Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007816.1 Hibiscus syriacus cultivar Beakdansim tig00110151_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: 3994936
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 14
Found at i:3399286 original size:8 final size:9
Alignment explanation
Indices: 3399273--3399313 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
3399263 AATAAAAACC
3399273 AATATA-AT
1 AATATATAT
3399281 AATATAATAT
1 AATAT-ATAT
3399291 AAT-TATACT
1 AATATATA-T
3399300 AATATATAT
1 AATATATAT
3399309 AATAT
1 AATAT
3399314 TTTTAAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 8 0.28
9 12 0.41
10 9 0.31
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (9 bp):
AATATATAT
Found at i:3399297 original size:19 final size:18
Alignment explanation
Indices: 3399275--3399311 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3399265 TAAAAACCAA
3399275 TATAATAATATAATATAAT
1 TATAATAATAT-ATATAAT
*
3399294 TATACTAATATATATAAT
1 TATAATAATATATATAAT
3399312 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TATAATAATATATATAAT
Found at i:3399456 original size:37 final size:37
Alignment explanation
Indices: 3399309--3399664 Score: 326
Period size: 37 Copynumber: 9.8 Consensus size: 37
3399299 TAATATATAT
* *
3399309 AATATTTTTAAAAAC--TATA-TA-ACATATATTCAA
1 AATATTTTCAAAAACTATATATTATATATATATTCAA
* * * * *
3399342 ATTGTTTTCAAAAATTATATATTAAATATATTTTTTCAA
1 AATATTTTCAAAAACTATATATT--ATATATATATTCAA
* *
3399381 AATGTTTTCAAAAACTATATA-TATATATATATTAAA
1 AATATTTTCAAAAACTATATATTATATATATATTCAA
3399417 AATATTTGT-AAAAACTATATATTATATATATATTCAA
1 AATATTT-TCAAAAACTATATATTATATATATATTCAA
* *
3399454 AATACTTTCAAAAACTATATA-T-TATATGT-TTC-A
1 AATATTTTCAAAAACTATATATTATATATATATTCAA
* * *
3399487 AATGTTTTTCAAAAACTATATATTATATATGT-TTGAAA
1 AAT-ATTTTCAAAAACTATATATTATATATATATT-CAA
* * *
3399525 AATGTTTTCAAAAACTATATATTATATATTTTTTCAA
1 AATATTTTCAAAAACTATATATTATATATATATTCAA
* * *
3399562 AACATTTTTTAAAAACTATATATTATATATATTTTCAA
1 AATA-TTTTCAAAAACTATATATTATATATATATTCAA
***
3399600 AACGCTTTCAAAAACTATATATTATATATATA-T--A
1 AATATTTTCAAAAACTATATATTATATATATATTCAA
* * *
3399634 TATGTTTTCTAAAACTATATATTATATATAT
1 AATATTTTCAAAAACTATATATTATATATAT
3399665 TAAATAGAAC
Statistics
Matches: 273, Mismatches: 34, Indels: 31
0.81 0.10 0.09
Matches are distributed among these distances:
33 15 0.05
34 47 0.17
35 11 0.04
36 42 0.15
37 88 0.32
38 42 0.15
39 28 0.10
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (37 bp):
AATATTTTCAAAAACTATATATTATATATATATTCAA
Found at i:3399497 original size:146 final size:146
Alignment explanation
Indices: 3399309--3399665 Score: 440
Period size: 146 Copynumber: 2.4 Consensus size: 146
3399299 TAATATATAT
* * ** * *
3399309 AATATTTTTAAAAACTATATAACATATATTCAAAT-TGTTTTCAAAAATTATATATTAAATATAT
1 AATACTTTCAAAAACTATATATTATATTTTCAAATGT-TTTTCAAAAACTATATATT-AATATAT
**
3399373 TTTTTCAAAATGTTTTCAAAAACTATATA-TATATATATATT-AAAA-ATATTTGTAAAAACTAT
64 TTTTGAAAAATGTTTTCAAAAACTATATATTATATATATATTCAAAACAT-TTTGTAAAAACTAT
3399435 ATATTATATATATATTCAA
128 ATATTATATATATATTCAA
*
3399454 AATACTTTCAAAAACTATATATTATATGTTTCAAATGTTTTTCAAAAACTATATATT-ATATATG
1 AATACTTTCAAAAACTATATATTATAT-TTTCAAATGTTTTTCAAAAACTATATATTAATATATT
* * *
3399518 TTTGAAAAATGTTTTCAAAAACTATATATTATATATTTTTTCAAAACATTTTTTAAAAACTATAT
65 TTTGAAAAATGTTTTCAAAAACTATATATTATATATATATTCAAAACATTTTGTAAAAACTATAT
*
3399583 ATTATATATATTTTCAA
130 ATTATATATATATTCAA
** * *
3399600 AACGCTTTCAAAAACTATATATTATATATATAT-ATATG-TTTTCTAAAACTATATATTATATAT
1 AATACTTTCAAAAACTATATATTATAT-T-T-TCAAATGTTTTTCAAAAACTATATATTA-ATAT
3399663 ATT
62 ATT
3399666 AAATAGAACC
Statistics
Matches: 184, Mismatches: 19, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
144 32 0.17
145 33 0.18
146 104 0.57
147 8 0.04
148 7 0.04
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (146 bp):
AATACTTTCAAAAACTATATATTATATTTTCAAATGTTTTTCAAAAACTATATATTAATATATTT
TTGAAAAATGTTTTCAAAAACTATATATTATATATATATTCAAAACATTTTGTAAAAACTATATA
TTATATATATATTCAA
Found at i:3399929 original size:29 final size:30
Alignment explanation
Indices: 3399887--3399950 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 30
3399877 ATAGAGGGGG
3399887 CGACTTCTTGTTGTTGAGCCATACTG-GGA
1 CGACTTCTTGTTGTTGAGCCATACTGTGGA
3399916 CGACTTCTTGTTGTTGAGCCATACTGTGGA
1 CGACTTCTTGTTGTTGAGCCATACTGTGGA
3399946 CGACT
1 CGACT
3399951 CAGGAATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 26 0.76
30 8 0.24
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (30 bp):
CGACTTCTTGTTGTTGAGCCATACTGTGGA
Found at i:3400508 original size:123 final size:123
Alignment explanation
Indices: 3400274--3400535 Score: 384
Period size: 123 Copynumber: 2.1 Consensus size: 123
3400264 ATCCTTCCTC
* * * * *
3400274 GTGAAGTTGAAATCGTGGATTGCTCCTTCGCTGTGAAGTTAAGCTTTGAATTGGATGTTCTTCGT
1 GTGAAATTGAAATTGTGGATGGCTCCTTCGCTGTGAAGTTAAGCTTTAAATTGGATGTACTTCGT
* *
3400339 TGTGAAGTTGAAATCCAATCTTGTAAATTGCCTCACCTCAAGTTTAATATATTTCATT
66 TGTGAAGTTGAAATCCAATCTTGTAAATTGCATCACCTCAAGTTTAATATATTTCACT
*
3400397 GTGAAATTGAAATTGTGGATGGCTCCTTCGCTGTGAAGTTGAGCTTTAAATTGGATGTCACTT-G
1 GTGAAATTGAAATTGTGGATGGCTCCTTCGCTGTGAAGTTAAGCTTTAAATTGGATGT-ACTTCG
* * * *
3400461 TTGTGAAGTTGAAATCCAATCTTGTAAATTGCATCGCTTCGATTTTAATATATTTCACT
65 TTGTGAAGTTGAAATCCAATCTTGTAAATTGCATCACCTCAAGTTTAATATATTTCACT
3400520 GT-AAAGTTGAAATTGT
1 GTGAAA-TTGAAATTGT
3400536 CTCTAACAAG
Statistics
Matches: 125, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
122 3 0.02
123 119 0.95
124 3 0.02
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (123 bp):
GTGAAATTGAAATTGTGGATGGCTCCTTCGCTGTGAAGTTAAGCTTTAAATTGGATGTACTTCGT
TGTGAAGTTGAAATCCAATCTTGTAAATTGCATCACCTCAAGTTTAATATATTTCACT
Found at i:3400705 original size:22 final size:22
Alignment explanation
Indices: 3400678--3400736 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
3400668 TGATGACTCT
3400678 TGATTCTAGAATCTTGAATTTC
1 TGATTCTAGAATCTTGAATTTC
3400700 TGATTCTAGAATCTTGAATTTC
1 TGATTCTAGAATCTTGAATTTC
*
3400722 TGATTCTTG-ATCTTG
1 TGATTCTAGAATCTTG
3400737 GATCTTCAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 6 0.17
22 30 0.83
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (22 bp):
TGATTCTAGAATCTTGAATTTC
Found at i:3410124 original size:14 final size:14
Alignment explanation
Indices: 3410105--3410132 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3410095 TTCGGGAGTC
3410105 GTTACAGTCAAGGA
1 GTTACAGTCAAGGA
3410119 GTTACAGTCAAGGA
1 GTTACAGTCAAGGA
3410133 AGGATTAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (14 bp):
GTTACAGTCAAGGA
Found at i:3410851 original size:30 final size:30
Alignment explanation
Indices: 3410817--3410883 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
3410807 CATTAAGGGC
3410817 AAAAATGGAATTTCTTATTGAATGGAATAA
1 AAAAATGGAATTTCTTATTGAATGGAATAA
3410847 AAAAATGGAATTTCTTATTGAATGGAATAA
1 AAAAATGGAATTTCTTATTGAATGGAATAA
3410877 AAAAATG
1 AAAAATG
3410884 TCATTATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.49, C:0.03, G:0.16, T:0.31
Consensus pattern (30 bp):
AAAAATGGAATTTCTTATTGAATGGAATAA
Found at i:3412621 original size:31 final size:32
Alignment explanation
Indices: 3412583--3412643 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
3412573 CCTAGTACAG
3412583 ATGGTGGACACGACCTTA-TGTCATACGGGTT
1 ATGGTGGACACGACCTTAGTGTCATACGGGTT
3412614 ATGGTGGACACGACCTTATGTGTCATACGG
1 ATGGTGGACACGACCTTA-GTGTCATACGG
3412644 ATTAGCACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 18 0.64
33 10 0.36
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (32 bp):
ATGGTGGACACGACCTTAGTGTCATACGGGTT
Found at i:3412743 original size:23 final size:23
Alignment explanation
Indices: 3412699--3412744 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3412689 CAGGGTTGTA
* * *
3412699 TATTGGCTATTGTCTATTGTTAT
1 TATTGGCTATGGTATATGGTTAT
*
3412722 TATTGTCTATGGTATATGGTTAT
1 TATTGGCTATGGTATATGGTTAT
3412745 GGAATAATGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.54
Consensus pattern (23 bp):
TATTGGCTATGGTATATGGTTAT
Found at i:3412880 original size:46 final size:45
Alignment explanation
Indices: 3412756--3412936 Score: 248
Period size: 46 Copynumber: 4.1 Consensus size: 45
3412746 GAATAATGAC
3412756 AAGTGTA-T-GTAAAATAAGCTTACGAGCTTATGG-ATAAATGGT
1 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTATAAATGGT
* *
3412798 AAGTATATTTGTAAAAT-AGCTTACGAGCTTATGGTATTAAATGGT
1 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTA-TAAATGGT
*
3412843 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTATTAAATTGT
1 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTA-TAAATGGT
* * *
3412889 AAGTATTTTGGT-AAATAAGC-TACGAGCTTATGGGATAAATGGT
1 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTATAAATGGT
3412932 AAGTG
1 AAGTG
3412937 ATTTTATTTT
Statistics
Matches: 125, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
42 6 0.05
43 29 0.23
44 22 0.18
45 31 0.25
46 37 0.30
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (45 bp):
AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTATAAATGGT
Found at i:3412896 original size:89 final size:86
Alignment explanation
Indices: 3412756--3412936 Score: 244
Period size: 89 Copynumber: 2.1 Consensus size: 86
3412746 GAATAATGAC
3412756 AAGTGTATGTAAAATAAGCTTACGAGCTTATGGATAAATGGTAAG-TATATTT-GTAAA-ATAGC
1 AAGTGTATGTAAAATAAGCTTACGAGCTTATGGATAAATGGTAAGATAT-TTTGGTAAATA-AGC
*
3412818 TTACGAGCTTATGGTATTAAATGGT
64 -TACGAGCTTATGGGA-TAAATGGT
*
3412843 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTATTAAATTGTAAG-TATTTTGGTAAATAA
1 AAGTGTA-T-GTAAAATAAGCTTACGAGCTTATGG-A-TAAATGGTAAGATATTTTGGTAAATAA
3412907 GCTACGAGCTTATGGGATAAATGGT
62 GCTACGAGCTTATGGGATAAATGGT
3412932 AAGTG
1 AAGTG
3412937 ATTTTATTTT
Statistics
Matches: 86, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
87 7 0.08
88 1 0.01
89 38 0.44
90 18 0.21
91 21 0.24
92 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (86 bp):
AAGTGTATGTAAAATAAGCTTACGAGCTTATGGATAAATGGTAAGATATTTTGGTAAATAAGCTA
CGAGCTTATGGGATAAATGGT
Found at i:3415886 original size:18 final size:20
Alignment explanation
Indices: 3415863--3415899 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3415853 TAAACAAAGA
3415863 TAAATT-AAA-AAAAATAAT
1 TAAATTCAAATAAAAATAAT
3415881 TAAATTCAAATAAAAATAA
1 TAAATTCAAATAAAAATAA
3415900 AAGAAACAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (20 bp):
TAAATTCAAATAAAAATAAT
Found at i:3417070 original size:18 final size:18
Alignment explanation
Indices: 3417047--3417087 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3417037 AAGTTAAAAG
*
3417047 ATAAAAAATAA-AAAATAA
1 ATAAAAAACAATAAAAT-A
3417065 ATAAAAAACAATAAAATA
1 ATAAAAAACAATAAAATA
3417083 ATAAA
1 ATAAA
3417088 CCAATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (18 bp):
ATAAAAAACAATAAAATA
Found at i:3417080 original size:8 final size:7
Alignment explanation
Indices: 3417030--3417087 Score: 55
Period size: 7 Copynumber: 8.0 Consensus size: 7
3417020 AACAGAAAAT
3417030 AAATAAA
1 AAATAAA
*
3417037 AAGTTAAA
1 AA-ATAAA
*
3417045 AGATAAA
1 AAATAAA
3417052 AAATAAA
1 AAATAAA
3417059 AAATAAA
1 AAATAAA
3417066 TAAA-AAA
1 -AAATAAA
*
3417073 CAATAAA
1 AAATAAA
3417080 ATAATAAA
1 A-AATAAA
3417088 CCAATATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
6 2 0.05
7 25 0.61
8 14 0.34
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (7 bp):
AAATAAA
Found at i:3417166 original size:24 final size:21
Alignment explanation
Indices: 3417124--3417166 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
3417114 TATAGTATAA
3417124 TATATAAATATTTTTAAAAAC
1 TATATAAATATTTTTAAAAAC
*
3417145 TATATAACATATATTTTCAAAA
1 TATATAA-ATAT-TTTTAAAAA
3417167 TGTTTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 8 0.42
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (21 bp):
TATATAAATATTTTTAAAAAC
Found at i:3417190 original size:40 final size:40
Alignment explanation
Indices: 3417145--3417421 Score: 118
Period size: 41 Copynumber: 7.4 Consensus size: 40
3417135 TTTTAAAAAC
*
3417145 TATATAACATATATTTTCAAAATGTTTTCAAAAA-TATATA
1 TATATAA-ATATATTTTCAAAATATTTTCAAAAACTATATA
* *
3417185 TATATATATATATTTTTTCAAATTATTTTCAAAAACTATATA
1 TATATA-A-ATATATTTTCAAAATATTTTCAAAAACTATATA
*
3417227 T-TAT--ATATATTTTCAAAA-A----C---TA-TATAT-
1 TATATAAATATATTTTCAAAATATTTTCAAAAACTATATA
** *** * *
3417254 TATATAGGT-T-TTCAAAATATT-TTTCAAAAACTATATA
1 TATATAAATATATTTTCAAAATATTTTCAAAAACTATATA
* * *
3417291 TCATATATATATATATTCAAAATGTTTTCAAAAACTATATA
1 T-ATATAAATATATTTTCAAAATATTTTCAAAAACTATATA
* * *
3417332 T-TAT--ATAT-TTTTTAAAATATTTTTTAAAAAACTATGTA
1 TATATAAATATATTTTCAAAATA--TTTTCAAAAACTATATA
* ** *
3417370 T-TAT--ATATATTTTTAAAATGCTTTCAAAAACTATGTA
1 TATATAAATATATTTTCAAAATATTTTCAAAAACTATATA
*
3417407 T-TATATATATGATTT
1 TATATAAATAT-ATTT
3417422 CTAAAATTAT
Statistics
Matches: 183, Mismatches: 30, Indels: 48
0.70 0.11 0.18
Matches are distributed among these distances:
27 1 0.01
28 13 0.07
29 2 0.01
30 1 0.01
32 2 0.01
35 1 0.01
36 14 0.08
37 36 0.20
38 29 0.16
39 18 0.10
40 15 0.08
41 44 0.24
42 7 0.04
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (40 bp):
TATATAAATATATTTTCAAAATATTTTCAAAAACTATATA
Found at i:3417214 original size:41 final size:42
Alignment explanation
Indices: 3417145--3417236 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 42
3417135 TTTTAAAAAC
* *
3417145 TATATA-ACATATATTTTCAAAATGTTTTCAAAAA-TATATA
1 TATATATATATATATTTTCAAAATATTTTCAAAAACTATATA
* *
3417185 TATATATATATATTTTTTCAAATTATTTTCAAAAACTATATA
1 TATATATATATATATTTTCAAAATATTTTCAAAAACTATATA
3417227 T-TATATATAT
1 TATATATATAT
3417237 TTTCAAAAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
40 6 0.13
41 33 0.72
42 7 0.15
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.48
Consensus pattern (42 bp):
TATATATATATATATTTTCAAAATATTTTCAAAAACTATATA
Found at i:3417257 original size:24 final size:26
Alignment explanation
Indices: 3417208--3417270 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
3417198 TTTTTCAAAT
3417208 TATTTTCAAAAACTATATATTATATA
1 TATTTTCAAAAACTATATATTATATA
3417234 TATTTTCAAAAACTATATATTATATA
1 TATTTTCAAAAACTATATATTATATA
**
3417260 GGTTTTCAAAA
1 TATTTTCAAAA
3417271 TATTTTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (26 bp):
TATTTTCAAAAACTATATATTATATA
Found at i:3417283 original size:38 final size:38
Alignment explanation
Indices: 3417231--3417416 Score: 207
Period size: 38 Copynumber: 4.8 Consensus size: 38
3417221 TATATATTAT
**
3417231 ATATATTTTCAAAAACTATATATTATATAGGTTTTCAAA
1 ATAT-TTTTCAAAAACTATATATTATATATATTTTCAAA
3417270 ATATTTTTCAAAAACTATATATCATATATATATATATTCAAA
1 ATATTTTTCAAAAACTATATAT--TATATATAT-T-TTCAAA
* *
3417312 AT-GTTTTCAAAAACTATATATTATATAT-TTTTTAAA
1 ATATTTTTCAAAAACTATATATTATATATATTTTCAAA
* * *
3417348 ATATTTTTTAAAAAACTATGTATTATATATATTTTTAAA
1 ATA-TTTTTCAAAAACTATATATTATATATATTTTCAAA
** *
3417387 AT-GCTTTCAAAAACTATGTATTATATATAT
1 ATATTTTTCAAAAACTATATATTATATATAT
3417417 GATTTCTAAA
Statistics
Matches: 130, Mismatches: 10, Indels: 16
0.83 0.06 0.10
Matches are distributed among these distances:
36 7 0.05
37 26 0.20
38 42 0.32
39 21 0.16
40 7 0.05
41 19 0.15
42 8 0.06
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (38 bp):
ATATTTTTCAAAAACTATATATTATATATATTTTCAAA
Found at i:3417319 original size:105 final size:101
Alignment explanation
Indices: 3417126--3417348 Score: 306
Period size: 105 Copynumber: 2.2 Consensus size: 101
3417116 TAGTATAATA
*
3417126 TATAAATATTTTTAAAAACTATATAACATATATTTTCAAAATGTTTTCAAAAATATATATATATA
1 TATATATATTTTTAAAAACTATATAACATATATTTTCAAAATGTTTTCAAAAATATATATATATA
* *
3417191 TATATATTTTTTCAAATTATTTTCAAAAACTATATAT
66 TATATA-TTATTCAAAATATTTTCAAAAACTATATAT
* ** *
3417228 TATATATATTTTCAAAAACTATATATTATATAGGTTTTCAAAATATTTTTCAAAAACTATATATC
1 TATATATATTTTTAAAAACTATATAACATATA--TTTTCAAAAT-GTTTTCAAAAA-TATATAT-
*
3417293 ATATATATATA-TATTCAAAATGTTTTCAAAAACTATATAT
61 ATATATATATATTATTCAAAATATTTTCAAAAACTATATAT
3417333 TATATAT-TTTTTAAAA
1 TATATATATTTTTAAAA
3417349 TATTTTTTAA
Statistics
Matches: 107, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
102 28 0.26
104 18 0.17
105 43 0.40
106 7 0.07
107 11 0.10
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (101 bp):
TATATATATTTTTAAAAACTATATAACATATATTTTCAAAATGTTTTCAAAAATATATATATATA
TATATATTATTCAAAATATTTTCAAAAACTATATAT
Found at i:3417331 original size:26 final size:26
Alignment explanation
Indices: 3417201--3417333 Score: 82
Period size: 26 Copynumber: 5.1 Consensus size: 26
3417191 TATATATTTT
*
3417201 TTCAAATTATTTTCAAAAACTATATA
1 TTCAAAATATTTTCAAAAACTATATA
*
3417227 TT-ATATATATTTTCAAAAACTATATA
1 TTCA-AAATATTTTCAAAAACTATATA
* *
3417253 TT--ATATAGGTTTTC-AAAA-TAT-TT
1 TTCAAAATA--TTTTCAAAAACTATATA
* *
3417276 TTCAAAAACTATATATCATATATA-TATATA
1 TTC-AAAA-TAT-TTTCA-A-AAACTATATA
*
3417306 TTCAAAATGTTTTCAAAAACTATATA
1 TTCAAAATATTTTCAAAAACTATATA
3417332 TT
1 TT
3417334 ATATATTTTT
Statistics
Matches: 84, Mismatches: 10, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
23 3 0.04
24 8 0.10
25 8 0.10
26 43 0.51
27 6 0.07
28 3 0.04
29 9 0.11
30 4 0.05
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (26 bp):
TTCAAAATATTTTCAAAAACTATATA
Found at i:3417353 original size:12 final size:12
Alignment explanation
Indices: 3417336--3417360 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3417326 TATATATTAT
3417336 ATATTTTTTAAA
1 ATATTTTTTAAA
3417348 ATATTTTTTAAA
1 ATATTTTTTAAA
3417360 A
1 A
3417361 AACTATGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTTTTTAAA
Found at i:3417416 original size:79 final size:77
Alignment explanation
Indices: 3417237--3417414 Score: 245
Period size: 79 Copynumber: 2.3 Consensus size: 77
3417227 TTATATATAT
* *
3417237 TTTCAAAAACTATATATTATATAGGTTTTCAAAATATTTTTCAAAAACTATATATCATATATATA
1 TTTCAAAAACTATATATTATATA-TTTTTCAAAATATTTTTAAAAAACTATATAT-ATATATATA
*
3417302 TATATTCAAAATGT
64 TATATTCAAAATGC
* *
3417316 TTTCAAAAACTATATATTATATATTTTTTAAAATATTTTTTAAAAAACTATGTAT-TATATATAT
1 TTTCAAAAACTATATATTATATATTTTTCAAAATA-TTTTTAAAAAACTATATATATATATATAT
*
3417380 -T-TTTAAAATGC
65 ATATTCAAAATGC
*
3417391 TTTCAAAAACTATGTATTATATAT
1 TTTCAAAAACTATATATTATATAT
3417415 ATGATTTCTA
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
75 31 0.34
76 1 0.01
77 9 0.10
78 10 0.11
79 40 0.44
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.46
Consensus pattern (77 bp):
TTTCAAAAACTATATATTATATATTTTTCAAAATATTTTTAAAAAACTATATATATATATATATA
TATTCAAAATGC
Found at i:3420571 original size:22 final size:22
Alignment explanation
Indices: 3420546--3420626 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 22
3420536 TAGATAACTA
3420546 AAGTGCCTTAGCACTAGTATTG
1 AAGTGCCTTAGCACTAGTATTG
* * *
3420568 AAGTGTCTCAGCACT-GATATAG
1 AAGTGCCTTAGCACTAG-TATTG
* * * * *
3420590 AAGTGCATTTGCACTAATACTA
1 AAGTGCCTTAGCACTAGTATTG
*
3420612 AAGTGTCTTAGCACT
1 AAGTGCCTTAGCACT
3420627 GTTGAGAATA
Statistics
Matches: 43, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
21 1 0.02
22 42 0.98
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (22 bp):
AAGTGCCTTAGCACTAGTATTG
Found at i:3420791 original size:20 final size:20
Alignment explanation
Indices: 3420766--3420803 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3420756 TACTGATCAT
3420766 TTTAGTATCGATATCAAACC
1 TTTAGTATCGATATCAAACC
*
3420786 TTTAGTATCGGTATCAAA
1 TTTAGTATCGATATCAAA
3420804 ATCGGTCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (20 bp):
TTTAGTATCGATATCAAACC
Found at i:3426861 original size:3 final size:3
Alignment explanation
Indices: 3426853--3426923 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
3426843 TATTTACAAT
3426853 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3426901 ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA AT
3426924 GGATAAGTGA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3426977 original size:23 final size:23
Alignment explanation
Indices: 3426924--3426971 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3426914 TAATAATAAT
3426924 GGATAAGTGAGGACTTAAACCTA
1 GGATAAGTGAGGACTTAAACCTA
3426947 GGATAAGTGAGGACTTAAACCTA
1 GGATAAGTGAGGACTTAAACCTA
3426970 GG
1 GG
3426972 TCAAGTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (23 bp):
GGATAAGTGAGGACTTAAACCTA
Found at i:3429313 original size:10 final size:9
Alignment explanation
Indices: 3429283--3429312 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3429273 AAGGTTATGA
3429283 TTTGGGATT
1 TTTGGGATT
3429292 TTTGGGATT
1 TTTGGGATT
*
3429301 TTTGGGCTT
1 TTTGGGATT
3429310 TTT
1 TTT
3429313 TATAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.07, C:0.03, G:0.30, T:0.60
Consensus pattern (9 bp):
TTTGGGATT
Found at i:3429971 original size:21 final size:21
Alignment explanation
Indices: 3429945--3429985 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3429935 TGACATGATG
*
3429945 TCTTTTAAAAATTTTAAAATT
1 TCTTTTAAAAATTTAAAAATT
3429966 TCTTTTAAAAATTTAAAAAT
1 TCTTTTAAAAATTTAAAAAT
3429986 ATTATAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
TCTTTTAAAAATTTAAAAATT
Found at i:3429983 original size:29 final size:28
Alignment explanation
Indices: 3429948--3430002 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
3429938 CATGATGTCT
* *
3429948 TTTAAAAATTTTAAAATTTCTTTTAAAAA
1 TTTAAAAATATTAAAACTT-TTTTAAAAA
*
3429977 TTTAAAAATATTATAACTTTTTTAAA
1 TTTAAAAATATTAAAACTTTTTTAAA
3430003 GAAAAAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTAAAAATATTAAAACTTTTTTAAAAA
Found at i:3438342 original size:14 final size:14
Alignment explanation
Indices: 3438307--3438349 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3438297 AGTAAAATCC
3438307 ATAAAATATCAAAG
1 ATAAAATATCAAAG
*
3438321 ATATAATATCAAA-
1 ATAAAATATCAAAG
*
3438334 ATGAAAATATCCAAG
1 AT-AAAATATCAAAG
3438349 A
1 A
3438350 ACCAAATACT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 2 0.08
14 21 0.88
15 1 0.04
ACGTcount: A:0.60, C:0.09, G:0.07, T:0.23
Consensus pattern (14 bp):
ATAAAATATCAAAG
Found at i:3439505 original size:6 final size:6
Alignment explanation
Indices: 3439485--3439527 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
3439475 TAAAAAAAAG
3439485 AAAG-A AAAG-A AAAGAA AAAGAA AAAGAA AAAGAA AAAGTAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA AA
3439528 CATTATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 9 0.25
6 23 0.64
7 4 0.11
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:3450304 original size:20 final size:21
Alignment explanation
Indices: 3450279--3450335 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
3450269 CTGATTCAAT
*
3450279 TAGTATCGATACCTA-TGAGG
1 TAGTATCGATACCTAGTAAGG
3450299 TAGTATCGATACCATAGTAAGG
1 TAGTATCGATACC-TAGTAAGG
*
3450321 -GGTATCGATACCTAG
1 TAGTATCGATACCTAG
3450336 AAATATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.48
21 13 0.39
22 4 0.12
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCTAGTAAGG
Found at i:3450486 original size:95 final size:96
Alignment explanation
Indices: 3450298--3450474 Score: 212
Period size: 95 Copynumber: 1.9 Consensus size: 96
3450288 TACCTATGAG
* * * * *
3450298 GTAGTATCGATACCATAGTAAGGGGTATCGATACCTAGAAATATTAAATCTAATATTGGTATCGA
1 GTAGTATCAATACCATAGTAAGGGGTATCAATACCTAGAAACATCAAACCTAATATTGGTATCGA
* *** *
3450363 TACCGGTAGGGGGTATCAGTACAATAGTAGT
66 CACCCAAAAGGGGTATCAGTACAATAGTAGT
* * * * *
3450394 GTAGTATCAATACCATGGTAA-GGGTATCAATACCTGGAAACATCGAACCTATTTTTGGTATCGA
1 GTAGTATCAATACCATAGTAAGGGGTATCAATACCTAGAAACATCAAACCTAATATTGGTATCGA
3450458 CACCCAAAAGGGGTATC
66 CACCCAAAAGGGGTATC
3450475 GGTATCATAG
Statistics
Matches: 66, Mismatches: 15, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
95 47 0.71
96 19 0.29
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28
Consensus pattern (96 bp):
GTAGTATCAATACCATAGTAAGGGGTATCAATACCTAGAAACATCAAACCTAATATTGGTATCGA
CACCCAAAAGGGGTATCAGTACAATAGTAGT
Found at i:3450910 original size:55 final size:55
Alignment explanation
Indices: 3450846--3451082 Score: 357
Period size: 55 Copynumber: 4.3 Consensus size: 55
3450836 ATGTGTGTTG
* *
3450846 CAGGCACTTTGTGTGCATATTCATGGAATTCATCATGAGTTGATGAATCACCGTA
1 CAGGCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTA
* *
3450901 CAAGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTA
1 CAGGCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTA
* *
3450956 CAGGCACTATGTGTGGATATTCACGAAATTCATCATGAGTTGATGAATCACCGTA
1 CAGGCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTA
* ** * *
3451011 TAGGCACTTTGAATGCATATTCACGAAATTCATCATGAGTCGATGAATCAGCGTA
1 CAGGCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTA
* *
3451066 CATGCACTATGTGTGCA
1 CAGGCACTTTGTGTGCA
3451083 GCCCACATAA
Statistics
Matches: 164, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 164 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (55 bp):
CAGGCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTA
Found at i:3450951 original size:27 final size:27
Alignment explanation
Indices: 3450921--3451006 Score: 68
Period size: 26 Copynumber: 3.1 Consensus size: 27
3450911 GTGTGCATAT
*
3450921 TCACGGAATTCATCATGAGTTGATGAA
1 TCACGAAATTCATCATGAGTTGATGAA
* ** * * *
3450948 TCACCGTACAGGCA-CTATGTGTGGAT-AT
1 TCA-CG-AAATTCATC-ATGAGTTGATGAA
3450976 TCACGAAATTCATCATGAGTTGATGAA
1 TCACGAAATTCATCATGAGTTGATGAA
3451003 TCAC
1 TCAC
3451007 CGTATAGGCA
Statistics
Matches: 41, Mismatches: 13, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
26 12 0.29
27 11 0.27
28 7 0.17
29 11 0.27
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (27 bp):
TCACGAAATTCATCATGAGTTGATGAA
Found at i:3457234 original size:20 final size:20
Alignment explanation
Indices: 3457205--3457260 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
3457195 ATATTCAATC
* *
3457205 AGTATTGATACCTA-TGAGG
1 AGTATCGATACCTAGTAAGG
3457224 TAGTATCGATACCATAGTAAGG
1 -AGTATCGATACC-TAGTAAGG
*
3457246 GGTATCGATACCTAG
1 AGTATCGATACCTAG
3457261 AAACATCGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
21 13 0.42
22 4 0.13
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (20 bp):
AGTATCGATACCTAGTAAGG
Found at i:3457737 original size:2 final size:2
Alignment explanation
Indices: 3457730--3457771 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3457720 TATGTTGTTA
3457730 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
3457772 TGCATCGATA
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:3457890 original size:55 final size:55
Alignment explanation
Indices: 3457805--3458037 Score: 371
Period size: 55 Copynumber: 4.3 Consensus size: 55
3457795 TGTACTGTAG
3457805 GCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACA-
1 GCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAT
* *
3457859 GACACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTACAT
1 G-CACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAT
* * * *
3457915 GCACTATGTGT-CATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAAAG
1 GCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAT
*
3457969 GCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCATCGTACAT
1 GCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAT
*
3458024 GCACTATGTGTGCA
1 GCACTTTGTGTGCA
3458038 ACCCAAAGAA
Statistics
Matches: 164, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
54 51 0.31
55 112 0.68
56 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (55 bp):
GCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAT
Found at i:3458008 original size:109 final size:110
Alignment explanation
Indices: 3457805--3458037 Score: 414
Period size: 109 Copynumber: 2.1 Consensus size: 110
3457795 TGTACTGTAG
* *
3457805 GCACTTTGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAGACACTTTGTG
1 GCACTATGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTAAAGACACTTTGTG
*
3457870 TGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTACAT
66 TGCATATTCACGAAATTCATCATGAGTTGATGAATCATCGTACAT
* *
3457915 GCACTATGTGT-CATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAAAGGCACTTTGTG
1 GCACTATGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTAAAGACACTTTGTG
3457979 TGCATATTCACGAAATTCATCATGAGTTGATGAATCATCGTACAT
66 TGCATATTCACGAAATTCATCATGAGTTGATGAATCATCGTACAT
3458024 GCACTATGTGTGCA
1 GCACTATGTGTGCA
3458038 ACCCAAAGAA
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
109 105 0.90
110 12 0.10
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (110 bp):
GCACTATGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTAAAGACACTTTGTG
TGCATATTCACGAAATTCATCATGAGTTGATGAATCATCGTACAT
Found at i:3458082 original size:109 final size:109
Alignment explanation
Indices: 3457828--3458067 Score: 374
Period size: 109 Copynumber: 2.2 Consensus size: 109
3457818 ATATTCACGA
* * *
3457828 AATTCATCATGAGTTGATGAATCACCGTACAGACACTTTGTGTGCATATTCACGGAATTCATCAT
1 AATTCATCATGAGTTGATGAATCACCGTAAAGGCACTTTGTGTGCATATTCACGAAATTCATCAT
** **
3457893 GAGTTGATGAATCATCGTACATGCACTATGTGTCATATTCACGG
66 GAGTTGATGAATCATCGTACATGCACTATGTGTCATACCCAAAG
3457937 AATTCATCATGAGTTGATGAATCACCGTAAAGGCACTTTGTGTGCATATTCACGAAATTCATCAT
1 AATTCATCATGAGTTGATGAATCACCGTAAAGGCACTTTGTGTGCATATTCACGAAATTCATCAT
3458002 GAGTTGATGAATCATCGTACATGCACTATGTGTGCA-ACCCAAAG
66 GAGTTGATGAATCATCGTACATGCACTATGTGT-CATACCCAAAG
* * *
3458046 AATTTATTATGGGTTGATGAAT
1 AATTCATCATGAGTTGATGAAT
3458068 TCTCGTATAG
Statistics
Matches: 120, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
109 118 0.98
110 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (109 bp):
AATTCATCATGAGTTGATGAATCACCGTAAAGGCACTTTGTGTGCATATTCACGAAATTCATCAT
GAGTTGATGAATCATCGTACATGCACTATGTGTCATACCCAAAG
Found at i:3458110 original size:13 final size:11
Alignment explanation
Indices: 3458074--3458104 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3458064 GAATTCTCGT
3458074 ATAG-GCACTA
1 ATAGTGCACTA
3458084 ATAGTGCACTA
1 ATAGTGCACTA
3458095 ATAGTGCACT
1 ATAGTGCACT
3458105 CTAATAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (11 bp):
ATAGTGCACTA
Found at i:3460742 original size:40 final size:40
Alignment explanation
Indices: 3460698--3460793 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
3460688 AATATTTCAC
** * *
3460698 CGTAGTGCTGAGGTCGAGCCTTGCTCATGTAATACTGCAT
1 CGTAGTGCTGAGGTCGAGCCTTGCTCACCTAATAATGCAA
*
3460738 CGTAGTGTTGAGGTCGAGCCTTGCTCACCTAATAATGCAA
1 CGTAGTGCTGAGGTCGAGCCTTGCTCACCTAATAATGCAA
*
3460778 CATAGTGCTGAGGTCG
1 CGTAGTGCTGAGGTCG
3460794 GGCTTTACCC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (40 bp):
CGTAGTGCTGAGGTCGAGCCTTGCTCACCTAATAATGCAA
Found at i:3461082 original size:21 final size:22
Alignment explanation
Indices: 3461048--3461089 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
3461038 AAAATAACAG
3461048 TTATGATAAACATCATATGTAT
1 TTATGATAAACATCATATGTAT
3461070 TTATGAT-AACATCATATGTA
1 TTATGATAAACATCATATGTA
3461090 ATAAACAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (22 bp):
TTATGATAAACATCATATGTAT
Found at i:3467569 original size:40 final size:40
Alignment explanation
Indices: 3467489--3467569 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
3467479 CTCGCTCAGG
* * *
3467489 TAATAATGCACCGTAGTGCTAAGGTCGAGCATTGCTCACC
1 TAATAATGCACCGTAGAGCTAAGGTCGAGCATTACCCACC
* * * *
3467529 TAATAATGCACCTTAGAGCTGAGGTCGGGCTTTACCCACC
1 TAATAATGCACCGTAGAGCTAAGGTCGAGCATTACCCACC
3467569 T
1 T
3467570 TATACACCAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
TAATAATGCACCGTAGAGCTAAGGTCGAGCATTACCCACC
Found at i:3472359 original size:17 final size:16
Alignment explanation
Indices: 3472320--3472367 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
3472310 GGTTACGTTC
3472320 AATGTATCGATACCTTG
1 AATGTATCGATA-CTTG
3472337 AATGTATCGATACTTAG
1 AATGTATCGATACTT-G
* *
3472354 ACTGTATCAATACT
1 AATGTATCGATACT
3472368 ATACTTCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 3 0.11
17 25 0.89
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (16 bp):
AATGTATCGATACTTG
Found at i:3472837 original size:41 final size:41
Alignment explanation
Indices: 3472792--3472870 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
3472782 GATGTAATCC
3472792 AAAATAATCCAAAGTGGCACAACCACAACAAAATAAAACTA
1 AAAATAATCCAAAGTGGCACAACCACAACAAAATAAAACTA
* *
3472833 AAAATAATCCAAAGTGGCATAGCCACAACAAAATAAAA
1 AAAATAATCCAAAGTGGCACAACCACAACAAAATAAAA
3472871 ATAATCCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.58, C:0.20, G:0.09, T:0.13
Consensus pattern (41 bp):
AAAATAATCCAAAGTGGCACAACCACAACAAAATAAAACTA
Found at i:3472877 original size:35 final size:37
Alignment explanation
Indices: 3472792--3472880 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 37
3472782 GATGTAATCC
3472792 AAAATAATCCAAAGTGGCACAACCACAACAAAATAAAACTA
1 AAAATAATCCAAAGTGGCACAACCACAAC---A-AAAACTA
* *
3472833 AAAATAATCCAAAGTGGCATAGCCACAAC-AAAA-TA
1 AAAATAATCCAAAGTGGCACAACCACAACAAAAACTA
3472868 AAAATAATCCAAA
1 AAAATAATCCAAA
3472881 ACAATCTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
35 15 0.33
36 4 0.09
41 27 0.59
ACGTcount: A:0.58, C:0.20, G:0.08, T:0.13
Consensus pattern (37 bp):
AAAATAATCCAAAGTGGCACAACCACAACAAAAACTA
Found at i:3476876 original size:21 final size:23
Alignment explanation
Indices: 3476850--3476901 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
3476840 TTCTAGAAAG
3476850 GGAATTTTGGATATA-AATTA-A
1 GGAATTTTGGATATACAATTAGA
** *
3476871 GGAATTCGGGTTATACAATTAGA
1 GGAATTTTGGATATACAATTAGA
3476894 GGAATTTT
1 GGAATTTT
3476902 AAAATTAGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 12 0.50
22 5 0.21
23 7 0.29
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.37
Consensus pattern (23 bp):
GGAATTTTGGATATACAATTAGA
Found at i:3476981 original size:29 final size:29
Alignment explanation
Indices: 3476944--3477038 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 29
3476934 GAAGTCCCAC
*
3476944 ACCGGTATATTTTGGTTACGTCCATATTA
1 ACCGCTATATTTTGGTTACGTCCATATTA
* ** *
3476973 ACCGCTATAGAGTTT--TCCCGTTCATATT-
1 ACCGCTAT--ATTTTGGTTACGTCCATATTA
3477001 A--GCTCATATTTTGGTTACGTCCATATTA
1 ACCGCT-ATATTTTGGTTACGTCCATATTA
3477029 ACCGCTATAT
1 ACCGCTATAT
3477039 GCATTGCTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 16
0.66 0.12 0.22
Matches are distributed among these distances:
25 4 0.08
26 3 0.06
27 12 0.24
28 2 0.04
29 21 0.43
30 3 0.06
31 4 0.08
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (29 bp):
ACCGCTATATTTTGGTTACGTCCATATTA
Found at i:3477218 original size:2 final size:2
Alignment explanation
Indices: 3477213--3477264 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
3477203 ACACACACAA
*
3477213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
3477255 AT AT AT AT AT
1 AT AT AT AT AT
3477265 TAAATATTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3477813 original size:2 final size:2
Alignment explanation
Indices: 3477806--3477831 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3477796 TTATTTTTAT
3477806 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
3477832 CTTTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3479203 original size:78 final size:78
Alignment explanation
Indices: 3479116--3479264 Score: 237
Period size: 78 Copynumber: 1.9 Consensus size: 78
3479106 ATATAGTAAG
*
3479116 TAAACATTAAAAGAATGTAATTTTAATTACAACTCTTTTAATGGATATTTAATTTAGAA-TAATT
1 TAAACATTAAAAGAATGTAATTTGAATTACAACTCTTTTAATGGATATTTAATTT-GAATTAATT
3479180 GAATAAGGATAAAA
65 GAATAAGGATAAAA
* * *
3479194 TAAACATTAAAAGAATGTCATTTGGATTATAACTCTTTTAATGGATATTTAATTTGAATTAATTG
1 TAAACATTAAAAGAATGTAATTTGAATTACAACTCTTTTAATGGATATTTAATTTGAATTAATTG
*
3479259 ATTAAG
66 AATAAG
3479265 AATTTAATTA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
77 3 0.05
78 62 0.95
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (78 bp):
TAAACATTAAAAGAATGTAATTTGAATTACAACTCTTTTAATGGATATTTAATTTGAATTAATTG
AATAAGGATAAAA
Found at i:3495596 original size:20 final size:20
Alignment explanation
Indices: 3495560--3495597 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3495550 ATCCTATTCC
**
3495560 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
3495580 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
3495598 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:3498828 original size:23 final size:23
Alignment explanation
Indices: 3498798--3498844 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
3498788 AATTTATAAA
*
3498798 ATTTAAAATTCTAAATGTAAATT
1 ATTTAAAATTTTAAATGTAAATT
3498821 ATTTAAAATTTTAAATGT-AATT
1 ATTTAAAATTTTAAATGTAAATT
3498843 AT
1 AT
3498845 AAATTAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (23 bp):
ATTTAAAATTTTAAATGTAAATT
Found at i:3498847 original size:29 final size:30
Alignment explanation
Indices: 3498815--3498874 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
3498805 ATTCTAAATG
*
3498815 TAAATTATTTAAAATTTTAAATGT-AATTA
1 TAAATTAGTTAAAATTTTAAATGTAAATTA
3498844 TAAATTAGTTAAAATTTTAAATGTAAATTA
1 TAAATTAGTTAAAATTTTAAATGTAAATTA
3498874 T
1 T
3498875 TTAAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (30 bp):
TAAATTAGTTAAAATTTTAAATGTAAATTA
Found at i:3503001 original size:2 final size:2
Alignment explanation
Indices: 3502994--3503018 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3502984 GAACAAAAAC
3502994 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
3503019 ACATCATACA
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:3503195 original size:23 final size:23
Alignment explanation
Indices: 3503169--3503270 Score: 109
Period size: 23 Copynumber: 4.4 Consensus size: 23
3503159 CATTGAAGTG
*
3503169 CCACTTAGAAATGTCCCGAAGGA
1 CCACTTAGAAATGTCCTGAAGGA
* *
3503192 CCACATAGATATGTCCTGAAGGA
1 CCACTTAGAAATGTCCTGAAGGA
* *
3503215 CC-GTGTAGATATGTCCTGAAGGA
1 CCACT-TAGAAATGTCCTGAAGGA
*
3503238 CC-GTGTAGAAATGTCCTGAAGGA
1 CCACT-TAGAAATGTCCTGAAGGA
*
3503261 CCACGTAGAA
1 CCACTTAGAA
3503271 TTATCCCGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (23 bp):
CCACTTAGAAATGTCCTGAAGGA
Found at i:3503236 original size:46 final size:46
Alignment explanation
Indices: 3503174--3503280 Score: 124
Period size: 46 Copynumber: 2.3 Consensus size: 46
3503164 AAGTGCCACT
*
3503174 TAGAAATGTCCCGAAGGACCACATAGATATGTCCTGAAGGACCGTG
1 TAGAAATGTCCCGAAGGACCACATAGAAATGTCCTGAAGGACCGTG
* * *** **
3503220 TAGATATGTCCTGAAGGACCGTGTAGAAATGTCCTGAAGGACCACG
1 TAGAAATGTCCCGAAGGACCACATAGAAATGTCCTGAAGGACCGTG
* *
3503266 TAGAATTATCCCGAA
1 TAGAAATGTCCCGAA
3503281 TGACTGCTTA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (46 bp):
TAGAAATGTCCCGAAGGACCACATAGAAATGTCCTGAAGGACCGTG
Found at i:3503463 original size:14 final size:14
Alignment explanation
Indices: 3503444--3503477 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3503434 TAGGTCAATG
3503444 TCACATAACTTATA
1 TCACATAACTTATA
*
3503458 TCACATAGCTTATA
1 TCACATAACTTATA
3503472 TCACAT
1 TCACAT
3503478 TTTCATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (14 bp):
TCACATAACTTATA
Found at i:3504508 original size:10 final size:10
Alignment explanation
Indices: 3504493--3504522 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
3504483 CTACTTCTCT
3504493 TTAAGCTTTC
1 TTAAGCTTTC
3504503 TTAAGCTTTC
1 TTAAGCTTTC
3504513 TTAAGCTTTC
1 TTAAGCTTTC
3504523 CTAACATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (10 bp):
TTAAGCTTTC
Found at i:3508445 original size:23 final size:22
Alignment explanation
Indices: 3508419--3508496 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
3508409 TCACCGAGTG
3508419 CCACGTAGAAATGTCCCAAAGGA
1 CCACGTAGAAATGTCCCAAA-GA
* * *
3508442 CCACAT-GATATGTCCCGAATGA
1 CCACGTAGAAATGTCCC-AAAGA
* *
3508464 CCGCGTAGAAATGTCTCGAAAGA
1 CCACGTAGAAATGTC-CCAAAGA
3508487 CCACGTAGAA
1 CCACGTAGAA
3508497 TTTCCCGAAG
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
22 15 0.35
23 27 0.63
24 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.17
Consensus pattern (22 bp):
CCACGTAGAAATGTCCCAAAGA
Found at i:3508953 original size:15 final size:16
Alignment explanation
Indices: 3508933--3508978 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3508923 TACTTGTACA
3508933 TTGGTATCGATAC-CC
1 TTGGTATCGATACTCC
*
3508948 TTGGTAAT-GTTACTCC
1 TTGGT-ATCGATACTCC
*
3508964 TTCGTATCGATACTC
1 TTGGTATCGATACTC
3508979 TTTTAAGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (16 bp):
TTGGTATCGATACTCC
Found at i:3513314 original size:50 final size:46
Alignment explanation
Indices: 3513214--3513336 Score: 147
Period size: 50 Copynumber: 2.6 Consensus size: 46
3513204 GTAACCATGC
*
3513214 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAAA
* * * **
3513260 AAATAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTGGTAAA
1 AAATAAGCTTATGAGCTTATGGAA---T-AATGGCAAGTATATTGAAAAA
*
3513310 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
3513337 AAGGTAAGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
46 24 0.37
47 1 0.02
49 1 0.02
50 39 0.60
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.31
Consensus pattern (46 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAAA
Found at i:3513807 original size:22 final size:22
Alignment explanation
Indices: 3513782--3513834 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
3513772 AAAGGGGTAC
3513782 CGATTCCCCTGCTACAGGGAAT
1 CGATTCCCCTGCTACAGGGAAT
3513804 CGATTCCCCTGCTACAGGGAAT
1 CGATTCCCCTGCTACAGGGAAT
*
3513826 CAATTCCCC
1 CGATTCCCC
3513835 CACTGTTCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.23
Consensus pattern (22 bp):
CGATTCCCCTGCTACAGGGAAT
Found at i:3515477 original size:5 final size:6
Alignment explanation
Indices: 3515448--3515478 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
3515438 TCCTTTTCTT
3515448 TTTTAA TTTTAA TTTTAA TTTTAA -TTTAA TT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TT
3515479 ATTTGGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:3520770 original size:29 final size:28
Alignment explanation
Indices: 3520738--3520793 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
3520728 ATTGGGCCTA
* *
3520738 TATATTATTATTAATAATAATATAATAAT
1 TATATTAATATTAAAAATAATA-AATAAT
3520767 TATATTAATATTAAAAATAATAAATAA
1 TATATTAATATTAAAAATAATAAATAA
3520794 AAAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
TATATTAATATTAAAAATAATAAATAAT
Found at i:3523660 original size:14 final size:14
Alignment explanation
Indices: 3523641--3523669 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3523631 AAAATGATGC
3523641 AACTAGGATTGCCA
1 AACTAGGATTGCCA
3523655 AACTAGGATTGCCA
1 AACTAGGATTGCCA
3523669 A
1 A
3523670 TTACTAGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (14 bp):
AACTAGGATTGCCA
Found at i:3524098 original size:85 final size:89
Alignment explanation
Indices: 3523990--3524164 Score: 268
Period size: 86 Copynumber: 2.0 Consensus size: 89
3523980 ATAGTATAAC
* *
3523990 AGGCTAGCTGAATATTATCCATAAAGTCGGGGCGATTAACCAATTGCTTTAG-GGGACAACTCAA
1 AGGCTAGCTGAATATTATCCATAAAGCCAGGGCGATTAACCAATTGCTTTAGAGGGACAACTCAA
* *
3524054 GCTTTATTGTATATATAATAATAT
66 GCTTTATTGCATACATAATAATAT
* *
3524078 AGGCTATCTGAATA-T-T-CATAAAGCCAGGGTGATTAACCAATTGCTTTAGAGGGACAACTCAA
1 AGGCTAGCTGAATATTATCCATAAAGCCAGGGCGATTAACCAATTGCTTTAGAGGGACAACTCAA
3524140 GCTTTATTGCATACATAATAATAT
66 GCTTTATTGCATACATAATAATAT
3524164 A
1 A
3524165 ATATGAATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
85 30 0.38
86 36 0.45
87 1 0.01
88 13 0.16
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (89 bp):
AGGCTAGCTGAATATTATCCATAAAGCCAGGGCGATTAACCAATTGCTTTAGAGGGACAACTCAA
GCTTTATTGCATACATAATAATAT
Found at i:3529399 original size:166 final size:167
Alignment explanation
Indices: 3529138--3529458 Score: 425
Period size: 166 Copynumber: 1.9 Consensus size: 167
3529128 ATTATAAAGA
**
3529138 AAAATATATGAAAATAATTTTTTATAAAACTAAAGTAATATATATATATTTAGGGATTTTTAAAA
1 AAAATATATGAAAATAATTTTAAATAAAACTAAAGTAATATATATATATTT---G-TTTTTAAAA
* * *
3529203 TAGGGTATTTATTTATTTAAAAAAATCAGAAAATGACATCTATTTACTTTAAGACAACCCCTTTC
62 TAAGGTATTTATTTATTTAAAAAAATCAGAAAAGGACATCTAGTTACTTTAAGACAACCCCTTTC
* **
3529268 TTAATATTAAAA-AAATAAATATTAATAAGAATATGATAAG
127 GTAATAGAAAAATAAATAAATATTAATAAGAATATGATAAG
* *
3529308 AAAATCATATTAAAATAA-TTTAAATAAAACTAAAGTAA-ATATATATTATTT-TTTTTATAATT
1 AAAAT-ATATGAAAATAATTTTAAATAAAACTAAAGTAATATATATA-TATTTGTTTTTA-AAAT
* ** *
3529370 AAGGTATTTATTTATTTAAAAATATCAGAAAAGGACATCTAGTTACTTTAAGACAGTCTCTTTCG
63 AAGGTATTTATTTATTTAAAAAAATCAGAAAAGGACATCTAGTTACTTTAAGACAACCCCTTTCG
3529435 TAATAGAAAAATAAATAAATATTA
128 TAATAGAAAAATAAATAAATATTA
3529459 TCCTTTAACT
Statistics
Matches: 133, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
165 6 0.05
166 69 0.52
167 12 0.09
169 7 0.05
170 28 0.21
171 11 0.08
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.38
Consensus pattern (167 bp):
AAAATATATGAAAATAATTTTAAATAAAACTAAAGTAATATATATATATTTGTTTTTAAAATAAG
GTATTTATTTATTTAAAAAAATCAGAAAAGGACATCTAGTTACTTTAAGACAACCCCTTTCGTAA
TAGAAAAATAAATAAATATTAATAAGAATATGATAAG
Found at i:3530687 original size:26 final size:26
Alignment explanation
Indices: 3530649--3530701 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
3530639 CGGAAGTATT
*
3530649 AATAATAATAATAATATAATAAATAAATA
1 AATAAAAATAA-AA-ATAA-AAATAAATA
3530678 AATAAAAATAAAAATAAAAATAAA
1 AATAAAAATAAAAATAAAAATAAA
3530702 CATGGGACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 4 0.17
28 2 0.09
29 10 0.43
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (26 bp):
AATAAAAATAAAAATAAAAATAAATA
Found at i:3530701 original size:6 final size:6
Alignment explanation
Indices: 3530649--3530701 Score: 52
Period size: 6 Copynumber: 8.0 Consensus size: 6
3530639 CGGAAGTATT
*
3530649 AATAAT AATAATA ATATAATA AATAAATA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATAA-A A-ATAA-A AAT-AA-A AATAAA AATAAA AATAAA AATAAA
3530702 CATGGGACAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
6 24 0.56
7 5 0.12
8 14 0.33
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (6 bp):
AATAAA
Found at i:3534971 original size:3 final size:3
Alignment explanation
Indices: 3534963--3535037 Score: 55
Period size: 3 Copynumber: 24.7 Consensus size: 3
3534953 CAAACTAAAT
* * * * *
3534963 TAA TAA TAA -AA TAA TAA T-A TAA TAA TAA CAA CAA CAA CAA CAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
*
3535010 TAT TATA TAA TAA TAA GTAA TAA TAA TA
1 TAA TA-A TAA TAA TAA -TAA TAA TAA TA
3535038 TATACTAAAC
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
2 4 0.06
3 51 0.81
4 8 0.13
ACGTcount: A:0.64, C:0.07, G:0.01, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:3535157 original size:17 final size:16
Alignment explanation
Indices: 3535118--3535157 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
3535108 AATGTAATAT
3535118 ATTATATTTTTCAAAA
1 ATTATATTTTTCAAAA
**
3535134 ACAATATGTTTTCAAAA
1 ATTATAT-TTTTCAAAA
3535151 ATTATAT
1 ATTATAT
3535158 ATATTATACA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (16 bp):
ATTATATTTTTCAAAA
Found at i:3535174 original size:45 final size:43
Alignment explanation
Indices: 3535125--3535208 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
3535115 TATATTATAT
* *
3535125 TTTTCAAAAACAATATGTTTTCAAAAATTATATATATTATACACG
1 TTTTCAAAAAC--TATATTTTCAAAAACTATATATATTATACACG
* *
3535170 TTTTCAAAATCTATATTTTCAAAAACTATTTATATTATA
1 TTTTCAAAAACTATATTTTCAAAAACTATATATATTATA
3535209 TTTATTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 25 0.71
45 10 0.29
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (43 bp):
TTTTCAAAAACTATATTTTCAAAAACTATATATATTATACACG
Found at i:3551045 original size:3 final size:3
Alignment explanation
Indices: 3551039--3551068 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
3551029 TTTTTTTTTC
3551039 ATA ATA ATA ATAA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT
3551069 TTTAAAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3551312 original size:45 final size:45
Alignment explanation
Indices: 3551257--3551911 Score: 997
Period size: 45 Copynumber: 14.7 Consensus size: 45
3551247 CTCAGAAGGT
* *
3551257 TTACAGATGACCCGGAGGCTTTGAAAACATCATGCACTGAAGGTC
1 TTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
* * * *
3551302 TTACAAATGACCCTAAGGTTTTGAAAACATCATGCACTGAAGGTC
1 TTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
* * *
3551347 TTA-TGAATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGTC
1 TTACAG-ATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
* * * *
3551392 TTATAGATGAGCCGAAGGTTTTG-AAACATCATGCATTGAAGGGC
1 TTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
*
3551436 TTACAGATTACCCGAAGGCTTTG-AAA-A-CATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
* *
3551478 TTACAGATGA-CCAAAGGTTTATGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGCTT-TGAAAACATCATGCACTGAAGGGC
3551523 TTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTG-AGGGC
1 TTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
*
3551567 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACT-AAGGGC
1 TTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
3551611 TTACAGAT-ACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
*
3551655 TTACAGATGACCTGAAGGCTTTGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
* * *
3551700 TTAAAGATGACCCGAAGGCTTTGAAAAAATCATACACTGAAGGGC
1 TTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
*
3551745 TTACCGATGACCCGAAAGGCTTTG-AAACATCATGCACTGAAGGGC
1 TTACAGATGACCCG-AAGGCTTTGAAAACATCATGCACTGAAGGGC
3551790 TTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
*
3551835 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGC
1 TTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
*
3551880 TTACAGATGACCCGAAGGTTTTGAAAACATCA
1 TTACAGATGACCCGAAGGCTTTGAAAACATCA
3551912 AAAGATCCCA
Statistics
Matches: 564, Mismatches: 34, Indels: 24
0.91 0.05 0.04
Matches are distributed among these distances:
41 8 0.01
42 25 0.04
43 32 0.06
44 120 0.21
45 361 0.64
46 18 0.03
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (45 bp):
TTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGGC
Found at i:3552812 original size:22 final size:22
Alignment explanation
Indices: 3552775--3552985 Score: 341
Period size: 22 Copynumber: 9.6 Consensus size: 22
3552765 AATAAAGCTT
* * *
3552775 TCATCTTTAAAAAGAGAATATA
1 TCATCTTTGAAGAGAGAATCTA
*
3552797 TTATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
3552819 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
3552841 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
3552863 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
3552885 TCATCTTTGAAGATAGAATATA
1 TCATCTTTGAAGAGAGAATCTA
*
3552907 TCATCTTTGAAGAGAGAATATA
1 TCATCTTTGAAGAGAGAATCTA
*
3552929 TCATCTTTGGAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
3552951 TCATCTTTGAAGAGATAATCTA
1 TCATCTTTGAAGAGAGAATCTA
3552973 TCATCTTTGAAGA
1 TCATCTTTGAAGA
3552986 ATGTAGATGT
Statistics
Matches: 177, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 177 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:3553466 original size:54 final size:54
Alignment explanation
Indices: 3553352--3553566 Score: 195
Period size: 54 Copynumber: 4.0 Consensus size: 54
3553342 AGAATAACTG
* * * * * * * * *
3553352 GTTCCTAAAACATTTGACAACACATTCA-TCATCTCATATGGTTTTTGCTCAGAT
1 GTTCGTAAAATATTTGACAACACATTCATTC-TTTCCTGTGGCTTCTGCACAGAC
* * * *
3553406 GCTCGTAAAATATTTGACAACACATTCATTCTTTACC-GTGGCTTCTGCCCATAT
1 GTTCGTAAAATATTTGACAACACATTCATTCTTT-CCTGTGGCTTCTGCACAGAC
* *
3553460 GTTCGT-AAATCATTTGACAACACATTCA-TCATTTCCTGTGGTTTCTTCACAGAC
1 GTTCGTAAAAT-ATTTGACAACACATTCATTC-TTTCCTGTGGCTTCTGCACAGAC
* * * *
3553514 GTTCGTAAAACATTTGACAACATATTCATCCTTTCCTGTGGCTTTTGCACAGA
1 GTTCGTAAAATATTTGACAACACATTCATTCTTTCCTGTGGCTTCTGCACAGA
3553567 TGTTTGCCAG
Statistics
Matches: 132, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
53 8 0.06
54 117 0.89
55 7 0.05
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (54 bp):
GTTCGTAAAATATTTGACAACACATTCATTCTTTCCTGTGGCTTCTGCACAGAC
Found at i:3553555 original size:108 final size:108
Alignment explanation
Indices: 3553352--3553557 Score: 281
Period size: 108 Copynumber: 1.9 Consensus size: 108
3553342 AGAATAACTG
* * *
3553352 GTTCCTAAAACATTTGACAACACATTCATCATCTCATATGGTTTTTGCTCAGATGCTCGTAAAAT
1 GTTCCTAAAACATTTGACAACACATTCATCATCTCATATGGTTTTTGCACAGACGCTCGTAAAAC
*
3553417 ATTTGACAACACATTCATTCTTTACCGTGGCTTCTGCCCATAT
66 ATTTGACAACACATTCATCCTTTACCGTGGCTTCTGCCCATAT
* * * * * *
3553460 GTTCGTAAATCATTTGACAACACATTCATCATTTCCTGTGGTTTCTT-CACAGACGTTCGTAAAA
1 GTTCCTAAAACATTTGACAACACATTCATCATCTCATATGGTTT-TTGCACAGACGCTCGTAAAA
*
3553524 CATTTGACAACATATTCATCCTTT-CCTGTGGCTT
65 CATTTGACAACACATTCATCCTTTACC-GTGGCTT
3553558 TTGCACAGAT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
107 2 0.02
108 81 0.95
109 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.37
Consensus pattern (108 bp):
GTTCCTAAAACATTTGACAACACATTCATCATCTCATATGGTTTTTGCACAGACGCTCGTAAAAC
ATTTGACAACACATTCATCCTTTACCGTGGCTTCTGCCCATAT
Found at i:3553909 original size:26 final size:26
Alignment explanation
Indices: 3553871--3553930 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
3553861 GCTGTTGTAG
* *
3553871 TGAAACACACATGATAAATAAAATATA
1 TGAAA-ACACATGATAAACAAAATAGA
3553898 TGAAAACACATGATAAACAAAATAGA
1 TGAAAACACATGATAAACAAAATAGA
3553924 TGAAAAC
1 TGAAAAC
3553931 TCAGTTCACC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 26 0.84
27 5 0.16
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.18
Consensus pattern (26 bp):
TGAAAACACATGATAAACAAAATAGA
Found at i:3554720 original size:75 final size:75
Alignment explanation
Indices: 3554455--3554700 Score: 386
Period size: 75 Copynumber: 3.3 Consensus size: 75
3554445 GATGTAGGCC
* * * *
3554455 TTCAGCATGTCCCAACATTTGCTAATA-TGAACGTTCAAAATGCTCCAATATTCCAATTTCTGAT
1 TTCAGCATGCCCCATCATTTGCTAATACAG-ACGTTCAAAATGCGCCAATATTCCAATTTCTGAT
*
3554519 TAAAATGGGCT
65 TGAAATGGGCT
* *
3554530 TTCAGCATGCCCTATCATTTGCTAATACAGACGTTCAAAATGCGCCAATATTCCAATTTTTGATT
1 TTCAGCATGCCCCATCATTTGCTAATACAGACGTTCAAAATGCGCCAATATTCCAATTTCTGATT
3554595 GAAATGGGCT
66 GAAATGGGCT
* *
3554605 TTCAGCATGCCCCAGCATTTGCTAATACAGACGTTCAAAATGCGCCAATATTCCAATTTCTGAAT
1 TTCAGCATGCCCCATCATTTGCTAATACAGACGTTCAAAATGCGCCAATATTCCAATTTCTGATT
3554670 GAAATGGGCT
66 GAAATGGGCT
*
3554680 TTCAGCTTGCCCCATCATTTG
1 TTCAGCATGCCCCATCATTTG
3554701 TTGATGTGAG
Statistics
Matches: 157, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
75 156 0.99
76 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (75 bp):
TTCAGCATGCCCCATCATTTGCTAATACAGACGTTCAAAATGCGCCAATATTCCAATTTCTGATT
GAAATGGGCT
Found at i:3556684 original size:21 final size:21
Alignment explanation
Indices: 3556660--3556705 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
3556650 CTGAGTGCTT
3556660 GTGTGAAGTTGACTATAACAG
1 GTGTGAAGTTGACTATAACAG
3556681 GTGTGAAGTTGACTATAACAG
1 GTGTGAAGTTGACTATAACAG
3556702 GTGT
1 GTGT
3556706 TTCGCAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (21 bp):
GTGTGAAGTTGACTATAACAG
Found at i:3559079 original size:41 final size:41
Alignment explanation
Indices: 3559000--3559080 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 41
3558990 ATTAGTTTGT
* * *
3559000 CATTTGCTCTTTGAATCATCTTGGAAATTTTTGGCTTGATC
1 CATTTGCTCTTTGAATCACCCTGGAAATTTTTGACTTGATC
* *
3559041 CATTTGTTCATTTGAATCACCCTGGAACTTTTT-ACTTGAT
1 CATTTGCTC-TTTGAATCACCCTGGAAATTTTTGACTTGAT
3559081 AAATCATATC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 14 0.41
42 20 0.59
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.46
Consensus pattern (41 bp):
CATTTGCTCTTTGAATCACCCTGGAAATTTTTGACTTGATC
Found at i:3559419 original size:15 final size:16
Alignment explanation
Indices: 3559387--3559419 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3559377 TGTAACATGA
*
3559387 AAATGCAAAAATGTAG
1 AAATGCAAAAATGAAG
3559403 AAATGCAAAAAT-AAG
1 AAATGCAAAAATGAAG
3559418 AA
1 AA
3559420 TGTAAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.64, C:0.06, G:0.15, T:0.15
Consensus pattern (16 bp):
AAATGCAAAAATGAAG
Found at i:3559466 original size:13 final size:14
Alignment explanation
Indices: 3559450--3559479 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3559440 AGCAAACAAC
3559450 AAATGCAAA-ATGA
1 AAATGCAAAGATGA
3559463 AAATGCAAAGATGA
1 AAATGCAAAGATGA
3559477 AAA
1 AAA
3559480 ATACAAATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (14 bp):
AAATGCAAAGATGA
Found at i:3561421 original size:2 final size:2
Alignment explanation
Indices: 3561414--3561439 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3561404 AGAAAATTAA
3561414 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
3561440 TAGGGTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3563198 original size:3 final size:3
Alignment explanation
Indices: 3563192--3563232 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
3563182 TTTTTATTTC
*
3563192 ATA ATA ATA ATA ATA ATA ATA ATAA ATT ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA A
3563233 AAATTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3577035 original size:16 final size:16
Alignment explanation
Indices: 3577014--3577046 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3577004 TAAATAGTAA
3577014 AGTAAAGAGATTAAAT
1 AGTAAAGAGATTAAAT
3577030 AGTAAAGAGATTAAAT
1 AGTAAAGAGATTAAAT
3577046 A
1 A
3577047 AAAGGGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (16 bp):
AGTAAAGAGATTAAAT
Found at i:3578122 original size:20 final size:20
Alignment explanation
Indices: 3578099--3578148 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
3578089 GAAACTTTTG
3578099 ATTTTGAAAATCAAAATGAA
1 ATTTTGAAAATCAAAATGAA
3578119 ATTTTGAAAATCAAAATGAA
1 ATTTTGAAAATCAAAATGAA
3578139 ATTTTGAAAA
1 ATTTTGAAAA
3578149 ATGATTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.32
Consensus pattern (20 bp):
ATTTTGAAAATCAAAATGAA
Found at i:3581029 original size:24 final size:24
Alignment explanation
Indices: 3580997--3581052 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
3580987 GATATTATTT
3580997 GATATTTGGATGGTTTTCATGTTG
1 GATATTTGGATGGTTTTCATGTTG
3581021 GATATTTGGATGGTTTTCATGTTG
1 GATATTTGGATGGTTTTCATGTTG
3581045 GATATTTG
1 GATATTTG
3581053 AACTTATATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.18, C:0.04, G:0.29, T:0.50
Consensus pattern (24 bp):
GATATTTGGATGGTTTTCATGTTG
Found at i:3581608 original size:85 final size:86
Alignment explanation
Indices: 3581507--3581677 Score: 281
Period size: 85 Copynumber: 2.0 Consensus size: 86
3581497 CATACTCAAT
* * *
3581507 CATTTTTCGGGATTTAAAGTCGAGTTTGTAAGAATTTATAGCTCAAAGGACCATTTCTTTAGTAA
1 CATTTTTCGGGATTTAAAGTCGAGTTTGTAAGAATTTATAGCTCAAAAGACCATTCCTTTAGCAA
3581572 AAGAATCGATCCCTTTGACCA
66 AAGAATCGATCCCTTTGACCA
* * *
3581593 CATTTTT-GGGATTTAAAGTCGAGTTTGTAAGAATTTTTGGCTCAAAAGATCATTCCTTTAGCAA
1 CATTTTTCGGGATTTAAAGTCGAGTTTGTAAGAATTTATAGCTCAAAAGACCATTCCTTTAGCAA
3581657 AAGAATCGATCCCTTTGACCA
66 AAGAATCGATCCCTTTGACCA
3581678 AAAGATCGAT
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
85 72 0.91
86 7 0.09
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (86 bp):
CATTTTTCGGGATTTAAAGTCGAGTTTGTAAGAATTTATAGCTCAAAAGACCATTCCTTTAGCAA
AAGAATCGATCCCTTTGACCA
Found at i:3581685 original size:21 final size:20
Alignment explanation
Indices: 3581635--3581712 Score: 79
Period size: 21 Copynumber: 3.9 Consensus size: 20
3581625 ATTTTTGGCT
* *
3581635 CAAAAGATC-ATTCCTTTAG
1 CAAAAGATCGATCCCTTTAC
3581654 CAAAAGAATCGATCCCTTTGAC
1 CAAAAG-ATCGATCCCTTT-AC
3581676 CAAAAGATCGATCCCTTTA-
1 CAAAAGATCGATCCCTTTAC
* *
3581695 GAAAAGGATCAATCCCTT
1 CAAAA-GATCGATCCCTT
3581713 CGATTCCAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
19 10 0.20
20 15 0.29
21 19 0.37
22 7 0.14
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (20 bp):
CAAAAGATCGATCCCTTTAC
Found at i:3581700 original size:41 final size:41
Alignment explanation
Indices: 3581635--3581712 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
3581625 ATTTTTGGCT
* *
3581635 CAAAAGATCATTCCTTTAGCAAAAGAATCGATCCCTTTGAC
1 CAAAAGATCATCCCTTTAGCAAAAGAATCAATCCCTTTGAC
*
3581676 CAAAAGATCGATCCCTTTAG-AAAAGGATCAATCCCTT
1 CAAAAGATC-ATCCCTTTAGCAAAAGAATCAATCCCTT
3581713 CGATTCCAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 24 0.73
42 9 0.27
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (41 bp):
CAAAAGATCATCCCTTTAGCAAAAGAATCAATCCCTTTGAC
Found at i:3587024 original size:49 final size:49
Alignment explanation
Indices: 3586969--3587146 Score: 302
Period size: 49 Copynumber: 3.6 Consensus size: 49
3586959 TTTATGCTGA
*
3586969 AAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACATTTTATGTCG
1 AAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATGTCG
*
3587018 AAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATGTCA
1 AAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATGTCG
* *
3587067 AAATGCACCATTATGCATTTAACTTTCATTAGTGGCACCTTTTATGCCG
1 AAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATGTCG
* *
3587116 AAATCCACAGTTATGCATTTAACTTTCATTA
1 AAATGCACCGTTATGCATTTAACTTTCATTA
3587147 TAGAGCAGTT
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 121 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (49 bp):
AAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATGTCG
Found at i:3587088 original size:98 final size:99
Alignment explanation
Indices: 3586949--3587146 Score: 317
Period size: 98 Copynumber: 2.0 Consensus size: 99
3586939 GAATACCATG
* * *
3586949 AGTGACACTTTTTATGCTGAAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACATTTTAT
1 AGTGACACCTTTTATGCTCAAAATGCACCATTATGCATTTAACTTTCATTAGTGGCACATTTTAT
* * *
3587014 GTCGAAATGCACCGTTATGCATTTAACTTTCATT
66 GCCGAAATCCACAGTTATGCATTTAACTTTCATT
* *
3587048 AGTGGCACCTTTTATG-TCAAAATGCACCATTATGCATTTAACTTTCATTAGTGGCACCTTTTAT
1 AGTGACACCTTTTATGCTCAAAATGCACCATTATGCATTTAACTTTCATTAGTGGCACATTTTAT
3587112 GCCGAAATCCACAGTTATGCATTTAACTTTCATT
66 GCCGAAATCCACAGTTATGCATTTAACTTTCATT
3587146 A
1 A
3587147 TAGAGCAGTT
Statistics
Matches: 91, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
98 77 0.85
99 14 0.15
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (99 bp):
AGTGACACCTTTTATGCTCAAAATGCACCATTATGCATTTAACTTTCATTAGTGGCACATTTTAT
GCCGAAATCCACAGTTATGCATTTAACTTTCATT
Found at i:3595308 original size:19 final size:20
Alignment explanation
Indices: 3595272--3595309 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3595262 TTTTTGTATA
*
3595272 TTTTCCCAATTATCTGTTAT
1 TTTTCCCAATTATATGTTAT
3595292 TTTTCCCAA-TATATGTTA
1 TTTTCCCAATTATATGTTA
3595310 AATAAGAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTCCCAATTATATGTTAT
Found at i:3595458 original size:49 final size:49
Alignment explanation
Indices: 3595385--3595528 Score: 225
Period size: 49 Copynumber: 2.9 Consensus size: 49
3595375 CAATGAGTCA
3595385 CACATTTTATGCCGAAAATGCACCGTTATGCATTTAACTTTCATTAGTGG
1 CACATTTTATGCCG-AAATGCACCGTTATGCATTTAACTTTCATTAGTGG
* *
3595435 CACATTTTATACTGAAATGCACCGTTATGCATTTAACTTTCATTAGTGG
1 CACATTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGG
* * * *
3595484 CACCTTTTATGCCAAAATGCATCGTTATTCATTTAACTTTCATTA
1 CACATTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
3595529 TAGAGCAGTT
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 74 0.86
50 12 0.14
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.39
Consensus pattern (49 bp):
CACATTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGG
Found at i:3601189 original size:8 final size:8
Alignment explanation
Indices: 3601176--3601222 Score: 94
Period size: 8 Copynumber: 5.9 Consensus size: 8
3601166 ACCAATTAGT
3601176 AAGAATGG
1 AAGAATGG
3601184 AAGAATGG
1 AAGAATGG
3601192 AAGAATGG
1 AAGAATGG
3601200 AAGAATGG
1 AAGAATGG
3601208 AAGAATGG
1 AAGAATGG
3601216 AAGAATG
1 AAGAATG
3601223 AAAGGGTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.36, T:0.13
Consensus pattern (8 bp):
AAGAATGG
Found at i:3601928 original size:19 final size:19
Alignment explanation
Indices: 3601906--3601946 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3601896 ATGGTATCGA
*
3601906 TACTGAAAGGGAGTATCAG
1 TACTGAAAAGGAGTATCAG
*
3601925 TACTGAAAAGGAGTATCGG
1 TACTGAAAAGGAGTATCAG
3601944 TAC
1 TAC
3601947 CATAGTATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.29, T:0.22
Consensus pattern (19 bp):
TACTGAAAAGGAGTATCAG
Found at i:3602456 original size:49 final size:48
Alignment explanation
Indices: 3602384--3602658 Score: 329
Period size: 49 Copynumber: 5.6 Consensus size: 48
3602374 AACTATTCTA
* *
3602384 TAATGAAAGTTAAATGCATAACGGTGCATTTTCGCATAAAAAGTGCCAC
1 TAATGAAAGTTAAATGCATAACAGTGCA-TTTCGCATAAAAGGTGCCAC
* * * *
3602433 TAATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAAGTTCAAC
1 TAATGAAAGTTAAATGCATAACAGTGCATTTC-GCATAAAAGGTGCCAC
* * *
3602482 TAATGAAAGTTAAATGTATAACAGTTCATTTTGACATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACAGTGCATTTCG-CATAAAAGGTGCCAC
* ** *
3602531 AAATGAAAGTTAAATGCATAAC-GACACATTTCGACATAAAAGGTGCCAT
1 TAATGAAAGTTAAATGCATAACAG-TGCATTTCG-CATAAAAGGTGCCAC
* *
3602580 TAATGAAAGTTAAATGCGTAACAGTGTATTTCGGCAT-AAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACAGTGCATTTC-GCATAAAAGGTGCCAC
* *
3602628 TAATGAAACTTAAATGCATAATAGTGCATTT
1 TAATGAAAGTTAAATGCATAACAGTGCATTT
3602659 TTAGTATAAA
Statistics
Matches: 196, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
48 43 0.22
49 151 0.77
50 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (48 bp):
TAATGAAAGTTAAATGCATAACAGTGCATTTCGCATAAAAGGTGCCAC
Found at i:3602676 original size:147 final size:147
Alignment explanation
Indices: 3602385--3602659 Score: 383
Period size: 147 Copynumber: 1.9 Consensus size: 147
3602375 ACTATTCTAT
***
3602385 AATGAAAGTTAAATGCATAACGGTGCATTTTCGCATAAAAAGTGCCACTAATGAAAGTTAAATGC
1 AATGAAAGTTAAATGCATAACGACACATTTTCGCATAAAAAGTGCCACTAATGAAAGTTAAATGC
* * * * *
3602450 ATAACGGTGCATTTCAGCATAAAAAGTTCAACTAATGAAAGTTAAATGTATAACAGTTCATTTTG
66 ATAACAGTGCATTTCAGCATAAAAAGTGCAACTAATGAAACTTAAATGCATAACAGTGCATTTTG
3602515 ACATAAAAGGTGCCACA
131 ACATAAAAGGTGCCACA
* *
3602532 AATGAAAGTTAAATGCATAACGACACA-TTTCGACATAAAAGGTGCCATTAATGAAAGTTAAATG
1 AATGAAAGTTAAATGCATAACGACACATTTTCG-CATAAAAAGTGCCACTAATGAAAGTTAAATG
* * * * * *
3602596 CGTAACAGTGTATTTCGGCAT-AAAGGTGCCACTAATGAAACTTAAATGCATAATAGTGCATTTT
65 CATAACAGTGCATTTCAGCATAAAAAGTGCAACTAATGAAACTTAAATGCATAACAGTGCATTTT
3602660 TAGTATAAAA
Statistics
Matches: 111, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
146 41 0.37
147 70 0.63
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (147 bp):
AATGAAAGTTAAATGCATAACGACACATTTTCGCATAAAAAGTGCCACTAATGAAAGTTAAATGC
ATAACAGTGCATTTCAGCATAAAAAGTGCAACTAATGAAACTTAAATGCATAACAGTGCATTTTG
ACATAAAAGGTGCCACA
Found at i:3609120 original size:49 final size:49
Alignment explanation
Indices: 3609043--3609386 Score: 476
Period size: 49 Copynumber: 7.0 Consensus size: 49
3609033 AATTGCTCTA
*
3609043 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGATGCATTTCGGCATAAAAGGTGCCAC
* *
3609092 TAATGAAAGTTAAACGCATAACGATGCATTTAGGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGATGCATTTCGGCATAAAAGGTGCCAC
*
3609141 TAATGAAAGTTAAATGCATAACGATGCATTTCAGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGATGCATTTCGGCATAAAAGGTGCCAC
* ** * *
3609190 TAATGAAAGTTAAATGCATAACAATG-AGTTTCAACATAAACGGTACCAC
1 TAATGAAAGTTAAATGCATAACGATGCA-TTTCGGCATAAAAGGTGCCAC
* * *
3609239 AAATGAAAGTTAAGTGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGATGCATTTCGGCATAAAAGGTGCCAC
* *
3609288 TAATGAAACTTAAATGCATAACGGTGCATTTCGGCAT-AAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGATGCATTTCGGCATAAAAGGTGCCAC
** *** *
3609336 TAATGAAAGTTAAATTTATAACGACATATTTTCAGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGATGCA-TTTCGGCATAAAAGGTGCCAC
3609386 T
1 T
3609387 CATGGTATTC
Statistics
Matches: 262, Mismatches: 29, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
48 33 0.13
49 216 0.82
50 13 0.05
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (49 bp):
TAATGAAAGTTAAATGCATAACGATGCATTTCGGCATAAAAGGTGCCAC
Found at i:3613116 original size:22 final size:22
Alignment explanation
Indices: 3613088--3613138 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
3613078 ACTGAAGTAT
3613088 AGTATCGATACCATAGTGAGGA
1 AGTATCGATACCATAGTGAGGA
* *
3613110 AGTATCGGTACCATATTGAGGA
1 AGTATCGATACCATAGTGAGGA
*
3613132 AATATCG
1 AGTATCG
3613139 GGTACTGGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (22 bp):
AGTATCGATACCATAGTGAGGA
Found at i:3613649 original size:45 final size:45
Alignment explanation
Indices: 3613529--3613637 Score: 110
Period size: 45 Copynumber: 2.4 Consensus size: 45
3613519 ATTGTTTTAC
* * * * * **
3613529 ATGATCTATGTGATTACATGAAAAGGTGATATAAACTATGTGGTA
1 ATGACCTATGTGACTATATGAATATGTGATATAAACTATGTGACA
* ** *
3613574 TTGGTCTATGTGACTATATGAATATATGATATAAACTATGTGACA
1 ATGACCTATGTGACTATATGAATATGTGATATAAACTATGTGACA
*
3613619 ATGACCTATGTGATTATAT
1 ATGACCTATGTGACTATAT
3613638 ATCTATGTGA
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (45 bp):
ATGACCTATGTGACTATATGAATATGTGATATAAACTATGTGACA
Found at i:3614943 original size:44 final size:44
Alignment explanation
Indices: 3614893--3614979 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
3614883 TCATTTCATC
*
3614893 ACGGAAGTGCCATA-GCACTAATACTAAAATGCCTCAGCACTGAT
1 ACGGAAGTG-CATATGCACTAATACTAAAATGACTCAGCACTGAT
* *
3614937 ACGGAAGTGCATATGCACTGATACTAAAATGACTTAGCACTGA
1 ACGGAAGTGCATATGCACTAATACTAAAATGACTCAGCACTGA
3614980 GAGAGAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
43 4 0.10
44 35 0.90
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (44 bp):
ACGGAAGTGCATATGCACTAATACTAAAATGACTCAGCACTGAT
Found at i:3614976 original size:22 final size:21
Alignment explanation
Indices: 3614905--3614979 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 21
3614895 GGAAGTGCCA
*
3614905 TAGCACTAATACTAAAATGCCT
1 TAGCACTGATACTAAAATG-CT
* ** * *
3614927 CAGCACTGATACGGAAGTGCA
1 TAGCACTGATACTAAAATGCT
3614948 TATGCACTGATACTAAAATGACT
1 TA-GCACTGATACTAAAATG-CT
3614971 TAGCACTGA
1 TAGCACTGA
3614980 GAGAGAAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
21 2 0.05
22 35 0.88
23 3 0.08
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.24
Consensus pattern (21 bp):
TAGCACTGATACTAAAATGCT
Found at i:3621945 original size:22 final size:22
Alignment explanation
Indices: 3621910--3621952 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3621900 GTTCATCACA
*
3621910 AAAGTGCCTTAGCACTAATACT
1 AAAGTGCCTCAGCACTAATACT
* *
3621932 AAAGTTCCTCAGCACTGATAC
1 AAAGTGCCTCAGCACTAATAC
3621953 GGAAGTGCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.26
Consensus pattern (22 bp):
AAAGTGCCTCAGCACTAATACT
Found at i:3622943 original size:13 final size:14
Alignment explanation
Indices: 3622924--3622971 Score: 62
Period size: 13 Copynumber: 3.4 Consensus size: 14
3622914 GAAGACTTGG
3622924 AGAAGAAGAAA-AA
1 AGAAGAAGAAATAA
*
3622937 GGAAGAAGAAATAA
1 AGAAGAAGAAATAA
*
3622951 AGAAGAATAAGATAA
1 AGAAGAAGAA-ATAA
3622966 AGAAGA
1 AGAAGA
3622972 CCTTCCCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 10 0.33
14 10 0.33
15 10 0.33
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (14 bp):
AGAAGAAGAAATAA
Found at i:3625214 original size:90 final size:90
Alignment explanation
Indices: 3625101--3625277 Score: 282
Period size: 90 Copynumber: 2.0 Consensus size: 90
3625091 TAATCCCGAA
* * * * *
3625101 TATTTAATTTCAATTAATTAAATATATATTTAATTAATTTGAAATAACAAAATCCCTGATATGAT
1 TATTTAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAACAAAAACCCTAATATGAC
3625166 TAGGGTAACTTGGATATAAAAGAAT
66 TAGGGTAACTTGGATATAAAAGAAT
*
3625191 TATTTAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTTAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAACAAAAACCCTAATATGAC
**
3625256 TAGGGTAACTTGTCTATAAAAG
66 TAGGGTAACTTGGATATAAAAG
3625278 GGTGTGTTAG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.38
Consensus pattern (90 bp):
TATTTAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAACAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGAAT
Found at i:3626897 original size:30 final size:30
Alignment explanation
Indices: 3626861--3626927 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
3626851 TAAAGTTTGG
3626861 AAAAGTTTATAGACTAAAAAG-GTAATTTTC
1 AAAAGTTTATAGAC-AAAAAGTGTAATTTTC
* *
3626891 AAAAGTTTATGGACCAAAAGTGTAATTTTC
1 AAAAGTTTATAGACAAAAAGTGTAATTTTC
3626921 AAAAGTT
1 AAAAGTT
3626928 ATGTATTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 5 0.15
30 29 0.85
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (30 bp):
AAAAGTTTATAGACAAAAAGTGTAATTTTC
Found at i:3636404 original size:23 final size:24
Alignment explanation
Indices: 3636356--3636411 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
3636346 ATAAGTCTTT
3636356 AATATATATTTAATTTGAATTAATTA
1 AATA-ATATTTAATTT-AATTAATTA
*
3636382 AATAATATTTTATTT-ATTAATTA
1 AATAATATTTAATTTAATTAATTA
*
3636405 AAAAATA
1 AATAATA
3636412 ACTTTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 14 0.50
25 10 0.36
26 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
AATAATATTTAATTTAATTAATTA
Found at i:3644157 original size:30 final size:30
Alignment explanation
Indices: 3644106--3644186 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 30
3644096 GTCTAGTGTG
*
3644106 AAAAGTATAAAGTTTTGAAAAGTTTATAGG-CC
1 AAAAGTAT-AA-TTTTCAAAAGTTTA-AGGACC
* *
3644138 AAAAAG-GTAATTTTCAAAAGTTTAGGGACC
1 -AAAAGTATAATTTTCAAAAGTTTAAGGACC
3644168 AAAAGTATAATTTTCAAAA
1 AAAAGTATAATTTTCAAAA
3644187 CTTATTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 7 0.17
30 27 0.64
31 2 0.05
32 1 0.02
33 5 0.12
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (30 bp):
AAAAGTATAATTTTCAAAAGTTTAAGGACC
Found at i:3651878 original size:29 final size:28
Alignment explanation
Indices: 3651845--3651929 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 28
3651835 TAAAATTTAT
* *
3651845 AACTTTTCAAAATTATATTTTGGTCCCTA
1 AACTTTTCAAAATTATATTTTAGT-CATA
* *
3651874 AACTTTTCAAAGTTTATACTTTAGTCATA
1 AACTTTTCAAA-ATTATATTTTAGTCATA
*
3651903 AAATTTTCAAAACTTATATTTTAGTCA
1 AACTTTTCAAAA-TTATATTTTAGTCA
3651930 ATAGTAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 37 0.79
30 10 0.21
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (28 bp):
AACTTTTCAAAATTATATTTTAGTCATA
Found at i:3673917 original size:12 final size:13
Alignment explanation
Indices: 3673892--3673919 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3673882 TCAAAACAAT
3673892 AAGAATTAAAAAA
1 AAGAATTAAAAAA
3673905 AAGAATTAAAAAA
1 AAGAATTAAAAAA
3673918 AA
1 AA
3673920 TTAACTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (13 bp):
AAGAATTAAAAAA
Found at i:3675773 original size:16 final size:16
Alignment explanation
Indices: 3675752--3675788 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3675742 ATGACACAAT
*
3675752 TAATAAAATGAATAAC
1 TAATAAAATAAATAAC
*
3675768 TAATAAAATAAATAAT
1 TAATAAAATAAATAAC
3675784 TAATA
1 TAATA
3675789 GAAAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (16 bp):
TAATAAAATAAATAAC
Found at i:3681932 original size:20 final size:20
Alignment explanation
Indices: 3681909--3681951 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3681899 ATTCTACCAC
*
3681909 ATGCAACTATATGCTCCTAA
1 ATGCAACTACATGCTCCTAA
* *
3681929 ATGCATCTACATGGTCCTAA
1 ATGCAACTACATGCTCCTAA
3681949 ATG
1 ATG
3681952 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTACATGCTCCTAA
Found at i:3682303 original size:30 final size:29
Alignment explanation
Indices: 3682242--3682299 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
3682232 TTTGTATTTC
*
3682242 ATTGGTTCGATTAACTCAACATATTTTTT
1 ATTGGTTCGATCAACTCAACATATTTTTT
*
3682271 ATTGGTTTGATCAACTCAACATATTTTTT
1 ATTGGTTCGATCAACTCAACATATTTTTT
3682300 TATTAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (29 bp):
ATTGGTTCGATCAACTCAACATATTTTTT
Done.