Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 24 of 226
Found at i:10900579 original size:2 final size:2
Alignment explanation
Indices: 10900514--10900568 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
10900504 TTCAATAAAC
10900514 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10900556 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
10900569 ATAACTATAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10900691 original size:8 final size:8
Alignment explanation
Indices: 10900680--10900718 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
10900670 CATACATACA
10900680 ATAATAAT
1 ATAATAAT
10900688 ATAATAAT
1 ATAATAAT
*
10900696 AATAGTAAT
1 -ATAATAAT
10900705 AT-ATAAT
1 ATAATAAT
10900712 ATAATAA
1 ATAATAA
10900719 CAAAGATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 6 0.22
8 14 0.52
9 7 0.26
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (8 bp):
ATAATAAT
Found at i:10917175 original size:12 final size:12
Alignment explanation
Indices: 10917158--10917182 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10917148 TTTTTATGGT
10917158 ATTCTTATTTTC
1 ATTCTTATTTTC
10917170 ATTCTTATTTTC
1 ATTCTTATTTTC
10917182 A
1 A
10917183 AACATAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTCTTATTTTC
Found at i:10936932 original size:25 final size:26
Alignment explanation
Indices: 10936898--10936946 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
10936888 AAGTCATCTC
10936898 CAGTTAGATTAC-TTCAAAATGCTGA
1 CAGTTAGATTACTTTCAAAATGCTGA
10936923 CAGTTAGATTACTTTCAAAATGCT
1 CAGTTAGATTACTTTCAAAATGCT
10936947 TTCCAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (26 bp):
CAGTTAGATTACTTTCAAAATGCTGA
Found at i:10946514 original size:13 final size:13
Alignment explanation
Indices: 10946496--10946529 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
10946486 TCTTCATTGT
10946496 TTTTGAAAAGTAC
1 TTTTGAAAAGTAC
*
10946509 TTTTGAGAAGTAC
1 TTTTGAAAAGTAC
10946522 TTTT-AAAA
1 TTTTGAAAA
10946530 AATTTGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 3 0.16
13 16 0.84
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (13 bp):
TTTTGAAAAGTAC
Found at i:10958759 original size:5 final size:5
Alignment explanation
Indices: 10958749--10958786 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
10958739 TACTTCTCTA
10958749 AACTC AACTC AACTC AACTC AACTC AACTC AACTC AAC
1 AACTC AACTC AACTC AACTC AACTC AACTC AACTC AAC
10958787 AGCATGGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.18
Consensus pattern (5 bp):
AACTC
Found at i:10959964 original size:2 final size:2
Alignment explanation
Indices: 10959957--10959985 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10959947 AAGACCGTTG
10959957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10959986 CGGATAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10961574 original size:21 final size:21
Alignment explanation
Indices: 10961527--10961567 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10961517 GTATGAACAT
10961527 ATTGAACCGGCTAAAAAATCA
1 ATTGAACCGGCTAAAAAATCA
* *
10961548 ATTGAACTGGCTGAAAAATC
1 ATTGAACCGGCTAAAAAATC
10961568 GGTTGAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (21 bp):
ATTGAACCGGCTAAAAAATCA
Found at i:10970772 original size:41 final size:39
Alignment explanation
Indices: 10970744--10970829 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
10970734 GAACACTACC
10970744 ATAAATATAATAAATATTTTATTATATTAAAAAATACAA
1 ATAAATATAATAAATATTTTATTATATTAAAAAATACAA
* *
10970783 ATAAGTATAATAAATATTTTATTATATTAAAATATA-AA
1 ATAAATATAATAAATATTTTATTATATTAAAAAATACAA
10970821 TATAAATAT
1 -ATAAATAT
10970830 TCTATATTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 2 0.05
39 41 0.95
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (39 bp):
ATAAATATAATAAATATTTTATTATATTAAAAAATACAA
Found at i:10973882 original size:21 final size:22
Alignment explanation
Indices: 10973824--10973887 Score: 103
Period size: 21 Copynumber: 3.0 Consensus size: 22
10973814 CAAAACAGCA
*
10973824 GTTTCTCCCCTCGTTCTTGCTG
1 GTTTCTCCCCTCGTTTTTGCTG
10973846 GTTTCT-CCCTCGTTTTTGCTG
1 GTTTCTCCCCTCGTTTTTGCTG
*
10973867 GTTTCTCCCCTCTTTTTTGCT
1 GTTTCTCCCCTCGTTTTTGCT
10973888 TTGTTCTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.00, C:0.33, G:0.16, T:0.52
Consensus pattern (22 bp):
GTTTCTCCCCTCGTTTTTGCTG
Found at i:10976280 original size:60 final size:59
Alignment explanation
Indices: 10976169--10976393 Score: 398
Period size: 60 Copynumber: 3.8 Consensus size: 59
10976159 CATCTTGACC
* *
10976169 TTTAAAAAT-AAAAAATATATGTAATATATTTTAAAAATAAAAAATATATGTAGTGTAT
1 TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATGTAGTGTAT
10976227 TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAAATATATGTAGTGTAT
1 TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAAT-AAAAAATATATGTAGTGTAT
10976287 TTTAAAAATAAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATGTAGTGTAT
1 TTTAAAAAT-AAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATGTAGTGTAT
10976347 TTTAAAAATAAAAAATATATATGTAGTGTATTTTAAAAATAAAAAAT
1 TTTAAAAATAAAAAA-ATATATGTAGTGTATTTTAAAAATAAAAAAT
10976394 TTAGTTTATA
Statistics
Matches: 161, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
58 9 0.06
59 33 0.20
60 89 0.55
61 30 0.19
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (59 bp):
TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATGTAGTGTAT
Found at i:10976393 original size:31 final size:30
Alignment explanation
Indices: 10976169--10976392 Score: 391
Period size: 29 Copynumber: 7.5 Consensus size: 30
10976159 CATCTTGACC
* *
10976169 TTTAAAAAT-AAAAAATATATGTAATATAT
1 TTTAAAAATAAAAAAATATATGTAGTGTAT
10976198 TTTAAAAAT-AAAAAATATATGTAGTGTAT
1 TTTAAAAATAAAAAAATATATGTAGTGTAT
10976227 TTTAAAAATAAAAAAATATATGTAGTGTAT
1 TTTAAAAATAAAAAAATATATGTAGTGTAT
10976257 TTTAAAAATAAAAAAATATATGTAGTGTAT
1 TTTAAAAATAAAAAAATATATGTAGTGTAT
10976287 TTTAAAAATAAAAAAAATATATGTAGTGTAT
1 TTTAAAAAT-AAAAAAATATATGTAGTGTAT
10976318 TTTAAAAAT-AAAAAATATATGTAGTGTAT
1 TTTAAAAATAAAAAAATATATGTAGTGTAT
10976347 TTTAAAAATAAAAAATATATATGTAGTGTAT
1 TTTAAAAATAAAAAA-ATATATGTAGTGTAT
10976378 TTTAAAAATAAAAAA
1 TTTAAAAATAAAAAA
10976393 TTTAGTTTAT
Statistics
Matches: 189, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
29 65 0.34
30 64 0.34
31 60 0.32
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (30 bp):
TTTAAAAATAAAAAAATATATGTAGTGTAT
Found at i:10978124 original size:11 final size:11
Alignment explanation
Indices: 10978108--10978167 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
10978098 TATTTTTTAA
10978108 TTTTAAAATAT
1 TTTTAAAATAT
10978119 TTTTAAAATACT
1 TTTTAAAATA-T
*** *
10978131 TTTT-TTTTAA
1 TTTTAAAATAT
10978141 TTTTAAAATAT
1 TTTTAAAATAT
10978152 TTTTAAAATACT
1 TTTTAAAATA-T
10978164 TTTT
1 TTTT
10978168 TTTATTTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
10 4 0.11
11 24 0.63
12 10 0.26
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:10978138 original size:33 final size:33
Alignment explanation
Indices: 10978100--10978170 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
10978090 AATATATTTA
10978100 TTTTTTAATTTTAAAATATTTTTAAAATACTTT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTT
10978133 TTTTTTAATTTTAAAATATTTTTAAAATACTTT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTT
10978166 TTTTT
1 TTTTT
10978171 ATTTTTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (33 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTT
Found at i:10978186 original size:40 final size:40
Alignment explanation
Indices: 10978132--10978208 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
10978122 TAAAATACTT
10978132 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTA
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTA
10978172 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
10978209 AATTTTTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (40 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTA
Found at i:10978227 original size:20 final size:20
Alignment explanation
Indices: 10978190--10978228 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10978180 ATTTTAAAAT
**
10978190 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATAAATTTTTA
10978210 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
10978229 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTAAAATAAATTTTTA
Found at i:10978235 original size:22 final size:20
Alignment explanation
Indices: 10978189--10978246 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
10978179 AATTTTAAAA
*
10978189 TATTTTTAAAAT-ACTTTTT
1 TATTTTTAAAATAAATTTTT
10978208 TAATTTTTAAAATAAATTTTT
1 T-ATTTTTAAAATAAATTTTT
10978229 GGTATTTATTAAAA-AAAT
1 --TATTT-TTAAAATAAAT
10978247 GGGCCGGGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 1 0.03
20 11 0.33
21 6 0.18
22 8 0.24
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTTTTAAAATAAATTTTT
Found at i:10980372 original size:17 final size:18
Alignment explanation
Indices: 10980352--10980386 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10980342 TCACATATTT
10980352 TAATA-ATTTTAAAAAAG
1 TAATAGATTTTAAAAAAG
10980369 TAATATGATTTTAAAAAA
1 TAATA-GATTTTAAAAAA
10980387 TTCTATTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
19 11 0.69
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
TAATAGATTTTAAAAAAG
Found at i:10983133 original size:15 final size:15
Alignment explanation
Indices: 10983113--10983145 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
10983103 TTAAAGTTTG
10983113 TTATTATAATTTTTT
1 TTATTATAATTTTTT
10983128 TTATTATAATTTTTT
1 TTATTATAATTTTTT
10983143 TTA
1 TTA
10983146 CAAATGCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTATAATTTTTT
Found at i:10996807 original size:3 final size:3
Alignment explanation
Indices: 10996799--10997040 Score: 112
Period size: 3 Copynumber: 80.7 Consensus size: 3
10996789 AGTTGTTTCT
* * **
10996799 TGC TGC TGC TGC TGC TG- TGGC TGC TGT TGT TG- TAAT TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC T-GC TGC TGC TGC TGC T-GC TGC TGC TGC
* * * * **
10996844 TGC TGC TGC TGT TGC AGC TGT TGT TGC TG- TAAT TGC TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC T-GC TGC TGC TGC TGC
* * * * * * ** **
10996889 TGC TGC TGT TGC AGC TGT TGT TGC TGA TGA TGC AAC TGC TGC TGC AAC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
** * * * **
10996937 TGC AAC TGC TGC TGT TGT TGT TGC TGC TGC TGC TGC TGC TGC AAC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
** * * *** **
10996985 AAC TGC TGC TGT TGT TGC TGC TGC AAT TGC AAC TGC TGC TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
10997033 TGC TGC TG
1 TGC TGC TG
10997041 GTTCATGTAA
Statistics
Matches: 178, Mismatches: 55, Indels: 12
0.73 0.22 0.05
Matches are distributed among these distances:
2 3 0.02
3 172 0.97
4 3 0.02
ACGTcount: A:0.09, C:0.24, G:0.30, T:0.36
Consensus pattern (3 bp):
TGC
Found at i:10996869 original size:42 final size:42
Alignment explanation
Indices: 10996799--10996977 Score: 190
Period size: 42 Copynumber: 4.4 Consensus size: 42
10996789 AGTTGTTTCT
*
10996799 TGCTGCTGCTGCTGCTG-TG--GCTGCTGTTGTTGTAATTGC
1 TGCTGCTGCTGCTGCTGTTGCAGCTGCTGTTGCTGTAATTGC
*
10996838 TGCTGCTGCTGCTGCTGTTGCAGCTGTTGTTGCTGTAATTGC
1 TGCTGCTGCTGCTGCTGTTGCAGCTGCTGTTGCTGTAATTGC
* *
10996880 TGCTGCTGCTGCTGCTGTTGCAGCTGTTGTTGCTG--A-TGA
1 TGCTGCTGCTGCTGCTGTTGCAGCTGCTGTTGCTGTAATTGC
** *** * * * **
10996919 TGCAACTGCTGCTGCAACTGCAACTGCTGCTGTTGTTGTTGC
1 TGCTGCTGCTGCTGCTGTTGCAGCTGCTGTTGCTGTAATTGC
10996961 TGCTGCTGCTGCTGCTG
1 TGCTGCTGCTGCTGCTG
10996978 CAACTGCAAC
Statistics
Matches: 116, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
39 45 0.39
40 3 0.03
42 68 0.59
ACGTcount: A:0.08, C:0.23, G:0.31, T:0.38
Consensus pattern (42 bp):
TGCTGCTGCTGCTGCTGTTGCAGCTGCTGTTGCTGTAATTGC
Found at i:10996979 original size:39 final size:39
Alignment explanation
Indices: 10996790--10997008 Score: 141
Period size: 42 Copynumber: 5.4 Consensus size: 39
10996780 TAGTGGTGAA
* ** *
10996790 GTTGTTTCTTGCTGCTGCTGCTGCTGTGGCTGCTGTTGTT
1 GTTGTTGC-TGCTGCTGCTGCTGCTGCAGCTGCTGCTGTT
* * * *
10996830 GTAATTGCTGCTGCTGCTGCTGCTGTTGCAGCTGTTGTTGCTGTA
1 G---TTGTTGCTGCTGCTGCTGCTGCTGCAGC---TGCTGCTGTT
* * * * * *
10996875 ATTGCTGCTGCTGCTGCTGCTGTTGCAGCTGTTGTTGCT
1 GTTGTTGCTGCTGCTGCTGCTGCTGCAGCTGCTGCTGTT
* * ** ** *
10996914 GATGATGCAACTGCTGCTGCAACTGCAACTGCTGCTGTT
1 GTTGTTGCTGCTGCTGCTGCTGCTGCAGCTGCTGCTGTT
* *
10996953 GTTGTTGCTGCTGCTGCTGCTGCTGCAACTGCAACTGCTGCT
1 GTTGTTGCTGCTGCTGCTGCTGCTGCAGCTG---CTGCTGTT
10996995 GTTGTTGCTGCTGC
1 GTTGTTGCTGCTGC
10997009 AATTGCAACT
Statistics
Matches: 139, Mismatches: 31, Indels: 16
0.75 0.17 0.09
Matches are distributed among these distances:
39 59 0.42
40 1 0.01
42 67 0.48
43 5 0.04
45 7 0.05
ACGTcount: A:0.08, C:0.23, G:0.30, T:0.38
Consensus pattern (39 bp):
GTTGTTGCTGCTGCTGCTGCTGCTGCAGCTGCTGCTGTT
Found at i:10996991 original size:42 final size:42
Alignment explanation
Indices: 10996819--10997008 Score: 143
Period size: 42 Copynumber: 4.5 Consensus size: 42
10996809 GCTGCTGTGG
*** *** *
10996819 CTGCTGTTGTTGTAATTGCTGCTGCTGCTGCTGCTGTTGCAG
1 CTGCTGTTGTTGTTGCTGCTGCTGCTGCTGCTGCAACTGCAA
* * *** ***
10996861 CTGTTGTTGCTGTAATTGCTGCTGCTGCTGCTGCTGTTGC-A
1 CTGCTGTTGTTGTTGCTGCTGCTGCTGCTGCTGCAACTGCAA
* * * **
10996902 --GCTGTTGTTGCTGATGATGCAACTGCTGCTGCAACTGCAA
1 CTGCTGTTGTTGTTGCTGCTGCTGCTGCTGCTGCAACTGCAA
10996942 CTGCTGCTGTTGTTGTTGCTGCTGCTGCTGCTGCTGCAACTGCAA
1 ---CTGCTGTTGTTGTTGCTGCTGCTGCTGCTGCTGCAACTGCAA
*
10996987 CTGCTGCTGTTGTTGCTGCTGC
1 CTGCTGTTGTTGTTGCTGCTGC
10997009 AATTGCAACT
Statistics
Matches: 121, Mismatches: 21, Indels: 12
0.79 0.14 0.08
Matches are distributed among these distances:
39 26 0.21
40 1 0.01
42 59 0.49
45 35 0.29
ACGTcount: A:0.09, C:0.24, G:0.29, T:0.37
Consensus pattern (42 bp):
CTGCTGTTGTTGTTGCTGCTGCTGCTGCTGCTGCAACTGCAA
Found at i:10996992 original size:30 final size:30
Alignment explanation
Indices: 10996958--10997038 Score: 135
Period size: 30 Copynumber: 2.7 Consensus size: 30
10996948 CTGTTGTTGT
10996958 TGCTGCTGCTGCTGCTGCTGCAACTGCAAC
1 TGCTGCTGCTGCTGCTGCTGCAACTGCAAC
* * *
10996988 TGCTGCTGTTGTTGCTGCTGCAATTGCAAC
1 TGCTGCTGCTGCTGCTGCTGCAACTGCAAC
10997018 TGCTGCTGCTGCTGCTGCTGC
1 TGCTGCTGCTGCTGCTGCTGC
10997039 TGGTTCATGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.10, C:0.30, G:0.28, T:0.32
Consensus pattern (30 bp):
TGCTGCTGCTGCTGCTGCTGCAACTGCAAC
Found at i:11006724 original size:4 final size:4
Alignment explanation
Indices: 11006715--11006759 Score: 81
Period size: 4 Copynumber: 11.2 Consensus size: 4
11006705 AATAACACAG
*
11006715 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GCAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
11006760 CCTTGCCTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:11010413 original size:24 final size:24
Alignment explanation
Indices: 11010385--11010434 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
11010375 CCTTGAAGAT
*
11010385 TTTAGTTCAACTTGTGTCTGATTC
1 TTTAGTTCAACTTGCGTCTGATTC
11010409 TTTAGTTCAACTTGCGTCTGATTC
1 TTTAGTTCAACTTGCGTCTGATTC
11010433 TT
1 TT
11010435 CGTTCAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.50
Consensus pattern (24 bp):
TTTAGTTCAACTTGCGTCTGATTC
Found at i:11017191 original size:22 final size:22
Alignment explanation
Indices: 11017146--11017201 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
11017136 TTCTAAAATT
**
11017146 TTATTATTTTAAAAACATTTTA
1 TTATTATTTTAAAAACATAATA
11017168 TTATTATTTTAAAAA-ATCAATA
1 TTATTATTTTAAAAACAT-AATA
11017190 -T-TTATTTTAAAA
1 TTATTATTTTAAAA
11017202 TATTTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.35
21 3 0.10
22 17 0.55
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTATTTTAAAAACATAATA
Found at i:11017214 original size:20 final size:19
Alignment explanation
Indices: 11017144--11017216 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
11017134 ACTTCTAAAA
11017144 TTTTATTATTTTAAAAACATT
1 TTTTATTATTTT-AAAA-ATT
*
11017165 TTATTATTATTTTAAAAAAT
1 TT-TTATTATTTTAAAAATT
***
11017185 CAATATTTATTTTAAAATATT
1 TTTTA-TTATTTTAAAA-ATT
11017206 TTTTATTATTT
1 TTTTATTATTT
11017217 GATTATTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
19 2 0.05
20 19 0.46
21 10 0.24
22 10 0.24
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTATTATTTTAAAAATT
Found at i:11017251 original size:29 final size:29
Alignment explanation
Indices: 11017188--11017252 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
11017178 AAAAAATCAA
11017188 TATTTA-TTTTAAAATATTTTTTATTATT
1 TATTTATTTTTAAAATATTTTTTATTATT
* *
11017216 TGA-TTATTTTTATAAT-TTTTTTCGTTATT
1 T-ATTTATTTTTAAAATATTTTTT-ATTATT
11017245 TATTTATT
1 TATTTATT
11017253 GCTGATAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
28 11 0.35
29 20 0.65
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (29 bp):
TATTTATTTTTAAAATATTTTTTATTATT
Found at i:11032615 original size:2 final size:2
Alignment explanation
Indices: 11032608--11032676 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
11032598 NNNNNNNNNN
11032608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
11032650 TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
11032677 GAGATTTCAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11034877 original size:24 final size:24
Alignment explanation
Indices: 11034845--11034893 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
11034835 GAGTTCCCCC
11034845 AGAACCGATGGTCTAAATTAAGTT
1 AGAACCGATGGTCTAAATTAAGTT
11034869 AGAACCGATGGTCTAAATTAAGTT
1 AGAACCGATGGTCTAAATTAAGTT
11034893 A
1 A
11034894 CATCGACTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (24 bp):
AGAACCGATGGTCTAAATTAAGTT
Found at i:11063458 original size:46 final size:46
Alignment explanation
Indices: 11063325--11063464 Score: 217
Period size: 46 Copynumber: 3.0 Consensus size: 46
11063315 CCATGGCAAA
* * *
11063325 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTAAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAG
11063371 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAG
* * * *
11063417 TTGTGAAAAATAGGTATGATATTTCAGTGAAGGAAACCATATTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAG
11063463 TT
1 TT
11063465 ATAGCATTGT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAG
Found at i:11069820 original size:94 final size:94
Alignment explanation
Indices: 11069657--11069842 Score: 329
Period size: 94 Copynumber: 2.0 Consensus size: 94
11069647 TTGAATCACA
11069657 CAACTCTAACACCTAACTATTCTAGTAGTGACACAATAAGATTTATCGAAGATACTGCTGCCAAA
1 CAACTCTAACACCTAACTATTCTAGTAGTGACACAATAAGATTTATCGAAGATACTGCTGCCAAA
11069722 GGTTTTTC-TACAACTTATATAATTATACG
66 GG-TTTTCGTACAACTTATATAATTATACG
* * *
11069751 CAACTCTAACACCTGACTATTCTAGTCGTGACACAATAAGATTTATCGAAGATACTGCTGCCAAG
1 CAACTCTAACACCTAACTATTCTAGTAGTGACACAATAAGATTTATCGAAGATACTGCTGCCAAA
11069816 GGTTTTCGTACAACTTATATAATTATA
66 GGTTTTCGTACAACTTATATAATTATA
11069843 TATATTGTTT
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 5 0.06
94 83 0.94
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (94 bp):
CAACTCTAACACCTAACTATTCTAGTAGTGACACAATAAGATTTATCGAAGATACTGCTGCCAAA
GGTTTTCGTACAACTTATATAATTATACG
Found at i:11073097 original size:20 final size:20
Alignment explanation
Indices: 11073060--11073098 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11073050 TATATTTAAA
* *
11073060 TATTTTAAATATAGTTTATT
1 TATTTTAAATAAAATTTATT
*
11073080 TATTTTAATTAAAATTTAT
1 TATTTTAAATAAAATTTAT
11073099 ACTTCATATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATTTTAAATAAAATTTATT
Found at i:11077452 original size:3 final size:3
Alignment explanation
Indices: 11077388--11077437 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
11077378 TTGGTTTATT
*
11077388 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11077436 TA
1 TA
11077438 TAAAACCATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:11077980 original size:46 final size:46
Alignment explanation
Indices: 11077908--11078092 Score: 318
Period size: 46 Copynumber: 4.0 Consensus size: 46
11077898 ACATTGCTAT
*
11077908 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
11077954 AACTCAGTATGGTTTTCTTCA-TGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACT-GAAATACCATACCTACTTTTCAC
* *
11078000 AACTCAGTATGGTTTTCTTCACTGAAACAACATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
*
11078046 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
11078092 A
1 A
11078093 CTTTGCCATG
Statistics
Matches: 131, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
46 130 0.99
47 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:11079364 original size:16 final size:17
Alignment explanation
Indices: 11079318--11079365 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
11079308 AAATTCTTTT
11079318 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
11079335 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
11079352 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
11079366 TTATAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:11081123 original size:533 final size:533
Alignment explanation
Indices: 11080117--11081183 Score: 2134
Period size: 533 Copynumber: 2.0 Consensus size: 533
11080107 GACACAAGCA
11080117 TATCAATTTATACACAATAGAATTTCCTCTCCATCTCATTTATCTAAGTCTTCATCTAGAGACCT
1 TATCAATTTATACACAATAGAATTTCCTCTCCATCTCATTTATCTAAGTCTTCATCTAGAGACCT
11080182 CAATTCTAGTTTACTAAGCAATTTAATACCCCTAAACAATCAATTAATTAAAAACACGCATACTA
66 CAATTCTAGTTTACTAAGCAATTTAATACCCCTAAACAATCAATTAATTAAAAACACGCATACTA
11080247 ACCTCAATTAACAGCTAGTATCACAATCAATCATCAAGAGAATTTAGAACAACATGGAATTCAAA
131 ACCTCAATTAACAGCTAGTATCACAATCAATCATCAAGAGAATTTAGAACAACATGGAATTCAAA
11080312 ATACAAGCAGCTATACTAAACATTCAATTGATACAAAATAAATAAGAACAAGAGTTTAGATATGC
196 ATACAAGCAGCTATACTAAACATTCAATTGATACAAAATAAATAAGAACAAGAGTTTAGATATGC
11080377 TCATTCATGGACAATAGTCCAATTGCAAAGCTAGAGCTTGTTTTGATTTCCATTTACATTGCCAT
261 TCATTCATGGACAATAGTCCAATTGCAAAGCTAGAGCTTGTTTTGATTTCCATTTACATTGCCAT
11080442 CAATAAGAAAGAGTTGCAAATGCTACAACAATCTTACTCTCTACAAAGTCTTTACAAAGAAATAT
326 CAATAAGAAAGAGTTGCAAATGCTACAACAATCTTACTCTCTACAAAGTCTTTACAAAGAAATAT
11080507 GAAAAGACCCTACAAATTCTCTCTAAAAAATCTCTTCCATCTCTTCTTAATTTATGATACAAAGG
391 GAAAAGACCCTACAAATTCTCTCTAAAAAATCTCTTCCATCTCTTCTTAATTTATGATACAAAGG
11080572 TGTTTTTTCATTTCCATGAGCTAAAAGACCTTTTGACCCTCTTTAAATTTAAGTGTTTTATAAGT
456 TGTTTTTTCATTTCCATGAGCTAAAAGACCTTTTGACCCTCTTTAAATTTAAGTGTTTTATAAGT
11080637 TGAAATGTCCAAT
521 TGAAATGTCCAAT
11080650 TATCAATTTATACACAATAGAATTTCCTCTCCATCTCATTTATCTAAGTCTTCATCTAGAGACCT
1 TATCAATTTATACACAATAGAATTTCCTCTCCATCTCATTTATCTAAGTCTTCATCTAGAGACCT
11080715 CAATTCTAGTTTACTAAGCAATTTAATACCCCTAAACAATCAATTAATTAAAAACACGCATACTA
66 CAATTCTAGTTTACTAAGCAATTTAATACCCCTAAACAATCAATTAATTAAAAACACGCATACTA
11080780 ACCTCAATTAACAGCTAGTATCACAATCAATCATCAAGAGAATTTAGAACAACATGGAATTCAAA
131 ACCTCAATTAACAGCTAGTATCACAATCAATCATCAAGAGAATTTAGAACAACATGGAATTCAAA
11080845 ATACAAGCAGCTATACTAAACATTCAATTGATACAAAATAAATAAGAACAAGAGTTTAGATATGC
196 ATACAAGCAGCTATACTAAACATTCAATTGATACAAAATAAATAAGAACAAGAGTTTAGATATGC
11080910 TCATTCATGGACAATAGTCCAATTGCAAAGCTAGAGCTTGTTTTGATTTCCATTTACATTGCCAT
261 TCATTCATGGACAATAGTCCAATTGCAAAGCTAGAGCTTGTTTTGATTTCCATTTACATTGCCAT
11080975 CAATAAGAAAGAGTTGCAAATGCTACAACAATCTTACTCTCTACAAAGTCTTTACAAAGAAATAT
326 CAATAAGAAAGAGTTGCAAATGCTACAACAATCTTACTCTCTACAAAGTCTTTACAAAGAAATAT
11081040 GAAAAGACCCTACAAATTCTCTCTAAAAAATCTCTTCCATCTCTTCTTAATTTATGATACAAAGG
391 GAAAAGACCCTACAAATTCTCTCTAAAAAATCTCTTCCATCTCTTCTTAATTTATGATACAAAGG
11081105 TGTTTTTTCATTTCCATGAGCTAAAAGACCTTTTGACCCTCTTTAAATTTAAGTGTTTTATAAGT
456 TGTTTTTTCATTTCCATGAGCTAAAAGACCTTTTGACCCTCTTTAAATTTAAGTGTTTTATAAGT
11081170 TGAAATGTCCAAT
521 TGAAATGTCCAAT
11081183 T
1 T
11081184 CCTTTAAAAT
Statistics
Matches: 534, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
533 534 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (533 bp):
TATCAATTTATACACAATAGAATTTCCTCTCCATCTCATTTATCTAAGTCTTCATCTAGAGACCT
CAATTCTAGTTTACTAAGCAATTTAATACCCCTAAACAATCAATTAATTAAAAACACGCATACTA
ACCTCAATTAACAGCTAGTATCACAATCAATCATCAAGAGAATTTAGAACAACATGGAATTCAAA
ATACAAGCAGCTATACTAAACATTCAATTGATACAAAATAAATAAGAACAAGAGTTTAGATATGC
TCATTCATGGACAATAGTCCAATTGCAAAGCTAGAGCTTGTTTTGATTTCCATTTACATTGCCAT
CAATAAGAAAGAGTTGCAAATGCTACAACAATCTTACTCTCTACAAAGTCTTTACAAAGAAATAT
GAAAAGACCCTACAAATTCTCTCTAAAAAATCTCTTCCATCTCTTCTTAATTTATGATACAAAGG
TGTTTTTTCATTTCCATGAGCTAAAAGACCTTTTGACCCTCTTTAAATTTAAGTGTTTTATAAGT
TGAAATGTCCAAT
Found at i:11082295 original size:46 final size:46
Alignment explanation
Indices: 11082192--11082444 Score: 433
Period size: 46 Copynumber: 5.6 Consensus size: 46
11082182 TACGTATGAT
* *
11082192 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
11082235 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
11082281 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
11082326 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAACTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
11082372 CACTTACCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
11082418 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
11082445 AGTACTCAAA
Statistics
Matches: 198, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
43 10 0.05
44 5 0.03
45 64 0.32
46 119 0.60
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:11082311 original size:91 final size:91
Alignment explanation
Indices: 11082192--11082444 Score: 447
Period size: 91 Copynumber: 2.8 Consensus size: 91
11082182 TACGTATGAT
*
11082192 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
*
11082255 GATCAGATAAGTGTAGCTAAAGCTAC
66 GATCAGATAAGTGTAGCTAAAACTAC
11082281 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
11082346 GATCAGATAAGTGTAGCTAAAACTAC
66 GATCAGATAAGTGTAGCTAAAACTAC
* *
11082372 CACTTACCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACT
11082437 TGATCAGA
65 TGATCAGA
11082445 AGTACTCAAA
Statistics
Matches: 157, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
89 10 0.06
90 5 0.03
91 109 0.69
92 33 0.21
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (91 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
GATCAGATAAGTGTAGCTAAAACTAC
Found at i:11100061 original size:4 final size:4
Alignment explanation
Indices: 11100052--11100076 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
11100042 GTCAATTATT
11100052 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
11100077 ATGGGTACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:11100448 original size:2 final size:2
Alignment explanation
Indices: 11100441--11100476 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11100431 TATCACATAA
11100441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11100477 TTACATGAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11108448 original size:3 final size:3
Alignment explanation
Indices: 11108440--11108506 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
11108430 GATAGGAAAG
11108440 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11108488 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
11108507 TAAGATATGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11120900 original size:27 final size:31
Alignment explanation
Indices: 11120863--11120921 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 31
11120853 TAATATTGAT
11120863 ATAAACTTATAA-TTATT-ATAAAA-TAATA
1 ATAAACTTATAATTTATTGATAAAATTAATA
*
11120891 ATAAA-TTATAATTTTTTGATAAAATTAATA
1 ATAAACTTATAATTTATTGATAAAATTAATA
11120921 A
1 A
11120922 AATATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 6 0.22
28 9 0.33
29 6 0.22
30 6 0.22
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (31 bp):
ATAAACTTATAATTTATTGATAAAATTAATA
Found at i:11120922 original size:27 final size:26
Alignment explanation
Indices: 11120863--11120927 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
11120853 TAATATTGAT
11120863 ATAAACTTATAATTATTATAAAATAATA
1 ATAAA-TTATAATTATTATAAAAT-ATA
*
11120891 ATAAATTATAATTTTTTGATAAAAT-TA
1 ATAAATTATAA-TTATT-ATAAAATATA
*
11120918 ATAAAATATA
1 ATAAATTATA
11120928 TTTAAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 17 0.52
28 9 0.27
29 7 0.21
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (26 bp):
ATAAATTATAATTATTATAAAATATA
Found at i:11120973 original size:30 final size:30
Alignment explanation
Indices: 11120911--11120975 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
11120901 ATTTTTTGAT
* *
11120911 AAAATTAATAAAATATATTTAAATTATTTA
1 AAAATTAATAAAACATATTTAAATTATATA
* *
11120941 AAAATTTATAAAACATA-TTATAATTCTATA
1 AAAATTAATAAAACATATTTA-AATTATATA
11120971 AAAAT
1 AAAAT
11120976 CATAAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAATTAATAAAACATATTTAAATTATATA
Found at i:11120985 original size:20 final size:19
Alignment explanation
Indices: 11120939--11121030 Score: 55
Period size: 20 Copynumber: 4.8 Consensus size: 19
11120929 TTAAATTATT
11120939 TAAAAATTTATAAAACATA
1 TAAAAATTTATAAAACATA
* *
11120958 TTATAATTCTATAAAA-ATCA
1 TAAAAATT-TATAAAACAT-A
**
11120978 TAAAAA-TTATACAAAGGTA
1 TAAAAATTTATA-AAACATA
* * * *
11120997 TTAAAATTGATATACACTTA
1 TAAAAATTTATA-AAACATA
11121017 TAAAAA-TTATAAAA
1 TAAAAATTTATAAAA
11121031 AAAATCATAA
Statistics
Matches: 54, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
18 6 0.11
19 22 0.41
20 26 0.48
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.34
Consensus pattern (19 bp):
TAAAAATTTATAAAACATA
Found at i:11122023 original size:29 final size:29
Alignment explanation
Indices: 11121989--11122048 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
11121979 TTTATTTTGC
11121989 ATACTTAGTCATTCATACTAATACTTTTT
1 ATACTTAGTCATTCATACTAATACTTTTT
11122018 ATACTTAGTCATTCATACTAATACTTTTT
1 ATACTTAGTCATTCATACTAATACTTTTT
11122047 AT
1 AT
11122049 TTCAATTCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.17, G:0.03, T:0.48
Consensus pattern (29 bp):
ATACTTAGTCATTCATACTAATACTTTTT
Found at i:11122365 original size:46 final size:46
Alignment explanation
Indices: 11122298--11122386 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
11122288 CACTTCCTGC
11122298 CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAACT
1 CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAACT
11122344 CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACA
1 CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACA
11122387 TTTTTCCATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (46 bp):
CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAACT
Found at i:11123658 original size:20 final size:19
Alignment explanation
Indices: 11123617--11123663 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
11123607 AATTTTGATA
* *
11123617 TTTTTAAAATTTTAATATT
1 TTTTTAAAATTCTAATACT
*
11123636 TTTTTAAGAATTCTAATGC-
1 TTTTTAA-AATTCTAATACT
11123655 TTTTTAAAA
1 TTTTTAAAA
11123664 AAAAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 14 0.58
20 8 0.33
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (19 bp):
TTTTTAAAATTCTAATACT
Found at i:11123728 original size:29 final size:29
Alignment explanation
Indices: 11123695--11123800 Score: 99
Period size: 29 Copynumber: 3.6 Consensus size: 29
11123685 AGATTTATTA
11123695 ATTTTTTTAAAAATTTATTAGAATTTTAT
1 ATTTTTTTAAAAATTTATTAGAATTTTAT
**
11123724 ATTTTTTATGTAAA-TTATTAGAATTTTAT
1 ATTTTTT-TAAAAATTTATTAGAATTTTAT
* *
11123753 ATTTTTGTTAAAAGTTT-TATAAATTATTTTAT
1 ATTTTT-TTAAAAATTTAT-TAGA--ATTTTAT
* *
11123785 ATTATTATAAAAATTT
1 ATTTTTTTAAAAATTT
11123801 TAATATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
29 32 0.52
30 10 0.16
31 8 0.13
32 12 0.19
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (29 bp):
ATTTTTTTAAAAATTTATTAGAATTTTAT
Found at i:11123792 original size:20 final size:19
Alignment explanation
Indices: 11123769--11123829 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 19
11123759 GTTAAAAGTT
11123769 TTATAAATTATTTTATATTA
1 TTATAAA-TATTTTATATTA
* *
11123789 TTATAAAAATTTTAATATTT
1 TTATAAATATTTT-ATATTA
*
11123809 TTATGAAAATATATTATATTA
1 TTAT--AAATATTTTATATTA
11123830 AATCATAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
19 5 0.15
20 16 0.48
21 5 0.15
22 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TTATAAATATTTTATATTA
Found at i:11131180 original size:33 final size:33
Alignment explanation
Indices: 11131143--11131210 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
11131133 AGAAACCGAT
11131143 GGCGGTGGTGGAGGAACTGACTGCGGCGGGGGC
1 GGCGGTGGTGGAGGAACTGACTGCGGCGGGGGC
11131176 GGCGGTGGTGGAGGAACTGACTGCGGCGGGGGC
1 GGCGGTGGTGGAGGAACTGACTGCGGCGGGGGC
11131209 GG
1 GG
11131211 ACTTACATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.12, C:0.18, G:0.59, T:0.12
Consensus pattern (33 bp):
GGCGGTGGTGGAGGAACTGACTGCGGCGGGGGC
Found at i:11132374 original size:29 final size:31
Alignment explanation
Indices: 11132327--11132394 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
11132317 AGTATAATTT
* *
11132327 AATTTTAAAATCTGAAAAA-TATAGAG-ATTA
1 AATTTTAAAATATAAAAAAGTATA-AGTATTA
11132357 AATTTTAAAA-ATAAAAAAGTATAAGTATTA
1 AATTTTAAAATATAAAAAAGTATAAGTATTA
11132387 AATTTTAA
1 AATTTTAA
11132395 GTTTATAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 8 0.24
30 26 0.76
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.35
Consensus pattern (31 bp):
AATTTTAAAATATAAAAAAGTATAAGTATTA
Found at i:11135160 original size:19 final size:17
Alignment explanation
Indices: 11135138--11135176 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
11135128 CACTAAAATT
11135138 ATTATAAATTATAAAAAAA
1 ATTAT-AATT-TAAAAAAA
*
11135157 ATTATGATTTAAAAAAA
1 ATTATAATTTAAAAAAA
11135174 ATT
1 ATT
11135177 GATGAAATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 3 0.16
19 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
ATTATAATTTAAAAAAA
Found at i:11144795 original size:5 final size:5
Alignment explanation
Indices: 11144758--11144791 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
11144748 CCTTTTAAAC
*
11144758 AACAA AACAA AACAA AACAA AACAA AACAG AACA
1 AACAA AACAA AACAA AACAA AACAA AACAA AACA
11144792 GAACTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.76, C:0.21, G:0.03, T:0.00
Consensus pattern (5 bp):
AACAA
Found at i:11149403 original size:124 final size:123
Alignment explanation
Indices: 11149165--11149410 Score: 318
Period size: 124 Copynumber: 2.0 Consensus size: 123
11149155 CAAAGAATCA
*
11149165 AGAACCAAGCTTCATTGAGTGATTGGAAAGAGAATCTGAGAAACCTTTAAAGTTCTCTTCTTTCT
1 AGAACCAAGCTTCATTGAGTGATTGAAAAGAGAATCTGAGAAACCTTTAAAGTTCTCTTCTTTCT
* * * * * *
11149230 GTAGGTCAGTAATAAGGCATGAATCCAGATAACATAGTATTGACATTGAATTTGTCTCG
66 GTAGCTAAGCAATAAGACATGAATCCAGATAACATAATATCGACATTGAA-TTGTCTCG
* *
11149289 AGAACCAAGCTTCATTGAGTGATTGTAAAAG-GCATCTGAGAAACCTTTAAAGTT-TCTTTTTTG
1 AGAACCAAGCTTCATTGAGTGATTG-AAAAGAGAATCTGAGAAACCTTTAAAGTTCTCTTCTTT-
* * * *
11149352 TTGTTGCTAAGCAATAAGATATGAATCCAGAT-ACTATAATATCGACCTTGAATTGTCTC
64 CTGTAGCTAAGCAATAAGACATGAATCCAGATAAC-ATAATATCGACATTGAATTGTCTC
11149411 AATTTCTAGA
Statistics
Matches: 106, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
123 16 0.15
124 86 0.81
125 4 0.04
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (123 bp):
AGAACCAAGCTTCATTGAGTGATTGAAAAGAGAATCTGAGAAACCTTTAAAGTTCTCTTCTTTCT
GTAGCTAAGCAATAAGACATGAATCCAGATAACATAATATCGACATTGAATTGTCTCG
Found at i:11163959 original size:8 final size:8
Alignment explanation
Indices: 11163948--11163974 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
11163938 AATCATTTAA
11163948 TTTTTCAT
1 TTTTTCAT
11163956 TTTTTCAT
1 TTTTTCAT
11163964 TTTTTCAT
1 TTTTTCAT
11163972 TTT
1 TTT
11163975 CTGGTCACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTCAT
Found at i:11167499 original size:25 final size:25
Alignment explanation
Indices: 11167471--11167519 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
11167461 CATCTTTTTA
*
11167471 TTAACTATTTAAGTGTTGGTGATAG
1 TTAACTATTTAAGTGTTGATGATAG
*
11167496 TTAACTATTTAATTGTTGATGATA
1 TTAACTATTTAAGTGTTGATGATA
11167520 AAAATATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (25 bp):
TTAACTATTTAAGTGTTGATGATAG
Found at i:11177388 original size:2 final size:2
Alignment explanation
Indices: 11177381--11177411 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
11177371 ACATTTTAGA
*
11177381 AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11177412 ATTTTCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:11183845 original size:12 final size:12
Alignment explanation
Indices: 11183828--11183852 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11183818 GGTGTTCATT
11183828 CGGTTAACCGAC
1 CGGTTAACCGAC
11183840 CGGTTAACCGAC
1 CGGTTAACCGAC
11183852 C
1 C
11183853 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:11184025 original size:9 final size:9
Alignment explanation
Indices: 11184011--11184096 Score: 111
Period size: 9 Copynumber: 9.4 Consensus size: 9
11184001 TTTGGTTAAA
11184011 AATTACCCG
1 AATTACCCG
11184020 AATTACCCG
1 AATTACCCG
11184029 AATTACCCG
1 AATTACCCG
*
11184038 AATTAACCG
1 AATTACCCG
*
11184047 AATTAACCG
1 AATTACCCG
*
11184056 AATTAACCG
1 AATTACCCG
11184065 AATTA-CCG
1 AATTACCCG
*
11184073 AAAAATACCCG
1 --AATTACCCG
11184084 AATTACCCG
1 AATTACCCG
11184093 AATT
1 AATT
11184097 TTTTTAATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
8 3 0.04
9 61 0.86
10 4 0.06
11 3 0.04
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:11185884 original size:2 final size:2
Alignment explanation
Indices: 11185877--11185901 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11185867 GTCATTTTCA
11185877 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
11185902 ACATGTGAAT
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:11186658 original size:2 final size:2
Alignment explanation
Indices: 11186651--11186680 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
11186641 CCGACTCAAT
11186651 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11186681 TTAAGTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:11190635 original size:21 final size:21
Alignment explanation
Indices: 11190611--11190651 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11190601 TAAAAACTTC
11190611 AAATA-TATATATAAAATAAAT
1 AAATATTA-ATATAAAATAAAT
*
11190632 AAATATTAATATTAAATAAA
1 AAATATTAATATAAAATAAA
11190652 AAAAAGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATATTAATATAAAATAAAT
Found at i:11191672 original size:26 final size:26
Alignment explanation
Indices: 11191623--11191673 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
11191613 AAAAAATATA
* *
11191623 ATTTAGGTACCAATTATGATAAAAAG
1 ATTTAGGTACCAAATAAGATAAAAAG
11191649 ATTTAGGTACCAAAATAAGA-AAAAA
1 ATTTAGGTACC-AAATAAGATAAAAA
11191674 TATATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.25
Consensus pattern (26 bp):
ATTTAGGTACCAAATAAGATAAAAAG
Found at i:11193029 original size:2 final size:2
Alignment explanation
Indices: 11193022--11193053 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11193012 GACAATAAAG
11193022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11193054 TAGACCTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11197270 original size:19 final size:17
Alignment explanation
Indices: 11197244--11197297 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
11197234 AAAGCTGTAT
11197244 ACAATTAGAACTCTAAG
1 ACAATTAGAACTCTAAG
* *
11197261 ACATAATTAGAAGCTGT-AT
1 AC--AATTAGAA-CTCTAAG
11197280 ACAATTAGAACTCTAAG
1 ACAATTAGAACTCTAAG
11197297 A
1 A
11197298 TTAAATAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
16 3 0.10
17 12 0.41
19 11 0.38
20 3 0.10
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (17 bp):
ACAATTAGAACTCTAAG
Found at i:11197275 original size:36 final size:36
Alignment explanation
Indices: 11197227--11197297 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
11197217 ATCAAAGGCT
11197227 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
*
11197263 ATAATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGA
11197298 TTAAATAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (36 bp):
ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:11197287 original size:17 final size:17
Alignment explanation
Indices: 11197229--11197289 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
11197219 CAAAGGCTAT
*
11197229 AATTAAAAGCTGTATAC
1 AATTAGAAGCTGTATAC
* *
11197246 AATTAGAA-CTCTAAGAC
1 AATTAGAAGCTGT-ATAC
11197263 ATAATTAGAAGCTGTATAC
1 --AATTAGAAGCTGTATAC
11197282 AATTAGAA
1 AATTAGAA
11197290 CTCTAAGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 3 0.09
17 18 0.51
19 11 0.31
20 3 0.09
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (17 bp):
AATTAGAAGCTGTATAC
Found at i:11210615 original size:25 final size:24
Alignment explanation
Indices: 11210580--11210628 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
11210570 ATATTAAAAT
*
11210580 TTATATAAATATTAAATAAATATAA
1 TTATATAAATATAAAATAAA-ATAA
*
11210605 TTATATTAATATAAAATAAAATAA
1 TTATATAAATATAAAATAAAATAA
11210629 GAATCCCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TTATATAAATATAAAATAAAATAA
Found at i:11212933 original size:15 final size:15
Alignment explanation
Indices: 11212913--11212946 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11212903 TATTCGAGTC
11212913 ATATATTT-TTTAATT
1 ATATATTTGTTT-ATT
11212928 ATATATTTGTTTATT
1 ATATATTTGTTTATT
11212943 ATAT
1 ATAT
11212947 TATAAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.83
16 3 0.17
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
ATATATTTGTTTATT
Found at i:11228027 original size:31 final size:31
Alignment explanation
Indices: 11227959--11228027 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
11227949 TTTTAAAATT
* * * *
11227959 TATATAATTGAATTAAAATTAAAATTTCATA
1 TATATATTTGAATCAAAATCAAAATATCATA
*
11227990 TATATATTTGAATCATAATCAAAATATCATA
1 TATATATTTGAATCAAAATCAAAATATCATA
11228021 TATATAT
1 TATATAT
11228028 ATATATATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (31 bp):
TATATATTTGAATCAAAATCAAAATATCATA
Found at i:11228273 original size:23 final size:24
Alignment explanation
Indices: 11228247--11228308 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 24
11228237 TATGGGCCCG
* *
11228247 TTTTTAATTAAAATTAAAATTATT
1 TTTTTAATTAAAATTAAAACTATA
11228271 TTTTTAA-TAAAATTAAAACTA-A
1 TTTTTAATTAAAATTAAAACTATA
*
11228293 TTGTT-ATTAAAATTAA
1 TTTTTAATTAAAATTAA
11228309 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.03
22 13 0.38
23 13 0.38
24 7 0.21
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTTTAATTAAAATTAAAACTATA
Found at i:11228321 original size:16 final size:16
Alignment explanation
Indices: 11228284--11228323 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
11228274 TTAATAAAAT
* *
11228284 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
11228300 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
11228316 TAAAATTA
1 TAAAATTA
11228324 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:11228385 original size:66 final size:67
Alignment explanation
Indices: 11228312--11228454 Score: 243
Period size: 68 Copynumber: 2.1 Consensus size: 67
11228302 AAATTAATTG
* *
11228312 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTGTTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
11228376 GA
66 GA
*
11228378 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
11228443 TGA
65 TGA
11228446 TTAGTAAAA
1 TTAGTAAAA
11228455 CAAACTTGAT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 26 0.37
68 45 0.63
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.45
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
GA
Found at i:11228408 original size:9 final size:9
Alignment explanation
Indices: 11228396--11228423 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
11228386 TTTATCAAAT
11228396 TATTAATTG
1 TATTAATTG
11228405 TATTAATTG
1 TATTAATTG
11228414 TATTAATTG
1 TATTAATTG
11228423 T
1 T
11228424 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:11238926 original size:15 final size:15
Alignment explanation
Indices: 11238890--11238926 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
11238880 TAATTTTTTA
11238890 AATAAAAT-TTAATT
1 AATAAAATATTAATT
*
11238904 TA-AAAATATTAATT
1 AATAAAATATTAATT
11238918 AATAAAATA
1 AATAAAATA
11238927 AAAACCCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 5 0.26
14 8 0.42
15 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAAAATATTAATT
Found at i:11259749 original size:24 final size:24
Alignment explanation
Indices: 11259717--11259771 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
11259707 TCCGATGCTT
11259717 CCCGTTAATTGCTCTTCGGAGCTA
1 CCCGTTAATTGCTCTTCGGAGCTA
**
11259741 CCCGTTAATTGCTCTTTTGAGCTA
1 CCCGTTAATTGCTCTTCGGAGCTA
11259765 CCCGTTA
1 CCCGTTA
11259772 TAGGCTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.36
Consensus pattern (24 bp):
CCCGTTAATTGCTCTTCGGAGCTA
Found at i:11259778 original size:24 final size:26
Alignment explanation
Indices: 11259717--11259799 Score: 86
Period size: 24 Copynumber: 3.4 Consensus size: 26
11259707 TCCGATGCTT
* *
11259717 CCCGTTA-ATTGCTCTTCG-GAGCTA
1 CCCGTTATATGGCTCTTTGTGAGCTA
*
11259741 CCCGTTA-ATTGCTCTTT-TGAGCTA
1 CCCGTTATATGGCTCTTTGTGAGCTA
*
11259765 CCCGTTATA-GGCTCTTTGTGAGCTT
1 CCCGTTATATGGCTCTTTGTGAGCTA
*
11259790 CTCGTTATAT
1 CCCGTTATAT
11259800 TTCCCGAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
24 36 0.71
25 15 0.29
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (26 bp):
CCCGTTATATGGCTCTTTGTGAGCTA
Found at i:11261337 original size:46 final size:46
Alignment explanation
Indices: 11261264--11261402 Score: 181
Period size: 46 Copynumber: 3.0 Consensus size: 46
11261254 ACAAGGCTAT
* *
11261264 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTAACCGAAATACCATACCTACTTTTCAC
* * * *
11261310 AACTCAATATGGTTTTCTTTACCGAAATACCATATCAACTTTTCAC
1 AACTCAGTATGGTTTTCTTAACCGAAATACCATACCTACTTTTCAC
* * *
11261356 AACTCAGTATGGTTTTCTTAACTGGAATATCATACCTA-TGTTTCAC
1 AACTCAGTATGGTTTTCTTAACCGAAATACCATACCTACT-TTTCAC
11261402 A
1 A
11261403 CCTTGCCATG
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
45 1 0.01
46 79 0.99
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTAACCGAAATACCATACCTACTTTTCAC
Found at i:11263533 original size:17 final size:17
Alignment explanation
Indices: 11263513--11263549 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
11263503 AATTTTTGAA
11263513 TTAGTGAATTCTGTGAT
1 TTAGTGAATTCTGTGAT
*
11263530 TTAGTGAATTTTGTGAT
1 TTAGTGAATTCTGTGAT
11263547 TTA
1 TTA
11263550 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTCTGTGAT
Found at i:11264146 original size:46 final size:46
Alignment explanation
Indices: 11264090--11264201 Score: 197
Period size: 46 Copynumber: 2.4 Consensus size: 46
11264080 CCATGGAAAT
*
11264090 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAGCCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
*
11264136 TTGTGCAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
*
11264182 TTGTGAAAAGCAGGTATGGT
1 TTGTGAAAAGTAGGTATGGT
11264202 AAAATAACAT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:11264616 original size:46 final size:46
Alignment explanation
Indices: 11264549--11264642 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
11264539 ACAGTGCTAT
* *
11264549 AACTCAATATGGTTTCCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAATATGGTTTCCTTCACTGAAACACCATACCTACATTTCAC
* * * *
11264595 AACTCAGTATGGTTTTCTTCACTGAAACACTATGCCTACATTTCAC
1 AACTCAATATGGTTTCCTTCACTGAAACACCATACCTACATTTCAC
11264641 AA
1 AA
11264643 TTTTCCATGG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.34
Consensus pattern (46 bp):
AACTCAATATGGTTTCCTTCACTGAAACACCATACCTACATTTCAC
Found at i:11268228 original size:28 final size:29
Alignment explanation
Indices: 11268169--11268228 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
11268159 GAATTGAAAA
*
11268169 TTTTAATTTTTTTATATTATTTGGTAAGT
1 TTTTAATTTTTTTATATTATTTGGAAAGT
*
11268198 TTTTAATTTTTTTA-ATTATTT-GAAATT
1 TTTTAATTTTTTTATATTATTTGGAAAGT
11268225 TTTT
1 TTTT
11268229 CCAAAGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 8 0.28
28 7 0.24
29 14 0.48
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (29 bp):
TTTTAATTTTTTTATATTATTTGGAAAGT
Found at i:11268305 original size:20 final size:20
Alignment explanation
Indices: 11268266--11268323 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
11268256 TTATATAATA
11268266 TTAA-TATTTTAAAAAAATT
1 TTAACTATTTTAAAAAAATT
**
11268285 TGTAAC-ATTTTAAAATTATT
1 T-TAACTATTTTAAAAAAATT
*
11268305 TTCACTATTTTAAATAAAA
1 TTAACTATTTTAAA-AAAA
11268324 ATATTTTTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 4 0.13
20 24 0.80
21 2 0.07
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (20 bp):
TTAACTATTTTAAAAAAATT
Found at i:11270727 original size:25 final size:25
Alignment explanation
Indices: 11270699--11270750 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
11270689 GATTTGAGTA
*
11270699 ACTTA-ACAAAAAAAATTTAAATATC
1 ACTTATACAAAAAAAA-GTAAATATC
*
11270724 ACTTATTATAAAAAAAAGTAAATATC
1 ACTTA-TACAAAAAAAAGTAAATATC
11270750 A
1 A
11270751 AATTGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 5 0.22
26 9 0.39
27 9 0.39
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (25 bp):
ACTTATACAAAAAAAAGTAAATATC
Found at i:11283160 original size:27 final size:29
Alignment explanation
Indices: 11283110--11283182 Score: 82
Period size: 27 Copynumber: 2.6 Consensus size: 29
11283100 ATTTTTTATC
**
11283110 AAGCTTAAACTCCGAAT-TTCAAATC-CG
1 AAGCTTAAACTCTAAATCTTCAAATCTCG
11283137 AAGCTTAAACTCTAAATCTT-AAATCTCG
1 AAGCTTAAACTCTAAATCTTCAAATCTCG
*
11283165 AACCTTAAA-TCTTAAATC
1 AAGCTTAAACTC-TAAATC
11283183 CTGAACGGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (29 bp):
AAGCTTAAACTCTAAATCTTCAAATCTCG
Found at i:11292319 original size:17 final size:17
Alignment explanation
Indices: 11292297--11292330 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11292287 AAATTTTTTG
*
11292297 TATAATTTAAAAAAAAT
1 TATAATATAAAAAAAAT
*
11292314 TATAATATAGAAAAAAT
1 TATAATATAAAAAAAAT
11292331 ACTAAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
TATAATATAAAAAAAAT
Found at i:11293133 original size:37 final size:38
Alignment explanation
Indices: 11293092--11293182 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 38
11293082 ACACATGAAT
* *
11293092 TTGAACTATTGATTTTTGTTTTGC-TGCATATAAGTTG
1 TTGAACTATTGATTTTTGGTATGCATGCATATAAGTTG
* * *
11293129 TTGAATTGTTGATTTTTGGTATGCAATGTATATAAGTTG
1 TTGAACTATTGATTTTTGGTATGC-ATGCATATAAGTTG
* *
11293168 TTAAACTAGTGATTT
1 TTGAACTATTGATTT
11293183 AGTAAGTTCT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
37 20 0.47
39 23 0.53
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.49
Consensus pattern (38 bp):
TTGAACTATTGATTTTTGGTATGCATGCATATAAGTTG
Found at i:11303750 original size:20 final size:20
Alignment explanation
Indices: 11303725--11303774 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
11303715 GCTGCTGCCT
*
11303725 TTGTCCCTTCCACCATGG-TG
1 TTGTCCCTTCCACCA-GGCTA
11303745 TTGTCCCTTCCACCAGGCTA
1 TTGTCCCTTCCACCAGGCTA
11303765 TTGTCCCTTC
1 TTGTCCCTTC
11303775 AATGGGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.10, C:0.38, G:0.16, T:0.36
Consensus pattern (20 bp):
TTGTCCCTTCCACCAGGCTA
Found at i:11303877 original size:17 final size:18
Alignment explanation
Indices: 11303843--11303889 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
11303833 TCAACTGGAA
*
11303843 AAGAGAGAGAAAGGAGAAG
1 AAGAGA-AGAAAGAAGAAG
11303862 AAGAGAAG-AAGAAGAAG
1 AAGAGAAGAAAGAAGAAG
11303879 AA-AGAAAGAAA
1 AAGAG-AAGAAA
11303890 AAAGGTAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 13 0.52
18 4 0.16
19 6 0.24
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
AAGAGAAGAAAGAAGAAG
Found at i:11303888 original size:14 final size:14
Alignment explanation
Indices: 11303843--11303884 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
11303833 TCAACTGGAA
*
11303843 AAGAGAGAGAAAGGAG
1 AAGA-AGAG-AAGAAG
11303859 AAGAAGAGAAGAAG
1 AAGAAGAGAAGAAG
11303873 AAGAAGA-AAGAA
1 AAGAAGAGAAGAA
11303885 AGAAAAAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 5 0.20
14 12 0.48
15 4 0.16
16 4 0.16
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
AAGAAGAGAAGAAG
Found at i:11304082 original size:60 final size:59
Alignment explanation
Indices: 11304016--11304147 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 59
11304006 ATAGTTTTGG
* * **
11304016 ATTAGTATTTTGTATGAATGTAAT-TTTTTTTGCT-TTTTATAATTATTTTAAAATTAATTT
1 ATTAGTATTTAGAAT-AATGTAATAAATTTTTG-TGTTTT-TAATTATTTTAAAATTAATTT
* * *
11304076 GTTAGTAATTTAGAATTATGTTATAAATTTTTGTGTTTTTAATTATTTTAAAATTAATTT
1 ATTAGT-ATTTAGAATAATGTAATAAATTTTTGTGTTTTTAATTATTTTAAAATTAATTT
11304136 ATTAGTAATTTA
1 ATTAGT-ATTTA
11304148 AATTTGTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
60 44 0.72
61 17 0.28
ACGTcount: A:0.33, C:0.01, G:0.09, T:0.58
Consensus pattern (59 bp):
ATTAGTATTTAGAATAATGTAATAAATTTTTGTGTTTTTAATTATTTTAAAATTAATTT
Found at i:11304902 original size:56 final size:56
Alignment explanation
Indices: 11304763--11304930 Score: 211
Period size: 56 Copynumber: 3.1 Consensus size: 56
11304753 AAATGGTATG
* * * *
11304763 TTTTTTGTAATCGTGCCTATCTGATAGGTGCCAATCAATTTTTTATATTAAAAAA-A
1 TTTTTT-TAATCGCGCCTATCTGACAGGCGCGAATCAATTTTTTATATTAAAAAATA
* * * *
11304819 ----ATTAATCGCGCCTATCTAACAGACGCGAATTAATTTTTTATATTAAAAAATA
1 TTTTTTTAATCGCGCCTATCTGACAGGCGCGAATCAATTTTTTATATTAAAAAATA
*
11304871 TTTTTTTAATCGCGCCTATCTGACAGGCGCGAATCAATTTTTTATATTAAAATATA
1 TTTTTTTAATCGCGCCTATCTGACAGGCGCGAATCAATTTTTTATATTAAAAAATA
11304927 TTTT
1 TTTT
11304931 GTTGTTTAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
51 41 0.44
52 2 0.02
56 51 0.54
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (56 bp):
TTTTTTTAATCGCGCCTATCTGACAGGCGCGAATCAATTTTTTATATTAAAAAATA
Found at i:11305211 original size:17 final size:17
Alignment explanation
Indices: 11305189--11305228 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
11305179 TTAACTCATT
*
11305189 TAATTTTTTATATAATG
1 TAATTTTTTATATAATA
11305206 TAA-TTTTTATATAATA
1 TAATTTTTTATATAATA
11305222 TAATTTT
1 TAATTTT
11305229 ATTTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TAATTTTTTATATAATA
Found at i:11309085 original size:29 final size:31
Alignment explanation
Indices: 11309052--11309109 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
11309042 CCTTTTTACT
11309052 TTTCCCT-CAAAACTTTTACT-CCTTCCCAC
1 TTTCCCTCCAAAACTTTTACTCCCTTCCCAC
11309081 TTTCCCTCCAAAACTTTTACTCCCTTCCC
1 TTTCCCTCCAAAACTTTTACTCCCTTCCC
11309110 CTCCCAAGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 7 0.26
30 13 0.48
31 7 0.26
ACGTcount: A:0.19, C:0.43, G:0.00, T:0.38
Consensus pattern (31 bp):
TTTCCCTCCAAAACTTTTACTCCCTTCCCAC
Found at i:11309249 original size:30 final size:31
Alignment explanation
Indices: 11309215--11309273 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
11309205 AACATTTTAT
*
11309215 TTTTCCCCAAAATTTTTACTCCC-TCCCACC
1 TTTTCCCCAAAACTTTTACTCCCTTCCCACC
* *
11309245 TTTTCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCAAAACTTTTACTCCCTTCCCA
11309274 TCCCACCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.39, G:0.00, T:0.41
Consensus pattern (31 bp):
TTTTCCCCAAAACTTTTACTCCCTTCCCACC
Found at i:11309386 original size:16 final size:17
Alignment explanation
Indices: 11309365--11309396 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11309355 ACTTTCCCTC
11309365 AAAC-TTTTATTTTCCA
1 AAACTTTTTATTTTCCA
11309381 AAACTTTTTATTTTCC
1 AAACTTTTTATTTTCC
11309397 CCCTAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (17 bp):
AAACTTTTTATTTTCCA
Found at i:11310949 original size:17 final size:18
Alignment explanation
Indices: 11310927--11310960 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
11310917 GCTTGCGCAT
11310927 ATTATTTT-TTTAATATA
1 ATTATTTTATTTAATATA
11310944 ATTATTTTATTTAATAT
1 ATTATTTTATTTAATAT
11310961 TTAGTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTATTTTATTTAATATA
Found at i:11327138 original size:27 final size:28
Alignment explanation
Indices: 11327080--11327148 Score: 122
Period size: 27 Copynumber: 2.5 Consensus size: 28
11327070 AAAAATAAAA
*
11327080 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTATCAAAATATTACAACTTTTTTTT
11327108 ATTTATCAAAATATTACAA-TTTTTTTT
1 ATTTATCAAAATATTACAACTTTTTTTT
11327135 ATTTATCAAAATAT
1 ATTTATCAAAATAT
11327149 ATAAAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTTATCAAAATATTACAACTTTTTTTT
Found at i:11327312 original size:19 final size:19
Alignment explanation
Indices: 11327285--11327354 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
11327275 TCAACTCATT
*
11327285 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
11327304 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
11327322 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
11327341 TTTTAATTTAATAA
1 TTTTAATTTAATAA
11327355 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:11327333 original size:37 final size:37
Alignment explanation
Indices: 11327290--11327360 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
11327280 TCATTTTTTT
11327290 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
11327327 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
11327361 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:11327948 original size:28 final size:27
Alignment explanation
Indices: 11327908--11327983 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 27
11327898 NNNNNNNNNT
11327908 TTTATATATTTTGGTAAATAAAAAAAA
1 TTTATATATTTTGGTAAATAAAAAAAA
11327935 GTTTATATATTTTGGTAAAT---AAAAA
1 -TTTATATATTTTGGTAAATAAAAAAAA
11327960 -TTATAATATTTTGGTAAATAAAAA
1 TTTAT-ATATTTTGGTAAATAAAAA
11327984 GTTGTAATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.09
24 14 0.32
25 5 0.11
27 2 0.05
28 19 0.43
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (27 bp):
TTTATATATTTTGGTAAATAAAAAAAA
Found at i:11327958 original size:24 final size:25
Alignment explanation
Indices: 11327908--11328002 Score: 115
Period size: 24 Copynumber: 3.7 Consensus size: 25
11327898 NNNNNNNNNT
11327908 TTTATATATTTTGGTAAATAAAAAAAAG
1 TTTATATATTTTGGTAAAT---AAAAAG
11327936 TTTATATATTTTGGTAAATAAAAA-
1 TTTATATATTTTGGTAAATAAAAAG
11327960 -TTATAATATTTTGGTAAATAAAAAG
1 TTTAT-ATATTTTGGTAAATAAAAAG
*
11327985 TTGTA-ATATTTTGATAAA
1 TT-TATATATTTTGGTAAA
11328003 ATTTTATTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 11
0.84 0.01 0.15
Matches are distributed among these distances:
23 4 0.06
24 19 0.31
25 17 0.27
26 1 0.02
27 2 0.03
28 19 0.31
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (25 bp):
TTTATATATTTTGGTAAATAAAAAG
Found at i:11327983 original size:25 final size:25
Alignment explanation
Indices: 11327909--11328002 Score: 104
Period size: 25 Copynumber: 3.7 Consensus size: 25
11327899 NNNNNNNNTT
11327909 TTAT-ATATTTTGGTAAATAAAAAAAA
1 TTATAATATTTTGGTAAAT--AAAAAA
11327935 GTT-TATATATTTTGGTAAAT-AAAAA
1 -TTATA-ATATTTTGGTAAATAAAAAA
*
11327960 TTATAATATTTTGGTAAATAAAAAG
1 TTATAATATTTTGGTAAATAAAAAA
* *
11327985 TTGTAATATTTTGATAAA
1 TTATAATATTTTGGTAAA
11328003 ATTTTATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
24 16 0.27
25 27 0.45
26 1 0.02
27 2 0.03
28 14 0.23
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.43
Consensus pattern (25 bp):
TTATAATATTTTGGTAAATAAAAAA
Found at i:11329205 original size:31 final size:31
Alignment explanation
Indices: 11329170--11329231 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
11329160 GCCCAGTAAA
* * * *
11329170 TTAAATAAAAATTTTTGAATAGTTCAGTGAC
1 TTAAATAAAAACTTTCGAATAGATCAATGAC
*
11329201 TTAAATGAAAACTTTCGAATAGATCAATGAC
1 TTAAATAAAAACTTTCGAATAGATCAATGAC
11329232 CAAAATTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (31 bp):
TTAAATAAAAACTTTCGAATAGATCAATGAC
Found at i:11342969 original size:28 final size:27
Alignment explanation
Indices: 11342928--11342995 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 27
11342918 TCATGTTACT
* *
11342928 TTTTTTTTTAATTTT-ATTAACTTTTTA
1 TTTTTTGTGAATTTTAATTAA-TTTTTA
11342955 TATTTTTGTGAATTTTGAATTAATTTTTA
1 T-TTTTTGTGAATTTT-AATTAATTTTTA
11342984 TTTTTTGTGAAT
1 TTTTTTGTGAAT
11342996 ATTTTCATGG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 1 0.03
28 23 0.64
29 7 0.19
30 5 0.14
ACGTcount: A:0.24, C:0.01, G:0.07, T:0.68
Consensus pattern (27 bp):
TTTTTTGTGAATTTTAATTAATTTTTA
Found at i:11343374 original size:6 final size:6
Alignment explanation
Indices: 11343363--11343387 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11343353 AATTAATTTA
11343363 TTATGG TTATGG TTATGG TTATGG T
1 TTATGG TTATGG TTATGG TTATGG T
11343388 GGAGGGAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TTATGG
Found at i:11343776 original size:6 final size:6
Alignment explanation
Indices: 11343765--11343791 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
11343755 TGGTGCGTTT
11343765 CTTTCC CTTTCC CTTTCC CTTTCC CTT
1 CTTTCC CTTTCC CTTTCC CTTTCC CTT
11343792 CACCCCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTTCC
Found at i:11345372 original size:3 final size:3
Alignment explanation
Indices: 11345364--11345421 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
11345354 GCATACTTCC
* * * *
11345364 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TGA TGA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11345412 TAA TAA TAA T
1 TAA TAA TAA T
11345422 GTGTTCCTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:11349679 original size:29 final size:29
Alignment explanation
Indices: 11349637--11349695 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
11349627 AAACGTGACG
11349637 TTGTCACCTGCTACTTAATTAAATTTCAC
1 TTGTCACCTGCTACTTAATTAAATTTCAC
*
11349666 TTGTCACCTGCTACTTATTTAAATTTCAC
1 TTGTCACCTGCTACTTAATTAAATTTCAC
11349695 T
1 T
11349696 GAAAGTGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.44
Consensus pattern (29 bp):
TTGTCACCTGCTACTTAATTAAATTTCAC
Found at i:11353474 original size:92 final size:94
Alignment explanation
Indices: 11353365--11353535 Score: 249
Period size: 95 Copynumber: 1.8 Consensus size: 94
11353355 TCTTTTTATA
* * * * *
11353365 AACACACTCGGTGCCATTCAC-G-ACTAC-AAAGAATGAACTATTCTTCATTTTAAATTCAATGC
1 AACACACTCGGTCCCATTCACAGTACGACAAAAGAACGAACTATTCTT-AATATAAATTCAATGC
11353427 AAACGCAACGCATCTTCAGGAGATTCATAG
65 AAACGCAACGCATCTTCAGGAGATTCATAG
*
11353457 AACACACTCGGTCCCATTCACGAGTACGACAAAAGAACGAATTATTCTTAATATAAATTCAATGC
1 AACACACTCGGTCCCATTCAC-AGTACGACAAAAGAACGAACTATTCTTAATATAAATTCAATGC
11353522 AAACGCAACGCATC
65 AAACGCAACGCATC
11353536 ATCATCAGAT
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
92 20 0.29
94 1 0.01
95 32 0.46
96 16 0.23
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (94 bp):
AACACACTCGGTCCCATTCACAGTACGACAAAAGAACGAACTATTCTTAATATAAATTCAATGCA
AACGCAACGCATCTTCAGGAGATTCATAG
Found at i:11357940 original size:24 final size:24
Alignment explanation
Indices: 11357913--11357959 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
11357903 TGGTGTGGCA
*
11357913 ACAGGAGTTGATGATGAAGCAGCT
1 ACAGGAGTTGATGATGAAACAGCT
11357937 ACAGGAGTTGATGATGAAACAGC
1 ACAGGAGTTGATGATGAAACAGC
11357960 ATCAGATGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.32, T:0.19
Consensus pattern (24 bp):
ACAGGAGTTGATGATGAAACAGCT
Found at i:11367786 original size:21 final size:21
Alignment explanation
Indices: 11367747--11367787 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11367737 CCACAAGAAA
* * *
11367747 CCTCTTTATAAATATATTTCT
1 CCTCTTTACAAAGAGATTTCT
11367768 CCTCTTTACAAAGAGATTTC
1 CCTCTTTACAAAGAGATTTC
11367788 ATAGGGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (21 bp):
CCTCTTTACAAAGAGATTTCT
Found at i:11376016 original size:4 final size:4
Alignment explanation
Indices: 11376009--11376048 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
11375999 TATATATATC
*
11376009 TATG TATG TATG TATG TATG TATG TACG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11376049 ACTGCCCTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:11376816 original size:18 final size:18
Alignment explanation
Indices: 11376793--11376832 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
11376783 CAATTCATCG
*
11376793 ATATAAA-TCTATAGATAT
1 ATATAAATTCAATA-ATAT
11376811 ATATAAATTCAATAATAT
1 ATATAAATTCAATAATAT
11376829 ATAT
1 ATAT
11376833 CCAAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (18 bp):
ATATAAATTCAATAATAT
Found at i:11380386 original size:26 final size:26
Alignment explanation
Indices: 11380336--11380395 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
11380326 CATAAATTAT
* *
11380336 GAAGCTCACAAAGAGCCTTTAATCGG
1 GAAGCTCACAAAGAGCCTATAATCGA
11380362 GAAGCTCACGAAA-AGCC-ATATATCGA
1 GAAGCTCAC-AAAGAGCCTATA-ATCGA
*
11380388 GATGCTCA
1 GAAGCTCA
11380396 TAAGAGCTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 2 0.07
26 24 0.83
27 3 0.10
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (26 bp):
GAAGCTCACAAAGAGCCTATAATCGA
Found at i:11380843 original size:5 final size:5
Alignment explanation
Indices: 11380815--11380853 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
11380805 AAATTTAGCA
* *
11380815 CAATT GAATA CAATT CATATT CAATT CAATT CAATT CAA
1 CAATT CAATT CAATT CA-ATT CAATT CAATT CAATT CAA
11380854 ATCCTAGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.36
Consensus pattern (5 bp):
CAATT
Found at i:11390845 original size:26 final size:27
Alignment explanation
Indices: 11390790--11390846 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
11390780 TATAGGGGTA
* * **
11390790 TGGTGCCTATTTGATAGGCGGCACTGG
1 TGGTGCCTATCTGATAGGCGACACCAG
11390817 TGGTG-CTATCTGATAGGCGACACCAG
1 TGGTGCCTATCTGATAGGCGACACCAG
11390843 TGGT
1 TGGT
11390847 ATTTTCCCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.18, C:0.19, G:0.35, T:0.28
Consensus pattern (27 bp):
TGGTGCCTATCTGATAGGCGACACCAG
Done.