Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 106 of 210
Found at i:30959034 original size:43 final size:42
Alignment explanation
Indices: 30958934--30959160 Score: 210
Period size: 43 Copynumber: 5.4 Consensus size: 42
30958924 TTCCCCGAGG
* * * *
30958934 GGTTGCTAAGTGCTGATTCCCTGAATTATTGACTGTAAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATCATTGATTGTAAAGGT
* * *
30958976 GGTTTCTAAGTGCTGATCCCACCGTATCTTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CCGTATCATTGATTGT-AAAGGT
* * * *
30959019 GGTTGCTAAGTGCTGATTCCTCGTATCACTGAATATAAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATCATTGATTGTAAAGGT
* * * *
30959061 GGTTGCTAAGTGCTGATTCCACTGAATCCTTAATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CCGTATCATTGATTGT-AAAGGT
* * * *
30959104 GGTTGCTATGTGTTGATTCCCCGTATCATTGAATT-T-ATGGC
1 GGTTGCTAAGTGCTGATTCCCCGTATCATTG-ATTGTAAAGGT
30959145 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
30959161 ATCCACCGAG
Statistics
Matches: 147, Mismatches: 31, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
40 3 0.02
41 19 0.13
42 57 0.39
43 58 0.39
44 10 0.07
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.35
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCCCGTATCATTGATTGTAAAGGT
Found at i:30959064 original size:85 final size:82
Alignment explanation
Indices: 30958931--30959169 Score: 280
Period size: 85 Copynumber: 2.8 Consensus size: 82
30958921 TGATTCCCCG
* * * *
30958931 AGGGGTTGCTAAGTGCTGATTCCCTGAATTATTGACTGTAAAGGTGGTTTCTAAGTGCTGATCCC
1 AGGGGTTGCTAAGTGCTGATTCCC-GTATCATTGAAT-TAAAGGTGGTTGCTAAGTGCTGAT-CC
* * *
30958996 ACCGTATCTTTGATTGTGAA
63 ACCGAATCCTTAATTGTGAA
*
30959016 AGGGGTTGCTAAGTGCTGATTCCTCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
1 AGGGGTTGCTAAGTGCTGATTCC-CGTATCATTGAAT-TAAAGGTGGTTGCTAAGTGCTGA-TCC
*
30959081 ACTGAATCCTTAATTGTGAA
63 ACCGAATCCTTAATTGTGAA
* * * * *
30959101 AGGGGTTGCTATGTGTTGATTCCCCGTATCATTGAATTTATGGCGGTTGCTAAGTGCTGAATCCA
1 AGGGGTTGCTAAGTGCTGATT-CCCGTATCATTGAATTAAAGGTGGTTGCTAAGTGCTG-ATCCA
30959166 CCGA
64 CCGA
30959170 GTAACGGATA
Statistics
Matches: 133, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
84 26 0.20
85 103 0.77
86 4 0.03
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (82 bp):
AGGGGTTGCTAAGTGCTGATTCCCGTATCATTGAATTAAAGGTGGTTGCTAAGTGCTGATCCACC
GAATCCTTAATTGTGAA
Found at i:30959065 original size:42 final size:41
Alignment explanation
Indices: 30958931--30959160 Score: 212
Period size: 42 Copynumber: 5.5 Consensus size: 41
30958921 TGATTCCCCG
* * * *
30958931 AGGGGTTGCTAAGTGCTGATTCCCTGAATTATTGACTGTAA
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGAATGTAA
* * * *
30958972 AGGTGGTTTCTAAGTGCTGATCCCACCGTATCTTTGATTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGAATGT-AA
* * *
30959016 AGGGGTTGCTAAGTGCTGATTCCTCGTATCACTGAATATAA
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGAATGTAA
* * *
30959057 AGGTGGTTGCTAAGTGCTGATTCCACTGAATCCTT-AATTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGAA-TGT-AA
* * *
30959101 AGGGGTTGCTATGTGTTGATTCCCCGTATCATTGAAT-TTA
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGAATGTAA
*
30959141 TGGCGGTTGCTAAGTGCTGA
1 AGG-GGTTGCTAAGTGCTGA
30959161 ATCCACCGAG
Statistics
Matches: 151, Mismatches: 29, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
40 3 0.02
41 23 0.15
42 59 0.39
43 56 0.37
44 10 0.07
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.35
Consensus pattern (41 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGAATGTAA
Found at i:30974172 original size:30 final size:30
Alignment explanation
Indices: 30974124--30974314 Score: 158
Period size: 30 Copynumber: 6.4 Consensus size: 30
30974114 TGGTTGACAC
* * *
30974124 ATCCCTTTTCGTAATTCGATAACCGAAGTT
1 ATCCCTTTTCATAGTTCGATAACCGAAGCT
* * *
30974154 ATCTCTTTTTATAGTTCGATAGCCGAAGCT
1 ATCCCTTTTCATAGTTCGATAACCGAAGCT
* * *
30974184 ATCCTTTTTCATTA-TTTGATAGCCGAAGCT
1 ATCCCTTTTCA-TAGTTCGATAACCGAAGCT
* *
30974214 ATCCCTTTTCATAGATCGATATA-CGAAGCC
1 ATCCCTTTTCATAGTTCGATA-ACCGAAGCT
* * * *
30974244 ATCCCTTTTCATAGTTCGATGATCGTCA-CC
1 ATCCCTTTTCATAGTTCGATAACCG-AAGCT
* *
30974274 ATCCATTTTCAT-GATT-GATAGCCGAAGCT
1 ATCCCTTTTCATAG-TTCGATAACCGAAGCT
30974303 ATCCCTTTTCAT
1 ATCCCTTTTCAT
30974315 TCGTCGATAA
Statistics
Matches: 129, Mismatches: 25, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
28 1 0.01
29 21 0.16
30 104 0.81
31 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCATAGTTCGATAACCGAAGCT
Found at i:30974258 original size:90 final size:89
Alignment explanation
Indices: 30974124--30974314 Score: 219
Period size: 90 Copynumber: 2.1 Consensus size: 89
30974114 TGGTTGACAC
* ** * * *
30974124 ATCCCTTTTCGTAATTCGATAACCGAAGTTATCTCTTTTTATAGTTCGAT-AGCCG-AAGCTATC
1 ATCCCTTTTCATAATTCGATAACCGAAGCCATCCCTTTTCATAGTTCGATGA-CCGTAA-CCATC
* *
30974187 CTTTTTCATTATTTGATAGCCGAAGCT
64 CATTTTCATGA-TTGATAGCCGAAGCT
* *
30974214 ATCCCTTTTCATAGA-TCGATATA-CGAAGCCATCCCTTTTCATAGTTCGATGATCGTCACCATC
1 ATCCCTTTTCATA-ATTCGATA-ACCGAAGCCATCCCTTTTCATAGTTCGATGACCGTAACCATC
30974277 CATTTTCATGATTGATAGCCGAAGCT
64 CATTTTCATGATTGATAGCCGAAGCT
30974303 ATCCCTTTTCAT
1 ATCCCTTTTCAT
30974315 TCGTCGATAA
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
89 27 0.31
90 56 0.64
91 4 0.05
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.38
Consensus pattern (89 bp):
ATCCCTTTTCATAATTCGATAACCGAAGCCATCCCTTTTCATAGTTCGATGACCGTAACCATCCA
TTTTCATGATTGATAGCCGAAGCT
Found at i:30981046 original size:30 final size:30
Alignment explanation
Indices: 30981005--30981231 Score: 196
Period size: 30 Copynumber: 7.6 Consensus size: 30
30980995 ACCATATTGT
*
30981005 ACCATCACTTTTCATAATTTGATAGTCGTC
1 ACCATCCCTTTTCATAATTTGATAGTCGTC
* *
30981035 ACCATCCCTTTTCATAATTTGATGGTCGAC
1 ACCATCCCTTTTCATAATTTGATAGTCGTC
* ** * * *
30981065 ATCATCCCTTTTCATTGTTCGATGGTCATC
1 ACCATCCCTTTTCATAATTTGATAGTCGTC
* *
30981095 ACCATCCATTTTCATAATTTGATAG-C-TGA
1 ACCATCCCTTTTCATAATTTGATAGTCGT-C
* * * *
30981124 AGCTATCCCTTTTAATAGA-TCGATAGTCG-A
1 A-CCATCCCTTTTCATA-ATTTGATAGTCGTC
* * *
30981154 AGCCATCCCTTTTCATAGTTTGATGGTCATC
1 A-CCATCCCTTTTCATAATTTGATAGTCGTC
*
30981185 ACCATTCCTTTTCAT--TGTTGATAGTCGTC
1 ACCATCCCTTTTCATAAT-TTGATAGTCGTC
30981214 ACCATCCCTTTTCATAAT
1 ACCATCCCTTTTCATAAT
30981232 CGATAGCTGG
Statistics
Matches: 156, Mismatches: 31, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
28 2 0.01
29 26 0.17
30 124 0.79
31 4 0.03
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (30 bp):
ACCATCCCTTTTCATAATTTGATAGTCGTC
Found at i:30981098 original size:60 final size:60
Alignment explanation
Indices: 30981005--30981231 Score: 223
Period size: 60 Copynumber: 3.8 Consensus size: 60
30980995 ACCATATTGT
* ** * *
30981005 ACCATCACTTTTCATAATTTGATAGTCGTCACCATCCCTTTTCATAATTTGATGGTCGAC
1 ACCATCCCTTTTCATTGTTCGATAGTCATCACCATCCCTTTTCATAATTTGATGGTCGAC
* * * *
30981065 ATCATCCCTTTTCATTGTTCGATGGTCATCACCATCCATTTTCATAATTTGATAG-CTGA-
1 ACCATCCCTTTTCATTGTTCGATAGTCATCACCATCCCTTTTCATAATTTGATGGTC-GAC
* * * * *
30981124 AGCTATCCCTTTTAATAGATCGATAGTCGA--AGCCATCCCTTTTCATAGTTTGATGGTC-ATC
1 A-CCATCCCTTTTCATTGTTCGATAGTC-ATCA-CCATCCCTTTTCATAATTTGATGGTCGA-C
* *
30981185 ACCATTCCTTTTCATTGTT-GATAGTCGTCACCATCCCTTTTCATAAT
1 ACCATCCCTTTTCATTGTTCGATAGTCATCACCATCCCTTTTCATAAT
30981232 CGATAGCTGG
Statistics
Matches: 133, Mismatches: 25, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
59 27 0.20
60 103 0.77
61 3 0.02
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (60 bp):
ACCATCCCTTTTCATTGTTCGATAGTCATCACCATCCCTTTTCATAATTTGATGGTCGAC
Found at i:30981249 original size:29 final size:30
Alignment explanation
Indices: 30981217--30981287 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
30981207 AGTCGTCACC
30981217 ATCCCTTTTCATAAT-CGATAG-CTGGAA-CT
1 ATCCCTTTTCATAATACGATAGCCT--AAGCT
* *
30981246 ATCCCTTTCCGT-ATACGATAGCCTAAGCT
1 ATCCCTTTTCATAATACGATAGCCTAAGCT
30981275 ATCCCTTTTCATA
1 ATCCCTTTTCATA
30981288 CGTCGATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
28 4 0.12
29 28 0.82
30 2 0.06
ACGTcount: A:0.25, C:0.28, G:0.11, T:0.35
Consensus pattern (30 bp):
ATCCCTTTTCATAATACGATAGCCTAAGCT
Found at i:30993609 original size:24 final size:23
Alignment explanation
Indices: 30993580--30993628 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
30993570 ATACATTATT
30993580 AAAATATA-GAAAATAGCAAATTGA
1 AAAATA-ACGAAAA-AGCAAATTGA
*
30993604 AAAATAACGAAAAATCAAATTGA
1 AAAATAACGAAAAAGCAAATTGA
30993627 AA
1 AA
30993629 TATCCCCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.18
Consensus pattern (23 bp):
AAAATAACGAAAAAGCAAATTGA
Found at i:30994849 original size:50 final size:50
Alignment explanation
Indices: 30994790--30995165 Score: 376
Period size: 50 Copynumber: 7.5 Consensus size: 50
30994780 TTTGAAAAGT
* * *
30994790 AAGATTTGCCATTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * * ** ** * * *
30994840 AAGATTTGCCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAAGT
1 AAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * *
30994890 AAGATTCACCATTGTAGCTTTAATCTTTTTAACTGCAATGTTGGGGAAGC
1 AAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * ** ** * * *
30994940 AAGATTTGCCGTTGT-GACTTTAATCTGTTCCACTGCACCGCCTGGGAAGT
1 AAGATTCGCCGTTGTAG-CTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
30994990 AAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * * * ** * * * * *
30995040 AAGATTCACCGCTGTGGCTTTAATCTATTCCACTGTACTGCCTGGGAAGT
1 AAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
***
30995090 AAGATTCATTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
*
30995140 AAGATTCGCCGTTGTGGCTTTAATCT
1 AAGATTCGCCGTTGTAGCTTTAATCT
30995166 GTTCCACTAT
Statistics
Matches: 252, Mismatches: 72, Indels: 4
0.77 0.22 0.01
Matches are distributed among these distances:
49 1 0.00
50 250 0.99
51 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (50 bp):
AAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
Found at i:30994961 original size:100 final size:100
Alignment explanation
Indices: 30994786--30995196 Score: 624
Period size: 100 Copynumber: 4.1 Consensus size: 100
30994776 AACTTTTGAA
** * *
30994786 AAGTAAGATTTGCCATTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTTGCCG
1 AAGTAAGATTCACCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCG
30994851 TTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
66 TTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
* *
30994886 AAGTAAGATTCACCATTGTAGCTTTAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTTGCCG
1 AAGTAAGATTCACCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCG
*
30994951 TTGTGACTTTAATCTGTTCCACTGCACCGCCTGGG
66 TTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
* * *
30994986 AAGTAAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
1 AAGTAAGATTCACCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCG
* * * *
30995051 CTGTGGCTTTAATCTATTCCACTGTACTGCCTGGG
66 TTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
***
30995086 AAGTAAGATTCATTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCG
1 AAGTAAGATTCACCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCG
** * * *
30995151 TTGTGGCTTTAATCTGTTCCACTATACTGCCAGGA
66 TTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
30995186 AAGTAAGATTC
1 AAGTAAGATTC
30995197 GCTATTCTCA
Statistics
Matches: 287, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 287 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (100 bp):
AAGTAAGATTCACCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCG
TTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
Found at i:30995379 original size:44 final size:44
Alignment explanation
Indices: 30995295--30995380 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
30995285 GATGTGATCT
* * *
30995295 ACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTCAATTC
1 ACTCCACTGCAACTTCAGAGAGATAAGATCTATGACTTCAATTC
* * *
30995339 ACTCCACTGCAACTTCAGGGAGATAGGAT-TACTGGCTTCAAT
1 ACTCCACTGCAACTTCAGAGAGATAAGATCTA-TGACTTCAAT
30995381 GTACCCCGCG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
43 2 0.06
44 33 0.94
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (44 bp):
ACTCCACTGCAACTTCAGAGAGATAAGATCTATGACTTCAATTC
Found at i:30995565 original size:131 final size:131
Alignment explanation
Indices: 30995314--30995557 Score: 303
Period size: 131 Copynumber: 1.9 Consensus size: 131
30995304 CAACTTCAGA
* * *
30995314 GAGATAAGATCTATTATTTCAATTCACTCCACTGCAACTTCAGGGAGATAGGATTACTGGCTTCA
1 GAGATAAGATCTATAATTTCAATTCACTCCACTGCAACTCCAGGGAGATAGAATTACTGGCTTCA
* * * * * *
30995379 ATGTACCCCGCGTATCCTTAGGGAGGTAAAATCCGCCATCTTTGATCTACTCCACTACTGCTTAG
66 ATCTACCCCACGTAACCTCAGGAAGGTAAAATCCGCCATCTTCGATCTACTCCACTACTGCTTAG
30995444 G
131 G
* * * * *
30995445 GAGATAAGATCTGTAATCTTCAATTTATTCCACTGCTAC-CCAGGGAGATAGAATTACT-TCTTC
1 GAGATAAGATCTATAAT-TTCAATTCACTCCACTGCAACTCCAGGGAGATAGAATTACTGGCTTC
* **
30995508 AATCTACTCCACTGTAACCTCAGGAAGGTAAAATTTGCCATCTTCGATCT
65 AATCTACCCCAC-GTAACCTCAGGAAGGTAAAATCCGCCATCTTCGATCT
30995558 GTTCCACTTG
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
130 13 0.14
131 63 0.67
132 18 0.19
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (131 bp):
GAGATAAGATCTATAATTTCAATTCACTCCACTGCAACTCCAGGGAGATAGAATTACTGGCTTCA
ATCTACCCCACGTAACCTCAGGAAGGTAAAATCCGCCATCTTCGATCTACTCCACTACTGCTTAG
G
Found at i:30995699 original size:22 final size:22
Alignment explanation
Indices: 30995671--30995823 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
30995661 TTTATTGTTC
*
30995671 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
30995693 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
30995715 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
30995737 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
30995759 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
30995781 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
30995803 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
30995824 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:30996029 original size:44 final size:42
Alignment explanation
Indices: 30995957--30996163 Score: 115
Period size: 44 Copynumber: 4.8 Consensus size: 42
30995947 NNNNNGCTTA
30995957 AATCTGCTTCC-CTACTCCT-GGGAAAGATAAGATTCGTCGTCTTT
1 AATCTGC-TCCACTACTCCTAGGG--AGATAAGATTCGT-GTCTTT
* *
30996001 GATCTGCTCCACTACTCCTTAGGGAGATAAGA-TC-TGTAATTT
1 AATCTGCTCCACTACTCC-TAGGGAGATAAGATTCGTGT-CTTT
* ** * * * *
30996043 CCAACCTATTCCACTGCTGACC-AGGGAGATAGGACTT-GTGGCTTA
1 --AATCTGCTCCACTACT--CCTAGGGAGATAAGA-TTCGTGTCTTT
*
30996088 AATCTGCTTCC-CTACTCCT-GGGAAGATAAGATTCGTCATCTTT
1 AATCTGC-TCCACTACTCCTAGGG-AGATAAGATTCGT-GTCTTT
* *
30996131 GATCTGCTCCACTACTGCTTAGGGAGATAAGAT
1 AATCTGCTCCACTACT-CCTAGGGAGATAAGAT
30996164 CTGTAATTTC
Statistics
Matches: 123, Mismatches: 21, Indels: 38
0.68 0.12 0.21
Matches are distributed among these distances:
41 9 0.07
42 16 0.13
43 27 0.22
44 57 0.46
45 6 0.05
46 8 0.07
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (42 bp):
AATCTGCTCCACTACTCCTAGGGAGATAAGATTCGTGTCTTT
Found at i:30996313 original size:44 final size:44
Alignment explanation
Indices: 30996265--30996553 Score: 180
Period size: 44 Copynumber: 6.6 Consensus size: 44
30996255 CGCCTTTGAT
* *
30996265 CTACTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAAC
1 CTACTCCACTGCTGCTTAGGGAGATAAGATCTGCAATCTTCAAC
* * * *
30996309 CTACTCCACTGTTGCTCAGGGAGATAAGGTCTACAATCTTCAAC
1 CTACTCCACTGCTGCTTAGGGAGATAAGATCTGCAATCTTCAAC
* * * * * * * *
30996353 ATATTCCACTGTTG-TCCAGGGAGATAGGAT-T--AGTGGCTTAAAT
1 CTACTCCACTGCTGCT-TAGGGAGATAAGATCTGCAAT--CTTCAAC
* * * * * ** * *
30996396 TTGCTTCC-CTACTTC-TGGGGAAGATAAGAT-TCGCTGTCTTCGAT
1 CTAC-TCCACTGCTGCTTAGGG-AGATAAGATCT-GCAATCTTCAAC
* * * *
30996440 CTGCTCCACTACTGCTTAAGGAGATAAGATCTGCAATTTTCAAC
1 CTACTCCACTGCTGCTTAGGGAGATAAGATCTGCAATCTTCAAC
* * *
30996484 CTACTCCACTGCTGCTTAAGGAGATAAGGTCTACAATCTTCAAC
1 CTACTCCACTGCTGCTTAGGGAGATAAGATCTGCAATCTTCAAC
*
30996528 CTATTCCACTGCTG-TCTAGGGAGATA
1 CTACTCCACTGCTGCT-TAGGGAGATA
30996554 GGACTAGTGG
Statistics
Matches: 191, Mismatches: 41, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
41 2 0.01
42 3 0.02
43 24 0.13
44 156 0.82
45 4 0.02
46 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
CTACTCCACTGCTGCTTAGGGAGATAAGATCTGCAATCTTCAAC
Found at i:30996329 original size:131 final size:131
Alignment explanation
Indices: 30995952--30996334 Score: 610
Period size: 130 Copynumber: 2.9 Consensus size: 131
30995942 NNNNNNNNNN
*
30995952 GCTTAAATCTGCTTCCCTACTCCTGGGAAAGATAAGATTCGTCGTCTTTGATCTGCTCCACTACT
1 GCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGTCGTCTTTGATCTGCTCCACTACT
* *
30996017 CCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTGT
66 GCTTAGGGAGATAAGATCTGTAATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTGT
30996082 G
131 G
*
30996083 GCTTAAATCTGCTTCCCTACTCCT-GGGAAGATAAGATTCGTCATCTTTGATCTGCTCCACTACT
1 GCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGTCGTCTTTGATCTGCTCCACTACT
*
30996147 GCTTAGGGAGATAAGATCTGTAA-TTTCTAACCTATTCCACTGCCGACCAGGGAGATAGGACTTG
66 GCTTAGGGAGATAAGATCTGTAATTTTC-AACCTATTCCACTGCTGACCAGGGAGATAGGACTTG
30996211 TG
130 TG
* * * * *
30996213 GCTTAAATCTGCATCCTTACTCCTGGGGAAGATAAGATTCGCCGCCTTTGATCTACTCCACTACT
1 GCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGTCGTCTTTGATCTGCTCCACTACT
* * *
30996278 GCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTGTTG-CTCAGGGAGATA
66 GCTTAGGGAGATAAGATCTGTAATTTTCAACCTATTCCACTGCTGAC-CAGGGAGATA
30996335 AGGTCTACAA
Statistics
Matches: 233, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
129 3 0.01
130 120 0.52
131 106 0.45
132 4 0.02
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (131 bp):
GCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGTCGTCTTTGATCTGCTCCACTACT
GCTTAGGGAGATAAGATCTGTAATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTGT
G
Found at i:30996332 original size:175 final size:175
Alignment explanation
Indices: 30996137--30996654 Score: 788
Period size: 175 Copynumber: 3.0 Consensus size: 175
30996127 CTTTGATCTG
* * ** * *
30996137 CTCCACTACTGCTTAGGGAGATAAGATCTGTAAT-TTCTAACCTATTCCACTGCCGACCAGGGAG
1 CTCCACTGCTGCTTAGGGAGATAAGGTCTACAATCTTC-AACCTATTCCACTGCTGTCCAGGGAG
* * * *
30996201 ATAGGACTTGTGGCTTAAATCTGCATCCTTACTCCTGGGGAAGATAAGATTCGCCGCCTTTGATC
65 ATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATC
*
30996266 TACTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTA
130 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTA
* * * *
30996312 CTCCACTGTTGCTCAGGGAGATAAGGTCTACAATCTTCAACATATTCCACTGTTGTCCAGGGAGA
1 CTCCACTGCTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGTCCAGGGAGA
* * *
30996377 TAGGA-TTAGTGGCTTAAATTTGCTTCCCTACTTCTGGGGAAGATAAGATTCGCTGTCTTCGATC
66 TAGGACTT-GTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATC
*
30996441 TGCTCCACTACTGCTTAAGGAGATAAGATCTGCAATTTTCAACCTA
130 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTA
* *
30996487 CTCCACTGCTGCTTAAGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGTCTAGGGAGA
1 CTCCACTGCTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGTCCAGGGAGA
* *
30996552 TAGGACTAGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCACCGTCTTCGATCT
66 TAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCT
*
30996617 GCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
131 GCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTT
30996655 TAAATTGCTC
Statistics
Matches: 308, Mismatches: 32, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
174 2 0.01
175 302 0.98
176 4 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (175 bp):
CTCCACTGCTGCTTAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGTCCAGGGAGA
TAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCT
GCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTA
Found at i:30998906 original size:8 final size:8
Alignment explanation
Indices: 30998873--30998949 Score: 52
Period size: 8 Copynumber: 9.6 Consensus size: 8
30998863 TTTTCTTTTC
30998873 TTTTTCTT
1 TTTTTCTT
*
30998881 TTTATCATT
1 TTTTTC-TT
**
30998890 TTGAT-TT
1 TTTTTCTT
30998897 TTTTTCTT
1 TTTTTCTT
30998905 TTTTTCTT
1 TTTTTCTT
30998913 TCTTTT-TT
1 T-TTTTCTT
*
30998921 GTTTT-TT
1 TTTTTCTT
*
30998928 TCTTTCTT
1 TTTTTCTT
*
30998936 ATTTTCATT
1 TTTTTC-TT
30998945 TTTTT
1 TTTTT
30998950 GATTTTTTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
7 14 0.26
8 24 0.44
9 16 0.30
ACGTcount: A:0.06, C:0.10, G:0.03, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:30998918 original size:19 final size:19
Alignment explanation
Indices: 30998896--30998949 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 19
30998886 CATTTTGATT
30998896 TTTTTTCTTTTTTTCTTTC
1 TTTTTTCTTTTTTTCTTTC
*
30998915 TTTTTTGTTTTTTTCTTTC
1 TTTTTTCTTTTTTTCTTTC
30998934 TTATTTTCATTTTTTT
1 TT-TTTTC-TTTTTTT
30998950 GATTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 20 0.65
20 4 0.13
21 7 0.23
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTTTTCTTTTTTTCTTTC
Found at i:30998959 original size:19 final size:19
Alignment explanation
Indices: 30998888--30998976 Score: 60
Period size: 17 Copynumber: 4.7 Consensus size: 19
30998878 CTTTTTATCA
30998888 TTTTGATTTTTTTTC-TTT
1 TTTTGATTTTTTTTCATTT
* **
30998906 TTTT-CTTTCTTTTTTGTTT
1 TTTTGATTT-TTTTTCATTT
**
30998925 TTTTCTTTCTTATTTTCATTT
1 TTTTGATT-TT-TTTTCATTT
30998946 TTTTGATTTTTTTT-A-TT
1 TTTTGATTTTTTTTCATTT
**
30998963 GATTGATTTTTTTT
1 TTTTGATTTTTTTT
30998977 ATATTTCGAT
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
17 17 0.30
18 10 0.18
19 11 0.19
20 5 0.09
21 14 0.25
ACGTcount: A:0.08, C:0.07, G:0.06, T:0.80
Consensus pattern (19 bp):
TTTTGATTTTTTTTCATTT
Found at i:30998987 original size:17 final size:16
Alignment explanation
Indices: 30998948--30998992 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
30998938 TTTCATTTTT
30998948 TTGATTTTTTTTATTGA
1 TTGATTTTTTTTATT-A
30998965 TTGATTTTTTTTA-TA
1 TTGATTTTTTTTATTA
30998980 TTTCGATTTTTTT
1 -TT-GATTTTTTT
30998993 ATTGAATCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.04
16 3 0.12
17 22 0.85
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.73
Consensus pattern (16 bp):
TTGATTTTTTTTATTA
Found at i:30999805 original size:25 final size:25
Alignment explanation
Indices: 30999755--30999820 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
30999745 AAGAAAATCC
* *
30999755 AAAAGAATGAAAGAATAATTATTCA
1 AAAAGAATAAAAGAATAATTACTCA
*
30999780 AAAAGAATAAAAGAAT-ATTGGCTCA
1 AAAAGAATAAAAGAATAATT-ACTCA
30999805 AAAACGAATACAAAGA
1 AAAA-GAATA-AAAGA
30999821 TGCATTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.09
25 22 0.63
26 5 0.14
27 5 0.14
ACGTcount: A:0.61, C:0.08, G:0.14, T:0.18
Consensus pattern (25 bp):
AAAAGAATAAAAGAATAATTACTCA
Found at i:31006006 original size:11 final size:11
Alignment explanation
Indices: 31005990--31006016 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
31005980 CTTAGAATTC
31005990 TTTAACGAAAG
1 TTTAACGAAAG
31006001 TTTAACGAAAG
1 TTTAACGAAAG
31006012 TTTAA
1 TTTAA
31006017 AAACCTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (11 bp):
TTTAACGAAAG
Found at i:31009113 original size:46 final size:46
Alignment explanation
Indices: 31009043--31009134 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
31009033 CAAAGAAAAG
31009043 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
*
31009089 ACCTCGACCCACTATCAAGGATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
31009135 TCGCCACACT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
Found at i:31013861 original size:39 final size:39
Alignment explanation
Indices: 31013817--31013892 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
31013807 AAATAATTCA
* * *
31013817 AATATTTATTAATAGTAAAGATTATTGAATAATATTATT
1 AATATTTATTAATAATAAAAATTATTGAAAAATATTATT
* *
31013856 AATATTTTTTAATAATAAAAATTATTTAAAAATATTA
1 AATATTTATTAATAATAAAAATTATTGAAAAATATTA
31013893 AAATACATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (39 bp):
AATATTTATTAATAATAAAAATTATTGAAAAATATTATT
Found at i:31015146 original size:24 final size:24
Alignment explanation
Indices: 31015106--31015151 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
31015096 GCCACATGGT
*
31015106 CGTGTGTCAGGCCGTGTGGTAGGC
1 CGTGTGTCAGGCCGTGTAGTAGGC
*
31015130 CGTGTGTC-GAGCGGTGTAGTAG
1 CGTGTGTCAG-GCCGTGTAGTAG
31015152 ACCATGTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.11, C:0.17, G:0.46, T:0.26
Consensus pattern (24 bp):
CGTGTGTCAGGCCGTGTAGTAGGC
Found at i:31016291 original size:5 final size:5
Alignment explanation
Indices: 31016283--31016325 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
31016273 TATCTTCAAC
* *
31016283 TCTGT TCTGT TCTAT TCTAT TCTGT TCTGT TCTGT TCTGT TCT
1 TCTGT TCTGT TCTGT TCTGT TCTGT TCTGT TCTGT TCTGT TCT
31016326 TTTTGTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.05, C:0.21, G:0.14, T:0.60
Consensus pattern (5 bp):
TCTGT
Found at i:31016314 original size:20 final size:20
Alignment explanation
Indices: 31016263--31016325 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
31016253 CATTCGCTGC
* * * *
31016263 TCTGTTCTGTTATCTTCAAC
1 TCTGTTCTGTTCTATTCTAT
31016283 TCTGTTCTGTTCTATTCTAT
1 TCTGTTCTGTTCTATTCTAT
* *
31016303 TCTGTTCTGTTCTGTTCTGT
1 TCTGTTCTGTTCTATTCTAT
31016323 TCT
1 TCT
31016326 TTTTGTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.08, C:0.22, G:0.13, T:0.57
Consensus pattern (20 bp):
TCTGTTCTGTTCTATTCTAT
Found at i:31018346 original size:100 final size:98
Alignment explanation
Indices: 31018162--31018346 Score: 289
Period size: 100 Copynumber: 1.9 Consensus size: 98
31018152 TTACCAAAAG
*
31018162 AAAAAAGAAAAGAAATAAAACCTAAAAGGAAATAGGCTATTGACATATTACAAATATATACAAAA
1 AAAAAAGAAAAGAAATAAAACCTAAAAGGAAATAGGATATTGACATATTACAAATATATACAAAA
* *
31018227 CCAGAATCGGTACCCATCCTAAACTTGACTCCA
66 CCAGAATCAGTACACATCCTAAACTTGACTCCA
* * *
31018260 AAAAAATGAAAATGAAATAAAGCCTAAAATGAAATAGTATATTGACATATTACAAATATATACAA
1 AAAAAA-GAAAA-GAAATAAAACCTAAAAGGAAATAGGATATTGACATATTACAAATATATACAA
*
31018325 AACCAGAATCAGTATACATCCT
64 AACCAGAATCAGTACACATCCT
31018347 CAATTGCCAA
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 6 0.08
99 5 0.06
100 67 0.86
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.22
Consensus pattern (98 bp):
AAAAAAGAAAAGAAATAAAACCTAAAAGGAAATAGGATATTGACATATTACAAATATATACAAAA
CCAGAATCAGTACACATCCTAAACTTGACTCCA
Found at i:31020877 original size:2 final size:2
Alignment explanation
Indices: 31020865--31020895 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
31020855 CACATCATAA
31020865 AT AT A- 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
31020896 TAAAAGGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31021818 original size:16 final size:16
Alignment explanation
Indices: 31021767--31021811 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 16
31021757 GAGTGAGAAG
31021767 TAAAAGTTTTGGGGGAAAA
1 TAAAAGTTTT-GGGG--AA
31021786 TAAAAAGTTTTGGGGAA
1 T-AAAAGTTTTGGGGAA
31021803 TAAAAGTTT
1 TAAAAGTTT
31021812 GAGGGAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.32
17 3 0.12
19 5 0.20
20 9 0.36
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (16 bp):
TAAAAGTTTTGGGGAA
Found at i:31021944 original size:30 final size:31
Alignment explanation
Indices: 31021905--31021964 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
31021895 AGAGGTGGGA
31021905 TGGGAAGGGAATAAA-AGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAATA-TTTTAGGGGAAAAG
* *
31021936 TGGG-AGGGAGTAAATATTTTGGGGGAAAA
1 TGGGAAGGGAATAAATATTTTAGGGGAAAA
31021965 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.22
Consensus pattern (31 bp):
TGGGAAGGGAATAAATATTTTAGGGGAAAAG
Found at i:31022137 original size:31 final size:30
Alignment explanation
Indices: 31022079--31022137 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
31022069 GGGAGGGGAG
* * **
31022079 TAAAAGTTTTGGGGGGAAAGTGGAAAGGAA
1 TAAAAGTTTTGAGGGAAAAGTAAAAAGGAA
31022109 TAAAAGTTTTTGAGGGAAAAGTAAAAAGG
1 TAAAAG-TTTTGAGGGAAAAGTAAAAAGG
31022138 TTTGAGAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (30 bp):
TAAAAGTTTTGAGGGAAAAGTAAAAAGGAA
Found at i:31022278 original size:9 final size:9
Alignment explanation
Indices: 31022261--31022291 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
31022251 TCGAGTTGAT
31022261 TCGAATAAC
1 TCGAATAAC
*
31022270 TCGATTAAC
1 TCGAATAAC
31022279 TCGAATAAC
1 TCGAATAAC
31022288 TCGA
1 TCGA
31022292 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:31023224 original size:10 final size:10
Alignment explanation
Indices: 31023202--31023251 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 10
31023192 AATTTTTAAT
31023202 TTAAAAATT-
1 TTAAAAATTA
31023211 TTAAAAATTA
1 TTAAAAATTA
31023221 TT-AAAA-TA
1 TTAAAAATTA
31023229 TATAAAAATTA
1 T-TAAAAATTA
* *
31023240 TAAAAAAATA
1 TTAAAAATTA
31023250 TT
1 TT
31023252 TTTATTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
8 3 0.09
9 14 0.41
10 14 0.41
11 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:31023226 original size:19 final size:20
Alignment explanation
Indices: 31023202--31023250 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
31023192 AATTTTTAAT
*
31023202 TTAAAAAT-TTTAAAAATTA
1 TTAAAAATATATAAAAATTA
31023221 TT-AAAATATATAAAAATTA
1 TTAAAAATATATAAAAATTA
*
31023240 -TAAAAAAATAT
1 TTAAAAATATAT
31023251 TTTTATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAAAATATATAAAAATTA
Found at i:31023543 original size:31 final size:31
Alignment explanation
Indices: 31023506--31023573 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
31023496 TTACGTTTGA
*
31023506 GGGTGGGTTTGGATGGACGATTAGGTGCGGT
1 GGGTGGGTTTGGATGGACGATGAGGTGCGGT
31023537 GGGTGGGTTTGGATGGACGATGAGGTGCGGT
1 GGGTGGGTTTGGATGGACGATGAGGTGCGGT
31023568 GCGGTG
1 G-GGTG
31023574 CGGTGCGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.12, C:0.07, G:0.54, T:0.26
Consensus pattern (31 bp):
GGGTGGGTTTGGATGGACGATGAGGTGCGGT
Found at i:31028747 original size:18 final size:18
Alignment explanation
Indices: 31028708--31028749 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
31028698 AATACTTTCT
*
31028708 AATTTATTTTAAATAATT
1 AATTTATTTTAAATAATA
*
31028726 AATTTATTTT-AGTAAGTA
1 AATTTATTTTAAATAA-TA
31028744 AATTTA
1 AATTTA
31028750 GTGAGCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (18 bp):
AATTTATTTTAAATAATA
Found at i:31028824 original size:20 final size:20
Alignment explanation
Indices: 31028773--31028829 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
31028763 ATCTAATAAC
*
31028773 GAGCTC-AATGAGTTGAATT
1 GAGCTCGAATGAGCTGAATT
* ** *
31028792 GAGCTTGTGTGAGCTGACTT
1 GAGCTCGAATGAGCTGAATT
31028812 GAGCTCGAATGAGCTGAA
1 GAGCTCGAATGAGCTGAA
31028830 CCGCATGGAA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.28
Consensus pattern (20 bp):
GAGCTCGAATGAGCTGAATT
Found at i:31029189 original size:19 final size:18
Alignment explanation
Indices: 31029155--31029193 Score: 51
Period size: 21 Copynumber: 2.0 Consensus size: 18
31029145 TTAGAAAGGC
31029155 ATTTTAAATAATATATAA
1 ATTTTAAATAATATATAA
31029173 ATTTTATAATATCATATATAA
1 ATTTTA-AATA--ATATATAA
31029194 TATTACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
21 8 0.44
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTTAAATAATATATAA
Found at i:31032333 original size:21 final size:19
Alignment explanation
Indices: 31032286--31032333 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
31032276 TCAAAAATTT
*
31032286 AAAATTAAAATTCAGAAAA
1 AAAATAAAAATTCAGAAAA
*
31032305 AAATATAAAAAGTTCATAAAA
1 AAA-ATAAAAA-TTCAGAAAA
31032326 ATAAATAA
1 A-AAATAA
31032334 TATTAGCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 3 0.12
20 6 0.25
21 13 0.54
22 2 0.08
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (19 bp):
AAAATAAAAATTCAGAAAA
Found at i:31034332 original size:2 final size:2
Alignment explanation
Indices: 31034327--31034361 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31034317 CAAGATGGTG
31034327 TA TA TA TA TA 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
31034362 CAACCATGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31036690 original size:76 final size:77
Alignment explanation
Indices: 31036596--31036737 Score: 166
Period size: 77 Copynumber: 1.9 Consensus size: 77
31036586 CAATATATGT
* *
31036596 TAACCAAAACGCAGCG-TTTGGCCTAGAG-GTATGTTACAATTTA-TGGCGCTT-ATGGGAAAAC
1 TAACCAAAACGCACCGTTTTGGCCTAG-GTGTATGTTAC-AGTTAGTGGCGCTTAAT-GGAAAAC
31036657 GCCGCAAAAATATCC
63 GCCGCAAAAATATCC
** * * *
31036672 TAACCAAAGTGCACCGTTTTGGTCTTGGTGTATGTTACAGTTAGTGGCGCTTAATGTAAAACGCC
1 TAACCAAAACGCACCGTTTTGGCCTAGGTGTATGTTACAGTTAGTGGCGCTTAATGGAAAACGCC
31036737 G
66 G
31036738 GTAAAGTATA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
76 18 0.33
77 35 0.64
78 2 0.04
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (77 bp):
TAACCAAAACGCACCGTTTTGGCCTAGGTGTATGTTACAGTTAGTGGCGCTTAATGGAAAACGCC
GCAAAAATATCC
Found at i:31037210 original size:229 final size:227
Alignment explanation
Indices: 31036730--31037262 Score: 514
Period size: 229 Copynumber: 2.3 Consensus size: 227
31036720 GCTTAATGTA
* * * * ** **
31036730 AAACGCCGGTAAAGTATAATATTAGCGGCG-TGTTGTGGTAAGCGCCGCAAAACCT-CTTAACCA
1 AAACGCCGCTAAAGCATAGTATTAGCGGCGCT-TTCTGACAAGCGCCGCAAAATATAC-TAACCA
* * * * **
31036793 AAACGCAGAGTTTGGT-CTTGAGGTATACTAGAATTAGTGGCGC---AAGCGA-ACACGCCACTA
64 AAACGCAGAGTTT-TTACATGAGGTATATTAGAATTAGTGGCACTTTTTG-GAGAC-CGCCACTA
*
31036853 ATGTATACTATTAGCGGCGCTTTTGTATAAGCGCCGCAAAAATTGACAACAAAAACGCAACGTTT
126 AAGTATACTATTAGCGGCGCTTTTGTATAAGCGCCGCAAAAATT-ACAACAAAAACGCAACGTTT
** **
31036918 TTGTCTCGATGTATACAGTTACTAGTGGCGCATATAAAG
190 AAGTCTCGATGTATACAGGAACTAGTGGCG-ATATAAAG
* * *
31036957 AAACGCCGCTAAATCATAGTATTAGTGGCGC-TTCTGCACAAGCGCCGCAAAATATACTCACCAA
1 AAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTCTG-ACAAGCGCCGCAAAATATACTAACCAA
* *
31037021 AACGCTGAGTTTTTACATGAGGTATATTAGAATTAGTGGCACTTTTTGGAGACCGCCGCTAAAGT
65 AACGCAGAGTTTTTACATGAGGTATATTAGAATTAGTGGCACTTTTTGGAGACCGCCACTAAAGT
* * * *
31037086 ATATTATTAGTGGCGCTCTTT-TATAAGCGCCGCAAAAGA-TATTAACAAAAACGCAGCGTTTAA
130 ATACTATTAGCGGCGCT-TTTGTATAAGCGCCGCAAAA-ATTA-CAACAAAAACGCAACGTTTAA
* * *
31037149 GTCTTGATGTATACTGGAATTAGTGGCG-T-TCACAAG
192 GTCTCGATGTATACAGGAACTAGTGGCGATAT-A-AAG
* * * * * * *
31037185 AAATCGCTGCTAAAGCATGGTATTAGCGGCGCTTTTTGATAAGCGCCGGAAAATGTATTAACCAA
1 AAA-CGCCGCTAAAGCATAGTATTAGCGGCGCTTTCTGACAAGCGCCGCAAAATATACTAACCAA
31037250 AACGCAGAGTTTT
65 AACGCAGAGTTTT
31037263 GGTCTTAACC
Statistics
Matches: 249, Mismatches: 42, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
226 6 0.02
227 82 0.33
228 8 0.03
229 142 0.57
230 11 0.04
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (227 bp):
AAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTCTGACAAGCGCCGCAAAATATACTAACCAAA
ACGCAGAGTTTTTACATGAGGTATATTAGAATTAGTGGCACTTTTTGGAGACCGCCACTAAAGTA
TACTATTAGCGGCGCTTTTGTATAAGCGCCGCAAAAATTACAACAAAAACGCAACGTTTAAGTCT
CGATGTATACAGGAACTAGTGGCGATATAAAG
Found at i:31037352 original size:21 final size:20
Alignment explanation
Indices: 31037328--31037366 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
31037318 TTTGGTCTAT
*
31037328 GGTTTATGGTTTAAAGGTTGG
1 GGTTTAAGGTTT-AAGGTTGG
31037349 GGTTTAAGGTTTAAGGTT
1 GGTTTAAGGTTTAAGGTT
31037367 AATATGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.44
Consensus pattern (20 bp):
GGTTTAAGGTTTAAGGTTGG
Found at i:31039934 original size:2 final size:2
Alignment explanation
Indices: 31039927--31039952 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31039917 AAGTAAAATA
31039927 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
31039953 TTGTTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31040147 original size:13 final size:13
Alignment explanation
Indices: 31040129--31040165 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
31040119 TTGAATGTTT
31040129 ATTAAAATATGTA
1 ATTAAAATATGTA
31040142 ATTAAAATATGTA
1 ATTAAAATATGTA
31040155 ATTAAAA-ATGT
1 ATTAAAATATGT
31040166 TTCCATGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
ATTAAAATATGTA
Found at i:31041002 original size:9 final size:9
Alignment explanation
Indices: 31040958--31041611 Score: 501
Period size: 9 Copynumber: 72.8 Consensus size: 9
31040948 AATTAAATAT
31040958 CTTACATAA
1 CTTACATAA
*
31040967 CTTACGTAA
1 CTTACATAA
*
31040976 ATTA-AGTTAA
1 CTTACA--TAA
*
31040986 -TTAAATAA
1 CTTACATAA
31040994 CTTACATAA
1 CTTACATAA
*
31041003 ATTA-AGTAA
1 CTTACA-TAA
* *
31041012 ATTAAATAA
1 CTTACATAA
31041021 CTTACATAA
1 CTTACATAA
31041030 CTTACATAA
1 CTTACATAA
*
31041039 ATTA-AGTAA
1 CTTACA-TAA
*
31041048 TTTACATAA
1 CTTACATAA
31041057 CTTACATAA
1 CTTACATAA
* * *
31041066 ATTAAATAT
1 CTTACATAA
*
31041075 CTTGCATAA
1 CTTACATAA
31041084 CTTACATAA
1 CTTACATAA
* * *
31041093 ATTAAATAT
1 CTTACATAA
31041102 CTTACATAA
1 CTTACATAA
31041111 CTTACATAA
1 CTTACATAA
* *
31041120 ATTAAATAA
1 CTTACATAA
31041129 CTTACATAA
1 CTTACATAA
31041138 CTTACATAA
1 CTTACATAA
*
31041147 ATTA-AGTAA
1 CTTACA-TAA
*
31041156 TTTACATAA
1 CTTACATAA
31041165 CTTACATAA
1 CTTACATAA
* * *
31041174 ATTAAATAT
1 CTTACATAA
31041183 CTTACATAA
1 CTTACATAA
*
31041192 CTTACGTAA
1 CTTACATAA
*
31041201 ATTA-AGTTAA
1 CTTACA--TAA
*
31041211 -TTAAATAA
1 CTTACATAA
31041219 CTTACATAA
1 CTTACATAA
*
31041228 ATTA-AGTAA
1 CTTACA-TAA
* *
31041237 ATTAAATAA
1 CTTACATAA
31041246 CTTACATAA
1 CTTACATAA
31041255 CTTACATAA
1 CTTACATAA
*
31041264 -ATA-AGTAA
1 CTTACA-TAA
*
31041272 TTTACATAA
1 CTTACATAA
31041281 C-TACATAA
1 CTTACATAA
* * *
31041289 ATTAAATAT
1 CTTACATAA
*
31041298 CTTGCATAA
1 CTTACATAA
*
31041307 CTTACGTAA
1 CTTACATAA
* *
31041316 ATTAAAGTTAA
1 CTTACA--TAA
*
31041327 -TTAAATAA
1 CTTACATAA
31041335 CTTACATAA
1 CTTACATAA
*
31041344 ATTA-AGTAA
1 CTTACA-TAA
* * *
31041353 ATTAAATAT
1 CTTACATAA
*
31041362 CTTGCATAA
1 CTTACATAA
31041371 CTTACATAA
1 CTTACATAA
*
31041380 ATTA-AGTAA
1 CTTACA-TAA
*
31041389 TTTACATAA
1 CTTACATAA
31041398 CTTACATAA
1 CTTACATAA
* * *
31041407 ATTAAATAT
1 CTTACATAA
*
31041416 CTTGCATAA
1 CTTACATAA
31041425 CTTACATAA
1 CTTACATAA
* * *
31041434 ATTAAATAT
1 CTTACATAA
31041443 CTTACATAA
1 CTTACATAA
31041452 CTTACATAA
1 CTTACATAA
* * *
31041461 ATTAAATAT
1 CTTACATAA
31041470 CTTACATAA
1 CTTACATAA
31041479 CTTACATAA
1 CTTACATAA
*
31041488 ATTA-AGTAA
1 CTTACA-TAA
* *
31041497 ATTAAATAA
1 CTTACATAA
31041506 CTTACATAA
1 CTTACATAA
31041515 CTTACATAA
1 CTTACATAA
31041524 CTTACATAA
1 CTTACATAA
*
31041533 ATTACATAA
1 CTTACATAA
31041542 CTTACATAA
1 CTTACATAA
31041551 CTTACATAA
1 CTTACATAA
31041560 CTTACATAA
1 CTTACATAA
* * *
31041569 ATTAAATAT
1 CTTACATAA
*
31041578 CTTACATCA
1 CTTACATAA
31041587 CTTACATAA
1 CTTACATAA
*
31041596 CTTACATTA
1 CTTACATAA
31041605 CTTACAT
1 CTTACAT
31041612 GGGGCATACA
Statistics
Matches: 512, Mismatches: 104, Indels: 58
0.76 0.15 0.09
Matches are distributed among these distances:
7 1 0.00
8 28 0.05
9 459 0.90
10 21 0.04
11 3 0.01
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (9 bp):
CTTACATAA
Found at i:31041042 original size:54 final size:54
Alignment explanation
Indices: 31040984--31041611 Score: 726
Period size: 54 Copynumber: 11.3 Consensus size: 54
31040974 AAATTAAGTT
* *
31040984 AATTAAATAACTTACATAAATTA-AGTAAATTAAATAACTTACATAACTTACATA
1 AATTAAATAACTTACATAACTTACA-TAAATTAAATATCTTACATAACTTACATA
* * *
31041038 AATTAAGTAATTTACATAACTTACATAAATTAAATATCTTGCATAACTTACATA
1 AATTAAATAACTTACATAACTTACATAAATTAAATATCTTACATAACTTACATA
* *
31041092 AATTAAATATCTTACATAACTTACATAAATTAAATAACTTACATAACTTACATA
1 AATTAAATAACTTACATAACTTACATAAATTAAATATCTTACATAACTTACATA
* *
31041146 AATTAAGTAATTTACATAACTTACATAAATTAAATATCTTACATAACTTACGTAAATTAA
1 AATTAAATAACTTACATAACTTACATAAATTAAATATCTTACATAACTTAC----A-T-A
* *
31041206 GTTAATTAAATAACTTACATAAATTA-AGTAAATTAAATAACTTACATAACTTACATA
1 ---AATTAAATAACTTACATAACTTACA-TAAATTAAATATCTTACATAACTTACATA
* * *
31041263 AA-TAAGTAATTTACATAAC-TACATAAATTAAATATCTTGCATAACTTACGTAAATTAAA
1 AATTAAATAACTTACATAACTTACATAAATTAAATATCTTACATAACTTAC----A-T--A
* *
31041322 GTTAATTAAATAACTTACATAAATTA-AGTAAATTAAATATCTTGCATAACTTACATA
1 ---AATTAAATAACTTACATAACTTACA-TAAATTAAATATCTTACATAACTTACATA
* * *
31041379 AATTAAGTAATTTACATAACTTACATAAATTAAATATCTTGCATAACTTACATA
1 AATTAAATAACTTACATAACTTACATAAATTAAATATCTTACATAACTTACATA
*
31041433 AATTAAATATCTTACATAACTTACATAAATTAAATATCTTACATAACTTACATA
1 AATTAAATAACTTACATAACTTACATAAATTAAATATCTTACATAACTTACATA
* * * * * * *
31041487 AATTAAGTAAATTAAATAACTTACATAACTTACATAACTTACATAAATTACATA
1 AATTAAATAACTTACATAACTTACATAAATTAAATATCTTACATAACTTACATA
* * *
31041541 ACTTACATAACTTACATAACTTACATAAATTAAATATCTTACATCACTTACATA
1 AATTAAATAACTTACATAACTTACATAAATTAAATATCTTACATAACTTACATA
* * *
31041595 ACTTACATTACTTACAT
1 AATTAAATAACTTACAT
31041612 GGGGCATACA
Statistics
Matches: 496, Mismatches: 52, Indels: 52
0.83 0.09 0.09
Matches are distributed among these distances:
52 26 0.05
53 15 0.03
54 350 0.71
55 2 0.00
56 1 0.00
57 3 0.01
58 2 0.00
59 4 0.01
60 2 0.00
62 3 0.01
63 60 0.12
64 28 0.06
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (54 bp):
AATTAAATAACTTACATAACTTACATAAATTAAATATCTTACATAACTTACATA
Found at i:31043654 original size:21 final size:21
Alignment explanation
Indices: 31043625--31043693 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
31043615 CAGCAACTTA
* *
31043625 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
* **
31043646 AAGTAGAGGCTACAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
*
31043667 AAGCAGATGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
31043688 AAGCAG
1 AAGCAG
31043694 CGAGAGAAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.42, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:31043695 original size:12 final size:12
Alignment explanation
Indices: 31043678--31043738 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
31043668 AGCAGATGCC
31043678 GCAGCGAGAGAA
1 GCAGCGAGAGAA
31043690 GCAGCGAGAGAA
1 GCAGCGAGAGAA
* **
31043702 GCA--AAG-GCT
1 GCAGCGAGAGAA
31043711 GCAGCGAGAGAA
1 GCAGCGAGAGAA
*
31043723 GCAGCGAGGGAA
1 GCAGCGAGAGAA
31043735 GCAG
1 GCAG
31043739 AGGTTCAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
9 4 0.10
10 2 0.05
11 2 0.05
12 31 0.79
ACGTcount: A:0.38, C:0.18, G:0.43, T:0.02
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:31043700 original size:33 final size:33
Alignment explanation
Indices: 31043658--31043741 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
31043648 GTAGAGGCTA
*
31043658 CAGCGAGAGAAGCAGATGCCGCAGCGAGAGAAG
1 CAGCGAGAGAAGCAGAGGCCGCAGCGAGAGAAG
* *
31043691 CAGCGAGAGAAGCAAAGGCTGCAGCGAGAGAAG
1 CAGCGAGAGAAGCAGAGGCCGCAGCGAGAGAAG
*
31043724 CAGCGAGGGAAGCAGAGG
1 CAGCGAGAGAAGCAGAGG
31043742 TTCAAAAGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.37, C:0.19, G:0.42, T:0.02
Consensus pattern (33 bp):
CAGCGAGAGAAGCAGAGGCCGCAGCGAGAGAAG
Found at i:31044263 original size:43 final size:41
Alignment explanation
Indices: 31044159--31044446 Score: 295
Period size: 43 Copynumber: 6.9 Consensus size: 41
31044149 GTTTGTGAAA
* **
31044159 TAAGCGCCGCTAAAGAACACT-ACTTTTAGCGGTGTTTTTGAA
1 TAAGCGCCGCTAAAGAACA-TGACTTTTAGCGGCGTTTTT-TC
* * * *
31044201 GAAGCGCCGCTATAGAACATTACTTTTAGAGGCGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTT-TT-C
* *
31044244 AAAGCGCCGCTAAATAACATGAGC-TTTAGCGGCGTTTATTT-
1 TAAGCGCCGCTAAAGAACATGA-CTTTTAGCGGCGTTT-TTTC
*
31044285 TAAGCGCCGCTAAAGAACATGA-TCTTTAACGGCGTTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGACT-TTTAGCGGCG--TTTTTTC
*
31044328 TAAGCGCCGCTAAAGAACATGA-TCTTTAGGGGCGTTTTTT-
1 TAAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGTTTTTTC
*
31044368 TAAGCGCCGCTAAAGAACATGA-TCTTTAGGGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGACT-TTTAGCGGCG-TTTTTTC
31044410 TAAGCGCCGCTAAAGAACATGAGC-TTTAGCGGCGTTT
1 TAAGCGCCGCTAAAGAACATGA-CTTTTAGCGGCGTTT
31044447 CTTTATGTAA
Statistics
Matches: 215, Mismatches: 17, Indels: 29
0.82 0.07 0.11
Matches are distributed among these distances:
40 34 0.16
41 45 0.21
42 66 0.31
43 68 0.32
44 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (41 bp):
TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTC
Found at i:31044408 original size:42 final size:42
Alignment explanation
Indices: 31044159--31044468 Score: 326
Period size: 42 Copynumber: 7.4 Consensus size: 42
31044149 GTTTGTGAAA
* ***
31044159 TAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGTGTTTTTGAA
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTTTT
* * * * **
31044201 GAAGCGCCGCTATAGAACATTA-CTTTTAGAGGCGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTTT
* * * *
31044244 AAAGCGCCGCTAAATAACATGAGCTTTAGCGGCG-TTTATTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTT
*
31044285 TAAGCGCCGCTAAAGAACATGATCTTTAACGGCGTTTTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTT
*
31044327 CTAAGCGCCGCTAAAGAACATGATCTTTAGGGGCG--TTTTTT
1 -TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTT
* *
31044368 TAAGCGCCGCTAAAGAACATGATCTTTAGGGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTT
* *
31044410 TAAGCGCCGCTAAAGAACATGAGCTTTAGCGGCGTTTCTTTATG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTT-TT
*
31044454 TAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAG
31044469 TTAGCGACGT
Statistics
Matches: 232, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
40 34 0.15
41 38 0.16
42 81 0.35
43 63 0.27
44 16 0.07
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTT
Found at i:31053305 original size:50 final size:50
Alignment explanation
Indices: 31053177--31053417 Score: 297
Period size: 50 Copynumber: 4.8 Consensus size: 50
31053167 GATAATAACA
* * ** * *
31053177 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * ** *
31053226 TGCCAATGCTATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* **
31053276 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
31053326 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
31053376 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31053418 TTACCCAAAT
Statistics
Matches: 165, Mismatches: 25, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
48 1 0.01
49 38 0.23
50 126 0.76
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:31057537 original size:42 final size:42
Alignment explanation
Indices: 31057449--31057608 Score: 126
Period size: 42 Copynumber: 3.8 Consensus size: 42
31057439 CTAGTTAGAT
* * * * ***
31057449 ATGATGCACAGAGGTGCCAAATATATTGCTTC-GAACTTTTGG
1 ATGATGCACTGAAGTGCCAGATATATTACTTCAGAA-TTTCCA
* * *
31057491 ATGATGCACTGAAGTGCCAGATATATTTCTTTAGAATTTCTA
1 ATGATGCACTGAAGTGCCAGATATATTACTTCAGAATTTCCA
* * ** * *
31057533 ATGATGCATTGAGGTGCTGGATATATTACTTCAGACTTTCCG
1 ATGATGCACTGAAGTGCCAGATATATTACTTCAGAATTTCCA
* *
31057575 ATAATGCACT-AAGGTGCCAAATATATTACTTCAG
1 ATGATGCACTGAA-GTGCCAGATATATTACTTCAG
31057609 TTATATTTCA
Statistics
Matches: 93, Mismatches: 23, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
41 1 0.01
42 89 0.96
43 3 0.03
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (42 bp):
ATGATGCACTGAAGTGCCAGATATATTACTTCAGAATTTCCA
Found at i:31063510 original size:24 final size:24
Alignment explanation
Indices: 31063483--31063532 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
31063473 AAGGGATGCT
31063483 AGAACTGGGAAAGAAATGAGCCAG
1 AGAACTGGGAAAGAAATGAGCCAG
31063507 AGAACTGGGAAAGAAATGAGCCAG
1 AGAACTGGGAAAGAAATGAGCCAG
31063531 AG
1 AG
31063533 GCTATTTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.34, T:0.08
Consensus pattern (24 bp):
AGAACTGGGAAAGAAATGAGCCAG
Found at i:31073364 original size:42 final size:42
Alignment explanation
Indices: 31073222--31073362 Score: 158
Period size: 43 Copynumber: 3.3 Consensus size: 42
31073212 GAACGGTACT
* *
31073222 TTTAGCGGCGTTTGTGATAAAAGTGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTCTGATAAAAGCGCCGCTAAAG-TCATGTTC
*
31073265 TTTAGCAGCGTTTCTGATAAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTCTGATAAAAGCGCCGCTAAA-GTCATGTTC
** * * * *
31073308 TTTAATGGCATTT-TTATAAAAGCACCGCTACAAGTCATGCTC
1 TTTAGCGGCGTTTCTGATAAAAGCGCCGCTA-AAGTCATGTTC
*
31073350 TATAGCGGCGTTT
1 TTTAGCGGCGTTT
31073363 TTCACATAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
42 32 0.39
43 49 0.60
44 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (42 bp):
TTTAGCGGCGTTTCTGATAAAAGCGCCGCTAAAGTCATGTTC
Found at i:31079319 original size:27 final size:27
Alignment explanation
Indices: 31079289--31079486 Score: 177
Period size: 27 Copynumber: 7.3 Consensus size: 27
31079279 CCTTGGGCTA
*
31079289 TAAAATTATTGAAATACCCTCAATGGG
1 TAAAATTACTGAAATACCCTCAATGGG
* * * *
31079316 TAAAATTACCGAAATACCATTAATGGA
1 TAAAATTACTGAAATACCCTCAATGGG
* **
31079343 TAAAATTATTGAAATACCCTTGATGGG
1 TAAAATTACTGAAATACCCTCAATGGG
* * **
31079370 TAAAATTAC-CATAATACCTTTGATGGG
1 TAAAATTACTGA-AATACCCTCAATGGG
*
31079397 TAAAATTACTGAAATACCCTCAATGAG
1 TAAAATTACTGAAATACCCTCAATGGG
*
31079424 -AAAATTTACTGAAATACCCTCGATGGG
1 TAAAA-TTACTGAAATACCCTCAATGGG
** ** *
31079451 TGGAATTACCAAAATACTCCTGAA-GGG
1 TAAAATTACTGAAATAC-CCTCAATGGG
31079478 TAAAATTAC
1 TAAAATTAC
31079487 CATTATACCC
Statistics
Matches: 138, Mismatches: 28, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 5 0.04
27 126 0.91
28 7 0.05
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (27 bp):
TAAAATTACTGAAATACCCTCAATGGG
Found at i:31079370 original size:54 final size:54
Alignment explanation
Indices: 31079288--31079429 Score: 198
Period size: 54 Copynumber: 2.6 Consensus size: 54
31079278 CCCTTGGGCT
31079288 ATAAAATTATTGAAATACCCTCAATGGGTAAAATTACCGA-AATACCATTAATGG
1 ATAAAATTATTGAAATACCCTCAATGGGTAAAATTACC-ATAATACCATTAATGG
** * *
31079342 ATAAAATTATTGAAATACCCTTGATGGGTAAAATTACCATAATACCTTTGATGG
1 ATAAAATTATTGAAATACCCTCAATGGGTAAAATTACCATAATACCATTAATGG
* * *
31079396 GTAAAATTACTGAAATACCCTCAATGAG-AAAATT
1 ATAAAATTATTGAAATACCCTCAATGGGTAAAATT
31079430 TACTGAAATA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
53 7 0.09
54 71 0.91
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (54 bp):
ATAAAATTATTGAAATACCCTCAATGGGTAAAATTACCATAATACCATTAATGG
Found at i:31079413 original size:81 final size:81
Alignment explanation
Indices: 31079311--31079487 Score: 223
Period size: 81 Copynumber: 2.2 Consensus size: 81
31079301 AATACCCTCA
* * *
31079311 ATGGGTAAAATTACCGAAATACCATTAATG-GATAAAATTATTGAAATACCCTTGATGGGTAAAA
1 ATGGGTAAAATTACCGAAATACCATCAATGAGA-AAAATTACTGAAATACCCTCGATGGGTAAAA
* *
31079375 TTACCATAATAC-CTTTG
65 TTACCAAAATACTC-CTG
* * * **
31079392 ATGGGTAAAATTACTGAAATACCCTCAATGAGAAAATTTACTGAAATACCCTCGATGGGTGGAAT
1 ATGGGTAAAATTACCGAAATACCATCAATGAGAAAAATTACTGAAATACCCTCGATGGGTAAAAT
31079457 TACCAAAATACTCCTG
66 TACCAAAATACTCCTG
*
31079473 AAGGGTAAAATTACC
1 ATGGGTAAAATTACC
31079488 ATTATACCCG
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
81 79 0.96
82 3 0.04
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (81 bp):
ATGGGTAAAATTACCGAAATACCATCAATGAGAAAAATTACTGAAATACCCTCGATGGGTAAAAT
TACCAAAATACTCCTG
Found at i:31080255 original size:19 final size:19
Alignment explanation
Indices: 31080214--31080257 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
31080204 TTCAAATAAG
*
31080214 TTTTCACAACAAACATTGT
1 TTTTCACAACAAACATCGT
*
31080233 TTTTCATAACAAACA-CGT
1 TTTTCACAACAAACATCGT
31080251 ATTTTCA
1 -TTTTCA
31080258 ACTTCAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (19 bp):
TTTTCACAACAAACATCGT
Found at i:31085456 original size:81 final size:81
Alignment explanation
Indices: 31085318--31085713 Score: 453
Period size: 81 Copynumber: 4.9 Consensus size: 81
31085308 GGCTTGGGCT
* * * **
31085318 GTAAAATTATCGAAATACTATTGATGGATAAAATTACCGAAATACGTTCGATGGGTAAAATTACT
1 GTAAAATTATCGAAATACCATCGATGGGTAAAATTACCGAAATACCCTCGATGGGTAAAATTACT
31085383 GAAATACCCTCGATGG
66 GAAATACCCTCGATGG
*
31085399 GTAAAATTATCGAAATACCATCGATGGGTAAAATTACCGAAATACCCTCGATAGGTAAAATTACT
1 GTAAAATTATCGAAATACCATCGATGGGTAAAATTACCGAAATACCCTCGATGGGTAAAATTACT
* *
31085464 -AATATACCCTTGATAG
66 GAA-ATACCCTCGATGG
* * * * * * *
31085480 CTAAAATTATCGAAATGCCATCGATAGGTAAAATTACCAAAATACCTTCAAAGGG-AAAATTACT
1 GTAAAATTATCGAAATACCATCGATGGGTAAAATTACCGAAATACCCTCGATGGGTAAAATTACT
31085544 GAAATACCCTCGATGG
66 GAAATACCCTCGATGG
* * * ** * *
31085560 G-AAAATTTATCGAAATACCCTCGATAGG-AAAATTTATCGAAATACCCTTAATGGGTGATATTA
1 GTAAAA-TTATCGAAATACCATCGATGGGTAAAA-TTACCGAAATACCCTCGATGGGTAAAATTA
* *
31085623 CTAAAATACCCTTGATGG
64 CTGAAATACCCTCGATGG
* * * *
31085641 GTAAAATTA-CTGAAATACCCTTGATGGG-AAAATTATCGAAATACCCTCGATGGGTGAAATTAC
1 GTAAAATTATC-GAAATACCATCGATGGGTAAAATTACCGAAATACCCTCGATGGGTAAAATTAC
*
31085704 CGAAATACCC
65 TGAAATACCC
31085714 CTAAAGGGTA
Statistics
Matches: 271, Mismatches: 37, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
79 8 0.03
80 96 0.35
81 163 0.60
82 4 0.01
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (81 bp):
GTAAAATTATCGAAATACCATCGATGGGTAAAATTACCGAAATACCCTCGATGGGTAAAATTACT
GAAATACCCTCGATGG
Found at i:31085713 original size:27 final size:27
Alignment explanation
Indices: 31085318--31085732 Score: 392
Period size: 27 Copynumber: 15.4 Consensus size: 27
31085308 GGCTTGGGCT
* ** *
31085318 GTAAAATTATCGAAATACTATTGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
* **
31085345 ATAAAATTACCGAAATACGTTCGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
*
31085372 GTAAAATTACTGAAATACCCTCGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
* *
31085399 GTAAAATTATCGAAATACCATCGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
*
31085426 GTAAAATTACCGAAATACCCTCGATAG
1 GTAAAATTACCGAAATACCCTCGATGG
* * *
31085453 GTAAAATTA-CTAATATACCCTTGATAG
1 GTAAAATTACCGAA-ATACCCTCGATGG
* * * * *
31085480 CTAAAATTATCGAAATGCCATCGATAG
1 GTAAAATTACCGAAATACCCTCGATGG
* * * *
31085507 GTAAAATTACCAAAATACCTTCAAAGG
1 GTAAAATTACCGAAATACCCTCGATGG
*
31085534 G-AAAATTACTGAAATACCCTCGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
* *
31085560 G-AAAATTTATCGAAATACCCTCGATAG
1 GTAAAA-TTACCGAAATACCCTCGATGG
* **
31085587 G-AAAATTTATCGAAATACCCTTAATGG
1 GTAAAA-TTACCGAAATACCCTCGATGG
* * ** *
31085614 GTGATATTACTAAAATACCCTTGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
* *
31085641 GTAAAATTACTGAAATACCCTTGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
*
31085668 G-AAAATTATCGAAATACCCTCGATGG
1 GTAAAATTACCGAAATACCCTCGATGG
* * *
31085694 GTGAAATTACCGAAATACCC-CTAAAGG
1 GTAAAATTACCGAAATACCCTC-GATGG
31085721 GTAAAATTACCG
1 GTAAAATTACCG
31085733 TTATACCCCT
Statistics
Matches: 324, Mismatches: 58, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
26 52 0.16
27 267 0.82
28 5 0.02
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (27 bp):
GTAAAATTACCGAAATACCCTCGATGG
Found at i:31085739 original size:134 final size:134
Alignment explanation
Indices: 31085346--31085740 Score: 424
Period size: 134 Copynumber: 2.9 Consensus size: 134
31085336 TATTGATGGA
* * ** *
31085346 TAAAATTACCGAAATACGTTCGATGGGTAAAATTACTGAAATACCCTCGATGGGTAAAATTATCG
1 TAAAATTATCAAAATACCATCGATGGGTAAAATTACTGAAATACCCTTGATGGG-AAAATTATCG
* ** *
31085411 AAATACCATCGATGGGTAAAATTACCGAAATACCCTCGATAGGTAAAATTACTAATATACCCTTG
65 AAATACCCTCGATGGGTAAAATTACCGAAATACCCTCGATAGGTAAAATTACCGATATACCCTTA
31085476 ATAGC
130 ATAGC
* * * ** * *
31085481 TAAAATTATCGAAATGCCATCGATAGGTAAAATTACCAAAATA-CCTTCAAAGGGAAAATTA-CT
1 TAAAATTATCAAAATACCATCGATGGGTAAAATTACTGAAATACCCTT-GATGGGAAAATTATC-
* * *
31085544 GAAATACCCTCGATGGG-AAAATTTATCGAAATACCCTCGATAGG-AAAATTTATCGAAATACCC
64 GAAATACCCTCGATGGGTAAAA-TTACCGAAATACCCTCGATAGGTAAAA-TTACCGATATACCC
* *
31085607 TTAATGGG
127 TTAATAGC
* * * *
31085615 TGATATTA-CTAAAATACCCTTGATGGGTAAAATTACTGAAATACCCTTGATGGGAAAATTATCG
1 TAAAATTATC-AAAATACCATCGATGGGTAAAATTACTGAAATACCCTTGATGGGAAAATTATCG
* * * *
31085679 AAATACCCTCGATGGGTGAAATTACCGAAATACCC-CTAAAGGGTAAAATTACCGTTATACCC
65 AAATACCCTCGATGGGTAAAATTACCGAAATACCCTCGATA-GGTAAAATTACCGATATACCC
31085741 CTAAAATATG
Statistics
Matches: 213, Mismatches: 37, Indels: 21
0.79 0.14 0.08
Matches are distributed among these distances:
133 13 0.06
134 148 0.69
135 52 0.24
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (134 bp):
TAAAATTATCAAAATACCATCGATGGGTAAAATTACTGAAATACCCTTGATGGGAAAATTATCGA
AATACCCTCGATGGGTAAAATTACCGAAATACCCTCGATAGGTAAAATTACCGATATACCCTTAA
TAGC
Found at i:31085754 original size:27 final size:27
Alignment explanation
Indices: 31085695--31085754 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
31085685 CCTCGATGGG
* *
31085695 TGAAATTACCGAAATACCCCTAAAGGG
1 TGAAATTACCGAAATACCCCTAAAAGA
* ** *
31085722 TAAAATTACCGTTATACCCCTAAAATA
1 TGAAATTACCGAAATACCCCTAAAAGA
31085749 TGAAAT
1 TGAAAT
31085755 AATTGTTATG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (27 bp):
TGAAATTACCGAAATACCCCTAAAAGA
Found at i:31085919 original size:29 final size:26
Alignment explanation
Indices: 31085887--31085942 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 26
31085877 ACTGTTTCTA
31085887 GTGGCTCTGCCACACTCATACTGATACTG
1 GTGGCTCTGCCACA-T-ATACTG-TACTG
*
31085916 GTGGCTTTGCCACATATACTGTACTG
1 GTGGCTCTGCCACATATACTGTACTG
31085942 G
1 G
31085943 CAGCTCTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 6 0.23
27 6 0.23
28 1 0.04
29 13 0.50
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (26 bp):
GTGGCTCTGCCACATATACTGTACTG
Found at i:31086296 original size:15 final size:15
Alignment explanation
Indices: 31086276--31086306 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31086266 CTGTGCAGGT
31086276 AATCCCCAACCTTAG
1 AATCCCCAACCTTAG
31086291 AATCCCCAACCTTAG
1 AATCCCCAACCTTAG
31086306 A
1 A
31086307 TGATTTGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.39, G:0.06, T:0.19
Consensus pattern (15 bp):
AATCCCCAACCTTAG
Found at i:31086527 original size:19 final size:19
Alignment explanation
Indices: 31086486--31086530 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
31086476 TTCAAGTAAG
*
31086486 TTTTCAAAACAAACACAGT
1 TTTTCAAAACAAACACACT
*
31086505 TTTTCATAACAAACAC-CT
1 TTTTCAAAACAAACACACT
31086523 ATTTTCAA
1 -TTTTCAA
31086531 CTTCAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.42, C:0.22, G:0.02, T:0.33
Consensus pattern (19 bp):
TTTTCAAAACAAACACACT
Found at i:31090693 original size:22 final size:22
Alignment explanation
Indices: 31090665--31090707 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
31090655 GCTTAATTGA
31090665 ATTATACAGTCACAAAGAAAGG
1 ATTATACAGTCACAAAGAAAGG
* *
31090687 ATTATACAGTCATAGAGAAAG
1 ATTATACAGTCACAAAGAAAG
31090708 AGTTACTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.21
Consensus pattern (22 bp):
ATTATACAGTCACAAAGAAAGG
Found at i:31104634 original size:411 final size:411
Alignment explanation
Indices: 31103866--31104679 Score: 1360
Period size: 411 Copynumber: 2.0 Consensus size: 411
31103856 TGAATTACAT
*
31103866 GGTAACAGAAAAAGAGTTACTTGCTATTGTGCTTGCTTTTGACAAGTTTCGAATCTATCTTGTAG
1 GGTAACAGAAAAAGAGTTACTTGCTATTGTGCTTGCTTTAGACAAGTTTCGAATCTATCTTGTAG
* * *
31103931 GTACCAAAGTGACTGTTTATATGGACCAGTCGACAGTTAAGTATTTACTTACCAAGAAAGACGCT
66 GTACCAAAGTGACTGTTTATACGGACCACTCGACAATTAAGTATTTACTTACCAAGAAAGACGCT
* * * * *
31103996 AAGCCGGGACTGATGTGATGGGTATTTCTACTTAAAGAGTTGGATCTAGAAATTCAAGATCAAAA
131 AAGCCGAGACTGATCTGATGGGCACTTCTACTTAAAGAGTTCGATCTAGAAATTCAAGATCAAAA
* *
31104061 GGGAGTGGAAAACCAAGTAGCAAACCACTTGTCCAAATTGGAGCCATAAGAATGGAACTCTCCTC
196 GGGAGTGCAAAACCAAGTAGCAAACCACTTGTCCAAATTGGAGCCATAAGAAGGGAACTCTCCTC
*
31104126 TTATACCAATTCAAGAGACGTTTCCAAATGAACACATACTGAAGATAAATCATGTTGATAATACC
261 TTATACCAATTCAAGAGACGTTTCCAAATGAACACATACTGAAGATAAATCATGTCGATAATACC
* * *
31104191 CCTTGGTTTGCTGATATTGCTTACTTTTTAGCTTGTGGTTTGATGCCGATTGATAAGATGTATCA
326 CCTTGGTTTGCTGATATTGATAACTTTTTAGCTTGTGGTTTGATGCCGATTGATAAGACGTATCA
31104256 TCAAAAGAAAAAGAGAGACAC
391 TCAAAAGAAAAAGAGAGACAC
* *
31104277 GGTAATAGAAAAAGAGTTACTTGCTATTGTGTTTGCTTTAGACAAGTTTCG-ATCTTATCTTGTA
1 GGTAACAGAAAAAGAGTTACTTGCTATTGTGCTTGCTTTAGACAAGTTTCGAATC-TATCTTGTA
* *
31104341 GGTACCAAAGTGACTGTTTATACGGACCACTCGACAATTAAGTATTTACTTGCCAAGAAAGACTC
65 GGTACCAAAGTGACTGTTTATACGGACCACTCGACAATTAAGTATTTACTTACCAAGAAAGACGC
**
31104406 TAAGCCGAGACTGATCTGATGGGCACTTCTACTTAAAGAGTTCGATCTAGAAATTCAAGATTGAA
130 TAAGCCGAGACTGATCTGATGGGCACTTCTACTTAAAGAGTTCGATCTAGAAATTCAAGATCAAA
* * *
31104471 AGGGAGTGCAAAACCAAGTAGCAGACCACTTGTTCAGATTGGAGCCATAAGAAGGGAACTCTCCT
195 AGGGAGTGCAAAACCAAGTAGCAAACCACTTGTCCAAATTGGAGCCATAAGAAGGGAACTCTCCT
* * * *
31104536 TTTATACCAATTCTAGAGACGTTTCCAGATGAACACATACTGAAGGTAAATCATGTCGATAATAC
260 CTTATACCAATTCAAGAGACGTTTCCAAATGAACACATACTGAAGATAAATCATGTCGATAATAC
31104601 CCCTTGGTTTGCTGATATTGATAACTTTTTAGCTTGTGGTTTGATGCCGATTGATAAGACGTATC
325 CCCTTGGTTTGCTGATATTGATAACTTTTTAGCTTGTGGTTTGATGCCGATTGATAAGACGTATC
31104666 ATCAAAAGAAAAAG
390 ATCAAAAGAAAAAG
31104680 TTTCTTTACG
Statistics
Matches: 374, Mismatches: 28, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
410 3 0.01
411 371 0.99
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (411 bp):
GGTAACAGAAAAAGAGTTACTTGCTATTGTGCTTGCTTTAGACAAGTTTCGAATCTATCTTGTAG
GTACCAAAGTGACTGTTTATACGGACCACTCGACAATTAAGTATTTACTTACCAAGAAAGACGCT
AAGCCGAGACTGATCTGATGGGCACTTCTACTTAAAGAGTTCGATCTAGAAATTCAAGATCAAAA
GGGAGTGCAAAACCAAGTAGCAAACCACTTGTCCAAATTGGAGCCATAAGAAGGGAACTCTCCTC
TTATACCAATTCAAGAGACGTTTCCAAATGAACACATACTGAAGATAAATCATGTCGATAATACC
CCTTGGTTTGCTGATATTGATAACTTTTTAGCTTGTGGTTTGATGCCGATTGATAAGACGTATCA
TCAAAAGAAAAAGAGAGACAC
Found at i:31107212 original size:19 final size:19
Alignment explanation
Indices: 31107190--31107227 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
31107180 TCCCTCATCC
31107190 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
31107209 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
31107228 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:31114591 original size:47 final size:48
Alignment explanation
Indices: 31114532--31114724 Score: 228
Period size: 48 Copynumber: 4.0 Consensus size: 48
31114522 TACTATGCGT
*
31114532 ACCGATAATCTGTTATGACACAAGGGTGGCA-GGACTGTGTGCAGGCC
1 ACCGATAATCTGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
* * *
31114579 ACCGATATTCTGTTTTGACACAAGGGTGGCACGGACTGTGTGCAGGCC
1 ACCGATAATCTGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
* * * * * * * *
31114627 ACCAATAA-CTTGTTAAGATACAAACGTGGAACAGACTATGTGTAGGCC
1 ACCGATAATC-TGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
* * *
31114675 ACCGAGAATCTGTTATTACACAAAGGTGGTACGGACTGTGTGCAGGCC
1 ACCGATAATCTGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
31114723 AC
1 AC
31114725 TGAGAAATCT
Statistics
Matches: 120, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
47 30 0.25
48 89 0.74
49 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (48 bp):
ACCGATAATCTGTTATGACACAAAGGTGGCACGGACTGTGTGCAGGCC
Found at i:31116110 original size:24 final size:24
Alignment explanation
Indices: 31116075--31116125 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
31116065 AAAGCAATGC
31116075 GCCGGCTCCCGC-TCGAAGGACTGT
1 GCCGGCTCCCGCGT-GAAGGACTGT
*
31116099 GCCGGCTTCCGCGTGAAGGACTGT
1 GCCGGCTCCCGCGTGAAGGACTGT
31116123 GCC
1 GCC
31116126 TGCGGAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.12, C:0.35, G:0.35, T:0.18
Consensus pattern (24 bp):
GCCGGCTCCCGCGTGAAGGACTGT
Found at i:31122126 original size:48 final size:47
Alignment explanation
Indices: 31122045--31122234 Score: 215
Period size: 48 Copynumber: 4.0 Consensus size: 47
31122035 TGTACTGATA
** *
31122045 ATCTGTTAGGACACAAGGGTGG-ATCGGATTGTGTGCAGGCCACCGAT
1 ATCTGTTTTGACACAAGGGTGGCA-CGGACTGTGTGCAGGCCACCGAT
31122092 ATTCTGTTTTGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGAT
1 A-TCTGTTTTGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGAT
* ** * *
31122140 AACTTGTTAAGATACAAGGGTGGCACGGACTATGTGCAGGCCACCCAGA-
1 ATC-TGTTTTGACACAAGGGTGGCACGGACTGTGTGCAGGCCA-CC-GAT
* *
31122189 ATCTGTTATT-ACACAAAGGTGGTACGGACTGTGTGCAGGCCACCGA
1 ATCTGTT-TTGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGA
31122235 GAAATCTATT
Statistics
Matches: 122, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
46 2 0.02
47 4 0.03
48 109 0.89
49 5 0.04
50 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.23
Consensus pattern (47 bp):
ATCTGTTTTGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGAT
Found at i:31122210 original size:96 final size:96
Alignment explanation
Indices: 31122048--31122234 Score: 261
Period size: 96 Copynumber: 1.9 Consensus size: 96
31122038 ACTGATAATC
* * * * * * *
31122048 TGTTAGGACACAAGGGTGGATCGGATTGTGTGCAGGCCACCGATATTCTGTTTTGACACAAGGGT
1 TGTTAAGACACAAGGGTGGATCGGACTATGTGCAGGCCACCCAGAATCTGTTTTGACACAAAGGT
31122113 GGCACGGACTGTGTGCAGGCCACCGATAACT
66 GGCACGGACTGTGTGCAGGCCACCGATAACT
*
31122144 TGTTAAGATACAAGGGTGGCA-CGGACTATGTGCAGGCCACCCAGAATCTGTTATT-ACACAAAG
1 TGTTAAGACACAAGGGTGG-ATCGGACTATGTGCAGGCCACCCAGAATCTGTT-TTGACACAAAG
*
31122207 GTGGTACGGACTGTGTGCAGGCCACCGA
64 GTGGCACGGACTGTGTGCAGGCCACCGA
31122235 GAAATCTATT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
96 77 0.96
97 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.22
Consensus pattern (96 bp):
TGTTAAGACACAAGGGTGGATCGGACTATGTGCAGGCCACCCAGAATCTGTTTTGACACAAAGGT
GGCACGGACTGTGTGCAGGCCACCGATAACT
Found at i:31128188 original size:19 final size:19
Alignment explanation
Indices: 31128166--31128203 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
31128156 TCACTCATCC
31128166 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
31128185 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
31128204 ACTATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:31136129 original size:21 final size:22
Alignment explanation
Indices: 31136105--31136147 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31136095 ACTCATCCCT
*
31136105 CATTCTTCA-TCCTTTCATTCA
1 CATTCTACATTCCTTTCATTCA
*
31136126 CATTCTACATTCCTTTCTTTCA
1 CATTCTACATTCCTTTCATTCA
31136148 TTCCATTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.49
Consensus pattern (22 bp):
CATTCTACATTCCTTTCATTCA
Found at i:31143880 original size:24 final size:23
Alignment explanation
Indices: 31143839--31143883 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
31143829 CCTACCCAAG
* *
31143839 CTCACCACCTTTTGTCTCCATCA
1 CTCACCACCTTATCTCTCCATCA
31143862 CTCACCTACCTTATCTCTCCAT
1 CTCACC-ACCTTATCTCTCCAT
31143884 GTAGGAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.18, C:0.44, G:0.02, T:0.36
Consensus pattern (23 bp):
CTCACCACCTTATCTCTCCATCA
Found at i:31146763 original size:104 final size:103
Alignment explanation
Indices: 31146500--31146755 Score: 399
Period size: 104 Copynumber: 2.5 Consensus size: 103
31146490 TAACCGTTAT
* *
31146500 TGGTGGATCCCGCACTTAGCACCA-CCACTGAATCGGGGAATCAGCACATAGCAACCTCTCGGGG
1 TGGTGGATCACGCACTTAGCACCACCCA-TGAATCGGGGAATCAGCACATAGCAACCGCTCGGGG
*
31146564 GAATCAGCAAATAGCAACCCCCTTTTCATTTCAAAGATA
65 GAATCAGCAAATAGCAACCCCCTTTACATTTCAAAGATA
* *
31146603 TGGTGGAT-ATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCGCTCGGG
1 TGGTGGATCA-CGCACTTAGCACCACCCATG-AATCGGGGAATCAGCACATAGCAACCGCTCGGG
*
31146667 GGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
64 GGAATCAGCAAATAGCAACCCCCTTT-ACATTTCAAAGATA
*
31146708 TGGTGGATCACGCACATAGCACCACCCATGAATCGGGGAATCAGCACA
1 TGGTGGATCACGCACTTAGCACCACCCATGAATCGGGGAATCAGCACA
31146756 CGGCAACCCC
Statistics
Matches: 139, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
103 24 0.17
104 75 0.54
105 39 0.28
106 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (103 bp):
TGGTGGATCACGCACTTAGCACCACCCATGAATCGGGGAATCAGCACATAGCAACCGCTCGGGGG
AATCAGCAAATAGCAACCCCCTTTACATTTCAAAGATA
Found at i:31153668 original size:27 final size:27
Alignment explanation
Indices: 31153624--31153675 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
31153614 CAATGAAATC
*
31153624 GGGGAATCAGCACTTAGCAACCCCTCG
1 GGGGAATCAGCACATAGCAACCCCTCG
*
31153651 GGGGAATCAGTACATAGCAACCCCT
1 GGGGAATCAGCACATAGCAACCCCT
31153676 TTTTCATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.31, G:0.25, T:0.15
Consensus pattern (27 bp):
GGGGAATCAGCACATAGCAACCCCTCG
Found at i:31153709 original size:104 final size:104
Alignment explanation
Indices: 31153547--31153856 Score: 489
Period size: 104 Copynumber: 3.0 Consensus size: 104
31153537 CCACTGAATC
* *
31153547 GGGGAATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATATGGTGGATATCACACTTAGCACC
1 GGGGAATCAGCACATAGCAACCCCTTTTTCATTTCAAAGATATGGTGGATATCGCACTTAGCACC
31153612 ACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCG
66 ACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCG
*
31153651 GGGGAATCAGTACATAGCAACCCCTTTTTCATTTCAAAGATATGGTGGATATCGCACTTAGCACC
1 GGGGAATCAGCACATAGCAACCCCTTTTTCATTTCAAAGATATGGTGGATATCGCACTTAGCACC
*
31153716 ACCAATGAAATCGGGGAATCAACACTTAGCAACCCCTCG
66 ACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCG
* ** *
31153755 GGGGAATCAGCACAAAGCAACCCCCTTTCACATTTCAAAGATATGGTGGATCA-CGCACATAGCA
1 GGGGAATCAGCACATAGCAA-CCCCTTTTTCATTTCAAAGATATGGTGGAT-ATCGCACTTAGCA
* **
31153819 CCACCCATG-AATCGGGGAATCAGCACACAGCAACCCCT
64 CCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCT
31153857 TTTATATACA
Statistics
Matches: 191, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
104 144 0.75
105 46 0.24
106 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.20
Consensus pattern (104 bp):
GGGGAATCAGCACATAGCAACCCCTTTTTCATTTCAAAGATATGGTGGATATCGCACTTAGCACC
ACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCG
Found at i:31176126 original size:40 final size:40
Alignment explanation
Indices: 31176071--31176151 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
31176061 GCTAGTTGAG
31176071 TTAGAGCACAAAGCATTTTGGACAAACAAGAAATAAAACA
1 TTAGAGCACAAAGCATTTTGGACAAACAAGAAATAAAACA
*
31176111 TTAGAGCACAAAGCATTTTGGATAAACAAGAAATAAAACA
1 TTAGAGCACAAAGCATTTTGGACAAACAAGAAATAAAACA
31176151 T
1 T
31176152 GGACTAGGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.52, C:0.14, G:0.15, T:0.20
Consensus pattern (40 bp):
TTAGAGCACAAAGCATTTTGGACAAACAAGAAATAAAACA
Found at i:31189002 original size:23 final size:23
Alignment explanation
Indices: 31188972--31189019 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
31188962 TGCTTTTTTG
*
31188972 AGTGGAGCAAAACTCCTTGTTTA
1 AGTGGAGCAAAACTCCCTGTTTA
*
31188995 AGTGGAGCAAAAGTCCCTGTTTA
1 AGTGGAGCAAAACTCCCTGTTTA
31189018 AG
1 AG
31189020 AGTAAATCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (23 bp):
AGTGGAGCAAAACTCCCTGTTTA
Found at i:31189727 original size:14 final size:14
Alignment explanation
Indices: 31189708--31189747 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
31189698 TTGTTTGCCA
31189708 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
31189722 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
31189736 GGAAAATGTTTT
1 GTAAAATGTTTT
31189748 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:31189760 original size:34 final size:35
Alignment explanation
Indices: 31189716--31189782 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
31189706 CAGTAAAATG
* *
31189716 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
*
31189750 TTTTCTGTAAAATAATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTT
31189783 TTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:31189768 original size:20 final size:20
Alignment explanation
Indices: 31189731--31189770 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
31189721 CGTAAAATGA
**
31189731 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATAATTTACT
*
31189751 TTTCTGTAAAATAATTTACT
1 TTTCTGGAAAATAATTTACT
31189771 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATAATTTACT
Found at i:31192473 original size:14 final size:14
Alignment explanation
Indices: 31192454--31192481 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31192444 TGGAAAAGGT
31192454 GGAAAATATTTTCC
1 GGAAAATATTTTCC
31192468 GGAAAATATTTTCC
1 GGAAAATATTTTCC
31192482 ACCAAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
GGAAAATATTTTCC
Found at i:31193200 original size:20 final size:21
Alignment explanation
Indices: 31193161--31193206 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
31193151 CGGAATGTAG
31193161 TCAACCTAACATGAATTAAAT
1 TCAACCTAACATGAATTAAAT
31193182 TCAACCTAA-ATTG-ATTAAAT
1 TCAACCTAACA-TGAATTAAAT
31193202 T-AACC
1 TCAACC
31193207 ATTCCAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.17
20 9 0.38
21 11 0.46
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (21 bp):
TCAACCTAACATGAATTAAAT
Found at i:31197717 original size:30 final size:30
Alignment explanation
Indices: 31197661--31197719 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
31197651 CTTTTTGAAT
* *
31197661 ATATTTACAAAAAGAGGCATCTAATTTTTA
1 ATATTTACAAAAAGAGGCACCAAATTTTTA
31197691 ATATTTACAAAAAGA-GCAACCAAATTTTT
1 ATATTTACAAAAAGAGGC-ACCAAATTTTT
31197720 TAAAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (30 bp):
ATATTTACAAAAAGAGGCACCAAATTTTTA
Found at i:31204162 original size:21 final size:20
Alignment explanation
Indices: 31204133--31204178 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
31204123 CAAAATGCAA
31204133 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
31204154 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
31204174 T-AACC
1 TCAACC
31204179 ATTCCAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:31209030 original size:14 final size:14
Alignment explanation
Indices: 31209007--31209039 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
31208997 TCTCCTCTCC
31209007 CTTTTT-CCTTCTT
1 CTTTTTCCCTTCTT
31209020 CTTTTTCCCTTCTT
1 CTTTTTCCCTTCTT
31209034 -TTTTTC
1 CTTTTTC
31209040 TCTCCTCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
CTTTTTCCCTTCTT
Found at i:31209197 original size:7 final size:7
Alignment explanation
Indices: 31209185--31209448 Score: 438
Period size: 7 Copynumber: 37.7 Consensus size: 7
31209175 TTTCATTCTT
31209185 TATTTCC
1 TATTTCC
31209192 TATTTCC
1 TATTTCC
31209199 TATTTCC
1 TATTTCC
31209206 TATTTCC
1 TATTTCC
31209213 TATTTCC
1 TATTTCC
31209220 TATTTCC
1 TATTTCC
31209227 TATTTCC
1 TATTTCC
31209234 TATTTCC
1 TATTTCC
31209241 TATTTCC
1 TATTTCC
31209248 TATTTCC
1 TATTTCC
31209255 TATTTCC
1 TATTTCC
31209262 TATTTCC
1 TATTTCC
31209269 TATTTCC
1 TATTTCC
31209276 TATTTCC
1 TATTTCC
31209283 TATTTCC
1 TATTTCC
31209290 TATTTCC
1 TATTTCC
31209297 TATTTCC
1 TATTTCC
31209304 TATTTCC
1 TATTTCC
31209311 TATTTCC
1 TATTTCC
31209318 TATTTCC
1 TATTTCC
31209325 TATTTCC
1 TATTTCC
31209332 TATTTCC
1 TATTTCC
31209339 TATTTCC
1 TATTTCC
31209346 TATTTCC
1 TATTTCC
31209353 TATTTCC
1 TATTTCC
31209360 TATTTCC
1 TATTTCC
31209367 TATTTCC
1 TATTTCC
*
31209374 TATTTCT
1 TATTTCC
*
31209381 TATTTCG
1 TATTTCC
*
31209388 TATTTCT
1 TATTTCC
*
31209395 TATTTCG
1 TATTTCC
*
31209402 TATTTCG
1 TATTTCC
*
31209409 TATTTCT
1 TATTTCC
* *
31209416 TGTTTCT
1 TATTTCC
31209423 TATTTCC
1 TATTTCC
*
31209430 TATTTCT
1 TATTTCC
*
31209437 TATTTCT
1 TATTTCC
31209444 TATTT
1 TATTT
31209449 TCATTAGTTA
Statistics
Matches: 248, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 248 1.00
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.60
Consensus pattern (7 bp):
TATTTCC
Found at i:31211222 original size:6 final size:5
Alignment explanation
Indices: 31211193--31211244 Score: 54
Period size: 5 Copynumber: 10.2 Consensus size: 5
31211183 ATTGAGTCAA
*
31211193 TTTAT TTTAT TTTAT TTTATT TTTACT TTTAT TTT-T TAT-T TTTAT GTTTAT
1 TTTAT TTTAT TTTAT TTTA-T TTTA-T TTTAT TTTAT TTTAT TTTAT -TTTAT
31211244 T
1 T
31211245 GTAATTTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 6 0.15
5 20 0.49
6 15 0.37
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:31213160 original size:14 final size:14
Alignment explanation
Indices: 31213141--31213168 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31213131 CTAATTTATT
31213141 AATGAATTATTAAA
1 AATGAATTATTAAA
31213155 AATGAATTATTAAA
1 AATGAATTATTAAA
31213169 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:31215596 original size:27 final size:26
Alignment explanation
Indices: 31215565--31215641 Score: 118
Period size: 27 Copynumber: 2.8 Consensus size: 26
31215555 TTAAAAAATG
31215565 GAAATATCCCCATAGGGTAAAATAACC
1 GAAATA-CCCCATAGGGTAAAATAACC
*
31215592 GAAATACTCCCATAGGGTAAAATAATC
1 GAAATAC-CCCATAGGGTAAAATAACC
31215619 GAAATACCTCCATAGGGTAAAAT
1 GAAATACC-CCATAGGGTAAAAT
31215642 GACTGTTATA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 2 0.04
27 45 0.96
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (26 bp):
GAAATACCCCATAGGGTAAAATAACC
Found at i:31230282 original size:30 final size:30
Alignment explanation
Indices: 31230246--31230303 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
31230236 CTGGGCAATT
*
31230246 CCACACGGGCTAGG-CACACGCCCGTGTGAG
1 CCACACGGGCT-GGCCACACGCCCATGTGAG
*
31230276 CCACACGGGCTGGCCACATGCCCATGTG
1 CCACACGGGCTGGCCACACGCCCATGTG
31230304 CCAACCCGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.19, C:0.38, G:0.31, T:0.12
Consensus pattern (30 bp):
CCACACGGGCTGGCCACACGCCCATGTGAG
Found at i:31233415 original size:20 final size:20
Alignment explanation
Indices: 31233390--31233429 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
31233380 TATCACCACT
31233390 CATAGACTCGTAGAGTCAAA
1 CATAGACTCGTAGAGTCAAA
31233410 CATAGACTCGTAGAGTCAAA
1 CATAGACTCGTAGAGTCAAA
31233430 TATATAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
CATAGACTCGTAGAGTCAAA
Found at i:31238283 original size:652 final size:652
Alignment explanation
Indices: 31237040--31238351 Score: 2295
Period size: 652 Copynumber: 2.0 Consensus size: 652
31237030 ATTACAGTAT
* * * * *
31237040 CAATATTCAATGCAGTAACAGATATACATTTTCGAATCCTACCCAGCCAGCATCTACACTCCAAT
1 CAATATTCAACGCAGTAACAAATATACAGTTTCAAATCCTACCCAGCCAACATCTACACTCCAAT
* *
31237105 TCTGTCCAACCCTACACTCCATGTGAGAATATAATCAATCCACCTATCCCTACACTCCAGAAAGT
66 TCTGTCCAACCCTACACTCCATGTGAGAATATAATCAACCCACCTATCCCCACACTCCAGAAAGT
* *
31237170 ACCGAATGCGGCACTAAATAGTAGTTTGCAGCAGAGCTGCCAGTAACTTAGGCTTGAGGCCTTTC
131 ACCGAATGCGGCACTAAACAGTAGTTCGCAGCAGAGCTGCCAGTAACTTAGGCTTGAGGCCTTTC
*
31237235 AGTACACTTCCTCCGAACATTATAATTCCCCAAACCCAATGTAATGCAATATACAGATATGACAT
196 AGTACACTTCCTCCGAACATTATAATTCCCCAAACCCAATGTAATGCAATATACAAATATGACAT
* *
31237300 GCTGTAACATAATATCATGCATGTAAATAGAGCATACAGTATCAAATCATTGTGACATCATCAGA
261 GCTGTAACATAATATCATGCATGTAAATAGAGCATACAGTATCAAATCATTGGGACATCATCAAA
* * * ***
31237365 CTTAATCATATCAGTCATACAGTCATTTTAGTCAATTAGGGGTCGAGGTAAACTTGTTGTCCCTA
326 CTTAATCATATCAGTCATAAAGTCATTTCAGTCAATTAGGAGTCGAGGTAAACTTACCGTCCCTA
31237430 CAGTAGGTTCAAAGTCGACTTGGCCGACCCGTGCAACCTTATCAATCAAACAGTGAAAATGGGCC
391 CAGTAGGTTCAAAGTCGACTTGGCCGACCCGTGCAACCTTATCAATCAAACAGTGAAAATGGGCC
31237495 TACGAGCCCAAAAGGTTCACTCATGTAGGCCCACACGCCCGTGTGGCCCACATGGCCCAAACTGA
456 TACGAGCCCAAAAGGTTCACTCATGTAGGCCCACACGCCCGTGTGGCCCACATGGCCCAAACTGA
31237560 CCATGGCCTCGTGATCCATTTTAGTATAACCCATGCTAGATAATTATTCATATGTGTTTGCCCTT
521 CCATGGCCTCGTGATCCATTTTAGTATAACCCATGCTAGATAATTATTCATATGTGTTTGCCCTT
* *
31237625 TTTACTTATAATCCTTCCAAGCTATCTACTTGAGTCACTGTTACTAAATTATTTGTATCTTAAGA
586 TTTACTTATAATCCTTCCAAGCTATCTACTTGAGTCACTGTTACTAAATTAATTGTATATTAAGA
31237690 TA
651 TA
* *
31237692 CAATATTCAACGCCGTAACAAATATACAGTTTCAAATCCTACCCAGCCAACCTCTACACTCCAAC
1 CAATATTCAACGCAGTAACAAATATACAGTTTCAAATCCTACCCAGCCAACATCTACACTCCAA-
* *
31237757 TTC-GTCCAACCCTACACTCCATGTGGGAATATAATCAACCCACCTATCCCCACACTCTAGAAAG
65 TTCTGTCCAACCCTACACTCCATGTGAGAATATAATCAACCCACCTATCCCCACACTCCAGAAAG
*
31237821 TACTGAATGCGGCACTAAACAGTAGTTCGCAGCAGAGCTGCCAGTAACTTAGGCTTGAGGCCTTT
130 TACCGAATGCGGCACTAAACAGTAGTTCGCAGCAGAGCTGCCAGTAACTTAGGCTTGAGGCCTTT
31237886 CAGTACACTTCCTCCGAACATTATAATTCCCCAAACCCAATGTAATGCAATATACAAATATGACA
195 CAGTACACTTCCTCCGAACATTATAATTCCCCAAACCCAATGTAATGCAATATACAAATATGACA
*
31237951 TGCTGTAACATAATATCATGCATGTAATTAGAGCATACAGTATCAAATCATTGGGACATCATCAA
260 TGCTGTAACATAATATCATGCATGTAAATAGAGCATACAGTATCAAATCATTGGGACATCATCAA
*
31238016 ACTTAATCATATCAGTCATAAAGTCATTTCAGTCAATTAGGAGTCTAGGTAAACTTACCGTCCCT
325 ACTTAATCATATCAGTCATAAAGTCATTTCAGTCAATTAGGAGTCGAGGTAAACTTACCGTCCCT
31238081 ACAGTAGGTTCAAAGTCGACTTGGCCGACCCGTGCAACCTTATCAATCAAACAGTGAAAATGGGC
390 ACAGTAGGTTCAAAGTCGACTTGGCCGACCCGTGCAACCTTATCAATCAAACAGTGAAAATGGGC
*
31238146 CTACGAGCCCAAAAGGTTCACTCATGTAGGCCCACACGCCCGTGTGGCCCACATGGCTCAAACTG
455 CTACGAGCCCAAAAGGTTCACTCATGTAGGCCCACACGCCCGTGTGGCCCACATGGCCCAAACTG
*
31238211 ACCATGGCCTCGTGATCCATTTTAGTATAACCCATGCTAGATAATTATTCATATGTGTTTTTCCC
520 ACCATGGCCTCGTGATCCATTTTAGTATAACCCATGCTAGATAATTATTCATATGTG-TTTGCCC
* *
31238276 -TTTTACTTATAATCCTTCCAAGCTGTCTACTTGCGTCACTGTTACTAAATTAATTGTATATTAA
584 TTTTTACTTATAATCCTTCCAAGCTATCTACTTGAGTCACTGTTACTAAATTAATTGTATATTAA
*
31238340 GCTA
649 GATA
*
31238344 CAAAATTC
1 CAATATTC
31238352 TGAATTAAGG
Statistics
Matches: 625, Mismatches: 33, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
652 616 0.99
653 9 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (652 bp):
CAATATTCAACGCAGTAACAAATATACAGTTTCAAATCCTACCCAGCCAACATCTACACTCCAAT
TCTGTCCAACCCTACACTCCATGTGAGAATATAATCAACCCACCTATCCCCACACTCCAGAAAGT
ACCGAATGCGGCACTAAACAGTAGTTCGCAGCAGAGCTGCCAGTAACTTAGGCTTGAGGCCTTTC
AGTACACTTCCTCCGAACATTATAATTCCCCAAACCCAATGTAATGCAATATACAAATATGACAT
GCTGTAACATAATATCATGCATGTAAATAGAGCATACAGTATCAAATCATTGGGACATCATCAAA
CTTAATCATATCAGTCATAAAGTCATTTCAGTCAATTAGGAGTCGAGGTAAACTTACCGTCCCTA
CAGTAGGTTCAAAGTCGACTTGGCCGACCCGTGCAACCTTATCAATCAAACAGTGAAAATGGGCC
TACGAGCCCAAAAGGTTCACTCATGTAGGCCCACACGCCCGTGTGGCCCACATGGCCCAAACTGA
CCATGGCCTCGTGATCCATTTTAGTATAACCCATGCTAGATAATTATTCATATGTGTTTGCCCTT
TTTACTTATAATCCTTCCAAGCTATCTACTTGAGTCACTGTTACTAAATTAATTGTATATTAAGA
TA
Found at i:31246408 original size:20 final size:20
Alignment explanation
Indices: 31246383--31246455 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
31246373 TGATGAACCT
31246383 TTCCATTTACTTACTTAT-CA
1 TTCCATTTACTTACTT-TCCA
*
31246403 TTCCATTTGCTTACTTTCCA
1 TTCCATTTACTTACTTTCCA
*
31246423 TTTCATTTACTTACTTTCCA
1 TTCCATTTACTTACTTTCCA
*
31246443 TTCTATTTACTTA
1 TTCCATTTACTTA
31246456 GCATAAGCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.02
20 46 0.98
ACGTcount: A:0.21, C:0.25, G:0.01, T:0.53
Consensus pattern (20 bp):
TTCCATTTACTTACTTTCCA
Found at i:31247909 original size:30 final size:30
Alignment explanation
Indices: 31247868--31247933 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
31247858 GTATGTCCGA
*
31247868 CCGTATACCTCTCAAAATGGCCCCACACGC
1 CCGTGTACCTCTCAAAATGGCCCCACACGC
** * *
31247898 CCGTGTACCTCTTGAAATGGCCTCACATGC
1 CCGTGTACCTCTCAAAATGGCCCCACACGC
31247928 CCGTGT
1 CCGTGT
31247934 GCCAGGCTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (30 bp):
CCGTGTACCTCTCAAAATGGCCCCACACGC
Found at i:31260210 original size:3 final size:3
Alignment explanation
Indices: 31260202--31260226 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31260192 TGAGGTTTTT
31260202 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
31260227 GATAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:31264192 original size:46 final size:46
Alignment explanation
Indices: 31264125--31264286 Score: 285
Period size: 46 Copynumber: 3.6 Consensus size: 46
31264115 TTTGAGTACT
31264125 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
31264171 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
31264217 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
31264262 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
31264287 ATCATACGTA
Statistics
Matches: 114, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
43 12 0.11
44 5 0.04
45 19 0.17
46 78 0.68
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:31265195 original size:27 final size:27
Alignment explanation
Indices: 31265156--31265376 Score: 275
Period size: 27 Copynumber: 8.2 Consensus size: 27
31265146 AGAGGTCGAT
*
31265156 AAATGACCAAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
31265183 AAATAACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
31265210 AAATGACCGAATTAGCCCCACAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
31265237 AAATGACCGAATTACCCCCACAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
31265264 AAATGACTG-AATACCCCTATAGGTTA
1 AAATGACCGAAATACCCCCATAGGGTA
31265290 AAATGACC-AAATTACCCCCATAGGGTA
1 AAATGACCGAAA-TACCCCCATAGGGTA
** ** * *
31265317 AAATGATTGAGTTACCCCCACAGAGTA
1 AAATGACCGAAATACCCCCATAGGGTA
31265344 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
31265371 AAATGA
1 AAATGA
31265377 TTGTTATACC
Statistics
Matches: 164, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
26 22 0.13
27 141 0.86
28 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:31265352 original size:107 final size:108
Alignment explanation
Indices: 31265166--31265390 Score: 319
Period size: 107 Copynumber: 2.1 Consensus size: 108
31265156 AAATGACCAA
* *
31265166 AATACCCCCATAGGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACCGAATTAGCCCCAC
1 AATACCCCTATAGGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACCGAATTACCCCCAC
* *
31265231 AGGGTAAAATGACCGAATTACCCCCACAGGGTAAAATGACTG-
66 AGAGTAAAATGACCGAAATACCCCCACAGGGTAAAATGACTGT
* * ** *
31265273 AATACCCCTATAGGTTAAAATGACC-AAATTACCCCCATAGGGTAAAATGATTGAGTTACCCCCA
1 AATACCCCTATAGGGTAAAATAACCGAAA-TACCCCCATAGGGTAAAATGACCGAATTACCCCCA
* *
31265337 CAGAGTAAAATGACCGAAATACCCCCATAGGGTAAAATGATTGT
65 CAGAGTAAAATGACCGAAATACCCCCACAGGGTAAAATGACTGT
*
31265381 TATACCCCTA
1 AATACCCCTA
31265391 GGAGATGAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
106 3 0.03
107 92 0.88
108 9 0.09
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (108 bp):
AATACCCCTATAGGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACCGAATTACCCCCAC
AGAGTAAAATGACCGAAATACCCCCACAGGGTAAAATGACTGT
Found at i:31265402 original size:54 final size:54
Alignment explanation
Indices: 31265167--31265404 Score: 211
Period size: 54 Copynumber: 4.4 Consensus size: 54
31265157 AATGACCAAA
* * * *
31265167 ATACCCCCATAGGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACCGAATT
1 ATACCCCCAGA-GATAAAATGACCGAAATACCCCCATAGGGTAAAATGACTG-ATT
* * * *
31265223 A-GCCCCACAG-GGTAAAATGACCGAATTACCCCCACAGGGTAAAATGACTGA--
1 ATACCCC-CAGAGATAAAATGACCGAAATACCCCCATAGGGTAAAATGACTGATT
* * * * *
31265274 ATACCCCTATAGGTTAAAATGACC-AAATTACCCCCATAGGGTAAAATGATTGAGT
1 ATACCCCCAGA-GATAAAATGACCGAAA-TACCCCCATAGGGTAAAATGACTGATT
* *
31265329 -TACCCCCACAGAGTAAAATGACCGAAATACCCCCATAGGGTAAAATGATTG-TT
1 ATACCCCCAGAGA-TAAAATGACCGAAATACCCCCATAGGGTAAAATGACTGATT
* *
31265382 ATACCCCTAGGAGATGAAATGAC
1 ATACCCCCA-GAGATAAAATGAC
31265405 TGTTATGGCC
Statistics
Matches: 151, Mismatches: 20, Indels: 24
0.77 0.10 0.12
Matches are distributed among these distances:
51 2 0.01
52 6 0.04
53 37 0.25
54 93 0.62
55 10 0.07
56 3 0.02
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (54 bp):
ATACCCCCAGAGATAAAATGACCGAAATACCCCCATAGGGTAAAATGACTGATT
Found at i:31281449 original size:50 final size:50
Alignment explanation
Indices: 31281300--31281546 Score: 156
Period size: 50 Copynumber: 4.8 Consensus size: 50
31281290 GATAATAACA
* * * ** * * *
31281300 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAACGCCATGTCCCACACATGGTCTTACAGGGGACCTCTCATAT-CGG
* * * * * **
31281349 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCACACATGGTCTTACAGGGGACCTCTCATATCGG
* * * * * * * *
31281399 TGCCCATGTCATGTCCCAGACATTGTCTTACGGGGGACCTTTCATCTCGG
1 TGCCAACGCCATGTCCCACACATGGTCTTACAGGGGACCTCTCATATCGG
* *
31281449 TGCCAACGCCATGTCCCACACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCACACATGGTCTTACAGGGGACCTCTCAT-A--TC---GG
* * * *
31281505 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCACACATGGTCTTACAGGGGACCTCT
31281547 TTACCCAAAT
Statistics
Matches: 156, Mismatches: 34, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
48 1 0.01
49 38 0.24
50 75 0.48
53 2 0.01
56 40 0.26
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCACACATGGTCTTACAGGGGACCTCTCATATCGG
Found at i:31287676 original size:3 final size:3
Alignment explanation
Indices: 31287663--31287699 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
31287653 AAGCACTAAG
* *
31287663 TGA TAA TGA TGA TGA TGA TGA TGA TGA TGA TAA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
31287700 AGAGCTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.27, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:31288848 original size:9 final size:9
Alignment explanation
Indices: 31288834--31288904 Score: 52
Period size: 9 Copynumber: 7.3 Consensus size: 9
31288824 AATGAATTTG
31288834 AAATTATTA
1 AAATTATTA
31288843 AAATTATTTTA
1 AAATTA--TTA
*
31288854 AAATAATTTA
1 AAATTA-TTA
31288864 AAATTATTA
1 AAATTATTA
* *
31288873 AAATGATTTTG
1 AAAT--TATTA
* *
31288884 AAATCAGTA
1 AAATTATTA
31288893 AAATTATTA
1 AAATTATTA
31288902 AAA
1 AAA
31288905 ATATAAAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
9 24 0.50
10 9 0.19
11 15 0.31
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (9 bp):
AAATTATTA
Found at i:31288868 original size:30 final size:30
Alignment explanation
Indices: 31288823--31288904 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
31288813 CCATGTCAGC
* *
31288823 AAATGAATTTGAAATTATTAAAATTATTTTA
1 AAAT-AATTTAAAATTATTAAAATGATTTTA
*
31288854 AAATAATTTAAAATTATTAAAATGATTTTG
1 AAATAATTTAAAATTATTAAAATGATTTTA
* *
31288884 AAATCA-GTAAAATTATTAAAA
1 AAATAATTTAAAATTATTAAAA
31288905 ATATAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 14 0.30
30 28 0.61
31 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.40
Consensus pattern (30 bp):
AAATAATTTAAAATTATTAAAATGATTTTA
Found at i:31292839 original size:18 final size:18
Alignment explanation
Indices: 31292795--31292859 Score: 91
Period size: 18 Copynumber: 3.8 Consensus size: 18
31292785 GTTTTTTCCG
31292795 AATATATATA-TTTAA-A
1 AATATATATATTTTAATA
31292811 AA-ATATATATTTTAATA
1 AATATATATATTTTAATA
*
31292828 AATATATGTATTTTAATA
1 AATATATATATTTTAATA
*
31292846 ATTATATATATTTT
1 AATATATATATTTT
31292860 GATAGGAGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
15 7 0.16
16 7 0.16
17 3 0.07
18 26 0.60
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
AATATATATATTTTAATA
Found at i:31293056 original size:15 final size:16
Alignment explanation
Indices: 31293004--31293059 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 16
31292994 TTTTATGTAT
31293004 TTTATATAATTTCTATA
1 TTTATATAATTTCTA-A
* **
31293021 GTTTGTATAATTTCTTC
1 -TTTATATAATTTCTAA
31293038 TTTATA-AATTTCTAA
1 TTTATATAATTTCTAA
31293053 TTTATAT
1 TTTATAT
31293060 TTGTTGAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 13 0.42
16 5 0.16
18 13 0.42
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (16 bp):
TTTATATAATTTCTAA
Found at i:31293158 original size:16 final size:17
Alignment explanation
Indices: 31293137--31293174 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
31293127 TTCTTAATAT
31293137 TTTTTTCTATT-TTCTA
1 TTTTTTCTATTATTCTA
*
31293153 TTTTTTCTATTATTTTA
1 TTTTTTCTATTATTCTA
31293170 TTTTT
1 TTTTT
31293175 AGATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCTATTATTCTA
Found at i:31294155 original size:18 final size:18
Alignment explanation
Indices: 31294134--31294170 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
31294124 TTTGCGCAAG
31294134 AACAGTAGCTTTTTAGCT
1 AACAGTAGCTTTTTAGCT
31294152 AACAGTAGCTTTTTAGCT
1 AACAGTAGCTTTTTAGCT
31294170 A
1 A
31294171 CTAACTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (18 bp):
AACAGTAGCTTTTTAGCT
Found at i:31298389 original size:39 final size:38
Alignment explanation
Indices: 31298303--31298402 Score: 112
Period size: 39 Copynumber: 2.6 Consensus size: 38
31298293 GAAATCCTTG
* *
31298303 TTATAATTATTTTAATTATAATTTACGATAGAATATTA
1 TTATAATTATTGTAATTATAATTTACGATAGAACATTA
* * *
31298341 TTATAATTATTGTAATTGTAATTTTTCGGTCA-AACATTA
1 TTATAATTATTGTAATTATAA-TTTACGAT-AGAACATTA
* *
31298380 TTATAATTATGGGAATTATAATT
1 TTATAATTATTGTAATTATAATT
31298403 ATTGTATTTG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
38 21 0.40
39 30 0.58
40 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (38 bp):
TTATAATTATTGTAATTATAATTTACGATAGAACATTA
Found at i:31301642 original size:25 final size:25
Alignment explanation
Indices: 31301614--31301669 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
31301604 AATGTATGTA
*
31301614 TGTACAGTGCATTGCTGTAAACTGT
1 TGTACAGTGCATTGCTGTAAACTAT
31301639 TGTACAGTGCATTGCTGTAAACTAT
1 TGTACAGTGCATTGCTGTAAACTAT
31301664 TGTACA
1 TGTACA
31301670 TACATGTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (25 bp):
TGTACAGTGCATTGCTGTAAACTAT
Found at i:31304366 original size:30 final size:30
Alignment explanation
Indices: 31304330--31304391 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
31304320 TGAGTGAATA
31304330 TAGTTACTAATTACATAAACAAAATTTAAC
1 TAGTTACTAATTACATAAACAAAATTTAAC
31304360 TAGTTACTAATTACATAAACAAAATTTAAC
1 TAGTTACTAATTACATAAACAAAATTTAAC
31304390 TA
1 TA
31304392 AGTATGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34
Consensus pattern (30 bp):
TAGTTACTAATTACATAAACAAAATTTAAC
Found at i:31305930 original size:14 final size:14
Alignment explanation
Indices: 31305911--31305937 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31305901 ATTCATCTAT
31305911 AAGGGAAGAATATA
1 AAGGGAAGAATATA
31305925 AAGGGAAGAATAT
1 AAGGGAAGAATAT
31305938 TCTCAATACT
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:0.56, C:0.00, G:0.30, T:0.15
Consensus pattern (14 bp):
AAGGGAAGAATATA
Found at i:31307753 original size:22 final size:22
Alignment explanation
Indices: 31307721--31307764 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31307711 AAAACAATTA
*
31307721 AAAACCTGATTATTAATGAAGC
1 AAAACCCGATTATTAATGAAGC
31307743 AAAACCCGATTATTAATGAAGC
1 AAAACCCGATTATTAATGAAGC
31307765 CAAGTGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (22 bp):
AAAACCCGATTATTAATGAAGC
Done.