Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 36 of 135
Found at i:13917219 original size:28 final size:28
Alignment explanation
Indices: 13917183--13917291 Score: 128
Period size: 28 Copynumber: 3.9 Consensus size: 28
13917173 CACAGGATCG
*
13917183 ATTTGCTCACACAAACTGCAATATTCGA
1 ATTTGCTCACACAAACTGTAATATTCGA
** *
13917211 ATTTGCTCACATGATCTGTAATATTCGA
1 ATTTGCTCACACAAACTGTAATATTCGA
* * * *
13917239 ATTTGCTCATACAAGCTATGATATTCGA
1 ATTTGCTCACACAAACTGTAATATTCGA
* *
13917267 ATTTGCTCACACAAGCTGTGATATT
1 ATTTGCTCACACAAACTGTAATATT
13917292 TGGGTTGCTC
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (28 bp):
ATTTGCTCACACAAACTGTAATATTCGA
Found at i:13917307 original size:27 final size:28
Alignment explanation
Indices: 13917185--13917308 Score: 97
Period size: 28 Copynumber: 4.5 Consensus size: 28
13917175 CAGGATCGAT
* *** *
13917185 TTGCTCACACAAACTGCAATATTCGAAT
1 TTGCTCACACAAGCTATGATATTCGAAG
** * * * *
13917213 TTGCTCACATGATCTGTAATATTCGAAT
1 TTGCTCACACAAGCTATGATATTCGAAG
* *
13917241 TTGCTCATACAAGCTATGATATTCGAAT
1 TTGCTCACACAAGCTATGATATTCGAAG
* * *
13917269 TTGCTCACACAAGCTGTGATATTTG-GG
1 TTGCTCACACAAGCTATGATATTCGAAG
13917296 TTGCTCACACAAG
1 TTGCTCACACAAG
13917309 TTGTAGGTTA
Statistics
Matches: 81, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
27 13 0.16
28 68 0.84
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (28 bp):
TTGCTCACACAAGCTATGATATTCGAAG
Found at i:13919553 original size:55 final size:55
Alignment explanation
Indices: 13919488--13919592 Score: 183
Period size: 55 Copynumber: 1.9 Consensus size: 55
13919478 AGGGTAAACT
*
13919488 ATATAAATGGTCACCAAACTATTCTCGTGTTCTTATTTTAGTTATTCAATAAATC
1 ATATAAATGGTCACCAAACTATGCTCGTGTTCTTATTTTAGTTATTCAATAAATC
* *
13919543 ATATAAATGGTCATCAAACTATGCTCGTGTTTTTATTTTAGTTATTCAAT
1 ATATAAATGGTCACCAAACTATGCTCGTGTTCTTATTTTAGTTATTCAAT
13919593 TTTAAAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.44
Consensus pattern (55 bp):
ATATAAATGGTCACCAAACTATGCTCGTGTTCTTATTTTAGTTATTCAATAAATC
Found at i:13923584 original size:19 final size:19
Alignment explanation
Indices: 13923560--13923602 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
13923550 AAATATAAAT
13923560 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
13923579 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
13923598 TAAAT
1 TAAAT
13923603 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:13931475 original size:19 final size:19
Alignment explanation
Indices: 13931451--13931493 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
13931441 AAACATAAAT
13931451 TAAATATAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
13931470 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
13931489 TAAAT
1 TAAAT
13931494 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:13933687 original size:34 final size:32
Alignment explanation
Indices: 13933649--13933712 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 32
13933639 AATTGATGAA
13933649 TTTAAAATT-AATAAAAATATATGAAATAATATAG
1 TTTAAAATTAAATAAAAA-A-AT-AAATAATATAG
13933683 TTTAAAATTGAAATAAAAAAATAAATAATA
1 TTTAAAATT-AAATAAAAAAATAAATAATA
13933713 ATTATACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
33 8 0.29
34 11 0.39
35 1 0.04
36 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (32 bp):
TTTAAAATTAAATAAAAAAATAAATAATATAG
Found at i:13938886 original size:12 final size:11
Alignment explanation
Indices: 13938855--13938894 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
13938845 AGTCCATGCA
13938855 TATTTAATTTT
1 TATTTAATTTT
*
13938866 TAATTAATTTT
1 TATTTAATTTT
13938877 TATTTGAATTTT
1 TATTT-AATTTT
13938889 T-TTTAA
1 TATTTAA
13938895 ATATAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 2 0.08
11 17 0.65
12 7 0.27
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (11 bp):
TATTTAATTTT
Found at i:13946072 original size:40 final size:43
Alignment explanation
Indices: 13945994--13946080 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 43
13945984 ATAAGATTAT
13945994 TATTAAATATAATTTAATAATATTTTTAATATAATTATTTTTA
1 TATTAAATATAATTTAATAATATTTTTAATATAATTATTTTTA
*
13946037 TATTAAAT-T-ATATTAA-AATA-TTTTAACTAT-TTTATTTTTA
1 TATTAAATATAAT-TTAATAATATTTTTAA-TATAATTATTTTTA
13946077 TATT
1 TATT
13946081 TTTAAATCCA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
40 19 0.46
41 9 0.22
42 5 0.12
43 8 0.20
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (43 bp):
TATTAAATATAATTTAATAATATTTTTAATATAATTATTTTTA
Found at i:13949364 original size:21 final size:21
Alignment explanation
Indices: 13949340--13949380 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13949330 ATTGCTCCTC
13949340 TCTCTTCT-TTTTTTTCTCTTT
1 TCTCTT-TATTTTTTTCTCTTT
*
13949361 TCTCTTTATTTTTTTTTCTT
1 TCTCTTTATTTTTTTCTCTT
13949381 CTCCTCCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (21 bp):
TCTCTTTATTTTTTTCTCTTT
Found at i:13949364 original size:23 final size:21
Alignment explanation
Indices: 13949338--13949380 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
13949328 TTATTGCTCC
*
13949338 TCTCTCTTCTTTTTTTTCTCTTT
1 TCTCT-TTATTTTTTTT-TCTTT
13949361 TCTCTTTATTTTTTTTTCTT
1 TCTCTTTATTTTTTTTTCTT
13949381 CTCCTCCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (21 bp):
TCTCTTTATTTTTTTTTCTTT
Found at i:13950849 original size:16 final size:16
Alignment explanation
Indices: 13950828--13950858 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
13950818 CGTTTTTCTA
13950828 TTTATGTATATAATTT
1 TTTATGTATATAATTT
13950844 TTTATGTATATAATT
1 TTTATGTATATAATT
13950859 CTAATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
TTTATGTATATAATTT
Found at i:13950863 original size:22 final size:23
Alignment explanation
Indices: 13950838--13950894 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
13950828 TTTATGTATA
*
13950838 TAATTTTTTATG-TATATAAT-TC
1 TAATTTTTTATGCTA-ACAATCTC
*
13950860 TAATTTATTAATGCTAACAATCTC
1 TAATTT-TTTATGCTAACAATCTC
13950884 TAATTTTTTAT
1 TAATTTTTTAT
13950895 TGATAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 6 0.21
23 13 0.45
24 10 0.34
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (23 bp):
TAATTTTTTATGCTAACAATCTC
Found at i:13957322 original size:21 final size:22
Alignment explanation
Indices: 13957268--13957324 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
13957258 TAAATTTGTC
*
13957268 ATAATTTTAATTTTATTAATATA
1 ATAATTTTAATATTATT-ATATA
13957291 AT-ATTTT-ATATTATT-T-TGA
1 ATAATTTTAATATTATTATAT-A
13957310 ATAATTTTAATATTA
1 ATAATTTTAATATTA
13957325 AATATACCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 1 0.03
19 4 0.13
20 5 0.17
21 13 0.43
22 5 0.17
23 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
ATAATTTTAATATTATTATATA
Found at i:13959119 original size:21 final size:19
Alignment explanation
Indices: 13959095--13959168 Score: 69
Period size: 21 Copynumber: 3.7 Consensus size: 19
13959085 TTTTAAATAC
13959095 AATTTTAATAAATGTATAAAA
1 AATTTTAATAAA--TATAAAA
* *
13959116 AATTTAAATAAATAAAAAA
1 AATTTTAATAAATATAAAA
*
13959135 AATTTATTATAAAATATAAAA
1 AATTT-TAAT-AAATATAAAA
*
13959156 AA-ATTAATAAATA
1 AATTTTAATAAATA
13959169 AACAGTGTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.11
19 14 0.32
20 3 0.07
21 22 0.50
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (19 bp):
AATTTTAATAAATATAAAA
Found at i:13959139 original size:40 final size:39
Alignment explanation
Indices: 13959095--13959170 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
13959085 TTTTAAATAC
* *
13959095 AATTT-TAATAAATGTATAAAAAATTTAAATAAATAAAAAA
1 AATTTATAATAAA-ATATAAAAAAATT-AATAAATAAAAAA
*
13959135 AATTTATTATAAAATATAAAAAAATTAATAAATAAA
1 AATTTATAATAAAATATAAAAAAATTAATAAATAAA
13959171 CAGTGTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 10 0.31
40 16 0.50
41 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (39 bp):
AATTTATAATAAAATATAAAAAAATTAATAAATAAAAAA
Found at i:13959158 original size:22 final size:19
Alignment explanation
Indices: 13959112--13959170 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
13959102 ATAAATGTAT
13959112 AAAAAATTTAAATAAATAA
1 AAAAAATTTAAATAAATAA
*
13959131 AAAAAATTTATTATAAAATATA
1 AAAAAATTTA-AAT-AAATA-A
13959153 AAAAAA-TT-AATAAATAA
1 AAAAAATTTAAATAAATAA
13959170 A
1 A
13959171 CAGTGTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 2 0.06
18 5 0.14
19 12 0.34
20 2 0.06
21 7 0.20
22 7 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAATTTAAATAAATAA
Found at i:13959276 original size:3 final size:3
Alignment explanation
Indices: 13959268--13959315 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
13959258 TCAAATACAC
13959268 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13959316 TGGTATTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:13972339 original size:9 final size:8
Alignment explanation
Indices: 13972314--13972360 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
13972304 TAATGCCATA
*
13972314 TTCTCTTT
1 TTCTATTT
13972322 TTCTATTT
1 TTCTATTT
13972330 TTCTATTT
1 TTCTATTT
13972338 TTC-ATTT
1 TTCTATTT
* *
13972345 TCCTTTTT
1 TTCTATTT
*
13972353 TTTTATTT
1 TTCTATTT
13972361 CTCGTTCCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
7 6 0.19
8 26 0.81
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCTATTT
Found at i:13972353 original size:15 final size:16
Alignment explanation
Indices: 13972319--13972360 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
13972309 CCATATTCTC
*
13972319 TTTTTCTATTTTTCTA
1 TTTTTCTATTTTCCTA
*
13972335 TTTTTC-ATTTTCCTT
1 TTTTTCTATTTTCCTA
*
13972350 TTTTTTTATTT
1 TTTTTCTATTT
13972361 CTCGTTCCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTCTATTTTCCTA
Found at i:13972459 original size:27 final size:27
Alignment explanation
Indices: 13972408--13972462 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
13972398 CTCCTCATCC
* **
13972408 TTTTCCCAATCCTAACCACTTCCAACA
1 TTTTCCCAACCCTAACCACCGCCAACA
*
13972435 TTTTCCCAACCCTAACCGCCGCCAACA
1 TTTTCCCAACCCTAACCACCGCCAACA
13972462 T
1 T
13972463 GCACCATAGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.04, T:0.25
Consensus pattern (27 bp):
TTTTCCCAACCCTAACCACCGCCAACA
Found at i:13973243 original size:19 final size:19
Alignment explanation
Indices: 13973203--13973243 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
13973193 AGAAACCCAG
**
13973203 AAATGTTGAATGAATTTGA
1 AAATGTTGAATGAATTCAA
13973222 AAATGTTGAATGAATTCAA
1 AAATGTTGAATGAATTCAA
13973241 AAA
1 AAA
13973244 AAAAAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.17, T:0.32
Consensus pattern (19 bp):
AAATGTTGAATGAATTCAA
Found at i:13973496 original size:22 final size:22
Alignment explanation
Indices: 13973454--13973494 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
13973444 AAAATGGAAA
13973454 TAATTTTTAAAAATATTTTTAT
1 TAATTTTTAAAAATATTTTTAT
*
13973476 TAATTTTT-AATATATTTTT
1 TAATTTTTAAAAATATTTTT
13973495 TAGATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TAATTTTTAAAAATATTTTTAT
Found at i:13979500 original size:6 final size:6
Alignment explanation
Indices: 13979489--13979517 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
13979479 GAATTTGAGA
13979489 GTGTGG GTGTGG GTGTGG GTGTGG GTGTG
1 GTGTGG GTGTGG GTGTGG GTGTGG GTGTG
13979518 AAACCTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (6 bp):
GTGTGG
Found at i:13984318 original size:17 final size:18
Alignment explanation
Indices: 13984293--13984327 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
13984283 CAGAAAAGGT
13984293 TTCCGTTTTG-CTTTTAA
1 TTCCGTTTTGTCTTTTAA
*
13984310 TTCCTTTTTGTCTTTTAA
1 TTCCGTTTTGTCTTTTAA
13984328 ATGAGATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.11, C:0.17, G:0.09, T:0.63
Consensus pattern (18 bp):
TTCCGTTTTGTCTTTTAA
Found at i:13993319 original size:50 final size:50
Alignment explanation
Indices: 13993262--13993390 Score: 154
Period size: 50 Copynumber: 2.5 Consensus size: 50
13993252 TTTTCCGATC
13993262 TGATGTTTTAAATAAATATAAATATTTATTGAAAGTGA-TTTGTTTAAATA
1 TGATGTTTTAAATAAA-ATAAATATTTATTGAAAGTGATTTTGTTTAAATA
* * * *
13993312 TGATGTTTTATATGAAAATAAATATTTATTTAAATTGATTTTGTTTAGATA
1 TGATGTTTTAAAT-AAAATAAATATTTATTGAAAGTGATTTTGTTTAAATA
*
13993363 TGTTAT-TTTTACATAAACATAAATATTT
1 TG--ATGTTTTAAATAAA-ATAAATATTT
13993391 CTTTATAATA
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
50 31 0.45
51 19 0.28
52 17 0.25
53 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.49
Consensus pattern (50 bp):
TGATGTTTTAAATAAAATAAATATTTATTGAAAGTGATTTTGTTTAAATA
Found at i:13993819 original size:21 final size:21
Alignment explanation
Indices: 13993772--13993822 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
13993762 ATATATTTTA
13993772 TATATTT-TTATTTTAATATG
1 TATATTTATTATTTTAATATG
* * *
13993792 CACTATTTATTATTTTCATTTG
1 TA-TATTTATTATTTTAATATG
13993814 TATATTTAT
1 TATATTTAT
13993823 ACTTACTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 12 0.48
22 12 0.48
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (21 bp):
TATATTTATTATTTTAATATG
Found at i:14000854 original size:6 final size:6
Alignment explanation
Indices: 14000843--14000873 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
14000833 TCTTACCAAC
14000843 GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT G
1 GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT G
14000874 AATGATGACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.16
Consensus pattern (6 bp):
GGCAAT
Found at i:14003329 original size:13 final size:13
Alignment explanation
Indices: 14003311--14003337 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14003301 TGTTGTTTGT
14003311 AAATATAAGTTTA
1 AAATATAAGTTTA
14003324 AAATATAAGTTTA
1 AAATATAAGTTTA
14003337 A
1 A
14003338 CATTTATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
AAATATAAGTTTA
Found at i:14008523 original size:21 final size:21
Alignment explanation
Indices: 14008484--14008524 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
14008474 TTAATATTTA
**
14008484 TATTTTTTTAATTTGATTTGT
1 TATTTTTTTAATTAAATTTGT
14008505 TATTTTTTTAATTAAATTTG
1 TATTTTTTTAATTAAATTTG
14008525 ATCTATCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (21 bp):
TATTTTTTTAATTAAATTTGT
Found at i:14008682 original size:10 final size:10
Alignment explanation
Indices: 14008669--14008702 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
14008659 AATTTAATAT
14008669 TTTTTTTTAA
1 TTTTTTTTAA
14008679 TTTTTTTTAA
1 TTTTTTTTAA
*
14008689 -TTTTTATAA
1 TTTTTTTTAA
14008698 TTTTT
1 TTTTT
14008703 AAAACATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:14012405 original size:21 final size:21
Alignment explanation
Indices: 14012379--14012426 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
14012369 GAGAAAGGGA
*
14012379 GAAGAAGAAGAAAAGGAAAAT
1 GAAGAAGAAGAAAAAGAAAAT
*
14012400 GAAGAA-ATGAAAAAGAAAAT
1 GAAGAAGAAGAAAAAGAAAAT
14012420 -AA-AAGAA
1 GAAGAAGAA
14012427 ATAAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.09
19 3 0.13
20 12 0.52
21 6 0.26
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (21 bp):
GAAGAAGAAGAAAAAGAAAAT
Found at i:14013503 original size:16 final size:16
Alignment explanation
Indices: 14013482--14013530 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
14013472 TGATGGAGAT
14013482 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
14013498 ATTATTTTTAT-ATT-
1 ATTATTTTGATAATTA
14013512 A-TATTTTGATAATTA
1 ATTATTTTGATAATTA
14013527 ATTA
1 ATTA
14013531 GTTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 8 0.29
14 4 0.14
15 4 0.14
16 12 0.43
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:14015236 original size:151 final size:150
Alignment explanation
Indices: 14014957--14015238 Score: 354
Period size: 151 Copynumber: 1.9 Consensus size: 150
14014947 GTGCATTGTG
* ** * *
14014957 TTCTTATGGCTTTTCAATTCTCTTGTTGCTCTTTCGTTTTGAGTTGCTTCTGTTATATTTTTTGG
1 TTCTTATGACTTTTCAATTCTCTCATTACTCTTTCGTTTCGAGTTGCTTCTGTTATATTTTTTGG
* * * * *
14015022 TGTCTTAGAGAATTTTCGAGAAAATTTTTACTCTTTGAGTGTTAGGTTGACTTATGAAGATTTGA
66 TGCCTTAGAGAATTTTCGAGAAAATTCTCACTCTTTGAGTGTAAGGTTGACTTAGGAAGATTTGA
14015087 AATACTTGATGTACATTGCT
131 AATACTTGATGTACATTGCT
* * *
14015107 TTCTTGTGACTTTTCAATTCTCTCATTACTCTTTTGTTTCGAGTTTCTT-TCGTTATATTTTTTT
1 TTCTTATGACTTTTCAATTCTCTCATTACTCTTTCGTTTCGAGTTGCTTCT-GTTATA-TTTTTT
* * * *
14015171 GGTGCCTTAGTGAATTTTTGGGAAAATTCTCACT-TTTCGAGTGTAATGTTGACTTAGGCAA-AT
64 GGTGCCTTAGAGAATTTTCGAGAAAATTCTCACTCTTT-GAGTGTAAGGTTGACTTAGG-AAGAT
14015234 TTGAA
127 TTGAA
14015239 GCAAAGTAAT
Statistics
Matches: 111, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
149 1 0.01
150 50 0.45
151 58 0.52
152 2 0.02
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (150 bp):
TTCTTATGACTTTTCAATTCTCTCATTACTCTTTCGTTTCGAGTTGCTTCTGTTATATTTTTTGG
TGCCTTAGAGAATTTTCGAGAAAATTCTCACTCTTTGAGTGTAAGGTTGACTTAGGAAGATTTGA
AATACTTGATGTACATTGCT
Found at i:14028434 original size:23 final size:23
Alignment explanation
Indices: 14028392--14028455 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
14028382 TAAGATCACT
*
14028392 ATATATAAAATTTCAATAAATAAAA
1 ATATAT-AAATTT-ATTAAATAAAA
**
14028417 ATATATAAATTTATTAAATTGAA
1 ATATATAAATTTATTAAATAAAA
*
14028440 ATAATATAAATATATT
1 AT-ATATAAATTTATT
14028456 TTTTAAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 10 0.29
24 18 0.53
25 6 0.18
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
ATATATAAATTTATTAAATAAAA
Found at i:14030031 original size:37 final size:37
Alignment explanation
Indices: 14029976--14030105 Score: 149
Period size: 37 Copynumber: 3.6 Consensus size: 37
14029966 ACAAAGCCTG
* * *
14029976 CTAGGCACATAACCTGAAAACACCGGCATGAAGCTTA
1 CTAGGCACAAAACTTGAAAACACCGGCACGAAGCTTA
* * * *
14030013 CTAGGCACAAAATTTGAAAACACTGGCACGAAGCCTG
1 CTAGGCACAAAACTTGAAAACACCGGCACGAAGCTTA
*
14030050 CTAGGCACAAAGCTTG-AAA-A-CGGCACGAAGCTTA
1 CTAGGCACAAAACTTGAAAACACCGGCACGAAGCTTA
* *
14030084 CTAGGCACAAAGCCTGAAAACA
1 CTAGGCACAAAACTTGAAAACA
14030106 TTGGCACAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
34 26 0.33
35 4 0.05
36 4 0.05
37 44 0.56
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.15
Consensus pattern (37 bp):
CTAGGCACAAAACTTGAAAACACCGGCACGAAGCTTA
Found at i:14030080 original size:34 final size:36
Alignment explanation
Indices: 14029964--14030119 Score: 147
Period size: 37 Copynumber: 4.3 Consensus size: 36
14029954 TGGGTCACCA
* *
14029964 GCACAAAGCCTGCTAGGCACATAA-CCTGAAAACACCG
1 GCACGAAGCCTACTAGGCACA-AAGCCTGAAAACA-CG
* * ***
14030001 GCATGAAGCTTACTAGGCACAAAATTTGAAAACACTG
1 GCACGAAGCCTACTAGGCACAAAGCCTGAAAACAC-G
* *
14030038 GCACGAAGCCTGCTAGGCACAAAGCTTG-AAA-ACG
1 GCACGAAGCCTACTAGGCACAAAGCCTGAAAACACG
* *
14030072 GCACGAAGCTTACTAGGCACAAAGCCTGAAAACATTG
1 GCACGAAGCCTACTAGGCACAAAGCCTGAAAACA-CG
*
14030109 GCACAAAGCCT
1 GCACGAAGCCT
14030120 GAAAATACCG
Statistics
Matches: 97, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
34 26 0.27
35 5 0.05
36 7 0.07
37 59 0.61
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (36 bp):
GCACGAAGCCTACTAGGCACAAAGCCTGAAAACACG
Found at i:14030093 original size:71 final size:74
Alignment explanation
Indices: 14029964--14030120 Score: 214
Period size: 71 Copynumber: 2.2 Consensus size: 74
14029954 TGGGTCACCA
* **
14029964 GCACAAAGCCTGCTAGGCACATAACCTGAAAACACCGGCATGAAGCTTACTAGGCACAAAATTTG
1 GCACAAAGCCTGCTAGGCACATAACCTGAAAACACCGGCACGAAGCTTACTAGGCACAAAACCTG
14030029 AAAACACTG
66 AAAACACTG
* * *
14030038 GCACGAAGCCTGCTAGGCACA-AAGCTTG-AAA-A-CGGCACGAAGCTTACTAGGCACAAAGCCT
1 GCACAAAGCCTGCTAGGCACATAA-CCTGAAAACACCGGCACGAAGCTTACTAGGCACAAAACCT
*
14030099 GAAAACATTG
65 GAAAACACTG
14030109 GCACAAAGCCTG
1 GCACAAAGCCTG
14030121 AAAATACCGG
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
71 45 0.61
72 1 0.01
73 5 0.07
74 23 0.31
ACGTcount: A:0.38, C:0.26, G:0.22, T:0.15
Consensus pattern (74 bp):
GCACAAAGCCTGCTAGGCACATAACCTGAAAACACCGGCACGAAGCTTACTAGGCACAAAACCTG
AAAACACTG
Found at i:14030132 original size:21 final size:21
Alignment explanation
Indices: 14030087--14030140 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
14030077 AAGCTTACTA
**
14030087 GGCACAAAGCCTGAAAACATT
1 GGCACAAAGCCTGAAAACACC
*
14030108 GGCACAAAGCCTGAAAATACC
1 GGCACAAAGCCTGAAAACACC
*
14030129 GGCACGAAGCCT
1 GGCACAAAGCCT
14030141 ACTAGGCACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.39, C:0.28, G:0.22, T:0.11
Consensus pattern (21 bp):
GGCACAAAGCCTGAAAACACC
Found at i:14030144 original size:58 final size:55
Alignment explanation
Indices: 14030053--14030178 Score: 162
Period size: 58 Copynumber: 2.2 Consensus size: 55
14030043 AAGCCTGCTA
* * *
14030053 GGCACAAAGCTTGAAAACGGCACGAAGCTTACTAGGCACAAAGCCTGAAAACATT
1 GGCACAAAGCCTGAAAACGGCACGAAGCCTACTAGGCACAAAGCCTGAAAACACT
* * *
14030108 GGCACAAAGCCTGAAAATACCGGCACGAAGCCTACTAGGCACACAGCCTGAATATACT
1 GGCACAAAGCCTG-AAA-A-CGGCACGAAGCCTACTAGGCACAAAGCCTGAAAACACT
*
14030166 GGCACGAAGCCTG
1 GGCACAAAGCCTG
14030179 CTAGGCACAC
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
55 12 0.20
56 3 0.05
57 1 0.02
58 45 0.74
ACGTcount: A:0.37, C:0.27, G:0.23, T:0.13
Consensus pattern (55 bp):
GGCACAAAGCCTGAAAACGGCACGAAGCCTACTAGGCACAAAGCCTGAAAACACT
Found at i:14030158 original size:37 final size:37
Alignment explanation
Indices: 14030108--14030226 Score: 184
Period size: 37 Copynumber: 3.2 Consensus size: 37
14030098 TGAAAACATT
* * *
14030108 GGCACAAAGCCTGAAAATACCGGCACGAAGCCTACTA
1 GGCACACAGCCTGAATATACCGGCACGAAGCCTGCTA
*
14030145 GGCACACAGCCTGAATATACTGGCACGAAGCCTGCTA
1 GGCACACAGCCTGAATATACCGGCACGAAGCCTGCTA
* *
14030182 GGCACACAGCCTGAATACACCGGCACGAAGTCTGCTA
1 GGCACACAGCCTGAATATACCGGCACGAAGCCTGCTA
14030219 GGCACACA
1 GGCACACA
14030227 ACCTAAATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 75 1.00
ACGTcount: A:0.33, C:0.31, G:0.24, T:0.13
Consensus pattern (37 bp):
GGCACACAGCCTGAATATACCGGCACGAAGCCTGCTA
Found at i:14032749 original size:2 final size:2
Alignment explanation
Indices: 14032744--14032774 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14032734 TCAGTAATTC
14032744 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14032775 TTGGCTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14034912 original size:4 final size:4
Alignment explanation
Indices: 14034903--14034948 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
14034893 TCCCATAAAC
* * *
14034903 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGC ATGC ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
14034949 AGTAAGAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (4 bp):
ATGT
Found at i:14036849 original size:17 final size:19
Alignment explanation
Indices: 14036821--14036855 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
14036811 AAGTGTTCGT
14036821 AGAATAAAATAT-TAAAAA
1 AGAATAAAATATATAAAAA
14036839 AGAAT-AAATATATAAAA
1 AGAATAAAATATATAAAA
14036856 TAAATGAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (19 bp):
AGAATAAAATATATAAAAA
Found at i:14041819 original size:20 final size:21
Alignment explanation
Indices: 14041794--14041834 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
14041784 TGACCATCTT
14041794 CTTCTT-TCTCATTTT-TCTCA
1 CTTCTTCTC-CATTTTCTCTCA
14041814 CTTCTTCTCCATTTTCTCTCA
1 CTTCTTCTCCATTTTCTCTCA
14041835 GCTCCATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.10, C:0.34, G:0.00, T:0.56
Consensus pattern (21 bp):
CTTCTTCTCCATTTTCTCTCA
Found at i:14042316 original size:68 final size:69
Alignment explanation
Indices: 14042207--14042344 Score: 163
Period size: 68 Copynumber: 2.0 Consensus size: 69
14042197 ATTTGCTGAG
* * * * **
14042207 AAGTCGCAATGATAATTTGGGAGTCTCACATCACTCGAAAAA-ATTATGGTTGTAATTTAAACAT
1 AAGTCGCAATGATAATTTGGGAGTCTCACAGCACTCAAAAAACACTAAGGTTGTAATGCAAACAT
14042271 TTGA
66 TTGA
* ** *
14042275 AAGTCGCAATGATAGTTTGGGAG-CATCGTAGCACTCAAAAAACCCTAAGGTTGTAATGCAAACA
1 AAGTCGCAATGATAATTTGGGAGTC-TCACAGCACTCAAAAAACACTAAGGTTGTAATGCAAACA
14042339 TTTGA
65 TTTGA
14042344 A
1 A
14042345 TGTTATTTGA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
67 1 0.02
68 35 0.60
69 22 0.38
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (69 bp):
AAGTCGCAATGATAATTTGGGAGTCTCACAGCACTCAAAAAACACTAAGGTTGTAATGCAAACAT
TTGA
Found at i:14043937 original size:21 final size:20
Alignment explanation
Indices: 14043909--14043947 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
14043899 ACATCATCAT
14043909 TAATTTTAATCTTATTATTA
1 TAATTTTAATCTTATTATTA
*
14043929 TAATATTTAATTTTATTAT
1 TAAT-TTTAATCTTATTAT
14043948 CATCATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATTTTAATCTTATTATTA
Found at i:14043944 original size:18 final size:18
Alignment explanation
Indices: 14043923--14043961 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
14043913 TTTAATCTTA
14043923 TTATTATAAT-ATTTAATT
1 TTATTATAATCA-TTAATT
*
14043941 TTATTATCATCATTAATT
1 TTATTATAATCATTAATT
14043959 TTA
1 TTA
14043962 ATTTTATCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTATAATCATTAATT
Found at i:14050326 original size:5 final size:5
Alignment explanation
Indices: 14050316--14050342 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
14050306 AAAAATCATA
14050316 ATATT ATATT ATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT AT
14050343 CATCAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:14050599 original size:20 final size:18
Alignment explanation
Indices: 14050576--14050627 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
14050566 AAAATCGTAA
14050576 AAAAATATTTAAAAACTACG
1 AAAAATATTTAAAAA-T-CG
*
14050596 AAAAAT-TATTAAAAATTG
1 AAAAATAT-TTAAAAATCG
14050614 AAAAATATTGTAAA
1 AAAAATATT-TAAA
14050628 TCCGATTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 8 0.29
19 7 0.25
20 13 0.46
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.29
Consensus pattern (18 bp):
AAAAATATTTAAAAATCG
Found at i:14052625 original size:15 final size:15
Alignment explanation
Indices: 14052605--14052634 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
14052595 CAAGCTCATC
*
14052605 CAAAGAAGGGGACAT
1 CAAAGAAGAGGACAT
14052620 CAAAGAAGAGGACAT
1 CAAAGAAGAGGACAT
14052635 ACCAAGGTTG
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:0.50, C:0.13, G:0.30, T:0.07
Consensus pattern (15 bp):
CAAAGAAGAGGACAT
Found at i:14055254 original size:15 final size:16
Alignment explanation
Indices: 14055230--14055265 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
14055220 TTTATAACAC
*
14055230 ATAATTTATTTTT-TT
1 ATAATATATTTTTATT
14055245 ATAATATATTTTTATT
1 ATAATATATTTTTATT
14055261 ATAAT
1 ATAAT
14055266 TTTAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATATATTTTTATT
Found at i:14057124 original size:71 final size:71
Alignment explanation
Indices: 14057043--14057184 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
14057033 AGTCGGGGTG
* *
14057043 CAACAAATATGATTGTCCTTTGAGGAAGAAGCAAAAGGAGAAGAAGAAAGTTATGGTAGCCACTT
1 CAACAAATATGATTGTCCTTTGAGGAAGAAGCAAAAGGAAAAGAAGAAAGTCATGGTAGCCACTT
14057108 GAAGTA
66 GAAGTA
14057114 CAACAAATATGATTGTCCTTTGAGGAAGAAGCAAAAGGAAAAGAAGAAAGTCATGGTAGCCACTT
1 CAACAAATATGATTGTCCTTTGAGGAAGAAGCAAAAGGAAAAGAAGAAAGTCATGGTAGCCACTT
14057179 GAAGTA
66 GAAGTA
14057185 ATAGTGACAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.43, C:0.12, G:0.25, T:0.20
Consensus pattern (71 bp):
CAACAAATATGATTGTCCTTTGAGGAAGAAGCAAAAGGAAAAGAAGAAAGTCATGGTAGCCACTT
GAAGTA
Found at i:14063719 original size:11 final size:11
Alignment explanation
Indices: 14063698--14063727 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
14063688 ATCTGATTAC
14063698 AATATATAAATA
1 AATA-ATAAATA
14063710 AATAATAAATA
1 AATAATAAATA
14063721 AATAATA
1 AATAATA
14063728 GAACATCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AATAATAAATA
Found at i:14066214 original size:29 final size:29
Alignment explanation
Indices: 14066159--14066214 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
14066149 TTAATGTCAA
*
14066159 TAATTATATACATGAATTTTGATTTTGTG
1 TAATTATATACATGAATTTTGAATTTGTG
*
14066188 TAATTTTATACATGAAATTTT-AATTTG
1 TAATTATATACATG-AATTTTGAATTTG
14066215 GTCCAATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.52
Consensus pattern (29 bp):
TAATTATATACATGAATTTTGAATTTGTG
Found at i:14074764 original size:25 final size:24
Alignment explanation
Indices: 14074736--14074786 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
14074726 TATTTATATA
*
14074736 ATAAATTTTTTAATTTTTAATATTT
1 ATAAATTTTTTAATTTATAAT-TTT
* *
14074761 ATAATTTTTTTAGTTTATAATTTT
1 ATAAATTTTTTAATTTATAATTTT
14074785 AT
1 AT
14074787 TTTTAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
ATAAATTTTTTAATTTATAATTTT
Found at i:14074765 original size:16 final size:16
Alignment explanation
Indices: 14074746--14074784 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
14074736 ATAAATTTTT
14074746 TAATTTTTAATA-TTTA
1 TAATTTTT-ATAGTTTA
*
14074762 TAATTTTTTTAGTTTA
1 TAATTTTTATAGTTTA
14074778 TAATTTT
1 TAATTTT
14074785 ATTTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TAATTTTTATAGTTTA
Found at i:14074807 original size:16 final size:16
Alignment explanation
Indices: 14074749--14074808 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 16
14074739 AATTTTTTAA
*
14074749 TTTTTAATATTTATAATT
1 TTTTTAAT-TTTAT-TTT
*
14074767 TTTTTAGTTTATAATTTT
1 TTTTTAATTT-T-ATTTT
14074785 ATTTTTAATTTTATTTT
1 -TTTTTAATTTTATTTT
14074802 TTTTTAA
1 TTTTTAA
14074809 AAATAATTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 7 0.19
17 7 0.19
18 11 0.31
19 11 0.31
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTTAATTTTATTTT
Found at i:14077741 original size:30 final size:30
Alignment explanation
Indices: 14077706--14077776 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
14077696 AAATCAATCA
14077706 ATTCAATCCTTTTGACTAAATTGATTCCTC
1 ATTCAATCCTTTTGACTAAATTGATTCCTC
14077736 ATTCAATCCTTTTGACTAAATTGATTCCTC
1 ATTCAATCCTTTTGACTAAATTGATTCCTC
14077766 ATTCAATCCTT
1 ATTCAATCCTT
14077777 AATCCAATCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
ATTCAATCCTTTTGACTAAATTGATTCCTC
Found at i:14083647 original size:2 final size:2
Alignment explanation
Indices: 14083640--14083665 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14083630 GTATACTATT
14083640 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
14083666 GGGAGATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14093633 original size:9 final size:10
Alignment explanation
Indices: 14093613--14093637 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
14093603 GGTACCAATT
14093613 AAGTTAAAAA
1 AAGTTAAAAA
14093623 AAGTTAAAAA
1 AAGTTAAAAA
14093633 AAGTT
1 AAGTT
14093638 CATGTATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (10 bp):
AAGTTAAAAA
Found at i:14105252 original size:46 final size:46
Alignment explanation
Indices: 14105194--14105282 Score: 144
Period size: 46 Copynumber: 1.9 Consensus size: 46
14105184 CTTACAATTC
* *
14105194 TATTATTTTCTTTTGTTCTCTCTATGTTGT-TTATATATAAATAGGG
1 TATTATTCTCTTTTGTCCTCTCTATGTTGTGTT-TATATAAATAGGG
14105240 TATTATTCTCTTTTGTCCTCTCTATGTTGTGTTTATATAAATA
1 TATTATTCTCTTTTGTCCTCTCTATGTTGTGTTTATATAAATA
14105283 AGGGAGGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
46 38 0.95
47 2 0.05
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.56
Consensus pattern (46 bp):
TATTATTCTCTTTTGTCCTCTCTATGTTGTGTTTATATAAATAGGG
Found at i:14105524 original size:53 final size:53
Alignment explanation
Indices: 14105444--14105550 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
14105434 AGGACCCACA
14105444 TCAACAATGGAAGGAACAAGAAATAACACATCATATTTTCAATTAAACCTTCT
1 TCAACAATGGAAGGAACAAGAAATAACACATCATATTTTCAATTAAACCTTCT
14105497 TCAACAATGGAAGGAACAAGAAATAACACATCATATTTTCAATTAAACCTTCT
1 TCAACAATGGAAGGAACAAGAAATAACACATCATATTTTCAATTAAACCTTCT
14105550 T
1 T
14105551 GCAAACCAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.27
Consensus pattern (53 bp):
TCAACAATGGAAGGAACAAGAAATAACACATCATATTTTCAATTAAACCTTCT
Found at i:14105793 original size:46 final size:46
Alignment explanation
Indices: 14105726--14105814 Score: 144
Period size: 46 Copynumber: 1.9 Consensus size: 46
14105716 ATTCCTCCCT
* *
14105726 TATTTATATAAACACAACATAGAGAGGACAAAAGAGAATAATACCC
1 TATTTATATAAACACAACATAGAGAGAACAAAAGAAAATAATACCC
14105772 TATTTATATATAA-ACAACATAGAGAGAACAAAAGAAAATAATA
1 TATTTATATA-AACACAACATAGAGAGAACAAAAGAAAATAATA
14105815 GAATTGTAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
46 38 0.95
47 2 0.05
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.21
Consensus pattern (46 bp):
TATTTATATAAACACAACATAGAGAGAACAAAAGAAAATAATACCC
Found at i:14117144 original size:22 final size:20
Alignment explanation
Indices: 14117113--14117157 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
14117103 AATTCATCCA
14117113 TTATAAATTTAAATATATAATT
1 TTATAAATTTAAA-ATA-AATT
* *
14117135 TTATATATTTGAAATAAATT
1 TTATAAATTTAAAATAAATT
14117155 TTA
1 TTA
14117158 ACAGAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 3 0.14
22 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TTATAAATTTAAAATAAATT
Found at i:14117273 original size:13 final size:13
Alignment explanation
Indices: 14117257--14117281 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14117247 AGTGATTTTG
14117257 AAAAAAAAAAGTT
1 AAAAAAAAAAGTT
14117270 AAAAAAAAAAGT
1 AAAAAAAAAAGT
14117282 ATTTTTACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AAAAAAAAAAGTT
Found at i:14117624 original size:29 final size:29
Alignment explanation
Indices: 14117566--14117624 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
14117556 TAGTACCTAA
* *
14117566 ATTTTTTTGTCACAATTGGTACCTAGATT
1 ATTTTTTTGTCACAATTGATACCTACATT
* *
14117595 ATTTTTTT-TCTCAATTTGATACCTCCATT
1 ATTTTTTTGTCACAA-TTGATACCTACATT
14117624 A
1 A
14117625 AGTCAAACCG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.24, C:0.17, G:0.08, T:0.51
Consensus pattern (29 bp):
ATTTTTTTGTCACAATTGATACCTACATT
Found at i:14117872 original size:7 final size:7
Alignment explanation
Indices: 14117858--14117890 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
14117848 TATATCTTTC
14117858 TCTTCTT
1 TCTTCTT
*
14117865 TTTTCTT
1 TCTTCTT
14117872 TCTTCTT
1 TCTTCTT
14117879 TCTTCTT
1 TCTTCTT
14117886 TCTTC
1 TCTTC
14117891 AGCAGACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TCTTCTT
Found at i:14119766 original size:30 final size:30
Alignment explanation
Indices: 14119723--14119787 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
14119713 TTAAACTTTT
14119723 TTTTTCCGATTTGGTACC-AAACTTGACAC
1 TTTTTCCGATTTGGTACCTAAACTTGACAC
* * *
14119752 TTTTTCCTATTTTGGTACCTAAATTTGATAC
1 TTTTTCCGA-TTTGGTACCTAAACTTGACAC
14119783 TTTTT
1 TTTTT
14119788 TTAAGTTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 8 0.26
30 9 0.29
31 14 0.45
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (30 bp):
TTTTTCCGATTTGGTACCTAAACTTGACAC
Found at i:14119811 original size:88 final size:89
Alignment explanation
Indices: 14119673--14119859 Score: 236
Period size: 88 Copynumber: 2.1 Consensus size: 89
14119663 TTAATATAAT
* * * * ** *
14119673 ATTTGGTATCTGAATTTGATATTTTTTCCTAATTTAGTATTTAAACTTTTTT-TTTCCGATTTGG
1 ATTTGGTACCTAAATTTGATATTTTTT-CTAAGTTAGTATTAAAACTTTTTTGGGTCCAATTTGG
14119737 TACC-AAACTTGACACTTTTTCCTA
65 TACCTAAACTTGACACTTTTTCCTA
* *
14119761 TTTTGGTACCTAAATTTGATACTTTTTT-TAAGTTGGTACTTAAAACTTTTTTGGGTCCAATTTG
1 ATTTGGTACCTAAATTTGATA-TTTTTTCTAAGTTAGTA-TTAAAACTTTTTTGGGTCCAATTTG
*
14119825 GTACCTAAACTTGACTCTTTTTCCTA
64 GTACCTAAACTTGACACTTTTTCCTA
14119851 ATTTGGTAC
1 ATTTGGTAC
14119860 TTAATTTTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
87 8 0.10
88 30 0.36
89 19 0.23
90 27 0.32
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (89 bp):
ATTTGGTACCTAAATTTGATATTTTTTCTAAGTTAGTATTAAAACTTTTTTGGGTCCAATTTGGT
ACCTAAACTTGACACTTTTTCCTA
Found at i:14120094 original size:60 final size:58
Alignment explanation
Indices: 14120014--14120164 Score: 191
Period size: 60 Copynumber: 2.6 Consensus size: 58
14120004 AAATTGAATC
*
14120014 TAAAAAAAA-TTAGGTACCAAATTAGGGAAAAAA-ACCAAGTTCAAGTGCCAAATTGGG
1 TAAAAAAAATTTAGGTACCAAATTA-GGAAAAAATACCAAGTTCAAGTACCAAATTGGG
** * *
14120071 TCAAAAAAAACTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTACTAAATTGGG
1 T-AAAAAAAA-TTTAGGTACCAAATTAGGAAAAAATACCAAGTTCAAGTACCAAATTGGG
*
14120131 TAAAAAAAAGTTTAGGTACCAAATTA-AAAAAAAT
1 TAAAAAAAA-TTTAGGTACCAAATTAGGAAAAAAT
14120165 GTAAAATTCA
Statistics
Matches: 83, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
57 1 0.01
58 15 0.18
59 32 0.39
60 35 0.42
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.23
Consensus pattern (58 bp):
TAAAAAAAATTTAGGTACCAAATTAGGAAAAAATACCAAGTTCAAGTACCAAATTGGG
Found at i:14120163 original size:28 final size:28
Alignment explanation
Indices: 14120073--14120163 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 28
14120063 AAATTGGGTC
*
14120073 AAAAAAAACTTTAGGTACCAAATTAGGAAA
1 AAAAAAAAGTTTAGGTACCAAATTA--AAA
*** * * ****
14120103 AAATGTCAAGTTCAGGTACTAAATTGGGT
1 AAA-AAAAAGTTTAGGTACCAAATTAAAA
14120132 AAAAAAAAGTTTAGGTACCAAATTAAAA
1 AAAAAAAAGTTTAGGTACCAAATTAAAA
14120160 AAAA
1 AAAA
14120164 TGTAAAATTC
Statistics
Matches: 41, Mismatches: 19, Indels: 4
0.64 0.30 0.06
Matches are distributed among these distances:
28 20 0.49
29 3 0.07
30 3 0.07
31 15 0.37
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.23
Consensus pattern (28 bp):
AAAAAAAAGTTTAGGTACCAAATTAAAA
Found at i:14120339 original size:22 final size:23
Alignment explanation
Indices: 14120293--14120344 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
14120283 TTTATGCGTT
*
14120293 TATTTTT-AAATTTATTAAATAA
1 TATTTTTAAAATTTATAAAATAA
14120315 TATTTTTAATAATTTA-AAAAT-A
1 TATTTTTAA-AATTTATAAAATAA
*
14120337 TATGTTTA
1 TATTTTTA
14120345 CTACTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 15 0.58
23 5 0.19
24 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TATTTTTAAAATTTATAAAATAA
Found at i:14123742 original size:29 final size:30
Alignment explanation
Indices: 14123661--14123750 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
14123651 TCTAGTCCCC
* * * *
14123661 AAACTTTCCAAAATTCTATTTTTGACCCCG
1 AAACTTTCAAAAATTCCATTTTTAACCCTG
* *
14123691 AAACTTCCAAAAATTACCA-TTTT-ACCCTT
1 AAACTTTCAAAAATT-CCATTTTTAACCCTG
*
14123720 AACCTTTCAAAAATTCCATTTTTAACCCTG
1 AAACTTTCAAAAATTCCATTTTTAACCCTG
14123750 A
1 A
14123751 TGTCACCCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
28 3 0.06
29 21 0.43
30 23 0.47
31 2 0.04
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (30 bp):
AAACTTTCAAAAATTCCATTTTTAACCCTG
Found at i:14123807 original size:29 final size:28
Alignment explanation
Indices: 14123657--14123894 Score: 98
Period size: 29 Copynumber: 8.1 Consensus size: 28
14123647 GCTCTCTAGT
*
14123657 CCCCAAACTTTCCAAAATTCTATTTTTGA
1 CCCCAAACTTTCCAAAATTCCATTTTT-A
14123686 CCCCGAAAC-TTCCAAAAATTACCA-TTTTA
1 CCCC-AAACTTTCC-AAAATT-CCATTTTTA
* * *
14123715 CCCTTAACCTTTCAAAAATTCCATTTTTA
1 CCC-CAAACTTTCCAAAATTCCATTTTTA
* ** *
14123744 ACCCTGA-TGTCACCCAAAATTACCA-TTTTA
1 CCCCAAACT-T--TCCAAAATT-CCATTTTTA
*
14123774 TCCCCAAACTTTTCAAAATTCCATTTTTGA
1 -CCCCAAACTTTCCAAAATTCCATTTTT-A
*
14123804 CCCC-GA-TTTCACCCAAAATTACCA-TTTTA
1 CCCCAAACTTT---CCAAAATT-CCATTTTTA
*
14123833 CCCTCGAACTTTCCAAATATT--ATTTTTA
1 CCC-CAAACTTTCCAAA-ATTCCATTTTTA
* * * * *
14123861 GCCCTAAATTTTCTCGAAATTACATTTTTG
1 -CCCCAAACTTTC-CAAAATTCCATTTTTA
14123891 CCCC
1 CCCC
14123895 CGAGAGCCAA
Statistics
Matches: 157, Mismatches: 25, Indels: 54
0.67 0.11 0.23
Matches are distributed among these distances:
27 5 0.03
28 22 0.14
29 61 0.39
30 51 0.32
31 14 0.09
32 4 0.03
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (28 bp):
CCCCAAACTTTCCAAAATTCCATTTTTA
Found at i:14123823 original size:30 final size:30
Alignment explanation
Indices: 14123729--14123835 Score: 84
Period size: 30 Copynumber: 3.6 Consensus size: 30
14123719 TAACCTTTCA
* *
14123729 AAAATT-CCATTTTTAACCCTGATGTCACCC
1 AAAATTACCATTTTT-ACCCCGATTTCACCC
* *
14123759 AAAATTACCA-TTTTATCCCCAAACTTT---TC
1 AAAATTACCATTTTTA-CCCC-GA-TTTCACCC
14123788 AAAATT-CCATTTTTGACCCCGATTTCACCC
1 AAAATTACCATTTTT-ACCCCGATTTCACCC
14123818 AAAATTACCA-TTTTACCC
1 AAAATTACCATTTTTACCC
14123836 TCGAACTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 21
0.69 0.07 0.24
Matches are distributed among these distances:
27 3 0.05
28 4 0.07
29 20 0.33
30 25 0.41
31 7 0.11
32 2 0.03
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.35
Consensus pattern (30 bp):
AAAATTACCATTTTTACCCCGATTTCACCC
Found at i:14123843 original size:59 final size:59
Alignment explanation
Indices: 14123660--14123849 Score: 233
Period size: 59 Copynumber: 3.2 Consensus size: 59
14123650 CTCTAGTCCC
* * *
14123660 CAAACTTTCCAAAATTCTATTTTTGACCCCGAAACTT--CCAAAAATTACCATTTTACCCT
1 CAAACTTTCCAAAATTCCATTTTTGACCCCG--ATTTCACCCAAAATTACCATTTTACCCT
* * * * * *
14123719 TAACCTTTCAAAAATTCCATTTTTAACCCTGATGTCACCCAAAATTACCATTTTATCCC-
1 CAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACCCAAAATTACCATTTTA-CCCT
*
14123778 CAAACTTTTCAAAATTCCATTTTTGACCCCGATTTCACCCAAAATTACCATTTTACCCT
1 CAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACCCAAAATTACCATTTTACCCT
*
14123837 CGAACTTTCCAAA
1 CAAACTTTCCAAA
14123850 TATTATTTTT
Statistics
Matches: 109, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
57 2 0.02
58 3 0.03
59 101 0.93
60 3 0.03
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (59 bp):
CAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACCCAAAATTACCATTTTACCCT
Found at i:14136416 original size:200 final size:200
Alignment explanation
Indices: 14136064--14137105 Score: 1541
Period size: 200 Copynumber: 5.2 Consensus size: 200
14136054 AAGAAACAGT
* * * *
14136064 GAGGCGATAATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTTAA-AGCGAGCAAA
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACA-CGAGCCAA
* * * *
14136128 TCTGCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGTTCGAAACAATAAAATGGTTAGCTTC
65 TCTTCGTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
* *
14136193 CTGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCTTGAGGAGATCTAGAGAAGCAAATTAAA
130 CTGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAA
*
14136258 ACAATA
195 ACAACA
14136264 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
* *
14136329 CTTCGTACCCAGCTTCTTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
66 CTTCGTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* *
14136394 TGATGAGATACAGAGAAGTGGACCAAATTTATCTTCCTGAGGAGATCCAGAGAAGCAAATGAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
14136459 CAACA
196 CAACA
*
14136464 GAGGCGGTCATCTTCCTAATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
14136529 CTTCGTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
66 CTTCGTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* *
14136594 TGATGAGATACAGAGAAGTGAACCAAATTTGTCTTCCTAAGGAGATCCAGAGAAGCAAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
*
14136659 TAACA
196 CAACA
* * *
14136664 GAGGCAGTCATCTTCCTGATGAGATACACAGAAGAATAACAACTCAACGCTCAACACGAGCCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
* * *
14136729 CTTCGTACCCAACTTCCTAATGAGACACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
66 CTTCGTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* * * * *
14136794 TGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCTTGAGGAGATCTAGAGAAGCGAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
14136859 CAAGC-
196 CAA-CA
* * * * ** *
14136864 GATGTGGCCATCTTCCTGATGAGACACAGAGAAGAATACCAACTCAACGCTCAATGCGAGCAAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
* * * *
14136929 CTTCGAACTCAGCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCC
66 CTTCGTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
** * * * *
14136994 TGATGAGATACAGAGAAGTGGACTGAATTCGTCTTCCTGAGGTGATCCAAAGAAGCGAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
* *
14137059 TAGATA
196 CA-ACA
* * * * *
14137065 -ATTGCGATCATCTTCCTGATAAGACACAGAGAAGAAGACCA
1 GA-GGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCA
14137106 GGTCAATGAA
Statistics
Matches: 768, Mismatches: 69, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
200 731 0.95
201 37 0.05
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (200 bp):
GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
CTTCGTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
TGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
CAACA
Found at i:14137494 original size:17 final size:17
Alignment explanation
Indices: 14137472--14137531 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
14137462 GTTAAAATGG
*
14137472 ATTTAAATTTATTTTAA
1 ATTTAAATTTAATTTAA
** *
14137489 ATTTAAATTTGCTCTAA
1 ATTTAAATTTAATTTAA
* *
14137506 ATTTAAGTTTAATTGAA
1 ATTTAAATTTAATTTAA
14137523 ATTTAAATT
1 ATTTAAATT
14137532 GATATTAACC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (17 bp):
ATTTAAATTTAATTTAA
Found at i:14138330 original size:58 final size:59
Alignment explanation
Indices: 14138153--14138425 Score: 446
Period size: 58 Copynumber: 4.7 Consensus size: 59
14138143 ATCATCTTCG
*
14138153 TTTTACCCCCAAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCACCCAAAATTACCA
1 TTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAATTACCA
*
14138211 TTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCCAAAATTACCA
1 TTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAATTACCA
*
14138270 TTTTACCCCTAAACTTTCCAAAATTCCA-TTTTAACCTCGATTTCACCCAAAATTACCA
1 TTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAATTACCA
* *
14138328 TTTTACCCCCAAACTTTCCAAAATTCCATTTTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTACCCCTAAACTTTCCAAAATTCCA-TTTTTAACCCCGATTTCACCCAAAATTACCA
*
14138388 TTTTA-CCCTCAAACTTTCC-AAATTCTATTTTTAACCCC
1 TTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCC
14138426 AAAATTTCCC
Statistics
Matches: 204, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
58 95 0.47
59 67 0.33
60 42 0.21
ACGTcount: A:0.32, C:0.32, G:0.01, T:0.35
Consensus pattern (59 bp):
TTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAATTACCA
Found at i:14138359 original size:117 final size:118
Alignment explanation
Indices: 14138153--14138425 Score: 453
Period size: 117 Copynumber: 2.3 Consensus size: 118
14138143 ATCATCTTCG
*
14138153 TTTTACCCCCAAACTTTCCAAAATTCCATTTTAACCCCGATTTCACCCAAAATTACCATTTTACC
1 TTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCGATTTCACCCAAAATTACCATTTTACC
* * *
14138218 CCTAAACTTTCCAAAATTCCA-TTTTTAACCTCGATTTCACCCAAAATTACCA
66 CCCAAACTTTCCAAAATTCCATTTTTTAACCCCGATTTCACCAAAAATTACCA
*
14138270 TTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCTCGATTTCACCCAAAATTACCATTTTACC
1 TTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCGATTTCACCCAAAATTACCATTTTACC
14138335 CCCAAACTTTCCAAAATTCCATTTTTTAACCCCGATTTCACCAAAAATTACCA
66 CCCAAACTTTCCAAAATTCCATTTTTTAACCCCGATTTCACCAAAAATTACCA
*
14138388 TTTTA-CCCTCAAACTTTCC-AAATTCTATTTTTAACCCC
1 TTTTACCCCT-AAACTTTCCAAAATTCCA-TTTTAACCCC
14138426 AAAATTTCCC
Statistics
Matches: 146, Mismatches: 7, Indels: 5
0.92 0.04 0.03
Matches are distributed among these distances:
117 94 0.64
118 52 0.36
ACGTcount: A:0.32, C:0.32, G:0.01, T:0.35
Consensus pattern (118 bp):
TTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCGATTTCACCCAAAATTACCATTTTACC
CCCAAACTTTCCAAAATTCCATTTTTTAACCCCGATTTCACCAAAAATTACCA
Found at i:14141377 original size:28 final size:27
Alignment explanation
Indices: 14141346--14141400 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
14141336 ACTAAGGCAG
14141346 GTACCAACTTG-GAAAAAAAATAGTTTAA
1 GTACC-ACTTGTGAAAAAAAA-AGTTTAA
14141374 GTACCACTTGTGAAAAAAAAAGTTTAA
1 GTACCACTTGTGAAAAAAAAAGTTTAA
14141401 ATACTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (27 bp):
GTACCACTTGTGAAAAAAAAAGTTTAA
Found at i:14141390 original size:27 final size:28
Alignment explanation
Indices: 14141346--14141400 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
14141336 ACTAAGGCAG
*
14141346 GTACCAACTTGGAAAAAAAATAGTTTAA
1 GTACCAACTTGGAAAAAAAAAAGTTTAA
14141374 GTACC-ACTTGTG-AAAAAAAAAGTTTAA
1 GTACCAACTTG-GAAAAAAAAAAGTTTAA
14141401 ATACTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (28 bp):
GTACCAACTTGGAAAAAAAAAAGTTTAA
Found at i:14141498 original size:24 final size:25
Alignment explanation
Indices: 14141444--14141496 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 25
14141434 AAGCTTATTT
14141444 AAAATAAAATCATATTTTTTAATAA
1 AAAATAAAATCATATTTTTTAATAA
14141469 AAAATAAAATCATA-TTTTTAGATAA
1 AAAATAAAATCATATTTTTTA-ATAA
14141494 AAA
1 AAA
14141497 TATATTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (25 bp):
AAAATAAAATCATATTTTTTAATAA
Found at i:14144973 original size:18 final size:17
Alignment explanation
Indices: 14144952--14144991 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
14144942 TGTCATTTTT
*
14144952 AATTTATATATTTTTTAA
1 AATTTATA-ATTTTCTAA
*
14144970 AATTTCTAATTTTCTAA
1 AATTTATAATTTTCTAA
14144987 AATTT
1 AATTT
14144992 TAAATGTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTATAATTTTCTAA
Found at i:14146071 original size:45 final size:44
Alignment explanation
Indices: 14146005--14146138 Score: 196
Period size: 45 Copynumber: 3.0 Consensus size: 44
14145995 TACGCCTAAT
*
14146005 ATGAGTAAGACCATAGCTGAAAGATGTTATGGGATCATGATAAAA
1 ATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCAT-ATAAAA
* * * *
14146050 ATGAGTAATACCATAGTTGAAAGATGCTATAGCATCATTATAAAA
1 ATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCA-TATAAAA
*
14146095 ATGAGTAAGACCATAGCTGAAAGATGTTATGACATCATATAAAA
1 ATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATATAAAA
14146139 GCGCATCAGA
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
44 7 0.09
45 70 0.90
46 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.26
Consensus pattern (44 bp):
ATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATATAAAA
Found at i:14146346 original size:27 final size:28
Alignment explanation
Indices: 14146316--14146385 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 28
14146306 GTCGAAACAC
*
14146316 TAAACACAAGATAGTCT-GATGGGACAA
1 TAAACACAAGATAGTCTCGACGGGACAA
*
14146343 TAAATA-ACAGATAGT-TCGACGGGACAA
1 TAAACACA-AGATAGTCTCGACGGGACAA
* *
14146370 TGAACACGAGATAGTC
1 TAAACACAAGATAGTC
14146386 CATCAGGATA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
26 2 0.06
27 32 0.94
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.19
Consensus pattern (28 bp):
TAAACACAAGATAGTCTCGACGGGACAA
Found at i:14148127 original size:13 final size:13
Alignment explanation
Indices: 14148109--14148133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14148099 GCATTTCCTC
14148109 CTTCCCTTCCCTA
1 CTTCCCTTCCCTA
14148122 CTTCCCTTCCCT
1 CTTCCCTTCCCT
14148134 TTCCAAAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.56, G:0.00, T:0.40
Consensus pattern (13 bp):
CTTCCCTTCCCTA
Found at i:14160734 original size:37 final size:36
Alignment explanation
Indices: 14160693--14160766 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 36
14160683 TTTATCATCC
*
14160693 TATTTAAGTTTTGGGATAAATCAATTAGTTTTTAAAT
1 TATTTAAGTTTTGGGATAAATCAACTAG-TTTTAAAT
*
14160730 TATTTAATTTTTGGGATAAATCAACTAGTTTTAAAT
1 TATTTAAGTTTTGGGATAAATCAACTAGTTTTAAAT
14160766 T
1 T
14160767 TTTTTATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 9 0.26
37 26 0.74
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (36 bp):
TATTTAAGTTTTGGGATAAATCAACTAGTTTTAAAT
Found at i:14161130 original size:19 final size:19
Alignment explanation
Indices: 14161108--14161157 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
14161098 TTTTTATAAA
14161108 TATTTTTAATTTAAAAAAT
1 TATTTTTAATTTAAAAAAT
* *
14161127 TATTTTGAATTTTTGAAAAAT
1 TATTTTTAA--TTTAAAAAAT
14161148 TA-TTTTAATT
1 TATTTTTAATT
14161158 ATTTTAACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.08
19 8 0.31
20 5 0.19
21 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
TATTTTTAATTTAAAAAAT
Found at i:14165464 original size:33 final size:33
Alignment explanation
Indices: 14165427--14165491 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
14165417 TTATTGATAA
*
14165427 ATTTACAATAATATTTAAAATTAATAATAAAGG
1 ATTTACAATAATATTTAAAATTAAGAATAAAGG
14165460 ATTTACAATAATATTTAAAATTAAGAATAAAG
1 ATTTACAATAATATTTAAAATTAAGAATAAAG
14165492 TATCACTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (33 bp):
ATTTACAATAATATTTAAAATTAAGAATAAAGG
Found at i:14166963 original size:6 final size:6
Alignment explanation
Indices: 14166952--14166981 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
14166942 AAGTACGAAC
14166952 TTTTCT TTTTCT TTTTCT GTTTTCT TTTTC
1 TTTTCT TTTTCT TTTTCT -TTTTCT TTTTC
14166982 AGATTGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:14166976 original size:13 final size:12
Alignment explanation
Indices: 14166952--14166981 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
14166942 AAGTACGAAC
14166952 TTTTCTTTTTCT
1 TTTTCTTTTTCT
14166964 TTTTCTGTTTTCT
1 TTTTCT-TTTTCT
14166977 TTTTC
1 TTTTC
14166982 AGATTGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:14168980 original size:105 final size:107
Alignment explanation
Indices: 14168797--14169018 Score: 330
Period size: 106 Copynumber: 2.1 Consensus size: 107
14168787 ACAAGAAAAT
14168797 TTTTTTTGGTGTAAGCCATTGCATGGTCGACACTCCCTTTTAATCTGATAAAAAAAATCAAATTT
1 TTTTTTTGGTGTAAGCCATTGCATGGTCGACACTCCCTTTTAATCTGATAAAAAAAATCAAATTT
* *
14168862 TTGCATGGTCGACACCCC-TTTTTGTCAGATAAAAAATTCAA
66 TTGCATGGCCGACACCCCTTTTTTGTCAGATAAAAAATCCAA
**
14168903 TTTTTTTGGTGTTGGCCA-TGCAATGG-CTGACAC-CCCTATTT-ATCTGAT-AAAAAAATCAAA
1 TTTTTTTGGTGTAAGCCATTGC-ATGGTC-GACACTCCCT-TTTAATCTGATAAAAAAAATCAAA
14168963 TTTTTGGCATGGCCGACACCCCTTTTTTGTCAGATAAAAAATCCAA
63 TTTTT-GCATGGCCGACACCCCTTTTTTGTCAGATAAAAAATCCAA
14169009 TTTTTTTGGT
1 TTTTTTTGGT
14169019 ATCGACCATG
Statistics
Matches: 107, Mismatches: 4, Indels: 10
0.88 0.03 0.08
Matches are distributed among these distances:
104 17 0.16
105 30 0.28
106 60 0.56
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (107 bp):
TTTTTTTGGTGTAAGCCATTGCATGGTCGACACTCCCTTTTAATCTGATAAAAAAAATCAAATTT
TTGCATGGCCGACACCCCTTTTTTGTCAGATAAAAAATCCAA
Found at i:14169002 original size:46 final size:46
Alignment explanation
Indices: 14168925--14169013 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
14168915 TGGCCATGCA
* *
14168925 ATGGCTGACACCCCTATTTATCTGATAAAAAAATCAAATTTTTGGC
1 ATGGCCGACACCCCTATTTATCAGATAAAAAAATCAAATTTTTGGC
* * *
14168971 ATGGCCGACACCCCTTTTTTGTCAGAT-AAAAAATCCAATTTTT
1 ATGGCCGACACCCC-TATTTATCAGATAAAAAAATCAAATTTTT
14169014 TTGGTATCGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
46 28 0.76
47 9 0.24
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (46 bp):
ATGGCCGACACCCCTATTTATCAGATAAAAAAATCAAATTTTTGGC
Found at i:14169140 original size:98 final size:96
Alignment explanation
Indices: 14169036--14169252 Score: 262
Period size: 97 Copynumber: 2.2 Consensus size: 96
14169026 ATGGTCAGAT
*
14169036 AAAAAAATTTCAAATTTTTTTGGTGTC-CCTTTTTAT-CTGAATAAAAAATCAAATTTTTGGGTG
1 AAAAAAATTTCAAATTTTTTTGGTGTCGCC-----ATGCTGAATAAAAAATCAAATTTTTGGGTA
*
14169099 TTGGTCATGCCATGACCGACAC-CCCTATTTATCAGA
61 TTGGTCATGCAATGACCGACACTCCCTATTTATCA-A
* * *
14169135 AAAAAAATTTTAAATTTTTTTTGTGTCGGCCATGCTGAATAAAAAATCAAATTTTTGGGTATTTG
1 AAAAAAATTTCAAATTTTTTTGGTGTC-GCCATGCTGAATAAAAAATCAAATTTTTGGGTATTGG
* *
14169200 TCATGCAATGACCGACACTCCCTTTTTGTCAA
65 TCATGCAATGACCGACACTCCCTATTTATCAA
*
14169232 ATAAAAAA-TTCGAATTTTTTT
1 A-AAAAAATTTCAAATTTTTTT
14169253 TGTATTGACC
Statistics
Matches: 104, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
96 2 0.02
97 59 0.57
98 16 0.15
99 25 0.24
101 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (96 bp):
AAAAAAATTTCAAATTTTTTTGGTGTCGCCATGCTGAATAAAAAATCAAATTTTTGGGTATTGGT
CATGCAATGACCGACACTCCCTATTTATCAA
Found at i:14169203 original size:97 final size:97
Alignment explanation
Indices: 14169072--14169255 Score: 273
Period size: 97 Copynumber: 1.9 Consensus size: 97
14169062 CCCTTTTTAT
* *
14169072 CTGAATAAAAAATCAAATTTTTGGGTGTTGGTCATGCCATGACCGACAC-CCCTATTTATCAGAA
1 CTGAATAAAAAATCAAATTTTTGGGTATTGGTCATGCAATGACCGACACTCCCTATTTATCA-AA
*
14169136 -AAAAAATTTTAAATTTTTTTTGTGTCGGCCATG
65 TAAAAAA-TTCAAATTTTTTTTGTGTCGGCCATG
* * *
14169169 CTGAATAAAAAATCAAATTTTTGGGTATTTGTCATGCAATGACCGACACTCCCTTTTTGTCAAAT
1 CTGAATAAAAAATCAAATTTTTGGGTATTGGTCATGCAATGACCGACACTCCCTATTTATCAAAT
*
14169234 AAAAAATTCGAATTTTTTTTGT
66 AAAAAATTCAAATTTTTTTTGT
14169256 ATTGACCATG
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
97 62 0.79
98 16 0.21
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (97 bp):
CTGAATAAAAAATCAAATTTTTGGGTATTGGTCATGCAATGACCGACACTCCCTATTTATCAAAT
AAAAAATTCAAATTTTTTTTGTGTCGGCCATG
Found at i:14170948 original size:24 final size:24
Alignment explanation
Indices: 14170917--14170971 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
14170907 TGGGTGTTAA
14170917 CATCATCACCCTCCACCGACCCCT
1 CATCATCACCCTCCACCGACCCCT
14170941 CATCATCACCCTCCACCGACCCCT
1 CATCATCACCCTCCACCGACCCCT
14170965 CATCATC
1 CATCATC
14170972 TAAGTCTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.22, C:0.56, G:0.04, T:0.18
Consensus pattern (24 bp):
CATCATCACCCTCCACCGACCCCT
Found at i:14174250 original size:17 final size:17
Alignment explanation
Indices: 14174228--14174298 Score: 99
Period size: 17 Copynumber: 4.1 Consensus size: 17
14174218 TTTAAGTGTG
* *
14174228 AATTTATAATAATTTTA
1 AATTTAAAATAAATTTA
14174245 AATTTAAAATAAATTTAA
1 AATTTAAAATAAATTT-A
14174263 AATTTAAAATAAATTT-
1 AATTTAAAATAAATTTA
14174279 AATCTTAAAATAAATTTA
1 AAT-TTAAAATAAATTTA
14174297 AA
1 AA
14174299 ATAGGTTTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
16 3 0.06
17 27 0.55
18 19 0.39
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:14174267 original size:35 final size:35
Alignment explanation
Indices: 14174228--14174300 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
14174218 TTTAAGTGTG
* *
14174228 AATTTATAATAATTTTAAAT-TTAAAATAAATTTAA
1 AATTTAAAATAAATTT-AATCTTAAAATAAATTTAA
14174263 AATTTAAAATAAATTTAATCTTAAAATAAATTTAA
1 AATTTAAAATAAATTTAATCTTAAAATAAATTTAA
14174298 AAT
1 AAT
14174301 AGGTTTAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 3 0.09
35 32 0.91
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (35 bp):
AATTTAAAATAAATTTAATCTTAAAATAAATTTAA
Found at i:14174308 original size:11 final size:11
Alignment explanation
Indices: 14174243--14174301 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
14174233 ATAATAATTT
14174243 TAAATTTAAAA
1 TAAATTTAAAA
14174254 TAAATTTAAAA
1 TAAATTTAAAA
* *
14174265 TTTAAA-ATAAAT
1 --TAAATTTAAAA
*
14174277 TTAATCTTAAAA
1 TAAAT-TTAAAA
14174289 TAAATTTAAAA
1 TAAATTTAAAA
14174300 TA
1 TA
14174302 GGTTTAACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
10 3 0.08
11 19 0.50
12 12 0.32
13 4 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:14174499 original size:6 final size:6
Alignment explanation
Indices: 14174490--14174557 Score: 77
Period size: 6 Copynumber: 11.3 Consensus size: 6
14174480 TTTTAATTTT
*
14174490 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* *
14174538 CTTTGA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
14174558 AAAAATTAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
5 8 0.15
6 39 0.74
8 6 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:14174511 original size:17 final size:16
Alignment explanation
Indices: 14174481--14174554 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
14174471 TAAATTGATT
*
14174481 TTTAATTTTATTTAAA
1 TTTAAATTTATTTAAA
14174497 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
*
14174514 TTTAAATTTAATT--A
1 TTTAAATTTATTTAAA
*
14174528 TTTAAATTTACTTTGAA
1 TTTAAATTTA-TTTAAA
14174545 TTTAAATTTA
1 TTTAAATTTA
14174555 AATAAAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.22
15 2 0.04
16 11 0.22
17 27 0.53
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:14174746 original size:15 final size:15
Alignment explanation
Indices: 14174728--14174758 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
14174718 TATGCTGTTG
14174728 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
14174743 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
14174758 C
1 C
14174759 CATACACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.55, G:0.13, T:0.13
Consensus pattern (15 bp):
CTGCCACCACCAGCT
Found at i:14175261 original size:15 final size:16
Alignment explanation
Indices: 14175227--14175269 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
14175217 TAACAGCAGC
14175227 ATTAATTAATAATATTA
1 ATTAATTAA-AATATTA
14175244 ATTAATTAAAAT-TTA
1 ATTAATTAAAATATTA
*
14175259 ATTAAATAAAA
1 ATTAATTAAAA
14175270 AAGAAATCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 13 0.52
16 3 0.12
17 9 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTAATTAAAATATTA
Found at i:14175905 original size:14 final size:16
Alignment explanation
Indices: 14175880--14175913 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
14175870 GAAATTTTAA
14175880 GAAATGAAAAAAAT-T
1 GAAATGAAAAAAATCT
14175895 GAAAT-AAAAAAATCT
1 GAAATGAAAAAAATCT
14175910 GAAA
1 GAAA
14175914 ATGTTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.03, G:0.12, T:0.18
Consensus pattern (16 bp):
GAAATGAAAAAAATCT
Found at i:14176390 original size:30 final size:30
Alignment explanation
Indices: 14176351--14176547 Score: 261
Period size: 30 Copynumber: 6.5 Consensus size: 30
14176341 CCCTAAATTG
* * **
14176351 TCCAGAAATTATCTTTCGACCCTGAAACTTT
1 TCCA-AAATTATATTTTGACCCCAAAACTTT
14176382 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
** * *
14176412 TCCAAAATTATATTTTGACTTCGAAACTTC
1 TCCAAAATTATATTTTGACCCCAAAACTTT
14176442 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
14176472 TCCGAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
* *
14176502 TCCAAAATTACATTTCGACCCCAAAAC-TT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
14176531 TCAAAAATTATCATTTT
1 TCCAAAATTAT-ATTTT
14176548 TCTCCCGAAT
Statistics
Matches: 146, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
29 11 0.08
30 131 0.90
31 4 0.03
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (30 bp):
TCCAAAATTATATTTTGACCCCAAAACTTT
Found at i:14176686 original size:59 final size:59
Alignment explanation
Indices: 14176534--14176907 Score: 500
Period size: 59 Copynumber: 6.4 Consensus size: 59
14176524 AAAACTTTCA
* * * * * *
14176534 AAAATTATCATTTTTCTCCCGAATCTTTTAAAATTCCGTTTTTAAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCGTTTTT-AACCCCGATTTCAACG
* * *
14176594 AAAATTACCATTTTACCCCCGAATCTTTT-AAATTCTGTTTTTAATCCCGATTTCAACG
1 AAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCGTTTTTAACCCCGATTTCAACG
* * * * *
14176652 AAAATTACCCTTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTTACCG
1 AAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCGTTTTTAACCCCGATTTCAACG
* *
14176711 AAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCTGTTTTTAACCCCGATTTCATCG
1 AAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCGTTTTTAACCCCGATTTCAACG
* * *
14176770 AAAATTGCCATTTTACCCCCGAAGCTTTTAAAATTCTGTTTTTAACCCCGATTTCATCG
1 AAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCGTTTTTAACCCCGATTTCAACG
* * * * *
14176829 AAAATTGCCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTAC-ACC
1 AAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCGTTTTTAACCCCGATTTCAACG
*
14176887 AAAATTACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
14176908 GGTATCCATA
Statistics
Matches: 283, Mismatches: 30, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
58 59 0.21
59 198 0.70
60 26 0.09
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.37
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCGTTTTTAACCCCGATTTCAACG
Found at i:14176694 original size:29 final size:29
Alignment explanation
Indices: 14176551--14176879 Score: 159
Period size: 30 Copynumber: 11.2 Consensus size: 29
14176541 TCATTTTTCT
* *
14176551 CCCGAATCTTTTAAAATTCCGTTTTTAAAC
1 CCCGAATCTTCTAAAATTCCATTTTT-AAC
* ** * *
14176581 CCCGATTTCACCAAAAATTACCA-TTTTACC
1 CCCGA-ATCTTCTAAAATT-CCATTTTTAAC
* ** *
14176611 CCCGAATCTT-TTAAATTCTGTTTTTAAT
1 CCCGAATCTTCTAAAATTCCATTTTTAAC
* ** * * *
14176639 CCCGATTTCAACGAAAATTACC-CTTTTACC
1 CCCGA-ATCTTCTAAAATT-CCATTTTTAAC
*
14176669 CCCGAAGCTTCTAAAATTCCATTTTTAAC
1 CCCGAATCTTCTAAAATTCCATTTTTAAC
* * *
14176698 CCCG-ATTTTACCGAAAATTACCA-TTTTACC
1 CCCGAATCTT--CTAAAATT-CCATTTTTAAC
* * **
14176728 CCCGAAGCTTTTAAAATTCTGTTTTTAAC
1 CCCGAATCTTCTAAAATTCCATTTTTAAC
* * * *
14176757 CCCGATTTCATCGAAAATTGCCA-TTTTACC
1 CCCGA-ATCTTCTAAAATT-CCATTTTTAAC
* * **
14176787 CCCGAAGCTTTTAAAATTCTGTTTTTAAC
1 CCCGAATCTTCTAAAATTCCATTTTTAAC
* * * *
14176816 CCCGATTTCATCGAAAATTGCCA-TTTTACC
1 CCCGA-ATCTTCTAAAATT-CCATTTTTAAC
*
14176846 CCCGAATCTTTTAAAATTCCATTTTTAAC
1 CCCGAATCTTCTAAAATTCCATTTTTAAC
14176875 CCCGA
1 CCCGA
14176880 TTACACCAAA
Statistics
Matches: 209, Mismatches: 72, Indels: 37
0.66 0.23 0.12
Matches are distributed among these distances:
27 1 0.00
28 25 0.12
29 78 0.37
30 82 0.39
31 21 0.10
32 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.36
Consensus pattern (29 bp):
CCCGAATCTTCTAAAATTCCATTTTTAAC
Found at i:14176833 original size:177 final size:176
Alignment explanation
Indices: 14176534--14176907 Score: 561
Period size: 177 Copynumber: 2.1 Consensus size: 176
14176524 AAAACTTTCA
* * * *
14176534 AAAATTATCATTTTTCTCCCGAATCTTTTAAAATTCCGTTTTTAAACCCCGATTTCACCAAAAAT
1 AAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCGTTTTTAAACCCCGATTTCACCAAAAAT
* * *
14176599 TACCATTTTACCCCCGAATCTTTTAAATTCTGTTTTTAATCCCGATTTCAACGAAAATTACCCTT
66 TACCATTTTACCCCCGAAGCTTTTAAATTCTGTTTTTAACCCCGATTTCAACGAAAATTACCATT
**
14176664 TTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTTACC
131 TTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTACACC
* * *
14176710 GAAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCTGTTTTT-AACCCCGATTTCATCGAAAA
1 -AAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCGTTTTTAAACCCCGATTTCACCAAAAA
* * *
14176774 TTGCCATTTTACCCCCGAAGCTTTTAAAATTCTGTTTTTAACCCCGATTTCATCGAAAATTGCCA
65 TTACCATTTTACCCCCGAAGCTTTT-AAATTCTGTTTTTAACCCCGATTTCAACGAAAATTACCA
* *
14176839 TTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACACC
129 TTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTACACC
*
14176887 AAAATTACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
14176908 GGTATCCATA
Statistics
Matches: 178, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
176 61 0.34
177 117 0.66
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.37
Consensus pattern (176 bp):
AAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCGTTTTTAAACCCCGATTTCACCAAAAAT
TACCATTTTACCCCCGAAGCTTTTAAATTCTGTTTTTAACCCCGATTTCAACGAAAATTACCATT
TTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTACACC
Found at i:14189900 original size:69 final size:68
Alignment explanation
Indices: 14189707--14190512 Score: 1223
Period size: 68 Copynumber: 11.8 Consensus size: 68
14189697 TCTTCATCTC
* * * *
14189707 TGAAATTGAAGTAAAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACATCGTCC
1 TGAAATTGAAGTAGAGTGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCGTCC
14189772 TCT
66 TCT
* * *
14189775 TGAAATTGAAGTAGAGTTGATATCAGGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCGTCC
1 TGAAATTGAAGTAGAGTGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCGTCC
14189840 TCT
66 TCT
* *
14189843 TGAAATTGAAGTAGAGTTGGATATCACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATC
1 TGAAATTGAAGTAGAG-TGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCGTC
14189908 CTCT
65 CTCT
14189912 TGAAATTGAAGTAGAGTGGATAAT-ACGTC-TTATCTCTG-AATTGAAGTAAGAGCAACGTCGTC
1 TGAAATTGAAGTAGAGTGGAT-ATCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCGTC
14189974 CTCT
65 CTCT
*
14189978 TGAAATTGAAGTAGAGTTGGATATCACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCGTC
1 TGAAATTGAAGTAGAG-TGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCGTC
14190043 CTCT
65 CTCT
* *
14190047 TGAAATTGAAGTAGAGTTGGATATCACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATC
1 TGAAATTGAAGTAGAG-TGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCGTC
14190112 CTCT
65 CTCT
* *
14190116 TGAAATTGAAGTAGAGTGGATAAT-ACGTCTTTATCTCTCAAATTGAAGTAAGAGCAACGTCATC
1 TGAAATTGAAGTAGAGTGGAT-ATCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCGTC
14190180 CTCT
65 CTCT
* * *
14190184 TGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGCAAGAGC-ACGTCATC
1 TGAAATTGAAGTAGAG-TGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCGTC
14190248 C-CT
65 CTCT
*
14190251 TGAAATTGAAGTAGAGTGGATAAT-ACGTCTTTATCTATGAAATTGAAGTAAGAGCAACGTCGTC
1 TGAAATTGAAGTAGAGTGGAT-ATCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCGTC
14190315 CTCT
65 CTCT
* *
14190319 TGAAATTGAAGTAGAGTGGATAAT-ACGTCTTTATCTCTAAAATTGAAGTAAGAGCCACGTCGTC
1 TGAAATTGAAGTAGAGTGGAT-ATCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCGTC
14190383 CTCT
65 CTCT
** *
14190387 TGAAATTGAAGTAGAGTTGGATATCAAATCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATC
1 TGAAATTGAAGTAGAG-TGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCGTC
*
14190452 CCCT
65 CTCT
* * * *
14190456 CGAAATTGAAATAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGCAAGAGCAA
1 TGAAATTGAAGTAGAGTGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
14190513 GATCATTTCC
Statistics
Matches: 687, Mismatches: 37, Indels: 28
0.91 0.05 0.04
Matches are distributed among these distances:
66 78 0.11
67 46 0.07
68 292 0.43
69 271 0.39
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (68 bp):
TGAAATTGAAGTAGAGTGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCGTCC
TCT
Found at i:14190174 original size:137 final size:137
Alignment explanation
Indices: 14189700--14190512 Score: 1220
Period size: 137 Copynumber: 6.0 Consensus size: 137
14189690 TAACAGGTCT
* * *
14189700 TCAT-CTC-TGAAATTGAAGTAAAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGC
1 TCATCCTCTTGAAATTGAAGTAGAGTTGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGC
* * * * *
14189762 AACATCGTCCTCTTGAAATTGAAGTAGAGTTGATATCAGGTCTTCATCTCTGAAATTGAAGTAAG
66 AACGTCATCCTCTTGAAATTGAAGTAGAGTGGATATCACGTCTTTATCTCTGAAATTGAAGTAAG
14189827 AGCAACG
131 AGCAACG
* *
14189834 TCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCACGTCTTCATCTCTGAAATTGAAGTAAGAGC
1 TCATCCTCTTGAAATTGAAGTAGAGTTGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGC
14189899 AACGTCATCCTCTTGAAATTGAAGTAGAGTGGATAAT-ACGTC-TTATCTCTG-AATTGAAGTAA
66 AACGTCATCCTCTTGAAATTGAAGTAGAGTGGAT-ATCACGTCTTTATCTCTGAAATTGAAGTAA
14189961 GAGCAACG
130 GAGCAACG
* *
14189969 TCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCACGTCTTCATCTCTGAAATTGAAGTAAGAGC
1 TCATCCTCTTGAAATTGAAGTAGAGTTGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGC
* *
14190034 AACGTCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCACGTCTTCATCTCTGAAATTGAAGTAA
66 AACGTCATCCTCTTGAAATTGAAGTAGAG-TGGATATCACGTCTTTATCTCTGAAATTGAAGTAA
14190099 GAGCAACG
130 GAGCAACG
*
14190107 TCATCCTCTTGAAATTGAAGTAGAG-TGGATAAT-ACGTCTTTATCTCTCAAATTGAAGTAAGAG
1 TCATCCTCTTGAAATTGAAGTAGAGTTGGAT-ATCACGTCTTTATCTCTGAAATTGAAGTAAGAG
* *
14190170 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGCA
65 CAACGTCATCCTCTTGAAATTGAAGTAGAG-TGGATATCACGTCTTTATCTCTGAAATTGAAGTA
14190235 AGAGC-ACG
129 AGAGCAACG
*
14190243 TCATCC-CTTGAAATTGAAGTAGAG-TGGATAAT-ACGTCTTTATCTATGAAATTGAAGTAAGAG
1 TCATCCTCTTGAAATTGAAGTAGAGTTGGAT-ATCACGTCTTTATCTCTGAAATTGAAGTAAGAG
* *
14190305 CAACGTCGTCCTCTTGAAATTGAAGTAGAGTGGATAAT-ACGTCTTTATCTCTAAAATTGAAGTA
65 CAACGTCATCCTCTTGAAATTGAAGTAGAGTGGAT-ATCACGTCTTTATCTCTGAAATTGAAGTA
*
14190369 AGAGCCACG
129 AGAGCAACG
* **
14190378 TCGTCCTCTTGAAATTGAAGTAGAGTTGGATATCAAATCTTTATCTCTGAAATTGAAGTAAGAGC
1 TCATCCTCTTGAAATTGAAGTAGAGTTGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGC
* * * * *
14190443 AACGTCATCCCCTCGAAATTGAAATAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGCAAG
66 AACGTCATCCTCTTGAAATTGAAGTAGAGTGGATATCACGTCTTTATCTCTGAAATTGAAGTAAG
14190508 AGCAA
131 AGCAA
14190513 GATCATTTCC
Statistics
Matches: 627, Mismatches: 37, Indels: 27
0.91 0.05 0.04
Matches are distributed among these distances:
134 36 0.06
135 210 0.33
136 63 0.10
137 271 0.43
138 47 0.07
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (137 bp):
TCATCCTCTTGAAATTGAAGTAGAGTTGGATATCACGTCTTTATCTCTGAAATTGAAGTAAGAGC
AACGTCATCCTCTTGAAATTGAAGTAGAGTGGATATCACGTCTTTATCTCTGAAATTGAAGTAAG
AGCAACG
Found at i:14190858 original size:6 final size:6
Alignment explanation
Indices: 14190849--14190916 Score: 77
Period size: 6 Copynumber: 11.3 Consensus size: 6
14190839 TTTTAATTTT
*
14190849 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* *
14190897 CTTTGA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
14190917 AAAAATTAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
5 8 0.15
6 39 0.74
8 6 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:14190870 original size:17 final size:16
Alignment explanation
Indices: 14190840--14190913 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
14190830 TAAATTGATT
*
14190840 TTTAATTTTATTTAAA
1 TTTAAATTTATTTAAA
14190856 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
*
14190873 TTTAAATTTAATT--A
1 TTTAAATTTATTTAAA
*
14190887 TTTAAATTTACTTTGAA
1 TTTAAATTTA-TTTAAA
14190904 TTTAAATTTA
1 TTTAAATTTA
14190914 AATAAAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.22
15 2 0.04
16 11 0.22
17 27 0.53
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:14191600 original size:15 final size:15
Alignment explanation
Indices: 14191567--14191610 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
14191557 TAACAGCAGC
14191567 ATTAATTAATAATATTA
1 ATTAATTAA-AA-ATTA
14191584 ATTAATTAAAAATTA
1 ATTAATTAAAAATTA
*
14191599 ATTAAATAAAAA
1 ATTAATTAAAAA
14191611 GAAACGAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 15 0.58
16 2 0.08
17 9 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAATTAAAAATTA
Found at i:14192242 original size:14 final size:16
Alignment explanation
Indices: 14192217--14192250 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
14192207 GAAATTTTAA
14192217 GAAATGAAAAAAAT-T
1 GAAATGAAAAAAATCT
14192232 GAAAT-AAAAAAATCT
1 GAAATGAAAAAAATCT
14192247 GAAA
1 GAAA
14192251 ATTTATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.03, G:0.12, T:0.18
Consensus pattern (16 bp):
GAAATGAAAAAAATCT
Found at i:14192734 original size:30 final size:30
Alignment explanation
Indices: 14192700--14192819 Score: 161
Period size: 30 Copynumber: 4.0 Consensus size: 30
14192690 ATTATCTTTC
*
14192700 GACCCCGAAACTTTTCCAAAATTACATTTT
1 GACCCCAAAACTTTTCCAAAATTACATTTT
*
14192730 GACCCCAAAACTTTTCCAAAATTATATTTT
1 GACCCCAAAACTTTTCCAAAATTACATTTT
* * * *
14192760 GACTCCGAAACTGTTCCAAAATTACATTTC
1 GACCCCAAAACTTTTCCAAAATTACATTTT
*
14192790 GACCCCAAAAC-TTTCAAAAATTATCATTTT
1 GACCCCAAAACTTTTCCAAAATTA-CATTTT
14192820 TCTCCCGATA
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
29 10 0.13
30 67 0.87
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (30 bp):
GACCCCAAAACTTTTCCAAAATTACATTTT
Found at i:14192770 original size:60 final size:59
Alignment explanation
Indices: 14192688--14192819 Score: 192
Period size: 60 Copynumber: 2.2 Consensus size: 59
14192678 AATTGTCCGG
* * * * *
14192688 AAATTATCTTTCGACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTATATTTTGACCCCGAAACTGTTCCAAAATTACATTTCGACCCCAAAAC-TTTCAA
*
14192748 AAATTATATTTTGACTCCGAAACTGTTCCAAAATTACATTTCGACCCCAAAACTTTCAA
1 AAATTATATTTTGACCCCGAAACTGTTCCAAAATTACATTTCGACCCCAAAACTTTCAA
14192807 AAATTATCATTTT
1 AAATTAT-ATTTT
14192820 TCTCCCGATA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 12 0.18
60 53 0.82
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (59 bp):
AAATTATATTTTGACCCCGAAACTGTTCCAAAATTACATTTCGACCCCAAAACTTTCAA
Found at i:14192867 original size:59 final size:58
Alignment explanation
Indices: 14192804--14193118 Score: 368
Period size: 59 Copynumber: 5.4 Consensus size: 58
14192794 CCAAAACTTT
* * * * **
14192804 CAAAAATTATCATTTTTCTCCCGATATTTTTAAAATTCTGTTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGA-ACTTTTAAAATTCCATTTTTAACCCCGATTTCAC
* *
14192863 CAAAAATTACCATTTTAACCCCCGGATCTTTTAAAATTCCA--TTTAATCCCGATTTCAC
1 CAAAAATTACCATTTT-ACCCCC-GAACTTTTAAAATTCCATTTTTAACCCCGATTTCAC
* * * * *
14192921 CGAAAATTACCTTTTTA-CCTCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTTAC
1 CAAAAATTACCATTTTACCCCCGAA-CTTTTAAAATTCCATTTTTAACCCCGATTTCAC
* * *
14192979 CAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCTATTTTTAACCCCGATTTCAT
1 CAAAAATTACCATTTTACCCCCGAA-CTTTTAAAATTCCATTTTTAACCCCGATTTCAC
* * *
14193038 CGAAAATTGCCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACAC
1 CAAAAATTACCATTTTACCCCCGAA-CTTTTAAAATTCCATTTTTAACCCCGATTTCAC
*
14193097 C-AAAATTACCATTTTGCCCCCG
1 CAAAAATTACCATTTTACCCCCG
14193119 GGTATCCATA
Statistics
Matches: 220, Mismatches: 30, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
55 2 0.01
56 16 0.07
57 1 0.00
58 79 0.36
59 105 0.48
60 15 0.07
61 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.37
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCCGAACTTTTAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:14193013 original size:29 final size:29
Alignment explanation
Indices: 14192865--14193090 Score: 144
Period size: 29 Copynumber: 7.8 Consensus size: 29
14192855 GATTTCACCA
* *
14192865 AAAATTACCA-TTTTAACCCCCGGATCTTTT
1 AAAATT-CCATTTTTAA-CCCCGAATCTTCT
* * ** *
14192895 AAAATTCCA--TTTAATCCCGATTTCACCG
1 AAAATTCCATTTTTAACCCCGA-ATCTTCT
* *
14192923 AAAATTACC-TTTTT-ACCTCGAAGCTTCT
1 AAAATT-CCATTTTTAACCCCGAATCTTCT
* *
14192951 AAAATTCCATTTTTAACCCCG-ATTTTACCA
1 AAAATTCCATTTTTAACCCCGAATCTT--CT
* *
14192981 AAAATTACCA-TTTTACCCCCGAAGCTTCT
1 AAAATT-CCATTTTTAACCCCGAATCTTCT
* * * *
14193010 AAAATTCTATTTTTAACCCCGATTTCATCG
1 AAAATTCCATTTTTAACCCCGA-ATCTTCT
* *
14193040 AAAATTGCCA-TTTTACCCCCGAATCTTTT
1 AAAATT-CCATTTTTAACCCCGAATCTTCT
14193069 AAAATTCCATTTTTAACCCCGA
1 AAAATTCCATTTTTAACCCCGA
14193091 TTACACCAAA
Statistics
Matches: 147, Mismatches: 35, Indels: 29
0.70 0.17 0.14
Matches are distributed among these distances:
27 6 0.04
28 34 0.23
29 53 0.36
30 46 0.31
31 8 0.05
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (29 bp):
AAAATTCCATTTTTAACCCCGAATCTTCT
Found at i:14193101 original size:29 final size:30
Alignment explanation
Indices: 14192844--14193111 Score: 95
Period size: 30 Copynumber: 9.1 Consensus size: 30
14192834 TAAAATTCTG
*
14192844 TTTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTTAACCCCGATTACACC-AAAATTACCA
***
14192875 -TTTTAACCCCCGGA-T-CTTTTAAAATT-CCA
1 TTTTTAA-CCCC-GATTAC-ACCAAAATTACCA
* *
14192904 --TTTAATCCCGATTTCACCGAAAATTACC-
1 TTTTTAACCCCGATTACACC-AAAATTACCA
* * *
14192932 TTTTT-ACCTCGA--AGCTTCTAAAATT-CCA
1 TTTTTAACCCCGATTA-C-ACCAAAATTACCA
**
14192960 TTTTTAACCCCGATTTTACCAAAAATTACCA
1 TTTTTAACCCCGATTACACC-AAAATTACCA
* * * *
14192991 -TTTTACCCCCGA--AGCTTCTAAAATT-CTA
1 TTTTTAACCCCGATTA-C-ACCAAAATTACCA
* * *
14193019 TTTTTAACCCCGATTTCATCGAAAATTGCCA
1 TTTTTAACCCCGATTACA-CCAAAATTACCA
* * ***
14193050 -TTTTACCCCCGAAT-CTTTTAAAATT-CCA
1 TTTTTAACCCCGATTAC-ACCAAAATTACCA
14193078 TTTTTAACCCCGATTACACCAAAATTACCA
1 TTTTTAACCCCGATTACACCAAAATTACCA
14193108 TTTT
1 TTTT
14193112 GCCCCCGGGT
Statistics
Matches: 171, Mismatches: 38, Indels: 57
0.64 0.14 0.21
Matches are distributed among these distances:
26 2 0.01
27 6 0.04
28 29 0.17
29 60 0.35
30 62 0.36
31 10 0.06
32 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (30 bp):
TTTTTAACCCCGATTACACCAAAATTACCA
Done.