Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_pilon, whole genome shotgun sequence
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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 62
Found at i:5377264 original size:3 final size:3
Alignment explanation
Indices: 5377256--5377285 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5377246 TCGGAGACCG
5377256 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5377286 CTACTACTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5381399 original size:21 final size:21
Alignment explanation
Indices: 5381375--5381426 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
5381365 GAATAAAGAC
5381375 TTAAATTAAATCTAAATC-AAT
1 TTAAATTAAAT-TAAATCAAAT
* *
5381396 TTAACTATAACTTAAATCAAAT
1 TTAAAT-TAAATTAAATCAAAT
*
5381418 TTCAATTAA
1 TTAAATTAA
5381427 TTGATTAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAATTAAATTAAATCAAAT
Found at i:5384150 original size:134 final size:134
Alignment explanation
Indices: 5383910--5384177 Score: 536
Period size: 134 Copynumber: 2.0 Consensus size: 134
5383900 CATGACCAAA
5383910 AATACATGTCAAATTTGCAAGTGCGGGCACTGTTTATGGTATTCCAAATTTGCTCAATCATTAAA
1 AATACATGTCAAATTTGCAAGTGCGGGCACTGTTTATGGTATTCCAAATTTGCTCAATCATTAAA
5383975 CTTACCACATTTGCTCTTGCTCCTGAAACACCAGATACATCAAAAGCACTCATAGTGTTAACATT
66 CTTACCACATTTGCTCTTGCTCCTGAAACACCAGATACATCAAAAGCACTCATAGTGTTAACATT
5384040 TGGG
131 TGGG
5384044 AATACATGTCAAATTTGCAAGTGCGGGCACTGTTTATGGTATTCCAAATTTGCTCAATCATTAAA
1 AATACATGTCAAATTTGCAAGTGCGGGCACTGTTTATGGTATTCCAAATTTGCTCAATCATTAAA
5384109 CTTACCACATTTGCTCTTGCTCCTGAAACACCAGATACATCAAAAGCACTCATAGTGTTAACATT
66 CTTACCACATTTGCTCTTGCTCCTGAAACACCAGATACATCAAAAGCACTCATAGTGTTAACATT
5384174 TGGG
131 TGGG
5384178 CACCGTGTTC
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 134 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (134 bp):
AATACATGTCAAATTTGCAAGTGCGGGCACTGTTTATGGTATTCCAAATTTGCTCAATCATTAAA
CTTACCACATTTGCTCTTGCTCCTGAAACACCAGATACATCAAAAGCACTCATAGTGTTAACATT
TGGG
Found at i:5391137 original size:18 final size:18
Alignment explanation
Indices: 5391114--5391151 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
5391104 TGTACCCAAA
5391114 CAGAATACGCGAGGACAC
1 CAGAATACGCGAGGACAC
5391132 CAGAATACGCGAGGACAC
1 CAGAATACGCGAGGACAC
5391150 CA
1 CA
5391152 CTTAAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.29, G:0.26, T:0.05
Consensus pattern (18 bp):
CAGAATACGCGAGGACAC
Found at i:5394128 original size:38 final size:37
Alignment explanation
Indices: 5394074--5394155 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 37
5394064 CTTCATAAAA
* *
5394074 TAATATTATTACATTATTAAATATTTAAA-ATATTTATT
1 TAATAATATTAAATTATTAAATATTTAAATATA-TTA-T
5394112 TAATAATATTAAATTATTAAATATTTAAATATATTAT
1 TAATAATATTAAATTATTAAATATTTAAATATATTAT
5394149 TAATAAT
1 TAATAAT
5394156 TTCCAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
37 8 0.20
38 30 0.73
39 3 0.07
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (37 bp):
TAATAATATTAAATTATTAAATATTTAAATATATTAT
Found at i:5394136 original size:15 final size:17
Alignment explanation
Indices: 5394088--5394147 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 17
5394078 ATTATTACAT
5394088 TATTAAATATTTAAAATA
1 TATTAAATATTT-AAATA
*
5394106 TTTATTTAATAATATTAAAT-
1 --TATTAAAT-AT-TTAAATA
5394126 TATTAAATATTTAAATA
1 TATTAAATATTTAAATA
5394143 TATTA
1 TATTA
5394148 TTAATAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 6 0.17
17 7 0.20
18 7 0.20
20 7 0.20
21 6 0.17
22 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTAAATATTTAAATA
Found at i:5394210 original size:22 final size:24
Alignment explanation
Indices: 5394176--5394221 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
5394166 TAATTTAATA
*
5394176 TTTTAATTTTAAT-ATTA-TATAT
1 TTTTAATTCTAATAATTATTATAT
*
5394198 TTTTTATTCTAATAATTATTATAT
1 TTTTAATTCTAATAATTATTATAT
5394222 AATTAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 4 0.20
24 5 0.25
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTAATTCTAATAATTATTATAT
Found at i:5394236 original size:26 final size:25
Alignment explanation
Indices: 5394207--5394261 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
5394197 TTTTTTATTC
*
5394207 TAATAATTATTA-TATAATTAATAAT
1 TAAT-ATTATTATTATAATAAATAAT
*
5394232 ATAATATTTTTATTATAATAAATAAT
1 -TAATATTATTATTATAATAAATAAT
5394258 TAAT
1 TAAT
5394262 CATATTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAATATTATTATTATAATAAATAAT
Found at i:5394269 original size:26 final size:26
Alignment explanation
Indices: 5394219--5394273 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
5394209 ATAATTATTA
* *
5394219 TATAATTAATAATATAATATTTTTAT
1 TATAATAAATAATATAATATATTTAT
5394245 TATAATAAATAAT-TAATCATATTTAT
1 TATAATAAATAATATAAT-ATATTTAT
5394271 TAT
1 TAT
5394274 TTTAGTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
TATAATAAATAATATAATATATTTAT
Found at i:5394557 original size:23 final size:21
Alignment explanation
Indices: 5394530--5394591 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 21
5394520 ACATAATATA
5394530 TAATAATTATTATTATTTAAAAC
1 TAATAATTATTATTATTT--AAC
*
5394553 TAATATATTTATTTATT-TTTAAT
1 TAATA-A-TTA-TTATTATTTAAC
5394576 TAATAA-TATTATTATT
1 TAATAATTATTATTATT
5394592 GTATTCGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
19 5 0.15
20 4 0.12
22 1 0.03
23 12 0.35
24 1 0.03
25 6 0.18
26 5 0.15
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATAATTATTATTATTTAAC
Found at i:5395506 original size:100 final size:99
Alignment explanation
Indices: 5395402--5395849 Score: 465
Period size: 97 Copynumber: 4.5 Consensus size: 99
5395392 TTTTAACTGG
* *
5395402 TTAAGTTATAAGACTTTAACTGTTTATATTATAATAATCTATAACAAATCCAATTTC-AGTGGTA
1 TTAAGTTATAAGACTTTAA-TG-TTATATTATAATAACCTATAACAAATCCAGTTTCGA-TGGTA
5395466 A-GTAATAGATTGCGCCTTGATTTTATTTTGAATCGA
63 ACGTAATAGATTGCGCCTTGATTTTATTTTGAATCGA
* * * *
5395502 TTAAGTTATAAGGCTTTAACCGTT-TA-TAT--TAACCTATGACAAATACAGTTTCGATGGTAAC
1 TTAAGTTATAAGACTTTAA-TGTTATATTATAATAACCTATAACAAATCCAGTTTCGATGGTAAC
* * * *
5395563 GTAATAGGTTGCGCCTTTATTTTATTTTTGAATTGG
65 GTAATAGATTGCGCCTTGATTTTA-TTTTGAATCGA
* *** *
5395599 TT-AGTTATAAGACTTTAATTGTTATATTATAAT--CCTATGACAAATATGGTTTC-AGTGATAA
1 TTAAGTTATAAGACTTTAA-TGTTATATTATAATAACCTATAACAAATCCAGTTTCGA-TGGTAA
* * * *
5395660 TGTAATAGGTTGCACC-TGATTTTATTTTGAA-CTA
64 CGTAATAGATTGCGCCTTGATTTTATTTTGAATCGA
5395694 GTTAAGTTATAAGACTTTAATCGTTATATTATAATAACCTATAACAAATCCAGTTTCGATGGTAA
1 -TTAAGTTATAAGACTTTAAT-GTTATATTATAATAACCTATAACAAATCCAGTTTCGATGGTAA
* * * * *
5395759 CGTAATA-AGTGTGCCTTGATTTTATTTTTAAACTGG
64 CGTAATAGATTGCGCCTTGATTTTATTTTGAATC-GA
*
5395795 TTAAGTTATAAGGCTTTAATCGTTTATATTATAATAACCTATAACAAATCC-GTTT
1 TTAAGTTATAAGACTTTAAT-G-TTATATTATAATAACCTATAACAAATCCAGTTT
5395850 ATATGTAATA
Statistics
Matches: 294, Mismatches: 36, Indels: 36
0.80 0.10 0.10
Matches are distributed among these distances:
95 25 0.09
96 51 0.17
97 53 0.18
98 46 0.16
99 43 0.15
100 48 0.16
101 28 0.10
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (99 bp):
TTAAGTTATAAGACTTTAATGTTATATTATAATAACCTATAACAAATCCAGTTTCGATGGTAACG
TAATAGATTGCGCCTTGATTTTATTTTGAATCGA
Found at i:5395761 original size:197 final size:196
Alignment explanation
Indices: 5395362--5395843 Score: 618
Period size: 197 Copynumber: 2.5 Consensus size: 196
5395352 GGTCGGGATA
* * * *
5395362 GTAACGTAAAAGGTTGTGCATTGA-TTTATTTTTTAACTGGTTAAGTTATAAGACTTTAACTGTT
1 GTAACGTAATAGGTTGTGCCTTGATTTTATTTTTAAACTGGTTAAGTTATAAGACTTTAATTGTT
* * * *
5395426 TATATTATAATAATCTATAACAAATCCAATTTCAGTGGTAAGTAATAGATTGCGCCTTGATTTTA
66 TATATTATAAT-ACCTATAACAAATACAATTTCAGTGATAAGTAATAGATTGCACCTTGATTTTA
* * *
5395491 TTTTGAATCGATTAAGTTATAAGGCTTTAACCGTTTATATTAACCTATGACAAATACAGTTTCGA
130 TTTTGAATAGATTAAGTTATAAGACTTTAACCGTTTATATTAACCTATAACAAATACAGTTTCGA
5395556 TG
195 TG
* * * *
5395558 GTAACGTAATAGGTTGCGCCTTTATTTTATTTTTGAATTGGTT-AGTTATAAGACTTTAATTG-T
1 GTAACGTAATAGGTTGTGCCTTGATTTTATTTTTAAACTGGTTAAGTTATAAGACTTTAATTGTT
* *** *
5395621 TATATTATAAT-CCTATGACAAATATGGTTTCAGTGATAATGTAATAGGTTGCACC-TGATTTTA
66 TATATTATAATACCTATAACAAATACAATTTCAGTGATAA-GTAATAGATTGCACCTTGATTTTA
* *
5395684 TTTTGAACTAG-TTAAGTTATAAGACTTTAATCGTTATATTATAATAACCTATAACAAATCCAGT
130 TTTTGAA-TAGATTAAGTTATAAGACTTTAACCGTT-TA-TAT--TAACCTATAACAAATACAGT
5395748 TTCGATG
190 TTCGATG
* * *
5395755 GTAACGTAATAAG-TGTGCCTTGATTTTATTTTTAAACTGGTTAAGTTATAAGGCTTTAATCGTT
1 GTAACGTAATAGGTTGTGCCTTGATTTTATTTTTAAACTGGTTAAGTTATAAGACTTTAATTGTT
5395819 TATATTATAATAACCTATAACAAAT
66 TATATTATAAT-ACCTATAACAAAT
5395844 CCGTTTATAT
Statistics
Matches: 246, Mismatches: 29, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
193 58 0.24
194 17 0.07
195 15 0.06
196 63 0.26
197 70 0.28
198 12 0.05
200 11 0.04
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (196 bp):
GTAACGTAATAGGTTGTGCCTTGATTTTATTTTTAAACTGGTTAAGTTATAAGACTTTAATTGTT
TATATTATAATACCTATAACAAATACAATTTCAGTGATAAGTAATAGATTGCACCTTGATTTTAT
TTTGAATAGATTAAGTTATAAGACTTTAACCGTTTATATTAACCTATAACAAATACAGTTTCGAT
G
Found at i:5395903 original size:19 final size:19
Alignment explanation
Indices: 5395876--5395913 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5395866 GTTATAACTA
* *
5395876 TTACTTAAATATTGATACT
1 TTACATAAATATCGATACT
5395895 TTACATAAATATCGATACT
1 TTACATAAATATCGATACT
5395914 ATCGAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.42
Consensus pattern (19 bp):
TTACATAAATATCGATACT
Found at i:5402027 original size:103 final size:106
Alignment explanation
Indices: 5401900--5402092 Score: 338
Period size: 103 Copynumber: 1.8 Consensus size: 106
5401890 TTTGGGTACT
*
5401900 CCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTT-TG-CTACGGGTTCACTCCCTTTTGCTTCA
1 CCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCACTCCCTCTTGCTTCA
5401963 -GGAGTAGAACTCGAACAATCTTCTACCTACGGGTTCTCTC
66 GGGAGTAGAACTCGAACAATCTTCTACCTACGGGTTCTCTC
* *
5402003 CCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCA
1 CCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCACTCCCTCTTGCTTCA
5402068 GGGAGTAGAACTCGAACAATCTTCT
66 GGGAGTAGAACTCGAACAATCTTCT
5402093 GGTATGATTC
Statistics
Matches: 84, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
103 34 0.40
104 2 0.02
105 24 0.29
106 24 0.29
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (106 bp):
CCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCACTCCCTCTTGCTTCA
GGGAGTAGAACTCGAACAATCTTCTACCTACGGGTTCTCTC
Found at i:5402045 original size:53 final size:52
Alignment explanation
Indices: 5401843--5402093 Score: 340
Period size: 53 Copynumber: 5.0 Consensus size: 52
5401833 TCTTTTAAAA
* *
5401843 ACGGGTTCGCTCCCTATTGCTTCAGGGAGTAGAAC-CG-A-AATCTTCTG-T
1 ACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCT
** *
5401891 TTGGG-T-ACT-CCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTT-TGCT
1 ACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCT
* *
5401939 ACGGGTTCACTCCCTTTTGCTTCA-GGAGTAGAACTCGAACAATCTTCTACCT
1 ACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT-GCT
*
5401991 ACGGGTTCTCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
1 ACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG-CT
*
5402044 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 ACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
5402094 GTATGATTCT
Statistics
Matches: 179, Mismatches: 13, Indels: 17
0.86 0.06 0.08
Matches are distributed among these distances:
45 21 0.12
46 4 0.02
47 4 0.02
48 13 0.07
49 1 0.01
50 25 0.14
51 12 0.07
52 24 0.13
53 75 0.42
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (52 bp):
ACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCT
Found at i:5402671 original size:41 final size:41
Alignment explanation
Indices: 5402604--5402690 Score: 140
Period size: 41 Copynumber: 2.1 Consensus size: 41
5402594 AAATTACCTT
5402604 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGACACG
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGAC-CG
* *
5402646 AAGGATTT-TTCATCATGCTCGAAAGACTTACTGATGGCCG
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGACCG
5402686 AAGGA
1 AAGGA
5402691 CTTGTAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 7 0.16
41 28 0.65
42 8 0.19
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (41 bp):
AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGACCG
Found at i:5402884 original size:36 final size:35
Alignment explanation
Indices: 5402839--5402915 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 35
5402829 GCTGTAAAGA
5402839 CTTACAGATGGATTTGCTTCACTACTC-TTCGTGAAGG
1 CTTACAGATGG---TGCTTCACTACTCTTTCGTGAAGG
*
5402876 CTTA-AGATGGTGCTTCACTACTCTTTGGTGAAGG
1 CTTACAGATGGTGCTTCACTACTCTTTCGTGAAGG
5402910 CTTACA
1 CTTACA
5402916 AATTACCCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
33 13 0.35
34 13 0.35
35 1 0.03
36 6 0.16
37 4 0.11
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (35 bp):
CTTACAGATGGTGCTTCACTACTCTTTCGTGAAGG
Found at i:5402967 original size:41 final size:41
Alignment explanation
Indices: 5402921--5403016 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
5402911 TTACAAATTA
*
5402921 CCCGAATGA-TTAATCATCATGCTCAAAAGACTTACTGATGG
1 CCCGAAGGACTTAATCATCATGCTCAAAAGACTTAC-GATGG
* * *
5402962 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACGATGA
1 CCCGAAGGACTTAATCATCATGCTCAAAAGACTTACGATGG
* *
5403003 CACTAAGGACTTAA
1 CCCGAAGGACTTAA
5403017 ATTGCTTACT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 23 0.49
42 24 0.51
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (41 bp):
CCCGAAGGACTTAATCATCATGCTCAAAAGACTTACGATGG
Found at i:5402994 original size:22 final size:21
Alignment explanation
Indices: 5402933--5402996 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
5402923 CGAATGATTA
*
5402933 ATCATCATGCTCAAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * *
5402954 A-C-TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
5402974 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
5402996 A
1 A
5402997 CGATGACACT
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 3 0.09
22 12 0.38
23 3 0.09
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:5419935 original size:21 final size:22
Alignment explanation
Indices: 5419893--5419946 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
5419883 AACAACAAAT
*
5419893 GGATCGATC-TTTTCTTTCGAG
1 GGATCGATCTTTTTCCTTCGAG
5419914 GGATCGATCTTTTTCCTT-GAG
1 GGATCGATCTTTTTCCTTCGAG
*
5419935 GGATTG-TCTTTT
1 GGATCGATCTTTT
5419947 GGAAAAGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 6 0.20
21 17 0.57
22 7 0.23
ACGTcount: A:0.13, C:0.17, G:0.24, T:0.46
Consensus pattern (22 bp):
GGATCGATCTTTTTCCTTCGAG
Found at i:5421120 original size:23 final size:23
Alignment explanation
Indices: 5421094--5421172 Score: 131
Period size: 23 Copynumber: 3.4 Consensus size: 23
5421084 ATTTATCTTT
*
5421094 TTTTTCCTCTCCTATTCTTCATA
1 TTTTCCCTCTCCTATTCTTCATA
*
5421117 TTTTCCCTCTCATATTCTTCATA
1 TTTTCCCTCTCCTATTCTTCATA
5421140 TTTTCCCTCTCCTATTCTTCATA
1 TTTTCCCTCTCCTATTCTTCATA
*
5421163 TTTTTCCTCT
1 TTTTCCCTCT
5421173 TGTGAGCTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.13, C:0.32, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTCCCTCTCCTATTCTTCATA
Found at i:5422387 original size:22 final size:21
Alignment explanation
Indices: 5422361--5422411 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
5422351 TTCTCTTTTC
*
5422361 CAGTGCTATGGAACTTTTGTAT
1 CAGTGCTATGCAA-TTTTGTAT
*
5422383 CAGTGCAAATGCAATTTTGTAT
1 CAGTGC-TATGCAATTTTGTAT
5422405 CAGTGCT
1 CAGTGCT
5422412 GAGGCACTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (21 bp):
CAGTGCTATGCAATTTTGTAT
Found at i:5425219 original size:22 final size:23
Alignment explanation
Indices: 5425183--5425227 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
5425173 ATGTTGTGCC
5425183 AAAGAACAAAAACATTATGTGTT
1 AAAGAACAAAAACATTATGTGTT
5425206 AAAGAAC-AAAACATTATGTGTT
1 AAAGAACAAAAACATTATGTGTT
5425228 TGTCATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (23 bp):
AAAGAACAAAAACATTATGTGTT
Found at i:5428808 original size:25 final size:25
Alignment explanation
Indices: 5428771--5428831 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
5428761 ATCTTTGACC
*
5428771 TTTGTATCCTATTGGATGAATAACA
1 TTTGTATCTTATTGGATGAATAACA
**
5428796 TTTGTATCTTATTGGATGAATAATT
1 TTTGTATCTTATTGGATGAATAACA
5428821 TTTGTATCTTA
1 TTTGTATCTTA
5428832 AGAAATACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (25 bp):
TTTGTATCTTATTGGATGAATAACA
Found at i:5432979 original size:15 final size:14
Alignment explanation
Indices: 5432953--5432982 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5432943 TTTATTCATC
5432953 AATAATGTATTTTT
1 AATAATGTATTTTT
*
5432967 AATAATGTAATTTT
1 AATAATGTATTTTT
5432981 AA
1 AA
5432983 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:5433327 original size:17 final size:17
Alignment explanation
Indices: 5433302--5433341 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
5433292 GAAAGATTTC
*
5433302 ATCAAATAGTATTGAAT
1 ATCAAATAGTATCGAAT
*
5433319 ATCATATAGTATCGAAT
1 ATCAAATAGTATCGAAT
5433336 ATCAAA
1 ATCAAA
5433342 AGATTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (17 bp):
ATCAAATAGTATCGAAT
Found at i:5433666 original size:98 final size:98
Alignment explanation
Indices: 5433538--5433880 Score: 344
Period size: 101 Copynumber: 3.5 Consensus size: 98
5433528 AAATCGATAT
* *
5433538 GTTAT-AGTGCTTATAACCATTTATATTATAATAACATATAACAAAT-CATGATTCTATGGTAAC
1 GTTATAAG-GCTT-TAACCGTTTATATTATAATAACATATAACAAATACA-GATTCTATGGTAAA
5433601 GTAATAGGTTGCGCCTTGATTTTTTGAATCAGTTAA
63 GTAATAGGTTGCGCCTTGATTTTTTGAATCAGTTAA
* * *
5433637 GTTATATA-GCTTTAACCGTTTATATTATAATAACCTATAATAAATACA-ATTTCAATGGTAAAG
1 GTTATA-AGGCTTTAACCGTTTATATTATAATAACATATAACAAATACAGA-TTCTATGGTAAAG
* *
5433700 TAATAGGTTGTGCCTT-ATTTTTTTTTTGAA-CTGGTTAA
64 TAATAGGTTGCGCCTTGA----TTTTTTGAATC-AGTTAA
* * * *
5433738 CTTATAAGGCTTTAATCGTTTATATTATAATAACATATAACAAATACAGTTTTTATGGTAAAGTA
1 GTTATAAGGCTTTAACCGTTTATATTATAATAACATATAACAAATACAGATTCTATGGTAAAGTA
* * * *
5433803 TTAGGTTGC-ACTGTGATTTTTT-TAT-TGTTTAA
66 ATAGGTTGCGCCT-TGATTTTTTGAATCAG-TTAA
** * *
5433835 GTTATAATTCGTTAACCGTTTATATTATAATAACCTATAACAAATA
1 GTTATAAGGCTTTAACCGTTTATATTATAATAACATATAACAAATA
5433881 TGGTTATGAG
Statistics
Matches: 204, Mismatches: 25, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
96 1 0.00
97 47 0.23
98 62 0.30
99 11 0.05
100 4 0.02
101 78 0.38
102 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (98 bp):
GTTATAAGGCTTTAACCGTTTATATTATAATAACATATAACAAATACAGATTCTATGGTAAAGTA
ATAGGTTGCGCCTTGATTTTTTGAATCAGTTAA
Found at i:5436056 original size:30 final size:31
Alignment explanation
Indices: 5436008--5436065 Score: 109
Period size: 30 Copynumber: 1.9 Consensus size: 31
5435998 TGATTTATTC
5436008 GGTTTAGTTCATTTTAATCCATGAATATCAT
1 GGTTTAGTTCATTTTAATCCATGAATATCAT
5436039 GGTTTAGTTCA-TTTAATCCATGAATAT
1 GGTTTAGTTCATTTTAATCCATGAATAT
5436066 AGTATCTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (31 bp):
GGTTTAGTTCATTTTAATCCATGAATATCAT
Found at i:5443516 original size:36 final size:36
Alignment explanation
Indices: 5443361--5443515 Score: 231
Period size: 36 Copynumber: 4.3 Consensus size: 36
5443351 AGTCAATCCT
*
5443361 AAGCCTTCACCGGAGAATAGTGAAGTAAACCATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
* *
5443397 AAGCCTTCACCGGAGAATAGTGAAGCAATCAATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
5443433 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCAT-
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATC-TG
* * *
5443469 AAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
*
5443505 AAGTCTTCACC
1 AAGCCTTCACC
5443516 AAAAAGTAGT
Statistics
Matches: 109, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
35 1 0.01
36 107 0.98
37 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (36 bp):
AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
Found at i:5443524 original size:36 final size:36
Alignment explanation
Indices: 5443361--5443549 Score: 177
Period size: 36 Copynumber: 5.2 Consensus size: 36
5443351 AGTCAATCCT
* * *
5443361 AAGCCTTCACCGGAGAATAGTGAAGTAAACCATCTG
1 AAGCCTTCACCGAAAAATAGTGAAGCAAACCATCTG
* * * *
5443397 AAGCCTTCACCGGAGAATAGTGAAGCAATCAATCTG
1 AAGCCTTCACCGAAAAATAGTGAAGCAAACCATCTG
* *
5443433 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCAT-
1 AAGCCTTCACCGAAAAATAGTGAAGCAAACCATC-TG
* * *
5443469 AAGTCTTCACC-AGAGAGTAGTGAAGCAAACCATCTG
1 AAGCCTTCACCGA-AAAATAGTGAAGCAAACCATCTG
* * * *
5443505 AAGTCTTCACC-AAAAAGTAGTGAAGCAGATCCATTTT
1 AAGCCTTCACCGAAAAA-TAGTGAAGCA-AACCATCTG
5443542 AAGCCTTC
1 AAGCCTTC
5443550 TCAGAAGAGT
Statistics
Matches: 134, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
35 3 0.02
36 117 0.87
37 14 0.10
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (36 bp):
AAGCCTTCACCGAAAAATAGTGAAGCAAACCATCTG
Found at i:5443526 original size:72 final size:72
Alignment explanation
Indices: 5443361--5443549 Score: 211
Period size: 72 Copynumber: 2.6 Consensus size: 72
5443351 AGTCAATCCT
* * * * *
5443361 AAGCCTTCACCGGAGAATAGTGAAGTAAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAT
1 AAGCCTTCACCGAAAAATAGTGAAGCAAACCATCTGAAGCCTTCACCAGAGAATAGTGAAGCAAA
5443426 CAATCTG
66 CAATCTG
* * * *
5443433 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCAT-AAGTCTTCACCAGAGAGTAGTGAAGCAA
1 AAGCCTTCACCGAAAAATAGTGAAGCAAACCATC-TGAAGCCTTCACCAGAGAATAGTGAAGCAA
*
5443497 ACCATCTG
65 ACAATCTG
* * * *
5443505 AAGTCTTCACC-AAAAAGTAGTGAAGCAGATCCATTTTAAGCCTTC
1 AAGCCTTCACCGAAAAA-TAGTGAAGCA-AACCATCTGAAGCCTTC
5443550 TCAGAAGAGT
Statistics
Matches: 101, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
71 3 0.03
72 85 0.84
73 13 0.13
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (72 bp):
AAGCCTTCACCGAAAAATAGTGAAGCAAACCATCTGAAGCCTTCACCAGAGAATAGTGAAGCAAA
CAATCTG
Found at i:5444000 original size:51 final size:51
Alignment explanation
Indices: 5443929--5444220 Score: 327
Period size: 51 Copynumber: 5.6 Consensus size: 51
5443919 TGAAGATATA
* *
5443929 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTAAAGATGTT
1 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTAAAGATGTT
* *
5443980 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATG-T
1 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT-AA-AGATGTT
* *
5444032 CTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TGAAGAGATGTT
1 C-GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTAA-AGATGTT
* * * *
5444084 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGATTATT
1 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTAAAGA-TGTT
* * * * **
5444136 TGAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCTGTAAGAAGAAGATGTT
1 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGT--TTA-AAGATGTT
* * *
5444190 CGAGTTCCATAATCCCTAGAGAAATAGGGAG
1 CGAGTTCCATACTCCCTAAAGAAAGAGGGAG
5444221 TAGACGCAAT
Statistics
Matches: 206, Mismatches: 26, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
51 86 0.42
52 46 0.22
53 40 0.19
54 30 0.15
55 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (51 bp):
CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTAAAGATGTT
Found at i:5444115 original size:104 final size:103
Alignment explanation
Indices: 5443930--5444220 Score: 388
Period size: 104 Copynumber: 2.8 Consensus size: 103
5443920 GAAGATATAC
* * * *
5443930 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTAA-AGATGTTCGAGTTCCATACTC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TGAAGAGATGTTCGAGTTCCATACTC
* * *
5443994 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGA-GATGTCT
65 CCTAAAGAAAGAGGGAGCGAACCCATTTGAAGATGAT-T-T
*
5444034 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCGAGTTCTATACTCC
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCGAGTTCCATACTCC
*
5444099 CTAAAGAAAGAGGGAGCGAACCCATTTGAAGATTATTT
66 CTAAAGAAAGAGGGAGCGAACCCATTTGAAGATGATTT
* * *
5444137 GAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCTGTAAGAAGAAGATGTTCGAGTTCCATAA
1 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT--GAAG-AGATGTTCGAGTTCCATAC
* *
5444202 TCCCTAGAGAAATAGGGAG
63 TCCCTAAAGAAAGAGGGAG
5444221 TAGACGCAAT
Statistics
Matches: 167, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
103 41 0.25
104 86 0.51
105 6 0.04
106 34 0.20
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (103 bp):
GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCGAGTTCCATACTCC
CTAAAGAAAGAGGGAGCGAACCCATTTGAAGATGATTT
Found at i:5444272 original size:53 final size:55
Alignment explanation
Indices: 5444208--5444333 Score: 157
Period size: 53 Copynumber: 2.3 Consensus size: 55
5444198 ATAATCCCTA
* * *
5444208 GAGAAATAGGGAGTAGACGCAATTGATGAAGATTG-T-GAGTCTTATACTCTCTG
1 GAGAAATAGGGAGTAGACCCAATTGATGAAGATTGTTCGAGTCTCATACTATCTG
* *
5444261 GAGAAATAGGGAGTAGACCCGATTGTTGAAGATTGTTCGAGTCTCATACTATCTG
1 GAGAAATAGGGAGTAGACCCAATTGATGAAGATTGTTCGAGTCTCATACTATCTG
* * * *
5444316 AAGGAATAAGGAGCAGAC
1 GAGAAATAGGGAGTAGAC
5444334 ACGTTTTCAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
53 32 0.52
54 1 0.02
55 29 0.47
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (55 bp):
GAGAAATAGGGAGTAGACCCAATTGATGAAGATTGTTCGAGTCTCATACTATCTG
Found at i:5448780 original size:73 final size:72
Alignment explanation
Indices: 5448634--5448894 Score: 278
Period size: 71 Copynumber: 3.6 Consensus size: 72
5448624 CATAATATAT
* * * *
5448634 GTATCTATATTTTAACTATTGATCATATCTTCAACTTCTTCTATA--TAAAAGTATCGATCATCA
1 GTATCAATATTTTAACT-TTGATCTTATCTTCAACTTTTTCAATACTTAAAAGTATCGATCATCA
*
5448697 GCGCATAA
65 CCGCATAA
* * * *
5448705 GTATCGATATTTTAAATTTCGATCTTATCTTCAACTCTTTCAATACTTAAAAATATCGATCATCA
1 GTATCAATATTTTAACTTT-GATCTTATCTTCAACTTTTTCAATACTTAAAAGTATCGATCATCA
* *
5448770 CCTCCTAA
65 CCGCATAA
* * * * * *
5448778 GTATCAATATATTAACTTTTGATCTTATCTT-TATTTTTTAAATAATTAAAAGTATTGATCATCA
1 GTATCAATATTTTAAC-TTTGATCTTATCTTCAACTTTTTCAATACTTAAAAGTATCGATCATCA
*
5448842 CCGCATGA
65 CCGCATAA
* *
5448850 GTATCAATA-TTTAACTTTAAATCTCATCTTCAACTTTTTCAATAC
1 GTATCAATATTTTAACTTT-GATCTTATCTTCAACTTTTTCAATAC
5448895 CTGAACGTGT
Statistics
Matches: 154, Mismatches: 30, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
70 5 0.03
71 50 0.32
72 50 0.32
73 46 0.30
74 3 0.02
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.42
Consensus pattern (72 bp):
GTATCAATATTTTAACTTTGATCTTATCTTCAACTTTTTCAATACTTAAAAGTATCGATCATCAC
CGCATAA
Found at i:5448807 original size:144 final size:144
Alignment explanation
Indices: 5448634--5448894 Score: 328
Period size: 144 Copynumber: 1.8 Consensus size: 144
5448624 CATAATATAT
* * **
5448634 GTATCTATATTTTAACTATTGATCATATCTTCAACTTCTTCTAT-A-TAAAAGTATCGATCATCA
1 GTATCAATATATTAACTATTGATCATATCTT-AACTTCTTAAATAATTAAAAGTATCGATCATCA
* * ** *
5448697 GCGCATAAGTATCGATATTTTAAATTTCGATCTTATCTTCAACTCTTTCAATACTTAAAAATATC
65 CCGCATAAGTATCAATA-TTTAAATTTAAATCTCATCTTCAACTCTTTCAATACTTAAAAATATC
5448762 GATCATCACCTCCTAA
129 GATCATCACCTCCTAA
* * * * * *
5448778 GTATCAATATATTAACTTTTGATCTTATCTTTATTTTTTAAATAATTAAAAGTATTGATCATCAC
1 GTATCAATATATTAACTATTGATCATATCTTAACTTCTTAAATAATTAAAAGTATCGATCATCAC
* * *
5448843 CGCATGAGTATCAATATTTAACTTTAAATCTCATCTTCAACTTTTTCAATAC
66 CGCATAAGTATCAATATTTAAATTTAAATCTCATCTTCAACTCTTTCAATAC
5448895 CTGAACGTGT
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
143 7 0.07
144 59 0.61
145 31 0.32
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.42
Consensus pattern (144 bp):
GTATCAATATATTAACTATTGATCATATCTTAACTTCTTAAATAATTAAAAGTATCGATCATCAC
CGCATAAGTATCAATATTTAAATTTAAATCTCATCTTCAACTCTTTCAATACTTAAAAATATCGA
TCATCACCTCCTAA
Found at i:5448853 original size:72 final size:72
Alignment explanation
Indices: 5448634--5448893 Score: 235
Period size: 72 Copynumber: 3.6 Consensus size: 72
5448624 CATAATATAT
* *
5448634 GTATCTATATTTTAACTATT-GATCATATCTTCAACTTCTTCT--AT-A-TAAAAGTATCGATCA
1 GTATCAATA-TTTAACT-TTCGATCTTATCTTCAAC-TCTT-TAAATAATTAAAAGTATCGATCA
*
5448694 TCAGCGCATAA
62 TCACCGCATAA
* * * * *
5448705 GTATCGATATTTTAAATTTCGATCTTATCTTCAACTCTTTCAATACTTAAAAATATCGATCATCA
1 GTATCAATA-TTTAACTTTCGATCTTATCTTCAACTCTTTAAATAATTAAAAGTATCGATCATCA
* *
5448770 CCTCCTAA
65 CCGCATAA
* * * * *
5448778 GTATCAATATATTAACTTTTGATCTTATCTT-TATTTTTTAAATAATTAAAAGTATTGATCATCA
1 GTATCAATAT-TTAACTTTCGATCTTATCTTCAACTCTTTAAATAATTAAAAGTATCGATCATCA
*
5448842 CCGCATGA
65 CCGCATAA
** * * *
5448850 GTATCAATATTTAACTTTAAATCTCATCTTCAACTTTTTCAATA
1 GTATCAATATTTAACTTTCGATCTTATCTTCAACTCTTTAAATA
5448894 CCTGAACGTG
Statistics
Matches: 155, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
69 1 0.01
70 6 0.04
71 48 0.31
72 52 0.34
73 48 0.31
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.42
Consensus pattern (72 bp):
GTATCAATATTTAACTTTCGATCTTATCTTCAACTCTTTAAATAATTAAAAGTATCGATCATCAC
CGCATAA
Found at i:5449420 original size:185 final size:184
Alignment explanation
Indices: 5449012--5449892 Score: 889
Period size: 185 Copynumber: 4.7 Consensus size: 184
5449002 GGCAACCGAT
** * *
5449012 TTTTATTAAACATAAAATTAACATTCCAAATCTTAACCTACTTTTTTAGCGACCCATAACATTTA
1 TTTTATTAAACATAAAATTAACATTCCAAATCACAACCTACTTTCTTAGCGA-CCATAACATTCA
* *
5449077 TGGGCGCAACATGATTTCTTATAGATATTCATAACATTTTTTTTATTTTAACTTATTTTGTTATC
65 TGGGCTCAACCTGATTTCTTATAGATATTCATAACA---TTTTTATTTTAACTTATTTTGTTATC
** * * * *
5449142 GTGGGAAATTCAAAAGCCTCATCAACTTAAACTTTGATAACATTTTAGGCGCAACCGA
127 GTGGGAAATTTGAAAGCCACATCAACTTAAACTCTGATAACATTTTAGGCACAATCGA
* * * **
5449200 TTTTATTAAATATAATACTAACATTCCAAATCACAACCTACTTTCTTAATGACACATAACATTCA
1 TTTTATTAAACATAAAATTAACATTCCAAATCACAACCTACTTTCTTAGCGAC-CATAACATTCA
* * * *
5449265 CGGGCTCAACCTGATTTCTTATAGATGTTCATAACATTTTTATTTTAACTTAGTTTGTTATTGTG
65 TGGGCTCAACCTGATTTCTTATAGATATTCATAACATTTTTATTTTAACTTATTTTGTTATCGTG
* * * * * *
5449330 TGAAATTTGAAAGTCC-CATCAGCTTGAACTCT-AGTAACATTTTAGGCATAGTTGA
130 GGAAATTTGAAAG-CCACATCAACTTAAACTCTGA-TAACATTTTAGGCACAATCGA
* * * *
5449385 TTTTATCAAACACAAAATTAACATTCCAGATCACAACCTACTTTCTTAGCAACCCATAACATTCA
1 TTTTATTAAACATAAAATTAACATTCCAAATCACAACCTACTTTCTTAGCGA-CCATAACATTCA
* * * * * * * *
5449450 TGGACGT-AACCTGAATTCTTATAGATATTCATAATATTTTTAATTTAACTTAATTTATTTTTGT
65 TGGGC-TCAACCTGATTTCTTATAGATATTCATAACATTTTTATTTTAACTTATTTTGTTATCGT
** ** * * * *
5449514 TAGAAATTCAAAATCC-CTATCAAATTAAACTCTGTTAACATTTTAGGCACAATCAA
129 GGGAAATTTGAAAGCCAC-ATCAACTTAAACTCTGATAACATTTTAGGCACAATCGA
* ** ** *
5449570 TTTTATCT-AACATAAAATTAACATTTCAGGTCGTAACCTACTTTCTTAGCGACCTATAACATTA
1 TTTTAT-TAAACATAAAATTAACATTCCAAATCACAACCTACTTTCTTAGCGACC-ATAACATTC
* * * *
5449634 ATGAGCACAACTTAATTT-TTATAGATATTCATAACAGTTTTTGATTTTAACTTATTTTGTTATC
64 ATGGGCTCAACCTGATTTCTTATAGATATTCATAACA-TTTTT-ATTTTAACTTATTTTGTTATC
* * * * *
5449698 GTGGGAAA-TTGAAAAGCCATATTAGCTTAAACTCTGGTAACATTTTAGGCTCAATCGA
127 GTGGGAAATTTG-AAAGCCACATCAACTTAAACTCTGATAACATTTTAGGCACAATCGA
* * * * * *
5449756 TTTTATTAGACATAAAACTAACATTCTATATCACAACCTACTTTATTGGCGACCATAGA-ATT-A
1 TTTTATTAAACATAAAATTAACATTCCAAATCACAACCTACTTTCTTAGCGACCATA-ACATTCA
* * *
5449819 TTGGATGCAACCTGATTTCTTATAGATATTCATAACAACTTTTATTTTAACTTATTTTGTTATCG
65 TGGGCT-CAACCTGATTTCTTATAGATATTCATAAC-ATTTTTATTTTAACTTATTTTGTTATCG
*
5449884 TGAGAAATT
128 TGGGAAATT
5449893 CAGAACCCCA
Statistics
Matches: 566, Mismatches: 107, Indels: 42
0.79 0.15 0.06
Matches are distributed among these distances:
184 26 0.05
185 324 0.57
186 128 0.23
187 2 0.00
188 86 0.15
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (184 bp):
TTTTATTAAACATAAAATTAACATTCCAAATCACAACCTACTTTCTTAGCGACCATAACATTCAT
GGGCTCAACCTGATTTCTTATAGATATTCATAACATTTTTATTTTAACTTATTTTGTTATCGTGG
GAAATTTGAAAGCCACATCAACTTAAACTCTGATAACATTTTAGGCACAATCGA
Found at i:5449611 original size:370 final size:369
Alignment explanation
Indices: 5448989--5449929 Score: 1033
Period size: 370 Copynumber: 2.5 Consensus size: 369
5448979 TATTATTGTG
* ** * **
5448989 GTAACGTTTTAGGGGCAACCGATTTTTATTAAACATAAAATTAACATTCCAAATCTTAACCTACT
1 GTAACATTTTAGGCTCAATCGA-TTTTATTAAACATAAAATTAACATTCCAAATCACAACCTACT
* * * *
5449054 TTTTTAGCGACCCATAACATTTATGGGCGCAACATGATTTCTTATAGATATTCATAACATTTTTT
65 TTATTAGCGACCCATAACA-TTATGGACGCAACCTGATTTCTTATAGATATTCATAAC--TATTT
* * * *
5449119 TTATTTTAACTTATTTTGTTATCGTGGGAAATTCAAAAGCCTCATCAACTTAAACTTTGATAACA
127 TTATTTTAACTTATTTTGTTATCGTGAGAAATTCAAAACCCT-ATCAAATTAAACTCTG-TAACA
* *
5449184 TTTTAGGCGCAACCGATTTTATTAAATATAATACTAACATTCCAAATCACAACCTACTTTCTTAA
190 TTTTAGGCACAACCAATTTTATTAAATATAATACTAACATTCCAAATCACAACCTACTTTCTTAA
* * * * * *
5449249 TGACAC-ATAACATTCACGGGCTCAACCTGATTTCTTATAGATGTTCATAACA-TTTTT-ATTTT
255 CGAC-CTATAACATTAACGAGCACAACCTAATTT-TTATAGATATTCATAACAGTTTTTGATTTT
* * *
5449311 AACTTAGTTTGTTATTGTGTGAAATTTG-AAAGTCC-CATCAGCTTGAACTCTA
318 AACTTAGTTTGTTATCGTGGGAAA-TTGAAAAG-CCACATCAGCTTAAACTCTA
* * * * *
5449363 GTAACATTTTAGGCAT-AGTTGATTTTATCAAACACAAAATTAACATTCCAGATCACAACCTACT
1 GTAACATTTTAGGC-TCAATCGATTTTATTAAACATAAAATTAACATTCCAAATCACAACCTACT
* * * *
5449427 TTCTTAGCAACCCATAACATTCATGGACGTAACCTGAATTCTTATAGATATTCATAA-TATTTTT
65 TTATTAGCGACCCATAACATT-ATGGACGCAACCTGATTTCTTATAGATATTCATAACTATTTTT
* * * * * *
5449491 AATTTAACTTAATTTATTTTTGTTAGAAATTCAAAATCCCTATCAAATTAAACTCTGTTAACATT
129 ATTTTAACTTATTTTGTTATCGTGAGAAATTCAAAA-CCCTATCAAATTAAACTCTG-TAACATT
* * * ** ** *
5449556 TTAGGCACAATCAATTTTATCTAACATA-AA-ATTAACATTTCAGGTCGTAACCTACTTTCTTAG
192 TTAGGCACAACCAATTTTAT-TAA-ATATAATACTAACATTCCAAATCACAACCTACTTTCTTAA
* *
5449619 CGACCTATAACATTAATGAGCACAACTTAATTTTTATAGATATTCATAACAGTTTTTGATTTTAA
255 CGACCTATAACATTAACGAGCACAACCTAATTTTTATAGATATTCATAACAGTTTTTGATTTTAA
* * * *
5449684 CTTATTTTGTTATCGTGGGAAATTGAAAAGCCATATTAGCTTAAACTCTG
320 CTTAGTTTGTTATCGTGGGAAATTGAAAAGCCACATCAGCTTAAACTCTA
* * * *
5449734 GTAACATTTTAGGCTCAATCGATTTTATTAGACATAAAACTAACATTCTATATCACAACCTACTT
1 GTAACATTTTAGGCTCAATCGATTTTATTAAACATAAAATTAACATTCCAAATCACAACCTACTT
* * * *
5449799 TATTGGCGA-CCATAGA-ATTATTGGATGCAACCTGATTTCTTATAGATATTCATAACAACTTTT
66 TATTAGCGACCCATA-ACATTA-TGGACGCAACCTGATTTCTTATAGATATTCATAACTATTTTT
* * * *
5449862 ATTTTAACTTATTTTGTTATCGTGAGAAATTCAGAACCCCATCATATT-AACTCTAGCAACATTT
129 ATTTTAACTTATTTTGTTATCGTGAGAAATTCAAAACCCTATCAAATTAAACTCT-GTAACATTT
5449926 TAGG
193 TAGG
5449930 TGCAATCGAT
Statistics
Matches: 472, Mismatches: 80, Indels: 35
0.80 0.14 0.06
Matches are distributed among these distances:
369 36 0.08
370 184 0.39
371 147 0.31
372 5 0.01
373 85 0.18
374 15 0.03
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (369 bp):
GTAACATTTTAGGCTCAATCGATTTTATTAAACATAAAATTAACATTCCAAATCACAACCTACTT
TATTAGCGACCCATAACATTATGGACGCAACCTGATTTCTTATAGATATTCATAACTATTTTTAT
TTTAACTTATTTTGTTATCGTGAGAAATTCAAAACCCTATCAAATTAAACTCTGTAACATTTTAG
GCACAACCAATTTTATTAAATATAATACTAACATTCCAAATCACAACCTACTTTCTTAACGACCT
ATAACATTAACGAGCACAACCTAATTTTTATAGATATTCATAACAGTTTTTGATTTTAACTTAGT
TTGTTATCGTGGGAAATTGAAAAGCCACATCAGCTTAAACTCTA
Found at i:5452396 original size:34 final size:34
Alignment explanation
Indices: 5452353--5452419 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
5452343 CCTTATTGAA
5452353 ACTGATCATTTGA-AGAGGCAAGCCAA-CAAATAAC
1 ACTGATCATTTGAGA-AGGCAAG-CAATCAAATAAC
*
5452387 ACTGGTCATTTGAGAAGGCAAGCAATCAAATAA
1 ACTGATCATTTGAGAAGGCAAGCAATCAAATAA
5452420 TCAGTCTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 3 0.10
34 26 0.87
35 1 0.03
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.19
Consensus pattern (34 bp):
ACTGATCATTTGAGAAGGCAAGCAATCAAATAAC
Found at i:5453167 original size:2 final size:2
Alignment explanation
Indices: 5453160--5453194 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5453150 TGGTATAACT
5453160 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5453195 TTGCATGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5463692 original size:36 final size:36
Alignment explanation
Indices: 5463643--5463712 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
5463633 GTCCCCCATG
* *
5463643 CCATCTTATGCCTTCACGAAAGAGTAGTGAAGCAAA
1 CCATCTTAAGCCTTCACAAAAGAGTAGTGAAGCAAA
5463679 CCATCTTAAGCCTTCACAAAAGAGTAGTGAAGCA
1 CCATCTTAAGCCTTCACAAAAGAGTAGTGAAGCA
5463713 GAATCACACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (36 bp):
CCATCTTAAGCCTTCACAAAAGAGTAGTGAAGCAAA
Found at i:5463840 original size:53 final size:53
Alignment explanation
Indices: 5463722--5463840 Score: 150
Period size: 53 Copynumber: 2.2 Consensus size: 53
5463712 AGAATCACAC
* *
5463722 CAGAAAATTGTTCGAGTTATACTCCCTAAAGTAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
* * * * * *
5463775 CAGAAGACTGTTCGAGTTCTACTCCCTGAAGAAAGAGGGAGTGAACCTGCTAGT
1 CAGAAGATTGTTCGAGTTATACTCCCTAAAGAAAGAGGGAGCGAACCCG-TAGG
5463829 C-GAAGATTGTTC
1 CAGAAGATTGTTC
5463841 AAAGAAGAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 52 0.93
54 4 0.07
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
Found at i:5464112 original size:2 final size:2
Alignment explanation
Indices: 5464105--5464129 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5464095 TGGTATAACT
5464105 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5464130 TTCATGAGTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5469074 original size:13 final size:13
Alignment explanation
Indices: 5469056--5469089 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
5469046 AATATTTTTG
*
5469056 TTTTGAAAATCAT
1 TTTTGAAAATCAA
5469069 TTTTG-AAATCAA
1 TTTTGAAAATCAA
5469081 TTTTGAAAA
1 TTTTGAAAA
5469090 ATTACTCCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTTGAAAATCAA
Found at i:5470850 original size:64 final size:65
Alignment explanation
Indices: 5470767--5470923 Score: 176
Period size: 65 Copynumber: 2.4 Consensus size: 65
5470757 ACTAAGAGTT
* *
5470767 CATCGATGCATCAAGTGCATTCGATGTTTT-A-AAATAGCCAGAGTGCATCGATGCATGGCT-GG
1 CATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCCACAGTGCATCGATGCATGG-TAGG
*
5470829 TG
64 AG
* * * * * * *
5470831 CATCGATACATCAAATGCATTCAATGTTTTCATAAAATCCTCAGTGCATTGGTGCATGGTATGAG
1 CATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGTAGGAG
*
5470896 CATCGATGCATGAAATGCATTCGATGTT
1 CATCGATGCATCAAATGCATTCGATGTT
5470924 CAATTTAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
64 28 0.36
65 46 0.60
66 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (65 bp):
CATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGTAGGAG
Found at i:5470964 original size:65 final size:63
Alignment explanation
Indices: 5470767--5470973 Score: 165
Period size: 65 Copynumber: 3.2 Consensus size: 63
5470757 ACTAAGAGTT
* * *
5470767 CATCGATGCATCAAGTGCATTCGATGTTT--TAAAATAGC-CAGAGTGCATCGATGCATGGCTGG
1 CATCGATGCATCAAATGCATTCAATGTTTCATAAAAT--CTC--AGTGCATCGATGCATGGTTGG
5470829 TG
62 TG
* * * *
5470831 CATCGATACATCAAATGCATTCAATGTTTTCATAAAATCCTCAGTGCATTGGTGCATGGTAT-GA
1 CATCGATGCATCAAATGCATTCAATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-TGGT
5470895 G
63 G
* * **
5470896 CATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGATTGG
1 CATCGATGCATCAAATGCATTCAATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-TTGG
5470959 TG
62 TG
*
5470961 CATCGGTGCATCA
1 CATCGATGCATCA
5470974 CTCTGAAAAA
Statistics
Matches: 115, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 43 0.37
65 57 0.50
66 2 0.02
67 7 0.06
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (63 bp):
CATCGATGCATCAAATGCATTCAATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTGGTG
Found at i:5477403 original size:22 final size:21
Alignment explanation
Indices: 5477361--5477400 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5477351 GAGTTTATTT
*
5477361 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
5477382 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
5477401 ACAATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:5477570 original size:22 final size:21
Alignment explanation
Indices: 5477528--5477567 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5477518 GAGTTTATTT
*
5477528 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
5477549 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
5477568 ACAATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:5479702 original size:65 final size:63
Alignment explanation
Indices: 5479504--5479704 Score: 160
Period size: 65 Copynumber: 3.1 Consensus size: 63
5479494 TGCACTAAGA
* * * ** * *
5479504 GTGCATCGATGCATCAAGTGCATTCGATGTTT--TAAAATAGGCAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGAATTCAATGTTTCATAAAAT---CTCAGTGCATTGATGCATGGTT
5479567 G
63 G
*
5479568 GTGCATCGATGCATCAAATGAATTCAATGTTTTCATAAAATCCTCAGTGCATTGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGAATTCAATG-TTTCATAAAAT-CTCAGTGCATTGATGCATGGT-T
5479633 -
63 G
* * * **
5479633 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATTGATGCATGGAT
1 GTGCATCGATGCATCAAATGAATTCAATGTTTC-ATAAAATCTCA--GTGCATTGATGCATGG-T
5479696 TG
62 TG
5479698 GTGCATC
1 GTGCATC
5479705 ACTCTGAAAA
Statistics
Matches: 113, Mismatches: 15, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 47 0.42
65 53 0.47
66 1 0.01
67 6 0.05
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGAATTCAATGTTTCATAAAATCTCAGTGCATTGATGCATGGTTG
Found at i:5480835 original size:19 final size:21
Alignment explanation
Indices: 5480811--5480856 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
5480801 TATATAGGTT
5480811 TCAAAACAAC-ATAA-TTAAA
1 TCAAAACAACAATAATTTAAA
5480830 TC-AAA-AACAATAATTTAAA
1 TCAAAACAACAATAATTTAAA
*
5480849 ACAAAACA
1 TCAAAACA
5480857 TATTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
17 3 0.14
18 7 0.32
19 8 0.36
20 3 0.14
21 1 0.05
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.20
Consensus pattern (21 bp):
TCAAAACAACAATAATTTAAA
Found at i:5481104 original size:20 final size:20
Alignment explanation
Indices: 5481066--5481104 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5481056 GAGTGGAATG
* *
5481066 TGATGTTGTTTGCACGATTT
1 TGATGATGTTAGCACGATTT
*
5481086 TGATGATGTTAGCAGGATT
1 TGATGATGTTAGCACGATT
5481105 AGAAGTTGAA
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:0.21, C:0.08, G:0.28, T:0.44
Consensus pattern (20 bp):
TGATGATGTTAGCACGATTT
Found at i:5482553 original size:65 final size:64
Alignment explanation
Indices: 5482419--5482578 Score: 177
Period size: 65 Copynumber: 2.5 Consensus size: 64
5482409 TGCACTAAGA
* * *
5482419 GTGCATCAATGCATGAAATGCATTCGATG-TTTCAAAATAGCCAGAGTGCGTCGATGCATGACT
1 GTGCATCGATGCATGAAATGCTTTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATGACT
* * *
5482482 GCTGCATCGACGCATCAAATGCTTTCGATGTTTTCATAAA-A-CTCGGAGTGCATCGATGCATAG
1 G-TGCATCGATGCATGAAATGCTTTCGATGTTTTCA-AAATAGC-CAGAGTGCATCGATGCAT-G
5482545 TA-T
62 -ACT
5482548 GTGCATCGATGCATGAAATG-TATTCGATGTT
1 GTGCATCGATGCATGAAATGCT-TTCGATGTT
5482579 CAATTTATTC
Statistics
Matches: 82, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
63 1 0.01
64 26 0.32
65 48 0.59
66 6 0.07
67 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCTTTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATGACT
Found at i:5482901 original size:14 final size:14
Alignment explanation
Indices: 5482878--5482911 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5482868 TAAGATTTTC
5482878 TTTG-AAAATAAAT
1 TTTGAAAAATAAAT
5482891 TTTGAAAAATAAAT
1 TTTGAAAAATAAAT
5482905 TTTGAAA
1 TTTGAAA
5482912 TTACTCCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (14 bp):
TTTGAAAAATAAAT
Found at i:5484783 original size:13 final size:13
Alignment explanation
Indices: 5484765--5484789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5484755 AATCAAAAAC
5484765 ATCAAATTTAGAA
1 ATCAAATTTAGAA
5484778 ATCAAATTTAGA
1 ATCAAATTTAGA
5484790 TTTTTTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (13 bp):
ATCAAATTTAGAA
Found at i:5488745 original size:13 final size:13
Alignment explanation
Indices: 5488727--5488752 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5488717 ATGTTATTTC
5488727 AATGTGCTTAGTT
1 AATGTGCTTAGTT
5488740 AATGTGCTTAGTT
1 AATGTGCTTAGTT
5488753 CTAGAGTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
AATGTGCTTAGTT
Found at i:5494129 original size:37 final size:37
Alignment explanation
Indices: 5494069--5494153 Score: 127
Period size: 37 Copynumber: 2.3 Consensus size: 37
5494059 ATAGCCAGAG
* *
5494069 TGCA-TCGATGCATGGCTGGTGCATCGATGCATCAAA
1 TGCATTCGATGTATGGCTGGTGCATCAATGCATCAAA
* *
5494105 TGCATTCGATGTATGGTTGTTGCATCAATGCATCAAA
1 TGCATTCGATGTATGGCTGGTGCATCAATGCATCAAA
5494142 TGCATTCGATGT
1 TGCATTCGATGT
5494154 TTTCATAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 4 0.09
37 40 0.91
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (37 bp):
TGCATTCGATGTATGGCTGGTGCATCAATGCATCAAA
Found at i:5494208 original size:102 final size:101
Alignment explanation
Indices: 5494031--5494218 Score: 267
Period size: 102 Copynumber: 1.9 Consensus size: 101
5494021 GAGTGCACCG
* *
5494031 ATGCATGAAATGCATTCGATGTTTTAAAATAGCCAGAGTGCATCGATGCATGGCTGGTGCATCGA
1 ATGCATCAAATGCATTCGATGTTTTAAAATAGCCAGAGTGCATCGATGCATAGCTGGTGCATCGA
5494096 TGCATCAAATGCATTCGATGTATGGTTGTTGCATCA
66 TGCATCAAATGCATTCGATGTATGGTTGTTGCATCA
*
5494132 ATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTA-AGTGCATCGATGCATAG-TATGTGC
1 ATGCATCAAATGCATTCGATGTTTT-A-AAATAGC-C-AGAGTGCATCGATGCATAGCT-GGTGC
*
5494193 ATCGATGCATGAAATGCATTCGATGT
61 ATCGATGCATCAAATGCATTCGATGT
5494219 TCAATTTATT
Statistics
Matches: 78, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
101 26 0.33
102 48 0.62
103 4 0.05
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Consensus pattern (101 bp):
ATGCATCAAATGCATTCGATGTTTTAAAATAGCCAGAGTGCATCGATGCATAGCTGGTGCATCGA
TGCATCAAATGCATTCGATGTATGGTTGTTGCATCA
Found at i:5501000 original size:23 final size:23
Alignment explanation
Indices: 5500973--5501025 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
5500963 TCCCGAAAGA
*
5500973 CCACATAGGTTTGCACCAAAGTG
1 CCACATAGGTTTACACCAAAGTG
*
5500996 CCACATAGGTTTACACCGAAGTG
1 CCACATAGGTTTACACCAAAGTG
5501019 CCACATA
1 CCACATA
5501026 ATTGTCCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (23 bp):
CCACATAGGTTTACACCAAAGTG
Found at i:5503071 original size:21 final size:21
Alignment explanation
Indices: 5503045--5503086 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5503035 CCACGATAGG
*
5503045 GGGTATCGGTACCCCTTCATA
1 GGGTATCAGTACCCCTTCATA
*
5503066 GGGTATCAGTACTCCTTCATA
1 GGGTATCAGTACCCCTTCATA
5503087 AAATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (21 bp):
GGGTATCAGTACCCCTTCATA
Found at i:5503154 original size:17 final size:18
Alignment explanation
Indices: 5503117--5503164 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
5503107 ATTGCAGCCA
*
5503117 GGGGGTATAGATACCCCT
1 GGGGGTATAGATACCCAT
*
5503135 GGGGGTATCGATA-CCAT
1 GGGGGTATAGATACCCAT
5503152 GGGGGTATAGATA
1 GGGGGTATAGATA
5503165 TCATCCGAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.25, C:0.15, G:0.38, T:0.23
Consensus pattern (18 bp):
GGGGGTATAGATACCCAT
Found at i:5506065 original size:664 final size:665
Alignment explanation
Indices: 5504530--5506515 Score: 2942
Period size: 663 Copynumber: 3.0 Consensus size: 665
5504520 CTGCAAGGCA
* * * *
5504530 AACTAAAAAAGGATGAAAAAAGCTGAAAAAGGAAATAATCGACATAAGCTATGCAAGAAAAGTTC
1 AACTAAAAAAGGATGAAAAAAGATGAAGAAGGAAACAATCGACCTAAGCTATGCAAGAAAAGTTC
* * * *
5504595 GCTCAAAAACTGCTCCAAGTATGGGAAACTTGGCTACAATAAGAGGACCTGTAGAGGAAAAATCG
66 GCTCGAAAACTGCTCCAAGTGTGGGAAACTTGGATACAATAAGAGGACTTGTAGAGGAAAAATCG
* * * *
5504660 GTGGTAATAGGAGACTAAACCAACATGAACTTAGATCCAACTAACGACATATAACTCTCAAACAA
131 GTGGTAATAGGAGACTAAACCAACATGAACTTAGATCCAACCAACGACATATAACTCACCAGCAA
5504725 CAAGCTCGACGTGCACGTAACCAACCAT-TCCAACAGCCAACTCCAAGGAACAACAAGTAAGGCA
196 CAAGCTCGACGTGCACGTAACCAACCATCT-CAACAGCCAACTCCAAGGAACAACAAGTAAGGCA
* *
5504789 CAAATTACCTATAAGGATGCCACTTAATCCACCTACAATAGTTTATTGGATTATGCTACCACCTA
260 CAAATTACCTATAAGGAGGCCACTTAATCCACCTACAATAGTTCATT-G----TG---CCACCTA
* *
5504854 CAACAATCCATACGATGCCTGCTAGTCAATAATATTTCTTTTTAACCCTCACACTCAAAAATTTT
317 CAACAATCCATACGATGACTGCTAGTCAAGAATATTTCTTTTTAACCCTCACACTCAAAAATTTT
* * * * *
5504919 ATACTACATCAAAGGATTGAAGTATGTCCAAGTAATTATGGAACCTTTTGTGTAATTTACTTGGG
382 ACACTACATCAAAGGATTGAAGTATGTCCAAGTGATGATGGAACTTTTTATGTAATTTACTTGGG
*
5504984 AACTTGACTTATTTTGTCATATACCTACTACTTATAGGATATATGTTATTTTGATTATAATGGCT
447 AACTTGACTTATTTTGTCATATACCTACTACTTATAGGATATATATTATTTTGATTATAATGGCT
5505049 TTTATGTATAACCATTCTTTTGTCCTTATTTTGACTTGAATTAAGCTTTGGCTTAATGTGATATT
512 TTTATGTATAACCATTCTTTTGTCCTTATTTTGACTTGAATTAAGCTTTGGCTTAATGTGATATT
* *
5505114 GAATTAGAGCAGGTTTGAC-AA--ATTA--TT--GTT-TT--AACTTGTATCAGTTTGAAAATTG
577 GAATTAGAGCAGGTTTGACAAATTATTATTTTAACTTGTTCAAACTTGTATCAGTTTGACAATTG
*
5505169 ATTTAAAGTTGAATTTCTTTTGCC
642 ATTTAAAGTTGAATTTCGTTTGCC
* * * *
5505193 AACTAAAAAAGGATGCAATAAGATGATGAAGAAAACAATCGACCTAAGCTATGCAAGAAAAGTTC
1 AACTAAAAAAGGATGAAAAAAGATGAAGAAGGAAACAATCGACCTAAGCTATGCAAGAAAAGTTC
* * *
5505258 GCTCGGAAACTACTCCAAGTGTGGAAAACTTGGATACAATAAGAGGACTTGTAGAGGAAAAATCG
66 GCTCGAAAACTGCTCCAAGTGTGGGAAACTTGGATACAATAAGAGGACTTGTAGAGGAAAAATCG
*
5505323 GTGGTAATAGGAGACTAAACCAACATGAACTTAGATCCAACCAACGACATATATCTCACCAGCAA
131 GTGGTAATAGGAGACTAAACCAACATGAACTTAGATCCAACCAACGACATATAACTCACCAGCAA
* * * * *
5505388 CAAGCTCGACGTGCACATAACCAGCCATCTCAACAACCAACTCCAAGGAACAACAACTAAGGCAA
196 CAAGCTCGACGTGCACGTAACCAACCATCTCAACAGCCAACTCCAAGGAACAACAAGTAAGGCAC
*
5505453 AAATTACCTATAAGGAGGCCACTTAATCCACCTACAATAGTTCATTG-G-CACCTACAATAATCC
261 AAATTACCTATAAGGAGGCCACTTAATCCACCTACAATAGTTCATTGTGCCACCTACAACAATCC
* * ** *
5505516 ATGCGATGACTGCCAGTCAAGAATATTTCTTTTTAACCCTTTCACTCAAAATTTTTACACTACAT
326 ATACGATGACTGCTAGTCAAGAATATTTCTTTTTAACCCTCACACTCAAAAATTTTACACTACAT
* *
5505581 CAAATGATTGAAGTATGTCCAAGTGATGATGGAACTTTTTATGTAATTTACTTTGGAACTTGACT
391 CAAAGGATTGAAGTATGTCCAAGTGATGATGGAACTTTTTATGTAATTTACTTGGGAACTTGACT
*
5505646 TATTTTGTCATATACCTAATACTTATAGGATATATATTATTTTGATTATAATGG-TTTTATGTAT
456 TATTTTGTCATATACCTACTACTTATAGGATATATATTATTTTGATTATAATGGCTTTTATGTAT
*
5505710 AACCATTCTTTTGTCCTTATTTTGACTTGAATTAAGCTTTGGATTAATGTGATATTGAATTAGAG
521 AACCATTCTTTTGTCCTTATTTTGACTTGAATTAAGCTTTGGCTTAATGTGATATTGAATTAGAG
* *
5505775 CAGGTTTGACAAATTATTATTTTAATTTGTATCAAACTTGTATCAGATTGACAATTGATTTAAAG
586 CAGGTTTGACAAATTATTATTTTAACTTGT-TCAAACTTGTATCAGTTTGACAATTGATTTAAAG
*
5505840 TTGAATTTCGTTTGCT
650 TTGAATTTCGTTTGCC
* * *
5505856 AACTAAAAAAAGGATGAAAGAAGTTGAAGAAGGAAACAATCGACCTAAGCTATGTAAGAAAAGTT
1 AACT-AAAAAAGGATGAAAAAAGATGAAGAAGGAAACAATCGACCTAAGCTATGCAAGAAAAGTT
* * *
5505921 CGCTCGAAAACTGCTCCAATTGTGGGAAACTTGGTTACAATAAGAGGACTTGTAAAGGAAAAATC
65 CGCTCGAAAACTGCTCCAAGTGTGGGAAACTTGGATACAATAAGAGGACTTGTAGAGGAAAAATC
** * *
5505986 TATGGTAATAGGAGACTAAACCAACATGAAGTTAGATCCAACCATCGACATATAACTCACCAGCA
130 GGTGGTAATAGGAGACTAAACCAACATGAACTTAGATCCAACCAACGACATATAACTCACCAGCA
* * * * * *
5506051 ACAAACTTGACGTGCATGTAACCAACCATCCCAATAGCTAACTCCAAGGAACAACAAGTAAGGCA
195 ACAAGCTCGACGTGCACGTAACCAACCATCTCAACAGCCAACTCCAAGGAACAACAAGTAAGGCA
*
5506116 CAAATTACCTATAAGGAGACCACTTAATCCACCTACAATAGTTCATTAGATGATGCCACCACCTA
260 CAAATTACCTATAAGGAGGCCACTTAATCCACCTACAATAGTTCA-T---TG-TG---CCACCTA
* *
5506181 AAACAATCCATACGAT-ACCTGCTAGTCAAGAATATTTCTTTTTAACCCTCCCACTCAAAAATTT
317 CAACAATCCATACGATGA-CTGCTAGTCAAGAATATTTCTTTTTAACCCTCACACTCAAAAATTT
5506245 TACACTACATCAAAGGATTGAAGTATGTCCAAGTGATGATGGAACTTTTTATGTAATTTACTTGG
381 TACACTACATCAAAGGATTGAAGTATGTCCAAGTGATGATGGAACTTTTTATGTAATTTACTTGG
* * * ** * *
5506310 GAACTTGACTTATTTTGTCATATACTTGCTAGTTATAGGATATCGATTATTTTGATTGTAATGGT
446 GAACTTGACTTATTTTGTCATATACCTACTACTTATAGGATATATATTATTTTGATTATAATGGC
* * *
5506375 TTTTATGTATAACCATTCATTTGTCCTTATTTTGACTTGAATTAAGCTTTGTCTTAATGTGATTT
511 TTTTATGTATAACCATTCTTTTGTCCTTATTTTGACTTGAATTAAGCTTTGGCTTAATGTGATAT
*
5506440 TGAATTAGAGCAGATTTGACAAATTATTATTTTAACTTGTGTCAAACTTGTATCAGTTTGACAAT
576 TGAATTAGAGCAGGTTTGACAAATTATTATTTTAACTTGT-TCAAACTTGTATCAGTTTGACAAT
5506505 TGA-TTAAAGTT
640 TGATTTAAAGTT
5506516 AATATGAAGT
Statistics
Matches: 1195, Mismatches: 103, Indels: 39
0.89 0.08 0.03
Matches are distributed among these distances:
652 84 0.07
653 184 0.15
655 4 0.00
657 3 0.00
659 2 0.00
660 1 0.00
661 1 0.00
662 1 0.00
663 324 0.27
664 272 0.23
665 1 0.00
668 2 0.00
670 1 0.00
673 1 0.00
674 189 0.16
675 125 0.10
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (665 bp):
AACTAAAAAAGGATGAAAAAAGATGAAGAAGGAAACAATCGACCTAAGCTATGCAAGAAAAGTTC
GCTCGAAAACTGCTCCAAGTGTGGGAAACTTGGATACAATAAGAGGACTTGTAGAGGAAAAATCG
GTGGTAATAGGAGACTAAACCAACATGAACTTAGATCCAACCAACGACATATAACTCACCAGCAA
CAAGCTCGACGTGCACGTAACCAACCATCTCAACAGCCAACTCCAAGGAACAACAAGTAAGGCAC
AAATTACCTATAAGGAGGCCACTTAATCCACCTACAATAGTTCATTGTGCCACCTACAACAATCC
ATACGATGACTGCTAGTCAAGAATATTTCTTTTTAACCCTCACACTCAAAAATTTTACACTACAT
CAAAGGATTGAAGTATGTCCAAGTGATGATGGAACTTTTTATGTAATTTACTTGGGAACTTGACT
TATTTTGTCATATACCTACTACTTATAGGATATATATTATTTTGATTATAATGGCTTTTATGTAT
AACCATTCTTTTGTCCTTATTTTGACTTGAATTAAGCTTTGGCTTAATGTGATATTGAATTAGAG
CAGGTTTGACAAATTATTATTTTAACTTGTTCAAACTTGTATCAGTTTGACAATTGATTTAAAGT
TGAATTTCGTTTGCC
Found at i:5507476 original size:17 final size:17
Alignment explanation
Indices: 5507454--5507500 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
5507444 TTTTTCTTTG
*
5507454 AATTTTAAATTT-ATTTT
1 AATTTT-AATTTGATTTC
5507471 AATTTTAATTTGATTTC
1 AATTTTAATTTGATTTC
*
5507488 AATTTCAATTTGA
1 AATTTTAATTTGA
5507501 AGGATATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (17 bp):
AATTTTAATTTGATTTC
Found at i:5512807 original size:22 final size:22
Alignment explanation
Indices: 5512779--5512826 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
5512769 ACTTTTTTTA
* * *
5512779 TCAAAGTTAACAGTTAGACCGG
1 TCAAAGTCAACAGTCAAACCGG
5512801 TCAAAGTCAACAGTCAAACCGG
1 TCAAAGTCAACAGTCAAACCGG
5512823 TCAA
1 TCAA
5512827 CGCTTCAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (22 bp):
TCAAAGTCAACAGTCAAACCGG
Found at i:5515172 original size:31 final size:31
Alignment explanation
Indices: 5515118--5515176 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
5515108 TTAGGTCCAT
* *
5515118 AATGAATTACCAGTCAGATCTGAACCTATAC
1 AATGAATTACCAGTCACAACTGAACCTATAC
5515149 AATGAATTACCAG-CAACAACTGAACCTA
1 AATGAATTACCAGTC-ACAACTGAACCTA
5515177 CCAGAGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.22
Consensus pattern (31 bp):
AATGAATTACCAGTCACAACTGAACCTATAC
Found at i:5517016 original size:20 final size:20
Alignment explanation
Indices: 5516993--5517056 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
5516983 TTAACTCGAG
*
5516993 TCGGGTCAGGTTGAATCGGT
1 TCGGGTCAGGTTGACTCGGT
* *
5517013 TCGGGTTTA-GTTGACTCGAT
1 TCGGG-TCAGGTTGACTCGGT
5517033 TCGGGTCAGGTTGACTCGGT
1 TCGGGTCAGGTTGACTCGGT
5517053 TCGG
1 TCGG
5517057 ACCGGGTTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.05
20 33 0.89
21 2 0.05
ACGTcount: A:0.12, C:0.17, G:0.38, T:0.33
Consensus pattern (20 bp):
TCGGGTCAGGTTGACTCGGT
Found at i:5517064 original size:20 final size:20
Alignment explanation
Indices: 5517022--5517065 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
5517012 TTCGGGTTTA
**
5517022 GTTGACTCGATTCGGGTCAG
1 GTTGACTCGATTCGGACCAG
* *
5517042 GTTGACTCGGTTCGGACCGG
1 GTTGACTCGATTCGGACCAG
5517062 GTTG
1 GTTG
5517066 GTCAGTTCAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.11, C:0.20, G:0.39, T:0.30
Consensus pattern (20 bp):
GTTGACTCGATTCGGACCAG
Found at i:5519424 original size:13 final size:13
Alignment explanation
Indices: 5519406--5519430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5519396 AGCCATTAGT
5519406 TTCATAATCAATA
1 TTCATAATCAATA
5519419 TTCATAATCAAT
1 TTCATAATCAAT
5519431 GTGACATGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCATAATCAATA
Found at i:5519909 original size:18 final size:18
Alignment explanation
Indices: 5519886--5519926 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
5519876 AGGCATTACA
* *
5519886 TCCTCTGGTTGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
5519904 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
5519922 TCCTC
1 TCCTC
5519927 ATGTTGTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.00, C:0.32, G:0.22, T:0.46
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:5527628 original size:16 final size:18
Alignment explanation
Indices: 5527593--5527629 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 18
5527583 ATATGCTTAG
5527593 AAAAATCATTTTCAAAATT
1 AAAAATCATTTT-AAAATT
5527612 AAAAATC-TTTT-AAATT
1 AAAAATCATTTTAAAATT
5527628 AA
1 AA
5527630 TTTGTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
18 4 0.22
19 7 0.39
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATCATTTTAAAATT
Found at i:5527864 original size:30 final size:30
Alignment explanation
Indices: 5527828--5527887 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
5527818 ATGTATTAAT
*
5527828 TTGTTATATCAAAACATCAAAATGTTTTCA
1 TTGTTATATCAAAACATCAAAATATTTTCA
5527858 TTGTTATATCAAAACATCAAAATATTTTCA
1 TTGTTATATCAAAACATCAAAATATTTTCA
5527888 ACAAACAACG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (30 bp):
TTGTTATATCAAAACATCAAAATATTTTCA
Found at i:5528379 original size:98 final size:99
Alignment explanation
Indices: 5528203--5528381 Score: 281
Period size: 98 Copynumber: 1.8 Consensus size: 99
5528193 GTATTATTAC
* * *
5528203 AATCGATTAAGTTATAGTGCTTTTAACCTTTTATATTATAATAACCTATAATAAATCCGGTTTTG
1 AATCGATTAAGTTATAGTGCTTTTAACCGTTTATATTATAATAACCTATAATAAATACAGTTTTG
**
5528268 ATGGTAACCTAATAGGTTGCGCCTTGATTTTTTG
66 ATGGTAAAATAATAGGTTGCGCCTTGATTTTTTG
*
5528302 AATCGGTTAAGTTATAAG-GC-TTTAACCGTTTATATTATAATAACCTATAATAAATACAGTTTT
1 AATCGATTAAGTTAT-AGTGCTTTTAACCGTTTATATTATAATAACCTATAATAAATACAGTTTT
5528365 GATGGTAAAATAATAGG
65 GATGGTAAAATAATAGG
5528382 CGATTTTCCC
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
98 55 0.75
99 16 0.22
100 2 0.03
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (99 bp):
AATCGATTAAGTTATAGTGCTTTTAACCGTTTATATTATAATAACCTATAATAAATACAGTTTTG
ATGGTAAAATAATAGGTTGCGCCTTGATTTTTTG
Found at i:5529772 original size:73 final size:73
Alignment explanation
Indices: 5529590--5529896 Score: 325
Period size: 72 Copynumber: 4.2 Consensus size: 73
5529580 CGATATAAAT
* * ** * * * *
5529590 TTAAAAGTATCGAACATCATAATATATGTATCGATATTTTAACTATCGATCATATCTTCAACAAT
1 TTAAAAGTATCGATCATCACAGCATAAGTATCGATAATTTAACTTTCGATCTTATCTTCAAC--T
*
5529655 TTCTTCTATA-
64 TT-TTCAATAC
* * * *
5529665 -TAAAAGCATCGATCATCAAAGCATAAATATCGATAATTTAACTTTCGATCTTATCTTCAACTCT
1 TTAAAAGTATCGATCATCACAGCATAAGTATCGATAATTTAACTTTCGATCTTATCTTCAACTTT
5529729 TTCAATAC
66 TTCAATAC
* * ** *
5529737 TTAAAAGTATCGATCATCACCGCATAAGTATCGATATTTTAACTTTCGATCTTAT-TTTTATTTT
1 TTAAAAGTATCGATCATCACAGCATAAGTATCGATAATTTAACTTTCGATCTTATCTTCAACTTT
* *
5529801 TTTAATAA
66 TTCAATAC
* * * * *
5529809 TTAAAAGTATTGATCATCACTGCATGAGTATCAAT-ATTTAACTTTCGATTTTATCTTCAACTTT
1 TTAAAAGTATCGATCATCACAGCATAAGTATCGATAATTTAACTTTCGATCTTATCTTCAACTTT
5529873 TTCAATAC
66 TTCAATAC
*
5529881 TTGAAAGTATCGATCA
1 TTAAAAGTATCGATCA
5529897 ACATAAATTA
Statistics
Matches: 193, Mismatches: 36, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
71 23 0.12
72 70 0.36
73 49 0.25
74 51 0.26
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (73 bp):
TTAAAAGTATCGATCATCACAGCATAAGTATCGATAATTTAACTTTCGATCTTATCTTCAACTTT
TTCAATAC
Found at i:5530359 original size:170 final size:169
Alignment explanation
Indices: 5530036--5530748 Score: 549
Period size: 185 Copynumber: 4.0 Consensus size: 169
5530026 AATCGCAACC
* * * *
5530036 TACTTTCTTAGCGACCCATAACATTCATGGGCGCAACATGATTTCTTATATATATTCATAACATT
1 TACTTTCTTAGCGACCCATAACATTCATGGGCGCAACCTAATTTCTTATAGATATTCATAATA-T
*** * *
5530101 TTTTATTTTAGCGTATTTTGTTATCGTG-GAAAATTCAAAAGCTCCATCAACGTAAACTCT-GAT
65 TTTTATTTTAATTTATTTTGTTATCGTGAG-AAATTCAAAAGCTCTATCAACTTAAACTCTAG-T
* *
5530164 AACATTTTAGGCA-CAACCGATTTTATTAAACATAAAACTAACA
128 AACATTTTAGG-AGCAA-TGATTTTATCAAACATAAAACTAACA
* * *
5530207 TACTTTCTTAACGACCCATAACATTCACGGGCTCAACCTAATTTCTTATAGATATTCATAATATT
1 TACTTTCTTAGCGACCCATAACATTCATGGGCGCAACCTAATTTCTTATAGATATTCATAATATT
* *
5530272 TTTATTTTAATTTATTTTGTTATCGTGAGAAATTCGAAA-CTACTATCAACTTAAAATCTAGTAA
66 TTTATTTTAATTTATTTTGTTATCGTGAGAAATTCAAAAGCT-CTATCAACTTAAACTCTAGTAA
*
5530336 CATTTTAGGAGCAGTTGATTTTATCAAACATAAAATTAACATTCCAGATTGCAACA
130 CATTTTAGGAGCA-ATGATTTTATCAAACAT---A--AA-A---C----T--AACA
* *
5530392 TACTTTCTTAGCGACCCATAACATTCATGGACGCAATCTAATTTCTTATAGATATTCATAATATT
1 TACTTTCTTAGCGACCCATAACATTCATGGGCGCAACCTAATTTCTTATAGATATTCATAATATT
* * ** * * * *
5530457 TTTATTTTAACTTAAATTT-TTATTTTAAGAAATTCAAAAGCCCTATCAACTTAAACTCAAGTAG
66 TTTATTTTAA-TTTATTTTGTTATCGTGAGAAATTCAAAAGCTCTATCAACTTAAACTCTAGTAA
* * *
5530521 CATTTTAGGTGCAATCAGTTTTATCAAACATAAAATTAACATTCCATGTCGCAACC
130 CATTTTAGGAGCAATGA-TTTTATCAAACAT---A--AA-A---C---T---AACA
* * * * * * * * *
5530577 TACTTTCTTAGTGACCTATAACATTAATGGACACAATCTGATTTCTTATAGATATTCATAACAAA
1 TACTTTCTTAGCGACCCATAACATTCATGGGCGCAACCTAATTTCTTATAGATATTCATAA-TAT
* ** * *** *
5530642 TTTGATTTTAATTTATTTTGTTATCGTGAGAAATTGGAAATC-CTCAT-TGGTTCAAACTCTGGT
65 TTTTATTTTAATTTATTTTGTTATCGTGAGAAATTCAAAAGCTCT-ATCAACTT-AAACTCTAGT
* *
5530705 AACATTTTAGGCGCAATCGATTTTATTAAACATAAAACTAACA
128 AACATTTTAGGAGCAAT-GATTTTATCAAACATAAAACTAACA
5530748 T
1 T
5530749 TTTAGATCGC
Statistics
Matches: 448, Mismatches: 65, Indels: 58
0.78 0.11 0.10
Matches are distributed among these distances:
169 3 0.01
170 77 0.17
171 62 0.14
173 1 0.00
174 1 0.00
175 2 0.00
176 1 0.00
177 1 0.00
179 1 0.00
180 1 0.00
181 2 0.00
183 2 0.00
184 3 0.01
185 219 0.49
186 71 0.16
187 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.37
Consensus pattern (169 bp):
TACTTTCTTAGCGACCCATAACATTCATGGGCGCAACCTAATTTCTTATAGATATTCATAATATT
TTTATTTTAATTTATTTTGTTATCGTGAGAAATTCAAAAGCTCTATCAACTTAAACTCTAGTAAC
ATTTTAGGAGCAATGATTTTATCAAACATAAAACTAACA
Found at i:5530761 original size:186 final size:185
Alignment explanation
Indices: 5530207--5530847 Score: 670
Period size: 185 Copynumber: 3.5 Consensus size: 185
5530197 AAAACTAACA
* * * * * *
5530207 TACTTTCTTAACGACCCATAACATTCACGGGCTCAACCTAATTTCTTATAGATATTCATAATATT
1 TACTTTCTTAGCGACCCATAACATTAATGGACACAATCTAATTTCTTATAGATATTCATAATATT
* *
5530272 TTTATTTTAATTTATTTTGTTATCGTGAGAAATTCGAAACTACT-ATCAACTTAAAATCTAGTAA
66 TTTATTTTAATTTATTTTGTTATCGTGAGAAATTCGAAA-TCCTCATCAACTTAAACTCTAGTAA
* * * *
5530336 CATTTTAGGAGCAGTTGATTTTATCAAACATAAAATTAACATTCCAGATTGCAACA
130 CATTTTAGGAGCAATCGATTTTATCAAACATAAAATTAACATTCCAGATCGCAACC
* *
5530392 TACTTTCTTAGCGACCCATAACATTCATGGACGCAATCTAATTTCTTATAGATATTCATAATATT
1 TACTTTCTTAGCGACCCATAACATTAATGGACACAATCTAATTTCTTATAGATATTCATAATATT
* * ** * * * *
5530457 TTTATTTTAACTTAAATTT-TTATTTTAAGAAATTCAAAAGCC-CTATCAACTTAAACTCAAGTA
66 TTTATTTTAA-TTTATTTTGTTATCGTGAGAAATTCGAAATCCTC-ATCAACTTAAACTCTAGTA
* *
5530520 GCATTTTAGGTGCAATC-AGTTTTATCAAACATAAAATTAACATTCCATG-TCGCAACC
129 ACATTTTAGGAGCAATCGA-TTTTATCAAACATAAAATTAACATTCCA-GATCGCAACC
* * * * *
5530577 TACTTTCTTAGTGACCTATAACATTAATGGACACAATCTGATTTCTTATAGATATTCATAACAAA
1 TACTTTCTTAGCGACCCATAACATTAATGGACACAATCTAATTTCTTATAGATATTCATAA-TAT
* * *** *
5530642 TTTGATTTTAATTTATTTTGTTATCGTGAGAAATTGGAAATCCTCAT-TGGTTCAAACTCTGGTA
65 TTTTATTTTAATTTATTTTGTTATCGTGAGAAATTCGAAATCCTCATCAACTT-AAACTCTAGTA
* * * **
5530706 ACATTTTAGGCGCAATCGATTTTATTAAACATAAAACTAACATTTTAGATCGCAACC
129 ACATTTTAGGAGCAATCGATTTTATCAAACATAAAATTAACATTCCAGATCGCAACC
* * * *** * * * *
5530763 TACTTTATT-GAC-AACCATAGCATGCTTGCG-CGCAACCTGATTTCTTATAGATATTCATTATA
1 TACTTTCTTAG-CGACCCATAACATTAATG-GACACAATCTAATTTCTTATAGATATTCATAATA
*
5530825 TTTTTTATTTTAACTTATTTTGT
64 -TTTTTATTTTAATTTATTTTGT
5530848 AATTGAAAAA
Statistics
Matches: 379, Mismatches: 63, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
184 3 0.01
185 272 0.72
186 102 0.27
187 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (185 bp):
TACTTTCTTAGCGACCCATAACATTAATGGACACAATCTAATTTCTTATAGATATTCATAATATT
TTTATTTTAATTTATTTTGTTATCGTGAGAAATTCGAAATCCTCATCAACTTAAACTCTAGTAAC
ATTTTAGGAGCAATCGATTTTATCAAACATAAAATTAACATTCCAGATCGCAACC
Found at i:5531017 original size:17 final size:17
Alignment explanation
Indices: 5530995--5531030 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5530985 AAATCTCCCC
*
5530995 TTCTTCTCTAAGTTCTT
1 TTCTTCTCTAAATTCTT
5531012 TTCTTCTCTAAATTCTT
1 TTCTTCTCTAAATTCTT
5531029 TT
1 TT
5531031 TCTCAATCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.22, G:0.03, T:0.61
Consensus pattern (17 bp):
TTCTTCTCTAAATTCTT
Found at i:5531299 original size:18 final size:19
Alignment explanation
Indices: 5531256--5531301 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
5531246 TCTGCCATTG
5531256 AAAAGCAGACAATGGTGAA
1 AAAAGCAGACAATGGTGAA
**
5531275 ATTAGCA-ACTAAT-GTGAA
1 AAAAGCAGAC-AATGGTGAA
5531293 AAAAGCAGA
1 AAAAGCAGA
5531302 AAAGTCGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.52, C:0.11, G:0.22, T:0.15
Consensus pattern (19 bp):
AAAAGCAGACAATGGTGAA
Found at i:5532273 original size:45 final size:45
Alignment explanation
Indices: 5532194--5532351 Score: 146
Period size: 45 Copynumber: 3.5 Consensus size: 45
5532184 ATATAACTTC
* * * *
5532194 TGAAGGAACGCCA-TTGGATAGCACAATAACTGATGACACTTTCAT
1 TGAAGGAAAG-CATTTGGATGGTACAATAATTGATGACACTTTCAT
* *
5532239 TGATGGAAAGCATTTGGATGGTACAATAATTGATGACAC-TGC-T
1 TGAAGGAAAGCATTTGGATGGTACAATAATTGATGACACTTTCAT
* * *
5532282 GCTGAAGGGAAGCATTTGGATGGTACAAT-ATCTGACGACACTGTT-AA
1 --TGAAGGAAAGCATTTGGATGGTACAATAAT-TGATGACACT-TTCAT
*
5532329 TGAAGGAAAGCATTTAGATGGTA
1 TGAAGGAAAGCATTTGGATGGTA
5532352 AAAAAACCGA
Statistics
Matches: 93, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
43 1 0.01
44 6 0.06
45 85 0.91
47 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (45 bp):
TGAAGGAAAGCATTTGGATGGTACAATAATTGATGACACTTTCAT
Found at i:5538705 original size:2 final size:2
Alignment explanation
Indices: 5538700--5538725 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5538690 TTTAGGAGTG
5538700 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
5538726 TCATTTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5546707 original size:2 final size:2
Alignment explanation
Indices: 5546700--5546731 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5546690 GTACATTCTT
5546700 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
5546732 CAAATTGTGT
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):
TA
Found at i:5547153 original size:18 final size:18
Alignment explanation
Indices: 5547130--5547169 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
5547120 GGTAGTTGTG
5547130 GGCCTAATGCTAAAAGTA
1 GGCCTAATGCTAAAAGTA
*
5547148 GGCCTAATGCTGAAAGTA
1 GGCCTAATGCTAAAAGTA
5547166 GGCC
1 GGCC
5547170 GAATACACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (18 bp):
GGCCTAATGCTAAAAGTA
Found at i:5551268 original size:15 final size:15
Alignment explanation
Indices: 5551233--5551276 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5551223 TTGCAAGCCA
5551233 AGGATCTCCTCAAAC
1 AGGATCTCCTCAAAC
* * *
5551248 ATGATCTTCTCAATC
1 AGGATCTCCTCAAAC
*
5551263 AGGATCTCCACAAA
1 AGGATCTCCTCAAA
5551277 TTCAAGTGCT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.25
Consensus pattern (15 bp):
AGGATCTCCTCAAAC
Found at i:5553489 original size:78 final size:77
Alignment explanation
Indices: 5553354--5553507 Score: 245
Period size: 78 Copynumber: 2.0 Consensus size: 77
5553344 GTACTCATAG
* * *
5553354 GATTATAAAACCCTAGTTTCAGGAAGAATAGAAGAGAATGAGAATGAAAGGGGAGAAGAAGGGAA
1 GATTATAAAACCCTACTTTCAGGAAGAATAAAAGAGAATGAGAATGAAAGGGAAGAAGAAGGGAA
5553419 ATCGAGATAATAC
66 ATCGAGA-AATAC
* * *
5553432 GATTCTAAAACCCTACTTTCAGGAATAATAAAAGAGGATGAGAATGAAAGGGAAGAAGAAGGGAA
1 GATTATAAAACCCTACTTTCAGGAAGAATAAAAGAGAATGAGAATGAAAGGGAAGAAGAAGGGAA
5553497 ATCGAGAAATA
66 ATCGAGAAATA
5553508 ACACAGGAGG
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
77 4 0.06
78 66 0.94
ACGTcount: A:0.48, C:0.08, G:0.27, T:0.17
Consensus pattern (77 bp):
GATTATAAAACCCTACTTTCAGGAAGAATAAAAGAGAATGAGAATGAAAGGGAAGAAGAAGGGAA
ATCGAGAAATAC
Found at i:5563759 original size:20 final size:18
Alignment explanation
Indices: 5563725--5563795 Score: 83
Period size: 20 Copynumber: 3.8 Consensus size: 18
5563715 GAGCAGTCAT
5563725 AGGTGTATGGATACACTAC
1 AGGTGTATGGATACACT-C
5563744 AGGTTGTATCGG-TACAC-C
1 AGG-TGTAT-GGATACACTC
5563762 AGGTGTATGGATACACTGC
1 AGGTGTATGGATACACT-C
5563781 AGGGTGTATGGATAC
1 A-GGTGTATGGATAC
5563796 CCTTTGACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.04
17 10 0.22
18 4 0.09
19 5 0.11
20 23 0.50
21 2 0.04
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (18 bp):
AGGTGTATGGATACACTC
Found at i:5564902 original size:14 final size:14
Alignment explanation
Indices: 5564883--5564912 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5564873 TGAATTCAAA
5564883 TTGATTCGAATAAT
1 TTGATTCGAATAAT
5564897 TTGATTCGAATAAT
1 TTGATTCGAATAAT
5564911 TT
1 TT
5564913 AAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (14 bp):
TTGATTCGAATAAT
Found at i:5564922 original size:2 final size:2
Alignment explanation
Indices: 5564915--5564956 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5564905 AATAATTTAA
5564915 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
5564957 TTGGAATCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5568668 original size:54 final size:54
Alignment explanation
Indices: 5568586--5568690 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
5568576 TTACCAAATA
* * * *
5568586 GGCACTAAGTGTGCATTTCACGGAATTCATCCTACGTGGATGAATGACCGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCCACGTAGATGAATAACCGTTTC
*
5568640 GGCACTAATTGTGCATTTCACAGAATTCATCCCACGTAGATGAATAACCGT
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCCACGTAGATGAATAACCGT
5568691 ACATGCACTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACAGAATTCATCCCACGTAGATGAATAACCGTTTC
Found at i:5568742 original size:55 final size:55
Alignment explanation
Indices: 5568678--5569559 Score: 1143
Period size: 55 Copynumber: 16.1 Consensus size: 55
5568668 ATCCCACGTA
* *
5568678 GATGAATAACCGTACATGCACTGTGTGTGCAAATCTACAGAATTCATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
* * * *
5568733 GATGGATAACCGTGCATGCACTATGTGTGCAAATCTACGGAATTCATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
* * *
5568788 AATGAATAACCGTATATGCACTATGTGTGCAAATCTAC-GAAATTCATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAG-AATTCATCATGAGTT
* * *
5568843 GATGAATAACCGTACAAGCACTATGTGTGCAAATCCACGGAATTCATCATGACTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
** * * * *
5568898 GATGAATAACTATACAGGCACGATGTGTACAAATCCA-TGAAATTCATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAG-AATTCATCATGAGTT
* * * * *
5568953 GATGAATAACCATACAGGCACTATATGTGCAAATCCATAGAATTTATCAT-ACGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATGA-GTT
* *
5569008 GATGAATAACCGTACAGGCACTATGTGTGCAAATCCACATAATTCATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
5569063 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
* *
5569118 GATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
*
5569173 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCACGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
* * *
5569228 GATGAATAACCGTACAAGTACTATGTGTGCAAATCCA-TGAAATTCATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAG-AATTCATCATGAGTT
* * * * *
5569283 GATGAAT---TGTAAAGGCACGATGTGTACAAATCCACAGAATTCATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
* * * *
5569335 GATGAATAACCGTACAGGCACTATGTATGCAAATCCACGGAATTCACCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
* * * * * *
5569390 GATGAATAATCGTACATACACTATGTTTACAAATCAAC-GAAATTTATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAG-AATTCATCATGAGTT
* *
5569445 GATGAATAACCGTATATGCACTATGTGTGCAAATCCACATAATTCATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
* * * * * * * **
5569500 GATGAATAATCATACAGGAACGATGTGT-CCAACCCATGGAATTCATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
5569554 GATGAA
1 GATGAA
5569560 CTACAGTATA
Statistics
Matches: 731, Mismatches: 83, Indels: 27
0.87 0.10 0.03
Matches are distributed among these distances:
52 43 0.06
53 1 0.00
54 32 0.04
55 652 0.89
56 3 0.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (55 bp):
GATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
Found at i:5569845 original size:68 final size:68
Alignment explanation
Indices: 5569736--5569925 Score: 299
Period size: 68 Copynumber: 2.8 Consensus size: 68
5569726 AAAGATTAAT
* *
5569736 GGCCTAGCTGTGCATTTAACAGAAAAGTGTCCATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAGCTGTGCATTTGACAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
5569801 TGA
66 TGA
* * * *
5569804 GGCCTAGCTGTGCAGTTGCCAGAAAAGTTTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTT
1 GGCCTAGCTGTGCATTTGACAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
5569869 TGA
66 TGA
* * *
5569872 GGACTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGG
1 GGCCTAGCTGTGCATTTGACAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGG
5569926 TTAAACGCAT
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 109 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (68 bp):
GGCCTAGCTGTGCATTTGACAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
TGA
Found at i:5571356 original size:19 final size:20
Alignment explanation
Indices: 5571332--5571371 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5571322 ATAAACGTTT
5571332 TATGAATAGTACT-ATACTG
1 TATGAATAGTACTGATACTG
* *
5571351 TATGAATTGTATTGATACTG
1 TATGAATAGTACTGATACTG
5571371 T
1 T
5571372 GCAAATAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (20 bp):
TATGAATAGTACTGATACTG
Found at i:5577687 original size:138 final size:138
Alignment explanation
Indices: 5577434--5577688 Score: 359
Period size: 138 Copynumber: 1.8 Consensus size: 138
5577424 TTGTATATAA
* * * * *
5577434 TTATCGATCGATTTTGTATAATGCATAATGGTGCATTTTCGTATCAGTACTATGTGTACTTTAGG
1 TTATCGATCGATTTTGTATAATGCATAACGGTGCATTTTCATATAAGCACTATATGTACTTTAGG
* *
5577499 CACTAGATGTGCAACCATGGTATTTATAATGAGTTTGTAAATTACCATTTCGACATACAATTATG
66 CACTAGATGTGCAACCATGGAATTCATAATGAGTTTGTAAATTACCATTTCGACATACAATTATG
5577564 TATGAAAG
131 TATGAAAG
* * * * *
5577572 TTATTGATCGATTTTGTTTAATGCATAACGGTGCATTTTTATATAAGCACTATATGTATTTTTGG
1 TTATCGATCGATTTTGTATAATGCATAACGGTGCATTTTCATATAAGCACTATATGTACTTTAGG
* * *
5577637 CACTATG-TGTGCATCCATGGAATTCATAATGAGTTTGTGAATTTCCATTTCG
66 CACTA-GATGTGCAACCATGGAATTCATAATGAGTTTGTAAATTACCATTTCG
5577689 GTACTTAGGT
Statistics
Matches: 101, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
138 100 0.99
139 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (138 bp):
TTATCGATCGATTTTGTATAATGCATAACGGTGCATTTTCATATAAGCACTATATGTACTTTAGG
CACTAGATGTGCAACCATGGAATTCATAATGAGTTTGTAAATTACCATTTCGACATACAATTATG
TATGAAAG
Found at i:5582773 original size:121 final size:121
Alignment explanation
Indices: 5582555--5582775 Score: 284
Period size: 121 Copynumber: 1.8 Consensus size: 121
5582545 GACGACACGA
* * * *
5582555 CTCATACGCGATGAAGAGTTCTGGTCGTCTAAGGGTGATACGGTTCCTACATAACGAAGAAATCT
1 CTCATACACGATGAAGAGTTCTGGTCATCTAAGGGTGACACGGCTCCTACATAACGAAGAAATCT
*
5582620 AGTCAGGGGATGACACTGCTCATAAGTAATGAAGAGTAGGAAGGGTGATAACATGG
66 AGTCAGGGGATGACACTGCTCATAAGCAATGAAGAGTAGGAAGGGTGATAACATGG
* * * * *
5582676 CTCATACATGATGAAGAGTTCTGGTTATC-AAGGGTTGACACGGCTCCTACATAATGAGGAGATC
1 CTCATACACGATGAAGAGTTCTGGTCATCTAAGGG-TGACACGGCTCCTACATAACGAAGAAATC
* * * *
5582740 TGGTCAGGTGATGACAC-GACTCATACGCGATGAAGA
65 TAGTCAGGGGATGACACTG-CTCATAAGCAATGAAGA
5582776 ATTCTGGCCA
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
120 6 0.07
121 78 0.93
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (121 bp):
CTCATACACGATGAAGAGTTCTGGTCATCTAAGGGTGACACGGCTCCTACATAACGAAGAAATCT
AGTCAGGGGATGACACTGCTCATAAGCAATGAAGAGTAGGAAGGGTGATAACATGG
Found at i:5582850 original size:42 final size:42
Alignment explanation
Indices: 5582799--5582991 Score: 110
Period size: 42 Copynumber: 4.6 Consensus size: 42
5582789 AAAGGTGATA
* * *
5582799 ACACGGTTCCTACGTGATGAGGACGGTTGGTTATCTGGGGTG
1 ACACAGTTCCTACGTAATGAGGACGGTTGGTTATCTGGGATG
* * * ** *
5582841 ACACAGTTCCTAAGCAATGAGGATGACTGG---TCAGGGATG
1 ACACAGTTCCTACGTAATGAGGACGGTTGGTTATCTGGGATG
* * * * ** *
5582880 ACACTGCTCATAC-T-ATGAAGA-GTGTTGGCCATCTAAAGGTGATA
1 ACACAGTTCCTACGTAATGAGGACG-GTTGGTTATCT---GG-GATG
* *
5582924 ACACAGTTCCTACGTGATGAGGACGGTTGGTTATCTGGGGTG
1 ACACAGTTCCTACGTAATGAGGACGGTTGGTTATCTGGGATG
* * *
5582966 ACACTGTTTCTACGCAATGAGGACGG
1 ACACAGTTCCTACGTAATGAGGACGG
5582992 CTGATTAGGG
Statistics
Matches: 109, Mismatches: 31, Indels: 22
0.67 0.19 0.14
Matches are distributed among these distances:
36 1 0.01
37 9 0.08
39 16 0.15
40 2 0.02
42 47 0.43
43 4 0.04
44 13 0.12
45 1 0.01
46 15 0.14
47 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (42 bp):
ACACAGTTCCTACGTAATGAGGACGGTTGGTTATCTGGGATG
Found at i:5582925 original size:125 final size:123
Alignment explanation
Indices: 5582728--5583037 Score: 424
Period size: 125 Copynumber: 2.4 Consensus size: 123
5582718 GCTCCTACAT
*
5582728 AATGAGGAGATCTGGTCAGGTGATGACAC-GACTCATACGCGATGAAGAATTCTGGCCATCTAAA
1 AATGAGGAGA-CTGGTCAGG-GATGACACTG-CTCATA--CTATGAAGAATT-TGGCCATCTAAA
*
5582792 GGTGATAACACGGTTCCTACGTGATGAGGACGGTTGGTTATCTGGGGTGACACAGTTCCTAAGC
60 GGTGATAACACAGTTCCTACGTGATGAGGACGGTTGGTTATCTGGGGTGACACAGTTCCTAAGC
*
5582856 AATGAGGATGACTGGTCAGGGATGACACTGCTCATACTATGAAGAGTGTTGGCCATCTAAAGGTG
1 AATGAGGA-GACTGGTCAGGGATGACACTGCTCATACTATGAAGAAT-TTGGCCATCTAAAGGTG
* * *
5582921 ATAACACAGTTCCTACGTGATGAGGACGGTTGGTTATCTGGGGTGACACTGTTTCTACGC
64 ATAACACAGTTCCTACGTGATGAGGACGGTTGGTTATCTGGGGTGACACAGTTCCTAAGC
* * * * *
5582981 AATGAGGACGGCTGATTAGGGATGACACTGCTTATACTATGATGAATCTTGGCCATC
1 AATGAGGA-GACTGGTCAGGGATGACACTGCTCATACTATGAAGAAT-TTGGCCATC
5583038 AAGGTTTTGG
Statistics
Matches: 165, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
125 130 0.79
126 1 0.01
127 14 0.08
128 18 0.11
129 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (123 bp):
AATGAGGAGACTGGTCAGGGATGACACTGCTCATACTATGAAGAATTTGGCCATCTAAAGGTGAT
AACACAGTTCCTACGTGATGAGGACGGTTGGTTATCTGGGGTGACACAGTTCCTAAGC
Found at i:5589082 original size:32 final size:32
Alignment explanation
Indices: 5589039--5589116 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 32
5589029 TACAATCAAG
* *
5589039 AGAAATAAGTTAGTGTACATAAACAAAAGGAA
1 AGAAATAAGTTAATGTACACAAACAAAAGGAA
*
5589071 AGAAATTAGTTAATGTACACAAACAAAAGGAA
1 AGAAATAAGTTAATGTACACAAACAAAAGGAA
5589103 AGAAATCAA-TTAAT
1 AGAAAT-AAGTTAAT
5589117 ACAGGTGATA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 40 0.98
33 1 0.02
ACGTcount: A:0.56, C:0.08, G:0.15, T:0.21
Consensus pattern (32 bp):
AGAAATAAGTTAATGTACACAAACAAAAGGAA
Found at i:5593006 original size:3 final size:3
Alignment explanation
Indices: 5592979--5593034 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
5592969 GCAAAATATG
* * *
5592979 TAA TAA -AA CTAA TTAA TAT TAA TAA TAA TAA TGA TAA TAG TAA TAA
1 TAA TAA TAA -TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
5593025 TAT TAA TAA T
1 TAA TAA TAA T
5593035 GACTCGGATA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
2 2 0.05
3 35 0.83
4 5 0.12
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:5609396 original size:23 final size:22
Alignment explanation
Indices: 5609344--5609396 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
5609334 TTTTTCGGTG
5609344 TTACTTTTTAGAACAAACACAT
1 TTACTTTTTAGAACAAACACAT
*
5609366 TTACTTTTTAGAACAAACGCAT
1 TTACTTTTTAGAACAAACACAT
*
5609388 TTTCTTTTT
1 TTACTTTTT
5609397 CTACAGGTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (22 bp):
TTACTTTTTAGAACAAACACAT
Found at i:5613132 original size:18 final size:18
Alignment explanation
Indices: 5613111--5613145 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5613101 CTCTTCTCTT
*
5613111 CTTCATTTCCAACGTGAA
1 CTTCATTGCCAACGTGAA
*
5613129 CTTCATTGCCAAGGTGA
1 CTTCATTGCCAACGTGA
5613146 GTAATTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (18 bp):
CTTCATTGCCAACGTGAA
Found at i:5614371 original size:23 final size:23
Alignment explanation
Indices: 5614317--5614379 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
5614307 TTTGAGGGAT
* * *
5614317 TCTATATGGTCCTTCGGGACAAT
1 TCTATGTGGTCATTCGGGACAAA
* *
5614340 TTTACGTGGTCATTCGGGACAAA
1 TCTATGTGGTCATTCGGGACAAA
5614363 TCTATGTGG-CACTTCGG
1 TCTATGTGGTCA-TTCGG
5614380 TGCATAATCT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
22 2 0.06
23 30 0.94
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (23 bp):
TCTATGTGGTCATTCGGGACAAA
Found at i:5614395 original size:24 final size:24
Alignment explanation
Indices: 5614361--5614412 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
5614351 ATTCGGGACA
*
5614361 AATCTATGTGGCACTTCGGTGCAT
1 AATCTACGTGGCACTTCGGTGCAT
*
5614385 AATCTACGTGGCACTTTGGTGCAT
1 AATCTACGTGGCACTTCGGTGCAT
5614409 AATC
1 AATC
5614413 CATGCGGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (24 bp):
AATCTACGTGGCACTTCGGTGCAT
Found at i:5616606 original size:23 final size:23
Alignment explanation
Indices: 5616533--5616596 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
5616523 AAGGACCGTG
5616533 TAGAATTATCCTGAAGGACCACA
1 TAGAATTATCCTGAAGGACCACA
5616556 TAGAATTATCCTGAAGGACCACA
1 TAGAATTATCCTGAAGGACCACA
*
5616579 TAGAATTGTCCTGAAGGA
1 TAGAATTATCCTGAAGGA
5616597 ACGTGTAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (23 bp):
TAGAATTATCCTGAAGGACCACA
Found at i:5621693 original size:23 final size:23
Alignment explanation
Indices: 5621662--5621740 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
5621652 CACCGAAGTT
* *
5621662 CCACATAGATTTGTCCCGAAGGA
1 CCACGTAGAATTGTCCCGAAGGA
* * *
5621685 CCGCGTAGAATTGTCTCGAAAGA
1 CCACGTAGAATTGTCCCGAAGGA
* * *
5621708 CCACATAGAATTATCCCAAAGGA
1 CCACGTAGAATTGTCCCGAAGGA
5621731 CCACGTAGAA
1 CCACGTAGAA
5621741 CCCTCGACTC
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.19
Consensus pattern (23 bp):
CCACGTAGAATTGTCCCGAAGGA
Found at i:5625971 original size:20 final size:20
Alignment explanation
Indices: 5625936--5625977 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5625926 GTAAAAATTG
*
5625936 ATATTTGAAAACTTTGAGTA
1 ATATTTGAAAACTTTGAATA
5625956 ATATTTGAAATA-TTTGAATA
1 ATATTTGAAA-ACTTTGAATA
5625976 AT
1 AT
5625978 TGAATCGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (20 bp):
ATATTTGAAAACTTTGAATA
Found at i:5626441 original size:16 final size:16
Alignment explanation
Indices: 5626420--5626468 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
5626410 AAAATCAAAC
5626420 ATCCAAAACACAAAAT
1 ATCCAAAACACAAAAT
**
5626436 ATCC-AAACAACTTAAT
1 ATCCAAAAC-ACAAAAT
5626452 ATCCAAAACACATAAAT
1 ATCCAAAACACA-AAAT
5626469 CCATCAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.18
Consensus pattern (16 bp):
ATCCAAAACACAAAAT
Found at i:5628413 original size:21 final size:21
Alignment explanation
Indices: 5628387--5628445 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
5628377 TGAAGAACAA
5628387 TATCGATACCTATTG-AAGAAG
1 TATCGATACCTA-TGCAAGAAG
* *
5628408 TATCGATA-CTATGCTAGTAG
1 TATCGATACCTATGCAAGAAG
5628428 TATCGATACCTA-GCAAGA
1 TATCGATACCTATGCAAGA
5628446 GAAATATCGG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.06
20 19 0.59
21 11 0.34
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (21 bp):
TATCGATACCTATGCAAGAAG
Found at i:5629219 original size:20 final size:20
Alignment explanation
Indices: 5629194--5629235 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
5629184 TCCATAATTC
*
5629194 GCATCCGAGAAGGCATGCAA
1 GCATCCAAGAAGGCATGCAA
5629214 GCATCCAAGAAGGCATGCAA
1 GCATCCAAGAAGGCATGCAA
5629234 GC
1 GC
5629236 TAAAGCTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.26, G:0.29, T:0.10
Consensus pattern (20 bp):
GCATCCAAGAAGGCATGCAA
Found at i:5645013 original size:23 final size:23
Alignment explanation
Indices: 5644987--5645035 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
5644977 ATAAAGAACC
*
5644987 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
5645010 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
5645033 AAA
1 AAA
5645036 CCAACCACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:5648319 original size:20 final size:20
Alignment explanation
Indices: 5648296--5648339 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5648286 AGAGAAAAGT
*
5648296 AAAAGTTAAAAATGAAATAG
1 AAAAGTTAAAAATGAAAGAG
**
5648316 AAAAGTTAAGGATGAAAGAG
1 AAAAGTTAAAAATGAAAGAG
5648336 AAAA
1 AAAA
5648340 AAAGTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAAGTTAAAAATGAAAGAG
Found at i:5655227 original size:23 final size:23
Alignment explanation
Indices: 5655201--5655249 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
5655191 ATAAAGAACC
*
5655201 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
5655224 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
5655247 AAA
1 AAA
5655250 CCAACTACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:5661364 original size:16 final size:17
Alignment explanation
Indices: 5661345--5661382 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5661335 AACATCCTTT
5661345 AAAA-AAATTTAAGACA
1 AAAATAAATTTAAGACA
* *
5661361 AAAATCATTTTAAGACA
1 AAAATAAATTTAAGACA
5661378 AAAAT
1 AAAAT
5661383 TGGTATGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24
Consensus pattern (17 bp):
AAAATAAATTTAAGACA
Found at i:5663841 original size:3 final size:3
Alignment explanation
Indices: 5663818--5663884 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
5663808 CTATAAAAAT
* * *
5663818 ATA A-A ATA A-A ATA TTA TTA ATA ATA ATA ATA ATA ATAA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
*
5663862 ATA ATAA ATA ATA ATA AAA ATA A
1 ATA AT-A ATA ATA ATA ATA ATA A
5663885 CTCGGACGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 4 0.07
3 44 0.81
4 6 0.11
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:5663864 original size:13 final size:13
Alignment explanation
Indices: 5663835--5663884 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
5663825 AAAATATTAT
5663835 TAATAAT-AATAA
1 TAATAATAAATAA
*
5663847 TAATAATAAATGA
1 TAATAATAAATAA
5663860 TAATAATAAATAA
1 TAATAATAAATAA
5663873 TAATAA-AAATAA
1 TAATAATAAATAA
5663885 CTCGGACGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
12 13 0.37
13 22 0.63
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:5663878 original size:16 final size:16
Alignment explanation
Indices: 5663836--5663884 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
5663826 AAATATTATT
5663836 AATAATAATAATAAT-
1 AATAATAATAATAATA
*
5663851 AATAAATGATAATAATA
1 AAT-AATAATAATAATA
*
5663868 AATAATAATAAAAATA
1 AATAATAATAATAATA
5663884 A
1 A
5663885 CTCGGACGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 3 0.10
16 23 0.79
17 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:5664148 original size:16 final size:17
Alignment explanation
Indices: 5664117--5664149 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5664107 CATGATGAGG
*
5664117 ATGACTAGCTTTTTTGA
1 ATGACTAGCTTCTTTGA
5664134 ATGACT-GCTTCTTTGA
1 ATGACTAGCTTCTTTGA
5664150 TTGTAGAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.45
Consensus pattern (17 bp):
ATGACTAGCTTCTTTGA
Found at i:5676384 original size:12 final size:12
Alignment explanation
Indices: 5676347--5676389 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
5676337 TTTTTAATTA
5676347 TTTAATTA-TTT
1 TTTAATTATTTT
* *
5676358 TTTAAATAGTATT
1 TTTAATTA-TTTT
5676371 TTTAATTATTTT
1 TTTAATTATTTT
5676383 TTTAATT
1 TTTAATT
5676390 TACACGTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 7 0.27
12 10 0.38
13 9 0.35
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTAATTATTTT
Found at i:5677099 original size:16 final size:16
Alignment explanation
Indices: 5677080--5677179 Score: 67
Period size: 16 Copynumber: 6.2 Consensus size: 16
5677070 AATTCGAACA
*
5677080 AAAAATAACCCAAACC
1 AAAAGTAACCCAAACC
* * *
5677096 AAAAGCAACCCGAACT
1 AAAAGTAACCCAAACC
** * *
5677112 AAATTTAACCTAATCC
1 AAAAGTAACCCAAACC
5677128 AAAAGTAACCCAAA-C
1 AAAAGTAACCCAAACC
** ** *
5677143 ATAATTTAACCTGATCC
1 A-AAAGTAACCCAAACC
5677160 AAAAGTAACCCAAACC
1 AAAAGTAACCCAAACC
5677176 AAAA
1 AAAA
5677180 TTAATCCGAA
Statistics
Matches: 57, Mismatches: 25, Indels: 4
0.66 0.29 0.05
Matches are distributed among these distances:
15 2 0.04
16 53 0.93
17 2 0.04
ACGTcount: A:0.53, C:0.27, G:0.05, T:0.15
Consensus pattern (16 bp):
AAAAGTAACCCAAACC
Found at i:5677110 original size:32 final size:32
Alignment explanation
Indices: 5677074--5677143 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
5677064 AAAAACAATT
5677074 CGAACAAAAAATAACCCAAACCAAAAGCAACC
1 CGAACAAAAAATAACCCAAACCAAAAGCAACC
* ** * * *
5677106 CGAACTAAATTTAACCTAATCCAAAAGTAACC
1 CGAACAAAAAATAACCCAAACCAAAAGCAACC
*
5677138 CAAACA
1 CGAACA
5677144 TAATTTAACC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.54, C:0.29, G:0.06, T:0.11
Consensus pattern (32 bp):
CGAACAAAAAATAACCCAAACCAAAAGCAACC
Found at i:5677149 original size:32 final size:32
Alignment explanation
Indices: 5677085--5677183 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
5677075 GAACAAAAAA
* * * *
5677085 TAACCCAAACCAAAAGCAACCCGAACTAAATT
1 TAACCTAATCCAAAAGTAACCCAAACTAAATT
5677117 TAACCTAATCCAAAAGTAACCCAAAC-ATAATT
1 TAACCTAATCCAAAAGTAACCCAAACTA-AATT
* * *
5677149 TAACCTGATCCAAAAGTAACCCAAACCAAAAT
1 TAACCTAATCCAAAAGTAACCCAAACTAAATT
5677181 TAA
1 TAA
5677184 TCCGAAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
31 1 0.02
32 57 0.97
33 1 0.02
ACGTcount: A:0.51, C:0.27, G:0.05, T:0.17
Consensus pattern (32 bp):
TAACCTAATCCAAAAGTAACCCAAACTAAATT
Found at i:5677730 original size:17 final size:17
Alignment explanation
Indices: 5677708--5677746 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
5677698 TTATTTGATC
*
5677708 AAATTTATATATCTGTT
1 AAATTTATATATCTATT
5677725 AAATTTATATATCTATT
1 AAATTTATATATCTATT
5677742 AAATT
1 AAATT
5677747 AAAAAGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTTATATATCTATT
Found at i:5677794 original size:4 final size:4
Alignment explanation
Indices: 5677785--5677809 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5677775 TTGAAAATAA
5677785 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
5677810 GCTACTTATA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Done.