bp):
CGTGTTTCCACAAATCTTCGTGTTTTTTC
Found at i:28733799 original size:18 final size:17
Alignment explanation
Indices: 28733776--28733963 Score: 152
Period size: 18 Copynumber: 10.7 Consensus size: 17
28733766 AAAAACCGTG
28733776 TTTCAAAAATCTTCCTGT
1 TTTCAAAAAT-TTCCTGT
*
28733794 TTTCAAAAA-TTCCGGT
1 TTTCAAAAATTTCCTGT
*
28733810 GTTTCAAAAATCTTCGTGT
1 -TTTCAAAAAT-TTCCTGT
28733829 TTTC-AAAATTTCCGGTGT
1 TTTCAAAAATTTCC--TGT
*
28733847 TTT-AAAAATTTTCGTGT
1 TTTCAAAAA-TTTCCTGT
* *
28733864 TTTCAAAAAATTCCCGT
1 TTTCAAAAATTTCCTGT
*
28733881 GTTTCAAAAATTTTCATGT
1 -TTTCAAAAA-TTTCCTGT
* *
28733900 TTTCAACAA-TTCCCGT
1 TTTCAAAAATTTCCTGT
*
28733916 GTTTCACAAATTTCCGTGT
1 -TTTCAAAAATTTCC-TGT
*
28733935 TTTCAAAAATTTTCGTGT
1 TTTCAAAAA-TTTCCTGT
28733953 TTT-AAAAATTT
1 TTTCAAAAATTT
28733964 TTGTGTTCTT
Statistics
Matches: 137, Mismatches: 19, Indels: 30
0.74 0.10 0.16
Matches are distributed among these distances:
16 17 0.12
17 37 0.27
18 63 0.46
19 20 0.15
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (17 bp):
TTTCAAAAATTTCCTGT
Found at i:28733962 original size:35 final size:35
Alignment explanation
Indices: 28733771--28734011 Score: 281
Period size: 35 Copynumber: 6.9 Consensus size: 35
28733761 TTTTAAAAAA
* *
28733771 CCGTGTTTCAAAAATCTTCCTGTTTTCAAAAATTC
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
* * *
28733806 CGGTGTTTCAAAAATCTTCGTGTTTTCAAAATTTC
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
* *
28733841 CGGTGTTTTAAAAATTTTCGTGTTTTCAAAAAATTC
1 CCGTGTTTCAAAAATTTTCGTGTTTTC-AAAAATTC
* *
28733877 CCGTGTTTCAAAAATTTTCATGTTTTCAACAATTC
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
* * *
28733912 CCGTGTTTCACAAATTTCCGTGTTTTCAAAAATTT
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
* * *
28733947 TCGTGTTTTAAAAATTTTTGTGTTCTT--AAAATTC
1 CCGTGTTTCAAAAATTTTCGTGTT-TTCAAAAATTC
* * *
28733981 TCGTATTTCAAAAGTTTTCGTG-TTTCAAAAA
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAA
28734012 AAATTCTCAT
Statistics
Matches: 177, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
32 2 0.01
33 1 0.01
34 28 0.16
35 113 0.64
36 33 0.19
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (35 bp):
CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
Found at i:28733965 original size:18 final size:17
Alignment explanation
Indices: 28733772--28734011 Score: 178
Period size: 17 Copynumber: 13.8 Consensus size: 17
28733762 TTTAAAAAAC
* *
28733772 CGTGTTTCAAAAATCTT
1 CGTGTTTTAAAAATTTT
* *
28733789 CCTGTTTTCAAAAA-TTC
1 CGTGTTTT-AAAAATTTT
* *
28733806 CGGTGTTTCAAAAATCTT
1 C-GTGTTTTAAAAATTTT
* *
28733824 CGTGTTTTCAAAATTTC
1 CGTGTTTTAAAAATTTT
28733841 CGGTGTTTTAAAAATTTT
1 C-GTGTTTTAAAAATTTT
**
28733859 CGTGTTTTCAAAAAATTCC
1 CGTGTTTT--AAAAATTTT
*
28733878 CGTGTTTCAAAAATTTT
1 CGTGTTTTAAAAATTTT
* * **
28733895 CATGTTTTCAACAATTCC
1 CGTGTTTT-AAAAATTTT
* * *
28733913 CGTGTTTCACAAATTTC
1 CGTGTTTTAAAAATTTT
28733930 CGTGTTTTCAAAAATTTT
1 CGTGTTTT-AAAAATTTT
28733948 CGTGTTTTAAAAATTTT
1 CGTGTTTTAAAAATTTT
* *
28733965 TGTGTTCTT-AAAATTCT
1 CGTGTT-TTAAAAATTTT
* * *
28733982 CGTATTTCAAAAGTTTT
1 CGTGTTTTAAAAATTTT
*
28733999 CGTGTTTCAAAAA
1 CGTGTTTTAAAAA
28734012 AAATTCTCAT
Statistics
Matches: 172, Mismatches: 41, Indels: 20
0.74 0.18 0.09
Matches are distributed among these distances:
16 1 0.01
17 101 0.59
18 56 0.33
19 14 0.08
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (17 bp):
CGTGTTTTAAAAATTTT
Found at i:28736328 original size:23 final size:24
Alignment explanation
Indices: 28736301--28736346 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
28736291 TAAATTTTGT
28736301 TCTATTATT-TAAA-TTTTATTTTA
1 TCTA-TATTATAAATTTTTATTTTA
28736324 TCTATATTATAAATTTTTATTTT
1 TCTATATTATAAATTTTTATTTT
28736347 TATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 8 0.38
24 9 0.43
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TCTATATTATAAATTTTTATTTTA
Found at i:28736356 original size:25 final size:22
Alignment explanation
Indices: 28736305--28736357 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 22
28736295 TTTTGTTCTA
28736305 TTATTTAAATTTTATTTTATCT
1 TTATTTAAATTTTATTTTATCT
* *
28736327 ATATTATAAATTTTTATTTTTATTT
1 TTATT-TAAA-TTTTA-TTTTATCT
28736352 TTATTT
1 TTATTT
28736358 TGATGTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 4 0.16
23 4 0.16
24 6 0.24
25 11 0.44
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATTTAAATTTTATTTTATCT
Found at i:28740246 original size:57 final size:58
Alignment explanation
Indices: 28740092--28740246 Score: 192
Period size: 57 Copynumber: 2.7 Consensus size: 58
28740082 TATATTATGA
*
28740092 TTTTTATT-AATTCATATTTTAATAATAATTATATTAAAA-ACGTTATTAAATTATATATT
1 TTTTTATTAAATT-ATATTTT-ATAATAATTATATTAAAATAC-TGATTAAATTATATATT
* * * * *
28740151 ATTTTATTAAATTATATTTAATAATAATTATGTTAAAATA-TGATTAAATTATTTGTT
1 TTTTTATTAAATTATATTTTATAATAATTATATTAAAATACTGATTAAATTATATATT
28740208 TTTTTATTAAATTATATTTTATAATAATCT-TATTAAAAT
1 TTTTTATTAAATTATATTTTATAATAAT-TATATTAAAAT
28740247 TTAATAATAA
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
57 48 0.57
58 18 0.21
59 14 0.17
60 4 0.05
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (58 bp):
TTTTTATTAAATTATATTTTATAATAATTATATTAAAATACTGATTAAATTATATATT
Found at i:28740254 original size:3 final size:3
Alignment explanation
Indices: 28740248--28740272 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28740238 TATTAAAATT
28740248 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
28740273 CATCTACCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:28740448 original size:16 final size:16
Alignment explanation
Indices: 28740419--28740469 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
28740409 TGAATTATTA
** *
28740419 ATTACAGCTTTATTTC
1 ATTACAGCCCTATTCC
*
28740435 ATTACAGTCCTATTCC
1 ATTACAGCCCTATTCC
28740451 ATTACAGCCCTATTCC
1 ATTACAGCCCTATTCC
28740467 ATT
1 ATT
28740470 CCCCCCAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.06, T:0.41
Consensus pattern (16 bp):
ATTACAGCCCTATTCC
Found at i:28740828 original size:30 final size:30
Alignment explanation
Indices: 28740792--28740851 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
28740782 ACTTAACAAG
28740792 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
28740822 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
28740852 TAATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.57, C:0.15, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:28741908 original size:14 final size:13
Alignment explanation
Indices: 28741883--28741912 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
28741873 ATAATTTATA
28741883 TATATTTATATTT
1 TATATTTATATTT
28741896 TATATTCTATATTT
1 TATATT-TATATTT
28741910 TAT
1 TAT
28741913 TATATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TATATTTATATTT
Found at i:28742464 original size:11 final size:10
Alignment explanation
Indices: 28742432--28742488 Score: 53
Period size: 11 Copynumber: 5.4 Consensus size: 10
28742422 TTAAAATTAT
28742432 AAAAATT-AA
1 AAAAATTAAA
* *
28742441 AATATTTATAA
1 AAAAATTA-AA
28742452 AAAAATTACAA
1 AAAAATTA-AA
28742463 AAAAATTAAA
1 AAAAATTAAA
28742473 AAAATTATTAAA
1 AAAA--ATTAAA
28742485 AAAA
1 AAAA
28742489 TAAAAACTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
9 5 0.13
10 6 0.15
11 18 0.46
12 10 0.26
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:28742472 original size:20 final size:20
Alignment explanation
Indices: 28742448--28742494 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
28742438 TAAAATATTT
28742448 ATAAAAAAATTA-CAAAAAA
1 ATAAAAAAATTATCAAAAAA
*
28742467 ATTAAAAAAATTATTAAAAAA
1 A-TAAAAAAATTATCAAAAAA
28742488 ATAAAAA
1 ATAAAAA
28742495 CTCTTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 17 0.68
21 7 0.28
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (20 bp):
ATAAAAAAATTATCAAAAAA
Found at i:28759145 original size:21 final size:21
Alignment explanation
Indices: 28759111--28759154 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28759101 TCTCTTTCCA
**
28759111 TTTCTTTTCTATAATTCAGTT
1 TTTCTTTTCTATAAAACAGTT
28759132 TTTCTTTT-TCATAAAACAGTT
1 TTTCTTTTCT-ATAAAACAGTT
28759153 TT
1 TT
28759155 GGACGTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.23, C:0.14, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTCTTTTCTATAAAACAGTT
Found at i:28767765 original size:6 final size:6
Alignment explanation
Indices: 28767754--28767779 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28767744 GTTAAGTCAT
28767754 ATTTTA ATTTTA ATTTTA ATTTTA AT
1 ATTTTA ATTTTA ATTTTA ATTTTA AT
28767780 ATCTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTA
Found at i:28773310 original size:11 final size:11
Alignment explanation
Indices: 28773262--28773326 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
28773252 TTTAAAATTT
28773262 TAAAAA-TAT-
1 TAAAAATTATA
28773271 TAAAAA--ATA
1 TAAAAATTATA
* *
28773280 TTAAAATTACA
1 TAAAAATTATA
28773291 TATAAAATTATA
1 TA-AAAATTATA
28773303 TAAAAATTA-A
1 TAAAAATTATA
*
28773313 CTAAAAATTTTA
1 -TAAAAATTATA
28773325 TA
1 TA
28773327 TTAATATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
8 2 0.04
9 11 0.24
10 1 0.02
11 20 0.44
12 11 0.24
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:28773335 original size:24 final size:24
Alignment explanation
Indices: 28773297--28773368 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
28773287 TACATATAAA
* *
28773297 ATTATATAAAAATTAACTAAAAATT
1 ATTATATTAATATTAACT-AAAATT
*
28773322 -TTATATTAATATTAAGTAAAATT
1 ATTATATTAATATTAACTAAAATT
28773345 CATTATATTAATATT-ACATAAAAT
1 -ATTATATTAATATTAAC-TAAAAT
28773369 AAAATAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 6 0.15
24 15 0.38
25 19 0.47
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (24 bp):
ATTATATTAATATTAACTAAAATT
Found at i:28773370 original size:5 final size:5
Alignment explanation
Indices: 28773362--28773391 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
28773352 TTAATATTAC
28773362 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
28773392 CTATCCCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:28783684 original size:28 final size:27
Alignment explanation
Indices: 28783651--28783749 Score: 112
Period size: 28 Copynumber: 3.6 Consensus size: 27
28783641 TAATGAGATT
28783651 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTTTAATTGAA
* *
28783678 ATGCACTAAGTGTGCGAGTATAAGGGTG-A
1 A-GCACTAAGTGTGCGAGTTTAA--TTGAA
*
28783707 AGCACTAAGTGTGCGAGTTTGATT-ATTA
1 AGCACTAAGTGTGCGAGTTTAATTGA--A
28783735 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
28783750 TACTTATCAA
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 55 0.90
29 2 0.03
30 2 0.03
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTTAATTGAA
Found at i:28784802 original size:47 final size:47
Alignment explanation
Indices: 28784730--28785072 Score: 460
Period size: 47 Copynumber: 7.3 Consensus size: 47
28784720 AAATTTGATA
28784730 TATAATGCTGTCC-ATTTTAAGTATATTGATGCTGTCTATTTTAATG
1 TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCTATTTTAATG
* * * *
28784776 TGTAATGCTGTCCAATTTTGAGTATATTGATGCTGCCCATTTTAATG
1 TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCTATTTTAATG
*
28784823 TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCATTTTAATG
1 TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCTATTTTAATG
*
28784870 TATAATGCTGTCCAATTTTGAGTATATTGATGCTG-CTCATTTTAATG
1 TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCT-ATTTTAATG
* * *
28784917 TATAATGCTGTCCAATTTTAAGTATATTTATGTTGTCCATTTTAATG
1 TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCTATTTTAATG
* * * * *
28784964 TATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCTAATTTGATG
1 TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCTATTTTAATG
* * *
28785011 TATAATGCTGTCC-ATTTTAAGCATATT-ATTGCTGTCTAATTTGATG
1 TATAATGCTGTCCAATTTTAAGTATATTGA-TGCTGTCTATTTTAATG
* *
28785057 AATAATTACTGTCCAA
1 TATAA-TGCTGTCCAA
28785073 AACAGGGTTG
Statistics
Matches: 267, Mismatches: 24, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
45 1 0.00
46 45 0.17
47 219 0.82
48 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (47 bp):
TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCTATTTTAATG
Found at i:28796867 original size:2 final size:2
Alignment explanation
Indices: 28796860--28796949 Score: 55
Period size: 2 Copynumber: 47.5 Consensus size: 2
28796850 TATAAAGATG
* * * *
28796860 TA TA TA TA TA TA TA TA TA -A TA -A GA TA TA AA AA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
28796900 TA TG TA TA TA AA GA TA TA TA TA TA -A TA -A GA TA TA -A AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
28796939 TA CA TA TA TA T
1 TA TA TA TA TA T
28796950 GTATGAAAAT
Statistics
Matches: 71, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
1 5 0.07
2 66 0.93
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (2 bp):
TA
Found at i:28800515 original size:29 final size:30
Alignment explanation
Indices: 28800476--28800533 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
28800466 AATTGGTCTC
28800476 TTCTTTTTGAGAA-ACTCTGTAATTATTCT
1 TTCTTTTTGAGAAGACTCTGTAATTATTCT
*
28800505 TTCTTTTTGAGAAGGTCTCTGTAATTATT
1 TTCTTTTTGAGAA-GACTCTGTAATTATT
28800534 ATAGTGAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
31 13 0.50
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (30 bp):
TTCTTTTTGAGAAGACTCTGTAATTATTCT
Found at i:28808787 original size:29 final size:31
Alignment explanation
Indices: 28808738--28808796 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
28808728 TAAAACTTTA
* *
28808738 GAATTTAGTCCCTATA-TTTTTAT-TTTCAG
1 GAATTTAGTCCATATACTTTTCATATTTCAG
*
28808767 GAATTTAGTCCATCTACTTTTCATATTTCA
1 GAATTTAGTCCATATACTTTTCATATTTCA
28808797 CTGTTTACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.56
30 6 0.24
31 5 0.20
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.49
Consensus pattern (31 bp):
GAATTTAGTCCATATACTTTTCATATTTCAG
Done.