Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008909.1 Hibiscus syriacus cultivar Beakdansim tig00112206_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: 2327114
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 8
Found at i:5414 original size:21 final size:20
Alignment explanation
Indices: 5388--5429 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5378 ATTCTGGGTT
* *
5388 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCC-TTCA
5409 AGGGGAACCGATACCCTTCA
1 AGGGGAACCGATACCCTTCA
5429 A
1 A
5430 CAAATATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (20 bp):
AGGGGAACCGATACCCTTCA
Found at i:5548 original size:67 final size:68
Alignment explanation
Indices: 5410--5559 Score: 171
Period size: 68 Copynumber: 2.2 Consensus size: 68
5400 ACCCATTCAA
* * * * *
5410 GGGGAACCGATA-CCCTTCAACAAATATGATTTCCAGAATGCTAGAGGGGAATCGGTACCCCAGG
1 GGGGAACCGATACCCCCTCAACAAATATGAATTCCAGAATGCTAGAAGGGAATCGATACCCCAGA
5474 GGG
66 GGG
* ** * *
5477 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAG-ATGCTTGAAGGGAATCGATACCCTA-
1 GGGGAACCGATACCCCCTCAACAAATATG-AATTCCAGAATGCTAGAAGGGAATCGATACCCCAG
5540 AGGG
65 AGGG
*
5544 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
5560 ATGACAAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
67 30 0.43
68 33 0.47
69 7 0.10
ACGTcount: A:0.29, C:0.25, G:0.28, T:0.19
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACAAATATGAATTCCAGAATGCTAGAAGGGAATCGATACCCCAGA
GGG
Found at i:5894 original size:29 final size:29
Alignment explanation
Indices: 5860--5931 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
5850 CATATTATGA
**
5860 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
5889 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
5918 TACATGACATGAAT
1 TACATGACATGAAT
5932 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:6299 original size:22 final size:23
Alignment explanation
Indices: 6223--6291 Score: 131
Period size: 23 Copynumber: 3.0 Consensus size: 23
6213 CTTATGGACA
6223 AAATTCTACGGGCACTTCGGTGC
1 AAATTCTACGGGCACTTCGGTGC
6246 AAATTCTACGGGCA-TTCGGTGC
1 AAATTCTACGGGCACTTCGGTGC
6268 AAATTCTACGGGCACTTCGGTGC
1 AAATTCTACGGGCACTTCGGTGC
6291 A
1 A
6292 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
22 22 0.49
23 23 0.51
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (23 bp):
AAATTCTACGGGCACTTCGGTGC
Found at i:10580 original size:2 final size:2
Alignment explanation
Indices: 10573--10599 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10563 TGGCAAAGTA
10573 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
10600 TTGTGCTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:15607 original size:16 final size:18
Alignment explanation
Indices: 15575--15607 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
15565 CCTTCGCTTT
15575 CCCTGCCCTTGTTCCAAA
1 CCCTGCCCTTGTTCCAAA
15593 CCCTG-CCTT-TTCCAA
1 CCCTGCCCTTGTTCCAA
15608 TCTGCATGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.15, C:0.45, G:0.09, T:0.30
Consensus pattern (18 bp):
CCCTGCCCTTGTTCCAAA
Found at i:17203 original size:7 final size:7
Alignment explanation
Indices: 17193--17237 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
17183 TTTATTATTA
17193 TTTAGGG
1 TTTAGGG
17200 TTTAGGG
1 TTTAGGG
17207 TTTAGGG
1 TTTAGGG
17214 TTTAGGG
1 TTTAGGG
*
17221 TTTAAGG
1 TTTAGGG
17228 TTTAGGG
1 TTTAGGG
17235 TTT
1 TTT
17238 TAAGTTAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:27239 original size:16 final size:16
Alignment explanation
Indices: 27218--27250 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
27208 TAATAAATAG
27218 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
27234 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
27250 A
1 A
27251 AAAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:27331 original size:10 final size:10
Alignment explanation
Indices: 27316--27390 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
27306 CATTTAATAA
27316 ATAAACGAAC
1 ATAAACGAAC
27326 ATAAACGAAC
1 ATAAACGAAC
27336 ----ACGAAC
1 ATAAACGAAC
27342 ATAAACGAAC
1 ATAAACGAAC
** *
27352 ACGAAC-ATAA
1 ATAAACGA-AC
27362 ATGAACACGAAC
1 AT-AA-ACGAAC
27374 ATAAACGAAC
1 ATAAACGAAC
27384 ATAAACG
1 ATAAACG
27391 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:27341 original size:16 final size:16
Alignment explanation
Indices: 27320--27384 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
27310 TAATAAATAA
27320 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
27336 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
27352 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
27368 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
27384 A
1 A
27385 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:28148 original size:14 final size:14
Alignment explanation
Indices: 28131--28182 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
28121 AATGAACATA
28131 AACGAACATAATCG
1 AACGAACATAATCG
28145 AACGAACATAA-C-
1 AACGAACATAATCG
*
28157 -A--AACATAACCG
1 AACGAACATAATCG
28168 AACGAACATAATCG
1 AACGAACATAATCG
28182 A
1 A
28183 CGTTCACGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
9 7 0.22
10 1 0.03
11 1 0.03
12 1 0.03
13 1 0.03
14 21 0.66
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.12
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:28169 original size:23 final size:23
Alignment explanation
Indices: 28110--28178 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
28100 AGATTGAGTT
* *
28110 AAACATAAAGGAATGAACATAAAC
1 AAACATAAACGAACGAACAT-AAC
* *
28134 GAACATAATCGAACGAACATAAC
1 AAACATAAACGAACGAACATAAC
*
28157 AAACATAACCGAACGAACATAA
1 AAACATAAACGAACGAACATAA
28179 TCGACGTTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 23 0.59
24 16 0.41
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.12
Consensus pattern (23 bp):
AAACATAAACGAACGAACATAAC
Found at i:31938 original size:2 final size:2
Alignment explanation
Indices: 31933--31973 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
31923 ATCTTTTTTC
31933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31974 TTTTTATTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34559 original size:2 final size:2
Alignment explanation
Indices: 34546--34575 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
34536 TTTGGAATCA
*
34546 AT AT AC 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
34576 TTCAATTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:43515 original size:2 final size:2
Alignment explanation
Indices: 43508--43544 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
43498 TTTGTTTAAT
43508 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
43545 ATATATATAT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:43549 original size:2 final size:2
Alignment explanation
Indices: 43544--43578 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
43534 TCTCTCTCTC
43544 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43579 TTTTGCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59278 original size:17 final size:17
Alignment explanation
Indices: 59252--59299 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
59242 TCTTATTTTC
*
59252 TTAATCATATATAAAAT
1 TTAATAATATATAAAAT
*
59269 TTAATAATATAT-ATAT
1 TTAATAATATATAAAAT
59285 TTATATAA-ATATAAA
1 TTA-ATAATATATAAA
59300 TTAATAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAATAATATATAAAAT
Found at i:65512 original size:26 final size:26
Alignment explanation
Indices: 65461--65510 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
65451 TGAAGCCTTT
*
65461 AAACCGAACCGAAACCGAACCGTTTA
1 AAACCAAACCGAAACCGAACCGTTTA
65487 AAACCAAACCG-AACCGAACCGTTT
1 AAACCAAACCGAAACCGAACCGTTT
65511 TACTCGGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.42, C:0.32, G:0.14, T:0.12
Consensus pattern (26 bp):
AAACCAAACCGAAACCGAACCGTTTA
Found at i:71796 original size:2 final size:2
Alignment explanation
Indices: 71791--71836 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
71781 ACACACACAC
71791 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
71833 AT AT
1 AT AT
71837 TAGAATTTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82781 original size:31 final size:31
Alignment explanation
Indices: 82715--82781 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
82705 TTAGCGATTG
** **
82715 AGGGACTAAAATCAAATAGATTGATAATGTC
1 AGGGACTAAAATCAAATAGATCAATAACATC
*
82746 AGGGACTAAAATCAAATAGATCAATAACATT
1 AGGGACTAAAATCAAATAGATCAATAACATC
82777 AGGGA
1 AGGGA
82782 TCATTCTCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.22
Consensus pattern (31 bp):
AGGGACTAAAATCAAATAGATCAATAACATC
Found at i:85365 original size:21 final size:21
Alignment explanation
Indices: 85327--85370 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
85317 AAACTATAAG
* *
85327 TTAGGGTTTAGAGGTTATTGT
1 TTAGGGTTTAGAAGTTATGGT
* *
85348 TTAGGGTTTATAATTTATGGT
1 TTAGGGTTTAGAAGTTATGGT
85369 TT
1 TT
85371 TAAGTTAGGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.52
Consensus pattern (21 bp):
TTAGGGTTTAGAAGTTATGGT
Found at i:88136 original size:18 final size:18
Alignment explanation
Indices: 88110--88153 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
88100 GTAAAATTTC
*
88110 AATTAAAAATACATAAAA
1 AATTTAAAATACATAAAA
* *
88128 AATTTAAAATATATAATA
1 AATTTAAAATACATAAAA
*
88146 ATTTTAAA
1 AATTTAAA
88154 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AATTTAAAATACATAAAA
Found at i:90924 original size:27 final size:27
Alignment explanation
Indices: 90884--90935 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
90874 TTGATGTTAC
*
90884 TTTTAAATCTGATTCGAGAATTATTAA
1 TTTTAAATCCGATTCGAGAATTATTAA
* *
90911 TTTTAGATCCGATTCGAGTATTATT
1 TTTTAAATCCGATTCGAGAATTATT
90936 TATACTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (27 bp):
TTTTAAATCCGATTCGAGAATTATTAA
Found at i:92720 original size:15 final size:15
Alignment explanation
Indices: 92700--92731 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
92690 AGAAAGCACA
92700 AATAAATCCTCAAGC
1 AATAAATCCTCAAGC
92715 AATAAATCCTCAAGC
1 AATAAATCCTCAAGC
92730 AA
1 AA
92732 GGTGAGTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (15 bp):
AATAAATCCTCAAGC
Found at i:109289 original size:31 final size:31
Alignment explanation
Indices: 109244--109346 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 31
109234 ATATTAATAG
109244 TAATACTTTT-ATAAGTTTAAGGATTATTTTA
1 TAATA-TTTTGATAAGTTTAAGGATTATTTTA
* * * *
109275 TAATATTTTGATAAGATTAAAGACCT-TTGTA
1 TAATATTTTGATAAGTTTAAGGA-TTATTTTA
* * * *
109306 TAATATTTTGATAAATTTTAGTGATCATGTTA
1 TAATATTTTGATAAGTTTAAG-GATTATTTTA
109338 TAATTATTT
1 TAA-TATTT
109347 AGTTAGTAGT
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
30 4 0.07
31 37 0.67
32 9 0.16
33 5 0.09
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.50
Consensus pattern (31 bp):
TAATATTTTGATAAGTTTAAGGATTATTTTA
Found at i:109515 original size:22 final size:21
Alignment explanation
Indices: 109474--109518 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
109464 TTTTAGTTAG
*
109474 TAATTTTTAAATATTATAAAA
1 TAATTATTAAATATTATAAAA
*
109495 TAATTATTAATATATTTTAAAA
1 TAATTATTAA-ATATTATAAAA
109517 TA
1 TA
109519 TCACAATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATTATTAAATATTATAAAA
Found at i:115118 original size:30 final size:30
Alignment explanation
Indices: 115084--115142 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
115074 ATTTAAATTT
115084 TCTTCGATTAATTATTTATTTTATAGATGG
1 TCTTCGATTAATTATTTATTTTATAGATGG
115114 TCTTCGATTAATTATTTATTTTATAGATG
1 TCTTCGATTAATTATTTATTTTATAGATG
115143 ATGTTCATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.07, G:0.12, T:0.54
Consensus pattern (30 bp):
TCTTCGATTAATTATTTATTTTATAGATGG
Found at i:115406 original size:16 final size:16
Alignment explanation
Indices: 115387--115419 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
115377 GAAATGAATC
*
115387 AAAAGTGAAACAAAAA
1 AAAAATGAAACAAAAA
115403 AAAAATGAAACAAAAA
1 AAAAATGAAACAAAAA
115419 A
1 A
115420 CTAAAGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.06, G:0.09, T:0.06
Consensus pattern (16 bp):
AAAAATGAAACAAAAA
Found at i:115769 original size:17 final size:19
Alignment explanation
Indices: 115729--115768 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
115719 TTTTCAATGG
115729 AAAATACATAGAAAATTTT
1 AAAATACATAGAAAATTTT
*
115748 AAAATATATA-AAAATTTT
1 AAAATACATAGAAAATTTT
115766 AAA
1 AAA
115769 TTAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAATACATAGAAAATTTT
Found at i:115778 original size:18 final size:18
Alignment explanation
Indices: 115740--115779 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
115730 AAATACATAG
* *
115740 AAAATTTTAAAATATATA
1 AAAATTTTAAAATAAAAA
*
115758 AAAATTTTAAATTAAAAA
1 AAAATTTTAAAATAAAAA
115776 AAAA
1 AAAA
115780 CAACTGTCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTTTAAAATAAAAA
Found at i:123995 original size:18 final size:19
Alignment explanation
Indices: 123966--124001 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
123956 AGATGGATGT
123966 TAATATGTTGTTTGAGATA
1 TAATATGTTGTTTGAGATA
123985 TAATA-GTTGTTTGAGAT
1 TAATATGTTGTTTGAGAT
124002 TCTAAGATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (19 bp):
TAATATGTTGTTTGAGATA
Found at i:137265 original size:2 final size:2
Alignment explanation
Indices: 137258--137310 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
137248 AATTTAAATT
137258 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
137300 TA TA TA TA TA T
1 TA TA TA TA TA T
137311 TAAAACGGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:141159 original size:122 final size:122
Alignment explanation
Indices: 140942--141188 Score: 476
Period size: 122 Copynumber: 2.0 Consensus size: 122
140932 ACACAGAGGG
140942 AAGTACAATGACAATTGCCCTTGTTGTGTCCCTTAACAAAGATGTAGGTGCAAGCGTTTCATACG
1 AAGTACAATGACAATTGCCCTTGTTGTGTCCCTTAACAAAGATGTAGGTGCAAGCGTTTCATACG
*
141007 CTGACGAGGCATCTAGGAACGATAAACAACAGCCTCAACCGACCAACAAGCAATTCT
66 CTAACGAGGCATCTAGGAACGATAAACAACAGCCTCAACCGACCAACAAGCAATTCT
*
141064 AAGTACAATGGCAATTGCCCTTGTTGTGTCCCTTAACAAAGATGTAGGTGCAAGCGTTTCATACG
1 AAGTACAATGACAATTGCCCTTGTTGTGTCCCTTAACAAAGATGTAGGTGCAAGCGTTTCATACG
141129 CTAACGAGGCATCTAGGAACGATAAACAACAGCCTCAACCGACCAACAAGCAATTCT
66 CTAACGAGGCATCTAGGAACGATAAACAACAGCCTCAACCGACCAACAAGCAATTCT
141186 AAG
1 AAG
141189 GGAAAATGCG
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 123 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (122 bp):
AAGTACAATGACAATTGCCCTTGTTGTGTCCCTTAACAAAGATGTAGGTGCAAGCGTTTCATACG
CTAACGAGGCATCTAGGAACGATAAACAACAGCCTCAACCGACCAACAAGCAATTCT
Found at i:142544 original size:32 final size:33
Alignment explanation
Indices: 142482--142545 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
142472 GCATTAAAAT
*
142482 AGAAATTAAACGAAAATATGGAAAACTAAAGAA
1 AGAAACTAAACGAAAATATGGAAAACTAAAGAA
* *
142515 AGAAACTAAACGTAAA-ATGGAAAAGTAAAGA
1 AGAAACTAAACGAAAATATGGAAAACTAAAGA
142546 GAGATAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.62, C:0.06, G:0.17, T:0.14
Consensus pattern (33 bp):
AGAAACTAAACGAAAATATGGAAAACTAAAGAA
Found at i:152433 original size:12 final size:11
Alignment explanation
Indices: 152401--152436 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
152391 TCTCGTCTCG
152401 GGTCGGGTCG-
1 GGTCGGGTCGT
152411 GGTCGGGTCGT
1 GGTCGGGTCGT
152422 GGTCGTGGTCGT
1 GGTCG-GGTCGT
152434 GGT
1 GGT
152437 AATACGTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.00, C:0.17, G:0.56, T:0.28
Consensus pattern (11 bp):
GGTCGGGTCGT
Found at i:152436 original size:6 final size:5
Alignment explanation
Indices: 152398--152432 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
152388 CTGTCTCGTC
152398 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG
152433 TGGTAATACG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:153178 original size:14 final size:16
Alignment explanation
Indices: 153139--153176 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
153129 TCGTTGACAG
153139 AATTTATTCATATATTT
1 AATTT-TTCATATATTT
153156 AATTTTTCATA-ATTT
1 AATTTTTCATATATTT
153171 AATTTT
1 AATTTT
153177 CAATTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.48
16 6 0.29
17 5 0.24
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTTTTCATATATTT
Found at i:158183 original size:20 final size:20
Alignment explanation
Indices: 158146--158184 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
158136 CTCTAAATCA
* *
158146 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
158166 TTTTTCAAAATCTAATTTT
1 TTTTTCAAAATCTAATTTT
158185 ACTTTCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:162751 original size:20 final size:20
Alignment explanation
Indices: 162728--162765 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
162718 AAAGTTTAAG
162728 TACTTAAT-TGATAGTTTATA
1 TACTTAATGTG-TAGTTTATA
*
162748 TACTTTATGTGTAGTTTA
1 TACTTAATGTGTAGTTTA
162766 CCCTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (20 bp):
TACTTAATGTGTAGTTTATA
Found at i:162930 original size:51 final size:50
Alignment explanation
Indices: 162841--162945 Score: 131
Period size: 51 Copynumber: 2.1 Consensus size: 50
162831 ATGAAAGGTG
*
162841 AACTAATCACTAGGGTGATGAATTTCAAGATAAAATA-TTTTTTTATTAA
1 AACTAATCACTAGGGTGATGAATTTCAAAATAAAATATTTTTTTTATTAA
* * * * *
162890 AACTCATCACGTAGGAGTGATGAGTTTTAAAATGATATATTTTTTTTATTAA
1 AACTAATCAC-TAGG-GTGATGAATTTCAAAATAAAATATTTTTTTTATTAA
162942 AACT
1 AACT
162946 TGTCATGCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 9 0.19
50 4 0.09
51 18 0.38
52 16 0.34
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (50 bp):
AACTAATCACTAGGGTGATGAATTTCAAAATAAAATATTTTTTTTATTAA
Found at i:163270 original size:30 final size:30
Alignment explanation
Indices: 163224--163280 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
163214 TTTCATTTAT
*
163224 GTACCTAAAATATA-TTTTGGTCAAAATAA
1 GTACCTAAAATATATTTTTGGCCAAAATAA
163253 GTACCTAAAATTATATTTTTGGCCAAAA
1 GTACCTAAAA-TATATTTTTGGCCAAAA
163281 ATTGGTACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 10 0.40
30 4 0.16
31 11 0.44
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (30 bp):
GTACCTAAAATATATTTTTGGCCAAAATAA
Found at i:173239 original size:18 final size:18
Alignment explanation
Indices: 173216--173256 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
173206 CCTATGATGG
173216 AAATAACATGAACAAATA
1 AAATAACATGAACAAATA
*
173234 AAATAACATGAACAGATA
1 AAATAACATGAACAAATA
173252 AAATA
1 AAATA
173257 TATTCTGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.66, C:0.10, G:0.07, T:0.17
Consensus pattern (18 bp):
AAATAACATGAACAAATA
Found at i:186119 original size:62 final size:62
Alignment explanation
Indices: 186024--186150 Score: 254
Period size: 62 Copynumber: 2.0 Consensus size: 62
186014 AGCACCATTA
186024 CTCCTCCTACCCATAACCAAAGGCCTAAATCCATGGGAATCGCGGACCGCAACTAGCTTATC
1 CTCCTCCTACCCATAACCAAAGGCCTAAATCCATGGGAATCGCGGACCGCAACTAGCTTATC
186086 CTCCTCCTACCCATAACCAAAGGCCTAAATCCATGGGAATCGCGGACCGCAACTAGCTTATC
1 CTCCTCCTACCCATAACCAAAGGCCTAAATCCATGGGAATCGCGGACCGCAACTAGCTTATC
186148 CTC
1 CTC
186151 GGTCACAAAC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.28, C:0.36, G:0.16, T:0.20
Consensus pattern (62 bp):
CTCCTCCTACCCATAACCAAAGGCCTAAATCCATGGGAATCGCGGACCGCAACTAGCTTATC
Found at i:187117 original size:19 final size:20
Alignment explanation
Indices: 187076--187126 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
187066 GAAACCCCTT
*
187076 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
187096 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
187115 TGAAGATACATG
1 TGAAAATACATG
187127 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:190052 original size:24 final size:24
Alignment explanation
Indices: 190002--190051 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
189992 AACACAACTC
* *
190002 TTGGCACTTCAAATGACGTTTCTT
1 TTGGAACTTCAAATGACGTATCTT
*
190026 TTGGAACTTCAAATGGCGTCATCTT
1 TTGGAACTTCAAATGACGT-ATCTT
190051 T
1 T
190052 GAAACATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (24 bp):
TTGGAACTTCAAATGACGTATCTT
Found at i:191346 original size:10 final size:11
Alignment explanation
Indices: 191328--191375 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
191318 TTTTTGAATT
191328 TTTTCTTTTTC
1 TTTTCTTTTTC
191339 TTTT-TTTTTC
1 TTTTCTTTTTC
**
191349 TTTTCTGATTC
1 TTTTCTTTTTC
*
191360 TTTTCTTCTTC
1 TTTTCTTTTTC
191371 TTTTC
1 TTTTC
191376 GTACTCCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 10 0.31
11 22 0.69
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:192126 original size:19 final size:20
Alignment explanation
Indices: 192085--192135 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
192075 GAAACCCCTT
*
192085 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
192105 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
192124 TGAAGATACATG
1 TGAAAATACATG
192136 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:195086 original size:15 final size:16
Alignment explanation
Indices: 195057--195086 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
195047 ATCTTTTTCA
195057 TTCTTTCCTTCTCTCT
1 TTCTTTCCTTCTCTCT
195073 TTCTTTCC-TCTCTC
1 TTCTTTCCTTCTCTC
195087 CATAAAAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (16 bp):
TTCTTTCCTTCTCTCT
Found at i:196455 original size:21 final size:21
Alignment explanation
Indices: 196430--196472 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
196420 CATTATCATG
196430 AACTACCAC-ATTAGTACCATA
1 AACTACCACGATTA-TACCATA
*
196451 AACTATCACGATTATACCATA
1 AACTACCACGATTATACCATA
196472 A
1 A
196473 CAATCAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (21 bp):
AACTACCACGATTATACCATA
Found at i:205264 original size:2 final size:2
Alignment explanation
Indices: 205257--205284 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
205247 AGCCAATGAG
205257 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
205285 GGGTAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:208430 original size:60 final size:60
Alignment explanation
Indices: 208317--208431 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
208307 ATAGCCATGT
* * * * ***
208317 GATCATTTTGTAACTTTTAATAGTCAGAGGACTTGACAAAATAATATTTTATAGTATGAG
1 GATCATTTTATAACTTTTAATAGTCAAAGAACTTAACAAAATAATACCATATAGTATGAG
* * *
208377 GATCATTTTATAATTTTTAATAGTCAAAGAACTTAATAAAGTAATACCATATAGT
1 GATCATTTTATAACTTTTAATAGTCAAAGAACTTAACAAAATAATACCATATAGT
208432 TGGACCATTT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (60 bp):
GATCATTTTATAACTTTTAATAGTCAAAGAACTTAACAAAATAATACCATATAGTATGAG
Found at i:209948 original size:18 final size:19
Alignment explanation
Indices: 209927--209967 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
209917 TAAAATCAAC
*
209927 ATGATGT-ATTATAAAATA
1 ATGATGTAATTAAAAAATA
*
209945 ATGATTTAATTAAAAAATA
1 ATGATGTAATTAAAAAATA
209964 ATGA
1 ATGA
209968 ACTTATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
ATGATGTAATTAAAAAATA
Found at i:213359 original size:19 final size:20
Alignment explanation
Indices: 213327--213366 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
213317 CGCATTGCCA
213327 TCGTTACCTCTTTC-CCAAC
1 TCGTTACCTCTTTCACCAAC
* *
213346 TCGTTTCCTTTTTCACCAAC
1 TCGTTACCTCTTTCACCAAC
213366 T
1 T
213367 GAGCTGGCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.15, C:0.38, G:0.05, T:0.42
Consensus pattern (20 bp):
TCGTTACCTCTTTCACCAAC
Found at i:216233 original size:2 final size:2
Alignment explanation
Indices: 216226--216258 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
216216 AAATAAGAAT
216226 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
216259 TGGGTCAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:216619 original size:20 final size:21
Alignment explanation
Indices: 216564--216608 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
216554 AAATTTTTAA
*
216564 AAAATTAA-AAGTTTAAGTACT
1 AAAATTAATAA-TTTAAATACT
216585 AAAATTAATAATTTAAATACT
1 AAAATTAATAATTTAAATACT
216606 AAA
1 AAA
216609 TAAGTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (21 bp):
AAAATTAATAATTTAAATACT
Found at i:221930 original size:23 final size:23
Alignment explanation
Indices: 221897--221940 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
221887 GAGTCGAGGG
221897 TCTACGCGGTCCTTCGGGACAAT
1 TCTACGCGGTCCTTCGGGACAAT
*
221920 TCTACGTGGTCCTTCGGGACA
1 TCTACGCGGTCCTTCGGGACA
221941 TATATGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGGGACAAT
Found at i:222305 original size:31 final size:31
Alignment explanation
Indices: 222238--222297 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
222228 CAATTTAAGG
*
222238 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
222269 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
222298 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:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:222503 original size:21 final size:21
Alignment explanation
Indices: 222477--222518 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
222467 ATTTGAATAT
*
222477 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
222498 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
222519 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:222580 original size:21 final size:21
Alignment explanation
Indices: 222547--222586 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
222537 GTTTTGCAGA
*
222547 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
222569 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
222587 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:222841 original size:34 final size:32
Alignment explanation
Indices: 222802--222871 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
222792 TTTTGTAAAG
* *
222802 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAAGTTCTAGCTTAGCCCG-G-AAAAACTA
*
222836 GGGAAAAGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
222868 GGGA
1 GGGA
222872 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (32 bp):
GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:224928 original size:99 final size:99
Alignment explanation
Indices: 224757--224955 Score: 371
Period size: 99 Copynumber: 2.0 Consensus size: 99
224747 TGTTAGGTAC
* *
224757 CTTAGGGTCCCTTTGGTAACTCGTAAACAATCTGCGAATGACTGCACAAGTTTTCTGGAAAGGAT
1 CTTAGGGTCCCTTTGGTAACTCGTAAAAAATCTGCGAATGACTGCACAAGTCTTCTGGAAAGGAT
224822 TAAAGAAAAATTAAGCCATTGGGCAAATAAATGA
66 TAAAGAAAAATTAAGCCATTGGGCAAATAAATGA
*
224856 CTTAGGGTCCCTTTGGTAACTCGTAAAAAATCTGCGAATGACTGCACAAGTCTTCTGGAAATGAT
1 CTTAGGGTCCCTTTGGTAACTCGTAAAAAATCTGCGAATGACTGCACAAGTCTTCTGGAAAGGAT
224921 TAAAGAAAAATTAAGCCATTGGGCAAATAAATGA
66 TAAAGAAAAATTAAGCCATTGGGCAAATAAATGA
224955 C
1 C
224956 ACAACTTGTG
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.26
Consensus pattern (99 bp):
CTTAGGGTCCCTTTGGTAACTCGTAAAAAATCTGCGAATGACTGCACAAGTCTTCTGGAAAGGAT
TAAAGAAAAATTAAGCCATTGGGCAAATAAATGA
Found at i:226486 original size:30 final size:30
Alignment explanation
Indices: 226451--226514 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
226441 TCTTAAACAT
*
226451 AAGTGTACTTAAATTGAATTATATTGTTTA
1 AAGTGTACTTAAATTGAATTATATGGTTTA
226481 AAGTGTACTTAAATTGAATTATATGGTTTA
1 AAGTGTACTTAAATTGAATTATATGGTTTA
226511 AAGT
1 AAGT
226515 AAGTGGCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.44
Consensus pattern (30 bp):
AAGTGTACTTAAATTGAATTATATGGTTTA
Found at i:238308 original size:16 final size:17
Alignment explanation
Indices: 238287--238320 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
238277 AATGACTATT
238287 TTATATTTTTT-AATAG
1 TTATATTTTTTAAATAG
238303 TTATATTTTTTAAATAG
1 TTATATTTTTTAAATAG
238320 T
1 T
238321 CAATGATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TTATATTTTTTAAATAG
Found at i:241171 original size:2 final size:2
Alignment explanation
Indices: 241164--241193 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
241154 ATAAAATTTA
241164 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
241194 GGAAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:243718 original size:22 final size:19
Alignment explanation
Indices: 243680--243723 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
243670 GTAGACAGGT
*
243680 AATTTTAATTTTTTTTTTA
1 AATTTTAATTTTTTTTTGA
243699 AATTGTTAATATTTTATTTTGA
1 AATT-TTAAT-TTTT-TTTTGA
243721 AAT
1 AAT
243724 CTACAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 5 0.24
21 4 0.19
22 8 0.38
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
AATTTTAATTTTTTTTTGA
Found at i:245374 original size:111 final size:110
Alignment explanation
Indices: 245236--245529 Score: 354
Period size: 111 Copynumber: 2.6 Consensus size: 110
245226 GCATGGAAAC
* * * * *
245236 TTGGAGGATCTTCATGCTGTAGGGGAAGTAGGTACCGATATGACTGAGTCAGAGGAGAACCCTGT
1 TTGGAGGATATTCATGCTGTAGAGGAAGCAGGTACAGATATG-CTGAGGCAGAGGAGAACCCTGT
*
245301 GATGGAAAGAAAAATTGTGAATAACGTGTCTGAACAAACTGAAAAT
65 GATGGAAAGAAAAATGGTGAATAACGTGTCTGAACAAACTGAAAAT
* ** * * * *
245347 TTGGAGGATATTCATGCTGTAGAGGAAGCAAGTATGGATATGGTCGAGGCAGAGGAGTACCTTTT
1 TTGGAGGATATTCATGCTGTAGAGGAAGCAGGTACAGATATGCT-GAGGCAGAGGAGAACCCTGT
* * *
245412 AATGGAAGGAAAAATGGTGAATAATGTGTCTGAACAAACTGAAAAT
65 GATGGAAAGAAAAATGGTGAATAACGTGTCTGAACAAACTGAAAAT
* * * * * * *
245458 TTGGAGGATATGCATGCTATAGAGGAAGCAGGTGCAGATACGGTTGAGGCAGAGGAGGACCCTGC
1 TTGGAGGATATTCATGCTGTAGAGGAAGCAGGTACAGATA-TGCTGAGGCAGAGGAGAACCCTGT
245523 GATGGAA
65 GATGGAA
245530 GAGGAATCGG
Statistics
Matches: 153, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
110 1 0.01
111 150 0.98
112 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.23
Consensus pattern (110 bp):
TTGGAGGATATTCATGCTGTAGAGGAAGCAGGTACAGATATGCTGAGGCAGAGGAGAACCCTGTG
ATGGAAAGAAAAATGGTGAATAACGTGTCTGAACAAACTGAAAAT
Found at i:267107 original size:2 final size:2
Alignment explanation
Indices: 267100--267139 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
267090 ATTCTACCCC
267100 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
267140 CATGCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:269043 original size:5 final size:5
Alignment explanation
Indices: 269033--269201 Score: 237
Period size: 5 Copynumber: 34.8 Consensus size: 5
269023 CATTCATTTA
269033 ATATT ATATT ATATT ATATT ATATT ATATT ATA-T -TATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
269081 ATATT AT-TT ATA-T AT-TAT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATAT-T ATATT ATATT ATATT ATATT ATATT ATATT
*
269129 ATATT ATATT ATA-T ATATT ATA-T -TATT ATATT ATATT ATGTT ATATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT-T
*
269177 TTATT ATATTT ATATT ATATT ATAT
1 ATATT ATA-TT ATATT ATATT ATAT
269202 ATTTGTCAAA
Statistics
Matches: 149, Mismatches: 4, Indels: 22
0.85 0.02 0.13
Matches are distributed among these distances:
3 4 0.03
4 15 0.10
5 120 0.81
6 10 0.07
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:269078 original size:66 final size:61
Alignment explanation
Indices: 269000--269204 Score: 207
Period size: 56 Copynumber: 3.4 Consensus size: 61
268990 AATTTACCCT
*
269000 TTATTATATTATACATTACAAGTCATTCATTTAATATTATATTATATTATATTATATTATATTAT
1 TTATTATATTATA-ATTA-TA-T-ATT-ATTTAATATTATATTATATTATATTATATTATATTAT
269065 A
61 A
269066 TTATTATATTAT-A-T-TATATTATTT-ATA-TAT-TATATATTATATTATATTATATTATA
1 TTATTATATTATAATTATATATTATTTAATATTATAT-TATATTATATTATATTATATTATA
* * *
269122 TTATATTATATTAT-ATTATATA-TATTATATTATTATATTATATTATGTTATATATTTATTATA
1 -T-TATTATATTATAATTATATATTATT-TAATATTATATTATATTATATTATAT-TATATTATA
269185 -T-TTATATTAT-ATTATATATT
1 TTATTATATTATAATTATATATT
269205 TGTCAAACTT
Statistics
Matches: 124, Mismatches: 4, Indels: 28
0.79 0.03 0.18
Matches are distributed among these distances:
55 1 0.01
56 27 0.22
57 4 0.03
58 16 0.13
59 25 0.20
60 8 0.06
61 3 0.02
62 17 0.14
63 10 0.08
64 1 0.01
66 12 0.10
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.59
Consensus pattern (61 bp):
TTATTATATTATAATTATATATTATTTAATATTATATTATATTATATTATATTATATTATA
Found at i:286444 original size:17 final size:17
Alignment explanation
Indices: 286418--286477 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 17
286408 GACTCGAAAT
286418 AATATATTTAATAAAAA
1 AATATATTTAATAAAAA
* *
286435 AATATTTTTATTCAATAAA
1 AATATATTTAAT-AA-AAA
286454 AATAGGTATTTAATTAAAAA
1 AATA--TATTTAA-TAAAAA
286474 AATA
1 AATA
286478 ATATATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
17 10 0.29
18 2 0.06
19 7 0.21
20 7 0.21
21 7 0.21
22 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (17 bp):
AATATATTTAATAAAAA
Found at i:295479 original size:23 final size:22
Alignment explanation
Indices: 295453--295503 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
295443 TATTCGTTTA
295453 TTTAACGTTC-GCAAATGTGTTCG
1 TTTAACGTTCAG-AAAT-TGTTCG
*
295476 TTTAATGTTCATGAAATTGTTCG
1 TTTAACGTTCA-GAAATTGTTCG
295499 TTTAA
1 TTTAA
295504 GTGTTTAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 20 0.80
24 4 0.16
25 1 0.04
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (22 bp):
TTTAACGTTCAGAAATTGTTCG
Found at i:295521 original size:24 final size:23
Alignment explanation
Indices: 295465--295514 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
295455 TAACGTTCGC
*
295465 AAATGTGTTCGTTTAATGTTCATG
1 AAAT-TGTTCGTTTAATGTTCAAG
*
295489 AAATTGTTCGTTTAAGTGTTTAAG
1 AAATTGTTCGTTTAA-TGTTCAAG
295513 AA
1 AA
295515 TATGTTCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (23 bp):
AAATTGTTCGTTTAATGTTCAAG
Found at i:300594 original size:59 final size:59
Alignment explanation
Indices: 300471--300601 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 59
300461 CGAGTGACTG
* * *
300471 TTTTGCAACTTTTAATAGTCGGGGACTTTAAAAAATAATATCCTATAATCAAGAGACCA
1 TTTTGTAACTTTTAATAGTCGAGGACTTCAAAAAATAATATCCTATAATCAAGAGACCA
* * * *
300530 TTTTGTAACTTTTAATAGTCGAAGGAC-TCAATAAAGTAATA-CTCTATAGTCGAGGGACCA
1 TTTTGTAACTTTTAATAGTCG-AGGACTTCAA-AAAATAATATC-CTATAATCAAGAGACCA
300590 TTTGTGT-ACTTT
1 TTT-TGTAACTTT
300602 ACCCTTAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
59 24 0.39
60 34 0.56
61 3 0.05
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (59 bp):
TTTTGTAACTTTTAATAGTCGAGGACTTCAAAAAATAATATCCTATAATCAAGAGACCA
Found at i:300881 original size:312 final size:312
Alignment explanation
Indices: 300316--300942 Score: 1218
Period size: 312 Copynumber: 2.0 Consensus size: 312
300306 TTTGAGTTGG
300316 ACATCAACCTGCTGACTAAGATACGATATATTATGAACCTAGAATCTCGAACGACTATCATATCC
1 ACATCAACCTGCTGACTAAGATACGATATATTATGAACCTAGAATCTCGAACGACTATCATATCC
300381 CGGTCAGCAGGTTAACGTCCAACTCAAACTACCATCAATTTTTTAATGAAAAAGGACGAGTTTGG
66 CGGTCAGCAGGTTAACGTCCAACTCAAACTACCATCAATTTTTTAATGAAAAAGGACGAGTTTGG
300446 AACACAATGAATAGCCGAGTGACTGTTTTGCAACTTTTAATAGTCGGGGACTTTAAAAAATAATA
131 AACACAATGAATAGCCGAGTGACTGTTTTGCAACTTTTAATAGTCGGGGACTTTAAAAAATAATA
*
300511 TCCTATAATCAAGAGACCATTTTGTAACTTTTAATAGTCGAAGGACTCAATAAAGTAATACTCTA
196 TCCTATAATCAAGAGACAATTTTGTAACTTTTAATAGTCGAAGGACTCAATAAAGTAATACTCTA
300576 TAGTCGAGGGACCATTTGTGTACTTTACCCTTAATTTAAATTAGGGTAAATT
261 TAGTCGAGGGACCATTTGTGTACTTTACCCTTAATTTAAATTAGGGTAAATT
300628 ACATCAACCTGCTGACTAAGATACGATATATTATGAACCTAGAATCTCGAACGACTATCATATCC
1 ACATCAACCTGCTGACTAAGATACGATATATTATGAACCTAGAATCTCGAACGACTATCATATCC
*
300693 CGGTCAGCAGGTTAACGTCCAACTCAAACTACCATCAATTTTTTAATGAAAAATGACGAGTTTGG
66 CGGTCAGCAGGTTAACGTCCAACTCAAACTACCATCAATTTTTTAATGAAAAAGGACGAGTTTGG
* *
300758 AACACAATGAATAGTCGAGTGACTGTTTTGTAACTTTTAATAGTCGGGGACTTTAAAAAATAATA
131 AACACAATGAATAGCCGAGTGACTGTTTTGCAACTTTTAATAGTCGGGGACTTTAAAAAATAATA
300823 TCCTATAATCAAGAGACAATTTTGTAACTTTTAATAGTCGAAGGACTCAATAAAGTAATACTCTA
196 TCCTATAATCAAGAGACAATTTTGTAACTTTTAATAGTCGAAGGACTCAATAAAGTAATACTCTA
300888 TAGTCGAGGGACCATTTGTGTACTTTACCCTTAATTTAAATTAGGGTAAATT
261 TAGTCGAGGGACCATTTGTGTACTTTACCCTTAATTTAAATTAGGGTAAATT
300940 ACA
1 ACA
300943 CCGATCATTA
Statistics
Matches: 311, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
312 311 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (312 bp):
ACATCAACCTGCTGACTAAGATACGATATATTATGAACCTAGAATCTCGAACGACTATCATATCC
CGGTCAGCAGGTTAACGTCCAACTCAAACTACCATCAATTTTTTAATGAAAAAGGACGAGTTTGG
AACACAATGAATAGCCGAGTGACTGTTTTGCAACTTTTAATAGTCGGGGACTTTAAAAAATAATA
TCCTATAATCAAGAGACAATTTTGTAACTTTTAATAGTCGAAGGACTCAATAAAGTAATACTCTA
TAGTCGAGGGACCATTTGTGTACTTTACCCTTAATTTAAATTAGGGTAAATT
Found at i:300913 original size:60 final size:59
Alignment explanation
Indices: 300768--300913 Score: 145
Period size: 59 Copynumber: 2.5 Consensus size: 59
300758 AACACAATGA
* ** * *
300768 ATAGTCGAGTGACTGTTTTGTAACTTTTAATAGTCGGGGACTTTAAAAAATAATATCCT
1 ATAGTCGAGAGACAATTTTGTAACTTTTAATAGTCGAGGACTTCAAAAAATAATATCCT
* * *
300827 ATAATCAAGAGACAATTTTGTAACTTTTAATAGTCGAAGGAC-TCAATAAAGTAATA-CTCT
1 ATAGTCGAGAGACAATTTTGTAACTTTTAATAGTCG-AGGACTTCAA-AAAATAATATC-CT
* *
300887 ATAGTCGAGGGACCATTTGTGT-ACTTT
1 ATAGTCGAGAGACAATTT-TGTAACTTT
300914 ACCCTTAATT
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
59 35 0.49
60 33 0.46
61 3 0.04
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (59 bp):
ATAGTCGAGAGACAATTTTGTAACTTTTAATAGTCGAGGACTTCAAAAAATAATATCCT
Found at i:304044 original size:13 final size:13
Alignment explanation
Indices: 304005--304036 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
303995 TTGTGTAATG
304005 AATTGAATTTATA
1 AATTGAATTTATA
304018 AATTGAATTTATA
1 AATTGAATTTATA
304031 AATTGA
1 AATTGA
304037 GTTGATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (13 bp):
AATTGAATTTATA
Found at i:305113 original size:60 final size:60
Alignment explanation
Indices: 305047--305160 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
305037 GATGGTCTCT
* *
305047 CGACTATAAGATA-TTATTTTATTGAGTC-CTTTAACTATTAAAAGTTATAAAATGATCCTC
1 CGACTATAAGA-AGTTACTTTATTGAGTCTC-TCAACTATTAAAAGTTATAAAATGATCCTC
* * *
305107 CGACTATAGGAAGTTACTTTGTTGAGTCTCTCGACTATTAAAAGTTATAAAATG
1 CGACTATAAGAAGTTACTTTATTGAGTCTCTCAACTATTAAAAGTTATAAAATG
305161 GTCACTTGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 1 0.02
60 45 0.96
61 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (60 bp):
CGACTATAAGAAGTTACTTTATTGAGTCTCTCAACTATTAAAAGTTATAAAATGATCCTC
Found at i:306249 original size:22 final size:22
Alignment explanation
Indices: 306224--306284 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
306214 GGCATGTGAA
*
306224 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
*
306246 ATTTGTCCCGAAGGACCTTTGT
1 ATTTGTCCCGAAGGACCTATGT
* *
306268 ATATATCCCGAAGGACC
1 ATTTGTCCCGAAGGACC
306285 GCGTAGACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGT
Found at i:311848 original size:17 final size:18
Alignment explanation
Indices: 311826--311869 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
311816 TTTTAAGAAT
311826 ATTAAATTCATA-TGAT-A
1 ATTAAATT-ATAGTGATAA
*
311843 ATTAAATTATAGTGTTAA
1 ATTAAATTATAGTGATAA
311861 ATTAAATTA
1 ATTAAATTA
311870 ACCTTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 11 0.46
18 10 0.42
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (18 bp):
ATTAAATTATAGTGATAA
Found at i:317167 original size:24 final size:24
Alignment explanation
Indices: 317119--317167 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
317109 TATCGCATTC
* *
317119 AAAATTGAATGTTATGTTTTGAAA
1 AAAATTGAAAGTTATGTTCTGAAA
317143 AAAATTGAAAGTTTATGTTCT-AAA
1 AAAATTGAAAG-TTATGTTCTGAAA
317167 A
1 A
317168 CTAATCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.39
Consensus pattern (24 bp):
AAAATTGAAAGTTATGTTCTGAAA
Found at i:317650 original size:214 final size:211
Alignment explanation
Indices: 317044--317724 Score: 863
Period size: 213 Copynumber: 3.2 Consensus size: 211
317034 TTTTATTATC
* * *
317044 AAAGTTTAATTTTTATTTTATTTTAGTACCA-CAGTTAAAAATTTTTAACTTTTGTTTCATTTTA
1 AAAGTTTAATTTTTATTTCATTTTAGTACCACCA-TTAAAAA-ATTTAATTTTTGTTTCATTTTA
* * * * *
317108 GTATCGCATTCAAAATTGAATGTTATGTTTTGAAAAAAATTGAAAGTTTATGTTCTAAAACTAAT
64 GTAT--CATTCAAAATTTAATGTTAAGTTTTGAAAAAAATTGAAAGTTTAAGTACTAAAACAAAT
* * * *
317173 CAAAACTGATAGTTTAGATACTGAACGGGTTAAGTTTTGATATGTTTTAGTACATAAACTTTCAG
127 CAAAATTGATAGTTTAGATACTGAACGGGTTAAGTTTTGATTTGTTTTAGTACCTAAACTTTTAG
* * *
317238 TTCATTTCAAAACCATGCCT
192 TTCTTTTCAAAATCATACCT
* **
317258 AAAGTTTAATTTTTATTTTATTTTAGTATCTGCCATTAAAAAATTTAATTTTTGTTTCATTTTAG
1 AAAGTTTAATTTTTATTTCATTTTAGTA-CCACCATTAAAAAATTTAATTTTTGTTTCATTTTAG
* * *
317323 TATCCATTCAAAATTTAATGTTAAATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACGAATCA
65 TAT-CATTCAAAATTTAATGTTAAGTTTTGAAAAAAATTGAAAGTTTAAGTACTAAAACAAATCA
* * * *
317388 AAATTGATAGTTTAAATATTGAACGGGTTAAGTTTTG-TTCTATTTTAGTACCTAAACTTTTAAT
129 AAATTGATAGTTTAGATACTGAACGGGTTAAGTTTTGATT-TGTTTTAGTACCTAAACTTTTAGT
317452 TCTTTTCAAAATCATACCT
193 TCTTTTCAAAATCATACCT
*
317471 AAAGTTTAATTTTTATTTCATTTTAGTACACACCATTAAAAAACTTTAATTTTTATTTCATTTTA
1 AAAGTTTAATTTTTATTTCATTTTAGTAC-CACCATTAAAAAA-TTTAATTTTTGTTTCATTTTA
* ** *
317536 ATATCATGTTCAAAATTTAACATTAAGTTTTG-AAAAAATTGAAAGTATAAGTACTAAAACAAA-
64 GTATCA--TTCAAAATTTAATGTTAAGTTTTGAAAAAAATTGAAAGTTTAAGTACTAAAACAAAT
* *
317599 CTAAAATTGATAGTTTAGATACTAAACGGGTTAAATTTTGATTTGTTTTAGTACCTAAAC--TTA
127 C-AAAATTGATAGTTTAGATACTGAACGGGTTAAGTTTTGATTTGTTTTAGTACCTAAACTTTTA
*
317662 GTT-TTTTCTAAAATCATACAT
191 GTTCTTTTC-AAAATCATACCT
* * *
317683 AAAATGTAATTTTTGTTTCATTTTAGTACCCACCATTAAAAA
1 AAAGTTTAATTTTTATTTCATTTTAGTA-CCACCATTAAAAA
317725 TTACAAAATG
Statistics
Matches: 413, Mismatches: 43, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
211 5 0.01
212 55 0.13
213 167 0.40
214 153 0.37
215 31 0.08
216 2 0.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (211 bp):
AAAGTTTAATTTTTATTTCATTTTAGTACCACCATTAAAAAATTTAATTTTTGTTTCATTTTAGT
ATCATTCAAAATTTAATGTTAAGTTTTGAAAAAAATTGAAAGTTTAAGTACTAAAACAAATCAAA
ATTGATAGTTTAGATACTGAACGGGTTAAGTTTTGATTTGTTTTAGTACCTAAACTTTTAGTTCT
TTTCAAAATCATACCT
Found at i:321990 original size:73 final size:72
Alignment explanation
Indices: 321902--322133 Score: 286
Period size: 73 Copynumber: 3.1 Consensus size: 72
321892 TTACCTAATA
* *
321902 TTTAGTTTTTGTTTCATTTTAGTATCAACCATTAAATTTATTTAATAGATCATACACAATATCTA
1 TTTATTTTTTCTTTCATTTTAGTATCAA-CATTAAATTTATTTAATAGATCATACACAATATCTA
*
321967 ATTTTTTT
65 ATTTTTCT
*
321975 TTTATTTTTTTTTTCATTTTAGTATCAATCATTAAATTTATTTAATAGATCATACACAATATCTA
1 TTTATTTTTTCTTTCATTTTAGTATCAA-CATTAAATTTATTTAATAGATCATACACAATATCTA
322040 ATTTTTCT
65 ATTTTTCT
* *** * *
322048 TTTATTTTAGTACCCACATTAGGTTTAGTA-CTTACACTAAATTTATTTAATAGATCATACACAA
1 TTTATTTT--TTCTTTCA-T---TTTAGTATC-AACATTAAATTTATTTAATAGATCATACACAA
322112 TATCTAATTTTTCT
59 TATCTAATTTTTCT
322126 TTTATTTT
1 TTTATTTT
322134 AGTACCCACA
Statistics
Matches: 141, Mismatches: 11, Indels: 9
0.88 0.07 0.06
Matches are distributed among these distances:
73 77 0.55
75 3 0.02
76 1 0.01
78 52 0.37
79 8 0.06
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.52
Consensus pattern (72 bp):
TTTATTTTTTCTTTCATTTTAGTATCAACATTAAATTTATTTAATAGATCATACACAATATCTAA
TTTTTCT
Found at i:322107 original size:78 final size:78
Alignment explanation
Indices: 321934--322164 Score: 323
Period size: 78 Copynumber: 3.0 Consensus size: 78
321924 TATCAACCAT
* *****
321934 TAAATTTATTTAATAGATCATACACAATATCTAATTTTTTTTTTATTTT--TTTTTTCA-T---T
1 TAAATTTATTTAATAGATCATACACAATATCTAATTTTTCTTTTATTTTAGTACCCACATTAGGT
* *
321993 TTAGTA-TCAATCAT
66 TTAGTACT-TA-CAC
322007 TAAATTTATTTAATAGATCATACACAATATCTAATTTTTCTTTTATTTTAGTACCCACATTAGGT
1 TAAATTTATTTAATAGATCATACACAATATCTAATTTTTCTTTTATTTTAGTACCCACATTAGGT
322072 TTAGTACTTACAC
66 TTAGTACTTACAC
322085 TAAATTTATTTAATAGATCATACACAATATCTAATTTTTCTTTTATTTTAGTACCCACATTAGGT
1 TAAATTTATTTAATAGATCATACACAATATCTAATTTTTCTTTTATTTTAGTACCCACATTAGGT
322150 TTAGTACTTACAC
66 TTAGTACTTACAC
322163 TA
1 TA
322165 TCAATTAGTA
Statistics
Matches: 143, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
73 48 0.34
75 3 0.02
76 1 0.01
78 82 0.57
79 8 0.06
80 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.48
Consensus pattern (78 bp):
TAAATTTATTTAATAGATCATACACAATATCTAATTTTTCTTTTATTTTAGTACCCACATTAGGT
TTAGTACTTACAC
Found at i:322343 original size:63 final size:63
Alignment explanation
Indices: 322278--322401 Score: 164
Period size: 63 Copynumber: 2.0 Consensus size: 63
322268 AACTTTAATT
* * *
322278 TTTTTTAAAAAA-A-TTAGCATTAAATTTTGAATAC-CTAATTATTAAAATGAAACAAAAACTA
1 TTTTTAAAAAAATATTTAACATTAAATTTTGAATACTCTAA-TACTAAAATGAAACAAAAACTA
* * *
322339 TTTTTAAAAAAATATTTAACGTTAAATTTTGAATACTTTGATACTAAAATGAAACAAAAACTA
1 TTTTTAAAAAAATATTTAACATTAAATTTTGAATACTCTAATACTAAAATGAAACAAAAACTA
322402 AACGTTGGTG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
61 11 0.20
62 1 0.02
63 40 0.74
64 2 0.04
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (63 bp):
TTTTTAAAAAAATATTTAACATTAAATTTTGAATACTCTAATACTAAAATGAAACAAAAACTA
Found at i:323296 original size:30 final size:30
Alignment explanation
Indices: 323260--323317 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
323250 ACCATATTCA
*
323260 TCGGTCAATTGAACCGGGTTGCCGTGCTCG
1 TCGGTCAATTGAACCGGGTTGCCATGCTCG
* **
323290 TCGGTCAGTTGAATGGGGTTGCCATGCT
1 TCGGTCAATTGAACCGGGTTGCCATGCT
323318 TGTCTCTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.14, C:0.22, G:0.34, T:0.29
Consensus pattern (30 bp):
TCGGTCAATTGAACCGGGTTGCCATGCTCG
Found at i:324020 original size:31 final size:31
Alignment explanation
Indices: 323934--324008 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
323924 AAATTACACA
*
323934 TTTAGTATCTAAATTATCAATTTTTATCTAT
1 TTTAGTATCTAAATTATCAATTTTTATCCAT
*
323965 TTTAATATCTAAATTATCAATTTTTATCCAT
1 TTTAGTATCTAAATTATCAATTTTTATCCAT
*
323996 TTTAGTATTTAAA
1 TTTAGTATCTAAA
324009 CTTCTAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTAGTATCTAAATTATCAATTTTTATCCAT
Found at i:324084 original size:40 final size:36
Alignment explanation
Indices: 324040--324122 Score: 121
Period size: 40 Copynumber: 2.2 Consensus size: 36
324030 TATTTAAAGT
*
324040 TTAATTTTTATTTCATTTTAATATCTCGATGTTAAAATA
1 TTAATTTTTATTTCATTTTAATACCTCG-T-TTAAAA-A
324079 GTTAATTTTTATTTCATTTTAATACCTCGTTTAAAAA
1 -TTAATTTTTATTTCATTTTAATACCTCGTTTAAAAA
324116 TTAATTT
1 TTAATTT
324123 CAAGTTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 7 0.17
37 1 0.02
38 6 0.14
39 1 0.02
40 27 0.64
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (36 bp):
TTAATTTTTATTTCATTTTAATACCTCGTTTAAAAA
Found at i:349114 original size:21 final size:22
Alignment explanation
Indices: 349073--349114 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
349063 TTTTCCCAGT
349073 GAATTTATATCGGACTTCACTA
1 GAATTTATATCGGACTTCACTA
* *
349095 GAATTTGTATCGTA-TTCACT
1 GAATTTATATCGGACTTCACT
349115 GTAAATTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (22 bp):
GAATTTATATCGGACTTCACTA
Found at i:350313 original size:21 final size:21
Alignment explanation
Indices: 350289--350337 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
350279 AGACTACCAC
* *
350289 GTCAGCATCATGGACTGTCAT
1 GTCAACATCATGAACTGTCAT
* *
350310 GTCAACATCGTGAATTGTCAT
1 GTCAACATCATGAACTGTCAT
*
350331 GTTAACA
1 GTCAACA
350338 CCGTAATGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (21 bp):
GTCAACATCATGAACTGTCAT
Found at i:353187 original size:20 final size:18
Alignment explanation
Indices: 353164--353205 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
353154 CATATAATAT
* *
353164 ATATAAATATGAATTTTA
1 ATATATATAAGAATTTTA
*
353182 ATATATTTAAGAATTTTA
1 ATATATATAAGAATTTTA
353200 ATATAT
1 ATATAT
353206 TTTTTACGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (18 bp):
ATATATATAAGAATTTTA
Found at i:353676 original size:56 final size:56
Alignment explanation
Indices: 353609--353720 Score: 147
Period size: 56 Copynumber: 2.0 Consensus size: 56
353599 TAAATGATTC
* * *
353609 ATCGACTATAGA-ATATTGTTTTGTTGAGTCTCAT-TACTATTAAAAGTTATAAAATG
1 ATCGACTATAGAGA-ATTGCTTTGTTGAGTC-CATCGACTATTAAAAGTTACAAAATG
* *
353665 ATCGACTATAGAGAGTTGCTTTGTTGAGTCCCTCGACTATTAAAAGTTACAAAATG
1 ATCGACTATAGAGAATTGCTTTGTTGAGTCCATCGACTATTAAAAGTTACAAAATG
353721 GTCACCCGAC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
55 2 0.04
56 46 0.94
57 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (56 bp):
ATCGACTATAGAGAATTGCTTTGTTGAGTCCATCGACTATTAAAAGTTACAAAATG
Found at i:355073 original size:4 final size:4
Alignment explanation
Indices: 355066--355100 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
355056 ATACACACAC
*
355066 ATGT ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
355101 AATGCAATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:356367 original size:19 final size:19
Alignment explanation
Indices: 356326--356369 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
356316 CTCTCTTTTA
*
356326 AAATTTAAAATTATTATAT
1 AAATTTTAAATTATTATAT
*
356345 --ATTTTAAATTTTTATAT
1 AAATTTTAAATTATTATAT
356362 AAATTTTA
1 AAATTTTA
356370 TTAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 15 0.71
19 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATTTTAAATTATTATAT
Found at i:356403 original size:40 final size:40
Alignment explanation
Indices: 356330--356407 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 40
356320 CTTTTAAAAT
*
356330 TTAAAATTATTATATATTTTAAATTTTTATATAAATTTTA
1 TTAAAATTATTATATATTTTAAATATTTATATAAATTTTA
*
356370 TTAAAATTTACTTTTATATTTTAAA-ATTT-TATAAATTT
1 TTAAAA-TTA-TTATATATTTTAAATATTTATATAAATTT
356408 ATTTATTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 15 0.44
41 6 0.18
42 13 0.38
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (40 bp):
TTAAAATTATTATATATTTTAAATATTTATATAAATTTTA
Found at i:357064 original size:43 final size:41
Alignment explanation
Indices: 356978--357291 Score: 166
Period size: 42 Copynumber: 7.3 Consensus size: 41
356968 GGGCTTAAAC
* * *
356978 TATAAAAGTAAAAAGT-ACGATTGAAAAAAATTAGGAACCTCAAT
1 TATAAAGGTAAAAAGTGA-GATT-AAAAAAATCA-G-ATCTCAAT
357022 TATAAAGGTAAAAAGTGAGATTAAAAAAATCAGATACATCAAT
1 TATAAAGGTAAAAAGTGAGATTAAAAAAATCAGAT-C-TCAAT
* * * *
357065 TTTAAAGGTGAAAAGTGAGATGAAAAAAAT-AGAGGTCTAAAT
1 TATAAAGGTAAAAAGTGAGATTAAAAAAATCAGA--TCTCAAT
* * * * * * *
357107 TATATACGAAAAAAATGGGATT-AAAAAATTAGGGTCTCAAT
1 TATAAAGGTAAAAAGTGAGATTAAAAAAATCA-GATCTCAAT
* * * *
357148 TATAAAGGTAGAAAGTAAGATTGAAAAAATCAAGAGCTCAAT
1 TATAAAGGTAAAAAGTGAGATTAAAAAAATC-AGATCTCAAT
* * * * * * * *
357190 TATAAACGTATAAACTAAGATTGAAAAACTTAGGGTCATCAAT
1 TATAAAGGTAAAAAGTGAGATTAAAAAAATCA-GATC-TCAAT
* * * * * *
357233 TGTAAATGTAAAAAAAGTGGGATTAGAAAAATTAAGAGCTTCAAT
1 TATAAAGGT--AAAAAGTGAGATTA-AAAAAATCAGATC-TCAAT
*
357278 TATAAAGATAAAAA
1 TATAAAGGTAAAAA
357292 ACATGATTAT
Statistics
Matches: 207, Mismatches: 49, Indels: 29
0.73 0.17 0.10
Matches are distributed among these distances:
41 30 0.14
42 66 0.32
43 61 0.29
44 20 0.10
45 23 0.11
46 7 0.03
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.25
Consensus pattern (41 bp):
TATAAAGGTAAAAAGTGAGATTAAAAAAATCAGATCTCAAT
Found at i:357175 original size:42 final size:42
Alignment explanation
Indices: 356978--357246 Score: 195
Period size: 42 Copynumber: 6.3 Consensus size: 42
356968 GGGCTTAAAC
* * **
356978 TATAAAAGTAAAAAGTACGATTGAAAAAAATTAGGAACCTCAAT
1 TATAAAGGTAAAAAGTAAGATTG-AAAAAATTAGG-GTCTCAAT
* * * *
357022 TATAAAGGTAAAAAGTGAGATTAAAAAAATCA-GATACATCAAT
1 TATAAAGGTAAAAAGTAAGATTGAAAAAATTAGGGT-C-TCAAT
* * * * *
357065 TTTAAAGGTGAAAAGTGAGA-TGAAAAAAATAGAGGTCTAAAT
1 TATAAAGGTAAAAAGTAAGATTGAAAAAATTAG-GGTCTCAAT
* * * * **
357107 TATATACGAAAAAAATGGGATT-AAAAAATTAGGGTCTCAAT
1 TATAAAGGTAAAAAGTAAGATTGAAAAAATTAGGGTCTCAAT
* * *
357148 TATAAAGGTAGAAAGTAAGATTGAAAAAATCAAGAG-CTCAAT
1 TATAAAGGTAAAAAGTAAGATTGAAAAAAT-TAGGGTCTCAAT
* * * *
357190 TATAAACGTATAAACTAAGATTGAAAAACTTAGGGTCATCAAT
1 TATAAAGGTAAAAAGTAAGATTGAAAAAATTAGGGTC-TCAAT
* *
357233 TGTAAATGTAAAAA
1 TATAAAGGTAAAAA
357247 AAGTGGGATT
Statistics
Matches: 176, Mismatches: 40, Indels: 19
0.75 0.17 0.08
Matches are distributed among these distances:
41 27 0.15
42 76 0.43
43 52 0.30
44 21 0.12
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.25
Consensus pattern (42 bp):
TATAAAGGTAAAAAGTAAGATTGAAAAAATTAGGGTCTCAAT
Found at i:357306 original size:43 final size:43
Alignment explanation
Indices: 357253--357335 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 43
357243 AAAAAAGTGG
357253 GATTAGAAAAATTAAGA-G-CTTCAATTATAAAGATAAAAAACAT
1 GATTAGAAAAA-TAAGAGGTCTT-AATTATAAAGATAAAAAACAT
* *
357296 GATTATAAAAATAAGAGGTCTTACTTATAAAGATAAAAAA
1 GATTAGAAAAATAAGAGGTCTTAATTATAAAGATAAAAAA
357336 AAATAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
42 5 0.14
43 28 0.78
44 3 0.08
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (43 bp):
GATTAGAAAAATAAGAGGTCTTAATTATAAAGATAAAAAACAT
Found at i:360306 original size:2 final size:2
Alignment explanation
Indices: 360299--360351 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
360289 TATTTAAAAG
360299 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
360340 AT AT AT AT AT AT
1 AT AT AT AT AT AT
360352 GATCATTTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:370581 original size:60 final size:60
Alignment explanation
Indices: 370517--370667 Score: 171
Period size: 61 Copynumber: 2.5 Consensus size: 60
370507 TGTTTTATTA
** * * * * *
370517 AGTCCCTCAACTATTAAAAATTACAAAATGGT-TATTCGACTATA-GATATTTGCTTTGTTG
1 AGTCCCTTGACTATTAAAAGTTACAAAATGGTCT-TTCGACTATATG-GAGTTGATTTGCTG
* * *
370577 AGTCCCTTGACAACTAAAAGTTACAAAAATGGTCTTTTGACTATATGGAGTTGATTTGCTG
1 AGTCCCTTGACTATTAAAAGTTAC-AAAATGGTCTTTCGACTATATGGAGTTGATTTGCTG
370638 AGTCCCTTGACTATTAAAAGTTACAAAATG
1 AGTCCCTTGACTATTAAAAGTTACAAAATG
370668 ATCACTTGGC
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
60 25 0.33
61 49 0.64
62 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (60 bp):
AGTCCCTTGACTATTAAAAGTTACAAAATGGTCTTTCGACTATATGGAGTTGATTTGCTG
Found at i:377772 original size:35 final size:35
Alignment explanation
Indices: 377732--377809 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
377722 GATATATGTA
* *
377732 ATAATTTGAAATTTAGGTATTAAAGAGTCTAATCC
1 ATAATTTGAAATTTAGGCATTAAAAAGTCTAATCC
377767 ATAATTTGAAATTTAGGCATTAAAAAGTCTAATCC
1 ATAATTTGAAATTTAGGCATTAAAAAGTCTAATCC
*
377802 ACAATTTG
1 ATAATTTG
377810 CCCAAAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (35 bp):
ATAATTTGAAATTTAGGCATTAAAAAGTCTAATCC
Found at i:386463 original size:12 final size:12
Alignment explanation
Indices: 386448--386482 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
386438 TTATTTTATT
386448 TTTAAAATTAAA
1 TTTAAAATTAAA
*
386460 TTTAAAATTATA
1 TTTAAAATTAAA
386472 TTTAAAATTAA
1 TTTAAAATTAA
386483 CTTTTAGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTAAAATTAAA
Found at i:387337 original size:17 final size:18
Alignment explanation
Indices: 387307--387351 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
387297 TATGATTAGA
* *
387307 GATTTTATGAAATTT-GG
1 GATTTTAAGAAATTTAAG
*
387324 GATTTTAAGTAATTTAAG
1 GATTTTAAGAAATTTAAG
387342 GATTTTAAGA
1 GATTTTAAGA
387352 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (18 bp):
GATTTTAAGAAATTTAAG
Found at i:387504 original size:63 final size:63
Alignment explanation
Indices: 387426--387574 Score: 203
Period size: 62 Copynumber: 2.4 Consensus size: 63
387416 TTAAACACTG
* * * * * *
387426 ATTGAAAAACG-ATTTTTTAACGTCTTTTGACGATTAAGTACCTTAAATGGTAACTTTAAAAT
1 ATTGAATAACGAATTTTTTAACGTCTTCTAACGATCAAGCACCTTAAATGATAACTTTAAAAT
387488 ATTGAATAACGAA-TTTTTAACGTCTTCTAACGATCAAGCACCTTAAATGATAACTTTAAAAT
1 ATTGAATAACGAATTTTTTAACGTCTTCTAACGATCAAGCACCTTAAATGATAACTTTAAAAT
* **
387550 GTTGGGTAACGAATTTTTTAACGTC
1 ATTGAATAACGAATTTTTTAACGTC
387575 GGTTAAATAC
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
62 64 0.84
63 12 0.16
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (63 bp):
ATTGAATAACGAATTTTTTAACGTCTTCTAACGATCAAGCACCTTAAATGATAACTTTAAAAT
Found at i:388972 original size:20 final size:20
Alignment explanation
Indices: 388947--388989 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
388937 CCTCTTATAT
388947 ACAAATATTTAACTTGCGAA
1 ACAAATATTTAACTTGCGAA
* *
388967 ACAAATGTTTAACTTGTGAA
1 ACAAATATTTAACTTGCGAA
388987 ACA
1 ACA
388990 TACTGCCAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (20 bp):
ACAAATATTTAACTTGCGAA
Found at i:400904 original size:21 final size:22
Alignment explanation
Indices: 400864--400910 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
400854 CGAGTGTAAT
*
400864 AAAATATTTAAATATATATA-A
1 AAAATATTGAAATATATATAGA
* *
400885 AAAATATTGAAATGTTTATAGA
1 AAAATATTGAAATATATATAGA
400907 AAAA
1 AAAA
400911 ATCTTTGTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (22 bp):
AAAATATTGAAATATATATAGA
Found at i:413798 original size:18 final size:19
Alignment explanation
Indices: 413763--413799 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
413753 CACGGAATGT
413763 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
413783 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
413800 GGATTATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:414020 original size:32 final size:31
Alignment explanation
Indices: 413935--414020 Score: 84
Period size: 37 Copynumber: 2.6 Consensus size: 31
413925 TTGTATAATA
413935 TTAC-AAATTATAAAATATTTATATATTTTCT
1 TTACAAAATTA-AAAATATTTATATATTTTCT
* *
413966 TTAAAAAATTAAATTCATAATATTTATATAATTTTTT
1 TTACAAAATT-AA---A-AATATTTATAT-ATTTTCT
414003 TTACAAAATTAAAAATAT
1 TTACAAAATTAAAAATAT
414021 AAAAAATGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
31 3 0.07
32 11 0.24
33 2 0.04
35 1 0.02
36 13 0.29
37 15 0.33
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (31 bp):
TTACAAAATTAAAAATATTTATATATTTTCT
Found at i:415333 original size:62 final size:62
Alignment explanation
Indices: 415249--415427 Score: 195
Period size: 62 Copynumber: 3.0 Consensus size: 62
415239 ATATATCTCC
* * * * * * *
415249 AAACTATAACT-T-TCATTTTAAATTGATCCTTAAATTTTTAAATATTCTAATTTTATCCTT
1 AAACTATGACTCTCTCATTCTAAATTAATCCTTAAACTTTTAAACATTCTAATTTCATCCAT
* *
415309 AAACTATGACTCTCTCATTCTAAATTAATGCTTAAACTTTTGAACATTCTAATTTCATCCAT
1 AAACTATGACTCTCTCATTCTAAATTAATCCTTAAACTTTTAAACATTCTAATTTCATCCAT
* ** ** *
415371 AAACTATGACTCTCT--TTCTAAATTAGTCCCCAAACTTTTGGACATTCCAATTTCATC
1 AAACTATGACTCTCTCATTCTAAATTAATCCTTAAACTTTTAAACATTCTAATTTCATC
415428 ACCAAATTCA
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
60 46 0.45
61 1 0.01
62 55 0.54
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.42
Consensus pattern (62 bp):
AAACTATGACTCTCTCATTCTAAATTAATCCTTAAACTTTTAAACATTCTAATTTCATCCAT
Found at i:415416 original size:60 final size:61
Alignment explanation
Indices: 415292--415427 Score: 184
Period size: 60 Copynumber: 2.2 Consensus size: 61
415282 ATTTTTAAAT
* * * **
415292 ATTCTAATTTTATCCTTAAACTATGACTCTCTCATTCTAAATTAATGCTTAAACTTTTGAAC
1 ATTCTAATTTCATCCATAAACTATGACTCTCT-ATTCTAAATTAATCCCCAAACTTTTGAAC
* *
415354 ATTCTAATTTCATCCATAAACTATGACTCTCT-TTCTAAATTAGTCCCCAAACTTTTGGAC
1 ATTCTAATTTCATCCATAAACTATGACTCTCTATTCTAAATTAATCCCCAAACTTTTGAAC
*
415414 ATTCCAATTTCATC
1 ATTCTAATTTCATC
415428 ACCAAATTCA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
60 36 0.55
62 30 0.45
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (61 bp):
ATTCTAATTTCATCCATAAACTATGACTCTCTATTCTAAATTAATCCCCAAACTTTTGAAC
Found at i:415647 original size:60 final size:62
Alignment explanation
Indices: 415548--415721 Score: 211
Period size: 60 Copynumber: 2.9 Consensus size: 62
415538 TGATTAGTAT
415548 ATAGGT-ATAGTTT-GGGATGAAATTGGAA-TGTTCAAAAAGTTTGGGGACTAATTTAGAATG
1 ATAGGTCATAGTTTAGGGATGAAATTGGAAGTGTT-AAAAAGTTTGGGGACTAATTTAGAATG
* * *
415608 A-AGGTCATAGTTTAGGGATGGAATT-GAAGTGTTAAAAAGTTTGAGGAATAATTTAGAATG
1 ATAGGTCATAGTTTAGGGATGAAATTGGAAGTGTTAAAAAGTTTGGGGACTAATTTAGAATG
** * *
415668 ATA-GTCATAGTTTAATGATGAAATTGGAAGAT-TT-AAAAGTTTAGGGACCAATTT
1 ATAGGTCATAGTTTAGGGATGAAATTGGAAG-TGTTAAAAAGTTTGGGGACTAATTT
415722 GAAAGGATGA
Statistics
Matches: 98, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
59 4 0.04
60 72 0.73
61 21 0.21
62 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (62 bp):
ATAGGTCATAGTTTAGGGATGAAATTGGAAGTGTTAAAAAGTTTGGGGACTAATTTAGAATG
Found at i:419814 original size:113 final size:112
Alignment explanation
Indices: 419479--419942 Score: 757
Period size: 112 Copynumber: 4.1 Consensus size: 112
419469 TTGTCGGTTT
* * * *
419479 GTGTCGATACTTTATAAAAATATATTGATTCATAACAATATAACAGGTAAAAAAATGTCAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
*
419544 GGTCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
419591 GCGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
* *
419656 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATTTATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
419703 TTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAAATGACAAAAT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAT
419768 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
419816 GTATCGATACTTTATAAAAATGTATCAATCTATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
* * *
419881 GGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
419928 GAGTCGATACTTTAT
1 GTGTCGATACTTTAT
419943 TATAAGTAGT
Statistics
Matches: 327, Mismatches: 24, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
112 222 0.68
113 105 0.32
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:419870 original size:225 final size:224
Alignment explanation
Indices: 419479--419942 Score: 757
Period size: 225 Copynumber: 2.1 Consensus size: 224
419469 TTGTCGGTTT
* * *
419479 GTGTCGATACTTTATAAAAATATATTGATTCATAACAATATAACAGGTAAAAAAATGTCAAAATC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
* *
419544 GGTCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAAGCGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGCATCGATACTTTATAAA
* *
419609 AATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATCGGTCTATAAATGACAAAA
131 AATGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAA
*
419674 CAGGTAAAGCGCTACCAGATTTATTGAAA
196 CAGGTAAAGCGCTACCAGATATATTGAAA
* * *
419703 TTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAAATGACAAAAT
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAT
*
419768 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTATCGATACTTTATAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGCATCGATACTTTATAA
* *
419833 AAATGTATCAATCTATAACAATATAACAGGTAAAAAAATGACAAAACCGGTTTATAAATGACAAA
130 AAATGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAA
* * *
419898 ACAGGTAAAGCGCTACCGGATATGTTGATA
195 ACAGGTAAAGCGCTACCAGATATATTGAAA
*
419928 GAGTCGATACTTTAT
1 GTGTCGATACTTTAT
419943 TATAAGTAGT
Statistics
Matches: 220, Mismatches: 19, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
224 43 0.20
225 177 0.80
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (224 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGCATCGATACTTTATAAA
AATGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAA
CAGGTAAAGCGCTACCAGATATATTGAAA
Found at i:420123 original size:179 final size:180
Alignment explanation
Indices: 419813--420265 Score: 660
Period size: 179 Copynumber: 2.5 Consensus size: 180
419803 GGATATATTG
* * * *
419813 AAAGTATCGATACTTTATAAAAATGTATCAATCTATAACAATATAACAGGTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * ** * * * *
419878 ACCGGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGAGTCGATACTTTAT
66 ACCGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGAGTCGATACTTTAT
419943 TATAAGTAGT-GACACTTTTGGAATTTAAAAG-AGAAGTTATAGATCT-AAT
131 TATAAGTA-TCGACACTTTTGGAATTTAAAAGAAGAAGTTATAG-TCTCAAT
*
419992 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
** * *
420057 ACCGATCTCGAAATGACAAAACCGGTAAAGAGCTATTAGATATGTTGAAAGTGTCGATATTTTAT
66 ACCGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGAGTCGATACTTTAT
*
420122 TATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGTGTCAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAG--AAGAAGTTATAGTCTCAAT
420174 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
420239 ATCGATCTCGAAATGATAAAATCGGTA
66 ACCGATCTCGAAATGACAAAACCGGTA
420266 GTAAAAAAAT
Statistics
Matches: 247, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
178 1 0.00
179 142 0.57
181 2 0.01
182 102 0.41
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (180 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGAGTCGATACTTTAT
TATAAGTATCGACACTTTTGGAATTTAAAAGAAGAAGTTATAGTCTCAAT
Found at i:430446 original size:22 final size:22
Alignment explanation
Indices: 430420--430463 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
430410 TAAATATTAT
430420 TCATTTAACTAAACGAATTTAA
1 TCATTTAACTAAACGAATTTAA
430442 TCATTTAACTAAACGAATTTAA
1 TCATTTAACTAAACGAATTTAA
430464 AATGATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (22 bp):
TCATTTAACTAAACGAATTTAA
Found at i:436264 original size:21 final size:21
Alignment explanation
Indices: 436240--436296 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
436230 TAAATGCATA
436240 CAAAATTCAACAAAAAGAACC
1 CAAAATTCAACAAAAAGAACC
* * *
436261 CAAATTTCGTAACAAAAAATAATC
1 CAAAATTC--AAC-AAAAAGAACC
436285 C-AAATTCAACAA
1 CAAAATTCAACAA
436297 GCTTGATGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 2 0.07
21 10 0.34
23 8 0.28
24 9 0.31
ACGTcount: A:0.58, C:0.21, G:0.04, T:0.18
Consensus pattern (21 bp):
CAAAATTCAACAAAAAGAACC
Found at i:437158 original size:38 final size:38
Alignment explanation
Indices: 437105--437182 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
437095 GTGGATCGGA
* *
437105 TCGAGTTCGGATCAGATGAAGGGTGTATTATTTTCAGG
1 TCGAGTTCGGATCAGATGAAGGATGTATAATTTTCAGG
* *
437143 TCGAGTTC-GAGTCAGATGGAGGATGTATAATTTTCGGG
1 TCGAGTTCGGA-TCAGATGAAGGATGTATAATTTTCAGG
437181 TC
1 TC
437183 TGGTTGACCG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 2 0.06
38 33 0.94
ACGTcount: A:0.23, C:0.12, G:0.32, T:0.33
Consensus pattern (38 bp):
TCGAGTTCGGATCAGATGAAGGATGTATAATTTTCAGG
Found at i:437935 original size:60 final size:60
Alignment explanation
Indices: 437871--438003 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
437861 TATGATGATC
* * * *
437871 ATTTTGTAACTTTTAATAGTCGAGGGACTCGACAAAGTAATACTCTATAGTCAAAGGACT
1 ATTTTGTAACTTTTAATAGTCAAGGGACTCAACAAAATAATACCCTATAGTCAAAGGACT
* * * * **
437931 ATTTTGTAACTTTTAATAGTTAAGGGAGTTAATAAAATAATACCCTATAGTCAGGGGACT
1 ATTTTGTAACTTTTAATAGTCAAGGGACTCAACAAAATAATACCCTATAGTCAAAGGACT
437991 ATTTATGT-ACTTT
1 ATTT-TGTAACTTT
438004 ACCCTATAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
60 59 0.95
61 3 0.05
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTCAAGGGACTCAACAAAATAATACCCTATAGTCAAAGGACT
Found at i:440964 original size:72 final size:73
Alignment explanation
Indices: 440834--440974 Score: 178
Period size: 72 Copynumber: 1.9 Consensus size: 73
440824 TGGGCATGTG
* * * * *
440834 GCCACCCTGAAATATAAATTTTTTTCTATTAGTTACTTATTTTACTGATGGTGCCCACC-TGAAA
1 GCCACCCTGAAATATAAATTTTCTTCGATTAGTTACTTATGTTACTGACGATGCCCACCTTGAAA
440898 TTTTCTGT
66 TTTTCTGT
* * * *
440906 GCCACTCTGAAATATGAGTTTTCTTCGATTAGTTACTTATGTTA-TGAACGATGTCCACCTTGAA
1 GCCACCCTGAAATATAAATTTTCTTCGATTAGTTACTTATGTTACTG-ACGATGCCCACCTTGAA
440970 ATTTT
65 ATTTT
440975 ATTTGTATCC
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
71 2 0.03
72 47 0.81
73 9 0.16
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (73 bp):
GCCACCCTGAAATATAAATTTTCTTCGATTAGTTACTTATGTTACTGACGATGCCCACCTTGAAA
TTTTCTGT
Found at i:441293 original size:2 final size:2
Alignment explanation
Indices: 441286--441381 Score: 192
Period size: 2 Copynumber: 48.0 Consensus size: 2
441276 TCCCGAAAGA
441286 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
441328 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
441370 AT AT AT AT AT AT
1 AT AT AT AT AT AT
441382 GTTTACGTGA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 94 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:445649 original size:24 final size:24
Alignment explanation
Indices: 445612--445721 Score: 116
Period size: 24 Copynumber: 4.6 Consensus size: 24
445602 TATAGATTGA
445612 TCTTG-ATTAGTGCATTCGTGCAC
1 TCTTGTATTAGTGCATTCGTGCAC
* *
445635 TCATGTATTAGTGCAATT-TTGCAC
1 TCTTGTATTAGTGC-ATTCGTGCAC
*
445659 TCTTGAATTAGTGCATTCGTGCAC
1 TCTTGTATTAGTGCATTCGTGCAC
* * * *
445683 TCTTGATTTTAGTTCATTCATGTAC
1 TCTTG-TATTAGTGCATTCGTGCAC
*
445708 TCCTGTATTAGTGC
1 TCTTGTATTAGTGC
445722 TTTGTTCTCT
Statistics
Matches: 70, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
23 7 0.10
24 42 0.60
25 21 0.30
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (24 bp):
TCTTGTATTAGTGCATTCGTGCAC
Done.