Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold130
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: 730134
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:171225 original size:97 final size:96
Alignment explanation
Indices: 171031--171245 Score: 272
Period size: 97 Copynumber: 2.2 Consensus size: 96
171021 CTCCTCGAAG
* * *
171031 GAATGGGGTTAGAATGTCCCCGACGATGGCAATTTAGGTGAAAATAAGATTTAATCTTGACAAGT
1 GAATGGGGTTAGAGTGTCCCCAACGATGACAATTTAGGTGAAAATAAGATTTAATCTTGACAAGT
* * * *
171096 TTAAAAACGGGGTTGGAGTATCCTCTCGAAA
66 TTAAAAACGAGATTAGAGTATCCTCTCAAAA
* * * * *
171127 GAATAGGGTTGGAGTGTCCCCAATGATGACACTTTGGGTGAAAATAAGATTTAAATCTTGACAAG
1 GAATGGGGTTAGAGTGTCCCCAACGATGACAATTTAGGTGAAAATAAGATTT-AATCTTGACAAG
171192 TTTAAAAACGAGATTAGAGTATTTCCT-T-AAAA
65 TTTAAAAACGAGATTAGAGTA--TCCTCTCAAAA
*
171224 GAATGGGGTTAGAGTATCCCCA
1 GAATGGGGTTAGAGTGTCCCCA
171246 TGAATAAAAT
Statistics
Matches: 101, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
96 44 0.44
97 52 0.51
98 1 0.01
99 4 0.04
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (96 bp):
GAATGGGGTTAGAGTGTCCCCAACGATGACAATTTAGGTGAAAATAAGATTTAATCTTGACAAGT
TTAAAAACGAGATTAGAGTATCCTCTCAAAA
Found at i:173982 original size:44 final size:41
Alignment explanation
Indices: 173934--174084 Score: 94
Period size: 44 Copynumber: 3.5 Consensus size: 41
173924 GTATAGACAA
173934 ACATGAAACAATGCAAATGTAAGCATCAATAAAGAGGCAAATG
1 ACATGAAACAATGCAAATG-AAGCATCAATAAAGAGG-AAATG
* ** * *
173977 CACATGATATGATGCAAATACGAATGTCATCTAA-AATATA-GATATG
1 -ACATGAAACAATGCAAAT--GAA-G-CATC-AATAA-AGAGGAAATG
*
174023 -CATGAAACGATGCAAATGCAAGCATCAATAAAGAGGTAAATG
1 ACATGAAACAATGCAAATG-AAGCATCAATAAAGAGG-AAATG
*
174065 TACAT-ACTACAATGCAAATG
1 -ACATGA-AACAATGCAAATG
174085 CCAATGTCAT
Statistics
Matches: 83, Mismatches: 11, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
40 4 0.05
41 7 0.08
42 6 0.07
43 3 0.04
44 44 0.53
45 2 0.02
46 6 0.07
47 7 0.08
48 4 0.05
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (41 bp):
ACATGAAACAATGCAAATGAAGCATCAATAAAGAGGAAATG
Found at i:174080 original size:88 final size:88
Alignment explanation
Indices: 173866--174171 Score: 319
Period size: 88 Copynumber: 3.5 Consensus size: 88
173856 GGTGTCTACA
* * * ** *
173866 CAAGCATCAATAAAGTGG-AAATGCATATGAAATGATGCAAATACAAATGTCATCTGAAGTATAG
1 CAAGCATCAATAAAGAGGCAAATGCACATGATACAATGCAAATACAAATGTCATCTAAAGTATAG
* ** *
173930 ACAAACATGAAACAATGCAAATG
66 ATATGCATGAAACGATGCAAATG
* ** * *
173953 TAAGCATCAATAAAGAGGCAAATGCACATGATATGATGCAAATACGAATGTCATCTAAAATATAG
1 CAAGCATCAATAAAGAGGCAAATGCACATGATACAATGCAAATACAAATGTCATCTAAAGTATAG
174018 ATATGCATGAAACGATGCAAATG
66 ATATGCATGAAACGATGCAAATG
* * * * * *
174041 CAAGCATCAATAAAGAGGTAAATGTACAT-ACTACAATGCAAATGCCAATGTCATTTAAAGTGTA
1 CAAGCATCAATAAAGAGGCAAATGCACATGA-TACAATGCAAATACAAATGTCATCTAAAGTATA
* * * * *
174105 GGTGTGCACGAAATGATCCAAATG
65 GATATGCATGAAACGATGCAAATG
* * * *
174129 CATGCATCAATAAAGAGGCAAATGCTCATGATGCGATGCAAAT
1 CAAGCATCAATAAAGAGGCAAATGCACATGATACAATGCAAAT
174172 GCTAATATGG
Statistics
Matches: 184, Mismatches: 32, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
87 17 0.09
88 166 0.90
89 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (88 bp):
CAAGCATCAATAAAGAGGCAAATGCACATGATACAATGCAAATACAAATGTCATCTAAAGTATAG
ATATGCATGAAACGATGCAAATG
Found at i:175183 original size:20 final size:21
Alignment explanation
Indices: 175160--175209 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
175150 ACCCTAAAAC
175160 TTCTTTTTTTCCTTT-TATT-T
1 TTCTTTTTTT-CTTTCTATTGT
*
175180 TTCTTTTTTTCTTTCTTTTGT
1 TTCTTTTTTTCTTTCTATTGT
175201 TTCTTTTTT
1 TTCTTTTTT
175210 GATTACTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 13 0.48
21 10 0.37
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (21 bp):
TTCTTTTTTTCTTTCTATTGT
Found at i:175218 original size:21 final size:21
Alignment explanation
Indices: 175179--175218 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
175169 TCCTTTTATT
** *
175179 TTTCTTTTTTTCTTTCTTTTG
1 TTTCTTTTTTGATTACTTTTG
175200 TTTCTTTTTTGATTACTTT
1 TTTCTTTTTTGATTACTTT
175219 ATCATGCTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTCTTTTTTGATTACTTTTG
Found at i:175540 original size:16 final size:16
Alignment explanation
Indices: 175521--175565 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
175511 TCATTTTATG
175521 TTTTTTTGTTTTCTTC
1 TTTTTTTGTTTTCTTC
175537 -TTTTTTGTTTTC--C
1 TTTTTTTGTTTTCTTC
*
175550 TTTTATTTGGTTTCTT
1 TTTT-TTTGTTTTCTT
175566 ATTTAGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
13 1 0.04
14 3 0.12
15 20 0.83
ACGTcount: A:0.02, C:0.11, G:0.09, T:0.78
Consensus pattern (16 bp):
TTTTTTTGTTTTCTTC
Found at i:175996 original size:20 final size:19
Alignment explanation
Indices: 175973--176047 Score: 80
Period size: 19 Copynumber: 3.8 Consensus size: 19
175963 CACACCCAGA
*
175973 TGTATCGATACATGCAGCTT
1 TGTATCGATACATG-AGCAT
**
175993 TGTATCGATACATGTTCAT
1 TGTATCGATACATGAGCAT
176012 TGTATCGATACATG-GCCAAAT
1 TGTATCGATACATGAG-C--AT
176033 TGTATCGATACATGA
1 TGTATCGATACATGA
176048 AACTGGCAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 17 0.36
20 14 0.30
21 16 0.34
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATGAGCAT
Found at i:176112 original size:13 final size:13
Alignment explanation
Indices: 176091--176121 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
176081 CGATACATGG
*
176091 TACAATGTATCGA
1 TACATTGTATCGA
176104 TACATTGTATCGA
1 TACATTGTATCGA
176117 TACAT
1 TACAT
176122 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:176117 original size:33 final size:32
Alignment explanation
Indices: 176075--176141 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
176065 CTATCACTAT
176075 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
176108 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
176141 T
1 T
176142 AGCATGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:182287 original size:13 final size:13
Alignment explanation
Indices: 182269--182296 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
182259 AAAACCCAGA
182269 TGTATCGATACAT
1 TGTATCGATACAT
182282 TGTATCGATACAT
1 TGTATCGATACAT
182295 TG
1 TG
182297 GGTACTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:184761 original size:13 final size:13
Alignment explanation
Indices: 184743--184769 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
184733 ACATGCTGCT
184743 TTGTATCGATACA
1 TTGTATCGATACA
184756 TTGTATCGATACA
1 TTGTATCGATACA
184769 T
1 T
184770 ATTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:184876 original size:13 final size:13
Alignment explanation
Indices: 184855--184885 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
184845 CGATACATGG
*
184855 TACAATGTATCGA
1 TACATTGTATCGA
184868 TACATTGTATCGA
1 TACATTGTATCGA
184881 TACAT
1 TACAT
184886 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:184881 original size:33 final size:32
Alignment explanation
Indices: 184839--184905 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
184829 CTATCACTAT
184839 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
184872 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
184905 T
1 T
184906 AGCATGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:184963 original size:13 final size:13
Alignment explanation
Indices: 184945--184970 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
184935 TTCAAATCAA
184945 TGTATCGATACAT
1 TGTATCGATACAT
184958 TGTATCGATACAT
1 TGTATCGATACAT
184971 AGCTACGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:188838 original size:20 final size:20
Alignment explanation
Indices: 188815--188888 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
188805 ACAATTCAAA
188815 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
188835 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
188856 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
188876 GTATCGATACATG
1 GTATCGATACATG
188889 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:188859 original size:21 final size:21
Alignment explanation
Indices: 188833--188908 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
188823 ACATGTTGCA
188833 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
188854 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
188874 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
188895 ATGTATCGATACAT
1 ATGTATCGATACAT
188909 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:188866 original size:41 final size:41
Alignment explanation
Indices: 188815--188908 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
188805 ACAATTCAAA
188815 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
188856 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
188897 GTATCGATACAT
1 GTATCGATACAT
188909 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:188965 original size:13 final size:13
Alignment explanation
Indices: 188947--188972 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
188937 TACAGCAAGT
188947 ATGTATCGATACA
1 ATGTATCGATACA
188960 ATGTATCGATACA
1 ATGTATCGATACA
188973 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:191206 original size:21 final size:21
Alignment explanation
Indices: 191173--191217 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
191163 TTGCAAGTTG
*
191173 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
191195 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
191215 AAA
1 AAA
191218 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:193041 original size:15 final size:15
Alignment explanation
Indices: 193021--193051 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
193011 TAAAAATGTC
*
193021 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
193036 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
193051 C
1 C
193052 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:195145 original size:20 final size:20
Alignment explanation
Indices: 195066--195145 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
195056 AATGTCCAAA
*
195066 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
195086 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
195111 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
195131 TTGTATCGATACATT
1 ATGTATCGATACATT
195146 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:195149 original size:13 final size:13
Alignment explanation
Indices: 195131--195169 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
195121 ACATTTTTCT
195131 TTGTATCGATACA
1 TTGTATCGATACA
195144 TTGTATCGATACA
1 TTGTATCGATACA
*
195157 CTGTATCGATACA
1 TTGTATCGATACA
195170 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:197642 original size:20 final size:20
Alignment explanation
Indices: 197619--197692 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
197609 ACAATTCAAA
197619 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
197639 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
197660 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
197680 GTATCGATACATG
1 GTATCGATACATG
197693 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:197663 original size:21 final size:21
Alignment explanation
Indices: 197637--197712 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
197627 ACATGTTGCA
197637 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
197658 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
197678 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
197699 ATGTATCGATACAT
1 ATGTATCGATACAT
197713 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:197670 original size:41 final size:41
Alignment explanation
Indices: 197619--197712 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
197609 ACAATTCAAA
197619 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
197660 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
197701 GTATCGATACAT
1 GTATCGATACAT
197713 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:197769 original size:13 final size:13
Alignment explanation
Indices: 197751--197776 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
197741 TACAGCAAGT
197751 ATGTATCGATACA
1 ATGTATCGATACA
197764 ATGTATCGATACA
1 ATGTATCGATACA
197777 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:198995 original size:34 final size:34
Alignment explanation
Indices: 198951--199019 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
198941 CGATTCGATG
* *
198951 ACTACTTAGGACTCGATTAAAGGGAAATTACCAA
1 ACTACCTAGGACTCAATTAAAGGGAAATTACCAA
** *
198985 ACTACCTAGGACTCAATTCTAGTGAAATTACCAA
1 ACTACCTAGGACTCAATTAAAGGGAAATTACCAA
199019 A
1 A
199020 ATATCCCTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (34 bp):
ACTACCTAGGACTCAATTAAAGGGAAATTACCAA
Found at i:200750 original size:20 final size:20
Alignment explanation
Indices: 200725--200778 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
200715 GTATCGATAC
**
200725 AATGTATCGATACATGACTA
1 AATGTATCGATACATGAAAA
*
200745 AATGTATCGATACTTGAAAA
1 AATGTATCGATACATGAAAA
200765 AATGTATCGATACA
1 AATGTATCGATACA
200779 AGTCATTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:200866 original size:33 final size:32
Alignment explanation
Indices: 200810--200877 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
200800 GTAGCTAAAT
*
200810 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
200842 TTGTATTGATACATCACAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
200875 TTG
1 TTG
200878 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 12 0.36
33 21 0.64
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:207495 original size:20 final size:21
Alignment explanation
Indices: 207463--207514 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
207453 CCCCTAGGCA
*
207463 GCACCCACCAGGTCGCGACC-G
1 GCACCC-CCAGGTCGCAACCGG
207484 GCACCCCCAGGTCGCAACCGG
1 GCACCCCCAGGTCGCAACCGG
207505 GCAGCCCCCA
1 GCA-CCCCCA
207515 CACTAGCAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.43
21 10 0.36
22 6 0.21
ACGTcount: A:0.19, C:0.50, G:0.27, T:0.04
Consensus pattern (21 bp):
GCACCCCCAGGTCGCAACCGG
Found at i:208946 original size:22 final size:23
Alignment explanation
Indices: 208921--208966 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
208911 CGAAATTGTT
208921 AAATTATTTT-ACTAAAGGGGAG
1 AAATTATTTTGACTAAAGGGGAG
* * *
208943 AAATTTTTTTGATTAAGGGGGAG
1 AAATTATTTTGACTAAAGGGGAG
208966 A
1 A
208967 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (23 bp):
AAATTATTTTGACTAAAGGGGAG
Found at i:209558 original size:20 final size:20
Alignment explanation
Indices: 209533--209586 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
209523 GTATCGATAC
**
209533 AATGTATCGATACATGACTA
1 AATGTATCGATACATGAAAA
*
209553 AATGTATCGATACTTGAAAA
1 AATGTATCGATACATGAAAA
209573 AATGTATCGATACA
1 AATGTATCGATACA
209587 AGTCATTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:209656 original size:13 final size:13
Alignment explanation
Indices: 209638--209663 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
209628 ACACACAATA
209638 TGTATCGATACAT
1 TGTATCGATACAT
209651 TGTATCGATACAT
1 TGTATCGATACAT
209664 CACAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:209674 original size:33 final size:32
Alignment explanation
Indices: 209618--209685 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 32
209608 GTAGCTAAAT
*
209618 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
209650 TTGTATCGATACATCACAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
209683 TTG
1 TTG
209686 GCTTGTAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.38
33 21 0.62
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:214214 original size:61 final size:60
Alignment explanation
Indices: 214098--214214 Score: 139
Period size: 61 Copynumber: 1.9 Consensus size: 60
214088 CATAAAATAG
* * * * *
214098 TAAAATAACAATGGAAATAAATTAAAGTAAATAACATGGACATGGAATAATAAAATGAAA
1 TAAAATAACAATGAAAATAAACTAAAGTAAAAAACATGAACATGAAATAATAAAATGAAA
*
214158 TAAAATAACAATGAAAAATAAACTAGAGTAAAAAAACATGAACAT-AAAGTAA-AAAAT
1 TAAAATAACAATG-AAAATAAACTAAAGT-AAAAAACATGAACATGAAA-TAATAAAAT
214215 ATAACATCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
60 13 0.27
61 19 0.40
62 16 0.33
ACGTcount: A:0.63, C:0.06, G:0.11, T:0.20
Consensus pattern (60 bp):
TAAAATAACAATGAAAATAAACTAAAGTAAAAAACATGAACATGAAATAATAAAATGAAA
Found at i:214840 original size:155 final size:163
Alignment explanation
Indices: 214597--214972 Score: 417
Period size: 155 Copynumber: 2.3 Consensus size: 163
214587 TAATAAAAAG
* * * * * * * *
214597 TTAAATAGAACATAAGCTTAAACATAAATAATAAAACATCACGTAAAACATTAATAGCTCAAAGT
1 TTAAATAGAATATAAACATAAAAAT-AACAATAAAACATCACTTAAAACATTAATAGCTAAAAGC
* * *
214662 TTGGCCACCCAAAAAGGTCATTACAACCTTGGCTCAAACAT-TC-C-A-TAATCTTAAGCTTAAA
65 TTGGCCACCCAAAAAGGTCATTACAACCTTAGCACAAACATCTCACTACTAAGCTTAAGCTTAAA
*
214723 ATCATCAAGCTTACAAT-TAA-AAATAA-AAAT-
130 ATCATCAAACTTACAATATAATAAATAACAAATA
* * *
214753 TTAAGTGGAATATAAACATAAACATAACAATAAAACATCACTTAAAACATTAATAGCTAAAAGCT
1 TTAAATAGAATATAAACATAAAAATAACAATAAAACATCACTTAAAACATTAATAGCTAAAAGCT
* ** * *
214818 TGGCTACCCTGAAAGGTTATTACAACCTTAGCACAAGCATCCTCTAAGCTTAAGCTTAAGCTTAA
66 TGGCCACCCAAAAAGGTCATTACAACCTTAGCACAAACAT-CTC--A-C-T-A-C-TAAGCTTAA
*
214883 GCTTAGAATCATCAAACTTACAATAATAATAAATAACAAATA
123 GCTTAAAATCATCAAACTTACAAT-ATAATAAATAACAAATA
214925 TTAAATAGAATATAAACATAAAAATAACAATAAAACATCACTTAAAAC
1 TTAAATAGAATATAAACATAAAAATAACAATAAAACATCACTTAAAAC
214973 GATAGCTCAA
Statistics
Matches: 181, Mismatches: 22, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
155 69 0.38
156 20 0.11
157 2 0.01
161 1 0.01
164 1 0.01
167 30 0.17
169 3 0.02
170 6 0.03
171 4 0.02
172 45 0.25
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.26
Consensus pattern (163 bp):
TTAAATAGAATATAAACATAAAAATAACAATAAAACATCACTTAAAACATTAATAGCTAAAAGCT
TGGCCACCCAAAAAGGTCATTACAACCTTAGCACAAACATCTCACTACTAAGCTTAAGCTTAAAA
TCATCAAACTTACAATATAATAAATAACAAATA
Found at i:214871 original size:6 final size:6
Alignment explanation
Indices: 214862--214887 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
214852 AAGCATCCTC
214862 TAAGCT TAAGCT TAAGCT TAAGCT TA
1 TAAGCT TAAGCT TAAGCT TAAGCT TA
214888 GAATCATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (6 bp):
TAAGCT
Found at i:218304 original size:21 final size:21
Alignment explanation
Indices: 218255--218304 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
218245 AAGTATGTTA
*
218255 TTTATTAATTATTTAATTAATT
1 TTTATT-ATTATTTAAATAATT
*
218277 TTT-TTATTTTTTAAATAATT
1 TTTATTATTATTTAAATAATT
218297 TTTATTAT
1 TTTATTAT
218305 AAAATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 16 0.64
21 6 0.24
22 3 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATTATTATTTAAATAATT
Found at i:218751 original size:10 final size:9
Alignment explanation
Indices: 218734--218760 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
218724 ATATGTTTGA
218734 TATTTTTTT
1 TATTTTTTT
218743 TATTTTTTT
1 TATTTTTTT
218752 TATTTTTTT
1 TATTTTTTT
218761 GACCAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TATTTTTTT
Found at i:218926 original size:16 final size:16
Alignment explanation
Indices: 218905--218936 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
218895 AATTAGAATA
*
218905 TAATTTAATAATAATT
1 TAATTTAACAATAATT
218921 TAATTTAACAATAATT
1 TAATTTAACAATAATT
218937 AAAGATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATTTAACAATAATT
Found at i:219894 original size:79 final size:81
Alignment explanation
Indices: 219805--219963 Score: 286
Period size: 80 Copynumber: 2.0 Consensus size: 81
219795 TTATTTGGTG
219805 TAAAAAAATTTAATCATTAAATATAT-AAAAAATAATATTTTTAATTGATATAATTAAGATATTA
1 TAAAAAAATTTAATCATTAAATATATCAAAAAATAATATTTTTAATTGATATAATTAAGATATTA
219869 TATTGA-TTAAAATTA
66 TATTGATTTAAAATTA
* *
219884 TAAAACAATTTAATCATTAAATATATCAAAAAATAATATTTTTAATTGATATCATTAAGATATTA
1 TAAAAAAATTTAATCATTAAATATATCAAAAAATAATATTTTTAATTGATATAATTAAGATATTA
219949 TATTGATTTAAAATT
66 TATTGATTTAAAATT
219964 TTATATGCAT
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
79 25 0.33
80 43 0.57
81 8 0.11
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (81 bp):
TAAAAAAATTTAATCATTAAATATATCAAAAAATAATATTTTTAATTGATATAATTAAGATATTA
TATTGATTTAAAATTA
Found at i:221972 original size:2 final size:2
Alignment explanation
Indices: 221965--221990 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
221955 TTGAATGTGC
221965 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
221991 TTGCTAAATA
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:224592 original size:14 final size:14
Alignment explanation
Indices: 224573--224625 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
224563 AATTAATATT
224573 TAAAATATATTTAA
1 TAAAATATATTTAA
*
224587 TAAAATA-AATT--
1 TAAAATATATTTAA
*
224598 TAAAATACATTTAA
1 TAAAATATATTTAA
224612 TAAAATATATTTAA
1 TAAAATATATTTAA
224626 AACCGAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 7 0.21
12 3 0.09
13 3 0.09
14 20 0.61
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAAATATATTTAA
Found at i:224602 original size:25 final size:25
Alignment explanation
Indices: 224561--224627 Score: 98
Period size: 25 Copynumber: 2.6 Consensus size: 25
224551 TTGAAATAAC
* *
224561 TAAATTAATATTTAAAATATATTTAA
1 TAAAATAA-ATTTAAAATACATTTAA
224587 TAAAATAAATTTAAAATACATTTAA
1 TAAAATAAATTTAAAATACATTTAA
*
224612 TAAAATATATTTAAAA
1 TAAAATAAATTTAAAA
224628 CCGAAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
25 31 0.82
26 7 0.18
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (25 bp):
TAAAATAAATTTAAAATACATTTAA
Found at i:231380 original size:22 final size:20
Alignment explanation
Indices: 231336--231384 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
231326 AAAATTTAAT
*
231336 ATATAAAAAAATTATATAAA
1 ATATAAAAAAATTAGATAAA
*
231356 ATATAAAATAAATTAAGATATA
1 ATATAAAA-AAATT-AGATAAA
231378 ATATAAA
1 ATATAAA
231385 TACAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.32
21 5 0.20
22 12 0.48
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
ATATAAAAAAATTAGATAAA
Found at i:231788 original size:8 final size:8
Alignment explanation
Indices: 231775--231800 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
231765 TTAATATGTA
231775 AAAAATAT
1 AAAAATAT
231783 AAAAATAT
1 AAAAATAT
231791 AAAAATAT
1 AAAAATAT
231799 AA
1 AA
231801 TATTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAATAT
Found at i:232247 original size:19 final size:18
Alignment explanation
Indices: 232207--232259 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
232197 ATGAATTGAG
* * *
232207 ATATAATACAAACTTAAC
1 ATATAATAAAAAATTAAA
232225 ATATATATAAAAAATTAAA
1 ATATA-ATAAAAAATTAAA
232244 ATATAACATAAAAAAT
1 ATAT-A-ATAAAAAAT
232260 AATAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 5 0.17
19 14 0.48
20 10 0.34
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (18 bp):
ATATAATAAAAAATTAAA
Found at i:232475 original size:22 final size:22
Alignment explanation
Indices: 232450--232501 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
232440 TACATAAAAT
232450 AAAATAAAT-TATTAATATATAA
1 AAAATAAATAT-TTAATATATAA
**
232472 AAAATATAATATTTTGTATATAA
1 AAAATA-AATATTTAATATATAA
232495 AAAATAA
1 AAAATAA
232502 CATAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 7 0.27
23 18 0.69
24 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
AAAATAAATATTTAATATATAA
Found at i:232540 original size:4 final size:4
Alignment explanation
Indices: 232533--232561 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
232523 TTTTTTTCTC
232533 CTTT CTTT CTTT CTTT -TTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
232562 CAGTTGCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:232739 original size:14 final size:14
Alignment explanation
Indices: 232720--232746 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
232710 ATTTAAAATT
232720 AAAATAAAAATATA
1 AAAATAAAAATATA
232734 AAAATAAAAATAT
1 AAAATAAAAATAT
232747 TTATAAATAT
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATAAAAATATA
Found at i:232975 original size:2 final size:2
Alignment explanation
Indices: 232968--233006 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
232958 ATAGGGTGGA
*
232968 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
233007 TCTGAAGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:239150 original size:22 final size:22
Alignment explanation
Indices: 239125--239178 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
239115 TAAATTTTTT
* *
239125 TATTTGAGTTAATTAAGTTTGA
1 TATTTAAGTTAATTAAGTTTAA
*
239147 TATTTAAATTAATTAAGTTTAA
1 TATTTAAGTTAATTAAGTTTAA
239169 TATTTAAGTT
1 TATTTAAGTT
239179 GATTCACTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (22 bp):
TATTTAAGTTAATTAAGTTTAA
Found at i:240850 original size:208 final size:208
Alignment explanation
Indices: 240492--241116 Score: 1250
Period size: 208 Copynumber: 3.0 Consensus size: 208
240482 GAATGGAAGC
240492 TGATGAGCTGAAAGTGAGAGTTGAAATACAAAAGGGAGTAAAGCCAAGAAAGAAGAAGCTACTGA
1 TGATGAGCTGAAAGTGAGAGTTGAAATACAAAAGGGAGTAAAGCCAAGAAAGAAGAAGCTACTGA
240557 AGCAAGAGCTGAAGAATGATGAGCTGAAGTTGGCTAGAAAATTATTCTCTAAATTCTCTTTCAAT
66 AGCAAGAGCTGAAGAATGATGAGCTGAAGTTGGCTAGAAAATTATTCTCTAAATTCTCTTTCAAT
240622 TCTTTTCTTTTCTGGTCTATCTTTTTCTTTTTTCTTCAATTTCTGATCTAAACATCACTTCAGCT
131 TCTTTTCTTTTCTGGTCTATCTTTTTCTTTTTTCTTCAATTTCTGATCTAAACATCACTTCAGCT
240687 ATTGTCATTGTTA
196 ATTGTCATTGTTA
240700 TGATGAGCTGAAAGTGAGAGTTGAAATACAAAAGGGAGTAAAGCCAAGAAAGAAGAAGCTACTGA
1 TGATGAGCTGAAAGTGAGAGTTGAAATACAAAAGGGAGTAAAGCCAAGAAAGAAGAAGCTACTGA
240765 AGCAAGAGCTGAAGAATGATGAGCTGAAGTTGGCTAGAAAATTATTCTCTAAATTCTCTTTCAAT
66 AGCAAGAGCTGAAGAATGATGAGCTGAAGTTGGCTAGAAAATTATTCTCTAAATTCTCTTTCAAT
240830 TCTTTTCTTTTCTGGTCTATCTTTTTCTTTTTTCTTCAATTTCTGATCTAAACATCACTTCAGCT
131 TCTTTTCTTTTCTGGTCTATCTTTTTCTTTTTTCTTCAATTTCTGATCTAAACATCACTTCAGCT
240895 ATTGTCATTGTTA
196 ATTGTCATTGTTA
240908 TGATGAGCTGAAAGTGAGAGTTGAAATACAAAAGGGAGTAAAGCCAAGAAAGAAGAAGCTACTGA
1 TGATGAGCTGAAAGTGAGAGTTGAAATACAAAAGGGAGTAAAGCCAAGAAAGAAGAAGCTACTGA
240973 AGCAAGAGCTGAAGAATGATGAGCTGAAGTTGGCTAGAAAATTATTCTCTAAATTCTCTTTCAAT
66 AGCAAGAGCTGAAGAATGATGAGCTGAAGTTGGCTAGAAAATTATTCTCTAAATTCTCTTTCAAT
241038 TCTTTTCTTTTCTGGTCTATCTTTTTCTTTTTTCTTCAATTTCTGATCTAAACATCACTTCAGCT
131 TCTTTTCTTTTCTGGTCTATCTTTTTCTTTTTTCTTCAATTTCTGATCTAAACATCACTTCAGCT
241103 ATTGTCATTGTTA
196 ATTGTCATTGTTA
241116 T
1 T
241117 TCTATGATAG
Statistics
Matches: 417, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
208 417 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (208 bp):
TGATGAGCTGAAAGTGAGAGTTGAAATACAAAAGGGAGTAAAGCCAAGAAAGAAGAAGCTACTGA
AGCAAGAGCTGAAGAATGATGAGCTGAAGTTGGCTAGAAAATTATTCTCTAAATTCTCTTTCAAT
TCTTTTCTTTTCTGGTCTATCTTTTTCTTTTTTCTTCAATTTCTGATCTAAACATCACTTCAGCT
ATTGTCATTGTTA
Found at i:251344 original size:33 final size:33
Alignment explanation
Indices: 251307--251373 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
251297 TTCAACGATT
251307 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
251340 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
251373 T
1 T
251374 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:251345 original size:13 final size:13
Alignment explanation
Indices: 251327--251351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
251317 CATAAAATGT
251327 TGTATCGATACAA
1 TGTATCGATACAA
251340 TGTATCGATACA
1 TGTATCGATACA
251352 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:251434 original size:13 final size:13
Alignment explanation
Indices: 251416--251440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
251406 ATTACTCACA
251416 TGTATCGATACAT
1 TGTATCGATACAT
251429 TGTATCGATACA
1 TGTATCGATACA
251441 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:251577 original size:52 final size:52
Alignment explanation
Indices: 251449--251569 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
251439 CACTGATCTT
*
251449 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
251501 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
251553 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
251570 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:256626 original size:27 final size:27
Alignment explanation
Indices: 256571--256631 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
256561 AAAAGCGAGG
* ** **
256571 TTGGAGTATCCCCTCGAAAGGATGGGA
1 TTGGAGTATCCCCTCAAAAAAATAAGA
256598 TTGGAGTATCCCCTCAAAAAAATAAGA
1 TTGGAGTATCCCCTCAAAAAAATAAGA
*
256625 TTAGAGT
1 TTGGAGT
256632 GTCCTCGCTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (27 bp):
TTGGAGTATCCCCTCAAAAAAATAAGA
Found at i:263528 original size:42 final size:42
Alignment explanation
Indices: 263469--263578 Score: 184
Period size: 42 Copynumber: 2.6 Consensus size: 42
263459 AAGAGAAAGA
* * *
263469 AGAGAGATGAGGAATGATAGGAGGAGAGACAGGAGAGATAGT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
263511 AGAGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
263553 AGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGAGAGGAGGGATGATAGGAGGAG
263579 GAGAGAAGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.11
Consensus pattern (42 bp):
AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
Found at i:263562 original size:18 final size:18
Alignment explanation
Indices: 263535--263584 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
263525 TGATAGGAGG
*
263535 AGAGACAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
263553 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
263571 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
263585 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.44, C:0.02, G:0.46, T:0.08
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:269094 original size:20 final size:21
Alignment explanation
Indices: 269056--269095 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
269046 GCTAGTGTGG
* *
269056 GGACTGCCCGGTTGTGACCTA
1 GGACTGCCCGGTCGCGACCTA
269077 GGACTG-CCGGTCGCGACCT
1 GGACTGCCCGGTCGCGACCT
269096 GGTGGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.12, C:0.33, G:0.35, T:0.20
Consensus pattern (21 bp):
GGACTGCCCGGTCGCGACCTA
Found at i:269556 original size:13 final size:12
Alignment explanation
Indices: 269538--269575 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
269528 ATAATCCCCC
269538 TGTATCGATACA
1 TGTATCGATACA
269550 GTGTATCGATACA
1 -TGTATCGATACA
269563 TGGTATCGATACA
1 T-GTATCGATACA
269576 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 1 0.04
13 23 0.96
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:273431 original size:20 final size:19
Alignment explanation
Indices: 273382--273431 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
273372 TTATATCATG
273382 AAAATATAATTAATATTTT
1 AAAATATAATTAATATTTT
*
273401 AAATTTATAATTAAT-TTATT
1 AAA-ATATAATTAATATT-TT
273421 AAAATACTAAT
1 AAAATA-TAAT
273432 AGAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAATATAATTAATATTTT
Found at i:276172 original size:13 final size:13
Alignment explanation
Indices: 276136--276174 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
276126 AAATAAATCA
276136 AATATAATAATAAT
1 AATATAA-AATAAT
276150 AATA-ATAAATAAT
1 AATATA-AAATAAT
276163 AATATAAAATAA
1 AATATAAAATAA
276175 ATAGAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATATAAAATAAT
Found at i:277087 original size:16 final size:16
Alignment explanation
Indices: 277063--277135 Score: 53
Period size: 16 Copynumber: 4.7 Consensus size: 16
277053 TATATAATTT
*
277063 TATTAAATATTTATCA
1 TATTTAATATTTATCA
*
277079 TATTTAATA-TCATACA
1 TATTTAATATTTAT-CA
* *
277095 TA-TTAAAAATTAT-A
1 TATTTAATATTTATCA
**
277109 TATTTAATATTTAAAA
1 TATTTAATATTTATCA
*
277125 TTTTTAATATT
1 TATTTAATATT
277136 ATTAATTAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
14 3 0.07
15 16 0.36
16 26 0.58
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTTAATATTTATCA
Found at i:277957 original size:11 final size:11
Alignment explanation
Indices: 277941--277999 Score: 55
Period size: 11 Copynumber: 4.9 Consensus size: 11
277931 AACTAAATTA
277941 ATATTTAAAAT
1 ATATTTAAAAT
277952 ATATTTAATAAAAT
1 ATA-TT--TAAAAT
*
277966 AAATTTAAAAT
1 ATATTTAAAAT
*
277977 ACATTTAATAAAT
1 ATATTT-A-AAAT
277990 ATATTTAAAA
1 ATATTTAAAA
278000 CCGAAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
11 17 0.43
12 4 0.10
13 11 0.28
14 8 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
ATATTTAAAAT
Found at i:277965 original size:14 final size:14
Alignment explanation
Indices: 277946--277997 Score: 58
Period size: 13 Copynumber: 4.0 Consensus size: 14
277936 AATTAATATT
277946 TAAAATATATTTAA
1 TAAAATATATTTAA
*
277960 TAAAATA-AATT--
1 TAAAATATATTTAA
*
277971 TAAAATACATTTAA
1 TAAAATATATTTAA
277985 T-AAATATATTTAA
1 TAAAATATATTTAA
277998 AACCGAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 7 0.22
12 3 0.09
13 14 0.44
14 8 0.25
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAAATATATTTAA
Found at i:277971 original size:25 final size:25
Alignment explanation
Indices: 277934--277999 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
277924 ATGAAATAAC
* *
277934 TAAATTAATATTTAAAATATATTTAA
1 TAAAATAA-ATTTAAAATACATTTAA
277960 TAAAATAAATTTAAAATACATTTAA
1 TAAAATAAATTTAAAATACATTTAA
*
277985 T-AAATATATTTAAAA
1 TAAAATAAATTTAAAA
278000 CCGAAAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 13 0.35
25 17 0.46
26 7 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
TAAAATAAATTTAAAATACATTTAA
Found at i:277995 original size:24 final size:25
Alignment explanation
Indices: 277941--277999 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
277931 AACTAAATTA
*
277941 ATATTTAAAATATATTTAATAAAAT
1 ATATTTAAAATACATTTAATAAAAT
*
277966 AAATTTAAAATACATTTAAT-AAAT
1 ATATTTAAAATACATTTAATAAAAT
277990 ATATTTAAAA
1 ATATTTAAAA
278000 CCGAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
24 13 0.42
25 18 0.58
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
ATATTTAAAATACATTTAATAAAAT
Found at i:280363 original size:21 final size:22
Alignment explanation
Indices: 280323--280369 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
280313 AAAATACAAC
** *
280323 AAAATTAT-AAAATTTTTAAAT
1 AAAATTATAAAAATAGTAAAAT
280344 AAAATTATAAAAATAGTAAAAT
1 AAAATTATAAAAATAGTAAAAT
280366 AAAA
1 AAAA
280370 AATCTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAATTATAAAAATAGTAAAAT
Found at i:285599 original size:19 final size:18
Alignment explanation
Indices: 285559--285621 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 18
285549 ATGAATTGAG
* * *
285559 ATATAATACAAACTTAAC
1 ATATAATAAAAAATTAAA
285577 ATATATATAAAAAATTAAA
1 ATATA-ATAAAAAATTAAA
285596 ATATAACATAAAAAATAATAAA
1 ATAT-A-ATAAAAAAT--TAAA
285618 ATAT
1 ATAT
285622 GGTACGAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.14
19 14 0.38
20 10 0.27
22 8 0.22
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
ATATAATAAAAAATTAAA
Found at i:285826 original size:22 final size:22
Alignment explanation
Indices: 285801--285852 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
285791 TACATAAAAT
285801 AAAATAAAT-TATTAATATATAA
1 AAAATAAATAT-TTAATATATAA
**
285823 AAAATATAATATTTTGTATATAA
1 AAAATA-AATATTTAATATATAA
285846 AAAATAA
1 AAAATAA
285853 CATAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 7 0.27
23 18 0.69
24 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
AAAATAAATATTTAATATATAA
Found at i:285892 original size:4 final size:4
Alignment explanation
Indices: 285883--285911 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
285873 TTTTTTTCTC
285883 CTTT CTTT CTTT CTTT -TTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
285912 CAGTTGCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:286088 original size:14 final size:14
Alignment explanation
Indices: 286069--286095 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
286059 ATTTAAAATT
286069 AAAATAAAAATATA
1 AAAATAAAAATATA
286083 AAAATAAAAATAT
1 AAAATAAAAATAT
286096 TTATAAATAT
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATAAAAATATA
Found at i:286324 original size:2 final size:2
Alignment explanation
Indices: 286317--286351 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
286307 ATAGGGTGGA
*
286317 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
286352 TCTGAAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:292496 original size:22 final size:22
Alignment explanation
Indices: 292471--292521 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
292461 AATTTTTTTT
* *
292471 TATTTGAATTAATTAAGTTTGA
1 TATTTAAATTAATTAAGTTTAA
292493 TATTTAAATTAATTAAGTTTAA
1 TATTTAAATTAATTAAGTTTAA
292515 TATTTAA
1 TATTTAA
292522 GTTGATTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (22 bp):
TATTTAAATTAATTAAGTTTAA
Found at i:297767 original size:18 final size:19
Alignment explanation
Indices: 297741--297786 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
297731 ATAAAACATT
297741 AACAAAAATATATT-AAAA-
1 AACAAAAATA-ATTGAAAAG
*
297759 AATAAAAATAATTGAAAAG
1 AACAAAAATAATTGAAAAG
297778 AACAAAAAT
1 AACAAAAAT
297787 TTTGATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 13 0.54
19 8 0.33
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (19 bp):
AACAAAAATAATTGAAAAG
Found at i:302961 original size:3 final size:3
Alignment explanation
Indices: 302953--302978 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
302943 ATGGGGTGAT
302953 GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GA
302979 AGAAGAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:312832 original size:42 final size:42
Alignment explanation
Indices: 312771--312889 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
312761 TAGCCCTCAA
* * *
312771 AGAGAAAGAAGAGAGAGGAGGAATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
312813 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
312855 AGAGATAATAGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
312890 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.44, C:0.02, G:0.45, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:312873 original size:18 final size:18
Alignment explanation
Indices: 312846--312895 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
312836 TGATAGGAGG
*
312846 AGAGACAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
312864 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
312882 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
312896 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.44, C:0.02, G:0.46, T:0.08
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:317079 original size:40 final size:41
Alignment explanation
Indices: 317033--317123 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 41
317023 TTTTCTTTCT
*
317033 CCCTTAATTAAAG-TAATTTTAACAAATTCATACATTCTCC
1 CCCTTAATTAAAGATAATTTTAACAAATTCACACATTCTCC
* * *
317073 CCCTTAA-T-AAGATAATTTTAGCAAATTTACGCATTCTCC
1 CCCTTAATTAAAGATAATTTTAACAAATTCACACATTCTCC
* *
317112 CCTTTTATTAAA
1 CCCTTAATTAAA
317124 AAAAAAATCT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
38 3 0.07
39 29 0.69
40 8 0.19
41 2 0.05
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.38
Consensus pattern (41 bp):
CCCTTAATTAAAGATAATTTTAACAAATTCACACATTCTCC
Found at i:318401 original size:20 final size:21
Alignment explanation
Indices: 318363--318402 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
318353 GCTAGTGTGG
* *
318363 GGACTGCCCGGTTGTGACCTA
1 GGACTGCCCGGTCGCGACCTA
318384 GGACTG-CCGGTCGCGACCT
1 GGACTGCCCGGTCGCGACCT
318403 GGTGGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.12, C:0.33, G:0.35, T:0.20
Consensus pattern (21 bp):
GGACTGCCCGGTCGCGACCTA
Found at i:318863 original size:13 final size:12
Alignment explanation
Indices: 318845--318882 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
318835 ATAATCCCCC
318845 TGTATCGATACA
1 TGTATCGATACA
318857 GTGTATCGATACA
1 -TGTATCGATACA
318870 TGGTATCGATACA
1 T-GTATCGATACA
318883 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 1 0.04
13 23 0.96
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:324362 original size:13 final size:13
Alignment explanation
Indices: 324344--324368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
324334 CAATTTTTTG
324344 TGTATCGATACAT
1 TGTATCGATACAT
324357 TGTATCGATACA
1 TGTATCGATACA
324369 AGTTTGACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:327327 original size:51 final size:51
Alignment explanation
Indices: 327233--327348 Score: 151
Period size: 51 Copynumber: 2.3 Consensus size: 51
327223 TTTTTACTAT
* * * * *
327233 TTGTATCGATACATTATGGGTTTTTACCCAGATGTATCGATACATTCTTTA
1 TTGTATCGATACATTATGGGTTTTCACCCAGATATATCAATACATTATTCA
* * *
327284 TTGTATCAATACATTTTGGGTTTTCACCTAGATATATCAATACATTATTCA
1 TTGTATCGATACATTATGGGTTTTCACCCAGATATATCAATACATTATTCA
*
327335 ATGTATCGATACAT
1 TTGTATCGATACAT
327349 GCAGGCATAT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (51 bp):
TTGTATCGATACATTATGGGTTTTCACCCAGATATATCAATACATTATTCA
Found at i:331924 original size:15 final size:15
Alignment explanation
Indices: 331904--331990 Score: 75
Period size: 15 Copynumber: 5.8 Consensus size: 15
331894 TGATCCTATC
331904 CATCCACCACCTGTT
1 CATCCACCACCTGTT
* *
331919 CATCCACCATCTATT
1 CATCCACCACCTGTT
* **
331934 CATCCATCACCCATT
1 CATCCACCACCTGTT
*
331949 CATCCACCATCTGTT
1 CATCCACCACCTGTT
* * * *
331964 TATTCATCACCCGTT
1 CATCCACCACCTGTT
*
331979 CATCTACCACCT
1 CATCCACCACCT
331991 ATTTACCTTG
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 53 1.00
ACGTcount: A:0.23, C:0.43, G:0.03, T:0.31
Consensus pattern (15 bp):
CATCCACCACCTGTT
Found at i:331939 original size:30 final size:30
Alignment explanation
Indices: 331899--331993 Score: 109
Period size: 30 Copynumber: 3.2 Consensus size: 30
331889 ACAACTGATC
* * *
331899 CTATCCATCCACCACCTGTTCATCCACCAT
1 CTATTCATCCATCACCCGTTCATCCACCAT
*
331929 CTATTCATCCATCACCCATTCATCCACCAT
1 CTATTCATCCATCACCCGTTCATCCACCAT
* * * * *
331959 CTGTTTATTCATCACCCGTTCATCTACCAC
1 CTATTCATCCATCACCCGTTCATCCACCAT
331989 CTATT
1 CTATT
331994 TACCTTGCTT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.23, C:0.41, G:0.03, T:0.33
Consensus pattern (30 bp):
CTATTCATCCATCACCCGTTCATCCACCAT
Found at i:332491 original size:9 final size:8
Alignment explanation
Indices: 332479--332536 Score: 50
Period size: 9 Copynumber: 7.1 Consensus size: 8
332469 ATAAAACTAA
332479 TTATTATAT
1 TTATTA-AT
332488 TTA-TAAT
1 TTATTAAT
*
332495 GTTATTATT
1 -TTATTAAT
332504 CTTATTAAT
1 -TTATTAAT
332513 TT-TTAA-
1 TTATTAAT
332519 TTATTATAT
1 TTATTA-AT
332528 TTATTAAT
1 TTATTAAT
332536 T
1 T
332537 CTTTTCAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
6 2 0.05
7 9 0.22
8 11 0.27
9 19 0.46
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (8 bp):
TTATTAAT
Found at i:332607 original size:17 final size:16
Alignment explanation
Indices: 332579--332632 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
332569 AAAATAGCAT
332579 TATAAATTAATAAGAA
1 TATAAATTAATAAGAA
*
332595 TATAAATTTAATAAAAA
1 TATAAA-TTAATAAGAA
* *
332612 TAAAAAATTAATAAGCA
1 T-ATAAATTAATAAGAA
332629 TATA
1 TATA
332633 TTTTTTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 8 0.26
17 19 0.61
18 4 0.13
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (16 bp):
TATAAATTAATAAGAA
Found at i:333117 original size:29 final size:29
Alignment explanation
Indices: 333062--333126 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
333052 CCCATGTGAC
*
333062 AAAATAACAGTATTTTGATAAAATATTTT
1 AAAATAACAGTATTTTGATAAAATATTTA
* **
333091 AAAATAACATTATTTT-AGTAATTTATTTA
1 AAAATAACAGTATTTTGA-TAAAATATTTA
333120 AAAATAA
1 AAAATAA
333127 GAGGTTGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.42
Consensus pattern (29 bp):
AAAATAACAGTATTTTGATAAAATATTTA
Found at i:333760 original size:19 final size:19
Alignment explanation
Indices: 333736--333780 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
333726 ACTGAAATTT
*
333736 AAATTATTATTTAATAAAA
1 AAATTATAATTTAATAAAA
* *
333755 AAATTA-AATTTAATTATA
1 AAATTATAATTTAATAAAA
333773 AAATTATA
1 AAATTATA
333781 TAAATATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTATAATTTAATAAAA
Found at i:334344 original size:32 final size:32
Alignment explanation
Indices: 334274--334345 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 32
334264 GGGTTCAGGC
* * **
334274 CTATTT-GGATTCGAAACTTTTCGAGTTTAGG
1 CTATTTCGGATTCGAAACTTTTCAAGTTCAAA
*
334305 C-ATTTTCGGATTCGAACCTTTTCAAGTTCAAA
1 CTA-TTTCGGATTCGAAACTTTTCAAGTTCAAA
334337 CTATTTCGG
1 CTATTTCGG
334346 GCTTAAGTCG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
30 1 0.03
31 4 0.12
32 27 0.82
33 1 0.03
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (32 bp):
CTATTTCGGATTCGAAACTTTTCAAGTTCAAA
Found at i:335288 original size:22 final size:22
Alignment explanation
Indices: 335235--335278 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
335225 TAAAGCTCAT
335235 GATATAATTTACTTTTTAATAA
1 GATATAATTTACTTTTTAATAA
*
335257 GATATAATTTACTTTTTGATAA
1 GATATAATTTACTTTTTAATAA
335279 ATTACTATTT
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:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (22 bp):
GATATAATTTACTTTTTAATAA
Found at i:335545 original size:15 final size:15
Alignment explanation
Indices: 335527--335560 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
335517 GTTCGAACTA
*
335527 TTTAAAATCAAATTT
1 TTTAAAATAAAATTT
*
335542 TTTAAATTAAAATTT
1 TTTAAAATAAAATTT
335557 TTTA
1 TTTA
335561 TTTTTTATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAAAATAAAATTT
Found at i:346057 original size:13 final size:13
Alignment explanation
Indices: 346039--346070 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
346029 CTTTGTATTG
346039 ATACATTATATCA
1 ATACATTATATCA
*
346052 ATACATTGTATCA
1 ATACATTATATCA
346065 ATACAT
1 ATACAT
346071 GGGTTACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.16, G:0.03, T:0.38
Consensus pattern (13 bp):
ATACATTATATCA
Found at i:346235 original size:20 final size:20
Alignment explanation
Indices: 346197--346236 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
346187 TTTCAAATTT
346197 CTTCATTTTCACTTCAAAATA
1 CTTCATTTTCAC-TCAAAATA
346218 CTTCATTTTTCA-TCAAAAT
1 CTTCA-TTTTCACTCAAAAT
346237 TATCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (20 bp):
CTTCATTTTCACTCAAAATA
Found at i:347982 original size:20 final size:21
Alignment explanation
Indices: 347945--347994 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
347935 TTTTAAACGA
347945 TTATCAAGGGGGAGGAAATTT
1 TTATCAAGGGGGAGGAAATTT
347966 TTATCAAGGGGGA-GAAATTT
1 TTATCAAGGGGGAGGAAATTT
347986 TTAATCAAG
1 TT-ATCAAG
347995 ACCTTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (21 bp):
TTATCAAGGGGGAGGAAATTT
Found at i:348622 original size:20 final size:20
Alignment explanation
Indices: 348578--348652 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
348568 GTATCAATAC
* **
348578 ATTGTATAGATACATGTTC-
1 ATTGTATCGATACATGCACA
348597 ATTGTATCGATACATGCACA
1 ATTGTATCGATACATGCACA
* *
348617 ATTGTATTGATACATGCATA
1 ATTGTATCGATACATGCACA
348637 ATTGTATCGATACATG
1 ATTGTATCGATACATG
348653 AAACTGGCAG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
19 16 0.33
20 33 0.67
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (20 bp):
ATTGTATCGATACATGCACA
Found at i:349158 original size:19 final size:19
Alignment explanation
Indices: 349131--349205 Score: 96
Period size: 19 Copynumber: 3.9 Consensus size: 19
349121 TGTATCGATA
*
349131 CATTGTATCGGTACATGTT
1 CATTGTATCGATACATGTT
* *
349150 CATTATATCAATACATGTT
1 CATTGTATCGATACATGTT
**
349169 CATTGTATCGATACATGGA
1 CATTGTATCGATACATGTT
349188 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
349206 AAAGTGGCAG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 32 0.67
20 16 0.33
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (19 bp):
CATTGTATCGATACATGTT
Found at i:349259 original size:20 final size:20
Alignment explanation
Indices: 349234--349307 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
349224 CTACCATTGT
*
349234 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
*
349254 TTGTATCGATACTTGATGAA
1 TTGTATCGATACATGATGAA
*
349274 TTGTATCGATACTTGATGAA
1 TTGTATCGATACATGATGAA
349294 TTGTATCGATACAT
1 TTGTATCGATACAT
349308 TGCTTGTAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
20 49 0.98
21 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:349615 original size:19 final size:19
Alignment explanation
Indices: 349588--349626 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
349578 TTTTGCTTTC
349588 ATTGCTGTTATTTTTTGAA
1 ATTGCTGTTATTTTTTGAA
*
349607 ATTGTTGTTATTTTTTGAA
1 ATTGCTGTTATTTTTTGAA
349626 A
1 A
349627 GCTCTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.59
Consensus pattern (19 bp):
ATTGCTGTTATTTTTTGAA
Found at i:354409 original size:21 final size:20
Alignment explanation
Indices: 354384--354437 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
354374 TTACAAGCCA
*
354384 ATGTATTGATACAAT-TTGGT
1 ATGTATCGATACAATCTT-GT
354404 CATGTATCGATAC-ATCTTGT
1 -ATGTATCGATACAATCTTGT
354424 ATGTATCGATACAA
1 ATGTATCGATACAA
354438 ACAGTTAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACAATCTTGT
Found at i:354525 original size:20 final size:21
Alignment explanation
Indices: 354478--354530 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
354468 GCCAATCACC
*
354478 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
*
354499 AGTATCGATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
354519 TGTATCGATACA
1 TGTATCGATACA
354531 ATGTATTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:357896 original size:21 final size:21
Alignment explanation
Indices: 357851--357896 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
357841 TTTTTGTCAA
* *
357851 AATGTATCGATACATGCCCTT
1 AATGTATCGATACAGGCCCTC
357872 AATGTATCGATACAAGGCCC-C
1 AATGTATCGATAC-AGGCCCTC
357893 AATG
1 AATG
357897 GTCAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (21 bp):
AATGTATCGATACAGGCCCTC
Found at i:357941 original size:24 final size:20
Alignment explanation
Indices: 357922--358027 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
357912 TTTTCACAAT
357922 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
357942 TTGTATCGATACATTCTGGGTTTACCCA
1 TTGTATCGATACA-T-T--G-TT---CA
* *
357970 GATATATCGATACATT-TTGCA
1 -TTGTATCGATACATTGTT-CA
*
357991 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
*
358011 TTGTATAGATACATTGT
1 TTGTATCGATACATTGT
358028 ATCGATATAT
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
20 43 0.63
21 4 0.06
22 1 0.01
23 2 0.03
24 1 0.01
25 2 0.03
27 1 0.01
28 3 0.04
29 11 0.16
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:360187 original size:80 final size:80
Alignment explanation
Indices: 360051--360252 Score: 236
Period size: 80 Copynumber: 2.5 Consensus size: 80
360041 TCTTCATCTC
* * * *
360051 GGGGATACT-CTAACCCCGATTTTATTTTCAAAATATCAATTTTTCATAATCGGGGATACTCCAA
1 GGGGATACTCCTAACCCCGATTTTATTTTCAAAACACCAATTTTTCATAATCAGGGATACCCCAA
360115 TCCC-GTTA-TTTCTGA
66 -CCCTGTTATTTTC-GA
* * * *
360130 GGGGATACTCCTAACCCTGATTTTTTTTTCAAAACACCAGTTTTTCATAATTAGGGATACCCCAA
1 GGGGATACTCCTAACCCCGATTTTATTTTCAAAACACCAATTTTTCATAATCAGGGATACCCCAA
360195 CCCTGTTATTTTCGA
66 CCCTGTTATTTTCGA
* *
360210 AGGGATACTCC-AACCCC-AGTTTTA-TTTCTAAAACACTAATTTT
1 GGGGATACTCCTAACCCCGA-TTTTATTTTC-AAAACACCAATTTT
360253 CCACAGTTGG
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
78 5 0.05
79 33 0.31
80 63 0.60
81 4 0.04
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (80 bp):
GGGGATACTCCTAACCCCGATTTTATTTTCAAAACACCAATTTTTCATAATCAGGGATACCCCAA
CCCTGTTATTTTCGA
Found at i:360273 original size:51 final size:52
Alignment explanation
Indices: 360211--360332 Score: 151
Period size: 51 Copynumber: 2.4 Consensus size: 52
360201 TATTTTCGAA
* * * *
360211 GGGATACTCCAACCCCAG-TTTTATTTCTAAAACACTAATTTTCCACAGTTG
1 GGGATACTCCAACCCCAGATTTTATTTCCAAAACACCAATTTTCCACAATCG
* * * *
360262 GGGATATTCCAA-CTCTGATTTTATTTCCAAAACACCAATTTTTCACAATCG
1 GGGATACTCCAACCCCAGATTTTATTTCCAAAACACCAATTTTCCACAATCG
360313 GGGATACTCCAACCCC-GATT
1 GGGATACTCCAACCCCAGATT
360333 ATTTCTGAGG
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
50 3 0.05
51 54 0.92
52 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (52 bp):
GGGATACTCCAACCCCAGATTTTATTTCCAAAACACCAATTTTCCACAATCG
Found at i:360294 original size:130 final size:128
Alignment explanation
Indices: 360130--360503 Score: 351
Period size: 131 Copynumber: 2.9 Consensus size: 128
360120 TTATTTCTGA
* * * * * * *
360130 GGGGATACTCCTAACCCTGATTTTTTTTTCAAAACACCAGTTTTTCATAATTAGGGATACCCCAA
1 GGGGATATTCC-AA-CCTGATTTTATTTCCAAAACACCAATTTTTCACAATCAGGGATACTCCAA
* *
360195 CCCTGTTATTTTCGAAGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATTT-TCCACAG
64 CCCTGTTATTTTCGAAGGGATACTCCAACCCC-GTTTTATTTCCAAAACACTAATTTCT-CACAA
*
360259 TT
127 TC
*
360261 GGGGATATTCCAACTCTGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATATTCCAAC-CTGATTTTATTTCCAAAACACCAATTTTTCACAATCAGGGATACTCCAAC
* * * * * * * *
360326 CCCGATTA-TTTCTGAGGGGATACTCCAATCTCGGCTTTATTTCCAAAATATTGATTTCTCACAA
65 CCTG-TTATTTTC-GAAGGGATACTCCAA-CCCCGTTTTATTTCCAAAACACTAATTTCTCACAA
360390 TC
127 TC
* *** * * * *
360392 AGGGATACTT-CAACCTCGGCCTTATTTCTAAATCATCAATTTTTCACAATCAGGGATACTGCAA
1 GGGGATA-TTCCAACCT-GATTTTATTTCCAAAACACCAATTTTTCACAATCAGGGATACTCCAA
* *
360456 CCTTGTTATTTTCG-AGGGAATACTCCAACCCCGATTTTATTTTCAAAA
64 CCCTGTTATTTTCGAAGGG-ATACTCCAACCCCG-TTTTATTTCCAAAA
360504 TATCGATTTT
Statistics
Matches: 198, Mismatches: 35, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
129 7 0.04
130 79 0.40
131 107 0.54
132 5 0.03
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (128 bp):
GGGGATATTCCAACCTGATTTTATTTCCAAAACACCAATTTTTCACAATCAGGGATACTCCAACC
CTGTTATTTTCGAAGGGATACTCCAACCCCGTTTTATTTCCAAAACACTAATTTCTCACAATC
Found at i:360398 original size:51 final size:51
Alignment explanation
Indices: 360342--360458 Score: 146
Period size: 51 Copynumber: 2.3 Consensus size: 51
360332 TATTTCTGAG
* * **
360342 GGGATACTCCAATCTCGGCTTTATTTCCAAAAT-ATTGATTTCTCACAATCA
1 GGGATACTCCAACCTCGGCCTTATTT-CAAAATCATCAATTTCTCACAATCA
* * *
360393 GGGATACTTCAACCTCGGCCTTATTTCTAAATCATCAATTTTTCACAATCA
1 GGGATACTCCAACCTCGGCCTTATTTCAAAATCATCAATTTCTCACAATCA
*
360444 GGGATACTGCAACCT
1 GGGATACTCCAACCT
360459 TGTTATTTTC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 5 0.09
51 52 0.91
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (51 bp):
GGGATACTCCAACCTCGGCCTTATTTCAAAATCATCAATTTCTCACAATCA
Found at i:360417 original size:131 final size:130
Alignment explanation
Indices: 360159--360528 Score: 340
Period size: 130 Copynumber: 2.8 Consensus size: 130
360149 ATTTTTTTTT
* * * * *
360159 CAAAACACCAGTTTTTCATAATTAGGGATACCCCAACCCTGTTATTTTCGAAGGG-ATACTCCAA
1 CAAAACACCAATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCG-AGGGAATACTCCAA
* * * * * * ** ***
360223 CCCC-AGTTTTATTTCTAAAACA-CTAATTTTCCACAGTTGGGGATA-TTCCAA-CTCTGATTTT
65 CCCCGA-CTTTATTTCCAAAATATC-GATTTTCTACAATCAGGGATACTT-CAACCTC-GGCCTT
360284 ATTTC
126 ATTTC
* *
360289 CAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGATTA-TTTCTGAGGGGATACTCCA
1 CAAAACACCAATTTTTCACAATCAGGGATACTCCAACCCCG-TTATTTTC-GAGGGAATACTCCA
* * * *
360353 ATCTCGGCTTTATTTCCAAAATATTGA-TTTCTCACAATCAGGGATACTTCAACCTCGGCCTTAT
64 ACCCCGACTTTATTTCCAAAATATCGATTTTCT-ACAATCAGGGATACTTCAACCTCGGCCTTAT
360417 TTC
128 TTC
* * * * **
360420 TAAATCATCAATTTTTCACAATCAGGGATACTGCAACCTTGTTATTTTCGAGGGAATACTCCAAC
1 CAAAACACCAATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCCAAC
* * *
360485 CCCGATTTTATTTTCAAAATATCGATTTTCTATAATCAGGGATA
66 CCCGACTTTATTTCCAAAATATCGATTTTCTACAATCAGGGATA
360529 GTCTAACCCT
Statistics
Matches: 194, Mismatches: 36, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
130 96 0.49
131 93 0.48
132 5 0.03
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (130 bp):
CAAAACACCAATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCCAAC
CCCGACTTTATTTCCAAAATATCGATTTTCTACAATCAGGGATACTTCAACCTCGGCCTTATTTC
Found at i:360485 original size:79 final size:78
Alignment explanation
Indices: 360392--360565 Score: 192
Period size: 79 Copynumber: 2.2 Consensus size: 78
360382 TCTCACAATC
* * * *
360392 AGGGATACTTCAACCTCGGCCTTA-TTTCTAAATCATCAATTTT-TCACAATCAGGGATACTGC-
1 AGGGATACTCCAACCCCGACCTTATTTTCAAAAT-ATCAATTTTCT-ACAATCAGGGATACT-CT
*
360454 AACCTTGTTATTTTCG
63 AACCCTGTTATTTTCG
** * * *
360470 AGGGAATACTCCAACCCCGATTTTATTTTCAAAATATCGATTTTCTATAATCAGGGATAGTCTAA
1 AGGG-ATACTCCAACCCCGACCTTATTTTCAAAATATCAATTTTCTACAATCAGGGATACTCTAA
360535 CCCTGTTATTTTCG
65 CCCTGTTATTTTCG
360549 AGGGGATACTCCAACCC
1 A-GGGATACTCCAACCC
360566 TGATTTTCTT
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
78 5 0.06
79 64 0.79
80 12 0.15
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (78 bp):
AGGGATACTCCAACCCCGACCTTATTTTCAAAATATCAATTTTCTACAATCAGGGATACTCTAAC
CCTGTTATTTTCG
Found at i:360571 original size:79 final size:79
Alignment explanation
Indices: 360430--360609 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 79
360420 TAAATCATCA
* * *
360430 ATTTTTCACAATCAGGGATACTGCAACCTTGTTATTTTCGAGGGAATACTCCAACCCCGATTTTA
1 ATTTTCCATAATCAGGGATACTGCAACCCTGTTATTTTCGAGGGAATACTCCAACCCCGATTTTA
* * *
360495 TTTTCAAAATATCG
66 TTTCCAAAACACCG
* * * *
360509 ATTTTCTATAATCAGGGATAGT-CTAACCCTGTTATTTTCGAGGGGATACTCCAACCCTGATTTT
1 ATTTTCCATAATCAGGGATACTGC-AACCCTGTTATTTTCGAGGGAATACTCCAACCCCGATTTT
*
360573 CTTTCCAAAACACCG
65 ATTTCCAAAACACCG
360588 ATTTTCCATAATC-GGGAATACT
1 ATTTTCCATAATCAGGG-ATACT
360610 CCAGCCCCGT
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
78 4 0.05
79 82 0.95
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (79 bp):
ATTTTCCATAATCAGGGATACTGCAACCCTGTTATTTTCGAGGGAATACTCCAACCCCGATTTTA
TTTCCAAAACACCG
Found at i:368277 original size:30 final size:28
Alignment explanation
Indices: 368243--368298 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
368233 TCGATGATTA
368243 GAAAATAAATCGAGATTGGAGTATCCCCTC
1 GAAAAT-AA-CGAGATTGGAGTATCCCCTC
* *
368273 GAAAATGACGGGATTGGAGTATCCCC
1 GAAAATAACGAGATTGGAGTATCCCC
368299 AATTATGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
29 1 0.04
30 6 0.25
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (28 bp):
GAAAATAACGAGATTGGAGTATCCCCTC
Found at i:368502 original size:107 final size:106
Alignment explanation
Indices: 368386--368732 Score: 284
Period size: 107 Copynumber: 3.3 Consensus size: 106
368376 CCGATGAAAT
* * *
368386 AACGAGGTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTTTGGAAATAAAATCAGAGTTGG
1 AACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTTTAGAAATAAAATCAGAGTTGG
*
368451 AGTATCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAA
66 AGTATCCCCGATTAAAGGGAAAATTGGTGTTTCGAAAATAA
* * * * *
368492 AACTGGGGTTGGAGTATCCCCGATTGTGGAAAAA-T--TAGTGTTTTAGCAATAAAA-CTGAGGT
1 AAC-GGGGTTGGAGTATCCTCGATTGT-GAAAAATTGGTATTTTTTTAGAAATAAAATCAGA-GT
* * * * * ** *
368553 TGGAGTATCCCCTCGGAAATAACGGG---GTTGGAGTATCCCCGATGAT-T
63 TGGAGTAT-CCC-C-G-ATTAAAGGGAAAATTGGTGT-T--TCGAAAATAA
* * *
368600 AACGGGGTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTTTAGAAATAAAATCGGAGTTA
1 AACGGGGTTGGAGTATCCTCGATTGTGAA-AAATTGGTATTTTTTTAGAAATAAAATCAGAGTTG
* *
368665 GAGTATCCCCGATTATA--GAAAATTAGTGTTTCGAAAATAA
65 GAGTATCCCCGATTAAAGGGAAAATTGGTGTTTCGAAAATAA
* *
368705 AATCGGAGTTGGAATAT-CTCCGATTGTG
1 AA-CGGGGTTGGAGTATCCT-CGATTGTG
368733 GAGAATTGAG
Statistics
Matches: 184, Mismatches: 36, Indels: 42
0.70 0.14 0.16
Matches are distributed among these distances:
104 9 0.05
105 29 0.16
106 39 0.21
107 54 0.29
108 12 0.07
109 14 0.08
110 24 0.13
111 3 0.02
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.31
Consensus pattern (106 bp):
AACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTTTAGAAATAAAATCAGAGTTGG
AGTATCCCCGATTAAAGGGAAAATTGGTGTTTCGAAAATAA
Found at i:368503 original size:53 final size:52
Alignment explanation
Indices: 368389--368564 Score: 169
Period size: 52 Copynumber: 3.3 Consensus size: 52
368379 ATGAAATAAC
* * * * *
368389 GAGGTTGGAGTATCCTCGATT-ATGAAAAATTGGTATTTTTTTGGAAATAAAA-T
1 GAGGTTGGAGTATCCCCGATTAAGGAAAAA-T--TAGTGTTTTAGAAATAAAACT
* * *
368442 CAGAGTTGGAGTATCCCCGATTAAAGGGAAAATTGGTGTTTT-GAAAATAAAACT
1 GAG-GTTGGAGTATCCCCGATT-AAGGAAAAATTAGTGTTTTAG-AAATAAAACT
* ** *
368496 GGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACT
1 GAGGTTGGAGTATCCCCGATTAAGGAAAAATTAGTGTTTTAGAAATAAAACT
368548 GAGGTTGGAGTATCCCC
1 GAGGTTGGAGTATCCCC
368565 TCGGAAATAA
Statistics
Matches: 102, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
52 41 0.40
53 35 0.34
54 19 0.19
55 1 0.01
56 6 0.06
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (52 bp):
GAGGTTGGAGTATCCCCGATTAAGGAAAAATTAGTGTTTTAGAAATAAAACT
Found at i:368582 original size:28 final size:27
Alignment explanation
Indices: 368550--368617 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
368540 ATAAAACTGA
**
368550 GGTTGGAGTATCCCCTCGGAAATAACGG
1 GGTTGGAGTATCCCCGAGG-AATAACGG
* *
368578 GGTTGGAGTATCCCCGATGATTAACGG
1 GGTTGGAGTATCCCCGAGGAATAACGG
368605 GGTTGGAGTATCC
1 GGTTGGAGTATCC
368618 TCGATTGTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 20 0.56
28 16 0.44
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.25
Consensus pattern (27 bp):
GGTTGGAGTATCCCCGAGGAATAACGG
Found at i:368656 original size:215 final size:213
Alignment explanation
Indices: 368335--368734 Score: 579
Period size: 215 Copynumber: 1.9 Consensus size: 213
368325 ATAAAGCCGG
* * *
368335 GGTTAGAGTATCCTCTCAGAAGTAATAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
1 GGTTAGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
* *
368400 ATCCTCGATTATGAAAAATTGGTATTTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTA
66 ATCCTCGATTATGAAAAATTGGTATTTTTTTAGAAATAAAATCAGAGTTAGAGTATCCCCGATTA
* * * *
368465 AAGGGAAAATTGGTGTTTTGAAAATAAAA-CTGGGGTTGGAGTATCCCCGATTGTGGAAAAATTA
131 AA--GAAAATTAGTGTTTCGAAAATAAAATC-GGAGTTGGAATATCCCCGATTGTGGAAAAATTA
368529 GTGTTTTAGCAATAAAACTGA
193 GTGTTTTAGCAATAAAACTGA
* * * * *
368550 GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGT
1 GGTTAGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
* * *
368614 ATCCTCGATTGTGAAGAAATTGGTGTTTTTTTAGAAATAAAATCGGAGTTAGAGTATCCCCGATT
66 ATCCTCGATTATGAA-AAATTGGTATTTTTTTAGAAATAAAATCAGAGTTAGAGTATCCCCGATT
* *
368679 ATAGAAAATTAGTGTTTCGAAAATAAAATCGGAGTTGGAATATCTCCGATTGTGGA
130 AAAGAAAATTAGTGTTTCGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
368735 GAATTGAGAA
Statistics
Matches: 164, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
213 46 0.28
214 30 0.18
215 88 0.54
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (213 bp):
GGTTAGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
ATCCTCGATTATGAAAAATTGGTATTTTTTTAGAAATAAAATCAGAGTTAGAGTATCCCCGATTA
AAGAAAATTAGTGTTTCGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTG
TTTTAGCAATAAAACTGA
Found at i:371117 original size:13 final size:13
Alignment explanation
Indices: 371099--371124 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
371089 ACAAAGATCC
371099 ATGTATCGATACA
1 ATGTATCGATACA
371112 ATGTATCGATACA
1 ATGTATCGATACA
371125 CAGAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:371187 original size:19 final size:18
Alignment explanation
Indices: 371163--371230 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
371153 CAGTAGCTAA
371163 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
371182 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
371197 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
371214 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
371231 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:371203 original size:13 final size:13
Alignment explanation
Indices: 371185--371209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
371175 ACAATACTTA
371185 TGTATCGATACAT
1 TGTATCGATACAT
371198 TGTATCGATACA
1 TGTATCGATACA
371210 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.