Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 33 of 105
Found at i:6469107 original size:17 final size:15
Alignment explanation
Indices: 6469077--6469112 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
6469067 AAAGTACTAT
6469077 TAATATTATATTAAA
1 TAATATTATATTAAA
6469092 TAATATTAATTATTAAA
1 TAATATT-A-TATTAAA
6469109 TAAT
1 TAAT
6469113 TAAAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
16 1 0.05
17 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATATTATATTAAA
Found at i:6469137 original size:37 final size:36
Alignment explanation
Indices: 6469078--6469154 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
6469068 AAGTACTATT
*
6469078 AATATTATATTAAATAATATTAATTATTAAATAATTAA
1 AATATTATATTAAATAACATTAA-TATT-AATAATTAA
* * *
6469116 AATATTAT-TTAAATAGCATTAATATTTATTATTAA
1 AATATTATATTAAATAACATTAATATTAATAATTAA
6469151 AATA
1 AATA
6469155 ATAATATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 11 0.31
36 4 0.11
37 12 0.34
38 8 0.23
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (36 bp):
AATATTATATTAAATAACATTAATATTAATAATTAA
Found at i:6469261 original size:20 final size:20
Alignment explanation
Indices: 6469223--6469261 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
6469213 TTTAATTAAA
6469223 ATTAAATAAAAATATTTTTT
1 ATTAAATAAAAATATTTTTT
*
6469243 ATTAATATAATAATATTTT
1 ATTAA-ATAAAAATATTTT
6469262 AGATCAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTAAATAAAAATATTTTTT
Found at i:6471211 original size:16 final size:15
Alignment explanation
Indices: 6471190--6471219 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6471180 AAATTTGTAA
6471190 ATTAAATATTATAAAC
1 ATTAAATATT-TAAAC
6471206 ATTAAATATTTAAA
1 ATTAAATATTTAAA
6471220 TACATAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTAAATATTTAAAC
Found at i:6473772 original size:395 final size:396
Alignment explanation
Indices: 6473041--6473827 Score: 1396
Period size: 395 Copynumber: 2.0 Consensus size: 396
6473031 AATGGAAAAA
* * *
6473041 AGTCATTTTTGAAAAGATAATTAAATAATTTTACTTAAAAATAATTTTTTTAAAAAATTTAAAAT
1 AGTCATTTTCGAAAAGATAATTAAATAATTTCACTTAAAAATAATTTTTTAAAAAAATTTAAAAT
* *
6473106 ATAAAAAAGAGGGTATAAATAGAAGTTCCCAAGACAAAAATGTCTAAAGTTGGATGTGATAAGCC
66 ATAAAAAAAAGGGTATAAATAAAAGTTCCCAAGACAAAAATGTCTAAAGTTGGATGTGATAAGCC
*
6473171 ACCTCACCCATTTCTCAGAAGTGGAAAAACGCACTCCCACTGGTGTCACATAAGCTCAATTGATC
131 ACCTCACCCATTTCTCAGAAGTGGAAAAACACACTCCCACTGGTGTCACATAAGCTCAATTGATC
* * *
6473236 AATGTCTTTGTTATCCAAACAAAAAACCATGATACAATTGCAACTAAAAGGTGCTTAATCGCACC
196 AATGCCTTTATTATCCAAACAAAAAACCATGATACAATTGCAACTAAAAGGTGCTTAATCGCAAC
*
6473301 GAAACATCACTCTGATTCAATCCATCCAACTATTTTCAAATGTGAACATTCACTTTACAACATTA
261 GAAACATCACTCCGATTCAATCCATCCAACTATTTTCAAATGTGAACATTCACTTTACAACATTA
* *
6473366 GAAAATTAACGATTTATTAGGCACATTCTCCCGTGTTGTAAGGTAAATATTTTAGTATTATGATA
326 GAAAATTAACGATTTATTAGGCACATGCTCCCATGTTGTAAGGTAAATATTTTAGTATTATGATA
6473431 TATTTT
391 TATTTT
6473437 AGTCATTTTCGAAAAGATAATTAAATAATTTCACTTAAAAATAATTTTTTAAAAAAATTTAAAAT
1 AGTCATTTTCGAAAAGATAATTAAATAATTTCACTTAAAAATAATTTTTTAAAAAAATTTAAAAT
*
6473502 ATAAAAAAAAGGGTATAAATAAAAGTTCCCAAGAC-AAAATGTCTAAAGTTGGATGTGATGAGCC
66 ATAAAAAAAAGGGTATAAATAAAAGTTCCCAAGACAAAAATGTCTAAAGTTGGATGTGATAAGCC
*
6473566 ACCTCACCTATTTCTCAGAAGTGGAAAAACACACTCCCACTGGTGTCACATAAGCTCAATTGATC
131 ACCTCACCCATTTCTCAGAAGTGGAAAAACACACTCCCACTGGTGTCACATAAGCTCAATTGATC
6473631 AATGCCTTTATTATCCAAACAAAAAACCATGATACAATTGCAACTAAAAGGTGCTTAATCGCAAC
196 AATGCCTTTATTATCCAAACAAAAAACCATGATACAATTGCAACTAAAAGGTGCTTAATCGCAAC
* * * *
6473696 GAAACATCATTCCGATTCAATCTATCTAGCTATTTTCAAATGTGAACATTCACTTTACAACATTA
261 GAAACATCACTCCGATTCAATCCATCCAACTATTTTCAAATGTGAACATTCACTTTACAACATTA
*
6473761 GAAAATTAACGATTTATTAGGCACATGCTCCCATGTTGTAGGGTAAATATTTTAGTATTATGATA
326 GAAAATTAACGATTTATTAGGCACATGCTCCCATGTTGTAAGGTAAATATTTTAGTATTATGATA
6473826 TA
391 TA
6473828 AAACTATTTT
Statistics
Matches: 372, Mismatches: 19, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
395 277 0.74
396 95 0.26
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.31
Consensus pattern (396 bp):
AGTCATTTTCGAAAAGATAATTAAATAATTTCACTTAAAAATAATTTTTTAAAAAAATTTAAAAT
ATAAAAAAAAGGGTATAAATAAAAGTTCCCAAGACAAAAATGTCTAAAGTTGGATGTGATAAGCC
ACCTCACCCATTTCTCAGAAGTGGAAAAACACACTCCCACTGGTGTCACATAAGCTCAATTGATC
AATGCCTTTATTATCCAAACAAAAAACCATGATACAATTGCAACTAAAAGGTGCTTAATCGCAAC
GAAACATCACTCCGATTCAATCCATCCAACTATTTTCAAATGTGAACATTCACTTTACAACATTA
GAAAATTAACGATTTATTAGGCACATGCTCCCATGTTGTAAGGTAAATATTTTAGTATTATGATA
TATTTT
Found at i:6474075 original size:3 final size:3
Alignment explanation
Indices: 6474069--6474108 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
6474059 TTTGTCAAAA
6474069 ATT ATT ATT ATT ATT ATT ATTT ATT ATTT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT A-TT ATT ATT ATT ATT
6474109 TTTAGTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 26 0.76
4 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:6474094 original size:19 final size:19
Alignment explanation
Indices: 6474070--6474109 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
6474060 TTGTCAAAAA
6474070 TTATTA-TTATTATTATTAT
1 TTATTATTTATTA-TATTAT
6474089 TTATTATTTATTATATTAT
1 TTATTATTTATTATATTAT
6474108 TT
1 TT
6474110 TTAGTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTATTTATTATATTAT
Found at i:6474131 original size:20 final size:23
Alignment explanation
Indices: 6474073--6474137 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
6474063 TCAAAAATTA
6474073 TTATTATTATTATTATTT-AT-TAT
1 TTATTA-TATTATT-TTTAATATAT
*
6474096 TTATTATATTATTTTTAGTATAT
1 TTATTATATTATTTTTAATATAT
6474119 TTA-TA-ATTA-TTTTAATATA
1 TTATTATATTATTTTTAATATA
6474138 AAAATTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 9 0.24
21 7 0.18
22 10 0.26
23 12 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
TTATTATATTATTTTTAATATAT
Found at i:6474434 original size:31 final size:31
Alignment explanation
Indices: 6474399--6474457 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
6474389 TTAATTTTTA
6474399 TTTTAT-TATAGTAATTTAATATGCAATTAAG
1 TTTTATATA-AGTAATTTAATATGCAATTAAG
* *
6474430 TTTTATATAATTAATTTAATATGTAATT
1 TTTTATATAAGTAATTTAATATGCAATT
6474458 TAATAAGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.53
Consensus pattern (31 bp):
TTTTATATAAGTAATTTAATATGCAATTAAG
Found at i:6475581 original size:12 final size:12
Alignment explanation
Indices: 6475564--6475609 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
6475554 TAAGATTCAA
6475564 TTGTTTATTTAG
1 TTGTTTATTTAG
6475576 TTGTTTATTTAG
1 TTGTTTATTTAG
**
6475588 TTTGTACATTTAG
1 -TTGTTTATTTAG
6475601 TATGTTTAT
1 T-TGTTTAT
6475610 ATGATTGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 13 0.46
13 15 0.54
ACGTcount: A:0.20, C:0.02, G:0.15, T:0.63
Consensus pattern (12 bp):
TTGTTTATTTAG
Found at i:6475617 original size:25 final size:25
Alignment explanation
Indices: 6475570--6475617 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
6475560 TCAATTGTTT
* *
6475570 ATTTAGTTGTTTATTTAGTTTGTAC
1 ATTTAGTTGTTTATATAGATTGTAC
6475595 ATTTAGTATGTTTATAT-GATTGT
1 ATTTAGT-TGTTTATATAGATTGT
6475618 TTAGGGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.23, C:0.02, G:0.17, T:0.58
Consensus pattern (25 bp):
ATTTAGTTGTTTATATAGATTGTAC
Found at i:6495381 original size:22 final size:22
Alignment explanation
Indices: 6495355--6495397 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
6495345 TGTATATTTA
*
6495355 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
6495377 TATTTGTATCCCTAGAATTAA
1 TATTTGTATCCCTAGAATTAA
6495398 AGAAGATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:6499613 original size:22 final size:22
Alignment explanation
Indices: 6499587--6499630 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6499577 TGTATATTTA
* *
6499587 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
6499609 TATTTGTATCCCTAAAATTAAG
1 TATTTGTATCCCTAAAATTAAG
6499631 GAAGATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:6506680 original size:11 final size:11
Alignment explanation
Indices: 6506664--6506697 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
6506654 TATGTTTGGA
6506664 TGATTATGTCC
1 TGATTATGTCC
6506675 TGATTATGTCC
1 TGATTATGTCC
6506686 TGATTATGTCC
1 TGATTATGTCC
6506697 T
1 T
6506698 AATTTTGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (11 bp):
TGATTATGTCC
Found at i:6509839 original size:19 final size:19
Alignment explanation
Indices: 6509811--6509849 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
6509801 CTTCACAGCT
*
6509811 AAATTGAAATTATTTGCTC
1 AAATTAAAATTATTTGCTC
6509830 AAATTAAAATTATTTGCTC
1 AAATTAAAATTATTTGCTC
6509849 A
1 A
6509850 TATACAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (19 bp):
AAATTAAAATTATTTGCTC
Found at i:6510832 original size:8 final size:8
Alignment explanation
Indices: 6510819--6510851 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
6510809 TCTTCTCCAT
6510819 ATTCTACC
1 ATTCTACC
6510827 ATTCTACC
1 ATTCTACC
6510835 ATTCTACC
1 ATTCTACC
6510843 ATTCTACC
1 ATTCTACC
6510851 A
1 A
6510852 GCCACCAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.27, C:0.36, G:0.00, T:0.36
Consensus pattern (8 bp):
ATTCTACC
Found at i:6514824 original size:15 final size:15
Alignment explanation
Indices: 6514804--6514834 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6514794 TTCAATATAC
6514804 TCTCATTTTTCCACA
1 TCTCATTTTTCCACA
6514819 TCTCATTTTTCCACA
1 TCTCATTTTTCCACA
6514834 T
1 T
6514835 GCTATCAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.32, G:0.00, T:0.48
Consensus pattern (15 bp):
TCTCATTTTTCCACA
Found at i:6519148 original size:22 final size:22
Alignment explanation
Indices: 6519122--6519163 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
6519112 TGTATATTTA
* *
6519122 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
6519144 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
6519164 GGATAGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:6519427 original size:25 final size:23
Alignment explanation
Indices: 6519375--6519434 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 23
6519365 AAAATTTTCA
* *
6519375 GCCTTCATTGCCGACTTTTTTAG
1 GCCTTCATTGCCGACCTGTTTAG
6519398 GCCTTCATTGCCGAATCCTGTTTAG
1 GCCTTCATTGCCG-A-CCTGTTTAG
6519423 GCCTTCATTGCC
1 GCCTTCATTGCC
6519435 AAACCCTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 13 0.39
24 1 0.03
25 19 0.58
ACGTcount: A:0.13, C:0.30, G:0.18, T:0.38
Consensus pattern (23 bp):
GCCTTCATTGCCGACCTGTTTAG
Found at i:6523104 original size:22 final size:22
Alignment explanation
Indices: 6523079--6523120 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
6523069 TATATATTTA
* *
6523079 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
6523101 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
6523121 GGATAGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:6530503 original size:25 final size:25
Alignment explanation
Indices: 6530462--6530523 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
6530452 AAAAATAAAT
* *
6530462 TAGGA-AATCA-AGCTGCATTAATG
1 TAGGAGAATCAGATCTGCACTAATG
6530485 TAGGAGAATCAGATCTGCACTAATG
1 TAGGAGAATCAGATCTGCACTAATG
*
6530510 TAAGAGAATCAGAT
1 TAGGAGAATCAGAT
6530524 TTCTACAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 5 0.15
24 5 0.15
25 24 0.71
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (25 bp):
TAGGAGAATCAGATCTGCACTAATG
Found at i:6534672 original size:51 final size:50
Alignment explanation
Indices: 6534613--6534710 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 50
6534603 ATTTAACAAG
* *
6534613 AAATTTTAATTGTTAGATTAAATCAATTTATAAAATAACAAATAAATGCTA
1 AAATTTTAATTATTAGAGTAAATCAATTTAT-AAATAACAAATAAATGCTA
* * *
6534664 AAATTTTAATTATTGGAGTAAATCAATTTATAAGTAACAAATTAATG
1 AAATTTTAATTATTAGAGTAAATCAATTTATAAATAACAAATAAATG
6534711 ACAAAAAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 14 0.33
51 28 0.67
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (50 bp):
AAATTTTAATTATTAGAGTAAATCAATTTATAAATAACAAATAAATGCTA
Found at i:6534728 original size:50 final size:51
Alignment explanation
Indices: 6534631--6534728 Score: 119
Period size: 50 Copynumber: 1.9 Consensus size: 51
6534621 ATTGTTAGAT
* ***
6534631 TAAATCAATTTATAAAATAACAAATAAATGCTAAAATTTTAATTATTGGAG
1 TAAATCAATTTATAAAATAACAAATAAATGCAAAAAGAATAATTATTGGAG
* *
6534682 TAAATCAATTTAT-AAGTAACAAATTAATGACAAAAAGAAT-ATTATTG
1 TAAATCAATTTATAAAATAACAAATAAATG-CAAAAAGAATAATTATTG
6534729 CACATCAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 21 0.52
51 19 0.47
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (51 bp):
TAAATCAATTTATAAAATAACAAATAAATGCAAAAAGAATAATTATTGGAG
Found at i:6535612 original size:29 final size:29
Alignment explanation
Indices: 6535549--6535614 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
6535539 AGTAAATATA
*
6535549 AAAACAAATAAAAAAAGAAACAAACAAAT
1 AAAACAAATAAAAAAAGAAACAAACAAAC
* * * *
6535578 AGAACAAATAAAAATATAAA-AAGCAAAGC
1 AAAACAAATAAAAAAAGAAACAAACAAA-C
6535607 AAAACAAA
1 AAAACAAA
6535615 AGTATTGAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.76, C:0.11, G:0.06, T:0.08
Consensus pattern (29 bp):
AAAACAAATAAAAAAAGAAACAAACAAAC
Found at i:6536487 original size:19 final size:18
Alignment explanation
Indices: 6536463--6536505 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
6536453 GTATATATAA
6536463 TTTTTTATAAATTAAAATT
1 TTTTTTATAAA-TAAAATT
* *
6536482 TTTTTTTTTAATAAAATT
1 TTTTTTATAAATAAAATT
6536500 TTTTTT
1 TTTTTT
6536506 GACATTGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTATAAATAAAATT
Found at i:6536595 original size:20 final size:23
Alignment explanation
Indices: 6536554--6536600 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 23
6536544 AGTTGCAAAA
6536554 TTTTGAAATTTCATTGGTGAAT-
1 TTTTGAAATTTCATTGGTGAATC
*
6536576 TTTTGAAA-TT-ATTTGTGAATC
1 TTTTGAAATTTCATTGGTGAATC
6536597 TTTT
1 TTTT
6536601 CAATTGTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 6 0.26
22 8 0.35
ACGTcount: A:0.26, C:0.04, G:0.15, T:0.55
Consensus pattern (23 bp):
TTTTGAAATTTCATTGGTGAATC
Found at i:6537172 original size:17 final size:17
Alignment explanation
Indices: 6537152--6537191 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
6537142 AAAATTTTTA
*
6537152 TTATTTATCTTTATAAG
1 TTATTTATCTTCATAAG
*
6537169 TTATTTATCTTCATTAG
1 TTATTTATCTTCATAAG
6537186 TTATTT
1 TTATTT
6537192 TAATTTAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.62
Consensus pattern (17 bp):
TTATTTATCTTCATAAG
Found at i:6537228 original size:21 final size:21
Alignment explanation
Indices: 6537202--6537247 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
6537192 TAATTTAGTA
6537202 ATTTATTTCTTATA-TATCTTT
1 ATTTATTTCTTA-ACTATCTTT
6537223 ATTTATTTCTTAACTATCTTT
1 ATTTATTTCTTAACTATCTTT
6537244 ATTT
1 ATTT
6537248 TTTTGAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTATTTCTTAACTATCTTT
Found at i:6541287 original size:19 final size:18
Alignment explanation
Indices: 6541255--6541291 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
6541245 GATGTTAGAG
*
6541255 AATTAAAAATAAAAAATT
1 AATTAAAAAAAAAAAATT
6541273 AATTAAAAAGAAAAAAATT
1 AATTAAAAA-AAAAAAATT
6541292 TTCATTCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (18 bp):
AATTAAAAAAAAAAAATT
Found at i:6541612 original size:15 final size:15
Alignment explanation
Indices: 6541592--6541749 Score: 70
Period size: 15 Copynumber: 10.9 Consensus size: 15
6541582 AGAAAAAGTT
6541592 CTAAAATCTAAAACC
1 CTAAAATCTAAAACC
*
6541607 CTAAAATCCAAAA-C
1 CTAAAATCTAAAACC
**
6541621 CTTGAATCCCTAAAACTC
1 CTAAAAT--CTAAAAC-C
*
6541639 C--AAATCCTAAAATC
1 CTAAAAT-CTAAAACC
* *
6541653 C-AAAACCTTGAAACC
1 CTAAAATC-TAAAACC
*
6541668 CTAAAATCCAAAACC
1 CTAAAATCTAAAACC
*
6541683 TTAAAACTCTAAAA--
1 CTAAAA-TCTAAAACC
6541697 CT----TC--AAACC
1 CTAAAATCTAAAACC
* *
6541706 CCAAAATCTAAGACC
1 CTAAAATCTAAAACC
6541721 CTAAAATCTAAAACC
1 CTAAAATCTAAAACC
* *
6541736 TTAAAATCCAAAAC
1 CTAAAATCTAAAAC
6541750 TTTGAAATCC
Statistics
Matches: 106, Mismatches: 21, Indels: 32
0.67 0.13 0.20
Matches are distributed among these distances:
7 3 0.03
9 3 0.03
13 2 0.02
14 10 0.09
15 67 0.63
16 19 0.18
18 2 0.02
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.20
Consensus pattern (15 bp):
CTAAAATCTAAAACC
Found at i:6541648 original size:38 final size:37
Alignment explanation
Indices: 6541637--6541737 Score: 105
Period size: 38 Copynumber: 2.7 Consensus size: 37
6541627 TCCCTAAAAC
*
6541637 TCCAAATCCTAAAATCCAAAACCTTGAAACCCTAAAA
1 TCCAAAACCTAAAATCCAAAACCTTGAAACCCTAAAA
* * *
6541674 TCCAAAACCTTAAAACTCTAAAA-CTTCAAACCCCAAAA
1 TCCAAAACC-TAAAA-TCCAAAACCTTGAAACCCTAAAA
* * *
6541712 TCTAAGACCCTAAAATCTAAAACCTT
1 TCCAA-AACCTAAAATCCAAAACCTT
6541738 AAAATCCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
37 15 0.28
38 30 0.56
39 9 0.17
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.21
Consensus pattern (37 bp):
TCCAAAACCTAAAATCCAAAACCTTGAAACCCTAAAA
Found at i:6541652 original size:24 final size:23
Alignment explanation
Indices: 6541595--6541653 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
6541585 AAAAGTTCTA
6541595 AAAT-CTAAAA-CCCTAAAATCC
1 AAATCCTAAAATCCCTAAAATCC
* **
6541616 AAAACCTTGAATCCCTAAAACTCC
1 AAATCCTAAAATCCCTAAAA-TCC
6541640 AAATCCTAAAATCC
1 AAATCCTAAAATCC
6541654 AAAACCTTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 3 0.10
22 4 0.14
23 8 0.28
24 14 0.48
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (23 bp):
AAATCCTAAAATCCCTAAAATCC
Found at i:6541705 original size:23 final size:23
Alignment explanation
Indices: 6541644--6541696 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
6541634 AACTCCAAAT
*
6541644 CCTAAAATCCAAAACCTTGAAAC
1 CCTAAAATCCAAAACCTTAAAAC
6541667 CCTAAAATCCAAAACCTTAAAAC
1 CCTAAAATCCAAAACCTTAAAAC
*
6541690 TCTAAAA
1 CCTAAAA
6541697 CTTCAAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.51, C:0.28, G:0.02, T:0.19
Consensus pattern (23 bp):
CCTAAAATCCAAAACCTTAAAAC
Found at i:6541757 original size:15 final size:15
Alignment explanation
Indices: 6541708--6541764 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
6541698 TTCAAACCCC
* * *
6541708 AAAATCTAAGACCCT
1 AAAATCCAAAACCTT
*
6541723 AAAATCTAAAACCTT
1 AAAATCCAAAACCTT
*
6541738 AAAATCCAAAACTTT
1 AAAATCCAAAACCTT
*
6541753 GAAATCCTAAAA
1 AAAATCC-AAAA
6541765 TGAGACCTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 32 0.89
16 4 0.11
ACGTcount: A:0.53, C:0.21, G:0.04, T:0.23
Consensus pattern (15 bp):
AAAATCCAAAACCTT
Found at i:6543209 original size:60 final size:60
Alignment explanation
Indices: 6543129--6543295 Score: 202
Period size: 60 Copynumber: 2.8 Consensus size: 60
6543119 TTTTATACAA
* *
6543129 AAAAATTGATACTTTCAACTTTTCTTTAAAAATATTTTTTCTT-CAAATTTTATTTTTC-AG
1 AAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTT-TTGAAAATTTTA-TTTTCAAG
* *
6543189 AAAAATTTG-TACTTCCAACTTTTCCTCAAGAAAT-TTTTTTTTGAAAATTTTATTTTCAAG
1 AAAAA-TTGATACTTTCAACTTTTCCTTAA-AAATATTTTTTTTGAAAATTTTATTTTCAAG
* *
6543249 AAAAATTGATACTTTCAATTTTTCCTTAAAAATA--CTTTTTGAAAATT
1 AAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTGAAAATT
6543296 GATACTTTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
58 12 0.13
59 14 0.15
60 60 0.65
61 7 0.08
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.48
Consensus pattern (60 bp):
AAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTGAAAATTTTATTTTCAAG
Found at i:6543327 original size:39 final size:40
Alignment explanation
Indices: 6543250--6543334 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
6543240 ATTTTCAAGA
* * *
6543250 AAAATTGATACTTTCAATTTTTCCTTAAAAATACTTTTTG
1 AAAATTGATACTTTCAACTTTCCCTCAAAAATACTTTTTG
* *
6543290 AAAATTGATACTTTTAACTTTCCCTCAAAAATA-TTTTTT
1 AAAATTGATACTTTCAACTTTCCCTCAAAAATACTTTTTG
6543329 AAAATT
1 AAAATT
6543335 TTTATGTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 11 0.28
40 29 0.73
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.46
Consensus pattern (40 bp):
AAAATTGATACTTTCAACTTTCCCTCAAAAATACTTTTTG
Found at i:6543367 original size:58 final size:59
Alignment explanation
Indices: 6543291--6543406 Score: 155
Period size: 58 Copynumber: 2.0 Consensus size: 59
6543281 TACTTTTTGA
* * * * *
6543291 AAATTGATACTTTTAACTTTCCCT-CAAAA-ATATTTTTTAAAATTTTTATGTTTAAAGG
1 AAATTAATACATTCAACTTTCCCTGAAAAATATATTTTTTAAAATTTTCAT-TTTAAAGG
*
6543349 AAATTAATACATTCAACTTTCCTTGAAAAATATATTTTTTAAAATTTTCATTTTAAAG
1 AAATTAATACATTCAACTTTCCCTGAAAAATATATTTTTTAAAATTTTCATTTTAAAG
6543407 AGATCATTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 20 0.40
59 11 0.22
60 19 0.38
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (59 bp):
AAATTAATACATTCAACTTTCCCTGAAAAATATATTTTTTAAAATTTTCATTTTAAAGG
Found at i:6543380 original size:98 final size:101
Alignment explanation
Indices: 6543205--6543394 Score: 230
Period size: 98 Copynumber: 1.9 Consensus size: 101
6543195 TTGTACTTCC
* * * * * *
6543205 AACTTTTCCTCAAGAAATTTTTTTTTGAAAATTTTATTTTCAAGAAAAATTGATACTTTCAATTT
1 AACTTTCCCTCAAGAAATTATTTTTTGAAAATTTTATTTTAAAGAAAAATTAATACATTCAATCT
*
6543270 TTCCTTAAAAATA-CTTTTTGAAAATTGATACTTTT
66 TTCCTTAAAAATATATTTTTGAAAATTGATACTTTT
*
6543305 AACTTTCCCTCAA-AAA-TATTTTTT-AAAATTTTTATGTTTAAAG-GAAATTAATACATTCAA-
1 AACTTTCCCTCAAGAAATTATTTTTTGAAAA-TTTTAT-TTTAAAGAAAAATTAATACATTCAAT
*
6543365 CTTTCCTTGAAAAATATATTTTTTAAAATT
64 CTTTCCTT-AAAAATATATTTTTGAAAATT
6543395 TTCATTTTAA
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
97 11 0.14
98 34 0.44
99 20 0.26
100 12 0.16
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.46
Consensus pattern (101 bp):
AACTTTCCCTCAAGAAATTATTTTTTGAAAATTTTATTTTAAAGAAAAATTAATACATTCAATCT
TTCCTTAAAAATATATTTTTGAAAATTGATACTTTT
Found at i:6544089 original size:29 final size:29
Alignment explanation
Indices: 6544028--6544088 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
6544018 AAATTCATCG
6544028 AAAACTAGAATTTTTCTAGAAATTTTCCA
1 AAAACTAGAATTTTTCTAGAAATTTTCCA
* *
6544057 AAAATCTAGGATTTTT-TAG-ATTTTTCCA
1 AAAA-CTAGAATTTTTCTAGAAATTTTCCA
6544085 AAAA
1 AAAA
6544089 AAAGCCCTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 12 0.41
29 7 0.24
30 10 0.34
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.39
Consensus pattern (29 bp):
AAAACTAGAATTTTTCTAGAAATTTTCCA
Found at i:6545053 original size:20 final size:20
Alignment explanation
Indices: 6545028--6545066 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6545018 CACCAAAGAG
*
6545028 TTCAAAGCTTCTTATTTGAA
1 TTCAAAGCTTCATATTTGAA
*
6545048 TTCAAAGGTTCATATTTGA
1 TTCAAAGCTTCATATTTGA
6545067 CAAATTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (20 bp):
TTCAAAGCTTCATATTTGAA
Found at i:6545146 original size:108 final size:107
Alignment explanation
Indices: 6544986--6545249 Score: 368
Period size: 108 Copynumber: 2.4 Consensus size: 107
6544976 GTATCCACCA
* * * * * *
6544986 TTTAAAGATTCTCATTTAAACTTTGAAGA-TCACACCAAAGAGTTCAAAGCTTCTTATTTGAATT
1 TTTAAAGCTTTTCATTTGAATTTTAAAGATTCACACCAAA-AGTTCAAAGCTTCTCATTTGAATT
6545050 CAAAGGTTCATATTTGACAAATTTAGGATTCACATCCAAAAAG
65 CAAAGGTTCATATTTGACAAATTTAGGATTCACATCCAAAAAG
* *
6545093 TTTAAAGCTTTTCATTTGTATTTTAAAGATTCACATCCAAAAGTTCAAAGCTTCTCGTTTGAATT
1 TTTAAAGCTTTTCATTTGAATTTTAAAGATTCACA-CCAAAAGTTCAAAGCTTCTCATTTGAATT
*
6545158 CAAAGGTTCATATTTGACAAATTTGGGATTCACATCCAAAAAG
65 CAAAGGTTCATATTTGACAAATTTAGGATTCACATCCAAAAAG
* * ** *
6545201 TTTAAAGTTTTTTATTTGAATTTTGGAGATTCAAACCCAAAAGTTCAAA
1 TTTAAAGCTTTTCATTTGAATTTTAAAGATTCACA-CCAAAAGTTCAAA
6545250 ACTTTCCATT
Statistics
Matches: 139, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
107 23 0.17
108 111 0.80
109 5 0.04
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (107 bp):
TTTAAAGCTTTTCATTTGAATTTTAAAGATTCACACCAAAAGTTCAAAGCTTCTCATTTGAATTC
AAAGGTTCATATTTGACAAATTTAGGATTCACATCCAAAAAG
Found at i:6546638 original size:22 final size:19
Alignment explanation
Indices: 6546606--6546658 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
6546596 TCAATTTGAG
* *
6546606 TCTTTCTTT-TTTTCTTTCA
1 TCTTTCTTTCATTT-TTTCT
6546625 TCTTT-TTTCATTTTTTCT
1 TCTTTCTTTCATTTTTTCT
6546643 TCTTTCTTTCATTTTT
1 TCTTTCTTTCATTTTT
6546659 CATTTTTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 12 0.40
19 18 0.60
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (19 bp):
TCTTTCTTTCATTTTTTCT
Found at i:6546654 original size:19 final size:19
Alignment explanation
Indices: 6546606--6546745 Score: 78
Period size: 18 Copynumber: 7.3 Consensus size: 19
6546596 TCAATTTGAG
*
6546606 TCTTTCTTT-TTTTCTTTCA
1 TCTTTCTTTCATTT-TTTCA
*
6546625 TCTTT-TTTCATTTTTTCT
1 TCTTTCTTTCATTTTTTCA
6546643 TCTTTCTTTCA-TTTTTCA
1 TCTTTCTTTCATTTTTTCA
*
6546661 TTTTTCCTCTT--TTTTTTCCA
1 TCTTT-CT-TTCATTTTTT-CA
* *
6546681 TCTATT-TTTCTTTTTTCTCT
1 TCT-TTCTTTCATTTTT-TCA
* *
6546701 TTTTTTTTTC-TTTTTTCA
1 TCTTTCTTTCATTTTTTCA
**
6546719 TCTTTCTCTTTTTTTTTCTCA
1 TCTTTCT-TTCATTTTT-TCA
6546740 TCTTTC
1 TCTTTC
6546746 ATCTATTATT
Statistics
Matches: 96, Mismatches: 11, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
18 31 0.32
19 30 0.31
20 23 0.24
21 12 0.12
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (19 bp):
TCTTTCTTTCATTTTTTCA
Found at i:6546664 original size:26 final size:24
Alignment explanation
Indices: 6546612--6546665 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 24
6546602 TGAGTCTTTC
*
6546612 TTTTTTTCTTTCATCTTTTTTCAT
1 TTTTTTTCTTTCATCATTTTTCAT
*
6546636 TTTTTCTTCTTTCTTTCATTTTTCAT
1 TTTTT-TTCTTTC-ATCATTTTTCAT
6546662 TTTT
1 TTTT
6546666 CCTCTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 5 0.19
25 7 0.27
26 14 0.54
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTTTCTTTCATCATTTTTCAT
Found at i:6546697 original size:7 final size:7
Alignment explanation
Indices: 6546608--6546732 Score: 62
Period size: 7 Copynumber: 17.4 Consensus size: 7
6546598 AATTTGAGTC
6546608 TTTCTTTT
1 TTTC-TTT
6546616 TTTCTTT
1 TTTCTTT
**
6546623 CATCTTT
1 TTTCTTT
6546630 TTTCATTT
1 TTTC-TTT
*
6546638 TTTCTTC
1 TTTCTTT
6546645 TTTC---
1 TTTCTTT
*
6546649 TTTCATT
1 TTTCTTT
6546656 TTTCATTT
1 TTTC-TTT
6546664 TTCCTCTTT
1 TT--TCTTT
*
6546673 TTT-TTC
1 TTTCTTT
**
6546679 CATCTATT
1 TTTCT-TT
6546687 TTTCTTT
1 TTTCTTT
*
6546694 TTTCTCT
1 TTTCTTT
6546701 TTT-TTT
1 TTTCTTT
6546707 TTTCTTT
1 TTTCTTT
6546714 TTTCATCTT
1 TTTC-T-TT
*
6546723 TCTCTTT
1 TTTCTTT
6546730 TTT
1 TTT
6546733 TTTCTCATCT
Statistics
Matches: 89, Mismatches: 16, Indels: 25
0.68 0.12 0.19
Matches are distributed among these distances:
4 4 0.04
6 8 0.09
7 44 0.49
8 21 0.24
9 10 0.11
10 2 0.02
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTCTTT
Found at i:6546701 original size:30 final size:28
Alignment explanation
Indices: 6546667--6546734 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
6546657 TTCATTTTTC
6546667 CTCTTTTTTTTCCATCTATTTTTCTTTTTT
1 CTCTTTTTTTT--ATCTATTTTTCTTTTTT
* * *
6546697 CTCTTTTTTTTTTCT-TTTTTCATCTTT
1 CTCTTTTTTTTATCTATTTTTCTTTTTT
6546724 CTCTTTTTTTT
1 CTCTTTTTTTT
6546735 TCTCATCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.60
28 3 0.09
30 11 0.31
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.76
Consensus pattern (28 bp):
CTCTTTTTTTTATCTATTTTTCTTTTTT
Found at i:6546735 original size:21 final size:22
Alignment explanation
Indices: 6546685--6546745 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
6546675 TTTCCATCTA
*
6546685 TTTTTCTTTTTTC-TCTTT-TT
1 TTTTTCTTTTTTCATCTTTCTC
6546705 TTTTTCTTTTTTCATCTTTCTC
1 TTTTTCTTTTTTCATCTTTCTC
*
6546727 TTTTT-TTTTCTCATCTTTC
1 TTTTTCTTTTTTCATCTTTC
6546746 ATCTATTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 13 0.35
21 18 0.49
22 6 0.16
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTCTTTTTTCATCTTTCTC
Found at i:6546735 original size:58 final size:56
Alignment explanation
Indices: 6546606--6546744 Score: 167
Period size: 58 Copynumber: 2.4 Consensus size: 56
6546596 TCAATTTGAG
6546606 TCTTTCT-TTTTTTCTTT-CATCTTTTTTCATTTTTTCTTCTTTCTTTCATTTTTCA
1 TCTTTCTCTTTTTT-TTTCCATCTTTTTTCATTTTTTCTTCTTTCTTTCATTTTTCA
* * * * *
6546661 TTTTTC-CTCTTTTTTTTCCATCTATTTTTCTTTTTTCTCTTTTTTTTTTCTTTTTTCA
1 TCTTTCTCT-TTTTTTTTCCATCT-TTTTTCATTTTT-TCTTCTTTCTTTCATTTTTCA
6546719 TCTTTCTCTTTTTTTTTCTCATCTTT
1 TCTTTCTCTTTTTTTTTC-CATCTTT
6546745 CATCTATTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
55 9 0.13
56 10 0.14
57 11 0.15
58 34 0.48
59 7 0.10
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (56 bp):
TCTTTCTCTTTTTTTTTCCATCTTTTTTCATTTTTTCTTCTTTCTTTCATTTTTCA
Found at i:6547121 original size:5 final size:5
Alignment explanation
Indices: 6547104--6547146 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
6547094 TGGCATTCAT
*
6547104 TTTTC TTTT- TTTTC TTTTC TTTAT- TTTGC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTT-TC TTTTC TTTTC TTTTC TTTT
6547147 TGCTTTCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 4 0.12
5 28 0.85
6 1 0.03
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:6547689 original size:22 final size:23
Alignment explanation
Indices: 6547664--6547707 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6547654 GTGAAATCCT
6547664 ATTGC-ATAAAAGAAATCCTAAC
1 ATTGCTATAAAAGAAATCCTAAC
* *
6547686 ATTGCTCTAAAAGAAATTCTAA
1 ATTGCTATAAAAGAAATCCTAA
6547708 AATGGCAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (23 bp):
ATTGCTATAAAAGAAATCCTAAC
Found at i:6550624 original size:14 final size:14
Alignment explanation
Indices: 6550605--6550631 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6550595 TAGACTAAAA
6550605 GCTATTCTTTTAGG
1 GCTATTCTTTTAGG
6550619 GCTATTCTTTTAG
1 GCTATTCTTTTAG
6550632 AGACTCTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.52
Consensus pattern (14 bp):
GCTATTCTTTTAGG
Found at i:6552300 original size:16 final size:16
Alignment explanation
Indices: 6552260--6552302 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
6552250 TTGTTCTTTC
* *
6552260 AAAATTTTTGATTTTT
1 AAAATTTTTAATTTAT
6552276 AAAATTTTTTAATTTAT
1 AAAA-TTTTTAATTTAT
*
6552293 ATAATTTTTA
1 AAAATTTTTA
6552303 CAAATAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
AAAATTTTTAATTTAT
Found at i:6564773 original size:46 final size:46
Alignment explanation
Indices: 6564678--6564774 Score: 124
Period size: 46 Copynumber: 2.1 Consensus size: 46
6564668 TGTCAATGTC
* * * *
6564678 CTTTTATTGATAAAATATCTACTATAAATTATTTTGGAGCATAATG
1 CTTTTATTGATAAAACATCGACTAGAAATTATTTTGGAACATAATG
* *
6564724 CTTTTATTGATAAAGCATCGACTAGAAATTATTTTTGAACAT-ATAG
1 CTTTTATTGATAAAACATCGACTAGAAATTATTTTGGAACATAAT-G
6564770 CTTTT
1 CTTTT
6564775 GTTAATTCCT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
45 2 0.05
46 42 0.95
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.43
Consensus pattern (46 bp):
CTTTTATTGATAAAACATCGACTAGAAATTATTTTGGAACATAATG
Found at i:6569877 original size:128 final size:130
Alignment explanation
Indices: 6569605--6569999 Score: 627
Period size: 128 Copynumber: 3.0 Consensus size: 130
6569595 GGCCATATAG
*
6569605 AAATAATAAGTACAAGTAAGAC--ATTCAATATTCAAGTATATTCAAGAAATCATAAAAGAATAT
1 AAATAATAAGTACAAGTAAAACATATTCAATATTCAAGTATATTCAAGAAATCATAAAAGAATAT
* *
6569668 AGAAATACCAATTTTAGGCCTTAAAATTTGTACGATCAAAATATATATATATATATATATATTAT
66 AGAAATACCAATTTTAGGCCTTAAAATTTGTACGATC-----A-A-AGA-ATATATATATATCAT
6569733 CCAAATAT
123 CCAAATAT
*
6569741 AAATAATAAGTACAAGTAAGACATATTCAATATTCAAGTATATTCAAGAAATCATAAAAGAATAT
1 AAATAATAAGTACAAGTAAAACATATTCAATATTCAAGTATATTCAAGAAATCATAAAAGAATAT
*
6569806 AGAAATACCAATTTTAGGCCTTAAAATTTGTACGATC-AA-AATATATATATATCATCTAAATAT
66 AGAAATACCAATTTTAGGCCTTAAAATTTGTACGATCAAAGAATATATATATATCATCCAAATAT
6569869 AAATAATAAGTACAAGTAAAACATATTCAATATTCAAGTATATTCAAGAAATCATAAAAGAATAT
1 AAATAATAAGTACAAGTAAAACATATTCAATATTCAAGTATATTCAAGAAATCATAAAAGAATAT
* *
6569934 AGAAATACCAATTTTAGGCCTTAAAATTTGTATGATCAAAGAAGATATATATATCATCCAAATAT
66 AGAAATACCAATTTTAGGCCTTAAAATTTGTACGATCAAAGAATATATATATATCATCCAAATAT
6569999 A
1 A
6570000 TTCAAGAATA
Statistics
Matches: 249, Mismatches: 6, Indels: 14
0.93 0.02 0.05
Matches are distributed among these distances:
128 121 0.49
129 3 0.01
130 24 0.10
131 1 0.00
136 22 0.09
138 78 0.31
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.31
Consensus pattern (130 bp):
AAATAATAAGTACAAGTAAAACATATTCAATATTCAAGTATATTCAAGAAATCATAAAAGAATAT
AGAAATACCAATTTTAGGCCTTAAAATTTGTACGATCAAAGAATATATATATATCATCCAAATAT
Found at i:6571256 original size:25 final size:24
Alignment explanation
Indices: 6571222--6571290 Score: 63
Period size: 25 Copynumber: 2.9 Consensus size: 24
6571212 AATGATATTC
6571222 TGATAATATTCTAGATTAATTTCAA
1 TGAT-ATATTCTAGATTAATTTCAA
* *
6571247 TGATATTATTCCAG-TAATATTTCAA
1 TGATA-TATTCTAGATTA-ATTTCAA
*
6571272 T-A-ATATTCTAGATTGATTT
1 TGATATATTCTAGATTAATTT
6571291 GATATTGATT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
22 11 0.31
23 2 0.06
24 4 0.11
25 19 0.53
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (24 bp):
TGATATATTCTAGATTAATTTCAA
Found at i:6571340 original size:22 final size:22
Alignment explanation
Indices: 6571287--6571340 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
6571277 TTCTAGATTG
6571287 ATTTGATATTGATTTAGAGAAT
1 ATTTGATATTGATTTAGAGAAT
* * *
6571309 ATTAGGTATTGATTTAG-TAAT
1 ATTTGATATTGATTTAGAGAAT
6571330 ATTCTGATATT
1 ATT-TGATATT
6571341 ATTCTATACT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (22 bp):
ATTTGATATTGATTTAGAGAAT
Found at i:6571413 original size:112 final size:112
Alignment explanation
Indices: 6571216--6571430 Score: 297
Period size: 112 Copynumber: 1.9 Consensus size: 112
6571206 ATGGTAAATG
* *
6571216 ATATTCTGATAATATTCTAGATTAATTTCAATGATATTATTCCAGTAATATTTCAATAATATTCT
1 ATATTCTGATAATATTCTAGACTAATTTCAATGATATTATTCCAATAATATTTCAATAATATTCT
* * * *
6571281 AGATTGATTTGATATTGATTTAGAGAATATTAGGTATTGATTTAGTA
66 AAATGGATTTGATATTGATTTAAAGAATATTAGATATTGATTTAGTA
* * * * *
6571328 ATATTCTGATATTATTCTATACTGATTTCAATGGTATTATTCTAATAATA-TTCAAGTAATATTC
1 ATATTCTGATAATATTCTAGACTAATTTCAATGATATTATTCCAATAATATTTCAA-TAATATTC
* *
6571392 TAAATGGATTTGCTATTGATTTAAAGAATTTTAGATATT
65 TAAATGGATTTGATATTGATTTAAAGAATATTAGATATT
6571431 AACTAATTAT
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
111 5 0.06
112 84 0.94
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (112 bp):
ATATTCTGATAATATTCTAGACTAATTTCAATGATATTATTCCAATAATATTTCAATAATATTCT
AAATGGATTTGATATTGATTTAAAGAATATTAGATATTGATTTAGTA
Found at i:6579107 original size:15 final size:15
Alignment explanation
Indices: 6579087--6579125 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
6579077 AAGTTTTTTA
6579087 TTCTTG-ATGAAGAGT
1 TTCTTGCAT-AAGAGT
6579102 TTCTTGCATAAGAGT
1 TTCTTGCATAAGAGT
6579117 TTCTTGCAT
1 TTCTTGCAT
6579126 TTGAAGCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 21 0.91
16 2 0.09
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.44
Consensus pattern (15 bp):
TTCTTGCATAAGAGT
Found at i:6580067 original size:17 final size:17
Alignment explanation
Indices: 6580045--6580108 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
6580035 AAAAGCTTGA
6580045 AAATTTAAATAAGCATT
1 AAATTTAAATAAGCATT
* *
6580062 AAATTTAAAT-TGCATGA
1 AAATTTAAATAAGCAT-T
*
6580079 AAATTTAAATTA-CA-T
1 AAATTTAAATAAGCATT
*
6580094 AAATGTAAA-AAGCAT
1 AAATTTAAATAAGCAT
6580109 AAAAAATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
14 1 0.03
15 10 0.27
16 4 0.11
17 22 0.59
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (17 bp):
AAATTTAAATAAGCATT
Found at i:6580124 original size:16 final size:16
Alignment explanation
Indices: 6580099--6580129 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6580089 TACATAAATG
6580099 TAAAAAGCATAAAAAA
1 TAAAAAGCATAAAAAA
*
6580115 TAAAATGCATAAAAA
1 TAAAAAGCATAAAAA
6580130 GGTAAATGAG
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:0.71, C:0.06, G:0.06, T:0.16
Consensus pattern (16 bp):
TAAAAAGCATAAAAAA
Found at i:6583863 original size:110 final size:112
Alignment explanation
Indices: 6583720--6583933 Score: 342
Period size: 110 Copynumber: 1.9 Consensus size: 112
6583710 GATATTCTGA
* *
6583720 TAATATTGTGGTAATATTCTATATTGATTTCAATGATATTATTCTAGTGATATTCCAATAATATT
1 TAATATTGTGGTAATATTCTATATTGATTTCAATGATATTATTCTAGTAATATTCCAATAATAAT
* * *
6583785 CTAGTTTGATTTTATATTGA-TTAGAGAATATT-GATATCGATTTAG
66 CTAGATTGATTTGATATTGATTTAAAGAATATTAGATATCGATTTAG
* * *
6583830 TAATATTTTGGTAATATTTTATATTGATTTCAATGATATTATTCTAGTAATATTTCAATAATAAT
1 TAATATTGTGGTAATATTCTATATTGATTTCAATGATATTATTCTAGTAATATTCCAATAATAAT
6583895 CTAGATTGATTTGATATTGATTTAAAGAATATTAGATAT
66 CTAGATTGATTTGATATTGATTTAAAGAATATTAGATAT
6583934 TAATTTACCT
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
110 78 0.83
111 11 0.12
112 5 0.05
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.48
Consensus pattern (112 bp):
TAATATTGTGGTAATATTCTATATTGATTTCAATGATATTATTCTAGTAATATTCCAATAATAAT
CTAGATTGATTTGATATTGATTTAAAGAATATTAGATATCGATTTAG
Found at i:6588941 original size:22 final size:22
Alignment explanation
Indices: 6588916--6588957 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6588906 TTTATTAAAG
6588916 ATTATATCAATTTT-AATTTTCA
1 ATTAT-TCAATTTTGAATTTTCA
*
6588938 ATTATTGAATTTTGAATTTT
1 ATTATTCAATTTTGAATTTT
6588958 GATAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (22 bp):
ATTATTCAATTTTGAATTTTCA
Found at i:6588950 original size:15 final size:14
Alignment explanation
Indices: 6588922--6588959 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
6588912 AAAGATTATA
6588922 TCAATTTT-AATTT
1 TCAATTTTGAATTT
6588935 TCAATTATTGAATTT
1 TCAATT-TTGAATTT
*
6588950 TGAATTTTGA
1 TCAATTTTGA
6588960 TAAAATTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 6 0.27
14 6 0.27
15 10 0.45
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (14 bp):
TCAATTTTGAATTT
Found at i:6589039 original size:10 final size:11
Alignment explanation
Indices: 6589024--6589057 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
6589014 GGACATAAAT
6589024 TTCATGCAA-A
1 TTCATGCAAGA
6589034 TTCATGCAAGA
1 TTCATGCAAGA
*
6589045 TCCATGCAAGA
1 TTCATGCAAGA
6589056 TT
1 TT
6589058 AGGACAAGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (11 bp):
TTCATGCAAGA
Found at i:6592922 original size:82 final size:84
Alignment explanation
Indices: 6592827--6592991 Score: 228
Period size: 85 Copynumber: 2.0 Consensus size: 84
6592817 TCCTATCTCT
* * * *
6592827 AATAGTTCGTTGGTGAGTTTAG-T-ATGTG-TGCCAAAAAAAGGTAGAATGATAATGGTTACCAA
1 AATAGTTCATTGGTGAGTCTAGTTAATATGTTG-CAAAAAAAGGTAGAATGATAATGGTCACCAA
6592889 TGACATAAGGAATTGATTGC
65 TGACATAAGGAATTGATTGC
* **
6592909 AATAGTTCATTGGTGAGTCTAGTTCAATATGTTGTAAAAAAAGGTAGAATGATGGTGGTCACCAA
1 AATAGTTCATTGGTGAGTCTAGTT-AATATGTTGCAAAAAAAGGTAGAATGATAATGGTCACCAA
6592974 TGACATAAGGAATTGATT
65 TGACATAAGGAATTGATT
6592992 ACAACAAGAA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
82 20 0.28
83 1 0.01
85 49 0.68
86 2 0.03
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (84 bp):
AATAGTTCATTGGTGAGTCTAGTTAATATGTTGCAAAAAAAGGTAGAATGATAATGGTCACCAAT
GACATAAGGAATTGATTGC
Found at i:6595746 original size:63 final size:63
Alignment explanation
Indices: 6595638--6595892 Score: 300
Period size: 63 Copynumber: 4.0 Consensus size: 63
6595628 TATAAGGTAT
* * *
6595638 AAATATAAAA-GTATTATTTAAGGTATTTTTTATACAAAAATGCCTTAAATAATCCATTTATAA
1 AAATATAAAATG-ATTATTTAAAGTATTTTCTATACAAAAACGCCTTAAATAATCCATTTATAA
** * *
6595701 AAATATAAAATGATTATTTAAAGCGTTTTCTATATAGAAACGCCTTAAATAATCCATTTATAA
1 AAATATAAAATGATTATTTAAAGTATTTTCTATACAAAAACGCCTTAAATAATCCATTTATAA
* * * * *
6595764 AAATATAAAATAATTATTT-AAGGAGTTTTCTATATAGAAACGCCTTAAATAATTCATTTTATAA
1 AAATATAAAATGATTATTTAAAGTA-TTTTCTATACAAAAACGCCTTAAATAATCCA-TTTATAA
* * * * *
6595828 AAATATAAAAGGATTATTT-AAGATATTTTTTATACAAAAATGCCTTAAATAATCCTTTTACAA
1 AAATATAAAATGATTATTTAAAG-TATTTTCTATACAAAAACGCCTTAAATAATCCATTTATAA
6595891 AA
1 AA
6595893 GTATTAACCT
Statistics
Matches: 167, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
62 3 0.02
63 110 0.66
64 53 0.32
65 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (63 bp):
AAATATAAAATGATTATTTAAAGTATTTTCTATACAAAAACGCCTTAAATAATCCATTTATAA
Found at i:6596056 original size:49 final size:50
Alignment explanation
Indices: 6595976--6596073 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 50
6595966 TTTTATAAAA
6595976 AGATTATTTAAGGCATTTTTACAAAAAAAAAG-TCTTAAATAAT-CTTTTG
1 AGATTATTTAAGGCATTTTTACAAAAAAAAAGCT-TTAAATAATCCTTTTG
*** *
6596025 AGATTATTTAAGGCATTTTCTA-TGTAGAAAAGCTTTAAATAATCCTTTT
1 AGATTATTTAAGGCATTTT-TACAAAAAAAAAGCTTTAAATAATCCTTTT
6596074 ATACAAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
49 34 0.81
50 8 0.19
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (50 bp):
AGATTATTTAAGGCATTTTTACAAAAAAAAAGCTTTAAATAATCCTTTTG
Found at i:6596126 original size:63 final size:63
Alignment explanation
Indices: 6596026--6596158 Score: 187
Period size: 63 Copynumber: 2.1 Consensus size: 63
6596016 AATCTTTTGA
* ** * * * *
6596026 GATTATTTAAGGCATTTTCTATGTAGAAAAGCTTTAAATAATCCTTTTATACAAATATAAATG
1 GATTATTGAAGGCATTTTCTATACAGAAAAGCCTTAAATAATCCATTTATAAAAATATAAAAG
6596089 GATTATTGAAGGCATTTTCTATACA-AAAATGCCTTAAATAATCCATTTATAAAAATATAAAAG
1 GATTATTGAAGGCATTTTCTATACAGAAAA-GCCTTAAATAATCCATTTATAAAAATATAAAAG
6596152 GATTATT
1 GATTATT
6596159 TAGGGTAATT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 4 0.06
63 58 0.94
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.38
Consensus pattern (63 bp):
GATTATTGAAGGCATTTTCTATACAGAAAAGCCTTAAATAATCCATTTATAAAAATATAAAAG
Found at i:6600907 original size:18 final size:19
Alignment explanation
Indices: 6600867--6600902 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6600857 ATTAAAGTAT
6600867 ATAAATA-ATTTTAAATTG
1 ATAAATATATTTTAAATTG
*
6600885 ATAAATATATTTTGAATT
1 ATAAATATATTTTAAATT
6600903 TTAAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (19 bp):
ATAAATATATTTTAAATTG
Found at i:6611308 original size:29 final size:29
Alignment explanation
Indices: 6611275--6611334 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
6611265 ACAATTACAT
*
6611275 TAACATGTTACTTGATTGAACTTAGCAAA
1 TAACATGTTACTTGATTGAACTTAACAAA
*
6611304 TAACATTTTACTTGATTGAACTTAACAAA
1 TAACATGTTACTTGATTGAACTTAACAAA
6611333 TA
1 TA
6611335 TATATAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (29 bp):
TAACATGTTACTTGATTGAACTTAACAAA
Found at i:6614017 original size:15 final size:15
Alignment explanation
Indices: 6613997--6614028 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6613987 ATACAAACAA
*
6613997 AAATAAATAAAGAAT
1 AAATAAATAAAAAAT
6614012 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
6614027 AA
1 AA
6614029 TGGACCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
AAATAAATAAAAAAT
Found at i:6618145 original size:30 final size:29
Alignment explanation
Indices: 6618072--6618161 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 29
6618062 TATCAACTTA
*
6618072 TTTTAATCTTTAATTT-TCATTTAAATAAAT
1 TTTTAAT-TTTAATTTAT-ATCTAAATAAAT
* *
6618102 TATTAGTTATTAATTTATATCTAAATAAAT
1 TTTTAATT-TTAATTTATATCTAAATAAAT
6618132 TTTTAAATTTTAATTTATATCTAAATAAAT
1 TTTT-AATTTTAATTTATATCTAAATAAAT
6618162 ACTTAATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
29 1 0.02
30 47 0.90
31 4 0.08
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (29 bp):
TTTTAATTTTAATTTATATCTAAATAAAT
Found at i:6621786 original size:19 final size:18
Alignment explanation
Indices: 6621764--6621806 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
6621754 ATCTAATTCT
*
6621764 AAAAAATAAATCAAACAAA
1 AAAAAATAAAGCAAA-AAA
* *
6621783 AAAAATTACAGCAAAAAA
1 AAAAAATAAAGCAAAAAA
6621801 AAAAAA
1 AAAAAA
6621807 GGTAAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.79, C:0.09, G:0.02, T:0.09
Consensus pattern (18 bp):
AAAAAATAAAGCAAAAAA
Found at i:6621817 original size:13 final size:13
Alignment explanation
Indices: 6621801--6621828 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6621791 CAGCAAAAAA
6621801 AAAAAAGGTAAAT
1 AAAAAAGGTAAAT
6621814 AAAAAAGGTAAAT
1 AAAAAAGGTAAAT
6621827 AA
1 AA
6621829 CACTAAGTGA
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:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAAAAGGTAAAT
Found at i:6621999 original size:6 final size:6
Alignment explanation
Indices: 6621986--6622036 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
6621976 TCATGCATTC
* * * *
6621986 ATATAT ACATAT ACATAC ATACAT ATATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
6622034 ATA
1 ATA
6622037 ACATCCAAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (6 bp):
ATATAT
Found at i:6622015 original size:4 final size:4
Alignment explanation
Indices: 6621986--6622036 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
6621976 TCATGCATTC
* * * *
6621986 ATAT ATAC ATAT ACAT ACAT ACAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
6622034 ATA
1 ATA
6622037 ACATCCAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (4 bp):
ATAT
Found at i:6625236 original size:170 final size:170
Alignment explanation
Indices: 6624954--6625283 Score: 633
Period size: 170 Copynumber: 1.9 Consensus size: 170
6624944 TAAAGACTTA
*
6624954 TCGGAAATCCATTTTTGAGAAGACTTAAAGCTTTTCGGAAATCAAAAAGCCTAAAGGTTTCTCAA
1 TCGGAAATCCATTTCTGAGAAGACTTAAAGCTTTTCGGAAATCAAAAAGCCTAAAGGTTTCTCAA
* *
6625019 AAATCCATTATCGAAAATCCTTAAAGTTTCTTGAAAATTCAAAAACCTAAAGGCTTCTCCAAAAT
66 AAATCCATTAACGAAAATCATTAAAGTTTCTTGAAAATTCAAAAACCTAAAGGCTTCTCCAAAAT
6625084 AGATTTCCAAGAAACCCTAAAACTAGGCTTTTTAAGCTTC
131 AGATTTCCAAGAAACCCTAAAACTAGGCTTTTTAAGCTTC
6625124 TCGGAAATCCATTTCTGAGAAGACTTAAAGCTTTTCGGAAATCAAAAAGCCTAAAGGTTTCTCAA
1 TCGGAAATCCATTTCTGAGAAGACTTAAAGCTTTTCGGAAATCAAAAAGCCTAAAGGTTTCTCAA
6625189 AAATCCATTAACGAAAATCATTAAAGTTTCTTGAAAATTCAAAAACCTAAAGGCTTCTCCAAAAT
66 AAATCCATTAACGAAAATCATTAAAGTTTCTTGAAAATTCAAAAACCTAAAGGCTTCTCCAAAAT
6625254 AGATTTCCAAGAAACCCTAAAACTAGGCTT
131 AGATTTCCAAGAAACCCTAAAACTAGGCTT
6625284 CTCGGAAATT
Statistics
Matches: 157, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
170 157 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (170 bp):
TCGGAAATCCATTTCTGAGAAGACTTAAAGCTTTTCGGAAATCAAAAAGCCTAAAGGTTTCTCAA
AAATCCATTAACGAAAATCATTAAAGTTTCTTGAAAATTCAAAAACCTAAAGGCTTCTCCAAAAT
AGATTTCCAAGAAACCCTAAAACTAGGCTTTTTAAGCTTC
Found at i:6627815 original size:3 final size:3
Alignment explanation
Indices: 6627809--6627855 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
6627799 ACATAAATGC
6627809 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6627856 TGCTAGTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6628574 original size:21 final size:22
Alignment explanation
Indices: 6628550--6628606 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
6628540 CATAATTTTT
6628550 ATTTTGATAACCTTT-AATGA-A
1 ATTTTGATAACCTTTCAAT-ATA
6628571 ATTTTGATAA-CTTTCAATATA
1 ATTTTGATAACCTTTCAATATA
* *
6628592 ATTTTGGTATCCTTT
1 ATTTTGATAACCTTT
6628607 GATACTAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 5 0.16
21 22 0.71
22 4 0.13
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (22 bp):
ATTTTGATAACCTTTCAATATA
Found at i:6628639 original size:21 final size:21
Alignment explanation
Indices: 6628587--6628639 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
6628577 ATAACTTTCA
*
6628587 ATATAATTTTGGTATCCTTTG
1 ATATAATTTTGCTATCCTTTG
*
6628608 ATACT-AGTTTGCTA-CCTTATG
1 ATA-TAATTTTGCTATCCTT-TG
6628629 ATATAATTTTG
1 ATATAATTTTG
6628640 ATAACTATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 5 0.19
21 20 0.77
22 1 0.04
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.49
Consensus pattern (21 bp):
ATATAATTTTGCTATCCTTTG
Found at i:6629191 original size:22 final size:22
Alignment explanation
Indices: 6629106--6629255 Score: 119
Period size: 22 Copynumber: 6.9 Consensus size: 22
6629096 AAATTAGTAT
6629106 TGATTTACTACTAAATTATAAA
1 TGATTTACTACTAAATTATAAA
* *
6629128 TTATTTACTACTAAGTTATAAA
1 TGATTTACTACTAAATTATAAA
* * *
6629150 TAATTTACTATTAAATTATTAA
1 TGATTTACTACTAAATTATAAA
* **
6629172 TGATTTACTACTAAGTTATTGA
1 TGATTTACTACTAAATTATAAA
** *
6629194 TGATTTGTTA-TAAAATTATAAT
1 TGATTTACTACT-AAATTATAAA
* * *
6629216 TGA-TTACCA-TTAATCTATCAA
1 TGATTTACTACTAAAT-TATAAA
6629237 TGATTTACTA-TAAAATTAT
1 TGATTTACTACT-AAATTAT
6629256 TAATAATTAA
Statistics
Matches: 100, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
20 3 0.03
21 12 0.12
22 82 0.82
23 3 0.03
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (22 bp):
TGATTTACTACTAAATTATAAA
Found at i:6629210 original size:44 final size:44
Alignment explanation
Indices: 6629106--6629268 Score: 154
Period size: 44 Copynumber: 3.7 Consensus size: 44
6629096 AAATTAGTAT
* *
6629106 TGATTTACTACT-AAATTATAAATTATTTACTACTAAGTTATAAA
1 TGATTTACTA-TAAAATTATTAATGATTTACTACTAAGTTATAAA
* * **
6629150 TAATTTACTATTAAATTATTAATGATTTACTACTAAGTTATTGA
1 TGATTTACTATAAAATTATTAATGATTTACTACTAAGTTATAAA
** * * *
6629194 TGATTTGTTATAAAATTA-TAATTGA-TTACCATTAA-TCTATCAA
1 TGATTTACTATAAAATTATTAA-TGATTTACTACTAAGT-TATAAA
* *
6629237 TGATTTACTATAAAATTATTAATAATTAACTA
1 TGATTTACTATAAAATTATTAATGATTTACTA
6629269 ATTTACTACT
Statistics
Matches: 96, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
42 1 0.01
43 34 0.35
44 61 0.64
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (44 bp):
TGATTTACTATAAAATTATTAATGATTTACTACTAAGTTATAAA
Found at i:6629338 original size:22 final size:22
Alignment explanation
Indices: 6629267--6629367 Score: 80
Period size: 22 Copynumber: 4.6 Consensus size: 22
6629257 AATAATTAAC
* **
6629267 TAATTTACTACTAAATTATCGT
1 TAATTTACTATTAAATTATCAA
* * *
6629289 TGATTTA-TAATTAAATTATTAG
1 TAATTTACT-ATTAAATTATCAA
* * * *
6629311 TGATTTTCTATTGAGTTATCAA
1 TAATTTACTATTAAATTATCAA
6629333 TAATTTAC-ATCTAAATTATCAA
1 TAATTTACTAT-TAAATTATCAA
6629355 TAATTTACTATTA
1 TAATTTACTATTA
6629368 TGTTATGATT
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
21 3 0.05
22 55 0.90
23 3 0.05
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.48
Consensus pattern (22 bp):
TAATTTACTATTAAATTATCAA
Found at i:6631308 original size:140 final size:140
Alignment explanation
Indices: 6631056--6631323 Score: 457
Period size: 140 Copynumber: 1.9 Consensus size: 140
6631046 AAGCAGGTCA
* ** * * *
6631056 GGTGCATGGGTTTCGGGTTTGGCTGTGAATTGGTATGCTAATCTTCAAGTCAACACATCATTTTG
1 GGTGCATGAGTTTCGGGTTTGGCTGCAAATTGATATACTAATCTTCAAGTCAACACATCATTTTA
*
6631121 TTTTTTTTTATATAAAATAACTTTTTTCAAATAATTTCATCCCTTTTTACTAAAAAAAAAAAACC
66 TTTTTTTATATATAAAATAACTTTTTTCAAATAATTTCATCCCTTTTTACTAAAAAAAAAAAACC
6631186 TTTCAAGTCT
131 TTTCAAGTCT
6631196 GGTGCATGAGTTTCGGGTTTGGCTGCAAATTGATATACTAATCTTCAAGTCAACACATCATTTTA
1 GGTGCATGAGTTTCGGGTTTGGCTGCAAATTGATATACTAATCTTCAAGTCAACACATCATTTTA
6631261 TTTTTTTATATA-AAAATAACTTTCTTTCAAATAATTTCATCCCTTTTTACTAAAAAAAAAAAA
66 TTTTTTTATATATAAAATAACTTT-TTTCAAATAATTTCATCCCTTTTTACTAAAAAAAAAAAA
6631324 ACCACCCTTC
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
139 11 0.09
140 109 0.91
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (140 bp):
GGTGCATGAGTTTCGGGTTTGGCTGCAAATTGATATACTAATCTTCAAGTCAACACATCATTTTA
TTTTTTTATATATAAAATAACTTTTTTCAAATAATTTCATCCCTTTTTACTAAAAAAAAAAAACC
TTTCAAGTCT
Found at i:6633171 original size:66 final size:66
Alignment explanation
Indices: 6633032--6633210 Score: 170
Period size: 67 Copynumber: 2.7 Consensus size: 66
6633022 GATTTTTTTA
** * *
6633032 GCTTTCTTTACCTTTTTGTTTTCTTCAA-TTTAAAAGTAATATTTATCTATTAATTGTATTTTCT
1 GCTTT-TTTACCTTTTCATTTTCTTCAATTTTAAAAATAATATTTATCTATTAATTGTATTATCT
6633096 TG
65 TG
*
6633098 GATTTTTTTACCTTTTCATTTTCTTCAATTTTAAAAATAATATTTAT-TAATTAATTGTGCA-TA
1 G-CTTTTTTACCTTTTCATTTTCTTCAATTTTAAAAATAATATTTATCT-ATTAATTGT--ATTA
6633161 T-TTG
62 TCTTG
* * * *
6633165 GCTTTTTTTTATCTTTTTGA-TTTCTTCACTTTTAAATATAATATTT
1 GC--TTTTTTA-CCTTTTCATTTTCTTCAATTTTAAAAATAATATTT
6633211 TATTTATTTA
Statistics
Matches: 95, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
66 22 0.23
67 33 0.35
68 33 0.35
69 7 0.07
ACGTcount: A:0.25, C:0.11, G:0.06, T:0.58
Consensus pattern (66 bp):
GCTTTTTTACCTTTTCATTTTCTTCAATTTTAAAAATAATATTTATCTATTAATTGTATTATCTT
G
Found at i:6633171 original size:67 final size:67
Alignment explanation
Indices: 6633032--6633210 Score: 188
Period size: 68 Copynumber: 2.7 Consensus size: 67
6633022 GATTTTTTTA
* ** * *
6633032 GCTTTCTTTACCTTTTTGTTTTCTTCAA-TTTAAAAGTAATATTTATCTATTAATTGTATTTTCT
1 GCTTTTTTTACCTTTTCATTTTCTTCAATTTTAAAAATAATATTTATCTATTAATTGTATTATCT
6633096 TG
66 TG
*
6633098 GATTTTTTTACCTTTTCATTTTCTTCAATTTTAAAAATAATATTTAT-TAATTAATTGTGCA-TA
1 GCTTTTTTTACCTTTTCATTTTCTTCAATTTTAAAAATAATATTTATCT-ATTAATTGT--ATTA
6633161 T-TTG
63 TCTTG
* * * *
6633165 GCTTTTTTTTATCTTTTTGA-TTTCTTCACTTTTAAATATAATATTT
1 GC-TTTTTTTA-CCTTTTCATTTTCTTCAATTTTAAAAATAATATTT
6633211 TATTTATTTA
Statistics
Matches: 96, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
66 25 0.26
67 30 0.31
68 34 0.35
69 7 0.07
ACGTcount: A:0.25, C:0.11, G:0.06, T:0.58
Consensus pattern (67 bp):
GCTTTTTTTACCTTTTCATTTTCTTCAATTTTAAAAATAATATTTATCTATTAATTGTATTATCT
TG
Found at i:6636189 original size:3 final size:3
Alignment explanation
Indices: 6636181--6636219 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
6636171 TTACTATTAT
6636181 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6636220 TAAATGTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6639854 original size:25 final size:25
Alignment explanation
Indices: 6639804--6639849 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
6639794 TTCAAAATTA
*
6639804 TATATTTTTTAATATTTAAAATTTT
1 TATATTTTATAATATTTAAAATTTT
6639829 TATATTTTAT-AT-TTTAAAATT
1 TATATTTTATAATATTTAAAATT
6639850 ATTTTTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 2 0.10
25 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TATATTTTATAATATTTAAAATTTT
Found at i:6639941 original size:23 final size:23
Alignment explanation
Indices: 6639870--6639941 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
6639860 ATTTTTAACT
*
6639870 TTTTAATATTAAAAATTATGAAAA
1 TTTTAATATTAAAAA-TATTAAAA
* * **
6639894 -TTTAATTTTATAAAAAATTTTAA
1 TTTTAATATTA-AAAATATTAAAA
*
6639917 TTTTAATATTAAATATATTAAAA
1 TTTTAATATTAAAAATATTAAAA
6639940 TT
1 TT
6639942 AAAAATTTTT
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
23 23 0.64
24 13 0.36
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (23 bp):
TTTTAATATTAAAAATATTAAAA
Found at i:6640212 original size:31 final size:31
Alignment explanation
Indices: 6640158--6640217 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
6640148 GAATATACTA
* *
6640158 AAAATTGTTTTTTATTTTTATTTTGAAATGT
1 AAAATTGTTTTTTATTTTAATTTTAAAATGT
6640189 AAAATTGTTTTTT-TTTATAATTTTAAAAT
1 AAAATTGTTTTTTATTT-TAATTTTAAAAT
6640218 ATTAATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (31 bp):
AAAATTGTTTTTTATTTTAATTTTAAAATGT
Found at i:6640269 original size:18 final size:18
Alignment explanation
Indices: 6640246--6640281 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6640236 AATATAAAAG
6640246 ATGATTTCTTTTAAAGCC
1 ATGATTTCTTTTAAAGCC
*
6640264 ATGATTTCTTTTAGAGCC
1 ATGATTTCTTTTAAAGCC
6640282 GTTTGGTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (18 bp):
ATGATTTCTTTTAAAGCC
Found at i:6644874 original size:22 final size:23
Alignment explanation
Indices: 6644839--6644882 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
6644829 CACTACGAGG
*
6644839 GTTTAGATTTTTAGTGACGTTTT
1 GTTTAGATATTTAGTGACGTTTT
*
6644862 GTTTA-ATATTTAGTGATGTTT
1 GTTTAGATATTTAGTGACGTTT
6644883 ATAAACGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.20, C:0.02, G:0.20, T:0.57
Consensus pattern (23 bp):
GTTTAGATATTTAGTGACGTTTT
Found at i:6645024 original size:17 final size:17
Alignment explanation
Indices: 6645004--6645059 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
6644994 ACGACATTTA
6645004 TATATGAAAAATGTTGC
1 TATATGAAAAATGTTGC
* * *
6645021 TATATTAATAACGTTTG-
1 TATATGAAAAATG-TTGC
* *
6645038 TATCTGAAAAATGTCGC
1 TATATGAAAAATGTTGC
6645055 TATAT
1 TATAT
6645060 TAATAATATT
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
16 2 0.07
17 23 0.82
18 3 0.11
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (17 bp):
TATATGAAAAATGTTGC
Found at i:6645063 original size:34 final size:34
Alignment explanation
Indices: 6644987--6645082 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 34
6644977 AAAATATTAT
** * * *
6644987 TATATTAACGACATTTATATATGAAAAATGTTGC
1 TATATTAATAACATTTGTATCTGAAAAATGTCGC
*
6645021 TATATTAATAACGTTTGTATCTGAAAAATGTCGC
1 TATATTAATAACATTTGTATCTGAAAAATGTCGC
*
6645055 TATATTAATAATATTTGTATCTAGAAAA
1 TATATTAATAACATTTGTATCT-GAAAA
6645083 CATCGTTATT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
34 48 0.91
35 5 0.09
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (34 bp):
TATATTAATAACATTTGTATCTGAAAAATGTCGC
Found at i:6648758 original size:134 final size:133
Alignment explanation
Indices: 6648475--6648829 Score: 419
Period size: 134 Copynumber: 2.7 Consensus size: 133
6648465 CGAAATGCCA
* * *
6648475 CTATTTTAGCGACGTTTGTATCTTTGAGATGCCGCTAAATTAATGGTA-TTTTTATGAGAAAAAC
1 CTATATTAGCGACGTTTGTATCTTTGAGACGCCGCT-AATTAGTGG-AGTTTTTATGAGAAAAAC
* ** * * *
6648539 ACCGTTGCTTTCAT-GCACTTGTAACTGAAAACACCACTACTTTAGAGGCGTTTGTATTTGAAAA
64 ACCATTGCTTTGGTGGCATTTGTAACTGAAAACACCACTACTTTAGAGGCATTTGTATATGAAAA
*
6648603 TACCT
129 CACCT
* * * *
6648608 CTATATT-GACGGCGTTTTTTTCTTTGAGACACCGCTAATCTAGTGGAGTTTTTATGAGAAAAAC
1 CTATATTAG-CGACGTTTGTATCTTTGAGACGCCGCTAAT-TAGTGGAGTTTTTATGAGAAAAAC
* * * *
6648672 ACCATTGCTTTGGTGGCATTTGTAATTGAAAACATCGCTACTTTGGAGGCATTTGTATATGAAAA
64 ACCATTGCTTTGGTGGCATTTGTAACTGAAAACACCACTACTTTAGAGGCATTTGTATATGAAAA
6648737 CACCT
129 CACCT
* * * * *
6648742 TTGTATTAGCGACGTTTGTATCTTTGAGACGCTGTTAATTTAGTGGCGTTTTTATGAGAAAAACA
1 CTATATTAGCGACGTTTGTATCTTTGAGACGCCGCTAA-TTAGTGGAGTTTTTATGAGAAAAACA
* *
6648807 CCATTGTTTTGGTGGCGTTTGTA
65 CCATTGCTTTGGTGGCATTTGTA
6648830 TAAAAATGTC
Statistics
Matches: 187, Mismatches: 29, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
132 5 0.03
133 60 0.32
134 120 0.64
135 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.37
Consensus pattern (133 bp):
CTATATTAGCGACGTTTGTATCTTTGAGACGCCGCTAATTAGTGGAGTTTTTATGAGAAAAACAC
CATTGCTTTGGTGGCATTTGTAACTGAAAACACCACTACTTTAGAGGCATTTGTATATGAAAACA
CCT
Found at i:6654524 original size:36 final size:33
Alignment explanation
Indices: 6654448--6654546 Score: 126
Period size: 33 Copynumber: 2.9 Consensus size: 33
6654438 CCTTTGTTCT
*
6654448 TGATACATTTGAGGTAGAGGATATATTTGAGGA
1 TGATACATTTGAGGTGGAGGATATATTTGAGGA
* * * *
6654481 TGATACATTTGTGGTGGAGGGTACATTTGTGGTAA
1 TGATACATTTGAGGTGGAGGATATATTTGAGG--A
6654516 CTGATACATTTGAGGTGGAGGATATATTTGA
1 -TGATACATTTGAGGTGGAGGATATATTTGA
6654547 AGAGGTGGAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
33 27 0.50
35 1 0.02
36 26 0.48
ACGTcount: A:0.28, C:0.05, G:0.31, T:0.35
Consensus pattern (33 bp):
TGATACATTTGAGGTGGAGGATATATTTGAGGA
Found at i:6654551 original size:21 final size:21
Alignment explanation
Indices: 6654527--6654567 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6654517 TGATACATTT
* *
6654527 GAGGTGGAGGATATATTTGAA
1 GAGGTGGAAGATACATTTGAA
6654548 GAGGTGGAAGATACATTTGA
1 GAGGTGGAAGATACATTTGA
6654568 GGTGGATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.37, T:0.27
Consensus pattern (21 bp):
GAGGTGGAAGATACATTTGAA
Found at i:6654571 original size:18 final size:18
Alignment explanation
Indices: 6654449--6654573 Score: 96
Period size: 18 Copynumber: 6.9 Consensus size: 18
6654439 CTTTGTTCTT
*
6654449 GATACATTTGAGGTAGAG
1 GATACATTTGAGGTGGAG
* *
6654467 GATATATTTGA---GGAT
1 GATACATTTGAGGTGGAG
*
6654482 GATACATTTGTGGTGGAG
1 GATACATTTGAGGTGGAG
* * * *
6654500 GGTACATTTGTGGT-AACT
1 GATACATTTGAGGTGGA-G
6654518 GATACATTTGAGGTGGAG
1 GATACATTTGAGGTGGAG
* *
6654536 GATATATTTGAAGAGGTGGAA
1 GATACATTT---GAGGTGGAG
6654557 GATACATTTGAGGTGGA
1 GATACATTTGAGGTGGA
6654574 TAATAACCAT
Statistics
Matches: 83, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
15 11 0.13
17 1 0.01
18 54 0.65
19 1 0.01
21 16 0.19
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.32
Consensus pattern (18 bp):
GATACATTTGAGGTGGAG
Found at i:6654928 original size:6 final size:6
Alignment explanation
Indices: 6654917--6654953 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
6654907 CCAAAATTTG
* *
6654917 CACCAT CACCAT CACCAT CTCCAT CACCAT CATCAT C
1 CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT C
6654954 TAGACTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.30, C:0.49, G:0.00, T:0.22
Consensus pattern (6 bp):
CACCAT
Found at i:6654940 original size:18 final size:18
Alignment explanation
Indices: 6654919--6654954 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6654909 AAAATTTGCA
6654919 CCATCACCATCACCATCT
1 CCATCACCATCACCATCT
*
6654937 CCATCACCATCATCATCT
1 CCATCACCATCACCATCT
6654955 AGACTTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.47, G:0.00, T:0.25
Consensus pattern (18 bp):
CCATCACCATCACCATCT
Found at i:6658412 original size:26 final size:26
Alignment explanation
Indices: 6658363--6658411 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
6658353 TTTCAAAAAT
*
6658363 TAAAAGTTTTCAAACTTATATTTTAA
1 TAAAAGTTTTCAAACCTATATTTTAA
6658389 TAAAA-TTTTCAAACCTATATTTT
1 TAAAAGTTTTCAAACCTATATTTT
6658412 TTATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (26 bp):
TAAAAGTTTTCAAACCTATATTTTAA
Found at i:6658666 original size:20 final size:19
Alignment explanation
Indices: 6658636--6658673 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
6658626 AAACAACAAA
6658636 AAAATTAAAATTAATATAC
1 AAAATTAAAATTAATATAC
6658655 AAAATTATAAATTAATATA
1 AAAATTA-AAATTAATATA
6658674 TAACACAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTAAAATTAATATAC
Found at i:6658959 original size:20 final size:20
Alignment explanation
Indices: 6658880--6658961 Score: 53
Period size: 20 Copynumber: 4.0 Consensus size: 20
6658870 ATACACCCTA
6658880 CCACACCCAATCCCTCCCCAC
1 CCACA-CCAATCCCTCCCCAC
* * *
6658901 CCCCATCAATCCCTCTCCAC
1 CCACACCAATCCCTCCCCAC
* * *
6658921 TTTCCCCCCCAA--CAT-CCCAC
1 ---CCACACCAATCCCTCCCCAC
6658941 CCACACCAATCCCTCCCCAC
1 CCACACCAATCCCTCCCCAC
6658961 C
1 C
6658962 TTCCTCCCAC
Statistics
Matches: 45, Mismatches: 10, Indels: 13
0.66 0.15 0.19
Matches are distributed among these distances:
17 7 0.16
19 2 0.04
20 23 0.51
21 6 0.13
23 7 0.16
ACGTcount: A:0.22, C:0.63, G:0.00, T:0.15
Consensus pattern (20 bp):
CCACACCAATCCCTCCCCAC
Found at i:6659052 original size:37 final size:36
Alignment explanation
Indices: 6658926--6659071 Score: 158
Period size: 36 Copynumber: 3.9 Consensus size: 36
6658916 TCCACTTTCC
*
6658926 CCCCCAACATCCCACC-CACACCAATCCCTCCCCACCTT
1 CCCCCAAC-CCCCACCACAC-CCAAT-CCTCCCCACCTT
6658964 CCTCCC-ACCCACCACCCAATCACCCAATCCT--CCACCTT
1 CC-CCCAACCC-CCA-CC-A-CACCCAATCCTCCCCACCTT
*
6659002 CCCCCAACACCCACCACACCCAATCCTCCCCACCTT
1 CCCCCAACCCCCACCACACCCAATCCTCCCCACCTT
6659038 CCCCCAACGCCCCACCACACCCAAT-CTCCCCACC
1 CCCCCAAC-CCCCACCACACCCAATCCTCCCCACC
6659072 CCCCCCCACC
Statistics
Matches: 95, Mismatches: 3, Indels: 22
0.79 0.03 0.18
Matches are distributed among these distances:
34 11 0.12
35 1 0.01
36 26 0.27
37 22 0.23
38 19 0.20
39 5 0.05
40 3 0.03
41 5 0.05
42 3 0.03
ACGTcount: A:0.24, C:0.64, G:0.01, T:0.12
Consensus pattern (36 bp):
CCCCCAACCCCCACCACACCCAATCCTCCCCACCTT
Found at i:6659068 original size:18 final size:18
Alignment explanation
Indices: 6659011--6659071 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
6659001 TCCCCCAACA
6659011 CCCACCACACCCAATCCTC
1 CCCACCACACCCAAT-CTC
* * *
6659030 CCCACCTTCCCCCAA-CGC
1 CCCACC-ACACCCAATCTC
6659048 CCCACCACACCCAATCTC
1 CCCACCACACCCAATCTC
6659066 CCCACC
1 CCCACC
6659072 CCCCCCCACC
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
17 6 0.18
18 16 0.47
19 6 0.18
20 6 0.18
ACGTcount: A:0.23, C:0.66, G:0.02, T:0.10
Consensus pattern (18 bp):
CCCACCACACCCAATCTC
Found at i:6660130 original size:21 final size:20
Alignment explanation
Indices: 6660090--6660131 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
6660080 AAAGATGTTT
*
6660090 TTATCACTAACCATTAATGA
1 TTATCACTAACCATCAATGA
*
6660110 TTATCATCTAACCATCGATGA
1 TTATCA-CTAACCATCAATGA
6660131 T
1 T
6660132 GTCTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (20 bp):
TTATCACTAACCATCAATGA
Found at i:6660449 original size:39 final size:39
Alignment explanation
Indices: 6660388--6660467 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
6660378 TATCATTACC
6660388 TGGACCTTTTTCCTCAGAAATTATCATAGACAATATAAA
1 TGGACCTTTTTCCTCAGAAATTATCATAGACAATATAAA
*
6660427 TGGACCTTTTTTCC-CAGGAATTATCATAGACAATATAAA
1 TGGACC-TTTTTCCTCAGAAATTATCATAGACAATATAAA
6660466 TG
1 TG
6660468 ACTATTGCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 32 0.82
40 7 0.18
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (39 bp):
TGGACCTTTTTCCTCAGAAATTATCATAGACAATATAAA
Found at i:6662630 original size:125 final size:123
Alignment explanation
Indices: 6662397--6662633 Score: 302
Period size: 125 Copynumber: 1.9 Consensus size: 123
6662387 TTGATTGGGA
* ** * *
6662397 TTATTAAAGGCGTCTTCTATTGAAAATGCCTTTAATATTACACAACTTAAATTTTAAAGGGTTAT
1 TTATTAAAGGCGTCTTCTACTGAAAATGCCTTTAATATTACACAACTTAAATTTTAAACAGATAG
* *
6662462 TGAAGGATTTTATTTTAGAAAAATGCCTTGACTAATTCGTTTTATTTCTTGAAGTAAT
66 TGAAGGATTTTATTATAGAAAAATGCCTTGACTAATGCGTTTTATTTCTTGAAGTAAT
* *
6662520 TTATTAAAGGCGTCTTCTACTGCAAAATG-CTTTCAATATTTCACTACTTAAATTTTAAGACAGA
1 TTATTAAAGGCGTCTTCTACTG-AAAATGCCTTT-AATATTACACAACTTAAATTTTAA-ACAGA
*
6662584 TAGTGAA-TATGTTTATTATAGAAAAATGCCATT-ACTAAATGC-TTTTATTT
63 TAGTGAAGGAT-TTTATTATAGAAAAATGCC-TTGACT-AATGCGTTTTATTT
6662634 TATTTTAAGT
Statistics
Matches: 98, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
123 25 0.26
124 30 0.31
125 37 0.38
126 6 0.06
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (123 bp):
TTATTAAAGGCGTCTTCTACTGAAAATGCCTTTAATATTACACAACTTAAATTTTAAACAGATAG
TGAAGGATTTTATTATAGAAAAATGCCTTGACTAATGCGTTTTATTTCTTGAAGTAAT
Found at i:6664703 original size:76 final size:80
Alignment explanation
Indices: 6664488--6664727 Score: 231
Period size: 76 Copynumber: 3.0 Consensus size: 80
6664478 TTAAATATTG
* ** * * *
6664488 TGGTTTGCTGAACCTTGTTGTCTTTTTTTTTTTTTTGCTAAATGGTATTGTATGATATT--GGGG
1 TGGTTTGCTGAACCATGTTG--TTTAATATTGTTTTGCTGAATGGTATTGTATGATATTGGGGGG
* * *
6664551 CTGAATCGTATGATAAA
64 CTGAATCATATGCTGAA
* * * * * *
6664568 TGATTTGTTGAACCTTGTTGTTTAATATTGTATTACCGAATGGTATTGTATGATATTGGGGGGCT
1 TGGTTTGCTGAACCATGTTGTTTAATATTGTTTTGCTGAATGGTATTGTATGATATTGGGGGGCT
6664633 GAATCATATGCTGAA
66 GAATCATATGCTGAA
* * * **
6664648 TGGTTTGCTGAA-CAT-TT-TTT-ATATTGTTTTGCTGAATGATTTTGCATGATATTGGGGAACT
1 TGGTTTGCTGAACCATGTTGTTTAATATTGTTTTGCTGAATGGTATTGTATGATATTGGGGGGCT
*
6664709 AAATCATATGCTGAA
66 GAATCATATGCTGAA
6664724 TGGT
1 TGGT
6664728 GTTTCTGAGT
Statistics
Matches: 133, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
76 51 0.38
77 3 0.02
78 31 0.23
79 2 0.02
80 46 0.35
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (80 bp):
TGGTTTGCTGAACCATGTTGTTTAATATTGTTTTGCTGAATGGTATTGTATGATATTGGGGGGCT
GAATCATATGCTGAA
Found at i:6668609 original size:281 final size:282
Alignment explanation
Indices: 6668094--6668643 Score: 757
Period size: 281 Copynumber: 2.0 Consensus size: 282
6668084 ACCAAAACTG
* ** * *
6668094 CCTTCAATAATCACCCCAAAAATTTATTGTGTGGAATATTAAAGGTGTTTTGGGAAAAAAATGCC
1 CCTTCAATAATCACACCAAAAATTTATTGTGTGGAATATTAAAGGCATTTTGAGAAAAAAATACC
** * * *
6668159 TTCAAGAATTCATTACATCTTTTTTGTATGGATTATTGAAGGCATTTTAAAAAAAACGCCTTCAA
66 TTCAAGAATTCATTACATCTTTTTTGTATAAATTATTAAAGGCATTTTAAAAAAAACACATTCAA
* * **
6668224 TAATACCAATTAAAAATTAATCGAATGGATTATGAAGGGCATTTTCCTATGGGTAACACCTTGAA
131 TAATACCAACTAAAAATTAATCGAATGGATTATAAAGGGCATTTTCCTACAGGTAACACCTTGAA
* * * * *
6668289 TAATTCATAACAAAATGTTATTGAAGGTGTTTTTGGATATAACTGCCTTCAATAA-TCCACCATT
196 TAATCCATAACAAAATATTATTGAAGGCGTATCTGGATATAACTGCCTTCAATAATTCCACCATT
6668353 AAAATTTATCATCTGGAGTATCA
261 -AAATTTATCATCTGGAGTATCA
* *
6668376 CCTTCAATAATCTCACCAAAAATTTATTGTGTGGAATATTAAAGGCATTTTGAGCAAAAAATACC
1 CCTTCAATAATCACACCAAAAATTTATTGTGTGGAATATTAAAGGCATTTTGAGAAAAAAATACC
* *
6668441 TTTAAGAA-TC-TGTCGCATCTTTTTTGTATAAATTATTAAAGGCA-TTTAAAAAAAACACATTC
66 TTCAAGAATTCAT-T-ACATCTTTTTTGTATAAATTATTAAAGGCATTTTAAAAAAAACACATTC
** **
6668503 AATAATACCAACTAAAAATTAATCGAATGGATTATAAAGGGTGTTTTCCTACAGGTAATGCCTTG
129 AATAATACCAACTAAAAATTAATCGAATGGATTATAAAGGGCATTTTCCTACAGGTAACACCTTG
* * * * *
6668568 AATAATCCCTAGCAAAATATTATTGAAGGCGTATCTGGATATAACTGCGTTCAATAATTCGATCA
194 AATAATCCATAACAAAATATTATTGAAGGCGTATCTGGATATAACTGCCTTCAATAATTCCACCA
6668633 TTAAATTTATC
259 TTAAATTTATC
6668644 GTTCGGAATA
Statistics
Matches: 233, Mismatches: 32, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
280 1 0.00
281 134 0.58
282 98 0.42
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (282 bp):
CCTTCAATAATCACACCAAAAATTTATTGTGTGGAATATTAAAGGCATTTTGAGAAAAAAATACC
TTCAAGAATTCATTACATCTTTTTTGTATAAATTATTAAAGGCATTTTAAAAAAAACACATTCAA
TAATACCAACTAAAAATTAATCGAATGGATTATAAAGGGCATTTTCCTACAGGTAACACCTTGAA
TAATCCATAACAAAATATTATTGAAGGCGTATCTGGATATAACTGCCTTCAATAATTCCACCATT
AAATTTATCATCTGGAGTATCA
Found at i:6668929 original size:306 final size:304
Alignment explanation
Indices: 6668376--6668952 Score: 723
Period size: 306 Copynumber: 1.9 Consensus size: 304
6668366 TGGAGTATCA
* * * *
6668376 CCTTCAATAATCTCACCAAAAATTTATTGTGTGGAATATTAAAGGCATTTTGAGCAAAAAATACC
1 CCTTCAATAATCCCACCAAAAATTTATTGTGTGAAATATTAAAGGCATTTTGAGAAAAAAAAACC
* *
6668441 TTTAAGAATCTGTCGCATCTTTTTTGTATAAATTATTAAAGGCATTTAAAAAAAACACATTCAAT
66 TTCAAGAATCTGTCGCATCTTTTTTATATAAATTATTAAAGGCATTTAAAAAAAACACATTCAAT
* *
6668506 AATACCAACTAAAAATTAATCGAATGGATTATAAAGGGTGTTTTCCTACAGGTAATGCCTTGAAT
131 AATACCAACTAAAAATTAATCAAATGGATTATAAAGGGTGTTTTCCTACAGGTAATGCCTTAAAT
* * * * *
6668571 AATCCCTAGCAAAATATTATTGAAGGCGTATCTGGATATAACTGCGTTCAATAAT-TCGATCATT
196 AATCCCTAACAAAATATTATTGAAGACATATCTGGATATAACTACGTTCAATAATCT-GACCATT
6668635 -AAATTTATCGTTCGGAATATCAATAGTATTTTTTACCAAAATCG
260 AAAATTTATCGTTCGGAATATCAATAGTATTTTTTACCAAAATCG
* * **
6668679 CCTTCAATAATCCCTCCAAAAATTTATTGTGTGAAATATTATAGGTGTTTTGAGAAAAAAAAAAA
1 CCTTCAATAATCCCACCAAAAATTTATTGTGTGAAATATTAAAGGCATTTTGAG--AAAAAAAAA
* * ** * ** * ** *
6668744 CTCCTTCAAGAATCTGTTGTGA-CTTTTTTATATGGATTATTGAAGGTGTTTTAAAAAAATGCCT
64 --CCTTCAAGAATCTGTCG-CATCTTTTTTATATAAATTATTAAAGGCATTTAAAAAAAACACAT
* * * *
6668808 TCAATAATACTAA-TAAAAATTAATCAAATGGATTATGAAGGGTGTTTTCCTA-TGAGTAGTGCC
126 TCAATAATACCAACTAAAAATTAATCAAATGGATTATAAAGGGTGTTTTCCTACAG-GTAATGCC
* * * * *
6668871 TTAAATAATCCCTAACAAAATGTTATTGAAGACATTTTTGGATATAATTACTTTCAATAATCTGA
190 TTAAATAATCCCTAACAAAATATTATTGAAGACATATCTGGATATAACTACGTTCAATAATCTGA
6668936 CCATTAAAATTTATCGT
255 CCATTAAAATTTATCGT
6668953 CTAAAATATT
Statistics
Matches: 229, Mismatches: 37, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
303 48 0.21
305 8 0.03
306 101 0.44
307 71 0.31
308 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (304 bp):
CCTTCAATAATCCCACCAAAAATTTATTGTGTGAAATATTAAAGGCATTTTGAGAAAAAAAAACC
TTCAAGAATCTGTCGCATCTTTTTTATATAAATTATTAAAGGCATTTAAAAAAAACACATTCAAT
AATACCAACTAAAAATTAATCAAATGGATTATAAAGGGTGTTTTCCTACAGGTAATGCCTTAAAT
AATCCCTAACAAAATATTATTGAAGACATATCTGGATATAACTACGTTCAATAATCTGACCATTA
AAATTTATCGTTCGGAATATCAATAGTATTTTTTACCAAAATCG
Found at i:6670313 original size:20 final size:20
Alignment explanation
Indices: 6670288--6670325 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6670278 AAATTAACAC
6670288 AGTAAAAATAT-ATTAAAATA
1 AGTAAAAAT-TCATTAAAATA
6670308 AGTAAAAATTCATTAAAA
1 AGTAAAAATTCATTAAAA
6670326 ATAATCTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
AGTAAAAATTCATTAAAATA
Found at i:6672560 original size:23 final size:23
Alignment explanation
Indices: 6672509--6672565 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
6672499 CTAAACAATC
6672509 AAAATAATAAA-AAATAAAATAAA
1 AAAAT-ATAAATAAATAAAATAAA
**
6672532 CCAATATAAATAAAT-AAATAAA
1 AAAATATAAATAAATAAAATAAA
*
6672554 TAAAATAGAAAT
1 -AAAATATAAAT
6672566 TGAACTCTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (23 bp):
AAAATATAAATAAATAAAATAAA
Found at i:6672776 original size:43 final size:43
Alignment explanation
Indices: 6672722--6672919 Score: 152
Period size: 43 Copynumber: 4.6 Consensus size: 43
6672712 TTACTTAACT
*
6672722 ACTTTAGAAAATTTAAAAGGCTCATTTCATCAAAGGCTTAATA
1 ACTTTAAAAAATTTAAAAGGCTCATTTCATCAAAGGCTTAATA
* * *
6672765 ACTTCAAAAAATTTAAAAGGCT-TTATTCATCAGAGG-TTCAATA
1 ACTTTAAAAAATTTAAAAGGCTCAT-TTCATCAAAGGCTT-AATA
* * * * * *
6672808 ACTTTAAAAATTTTAAAAAGTTGC-TCTCATTAGAGGCTTAATA
1 ACTTTAAAAAATTTAAAAGGCT-CATTTCATCAAAGGCTTAATA
* ** * * *
6672851 ACTTTTAAAAAATATAAAAAACTTATTTCATCAGAA-GCTCAACA
1 AC-TTTAAAAAATTTAAAAGGCTCATTTCATCA-AAGGCTTAATA
* * *
6672895 ACTATGAAAATTTTAAAAGGCTCAT
1 ACTTTAAAAAATTTAAAAGGCTCAT
6672920 CTTATCAGAA
Statistics
Matches: 120, Mismatches: 27, Indels: 16
0.74 0.17 0.10
Matches are distributed among these distances:
42 3 0.03
43 83 0.69
44 33 0.28
45 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (43 bp):
ACTTTAAAAAATTTAAAAGGCTCATTTCATCAAAGGCTTAATA
Found at i:6673021 original size:42 final size:42
Alignment explanation
Indices: 6672957--6673052 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
6672947 ATTTTAAAGG
6672957 CTTCAAAAAATTTAAAAAACTCATCTCATCAAAGG-TTATAAAA
1 CTTC-AAAAATTTAAAAAACTCATCTCATCAAAGGCTTA-AAAA
* * * *
6673000 CTTTAAAAATTTAAAAAACTCATTTCATCAGAGGCTTAATAA
1 CTTCAAAAATTTAAAAAACTCATCTCATCAAAGGCTTAAAAA
6673042 CTTCAAAAATT
1 CTTCAAAAATT
6673053 GTTCACAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
42 41 0.87
43 6 0.13
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (42 bp):
CTTCAAAAATTTAAAAAACTCATCTCATCAAAGGCTTAAAAA
Found at i:6676947 original size:23 final size:25
Alignment explanation
Indices: 6676896--6676947 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
6676886 TGGATTAGGA
* *
6676896 CAAAATAAAATTTTCAAGGGCTTAC
1 CAAAATAAAAATTTCAAGGGCATAC
*
6676921 CAAAA-AAAAATTTC-AGGGCATAT
1 CAAAATAAAAATTTCAAGGGCATAC
6676944 CAAA
1 CAAA
6676948 TCCCTGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.46
24 8 0.33
25 5 0.21
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.23
Consensus pattern (25 bp):
CAAAATAAAAATTTCAAGGGCATAC
Found at i:6682656 original size:22 final size:22
Alignment explanation
Indices: 6682630--6682805 Score: 89
Period size: 22 Copynumber: 8.1 Consensus size: 22
6682620 TAACAGTAGA
*
6682630 AAATCATAAATAATTTAATAAT
1 AAATCATAGATAATTTAATAAT
*
6682652 AAATCA-ATGATAATTTAATAGT
1 AAATCATA-GATAATTTAATAAT
* * * * *
6682674 AAGTAATTGATAATTTAGTAGT
1 AAATCATAGATAATTTAATAAT
* * *
6682696 TAATTATTA-AAAATTTAA-AAT
1 AAATCA-TAGATAATTTAATAAT
* *
6682717 AAATCAATAG--AACTTAATAGT
1 AAATC-ATAGATAATTTAATAAT
* * *
6682738 AAATCATATATAATATAATAGT
1 AAATCATAGATAATTTAATAAT
* **
6682760 TAATCA-ATGATAAAATAATAAT
1 AAATCATA-GATAATTTAATAAT
6682782 AAATCAT-GTATAATTTAAT-AT
1 AAATCATAG-ATAATTTAATAAT
6682803 AAA
1 AAA
6682806 AATTATTGTA
Statistics
Matches: 116, Mismatches: 27, Indels: 23
0.70 0.16 0.14
Matches are distributed among these distances:
20 9 0.08
21 22 0.19
22 84 0.72
23 1 0.01
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.36
Consensus pattern (22 bp):
AAATCATAGATAATTTAATAAT
Found at i:6682751 original size:64 final size:67
Alignment explanation
Indices: 6682636--6682763 Score: 165
Period size: 64 Copynumber: 2.0 Consensus size: 67
6682626 TAGAAAATCA
* * * * *
6682636 TAAATAATTTAATAATAAATCAATGATAATTTAATAGTAAGTAATTGATAATTTAGTAGTTAATT
1 TAAATAATTTAATAATAAATCAATGAGAACTTAATAGTAAATAATTGATAATATAATAGTTAATT
6682701 AT
66 AT
*
6682703 TAAA-AATTTAA-AATAAATCAAT-AGAACTTAATAGTAAATCATAT-ATAATATAATAGTTAAT
1 TAAATAATTTAATAATAAATCAATGAGAACTTAATAGTAAATAAT-TGATAATATAATAGTTAAT
6682764 CAATGATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
64 31 0.57
65 12 0.22
66 7 0.13
67 4 0.07
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (67 bp):
TAAATAATTTAATAATAAATCAATGAGAACTTAATAGTAAATAATTGATAATATAATAGTTAATT
AT
Found at i:6684486 original size:11 final size:11
Alignment explanation
Indices: 6684455--6684493 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6684445 TTTCAAAAAC
*
6684455 AAAATTTTAATT
1 AAAATATTAA-T
*
6684467 AAAAAATTAAT
1 AAAATATTAAT
6684478 AAAATATTAAT
1 AAAATATTAAT
6684489 AAAAT
1 AAAAT
6684494 TTCTGACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAATATTAAT
Found at i:6684508 original size:209 final size:205
Alignment explanation
Indices: 6684109--6684492 Score: 510
Period size: 209 Copynumber: 1.9 Consensus size: 205
6684099 TTTATCCGAC
* * * *
6684109 GATGAGATTCAAAGGTATTCCGAGTAGTGATGCCTACGAAATCTCTAGGTGAGAAGATTTTTTTA
1 GATGAGATTCAAAAGTATTCCGAGCAGAGATGCCTAAGAAATCTCTAGGTGAGAAGATTTTTTTA
* * * *
6684174 AAATACTACCAGCGTATTGGAGTATTTATAAAAAATTTTCAATACAGTAAAGATTTTCTTTTTTT
66 AAATACTACCAGCGTATTGGAATATTTATAAAAAATCTTCAATACAATAAAGATTTCCTTTTTTT
* * *
6684239 TAATAATAAATAAAAATTAGTTAATAAATTAAAAATATATGTAATAAAAATATGAAGGAAAGAAA
131 T-ATAATAAACAAAAATTAATTAAAAAATTAAAAATATATGTAATAAAAATATGAAGGAAAGAAA
6684304 TTTAATCCAAT
195 TTTAATCCAAT
**
6684315 GATGAGATTCTAAAAGTATTCCGAGCAGAGATGTTTTAAGAAATCTCTAGGTGAGAAGATTTTTT
1 GATGAGATTC-AAAAGTATTCCGAGCAGAGATG-CCTAAGAAATCTCTAGGTGAGAAGATTTTTT
* * *
6684380 GTAAAATATTACCAGCGTATTGGAATATTTATAAAAAATCTTCAATATAATTAA-A-TTCCTTTT
64 -TAAAATACTACCAGCGTATTGGAATATTTATAAAAAATCTTCAATACAATAAAGATTTCCTTTT
*
6684443 TTTT-TCAA-AAACAAAATTTTAATTAAAAAATTAATAAA-ATAT-TAATAAAA
128 TTTTAT-AATAAACAAAA-ATTAATTAAAAAATTAA-AAATATATGTAATAAAA
6684493 TTTCTGACAA
Statistics
Matches: 155, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
205 16 0.10
206 30 0.19
207 33 0.21
208 29 0.19
209 47 0.30
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.35
Consensus pattern (205 bp):
GATGAGATTCAAAAGTATTCCGAGCAGAGATGCCTAAGAAATCTCTAGGTGAGAAGATTTTTTTA
AAATACTACCAGCGTATTGGAATATTTATAAAAAATCTTCAATACAATAAAGATTTCCTTTTTTT
TATAATAAACAAAAATTAATTAAAAAATTAAAAATATATGTAATAAAAATATGAAGGAAAGAAAT
TTAATCCAAT
Done.