Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009066.1 Hibiscus syriacus cultivar Beakdansim tig00112490_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: 821833
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:379123 original size:15 final size:15
Alignment explanation
Indices: 379100--379135 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
379090 ATGCTCAAAA
*
379100 TATCAAGTCTACTGC
1 TATCTAGTCTACTGC
379115 TATCTAGTCTACTGC
1 TATCTAGTCTACTGC
379130 TATCTA
1 TATCTA
379136 CCCTGCTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (15 bp):
TATCTAGTCTACTGC
Found at i:389804 original size:45 final size:45
Alignment explanation
Indices: 389754--389858 Score: 142
Period size: 45 Copynumber: 2.3 Consensus size: 45
389744 TTGGACCCTT
389754 AGTGCATCGATGCATCAAATACATTCGATG-TTTCA-AAATAGCCAG
1 AGTGCATCGATGCATCAAATACATTCGATGTTTTCATAAA-A-CCAG
* * * *
389799 AGTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAATCTG
1 AGTGCATCGATGCATCAAATACATTCGATGTTTTCATAAAACCAG
389844 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
389859 AGTATGTGCA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
45 45 0.83
46 6 0.11
47 3 0.06
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATACATTCGATGTTTTCATAAAACCAG
Found at i:390493 original size:15 final size:15
Alignment explanation
Indices: 390473--390502 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
390463 ACACTTCTCC
390473 CCTTTAAAATTTTTA
1 CCTTTAAAATTTTTA
*
390488 CCTTTAACATTTTTA
1 CCTTTAAAATTTTTA
390503 TATTTCTCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (15 bp):
CCTTTAAAATTTTTA
Found at i:392423 original size:23 final size:22
Alignment explanation
Indices: 392393--392472 Score: 101
Period size: 21 Copynumber: 3.6 Consensus size: 22
392383 GCATGACCTT
392393 GTGCATCGATGCACATTCAATG
1 GTGCATCGATGCACATTCAATG
* *
392415 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAATG
*
392437 GTGTATCGATGCACATTCAA-G
1 GTGCATCGATGCACATTCAATG
392458 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
392473 TGTTAGGTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
21 17 0.35
22 16 0.33
23 16 0.33
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAATG
Found at i:392447 original size:44 final size:42
Alignment explanation
Indices: 392397--392491 Score: 122
Period size: 42 Copynumber: 2.2 Consensus size: 42
392387 GACCTTGTGC
*
392397 ATCGATGCACATTCAATGCG-TGCATCGGTGCACCT-TCATGGTGT
1 ATCGATGCACATTCAA-G-GATGCATCGATGCA-CTGTCA-GGTGT
*
392441 ATCGATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
392483 ATCGATGCA
1 ATCGATGCA
392492 TTAAGCAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
42 17 0.36
43 14 0.30
44 16 0.34
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
Found at i:392488 original size:20 final size:21
Alignment explanation
Indices: 392397--392491 Score: 86
Period size: 21 Copynumber: 4.4 Consensus size: 21
392387 GACCTTGTGC
*
392397 ATCGATGCACATTCAATGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* * *
392420 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
*
392441 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
392463 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
392483 ATCGATGCA
1 ATCGATGCA
392492 TTAAGCAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 22 0.37
22 14 0.23
23 13 0.22
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:401124 original size:53 final size:53
Alignment explanation
Indices: 401043--401144 Score: 168
Period size: 53 Copynumber: 1.9 Consensus size: 53
401033 TACTTTCGGC
* *
401043 ACTATGTATGCACCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCAGA
1 ACTATGTATGCACCCATAGAATTCATAATGAGTTTGTGAATTACCATTTCAGA
* *
401096 ACTATGTGTGCATCCATAGAATTCATAATGAGTTTGTGAATTACCATTT
1 ACTATGTATGCACCCATAGAATTCATAATGAGTTTGTGAATTACCATTT
401145 TGGCACTTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (53 bp):
ACTATGTATGCACCCATAGAATTCATAATGAGTTTGTGAATTACCATTTCAGA
Found at i:401361 original size:27 final size:27
Alignment explanation
Indices: 401319--401370 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
401309 TATTATTATG
*
401319 ATTTATATGATTTAATTCATATTTTGAT
1 ATTTATATGATATAATTC-TATTTTGAT
401347 ATTT-TATGATATAATTCTATTTTG
1 ATTTATATGATATAATTCTATTTTG
401371 GTTACACCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
27 12 0.52
28 4 0.17
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.58
Consensus pattern (27 bp):
ATTTATATGATATAATTCTATTTTGAT
Found at i:406715 original size:31 final size:31
Alignment explanation
Indices: 406649--406708 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
406639 CAATTTAAGG
*
406649 CAAAATAGTTTTTGGACTTGAATTGAATTTA
1 CAAAATAGTATTTGGACTTGAATTGAATTTA
406680 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATAGTATTTGGACTTGAATTGAATTTA
406709 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (31 bp):
CAAAATAGTATTTGGACTTGAATTGAATTTA
Found at i:406909 original size:21 final size:21
Alignment explanation
Indices: 406885--406926 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
406875 ATTTGAATAT
**
406885 TATGAAGGGGTATTGATTCCC
1 TATGAAGGGGTACCGATTCCC
406906 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
406927 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:409068 original size:21 final size:21
Alignment explanation
Indices: 409042--409081 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
409032 ATTGATACTT
409042 TAGTAGGGGTATCGATACTCC
1 TAGTAGGGGTATCGATACTCC
409063 TAGTAGGGGTATCGATACT
1 TAGTAGGGGTATCGATACT
409082 AAGGCATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (21 bp):
TAGTAGGGGTATCGATACTCC
Found at i:413634 original size:38 final size:39
Alignment explanation
Indices: 413552--413634 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
413542 AAAGGGTACC
* *
413552 TGAAAA-TTCAAATAAAAATAAATCAAAAAACTAAAAAT
1 TGAAAATTTAAAATAAAAATAAATCAAAAAACGAAAAAT
* * *
413590 TTAAAATTTAAAATAAAAA-AAATTGAACAAACGAAAAA-
1 TGAAAATTTAAAATAAAAATAAA-TCAAAAAACGAAAAAT
413628 TGAAAAT
1 TGAAAAT
413635 AAAATGAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
38 14 0.38
39 23 0.62
ACGTcount: A:0.67, C:0.06, G:0.05, T:0.22
Consensus pattern (39 bp):
TGAAAATTTAAAATAAAAATAAATCAAAAAACGAAAAAT
Found at i:414530 original size:17 final size:18
Alignment explanation
Indices: 414478--414546 Score: 131
Period size: 18 Copynumber: 3.9 Consensus size: 18
414468 CAAAGTCAAT
414478 TTTTGATTTTGAAAATTG
1 TTTTGATTTTGAAAATTG
414496 TTTTGATTTTGAAAATTG
1 TTTTGATTTTGAAAATTG
414514 TTTTGATTTTG-AAATTG
1 TTTTGATTTTGAAAATTG
414531 TTTTGATTTTGAAAAT
1 TTTTGATTTTGAAAAT
414547 AAGCGCAGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
17 17 0.34
18 33 0.66
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.57
Consensus pattern (18 bp):
TTTTGATTTTGAAAATTG
Found at i:414536 original size:35 final size:36
Alignment explanation
Indices: 414478--414546 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
414468 CAAAGTCAAT
414478 TTTTGATTTTGAAAATTGTTTTGATTTTGAAAATTG
1 TTTTGATTTTGAAAATTGTTTTGATTTTGAAAATTG
414514 TTTTGATTTTG-AAATTGTTTTGATTTTGAAAAT
1 TTTTGATTTTGAAAATTGTTTTGATTTTGAAAAT
414547 AAGCGCAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 22 0.67
36 11 0.33
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.57
Consensus pattern (36 bp):
TTTTGATTTTGAAAATTGTTTTGATTTTGAAAATTG
Found at i:416713 original size:5 final size:5
Alignment explanation
Indices: 416699--416728 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
416689 GTAACAAAAG
*
416699 AATCA GATCA AATCA AATCA AATCA AATCA
1 AATCA AATCA AATCA AATCA AATCA AATCA
416729 GAAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.20, G:0.03, T:0.20
Consensus pattern (5 bp):
AATCA
Found at i:417053 original size:41 final size:41
Alignment explanation
Indices: 416996--417077 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
416986 GAGTGTGAAA
416996 ATGGCATTGGGAACGATAAAGAAGGAAAGGAAGAAGGAATT
1 ATGGCATTGGGAACGATAAAGAAGGAAAGGAAGAAGGAATT
417037 ATGGCATTGGGAACGATAAAGAAGGAAAGGAAGAAGGAATT
1 ATGGCATTGGGAACGATAAAGAAGGAAAGGAAGAAGGAATT
417078 TGAACAAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.46, C:0.05, G:0.34, T:0.15
Consensus pattern (41 bp):
ATGGCATTGGGAACGATAAAGAAGGAAAGGAAGAAGGAATT
Found at i:419938 original size:38 final size:37
Alignment explanation
Indices: 419874--420275 Score: 325
Period size: 36 Copynumber: 10.9 Consensus size: 37
419864 ATTAATATAG
* * *
419874 TATAGTTTCTGAAAATA-TTTTTGAAAAAATATAATA
1 TATAGTTTTTGAAAACATTTTTTGAAAACATATAATA
* *
419910 TATAGTTTTTAGAAAACGTTTTTTGAAAACGTATAATA
1 TATAGTTTTT-GAAAACATTTTTTGAAAACATATAATA
* * * *
419948 TATACTTTTTGAAAACAATTTTTGAATATATATATATTA
1 TATAGTTTTTGAAAACATTTTTTGAA-A-ACATATAATA
** *
419987 TATAG-TTTTGAAAACATTTTTTGAAAGTATATATTA
1 TATAGTTTTTGAAAACATTTTTTGAAAACATATAATA
** * * *
420023 TATAG-TTTTGAAAACGGTTTTAGAATATATATATATA
1 TATAGTTTTTGAAAACATTTTTTGAAAACATATA-ATA
* *
420060 TATATGGTTTTGAAAACATATTTTTG--AA-A-AT-GTA
1 TATA-GTTTTTGAAAACAT-TTTTTGAAAACATATAATA
* *
420094 TATAGTTTTT-AAAATA-TTTTTGAAAACGTAT-ATAA
1 TATAGTTTTTGAAAACATTTTTTGAAAACATATAAT-A
420129 TATAG-TTTTGAAAACATATTTTTTTGAAAACATATAATA
1 TATAGTTTTTGAAAAC--A-TTTTTTGAAAACATATAATA
420168 TATAG-TTTTGAAAACATATTTTTTTTGAAAACATATAATA
1 TATAGTTTTTGAAAAC--A--TTTTTTGAAAACATATAATA
* *
420208 TATAGTTTTTTAAAATA-TTTTTGAAAACATATAATA
1 TATAGTTTTTGAAAACATTTTTTGAAAACATATAATA
* *
420244 TAAAG-TTTT-AAAATGA-TTTTTGAAAACATATA
1 TATAGTTTTTGAAAA-CATTTTTTGAAAACATATA
420276 GTTTTTTAAA
Statistics
Matches: 309, Mismatches: 35, Indels: 45
0.79 0.09 0.12
Matches are distributed among these distances:
30 6 0.02
32 7 0.02
33 5 0.02
34 17 0.06
35 31 0.10
36 71 0.23
37 28 0.09
38 48 0.16
39 55 0.18
40 33 0.11
41 8 0.03
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (37 bp):
TATAGTTTTTGAAAACATTTTTTGAAAACATATAATA
Found at i:420096 original size:32 final size:30
Alignment explanation
Indices: 420060--420127 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
420050 TATATATATA
* *
420060 TATATGGTTTTGAAAACATATTTTTGAAAATG
1 TATATAGTTTT-AAAA-ATATTTTTGAAAACG
*
420092 TATATAGTTTTTAAAATATTTTTGAAAACG
1 TATATAGTTTTAAAAATATTTTTGAAAACG
420122 TATATA
1 TATATA
420128 ATATAGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 20 0.61
31 3 0.09
32 10 0.30
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.46
Consensus pattern (30 bp):
TATATAGTTTTAAAAATATTTTTGAAAACG
Found at i:420132 original size:106 final size:109
Alignment explanation
Indices: 419874--420275 Score: 323
Period size: 113 Copynumber: 3.6 Consensus size: 109
419864 ATTAATATAG
* ** * *
419874 TATAGTTTCTGAAAATATTTTTGAAAAAATATA-ATATATAGTTTTTAGAAAAC-GTTTTTTGAA
1 TATAGTTT-TTAAAATATTTTTGAAAACGTATATA-ATATAG-TTTT-GAAAACAGGTTTTAGAA
* * *
419937 AACGTATAATATATACTTTTTGAAAACA-A-TTTTTGAATATATATATATTA
62 AACATATAATATATA-GTTTTGAAAACATATTTTTTGAA-ACATATA-A-TA
* *
419987 TATAGTTTTGAAAACATTTTTTG-AAA-GTATATATTATATAGTTTTGAAAAC-GGTTTTAGAAT
1 TATAGTTTTTAAAATA-TTTTTGAAAACGTATATA--ATATAGTTTTGAAAACAGGTTTTAGAA-
* * *
420049 ATATATATATATATATGGTTTTGAAAACATA-TTTTTG-AA-A-AT-GTA
62 A-ACATATA-ATATATAGTTTTGAAAACATATTTTTTGAAACATATAATA
** *
420094 TATAGTTTTTAAAATATTTTTGAAAACGTATATAATATAGTTTTGAAAACATATTTTTTTGAAAA
1 TATAGTTTTTAAAATATTTTTGAAAACGTATATAATATAGTTTTGAAAAC--AGGTTTTAGAAAA
420159 CATATAATATATAGTTTTGAAAACATATTTTTTTTGAAAACATATAATA
64 CATATAATATATAGTTTTGAAAACATA--TTTTTTG-AAACATATAATA
* * *
420208 TATAGTTTTTTAAAATATTTTTGAAAAC--ATATAATATAAAGTTTT-AAAA-TGATTTTTGAAA
1 TATAG-TTTTTAAAATATTTTTGAAAACGTATATAATAT--AGTTTTGAAAACAGGTTTTAGAAA
420269 ACATATA
63 ACATATA
420276 GTTTTTTAAA
Statistics
Matches: 246, Mismatches: 20, Indels: 48
0.78 0.06 0.15
Matches are distributed among these distances:
106 42 0.17
107 25 0.10
108 8 0.03
109 13 0.05
110 2 0.01
111 37 0.15
112 18 0.07
113 49 0.20
114 24 0.10
115 28 0.11
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (109 bp):
TATAGTTTTTAAAATATTTTTGAAAACGTATATAATATAGTTTTGAAAACAGGTTTTAGAAAACA
TATAATATATAGTTTTGAAAACATATTTTTTGAAACATATAATA
Found at i:420138 original size:23 final size:22
Alignment explanation
Indices: 420111--420209 Score: 71
Period size: 23 Copynumber: 5.0 Consensus size: 22
420101 TTTAAAATAT
420111 TTTTGAAAACGTATATAATATAG
1 TTTTGAAAAC-TATATAATATAG
420134 TTTTGAAAAC-ATAT--T-T--
1 TTTTGAAAACTATATAATATAG
420150 TTTTGAAAAC-ATATAATATATAG
1 TTTTGAAAACTATAT-A-ATATAG
*
420173 TTTTGAAAAC-ATAT--T-T-T
1 TTTTGAAAACTATATAATATAG
420190 TTTTGAAAAC-ATATAATATA
1 TTTTGAAAACTATATAATATA
420210 TAGTTTTTTA
Statistics
Matches: 64, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
16 14 0.22
17 14 0.22
18 2 0.03
19 3 0.05
20 2 0.03
21 5 0.08
23 24 0.38
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (22 bp):
TTTTGAAAACTATATAATATAG
Found at i:420216 original size:23 final size:23
Alignment explanation
Indices: 420150--420216 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
420140 AAACATATTT
420150 TTTTGAAAACATATAATATATAG
1 TTTTGAAAACATATAATATATAG
420173 TTTTGAAAACATAT--T-T-T--
1 TTTTGAAAACATATAATATATAG
420190 TTTTGAAAACATATAATATATAG
1 TTTTGAAAACATATAATATATAG
420213 TTTT
1 TTTT
420217 TTAAAATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
17 14 0.37
19 2 0.05
20 2 0.05
21 2 0.05
23 18 0.47
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.46
Consensus pattern (23 bp):
TTTTGAAAACATATAATATATAG
Found at i:420303 original size:32 final size:30
Alignment explanation
Indices: 420207--420312 Score: 124
Period size: 32 Copynumber: 3.3 Consensus size: 30
420197 AACATATAAT
420207 ATATAGTTTTTTAAAAT-ATTTTTGAAAAC
1 ATATAGTTTTTTAAAATGATTTTTGAAAAC
*
420236 ATATAATATAAAGTTTTAAAATGATTTTTGAAAAC
1 ATATAGT-T----TTTTAAAATGATTTTTGAAAAC
*
420271 ATATAGTTTTTTAAAATGATTTTTTTGGAAAC
1 ATATAGTTTTTTAAAATGA--TTTTTGAAAAC
420303 ATATAGTTTT
1 ATATAGTTTT
420313 AGAAATGCAT
Statistics
Matches: 66, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
29 6 0.09
30 12 0.18
32 20 0.30
34 10 0.15
35 18 0.27
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (30 bp):
ATATAGTTTTTTAAAATGATTTTTGAAAAC
Found at i:420313 original size:30 final size:30
Alignment explanation
Indices: 420247--420326 Score: 101
Period size: 32 Copynumber: 2.6 Consensus size: 30
420237 TATAATATAA
420247 AGTTTTAAAATGA--TTTTTGAAAACATAT
1 AGTTTTAAAATGATTTTTTTGAAAACATAT
*
420275 AGTTTTTTAAAATGATTTTTTTGGAAACATAT
1 AG--TTTTAAAATGATTTTTTTGAAAACATAT
420307 AGTTTTAGAAATGCATTTTT
1 AGTTTTA-AAATG-ATTTTT
420327 CGACATATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
28 2 0.04
30 16 0.36
31 5 0.11
32 22 0.49
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.47
Consensus pattern (30 bp):
AGTTTTAAAATGATTTTTTTGAAAACATAT
Found at i:421506 original size:5 final size:5
Alignment explanation
Indices: 421487--421524 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
421477 TATTTCCTTA
*
421487 ATTTT ATTTT -TATTT AATTT ATTTT ATTTT ATTTT ATT
1 ATTTT ATTTT AT-TTT ATTTT ATTTT ATTTT ATTTT ATT
421525 GCTTTTCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 1 0.03
5 28 0.97
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:421672 original size:12 final size:12
Alignment explanation
Indices: 421657--421681 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
421647 GAATCGAAAT
421657 TTTAAATTTCAA
1 TTTAAATTTCAA
421669 TTTAAATTTCAA
1 TTTAAATTTCAA
421681 T
1 T
421682 GTTTTGCAAT
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAAATTTCAA
Found at i:424445 original size:98 final size:98
Alignment explanation
Indices: 424261--424455 Score: 302
Period size: 98 Copynumber: 2.0 Consensus size: 98
424251 CGTATACTAA
* * *
424261 GATTATAATATTATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACAACTCGGCT
1 GATTATAATATTATACAATAAAGCTTGAGTTGTCCCTCTAGAACAATTAGTTAAACAACCCGGCT
424326 TTATGGATAAGATTCAACTAG-CTGATAAAGGT
66 TTATGGATAAGATTCAACTAGCCTGATAAAGGT
* * **
424358 GATTATAATGTATATACAATAAAGCTTGAGTTGTCCCTCTAGAACAATTAGTTAATCGCCCCGGC
1 GATTATAATAT-TATACAATAAAGCTTGAGTTGTCCCTCTAGAACAATTAGTTAAACAACCCGGC
*
424423 TTTATGGATAAGATTCAGCTAGCCTGATAAAGG
65 TTTATGGATAAGATTCAACTAGCCTGATAAAGG
424456 CAAATTACAA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
97 10 0.11
98 68 0.77
99 10 0.11
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (98 bp):
GATTATAATATTATACAATAAAGCTTGAGTTGTCCCTCTAGAACAATTAGTTAAACAACCCGGCT
TTATGGATAAGATTCAACTAGCCTGATAAAGGT
Found at i:425887 original size:85 final size:85
Alignment explanation
Indices: 425739--426508 Score: 1033
Period size: 85 Copynumber: 9.1 Consensus size: 85
425729 AAACTATTCG
* *
425739 CAGCTTAGCTCAAGGC-AGCAAGGGCTATCTGTCAACAAAAACCTTCGAGTTTGATTACATTCAG
1 CAGCATAGCTCAAGGCGAG-AAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAG
* *
425803 CTCAAGGGTATATCAAACTTA
65 CTCAAGGGCATATCAAATTTA
** * ** * *
425824 CAATATAGCTCAAGGCGAGAAGGGTTATCTGTCAATGAAAACCTTCAAGTTCAATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
* *
425889 TCAAAGGCATGTCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * *
425909 CAGCATAGCTCAAGGCTAGAAGAGCTATCTGTCAACAAAAACCTTTGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
425974 TCAAGGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * * * **
425994 CAGCATAGCTCAAGGTGAGGAGGGCTATCTATC-A-AAAAACCTTCAAGTTCGATTACATTTTGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
426057 TCAAGGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * * * * * **
426077 CAGCATAGATCAATGCGAGAAGGGTTATCTGTCAATAAAAACCTTCAAGTTTGATTACATTTTGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
426142 TCAAGGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * * * * * * * *
426162 CAGCATAGATCAATGCGAAAAGGGTTACCTGCCAATAAAAACCTTCAAGTTCGATTACATTCGGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
*
426227 TCAATGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * *
426247 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTTAACAAAAACCTTCGAGGTCGATTATATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
*
426312 TCGAGGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * * *
426332 CAACATAGCTTAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCACC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
*
426397 TCAATGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
** *
426417 CATAATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAAC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
*
426482 TCAAGAGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
426502 CAGCATA
1 CAGCATA
426509 TCAAATTTAC
Statistics
Matches: 602, Mismatches: 80, Indels: 6
0.88 0.12 0.01
Matches are distributed among these distances:
83 72 0.12
84 2 0.00
85 526 0.87
86 2 0.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (85 bp):
CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
TCAAGGGCATATCAAATTTA
Found at i:426270 original size:170 final size:170
Alignment explanation
Indices: 425739--426669 Score: 1123
Period size: 170 Copynumber: 5.4 Consensus size: 170
425729 AAACTATTCG
* *
425739 CAGCTTAGCTCAAGGC-AGCAAGGGCTATCTGTCAACAAAAACCTTCGAGTTTGATTACATTCAG
1 CAGCATAGCTCAAGGCGAG-AAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAG
* * ** *
425803 CTCAAGGGTATATCAAACTTACAATATAGCTCAAGGCGAGAAGGGTTATCTGTCAATGAAAACCT
65 CTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAAACCT
* * *
425868 TCAAGTTCAATTACATTCAGCTCAAAGGCATGTCAAATTTA
130 TCAAGTTCGATTACATTCAGCTCAATGGCATATCAAATTTA
* * *
425909 CAGCATAGCTCAAGGCTAGAAGAGCTATCTGTCAACAAAAACCTTTGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
* * * *
425974 TCAAGGGCATATCAAATTTACAGCATAGCTCAAGGTGAGGAGGGCTATCTATC-A-AAAAACCTT
66 TCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAAACCTT
** *
426037 CAAGTTCGATTACATTTTGCTCAAGGGCATATCAAATTTA
131 CAAGTTCGATTACATTCAGCTCAATGGCATATCAAATTTA
* * * * * * **
426077 CAGCATAGATCAATGCGAGAAGGGTTATCTGTCAATAAAAACCTTCAAGTTTGATTACATTTTGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
* * * * *
426142 TCAAGGGCATATCAAATTTACAGCATAGATCAATGCGAAAAGGGTTACCTGCCAATAAAAACCTT
66 TCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAAACCTT
*
426207 CAAGTTCGATTACATTCGGCTCAATGGCATATCAAATTTA
131 CAAGTTCGATTACATTCAGCTCAATGGCATATCAAATTTA
* * *
426247 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTTAACAAAAACCTTCGAGGTCGATTATATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
* * * *
426312 TCGAGGGCATATCAAATTTACAACATAGCTTAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTT
66 TCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAAACCTT
* *
426377 CGAGTTCGATTACATTCACCTCAATGGCATATCAAATTTA
131 CAAGTTCGATTACATTCAGCTCAATGGCATATCAAATTTA
** *
426417 CATAATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAAC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
* * * * **
426482 TCAAGAGCATATCAAATTTACAGCATATCAAATTTACAACATATCTCAAGGTGATAAGGCCTATC
66 TCAAG-G---------------GCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATC
*** *
426547 TGTCAGCGAAAACCTTCGAGTTCGATTACATTCAGCTCAA-GAGCATATCAAATTTA
115 TGTCAATAAAAACCTTCAAGTTCGATTACATTCAGCTCAATG-GCATATCAAATTTA
* * * * *
426603 CATCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGATTTTGATTCCATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
426668 TC
66 TC
426670 GATGACAACA
Statistics
Matches: 655, Mismatches: 86, Indels: 24
0.86 0.11 0.03
Matches are distributed among these distances:
168 141 0.22
169 2 0.00
170 359 0.55
171 3 0.00
185 1 0.00
186 149 0.23
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (170 bp):
CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
TCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAAACCTT
CAAGTTCGATTACATTCAGCTCAATGGCATATCAAATTTA
Found at i:426506 original size:16 final size:16
Alignment explanation
Indices: 426487--426526 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
426477 TCAACTCAAG
426487 AGCATATCAAATTTAC
1 AGCATATCAAATTTAC
426503 AGCATATCAAATTTAC
1 AGCATATCAAATTTAC
*
426519 AACATATC
1 AGCATATC
426527 TCAAGGTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (16 bp):
AGCATATCAAATTTAC
Found at i:426578 original size:101 final size:101
Alignment explanation
Indices: 426403--426609 Score: 326
Period size: 101 Copynumber: 2.0 Consensus size: 101
426393 CACCTCAATG
*
426403 GCATATCAAATTTACATAATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTT
1 GCATATCAAATTTACATAATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGTT
426468 CGATTACATTCAACTCAAGAGCATATCAAATTTACA
66 CGATTACATTCAACTCAAGAGCATATCAAATTTACA
* * * * *
426504 GCATATCAAATTTACA-ACATATCTCAAGGTGATAAGGCCTATCTGTCAGCGAAAACCTTCGAGT
1 GCATATCAAATTTACATA-ATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGT
*
426568 TCGATTACATTCAGCTCAAGAGCATATCAAATTTACA
65 TCGATTACATTCAACTCAAGAGCATATCAAATTTACA
*
426605 TCATA
1 GCATA
426610 GCTCAAGGCG
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
100 1 0.01
101 96 0.99
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (101 bp):
GCATATCAAATTTACATAATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGTT
CGATTACATTCAACTCAAGAGCATATCAAATTTACA
Found at i:426634 original size:186 final size:186
Alignment explanation
Indices: 426318--426665 Score: 554
Period size: 186 Copynumber: 1.9 Consensus size: 186
426308 CAGCTCGAGG
* **
426318 GCATATCAAATTTACAACATAGCTTAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTT
1 GCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGTT
426383 CGATTACATTCACCTCAATGGCATATCAAATTTACATAATAGCTCAAGGCGAGAAGGGCTATCTG
66 CGATTACATTCACCTCAATGGCATATCAAATTTACATAATAGCTCAAGGCGAGAAGGGCTATCTG
426448 TCAACAAAAACCTTCGAGTTCGATTACATTCAACTCAAGAGCATATCAAATTTACA
131 TCAACAAAAACCTTCGAGTTCGATTACATTCAACTCAAGAGCATATCAAATTTACA
* * * * *
426504 GCATATCAAATTTACAACATATCTCAAGGTGATAAGGCCTATCTGTCAGCGAAAACCTTCGAGTT
1 GCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGTT
* * *
426569 CGATTACATTCAGCTCAA-GAGCATATCAAATTTACATCATAGCTCAAGGCGAGAAGGGTTATCT
66 CGATTACATTCACCTCAATG-GCATATCAAATTTACATAATAGCTCAAGGCGAGAAGGGCTATCT
* * *
426633 GTCAACAAAAACCTTCGATTTTGATTCCATTCA
130 GTCAACAAAAACCTTCGAGTTCGATTACATTCA
426666 GCTCGATGAC
Statistics
Matches: 147, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
185 1 0.01
186 146 0.99
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (186 bp):
GCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGTT
CGATTACATTCACCTCAATGGCATATCAAATTTACATAATAGCTCAAGGCGAGAAGGGCTATCTG
TCAACAAAAACCTTCGAGTTCGATTACATTCAACTCAAGAGCATATCAAATTTACA
Found at i:426646 original size:85 final size:85
Alignment explanation
Indices: 426503--426669 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 85
426493 TCAAATTTAC
* * * * *
426503 AGCATATCAAATTTACAACATATCTCAAGGTGATAAGGCCTATCTGTCAGCGAAAACCTTCGAGT
1 AGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGT
426568 TCGATTACATTCAGCTCAAG
66 TCGATTACATTCAGCTCAAG
* ** *
426588 AGCATATCAAATTTACATCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGATT
1 AGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGT
* *
426653 TTGATTCCATTCAGCTC
66 TCGATTACATTCAGCTC
426670 GATGACAACA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (85 bp):
AGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGCCTATCTGTCAACAAAAACCTTCGAGT
TCGATTACATTCAGCTCAAG
Found at i:427382 original size:37 final size:37
Alignment explanation
Indices: 427249--427546 Score: 202
Period size: 37 Copynumber: 7.9 Consensus size: 37
427239 ATTAATATAG
* * *
427249 TATAGTTTTTG-AAA-ATGTTTTTGAAAAAATATAATA
1 TATAG-TTTTGAAAACATATTTTTGAAAATATATATTA
**
427285 TATAGTTTTTAGAAAAC-GGTTTTTGAAAACGTATA-ATT-
1 TATAG-TTTT-GAAAACATATTTTTGAAAA--TATATATTA
*
427323 TATACTTTTTGAAAACA-ATTTTTGAAAATATATATTA
1 TATA-GTTTTGAAAACATATTTTTGAAAATATATATTA
* *
427360 TATAGTTTTGAAAACATTTTTTTGAAAGTATATATTA
1 TATAGTTTTGAAAACATATTTTTGAAAATATATATTA
* ** *
427397 TATAGTTCTGAAAAC-GGTTTTAGAATATATATATATATATA
1 TATAGTTTTGAAAACATATTTTTG-A-A-A-ATATATAT-TA
* *
427438 TAATATGGTTTTAAAAACATATTTTTGAAAATGTATATAATA
1 T-ATA--GTTTTGAAAACATATTTTTGAAAA--TATATATTA
* * * *
427480 TATAGTTTT-TAAA-ATATATTTGAAAACATATATAA
1 TATAGTTTTGAAAACATATTTTTGAAAATATATATTA
* *
427515 TATAGTTTTAAAAACATATTTTTTAAAA-ATAT
1 TATAGTTTTGAAAACATATTTTTGAAAATATAT
427547 TTTTGAAAAC
Statistics
Matches: 212, Mismatches: 27, Indels: 46
0.74 0.09 0.16
Matches are distributed among these distances:
35 19 0.09
36 36 0.17
37 77 0.36
38 26 0.12
39 8 0.04
40 10 0.05
41 7 0.03
42 7 0.03
43 7 0.03
44 10 0.05
45 5 0.02
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.44
Consensus pattern (37 bp):
TATAGTTTTGAAAACATATTTTTGAAAATATATATTA
Found at i:427516 original size:21 final size:22
Alignment explanation
Indices: 427492--427533 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
427482 TAGTTTTTAA
*
427492 AATATA-TTTGAAAACATATAT
1 AATATAGTTTAAAAACATATAT
427513 AATATAGTTTTAAAAACATAT
1 AATATAG-TTTAAAAACATAT
427534 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
23 12 0.67
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (22 bp):
AATATAGTTTAAAAACATATAT
Found at i:427518 original size:81 final size:81
Alignment explanation
Indices: 427350--427518 Score: 191
Period size: 81 Copynumber: 2.1 Consensus size: 81
427340 ATTTTTGAAA
* * * * *
427350 ATATATATTATATAGTTTTGAAAACATTTTTTTGAAAGTATATATTATATAGTTCTGAAAACGGT
1 ATATATATAATATAGTTTTAAAAACATATTTTTGAAAGTATATAATATATAGTTCTGAAAACGAT
* *
427415 TTTAGAATATATATAT
66 TTTAGAAAACATATAT
* * * *
427431 ATATATATAATATGGTTTTAAAAACATATTTTTGAAAATGTATATAATATATAGTTTTTAAAA-T
1 ATATATATAATATAGTTTTAAAAACATATTTTTG-AAA-GTATATAATATATAGTTCTGAAAACG
427495 ATATTT-GAAAACATATAT
64 AT-TTTAGAAAACATATAT
427513 A-ATATA
1 ATATATA
427519 GTTTTAAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
81 35 0.47
82 15 0.20
83 24 0.32
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (81 bp):
ATATATATAATATAGTTTTAAAAACATATTTTTGAAAGTATATAATATATAGTTCTGAAAACGAT
TTTAGAAAACATATAT
Found at i:427546 original size:13 final size:14
Alignment explanation
Indices: 427520--427560 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
427510 TATAATATAG
427520 TTTTAAAAACATAT
1 TTTTAAAAACATAT
*
427534 TTTTTAAAA-ATAT
1 TTTTAAAAACATAT
*
427547 TTTTGAAAACATAT
1 TTTTAAAAACATAT
427561 AATATAAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (14 bp):
TTTTAAAAACATAT
Found at i:427608 original size:31 final size:31
Alignment explanation
Indices: 427520--427633 Score: 119
Period size: 31 Copynumber: 3.6 Consensus size: 31
427510 TATAATATAG
* *
427520 TTTTAAAAACATAT--TTTTTAAAAAT-A-T
1 TTTTGAAAACATATAGTTTTTTAAAATGATT
*
427547 TTTTGAAAACATATAATATAAGGTTTTAAAATGATT
1 TTTTGAAAACATATAGT-T----TTTTAAAATGATT
*
427583 TTTTGAAAACATGTAGTTTTTTAAAATGATT
1 TTTTGAAAACATATAGTTTTTTAAAATGATT
427614 TTTTGAAAACATATAGTTTT
1 TTTTGAAAACATATAGTTTT
427634 GGAAATGCAT
Statistics
Matches: 73, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
27 13 0.18
29 1 0.01
30 1 0.01
31 32 0.44
34 8 0.11
35 2 0.03
36 16 0.22
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (31 bp):
TTTTGAAAACATATAGTTTTTTAAAATGATT
Found at i:427646 original size:31 final size:31
Alignment explanation
Indices: 427570--427647 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
427560 TAATATAAGG
*
427570 TTTT-AAAATGATTTTTTGAAAACATGTAGT
1 TTTTGAAAATGATTTTTTGAAAACATATAGT
*
427600 TTTTTAAAATGATTTTTTGAAAACATATAG-
1 TTTTGAAAATGATTTTTTGAAAACATATAGT
*
427630 TTTTGGAAATGCATTTTT
1 TTTTGAAAATG-ATTTTT
427648 CGACATATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 13 0.30
31 30 0.70
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (31 bp):
TTTTGAAAATGATTTTTTGAAAACATATAGT
Found at i:427701 original size:23 final size:21
Alignment explanation
Indices: 427667--427739 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 21
427657 TACATATTAT
427667 TATTTTATTTTTATTTTTTTC
1 TATTTTATTTTTATTTTTTTC
427688 TATTTTCCATTTTTATTTTATTTAC
1 TATTTT--ATTTTTATTTT-TTT-C
427713 T-TGTTTATTTTTA-TTTTTTC
1 TAT-TTTATTTTTATTTTTTTC
427733 TTATTTT
1 -TATTTT
427740 TAGTCCAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
20 1 0.02
21 13 0.29
22 4 0.09
23 18 0.40
24 4 0.09
25 5 0.11
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.77
Consensus pattern (21 bp):
TATTTTATTTTTATTTTTTTC
Found at i:428924 original size:202 final size:205
Alignment explanation
Indices: 428549--428955 Score: 736
Period size: 203 Copynumber: 2.0 Consensus size: 205
428539 CAATTTGATC
428549 CTTCGTTATATTTGTTATATTTTACGATTTAATCCCCTAACTTTTTGTTTTCTTTGGCAAATCAT
1 CTTCGTTATATTTGTTATATTTTACGATTTAATCCCCTAACTTTTTGTTTTCTTTGGCAAATCAT
428614 TTCTAATATTAATTCAAGCCATAAATATATTAATTCAATTCGGTCCTTTTTATTTGTTTTTTTAG
66 TTCTAATATTAATTCAAGCCATAAATATATTAATTCAATTCGGTCCTTTTTATTTGTTTTTTTAG
428679 CATTTTTTAAACATTTTTTCTTCCTTTTAATACTTTTTCTTCTTTTTTTCTCTCTTTT-AAATTT
131 CATTTTTTAAACATTTTTTCTTCCTTTTAATACTTTTTCTTCTTTTTTTCTCTCTTTTAAAATTT
428743 ACCATTTTTT
196 ACCATTTTTT
428753 CTTCGTTAT-TTTGTTATATTTTACGATTTAAT-CCCTAAC-TTTTG-TTTCTTTGGCAAATCAC
1 CTTCGTTATATTTGTTATATTTTACGATTTAATCCCCTAACTTTTTGTTTTCTTTGGCAAATCA-
428814 TTTCTAATATTAATTCAAGCCATAAATATAATTAATTCAATTCGGTCCTTTTTTATTTGTTTTTT
65 TTTCTAATATTAATTCAAGCCATAAATAT-ATTAATTCAATTCGGTCC-TTTTTATTTGTTTTTT
*
428879 TAGCATTTTTTAAACA-TTTTTCTTCCTTTTAATATTTTTTCTTCTTTTTTTCTCTCTTTTAAAA
128 TAGCATTTTTTAAACATTTTTTCTTCCTTTTAATACTTTTTCTTCTTTTTTTCTCTCTTTTAAAA
428943 TTTACCATTTTTT
193 TTTACCATTTTTT
428956 TAGTTTATTC
Statistics
Matches: 198, Mismatches: 1, Indels: 9
0.95 0.00 0.04
Matches are distributed among these distances:
200 16 0.08
201 34 0.17
202 68 0.34
203 71 0.36
204 9 0.05
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.56
Consensus pattern (205 bp):
CTTCGTTATATTTGTTATATTTTACGATTTAATCCCCTAACTTTTTGTTTTCTTTGGCAAATCAT
TTCTAATATTAATTCAAGCCATAAATATATTAATTCAATTCGGTCCTTTTTATTTGTTTTTTTAG
CATTTTTTAAACATTTTTTCTTCCTTTTAATACTTTTTCTTCTTTTTTTCTCTCTTTTAAAATTT
ACCATTTTTT
Found at i:429073 original size:16 final size:16
Alignment explanation
Indices: 429054--429084 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
429044 TTGTTTTTCA
429054 TTTATTTTAACATTTT
1 TTTATTTTAACATTTT
*
429070 TTTATTTTACCATTT
1 TTTATTTTAACATTT
429085 AATAGTTAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTTTAACATTTT
Found at i:429920 original size:10 final size:10
Alignment explanation
Indices: 429904--429977 Score: 94
Period size: 10 Copynumber: 7.1 Consensus size: 10
429894 CTGGTTCACT
429904 GGTTCAACCG
1 GGTTCAACCG
*
429914 AGTTCAACCG
1 GGTTCAACCG
*
429924 CGGTTCAATCG
1 -GGTTCAACCG
429935 GGTTCAACCG
1 GGTTCAACCG
429945 CGGTTCAACCG
1 -GGTTCAACCG
429956 GGTTCAACCG
1 GGTTCAACCG
*
429966 CGGTTGAACCG
1 -GGTTCAACCG
429977 G
1 G
429978 ATTTTATATA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
10 29 0.52
11 27 0.48
ACGTcount: A:0.20, C:0.30, G:0.30, T:0.20
Consensus pattern (10 bp):
GGTTCAACCG
Found at i:429929 original size:21 final size:21
Alignment explanation
Indices: 429904--429977 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
429894 CTGGTTCACT
*
429904 GGTTCAACCGAGTTCAACCGC
1 GGTTCAACCGGGTTCAACCGC
*
429925 GGTTCAATCGGGTTCAACCGC
1 GGTTCAACCGGGTTCAACCGC
429946 GGTTCAACCGGGTTCAACCGC
1 GGTTCAACCGGGTTCAACCGC
*
429967 GGTTGAACCGG
1 GGTTCAACCGG
429978 ATTTTATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.20, C:0.30, G:0.30, T:0.20
Consensus pattern (21 bp):
GGTTCAACCGGGTTCAACCGC
Found at i:430486 original size:24 final size:24
Alignment explanation
Indices: 430454--430509 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
430444 CTATTCTTTC
430454 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
430478 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
430502 GCTTCAAT
1 GCTTCAAT
430510 CGAACTTCTA
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:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:432174 original size:130 final size:130
Alignment explanation
Indices: 431941--432203 Score: 517
Period size: 130 Copynumber: 2.0 Consensus size: 130
431931 ATCCCCTCTT
431941 TGCGGCGGGATTGTGTGATTGAATAATCATCAGTTTTACAGAAAAATGGAATAATAAAGTTTTAA
1 TGCGGCGGGATTGTGTGATTGAATAATCATCAGTTTTACAGAAAAATGGAATAATAAAGTTTTAA
432006 TCTCAGTTATTTATTTAGATTCATCCCATAGTAATATTTTCGTGCAAAACTTACGAGTTTCACCG
66 TCTCAGTTATTTATTTAGATTCATCCCATAGTAATATTTTCGTGCAAAACTTACGAGTTTCACCG
432071 TGCGGCGGGATTGTGTGATTGAATAATCATCAGTTTTACAGAAAAATGGAATAATAAAGTTTTAA
1 TGCGGCGGGATTGTGTGATTGAATAATCATCAGTTTTACAGAAAAATGGAATAATAAAGTTTTAA
*
432136 TCTCAGTTATTTATTTAGATTCATCCCATAGTTATATTTTCGTGCAAAACTTACGAGTTTCACCG
66 TCTCAGTTATTTATTTAGATTCATCCCATAGTAATATTTTCGTGCAAAACTTACGAGTTTCACCG
432201 TGC
1 TGC
432204 AAGCGGGTCC
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 132 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (130 bp):
TGCGGCGGGATTGTGTGATTGAATAATCATCAGTTTTACAGAAAAATGGAATAATAAAGTTTTAA
TCTCAGTTATTTATTTAGATTCATCCCATAGTAATATTTTCGTGCAAAACTTACGAGTTTCACCG
Found at i:435406 original size:224 final size:229
Alignment explanation
Indices: 435007--435462 Score: 818
Period size: 224 Copynumber: 2.0 Consensus size: 229
434997 TAGAATGATT
435007 ACAAAGCAGTATTAATTTATAATCCTTCTTAACCTTTAATATTGCACGTACATTACAAATGTAAC
1 ACAAAGCAGTATTAATTTATAATCCTTCTTAACCTTTAATATTG-ACGTACATTACAAATGTAAC
435072 TACTTGAATTTAAGAATTCTAATAAAATTAATATTTTTTTAATTACTGAAATTATTTGACAAGTT
65 TACTTGAATTTAAGAATTCTAAT-AAATT-ATATTTTTTTAATTACTGAAATTATTTGACAAGTT
435137 AAATACTACTAAATATATCTAAATGAATCTTAAAGCTTA-TTTTTTTCTTTAAAAAAATGACTAT
128 AAATACTACTAAATATATCTAAATGAATCTTAAAGCTTATTTTTTTTCTTT-AAAAAATGACTAT
435201 TACATGCTTTGAATGGTAGTTGGTAATATTAAATTGAAA
192 TACATGCTTTGAATGGTAGTTGGTAAT-TTAAATTGAAA
435240 ACAAAGCAGTATTAATTTATAATCCTTCTTAACCTTT-AT-TTG-CGTACATTACAAATGTAACT
1 ACAAAGCAGTATTAATTTATAATCCTTCTTAACCTTTAATATTGACGTACATTACAAATGTAACT
435302 ACTTGAATTTAAGAATTCTAAT-AATT-TATTTTTTTAATTACTGAAATTA-TTGACAAGTTAAA
66 ACTTGAATTTAAGAATTCTAATAAATTATATTTTTTTAATTACTGAAATTATTTGACAAGTTAAA
435364 TACTACTAAATATATCTAAATGAATCTTAAAGCTTATTTTTTTTCTTTAAAAAATGACTATTACA
131 TACTACTAAATATATCTAAATGAATCTTAAAGCTTATTTTTTTTCTTTAAAAAATGACTATTACA
435429 TGCTTTGAATGGTAGTTGGTAATTTAAATTGAAA
196 TGCTTTGAATGGTAGTTGGTAATTTAAATTGAAA
435463 TAATTAAAAT
Statistics
Matches: 222, Mismatches: 0, Indels: 12
0.95 0.00 0.05
Matches are distributed among these distances:
223 11 0.05
224 89 0.40
225 34 0.15
227 4 0.02
229 42 0.19
231 3 0.01
232 2 0.01
233 37 0.17
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (229 bp):
ACAAAGCAGTATTAATTTATAATCCTTCTTAACCTTTAATATTGACGTACATTACAAATGTAACT
ACTTGAATTTAAGAATTCTAATAAATTATATTTTTTTAATTACTGAAATTATTTGACAAGTTAAA
TACTACTAAATATATCTAAATGAATCTTAAAGCTTATTTTTTTTCTTTAAAAAATGACTATTACA
TGCTTTGAATGGTAGTTGGTAATTTAAATTGAAA
Found at i:436923 original size:2 final size:2
Alignment explanation
Indices: 436916--436946 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
436906 CTAAGTGAAA
436916 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
436947 TTTAACTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:437080 original size:24 final size:24
Alignment explanation
Indices: 437033--437097 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
437023 TAAATGACTG
437033 AAATTATAA-T-TAATAATAAAATT
1 AAATTATAATTCTAA-AATAAAATT
*
437056 AAATTGAT-ATTCTAAAATAAGATT
1 AAATT-ATAATTCTAAAATAAAATT
437080 AAATTATAAATTCTAAAA
1 AAATTAT-AATTCTAAAA
437098 AGCAGTATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
23 8 0.22
24 16 0.44
25 12 0.33
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (24 bp):
AAATTATAATTCTAAAATAAAATT
Found at i:437395 original size:10 final size:10
Alignment explanation
Indices: 437380--437427 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
437370 AAGCATTTCG
437380 TTCTTCTTTT
1 TTCTTCTTTT
437390 TTCTTCTTCTT
1 TTCTTCTT-TT
437401 TT-TTC-TTT
1 TTCTTCTTTT
*
437409 TTCTT-TTTA
1 TTCTTCTTTT
437418 TT-TTCTTTT
1 TTCTTCTTTT
437427 T
1 T
437428 CTTTTTGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
8 6 0.19
9 11 0.34
10 11 0.34
11 4 0.12
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (10 bp):
TTCTTCTTTT
Found at i:437398 original size:13 final size:13
Alignment explanation
Indices: 437375--437416 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
437365 AGATAAAGCA
437375 TTTCGTTCTTCTTT
1 TTTC-TTCTTCTTT
437389 TTTCTTCTTCTTT
1 TTTCTTCTTCTTT
*
437402 TTTCTTTTTCTTT
1 TTTCTTCTTCTTT
437415 TT
1 TT
437417 ATTTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 23 0.85
14 4 0.15
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTCTTCTTCTTT
Found at i:437409 original size:6 final size:6
Alignment explanation
Indices: 437387--437433 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
437377 TCGTTCTTCT
* *
437387 TTTTTC TTCTTC TTTTTTC TTTTTC TTTTT- ATTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
437434 GAATCTCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 4 0.11
6 26 0.74
7 5 0.14
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:438981 original size:31 final size:31
Alignment explanation
Indices: 438946--439004 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
438936 TTGTCTCCTG
* * *
438946 AAATTTTATAAGTTCAAGTTTGTTCTCTCTA
1 AAATTTTAAAAATTCAAGTTCGTTCTCTCTA
438977 AAATTTTAAAAATTCAAGTTCGTTCTCT
1 AAATTTTAAAAATTCAAGTTCGTTCTCT
439005 AACATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (31 bp):
AAATTTTAAAAATTCAAGTTCGTTCTCTCTA
Found at i:440943 original size:2 final size:2
Alignment explanation
Indices: 440938--440968 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
440928 AATGAAGTAA
440938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
440969 AGCAAGATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:442643 original size:39 final size:39
Alignment explanation
Indices: 442599--442680 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
442589 GTTGAACAAG
*
442599 TTCTT-CTCCTTCAGATGAGTTCTTCTCATTATGAACTTC
1 TTCTTCCT-CTTCAGATGAGTTCTTCTCATTACGAACTTC
* *
442638 TTCTTCCTCTTCAGGTGAGTTCTTCTTATTACGAACTTC
1 TTCTTCCTCTTCAGATGAGTTCTTCTCATTACGAACTTC
442677 TTCT
1 TTCT
442681 GGAAATGTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
39 37 0.95
40 2 0.05
ACGTcount: A:0.16, C:0.26, G:0.11, T:0.48
Consensus pattern (39 bp):
TTCTTCCTCTTCAGATGAGTTCTTCTCATTACGAACTTC
Found at i:442771 original size:36 final size:36
Alignment explanation
Indices: 442731--443075 Score: 230
Period size: 36 Copynumber: 9.5 Consensus size: 36
442721 AGTGAAACTG
* * *
442731 TCTCAAGCGAGACGAATCTTGTTTTAAAAAAAACAA
1 TCTCAAGCGAGACAAATGTTGTTTTAAGAAAAACAA
* * * **
442767 TCTCAAGTGAGATAAATTGTTG-TTT-CGAATGAAACTG
1 TCTCAAGCGAGACAAA-TGTTGTTTTAAGAA--AAACAA
*
442804 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATGTTGTTTTAAGAAAAACAA
* * ** ** **
442840 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTG
1 TCTCAAGCGAGACAAA-TGTTGTTTTAAGAAAAACAA
** *
442877 TCTCAAGCGAGACGCATTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATGTTGTTTTAAGAAAAACAA
* * * ** ** **
442913 TCTCAAGTGAGATAAATTATTGTTTCGAGTGAAACTG
1 TCTCAAGCGAGACAAA-TGTTGTTTTAAGAAAAACAA
*
442950 TCTCAAGCGAGACACAAT-TTCTTTTAAGAAAAACAA
1 TCTCAAGCGAGACA-AATGTTGTTTTAAGAAAAACAA
* * ** ** **
442986 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTG
1 TCTCAAGCGAGACAAA-TGTTGTTTTAAGAAAAACAA
443023 TCTCAAGCGAGACACAAT-TTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACA-AATGTTGTTTTAAGAAAAACAA
* *
443059 TCTCAAGTGAGATAAAT
1 TCTCAAGCGAGACAAAT
443076 TACTATTTGA
Statistics
Matches: 225, Mismatches: 73, Indels: 23
0.70 0.23 0.07
Matches are distributed among these distances:
35 7 0.03
36 111 0.49
37 100 0.44
38 7 0.03
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (36 bp):
TCTCAAGCGAGACAAATGTTGTTTTAAGAAAAACAA
Found at i:442826 original size:73 final size:73
Alignment explanation
Indices: 442714--443076 Score: 613
Period size: 73 Copynumber: 5.0 Consensus size: 73
442704 TGGAAATTTA
* * * *
442714 TGTTTCTAGTGAAACTGTCTCAAGCGAGACGAATCTTGTTTTAAAAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
442779 TAAATTGT
66 TAAATTGT
*
442787 TGTTTCGAATGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
442852 TAAATTGT
66 TAAATTGT
**
442860 TGTTTCGAGTGAAACTGTCTCAAGCGAGACGCATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
*
442925 TAAATTAT
66 TAAATTGT
*
442933 TGTTTCGAGTGAAACTGTCTCAAGCGAGACACAA-TTTCTTTTAAGAAAAACAATCTCAAGTGAG
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACA-AATTTTGTTTTAAGAAAAACAATCTCAAGTGAG
442997 ATAAATTGT
65 ATAAATTGT
443006 TGTTTCGAGTGAAACTGTCTCAAGCGAGACACAA-TTTGTTTTAAGAAAAACAATCTCAAGTGAG
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACA-AATTTTGTTTTAAGAAAAACAATCTCAAGTGAG
443070 ATAAATT
65 ATAAATT
443077 ACTATTTGAA
Statistics
Matches: 275, Mismatches: 14, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
73 274 1.00
74 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (73 bp):
TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
TAAATTGT
Found at i:443856 original size:22 final size:22
Alignment explanation
Indices: 443796--443857 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
443786 GGAATCCAAT
*
443796 AAATCT-T-ATCTTTGAAAAGA
1 AAATCTATCATCTTTGAAGAGA
*
443816 AAATCTATCATTTTTGAAGAGA
1 AAATCTATCATCTTTGAAGAGA
443838 AAATCTATCATCTTTGAAGA
1 AAATCTATCATCTTTGAAGA
443858 ATATAGATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 6 0.16
21 1 0.03
22 30 0.81
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.35
Consensus pattern (22 bp):
AAATCTATCATCTTTGAAGAGA
Found at i:444307 original size:54 final size:53
Alignment explanation
Indices: 444225--444386 Score: 227
Period size: 54 Copynumber: 3.0 Consensus size: 53
444215 ATAATCACTG
*
444225 GTTCGTAAAACATGTGATAATACATTCATCTTTTCTCGTGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGATAATACATTCATCTTTTCT-GTGGTTTCTGCACAGAT
* * *
444279 GTTCGTAAAACATTTGATAACACATTCATCTTTTCTTATGGCTTCTGGC-CAGAT
1 GTTCGTAAAACATTTGATAATACATTCATCTTTTC-TGTGGTTTCT-GCACAGAT
* *
444333 GTTCGTAAAGCATTTGACAATACATTCATCATTTTCTGTGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGATAATACATTCATC-TTTTCTGTGGTTTCTGCACAGAT
444387 TTATGATCAA
Statistics
Matches: 95, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
53 2 0.02
54 85 0.89
55 8 0.08
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (53 bp):
GTTCGTAAAACATTTGATAATACATTCATCTTTTCTGTGGTTTCTGCACAGAT
Found at i:451812 original size:25 final size:26
Alignment explanation
Indices: 451762--451825 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 26
451752 TTAATACATG
451762 AAAATAA-A-ATAAAGATATTAATAA
1 AAAATAATATATAAAGATATTAATAA
451786 AAAATAATATATAAA-ATATT-ATGAA
1 AAAATAATATATAAAGATATTAAT-AA
451811 AATAATAAGTATATA
1 AA-AATAA-TATATA
451826 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
24 9 0.26
25 10 0.29
26 10 0.29
27 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (26 bp):
AAAATAATATATAAAGATATTAATAA
Found at i:451816 original size:23 final size:24
Alignment explanation
Indices: 451759--451818 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
451749 AATTTAATAC
451759 ATGAAAATAA-AATAAAGATATTA
1 ATGAAAATAATAATAAAGATATTA
*
451782 ATAAAAAATAATATATAAA-ATATT-
1 AT-GAAAATAATA-ATAAAGATATTA
451806 ATGAAAATAATAA
1 ATGAAAATAATAA
451819 GTATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 1 0.03
23 11 0.34
24 9 0.28
25 6 0.19
26 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (24 bp):
ATGAAAATAATAATAAAGATATTA
Found at i:452512 original size:2 final size:2
Alignment explanation
Indices: 452507--452535 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
452497 AATGAAGTAA
452507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
452536 CATGATATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:452577 original size:161 final size:158
Alignment explanation
Indices: 452382--452786 Score: 429
Period size: 157 Copynumber: 2.6 Consensus size: 158
452372 TAAATAGAAC
**
452382 ATTTATTTA--TTTACAAATATCAGAA-AATGACATCTAGTTATTTTAAGAATGTCTTTTCTTTA
1 ATTTATTTATTTTTA-AAATATCAGAATAA-GACATCTAGTTGCTTTAAGAATGTCTTTTCTTTA
*
452444 ATATTAATAAATAAATAAATATTAATAAGAATATAATAATTTTCCTAA-AAAATAATGAAGT-AA
64 ATATTAA-AAATAAATAAATATT-ATAA-AA-ATAATAATTTTCCTAAGAAAATAATGAAATAAA
*
452507 A-TATATATATATATATA-TATATATATA-TACATGAT
125 ACAATATATAT-TATATAGTATATATA-AGTA-AT-AT
* *
452542 ATTTATTTATTTTTAAAATATCAGAATAAGACATCTAGTTGCTTTAAGACTGTCCTTTC-TTAAT
1 ATTTATTTATTTTTAAAATATCAGAATAAGACATCTAGTTGCTTTAAGAATGTCTTTTCTTTAAT
* * *
452606 ATTTGAAAAATAAATAAATA-T-TAAAAATAATAATTTTCCTAAGAAGATATTTAAATAAAACAA
66 A-TT-AAAAATAAATAAATATTATAAAAATAATAATTTTCCTAAGAAAATAATGAAATAAAACAA
* * * * *
452669 TATGTATTTTCTAGTTTTTATAAGTAATAT
129 TATATATTATATAGTATATATAAGTAATAT
* * * * *
452699 ATTTATTTATTTTTAAAATACCATAATAAGACATCTAGTTGCTTTAA-AACTGCCCTTTTATTTG
1 ATTTATTTATTTTTAAAATATCAGAATAAGACATCTAGTTGCTTTAAGAA-TG-TCTTTTCTTTA
452763 ATATTAAAAATAAATAAATATTAT
64 ATATTAAAAATAAATAAATATTAT
452787 TATCTAATCA
Statistics
Matches: 209, Mismatches: 21, Indels: 31
0.80 0.08 0.12
Matches are distributed among these distances:
156 17 0.08
157 75 0.36
158 20 0.10
159 21 0.10
160 16 0.08
161 52 0.25
162 8 0.04
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.42
Consensus pattern (158 bp):
ATTTATTTATTTTTAAAATATCAGAATAAGACATCTAGTTGCTTTAAGAATGTCTTTTCTTTAAT
ATTAAAAATAAATAAATATTATAAAAATAATAATTTTCCTAAGAAAATAATGAAATAAAACAATA
TATATTATATAGTATATATAAGTAATAT
Found at i:464816 original size:2 final size:2
Alignment explanation
Indices: 464809--464833 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
464799 AAATAAATAA
464809 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
464834 AACTTGGAAT
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:466235 original size:18 final size:18
Alignment explanation
Indices: 466214--466251 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
466204 GTGCTGATGT
*
466214 TGTTGTTGTTGCTGCTGC
1 TGTTGTTGATGCTGCTGC
*
466232 TGTTGTTGATGCTGTTGC
1 TGTTGTTGATGCTGCTGC
466250 TG
1 TG
466252 GTGCATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.13, G:0.34, T:0.50
Consensus pattern (18 bp):
TGTTGTTGATGCTGCTGC
Found at i:466237 original size:15 final size:15
Alignment explanation
Indices: 466198--466245 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
466188 AATGTTGCTC
* *
466198 CTGCTGGTGCTGATG
1 CTGCTGTTGTTGATG
* * *
466213 TTGTTGTTGTTGCTG
1 CTGCTGTTGTTGATG
466228 CTGCTGTTGTTGATG
1 CTGCTGTTGTTGATG
466243 CTG
1 CTG
466246 TTGCTGGTGC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.04, C:0.15, G:0.35, T:0.46
Consensus pattern (15 bp):
CTGCTGTTGTTGATG
Found at i:471108 original size:134 final size:134
Alignment explanation
Indices: 470839--471276 Score: 565
Period size: 134 Copynumber: 3.3 Consensus size: 134
470829 AAACGTCGAC
* * * * * * * * * *
470839 TCATCCCATTGTTCTCCACGGAAGATTGAATCAAGGAAGACTTGTTTCATTGTTCCTCAGGGAAG
1 TCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAAT
* * * * *
470904 ATCAAATCTGGAAAAAAAGAGGGATTTGTTTCACTTTTTCTTGAGGGAAAATCAGATCTGGGGAC
66 ATCAAATCTTG--AAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGAC
470969 GTTGAT
129 GTTGAT
* * *
470975 TCATTCCACTATTCTTCAGGGAAGATTGAATTGAGGCAGACTTGTTCTACTGTTAC-CTAGGGAA
1 TCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTC-AGGGAA
* * * * *
471039 TATTAAATCTTGAACGAGAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTGGGAACA
65 TATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGACG
471104 TTGAT
130 TTGAT
** *
471109 TCATTCCACTGTTACTT-AGGGAAGATTGAATCGAGGTTGATTTGTTCCACTGTTACTCAGGGAA
1 TCATTCCACTGTT-CTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAA
* * *
471173 TATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTTTTGAGGGAAAATCATATATGGGGACG
65 TATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGACG
471238 TTGAT
130 TTGAT
471243 TCATTCCACTGTTCTTCAGGGAAGATTGAATCGA
1 TCATTCCACTGTTCTTCAGGGAAGATTGAATCGA
471277 ATTCGATTTT
Statistics
Matches: 261, Mismatches: 37, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
133 3 0.01
134 194 0.74
135 5 0.02
136 59 0.23
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (134 bp):
TCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAAT
ATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGACGT
TGAT
Found at i:473019 original size:13 final size:14
Alignment explanation
Indices: 472996--473024 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
472986 AATAAATTCA
472996 CTCACCTATTATGC
1 CTCACCTATTATGC
473010 CTCA-CTATTATGC
1 CTCACCTATTATGC
473023 CT
1 CT
473025 TACTGATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.34, G:0.07, T:0.38
Consensus pattern (14 bp):
CTCACCTATTATGC
Found at i:474653 original size:233 final size:232
Alignment explanation
Indices: 474222--475385 Score: 1582
Period size: 233 Copynumber: 5.0 Consensus size: 232
474212 CAACCTGAAA
* **
474222 GATTTAAGCATAAT-CTTCGAAAGACTTACTGATAACCCGAAGGACTTACCAATTTTGGAAATAG
1 GATTTAAGCATCATGC-TCGAAAGACTTACTGAT-GTCCGAAGGACTTACCAATTTTGGAAATAG
* * * * * *
474286 TTTACTAGG-ATAGAAACTTTTCATACTATTCAAAAATTTTAAATTTCAGATTCAAATGAGAAAT
64 TTTACTAGGCA-AGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAC
* * * *
474350 TTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTACCCGAAGATCTTATAGATGCCCCGAAGG
128 TTTTCTCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGG
*
474415 ACTTATTATCTTGCTCGAAAGACTTACAGATGACCCGAAG
193 ACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAG
* * * *
474455 GATTTAAGCATCATGCTCAAAAGCCTTTCTGATTGTCCGAATGACTTACCAATTTTGGAAATAGT
1 GATTTAAGCATCATGCTCGAAAGACTTACTGA-TGTCCGAAGGACTTACCAATTTTGGAAATAGT
* * * * *
474520 TTACTAGGTAATAAACTTTTTTTACTTTTTAAAAATTTCAATTTTCAAATTTAAATGAGAAACTT
65 TTACTAGGCAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTT
** * *
474585 TTCTCATTTTTCGAAAAACATGTGAAAACATCCTGCTTGAAGGTCTTATGGATGGCCCGAATGAC
130 TTCTCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGAC
* * **
474650 TTATTATCTTGCTTGAAAGACTTACAGATGACCTTAAG
195 TTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAG
* *
474688 GATTTAAGCATCATGCGCGAAAGACTTA-TGATGGCCCGAAGGACTTACCAATTTTGGAAATAGT
1 GATTTAAGCATCATGCTCGAAAGACTTACTGAT-GTCCGAAGGACTTACCAATTTTGGAAATAGT
* **
474752 TTACTAGGCAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAAAGT
65 TTACTAGGCAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTT
*
474817 TTCTCACTTTTCGAAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGA
130 TTCTCATTTTTCG-AAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGA
*
474882 CTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAA
194 CTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAG
* * *
474921 GATTTAAGCATCATACTCGAAAGACTTACAGATGTCCCTAAGGACTTACCAATTTTGGAAATAGT
1 GATTTAAGCATCATGCTCGAAAGACTTACTGATGT-CCGAAGGACTTACCAATTTTGGAAATAGT
* * * *
474986 TTAATAGGCAAGAAACTTTTTTTACTTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAATTT
65 TTACTAGGCAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTT
* * * * *
475051 TTCTCATTTTTTGAAAAACATTTAAAAACATCCTGCCCGAAGGTCTTGTAGATGGCCCAAAGGAC
130 TTCTCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGAC
*
475116 TCATCATCTTGCTCGAAAGACTTACAGATGACCCGAAG
195 TTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAG
* * * ** *
475154 GATTTAAGCATCAAGCTCGAAAGACTTACTGATGGCTCGAATGACTTACCAATTGGGGAAATTGT
1 GATTTAAGCATCATGCTCGAAAGACTTACTGATGTC-CGAAGGACTTACCAATTTTGGAAATAGT
* * * *
475219 TTACTAGGAAAGAAACTTTTCTTATTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACAT
65 TTACTAGGCAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTT
* * * * * *
475284 TTCTCA-TTTTCGAAAAACATAT-ATAAACATTCTTCCCGAAGGTCTTATGGATGTCCCGAATGA
130 TTCTCATTTTTCGAAAAACATGTGA-AAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGA
* * *
475347 CTTATCATTTTGCTCGAAAGACTTACTGATGGCCCGAAG
194 CTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAG
475386 AACTTACCAA
Statistics
Matches: 822, Mismatches: 100, Indels: 19
0.87 0.11 0.02
Matches are distributed among these distances:
231 2 0.00
232 184 0.22
233 532 0.65
234 104 0.13
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (232 bp):
GATTTAAGCATCATGCTCGAAAGACTTACTGATGTCCGAAGGACTTACCAATTTTGGAAATAGTT
TACTAGGCAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTT
TCTCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGACT
TATCATCTTGCTCGAAAGACTTACAGATGACCCGAAG
Found at i:474921 original size:20 final size:20
Alignment explanation
Indices: 474896--474969 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
474886 TCATCTTGCT
474896 CGAAAGACTTACAGATGACC
1 CGAAAGACTTACAGATGACC
* * *
474916 CGAAAGATTTA-AGCATCATACT
1 CGAAAGACTTACAG-AT--GACC
*
474938 CGAAAGACTTACAGATGTCC
1 CGAAAGACTTACAGATGACC
* *
474958 CTAAGGACTTAC
1 CGAAAGACTTAC
474970 CAATTTTGGA
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
19 2 0.05
20 23 0.56
22 14 0.34
23 2 0.05
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (20 bp):
CGAAAGACTTACAGATGACC
Found at i:475576 original size:191 final size:190
Alignment explanation
Indices: 475168--475576 Score: 502
Period size: 190 Copynumber: 2.1 Consensus size: 190
475158 TAAGCATCAA
* * * *
475168 GCTCGAAAGACTTACTGATGGCTCGAATG-ACTTACCAATTGGGGAAATTGTTTACTAGGAAAGA
1 GCTCGAAAGACTTACAGATGACCCGAA-GAACTTACCAATTGGGGAAATAGTTTACTAGGAAAGA
* * * * * *
475232 AACTTTTCTTATTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACATTTCTCATTTTCGA
65 AACTTTTATTACTTTTCAAAAATTTAAATTTCCAGATTTAAATGAGAAACATTTCCCATTTTCGA
* ** * *
475297 AAAACATATATAAACATTCTTCCCGAAGGTCTTATGGATGTCCCGAATGACTTATCATTTT
130 AAAACATATATAAACATTCTGCCCGAAGGTCTTATAAATGGCCCGAATAACTTATCATTTT
* * ** * *
475358 GCTCGAAAGACTTACTGATGGCCCGAAGAACTTACCAATTTTGGAAATAGTTTACTAGGTAATAA
1 GCTCGAAAGACTTACAGATGACCCGAAGAACTTACCAATTGGGGAAATAGTTTACTAGGAAAGAA
* * *
475423 ACTTTTATTACTTTTCAAAACTTTAAATTTCCAGATTTAAATGAGAATCGTTTCCCATTTTTC-A
66 ACTTTTATTACTTTTCAAAAATTTAAATTTCCAGATTTAAATGAGAAACATTTCCCA-TTTTCGA
*
475487 AAAA-ATATGTGAAAACATT-TGGCCCGAAGGTCTTATAAATGGCCCGAATAACTTATCATTTT
130 AAAACATATAT--AAACATTCT-GCCCGAAGGTCTTATAAATGGCCCGAATAACTTATCATTTT
* *
475549 GCTCGAGAGTCTTACAGATGACCCGAAG
1 GCTCGAAAGACTTACAGATGACCCGAAG
475577 GATTTAAGCA
Statistics
Matches: 189, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
189 6 0.03
190 111 0.59
191 72 0.38
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (190 bp):
GCTCGAAAGACTTACAGATGACCCGAAGAACTTACCAATTGGGGAAATAGTTTACTAGGAAAGAA
ACTTTTATTACTTTTCAAAAATTTAAATTTCCAGATTTAAATGAGAAACATTTCCCATTTTCGAA
AAACATATATAAACATTCTGCCCGAAGGTCTTATAAATGGCCCGAATAACTTATCATTTT
Found at i:475767 original size:233 final size:232
Alignment explanation
Indices: 475357--476009 Score: 879
Period size: 233 Copynumber: 2.8 Consensus size: 232
475347 CTTATCATTT
* *
475357 TGCTCGAAAGACTTACTGATGGCCCGAAGAACTTACCAATTTTGGAAATAGTTTACTAGGTAATA
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGA
* * * * *
475422 AACTTTTATTACTTTTCAAAACTTTAAATTTCCAGATTTAAATGAG-AATCGTTTCCCATTTTTC
66 AACTTTTATTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAT-TTTTCTCATTTTTC
* * * * *
475486 AAAAAATATGTGAAAACAT-TTGGCCCGAAGGTCTTATAAATGGCCCGAATAACTTATCATTTTG
130 AAAAAA-ATGTGAAAACATCAT-GCCTGAAGGTCTTATAGATGGCCCGAAGAACTTATCATCTTG
* * * * *
475550 CTCGAGAGTCTTACAGATGACCCGAAGGATTTAAGCATCA
193 CTCGAAAGACTTACAGATAACCCAAAGGATTTAACCATCA
* *
475590 TGCTCGAAATACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGA
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGA
* *
475655 AACTTTTCTTACTTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAATTTTTCTCATTTTTCG
66 AACTTTTATTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAATTTTTCTCATTTTTC-
* * * * * *
475720 AAAAACATGTGAAAACATCCTGCCTGAAGGTCTTATGGATTGCCCGAAGGACTTATCATCTTGTT
130 AAAAAAATGTGAAAACATCATGCCTGAAGGTCTTATAGATGGCCCGAAGAACTTATCATCTTGCT
*
475785 CGAAAGACTTACAGATAACTCAAAGGATTTAACCATCA
195 CGAAAGACTTACAGATAACCCAAAGGATTTAACCATCA
* * * *
475823 TGCTCAAAAGAATTACTGATGGCCCGAATGACTTACCAATTTTGGAAGTAGTTTACTAGGTAAGA
1 TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGA
* *
475888 AACTTTTTTTACTTTTCAAAAATTTCAA-TTTCAGATTTAAATGAGAAACTTTTCTCA--TTT-A
66 AACTTTTATTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAATTTTTCTCATTTTTCA
* * *
475949 AAAAAATATGAAAACATCATGCCAT-AAGGTCTTATAGATGGCCCGAAGGACTTATTATCTT
131 AAAAAATGTGAAAACATCATGCC-TGAAGGTCTTATAGATGGCCCGAAGAACTTATCATCTT
476010 TGGAAATAGT
Statistics
Matches: 374, Mismatches: 42, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
228 54 0.14
229 1 0.00
230 3 0.01
232 27 0.07
233 280 0.75
234 9 0.02
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (232 bp):
TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGA
AACTTTTATTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAATTTTTCTCATTTTTCA
AAAAAATGTGAAAACATCATGCCTGAAGGTCTTATAGATGGCCCGAAGAACTTATCATCTTGCTC
GAAAGACTTACAGATAACCCAAAGGATTTAACCATCA
Found at i:477728 original size:2 final size:2
Alignment explanation
Indices: 477721--477749 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
477711 AGCTTTATTG
477721 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
477750 ATCTCCTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:484376 original size:111 final size:107
Alignment explanation
Indices: 484114--484403 Score: 386
Period size: 107 Copynumber: 2.7 Consensus size: 107
484104 AATGTTAGTT
* *
484114 GTTAATGGTTAGCAGAGTCC-AGACCATAATAATGTGGACCGTACCCCAGATCGGGTCACCACAA
1 GTTAGTGGTTAGCAGAGTCCGA-ACCATAATAATGTGGATCGTACCCCAGATCGGGTCACCACAA
* * *
484178 AGTCGAATAATAATTCAAACAAATTAATGAAAAAATAAAAAAA
65 GGTCGAATAATAAATCAAACAAATTAATAAAAAAATAAAAAAA
* * * *
484221 GTTAGTGGTTAGCAGAGTTCGAACCATAATAATGTGGATCGTACCCCATATTGAGTCACCACAAG
1 GTTAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCGTACCCCAGATCGGGTCACCACAAG
*
484286 GTCGAATAATAAATCAATCAAATTAATAAAAATAATAAAAAAAA
66 GTCGAATAATAAATCAAACAAATTAATAAAAA-AAT-AAAAAAA
* * * *
484330 TGGTTAG-GAGTTAGTAGAGTCCGAACAATAATAATGTGGATTGTACCCCGGATCGGGTCACCAC
1 --GTTAGTG-GTTAGCAGAGTCCGAACCATAATAATGTGGATCGTACCCCAGATCGGGTCACCAC
484394 AAGGTCGAAT
63 AAGGTCGAAT
484404 CAAATATGAG
Statistics
Matches: 159, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
107 85 0.53
108 4 0.03
109 7 0.04
110 1 0.01
111 62 0.39
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (107 bp):
GTTAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCGTACCCCAGATCGGGTCACCACAAG
GTCGAATAATAAATCAAACAAATTAATAAAAAAATAAAAAAA
Found at i:496880 original size:102 final size:105
Alignment explanation
Indices: 496696--496903 Score: 377
Period size: 103 Copynumber: 2.0 Consensus size: 105
496686 AGATCCAAGA
*
496696 TGAATCCTGGCACTTCTACAACCTCTACCACGACTTCAAGATCTGAGCATTTCCAAACTGCTGAG
1 TGAATCCTGGCACTTCTACAACCTCTACCACGACTTCAAGATCCGAGCATTTCCAAACTGCTGAG
496761 GCTAAGGCACAGT-AAAAAACCCTATAGAAATGGCAAGTT
66 GCTAAGGCACAGTAAAAAAACCCTATAGAAATGGCAAGTT
496800 TGAATCCTGGCACTTCTACAACCTCTACC-CGACTTCAAGATCCGAGCATTT-CAAACTGCTGAG
1 TGAATCCTGGCACTTCTACAACCTCTACCACGACTTCAAGATCCGAGCATTTCCAAACTGCTGAG
*
496863 GCTTAGGCACAGTAAAAAAACCCTATAGAAATGGCAAGTT
66 GCTAAGGCACAGTAAAAAAACCCTATAGAAATGGCAAGTT
496903 T
1 T
496904 ATTGGAGGAT
Statistics
Matches: 101, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
102 24 0.24
103 48 0.48
104 29 0.29
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (105 bp):
TGAATCCTGGCACTTCTACAACCTCTACCACGACTTCAAGATCCGAGCATTTCCAAACTGCTGAG
GCTAAGGCACAGTAAAAAAACCCTATAGAAATGGCAAGTT
Found at i:505251 original size:21 final size:23
Alignment explanation
Indices: 505222--505269 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
505212 TTCATAACGT
*
505222 AAATGACAA-TCTTAA-CACTTCA
1 AAATGACAACTCTAAATC-CTTCA
505244 AAAT-ACAACTCTAAATCCTTCA
1 AAATGACAACTCTAAATCCTTCA
505266 AAAT
1 AAAT
505270 TCAAATCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 18 0.78
23 1 0.04
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (23 bp):
AAATGACAACTCTAAATCCTTCA
Found at i:506228 original size:2 final size:2
Alignment explanation
Indices: 506221--506280 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
506211 TCTAACCATA
506221 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
506263 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
506281 TCTTTCATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:506806 original size:160 final size:155
Alignment explanation
Indices: 506561--506868 Score: 438
Period size: 160 Copynumber: 2.0 Consensus size: 155
506551 TATGGTAGAT
* *** *
506561 GAGCATGTGGTTCAAATTTGTTAAAAAGGGACTTAAAATAAATCAAAAATTGAAGGAATAAAGAG
1 GAGCATGTGGCTCAAATTTGTTAAAAACAAACTTAAAATAAATCAAAAATTGAAGAAATAAAGAG
* * *
506626 ATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAAAATTGTTATCAAAAAGAGGAATTGAA
66 ATTATGAAAAACTAAAGGACTAAATTG-AAAAT-AAAAAAA-TGTTATCAAAAAGAGAAATTGAA
506691 AGTACACATGTATTCTACTATCTTTAAG
128 AGTACACATGTATTCTACTATCTTTAAG
* **
506719 GAGCATGTGGCTCAAATTTGGTTAAAATACAAACTTAAAATAAATGATGAATTGAAGAAAT-AAG
1 GAGCATGTGGCTCAAATTT-GTTAAAA-ACAAACTTAAAATAAATCAAAAATTGAAGAAATAAAG
* *
506783 TAGATTATGAAAAACTAAAGGACTAAATTGAAAATTAAAAAATGTTATCAAAAATAGAAATTGAA
64 -AGATTATGAAAAACTAAAGGACTAAATTGAAAATAAAAAAATGTTATCAAAAAGAGAAATTGAA
506848 AGTACACATGTATTCTACTAT
128 AGTACACATGTATTCTACTAT
506869 AGTGTAGAAT
Statistics
Matches: 134, Mismatches: 13, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
157 42 0.31
158 24 0.18
159 15 0.11
160 53 0.40
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (155 bp):
GAGCATGTGGCTCAAATTTGTTAAAAACAAACTTAAAATAAATCAAAAATTGAAGAAATAAAGAG
ATTATGAAAAACTAAAGGACTAAATTGAAAATAAAAAAATGTTATCAAAAAGAGAAATTGAAAGT
ACACATGTATTCTACTATCTTTAAG
Found at i:506892 original size:157 final size:159
Alignment explanation
Indices: 506562--506896 Score: 448
Period size: 157 Copynumber: 2.1 Consensus size: 159
506552 ATGGTAGATG
*** *
506562 AGCATGTGGTTCAAATTT-GTTAAAAAGGGACTTAAAATAAATCAAAAATTGAAGGAATAAAGAG
1 AGCATGTGGTTCAAATTTGGTTAAAAACAAACTTAAAATAAATCAAAAATTGAAGAAATAAAGAG
* * *
506626 ATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAAAATTGTTATCAAAAAGAGGAATTGAA
66 ATTATGAAAAACTAAAGGACTAAATTGAAAAATAAAAAAAATTGTTATCAAAAAGAGAAATTGAA
* *
506691 AGTACACATGTATTCTACTATCTTTAAGG
131 AGTACACATGTATTCTACTATCTGTAAGA
* * **
506720 AGCATGTGGCTCAAATTTGGTTAAAATACAAACTTAAAATAAATGATGAATTGAAGAAAT-AAGT
1 AGCATGTGGTTCAAATTTGGTTAAAA-ACAAACTTAAAATAAATCAAAAATTGAAGAAATAAAG-
* *
506784 AGATTATGAAAAACTAAAGGACTAAATTG-AAAAT-TAAAAAA-TGTTATCAAAAATAGAAATTG
64 AGATTATGAAAAACTAAAGGACTAAATTGAAAAATAAAAAAAATTGTTATCAAAAAGAGAAATTG
*
506846 AAAGTACACATGTATTCTACTATAGTGT-AGA
129 AAAGTACACATGTATTCTACTAT-CTGTAAGA
*
506877 ATCATGTGGTTCAAATTTGG
1 AGCATGTGGTTCAAATTTGG
506897 GAAAAATAGA
Statistics
Matches: 155, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
157 62 0.40
158 25 0.16
159 15 0.10
160 53 0.34
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.28
Consensus pattern (159 bp):
AGCATGTGGTTCAAATTTGGTTAAAAACAAACTTAAAATAAATCAAAAATTGAAGAAATAAAGAG
ATTATGAAAAACTAAAGGACTAAATTGAAAAATAAAAAAAATTGTTATCAAAAAGAGAAATTGAA
AGTACACATGTATTCTACTATCTGTAAGA
Found at i:506938 original size:157 final size:160
Alignment explanation
Indices: 506624--506933 Score: 416
Period size: 157 Copynumber: 2.0 Consensus size: 160
506614 AGGAATAAAG
* * *
506624 AGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAAAATTGTTATCAAAAAGAGGAATTG
1 AGATTATGAAAAACTAAAGGACTAAATTGAAAAATAAAAAAAATTGTTATCAAAAAGAGAAATTG
* * * *
506689 AAAGTACACATGTATTCTACTATCTTTAAGGAGCATGTGGCTCAAATTTGGTTAAAATACAAACT
66 AAAGTACACATGTATTCTACTATCTGTAAGAAGCATGTGGCTCAAATTTGGTGAAAATACAAACC
* *
506754 TAAAATAAATGATGAATTGAAGAAATAAGT
131 TAAAATAAATGAGGAATTGAAAAAATAAGT
* *
506784 AGATTATGAAAAACTAAAGGACTAAATTG-AAAAT-TAAAAAA-TGTTATCAAAAATAGAAATTG
1 AGATTATGAAAAACTAAAGGACTAAATTGAAAAATAAAAAAAATTGTTATCAAAAAGAGAAATTG
* * * * *
506846 AAAGTACACATGTATTCTACTATAGTGT-AGAATCATGTGGTTCAAATTTGG-GAAAA-ATAGAC
66 AAAGTACACATGTATTCTACTAT-CTGTAAGAAGCATGTGGCTCAAATTTGGTGAAAATACAAAC
*
506908 CTAAAATGAATGAGGAATTGAAAAAA
130 CTAAAATAAATGAGGAATTGAAAAAA
506934 AATAATGAAA
Statistics
Matches: 132, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
155 26 0.20
156 4 0.03
157 62 0.47
158 8 0.06
159 5 0.04
160 27 0.20
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.27
Consensus pattern (160 bp):
AGATTATGAAAAACTAAAGGACTAAATTGAAAAATAAAAAAAATTGTTATCAAAAAGAGAAATTG
AAAGTACACATGTATTCTACTATCTGTAAGAAGCATGTGGCTCAAATTTGGTGAAAATACAAACC
TAAAATAAATGAGGAATTGAAAAAATAAGT
Found at i:507941 original size:2 final size:2
Alignment explanation
Indices: 507934--507970 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
507924 ATGGTCAATA
507934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
507971 AGTTCCAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:521189 original size:19 final size:19
Alignment explanation
Indices: 521165--521212 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
521155 GTCTACAATG
521165 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
521184 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
521203 TCGTTGCGAT
1 TCGTTGCGAT
521213 AGTTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:521324 original size:5 final size:5
Alignment explanation
Indices: 521302--521346 Score: 72
Period size: 5 Copynumber: 8.6 Consensus size: 5
521292 ACCACAACCA
521302 CGACC ACGACC ACGACC CGACC CGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC CGACC CGA
521347 GACGAGACGA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
5 28 0.72
6 11 0.28
ACGTcount: A:0.24, C:0.56, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:521352 original size:5 final size:5
Alignment explanation
Indices: 521344--521373 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
521334 CGACCCGACC
521344 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA
521374 TGGACGGACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:521524 original size:39 final size:39
Alignment explanation
Indices: 521468--521563 Score: 183
Period size: 39 Copynumber: 2.5 Consensus size: 39
521458 TTCTCAATAG
*
521468 TGTTTCCAATACTATGTGGGATTGAGCATTACCAACACT
1 TGTTTCCAATACAATGTGGGATTGAGCATTACCAACACT
521507 TGTTTCCAATACAATGTGGGATTGAGCATTACCAACACT
1 TGTTTCCAATACAATGTGGGATTGAGCATTACCAACACT
521546 TGTTTCCAATACAATGTG
1 TGTTTCCAATACAATGTG
521564 ATTATTCAGG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (39 bp):
TGTTTCCAATACAATGTGGGATTGAGCATTACCAACACT
Found at i:521912 original size:6 final size:6
Alignment explanation
Indices: 521901--521948 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
521891 TCTCGTCTCG
521901 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
521949 ACATGTCTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:522081 original size:21 final size:21
Alignment explanation
Indices: 522052--522207 Score: 129
Period size: 21 Copynumber: 7.6 Consensus size: 21
522042 GAACTGGAAA
522052 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
522073 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
522094 ATCGCAACGCGAACTGGAA-A
1 ATCGCAACGCGATTTTCAACT
** ** *
522114 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
* ** ** *
522134 ATCGCAACTCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
522154 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
522175 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
522196 ATCGCAACGCGA
1 ATCGCAACGCGA
522208 ATTTGCGATT
Statistics
Matches: 118, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
20 52 0.44
21 66 0.56
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:522119 original size:20 final size:20
Alignment explanation
Indices: 522094--522165 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
522084 ATTTTCAACT
*
522094 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
522114 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
522134 ATCGCAACTCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
522154 ATCGCAACGCGA
1 ATCGCAACGCGA
522166 TTTTCAACTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:536336 original size:18 final size:18
Alignment explanation
Indices: 536313--536347 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
536303 GCGTATAATT
536313 TGTCCCAAATGACCACTA
1 TGTCCCAAATGACCACTA
*
536331 TGTCCCGAATGACCACT
1 TGTCCCAAATGACCACT
536348 CTTTAAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.14, T:0.23
Consensus pattern (18 bp):
TGTCCCAAATGACCACTA
Found at i:536427 original size:21 final size:21
Alignment explanation
Indices: 536401--536440 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
536391 CCGAAGTACC
*
536401 ACATATATGTTCCAAAGGATT
1 ACATATATGTCCCAAAGGATT
*
536422 ACATATATGTCCCGAAGGA
1 ACATATATGTCCCAAAGGA
536441 CCACGTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
ACATATATGTCCCAAAGGATT
Found at i:536597 original size:30 final size:31
Alignment explanation
Indices: 536557--536620 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
536547 ACATATGCAT
* *
536557 ATAATCTCATGTCACGTTCTCATATGATCAC
1 ATAATCTCATGTCACATTATCATATGATCAC
*
536588 ATAA-CTCATGTCACATTATCATATGGTCAC
1 ATAATCTCATGTCACATTATCATATGATCAC
536618 ATA
1 ATA
536621 GATCATATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.34
Consensus pattern (31 bp):
ATAATCTCATGTCACATTATCATATGATCAC
Found at i:536632 original size:30 final size:30
Alignment explanation
Indices: 536557--536633 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
536547 ACATATGCAT
* * *
536557 ATAATCTCATGTCACGTTCTCATATGATCAC
1 ATAA-CTCATATCACATTATCATATGATCAC
* *
536588 ATAACTCATGTCACATTATCATATGGTCAC
1 ATAACTCATATCACATTATCATATGATCAC
536618 ATAGA-TCATATCACAT
1 ATA-ACTCATATCACAT
536634 AATTGATATC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
30 36 0.88
31 5 0.12
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (30 bp):
ATAACTCATATCACATTATCATATGATCAC
Found at i:540210 original size:2 final size:2
Alignment explanation
Indices: 540203--540227 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
540193 CATGTAACAA
540203 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
540228 AATACTAATA
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:540807 original size:30 final size:30
Alignment explanation
Indices: 540773--540837 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
540763 TGCATATAAT
**
540773 CTCATGTCATGTTCTCATATGGTCACATAG
1 CTCATGTCACATTCTCATATGGTCACATAG
540803 CTCATGTCACATTCTCATATGGTCACATAG
1 CTCATGTCACATTCTCATATGGTCACATAG
*
540833 ATCAT
1 CTCAT
540838 ATCGCATAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (30 bp):
CTCATGTCACATTCTCATATGGTCACATAG
Found at i:540829 original size:16 final size:16
Alignment explanation
Indices: 540784--540830 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
540774 TCATGTCATG
540784 TTCTCATATGGTCACA
1 TTCTCATATGGTCACA
*
540800 TAGCTC--AT-GTCACA
1 T-TCTCATATGGTCACA
540814 TTCTCATATGGTCACA
1 TTCTCATATGGTCACA
540830 T
1 T
540831 AGATCATATC
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
13 3 0.12
14 7 0.28
15 4 0.16
16 8 0.32
17 3 0.12
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36
Consensus pattern (16 bp):
TTCTCATATGGTCACA
Found at i:540839 original size:17 final size:17
Alignment explanation
Indices: 540786--540839 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
540776 ATGTCATGTT
540786 CTCATATGGTCACATAG
1 CTCATATGGTCACATAG
*
540803 CTC--AT-GTCACAT-T
1 CTCATATGGTCACATAG
540816 CTCATATGGTCACATAG
1 CTCATATGGTCACATAG
*
540833 ATCATAT
1 CTCATAT
540840 CGCATAGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 4 0.13
16 7 0.23
17 9 0.30
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (17 bp):
CTCATATGGTCACATAG
Found at i:541994 original size:31 final size:31
Alignment explanation
Indices: 541956--542080 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
541946 CCCGAAGAAC
* * *
541956 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
541987 CAGTCCATATATCCTGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
542018 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
542049 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
542080 C
1 C
542081 CCTCGACCCT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 86 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:546261 original size:31 final size:31
Alignment explanation
Indices: 546223--546378 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
546213 CCCGAAGGAC
* * *
546223 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
546254 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
546285 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
546316 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
546347 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
546378 C
1 C
546379 CCTCGACCCT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 119 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:547197 original size:21 final size:21
Alignment explanation
Indices: 547173--547217 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
547163 TGTTGTTCGT
* *
547173 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
547194 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
547215 TTG
1 TTG
547218 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:548158 original size:20 final size:21
Alignment explanation
Indices: 548133--548187 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
548123 CTATGTTGTC
548133 TGGTATCGATACCCT-TAAC-A
1 TGGTATCGATACCCTAT-ACTA
*
548153 TGGTATCGATACTACTATACTA
1 TGGTATCGATAC-CCTATACTA
548175 TGGTATCGATACC
1 TGGTATCGATACC
548188 TCCTCATTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 12 0.40
21 4 0.13
22 14 0.47
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (21 bp):
TGGTATCGATACCCTATACTA
Found at i:551010 original size:2 final size:2
Alignment explanation
Indices: 551003--551092 Score: 173
Period size: 2 Copynumber: 45.5 Consensus size: 2
550993 TAACAAACAA
551003 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
551045 AC AC AC AC AC AC -C AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
551086 AC AC AC A
1 AC AC AC A
551093 TATATACACT
Statistics
Matches: 87, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 86 0.99
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:551681 original size:14 final size:14
Alignment explanation
Indices: 551662--551704 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
551652 ATTTCATATG
*
551662 ATCACATAGATCAT
1 ATCACATAGTTCAT
**
551676 ATCACATAGTTGTT
1 ATCACATAGTTCAT
551690 ATCACATAGTTCAT
1 ATCACATAGTTCAT
551704 A
1 A
551705 AACATTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (14 bp):
ATCACATAGTTCAT
Found at i:553169 original size:71 final size:72
Alignment explanation
Indices: 553053--553194 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 72
553043 TCAAATTTGT
553053 CCATTGTAATGGACAATCGTTAAAACTTGTCACTCATTTTCTTTGCATGTTC-AAAACATATATA
1 CCATTGTAATGGACAATCGTTAAAACTTGTCACTCATTTTCTTTGCATGTTCAAAAACATATATA
553117 TTTTGAA
66 TTTTGAA
553124 CCATTGTAATGGACAATCGTTAAAACTTGTCACTCATTTTCTTTGCATGTTCAAAAACATATATA
1 CCATTGTAATGGACAATCGTTAAAACTTGTCACTCATTTTCTTTGCATGTTCAAAAACATATATA
553189 TTTTGA
66 TTTTGA
553195 CAAAATGCAT
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 52 0.74
72 18 0.26
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (72 bp):
CCATTGTAATGGACAATCGTTAAAACTTGTCACTCATTTTCTTTGCATGTTCAAAAACATATATA
TTTTGAA
Found at i:554356 original size:17 final size:17
Alignment explanation
Indices: 554334--554391 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
554324 TACTTTTTGA
554334 AATTTAGTTTTTATATT
1 AATTTAGTTTTTATATT
* *
554351 AATTTAATTTGTATATTATA
1 AATTTAGTTT-T-TA-TATT
554371 AATTT-GATTTTTATATT
1 AATTTAG-TTTTTATATT
554388 AATT
1 AATT
554392 CAATTCTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 16 0.48
18 3 0.09
19 3 0.09
20 11 0.33
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
AATTTAGTTTTTATATT
Found at i:554380 original size:20 final size:20
Alignment explanation
Indices: 554351--554388 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
554341 TTTTTATATT
554351 AATTTAATTTGTATATTATA
1 AATTTAATTTGTATATTATA
* *
554371 AATTTGATTTTTATATTA
1 AATTTAATTTGTATATTA
554389 ATTCAATTCT
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:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
AATTTAATTTGTATATTATA
Found at i:554420 original size:37 final size:37
Alignment explanation
Indices: 554342--554421 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
554332 GAAATTTAGT
* * * *
554342 TTTTATATTAATTTAATTTGTATATTATAAATTTGAT
1 TTTTATATTAATTCAATTTGTATATTATAAATATAAA
* *
554379 TTTTATATTAATTCAATTCTTTATA-TATATATATAAA
1 TTTTATATTAATTCAATT-TGTATATTATAAATATAAA
554416 TTTTAT
1 TTTTAT
554422 TTATAATCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
37 31 0.86
38 5 0.14
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (37 bp):
TTTTATATTAATTCAATTTGTATATTATAAATATAAA
Found at i:555022 original size:23 final size:23
Alignment explanation
Indices: 554992--555044 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
554982 GCAGCAACTG
554992 GCAAGCATCACCATATCAATTCA
1 GCAAGCATCACCATATCAATTCA
***
555015 GCAAGCATCATTGTATCAATTCA
1 GCAAGCATCACCATATCAATTCA
555038 GCAAGCA
1 GCAAGCA
555045 ACATGCATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (23 bp):
GCAAGCATCACCATATCAATTCA
Found at i:555056 original size:23 final size:23
Alignment explanation
Indices: 555006--555052 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
554996 GCATCACCAT
* *
555006 ATCAATTCAGCAAGCATCATTGT
1 ATCAATTCAGCAAGCAACATTGC
555029 ATCAATTCAGCAAGCAACA-TGC
1 ATCAATTCAGCAAGCAACATTGC
555051 AT
1 AT
555053 TCAAAAAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (23 bp):
ATCAATTCAGCAAGCAACATTGC
Found at i:555428 original size:20 final size:18
Alignment explanation
Indices: 555403--555453 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
555393 AATTAAAAGG
555403 AAAATTAAAATAATTAATT
1 AAAATTAAAATAATTAA-T
*
555422 AACAATTTGAAAT-ATTAAT
1 AA-AA-TTAAAATAATTAAT
*
555441 AAAATTAACATAA
1 AAAATTAAAATAA
555454 AAAACAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
17 5 0.19
18 3 0.12
19 5 0.19
20 7 0.27
21 6 0.23
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAATTAAAATAATTAAT
Found at i:558196 original size:3 final size:3
Alignment explanation
Indices: 558183--558262 Score: 62
Period size: 3 Copynumber: 28.0 Consensus size: 3
558173 TATAATATTT
* * *
558183 ATA AT- ATA ATA AT- ATA ATA ATA TTA ATA TATA ATG ATA GTA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
* * *
558226 ATA GTA ATA AT- ATA ATA ATA GTA AT- ATT ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
558263 TCAACTCATA
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
2 10 0.17
3 47 0.78
4 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:558196 original size:8 final size:8
Alignment explanation
Indices: 558183--558263 Score: 94
Period size: 8 Copynumber: 9.9 Consensus size: 8
558173 TATAATATTT
558183 ATAATATA
1 ATAATATA
558191 ATAATATA
1 ATAATATA
558199 ATAATATTA
1 ATAATA-TA
558208 AT-ATATA
1 ATAATATA
*
558215 ATGATAGTA
1 ATAATA-TA
558224 AT-ATAGTA
1 ATAATA-TA
558232 ATAATATA
1 ATAATATA
558240 ATAATAGTA
1 ATAATA-TA
*
558249 ATATTATA
1 ATAATATA
558257 ATAATAT
1 ATAATAT
558264 CAACTCATAC
Statistics
Matches: 66, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
7 4 0.06
8 44 0.67
9 18 0.27
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (8 bp):
ATAATATA
Found at i:558204 original size:11 final size:11
Alignment explanation
Indices: 558188--558263 Score: 61
Period size: 11 Copynumber: 6.9 Consensus size: 11
558178 TATTTATAAT
558188 ATAATAATATA
1 ATAATAATATA
558199 ATAAT-AT-TA
1 ATAATAATATA
558208 ATATATAATGATA
1 ATA-ATAAT-ATA
*
558221 GTAAT-ATAGTA
1 ATAATAATA-TA
558232 ATAAT-ATAATA
1 ATAATAAT-ATA
* *
558243 ATAGTAATATT
1 ATAATAATATA
558254 ATAATAATAT
1 ATAATAATAT
558264 CAACTCATAC
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
9 5 0.09
10 5 0.09
11 34 0.64
12 5 0.09
13 4 0.08
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (11 bp):
ATAATAATATA
Found at i:558205 original size:25 final size:26
Alignment explanation
Indices: 558174--558263 Score: 116
Period size: 25 Copynumber: 3.6 Consensus size: 26
558164 CCCCGATTTT
*
558174 ATAATATTTATAATATAATAATA-TA
1 ATAATATTAATAATATAATAATAGTA
*
558199 ATAATATTAAT-ATATAATGATAGTA
1 ATAATATTAATAATATAATAATAGTA
*
558224 AT-ATAGTAATAATATAATAATAGTA
1 ATAATATTAATAATATAATAATAGTA
*
558249 ATATTA-TAATAATAT
1 ATAATATTAATAATAT
558264 CAACTCATAC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
24 17 0.30
25 38 0.67
26 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (26 bp):
ATAATATTAATAATATAATAATAGTA
Found at i:558209 original size:14 final size:14
Alignment explanation
Indices: 558174--558259 Score: 60
Period size: 14 Copynumber: 6.4 Consensus size: 14
558164 CCCCGATTTT
558174 ATAATATT--TATA
1 ATAATATTAATATA
*
558186 AT-ATAATAATATA
1 ATAATATTAATATA
558199 ATAATATTAATAT-
1 ATAATATTAATATA
558212 ATAATGATAGTAATATA
1 ATAAT-AT--TAATATA
*
558229 GT-A-A-TAATATA
1 ATAATATTAATATA
* *
558240 ATAATAGTAATATT
1 ATAATATTAATATA
558254 ATAATA
1 ATAATA
558260 ATATCAACTC
Statistics
Matches: 59, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
11 12 0.20
12 3 0.05
13 12 0.20
14 24 0.41
16 7 0.12
17 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (14 bp):
ATAATATTAATATA
Found at i:558599 original size:116 final size:114
Alignment explanation
Indices: 558394--558696 Score: 396
Period size: 116 Copynumber: 2.6 Consensus size: 114
558384 AATCAAAAAT
* * **
558394 AAAAACATCGTACCTTGAGGTTTTACAGATGA-CCGGAGGCTTTACAAATCACCCG-GAGGATTT
1 AAAAACATCCTACCTTGAGGTTTTACAGATGACCCGGAGGCTTTACAAAT---TCGTG-GGAAAT
* * *
558457 AATTTTCTAGAACATTAATGAGAACTTTGAAAATCGCTTCATCATTTTCATGC
62 AATTTACTAGGACATAAATGAGAACTTTGAAAATCGCTTCATCATTTTCATGC
* * *
558510 GAAAACATCCTACCTTTAGGTTTTACAAATGACCCGGAGGCTTTACAAATTCGTGGGAAATAATT
1 AAAAACATCCTACCTTGAGGTTTTACAGATGACCCGGAGGCTTTACAAATTCGTGGGAAATAATT
*
558575 TACTAGGACAATAAATGAGAAACTTTGAAAATCGCTTCTTCATTTTCATGC
66 TACTAGGAC-ATAAATGAG-AACTTTGAAAATCGCTTCATCATTTTCATGC
* * * *
558626 AAAAACATCCTACCCTGAGG-TTTACAGATGGCCCAGAGGTTTTACAAATTCGTGGGAAATAATT
1 AAAAACATCCTACCTTGAGGTTTTACAGATGACCCGGAGGCTTTACAAATTCGTGGGAAATAATT
558690 TACTAGG
66 TACTAGG
558697 TAAGAAACCT
Statistics
Matches: 165, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
114 17 0.10
115 56 0.34
116 75 0.45
117 17 0.10
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (114 bp):
AAAAACATCCTACCTTGAGGTTTTACAGATGACCCGGAGGCTTTACAAATTCGTGGGAAATAATT
TACTAGGACATAAATGAGAACTTTGAAAATCGCTTCATCATTTTCATGC
Found at i:558722 original size:116 final size:116
Alignment explanation
Indices: 558479--558705 Score: 305
Period size: 115 Copynumber: 2.0 Consensus size: 116
558469 CATTAATGAG
* * * *
558479 AACTTTGAAAATCGCTTCATCATTTTCATGCGAAAACATCCTACCTTTAGGTTTTACAAATGACC
1 AACTTTAAAAATCGCTTCATCATTTTCATGCAAAAACATCCTACCCTGAGGTTTTACAAATGACC
* * ** *
558544 CGGAGGCTTTACAAATTCGTGGGAAATAATTTACTAGGACAATAAATGAGA
66 CAGAGGCTTTACAAATTCGTGGGAAATAATTTACTAGGACAAGAAACCACA
* * * *
558595 AACTTTGAAAATCGCTTCTTCATTTTCATGCAAAAACATCCTACCCTGAGG-TTTACAGATGGCC
1 AACTTTAAAAATCGCTTCATCATTTTCATGCAAAAACATCCTACCCTGAGGTTTTACAAATGACC
* *
558659 CAGAGGTTTTACAAATTCGTGGGAAATAATTTACTAGG-TAAGAAACC
66 CAGAGGCTTTACAAATTCGTGGGAAATAATTTACTAGGACAAGAAACC
558706 TCTTACTTTT
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
114 5 0.05
115 47 0.47
116 47 0.47
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (116 bp):
AACTTTAAAAATCGCTTCATCATTTTCATGCAAAAACATCCTACCCTGAGGTTTTACAAATGACC
CAGAGGCTTTACAAATTCGTGGGAAATAATTTACTAGGACAAGAAACCACA
Found at i:559568 original size:66 final size:68
Alignment explanation
Indices: 559462--559599 Score: 262
Period size: 66 Copynumber: 2.1 Consensus size: 68
559452 TTGACCATCG
559462 TTCAATCTTAGTTGGCTCTACTAGTTTCTTGTTGTTGAAGTTCCAGCG-T-TTTTGTGGAAGGAA
1 TTCAATCTTAGTTGGCTCTACTAGTTTCTTGTTGTTGAAGTTCCAGCGTTCTTTTGTGGAAGGAA
559525 ATC
66 ATC
559528 TTCAATCTTAGTTGGCTCTACTAGTTTCTTGTTGTTGAAGTTCCAGCGTTCTTTTGTGGAAGGAA
1 TTCAATCTTAGTTGGCTCTACTAGTTTCTTGTTGTTGAAGTTCCAGCGTTCTTTTGTGGAAGGAA
559593 ATC
66 ATC
559596 TTCA
1 TTCA
559600 TCATTTCTCA
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
66 48 0.69
67 1 0.01
68 21 0.30
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.43
Consensus pattern (68 bp):
TTCAATCTTAGTTGGCTCTACTAGTTTCTTGTTGTTGAAGTTCCAGCGTTCTTTTGTGGAAGGAA
ATC
Found at i:561766 original size:21 final size:21
Alignment explanation
Indices: 561719--561766 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
561709 TCATAACCTT
*
561719 AAAAGCAACACACTTTTATAA
1 AAAAGGAACACACTTTTATAA
*
561740 AAAAGGAACACACTTTTATCA
1 AAAAGGAACACACTTTTATAA
561761 AAAAGG
1 AAAAGG
561767 CGGAGAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (21 bp):
AAAAGGAACACACTTTTATAA
Found at i:567466 original size:3 final size:3
Alignment explanation
Indices: 567454--567494 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
567444 GTAATATTTG
*
567454 TAA T-A TAA TAA TAA TAA TAA TAA T-A TAG TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
567495 TATTATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 6 0.18
3 27 0.82
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:568736 original size:6 final size:6
Alignment explanation
Indices: 568719--568831 Score: 75
Period size: 6 Copynumber: 18.8 Consensus size: 6
568709 GTTTGGACTC
* * ** * *
568719 GGGTTT GGGTTT GGGTTT GGGATC AAGTTC GGGTTT AGGTTT -GGTTT
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT
** * * * * *
568766 CATGTTT GGGTTC GGGTTT AGTTTT GGGTTT GGGTTT TGGTTA GGGTTT
1 -GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT
* *
568815 GGGTTA GGGTTA GGGTT
1 GGGTTT GGGTTT GGGTT
568832 ATAGAAGATG
Statistics
Matches: 82, Mismatches: 23, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
5 5 0.06
6 73 0.89
7 4 0.05
ACGTcount: A:0.08, C:0.04, G:0.42, T:0.46
Consensus pattern (6 bp):
GGGTTT
Found at i:568752 original size:24 final size:24
Alignment explanation
Indices: 568675--568762 Score: 90
Period size: 24 Copynumber: 3.7 Consensus size: 24
568665 CAAATTCGGA
* *
568675 TTCGGGTTT-GGATTGGGTTCAAG
1 TTCGGGTTTGGGTTTGGGATCAAG
* **
568698 TTCGGGTTCGGGTTT-GGACTCGGG
1 TTCGGGTTTGGGTTTGGGA-TCAAG
*
568722 TTTGGGTTTGGGTTTGGGATCAAG
1 TTCGGGTTTGGGTTTGGGATCAAG
*
568746 TTCGGGTTTAGGTTTGG
1 TTCGGGTTTGGGTTTGG
568763 TTTCATGTTT
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
23 10 0.20
24 38 0.75
25 3 0.06
ACGTcount: A:0.09, C:0.09, G:0.42, T:0.40
Consensus pattern (24 bp):
TTCGGGTTTGGGTTTGGGATCAAG
Done.