Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1092
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: 788722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:399820 original size:60 final size:61
Alignment explanation
Indices: 399717--399882 Score: 210
Period size: 61 Copynumber: 2.8 Consensus size: 61
399707 GGCACCACGG
* * * *
399717 AGTTGTGGACTTAGAA-AGATAAGGTGCCATGGAGTTGTAGACTTAAAATGGTGCCAC-AA
1 AGTTGTGGACTTAAAAGAGAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACTAA
* *** *
399776 AGTTGTGGACTTAAAAGAGAAAAAGTGCCACAAAGTTGTGGACTTAAAAGGGTGCCACTGA
1 AGTTGTGGACTTAAAAGAGAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACTAA
* * *
399837 AGTTATGGACTTAAAAGGGAAAAGGTACCATGGAGTTGTGGACTTA
1 AGTTGTGGACTTAAAAGAGAAAAGGTGCCATGGAGTTGTGGACTTA
399883 GAAAAAAAAG
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
59 15 0.17
60 34 0.38
61 40 0.45
ACGTcount: A:0.36, C:0.11, G:0.29, T:0.24
Consensus pattern (61 bp):
AGTTGTGGACTTAAAAGAGAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACTAA
Found at i:400662 original size:22 final size:20
Alignment explanation
Indices: 400632--400675 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
400622 AATTCAAAAT
400632 TTTCACAATTTGTATCGATACA
1 TTTCACAA--TGTATCGATACA
*
400654 TTTCTCAATGTATCGATACA
1 TTTCACAATGTATCGATACA
400674 TT
1 TT
400676 CAAGCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (20 bp):
TTTCACAATGTATCGATACA
Found at i:403110 original size:79 final size:78
Alignment explanation
Indices: 402977--403366 Score: 451
Period size: 79 Copynumber: 4.9 Consensus size: 78
402967 TCATTGATGT
* *
402977 TTTTATTTCTAAAACACCGATTTTTCACAATCGAGAATACTCCAACCCCATTATTTTTTAGGGGA
1 TTTTATTTCTAAAACACCGATTTTTCACAATCG-GGATACTCCAACCCCATTATTTTTGAGGGGA
*
403042 TACTCTAACCCCAA
65 TACTCCAACCCCAA
* * *
403056 TTTTATTT-TCAAAACACCGATTTTTCACAATCAGGGATACTCCAACCCCTTTATTTCTGA-GAG
1 TTTTATTTCT-AAAACACCGATTTTTCACAATC-GGGATACTCCAACCCCATTATTTTTGAGGGG
* ** *
403119 ACACTCCAACTACAG
64 ATACTCCAACCCCAA
* * * * * * *
403134 TTTTATTTCTAAAACATCGATTTTCCACCATTAGGGATACTCTAACCCCGTTATTTTTGAGGGAA
1 TTTTATTTCTAAAACACCGATTTTTCA-CAATCGGGATACTCCAACCCCATTATTTTTGAGGGGA
* *
403199 TACTCCAACTCCGA
65 TACTCCAACCCCAA
* *
403213 TTTTATTTCTAAAACATCGATTTTTCATAATCGGAGATACTCCAACCCCATTATTTTTGAGGGGA
1 TTTTATTTCTAAAACACCGATTTTTCACAATCGG-GATACTCCAACCCCATTATTTTTGAGGGGA
*
403278 TACTCCAACCCTAA
65 TACTCCAACCCCAA
* * * * * * *
403292 TTTTATTTCTAAAACACTGATTTTTCACTATTGGGGATACTCTAATCCCGTTACTTTTGAGGGGA
1 TTTTATTTCTAAAACACCGATTTTTCAC-AATCGGGATACTCCAACCCCATTATTTTTGAGGGGA
403357 TACTCCAACC
65 TACTCCAACC
403367 TCGTTTTGAC
Statistics
Matches: 262, Mismatches: 42, Indels: 14
0.82 0.13 0.04
Matches are distributed among these distances:
78 64 0.24
79 193 0.74
80 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (78 bp):
TTTTATTTCTAAAACACCGATTTTTCACAATCGGGATACTCCAACCCCATTATTTTTGAGGGGAT
ACTCCAACCCCAA
Found at i:403267 original size:157 final size:156
Alignment explanation
Indices: 402977--403366 Score: 475
Period size: 157 Copynumber: 2.5 Consensus size: 156
402967 TCATTGATGT
* * * * * *
402977 TTTTATTTCTAAAACACCGATTTTTCA-CAATCGAGAATACTCCAACCCCATTATTTTTTAGGGG
1 TTTTATTTCTAAAACA-CGATTTTTCACCATTAG-GGATACTCTAACCCCGTTATTTTTGAGGGG
* *
403041 ATACTCTAACCCCAATTTTATTTTCAAAACACCGATTTTTCACAATCAGGGATACTCCAACCCCT
64 ATACTCCAACCCCAATTTTATTTTCAAAACACCGATTTTTCACAATCAGGGATACTCCAACCCCA
403106 TTATTTCTGA-GAGACACTCCAA-CTACA
129 TTATTTCTGAGGAGACACTCCAACCTA-A
* *
403133 GTTTTATTTCTAAAACATCGATTTTCCACCATTAGGGATACTCTAACCCCGTTATTTTTGAGGGA
1 -TTTTATTTCTAAAACA-CGATTTTTCACCATTAGGGATACTCTAACCCCGTTATTTTTGAGGGG
* * * *
403198 ATACTCCAACTCCGATTTTA-TTTCTAAAACATCGATTTTTCATAATC-GGAGATACTCCAACCC
64 ATACTCCAACCCCAATTTTATTTTC-AAAACACCGATTTTTCACAATCAGG-GATACTCCAACCC
* * *
403261 CATTATTTTTGAGGGGATACTCCAACCCTAA
127 CATTATTTCTGAGGAGACACTCCAA-CCTAA
* * * *
403292 TTTTATTTCTAAAACACTGATTTTTCACTATTGGGGATACTCTAATCCCGTTACTTTTGAGGGGA
1 TTTTATTTCTAAAACAC-GATTTTTCACCATTAGGGATACTCTAACCCCGTTATTTTTGAGGGGA
403357 TACTCCAACC
65 TACTCCAACC
403367 TCGTTTTGAC
Statistics
Matches: 201, Mismatches: 25, Indels: 13
0.84 0.10 0.05
Matches are distributed among these distances:
156 6 0.03
157 111 0.55
158 80 0.40
159 1 0.00
160 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (156 bp):
TTTTATTTCTAAAACACGATTTTTCACCATTAGGGATACTCTAACCCCGTTATTTTTGAGGGGAT
ACTCCAACCCCAATTTTATTTTCAAAACACCGATTTTTCACAATCAGGGATACTCCAACCCCATT
ATTTCTGAGGAGACACTCCAACCTAA
Found at i:403434 original size:236 final size:235
Alignment explanation
Indices: 402977--403439 Score: 501
Period size: 236 Copynumber: 2.0 Consensus size: 235
402967 TCATTGATGT
*
402977 TTTTATTTCTAAAACACCGATTTTTCACAATCGAGAATACTCCAACCCCATTATTTTTTAGGGGA
1 TTTTATTTCTAAAACACCGATTTTTCACAATCGAGAATACTCCAACCCCATTATTTTTGAGGGGA
* *
403042 TACTCTAACCCCAATTTTATTTTCAAAACACCGATTTTTCACAATCAGGGATACTCCAACCCCTT
66 TACTCCAACCCCAATTTTATTTTCAAAACACCGATTTTTCACAATCAGGGATACTCCAACCCCGT
** * ** *
403107 TATTTCTGAGAGACACTCCAACTACAGTTTTATTTCTAAAACATCGATTTTCCACCATTAGGGAT
131 TATTTCTGAGAGACACTCCAACTACAGTTTTACCTCCAAAACATAAATTTTCCACCA-GAGGGAT
* ****
403172 ACTCTAACCCCGTTATTTTTGAGGGAATACTCCAACTCCGA
195 ACTCCAACCCCGTTATCCCCGAGGGAATACTCCAACTCCGA
* *
403213 TTTTATTTCTAAAACATCGATTTTTCATAATCG-GAGATACTCCAACCCCATTATTTTTGAGGGG
1 TTTTATTTCTAAAACACCGATTTTTCACAATCGAGA-ATACTCCAACCCCATTATTTTTGAGGGG
* * * ** * *
403277 ATACTCCAACCCTAATTTTA-TTTCTAAAACACTGATTTTTCACTATTGGGGATACTCTAATCCC
65 ATACTCCAACCCCAATTTTATTTTC-AAAACACCGATTTTTCACAATCAGGGATACTCCAACCCC
* * * * *
403341 GTTACTTT-TGAGGGGATACTCCAACCT-C-GTTTTGACCTCCAAAATATTAAATTTTTCATC-G
129 GTTA-TTTCTGA-GAGACACTCCAA-CTACAGTTTT-ACCTCCAAAACA-TAAATTTTCCACCAG
***
403402 AGGGATGTACTCCAATTGCG-TA-CCCCGAGGGAATACTC
189 AGGGA--TACTCCAACCCCGTTATCCCCGAGGGAATACTC
403440 TAACCATGTT
Statistics
Matches: 187, Mismatches: 31, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
235 6 0.03
236 137 0.73
237 24 0.13
238 20 0.11
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.35
Consensus pattern (235 bp):
TTTTATTTCTAAAACACCGATTTTTCACAATCGAGAATACTCCAACCCCATTATTTTTGAGGGGA
TACTCCAACCCCAATTTTATTTTCAAAACACCGATTTTTCACAATCAGGGATACTCCAACCCCGT
TATTTCTGAGAGACACTCCAACTACAGTTTTACCTCCAAAACATAAATTTTCCACCAGAGGGATA
CTCCAACCCCGTTATCCCCGAGGGAATACTCCAACTCCGA
Found at i:405246 original size:15 final size:15
Alignment explanation
Indices: 405228--405286 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 15
405218 TTGCCTTTGC
405228 ATTTTTTTTTGTTTT
1 ATTTTTTTTTGTTTT
*
405243 A-TTTTTTTGGTTTT
1 ATTTTTTTTTGTTTT
* *
405257 -TTGTTTGTTGTTTT
1 ATTTTTTTTTGTTTT
*
405271 GTTTTTTGTTT-TTTT
1 ATTTTTT-TTTGTTTT
405286 A
1 A
405287 GTATTTTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
14 22 0.65
15 10 0.29
16 2 0.06
ACGTcount: A:0.05, C:0.00, G:0.14, T:0.81
Consensus pattern (15 bp):
ATTTTTTTTTGTTTT
Found at i:405251 original size:25 final size:25
Alignment explanation
Indices: 405205--405265 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
405195 TTTGTTGTTC
405205 TTTTTT-TTTTATTTTGCCTTTGCATTT
1 TTTTTTGTTTTATTTT--CTTTG-ATTT
*
405232 TTTTTTGTTTTATTTT-TTTGGTTT
1 TTTTTTGTTTTATTTTCTTTGATTT
405256 TTTGTTTGTT
1 TTT-TTTGTT
405266 GTTTTGTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 6 0.19
25 10 0.32
27 6 0.19
28 9 0.29
ACGTcount: A:0.05, C:0.05, G:0.11, T:0.79
Consensus pattern (25 bp):
TTTTTTGTTTTATTTTCTTTGATTT
Found at i:405284 original size:7 final size:7
Alignment explanation
Indices: 405232--405284 Score: 58
Period size: 7 Copynumber: 7.9 Consensus size: 7
405222 CTTTGCATTT
405232 TTTTTTG
1 TTTTTTG
405239 TTTTATT-
1 TTTT-TTG
*
405246 TTTTTGG
1 TTTTTTG
405253 TTTTTTG
1 TTTTTTG
*
405260 TTTGTTG
1 TTTTTTG
405267 --TTTTG
1 TTTTTTG
405272 TTTTTTG
1 TTTTTTG
405279 TTTTTT
1 TTTTTT
405285 TAGTATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 4 0.11
6 1 0.03
7 31 0.82
8 2 0.05
ACGTcount: A:0.02, C:0.00, G:0.15, T:0.83
Consensus pattern (7 bp):
TTTTTTG
Found at i:410116 original size:14 final size:15
Alignment explanation
Indices: 410097--410131 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
410087 AATAGATTTA
410097 ATATTTAAATTTTT-
1 ATATTTAAATTTTTG
410111 ATATTTAAATTTTTG
1 ATATTTAAATTTTTG
410126 ATATTT
1 ATATTT
410132 TATGTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
ATATTTAAATTTTTG
Found at i:410124 original size:15 final size:14
Alignment explanation
Indices: 410097--410131 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
410087 AATAGATTTA
*
410097 ATATTTAAATTTTT
1 ATATTTAAATTTTG
410111 ATATTTAAATTTTTG
1 ATATTTAAA-TTTTG
410126 ATATTT
1 ATATTT
410132 TATGTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
ATATTTAAATTTTG
Found at i:410700 original size:22 final size:20
Alignment explanation
Indices: 410672--410746 Score: 80
Period size: 22 Copynumber: 3.6 Consensus size: 20
410662 CATGATTCTC
410672 AAAATATTTATTATTTATTTTT
1 AAAATATTT-TTA-TTATTTTT
**
410694 AAAATATTTTTA-TATTAAT
1 AAAATATTTTTATTATTTTT
*
410713 AAATATATATTTTATAATTTTT
1 AAA-ATAT-TTTTATTATTTTT
410735 AAAATATTTTTA
1 AAAATATTTTTA
410747 ACATTAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
19 8 0.18
20 9 0.20
21 12 0.27
22 16 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAAATATTTTTATTATTTTT
Found at i:414130 original size:31 final size:31
Alignment explanation
Indices: 414095--414191 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 31
414085 TTTTGGCTTA
414095 ATAATGCCACTTGATGTAAGCAGTTACATTG
1 ATAATGCCACTTGATGTAAGCAGTTACATTG
* *** * *
414126 ATAATCTGTCACTTG--G-ATAGTTTTTGC-TTA
1 ATAA--TGCCACTTGATGTA-AGCAGTTACATTG
*
414156 ATAATGCCACTAGATGTAAGCAGTTACATTG
1 ATAATGCCACTTGATGTAAGCAGTTACATTG
414187 ATAAT
1 ATAAT
414192 CTTCACTTGG
Statistics
Matches: 46, Mismatches: 13, Indels: 14
0.63 0.18 0.19
Matches are distributed among these distances:
28 7 0.15
30 13 0.28
31 18 0.39
33 8 0.17
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (31 bp):
ATAATGCCACTTGATGTAAGCAGTTACATTG
Found at i:414160 original size:61 final size:60
Alignment explanation
Indices: 414085--414201 Score: 207
Period size: 61 Copynumber: 1.9 Consensus size: 60
414075 ACAACTAAAC
*
414085 TTTTGGCTTAATAATGCCACTTGATGTAAGCAGTTACATTGATAATCTGTCACTTGGATAG
1 TTTTGGCTTAATAATGCCACTAGATGTAAGCAGTTACATTGATAATCT-TCACTTGGATAG
*
414146 TTTTTGCTTAATAATGCCACTAGATGTAAGCAGTTACATTGATAATCTTCACTTGG
1 TTTTGGCTTAATAATGCCACTAGATGTAAGCAGTTACATTGATAATCTTCACTTGG
414202 GTTATTGCAC
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
60 8 0.15
61 46 0.85
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (60 bp):
TTTTGGCTTAATAATGCCACTAGATGTAAGCAGTTACATTGATAATCTTCACTTGGATAG
Found at i:415578 original size:15 final size:15
Alignment explanation
Indices: 415558--415588 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
415548 TTTTTGAAAG
415558 ATAGGTTACAGCATT
1 ATAGGTTACAGCATT
415573 ATAGGTTACAGCATT
1 ATAGGTTACAGCATT
415588 A
1 A
415589 ACTATCTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (15 bp):
ATAGGTTACAGCATT
Found at i:415945 original size:2 final size:2
Alignment explanation
Indices: 415938--415965 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
415928 TAAATATTGA
415938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
415966 TGAAATTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:429816 original size:55 final size:55
Alignment explanation
Indices: 429751--430008 Score: 283
Period size: 55 Copynumber: 4.6 Consensus size: 55
429741 CTCCTTTCAC
429751 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
429805 CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTCTAAGCCCACACAAGTTGATGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
429860 CTTTTCTAGTCCTCAAAGAGCAGGATACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTC-AGTCCTCAAAGAGCAGG--A-C---GCCTTTCAAAGCCCACACAAGTTGGTGGCA
** * * *
429922 TTTTTTTA-TACCTCAAAGAGCAGGATGCCATTT-AAAGCCCACACAAATTGGTGGCA
1 -CCTTTCAGT-CCTCAAAGAGCAGGACGCC-TTTCAAAGCCCACACAAGTTGGTGGCA
*
429978 -CTTCCCAGTCCTCAAAGAGCAGGACG-CTTTC
1 CCTT-TCAGTCCTCAAAGAGCAGGACGCCTTTC
430009 TCTTTTCGCC
Statistics
Matches: 173, Mismatches: 17, Indels: 28
0.79 0.08 0.13
Matches are distributed among these distances:
53 3 0.02
54 8 0.05
55 68 0.39
56 41 0.24
57 3 0.02
58 1 0.01
59 1 0.01
60 1 0.01
61 1 0.01
62 42 0.24
63 4 0.02
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (55 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:429988 original size:117 final size:117
Alignment explanation
Indices: 429776--430001 Score: 314
Period size: 117 Copynumber: 1.9 Consensus size: 117
429766 GAGCAGGACG
*
429776 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACGCCTTTCTAAG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACGCCTTTCAAAG
* * *
429841 CCCACACAAGTTGATGGCACTTTTCTAGTCCTCAAAGAGCAGGATACCTTTT
66 CCCACACAAATTGATGGCACTTTCCCAGTCCTCAAAGAGCAGGATACCTTTT
** * * *
429893 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTA-TACCTCAAAGAGCAGGATGCCATTT-A
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTTCAGT-CCTCAAAGAGCAAGACGCC-TTTCA
*
429956 AAGCCCACACAAATTGGTGGCAC-TTCCCAGTCCTCAAAGAGCAGGA
63 AAGCCCACACAAATTGATGGCACTTTCCCAGTCCTCAAAGAGCAGGA
430002 CGCTTTCTCT
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
117 51 0.53
118 42 0.44
119 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.25
Consensus pattern (117 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACGCCTTTCAAAG
CCCACACAAATTGATGGCACTTTCCCAGTCCTCAAAGAGCAGGATACCTTTT
Found at i:430064 original size:212 final size:214
Alignment explanation
Indices: 429812--430232 Score: 629
Period size: 212 Copynumber: 2.0 Consensus size: 214
429802 GCACCTTTCA
* *
429812 GTCCTCAAAGAGCAAGACGCCTTTCTAAGCCCACACAAGTTGATGGCACTTTTCTAGTCCTCAAA
1 GTCCACAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGATGGCACTTTTCTAGTCCTCAAA
* * *
429877 GAGCAGGATACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTA-TACCTCAAAGA
66 GAGCAGGACACATTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTTCAGT-CCTCAAAGA
*
429941 GCAGGATGC-C-ATTT-AAAGCCCACACAAATTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGA
129 GCAGGATGCTCTATTTCAAAGCCCACACAAATTGGTGGCATCTT-CCACTCCTCAAAGAGCAGGA
430002 CG-CTTTCTCTTTTCGCCCTTAT
193 CGCCTTTC-CTTTTCGCCCTTAT
* *
430024 GTCCACAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAA
1 GTCCACAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGATGGCACTTTTCTAGTCCTCAAA
430089 GAGCAGGACACATTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGC
66 GAGCAGGACACATTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGC
* * * *
430154 ATGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCATCTTTCACTCCTCAAAGAGCAGGA
131 AGGATGC--TCTATTT-CAAAGCCCACACAAATTGGTGGCATCTTCCACTCCTCAAAGAGCAGGA
430219 CGCCTTTCCTTTTC
193 CGCCTTTCCTTTTC
430233 AAAGCCCACA
Statistics
Matches: 188, Mismatches: 12, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
211 23 0.12
212 105 0.56
214 1 0.01
215 3 0.02
217 48 0.26
218 8 0.04
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (214 bp):
GTCCACAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGATGGCACTTTTCTAGTCCTCAAA
GAGCAGGACACATTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGC
AGGATGCTCTATTTCAAAGCCCACACAAATTGGTGGCATCTTCCACTCCTCAAAGAGCAGGACGC
CTTTCCTTTTCGCCCTTAT
Found at i:430149 original size:156 final size:150
Alignment explanation
Indices: 429893--430169 Score: 387
Period size: 156 Copynumber: 1.8 Consensus size: 150
429883 GATACCTTTT
* *
429893 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTATACCTCAAAGAGCAGGATGCCATTTAAA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTATACCTCAAAGAGCAGGATGCCATTTAAA
429958 GCCCACACAAATTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCTTTCTCTTTTCGCCCTTA
66 GCCCACACAAATTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCTTTCTCTTTTCGCCCTTA
430023 TGTCCACAAAGAGCAGGACG
131 TGTCCACAAAGAGCAGGACG
*
430043 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGT-CCTCAAAGAGCAGGACACATTTTCC
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTA-TACCTCAAAGAGCAGG----A--TGCC
* * ** * *
430107 -TTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCATGATGCTTTCTCTTT
59 ATTT-AAAGCCCACACAAATTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCTTTCTCTTT
430170 GCAAAGCCCA
Statistics
Matches: 110, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
150 49 0.45
151 1 0.01
154 1 0.01
155 3 0.03
156 56 0.51
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (150 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTATACCTCAAAGAGCAGGATGCCATTTAAA
GCCCACACAAATTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCTTTCTCTTTTCGCCCTTA
TGTCCACAAAGAGCAGGACG
Found at i:430175 original size:61 final size:60
Alignment explanation
Indices: 430044--430279 Score: 341
Period size: 61 Copynumber: 3.9 Consensus size: 60
430034 AGCAGGACGC
* *
430044 CTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACACATTT-T
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTTC-AGTCCTCAAAGAGCAGGACGC-TTTCT
* *
430105 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCATGATGCTTTCT
1 -CTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGCTTTCT
* *
430166 CTTTGCAAAGCCCACACAAGTTGGTGGCATCTTTCACTCCTCAAAGAGCAGGACGCCTTTC-
1 CTTT-CAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACG-CTTTCT
*
430227 CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA
1 C-TTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGA
430280 TGCACTTTAT
Statistics
Matches: 159, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
60 7 0.04
61 111 0.70
62 41 0.26
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (60 bp):
CTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGCTTTCT
Found at i:430266 original size:122 final size:122
Alignment explanation
Indices: 430044--430282 Score: 385
Period size: 122 Copynumber: 2.0 Consensus size: 122
430034 AGCAGGACGC
* *
430044 CTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACACATTTTCCTT
1 CTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTACTCCTCAAAGAGCAGGACACACTTTCCTT
* *
430109 TCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCATGATGCTTTCT
66 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTTTCT
*
430166 CTTTGCAAAGCCCACACAAGTTGGTGGCA-TCTTTC-ACTCCTCAAAGAGCAGGACGC-CTTTCC
1 CTTT-CAAAGCCCACACAAGTTGGTGGCACT-TTTCTACTCCTCAAAGAGCAGGACACACTTTCC
430228 TTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGC
64 -TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGC
430283 ACTTTATTTT
Statistics
Matches: 109, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
121 5 0.05
122 76 0.70
123 28 0.26
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (122 bp):
CTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTACTCCTCAAAGAGCAGGACACACTTTCCTT
TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTTTCT
Found at i:430314 original size:42 final size:43
Alignment explanation
Indices: 430263--430539 Score: 269
Period size: 42 Copynumber: 6.4 Consensus size: 43
430253 GCATTTTCCA
**
430263 GTCCTCAAAGAGCAGGATGCACTTTATTTTCC-TCTTTCCTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTTCCTTCTTTCCTTT
* * *
430305 GTCCTCAAAGAGCAAGACACACTTCA-TTCCCTTCTTTTCTCTTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTTCCTTC-TTTC-C-TTT
*
430350 GTCCTCAAAGAGCATGACACACTTTATTTTCC-TCTTTCCTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTTCCTTCTTTCCTTT
* * *
430392 GTCCTCAAAGAGCAGGACACACTTCA-ATCCCTTCTTTTCTCTTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTTCCTTC-TTTC-C-TTT
* ** *
430437 GTCCTCAAAGAGTAGGATGCACTTTATTTTCC-TCTTTCTTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTTCCTTCTTTCCTTT
* * * * * *
430479 GTCTTCAAAAAGCAGGACGCATTTTGTTTTCCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTTCCTTCTTTCCTTT
*
430522 ATCCTCGAAA-AGCAGGAC
1 GTCCTC-AAAGAGCAGGAC
430540 GTACTCTTTT
Statistics
Matches: 194, Mismatches: 29, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
41 7 0.04
42 82 0.42
43 29 0.15
44 13 0.07
45 56 0.29
46 7 0.04
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.39
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACACACTTTATTTTCCTTCTTTCCTTT
Found at i:430360 original size:45 final size:45
Alignment explanation
Indices: 430302--430448 Score: 212
Period size: 45 Copynumber: 3.3 Consensus size: 45
430292 TCCTCTTTCC
430302 TTTGTCCTCAAAGAGCAAGACACACTTCATTCCCTTCTTTTCTCT
1 TTTGTCCTCAAAGAGCAAGACACACTTCATTCCCTTCTTTTCTCT
* * *
430347 TTTGTCCTCAAAGAGCATGACACACTTTATTTTCC-TC-TTTC-C-
1 TTTGTCCTCAAAGAGCAAGACACACTTCA-TTCCCTTCTTTTCTCT
* *
430389 TTTGTCCTCAAAGAGCAGGACACACTTCAATCCCTTCTTTTCTCT
1 TTTGTCCTCAAAGAGCAAGACACACTTCATTCCCTTCTTTTCTCT
430434 TTTGTCCTCAAAGAG
1 TTTGTCCTCAAAGAG
430449 TAGGATGCAC
Statistics
Matches: 90, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
41 3 0.03
42 29 0.32
43 5 0.06
44 5 0.06
45 44 0.49
46 4 0.04
ACGTcount: A:0.22, C:0.29, G:0.11, T:0.37
Consensus pattern (45 bp):
TTTGTCCTCAAAGAGCAAGACACACTTCATTCCCTTCTTTTCTCT
Found at i:430517 original size:87 final size:87
Alignment explanation
Indices: 430263--430496 Score: 387
Period size: 87 Copynumber: 2.7 Consensus size: 87
430253 GCATTTTCCA
*
430263 GTCCTCAAAGAGCAGGATGCACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAAGACACACT
1 GTCCTCAAAGAGCAGGATGCACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGACACACT
430328 TCATTCCCTTCTTTTCTCTTTT
66 TCATTCCCTTCTTTTCTCTTTT
* **
430350 GTCCTCAAAGAGCATGACACACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGACACACT
1 GTCCTCAAAGAGCAGGATGCACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGACACACT
*
430415 TCAATCCCTTCTTTTCTCTTTT
66 TCATTCCCTTCTTTTCTCTTTT
* * * *
430437 GTCCTCAAAGAGTAGGATGCACTTTATTTTCCTCTTTCTTTTGTCTTCAAAAAGCAGGAC
1 GTCCTCAAAGAGCAGGATGCACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGAC
430497 GCATTTTGTT
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 135 1.00
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.38
Consensus pattern (87 bp):
GTCCTCAAAGAGCAGGATGCACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGACACACT
TCATTCCCTTCTTTTCTCTTTT
Found at i:431242 original size:13 final size:13
Alignment explanation
Indices: 431224--431251 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
431214 TTTTCACAAT
431224 TTGTATCGATACA
1 TTGTATCGATACA
431237 TTGTATCGATACA
1 TTGTATCGATACA
431250 TT
1 TT
431252 CTGGGTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:431292 original size:20 final size:20
Alignment explanation
Indices: 431266--431320 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
431256 GTTTACCTAG
*
431266 ATGTATCGATACATTTTGCA
1 ATGTATCGATACATTTTACA
*
431286 TTGTATCGATACATTTTACA
1 ATGTATCGATACATTTTACA
431306 ATGTATCGATACATT
1 ATGTATCGATACATT
431321 CAGGTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTACA
Found at i:433916 original size:51 final size:51
Alignment explanation
Indices: 433824--433920 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 51
433814 CACTCCAACC
* * * * * **
433824 CCGATTTTATTTCTAAAATACTAATTTTTTACAATTGGGGATACTCGAGCT
1 CCGATTTTATTTCCAAAACACCAATTTCTCACAATCAGGGATACTCGAGCT
*
433875 CCGATTTTATTTCCAAAACACCAATTTCTCCCAATCAGGGATACTC
1 CCGATTTTATTTCCAAAACACCAATTTCTCACAATCAGGGATACTC
433921 CAACCCCGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 38 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (51 bp):
CCGATTTTATTTCCAAAACACCAATTTCTCACAATCAGGGATACTCGAGCT
Found at i:434015 original size:130 final size:130
Alignment explanation
Indices: 433782--434016 Score: 298
Period size: 130 Copynumber: 1.8 Consensus size: 130
433772 TTATTTCATC
* **
433782 GGGATACTCCAATCCCGTTATTTCCGAGGGGACACTCCAACCCCGATTTTATTTCTAAAATACTA
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGACCTTATTTCTAAAATACTA
* *** * *
433847 ATTTTTTACAATTGGGGATACTCGAGCTCCGATTTTATTTCCAAAACACCAATTTCTCCCAATCA
66 ATTTTTCACAATCAAGGATACTCAACCTCCGATTTTATTTCCAAAACACCAATTTCTCCCAATCA
* *
433912 GGGATACTCCAACCCCGTTATTTTC-ACGGGGATACTCCAACCCCGACCTTATTTCTAAAGCAT-
1 GGGATACTCCAACCCCGTTATTTCCGA-GGGGACACTCCAACCCCGACCTTATTTCTAAA--ATA
*
433975 C-GATTTTTCACAATCAAGGATACTCCAACCT-CGATTTTATTT
63 CTAATTTTTCACAATCAAGGATACT-CAACCTCCGATTTTATTT
434017 TCAGAATATC
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
129 1 0.01
130 81 0.91
131 5 0.06
132 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (130 bp):
GGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGACCTTATTTCTAAAATACTA
ATTTTTCACAATCAAGGATACTCAACCTCCGATTTTATTTCCAAAACACCAATTTCTCCCAATCA
Found at i:436217 original size:34 final size:31
Alignment explanation
Indices: 436158--436234 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 31
436148 CTTTTGAAGG
*
436158 CTAAGATAAAACCTCCCTATCTTTTCACAAC
1 CTAAGATAGAACCTCCCTATCTTTTCACAAC
**
436189 CTAAGATAGAACCTCTTCACTATCTTTTCACAGG
1 CTAAGATAGAACCTC--C-CTATCTTTTCACAAC
436223 CTAAGATAGAAC
1 CTAAGATAGAAC
436235 TTTTTCTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 14 0.35
33 1 0.03
34 25 0.62
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.29
Consensus pattern (31 bp):
CTAAGATAGAACCTCCCTATCTTTTCACAAC
Found at i:436262 original size:37 final size:35
Alignment explanation
Indices: 436170--436276 Score: 119
Period size: 34 Copynumber: 3.0 Consensus size: 35
436160 AAGATAAAAC
*
436170 CTCCCTATCTTTTCACAA-CCTAAGATAGAACCTCT
1 CTCCCTATCTTTTCA-AAGGCTAAGATAGAACCTCT
* * * *
436205 -TCACTATCTTTTCACAGGCTAAGATAGAACTTTTT
1 CTCCCTATCTTTTCAAAGGCTAAGATAGAAC-CTCT
*
436240 CTCCCTATCTTTTTCAAAGGCTAAGATAGAATCTCT
1 CTCCCTATC-TTTTCAAAGGCTAAGATAGAACCTCT
436276 C
1 C
436277 AATCACTTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
33 1 0.02
34 25 0.43
35 2 0.03
36 10 0.17
37 20 0.34
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (35 bp):
CTCCCTATCTTTTCAAAGGCTAAGATAGAACCTCT
Found at i:436987 original size:50 final size:49
Alignment explanation
Indices: 436912--437024 Score: 181
Period size: 50 Copynumber: 2.3 Consensus size: 49
436902 TTTCACAATT
* * *
436912 TGTATCGATACATTGTTCATTGTATCAATACATTCTGAGTTTTACCTAGA
1 TGTATCGATACATTATTCATTGTATCAATACATTCTG-GGTTTACCCAGA
*
436962 TGTATCGATACATTATTCATTGTATCGATACATTCTGGGTTTACCCAGA
1 TGTATCGATACATTATTCATTGTATCAATACATTCTGGGTTTACCCAGA
437011 TGTATCGATACATT
1 TGTATCGATACATT
437025 TGTCAATGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 24 0.41
50 35 0.59
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (49 bp):
TGTATCGATACATTATTCATTGTATCAATACATTCTGGGTTTACCCAGA
Found at i:437024 original size:49 final size:49
Alignment explanation
Indices: 436912--437045 Score: 189
Period size: 49 Copynumber: 2.7 Consensus size: 49
436902 TTTCACAATT
* * *
436912 TGTATCGATACATTGTTCATTGTATCAATACATTCTGAGTTTTACCTAGA
1 TGTATCGATACATT-TTCATTGTATCGATACATTCTGAGGTTTACCCAGA
436962 TGTATCGATACATTATTCATTGTATCGATACATTCTG-GGTTTACCCAGA
1 TGTATCGATACATT-TTCATTGTATCGATACATTCTGAGGTTTACCCAGA
* *
437011 TGTATCGATACATTTGTCAATGTATTGATACATTC
1 TGTATCGATACATTT-TCATTGTATCGATACATTC
437046 AGGCATTTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
48 1 0.01
49 41 0.53
50 35 0.45
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (49 bp):
TGTATCGATACATTTTCATTGTATCGATACATTCTGAGGTTTACCCAGA
Found at i:439655 original size:78 final size:78
Alignment explanation
Indices: 439378--439679 Score: 274
Period size: 79 Copynumber: 3.8 Consensus size: 78
439368 TTCATTTCGA
* * * *
439378 GGATACTCCAACCTCGGTTTTATTTCCAAAACATCAATTTATCGTAATCAGGGATACTCTAA-TC
1 GGATACTCCAACCTCGGTTTTATTT-CAAAATATCAATTTATCATAATCAGGGATACTCCAACCC
*
439442 TCGTTATTTCCGAGG
65 T-GTTATTTTCGAGG
* * ** * * *
439457 GGATACTCCAACCTTGGCTTTATTTCTAAAATATTGATTTCTCACAATC-GGAGGTACTCCAACC
1 GGATACTCCAACCTCGGTTTTATTTC-AAAATATCAATTTATCATAATCAGG-GATACTCCAACC
* *
439521 CTGTTATTTTGGCA-T
64 CTGTTATTTTCG-AGG
* * ** * * *
439536 GGATACTCCAACCTCGG-CTTATTTCTAAAGCTTAGATTTTTCATAATC-GAGGATACTCTAACC
1 GGATACTCCAACCTCGGTTTTATTTCAAAATATCA-ATTTATCATAATCAG-GGATACTCCAACC
439599 CTGTTATTTTCGAGG
64 CTGTTATTTTCGAGG
* *
439614 GGATACTCCAACCCCGATTTTATTTTCAAAATATCAATTT-TCTATAATCAGGGATACTCCAACC
1 GGATACTCCAACCTCGGTTTTA-TTTCAAAATATCAATTTATC-ATAATCAGGGATACTCCAACC
439678 CT
64 CT
439680 AATTTTATTT
Statistics
Matches: 178, Mismatches: 34, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
77 6 0.03
78 60 0.34
79 99 0.56
80 13 0.07
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (78 bp):
GGATACTCCAACCTCGGTTTTATTTCAAAATATCAATTTATCATAATCAGGGATACTCCAACCCT
GTTATTTTCGAGG
Found at i:439675 original size:51 final size:51
Alignment explanation
Indices: 439613--439725 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
439603 TATTTTCGAG
* * * *
439613 GGGATACTCCAACCCCGATTTTATTTTCAAAATATCAA-TTTTCTATAATCA
1 GGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTTTC-ATAATCA
* * * *
439664 GGGATACTCCAACCCTAATTTTATTTCCAGAACACCGATTTTTCATAATCG
1 GGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTTTCATAATCA
439715 GGGATACTCCA
1 GGGATACTCCA
439726 GCCCTATTGT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 48 0.91
52 5 0.09
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (51 bp):
GGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTTTCATAATCA
Found at i:440880 original size:32 final size:33
Alignment explanation
Indices: 440839--440902 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
440829 CATTTTATGG
*
440839 TGTATTGATACAAAG-AACATGTATCGATACAA
1 TGTATTGATACAAAGCAACATGTATCAATACAA
*
440871 TGTATTGATACAAAGCAATATGTATCAATACA
1 TGTATTGATACAAAGCAACATGTATCAATACA
440903 TTTGGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATTGATACAAAGCAACATGTATCAATACAA
Found at i:441899 original size:35 final size:36
Alignment explanation
Indices: 441844--441919 Score: 127
Period size: 35 Copynumber: 2.1 Consensus size: 36
441834 GATCTATGAC
*
441844 TAATCATCATTGGGGTTAGTTGGAGCAAGACGGATG
1 TAATCATCACTGGGGTTAGTTGGAGCAAGACGGATG
*
441880 TAATCATCACT-GGGTTAGTTGGAGCATGACGGATG
1 TAATCATCACTGGGGTTAGTTGGAGCAAGACGGATG
441915 TAATC
1 TAATC
441920 CTCTATTGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 28 0.74
36 10 0.26
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.29
Consensus pattern (36 bp):
TAATCATCACTGGGGTTAGTTGGAGCAAGACGGATG
Found at i:443486 original size:32 final size:32
Alignment explanation
Indices: 443431--443491 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
443421 ATAGTCGAAA
* *
443431 TGTATCGATATAATTTTAATGTATTGATACAT
1 TGTATCGATACAATTTTAATGTATCGATACAT
*
443463 TGTATCGATACAATTTCT-TTGTATCGATA
1 TGTATCGATACAATTT-TAATGTATCGATA
443492 GATCTGGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 24 0.96
33 1 0.04
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (32 bp):
TGTATCGATACAATTTTAATGTATCGATACAT
Found at i:444651 original size:21 final size:21
Alignment explanation
Indices: 444623--444674 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
444613 AGTTAATTCA
444623 TCATTT-TTTTC--TTACAAC
1 TCATTTCTTTTCTTTTACAAC
*
444641 TCATTTCTTTTCTTTTCCAAC
1 TCATTTCTTTTCTTTTACAAC
444662 TCA-TTCATTTTCT
1 TCATTTC-TTTTCT
444675 CCTTTAGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.21
19 5 0.17
20 3 0.10
21 15 0.52
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (21 bp):
TCATTTCTTTTCTTTTACAAC
Found at i:446324 original size:30 final size:31
Alignment explanation
Indices: 446290--446366 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 31
446280 CCTTACAACA
*
446290 CTATCTTTTGA-AAGCTAACATAGAACCTCC
1 CTATCTTTTCACAAGCTAACATAGAACCTCC
*
446320 CTATCTTTTCACAAGCTAAGATAGAACCTCTTC
1 CTATCTTTTCACAAGCTAACATAGAACCTC--C
446353 ACTATCTTTTCACA
1 -CTATCTTTTCACA
446367 GGTTATGATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 10 0.24
31 17 0.41
33 1 0.02
34 13 0.32
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (31 bp):
CTATCTTTTCACAAGCTAACATAGAACCTCC
Found at i:446363 original size:34 final size:34
Alignment explanation
Indices: 446288--446420 Score: 130
Period size: 34 Copynumber: 4.0 Consensus size: 34
446278 AACCTTACAA
* *
446288 CACTATCTTTTGA-AAGCTAACATAGAACCTC--
1 CACTATCTTTTCACAAGCTAAGATAGAACCTCTT
446319 C-CTATCTTTTCACAAGCTAAGATAGAACCTCTT
1 CACTATCTTTTCACAAGCTAAGATAGAACCTCTT
* * * *
446352 CACTATCTTTTCACAGGTTATGATAGAACCTTTCT
1 CACTATCTTTTCACAAGCTAAGATAGAACCTCT-T
* * * *
446387 CCCTATATTTTTTAAAAGCTAAGATAGAACCTCT
1 CACTAT-CTTTTCACAAGCTAAGATAGAACCTCT
446421 CAATCACTTC
Statistics
Matches: 82, Mismatches: 14, Indels: 7
0.80 0.14 0.07
Matches are distributed among these distances:
30 10 0.12
31 18 0.22
33 1 0.01
34 27 0.33
35 6 0.07
36 20 0.24
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.35
Consensus pattern (34 bp):
CACTATCTTTTCACAAGCTAAGATAGAACCTCTT
Found at i:449872 original size:9 final size:9
Alignment explanation
Indices: 449858--449887 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
449848 ATAGGATTAA
449858 TTCATTTAG
1 TTCATTTAG
449867 TTCATTTAG
1 TTCATTTAG
449876 TTCATTTAG
1 TTCATTTAG
449885 TTC
1 TTC
449888 TTATTTCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.57
Consensus pattern (9 bp):
TTCATTTAG
Found at i:453521 original size:33 final size:33
Alignment explanation
Indices: 453453--453529 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
453443 CCTTTATATG
* * *
453453 TATTAATACTTTCCTTTAAGGTATTGCTACCAA
1 TATTAATACTTTCCTTTAAGGAATCGATACCAA
* *
453486 TATTGATACTTTCCTTTGAA-GAATCGATACTAA
1 TATTAATACTTTCCTTT-AAGGAATCGATACCAA
453519 TATTAATACTT
1 TATTAATACTT
453530 GATGAACAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
33 35 0.95
34 2 0.05
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (33 bp):
TATTAATACTTTCCTTTAAGGAATCGATACCAA
Found at i:454028 original size:51 final size:50
Alignment explanation
Indices: 453972--454126 Score: 136
Period size: 50 Copynumber: 3.1 Consensus size: 50
453962 TTACGAATCT
* *
453972 TAGAAAAAAGTGCACCTATTTCATTTAGATATGCATATTTCATAAAGTCCC
1 TAGAAAAAAGTGCACCTATTTCATTTAG-TGTGCATATTTCATAAAATCCC
** * * *
454023 TAG-AAAAAGTGCATTTTTTTCCATTTAG-GTGCACCTTTTTCATAAAATCCT
1 TAGAAAAAAGTGCACCTATTT-CATTTAGTGTGCA--TATTTCATAAAATCCC
* * * * *
454074 TAGAAAAGAGGGCACCTATTTTA-TTAGGTGTGCCTATTTCATAAAATCTC
1 TAGAAAAAAGTGCACCTATTTCATTTA-GTGTGCATATTTCATAAAATCCC
454124 TAG
1 TAG
454127 TTCAAAAAGA
Statistics
Matches: 81, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
49 4 0.05
50 33 0.41
51 28 0.35
52 16 0.20
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (50 bp):
TAGAAAAAAGTGCACCTATTTCATTTAGTGTGCATATTTCATAAAATCCC
Found at i:454285 original size:34 final size:34
Alignment explanation
Indices: 454242--454324 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
454232 GGATATAGGC
* *
454242 TTGATTCTTTTAACTCATTTAGTAAGACACAAGT
1 TTGACTCTTTTAACTCATTCAGTAAGACACAAGT
* ** * **
454276 TTGAGTCTTTTAACTTGTTCAGTAGGACATGAGT
1 TTGACTCTTTTAACTCATTCAGTAAGACACAAGT
454310 TTGACTCTTTTAACT
1 TTGACTCTTTTAACT
454325 TGTTCAGAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (34 bp):
TTGACTCTTTTAACTCATTCAGTAAGACACAAGT
Found at i:454350 original size:34 final size:32
Alignment explanation
Indices: 454270--454485 Score: 103
Period size: 34 Copynumber: 6.4 Consensus size: 32
454260 TTAGTAAGAC
* *
454270 ACAAGTTTGAGTCTTTTAACTTGTTCAGTAGG
1 ACAAGTTTGACTCTTTTAACTTGTTCAGAAGG
454302 ACATGAGTTTGACTCTTTTAACTTGTTCAGAAGGG
1 ACA--AGTTTGACTCTTTTAACTTGTTCAGAA-GG
* * * *
454337 TACAAGTTCGACTC-TTGATC-TGTTCAAAAGG
1 -ACAAGTTTGACTCTTTTAACTTGTTCAGAAGG
* ** * * *
454368 GCATACGCATGACTCTTTTTAAACTTATTAAGTAGG
1 ACA-A-GTTTGACTC-TTTT-AACTTGTTCAGAAGG
*** * * *
454404 ACACAAGTTTGACTCCACTAACTTGCTCAAAAGT
1 --ACAAGTTTGACTCTTTTAACTTGTTCAGAAGG
* * *
454438 ACATAAGTTTGACTTTTTTAACTTGTTTAAAAGG
1 AC--AAGTTTGACTCTTTTAACTTGTTCAGAAGG
454472 ACACAAGTTTGACT
1 --ACAAGTTTGACT
454486 ATTGACCTGT
Statistics
Matches: 133, Mismatches: 35, Indels: 30
0.67 0.18 0.15
Matches are distributed among these distances:
30 2 0.02
31 3 0.02
32 19 0.14
33 4 0.03
34 78 0.59
35 5 0.04
36 19 0.14
37 1 0.01
38 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36
Consensus pattern (32 bp):
ACAAGTTTGACTCTTTTAACTTGTTCAGAAGG
Found at i:454462 original size:136 final size:134
Alignment explanation
Indices: 454181--454496 Score: 344
Period size: 136 Copynumber: 2.3 Consensus size: 134
454171 CAGGTTTAAG
* * * * * * * *
454181 TCTTTTAACTTGTTCAAAAGGATATAAGTTCAACTTTTGACCTATTTAAAAGGATATAGGCTTGA
1 TCTTTTAACTTGTTCAAAAGGATACAAGTTCGACTATTGACCTGTTCAAAAGGACATACGCATGA
* * * *** * ** *
454246 TTCTTTTAACTCATTTAGTAAGACACAAGTTTGAGTCTTTTAACTTGTTCAGTAGGACATGAGTT
66 CTCTTTTAACTCATTAAGTAAGACACAAGTTTGACTCCACTAACTTGCTCAAAAGGACATAAGTT
454311 TGAC
131 TGAC
* * * * *
454315 TCTTTTAACTTGTTCAGAAGGGTACAAGTTCGACTCTTGATCTGTTCAAAAGGGCATACGCATGA
1 TCTTTTAACTTGTTCAAAAGGATACAAGTTCGACTATTGACCTGTTCAAAAGGACATACGCATGA
* * *
454380 CTCTTTTTAAACTTATTAAGTAGGACACAAGTTTGACTCCACTAACTTGCTCAAAAGTACATAAG
66 CTC-TTTT-AACTCATTAAGTAAGACACAAGTTTGACTCCACTAACTTGCTCAAAAGGACATAAG
454445 TTTGAC
129 TTTGAC
* * * *
454451 TTTTTTAACTTGTTTAAAAGGACACAAGTTTGACTATTGACCTGTT
1 TCTTTTAACTTGTTCAAAAGGATACAAGTTCGACTATTGACCTGTT
454497 TAGATATGTA
Statistics
Matches: 147, Mismatches: 33, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
134 55 0.37
135 4 0.03
136 88 0.60
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (134 bp):
TCTTTTAACTTGTTCAAAAGGATACAAGTTCGACTATTGACCTGTTCAAAAGGACATACGCATGA
CTCTTTTAACTCATTAAGTAAGACACAAGTTTGACTCCACTAACTTGCTCAAAAGGACATAAGTT
TGAC
Found at i:457048 original size:24 final size:26
Alignment explanation
Indices: 457021--457071 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
457011 ATCAAAATTT
457021 TATTCAT-C-GGGGACACTCCAACCC
1 TATTCATCCAGGGGACACTCCAACCC
*
457045 TATTCCTCCGAGGGGACACTCCAACCC
1 TATTCATCC-AGGGGACACTCCAACCC
457072 CGTTTTCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 1 0.04
27 16 0.70
ACGTcount: A:0.24, C:0.39, G:0.18, T:0.20
Consensus pattern (26 bp):
TATTCATCCAGGGGACACTCCAACCC
Found at i:462128 original size:16 final size:17
Alignment explanation
Indices: 462107--462138 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
462097 AAGAAATTAT
462107 TTATTA-TTTTATTTTA
1 TTATTATTTTTATTTTA
462123 TTATTATTTTTATTTT
1 TTATTATTTTTATTTT
462139 TGAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTATTATTTTTATTTTA
Found at i:463229 original size:21 final size:21
Alignment explanation
Indices: 463203--463256 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
463193 CTGTCTTTAG
*
463203 CTGCTGTTGGTGGTGGTGCTA
1 CTGCTGCTGGTGGTGGTGCTA
* * *
463224 CTGCTGCGGGTGGTGGTGGTG
1 CTGCTGCTGGTGGTGGTGCTA
*
463245 CTGCTGGTGGTG
1 CTGCTGCTGGTG
463257 CTGTTTTGCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.15, G:0.50, T:0.33
Consensus pattern (21 bp):
CTGCTGCTGGTGGTGGTGCTA
Found at i:463237 original size:18 final size:18
Alignment explanation
Indices: 463214--463258 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
463204 TGCTGTTGGT
463214 GGTGGTGCTACTGCTGCG
1 GGTGGTGCTACTGCTGCG
* ** *
463232 GGTGGTGGTGGTGCTGCT
1 GGTGGTGCTACTGCTGCG
463250 GGTGGTGCT
1 GGTGGTGCT
463259 GTTTTGCTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.02, C:0.16, G:0.51, T:0.31
Consensus pattern (18 bp):
GGTGGTGCTACTGCTGCG
Found at i:463705 original size:22 final size:22
Alignment explanation
Indices: 463675--463716 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
463665 TAGTGTTTCA
463675 TGTTAGAGCTGCTGTCGTTGGC
1 TGTTAGAGCTGCTGTCGTTGGC
* *
463697 TGTTGGAGCTGCTGTTGTTG
1 TGTTAGAGCTGCTGTCGTTG
463717 CTAGAGATAT
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:0.07, C:0.14, G:0.38, T:0.40
Consensus pattern (22 bp):
TGTTAGAGCTGCTGTCGTTGGC
Found at i:464571 original size:8 final size:8
Alignment explanation
Indices: 464542--464756 Score: 54
Period size: 8 Copynumber: 26.0 Consensus size: 8
464532 GCCATCATCT
*
464542 TTATTTCA
1 TTATTTTA
464550 TT-TTTTA
1 TTATTTTA
* *
464557 TTGTTTTG
1 TTATTTTA
464565 TTATTTT-
1 TTATTTTA
* *
464572 TTGTTATTT
1 TTATT-TTA
*
464581 TTGTTTTA
1 TTATTTTA
464589 TTATTTTA
1 TTATTTTA
464597 TTATTTTAA
1 TTATTTT-A
* *
464606 TTAATAATAA
1 TT-AT-TTTA
*
464616 TAATTTT-
1 TTATTTTA
464623 TTATTTTGA
1 TTATTTT-A
464632 TT-TTTT-
1 TTATTTTA
464638 TTATTTT-
1 TTATTTTA
*
464645 TTCGGTTTTTCAA
1 TT---ATTTT--A
*
464658 TTTTTTTA
1 TTATTTTA
*
464666 TTTTTTTA
1 TTATTTTA
*
464674 TT-TTTTG
1 TTATTTTA
*
464681 TTGATTTTT
1 TT-ATTTTA
*
464690 TTATTTTT
1 TTATTTTA
464698 TTATTTT-
1 TTATTTTA
464705 TTGAGTTTTTA
1 TT-A--TTTTA
*
464716 TGATTTT-
1 TTATTTTA
*
464723 TTATTTTT
1 TTATTTTA
464731 TTGATTATTA
1 TT-ATT-TTA
464741 -TATTATTA
1 TTATT-TTA
464749 TTATTTTA
1 TTATTTTA
464757 ATTTTATATA
Statistics
Matches: 164, Mismatches: 18, Indels: 50
0.71 0.08 0.22
Matches are distributed among these distances:
6 2 0.01
7 36 0.22
8 76 0.46
9 26 0.16
10 20 0.12
11 2 0.01
13 2 0.01
ACGTcount: A:0.19, C:0.01, G:0.06, T:0.73
Consensus pattern (8 bp):
TTATTTTA
Found at i:464572 original size:9 final size:10
Alignment explanation
Indices: 464550--464603 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
464540 CTTTATTTCA
464550 TTTT-TTATT
1 TTTTGTTATT
464559 GTTTTGTTATT
1 -TTTTGTTATT
464570 TTTTGTTATT
1 TTTTGTTATT
*
464580 TTTGTTTTATT
1 TTT-TGTTATT
*
464591 ATTTTATTATT
1 -TTTTGTTATT
464602 TT
1 TT
464604 AATTAATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 19 0.49
11 17 0.44
12 3 0.08
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (10 bp):
TTTTGTTATT
Found at i:464704 original size:26 final size:25
Alignment explanation
Indices: 464626--464755 Score: 111
Period size: 25 Copynumber: 5.0 Consensus size: 25
464616 TAATTTTTTA
***
464626 TTTTGATTTTTTTTATTTTTTCGGTT
1 TTTTGA-TTTTTTTATTTTTTTATTT
**
464652 TTTCAATTTTTTTATTTTTTTATTT
1 TTTTGATTTTTTTATTTTTTTATTT
464677 TTTGTTGATTTTTTTATTTTTTTA-TT
1 -TT-TTGATTTTTTTATTTTTTTATTT
*
464703 TTTTGA-GTTTTTATGATTTTTTATTT
1 TTTTGATTTTTTTAT--TTTTTTATTT
* * *
464729 TTTTGATTATTATATTATTATTATTT
1 TTTTGATTTTTTTATT-TTTTTATTT
464755 T
1 T
464756 AATTTTATAT
Statistics
Matches: 85, Mismatches: 12, Indels: 14
0.77 0.11 0.13
Matches are distributed among these distances:
23 7 0.08
24 4 0.05
25 26 0.31
26 25 0.29
27 23 0.27
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.76
Consensus pattern (25 bp):
TTTTGATTTTTTTATTTTTTTATTT
Found at i:464755 original size:33 final size:33
Alignment explanation
Indices: 464686--464755 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
464676 TTTTGTTGAT
* *
464686 TTTTTTATTTTTTTATTTTTTGAGTTTTTATGA
1 TTTTTTATTTTTTTATTTTATGAGTTATTATGA
*
464719 TTTTTTATTTTTTTGATTATTAT-A-TTATTATTA
1 TTTTTTATTTTTTT-ATT-TTATGAGTTATTATGA
464752 TTTT
1 TTTT
464756 AATTTTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 25 0.78
34 4 0.12
35 3 0.09
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.76
Consensus pattern (33 bp):
TTTTTTATTTTTTTATTTTATGAGTTATTATGA
Found at i:468678 original size:21 final size:21
Alignment explanation
Indices: 468652--468703 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
468642 CAAGTATGGA
* *
468652 TGTATCGATACATTCT-GAAAT
1 TGTATCGATACATT-TACAAAG
*
468673 TGTATCAATACATTTACAAAG
1 TGTATCGATACATTTACAAAG
468694 TGTATCGATA
1 TGTATCGATA
468704 TAACTGAGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (21 bp):
TGTATCGATACATTTACAAAG
Found at i:468781 original size:20 final size:20
Alignment explanation
Indices: 468756--468803 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
468746 TCACATGATT
468756 TATCGATACATTGTAATATG
1 TATCGATACATTGTAATATG
* * * *
468776 TATCGAAACATTTTCATGTG
1 TATCGATACATTGTAATATG
468796 TATCGATA
1 TATCGATA
468804 TAAATGAGGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (20 bp):
TATCGATACATTGTAATATG
Found at i:470308 original size:19 final size:19
Alignment explanation
Indices: 470284--470351 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
470274 AATTCAACAA
470284 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
470303 TTTGTATTGATAC--AA--
1 TTTGTATCGATACATAAGT
470318 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
470335 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
470352 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:470327 original size:32 final size:32
Alignment explanation
Indices: 470286--470348 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
470276 TTCAACAATT
* *
470286 TGTATCGATACATAAGTTTTGTATTGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
470318 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
470349 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:470405 original size:20 final size:20
Alignment explanation
Indices: 470382--470445 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
470372 ATATCAATAT
470382 ATTTTTCTGTGTATCGATAC
1 ATTTTTCTGTGTATCGATAC
470402 ATTTTTCTGTGTATCGATAC
1 ATTTTTCTGTGTATCGATAC
*** *
470422 ATGGATCTTTGTATCGATAC
1 ATTTTTCTGTGTATCGATAC
470442 ATTT
1 ATTT
470446 GGAAATTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (20 bp):
ATTTTTCTGTGTATCGATAC
Found at i:473009 original size:51 final size:51
Alignment explanation
Indices: 472954--473155 Score: 174
Period size: 51 Copynumber: 4.0 Consensus size: 51
472944 TAACCTTGAC
* *
472954 TTTATTTCCAAAATATTGATTTTTCATAATCGGGGATACTCCAACCCCGGT
1 TTTATTTCCAAAACACTGATTTTTCATAATCGGGGATACTCCAACCCCGGT
* * * * * *
473005 TTTATTGCTAAAACACTAATTTTTCCACAATCGGGGATACTCTAACCCCGAT
1 TTTATTTCCAAAACACTGATTTTT-CATAATCGGGGATACTCCAACCCCGGT
* * * **** * *
473057 TTTATTTTCAAAACACT-AATTTTCCTCCGAGGGGATACTCTAACCCCGGC
1 TTTATTTCCAAAACACTGATTTTTCATAATCGGGGATACTCCAACCCCGGT
* * * **
473107 TTTATTCCCAAAATA-TCGATTTCTCATAATTAGGGATACTCCAACCCCG
1 TTTATTTCCAAAACACT-GATTTTTCATAATCGGGGATACTCCAACCCCG
473156 TTATTTCTGA
Statistics
Matches: 116, Mismatches: 32, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
49 1 0.01
50 31 0.27
51 46 0.40
52 38 0.33
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (51 bp):
TTTATTTCCAAAACACTGATTTTTCATAATCGGGGATACTCCAACCCCGGT
Found at i:473045 original size:52 final size:52
Alignment explanation
Indices: 472972--473119 Score: 171
Period size: 52 Copynumber: 2.9 Consensus size: 52
472962 CAAAATATTG
* *
472972 ATTTTT-CATAATCGGGGATACTCCAACCCCGGTTTTATTGCT-AAAACACTA
1 ATTTTTCCACAATCGGGGATACTCTAACCCCGGTTTTATT-CTCAAAACACTA
* *
473023 ATTTTTCCACAATCGGGGATACTCTAACCCCGATTTTATTTTCAAAACACTA
1 ATTTTTCCACAATCGGGGATACTCTAACCCCGGTTTTATTCTCAAAACACTA
* * * *
473075 A-TTTTCCTCCGA--GGGGATACTCTAACCCCGGCTTTATTCCCAAAA
1 ATTTTTCC-ACAATCGGGGATACTCTAACCCCGGTTTTATTCTCAAAA
473120 TATCGATTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
50 29 0.35
51 13 0.15
52 42 0.50
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (52 bp):
ATTTTTCCACAATCGGGGATACTCTAACCCCGGTTTTATTCTCAAAACACTA
Found at i:486950 original size:52 final size:52
Alignment explanation
Indices: 486870--486989 Score: 204
Period size: 52 Copynumber: 2.3 Consensus size: 52
486860 AAAAGTTGCT
* * *
486870 TGCATGTATCGATACATTTAATAGTGTATTGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTACC
*
486922 TGCATGTATCGATACATTTTATAATGTATCGATACATCTAGGCAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTACC
486974 TGCATGTATCGATACA
1 TGCATGTATCGATACA
486990 AAGATCAGTG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTACC
Found at i:487002 original size:52 final size:51
Alignment explanation
Indices: 486870--487009 Score: 192
Period size: 52 Copynumber: 2.7 Consensus size: 51
486860 AAAAGTTGCT
* *
486870 TGCATGTATCGATACATTTAATAGTGTATTGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAATTTACC
* *
486922 TGCATGTATCGATACATTTTATAATGTATCGATACATCTAGGCAAATTTACC
1 TGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAATTTACC
*
486974 TGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TGCATGTATCGATACATTA-AT-AGTGTATCGATACA
487010 ATGTATCGAT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.03
52 77 0.97
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (51 bp):
TGCATGTATCGATACATTAATAGTGTATCGATACATCTAGGCAAATTTACC
Found at i:487016 original size:13 final size:13
Alignment explanation
Indices: 486998--487022 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
486988 CAAAGATCAG
486998 TGTATCGATACAA
1 TGTATCGATACAA
487011 TGTATCGATACA
1 TGTATCGATACA
487023 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:487090 original size:20 final size:20
Alignment explanation
Indices: 487061--487118 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
487051 GCAGTAGCTT
487061 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
487080 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
487100 CTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
487119 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:489994 original size:10 final size:10
Alignment explanation
Indices: 489981--490032 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
489971 AAAAAAGGCA
489981 AAAAAAAAAG
1 AAAAAAAAAG
489991 AAAAAAAAA-
1 AAAAAAAAAG
* *
490000 CAAAACAAAG
1 AAAAAAAAAG
* *
490010 AAAAAGAGAG
1 AAAAAAAAAG
490020 AAAAGAAAAAG
1 AAAA-AAAAAG
490031 AA
1 AA
490033 CATGCTTAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
9 7 0.21
10 20 0.61
11 6 0.18
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:491297 original size:176 final size:177
Alignment explanation
Indices: 491003--492007 Score: 1357
Period size: 176 Copynumber: 5.7 Consensus size: 177
490993 CTTTTAGCCA
*
491003 TCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAA
1 TCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
*
491067 AGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGAC
66 AGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGAC
*
491132 GCCTTCTCCTTTTAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCC
131 GCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
* * * *
491179 TCAAAGAGCAGGACG-CTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCGTCCCCAA
1 TCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
491243 AGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGAC
66 AGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGAC
*
491308 GCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCT
131 GCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
* * * * *
491355 TCAAAGAGCGGGACGCCTTTT-CTTTCAAAGCCCACACAAGTTGGTGGAACCTTTCCGTCCCCAA
1 TCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
491419 AGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGAC
66 AGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGAC
* *
491484 GCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCC
131 GCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
* * * *
491531 TCAAAGAGCAGAACGCCTTCTCCTTTTAAAGCCTACACAAGTTGGTGGCA-TTTTCCAGTCCTCA
1 TCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCA
* * * *
491595 AAGAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC-GTCCCCAAAGA
65 AAGAGCAGGAC-CC----CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGA
*
491659 GCAGGA---C--C-CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCC
124 GCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
* * * *
491707 TCAAACAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTAGCA-TTTTCGAGTCCTCA
1 TCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCA
* * *
491771 AAGAGCGGGACGCCTTTTCTTTTAAAGCCCCCACAAGTTGGTGGCACCT-CCAGTCCTCAAAGAG
65 AAGAGCAGGAC-CC----CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAG
* * * * *
491835 CGGGACGCCTT-TTCTTTCAAAGCCTACACAAGTTTGTGGCATTTTCCAGTCC
125 CAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
* *
491887 TCAAAGAGCAAGACACC---T-C--TTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
1 TCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
* * * ***
491946 AGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAG
66 AGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAG
492008 AATACACTTT
Statistics
Matches: 754, Mismatches: 55, Indels: 46
0.88 0.06 0.05
Matches are distributed among these distances:
169 27 0.04
170 15 0.02
173 1 0.00
174 44 0.06
175 56 0.07
176 461 0.61
177 49 0.06
178 3 0.00
179 1 0.00
180 49 0.06
182 43 0.06
183 5 0.01
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (177 bp):
TCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
AGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGAC
GCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
Found at i:491500 original size:237 final size:238
Alignment explanation
Indices: 491003--492007 Score: 1373
Period size: 237 Copynumber: 4.3 Consensus size: 238
490993 CTTTTAGCCA
* *
491003 TCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT--CAGTCCTCA
1 TCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCA
* * *
491066 AAGAGCAGGA------CACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGA
65 AAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGA
* * * * * *
491125 GCAGGACGCCTTCTCCTTTTAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAG
130 GCGGGACGCCTT-TTCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCCCAAAGAGCAG
* *
491190 GACGCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC-GTCC
194 GAC-C----CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCC
*
491239 CCAAAGAGCAGGA---C--C-CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAA
1 TCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAA
*
491298 AGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCTTCAAAGAG
66 AGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAG
*
491363 CGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGAACCTTTCC-GTCCCCAAAGAGCAGG
131 CGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCCCAAAGAGCAGG
*
491427 ACCCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCC
195 ACCCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCC
491470 TCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAA
1 TCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAA
* *
491535 AGAGCAGAACGCCTTCTCCTTTTAAAGCCTACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAG
66 AGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAG
491600 CGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC-GTCCCCAAAGAGCAGG
131 CGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCCCAAAGAGCAGG
491664 ACCCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCC
195 ACCCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCC
* * * * *
491707 TCAAACAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTAGCATTTTCGAGTCCTCAA
1 TCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAA
* * * **
491772 AGAGCGGGACGCCTT-TTCTTTTAAAGCCCCCACAAGTTGGTGGCA-CCTCCAGTCCTCAAAGAG
66 AGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAG
* * * * *
491835 CGGGACGCCTTTTCTTTCAAAGCCTACACAAGTTTGTGGCATTTTCCAGTCCTCAAAGAGCAAGA
131 CGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCCCAAAGAGCAGGA
* *
491900 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCC
196 CCCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCC
* ***
491942 TCAAAGAGCAGGACGCCTT-T-C----AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAA
1 TCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAA
492001 AGAGCAG
66 AGAGCAG
492008 AATACACTTT
Statistics
Matches: 703, Mismatches: 48, Indels: 43
0.89 0.06 0.05
Matches are distributed among these distances:
229 42 0.06
230 34 0.05
231 62 0.09
233 2 0.00
234 7 0.01
235 124 0.18
236 87 0.12
237 345 0.49
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (238 bp):
TCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAA
AGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAG
CGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCCCAAAGAGCAGGA
CCCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCC
Found at i:492757 original size:21 final size:21
Alignment explanation
Indices: 492731--492807 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
492721 AAAAAATTCA
492731 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
492752 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
492773 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
492794 AATGTATCGATACA
1 AATGTATCGATACA
492808 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:492867 original size:19 final size:19
Alignment explanation
Indices: 492843--492910 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
492833 AATTCAACAA
492843 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
492862 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
492877 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
492894 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
492911 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:492882 original size:13 final size:13
Alignment explanation
Indices: 492864--492888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
492854 ACATAAGTTT
492864 TGTATCGATACAA
1 TGTATCGATACAA
492877 TGTATCGATACA
1 TGTATCGATACA
492889 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:492886 original size:32 final size:32
Alignment explanation
Indices: 492845--492907 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
492835 TTCAACAATT
*
492845 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
492877 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
492908 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:492968 original size:13 final size:13
Alignment explanation
Indices: 492950--492975 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
492940 CATTTTTCTG
492950 TGTATCGATACAT
1 TGTATCGATACAT
492963 TGTATCGATACAT
1 TGTATCGATACAT
492976 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:492972 original size:33 final size:33
Alignment explanation
Indices: 492930--492996 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
492920 GCCAAGGAAA
***
492930 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
492963 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
492996 T
1 T
492997 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:495454 original size:55 final size:51
Alignment explanation
Indices: 495320--495454 Score: 164
Period size: 51 Copynumber: 2.6 Consensus size: 51
495310 TTGAGTTTCT
* * *
495320 CAATTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACAC
1 CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTTAAAAACAC
* * *
495371 TAATT-TTCTATAATCGGGGATACTCCAACTCCGTTTTTATTTCTAAAAAAACAC
1 CAATTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTT-T--AAAAACAC
495425 CAATTTCTTCACAATCGGGGATACTCCAAC
1 CAA-TTCTTCACAATCGGGGATACTCCAAC
495455 CCCATTATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
50 2 0.03
51 34 0.49
52 1 0.01
54 9 0.13
55 21 0.30
56 3 0.04
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (51 bp):
CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTTAAAAACAC
Found at i:495529 original size:51 final size:52
Alignment explanation
Indices: 495469--495614 Score: 186
Period size: 52 Copynumber: 2.8 Consensus size: 52
495459 TTATTTCTGA
* ** * * * *
495469 GGGGATACTCCAACCTCGACTTTATTTCCAAAATATTGATTTTT-CATAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCCACAATC
* *
495520 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCCACAATC
* *
495572 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTT
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTT
495615 CCTCTGAGGG
Statistics
Matches: 81, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
51 36 0.44
52 45 0.56
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.34
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCCACAATC
Found at i:495598 original size:134 final size:132
Alignment explanation
Indices: 495335--495588 Score: 345
Period size: 134 Copynumber: 1.9 Consensus size: 132
495325 CTCCACAATC
* * *
495335 GGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGACTTTATTTCCAAAACACTAATTTTCTATAATCGGGGATACTCCAAC
* * *
495400 TCCGTTTTTATTTCTAAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCATTATTT
66 CCCGGTTTTATTGCT--AAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCATTATTT
495465 CTGA
129 CTGA
* * *
495469 GGGGATACTCCAAC-CTCGACTTTATTTCCAAAATATTGATTTT-TCATAATCGGGGATACTCCA
1 GGGGATACTCCAACTC-CGACTTTATTTCCAAAACACTAATTTTCT-ATAATCGGGGATACTCCA
*
495532 ACCCCGGTTTTATTGCT-AAAACACTAATTT-TTCCACAATCGGGGATACTCCAACCCC
64 ACCCCGGTTTTATTGCTAAAAACACCAATTTCTT-CACAATCGGGGATACTCCAACCCC
495589 GGTTTTATTT
Statistics
Matches: 107, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
130 2 0.02
131 36 0.34
133 2 0.02
134 67 0.63
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.33
Consensus pattern (132 bp):
GGGGATACTCCAACTCCGACTTTATTTCCAAAACACTAATTTTCTATAATCGGGGATACTCCAAC
CCCGGTTTTATTGCTAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCATTATTTCT
GA
Found at i:496865 original size:20 final size:20
Alignment explanation
Indices: 496840--496890 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
496830 ACCCTGAAAA
496840 GTATCGATACACATT-TAAAT
1 GTATCGATACACATTGT-AAT
* *
496860 GTATCGATACAGATTGTATT
1 GTATCGATACACATTGTAAT
496880 GTATCGATACA
1 GTATCGATACA
496891 TTGTATCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
GTATCGATACACATTGTAAT
Found at i:496895 original size:13 final size:13
Alignment explanation
Indices: 496877--496904 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
496867 TACAGATTGT
496877 ATTGTATCGATAC
1 ATTGTATCGATAC
496890 ATTGTATCGATAC
1 ATTGTATCGATAC
496903 AT
1 AT
496905 GACCAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:496895 original size:18 final size:19
Alignment explanation
Indices: 496840--496896 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
496830 ACCCTGAAAA
*
496840 GTATCGATACACATT-TAAAT
1 GTATCGATACA-ATTGT-ATT
496860 GTATCGATACAGATTGTATT
1 GTATCGATACA-ATTGTATT
496880 GTATCGATAC-ATTGTAT
1 GTATCGATACAATTGTAT
496897 CGATACATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.21
20 26 0.76
21 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (19 bp):
GTATCGATACAATTGTATT
Found at i:496940 original size:21 final size:20
Alignment explanation
Indices: 496892--496944 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
496882 ATCGATACAT
**
496892 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
* *
496912 TATATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAA-AA
496933 TGTATCGATACA
1 TGTATCGATACA
496945 AGTCATTGGC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:503233 original size:13 final size:13
Alignment explanation
Indices: 503214--503252 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
503204 ATAGCATTCT
503214 CTGTATCGATACA
1 CTGTATCGATACA
*
503227 TTGTATCGATACA
1 CTGTATCGATACA
503240 CTGTATCGATACA
1 CTGTATCGATACA
503253 AGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:503718 original size:20 final size:22
Alignment explanation
Indices: 503693--503737 Score: 76
Period size: 20 Copynumber: 2.1 Consensus size: 22
503683 GCAGCACCTA
503693 CCAGGTCGCAACC-GGCA-CCC
1 CCAGGTCGCAACCGGGCAGCCC
503713 CCAGGTCGCAACCGGGCAGCCC
1 CCAGGTCGCAACCGGGCAGCCC
503735 CCA
1 CCA
503738 CACTAGCAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.57
21 4 0.17
22 6 0.26
ACGTcount: A:0.20, C:0.49, G:0.27, T:0.04
Consensus pattern (22 bp):
CCAGGTCGCAACCGGGCAGCCC
Found at i:505165 original size:22 final size:21
Alignment explanation
Indices: 505116--505168 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
505106 ATTATTTTAC
505116 TAAGGGGGAGAAACGTTTGAT
1 TAAGGGGGAGAAACGTTTGAT
**
505137 TAAGGGGGAGAAATTTTTGAT
1 TAAGGGGGAGAAACGTTTGAT
*
505158 TTAGGGGGAGA
1 TAAGGGGGAGA
505169 GAAAAGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.02, G:0.40, T:0.26
Consensus pattern (21 bp):
TAAGGGGGAGAAACGTTTGAT
Found at i:505708 original size:20 final size:20
Alignment explanation
Indices: 505677--505733 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
505667 GTCAAAACCC
*
505677 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
505697 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
505717 TGCATTGTATCGATACA
1 TGAAATGTATCGATACA
505734 TGACCAAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:505745 original size:20 final size:21
Alignment explanation
Indices: 505722--505774 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
505712 CAGATTGCAT
**
505722 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
505742 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
505763 TGTATCGATACA
1 TGTATCGATACA
505775 AGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:505844 original size:13 final size:13
Alignment explanation
Indices: 505826--505851 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
505816 ACACACAGTA
505826 TGTATCGATACAT
1 TGTATCGATACAT
505839 TGTATCGATACAT
1 TGTATCGATACAT
505852 CATAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:505867 original size:33 final size:32
Alignment explanation
Indices: 505806--505873 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
505796 GTAGCCAAAC
**
505806 TTGTATCGATACACACAGTATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
505838 TTGTATCGATACATCATAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
505871 TTG
1 TTG
505874 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:510411 original size:22 final size:21
Alignment explanation
Indices: 510381--510423 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
510371 GTTTGTGGGC
510381 TGGAAGCTG-CTGTTTGCTGGAG
1 TGGAAGCTGTC-G-TTGCTGGAG
*
510403 TGGATGCTGTCGTTGCTGGAG
1 TGGAAGCTGTCGTTGCTGGAG
510424 CTATTGCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 9 0.47
23 1 0.05
ACGTcount: A:0.12, C:0.14, G:0.42, T:0.33
Consensus pattern (21 bp):
TGGAAGCTGTCGTTGCTGGAG
Found at i:510420 original size:64 final size:64
Alignment explanation
Indices: 510352--510472 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 64
510342 ATACTATTGC
* * * *
510352 TGCTGGAGCTGCTT-CCGGTGTTTGTGGGCTGGAAGCTGCTGTTTGCTGGAGTGGATGCTGTCGT
1 TGCTGGAGCT-ATTGCCGGTGTTCGTGGGCTAGAAGCTGCTGATTGCTGGAGTGGATGCTGTCGT
* * *
510416 TGCTGGAGCTATTGCTGGTGTTCGTTGGCTAGAAGCTGCTGATTGTTGGAGTGGATG
1 TGCTGGAGCTATTGCCGGTGTTCGTGGGCTAGAAGCTGCTGATTGCTGGAGTGGATG
510473 TTGGAAGCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
63 2 0.04
64 47 0.96
ACGTcount: A:0.11, C:0.15, G:0.40, T:0.35
Consensus pattern (64 bp):
TGCTGGAGCTATTGCCGGTGTTCGTGGGCTAGAAGCTGCTGATTGCTGGAGTGGATGCTGTCGT
Found at i:510494 original size:29 final size:29
Alignment explanation
Indices: 510447--510504 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
510437 TCGTTGGCTA
*
510447 GAAGCTGCTGATTGTTGGAGTGGATGTTG
1 GAAGCTGCTGATTGCTGGAGTGGATGTTG
* *
510476 GAAGCTGTTGCTTGCTGGAGTGGATGTTG
1 GAAGCTGCTGATTGCTGGAGTGGATGTTG
510505 TCATTGTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.09, G:0.41, T:0.34
Consensus pattern (29 bp):
GAAGCTGCTGATTGCTGGAGTGGATGTTG
Found at i:510570 original size:26 final size:26
Alignment explanation
Indices: 510534--510584 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
510524 GAGCTCATAG
510534 GCTGGAAGCTGCTTGCTGGAGTGGAC
1 GCTGGAAGCTGCTTGCTGGAGTGGAC
*
510560 GCTGGAAGCTGCTTGTTGGAGTGGA
1 GCTGGAAGCTGCTTGCTGGAGTGGA
510585 TGCTACTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.16, C:0.16, G:0.43, T:0.25
Consensus pattern (26 bp):
GCTGGAAGCTGCTTGCTGGAGTGGAC
Found at i:511424 original size:11 final size:11
Alignment explanation
Indices: 511410--511435 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
511400 AAATTTTTTG
511410 ATTTATTATTA
1 ATTTATTATTA
511421 ATTTATTATTA
1 ATTTATTATTA
511432 ATTT
1 ATTT
511436 TTTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTATTATTA
Found at i:511998 original size:43 final size:43
Alignment explanation
Indices: 511951--513309 Score: 826
Period size: 43 Copynumber: 31.8 Consensus size: 43
511941 AAAAGGTGGT
** * * *
511951 AAAGTCTCCAAAGTCAAAGCCAACAGGTAGACTGAAGGGTAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * * * *
511994 AAAGTCTCCAAGGTTAAAGCCGATAGGCAGACTG-AGGGTAAG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* ** * * * * * **
512036 AAAATCTTAAAGGTTAAAACTGACCA-GCAAACTTTA-GAT-GTG
1 AAAGTCTCCAGGGTCAAAGCCGA-CAGGCAGACTGAAGGATAG-G
** * **
512078 GTAGTCTCCAGGGTCAAAGCTGACAGGCAGACT-AAAAAGTAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGA-TAGG
* * * * * * * *
512121 AAAGTCTCTAGGGTCAAAGTCTACAGGTAGACTTAGGGACAAG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * * * * *
512164 AAAATCTCCAAGGTCAAAGCCGATAGGCAAAATGAAGGATTGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * * **
512207 AAAGTCTCCAGGGTTAAAGCCAATAGGCAGACTTTA-GATGAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGAT-AGG
* * * *
512250 -TAGTCTCCAAGGTCAAAGCCGATAGGCAGACT-AAGGGTAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* ** * **
512291 AAAGTCTCCAGGATCAAAATCGACAGGCAAACTTTA-GATGAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGAT-AGG
* * * *
512334 -CAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGGTAAG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * **
512376 AAAGTCTCTAGGGTCAAAGCTGACAGGCAGACTTTA-GATAAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGAT-AGG
* * * *
512419 -CAGTCTCCAGGGTCAAAGTCGACAAGTAGACTGAAGGATAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * * **
512461 AAAGTCTTCAGGGTCAAAGCCGATAGGCAAACTTTA-GATGAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGAT-AGG
* * * * *
512504 -CAGTCTCCAAGGTCAAAGCCAACAGACAGACTGAAGGATAGA
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * * * * **
512546 AAAGTCTCCAGGGTTAAAGCCAATAGACAAACTTTA-GATGAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGAT-AGG
* * ** *
512589 -TAGTCTCCAAGGTCAAAGCCGACATACAGATTGAA-GATAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * * * **
512630 AAAGTCTCTAGGGTCCAAGCTGACAGGTAGACTTTA-GATGAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGAT-AGG
* * * * *
512673 -CAGTCTCCAAGGTCAAAGCCAACAAGCAGACTCAAGGATAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* ** * * * *
512715 AAAGTCTACAGGGTCAAAGCTAACAAGTAGACTTAGGGATAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * * * * * *
512758 AAAGCCTCTAGGGTCAAAGCCGATAAGCATATTGAAGGATAGA
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * * *
512801 AAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTTAAGGATAAG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * * * * *
512844 AAAGTCTCCAAGGTCAAAGCCGACAAGTAAACTTAGGGATAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * * * * *
512887 AAAGTCTCCGGGGTCAAAACCAATAGGCAAACTTAAAATAGG-TAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGAC-T--GA-AGGATAGG
* * **
512933 AAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTTTA-GATGAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGAT-AGG
* * * **
512976 -CAGTCTCTAAGGTCAAAGCCGACAGGCAGACTTTA-GATGAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGAT-AGG
* * * * * *
513018 -CAGTCTCTAAGGTCAAAGCTGACAGGCAGACTGAAAGATAAG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * * **
513060 AAAGTTTCCAGGATCAAAGCCGACAAGCAGACTTTA-GATGAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGAT-AGG
* * * * *
513103 -CAGTCTCTACGGTTAAAGCCAACAGGCAGACTGAAGGATAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * * *
513145 AAAGTCTCCAAGGTCAAAGCCAACAGGTAGACTGAAGGATAAG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * * * *
513188 AAAGTCTCTAGGGTCAAAGCCGACAAGTAGACTTAGGGATAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
* * * * **
513231 AAAGTCTCTAGGGTCAAAGCCCATAGGCAGACTTAAAATGGGCAGG
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGAC-T-GAA-GGATAGG
* *
513277 AAAGTCTCCAGAGTCAAAGCCTACAGGCAGACT
1 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT
513310 TAGAATAATG
Statistics
Matches: 1011, Mismatches: 265, Indels: 78
0.75 0.20 0.06
Matches are distributed among these distances:
41 11 0.01
42 400 0.40
43 527 0.52
44 5 0.00
45 3 0.00
46 63 0.06
47 2 0.00
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (43 bp):
AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGG
Found at i:512420 original size:85 final size:85
Alignment explanation
Indices: 511996--513309 Score: 1063
Period size: 85 Copynumber: 15.4 Consensus size: 85
511986 AGGGTAGGAA
* * * * * * * * *
511996 AGTCTCCAAGGTTAAAGCCGATAGGCAGACTG-AGGGTAAGAAAATCT-TAAAGGTTAAAACTGA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCT-AGGGTCAAAGCCGA
* * *
512059 CCA-GCAAACTTTAGATGTGGT
65 -CAGGCAGACTTTAGATGAGGC
* * ** * *
512080 AGTCTCCAGGGTCAAAGCTGACAGGCAGACT-AAAAAGTAGGAAAGTCTCTAGGGTCAAAGTCTA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGA-TAGGAAAGTCTCTAGGGTCAAAGCCGA
* ** **
512144 CAGGTAGAC-TTAGGGACAAGAA
65 CAGGCAGACTTTA--GATGAGGC
* * * * * * * * *
512166 AATCTCCAAGGTCAAAGCCGATAGGCAAAATGAAGGATTGGAAAGTCTCCAGGGTTAAAGCCAAT
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCTAGGGTCAAAGCCGAC
*
512231 AGGCAGACTTTAGATGAGGT
66 AGGCAGACTTTAGATGAGGC
* * * * **
512251 AGTCTCCAAGGTCAAAGCCGATAGGCAGACT-AAGGGTAGGAAAGTCTCCAGGATCAAAATCGAC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCTAGGGTCAAAGCCGAC
*
512315 AGGCAAACTTTAGATGAGGC
66 AGGCAGACTTTAGATGAGGC
* * *
512335 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGGTAAGAAAGTCTCTAGGGTCAAAGCTGAC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCTAGGGTCAAAGCCGAC
*
512400 AGGCAGACTTTAGATAAGGC
66 AGGCAGACTTTAGATGAGGC
* * * *
512420 AGTCTCCAGGGTCAAAGTCGACAAGTAGACTGAAGGATAGGAAAGTCT-TCAGGGTCAAAGCCGA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCT-AGGGTCAAAGCCGA
* *
512484 TAGGCAAACTTTAGATGAGGC
65 CAGGCAGACTTTAGATGAGGC
* * * * * * *
512505 AGTCTCCAAGGTCAAAGCCAACAGACAGACTGAAGGATAGAAAAGTCTCCAGGGTTAAAGCCAAT
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCTAGGGTCAAAGCCGAC
* * *
512570 AGACAAACTTTAGATGAGGT
66 AGGCAGACTTTAGATGAGGC
** * * *
512590 AGTCTCCAAGGTCAAAGCCGACATACAGATTGAA-GATAGGAAAGTCTCTAGGGTCCAAGCTGAC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCTAGGGTCAAAGCCGAC
*
512654 AGGTAGACTTTAGATGAGGC
66 AGGCAGACTTTAGATGAGGC
* * * **
512674 AGTCTCCAAGGTCAAAGCCAACAAGCAGACTCAAGGATAGGAAAGTCTAC-AGGGTCAAAGCTAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCT-CTAGGGTCAAAGCCGA
* * *
512738 CAAGTAGAC-TTAGGGAT-AGGAA
65 CAGGCAGACTTTA--GATGAGG-C
* * * * * * * *
512760 AGCCTCTAGGGTCAAAGCCGATAAGCATATTGAAGGATAGAAAAGTCTCTAGGGTCAAAGCCGAC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCTAGGGTCAAAGCCGAC
* * * **
512825 AGGTAGACTTAAGGATAAGAA
66 AGGCAGACTTTA-GATGAGGC
* * * * * ** * * *
512846 AGTCTCCAAGGTCAAAGCCGACAAGTAAACTTAGGGATAGGAAAGTCTCCGGGGTCAAAACCAAT
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCTAGGGTCAAAGCCGAC
* * * *
512911 AGGCAAACTTAAAATAGGTAGGAA
66 AGGCAGACTTTAGAT--G-AGG-C
* * * ** * *
512935 AGTCTCTAGGGTCAAAGCCGACAGGTAGACTTTA-GATGAGG-CAGTCTCTAAGGTCAAAGCCGA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGAT-AGGAAAGTCTCTAGGGTCAAAGCCGA
512998 CAGGCAGACTTTAGATGAGGC
65 CAGGCAGACTTTAGATGAGGC
* * * * * * *
513019 AGTCTCTAAGGTCAAAGCTGACAGGCAGACTGAAAGATAAGAAAGTTTCCAGGATCAAAGCCGAC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCTAGGGTCAAAGCCGAC
*
513084 AAGCAGACTTTAGATGAGGC
66 AGGCAGACTTTAGATGAGGC
* * * * * * *
513104 AGTCTCTACGGTTAAAGCCAACAGGCAGACTGAAGGATAGGAAAGTCTCCAAGGTCAAAGCCAAC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCTAGGGTCAAAGCCGAC
* ** * **
513169 AGGTAGACTGAAGGATAAGAA
66 AGGCAGACTTTA-GATGAGGC
* * * * * * * *
513190 AGTCTCTAGGGTCAAAGCCGACAAGTAGACTTAGGGATAGGAAAGTCTCTAGGGTCAAAGCCCAT
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCTAGGGTCAAAGCCGAC
* * *
513255 AGGCAGACTTAAAATGGGCAGGAA
66 AGGCAGACTTTAGAT--G-AGG-C
*
513279 AGTCTCC-AGAGTCAAAGCCTACAGGCAGACT
1 AGTCTCCAAG-GTCAAAGCCGACAGGCAGACT
513310 TAGAATAATG
Statistics
Matches: 989, Mismatches: 209, Indels: 59
0.79 0.17 0.05
Matches are distributed among these distances:
84 209 0.21
85 421 0.43
86 256 0.26
87 10 0.01
88 36 0.04
89 57 0.06
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (85 bp):
AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCTAGGGTCAAAGCCGAC
AGGCAGACTTTAGATGAGGC
Found at i:522715 original size:33 final size:32
Alignment explanation
Indices: 522669--522736 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
522659 CCGTTAGAAG
522669 AATGTATCAATACAAT-TCATCATGTATCGATAC
1 AATGTATCAATACAATATC--CATGTATCGATAC
**
522702 AATGTATTGATACAATATGCCATGTATCGATAC
1 AATGTATCAATACAATAT-CCATGTATCGATAC
522735 AA
1 AA
522737 ATAGTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (32 bp):
AATGTATCAATACAATATCCATGTATCGATAC
Found at i:523442 original size:22 final size:20
Alignment explanation
Indices: 523404--523445 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
523394 GGCTCTCATT
*
523404 AAAAATTTCCCCTTTGATAA
1 AAAAATTTCCCCCTTGATAA
523424 AAAAATTTCTCCCCCTTGATAA
1 AAAAA-TT-TCCCCCTTGATAA
523446 TCGATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAAATTTCCCCCTTGATAA
Found at i:525233 original size:13 final size:13
Alignment explanation
Indices: 525215--525240 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
525205 CAATTTTTTG
525215 TGTATCGATACAT
1 TGTATCGATACAT
525228 TGTATCGATACAT
1 TGTATCGATACAT
525241 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:525326 original size:20 final size:20
Alignment explanation
Indices: 525301--525373 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
525291 ATCTTTTTTT
525301 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
525321 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
525342 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
525362 ATGTATCGATAC
1 ATGTATCGATAC
525374 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:525352 original size:41 final size:42
Alignment explanation
Indices: 525279--525373 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
525269 CTGCCAAGAA
*
525279 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
525321 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
525362 ATGTATCGATAC
1 ATGTATCGATAC
525374 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:527851 original size:13 final size:13
Alignment explanation
Indices: 527833--527871 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
527823 ATAATCACCC
*
527833 TGTATCGATACAG
1 TGTATCGATACAA
527846 TGTATCGATACAA
1 TGTATCGATACAA
527859 TGTATCGATACAA
1 TGTATCGATACAA
527872 CAAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:527882 original size:20 final size:20
Alignment explanation
Indices: 527857--527935 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
527847 GTATCGATAC
527857 AATGTATCGATACAACAAAA
1 AATGTATCGATACAACAAAA
* *
527877 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACA-ACAA----AA
*
527902 GATGTATCGATAC-ACAAAA
1 AATGTATCGATACAACAAAA
527921 ACATGTATCGATACA
1 A-ATGTATCGATACA
527936 TTTTGGACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 26 0.57
21 3 0.07
23 3 0.07
25 13 0.28
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAACAAAA
Found at i:529970 original size:15 final size:15
Alignment explanation
Indices: 529950--529980 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
529940 ATTTCGTTTG
*
529950 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
529965 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
529980 G
1 G
529981 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:534060 original size:13 final size:13
Alignment explanation
Indices: 534042--534067 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
534032 CAATTTTTTG
534042 TGTATCGATACAT
1 TGTATCGATACAT
534055 TGTATCGATACAT
1 TGTATCGATACAT
534068 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:534153 original size:20 final size:20
Alignment explanation
Indices: 534128--534200 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
534118 ATCTTTTTTT
534128 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
534148 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
534169 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
534189 ATGTATCGATAC
1 ATGTATCGATAC
534201 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:534179 original size:41 final size:42
Alignment explanation
Indices: 534106--534200 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
534096 CTGCCAAGAA
*
534106 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
534148 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
534189 ATGTATCGATAC
1 ATGTATCGATAC
534201 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:535196 original size:22 final size:21
Alignment explanation
Indices: 535161--535210 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
535151 TTTGTTGATG
*
535161 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
535181 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
535202 AATTTGAAG
1 ATTTTGAAG
535211 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:535207 original size:21 final size:22
Alignment explanation
Indices: 535168--535210 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
535158 ATGATTTTGA
* *
535168 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
535190 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
535211 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:541498 original size:33 final size:33
Alignment explanation
Indices: 541473--541552 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
541463 TACAATTCAT
*
541473 CATGTATCGATACTTTGTATCGATACAATGTGC
1 CATGTATCGATACATTGTATCGATACAATGTGC
**
541506 CATGTATCGATACATTAAATCGATACAATGTGC
1 CATGTATCGATACATTGTATCGATACAATGTGC
541539 CATGTATCGATACA
1 CATGTATCGATACA
541553 AACAGTGGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (33 bp):
CATGTATCGATACATTGTATCGATACAATGTGC
Found at i:541513 original size:20 final size:20
Alignment explanation
Indices: 541488--541553 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
541478 ATCGATACTT
541488 TGTATCGATACAATGTGCCA
1 TGTATCGATACAATGTGCCA
541508 TGTATCGATAC-AT-T---A
1 TGTATCGATACAATGTGCCA
*
541523 --AATCGATACAATGTGCCA
1 TGTATCGATACAATGTGCCA
541541 TGTATCGATACAA
1 TGTATCGATACAA
541554 ACAGTGGTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 8 0.22
14 2 0.05
15 2 0.05
18 2 0.05
19 2 0.05
20 21 0.57
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (20 bp):
TGTATCGATACAATGTGCCA
Found at i:541640 original size:13 final size:13
Alignment explanation
Indices: 541622--541648 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
541612 TATAATGAAT
541622 ATGTATCGATACA
1 ATGTATCGATACA
541635 ATGTATCGATACA
1 ATGTATCGATACA
541648 A
1 A
541649 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:546463 original size:174 final size:174
Alignment explanation
Indices: 546173--546522 Score: 700
Period size: 174 Copynumber: 2.0 Consensus size: 174
546163 TTAATGTTCA
546173 TTAAACTTTCCTAAATTAGCGATTCAGTCCCTTCATAAAAAAACTACAAAAATTAAATGTTATAC
1 TTAAACTTTCCTAAATTAGCGATTCAGTCCCTTCATAAAAAAACTACAAAAATTAAATGTTATAC
546238 ATCAAAATCAAAAGTGAAAACACATCAAGAATTTATTCCAAACATTCGGCCAAGCAACACATACC
66 ATCAAAATCAAAAGTGAAAACACATCAAGAATTTATTCCAAACATTCGGCCAAGCAACACATACC
546303 ATGAGTCAAAATTTTTGACATTTTTGTAATTTAGTCCCCATCTT
131 ATGAGTCAAAATTTTTGACATTTTTGTAATTTAGTCCCCATCTT
546347 TTAAACTTTCCTAAATTAGCGATTCAGTCCCTTCATAAAAAAACTACAAAAATTAAATGTTATAC
1 TTAAACTTTCCTAAATTAGCGATTCAGTCCCTTCATAAAAAAACTACAAAAATTAAATGTTATAC
546412 ATCAAAATCAAAAGTGAAAACACATCAAGAATTTATTCCAAACATTCGGCCAAGCAACACATACC
66 ATCAAAATCAAAAGTGAAAACACATCAAGAATTTATTCCAAACATTCGGCCAAGCAACACATACC
546477 ATGAGTCAAAATTTTTGACATTTTTGTAATTTAGTCCCCATCTT
131 ATGAGTCAAAATTTTTGACATTTTTGTAATTTAGTCCCCATCTT
546521 TT
1 TT
546523 CCAATGTTTG
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 176 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.31
Consensus pattern (174 bp):
TTAAACTTTCCTAAATTAGCGATTCAGTCCCTTCATAAAAAAACTACAAAAATTAAATGTTATAC
ATCAAAATCAAAAGTGAAAACACATCAAGAATTTATTCCAAACATTCGGCCAAGCAACACATACC
ATGAGTCAAAATTTTTGACATTTTTGTAATTTAGTCCCCATCTT
Found at i:547301 original size:23 final size:23
Alignment explanation
Indices: 547258--547311 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
547248 AGCTACTGTT
**
547258 GTTGCTGTCGTGCTATTG-TTTC
1 GTTGCTGTCGTGCTAGGGTTTTC
*
547280 GTTGCTGTTCGTGCTGGGGTTTTC
1 GTTGCTG-TCGTGCTAGGGTTTTC
547304 GATTGCTG
1 G-TTGCTG
547312 GAGGTTACGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 7 0.27
23 8 0.31
24 5 0.19
25 6 0.23
ACGTcount: A:0.04, C:0.17, G:0.33, T:0.46
Consensus pattern (23 bp):
GTTGCTGTCGTGCTAGGGTTTTC
Found at i:547377 original size:26 final size:25
Alignment explanation
Indices: 547320--547381 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
547310 TGGAGGTTAC
* *
547320 GGAGCTGCTGGCGTGCTCGTGAGCT
1 GGAGCTGCTGGAGTGCTCGAGAGCT
547345 GGAAGCTGCTGGAGTGCTCGA-AGGCT
1 GG-AGCTGCTGGAGTGCTCGAGA-GCT
547371 AGGAGCTGCTG
1 -GGAGCTGCTG
547382 CTGCTGTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 3 0.09
26 27 0.84
27 2 0.06
ACGTcount: A:0.15, C:0.21, G:0.44, T:0.21
Consensus pattern (25 bp):
GGAGCTGCTGGAGTGCTCGAGAGCT
Found at i:548267 original size:8 final size:8
Alignment explanation
Indices: 548254--548278 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
548244 TGCAATACAT
548254 AGCATGAA
1 AGCATGAA
548262 AGCATGAA
1 AGCATGAA
548270 AGCATGAA
1 AGCATGAA
548278 A
1 A
548279 TGTTTATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.24, T:0.12
Consensus pattern (8 bp):
AGCATGAA
Found at i:548458 original size:7 final size:7
Alignment explanation
Indices: 548441--548520 Score: 63
Period size: 7 Copynumber: 11.0 Consensus size: 7
548431 CCATTTCTTT
548441 TTTTATTA
1 TTTT-TTA
548449 TTTTTTA
1 TTTTTTA
548456 TTTTTTGA
1 TTTTTT-A
***
548464 TAAATT-
1 TTTTTTA
*
548470 TTTTTGA
1 TTTTTTA
548477 TTTTTTA
1 TTTTTTA
*
548484 TTAATTTA
1 TT-TTTTA
*
548492 TTATTTA
1 TTTTTTA
548499 TTTTTTA
1 TTTTTTA
548506 TTTTTTTA
1 -TTTTTTA
548514 TTTTTTA
1 TTTTTTA
548521 AAAAAAAACG
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
6 2 0.03
7 35 0.60
8 21 0.36
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (7 bp):
TTTTTTA
Found at i:548460 original size:8 final size:8
Alignment explanation
Indices: 548438--548519 Score: 53
Period size: 8 Copynumber: 9.8 Consensus size: 8
548428 CAGCCATTTC
548438 TTTTTTTA
1 TTTTTTTA
548446 TTATTTTTTA
1 -T-TTTTTTA
548456 TTTTTTGATAAA
1 TTTTTT--T--A
548468 TTTTTTTGA
1 TTTTTTT-A
548477 -TTTTTTA
1 TTTTTTTA
**
548484 TTAATTTA
1 TTTTTTTA
*
548492 -TTATTTA
1 TTTTTTTA
548499 -TTTTTTA
1 TTTTTTTA
548506 TTTTTTTA
1 TTTTTTTA
548514 TTTTTT
1 TTTTTT
548520 AAAAAAAAAC
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
7 13 0.21
8 29 0.48
9 3 0.05
10 9 0.15
12 7 0.11
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTTTTA
Found at i:548479 original size:21 final size:19
Alignment explanation
Indices: 548449--548520 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
548439 TTTTTTATTA
548449 TTTTTTATTTTTTGATAAAT
1 TTTTTTATTTTTT-ATAAAT
*
548469 TTTTTTGATTTTTTATTAA-
1 TTTTTT-ATTTTTTATAAAT
* **
548488 TTTATTATTTATTT-TTTAT
1 TTTTTTATTT-TTTATAAAT
548507 TTTTTTATTTTTTA
1 TTTTTTATTTTTTA
548521 AAAAAAAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
18 10 0.23
19 17 0.39
20 10 0.23
21 7 0.16
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTTTTATTTTTTATAAAT
Found at i:548515 original size:22 final size:22
Alignment explanation
Indices: 548446--548507 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
548436 TCTTTTTTTA
* *
548446 TTATTTTTTATTTTTTGATAAAT
1 TTATTATTTATTTTTT-ATTAAT
*
548469 TT-TT-TTGATTTTTTATTAAT
1 TTATTATTTATTTTTTATTAAT
548489 TTATTATTTATTTTTTATT
1 TTATTATTTATTTTTTATT
548508 TTTTTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 7 0.21
21 11 0.32
22 14 0.41
23 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (22 bp):
TTATTATTTATTTTTTATTAAT
Done.