Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 28 of 50
Found at i:12398161 original size:67 final size:67
Alignment explanation
Indices: 12398025--12398164 Score: 151
Period size: 67 Copynumber: 2.1 Consensus size: 67
12398015 TGATCTTGTG
* * * * **
12398025 AAAAGCATTGTAAGGGTTTCGCTTGATCTTGTGAGAAAACCTTGTGGGGGTTTCGCTTAATCTTG
1 AAAAGCATTGTAAGGGTTTAGCTTGATCTTGTGAGAAAACATTGTGAGGGTTTCACTTAATCTCA
12398090 TA
66 TA
* * *
12398092 AAAAGCATTGTGAGGGTTTAGCTTGATC-T-TGA-AAAATGCTATTGTGAGGGTTTCACTTGATG
1 AAAAGCATTGTAAGGGTTTAGCTTGATCTTGTGAGAAAA--C-ATTGTGAGGGTTTCACTTAATC
12398154 TCATA
63 TCATA
12398159 AAAAGC
1 AAAAGC
12398165 TTATTTCCCT
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
64 4 0.07
65 3 0.05
66 2 0.03
67 52 0.85
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (67 bp):
AAAAGCATTGTAAGGGTTTAGCTTGATCTTGTGAGAAAACATTGTGAGGGTTTCACTTAATCTCA
TA
Found at i:12400233 original size:73 final size:73
Alignment explanation
Indices: 12400130--12400311 Score: 258
Period size: 73 Copynumber: 2.5 Consensus size: 73
12400120 TGTTAAAAAA
* * *
12400130 CATG-AAAAATTCCAAGATTTAAGAAGCCATAGTCGATCCATTAGATCCTATAGTCGACCTTAAG
1 CATGAAAAAACTCTAAGATTTAAGAAGCCATAGTCGATCCATTAGATCCTAGAGTCGACCTTAAG
12400194 GTAGATTG
66 GTAGATTG
* * * * * *
12400202 CATGAAAAAACTCTAAGATTTGAGAAGCCATAGTCAATCCGTTAGCTCTTGGAGTCGACCTTAAG
1 CATGAAAAAACTCTAAGATTTAAGAAGCCATAGTCGATCCATTAGATCCTAGAGTCGACCTTAAG
12400267 GTAGATTG
66 GTAGATTG
* *
12400275 CGTGAAAAAACTCTAAGATTTAAGAAGCTATAGTCGA
1 CATGAAAAAACTCTAAGATTTAAGAAGCCATAGTCGA
12400312 CCTCCTAACC
Statistics
Matches: 96, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 4 0.04
73 92 0.96
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (73 bp):
CATGAAAAAACTCTAAGATTTAAGAAGCCATAGTCGATCCATTAGATCCTAGAGTCGACCTTAAG
GTAGATTG
Found at i:12401531 original size:36 final size:35
Alignment explanation
Indices: 12401472--12401576 Score: 131
Period size: 36 Copynumber: 2.9 Consensus size: 35
12401462 TATTCTTCAT
* *
12401472 GAATATGGCCCAAATGTGAGGGTAAGAATACTATAC
1 GAATATGGCCCAGATGTG-GGGTAAGAATACCATAC
* *
12401508 GAATTTGGCCCAGATGTAGGGGT-AGAATTACCATAT
1 GAATATGGCCCAGATGT-GGGGTAAGAA-TACCATAC
12401544 GAATATGGCCCAGATGTGGGGGTAAGAATACCA
1 GAATATGGCCCAGATGT-GGGGTAAGAATACCA
12401577 CACGTGTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
35 4 0.07
36 51 0.85
37 5 0.08
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (35 bp):
GAATATGGCCCAGATGTGGGGTAAGAATACCATAC
Found at i:12424529 original size:19 final size:21
Alignment explanation
Indices: 12424505--12424547 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
12424495 CTAGGGTTTG
12424505 TGTTCTT-CTT-TTCTTCCTT
1 TGTTCTTGCTTCTTCTTCCTT
12424524 TGTTCTTGCTTCGTTCTTCCTT
1 TGTTCTTGCTTC-TTCTTCCTT
12424546 TG
1 TG
12424548 GCTGGCCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 3 0.14
22 11 0.52
ACGTcount: A:0.00, C:0.26, G:0.12, T:0.63
Consensus pattern (21 bp):
TGTTCTTGCTTCTTCTTCCTT
Found at i:12426001 original size:20 final size:21
Alignment explanation
Indices: 12425956--12426002 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
12425946 AGATGTCTAA
*
12425956 AATAATTATTTGAAATGAAAT
1 AATAATTATTTGAAATAAAAT
* *
12425977 TATAATTGTTTG-AATAAAAT
1 AATAATTATTTGAAATAAAAT
12425997 AATAAT
1 AATAAT
12426003 ATTCAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (21 bp):
AATAATTATTTGAAATAAAAT
Found at i:12431366 original size:461 final size:460
Alignment explanation
Indices: 12430504--12431426 Score: 1837
Period size: 461 Copynumber: 2.0 Consensus size: 460
12430494 ATGCTTGGAC
12430504 ATAAAATATGGTTTCTACAACAAGGCTATAAAAACCTTCTAAAAGGTTCATTTTAGCTTCTGAAA
1 ATAAAATATGGTTTCTACAACAAGGCTATAAAAACCTTCTAAAAGGTTCATTTTAGCTTCTGAAA
12430569 ATTGCAAAACATTTAAAACTGTTGAAAATAAAATGTCCTTTGACATAATGCTCAAAAAAGTCCTT
66 ATTGCAAAACATTTAAAACTGTTGAAAATAAAATGTCCTTTGACATAATGCTCAAAAAAGTCCTT
12430634 AAACTATTCAAAAAATTCAAATAAACTCTTATTCTTTTGTTATGTTCAATCAAGCTCTTGCACTT
131 AAACTATTCAAAAAATTCAAATAAACTCTTATTCTTTTGTTATGTTCAATCAAGCTCTTGCACTT
12430699 TTATTTTAAATCTAATAAGCCTTTATGGTTAATGATTGACTAATTGTCATTAGTCAAATTGCCTC
196 TTATTTTAAATCTAATAAGCCTTTATGGTTAATGATTGACTAATTGTCATTAGTCAAATTGCCTC
12430764 TTATCATTTTATATCCACATGGCACTAACACAGCGTTATTGTAGAAGATGAAAAATACCACATGA
261 TTATCATTTTATATCCACATGGCACTAACACAGCGTTATTGTAGAAGATGAAAAATACCACATGA
12430829 TCAGGTTGTTATGCCAACTTCGCATGTCATGTCATCATTGCTTATGATATGTCAGCATACCACAT
326 TCAGGTTGTTATGCCAACTTCGCATGTCATGTCATCATTGCTTATGATATGTCAGCATACCACAT
12430894 CATCATCAATTATGATATATTAACATGCCACGTTAGTGTTATGCAACATAAAATGACAAATGACA
391 CATCATCAATTATGATATATTAACATGCCACGTTAGTGTTATGCAACATAAAATGACAAATGACA
12430959 TTTTA
456 TTTTA
12430964 NATAAAATATGGTTTCTACAACAAGGCTATAAAAACCTTCTAAAAGGTTCATTTTAGCTTCTGAA
1 -ATAAAATATGGTTTCTACAACAAGGCTATAAAAACCTTCTAAAAGGTTCATTTTAGCTTCTGAA
12431029 AATTGCAAAACATTTAAAACTGTTGAAAATAAAATGTCCTTTGACATAATGCTCAAAAAAGTCCT
65 AATTGCAAAACATTTAAAACTGTTGAAAATAAAATGTCCTTTGACATAATGCTCAAAAAAGTCCT
12431094 TAAACTATTCAAAAAATTCAAATAAACTCTTATTCTTTTGTTATGTTCAATCAAGCTCTTGCACT
130 TAAACTATTCAAAAAATTCAAATAAACTCTTATTCTTTTGTTATGTTCAATCAAGCTCTTGCACT
12431159 TTTATTTTAAATCTAATAAGCCTTTATGGTTAATGATTGACTAATTGTCATTAGTCAAATTGCCT
195 TTTATTTTAAATCTAATAAGCCTTTATGGTTAATGATTGACTAATTGTCATTAGTCAAATTGCCT
12431224 CTTATCATTTTATATCCACATGGCACTAACACAGCGTTATTGTAGAAGATGAAAAATACCACATG
260 CTTATCATTTTATATCCACATGGCACTAACACAGCGTTATTGTAGAAGATGAAAAATACCACATG
12431289 ATCAGGTTGTTATGCCAACTTCGCATGTCATGTCATCATTGCTTATGATATGTCAGCATACCACA
325 ATCAGGTTGTTATGCCAACTTCGCATGTCATGTCATCATTGCTTATGATATGTCAGCATACCACA
12431354 TCATCATCAATTATGATATATTAACATGCCACGTTAGTGTTATGCAACATAAAATGACAAATGAC
390 TCATCATCAATTATGATATATTAACATGCCACGTTAGTGTTATGCAACATAAAATGACAAATGAC
12431419 ATTTTA
455 ATTTTA
12431425 AT
1 AT
12431427 TTAGTCAATC
Statistics
Matches: 462, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
460 2 0.00
461 460 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (460 bp):
ATAAAATATGGTTTCTACAACAAGGCTATAAAAACCTTCTAAAAGGTTCATTTTAGCTTCTGAAA
ATTGCAAAACATTTAAAACTGTTGAAAATAAAATGTCCTTTGACATAATGCTCAAAAAAGTCCTT
AAACTATTCAAAAAATTCAAATAAACTCTTATTCTTTTGTTATGTTCAATCAAGCTCTTGCACTT
TTATTTTAAATCTAATAAGCCTTTATGGTTAATGATTGACTAATTGTCATTAGTCAAATTGCCTC
TTATCATTTTATATCCACATGGCACTAACACAGCGTTATTGTAGAAGATGAAAAATACCACATGA
TCAGGTTGTTATGCCAACTTCGCATGTCATGTCATCATTGCTTATGATATGTCAGCATACCACAT
CATCATCAATTATGATATATTAACATGCCACGTTAGTGTTATGCAACATAAAATGACAAATGACA
TTTTA
Found at i:12431478 original size:30 final size:28
Alignment explanation
Indices: 12431444--12431506 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 28
12431434 ATCATTAGTC
*
12431444 ATAAAGGCTTATTTGATTCAAAATAAAAGT
1 ATAAAGGCTTATTTGACTC-AAA-AAAAGT
*
12431474 ATAAAGGCTTATTTGGCTCAAAAAAAGT
1 ATAAAGGCTTATTTGACTCAAAAAAAGT
12431502 ATAAA
1 ATAAA
12431507 AATTTGATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 11 0.35
29 3 0.10
30 17 0.55
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (28 bp):
ATAAAGGCTTATTTGACTCAAAAAAAGT
Found at i:12435022 original size:70 final size:70
Alignment explanation
Indices: 12434869--12435031 Score: 220
Period size: 70 Copynumber: 2.3 Consensus size: 70
12434859 AATAAAGCCC
* *
12434869 GATGTGGGGGTAAGAATACCACAAGACCAAGATAGGCGAATGTACCCATTCTTGTCTCCTTTTAA
1 GATGTGGGGGTAAGAATACCACAAGACCAAGATAGGCAAATGTACCCATTATTGTCTCCTTTTAA
** *
12434934 TGCTT
66 AACCT
* * ** *
12434939 GGTGTAGTTGTAAGAATACCACAAGACCAAGATGGGCAAATGTACCCATTATTGTC-CCTTTCTA
1 GATGTGGGGGTAAGAATACCACAAGACCAAGATAGGCAAATGTACCCATTATTGTCTCCTTT-TA
12435003 AAACCT
65 AAACCT
12435009 GATGTGGGGGTAAGAATACCACA
1 GATGTGGGGGTAAGAATACCACA
12435032 GGGTCTAGTT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
69 5 0.06
70 73 0.94
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (70 bp):
GATGTGGGGGTAAGAATACCACAAGACCAAGATAGGCAAATGTACCCATTATTGTCTCCTTTTAA
AACCT
Found at i:12436729 original size:21 final size:21
Alignment explanation
Indices: 12436686--12436729 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
12436676 GTCATAATAG
* * *
12436686 ATGGTAAGATGGTATGTTGAT
1 ATGGTAAGATGATATGATCAT
*
12436707 ATGGTATGATGATATGATCAT
1 ATGGTAAGATGATATGATCAT
12436728 AT
1 AT
12436730 CACATTTTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.27, T:0.39
Consensus pattern (21 bp):
ATGGTAAGATGATATGATCAT
Found at i:12437087 original size:2 final size:2
Alignment explanation
Indices: 12437080--12437113 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12437070 TTTGTAATTA
12437080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12437114 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12444558 original size:33 final size:33
Alignment explanation
Indices: 12444498--12444560 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
12444488 ACATATTAAC
** *
12444498 ATATTATAATAGATGATGATGTGATATGCTGAT
1 ATATTATAATAGATGATGACATAATATGCTGAT
12444531 ATATTATAATTA-ATGATGACATAATATGCT
1 ATATTATAA-TAGATGATGACATAATATGCT
12444561 AATTTGACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 24 0.92
34 2 0.08
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (33 bp):
ATATTATAATAGATGATGACATAATATGCTGAT
Found at i:12450315 original size:43 final size:43
Alignment explanation
Indices: 12450251--12450387 Score: 150
Period size: 43 Copynumber: 3.2 Consensus size: 43
12450241 AGTTGGGTCA
* *
12450251 TCATCATCGGCTTAAGCGCACTCCCTACTCACACATAGCTAGG
1 TCATCATCGGCTTATGTGCACTCCCTACTCACACATAGCTAGG
* * *
12450294 TCATCATTGGCTTATGTGCACTCCCTACTCTCACATAGCCAGG
1 TCATCATCGGCTTATGTGCACTCCCTACTCACACATAGCTAGG
* ** * * * *
12450337 TCATTATCAACTCATGTGCAATCTC-ACATCGCACATAGCTAGG
1 TCATCATCGGCTTATGTGCACTCCCTAC-TCACACATAGCTAGG
12450380 TCATCATC
1 TCATCATC
12450388 ATCACACAAC
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 2 0.03
43 76 0.97
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.28
Consensus pattern (43 bp):
TCATCATCGGCTTATGTGCACTCCCTACTCACACATAGCTAGG
Found at i:12451638 original size:60 final size:61
Alignment explanation
Indices: 12451530--12451678 Score: 180
Period size: 60 Copynumber: 2.4 Consensus size: 61
12451520 ACAAGTCCAG
* * *
12451530 CTTTCTCT-TTTTTGTTTCCTTTCTTTCTTTCTTTCTTTTCTCTCCTTGGT-TCGACCGAGCTTC
1 CTTTCTCTCTTTTTCTTTCCTTTC-TTCCTTC-TTCTTTTCTCTCCTTGGTCT-GACCGAAC-TC
**
12451593 C-TTCTCTCTTTTTCTTTCCTTTCTTCCTTC-TCTTTTCTCTCCTTGGTCTGGTCGAACTC
1 CTTTCTCTCTTTTTCTTTCCTTTCTTCCTTCTTCTTTTCTCTCCTTGGTCTGACCGAACTC
*
12451652 CTTTCTCTCTTTTTCTTTTCTTTCTTC
1 CTTTCTCTCTTTTTCTTTCCTTTCTTC
12451679 TTTTTTTCTT
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
59 3 0.04
60 46 0.60
61 1 0.01
62 12 0.16
63 15 0.19
ACGTcount: A:0.03, C:0.31, G:0.07, T:0.59
Consensus pattern (61 bp):
CTTTCTCTCTTTTTCTTTCCTTTCTTCCTTCTTCTTTTCTCTCCTTGGTCTGACCGAACTC
Found at i:12451676 original size:19 final size:20
Alignment explanation
Indices: 12451652--12451689 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12451642 GGTCGAACTC
12451652 CTTTC-TCTCTTTTTCTTTT
1 CTTTCTTCTCTTTTTCTTTT
*
12451671 CTTTCTTCTTTTTTTCTTT
1 CTTTCTTCTCTTTTTCTTT
12451690 CCCTCATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
CTTTCTTCTCTTTTTCTTTT
Found at i:12451677 original size:15 final size:15
Alignment explanation
Indices: 12451653--12451690 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
12451643 GTCGAACTCC
*
12451653 TTTCTCTCTT-TTTCT
1 TTTCTTTCTTCTTT-T
12451668 TTTCTTTCTTCTTTT
1 TTTCTTTCTTCTTTT
12451683 TTTCTTTC
1 TTTCTTTC
12451691 CCTCATTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTCTTTCTTCTTTT
Found at i:12475043 original size:20 final size:21
Alignment explanation
Indices: 12475004--12475046 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
12474994 GATATTGAGA
*
12475004 ATGAATAATGAATGCTTGATG
1 ATGAATAATGAATACTTGATG
*
12475025 ATGAATGAT-AATACTTGATG
1 ATGAATAATGAATACTTGATG
12475045 AT
1 AT
12475047 AATTGAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (21 bp):
ATGAATAATGAATACTTGATG
Found at i:12479266 original size:68 final size:68
Alignment explanation
Indices: 12479053--12479319 Score: 239
Period size: 68 Copynumber: 3.9 Consensus size: 68
12479043 CATGTTTGGT
* * * * * * *
12479053 ATGATAAATGCCAAAAGATTTTGTGTATGATGTAAATTTCATATACCATATGAGATGATTAAGCA
1 ATGATGAATGCCATAAGATTATGTATATGATGTAAATTCCATATACAATATGAGATGATTAAGAA
12479118 TGC
66 TGC
* * * * * * * *
12479121 ATGATGAATACCATAAGATTGTATATATGATGTAAATTCCACATAGAATATAAGGTGATTAAGTA
1 ATGATGAATGCCATAAGATTATGTATATGATGTAAATTCCATATACAATATGAGATGATTAAGAA
12479186 TGC
66 TGC
* ** * * *
12479189 ATGATGAATGCCATGAGATTATGTATATGATGTGTATTCCATATACTACATGAGATGATTGAGAA
1 ATGATGAATGCCATAAGATTATGTATATGATGTAAATTCCATATACAATATGAGATGATTAAGAA
*
12479254 AGC
66 TGC
* * * ** * ** *
12479257 ATGATGAATGCTAGGAA-ATTATGTATATGATCTATTTTTCATATACCTTATGAGATGAGTAAG
1 ATGATGAATGCCA-TAAGATTATGTATATGATGTAAATTCCATATACAATATGAGATGATTAAG
12479320 CTTGTTTGTG
Statistics
Matches: 158, Mismatches: 40, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
68 157 0.99
69 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.34
Consensus pattern (68 bp):
ATGATGAATGCCATAAGATTATGTATATGATGTAAATTCCATATACAATATGAGATGATTAAGAA
TGC
Found at i:12479703 original size:20 final size:21
Alignment explanation
Indices: 12479664--12479723 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
12479654 GCTTTCTATG
*
12479664 TGAAATGTATCGATATATTCT
1 TGAAATGTATCGATACATTCT
*
12479685 TGAAA-GTATCTATACATTC-
1 TGAAATGTATCGATACATTCT
*
12479704 -GAGAATGTATCGATAGATTC
1 TGA-AATGTATCGATACATTC
12479724 ATTATAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 24 0.73
21 5 0.15
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (21 bp):
TGAAATGTATCGATACATTCT
Found at i:12495325 original size:20 final size:20
Alignment explanation
Indices: 12495300--12495337 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
12495290 AAAAAAAAAA
12495300 ATTTAATAAAATAATATTTT
1 ATTTAATAAAATAATATTTT
12495320 ATTTAATAAAATAATATT
1 ATTTAATAAAATAATATT
12495338 AAAATATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTAATAAAATAATATTTT
Found at i:12495389 original size:22 final size:21
Alignment explanation
Indices: 12495352--12495401 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
12495342 TATTACTAAT
12495352 AATAAAAAAAATAAATGAATA
1 AATAAAAAAAATAAATGAATA
*
12495373 AATAAATAAAATGAAATGAATA
1 AATAAAAAAAAT-AAATGAATA
*
12495395 AAGAAAA
1 AATAAAA
12495402 GATGAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (21 bp):
AATAAAAAAAATAAATGAATA
Found at i:12495408 original size:15 final size:15
Alignment explanation
Indices: 12495388--12495417 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12495378 ATAAAATGAA
12495388 ATGAATAAAGAAAAG
1 ATGAATAAAGAAAAG
*
12495403 ATGAATAATGAAAAG
1 ATGAATAAAGAAAAG
12495418 GTTGGACAGG
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:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (15 bp):
ATGAATAAAGAAAAG
Found at i:12503879 original size:23 final size:23
Alignment explanation
Indices: 12503834--12503878 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
12503824 AGCAAATAAA
*
12503834 AGAGGGAAAATGAGCTGATTTTG
1 AGAGGGAAAAGGAGCTGATTTTG
*
12503857 AGAGAGGAAAAGGGGCTGATTT
1 AGAG-GGAAAAGGAGCTGATTT
12503879 GCTACCGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.36, C:0.04, G:0.38, T:0.22
Consensus pattern (23 bp):
AGAGGGAAAAGGAGCTGATTTTG
Found at i:12513709 original size:43 final size:43
Alignment explanation
Indices: 12513642--12513753 Score: 163
Period size: 43 Copynumber: 2.6 Consensus size: 43
12513632 CATTCACTCG
* * *
12513642 GCTATGTGCGAGTAGGGAGCGCGCATAAGCCGAG-GATGACCTG
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGATGACCTA
*
12513685 GTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCTA
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCTA
*
12513728 GCCATGTGCGAGTAGGGAGTGCGCAT
1 GCTATGTGCGAGTAGGGAGTGCGCAT
12513754 GAACTTGTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.02
43 61 0.98
ACGTcount: A:0.22, C:0.20, G:0.38, T:0.20
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCTA
Found at i:12527595 original size:13 final size:13
Alignment explanation
Indices: 12527577--12527601 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12527567 AGAGAAATTG
12527577 TGATTTTATAAAA
1 TGATTTTATAAAA
12527590 TGATTTTATAAA
1 TGATTTTATAAA
12527602 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:12532972 original size:22 final size:22
Alignment explanation
Indices: 12532930--12532972 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
12532920 GTGGAGAATT
* *
12532930 TCAAGGGAAAAAGTGTGAAAAA
1 TCAAGGAAAAAAGTGTAAAAAA
12532952 TCAAGGAAAACAAGTG-AAAAA
1 TCAAGGAAAA-AAGTGTAAAAA
12532973 TGTAGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.58, C:0.07, G:0.23, T:0.12
Consensus pattern (22 bp):
TCAAGGAAAAAAGTGTAAAAAA
Found at i:12547199 original size:126 final size:126
Alignment explanation
Indices: 12546975--12547202 Score: 305
Period size: 126 Copynumber: 1.8 Consensus size: 126
12546965 TGATGTCCCA
* * * *
12546975 AATTGTTCTCAACATAATTTGTTGTTGTAAACTAACTCACATTTACATGAATGAGGTTTACAGCA
1 AATTGGTCTCAACATAATTTATTGTGGTAAACTAACTCACATCTACATGAATGAGGTTTACAGCA
** * * * *
12547040 GCAATGGTACAAAATTCTGTGTCGCCCTTTATTTACACCCTATTTATTAAACTATGTCGTC
66 AAAATGGTACAAAATTCTGCGTCACCATCTATTTACACCCTATTTATTAAACTATGTCGTC
* *
12547101 AATTGGTCTCAACATAATTTATTGTGGTAAACTAA-TGCTCATCTACATGAATGAGGTTTACAGT
1 AATTGGTCTCAACATAATTTATTGTGGTAAACTAACT-CACATCTACATGAATGAGGTTTACAGC
* **
12547165 AAAAATGGTACAAAATTTTGCGTCATGATCTATTTACA
65 AAAAATGGTACAAAATTCTGCGTCACCATCTATTTACA
12547203 GCTATTACTA
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
125 1 0.01
126 85 0.99
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (126 bp):
AATTGGTCTCAACATAATTTATTGTGGTAAACTAACTCACATCTACATGAATGAGGTTTACAGCA
AAAATGGTACAAAATTCTGCGTCACCATCTATTTACACCCTATTTATTAAACTATGTCGTC
Found at i:12550034 original size:39 final size:39
Alignment explanation
Indices: 12549981--12550060 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
12549971 AACCAATCCT
* *
12549981 TTCAGTCCCACTAAGCATTCTGGTTAATTTTCCATTTTG
1 TTCAATCCCACTAAGCATTCTGGTAAATTTTCCATTTTG
* *
12550020 TTCAATCCCCCTAAGCATTCTGGTAAATTTTCTATTTTG
1 TTCAATCCCACTAAGCATTCTGGTAAATTTTCCATTTTG
12550059 TT
1 TT
12550061 GACTGACTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (39 bp):
TTCAATCCCACTAAGCATTCTGGTAAATTTTCCATTTTG
Found at i:12554073 original size:2 final size:2
Alignment explanation
Indices: 12554066--12554140 Score: 136
Period size: 2 Copynumber: 38.5 Consensus size: 2
12554056 ATGATCTATC
12554066 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12554108 TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12554141 GTGAATTTTG
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 69 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12555128 original size:2 final size:2
Alignment explanation
Indices: 12555121--12555158 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
12555111 ATAATTATGC
12555121 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12555159 GCGAAAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12558541 original size:12 final size:12
Alignment explanation
Indices: 12558524--12558548 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12558514 GAAGTCAAAC
12558524 ATATACATATAT
1 ATATACATATAT
12558536 ATATACATATAT
1 ATATACATATAT
12558548 A
1 A
12558549 CACCCAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATACATATAT
Found at i:12559128 original size:30 final size:30
Alignment explanation
Indices: 12559087--12559152 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
12559077 TTTATTACGT
* *
12559087 TCAATTAAATCCATATACTTT-TATTTTGAA
1 TCAAATAAATCCATATA-TTTGTATTTTAAA
* *
12559117 TTAAATAAATCCTTATATTTGTATTTTAAA
1 TCAAATAAATCCATATATTTGTATTTTAAA
12559147 TCAAAT
1 TCAAAT
12559153 TAACTCTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (30 bp):
TCAAATAAATCCATATATTTGTATTTTAAA
Found at i:12560936 original size:35 final size:35
Alignment explanation
Indices: 12560883--12560961 Score: 86
Period size: 35 Copynumber: 2.3 Consensus size: 35
12560873 ATAGTTATTG
* * * * * **
12560883 TATTCATGTATTATTATTGGATACCTGAATTGGTA
1 TATTCATATATCACTATTGCATACATGAATCAGTA
12560918 TATTCATATATCACTATTGCATACATGAATCAGTA
1 TATTCATATATCACTATTGCATACATGAATCAGTA
*
12560953 GATTCATAT
1 TATTCATAT
12560962 TCGTGTATCT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (35 bp):
TATTCATATATCACTATTGCATACATGAATCAGTA
Found at i:12561519 original size:32 final size:32
Alignment explanation
Indices: 12561474--12561542 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
12561464 TAGTCATTTA
* * * *
12561474 TTTCATAAGATGACTATTCAAAAGTTGTTTCC
1 TTTCAAAAAATGACTATTCAAAAGTTATTACC
12561506 TTTCAAAAAATGACTATTCAAAAGTTATTACC
1 TTTCAAAAAATGACTATTCAAAAGTTATTACC
12561538 TTTCA
1 TTTCA
12561543 TAATACAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (32 bp):
TTTCAAAAAATGACTATTCAAAAGTTATTACC
Found at i:12561554 original size:32 final size:32
Alignment explanation
Indices: 12561486--12561557 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
12561476 TCATAAGATG
* * **
12561486 ACTATTCAAAAGTTGTTTCCTTTCAAAAAATG
1 ACTATTCAAAAGTTATTACCTTTCAAAAAACA
* *
12561518 ACTATTCAAAAGTTATTACCTTTCATAATACA
1 ACTATTCAAAAGTTATTACCTTTCAAAAAACA
12561550 ACTATTCA
1 ACTATTCA
12561558 TAAAAATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.38
Consensus pattern (32 bp):
ACTATTCAAAAGTTATTACCTTTCAAAAAACA
Found at i:12561592 original size:41 final size:39
Alignment explanation
Indices: 12561535--12561615 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 39
12561525 AAAAGTTATT
12561535 ACCTTTCATAATACAACTATTCATAAAAATTATATTGAATA
1 ACCTTTCATAATACAACTATT-A-AAAAATTATATTGAATA
* *
12561576 ACCTTTCATAATACAACTATTAAAAAGTTATATTTAATA
1 ACCTTTCATAATACAACTATTAAAAAATTATATTGAATA
12561615 A
1 A
12561616 GGTAATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 16 0.42
40 1 0.03
41 21 0.55
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (39 bp):
ACCTTTCATAATACAACTATTAAAAAATTATATTGAATA
Found at i:12561846 original size:45 final size:45
Alignment explanation
Indices: 12561737--12561831 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
12561727 TTTAATGAAA
* * * *
12561737 TTACACGCCATGTACAAAAACACGTTACACTTCATGATTAGGTTG
1 TTACACGTCATATACAAAAACACGTGACACGTCATGATTAGGTTG
* *
12561782 TTACACGTCATATACAAAAACATGTGACACGTCATGGTTAGGTTG
1 TTACACGTCATATACAAAAACACGTGACACGTCATGATTAGGTTG
12561827 TTACA
1 TTACA
12561832 TGATATGTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (45 bp):
TTACACGTCATATACAAAAACACGTGACACGTCATGATTAGGTTG
Found at i:12561906 original size:77 final size:77
Alignment explanation
Indices: 12561778--12562029 Score: 272
Period size: 77 Copynumber: 3.2 Consensus size: 77
12561768 TCATGATTAG
** * * **
12561778 GTTGTTACACGTCATATACAAAAACATGTGACACGTCATGGTTAGGTTGTTACATGATATGTTGA
1 GTTGTTACACACCATGTACAAAAACATGTTACACGTCATGGTTAGGTTGTTACATGCCATGTTGA
12561843 AAAAAAAATATT
66 AAAAAAAATATT
* * * * * * *
12561855 ATTGTTACACACCATGTACAAAAACATATTACATGCCATGGTTAGGTTGTTACACGCCGTATTGA
1 GTTGTTACACACCATGTACAAAAACATGTTACACGTCATGGTTAGGTTGTTACATGCCATGTTGA
*
12561920 AAACAAAATATT
66 AAAAAAAATATT
* * * * * *
12561932 GTTATTACACACTATGTATAAAAACATGTTGCACGTCATGATTAAAAAAGGTTATTACATGCCAT
1 GTTGTTACACACCATGTACAAAAACATGTTACACGTCATGGTT-----AGGTTGTTACATGCCAT
12561997 GTTG-AAAAAAAATATT
61 GTTGAAAAAAAAATATT
12562013 GTTGTTACACACCATGT
1 GTTGTTACACACCATGT
12562030 TGAAAACATA
Statistics
Matches: 140, Mismatches: 30, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
77 97 0.69
81 26 0.19
82 17 0.12
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (77 bp):
GTTGTTACACACCATGTACAAAAACATGTTACACGTCATGGTTAGGTTGTTACATGCCATGTTGA
AAAAAAAATATT
Found at i:12562035 original size:29 final size:30
Alignment explanation
Indices: 12561993--12562051 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
12561983 TTATTACATG
12561993 CCATGTTGAAAAAAAATATTGTTGTTACACA
1 CCATGTTG-AAAAAAATATTGTTGTTACACA
*
12562024 CCATGTTG-AAAACATATTGTTGTTACAC
1 CCATGTTGAAAAAAATATTGTTGTTACAC
12562052 GCTATATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 19 0.70
31 8 0.30
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (30 bp):
CCATGTTGAAAAAAATATTGTTGTTACACA
Found at i:12562064 original size:29 final size:30
Alignment explanation
Indices: 12562002--12562076 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
12561992 GCCATGTTGA
* *
12562002 AAAAAAATATTGTTGTTACACACCATGTT-
1 AAAAACATATTGTTGTTACACACCATATTC
* * *
12562031 GAAAACATATTGTTGTTACACGCTATATTC
1 AAAAACATATTGTTGTTACACACCATATTC
*
12562061 AAAAACATTTTGTTGT
1 AAAAACATATTGTTGT
12562077 ACTTTAATAC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 24 0.63
30 14 0.37
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (30 bp):
AAAAACATATTGTTGTTACACACCATATTC
Found at i:12563431 original size:21 final size:21
Alignment explanation
Indices: 12563403--12563457 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
12563393 AAATTGCTTC
12563403 AATGATCTTT-AAGCTTCTTTG
1 AATGATCTTTGAA-CTTCTTTG
* *
12563424 AGTGATCTTTGAACTTGTTTG
1 AATGATCTTTGAACTTCTTTG
*
12563445 AATGATTTTTGAA
1 AATGATCTTTGAA
12563458 GATGTTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.47
Consensus pattern (21 bp):
AATGATCTTTGAACTTCTTTG
Found at i:12563463 original size:21 final size:21
Alignment explanation
Indices: 12563403--12563467 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
12563393 AAATTGCTTC
* *
12563403 AATGATCTTT-AAGCTTCTTTG
1 AATGATCTTTGAA-CATGTTTG
* *
12563424 AGTGATCTTTGAACTTGTTTG
1 AATGATCTTTGAACATGTTTG
* *
12563445 AATGATTTTTGAAGATGTTTG
1 AATGATCTTTGAACATGTTTG
12563466 AA
1 AA
12563468 AATTTTTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46
Consensus pattern (21 bp):
AATGATCTTTGAACATGTTTG
Found at i:12563583 original size:21 final size:21
Alignment explanation
Indices: 12563559--12563632 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
12563549 ATAATCAAAA
* *
12563559 TTGTTTAAATGATCTTTGAAC
1 TTGTTTAAATGATTTTTAAAC
* * *
12563580 TTGTTTGAATAATTTTTAAAG
1 TTGTTTAAATGATTTTTAAAC
*
12563601 TTGTTTGAATGAGTTTTTAAAC
1 TTGTTTAAATGA-TTTTTAAAC
*
12563623 TTTTTTAAAT
1 TTGTTTAAAT
12563633 AAGTTTTGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 27 0.63
22 16 0.37
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.53
Consensus pattern (21 bp):
TTGTTTAAATGATTTTTAAAC
Found at i:12563620 original size:22 final size:21
Alignment explanation
Indices: 12563577--12563639 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
12563567 ATGATCTTTG
*
12563577 AACTTGTTTGAATAATTTTTA
1 AACTTGTTTGAATAGTTTTTA
*
12563598 AAGTTGTTTGAATGAGTTTTTA
1 AACTTGTTTGAAT-AGTTTTTA
* *
12563620 AACTTTTTTAAATAAGTTTT
1 AACTTGTTTGAAT-AGTTTT
12563640 GAAGTGCCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 12 0.34
22 23 0.66
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (21 bp):
AACTTGTTTGAATAGTTTTTA
Found at i:12563699 original size:22 final size:22
Alignment explanation
Indices: 12563673--12563718 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12563663 GAAAAGTTTC
12563673 AAAATTACTTGAATGAGT-TTTG
1 AAAATTACTTGAATGA-TATTTG
* *
12563695 AAAATTGCTTTAATGATATTTG
1 AAAATTACTTGAATGATATTTG
12563717 AA
1 AA
12563719 CTTGTTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.41
Consensus pattern (22 bp):
AAAATTACTTGAATGATATTTG
Found at i:12563728 original size:119 final size:118
Alignment explanation
Indices: 12563517--12563757 Score: 281
Period size: 119 Copynumber: 2.0 Consensus size: 118
12563507 ATACATTTTC
* * ** *
12563517 TTTTGGAGTGCATAAGTGTTTCTATGTGAAAAATAATCAAAATTGTTTAAATGATCTTTGAACTT
1 TTTTGAAGTGCATAAGTGTTTCCATGTGAAAAATAATCAAAATTACTTAAATGATCTTTGAAATT
* * * *
12563582 GTTTGAATAATTTTTAAAGTTGTTTGAATGAGTTTTTAAACTTTTTTAAATAAG
66 GTTTGAATAATATTTAAACTTGTTTGAAT-AGCTTTTAAACTTGTTTAAATAAG
* * * *
12563636 TTTTGAAGTGCCTAAGTGTTTCCATGTGAAAAGT-TTCAAAATTACTTGAATGAGT-TTTGAAAA
1 TTTTGAAGTGCATAAGTGTTTCCATGTGAAAAATAATCAAAATTACTTAAATGA-TCTTTG-AAA
* * *
12563699 TTGCTTT-AATGATATTTGAACTTGTTTGAATAGCTTTTAAACTTGTTTAAATTAG
64 TTG-TTTGAATAATATTTAAACTTGTTTGAATAGCTTTTAAACTTGTTTAAATAAG
12563754 TTTT
1 TTTT
12563758 AACCTTCCTT
Statistics
Matches: 103, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
118 44 0.43
119 56 0.54
120 3 0.03
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (118 bp):
TTTTGAAGTGCATAAGTGTTTCCATGTGAAAAATAATCAAAATTACTTAAATGATCTTTGAAATT
GTTTGAATAATATTTAAACTTGTTTGAATAGCTTTTAAACTTGTTTAAATAAG
Found at i:12563743 original size:21 final size:21
Alignment explanation
Indices: 12563717--12563759 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
12563707 ATGATATTTG
*
12563717 AACTTGTTTGAA-TAGCTTTTA
1 AACTTGTTTAAATTAG-TTTTA
12563738 AACTTGTTTAAATTAGTTTTA
1 AACTTGTTTAAATTAGTTTTA
12563759 A
1 A
12563760 CCTTCCTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.49
Consensus pattern (21 bp):
AACTTGTTTAAATTAGTTTTA
Found at i:12564309 original size:32 final size:32
Alignment explanation
Indices: 12564253--12564375 Score: 113
Period size: 32 Copynumber: 3.7 Consensus size: 32
12564243 TAAGAGAGAA
* *
12564253 AAGGTTGTGCCTT-AACCTTTAAAGGCATTGTG
1 AAGGTTGTG-CTTGATCCTTAAAAGGCATTGTG
*
12564285 AAGGTTGTGCTTGATCCATAAAAGGCATTGTATTG
1 AAGGTTGTGCTTGATCCTTAAAAGGCATTG---TG
* * * *
12564320 AGAGGTTGTGTTTGATCCTTGAAAGACATTGTA
1 A-AGGTTGTGCTTGATCCTTAAAAGGCATTGTG
* *
12564353 AAGGTTATGCTTGAGCCTTAAAA
1 AAGGTTGTGCTTGATCCTTAAAA
12564376 AGTATTTTTC
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
31 3 0.04
32 41 0.55
33 2 0.03
35 3 0.04
36 25 0.34
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.34
Consensus pattern (32 bp):
AAGGTTGTGCTTGATCCTTAAAAGGCATTGTG
Found at i:12567509 original size:63 final size:62
Alignment explanation
Indices: 12567410--12567534 Score: 225
Period size: 63 Copynumber: 2.0 Consensus size: 62
12567400 ATATATAGTT
12567410 CCATGGGCTTTATCTATATAAGTACAAAAAGTAATTAAATTACAAACTTATGGATAAAGAAC
1 CCATGGGCTTTATCTATATAAGTACAAAAAGTAATTAAATTACAAACTTATGGATAAAGAAC
12567472 NCCATGGGCTTTATCTACT-TAAGTACAAAAAGTAATTAAATTACAAACTTATGGATAAAGAAC
1 -CCATGGGCTTTATCTA-TATAAGTACAAAAAGTAATTAAATTACAAACTTATGGATAAAGAAC
12567535 TACTTCAATG
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
63 60 0.98
64 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (62 bp):
CCATGGGCTTTATCTATATAAGTACAAAAAGTAATTAAATTACAAACTTATGGATAAAGAAC
Found at i:12568100 original size:2 final size:2
Alignment explanation
Indices: 12568093--12568138 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
12568083 CCTTACTTCT
* *
12568093 TC TC TC TC TC TC T- TC TC TC TC TT TC TC TC TT TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12568134 TC TC T
1 TC TC T
12568139 ACCACTCCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (2 bp):
TC
Found at i:12573772 original size:34 final size:32
Alignment explanation
Indices: 12573720--12573782 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 32
12573710 TCCCATAATT
*
12573720 TTATATAATATAATTAATTATATTAAAATATATA
1 TTATATAATATAAATAATTA-A-TAAAATATATA
12573754 TTATATAAT-TAAAATAATTAATAAAATAT
1 TTATATAATAT-AAATAATTAATAAAATAT
12573783 TTTTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 8 0.30
33 2 0.07
34 17 0.63
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
TTATATAATATAAATAATTAATAAAATATATA
Found at i:12578140 original size:11 final size:11
Alignment explanation
Indices: 12578124--12578149 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12578114 TTATATTTTT
12578124 TAATTTTTATA
1 TAATTTTTATA
12578135 TAATTTTTATA
1 TAATTTTTATA
12578146 TAAT
1 TAAT
12578150 AAATTATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:12578141 original size:18 final size:17
Alignment explanation
Indices: 12578102--12578143 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
12578092 TTTTATCAAT
*
12578102 TATTTTTTATTTTTATA
1 TATTTTTAATTTTTATA
12578119 T-TTTTTAATTTTTATA
1 TATTTTTAATTTTTATA
12578135 TAATTTTTA
1 T-ATTTTTA
12578144 TATAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 15 0.68
17 1 0.05
18 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTTTAATTTTTATA
Found at i:12589620 original size:2 final size:2
Alignment explanation
Indices: 12589613--12589656 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12589603 TAAAATACAA
12589613 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12589655 AT
1 AT
12589657 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12591909 original size:73 final size:73
Alignment explanation
Indices: 12591827--12591967 Score: 264
Period size: 73 Copynumber: 1.9 Consensus size: 73
12591817 CATTTTACCG
*
12591827 AACATGCATTGCTGGCTAATATTTTTCCAGTTCAGGGTAAGGTAACCCTCGTATTGCTAAATTAC
1 AACATGCATTGCTGGCTAATATATTTCCAGTTCAGGGTAAGGTAACCCTCGTATTGCTAAATTAC
12591892 ATTCTGCT
66 ATTCTGCT
*
12591900 AACATGCATTGCTGGCTAATATATTTCCAGTTCAGGGTAAGGTAACCCTTGTATTGCTAAATTAC
1 AACATGCATTGCTGGCTAATATATTTCCAGTTCAGGGTAAGGTAACCCTCGTATTGCTAAATTAC
12591965 ATT
66 ATT
12591968 ATGCAAAATG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (73 bp):
AACATGCATTGCTGGCTAATATATTTCCAGTTCAGGGTAAGGTAACCCTCGTATTGCTAAATTAC
ATTCTGCT
Found at i:12612602 original size:2 final size:2
Alignment explanation
Indices: 12612595--12612619 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12612585 TAATTAAAGA
12612595 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12612620 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12619348 original size:24 final size:24
Alignment explanation
Indices: 12619320--12619374 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
12619310 AGATAGCCGA
12619320 TTGCATCAAGGACTTCAGTTAGCC
1 TTGCATCAAGGACTTCAGTTAGCC
12619344 TTGCATCAAGGACTTCAGTTAGCC
1 TTGCATCAAGGACTTCAGTTAGCC
12619368 TTGCATC
1 TTGCATC
12619375 GACAAAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (24 bp):
TTGCATCAAGGACTTCAGTTAGCC
Found at i:12619812 original size:22 final size:21
Alignment explanation
Indices: 12619774--12619816 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
12619764 TTCGATTGGT
*
12619774 ATCAGAGCATTTGGTTTTAAAG
1 ATCAGAGCATTTAG-TTTAAAG
12619796 ATCAGAG-ATTTTAGTTTAAAG
1 ATCAGAGCA-TTTAGTTTAAAG
12619817 CTTTGGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (21 bp):
ATCAGAGCATTTAGTTTAAAG
Found at i:12619847 original size:15 final size:15
Alignment explanation
Indices: 12619810--12619847 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
12619800 GAGATTTTAG
*
12619810 TTTAAAGCTTTGGAT
1 TTTAAAGTTTTGGAT
*
12619825 TTTAAAGTTTTTGAT
1 TTTAAAGTTTTGGAT
12619840 TTTAAAGT
1 TTTAAAGT
12619848 CGTTTTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTAAAGTTTTGGAT
Found at i:12626105 original size:13 final size:13
Alignment explanation
Indices: 12626087--12626113 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12626077 TGAATAAATG
12626087 TGATTTTATAAAA
1 TGATTTTATAAAA
12626100 TGATTTTATAAAA
1 TGATTTTATAAAA
12626113 T
1 T
12626114 TTTAGAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:12637294 original size:26 final size:26
Alignment explanation
Indices: 12637265--12637323 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
12637255 ATTTTCTAGT
* *
12637265 TTTCCTTTGT-TTTTCTCTTTTCTTCC
1 TTTCCTTTCTATTTTCTCTCTTCTT-C
* *
12637291 TTTCCTCTCTATTTTCTCTCTTGTTC
1 TTTCCTTTCTATTTTCTCTCTTCTTC
12637317 TTTCCTT
1 TTTCCTT
12637324 ATGGCTGGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTCCTTTCTATTTTCTCTCTTCTTC
Found at i:12637582 original size:29 final size:30
Alignment explanation
Indices: 12637544--12637606 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
12637534 TTTTTGAAAT
* **
12637544 TTACACTTTTGCCCCCGAAAAAGTGAAAAA
1 TTACACTTTTGACCCAAAAAAAGTGAAAAA
* *
12637574 TTACA-TTTTTACCCAAAAAAATTGAAAAA
1 TTACACTTTTGACCCAAAAAAAGTGAAAAA
12637603 TTAC
1 TTAC
12637607 CCATAGACAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (30 bp):
TTACACTTTTGACCCAAAAAAAGTGAAAAA
Found at i:12639326 original size:18 final size:20
Alignment explanation
Indices: 12639289--12639398 Score: 72
Period size: 18 Copynumber: 5.5 Consensus size: 20
12639279 TAAACTACAA
12639289 TAATATAATATAGCTTATAT
1 TAATATAATATAGCTTATAT
*
12639309 TAATATAGTA-AG-TTATAT
1 TAATATAATATAGCTTATAT
* *
12639327 TAAATTATTAATATCAG--AATAC
1 T-AA-TA-TAATAT-AGCTTATAT
12639349 T-ATAGTAATATAGCTTATAT
1 TAATA-TAATATAGCTTATAT
* *
12639369 TACTA-AAT-TAACTTATAT
1 TAATATAATATAGCTTATAT
12639387 TAATATTAATAT
1 TAATA-TAATAT
12639399 TATATAATAA
Statistics
Matches: 69, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
18 22 0.32
19 15 0.22
20 19 0.28
21 7 0.10
22 4 0.06
23 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (20 bp):
TAATATAATATAGCTTATAT
Found at i:12639586 original size:20 final size:20
Alignment explanation
Indices: 12639561--12639601 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
12639551 TAATTAATCA
*
12639561 ATAACAATATATTATTATAT
1 ATAACAATATACTATTATAT
12639581 ATAACAATATACTATTATAT
1 ATAACAATATACTATTATAT
12639601 A
1 A
12639602 GTATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAACAATATACTATTATAT
Found at i:12644035 original size:12 final size:15
Alignment explanation
Indices: 12644012--12644050 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 15
12644002 TTTATATAAA
12644012 AATACT-ATATTTT-
1 AATACTAATATTTTG
12644025 AAT-C-AATATTTTG
1 AATACTAATATTTTG
12644038 AATACTAATATTT
1 AATACTAATATTT
12644051 GTTTATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 8 0.36
13 6 0.27
14 1 0.05
15 7 0.32
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (15 bp):
AATACTAATATTTTG
Found at i:12645239 original size:45 final size:46
Alignment explanation
Indices: 12645165--12645261 Score: 135
Period size: 45 Copynumber: 2.1 Consensus size: 46
12645155 CATTCATCGT
*
12645165 CATAGCCGGGTGATCATCTTCGACTTATGCGCACTCCCTACT-TGCA
1 CATAGCCGGGTGATCATCATCGACTTATGCGCACTCCCTACTCT-CA
* **
12645211 CATAGCCGGGT-CTCATCATCGGTTTATGCGCACTCCCTACTCTCA
1 CATAGCCGGGTGATCATCATCGACTTATGCGCACTCCCTACTCTCA
12645256 CATAGC
1 CATAGC
12645262 TAGGTCATCA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
45 34 0.74
46 12 0.26
ACGTcount: A:0.20, C:0.34, G:0.19, T:0.28
Consensus pattern (46 bp):
CATAGCCGGGTGATCATCATCGACTTATGCGCACTCCCTACTCTCA
Found at i:12654332 original size:26 final size:26
Alignment explanation
Indices: 12654303--12654361 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
12654293 ATTTTTTAGT
* *
12654303 TTTCCTTTGT-TTTTCTCTTTTCTTCC
1 TTTCCTTTCTATTTTCTCTCTTCTT-C
* *
12654329 TTTCCTCTCTATTTTCTCTCTTGTTC
1 TTTCCTTTCTATTTTCTCTCTTCTTC
12654355 TTTCCTT
1 TTTCCTT
12654362 ATGGCCGGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTCCTTTCTATTTTCTCTCTTCTTC
Found at i:12654503 original size:21 final size:22
Alignment explanation
Indices: 12654463--12654503 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12654453 CCATTGGCTC
*
12654463 GTTTTTAAAATTTCATCCATTT
1 GTTTTCAAAATTTCATCCATTT
*
12654485 GTTTTCAAATTTTCA-CCAT
1 GTTTTCAAAATTTCATCCAT
12654504 ACACTTGTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (22 bp):
GTTTTCAAAATTTCATCCATTT
Found at i:12658459 original size:43 final size:43
Alignment explanation
Indices: 12658394--12658486 Score: 141
Period size: 43 Copynumber: 2.2 Consensus size: 43
12658384 TGCAATATCA
* * *
12658394 TCATCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGG
1 TCATCATCAGCTCATGTACACTCCCACACCGCACATAGCTAGG
* *
12658437 TCATCATCAGCTCATGTACACTCCTAGACCGCACATAGCTAGG
1 TCATCATCAGCTCATGTACACTCCCACACCGCACATAGCTAGG
12658480 TCATCAT
1 TCATCAT
12658487 TATCACATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (43 bp):
TCATCATCAGCTCATGTACACTCCCACACCGCACATAGCTAGG
Found at i:12659289 original size:20 final size:20
Alignment explanation
Indices: 12659264--12659305 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
12659254 ATGAGAAGAA
*
12659264 GAAGAAGCTGCTGGAGAAAT
1 GAAGAAGCTGCTGGAAAAAT
* *
12659284 GAAGAAGTTGCTTGAAAAAT
1 GAAGAAGCTGCTGGAAAAAT
12659304 GA
1 GA
12659306 TATTTTTAGC
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:0.43, C:0.07, G:0.31, T:0.19
Consensus pattern (20 bp):
GAAGAAGCTGCTGGAAAAAT
Found at i:12679191 original size:30 final size:29
Alignment explanation
Indices: 12679155--12679213 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
12679145 CCTTTGCACA
*
12679155 CACACACACACACAGACATATATATATAT
1 CACACACACACACACACATATATATATAT
12679184 NCACACACACACACACACATATATATATAT
1 -CACACACACACACACACATATATATATAT
12679214 ATATATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.20
Consensus pattern (29 bp):
CACACACACACACACACATATATATATAT
Found at i:12679207 original size:2 final size:2
Alignment explanation
Indices: 12679202--12679242 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
12679192 ACACACACAC
12679202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12679243 GGCAGTAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12681345 original size:72 final size:73
Alignment explanation
Indices: 12681228--12681425 Score: 251
Period size: 72 Copynumber: 2.7 Consensus size: 73
12681218 GTATTGAGAA
* **
12681228 ACAGAACCGACTTAGTCGACCAAGATGTGAGTTAGTCGACTAAATGCTTTCTGCCA-AAGTCTG-
1 ACAGAACCAACTTAGTCGACCAAGAAATGAGTTAGTCGACTAAATGCTTTCTGCCAGAA-TCTGC
**
12681291 GACTTCAAG
65 GACCACAAG
* *
12681300 ACAGAACCAACTTAGTCGACCAAGAAATGAGTTAGTCGACTAAATGCTCTCTACCAGAATCTGCG
1 ACAGAACCAACTTAGTCGACCAAGAAATGAGTTAGTCGACTAAATGCTTTCTGCCAGAATCTGCG
*
12681365 ACCAGAAG
66 ACCACAAG
* *
12681373 ATAGAACCAACTTAGTCGACCAAGAAGA-AAGTTAGTCGACTAAGA-GCTTTCTG
1 ACAGAACCAACTTAGTCGACCAAGAA-ATGAGTTAGTCGACTAA-ATGCTTTCTG
12681426 TCTGTAATTT
Statistics
Matches: 110, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
72 55 0.50
73 53 0.48
74 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (73 bp):
ACAGAACCAACTTAGTCGACCAAGAAATGAGTTAGTCGACTAAATGCTTTCTGCCAGAATCTGCG
ACCACAAG
Found at i:12687405 original size:13 final size:13
Alignment explanation
Indices: 12687387--12687412 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12687377 CTTACTTTTT
12687387 TTTTATTTATTTA
1 TTTTATTTATTTA
12687400 TTTTATTTATTTA
1 TTTTATTTATTTA
12687413 ATTATTAAAT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:12687408 original size:17 final size:17
Alignment explanation
Indices: 12687383--12687418 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12687373 CTAACTTACT
* *
12687383 TTTTTTTTATTTATTTA
1 TTTTATTTATTTAATTA
12687400 TTTTATTTATTTAATTA
1 TTTTATTTATTTAATTA
12687417 TT
1 TT
12687419 AAATTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTATTTAATTA
Found at i:12687809 original size:48 final size:50
Alignment explanation
Indices: 12687736--12687829 Score: 147
Period size: 48 Copynumber: 1.9 Consensus size: 50
12687726 GGCAGGCCGT
*
12687736 AGCCCCCTTTGATGTGGGCTACCAACAATGGGCAGCCCAC-TACCCCATA
1 AGCCCCCTTTGAAGTGGGCTACCAACAATGGGCAGCCCACTTACCCCATA
* *
12687785 AGCCCCC-TTGAAGTGGGCTGCCAACAATGGGCTGCCCACTTACCC
1 AGCCCCCTTTGAAGTGGGCTACCAACAATGGGCAGCCCACTTACCC
12687830 ACTTACCCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 29 0.71
49 12 0.29
ACGTcount: A:0.22, C:0.37, G:0.22, T:0.18
Consensus pattern (50 bp):
AGCCCCCTTTGAAGTGGGCTACCAACAATGGGCAGCCCACTTACCCCATA
Found at i:12693586 original size:25 final size:25
Alignment explanation
Indices: 12693557--12693611 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
12693547 CACAACCACA
**
12693557 TATATCAACTTGTGGCCTAGCCATG
1 TATATCAACCCGTGGCCTAGCCATG
* *
12693582 TATATTAACCCGTGGCCTTGCCATG
1 TATATCAACCCGTGGCCTAGCCATG
12693607 TATAT
1 TATAT
12693612 ATCACAGACC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (25 bp):
TATATCAACCCGTGGCCTAGCCATG
Found at i:12696283 original size:37 final size:37
Alignment explanation
Indices: 12696242--12696351 Score: 103
Period size: 37 Copynumber: 3.0 Consensus size: 37
12696232 AAAATGTTGT
* **
12696242 ATGATGATAATGAGGTGTGCGAGTAGGGAGTGCACAC
1 ATGATGATATTGAAATGTGCGAGTAGGGAGTGCACAC
* * * *
12696279 ATGATGACATTAAAATGTGCGAATAGGGAGTGCACAT
1 ATGATGATATTGAAATGTGCGAGTAGGGAGTGCACAC
* * *** *
12696316 ATGGTGGTATTGCCTTGTGCGTGTAGGGAGTGCACA
1 ATGATGATATTGAAATGTGCGAGTAGGGAGTGCACA
12696352 AGAACTGAGG
Statistics
Matches: 57, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.28, C:0.12, G:0.35, T:0.25
Consensus pattern (37 bp):
ATGATGATATTGAAATGTGCGAGTAGGGAGTGCACAC
Found at i:12703313 original size:2 final size:2
Alignment explanation
Indices: 12703306--12703352 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
12703296 TGGACATTCT
12703306 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12703348 AG AG A
1 AG AG A
12703353 CTTTCCACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12713219 original size:22 final size:22
Alignment explanation
Indices: 12713177--12713236 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
12713167 TCCCTTTTAG
* *
12713177 CTTTCCTTCTTTC-TCCCTTCTC
1 CTTT-CTTCTTTCTTTCTTTCTC
12713199 CTTT-TTCTTTTCTTTCTTTCTC
1 CTTTCTTC-TTTCTTTCTTTCTC
*
12713221 TTTTCTTCTTTCTTTC
1 CTTTCTTCTTTCTTTC
12713237 AAGCCGATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
20 3 0.09
21 4 0.12
22 22 0.69
23 3 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (22 bp):
CTTTCTTCTTTCTTTCTTTCTC
Found at i:12713222 original size:15 final size:14
Alignment explanation
Indices: 12713177--12713233 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
12713167 TCCCTTTTAG
*
12713177 CTTTCCTTCTTTCT
1 CTTTTCTTCTTTCT
** * *
12713191 CCCTTCTCCTTTTT
1 CTTTTCTTCTTTCT
12713205 CTTTTCTTTCTTTCT
1 CTTTTC-TTCTTTCT
12713220 CTTTTCTTCTTTCT
1 CTTTTCTTCTTTCT
12713234 TTCAAGCCGA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
CTTTTCTTCTTTCT
Found at i:12714287 original size:17 final size:19
Alignment explanation
Indices: 12714247--12714293 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
12714237 TTAATATTTT
12714247 AATATTATTTTATTCATAA
1 AATATTATTTTATTCATAA
12714266 AATATTATTTTATTC-T-A
1 AATATTATTTTATTCATAA
*
12714283 AATATTCTTTT
1 AATATTATTTT
12714294 CACATGTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 11 0.41
18 1 0.04
19 15 0.56
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:12718958 original size:40 final size:40
Alignment explanation
Indices: 12718903--12718986 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
12718893 AAGCCAAGGA
12718903 CTTAAATGTTATAACTTTGGATGAAATTTGTGGTTCTCTC
1 CTTAAATGTTATAACTTTGGATGAAATTTGTGGTTCTCTC
*
12718943 CTTAAATGTTATAACTTTGGATGAAATTTGTGGTTTTCTC
1 CTTAAATGTTATAACTTTGGATGAAATTTGTGGTTCTCTC
12718983 CTTA
1 CTTA
12718987 CTCATGAGCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (40 bp):
CTTAAATGTTATAACTTTGGATGAAATTTGTGGTTCTCTC
Found at i:12727631 original size:14 final size:14
Alignment explanation
Indices: 12727612--12727638 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12727602 AAGAAGAACA
12727612 AGCTAAAAGGAAAC
1 AGCTAAAAGGAAAC
12727626 AGCTAAAAGGAAA
1 AGCTAAAAGGAAA
12727639 GCACAAAAGT
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:0.59, C:0.11, G:0.22, T:0.07
Consensus pattern (14 bp):
AGCTAAAAGGAAAC
Found at i:12728578 original size:17 final size:17
Alignment explanation
Indices: 12728552--12728587 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12728542 AAGTAAAATA
12728552 AGCACACACTAAGGGGG
1 AGCACACACTAAGGGGG
* *
12728569 AGCACTCACTTAGGGGG
1 AGCACACACTAAGGGGG
12728586 AG
1 AG
12728588 AAATCCTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.36, T:0.11
Consensus pattern (17 bp):
AGCACACACTAAGGGGG
Found at i:12734845 original size:43 final size:43
Alignment explanation
Indices: 12734727--12734848 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
12734717 TGACTCGACT
* **
12734727 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
12734770 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
12734813 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
12734849 TGATGATGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:12734859 original size:20 final size:19
Alignment explanation
Indices: 12734834--12734896 Score: 90
Period size: 20 Copynumber: 3.2 Consensus size: 19
12734824 GGGAGTGCGC
12734834 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGA-GATGATG
12734854 ATGAGCTGGTGACGATGATG
1 ATGAGCTGGTGA-GATGATG
* *
12734874 ATGGGTTGGTGAGATGATG
1 ATGAGCTGGTGAGATGATG
12734893 ATGA
1 ATGA
12734897 TGTGTATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 10 0.26
20 29 0.74
ACGTcount: A:0.25, C:0.05, G:0.41, T:0.29
Consensus pattern (19 bp):
ATGAGCTGGTGAGATGATG
Found at i:12737643 original size:43 final size:42
Alignment explanation
Indices: 12737572--12737693 Score: 183
Period size: 43 Copynumber: 2.9 Consensus size: 42
12737562 GTAATTATGT
* *
12737572 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCT-GAGAA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAA-CTAGAG-A
*
12737615 TGACCCGGTTATGTGCGAGTAGGAAGTGCGCATAACTAGATGA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACTAGA-GA
12737658 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAAC
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAAC
12737694 CCGGTGATGA
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
42 2 0.03
43 70 0.96
44 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.22
Consensus pattern (42 bp):
TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACTAGAGA
Found at i:12737702 original size:43 final size:43
Alignment explanation
Indices: 12737572--12737728 Score: 181
Period size: 43 Copynumber: 3.7 Consensus size: 43
12737562 GTAATTATGT
* * * *
12737572 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCTGAG-AA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCAG-GTGA
* * * *
12737615 TGACCCGGTTATGTGCGAGTAGGAAGTGCGCATAACTAGATGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCAGGTGA
* *
12737658 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCAGGTGA
* * *
12737701 TGACCCAGCCATGTGCGAGTAAGGAGTG
1 TGACCCGGCTATGTGCGAGTAGGGAGTG
12737729 TTCATGAGCT
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 97 1.00
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCAGGTGA
Found at i:12738119 original size:43 final size:42
Alignment explanation
Indices: 12738048--12738151 Score: 140
Period size: 43 Copynumber: 2.4 Consensus size: 42
12738038 CTATGTGTGG
*
12738048 GTAGGGAGTGCGCATAAGCTGAGAATGACCCGGTTAGGTGCGA
1 GTAGGAAGTGCGCATAA-CTGAGAATGACCCGGTTAGGTGCGA
*
12738091 GTAGGAAGTGCGCATAACT-AGATGATGACCCGGTTATGTGCGA
1 GTAGGAAGTGCGCATAACTGAGA--ATGACCCGGTTAGGTGCGA
12738134 GTAGGGAA-TGCGCATAAC
1 GTA-GGAAGTGCGCATAAC
12738152 CCGGTGATGA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
41 3 0.05
42 2 0.04
43 47 0.84
44 4 0.07
ACGTcount: A:0.28, C:0.16, G:0.36, T:0.20
Consensus pattern (42 bp):
GTAGGAAGTGCGCATAACTGAGAATGACCCGGTTAGGTGCGA
Found at i:12738148 original size:458 final size:458
Alignment explanation
Indices: 12737287--12738200 Score: 1661
Period size: 459 Copynumber: 2.0 Consensus size: 458
12737277 TGAGACGTCA
* *
12737287 GGAAAAGGCAAAGGAATTGCGCCTGAGGACTATTAGTCCGAGTGCACTCGGAATCTAGATTTTCG
1 GGAAAAGGCAAAGGAATTGCCCCTGAGGACTATTAGTCCGAGTGCACTCGGAATCCAGATTTTCG
* *
12737352 ACACCTGTGAGTGGACTGCCTATCAAAATTGTTTTGGGAATATAACTATTTTGAACAAAGTGTTT
66 ACACATGTGAGTGGACTGCCTATCAAAATTGTTTTGGGAATATAACTATGTTGAACAAAGTGTTT
*
12737417 GAATGATTTTATGCAATTTTTCATGAAAATGAATGCCTTGGGAACAAGCTTTTGAGAAAAGGTTT
131 GAATGATTTTATGCAATTTTTCATGAAAATGAATGCCTTGGGAACAAGCTTTTGAGAAAAGGTGT
12737482 ATGTTATGAAATGTGGTTATTATGGATTTCTATGTGGCTGCATTATGTTGATATACATATATGCT
196 ATGTTATGAAATGTGGTTATTATGGATTTCTATGTGGCTGCATTATGTTGATATACATATATGCT
12737547 TGAATATAATGTTGTGTAATTATGTTGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCTGA
261 TGAATATAATGTTGTGTAATTATGTTGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCTGA
*
12737612 GAATGACCCGGTTATGTGCGAGTAGGAAGTGCGCATAACTAGATGATGACCCGGTTATGTGCGAG
326 GAATGACCCGGTTAGGTGCGAGTAGGAAGTGCGCATAACTAGATGATGACCCGGTTATGTGCGAG
*
12737677 TAGGGAGTGCGCATAACCCGGTGATGA-CCCAGCCATGTGCGAGTAAGGAGTGTTCATGAGCTGG
391 TAGGGAATGCGCATAACCCGGTGATGACCCCAGCCATGTGCGAGTAAGGAGTGTTCATGAGCTGG
12737741 TNTC
456 T-TC
*
12737745 GGAAAAGGCAAAGGAATTGCCCCTGAGGACTATTAGTCTGAGTGCACTCGGAATCCAGATTTTTC
1 GGAAAAGGCAAAGGAATTGCCCCTGAGGACTATTAGTCCGAGTGCACTCGGAATCCAGA-TTTTC
* *
12737810 GACACATGTGAGTTGACTGCCTATCAAAATTGTTTTGGGAATATGACTATGTTGAACAAAGTGTT
65 GACACATGTGAGTGGACTGCCTATCAAAATTGTTTTGGGAATATAACTATGTTGAACAAAGTGTT
12737875 TGAATGATTTTATGCAATTTTTCATGAAAATGAATGCCTTGGGAACAAGCTTTTGAGAAAAGGTG
130 TGAATGATTTTATGCAATTTTTCATGAAAATGAATGCCTTGGGAACAAGCTTTTGAGAAAAGGTG
* *
12737940 TATGTTATGAAATGTGGTTATTATGGATTTCTATTTGGCTGCATTTTGTTGATATACATATATGC
195 TATGTTATGAAATGTGGTTATTATGGATTTCTATGTGGCTGCATTATGTTGATATACATATATGC
* * *
12738005 TTGGATATAATGTTGTGTAATTAT-TTGACTCGGCTATGTGTGGGTAGGGAGTGCGCATAAGCTG
260 TTGAATATAATGTTGTGTAATTATGTTGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCTG
12738069 AGAATGACCCGGTTAGGTGCGAGTAGGAAGTGCGCATAACTAGATGATGACCCGGTTATGTGCGA
325 AGAATGACCCGGTTAGGTGCGAGTAGGAAGTGCGCATAACTAGATGATGACCCGGTTATGTGCGA
12738134 GTAGGGAATGCGCATAACCCGGTGATGACCCCAGCCATGTGCGAGTAAGGAGTGTTCATGAGCTG
390 GTAGGGAATGCGCATAACCCGGTGATGACCCCAGCCATGTGCGAGTAAGGAGTGTTCATGAGCTG
12738199 GT
455 GT
12738201 GATGATGATG
Statistics
Matches: 439, Mismatches: 15, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
458 185 0.42
459 254 0.58
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (458 bp):
GGAAAAGGCAAAGGAATTGCCCCTGAGGACTATTAGTCCGAGTGCACTCGGAATCCAGATTTTCG
ACACATGTGAGTGGACTGCCTATCAAAATTGTTTTGGGAATATAACTATGTTGAACAAAGTGTTT
GAATGATTTTATGCAATTTTTCATGAAAATGAATGCCTTGGGAACAAGCTTTTGAGAAAAGGTGT
ATGTTATGAAATGTGGTTATTATGGATTTCTATGTGGCTGCATTATGTTGATATACATATATGCT
TGAATATAATGTTGTGTAATTATGTTGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCTGA
GAATGACCCGGTTAGGTGCGAGTAGGAAGTGCGCATAACTAGATGATGACCCGGTTATGTGCGAG
TAGGGAATGCGCATAACCCGGTGATGACCCCAGCCATGTGCGAGTAAGGAGTGTTCATGAGCTGG
TTC
Found at i:12738160 original size:43 final size:43
Alignment explanation
Indices: 12738048--12738164 Score: 139
Period size: 43 Copynumber: 2.7 Consensus size: 43
12738038 CTATGTGTGG
* * *
12738048 GTAGGGAGTGCGCATAAGCTGA-GAATGACCCGGTTAGGTGCGA
1 GTAGGAAGTGCGCATAACCAGATG-ATGACCCGGTTAGGTGCGA
* *
12738091 GTAGGAAGTGCGCATAACTAGATGATGACCCGGTTATGTGCGA
1 GTAGGAAGTGCGCATAACCAGATGATGACCCGGTTAGGTGCGA
* *
12738134 GTAGGGAA-TGCGCATAACCCGGTGATGACCC
1 GTA-GGAAGTGCGCATAACCAGATGATGACCC
12738165 CAGCCATGTG
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 59 0.92
44 5 0.08
ACGTcount: A:0.26, C:0.19, G:0.35, T:0.20
Consensus pattern (43 bp):
GTAGGAAGTGCGCATAACCAGATGATGACCCGGTTAGGTGCGA
Found at i:12738216 original size:20 final size:20
Alignment explanation
Indices: 12738191--12738255 Score: 94
Period size: 20 Copynumber: 3.1 Consensus size: 20
12738181 AGGAGTGTTC
12738191 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
12738211 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
* *
12738231 ATGCGTTGGTGGGATGATGATG
1 ATGAGCTGGT--GATGATGATG
12738253 ATG
1 ATG
12738256 GGTATATACG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
20 28 0.68
22 13 0.32
ACGTcount: A:0.23, C:0.05, G:0.42, T:0.31
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:12743610 original size:43 final size:43
Alignment explanation
Indices: 12743556--12743680 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 43
12743546 TCATTCATCG
*
12743556 TCATGTGCACTCCTTACTCGCACATAGCCGGGTCATCATC-GAC
1 TCATGCGCACTCCTTACTCGCACATAGCCGGGTCATCATCAG-C
* * *
12743599 TTATGCGCACTCCTTACTCGCACATAACCGAGTCATCATCAGC
1 TCATGCGCACTCCTTACTCGCACATAGCCGGGTCATCATCAGC
* * * *
12743642 TCATGTGCACTCC-CACACTGCACATAGCTGGGTCATCAT
1 TCATGCGCACTCCTTACTC-GCACATAGCCGGGTCATCAT
12743681 TATCACACAA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 3 0.04
43 65 0.94
44 1 0.01
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (43 bp):
TCATGCGCACTCCTTACTCGCACATAGCCGGGTCATCATCAGC
Found at i:12749271 original size:22 final size:22
Alignment explanation
Indices: 12749246--12749294 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
12749236 TCGTTACAGC
*
12749246 GAGAATCCAT-TTTCACTGTAGT
1 GAGAATCC-TCTTTCACTGCAGT
*
12749268 GAGAATTCTCTTTCACTGCAGT
1 GAGAATCCTCTTTCACTGCAGT
12749290 GAGAA
1 GAGAA
12749295 ACAGGGCTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (22 bp):
GAGAATCCTCTTTCACTGCAGT
Found at i:12758069 original size:16 final size:16
Alignment explanation
Indices: 12758050--12758084 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12758040 GTATAAATCT
*
12758050 CATTTTTATTAAAAAA
1 CATTTTAATTAAAAAA
*
12758066 CATTTTAATTAGAAAA
1 CATTTTAATTAAAAAA
12758082 CAT
1 CAT
12758085 AATATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.40
Consensus pattern (16 bp):
CATTTTAATTAAAAAA
Found at i:12779042 original size:74 final size:72
Alignment explanation
Indices: 12778865--12779059 Score: 205
Period size: 73 Copynumber: 2.7 Consensus size: 72
12778855 TTGGTCAGTC
* * * * *
12778865 CAGAAATAGAAAAAACTTAGTCGACCAATAATCATGGTTAGTCGACTAATGTTCACTACCAGAAA
1 CAGAAATAGAAAAGACTTAGTCGACCAAGAAGCATGGTTAGTCGACTAATGCTCACTACCAAAAA
*
12778930 CTTCAAT
66 CTTAAAT
* * *
12778937 CAGAAAACAGAGAAGACTTAGTCGACCAAGAAGCATGGTTAGTTGACTAAGTGCTCACTACCAAA
1 CAG-AAATAGAAAAGACTTAGTCGACCAAGAAGCATGGTTAGTCGACTAA-TGCTCACTACCAAA
12779002 AAC-TAAGAT
64 AACTTAA-AT
* * * ** *
12779011 TAGAAGATAGAAAAGACTTTGTCGACTAAGAATTAT-GTTAGTCAACTAA
1 CAGAA-ATAGAAAAGACTTAGTCGACCAAGAAGCATGGTTAGTCGACTAA
12779060 GAGCACACTA
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
72 3 0.03
73 55 0.54
74 43 0.43
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (72 bp):
CAGAAATAGAAAAGACTTAGTCGACCAAGAAGCATGGTTAGTCGACTAATGCTCACTACCAAAAA
CTTAAAT
Found at i:12819890 original size:31 final size:32
Alignment explanation
Indices: 12819833--12819895 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 32
12819823 TATTTCAGCA
*
12819833 TAAAAATACAGCATGAAAACATAAACATTGTT
1 TAAAAACACAGCATGAAAACATAAACATTGTT
*
12819865 TAAAAACACAGCAT-AAAGCATAAACATTGTT
1 TAAAAACACAGCATGAAAACATAAACATTGTT
12819896 CAACCTAGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 16 0.55
32 13 0.45
ACGTcount: A:0.52, C:0.14, G:0.10, T:0.24
Consensus pattern (32 bp):
TAAAAACACAGCATGAAAACATAAACATTGTT
Found at i:12820890 original size:73 final size:73
Alignment explanation
Indices: 12820771--12820920 Score: 212
Period size: 73 Copynumber: 2.1 Consensus size: 73
12820761 ATTGAGAAAC
* * *
12820771 AGAAAAGGCTTAGTCGACTAAGAGCCTATTATCAGAAATCTGGACTTCAAGACA-AAACCAACTT
1 AGAAAAGGCTTAGTCGACTAAAAGCCTACTACCAGAAATCTGGACTTCAAGACAGAAA-CAACTT
12820835 AATCGACTA
65 AATCGACTA
* * * * *
12820844 AGAAAAGGGTTAGTCGACTAAAAGGCTACTGCCAGAAATTTGGACTTCAAGACAGAAATAACTTA
1 AGAAAAGGCTTAGTCGACTAAAAGCCTACTACCAGAAATCTGGACTTCAAGACAGAAACAACTTA
12820909 ATCGACTA
66 ATCGACTA
12820917 AGAA
1 AGAA
12820921 GAAAATTAGT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
73 65 0.96
74 3 0.04
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (73 bp):
AGAAAAGGCTTAGTCGACTAAAAGCCTACTACCAGAAATCTGGACTTCAAGACAGAAACAACTTA
ATCGACTA
Found at i:12820930 original size:73 final size:73
Alignment explanation
Indices: 12820771--12820958 Score: 195
Period size: 73 Copynumber: 2.6 Consensus size: 73
12820761 ATTGAGAAAC
** * * *
12820771 AGAAAAGGCTTAGTCGACTAAGAGCCTATTATCAGAAATCTGGACTTCAAGACAAAACCAACTTA
1 AGAAAAGAATTAGTCGACTAAAAGCCTACTACCAGAAATCTGGACTTCAAGACAAAACCAACTTA
12820836 ATCGACTA
66 ATCGACTA
** * * * *
12820844 AGAAAAGGGTTAGTCGACTAAAAGGCTACTGCCAGAAATTTGGACTTCAAGACAGAAA-TAACTT
1 AGAAAAGAATTAGTCGACTAAAAGCCTACTACCAGAAATCTGGACTTCAAGACA-AAACCAACTT
12820908 AATCGACTA
65 AATCGACTA
* **
12820917 AGAAGAA-AATTAGTCAACTAAGTG-CTCACTACCAGAAA-CTGG
1 AGAA-AAGAATTAGTCGACTAAAAGCCT-ACTACCAGAAATCTGG
12820959 GATCAGAAAA
Statistics
Matches: 97, Mismatches: 15, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
72 5 0.05
73 87 0.90
74 5 0.05
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (73 bp):
AGAAAAGAATTAGTCGACTAAAAGCCTACTACCAGAAATCTGGACTTCAAGACAAAACCAACTTA
ATCGACTA
Found at i:12826801 original size:14 final size:14
Alignment explanation
Indices: 12826778--12826812 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
12826768 GATAAAGATG
*
12826778 AAAGATAGAAAAGA
1 AAAGAAAGAAAAGA
*
12826792 TAAGAAAGAAAAGA
1 AAAGAAAGAAAAGA
12826806 AAAGAAA
1 AAAGAAA
12826813 AGTCAAAGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (14 bp):
AAAGAAAGAAAAGA
Found at i:12826808 original size:19 final size:19
Alignment explanation
Indices: 12826755--12826810 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
12826745 GCCAAGTTAG
*
12826755 TAAGAAAGAATGAGATAAAGA
1 TAAGAAAGAA-AAGA-AAAGA
*
12826776 T--GAAAG-ATAGAAAAGA
1 TAAGAAAGAAAAGAAAAGA
12826792 TAAGAAAGAAAAGAAAAGA
1 TAAGAAAGAAAAGAAAAGA
12826811 AAAGTCAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
16 6 0.20
17 3 0.10
18 6 0.20
19 14 0.47
21 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (19 bp):
TAAGAAAGAAAAGAAAAGA
Found at i:12827412 original size:24 final size:25
Alignment explanation
Indices: 12827352--12827423 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
12827342 AAAGAAGAAA
* *
12827352 AAGAAAAGAGTGGGCATAGCCTAAT
1 AAGAAAAGAATGGGCATAGCCCAAT
*
12827377 AAGAAAAGAATGGGCATGGCCCAAT
1 AAGAAAAGAATGGGCATAGCCCAAT
* *
12827402 -AG-AAAGAAATGGGAAGAGCCCA
1 AAGAAAAG-AATGGGCATAGCCCA
12827424 TGGAAAGGGC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 4 0.10
24 14 0.35
25 22 0.55
ACGTcount: A:0.46, C:0.14, G:0.29, T:0.11
Consensus pattern (25 bp):
AAGAAAAGAATGGGCATAGCCCAAT
Found at i:12833008 original size:19 final size:19
Alignment explanation
Indices: 12832984--12833021 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12832974 CCATTTGACA
12832984 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
12833003 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
12833022 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:12844363 original size:137 final size:136
Alignment explanation
Indices: 12844117--12844389 Score: 456
Period size: 137 Copynumber: 2.0 Consensus size: 136
12844107 ATATGGCAAA
* * *
12844117 AACCAGCCAAATGATAAGTGGAACAAAAATTTTTATTCTCGCTGTAGCGAGAAACAGAGCAACAA
1 AACCAGCCAAATGATAAGCGGAACAAAAAGTTTCATTCTCGCTGTAGCGAGAAACAGAGCAACAA
* *
12844182 GAAAGACTTCCTTTCATCTCAAATAAACCATTTCACTGCAATGCAAATCAATTTGGAACACTAAA
66 GAAAGACTTCCTTTCATCCCAAATAAACCATTTCACTGCAATGCAAATCAATTTAGAACACTAAA
12844247 AAAAAT
131 AAAAAT
* * *
12844253 NAACCAGCCAAGTGATAAGCGGCACAGAAAGTTTCATTCTCGCTGTAGCGAGAAACAGAGCAACA
1 -AACCAGCCAAATGATAAGCGGAACAAAAAGTTTCATTCTCGCTGTAGCGAGAAACAGAGCAACA
*
12844318 AGCAAGACTTCCTTTCATCCCAAATAAACCATTTCACTGCAATGCAAATCAATTTAGAACACTAA
65 AGAAAGACTTCCTTTCATCCCAAATAAACCATTTCACTGCAATGCAAATCAATTTAGAACACTAA
12844383 AAAAAAT
130 AAAAAAT
12844390 GCTCAAGGTT
Statistics
Matches: 127, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
137 127 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (136 bp):
AACCAGCCAAATGATAAGCGGAACAAAAAGTTTCATTCTCGCTGTAGCGAGAAACAGAGCAACAA
GAAAGACTTCCTTTCATCCCAAATAAACCATTTCACTGCAATGCAAATCAATTTAGAACACTAAA
AAAAAT
Found at i:12844590 original size:42 final size:42
Alignment explanation
Indices: 12844495--12844661 Score: 192
Period size: 42 Copynumber: 4.0 Consensus size: 42
12844485 TCTCCCATCG
* * * * * *
12844495 TCATCAGCTCATGTGCACTCCCAACTAGCACATGGCTGGGTCA
1 TCATCAGCTTATGCGCACT-CCTACTCGCACATAGCCGGGTCA
* * *
12844538 GCATCGGCTTATGCGCACTCCTACTCGCACATAGCCGGGTTA
1 TCATCAGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCA
* *
12844580 TCATCAGCTTATGCGCACTCTTACTCGCACATAGTCGGGTCA
1 TCATCAGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCA
** *
12844622 T-ATTGGCTTATGCGCACTCCTACTCGCACATAGTCGGGTC
1 TCATCAGCTTATGCGCACTCCTACTCGCACATAGCCGGGTC
12844662 CACATCAACA
Statistics
Matches: 107, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 36 0.34
42 56 0.52
43 15 0.14
ACGTcount: A:0.20, C:0.32, G:0.22, T:0.26
Consensus pattern (42 bp):
TCATCAGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCA
Found at i:12844646 original size:41 final size:42
Alignment explanation
Indices: 12844532--12844661 Score: 199
Period size: 42 Copynumber: 3.1 Consensus size: 42
12844522 GCACATGGCT
* *
12844532 GGGTCAGCATCGGCTTATGCGCACTCCTACTCGCACATAGCC
1 GGGTCATCATCGGCTTATGCGCACTCCTACTCGCACATAGTC
* * *
12844574 GGGTTATCATCAGCTTATGCGCACTCTTACTCGCACATAGTC
1 GGGTCATCATCGGCTTATGCGCACTCCTACTCGCACATAGTC
*
12844616 GGGTCAT-ATTGGCTTATGCGCACTCCTACTCGCACATAGTC
1 GGGTCATCATCGGCTTATGCGCACTCCTACTCGCACATAGTC
12844657 GGGTC
1 GGGTC
12844662 CACATCAACA
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 36 0.46
42 43 0.54
ACGTcount: A:0.19, C:0.31, G:0.23, T:0.27
Consensus pattern (42 bp):
GGGTCATCATCGGCTTATGCGCACTCCTACTCGCACATAGTC
Found at i:12853743 original size:73 final size:73
Alignment explanation
Indices: 12853618--12853790 Score: 197
Period size: 73 Copynumber: 2.4 Consensus size: 73
12853608 AATAGAGAAG
* * * * *
12853618 ACTTAGTCGACCAAGAAATATGTTAGTTGACTAAGAGCCTACTGCTAGAAATCTAGATTTCAAGA
1 ACTTAATCGACCAAGAAATAGGTTAGTAGACTAAGAGCCTACTGCTAAAAATCTAGACTTCAAGA
* *
12853683 CAGAACCA
66 CAAAAACA
* * *
12853691 ACTTAATCGACCAAGAAA-AGGGTTAGTAGACTAAGAGGCTATTG-TCAAAAATCTGGACTTCAA
1 ACTTAATCGACCAAGAAATA-GGTTAGTAGACTAAGAGCCTACTGCT-AAAAATCTAGACTTCAA
12853754 GACAAAAACA
64 GACAAAAACA
* * *
12853764 ACTTAATCGACTAAGAAGTAAGTTAGT
1 ACTTAATCGACCAAGAAATAGGTTAGT
12853791 CGATTAAGTG
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
72 2 0.02
73 81 0.96
74 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (73 bp):
ACTTAATCGACCAAGAAATAGGTTAGTAGACTAAGAGCCTACTGCTAAAAATCTAGACTTCAAGA
CAAAAACA
Found at i:12854185 original size:73 final size:73
Alignment explanation
Indices: 12854060--12854240 Score: 195
Period size: 73 Copynumber: 2.5 Consensus size: 73
12854050 AATAGAAAAG
* * * * *
12854060 ACTTAGTCGACCAAGAAATATGTTAGTTGACTAAGAGCCTACTGCTAGAAATCTAGATTTCAAGA
1 ACTTAATCGACCAAGAAATAGGTTAGTAGACTAAGAGCCTACTGCTAAAAATCTAGACTTCAAGA
* *
12854125 CAGAACCA
66 CAAAAACA
* * *
12854133 ACTTAATCGACCAAGAAA-AGGGTTAGTAGACTAAGAGGCTATTG-TCAAAAATCTGGACTTCAA
1 ACTTAATCGACCAAGAAATA-GGTTAGTAGACTAAGAGCCTACTGCT-AAAAATCTAGACTTCAA
12854196 GACAAAAACA
64 GACAAAAACA
* ** * *
12854206 ACTTAATCGACTAAGAAGGAAGTTAGTCGACTAAG
1 ACTTAATCGACCAAGAAATAGGTTAGTAGACTAAG
12854241 TGCTCACTGC
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
72 2 0.02
73 88 0.97
74 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (73 bp):
ACTTAATCGACCAAGAAATAGGTTAGTAGACTAAGAGCCTACTGCTAAAAATCTAGACTTCAAGA
CAAAAACA
Found at i:12876656 original size:20 final size:20
Alignment explanation
Indices: 12876631--12876671 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
12876621 CCTTTATTTC
*
12876631 TTTCTTTTCC-TTCCATTCTT
1 TTTCTTCTCCTTTCC-TTCTT
12876651 TTTCTTCTCCTTTCCTTCTT
1 TTTCTTCTCCTTTCCTTCTT
12876671 T
1 T
12876672 CTCCAACCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTCTTCTCCTTTCCTTCTT
Found at i:12877298 original size:47 final size:46
Alignment explanation
Indices: 12877234--12877326 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 46
12877224 TTTTTTTTTA
* *
12877234 TTTCTCTTTTTCCTTTATTGTTTCATTTGGCCAACCCCTACCATCC
1 TTTCTCTTCTTCCTTTATTGTTTCATTTAGCCAACCCCTACCATCC
* * **
12877280 TTTCTTCTTCTTCTTTTATTGTTTTATTTAGCCGGCCCCTACCATCC
1 TTTC-TCTTCTTCCTTTATTGTTTCATTTAGCCAACCCCTACCATCC
12877327 ATTCACAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 4 0.10
47 36 0.90
ACGTcount: A:0.12, C:0.31, G:0.08, T:0.49
Consensus pattern (46 bp):
TTTCTCTTCTTCCTTTATTGTTTCATTTAGCCAACCCCTACCATCC
Found at i:12877447 original size:22 final size:19
Alignment explanation
Indices: 12877405--12877443 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
12877395 CATTCTTCCC
12877405 TTATTTTATTATTTATTTA
1 TTATTTTATTATTTATTTA
12877424 TTATTATTATATATTTATTT
1 TTATT-TTAT-TATTTATTT
12877444 TATTTAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATTTTATTATTTATTTA
Found at i:12877851 original size:18 final size:19
Alignment explanation
Indices: 12877804--12877851 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
12877794 TTAATATTTT
12877804 AATATTATTTTATTCATAA
1 AATATTATTTTATTCATAA
* *
12877823 AATAATATTTTATT-TTAA
1 AATATTATTTTATTCATAA
*
12877841 AATATTCTTTT
1 AATATTATTTT
12877852 CGCCCCGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:12879447 original size:20 final size:21
Alignment explanation
Indices: 12879406--12879450 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
12879396 CCTAGGTCAA
12879406 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGTGTG
12879427 AAAATTCAA-GGAAACAG-GTG
1 AAAATTCAAGGGAAA-AGTGTG
12879447 AAAA
1 AAAA
12879451 AAGGGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.53, C:0.07, G:0.24, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGTGTG
Found at i:12879451 original size:21 final size:22
Alignment explanation
Indices: 12879405--12879451 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
12879395 CCCTAGGTCA
12879405 AAAAATTCAAGGGAAAAGTGTG
1 AAAAATTCAAGGGAAAAGTGTG
12879427 -AAAATTCAA-GGAAACAG-GTG
1 AAAAATTCAAGGGAAA-AGTGTG
12879447 AAAAA
1 AAAAA
12879452 AGGGTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.55, C:0.06, G:0.23, T:0.15
Consensus pattern (22 bp):
AAAAATTCAAGGGAAAAGTGTG
Found at i:12881809 original size:5 final size:5
Alignment explanation
Indices: 12881799--12881824 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12881789 CAGTGTGGCC
12881799 TAAGT TAAGT TAAGT TAAGT TAAGT T
1 TAAGT TAAGT TAAGT TAAGT TAAGT T
12881825 TGATAGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.42
Consensus pattern (5 bp):
TAAGT
Found at i:12889170 original size:22 final size:21
Alignment explanation
Indices: 12889131--12889171 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12889121 CCTAGGTCAA
**
12889131 AAAATTCAAGGGCAAAGTGTG
1 AAAATTCAAGGAAAAAGTGTG
12889152 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAA-AAGTG
12889172 AAAAAAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.49, C:0.10, G:0.24, T:0.17
Consensus pattern (21 bp):
AAAATTCAAGGAAAAAGTGTG
Found at i:12889177 original size:22 final size:21
Alignment explanation
Indices: 12889129--12889177 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
12889119 ACCCTAGGTC
**
12889129 AAAAAATTCAAGGGCAAAGTG
1 AAAAAATTCAAGGAAAAAGTG
**
12889150 TGAAAATTCAAGGAAACAAGTG
1 AAAAAATTCAAGGAAA-AAGTG
12889172 AAAAAA
1 AAAAAA
12889178 GGGTAAAAAT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.57, C:0.08, G:0.20, T:0.14
Consensus pattern (21 bp):
AAAAAATTCAAGGAAAAAGTG
Found at i:12891820 original size:19 final size:19
Alignment explanation
Indices: 12891796--12891833 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12891786 CCATTTAACT
*
12891796 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
12891815 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
12891834 GGTTTGGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:12893577 original size:30 final size:30
Alignment explanation
Indices: 12893543--12893600 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
12893533 AACAATCATC
* *
12893543 AAAGAATGTATGAGTTTTCTACACTTAGTT
1 AAAGAATGCATGAGTTTTCTACAATTAGTT
*
12893573 AAAGATTGCATGAGTTTTCTACAATTAG
1 AAAGAATGCATGAGTTTTCTACAATTAG
12893601 ATACAATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (30 bp):
AAAGAATGCATGAGTTTTCTACAATTAGTT
Found at i:12894536 original size:22 final size:22
Alignment explanation
Indices: 12894508--12894556 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
12894498 GATAAGCTTG
12894508 AGCTTTTTATCATATTTCCAGT
1 AGCTTTTTATCATATTTCCAGT
12894530 AGCTTTTTATCATATTTCCAGT
1 AGCTTTTTATCATATTTCCAGT
12894552 AGCTT
1 AGCTT
12894557 CTTCTTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.49
Consensus pattern (22 bp):
AGCTTTTTATCATATTTCCAGT
Done.