Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 105 of 126
Found at i:31633749 original size:23 final size:23
Alignment explanation
Indices: 31633652--31633801 Score: 123
Period size: 23 Copynumber: 6.6 Consensus size: 23
31633642 AGTGCTGAGA
31633652 AAACAGTAAGCACAC-ACAGTGC-
1 AAACAGTAAGCACACGA-AGTGCG
*
31633674 AATCCAGTAAGCACAC-ACAGTGC-
1 AA-ACAGTAAGCACACGA-AGTGCG
** * * *
31633697 AATTAGTAGGCGCAC-ATAGCGC-
1 AAACAGTAAGCACACGA-AGTGCG
* *
31633719 AAATCAGTAGGCACACGAGGTGCG
1 AAA-CAGTAAGCACACGAAGTGCG
31633743 AAACAGTAAGCACACGAAGTGCG
1 AAACAGTAAGCACACGAAGTGCG
* *
31633766 AAACAGTAAGCATACAAAGTGCG
1 AAACAGTAAGCACACGAAGTGCG
31633789 AAACAGTAAGCAC
1 AAACAGTAAGCAC
31633802 GCTAGAGTTC
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
22 18 0.17
23 85 0.79
24 4 0.04
ACGTcount: A:0.41, C:0.23, G:0.23, T:0.12
Consensus pattern (23 bp):
AAACAGTAAGCACACGAAGTGCG
Found at i:31641161 original size:16 final size:16
Alignment explanation
Indices: 31641140--31641170 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31641130 AACAAGGGGA
*
31641140 ATTTTCAATCAATCAT
1 ATTTTCAACCAATCAT
31641156 ATTTTCAACCAATCA
1 ATTTTCAACCAATCA
31641171 AAAAGCACAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTTTCAACCAATCAT
Found at i:31642597 original size:15 final size:15
Alignment explanation
Indices: 31642556--31642607 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 15
31642546 TAAAATAGTG
31642556 AATTTTAATTAAAATA
1 AATTTTAA-TAAAATA
* *
31642572 TTATTTCAATAAAATA
1 -AATTTTAATAAAATA
31642588 AATTTTAAT-AAAT-
1 AATTTTAATAAAATA
31642601 AATTTTA
1 AATTTTA
31642608 TATTTGTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 7 0.23
14 4 0.13
15 7 0.23
16 7 0.23
17 6 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTTTAATAAAATA
Found at i:31644010 original size:21 final size:21
Alignment explanation
Indices: 31643986--31644036 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
31643976 GAATAAGTTT
* *
31643986 TACCGATACAACTCTACGT-AC
1 TACCGATACAAC-ATAAGTAAC
31644007 TACCGATACAACATAAGTAAC
1 TACCGATACAACATAAGTAAC
31644028 TACCGATAC
1 TACCGATAC
31644037 TAAAACTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (21 bp):
TACCGATACAACATAAGTAAC
Found at i:31648577 original size:27 final size:27
Alignment explanation
Indices: 31648547--31648603 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
31648537 GGGTCAAAGC
*
31648547 CAACTCGGGTCAACGAGTCGGGTTGAT
1 CAACTCGGGTCAACGAGTCGGGTCGAT
31648574 CAACTCGGGTCAACGAGTCGGGTCGAT
1 CAACTCGGGTCAACGAGTCGGGTCGAT
31648601 CAA
1 CAA
31648604 TAGGCGAGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.32, T:0.19
Consensus pattern (27 bp):
CAACTCGGGTCAACGAGTCGGGTCGAT
Found at i:31650513 original size:25 final size:25
Alignment explanation
Indices: 31650460--31650506 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
31650450 GCTGGGATCT
**
31650460 TTAT-TTTATTTAATATTGATATAA
1 TTATATTTATTTAATATAAATATAA
31650484 TTATATTTATTTAATATAAATAT
1 TTATATTTATTTAATATAAATAT
31650507 GAATATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TTATATTTATTTAATATAAATATAA
Found at i:31656039 original size:16 final size:17
Alignment explanation
Indices: 31656015--31656049 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
31656005 TGAGTAAAAG
31656015 AAAACATTTTA-TTTAA
1 AAAACATTTTATTTTAA
*
31656031 AAAATATTTTATTTTAA
1 AAAACATTTTATTTTAA
31656048 AA
1 AA
31656050 TTTGTTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
AAAACATTTTATTTTAA
Found at i:31660845 original size:34 final size:35
Alignment explanation
Indices: 31660807--31660877 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
31660797 CAAAAAAATA
31660807 TTTATTT-ACTAAAATAATATAAAAAATTATTTAT
1 TTTATTTGACTAAAATAATATAAAAAATTATTTAT
*
31660841 TTTATTTGACTAAAATAATATTAAAAATTATTTAT
1 TTTATTTGACTAAAATAATATAAAAAATTATTTAT
31660876 TT
1 TT
31660878 AATAAAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 7 0.20
35 28 0.80
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (35 bp):
TTTATTTGACTAAAATAATATAAAAAATTATTTAT
Found at i:31660876 original size:30 final size:30
Alignment explanation
Indices: 31660782--31660888 Score: 103
Period size: 29 Copynumber: 3.5 Consensus size: 30
31660772 GTTAGAGTTT
** *
31660782 TTTACTAATTTAATACAAAAAAA-TATTTA
1 TTTACTAAAATAATATAAAAAAATTATTTA
31660811 TTTACTAAAATAATATAAAAAATTATTTATTTTA
1 TTTACTAAAATAATATAAAAAA--A-TTA-TTTA
*
31660845 TTTGACTAAAATAATAT-TAAAAATTATTTA
1 TTT-ACTAAAATAATATAAAAAAATTATTTA
*
31660875 TTTAATAAAA-AATA
1 TTTACTAAAATAATA
31660889 AAATTAAATA
Statistics
Matches: 67, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
28 4 0.06
29 25 0.37
30 7 0.10
31 4 0.06
32 1 0.01
33 2 0.03
34 11 0.16
35 13 0.19
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (30 bp):
TTTACTAAAATAATATAAAAAAATTATTTA
Found at i:31661029 original size:3 final size:3
Alignment explanation
Indices: 31661019--31661061 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
31661009 ATTAAAAAAT
31661019 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
31661062 GTGGTGCCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:31661154 original size:3 final size:3
Alignment explanation
Indices: 31661148--31661223 Score: 100
Period size: 3 Copynumber: 25.3 Consensus size: 3
31661138 AAAAAATCCA
*
31661148 AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
31661196 AAG AAC AGAG GAG AA- AAG GAG AAG AAG A
1 AAG AAG A-AG AAG AAG AAG AAG AAG AAG A
31661224 GGAGAATTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.03
3 60 0.95
4 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:31661185 original size:27 final size:28
Alignment explanation
Indices: 31661146--31661223 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
31661136 AAAAAAAATC
31661146 CAAAGAAGAAGAAGAAGAAGAAGAAGAA
1 CAAAGAAGAAGAAGAAGAAGAAGAAGAA
31661174 -AAAGAAGAAGAAGAAGAAGAAGAAGAA
1 CAAAGAAGAAGAAGAAGAAGAAGAAGAA
* * *
31661201 CAGAGGAGAA-AAGGAGAAGAAGA
1 CAAAGAAGAAGAAGAAGAAGAAGA
31661224 GGAGAATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 39 0.85
28 7 0.15
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (28 bp):
CAAAGAAGAAGAAGAAGAAGAAGAAGAA
Found at i:31664061 original size:26 final size:26
Alignment explanation
Indices: 31664029--31664080 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
31664019 ATGAATTTGA
*
31664029 AATTAATTATGTTTAAT-TTTGTATTT
1 AATTAATAAT-TTTAATGTTTGTATTT
*
31664055 AATTAATAATTTTTATGTTTGTATTT
1 AATTAATAATTTTAATGTTTGTATTT
31664081 TAGTTTAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (26 bp):
AATTAATAATTTTAATGTTTGTATTT
Found at i:31664110 original size:28 final size:26
Alignment explanation
Indices: 31664078--31664164 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 26
31664068 TATGTTTGTA
31664078 TTTTAGTTTAAGGGTTTCGAATTTAAGG
1 TTTTA-TTTAAGGGTTT-GAATTTAAGG
31664106 TTTTATGTTAAGGGTTATGAATTTAAGG
1 TTTTAT-TTAAGGGTT-TGAATTTAAGG
*
31664134 TTTTGAATTT-AGGGTTTAAGATTTAAGG
1 TTTT--ATTTAAGGGTTTGA-ATTTAAGG
31664162 TTT
1 TTT
31664165 CAAGTTTTGA
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
27 3 0.06
28 45 0.85
29 3 0.06
30 2 0.04
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.48
Consensus pattern (26 bp):
TTTTATTTAAGGGTTTGAATTTAAGG
Found at i:31664135 original size:14 final size:13
Alignment explanation
Indices: 31664084--31664164 Score: 65
Period size: 14 Copynumber: 5.8 Consensus size: 13
31664074 TGTATTTTAG
31664084 TTTAAGGGTTTCGAA
1 TTTAA-GGTTT-GAA
*
31664099 TTTAAGGTTT-TA
1 TTTAAGGTTTGAA
31664111 TGTTAAGGGTTATGAA
1 T-TTAA-GGTT-TGAA
31664127 TTTAAGGTTTTGAA
1 TTTAAGG-TTTGAA
* *
31664141 TTTAGGGTTTAAGA
1 TTTAAGGTTTGA-A
31664155 TTTAAGGTTT
1 TTTAAGGTTT
31664165 CAAGTTTTGA
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
12 2 0.04
13 8 0.15
14 31 0.56
15 12 0.22
16 2 0.04
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (13 bp):
TTTAAGGTTTGAA
Found at i:31664192 original size:14 final size:14
Alignment explanation
Indices: 31664140--31664193 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
31664130 AAGGTTTTGA
31664140 ATTTAGGGTTTAAG
1 ATTTAGGGTTTAAG
*
31664154 ATTTAAGGTTTCAAG
1 ATTTAGGGTTT-AAG
* *
31664169 -TTTTGAGTTTAAG
1 ATTTAGGGTTTAAG
31664182 ATTTAGGGTTTA
1 ATTTAGGGTTTA
31664194 TAAGTATGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 3 0.09
14 26 0.81
15 3 0.09
ACGTcount: A:0.28, C:0.02, G:0.24, T:0.46
Consensus pattern (14 bp):
ATTTAGGGTTTAAG
Found at i:31666821 original size:20 final size:19
Alignment explanation
Indices: 31666792--31666829 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
31666782 AATAAATCAA
*
31666792 TCACATTAAACAATAAAATT
1 TCACAATAAAC-ATAAAATT
31666812 TCACAATAAACATAAAAT
1 TCACAATAAACATAAAAT
31666830 CAAATTACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (19 bp):
TCACAATAAACATAAAATT
Found at i:31667079 original size:27 final size:27
Alignment explanation
Indices: 31667049--31667100 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
31667039 AAATCCCAAT
* *
31667049 GTGCCGTCACTTGAAAACCCTCCATGA
1 GTGCCGCCACTTCAAAACCCTCCATGA
**
31667076 GTGCCGCCGTTTCAAAACCCTCCAT
1 GTGCCGCCACTTCAAAACCCTCCAT
31667101 CTGTGTGTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (27 bp):
GTGCCGCCACTTCAAAACCCTCCATGA
Found at i:31680835 original size:20 final size:20
Alignment explanation
Indices: 31680810--31680865 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
31680800 CTACCCTGAG
*
31680810 ACTTTTA-CTGATAGAACTTC
1 ACTTTTACCT-ATACAACTTC
31680830 ACTTTTACCTATACAACTTC
1 ACTTTTACCTATACAACTTC
* * *
31680850 AGTTCTACCGATACAA
1 ACTTTTACCTATACAA
31680866 GTATGCTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (20 bp):
ACTTTTACCTATACAACTTC
Found at i:31692384 original size:17 final size:17
Alignment explanation
Indices: 31692362--31692394 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31692352 GAAAATAACT
31692362 TGATAGA-TTGAGAAAAA
1 TGATAGAGTT-AGAAAAA
31692379 TGATAGAGTTAGAAAA
1 TGATAGAGTTAGAAAA
31692395 TATAATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
TGATAGAGTTAGAAAAA
Found at i:31693113 original size:3 final size:3
Alignment explanation
Indices: 31693105--31693141 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
31693095 TTTTAATACT
31693105 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
31693142 TTTTAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:31701579 original size:13 final size:13
Alignment explanation
Indices: 31701560--31701612 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
31701550 TTGCCACTTT
31701560 TATTAAATTTTAA
1 TATTAAATTTTAA
* **
31701573 AATTAAAATTTTTT
1 TATT-AAATTTTAA
*
31701587 TATTAAATTTTAC
1 TATTAAATTTTAA
*
31701600 TATTCAATTTTAA
1 TATTAAATTTTAA
31701613 CTTAAATTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
13 21 0.68
14 10 0.32
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTAAATTTTAA
Found at i:31711860 original size:45 final size:45
Alignment explanation
Indices: 31711809--31711895 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
31711799 AATTCCTCTA
*
31711809 CTTTTATTTAAAAAAATTTAATCCCTCTAATTTTCAATTTTAATT
1 CTTTTATTTAAAAAAAATTAATCCCTCTAATTTTCAATTTTAATT
** *
31711854 CTTTTATTTAAAAAAAATTAATCTTTCTAATTTTTAATTTTA
1 CTTTTATTTAAAAAAAATTAATCCCTCTAATTTTCAATTTTA
31711896 TAAATATGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (45 bp):
CTTTTATTTAAAAAAAATTAATCCCTCTAATTTTCAATTTTAATT
Found at i:31715051 original size:69 final size:69
Alignment explanation
Indices: 31714940--31715075 Score: 254
Period size: 69 Copynumber: 2.0 Consensus size: 69
31714930 CCTAAAAGGA
* *
31714940 TAAAACATCAAAACAGTAGCCCCAAATCCCACTTTTTTTGGTAAACAGTTCAGGAAAAAAGATTT
1 TAAAACATCAAAACAGTAGCCCCAAATCCCAATTTTTTTGGTAAACAGTTCAAGAAAAAAGATTT
31715005 TGGC
66 TGGC
31715009 TAAAACATCAAAACAGTAGCCCCAAATCCCAATTTTTTTGGTAAACAGTTCAAGAAAAAAGATTT
1 TAAAACATCAAAACAGTAGCCCCAAATCCCAATTTTTTTGGTAAACAGTTCAAGAAAAAAGATTT
31715074 TG
66 TG
31715076 CAAGCCAATT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.26
Consensus pattern (69 bp):
TAAAACATCAAAACAGTAGCCCCAAATCCCAATTTTTTTGGTAAACAGTTCAAGAAAAAAGATTT
TGGC
Found at i:31722169 original size:8 final size:7
Alignment explanation
Indices: 31722152--31722205 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 7
31722142 CTCCAACTAT
31722152 GAAGAGAA
1 GAAGA-AA
31722160 GAAGATAA
1 GAAGA-AA
*
31722168 GAAGAAG
1 GAAGAAA
31722175 GAAGAAA
1 GAAGAAA
31722182 GAA-AAA
1 GAAGAAA
31722188 -AA-AAA
1 GAAGAAA
31722193 GAAG-AA
1 GAAGAAA
31722199 GAAGAAA
1 GAAGAAA
31722206 AGGTGTAGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
5 5 0.12
6 11 0.28
7 12 0.30
8 12 0.30
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (7 bp):
GAAGAAA
Found at i:31722183 original size:14 final size:13
Alignment explanation
Indices: 31722156--31722205 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
31722146 AACTATGAAG
31722156 AGAAGAAGATAAGA
1 AGAAGAAGA-AAGA
31722170 AGAAGGAAGAAAGA
1 AGAA-GAAGAAAGA
*
31722184 A-AA-AAAAAAGA
1 AGAAGAAGAAAGA
31722195 AGAAGAAGAAA
1 AGAAGAAGAAA
31722206 AGGTGTAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 8 0.26
12 2 0.06
13 7 0.23
14 9 0.29
15 5 0.16
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (13 bp):
AGAAGAAGAAAGA
Found at i:31726981 original size:16 final size:16
Alignment explanation
Indices: 31726960--31727022 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
31726950 TTTACTAATC
31726960 TATGTATAAAAATATA
1 TATGTATAAAAATATA
* *
31726976 TATGTATATAAAAAAAA
1 TATGTATA-AAAATATA
31726993 TATGTA-AAAAATATA
1 TATGTATAAAAATATA
*
31727008 CAATGT-TAAAAATAT
1 -TATGTATAAAAATAT
31727023 GAATATAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 6 0.15
16 21 0.54
17 12 0.31
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (16 bp):
TATGTATAAAAATATA
Found at i:31726995 original size:17 final size:16
Alignment explanation
Indices: 31726960--31727003 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
31726950 TTTACTAATC
* *
31726960 TATGTATAAAAATATA
1 TATGTATAAAAAAAAA
31726976 TATGTATATAAAAAAAA
1 TATGTATA-AAAAAAAA
31726993 TATGTA-AAAAA
1 TATGTATAAAAA
31727004 TATACAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.16
16 9 0.36
17 12 0.48
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (16 bp):
TATGTATAAAAAAAAA
Found at i:31727548 original size:2 final size:2
Alignment explanation
Indices: 31727543--31727567 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31727533 TATATATATA
31727543 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
31727568 ACATAAAACA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:31736639 original size:18 final size:19
Alignment explanation
Indices: 31736607--31736642 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
31736597 TTGAACTTTA
*
31736607 TTTAATATTTTTTATAAAT
1 TTTAATATTTGTTATAAAT
31736626 TTTAATA-TTGTTATAAA
1 TTTAATATTTGTTATAAA
31736643 AATTTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTAATATTTGTTATAAAT
Found at i:31736648 original size:19 final size:19
Alignment explanation
Indices: 31736606--31736648 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
31736596 TTTGAACTTT
*
31736606 ATTTAATATTTTTTATAAA
1 ATTTAATATTTTATATAAA
*
31736625 TTTTAATATTGTTATA-AAA
1 ATTTAATATT-TTATATAAA
31736644 ATTTA
1 ATTTA
31736649 TAAAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTAATATTTTATATAAA
Found at i:31737319 original size:12 final size:12
Alignment explanation
Indices: 31737302--31737391 Score: 74
Period size: 12 Copynumber: 7.6 Consensus size: 12
31737292 ATAACATTCA
*
31737302 AACAACCAAAAT
1 AACAACAAAAAT
*
31737314 AACAACCAAAAT
1 AACAACAAAAAT
* **
31737326 AATAGTAAAAAT
1 AACAACAAAAAT
*
31737338 AACAAC-AAAAC
1 AACAACAAAAAT
*
31737349 AACAATAAAAAT
1 AACAACAAAAAT
* * *
31737361 AGCAATAAAAAC
1 AACAACAAAAAT
*
31737373 AGCAACAAAAAT
1 AACAACAAAAAT
31737385 AACAACA
1 AACAACA
31737392 TCAAAACAGT
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
11 9 0.15
12 53 0.85
ACGTcount: A:0.69, C:0.18, G:0.03, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:31737346 original size:23 final size:23
Alignment explanation
Indices: 31737309--31737391 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
31737299 TCAAACAACC
* * *
31737309 AAAATAACAACCAAAATAATAGTA
1 AAAATAACAA-CAAAACAACAATA
31737333 AAAATAACAACAAAACAACAATA
1 AAAATAACAACAAAACAACAATA
* * * *
31737356 AAAATAGCAATAAAAACAGCAACA
1 AAAATAACAA-CAAAACAACAATA
31737380 AAAATAACAACA
1 AAAATAACAACA
31737392 TCAAAACAGT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
23 20 0.41
24 29 0.59
ACGTcount: A:0.70, C:0.16, G:0.04, T:0.11
Consensus pattern (23 bp):
AAAATAACAACAAAACAACAATA
Found at i:31737423 original size:26 final size:27
Alignment explanation
Indices: 31737363--31737423 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
31737353 ATAAAAATAG
*
31737363 CAATAAAAACAGCAACAAAAATAACAA
1 CAATAAAAACAGCAACAAAAACAACAA
* *
31737390 C-ATCAAAACAGTAA-AAAAACCAA-AA
1 CAATAAAAACAGCAACAAAAA-CAACAA
31737415 CAATAAAAA
1 CAATAAAAA
31737424 ATAATACCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
25 8 0.29
26 19 0.68
27 1 0.04
ACGTcount: A:0.70, C:0.18, G:0.03, T:0.08
Consensus pattern (27 bp):
CAATAAAAACAGCAACAAAAACAACAA
Found at i:31737479 original size:22 final size:22
Alignment explanation
Indices: 31737408--31737479 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
31737398 CAGTAAAAAA
* *
31737408 ACCAAAACAATAAAAAATAA-T
1 ACCAAAACAGTAAAAAAAAAGT
* * *
31737429 ACCAAAACAG-CAAAAAACAGCA
1 ACCAAAACAGTAAAAAAAAAG-T
*
31737451 ACTAAAACAGTAAAAAAAAAGT
1 ACCAAAACAGTAAAAAAAAAGT
31737473 ACCAAAA
1 ACCAAAA
31737480 TAATAATATA
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
20 6 0.16
21 9 0.24
22 15 0.39
23 8 0.21
ACGTcount: A:0.68, C:0.18, G:0.06, T:0.08
Consensus pattern (22 bp):
ACCAAAACAGTAAAAAAAAAGT
Found at i:31738040 original size:15 final size:14
Alignment explanation
Indices: 31738011--31738049 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
31738001 TAATAGTATA
31738011 AATAAATAT-TTTT
1 AATAAATATATTTT
31738024 AATAAATATAATTTT
1 AATAAATAT-ATTTT
*
31738039 AATATATATAT
1 AATAAATATAT
31738050 ATTCTTACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 9 0.39
14 2 0.09
15 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AATAAATATATTTT
Found at i:31752560 original size:19 final size:19
Alignment explanation
Indices: 31752512--31752562 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
31752502 CTATGACTTC
31752512 TATTTAGATTAGAAATTGTAT
1 TATTTA-ATTA-AAATTGTAT
*
31752533 T-TTTTATTAAAATAT-TAT
1 TATTTAATTAAAAT-TGTAT
31752551 TATTTAATTAAA
1 TATTTAATTAAA
31752563 TCTTATTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 8 0.31
19 14 0.54
20 3 0.12
21 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
TATTTAATTAAAATTGTAT
Found at i:31759284 original size:20 final size:19
Alignment explanation
Indices: 31759261--31759332 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 19
31759251 TTTCTTAGGA
31759261 TTTATCAAAATTTATAAGAT
1 TTTATCAAAATTT-TAAGAT
*
31759281 TTTACCAAAATATTTAAGGA-
1 TTTATCAAAAT-TTTAA-GAT
*
31759301 GTTATCAAAATTTCTAA-AGT
1 TTTATCAAAATTT-TAAGA-T
*
31759321 TTTATAAAAATT
1 TTTATCAAAATT
31759333 CTAAAAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
18 1 0.02
19 2 0.05
20 35 0.83
21 4 0.10
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (19 bp):
TTTATCAAAATTTTAAGAT
Found at i:31759343 original size:20 final size:20
Alignment explanation
Indices: 31759302--31759343 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
31759292 ATTTAAGGAG
* *
31759302 TTATCAAAATTTCTAAAGTT
1 TTATCAAAAATTCTAAAATT
31759322 TTAT-AAAAATTCTAAAAATT
1 TTATCAAAAATTCT-AAAATT
31759342 TT
1 TT
31759344 CTTAGTGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (20 bp):
TTATCAAAAATTCTAAAATT
Found at i:31759530 original size:20 final size:19
Alignment explanation
Indices: 31759505--31759656 Score: 59
Period size: 20 Copynumber: 8.0 Consensus size: 19
31759495 ATACCACTTC
31759505 ACCAAAATTTCTAAAGATTT
1 ACCAAAATTT-TAAAGATTT
31759525 ACC-AAATTTT--A-A---
1 ACCAAAATTTTAAAGATTT
*
31759537 ACCAAAATTTTTAAGATTAT
1 ACCAAAATTTTAAAGATT-T
** * *
31759557 ACCAATTTTTTTAAGGGTTT
1 ACCAA-AATTTTAAAGATTT
* *
31759577 ACCGATA-TTTATAAGACTTT
1 ACCAAAATTTTA-AAGA-TTT
*
31759597 ACCAAAATTTTTAAAAATTT
1 ACCAAAA-TTTTAAAGATTT
* * * *
31759617 AACAATATTATTAAAGGTTC
1 ACCAAAATT-TTAAAGATTT
*
31759637 ACCAATATTTCTAAAGATTT
1 ACCAAAATTT-TAAAGATTT
31759657 CCCTAATGAC
Statistics
Matches: 97, Mismatches: 20, Indels: 30
0.66 0.14 0.20
Matches are distributed among these distances:
12 3 0.03
13 7 0.07
15 2 0.02
16 2 0.02
18 5 0.05
19 12 0.12
20 51 0.53
21 11 0.11
22 4 0.04
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (19 bp):
ACCAAAATTTTAAAGATTT
Found at i:31759564 original size:31 final size:32
Alignment explanation
Indices: 31759505--31759566 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
31759495 ATACCACTTC
31759505 ACCAAAATTTCTAAAGATTTACCAAATTTTAA
1 ACCAAAATTTCTAAAGATTTACCAAATTTTAA
* *
31759537 ACCAAAATTT-TTAAGATTATACCAATTTTT
1 ACCAAAATTTCTAAAGATT-TACCAAATTTT
31759567 TTAAGGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.39
Consensus pattern (32 bp):
ACCAAAATTTCTAAAGATTTACCAAATTTTAA
Found at i:31761111 original size:38 final size:38
Alignment explanation
Indices: 31761044--31761119 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
31761034 ATTGTTTCAA
* * *
31761044 TGTTTGTTTTTATTTGAATAGTTGCCCACCACTATAGG
1 TGTTTATTTTTATTTGAATAATTGCCCACCAATATAGG
*
31761082 TGTTTATTTTTATTTGATTAATT-CTCCACCAATATAGG
1 TGTTTATTTTTATTTGAATAATTGC-CCACCAATATAGG
31761120 AGAACATGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (38 bp):
TGTTTATTTTTATTTGAATAATTGCCCACCAATATAGG
Found at i:31764211 original size:2 final size:2
Alignment explanation
Indices: 31764199--31764240 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
31764189 GAGGGTTGAA
*
31764199 AT AT TT 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
31764241 TTGTTCGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:31771936 original size:12 final size:12
Alignment explanation
Indices: 31771919--31771953 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
31771909 CGGCCCACCC
31771919 ATATTAATTTTT
1 ATATTAATTTTT
31771931 ATATT-ATTTTT
1 ATATTAATTTTT
31771942 ATA-TAATTTTT
1 ATATTAATTTTT
31771953 A
1 A
31771954 AATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 16 0.73
12 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:31772105 original size:30 final size:30
Alignment explanation
Indices: 31772071--31772135 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
31772061 CAACTTAACA
*
31772071 AACAAAT-ACGTATAAAATAGTAACAAAATT
1 AACAAATGAC-TATAAAATAATAACAAAATT
* *
31772101 AACAAATGACTCTAGAATAATAACAAAATT
1 AACAAATGACTATAAAATAATAACAAAATT
31772131 AACAA
1 AACAA
31772136 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.60, C:0.12, G:0.06, T:0.22
Consensus pattern (30 bp):
AACAAATGACTATAAAATAATAACAAAATT
Found at i:31794126 original size:228 final size:228
Alignment explanation
Indices: 31793729--31794173 Score: 804
Period size: 228 Copynumber: 2.0 Consensus size: 228
31793719 TTGAGACTTC
* *
31793729 AAGTGGACCTGTAAACAAACTTATAGCCAAACCCATGCCTTATCTTACTAACTAATCTGGTAAAT
1 AAGTGGACCTGTAAACAAACTTATAGCCAAACCCATGCCCTATCTTACTAACTAATCTCGTAAAT
31793794 AAACTTTACCTATCTCATCTACTAAAATTGTTTCACAAAACCAACGGCCATGAAAAAAAACACTA
66 AAACTTTACCTATCTCATCTACTAAAATTGTTTCACAAAACCAACGGCCATGAAAAAAAACACTA
*
31793859 AAAAACATTCCAAAAAACCATCAGCCATGAAATGAAATTAAAGAAATAAAGTCTTGGAAAGATAA
131 AAAAACATTCCAAAAAACCATCAGCCATGAAAAGAAATTAAAGAAATAAAGTCTTGGAAAGATAA
31793924 AAAGTAAAACATAATAACTTTGAAAAGAAATTT
196 AAAGTAAAACATAATAACTTTGAAAAGAAATTT
*
31793957 AAGTGGATCC-GTAAACAAACTTATAGCCAGACCCATGCCCTATCTTACTAACTAATCTCGTAAA
1 AAGTGGA-CCTGTAAACAAACTTATAGCCAAACCCATGCCCTATCTTACTAACTAATCTCGTAAA
31794021 TAAACTTTACCTATCTCATCTAACT-AAATTGTTTCACAAAACCAACGGCCATGAAAAAAAACAC
65 TAAACTTTACCTATCTCATCT-ACTAAAATTGTTTCACAAAACCAACGGCCATGAAAAAAAACAC
* *
31794085 TAAAAACCATTCCAAAAAACCGTCAGCCATGAAAAGAAATTAAAGAAATAAAGTCTTGGAAAGAT
129 TAAAAAACATTCCAAAAAACCATCAGCCATGAAAAGAAATTAAAGAAATAAAGTCTTGGAAAGAT
31794150 AAAAAGTAAAACATAATAACTTTG
194 AAAAAGTAAAACATAATAACTTTG
31794174 CCCACTCTCT
Statistics
Matches: 209, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
228 204 0.98
229 5 0.02
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.24
Consensus pattern (228 bp):
AAGTGGACCTGTAAACAAACTTATAGCCAAACCCATGCCCTATCTTACTAACTAATCTCGTAAAT
AAACTTTACCTATCTCATCTACTAAAATTGTTTCACAAAACCAACGGCCATGAAAAAAAACACTA
AAAAACATTCCAAAAAACCATCAGCCATGAAAAGAAATTAAAGAAATAAAGTCTTGGAAAGATAA
AAAGTAAAACATAATAACTTTGAAAAGAAATTT
Found at i:31795343 original size:19 final size:19
Alignment explanation
Indices: 31795315--31795358 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
31795305 TTAGATTTTA
* *
31795315 AAATTTAATTACATTTAGT
1 AAATTAAATTACATTGAGT
**
31795334 AAATTAAATTTTATTGAGT
1 AAATTAAATTACATTGAGT
31795353 AAATTA
1 AAATTA
31795359 CACTCATAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (19 bp):
AAATTAAATTACATTGAGT
Found at i:31796314 original size:37 final size:37
Alignment explanation
Indices: 31796273--31796345 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
31796263 CTTTGCACCA
* * * *
31796273 GTGTTATCAGGCTTTGTGCCTAGTATGCTTTGTGCCG
1 GTGTTATCAAGCTTTGTGCCTAATAGGCTTTATGCCG
31796310 GTGTTATCAAGCTTTGTGCCTAATAGGCTTTATGCC
1 GTGTTATCAAGCTTTGTGCCTAATAGGCTTTATGCC
31796346 AGTGATCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.15, C:0.19, G:0.26, T:0.40
Consensus pattern (37 bp):
GTGTTATCAAGCTTTGTGCCTAATAGGCTTTATGCCG
Found at i:31799749 original size:30 final size:30
Alignment explanation
Indices: 31799713--31799772 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
31799703 TTAATAATAC
31799713 TTTTAGACCAATCCATCAAACCACGACGTA
1 TTTTAGACCAATCCATCAAACCACGACGTA
31799743 TTTTAGACCAATCCATCAAACCACGACGTA
1 TTTTAGACCAATCCATCAAACCACGACGTA
31799773 CCACCCCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.30, G:0.10, T:0.23
Consensus pattern (30 bp):
TTTTAGACCAATCCATCAAACCACGACGTA
Found at i:31807457 original size:13 final size:13
Alignment explanation
Indices: 31807441--31807483 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
31807431 ACTCTAATAA
31807441 TTTAATATAATTT
1 TTTAATATAATTT
*
31807454 TTTAATA-AAATT
1 TTTAATATAATTT
*
31807466 TTAAATAT-ATTT
1 TTTAATATAATTT
31807478 TTTAAT
1 TTTAAT
31807484 GTTTACATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 18 0.72
13 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTAATATAATTT
Found at i:31808781 original size:3 final size:3
Alignment explanation
Indices: 31808775--31808809 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
31808765 GCAACAAAAA
31808775 ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31808810 TTGTGAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:31808799 original size:17 final size:17
Alignment explanation
Indices: 31808777--31808809 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31808767 AACAAAAAAT
31808777 TATTATTATTATTATTA
1 TATTATTATTATTATTA
31808794 TATTATTATTATTATT
1 TATTATTATTATTATT
31808810 TTGTGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:31809503 original size:21 final size:21
Alignment explanation
Indices: 31809479--31809519 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31809469 TAAAAAAAAA
*
31809479 TTTAAAATTCAAAAAAATTAT
1 TTTAAAAATCAAAAAAATTAT
*
31809500 TTTAAAAATGAAAAAAATTA
1 TTTAAAAATCAAAAAAATTA
31809520 AAAATATTTA
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:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
TTTAAAAATCAAAAAAATTAT
Found at i:31809534 original size:10 final size:10
Alignment explanation
Indices: 31809517--31809566 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
31809507 ATGAAAAAAA
31809517 TTAAAAATAT
1 TTAAAAATAT
31809527 TTAAAAATAT
1 TTAAAAATAT
*
31809537 ATAAAAAATATT
1 -TTAAAAATA-T
* *
31809549 TTAAATATTT
1 TTAAAAATAT
31809559 TTAAAAAT
1 TTAAAAAT
31809567 TAATTAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
10 18 0.55
11 14 0.42
12 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:31809564 original size:21 final size:21
Alignment explanation
Indices: 31809516--31809566 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
31809506 AATGAAAAAA
31809516 ATTAAAAATATTTAAAAATAT
1 ATTAAAAATATTTAAAAATAT
* *
31809537 ATAAAAAATATTT-TAAATATT
1 ATTAAAAATATTTAAAAATA-T
*
31809558 TTTAAAAAT
1 ATTAAAAAT
31809567 TAATTAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAAAAATATTTAAAAATAT
Found at i:31812200 original size:27 final size:27
Alignment explanation
Indices: 31812170--31812262 Score: 81
Period size: 27 Copynumber: 3.6 Consensus size: 27
31812160 AGTCTATAAA
*
31812170 CCTCCTCCAGTTCCAGTAAAACCACTT
1 CCTCCACCAGTTCCAGTAAAACCACTT
* *
31812197 CCTCCACCTGTTCCAATCTATAAA-C-C-T
1 CCTCCACCAGTTCC-A-GTA-AAACCACTT
31812224 CCT---CCAGTTCCAGTAAAACCACTT
1 CCTCCACCAGTTCCAGTAAAACCACTT
*
31812248 CCTCCACCTGTTCCA
1 CCTCCACCAGTTCCA
31812263 ATCTACAAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
21 3 0.06
22 3 0.06
23 2 0.04
24 11 0.22
27 24 0.47
28 2 0.04
29 3 0.06
30 3 0.06
ACGTcount: A:0.25, C:0.42, G:0.06, T:0.27
Consensus pattern (27 bp):
CCTCCACCAGTTCCAGTAAAACCACTT
Found at i:31812299 original size:48 final size:49
Alignment explanation
Indices: 31812146--31812332 Score: 250
Period size: 51 Copynumber: 3.8 Consensus size: 49
31812136 AATCTATAAA
* * *
31812146 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTAAAACCACTT
1 CCTCCACCTGTTCCAATCTATAAACCTCCACCAGTT-C-GTAAAACCACTT
*
31812197 CCTCCACCTGTTCCAATCTATAAACCTCCTCCAGTTCCAGTAAAACCACTT
1 CCTCCACCTGTTCCAATCTATAAACCTCCACCAGTT-C-GTAAAACCACTT
* * *
31812248 CCTCCACCTGTTCCAATCTACAAACCTCCACCAGTT-GAAAAACCACAT
1 CCTCCACCTGTTCCAATCTATAAACCTCCACCAGTTCGTAAAACCACTT
* *
31812296 CCTCCACCTGTTCCAGTCTATAAACCTCCACCGGTTC
1 CCTCCACCTGTTCCAATCTATAAACCTCCACCAGTTC
31812333 CAGTATACAA
Statistics
Matches: 126, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
48 43 0.34
51 83 0.66
ACGTcount: A:0.27, C:0.40, G:0.07, T:0.25
Consensus pattern (49 bp):
CCTCCACCTGTTCCAATCTATAAACCTCCACCAGTTCGTAAAACCACTT
Found at i:31812302 original size:99 final size:100
Alignment explanation
Indices: 31812146--31812451 Score: 283
Period size: 99 Copynumber: 2.9 Consensus size: 100
31812136 AATCTATAAA
* * * * *
31812146 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTAAAACCACTTCCTCCACCTGTTCC
1 CCTCCACCAGTTCCAATCTACAAACCTCCACCAGTT-C-GAAAAACCACATCCTCCACCTGTTCC
*
31812211 AATCTATAAACCTCCTCCAGTTCCAGTAAAACCACTT
64 AATCTATAAACCTCCACCAGTTCCAGTAAAACCACTT
* *
31812248 CCTCCACCTGTTCCAATCTACAAACCTCCACCAGTT-GAAAAACCACATCCTCCACCTGTTCCAG
1 CCTCCACCAGTTCCAATCTACAAACCTCCACCAGTTCGAAAAACCACATCCTCCACCTGTTCCAA
*
31812312 TCTATAAACCTCCACCGGTTCCAGTATACAAGAAACCA-TGT
66 TCTATAAACCTCCACCAGTTCCAG--T---A-AAACCACT-T
* * * * **
31812353 CCTCCACCGGTTCCAGTCTATAAACCTCCACCCGTTCCAGTATACAAGAAACCATGTCCTCCACC
1 CCTCCACCAGTTCCAATCTACAAACCTCCACCAGTT-C-G-----AA-AAACCACATCCTCCACC
* * *
31812418 AGTTCCAGTCTATAAACCTCCACCCGTTCCAGTA
58 TGTTCCAATCTATAAACCTCCACCAGTTCCAGTA
31812452 TACAAGAAAC
Statistics
Matches: 171, Mismatches: 17, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
99 47 0.27
101 1 0.01
102 32 0.19
104 2 0.01
105 39 0.23
108 1 0.01
109 1 0.01
112 1 0.01
113 2 0.01
114 45 0.26
ACGTcount: A:0.28, C:0.39, G:0.09, T:0.24
Consensus pattern (100 bp):
CCTCCACCAGTTCCAATCTACAAACCTCCACCAGTTCGAAAAACCACATCCTCCACCTGTTCCAA
TCTATAAACCTCCACCAGTTCCAGTAAAACCACTT
Found at i:31812335 original size:24 final size:24
Alignment explanation
Indices: 31812131--31812336 Score: 107
Period size: 24 Copynumber: 8.3 Consensus size: 24
31812121 AAACCCGCCT
*
31812131 GTTCCAATCTATAAACCTCCACCA
1 GTTCCAGTCTATAAACCTCCACCA
*
31812155 GTTCCAGTCTATAAACCTCCTCCA
1 GTTCCAGTCTATAAACCTCCACCA
* *
31812179 GTTCCAG--TAAAACCACTTCCTCCACCT
1 GTTCCAGTCTATAA--A---CCTCCACCA
* *
31812206 GTTCCAATCTATAAACCTCCTCCA
1 GTTCCAGTCTATAAACCTCCACCA
* *
31812230 GTTCCAG--TAAAACCACTTCCTCCACCT
1 GTTCCAGTCTATAA--A---CCTCCACCA
* *
31812257 GTTCCAATCTACAAACCTCCACCA
1 GTTCCAGTCTATAAACCTCCACCA
** ** * * * *
31812281 GTTGAAAAACCA-CATCCTCCACCT
1 GTT-CCAGTCTATAAACCTCCACCA
*
31812305 GTTCCAGTCTATAAACCTCCACCG
1 GTTCCAGTCTATAAACCTCCACCA
31812329 GTTCCAGT
1 GTTCCAGT
31812337 ATACAAGAAA
Statistics
Matches: 135, Mismatches: 31, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
22 8 0.06
23 3 0.02
24 84 0.62
25 4 0.03
27 28 0.21
29 8 0.06
ACGTcount: A:0.28, C:0.38, G:0.08, T:0.26
Consensus pattern (24 bp):
GTTCCAGTCTATAAACCTCCACCA
Found at i:31812362 original size:33 final size:33
Alignment explanation
Indices: 31812320--31812606 Score: 196
Period size: 33 Copynumber: 9.5 Consensus size: 33
31812310 AGTCTATAAA
*
31812320 CCTCCACCGGTTCCAGTATACAAGAAACCATGT
1 CCTCCACCAGTTCCAGTATACAAGAAACCATGT
* * *
31812353 CCTCCACCGGTTCCAG--T-CTA-TAA--A---
1 CCTCCACCAGTTCCAGTATACAAGAAACCATGT
*
31812377 CCTCCACCCGTTCCAGTATACAAGAAACCATGT
1 CCTCCACCAGTTCCAGTATACAAGAAACCATGT
* *
31812410 CCTCCACCAGTTCCAG--T-CTA-TAA--A---
1 CCTCCACCAGTTCCAGTATACAAGAAACCATGT
*
31812434 CCTCCACCCGTTCCAGTATACAAGAAACCATGT
1 CCTCCACCAGTTCCAGTATACAAGAAACCATGT
* *
31812467 CCTCCACCAGTTCCAGTCTA-TA-AAA-C---T
1 CCTCCACCAGTTCCAGTATACAAGAAACCATGT
* **
31812494 CCT---CCGGTTCCAGTATACAAGAAACCACAT
1 CCTCCACCAGTTCCAGTATACAAGAAACCATGT
* * * **
31812524 CCTCCTCCAGTTCCAGTCTATAAGAAACCACAT
1 CCTCCACCAGTTCCAGTATACAAGAAACCATGT
* *
31812557 CCACCGCCAGTTCCAGTATACAAGAAACCATGT
1 CCTCCACCAGTTCCAGTATACAAGAAACCATGT
*
31812590 CCTCCCCCAGTTCCAGT
1 CCTCCACCAGTTCCAGT
31812607 CCATAAGCCT
Statistics
Matches: 199, Mismatches: 28, Indels: 54
0.71 0.10 0.19
Matches are distributed among these distances:
24 42 0.21
25 1 0.01
26 5 0.03
27 11 0.06
28 4 0.02
29 4 0.02
30 11 0.06
31 5 0.03
32 1 0.01
33 115 0.58
ACGTcount: A:0.29, C:0.37, G:0.12, T:0.22
Consensus pattern (33 bp):
CCTCCACCAGTTCCAGTATACAAGAAACCATGT
Found at i:31812375 original size:57 final size:57
Alignment explanation
Indices: 31812146--31812725 Score: 508
Period size: 57 Copynumber: 10.4 Consensus size: 57
31812136 AATCTATAAA
* *
31812146 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAG--T---A-AAACCACT-T
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCGGTTCCAGTATACAAGAAACCA-TGT
* * * *
31812197 CCTCCACCTGTTCCAATCTATAAACCTCCTCCAGTTCCAG--T---A-AAACCACT-T
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCGGTTCCAGTATACAAGAAACCA-TGT
* * * * **
31812248 CCTCCACCTGTTCCAATCTACAAACCTCCA------CCAGT-T-GAA-AAACCACAT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCGGTTCCAGTATACAAGAAACCATGT
*
31812296 CCTCCACCTGTTCCAGTCTATAAACCTCCACCGGTTCCAGTATACAAGAAACCATGT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCGGTTCCAGTATACAAGAAACCATGT
* *
31812353 CCTCCACCGGTTCCAGTCTATAAACCTCCACCCGTTCCAGTATACAAGAAACCATGT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCGGTTCCAGTATACAAGAAACCATGT
*
31812410 CCTCCACCAGTTCCAGTCTATAAACCTCCACCCGTTCCAGTATACAAGAAACCATGT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCGGTTCCAGTATACAAGAAACCATGT
* * **
31812467 CCTCCACCAGTTCCAGTCTATAAAACTCCTCCGGTTCCAGTATACAAGAAACCACAT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCGGTTCCAGTATACAAGAAACCATGT
*
31812524 CCTCCTCCAGTTCCAGTCTATAAGAAACCACATCCACCGCCAGTTCCAGTATACAAGAAACCATG
1 CCTCCACCAGTTCCAGTCTAT---AAA-C-C-TCCACCG---GTTCCAGTATACAAGAAACCATG
31812589 T
57 T
* * * * * *
31812590 CCTCCCCCAGTTCCAGTCCATAAGCCTCCTCCAGTTCCGGTATACAAGAAACCA-GT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCGGTTCCAGTATACAAGAAACCATGT
* * * * * * * * * * *
31812646 CCCTCCTCCGGTTCCAATCTACAAGCCCCCTCCAGTTCCTGTATACAACAAACCACT-A
1 -CCTCCACCAGTTCCAGTCTATAAACCTCCACCGGTTCCAGTATACAAGAAACCA-TGT
* *
31812704 CCTCCCCCAGTTCCAGTGTATA
1 CCTCCACCAGTTCCAGTCTATA
31812726 CGAAGCCACT
Statistics
Matches: 461, Mismatches: 43, Indels: 44
0.84 0.08 0.08
Matches are distributed among these distances:
45 4 0.01
46 1 0.00
48 36 0.08
51 77 0.17
54 5 0.01
55 1 0.00
56 4 0.01
57 273 0.59
60 8 0.02
61 1 0.00
62 2 0.00
63 8 0.02
66 41 0.09
ACGTcount: A:0.28, C:0.38, G:0.10, T:0.23
Consensus pattern (57 bp):
CCTCCACCAGTTCCAGTCTATAAACCTCCACCGGTTCCAGTATACAAGAAACCATGT
Found at i:31812487 original size:114 final size:114
Alignment explanation
Indices: 31812146--31812725 Score: 560
Period size: 114 Copynumber: 5.2 Consensus size: 114
31812136 AATCTATAAA
*
31812146 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAG--T---A-AAACCACTTCCTCCACC
1 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCACATCCTCCACC
* * *
31812205 TGTTCCAATCTATAAACCTCCTCCAGTTCCAG--T---A-AAACCACT-T
66 AGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAAACCA-TGT
* * * *
31812248 CCTCCACCTGTTCCAATCTACAAA---CCTCCA---CCAGT-T-GAA-AAACCACATCCTCCACC
1 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCACATCCTCCACC
* *
31812304 TGTTCCAGTCTATAAACCTCCACCGGTTCCAGTATACAAGAAACCATGT
66 AGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAAACCATGT
* * * **
31812353 CCTCCACCGGTTCCAGTCTATAAACCTCCACCCGTTCCAGTATACAAGAAACCATGTCCTCCACC
1 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCACATCCTCCACC
*
31812418 AGTTCCAGTCTATAAACCTCCACCCGTTCCAGTATACAAGAAACCATGT
66 AGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAAACCATGT
* * *
31812467 CCTCCACCAGTTCCAGTCTATAAAACTCCTCCGGTTCCAGTATACAAGAAACCACATCCTCCTCC
1 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCACATCCTCCACC
31812532 AGTTCCAGTCTATAAGAAACCACATCCACCGCCAGTTCCAGTATACAAGAAACCATGT
66 AGTTCCAGTCTAT---AAA-C-C-TCCA---CCAGTTCCAGTATACAAGAAACCATGT
* * * * * *
31812590 CCTCCCCCAGTTCCAGTCCATAAGCCTCCTCCAGTTCCGGTATACAAGAAACCA-GTCCCTCCTC
1 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCACAT-CCTCCAC
* * * * * * * * *
31812654 CGGTTCCAATCTACAAGCCCCCTCCAGTTCCTGTATACAACAAACCACT-A
65 CAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAAACCA-TGT
* *
31812704 CCTCCCCCAGTTCCAGTGTATA
1 CCTCCACCAGTTCCAGTCTATA
31812726 CGAAGCCACT
Statistics
Matches: 405, Mismatches: 43, Indels: 48
0.82 0.09 0.10
Matches are distributed among these distances:
96 4 0.01
97 1 0.00
99 52 0.13
101 1 0.00
102 21 0.05
104 2 0.00
105 28 0.07
108 4 0.01
111 5 0.01
112 1 0.00
113 2 0.00
114 175 0.43
115 1 0.00
117 5 0.01
118 2 0.00
119 2 0.00
120 6 0.01
122 1 0.00
123 92 0.23
ACGTcount: A:0.28, C:0.38, G:0.10, T:0.23
Consensus pattern (114 bp):
CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCACATCCTCCACC
AGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAAACCATGT
Found at i:31812678 original size:147 final size:147
Alignment explanation
Indices: 31812527--31812808 Score: 334
Period size: 147 Copynumber: 1.9 Consensus size: 147
31812517 ACCACATCCT
* * * *
31812527 CCTCCAGTTCCAGTCTATAAGAAACCAC-ATCCACCGCCAGTTCCAGTATACAAGAAACCA-TGT
1 CCTCCAGTTCCAGTATACAACAAACCACTA-CCACCCCCAGTTCCAGTATACAAGAAACCACT-T
* * * * * * * * *
31812590 CCTCCCCCAGTTCCAGTCCATAAGCCTCCTCCAGTTCCGGTATACAAGAAACCAGTCCCTCCTCC
64 CCACCACCAGTTCCAATCCACAAGCCCCCTCCAGTTCCGGTATACAACAAACCACTACCTCCCCC
31812655 GGTTCCAATCTACAAGCCC
129 GGTTCCAATCTACAAGCCC
* * * * * *
31812674 CCTCCAGTTCCTGTATACAACAAACCACTACCTCCCCCAGTTCCAGTGTATACGAAGCCACTTCC
1 CCTCCAGTTCCAGTATACAACAAACCACTACCACCCCCAGTTCCAGTATACAAGAAACCACTTCC
* * *
31812739 ACCACCTGTTCCAATCTACAAGCCCCCTCCAGTTCCTGTATACAACAAACCACTACCTCCCCCGG
66 ACCACCAGTTCCAATCCACAAGCCCCCTCCAGTTCCGGTATACAACAAACCACTACCTCCCCCGG
31812804 TTCCA
131 TTCCA
31812809 GTGTATACGA
Statistics
Matches: 111, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
147 109 0.98
148 2 0.02
ACGTcount: A:0.27, C:0.40, G:0.11, T:0.22
Consensus pattern (147 bp):
CCTCCAGTTCCAGTATACAACAAACCACTACCACCCCCAGTTCCAGTATACAAGAAACCACTTCC
ACCACCAGTTCCAATCCACAAGCCCCCTCCAGTTCCGGTATACAACAAACCACTACCTCCCCCGG
TTCCAATCTACAAGCCC
Found at i:31812692 original size:180 final size:175
Alignment explanation
Indices: 31812295--31812760 Score: 505
Period size: 180 Copynumber: 2.6 Consensus size: 175
31812285 AAAAACCACA
* * * * * *
31812295 TCCTCCACCTGTTCCAGTCTA-TAAACCTCCACCGGTTCCAGTATACAAGAAACCATGTCCTCCA
1 TCCTCCACCAGTTCCAATCTACAAAACC-CCTCCAGTTCCAGTATACAAGAAACCA-CTCCTCCA
*
31812359 CCGGTTCCAGTCTAT--AAA-C-CTCCA-CCCGTTCCAGTATACAAGAAACCATGTCCTCCACCA
64 CCAGTTCCAGTCTATAGAAACCACTCCACCCCGTTCCAGTATACAAGAAACCATGTCCTCCACCA
* *
31812419 GTTCCAGTCTATAAACCTCCACCCGTTCCAGTATACAAGAAACCATG
129 GTTCCAGTCCATAAACCTCCACCAGTTCCAGTATACAAGAAACCATG
* * * * *
31812466 TCCTCCACCAGTTCCAGTCTATAAAACTCCTCCGGTTCCAGTATACAAGAAACCACATCCTCCTC
1 TCCTCCACCAGTTCCAATCTACAAAACCCCTCCAGTTCCAGTATACAAGAAACCAC-TCCTCCAC
*
31812531 CAGTTCCAGTCTATAAGAAACCACATCCACCGCCAGTTCCAGTATACAAGAAACCATGTCCTCCC
65 CAGTTCCAGTCTAT-AGAAACCAC-TCCACC-CC-GTTCCAGTATACAAGAAACCATGTCCTCCA
* * *
31812596 CCAGTTCCAGTCCATAAGCCTCCTCCAGTTCCGGTATACAAGAAACCA-G
126 CCAGTTCCAGTCCATAAACCTCCACCAGTTCCAGTATACAAGAAACCATG
* * ** * * *
31812645 TCCCTCCTCCGGTTCCAATCTACAAGCCCCCTCCAGTTCCTGTATACAACAAACCACTACCTCCC
1 T-CCTCCACCAGTTCCAATCTACAAAACCCCTCCAGTTCCAGTATACAAGAAACCACT-CCTCCA
* * * *
31812710 CCAGTTCCAGTGTATACGAAGCCACTTCCACCACCTGTTCCAATCTACAAG
64 CCAGTTCCAGTCTATA-GAAACCAC-TCCACC-CC-GTTCCAGTATACAAG
31812761 CCCCCTCCAG
Statistics
Matches: 250, Mismatches: 31, Indels: 19
0.83 0.10 0.06
Matches are distributed among these distances:
171 66 0.26
172 4 0.02
174 3 0.01
175 1 0.00
176 1 0.00
177 4 0.02
178 1 0.00
179 6 0.02
180 164 0.66
ACGTcount: A:0.28, C:0.38, G:0.12, T:0.23
Consensus pattern (175 bp):
TCCTCCACCAGTTCCAATCTACAAAACCCCTCCAGTTCCAGTATACAAGAAACCACTCCTCCACC
AGTTCCAGTCTATAGAAACCACTCCACCCCGTTCCAGTATACAAGAAACCATGTCCTCCACCAGT
TCCAGTCCATAAACCTCCACCAGTTCCAGTATACAAGAAACCATG
Found at i:31812708 original size:90 final size:90
Alignment explanation
Indices: 31812614--31812849 Score: 323
Period size: 90 Copynumber: 2.6 Consensus size: 90
31812604 AGTCCATAAG
* * * *
31812614 CCTCCTCCAGTTCC-G-GTATACAAGAAACCAGTCCCTCCTCCGGTTCCAATCTACAAGCCCCCT
1 CCTCCCCCAGTTCCAGTGTATAC--GAAACCACTCCCACCACCGGTTCCAATCTACAAGCCCCCT
31812677 CCAGTTCCTGTATACAACAAACCACTA
64 CCAGTTCCTGTATACAACAAACCACTA
* * *
31812704 CCTCCCCCAGTTCCAGTGTATACGAAGCCACTTCCACCACCTGTTCCAATCTACAAGCCCCCTCC
1 CCTCCCCCAGTTCCAGTGTATACGAAACCACTCCCACCACCGGTTCCAATCTACAAGCCCCCTCC
31812769 AGTTCCTGTATACAACAAACCACTA
66 AGTTCCTGTATACAACAAACCACTA
* * * * * *
31812794 CCTCCCCCGGTTCCAGTGTATACGAAGCCACTTCCACCTCCTGTTCCAACCTACAA
1 CCTCCCCCAGTTCCAGTGTATACGAAACCACTCCCACCACCGGTTCCAATCTACAA
31812850 CCCAAAACCC
Statistics
Matches: 134, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
90 127 0.95
91 1 0.01
92 6 0.04
ACGTcount: A:0.25, C:0.41, G:0.11, T:0.22
Consensus pattern (90 bp):
CCTCCCCCAGTTCCAGTGTATACGAAACCACTCCCACCACCGGTTCCAATCTACAAGCCCCCTCC
AGTTCCTGTATACAACAAACCACTA
Found at i:31812735 original size:33 final size:32
Alignment explanation
Indices: 31812698--31812825 Score: 76
Period size: 33 Copynumber: 4.2 Consensus size: 32
31812688 ATACAACAAA
31812698 CCACTACCTCCCCCAGTTCCAGTGTATACGAAG
1 CCACTACCTCCCCCAGTTCCA-TGTATACGAAG
* * * * * *
31812731 CCACTTCCACCACCTGTTCCA-ATCTAC-AAG
1 CCACTACCTCCCCCAGTTCCATGTATACGAAG
* *
31812761 CC-C--CCT---CCAGTTCC-TGTATACAACAAA
1 CCACTACCTCCCCCAGTTCCATGTATAC--GAAG
*
31812788 CCACTACCTCCCCCGGTTCCAGTGTATACGAAG
1 CCACTACCTCCCCCAGTTCCA-TGTATACGAAG
31812821 CCACT
1 CCACT
31812826 TCCACCTCCT
Statistics
Matches: 69, Mismatches: 14, Indels: 24
0.64 0.13 0.22
Matches are distributed among these distances:
24 11 0.16
27 6 0.09
28 1 0.01
29 1 0.01
30 8 0.12
31 4 0.06
33 31 0.45
35 7 0.10
ACGTcount: A:0.25, C:0.41, G:0.12, T:0.22
Consensus pattern (32 bp):
CCACTACCTCCCCCAGTTCCATGTATACGAAG
Found at i:31812908 original size:18 final size:18
Alignment explanation
Indices: 31812885--31812920 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
31812875 TACAAGCCAC
31812885 TCCCTCCACTTCCC-AAGA
1 TCCCTCCA-TTCCCTAAGA
31812903 TCCCTCCATTCCCTAAGA
1 TCCCTCCATTCCCTAAGA
31812921 AGCCATGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.22, C:0.47, G:0.06, T:0.25
Consensus pattern (18 bp):
TCCCTCCATTCCCTAAGA
Found at i:31813132 original size:60 final size:60
Alignment explanation
Indices: 31812932--31813110 Score: 324
Period size: 60 Copynumber: 3.0 Consensus size: 60
31812922 GCCATGCCCT
*
31812932 CCCCTTCCTAAGCTACCCCCTCTTCCC-AAGATTCCTCCCAAGTATTTCCACCACCACCCA
1 CCCCTTCCTAAGCTACCTCCTC-TCCCTAAGATTCCTCCCAAGTATTTCCACCACCACCCA
*
31812992 CCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCACCCT
1 CCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCACCCA
31813052 CCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCACCC
1 CCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCACCC
31813111 CAAGTTCGGA
Statistics
Matches: 116, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
59 4 0.03
60 112 0.97
ACGTcount: A:0.21, C:0.49, G:0.05, T:0.25
Consensus pattern (60 bp):
CCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCACCCA
Found at i:31821103 original size:3 final size:3
Alignment explanation
Indices: 31821095--31821135 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
31821085 CCATTTAAAT
31821095 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
31821136 GCCAACTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:31821803 original size:24 final size:24
Alignment explanation
Indices: 31821775--31821823 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
31821765 TGATGTGAAA
31821775 CTAGTAGAAAATGAAGATCCAACT
1 CTAGTAGAAAATGAAGATCCAACT
31821799 CTAGTAGAAAATGAAGATCCAACT
1 CTAGTAGAAAATGAAGATCCAACT
31821823 C
1 C
31821824 CGTGTATGGT
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:0.45, C:0.18, G:0.16, T:0.20
Consensus pattern (24 bp):
CTAGTAGAAAATGAAGATCCAACT
Found at i:31822533 original size:25 final size:27
Alignment explanation
Indices: 31822505--31822560 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
31822495 TTACTCAACT
*
31822505 AAATAAAAAAATTAAA-T-AACAAATC
1 AAATAAAAAAATTAAATTAAACAAAAC
31822530 AAAT--AAAAATTAAATTAAACAAAAC
1 AAATAAAAAAATTAAATTAAACAAAAC
31822555 AAATAA
1 AAATAA
31822561 CTTAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 10 0.38
24 1 0.04
25 15 0.58
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (27 bp):
AAATAAAAAAATTAAATTAAACAAAAC
Found at i:31823846 original size:5 final size:5
Alignment explanation
Indices: 31823836--31823886 Score: 102
Period size: 5 Copynumber: 10.2 Consensus size: 5
31823826 CAATATTATA
31823836 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
31823886 A
1 A
31823887 ATATATGTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:31827440 original size:18 final size:19
Alignment explanation
Indices: 31827417--31827452 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
31827407 CAAAGTAGTT
*
31827417 TTGCAAGCC-TATATTTTG
1 TTGCAAACCATATATTTTG
31827435 TTGCAAACCATATATTTT
1 TTGCAAACCATATATTTT
31827453 TAGTGATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (19 bp):
TTGCAAACCATATATTTTG
Found at i:31834403 original size:22 final size:22
Alignment explanation
Indices: 31834375--31834431 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
31834365 GTGCCCTCTG
31834375 TTCAGCATTGTGTGTGCTTCTA
1 TTCAGCATTGTGTGTGCTTCTA
*
31834397 TTCAGCACTGTGTGTGCTTCTA
1 TTCAGCATTGTGTGTGCTTCTA
*
31834419 TTCATCATTGTGT
1 TTCAGCATTGTGT
31834432 ATGCCTACTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.46
Consensus pattern (22 bp):
TTCAGCATTGTGTGTGCTTCTA
Found at i:31835828 original size:40 final size:39
Alignment explanation
Indices: 31835760--31835894 Score: 107
Period size: 40 Copynumber: 3.4 Consensus size: 39
31835750 ACCAGAATGG
* *
31835760 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGTAATAAAGTGA
* *
31835800 CACCCAGTGTCTCATCGGCCTAGCCGAAG---TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGTAATAAAGTGA
* * * * *
31835837 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGTAATAA-AGTGA
*
31835878 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
31835895 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGTAATAAAGTGA
Found at i:31835892 original size:41 final size:40
Alignment explanation
Indices: 31835784--31835895 Score: 113
Period size: 37 Copynumber: 2.8 Consensus size: 40
31835774 TCGGATAGTT
*
31835784 CGAAGTAATAAAGTGACACCCAGTGTCTCATCG-GCCTAGC
1 CGAAGTAA-AAAGTGACACCCAGTGTCTCATCGAACCTAGC
** ** * *
31835824 CGAAGT--AAAGTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAAAAAGTGACACCCAGTGTCTCATCGAACCTAGC
*
31835862 CGAAGTAAAATAATGACACCCAGTGTCTCATCGA
1 CGAAGTAAAA-AGTGACACCCAGTGTCTCATCGA
31835896 CTCGAGGTCG
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
37 20 0.36
38 10 0.18
40 8 0.14
41 18 0.32
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (40 bp):
CGAAGTAAAAAGTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:31836816 original size:13 final size:12
Alignment explanation
Indices: 31836746--31836827 Score: 60
Period size: 13 Copynumber: 6.6 Consensus size: 12
31836736 TTCATATACA
*
31836746 TATATATATTAGT
1 TATA-ATATTAAT
*
31836759 TAATAATAATAA-
1 T-ATAATATTAAT
*
31836771 TATAATACTAAT
1 TATAATATTAAT
*
31836783 TA-AATAATAATT
1 TATAATATTAA-T
*
31836795 TATATTATTATAT
1 TATAATATTA-AT
31836808 TATAATATTAAT
1 TATAATATTAAT
31836820 TAATAATA
1 T-ATAATA
31836828 AATAAATAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
11 16 0.29
12 9 0.16
13 27 0.48
14 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (12 bp):
TATAATATTAAT
Found at i:31841958 original size:40 final size:39
Alignment explanation
Indices: 31841890--31842024 Score: 107
Period size: 40 Copynumber: 3.4 Consensus size: 39
31841880 ACCAGAATGG
* *
31841890 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGTAATAAAGTGA
* *
31841930 CACCCAGTGTCTCATCGGCCTAGCCGAAG---TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGTAATAAAGTGA
* * * * *
31841967 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGTAATAA-AGTGA
*
31842008 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
31842025 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGTAATAAAGTGA
Found at i:31842022 original size:41 final size:40
Alignment explanation
Indices: 31841914--31842025 Score: 113
Period size: 37 Copynumber: 2.8 Consensus size: 40
31841904 TCGGATAGTT
*
31841914 CGAAGTAATAAAGTGACACCCAGTGTCTCATCG-GCCTAGC
1 CGAAGTAA-AAAGTGACACCCAGTGTCTCATCGAACCTAGC
** ** * *
31841954 CGAAGT--AAAGTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAAAAAGTGACACCCAGTGTCTCATCGAACCTAGC
*
31841992 CGAAGTAAAATAATGACACCCAGTGTCTCATCGA
1 CGAAGTAAAA-AGTGACACCCAGTGTCTCATCGA
31842026 CTCGAGGTCG
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
37 20 0.36
38 10 0.18
40 8 0.14
41 18 0.32
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (40 bp):
CGAAGTAAAAAGTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:31842946 original size:13 final size:12
Alignment explanation
Indices: 31842876--31842957 Score: 60
Period size: 13 Copynumber: 6.6 Consensus size: 12
31842866 TTCATATACA
*
31842876 TATATATATTAGT
1 TATA-ATATTAAT
*
31842889 TAATAATAATAA-
1 T-ATAATATTAAT
*
31842901 TATAATACTAAT
1 TATAATATTAAT
*
31842913 TA-AATAATAATT
1 TATAATATTAA-T
*
31842925 TATATTATTATAT
1 TATAATATTA-AT
31842938 TATAATATTAAT
1 TATAATATTAAT
31842950 TAATAATA
1 T-ATAATA
31842958 AATAAATAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
11 16 0.29
12 9 0.16
13 27 0.48
14 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (12 bp):
TATAATATTAAT
Found at i:31844372 original size:28 final size:27
Alignment explanation
Indices: 31844336--31844389 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
31844326 TTTAATAGTT
* * *
31844336 TATATTTTTATTATTTTTAATATTAAAG
1 TATAATTTTAATATTATTAAT-TTAAAG
31844364 TATAATTTTAATATTATTAATTTAAA
1 TATAATTTTAATATTATTAATTTAAA
31844390 TTTTTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
TATAATTTTAATATTATTAATTTAAAG
Found at i:31850850 original size:30 final size:29
Alignment explanation
Indices: 31850788--31850850 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
31850778 AACATATATT
* * *
31850788 TTTTTTTGATCAAAAAAAAAAAACATATA
1 TTTTTTTAATCAAAAAAAAAAAAAATACA
31850817 TTTTTTTAAT-AAAAAATAAAGAAAAATACA
1 TTTTTTTAATCAAAAAA-AAA-AAAAATACA
31850847 TTTT
1 TTTT
31850851 AATGACATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 12 0.41
30 11 0.38
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (29 bp):
TTTTTTTAATCAAAAAAAAAAAAAATACA
Found at i:31862146 original size:24 final size:24
Alignment explanation
Indices: 31862113--31862198 Score: 100
Period size: 24 Copynumber: 3.6 Consensus size: 24
31862103 CGTTATTCTG
* *
31862113 ATTCTAGGCTTGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
31862137 ATTCTGGGCTCATAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
* * *
31862161 GTTCTGGGCTCGTAGGAGCTAACT
1 ATTCTGGGCTCGTAAGAGCTAACC
* *
31862185 GTTCTAGGCTCGTA
1 ATTCTGGGCTCGTA
31862199 TGGGCTAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCTAACC
Found at i:31865560 original size:18 final size:18
Alignment explanation
Indices: 31865537--31865573 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31865527 ACAATTCATA
31865537 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
31865555 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
31865573 T
1 T
31865574 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:31871140 original size:24 final size:24
Alignment explanation
Indices: 31871108--31871162 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
31871098 TTTAGCCAAC
*
31871108 ACGAGCCTAGAATGATTATCTCTT
1 ACGAGCCTAGAATGATTAGCTCTT
31871132 ACGAGCCTAGAATGATTAGCTCTT
1 ACGAGCCTAGAATGATTAGCTCTT
31871156 ACGAGCC
1 ACGAGCC
31871163 CAGATAGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (24 bp):
ACGAGCCTAGAATGATTAGCTCTT
Found at i:31882233 original size:15 final size:16
Alignment explanation
Indices: 31882198--31882232 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31882188 TTACAATCCC
31882198 AAAATAAAATAATAGA
1 AAAATAAAATAATAGA
* *
31882214 AAAATAACATAATTGA
1 AAAATAAAATAATAGA
31882230 AAA
1 AAA
31882233 TCCCAAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (16 bp):
AAAATAAAATAATAGA
Found at i:31883407 original size:28 final size:29
Alignment explanation
Indices: 31883373--31883429 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
31883363 TAATGAGTCA
*
31883373 GGTTCGGTTCGA-TTTGGTTTGGGTCAAT
1 GGTTCGGTTCGACTTGGGTTTGGGTCAAT
31883401 GGTTCGGTTCGAGCTTGGGTTTGGGTCAA
1 GGTTCGGTTCGA-CTTGGGTTTGGGTCAA
31883430 ATGATTTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.11, C:0.12, G:0.39, T:0.39
Consensus pattern (29 bp):
GGTTCGGTTCGACTTGGGTTTGGGTCAAT
Found at i:31895741 original size:16 final size:17
Alignment explanation
Indices: 31895722--31895762 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
31895712 TAATTTTTTA
31895722 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
* *
31895738 AAAA-TATTAAAATGGT
1 AAAATTATAAAAATGAT
31895754 AAAATTATA
1 AAAATTATA
31895763 TTTTTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 8 0.40
16 9 0.45
17 3 0.15
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:31895798 original size:23 final size:23
Alignment explanation
Indices: 31895754--31895798 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
31895744 TTAAAATGGT
* *
31895754 AAAATTATATTTTTATTATTGTA
1 AAAATTATAATTTAATTATTGTA
31895777 AAAATATATAATTTAATT-TTGT
1 AAAAT-TATAATTTAATTATTGT
31895799 TCCTTCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
AAAATTATAATTTAATTATTGTA
Found at i:31899443 original size:18 final size:18
Alignment explanation
Indices: 31899420--31899463 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
31899410 TAGAGGAACG
* *
31899420 GCCTCGGGGAGAGGAGCA
1 GCCTCGGGCAGAGGAGAA
* *
31899438 GTCTCGAGCAGAGGAGAA
1 GCCTCGGGCAGAGGAGAA
31899456 GCCTCGGG
1 GCCTCGGG
31899464 AGCCGAGTGG
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.45, T:0.09
Consensus pattern (18 bp):
GCCTCGGGCAGAGGAGAA
Found at i:31900286 original size:49 final size:49
Alignment explanation
Indices: 31900233--31900493 Score: 199
Period size: 49 Copynumber: 5.3 Consensus size: 49
31900223 GCCATTGTGG
* ** *
31900233 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCTATTGCAA
1 CTTAAACCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGA
* * * * *
31900282 CTTAAACCTTTCCCTT--TG-TATCTTCATGGTACTAGATTCGCCGTCGCGG
1 CTTAAACCTTTCCCTTCATGCT-TC-TGA-GGTACAAGGTTCGCCGTTGCGA
* * * * * *
31900331 CTTAAATCTTTCCATTCGTG-TCTCTGAGATACAAGGTTCACCGTTGTGA
1 CTTAAACCTTTCCCTTCATGCT-TCTGAGGTACAAGGTTCGCCGTTGCGA
* * * * * *
31900380 CTTAAACCTTTCCCTCCATTATCTT-TGTGGTACTAGATTCGCCGTTGCGG
1 CTTAAACCTTTCCCTTCA-T-GCTTCTGAGGTACAAGGTTCGCCGTTGCGA
* * * * *
31900430 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAATGTTTGCCGTTACAA
1 CTTAAACCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGA
31900479 CTTAAACCTTTCCCT
1 CTTAAACCTTTCCCT
31900494 CCATTATCTT
Statistics
Matches: 159, Mismatches: 44, Indels: 18
0.72 0.20 0.08
Matches are distributed among these distances:
46 1 0.01
47 4 0.03
48 5 0.03
49 105 0.66
50 37 0.23
51 6 0.04
52 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (49 bp):
CTTAAACCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGA
Found at i:31900441 original size:99 final size:99
Alignment explanation
Indices: 31900209--31900545 Score: 446
Period size: 99 Copynumber: 3.4 Consensus size: 99
31900199 CAATGTCATC
* *
31900209 GTGGTACTAGATTCGCCATTGTGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGC
1 GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGC
** * *
31900274 TATTGCAACTTAAACCTTTCCCT--TTGTATCTTC
66 CGTTGCAACTTAAACCTTTCCCTCCAT-TATCTTT
* * * * * *
31900307 ATGGTACTAGATTCGCCGTCGCGGCTTAAATCTTTCCATTCGTG-TCTCTGAGATACAAGGTTCA
1 GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTGAGGTACAAGGTTCG
**
31900371 CCGTTGTGACTTAAACCTTTCCCTCCATTATCTTT
65 CCGTTGCAACTTAAACCTTTCCCTCCATTATCTTT
* *
31900406 GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAATGTTTGC
1 GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGC
*
31900471 CGTTACAACTTAAACCTTTCCCTCCATTATCTTT
66 CGTTGCAACTTAAACCTTTCCCTCCATTATCTTT
* * * *
31900505 GCGGTGCTGGATTCGTCGTTGCGGCTTAAATCTTTCCCTTC
1 GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTC
31900546 GTGTCTTATG
Statistics
Matches: 206, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
97 1 0.00
98 74 0.36
99 129 0.63
100 2 0.01
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (99 bp):
GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGC
CGTTGCAACTTAAACCTTTCCCTCCATTATCTTT
Found at i:31900996 original size:18 final size:18
Alignment explanation
Indices: 31900969--31901005 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31900959 AAAAATTGCC
*
31900969 AAATATTTACAAGGAACA
1 AAATAATTACAAGGAACA
*
31900987 AAATAATTACTAGGAACA
1 AAATAATTACAAGGAACA
31901005 A
1 A
31901006 TATTAGATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.22
Consensus pattern (18 bp):
AAATAATTACAAGGAACA
Found at i:31907087 original size:6 final size:6
Alignment explanation
Indices: 31907051--31907133 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
31907041 GACTTTGATT
* * * *
31907051 TTTAAG TTTAAA -TTAAT TTTAAA TTT-TA TTTAGA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
31907095 TCTTAAA TTT-AC TTTAAA TTTAAA TTTAATA TTAAAA TT
1 T-TTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TT
31907134 AATAAATTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 14
0.73 0.11 0.17
Matches are distributed among these distances:
4 2 0.03
5 14 0.23
6 38 0.62
7 7 0.11
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:31907088 original size:28 final size:28
Alignment explanation
Indices: 31907051--31907130 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 28
31907041 GACTTTGATT
* *
31907051 TTTAAGTTTAAATTAATTTTAAATTTTA-
1 TTTAAATTTAAATTAATATTAAA-TTTAC
* * *
31907079 TTTAGATTTAAATTTATCTTAAATTTAC
1 TTTAAATTTAAATTAATATTAAATTTAC
31907107 TTTAAATTTAAATTTAATATTAAA
1 TTTAAATTTAAA-TTAATATTAAA
31907131 ATTAATAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 4 0.09
28 30 0.70
29 9 0.21
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (28 bp):
TTTAAATTTAAATTAATATTAAATTTAC
Found at i:31907104 original size:17 final size:17
Alignment explanation
Indices: 31907063--31907123 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
31907053 TAAGTTTAAA
*
31907063 TTAATTTTAAATTTTAT
1 TTAAATTTAAATTTTAT
*
31907080 TTAGATTTAAA-TTTAT
1 TTAAATTTAAATTTTAT
* *
31907096 CTTAAATTT-ACTTTAAAT
1 -TTAAATTTAAATTT-TAT
31907114 TTAAATTTAA
1 TTAAATTTAA
31907124 TATTAAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 6 0.17
17 26 0.74
18 3 0.09
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAAATTTAAATTTTAT
Found at i:31909214 original size:30 final size:30
Alignment explanation
Indices: 31908986--31909217 Score: 277
Period size: 30 Copynumber: 7.7 Consensus size: 30
31908976 AAATTGTCCA
* ** *
31908986 AAAATTACATTTTGACCTTAAAAC-TTTCTA
1 AAAATTATATTTTGACCCCAAAACTTTTC-C
* *
31909016 AAAATTATATTTTGACCCCTAAACTTTTTC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
31909046 AAAATTATATTTTGACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* * **
31909076 AAAATTATATTTAGACCCTAAAACTTTTTG
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* * *
31909106 GAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* * * *
31909136 AAAGTTACATTTTAACCCCAAAACTTTTTC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
*
31909166 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
*
31909196 AAAATCATATTTTGACCCCAAA
1 AAAATTATATTTTGACCCCAAA
31909218 TTTCCAAAAA
Statistics
Matches: 174, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
30 171 0.98
31 3 0.02
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCAAAACTTTTCC
Found at i:31909215 original size:60 final size:60
Alignment explanation
Indices: 31908986--31909217 Score: 322
Period size: 60 Copynumber: 3.9 Consensus size: 60
31908976 AAATTGTCCA
** * *
31908986 AAAATTACATTTTGACCTTAAAAC-TTTCTAAAAATTATATTTTGACCCCTAAACTTTTTC
1 AAAATTACATTTTGACCCCAAAACTTTTC-CAAAATTATATTTTGACCCCAAAACTTTTTC
* * * *
31909046 AAAATTATATTTTGACCCCAAAACTTTTCCAAAATTATATTTAGACCCTAAAACTTTTTG
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTTC
* * * * *
31909106 GAAATTACATTTTGACCCTAAAACTTTTCCAAAGTTACATTTTAACCCCAAAACTTTTTC
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTTC
*
31909166 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATCATATTTTGACCCCAAA
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAA
31909218 TTTCCAAAAA
Statistics
Matches: 148, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
60 144 0.97
61 4 0.03
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (60 bp):
AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTTC
Found at i:31909238 original size:30 final size:31
Alignment explanation
Indices: 31908985--31909258 Score: 91
Period size: 30 Copynumber: 9.1 Consensus size: 31
31908975 TAAATTGTCC
** *
31908985 AAAAATTACATTTTGACCTTAAAACTTT-C-T
1 AAAAATT-CATTTTGACCCCAAAACTTTCCAA
* * *
31909015 AAAAATTATATTTTGACCCCTAAACTTTTTCAA
1 AAAAATT-CATTTTGACCCCAAAAC-TTTCCAA
**
31909048 AATTA-T-ATTTTGACCCCAAAACTTTTCCAA
1 AAAAATTCATTTTGACCCCAAAAC-TTTCCAA
** * * **
31909078 AATTA-T-ATTTAGACCCTAAAACTTT--TT
1 AAAAATTCATTTTGACCCCAAAACTTTCCAA
** *
31909105 GGAAATTACATTTTGACCCTAAAACTTTTCC--
1 AAAAATT-CATTTTGACCCCAAAAC-TTTCCAA
* * *
31909136 -AAAGTTACATTTTAACCCCAAAACTTTTTC--
1 AAAAATT-CATTTTGACCCCAAAAC-TTTCCAA
31909166 -AAAATTACATTTTGACCCCAAAACTTTTCCAA
1 AAAAATT-CATTTTGACCCCAAAAC-TTTCCAA
**
31909198 AATCA-T-ATTTTGACCCC-AAA-TTTCCAA
1 AAAAATTCATTTTGACCCCAAAACTTTCCAA
* * *
31909225 AAAAATTGCATTTTTACCTCGAAACTTT-CAA
1 AAAAATT-CATTTTGACCCCAAAACTTTCCAA
31909256 AAA
1 AAA
31909259 TTACCATTTT
Statistics
Matches: 195, Mismatches: 32, Indels: 33
0.75 0.12 0.13
Matches are distributed among these distances:
27 11 0.06
28 2 0.01
29 6 0.03
30 150 0.77
31 15 0.08
32 6 0.03
33 5 0.03
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.36
Consensus pattern (31 bp):
AAAAATTCATTTTGACCCCAAAACTTTCCAA
Found at i:31909330 original size:28 final size:29
Alignment explanation
Indices: 31909255--31909344 Score: 78
Period size: 30 Copynumber: 3.1 Consensus size: 29
31909245 GAAACTTTCA
*
31909255 AAAATTACCATTTTACCCCTAAACTTCCCT
1 AAAATTACCATTTTACCCC-AAACTTCACT
* * *
31909285 -AAA-TCCCATTTTAAACCCC-AATTTTACT
1 AAAATTACCATTTT--ACCCCAAACTTCACT
*
31909313 AAAATTACCATTTTACCCTCAAACTTCCCT
1 AAAATTACCATTTTACCC-CAAACTTCACT
31909343 AA
1 AA
31909345 GTCCCATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
28 18 0.39
29 7 0.15
30 21 0.46
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCAAACTTCACT
Found at i:31913403 original size:11 final size:11
Alignment explanation
Indices: 31913383--31913426 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
31913373 AAGTCACGTG
*
31913383 GCTGATGTGGC
1 GCTGACGTGGC
31913394 GCTGACGTGGC
1 GCTGACGTGGC
* *
31913405 ACTGACGTGGA
1 GCTGACGTGGC
31913416 GCTGACGTGGC
1 GCTGACGTGGC
31913427 TAGCACTGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.14, C:0.23, G:0.43, T:0.20
Consensus pattern (11 bp):
GCTGACGTGGC
Found at i:31913414 original size:22 final size:22
Alignment explanation
Indices: 31913384--31913426 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
31913374 AGTCACGTGG
* *
31913384 CTGATGTGGCGCTGACGTGGCA
1 CTGACGTGGAGCTGACGTGGCA
31913406 CTGACGTGGAGCTGACGTGGC
1 CTGACGTGGAGCTGACGTGGC
31913427 TAGCACTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.23, G:0.42, T:0.21
Consensus pattern (22 bp):
CTGACGTGGAGCTGACGTGGCA
Found at i:31913615 original size:6 final size:6
Alignment explanation
Indices: 31913604--31913635 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
31913594 AATTTGAGAA
31913604 TTTTAT TTTTAT TTTTAT TTATTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TT-TTAT TTTTAT T
31913636 ATTTTTTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:31913628 original size:13 final size:12
Alignment explanation
Indices: 31913604--31913635 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
31913594 AATTTGAGAA
31913604 TTTTATTTTTAT
1 TTTTATTTTTAT
31913616 TTTTATTTATTAT
1 TTTTATTT-TTAT
31913629 TTTTATT
1 TTTTATT
31913636 ATTTTTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTATTTTTAT
Found at i:31913635 original size:9 final size:9
Alignment explanation
Indices: 31913606--31913641 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
31913596 TTTGAGAATT
31913606 TTATTTTTA
1 TTATTTTTA
*
31913615 TTTTTATTTA
1 TTATT-TTTA
31913625 TTATTTTTA
1 TTATTTTTA
31913634 TTATTTTT
1 TTATTTTT
31913642 TGGGTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTATTTTTA
Found at i:31913637 original size:12 final size:12
Alignment explanation
Indices: 31913604--31913642 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
31913594 AATTTGAGAA
*
31913604 TTTTATTTTTAT
1 TTTTATTATTAT
31913616 TTTTATTTATTAT
1 TTTTA-TTATTAT
31913629 TTTTATTATT-T
1 TTTTATTATTAT
31913640 TTT
1 TTT
31913643 GGGTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 4 0.16
12 10 0.40
13 11 0.44
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:31913651 original size:14 final size:14
Alignment explanation
Indices: 31913634--31913660 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31913624 ATTATTTTTA
31913634 TTATTTTTTGGGTT
1 TTATTTTTTGGGTT
31913648 TTATTTTTTGGGT
1 TTATTTTTTGGGT
31913661 CCGGTCAAAA
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:0.07, C:0.00, G:0.22, T:0.70
Consensus pattern (14 bp):
TTATTTTTTGGGTT
Found at i:31914173 original size:27 final size:27
Alignment explanation
Indices: 31914136--31914187 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
31914126 AGCAAATTTC
*
31914136 TTTTGTTATAAGTGATATCTAAACCGT
1 TTTTATTATAAGTGATATCTAAACCGT
31914163 TTTTATTATAAGTGATATCTAAACC
1 TTTTATTATAAGTGATATCTAAACC
31914188 ACTTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (27 bp):
TTTTATTATAAGTGATATCTAAACCGT
Found at i:31914193 original size:27 final size:26
Alignment explanation
Indices: 31914135--31914206 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 26
31914125 TAGCAAATTT
*
31914135 CTTTTGTTATAAGTGATATCTAAACCG
1 CTTTT-TTATAAGTGATATCTAAACCA
*
31914162 TTTTTATTATAAGTGATATCTAAACCA
1 CTTTT-TTATAAGTGATATCTAAACCA
*
31914189 CTTTTTTTTAAGTAGATA
1 CTTTTTTATAAGT-GATA
31914207 CCTCTATTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 7 0.18
27 32 0.82
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (26 bp):
CTTTTTTATAAGTGATATCTAAACCA
Found at i:31916775 original size:12 final size:12
Alignment explanation
Indices: 31916758--31916782 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31916748 CATTTCTGTC
31916758 TTGCCAAACAAA
1 TTGCCAAACAAA
31916770 TTGCCAAACAAA
1 TTGCCAAACAAA
31916782 T
1 T
31916783 GCAATCTTCC
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:0.48, C:0.24, G:0.08, T:0.20
Consensus pattern (12 bp):
TTGCCAAACAAA
Found at i:31917729 original size:31 final size:31
Alignment explanation
Indices: 31917691--31917752 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
31917681 TTGGGTCAAA
31917691 CAGTTTGCCTCTGTTCAGAAACCAAATATAG
1 CAGTTTGCCTCTGTTCAGAAACCAAATATAG
31917722 CAGTTTGCCTCTGTTCAGAAACCAAATATAG
1 CAGTTTGCCTCTGTTCAGAAACCAAATATAG
31917753 ATAAGAGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (31 bp):
CAGTTTGCCTCTGTTCAGAAACCAAATATAG
Found at i:31919035 original size:62 final size:60
Alignment explanation
Indices: 31918923--31919042 Score: 161
Period size: 62 Copynumber: 2.0 Consensus size: 60
31918913 ATCACTTTAA
* * *
31918923 TATTAAATTAATATAATATTTATCAAAATAAATATTAAATTAAATTTAATA-TTAAATCT
1 TATTAAAATAATAGAATATTTATCAAAATAAACATTAAATTAAATTTAATATTTAAATCT
* *
31918982 TATTAAAATAATAGAATGTTTATCTACAAGATAACCATTAAATTAAATTTAATATTTAAAT
1 TATTAAAATAATAGAATATTTATC-A-AA-ATAAACATTAAATTAAATTTAATATTTAAAT
31919043 AATCACTTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 21 0.40
60 1 0.02
61 2 0.04
62 22 0.42
63 6 0.12
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (60 bp):
TATTAAAATAATAGAATATTTATCAAAATAAACATTAAATTAAATTTAATATTTAAATCT
Found at i:31920639 original size:95 final size:95
Alignment explanation
Indices: 31920534--31920741 Score: 262
Period size: 95 Copynumber: 2.2 Consensus size: 95
31920524 AACTTTGCAA
* *
31920534 AATTTAGCTAAGTGCCTTAAGT-GGCTTAGTAGTGTATCTGGC-ATTAGACCTAGCAAACAGTTT
1 AATTTAGCTAAGTGCCTTAA-TAGGCTTAGCAGTATATCT-GCTATTAGACCTAGCAAACAGTTT
*
31920597 CCTCTC-GAGGTGTCTGCTTTATAACTTCATTG
64 CCTCTCAGA-GTGTCTACTTTATAACTTCATTG
* * * *
31920629 AATTTAGCTAAGTGCCTTAATAGGCTTAGCAGTATATCTGCTATTAGACTTAGCGAGCAGTTTTC
1 AATTTAGCTAAGTGCCTTAATAGGCTTAGCAGTATATCTGCTATTAGACCTAGCAAACAGTTTCC
* **
31920694 TCTCAGAGTGTCTATTTTATAACTTTGTTG
66 TCTCAGAGTGTCTACTTTATAACTTCATTG
*
31920724 AATTTAGC-AAGTGGCTTA
1 AATTTAGCTAAGTGCCTTA
31920742 GTAGTGTATC
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
94 12 0.12
95 85 0.86
96 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (95 bp):
AATTTAGCTAAGTGCCTTAATAGGCTTAGCAGTATATCTGCTATTAGACCTAGCAAACAGTTTCC
TCTCAGAGTGTCTACTTTATAACTTCATTG
Found at i:31922348 original size:22 final size:22
Alignment explanation
Indices: 31922323--31922366 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
31922313 TCACTAAACT
*
31922323 TCAAATTATTCTA-GTTATATCA
1 TCAAATTA-TCAATGTTATATCA
31922345 TCAAATTATCAATGTTATATCA
1 TCAAATTATCAATGTTATATCA
31922367 ATTAGGTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.43
Consensus pattern (22 bp):
TCAAATTATCAATGTTATATCA
Found at i:31927893 original size:57 final size:57
Alignment explanation
Indices: 31927824--31927960 Score: 274
Period size: 57 Copynumber: 2.4 Consensus size: 57
31927814 TCGTTTTAAA
31927824 TTCAAATTTTATTAGTGTGTGAATTTTTAAAACACTGATTCGAAATTGCATATGCAG
1 TTCAAATTTTATTAGTGTGTGAATTTTTAAAACACTGATTCGAAATTGCATATGCAG
31927881 TTCAAATTTTATTAGTGTGTGAATTTTTAAAACACTGATTCGAAATTGCATATGCAG
1 TTCAAATTTTATTAGTGTGTGAATTTTTAAAACACTGATTCGAAATTGCATATGCAG
31927938 TTCAAATTTTATTAGTGTGTGAA
1 TTCAAATTTTATTAGTGTGTGAA
31927961 GTTAAGATGA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 80 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (57 bp):
TTCAAATTTTATTAGTGTGTGAATTTTTAAAACACTGATTCGAAATTGCATATGCAG
Found at i:31930316 original size:30 final size:30
Alignment explanation
Indices: 31930282--31930503 Score: 318
Period size: 30 Copynumber: 7.4 Consensus size: 30
31930272 ACCGGGGTCA
*
31930282 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
1 AAAATATAATTTTGGAAAAGTTTTGGGGTT
* * **
31930312 AAAATGTAATTTTGGATAAGTTTTAAGGTT
1 AAAATATAATTTTGGAAAAGTTTTGGGGTT
*
31930342 AAAATATAATTTTGGAAAAGTTTTGGGGTC
1 AAAATATAATTTTGGAAAAGTTTTGGGGTT
**
31930372 AAAATATAATTTTGGAAAAGTTTTAAGGTT
1 AAAATATAATTTTGGAAAAGTTTTGGGGTT
*
31930402 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
1 AAAATATAATTTTGGAAAAGTTTTGGGGTT
**
31930432 AAAATATAATTTTGGAAAAGTTTTAAGGTT
1 AAAATATAATTTTGGAAAAGTTTTGGGGTT
* * *
31930462 AAAATGTAATTTTGGAAAAGTTTTGGTGTC
1 AAAATATAATTTTGGAAAAGTTTTGGGGTT
31930492 AAAATATAATTT
1 AAAATATAATTT
31930504 CTAGATAGTT
Statistics
Matches: 169, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 169 1.00
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.40
Consensus pattern (30 bp):
AAAATATAATTTTGGAAAAGTTTTGGGGTT
Found at i:31930352 original size:90 final size:88
Alignment explanation
Indices: 31930223--31930450 Score: 257
Period size: 90 Copynumber: 2.6 Consensus size: 88
31930213 ATCGAGGCTA
* * ** *
31930223 AAAATGGAATTTTAGAAAGTTCAAAGG-TAAAATGGTAATTTTTGGTAAAA-CCGGGGTCAAAAA
1 AAAATGTAATTTTGGAAAGTTTTAAGGTTAAAAT-ATAATTTTTGG-AAAATCCGGGGTC-AAAA
* **
31930286 TGTAATTTTGGAAAAGTTTTGGGGTT
63 TATAATTTTGGAAAAGTTTTAAGGTT
**
31930312 AAAATGTAATTTTGGATAAGTTTTAAGGTTAAAATATAA-TTTTGGAAAAGTTTTGGGGTCAAAA
1 AAAATGTAATTTTGGA-AAGTTTTAAGGTTAAAATATAATTTTTGGAAAA--TCCGGGGTCAAAA
31930376 TATAATTTTGGAAAAGTTTTAAGGTT
63 TATAATTTTGGAAAAGTTTTAAGGTT
**
31930402 AAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATATAA-TTTTGGAAAA
1 AAAATGTAATTTTGG-AAAGTTTTAAGGTTAAAATATAATTTTTGGAAAA
31930451 GTTTTAAGGT
Statistics
Matches: 121, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
88 4 0.03
89 20 0.17
90 84 0.69
91 13 0.11
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (88 bp):
AAAATGTAATTTTGGAAAGTTTTAAGGTTAAAATATAATTTTTGGAAAATCCGGGGTCAAAATAT
AATTTTGGAAAAGTTTTAAGGTT
Found at i:31930514 original size:60 final size:60
Alignment explanation
Indices: 31930282--31930503 Score: 390
Period size: 60 Copynumber: 3.7 Consensus size: 60
31930272 ACCGGGGTCA
* * *
31930282 AAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATGTAATTTTGGATAAGTTTTAAGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTAAGGTT
*
31930342 AAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTAAGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTAAGGTT
*
31930402 AAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGTTTTAAGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTAAGGTT
*
31930462 AAAATGTAATTTTGGAAAAGTTTTGGTGTCAAAATATAATTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTT
31930504 CTAGATAGTT
Statistics
Matches: 154, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 154 1.00
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.40
Consensus pattern (60 bp):
AAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTAAGGTT
Found at i:31931966 original size:17 final size:17
Alignment explanation
Indices: 31931943--31931995 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
31931933 GGCTTTTATT
31931943 TTTAAATTTATAA-T-AA
1 TTTAAATTTA-AATTAAA
31931959 TGTTAAATTTAAATTAAA
1 T-TTAAATTTAAATTAAA
*
31931977 TTTAAATTTAAATTGAA
1 TTTAAATTTAAATTAAA
31931994 TT
1 TT
31931996 CAAAATAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 3 0.09
17 27 0.82
18 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:31931970 original size:6 final size:6
Alignment explanation
Indices: 31931961--31932026 Score: 59
Period size: 6 Copynumber: 11.7 Consensus size: 6
31931951 TATAATAATG
* * *
31931961 TTAAAT TTAAA- TTAAAT TTAAAT TTAAA- TTGAAT TCAAA- ATAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
31932006 TTAAAA TTAAA- ATAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAA
31932027 TTTCAAAATG
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
5 16 0.34
6 31 0.66
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (6 bp):
TTAAAT
Done.