Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008752.1 Hibiscus syriacus cultivar Beakdansim tig00111843_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: 1143363
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:401158 original size:30 final size:26
Alignment explanation
Indices: 401078--401141 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
401068 GCATGGTTGG
*
401078 AGGTCGCCATGCAATCTAACCAAGCA
1 AGGTCGCCATGTAATCTAACCAAGCA
401104 AGGTCGCCATGTAATCTAACCAAGCA
1 AGGTCGCCATGTAATCTAACCAAGCA
401130 AGGTCGCCATGT
1 AGGTCGCCATGT
401142 GATTGCTGCG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (26 bp):
AGGTCGCCATGTAATCTAACCAAGCA
Found at i:403413 original size:19 final size:19
Alignment explanation
Indices: 403389--403426 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
403379 AAGCCATTAG
403389 GCCCTGGTGCCTTATCCTT
1 GCCCTGGTGCCTTATCCTT
*
403408 GCCCTGGTGTCTTATCCTT
1 GCCCTGGTGCCTTATCCTT
403427 ATCCTCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.34, G:0.21, T:0.39
Consensus pattern (19 bp):
GCCCTGGTGCCTTATCCTT
Found at i:404865 original size:60 final size:59
Alignment explanation
Indices: 404763--404887 Score: 187
Period size: 60 Copynumber: 2.1 Consensus size: 59
404753 AAATCCATGA
* * * *
404763 ATAAAAACTATGTGAATGATAAGGAGTTAATGCTCAACTATGTTACTAGGTAAGCCAAG
1 ATAAAAACCATGTGAATGATAAAGAGCTAAGGCTCAACTATGTTACTAGGTAAGCCAAG
* *
404822 ATAAGAAACCATGTGAATGATAAAGAGCTAAGGCTCAACTATGTTACTTGGTACGCCAAG
1 ATAA-AAACCATGTGAATGATAAAGAGCTAAGGCTCAACTATGTTACTAGGTAAGCCAAG
404882 ATAAAA
1 ATAAAA
404888 TTCGTATGTG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 6 0.10
60 53 0.90
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.25
Consensus pattern (59 bp):
ATAAAAACCATGTGAATGATAAAGAGCTAAGGCTCAACTATGTTACTAGGTAAGCCAAG
Found at i:406331 original size:76 final size:75
Alignment explanation
Indices: 406181--406379 Score: 285
Period size: 75 Copynumber: 2.6 Consensus size: 75
406171 AGAAACATAT
* *
406181 TTTTAGGTTGCAACCTAATTTATCATATAGAAACCTGAATTTCTAGGTTACAACCTGATTATCAT
1 TTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGAATTTCTAGGTCACAACCTGATTATCAT
*
406246 AAAACCTGAAA
66 AAAAACTG-AA
* *
406257 TTTTAGGTTGCAACCTGATTTATCATATAGAAACTTGAATTTCTAGG-CGCAACCTGATTATCAT
1 TTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGAATTTCTAGGTCACAACCTGATTATCAT
406321 ATAAAACTGAA
66 A-AAAACTGAA
* * *
406332 TTCTAGGTTGCAACCTGATTTATCATATGGAAACCCGAACTTT-TAGGT
1 TTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGAA-TTTCTAGGT
406380 TGCAGTCTGA
Statistics
Matches: 111, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
75 57 0.51
76 54 0.49
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (75 bp):
TTTTAGGTTGCAACCTGATTTATCATATAGAAACCTGAATTTCTAGGTCACAACCTGATTATCAT
AAAAACTGAA
Found at i:406378 original size:115 final size:112
Alignment explanation
Indices: 406181--406432 Score: 303
Period size: 115 Copynumber: 2.2 Consensus size: 112
406171 AGAAACATAT
*
406181 TTTTAGGTTGCAACCTAATTTATCATATAGAAACCTGAATTTCTAGGTTACAACCTGATTATCAT
1 TTTTAGG-CGCAACCTAA-TTATCATATAGAAACCTGAATTTCTAGGTTACAACCTGATTATCAT
* * *
406246 AAAACCTGAAATTTTAGGTTGCAACCTGATTTATCATATAGAAACTTGAA
64 AAAACCCGAAATTTTAGGTTGCAACCTGATTGATCATATAGAAACCTG-A
* *
406296 TTTCTAGGCGCAACCTGATTATCATATA-AAA-CTGAA-TTCTAGGTTGCAACCTGATTTATCAT
1 TTT-TAGGCGCAACCTAATTATCATATAGAAACCTGAATTTCTAGGTTACAACCTGA-TTATCAT
* ** *
406358 ATGGAAACCCGAACTTTTAGGTTGCAGTCTGATTGATCATGTAGAAACCTGA
64 A---AAACCCGAAATTTTAGGTTGCAACCTGATTGATCATATAGAAACCTGA
**
406410 TTTTAGTTGCAACCTAATTATCA
1 TTTTAGGCGCAACCTAATTATCA
406433 CATTGTAACT
Statistics
Matches: 119, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
111 17 0.14
112 13 0.11
113 20 0.17
114 14 0.12
115 51 0.43
116 4 0.03
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (112 bp):
TTTTAGGCGCAACCTAATTATCATATAGAAACCTGAATTTCTAGGTTACAACCTGATTATCATAA
AACCCGAAATTTTAGGTTGCAACCTGATTGATCATATAGAAACCTGA
Found at i:406505 original size:115 final size:114
Alignment explanation
Indices: 406190--406506 Score: 292
Period size: 115 Copynumber: 2.8 Consensus size: 114
406180 TTTTTAGGTT
* * *
406190 GCAACCTAATTTATCATATAGAAACCTGAATTTCTAGGTTACAACCTGA-TTAT-CATA-AAACC
1 GCAACCTAA-TTATCACATA-AAA-CTGAA-TTCTAGGTTGCAACCTGATTTATATATAGAAACC
* * *
406252 TGAAATTTTAGGTTGCAACCTGATTTATCATATAGAAACTTGAATTTCTAGGC
62 CGAAATTTTAGGTTGCAACCTGATTGATCATATAGAAACCTGAATTTCTAGGC
* * *
406305 GCAACCTGATTATCATATAAAACTGAATTCTAGGTTGCAACCTGATTTATCATATGGAAACCCGA
1 GCAACCTAATTATCACATAAAACTGAATTCTAGGTTGCAACCTGATTTAT-ATATAGAAACCCGA
* ** * **
406370 ACTTTTAGGTTGCAGTCTGATTGATCATGTAGAAACCTG-ATTT-TAGTT
65 AATTTTAGGTTGCAACCTGATTGATCATATAGAAACCTGAATTTCTAGGC
** * *
406418 GCAACCTAATTATCACATTGTAACTTGATTTCTTTTCA-GTTGCAACCTTATTT-TATTATAGAA
1 GCAACCTAATTATCACA-TAAAAC-TGAATTC---T-AGGTTGCAACCTGATTTATA-TATAGAA
406481 A-CC-AAATTTTAGGTTGCAACCTGATT
59 ACCCGAAATTTTAGGTTGCAACCTGATT
406507 TTTCATATGG
Statistics
Matches: 168, Mismatches: 23, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
111 17 0.10
112 9 0.05
113 21 0.12
114 20 0.12
115 74 0.44
116 3 0.02
117 8 0.05
118 15 0.09
119 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (114 bp):
GCAACCTAATTATCACATAAAACTGAATTCTAGGTTGCAACCTGATTTATATATAGAAACCCGAA
ATTTTAGGTTGCAACCTGATTGATCATATAGAAACCTGAATTTCTAGGC
Found at i:410314 original size:12 final size:12
Alignment explanation
Indices: 410297--410365 Score: 81
Period size: 12 Copynumber: 5.9 Consensus size: 12
410287 GTATATTTTC
410297 TCTGATTTCTGT
1 TCTGATTTCTGT
410309 TCTGATTTC--T
1 TCTGATTTCTGT
*
410319 TCTGATTTCTAT
1 TCTGATTTCTGT
* *
410331 TCTAATTTCTGC
1 TCTGATTTCTGT
410343 TCTGATTTCTGCT
1 TCTGATTTCTG-T
410356 T-TGATTTCTG
1 TCTGATTTCTG
410366 ATATCTCCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
10 10 0.20
12 38 0.78
13 1 0.02
ACGTcount: A:0.12, C:0.19, G:0.13, T:0.57
Consensus pattern (12 bp):
TCTGATTTCTGT
Found at i:410322 original size:22 final size:22
Alignment explanation
Indices: 410293--410364 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 22
410283 ACATGTATAT
410293 TTTC-TCTGATTTCTGTTCTGA
1 TTTCTTCTGATTTCTGTTCTGA
* *
410314 TTTCTTCTGATTTCTATTCTAA
1 TTTCTTCTGATTTCTGTTCTGA
410336 TTTCTGCTCTGATTTCTGCTT-TGA
1 TTTCT--TCTGATTTCTG-TTCTGA
410360 TTTCT
1 TTTCT
410365 GATATCTCCG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
21 4 0.09
22 20 0.47
24 17 0.40
25 2 0.05
ACGTcount: A:0.11, C:0.19, G:0.11, T:0.58
Consensus pattern (22 bp):
TTTCTTCTGATTTCTGTTCTGA
Found at i:410542 original size:31 final size:31
Alignment explanation
Indices: 410504--410591 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 31
410494 TAAGGCGACC
** * *
410504 CTTGGGTAGGCTCTAG-GGCCCTGAGATTTTT
1 CTTGGGTAGGCTCT-GTGGCCCCAAGAATTGT
*
410535 CTTGGGTAAGCCTCTGTGGCCCCAAGAATTGT
1 CTTGGGT-AGGCTCTGTGGCCCCAAGAATTGT
**
410567 CTTGGGTAGGCTCTCAGGCCCCAAG
1 CTTGGGTAGGCTCTGTGGCCCCAAG
410592 GTAATCCTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
31 23 0.49
32 24 0.51
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.28
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGTGGCCCCAAGAATTGT
Found at i:414148 original size:12 final size:12
Alignment explanation
Indices: 414128--414187 Score: 93
Period size: 12 Copynumber: 5.0 Consensus size: 12
414118 TGGATATTTT
414128 CTCTGATTTCTG
1 CTCTGATTTCTG
* *
414140 TTTTGATTTCTG
1 CTCTGATTTCTG
414152 CTCTGATTTCTG
1 CTCTGATTTCTG
*
414164 TTCTGATTTCTG
1 CTCTGATTTCTG
414176 CTCTGATTTCTG
1 CTCTGATTTCTG
414188 ATATCCCCAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.08, C:0.20, G:0.17, T:0.55
Consensus pattern (12 bp):
CTCTGATTTCTG
Found at i:414156 original size:24 final size:24
Alignment explanation
Indices: 414128--414187 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
414118 TGGATATTTT
*
414128 CTCTGATTTCTGTTTTGATTTCTG
1 CTCTGATTTCTGTTCTGATTTCTG
414152 CTCTGATTTCTGTTCTGATTTCTG
1 CTCTGATTTCTGTTCTGATTTCTG
414176 CTCTGATTTCTG
1 CTCTGATTTCTG
414188 ATATCCCCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.08, C:0.20, G:0.17, T:0.55
Consensus pattern (24 bp):
CTCTGATTTCTGTTCTGATTTCTG
Found at i:414832 original size:12 final size:12
Alignment explanation
Indices: 414815--414869 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
414805 GATATTTTCA
414815 CTGATTTCTGTT
1 CTGATTTCTGTT
*
414827 CTGATTTCTGCT
1 CTGATTTCTGTT
*
414839 ATGATTTCTGTT
1 CTGATTTCTGTT
* **
414851 CTCATTTCTAAT
1 CTGATTTCTGTT
414863 CTGATTT
1 CTGATTT
414870 TCGATATCTC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.15, C:0.18, G:0.13, T:0.55
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:414867 original size:24 final size:24
Alignment explanation
Indices: 414815--414869 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
414805 GATATTTTCA
* **
414815 CTGATTTCTGTTCTGATTTCTGCT
1 CTGATTTCTGTTCTCATTTCTAAT
*
414839 ATGATTTCTGTTCTCATTTCTAAT
1 CTGATTTCTGTTCTCATTTCTAAT
414863 CTGATTT
1 CTGATTT
414870 TCGATATCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.15, C:0.18, G:0.13, T:0.55
Consensus pattern (24 bp):
CTGATTTCTGTTCTCATTTCTAAT
Found at i:416988 original size:33 final size:34
Alignment explanation
Indices: 416938--417033 Score: 126
Period size: 34 Copynumber: 2.8 Consensus size: 34
416928 ATATATATAT
**
416938 ATATATATAATAGTTTTTGAAAATGTTTTAAAAAC-
1 ATATA-ATAATAGTTTTTGAAAACATTTT-AAAACG
416973 ATATAATAATA-TTTTTGAAAACATTTTAAAACG
1 ATATAATAATAGTTTTTGAAAACATTTTAAAACG
417006 TATATAAT-ATAGTTTTTGAAAACATTTT
1 -ATATAATAATAGTTTTTGAAAACATTTT
417034 GAAATATATT
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
32 5 0.09
33 17 0.30
34 29 0.52
35 5 0.09
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (34 bp):
ATATAATAATAGTTTTTGAAAACATTTTAAAACG
Found at i:417061 original size:38 final size:37
Alignment explanation
Indices: 416932--417209 Score: 169
Period size: 38 Copynumber: 7.7 Consensus size: 37
416922 AAATATATAT
**
416932 ATATATATATATATAATAGTTTTTGAAAATGTTTT-AAA
1 ATATATATATATAT-ATAG-TTTTGAAAACATTTTGAAA
* *
416970 A-ACATATA-ATA-ATATTTTTGAAAACATTTT--AA
1 ATATATATATATATATAGTTTTGAAAACATTTTGAAA
**
417002 A-ACGTATATA-ATATAGTTTTTGAAAACATTTTGAAA
1 ATATATATATATATATAG-TTTTGAAAACATTTTGAAA
* *
417038 TATATTTATATATATATAGTTTTGAAAACAATTTG-AA
1 -ATATATATATATATATAGTTTTGAAAACATTTTGAAA
* * ** *
417075 A-ATATATATA-GT-T--TTTAGAAATGATTTTTGAAT
1 ATATATATATATATATAGTTTTGAAAACA-TTTTGAAA
* *
417108 ATATATATA-CTATAT-GATTTTGAAAATGATTTTTGAAA
1 ATATATATATATATATAG-TTTTGAAAA-CA-TTTTGAAA
* *
417146 ATATATATAT-TATATGGTTTTGAAAACAATTTTTAAA
1 ATATATATATATATATAGTTTTGAAAAC-ATTTTGAAA
* *
417183 A-ACATATATAATATATAGTTTTAAAAA
1 ATATATATAT-ATATATAGTTTTGAAAA
417210 TGATATTTTT
Statistics
Matches: 193, Mismatches: 26, Indels: 42
0.74 0.10 0.16
Matches are distributed among these distances:
31 8 0.04
32 14 0.07
33 20 0.10
34 27 0.14
35 9 0.05
36 13 0.07
37 24 0.12
38 71 0.37
39 7 0.04
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (37 bp):
ATATATATATATATATAGTTTTGAAAACATTTTGAAA
Found at i:417082 original size:105 final size:108
Alignment explanation
Indices: 416930--417194 Score: 274
Period size: 105 Copynumber: 2.5 Consensus size: 108
416920 TGAAATATAT
*** *
416930 ATATATATATATATATAATAGTTTTTGAAAATGTTTTAAAAACATATAATAATATTTTTGAAAAC
1 ATATATATATATATAT-ATAG-TTTTGAAAACAATTTAAAAACATAT-ATAAT-TTTTAGAAAAC
* *
416995 A-TTTT-AAAACGTATATAATATA-GTTTTTGAAAA-CA-TTTTGAA
62 ATTTTTGAAAACATATATAATATATGATTTTGAAAATCATTTTTGAA
* * * * **
417037 ATATATTTATATATATATAGTTTTGAAAACAATTTGAAAATATATATAGTTTTTAGAAATGATTT
1 ATATATATATATATATATAGTTTTGAAAACAATTTAAAAACATATATAATTTTTAGAAAACATTT
* * * *
417102 TTGAATATATATATACTATATGATTTTGAAAATGATTTTTGAA
66 TTGAAAACATATATAATATATGATTTTGAAAATCATTTTTGAA
*
417145 A-ATATATATAT-TATATGGTTTTGAAAACAATTTTTAAAAACATATATAAT
1 ATATATATATATATATATAGTTTTGAAAACAA--TTTAAAAACATATATAAT
417195 ATATAGTTTT
Statistics
Matches: 130, Mismatches: 21, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
103 9 0.07
104 8 0.06
105 33 0.25
106 32 0.25
107 25 0.19
108 23 0.18
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (108 bp):
ATATATATATATATATATAGTTTTGAAAACAATTTAAAAACATATATAATTTTTAGAAAACATTT
TTGAAAACATATATAATATATGATTTTGAAAATCATTTTTGAA
Found at i:417129 original size:68 final size:69
Alignment explanation
Indices: 416940--417154 Score: 173
Period size: 68 Copynumber: 3.1 Consensus size: 69
416930 ATATATATAT
** * * *
416940 ATATATAATAGTTTTTGAAAATGTTTT-AAAAACA-TATA-ATA-ATATTTTTGAAAA-CAT-TT
1 ATATAT-ATAGTTTTTGAAAACATTTTGAAATATATTATATATATATAGTTTTGAAAATCATATT
*
416999 TAAAA
65 TGAAA
417004 CGTATATAATATAGTTTTTGAAAACATTTTGAAATATATTTATATATATATAGTTTTGAAAA-CA
1 ---ATAT-ATATAGTTTTTGAAAACATTTTGAAATATA-TTATATATATATAGTTTTGAAAATCA
417068 -ATTTGAAA
61 TATTTGAAA
** *
417076 ATATATATAGTTTTTAGAAATGATTTTTG-AATATA-TATATACTATAT-GATTTTGAAAATGAT
1 ATATATATAGTTTTT-GAAAACA-TTTTGAAATATATTATATA-TATATAG-TTTTGAAAATCAT
*
417138 TTTTGAAA
62 ATTTGAAA
417146 ATATATATA
1 ATATATATA
417155 TTATATGGTT
Statistics
Matches: 125, Mismatches: 10, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
67 29 0.23
68 32 0.26
69 16 0.13
70 25 0.20
71 3 0.02
72 20 0.16
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (69 bp):
ATATATATAGTTTTTGAAAACATTTTGAAATATATTATATATATATAGTTTTGAAAATCATATTT
GAAA
Found at i:417230 original size:15 final size:14
Alignment explanation
Indices: 417212--417282 Score: 65
Period size: 14 Copynumber: 5.0 Consensus size: 14
417202 TTTAAAAATG
417212 ATATTTTTATATATT
1 ATATTTTTAT-TATT
**
417227 ATATTAATATTATT
1 ATATTTTTATTATT
417241 -TATTTTTATTTATT
1 ATATTTTTA-TTATT
* *
417255 TTATTTTTATTTTT
1 ATATTTTTATTATT
417269 AT-TTATTTATTATT
1 ATATT-TTTATTATT
417283 TTTATTTATT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
13 8 0.17
14 22 0.48
15 16 0.35
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
ATATTTTTATTATT
Found at i:417245 original size:4 final size:4
Alignment explanation
Indices: 417217--417297 Score: 60
Period size: 4 Copynumber: 19.8 Consensus size: 4
417207 AAATGATATT
* * *
417217 TTTA TATA TTATA TTAA TATTA TTTA -TT- TTTA TTTA TTTTA TTT- TTATT
1 TTTA TTTA TT-TA TTTA T-TTA TTTA TTTA TTTA TTTA -TTTA TTTA TT-TA
*
417266 TTTA TTTA TTTA TTATT TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTT
417298 TCGTTTCAGG
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
3 6 0.10
4 40 0.65
5 16 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:417254 original size:28 final size:26
Alignment explanation
Indices: 417213--417298 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 26
417203 TTAAAAATGA
*
417213 TATTTTTATATATTATATTAATATTATT
1 TATTTTTATTTATTATATT-AT-TTATT
*
417241 TATTTTTATTTATTTTATT-TTTATT
1 TATTTTTATTTATTATATTATTTATT
*
417266 T-TTATTTATTTATTATTTTTATTTATT
1 TATT-TTTATTTATTA-TATTATTTATT
417293 TATTTT
1 TATTTT
417299 CGTTTCAGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
24 2 0.04
25 16 0.32
26 4 0.08
27 9 0.18
28 19 0.38
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (26 bp):
TATTTTTATTTATTATATTATTTATT
Found at i:417269 original size:17 final size:16
Alignment explanation
Indices: 417213--417293 Score: 92
Period size: 17 Copynumber: 4.9 Consensus size: 16
417203 TTAAAAATGA
*
417213 TATTTTTATATATTATAT
1 TATTTTTATTTATT-T-T
* *
417231 TAATATTATTTATTTT
1 TATTTTTATTTATTTT
*
417247 TATTTAT-TTTATTTT
1 TATTTTTATTTATTTT
417262 TATTTTTATTTATTTAT
1 TATTTTTATTTATTT-T
417279 TATTTTTATTTATTT
1 TATTTTTATTTATTT
417294 ATTTTCGTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
15 14 0.26
16 12 0.22
17 17 0.31
18 11 0.20
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTTATTTATTTT
Found at i:418615 original size:36 final size:34
Alignment explanation
Indices: 418552--418627 Score: 89
Period size: 36 Copynumber: 2.2 Consensus size: 34
418542 ATTAATATTC
418552 TTATTTTATTTATTCTTTACTTATTTATCTATTTAT
1 TTATTTTATTTATTCTTTACTTATTTA--TATTTAT
* * * *
418588 TTATTTTATTTTTTTTTTCCTTTTTTATATTTAT
1 TTATTTTATTTATTCTTTACTTATTTATATTTAT
*
418622 ATATTT
1 TTATTT
418628 CACCATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 12 0.34
36 23 0.66
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.74
Consensus pattern (34 bp):
TTATTTTATTTATTCTTTACTTATTTATATTTAT
Found at i:423920 original size:85 final size:85
Alignment explanation
Indices: 423772--424319 Score: 778
Period size: 85 Copynumber: 6.5 Consensus size: 85
423762 CATAACTCAA
* * *
423772 CTATCTGTCAACAAAAACCTTCAAGTTCGATTATATTCAGCTTAAGGGCATATCAAATTTACAGC
1 CTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGC
*
423837 ATAGCTCAAGGCGAGAAGGA
66 ATAGCTCAAGGCGAGAAGGG
* *
423857 CTAACTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATATACAGC
1 CTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGC
423922 ATAGCTCAAGGCGAGAAGGG
66 ATAGCTCAAGGCGAGAAGGG
* * *
423942 TTATCTGTCAACAAAAACCTTCGAGTTCGATTATATTCAGCTCAATGGCATATCAAATTTACAGC
1 CTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGC
*
424007 ATAGCTTAAGGCGAGAAGGG
66 ATAGCTCAAGGCGAGAAGGG
* * * * *
424027 TTATTTGTCAACAAAAACCTTCAAGTTTGATTACATTCAGCTCAAGGGCATATCAAATTTACAGA
1 CTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGC
*
424092 ATAGCTCAAGACGAGAAGGG
66 ATAGCTCAAGGCGAGAAGGG
* * * * *
424112 CTACCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAACTCATGGGCATATCACATTTACAGG
1 CTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGC
* *
424177 ATAACTCAAGGCGATAAGGG
66 ATAGCTCAAGGCGAGAAGGG
* * * * *
424197 CTATCTGTCAACAAAAACCTTCCAATTCGATTCCATTCAGCTCAAGGGAATACCAAATTTACAGC
1 CTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGC
* *
424262 ATAGCTCAAGGCGATAATGG
66 ATAGCTCAAGGCGAGAAGGG
* * *
424282 -T-TATGGCAAC-AAAACCTTCGAGTTCGATTCCATTCAGC
1 CTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
424320 AATGACAACG
Statistics
Matches: 415, Mismatches: 48, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
82 26 0.06
83 7 0.02
84 1 0.00
85 381 0.92
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (85 bp):
CTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGC
ATAGCTCAAGGCGAGAAGGG
Found at i:424964 original size:38 final size:37
Alignment explanation
Indices: 424879--425192 Score: 226
Period size: 37 Copynumber: 8.5 Consensus size: 37
424869 ATATATATAT
* *
424879 ATATATAATATAGTTTTTGAAAGCATTTT-AAAA-AC
1 ATATATTATATAGTTTTTGAAAACATTTTGAAAATAC
424914 ATATATGATATATAGTTTTTGAAAACATTTTGAAAAATAC
1 ATATAT--TATATAGTTTTTGAAAACATTTTG-AAAATAC
* *
424954 ATATATTATATA-ATTTTGAAAACATTTTTGAATATATAT
1 ATATATTATATAGTTTTTGAAAACA-TTTTGAA-A-ATAC
* *
424993 ATATATATATTATAG-TTTTGAAAATATTTTGAAAACATAT
1 ATATAT-TA-TATAGTTTTTGAAAACATTTTG-AAA-ATAC
* *
425033 ATATAATATATAGTTTTTGAAAATAGTTTT--AAA-A-
1 ATATATTATATAGTTTTTGAAAACA-TTTTGAAAATAC
***
425067 ATATATTATATAG-TTTT-AAATTTTTTTGAAAAT--
1 ATATATTATATAGTTTTTGAAAACATTTTGAAAATAC
* * * *
425100 ATATATTATATAG-TTTTAAAAATGATTTTTGAATATAT
1 ATATATTATATAGTTTTTGAAAA-CA-TTTTGAAAATAC
* *
425138 ATATATTATAT-GGTTTTGAAAACAATTTTGAAAA-GC
1 ATATATTATATAGTTTTTGAAAAC-ATTTTGAAAATAC
425174 ATATATGATATATAGTTTT
1 ATATAT--TATATAGTTTT
425193 AAAAATGATT
Statistics
Matches: 232, Mismatches: 20, Indels: 50
0.77 0.07 0.17
Matches are distributed among these distances:
31 4 0.02
32 4 0.02
33 24 0.10
34 15 0.06
35 7 0.03
36 16 0.07
37 45 0.19
38 42 0.18
39 30 0.13
40 29 0.12
41 16 0.07
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (37 bp):
ATATATTATATAGTTTTTGAAAACATTTTGAAAATAC
Found at i:425007 original size:79 final size:79
Alignment explanation
Indices: 424914--425078 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
424904 TTTTAAAAAC
*
424914 ATATATGATATATAGTTTTTGAAAACATTTTGAAAA-ATACATATATTATATA-ATTTTGAAAAC
1 ATATAT-ATATATAG-TTTTGAAAACATTTTGAAAACATACATATAATATATAGATTTTGAAAAC
* * *
424977 ATTTTTGAATATATAT
64 AGTTTTAAAAATATAT
* * * *
424993 ATATATATATTATAGTTTTGAAAATATTTTGAAAACATATATATAATATATAGTTTTTGAAAATA
1 ATATATATA-TATAGTTTTGAAAACATTTTGAAAACATACATATAATATATAGATTTTGAAAACA
425058 GTTTTAAAAATATAT
65 GTTTTAAAAATATAT
425073 -TATATA
1 ATATATA
425079 GTTTTAAATT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 22 0.29
79 31 0.41
80 22 0.29
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (79 bp):
ATATATATATATAGTTTTGAAAACATTTTGAAAACATACATATAATATATAGATTTTGAAAACAG
TTTTAAAAATATAT
Found at i:425091 original size:41 final size:39
Alignment explanation
Indices: 424929--425101 Score: 129
Period size: 41 Copynumber: 4.3 Consensus size: 39
424919 TGATATATAG
* * *
424929 TTTTTGAAAACATTTTGAAAA-ATA-CATATATTATATAA
1 TTTTTGAAAATATTTTGAAAATATATTATATATTTTA-AA
* * * *
424967 -TTTTGAAAACATTTTTGAATATATATATATATATATTATA
1 TTTTTGAAAATA-TTTTGAAAATATAT-TATATATTTTAAA
* * * * *
425007 GTTTTGAAAATATTTTGAAAACATA-TATATAATATATAG
1 TTTTTGAAAATATTTTGAAAATATATTATATATTTTA-AA
*
425046 TTTTTGAAAATAGTTTTAAAAATATATTATATAGTTTTAAA
1 TTTTTGAAAATA-TTTTGAAAATATATTATATA-TTTTAAA
425087 TTTTTTTGAAAATAT
1 --TTTTTGAAAATAT
425102 ATATTATATA
Statistics
Matches: 105, Mismatches: 19, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
37 11 0.10
38 16 0.15
39 14 0.13
40 23 0.22
41 25 0.24
42 4 0.04
43 12 0.11
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (39 bp):
TTTTTGAAAATATTTTGAAAATATATTATATATTTTAAA
Found at i:425102 original size:31 final size:33
Alignment explanation
Indices: 424991--425119 Score: 109
Period size: 33 Copynumber: 3.7 Consensus size: 33
424981 TTGAATATAT
* *
424991 ATATATATATATTATAGTTTTGAAAATATTTTGAAAA
1 ATATATAT-TA-TATAGTTTT--AAATTTTTTTAAAA
**
425028 CATATATATAATATATAGTTTTTGAAAATAGTTTT-AAA
1 -ATATATAT--TATATAG-TTTT--AAATTTTTTTAAAA
*
425066 A-ATATATTATATAGTTTTAAATTTTTTTGAAA
1 ATATATATTATATAGTTTTAAATTTTTTTAAAA
425098 ATATATATTATATAGTTTTAAA
1 ATATATATTATATAGTTTTAAA
425120 AATGATTTTT
Statistics
Matches: 83, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
31 8 0.10
32 4 0.05
33 24 0.29
34 7 0.08
36 6 0.07
37 1 0.01
38 16 0.19
39 17 0.20
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (33 bp):
ATATATATTATATAGTTTTAAATTTTTTTAAAA
Found at i:425204 original size:38 final size:35
Alignment explanation
Indices: 424877--425204 Score: 245
Period size: 38 Copynumber: 8.8 Consensus size: 35
424867 AAATATATAT
** *
424877 ATATATATAATATAGTTTTTGAAAGCATTTTAAAAAC
1 ATATATAT-ATATAG-TTTTGAAAATATTTTGAAAAC
*
424914 ATATATGATATATAGTTTTTGAAAACATTTTGAAAA-
1 ATATAT-ATATATAG-TTTTGAAAATATTTTGAAAAC
* * *
424950 ATACATATATTATATAATTTTGAAAACATTTTTGAATATATAT
1 AT--ATATA-TATATAGTTTTGAAAATA-TTTTG-A-A-A-AC
424993 ATATATATATTATAGTTTTGAAAATATTTTGAAAAC
1 ATATATATA-TATAGTTTTGAAAATATTTTGAAAAC
425029 ATATATATAATATATAGTTTTTGAAAATAGTTTT-AAAA-
1 --ATATAT-ATATATAG-TTTTGAAAATA-TTTTGAAAAC
* * *
425067 ATATAT-TATATAGTTTT-AAATTTTTTTGAAAAT
1 ATATATATATATAGTTTTGAAAATATTTTGAAAAC
* * *
425100 ATATAT-TATATAGTTTTAAAAATGATTTTTGAATAT
1 ATATATATATATAGTTTTGAAAAT-A-TTTTGAAAAC
* *
425136 ATATATATTATATGGTTTTGAAAACAATTTTGAAAAGC
1 ATATATA-TATATAGTTTTGAAAA-TATTTTGAAAA-C
*
425174 ATATATGATATATAGTTTTAAAAATGATTTT
1 ATATAT-ATATATAGTTTTGAAAAT-ATTTT
425205 TTATATCTTA
Statistics
Matches: 245, Mismatches: 19, Indels: 53
0.77 0.06 0.17
Matches are distributed among these distances:
31 4 0.02
32 8 0.03
33 21 0.09
34 11 0.04
36 24 0.10
37 52 0.21
38 69 0.28
39 21 0.09
40 12 0.05
41 20 0.08
42 1 0.00
43 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (35 bp):
ATATATATATATAGTTTTGAAAATATTTTGAAAAC
Found at i:425243 original size:28 final size:30
Alignment explanation
Indices: 425200--425272 Score: 105
Period size: 28 Copynumber: 2.5 Consensus size: 30
425190 TTTAAAAATG
* *
425200 ATTTTTTATATCTTATATTAATA-TTATTT
1 ATTTTTTATTTATTATATTAATATTTATTT
425229 A-TTTTTATTTATTATATTAATATTTTATTT
1 ATTTTTTATTTATTATATTAATA-TTTATTT
425259 ATTTTTTATTTATT
1 ATTTTTTATTTATT
425273 TTCTTGTCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 19 0.49
29 1 0.03
30 7 0.18
31 12 0.31
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (30 bp):
ATTTTTTATTTATTATATTAATATTTATTT
Found at i:425269 original size:11 final size:11
Alignment explanation
Indices: 425223--425274 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
425213 TATATTAATA
425223 TTATTTA-TTT
1 TTATTTATTTT
425233 TTATTTA--TT
1 TTATTTATTTT
* * *
425242 ATATTAATATT
1 TTATTTATTTT
425253 TTATTTATTTT
1 TTATTTATTTT
425264 TTATTTATTTT
1 TTATTTATTTT
425275 CTTGTCAGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 7 0.20
10 7 0.20
11 21 0.60
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTATTTATTTT
Found at i:426126 original size:13 final size:13
Alignment explanation
Indices: 426108--426133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
426098 TTCATTTTGG
426108 TATTTTCAATTTA
1 TATTTTCAATTTA
426121 TATTTTCAATTTA
1 TATTTTCAATTTA
426134 ATTCATGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTTCAATTTA
Found at i:426284 original size:16 final size:15
Alignment explanation
Indices: 426259--426302 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
426249 TCCTTTGATT
* *
426259 TTTATCTATTTATGTA
1 TTTATTTATTT-TCTA
426275 TTTATTTATTTTCTA
1 TTTATTTATTTTCTA
426290 TTTATTTTATTTT
1 TTTA-TTTATTTT
426303 ATTAACATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTATTTATTTTCTA
Found at i:426312 original size:16 final size:16
Alignment explanation
Indices: 426293--426330 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
426283 TTTTCTATTT
426293 ATTTTATTTTATTAAC
1 ATTTTATTTTATTAAC
*
426309 A-TTTATTTTCTTAAC
1 ATTTTATTTTATTAAC
426324 ATTTTAT
1 ATTTTAT
426331 ATATTTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTTATTTTATTAAC
Found at i:426374 original size:6 final size:6
Alignment explanation
Indices: 426365--426455 Score: 53
Period size: 6 Copynumber: 14.8 Consensus size: 6
426355 AAATTTAAAT
* * * * *
426365 TTTTTC TTTTTA TTTTT- TATTTCA TTTTTA TTGTAATA TTCTTA ATTTTA
1 TTTTTA TTTTTA TTTTTA T-TTTTA TTTTTA TT-T-TTA TTTTTA TTTTTA
* *
426415 TTTATC TTTAATTA TTTTTA -TTTTA -TTTTA TTTTTA TTTTT
1 TTTTTA TTT--TTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
426456 TCCCTTTTTA
Statistics
Matches: 65, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
5 11 0.17
6 44 0.68
7 2 0.03
8 8 0.12
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (6 bp):
TTTTTA
Found at i:426404 original size:26 final size:25
Alignment explanation
Indices: 426375--426456 Score: 71
Period size: 26 Copynumber: 3.3 Consensus size: 25
426365 TTTTTCTTTT
*
426375 TATTTTTTATTTCATTTTTATTGTAA
1 TATTTTTTATTTTATTTTTATT-TAA
* * * *
426401 TATTCTTAATTTTATTTATCTTTAA
1 TATTTTTTATTTTATTTTTATTTAA
*
426426 T-TATTTTTATTTTA-TTTTATTT-T
1 TAT-TTTTTATTTTATTTTTATTTAA
426449 TATTTTTT
1 TATTTTTT
426457 CCCTTTTTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
23 6 0.14
24 8 0.18
25 13 0.30
26 17 0.39
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (25 bp):
TATTTTTTATTTTATTTTTATTTAA
Found at i:426427 original size:16 final size:15
Alignment explanation
Indices: 426379--426447 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 15
426369 TCTTTTTATT
*
426379 TTTTATTTCATTTTTA
1 TTTTATTT-ATTTTAA
* *
426395 TTGTA-ATATTCTTAA
1 TTTTATTTATT-TTAA
426410 TTTTATTTATCTTTAA
1 TTTTATTTAT-TTTAA
426426 TTATT-TTTATTTT-A
1 TT-TTATTTATTTTAA
426440 TTTTATTT
1 TTTTATTT
426448 TTATTTTTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
13 2 0.05
14 9 0.21
15 11 0.26
16 18 0.42
17 3 0.07
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.71
Consensus pattern (15 bp):
TTTTATTTATTTTAA
Found at i:427120 original size:35 final size:35
Alignment explanation
Indices: 427077--427147 Score: 85
Period size: 35 Copynumber: 2.0 Consensus size: 35
427067 GTTGTCGAAC
*
427077 ATCGATATTTCT-TATTATT-TTTTTTAATTTT-AAT
1 ATCGATATTTATATATT-TTGTTTTTT-ATTTTCAAT
427111 ATCGAATATTTATATATTTTGTTTTTTATTTTCAAT
1 ATCG-ATATTTATATATTTTGTTTTTTATTTTCAAT
427147 A
1 A
427148 AATCTTCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
34 4 0.12
35 14 0.44
36 14 0.44
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (35 bp):
ATCGATATTTATATATTTTGTTTTTTATTTTCAAT
Found at i:427902 original size:18 final size:19
Alignment explanation
Indices: 427881--427927 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
427871 TTAAAAGATA
*
427881 AAAATATATTATCAATA-T
1 AAAATATATTATAAATACT
*
427899 AAAATATAATATAAATATCT
1 AAAATATATTATAAATA-CT
427919 AAAATATAT
1 AAAATATAT
427928 AATGATTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
20 9 0.38
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATATATTATAAATACT
Found at i:434978 original size:23 final size:24
Alignment explanation
Indices: 434943--434991 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
434933 TCACCTGAAA
434943 AATACATATATAAAATTATATATT
1 AATACATATATAAAATTATATATT
*
434967 AATACA-ATATAATATTATATATT
1 AATACATATATAAAATTATATATT
434990 AA
1 AA
434992 ATCAAAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (24 bp):
AATACATATATAAAATTATATATT
Found at i:437897 original size:15 final size:15
Alignment explanation
Indices: 437871--437910 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
437861 ATATAATAAT
*
437871 AAAAATAAAATAAATGA
1 AAAAATAATA-AAAT-A
437888 AAAAATAATAAAATA
1 AAAAATAATAAAATA
437903 AAAAATAA
1 AAAAATAA
437911 AAGTAGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 4 0.18
17 9 0.41
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (15 bp):
AAAAATAATAAAATA
Found at i:437907 original size:17 final size:18
Alignment explanation
Indices: 437835--437907 Score: 64
Period size: 17 Copynumber: 4.2 Consensus size: 18
437825 GTTAGATTGT
*
437835 AAAAAAT-ATATATATAA
1 AAAAAATAATATAAATAA
*
437852 AAAATATTAATAT-AATAA
1 AAAA-AATAATATAAATAA
* * *
437870 TAAAAATAAAATAAAT-G
1 AAAAAATAATATAAATAA
437887 AAAAAATAATA-AAATAA
1 AAAAAATAATATAAATAA
437904 AAAA
1 AAAA
437908 TAAAAGTAGA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
16 4 0.09
17 23 0.53
18 12 0.28
19 4 0.09
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (18 bp):
AAAAAATAATATAAATAA
Found at i:437961 original size:18 final size:17
Alignment explanation
Indices: 437869--438004 Score: 77
Period size: 17 Copynumber: 7.9 Consensus size: 17
437859 TAATATAATA
437869 ATAAAAATAAAATAAATG
1 ATAAAAATAAAA-AAATG
*
437887 A-AAAAATAATAAAAT-
1 ATAAAAATAAAAAAATG
*
437902 A-AAAAATAAAAGTAGAAAG
1 ATAAAAATAAAA--A-AATG
* *
437921 GTAAAAGTAAAAGAAATG
1 ATAAAAATAAAA-AAATG
*
437939 A-AAAACTAAAAAAATG
1 ATAAAAATAAAAAAATG
*
437955 AATAAAAAGAAAAAAAT-
1 -ATAAAAATAAAAAAATG
* *
437972 AGTTAAAGTAAAAAACATG
1 A-TAAAAATAAAAAA-ATG
*
437991 A-AATAATAAAAAAA
1 ATAAAAATAAAAAAA
438005 CCTAAAAAGG
Statistics
Matches: 91, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
15 10 0.11
16 11 0.12
17 39 0.43
18 20 0.22
19 2 0.02
20 9 0.10
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.16
Consensus pattern (17 bp):
ATAAAAATAAAAAAATG
Found at i:438237 original size:26 final size:26
Alignment explanation
Indices: 438207--438307 Score: 107
Period size: 26 Copynumber: 4.0 Consensus size: 26
438197 AACACACCTT
* *
438207 AAACCACTATACCTTTTAAAATAATC
1 AAACCACTACACCTATTAAAATAATC
* *
438233 AAACCACTACACTTATTAAAGTAATC
1 AAACCACTACACCTATTAAAATAATC
***
438259 AAATTTCTACACCTATTAAAATAATC
1 AAACCACTACACCTATTAAAATAATC
* *
438285 AAACCA--ATATCTATTAAAATAAT
1 AAACCACTACACCTATTAAAATAAT
438308 TAACTCAAAC
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
24 15 0.25
26 46 0.75
ACGTcount: A:0.49, C:0.20, G:0.01, T:0.31
Consensus pattern (26 bp):
AAACCACTACACCTATTAAAATAATC
Found at i:438450 original size:2 final size:2
Alignment explanation
Indices: 438443--438476 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
438433 ATGTTAGGTA
438443 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
438477 TTAATAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:438669 original size:18 final size:18
Alignment explanation
Indices: 438648--438686 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
438638 AAAAAAATAG
438648 TAAAAAATAAAATAAAAA
1 TAAAAAATAAAATAAAAA
* * *
438666 TAAAATATATAATAATAA
1 TAAAAAATAAAATAAAAA
438684 TAA
1 TAA
438687 CCAAAAGGGC
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAAAATAAAATAAAAA
Found at i:439190 original size:14 final size:14
Alignment explanation
Indices: 439099--439181 Score: 64
Period size: 14 Copynumber: 5.6 Consensus size: 14
439089 TTAGATTGCA
439099 AAAAAAT-ATAAA-
1 AAAAAATAATAAAT
439111 AAAAGAATAATAAA-
1 AAAA-AATAATAAAT
* *
439125 AAATATTAATATAAT
1 AAAAAATAATA-AAT
439140 AATAACAATAACATAAAT
1 AA-AA-AAT-A-ATAAAT
439158 GAAAAAATAATAAAT
1 -AAAAAATAATAAAT
439173 AAAAAATAA
1 AAAAAATAA
439182 AAGGTAAAAG
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
12 4 0.07
13 9 0.16
14 19 0.33
15 8 0.14
16 2 0.03
17 5 0.09
18 6 0.10
19 5 0.09
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (14 bp):
AAAAAATAATAAAT
Found at i:439223 original size:16 final size:15
Alignment explanation
Indices: 439204--439299 Score: 50
Period size: 17 Copynumber: 5.9 Consensus size: 15
439194 AAAGAAATAA
439204 AAAAAACTAAAAAACT
1 AAAAAACTAAAAAA-T
*
439220 AAAAAA-TGAATAAAAAG
1 AAAAAACT--A-AAAAAT
* *
439237 AAAAAAATAATTAAATT
1 AAAAAACTAA--AAAAT
*
439254 AAAAAACATGAAATAAT
1 AAAAAAC-T-AAAAAAT
*
439271 AAAAACCTAAAATAAT
1 AAAAAACTAAAA-AAT
*
439287 AAAAACCTAAAAA
1 AAAAAACTAAAAA
439300 TGATTATCTA
Statistics
Matches: 63, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
15 6 0.10
16 23 0.37
17 25 0.40
18 7 0.11
19 2 0.03
ACGTcount: A:0.73, C:0.07, G:0.03, T:0.17
Consensus pattern (15 bp):
AAAAAACTAAAAAAT
Found at i:439274 original size:15 final size:16
Alignment explanation
Indices: 439255--439298 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
439245 AATTAAATTA
*
439255 AAAAACATGAAATAAT
1 AAAAACATAAAATAAT
*
439271 AAAAACCTAAAATAAT
1 AAAAACATAAAATAAT
*
439287 AAAAACCTAAAA
1 AAAAACATAAAA
439299 ATGATTATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.70, C:0.11, G:0.02, T:0.16
Consensus pattern (16 bp):
AAAAACATAAAATAAT
Found at i:439392 original size:18 final size:20
Alignment explanation
Indices: 439371--439413 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
439361 TAAAACAATT
439371 TAAAAAAG-AA-AAAAGGAA
1 TAAAAAAGAAATAAAAGGAA
*
439389 TAAAAATGAAATAAAAGGAA
1 TAAAAAAGAAATAAAAGGAA
439409 -AAAAA
1 TAAAAA
439414 GGACACGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (20 bp):
TAAAAAAGAAATAAAAGGAA
Found at i:439541 original size:26 final size:26
Alignment explanation
Indices: 439505--439579 Score: 127
Period size: 26 Copynumber: 3.0 Consensus size: 26
439495 AACCCACCCT
439505 AAACCACTACACCTATTAAAATAATC
1 AAACCACTACACCTATTAAAATAATC
*
439531 AAACCACTACACTTATTAAAATAATC
1 AAACCACTACACCTATTAAAATAATC
439557 AAACCACT--ACCTATTAAAATAAT
1 AAACCACTACACCTATTAAAATAAT
439580 TAAATCAAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.30
26 33 0.70
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (26 bp):
AAACCACTACACCTATTAAAATAATC
Found at i:439840 original size:2 final size:2
Alignment explanation
Indices: 439833--439857 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
439823 AGAACAAATA
439833 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
439858 AACGTTAGGA
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:441148 original size:2 final size:2
Alignment explanation
Indices: 441143--441173 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
441133 CTCCTAATGT
441143 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
441174 GTTGTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:441467 original size:40 final size:42
Alignment explanation
Indices: 441407--441489 Score: 143
Period size: 40 Copynumber: 2.0 Consensus size: 42
441397 TTAATTTTGT
441407 GGTGGGTTTGATTTAATTATTTTAATA-G-GTAGTGGTTTAG
1 GGTGGGTTTGATTTAATTATTTTAATAGGTGTAGTGGTTTAG
*
441447 GGTGTGTTTGATTTAATTATTTTAATAGGTGTAGTGGTTTAG
1 GGTGGGTTTGATTTAATTATTTTAATAGGTGTAGTGGTTTAG
441489 G
1 G
441490 TTGAATTTGG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 26 0.65
41 1 0.03
42 13 0.32
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (42 bp):
GGTGGGTTTGATTTAATTATTTTAATAGGTGTAGTGGTTTAG
Found at i:441505 original size:42 final size:40
Alignment explanation
Indices: 441413--441509 Score: 122
Period size: 42 Copynumber: 2.4 Consensus size: 40
441403 TTGTGGTGGG
* **
441413 TTTGATTTAATTATTTTAATAGGTAGTGGTTTAGGGTGTG
1 TTTGAGTTAATTATTTTAATAGGTAGTGGTTTAGGGTGAA
* *
441453 TTTGATTTAATTATTTTAATAGGTGTAGTGGTTTAGGTTGAA
1 TTTGAGTTAATTATTTTAATA-G-GTAGTGGTTTAGGGTGAA
*
441495 TTTGGGTTAATTATT
1 TTTGAGTTAATTATT
441510 ATCTTTTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
40 21 0.42
41 1 0.02
42 28 0.56
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.52
Consensus pattern (40 bp):
TTTGAGTTAATTATTTTAATAGGTAGTGGTTTAGGGTGAA
Found at i:441564 original size:29 final size:29
Alignment explanation
Indices: 441532--441588 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
441522 GAATTTTGTG
*
441532 TCCTTATTTCCTTTTATTATATT-TTTTAT
1 TCCTTATTTCCTTTT-TTAAATTGTTTTAT
* *
441561 TCCTTTTTTTCTTTTTTAAATTGTTTTA
1 TCCTTATTTCCTTTTTTAAATTGTTTTA
441589 AATATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.70
Consensus pattern (29 bp):
TCCTTATTTCCTTTTTTAAATTGTTTTAT
Found at i:441716 original size:11 final size:11
Alignment explanation
Indices: 441678--441829 Score: 61
Period size: 11 Copynumber: 12.6 Consensus size: 11
441668 ATTTAACTAT
441678 TTTTTCTTTTTA
1 TTTTT-TTTTTA
** *
441690 TTCATTTTTAA
1 TTTTTTTTTTA
*
441701 GTTTTTTTTTA
1 TTTTTTTTTTA
*
441712 TTTTTTATTTA
1 TTTTTTTTTTA
**
441723 TTTTACTTTTA
1 TTTTTTTTTTA
*
441734 CCTTTTTACTTTTA
1 --TTTTT-TTTTTA
*
441748 TTTTTTATTTA
1 TTTTTTTTTTA
*
441759 TTATTTTTTTCA
1 TT-TTTTTTTTA
441771 TTTAATTTAATTTTA
1 TTT--TTT--TTTTA
**
441786 TTATTATATTAATA
1 TT-TT-T-TTTTTA
* *
441800 TATTTTTATTA
1 TTTTTTTTTTA
441811 TTCTTTTTTTTA
1 TT-TTTTTTTTA
441823 TTTTTTT
1 TTTTTTT
441830 ACAATCTAAC
Statistics
Matches: 104, Mismatches: 24, Indels: 25
0.68 0.16 0.16
Matches are distributed among these distances:
11 47 0.45
12 28 0.27
13 9 0.09
14 11 0.11
15 7 0.07
16 2 0.02
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:445799 original size:99 final size:99
Alignment explanation
Indices: 445692--445889 Score: 229
Period size: 99 Copynumber: 2.0 Consensus size: 99
445682 TTGTAATATT
* *
445692 ATATATATACAACAAAGCTTGAACTATCCCTATAA-AGCAATTGGTTAAACGCCT-CGGCTTTAT
1 ATATATATACAACAAAACTTGAACTATCCCTATAAGA-CAATTGGTTAAAC-ACTGCGGCTTTAT
* *
445755 GGATAATATTCACCTAGCCTGATAAAGGTGATTATA
64 GGATAAGATTCACCTAACCTGATAAAGGTGATTATA
* * ** * * * *
445791 ATATATATACAATAAAATTTGAGTTGTTCGTCTAAGACAATTGGTTAAACACTGCGGCTTTATGG
1 ATATATATACAACAAAACTTGAACTATCCCTATAAGACAATTGGTTAAACACTGCGGCTTTATGG
* * *
445856 ATAAGATTCAGCTAACTTGATAAAGGTGTTTATA
66 ATAAGATTCACCTAACCTGATAAAGGTGATTATA
445890 TATTGAGTTG
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
98 2 0.02
99 79 0.96
100 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (99 bp):
ATATATATACAACAAAACTTGAACTATCCCTATAAGACAATTGGTTAAACACTGCGGCTTTATGG
ATAAGATTCACCTAACCTGATAAAGGTGATTATA
Found at i:447381 original size:85 final size:85
Alignment explanation
Indices: 447138--448052 Score: 1165
Period size: 85 Copynumber: 10.8 Consensus size: 85
447128 GAACTGTTGG
* **
447138 CAGCATAACTCATGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTCGATTACATTCAGC
* *
447203 TCAAAGGAATATTAAATTTA
66 TCAAAGGCATATCAAATTTA
* * * *
447223 CAACATAGCTC-AGGCGAGAA-GGTCTATCTATCAACAAAGACCTTCGAGTTCGATTACATTCAG
1 CAGCATAACTCAAGGCGAGAAGGGT-TATCTGTCAATAAAGACCTTCGAGTTCGATTACATTCAG
*
447286 CTCAAAGGCACATCAAATTTA
65 CTCAAAGGCATATCAAATTTA
* * * * *
447307 CAGCATAACTCAAGGTGAGAAGGGTTATCTGTCAATGAAGTCCTTCAAGTTCGATTACATTTAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTCGATTACATTCAGC
* *
447372 TCAAAGGCACATCAAATTTG
66 TCAAAGGCATATCAAATTTA
* * *
447392 CAGCATAGCTCAAGGCGAGAAGGGTTATCTTTCAATAAAGACCTTTGAGTTCGATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTCGATTACATTCAGC
447457 TCAAAGGCATATCAAATTTA
66 TCAAAGGCATATCAAATTTA
* * *** * * *
447477 CAGCATAGCTCAAGGCAAGAAGTACTATATGTCAACAAAGACATTCGAGTTCGATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTCGATTACATTCAGC
447542 TCAAAGGCATATCAAATTTA
66 TCAAAGGCATATCAAATTTA
*
447562 CAGCATAACTCAAGGCGAGAAGGGTTATCTATCAATAAAGACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTCGATTACATTCAGC
*
447627 TCAAAGACATATCAAATTTA
66 TCAAAGGCATATCAAATTTA
* *
447647 CAACATAACTCAAGGCGAGAAGGGTTATCTATCAAT--AGACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTCGATTACATTCAGC
*
447710 TCAAAGACATATCAAATTTA
66 TCAAAGGCATATCAAATTTA
* * * * * *
447730 CAGCATAGCTCAAGGCGAGAAGGGCTATATGTCAACAAAGACTTTCGAGTTCGATTACATTCAAC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTCGATTACATTCAGC
*
447795 TCAAAGGCATATTAAATTTA
66 TCAAAGGCATATCAAATTTA
* * * * * *
447815 CAACATAACTCATGGAGAGAAGGGTTATATGTTAATAAAGACCTTCGAGTTCAATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTCGATTACATTCAGC
*
447880 TTAAAGGCATATCAAATTTA
66 TCAAAGGCATATCAAATTTA
* * * * * * *
447900 CATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAATACCTTCGAGTTTGATTCCATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTCGATTACATTCAGC
* *
447965 TCAATGGCATGTCAAATTTA
66 TCAAAGGCATATCAAATTTA
* * * ** ** * * * *
447985 CAGCTTAGCTTAAGTTGAGAAAAGCTATCTGTCAA-CAAGAAACTGTCGAGTTCGATTCCATTCA
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAATAAAG-ACCT-TCGAGTTCGATTACATTCA
448049 GCTC
64 GCTC
448053 GATGACACAT
Statistics
Matches: 727, Mismatches: 96, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
83 80 0.11
84 74 0.10
85 548 0.75
86 25 0.03
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (85 bp):
CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTCGATTACATTCAGC
TCAAAGGCATATCAAATTTA
Found at i:447935 original size:423 final size:424
Alignment explanation
Indices: 447138--448052 Score: 1257
Period size: 423 Copynumber: 2.2 Consensus size: 424
447128 GAACTGTTGG
* * *
447138 CAGCATAACTCATGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTACATTCAGC
* *
447203 TCAAAGGAATATTAAATTTACAACATAGCTCAGGCGAGAAGGTCTATCTATCAACAAAGACCTTC
66 TCAAAGGAATATCAAATTTACAACATAACTCAGGCGAGAAGGTCTATCTATCAACAAAGACCTTC
* * *
447268 GAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGCATAACTCAAGGTGAGAAGGGTT
131 GAGTTCGATTACATTCAGCTCAAAGACACATCAAATTTACAGCATAACTCAAGGCGAGAAGGGCT
* ** * * * * *
447333 ATCTGTCAATGAAGTCCTTCAAGTTCGATTACATTTAGCTCAAAGGCACATCAAATTTGCAGCAT
196 ATATGTCAACAAAGACCTTCAAGTTCGATTACATTCAACTCAAAGGCACATCAAATTTACAACAT
* * * * *
447398 AGCTCAAGGCGAGAAGGGTTATCTTTCAATAAAGACCTTTGAGTTCGATTACATTCAGCTCAAAG
261 AACTCAAGGAGAGAAGGGTTATATTTCAATAAAGACCTTCGAGTTCAATTACATTCAGCTCAAAG
*
447463 GCATATCAAATTTACAGCATAGCTCAAGGCAAGAAGTACTATATGTCAACAAAGACATTCGAGTT
326 GCATATCAAATTTACAGCATAGCTCAAGGCAAGAAGGACTATATGTCAACAAAGACATTCGAGTT
447528 CGATTACATTCAGCTCAAAGGCATATCAAATTTA
391 CGATTACATTCAGCTCAAAGGCATATCAAATTTA
*
447562 CAGCATAACTCAAGGCGAGAAGGGTTATCTATCAATAAAGACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTACATTCAGC
*
447627 TCAAA-GACATATCAAATTTACAACATAACTCAAGGCGAGAAGGGT-TATCTATC-A-ATAGACC
66 TCAAAGGA-ATATCAAATTTACAACATAACTC-AGGCGAGAA-GGTCTATCTATCAACAAAGACC
* *
447688 TTCGAGTTCGATTACATTCAGCTCAAAGACATATCAAATTTACAGCATAGCTCAAGGCGAGAAGG
128 TTCGAGTTCGATTACATTCAGCTCAAAGACACATCAAATTTACAGCATAACTCAAGGCGAGAAGG
* * * *
447753 GCTATATGTCAACAAAGACTTTCGAGTTCGATTACATTCAACTCAAAGGCATATTAAATTTACAA
193 GCTATATGTCAACAAAGACCTTCAAGTTCGATTACATTCAACTCAAAGGCACATCAAATTTACAA
* *
447818 CATAACTCATGGAGAGAAGGGTTATATGTT-AATAAAGACCTTCGAGTTCAATTACATTCAGCTT
258 CATAACTCAAGGAGAGAAGGGTTATAT-TTCAATAAAGACCTTCGAGTTCAATTACATTCAGCTC
* * * * * *
447882 AAAGGCATATCAAATTTACATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAATACCTTCG
322 AAAGGCATATCAAATTTACAGCATAGCTCAAGGCAAGAAGGACTATATGTCAACAAAGACATTCG
* * * *
447947 AGTTTGATTCCATTCAGCTCAATGGCATGTCAAATTTA
387 AGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTA
* * * ** ** * * * *
447985 CAGCTTAGCTTAAGTTGAGAAAAGCTATCTGTCAAC-AAGAAACTGTCGAGTTCGATTCCATTCA
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTATCAACAAAG-ACCT-TCGAGTTCGATTACATTCA
448049 GCTC
64 GCTC
448053 GATGACACAT
Statistics
Matches: 431, Mismatches: 54, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
422 3 0.01
423 296 0.69
424 112 0.26
425 17 0.04
426 3 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (424 bp):
CAGCATAACTCAAGGCGAGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTACATTCAGC
TCAAAGGAATATCAAATTTACAACATAACTCAGGCGAGAAGGTCTATCTATCAACAAAGACCTTC
GAGTTCGATTACATTCAGCTCAAAGACACATCAAATTTACAGCATAACTCAAGGCGAGAAGGGCT
ATATGTCAACAAAGACCTTCAAGTTCGATTACATTCAACTCAAAGGCACATCAAATTTACAACAT
AACTCAAGGAGAGAAGGGTTATATTTCAATAAAGACCTTCGAGTTCAATTACATTCAGCTCAAAG
GCATATCAAATTTACAGCATAGCTCAAGGCAAGAAGGACTATATGTCAACAAAGACATTCGAGTT
CGATTACATTCAGCTCAAAGGCATATCAAATTTA
Found at i:448688 original size:2 final size:2
Alignment explanation
Indices: 448681--448709 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
448671 AATTTTCGTC
448681 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
448710 TACTTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:449818 original size:23 final size:23
Alignment explanation
Indices: 449789--449837 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
449779 ATTATTATTA
449789 TATATTTCAT-TTCATTTCATTTT
1 TATATTT-ATATTCATTTCATTTT
* *
449812 TATATTTATATTTATTTTATTTT
1 TATATTTATATTCATTTCATTTT
449835 TAT
1 TAT
449838 TTTTTTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (23 bp):
TATATTTATATTCATTTCATTTT
Found at i:449831 original size:17 final size:15
Alignment explanation
Indices: 449808--449851 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
449798 TTTCATTTCA
449808 TTTTTATATTTATATT
1 TTTTTATATTT-TATT
449824 TATTTTAT-TTTTATT
1 T-TTTTATATTTTATT
449839 TTTTTACTATTTT
1 TTTTTA-TATTTT
449852 TTCGTTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.20
15 6 0.24
16 8 0.32
17 6 0.24
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTATATTTTATT
Found at i:449852 original size:17 final size:16
Alignment explanation
Indices: 449808--449852 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
449798 TTTCATTTCA
*
449808 TTTTTATATTTATATT
1 TTTTTATATTTTTATT
*
449824 TATTT-TATTTTTATT
1 TTTTTATATTTTTATT
449839 TTTTTACTATTTTT
1 TTTTTA-TATTTTT
449853 TCGTTTTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 13 0.54
16 4 0.17
17 7 0.29
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTATATTTTTATT
Found at i:449908 original size:2 final size:2
Alignment explanation
Indices: 449901--449973 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
449891 CCTAACGTTT
449901 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
449943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
449974 TTATTTGTTC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:450355 original size:12 final size:12
Alignment explanation
Indices: 450331--450383 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
450321 ATTAGATTGT
450331 AAAA-AATATATA
1 AAAATAATA-ATA
450343 AAAATAATAATA
1 AAAATAATAATA
*
450355 AAAATATTAATA
1 AAAATAATAATA
*
450367 TAATAATAAGAATA
1 -AA-AATAATAATA
450381 AAA
1 AAA
450384 TAAATGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
12 19 0.54
13 8 0.23
14 8 0.23
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:450356 original size:23 final size:23
Alignment explanation
Indices: 450330--450411 Score: 69
Period size: 26 Copynumber: 3.4 Consensus size: 23
450320 TATTAGATTG
450330 TAAAAAATATATAAAAATAATAA
1 TAAAAAATATATAAAAATAATAA
450353 T-AAAAATAT-TAATATAATAATAA
1 TAAAAAATATATAA-A-AATAATAA
* * *
450376 GAATAAAATAAATGAAAAAATAAAAAA
1 TAA-AAAATATAT--AAAAAT-AATAA
450403 TAAAAAATA
1 TAAAAAATA
450412 AAAGGTAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
21 3 0.06
22 9 0.19
23 9 0.19
24 1 0.02
25 6 0.13
26 10 0.21
27 7 0.15
28 2 0.04
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (23 bp):
TAAAAAATATATAAAAATAATAA
Found at i:450369 original size:20 final size:22
Alignment explanation
Indices: 450332--450412 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 22
450322 TTAGATTGTA
450332 AAAAATATATAAAAATAATAAT
1 AAAAATATATAAAAATAATAAT
*
450354 AAAAATAT-T-AATATAATAAT
1 AAAAATATATAAAAATAATAAT
* *
450374 AAGAATA-A-AATAAATGAAAAAAT
1 AAAAATATATAA-AAAT--AATAAT
450397 AAAAA-ATA-AAAAATAA
1 AAAAATATATAAAAATAA
450413 AAGGTAAAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
20 19 0.40
21 4 0.08
22 13 0.27
23 12 0.25
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (22 bp):
AAAAATATATAAAAATAATAAT
Found at i:450400 original size:6 final size:6
Alignment explanation
Indices: 450340--450463 Score: 51
Period size: 6 Copynumber: 20.2 Consensus size: 6
450330 TAAAAAATAT
* * * * *
450340 ATAAAA ATAATA ATAAAA ATATTAAT ATAATA ATAAGA AT-AAA ATAAATG
1 ATAAAA ATAAAA ATAAAA ATA--AAA ATAAAA ATAAAA ATAAAA ATAAA-A
* *
450390 A-AAAA ATAAAAA ATAAAAA ATAAAA GGTAAAA GTAAAA GA-AATAA A-AAAA
1 ATAAAA AT-AAAA AT-AAAA ATAAAA -ATAAAA ATAAAA -ATAA-AA ATAAAA
* * *
450440 CTAAAA A-ATAA ATAAAA AGAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
450464 AATAGTTAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
5 11 0.12
6 54 0.59
7 21 0.23
8 5 0.05
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:450402 original size:7 final size:7
Alignment explanation
Indices: 450385--450451 Score: 55
Period size: 7 Copynumber: 9.0 Consensus size: 7
450375 AGAATAAAAT
450385 AAATGAAA
1 AAAT-AAA
450393 AAATAAA
1 AAATAAA
450400 AAATAAA
1 AAATAAA
450407 AAATAAA
1 AAATAAA
**
450414 AGGTAAA
1 AAATAAA
*
450421 AGTAA-AAG
1 A--AATAAA
450429 AAATAAAA
1 AAAT-AAA
450437 AAACTAAA
1 AAA-TAAA
450445 AAATAAA
1 AAATAAA
450452 TAAAAAGAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
6 2 0.04
7 27 0.56
8 18 0.38
9 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.07, T:0.13
Consensus pattern (7 bp):
AAATAAA
Found at i:452499 original size:85 final size:85
Alignment explanation
Indices: 452344--453176 Score: 1058
Period size: 85 Copynumber: 9.8 Consensus size: 85
452334 ATGTGTCATC
* * * *** ** ** *
452344 GAGCTGAATGGAATCGAACTCGATA-GTTTCTTGTTGACATATAGTTTTTCTCAACTCAAGCTAA
1 GAGCTGAATGTAATCGAACTCGA-AGGTCT-TTGTTGACAGATAGCCCTTCTCGCCTTGAGCTAT
* *
452408 GCTGTAAATTTGACATGCCCTT
64 GCTGTAAATTTGATATGCCTTT
* * * *
452430 GAGCTGAATGAAATCGAACTCGAAGGTATTTGTTGACAGATAGCCCTTATCGCCTTAAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
452495 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * * *
452515 GAGCTGAATGTAATCGAACTCGAAGGTCTTTATTGACAGATAACTCTTCTCGCCTTAAGTTAT-C
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
*
452579 TTGTAAATTTGATATGTCTTT
66 -TGTAAATTTGATATGCCTTT
* * * *
452600 GAGTTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGTCATTCTCGCCTTAAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
*
452665 TGTAAATTTGATATGTCTTT
66 TGTAAATTTGATATGCCTTT
* * * * * *
452685 GAGCTGAATGTAATCGAACTCGAAGGTCATTATTGACAGATAACCCTTCTCACCTTGAGTTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
*
452750 TGTAAATTTGATATTCCTTT
66 TGTAAATTTGATATGCCTTT
* *
452770 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTAACAGATAGCCCTTCTTGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
* *
452835 TGTAAATTTAATATGACTTT
66 TGTAAATTTGATATGCCTTT
* * * *
452855 GAGCTGAATGTAATCGAACTCGAAGGTCTTTATTGACAGATAGCCATTCTCTCCTTGAGCTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
* * * *
452920 TGCAAATTTAATGTGTCTTT
66 TGTAAATTTGATATGCCTTT
* * * * *
452940 AAGCTGAATATAATTGAACTCGAAGGTCTTTTTTGACAGATAGCCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
* * *
453005 TATAAATTTGATGTGCATTT
66 TGTAAATTTGATATGCCTTT
* *
453025 GAGCTGAATGTAATCGAACTCGAAGGACTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
453090 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * ** *
453110 GAGCTGACTGTAATCGAACTCGAAGGTCTTGGTTGATAGATAAACCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
453175 TG
66 TG
453177 CCAATAGTTC
Statistics
Matches: 655, Mismatches: 89, Indels: 7
0.87 0.12 0.01
Matches are distributed among these distances:
84 1 0.00
85 628 0.96
86 26 0.04
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCTTT
Found at i:455980 original size:21 final size:21
Alignment explanation
Indices: 455934--455980 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
455924 CATTCATTTG
* *
455934 GTCCTCCAATTGTTTGATTTT
1 GTCCTCCAATTCTTTGACTTT
*
455955 CTCCTCCATATTCTTTG-CTTT
1 GTCCTCCA-ATTCTTTGACTTT
455976 GTCCT
1 GTCCT
455981 TTTTGTCTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.11, C:0.28, G:0.11, T:0.51
Consensus pattern (21 bp):
GTCCTCCAATTCTTTGACTTT
Found at i:457695 original size:12 final size:12
Alignment explanation
Indices: 457678--457710 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
457668 GTTAGATTGT
457678 AAAAAATATATA
1 AAAAAATATATA
457690 AAAAAATA-ATA
1 AAAAAATATATA
457701 AAAAAA-ATAT
1 AAAAAATATAT
457711 TAATATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 11 0.55
12 8 0.40
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAAATATATA
Found at i:457720 original size:23 final size:25
Alignment explanation
Indices: 457678--457743 Score: 82
Period size: 23 Copynumber: 2.7 Consensus size: 25
457668 GTTAGATTGT
457678 AAAAAATATATAAAAAAATAATAA-
1 AAAAAATATATAAAAAAATAATAAC
* *
457702 AAAAAATAT-TAATATAATAATAAC
1 AAAAAATATATAAAAAAATAATAAC
*
457726 AATAAAATAAATAAAAAA
1 AA-AAAATATATAAAAAA
457744 TAAAAGTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 12 0.35
24 11 0.32
25 6 0.18
26 5 0.15
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.23
Consensus pattern (25 bp):
AAAAAATATATAAAAAAATAATAAC
Found at i:458035 original size:26 final size:24
Alignment explanation
Indices: 458006--458054 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
457996 AATTCAACCT
458006 AAACCACTACACTTATTAAAATAATA
1 AAACCACTAC-C-TATTAAAATAATA
*
458032 AAACCATTACCTATTAAAATAAT
1 AAACCACTACCTATTAAAATAAT
458055 TAAATCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 1 0.05
26 9 0.41
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (24 bp):
AAACCACTACCTATTAAAATAATA
Found at i:458213 original size:2 final size:2
Alignment explanation
Indices: 458206--458235 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
458196 ATGTTAGGTA
458206 AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
458236 GTATTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:462904 original size:21 final size:21
Alignment explanation
Indices: 462866--462906 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
462856 GTTATAACAT
* **
462866 TGACATGACACTTTACAATGC
1 TGACATGACAATCCACAATGC
462887 TGACATGACAATCCACAATG
1 TGACATGACAATCCACAATG
462907 GTTAGTGATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (21 bp):
TGACATGACAATCCACAATGC
Found at i:470505 original size:22 final size:22
Alignment explanation
Indices: 470480--470522 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
470470 TGTAACAGAG
470480 TTGCA-CATATTGTAGTTCTTAA
1 TTGCACCATATTG-AGTTCTTAA
470502 TTGCATCCATATTGAGTTCTT
1 TTGCA-CCATATTGAGTTCTT
470523 TTGTTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 7 0.37
24 7 0.37
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (22 bp):
TTGCACCATATTGAGTTCTTAA
Found at i:475735 original size:15 final size:17
Alignment explanation
Indices: 475704--475735 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
475694 ATGTATTTTT
475704 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
475721 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
475736 TTATTATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:475846 original size:21 final size:20
Alignment explanation
Indices: 475820--475859 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
475810 GTAACAAAGA
475820 AAAAGAAAGAAAAGAAATAAC
1 AAAAGAAAGAAAA-AAATAAC
*
475841 AAAAGAAATAAAAAAATAA
1 AAAAGAAAGAAAAAAATAA
475860 AAATCATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (20 bp):
AAAAGAAAGAAAAAAATAAC
Found at i:479017 original size:14 final size:14
Alignment explanation
Indices: 478998--479024 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
478988 TAATTAAGCT
478998 ATTAAGTTTGTAAC
1 ATTAAGTTTGTAAC
479012 ATTAAGTTTGTAA
1 ATTAAGTTTGTAA
479025 ATATCAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (14 bp):
ATTAAGTTTGTAAC
Found at i:479525 original size:3 final size:3
Alignment explanation
Indices: 479513--479554 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
479503 ATTTATAACA
479513 TAT TATT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT T-T TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
479555 TGTGGAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:479538 original size:17 final size:16
Alignment explanation
Indices: 479513--479549 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
479503 ATTTATAACA
479513 TATTATTTATTATTAT
1 TATTATTTATTATTAT
479529 TATTATTTTATTATTAT
1 TATTA-TTTATTATTAT
479546 TATT
1 TATT
479550 TTATTTGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTATTTATTATTAT
Found at i:479539 original size:14 final size:14
Alignment explanation
Indices: 479513--479554 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
479503 ATTTATAACA
*
479513 TATTATT-TATTAT
1 TATTATTATTTTAT
479526 TATTATTATTTTAT
1 TATTATTATTTTAT
479540 TATTATTATTTTAT
1 TATTATTATTTTAT
479554 T
1 T
479555 TGTGGAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 7 0.26
14 20 0.74
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATTATTTTAT
Found at i:486975 original size:57 final size:57
Alignment explanation
Indices: 486509--486969 Score: 688
Period size: 57 Copynumber: 8.1 Consensus size: 57
486499 AACTTCTCAG
* * * * *
486509 TTTTTGAACATAAAGTGCTCATACGAAAATTCATAAACTAATTATGAATTTCTTAAC
1 TTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAAC
* * * *
486566 TTTTTGCACACAAAGTGTCTATACGGAAATTCATAAACTTGTTATGAATTTCTTAGC
1 TTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAAC
* *
486623 TTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTTTTAAC
1 TTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAAC
* * * *
486680 TTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTAATTATAAATTTTTTAAC
1 TTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAAC
* * * *
486737 TTTTTGCACACAAAGTGCCCATACAGAAATTTATAAACTTATTATGAATTTCGTAGC
1 TTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAAC
* * *
486794 TTTTTGCAAACAAAGTGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGC
1 TTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAAC
* * *
486851 TTTTTGCACACAAAGTGCCCATATGGAAATTCATAAACTTATTATAAATTTCTTAGC
1 TTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAAC
*
486908 TTTTTGTACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAAC
1 TTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAAC
486965 TTTTT
1 TTTTT
486970 ATACACTCGG
Statistics
Matches: 368, Mismatches: 36, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 368 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (57 bp):
TTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAAC
Found at i:492198 original size:2 final size:2
Alignment explanation
Indices: 492185--492296 Score: 91
Period size: 2 Copynumber: 59.5 Consensus size: 2
492175 AATAATAATA
* * *
492185 AT AT AT ACT AT AT ACT AT AT A- AT CT AT AA AT GT AT AT A- AT AT
1 AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
492227 A- AT AT A- AT AT AT -T AT A- AT AT AT AT A- AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
492263 AT ACT AT AT AT AT AT -T AT AT A- AT AT AT AC AT AT A
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
492297 AAAACAAAAA
Statistics
Matches: 89, Mismatches: 8, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
1 10 0.11
2 73 0.82
3 6 0.07
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:492198 original size:7 final size:7
Alignment explanation
Indices: 492186--492296 Score: 63
Period size: 7 Copynumber: 15.9 Consensus size: 7
492176 ATAATAATAA
492186 TATATAC
1 TATATAC
492193 TATATAC
1 TATATAC
492200 TATATAATC
1 TATAT-A-C
* *
492209 TATAAATG
1 TATATA-C
*
492217 TATATAA
1 TATATAC
492224 TATAATA-
1 TAT-ATAC
*
492231 TAATATAT
1 T-ATATAC
492239 TATAATA-
1 TAT-ATAC
*
492246 TATATAA
1 TATATAC
*
492253 TATATAT
1 TATATAC
492260 TATATAC
1 TATATAC
492267 TATATA-
1 TATATAC
492273 TATAT--
1 TATATAC
*
492278 TATATAA
1 TATATAC
492285 TATATAC
1 TATATAC
492292 -ATATA
1 TATATA
492297 AAAACAAAAA
Statistics
Matches: 88, Mismatches: 7, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
5 5 0.06
6 13 0.15
7 48 0.55
8 17 0.19
9 5 0.06
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.45
Consensus pattern (7 bp):
TATATAC
Found at i:492226 original size:29 final size:29
Alignment explanation
Indices: 492176--492297 Score: 85
Period size: 29 Copynumber: 4.1 Consensus size: 29
492166 ATGGTAAATA
492176 ATAATAATAATATA-TACTATATACTATATAAT
1 ATAAT-ATAATATATTA-TA-ATA-TATATAAT
* *
492208 CT-ATA-AATGTA-TATAATATAATATAAT
1 ATAATATAATATATTATAATAT-ATATAAT
* *
492235 ATATTATAATATA-TATAATATATATTAT
1 ATAATATAATATATTATAATATATATAAT
*
492263 ATACTATATATATATTAT-ATAATATATACAT
1 ATAATATA-ATATATTATAAT-ATATATA-AT
492294 ATAA
1 ATAA
492298 AAACAAAAAG
Statistics
Matches: 74, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
26 1 0.01
27 11 0.15
28 17 0.23
29 27 0.36
30 10 0.14
31 7 0.09
32 1 0.01
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (29 bp):
ATAATATAATATATTATAATATATATAAT
Found at i:492228 original size:5 final size:5
Alignment explanation
Indices: 492218--492288 Score: 78
Period size: 5 Copynumber: 15.0 Consensus size: 5
492208 CTATAAATGT
* *
492218 ATATA ATATA ATATA ATATA TTATA ATAT- ATATA ATAT- ATATT ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* *
492266 CTAT- ATAT- ATATT ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
492289 TACATATAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
4 15 0.26
5 42 0.74
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (5 bp):
ATATA
Found at i:493841 original size:14 final size:15
Alignment explanation
Indices: 493818--493848 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
493808 TTTATTTTTC
493818 TTTTCTTTTTTCAAT
1 TTTTCTTTTTTCAAT
493833 TTTTC-TTTTTCAAT
1 TTTTCTTTTTTCAAT
493847 TT
1 TT
493849 AGAGCGCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTCTTTTTTCAAT
Found at i:505367 original size:13 final size:13
Alignment explanation
Indices: 505349--505373 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
505339 TGGCTCGATG
505349 GGCTTCCCGAGTT
1 GGCTTCCCGAGTT
505362 GGCTTCCCGAGT
1 GGCTTCCCGAGT
505374 CAGACTAGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.32, G:0.32, T:0.28
Consensus pattern (13 bp):
GGCTTCCCGAGTT
Found at i:506881 original size:6 final size:6
Alignment explanation
Indices: 506870--506901 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
506860 TCATAATATC
506870 TATGTA TATGTA TATGTA TATGTA TATGTA TA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TA
506902 GGGATAGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TATGTA
Found at i:508287 original size:20 final size:20
Alignment explanation
Indices: 508262--508299 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
508252 ATCCTATCCC
*
508262 CTGATAATCTTACATTCCTA
1 CTGATAATCGTACATTCCTA
508282 CTGATAATCGTACATTCC
1 CTGATAATCGTACATTCC
508300 GTGAACCAAA
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:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (20 bp):
CTGATAATCGTACATTCCTA
Found at i:509400 original size:19 final size:19
Alignment explanation
Indices: 509376--509414 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
509366 AAAGTTTGTC
509376 ACCTAACATAAAATTTTAA
1 ACCTAACATAAAATTTTAA
509395 ACCTAACATAAAATTTTAA
1 ACCTAACATAAAATTTTAA
509414 A
1 A
509415 AGAGTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (19 bp):
ACCTAACATAAAATTTTAA
Found at i:514771 original size:29 final size:30
Alignment explanation
Indices: 514724--514828 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 30
514714 ATTAAAATTG
* * *
514724 AAAAACATACACTTAAAGGGCCAAAATAGT
1 AAAAACAAAAACTTAAAGGGCCAAAATAGC
* *
514754 AAAAACAAAAACTT-AAGGGTCTAAATAGC
1 AAAAACAAAAACTTAAAGGGCCAAAATAGC
* * * * * *
514783 AAATACAAATATTTAAAGGACTAAAATAAC
1 AAAAACAAAAACTTAAAGGGCCAAAATAGC
* *
514813 AAAAATAGAAACTTAA
1 AAAAACAAAAACTTAA
514829 GGACTAAAAT
Statistics
Matches: 56, Mismatches: 18, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 23 0.41
30 33 0.59
ACGTcount: A:0.58, C:0.12, G:0.10, T:0.19
Consensus pattern (30 bp):
AAAAACAAAAACTTAAAGGGCCAAAATAGC
Found at i:515646 original size:15 final size:14
Alignment explanation
Indices: 515604--515655 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
515594 ATGTTCTTTG
*
515604 TTTGATTTTCTCTT
1 TTTGTTTTTCTCTT
*
515618 TTTGATCTTT-TCTT
1 TTTG-TTTTTCTCTT
515632 TTTGTTTATTCTCTT
1 TTTGTTT-TTCTCTT
*
515647 GTTGTTTTT
1 TTTGTTTTT
515656 TTTTCTCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
13 2 0.06
14 16 0.52
15 13 0.42
ACGTcount: A:0.06, C:0.12, G:0.10, T:0.73
Consensus pattern (14 bp):
TTTGTTTTTCTCTT
Found at i:516743 original size:82 final size:83
Alignment explanation
Indices: 516583--516780 Score: 256
Period size: 82 Copynumber: 2.4 Consensus size: 83
516573 ATCTTTAGGG
* * ** * **
516583 AGGGTGATAACACGGTTCCTACGTGATGAGAATGGCTGGTTATCTAGGGGTGACACGGCTCCTAC
1 AGGG-GATGACACGGTTCCTACGTGATGAGGACAGATGGTTATCTAGGGGTGACACAACTCCTAC
516648 GTGATGAGAAGGTCTGGTC
65 GTGATGAGAAGGTCTGGTC
* *
516667 -GGTGGATGACACGGTTCCTACGCGATGAGGACAGATGGTTATC-AGGGGTGACACAACTTCTAC
1 AGG-GGATGACACGGTTCCTACGTGATGAGGACAGATGGTTATCTAGGGGTGACACAACTCCTAC
*
516730 GTGATGAGGAGGTCTGGTC
65 GTGATGAGAAGGTCTGGTC
* *
516749 AGGGGGTGATACGGTTCCTACGTGATGAGGAC
1 AGGGGATGACACGGTTCCTACGTGATGAGGAC
516781 GACATGCCAT
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
82 61 0.62
83 37 0.37
84 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.24
Consensus pattern (83 bp):
AGGGGATGACACGGTTCCTACGTGATGAGGACAGATGGTTATCTAGGGGTGACACAACTCCTACG
TGATGAGAAGGTCTGGTC
Found at i:516778 original size:40 final size:40
Alignment explanation
Indices: 516592--516909 Score: 157
Period size: 40 Copynumber: 7.6 Consensus size: 40
516582 GAGGGTGATA
* *
516592 ACACGGTTCCTACGTGATGAGAATGGCTGGTTATCTAGGGGTG
1 ACACGGTTCCTACGTGATGAGGACGGCTGG-T-TC-AGGGGTG
* *
516635 ACACGGCTCCTACGTGATGA-GAAGGTCTGG-TC-GGTGGATG
1 ACACGGTTCCTACGTGATGAGGACGG-CTGGTTCAGG-GG-TG
* * *
516675 ACACGGTTCCTACGCGATGAGGACAGATGGTTATCAGGGGTG
1 ACACGGTTCCTACGTGATGAGGACGGCTGG-T-TCAGGGGTG
**
516717 ACACAACTT-CTACGTGATGAGGA-GGTCTGG-TCAGGGGGTG
1 ACAC-GGTTCCTACGTGATGAGGACGG-CTGGTTCA-GGGGTG
* * * * * *
516757 ATACGGTTCCTACGTGATGAGGACGACATGCCATCTTTAGGAATGATA
1 ACACGGTTCCTACGTGATGAGGACGGC-TG----GTTCAGG---GGTG
* * *
516805 ACAAGGTTCCTATGTGATGAGGACGGCTGGTTATTAGGGGTG
1 ACACGGTTCCTACGTGATGAGGACGGCTGG-T-TCAGGGGTG
* * * *
516847 ACATGGCTCCTACGTGATGAAGA-GGTCTGG-TCGGGGGATG
1 ACACGGTTCCTACGTGATGAGGACGG-CTGGTTCAGGGG-TG
**
516887 ACATTGTTCCTACGTGATGAGGA
1 ACACGGTTCCTACGTGATGAGGA
516910 TGGCATGCCA
Statistics
Matches: 212, Mismatches: 37, Indels: 55
0.70 0.12 0.18
Matches are distributed among these distances:
38 2 0.01
39 12 0.06
40 71 0.33
41 9 0.04
42 50 0.24
43 29 0.14
44 3 0.01
45 7 0.03
46 2 0.01
47 2 0.01
48 25 0.12
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.25
Consensus pattern (40 bp):
ACACGGTTCCTACGTGATGAGGACGGCTGGTTCAGGGGTG
Found at i:516836 original size:130 final size:130
Alignment explanation
Indices: 516679--516929 Score: 351
Period size: 130 Copynumber: 1.9 Consensus size: 130
516669 TGGATGACAC
* *
516679 GGTTCCTACGCGATGAGGACAGATGGTTATCAGGGGTGACACAACTTCTACGTGATGAGGAGGTC
1 GGTTCCTACGCGATGAGGACAGATGGTTATCAGGGGTGACACAACTCCTACGTGATGAAGAGGTC
*
516744 TGGTCAGGGGG-TGATACGGTTCCTACGTGATGAGGACGACATGCCATCTTTAGGAATGATAACA
66 TGGTC-GGGGGATGACACGGTTCCTACGTGATGAGGACGACATGCCATCTTTAGGAATGATAACA
516808 A
130 A
* * * * * ***
516809 GGTTCCTATGTGATGAGGACGGCTGGTTATTAGGGGTGACATGGCTCCTACGTGATGAAGAGGTC
1 GGTTCCTACGCGATGAGGACAGATGGTTATCAGGGGTGACACAACTCCTACGTGATGAAGAGGTC
** * *
516874 TGGTCGGGGGATGACATTGTTCCTACGTGATGAGGATGGCATGCCATCTTTAGGAA
66 TGGTCGGGGGATGACACGGTTCCTACGTGATGAGGACGACATGCCATCTTTAGGAA
516930 GGGATTTTGG
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
129 5 0.05
130 100 0.95
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.26
Consensus pattern (130 bp):
GGTTCCTACGCGATGAGGACAGATGGTTATCAGGGGTGACACAACTCCTACGTGATGAAGAGGTC
TGGTCGGGGGATGACACGGTTCCTACGTGATGAGGACGACATGCCATCTTTAGGAATGATAACAA
Found at i:517103 original size:67 final size:61
Alignment explanation
Indices: 517030--517248 Score: 212
Period size: 67 Copynumber: 3.4 Consensus size: 61
517020 AAAGATGTTT
517030 ATTTTGTTTCAAATGAAACAAACTCAAAGATGGGTGTTTTCAAAAGAAATTATCTCGAGAGACAA
1 ATTTTGTTTCAAA-GAAACAAACTCAAAGAT---T-TTTTCAAAAGAAATTATCTCGAGAGA-AA
517095 AA
60 AA
* * *
517097 ATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTTTCTCAAGAGAGATAA
1 ATTTTGTTTCAAA-GAAACAAACTCAAAGA-TTTTT-TCAAAAGAAATTATCTCGAGAGA-AAAA
* * * * *
517162 ATATTTATTTCCAGAGAAACAGACTCAAAGA-TTTTT-AAAAGAAACTGTCTCGAGAG-AAAA
1 AT-TTTGTTT-CAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAATTATCTCGAGAGAAAAA
*
517222 ATTTTGTATCAAGAGAAAC-AACTCAAA
1 ATTTTGTTTCAA-AGAAACAAACTCAAA
517249 TGATACTAAT
Statistics
Matches: 131, Mismatches: 16, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
58 9 0.07
59 11 0.08
60 5 0.04
62 17 0.13
63 1 0.01
64 7 0.05
65 27 0.21
66 21 0.16
67 32 0.24
68 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (61 bp):
ATTTTGTTTCAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAATTATCTCGAGAGAAAAA
Found at i:518517 original size:27 final size:26
Alignment explanation
Indices: 518423--518552 Score: 91
Period size: 27 Copynumber: 4.7 Consensus size: 26
518413 GCACTTCTTA
*
518423 TCTTTTTTCTTTCTTTTGTTTTTTAT-T
1 TCTTTTTTCTTTGTTTT-TTTTTT-TCT
* *
518450 TATTTTTTCTTTGATTTGACTTTTTTTCT
1 TCTTTTTTCTTTG-TTT--TTTTTTTTCT
***
518479 TCTTTGCACTTTGTTTTTTTGTTTTCT
1 TCTTTTTTCTTTGTTTTTTT-TTTTCT
*
518506 TCTTTTTTCTTTATTTTTTTTTCATTTGCT
1 TCTTTTTTCTTT-GTTTTTTTT--TTT-CT
*
518536 TCTTTTCTCTTTGTTTT
1 TCTTTTTTCTTTGTTTT
518553 GATTGGATCT
Statistics
Matches: 80, Mismatches: 14, Indels: 16
0.73 0.13 0.15
Matches are distributed among these distances:
26 3 0.04
27 27 0.34
28 14 0.17
29 23 0.29
30 13 0.16
ACGTcount: A:0.05, C:0.13, G:0.06, T:0.75
Consensus pattern (26 bp):
TCTTTTTTCTTTGTTTTTTTTTTTCT
Found at i:518526 original size:30 final size:30
Alignment explanation
Indices: 518441--518552 Score: 80
Period size: 30 Copynumber: 3.5 Consensus size: 30
518431 CTTTCTTTTG
* * *
518441 TTTTTTATTTATTTTTTCTTTGATTTGACTTT
1 TTTTTTCTTTATTTTTTTTTTG-TTT-ACTTC
*
518473 TTTTCTTCTTTGCACTTTGTTTTTTTGTTTTCTTC
1 TTTT-TTCTTT--A-TTT-TTTTTTTGTTTACTTC
** *
518508 TTTTTTCTTTATTTTTTTTTCATTTGCTTC
1 TTTTTTCTTTATTTTTTTTTTGTTTACTTC
* *
518538 TTTTCTCTTTGTTTT
1 TTTTTTCTTTATTTT
518553 GATTGGATCT
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
30 26 0.39
31 3 0.05
32 5 0.08
33 5 0.08
34 6 0.09
35 8 0.12
36 6 0.09
37 7 0.11
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.75
Consensus pattern (30 bp):
TTTTTTCTTTATTTTTTTTTTGTTTACTTC
Found at i:523553 original size:6 final size:6
Alignment explanation
Indices: 523542--523616 Score: 71
Period size: 6 Copynumber: 12.5 Consensus size: 6
523532 AGTGGAGCCA
* * * * *
523542 AAATTG AAATTG AAATTC AAACTC AAATTA AAATTA AAATTG AAATTG
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG
* *
523590 AAATT- CAATCTC AAATTG AAATTG AAA
1 AAATTG AAAT-TG AAATTG AAATTG AAA
523617 ACTACATAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
5 3 0.05
6 53 0.90
7 3 0.05
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (6 bp):
AAATTG
Found at i:523575 original size:18 final size:18
Alignment explanation
Indices: 523548--523612 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
523538 GCCAAAATTG
523548 AAATTGAAATTCAAACTC
1 AAATTGAAATTCAAACTC
* * * *
523566 AAATTAAAATTAAAATTG
1 AAATTGAAATTCAAACTC
*
523584 AAATTGAAATTCAATCTC
1 AAATTGAAATTCAAACTC
523602 AAATTGAAATT
1 AAATTGAAATT
523613 GAAAACTACA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.32
Consensus pattern (18 bp):
AAATTGAAATTCAAACTC
Found at i:523588 original size:36 final size:37
Alignment explanation
Indices: 523541--523617 Score: 129
Period size: 36 Copynumber: 2.1 Consensus size: 37
523531 TAGTGGAGCC
523541 AAAATTGAAATTGAAATTCAAACTCAAATTAAAATT-
1 AAAATTGAAATTGAAATTCAAACTCAAATTAAAATTG
* *
523577 AAAATTGAAATTGAAATTCAATCTCAAATTGAAATTG
1 AAAATTGAAATTGAAATTCAAACTCAAATTAAAATTG
523614 AAAA
1 AAAA
523618 CTACATAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 34 0.89
37 4 0.11
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.30
Consensus pattern (37 bp):
AAAATTGAAATTGAAATTCAAACTCAAATTAAAATTG
Found at i:525709 original size:2 final size:2
Alignment explanation
Indices: 525702--525739 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
525692 GATTCTGGAG
525702 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
525740 CATTCCCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:532448 original size:206 final size:206
Alignment explanation
Indices: 532094--532508 Score: 812
Period size: 206 Copynumber: 2.0 Consensus size: 206
532084 AAGTTGGAAT
532094 GTAAAGATTGTAACAAAGTTATACTAGTGGGATATAAAATTACCTAAAATAATATTTTATTAAAT
1 GTAAAGATTGTAACAAAGTTATACTAGTGGGATATAAAATTACCTAAAATAATATTTTATTAAAT
532159 TGTTGTTTAATATTAAAGTAGAAGATGTTGATATGAAAGTCGACCCGAGAGAGATTGGTTAGACC
66 TGTTGTTTAATATTAAAGTAGAAGATGTTGATATGAAAGTCGACCCGAGAGAGATTGGTTAGACC
532224 CCTTACAAGTTAGGATTGTAAAGAAAAATGGATGTCCCTTTTTCCCATATGTATGGGATAAGAGG
131 CCTTACAAGTTAGGATTGTAAAGAAAAATGGATGTCCCTTTTTCCCATATGTATGGGATAAGAGG
532289 GAGGTAAGATA
196 GAGGTAAGATA
532300 GTAAAGATTGTAACAAAGTTATACTAGTGGGATATAAAATTACCTAAAATAATATTTTATTAAAT
1 GTAAAGATTGTAACAAAGTTATACTAGTGGGATATAAAATTACCTAAAATAATATTTTATTAAAT
532365 TGTTGTTTAATATTAAAGTAGAAGATGTTGATATGAAAGTCGACCCGAGAGAGATTGGTTAGACC
66 TGTTGTTTAATATTAAAGTAGAAGATGTTGATATGAAAGTCGACCCGAGAGAGATTGGTTAGACC
* *
532430 CCTTACAAGTTAGGATTGTAAAGAAAAATGGATGTCCCTTTTTTCCATATGTATGGGGTAAGAGG
131 CCTTACAAGTTAGGATTGTAAAGAAAAATGGATGTCCCTTTTTCCCATATGTATGGGATAAGAGG
532495 GAGGTAAGATA
196 GAGGTAAGATA
532506 GTA
1 GTA
532509 GGTTGTCCCC
Statistics
Matches: 207, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
206 207 1.00
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.32
Consensus pattern (206 bp):
GTAAAGATTGTAACAAAGTTATACTAGTGGGATATAAAATTACCTAAAATAATATTTTATTAAAT
TGTTGTTTAATATTAAAGTAGAAGATGTTGATATGAAAGTCGACCCGAGAGAGATTGGTTAGACC
CCTTACAAGTTAGGATTGTAAAGAAAAATGGATGTCCCTTTTTCCCATATGTATGGGATAAGAGG
GAGGTAAGATA
Found at i:534691 original size:32 final size:32
Alignment explanation
Indices: 534650--534710 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
534640 CAAAAAATGA
534650 CACAAACAAAAGAAAAGAAATAAGTTAGTGTT
1 CACAAACAAAAGAAAAGAAATAAGTTAGTGTT
*
534682 CACAAACAAAAGAAAAGAAATTAGTTAGT
1 CACAAACAAAAGAAAAGAAATAAGTTAGT
534711 ACAAGAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.18
Consensus pattern (32 bp):
CACAAACAAAAGAAAAGAAATAAGTTAGTGTT
Found at i:536443 original size:13 final size:14
Alignment explanation
Indices: 536415--536448 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
536405 AAAATATTAC
536415 AAATCAAAATACAAT
1 AAAT-AAAATACAAT
536430 AAATAAAA-ACAAT
1 AAATAAAATACAAT
536443 AAATAA
1 AAATAA
536449 TCATATTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
14 4 0.21
15 4 0.21
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (14 bp):
AAATAAAATACAAT
Found at i:537609 original size:24 final size:23
Alignment explanation
Indices: 537566--537624 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 23
537556 TCATTTCTTC
* *
537566 TTCTTTCTCTTTTTCTTATTA--
1 TTCTTTCTATTTTTCTTCTTATT
*
537587 TT-TTTCTTTTTTTCTTCTATATT
1 TTCTTTCTATTTTTCTTCT-TATT
537610 TTCTTTCTATTTTTC
1 TTCTTTCTATTTTTC
537625 GAGATCCAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 14 0.45
21 4 0.13
23 2 0.06
24 11 0.35
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (23 bp):
TTCTTTCTATTTTTCTTCTTATT
Found at i:538133 original size:3 final size:3
Alignment explanation
Indices: 538125--538152 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
538115 TTTGTATTAA
538125 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
538153 TTTTTGTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:538287 original size:2 final size:2
Alignment explanation
Indices: 538280--538312 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
538270 ACTAACTAAC
538280 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
538313 TAGAAGACTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:539396 original size:110 final size:110
Alignment explanation
Indices: 539203--539422 Score: 440
Period size: 110 Copynumber: 2.0 Consensus size: 110
539193 AAATAACTCA
539203 TTGAAACACTTATTATTGTTTTAAAACACACTGGTTCCCTTTGAAAGATAATAAACGCTATATAA
1 TTGAAACACTTATTATTGTTTTAAAACACACTGGTTCCCTTTGAAAGATAATAAACGCTATATAA
539268 GAAATATAAAGCTTACTGTTAGCATCCAAGTATCATTTTCTACTT
66 GAAATATAAAGCTTACTGTTAGCATCCAAGTATCATTTTCTACTT
539313 TTGAAACACTTATTATTGTTTTAAAACACACTGGTTCCCTTTGAAAGATAATAAACGCTATATAA
1 TTGAAACACTTATTATTGTTTTAAAACACACTGGTTCCCTTTGAAAGATAATAAACGCTATATAA
539378 GAAATATAAAGCTTACTGTTAGCATCCAAGTATCATTTTCTACTT
66 GAAATATAAAGCTTACTGTTAGCATCCAAGTATCATTTTCTACTT
539423 CACGGGGATT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 110 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (110 bp):
TTGAAACACTTATTATTGTTTTAAAACACACTGGTTCCCTTTGAAAGATAATAAACGCTATATAA
GAAATATAAAGCTTACTGTTAGCATCCAAGTATCATTTTCTACTT
Found at i:540913 original size:6 final size:6
Alignment explanation
Indices: 540902--541131 Score: 291
Period size: 6 Copynumber: 38.5 Consensus size: 6
540892 AGAACAAAAA
540902 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* ** *
540950 TTCTTC TTCCTC TTCTTC CACTTC TTCTTC TTCTTC TTCTTC CTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* ** * * * *
540998 CTCCAC TTCTTC TTCTTC CTCTTC TTCCTC TTCCTC TTCTTC CTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * * *
541046 TTCCTC TTCCTC TTCTTC CTCTTC TTCTTC CTCTTC TTC-TC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * *
541093 TTCCTC TTCTTC TTCTTC TTCCTC TTCTTC CTCTTC TTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTC
541132 CTCTCACTTT
Statistics
Matches: 193, Mismatches: 30, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
5 5 0.03
6 188 0.97
ACGTcount: A:0.01, C:0.40, G:0.00, T:0.59
Consensus pattern (6 bp):
TTCTTC
Found at i:540916 original size:9 final size:9
Alignment explanation
Indices: 540902--541131 Score: 291
Period size: 9 Copynumber: 25.7 Consensus size: 9
540892 AGAACAAAAA
540902 TTCTTCTTC
1 TTCTTCTTC
540911 TTCTTCTTC
1 TTCTTCTTC
540920 TTCTTCTTC
1 TTCTTCTTC
540929 TTCTTCTTC
1 TTCTTCTTC
540938 TTCTTCTTC
1 TTCTTCTTC
540947 TTCTTCTTC
1 TTCTTCTTC
*
540956 TTCCTCTTC
1 TTCTTCTTC
**
540965 TTCCACTTC
1 TTCTTCTTC
540974 TTCTTCTTC
1 TTCTTCTTC
540983 TTCTTCTTC
1 TTCTTCTTC
* *
540992 CTCTTCCTC
1 TTCTTCTTC
**
541001 CACTTCTTC
1 TTCTTCTTC
*
541010 TTCTTCCTC
1 TTCTTCTTC
*
541019 TTCTTCCTC
1 TTCTTCTTC
*
541028 TTCCTCTTC
1 TTCTTCTTC
*
541037 TTCCTCTTC
1 TTCTTCTTC
*
541046 TTCCTCTTC
1 TTCTTCTTC
*
541055 CTCTTCTTC
1 TTCTTCTTC
*
541064 CTCTTCTTC
1 TTCTTCTTC
*
541073 TTCCTCTTC
1 TTCTTCTTC
541082 TTC-TCTTC
1 TTCTTCTTC
*
541090 TTCTTCCTC
1 TTCTTCTTC
541099 TTCTTCTTC
1 TTCTTCTTC
*
541108 TTCTTCCTC
1 TTCTTCTTC
*
541117 TTCTTCCTC
1 TTCTTCTTC
541126 TTCTTC
1 TTCTTC
541132 CTCTCACTTT
Statistics
Matches: 200, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
8 8 0.04
9 192 0.96
ACGTcount: A:0.01, C:0.40, G:0.00, T:0.59
Consensus pattern (9 bp):
TTCTTCTTC
Found at i:540922 original size:15 final size:15
Alignment explanation
Indices: 540902--541131 Score: 291
Period size: 15 Copynumber: 15.4 Consensus size: 15
540892 AGAACAAAAA
540902 TTCTTCTTCTTCTTC
1 TTCTTCTTCTTCTTC
540917 TTCTTCTTCTTCTTC
1 TTCTTCTTCTTCTTC
540932 TTCTTCTTCTTCTTC
1 TTCTTCTTCTTCTTC
*
540947 TTCTTCTTCTTCCTC
1 TTCTTCTTCTTCTTC
**
540962 TTCTTCCACTTCTTC
1 TTCTTCTTCTTCTTC
540977 TTCTTCTTCTTCTTC
1 TTCTTCTTCTTCTTC
* * **
540992 CTCTTCCTCCACTTC
1 TTCTTCTTCTTCTTC
*
541007 TTCTTCTTCCTCTTC
1 TTCTTCTTCTTCTTC
* *
541022 TTCCTCTTCCTCTTC
1 TTCTTCTTCTTCTTC
* *
541037 TTCCTCTTCTTCCTC
1 TTCTTCTTCTTCTTC
* *
541052 TTCCTCTTCTTCCTC
1 TTCTTCTTCTTCTTC
*
541067 TTCTTCTTCCTCTTC
1 TTCTTCTTCTTCTTC
541082 TTC-TCTTCTTCTTC
1 TTCTTCTTCTTCTTC
*
541096 CTCTTCTTCTTCTTC
1 TTCTTCTTCTTCTTC
* *
541111 TTCCTCTTCTTCCTC
1 TTCTTCTTCTTCTTC
541126 TTCTTC
1 TTCTTC
541132 CTCTCACTTT
Statistics
Matches: 189, Mismatches: 25, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
14 12 0.06
15 177 0.94
ACGTcount: A:0.01, C:0.40, G:0.00, T:0.59
Consensus pattern (15 bp):
TTCTTCTTCTTCTTC
Found at i:562516 original size:3 final size:3
Alignment explanation
Indices: 562508--562560 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
562498 TGAGTTGTTT
* * * * * *
562508 TTA TTA TTA TTA TCA TCA TCA TTA TTA TTA TTA CTA ATA TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
562556 TTA TT
1 TTA TT
562561 TTCATATTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:562549 original size:18 final size:21
Alignment explanation
Indices: 562508--562559 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 21
562498 TGAGTTGTTT
*
562508 TTATTATTATTATCATCATCA
1 TTATTATTATTATCATAATCA
562529 TTATTATTATTA-C-TAAT-A
1 TTATTATTATTATCATAATCA
*
562547 TTATTTTTATTAT
1 TTATTATTATTAT
562560 TTTCATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 12 0.43
19 3 0.11
20 1 0.04
21 12 0.43
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATTATTATTATCATAATCA
Found at i:562556 original size:21 final size:23
Alignment explanation
Indices: 562505--562560 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
562495 ATCTGAGTTG
*
562505 TTTTTATTATTATTATCATCATCA
1 TTTTTATTATTACTA-CATCATCA
* *
562529 TTATTATTATTACTA-AT-ATTA
1 TTTTTATTATTACTACATCATCA
562550 TTTTTATTATT
1 TTTTTATTATT
562561 TTCATATTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 13 0.46
22 2 0.07
24 13 0.46
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTTATTATTACTACATCATCA
Found at i:566552 original size:13 final size:13
Alignment explanation
Indices: 566534--566564 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
566524 TTTCAAGGAA
566534 GAAGCTCCGAGAC
1 GAAGCTCCGAGAC
*
566547 GAAGCTCCGAGAT
1 GAAGCTCCGAGAC
566560 GAAGC
1 GAAGC
566565 ATTGACCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.32, T:0.10
Consensus pattern (13 bp):
GAAGCTCCGAGAC
Found at i:569044 original size:43 final size:43
Alignment explanation
Indices: 568976--569059 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 43
568966 TTCTTAATAT
* * *
568976 TAAAAAATAAATAAATATTAATAAAA-ATAAGATATTTTTTCC
1 TAAAAAATAAATAAATATGAATAAAACAAAAAATATTTTTTCC
*
569018 TAAAAAATAATGTAAATA-GAACTAAAACAAAAAATATTTTTT
1 TAAAAAATAA-ATAAATATGAA-TAAAACAAAAAATATTTTTT
569060 TTATATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
42 12 0.34
43 11 0.31
44 12 0.34
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (43 bp):
TAAAAAATAAATAAATATGAATAAAACAAAAAATATTTTTTCC
Done.