Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 130 of 185
Found at i:39919917 original size:31 final size:29
Alignment explanation
Indices: 39919832--39919927 Score: 92
Period size: 31 Copynumber: 3.3 Consensus size: 29
39919822 TATTTTTTTC
*
39919832 CTTTC-TTTTTC-TT-TTTTCTTTTTCTTT
1 CTTTCTTTTTTCTTTCTTTTCCTTTTC-TT
* *
39919859 CCTTTTTTTTTTCTTTTTTTTCC-TTTCTT
1 -CTTTCTTTTTTCTTTCTTTTCCTTTTCTT
*
39919888 CTTTCTTTTTTCTTTCCTTTTCCGTTTTCTC
1 CTTTCTTTTTTCTTT-CTTTTCC-TTTTCTT
39919919 CTTTCTTTT
1 CTTTCTTTT
39919928 CCGTTCAGCC
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
28 18 0.32
29 14 0.25
30 6 0.11
31 19 0.33
ACGTcount: A:0.00, C:0.23, G:0.01, T:0.76
Consensus pattern (29 bp):
CTTTCTTTTTTCTTTCTTTTCCTTTTCTT
Found at i:39920471 original size:29 final size:29
Alignment explanation
Indices: 39920417--39920491 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
39920407 GAAAAATATG
* * *
39920417 GGGCCAAAATGTAATTTATGGAAAGTTTAA
1 GGGCTAAAATATAA-TTATGAAAAGTTTAA
* *
39920447 GGGCTCAAATATAATTATGAAAAGTTTAG
1 GGGCTAAAATATAATTATGAAAAGTTTAA
*
39920476 GGGTTAAAATATAATT
1 GGGCTAAAATATAATT
39920492 TTTTTAAGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 27 0.71
30 11 0.29
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.32
Consensus pattern (29 bp):
GGGCTAAAATATAATTATGAAAAGTTTAA
Found at i:39920930 original size:75 final size:75
Alignment explanation
Indices: 39920851--39921662 Score: 951
Period size: 75 Copynumber: 10.7 Consensus size: 75
39920841 GTGATTTAAA
* * * *
39920851 GCTCAATTCACCTCTCGGATTATGAGTTGATATTTGAGAAACAGAAATTGAAAATACCTCAGCGT
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
*
39920916 GTGACTCGAG
66 GTGACCCGAG
* * *
39920926 GCTCAACTCACCTCCCGGATTATGAGTTGATTTTTGAAAAACATAAATTGAAAATACCTCAGCGT
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
39920991 GTGA-CCGAAG
66 GTGACCCG-AG
* * *** * *
39921001 GCTCAACTCACCACTCGCATTATGAGTTAATTTTTTTTAAA-TGAAATTGAAAAATACCTCAGCA
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTG-AAAATACCTCAGCG
*
39921065 TGTG-TCCGAG
65 TGTGACCCGAG
*
39921075 GCTCGACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
39921140 GTGACCCGAG
66 GTGACCCGAG
* *
39921150 GCTCAACTCACCTCTCGCATTATGAGTTAATTTTTGAAAAAACAGAAATTGAAAAATACCAC-G-
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTG-AAAAACAGAAATTG-AAAATACCTCAGC
* *
39921213 GTGTGCGCCCGTG
64 GTGTG-ACCCGAG
* * * * *
39921226 GCTCAA-TCACGTCTCGCATTATGAGTTGATTTTTTTTAAAAAAATGAAATTGAAAAATGCCTCG
1 GCTCAACTCACCTCTCGCATTATGAGTTGA--TTTTTGAAAAACA-GAAATTG-AAAATACCTCA
* * *
39921290 GCATGTG-TCTGAG
62 GCGTGTGACCCGAG
* *
39921303 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAATACAGAAATTGAAAATACCTCAGCAT
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
*
39921368 GTGACCTGAG
66 GTGACCCGAG
* ** * * *
39921378 GCTCAACTCACCTCTCCCATTATGAGTTGATTTTAAAAAAAAATAGAAATTGAAAAATGCCTCGG
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTT--TGAAAAACAGAAATTG-AAAATACCTCAG
39921443 CGTGT--CCCTGAG
63 CGTGTGACCC-GAG
* *
39921455 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAAAATAGAAATTGAAAATACCTCGG
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTG---AAAAACAGAAATTGAAAATACCTCAG
39921520 CGTGTG-CCCGAG
63 CGTGTGACCCGAG
* * * *
39921532 GCTCAACTCATCTCTAGCATTATGAGTTGATTTTTGAAAAAACAAAAATTGAAAATACCTCGGCG
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTG-AAAAACAGAAATTGAAAATACCTCAGCG
39921597 TGTGACCCGAG
65 TGTGACCCGAG
* * ** *
39921608 ACTCAACTCACCTCTCGCATTATGAGTTCATTTTAAAAAAAATAGAAATTGAAAA
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTT-TGAAAAACAGAAATTGAAAA
39921663 ATAATTCTTG
Statistics
Matches: 640, Mismatches: 72, Indels: 49
0.84 0.09 0.06
Matches are distributed among these distances:
74 78 0.12
75 268 0.42
76 96 0.15
77 140 0.22
78 54 0.08
79 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (75 bp):
GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
GTGACCCGAG
Found at i:39921373 original size:228 final size:229
Alignment explanation
Indices: 39920851--39921665 Score: 1119
Period size: 228 Copynumber: 3.6 Consensus size: 229
39920841 GTGATTTAAA
* * * *
39920851 GCTCAATTCACCTCTCGGATTATGAGTTGATATTTGAGAAACAGAAATTGAAAATACCTCAGCGT
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
* * * ** *
39920916 GTGACTCGAGGCTCAACTCACCTCCCGGATTATGAGTTGATTTT-TGAAAAACATAAATTG-AAA
66 GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTAAAAAAAACAGAAATTGAAAA
* * * * *
39920979 ATACCTCAGCGTGTGACCGAAGGCTCAACTCACCACTCGCATTATGAGTTAATTTTTTTT----A
131 ATACCTCGGCGTGCGCCCG-AGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTAAAAA
*
39921040 AATGAAATTGAAAAATACCTCAGCATGTGTCCGAG
195 AATGAAATTGAAAAATACCTCGGCATGTGTCCGAG
*
39921075 GCTCGACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
* **
39921140 GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTAATTTTTGAAAAAACAGAAATTGAAAA
66 GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTAAAAAAAACAGAAATTGAAAA
* * * *
39921205 ATACCACGGTGTGCGCCCGTGGCTCAA-TCACGTCTCGCATTATGAGTTGATTTTTTTTAAAAAA
131 ATACCTCGGCGTGCGCCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTAAAAAA
* *
39921269 ATGAAATTGAAAAATGCCTCGGCATGTGTCTGAG
196 ATGAAATTGAAAAATACCTCGGCATGTGTCCGAG
* *
39921303 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAATACAGAAATTGAAAATACCTCAGCAT
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
* * *
39921368 GTGACCTGAGGCTCAACTCACCTCTCCCATTATGAGTTGATTTTAAAAAAAAATAGAAATTGAAA
66 GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTT-AAAAAAAACAGAAATTGAAA
* * **
39921433 AATGCCTCGGCGTGTC-CCTGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTGAAAAA
130 AATACCTCGGCGTG-CGCCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTAAAA
* *
39921496 AAATAGAAATTG-AAAATACCTCGGCGTGTGCCCGAG
194 AAAT-GAAATTGAAAAATACCTCGGCATGTGTCCGAG
* * * *
39921532 GCTCAACTCATCTCTAGCATTATGAGTTGATTTTTGAAAAAACAAAAATTGAAAATACCTCGGCG
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTG-AAAAACAGAAATTGAAAATACCTCAGCG
* * *
39921597 TGTGACCCGAGACTCAACTCACCTCTCGCATTATGAGTTCATTTTAAAAAAAATAGAAATTGAAA
65 TGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTAAAAAAAACAGAAATTGAAA
39921662 AATA
130 AATA
39921666 ATTCTTGAAA
Statistics
Matches: 524, Mismatches: 56, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
224 128 0.24
225 20 0.04
226 17 0.03
228 136 0.26
229 128 0.24
230 95 0.18
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (229 bp):
GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTAAAAAAAACAGAAATTGAAAA
ATACCTCGGCGTGCGCCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTAAAAAA
ATGAAATTGAAAAATACCTCGGCATGTGTCCGAG
Found at i:39933820 original size:20 final size:19
Alignment explanation
Indices: 39933779--39933823 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
39933769 AGAATGGGCA
*
39933779 TTTTTC-TCCTTTTTCTTT
1 TTTTTCTTCCTTTTTCCTT
39933797 TTTTTCTTCCTTTCTTCCTT
1 TTTTTCTTCCTTT-TTCCTT
39933817 TTTTTCT
1 TTTTTCT
39933824 GGCTGGGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 6 0.25
19 6 0.25
20 12 0.50
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTCTTCCTTTTTCCTT
Found at i:39934334 original size:21 final size:21
Alignment explanation
Indices: 39934288--39934335 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
39934278 CTTTCTTCTT
*
39934288 TGCTGTTCTTTTTTGTTATTTT
1 TGCT-TTCTTTTTTGTTATTTA
*
39934310 TGCTTTCTATTTTT-TTGTTTA
1 TGCTTTCT-TTTTTGTTATTTA
39934331 TGCTT
1 TGCTT
39934336 GTTTGGCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.06, C:0.10, G:0.12, T:0.71
Consensus pattern (21 bp):
TGCTTTCTTTTTTGTTATTTA
Found at i:39934752 original size:29 final size:29
Alignment explanation
Indices: 39934705--39934779 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
39934695 GAAAAATATA
* *
39934705 GGGCCAAAATACAATTTATG-ATAAGTTTAG
1 GGGCTAAAATATAA-TTATGAAT-AGTTTAG
* *
39934735 GGGCTTAAATATAATTATGAATCGTTTAG
1 GGGCTAAAATATAATTATGAATAGTTTAG
39934764 GGGCTAAAATATAATT
1 GGGCTAAAATATAATT
39934780 TTTTTAAAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 26 0.67
30 13 0.33
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (29 bp):
GGGCTAAAATATAATTATGAATAGTTTAG
Found at i:39952075 original size:21 final size:21
Alignment explanation
Indices: 39952050--39952143 Score: 61
Period size: 21 Copynumber: 4.5 Consensus size: 21
39952040 TGTGTTTGCT
*
39952050 TTTAGTTTAGCTCTTATGAGC
1 TTTAGTTTAACTCTTATGAGC
* *
39952071 TTTAG-CTAACTCATATGAG-
1 TTTAGTTTAACTCTTATGAGC
* *
39952090 TTTCAGTTTAAC-CCTACT-AGG
1 TTT-AGTTTAACTCTTA-TGAGC
* *
39952111 TTTCAGTTTAGCTCTTTTGAGC
1 TTT-AGTTTAACTCTTATGAGC
*
39952133 TTCAGTTTAAC
1 TTTAGTTTAAC
39952144 CCTTGTGGGT
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
19 3 0.05
20 18 0.32
21 29 0.52
22 6 0.11
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (21 bp):
TTTAGTTTAACTCTTATGAGC
Found at i:39952189 original size:42 final size:43
Alignment explanation
Indices: 39952084--39952189 Score: 135
Period size: 42 Copynumber: 2.5 Consensus size: 43
39952074 AGCTAACTCA
* * *
39952084 TATGAGTTTCAGTTTAACCCTACTAGGTTTCAGTTTAGCTCTT
1 TATGAGCTTCAGTTTAACCCTTCTAGGTTTCAGTTCAGCTCTT
* * *
39952127 T-TGAGCTTCAGTTTAACCCTTGTGGGTTTCCGTTCAGCT-TT
1 TATGAGCTTCAGTTTAACCCTTCTAGGTTTCAGTTCAGCTCTT
*
39952168 TATGAGCTTCTGTTTAACCCTT
1 TATGAGCTTCAGTTTAACCCTT
39952190 AAGGGTTTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
41 3 0.05
42 51 0.93
43 1 0.02
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (43 bp):
TATGAGCTTCAGTTTAACCCTTCTAGGTTTCAGTTCAGCTCTT
Found at i:39952196 original size:42 final size:43
Alignment explanation
Indices: 39952084--39952202 Score: 129
Period size: 42 Copynumber: 2.8 Consensus size: 43
39952074 AGCTAACTCA
* * *
39952084 TATGAGTTTCAGTTTAACCC-TACTA-GGTTTCAGTTTAGCTCTT
1 TATGAGCTTCAGTTTAACCCTTA--AGGGTTTCCGTTCAGCTCTT
**
39952127 T-TGAGCTTCAGTTTAACCCTTGTGGGTTTCCGTTCAGCT-TT
1 TATGAGCTTCAGTTTAACCCTTAAGGGTTTCCGTTCAGCTCTT
* *
39952168 TATGAGCTTCTGTTTAACCCTTAAGGGTTTTCGTT
1 TATGAGCTTCAGTTTAACCCTTAAGGGTTTCCGTT
39952203 TAACACTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 3 0.05
42 59 0.92
43 2 0.03
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (43 bp):
TATGAGCTTCAGTTTAACCCTTAAGGGTTTCCGTTCAGCTCTT
Found at i:39959955 original size:44 final size:43
Alignment explanation
Indices: 39959866--39959959 Score: 145
Period size: 44 Copynumber: 2.2 Consensus size: 43
39959856 ACAGTCGCAC
39959866 ATTAGTAATTAACGATTCTTCCCTACTGTAAACTTCCTACAAT
1 ATTAGTAATTAACGATTCTTCCCTACTGTAAACTTCCTACAAT
* *
39959909 ATTAGTAATTAACGATTTTGTTCCC-ACTGTAAACTTCCTACCAT
1 ATTAGTAATTAACGA--TTCTTCCCTACTGTAAACTTCCTACAAT
39959953 ATTAGTA
1 ATTAGTA
39959960 CACCATCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 15 0.32
44 25 0.53
45 7 0.15
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (43 bp):
ATTAGTAATTAACGATTCTTCCCTACTGTAAACTTCCTACAAT
Found at i:39962218 original size:24 final size:24
Alignment explanation
Indices: 39962191--39962238 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
39962181 TTTTGCAAAC
39962191 TAAACCAAACCA-AAAATAAATAAA
1 TAAA-CAAACCAGAAAATAAATAAA
* *
39962215 TAAATAAACCAGAAAATTAATAAA
1 TAAACAAACCAGAAAATAAATAAA
39962239 AGTAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.69, C:0.12, G:0.02, T:0.17
Consensus pattern (24 bp):
TAAACAAACCAGAAAATAAATAAA
Found at i:39967806 original size:19 final size:20
Alignment explanation
Indices: 39967766--39967809 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
39967756 GTTTCTTTTG
* *
39967766 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
39967785 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
39967804 GCATTA
1 GCATTA
39967810 GACTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:39972072 original size:86 final size:86
Alignment explanation
Indices: 39971927--39972276 Score: 565
Period size: 86 Copynumber: 4.1 Consensus size: 86
39971917 AGTAAAAATT
* * * * * *
39971927 GAAGATAAACCTTGCCTCTCTCGGTCGTAGCAGAGCTGGTTGAAGTTATCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
39971992 GCATTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
*
39972013 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
39972078 GCATTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
*
39972099 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
*
39972164 GCACTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
* * *
39972185 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCTTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
* *
39972250 GTATTTGGCAGCGAAGCAGATC
66 GCA-TTGACAGCGAAGCAGATC
39972272 GAAGA
1 GAAGA
39972277 TGGCAGATTT
Statistics
Matches: 248, Mismatches: 15, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
86 227 0.92
87 21 0.08
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (86 bp):
GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
GCATTGACAGCGAAGCAGATC
Found at i:39972114 original size:42 final size:42
Alignment explanation
Indices: 39971981--39972201 Score: 107
Period size: 42 Copynumber: 5.2 Consensus size: 42
39971971 GTTATCAGAT
39971981 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
* * * * * * * * *
39972023 CTTGCC-ACTCT-CGTTTG-TAG-TAGAGCTGGTTGAAGATAGCAGAT
1 CTTGCCTTC-CTGC-ATTGACAGCGA-AGCAGATCGAAG--A-CAAAC
39972067 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
* * * * * * * * *
39972109 CTTGCC-ACTCT-CGTTTG-TAG-TAGAGCTGGTTGAAGATAGCAGAT
1 CTTGCCTTC-CTGC-ATTGACAGCGA-AGCAGATCGAAG--A-CAAAC
*
39972153 CTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
39972195 CTTGCCT
1 CTTGCCT
39972202 CTCTCGTTTG
Statistics
Matches: 122, Mismatches: 37, Indels: 40
0.61 0.19 0.20
Matches are distributed among these distances:
40 2 0.02
41 26 0.21
42 35 0.29
43 4 0.03
44 27 0.22
45 26 0.21
46 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (42 bp):
CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
Found at i:39972465 original size:134 final size:134
Alignment explanation
Indices: 39972224--39972499 Score: 491
Period size: 134 Copynumber: 2.1 Consensus size: 134
39972214 GCAGAGCTGG
*
39972224 TTGAAGATATCAGATCTTGCTTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
1 TTGAAGATATCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
*
39972289 CCTCCCTGACAACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
66 CCTCCCTGACAACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGCATTTGGCAGTGGAA
39972354 TAGA
131 TAGA
39972358 TTGAAGAT-TGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTT
1 TTGAAGATAT-CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTT
* *
39972422 ACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGCATTTGGCAGTGGA
65 ACCTCCCTGACAACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGCATTTGGCAGTGGA
39972487 ATAGA
130 ATAGA
*
39972492 TTAAAGAT
1 TTGAAGAT
39972500 CAAAGATGGC
Statistics
Matches: 136, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
133 1 0.01
134 135 0.99
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (134 bp):
TTGAAGATATCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
CCTCCCTGACAACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGCATTTGGCAGTGGAA
TAGA
Found at i:39972486 original size:45 final size:44
Alignment explanation
Indices: 39972435--39972592 Score: 122
Period size: 45 Copynumber: 3.4 Consensus size: 44
39972425 TCCCTGACTA
*
39972435 CAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGCATTTGG
1 CAGTGGAATACATTGAAGCCGATAATTCTATCTCCCTG-ATTTGG
* * * * * * *
39972480 CAGTGGAATAGATTAAAGATCAAAGATGGCAGATTTTACCTCCCTGA-CT-A
1 CAGTGGAATACATTGAAG--C--CGAT---A-ATTCTATCTCCCTGATTTGG
*
39972530 CAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGG
1 CAGTGGAATACATTGAAGCCGATAATTCTATCTCCCTG-ATTTGG
*
39972575 CAGTGGAATAGATTGAAG
1 CAGTGGAATACATTGAAG
39972593 ATTACAGATC
Statistics
Matches: 84, Mismatches: 18, Indels: 22
0.68 0.15 0.18
Matches are distributed among these distances:
42 12 0.14
43 2 0.02
44 1 0.01
45 31 0.37
46 3 0.04
47 1 0.01
48 1 0.01
49 3 0.04
50 15 0.18
51 1 0.01
52 2 0.02
53 12 0.14
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (44 bp):
CAGTGGAATACATTGAAGCCGATAATTCTATCTCCCTGATTTGG
Found at i:39972510 original size:95 final size:95
Alignment explanation
Indices: 39972401--39972594 Score: 361
Period size: 95 Copynumber: 2.0 Consensus size: 95
39972391 GCAGCGAAGC
*
39972401 AGATCGAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTAT
39972466 CTCCCTGCATTTGGCAGTGGAATAGATTAA
66 CTCCCTGCATTTGGCAGTGGAATAGATTAA
39972496 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTAT
* *
39972561 CTCCCTGTATTTGGCAGTGGAATAGATTGA
66 CTCCCTGCATTTGGCAGTGGAATAGATTAA
39972591 AGAT
1 AGAT
39972595 TACAGATCTT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (95 bp):
AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTAT
CTCCCTGCATTTGGCAGTGGAATAGATTAA
Found at i:39972680 original size:132 final size:129
Alignment explanation
Indices: 39972502--39972758 Score: 363
Period size: 132 Copynumber: 2.0 Consensus size: 129
39972492 TTAAAGATCA
*
39972502 AAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTA-TCTCCC
1 AAGACGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTACT-TCCC
* *** *
39972566 TGTATTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAATGGAGTAGG
65 TGGA--AAACAGTGGAATAGATCGAAGATTACA-ATCTTATCTCCCTAAGCAATAATGGAGTAGG
39972631 TTG
127 TTG
* * * * *
39972634 AAGACGGCGGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTCTACTTCCCT
1 AAGACGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTACTTCCCT
*
39972699 GGAAAACAGTGGAATAGATCGAAGATTACAATCTTATCTCCCTAAGCAGTAATGGAGTAG
66 GGAAAACAGTGGAATAGATCGAAGATTACAATCTTATCTCCCTAAGCAATAATGGAGTAG
39972759 ATCGTATTAA
Statistics
Matches: 112, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
129 29 0.26
130 23 0.21
132 59 0.53
133 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (129 bp):
AAGACGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTACTTCCCT
GGAAAACAGTGGAATAGATCGAAGATTACAATCTTATCTCCCTAAGCAATAATGGAGTAGGTTG
Found at i:39972761 original size:43 final size:40
Alignment explanation
Indices: 39972708--39972875 Score: 124
Period size: 40 Copynumber: 4.1 Consensus size: 40
39972698 TGGAAAACAG
*
39972708 TGGAATAGATCGAAGATTACAATCTTATCTCCCTAAGCAGTAA
1 TGGAGTAGATCG--GATTA-AATCTTATCTCCCTAAGCAGTAA
* * *
39972751 TGGAGTAGATCGTATTAAGTCTTATCTCCCTAAGCAGTAG
1 TGGAGTAGATCGGATTAAATCTTATCTCCCTAAGCAGTAA
* * ** * * *
39972791 TGGAGCAGA-C-AACCACAGATCTTATTTCCCTAAGCAATAG
1 TGGAGTAGATCGGATTA-A-ATCTTATCTCCCTAAGCAGTAA
* * * * * *
39972831 TGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGTAGTAG
1 TGGAGTAGATCGGATTAAATCTTATCTCCCTAAGCAGTAA
39972871 TGGAG
1 TGGAG
39972876 CAGACTAAAA
Statistics
Matches: 104, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 80 0.77
41 6 0.06
42 3 0.03
43 11 0.11
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (40 bp):
TGGAGTAGATCGGATTAAATCTTATCTCCCTAAGCAGTAA
Found at i:39972781 original size:40 final size:40
Alignment explanation
Indices: 39972730--39972879 Score: 187
Period size: 40 Copynumber: 3.8 Consensus size: 40
39972720 AAGATTACAA
* * * *
39972730 TCTTATCTCCCTAAGCAGTAATGGAGTAGATCGTATTAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAATCAAG
*
39972770 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-C-AACCACAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAATCA-AG
* * *
39972809 ATCTTATTTCCCTAAGCAATAGTGGAGCAGATCGCATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAATCAAG
*
39972850 TCTTATCTCCCTAAGTAGTAGTGGAGCAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA
39972880 CTAAAAACAC
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 3 0.03
40 83 0.88
41 3 0.03
42 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAATCAAG
Found at i:39972821 original size:80 final size:80
Alignment explanation
Indices: 39972729--39972880 Score: 241
Period size: 80 Copynumber: 1.9 Consensus size: 80
39972719 GAAGATTACA
* * * *
39972729 ATCTTATCTCCCTAAGCAGTAATGGAGTAGATCGTATTAAGTCTTATCTCCCTAAGCAGTAGTGG
1 ATCTTATCTCCCTAAGCAATAATGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGG
39972794 AGCAGACAACCACAG
66 AGCAGACAACCACAG
* * *
39972809 ATCTTATTTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGTAGTAGTGG
1 ATCTTATCTCCCTAAGCAATAATGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGG
39972874 AGCAGAC
66 AGCAGAC
39972881 TAAAAACACA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.27
Consensus pattern (80 bp):
ATCTTATCTCCCTAAGCAATAATGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGG
AGCAGACAACCACAG
Found at i:39983214 original size:27 final size:26
Alignment explanation
Indices: 39983151--39983219 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 26
39983141 AACAATAGCA
* *
39983151 TTTTTACCAAAATAAAATAAATAAAT
1 TTTTTATCAAAATAATATAAATAAAT
* *
39983177 ATTTT-TC-AAATAATATAAATAATCT
1 TTTTTATCAAAATAATATAAATAA-AT
39983202 TTTTTATCAAAATAATAT
1 TTTTTATCAAAATAATAT
39983220 GTTTAAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 14 0.40
25 6 0.17
26 6 0.17
27 9 0.26
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (26 bp):
TTTTTATCAAAATAATATAAATAAAT
Found at i:39984894 original size:6 final size:6
Alignment explanation
Indices: 39984870--39984913 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
39984860 TGCCTTCTTC
* * *
39984870 TCCCCTT TCCCCT TTCCCT TCCCCT TCCCTT TTCCCT TCCCCT T
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
39984914 GGATTGCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (6 bp):
TCCCCT
Found at i:39984897 original size:18 final size:18
Alignment explanation
Indices: 39984870--39984913 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
39984860 TGCCTTCTTC
39984870 TCCCCTTTCCCCTTTCCCT
1 TCCCC-TTCCCCTTTCCCT
*
39984889 TCCCCTTCCCTTTTCCCT
1 TCCCCTTCCCCTTTCCCT
39984907 TCCCCTT
1 TCCCCTT
39984914 GGATTGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (18 bp):
TCCCCTTCCCCTTTCCCT
Found at i:39985007 original size:25 final size:25
Alignment explanation
Indices: 39984973--39985022 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
39984963 CAGGTAAGGC
*
39984973 TCCTTCTTCTTCTTCCGTTTTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
* *
39984998 TCCTTTTTCTTCTTCTGTTCTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
39985023 CTTCTCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.04, C:0.30, G:0.04, T:0.62
Consensus pattern (25 bp):
TCCTTCTTCTTCTTCCGTTCTTCAT
Found at i:39985225 original size:11 final size:11
Alignment explanation
Indices: 39985209--39985234 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39985199 TTGCTGGATG
39985209 ATATTTTGGTT
1 ATATTTTGGTT
39985220 ATATTTTGGTT
1 ATATTTTGGTT
39985231 ATAT
1 ATAT
39985235 ACAGATGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (11 bp):
ATATTTTGGTT
Found at i:39988309 original size:15 final size:15
Alignment explanation
Indices: 39988270--39988322 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 15
39988260 GAACATTTGG
39988270 AATTTAATTAGATAAAA
1 AATTT-ATTA-ATAAAA
39988287 AACTTTTATTAATAAAA
1 AA--TTTATTAATAAAA
*
39988304 AATTTATTTATAAATA
1 AATTTATTAATAAA-A
39988320 AAT
1 AAT
39988323 CATTGCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.34
16 4 0.12
17 10 0.31
18 4 0.12
19 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
AATTTATTAATAAAA
Found at i:39988396 original size:22 final size:20
Alignment explanation
Indices: 39988353--39988391 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39988343 TAATTTAAAA
39988353 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
39988373 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
39988392 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:39988505 original size:20 final size:20
Alignment explanation
Indices: 39988480--39988519 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39988470 AATATTTTCC
*
39988480 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
39988500 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
39988520 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:39988525 original size:34 final size:35
Alignment explanation
Indices: 39988468--39988534 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
39988458 CAAACACCAA
*
39988468 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
39988503 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
39988535 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:39988526 original size:14 final size:14
Alignment explanation
Indices: 39988503--39988542 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
39988493 ACAGAAAAGT
*
39988503 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
39988517 AAATCATTTTACGG
1 AAAACATTTTACAG
39988531 AAAACATTTTAC
1 AAAACATTTTAC
39988543 TGCCAATCAA
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:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:39988635 original size:28 final size:28
Alignment explanation
Indices: 39988595--39988693 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
39988585 TGATTTTCGA
39988595 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAATTTAATTGTAAAG
* * *
39988623 CACTAAGTGTGCGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAATTTAATTGTAAAG
* * * **
39988651 CACTAAGTGTGCGAGTTTTATTATTGAG
1 CACTAAGTGTGCGAATTTAATTGTAAAG
39988679 CACTAAGTGTGCGAA
1 CACTAAGTGTGCGAA
39988694 CTTATTAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (28 bp):
CACTAAGTGTGCGAATTTAATTGTAAAG
Found at i:39988872 original size:2 final size:2
Alignment explanation
Indices: 39988867--39988891 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39988857 GGAAAAAAAA
39988867 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39988892 GTATGATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39989464 original size:23 final size:23
Alignment explanation
Indices: 39989437--39990060 Score: 390
Period size: 23 Copynumber: 26.6 Consensus size: 23
39989427 TTATGCTTAA
*
39989437 ATGCTGTCCAATTTGTTGTATTT
1 ATGCTGTCCAATTTGTTGTATAT
*
39989460 ATGCTG-CCAAAATTGTTGTATAT
1 ATGCTGTCC-AATTTGTTGTATAT
* *
39989483 ATGCTGTCCAATTTTGATGTA-AA
1 ATGCTGTCCAA-TTTGTTGTATAT
* * *
39989506 ATGCTG-CTCAATTTGGTATATGT
1 ATGCTGTC-CAATTTGTTGTATAT
* * * *
39989529 ATGCTGCCCAAATTGTTGCACAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
39989552 ATGCTGTCAAATTTTTATGCTA-AA
1 ATGCTGTCCAATTTGT-TG-TATAT
*
39989576 ATGCTGTCCAATTTGTTGTATTT
1 ATGCTGTCCAATTTGTTGTATAT
* *
39989599 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* *
39989622 ATGCTGTCCAATTTTGATGTA-AA
1 ATGCTGTCCAA-TTTGTTGTATAT
*
39989645 ATGCTG-CTCAATTTGGTATATATAT
1 ATGCTGTC-CAATTT-GT-TGTATAT
* * * *
39989670 ATGCTGCCCAAATTGTTGCACAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
39989693 ATGCTGTCAAATTTTTATGCTA-AA
1 ATGCTGTCCAATTTGT-TG-TATAT
* *
39989717 ATGTTGTCCAATTTGTTGTATTT
1 ATGCTGTCCAATTTGTTGTATAT
* * * *
39989740 ATGCTGCCCAAATTGGTGCATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * * *
39989763 ATGTTGTCAAATTTTTATGCTA-AA
1 ATGCTGTCCAATTTGT-TG-TATAT
*
39989787 ATGCTGTCCAATTTGTTGTATTT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
39989810 ATGCTGCCCAAATTGTTGCATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
39989833 ATGTTGTCCAATTTTTATGCT-TAA
1 ATGCTGTCCAATTTGT-TG-TATAT
* * *
39989857 ATGCTGCCCAATTTGTTTTATTT
1 ATGCTGTCCAATTTGTTGTATAT
* *
39989880 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * * *
39989903 ATGTTGTCCAATTTTGATGTAAAA
1 ATGCTGTCCAA-TTTGTTGTATAT
*
39989927 ATGCTG-CTCAATTTGATATATATAT
1 ATGCTGTC-CAATTTG-T-TGTATAT
* *
39989952 ATAGGCTGCCCAAATTGTTGTATAT
1 AT--GCTGTCCAATTTGTTGTATAT
* * *
39989977 ATGCTGTCTAATTTTTATGCTA-AA
1 ATGCTGTCCAATTTGT-TG-TATAT
*
39990001 ATGCTG-CTCAATTTGATGTATAT
1 ATGCTGTC-CAATTTGTTGTATAT
* *
39990024 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
39990047 ATGCTGTCCAATTT
1 ATGCTGTCCAATTT
39990061 TTGGTGTGAA
Statistics
Matches: 451, Mismatches: 114, Indels: 72
0.71 0.18 0.11
Matches are distributed among these distances:
22 23 0.05
23 265 0.59
24 119 0.26
25 31 0.07
26 2 0.00
27 10 0.02
28 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.42
Consensus pattern (23 bp):
ATGCTGTCCAATTTGTTGTATAT
Found at i:39989602 original size:70 final size:69
Alignment explanation
Indices: 39989422--39990062 Score: 838
Period size: 70 Copynumber: 9.1 Consensus size: 69
39989412 ATGTTCATGT
* *
39989422 AATTTTTATGCTTAAATGCTGTCCAATTTGTTGTATTTATGCTGCCAAAATTGTTGTATATATGC
1 AATTTTTATGCTAAAATGCTG-CCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
39989487 TGTCC
65 TGTCC
* * * * * *
39989492 AATTTTGATG-TAAAATGCTGCTCAATTTGGTATATGTATGCTGCCCAAATTGTTGCACATATGC
1 AATTTTTATGCTAAAATGCTGC-CAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
*
39989556 TGTCA
65 TGTCC
39989561 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
1 AATTTTTATGCTAAAATGCTG-CCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
39989626 TGTCC
65 TGTCC
* * * * *
39989631 AATTTTGATG-TAAAATGCTGCTCAATTTGGTATATATATATGCTGCCCAAATTGTTGCACATAT
1 AATTTTTATGCTAAAATGCTGC-CAATTT-GT-TGTATTTATGCTGCCCAAATTGTTGTATATAT
*
39989695 GCTGTCA
63 GCTGTCC
* * * *
39989702 AATTTTTATGCTAAAATGTTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGGTGCATATATGT
1 AATTTTTATGCTAAAATGCTG-CCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
*
39989767 TGTCA
65 TGTCC
* *
39989772 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATGT
1 AATTTTTATGCTAAAATGCTG-CCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
39989837 TGTCC
65 TGTCC
* * *
39989842 AATTTTTATGCTTAAATGCTGCCCAATTTGTTTTATTTATGCTGCCCAAATTGTTGTATATATGT
1 AATTTTTATGCTAAAATGCTG-CCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
39989907 TGTCC
65 TGTCC
* * *
39989912 AATTTTGATG-TAAAAATGCTGCTCAATTTGATATATATATATAGGCTGCCCAAATTGTTGTATA
1 AATTTTTATGCT-AAAATGCTGC-CAATTTG-T-TGTAT-T-TATGCTGCCCAAATTGTTGTATA
*
39989976 TATGCTGTCT
60 TATGCTGTCC
* *
39989986 AATTTTTATGCTAAAATGCTGCTCAATTTGATGTATATATGCTGCCCAAATTGTTGTATATATGC
1 AATTTTTATGCTAAAATGCTGC-CAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
39990051 TGTCC
65 TGTCC
39990056 AATTTTT
1 AATTTTT
39990063 GGTGTGAAAA
Statistics
Matches: 508, Mismatches: 48, Indels: 30
0.87 0.08 0.05
Matches are distributed among these distances:
68 2 0.00
69 76 0.15
70 300 0.59
71 47 0.09
72 23 0.05
73 2 0.00
74 57 0.11
75 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (69 bp):
AATTTTTATGCTAAAATGCTGCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGCT
GTCC
Found at i:39991281 original size:20 final size:18
Alignment explanation
Indices: 39991225--39991283 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
39991215 TTAATTTAAA
* * *
39991225 TTTAATATGCATAATTAA
1 TTTAATATACACAATTAT
*
39991243 ATTAATATACACAATTAT
1 TTTAATATACACAATTAT
*
39991261 TTTAATATTCAC-ATTAT
1 TTTAATATACACAATTAT
39991278 TATTAA
1 T-TTAA
39991284 ATTAAATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 6 0.18
18 28 0.82
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (18 bp):
TTTAATATACACAATTAT
Found at i:39991283 original size:18 final size:19
Alignment explanation
Indices: 39991243--39991283 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
39991233 GCATAATTAA
39991243 ATTAATATACACAATTATT
1 ATTAATATACACAATTATT
*
39991262 -TTAATATTCAC-ATTATT
1 ATTAATATACACAATTATT
39991279 ATTAA
1 ATTAA
39991284 ATTAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTAATATACACAATTATT
Found at i:39992605 original size:35 final size:35
Alignment explanation
Indices: 39992552--39992651 Score: 105
Period size: 35 Copynumber: 2.8 Consensus size: 35
39992542 TTATGCTGCC
* *
39992552 TATTGTCCTTTTTATGTTTTTTATTTGTTTTTTCTT
1 TATT-TCCTTTTTATGTTTTTTATTTGTTTTGTCCT
*
39992588 TATTTCCTTTTTCTGTTTTTTATTT-TTTTGTCCT
1 TATTTCCTTTTTATGTTTTTTATTTGTTTTGTCCT
* * *
39992622 T-TTTCTGTTTTTTTATTTGTTTATTTGTTT
1 TATTTC-CTTTTTATGTTT-TTTATTTGTTT
39992652 ATAATATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.07
34 17 0.31
35 27 0.49
36 7 0.13
ACGTcount: A:0.07, C:0.09, G:0.08, T:0.76
Consensus pattern (35 bp):
TATTTCCTTTTTATGTTTTTTATTTGTTTTGTCCT
Found at i:39992608 original size:26 final size:25
Alignment explanation
Indices: 39992577--39992635 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 25
39992567 GTTTTTTATT
* *
39992577 TGTTTTTTCTTTATT-TCCTTTTTC
1 TGTTTTTTTTTTTTTGTCCTTTTTC
39992601 TGTTTTTTATTTTTTTGTCCTTTTTC
1 TGTTTTTT-TTTTTTTGTCCTTTTTC
39992627 TGTTTTTTT
1 TGTTTTTTT
39992636 ATTTGTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 8 0.26
25 6 0.19
26 17 0.55
ACGTcount: A:0.03, C:0.12, G:0.07, T:0.78
Consensus pattern (25 bp):
TGTTTTTTTTTTTTTGTCCTTTTTC
Found at i:39993595 original size:25 final size:25
Alignment explanation
Indices: 39993549--39993605 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
39993539 ACAATCCATG
*** * *
39993549 TAAATCATGTATTTCATGTAACTTT
1 TAAATCATGTAAACCATATAACATT
39993574 TAAATCATGTAAACCATATAACATT
1 TAAATCATGTAAACCATATAACATT
*
39993599 TATATCA
1 TAAATCA
39993606 ATTCTTTCCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.40
Consensus pattern (25 bp):
TAAATCATGTAAACCATATAACATT
Found at i:39993897 original size:23 final size:22
Alignment explanation
Indices: 39993844--39993935 Score: 112
Period size: 23 Copynumber: 3.9 Consensus size: 22
39993834 GAGCCATGAC
39993844 CGGTAAGCTCATTCTGAGCTGATAAA
1 CGGTAAGCTCA-TC-GAGCTG--AAA
39993870 CGGTAAGCTCTATCGAGCTGAAA
1 CGGTAAGCTC-ATCGAGCTGAAA
*
39993893 CGGTAAGCTCCATAGAGCTGAAA
1 CGGTAAGCT-CATCGAGCTGAAA
39993916 CGGTAAGCTCATACGAGCTG
1 CGGTAAGCTCAT-CGAGCTG
39993936 TGGTGAGTCC
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
22 3 0.05
23 38 0.62
24 1 0.02
25 6 0.10
26 12 0.20
27 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (22 bp):
CGGTAAGCTCATCGAGCTGAAA
Found at i:40000928 original size:25 final size:25
Alignment explanation
Indices: 40000882--40000938 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
40000872 ACAATCCATG
*** * *
40000882 TAAATCATGTATTTCATGTAACTTT
1 TAAATCATGTAAACCATATAACATT
40000907 TAAATCATGTAAACCATATAACATT
1 TAAATCATGTAAACCATATAACATT
*
40000932 TATATCA
1 TAAATCA
40000939 ATTCTTTCCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.40
Consensus pattern (25 bp):
TAAATCATGTAAACCATATAACATT
Found at i:40001233 original size:23 final size:22
Alignment explanation
Indices: 40001176--40001266 Score: 85
Period size: 23 Copynumber: 3.9 Consensus size: 22
40001166 GAGCCATGAT
40001176 CGGTAAGCTCATTCTGAGCTGATAAA
1 CGGTAAGCTCA-TC-GAGCTG--AAA
*
40001202 TGGTAAGCTCTATCGAGCTGAAA
1 CGGTAAGCTC-ATCGAGCTGAAA
*
40001225 CGGTAAGCTCCATAGAGCT-AAA
1 CGGTAAGCT-CATCGAGCTGAAA
*
40001247 CGATAAGCTCATACGAGCTG
1 CGGTAAGCTCAT-CGAGCTG
40001267 TGGTGAGTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
21 3 0.05
22 16 0.29
23 18 0.32
24 1 0.02
25 6 0.11
26 11 0.20
27 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (22 bp):
CGGTAAGCTCATCGAGCTGAAA
Found at i:40001253 original size:22 final size:23
Alignment explanation
Indices: 40001205--40001266 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
40001195 TGATAAATGG
* * *
40001205 TAAGCTCTATCGAGCTGAAACGG
1 TAAGCTCCATAGAGCTGAAACGA
40001228 TAAGCTCCATAGAGCT-AAACGA
1 TAAGCTCCATAGAGCTGAAACGA
40001250 TAAGCT-CATACGAGCTG
1 TAAGCTCCATA-GAGCTG
40001267 TGGTGAGTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.12
22 16 0.47
23 14 0.41
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (23 bp):
TAAGCTCCATAGAGCTGAAACGA
Found at i:40008820 original size:210 final size:210
Alignment explanation
Indices: 40008458--40008841 Score: 705
Period size: 210 Copynumber: 1.8 Consensus size: 210
40008448 ATCTATTTAG
40008458 ATTCGCTCGAATTAACCCTTCTCATAATGAGAATTTATATAGCCCTATTTCGGTATGGAATAAAC
1 ATTCGCTCGAATTAACCCTTCTCATAATGAGAATTTATATAGCCCTATTTCGGTATGGAATAAAC
*
40008523 TTAAAATAATGGAATTGACTCGCTCATCAAGTTATAGATTATAAGTTGATAACCCCAGCCCATTC
66 TTAAAATAATGGAATTGACTCGCTCATCAAGTTATAGATTATAAGTTGATAACCCCAACCCATTC
40008588 CCATTTTGGGTGAAATAGATCTACTAATTCTTTCATTCCAGTTAAAGCAGGAACTAAAAAATAGA
131 CCATTTTGGGTGAAATAGATCTACTAATTCTTTCATTCCAGTTAAAGCAGGAACTAAAAAATAGA
40008653 TCTACTAATTCTTTC
196 TCTACTAATTCTTTC
* * *
40008668 ATTCGCTCGAATTAACCCTTCTCATAATGAGAATTTATATAGCGCTGTTTTGGTATGGAATAAAC
1 ATTCGCTCGAATTAACCCTTCTCATAATGAGAATTTATATAGCCCTATTTCGGTATGGAATAAAC
* *
40008733 TTAAAATAATGGAATTGACTCGCTCATCAAGTTATAGATTATAAGTTTATAACCCTAACCCATTC
66 TTAAAATAATGGAATTGACTCGCTCATCAAGTTATAGATTATAAGTTGATAACCCCAACCCATTC
*
40008798 CCATTTTGGGTGAAATAGATCTATTAATTCTTTCATTCCAGTTA
131 CCATTTTGGGTGAAATAGATCTACTAATTCTTTCATTCCAGTTA
40008842 GTAAAGCAGG
Statistics
Matches: 167, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
210 167 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (210 bp):
ATTCGCTCGAATTAACCCTTCTCATAATGAGAATTTATATAGCCCTATTTCGGTATGGAATAAAC
TTAAAATAATGGAATTGACTCGCTCATCAAGTTATAGATTATAAGTTGATAACCCCAACCCATTC
CCATTTTGGGTGAAATAGATCTACTAATTCTTTCATTCCAGTTAAAGCAGGAACTAAAAAATAGA
TCTACTAATTCTTTC
Found at i:40011921 original size:22 final size:23
Alignment explanation
Indices: 40011868--40011923 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
40011858 TTTAATTAAA
* * *
40011868 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
40011891 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
40011913 ATTAAAATTAA
1 ATTAAAATTAA
40011924 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:40011936 original size:16 final size:16
Alignment explanation
Indices: 40011899--40011938 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
40011889 TTAATAAAAT
* *
40011899 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
40011915 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
40011931 TAAAATTA
1 TAAAATTA
40011939 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:40012017 original size:59 final size:59
Alignment explanation
Indices: 40011949--40012118 Score: 304
Period size: 59 Copynumber: 2.9 Consensus size: 59
40011939 TCAAATTATT
* *
40011949 AATTGTTAATTGTATTAATTCTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
40012008 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
**
40012067 AATTATTAATTGTATTAATTGTTGTAACCAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
40012119 ACAAACTTGA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 107 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:40012660 original size:24 final size:24
Alignment explanation
Indices: 40012628--40012678 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
40012618 AATTTAACCT
40012628 AGAAAATGTTGTGCATTGTGAATG
1 AGAAAATGTTGTGCATTGTGAATG
40012652 AGAAAATGTTGTGCATTGTGAATG
1 AGAAAATGTTGTGCATTGTGAATG
40012676 AGA
1 AGA
40012679 TTGAAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.31
Consensus pattern (24 bp):
AGAAAATGTTGTGCATTGTGAATG
Found at i:40031194 original size:23 final size:22
Alignment explanation
Indices: 40031147--40031197 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 22
40031137 GGAGAGGTAG
40031147 AAAAAGCTTACTTTAATGGACAGA
1 AAAAAGCTTACTTTAA--GACAGA
40031171 AAAAAGCTTACTTTGAA-ACAAGA
1 AAAAAGCTTACTTT-AAGAC-AGA
40031194 AAAA
1 AAAA
40031198 TAAAATGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 2 0.08
23 7 0.28
24 14 0.56
25 2 0.08
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.22
Consensus pattern (22 bp):
AAAAAGCTTACTTTAAGACAGA
Found at i:40037395 original size:28 final size:28
Alignment explanation
Indices: 40037342--40037396 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
40037332 AATAAATAAA
**
40037342 TATTTTTTAATTTTAAAATATTTTTTTT
1 TATTTTTTAATTTTAAAATAAATTTTTT
* *
40037370 TATTTTTTTATTTTTAAATAAATTTTT
1 TATTTTTTAATTTTAAAATAAATTTTT
40037397 AGTGTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (28 bp):
TATTTTTTAATTTTAAAATAAATTTTTT
Found at i:40039486 original size:3 final size:3
Alignment explanation
Indices: 40039478--40039502 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40039468 TTAAAAGAGT
40039478 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
40039503 AGAGCGGGTC
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:40040231 original size:18 final size:17
Alignment explanation
Indices: 40040200--40040239 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
40040190 GTGTTTGCAG
40040200 GAGA-CTGGCGGTGGCA
1 GAGAGCTGGCGGTGGCA
40040216 GAGAGCTGGACGGTGGCA
1 GAGAGCTGG-CGGTGGCA
40040234 GAGAGC
1 GAGAGC
40040240 AGGTGGCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 4 0.18
17 4 0.18
18 14 0.64
ACGTcount: A:0.23, C:0.17, G:0.50, T:0.10
Consensus pattern (17 bp):
GAGAGCTGGCGGTGGCA
Found at i:40040447 original size:19 final size:20
Alignment explanation
Indices: 40040394--40040449 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
40040384 CTGTGGGTTA
40040394 GTTTGTTGGGTCTTGGGTCT
1 GTTTGTTGGGTCTTGGGTCT
*
40040414 GTTTG--GGTGTATTGGG-CT
1 GTTTGTTGG-GTCTTGGGTCT
*
40040432 GTTTGTTGGGCCTTGGGT
1 GTTTGTTGGGTCTTGGGT
40040450 ATTTATTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
18 9 0.31
19 13 0.45
20 7 0.24
ACGTcount: A:0.02, C:0.09, G:0.43, T:0.46
Consensus pattern (20 bp):
GTTTGTTGGGTCTTGGGTCT
Found at i:40045782 original size:50 final size:50
Alignment explanation
Indices: 40045705--40045819 Score: 153
Period size: 50 Copynumber: 2.3 Consensus size: 50
40045695 GACACACCAT
* *
40045705 AGCTCTCTTGAGCTTCCCGATACTTGGCTCT-CATGAGCTTCCCGAT-TAAC
1 AGCTCTCTTGAGCTTCCCAATACTTGGCT-TGCAAGAGCTTCCCGATAT-AC
*
40045755 AGCTCTCTTGAGCTTCCCAATATTTGGCTTGCAAGAGCTTCCCGATATAC
1 AGCTCTCTTGAGCTTCCCAATACTTGGCTTGCAAGAGCTTCCCGATATAC
* *
40045805 AGCTCACATGAGCTT
1 AGCTCTCTTGAGCTT
40045820 TCCGTTATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
49 1 0.02
50 56 0.97
51 1 0.02
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.31
Consensus pattern (50 bp):
AGCTCTCTTGAGCTTCCCAATACTTGGCTTGCAAGAGCTTCCCGATATAC
Found at i:40045817 original size:25 final size:25
Alignment explanation
Indices: 40045705--40045828 Score: 92
Period size: 25 Copynumber: 5.0 Consensus size: 25
40045695 GACACACCAT
* *
40045705 AGCTCTCTTGAGCTTCCCGATACT-T
1 AGCTCTCATGAGCTTCCCGATA-TAC
*
40045730 GGCTCTCATGAGCTTCCCGAT-TAAC
1 AGCTCTCATGAGCTTCCCGATAT-AC
* * **
40045755 AGCTCTCTTGAGCTTCCCAATATTT
1 AGCTCTCATGAGCTTCCCGATATAC
* *
40045780 GGCT-TGCAAGAGCTTCCCGATATAC
1 AGCTCT-CATGAGCTTCCCGATATAC
* * *
40045805 AGCTCACATGAGCTTTCCGTTATA
1 AGCTCTCATGAGCTTCCCGATATA
40045829 TGGCTCGAAA
Statistics
Matches: 75, Mismatches: 19, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
23 1 0.01
24 1 0.01
25 72 0.96
26 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (25 bp):
AGCTCTCATGAGCTTCCCGATATAC
Found at i:40045833 original size:50 final size:50
Alignment explanation
Indices: 40045713--40045844 Score: 124
Period size: 50 Copynumber: 2.6 Consensus size: 50
40045703 ATAGCTCTCT
* ** * * *
40045713 TGAGCTTCCCGATACT-TGGCTCTCATGAGCTTCCCGATTAACAGCTCTCT
1 TGAGCTTCCCAATA-TATGGCTCGAAAGAGCTTCCCGATTAACAGCTCACA
* * *
40045763 TGAGCTTCCCAATATTTGGCTTGCAAGAGCTTCCCGA-TATACAGCTCACA
1 TGAGCTTCCCAATATATGGCTCGAAAGAGCTTCCCGATTA-ACAGCTCACA
* **
40045813 TGAGCTTTCCGTTATATGGCTCGAAAGAGCTT
1 TGAGCTTCCCAATATATGGCTCGAAAGAGCTT
40045845 TTCGCTTACA
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
49 3 0.04
50 65 0.96
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (50 bp):
TGAGCTTCCCAATATATGGCTCGAAAGAGCTTCCCGATTAACAGCTCACA
Found at i:40058547 original size:6 final size:6
Alignment explanation
Indices: 40058536--40058581 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
40058526 TGCCCTTACC
40058536 CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG CCAA
1 CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG CCAAAG CCAA
40058582 GGTCTCTCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.50, C:0.35, G:0.15, T:0.00
Consensus pattern (6 bp):
CCAAAG
Found at i:40058682 original size:2 final size:2
Alignment explanation
Indices: 40058675--40058710 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40058665 CCTTCGCCAA
40058675 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
40058711 ACTTATTCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:40075626 original size:90 final size:90
Alignment explanation
Indices: 40075333--40075609 Score: 333
Period size: 90 Copynumber: 3.1 Consensus size: 90
40075323 GATTAATTAT
* * * * * * *
40075333 CTGCAACTCTGGTGATTCATCCA-CAACTTATCTAGAAACTTTAATCTGCAAATATGTTGTGCAT
1 CTGCAACACTGGTGGTTCATCCACCCACAT-TCTGGAAACTTTCATATGCAAATATGTTGTGCAT
*
40075397 TCACAACCATCTGACAACGTATTAAC
65 TCACAACCATCTGACAGCGTATTAAC
* * * *
40075423 TTGCAACACTGGTGGTTCATCCACCCATATTCTGGCAACTTTCATATGCAAATATGTTGTGTATT
1 CTGCAACACTGGTGGTTCATCCACCCACATTCTGGAAACTTTCATATGCAAATATGTTGTGCATT
* * * * *
40075488 TAGAGCCATTTGACAGTGTATTAAC
66 CACAACCATCTGACAGCGTATTAAC
40075513 CTGCAACACTGGTGGTTCATCCACCCACATTCTGGAAACTCTT-ATATGCAAATATGTTGTGCAT
1 CTGCAACACTGGTGGTTCATCCACCCACATTCTGGAAACT-TTCATATGCAAATATGTTGTGCAT
** *
40075577 TCACAACCATCTGGTAGCATATTAAC
65 TCACAACCATCTGACAGCGTATTAAC
*
40075603 CTACAAC
1 CTGCAAC
40075610 TTTTGTGGTT
Statistics
Matches: 155, Mismatches: 30, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
90 150 0.97
91 5 0.03
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.32
Consensus pattern (90 bp):
CTGCAACACTGGTGGTTCATCCACCCACATTCTGGAAACTTTCATATGCAAATATGTTGTGCATT
CACAACCATCTGACAGCGTATTAAC
Found at i:40077515 original size:8 final size:8
Alignment explanation
Indices: 40077501--40077530 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
40077491 ATAAAATTTT
40077501 AATATATA
1 AATATATA
*
40077509 TATATATA
1 AATATATA
40077517 AATATATA
1 AATATATA
40077525 AATATA
1 AATATA
40077531 AAGAATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
AATATATA
Found at i:40078158 original size:25 final size:27
Alignment explanation
Indices: 40078115--40078171 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
40078105 TGAACTTGCA
*
40078115 TTTTGTTTTTTAGAAAGATAAATAT-AT
1 TTTTATTTTTTAG-AAGATAAATATCAT
*
40078142 TTTTATTTTTTAG-AGATAAATTTCAT
1 TTTTATTTTTTAGAAGATAAATATCAT
40078168 TTTT
1 TTTT
40078172 TAAAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 9 0.33
26 6 0.22
27 12 0.44
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.58
Consensus pattern (27 bp):
TTTTATTTTTTAGAAGATAAATATCAT
Found at i:40086021 original size:49 final size:50
Alignment explanation
Indices: 40085905--40086123 Score: 277
Period size: 50 Copynumber: 4.4 Consensus size: 50
40085895 TATCCTAGAT
* ** * *
40085905 ATGGTCTTACATGAGAGTTCTCATATAGGTGCCCA-TGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACT-CCATGTCCCAGAC
*
40085955 ATGGTCTTAC-GGAGGACCTCTCATCTAGGTGCCAACTCCATGT-CCAGAC
1 ATGGTCTTACATG-GGACCTCTCATCTAGGTGCCAACTCCATGTCCCAGAC
* * *
40086004 ATGGTCTTACATGGGACCTCTAATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACTCCATGTCCCAGAC
*
40086054 ATGGTCTTAC-GGAGGACCTCTCATCTAGGTGCCAACTCCATGT-CCAGAC
1 ATGGTCTTACATG-GGACCTCTCATCTAGGTGCCAACTCCATGTCCCAGAC
*
40086103 ATGGTCTTACATGGGATCTCT
1 ATGGTCTTACATGGGACCTCT
40086124 TTACCCAAAT
Statistics
Matches: 147, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
49 68 0.46
50 78 0.53
51 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACTCCATGTCCCAGAC
Found at i:40086116 original size:99 final size:99
Alignment explanation
Indices: 40085905--40086123 Score: 357
Period size: 99 Copynumber: 2.2 Consensus size: 99
40085895 TATCCTAGAT
* ** * * *
40085905 ATGGTCTTACATGAGAGTTCTCATATAGGTGCCCATGCCATGTCCCAGACATGGTCTTACGGAGG
1 ATGGTCTTACATGGGACCTCTAATATAGGTGCCAACGCCATGTCCCAGACATGGTCTTACGGAGG
40085970 ACCTCTCATCTAGGTGCCAACTCCATGTCCAGAC
66 ACCTCTCATCTAGGTGCCAACTCCATGTCCAGAC
* *
40086004 ATGGTCTTACATGGGACCTCTAATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACGGAGG
1 ATGGTCTTACATGGGACCTCTAATATAGGTGCCAACGCCATGTCCCAGACATGGTCTTACGGAGG
40086069 ACCTCTCATCTAGGTGCCAACTCCATGTCCAGAC
66 ACCTCTCATCTAGGTGCCAACTCCATGTCCAGAC
*
40086103 ATGGTCTTACATGGGATCTCT
1 ATGGTCTTACATGGGACCTCT
40086124 TTACCCAAAT
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
99 111 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.26
Consensus pattern (99 bp):
ATGGTCTTACATGGGACCTCTAATATAGGTGCCAACGCCATGTCCCAGACATGGTCTTACGGAGG
ACCTCTCATCTAGGTGCCAACTCCATGTCCAGAC
Found at i:40087606 original size:37 final size:37
Alignment explanation
Indices: 40087549--40087700 Score: 173
Period size: 37 Copynumber: 3.9 Consensus size: 37
40087539 TATGATCACT
*
40087549 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
40087584 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
40087621 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
*
40087666 TTATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
40087701 GAAGCTATCA
Statistics
Matches: 100, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
35 6 0.06
36 4 0.04
37 54 0.54
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 32 0.32
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:40087684 original size:46 final size:46
Alignment explanation
Indices: 40087617--40087885 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
40087607 TAAGTGTAGC
* **
40087617 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
40087663 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
40087709 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
40087761 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
40087807 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
40087859 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
40087886 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:40087736 original size:52 final size:52
Alignment explanation
Indices: 40087660--40087879 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
40087650 TAGCTAAAGC
* *
40087660 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
40087713 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
40087765 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
40087811 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
40087863 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
40087880 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:40087782 original size:98 final size:98
Alignment explanation
Indices: 40087617--40087885 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
40087607 TAAGTGTAGC
* * *
40087617 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
40087682 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
40087716 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
40087781 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
40087814 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
40087879 GATCAGA
66 GATCAGA
40087886 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:40090839 original size:29 final size:28
Alignment explanation
Indices: 40090780--40090839 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
40090770 AATTAAAATG
* * *
40090780 AATTTCAAATAAATAATATATATATGAA
1 AATTTAAAATAAATAAAATATATATAAA
40090808 AATTTAAAATAAATCAAAATATAGT-TAAA
1 AATTTAAAATAAAT-AAAATATA-TATAAA
40090837 AAT
1 AAT
40090840 AAATACTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 13 0.48
29 13 0.48
30 1 0.04
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (28 bp):
AATTTAAAATAAATAAAATATATATAAA
Found at i:40098194 original size:13 final size:14
Alignment explanation
Indices: 40098171--40098200 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
40098161 ATAAATATTA
40098171 TTTATTAAATTAAT
1 TTTATTAAATTAAT
40098185 TTTATT-AATTAAT
1 TTTATTAAATTAAT
40098198 TTT
1 TTT
40098201 CCAATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTATTAAATTAAT
Found at i:40101746 original size:190 final size:190
Alignment explanation
Indices: 40101410--40101787 Score: 605
Period size: 190 Copynumber: 2.0 Consensus size: 190
40101400 GACCACTAAG
* * * *
40101410 TGCTTCTTAGAACACTAGGCCATTAGGTTACCTCTAAAAAATATACAGAACTCAATTATGGATCT
1 TGCTTCCTAGAACACTAGGCCATTAGGCTACCTCCAAAAAATATACAGAACCCAATTATGGATCT
* * *
40101475 TCTACCTTCAGGACAAGATGCCTAGTTTGCATCAGCAAAACATTCTAACTTAAGAACATTAGTTT
66 TCTACCTTCAGGACAAGATGCCCAGTTTGCATCAGCAAAACATTCTAACTTAAGAACAATAGTTC
* * * *
40101540 TTTTGTATTCCAAAGCATTGCTTAAAGTGCTTTTGAGGTATCTTAAAATCCTTTTAACCT
131 TTTTGTAATCCAAAGCATTGCTTAAAGTGCCTTTGAGATACCTTAAAATCCTTTTAACCT
* *
40101600 TGCTTCCTAGAACACTAGGCCATTAGGCTACCTCCAAAAAATATTCAGAACCCAATTGTGGATCT
1 TGCTTCCTAGAACACTAGGCCATTAGGCTACCTCCAAAAAATATACAGAACCCAATTATGGATCT
*
40101665 TCTACCTTCAGGGCAAGATGCCCAGTTTGCATCAGCAAAACATTCTAACTTAAGAACAATAGTTC
66 TCTACCTTCAGGACAAGATGCCCAGTTTGCATCAGCAAAACATTCTAACTTAAGAACAATAGTTC
*
40101730 TTTTGTACAT-CAAAGCATTGTTTAAAGTGCCTTTGAGATACCTTAAAATCCTTTTAAC
131 TTTTGTA-ATCCAAAGCATTGCTTAAAGTGCCTTTGAGATACCTTAAAATCCTTTTAAC
40101788 AGCTTGTCAG
Statistics
Matches: 172, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
190 171 0.99
191 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (190 bp):
TGCTTCCTAGAACACTAGGCCATTAGGCTACCTCCAAAAAATATACAGAACCCAATTATGGATCT
TCTACCTTCAGGACAAGATGCCCAGTTTGCATCAGCAAAACATTCTAACTTAAGAACAATAGTTC
TTTTGTAATCCAAAGCATTGCTTAAAGTGCCTTTGAGATACCTTAAAATCCTTTTAACCT
Found at i:40104477 original size:26 final size:26
Alignment explanation
Indices: 40104441--40104494 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
40104431 TCACTGCGGA
40104441 TAGTTATACATGTGATTTATTTTTCT
1 TAGTTATACATGTGATTTATTTTTCT
40104467 TAGTTATACATGTGATTTATTTTTCT
1 TAGTTATACATGTGATTTATTTTTCT
40104493 TA
1 TA
40104495 CTTCATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.24, C:0.07, G:0.11, T:0.57
Consensus pattern (26 bp):
TAGTTATACATGTGATTTATTTTTCT
Found at i:40116416 original size:10 final size:10
Alignment explanation
Indices: 40116388--40116444 Score: 57
Period size: 10 Copynumber: 6.0 Consensus size: 10
40116378 ATGAGAAAAA
40116388 ATATATTTTT
1 ATATATTTTT
*
40116398 AT-TA-ATTT
1 ATATATTTTT
40116406 ATATATTTTT
1 ATATATTTTT
*
40116416 AAATATTTTT
1 ATATATTTTT
*
40116426 -TTTATTTTT
1 ATATATTTTT
*
40116435 ATTTATTTTT
1 ATATATTTTT
40116445 TCACGTAGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
8 5 0.13
9 11 0.28
10 23 0.59
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
ATATATTTTT
Found at i:40116431 original size:19 final size:19
Alignment explanation
Indices: 40116409--40116445 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40116399 TTAATTTATA
40116409 TATTTTTAAATATTTTTTT
1 TATTTTTAAATATTTTTTT
**
40116428 TATTTTTATTTATTTTTT
1 TATTTTTAAATATTTTTT
40116446 CACGTAGCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
TATTTTTAAATATTTTTTT
Found at i:40124272 original size:21 final size:21
Alignment explanation
Indices: 40124243--40124292 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
40124233 GGACCAACTC
*
40124243 TTACAAGCTTCTGTTCAGCTT
1 TTACAAGCTTCTATTCAGCTT
* *
40124264 TTACGAGCTTCTATTTAGC-T
1 TTACAAGCTTCTATTCAGCTT
40124284 TT-CAAGCTT
1 TTACAAGCTT
40124293 TTGTTGACGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 6 0.24
20 3 0.12
21 16 0.64
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (21 bp):
TTACAAGCTTCTATTCAGCTT
Found at i:40128506 original size:33 final size:33
Alignment explanation
Indices: 40128469--40128541 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
40128459 TTACATTTGA
**
40128469 GAGATTAGCGGAACTATATATATCTGAGATTGT
1 GAGATTAGAAGAACTATATATATCTGAGATTGT
*
40128502 GAGATTAGAAGAACTATATATATCTTAGATTGT
1 GAGATTAGAAGAACTATATATATCTGAGATTGT
40128535 GAGATTA
1 GAGATTA
40128542 CACGGAGTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (33 bp):
GAGATTAGAAGAACTATATATATCTGAGATTGT
Found at i:40133449 original size:47 final size:47
Alignment explanation
Indices: 40133380--40133474 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
40133370 GAGATATAAT
40133380 AGGTTTTGTGAGACAAGGTCAGAATGATTTCGGGTTCCCATATTCTG
1 AGGTTTTGTGAGACAAGGTCAGAATGATTTCGGGTTCCCATATTCTG
*
40133427 AGGTTTTGTGAGACAAGGTCAGAATGATTTCGGGTTCCCCTATTCTG
1 AGGTTTTGTGAGACAAGGTCAGAATGATTTCGGGTTCCCATATTCTG
40133474 A
1 A
40133475 CTTTGGAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (47 bp):
AGGTTTTGTGAGACAAGGTCAGAATGATTTCGGGTTCCCATATTCTG
Found at i:40135893 original size:18 final size:18
Alignment explanation
Indices: 40135870--40135906 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40135860 TAATAAACTG
40135870 TGTATAA-TAAAATTAAAA
1 TGTATAAGT-AAATTAAAA
40135888 TGTATAAGTAAATTAAAA
1 TGTATAAGTAAATTAAAA
40135906 T
1 T
40135907 AAAACTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (18 bp):
TGTATAAGTAAATTAAAA
Found at i:40148497 original size:19 final size:20
Alignment explanation
Indices: 40148465--40148507 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
40148455 AATAAAATAA
*
40148465 TTTCTGGAAAATGATTTAGT
1 TTTCTGGAAAATGATTTACT
40148485 TTTCTGG-AAATGATTTACT
1 TTTCTGGAAAATGATTTACT
40148504 TTTC
1 TTTC
40148508 GGTGTTTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.49
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:40149093 original size:48 final size:48
Alignment explanation
Indices: 40149034--40149138 Score: 203
Period size: 48 Copynumber: 2.2 Consensus size: 48
40149024 CAGCCAGCTT
40149034 CCTAGGCCCGGACACGGCCCGAAATATGGGCCCGATAATTTGTCCAAG
1 CCTAGGCCCGGACACGGCCCGAAATATGGGCCCGATAATTTGTCCAAG
40149082 CCTAGGCCCGGACACGGCCCGAAATATGGGCCCGATAATTTGTCCAAG
1 CCTAGGCCCGGACACGGCCCGAAATATGGGCCCGATAATTTGTCCAAG
40149130 CCTA-GCCCG
1 CCTAGGCCCG
40149139 AGAAAAAAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 5 0.09
48 52 0.91
ACGTcount: A:0.24, C:0.33, G:0.27, T:0.16
Consensus pattern (48 bp):
CCTAGGCCCGGACACGGCCCGAAATATGGGCCCGATAATTTGTCCAAG
Found at i:40149241 original size:16 final size:16
Alignment explanation
Indices: 40149204--40149243 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
40149194 TTGATAAAAT
* *
40149204 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
40149220 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
40149236 TAAAATTA
1 TAAAATTA
40149244 TCAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:40149476 original size:16 final size:16
Alignment explanation
Indices: 40149455--40149488 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
40149445 TATATATTTT
40149455 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
40149471 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
40149487 AA
1 AA
40149489 CTAGTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.18
Consensus pattern (16 bp):
AAACATAAAAAACTTA
Found at i:40155322 original size:25 final size:25
Alignment explanation
Indices: 40155285--40155333 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
40155275 TTTAATTTTT
*
40155285 TTTTAAAAATAATTATTTTATTATA
1 TTTTAAAAATAATAATTTTATTATA
* *
40155310 TTTTAATATTAATAATTTTATTAT
1 TTTTAAAAATAATAATTTTATTAT
40155334 TTATTTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTAAAAATAATAATTTTATTATA
Found at i:40157108 original size:22 final size:22
Alignment explanation
Indices: 40157085--40157126 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40157075 AAATTAATTA
40157085 AAAG-GATATAAGT-AAATAAAT
1 AAAGCGATATAA-TAAAATAAAT
40157106 AAAGCGATATAATAAAATAAA
1 AAAGCGATATAATAAAATAAA
40157127 CGTATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.64, C:0.02, G:0.12, T:0.21
Consensus pattern (22 bp):
AAAGCGATATAATAAAATAAAT
Found at i:40157844 original size:20 final size:21
Alignment explanation
Indices: 40157819--40157858 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
40157809 TCGTCTTTTA
40157819 TATATATATATATC-ATATGT
1 TATATATATATATCTATATGT
*
40157839 TATATATATTTATCTATATG
1 TATATATATATATCTATATG
40157859 CAGTTCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (21 bp):
TATATATATATATCTATATGT
Found at i:40158879 original size:143 final size:143
Alignment explanation
Indices: 40158563--40159570 Score: 1392
Period size: 143 Copynumber: 7.1 Consensus size: 143
40158553 TCACTTTAGG
** * * * *
40158563 GAGATAAAACTGGTGGCTTCAATCTGCTCCACTACAACTTTAGGAAGATAAGATCCACCATAATT
1 GAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATT
* * * * *
40158628 TGTAGCTTTAATTTATTCCACTGCAACG-CAGGGAAATAAGATCCGCTGTCTTTAGTCTGCTCCG
66 TGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCG
* * *
40158692 CCGCAACTTTAGG
131 CTGCAACTTCAGA
*
40158705 GAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGATTCGCCATAATT
1 GAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATT
* * * *
40158770 TGTAGCTTTAATCTGTTCCATTACAACGCCATGGAAATAAGATTAGTTGTCTTCAGTCTGCTCCG
66 TGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCG
*
40158835 CTGCAACTTCAAA
131 CTGCAACTTCAGA
* * * *
40158848 GAGATAAGGTTGGTGGCTTCAATTTGCTCCACTGCAACTTCAAGAAGATAAGATCCGCCATAATT
1 GAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATT
* * *
40158913 TGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTTGCTGTCTTCAGTCTGCTTCG
66 TGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCG
* * * *
40158978 GTACCACTTCAGG
131 CTGCAACTTCAGA
* * *
40158991 GAGATAAGGCTGGTGGCTTCAATCTGCTTCACTGCAACTTCAGGAAGATAAGATCCGCCACAATT
1 GAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATT
* * * * *
40159056 TGTAGCTTTAATTTGTTCCACTGCAATGCTAGGGAAATAAGATTTGTTGTATTCAGTCTGCTCCG
66 TGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCG
* *
40159121 CTGTAACTTCAAA
131 CTGCAACTTCAGA
* *
40159134 GTGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGAAAAGA-TCTGCCATAAT
1 GAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTC-GCCATAAT
* * *
40159198 TTGTAACTTTAATTTGTTCCACTGCAACGCCAAGGAAATAAGATTCGTTGTCTTCAGTCTGCTCC
65 TTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCC
* *
40159263 GCTGTAACTTCAGG
130 GCTGCAACTTCAGA
* * *
40159277 GAGATAAGGCCGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAATATTTGCCATAATT
1 GAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATT
* * * * *
40159342 TGTAGCTTTAATCTGTTCCACTGCAATGCTAGGGAAATAAGCTTCGATGTCTTTAGTCTGCTCCG
66 TGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCG
40159407 CTGCAACTTCAGA
131 CTGCAACTTCAGA
* * *
40159420 GAGATAAGGCCGGTGGCTTCAATCTGCTCCATTGCAACTTCAGGAAGATAAGA-TCTGTCATAAT
1 GAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTC-GCCATAAT
* ** *
40159484 TTGTAGCTTTAATCTGTTCCACTGCAAGGTGAAGGAAATAAGATTCGTTGTCTTCAGTCTGCTCC
65 TTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCC
*
40159549 GCTGCAACTTCAGG
130 GCTGCAACTTCAGA
*
40159563 GAAATAAG
1 GAGATAAG
40159571 ATTGTCATTT
Statistics
Matches: 770, Mismatches: 92, Indels: 7
0.89 0.11 0.01
Matches are distributed among these distances:
142 84 0.11
143 685 0.89
144 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (143 bp):
GAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATT
TGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCG
CTGCAACTTCAGA
Found at i:40167280 original size:22 final size:21
Alignment explanation
Indices: 40167251--40167293 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
40167241 AAATCAATTA
40167251 AAAGGATATAAGT-AAATAAAT
1 AAAGGATATAA-TAAAATAAAT
40167272 AAAGCGATATAATAAAATAAAT
1 AAAG-GATATAATAAAATAAAT
40167294 GTATTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.23
Consensus pattern (21 bp):
AAAGGATATAATAAAATAAAT
Found at i:40168807 original size:16 final size:17
Alignment explanation
Indices: 40168788--40168820 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
40168778 AAACTCACAA
40168788 AACAAAATTCT-TTTAT
1 AACAAAATTCTCTTTAT
40168804 AACAAAATTCTCTTTAT
1 AACAAAATTCTCTTTAT
40168821 TATTTTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (17 bp):
AACAAAATTCTCTTTAT
Found at i:40170497 original size:20 final size:21
Alignment explanation
Indices: 40170474--40170520 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
40170464 TTCCACATCA
*
40170474 ATTTAATATTAAA-GAATAAT
1 ATTTAATATCAAACGAATAAT
** *
40170494 ATTTTCTATCAAACTAATAAT
1 ATTTAATATCAAACGAATAAT
40170515 ATTTAA
1 ATTTAA
40170521 ATATAAATTA
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTTAATATCAAACGAATAAT
Found at i:40170542 original size:15 final size:16
Alignment explanation
Indices: 40170515--40170555 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
40170505 AACTAATAAT
40170515 ATTTAA-ATATAAATT-
1 ATTTAATAT-TAAATTA
*
40170530 ATTTTATATTAAATTA
1 ATTTAATATTAAATTA
40170546 ATTTAATATT
1 ATTTAATATT
40170556 TTATGATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTAATATTAAATTA
Found at i:40170557 original size:23 final size:22
Alignment explanation
Indices: 40170529--40170619 Score: 85
Period size: 23 Copynumber: 3.9 Consensus size: 22
40170519 AAATATAAAT
40170529 TATTTTATATTAAATTAATTTAA
1 TATTTTATA-TAAATTAATTTAA
*
40170552 TATTTTATGATAAATTATTTTAA
1 TATTTTAT-ATAAATTAATTTAA
* **
40170575 TATTTTCTA-AAATTTGAAAATAA
1 TATTTTATATAAA-TT-AATTTAA
40170598 TATTTTATACTAAATTATATTT
1 TATTTTATA-TAAATTA-ATTT
40170620 GTAATGGCCC
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
21 3 0.06
22 3 0.06
23 40 0.74
24 5 0.09
25 3 0.06
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TATTTTATATAAATTAATTTAA
Found at i:40173018 original size:26 final size:26
Alignment explanation
Indices: 40172962--40173019 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
40172952 AAAATGGATG
* * *
40172962 AATTTGAAATAATGACACATAGAAAT
1 AATTTGAAATAATAAAACATAGAAAA
40172988 AATTTGAAATAA-AAAACATAGAAAA
1 AATTTGAAATAATAAAACATAGAAAA
40173013 ATATTTG
1 A-ATTTG
40173020 TTAAAAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28
Consensus pattern (26 bp):
AATTTGAAATAATAAAACATAGAAAA
Found at i:40173294 original size:14 final size:15
Alignment explanation
Indices: 40173266--40173298 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
40173256 AAGGTTTATA
40173266 GATTATGGAATTAGG
1 GATTATGGAATTAGG
40173281 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
40173295 GATT
1 GATT
40173299 CTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:40173543 original size:14 final size:13
Alignment explanation
Indices: 40173524--40173583 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 13
40173514 TAAATAAGGT
40173524 TTAGGGGTTAGTAG
1 TTAGGGGTTAG-AG
* *
40173538 TTAGGGGATAGGGG
1 TTAGGGGTTA-GAG
40173552 TTAGGGGTTAGATG
1 TTAGGGGTTAGA-G
40173566 TTAGGGGTTAGATG
1 TTAGGGGTTAGA-G
40173580 TTAG
1 TTAG
40173584 ATGTTAGAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
13 1 0.03
14 38 0.95
15 1 0.03
ACGTcount: A:0.22, C:0.00, G:0.45, T:0.33
Consensus pattern (13 bp):
TTAGGGGTTAGAG
Found at i:40173559 original size:7 final size:7
Alignment explanation
Indices: 40173524--40173576 Score: 61
Period size: 7 Copynumber: 7.6 Consensus size: 7
40173514 TAAATAAGGT
40173524 TTAGGGG
1 TTAGGGG
**
40173531 TTAGTAG
1 TTAGGGG
40173538 TTAGGGG
1 TTAGGGG
*
40173545 ATAGGGG
1 TTAGGGG
40173552 TTAGGGG
1 TTAGGGG
**
40173559 TTAGATG
1 TTAGGGG
40173566 TTAGGGG
1 TTAGGGG
40173573 TTAG
1 TTAG
40173577 ATGTTAGATG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:40173561 original size:21 final size:21
Alignment explanation
Indices: 40173525--40173604 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
40173515 AAATAAGGTT
* *
40173525 TAGGGGTTAGTAGTTAGGGGA
1 TAGGGGTTAGGAGTTAGAGGA
* * *
40173546 TAGGGGTTAGGGGTTAGATGT
1 TAGGGGTTAGGAGTTAGAGGA
* *
40173567 TAGGGGTTA-GATGTTAGATGT
1 TAGGGGTTAGGA-GTTAGAGGA
* *
40173588 TAGAGGTTAAGAGTTAG
1 TAGGGGTTAGGAGTTAG
40173605 TGATTTAGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 1 0.02
21 47 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (21 bp):
TAGGGGTTAGGAGTTAGAGGA
Found at i:40173582 original size:7 final size:7
Alignment explanation
Indices: 40173558--40173596 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
40173548 GGGGTTAGGG
40173558 GTTAGAT
1 GTTAGAT
**
40173565 GTTAGGG
1 GTTAGAT
40173572 GTTAGAT
1 GTTAGAT
40173579 GTTAGAT
1 GTTAGAT
*
40173586 GTTAGAG
1 GTTAGAT
40173593 GTTA
1 GTTA
40173597 AGAGTTAGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (7 bp):
GTTAGAT
Found at i:40173589 original size:14 final size:14
Alignment explanation
Indices: 40173551--40173596 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
40173541 GGGGATAGGG
*
40173551 GTTAGGGGTTAGAT
1 GTTAGAGGTTAGAT
*
40173565 GTTAGGGGTTAGAT
1 GTTAGAGGTTAGAT
* *
40173579 GTTAGATGTTAGAG
1 GTTAGAGGTTAGAT
40173593 GTTA
1 GTTA
40173597 AGAGTTAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.37
Consensus pattern (14 bp):
GTTAGAGGTTAGAT
Found at i:40173603 original size:14 final size:14
Alignment explanation
Indices: 40173558--40173604 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
40173548 GGGGTTAGGG
* *
40173558 GTTAGATGTTAGGG
1 GTTAGATGTTAAGA
40173572 GTTAGATGTT-AGA
1 GTTAGATGTTAAGA
*
40173585 TGTTAGAGGTTAAGA
1 -GTTAGATGTTAAGA
40173600 GTTAG
1 GTTAG
40173605 TGATTTAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 1 0.04
14 24 0.86
15 3 0.11
ACGTcount: A:0.28, C:0.00, G:0.36, T:0.36
Consensus pattern (14 bp):
GTTAGATGTTAAGA
Found at i:40181682 original size:10 final size:11
Alignment explanation
Indices: 40181667--40181695 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
40181657 TCCAAAGATG
40181667 TGAATTGAAT-
1 TGAATTGAATA
40181677 TGAATTGAATA
1 TGAATTGAATA
40181688 TGAATTGA
1 TGAATTGA
40181696 TGTTAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (11 bp):
TGAATTGAATA
Found at i:40188532 original size:3 final size:3
Alignment explanation
Indices: 40188526--40188554 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40188516 CATCATCATC
40188526 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
40188555 ACTCCTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:40188980 original size:31 final size:32
Alignment explanation
Indices: 40188941--40189013 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 32
40188931 TAATTTTTAG
40188941 AGGA-TGATTAATAC-AAT-CATTGAAGAAATT
1 AGGATTGATTAATACAAATAC-TTGAAGAAATT
40188971 AGGATTGATTAATACAAATACTTGAAGAAATT
1 AGGATTGATTAATACAAATACTTGAAGAAATT
*
40189003 AAGATTGATTA
1 AGGATTGATTA
40189014 GAAATTTAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
30 4 0.10
31 10 0.26
32 24 0.62
33 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.32
Consensus pattern (32 bp):
AGGATTGATTAATACAAATACTTGAAGAAATT
Found at i:40190935 original size:31 final size:31
Alignment explanation
Indices: 40190897--40190958 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
40190887 GGATGCAATG
40190897 ATTGCTTATAAATCCTTTCATAAGCTTTTCT
1 ATTGCTTATAAATCCTTTCATAAGCTTTTCT
40190928 ATTGCTTATAAATCCTTTCATAAGCTTTTCT
1 ATTGCTTATAAATCCTTTCATAAGCTTTTCT
40190959 GTTTAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (31 bp):
ATTGCTTATAAATCCTTTCATAAGCTTTTCT
Found at i:40196695 original size:11 final size:10
Alignment explanation
Indices: 40196655--40196707 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
40196645 GGCCCATTTT
40196655 TATTTTAAAA
1 TATTTTAAAA
*
40196665 TTTTTTTAAAA
1 -TATTTTAAAA
*
40196676 T-TTTAAAAA
1 TATTTTAAAA
40196685 GTATTTTAAAAA
1 -TATTTT-AAAA
40196697 TATTTTAAAA
1 TATTTTAAAA
40196707 T
1 T
40196708 TAAAAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
9 7 0.19
10 7 0.19
11 18 0.50
12 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:40196724 original size:28 final size:29
Alignment explanation
Indices: 40196692--40196764 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
40196682 AAAGTATTTT
40196692 AAAAA-TATTTTAAAATTAAAAAAAATT-A
1 AAAAAGTATTTTAAAATT-AAAAAAATTAA
40196720 AAAAAGTATTTTAAAATTAAAAAAATTAA
1 AAAAAGTATTTTAAAATTAAAAAAATTAA
40196749 AAAAAGTATTTTAAAA
1 AAAAAGTATTTTAAAA
40196765 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 14 0.33
29 29 0.67
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAAAGTATTTTAAAATTAAAAAAATTAA
Found at i:40196731 original size:40 final size:40
Alignment explanation
Indices: 40196680--40196825 Score: 140
Period size: 40 Copynumber: 3.9 Consensus size: 40
40196670 TTAAAATTTT
40196680 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATTA
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATTA
40196720 AAAAAG-----------TATTTTAAAATT-AAAAAAATTAA
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATT-A
40196749 AAAAAGTATTTTAAAAATAT-TT-TAAAATTTAAAAAAAATTA
1 AAAAAGTATTTT-AAAA-ATATTTTAAAA-TTAAAAAAAATTA
* *
40196790 AAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAA
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAA
40196826 TAAATATATT
Statistics
Matches: 86, Mismatches: 2, Indels: 36
0.69 0.02 0.29
Matches are distributed among these distances:
28 9 0.10
29 19 0.22
39 2 0.02
40 26 0.30
41 20 0.23
42 10 0.12
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (40 bp):
AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATTA
Found at i:40196743 original size:8 final size:9
Alignment explanation
Indices: 40196703--40196753 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
40196693 AAAATATTTT
40196703 AAAATTAAAA
1 AAAATT-AAA
40196713 AAAATTAAA
1 AAAATTAAA
**
40196722 AAAGTATT-TT
1 AAA--ATTAAA
40196732 AAAATTAAA
1 AAAATTAAA
40196741 AAAATTAAA
1 AAAATTAAA
40196750 AAAA
1 AAAA
40196754 GTATTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
8 3 0.09
9 19 0.56
10 9 0.26
11 3 0.09
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (9 bp):
AAAATTAAA
Found at i:40196816 original size:11 final size:11
Alignment explanation
Indices: 40196655--40196706 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 11
40196645 GGCCCATTTT
40196655 TATTTT-AAAA
1 TATTTTAAAAA
**
40196665 T-TTTTTTAAA
1 TATTTTAAAAA
40196675 -ATTTTAAAAA
1 TATTTTAAAAA
40196685 GTATTTTAAAAA
1 -TATTTTAAAAA
40196697 TATTTTAAAA
1 TATTTTAAAA
40196707 TTAAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
9 4 0.11
10 11 0.31
11 10 0.29
12 10 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:40197084 original size:10 final size:9
Alignment explanation
Indices: 40197060--40197095 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
40197050 TTTATTATAT
40197060 AATTTTTAG
1 AATTTTTAG
40197069 AATTTTTAG
1 AATTTTTAG
40197078 AATTTTTATG
1 AATTTTTA-G
40197088 AATTTTTA
1 AATTTTTA
40197096 ATTAAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (9 bp):
AATTTTTAG
Found at i:40197090 original size:19 final size:18
Alignment explanation
Indices: 40197060--40197095 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
40197050 TTTATTATAT
40197060 AATTTTTAGAATTTTTAG
1 AATTTTTAGAATTTTTAG
40197078 AATTTTTATGAATTTTTA
1 AATTTTTA-GAATTTTTA
40197096 ATTAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (18 bp):
AATTTTTAGAATTTTTAG
Found at i:40197213 original size:20 final size:21
Alignment explanation
Indices: 40197159--40197214 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
40197149 TTAAATTGAA
*
40197159 TTTTTAGACATTTTTAAGATTC
1 TTTTTA-ATATTTTTAAGATTC
* *
40197181 TTTTTTATGTTTTT-AGATT-
1 TTTTTAATATTTTTAAGATTC
40197200 TTTTTAATAATTTTT
1 TTTTTAAT-ATTTTT
40197215 CCAGAATCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 7 0.25
20 10 0.36
21 6 0.21
22 5 0.18
ACGTcount: A:0.23, C:0.04, G:0.07, T:0.66
Consensus pattern (21 bp):
TTTTTAATATTTTTAAGATTC
Found at i:40198324 original size:23 final size:24
Alignment explanation
Indices: 40198289--40198338 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
40198279 GAAACAATAT
*
40198289 AAAAAATACACAAAAATAACAACA
1 AAAAAATACACAAAAACAACAACA
* *
40198313 AAAAAATA-ACAATAACAACACCA
1 AAAAAATACACAAAAACAACAACA
40198336 AAA
1 AAA
40198339 CACTAGGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.74, C:0.18, G:0.00, T:0.08
Consensus pattern (24 bp):
AAAAAATACACAAAAACAACAACA
Found at i:40199414 original size:19 final size:20
Alignment explanation
Indices: 40199390--40199429 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
40199380 GTTTTTGTAT
*
40199390 TTTTAAGTAATATA-ATTTA
1 TTTTAAATAATATATATTTA
*
40199409 TTTTAAATATTATATATTTA
1 TTTTAAATAATATATATTTA
40199429 T
1 T
40199430 ATATAGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTAAATAATATATATTTA
Found at i:40201152 original size:31 final size:31
Alignment explanation
Indices: 40201059--40201154 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
40201049 GGCAAATTAC
*
40201059 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
40201090 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
40201122 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
40201153 AA
1 AA
40201155 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:40213795 original size:36 final size:37
Alignment explanation
Indices: 40213722--40213795 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
40213712 AGACCGAAGA
* * *
40213722 TTTGGGAATTTGGAGTTGTTGAAATGAATTGGGGAAT
1 TTTGGGAATTAGGAGTTGCTGAAATGAATTGGAGAAT
*
40213759 TTTGGTAATTAGG-GTTGCTGAAATGAATAT-GAGAAT
1 TTTGGGAATTAGGAGTTGCTGAAATGAAT-TGGAGAAT
40213795 T
1 T
40213796 GTCATGTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 20 0.62
37 12 0.38
ACGTcount: A:0.30, C:0.01, G:0.31, T:0.38
Consensus pattern (37 bp):
TTTGGGAATTAGGAGTTGCTGAAATGAATTGGAGAAT
Found at i:40218291 original size:19 final size:20
Alignment explanation
Indices: 40218261--40218300 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
40218251 TAAATTTTAA
40218261 AAATTAATTTAAAAAAATAT
1 AAATTAATTTAAAAAAATAT
*
40218281 AAATTAA-TTAAAAAAGTAT
1 AAATTAATTTAAAAAAATAT
40218300 A
1 A
40218301 CATTTTTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAATTAATTTAAAAAAATAT
Found at i:40218384 original size:26 final size:27
Alignment explanation
Indices: 40218329--40218387 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
40218319 TGAACCTTGA
* * *
40218329 TTAAAATTTATATATATTTTTATTTTT
1 TTAAAATTTATATAAATTTTTATCTAT
*
40218356 TTAAAATTTTTA-AAATTTTTATCTAT
1 TTAAAATTTATATAAATTTTTATCTAT
40218382 TTAAAA
1 TTAAAA
40218388 ACGGTCACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TTAAAATTTATATAAATTTTTATCTAT
Found at i:40220394 original size:3 final size:3
Alignment explanation
Indices: 40220386--40220413 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40220376 CTGCTTTTGA
40220386 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
40220414 CCTGCATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:40225798 original size:43 final size:41
Alignment explanation
Indices: 40225738--40225894 Score: 176
Period size: 43 Copynumber: 3.7 Consensus size: 41
40225728 TATGTATTTT
40225738 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTATA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TTGTG-ATA
* * *
40225781 CGTGTAAGACCATGTCTGGGACATTGGCATCGTATT-TGATT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCG-ATTGTGATA
* *
40225822 TGTGTAAGACC-CTGTCTGGGATAG-TGGCATCGATATGTGATTA
1 CGTGTAAGACCAC-GTCTGGGA-CGTTGGCATCGAT-TGTGA-TA
*
40225865 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
40225895 TGTACGAGTC
Statistics
Matches: 95, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
40 2 0.02
41 29 0.31
42 6 0.06
43 56 0.59
44 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.30
Consensus pattern (41 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATTGTGATA
Done.