Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 57 of 173
Found at i:16169019 original size:142 final size:142
Alignment explanation
Indices: 16168763--16169039 Score: 482
Period size: 142 Copynumber: 2.0 Consensus size: 142
16168753 GACCTGTTAT
16168763 GATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTATTCTAATCCGCTCCACTATAATCTC
1 GATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTATTCTAATCCGCTCCACTATAATCTC
* *
16168828 AGGGAAATAAGATTACTGGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAAGATTTCTGGCT
66 AGGGAAATAAGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCT
16168893 TCAATTTGATGC
131 TCAATTTGATGC
* * * *
16168905 GATCTACTCTATTGTAACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATCTC
1 GATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTATTCTAATCCGCTCCACTATAATCTC
* *
16168970 AGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCT
66 AGGGAAATAAGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCT
16169035 TCAAT
131 TCAAT
16169040 CTGCTCCACT
Statistics
Matches: 127, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 127 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (142 bp):
GATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTATTCTAATCCGCTCCACTATAATCTC
AGGGAAATAAGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCT
TCAATTTGATGC
Found at i:16170386 original size:13 final size:14
Alignment explanation
Indices: 16170359--16170416 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
16170349 CCTCAACCTC
16170359 TTCATTTTTACTTT
1 TTCATTTTTACTTT
16170373 TTCATTTTTA-TTT
1 TTCATTTTTACTTT
16170386 TTCCATTTTCT-CTTT
1 TT-CATTTT-TACTTT
** *
16170401 TTTGTTTTTTCTTT
1 TTCATTTTTACTTT
16170415 TT
1 TT
16170417 TTCTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 6 0.16
14 26 0.68
15 6 0.16
ACGTcount: A:0.09, C:0.14, G:0.02, T:0.76
Consensus pattern (14 bp):
TTCATTTTTACTTT
Found at i:16170408 original size:22 final size:22
Alignment explanation
Indices: 16170377--16170425 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
16170367 TACTTTTTCA
16170377 TTTTTATTTTTCCATTTTCTCT
1 TTTTTATTTTTCCATTTTCTCT
* * * *
16170399 TTTTTGTTTTTTCTTTTTTTCT
1 TTTTTATTTTTCCATTTTCTCT
16170421 TTTTT
1 TTTTT
16170426 TCTCAAAGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.82
Consensus pattern (22 bp):
TTTTTATTTTTCCATTTTCTCT
Found at i:16170428 original size:8 final size:8
Alignment explanation
Indices: 16170391--16170428 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
16170381 TATTTTTCCA
16170391 TTTTCTCTT
1 TTTTCT-TT
*
16170400 TTTT-GTT
1 TTTTCTTT
16170407 TTTTCTTT
1 TTTTCTTT
16170415 TTTTCTTT
1 TTTTCTTT
16170423 TTTTCT
1 TTTTCT
16170429 CAAAGTCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 6 0.23
8 16 0.62
9 4 0.15
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (8 bp):
TTTTCTTT
Found at i:16170428 original size:16 final size:16
Alignment explanation
Indices: 16170391--16170425 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
16170381 TATTTTTCCA
16170391 TTTTCTCTTTTTTGTT
1 TTTTCTCTTTTTTGTT
*
16170407 TTTTCT-TTTTTTCTT
1 TTTTCTCTTTTTTGTT
16170422 TTTT
1 TTTT
16170426 TCTCAAAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTTCTCTTTTTTGTT
Found at i:16171239 original size:7 final size:7
Alignment explanation
Indices: 16171217--16171259 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
16171207 TGGCTTCTCC
16171217 TTCTTTT
1 TTCTTTT
*
16171224 TCCTTTT
1 TTCTTTT
16171231 TTCTTTT
1 TTCTTTT
*
16171238 TTCTTCT
1 TTCTTTT
*
16171245 CTCTTTT
1 TTCTTTT
16171252 TTCATTTT
1 TTC-TTTT
16171260 CATTTTGACT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
7 25 0.86
8 4 0.14
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (7 bp):
TTCTTTT
Found at i:16181987 original size:43 final size:43
Alignment explanation
Indices: 16181926--16182012 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
16181916 GAATCGGGTT
*
16181926 TGTGAATCGAGAGAGAGTGGTCATGCCTTAATTTTTTAAATTA
1 TGTGAATCGAGAGAGAGTGATCATGCCTTAATTTTTTAAATTA
16181969 TGTGAATCGAGAGAGAGTGATCATGCCTTAATTTTTTAAATTA
1 TGTGAATCGAGAGAGAGTGATCATGCCTTAATTTTTTAAATTA
16182012 T
1 T
16182013 CTATGCATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (43 bp):
TGTGAATCGAGAGAGAGTGATCATGCCTTAATTTTTTAAATTA
Found at i:16197818 original size:28 final size:26
Alignment explanation
Indices: 16197773--16197824 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
16197763 CTATTCAGTA
16197773 ACAGTACAGTATGGCCTTAGCCCAAT
1 ACAGTACAGTATGGCCTTAGCCCAAT
*
16197799 ACAGTAACAGTGTGGGCCTTAGCCCA
1 ACAGT-ACAGTAT-GGCCTTAGCCCA
16197825 TTATAGTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 5 0.22
27 6 0.26
28 12 0.52
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (26 bp):
ACAGTACAGTATGGCCTTAGCCCAAT
Found at i:16197983 original size:26 final size:27
Alignment explanation
Indices: 16197948--16198013 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 27
16197938 AATATAGCAA
*
16197948 CAAAGTTGCCAGTAAT-AGTAAT-GCAG
1 CAAAGCTGCCAGTAATCAGT-ATCGCAG
16197974 CAAAGCTGCCAGT-ATCAGTATCGCAG
1 CAAAGCTGCCAGTAATCAGTATCGCAG
*
16198000 CAAAACTGCCAGTA
1 CAAAGCTGCCAGTA
16198014 CAGTATACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 4 0.11
26 31 0.89
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (27 bp):
CAAAGCTGCCAGTAATCAGTATCGCAG
Found at i:16200811 original size:26 final size:26
Alignment explanation
Indices: 16200782--16200851 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
16200772 CATTCTGACC
*
16200782 CACAGCTCGTGTGAGCAAGCCCATTT
1 CACAGCTCGTGTGAGCAAACCCATTT
*
16200808 CACAGCTCGTGTGAGCAAACTCATTT
1 CACAGCTCGTGTGAGCAAACCCATTT
*
16200834 CACAGCTTGTGTGAGCAA
1 CACAGCTCGTGTGAGCAA
16200852 CGATGTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCAAACCCATTT
Found at i:16201534 original size:21 final size:21
Alignment explanation
Indices: 16201508--16201550 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
16201498 TGTTGAAATA
16201508 GTCAAGTAAAAGTATATGTTG
1 GTCAAGTAAAAGTATATGTTG
16201529 GTCAAGTAAAAGTATATGTTG
1 GTCAAGTAAAAGTATATGTTG
16201550 G
1 G
16201551 ATGACCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.33
Consensus pattern (21 bp):
GTCAAGTAAAAGTATATGTTG
Found at i:16205580 original size:31 final size:32
Alignment explanation
Indices: 16205545--16205606 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
16205535 CATAATTAAA
16205545 AAACACTTA-AA-ATAAATAAAACCCTAAACTT
1 AAACACTTACAATATAAA-AAAACCCTAAACTT
*
16205576 AAACACTTACAATCTAAAAAAACCCTAAACT
1 AAACACTTACAATATAAAAAAACCCTAAACT
16205607 CTAATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 9 0.32
32 15 0.54
33 4 0.14
ACGTcount: A:0.56, C:0.23, G:0.00, T:0.21
Consensus pattern (32 bp):
AAACACTTACAATATAAAAAAACCCTAAACTT
Found at i:16206131 original size:46 final size:45
Alignment explanation
Indices: 16206075--16206199 Score: 144
Period size: 46 Copynumber: 2.7 Consensus size: 45
16206065 CAGGTCTTAT
*
16206075 TATACCTGTATTCTCGAGTCTGCAACACATGCTGGAGCTCGAAACC
1 TATACTTGTATTCTCGAGTCTGCAACA-ATGCTGGAGCTCGAAACC
* ** * *
16206121 TATACTTGTATTCTTGAGTCCACAACAATTGTTGTAGCTCGAAACC
1 TATACTTGTATTCTCGAGTCTGCAACAA-TGCTGGAGCTCGAAACC
*
16206167 TATA-TCTATATTCTCGAGTCTGCAACATATGCT
1 TATACT-TGTATTCTCGAGTCTGCAACA-ATGCT
16206200 AGCACTCAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
45 2 0.03
46 62 0.95
47 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (45 bp):
TATACTTGTATTCTCGAGTCTGCAACAATGCTGGAGCTCGAAACC
Found at i:16206212 original size:46 final size:45
Alignment explanation
Indices: 16206083--16206213 Score: 131
Period size: 46 Copynumber: 2.8 Consensus size: 45
16206073 ATTATACCTG
* *
16206083 TATTCTCGAGTCTGCAACACATGCTGGAGCTCGAAACCTATACTTG
1 TATTCTCGAGTCTGCAACA-ATGCTGCAGCTCGAAACCTATACTTA
* ** * *
16206129 TATTCTTGAGTCCACAACAATTGTTGTAGCTCGAAACCTATA-TCTA
1 TATTCTCGAGTCTGCAACAA-TGCTGCAGCTCGAAACCTATACT-TA
*
16206175 TATTCTCGAGTCTGCAACATATGCTAGCA-CTCAAAACCT
1 TATTCTCGAGTCTGCAACA-ATGCT-GCAGCTCGAAACCT
16206214 GGGGTAATAA
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
45 2 0.03
46 64 0.93
47 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (45 bp):
TATTCTCGAGTCTGCAACAATGCTGCAGCTCGAAACCTATACTTA
Found at i:16209983 original size:31 final size:29
Alignment explanation
Indices: 16209948--16210038 Score: 92
Period size: 32 Copynumber: 2.9 Consensus size: 29
16209938 GAAGGAGAAG
*
16209948 AGGTTGTGTTTGGGATTTGAGAAAAGAATTA
1 AGGTTGTGTTTGGG-TTTGA-AAAAAAATTA
16209979 AGGTTGTGTTTAGGGTTTGAAAAAAAATTA
1 AGGTTGTGTTT-GGGTTTGAAAAAAAATTA
* *
16210009 AGAGATTGTATTTGGGGTTAGAAGAAAAAA
1 AG-G-TTGTGTTT-GGGTTTGAA-AAAAAA
16210039 ATCATAAAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.21
31 17 0.33
32 18 0.35
33 6 0.12
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (29 bp):
AGGTTGTGTTTGGGTTTGAAAAAAAATTA
Found at i:16210976 original size:12 final size:12
Alignment explanation
Indices: 16210959--16210983 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16210949 TTTTGTAATG
16210959 AAAATTTATTGT
1 AAAATTTATTGT
16210971 AAAATTTATTGT
1 AAAATTTATTGT
16210983 A
1 A
16210984 TCACATTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
AAAATTTATTGT
Found at i:16212834 original size:33 final size:33
Alignment explanation
Indices: 16212791--16212871 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
16212781 TGTAGTATAG
* *
16212791 CACTCCTCCCGGCTCTTATCCACCGCATTACTC
1 CACTCCTCCCGGCTCGTATCCACCGCAATACTC
* *
16212824 TACTCCTCCCGGCTCGTATCCACCGTAATACTC
1 CACTCCTCCCGGCTCGTATCCACCGCAATACTC
*
16212857 CACTCCTCCCAGCTC
1 CACTCCTCCCGGCTC
16212872 AAATTCATCA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.16, C:0.48, G:0.10, T:0.26
Consensus pattern (33 bp):
CACTCCTCCCGGCTCGTATCCACCGCAATACTC
Found at i:16213226 original size:26 final size:26
Alignment explanation
Indices: 16213189--16213240 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
16213179 ACATTACTAC
16213189 ATTAAAACGAGGAACAAACTTTGTAA
1 ATTAAAACGAGGAACAAACTTTGTAA
* *
16213215 ATTAAAATGAGGAACGAACTTTGTAA
1 ATTAAAACGAGGAACAAACTTTGTAA
16213241 TATAGATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (26 bp):
ATTAAAACGAGGAACAAACTTTGTAA
Found at i:16213286 original size:48 final size:48
Alignment explanation
Indices: 16213215--16213346 Score: 192
Period size: 48 Copynumber: 2.8 Consensus size: 48
16213205 AACTTTGTAA
* *
16213215 ATTAAAATGAGGAACGAACTTTGTAATATAGATTAGATACATTACAAC
1 ATTAAAATGAGGAACAAACTTTGTAATATAAATTAGATACATTACAAC
*
16213263 ATTAAAATGAGGAACAAACTTTGTAATATAAATTAGATACATTGCAAC
1 ATTAAAATGAGGAACAAACTTTGTAATATAAATTAGATACATTACAAC
* * * * *
16213311 ATTAAAACGATGAACATACTTTATTATATAAATTAG
1 ATTAAAATGAGGAACAAACTTTGTAATATAAATTAG
16213347 GTGCATTAGA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 76 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (48 bp):
ATTAAAATGAGGAACAAACTTTGTAATATAAATTAGATACATTACAAC
Found at i:16217110 original size:10 final size:11
Alignment explanation
Indices: 16217086--16217112 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16217076 ACTTACTAAC
16217086 AAAATAACTTA
1 AAAATAACTTA
16217097 AAAATAACTTA
1 AAAATAACTTA
16217108 AAAAT
1 AAAAT
16217113 TAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAATAACTTA
Found at i:16217323 original size:4 final size:4
Alignment explanation
Indices: 16217314--16217377 Score: 69
Period size: 4 Copynumber: 15.5 Consensus size: 4
16217304 AAAAATACAT
*
16217314 TTTC TTTC TTTC -TT- TTTC TTCTCC TTTC TTTC TTTA TTTC TTCTCC
1 TTTC TTTC TTTC TTTC TTTC TT-T-C TTTC TTTC TTTC TTTC TT-T-C
16217360 TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TT
16217378 CTCCCTCTCT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
3 4 0.08
4 38 0.73
5 4 0.08
6 6 0.12
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:16217332 original size:14 final size:14
Alignment explanation
Indices: 16217313--16217370 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
16217303 TAAAAATACA
16217313 TTTTCTTTCTTTCT
1 TTTTCTTTCTTTCT
16217327 TTTTCTTCTCCTTTC-
1 TTTTCTT-T-CTTTCT
*
16217342 -TTTCTTTATTTCT
1 TTTTCTTTCTTTCT
* *
16217355 TCTCCTTTCTTTCT
1 TTTTCTTTCTTTCT
16217369 TT
1 TT
16217371 CTTTCTTCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
12 4 0.11
13 1 0.03
14 24 0.69
15 1 0.03
16 5 0.14
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCTTTCTTTCT
Found at i:16217356 original size:22 final size:21
Alignment explanation
Indices: 16217317--16217381 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 21
16217307 AATACATTTT
16217317 CTTTCTTTC-TTTTTCTTCTC
1 CTTTCTTTCTTTTTTCTTCTC
16217337 CTTTCTTTCTTTATTTCTTCTC
1 CTTTCTTTCTTT-TTTCTTCTC
16217359 CTTTCTTTCTTTCTTTCTTCTC
1 CTTTCTTTCTTT-TTTCTTCTC
16217381 C
1 C
16217382 CTCTCTTCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
20 9 0.21
21 2 0.05
22 31 0.74
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.68
Consensus pattern (21 bp):
CTTTCTTTCTTTTTTCTTCTC
Found at i:16217543 original size:27 final size:27
Alignment explanation
Indices: 16217470--16217543 Score: 130
Period size: 27 Copynumber: 2.7 Consensus size: 27
16217460 TTAATGCACT
* *
16217470 AGTGTCGCCTATCAGATAGAGGTCACC
1 AGTGCCGCCTATCAGATAGGGGTCACC
16217497 AGTGCCGCCTATCAGATAGGGGTCACC
1 AGTGCCGCCTATCAGATAGGGGTCACC
16217524 AGTGCCGCCTATCAGATAGG
1 AGTGCCGCCTATCAGATAGG
16217544 CACCACACCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.24, C:0.27, G:0.28, T:0.20
Consensus pattern (27 bp):
AGTGCCGCCTATCAGATAGGGGTCACC
Found at i:16222654 original size:34 final size:34
Alignment explanation
Indices: 16222611--16222680 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
16222601 TTGAGACTTG
* *
16222611 AAAATTTTGAAGGTGAAGACATTTTTTTAACCTC
1 AAAATTTTGAAGATGAAGACATTTTTTGAACCTC
* *
16222645 AAAATTTTGAAGATGAGGACCTTTTTTGAACCTC
1 AAAATTTTGAAGATGAAGACATTTTTTGAACCTC
16222679 AA
1 AA
16222681 CTAATTGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (34 bp):
AAAATTTTGAAGATGAAGACATTTTTTGAACCTC
Found at i:16224885 original size:21 final size:21
Alignment explanation
Indices: 16224859--16224900 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16224849 CAATGTGGCA
* * *
16224859 AGTTAATTGGCCACGTCAGCT
1 AGTTAACTAGCCACATCAGCT
16224880 AGTTAACTAGCCACATCAGCT
1 AGTTAACTAGCCACATCAGCT
16224901 GTCCCGTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
AGTTAACTAGCCACATCAGCT
Found at i:16231219 original size:19 final size:19
Alignment explanation
Indices: 16231186--16231224 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16231176 GTAAAATTTA
*
16231186 ATTTTAATATATAAAGTAT
1 ATTTTAATATATAAAATAT
16231205 ATTTTAA-ATATTAAAATAT
1 ATTTTAATATA-TAAAATAT
16231224 A
1 A
16231225 ACCATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTTTAATATATAAAATAT
Found at i:16231895 original size:2 final size:2
Alignment explanation
Indices: 16231890--16231920 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16231880 GTGTGTGTGT
16231890 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
16231921 GGGGGGGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16235859 original size:19 final size:19
Alignment explanation
Indices: 16235835--16235877 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
16235825 AGTTGGGGAA
*
16235835 AGTGGCGAGCTAGGAGCGG
1 AGTGGCGAGCGAGGAGCGG
16235854 AGTGGCGAGCGAGGAGCGG
1 AGTGGCGAGCGAGGAGCGG
16235873 AGTGG
1 AGTGG
16235878 TGCAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.21, C:0.14, G:0.56, T:0.09
Consensus pattern (19 bp):
AGTGGCGAGCGAGGAGCGG
Found at i:16240944 original size:34 final size:34
Alignment explanation
Indices: 16240904--16241294 Score: 125
Period size: 34 Copynumber: 11.5 Consensus size: 34
16240894 TAAATAAAAG
* *
16240904 CGTGATCTTAAATCACCGTGCTATGTAAATTAGT
1 CGTGATCTTAAATCAGCGTGCTATGTAAATTAGC
* * * * *
16240938 TGTGATCTTAAAACAACATG-T-TGTAAGA-TAGGAG
1 CGTGATCTTAAATCAGCGTGCTATGTAA-ATTA-G-C
* * ** *
16240972 CGTGATCTTAAATCAGCATCCTATGTAGGTTAAC
1 CGTGATCTTAAATCAGCGTGCTATGTAAATTAGC
* *
16241006 CGTGATCTTAAATCAACG-GAT-TGTAAGATATGAG-
1 CGTGATCTTAAATCAGCGTGCTATGTAA-AT-T-AGC
* ** *
16241040 TGTGATCTTAAATTGGCGTGCTATGTAGATTAGC
1 CGTGATCTTAAATCAGCGTGCTATGTAAATTAGC
* *
16241074 CGTGATCTTAAATCAGCGAT-CTA--TAAAATAGG
1 CGTGATCTTAAATCAGCG-TGCTATGTAAATTAGC
* * *
16241106 GGTGCAATCTTAAATC-GACATGCTATGTAAATTAGT
1 CGTG--ATCTTAAATCAG-CGTGCTATGTAAATTAGC
** * * *
16241142 TATGATCTTAAATCAGTGGGCTA--TAAGATAAG-
1 CGTGATCTTAAATCAGCGTGCTATGTAA-ATTAGC
* ** * ** *
16241174 AGTGCGATCTTAAATTGGCGTGCTATATAGGTTAAC
1 CGT--GATCTTAAATCAGCGTGCTATGTAAATTAGC
* * * *
16241210 CATGATATTAAATCA--GTG-AACTGT-AATATAGGAG
1 CGTGATCTTAAATCAGCGTGCTA-TGTAAAT-TA-G-C
16241244 CGAT-ATCTTAAATCAGCGTGCTATGTAAATTAGC
1 CG-TGATCTTAAATCAGCGTGCTATGTAAATTAGC
* *
16241278 TGTGATCTTCAATCAGC
1 CGTGATCTTAAATCAGC
16241295 AGACTATAAA
Statistics
Matches: 252, Mismatches: 69, Indels: 72
0.64 0.18 0.18
Matches are distributed among these distances:
31 2 0.01
32 31 0.12
33 14 0.06
34 159 0.63
35 12 0.05
36 30 0.12
37 4 0.02
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (34 bp):
CGTGATCTTAAATCAGCGTGCTATGTAAATTAGC
Found at i:16241105 original size:136 final size:134
Alignment explanation
Indices: 16240920--16241596 Score: 585
Period size: 136 Copynumber: 5.0 Consensus size: 134
16240910 CTTAAATCAC
* * *
16240920 CGTGCTATGTAAATTAGTTGTGATCTTAAAACAAC-ATGTTGTAAGATAGGAGCGTGATCTTAAA
1 CGTGCTATGTAAATTAGTCGTGATCTTAAATCAGCGA--TTGTAAGATAGGAGCGTGATCTTAAA
* *** * * * *
16240984 TCAGCATCCTATGTAGGTTAACCGTGATCTTAAATCAACGGATTGTAAGATATGAGTGTGATCTT
64 TCAGCATGCTATGTAGGTTAGTTGTGATCTTAAATCAACGGACTATAAAATA-GAGTGCGATCTT
16241049 AAATTGG
128 AAATTGG
* * * *
16241056 CGTGCTATGTAGATTAGCCGTGATCTTAAATCAGCGATCTATAAAATAGG-G-GTGCAATCTTAA
1 CGTGCTATGTAAATTAGTCGTGATCTTAAATCAGCGAT-TGTAAGATAGGAGCGTG--ATCTTAA
** * ** * *
16241119 ATC-GACATGCTATGTAAATTAGTTATGATCTTAAATCAGTGGGCTATAAGATAAGAGTGCGATC
63 ATCAG-CATGCTATGTAGGTTAGTTGTGATCTTAAATCAACGGACTATAAAAT-AGAGTGCGATC
16241183 TTAAATTGG
126 TTAAATTGG
* ** ** * * * * *
16241192 CGTGCTATATAGGTTAACCATGATATTAAATCAGTGAACTGTAATATAGGAGCGAT-ATCTTAAA
1 CGTGCTATGTAAATTAGTCGTGATCTTAAATCAGCG-ATTGTAAGATAGGAGCG-TGATCTTAAA
* ** * * * * *
16241256 TCAGCGTGCTATGTAAATTAGCTGTGATCTTCAATCAGCAGACTATAAAATAAAGGTGCGATCTT
64 TCAGCATGCTATGTAGGTTAGTTGTGATCTTAAATCAACGGACTATAAAATAGA-GTGCGATCTT
*
16241321 AAATTGA
128 AAATTGG
* * * *
16241328 TGTGCTATAG-AAATTAGTCATGATCTTAAATCAGTGGATTGTAAGATAGGAGCGCGATCTTAAA
1 CGTGCTAT-GTAAATTAGTCGTGATCTTAAATCAG-CGATTGTAAGATAGGAGCGTGATCTTAAA
** * * *
16241392 TCAGTGTGCTATGTAGGTTAGTTGTGATCTTAAATCAACGAACTATAAAATAG-GGGCGCAATAT
64 TCAGCATGCTATGTAGGTTAGTTGTGATCTTAAATCAACGGACTATAAAATAGAGTGCG--ATCT
16241456 TAAATTGG
127 TAAATTGG
* * * * *
16241464 TGTGCTATGTAAATTAGTCGTGATGTTAAATTAGTAGGTTGTAAGATAGGAGCGTGATCTTAAAT
1 CGTGCTATGTAAATTAGTCGTGATCTTAAATCAG-CGATTGTAAGATAGGAGCGTGATCTTAAAT
* * * * ** * *
16241529 CGGCATGCTATGTAGGTAAGTCGTGATATTAAATCAACAAACTATAAAATAAGGGTGTGATCTTA
65 CAGCATGCTATGTAGGTTAGTTGTGATCTTAAATCAACGGACTATAAAAT-AGAGTGCGATCTTA
16241594 AAT
129 AAT
16241597 CGCTAACTCT
Statistics
Matches: 443, Mismatches: 78, Indels: 40
0.79 0.14 0.07
Matches are distributed among these distances:
134 7 0.02
135 6 0.01
136 417 0.94
137 8 0.02
138 4 0.01
139 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (134 bp):
CGTGCTATGTAAATTAGTCGTGATCTTAAATCAGCGATTGTAAGATAGGAGCGTGATCTTAAATC
AGCATGCTATGTAGGTTAGTTGTGATCTTAAATCAACGGACTATAAAATAGAGTGCGATCTTAAA
TTGG
Found at i:16241265 original size:204 final size:204
Alignment explanation
Indices: 16240908--16241494 Score: 615
Period size: 204 Copynumber: 2.9 Consensus size: 204
16240898 TAAAAGCGTG
* * ****
16240908 ATCTTAAATC-ACCGTGCTATGTAAATTAGTTGTGATCTTAAAACAACATGTTGTAAGATAGGAG
1 ATCTTAAATCGA-CGTGCTATGTAAATTAGTTATGATCTTAAATCAGTGGGTTGTAAGATAGGAG
* * * * * * * *
16240972 CGTGATCTTAAATCAGCATCCTATGTAGGTTAACCGTGATCTTAAATCAACGGATTGTAAGATAT
65 CGCGATCTTAAATCAGCGTGCTATGTAGGTTAACCATGATATTAAATCAACGAACTGTAAGATAG
* ** *
16241037 GAGTGTGATCTTAAATTGGCGTGCTATGTAGATTAGCCGTGATCTTAAATCAGC-GATCTATAAA
130 GAGCGTGATCTTAAATCAGCGTGCTATGTAAATTAGCCGTGATCTTAAATCAGCAGA-CTATAAA
**
16241101 ATAGGGGTGCA
194 ATAAAGGTGCA
* * * * *
16241112 ATCTTAAATCGACATGCTATGTAAATTAGTTATGATCTTAAATCAGTGGGCTATAAGATAAGAGT
1 ATCTTAAATCGACGTGCTATGTAAATTAGTTATGATCTTAAATCAGTGGGTTGTAAGATAGGAGC
** * ** *
16241177 GCGATCTTAAATTGGCGTGCTATATAGGTTAACCATGATATTAAATCAGTGAACTGTAATATAGG
66 GCGATCTTAAATCAGCGTGCTATGTAGGTTAACCATGATATTAAATCAACGAACTGTAAGATAGG
* *
16241242 AGCGAT-ATCTTAAATCAGCGTGCTATGTAAATTAGCTGTGATCTTCAATCAGCAGACTATAAAA
131 AGCG-TGATCTTAAATCAGCGTGCTATGTAAATTAGCCGTGATCTTAAATCAGCAGACTATAAAA
*
16241306 TAAAGGTGCG
195 TAAAGGTGCA
* * * *
16241316 ATCTTAAATTGATGTGCTATAG-AAATTAGTCATGATCTTAAATCAGTGGATTGTAAGATAGGAG
1 ATCTTAAATCGACGTGCTAT-GTAAATTAGTTATGATCTTAAATCAGTGGGTTGTAAGATAGGAG
* **** * * *
16241380 CGCGATCTTAAATCAGTGTGCTATGTAGGTTAGTTGTGATCTTAAATCAACGAACTATAAAATAG
65 CGCGATCTTAAATCAGCGTGCTATGTAGGTTAACCATGATATTAAATCAACGAACTGTAAGATAG
* ** * ** * * *
16241445 GGGCGCAATATTAAATTGGTGTGCTATGTAAATTAGTCGTGATGTTAAAT
130 GAGCGTGATCTTAAATCAGCGTGCTATGTAAATTAGCCGTGATCTTAAAT
16241495 TAGTAGGTTG
Statistics
Matches: 312, Mismatches: 66, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
204 307 0.98
205 5 0.02
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (204 bp):
ATCTTAAATCGACGTGCTATGTAAATTAGTTATGATCTTAAATCAGTGGGTTGTAAGATAGGAGC
GCGATCTTAAATCAGCGTGCTATGTAGGTTAACCATGATATTAAATCAACGAACTGTAAGATAGG
AGCGTGATCTTAAATCAGCGTGCTATGTAAATTAGCCGTGATCTTAAATCAGCAGACTATAAAAT
AAAGGTGCA
Found at i:16241589 original size:68 final size:68
Alignment explanation
Indices: 16240843--16241598 Score: 384
Period size: 68 Copynumber: 11.1 Consensus size: 68
16240833 AGGTTGTGAC
* ** * * * * * * * *
16240843 CTTAAATCGGCTTGCTACATATATCAATCGTGATTTTAAATTAGTGGACTATAAATAAAAGCGT-
1 CTTAAATCGGCGTGCTATGTAGATTAGTCGTGATCTTAAATCAGCGGACTATAAA-ATAAGGGTG
16240907 -GAT
65 CGAT
** * * * * * * * * *
16240910 CTTAAATCACCGTGCTATGTAAATTAGTTGTGATCTTAAAACAACATG-TTGTAAGAT-AGGAGC
1 CTTAAATCGGCGTGCTATGTAGATTAGTCGTGATCTTAAATCAGC-GGACTATAAAATAAGG-GT
*
16240973 GTGAT
64 GCGAT
* * * * ** * * * * * * *
16240978 CTTAAATCAGCATCCTATGTAGGTTAACCGTGATCTTAAATCAACGGATTGTAAGATATGAGTGT
1 CTTAAATCGGCGTGCTATGTAGATTAGTCGTGATCTTAAATCAGCGGACTATAAAATAAGGGTGC
16241043 GAT
66 GAT
* * *
16241046 CTTAAATTGGCGTGCTATGTAGATTAGCCGTGATCTTAAATCAGC-GATCTATAAAATAGGGGTG
1 CTTAAATCGGCGTGCTATGTAGATTAGTCGTGATCTTAAATCAGCGGA-CTATAAAATAAGGGTG
*
16241110 CAAT
65 CGAT
* * * ** * * * *
16241114 CTTAAATCGACATGCTATGTAAATTAGTTATGATCTTAAATCAGTGGGCTATAAGATAAGAGTGC
1 CTTAAATCGGCGTGCTATGTAGATTAGTCGTGATCTTAAATCAGCGGACTATAAAATAAGGGTGC
16241179 GAT
66 GAT
* * * ** * * * * * * *
16241182 CTTAAATTGGCGTGCTATATAGGTTAACCATGATATTAAATCAGTGAACTGTAATAT-A-GGAGC
1 CTTAAATCGGCGTGCTATGTAGATTAGTCGTGATCTTAAATCAGCGGACTATAAAATAAGGGTGC
16241245 GATAT
66 G--AT
* * * * *
16241250 CTTAAATCAGCGTGCTATGTAAATTAG-CTGTGATCTTCAATCAGCAGACTATAAAATAAAGGTG
1 CTTAAATCGGCGTGCTATGTAGATTAGTC-GTGATCTTAAATCAGCGGACTATAAAATAAGGGTG
16241314 CGAT
65 CGAT
* ** * * * * * * *
16241318 CTTAAATTGATGTGCTATAG-AAATTAGTCATGATCTTAAATCAGTGGATTGTAAGAT-AGGAGC
1 CTTAAATCGGCGTGCTAT-GTAGATTAGTCGTGATCTTAAATCAGCGGACTATAAAATAAGG-GT
16241381 GCGAT
64 GCGAT
* * * * * * * *
16241386 CTTAAATCAGTGTGCTATGTAGGTTAGTTGTGATCTTAAATCAACGAACTATAAAATAGGGGCGC
1 CTTAAATCGGCGTGCTATGTAGATTAGTCGTGATCTTAAATCAGCGGACTATAAAATAAGGGTGC
*
16241451 AAT
66 GAT
* * * * * * * * * * *
16241454 ATTAAATTGGTGTGCTATGTAAATTAGTCGTGATGTTAAATTAGTAGG-TTGTAAGAT-AGGAGC
1 CTTAAATCGGCGTGCTATGTAGATTAGTCGTGATCTTAAATCAG-CGGACTATAAAATAAGG-GT
*
16241517 GTGAT
64 GCGAT
* * * * * ** *
16241522 CTTAAATCGGCATGCTATGTAGGTAAGTCGTGATATTAAATCAACAAACTATAAAATAAGGGTGT
1 CTTAAATCGGCGTGCTATGTAGATTAGTCGTGATCTTAAATCAGCGGACTATAAAATAAGGGTGC
16241587 GAT
66 GAT
16241590 CTTAAATCG
1 CTTAAATCG
16241599 CTAACTCTAA
Statistics
Matches: 513, Mismatches: 154, Indels: 43
0.72 0.22 0.06
Matches are distributed among these distances:
65 2 0.00
66 6 0.01
67 45 0.09
68 444 0.87
69 11 0.02
70 5 0.01
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.32
Consensus pattern (68 bp):
CTTAAATCGGCGTGCTATGTAGATTAGTCGTGATCTTAAATCAGCGGACTATAAAATAAGGGTGC
GAT
Found at i:16245303 original size:16 final size:17
Alignment explanation
Indices: 16245282--16245325 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
16245272 TTGGGTTCAG
16245282 TCCAATGTATCA-TTCT
1 TCCAATGTATCAGTTCT
16245298 TCCAATG-AGT-AGTTCT
1 TCCAATGTA-TCAGTTCT
16245314 TCCAATGTATCA
1 TCCAATGTATCA
16245326 ACATGAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 2 0.08
16 20 0.83
17 2 0.08
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (17 bp):
TCCAATGTATCAGTTCT
Found at i:16257753 original size:15 final size:14
Alignment explanation
Indices: 16257724--16257786 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 14
16257714 TTTCTTCCAA
16257724 ATTATTATTCATTC
1 ATTATTATTCATTC
*
16257738 ATTATTCATTCGTTC
1 ATTATT-ATTCATTC
* * *
16257753 ATTATCATATGATAC
1 ATTATTAT-TCATTC
16257768 AAATTATTATTCATTC
1 --ATTATTATTCATTC
16257784 ATT
1 ATT
16257787 CATAATCATA
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
14 11 0.30
15 15 0.41
16 4 0.11
17 7 0.19
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (14 bp):
ATTATTATTCATTC
Found at i:16257781 original size:35 final size:35
Alignment explanation
Indices: 16257738--16257816 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
16257728 TTATTCATTC
* * *
16257738 ATTATTCATTCGTTCATTATCATATGATACAAATT
1 ATTATTCATTCATTCATAATCATATGATACAAATA
16257773 ATTATTCATTCATTCATAATCATATGATACAAATA
1 ATTATTCATTCATTCATAATCATATGATACAAATA
16257808 ATTATTCAT
1 ATTATTCAT
16257817 GAATTTATAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (35 bp):
ATTATTCATTCATTCATAATCATATGATACAAATA
Found at i:16258562 original size:15 final size:15
Alignment explanation
Indices: 16258542--16258576 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16258532 AATGAAAATG
*
16258542 AAAAAAGAGAGAAGAA
1 AAAAAAG-GAAAAGAA
16258558 AAAAAAGGAAAAGAA
1 AAAAAAGGAAAAGAA
16258573 AAAA
1 AAAA
16258577 GAAAATGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAAAGGAAAAGAA
Found at i:16259430 original size:7 final size:7
Alignment explanation
Indices: 16259418--16259471 Score: 85
Period size: 7 Copynumber: 8.0 Consensus size: 7
16259408 TCTAAGTCAA
16259418 AAAAATG
1 AAAAATG
16259425 AAAAATG
1 AAAAATG
*
16259432 -AGAATG
1 AAAAATG
16259438 AAAAATG
1 AAAAATG
16259445 AAAAATG
1 AAAAATG
16259452 -AAAATG
1 AAAAATG
16259458 AAAAATG
1 AAAAATG
16259465 AAAAATG
1 AAAAATG
16259472 GAGAGGCTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 11 0.26
7 32 0.74
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:16259439 original size:13 final size:14
Alignment explanation
Indices: 16259418--16259471 Score: 85
Period size: 13 Copynumber: 4.0 Consensus size: 14
16259408 TCTAAGTCAA
16259418 AAAAATGAAAAATG
1 AAAAATGAAAAATG
*
16259432 -AGAATGAAAAATG
1 AAAAATGAAAAATG
16259445 AAAAATG-AAAATG
1 AAAAATGAAAAATG
16259458 AAAAATGAAAAATG
1 AAAAATGAAAAATG
16259472 GAGAGGCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
13 25 0.69
14 11 0.31
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.15
Consensus pattern (14 bp):
AAAAATGAAAAATG
Found at i:16259443 original size:20 final size:20
Alignment explanation
Indices: 16259418--16259471 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
16259408 TCTAAGTCAA
*
16259418 AAAAATGAAAAATGAGAATG
1 AAAAATGAAAAATGAAAATG
16259438 AAAAATGAAAAATGAAAATG
1 AAAAATGAAAAATGAAAATG
16259458 AAAAATGAAAAATG
1 AAAAATGAAAAATG
16259472 GAGAGGCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAAATGAAAAATGAAAATG
Found at i:16261300 original size:347 final size:347
Alignment explanation
Indices: 16260664--16261508 Score: 1341
Period size: 347 Copynumber: 2.4 Consensus size: 347
16260654 AGATCAGTGA
* * *
16260664 AGATCGAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGGAGCTAGTTAAAGATAGCAGATCTTTC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* * *
16260729 CTTCCCGCATTGACAACGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
66 CTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
* * *
16260794 AGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCAAAGCAAATCGAAAATAAAGCCTTGC
131 GGTTAAAGATAGCAG-TCTTGCCTTCCTGCATTAACAGCAAAGCAAATCAAAAACAAAGCCTTGC
* * * *
16260859 CTCCATCGGTTGCAGTGGAGCTAGTTAAAGATAGCAGATTTTGCCTTCCCGCATTGACAGTGAAG
195 CACCATCGGTTGCAATGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCCGCATTGACAGCGAAG
*
16260924 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAACTGGTTAAAGATAGTAGATATTG
260 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAACTGGTTAAAGATAGCAGATATTG
16260989 CCTTCCTGCATTAACAGA-GAAGC
325 CCTTCCTGCATTAACA-ACGAAGC
* * *
16261012 AGATCGAAAACAAAACATTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGTAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
16261077 CTTCCTGCATTAACAGCAAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
66 CTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
* * *
16261142 GGTTAAAGATAGCAGTCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAGCCTTTCC
131 GGTTAAAGATAGCAGTCTTGCCTTCCTGCATTAACAGCAAAGCAAATCAAAAACAAAGCCTTGCC
* **
16261207 ACCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCTTGCATTGACAGCGAAGC
196 ACCATCGGTTGCAATGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCCGCATTGACAGCGAAGC
* * *
16261272 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCATTGGAGCTGGTTAAAGATAGCAGATCTTGC
261 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAACTGGTTAAAGATAGCAGATATTGC
*
16261337 CTTCCTGCATTAACAACGAAGT
326 CTTCCTGCATTAACAACGAAGC
* *
16261359 GGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* * *
16261424 CTTCTTGCATTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCAGCAGTTGCAGTGGAGCT
66 CTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
*
16261489 GGTTAAAGATAACAGGTCTT
131 GGTTAAAGATAGCA-GTCTT
16261509 ATCTCCATGA
Statistics
Matches: 455, Mismatches: 40, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
346 1 0.00
347 316 0.69
348 138 0.30
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (347 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
GGTTAAAGATAGCAGTCTTGCCTTCCTGCATTAACAGCAAAGCAAATCAAAAACAAAGCCTTGCC
ACCATCGGTTGCAATGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCCGCATTGACAGCGAAGC
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAACTGGTTAAAGATAGCAGATATTGC
CTTCCTGCATTAACAACGAAGC
Found at i:16261536 original size:87 final size:87
Alignment explanation
Indices: 16260664--16261508 Score: 1314
Period size: 87 Copynumber: 9.7 Consensus size: 87
16260654 AGATCAGTGA
* * *
16260664 AGATCGAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGGAGCTAGTTAAAGATAGCAGATCTTTC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* * *
16260729 CTTCCCGCATTGACAACGAAGC
66 CTTCCTGCATTAACAGCGAAGC
* *
16260751 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTAGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
16260816 CTTCCTGCATTAACAGCAAAGC
66 CTTCCTGCATTAACAGCGAAGC
* * * *
16260838 AAATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTAGTTAAAGATAGCAGATTTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* * *
16260903 CTTCCCGCATTGACAGTGAAGC
66 CTTCCTGCATTAACAGCGAAGC
* * *
16260925 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAACTGGTTAAAGATAGTAGATATTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
16260990 CTTCCTGCATTAACAGAGAAGC
66 CTTCCTGCATTAACAGCGAAGC
* * *
16261012 AGATCGAAAACAAAACATTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGTAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
16261077 CTTCCTGCATTAACAGCAAAGC
66 CTTCCTGCATTAACAGCGAAGC
16261099 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAG-TCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
16261163 CTTCCTGCATTAACAGCGAAGC
66 CTTCCTGCATTAACAGCGAAGC
* * * *
16261185 AGATCAAAAACAAAGCCTTTCCACCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
16261250 CTTCTTGCATTGACAGCGAAGC
66 CTTCCTGCATTAACAGCGAAGC
*
16261272 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCATTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
16261337 CTTCCTGCATTAACAACGAAGT
66 CTTCCTGCATTAACAGCGAAGC
* *
16261359 GGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
16261424 CTTCTTGCATTAACAGCGAAGC
66 CTTCCTGCATTAACAGCGAAGC
* * * * *
16261446 AGATCAAAAACAAAGCCTTGCCTCCAGCAGTTGCAGTGGAGCTGGTTAAAGATAACAGGTCTT
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTT
16261509 ATCTCCATGA
Statistics
Matches: 697, Mismatches: 60, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
86 81 0.12
87 616 0.88
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (87 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCATTAACAGCGAAGC
Found at i:16261536 original size:434 final size:435
Alignment explanation
Indices: 16260664--16261509 Score: 1334
Period size: 434 Copynumber: 1.9 Consensus size: 435
16260654 AGATCAGTGA
*
16260664 AGATCGAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGGAGCTAGTTAAAGATAGCAGATCTTTC
1 AGATCGAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGGAGCTAGTTAAAGATAGCAGATCTTGC
* * *
16260729 CTTCCCGCATTGACAACGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
66 CTTCCCGCATTAACAACGAAGCAGATCAAAAACAAAGCCTTGCCACCATCGGTTGCAATGGAGCT
*
16260794 AGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCAAAGCAAATCGAAAATAAAGCCTTGC
131 AGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCAAAGCAAATCGAAAACAAAGCCTTGC
* * **
16260859 CTCCATCGGTTGCAGTGGAGCTAGTTAAAGATAGCAGATTTTGCCTTCCCGCATTGACAGTGAAG
196 CTCCATCGGTTGCAGTGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCCGCATTAACAACGAAG
* *
16260924 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAACTGGTTAAAGATAGTAGATATTG
261 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAACTGGTTAAAGATAGCAGATATTG
* * *
16260989 CCTTCCTGCATTAACAGAGAAGCAGATCGAAAACAAAACATTGCCTCCATCGGTTGCAGTGGAGC
326 CCTTCCTGCATTAACAGAGAAGCAGATCAAAAACAAAACATTGCCTCCAGCAGTTGCAGTGGAGC
** *
16261054 TGGTTAAAGATAGTAGATCTTGCCTTCCTGCATTAACAGCAAAGC
391 TGGTTAAAGATAACAGATCTTACCTTCCTGCATTAACAGCAAAGC
* *
16261099 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAG-TCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGGAGCTAGTTAAAGATAGCAGATCTTGC
* * *
16261163 CTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAGCCTTTCCACCATCGGTTGCAATGGAGCT
66 CTTCCCGCATTAACAACGAAGCAGATCAAAAACAAAGCCTTGCCACCATCGGTTGCAATGGAGCT
* * * * *
16261228 GGTTAAAGATAGCAGATCTTGCCTTCTTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGC
131 AGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCAAAGCAAATCGAAAACAAAGCCTTGC
* * *
16261293 CTCCATCGGTTGCATTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAACGAAG
196 CTCCATCGGTTGCAGTGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCCGCATTAACAACGAAG
** * *
16261358 TGGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTG
261 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAACTGGTTAAAGATAGCAGATATTG
* * * *
16261423 CCTTCTTGCATTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCAGCAGTTGCAGTGGAGC
326 CCTTCCTGCATTAACAGAGAAGCAGATCAAAAACAAAACATTGCCTCCAGCAGTTGCAGTGGAGC
*
16261488 TGGTTAAAGATAACAGGTCTTA
391 TGGTTAAAGATAACAGATCTTA
16261510 TCTCCATGAG
Statistics
Matches: 372, Mismatches: 39, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
434 316 0.85
435 56 0.15
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (435 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGGAGCTAGTTAAAGATAGCAGATCTTGC
CTTCCCGCATTAACAACGAAGCAGATCAAAAACAAAGCCTTGCCACCATCGGTTGCAATGGAGCT
AGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCAAAGCAAATCGAAAACAAAGCCTTGC
CTCCATCGGTTGCAGTGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCCGCATTAACAACGAAG
CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAACTGGTTAAAGATAGCAGATATTG
CCTTCCTGCATTAACAGAGAAGCAGATCAAAAACAAAACATTGCCTCCAGCAGTTGCAGTGGAGC
TGGTTAAAGATAACAGATCTTACCTTCCTGCATTAACAGCAAAGC
Found at i:16261600 original size:44 final size:44
Alignment explanation
Indices: 16261479--16261601 Score: 108
Period size: 44 Copynumber: 2.8 Consensus size: 44
16261469 CCAGCAGTTG
* *
16261479 CAGTGGAGCTGGTTAAAGATAACAGG-TCTTATCTCCATGAGATTA
1 CAGTGGAGCAGATTAAA-ATAA-AGGATCTTATCTCCATGAGATTA
* * ** * * *
16261524 TAGCGGAGCAGATTGAAGCT--AGTAATCCTATCTCCTTGAGATTA
1 CAGTGGAGCAGATT-AAAATAAAG-GATCTTATCTCCATGAGATTA
16261568 CAGTGGAGCAGATTAAAATAAAGGATCTTATCTC
1 CAGTGGAGCAGATTAAAATAAAGGATCTTATCTC
16261602 TCTGAAGTTA
Statistics
Matches: 58, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
42 2 0.03
43 3 0.05
44 38 0.66
45 13 0.22
46 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (44 bp):
CAGTGGAGCAGATTAAAATAAAGGATCTTATCTCCATGAGATTA
Found at i:16263664 original size:28 final size:27
Alignment explanation
Indices: 16263610--16263671 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
16263600 CCGTATTATT
16263610 TAATTTATTTCAAATTTTCATTTATATA
1 TAATTTATTTCAAATTTT-ATTTATATA
* *
16263638 TTATTTATTTTAAA-TTTATTTTAATATA
1 TAATTTATTTCAAATTTTA-TTT-ATATA
16263666 TAATTT
1 TAATTT
16263672 CCTTTCTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 6 0.21
28 22 0.76
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATTTATTTCAAATTTTATTTATATA
Found at i:16266692 original size:43 final size:43
Alignment explanation
Indices: 16266619--16266717 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
16266609 TATGAGAATT
* * * * *
16266619 CATGTAAGACCATGTCTGGTACATTAGCATCGGTATGTGATTT
1 CATGTAAGACCATGGCTGGTACATTAGCATCGATACGAGATTA
* * *
16266662 CGTGTAAGACCATGGCTGG-GCTATTGGCATCGATACGAGATTA
1 CATGTAAGACCATGGCTGGTAC-ATTAGCATCGATACGAGATTA
16266705 CATGTAAGACCAT
1 CATGTAAGACCAT
16266718 ATCTGGATAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
42 1 0.02
43 45 0.98
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (43 bp):
CATGTAAGACCATGGCTGGTACATTAGCATCGATACGAGATTA
Found at i:16274361 original size:22 final size:22
Alignment explanation
Indices: 16274346--16274408 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 22
16274336 TTGTTTTGAT
16274346 ATTGTTCTTGATTTGTTCTGGAA
1 ATTGTT-TTGATTTGTTCTGGAA
* *
16274369 ATTGTTTTGA-TAGTCTGCTAGAA
1 ATTGTTTTGATTTGT-T-CTGGAA
16274392 ATTGTTCTTGATTTGTT
1 ATTGTT-TTGATTTGTT
16274409 AGTGAGTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 3 0.09
22 5 0.15
23 17 0.52
24 5 0.15
25 3 0.09
ACGTcount: A:0.19, C:0.08, G:0.21, T:0.52
Consensus pattern (22 bp):
ATTGTTTTGATTTGTTCTGGAA
Found at i:16274468 original size:22 final size:22
Alignment explanation
Indices: 16274427--16274515 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 22
16274417 GAAGATGAAA
16274427 CTGGAAATTG--TTGCATTTGTT
1 CTGGAAATTGTTTTG-ATTTGTT
* *
16274448 -TTGATATTGTTCTTGATTTGTT
1 CTGGAAATTGTT-TTGATTTGTT
*
16274470 CTGGAAATTGTTTTGA-TAGTCT
1 CTGGAAATTGTTTTGATTTGT-T
16274492 ACTGGAAATTGTTCTTGATTTGTT
1 -CTGGAAATTGTT-TTGATTTGTT
16274516 AGTGAGTAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
20 7 0.13
21 3 0.06
22 12 0.22
23 24 0.44
24 5 0.09
25 3 0.06
ACGTcount: A:0.19, C:0.08, G:0.21, T:0.52
Consensus pattern (22 bp):
CTGGAAATTGTTTTGATTTGTT
Found at i:16274500 original size:107 final size:107
Alignment explanation
Indices: 16274314--16274543 Score: 433
Period size: 107 Copynumber: 2.1 Consensus size: 107
16274304 GCTGTTTTCA
*
16274314 ATGAAACTAGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
1 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
*
16274379 TAGTCTGCTAGAAATTGTTCTTGATTTGTTAGTGAGTAGAAG
66 TAGTCTACTAGAAATTGTTCTTGATTTGTTAGTGAGTAGAAG
16274421 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
1 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
*
16274486 TAGTCTACTGGAAATTGTTCTTGATTTGTTAGTGAGTAGAAG
66 TAGTCTACTAGAAATTGTTCTTGATTTGTTAGTGAGTAGAAG
16274528 ATGAAACTGGAAATTG
1 ATGAAACTGGAAATTG
16274544 CAAGTATAGT
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 120 1.00
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.44
Consensus pattern (107 bp):
ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
TAGTCTACTAGAAATTGTTCTTGATTTGTTAGTGAGTAGAAG
Found at i:16276123 original size:47 final size:47
Alignment explanation
Indices: 16276070--16276221 Score: 154
Period size: 47 Copynumber: 3.3 Consensus size: 47
16276060 TCATATAAGA
*
16276070 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTAATATTAAGAATTTTATGAAATTATATATCATTATTAAATT
** *
16276117 ATATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--
1 ATATTTAATATTAAGAATTTTATGAAATTATATATCATT-AT-TAA-ATT
* ** * *
16276161 AAATTTGTTATCAAGAATTTTATGAAATTATATATCATTACTAAATT
1 ATATTTAATATTAAGAATTTTATGAAATTATATATCATTATTAAATT
16276208 ATATTTAATATTAA
1 ATATTTAATATTAA
16276222 TTATTTTAAA
Statistics
Matches: 80, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
43 3 0.04
44 23 0.29
45 8 0.10
46 8 0.10
47 35 0.44
48 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (47 bp):
ATATTTAATATTAAGAATTTTATGAAATTATATATCATTATTAAATT
Found at i:16276177 original size:91 final size:89
Alignment explanation
Indices: 16276056--16276335 Score: 393
Period size: 91 Copynumber: 3.2 Consensus size: 89
16276046 TGATTTTAGC
*
16276056 AAATTCATATAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATAT
1 AAATTCATATAAGAAAATTT-TTA-TAAGAATTTTATGAAATTATATATCATTATTAAATTATAT
16276121 TTAATATTAATTATTTTAAATTATAT
64 TTAATATTAATTATTTTAAATTATAT
*
16276147 AAATTCATATAAGAAAATTTGTTATCAAGAATTTTATGAAATTATATATCATTACTAAATTATAT
1 AAATTCATATAAGAAAATTT-TTAT-AAGAATTTTATGAAATTATATATCATTATTAAATTATAT
16276212 TTAATATTAATTATTTTAAATTATAT
64 TTAATATTAATTATTTTAAATTATAT
*
16276238 AAATTCATATAAGAAAATTTTTAT--GAA----AT--TATT-TAT-T-ATTATTAAATTATATTT
1 AAATTCATATAAGAAAATTTTTATAAGAATTTTATGAAATTATATATCATTATTAAATTATATTT
* * *
16276292 AATAATAATTATATTAAATTATAC
66 AATATTAATTATTTTAAATTATAT
16276316 AAATTCATATAAGAAAATTT
1 AAATTCATATAAGAAAATTT
16276336 ATTACTAATA
Statistics
Matches: 180, Mismatches: 8, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
78 57 0.32
79 1 0.01
80 3 0.02
81 3 0.02
83 2 0.01
87 3 0.02
90 5 0.03
91 106 0.59
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (89 bp):
AAATTCATATAAGAAAATTTTTATAAGAATTTTATGAAATTATATATCATTATTAAATTATATTT
AATATTAATTATTTTAAATTATAT
Found at i:16276181 original size:44 final size:43
Alignment explanation
Indices: 16276133--16276261 Score: 109
Period size: 47 Copynumber: 2.9 Consensus size: 43
16276123 AATATTAATT
16276133 ATTTTAAATTATATAAATTCATATAAGAAAATTTGTTATCAAGA
1 ATTTTAAATTATATAAATTCATATAAGAAAATTT-TTATCAAGA
* ** * * * **
16276177 ATTTTATGAAATTATATATCATT-ACTA-AATTATATTTAATATTAATT
1 A-TTT-T-AAATTATATA-AATTCA-TATAAGAAAATTT-TTATCAAGA
16276224 ATTTTAAATTATATAAATTCATATAAGAAAATTTTTAT
1 ATTTTAAATTATATAAATTCATATAAGAAAATTTTTAT
16276262 GAAATTATTT
Statistics
Matches: 64, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
43 8 0.12
44 19 0.30
45 4 0.06
46 4 0.06
47 24 0.38
48 5 0.08
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (43 bp):
ATTTTAAATTATATAAATTCATATAAGAAAATTTTTATCAAGA
Found at i:16276284 original size:78 final size:78
Alignment explanation
Indices: 16276178--16276335 Score: 262
Period size: 78 Copynumber: 2.0 Consensus size: 78
16276168 TTATCAAGAA
* * *
16276178 TTTTATGAAATTATATATCATTACTAAATTATATTTAATATTAATTATTTTAAATTATATAAATT
1 TTTTATGAAATTATATATCATTACTAAATTATATTTAATAATAATTATATTAAATTATACAAATT
16276243 CATATAAGAAAAT
66 CATATAAGAAAAT
* * *
16276256 TTTTATGAAATTATTTATTATTATTAAATTATATTTAATAATAATTATATTAAATTATACAAATT
1 TTTTATGAAATTATATATCATTACTAAATTATATTTAATAATAATTATATTAAATTATACAAATT
16276321 CATATAAGAAAAT
66 CATATAAGAAAAT
16276334 TT
1 TT
16276336 ATTACTAATA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (78 bp):
TTTTATGAAATTATATATCATTACTAAATTATATTTAATAATAATTATATTAAATTATACAAATT
CATATAAGAAAAT
Found at i:16276501 original size:18 final size:17
Alignment explanation
Indices: 16276473--16276507 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
16276463 AGTATTAAGA
*
16276473 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
16276490 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
16276508 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:16291050 original size:15 final size:15
Alignment explanation
Indices: 16291019--16291052 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
16291009 ACATTGATCA
* *
16291019 TCATCATCATCATCT
1 TCATCATCATAAACT
16291034 TCATCATCATAAACT
1 TCATCATCATAAACT
16291049 TCAT
1 TCAT
16291053 AGTCACTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (15 bp):
TCATCATCATAAACT
Found at i:16292210 original size:30 final size:31
Alignment explanation
Indices: 16292154--16292219 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
16292144 TAAAATTTTA
* * *
16292154 AAATTCAAAAACTATAAAATATAAATTGA-C
1 AAATTCAAAAAATACAAAATATAAATTAATC
*
16292184 AAATTTAAAAAATACAAAACTA-AAATTAATC
1 AAATTCAAAAAATACAAAA-TATAAATTAATC
16292215 AAATT
1 AAATT
16292220 AAAGTTTAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.27
Consensus pattern (31 bp):
AAATTCAAAAAATACAAAATATAAATTAATC
Found at i:16293581 original size:1 final size:1
Alignment explanation
Indices: 16293575--16293600 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
16293565 TGGCTTCTTC
16293575 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
16293601 GCAGCAAGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16300158 original size:26 final size:26
Alignment explanation
Indices: 16300129--16300185 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
16300119 CCCTCTTAGA
16300129 TGTTATCCAATGGTCCAAACCAGGGT
1 TGTTATCCAATGGTCCAAACCAGGGT
16300155 TGTTATCCAATGGTCCAAACCAGGGT
1 TGTTATCCAATGGTCCAAACCAGGGT
16300181 TGTTA
1 TGTTA
16300186 ATGTAGACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (26 bp):
TGTTATCCAATGGTCCAAACCAGGGT
Found at i:16304238 original size:10 final size:11
Alignment explanation
Indices: 16304213--16304241 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
16304203 ATTTCAAATC
16304213 ATCAAGAATAA
1 ATCAAGAATAA
16304224 ATCAAGAAT-A
1 ATCAAGAATAA
16304234 ATCAAGAA
1 ATCAAGAA
16304242 CAAAACCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (11 bp):
ATCAAGAATAA
Found at i:16308854 original size:49 final size:49
Alignment explanation
Indices: 16308766--16309264 Score: 749
Period size: 49 Copynumber: 10.3 Consensus size: 49
16308756 TATGTAATCC
* * * ** *
16308766 AATGTACCTAATTTA-AATTACAAAGTTTGTTCCTCGTTTTAATGTTGC
1 AATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
16308814 AATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
1 AATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
* *
16308863 AATGTATCTAATTTAT-ATTACAAAGTTTGTTTCAAGTTTTAATGTTGT
1 AATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
*
16308911 AATGTATCTAATTTATGAGCACAAAGTTTGTTCCAAGTTTTAATGTTGT
1 AATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
16308960 AATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
1 AATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
* * *
16309009 AATGTATCTAATTTAT-ATTACAAAGTTTGTTCCAATTTTTAATTTTGT
1 AATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
* *
16309057 AATGTAACTAATTTAT-ATTACAAAGTTTGTTCCAAGTTTTAATGTTGT
1 AATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
16309105 AATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
1 AATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
** * *
16309154 AATGTATCTAATTTATGGCCACAAAGTGTT-TTCTAAGTTTTAATCTTGT
1 AATGTATCTAATTTATGATCACAAAGT-TTGTTCCAAGTTTTAATGTTGT
* * *
16309203 AATGTATCTAATTTATGACCACAAAGTTTGTTCCAAGTTTTAATATTGC
1 AATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
16309252 AAT-TAATCTAATT
1 AATGT-ATCTAATT
16309265 AAATAAATAC
Statistics
Matches: 417, Mismatches: 28, Indels: 11
0.91 0.06 0.02
Matches are distributed among these distances:
48 152 0.36
49 263 0.63
50 2 0.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (49 bp):
AATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
Found at i:16308934 original size:97 final size:97
Alignment explanation
Indices: 16308766--16309264 Score: 761
Period size: 97 Copynumber: 5.1 Consensus size: 97
16308756 TATGTAATCC
* * ** *
16308766 AATGTACCTAATTTAAATTACAAAGTTTGTTCCTCGTTTTAATGTTGCAATGTATCTAATTTATG
1 AATGTATCTAATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATG
16308831 ATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
66 ATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
*
16308863 AATGTATCTAATTTATATTACAAAGTTTGTTTCAAGTTTTAATGTTGTAATGTATCTAATTTATG
1 AATGTATCTAATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATG
*
16308928 AGCACAAAGTTTGTTCCAAGTTTTAATGTTGT
66 ATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
*
16308960 AATGTATCTAATTTATGATCACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTAT
1 AATGTATCTAATTTAT-ATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTAT
* * *
16309025 -ATTACAAAGTTTGTTCCAATTTTTAATTTTGT
65 GATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
*
16309057 AATGTAACTAATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATG
1 AATGTATCTAATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATG
16309122 ATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
66 ATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
*** * *
16309154 AATGTATCTAATTTATGGCCACAAAGTGTT-TTCTAAGTTTTAATCTTGTAATGTATCTAATTTA
1 AATGTATCTAATTTAT-ATTACAAAGT-TTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTA
* * *
16309218 TGACCACAAAGTTTGTTCCAAGTTTTAATATTGC
64 TGATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
16309252 AAT-TAATCTAATT
1 AATGT-ATCTAATT
16309265 AAATAAATAC
Statistics
Matches: 370, Mismatches: 27, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
96 47 0.13
97 194 0.52
98 127 0.34
99 2 0.01
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (97 bp):
AATGTATCTAATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATG
ATCACAAAGTTTGTTCCAAGTTTTAATGTTGT
Found at i:16309601 original size:33 final size:33
Alignment explanation
Indices: 16309531--16309603 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
16309521 TTGAGCCGGG
* * *
16309531 AGGAGTGGAGTATTGCGGTGGATACGAGCGAGG
1 AGGAGTGGAGTAATGCGGTAGATACGAGCGAGA
* **
16309564 AGGAGTGGAGTAATGCGGTAGATACGGGCTTGA
1 AGGAGTGGAGTAATGCGGTAGATACGAGCGAGA
16309597 AGGAGTG
1 AGGAGTG
16309604 ATGTACTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.26, C:0.08, G:0.47, T:0.19
Consensus pattern (33 bp):
AGGAGTGGAGTAATGCGGTAGATACGAGCGAGA
Found at i:16309783 original size:24 final size:24
Alignment explanation
Indices: 16309751--16309797 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
16309741 TCTAGTTTTG
*
16309751 GCTCAGGTTCAAGGTTGGGCTCGA
1 GCTCAGGTTCAAGGTCGGGCTCGA
* * *
16309775 GCTCGGGTTTAGGGTCGGGCTCG
1 GCTCAGGTTCAAGGTCGGGCTCG
16309798 TATGCCCTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.43, T:0.26
Consensus pattern (24 bp):
GCTCAGGTTCAAGGTCGGGCTCGA
Found at i:16310432 original size:14 final size:14
Alignment explanation
Indices: 16310413--16310446 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
16310403 AAATTACATG
16310413 TTAGAATAGTATCA
1 TTAGAATAGTATCA
16310427 TTAGAATAGTATCA
1 TTAGAATAGTATCA
16310441 TTAGAA
1 TTAGAA
16310447 AAAAAAGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (14 bp):
TTAGAATAGTATCA
Found at i:16311254 original size:26 final size:26
Alignment explanation
Indices: 16311225--16311277 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
16311215 TTATTATAAC
16311225 ATAATTTAGTTTCGTAAATGACGTGG
1 ATAATTTAGTTTCGTAAATGACGTGG
*
16311251 ATAATTTATTTTCGTAAATGACGTGG
1 ATAATTTAGTTTCGTAAATGACGTGG
16311277 A
1 A
16311278 ACTTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.40
Consensus pattern (26 bp):
ATAATTTAGTTTCGTAAATGACGTGG
Found at i:16312643 original size:20 final size:22
Alignment explanation
Indices: 16312601--16312651 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
16312591 ATATTAAAAA
*
16312601 TTAATTTTTATATTAATAATTT
1 TTAATTTTTATATAAATAATTT
*
16312623 TTAATTTTTA-A-AAATATTTT
1 TTAATTTTTATATAAATAATTT
*
16312643 TTTATTTTT
1 TTAATTTTT
16312652 TTTGAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 15 0.58
21 1 0.04
22 10 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTAATTTTTATATAAATAATTT
Found at i:16319219 original size:50 final size:50
Alignment explanation
Indices: 16319100--16319333 Score: 168
Period size: 50 Copynumber: 4.6 Consensus size: 50
16319090 CATGGCAAAT
* * * *
16319100 CCATGTCCCAGACATGGTCTTAGATGGGA-TGTTTCTTGTAC--TGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACT-TCTCATAT-CGGTGCCAATG
* * * *
16319149 CCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATG
1 CCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCGGTGCCAATG
* * ** * * * *
16319199 CTATGTCCCATACATGGTCTTACGGGGGACCTCTCATCTCGGTGTCAACG
1 CCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCGGTGCCAATG
* * * *
16319249 CCATGTCCTAGACATGTTCTTACATGGGACATCTCATAATCTCAATGATGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACTTCTCAT-A--TC---GGTGCCAATG
* * *
16319305 TCACGTCCTAGACATGGTCTTACATGGGA
1 CCATGTCCCAGACATGGTCTTACATGGGA
16319334 TCTCTTTACC
Statistics
Matches: 143, Mismatches: 33, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
48 1 0.01
49 31 0.22
50 76 0.53
53 2 0.01
56 33 0.23
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.30
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCGGTGCCAATG
Found at i:16324878 original size:39 final size:40
Alignment explanation
Indices: 16324801--16324947 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
16324791 TAGCTCCTCG
* * *
16324801 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
16324841 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
16324880 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
16324920 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
16324948 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:16324958 original size:80 final size:80
Alignment explanation
Indices: 16324847--16325027 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
16324837 CTCATTCAAT
* * *
16324847 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
16324910 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
16324926 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
16324990 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
16325007 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
16325028 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:16324987 original size:40 final size:40
Alignment explanation
Indices: 16324844--16325027 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
16324834 TAACTCATTC
* *
16324844 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
16324884 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
16324924 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
16324964 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
16325005 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
16325028 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:16332728 original size:39 final size:40
Alignment explanation
Indices: 16332651--16332797 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
16332641 TAGCTCCTCG
* * *
16332651 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
16332691 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
16332730 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
16332770 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
16332798 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:16332808 original size:80 final size:80
Alignment explanation
Indices: 16332697--16332877 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
16332687 CTCATTCAAT
* * *
16332697 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
16332760 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
16332776 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
16332840 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
16332857 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
16332878 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:16332837 original size:40 final size:40
Alignment explanation
Indices: 16332694--16332877 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
16332684 TAACTCATTC
* *
16332694 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
16332734 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
16332774 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
16332814 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
16332855 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
16332878 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:16337702 original size:50 final size:50
Alignment explanation
Indices: 16337585--16337819 Score: 197
Period size: 50 Copynumber: 4.6 Consensus size: 50
16337575 ACATGCTAAA
* * * * * *
16337585 GCCATGTCCCAAACATGGTCTTAGATGGGA-TGTTTCTTGT-ACTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACT-TCTCATATCAGTGCCAAT
* * * *
16337634 GCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCAGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCAGTGCCAAT
* * * * *
16337684 GCCATGTCCCACACATGGTCTTACGA-GGGACCTCTCATCTCGGTGCCAAG
1 GCCATGTCCCAGACATGGTCTTAC-ATGGGACTTCTCATATCAGTGCCAAT
* * *
16337734 GCCATGTCCTAGACATGTTCTTACATGGGACATCTCATAATCTCAATGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACTTCTCAT-A--TC-A-G-TGCCAAT
* *
16337790 GTCATGTCCTAGACATGGTCTTACATGGGA
1 GCCATGTCCCAGACATGGTCTTACATGGGA
16337820 TCTCTTTGCC
Statistics
Matches: 149, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
49 32 0.21
50 79 0.53
51 1 0.01
53 2 0.01
55 1 0.01
56 34 0.23
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCAGTGCCAAT
Found at i:16342324 original size:233 final size:233
Alignment explanation
Indices: 16341917--16342382 Score: 878
Period size: 233 Copynumber: 2.0 Consensus size: 233
16341907 AAATGCAAAA
*
16341917 CTTTAGGGGTATTGAAAAATAAAATTTCATAGGTTCAAAAATATCATGGCATAACATAAAAAATA
1 CTTTAGGGGTATTGAAAAATAAAATTTCATAGGTTCAAAAATATCATGGCATAACATAAAAAAGA
*
16341982 TTTGGTATTGATAAATTATTTAAAATAATTAATTAGATCAAGAATTGAATCAAATTGGAGATAAT
66 TTTGGTATTGATAAATTATTTAAAATAATTAATTAGATCAAGAATTGAATCAAACTGGAGATAAT
16342047 CAAGAAAAAACAAAAATTATCGATTAGTCCCTGAAGATTCAATTTGTTTACTATTTTTCCAGATA
131 CAAGAAAAAACAAAAATTATCGATTAGTCCCTGAAGATTCAATTTGTTTACTATTTTTCCAGATA
16342112 AGTTCATATGGTATATATATGTGTTTAAATAATTATGT
196 AGTTCATATGGTATATATATGTGTTTAAATAATTATGT
*
16342150 CTTTAGGGGTATTGAAAAATAAAATTTCATAGGTTCAAAAATATCATGGCATAACATAAAAAAGG
1 CTTTAGGGGTATTGAAAAATAAAATTTCATAGGTTCAAAAATATCATGGCATAACATAAAAAAGA
16342215 TTTGGTATTGATAAATTATTTAAAATAATTAATTAGATCAAGAATTGAATCAAACTGGAGATAAT
66 TTTGGTATTGATAAATTATTTAAAATAATTAATTAGATCAAGAATTGAATCAAACTGGAGATAAT
* * *
16342280 CAAGGAAAAATAAAAATTATCGATTAGTCCCTGAAGATTCAATTTGTTTACTGTTTTTCCAGATA
131 CAAGAAAAAACAAAAATTATCGATTAGTCCCTGAAGATTCAATTTGTTTACTATTTTTCCAGATA
16342345 AGTTCATATGGTATATATATGTGTTTAAATAATTATGT
196 AGTTCATATGGTATATATATGTGTTTAAATAATTATGT
16342383 GTTTGATTTG
Statistics
Matches: 227, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
233 227 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (233 bp):
CTTTAGGGGTATTGAAAAATAAAATTTCATAGGTTCAAAAATATCATGGCATAACATAAAAAAGA
TTTGGTATTGATAAATTATTTAAAATAATTAATTAGATCAAGAATTGAATCAAACTGGAGATAAT
CAAGAAAAAACAAAAATTATCGATTAGTCCCTGAAGATTCAATTTGTTTACTATTTTTCCAGATA
AGTTCATATGGTATATATATGTGTTTAAATAATTATGT
Found at i:16343777 original size:11 final size:11
Alignment explanation
Indices: 16343761--16343785 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16343751 CAACCCCCTA
16343761 GTTATATTAAG
1 GTTATATTAAG
16343772 GTTATATTAAG
1 GTTATATTAAG
16343783 GTT
1 GTT
16343786 GGAAATGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (11 bp):
GTTATATTAAG
Found at i:16350428 original size:17 final size:18
Alignment explanation
Indices: 16350391--16350434 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
16350381 ATAAATCTGT
*
16350391 ATAAATTATATATTTAAA
1 ATAAAATATATATTTAAA
* *
16350409 ATAACATATA-ATTTATA
1 ATAAAATATATATTTAAA
16350426 ATAAAATAT
1 ATAAAATAT
16350435 GTGGTTCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAAAATATATATTTAAA
Found at i:16353048 original size:26 final size:25
Alignment explanation
Indices: 16353019--16353067 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
16353009 TATGAGAAAG
16353019 CTTACACCCAAAATTTAGTAGTAGCC
1 CTTACACCCAAAATTTAG-AGTAGCC
*
16353045 CTTACACTCAAAATTTAGAGTAG
1 CTTACACCCAAAATTTAGAGTAG
16353068 GGGTTTAGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (25 bp):
CTTACACCCAAAATTTAGAGTAGCC
Found at i:16361133 original size:15 final size:16
Alignment explanation
Indices: 16361107--16361136 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16361097 TTTGGTTGAG
16361107 AAAATAATTTAATTAA
1 AAAATAATTTAATTAA
16361123 AAAATAA-TTAATTA
1 AAAATAATTTAATTA
16361137 TATTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATAATTTAATTAA
Found at i:16362261 original size:3 final size:3
Alignment explanation
Indices: 16362202--16362245 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
16362192 AACCTCTCAT
16362202 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
16362246 TTCATAAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:16362907 original size:27 final size:27
Alignment explanation
Indices: 16362877--16362931 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
16362867 TAGGCAATCC
16362877 TCGAGCAATGTTATCTTTAAAGGAACT
1 TCGAGCAATGTTATCTTTAAAGGAACT
**
16362904 TCGAGTGATGTTATCTTTAAAGGAACT
1 TCGAGCAATGTTATCTTTAAAGGAACT
16362931 T
1 T
16362932 TGCATGTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (27 bp):
TCGAGCAATGTTATCTTTAAAGGAACT
Found at i:16366440 original size:40 final size:40
Alignment explanation
Indices: 16366382--16366457 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
16366372 TTCAAATTAA
*
16366382 GTTAGAATGATGGTCAAATGTTACACGATTATTAGTTCGT
1 GTTAGAATGATGGCCAAATGTTACACGATTATTAGTTCGT
16366422 GTTAGAATGATGGCCAAATGTTACACGATTATTAGT
1 GTTAGAATGATGGCCAAATGTTACACGATTATTAGT
16366458 ACATGTGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.36
Consensus pattern (40 bp):
GTTAGAATGATGGCCAAATGTTACACGATTATTAGTTCGT
Found at i:16374940 original size:17 final size:17
Alignment explanation
Indices: 16374895--16374931 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16374885 GCCTGGCGGG
* *
16374895 TAGAATTACTTGACGAA
1 TAGAATTACCTAACGAA
16374912 TAGAATTACCTAACGAA
1 TAGAATTACCTAACGAA
16374929 TAG
1 TAG
16374932 GATTGCCTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (17 bp):
TAGAATTACCTAACGAA
Found at i:16376705 original size:18 final size:18
Alignment explanation
Indices: 16376682--16376719 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
16376672 GTAAGTTTCC
16376682 AAAATTGGAAATAGAAAT
1 AAAATTGGAAATAGAAAT
*
16376700 AAAATTGGAAATGGAAAT
1 AAAATTGGAAATAGAAAT
16376718 AA
1 AA
16376720 TAAAGAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (18 bp):
AAAATTGGAAATAGAAAT
Found at i:16376735 original size:24 final size:24
Alignment explanation
Indices: 16376682--16376736 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
16376672 GTAAGTTTCC
*
16376682 AAAATTGGAAATAGAAATAAAATTG
1 AAAA-TGGAAATAGAAAGAAAATTG
* *
16376707 GAAATGGAAATAATAAAGAAAA-TG
1 AAAATGGAAAT-AGAAAGAAAATTG
16376731 AAAATG
1 AAAATG
16376737 ATCCATTTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.20
Consensus pattern (24 bp):
AAAATGGAAATAGAAAGAAAATTG
Found at i:16376930 original size:26 final size:26
Alignment explanation
Indices: 16376879--16376943 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
16376869 TGAACATATT
**
16376879 TTGTCAAAATTTTATTAGGGGCAAAA
1 TTGTCAAAATTTTACAAGGGGCAAAA
* *
16376905 TTGTCAAAATTTTACAATGGGTAAAA
1 TTGTCAAAATTTTACAAGGGGCAAAA
**
16376931 TCATCAAAATTTT
1 TTGTCAAAATTTT
16376944 GTTGAGGGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (26 bp):
TTGTCAAAATTTTACAAGGGGCAAAA
Found at i:16377292 original size:21 final size:21
Alignment explanation
Indices: 16377266--16377305 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16377256 AATAAATACC
*
16377266 AAAAAATTATTTTAAAAATTA
1 AAAAAAGTATTTTAAAAATTA
16377287 AAAAAAGTATTTTAAAAAT
1 AAAAAAGTATTTTAAAAAT
16377306 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
AAAAAAGTATTTTAAAAATTA
Found at i:16377308 original size:11 final size:11
Alignment explanation
Indices: 16377267--16377392 Score: 89
Period size: 11 Copynumber: 12.4 Consensus size: 11
16377257 ATAAATACCA
16377267 AAAAATTATTTT
1 AAAAA-TATTTT
**
16377279 -AAAA-ATTAA
1 AAAAATATTTT
16377288 AAAAAGTATTTT
1 AAAAA-TATTTT
16377300 AAAAATATTTT
1 AAAAATATTTT
16377311 --AAA-A--TT
1 AAAAATATTTT
16377317 AAAAAT-TTTT
1 AAAAATATTTT
16377327 AAAAATATTTT
1 AAAAATATTTT
16377338 AAAAATATTTT
1 AAAAATATTTT
*
16377349 --AAA-A-TTA
1 AAAAATATTTT
* *
16377356 AAAAATA-ATA
1 AAAAATATTTT
16377366 AAAAAGTATTTT
1 AAAAA-TATTTT
16377378 AAAAATATTTT
1 AAAAATATTTT
16377389 AAAA
1 AAAA
16377393 TTAAAAAAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 29
0.71 0.06 0.22
Matches are distributed among these distances:
6 2 0.02
7 2 0.02
8 5 0.05
9 12 0.13
10 20 0.22
11 37 0.40
12 14 0.15
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:16377319 original size:38 final size:38
Alignment explanation
Indices: 16377277--16377399 Score: 185
Period size: 38 Copynumber: 3.2 Consensus size: 38
16377267 AAAAATTATT
16377277 TTAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
**
16377315 TTAAAAATTTTTAAAAA-TATTTTAAAAATATTTTAAAA
1 TTAAAAA-TTAAAAAAAGTATTTTAAAAATATTTTAAAA
*
16377353 TTAAAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAA
1 TT-AAAAATTA-AAAAAAGTATTTTAAAAATATTTTAAAA
16377393 TTAAAAA
1 TTAAAAA
16377400 AATTTAAAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
38 31 0.41
39 22 0.29
40 23 0.30
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (38 bp):
TTAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:16377422 original size:17 final size:17
Alignment explanation
Indices: 16377299--16377422 Score: 59
Period size: 17 Copynumber: 6.7 Consensus size: 17
16377289 AAAAGTATTT
* *
16377299 TAAAAATATTTTAAAAT
1 TAAAAATATTTAAAAAA
*
16377316 TAAAAATTTTTAAAAATA
1 TAAAAATATTTAAAAA-A
* *
16377334 TTTTAAAAATATTTTAAAAT
1 ---TAAAAATATTTAAAAAA
* *
16377354 TAAAAAATAATAAAAAAGTA
1 T-AAAAATATTTAAAAA--A
* *
16377374 TTTTAAAAATATTTTAAAAT
1 ---TAAAAATATTTAAAAAA
*
16377394 TAAAAAAATTTAAAAAA
1 TAAAAATATTTAAAAAA
*
16377411 TAAATATATTTA
1 TAAAAATATTTA
16377423 TTATATCGGG
Statistics
Matches: 78, Mismatches: 19, Indels: 20
0.67 0.16 0.17
Matches are distributed among these distances:
17 39 0.50
18 12 0.15
21 14 0.18
22 12 0.15
23 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (17 bp):
TAAAAATATTTAAAAAA
Found at i:16380572 original size:20 final size:20
Alignment explanation
Indices: 16380523--16380588 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
16380513 GCTACGATGT
** *
16380523 CTCTGTTTGCACTTCTGTGC
1 CTCTGTTTGCACAACAGTGC
**
16380543 CTCTAATTGCACAAGCA-TGC
1 CTCTGTTTGCACAA-CAGTGC
*
16380563 CTCTGTTTGCACTACAGTGC
1 CTCTGTTTGCACAACAGTGC
16380583 CTCTGT
1 CTCTGT
16380589 ATAGAGTTAC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.06
20 33 0.92
21 1 0.03
ACGTcount: A:0.15, C:0.30, G:0.18, T:0.36
Consensus pattern (20 bp):
CTCTGTTTGCACAACAGTGC
Found at i:16383827 original size:22 final size:22
Alignment explanation
Indices: 16383797--16383842 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
16383787 AATGGTAAAC
*
16383797 TAGCTTTGTTA-TGGATTTGTAG
1 TAGCATTGTTACTGGATTTG-AG
*
16383819 TAGCATTGTTACTGTATTTGAG
1 TAGCATTGTTACTGGATTTGAG
16383841 TA
1 TA
16383843 TTCTCAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.48
Consensus pattern (22 bp):
TAGCATTGTTACTGGATTTGAG
Found at i:16388157 original size:90 final size:90
Alignment explanation
Indices: 16388028--16388206 Score: 315
Period size: 90 Copynumber: 2.0 Consensus size: 90
16388018 GAAAATTACT
*
16388028 AATTGCATGTTAGTTTCGTGAACATCTTATATTTGTTTAATGTGAAAGAAAATAATTGATATGTT
1 AATTGCATGTTAGTTTCGTGAACATCTTATATATGTTTAATGTGAAAGAAAATAATTGATATGTT
* *
16388093 GTTACTAATTTTCTTTCGGATTGGA
66 ATTACTAATTTTCTTTCGAATTGGA
16388118 AATTGCATGTTAGTTTCGTGAACATCTGT-TATATGTTTAATGTGAAAGAAAATAATTGATATGT
1 AATTGCATGTTAGTTTCGTGAACATCT-TATATATGTTTAATGTGAAAGAAAATAATTGATATGT
16388182 TATTACTAATTTTCTTTCGAATTGG
65 TATTACTAATTTTCTTTCGAATTGG
16388207 GCAAGCATAT
Statistics
Matches: 85, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
90 84 0.99
91 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (90 bp):
AATTGCATGTTAGTTTCGTGAACATCTTATATATGTTTAATGTGAAAGAAAATAATTGATATGTT
ATTACTAATTTTCTTTCGAATTGGA
Found at i:16391847 original size:21 final size:21
Alignment explanation
Indices: 16391817--16391866 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
16391807 TAAAATTTAA
*
16391817 AAAAATTAATTTTTTTAAATAT
1 AAAAA-TAATTTTTTAAAATAT
16391839 AAAAATAA--TTTTAAAATAT
1 AAAAATAATTTTTTAAAATAT
16391858 AAAAA-AATT
1 AAAAATAATT
16391867 CTAAAATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
19 15 0.60
21 3 0.12
22 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAATAATTTTTTAAAATAT
Found at i:16391855 original size:19 final size:18
Alignment explanation
Indices: 16391828--16391873 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
16391818 AAAATTAATT
*
16391828 TTTTTAAATATAAAAATAA
1 TTTTAAAATATAAAAA-AA
16391847 TTTTAAAATATAAAAAAA
1 TTTTAAAATATAAAAAAA
*
16391865 TTCTAAAAT
1 TTTTAAAAT
16391874 TCAATGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTTAAAATATAAAAAAA
Found at i:16391872 original size:18 final size:19
Alignment explanation
Indices: 16391833--16391873 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
16391823 TAATTTTTTT
*
16391833 AAATATAAAAATAATTTTA
1 AAATATAAAAATAATTCTA
16391852 AAATATAAAAA-AATTCTA
1 AAATATAAAAATAATTCTA
16391870 AAAT
1 AAAT
16391874 TCAATGTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATATAAAAATAATTCTA
Found at i:16392290 original size:7 final size:8
Alignment explanation
Indices: 16392270--16392299 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
16392260 AATTTTGAAT
16392270 TTTTTCATA
1 TTTTTC-TA
16392279 TTTTTCTA
1 TTTTTCTA
16392287 TTTTTCTA
1 TTTTTCTA
16392295 TTTTT
1 TTTTT
16392300 GAATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCTA
Found at i:16392305 original size:16 final size:17
Alignment explanation
Indices: 16392262--16392306 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
16392252 TAACATTGAA
16392262 TTTTGAATTTTTTCATAT
1 TTTTGAA-TTTTTCATAT
**
16392280 TTTTCTATTTTTC-TAT
1 TTTTGAATTTTTCATAT
16392296 TTTTGAATTTT
1 TTTTGAATTTT
16392307 AAAGAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 12 0.52
17 6 0.26
18 5 0.22
ACGTcount: A:0.18, C:0.07, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTTGAATTTTTCATAT
Found at i:16397179 original size:132 final size:132
Alignment explanation
Indices: 16396934--16397565 Score: 1030
Period size: 132 Copynumber: 4.8 Consensus size: 132
16396924 TCCATTCCAC
*
16396934 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * * *
16396999 TATTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAACGACTTAAATCTGCTTCTCCACTG
66 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
16397064 TA
131 TA
* * *
16397066 TTGGAAAGATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACGGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * *
16397131 TCTTCGACCTATTCCACTACTGTTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
66 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
16397196 TA
131 TA
* * * *
16397198 TTGGGAAGATAAGATTCACCATCTTTGATCTACTCCACTACTGTTTAGGGTGACAGAATCTACAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * * * *
16397263 TCTTCGACCTATTCCACTATTGTTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTG
66 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
16397328 TA
131 TA
16397330 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* *
16397395 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCACTG
66 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
16397460 TA
131 TA
* * *
16397462 TTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGATAGAATTTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
*
16397527 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACT
66 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACT
16397566 GCTTAGGGAG
Statistics
Matches: 465, Mismatches: 35, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 465 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (132 bp):
TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
TA
Found at i:16397279 original size:44 final size:44
Alignment explanation
Indices: 16397099--16397294 Score: 127
Period size: 44 Copynumber: 4.5 Consensus size: 44
16397089 TTCGATCTGC
* * *
16397099 TCCACTACTGCTTAGGGTGACGGAATCTGCAATCTTCGACCTAT
1 TCCACTACTGTTTAGGGTGACAGAATCTACAATCTTCGACCTAT
* * ** * *
16397143 TCCACTACTGTTTAGGGTGATAGGA-CT--AATGGCTTAAATCTGCT
1 TCCACTACTGTTTAGGGTGACAGAATCTACAAT--CTTCGACCT-AT
* * * * * * *
16397187 TCTC-C-ACTGTATT-GGGAAGATAAGATTC-ACCATCTTTGATCTAC
1 TC-CACTACTGT-TTAGGG-TGA-CAGAATCTACAATCTTCGACCTAT
16397231 TCCACTACTGTTTAGGGTGACAGAATCTACAATCTTCGACCTAT
1 TCCACTACTGTTTAGGGTGACAGAATCTACAATCTTCGACCTAT
*
16397275 TCCACTATTGTTTAGGGTGA
1 TCCACTACTGTTTAGGGTGA
16397295 TAAGACTAAT
Statistics
Matches: 113, Mismatches: 25, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
41 3 0.03
43 22 0.19
44 67 0.59
45 18 0.16
46 1 0.01
47 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (44 bp):
TCCACTACTGTTTAGGGTGACAGAATCTACAATCTTCGACCTAT
Found at i:16397572 original size:18 final size:18
Alignment explanation
Indices: 16397549--16397583 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16397539 TCCACTACTA
*
16397549 CTTAGGGTGATAGGACTG
1 CTTAGGGAGATAGGACTG
16397567 CTTAGGGAGATAGGACT
1 CTTAGGGAGATAGGACT
16397584 AGATGCGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.37, T:0.26
Consensus pattern (18 bp):
CTTAGGGAGATAGGACTG
Found at i:16397715 original size:50 final size:50
Alignment explanation
Indices: 16397657--16398530 Score: 323
Period size: 50 Copynumber: 17.7 Consensus size: 50
16397647 TGCAATGTTG
* *
16397657 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTATTCCATTACACCGCCT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* ** ** *
16397707 GGGAAGTAAGATTCGCCGTTGT-GACTTCAATCTTTTTAATTGCAATG-TT
1 GGGAAGTAAGATTCGCCGTTGTAG-CTTCAATCTATTCCATTGCACCGCCT
* *
16397756 GGTGAAAG-AAGATTTGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCCT
1 GG-G-AAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* ** * **
16397807 -GGAATGTAAGATTTGTTGTTGTAGCTTCAATCTTTTTAATTG--CCG---
1 GGGAA-GTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* * * * * *
16397852 GGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* * * * * ** ** *
16397901 AAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATG-TT
1 -GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* * * ** * ** * *
16397951 AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGTAATGTCA
1 -GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* * * * * *
16398002 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTACAACG-CT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* * * * ** **** *
16398051 AAGAAAGTAAGA-TCTGCTGTTGTAGCTTCAATCTTTTTAATTGCAATATCA
1 -GGGAAGTAAGATTC-GCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* * * * *
16398102 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* * * * ** * ** * ** * *
16398151 AAGAAAGTAAAATCCGTTGTTGTAGCTTCAATCTTTTTAATTACAATGTCA
1 -GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* * * ** **** *
16398202 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATATCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* * * * * * *
16398252 GGGAAGTAAGATCCGCTGTTATAGCTTCAATCTGTTCCACTGCAACG-TT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* * * * * ** ** * *
16398301 AAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCA
1 -GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* * * * * *
16398352 GGGAAGTAAGATCCGCTGCTGTAGCTTCAATCTGTTCCACTGCAACG-CT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* * * * * * *
16398401 AAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT-TT---TT-AACTGCCA
1 -GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* * * * * * *
16398447 GGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTACACTGCCT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
* ** *
16398497 GGAAAGGTAAGATTCATCGTTGTGGCTTCAATCT
1 GGGAA-GTAAGATTCGCCGTTGTAGCTTCAATCT
16398531 TTTAATTGAA
Statistics
Matches: 654, Mismatches: 140, Indels: 59
0.77 0.16 0.07
Matches are distributed among these distances:
45 61 0.09
46 8 0.01
47 2 0.00
48 5 0.01
49 13 0.02
50 535 0.82
51 30 0.05
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (50 bp):
GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTCCATTGCACCGCCT
Found at i:16397807 original size:100 final size:98
Alignment explanation
Indices: 16397634--16398538 Score: 634
Period size: 100 Copynumber: 9.2 Consensus size: 98
16397624 CTGCCATCTC
* * * * * *
16397634 CAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTATTCCATTA
1 CAATCTTTTTAATTGCAATGTT-GGGAAGTAAGATCCGCCGTTGTAGCTTCAATCTATTCCACTG
*
16397699 CACCGCCTGGGAAGTAAGATTCGCCGTTGT-GACTT
65 CACCGCCT-GGAAGTAAGATTCGCTGTTGTAG-CTT
**
16397734 CAATCTTTTTAATTGCAATGTTGGTGAAAG-AAGATTTGCCGTTGTAGCTTCAATCTATTCCACT
1 CAATCTTTTTAATTGCAATGTTGG-G-AAGTAAGATCCGCCGTTGTAGCTTCAATCTATTCCACT
* *
16397798 GCACCGCCTGGAATGTAAGATTTGTTGTTGTAGCTT
64 GCACCGCCTGGAA-GTAAGATTCGCTGTTGTAGCTT
* * * *
16397834 CAATCTTTTTAATTGC--CG--GGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGC
1 CAATCTTTTTAATTGCAATGTTGGGAAGTAAGATCCGCCGTTGTAGCTTCAATCTATTCCACTGC
* * *
16397895 AACG-CTAAGAAAGTAAGATCCGCTGTTGTAGCTT
66 ACCGCCT--GGAAGTAAGATTCGCTGTTGTAGCTT
* * ** *
16397929 CAATCTTTTTAATTGCAATGTTAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTG
1 CAATCTTTTTAATTGCAATGTT-GGGAAGTAAGATCCGCCGTTGTAGCTTCAATCTATTCCACTG
* ** ** *
16397994 TAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTT
65 CACCG-CCTGGAAGTAAGATTCGCTGTTGTAGCTT
* ** * * * ** * * * * ** *
16398029 CAATCTGTTCCACTACAACGCTAAGAAAGTAAGATCTGCTGTTGTAGCTTCAATCTTTTTAATTG
1 CAATCTTTTTAATTGCAATG-TTGGGAAGTAAGATCCGCCGTTGTAGCTTCAATCTATTCCACTG
*** ** *
16398094 CAATATCAGGGAAGTAAGATCCGCTGTTGTAGCTT
65 C-ACCGCCTGGAAGTAAGATTCGCTGTTGTAGCTT
* ** * * ** * * ** * ** * *
16398129 CAATCTGTTCCACTGCAACGCTAAGAAAGTAAAATCCGTTGTTGTAGCTTCAATCTTTTTAATTA
1 CAATCTTTTTAATTGCAATG-TTGGGAAGTAAGATCCGCCGTTGTAGCTTCAATCTATTCCACTG
** ** *
16398194 CAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTT
65 CACCG-CCTGGAAGTAAGATTCGCTGTTGTAGCTT
* * * * *
16398229 CAATCTTTTTAATTGCAATATCAGGGAAGTAAGATCCGCTGTTATAGCTTCAATCTGTTCCACTG
1 CAATCTTTTTAATTGCAATGT-TGGGAAGTAAGATCCGCCGTTGTAGCTTCAATCTATTCCACTG
* * * *
16398294 CAACG-TTAAGAAAGTAAGATCCGCTGTTGTAGCTT
65 CACCGCCT--GGAAGTAAGATTCGCTGTTGTAGCTT
* * * *
16398329 CAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGCTGTAGCTTCAATCTGTTCCACTG
1 CAATCTTTTTAATTGCAATGT-TGGGAAGTAAGATCCGCCGTTGTAGCTTCAATCTATTCCACTG
* * *
16398394 CAACG-CTAAGAAAGTAAGATCCGCTGTTGTAGCTT
65 CACCGCCT--GGAAGTAAGATTCGCTGTTGTAGCTT
* * * * * *
16398429 CAATCTTTTTAACTGCCA----GGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTAC
1 CAATCTTTTTAATTGCAATGTTGGGAAGTAAGATCCGCCGTTGTAGCTTCAATCTATTCCACTGC
* * *
16398490 ACTGCCTGGAAAGGTAAGATTC-ATCGTTGTGGCTT
66 ACCGCCTGG-AA-GTAAGATTCGCT-GTTGTAGCTT
16398525 CAATC-TTTTAATTG
1 CAATCTTTTTAATTG
16398539 AAGACTATAG
Statistics
Matches: 693, Mismatches: 88, Indels: 53
0.83 0.11 0.06
Matches are distributed among these distances:
94 6 0.01
95 124 0.18
96 29 0.04
97 1 0.00
98 1 0.00
99 8 0.01
100 518 0.75
101 6 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (98 bp):
CAATCTTTTTAATTGCAATGTTGGGAAGTAAGATCCGCCGTTGTAGCTTCAATCTATTCCACTGC
ACCGCCTGGAAGTAAGATTCGCTGTTGTAGCTT
Found at i:16398057 original size:150 final size:149
Alignment explanation
Indices: 16397823--16398490 Score: 746
Period size: 150 Copynumber: 4.5 Consensus size: 149
16397813 TAAGATTTGT
* *
16397823 TGTTGTAGCTTCAATCTTTTTAAT----TGCCGGGGAAGCAAGATCCGCTGTTGTAGCTTCAATC
1 TGTTGTAGCTTCAATCTTTTTAATGCAATGCCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATC
*
16397884 TGTTCCACTGCAACG-CTAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAAT
66 TGTTCCACTACAACGTC-AAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAAT
* *
16397948 GTTAGGGAAGTAAGATCCGC
130 ATCAGGGAAGTAAGATCCGC
* *
16397968 TGTTGTAGCTTCAATCTTTTTAATTGTAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAAT
1 TGTTGTAGCTTCAATCTTTTTAA-TGCAATGCCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAAT
*
16398033 CTGTTCCACTACAACG-CTAAGAAAGTAAGATCTGCTGTTGTAGCTTCAATCTTTTTAATTGCAA
65 CTGTTCCACTACAACGTC-AAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAA
16398097 TATCAGGGAAGTAAGATCCGC
129 TATCAGGGAAGTAAGATCCGC
** * * * * * * *
16398118 TGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAAGAAAGTAAAATCCGTTGTTGTAGCTTCAAT
1 TGTTGTAGCTTCAATCT-TTTTAATGCAATGCCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAAT
* ** * * * *
16398183 CTTTTTAATTACAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAAT
65 CTGTTCCACTACAACGTCAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAAT
16398248 ATCAGGGAAGTAAGATCCGC
130 ATCAGGGAAGTAAGATCCGC
* ** * * ** * *
16398268 TGTTATAGCTTCAATCTGTTCCACTGCAACGTTAAGAAAGTAAGATCCGCTGTTGTAGCTTCAAT
1 TGTTGTAGCTTCAATCT-TTTTAATGCAATGCCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAAT
* ** * * * * * * * ** *
16398333 CTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGCTGTAGCTTCAATCTGTTCCACTGCAA-
65 CTGTTCCACTACAACGTCAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAAT
** * *
16398397 CGCTAAGAAAGTAAGATCCGC
130 ATC-AGGGAAGTAAGATCCGC
*
16398418 TGTTGTAGCTTCAATCTTTTTAA--C--TGCCAGGGAAGCAAGATCCGCTGTTGTAGCTTCAATC
1 TGTTGTAGCTTCAATCTTTTTAATGCAATGCCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATC
16398479 TGTTCCACTACA
66 TGTTCCACTACA
16398491 CTGCCTGGAA
Statistics
Matches: 460, Mismatches: 55, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
145 61 0.13
146 1 0.00
147 1 0.00
149 4 0.01
150 389 0.85
151 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (149 bp):
TGTTGTAGCTTCAATCTTTTTAATGCAATGCCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATC
TGTTCCACTACAACGTCAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATA
TCAGGGAAGTAAGATCCGC
Found at i:16399639 original size:53 final size:53
Alignment explanation
Indices: 16399571--16399676 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
16399561 CATTCTGAGT
16399571 TTGACATGTGTTTAGGAGATCTTCAGGACTTTGTCGATGCTCCAAGATGTCGC
1 TTGACATGTGTTTAGGAGATCTTCAGGACTTTGTCGATGCTCCAAGATGTCGC
* *
16399624 TTGATATGTGTTTAGGAGATCTTCGGGACTTTGTCGATGCTCCAAGATGTCGC
1 TTGACATGTGTTTAGGAGATCTTCAGGACTTTGTCGATGCTCCAAGATGTCGC
16399677 CTACCTTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (53 bp):
TTGACATGTGTTTAGGAGATCTTCAGGACTTTGTCGATGCTCCAAGATGTCGC
Found at i:16401121 original size:23 final size:23
Alignment explanation
Indices: 16401095--16401156 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
16401085 TTTTTTTTCT
**
16401095 TTTTTTTTCTATTTTGACTTTGA
1 TTTTTTTGATATTTTGACTTTGA
* *
16401118 TTTTTTTGATTTTTTGATTTTGA
1 TTTTTTTGATATTTTGACTTTGA
* *
16401141 TTTATTT-ATTTTTTGA
1 TTTTTTTGATATTTTGA
16401157 GTCTGAACTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 9 0.26
23 25 0.74
ACGTcount: A:0.15, C:0.03, G:0.10, T:0.73
Consensus pattern (23 bp):
TTTTTTTGATATTTTGACTTTGA
Found at i:16401138 original size:14 final size:14
Alignment explanation
Indices: 16401104--16401152 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
16401094 TTTTTTTTTC
16401104 TATTTTGACTTTGATT
1 TATTTTGA-TTT-ATT
16401120 T-TTTTGATTT-TT
1 TATTTTGATTTATT
16401132 TGATTTTGATTTATT
1 T-ATTTTGATTTATT
16401147 TATTTT
1 TATTTT
16401153 TTGAGTCTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.10
14 17 0.57
15 9 0.30
16 1 0.03
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.71
Consensus pattern (14 bp):
TATTTTGATTTATT
Found at i:16409928 original size:46 final size:46
Alignment explanation
Indices: 16409861--16409949 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
16409851 AGGCACACGG
* *
16409861 GTTGGGCTTTCCCACACGGGTTGGACACACGACTATGAGCCAACGA
1 GTTGGGCTTTCCCACAAGGGTTGGACACACGACCATGAGCCAACGA
* *
16409907 GTTGGGCTTTCCCAGAAGGGTTGGACACACGGCCATGAGCCAA
1 GTTGGGCTTTCCCACAAGGGTTGGACACACGACCATGAGCCAA
16409950 ACTGTGCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.19
Consensus pattern (46 bp):
GTTGGGCTTTCCCACAAGGGTTGGACACACGACCATGAGCCAACGA
Found at i:16426487 original size:37 final size:37
Alignment explanation
Indices: 16426403--16426487 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
16426393 AGATAATCTA
* *
16426403 CTGGACTTGTCCTCATGTTTGAAGCTAAGACAGTCTG
1 CTGGACTTGTCCTCATGTTTCAAGCTAAGACAGTCCG
16426440 CTGGACTTGTCCTCATGTTTCAAGCTAAGATCA-TCCG
1 CTGGACTTGTCCTCATGTTTCAAGCTAAGA-CAGTCCG
* *
16426477 TTGGAATTGTC
1 CTGGACTTGTC
16426488 TCCAAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 41 0.95
38 2 0.05
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (37 bp):
CTGGACTTGTCCTCATGTTTCAAGCTAAGACAGTCCG
Found at i:16426654 original size:42 final size:42
Alignment explanation
Indices: 16426603--16426688 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
16426593 TATCTATAAA
* *
16426603 TCTGGATATATGAAT-TCGTACTTATGAATCCGCATATGTGAT
1 TCTGCATATATGAATCT-ATACTTATGAATCCGCATATGTGAT
**
16426645 TCTGCATATATGAATCTATACTTATGAATCTTCATATGTGAT
1 TCTGCATATATGAATCTATACTTATGAATCCGCATATGTGAT
16426687 TC
1 TC
16426689 ATATGTGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 38 0.97
43 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (42 bp):
TCTGCATATATGAATCTATACTTATGAATCCGCATATGTGAT
Found at i:16426691 original size:11 final size:11
Alignment explanation
Indices: 16426675--16426699 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16426665 CTTATGAATC
16426675 TTCATATGTGA
1 TTCATATGTGA
16426686 TTCATATGTGA
1 TTCATATGTGA
16426697 TTC
1 TTC
16426700 TGTATCTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (11 bp):
TTCATATGTGA
Found at i:16431159 original size:21 final size:20
Alignment explanation
Indices: 16431135--16431185 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
16431125 ATTTATAACA
*
16431135 TATTCAATTCTCATCACTTGC
1 TATTCAAATCTCAT-ACTTGC
16431156 TATTTCAAATCTCATACTTGC
1 TA-TTCAAATCTCATACTTGC
*
16431177 TATACAAAT
1 TATTCAAAT
16431186 AGCTTTTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 6 0.22
21 10 0.37
22 11 0.41
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (20 bp):
TATTCAAATCTCATACTTGC
Found at i:16431162 original size:22 final size:21
Alignment explanation
Indices: 16431137--16431179 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
16431127 TTATAACATA
*
16431137 TTCAATTCTCATCACTTGCTAT
1 TTCAAATCTCAT-ACTTGCTAT
16431159 TTCAAATCTCATACTTGCTAT
1 TTCAAATCTCATACTTGCTAT
16431180 ACAAATAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (21 bp):
TTCAAATCTCATACTTGCTAT
Found at i:16431716 original size:12 final size:12
Alignment explanation
Indices: 16431699--16431729 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
16431689 AATATCAATT
16431699 ACTTACCTCAAC
1 ACTTACCTCAAC
16431711 ACTTACCTCAAC
1 ACTTACCTCAAC
16431723 ACTTACC
1 ACTTACC
16431730 ATATACATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.42, G:0.00, T:0.26
Consensus pattern (12 bp):
ACTTACCTCAAC
Found at i:16432427 original size:5 final size:5
Alignment explanation
Indices: 16432419--16432494 Score: 145
Period size: 5 Copynumber: 15.4 Consensus size: 5
16432409 TTATTTTAGT
16432419 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
16432469 TAATA TAATA TAATA TAATA T-ATA TA
1 TAATA TAATA TAATA TAATA TAATA TA
16432495 CTTAACATTT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.06
5 66 0.94
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:16432543 original size:38 final size:37
Alignment explanation
Indices: 16432477--16432556 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 37
16432467 TATAATATAA
16432477 TATAATATAATATATATACTTAACATTTAAGTTTTAT
1 TATAATATAATATATATACTTAACATTTAAGTTTTAT
* * *
16432514 TATAATATTATATTATATATTTTAA-ATTTAATTTTTAT
1 TATAATATAATA-TATATA-CTTAACATTTAAGTTTTAT
*
16432552 AATAA
1 TATAA
16432557 AATACACTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 11 0.30
38 22 0.59
39 4 0.11
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (37 bp):
TATAATATAATATATATACTTAACATTTAAGTTTTAT
Found at i:16433768 original size:40 final size:40
Alignment explanation
Indices: 16433649--16433788 Score: 135
Period size: 40 Copynumber: 3.6 Consensus size: 40
16433639 ACTTCGAGTC
* * *
16433649 GATGAGACACTAGGTGTCAAATTATTACTTCGGATATATTT
1 GATGAGACACTAGGTGCCAAACTATTACTTCGGAT-TATCT
* * * *
16433690 GATGAGGCAATAGGTGCC--A--ATTACTTCGGTTTAGCT
1 GATGAGACACTAGGTGCCAAACTATTACTTCGGATTATCT
* * *
16433726 GATGAGACATTGGGTGCCAAACTATTACTTCGAATTATCT
1 GATGAGACACTAGGTGCCAAACTATTACTTCGGATTATCT
* *
16433766 GATGAGGCACTGGGTGCCAAACT
1 GATGAGACACTAGGTGCCAAACT
16433789 GGTGTGTTTG
Statistics
Matches: 81, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
36 18 0.22
37 11 0.14
38 1 0.01
39 1 0.01
40 35 0.43
41 15 0.19
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (40 bp):
GATGAGACACTAGGTGCCAAACTATTACTTCGGATTATCT
Found at i:16434178 original size:18 final size:17
Alignment explanation
Indices: 16434157--16434197 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
16434147 AATTACAAAA
*
16434157 AAAATCAAAATAATTTTT
1 AAAATCAAAAT-ATTTAT
16434175 AAAATTCAAAATATTTAT
1 AAAA-TCAAAATATTTAT
16434193 AAAAT
1 AAAAT
16434198 ATATAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 13 0.62
19 7 0.33
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATCAAAATATTTAT
Found at i:16434178 original size:19 final size:18
Alignment explanation
Indices: 16434156--16434196 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
16434146 AAATTACAAA
*
16434156 AAAAATCAAAATAATTTTT
1 AAAAATCAAAAT-ATTTAT
*
16434175 AAAATTCAAAATATTTAT
1 AAAAATCAAAATATTTAT
16434193 AAAA
1 AAAA
16434197 TATATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATCAAAATATTTAT
Found at i:16434232 original size:10 final size:10
Alignment explanation
Indices: 16434217--16434274 Score: 62
Period size: 11 Copynumber: 5.5 Consensus size: 10
16434207 TTATATTTTA
16434217 AAAAAATTAT
1 AAAAAATTAT
*
16434227 AAAAAATTCT
1 AAAAAATTAT
*
16434237 ACAAAAATTCT
1 A-AAAAATTAT
16434248 AAAAAATATAT
1 AAAAAAT-TAT
*
16434259 AAAGAAATTTT
1 AAA-AAATTAT
16434270 AAAAA
1 AAAAA
16434275 TTAAAAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
10 18 0.43
11 20 0.48
12 4 0.10
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (10 bp):
AAAAAATTAT
Done.