Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, 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: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 25 of 31
Found at i:11973579 original size:212 final size:212
Alignment explanation
Indices: 11973207--11973632 Score: 735
Period size: 212 Copynumber: 2.0 Consensus size: 212
11973197 AATGATTTTT
* *
11973207 TTTTTGTTCATCAATTGCTCTAGTTAAGTCAAATGCTTACACGACTTTTAATCTTGCTTGACCTT
1 TTTTGGTTCATCAATTGCTCTAGTCAAGTCAAATGCTTACACGACTTTTAATCTTGCTTGACCTT
11973272 AATGATTGAAGTCTATAACTTAACATAAGTGATAGAATTGCTTATAGTGCTTAATTTCATAATTC
66 AATGATTGAAGTCTATAACTTAACATAAGTGATAGAATTGCTTATAGTGCTTAATTTCATAATTC
*
11973337 AAGTCAAGTTTGATCATGAAATAGAGTTTGTGTTGACATAATTGAAATATCCTTTGAATACGCAT
131 AAGTCAAGTTTGATCAGGAAATAGAGTTTGTGTTGACATAATTGAAATATCCTTTGAATACGCAT
11973402 TTGAATATTACTATGTC
196 TTGAATATTACTATGTC
* * * *
11973419 TTTTGGTTCATCTATTGCTCTGGTCAAGTCAAATGCTTACATGACTTTTAATCTTGCTTGACTTT
1 TTTTGGTTCATCAATTGCTCTAGTCAAGTCAAATGCTTACACGACTTTTAATCTTGCTTGACCTT
* *
11973484 AATGATTGAAGTCTATAACTTGACTTAAGTGATAGAATTGCTTATAGTGCTTAATTTCATAATTC
66 AATGATTGAAGTCTATAACTTAACATAAGTGATAGAATTGCTTATAGTGCTTAATTTCATAATTC
* * * *
11973549 AAGTCGAGTTTGATCAGGACATAGAGTTTGTGTTGACATATTTGAAATATCCTTTGAATATGCAT
131 AAGTCAAGTTTGATCAGGAAATAGAGTTTGTGTTGACATAATTGAAATATCCTTTGAATACGCAT
11973614 TTGAATATTACTATGTC
196 TTGAATATTACTATGTC
11973631 TT
1 TT
11973633 CATTGAGCCT
Statistics
Matches: 201, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
212 201 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (212 bp):
TTTTGGTTCATCAATTGCTCTAGTCAAGTCAAATGCTTACACGACTTTTAATCTTGCTTGACCTT
AATGATTGAAGTCTATAACTTAACATAAGTGATAGAATTGCTTATAGTGCTTAATTTCATAATTC
AAGTCAAGTTTGATCAGGAAATAGAGTTTGTGTTGACATAATTGAAATATCCTTTGAATACGCAT
TTGAATATTACTATGTC
Found at i:11975033 original size:22 final size:22
Alignment explanation
Indices: 11974975--11975036 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
11974965 TAGAAGGACA
* *
11974975 AATTAGGTTGATGAGGCTAAAC
1 AATTAGGTTGATTAGGTTAAAC
* *
11974997 AACTAGGTTCATTAGGTTAAAC
1 AATTAGGTTGATTAGGTTAAAC
*
11975019 AATTAGGTTGGTTAGGTT
1 AATTAGGTTGATTAGGTT
11975037 GAATAGCTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (22 bp):
AATTAGGTTGATTAGGTTAAAC
Found at i:11975150 original size:15 final size:15
Alignment explanation
Indices: 11975106--11975150 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
11975096 CTGATTTAGT
11975106 TGTTTCTATGCTGAA
1 TGTTTCTATGCTGAA
*
11975121 TGTTT-T-TGTTGAA
1 TGTTTCTATGCTGAA
11975134 TGTTTCTATGCTGAA
1 TGTTTCTATGCTGAA
11975149 TG
1 TG
11975151 GTGCTTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 11 0.42
14 2 0.08
15 13 0.50
ACGTcount: A:0.18, C:0.09, G:0.22, T:0.51
Consensus pattern (15 bp):
TGTTTCTATGCTGAA
Found at i:11980943 original size:30 final size:30
Alignment explanation
Indices: 11980909--11981003 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
11980899 TATGTGTGTG
11980909 ATGCTTAGTTATGGTTTTGTTGAACAATAC
1 ATGCTTAGTTATGGTTTTGTTGAACAATAC
* * *
11980939 ATGCTACTTA-TTATGG--ATGTTCAA-TATATC
1 ATG---CTTAGTTATGGTTTTGTTGAACAATA-C
*
11980969 TTGCTTAGTTATGGTTTTGTTGAACAATAC
1 ATGCTTAGTTATGGTTTTGTTGAACAATAC
11980999 ATGCT
1 ATGCT
11981004 ACTTATTATG
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
27 4 0.08
28 6 0.12
29 3 0.06
30 23 0.47
31 3 0.06
32 6 0.12
33 4 0.08
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (30 bp):
ATGCTTAGTTATGGTTTTGTTGAACAATAC
Found at i:11980964 original size:27 final size:27
Alignment explanation
Indices: 11980933--11981024 Score: 87
Period size: 27 Copynumber: 3.2 Consensus size: 27
11980923 TTTTGTTGAA
11980933 CAATACATGCTACTTATTATGGATGTT
1 CAATACATGCTACTTATTATGGATGTT
* * *
11980960 CAATATAT-CTTGCTTAGTTATGGTTTTGTT
1 CAATACATGC-TACTTA-TTATGG--ATGTT
11980990 GAACAATACATGCTACTTATTATGGATGTT
1 ---CAATACATGCTACTTATTATGGATGTT
11981020 CAATA
1 CAATA
11981025 TATCTTGCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
26 1 0.02
27 17 0.33
28 6 0.12
30 8 0.16
32 6 0.12
33 12 0.24
34 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (27 bp):
CAATACATGCTACTTATTATGGATGTT
Found at i:11980983 original size:60 final size:60
Alignment explanation
Indices: 11980910--11981036 Score: 254
Period size: 60 Copynumber: 2.1 Consensus size: 60
11980900 ATGTGTGTGA
11980910 TGCTTAGTTATGGTTTTGTTGAACAATACATGCTACTTATTATGGATGTTCAATATATCT
1 TGCTTAGTTATGGTTTTGTTGAACAATACATGCTACTTATTATGGATGTTCAATATATCT
11980970 TGCTTAGTTATGGTTTTGTTGAACAATACATGCTACTTATTATGGATGTTCAATATATCT
1 TGCTTAGTTATGGTTTTGTTGAACAATACATGCTACTTATTATGGATGTTCAATATATCT
11981030 TGCTTAG
1 TGCTTAG
11981037 CTACTATGGA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (60 bp):
TGCTTAGTTATGGTTTTGTTGAACAATACATGCTACTTATTATGGATGTTCAATATATCT
Found at i:12000816 original size:109 final size:109
Alignment explanation
Indices: 12000689--12000915 Score: 454
Period size: 109 Copynumber: 2.1 Consensus size: 109
12000679 GCAACAAATA
12000689 AAGTTAATTAATTTAATTTTAATTTACAATGACTTAATTAAAAGGTTTAATTAAGTGTTGGGCCA
1 AAGTTAATTAATTTAATTTTAATTTACAATGACTTAATTAAAAGGTTTAATTAAGTGTTGGGCCA
12000754 ATATTATATATAGTTATAATACTGAGGCCTAATTGCAGTTAAAG
66 ATATTATATATAGTTATAATACTGAGGCCTAATTGCAGTTAAAG
12000798 AAGTTAATTAATTTAATTTTAATTTACAATGACTTAATTAAAAGGTTTAATTAAGTGTTGGGCCA
1 AAGTTAATTAATTTAATTTTAATTTACAATGACTTAATTAAAAGGTTTAATTAAGTGTTGGGCCA
12000863 ATATTATATATAGTTATAATACTGAGGCCTAATTGCAGTTAAAG
66 ATATTATATATAGTTATAATACTGAGGCCTAATTGCAGTTAAAG
12000907 AAGTTAATT
1 AAGTTAATT
12000916 TAACCTTGGT
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 118 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.40
Consensus pattern (109 bp):
AAGTTAATTAATTTAATTTTAATTTACAATGACTTAATTAAAAGGTTTAATTAAGTGTTGGGCCA
ATATTATATATAGTTATAATACTGAGGCCTAATTGCAGTTAAAG
Found at i:12003494 original size:35 final size:35
Alignment explanation
Indices: 12003394--12003499 Score: 106
Period size: 35 Copynumber: 3.0 Consensus size: 35
12003384 GTAAAAATAT
* * *
12003394 CACTTGATCATAGCCCATCGTATGGGTAAAAGTAC
1 CACTTGATTATAGCCCATCGTAGGGGTAAGAGTAC
* * ** *
12003429 CACTTAATTATAACATATTGT-GGGGTTAAGAGTAC
1 CACTTGATTATAGCCCATCGTAGGGG-TAAGAGTAC
* *
12003464 CACTTGATTATAGCCCATCATAGGGGTAAGAATAC
1 CACTTGATTATAGCCCATCGTAGGGGTAAGAGTAC
12003499 C
1 C
12003500 TCATAAACGA
Statistics
Matches: 54, Mismatches: 15, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
34 3 0.06
35 47 0.87
36 4 0.07
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (35 bp):
CACTTGATTATAGCCCATCGTAGGGGTAAGAGTAC
Found at i:12005186 original size:43 final size:43
Alignment explanation
Indices: 12005121--12005216 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
12005111 GCTGTTGTTG
* * * ** **
12005121 TTTTAACAACGTGATTGTTGTTGTTATTGGTGGTGTTTTTGTA
1 TTTTTACAATGTGATTGTTGTTGTTAATGGTAATGTTAATGTA
* *
12005164 TTTTTACAATGTGGTTGTTGTTGTTAATGTTAATGTTAATGTA
1 TTTTTACAATGTGATTGTTGTTGTTAATGGTAATGTTAATGTA
12005207 TTTTTACAAT
1 TTTTTACAAT
12005217 AGGTGTTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.21, C:0.04, G:0.21, T:0.54
Consensus pattern (43 bp):
TTTTTACAATGTGATTGTTGTTGTTAATGGTAATGTTAATGTA
Found at i:12005276 original size:37 final size:38
Alignment explanation
Indices: 12005206--12005289 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 38
12005196 ATGTTAATGT
* *
12005206 ATTTTTACAATAGGTGTTTTAAAAATTGGTGTTGTTAC
1 ATTTTTACAATAGGTGTTATAAAAATTAGTGTTGTTAC
* **
12005244 ATTTTTACAAT--GTGGTTATAAAAATTATTGTTGTTGT
1 ATTTTTACAATAGGT-GTTATAAAAATTAGTGTTGTTAC
12005281 ATTTTTACA
1 ATTTTTACA
12005290 GTGGTTGTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
36 2 0.05
37 27 0.68
38 11 0.28
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (38 bp):
ATTTTTACAATAGGTGTTATAAAAATTAGTGTTGTTAC
Found at i:12006967 original size:12 final size:12
Alignment explanation
Indices: 12006929--12006973 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
12006919 TGTTCATTGG
12006929 TATTATT-AT-T
1 TATTATTAATAT
12006939 TATATACTTAA-AT
1 TAT-TA-TTAATAT
12006952 TATTATTAATAT
1 TATTATTAATAT
12006964 TATTATTAAT
1 TATTATTAAT
12006974 GTATATAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 3 0.10
11 6 0.20
12 16 0.53
13 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATTAATAT
Found at i:12007147 original size:21 final size:22
Alignment explanation
Indices: 12007121--12007176 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
12007111 TGTTATTTAC
12007121 TTATATTATTAACAATATA-TA
1 TTATATTATTAACAATATAGTA
* *
12007142 TTATATGTAATTTATAATATAGTA
1 TTATAT-T-ATTAACAATATAGTA
*
12007166 TAATATTATTA
1 TTATATTATTA
12007177 TGTAACAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 6 0.21
22 4 0.14
23 11 0.39
24 7 0.25
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (22 bp):
TTATATTATTAACAATATAGTA
Found at i:12012514 original size:30 final size:31
Alignment explanation
Indices: 12012459--12012525 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
12012449 CAATCAAGTT
* *
12012459 TTTATAGTTTTTATTTTACACCAAATAATCC
1 TTTATAGTTTTTATTTGACACCAAATAAGCC
* * *
12012490 TTTATA-TTTTTATTTGAGATCAAATAAGCT
1 TTTATAGTTTTTATTTGACACCAAATAAGCC
12012520 TTTATA
1 TTTATA
12012526 ACTAATGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 25 0.81
31 6 0.19
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (31 bp):
TTTATAGTTTTTATTTGACACCAAATAAGCC
Found at i:12015891 original size:30 final size:29
Alignment explanation
Indices: 12015857--12015942 Score: 84
Period size: 28 Copynumber: 2.9 Consensus size: 29
12015847 AAATAGCTTT
12015857 AATATATTTGTCTAAATTTAAGACAAGAAA
1 AATATATTTGTCTAAATTT-AGACAAGAAA
* * * * *
12015887 AATATGTTTTGTCTTAACTGAGATAAG-AA
1 AATAT-ATTTGTCTAAATTTAGACAAGAAA
* *
12015916 AATATATTTATCTCAATTTAGACAAGA
1 AATATATTTGTCTAAATTTAGACAAGA
12015943 TAACATGTTT
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
28 15 0.35
29 7 0.16
30 11 0.26
31 10 0.23
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (29 bp):
AATATATTTGTCTAAATTTAGACAAGAAA
Found at i:12019276 original size:28 final size:28
Alignment explanation
Indices: 12019240--12019293 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
12019230 TAAGAATACC
*
12019240 TTTACCCCACAAGAAATGAATGAATATT
1 TTTAACCCACAAGAAATGAATGAATATT
* *
12019268 TTTAACCCACCAGAAATGGATGAATA
1 TTTAACCCACAAGAAATGAATGAATA
12019294 ATAAAAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.26
Consensus pattern (28 bp):
TTTAACCCACAAGAAATGAATGAATATT
Found at i:12023033 original size:38 final size:40
Alignment explanation
Indices: 12022959--12023039 Score: 121
Period size: 38 Copynumber: 2.0 Consensus size: 40
12022949 GAATAAAAGA
**
12022959 TGAGCTAAGGAAAAAATGAGGGAAAAAATAATTTCAAAATT
1 TGAGCTAAGGAAAAAA-GAAAGAAAAAATAATTTCAAAATT
12023000 TGAGCTAAGGAAAAAA-AAAG-AAAAATAATTTCAAAATT
1 TGAGCTAAGGAAAAAAGAAAGAAAAAATAATTTCAAAATT
12023038 TG
1 TG
12023040 GACTTAGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 20 0.53
39 2 0.05
41 16 0.42
ACGTcount: A:0.56, C:0.05, G:0.17, T:0.22
Consensus pattern (40 bp):
TGAGCTAAGGAAAAAAGAAAGAAAAAATAATTTCAAAATT
Found at i:12043032 original size:43 final size:43
Alignment explanation
Indices: 12042984--12043069 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
12042974 AAGATGAACA
* * *
12042984 CACAATAAGATAACATTTCAATTAAGTCACATTCCAAAA-TAAG
1 CACAATAAGATAACACTCCAATTAAATCACATT-CAAAAGTAAG
* *
12043027 CACAATAGGATAATACTCCAATTAAATCACATTCAAAAGTAAG
1 CACAATAAGATAACACTCCAATTAAATCACATTCAAAAGTAAG
12043070 AAGGAAGTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
42 5 0.14
43 32 0.86
ACGTcount: A:0.49, C:0.19, G:0.08, T:0.24
Consensus pattern (43 bp):
CACAATAAGATAACACTCCAATTAAATCACATTCAAAAGTAAG
Found at i:12045875 original size:60 final size:61
Alignment explanation
Indices: 12045760--12045881 Score: 147
Period size: 60 Copynumber: 2.0 Consensus size: 61
12045750 AGAGATCAAC
* * *
12045760 ACATCTCAAGAGATCAACATATCCTCTTGATAAAATGAACATACAACAAAATGATATTCCA
1 ACATCTCAAAAGATCAACATATCCTCTTAATAAAATGAACACACAACAAAATGATATTCCA
* * ** * **
12045821 ACATCTCAAAAGATCAACTTATCTTC-TAATAGGATGAATACACAACAACTTGATATTCCA
1 ACATCTCAAAAGATCAACATATCCTCTTAATAAAATGAACACACAACAAAATGATATTCCA
12045881 A
1 A
12045882 TCAAGTCACA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
60 28 0.55
61 23 0.45
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.26
Consensus pattern (61 bp):
ACATCTCAAAAGATCAACATATCCTCTTAATAAAATGAACACACAACAAAATGATATTCCA
Found at i:12050952 original size:19 final size:18
Alignment explanation
Indices: 12050909--12050964 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
12050899 ATTTTCAAAC
**
12050909 TTTAATTTTTTTTTATAA
1 TTTAATTTTGATTTATAA
*
12050927 ATTAATTTTGATTTATTAA
1 TTTAATTTTGATTTA-TAA
* *
12050946 TTTAATTTTCATTAATAA
1 TTTAATTTTGATTTATAA
12050964 T
1 T
12050965 ATATATAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 16 0.52
19 15 0.48
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTAATTTTGATTTATAA
Found at i:12057189 original size:24 final size:24
Alignment explanation
Indices: 12057148--12057212 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 24
12057138 TCTTTTTTGT
* *
12057148 TTTTTTTACATTTTTTCCTTCTTGCC
1 TTTTTTT-C-TTTCTTCCTTCCTGCC
12057174 TTTTTTTCTTTCTTCCTTCCTGCC
1 TTTTTTTCTTTCTTCCTTCCTGCC
*
12057198 TTTTTCTCTTTCTTC
1 TTTTTTTCTTTCTTC
12057213 TCACTTTGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 28 0.78
25 1 0.03
26 7 0.19
ACGTcount: A:0.03, C:0.28, G:0.03, T:0.66
Consensus pattern (24 bp):
TTTTTTTCTTTCTTCCTTCCTGCC
Found at i:12057191 original size:16 final size:17
Alignment explanation
Indices: 12057158--12057191 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12057148 TTTTTTTACA
12057158 TTTTTTCCTTCTTGCCT
1 TTTTTTCCTTCTTGCCT
*
12057175 TTTTTTCTTTCTT-CCT
1 TTTTTTCCTTCTTGCCT
12057191 T
1 T
12057192 CCTGCCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTTCCTTCTTGCCT
Found at i:12057222 original size:25 final size:25
Alignment explanation
Indices: 12057169--12057242 Score: 91
Period size: 25 Copynumber: 3.0 Consensus size: 25
12057159 TTTTTCCTTC
*
12057169 TTGCCTTTTTTTCTTTC-T-TC-CT
1 TTGCCTTTTTCTCTTTCTTCTCACT
12057191 TCCTGCCTTTTTCTCTTTCTTCTCACT
1 T--TGCCTTTTTCTCTTTCTTCTCACT
*
12057218 TTGCCTTTTTCTCCTTCTTCTCACT
1 TTGCCTTTTTCTCTTTCTTCTCACT
12057243 GTTCGCAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
22 1 0.02
24 15 0.33
25 24 0.53
26 2 0.04
27 3 0.07
ACGTcount: A:0.03, C:0.34, G:0.04, T:0.59
Consensus pattern (25 bp):
TTGCCTTTTTCTCTTTCTTCTCACT
Found at i:12060319 original size:6 final size:6
Alignment explanation
Indices: 12060310--12060339 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
12060300 AATTAATAGT
12060310 AATTAG AATTAG AATTAG AATTAG AATTAG
1 AATTAG AATTAG AATTAG AATTAG AATTAG
12060340 TGGATGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
AATTAG
Found at i:12066366 original size:19 final size:18
Alignment explanation
Indices: 12066328--12066366 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12066318 TTTGAAAAGA
* *
12066328 TTTTTAAAAAAGTAACTT
1 TTTTTAAAAAAATAAATT
*
12066346 TTTTTAAAAAAATAAAAT
1 TTTTTAAAAAAATAAATT
12066364 TTT
1 TTT
12066367 AGAAAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (18 bp):
TTTTTAAAAAAATAAATT
Found at i:12074928 original size:2 final size:2
Alignment explanation
Indices: 12074915--12074948 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
12074905 CTCATATTCA
*
12074915 AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12074949 TCTCTCTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:12075116 original size:4 final size:4
Alignment explanation
Indices: 12075107--12075133 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
12075097 TTTAACACAA
12075107 AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAA
12075134 AGGTGGTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:12090683 original size:22 final size:22
Alignment explanation
Indices: 12090619--12090686 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 22
12090609 CCATATTTAA
12090619 ATGACACTACAACA--CTCGAGG
1 ATGACACTACAA-ATGCTCGAGG
* *
12090640 ATGACACTGC-AATGCTTGAGG
1 ATGACACTACAAATGCTCGAGG
*
12090661 ATGACACTACAAATGCTCAAGG
1 ATGACACTACAAATGCTCGAGG
12090683 ATGA
1 ATGA
12090687 TGTTGCATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 24 0.62
22 13 0.33
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (22 bp):
ATGACACTACAAATGCTCGAGG
Found at i:12095203 original size:31 final size:31
Alignment explanation
Indices: 12095168--12095233 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
12095158 TAGTGTTGTA
* *
12095168 ACACGCCATGTCTTAAGAGGTAATTGTTGCT
1 ACACGCCATGCCTTAAGAGGCAATTGTTGCT
* ** *
12095199 ACACGGCATGCCTTATTAGGCCATTGTTGCT
1 ACACGCCATGCCTTAAGAGGCAATTGTTGCT
12095230 ACAC
1 ACAC
12095234 TTCATGTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (31 bp):
ACACGCCATGCCTTAAGAGGCAATTGTTGCT
Found at i:12096607 original size:29 final size:29
Alignment explanation
Indices: 12096575--12096630 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
12096565 CGATTGAGCG
*
12096575 ACACACCATGCTTAACATGT-GAATATGCA
1 ACACACCATGCCTAACAT-TCGAATATGCA
*
12096604 ACACATCATGCCTAACATTCGAATATG
1 ACACACCATGCCTAACATTCGAATATG
12096631 TGACAGGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (29 bp):
ACACACCATGCCTAACATTCGAATATGCA
Found at i:12101366 original size:29 final size:29
Alignment explanation
Indices: 12101276--12101367 Score: 93
Period size: 29 Copynumber: 3.3 Consensus size: 29
12101266 AGATACTAGG
*
12101276 CAATTACAGTCCATGCCTATATATATTGT
1 CAATTACAATCCATGCCTATATATATTGT
* * * *
12101305 CAA-T--ATTACATGCCAATAT-TATTTAT
1 CAATTACAATCCATGCCTATATATA-TTGT
*
12101331 CACTTACAATCCATGCCTATATATATTGT
1 CAATTACAATCCATGCCTATATATATTGT
12101360 CAATTACA
1 CAATTACA
12101368 TGCCAGTTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
25 2 0.04
26 17 0.35
27 1 0.02
28 1 0.02
29 25 0.52
30 2 0.04
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.38
Consensus pattern (29 bp):
CAATTACAATCCATGCCTATATATATTGT
Found at i:12110056 original size:321 final size:321
Alignment explanation
Indices: 12109459--12110039 Score: 830
Period size: 321 Copynumber: 1.8 Consensus size: 321
12109449 CATGTTTAAA
* * * * *
12109459 TTACCAATGTTGCTACACGCCATGCCAACAAATAAAGTTGTTACACGCCATGTGTAAGAATTTGA
1 TTACCAATGTTGCTACACGCCATGCCAACAAATAAAGTAGTTACACACCATGCGTAACAATCTGA
** * *
12109524 CGGATGGCTTGTATGTTCATGTGTTTGATTGAAAGCATTATACCAAGAAGCACTTGTATTCATCC
66 CAAATGGCTTGTATGTTCATGTGTTTGATTGAAAGCATCATACCAAGAAGCACTTGTATGCATCC
*
12109589 AACAACTTTAAATTTAGATACAAAGTTTTGAGACATTAAATCAATAGTTTTAATTCTCATTACTA
131 AACAACTTTAAATTTAGATACAAAGTTTTGAGACATTAAATCAATAGTCTTAATTCTCATTACTA
* * * *
12109654 TGATTAAATGTATAGAGACTAAATGTCTTTTCACCTACTTTCCTTGGAAATTGTTTCATTTTGAA
196 TGATTAAATGTAAAGAGACTAAATGTCTCTTCACCTACTTTCCTTGAAAACTGTTTCATTTTGAA
*
12109719 CCTGCTCCATTTTGAATATTAATTTATTTATATGTTTTCTATCTAGCTAAACTTTTTCACT
261 CCTACTCCATTTTGAATATTAATTTATTTATATGTTTTCTATCTAGCTAAACTTTTTCACT
* * * *
12109780 TTACCAAATGTTGCTATATGCCATGCCAACAAATAGAGTAGTTACGCACCATGCGTAACAA-CTG
1 TTACC-AATGTTGCTACACGCCATGCCAACAAATAAAGTAGTTACACACCATGCGTAACAATCTG
*
12109844 ACAAATGGCTT-TCATGTTCATGTGTTTGATTGAAAGTATCATACCAAGAAGCACTTGTATGCAT
65 ACAAATGGCTTGT-ATGTTCATGTGTTTGATTGAAAGCATCATACCAAGAAGCACTTGTATGCAT
* * * * * *
12109908 CCAACAACTTTAAATTTAGTTGA-AGAGTTTTGAGACGTTAAATCAGTAGTCTTGATTTTCATTA
129 CCAACAACTTTAAATTTAGAT-ACAAAGTTTTGAGACATTAAATCAATAGTCTTAATTCTCATTA
* *
12109972 CTATTATTAAATGTACAAG-GACTAAATGTCTCTTCACTTAAC-TTCCTTGAAAACTGTTTCATT
193 CTATGATTAAATGTA-AAGAGACTAAATGTCTCTTCACCT-ACTTTCCTTGAAAACTGTTTCATT
12110035 TTGAA
256 TTGAA
12110040 GTTACTTTAT
Statistics
Matches: 228, Mismatches: 27, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
320 1 0.00
321 175 0.77
322 52 0.23
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (321 bp):
TTACCAATGTTGCTACACGCCATGCCAACAAATAAAGTAGTTACACACCATGCGTAACAATCTGA
CAAATGGCTTGTATGTTCATGTGTTTGATTGAAAGCATCATACCAAGAAGCACTTGTATGCATCC
AACAACTTTAAATTTAGATACAAAGTTTTGAGACATTAAATCAATAGTCTTAATTCTCATTACTA
TGATTAAATGTAAAGAGACTAAATGTCTCTTCACCTACTTTCCTTGAAAACTGTTTCATTTTGAA
CCTACTCCATTTTGAATATTAATTTATTTATATGTTTTCTATCTAGCTAAACTTTTTCACT
Found at i:12111931 original size:6 final size:6
Alignment explanation
Indices: 12111908--12111933 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12111898 AGTTTATTAG
12111908 TTTTAA TTTTAA TTTTAA TTTTAA TT
1 TTTTAA TTTTAA TTTTAA TTTTAA TT
12111934 GTTTAGGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:12118515 original size:15 final size:15
Alignment explanation
Indices: 12118482--12118515 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12118472 ATTACTATTG
* *
12118482 TATATATACTTTTAG
1 TATATATACTTTAAA
12118497 TATATATACTTTAAA
1 TATATATACTTTAAA
12118512 TATA
1 TATA
12118516 AACATATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (15 bp):
TATATATACTTTAAA
Found at i:12120365 original size:28 final size:28
Alignment explanation
Indices: 12120333--12120389 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
12120323 TAAAATGTAT
* *
12120333 AAATAAAAAAGAAATATAAGAAATAAAA
1 AAATAAAAAAGAAAAATAAAAAATAAAA
* *
12120361 AAATAAAAAATAAAAATAAAAAATGAAA
1 AAATAAAAAAGAAAAATAAAAAATAAAA
12120389 A
1 A
12120390 TATTAAATGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (28 bp):
AAATAAAAAAGAAAAATAAAAAATAAAA
Found at i:12120368 original size:7 final size:7
Alignment explanation
Indices: 12120333--12120389 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
12120323 TAAAATGTAT
12120333 AAATAAA
1 AAATAAA
*
12120340 AAA-GAA
1 AAATAAA
* *
12120346 ATATAAG
1 AAATAAA
12120353 AAATAAAA
1 AAAT-AAA
12120361 AAATAAA
1 AAATAAA
12120368 AAAT-AA
1 AAATAAA
12120374 AAATAAA
1 AAATAAA
*
12120381 AAATGAA
1 AAATAAA
12120388 AA
1 AA
12120390 TATTAAATGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
6 10 0.25
7 24 0.60
8 6 0.15
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (7 bp):
AAATAAA
Found at i:12120390 original size:13 final size:13
Alignment explanation
Indices: 12120333--12120391 Score: 64
Period size: 13 Copynumber: 4.4 Consensus size: 13
12120323 TAAAATGTAT
*
12120333 AAATAAAAAAGAA
1 AAATAAAAAATAA
* *
12120346 ATATAAGAAATAAAA
1 AAATAA-AAA-ATAA
12120361 AAATAAAAAATAA
1 AAATAAAAAATAA
*
12120374 AAATAAAAAATGA
1 AAATAAAAAATAA
12120387 AAATA
1 AAATA
12120392 TTAAATGCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
13 25 0.64
14 6 0.15
15 8 0.21
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:12121878 original size:36 final size:38
Alignment explanation
Indices: 12121838--12121920 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
12121828 GGATAAGAAA
*
12121838 TTTAAACA-ATTT-TGTTTTAGTTTTGAGTACCCTATT
1 TTTAAACAGATTTGTGTTTTAGTTTTGAATACCCTATT
* * *
12121874 TTTAAGCAGTTTTGTGTTTTGGTTTTGAATACCCTATT
1 TTTAAACAGATTTGTGTTTTAGTTTTGAATACCCTATT
*
12121912 TCTAAACAG
1 TTTAAACAG
12121921 TTTCAGTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
36 7 0.18
37 3 0.08
38 29 0.74
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.49
Consensus pattern (38 bp):
TTTAAACAGATTTGTGTTTTAGTTTTGAATACCCTATT
Found at i:12121899 original size:38 final size:38
Alignment explanation
Indices: 12121850--12121923 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
12121840 TAAACAATTT
* * *
12121850 TGTTTTAGTTTTGAGTACCCTATTTTTAAGCAGTTTTG
1 TGTTTTAGTTTTGAATACCCTATTTCTAAACAGTTTTG
*
12121888 TGTTTTGGTTTTGAATACCCTATTTCTAAACAGTTT
1 TGTTTTAGTTTTGAATACCCTATTTCTAAACAGTTT
12121924 CAGTTTTAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.51
Consensus pattern (38 bp):
TGTTTTAGTTTTGAATACCCTATTTCTAAACAGTTTTG
Found at i:12124565 original size:31 final size:31
Alignment explanation
Indices: 12124530--12124593 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
12124520 TGTTCCACGA
*
12124530 TATAAGGACTAAATTGAATAAAAATGTAAAG
1 TATAAGGACTAAATTGAACAAAAATGTAAAG
*
12124561 TATAAGGACTAAATTGAACAAAATTGTAAAG
1 TATAAGGACTAAATTGAACAAAAATGTAAAG
12124592 TA
1 TA
12124594 CATGGAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.27
Consensus pattern (31 bp):
TATAAGGACTAAATTGAACAAAAATGTAAAG
Found at i:12124605 original size:31 final size:31
Alignment explanation
Indices: 12124533--12124606 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
12124523 TCCACGATAT
* * *
12124533 AAGGACTAAATTGAATAAAAATGTAAAGTAT
1 AAGGAATAAATTGAACAAAAATGTAAAGTAC
* *
12124564 AAGGACTAAATTGAACAAAATTGTAAAGTAC
1 AAGGAATAAATTGAACAAAAATGTAAAGTAC
*
12124595 ATGGAATAAATT
1 AAGGAATAAATT
12124607 AGGTACTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (31 bp):
AAGGAATAAATTGAACAAAAATGTAAAGTAC
Found at i:12126535 original size:458 final size:456
Alignment explanation
Indices: 12125603--12126961 Score: 2305
Period size: 458 Copynumber: 3.0 Consensus size: 456
12125593 CTTTTCTAGG
*
12125603 CTAAGACTTAACCTGTTTACCTTTCTATGATTAAGGTATAACCAAACAATAATACCTTTTGGAGG
1 CTAAGACTTAACCTGTTTACCTTTTTATGATTAAGGTATAACCAAACAATAATACCTTTTGGAGG
* *
12125668 TTAAGGTAGAACATTTTCCATCAAATACAAGAGTGATGAGATGAAAGCTCTAATGCCTATAGAAA
66 TTAAGGTAGAACATTTTCAATCAAATACAAGAGTGATGAGATGAAAGCTCTAATGCCTCTAGAAA
*
12125733 GCTTATAGTTTTAGTGAGTATAAGATGTTTACAAGGAATATCACAAAAGAATAAAGAAAGTCAAA
131 GCTTATAGTTTTAGTGAATATAAGATGTTTACAAGGAATATCACAAAAGAATAAAGAAAGTCAAA
* *
12125798 GCTTTAAGAGTGATACAATGAAAAGCCATAAAAGT--GAGAGAGAATTTGATGATTTTAATTATG
196 GCTTTAAGAGTGATACAATGAGAAGCTATAAAAGTGAGAGAGAGAATTTGATGATTTTAATTATG
* *
12125861 ATTCTTATTCTTTATTCAAAAGAATGTTTTTCAATGCCTTCTTATTTGTCAATCAAGTTGAAAAC
261 ATTCTTATTCTTTATTCAAAAGAATGTTTTTCAATGCCTTCTCATTTGTTAATCAAGTTGAAAAC
* * ** *
12125926 TTATATTTAAACTCTGAAAGTTCTTGAGAACTATTTAAGTTAATTTGTACAAAAAATAACTGTTA
326 TTATATTTATACTCTG-AAGTTCTTGGGAACCGTTTAAGTTAATTTGTACCAAAAATAACTGTTA
12125991 TTTGTGTCTTTCCACGCTTGTTTGTCTTAAGGTGTCGATCCTTTTTGACTAGGTATCAAAGAAAA
390 TTTGTGTCTTTCCACGCTTGTTTGTCTTAAGGTGTCGATCCTTTTTGACTAGGTATCAAAGAAAA
12126056 GA
455 GA
*
12126058 CTGAGACTTAACCTGTTTACCTTCTTTATGATTAAGGTATAACCAAACAATAATACCTTTTGGAG
1 CTAAGACTTAACCTGTTTACCTT-TTTATGATTAAGGTATAACCAAACAATAATACCTTTTGGAG
*
12126123 GTTAAGGTAGAACATTTTCAATCAAATGCAAGAGTGATGAGATGAAAGCTCTAATGCCTCTAGAA
65 GTTAAGGTAGAACATTTTCAATCAAATACAAGAGTGATGAGATGAAAGCTCTAATGCCTCTAGAA
12126188 AGCTTATAGTTTTAGTGAATATAAGATGTTTACAAGGAATATCACAAAAGAATAAAGAAAGTCAA
130 AGCTTATAGTTTTAGTGAATATAAGATGTTTACAAGGAATATCACAAAAGAATAAAGAAAGTCAA
12126253 AGCTTTAAGAGTGATACAATGAGAAGCTATAAAAGTGAGAGAGAGAATTTGATGATTTTAATTAT
195 AGCTTTAAGAGTGATACAATGAGAAGCTATAAAAGTGAGAGAGAGAATTTGATGATTTTAATTAT
* *
12126318 GATTCTTATTCTTTGTTCAAAGGAATGTTTTTCAATGCCTTCTCATTTGTTAATCAAGTTGAAAA
260 GATTCTTATTCTTTATTCAAAAGAATGTTTTTCAATGCCTTCTCATTTGTTAATCAAGTTGAAAA
*
12126383 TTTATATTTATACTCTAGAAGTTCTTGGGAACCGTTTAAGTTAATTTGTACCAAAAATAACTGTT
325 CTTATATTTATACTCT-GAAGTTCTTGGGAACCGTTTAAGTTAATTTGTACCAAAAATAACTGTT
* * *
12126448 ATTTGTGTCTTTCCACGCTTGTTTGTCTTAAGGTATCGATCCTTTTGGACTAAGTATCAAAGAAA
389 ATTTGTGTCTTTCCACGCTTGTTTGTCTTAAGGTGTCGATCCTTTTTGACTAGGTATCAAAGAAA
12126513 AGA
454 AGA
* * *
12126516 CTAAGACTTAACCTGTTTACCTTTTCTATGCTTAATGTATAACCGAACAATAATACCTTTTGGAG
1 CTAAGACTTAACCTGTTTACCTTTT-TATGATTAAGGTATAACCAAACAATAATACCTTTTGGAG
* *
12126581 GTTAAGGTAGAACATTTTCAATCCAATACAAGAGTGATGAGATGAAAGCTCTAATGCCTCTAAAA
65 GTTAAGGTAGAACATTTTCAATCAAATACAAGAGTGATGAGATGAAAGCTCTAATGCCTCTAGAA
*
12126646 AGCTTATAGTTTTAGT-AAGTATAAGATGCTTACAAGGAATATCACAAAAGAATAAAGAAAGTCA
130 AGCTTATAGTTTTAGTGAA-TATAAGATGTTTACAAGGAATATCACAAAAGAATAAAGAAAGTCA
*
12126710 AAGCTTTAAGAGTGATACAATGAGAAGCTATAAAAGTGAGAGAGAGAATTTGATGATTTTAATGA
194 AAGCTTTAAGAGTGATACAATGAGAAGCTATAAAAGTGAGAGAGAGAATTTGATGATTTTAATTA
12126775 TGATTCTTATTCTTTATTCAAAAGAATG-TTTTCAATGCCTTCTCATTTGTTAATCAAGTTGAAA
259 TGATTCTTATTCTTTATTCAAAAGAATGTTTTTCAATGCCTTCTCATTTGTTAATCAAGTTGAAA
* * *
12126839 ACTTGTATTTATACTTTGGAAGTTCTTGGGAATCGTTTAAGTTAATTTG-ATCCAAAAATAACTG
324 ACTTATATTTATACTCT-GAAGTTCTTGGGAACCGTTTAAGTTAATTTGTA-CCAAAAATAACTG
* * * *
12126903 TTATTTATGTCTTTCCATGCTTATTTGTCTTAAGATGTCGATCCTTTTTGACTAGGTAT
387 TTATTTGTGTCTTTCCACGCTTGTTTGTCTTAAGGTGTCGATCCTTTTTGACTAGGTAT
12126962 AAATACTTTG
Statistics
Matches: 853, Mismatches: 44, Indels: 12
0.94 0.05 0.01
Matches are distributed among these distances:
455 22 0.03
456 201 0.24
457 149 0.17
458 480 0.56
459 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (456 bp):
CTAAGACTTAACCTGTTTACCTTTTTATGATTAAGGTATAACCAAACAATAATACCTTTTGGAGG
TTAAGGTAGAACATTTTCAATCAAATACAAGAGTGATGAGATGAAAGCTCTAATGCCTCTAGAAA
GCTTATAGTTTTAGTGAATATAAGATGTTTACAAGGAATATCACAAAAGAATAAAGAAAGTCAAA
GCTTTAAGAGTGATACAATGAGAAGCTATAAAAGTGAGAGAGAGAATTTGATGATTTTAATTATG
ATTCTTATTCTTTATTCAAAAGAATGTTTTTCAATGCCTTCTCATTTGTTAATCAAGTTGAAAAC
TTATATTTATACTCTGAAGTTCTTGGGAACCGTTTAAGTTAATTTGTACCAAAAATAACTGTTAT
TTGTGTCTTTCCACGCTTGTTTGTCTTAAGGTGTCGATCCTTTTTGACTAGGTATCAAAGAAAAG
A
Found at i:12127821 original size:31 final size:31
Alignment explanation
Indices: 12127786--12127861 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
12127776 ATAATAGATC
12127786 TTTATTCAATTTAATCCTTATACTCTACAAT
1 TTTATTCAATTTAATCCTTATACTCTACAAT
* * * *
12127817 TTTATTTAATTTAATCTTTGTACTCTACATT
1 TTTATTCAATTTAATCCTTATACTCTACAAT
*
12127848 TTTGTTCAATTTAA
1 TTTATTCAATTTAA
12127862 CACTTATGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.29, C:0.14, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTATTCAATTTAATCCTTATACTCTACAAT
Found at i:12129223 original size:21 final size:21
Alignment explanation
Indices: 12129182--12129260 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 21
12129172 AACTTTAGAT
** *
12129182 GTTGTCTTAATCAAAATAAGA
1 GTTGTCTTAATTTAAACAAGA
12129203 GTTGTCTTAATTTAAACAAGAA
1 GTTGTCTTAATTTAAACAAG-A
* * * *
12129225 TATATGTGTTATTTTGATACAAGA
1 -GT-TGTCTTAATTT-AAACAAGA
12129249 GTTGTCTTAATT
1 GTTGTCTTAATT
12129261 ACATATTTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
21 17 0.39
22 9 0.20
23 2 0.05
24 10 0.23
25 6 0.14
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (21 bp):
GTTGTCTTAATTTAAACAAGA
Found at i:12131446 original size:19 final size:20
Alignment explanation
Indices: 12131411--12131449 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
12131401 TTATATTAGT
12131411 ATTATTATTTATGTTTTTCA
1 ATTATTATTTATGTTTTTCA
12131431 ATTA-TATTCTAT-TTTTTCA
1 ATTATTATT-TATGTTTTTCA
12131450 TATATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.64
Consensus pattern (20 bp):
ATTATTATTTATGTTTTTCA
Found at i:12133019 original size:27 final size:27
Alignment explanation
Indices: 12132988--12133050 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
12132978 AGTCTATTTA
12132988 ATTTAAAATAA-AA-AATATAAGAGTTTG
1 ATTTAAAATAATAATAAT-TAA-AGTTTG
* * *
12133015 ATTTAACATAATAATAATTAAATTTTT
1 ATTTAAAATAATAATAATTAAAGTTTG
12133042 ATTTAAAAT
1 ATTTAAAAT
12133051 TTTTTAACTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 22 0.73
28 5 0.17
29 3 0.10
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (27 bp):
ATTTAAAATAATAATAATTAAAGTTTG
Found at i:12133379 original size:2 final size:2
Alignment explanation
Indices: 12133372--12133396 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12133362 TCATTACAAA
12133372 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12133397 GTGGTTGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12134741 original size:18 final size:19
Alignment explanation
Indices: 12134699--12134741 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
12134689 TAATATGTTA
* *
12134699 ATTTTGAAAACAAGAAATC
1 ATTTTTAAAACAAAAAATC
*
12134718 ATTTTTAAAATAAAAAAT-
1 ATTTTTAAAACAAAAAATC
12134736 ATTTTT
1 ATTTTT
12134742 GACAATATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (19 bp):
ATTTTTAAAACAAAAAATC
Found at i:12141993 original size:15 final size:15
Alignment explanation
Indices: 12141973--12142001 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12141963 CAGTAAAACT
12141973 TTGATAAATTAATAC
1 TTGATAAATTAATAC
12141988 TTGATAAATTAATA
1 TTGATAAATTAATA
12142002 ACTTCAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.41
Consensus pattern (15 bp):
TTGATAAATTAATAC
Found at i:12145788 original size:21 final size:19
Alignment explanation
Indices: 12145764--12145807 Score: 70
Period size: 21 Copynumber: 2.2 Consensus size: 19
12145754 TCAAATGCTA
12145764 AATTCATTAAAAGCATCATG
1 AATTCATTAAAAGCAT-ATG
12145784 CAATTCATTAAAAGCATATG
1 -AATTCATTAAAAGCATATG
12145804 AATT
1 AATT
12145808 AAGTTTGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.17
20 3 0.13
21 16 0.70
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (19 bp):
AATTCATTAAAAGCATATG
Found at i:12147290 original size:20 final size:20
Alignment explanation
Indices: 12147261--12147301 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12147251 TTCACTTCCT
**
12147261 TCAACCTTAACTGATTAAAA
1 TCAACCTTAACCAATTAAAA
*
12147281 TCAACTTTAACCAATTAAAA
1 TCAACCTTAACCAATTAAAA
12147301 T
1 T
12147302 TCTTTGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (20 bp):
TCAACCTTAACCAATTAAAA
Found at i:12148346 original size:15 final size:15
Alignment explanation
Indices: 12148326--12148367 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
12148316 TAATGTTATA
12148326 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
12148341 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
*
12148356 A-TAATATAAAAA
1 ATTAAAATAAAAA
12148368 TCAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:12148351 original size:5 final size:5
Alignment explanation
Indices: 12148328--12148405 Score: 52
Period size: 5 Copynumber: 15.2 Consensus size: 5
12148318 ATGTTATAAT
* * *
12148328 TAAAA TAAAA -AATAT TAAAA TAAAA T-ATA TAATA TAAAAA TCAAAAA
1 TAAAA TAAAA TAA-AA TAAAA TAAAA TAAAA TAAAA T-AAAA T--AAAA
* * *
12148375 TAAAA TAAAA TAAAA TATAA GAAAT TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T
12148406 TTATACAATA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
4 5 0.09
5 41 0.71
6 6 0.10
7 6 0.10
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (5 bp):
TAAAA
Found at i:12148353 original size:20 final size:19
Alignment explanation
Indices: 12148328--12148405 Score: 61
Period size: 20 Copynumber: 4.1 Consensus size: 19
12148318 ATGTTATAAT
12148328 TAAAATAAAAAATATTAAAA
1 TAAAATAAAAAA-ATTAAAA
* * *
12148348 TAAAATATATAATATAAAAA
1 TAAAATA-AAAAAATTAAAA
* *
12148368 TCAAA-AATAAAA-TAAAA
1 TAAAATAAAAAAATTAAAA
*
12148385 TAAAATATAAGAAATTAAAA
1 TAAAATA-AAAAAATTAAAA
12148405 T
1 T
12148406 TTATACAATA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
17 8 0.18
18 6 0.13
19 5 0.11
20 23 0.51
21 3 0.07
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (19 bp):
TAAAATAAAAAAATTAAAA
Found at i:12148384 original size:32 final size:31
Alignment explanation
Indices: 12148343--12148404 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
12148333 TAAAAAATAT
12148343 TAAAATAAAATATATAATATAA-AAATCAAAAA
1 TAAAATAAAATA-A-AATATAAGAAATCAAAAA
*
12148375 TAAAATAAAATAAAATATAAGAAATTAAAA
1 TAAAATAAAATAAAATATAAGAAATCAAAA
12148405 TTTATACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.25
31 9 0.32
32 12 0.43
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (31 bp):
TAAAATAAAATAAAATATAAGAAATCAAAAA
Found at i:12148394 original size:7 final size:7
Alignment explanation
Indices: 12148328--12148381 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
12148318 ATGTTATAAT
12148328 TAAAATA
1 TAAAATA
*
12148335 AAAAATA
1 TAAAATA
*
12148342 TTAAA-A
1 TAAAATA
12148348 TAAAATA
1 TAAAATA
*
12148355 TATAATA
1 TAAAATA
12148362 TAAAA-A
1 TAAAATA
12148368 TCAAAA-A
1 T-AAAATA
12148375 TAAAATA
1 TAAAATA
12148382 AAATAAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 11 0.29
7 27 0.71
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (7 bp):
TAAAATA
Found at i:12148480 original size:5 final size:6
Alignment explanation
Indices: 12148467--12148519 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
12148457 TATATTAAAG
* * *
12148467 AAATAA AAATAA AAATAA AATATATA AGATTA TAATAA TAAATAA AAATAA
1 AAATAA AAATAA AAATAA AA-ATA-A AAATAA AAATAA -AAATAA AAATAA
12148518 AA
1 AA
12148520 TATATGACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 26 0.68
7 10 0.26
8 2 0.05
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (6 bp):
AAATAA
Found at i:12148490 original size:40 final size:40
Alignment explanation
Indices: 12148426--12148523 Score: 117
Period size: 40 Copynumber: 2.5 Consensus size: 40
12148416 TCGGTAAAAT
* ** *
12148426 AAATTAAAATAAAATATATCATATAAAAAATTATATTAAAG
1 AAATAAAAATAAAATATAAAATATAAAAAATTATAAT-AAG
* * *
12148467 AAATAAAAATAAAA-ATAAAATATATAAGATTATAATAAT
1 AAATAAAAATAAAATATAAAATATAAAAAATTATAATAAG
12148506 AAATAAAAATAAAATATA
1 AAATAAAAATAAAATATA
12148524 TGACATTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 16 0.33
40 20 0.41
41 13 0.27
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (40 bp):
AAATAAAAATAAAATATAAAATATAAAAAATTATAATAAG
Found at i:12148764 original size:15 final size:15
Alignment explanation
Indices: 12148741--12148780 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
12148731 ATTTTTTCTA
* *
12148741 TAATTACATTATTTG
1 TAATCACATTACTTG
12148756 TAATCACATTACTTG
1 TAATCACATTACTTG
12148771 TAATCACATT
1 TAATCACATT
12148781 GTATTGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (15 bp):
TAATCACATTACTTG
Found at i:12151557 original size:32 final size:32
Alignment explanation
Indices: 12151521--12151581 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
12151511 GAATGGAAAG
* *
12151521 TTAAAACTTTGTAAAGTGTTTGAATTTTTCCA
1 TTAAAACTTTGTAAAATATTTGAATTTTTCCA
12151553 TTAAAACTTTGTAAAATATTTGAATTTTT
1 TTAAAACTTTGTAAAATATTTGAATTTTT
12151582 ATTCGATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (32 bp):
TTAAAACTTTGTAAAATATTTGAATTTTTCCA
Found at i:12168457 original size:2 final size:2
Alignment explanation
Indices: 12168444--12168476 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
12168434 GTGAAGACAC
*
12168444 AT AT AT AA AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12168477 GGTGTAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:12180927 original size:78 final size:79
Alignment explanation
Indices: 12180788--12180998 Score: 295
Period size: 78 Copynumber: 2.7 Consensus size: 79
12180778 AAGATGTTAA
* * * **
12180788 ATTTACATATTGGCACCATTATACCTTCATGTATAATAAGAA-GGCCACATGCCCATTTATCACA
1 ATTTACATATTGGCATCATTATACCTTAATGTATAATAAGAATAGCCACATGCCCACCTATCACA
*
12180852 TTG-ACTTTGATGGT
66 -TGAACCTTGATGGT
* * *
12180866 ATTTACATATTGGCATTATTATACCTTAATGTATAATAAGAATAG-TACATGTCCACCTATCACA
1 ATTTACATATTGGCATCATTATACCTTAATGTATAATAAGAATAGCCACATGCCCACCTATCACA
12180930 TGAACCTTGATGGT
66 TGAACCTTGATGGT
*
12180944 ATTTACATATTGGCATCATTATACCTTAATGTATAATAGGAAT-GCCACATGCCCA
1 ATTTACATATTGGCATCATTATACCTTAATGTATAATAAGAATAGCCACATGCCCA
12180999 TGCCTTATGT
Statistics
Matches: 117, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
77 3 0.03
78 113 0.97
79 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (79 bp):
ATTTACATATTGGCATCATTATACCTTAATGTATAATAAGAATAGCCACATGCCCACCTATCACA
TGAACCTTGATGGT
Found at i:12186109 original size:20 final size:21
Alignment explanation
Indices: 12186086--12186126 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
12186076 AATTATCGTT
12186086 ATATTT-TTTTTAAAAAAAAA
1 ATATTTATTTTTAAAAAAAAA
12186106 ATATTTGATTTTTAAAAAAAA
1 ATATTT-ATTTTTAAAAAAAA
12186127 TTAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
22 13 0.68
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATTTATTTTTAAAAAAAAA
Found at i:12186160 original size:16 final size:17
Alignment explanation
Indices: 12186118--12186164 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
12186108 ATTTGATTTT
12186118 TAAAA-AAAATTAATAA
1 TAAAATAAAATTAATAA
*
12186134 TAATTATTAAAATTAATAA
1 TAA--AATAAAATTAATAA
12186153 -AAAATAAAATTA
1 TAAAATAAAATTA
12186165 TTATTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 12 0.46
18 3 0.12
19 11 0.42
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATAAAATTAATAA
Found at i:12192749 original size:62 final size:61
Alignment explanation
Indices: 12192683--12192812 Score: 154
Period size: 62 Copynumber: 2.1 Consensus size: 61
12192673 GCAGAGTTGG
* * * **
12192683 GGGATTGGCTCTGCAGTGCTGTAGATGCT-GGAGGGGAAGTTTTGGCAATGCTGCAGCACTAA
1 GGGATTGGCGCTGCAGCGCTGCAGATGCTGGGAGGGG-AG-TTTGGCAACACTGCAGCACTAA
* * **
12192745 GGGATTGGCGCTGCAGCGCTGCAGCTGCTGGGATGGGAGTTTGGCAACACTGCAGCACTGG
1 GGGATTGGCGCTGCAGCGCTGCAGATGCTGGGAGGGGAGTTTGGCAACACTGCAGCACTAA
12192806 GGGATTG
1 GGGATTG
12192813 ACACTGTGGC
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
61 25 0.43
62 27 0.47
63 6 0.10
ACGTcount: A:0.18, C:0.18, G:0.40, T:0.23
Consensus pattern (61 bp):
GGGATTGGCGCTGCAGCGCTGCAGATGCTGGGAGGGGAGTTTGGCAACACTGCAGCACTAA
Found at i:12192799 original size:123 final size:122
Alignment explanation
Indices: 12192579--12192812 Score: 301
Period size: 123 Copynumber: 1.9 Consensus size: 122
12192569 CAAGTCTAGT
* * *
12192579 TGTAGGTGCTGGAGGGGGAGTTTTGGCAGCGCTGCAGCACTGGGAAATTGGCACTGCAACGCTAC
1 TGTAGATGCTGGAGGGGAAGTTTTGGCAACGCTGCAGCACTGGG-AATTGGCACTGCAACGCTAC
**** *
12192644 AGCTGCTAGGATGGGAGTTTGGCAGTGTTGCAG-AGTTGGGGGATTGGCTCTGCAGTGC
65 AGCTGCTAGGATGGGAGTTTGGCAACACTGCAGCA-CTGGGGGATTGGCTCTGCAGTGC
* * * *
12192702 TGTAGATGCTGGAGGGGAAGTTTTGGCAATGCTGCAGCACTAAGGG-ATTGGCGCTGCAGCGCTG
1 TGTAGATGCTGGAGGGGAAGTTTTGGCAACGCTGCAGCACT--GGGAATTGGCACTGCAACGCTA
*
12192766 CAGCTGCTGGGATGGGAGTTTGGCAACACTGCAGCACTGGGGGATTG
64 CAGCTGCTAGGATGGGAGTTTGGCAACACTGCAGCACTGGGGGATTG
12192813 ACACTGTGGC
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
123 91 0.96
124 1 0.01
125 3 0.03
ACGTcount: A:0.19, C:0.18, G:0.40, T:0.24
Consensus pattern (122 bp):
TGTAGATGCTGGAGGGGAAGTTTTGGCAACGCTGCAGCACTGGGAATTGGCACTGCAACGCTACA
GCTGCTAGGATGGGAGTTTGGCAACACTGCAGCACTGGGGGATTGGCTCTGCAGTGC
Found at i:12192825 original size:61 final size:61
Alignment explanation
Indices: 12192585--12192831 Score: 221
Period size: 61 Copynumber: 4.0 Consensus size: 61
12192575 TAGTTGTAGG
* * ** * *
12192585 TGCTGGAGGGGGAGTTTTGGCAGCGCTGCAGCACTGGGAAATTGGCACTGCAACGCTACAGC
1 TGCTGGA-TGGGAGTTTTGGCAACGCTGCAGCACTGGGGGATTGGCACTGCAGCGCTGCAGC
** * * * * * *
12192647 TGCTAGGATGGGAG-TTTGGCAGTGTTGCAG-AGTTGGGGGATTGGCTCTGCAGTGCTGTAGA
1 TGCT-GGATGGGAGTTTTGGCAACGCTGCAGCA-CTGGGGGATTGGCACTGCAGCGCTGCAGC
* * ** *
12192708 TGCTGGAGGGGAAGTTTTGGCAATGCTGCAGCACTAAGGGATTGGCGCTGCAGCGCTGCAGC
1 TGCTGGATGGG-AGTTTTGGCAACGCTGCAGCACTGGGGGATTGGCACTGCAGCGCTGCAGC
* * **
12192770 TGCTGGGATGGGAG-TTTGGCAACACTGCAGCACTGGGGGATTGACACTGTGGCGCTGCAGC
1 TGCT-GGATGGGAGTTTTGGCAACGCTGCAGCACTGGGGGATTGGCACTGCAGCGCTGCAGC
12192831 T
1 T
12192832 TCTGTTTCCA
Statistics
Matches: 148, Mismatches: 31, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
60 7 0.05
61 80 0.54
62 51 0.34
63 10 0.07
ACGTcount: A:0.19, C:0.19, G:0.39, T:0.23
Consensus pattern (61 bp):
TGCTGGATGGGAGTTTTGGCAACGCTGCAGCACTGGGGGATTGGCACTGCAGCGCTGCAGC
Found at i:12195819 original size:2 final size:2
Alignment explanation
Indices: 12195812--12195844 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12195802 TTCACATTCC
12195812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12195845 CAGTTCTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12200438 original size:2 final size:2
Alignment explanation
Indices: 12200431--12200458 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12200421 CAGTAGCATG
12200431 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
12200459 GTGATATAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12200473 original size:2 final size:2
Alignment explanation
Indices: 12200468--12200494 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12200458 TGTGATATAG
12200468 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
12200495 CGCATTGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12205676 original size:2 final size:2
Alignment explanation
Indices: 12205669--12205700 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12205659 AAATATGAGG
12205669 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12205701 TACAAAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12217895 original size:61 final size:63
Alignment explanation
Indices: 12217800--12217952 Score: 159
Period size: 61 Copynumber: 2.5 Consensus size: 63
12217790 TGGAAACAGA
** * * ** *
12217800 AGCTGCAGCGCCACAGTGTCAATCCCCCAGTGCTGCAGTGTTGCC-AAAC-T-CCCATCCCAGC
1 AGCTGCAGCGCTGCAGAGCCAATCCCCCAGTGCTGCAGCATTGCCAAAACTTCCCCCT-CCAGC
* **
12217861 AGCTGCAGCGCTGCAGCGCCAATCCCTTAGTGCTGCAGCATTGCCAAAACTTCCCCCTCCAGC
1 AGCTGCAGCGCTGCAGAGCCAATCCCCCAGTGCTGCAGCATTGCCAAAACTTCCCCCTCCAGC
* * *
12217924 ATCTACAGCACTGCAGAGCCAATCCCCCA
1 AGCTGCAGCGCTGCAGAGCCAATCCCCCA
12217953 ACTCTGCAAC
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
61 37 0.50
62 4 0.05
63 29 0.39
64 4 0.05
ACGTcount: A:0.23, C:0.40, G:0.20, T:0.18
Consensus pattern (63 bp):
AGCTGCAGCGCTGCAGAGCCAATCCCCCAGTGCTGCAGCATTGCCAAAACTTCCCCCTCCAGC
Found at i:12218391 original size:13 final size:13
Alignment explanation
Indices: 12218364--12218397 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
12218354 GGCCATCCCT
12218364 ATCCCCATC-GCC
1 ATCCCCATCGGCC
12218376 ATCCCCATCGGCC
1 ATCCCCATCGGCC
12218389 AT-CCCATCG
1 ATCCCCATCG
12218398 CTCGTGGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.18, C:0.53, G:0.12, T:0.18
Consensus pattern (13 bp):
ATCCCCATCGGCC
Found at i:12218696 original size:19 final size:19
Alignment explanation
Indices: 12218651--12218690 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12218641 ACTTTCTCAA
12218651 ATCC-CCATCCCTATCCCC
1 ATCCGCCATCCCTATCCCC
12218669 ATCCGCCATCCC-ATCGCCC
1 ATCCGCCATCCCTATC-CCC
12218688 ATC
1 ATC
12218691 GACCATTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.17, C:0.57, G:0.05, T:0.20
Consensus pattern (19 bp):
ATCCGCCATCCCTATCCCC
Found at i:12218773 original size:21 final size:21
Alignment explanation
Indices: 12218749--12218789 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12218739 GGACCCCAAC
*
12218749 CCCATC-CCCATTGGCGATCGG
1 CCCATCACCCATCGGC-ATCGG
12218770 CCCATCACCCATCGGCATCG
1 CCCATCACCCATCGGCATCG
12218790 CACCTTGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.17, C:0.46, G:0.20, T:0.17
Consensus pattern (21 bp):
CCCATCACCCATCGGCATCGG
Found at i:12219343 original size:62 final size:62
Alignment explanation
Indices: 12219243--12219363 Score: 170
Period size: 62 Copynumber: 2.0 Consensus size: 62
12219233 TCCAGCATGG
* *
12219243 CAGCACCTGCAGAGCTGCAGCACAAATCTCCCAACGCTGCAGCGTTACCAAAACTTCCCATC
1 CAGCACCTGCAGAGCTGCAGCACAAATCCCCCAACGCTGCAGCGCTACCAAAACTTCCCATC
* * * * * *
12219305 CAGCACCTGTAGCGCTGCAGCGCCAATCCCCCAGCGCTGCAGCGCTGCCAAAACTTCCC
1 CAGCACCTGCAGAGCTGCAGCACAAATCCCCCAACGCTGCAGCGCTACCAAAACTTCCC
12219364 CTTCAGTAGC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.25, C:0.41, G:0.19, T:0.15
Consensus pattern (62 bp):
CAGCACCTGCAGAGCTGCAGCACAAATCCCCCAACGCTGCAGCGCTACCAAAACTTCCCATC
Found at i:12222243 original size:16 final size:17
Alignment explanation
Indices: 12222213--12222253 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
12222203 CAAACAATCA
*
12222213 AAATC-AAATAATTAATT
1 AAATCTAAA-AATTAACT
12222230 AAA-CTAAAAATTAACT
1 AAATCTAAAAATTAACT
12222246 AAATCTAA
1 AAATCTAA
12222254 TTAACAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATCTAAAAATTAACT
Found at i:12236555 original size:19 final size:19
Alignment explanation
Indices: 12236531--12236572 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12236521 AAGTTTTCTC
* *
12236531 AATTAGTATCTAGCTTTAA
1 AATTAGCATCAAGCTTTAA
*
12236550 AATTAGCATCAAGCTTTAT
1 AATTAGCATCAAGCTTTAA
12236569 AATT
1 AATT
12236573 GTCTCTTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (19 bp):
AATTAGCATCAAGCTTTAA
Found at i:12238595 original size:73 final size:73
Alignment explanation
Indices: 12238432--12238596 Score: 187
Period size: 73 Copynumber: 2.2 Consensus size: 73
12238422 GAGTAAAGCA
* * *
12238432 GATTGCAAGACAAAGAAGACTTAATCGACTAAAAAGTATGTTTAGCCAACTAAAAGCTCACTATC
1 GATTGCAAGACAAA-AAGACTTAATCAACTAAAAAGTATGTTTAACCAACTAAAAACTCACTATC
12238497 AGAGAATTT
65 AGAGAATTT
* *
12238506 GATTGCGAGA-AGAAAAGACTTAATCAACTAAGAAA-TATAG-TTAACCAACTAAAAACTCATTA
1 GATTGCAAGACA-AAAAGACTTAATCAACTAA-AAAGTAT-GTTTAACCAACTAAAAACTCACTA
12238568 TCAGA-AATTT
63 TCAGAGAATTT
*
12238578 GAATT-TAAGCACAAAAAGA
1 G-ATTGCAAG-ACAAAAAGA
12238597 TAAAATAATT
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
72 8 0.10
73 54 0.69
74 16 0.21
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (73 bp):
GATTGCAAGACAAAAAGACTTAATCAACTAAAAAGTATGTTTAACCAACTAAAAACTCACTATCA
GAGAATTT
Found at i:12241438 original size:24 final size:22
Alignment explanation
Indices: 12241402--12241446 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
12241392 AAAATAAATA
12241402 AATAATTAATAAAAATTATATAAT
1 AATAATTAAT-AAAATTA-ATAAT
**
12241426 AATAATTTTTAAAATTAATAA
1 AATAATTAATAAAATTAATAA
12241447 AGGATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 7 0.37
24 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAATTAATAAAATTAATAAT
Found at i:12244825 original size:27 final size:27
Alignment explanation
Indices: 12244794--12244847 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
12244784 ACTTGAAAAG
12244794 ATAGACAACATACATCAAACACTTGCT
1 ATAGACAACATACATCAAACACTTGCT
12244821 ATAGACAACATACATCAAACACTTGCT
1 ATAGACAACATACATCAAACACTTGCT
12244848 TCCAAACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.22
Consensus pattern (27 bp):
ATAGACAACATACATCAAACACTTGCT
Found at i:12248693 original size:84 final size:84
Alignment explanation
Indices: 12248552--12248711 Score: 250
Period size: 84 Copynumber: 1.9 Consensus size: 84
12248542 ATAAATAGCA
* * * *
12248552 CTCACTTCATTCTTAAATACACATTCGAATAATATTTTCTCATTTTCTTAATACTTTTTTCTCAT
1 CTCACTTCATTCTTAAATACACACTCGAATAAGATCTTCTCATTTTCTTAATACTTTTCTCTCAT
*
12248617 AATTGTTTTTTCATGTTCT
66 AATTATTTTTTCATGTTCT
*
12248636 CTCACTTCATT-TATAAATACACACTCGAATAAGATCTTCTCATTTTCTTAATGCTTTTCTCTCA
1 CTCACTTCATTCT-TAAATACACACTCGAATAAGATCTTCTCATTTTCTTAATACTTTTCTCTCA
12248700 TAATTATTTTTT
65 TAATTATTTTTT
12248712 TAAATTATAT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
83 1 0.01
84 68 0.99
ACGTcount: A:0.26, C:0.20, G:0.04, T:0.50
Consensus pattern (84 bp):
CTCACTTCATTCTTAAATACACACTCGAATAAGATCTTCTCATTTTCTTAATACTTTTCTCTCAT
AATTATTTTTTCATGTTCT
Found at i:12248873 original size:93 final size:93
Alignment explanation
Indices: 12248672--12248857 Score: 259
Period size: 93 Copynumber: 2.0 Consensus size: 93
12248662 GAATAAGATC
* * * *
12248672 TTCTCATTTTCTTAATGCTTTTCTCTCATAATTATTTTTTTAAATTATATTTTACAACACGCATT
1 TTCTCATTTTATTAAAGTTTTTCTCTCATAATTATTTTTTCAAATTATATTTTACAACACGCATT
*
12248737 ACCAGCACGATTCTCTAATCTCTTAAGT
66 ACCAACACGATTCTCTAATCTCTTAAGT
* * * *
12248765 TTCTCATTTTCTTAAAGTTTTTCTCTTATAATTGTTTTTTCAAGTTATATTTTACAACAC-C-TT
1 TTCTCATTTTATTAAAGTTTTTCTCTCATAATTATTTTTTCAAATTATATTTTACAACACGCATT
* *
12248828 ATCAATACGATTCTCTAATCTCTTAAGT
66 ACCAACACGATTCTCTAATCTCTTAAGT
12248856 TT
1 TT
12248858 TAATATTATT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
91 29 0.35
92 1 0.01
93 54 0.64
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.49
Consensus pattern (93 bp):
TTCTCATTTTATTAAAGTTTTTCTCTCATAATTATTTTTTCAAATTATATTTTACAACACGCATT
ACCAACACGATTCTCTAATCTCTTAAGT
Found at i:12260013 original size:181 final size:181
Alignment explanation
Indices: 12259664--12260047 Score: 499
Period size: 181 Copynumber: 2.1 Consensus size: 181
12259654 ACTCTCAATT
* * *
12259664 CTCAAGAGATGCTACAAACTCTAATCTGTCAAAAAAACTAGAAGAATGAACAAACTTCGTGCTTT
1 CTCAAGAGATGCTACAAACTCCAATCTGTCAAAAAAACCAGAAGAATGAACAAACTTCGTGCTTC
* *
12259729 ATTTCTCTTTGAATAGTGTTTTCCTTATTTCTCTCAAAACAAAGAAACTTAAGGAAATCAAAAGG
66 AATTCTCTTTGAAAAGTGTTTTCCTTATTTCTCTCAAAACAAAGAAACTTAAGGAAATCAAAAGG
* * * *
12259794 TCCATGAGTTTTCAAGATTCTTTCTTCTGAGCCATCAACTACAAAAGGAAC
131 TCCATGAGTTTTCAAGACTCCTACTTCTGAGCCATCAACTACAAAAAGAAC
* * * * *
12259845 CTTAAGAGATGCTACAAACTCCAATCTGTGAAAAGAACCAGAAGAATGAACAAACTTCTTTCTTC
1 CTCAAGAGATGCTACAAACTCCAATCTGTCAAAAAAACCAGAAGAATGAACAAACTTCGTGCTTC
* * * *
12259910 AATTCT-TTCTGAACAAG-G-TTTCCTTTGTTTCTTTCAAAGACAGAGAAACTTAGGGAAA-CTA
66 AATTCTCTT-TGAA-AAGTGTTTTCC-TTATTTCTCTCAAA-ACAAAGAAACTTAAGGAAATC-A
* * *
12259971 AGAGGTCCATGAGTTTTCCAGACTCCTACTTCTTAG-CATCAACTACAAAAAGAAC
126 AAAGGTCCATGAGTTTTCAAGACTCCTACTTCTGAGCCATCAACTACAAAAAGAAC
12260026 CTCAAGAGATGCTACAAACTCC
1 CTCAAGAGATGCTACAAACTCC
12260048 TTCTGACCAA
Statistics
Matches: 176, Mismatches: 22, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
180 7 0.04
181 119 0.68
182 50 0.28
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (181 bp):
CTCAAGAGATGCTACAAACTCCAATCTGTCAAAAAAACCAGAAGAATGAACAAACTTCGTGCTTC
AATTCTCTTTGAAAAGTGTTTTCCTTATTTCTCTCAAAACAAAGAAACTTAAGGAAATCAAAAGG
TCCATGAGTTTTCAAGACTCCTACTTCTGAGCCATCAACTACAAAAAGAAC
Found at i:12266829 original size:2 final size:2
Alignment explanation
Indices: 12266822--12266850 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12266812 TCTTACTTAT
12266822 AC AC AC AC AC AC AC AC AC AC AC AC A- AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12266851 TGAGGAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12271392 original size:3 final size:3
Alignment explanation
Indices: 12271384--12271430 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
12271374 TTAATTGGTA
12271384 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12271431 CCGTCATCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:12284296 original size:58 final size:59
Alignment explanation
Indices: 12284222--12284425 Score: 205
Period size: 58 Copynumber: 3.6 Consensus size: 59
12284212 AATAAAAATA
*
12284222 TAAAATATAAAATTATAATAATAAATAA-AAATAAAATATATGATATTAAAAATATATT
1 TAAAATATAATATTATAATAATAAATAATAAATAAAATATATGATATTAAAAATATATT
* *
12284280 TAAAATATGATATTAT-ATAA-AAATAATAATATAAATTATAAT-ATATTAAAAATA-A--
1 TAAAATATAATATTATAATAATAAATAATAA-ATAAAATAT-ATGATATTAAAAATATATT
* * * *
12284335 -AATATAAAATATTATAATAATAAATAATAAA-AATA-ATATGAACATTAAAAATATATT
1 TAAAATATAATATTATAATAATAAATAATAAATAAAATATATG-ATATTAAAAATATATT
* * *
12284392 TAAGAA-ATGATATTATAAAAATTAATAATAAATA
1 TAA-AATATAATATTATAATAATAAATAATAAATA
12284426 TATTAAAAAT
Statistics
Matches: 119, Mismatches: 14, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
52 2 0.02
53 2 0.02
54 25 0.21
55 6 0.05
56 15 0.13
57 7 0.06
58 58 0.49
59 4 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (59 bp):
TAAAATATAATATTATAATAATAAATAATAAATAAAATATATGATATTAAAAATATATT
Found at i:12284335 original size:103 final size:104
Alignment explanation
Indices: 12284222--12284543 Score: 376
Period size: 100 Copynumber: 3.0 Consensus size: 104
12284212 AATAAAAATA
12284222 TAAAATATAAAATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAA-AAT
1 TAAAATATAAAATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAA-
12284286 ATGATATTATATAAAAATAATAATATAAATTATAATATAT
65 ATGATATTATATAAAAATAATAATATAAATTATAATATAT
* *
12284326 TAAAA-ATAAAATATAAAATATTATAATAATAAATAATAAAAATAATATGAACATTAAAAATATA
1 TAAAATATAAAAT-TATAATA--AT-A-AATAAA-AAT-AAAAT-ATATG-ATATTAAAAATATA
* *
12284390 TTTAAGAAATGATATTATA-AAAATTAAT-A-ATAAATATATTAA-A-AA
57 TTTAAGAAATGATATTATATAAAAATAATAATATAAAT-TA-TAATATAT
12284435 TAAAATATAAAATATTATAATAATAAATAAAAAT---ATATATGATATTAAAAATATATTTAAGA
1 TAAAATAT-AAA-ATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGA
* *
12284497 AATGATATTATATAAAAATTAATAATAAAAAATATAAATATAT
64 AATGATATTATATAAAAA-TAATAATATAAATTAT-AATATAT
12284540 TAAA
1 TAAA
12284544 CTTATATTTT
Statistics
Matches: 186, Mismatches: 10, Indels: 43
0.78 0.04 0.18
Matches are distributed among these distances:
100 32 0.17
101 9 0.05
102 7 0.04
103 12 0.06
104 16 0.09
105 5 0.03
106 5 0.03
107 7 0.04
108 7 0.04
109 17 0.09
110 11 0.06
111 25 0.13
112 31 0.17
113 2 0.01
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (104 bp):
TAAAATATAAAATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAA
TGATATTATATAAAAATAATAATATAAATTATAATATAT
Found at i:12284343 original size:12 final size:13
Alignment explanation
Indices: 12284211--12284370 Score: 60
Period size: 13 Copynumber: 11.6 Consensus size: 13
12284201 TATATTAAAG
12284211 AAATA-AAAATATA
1 AAATATAAAA-ATA
*
12284224 AAATATAAAATTA
1 AAATATAAAAATA
* *
12284237 TAATA-ATAAATA
1 AAATATAAAAATA
12284249 AAA-ATAAAATATA
1 AAATATAAAA-ATA
**
12284262 TGATATTAAAAAT-
1 AAATA-TAAAAATA
* *
12284275 ATATTTAAAATATGA
1 AAATATAAAA-AT-A
*
12284290 TATTATATAAAAATA
1 -A-AATATAAAAATA
*
12284305 ATAATATAAATTATA
1 A-AATATAAA-AATA
*
12284320 ATATATTAAAAATA
1 AAATA-TAAAAATA
12284334 AAATATAAAATATTA
1 AAATATAAAA-A-TA
*
12284349 TAATAATAAATAATA
1 AAAT-ATAAA-AATA
12284364 AAA-ATAA
1 AAATATAA
12284371 TATGAACATT
Statistics
Matches: 112, Mismatches: 19, Indels: 32
0.69 0.12 0.20
Matches are distributed among these distances:
11 1 0.01
12 15 0.13
13 28 0.25
14 27 0.24
15 23 0.21
16 9 0.08
17 9 0.08
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (13 bp):
AAATATAAAAATA
Found at i:12284355 original size:34 final size:34
Alignment explanation
Indices: 12284317--12284469 Score: 140
Period size: 33 Copynumber: 4.5 Consensus size: 34
12284307 AATATAAATT
12284317 ATAATATATTAAAAATAAAATATAAAATATTATA
1 ATAATATATTAAAAATAAAATATAAAATATTATA
* * *
12284351 ATAATA-AATAATAAA-AATAATAT-GAACATTA-A
1 ATAATATATTAA-AAATAA-AATATAAAATATTATA
* *
12284383 A-AATATATTTAAGAAATGATATTATAAAA-ATTAATA
1 ATAATATA-TTAA-AAAT-AAAATATAAAATATT-ATA
12284419 ATAAATATATTAAAAATAAAATATAAAATATTATA
1 AT-AATATATTAAAAATAAAATATAAAATATTATA
*
12284454 ATAATA-AATAAAAATA
1 ATAATATATTAAAAATA
12284470 TATATGATAT
Statistics
Matches: 96, Mismatches: 11, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
31 4 0.04
32 3 0.03
33 27 0.28
34 25 0.26
35 18 0.19
36 9 0.09
37 4 0.04
38 6 0.06
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.33
Consensus pattern (34 bp):
ATAATATATTAAAAATAAAATATAAAATATTATA
Found at i:12284364 original size:23 final size:23
Alignment explanation
Indices: 12284296--12284366 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 23
12284286 ATGATATTAT
* *
12284296 ATAAAA-ATAATAAT-ATAAATT
1 ATAAAATATTATAATAATAAATA
*
12284317 ATAATATATTA-AA-AATAAA-A
1 ATAAAATATTATAATAATAAATA
12284337 TATAAAATATTATAATAATAAATA
1 -ATAAAATATTATAATAATAAATA
12284361 ATAAAA
1 ATAAAA
12284367 ATAATATGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
21 22 0.55
22 5 0.12
23 12 0.30
24 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
ATAAAATATTATAATAATAAATA
Found at i:12284385 original size:112 final size:109
Alignment explanation
Indices: 12284216--12284543 Score: 446
Period size: 103 Copynumber: 3.0 Consensus size: 109
12284206 TAAAGAAATA
*
12284216 AAAATATAAAATAT-AAA-ATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATAT
1 AAAA-ATAAAATATAAAATATTATAATAATAAATAAAAA-AATA-ATATGATATTAAAAATATAT
12284279 TTAA-AATATGATATTATATAAAAATAATAATATAAATTATAATATATT
63 TTAAGAA-ATGATATTATATAAAAATAATAATATAAA-TATAATATATT
*
12284327 AAAAATAAAATATAAAATATTATAATAATAAATAATAAAAATAATATGAACATTAAAAATATATT
1 AAAAATAAAATATAAAATATTATAATAATAAATAA-AAAAATAATATG-ATATTAAAAATATATT
12284392 TAAGAAATGATA-T-TATAAAAAT--T-A-AT-AATA-AATATATT
64 TAAGAAATGATATTATATAAAAATAATAATATAAATATAATATATT
*
12284430 AAAAATAAAATATAAAATATTATAATAATAAATAAAAATAT-ATATGATATTAAAAATATATTTA
1 AAAAATAAAATATAAAATATTATAATAATAAATAAAAAAATAATATGATATTAAAAATATATTTA
*
12284494 AGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATT
66 AGAAATGATATTATATAAAAA-TAATAAT-ATAAATAT-AATATATT
12284541 AAA
1 AAA
12284544 CTTATATTTT
Statistics
Matches: 196, Mismatches: 5, Indels: 32
0.84 0.02 0.14
Matches are distributed among these distances:
100 27 0.14
101 6 0.03
102 13 0.07
103 44 0.22
104 2 0.01
105 3 0.02
106 3 0.02
107 1 0.01
108 2 0.01
109 4 0.02
110 18 0.09
111 24 0.12
112 44 0.22
113 5 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (109 bp):
AAAAATAAAATATAAAATATTATAATAATAAATAAAAAAATAATATGATATTAAAAATATATTTA
AGAAATGATATTATATAAAAATAATAATATAAATATAATATATT
Found at i:12284387 original size:24 final size:24
Alignment explanation
Indices: 12284333--12284389 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
12284323 TATTAAAAAT
* *
12284333 AAAATATAAAATATTATAATAATA
1 AAAATATAAAATAATATAACAATA
*
12284357 AATAATA-AAAATAATATGAACATTA
1 AA-AATATAAAATAATAT-AACAATA
12284382 AAAATATA
1 AAAATATA
12284390 TTTAAGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAATATAAAATAATATAACAATA
Found at i:12284413 original size:14 final size:12
Alignment explanation
Indices: 12284379--12284436 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
12284369 AATATGAACA
12284379 TTAAAAATATAT
1 TTAAAAATATAT
12284391 TTAAGAAATGATAT
1 TTAA-AAAT-ATAT
12284405 TATAAAAAT-TA-
1 T-TAAAAATATAT
*
12284416 ATAATAAATATA-
1 TTAA-AAATATAT
12284428 TTAAAAATA
1 TTAAAAATA
12284437 AAATATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
10 3 0.08
11 9 0.23
12 11 0.28
13 4 0.10
14 9 0.23
15 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (12 bp):
TTAAAAATATAT
Found at i:12284441 original size:23 final size:22
Alignment explanation
Indices: 12284407--12284472 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
12284397 AATGATATTA
*
12284407 TAAAAATTAATAATAAATATAT
1 TAAAAATAAATAATAAATATAT
12284429 TAAAAATAAA-ATATAAA-ATAT
1 TAAAAATAAATA-ATAAATATAT
12284450 TATAATAATAAATAA-AAATATAT
1 TA-AA-AATAAATAATAAATATAT
12284473 ATGATATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 7 0.18
22 19 0.50
23 11 0.29
24 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAAATAAATAATAAATATAT
Found at i:12284442 original size:16 final size:15
Alignment explanation
Indices: 12284412--12284543 Score: 53
Period size: 15 Copynumber: 8.4 Consensus size: 15
12284402 TATTATAAAA
*
12284412 ATTAATAATAAATAT
1 ATTAAAAATAAATAT
12284427 ATTAAAAATAAA-AT
1 ATTAAAAATAAATAT
12284441 A-TAAAATATTATAATAAT
1 ATTAAAA-A-TA-AAT-AT
*
12284459 AAATAAAAATATATATGAT
1 -ATTAAAAATA-A-AT-AT
12284478 ATTAAAAAT--ATAT
1 ATTAAAAATAAATAT
*
12284491 -TTAAGAAAT-GATATT
1 ATTAA-AAATAAATA-T
*
12284506 ATATAAAAATTAATA-
1 AT-TAAAAATAAATAT
*
12284521 ATAAAAAATATAAATAT
1 AT-TAAAA-ATAAATAT
12284538 ATTAAA
1 ATTAAA
12284544 CTTATATTTT
Statistics
Matches: 94, Mismatches: 7, Indels: 31
0.71 0.05 0.23
Matches are distributed among these distances:
12 4 0.04
13 11 0.12
14 9 0.10
15 21 0.22
16 16 0.17
17 8 0.09
18 14 0.15
19 6 0.06
20 5 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
ATTAAAAATAAATAT
Found at i:12284713 original size:15 final size:15
Alignment explanation
Indices: 12284693--12284761 Score: 93
Period size: 15 Copynumber: 4.6 Consensus size: 15
12284683 TTTTCTCTGT
* *
12284693 AATCACATTGCTTGC
1 AATCACATTACGTGC
*
12284708 AATCACATTACTTGC
1 AATCACATTACGTGC
*
12284723 AATCACATTACGTGT
1 AATCACATTACGTGC
*
12284738 AATCACATTACGTGT
1 AATCACATTACGTGC
12284753 AATCACATT
1 AATCACATT
12284762 GCATTGTAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 51 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (15 bp):
AATCACATTACGTGC
Found at i:12286220 original size:45 final size:45
Alignment explanation
Indices: 12286169--12286286 Score: 202
Period size: 45 Copynumber: 2.6 Consensus size: 45
12286159 AAATAGAGAT
12286169 GAAAATTGCTTCTTGCTTGAAAATCCCTCACTTGGATCTTTAAAG
1 GAAAATTGCTTCTTGCTTGAAAATCCCTCACTTGGATCTTTAAAG
* *
12286214 GAAAATTGCTTCTTGCTTGAAAATCCTTTACTTGGATCTTTAAAG
1 GAAAATTGCTTCTTGCTTGAAAATCCCTCACTTGGATCTTTAAAG
12286259 GAAAATTGCTTCTTGCTT-AAGAATCCCT
1 GAAAATTGCTTCTTGCTTGAA-AATCCCT
12286287 TAGATATATT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
44 2 0.03
45 67 0.97
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (45 bp):
GAAAATTGCTTCTTGCTTGAAAATCCCTCACTTGGATCTTTAAAG
Found at i:12296089 original size:35 final size:34
Alignment explanation
Indices: 12296036--12296102 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 34
12296026 TTTAAGTCGT
*
12296036 TATTTGAATATTTATTTTTAGTTATTTAAATTGA
1 TATTTGAATATTTATTTTTAATTATTTAAATTGA
12296070 TATTTGAGATATTTATTTTTAATTATTTAAATT
1 TATTTGA-ATATTTATTTTTAATTATTTAAATT
12296103 AAAATTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 7 0.23
35 24 0.77
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (34 bp):
TATTTGAATATTTATTTTTAATTATTTAAATTGA
Found at i:12302990 original size:19 final size:19
Alignment explanation
Indices: 12302954--12302989 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12302944 ATATATTAAT
12302954 TTTTAAAATAAATATTTTA
1 TTTTAAAATAAATATTTTA
*
12302973 TTTTAAAA-AATTATTTT
1 TTTTAAAATAAATATTTT
12302990 TTATTAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAAAATAAATATTTTA
Found at i:12309178 original size:2 final size:2
Alignment explanation
Indices: 12309171--12309196 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12309161 GAAAAATAGA
12309171 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
12309197 GGACGGGGCC
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):
AG
Found at i:12311812 original size:2 final size:2
Alignment explanation
Indices: 12311805--12311839 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12311795 TTTCATCATT
12311805 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12311840 AAGTTGCATA
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:12330839 original size:26 final size:27
Alignment explanation
Indices: 12330782--12330840 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
12330772 GGCAAGAAAG
* *
12330782 AGAACAAAAACAGAAAAATGAGAGACA
1 AGAACAAAAACAGAAAAATAAAAGACA
12330809 A-AACAAAAA-AGAAAGAATAAAAGA-A
1 AGAACAAAAACAGAAA-AATAAAAGACA
12330834 AGAACAA
1 AGAACAA
12330841 CATTTTGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 7 0.25
26 20 0.71
27 1 0.04
ACGTcount: A:0.73, C:0.08, G:0.15, T:0.03
Consensus pattern (27 bp):
AGAACAAAAACAGAAAAATAAAAGACA
Found at i:12331288 original size:119 final size:118
Alignment explanation
Indices: 12331088--12331313 Score: 303
Period size: 119 Copynumber: 1.9 Consensus size: 118
12331078 TGAAAAAAAG
* * * *
12331088 GTGAAAGATTTATTTCAATATAGAAACAAAAACTAATATTTTAAACAGTAAAAATTAAAATAAAA
1 GTGAAAGAGTTATTTCAATATAAAAACAAAAACTAATATTTTAAACAGTAAAAATCAAAACAAAA
* *
12331153 TGCATCTATAATTTTAAAAGCCACACGTATTATTTAGGGTAATATGTTCTCAA
66 TACATCCATAATTTTAAAAGCCACACGTATTATTTAGGGTAATATGTTCTCAA
* *
12331206 GTGAAAGAGTTATTTCAATATAAAAACTAAGAAA-TTATATTTTAAAC-GATAGAAATCAAAACA
1 GTGAAAGAGTTATTTCAATATAAAAAC-AA-AAACTAATATTTTAAACAG-TAAAAATCAAAACA
* * * *
12331269 ATATACGTCCATAATTTTAAAAGCTACATGTATTATTTAGGGTAA
63 AAATACATCCATAATTTTAAAAGCCACACGTATTATTTAGGGTAA
12331314 AATACTCTCA
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
118 26 0.28
119 64 0.69
120 3 0.03
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (118 bp):
GTGAAAGAGTTATTTCAATATAAAAACAAAAACTAATATTTTAAACAGTAAAAATCAAAACAAAA
TACATCCATAATTTTAAAAGCCACACGTATTATTTAGGGTAATATGTTCTCAA
Found at i:12331641 original size:19 final size:19
Alignment explanation
Indices: 12331619--12331662 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
12331609 ATAAAATTTC
12331619 TTCTCTCCCCTTAAATACT
1 TTCTCTCCCCTTAAATACT
* *
12331638 TTCTTTCCCTTTAAATACT
1 TTCTCTCCCCTTAAATACT
12331657 TTCTCT
1 TTCTCT
12331663 TATATTTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (19 bp):
TTCTCTCCCCTTAAATACT
Found at i:12336657 original size:19 final size:19
Alignment explanation
Indices: 12336630--12336673 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
12336620 ATAAGATTTC
12336630 TTCTCTCCCCGTAAATACT
1 TTCTCTCCCCGTAAATACT
* **
12336649 TTCTTTCCCTTTAAATACT
1 TTCTCTCCCCGTAAATACT
12336668 TTCTCT
1 TTCTCT
12336674 TATAGTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.02, T:0.48
Consensus pattern (19 bp):
TTCTCTCCCCGTAAATACT
Found at i:12336829 original size:29 final size:30
Alignment explanation
Indices: 12336787--12336844 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
12336777 AAGGGTAGGA
12336787 AGCACTAATTTGGTGCTCC-CTCCCTTGAG
1 AGCACTAATTTGGTGCTCCTCTCCCTTGAG
*
12336816 AGCACTAGA-TTGGTGCTCCTCTCTCTTGA
1 AGCACTA-ATTTGGTGCTCCTCTCCCTTGA
12336845 TCGATGCTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.33
Consensus pattern (30 bp):
AGCACTAATTTGGTGCTCCTCTCCCTTGAG
Found at i:12347827 original size:13 final size:13
Alignment explanation
Indices: 12347803--12347835 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
12347793 AAAGGTTTCC
12347803 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
12347816 TT-TTTTTCTCTTT
1 TTCTTTTT-TCTTT
12347829 TTCTTTT
1 TTCTTTT
12347836 AATTTTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 9 0.50
14 4 0.22
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTCTTTTTTCTTT
Found at i:12347841 original size:19 final size:18
Alignment explanation
Indices: 12347803--12347844 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
12347793 AAAGGTTTCC
**
12347803 TTCTTTTTTCTTTTTTTT
1 TTCTTTTTTCTTTTAATT
12347821 TTCTCTTTTTCTTTTAATT
1 TTCT-TTTTTCTTTTAATT
12347840 TTCTT
1 TTCTT
12347845 AATTTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (18 bp):
TTCTTTTTTCTTTTAATT
Found at i:12361341 original size:50 final size:49
Alignment explanation
Indices: 12361282--12361399 Score: 182
Period size: 50 Copynumber: 2.4 Consensus size: 49
12361272 TTTCCAGATA
* * *
12361282 GAGTTCCTGGTTGAATCTTCTGTCATTGGTTTCTATTGAAGAAGCTTTTT
1 GAGTTCCTGGTTGAAACTTCTGTCATTGGTTTCTATTAAAGAAGC-TATT
*
12361332 GAGTTCCTGGTTGAAACTTCTGTCATTTGTTTCTATTAAAGAAGCTATT
1 GAGTTCCTGGTTGAAACTTCTGTCATTGGTTTCTATTAAAGAAGCTATT
*
12361381 GAGTTCCTGGTTGCAACTT
1 GAGTTCCTGGTTGAAACTT
12361400 GCGGCTTGTA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
49 21 0.33
50 42 0.67
ACGTcount: A:0.20, C:0.15, G:0.21, T:0.43
Consensus pattern (49 bp):
GAGTTCCTGGTTGAAACTTCTGTCATTGGTTTCTATTAAAGAAGCTATT
Found at i:12362854 original size:33 final size:33
Alignment explanation
Indices: 12362812--12362888 Score: 129
Period size: 33 Copynumber: 2.3 Consensus size: 33
12362802 CTCCACCATC
12362812 TCCTCTGCCCCTTCTTTC-CTCGTCGCTACCACT
1 TCCTCTGCCCCTTCTTTCTC-CGTCGCTACCACT
*
12362845 TCCTCTGCCCCTTCTTTCTCCGTCTCTACCACT
1 TCCTCTGCCCCTTCTTTCTCCGTCGCTACCACT
12362878 TCCTCTGCCCC
1 TCCTCTGCCCC
12362889 GCTCTCCTCC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
33 41 0.98
34 1 0.02
ACGTcount: A:0.05, C:0.51, G:0.08, T:0.36
Consensus pattern (33 bp):
TCCTCTGCCCCTTCTTTCTCCGTCGCTACCACT
Found at i:12362899 original size:33 final size:32
Alignment explanation
Indices: 12362812--12362903 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 32
12362802 CTCCACCATC
* *
12362812 TCCTCTGCCCCTTCTTTCCT-CGTCGCTACCACT
1 TCCTCTGCCCC--CTCTCCTCCGTCTCTACCACT
* *
12362845 TCCTCTGCCCCTTCTTTCTCCGTCTCTACCACT
1 TCCTCTGCCCCCTC-TCCTCCGTCTCTACCACT
12362878 TCCTCTGCCCCGCTCTCCTCCGTCTC
1 TCCTCTGCCCC-CTCTCCTCCGTCTC
12362904 CATCTTCTCC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
31 1 0.02
32 3 0.06
33 44 0.88
34 2 0.04
ACGTcount: A:0.04, C:0.51, G:0.09, T:0.36
Consensus pattern (32 bp):
TCCTCTGCCCCCTCTCCTCCGTCTCTACCACT
Found at i:12364420 original size:21 final size:19
Alignment explanation
Indices: 12364388--12364427 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
12364378 ATAAATATTT
12364388 ATTTAAAATTTTTAAAATA
1 ATTTAAAATTTTTAAAATA
12364407 ATTTAAATACTTTTTAAAATA
1 ATTTAAA-A-TTTTTAAAATA
12364428 TTATGCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 1 0.05
21 11 0.58
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAAATTTTTAAAATA
Found at i:12368279 original size:71 final size:70
Alignment explanation
Indices: 12368170--12368373 Score: 264
Period size: 71 Copynumber: 2.9 Consensus size: 70
12368160 ATTAAGTTGT
* * *
12368170 GCCTAATTCATTAAATTGTTTAATTAAGTTATTGGGCCTAATTAATTAAATTAAGCAATTAAATT
1 GCCTAATTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAAACAATTAAATT
12368235 ATTGA
66 ATTGA
* * * *** * *
12368240 GCCTAATTGATTAAATTTGTTTGATCAAGTTATTAGGCCTAATTGATTAAATTTATTTAATCAAG
1 GCCTAATTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAATTGATTAAA-TTAAACAATTAAA
* *
12368305 TTGTTGG
64 TTATTGA
*
12368312 GCTTAATTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAAACAATTAA
1 GCCTAATTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAAACAATTAA
12368374 GTTAATTAGG
Statistics
Matches: 112, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
70 22 0.20
71 63 0.56
72 27 0.24
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.43
Consensus pattern (70 bp):
GCCTAATTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAAACAATTAAATT
ATTGA
Found at i:12368325 original size:107 final size:106
Alignment explanation
Indices: 12368170--12368363 Score: 271
Period size: 107 Copynumber: 1.8 Consensus size: 106
12368160 ATTAAGTTGT
* *
12368170 GCCTAATTCATTAAATTGTTTAATTAAGTTATTGGGCCTAATTAATTAAATTAAGCAATTAAATT
1 GCCTAATTCATTAAATTATTTAATCAAGTTATTGGGCCTAATTAATTAAATTAAGCAATTAAATT
12368235 ATTGAGCCTAATTGATTAAATTTGTTTGATCAAGTTATTAG
66 ATTGAGCCTAATTGATTAAATTTGTTTGATCAAGTTATTAG
* * * * **** *
12368276 GCCTAATTGATTAAATTTATTTAATCAAGTTGTTGGGCTTAATTGATTAAATTGTTTAATTAAGT
1 GCCTAATTCATTAAA-TTATTTAATCAAGTTATTGGGCCTAATTAATTAAATTAAGCAATTAAAT
*
12368341 TATTGGGCCTAATTGATTAAATT
65 TATTGAGCCTAATTGATTAAATT
12368364 AAACAATTAA
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
106 14 0.19
107 61 0.81
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (106 bp):
GCCTAATTCATTAAATTATTTAATCAAGTTATTGGGCCTAATTAATTAAATTAAGCAATTAAATT
ATTGAGCCTAATTGATTAAATTTGTTTGATCAAGTTATTAG
Found at i:12368377 original size:35 final size:35
Alignment explanation
Indices: 12368143--12368364 Score: 243
Period size: 35 Copynumber: 6.3 Consensus size: 35
12368133 TTTCAAGCAC
*
12368143 TTGATTAAAATTATTTAATTAAG---TTGTGCCTAA
1 TTGATT-AAATTATTTAATTAAGTTATTGGGCCTAA
* *
12368176 TTCATTAAATTGTTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAATTATTTAATTAAGTTATTGGGCCTAA
* *** * *
12368211 TTAATTAAATTAAGCAATTAAATTATTGAGCCTAA
1 TTGATTAAATTATTTAATTAAGTTATTGGGCCTAA
* * * *
12368246 TTGATTAAATTTGTTTGATCAAGTTATTAGGCCTAA
1 TTGATTAAA-TTATTTAATTAAGTTATTGGGCCTAA
* * *
12368282 TTGATTAAATTTATTTAATCAAGTTGTTGGGCTTAA
1 TTGATTAAA-TTATTTAATTAAGTTATTGGGCCTAA
*
12368318 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAATTATTTAATTAAGTTATTGGGCCTAA
12368353 TTGATTAAATTA
1 TTGATTAAATTA
12368365 AACAATTAAG
Statistics
Matches: 155, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
32 15 0.10
33 5 0.03
35 78 0.50
36 57 0.37
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.45
Consensus pattern (35 bp):
TTGATTAAATTATTTAATTAAGTTATTGGGCCTAA
Found at i:12370885 original size:25 final size:24
Alignment explanation
Indices: 12370825--12370886 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 24
12370815 TATTAATTAA
*
12370825 CATAATTATAAGAATTAGGAATCAC
1 CATAATTAT-AGAATTAGAAATCAC
*
12370850 CATAATTATAGCAATTATAAATCAC
1 CATAATTATAG-AATTAGAAATCAC
12370875 CATAATTATAGA
1 CATAATTATAGA
12370887 GATTTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 3 0.09
25 31 0.91
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (24 bp):
CATAATTATAGAATTAGAAATCAC
Found at i:12372942 original size:6 final size:6
Alignment explanation
Indices: 12372931--12372956 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12372921 CCACTTGGGA
12372931 TTCTTT TTCTTT TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TT
12372957 TTTCTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTCTTT
Found at i:12380213 original size:12 final size:12
Alignment explanation
Indices: 12380171--12380219 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
12380161 GAATGCTAAA
12380171 TTTTTCTTCTCTT
1 TTTTTCTTCT-TT
*
12380184 TTTTGGCTTCTTT
1 TTTT-TCTTCTTT
*
12380197 CTTTTCTTCTTT
1 TTTTTCTTCTTT
12380209 TTTTT-TTCTTT
1 TTTTTCTTCTTT
12380220 CATTTCAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 6 0.19
12 11 0.35
13 9 0.29
14 5 0.16
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTTCTTCTTT
Found at i:12380217 original size:23 final size:25
Alignment explanation
Indices: 12380172--12380225 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
12380162 AATGCTAAAT
12380172 TTTTCTTCTCTTTTTTGGCTTCTTTC
1 TTTTCTTCTCTTTTTT-GCTTCTTTC
*
12380198 TTTTCTTCT-TTTTTT-TTTCTTTC
1 TTTTCTTCTCTTTTTTGCTTCTTTC
*
12380221 ATTTC
1 TTTTC
12380226 AAGTTCATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.42
25 6 0.23
26 9 0.35
ACGTcount: A:0.02, C:0.20, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTTCTTCTCTTTTTTGCTTCTTTC
Found at i:12384178 original size:15 final size:15
Alignment explanation
Indices: 12384158--12384188 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12384148 AGAAGTGATC
12384158 ATGGAGATGAGTTTG
1 ATGGAGATGAGTTTG
*
12384173 ATGGAGATGATTTTG
1 ATGGAGATGAGTTTG
12384188 A
1 A
12384189 AAATTTTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (15 bp):
ATGGAGATGAGTTTG
Done.