Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 84 of 145
Found at i:27985752 original size:10 final size:10
Alignment explanation
Indices: 27985737--27985761 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
27985727 TTTTTCATTC
27985737 TTTAATTTTG
1 TTTAATTTTG
27985747 TTTAATTTTG
1 TTTAATTTTG
27985757 TTTAA
1 TTTAA
27985762 ACTTTCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (10 bp):
TTTAATTTTG
Found at i:27989032 original size:801 final size:801
Alignment explanation
Indices: 27987491--27989092 Score: 3188
Period size: 801 Copynumber: 2.0 Consensus size: 801
27987481 GTGGTGCAAA
27987491 GGTAGCAAGGGTTGTGCGGGTAATGTGTGTGAAGCAAGAGTGTGCACGAGCTAGGGGCAAGAAGC
1 GGTAGCAAGGGTTGTGCGGGTAATGTGTGTGAAGCAAGAGTGTGCACGAGCTAGGGGCAAGAAGC
27987556 AATAGCACCGCGAGGGCTAGAATGCTAGACACATCAGCATCATGTGAATGCTAGGGTGCTGGAAG
66 AATAGCACCGCGAGGGCTAGAATGCTAGACACATCAGCATCATGTGAATGCTAGGGTGCTGGAAG
27987621 TAGCGGCGATGGCACGTGAGTAGCAGGGTGCGCAAGCAGGGCAGAGCTGTCTGAGCTAGTGCGCA
131 TAGCGGCGATGGCACGTGAGTAGCAGGGTGCGCAAGCAGGGCAGAGCTGTCTGAGCTAGTGCGCA
27987686 AGGGAGCAATGGTGCTTACGATGGTGGCTGCTGGTAGGTGCTATGGACAGTTGCCAATGATGGTA
196 AGGGAGCAATGGTGCTTACGATGGTGGCTGCTGGTAGGTGCTATGGACAGTTGCCAATGATGGTA
27987751 GGTGGGGGCTAGGGCACTAGGTAGTTTGGGGGGTAGATGGTGTTAAAGGTGATGGAAGAAAAAGG
261 GGTGGGGGCTAGGGCACTAGGTAGTTTGGGGGGTAGATGGTGTTAAAGGTGATGGAAGAAAAAGG
27987816 TGTACGGGAAGGTGGTTTTTAAAGTGTGAGTATAGAGGTGTTCAACTTAAAATCTTAGAAGAAAT
326 TGTACGGGAAGGTGGTTTTTAAAGTGTGAGTATAGAGGTGTTCAACTTAAAATCTTAGAAGAAAT
27987881 AATAATAAAATACTATAACTCCTAATCTTATTTAAAGATAATACAATTAATTTTATAATATAAAG
391 AATAATAAAATACTATAACTCCTAATCTTATTTAAAGATAATACAATTAATTTTATAATATAAAG
27987946 TATATTAATATATTACTTGGTATTATATTATTTATTGGAAAAAAATTCTTGAATGAAATAATGAT
456 TATATTAATATATTACTTGGTATTATATTATTTATTGGAAAAAAATTCTTGAATGAAATAATGAT
27988011 AAAATATTAAACAATTCGAATCCTATACAAAGTTGATAATAATTAATATATATTATCATAAATAT
521 AAAATATTAAACAATTCGAATCCTATACAAAGTTGATAATAATTAATATATATTATCATAAATAT
27988076 ATTTATATATTAATTGTAATAATATTATTTATTAAAATTAAATAAATAAATAAACTTTATTTTAG
586 ATTTATATATTAATTGTAATAATATTATTTATTAAAATTAAATAAATAAATAAACTTTATTTTAG
27988141 CAGTTTTAAAGACAATCAATTTCAATATTTACAAAAAAAAAAGAGTCAATTATTGCAAACAATTC
651 CAGTTTTAAAGACAATCAATTTCAATATTTACAAAAAAAAAAGAGTCAATTATTGCAAACAATTC
27988206 AATTAAGTACATGGACTTAAAAATTGGATCAAATTTGACATTTTTATTTGAAAGATTAAAAATTT
716 AATTAAGTACATGGACTTAAAAATTGGATCAAATTTGACATTTTTATTTGAAAGATTAAAAATTT
27988271 ATTTTGTCACTTAGGAAATAC
781 ATTTTGTCACTTAGGAAATAC
27988292 GGTAGCAAGGGTTGTGCGGGTAATGTGTGTGAAGCAAGAGTGTGCACGAGCTAGGGGCAAGAAGC
1 GGTAGCAAGGGTTGTGCGGGTAATGTGTGTGAAGCAAGAGTGTGCACGAGCTAGGGGCAAGAAGC
27988357 AATAGCACCGCGAGGGCTAGAATGCTAGACACATCAGCATCATGTGAATGCTAGGGTGCTGGAAG
66 AATAGCACCGCGAGGGCTAGAATGCTAGACACATCAGCATCATGTGAATGCTAGGGTGCTGGAAG
27988422 TAGCGGCGATGGCACGTGAGTAGCAGGGTGCGCAAGCAGGGCAGAGCTGTCTGAGCTAGTGCGCA
131 TAGCGGCGATGGCACGTGAGTAGCAGGGTGCGCAAGCAGGGCAGAGCTGTCTGAGCTAGTGCGCA
27988487 AGGGAGCAATGGTGCTTACGATGGTGGCTGCTGGTAGGTGCTATGGACAGTTGCCAATGATGGTA
196 AGGGAGCAATGGTGCTTACGATGGTGGCTGCTGGTAGGTGCTATGGACAGTTGCCAATGATGGTA
27988552 GGTGGGGGCTAGGGCACTAGGTAGTTTGGGGGGTAGATGGTGTTAAAGGTGATGGAAGAAAAAGG
261 GGTGGGGGCTAGGGCACTAGGTAGTTTGGGGGGTAGATGGTGTTAAAGGTGATGGAAGAAAAAGG
27988617 TGTACGGGAAGGTGGTTTTTAAAGTGTGAGTATAGAGGTGTTCAACTTAAAATCTTAGAAGAAAT
326 TGTACGGGAAGGTGGTTTTTAAAGTGTGAGTATAGAGGTGTTCAACTTAAAATCTTAGAAGAAAT
27988682 AATAATAAAATACTATAACTCCTAATCTTATTTAAAGATAATAACAATTAA-TTTATAATATAAA
391 AATAATAAAATACTATAACTCCTAATCTTATTTAAAGATAAT-ACAATTAATTTTATAATATAAA
27988746 GTATATTAATATATTACTTGGTATTATATTATTTATTGGAAAAAAATTCTTGAATGAAATAATGA
455 GTATATTAATATATTACTTGGTATTATATTATTTATTGGAAAAAAATTCTTGAATGAAATAATGA
27988811 TAAAATATTAAACAATTCGAATCCTATACAAAGTTGATAATAATTAATATATATTATCATAAATA
520 TAAAATATTAAACAATTCGAATCCTATACAAAGTTGATAATAATTAATATATATTATCATAAATA
27988876 TATTTATATATTAATTGTAATAATATTATTTATTAAAATTAAATAAATAAATAAACTTTATTTTA
585 TATTTATATATTAATTGTAATAATATTATTTATTAAAATTAAATAAATAAATAAACTTTATTTTA
27988941 GCAGTTTTAAAGACAATCAATTTCAATATTTACAAAAAAAAAAGAGTCAATTATTGCAAACAATT
650 GCAGTTTTAAAGACAATCAATTTCAATATTTACAAAAAAAAAAGAGTCAATTATTGCAAACAATT
27989006 CAATTAAGTACATGGACTTAAAAATTGGATCAAATTTGACATTTTTATTTGAAAGATTAAAAATT
715 CAATTAAGTACATGGACTTAAAAATTGGATCAAATTTGACATTTTTATTTGAAAGATTAAAAATT
27989071 TATTTTGTCACTTAGGAAATAC
780 TATTTTGTCACTTAGGAAATAC
27989093 TTTCTTGGAA
Statistics
Matches: 800, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
801 792 0.99
802 8 0.01
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (801 bp):
GGTAGCAAGGGTTGTGCGGGTAATGTGTGTGAAGCAAGAGTGTGCACGAGCTAGGGGCAAGAAGC
AATAGCACCGCGAGGGCTAGAATGCTAGACACATCAGCATCATGTGAATGCTAGGGTGCTGGAAG
TAGCGGCGATGGCACGTGAGTAGCAGGGTGCGCAAGCAGGGCAGAGCTGTCTGAGCTAGTGCGCA
AGGGAGCAATGGTGCTTACGATGGTGGCTGCTGGTAGGTGCTATGGACAGTTGCCAATGATGGTA
GGTGGGGGCTAGGGCACTAGGTAGTTTGGGGGGTAGATGGTGTTAAAGGTGATGGAAGAAAAAGG
TGTACGGGAAGGTGGTTTTTAAAGTGTGAGTATAGAGGTGTTCAACTTAAAATCTTAGAAGAAAT
AATAATAAAATACTATAACTCCTAATCTTATTTAAAGATAATACAATTAATTTTATAATATAAAG
TATATTAATATATTACTTGGTATTATATTATTTATTGGAAAAAAATTCTTGAATGAAATAATGAT
AAAATATTAAACAATTCGAATCCTATACAAAGTTGATAATAATTAATATATATTATCATAAATAT
ATTTATATATTAATTGTAATAATATTATTTATTAAAATTAAATAAATAAATAAACTTTATTTTAG
CAGTTTTAAAGACAATCAATTTCAATATTTACAAAAAAAAAAGAGTCAATTATTGCAAACAATTC
AATTAAGTACATGGACTTAAAAATTGGATCAAATTTGACATTTTTATTTGAAAGATTAAAAATTT
ATTTTGTCACTTAGGAAATAC
Found at i:27999844 original size:16 final size:16
Alignment explanation
Indices: 27999823--27999854 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
27999813 TCGTAGTCGA
27999823 AGTAAACCTGAACTCT
1 AGTAAACCTGAACTCT
27999839 AGTAAACCTGAACTCT
1 AGTAAACCTGAACTCT
27999855 GCCTATCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (16 bp):
AGTAAACCTGAACTCT
Found at i:28004176 original size:18 final size:19
Alignment explanation
Indices: 28004140--28004176 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28004130 GAATGCAAAA
*
28004140 TTGGTATTGATATAAATTT
1 TTGGTATCGATATAAATTT
28004159 TTGGTATCGATA-AAATTT
1 TTGGTATCGATATAAATTT
28004177 AATAAGTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGGTATCGATATAAATTT
Found at i:28004205 original size:20 final size:20
Alignment explanation
Indices: 28004161--28004210 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
28004151 ATAAATTTTT
28004161 GGTATCGATAAAATTTAATAA
1 GGTATCGATAAAATTT-ATAA
*
28004182 -GTATCGATATAATTT-TCAA
1 GGTATCGATAAAATTTAT-AA
*
28004201 GGTATTGATA
1 GGTATCGATA
28004211 CTTATTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 1 0.04
19 2 0.08
20 22 0.88
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (20 bp):
GGTATCGATAAAATTTATAA
Found at i:28004841 original size:30 final size:30
Alignment explanation
Indices: 28004807--28004866 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
28004797 TTTTATGTAA
28004807 AATTTGACACATTTATGTACATGAGTCATG
1 AATTTGACACATTTATGTACATGAGTCATG
28004837 AATTTGACACATTTATGTACATGAGTCATG
1 AATTTGACACATTTATGTACATGAGTCATG
28004867 TTCTTATTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (30 bp):
AATTTGACACATTTATGTACATGAGTCATG
Found at i:28005110 original size:71 final size:72
Alignment explanation
Indices: 28005026--28005169 Score: 272
Period size: 71 Copynumber: 2.0 Consensus size: 72
28005016 TTTAGTATTG
28005026 TGTTTTTTTTTTCACAAACAAGTATTATAAATCTATATAACGGCTTAATAATTTACTTCAC-AAA
1 TGTTTTTTTTTTCACAAACAAGTATTATAAATCTATATAACGGCTTAATAATTTACTTCACAAAA
28005090 ATTTGAT
66 ATTTGAT
28005097 TGTTTTTTTTTTCACAAACAAGTATTATAAATCTATATAACGGCTTAATAATTTACTTCACATAA
1 TGTTTTTTTTTTCACAAACAAGTATTATAAATCTATATAACGGCTTAATAATTTACTTCACA-AA
28005162 AATTTGAT
65 AATTTGAT
28005170 ATGTCGAAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
71 61 0.86
73 10 0.14
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (72 bp):
TGTTTTTTTTTTCACAAACAAGTATTATAAATCTATATAACGGCTTAATAATTTACTTCACAAAA
ATTTGAT
Found at i:28005961 original size:21 final size:22
Alignment explanation
Indices: 28005907--28005959 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
28005897 CTTTCTAAGT
28005907 TAATTTTTTTATGTAAAAGACA
1 TAATTTTTTTATGTAAAAGACA
28005929 TAATTTTTTTATGTAAAAGACA
1 TAATTTTTTTATGTAAAAGACA
28005951 TAATTTTTT
1 TAATTTTTT
28005960 ATTAGATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.51
Consensus pattern (22 bp):
TAATTTTTTTATGTAAAAGACA
Found at i:28013518 original size:14 final size:15
Alignment explanation
Indices: 28013495--28013523 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28013485 CTTTATTTTG
28013495 CTTTTAACTTTTTCA
1 CTTTTAACTTTTTCA
28013510 CTTTT-ACTTTTTCA
1 CTTTTAACTTTTTCA
28013524 TCTCAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (15 bp):
CTTTTAACTTTTTCA
Found at i:28014821 original size:12 final size:12
Alignment explanation
Indices: 28014787--28014823 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
28014777 GTAAAGGAAA
28014787 TAAA-AATA-TT
1 TAAATAATATTT
28014797 TAAATAATGATTT
1 TAAATAAT-ATTT
28014810 TAAATAATATTT
1 TAAATAATATTT
28014822 TA
1 TA
28014824 TTAAGAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.17
11 3 0.12
12 7 0.29
13 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (12 bp):
TAAATAATATTT
Found at i:28019244 original size:16 final size:16
Alignment explanation
Indices: 28019219--28019249 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28019209 TCAAAAAAGT
28019219 TTTCAAATATATATAG
1 TTTCAAATATATATAG
*
28019235 TTTCACATATATATA
1 TTTCAAATATATATA
28019250 CATATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (16 bp):
TTTCAAATATATATAG
Found at i:28020234 original size:23 final size:21
Alignment explanation
Indices: 28020204--28020246 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
28020194 TTCTTTAAAT
28020204 AAATTAAAAATATAGAAAAAAA
1 AAATTAAAAATATA-AAAAAAA
*
28020226 AAATGTAAAATTATAAAAAAA
1 AAAT-TAAAAATATAAAAAAA
28020247 TCCTAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (21 bp):
AAATTAAAAATATAAAAAAAA
Found at i:28020469 original size:19 final size:20
Alignment explanation
Indices: 28020444--28020488 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
28020434 GAACAAAAAT
28020444 GAAAAAAGAAAA-AAAATCA
1 GAAAAAAGAAAAGAAAATCA
*
28020463 TAAAAAAGAAAAGAAAATCA
1 GAAAAAAGAAAAGAAAATCA
28020483 GAAAAA
1 GAAAAA
28020489 TAGTCATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.78, C:0.04, G:0.11, T:0.07
Consensus pattern (20 bp):
GAAAAAAGAAAAGAAAATCA
Found at i:28021160 original size:206 final size:207
Alignment explanation
Indices: 28020806--28021220 Score: 823
Period size: 206 Copynumber: 2.0 Consensus size: 207
28020796 GACAAGTATC
28020806 TTATAAGAGTATAGTAAAATGTTAAAAAATATTTTTTTAAAAGTGGCAAATGACAATTTTCTAAA
1 TTATAAGAGTATAGTAAAATGTTAAAAAATATTTTTTTAAAAGTGGCAAATGACAATTTTCTAAA
28020871 ATTTCTTGTGGAATAAAAAAAAAGTATATTGTCATTGTATTAAATACTAACCCTATATATATTTA
66 ATTTCTTGTGGAATAAAAAAAAAGTATATTGTCATTGTATTAAATACTAACCCTATATATATTTA
28020936 AAAAAGGAAAGTATATTTTTAAAATTTCTAAAATTTTCTATATTTTCTAATTTTTTTTAAAAGTG
131 AAAAAGGAAAGTATATTTTTAAAATTTCTAAAATTTTCTATATTTTCTAATTTTTTTTAAAAGTG
28021001 A-ATTTTTTCTA
196 ACATTTTTTCTA
28021012 TTATAAGAGTATAGTAAAATGTTAAAAAATATTTTTTTAAAAGTGGCAAATGACAATTTTCTAAA
1 TTATAAGAGTATAGTAAAATGTTAAAAAATATTTTTTTAAAAGTGGCAAATGACAATTTTCTAAA
28021077 ATTTCTTGTGGAATAAAAAAAAAGTATATTGTCATTGTATTAAATACTAACCCTATATATATTTA
66 ATTTCTTGTGGAATAAAAAAAAAGTATATTGTCATTGTATTAAATACTAACCCTATATATATTTA
28021142 AAAAAGGAAAGTATATTTTTAAAATTTCTAAAATTTTCTATATTTTCTAATTTTTTTTAAAAGTG
131 AAAAAGGAAAGTATATTTTTAAAATTTCTAAAATTTTCTATATTTTCTAATTTTTTTTAAAAGTG
28021207 ACATTTTTTCTA
196 ACATTTTTTCTA
28021219 TT
1 TT
28021221 TTTGGATATT
Statistics
Matches: 208, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
206 196 0.94
207 12 0.06
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (207 bp):
TTATAAGAGTATAGTAAAATGTTAAAAAATATTTTTTTAAAAGTGGCAAATGACAATTTTCTAAA
ATTTCTTGTGGAATAAAAAAAAAGTATATTGTCATTGTATTAAATACTAACCCTATATATATTTA
AAAAAGGAAAGTATATTTTTAAAATTTCTAAAATTTTCTATATTTTCTAATTTTTTTTAAAAGTG
ACATTTTTTCTA
Found at i:28029307 original size:26 final size:26
Alignment explanation
Indices: 28029271--28029329 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
28029261 CTGTCATCAG
28029271 ACCATCGTCGTCACTACCGTAGCACT
1 ACCATCGTCGTCACTACCGTAGCACT
*
28029297 ACCATCGTCGTCGCTACCGTAGCACT
1 ACCATCGTCGTCACTACCGTAGCACT
28029323 ACCATCG
1 ACCATCG
28029330 ATGATTGTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.22, C:0.39, G:0.17, T:0.22
Consensus pattern (26 bp):
ACCATCGTCGTCACTACCGTAGCACT
Found at i:28030297 original size:19 final size:19
Alignment explanation
Indices: 28030273--28030309 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28030263 CTTACATGCC
*
28030273 AAAGTGAAAAATTGATTTG
1 AAAGTGAAAAAGTGATTTG
28030292 AAAGTGAAAAAGTGATTT
1 AAAGTGAAAAAGTGATTT
28030310 TTATGGCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.30
Consensus pattern (19 bp):
AAAGTGAAAAAGTGATTTG
Found at i:28031457 original size:15 final size:15
Alignment explanation
Indices: 28031437--28031469 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28031427 TATTTATACT
*
28031437 TGAAACTTTAGATTA
1 TGAAACCTTAGATTA
28031452 TGAAACCTTAGATTA
1 TGAAACCTTAGATTA
28031467 TGA
1 TGA
28031470 GATGATATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (15 bp):
TGAAACCTTAGATTA
Found at i:28035524 original size:28 final size:28
Alignment explanation
Indices: 28035462--28035517 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
28035452 GTTTGAAATG
28035462 GTGAAATAGAGGTATAAGAAGATGAAAA
1 GTGAAATAGAGGTATAAGAAGATGAAAA
28035490 GTGAAATAGAGGTATAAGAAGATGAAAA
1 GTGAAATAGAGGTATAAGAAGATGAAAA
28035518 AGGAAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.18
Consensus pattern (28 bp):
GTGAAATAGAGGTATAAGAAGATGAAAA
Found at i:28036289 original size:29 final size:30
Alignment explanation
Indices: 28036257--28036333 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
28036247 TTTATGGTCC
**
28036257 AAGTGTAAATATTTAAAATGT-AAGGGTTA
1 AAGTGTAAATATTTAAAATGTAAAGGGCCA
* ** *
28036286 AAGTATAAATATGAAAAATTTAAAGGGCCA
1 AAGTGTAAATATTTAAAATGTAAAGGGCCA
28036316 ATAGTGTAAATATCTTAA
1 A-AGTGTAAATAT-TTAA
28036334 GGATGGAAGG
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
29 17 0.47
30 7 0.19
31 10 0.28
32 2 0.06
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (30 bp):
AAGTGTAAATATTTAAAATGTAAAGGGCCA
Found at i:28039851 original size:42 final size:43
Alignment explanation
Indices: 28039805--28039890 Score: 102
Period size: 46 Copynumber: 2.0 Consensus size: 43
28039795 AGCTTATGTA
*
28039805 GTTCAACC-CAAATGACGATGCTCCTAAGCACGAGTTTAAATT
1 GTTCAACCACAAATGACGATGCTCCTAAGCACGAGCTTAAATT
* * *
28039847 GTTCATCCAAAATAAATGATGATGCTCCTAAGCACGAGCTTAAA
1 GTTCAACC---ACAAATGACGATGCTCCTAAGCACGAGCTTAAA
28039891 CTATTCACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 7 0.19
46 29 0.81
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (43 bp):
GTTCAACCACAAATGACGATGCTCCTAAGCACGAGCTTAAATT
Found at i:28045635 original size:41 final size:42
Alignment explanation
Indices: 28045571--28045652 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 42
28045561 GGTCTATAGC
* *
28045571 GGCGCTTTTCCCACAAACGCCGCTAAAGAA-TAAACCTTTAAT
1 GGCGCTTCTCCCAAAAACGCCGCTAAA-AACTAAACCTTTAAT
*
28045613 GGCGCTTCT-CCAAAAACGCCGCTAAAAACTTAACCTTTAA
1 GGCGCTTCTCCCAAAAACGCCGCTAAAAACTAAACCTTTAA
28045653 AAAAATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 2 0.06
41 26 0.72
42 8 0.22
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.23
Consensus pattern (42 bp):
GGCGCTTCTCCCAAAAACGCCGCTAAAAACTAAACCTTTAAT
Found at i:28051751 original size:17 final size:17
Alignment explanation
Indices: 28051729--28051762 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28051719 TAAAAGAACA
28051729 TTCTACATACCAGTCAG
1 TTCTACATACCAGTCAG
28051746 TTCTACATACCAGTCAG
1 TTCTACATACCAGTCAG
28051763 CAAAATCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (17 bp):
TTCTACATACCAGTCAG
Found at i:28053074 original size:24 final size:24
Alignment explanation
Indices: 28053042--28053091 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
28053032 GTGGATACAC
28053042 TGGCATTGGGATAAACAACATTTT
1 TGGCATTGGGATAAACAACATTTT
28053066 TGGCATTGGGATAAACAACATTTT
1 TGGCATTGGGATAAACAACATTTT
28053090 TG
1 TG
28053092 AACAGTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (24 bp):
TGGCATTGGGATAAACAACATTTT
Found at i:28053603 original size:7 final size:7
Alignment explanation
Indices: 28053584--28053629 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
28053574 AGGAACGAGA
28053584 GAAA-GG
1 GAAAGGG
*
28053590 GATAGGG
1 GAAAGGG
28053597 GAAAGGG
1 GAAAGGG
28053604 GAAAGGG
1 GAAAGGG
*
28053611 CAAAGGG
1 GAAAGGG
*
28053618 CAAAGGG
1 GAAAGGG
28053625 GAAAG
1 GAAAG
28053630 CGTAATAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
6 3 0.09
7 32 0.91
ACGTcount: A:0.43, C:0.04, G:0.50, T:0.02
Consensus pattern (7 bp):
GAAAGGG
Found at i:28053617 original size:21 final size:20
Alignment explanation
Indices: 28053584--28053629 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
28053574 AGGAACGAGA
* *
28053584 GAAAGGGATAGGGGAAAGGG
1 GAAAGGGAAAGGGCAAAGGG
28053604 GAAAGGGCAAAGGGCAAAGGG
1 GAAAGGG-AAAGGGCAAAGGG
28053625 GAAAG
1 GAAAG
28053630 CGTAATAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.43, C:0.04, G:0.50, T:0.02
Consensus pattern (20 bp):
GAAAGGGAAAGGGCAAAGGG
Found at i:28054400 original size:7 final size:7
Alignment explanation
Indices: 28054390--28054421 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
28054380 CTCTTAATCT
28054390 CTAACCC
1 CTAACCC
28054397 CTAACCC
1 CTAACCC
28054404 CTAACCC
1 CTAACCC
*
28054411 TTAACCC
1 CTAACCC
28054418 CTAA
1 CTAA
28054422 ATCCCCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.31, C:0.50, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAACCC
Found at i:28054418 original size:134 final size:134
Alignment explanation
Indices: 28054178--28054421 Score: 323
Period size: 134 Copynumber: 1.8 Consensus size: 134
28054168 NNNNNNNNNN
* * * * * *
28054178 AAAAATACTAATTAATCTAAACCTTAAACCCTAACCCGACCCTGAATCTCTAAACCTTAAGTCAC
1 AAAAACACTAATTAATCTAAACCCTAAACCCTAACCCGAACCTGAATCTATAAACCCTAAATCAC
* *
28054243 TCACTCTTAACCTCTAACCTCTAACCCTAAACCCTAAACCCCTAACTACTAACATTTAATATATA
66 TAACTCTTAACCTCTAACCCCTAACCCTAAACCCTAAACCCCTAACTACTAACATTTAATATATA
28054308 AATT
131 AATT
* **
28054312 AAAAACACTAATTAATCTAAACCCTAAACTCTAACTTGATACC-GAATCTATAAACCCTAAATC-
1 AAAAACACTAATTAATCTAAACCCTAAACCCTAACCCGA-ACCTGAATCTATAAACCCTAAATCA
* *
28054375 CTTAACTCTTAATCTCTAACCCCTAACCCCT-AACCCTTAACCCCTAA
65 C-TAACTCTTAACCTCTAACCCCTAA-CCCTAAACCCTAAACCCCTAA
28054422 ATCCCCTTAA
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
133 1 0.01
134 87 0.93
135 6 0.06
ACGTcount: A:0.39, C:0.32, G:0.02, T:0.27
Consensus pattern (134 bp):
AAAAACACTAATTAATCTAAACCCTAAACCCTAACCCGAACCTGAATCTATAAACCCTAAATCAC
TAACTCTTAACCTCTAACCCCTAACCCTAAACCCTAAACCCCTAACTACTAACATTTAATATATA
AATT
Found at i:28054460 original size:14 final size:15
Alignment explanation
Indices: 28054441--28054473 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
28054431 AACCAACCAG
28054441 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
28054455 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
28054470 AATC
1 AATC
28054474 TTTAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:28062469 original size:35 final size:36
Alignment explanation
Indices: 28062394--28062475 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 36
28062384 TCAATGAGAT
*
28062394 TGAAGTTTAT-TAATTTGAATACATTTGATTCTGAA
1 TGAAGTTTATATAATTTGAATACATTTGATTCTCAA
* * *
28062429 GGAAGTTTATAT-GTTTGAATAGATTTGATT-TCCAA
1 TGAAGTTTATATAATTTGAATACATTTGATTCT-CAA
28062464 TGAAGTTTATAT
1 TGAAGTTTATAT
28062476 CGATAAGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 1 0.03
35 38 0.95
36 1 0.03
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (36 bp):
TGAAGTTTATATAATTTGAATACATTTGATTCTCAA
Found at i:28064379 original size:10 final size:10
Alignment explanation
Indices: 28064366--28064399 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
28064356 GAAAAACTGC
28064366 AAAGAAAACT
1 AAAGAAAACT
28064376 AAAGAAAACCT
1 AAAGAAAA-CT
*
28064387 AGAGAAAACT
1 AAAGAAAACT
28064397 AAA
1 AAA
28064400 CCTAAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.68, C:0.12, G:0.12, T:0.09
Consensus pattern (10 bp):
AAAGAAAACT
Found at i:28064673 original size:20 final size:20
Alignment explanation
Indices: 28064648--28064702 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
28064638 CTTGGGAGAT
28064648 GGATATCGCGATACCCAAGG
1 GGATATCGCGATACCCAAGG
28064668 GGATATCGCGATACCCAAGG
1 GGATATCGCGATACCCAAGG
*
28064688 GGATATCGCAATACC
1 GGATATCGCGATACC
28064703 AATGAAGAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.16
Consensus pattern (20 bp):
GGATATCGCGATACCCAAGG
Found at i:28071613 original size:13 final size:13
Alignment explanation
Indices: 28071595--28071620 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28071585 CCCCTTTTTA
28071595 GTTACAAACCATT
1 GTTACAAACCATT
28071608 GTTACAAACCATT
1 GTTACAAACCATT
28071621 CTTCTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
GTTACAAACCATT
Found at i:28078911 original size:16 final size:16
Alignment explanation
Indices: 28078890--28078943 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
28078880 TTTGGTTCGC
28078890 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
28078906 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGG
*
28078922 TGTAATGAAATAGAGG
1 TGTAATGGAATAGAGG
*
28078938 CGTAAT
1 TGTAAT
28078944 AGTAATGCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.39, C:0.04, G:0.31, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:28078973 original size:45 final size:44
Alignment explanation
Indices: 28078922--28079018 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 44
28078912 GGAATAGAGC
28078922 TGTAATGAAATAGAGGCGTAATAGTAATGCAAT-TGTTTGGTTGAA
1 TGTAATGAAATAGAGGCGTAATAGT-ATGC-ATGTGTTTGGTTGAA
* * * *
28078967 TGTAATGGAATAGATGCGTAATAGTATTCTTGTGTTTGGTTGAA
1 TGTAATGAAATAGAGGCGTAATAGTATGCATGTGTTTGGTTGAA
*
28079011 TGAAATGA
1 TGTAATGA
28079019 TGTTGTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.47
45 23 0.51
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (44 bp):
TGTAATGAAATAGAGGCGTAATAGTATGCATGTGTTTGGTTGAA
Found at i:28082618 original size:17 final size:18
Alignment explanation
Indices: 28082578--28082625 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
28082568 TCCAGATTTG
*
28082578 AGCACAAGCAAAAGCAAA
1 AGCAAAAGCAAAAGCAAA
28082596 AGCAAAAGCAAAA-CAAA
1 AGCAAAAGCAAAAGCAAA
* *
28082613 ATCAAAATCAAAA
1 AGCAAAAGCAAAA
28082626 TTGATTTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.67, C:0.19, G:0.10, T:0.04
Consensus pattern (18 bp):
AGCAAAAGCAAAAGCAAA
Found at i:28082626 original size:6 final size:6
Alignment explanation
Indices: 28082578--28082625 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
28082568 TCCAGATTTG
* * *
28082578 AGCACA AGCAAA AGCAAA AGCAAA AGCAAA A-CAAA ATCAAA ATCAAA
1 AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA
28082625 A
1 A
28082626 TTGATTTTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
5 5 0.12
6 35 0.88
ACGTcount: A:0.67, C:0.19, G:0.10, T:0.04
Consensus pattern (6 bp):
AGCAAA
Found at i:28089655 original size:16 final size:16
Alignment explanation
Indices: 28089606--28089647 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
28089596 AAAATAAACC
28089606 TAAAACCTAAGAAGAAA
1 TAAAA-CTAAGAAGAAA
28089623 TAAAACTAAGAAGAAA
1 TAAAACTAAGAAGAAA
28089639 TAAAACTAA
1 TAAAACTAA
28089648 ACTGAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.14
Consensus pattern (16 bp):
TAAAACTAAGAAGAAA
Found at i:28090198 original size:30 final size:30
Alignment explanation
Indices: 28090156--28090228 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
28090146 TTAATTAAAT
* *
28090156 AATATATTTGCTTTCAAGCTCCTAAATATTT
1 AATATAATTGCTTTCAAGCTCCTAAA-ATTA
28090187 AAT-TAATTGCTTTCAAGCTCCTAAAATTA
1 AATATAATTGCTTTCAAGCTCCTAAAATTA
*
28090216 AATATATTTGCTT
1 AATATAATTGCTT
28090229 AAAGATTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.16
30 29 0.76
31 3 0.08
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (30 bp):
AATATAATTGCTTTCAAGCTCCTAAAATTA
Found at i:28090308 original size:16 final size:17
Alignment explanation
Indices: 28090281--28090315 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
28090271 TAGACTTGGG
*
28090281 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
28090298 TTGAG-AAATTAATTAA
1 TTGAGAAAATTAATTAA
28090314 TT
1 TT
28090316 TAAATTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:28093552 original size:50 final size:50
Alignment explanation
Indices: 28093431--28093821 Score: 494
Period size: 50 Copynumber: 7.8 Consensus size: 50
28093421 TAATAACATC
* ** *
28093431 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTG
* * * * ** *
28093482 CCCATGCCAAGTCCTAGACATGGTCTTACGGGGGACCTTTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
28093532 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* ** *
28093582 CCAACGCCATGTCCCAGACATGGTCTTTCATGGGAATTCTCATTTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * * ** *
28093632 CCAACGCCATGTCCTAGACTTTGTCTTACATAAGACATCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * * * * *
28093682 CCAATGTCATGTCCTAAACATGATCTTACATAGGACCTCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * *
28093732 CCAACGCCATGTCCCAGACTTGGTCTTTCATGGGACCTCTCAACTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
*
28093782 CCAACGCCATGTCTCAGACATGGTCTTACATGGGACCTCT
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
28093822 TTACCCAAAT
Statistics
Matches: 290, Mismatches: 50, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
50 261 0.90
51 29 0.10
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
Found at i:28097204 original size:318 final size:318
Alignment explanation
Indices: 28096627--28097263 Score: 1040
Period size: 318 Copynumber: 2.0 Consensus size: 318
28096617 TACTCGGATG
*
28096627 ATAATCAATAACCAATTCATAATCTTTTATCAATTCTAGCCATCTGCGTTGTCTCAAATTCAAAT
1 ATAATCAATAACCAATTCATAATCTTTTATCAATTCTAGCCATCTACGTTGTCTCAAATTCAAAT
28096692 CTTTCTGTGTCATCAAATACTTCAAGATTTTATGATCAGTATAAATATGACACTTTTCAACATAA
66 CTTTCTGTGTCATCAAATACTTCAAGATTTTATGATCAGTATAAATATGACACTTTTCAACATAA
* * * * * *
28096757 AAATGATGCCTCCATATTTTCAATGCAAATACAGTAGCAACTAATTTAAGATCATGTACCGGGCA
131 AAATAATGCCGCCATATTTTCAATGCAAACACAATAGCAACTAATTCAAGATCATGTACCGCGCA
*
28096822 GTTTCTTTCATGTGGCTTAAGTTGTCTTGAAGCATAGCCTATTACTTTATCTTCTTGCATCAAGA
196 GCTTCTTTCATGTGGCTTAAGTTGTCTTGAAGCATAGCCTATTACTTTATCTTCTTGCATCAAGA
* *
28096887 CACAACCCAAACCATTTAATGATGCATTACTATAAATAATAAATTCCTTACCAGATTC
261 CACAACCCAAACCATTTAATAATGCATCACTATAAATAATAAATTCCTTACCAGATTC
* *
28096945 ATAATCAATAACGAATTCATAATCTTTTATGAATTCTAGCCATCTACGTTGTCTCAAATTCAAAT
1 ATAATCAATAACCAATTCATAATCTTTTATCAATTCTAGCCATCTACGTTGTCTCAAATTCAAAT
* * *
28097010 CTTTCTGTGTCATCAAATACTTCAAGCTTTTATGATCAGTATAAATATGACACTTTTCACCATAC
66 CTTTCTGTGTCATCAAATACTTCAAGATTTTATGATCAGTATAAATATGACACTTTTCAACATAA
* * * *
28097075 AAATAATGCCGCCATATTTTCAATGCAAACATAATAGCAGCTAATTCAAGATCATGTACTGCGTA
131 AAATAATGCCGCCATATTTTCAATGCAAACACAATAGCAACTAATTCAAGATCATGTACCGCGCA
* * *
28097140 GCTTCTTTCATGTTGCTTAAGTTGTCTTGAAGCATAGCCTATTACTTTGTCTTCTTGTATCAAGA
196 GCTTCTTTCATGTGGCTTAAGTTGTCTTGAAGCATAGCCTATTACTTTATCTTCTTGCATCAAGA
* * * *
28097205 CACAACCCAAACCATTTAATAATGCATCAGTATAAATAATAATTTTCTTACCCGATTC
261 CACAACCCAAACCATTTAATAATGCATCACTATAAATAATAAATTCCTTACCAGATTC
28097263 A
1 A
28097264 GGCTGTACCA
Statistics
Matches: 293, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
318 293 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (318 bp):
ATAATCAATAACCAATTCATAATCTTTTATCAATTCTAGCCATCTACGTTGTCTCAAATTCAAAT
CTTTCTGTGTCATCAAATACTTCAAGATTTTATGATCAGTATAAATATGACACTTTTCAACATAA
AAATAATGCCGCCATATTTTCAATGCAAACACAATAGCAACTAATTCAAGATCATGTACCGCGCA
GCTTCTTTCATGTGGCTTAAGTTGTCTTGAAGCATAGCCTATTACTTTATCTTCTTGCATCAAGA
CACAACCCAAACCATTTAATAATGCATCACTATAAATAATAAATTCCTTACCAGATTC
Found at i:28101424 original size:50 final size:50
Alignment explanation
Indices: 28101317--28101500 Score: 197
Period size: 50 Copynumber: 3.7 Consensus size: 50
28101307 ATGCCAAAGC
** * * * * *
28101317 CATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGT
1 CATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGATACCAACGT
* * ** *
28101368 CATGTCCTAGACATGGTCTAACGGGGGACCTCTCATCTTGATACCAACGT
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATACCAACGT
* * * * *
28101418 CATGTCCCAGACTTGGTCTTTCATGGGACCTCTCATCTCGGTGCCAACGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATACCAACGT
*
28101468 CATGCCCCAGACATGGTCTTACATGGGACCTCT
1 CATGTCCCAGACATGGTCTTACATGGGACCTCT
28101501 TTACCCAAAT
Statistics
Matches: 108, Mismatches: 25, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
50 84 0.78
51 24 0.22
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATACCAACGT
Found at i:28101496 original size:100 final size:101
Alignment explanation
Indices: 28101317--28101500 Score: 244
Period size: 100 Copynumber: 1.8 Consensus size: 101
28101307 ATGCCAAAGC
** * * * * *
28101317 CATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGTCATGTCCTAGACAT
1 CATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAACGCCATGCCCCAGACAT
*
28101382 GGTCTAACGGGGGACCTCTCATCTTGATACCAACGT
66 GGTCTAACAGGGGACCTCTCATCTTGATACCAACGT
* * *
28101418 CATGTCCCAGACTTGGTCTTTCATGGGA-CCTCTCATCTCGGTGCCAACGCCATGCCCCAGACAT
1 CATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAACGCCATGCCCCAGACAT
* *
28101482 GGTCTTACATGGGACCTCT
66 GGTCTAACAGGGGACCTCT
28101501 TTACCCAAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
100 44 0.63
101 26 0.37
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (101 bp):
CATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAACGCCATGCCCCAGACAT
GGTCTAACAGGGGACCTCTCATCTTGATACCAACGT
Found at i:28106027 original size:48 final size:48
Alignment explanation
Indices: 28105939--28106134 Score: 196
Period size: 48 Copynumber: 4.1 Consensus size: 48
28105929 TAGATTTCTC
* * * * * * *
28105939 GGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAATAACAG-ATACTC
1 GGTGGTCTGCACACAGTCCGTGCCACCCTTATATCATAACAGAATA-TT
* * * * * **
28105987 AGTGGTCTACACATAGTCTGTGCCACCCTTATATCTTAACAGTTTATT
1 GGTGGTCTGCACACAGTCCGTGCCACCCTTATATCATAACAGAATATT
* * *
28106035 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAATAGAATATT
1 GGTGGTCTGCACACAGTCCGTGCCACCCTTATATCATAACAGAATATT
* * *
28106083 GGTGGTCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGAATATC
1 GGTGGTCTGCACACAGTCCGTGCCACCCTTATATCATAACAGAATATT
28106131 GGTG
1 GGTG
28106135 CGCATAGTAG
Statistics
Matches: 120, Mismatches: 27, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
48 118 0.98
49 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.29
Consensus pattern (48 bp):
GGTGGTCTGCACACAGTCCGTGCCACCCTTATATCATAACAGAATATT
Found at i:28106106 original size:96 final size:96
Alignment explanation
Indices: 28105939--28106112 Score: 242
Period size: 96 Copynumber: 1.8 Consensus size: 96
28105929 TAGATTTCTC
* * *
28105939 GGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAATAACAGATACTCAGTGGTCTACACATAGT
1 GGTGGCCTGCACACAGTCCGTACCACCCTTGTATAATAACAGATACTCAGTGGTCTACACACAGT
*
28106004 CTGTGCCACCCTTATATCTTAACAGTTTATT
66 CCGTGCCACCCTTATATCTTAACAGTTTATT
* * * ** *
28106035 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAATAGAATA-TTGGTGGTCTGCACACAG
1 GGTGGCCTGCACACAGTCCGTACCACCCTTGTATAATAACAG-ATACTCAGTGGTCTACACACAG
28106099 TCCGTGCCACCCTT
65 TCCGTGCCACCCTT
28106113 GTGTCATAAC
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
96 64 0.96
97 3 0.04
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (96 bp):
GGTGGCCTGCACACAGTCCGTACCACCCTTGTATAATAACAGATACTCAGTGGTCTACACACAGT
CCGTGCCACCCTTATATCTTAACAGTTTATT
Found at i:28109051 original size:48 final size:48
Alignment explanation
Indices: 28108992--28109189 Score: 202
Period size: 48 Copynumber: 4.1 Consensus size: 48
28108982 AATAGATTTC
* * *
28108992 TCGGTGGCCTGCACACAGTCCGTAG-CACCTTTGTGTAATAACAGATTC
1 TCGGTGGCCTGCACACAGTCCGT-GCCACCCTTGTATAATAACAGATTA
* * * * * *
28109040 TCGGTGGCCTGCACATACTCTGTGCCACCATTGTATATTAACAGTTTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATAATAACAGATTA
* * *
28109088 TTGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACAGAATA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATAATAACAGATTA
* * * * * *
28109136 GT-GGTGGCTTACACACAGTCCATGCCACCCTTGTGTCATAACAGAATA
1 -TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATAATAACAGATTA
28109184 TCGGTG
1 TCGGTG
28109190 CGCATAGTAG
Statistics
Matches: 126, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
47 2 0.02
48 123 0.98
49 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.28
Consensus pattern (48 bp):
TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATAATAACAGATTA
Found at i:28110460 original size:21 final size:21
Alignment explanation
Indices: 28110408--28110461 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
28110398 ACAACGTATA
*
28110408 TGCAATTCAGGGGTACTAATG
1 TGCAATTCAGGGGCACTAATG
* *
28110429 TACAAAT-AGGGGCAC-ATATG
1 TGCAATTCAGGGGCACTA-ATG
28110449 TGCAATTCAGGGG
1 TGCAATTCAGGGG
28110462 TAACGAAGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 15 0.58
21 10 0.38
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (21 bp):
TGCAATTCAGGGGCACTAATG
Found at i:28110460 original size:41 final size:41
Alignment explanation
Indices: 28110408--28110580 Score: 197
Period size: 41 Copynumber: 4.2 Consensus size: 41
28110398 ACAACGTATA
* *
28110408 TGCAATTCAGGGGTACTAATGTACAAATAGGGGCACATATG
1 TGCAATTCAGGGGTACTAAAGTACAAACAGGGGCACATATG
* ** *
28110449 TGCAATTCAGGGGTAAC-GAAGTACAAACAGGGGCATGTGTG
1 TGCAATTCAGGGGT-ACTAAAGTACAAACAGGGGCACATATG
* * *
28110490 TGCAATTTAGGGGTA-TCAAAGTACAAACAGGGGCACGTAAG
1 TGCAATTCAGGGGTACT-AAAGTACAAACAGGGGCACATATG
* * * *
28110531 TGCAATTCAGTGGTACCAAAGTACAAATAGGGGCACATTTG
1 TGCAATTCAGGGGTACTAAAGTACAAACAGGGGCACATATG
28110572 TGCAATTCA
1 TGCAATTCA
28110581 ACAATATTCT
Statistics
Matches: 110, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
40 1 0.01
41 107 0.97
42 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.23
Consensus pattern (41 bp):
TGCAATTCAGGGGTACTAAAGTACAAACAGGGGCACATATG
Found at i:28110553 original size:82 final size:82
Alignment explanation
Indices: 28110408--28110580 Score: 222
Period size: 82 Copynumber: 2.1 Consensus size: 82
28110398 ACAACGTATA
* * * *
28110408 TGCAATTCAGGGGTACTAATGTACAAATAGGGGCACATATGTGCAATTCAGGGGTAACGAAGTAC
1 TGCAATTCAGGGGTACTAAAGTACAAACAGGGGCACATAAGTGCAATTCAGGGGTAACAAAGTAC
28110473 AAACAGGGGCATGTGTG
66 AAACAGGGGCATGTGTG
* * * *
28110490 TGCAATTTAGGGGTA-TCAAAGTACAAACAGGGGCACGTAAGTGCAATTCAGTGGTACCAAAGTA
1 TGCAATTCAGGGGTACT-AAAGTACAAACAGGGGCACATAAGTGCAATTCAGGGGTAACAAAGTA
* ** *
28110554 CAAATAGGGGCACATTTG
65 CAAACAGGGGCATGTGTG
28110572 TGCAATTCA
1 TGCAATTCA
28110581 ACAATATTCT
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 1 0.01
82 76 0.99
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.23
Consensus pattern (82 bp):
TGCAATTCAGGGGTACTAAAGTACAAACAGGGGCACATAAGTGCAATTCAGGGGTAACAAAGTAC
AAACAGGGGCATGTGTG
Found at i:28119148 original size:42 final size:43
Alignment explanation
Indices: 28119011--28119160 Score: 155
Period size: 42 Copynumber: 3.6 Consensus size: 43
28119001 AACCGTAACT
* * *
28119011 CGGTGGAATCAGCACTTAGCAACCACC-TTATATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTACAATCAATGATA
* * * * *
28119053 CGG-GGAATCAACACATAACAACCA-CTTTCACAATTAAGGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTT-ACAATCAATGATA
* * * *
28119095 CGGTGGAATCAGCACTTAGCAACCACCTTTAGAAGCAATAATT
1 CGGTGGAATCAGCACTTAGCAACCACCTTTACAATCAATGATA
28119138 CGG-GGAATCAGCACTTAGCAACC
1 CGGTGGAATCAGCACTTAGCAACC
28119161 CCTCGAGGAA
Statistics
Matches: 87, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
40 1 0.01
41 20 0.23
42 34 0.39
43 28 0.32
44 4 0.05
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (43 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTACAATCAATGATA
Found at i:28119224 original size:41 final size:41
Alignment explanation
Indices: 28119167--28119354 Score: 277
Period size: 41 Copynumber: 4.6 Consensus size: 41
28119157 AACCCCTCGA
* *
28119167 GGAATTTGCACTTAGCAACCCCTTTTTGATCAGAGTTTCAG
1 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTCAG
*
28119208 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGTTTCAG
1 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTCAG
* * * * *
28119249 TGAATCTGTACTTGGCAACCCCTTTTTGATCAGTGATTCGG
1 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTCAG
* *
28119290 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGTGATTCGG
1 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTCAG
*
28119331 GGAATCTGCACTAAGCAACCCCTT
1 GGAATCTGCACTTAGCAACCCCTT
28119355 ACATTCAATG
Statistics
Matches: 136, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 136 1.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.32
Consensus pattern (41 bp):
GGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGATTCAG
Found at i:28126848 original size:41 final size:41
Alignment explanation
Indices: 28126803--28126994 Score: 226
Period size: 41 Copynumber: 4.7 Consensus size: 41
28126793 TAACAACCCC
*
28126803 TCGGGGAATCTGCACTTAGCAACCTCTTTTTGATAAGAGTT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATAAGAGTT
* *
28126844 TCGGGGAATCTGCACTTACCAACCCCTTTTTGATCAGAGTT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATAAGAGTT
*** * * * *
28126885 TCAAAGAATCTGCACTTGGCAACCTCTTTTTGATTAGTGATT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATAAGAG-TT
* *
28126927 T-GGGGAATCTGCACTTAGCAACCCCTTTTTGA-ACAGTGAT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATA-AGAGTT
* *
28126967 TCAGGGAATCTGCACTAAGCAACCCCTT
1 TCGGGGAATCTGCACTTAGCAACCCCTT
28126995 ACATTTAATG
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
40 2 0.02
41 123 0.96
42 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (41 bp):
TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATAAGAGTT
Found at i:28126949 original size:82 final size:82
Alignment explanation
Indices: 28126808--28126990 Score: 260
Period size: 82 Copynumber: 2.2 Consensus size: 82
28126798 ACCCCTCGGG
28126808 GAATCTGCACTTAGCAACCTCTTTTTGATAAGAGTTTCGGGGAATCTGCACTTACCAACCCCTTT
1 GAATCTGCACTTAGCAACCTCTTTTTGATAAGAGTTTCGGGGAATCTGCACTTACCAACCCCTTT
* *
28126873 TTGATCAGAGTTTCAAA
66 TTGAACAGAGATTCAAA
* * * *
28126890 GAATCTGCACTTGGCAACCTCTTTTTGATTAGTGATTT-GGGGAATCTGCACTTAGCAACCCCTT
1 GAATCTGCACTTAGCAACCTCTTTTTGATAAGAG-TTTCGGGGAATCTGCACTTACCAACCCCTT
* **
28126954 TTTGAACAGTGATTCAGG
65 TTTGAACAGAGATTCAAA
*
28126972 GAATCTGCACTAAGCAACC
1 GAATCTGCACTTAGCAACC
28126991 CCTTACATTT
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
82 86 0.97
83 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (82 bp):
GAATCTGCACTTAGCAACCTCTTTTTGATAAGAGTTTCGGGGAATCTGCACTTACCAACCCCTTT
TTGAACAGAGATTCAAA
Found at i:28133913 original size:27 final size:27
Alignment explanation
Indices: 28133875--28133930 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
28133865 CGAGATCCCC
*
28133875 GATACCTGTATTTATTTCTCCAGACTA
1 GATACATGTATTTATTTCTCCAGACTA
28133902 GATACATGTATTTATTTCTCCAGACTA
1 GATACATGTATTTATTTCTCCAGACTA
28133929 GA
1 GA
28133931 GATACTCAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (27 bp):
GATACATGTATTTATTTCTCCAGACTA
Found at i:28148514 original size:20 final size:19
Alignment explanation
Indices: 28148486--28148544 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
28148476 ATAGTATTTT
28148486 ATTAACTTAATATTAAAGTA
1 ATTAACTTAATATTAAA-TA
*
28148506 ATTATCTTAATATTAAATTAA
1 ATTAACTTAATATTAAA-T-A
*
28148527 ATTAAATTAA-ATTAAATA
1 ATTAACTTAATATTAAATA
28148545 TTTATCTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 23 0.68
21 9 0.26
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTAACTTAATATTAAATA
Found at i:28148527 original size:5 final size:5
Alignment explanation
Indices: 28148512--28148543 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
28148502 AGTAATTATC
28148512 TTAATA TTAAA TTAAA TTAAA TTAAA TTAAA T
1 TTAA-A TTAAA TTAAA TTAAA TTAAA TTAAA T
28148544 ATTTATCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:28161814 original size:25 final size:26
Alignment explanation
Indices: 28161741--28161815 Score: 91
Period size: 26 Copynumber: 2.9 Consensus size: 26
28161731 TCTCATCTGT
*
28161741 ATTTTACCCCTA-TCAAAATTTTGACG
1 ATTTTATCCCTAGT-AAAATTTTGACG
* *
28161767 ATTTTATCCCTTGTAAAAATTTGACG
1 ATTTTATCCCTAGTAAAATTTTGACG
*
28161793 ATTTT-TTCCTAGTAAAATTTTGA
1 ATTTTATCCCTAGTAAAATTTTGA
28161816 AAAAATATGT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 15 0.36
26 26 0.62
27 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (26 bp):
ATTTTATCCCTAGTAAAATTTTGACG
Found at i:28161983 original size:18 final size:18
Alignment explanation
Indices: 28161960--28161996 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
28161950 TGCAAATGGA
*
28161960 TCATTTCCATTTTAATTT
1 TCATTTCCATTTCAATTT
28161978 TCATTTCCATTTCAATTT
1 TCATTTCCATTTCAATTT
28161996 T
1 T
28161997 TGGAAACCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (18 bp):
TCATTTCCATTTCAATTT
Found at i:28162788 original size:26 final size:26
Alignment explanation
Indices: 28162758--28162814 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
28162748 TCTCATCCTT
28162758 ATTTTAACCCTAACAAAATTTTAACG
1 ATTTTAACCCTAACAAAATTTTAACG
* *** *
28162784 ATTTTACCCCTTGTAAAATTTTGACG
1 ATTTTAACCCTAACAAAATTTTAACG
28162810 ATTTT
1 ATTTT
28162815 TCCCTGGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (26 bp):
ATTTTAACCCTAACAAAATTTTAACG
Found at i:28162825 original size:25 final size:26
Alignment explanation
Indices: 28162772--28162832 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 26
28162762 TAACCCTAAC
* *
28162772 AAAATTTTAACGATTTTACCCCTTGT
1 AAAATTTTGACGATTTTACCCCTGGT
*
28162798 AAAATTTTGACGATTTT-TCCCTGGT
1 AAAATTTTGACGATTTTACCCCTGGT
28162823 AAAATTTTGA
1 AAAATTTTGA
28162833 GAAAATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 16 0.50
26 16 0.50
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (26 bp):
AAAATTTTGACGATTTTACCCCTGGT
Found at i:28174320 original size:22 final size:22
Alignment explanation
Indices: 28174292--28174340 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
28174282 ACTGGTGTCG
*
28174292 TGACACCCTAGTGTTTATGTAA
1 TGACACCCTAGTGTCTATGTAA
* *
28174314 TGACACCCTATTGTCTATGTCA
1 TGACACCCTAGTGTCTATGTAA
28174336 TGACA
1 TGACA
28174341 TTGAAGGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (22 bp):
TGACACCCTAGTGTCTATGTAA
Found at i:28175077 original size:14 final size:14
Alignment explanation
Indices: 28175058--28175088 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
28175048 AAGATTGGAC
28175058 TATACAAGTGTGAA
1 TATACAAGTGTGAA
28175072 TATACAAGTGTGAA
1 TATACAAGTGTGAA
28175086 TAT
1 TAT
28175089 TTCATAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (14 bp):
TATACAAGTGTGAA
Found at i:28175536 original size:103 final size:104
Alignment explanation
Indices: 28175357--28175565 Score: 411
Period size: 103 Copynumber: 2.0 Consensus size: 104
28175347 AATTAAATTA
28175357 ATTATTGAATTAATTTAATTTGATCGTTAAATATGAATCACATATATGTACAAACTTGTACACAA
1 ATTATTGAATTAATTTAATTTGATCGTTAAATATGAATCACATATATGTACAAACTTGTACACAA
28175422 ATAGAGAACATAGATAAAATTAATATAT-AATTTGATTC
66 ATAGAGAACATAGATAAAATTAATATATGAATTTGATTC
28175460 ATTATTGAATTAATTTAATTTGATCGTTAAATATGAATCACATATATGTACAAACTTGTACACAA
1 ATTATTGAATTAATTTAATTTGATCGTTAAATATGAATCACATATATGTACAAACTTGTACACAA
28175525 ATAGAGAACATAGATAAAATTAATATATGAATTTGATTC
66 ATAGAGAACATAGATAAAATTAATATATGAATTTGATTC
28175564 AT
1 AT
28175566 ACAAAATATT
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
103 93 0.89
104 12 0.11
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (104 bp):
ATTATTGAATTAATTTAATTTGATCGTTAAATATGAATCACATATATGTACAAACTTGTACACAA
ATAGAGAACATAGATAAAATTAATATATGAATTTGATTC
Found at i:28176818 original size:51 final size:51
Alignment explanation
Indices: 28176742--28176886 Score: 290
Period size: 51 Copynumber: 2.8 Consensus size: 51
28176732 AAATGTTTCA
28176742 TTCAACTTCATAAGAGAAAGAATGTATGAGTAAGATTCCATATCATTTCCC
1 TTCAACTTCATAAGAGAAAGAATGTATGAGTAAGATTCCATATCATTTCCC
28176793 TTCAACTTCATAAGAGAAAGAATGTATGAGTAAGATTCCATATCATTTCCC
1 TTCAACTTCATAAGAGAAAGAATGTATGAGTAAGATTCCATATCATTTCCC
28176844 TTCAACTTCATAAGAGAAAGAATGTATGAGTAAGATTCCATAT
1 TTCAACTTCATAAGAGAAAGAATGTATGAGTAAGATTCCATAT
28176887 GCTTCGACTA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 94 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (51 bp):
TTCAACTTCATAAGAGAAAGAATGTATGAGTAAGATTCCATATCATTTCCC
Found at i:28179008 original size:119 final size:119
Alignment explanation
Indices: 28178794--28179033 Score: 453
Period size: 119 Copynumber: 2.0 Consensus size: 119
28178784 TCACTTGGCG
*
28178794 TTAGATATATGATTGATTGGTCTTAGTGTTAGTGGGATATTGTTAGAGTATGCCTAAAGATTAAT
1 TTAGATATATGATTGATTGGTCTTAGTGTTAGTGGGATATTGTTAGAGTATGCCTAAAGACTAAT
*
28178859 CATGAGATGATTGTAATCACATACTTGTTTTACCCTATTTGCTAATATAAGGCA
66 CATGAGATGATTGTAATCACATACTCGTTTTACCCTATTTGCTAATATAAGGCA
28178913 TTAGATATATGATTGATTGGTCTTAGTGTTAGTGGGATATTGTTAGAGTATGCCTAAAGACTAAT
1 TTAGATATATGATTGATTGGTCTTAGTGTTAGTGGGATATTGTTAGAGTATGCCTAAAGACTAAT
*
28178978 CATGAGATTATTGTAATCACATACTCGTTTTACCCTATTTGCTAATATAAGGCA
66 CATGAGATGATTGTAATCACATACTCGTTTTACCCTATTTGCTAATATAAGGCA
28179032 TT
1 TT
28179034 GTCATTTTTA
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 118 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.40
Consensus pattern (119 bp):
TTAGATATATGATTGATTGGTCTTAGTGTTAGTGGGATATTGTTAGAGTATGCCTAAAGACTAAT
CATGAGATGATTGTAATCACATACTCGTTTTACCCTATTTGCTAATATAAGGCA
Found at i:28181342 original size:59 final size:59
Alignment explanation
Indices: 28181256--28181403 Score: 154
Period size: 59 Copynumber: 2.5 Consensus size: 59
28181246 AAACTATAAT
* * ** **
28181256 ATTCTAAAAATCTTGTAACCAGGGTAAAC-AGTTGTGATTGTAAATCAACGAATTGCAAG
1 ATTCTAAAAATATTGTAAGCAAAGTAAACGA-TTGTGATTGTAAATCAACGAACCGCAAG
* * * * ** **
28181315 ATTCTGAAAATCTTGTATGCGAAGTAAACGATTGTTTTTGTAAATCAGTGAACCGCAAG
1 ATTCTAAAAATATTGTAAGCAAAGTAAACGATTGTGATTGTAAATCAACGAACCGCAAG
28181374 ATTCTAAAAATATTGTAAGCAAAGTAAACG
1 ATTCTAAAAATATTGTAAGCAAAGTAAACG
28181404 TTTATGATCA
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 71 0.99
60 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (59 bp):
ATTCTAAAAATATTGTAAGCAAAGTAAACGATTGTGATTGTAAATCAACGAACCGCAAG
Found at i:28181418 original size:59 final size:59
Alignment explanation
Indices: 28181310--28181425 Score: 142
Period size: 59 Copynumber: 2.0 Consensus size: 59
28181300 TCAACGAATT
* * * * * ** **
28181310 GCAAGATTCTGAAAATCTTGTATGCGAAGTAAACGATTGTTTTTGTAAATCAGTGAACC
1 GCAAGATTCTAAAAATATTGTAAGCAAAGTAAACGATTATGATCATAAATCAGTGAACC
*
28181369 GCAAGATTCTAAAAATATTGTAAGCAAAGTAAACGTTTATGATCATAAATCAGTGAA
1 GCAAGATTCTAAAAATATTGTAAGCAAAGTAAACGATTATGATCATAAATCAGTGAA
28181426 ACTTAAGTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (59 bp):
GCAAGATTCTAAAAATATTGTAAGCAAAGTAAACGATTATGATCATAAATCAGTGAACC
Found at i:28186015 original size:28 final size:28
Alignment explanation
Indices: 28185977--28186033 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
28185967 CGTTTACCTT
28185977 AATTAAATAAAAAATGTTTAATTAATTA
1 AATTAAATAAAAAATGTTTAATTAATTA
* * * * *
28186005 AATTAATTAAACATTTTTTATTTAATTA
1 AATTAAATAAAAAATGTTTAATTAATTA
28186033 A
1 A
28186034 GGTAAACGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (28 bp):
AATTAAATAAAAAATGTTTAATTAATTA
Found at i:28187055 original size:114 final size:113
Alignment explanation
Indices: 28186844--28187343 Score: 285
Period size: 114 Copynumber: 4.4 Consensus size: 113
28186834 GGCGTTTGAC
28186844 AAGCGCCACAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGC
1 AAGCGCCACAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGC
* * *
28186909 GCAAAGCGAACACGCCACTAAGGCATACTATTAGCGGCACTTTGGGCT
66 GCAAAGCGAAAACGCCACTAACGCACACTATTAGCGGCACTTTGGGCT
** * * * * * * *
28186957 AAGCGCCGTAAAATTTCTTAACGAAAACGTAGCGTTTCTGTCTTGATGTATACTATAATTAGTGG
1 AAGCGCCACAAAATATCTTAACCAAAACGCAGAGTTT-GGTCTTGAGGTATACTAGAATTAGTGG
* * * * * ** ***
28187022 CGCATA-CTGGAAAACGCCGCTAACTC-CAGTATTAGTGGTGCTTT-TAAT
65 CGCAAAGC--GAAAACGCCACTAACGCACACTATTAGCGGCACTTTGGGCT
* * * * ** *
28187070 AAAACGCCGCAAAATATAC-TCACCAAAACGCAGAGTTTTGTCTTGAGGTATGTTAGTATTAGTG
1 -AAGCGCCACAAAATAT-CTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTG
* * * ** ** * * * * **
28187134 GCGCTTATGGGAGCATACCGCTAAAGAATACTATTAGCGG-AGCGTTCTTAG--
64 GCGC-AAAGCGAAAACGCCACTAACGCACACTATTAGCGGCA-C-TT-TGGGCT
* * * * * *
28187185 AAGCGCCGCAAAATATATTAACCAAAACGCAGCGTTTAGGTCTTGATGTATAGTGGAATTAGTGG
1 AAGCGCCACAAAATATCTTAACCAAAACGCAGAGTTT-GGTCTTGAGGTATACTAGAATTAGTGG
* * * * * * * * ** **
28187250 CGTCCAAGAGAAATCGCCTCTAAAGCATAGTATTAGCGGCGCTTTTTGAG
65 CG-CAAAGCGAAAACGCCACTAACGCACACTATTAGCGGCACTTTGGGCT
**
28187300 AAGCGCCGGAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTT
1 AAGCGCCACAAAATATCTTAACCAAAACGCAGAG-TTTGGTCTT
28187344 AACCATGCAT
Statistics
Matches: 291, Mismatches: 77, Indels: 36
0.72 0.19 0.09
Matches are distributed among these distances:
113 71 0.24
114 114 0.39
115 101 0.35
116 5 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (113 bp):
AAGCGCCACAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGC
GCAAAGCGAAAACGCCACTAACGCACACTATTAGCGGCACTTTGGGCT
Found at i:28189745 original size:8 final size:8
Alignment explanation
Indices: 28189732--28189758 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
28189722 TACCAGTTTG
28189732 TTTGGGAA
1 TTTGGGAA
28189740 TTTGGGAA
1 TTTGGGAA
28189748 TTTGGGAA
1 TTTGGGAA
28189756 TTT
1 TTT
28189759 TTGTATGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (8 bp):
TTTGGGAA
Found at i:28191007 original size:7 final size:6
Alignment explanation
Indices: 28190981--28191005 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28190971 GAGAGAGAAG
28190981 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
28191006 TACGAATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:28191953 original size:9 final size:9
Alignment explanation
Indices: 28191939--28192057 Score: 161
Period size: 9 Copynumber: 13.4 Consensus size: 9
28191929 TAGTAACCAA
28191939 ATAACTTAC
1 ATAACTTAC
28191948 ATAACTTAC
1 ATAACTTAC
28191957 ATAACTTAC
1 ATAACTTAC
* * *
28191966 AAAAATTAA
1 ATAACTTAC
28191975 ATAACTTAC
1 ATAACTTAC
28191984 ATAACTTAC
1 ATAACTTAC
* *
28191993 ATAAATTAA
1 ATAACTTAC
28192002 ATAACTTAC
1 ATAACTTAC
28192011 ATAACTTAC
1 ATAACTTAC
28192020 ATAACTTAC
1 ATAACTTAC
* *
28192029 ATAAATTAA
1 ATAACTTAC
28192038 ATAACTTAC
1 ATAACTTAC
28192047 A-AA-TTAC
1 ATAACTTAC
28192054 ATAA
1 ATAA
28192058 NNNNNNNNNN
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
7 5 0.05
8 4 0.04
9 86 0.91
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:28192190 original size:25 final size:24
Alignment explanation
Indices: 28192162--28192268 Score: 94
Period size: 25 Copynumber: 4.3 Consensus size: 24
28192152 ATTAATATTA
*
28192162 TACACAACTTACATAATACATTACT
1 TACATAACTTACATAATACA-TACT
* *
28192187 TACATAACTTACAGTACTTACATA-A
1 TACATAACTTACA-TA-ATACATACT
*
28192212 TACATAACTTACAGTACTTACAGTACT
1 TACATAACTTACA-TA-ATACA-TACT
28192239 TACATAA--TACATAATACATAACT
1 TACATAACTTACATAATACAT-ACT
28192262 TACATAA
1 TACATAA
28192269 TACAAATTTC
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
22 1 0.01
23 14 0.19
24 2 0.03
25 38 0.53
26 6 0.08
27 11 0.15
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.32
Consensus pattern (24 bp):
TACATAACTTACATAATACATACT
Found at i:28192211 original size:34 final size:34
Alignment explanation
Indices: 28192168--28192265 Score: 148
Period size: 34 Copynumber: 2.9 Consensus size: 34
28192158 ATTATACACA
28192168 ACTTACATAATACATTACTTACATAACTTACAGT
1 ACTTACATAATACATTACTTACATAACTTACAGT
*
28192202 ACTTACATAATACATAACTTACAGT-ACTTACAGT
1 ACTTACATAATACATTACTTACA-TAACTTACAGT
*
28192236 ACTTACATAATACA-TA-ATACATAACTTACA
1 ACTTACATAATACATTACTTACATAACTTACA
28192266 TAATACAAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
31 1 0.02
32 11 0.19
33 1 0.02
34 45 0.76
35 1 0.02
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.33
Consensus pattern (34 bp):
ACTTACATAATACATTACTTACATAACTTACAGT
Found at i:28192251 original size:7 final size:7
Alignment explanation
Indices: 28192239--28192272 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
28192229 TTACAGTACT
28192239 TACATAA
1 TACATAA
28192246 TACATAA
1 TACATAA
28192253 TACATAA
1 TACATAA
28192260 CTTACATAA
1 --TACATAA
28192269 TACA
1 TACA
28192273 AATTTCTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 18 0.72
9 7 0.28
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (7 bp):
TACATAA
Found at i:28192267 original size:9 final size:9
Alignment explanation
Indices: 28192162--28192268 Score: 92
Period size: 9 Copynumber: 12.8 Consensus size: 9
28192152 ATTAATATTA
*
28192162 TACACAACT
1 TACATAACT
28192171 TACATAA--
1 TACATAACT
*
28192178 TACATTACT
1 TACATAACT
28192187 TACATAACT
1 TACATAACT
28192196 TACAGT-ACT
1 TACA-TAACT
28192205 TACATAA--
1 TACATAACT
28192212 TACATAACT
1 TACATAACT
28192221 TACAGT-ACT
1 TACA-TAACT
28192230 TACAGT-ACT
1 TACA-TAACT
28192239 TACATAA--
1 TACATAACT
28192246 TACATAA--
1 TACATAACT
28192253 TACATAACT
1 TACATAACT
28192262 TACATAA
1 TACATAA
28192269 TACAAATTTC
Statistics
Matches: 85, Mismatches: 3, Indels: 20
0.79 0.03 0.19
Matches are distributed among these distances:
7 27 0.32
8 2 0.02
9 54 0.64
10 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:28198313 original size:21 final size:21
Alignment explanation
Indices: 28198287--28198355 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
28198277 CAACTTAAAA
* *
28198287 CAGAGGCGGCAGCGAGGGAAG
1 CAGAGGCCGCAGCGAGAGAAG
**
28198308 CAGAGGTTGCAGCGAGAGAAG
1 CAGAGGCCGCAGCGAGAGAAG
28198329 CAGAGGCCGCAGCGAGAGAAG
1 CAGAGGCCGCAGCGAGAGAAG
28198350 CAGAGG
1 CAGAGG
28198356 TTCAAAAGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.32, C:0.19, G:0.46, T:0.03
Consensus pattern (21 bp):
CAGAGGCCGCAGCGAGAGAAG
Found at i:28198799 original size:43 final size:42
Alignment explanation
Indices: 28198733--28198872 Score: 165
Period size: 43 Copynumber: 3.3 Consensus size: 42
28198723 AATCCCAAAA
* * *
28198733 TTAGTGGCGTTTGTGAAATAAGCGCCGCGAAAGAACACTACTT
1 TTAGCGGCGTTTGT-AAATAAGCGCCGCTAAAGAACATTACTT
*
28198776 TTAGCGGCGTTTGTAGATGAAGCGCCGCTAAAGAACATTACTT
1 TTAGCGGCGTTTGTAAAT-AAGCGCCGCTAAAGAACATTACTT
* ** * *
28198819 TTAGCGGCGTTT-TCTACCAAGCGCCACTATAGAACATTACTT
1 TTAGCGGCGTTTGT-AAATAAGCGCCGCTAAAGAACATTACTT
28198861 TTAGCGGCGTTT
1 TTAGCGGCGTTT
28198873 TTTTCCTAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
42 38 0.45
43 47 0.55
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (42 bp):
TTAGCGGCGTTTGTAAATAAGCGCCGCTAAAGAACATTACTT
Found at i:28198854 original size:42 final size:42
Alignment explanation
Indices: 28198752--28199004 Score: 240
Period size: 43 Copynumber: 5.9 Consensus size: 42
28198742 TTTGTGAAAT
* * ** **
28198752 AAGCGCCGCGAAAGAACACTACTTTTAGCGGCGTTTGTAGATG
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTT-TTTACC
*
28198795 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTCTACC
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
* * *
28198837 AAGCGCCACTATAGAACATTACTTTTAGCGGCGTTTTTTTCC
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
* * * * * *
28198879 TAAACTCCGCTAAGGATCATGTTC-TTTAGCGGCGTTTTTTCCC
1 -AAGCGCCGCTAAAGAACAT-TACTTTTAGCGGCGTTTTTTACC
* * *
28198922 AAGCGCCGCTAAAGAACATGA-TCATTAGCGGCGTTTTTTTTCC
1 AAGCGCCGCTAAAGAACATTACT-TTTAGCGGCG-TTTTTTACC
* * *
28198965 TAAGCGCCGCTAAAGAAAATGACCTTTAGCGGCGTTTTTT
1 -AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTT
28199005 TGTAAGCGCC
Statistics
Matches: 174, Mismatches: 29, Indels: 14
0.80 0.13 0.06
Matches are distributed among these distances:
42 64 0.37
43 79 0.45
44 31 0.18
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
Found at i:28198961 original size:44 final size:42
Alignment explanation
Indices: 28198795--28199005 Score: 219
Period size: 42 Copynumber: 4.9 Consensus size: 42
28198785 TTTGTAGATG
* * *
28198795 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCG-TTTTCTACC
1 AAGCGCCGCTAAAGAACATGAC-TTTAGCGGCGTTTTTTTCCC
* * * *
28198837 AAGCGCCACTATAGAACATTACTTTTAGCGGCGTTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGAC-TTTAGCGGCGTTTTTTTCCC
* * * * *
28198880 AAACTCCGCTAAGGATCATGTTCTTTAGCGGCG-TTTTTTCCC
1 AAGCGCCGCTAAAGAACATG-ACTTTAGCGGCGTTTTTTTCCC
* *
28198922 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGA-CTTTAGCGGCG-TTTTTTTCCC
*
28198966 AAGCGCCGCTAAAGAAAATGACCTTTAGCGGCGTTTTTTT
1 AAGCGCCGCTAAAGAACATGA-CTTTAGCGGCGTTTTTTT
28199006 GTAAGCGCCG
Statistics
Matches: 140, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
42 65 0.46
43 36 0.26
44 39 0.28
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGACTTTAGCGGCGTTTTTTTCCC
Found at i:28199015 original size:86 final size:85
Alignment explanation
Indices: 28198752--28199004 Score: 260
Period size: 85 Copynumber: 3.0 Consensus size: 85
28198742 TTTGTGAAAT
* * * *** *
28198752 AAGCGCCGCGAAAGAACACT-ACTTTTAGCGGCG-TTTGTAGATGAAGCGCCGCTAAAGAACATT
1 AAGCGCCGCTAAAGAACA-TGACTATTAGCGGCGTTTTTTTCCT-AAGCGCCGCTAAAGAACATG
* *
28198815 ACTTTTAGCGGCGTTTTCTACC
64 ACCTTTAGCGGCGTTTTTTACC
* * * * * * * * **
28198837 AAGCGCCACTATAGAACATTACTTTTAGCGGCGTTTTTTTCCTAAACTCCGCTAAGGATCATGTT
1 AAGCGCCGCTAAAGAACATGACTATTAGCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGAC
*
28198902 CTTTAGCGGCGTTTTTTCCC
66 CTTTAGCGGCGTTTTTTACC
*
28198922 AAGCGCCGCTAAAGAACATGA-TCATTAGCGGCGTTTTTTTTCCTAAGCGCCGCTAAAGAAAATG
1 AAGCGCCGCTAAAGAACATGACT-ATTAGCGGCG-TTTTTTTCCTAAGCGCCGCTAAAGAACATG
28198986 ACCTTTAGCGGCGTTTTTT
64 ACCTTTAGCGGCGTTTTTT
28199005 TGTAAGCGCC
Statistics
Matches: 136, Mismatches: 28, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
84 2 0.01
85 87 0.64
86 47 0.35
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (85 bp):
AAGCGCCGCTAAAGAACATGACTATTAGCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGAC
CTTTAGCGGCGTTTTTTACC
Found at i:28199766 original size:30 final size:30
Alignment explanation
Indices: 28199732--28199791 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
28199722 TATTTTATTA
28199732 TTAATTTTGTTATTATTTTAAAGACATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
* *
28199762 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
28199792 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGACATTTG
Found at i:28206856 original size:149 final size:146
Alignment explanation
Indices: 28206585--28206851 Score: 367
Period size: 149 Copynumber: 1.8 Consensus size: 146
28206575 CATTATATAA
* * *
28206585 AATATTATTATATATTAGTTATTATCATTTTATTTATTACAAAGAAATTAAAAACATTTATTTTA
1 AATATAATTATATATTAGTTATTATCATCTTATTTATTAAAAAGAAATTAAAAACATTTATTTTA
* * * * *
28206650 GCTTTTTTTTTTTAAATATTTATAGAAAAAAAACAACTAATTTTAGTATTTATAAAAGAACAACC
66 G--TTTGTTTTTAAAATATTTACAG-AAAAAAACAACTAATTTTAATATTTAAAAAAGAACAACC
28206715 AAAATTTTCAAATTTAATT
128 AAAATTTTCAAATTTAATT
* *
28206734 AATATAATTATATATTAGTTATTATCATCTTATTTATTAAAAATAAATTAAAAACCTTTATTTTA
1 AATATAATTATATATTAGTTATTATCATCTTATTTATTAAAAAGAAATTAAAAACATTTATTTTA
* * *
28206799 G-TTGTTTTTAAAATATTTACAG-AGAAGACATCTAATTTTAATATTTACAAAAA
66 GTTTGTTTTTAAAATATTTACAGAAAAAAACAACTAATTTTAATATTTA-AAAAA
28206852 AAAAGTCCCT
Statistics
Matches: 104, Mismatches: 13, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
144 21 0.20
145 4 0.04
146 18 0.17
149 61 0.59
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (146 bp):
AATATAATTATATATTAGTTATTATCATCTTATTTATTAAAAAGAAATTAAAAACATTTATTTTA
GTTTGTTTTTAAAATATTTACAGAAAAAAACAACTAATTTTAATATTTAAAAAAGAACAACCAAA
ATTTTCAAATTTAATT
Found at i:28212912 original size:23 final size:22
Alignment explanation
Indices: 28212875--28212917 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
28212865 GTGAAATAAA
28212875 AACTAAAAAATTAAATAAGTACT
1 AACTAAAAAATTAAA-AAGTACT
28212898 AACTAAGAAAA-TAAAAAGTA
1 AACTAA-AAAATTAAAAAGTA
28212918 AAATTCCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.21
Consensus pattern (22 bp):
AACTAAAAAATTAAAAAGTACT
Found at i:28214111 original size:21 final size:22
Alignment explanation
Indices: 28214080--28214130 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
28214070 TTAGTTTTAA
28214080 ATGTTATTTAGTCC-TTAAAAC-C
1 ATGTT-TTTAG-CCATTAAAACAC
*
28214102 ATGTTTTTAGCCATTAAATCAC
1 ATGTTTTTAGCCATTAAAACAC
28214124 ATGTTTT
1 ATGTTTT
28214131 AAATAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 11 0.42
22 13 0.50
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (22 bp):
ATGTTTTTAGCCATTAAAACAC
Found at i:28214857 original size:190 final size:190
Alignment explanation
Indices: 28214521--28214902 Score: 620
Period size: 190 Copynumber: 2.0 Consensus size: 190
28214511 TAATGAATCC
* * * * *
28214521 TTGGCTAATTTTTGGATGTATTGTTGTGCGAATTTATTATTTTGAAGTTCTAGATTTGATAGAAT
1 TTGGATAATTTTTGGATGTATTGTTGTGCGAATTTATTATGTTGAAGTTCCAGATTCGATAGAAC
* *
28214586 CTTCTACGAGTAGAGATAAAGGCAAGGAAAAGCTAGTTTGAGCATTCGGCTTTTAAGCAAAAGCG
66 CTTCTACGAGTAGAGATAAAGGCAAGGAAAAGCTAGTTTGAGCATTCAGCTTTTAAGCAAAAGCA
* *
28214651 TAATTGGTGACTGTATGGAATAATTGCTTGTGGACATGCTTCAATGCATTATTTGGGAAT
131 TAATTAGTGACTGTATGGAATAATTACTTGTGGACATGCTTCAATGCATTATTTGGGAAT
* *
28214711 TTGGATAATTTTTGGATGTATTGTTGTGTGAATTTATTGTGTTGAAGTTCCAGATTCGATAGAAC
1 TTGGATAATTTTTGGATGTATTGTTGTGCGAATTTATTATGTTGAAGTTCCAGATTCGATAGAAC
* * *
28214776 CTTCTATGAGTAGAGATAAAGGCAAGGAAAAGCTAGTTTGAGCTTTCAGCTTTTAGGCAAAAGCA
66 CTTCTACGAGTAGAGATAAAGGCAAGGAAAAGCTAGTTTGAGCATTCAGCTTTTAAGCAAAAGCA
* *
28214841 TAATTAGTGGCTGTATGGAATAATTACTTGTGGACATGCTTCAATGCGTTATTTGGGAAT
131 TAATTAGTGACTGTATGGAATAATTACTTGTGGACATGCTTCAATGCATTATTTGGGAAT
28214901 TT
1 TT
28214903 AGTAGTAGCC
Statistics
Matches: 176, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
190 176 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (190 bp):
TTGGATAATTTTTGGATGTATTGTTGTGCGAATTTATTATGTTGAAGTTCCAGATTCGATAGAAC
CTTCTACGAGTAGAGATAAAGGCAAGGAAAAGCTAGTTTGAGCATTCAGCTTTTAAGCAAAAGCA
TAATTAGTGACTGTATGGAATAATTACTTGTGGACATGCTTCAATGCATTATTTGGGAAT
Found at i:28220607 original size:17 final size:15
Alignment explanation
Indices: 28220569--28220611 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
28220559 AATGAATTCA
28220569 TTTTTTTCTCTCTTC
1 TTTTTTTCTCTCTTC
* *
28220584 ATCTTTTCTCTCTTCCC
1 TTTTTTTCTCTCTT--C
28220601 TTTTTTTCTCT
1 TTTTTTTCTCT
28220612 ACTCCTCCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.55
17 10 0.45
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTTCTCTCTTC
Found at i:28222867 original size:48 final size:48
Alignment explanation
Indices: 28222796--28222897 Score: 186
Period size: 48 Copynumber: 2.1 Consensus size: 48
28222786 AACTACCCTA
*
28222796 CATCCCCAATCCCCACATTCAACCTAACTAGACGAGTAGGAGAAATCT
1 CATCCCCAATCCCCACATTCAACCTAACTAGACGAGTAGGAAAAATCT
*
28222844 CATCCCCAATCCCCATATTCAACCTAACTAGACGAGTAGGAAAAATCT
1 CATCCCCAATCCCCACATTCAACCTAACTAGACGAGTAGGAAAAATCT
28222892 CATCCC
1 CATCCC
28222898 TTATTGGTCT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.35, C:0.34, G:0.11, T:0.20
Consensus pattern (48 bp):
CATCCCCAATCCCCACATTCAACCTAACTAGACGAGTAGGAAAAATCT
Found at i:28225069 original size:23 final size:22
Alignment explanation
Indices: 28225041--28225092 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
28225031 CCTTTGTGGC
*
28225041 GCATTCTAAATTTGGCGTTTATG
1 GCATTCT-AATTTGGCCTTTATG
** *
28225064 GCATTCTGGTTTGGCCTTTGTG
1 GCATTCTAATTTGGCCTTTATG
28225086 GCATTCT
1 GCATTCT
28225093 GTTAGCCCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.44
Consensus pattern (22 bp):
GCATTCTAATTTGGCCTTTATG
Found at i:28225087 original size:22 final size:22
Alignment explanation
Indices: 28225051--28225093 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28225041 GCATTCTAAA
*
28225051 TTTGGCGTTTATGGCATTCTGG
1 TTTGGCCTTTATGGCATTCTGG
*
28225073 TTTGGCCTTTGTGGCATTCTG
1 TTTGGCCTTTATGGCATTCTG
28225094 TTAGCCCTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.07, C:0.16, G:0.30, T:0.47
Consensus pattern (22 bp):
TTTGGCCTTTATGGCATTCTGG
Found at i:28225106 original size:20 final size:20
Alignment explanation
Indices: 28225016--28225127 Score: 80
Period size: 20 Copynumber: 5.2 Consensus size: 20
28225006 AGGTGCTTGG
*
28225016 GTGGCATTTTGTTAGCCTTT
1 GTGGCATTCTGTTAGCCTTT
* * *
28225036 GTGGCGCATTCTAAATTTGGCGTTT
1 GT-G-GCATTCT---GTTAGCCTTT
* *
28225061 ATGGCATTCTGGTTTGGCCTTT
1 GTGGCATTCT-G-TTAGCCTTT
*
28225083 GTGGCATTCTGTTAGCCCTT
1 GTGGCATTCTGTTAGCCTTT
* *
28225103 GTGGCAATCTGTTAACCTTT
1 GTGGCATTCTGTTAGCCTTT
28225123 GTGGC
1 GTGGC
28225128 GTATTCTATA
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
20 31 0.43
21 2 0.03
22 23 0.32
23 7 0.10
24 1 0.01
25 8 0.11
ACGTcount: A:0.12, C:0.19, G:0.27, T:0.42
Consensus pattern (20 bp):
GTGGCATTCTGTTAGCCTTT
Found at i:28243457 original size:3 final size:3
Alignment explanation
Indices: 28243449--28243497 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
28243439 TTCTTTTTAT
28243449 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28243497 T
1 T
28243498 CACATACGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28243952 original size:23 final size:23
Alignment explanation
Indices: 28243912--28243958 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
28243902 AGAATTTAGG
* *
28243912 TTTTTTATATTAAGTTTTGTTTT
1 TTTTTTAGATTAAGTTTTGATTT
28243935 TTTTTTAGATTATA-TTTTGATTT
1 TTTTTTAGATTA-AGTTTTGATTT
28243958 T
1 T
28243959 GAAATCTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (23 bp):
TTTTTTAGATTAAGTTTTGATTT
Found at i:28245425 original size:15 final size:15
Alignment explanation
Indices: 28245405--28245434 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28245395 TTAAGATTAA
28245405 TTAAAAGAACATGAG
1 TTAAAAGAACATGAG
28245420 TTAAAAGAACATGAG
1 TTAAAAGAACATGAG
28245435 AACTCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (15 bp):
TTAAAAGAACATGAG
Found at i:28248616 original size:6 final size:6
Alignment explanation
Indices: 28248583--28248615 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
28248573 TATTAGTTTA
*
28248583 ATTGAC ATTGAC ATTGAC ATTGAC ATTAAC ATT
1 ATTGAC ATTGAC ATTGAC ATTGAC ATTGAC ATT
28248616 ATTATCAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (6 bp):
ATTGAC
Found at i:28249754 original size:21 final size:22
Alignment explanation
Indices: 28249730--28249777 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
28249720 TATAAAAGAG
28249730 TTTGAATAAC-TTATATAAAAT
1 TTTGAATAACTTTATATAAAAT
* * * *
28249751 TTTGGATTACTTTTTATATAAT
1 TTTGAATAACTTTATATAAAAT
28249773 TTTGA
1 TTTGA
28249778 GCTGAAACTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.52
Consensus pattern (22 bp):
TTTGAATAACTTTATATAAAAT
Found at i:28251573 original size:17 final size:18
Alignment explanation
Indices: 28251535--28251576 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
28251525 TGCTTCTAAG
28251535 AAGCACTTTTAGGACAAA
1 AAGCACTTTTAGGACAAA
*
28251553 AAGCACTTTTGGGAC-AA
1 AAGCACTTTTAGGACAAA
28251570 AAGCACT
1 AAGCACT
28251577 CTTAAACAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (18 bp):
AAGCACTTTTAGGACAAA
Found at i:28254279 original size:50 final size:49
Alignment explanation
Indices: 28254220--28254499 Score: 341
Period size: 50 Copynumber: 5.7 Consensus size: 49
28254210 GGCAGTGAGT
*
28254220 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGA-CGAGGA
** *
28254270 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCAACACGGACAGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAC-GAGGA
* * * * *
28254320 GAG-TCAGTGTAAGACCATGTTTGGGACATGACATCGGCTC-GA-GATGA
1 GTGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGA
* *
28254367 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGTA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGA-CGAGGA
*
28254417 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGACAGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAC-GAGGA
* * * * *
28254467 GAGTTAGTGTAAGATCACGTTTGGGACATGGCA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCA
28254500 AAGGCACCGA
Statistics
Matches: 197, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
47 38 0.19
48 2 0.01
49 5 0.03
50 152 0.77
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.20
Consensus pattern (49 bp):
GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGA
Found at i:28254400 original size:97 final size:98
Alignment explanation
Indices: 28254224--28254499 Score: 333
Period size: 97 Copynumber: 2.8 Consensus size: 98
28254214 GTGAGTGTGC
*
28254224 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGGAGTGCTAGTGTAAGACCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGA-CGAGGAGTGCCAGTGTAAGACCATG
*
28254289 TCTGGGACATGGCATCAACACGGA-CAGAGGAGAG
65 TCTGGGACATGGCATCAACACAGATC-GAGGAGAG
* * * *
28254323 TCAGTGTAAGACCATGTTTGGGACATGACATCGGCTC-GA-GATGAGTGCCAGTGTAAGACCATG
1 -CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGAGTGCCAGTGTAAGACCATG
** * *
28254386 TCTGGGACATGGCATCGGCACAGATCGAGTAGTG
65 TCTGGGACATGGCATCAACACAGATCGAGGAGAG
* * ** * *
28254420 CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGACAGAGGAGAGTTAGTGTAAGATCAC
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAC-GAGGAGTGCCAGTGTAAGACCAT
*
28254485 GTTTGGGACATGGCA
64 GTCTGGGACATGGCA
28254500 AAGGCACCGA
Statistics
Matches: 151, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
96 1 0.01
97 81 0.54
98 3 0.02
99 2 0.01
100 64 0.42
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.20
Consensus pattern (98 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGAGTGCCAGTGTAAGACCATGT
CTGGGACATGGCATCAACACAGATCGAGGAGAG
Found at i:28254489 original size:147 final size:147
Alignment explanation
Indices: 28254220--28254496 Score: 500
Period size: 147 Copynumber: 1.9 Consensus size: 147
28254210 GGCAGTGAGT
28254220 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGGAGTGCTAGTGTAAGAC
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGGAGTGCTAGTGTAAGAC
*
28254285 CATGTCTGGGACATGGCATCAACACGGACAGAGGAGAGTCAGTGTAAGACCATGTTTGGGACATG
66 CATGTCTGGGACATGGCATCAACACGGACAGAGGAGAGTCAGTGTAAGACCACGTTTGGGACATG
28254350 ACATCGGCTCGAGATGA
131 ACATCGGCTCGAGATGA
*
28254367 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGTAGTGCTAGTGTAAGAC
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGGAGTGCTAGTGTAAGAC
** * *
28254432 CATGTCTGGGACATGGCATCGGCACGGACAGAGGAGAGTTAGTGTAAGATCACGTTTGGGACATG
66 CATGTCTGGGACATGGCATCAACACGGACAGAGGAGAGTCAGTGTAAGACCACGTTTGGGACATG
28254497 GCAAAGGCAC
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
147 124 1.00
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.21
Consensus pattern (147 bp):
GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATCGAGGAGTGCTAGTGTAAGAC
CATGTCTGGGACATGGCATCAACACGGACAGAGGAGAGTCAGTGTAAGACCACGTTTGGGACATG
ACATCGGCTCGAGATGA
Found at i:28259768 original size:8 final size:8
Alignment explanation
Indices: 28259755--28259779 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28259745 GAGGATCAAT
28259755 TTGTTAAA
1 TTGTTAAA
28259763 TTGTTAAA
1 TTGTTAAA
28259771 TTGTTAAA
1 TTGTTAAA
28259779 T
1 T
28259780 GTTTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TTGTTAAA
Found at i:28260648 original size:20 final size:19
Alignment explanation
Indices: 28260625--28260679 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
28260615 GGTGCCTTTG
28260625 TTTGCACTTCGATGCCCCTA
1 TTTGCACTTCG-TGCCCCTA
* *
28260645 TTTGTACATTTGTGCCCCTA
1 TTTGCAC-TTCGTGCCCCTA
*
28260665 TCTGCACTTCAGTGC
1 TTTGCACTTC-GTGC
28260680 TCTTGTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 23 0.82
21 3 0.11
ACGTcount: A:0.15, C:0.31, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTGCACTTCGTGCCCCTA
Found at i:28261491 original size:20 final size:20
Alignment explanation
Indices: 28261451--28261492 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
28261441 ATAATGGTAT
* * *
28261451 GTATAGGATGTTTTGTTATG
1 GTATAGGATGATATGTAATG
28261471 GTATAGGATGATATGTAATG
1 GTATAGGATGATATGTAATG
28261491 GT
1 GT
28261493 GATTTGGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (20 bp):
GTATAGGATGATATGTAATG
Found at i:28266462 original size:13 final size:13
Alignment explanation
Indices: 28266444--28266468 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28266434 TCGTAACATT
28266444 CTTGTTTTATTTA
1 CTTGTTTTATTTA
28266457 CTTGTTTTATTT
1 CTTGTTTTATTT
28266469 TGCACATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.72
Consensus pattern (13 bp):
CTTGTTTTATTTA
Found at i:28270616 original size:24 final size:24
Alignment explanation
Indices: 28270589--28270640 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
28270579 TTAGTAAGTC
*
28270589 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* * *
28270613 AAATATATTGTACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
28270637 AAAT
1 AAAT
28270641 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:28270813 original size:18 final size:18
Alignment explanation
Indices: 28270790--28270827 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28270780 GTATGTGTAA
*
28270790 GGTTTGGAAAGCTATGTT
1 GGTTTGAAAAGCTATGTT
*
28270808 GGTTTGAAAAGCTTTGTT
1 GGTTTGAAAAGCTATGTT
28270826 GG
1 GG
28270828 AAAGCTATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.34, T:0.39
Consensus pattern (18 bp):
GGTTTGAAAAGCTATGTT
Found at i:28278398 original size:50 final size:49
Alignment explanation
Indices: 28278304--28278398 Score: 145
Period size: 50 Copynumber: 1.9 Consensus size: 49
28278294 AAAGTGAAAG
* *
28278304 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAA
1 TGATGGTCACATGTGTAGTACTATATGCAGGCTACTACGCGTACCAGAA
* *
28278353 TGATAGGTCGCATGTGTAGTACTATATGCAGGCTACTATGCGTACC
1 TGAT-GGTCACATGTGTAGTACTATATGCAGGCTACTACGCGTACC
28278399 GGATAGCTCG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 4 0.10
50 37 0.90
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.29
Consensus pattern (49 bp):
TGATGGTCACATGTGTAGTACTATATGCAGGCTACTACGCGTACCAGAA
Found at i:28278568 original size:33 final size:33
Alignment explanation
Indices: 28278526--28278884 Score: 187
Period size: 33 Copynumber: 10.6 Consensus size: 33
28278516 ACATAAAAGG
28278526 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
28278559 GGTTGCTAAGTGCTGATTCCACTGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
* *
28278601 GGTTGCTAGGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
28278628 GGTTGCTAAGTGCTGATTCTCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
28278661 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
* *
28278703 GGTTGCTAAGTGCTGACTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
28278730 GGTTGCTAAGTGCTGATTCTCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * * *
28278763 GGTTGCTAAGTGTTGATTCCATCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
*
28278805 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
28278832 GGTTGCTAAGTGCTGATTCTCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
28278865 GGTTGCTAAGTGTTGATTCC
1 GGTTGCTAAGTGCTGATTCC
28278885 ATGAAAATTT
Statistics
Matches: 249, Mismatches: 32, Indels: 90
0.67 0.09 0.24
Matches are distributed among these distances:
27 61 0.24
28 6 0.02
31 6 0.02
32 6 0.02
33 78 0.31
34 7 0.03
35 3 0.01
37 6 0.02
38 6 0.02
39 3 0.01
41 4 0.02
42 63 0.25
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.35
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:28278886 original size:102 final size:102
Alignment explanation
Indices: 28278522--28278886 Score: 660
Period size: 102 Copynumber: 3.6 Consensus size: 102
28278512 TTGAACATAA
*
28278522 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCA-CTGTAT
1 AAGGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCATC-GTAT
*
28278586 TTTAAATGTGAAGGGGGTTGCTAGGTGCTGATTCCCCC
65 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
*
28278624 AAGGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCATCGTATT
*
28278689 TTAAATGTGAAGGGGGTTGCTAAGTGCTGACTCCCCC
66 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
*
28278726 AAGGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCATCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCATCGTATT
28278791 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
*
28278828 AAGGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCAT
1 AAGGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCAT
28278887 GAAAATTTGA
Statistics
Matches: 256, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
102 255 1.00
103 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (102 bp):
AAGGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCATCGTATT
TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:28279709 original size:49 final size:49
Alignment explanation
Indices: 28279625--28279725 Score: 123
Period size: 49 Copynumber: 2.1 Consensus size: 49
28279615 ACGAGTACTT
* * * * *
28279625 TCGGTAAGTGATATGTGATTCCGTATAGGAGCATAGCTGGGCTATGGCA
1 TCGGTAAGTGATATGTGATTACATATAAGACCATAGCTGGACTATGGCA
* *
28279674 TCGGTATA-TGATATGTGATTACATGTAAGACCATAGTTGGACTATGGCA
1 TCGGTA-AGTGATATGTGATTACATATAAGACCATAGCTGGACTATGGCA
28279723 TCG
1 TCG
28279726 AGAAAACGAG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 43 0.98
50 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (49 bp):
TCGGTAAGTGATATGTGATTACATATAAGACCATAGCTGGACTATGGCA
Found at i:28285165 original size:30 final size:30
Alignment explanation
Indices: 28285129--28285185 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
28285119 AAGACACGAC
*
28285129 CATGTGTCCTTAGTTCGAAGGTTACACAGT
1 CATGTGTCCCTAGTTCGAAGGTTACACAGT
* *
28285159 CATGTGTCCCTAGTTTGAATGTTACAC
1 CATGTGTCCCTAGTTCGAAGGTTACAC
28285186 GACTGTGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (30 bp):
CATGTGTCCCTAGTTCGAAGGTTACACAGT
Found at i:28290626 original size:18 final size:17
Alignment explanation
Indices: 28290594--28290633 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
28290584 ATAAAAAACA
28290594 ATTAAAATCATATTTAT
1 ATTAAAATCATATTTAT
*
28290611 ATTAAATATTATATTTAT
1 ATTAAA-ATCATATTTAT
28290629 ATTAA
1 ATTAA
28290634 TGTTAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTAAAATCATATTTAT
Found at i:28294066 original size:89 final size:88
Alignment explanation
Indices: 28293955--28294121 Score: 244
Period size: 89 Copynumber: 1.9 Consensus size: 88
28293945 TAGTGAAAAA
* * *
28293955 AATTGTATGGTCGCAATAATAATTAATAATAGTGACATGATATGTTATCACTATTACATCAGTTC
1 AATTGTATGGCCACAATAATAATTAATAATAGTGACATGATATGATATCACTATTACATCAGTTC
28294020 TCAAGAAAAAAAAACTTGAAGGC
66 TCAAGAAAAAAAAACTTGAAGGC
* * * *
28294043 AATTCGTATGGCCACAATAATAATTAATAATAGTGACTTTATATGATGTCACTATTACATCATTT
1 AATT-GTATGGCCACAATAATAATTAATAATAGTGACATGATATGATATCACTATTACATCAGTT
* *
28294108 CTCGAGGAAAAAAA
65 CTCAAGAAAAAAAA
28294122 GAATTTGGAG
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
88 4 0.06
89 65 0.94
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (88 bp):
AATTGTATGGCCACAATAATAATTAATAATAGTGACATGATATGATATCACTATTACATCAGTTC
TCAAGAAAAAAAAACTTGAAGGC
Found at i:28313468 original size:27 final size:27
Alignment explanation
Indices: 28313429--28313505 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
28313419 TTCCTTTCCT
* * *
28313429 TAGATCGCTACAAAGGCTTCTATCTCA
1 TAGATTGCCACAAAGGCTTCCATCTCA
*
28313456 TAGATTGCCACAAATGCTTCCATCTCA
1 TAGATTGCCACAAAGGCTTCCATCTCA
* *
28313483 TAGGTTGCCACAAAGACTTCCAT
1 TAGATTGCCACAAAGGCTTCCAT
28313506 TTTCCAGCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
TAGATTGCCACAAAGGCTTCCATCTCA
Found at i:28316631 original size:30 final size:29
Alignment explanation
Indices: 28316596--28316652 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
28316586 CTTTCAGATG
28316596 ACACACGGCC-ATGTCACCAGGCCATGTGCC
1 ACACAC-GCCTATGTC-CCAGGCCATGTGCC
*
28316626 ACACACGCCTATGTCCCAGGCTATGTG
1 ACACACGCCTATGTCCCAGGCCATGTG
28316653 TACCAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.23, C:0.37, G:0.23, T:0.18
Consensus pattern (29 bp):
ACACACGCCTATGTCCCAGGCCATGTGCC
Found at i:28323454 original size:18 final size:19
Alignment explanation
Indices: 28323428--28323469 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
28323418 TCAAATTTCT
*
28323428 TAATTAAAAAATAT-AAAA
1 TAATAAAAAAATATAAAAA
* *
28323446 TAATAAAAACATTTAAAAA
1 TAATAAAAAAATATAAAAA
28323465 TAATA
1 TAATA
28323470 TTTTCTTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
TAATAAAAAAATATAAAAA
Found at i:28324947 original size:25 final size:25
Alignment explanation
Indices: 28324919--28324970 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
28324909 ACCCAGAAAG
28324919 ATTGTCATAATTAGCTTCAAATGGC
1 ATTGTCATAATTAGCTTCAAATGGC
28324944 ATTGTCATAATTAGCTTCAAATGGC
1 ATTGTCATAATTAGCTTCAAATGGC
28324969 AT
1 AT
28324971 CTCATGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (25 bp):
ATTGTCATAATTAGCTTCAAATGGC
Found at i:28326932 original size:15 final size:15
Alignment explanation
Indices: 28326912--28326941 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28326902 AGGCGAGTAG
*
28326912 TGGATGTGTCGGTAT
1 TGGATGTGCCGGTAT
28326927 TGGATGTGCCGGTAT
1 TGGATGTGCCGGTAT
28326942 AAAGTGAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.40, T:0.37
Consensus pattern (15 bp):
TGGATGTGCCGGTAT
Found at i:28327932 original size:4 final size:4
Alignment explanation
Indices: 28327912--28327962 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
28327902 AAACAAATGA
28327912 AAAT AAAT --AT AATAT AAAT AAGA- ATAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AA-AT AAAT AA-AT A-AAT AAAT AAAT AAAT AAAT AAAT
28327960 AAA
1 AAA
28327963 ATAAGGAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
2 2 0.05
4 32 0.78
5 7 0.17
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:28334236 original size:13 final size:13
Alignment explanation
Indices: 28334218--28334245 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28334208 ATCTACAGTG
28334218 TACACTTGCACAT
1 TACACTTGCACAT
28334231 TACACTTGCACAT
1 TACACTTGCACAT
28334244 TA
1 TA
28334246 TTGTTGTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (13 bp):
TACACTTGCACAT
Done.